Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 168 of 211
Found at i:52331844 original size:25 final size:26
Alignment explanation
Indices: 52331785--52331845 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 26
52331775 ATTTTGTTTT
* *
52331785 AAATGTAGTGTATTTTAAAAATAAAA
1 AAATATAGTATATTTTAAAAATAAAA
52331811 AATATATAGTATATTTTAAAAAT-AAA
1 AA-ATATAGTATATTTTAAAAATAAAA
52331837 AAATATAGT
1 AAATATAGT
52331846 TTTTATTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 7 0.22
26 7 0.22
27 18 0.56
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (26 bp):
AAATATAGTATATTTTAAAAATAAAA
Found at i:52331852 original size:27 final size:27
Alignment explanation
Indices: 52331790--52331843 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
52331780 GTTTTAAATG
*
52331790 TAGTGTATTTTAAAAATAAAAAATATA
1 TAGTATATTTTAAAAATAAAAAATATA
52331817 TAGTATATTTTAAAAATAAAAAATATA
1 TAGTATATTTTAAAAATAAAAAATATA
52331844 GTTTTTATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (27 bp):
TAGTATATTTTAAAAATAAAAAATATA
Found at i:52331943 original size:9 final size:9
Alignment explanation
Indices: 52331918--52331963 Score: 65
Period size: 9 Copynumber: 5.0 Consensus size: 9
52331908 CAAAAGAAAA
52331918 AATTCGAATT
1 AATTCG-ATT
*
52331928 GATTCGATT
1 AATTCGATT
52331937 AATTCGATT
1 AATTCGATT
52331946 AATTCGATT
1 AATTCGATT
*
52331955 AACTCGATT
1 AATTCGATT
52331964 CGAATAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
9 28 0.85
10 5 0.15
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (9 bp):
AATTCGATT
Found at i:52360034 original size:31 final size:31
Alignment explanation
Indices: 52359984--52360063 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
52359974 GTTAATATTC
* *
52359984 CATTT-GGTATTTGAGTTTGGCTTCAATGTT
1 CATTTAGGTACTTGAATTTGGCTTCAATGTT
* *
52360014 CATTTAGGTACTTGAATTTGGTTTCAGTGTT
1 CATTTAGGTACTTGAATTTGGCTTCAATGTT
52360045 CATTTAGGTACTTGAATTT
1 CATTTAGGTACTTGAATTT
52360064 TTTCAATTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 5 0.11
31 40 0.89
ACGTcount: A:0.20, C:0.10, G:0.21, T:0.49
Consensus pattern (31 bp):
CATTTAGGTACTTGAATTTGGCTTCAATGTT
Found at i:52368448 original size:34 final size:35
Alignment explanation
Indices: 52368402--52368468 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
52368392 CTGTAAAATG
52368402 TTTTCTGGAAAATAATTT-CTGAAAAATATTTTAC
1 TTTTCTGGAAAATAATTTACTGAAAAATATTTTAC
* * *
52368436 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCTGGAAAATAATTTACTGAAAAATATTTT
52368469 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCTGGAAAATAATTTACTGAAAAATATTTTAC
Found at i:52368571 original size:20 final size:20
Alignment explanation
Indices: 52368543--52368619 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
52368533 TCCGGAAAAG
52368543 TTATTTTTACATATATTAAA
1 TTATTTTTACATATATTAAA
* *
52368563 TTGTTTTTACATATATATTAA
1 TTATTTTTACATATAT-TAAA
* *
52368584 TAAATTTTT--ATATTTTAAA
1 T-TATTTTTACATATATTAAA
52368603 TTATTTTTACATATATT
1 TTATTTTTACATATATT
52368620 GCAATGATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
18 6 0.13
19 4 0.09
20 26 0.58
21 4 0.09
22 5 0.11
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (20 bp):
TTATTTTTACATATATTAAA
Found at i:52368658 original size:18 final size:18
Alignment explanation
Indices: 52368635--52368670 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
52368625 GATTTATTTA
52368635 TAAATAAATAAATCAAAT
1 TAAATAAATAAATCAAAT
* *
52368653 TAAATATATCAATCAAAT
1 TAAATAAATAAATCAAAT
52368671 GGTTTAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAATAAATAAATCAAAT
Found at i:52370819 original size:13 final size:13
Alignment explanation
Indices: 52370801--52370836 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
52370791 GCCGACGGTT
52370801 GACGGAGATGACG
1 GACGGAGATGACG
52370814 GACGGAGATGACG
1 GACGGAGATGACG
52370827 GACGGAGATG
1 GACGGAGATG
52370837 GTGAGGTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.14, G:0.47, T:0.08
Consensus pattern (13 bp):
GACGGAGATGACG
Found at i:52370868 original size:26 final size:25
Alignment explanation
Indices: 52370802--52370868 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
52370792 CCGACGGTTG
* *
52370802 ACGGAGATGACGGACGGAGATGACGG
1 ACGGAGATGA-GGAGGGAGATGACGA
*
52370828 ACGGAGATG-GTGAGGTGAGGTGACGA
1 ACGGAGATGAG-GAGG-GAGATGACGA
52370854 ACGGAGATGAGGAGG
1 ACGGAGATGAGGAGG
52370869 CAGAGGATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
24 1 0.03
25 3 0.09
26 30 0.86
27 1 0.03
ACGTcount: A:0.30, C:0.10, G:0.49, T:0.10
Consensus pattern (25 bp):
ACGGAGATGAGGAGGGAGATGACGA
Found at i:52370915 original size:21 final size:22
Alignment explanation
Indices: 52370881--52370926 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
52370871 GAGGATGTGG
52370881 AAGAAGATTTGCTTAGAAGAGA
1 AAGAAGATTTGCTTAGAAGAGA
52370903 AAGAAGA-TTGCTTAGAAGAGA
1 AAGAAGATTTGCTTAGAAGAGA
52370924 AAG
1 AAG
52370927 GAGAAAGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.48, C:0.04, G:0.28, T:0.20
Consensus pattern (22 bp):
AAGAAGATTTGCTTAGAAGAGA
Found at i:52373431 original size:3 final size:3
Alignment explanation
Indices: 52373425--52373474 Score: 73
Period size: 3 Copynumber: 16.3 Consensus size: 3
52373415 CATCATCATC
**
52373425 ATT ATT ATT ATT ATT ATT ATTT ATT ACC ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
52373471 ATT A
1 ATT A
52373475 AATTTTTTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:52375845 original size:5 final size:6
Alignment explanation
Indices: 52375829--52375853 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
52375819 TTGAAATAGA
52375829 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
52375854 CTCTATCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:52378273 original size:2 final size:2
Alignment explanation
Indices: 52378266--52378307 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
52378256 TTTCCTGCCT
*
52378266 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC AC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
52378308 AATTCTCTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:52379394 original size:305 final size:305
Alignment explanation
Indices: 52378843--52379454 Score: 1109
Period size: 305 Copynumber: 2.0 Consensus size: 305
52378833 GGCCCGAATA
*
52378843 TATAATAAATATATTTTTTATTTTTTATTTTAAAATATTTTTAAAATACTCTTTTGGTGTTTATT
1 TATAATAAATATATATTTTATTTTTTATTTTAAAATATTTTTAAAATACTCTTTTGGTGTTTATT
*
52378908 AAAAAAATGGGTCGGGCTCGGGCTTAGAAATTTTTTTCCCCGACCGGGCCTAGACAAAATTTCAG
66 AAAAAAATGGGTCGGGCTCGGGCTTAGAAATTTTTTTCCCCGACCGGGCCTAGACAAAATTTCAA
* *
52378973 GCTCATATTTTGGGCAGGGCCGGGCTCGAGCCTAGGACACGGGCCGAAATCAAAAGTAATATATT
131 GCCCATATTTTGGACAGGGCCGGGCTCGAGCCTAGGACACGGGCCGAAATCAAAAGTAATATATT
52379038 TTAATGGTGAAAAAAAGTAACATATTTGTTATACAAGGAATACAGAACACGTTACGTGTCATAGC
196 TTAATGGTGAAAAAAAGTAACATATTTGTTATACAAGGAATACAGAACACGTTACGTGTCATAGC
52379103 TCGCCACTTATATGGTTCTATCCTGCTCGTCCATATCTTCTGAGG
261 TCGCCACTTATATGGTTCTATCCTGCTCGTCCATATCTTCTGAGG
52379148 TATAATAAATATATATTTTATTTTTTATTTTAAAATATTTTTAAAATACTCTTTTGGTGTTTATT
1 TATAATAAATATATATTTTATTTTTTATTTTAAAATATTTTTAAAATACTCTTTTGGTGTTTATT
* * * *
52379213 AAAAAAATGGGTCGGGCTCGGGCTTAGAATTTTTTTTCCCCGGCCGGGCCTGGACAAAATTTTAA
66 AAAAAAATGGGTCGGGCTCGGGCTTAGAAATTTTTTTCCCCGACCGGGCCTAGACAAAATTTCAA
* *
52379278 GCCCATATTTTGGACAGGGCCGGGCTCGGGCCTAGGACGA-GGGCCGAAATCAAAAGTTATATAT
131 GCCCATATTTTGGACAGGGCCGGGCTCGAGCCTAGGAC-ACGGGCCGAAATCAAAAGTAATATAT
*
52379342 TTTAATGGTGAAAAAAAGTAACATATTTGTTATACAAGGAATACATAACACGTTACGTGTCATAG
195 TTTAATGGTGAAAAAAAGTAACATATTTGTTATACAAGGAATACAGAACACGTTACGTGTCATAG
52379407 CTCGCCACTTATATGGTTCTATCCTGCTCGTCCATATCTTCTGAGG
260 CTCGCCACTTATATGGTTCTATCCTGCTCGTCCATATCTTCTGAGG
52379453 TA
1 TA
52379455 CTAGTGATCG
Statistics
Matches: 295, Mismatches: 11, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
305 294 1.00
306 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (305 bp):
TATAATAAATATATATTTTATTTTTTATTTTAAAATATTTTTAAAATACTCTTTTGGTGTTTATT
AAAAAAATGGGTCGGGCTCGGGCTTAGAAATTTTTTTCCCCGACCGGGCCTAGACAAAATTTCAA
GCCCATATTTTGGACAGGGCCGGGCTCGAGCCTAGGACACGGGCCGAAATCAAAAGTAATATATT
TTAATGGTGAAAAAAAGTAACATATTTGTTATACAAGGAATACAGAACACGTTACGTGTCATAGC
TCGCCACTTATATGGTTCTATCCTGCTCGTCCATATCTTCTGAGG
Found at i:52384459 original size:13 final size:13
Alignment explanation
Indices: 52384441--52384467 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52384431 TTTCGGTTTA
52384441 ATTTAAACAATAT
1 ATTTAAACAATAT
52384454 ATTTAAACAATAT
1 ATTTAAACAATAT
52384467 A
1 A
52384468 GTTGTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTTAAACAATAT
Found at i:52386035 original size:23 final size:23
Alignment explanation
Indices: 52386000--52386044 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
52385990 CCTTATTTAA
**
52386000 TTCAAATTGATTAT-AATATTATT
1 TTCAAATAAATTATCAA-ATTATT
52386023 TTCAAATAAATTATCAAATTAT
1 TTCAAATAAATTATCAAATTAT
52386045 AAAATGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
TTCAAATAAATTATCAAATTATT
Found at i:52389347 original size:92 final size:90
Alignment explanation
Indices: 52389190--52389398 Score: 271
Period size: 92 Copynumber: 2.3 Consensus size: 90
52389180 TTGATTTTAG
* *
52389190 TAAATTCATATAAAAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAAAA-A-TTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
52389255 ATTTAAT-ATTAATTATTTTAAATTGTA
64 ATGTAATAATT-ATTATTTTAAATTATA
*
52389282 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAA-AAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
52389346 TATGTAATAATTATTATTTTAAATTATA
63 TATGTAATAATTATTATTTTAAATTATA
*
52389374 CAAATTCATA-AAATATAATTTATTA
1 TAAATTCATATAAA-A-AATTTATTA
52389399 GTTATAATTA
Statistics
Matches: 105, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
90 2 0.02
91 31 0.30
92 66 0.63
93 6 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (90 bp):
TAAATTCATATAAAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATAT
GTAATAATTATTATTTTAAATTATA
Found at i:52389361 original size:24 final size:25
Alignment explanation
Indices: 52389326--52389373 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
52389316 TTATGAAATT
52389326 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
52389350 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
52389374 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:52389527 original size:66 final size:64
Alignment explanation
Indices: 52389452--52389659 Score: 176
Period size: 66 Copynumber: 3.4 Consensus size: 64
52389442 AAATATATTT
52389452 AATATTAATTATTTCAAATTTTCATTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
52389517 G
64 G
* * * *
52389518 AATATTAATTATTAAGAATTTTA-TTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT---
1 AATATTAATTATTTA-AATTTTATTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* * *
52389570 -TTAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCGTATA
1 AATATTAATTAT-TTAAATTT-TA-TTTACAGTATCATATATTATGATTTGAGTAAATTCATATA
52389633 AG
63 AG
*
52389635 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
52389660 AAATTATATA
Statistics
Matches: 108, Mismatches: 14, Indels: 41
0.66 0.09 0.25
Matches are distributed among these distances:
50 5 0.05
51 11 0.10
52 1 0.01
53 3 0.03
54 1 0.01
55 4 0.04
56 10 0.09
57 6 0.06
58 2 0.02
59 2 0.02
60 6 0.06
61 10 0.09
62 3 0.03
63 1 0.01
64 3 0.03
65 5 0.05
66 30 0.28
67 5 0.05
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.49
Consensus pattern (64 bp):
AATATTAATTATTTAAATTTTATTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:52389556 original size:120 final size:119
Alignment explanation
Indices: 52389421--52389703 Score: 459
Period size: 117 Copynumber: 2.4 Consensus size: 119
52389411 TTAAATTATT
* *
52389421 TTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-TTTACAG
1 TTAAATTATATATTTTAATTATAATATATTTAATA-TAATTATGTT--AATTTAT-ATTTTACAG
52389483 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
62 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
52389541 TTAAATTATATATTTTAATTATAATATATTT-A-ATAATTATGTTAATTTATATTTTACAGTATC
1 TTAAATTATATATTTTAATTATAATATATTTAATATAATTATGTTAATTTATATTTTACAGTATC
*
52389604 ATATATTATGATTTGAGTAAATTCGTATAAGAATATTAATTATTAAGAATTTTA
66 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
52389658 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 TTAAATTATATATTTTAATTATAATATATTTAAT-ATAATTATGTT
52389704 TAAATATGAT
Statistics
Matches: 154, Mismatches: 3, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
116 6 0.04
117 103 0.67
118 4 0.03
119 1 0.01
120 40 0.26
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (119 bp):
TTAAATTATATATTTTAATTATAATATATTTAATATAATTATGTTAATTTATATTTTACAGTATC
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
Found at i:52389686 original size:16 final size:16
Alignment explanation
Indices: 52389665--52389706 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
52389655 TTATTAAATT
*
52389665 ATATATTTTAATTATA
1 ATATATTTTAATAATA
52389681 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
52389696 AT-TATGTTTAA
1 ATATAT-TTTAA
52389707 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:52389691 original size:15 final size:15
Alignment explanation
Indices: 52389656--52389697 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
52389646 TTAAGAATTT
*
52389656 TATTAAATTAT-ATA
1 TATTTAATTATAATA
52389670 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
52389684 TATTTAATAATAAT
1 TATTTAATTATAAT
52389698 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:52389817 original size:156 final size:157
Alignment explanation
Indices: 52389640--52389955 Score: 589
Period size: 156 Copynumber: 2.0 Consensus size: 157
52389630 ATAAGAATAT
*
52389640 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
52389705 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
52389770 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
52389797 TAATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
52389861 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
52389926 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
52389953 TAA
1 TAA
52389956 GGGTATTCTA
Statistics
Matches: 155, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
156 149 0.96
157 6 0.04
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:52389836 original size:18 final size:17
Alignment explanation
Indices: 52389808--52389842 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52389798 AATTATAAGA
*
52389808 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
52389825 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
52389843 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:52393716 original size:140 final size:140
Alignment explanation
Indices: 52393396--52393706 Score: 385
Period size: 140 Copynumber: 2.2 Consensus size: 140
52393386 CAATTCATTG
* ** * * * * ** ** * *
52393396 ATTTATGATCATGAATTATTCACTCATAGCTCACGAATTTACAATTGCAACTTTATTTAAACAGT
1 ATTTACGATCATGAACGATTAATTCATAGCTCACCAATTTACGATCACCGCTTTACTTAAACAAT
* * * *
52393461 GTGTTGATTTAAGATCATAATGGATATTTTAGATCTCACTAATGTAATATCGCAACTCCACCCAA
66 ATGTTGATTTAAGATCACAATGGATATTTTAGATCTCACTAATGTAAGATCACAACTCCACCCAA
52393526 CAGTTTATTA
131 CAGTTTATTA
*
52393536 ATTTACGATCATGAACGATTAATTCATCGCTCACCAATTTACGATCACCGCTTTACTTAAACAAT
1 ATTTACGATCATGAACGATTAATTCATAGCTCACCAATTTACGATCACCGCTTTACTTAAACAAT
*
52393601 ATGTTGATTTAAGATCACAACT-GATATTTTAGAGT-TCACTAATTTAAGATCACAACTCCACCC
66 ATGTTGATTTAAGATCACAA-TGGATATTTTAGA-TCTCACTAATGTAAGATCACAACTCCACCC
*
52393664 AATAGTTCT-TTA
129 AACAGTT-TATTA
*
52393676 ATTTACGATCATGAACGATTCATTCATAGCT
1 ATTTACGATCATGAACGATTAATTCATAGCT
52393707 TGTTAATTTA
Statistics
Matches: 146, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
140 143 0.98
141 3 0.02
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (140 bp):
ATTTACGATCATGAACGATTAATTCATAGCTCACCAATTTACGATCACCGCTTTACTTAAACAAT
ATGTTGATTTAAGATCACAATGGATATTTTAGATCTCACTAATGTAAGATCACAACTCCACCCAA
CAGTTTATTA
Found at i:52396402 original size:20 final size:20
Alignment explanation
Indices: 52396362--52396398 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
52396352 CCACGTCAAC
*
52396362 AAATAATTTAAAAATCATAA
1 AAATAATTTAAAAATAATAA
52396382 AAAT-ATTTAAAAATAAT
1 AAATAATTTAAAAATAAT
52396399 TAAATTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAATTTAAAAATAATAA
Found at i:52401114 original size:24 final size:24
Alignment explanation
Indices: 52401052--52401119 Score: 57
Period size: 24 Copynumber: 2.8 Consensus size: 24
52401042 GTCTCGTTAT
*
52401052 TAGCTCTCTTGAGCTTCCCGTTAAA
1 TAGCTCT-TTGAGCTTCCCCTTAAA
* * *
52401077 TGGTTCTTGCGAGCTTCCCCTT-AA
1 TAGCTCTT-TGAGCTTCCCCTTAAA
*
52401101 TAGCTCTTTAGAGCATCCC
1 TAGCTCTTT-GAGCTTCCC
52401120 GATTGGTTGT
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
24 17 0.52
25 16 0.48
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (24 bp):
TAGCTCTTTGAGCTTCCCCTTAAA
Found at i:52401238 original size:25 final size:25
Alignment explanation
Indices: 52401181--52401239 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
52401171 GTCTCGGTAT
*
52401181 ATGGCTCCTTGGAGCTTCCAGATTA
1 ATGGCTCTTTGGAGCTTCCAGATTA
* *
52401206 AAGGCTCTTATGG-GCTTCCTGATTA
1 ATGGCTCTT-TGGAGCTTCCAGATTA
52401231 ATGGCTCTT
1 ATGGCTCTT
52401240 CAGAGCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 26 0.90
26 3 0.10
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.36
Consensus pattern (25 bp):
ATGGCTCTTTGGAGCTTCCAGATTA
Found at i:52401247 original size:25 final size:25
Alignment explanation
Indices: 52401192--52401247 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
52401182 TGGCTCCTTG
52401192 GAGCTTCCAGATTAAAGGCTCTTAT
1 GAGCTTCCAGATTAAAGGCTCTTAT
* * *
52401217 GGGCTTCCTGATTAATGGCTCTTCA-
1 GAGCTTCCAGATTAAAGGCTCTT-AT
52401242 GAGCTT
1 GAGCTT
52401248 TTCGATATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (25 bp):
GAGCTTCCAGATTAAAGGCTCTTAT
Found at i:52403367 original size:89 final size:89
Alignment explanation
Indices: 52403262--52404128 Score: 854
Period size: 89 Copynumber: 9.7 Consensus size: 89
52403252 TGGAGTAGGT
* * *
52403262 TGAAGATAACAGATCTTGCATTCTTGTACTGACAGCGAAACAGATCGAAGACACCAGCCTTGCCT
1 TGAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* ** * *
52403327 TCCTGTACTGACATCAGAGCAGAC
66 CCCTGTGTTGACAGCGGAGCAGAC
* * * * *
52403351 TGAAGATAACACATCTTGCATTCATGTATTGACAGCGAAGCAGATCGAATACACCAGCCTTGCCT
1 TGAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* ** *
52403416 TCCTGTACTGACAGCTGAGCAGAC
66 CCCTGTGTTGACAGCGGAGCAGAC
* *
52403440 TGAAGATAAAAGATCTTGCCTTCCTGTACTGACAGCGAAGCAAATCGAAGACACCAGCCTTGCCT
1 TGAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
52403505 CCCTG-GTTTGACAGCGGAGCAGAC
66 CCCTGTG-TTGACAGCGGAGCAGAC
** * * * *
52403529 TGAAGATAGTAGATCTTGCCTTCCTCTACTGGCAGCGAAGCAGATCGAAGACACTAGCCTTTCCT
1 TGAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
52403594 CCCTAG-GTTTG-TAGTGGAACAGAC
66 CCCT-GTG-TTGACAGCGGAGCAGAC
** **
52403618 TGAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACAAGAGTATTGCCT
1 TGAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * * * *
52403683 CCCTGGGTTGATAGCGAAGTAGAG
66 CCCTGTGTTGACAGCGGAGCAGAC
** * * *
52403707 TGAAGATAGTAGATATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCGGCCTTACCT
1 TGAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
52403772 CCCTGGGTTTACAACGGAGCAGAC
66 CCCTGTGTTGACAGCGGAGCAGAC
* * *
52403796 TGAAGATAGCAGATATTGCCTTCTTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TGAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
52403861 TCCTGGGTTGACAGCGGAGCAGAC
66 CCCTGTGTTGACAGCGGAGCAGAC
** * * * * *
52403885 TGAAGATAGTAGATTTTGCCTTCCTGTACTGATAGTGAAGGAGATCGAAGACACTAGCCTTGCCT
1 TGAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
52403950 CCCTGAGTTTG-CAG-GAGAGCAGAC
66 CCCTGTG-TTGACAGCG-GAGCAGAC
* *** * * * * * *
52403974 TAAAGATAAC-GTATCATTATTTTCCTGTATTGGCAGCAAAGCA-ATCGAAGACACTAGGCTTGT
1 TGAAGATAACAG-ATC-TTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGC
* * * *
52404037 CTCTCTGAGTTTG-CAGTGGAGTAGAC
64 CTCCCTGTG-TTGACAGCGGAGCAGAC
* * * * * * * *
52404063 TAAAAATAGCAGATCTTGTCTTCCTGTACT-AGTAGTGAAGCATATCTACA-ACACCAGCCTTGC
1 TGAAGATAACAGATCTTGCCTTCCTGTACTGA-CAGCGAAGCAGATCGA-AGACACCAGCCTTGC
52404126 CTC
64 CTC
52404129 TCTGAGTGTG
Statistics
Matches: 662, Mismatches: 103, Indels: 26
0.84 0.13 0.03
Matches are distributed among these distances:
88 25 0.04
89 607 0.92
90 30 0.05
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (89 bp):
TGAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTGTGTTGACAGCGGAGCAGAC
Found at i:52403393 original size:45 final size:44
Alignment explanation
Indices: 52403262--52403935 Score: 283
Period size: 45 Copynumber: 15.1 Consensus size: 44
52403252 TGGAGTAGGT
* * * *
52403262 TGAAGATAACAGATCTTGCATTCTTGTACTGACAGCGAAACAGA
1 TGAAGATAACACATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
* * *
52403306 TCGAAGA-CAC-CAGCCTTGCCTTCCTGTACTGACATC-AGAGCAGA
1 T-GAAGATAACACA-TCTTGCCTTCCTGTACTGACAGCGA-AGCAGA
* * *
52403350 CTGAAGATAACACATCTTGCATTCATGTATTGACAGCGAAGCAGA
1 -TGAAGATAACACATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
*
52403395 TCG-A-AT-ACACCAGCCTTGCCTTCCTGTACTGACAGCTG-AGCAGA
1 T-GAAGATAACA-CA-TCTTGCCTTCCTGTACTGACAGC-GAAGCAGA
* * *
52403439 CTGAAGATAAAAGATCTTGCCTTCCTGTACTGACAGCGAAGCAAA
1 -TGAAGATAACACATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
* * * * *
52403484 TCGAAGA-CAC-CAGCCTTGCCTCCCTGGT-TTGACAGCGGAGCAGA
1 T-GAAGATAACACA-TCTTGCCTTCCT-GTACTGACAGCGAAGCAGA
** * * *
52403528 CTGAAGATAGTAGATCTTGCCTTCCTCTACTGGCAGCGAAGCAGA
1 -TGAAGATAACACATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
* * * * * *
52403573 TCGAAG---ACACTAGCCTTTCCTCCCTAGGT-TTG-TAGTGGAA-CAGA
1 T-GAAGATAACAC-A-TCTTGCCTTCCT--GTACTGACAG-CGAAGCAGA
*
52403617 CTGAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
1 -TGAAGATAACACATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
* * * * * *** * *
52403662 TCGAAGACAAGA-GTATTGCCTCCCTGGGTTGATAGCGAAGTAGA
1 T-GAAGATAACACATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
** * *
52403706 GTGAAGATAGTAGATATTGCCTTCCTGTACTGACAGCGAAGCAGA
1 -TGAAGATAACACATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
* ** * * *** * * *
52403751 TCGAAGA-CAC-CGGCCTTACCTCCCTGGGTTTACAACGGAGCAGA
1 T-GAAGATAACAC-ATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
* * * *
52403795 CTGAAGATAGCAGATATTGCCTTCTTGTACTGACAGCGAAGCAGA
1 -TGAAGATAACACATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
* * *** *
52403840 TCGAAGA-CAC-CAGCCTTGCCTTCCTGGGTTGACAGCGGAGCAGA
1 T-GAAGATAACACA-TCTTGCCTTCCTGTACTGACAGCGAAGCAGA
** * * * * *
52403884 CTGAAGATAGTAGATTTTGCCTTCCTGTACTGATAGTGAAGGAGA
1 -TGAAGATAACACATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
52403929 TCGAAGA
1 T-GAAGA
52403936 CACTAGCCTT
Statistics
Matches: 451, Mismatches: 129, Indels: 99
0.66 0.19 0.15
Matches are distributed among these distances:
42 4 0.01
43 11 0.02
44 208 0.46
45 213 0.47
46 10 0.02
47 5 0.01
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (44 bp):
TGAAGATAACACATCTTGCCTTCCTGTACTGACAGCGAAGCAGA
Found at i:52404823 original size:22 final size:23
Alignment explanation
Indices: 52404781--52404823 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
52404771 TTCCGTACCT
* *
52404781 GCAAAGAATACGAAGACAACACA
1 GCAAAGAATAAGAAGAAAACACA
52404804 GCAAAGAA-AAGAAGAAAACA
1 GCAAAGAATAAGAAGAAAACA
52404824 ATGTATTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.63, C:0.16, G:0.19, T:0.02
Consensus pattern (23 bp):
GCAAAGAATAAGAAGAAAACACA
Found at i:52405681 original size:9 final size:9
Alignment explanation
Indices: 52405667--52405721 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
52405657 TTAATTTATC
52405667 ATTATTACT
1 ATTATTACT
52405676 ATTATTACT
1 ATTATTACT
*
52405685 ATCGTTATTATT
1 A---TTATTACT
*
52405697 ATTATTAAT
1 ATTATTACT
52405706 ATTATTACT
1 ATTATTACT
*
52405715 ACTATTA
1 ATTATTA
52405722 TTTTTATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 31 0.79
12 8 0.21
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.55
Consensus pattern (9 bp):
ATTATTACT
Found at i:52405698 original size:6 final size:6
Alignment explanation
Indices: 52405662--52405755 Score: 71
Period size: 6 Copynumber: 15.7 Consensus size: 6
52405652 TAATATTAAT
* * * ** *
52405662 TTATCA TTATTA CTATTA TTACTA TCGTTA TTATTA TTATTA ATATTA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
* * * * * * *
52405710 TTACTA CTATTA TTTTTA TTATTA GTATTT TTATTT TTATTT TTAT
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTAT
52405756 CAATTTACGT
Statistics
Matches: 68, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (6 bp):
TTATTA
Found at i:52405703 original size:30 final size:30
Alignment explanation
Indices: 52405662--52405738 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
52405652 TAATATTAAT
* * *
52405662 TTATCATTATTACTATTATTACTA-TCGTTA
1 TTATTATTATTAATATTATTACTACT-ATTA
52405692 TTATTATTATTAATATTATTACTACTATTA
1 TTATTATTATTAATATTATTACTACTATTA
* *
52405722 TTTTTATTATTAGTATT
1 TTATTATTATTAATATT
52405739 TTTATTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
30 40 0.98
31 1 0.02
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (30 bp):
TTATTATTATTAATATTATTACTACTATTA
Found at i:52405729 original size:21 final size:21
Alignment explanation
Indices: 52405696--52405750 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
52405686 TCGTTATTAT
**
52405696 TATTATTAATATTATTACTAC
1 TATTATTTTTATTATTACTAC
* *
52405717 TATTATTTTTATTATTAGTAT
1 TATTATTTTTATTATTACTAC
*
52405738 TTTTATTTTTATT
1 TATTATTTTTATT
52405751 TTTATCAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (21 bp):
TATTATTTTTATTATTACTAC
Found at i:52412795 original size:45 final size:45
Alignment explanation
Indices: 52412682--52415485 Score: 815
Period size: 45 Copynumber: 62.6 Consensus size: 45
52412672 TTAAAAATAA
* * * * *
52412682 CAGATCTTGCCTTTCTGTACTGACAG-TGAAGCAGATTGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACTGAAGATAG
* * * *
52412727 CAGCT-TTACCTTCCTGTACTGACAGCGGAGCCGACTGAAGATAG
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
* * * * * *
52412771 TAGATCTTACCTTCCTATACTGACAG-TGAAGCAGA-TCGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAG
* * *
52412816 CAG-CCTTGCCTTCCTGTACTGATAGCAGAACAGACTGAAGATAG
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
*
52412860 CAGATCTTGCCTTCCTGTACTGACAGCAGAACAGACTGAAGATAG
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
* * * *
52412905 CAGATCTTGCCTTCCTGTACTGAAAGC-GAAGCA-AATCGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAG
* * * ** *
52412950 CAG-CCTTGCC-TCACTGGGT-TTG-CAGTGGAGTAGACTAAAGATAG
1 CAGATCTTGCCTTC-CT--GTACTGACAGCGGAACAGACTGAAGATAG
* * * * * * *
52412994 CAGATTTTTCCTTTCTGTACTAACAGC-GAAGCAGA-TCGAAAACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAG
* * **
52413039 CAG-CCTTGCCTT-CT-TAGGTTGACAGCAAAACAGACTGAAGATAG
1 CAGATCTTGCCTTCCTGTA--CTGACAGCGGAACAGACTGAAGATAG
* * * * *
52413083 TAGATCTTGCCTTCTTGTACTGATAGC-GAAGTAGATCT-AAGACA-
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGA-CTGAAGATAG
* * *
52413127 CTAG-CCTTGCCTTCCTAGGT--TTACAGCGGAGCAGACTGAAGATAG
1 C-AGATCTTGCCTTCCT--GTACTGACAGCGGAACAGACTGAAGATAG
* * * *
52413172 TAGATCTTTCCATT-CTGTACTGACAGC-GAAGCAGA-TCGAAGACAT
1 CAGATCTTGCC-TTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAG
* * *
52413217 CAG-TCTTGCCTTCCTAGGT--TGACAGCAGAGCAAACTGAAGATAG
1 CAGATCTTGCCTTCCT--GTACTGACAGCGGAACAGACTGAAGATAG
* * * * * *
52413261 CAGATCTTACCTTCCTGTACTGACAG-TGAAGTAGATTGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACTGAAGATAG
* * * *
52413306 CAG-CCTTGCCTTCCTGTACTGACAGCGGAGCAGACTAAAGATAA
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
* ** * * *
52413350 CATATCTTGCCTTAATGTACTGACAAC-GAAGCAGA-TCGAATACA-
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAG
* * * * * *
52413394 CTAG-CCTTGCC-TCCTTGGATTTG-CAGCGGAGCAAACTAAAGATAG
1 C-AGATCTTGCCTTCC-TGTA-CTGACAGCGGAACAGACTGAAGATAG
* * * *
52413439 CAGATCTTGCATTCCTGTACTGACAGC-AAAGCAGA-TCGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAG
* * * ** ** * *
52413484 CAG-CCTTGCCTCCCTGGGT-TTG-CAGTAGAGTAGACTAAATATAG
1 CAGATCTTGCCTTCCT--GTACTGACAGCGGAACAGACTGAAGATAG
* * * * * *
52413528 CAGATTTTTCCTTCCTGTACTAACAGC-GAAGCAGATTGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACTGAAGATAG
* * *** *
52413573 CAG-CCTTGCCTTTCTGGGTTGACAGC-AAAGCAGACTGAAGATAG
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACTGAAGATAG
* * * *
52413617 TAGATCTTGCCTTCCTGTACTGATAGCGAAACAGATCT-AAGACA-
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAACAGA-CTGAAGATAG
* *** * **
52413661 CTAG-CCTTGCC-TCCTTGGGTTTACAGCGGAGTAGACTGAAGATAG
1 C-AGATCTTGCCTTCC-TGTACTGACAGCGGAACAGACTGAAGATAG
* * * *
52413706 TAGATCTTTCCATT-CTGTATTGACAGC-GAAGCAGA-TCGAAGA-CG
1 CAGATCTTGCC-TTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAG
* **
52413750 TCAG-TCTTGCCTTCCTAGGT--TGACAGCAGAGTAGACTGAAGATAG
1 -CAGATCTTGCCTTCCT--GTACTGACAGCGGAACAGACTGAAGATAG
* * * * *
52413795 CAGATCTTGCCTTCCTGTACTGACAGTGAAACAGATTGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
* * * * *
52413840 CAG-TCTTGCCTTCTTGTACTGACAGTGGAGCAGACTAAAGATAA
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
* ** * * * *
52413884 CACATCTTGCCTTAATGTACTGACAAC-GAAGCAGA-TCGAATACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAG
* * * * * * *
52413929 CAGCT-TTGCCTCCCTGGGT-TTG-CAGCGGAGCAAACTAAATATAG
1 CAGATCTTGCCTTCCT--GTACTGACAGCGGAACAGACTGAAGATAG
* * * * * * *
52413973 CAGATCTTACCTTCTTGTACTGACAGC-GAAGTAAATTGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACTGAAGATAG
* *** *
52414018 CAG-TCTTGCC-TCATTGGGTTGACAGCGGAGCAGACTGAAGATAG
1 CAGATCTTGCCTTC-CTGTACTGACAGCGGAACAGACTGAAGATAG
* * * *
52414062 CAGATCTTACCTTCCTGTAATGACAG-TGAAGCAGA-TCGAAGATAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAG
*** * * * *
52414107 CAG-TCTTGCC-TCTCTGGGTTAACAACGGAGCAAACTGAAGATAG
1 CAGATCTTGCCTTC-CTGTACTGACAGCGGAACAGACTGAAGATAG
* * * * * *
52414151 TAGATCTTGCCTTTCTGTACTGACAAC-GAAGCAAATCT-AAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGA-CTGAAGATAG
* * * *
52414196 CAG-TCTTGCCTCCCTGGGT-TTG-CAAC-GAAGCAAACTGAAGATAG
1 CAGATCTTGCCTTCCT--GTACTGACAGCGGAA-CAGACTGAAGATAG
* * *
52414240 CAGATCTTGTCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAA
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
* * * *
52414285 CAGATCTTGCCTTCCTGTACTGACAGC-GAAGCAGATTTAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACTGAAGATAG
* * * * * * *
52414330 CAGATCTTGCATTCCTTTGCTGAAAGTGGAGCAGATTGAAGATAG
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
* * * * *
52414375 CAGATCTTGCCTTCCTGTACTGACAGCGAAACAGATTGAAAACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
* * * ** * * *
52414420 CAGATCTTGCATTCTTTTACTGACAGCGGAGTAAACTGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
* * * * *
52414465 CAG-CCTTGCATTCCTGTACTGACA-CCGAAGCAGA-TCGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAG
* * * * *
52414509 CAG-CCTTACCTCCCTAGGT-TTG-CAGC-GAAGCAGACTAAAGATAG
1 CAGATCTTGCCTTCCT--GTACTGACAGCGGAA-CAGACTGAAGATAG
* * * * * *
52414553 CAGATCAAAGATACCAGTCTTGCCTCT-CTGGGTTA-ACAACGGAGCAAACTGAAGATAG
1 CAGATC-----T---TGCCTT-CCTGTACT--G--ACA-G-CGGAACAGACTGAAGATAG
* * * * * * *
52414611 TAGATCTTACCTTTCTGTACTGACAAC-GAAGCAAATCT-AAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGA-CTGAAGATAG
* * * **
52414656 CAG-TCTTACCTCCCTGGGT-TTG-CA-ATGAAGCAGACTGAAGATAG
1 CAGATCTTGCCTTCCT--GTACTGACAGCGGAA-CAGACTGAAGATAG
* *
52414700 CAGATCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAA
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
*
52414745 CAGATCTTGCCTTCCTGTACTGACAGC-GAAGCAGATCT-AAGACA-
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGA-CTGAAGATAG
* * * * *
52414789 CTAGATCTTGCATTCCTTTGCTGACAGTGGAGCAGACTGAAGATAG
1 C-AGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
* * * * *
52414835 CAGATCTTGCCTTCCTGTACTGACAGCGAAACAGATTGAAAACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
* * * ** * * *
52414880 CAGATCTTGCATTCTTTTACTGACAGCGGAGTAAACTGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
* * * * *
52414925 CAG-CCTTGCATTCCTGTACTGACA-CCGAAGCAGA-TCGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAG
* * * * * *
52414969 CAG-CCTTACCTCCCTAGGT-TTG-CAG-TGAAGCAGACTAAAGATAG
1 CAGATCTTGCCTTCCT--GTACTGACAGCGGAA-CAGACTGAAGATAG
* * * * * *
52415013 CAGATTTTACCTTCTTGTACTGACAGC-GAAGCAGA-TCGAAAACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAG
* * *** * *
52415058 CAG-CCTTGCCTCCCTGGGTTGACAGCGGAGCAGACTAAAGATAG
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
** * * ** *
52415102 C-GTATCATTGTTTTCCTATATTGGTAGC-GAAGCA-A-TCGAAGACA-
1 CAG-ATC-TTGCCTTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAG
* * * * * *
52415146 CTAG-CCTTGCCTCCCTG-AGTTTG-TAGCGGAGCAGACTAAAGATAG
1 C-AGATCTTGCCTTCCTGTA--CTGACAGCGGAACAGACTGAAGATAG
* ** ** *
52415191 C-GTACCATTGTTTTCCTGTACTGGTAGC-GAAGCA-A-TCGAAGACA-
1 CAG-ATC-TTGCCTTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAG
* * *** * * *
52415235 CTAG-CCTTGCCTCCCTGGGTTGACAGCGGAGCAGAGTGAATATAG
1 C-AGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
* * * * *
52415280 TAGATATTGCCTTCCTATGCTGACAGC-GAAGCAGA-TCGAAGATAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAG
* * * *
52415325 CAG-CCTTGCCTCCCTGGGT-TTG-CAGCGGAGCAGACTGAAGATAG
1 CAGATCTTGCCTTCCT--GTACTGACAGCGGAACAGACTGAAGATAG
* * *
52415369 CAGATCTTGCCTTCCTGTACTGATAGC-GAAGCAGA-TCGAAGACAC
1 CAGATCTTGCCTTCCTGTACTGACAGCGGAA-CAGACT-GAAGATAG
* * *
52415414 CA-ACCTTGCC-TCTCTAGGT--TTACAGCGGAGCAGACTGAAGATAG
1 CAGATCTTGCCTTC-CT--GTACTGACAGCGGAACAGACTGAAGATAG
52415458 CAGATCTTGCCTTCCTGTACTGACAGCG
1 CAGATCTTGCCTTCCTGTACTGACAGCG
52415486 AAGCAGATCG
Statistics
Matches: 2001, Mismatches: 528, Indels: 460
0.67 0.18 0.15
Matches are distributed among these distances:
42 3 0.00
43 86 0.04
44 771 0.39
45 1005 0.50
46 91 0.05
47 5 0.00
48 1 0.00
49 3 0.00
50 6 0.00
52 2 0.00
53 3 0.00
54 4 0.00
56 1 0.00
58 18 0.01
59 2 0.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (45 bp):
CAGATCTTGCCTTCCTGTACTGACAGCGGAACAGACTGAAGATAG
Found at i:52412958 original size:89 final size:89
Alignment explanation
Indices: 52412687--52414498 Score: 1389
Period size: 89 Copynumber: 20.3 Consensus size: 89
52412677 AATAACAGAT
* * * * * * * * *
52412687 CTTGCCTTTCTGTACTGACAGTGAAGCAGATTGAAGACACCAGCT-TTACCTTCCTGTACTGACA
1 CTTGCCTTCCTGTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
* * * ** *
52412751 GCGGAGCCGA-CTGAAGATAGTAGAT
66 GCGAAGCAGATC-GAAGACACCAG-C
* * * * * * * * *
52412776 CTTACCTTCCTATACTGACAGTGAAGCAGA-TCGAAGACACCAG-CCTTGCCTTCCTGTACTGAT
1 CTTGCCTTCCTGTATTGACAGCGGAGCAGACT-GAAGATAGCAGATCTTGCCTTCCTGTACTGAC
* * *
52412839 AGCAGAA-CAGA-CTGAAGATAGCAGAT
65 AGC-GAAGCAGATC-GAAGACACCAG-C
* * * *
52412865 CTTGCCTTCCTGTACTGACAGCAGAACAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAAA
1 CTTGCCTTCCTGTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
*
52412930 GCGAAGCAAATCGAAGACACCAGC
66 GCGAAGCAGATCGAAGACACCAGC
* * * * * * *
52412954 CTTGCC-TCACTGGGT-TTG-CAGTGGAGTAGACTAAAGATAGCAGATTTTTCCTTTCTGTACTA
1 CTTGCCTTC-CT--GTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTG
*
52413016 ACAGCGAAGCAGATCGAAAACACCAGC
63 ACAGCGAAGCAGATCGAAGACACCAGC
** * * *
52413043 CTTGCCTT-CT-TAGGTTGACAGCAAAACAGACTGAAGATAGTAGATCTTGCCTTCTTGTACTGA
1 CTTGCCTTCCTGTA--TTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGA
* * * *
52413106 TAGCGAAGTAGATCTAAGACACTAGC
64 CAGCGAAGCAGATCGAAGACACCAGC
* *
52413132 CTTGCCTTCCTAGGT-TT-ACAGCGGAGCAGACTGAAGATAGTAGATCTTTCCATT-CTGTACTG
1 CTTGCCTTCCT--GTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCC-TTCCTGTACTG
* *
52413194 ACAGCGAAGCAGATCGAAGACATCAGT
63 ACAGCGAAGCAGATCGAAGACACCAGC
* * * *
52413221 CTTGCCTTCCTAG-GTTGACAGCAGAGCAAACTGAAGATAGCAGATCTTACCTTCCTGTACTGAC
1 CTTGCCTTCCT-GTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
* * *
52413285 AGTGAAGTAGATTGAAGACACCAGC
65 AGCGAAGCAGATCGAAGACACCAGC
* * * * **
52413310 CTTGCCTTCCTGTACTGACAGCGGAGCAGACTAAAGATAACATATCTTGCCTTAATGTACTGACA
1 CTTGCCTTCCTGTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
* * *
52413375 ACGAAGCAGATCGAATACACTAGC
66 GCGAAGCAGATCGAAGACACCAGC
* * * *
52413399 CTTGCC-TCCTTGGATTTG-CAGCGGAGCAAACTAAAGATAGCAGATCTTGCATTCCTGTACTGA
1 CTTGCCTTCC-TGTA-TTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGA
*
52413462 CAGCAAAGCAGATCGAAGACACCAGC
64 CAGCGAAGCAGATCGAAGACACCAGC
* ** * * * * * *
52413488 CTTGCCTCCCTGGGT-TTG-CAGTAGAGTAGACTAAATATAGCAGATTTTTCCTTCCTGTACTAA
1 CTTGCCTTCCT--GTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGA
*
52413551 CAGCGAAGCAGATTGAAGACACCAGC
64 CAGCGAAGCAGATCGAAGACACCAGC
* ** ** * *
52413577 CTTGCCTTTCTGGGTTGACAGCAAAGCAGACTGAAGATAGTAGATCTTGCCTTCCTGTACTGATA
1 CTTGCCTTCCTGTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
* * *
52413642 GCGAAACAGATCTAAGACACTAGC
66 GCGAAGCAGATCGAAGACACCAGC
** * * * * *
52413666 CTTGCC-TCCTTGGGTTTACAGCGGAGTAGACTGAAGATAGTAGATCTTTCCATT-CTGTATTGA
1 CTTGCCTTCC-TGTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCC-TTCCTGTACTGA
** *
52413729 CAGCGAAGCAGATCGAAGACGTCAGT
64 CAGCGAAGCAGATCGAAGACACCAGC
* * *
52413755 CTTGCCTTCCTAG-GTTGACAGCAGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
1 CTTGCCTTCCT-GTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
* * * *
52413819 AGTGAAACAGATTGAAGACACCAGT
65 AGCGAAGCAGATCGAAGACACCAGC
* * * * * * **
52413844 CTTGCCTTCTTGTACTGACAGTGGAGCAGACTAAAGATAACACATCTTGCCTTAATGTACTGACA
1 CTTGCCTTCCTGTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
* *
52413909 ACGAAGCAGATCGAATACACCAGC
66 GCGAAGCAGATCGAAGACACCAGC
* * * * * * *
52413933 TTTGCCTCCCTGGGT-TTG-CAGCGGAGCAAACTAAATATAGCAGATCTTACCTTCTTGTACTGA
1 CTTGCCTTCCT--GTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGA
* * * *
52413996 CAGCGAAGTAAATTGAAGACACCAGT
64 CAGCGAAGCAGATCGAAGACACCAGC
* ** * *
52414022 CTTGCC-TCATTGGGTTGACAGCGGAGCAGACTGAAGATAGCAGATCTTACCTTCCTGTAATGAC
1 CTTGCCTTC-CTGTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
* * *
52414086 AGTGAAGCAGATCGAAGATACCAGT
65 AGCGAAGCAGATCGAAGACACCAGC
** * * * * *
52414111 CTTGCC-TCTCTGGGTTAACAACGGAGCAAACTGAAGATAGTAGATCTTGCCTTTCTGTACTGAC
1 CTTGCCTTC-CTGTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
* * * *
52414175 AACGAAGCAAATCTAAGACACCAGT
65 AGCGAAGCAGATCGAAGACACCAGC
* * * * *
52414200 CTTGCCTCCCTGGGT-TTG-CAACGAAGCAAACTGAAGATAGCAGATCTTGTCTTCCTGTACTGA
1 CTTGCCTTCCT--GTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGA
* * * *
52414263 CAGCGGAGCAGA-CTGAAGATAACAGAT
64 CAGCGAAGCAGATC-GAAGACACCAG-C
* * * * * * * * * *
52414290 CTTGCCTTCCTGTACTGACAGCGAAGCAGATTTAAGACACCAGATCTTGCATTCCTTTGCTGAAA
1 CTTGCCTTCCTGTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
* * * * * *
52414355 GTGGAGCAGATTGAAGATAGCAGAT
66 GCGAAGCAGATCGAAGACACCAG-C
* * * * * * * * * *
52414380 CTTGCCTTCCTGTACTGACAGCGAAACAGATTGAAAACACCAGATCTTGCATTCTTTTACTGACA
1 CTTGCCTTCCTGTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
* * *
52414445 GCGGAGTA-AACTGAAGACACCAGC
66 GCGAAGCAGATC-GAAGACACCAGC
* * * *
52414469 CTTGCATTCCTGTACTGACACCGAAGCAGA
1 CTTGCCTTCCTGTATTGACAGCGGAGCAGA
52414499 TCGAAGACAC
Statistics
Matches: 1408, Mismatches: 264, Indels: 102
0.79 0.15 0.06
Matches are distributed among these distances:
85 1 0.00
87 2 0.00
88 32 0.02
89 1163 0.83
90 202 0.14
91 7 0.00
93 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (89 bp):
CTTGCCTTCCTGTATTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
GCGAAGCAGATCGAAGACACCAGC
Found at i:52413049 original size:178 final size:177
Alignment explanation
Indices: 52412824--52414933 Score: 1429
Period size: 178 Copynumber: 11.8 Consensus size: 177
52412814 ACCAGCCTTG
* * * * *
52412824 CCTTCCTGTACTGATAGCAGAA-CAGA-CTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGC
1 CCTTCCTGTACTGACAGC-GAAGCAGATC-GAAGACACCAG-CCTTGCCTTCCTGTATTGACAGC
* * *
52412887 AGAACAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAAAGCGAAGCAAATCGAAGACACCA
63 AGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCA
* * *
52412952 GCCTTGCCTCACTGGGTTTGCAGTGGAGTAGACTAAAGATAGCAGATTTTT
128 GCCTTGCCTC-CTGGGTTTGCAGCGGAGCAGACTAAAGATAGCAGATCTTT
* * *
52413003 CCTTTCTGTACTAACAGCGAAGCAGATCGAAAACACCAGCCTTGCCTT-CT-TAGGTTGACAGCA
1 CCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTA--TTGACAGCA
* * * * * * * *
52413066 AAACAGACTGAAGATAGTAGATCTTGCCTTCTTGTACTGATAGCGAAGTAGATCTAAGACACTAG
64 GAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAG
* * * *
52413131 CCTTGCCTTCCTAGGTTTACAGCGGAGCAGACTGAAGATAGTAGATCTTT
129 CCTTGCC-TCCTGGGTTTGCAGCGGAGCAGACTAAAGATAGCAGATCTTT
* * *
52413181 CCATT-CTGTACTGACAGCGAAGCAGATCGAAGACATCAGTCTTGCCTTCCTAG-GTTGACAGCA
1 CC-TTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCT-GTATTGACAGCA
* * * * *
52413244 GAGCAAACTGAAGATAGCAGATCTTACCTTCCTGTACTGACAGTGAAGTAGATTGAAGACACCAG
64 GAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAG
* * * *
52413309 CCTTGCCTTCCT--GTACTGACAGCGGAGCAGACTAAAGATAACATATCTTG
129 CCTTGCC-TCCTGGGT-TTG-CAGCGGAGCAGACTAAAGATAGCAGATCTTT
** * * * * *
52413359 CCTTAATGTACTGACAACGAAGCAGATCGAATACACTAGCCTTGCC-TCCTTGGATTTG-CAGCG
1 CCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCC-TGTA-TTGACAGCA
* * * *
52413422 GAGCAAACTAAAGATAGCAGATCTTGCATTCCTGTACTGACAGCAAAGCAGATCGAAGACACCAG
64 GAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAG
** * * *
52413487 CCTTGCCTCCCTGGGTTTGCAGTAGAGTAGACTAAATATAGCAGATTTTT
129 CCTTGCCT-CCTGGGTTTGCAGCGGAGCAGACTAAAGATAGCAGATCTTT
* * * ** *
52413537 CCTTCCTGTACTAACAGCGAAGCAGATTGAAGACACCAGCCTTGCCTTTCTGGGTTGACAGCAAA
1 CCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTATTGACAGCAGA
* * * * *
52413602 GCAGACTGAAGATAGTAGATCTTGCCTTCCTGTACTGATAGCGAAACAGATCTAAGACACTAGCC
66 GCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCC
* * * *
52413667 TTGCCTCCTTGGGTTTACAGCGGAGTAGACTGAAGATAGTAGATCTTT
131 TTGCCTCC-TGGGTTTGCAGCGGAGCAGACTAAAGATAGCAGATCTTT
* ** * *
52413715 CCATT-CTGTATTGACAGCGAAGCAGATCGAAGACGTCAGTCTTGCCTTCCTAG-GTTGACAGCA
1 CC-TTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCT-GTATTGACAGCA
* * * *
52413778 GAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAACAGATTGAAGACACCAG
64 GAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAG
* * * * * * * *
52413843 TCTTGCCTTCT-TGTACTGACAGTGGAGCAGACTAAAGATAACACATCTTG
129 CCTTGCCTCCTGGGT-TTG-CAGCGGAGCAGACTAAAGATAGCAGATCTTT
** * * * * *
52413893 CCTTAATGTACTGACAACGAAGCAGATCGAATACACCAGCTTTGCCTCCCTGGGT-TTG-CAGCG
1 CCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCT--GTATTGACAGCA
* * * * * * * *
52413956 GAGCAAACTAAATATAGCAGATCTTACCTTCTTGTACTGACAGCGAAGTAAATTGAAGACACCAG
64 GAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAG
* * * *
52414021 TCTTGCCTCATTGGG-TTGACAGCGGAGCAGACTGAAGATAGCAGATCTTA
129 CCTTGCCTC-CTGGGTTTG-CAGCGGAGCAGACTAAAGATAGCAGATCTTT
* * * * ** * * *
52414071 CCTTCCTGTAATGACAGTGAAGCAGATCGAAGATACCAGTCTTGCC-TCTCTGGGTTAACAACGG
1 CCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTC-CTGTATTGACAGCAG
* * * * * * *
52414135 AGCAAACTGAAGATAGTAGATCTTGCCTTTCTGTACTGACAACGAAGCAAATCTAAGACACCAGT
65 AGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGC
* * * *
52414200 CTTGCCTCCCTGGGTTTGCAACGAAGCAAACTGAAGATAGCAGATCTTGT
130 CTTGCCT-CCTGGGTTTGCAGCGGAGCAGACTAAAGATAGCAGATCTT-T
* * * * *
52414250 -CTTCCTGTACTGACAGCGGAGCAGA-CTGAAGATAACAGATCTTGCCTTCCTGTACTGACAGC-
1 CCTTCCTGTACTGACAGCGAAGCAGATC-GAAGACACCAG-CCTTGCCTTCCTGTATTGACAGCA
* * * * * * * * * * * * *
52414312 GAAGCAGATTTAAGACACCAGATCTTGCATTCCTTTGCTGAAAGTGGAGCAGATTGAAGATAGCA
64 G-AGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCA
* * * * * * * *
52414377 GATCTTGCCTTCCT--GTACTGACAGCGAAACAGATTGAAA-ACACCAGATCTTG
128 G-CCTTGCC-TCCTGGGT-TTG-CAGCGGAGCAGACT-AAAGATAGCAGATCTTT
* * * * * * * * *
52414429 CATTCTTTTACTGACAGCGGAGTA-AACTGAAGACACCAGCCTTGCATTCCTGTACTGACA-CCG
1 CCTTCCTGTACTGACAGCGAAGCAGATC-GAAGACACCAGCCTTGCCTTCCTGTATTGACAGCAG
* * * * *
52414492 AAGCAGA-TCGAAGACACCAG-CCTTACCTCCCTAGGTTTGCAGC-GAAGCAGACTAAAGATAGC
65 -AGCAGACT-GAAGATAGCAGATCTTGCCTTCCT--G--T--A-CTG-A-CAG-C----GA-AGC
* * * ** * * * *
52414554 AGATCAAAGATACCAGTCTTGCCTCTCTGGGTTAACAACGGAGCAAACTGAAGATAGTAGATCTT
113 AGATCGAAGACACCAGCCTTGCCTC-CTGGGTTTGCAGCGGAGCAGACTAAAGATAGCAGATCTT
*
52414619 A
177 T
* * * * * * *
52414620 CCTTTCTGTACTGACAACGAAGCAAATCTAAGACACCAGTCTTACCTCCCTGGGT-TTG-CA--A
1 CCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCT--GTATTGACAGCA
* * *
52414681 TGAAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGGAGCAGA-CTGAAGATAA
64 -G-AGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATC-GAAGACAC
* * * * *
52414745 CAGATCTTGCCTTCCT--GTACTGACAGCGAAGCAGATCT-AAGACA-CTAGATCTTG
126 CAG-CCTTGCC-TCCTGGGT-TTG-CAGCGGAGCAGA-CTAAAGATAGC-AGATCTTT
* * * * * * * * *
52414799 CATTCCTTTGCTGACAGTGGAGCAGA-CTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGC-
1 CCTTCCTGTACTGACAGCGAAGCAGATC-GAAGACACCAG-CCTTGCCTTCCTGTATTGACAGCA
* * * * * * * * * * *
52414862 GAAACAGATTGAAAACACCAGATCTTGCATTCTTTTACTGACAGCGGAGTA-AACTGAAGACACC
64 G-AGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATC-GAAGACACC
52414926 AGCCTTGC
127 AGCCTTGC
52414934 ATTCCTGTAC
Statistics
Matches: 1531, Mismatches: 311, Indels: 178
0.76 0.15 0.09
Matches are distributed among these distances:
176 7 0.00
177 26 0.02
178 1007 0.66
179 217 0.14
180 135 0.09
181 3 0.00
182 1 0.00
183 1 0.00
184 4 0.00
185 4 0.00
186 4 0.00
188 1 0.00
190 5 0.00
191 82 0.05
192 30 0.02
193 4 0.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (177 bp):
CCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTATTGACAGCAGA
GCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCC
TTGCCTCCTGGGTTTGCAGCGGAGCAGACTAAAGATAGCAGATCTTT
Found at i:52413073 original size:223 final size:223
Alignment explanation
Indices: 52412682--52415073 Score: 637
Period size: 223 Copynumber: 10.7 Consensus size: 223
52412672 TTAAAAATAA
* * * * * *
52412682 CAGATCTTGCCTTTCTGTACTGACAGTGAAGCAGATTGAAGACACCAGCTTTACCTTCCTGTACT
1 CAGATCTTGCCTTCCTGTACTGAAAGCGAAGCAAATCGAAGACACCAGCCTTACCTTCCTGTACT
* * * * * *
52412747 GACAGCGGAGCCGACTGAAGATAGTAGATCTTACCTTCCTATACTGACAGTGAAGCAGATCGAAG
66 GACAGCGGAGCAGACTAAAGATAGCAGATCTTACCTTCCTATACTAACAGCGAAGCAGATCGAAA
* *
52412812 ACACCAGCCTTGCCTTCCTGTACTGATAGCAGAACAGACTGAAGATAGCAGATCTTGCCTTCCTG
131 ACACCAGCCTTGCCTTCCTGTACTGACAGCAAAACAGACTGAAGATAGCAGATCTTGCCTTCCTG
52412877 TACTGACAGCAGAACAGACTGAAGATAG
196 TACTGACAGCAGAACAGACTGAAGATAG
*
52412905 CAGATCTTGCCTTCCTGTACTGAAAGCGAAGCAAATCGAAGACACCAGCCTTGCC-TCACTGGGT
1 CAGATCTTGCCTTCCTGTACTGAAAGCGAAGCAAATCGAAGACACCAGCCTTACCTTC-CT--GT
* * * * * * *
52412969 -TTG-CAGTGGAGTAGACTAAAGATAGCAGATTTTTCCTTTCTGTACTAACAGCGAAGCAGATCG
63 ACTGACAGCGGAGCAGACTAAAGATAGCAGATCTTACCTTCCTATACTAACAGCGAAGCAGATCG
* *
52413032 AAAACACCAGCCTTGCCTT-CT-TAGGTTGACAGCAAAACAGACTGAAGATAGTAGATCTTGCCT
128 AAAACACCAGCCTTGCCTTCCTGTA--CTGACAGCAAAACAGACTGAAGATAGCAGATCTTGCCT
* * * *
52413095 TCTTGTACTGATAGC-GAAGTAGATCT-AAGACA-
191 TCCTGTACTGACAGCAGAA-CAGA-CTGAAGATAG
* * * * * * ** * *
52413127 CTAG-CCTTGCCTTCCTAGGT--TTACAGCGGAGCAGA-CTGAAGATAGTAGATCTTTCCATT-C
1 C-AGATCTTGCCTTCCT--GTACTGAAAGCGAAGCAAATC-GAAGACACCAG-CCTTACC-TTCC
* * * * * *** *
52413187 TGTACTGACAGCGAAGCAGA-TCGAAGACATCAG-TCTTGCCTTCCTAGGTTGACAGC-AGAGCA
60 TGTACTGACAGCGGAGCAGACT-AAAGATAGCAGATCTTACCTTCCTATACTAACAGCGA-AGCA
* * * * * * ** ** * * * *
52413249 -AACTGAAGATAGCAGATCTTACCTTCCTGTACTGACAGTGAAGTAGATTGAAGACACCAG-CCT
123 GATC-GAAAACACCAG-CCTTGCCTTCCTGTACTGACAGCAAAACAGACTGAAGATAGCAGATCT
* * * *
52413312 TGCCTTCCTGTACTGACAGCGGAGCAGACTAAAGATAA
186 TGCCTTCCTGTACTGACAGCAGAACAGACTGAAGATAG
* ** * * * * *
52413350 CATATCTTGCCTTAATGTACTGACAA-CGAAGCAGATCGAATACACTAGCCTTGCC-TCCTTGGA
1 CAGATCTTGCCTTCCTGTACTGA-AAGCGAAGCAAATCGAAGACACCAGCCTTACCTTCC-TGTA
* * * * * * *
52413413 TTTG-CAGCGGAGCAAACTAAAGATAGCAGATCTTGCATTCCTGTACTGACAGCAAAGCAGATCG
64 -CTGACAGCGGAGCAGACTAAAGATAGCAGATCTTACCTTCCTATACTAACAGCGAAGCAGATCG
* * * * * ** * * * *
52413477 AAGACACCAGCCTTGCCTCCCTGGGT-TTG-CAGTAGAGTAGACTAAATATAGCAGATTTTTCCT
128 AAAACACCAGCCTTGCCTTCCT--GTACTGACAGCAAAACAGACTGAAGATAGCAGATCTTGCCT
* * * *
52413540 TCCTGTACTAACAGC-GAAGCAGATTGAAGACAC
191 TCCTGTACTGACAGCAGAA-CAGACTGAAGATAG
* * *** * * * * ** * *
52413573 CAG-CCTTGCCTTTCTGGGTTGACAGCAAAGCAGA-CTGAAGATAGTAGATCTTGCCTTCCTGTA
1 CAGATCTTGCCTTCCTGTACTGAAAGCGAAGCAAATC-GAAGACACCAG-CCTTACCTTCCTGTA
* * * * * * ** * * *
52413636 CTGATAGCGAAACAGATCT-AAGACA-CTAG-CCTTGCC-TCCT-TGGGTTTACAGCGGAGTAGA
64 CTGACAGCGGAGCAGA-CTAAAGATAGC-AGATCTTACCTTCCTAT--ACTAACAGCGAAGCAGA
* * ** * * * * * *
52413696 -CTGAAGATAGTAGATCTTTCCATT-CTGTATTGACAGCGAAGCAGA-TCGAAGA-CGTCAG-TC
125 TC-GAAAACACCAG-CCTTGCC-TTCCTGTACTGACAGCAAAACAGACT-GAAGATAG-CAGATC
**
52413756 TTGCCTTCCTAGGT--TGACAGCAGAGTAGACTGAAGATAG
185 TTGCCTTCCT--GTACTGACAGCAGAACAGACTGAAGATAG
* * * * * * * *
52413795 CAGATCTTGCCTTCCTGTACTGACAGTGAAACAGATTGAAGACACCAGTCTTGCCTTCTTGTACT
1 CAGATCTTGCCTTCCTGTACTGAAAGCGAAGCAAATCGAAGACACCAGCCTTACCTTCCTGTACT
* * * * ** * * * *
52413860 GACAGTGGAGCAGACTAAAGATAACACATCTTGCCTTAATGTACTGACAACGAAGCAGATCGAAT
66 GACAGCGGAGCAGACTAAAGATAGCAGATCTTACCTTCCTATACTAACAGCGAAGCAGATCGAAA
* * * ** * * * * * *
52413925 ACACCAGCTTTGCCTCCCTGGGT-TTG-CAGCGGAGCAAACTAAATATAGCAGATCTTACCTTCT
131 ACACCAGCCTTGCCTTCCT--GTACTGACAGCAAAACAGACTGAAGATAGCAGATCTTGCCTTCC
* * * * *
52413988 TGTACTGACAGC-GAAGTAAATTGAAGACAC
194 TGTACTGACAGCAGAA-CAGACTGAAGATAG
* *** * * * * * *
52414018 CAG-TCTTGCC-TCATTGGGTTGACAGCGGAGCAGA-CTGAAGATAGCAGATCTTACCTTCCTGT
1 CAGATCTTGCCTTC-CTGTACTGAAAGCGAAGCAAATC-GAAGACACCAG-CCTTACCTTCCTGT
* * * * * * **** * * *
52414080 AATGACAGTGAAGCAGA-TCGAAGATACCAG-TCTTGCC-TCTCTGGGTTAACAACGGAGCA-AA
63 ACTGACAGCGGAGCAGACT-AAAGATAGCAGATCTTACCTTC-CTATACTAACAGCGAAGCAGAT
* * ** * * * * * * * *
52414141 CTGAAGATAGTAGATCTTGCCTTTCTGTACTGACAACGAAGCAAATCT-AAGACACCAG-TCTTG
126 C-GAAAACACCAG-CCTTGCCTTCCTGTACTGACAGCAAAACAGA-CTGAAGATAGCAGATCTTG
* * * *
52414204 CCTCCCTGGGT-TTG-CAAC-GAAGCAAACTGAAGATAG
188 CCTTCCT--GTACTGACAGCAGAA-CAGACTGAAGATAG
* * * * * * * *
52414240 CAGATCTTGTCTTCCTGTACTGACAGCGGAGCAGA-CTGAAGATAACAGATCTTGCCTTCCTGTA
1 CAGATCTTGCCTTCCTGTACTGAAAGCGAAGCAAATC-GAAGACACCAG-CCTTACCTTCCTGTA
* * * * * * * * * * * *
52414304 CTGACAGCGAAGCAGATTTAAGACACCAGATCTTGCATTCCTTTGCTGAA-AGTGGAGCAGATTG
64 CTGACAGCGGAGCAGACTAAAGATAGCAGATCTTACCTTCCTATACT-AACAGCGAAGCAGATCG
* * * * * * * * * *
52414368 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAACAGATTGAAAACACCAGATCTTGCATT
128 AAAACACCAG-CCTTGCCTTCCTGTACTGACAGCAAAACAGACTGAAGATAGCAGATCTTGCCTT
* * * ** * * *
52414433 CTTTTACTGACAGCGGAGTAAACTGAAGACAC
192 CCTGTACTGACAGCAGAACAGACTGAAGATAG
* * * * * *
52414465 CAG-CCTTGCATTCCTGTACTGACACCGAAGCAGATCGAAGACACCAGCCTTACCTCCCTAGGT-
1 CAGATCTTGCCTTCCTGTACTGAAAGCGAAGCAAATCGAAGACACCAGCCTTACCTTCCT--GTA
* * * *
52414528 TTG-CAGCGAAGCAGACTAAAGATAGCAGATCAAAGATACCAGTCTTGCCTCT-CTGGGTTAACA
64 CTGACAGCGGAGCAGACTAAAGATAGCAGATC----TTA-C---CTT-CCTATAC-----TAACA
* * * * * ** * * * * * * * *
52414591 ACGGAGCA-AACTGAAGATAGTAGATCTTACCTTTCTGTACTGACAACGAAGCAAATCT-AAGAC
115 GCGAAGCAGATC-GAAAACACCAG-CCTTGCCTTCCTGTACTGACAGCAAAACAGA-CTGAAGAT
* * * *
52414654 ACCAG-TCTTACCTCCCTGGGT-TTG-CA--ATGAAGCAGACTGAAGATAG
177 AGCAGATCTTGCCTTCCT--GTACTGACAGCA-GAA-CAGACTGAAGATAG
* * * * * * *
52414700 CAGATCTTGCCTTCCTGTACTGACAGCGGAGCAGA-CTGAAGATAACAGATCTTGCCTTCCTGTA
1 CAGATCTTGCCTTCCTGTACTGAAAGCGAAGCAAATC-GAAGACACCAG-CCTTACCTTCCTGTA
* * * * * * * * *
52414764 CTGACAGCGAAGCAGATCT-AAGACA-CTAGATCTTGCATTCCTTTGCTGACAGTGGAGCAGA-C
64 CTGACAGCGGAGCAGA-CTAAAGATAGC-AGATCTTACCTTCCTATACTAACAGCGAAGCAGATC
* * * * * * * * * *
52414826 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAACAGATTGAAAACACCAGATCTTGCA
127 -GAAAACACCAG-CCTTGCCTTCCTGTACTGACAGCAAAACAGACTGAAGATAGCAGATCTTGCC
* * * ** * * *
52414891 TTCTTTTACTGACAGCGGAGTAAACTGAAGACAC
190 TTCCTGTACTGACAGCAGAACAGACTGAAGATAG
* * * * * *
52414925 CAG-CCTTGCATTCCTGTACTGACACCGAAGCAGATCGAAGACACCAGCCTTACCTCCCTAGGT-
1 CAGATCTTGCCTTCCTGTACTGAAAGCGAAGCAAATCGAAGACACCAGCCTTACCTTCCT--GTA
* * * * * * *
52414988 TTG-CAGTGAAGCAGACTAAAGATAGCAGATTTTACCTTCTTGTACTGACAGCGAAGCAGATCGA
64 CTGACAGCGGAGCAGACTAAAGATAGCAGATCTTACCTTCCTATACTAACAGCGAAGCAGATCGA
*
52415052 AAACACCAGCCTTGCCTCCCTG
129 AAACACCAGCCTTGCCTTCCTG
52415074 GGTTGACAGC
Statistics
Matches: 1615, Mismatches: 408, Indels: 293
0.70 0.18 0.13
Matches are distributed among these distances:
220 2 0.00
221 34 0.02
222 400 0.25
223 691 0.43
224 238 0.15
225 67 0.04
226 4 0.00
227 1 0.00
228 5 0.00
229 3 0.00
231 3 0.00
232 5 0.00
233 1 0.00
234 2 0.00
235 29 0.02
236 95 0.06
237 33 0.02
238 2 0.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (223 bp):
CAGATCTTGCCTTCCTGTACTGAAAGCGAAGCAAATCGAAGACACCAGCCTTACCTTCCTGTACT
GACAGCGGAGCAGACTAAAGATAGCAGATCTTACCTTCCTATACTAACAGCGAAGCAGATCGAAA
ACACCAGCCTTGCCTTCCTGTACTGACAGCAAAACAGACTGAAGATAGCAGATCTTGCCTTCCTG
TACTGACAGCAGAACAGACTGAAGATAG
Found at i:52413202 original size:267 final size:267
Alignment explanation
Indices: 52412894--52414301 Score: 1545
Period size: 267 Copynumber: 5.3 Consensus size: 267
52412884 AGCAGAACAG
* * * *
52412894 ACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAAAGCGAAGCAAATCGAAGACACCAGCCTTGC
1 ACTGAAGATAGCAGATCTTTCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGC
** * * * * * *
52412959 CTCACTGGGTTTG-CAGTGGAGTAGACTAAAGATAGCAGATTTTTCCTTTCTGTACTAACAGCGA
66 CTC-CTGGG-TTGACAGCAGAGTAGACTGAAGATAGCAGATCTTACCTTCCTGTACTGACAGTGA
* * ** *
52413023 AGCAGATCGAAAACACCAGCCTTGCCTTCT-TAGGTTGACAGCAAAACAGACTGAAGATAGTAGA
129 AGCAGATTGAAGACACCAGCCTTGCCTTCTCTAGGTTGACAGCGGAGCAGACTGAAGATAGTAGA
** * * * *
52413087 TCTTGCCTTCTTGTACTGATAGCGAAGTAGATCTAAGACACTAGCCTTGCCTTCCTAGGTTTACA
194 TCTTGCCTTAATGTACTGACAACGAAGCAGATCTAAGACACTAGCCTTGCCTTCCTGGGTTTACA
*
52413152 GCGGAGCAG
259 GCGGAGCAA
* *
52413161 ACTGAAGATAGTAGATCTTTCCATT-CTGTACTGACAGCGAAGCAGATCGAAGACATCAGTCTTG
1 ACTGAAGATAGCAGATCTTTCC-TTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTG
* * *
52413225 CCTTCCTAGGTTGACAGCAGAGCAAACTGAAGATAGCAGATCTTACCTTCCTGTACTGACAGTGA
65 CC-TCCTGGGTTGACAGCAGAGTAGACTGAAGATAGCAGATCTTACCTTCCTGTACTGACAGTGA
* * **
52413290 AGTAGATTGAAGACACCAGCCTTGCCTTC-CT--GTACTGACAGCGGAGCAGACTAAAGATAACA
129 AGCAGATTGAAGACACCAGCCTTGCCTTCTCTAGGT--TGACAGCGGAGCAGACTGAAGATAGTA
* * * *
52413352 TATCTTGCCTTAATGTACTGACAACGAAGCAGATCGAATACACTAGCCTTGCC-TCCTTGGATTT
192 GATCTTGCCTTAATGTACTGACAACGAAGCAGATCTAAGACACTAGCCTTGCCTTCC-TGGGTTT
*
52413416 GCAGCGGAGCAA
256 ACAGCGGAGCAA
* * * * *
52413428 ACTAAAGATAGCAGATCTTGCATTCCTGTACTGACAGCAAAGCAGATCGAAGACACCAGCCTTGC
1 ACTGAAGATAGCAGATCTTTCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGC
* * * * * * *
52413493 CTCCCTGGGTTTG-CAGTAGAGTAGACTAAATATAGCAGATTTTTCCTTCCTGTACTAACAGCGA
66 CT-CCTGGG-TTGACAGCAGAGTAGACTGAAGATAGCAGATCTTACCTTCCTGTACTGACAGTGA
* **
52413557 AGCAGATTGAAGACACCAGCCTTGCCTT-TCTGGGTTGACAGCAAAGCAGACTGAAGATAGTAGA
129 AGCAGATTGAAGACACCAGCCTTGCCTTCTCTAGGTTGACAGCGGAGCAGACTGAAGATAGTAGA
** * * *
52413621 TCTTGCCTTCCTGTACTGATAGCGAAACAGATCTAAGACACTAGCCTTGCC-TCCTTGGGTTTAC
194 TCTTGCCTTAATGTACTGACAACGAAGCAGATCTAAGACACTAGCCTTGCCTTCC-TGGGTTTAC
* *
52413685 AGCGGAGTAG
258 AGCGGAGCAA
* * **
52413695 ACTGAAGATAGTAGATCTTTCCATT-CTGTATTGACAGCGAAGCAGATCGAAGACGTCAGTCTTG
1 ACTGAAGATAGCAGATCTTTCC-TTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTG
* *
52413759 CCTTCCTAGGTTGACAGCAGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGA
65 CC-TCCTGGGTTGACAGCAGAGTAGACTGAAGATAGCAGATCTTACCTTCCTGTACTGACAGTGA
* * * * **
52413824 AACAGATTGAAGACACCAGTCTTGCCTTCT-T--GTACTGACAGTGGAGCAGACTAAAGATAACA
129 AGCAGATTGAAGACACCAGCCTTGCCTTCTCTAGGT--TGACAGCGGAGCAGACTGAAGATAGTA
* * * * * * *
52413886 CATCTTGCCTTAATGTACTGACAACGAAGCAGATCGAATACACCAGCTTTGCCTCCCTGGGTTTG
192 GATCTTGCCTTAATGTACTGACAACGAAGCAGATCTAAGACACTAGCCTTGCCTTCCTGGGTTTA
52413951 CAGCGGAGCAA
257 CAGCGGAGCAA
* * * * * * *
52413962 ACTAAATATAGCAGATCTTACCTTCTTGTACTGACAGCGAAGTAAATTGAAGACACCAGTCTTGC
1 ACTGAAGATAGCAGATCTTTCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGC
* * * *
52414027 CTCATTGGGTTGACAGCGGAGCAGACTGAAGATAGCAGATCTTACCTTCCTGTAATGACAGTGAA
66 CTC-CTGGGTTGACAGCAGAGTAGACTGAAGATAGCAGATCTTACCTTCCTGTACTGACAGTGAA
* * * * * * *
52414092 GCAGATCGAAGATACCAGTCTTGCC-TCTCTGGGTTAACAACGGAGCAAACTGAAGATAGTAGAT
130 GCAGATTGAAGACACCAGCCTTGCCTTCTCTAGGTTGACAGCGGAGCAGACTGAAGATAGTAGAT
** * * * * * *
52414156 CTTGCCTTTCTGTACTGACAACGAAGCAAATCTAAGACACCAGTCTTGCCTCCCTGGGTTTGCAA
195 CTTGCCTTAATGTACTGACAACGAAGCAGATCTAAGACACTAGCCTTGCCTTCCTGGGTTTACAG
*
52414221 CGAAGCAA
260 CGGAGCAA
* * *
52414229 ACTGAAGATAGCAGATCTTGT-CTTCCTGTACTGACAGCGGAGCAGA-CTGAAGATAACAGATCT
1 ACTGAAGATAGCAGATCTT-TCCTTCCTGTACTGACAGCGAAGCAGATC-GAAGACACCAG-TCT
52414292 TGCCTTCCTG
63 TGCC-TCCTG
52414302 TACTGACAGC
Statistics
Matches: 952, Mismatches: 160, Indels: 57
0.81 0.14 0.05
Matches are distributed among these distances:
265 4 0.00
266 19 0.02
267 901 0.95
268 22 0.02
269 6 0.01
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (267 bp):
ACTGAAGATAGCAGATCTTTCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGC
CTCCTGGGTTGACAGCAGAGTAGACTGAAGATAGCAGATCTTACCTTCCTGTACTGACAGTGAAG
CAGATTGAAGACACCAGCCTTGCCTTCTCTAGGTTGACAGCGGAGCAGACTGAAGATAGTAGATC
TTGCCTTAATGTACTGACAACGAAGCAGATCTAAGACACTAGCCTTGCCTTCCTGGGTTTACAGC
GGAGCAA
Found at i:52414604 original size:460 final size:460
Alignment explanation
Indices: 52414091--52415017 Score: 1755
Period size: 460 Copynumber: 2.0 Consensus size: 460
52414081 ATGACAGTGA
*
52414091 AGCAGATCGAAGATACCAGTCTTGCCTCTCTGGGTTAACAACGGAGCAAACTGAAGATAGTAGAT
1 AGCAGATCAAAGATACCAGTCTTGCCTCTCTGGGTTAACAACGGAGCAAACTGAAGATAGTAGAT
* *
52414156 CTTGCCTTTCTGTACTGACAACGAAGCAAATCTAAGACACCAGTCTTGCCTCCCTGGGTTTGCAA
66 CTTACCTTTCTGTACTGACAACGAAGCAAATCTAAGACACCAGTCTTACCTCCCTGGGTTTGCAA
*
52414221 CGAAGCAAACTGAAGATAGCAGATCTTGTCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAAC
131 CGAAGCAAACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAAC
*
52414286 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATTTAAGACACCAGATCTTGCATTCCTTTGCT
196 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCTAAGACACCAGATCTTGCATTCCTTTGCT
*
52414351 GAAAGTGGAGCAGATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAACAGATTGAAA
261 GAAAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAACAGATTGAAA
52414416 ACACCAGATCTTGCATTCTTTTACTGACAGCGGAGTAAACTGAAGACACCAGCCTTGCATTCCTG
326 ACACCAGATCTTGCATTCTTTTACTGACAGCGGAGTAAACTGAAGACACCAGCCTTGCATTCCTG
52414481 TACTGACACCGAAGCAGATCGAAGACACCAGCCTTACCTCCCTAGGTTTGCAGCGAAGCAGACTA
391 TACTGACACCGAAGCAGATCGAAGACACCAGCCTTACCTCCCTAGGTTTGCAGCGAAGCAGACTA
52414546 AAGAT
456 AAGAT
52414551 AGCAGATCAAAGATACCAGTCTTGCCTCTCTGGGTTAACAACGGAGCAAACTGAAGATAGTAGAT
1 AGCAGATCAAAGATACCAGTCTTGCCTCTCTGGGTTAACAACGGAGCAAACTGAAGATAGTAGAT
52414616 CTTACCTTTCTGTACTGACAACGAAGCAAATCTAAGACACCAGTCTTACCTCCCTGGGTTTGCAA
66 CTTACCTTTCTGTACTGACAACGAAGCAAATCTAAGACACCAGTCTTACCTCCCTGGGTTTGCAA
* *
52414681 TGAAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAAC
131 CGAAGCAAACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAAC
*
52414746 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCTAAGACACTAGATCTTGCATTCCTTTGCT
196 AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCTAAGACACCAGATCTTGCATTCCTTTGCT
*
52414811 GACAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAACAGATTGAAA
261 GAAAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAACAGATTGAAA
52414876 ACACCAGATCTTGCATTCTTTTACTGACAGCGGAGTAAACTGAAGACACCAGCCTTGCATTCCTG
326 ACACCAGATCTTGCATTCTTTTACTGACAGCGGAGTAAACTGAAGACACCAGCCTTGCATTCCTG
*
52414941 TACTGACACCGAAGCAGATCGAAGACACCAGCCTTACCTCCCTAGGTTTGCAGTGAAGCAGACTA
391 TACTGACACCGAAGCAGATCGAAGACACCAGCCTTACCTCCCTAGGTTTGCAGCGAAGCAGACTA
52415006 AAGAT
456 AAGAT
52415011 AGCAGAT
1 AGCAGAT
52415018 TTTACCTTCT
Statistics
Matches: 456, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
460 456 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (460 bp):
AGCAGATCAAAGATACCAGTCTTGCCTCTCTGGGTTAACAACGGAGCAAACTGAAGATAGTAGAT
CTTACCTTTCTGTACTGACAACGAAGCAAATCTAAGACACCAGTCTTACCTCCCTGGGTTTGCAA
CGAAGCAAACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAAC
AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCTAAGACACCAGATCTTGCATTCCTTTGCT
GAAAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAACAGATTGAAA
ACACCAGATCTTGCATTCTTTTACTGACAGCGGAGTAAACTGAAGACACCAGCCTTGCATTCCTG
TACTGACACCGAAGCAGATCGAAGACACCAGCCTTACCTCCCTAGGTTTGCAGCGAAGCAGACTA
AAGAT
Found at i:52414718 original size:89 final size:89
Alignment explanation
Indices: 52414551--52414724 Score: 231
Period size: 89 Copynumber: 2.0 Consensus size: 89
52414541 GACTAAAGAT
* * * * * *
52414551 AGCAGATCAAAGATACCAGTCTTGCCTCTCTGGGTTAACAACGGAGCAAACTGAAGATAGTAGAT
1 AGCAAATCAAAGACACCAGTCTTACCTCCCTGGGTTAACAACGAAGCAAACTGAAGATAGCAGAT
*
52414616 CTTACCTTTCTGTACTGACAACGA
66 CTTACCTTCCTGTACTGACAACGA
* ** * *
52414640 AGCAAATCTAAGACACCAGTCTTACCTCCCTGGGTTTGCAATGAAGCAGACTGAAGATAGCAGAT
1 AGCAAATCAAAGACACCAGTCTTACCTCCCTGGGTTAACAACGAAGCAAACTGAAGATAGCAGAT
*
52414705 CTTGCCTTCCTGTACTGACA
66 CTTACCTTCCTGTACTGACA
52414725 GCGGAGCAGA
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
89 72 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (89 bp):
AGCAAATCAAAGACACCAGTCTTACCTCCCTGGGTTAACAACGAAGCAAACTGAAGATAGCAGAT
CTTACCTTCCTGTACTGACAACGA
Found at i:52415034 original size:89 final size:88
Alignment explanation
Indices: 52414723--52415705 Score: 912
Period size: 89 Copynumber: 11.0 Consensus size: 88
52414713 CCTGTACTGA
* * * *
52414723 CAGCGGAGCAGACTGAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCTAAGAC
1 CAGCGGAGCAGACTAAAGATAGCAGATATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGAC
* * * *
52414788 ACTAGATCTTGCATTCCT--TTGCTG
66 ACCAG-CCTTGCCTCCCTGGTT--TG
* * * * * *
52414812 ACAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAACAGATTGAAAA
1 -CAGCGGAGCAGACTAAAGATAGCAGATATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
* * * *
52414877 CACCAGATCTTGCAT-TCT-TTTACTG
65 CACCAG-CCTTGCCTCCCTGGTT--TG
* * * * * ** * *
52414902 ACAGCGGAGTAAACTGAAGACACCAG-CCTTGCATTCCTGTACTGACACCGAAGCAGATCGAAGA
1 -CAGCGGAGCAGACTAAAGATAGCAGATATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
*
52414966 CACCAGCCTTACCTCCCTAGGTTTG
65 CACCAGCCTTGCCTCCCT-GGTTTG
* * * * * *
52414991 CAGTGAAGCAGACTAAAGATAGCAGATTTTACCTTCTTGTACTGACAGCGAAGCAGATCGAAAAC
1 CAGCGGAGCAGACTAAAGATAGCAGATATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGAC
*
52415056 ACCAGCCTTGCCTCCCTGGGTTG
66 ACCAGCCTTGCCTCCCTGGTTTG
** * * **
52415079 ACAGCGGAGCAGACTAAAGATAGC-GTATCATTGTTTTCCTATATTGGTAGCGAAGCA-ATCGAA
1 -CAGCGGAGCAGACTAAAGATAGCAG-AT-ATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAA
*
52415142 GACACTAGCCTTGCCTCCCTGAGTTTG
63 GACACCAGCCTTGCCTCCCTG-GTTTG
* * ** **
52415169 TAGCGGAGCAGACTAAAGATAGC-GTACCATTGTTTTCCTGTACTGGTAGCGAAGCA-ATCGAAG
1 CAGCGGAGCAGACTAAAGATAGCAG-A-TATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAG
* *
52415232 ACACTAGCCTTGCCTCCCTGGGTTG
64 ACACCAGCCTTGCCTCCCTGGTTTG
* * * * * *
52415257 ACAGCGGAGCAGAGTGAATATAGTAGATATTGCCTTCCTATGCTGACAGCGAAGCAGATCGAAGA
1 -CAGCGGAGCAGACTAAAGATAGCAGATATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
*
52415322 TACCAGCCTTGCCTCCCTGGGTTTG
65 CACCAGCCTTGCCTCCCT-GGTTTG
* * *
52415347 CAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGATAGCGAAGCAGATCGAAGAC
1 CAGCGGAGCAGACTAAAGATAGCAGATATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGAC
* * *
52415412 ACCAACCTTGCCTCTCTAGGTTTA
66 ACCAGCCTTGCCTCCCT-GGTTTG
* *
52415436 CAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGAC
1 CAGCGGAGCAGACTAAAGATAGCAGATATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGAC
* * **
52415501 ACTAGACTTGCCTCTTTGAGTTTG
66 ACCAGCCTTGCCTCCCTG-GTTTG
** * ** *
52415525 CAGCGGAGCAGACTAAAGATAGC-GTATCATTGTTTTCCTGTATTGGTAGTGAAGCA-ATCGAAG
1 CAGCGGAGCAGACTAAAGATAGCAG-AT-ATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAG
*
52415588 ACACTAGCCTTGCCTCCCTGAGTTTG
64 ACACCAGCCTTGCCTCCCTG-GTTTG
* * * * *
52415614 CAGCGGAGTAGACTAACA-ACAGCAAATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATCGACA-
1 CAGCGGAGCAGACTAA-AGATAGCAGATATTGCCTTCCTGTACTGACAGCGAAGCAGATCGA-AG
*
52415677 ACACCAGCCTTGCCTCTCTGAGTTTG
64 ACACCAGCCTTGCCTCCCTG-GTTTG
52415703 CAG
1 CAG
52415706 TGGAATAGGT
Statistics
Matches: 757, Mismatches: 115, Indels: 43
0.83 0.13 0.05
Matches are distributed among these distances:
88 79 0.10
89 526 0.69
90 150 0.20
91 2 0.00
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (88 bp):
CAGCGGAGCAGACTAAAGATAGCAGATATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGAC
ACCAGCCTTGCCTCCCTGGTTTG
Found at i:52415722 original size:356 final size:356
Alignment explanation
Indices: 52414720--52415710 Score: 1139
Period size: 356 Copynumber: 2.8 Consensus size: 356
52414710 CTTCCTGTAC
* *
52414720 TGACAGCGGAGCAGACTGAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCTAA
1 TGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAA
* * * * *
52414785 GACACTAGATCTTGCATTCCTTT--G-CTGACAGTGGAGCAGACTGAAGATAGCAG-ATC-TTGC
66 GACACTAGA-CTTGC-CT-CTTTGAGTTTG-CAGCGGAGCAGACTAAAGATAGC-GTATCATTGT
* ** * * * * * * * *
52414845 CTTCCTGTACTGACAGCGAAACAGATTGAAAACACCAGATCTTGCAT-TCT-TTTACTGACAGCG
126 TTTCCTGTACTGGTAGCGAAGCA-ATCGAAGACACTAG-CCTTGCCTCCCTGGTT--TGACAGCG
* * * ** * *
52414908 GAGTAAACTGAAGACA-CCAGCCTTGCATTCCTGTACTGACACCGAAGCAGATCGAAGACACCAG
187 GAGTAGACTGAAAACAGCAAATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAG
* * * *
52414972 CCTTACCTCCCT-AGGTTTGCAGT-GAAGCAGACTAAAGATAGCAGATTTTACCTTCTTGTACTG
252 CCTTGCCTCCCTGA-GTTTGCAGTGGAA-CAGACTGAAGATAGCAGATCTTACCTTCCTGTACTG
* *
52415035 ACAGCGAAGCAGATCGAAAACACCAGCCTTGCCTCCCTGGGT
315 ACAGCGAAGCAGATCGAAAACACCAACCTTGCCTCCCTAGGT
* ** * * **
52415077 TGACAGCGGAGCAGACTAAAGATAGC-GTATCATTGTTTTCCTATATTGGTAGCGAAGCA-ATCG
1 TGACAGCGGAGCAGACTGAAGATAGCAG-ATC-TTGCCTTCCTGTACTGACAGCGAAGCAGATCG
* ** * *
52415140 AAGACACTAGCCTTGCCTCCCTGAGTTTGTAGCGGAGCAGACTAAAGATAGCGTACCATTGTTTT
64 AAGACACTAGACTTGCCTCTTTGAGTTTGCAGCGGAGCAGACTAAAGATAGCGTATCATTGTTTT
* *
52415205 CCTGTACTGGTAGCGAAGCAATCGAAGACACTAGCCTTGCCTCCCTGGGTTGACAGCGGAGCAGA
129 CCTGTACTGGTAGCGAAGCAATCGAAGACACTAGCCTTGCCTCCCTGGTTTGACAGCGGAGTAGA
* * * * * * * * *
52415270 GTGAATATAGTAGATATTGCCTTCCTATGCTGACAGCGAAGCAGATCGAAGATACCAGCCTTGCC
194 CTGAAAACAGCAAATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCC
* * * * *
52415335 TCCCTGGGTTTGCAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGATAGCGAAG
259 TCCCTGAGTTTGCAGTGGAACAGACTGAAGATAGCAGATCTTACCTTCCTGTACTGACAGCGAAG
* *
52415400 CAGATCGAAGACACCAACCTTGCCTCTCTAGGT
324 CAGATCGAAAACACCAACCTTGCCTCCCTAGGT
*
52415433 TTACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAA
1 TGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAA
52415498 GACACTAGACTTGCCTCTTTGAGTTTGCAGCGGAGCAGACTAAAGATAGCGTATCATTGTTTTCC
66 GACACTAGACTTGCCTCTTTGAGTTTGCAGCGGAGCAGACTAAAGATAGCGTATCATTGTTTTCC
* *
52415563 TGTATTGGTAGTGAAGCAATCGAAGACACTAGCCTTGCCTCCCTGAGTTTG-CAGCGGAGTAGAC
131 TGTACTGGTAGCGAAGCAATCGAAGACACTAGCCTTGCCTCCCTG-GTTTGACAGCGGAGTAGAC
*
52415627 T-AACAACAGCAAATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATCGACA-ACACCAGCCTTGC
195 TGAA-AACAGCAAATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGA-AGACACCAGCCTTGC
*
52415690 CTCTCTGAGTTTGCAGTGGAA
258 CTCCCTGAGTTTGCAGTGGAA
52415711 TAGGTTGAAG
Statistics
Matches: 526, Mismatches: 91, Indels: 35
0.81 0.14 0.05
Matches are distributed among these distances:
354 2 0.00
355 50 0.10
356 380 0.72
357 73 0.14
358 21 0.04
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (356 bp):
TGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAA
GACACTAGACTTGCCTCTTTGAGTTTGCAGCGGAGCAGACTAAAGATAGCGTATCATTGTTTTCC
TGTACTGGTAGCGAAGCAATCGAAGACACTAGCCTTGCCTCCCTGGTTTGACAGCGGAGTAGACT
GAAAACAGCAAATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTC
CCTGAGTTTGCAGTGGAACAGACTGAAGATAGCAGATCTTACCTTCCTGTACTGACAGCGAAGCA
GATCGAAAACACCAACCTTGCCTCCCTAGGT
Found at i:52417265 original size:3 final size:3
Alignment explanation
Indices: 52417246--52417303 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
52417236 TAATATTAAT
* * *
52417246 TTA TCA TTA TTA CTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
52417295 TTA TTA TTA
1 TTA TTA TTA
52417304 CTACTACTAC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:52417265 original size:9 final size:9
Alignment explanation
Indices: 52417251--52417330 Score: 79
Period size: 9 Copynumber: 8.8 Consensus size: 9
52417241 TTAATTTATC
52417251 ATTATTACT
1 ATTATTACT
52417260 ATTATTACT
1 ATTATTACT
*
52417269 ATTATTATT
1 ATTATTACT
*
52417278 ATTATTATT
1 ATTATTACT
*
52417287 ATTATTTATT
1 ATTA-TTACT
52417297 ATTATTACT
1 ATTATTACT
* *
52417306 ACTACTACT
1 ATTATTACT
* **
52417315 ATCATTTTT
1 ATTATTACT
52417324 ATTATTA
1 ATTATTA
52417331 GTTTTTTTTA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
9 50 0.85
10 9 0.15
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.59
Consensus pattern (9 bp):
ATTATTACT
Found at i:52421718 original size:17 final size:16
Alignment explanation
Indices: 52421692--52421726 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
52421682 ATCGTAATAT
52421692 ATTATTAATTAATAAA
1 ATTATTAATTAATAAA
*
52421708 ATTATTTAATTTATAAA
1 ATTA-TTAATTAATAAA
52421725 AT
1 AT
52421727 CAAATAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTATTAATTAATAAA
Found at i:52429533 original size:21 final size:21
Alignment explanation
Indices: 52429501--52429541 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
52429491 GAACATTTGG
52429501 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
52429522 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
52429542 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:52432717 original size:81 final size:81
Alignment explanation
Indices: 52432630--52433370 Score: 1104
Period size: 81 Copynumber: 9.1 Consensus size: 81
52432620 GAGACCTTAA
* * *
52432630 CAGACAAGGAAGAGCAAGAGAAGGTGCAGCAGCCCCAGAGTTTACCAGACAAGGAAGGGAAAGAT
1 CAGACAAGGAAGAGAAAGAGAAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGGGAAAGAT
* *
52432695 GCGCCTAAGATTTTAC
66 GCGCCCAAGAGTTTAC
* *
52432711 TAGACAAGGAAGAGAAAGAGAAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGAAAGGGAAAGAT
1 CAGACAAGGAAGAGAAAGAGAAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGGGAAAGAT
52432776 GCGCCCAAGAGTTTAC
66 GCGCCCAAGAGTTTAC
52432792 CAGACAAGGAAGAGAAAGAGAAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGGGAAAGAT
1 CAGACAAGGAAGAGAAAGAGAAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGGGAAAGAT
52432857 GCGCCCAAGAGTTTAC
66 GCGCCCAAGAGTTTAC
* *
52432873 CAGACAAGGAAGAGAAAGAGAAGGCGCAGCAGCCCGAGAGTTTACTAGACAAGGAAGGGAAAAAT
1 CAGACAAGGAAGAGAAAGAGAAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGGGAAAGAT
** *
52432938 GCATCTAAGAGTTTAC
66 GCGCCCAAGAGTTTAC
52432954 CAGACAAGGAAGAGAAAGAGAAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGGGAAAGAT
1 CAGACAAGGAAGAGAAAGAGAAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGGGAAAGAT
* *
52433019 ACACCCAAGAGTTTAC
66 GCGCCCAAGAGTTTAC
* * *
52433035 CAGACAAGGAAGAGAAAGAGAAGGCGCAGCAACCCGAGAGTTTACTAGACAAGGAAAGGAAAGAT
1 CAGACAAGGAAGAGAAAGAGAAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGGGAAAGAT
* *
52433100 GCGCCTAAGAGTTTAT
66 GCGCCCAAGAGTTTAC
* * * ** *
52433116 CAGACAAGGAAGAGAAAGAGGAGGTGCAGCAGCCCGAGAGTTTACAAGACAAAAAAGAGAAAGAT
1 CAGACAAGGAAGAGAAAGAGAAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGGGAAAGAT
*
52433181 GTGCCCAAGAGTTTAC
66 GCGCCCAAGAGTTTAC
* * * * * ** * *
52433197 TAGACAATGAAGAGAAAGAGGAGGCACAACAGCGAGAGAGTTTACCAAACAAGGAAGAGAAAGAT
1 CAGACAAGGAAGAGAAAGAGAAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGGGAAAGAT
52433262 GCGCCCAAGAGTTTAC
66 GCGCCCAAGAGTTTAC
* * * * * *
52433278 CAGACAAGGAAGTGAATGAGGAGGCGCAGCAGCCTGAGAGTTTACCAGATAAGGAAGAGAAAGAT
1 CAGACAAGGAAGAGAAAGAGAAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGGGAAAGAT
*
52433343 ACGCCCAAGAGTTTAC
66 GCGCCCAAGAGTTTAC
52433359 CAGACAAGGAAG
1 CAGACAAGGAAG
52433371 GCACAGCAGC
Statistics
Matches: 600, Mismatches: 60, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 600 1.00
ACGTcount: A:0.41, C:0.18, G:0.30, T:0.11
Consensus pattern (81 bp):
CAGACAAGGAAGAGAAAGAGAAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGGGAAAGAT
GCGCCCAAGAGTTTAC
Found at i:52433193 original size:36 final size:36
Alignment explanation
Indices: 52433147--52433215 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
52433137 AGGTGCAGCA
*
52433147 GCCCGAGAGTTTACAAGACAAAAAAGAGAAAGATGT
1 GCCCAAGAGTTTACAAGACAAAAAAGAGAAAGATGT
* **
52433183 GCCCAAGAGTTTACTAGACAATGAAGAGAAAGA
1 GCCCAAGAGTTTACAAGACAAAAAAGAGAAAGA
52433216 GGAGGCACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.46, C:0.14, G:0.25, T:0.14
Consensus pattern (36 bp):
GCCCAAGAGTTTACAAGACAAAAAAGAGAAAGATGT
Found at i:52433273 original size:36 final size:36
Alignment explanation
Indices: 52433233--52433401 Score: 146
Period size: 36 Copynumber: 4.5 Consensus size: 36
52433223 CAACAGCGAG
*
52433233 AGAGTTTACCAAACAAGGAAGAGAAAGATGCGCCCA
1 AGAGTTTACCAGACAAGGAAGAGAAAGATGCGCCCA
* * *
52433269 AGAGTTTACCAGACAAGGAAGTGAATGAGGAGGCGCAGCAGCCTG
1 AGAGTTTACCAGACAAGGAAGAGAA--A-GA--TGC-GC--CC-A
* *
52433314 AGAGTTTACCAGATAAGGAAGAGAAAGATACGCCCA
1 AGAGTTTACCAGACAAGGAAGAGAAAGATGCGCCCA
* * *
52433350 AGAGTTTACCAGACAAGGAAG-G-CACA-GCAGCCCG
1 AGAGTTTACCAGACAAGGAAGAGAAAGATGC-GCCCA
52433384 AGAGTTTACCAGACAAGG
1 AGAGTTTACCAGACAAGG
52433402 CTGCAAATCC
Statistics
Matches: 109, Mismatches: 14, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
33 1 0.01
34 24 0.22
35 1 0.01
36 43 0.39
37 2 0.02
38 1 0.01
39 4 0.04
40 1 0.01
41 2 0.02
42 4 0.04
43 1 0.01
44 2 0.02
45 23 0.21
ACGTcount: A:0.39, C:0.20, G:0.29, T:0.12
Consensus pattern (36 bp):
AGAGTTTACCAGACAAGGAAGAGAAAGATGCGCCCA
Found at i:52433393 original size:34 final size:34
Alignment explanation
Indices: 52433299--52433401 Score: 118
Period size: 34 Copynumber: 3.0 Consensus size: 34
52433289 GTGAATGAGG
* * *
52433299 AGGCGCAGCAGCCTGAGAGTTTACCAGATAAGGA
1 AGGCACAGCAGCCCGAGAGTTTACCAGACAAGGA
* * *
52433333 AGAG-AAAGATACGCCCAAGAGTTTACCAGACAAGGA
1 AG-GCACAG-CA-GCCCGAGAGTTTACCAGACAAGGA
52433369 AGGCACAGCAGCCCGAGAGTTTACCAGACAAGG
1 AGGCACAGCAGCCCGAGAGTTTACCAGACAAGG
52433402 CTGCAAATCC
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
34 26 0.46
35 4 0.07
36 26 0.46
ACGTcount: A:0.37, C:0.22, G:0.29, T:0.12
Consensus pattern (34 bp):
AGGCACAGCAGCCCGAGAGTTTACCAGACAAGGA
Found at i:52435070 original size:35 final size:35
Alignment explanation
Indices: 52435024--52435090 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
52435014 ACCTAACTAC
52435024 AAACTTCATTTATTTTTTAAACATTTTCTGTGTGG
1 AAACTTCATTTATTTTTTAAACATTTTCTGTGTGG
52435059 AAACTTCATTTATTTTTTAAACATTTTCTGTG
1 AAACTTCATTTATTTTTTAAACATTTTCTGTG
52435091 GATTTTATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (35 bp):
AAACTTCATTTATTTTTTAAACATTTTCTGTGTGG
Found at i:52435522 original size:18 final size:18
Alignment explanation
Indices: 52435493--52435531 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
52435483 TTACTTAGTG
52435493 TTTATTTTATTATTT-TT
1 TTTATTTTATTATTTCTT
52435510 TTTATTATTATTATTTCTT
1 TTTATT-TTATTATTTCTT
52435529 TTT
1 TTT
52435532 GGATGTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 9 0.45
19 5 0.25
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTATTTTATTATTTCTT
Found at i:52435989 original size:13 final size:13
Alignment explanation
Indices: 52435971--52436020 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
52435961 AGGATTAAGT
52435971 GCCACACGGCCTA
1 GCCACACGGCCTA
*
52435984 GCCACATGGCCTA
1 GCCACACGGCCTA
*
52435997 GCCACATGGCCTA
1 GCCACACGGCCTA
52436010 GCCACACGGCC
1 GCCACACGGCC
52436021 GTGTGGCTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.22, C:0.44, G:0.24, T:0.10
Consensus pattern (13 bp):
GCCACACGGCCTA
Found at i:52442897 original size:16 final size:16
Alignment explanation
Indices: 52442876--52442917 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
52442866 CACACGAGCA
52442876 TGTTTGTGACAATATC
1 TGTTTGTGACAATATC
52442892 TGTTTGTGACAATATC
1 TGTTTGTGACAATATC
52442908 TGTTTGTGAC
1 TGTTTGTGAC
52442918 TTAGGACAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.45
Consensus pattern (16 bp):
TGTTTGTGACAATATC
Found at i:52453148 original size:29 final size:29
Alignment explanation
Indices: 52453106--52453176 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
52453096 ACACGAGCAT
* *
52453106 AGGCCGTGTAAGCCACATGGTCGTGTGAC
1 AGGCCGTGTAAGCCACACGGTCATGTGAC
* *
52453135 AGGCCGTGTGAGCCACACGGTCATGTGAT
1 AGGCCGTGTAAGCCACACGGTCATGTGAC
*
52453164 AGGCCATGTAAGC
1 AGGCCGTGTAAGC
52453177 GACCGTATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.23, C:0.24, G:0.34, T:0.20
Consensus pattern (29 bp):
AGGCCGTGTAAGCCACACGGTCATGTGAC
Found at i:52459267 original size:7 final size:7
Alignment explanation
Indices: 52459255--52459281 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
52459245 ATCATTTCAA
52459255 TTTTATT
1 TTTTATT
52459262 TTTTATT
1 TTTTATT
52459269 TTTTATT
1 TTTTATT
52459276 TTTTAT
1 TTTTAT
52459282 AATAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:52460992 original size:41 final size:40
Alignment explanation
Indices: 52460947--52461049 Score: 145
Period size: 41 Copynumber: 2.5 Consensus size: 40
52460937 TTTCCGAATC
* *
52460947 AATGAAAAAGTTGAAAAGGATGTTATCTGAAAAGGATATCA
1 AATGAAAAAGTTGAAAAGGATATTATCCGAAAAGGATAT-A
*
52460988 AATGAGAAAGTTGAAAAGGATATTATCCGAAAAGGATATA
1 AATGAAAAAGTTGAAAAGGATATTATCCGAAAAGGATATA
*
52461028 AATG-AAAAGATCGAAAAGGATA
1 AATGAAAAAG-TTGAAAAGGATA
52461050 GCAATGAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
39 4 0.07
40 16 0.29
41 36 0.64
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.21
Consensus pattern (40 bp):
AATGAAAAAGTTGAAAAGGATATTATCCGAAAAGGATATA
Found at i:52461042 original size:24 final size:24
Alignment explanation
Indices: 52461015--52461065 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
52461005 GGATATTATC
*
52461015 CGAAAAGGATATAAATGAAAAGAT
1 CGAAAAGGATAGAAATGAAAAGAT
* *
52461039 CGAAAAGGATAGCAATGAAAAGGT
1 CGAAAAGGATAGAAATGAAAAGAT
52461063 CGA
1 CGA
52461066 TAACTCATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.08, G:0.25, T:0.14
Consensus pattern (24 bp):
CGAAAAGGATAGAAATGAAAAGAT
Found at i:52468081 original size:46 final size:46
Alignment explanation
Indices: 52468015--52468328 Score: 395
Period size: 46 Copynumber: 6.6 Consensus size: 46
52468005 TTTGAGTACT
52468015 TCTGATC-AGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
52468060 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
52468106 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAAGTGGTAGCTTTAGC-TA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTT-A--GCTA-C---A-CTTA
* * **
52468159 CACTTATCTGATCAAATGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 -TCTGATC--A--AGT-GACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
52468211 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
52468257 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
52468302 TCTGATC-AGGGAC-AAGTGATAAGTGGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGT
52468329 CATACATAAG
Statistics
Matches: 239, Mismatches: 14, Indels: 34
0.83 0.05 0.12
Matches are distributed among these distances:
43 14 0.06
44 5 0.02
45 26 0.11
46 138 0.58
47 2 0.01
49 4 0.02
50 1 0.00
51 6 0.03
52 3 0.01
53 3 0.01
54 6 0.03
55 1 0.00
56 4 0.02
58 2 0.01
59 24 0.10
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:52468145 original size:13 final size:13
Alignment explanation
Indices: 52468127--52468154 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52468117 GACAAAGTGA
52468127 TAAGTGGTAGCTT
1 TAAGTGGTAGCTT
52468140 TAAGTGGTAGCTT
1 TAAGTGGTAGCTT
52468153 TA
1 TA
52468155 GCTACACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.07, G:0.29, T:0.39
Consensus pattern (13 bp):
TAAGTGGTAGCTT
Found at i:52468173 original size:59 final size:59
Alignment explanation
Indices: 52468081--52468200 Score: 231
Period size: 59 Copynumber: 2.0 Consensus size: 59
52468071 GACAAAGTGA
*
52468081 TAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTT
1 TAAGTGGTAGCTTTAGCTACACTTATCTGATCAAATGACAAAGTGATAAGTGGTAGCTT
52468140 TAAGTGGTAGCTTTAGCTACACTTATCTGATCAAATGACAAAGTGATAAGTGGTAGCTT
1 TAAGTGGTAGCTTTAGCTACACTTATCTGATCAAATGACAAAGTGATAAGTGGTAGCTT
52468199 TA
1 TA
52468201 GCTACACTTA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.33
Consensus pattern (59 bp):
TAAGTGGTAGCTTTAGCTACACTTATCTGATCAAATGACAAAGTGATAAGTGGTAGCTT
Found at i:52468205 original size:105 final size:100
Alignment explanation
Indices: 52468034--52468328 Score: 432
Period size: 105 Copynumber: 3.0 Consensus size: 100
52468024 TGACAAAGTG
52468034 ATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGA-GACAAAGTGATAAGTGGTAGCTTTAGC
1 ATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA-ATGACAAAGTGATAAGTGGTAGCTTTAGC
52468098 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGGT
65 TACACTTATCTGATCAAGTGAC-AAGTGATAAGTGGT
52468135 AGCTTTAAGTGGTAGCTTTAGCTACACTTATCTGATCAAATGACAAAGTGATAAGTGGTAGCTTT
1 A----TAAGTGGTAGCTTTAGCTACACTTATCTGATCAAATGACAAAGTGATAAGTGGTAGCTTT
52468200 AGCTACACTTATCTGATCAAGTGAC-----A-AAGT-G-
62 AGCTACACTTATCTGATCAAGTGACAAGTGATAAGTGGT
* *
52468231 ATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCT
1 ATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAATGACAAAGTGATAAGTGGTAGCTTTAGCT
*
52468295 ACACTTATCTGATC-AGGGACAAGTGATAAGTGGT
66 ACACTTATCTGATCAAGTGACAAGTGATAAGTGGT
52468329 CATACATAAG
Statistics
Matches: 178, Mismatches: 3, Indels: 29
0.85 0.01 0.14
Matches are distributed among these distances:
90 5 0.03
91 19 0.11
92 56 0.31
95 1 0.01
96 5 0.03
97 2 0.01
98 4 0.02
99 1 0.01
101 1 0.01
104 1 0.01
105 83 0.47
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (100 bp):
ATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAATGACAAAGTGATAAGTGGTAGCTTTAGCT
ACACTTATCTGATCAAGTGACAAGTGATAAGTGGT
Found at i:52469531 original size:24 final size:21
Alignment explanation
Indices: 52469468--52469522 Score: 87
Period size: 19 Copynumber: 2.7 Consensus size: 21
52469458 ATCTTCAAGG
*
52469468 ATATTCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
52469487 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
52469508 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
52469523 AGATATGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 18 0.55
21 15 0.45
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:52469793 original size:23 final size:23
Alignment explanation
Indices: 52469749--52469793 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
52469739 TCTTATTTTG
* *
52469749 TTGATTTATGTATAATTTATTTA
1 TTGATTTATATATAATTGATTTA
* *
52469772 TTGATTTGTATATTATTGATTT
1 TTGATTTATATATAATTGATTT
52469794 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.62
Consensus pattern (23 bp):
TTGATTTATATATAATTGATTTA
Found at i:52477247 original size:17 final size:17
Alignment explanation
Indices: 52477225--52477258 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
52477215 TCATTTTGTA
52477225 TTGGGATTATTCATTAG
1 TTGGGATTATTCATTAG
52477242 TTGGGATTATTCATTAG
1 TTGGGATTATTCATTAG
52477259 ATACAATCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (17 bp):
TTGGGATTATTCATTAG
Found at i:52485366 original size:12 final size:11
Alignment explanation
Indices: 52485349--52485381 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
52485339 AACAAATCCT
52485349 CTCTCATATTTC
1 CTCTCA-ATTTC
52485361 CTCTCAA-TTC
1 CTCTCAATTTC
52485371 CTCTCAATTTC
1 CTCTCAATTTC
52485382 TTTCCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 4 0.20
12 6 0.30
ACGTcount: A:0.18, C:0.36, G:0.00, T:0.45
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:52485397 original size:22 final size:22
Alignment explanation
Indices: 52485366--52485443 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
52485356 ATTTCCTCTC
*
52485366 AATTCCTCTCAATTTCTTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
*
52485389 AATTATCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
*
52485411 AATTCTCTTAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
52485433 AATTCTCTCAA
1 AATTCTCTCAA
52485444 ATCCATATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 46 0.92
23 4 0.08
ACGTcount: A:0.29, C:0.28, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:52487867 original size:29 final size:29
Alignment explanation
Indices: 52487831--52488221 Score: 526
Period size: 29 Copynumber: 13.5 Consensus size: 29
52487821 GTTTATTCCT
*
52487831 AACCCTAACCCTAACCAAACTTTATTAAA
1 AACCCTAACCCTAACCAAACTTAATTAAA
* *
52487860 AACACTAACCCTAACCAAACTCAATTAAA
1 AACCCTAACCCTAACCAAACTTAATTAAA
*
52487889 AACCCT-ACCCTAACCTAACTTAATTAAA
1 AACCCTAACCCTAACCAAACTTAATTAAA
* *
52487917 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCAAACTTAATTAAA
52487946 AACCCTAACCCTAACCAAACTTAATTAAAAA
1 AACCCTAACCCTAACCAAACTTAATT--AAA
*
52487977 CCCTAACCCTAACCCTAACCAAACTCAATTAAA
1 ----AACCCTAACCCTAACCAAACTTAATTAAA
52488010 AACCCTAACCCTAACCAAACTTAATTAAA
1 AACCCTAACCCTAACCAAACTTAATTAAA
*
52488039 AACCCTAA-CCT-----AACTCAATTAAA
1 AACCCTAACCCTAACCAAACTTAATTAAA
*
52488062 AATCCTAACCCTAACCAAACTTAATTAAA
1 AACCCTAACCCTAACCAAACTTAATTAAA
* *
52488091 AACCCTAACCCTAACCTAACTCAATTAAA
1 AACCCTAACCCTAACCAAACTTAATTAAA
*
52488120 AACCCTAACCCTAACCAAACTCAATTAAA
1 AACCCTAACCCTAACCAAACTTAATTAAA
* * * *
52488149 AACCCTAACCTTAGCCTAATTTAATTAAA
1 AACCCTAACCCTAACCAAACTTAATTAAA
*
52488178 AACCCTAACCCTAACCTAACTTAATTAAA
1 AACCCTAACCCTAACCAAACTTAATTAAA
52488207 AACCCTAACCCTAAC
1 AACCCTAACCCTAAC
52488222 TCAATTGATA
Statistics
Matches: 323, Mismatches: 26, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
23 18 0.06
24 3 0.01
28 29 0.09
29 242 0.75
31 3 0.01
33 3 0.01
35 25 0.08
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (29 bp):
AACCCTAACCCTAACCAAACTTAATTAAA
Found at i:52488253 original size:19 final size:19
Alignment explanation
Indices: 52488229--52488328 Score: 84
Period size: 19 Copynumber: 5.4 Consensus size: 19
52488219 AACTCAATTG
52488229 ATAATTTCACTAACCATTA
1 ATAATTTCACTAACCATTA
* ** *
52488248 ATAATTTTA-T-ATGATTTC
1 ATAATTTCACTAACCA-TTA
52488266 ATAATTTCACTAACCATTA
1 ATAATTTCACTAACCATTA
* *
52488285 ATAATTTTA-TATA--ATTTC
1 ATAATTTCACTA-ACCA-TTA
52488303 ATAATTTCACTAACCATTA
1 ATAATTTCACTAACCATTA
52488322 ATAATTT
1 ATAATTT
52488329 TATATAATTT
Statistics
Matches: 61, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
17 3 0.05
18 24 0.39
19 31 0.51
20 3 0.05
ACGTcount: A:0.40, C:0.14, G:0.01, T:0.45
Consensus pattern (19 bp):
ATAATTTCACTAACCATTA
Found at i:52488279 original size:37 final size:37
Alignment explanation
Indices: 52488229--52488338 Score: 211
Period size: 37 Copynumber: 3.0 Consensus size: 37
52488219 AACTCAATTG
*
52488229 ATAATTTCACTAACCATTAATAATTTTATATGATTTC
1 ATAATTTCACTAACCATTAATAATTTTATATAATTTC
52488266 ATAATTTCACTAACCATTAATAATTTTATATAATTTC
1 ATAATTTCACTAACCATTAATAATTTTATATAATTTC
52488303 ATAATTTCACTAACCATTAATAATTTTATATAATTT
1 ATAATTTCACTAACCATTAATAATTTTATATAATTT
52488339 GAGTCTGCAC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.40, C:0.13, G:0.01, T:0.46
Consensus pattern (37 bp):
ATAATTTCACTAACCATTAATAATTTTATATAATTTC
Found at i:52491559 original size:123 final size:124
Alignment explanation
Indices: 52491269--52491644 Score: 603
Period size: 124 Copynumber: 3.0 Consensus size: 124
52491259 CCCAAACATT
**
52491269 CTACTGTAGCAAAAGCGCGCCCACGAGGCCGGGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGCCCACGAGGCCGCAATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *
52491334 TAGAAGTGATTTTATACTATTTGGTCAGAAAAGTCAAAAAAAATTATTTCTTACATGAC
66 TAAAAGCGATTTTATACTATTTGCTCAGAAAAGTCAAAAAAAATTATTTCTTACATGAC
*
52491393 CTACTGTAGCAAAAGCGCGTCCACGAGGCCGCAATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGCCCACGAGGCCGCAATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
52491458 TAAAAGGGATTTTATACTATTTGCTCAGAAAAGT-AAAAAAAATTATTTCTTACATGAC
66 TAAAAGCGATTTTATACTATTTGCTCAGAAAAGTCAAAAAAAATTATTTCTTACATGAC
52491516 CTACTGTAGCAAAAGCGCGCCCACGAGGCCGCAATTTCACAAATTCTTCTCAAATAGCAATCCTG
1 CTACTGTAGCAAAAGCGCGCCCACGAGGCCGCAATTTCACAAATTCTTCTCAAATAGC-ATCCTG
* ** * *
52491581 CTAAAAGCGATTTTATACTATTTGTTCAGAAACA-TCAACCCAAAATTATTTCTTCCAGGAC
65 CTAAAAGCGATTTTATACTATTTGCTCAGAAA-AGTCAA-AAAAAATTATTTCTTACATGAC
52491642 CTA
1 CTA
52491645 AAAACCCTAA
Statistics
Matches: 235, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
123 81 0.34
124 130 0.55
125 3 0.01
126 21 0.09
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGCCCACGAGGCCGCAATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAAAAGCGATTTTATACTATTTGCTCAGAAAAGTCAAAAAAAATTATTTCTTACATGAC
Found at i:52503613 original size:21 final size:21
Alignment explanation
Indices: 52503563--52503636 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
52503553 CTTGATGCAA
*
52503563 CCACTGCTCCAGTTGAATCTT
1 CCACTGCTCCAATTGAATCTT
52503584 CCA-TGGCTCCAATTGAATCTT
1 CCACT-GCTCCAATTGAATCTT
* * **
52503605 CAACTGCTCTAATTGACCCTT
1 CCACTGCTCCAATTGAATCTT
52503626 CCACTGCTCCA
1 CCACTGCTCCA
52503637 TCCCTTCCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.02
21 42 0.95
22 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.12, T:0.31
Consensus pattern (21 bp):
CCACTGCTCCAATTGAATCTT
Found at i:52508857 original size:27 final size:31
Alignment explanation
Indices: 52508799--52508858 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
52508789 TATTTAATTA
52508799 TTTATATTTAATAATATAATAATTTATTAAAAT
1 TTTATATTTAATAATATAAT-ATTTA-TAAAAT
52508832 TTTAT-TTTAATAATA-AAT-TTTA-AAAAT
1 TTTATATTTAATAATATAATATTTATAAAAT
52508859 AATATTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
27 5 0.19
29 4 0.15
31 3 0.11
32 10 0.37
33 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTATATTTAATAATATAATATTTATAAAAT
Found at i:52520378 original size:41 final size:41
Alignment explanation
Indices: 52520333--52520434 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 41
52520323 GCATAGCGCT
* * *
52520333 TAGCAAGCTTATTGCCGGTGAAACGTTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACATTTCAGACTATATGTC
*
52520374 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACATTTCAGACTATATGTC
52520415 TAGCAGGC-TAAGTGCCGGTG
1 TAGCAGGCTTAA-TGCCGGTG
52520435 TACTGAATCA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
40 3 0.05
41 53 0.95
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAACATTTCAGACTATATGTC
Found at i:52523788 original size:3 final size:3
Alignment explanation
Indices: 52523775--52523816 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
52523765 GCATTTCCAT
52523775 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
52523817 ATTGCCCAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:52532777 original size:20 final size:20
Alignment explanation
Indices: 52532752--52532791 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
52532742 AGAACAATGC
52532752 AACAAAACAAAAGATACTGT
1 AACAAAACAAAAGATACTGT
52532772 AACAAAACAAAAGATACTGT
1 AACAAAACAAAAGATACTGT
52532792 TACACACTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.15, G:0.10, T:0.15
Consensus pattern (20 bp):
AACAAAACAAAAGATACTGT
Found at i:52537739 original size:5 final size:5
Alignment explanation
Indices: 52537724--52537753 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
52537714 ACCTTTTTTA
52537724 AAAACT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAA-T AAAAT AAAAT AAAAT AAAAT AAAA
52537754 AATAAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:52539335 original size:43 final size:42
Alignment explanation
Indices: 52539275--52539431 Score: 176
Period size: 43 Copynumber: 3.7 Consensus size: 42
52539265 TATGTATTTT
52539275 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGTGTATA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGTG-ATA
* * * * *
52539318 CGTGTAATACCATGTCTGGGACATTGGCATCGTATT-TGATT
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGTGATA
* **
52539359 TGTGTAAGACCTTGTCTGGGACAG-TGGCATC-AATATGTGATTA
1 CGTGTAAGACCACGTCTGGGAC-GTTGGCATCGAAT-TGTGA-TA
*
52539402 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
52539432 TGTACGAGCA
Statistics
Matches: 94, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
40 2 0.02
41 29 0.31
42 6 0.06
43 57 0.61
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGTGATA
Found at i:52539376 original size:84 final size:84
Alignment explanation
Indices: 52539276--52539431 Score: 210
Period size: 84 Copynumber: 1.9 Consensus size: 84
52539266 ATGTATTTTC
* * *
52539276 GTGTAAGACCACGTCTGGGAC-GTTGGCATCGAAT-TGTG-TATACGTGTAATACCATGTCTGGG
1 GTGTAAGACCACGTCTGGGACAG-TGGCATC-AATATGTGAT-TACATGTAAGACCACGTCTGGG
52539338 ACATTGGCATCGTATTTGATTT
63 ACATTGGCATCGTATTTGATTT
** *
52539360 GTGTAAGACCTTGTCTGGGACAGTGGCATCAATATGTGATTACATGTAAGACCACGTCTGGGACG
1 GTGTAAGACCACGTCTGGGACAGTGGCATCAATATGTGATTACATGTAAGACCACGTCTGGGACA
52539425 TTGGCAT
66 TTGGCAT
52539432 TGTACGAGCA
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
83 3 0.05
84 58 0.92
85 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (84 bp):
GTGTAAGACCACGTCTGGGACAGTGGCATCAATATGTGATTACATGTAAGACCACGTCTGGGACA
TTGGCATCGTATTTGATTT
Found at i:52545501 original size:18 final size:17
Alignment explanation
Indices: 52545478--52545544 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 17
52545468 TTAAAATTTA
52545478 TAAAAATATTCAAAAAAT
1 TAAAAATATT-AAAAAAT
*
52545496 TAAAAAT-TAAAAAAAAT
1 TAAAAATAT-TAAAAAAT
52545513 CT-AAAA-ATTAAAAAA-
1 -TAAAAATATTAAAAAAT
*
52545528 TAAAAA-ATAAAAAAAT
1 TAAAAATATTAAAAAAT
52545544 T
1 T
52545545 CATGAAAGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 1 0.02
15 12 0.29
16 7 0.17
17 13 0.32
18 8 0.20
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAAATATTAAAAAAT
Found at i:52546052 original size:2 final size:2
Alignment explanation
Indices: 52546045--52546076 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52546035 AATAAGTAGG
52546045 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52546077 AAATTCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52553585 original size:38 final size:38
Alignment explanation
Indices: 52553534--52553611 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 38
52553524 CTTCTACTTT
*
52553534 AATTAGTAATTAAAGGTTTTATCTTTATCATGAATATG
1 AATTAGTAATTAAAGATTTTATCTTTATCATGAATATG
* * * *
52553572 AATTAGTAATTAAATATTTTATTTTTATTATGAGTATG
1 AATTAGTAATTAAAGATTTTATCTTTATCATGAATATG
52553610 AA
1 AA
52553612 ATAATTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (38 bp):
AATTAGTAATTAAAGATTTTATCTTTATCATGAATATG
Found at i:52555572 original size:14 final size:16
Alignment explanation
Indices: 52555540--52555574 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
52555530 TGTAAGATTT
52555540 TTTTTATTTTCATTAA
1 TTTTTATTTTCATTAA
52555556 TTTTTATTTT-A-TAA
1 TTTTTATTTTCATTAA
52555570 TTTTT
1 TTTTT
52555575 TAAAGTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.42
15 1 0.05
16 10 0.53
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTATTTTCATTAA
Found at i:52560771 original size:20 final size:21
Alignment explanation
Indices: 52560730--52560773 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
52560720 TTGTGTACAA
*
52560730 TAAAAATGAACAAAATTGTGT
1 TAAAAATGAACAAAATTATGT
*
52560751 TAAAAATGAATAAAA-TATGT
1 TAAAAATGAACAAAATTATGT
52560771 TAA
1 TAA
52560774 CGAGGTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (21 bp):
TAAAAATGAACAAAATTATGT
Found at i:52565071 original size:31 final size:31
Alignment explanation
Indices: 52565033--52565164 Score: 140
Period size: 31 Copynumber: 4.2 Consensus size: 31
52565023 TTATATATCT
*
52565033 ATATACAAATCAAATTCGGTAATGTATAACC
1 ATATACAAATCAAATTCGGCAATGTATAACC
* * *
52565064 ATATACAAATCAAATTCGGCAATATATATCT
1 ATATACAAATCAAATTCGGCAATGTATAACC
* * * *
52565095 ATA-AAAAATTCAAATTCGACAATGTATATCT
1 ATATACAAA-TCAAATTCGGCAATGTATAACC
* * *
52565126 ATAAACAAATCAAATTTGGCAATGTATAAAAC
1 ATATACAAATCAAATTCGGCAATGTAT-AACC
52565158 ATATACA
1 ATATACA
52565165 TTTAAATTCA
Statistics
Matches: 84, Mismatches: 14, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
30 4 0.05
31 69 0.82
32 11 0.13
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (31 bp):
ATATACAAATCAAATTCGGCAATGTATAACC
Found at i:52565121 original size:62 final size:62
Alignment explanation
Indices: 52565024--52565153 Score: 172
Period size: 62 Copynumber: 2.1 Consensus size: 62
52565014 GAGCTAGCTT
* ** *
52565024 TATATATCTATATACAAATCAAATTCGGTAATGTATAACCATATACAAATCAAATTCGGCAA
1 TATATATCTATATAAAAATCAAATTCGACAATGTATAACCATAAACAAATCAAATTCGGCAA
* * *
52565086 TATATATCTATA-AAAAATTCAAATTCGACAATGTATATCTATAAACAAATCAAATTTGGCAA
1 TATATATCTATATAAAAA-TCAAATTCGACAATGTATAACCATAAACAAATCAAATTCGGCAA
*
52565148 TGTATA
1 TATATA
52565154 AAACATATAC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
61 4 0.07
62 55 0.93
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (62 bp):
TATATATCTATATAAAAATCAAATTCGACAATGTATAACCATAAACAAATCAAATTCGGCAA
Found at i:52566439 original size:17 final size:19
Alignment explanation
Indices: 52566417--52566452 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
52566407 TCATCCTCAA
52566417 AACCTT-AAATA-ATAAAC
1 AACCTTAAAATACATAAAC
52566434 AACCTTAAAATACATAAAC
1 AACCTTAAAATACATAAAC
52566453 CCAAAGAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 5 0.29
19 6 0.35
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.22
Consensus pattern (19 bp):
AACCTTAAAATACATAAAC
Found at i:52566491 original size:20 final size:20
Alignment explanation
Indices: 52566468--52566506 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
52566458 GAACCATAAA
52566468 CCTA-AAAAGCAAACCCTAAC
1 CCTAGAAAA-CAAACCCTAAC
52566488 CCTAGAAAACAAACCCTAA
1 CCTAGAAAACAAACCCTAA
52566507 AAACTCTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.51, C:0.33, G:0.05, T:0.10
Consensus pattern (20 bp):
CCTAGAAAACAAACCCTAAC
Found at i:52567118 original size:9 final size:9
Alignment explanation
Indices: 52567104--52567131 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
52567094 TGACATGTGT
52567104 TTTTTTTAA
1 TTTTTTTAA
52567113 TTTTTTTAA
1 TTTTTTTAA
52567122 TTTTTTTAA
1 TTTTTTTAA
52567131 T
1 T
52567132 ATCCCATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:52569072 original size:106 final size:106
Alignment explanation
Indices: 52568854--52569082 Score: 241
Period size: 106 Copynumber: 2.2 Consensus size: 106
52568844 TCGTTGCCGA
* * * * *
52568854 GCAATCCAGGATGACATAAATGAATTAAGAAATCATCATTGTCGGGAAATCCAGGGTGGTAAGTC
1 GCAATCCAGGATGACATAAATGAATTAAGAAACCACCATTATCGAGAAATCCAGGGTGGTAAGCC
* * * * * *
52568919 GTCTTTGTAGGGAAACTGAGGGTGGCAATCATCATTGTCGG
66 ATCATTGTAGGCAAACCGAGGGTAGCAATCACCATTGTCGG
* *
52568960 GTAATCCAGGATGACATAAATGAATTGAGAAACCACCATTATCGAGAAATCC-GAGGTGGTAAGC
1 GCAATCCAGGATGACATAAATGAATTAAGAAACCACCATTATCGAGAAATCCAG-GGTGGTAAGC
* * *
52569024 CATCATTGCCTA-GCAACCCGA-GGTAGCAGTCACCGTT-TCTGG
65 CATCATTG--TAGGCAAACCGAGGGTAGCAATCACCATTGTC-GG
*
52569066 GCAATCCTGGATGACAT
1 GCAATCCAGGATGACAT
52569083 CAAGAAGTGA
Statistics
Matches: 101, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
105 3 0.03
106 90 0.89
107 6 0.06
108 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (106 bp):
GCAATCCAGGATGACATAAATGAATTAAGAAACCACCATTATCGAGAAATCCAGGGTGGTAAGCC
ATCATTGTAGGCAAACCGAGGGTAGCAATCACCATTGTCGG
Found at i:52577462 original size:126 final size:124
Alignment explanation
Indices: 52577237--52577490 Score: 447
Period size: 126 Copynumber: 2.0 Consensus size: 124
52577227 CAAAGAATCT
* *
52577237 CTTAGAGGCATATTAACTTTAAGGCTTTGCTTGGTAAGGTGAAAAGAAAATTGGAAAAATGGAAA
1 CTTAGAGGCATATTAACTTTAAGGCTTTGCTTGGTAAGGTGAAAAGAAAATCGGAAAAACGGAAA
52577302 ACTAAAGGGGGAGAAAAATAGAAAGATAGAAAAAAAAATACTTTTTATTTTCATTGGCATG
66 ACTAAAGGGGGAGAAAAATAGAAAGATAG-AAAAAAAATACTTTTT-TTTTCATTGGCATG
52577363 CTTAGAGGCATATTAACTTTAAGGCTTTGCTTGGTAAGGTGAAAAGAAAATCGGAAAAACGGAAA
1 CTTAGAGGCATATTAACTTTAAGGCTTTGCTTGGTAAGGTGAAAAGAAAATCGGAAAAACGGAAA
* *
52577428 ATTAAA-GGGGAGAAAAATAGAAAGATAGAAAAAAAATACTTTTTTTTTTATTGGCATG
66 ACTAAAGGGGGAGAAAAATAGAAAGATAGAAAAAAAATACTTTTTTTTTCATTGGCATG
52577486 CTTAG
1 CTTAG
52577491 TAGGAAAGAT
Statistics
Matches: 124, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
123 18 0.15
124 16 0.13
125 22 0.18
126 68 0.55
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (124 bp):
CTTAGAGGCATATTAACTTTAAGGCTTTGCTTGGTAAGGTGAAAAGAAAATCGGAAAAACGGAAA
ACTAAAGGGGGAGAAAAATAGAAAGATAGAAAAAAAATACTTTTTTTTTCATTGGCATG
Found at i:52586990 original size:20 final size:20
Alignment explanation
Indices: 52586967--52587033 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
52586957 AAGTTATTTT
52586967 AAAAT-TTAAAAACTATTAAA
1 AAAATATTAAAAA-TATTAAA
*
52586987 AAAATCA-T-AAAATTTATAAA
1 AAAAT-ATTAAAAATAT-TAAA
*
52587007 AAAATTATTAAAAAAATTAAA
1 AAAA-TATTAAAAATATTAAA
52587028 AAAATA
1 AAAATA
52587034 AATTTTATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
19 2 0.05
20 20 0.53
21 11 0.29
22 5 0.13
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATATTAAAAATATTAAA
Found at i:52587012 original size:12 final size:12
Alignment explanation
Indices: 52586995--52587049 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
52586985 AAAAAATCAT
52586995 AAAATTTATAAA
1 AAAATTTATAAA
52587007 AAAA-TTATTAAA
1 AAAATTTA-TAAA
* *
52587019 AAAATTAAAAAA
1 AAAATTTATAAA
52587031 ATAAATTTTATAAA
1 A-AAA-TTTATAAA
52587045 AAAAT
1 AAAAT
52587050 AACAATACTG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
11 3 0.09
12 17 0.49
13 8 0.23
14 7 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTTATAAA
Found at i:52587651 original size:14 final size:14
Alignment explanation
Indices: 52587632--52587710 Score: 51
Period size: 13 Copynumber: 5.8 Consensus size: 14
52587622 AATTAATTAC
52587632 TAATTATAAAAATA
1 TAATTATAAAAATA
*
52587646 TAATTA-ACAAA-A
1 TAATTATAAAAATA
*
52587658 TAATT-TATATAATA
1 TAATTATA-AAAATA
*
52587672 TTAATTATATAAATA
1 -TAATTATAAAAATA
* *
52587687 T-TTTATAAAAAAA
1 TAATTATAAAAATA
52587700 T-ATATATAAAA
1 TAAT-TATAAAA
52587711 GCATATTATT
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
12 7 0.14
13 17 0.34
14 15 0.30
15 9 0.18
16 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATTATAAAAATA
Found at i:52587665 original size:27 final size:28
Alignment explanation
Indices: 52587635--52587697 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
52587625 TAATTACTAA
52587635 TTATAAAAATA-TAATTA-ACAAAATAAT
1 TTATAAAAATATTAATTATA-AAAATAAT
* * *
52587662 TTAT-ATAATATTAATTATATAAATATT
1 TTATAAAAATATTAATTATAAAAATAAT
52587689 TTATAAAAA
1 TTATAAAAA
52587698 AATATATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 5 0.17
27 20 0.69
28 4 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
TTATAAAAATATTAATTATAAAAATAAT
Found at i:52587676 original size:15 final size:15
Alignment explanation
Indices: 52587632--52587688 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
52587622 AATTAATTAC
*
52587632 TAATTATAAAAATA-
1 TAATTATATAAATAT
*
52587646 TAATTA-ACAAA-A-
1 TAATTATATAAATAT
52587658 TAATT-TATATAATAT
1 TAATTATATA-AATAT
52587673 TAATTATATAAATAT
1 TAATTATATAAATAT
52587688 T
1 T
52587689 TTATAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
12 8 0.22
13 6 0.17
14 7 0.19
15 11 0.31
16 4 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATTATATAAATAT
Found at i:52588232 original size:34 final size:33
Alignment explanation
Indices: 52588190--52588287 Score: 128
Period size: 34 Copynumber: 2.9 Consensus size: 33
52588180 GAATTTAAAA
52588190 AAAATTAATTAAATTAGGTTTAAAGGGTTTTAAG
1 AAAATTAATTAAATTAGGTTT-AAGGGTTTTAAG
* *
52588224 TAAATTAATTAAATTAAGGTTT-AGATGTTTTAAG
1 AAAATTAATTAAATT-AGGTTTAAG-GGTTTTAAG
52588258 AAAATTAATTAAATTAGGATTT-AGGGTTTT
1 AAAATTAATTAAATTAGG-TTTAAGGGTTTT
52588288 TTAAAAATAA
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
33 10 0.18
34 41 0.72
35 6 0.11
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (33 bp):
AAAATTAATTAAATTAGGTTTAAGGGTTTTAAG
Found at i:52592598 original size:7 final size:7
Alignment explanation
Indices: 52592588--52592613 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52592578 TTATATACAT
52592588 AATACTA
1 AATACTA
52592595 AATACTA
1 AATACTA
52592602 AATACTA
1 AATACTA
52592609 AATAC
1 AATAC
52592614 GAAACGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:52595964 original size:44 final size:44
Alignment explanation
Indices: 52595901--52595995 Score: 163
Period size: 44 Copynumber: 2.2 Consensus size: 44
52595891 GAAAGAGCTA
*
52595901 TTATATTATTACCTAAAGGTAAAAAATTTGTCATTGGTGATGCT
1 TTATATTATTACCTAAAGGTAAAAAATTTGTCATTGATGATGCT
* *
52595945 TTATATTATTACCTAAAGGTAGAAAATTTGTCATTGATGATGTT
1 TTATATTATTACCTAAAGGTAAAAAATTTGTCATTGATGATGCT
52595989 TTATATT
1 TTATATT
52595996 TCACTAAGTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (44 bp):
TTATATTATTACCTAAAGGTAAAAAATTTGTCATTGATGATGCT
Found at i:52601022 original size:53 final size:53
Alignment explanation
Indices: 52600958--52601058 Score: 184
Period size: 53 Copynumber: 1.9 Consensus size: 53
52600948 AAGGTATCTG
*
52600958 TAGAAGGGCAGGAGATGCTGAACTTTAGCTACTGACTTGACTTGTTTCGATGA
1 TAGAAGGGCAGGAGATGCTGAACTATAGCTACTGACTTGACTTGTTTCGATGA
*
52601011 TAGAAGTGCAGGAGATGCTGAACTATAGCTACTGACTTGACTTGTTTC
1 TAGAAGGGCAGGAGATGCTGAACTATAGCTACTGACTTGACTTGTTTC
52601059 AGTAAAAGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (53 bp):
TAGAAGGGCAGGAGATGCTGAACTATAGCTACTGACTTGACTTGTTTCGATGA
Found at i:52614705 original size:40 final size:40
Alignment explanation
Indices: 52614661--52614739 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
52614651 TTACGTGGAC
*
52614661 GCAAAACGCGCTGACGTCCACGCGATTTTCTGACACATCA
1 GCAAAACGCGCTGACGTCCACGCGATTTGCTGACACATCA
*
52614701 GCAAAACGCGCTGATGTCCACGCGATTTGCTGACACATC
1 GCAAAACGCGCTGACGTCCACGCGATTTGCTGACACATC
52614740 CCTTGACATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.20
Consensus pattern (40 bp):
GCAAAACGCGCTGACGTCCACGCGATTTGCTGACACATCA
Found at i:52614938 original size:19 final size:21
Alignment explanation
Indices: 52614909--52614966 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
52614899 TGTATTACTG
52614909 TAATA-TGTAGTTCAAATT-A
1 TAATATTGTAGTTCAAATTCA
*
52614928 T-GTATTGTAGTT-AATATTCA
1 TAATATTGTAGTTCAA-ATTCA
*
52614948 TAATATTGTAGCTCAAATT
1 TAATATTGTAGTTCAAATT
52614967 GTCAATCCGT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 4 0.13
19 11 0.35
20 2 0.06
21 12 0.39
22 2 0.06
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (21 bp):
TAATATTGTAGTTCAAATTCA
Found at i:52616563 original size:12 final size:10
Alignment explanation
Indices: 52616529--52616565 Score: 58
Period size: 11 Copynumber: 3.7 Consensus size: 10
52616519 TTGTTTTAAC
52616529 ATAATTTTTA
1 ATAATTTTTA
52616539 ATATATTTTTA
1 ATA-ATTTTTA
52616550 ATAA-TTTTA
1 ATAATTTTTA
52616559 ATAATTT
1 ATAATTT
52616566 ATATTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.36
10 6 0.24
11 10 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:52616572 original size:23 final size:21
Alignment explanation
Indices: 52616529--52616572 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
52616519 TTGTTTTAAC
*
52616529 ATAATTTTTAATATATTTTTA
1 ATAATTTTTAATATATATTTA
*
52616550 ATAATTTTAATAATTTATATTTA
1 ATAATTTT--TAATATATATTTA
52616573 TTTTAAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATAATTTTTAATATATATTTA
Found at i:52616575 original size:19 final size:20
Alignment explanation
Indices: 52616529--52616578 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
52616519 TTGTTTTAAC
*
52616529 ATAATTTTTAATATATTTTTA
1 ATAA-TTTTAATATATTTATA
52616550 ATAATTTTAATA-ATTTATA
1 ATAATTTTAATATATTTATA
* *
52616569 TTTATTTTAA
1 ATAATTTTAA
52616579 AGATTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 14 0.54
20 8 0.31
21 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATAATTTTAATATATTTATA
Found at i:52620563 original size:32 final size:32
Alignment explanation
Indices: 52620522--52620582 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
52620512 TTTTTTGAAA
52620522 AATAATTATAACTATTTAAAT-AAT-ATTATTTG
1 AATAATTATAA-TA-TTAAATGAATAATTATTTG
*
52620554 AATAGTTATAATATTAAATGAATAATTAT
1 AATAATTATAATATTAAATGAATAATTAT
52620583 ATGTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 6 0.23
31 5 0.19
32 15 0.58
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (32 bp):
AATAATTATAATATTAAATGAATAATTATTTG
Found at i:52620564 original size:20 final size:20
Alignment explanation
Indices: 52620541--52620583 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
52620531 AACTATTTAA
** *
52620541 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
52620561 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
52620581 ATA
1 ATA
52620584 TGTTTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:52620952 original size:28 final size:28
Alignment explanation
Indices: 52620912--52620974 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
52620902 TTGCACACCG
52620912 AAGATAGGTGGGGGCTAATATAACCTTA
1 AAGATAGGTGGGGGCTAATATAACCTTA
52620940 AAGATAGGTGGGGGCTAATATAACCTTA
1 AAGATAGGTGGGGGCTAATATAACCTTA
52620968 AAGATAG
1 AAGATAG
52620975 TGACTTGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.38, C:0.10, G:0.29, T:0.24
Consensus pattern (28 bp):
AAGATAGGTGGGGGCTAATATAACCTTA
Found at i:52631124 original size:20 final size:19
Alignment explanation
Indices: 52631099--52631147 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
52631089 TTCGAGGATC
52631099 ATTTTGAAACAAATCAAAAA
1 ATTTTGAAA-AAATCAAAAA
* **
52631119 ATTTTGGAAAAATTGAAAA
1 ATTTTGAAAAAATCAAAAA
52631138 ATTTTGAAAA
1 ATTTTGAAAA
52631148 CAGGGGTCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.55, C:0.04, G:0.10, T:0.31
Consensus pattern (19 bp):
ATTTTGAAAAAATCAAAAA
Found at i:52632126 original size:9 final size:9
Alignment explanation
Indices: 52632112--52632137 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
52632102 AATTTAACTC
52632112 AATTTATAT
1 AATTTATAT
52632121 AATTTATAT
1 AATTTATAT
52632130 AATTTATA
1 AATTTATA
52632138 AAAGTTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
AATTTATAT
Found at i:52636397 original size:40 final size:40
Alignment explanation
Indices: 52636333--52636409 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
52636323 AACAAGGTAA
* *
52636333 AAATGTGCAATCAGGGGCACCGTAGTACAAACAGGAGCAC
1 AAATATGCAATCAGGAGCACCGTAGTACAAACAGGAGCAC
* * * *
52636373 AAATATGCTATCAGGAGCATCGTAGTGCTAACAGGAG
1 AAATATGCAATCAGGAGCACCGTAGTACAAACAGGAG
52636410 TACGAAAGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.17
Consensus pattern (40 bp):
AAATATGCAATCAGGAGCACCGTAGTACAAACAGGAGCAC
Found at i:52639089 original size:12 final size:12
Alignment explanation
Indices: 52639072--52639096 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52639062 TAGGCAAGTG
52639072 AGACCGATAGGT
1 AGACCGATAGGT
52639084 AGACCGATAGGT
1 AGACCGATAGGT
52639096 A
1 A
52639097 ATCTTGTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (12 bp):
AGACCGATAGGT
Found at i:52643834 original size:15 final size:15
Alignment explanation
Indices: 52643790--52643841 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
52643780 GTCCAAGATT
*
52643790 AATATGTGCAACATC
1 AATATGTGCAACATG
* *
52643805 AAGATGTACAACATG
1 AATATGTGCAACATG
*
52643820 GATATGTGCAACATG
1 AATATGTGCAACATG
*
52643835 AACATGT
1 AATATGT
52643842 ACAGGATTGA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.25
Consensus pattern (15 bp):
AATATGTGCAACATG
Found at i:52653258 original size:2 final size:2
Alignment explanation
Indices: 52653246--52653275 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
52653236 TTCTATAATC
52653246 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA T
52653276 GCATTCCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52659207 original size:43 final size:43
Alignment explanation
Indices: 52659138--52659281 Score: 180
Period size: 43 Copynumber: 3.3 Consensus size: 43
52659128 TTTTTCACAT
** ** *
52659138 AAACACCGCTAAAAAACATGACCTTTAGCGGCGCTTTTATCAC
1 AAACACCGCTAAAAGCCATGTTCTTTAGCGGCGCTTTTATAAC
* *
52659181 AAACCCCGCTAAAAGCCATGTTCTTTAGAGGCGCTTTTATAAC
1 AAACACCGCTAAAAGCCATGTTCTTTAGCGGCGCTTTTATAAC
* * **
52659224 AAACACCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATGGC
1 AAACACCGCTAAAAGCCATGTTCTTTAGCGGCGCTTTTATAAC
*
52659267 AAACGCCGCTAAAAG
1 AAACACCGCTAAAAG
52659282 TACCGTTCTT
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 86 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
AAACACCGCTAAAAGCCATGTTCTTTAGCGGCGCTTTTATAAC
Found at i:52659290 original size:43 final size:42
Alignment explanation
Indices: 52659160--52659303 Score: 157
Period size: 43 Copynumber: 3.4 Consensus size: 42
52659150 AAAACATGAC
* *
52659160 CTTTAGCGGCGCTTTTATCACAAACCCCGCTAAAAG-CCATGTT
1 CTTTAGCGGCGCTTTTATAACAAACACCGCTAAAAGTCC--GTT
* * *
52659203 CTTTAGAGGCGCTTTTATAACAAACACCGCTAAAGGTCATGTT
1 CTTTAGCGGCGCTTTTATAACAAACACCGCTAAAAGTC-CGTT
** *
52659246 CTTTAGCGGCGCTTTTATGGCAAACGCCGCTAAAAGTACCGTT
1 CTTTAGCGGCGCTTTTATAACAAACACCGCTAAAAGT-CCGTT
*
52659289 CTTTAGTGGCG-TTTT
1 CTTTAGCGGCGCTTTT
52659304 GCAGAAAATG
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
42 4 0.05
43 80 0.93
44 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (42 bp):
CTTTAGCGGCGCTTTTATAACAAACACCGCTAAAAGTCCGTT
Found at i:52660093 original size:13 final size:14
Alignment explanation
Indices: 52660065--52660093 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52660055 ACAAATGACG
52660065 AATTAAACCATTAT
1 AATTAAACCATTAT
52660079 AATTAAACC-TTAT
1 AATTAAACCATTAT
52660092 AA
1 AA
52660094 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Done.