Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, whole genome shotgun sequence
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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 18 of 138
Found at i:4983025 original size:29 final size:30
Alignment explanation
Indices: 4982993--4983065 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
4982983 AATTAATAAA
*
4982993 TTTATAATTTAATTATTATATTAGATA-TT
1 TTTATAATTTAATTATTATATTAAATATTT
* * * * *
4983022 TTTAAAAATAAAATATTATTTTAAATATTT
1 TTTATAATTTAATTATTATATTAAATATTT
4983052 TATTATAATTTAAT
1 T-TTATAATTTAAT
4983066 GCATGATATT
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
29 21 0.66
30 3 0.09
31 8 0.25
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (30 bp):
TTTATAATTTAATTATTATATTAAATATTT
Found at i:4989647 original size:14 final size:15
Alignment explanation
Indices: 4989626--4989660 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
4989616 GATTGAAATT
4989626 TAAA-TAATAGA-GA
1 TAAATTAATAGAGGA
4989639 TAAATTAATAGAGGA
1 TAAATTAATAGAGGA
4989654 TAAATTA
1 TAAATTA
4989661 TATAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.20
14 7 0.35
15 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (15 bp):
TAAATTAATAGAGGA
Found at i:4990884 original size:25 final size:25
Alignment explanation
Indices: 4990855--4990905 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
4990845 ATAGTTCATT
*
4990855 CACATTTACCCAAAAAGAACTATAC
1 CACATTCACCCAAAAAGAACTATAC
*
4990880 CACATTCACCTAAAAAGAACTATAC
1 CACATTCACCCAAAAAGAACTATAC
4990905 C
1 C
4990906 CTAAATTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.47, C:0.29, G:0.04, T:0.20
Consensus pattern (25 bp):
CACATTCACCCAAAAAGAACTATAC
Found at i:4992135 original size:2 final size:2
Alignment explanation
Indices: 4992110--4992172 Score: 80
Period size: 2 Copynumber: 33.5 Consensus size: 2
4992100 AATTGAAATC
* *
4992110 AT AT AT A- AT AT -T AT AT -T AC A- AT AT AT AT CT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4992148 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4992173 AACCTAATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
1 4 0.07
2 50 0.93
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4992484 original size:77 final size:74
Alignment explanation
Indices: 4992400--4992559 Score: 164
Period size: 77 Copynumber: 2.1 Consensus size: 74
4992390 CTAATTTAAA
* * * *
4992400 TATATTATTTTAAAA-AATGCATTTTCAAATAATCTAAATATATAT-TTTTATAAATTTAAAATT
1 TATATTATTTTAAAATAA-G--TTTGCAAATAATATAAATATATATCTTTT-TAAACTTAAAAAT
*
4992463 TTCAAATATAGTG
62 CTCAAATATAGTG
* *
4992476 TTATATTATCTTTTAAAATAAGTTTGCTAATAATATTAATATATATCTTTTTAAACTTAAAAATC
1 -TATATTA--TTTTAAAATAAGTTTGCAAATAATATAAATATATATCTTTTTAAACTTAAAAATC
*
4992541 TCAAATGTAGTG
63 TCAAATATAGTG
4992553 -ATATTAT
1 TATATTAT
4992560 GAAGTGAATT
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
73 1 0.01
75 6 0.08
77 49 0.69
78 4 0.06
79 9 0.13
80 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.46
Consensus pattern (74 bp):
TATATTATTTTAAAATAAGTTTGCAAATAATATAAATATATATCTTTTTAAACTTAAAAATCTCA
AATATAGTG
Found at i:4993488 original size:20 final size:20
Alignment explanation
Indices: 4993456--4993507 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
4993446 GCAATAAGAT
*
4993456 TTTAAAATAATTA-TTCAAAA
1 TTTAAAATTATTACTT-AAAA
*
4993476 TTTAATATTATTACTTAAAA
1 TTTAAAATTATTACTTAAAA
4993496 TTTAAAATTATT
1 TTTAAAATTATT
4993508 TCATTTCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTAAAATTATTACTTAAAA
Found at i:4993934 original size:64 final size:63
Alignment explanation
Indices: 4993819--4993938 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 63
4993809 ATTAAATAGG
* * *
4993819 ATTATTGAAAGTATTTTTAGTAAAAAACGCTTTCAATAATCCATTTAAAAAATTTTGGAGAGGA
1 ATTATTGAAAGTATTTTCAGTAAAAAAAGCCTTCAATAATCCA-TTAAAAAATTTTGGAGAGGA
* *
4993883 ATTATTGAAGGTATTTTCAGTAAAAAAAAGCCTTCAATAATTCA-TACAAAAATTTT
1 ATTATTGAAAGTATTTTCAGT-AAAAAAAGCCTTCAATAATCCATTA-AAAAATTTT
4993939 TGTATGGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
63 2 0.04
64 28 0.57
65 19 0.39
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (63 bp):
ATTATTGAAAGTATTTTCAGTAAAAAAAGCCTTCAATAATCCATTAAAAAATTTTGGAGAGGA
Found at i:4994169 original size:365 final size:363
Alignment explanation
Indices: 4993595--4994302 Score: 959
Period size: 365 Copynumber: 1.9 Consensus size: 363
4993585 ATAGTGACGG
* * *
4993595 TTAAATTACATTAGTAAAAGAGATTTTATTGATGAATTTTTAATGCCATCAGAATCTATCATACT
1 TTAAATTACATCAGTAAAAGAGATTTTATTGATGAATTTTTAATACCATCAGAATATATCATACT
* * *
4993660 TATACCAATATTTTATTTAATCGTCGGTATAAATAAATTTTTTCTGATGGTATATGACTATCTAT
66 TATACCAACATTTTATTTAATCATCGGTATAAATAAATTTTTTCTGATGGTATATGACTATCCAT
* * * * *
4993725 CAGTATAAATATGTTATATATTGACGATTATTAATGTAACTGTCAGTATAGGCTCAAAACAAAAA
131 CAGTATAAATATGTTATATACTGACGATTATTAATGCAACCGTCAGTAGAAGCTCAAAACAAAAA
4993790 AGCTATTAGCTTACAAAAAATTAAATAGGATTATTGAAAGTATTTTT-AGT-AAAAAA-CGCTTT
196 AGCTATTAGCTTACAAAAAATTAAAT-GGATTATTG-AAGTATTTTTGA-TCAAAAAAGC-CTTT
* *
4993852 CAATAATCCATTTAAAAAATTTTGGAGAG-GAATTATTGAAGGTATTTTC-AGTAAAAAAAAGCC
257 -AATAATCCATTCAAAAAATTTTGGAGAGAGAA-TATTGAAGGTATTTTCGA-T-AAAAAAAGCA
*
4993915 TTCAATAAT-TCATACAAAAATTTTTGTATGGATTATTTACTGACAA
318 TTCAATAATCT-ATACAAAAAATTTTGTATGGATTATTTACTGACAA
* * ** *
4993961 TTAAATTTCATCAGTAAAAGAGACTTTTATTGATGATTTTTTAATACTGTTAGAATATA-CTATA
1 TTAAATTACATCAGTAAAAGAGA-TTTTATTGATGAATTTTTAATACCATCAGAATATATC-ATA
*
4994025 CTTATACCAACATTTTATTTAATCATCGGTATAAAT-AATTTTTT-TTATGGTATATGACTATCC
64 CTTATACCAACATTTTATTTAATCATCGGTATAAATAAATTTTTTCTGATGGTATATGACTATCC
* *
4994088 ATCAGTATAAATTTGTTATATACTGACGGTTATTAATGCAACCGTCAGTAGAAGCTCAAAACATA
129 ATCAGTATAAATATGTTATATACTGACGATTATTAATGCAACCGTCAGTAGAAGCTCAAAACA-A
* * * *
4994153 AAAA-CTATTGGCTTACAAAAAATTGAATGGATTATTGAGGTGTTTTTGATCAAAAAAGCCTTTA
193 AAAAGCTATTAGCTTACAAAAAATTAAATGGATTATTGAAGTATTTTTGATCAAAAAAGCCTTTA
** * * *
4994217 ATAATTTATTCAAAAAATTTTGGTGAGAGAATATTGAAGGTATTTTCGATCAAAAACGCATTCAA
258 ATAATCCATTCAAAAAATTTTGGAGAGAGAATATTGAAGGTATTTTCGATAAAAAAAGCATTCAA
4994282 TAATCTATACAAAAAATTTTG
323 TAATCTATACAAAAAATTTTG
4994303 GAGGAGATTA
Statistics
Matches: 302, Mismatches: 31, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
362 30 0.10
363 51 0.17
364 24 0.08
365 96 0.32
366 35 0.12
367 66 0.22
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.38
Consensus pattern (363 bp):
TTAAATTACATCAGTAAAAGAGATTTTATTGATGAATTTTTAATACCATCAGAATATATCATACT
TATACCAACATTTTATTTAATCATCGGTATAAATAAATTTTTTCTGATGGTATATGACTATCCAT
CAGTATAAATATGTTATATACTGACGATTATTAATGCAACCGTCAGTAGAAGCTCAAAACAAAAA
AGCTATTAGCTTACAAAAAATTAAATGGATTATTGAAGTATTTTTGATCAAAAAAGCCTTTAATA
ATCCATTCAAAAAATTTTGGAGAGAGAATATTGAAGGTATTTTCGATAAAAAAAGCATTCAATAA
TCTATACAAAAAATTTTGTATGGATTATTTACTGACAA
Found at i:4994284 original size:64 final size:62
Alignment explanation
Indices: 4994196--4994365 Score: 198
Period size: 63 Copynumber: 2.7 Consensus size: 62
4994186 ATTGAGGTGT
* * * * * *
4994196 TTTTGATCAAAAAAGCCTTTAATAATTTATTCAAAAAATTTTGGTGAGAGAATATTGAAGGTA
1 TTTTGATCAAAAACGCATTCAATAATCTATACAAAAAATTTTGGAG-GAGAATATTGAAGGTA
* *
4994259 TTTTCGATCAAAAACGCATTCAATAATCTATACAAAAAATTTTGGAGGAGATTATTGAAGGCA
1 TTTT-GATCAAAAACGCATTCAATAATCTATACAAAAAATTTTGGAGGAGAATATTGAAGGTA
* * *
4994322 TTTTTATCCAAAAACG-ACTTCAATAATCAAAACAAAAAATTTTG
1 TTTTGAT-CAAAAACGCA-TTCAATAATCTATACAAAAAATTTTG
4994366 TTGAGGTTGA
Statistics
Matches: 93, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
62 3 0.03
63 54 0.58
64 36 0.39
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (62 bp):
TTTTGATCAAAAACGCATTCAATAATCTATACAAAAAATTTTGGAGGAGAATATTGAAGGTA
Found at i:4994509 original size:63 final size:62
Alignment explanation
Indices: 4994381--4994533 Score: 145
Period size: 63 Copynumber: 2.5 Consensus size: 62
4994371 GTTGAGAGTG
* * * *
4994381 TTTTTAGC-CAAAAACGCCTTCAATGAT--TCCTAAAAAAATTTGGAAGGGATTATTGAATAC
1 TTTTT-GCTCAAAAACGCCTTTAATAATCCTCCTAAAAAAATTTGGAAGAGATTATTAAATAC
* *
4994441 GTTTTTGACT-AAAAACGCCTTTAATAATCCTCTTAACAAAATTTGGAAGAGATTATTAAAGGTA
1 -TTTTTG-CTCAAAAACGCCTTTAATAATCCTCCTAAAAAAATTTGGAAGAGATTATTAAA--TA
4994505 -
62 C
* **
4994505 TTTTTGGTCAAAAATACCTTTAATAATCC
1 TTTTTGCTCAAAAACGCCTTTAATAATCC
4994534 CCAAAATTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
60 1 0.01
61 22 0.29
62 1 0.01
63 50 0.66
65 2 0.03
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (62 bp):
TTTTTGCTCAAAAACGCCTTTAATAATCCTCCTAAAAAAATTTGGAAGAGATTATTAAATAC
Found at i:4994842 original size:10 final size:10
Alignment explanation
Indices: 4994827--4994860 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
4994817 CTTAATCTCC
4994827 ACTCTCACCA
1 ACTCTCACCA
*
4994837 ACTCTCTCCA
1 ACTCTCACCA
*
4994847 TCTCTCACCA
1 ACTCTCACCA
4994857 ACTC
1 ACTC
4994861 CACAAGCTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.24, C:0.50, G:0.00, T:0.26
Consensus pattern (10 bp):
ACTCTCACCA
Found at i:4994853 original size:20 final size:19
Alignment explanation
Indices: 4994822--4994860 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
4994812 ACATACTTAA
4994822 TCTCCACTCTCACCAACTC
1 TCTCCACTCTCACCAACTC
4994841 TCTCCATCTCTCACCAACTC
1 TCTCCA-CTCTCACCAACTC
4994861 CACAAGCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.21, C:0.51, G:0.00, T:0.28
Consensus pattern (19 bp):
TCTCCACTCTCACCAACTC
Found at i:4997288 original size:31 final size:31
Alignment explanation
Indices: 4997253--4997314 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
4997243 TATGGATGCA
* *
4997253 TGAATTTA-AGGATTTAATTTCAAGCCAAATC
1 TGAATTTACAGG-TCTAATCTCAAGCCAAATC
4997284 TGAATTTACAGGTCTAATCTCAAGCCAAATC
1 TGAATTTACAGGTCTAATCTCAAGCCAAATC
4997315 AGATTCTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (31 bp):
TGAATTTACAGGTCTAATCTCAAGCCAAATC
Found at i:5000325 original size:2 final size:2
Alignment explanation
Indices: 5000318--5000349 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5000308 TACAAGACCA
5000318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5000350 TCGTTTCCTA
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):
AT
Found at i:5001633 original size:15 final size:16
Alignment explanation
Indices: 5001600--5001633 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5001590 TGGTTCAGCT
*
5001600 TAATTTGCAATTACTA
1 TAATTTGCAATTACCA
5001616 TAATTTGC-ATTACCA
1 TAATTTGCAATTACCA
5001631 TAA
1 TAA
5001634 CCCAATAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (16 bp):
TAATTTGCAATTACCA
Found at i:5005793 original size:21 final size:21
Alignment explanation
Indices: 5005751--5005794 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
5005741 AATTTATTTT
***
5005751 ATTTTAAGAAAACATTTTTAA
1 ATTTTAAGAAAACATAAATAA
*
5005772 ATTTTAAGAAAAGATAAATAA
1 ATTTTAAGAAAACATAAATAA
5005793 AT
1 AT
5005795 AAAAAATAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (21 bp):
ATTTTAAGAAAACATAAATAA
Found at i:5006759 original size:21 final size:22
Alignment explanation
Indices: 5006733--5006774 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
5006723 AAAGTAATAA
5006733 AATAAAAAACAAAAA-ACTATC
1 AATAAAAAACAAAAAGACTATC
5006754 AATAAAAAACAAAAAGACTAT
1 AATAAAAAACAAAAAGACTAT
5006775 TGTCGAGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.71, C:0.12, G:0.02, T:0.14
Consensus pattern (22 bp):
AATAAAAAACAAAAAGACTATC
Found at i:5007028 original size:34 final size:34
Alignment explanation
Indices: 5006991--5007244 Score: 160
Period size: 33 Copynumber: 7.6 Consensus size: 34
5006981 TCAAAAGTAA
*
5006991 AAAAAATGAAATGACTTGGTTTTACCCAAAGTC-
1 AAAAAATGAAATGACTTGGTTTTAGCCAAAGTCG
* *
5007024 AAAAAAT-AAGATGACTTGGTCTTGGCCAAAG-CTG
1 AAAAAATGAA-ATGACTTGGTTTTAGCCAAAGTC-G
* * **
5007058 GAAAGATGAAATGACTTGGTTTTAGTTAAAGT-G
1 AAAAAATGAAATGACTTGGTTTTAGCCAAAGTCG
* * * * ** *
5007091 AGAAAAGGAAATGACTTAGTCTTAGCGGAAGTTG
1 AAAAAATGAAATGACTTGGTTTTAGCCAAAGTCG
* * **
5007125 AAAAAATAAAATGACTTGATTTTAGCCGGAGTC-
1 AAAAAATGAAATGACTTGGTTTTAGCCAAAGTCG
* * ** ** *
5007158 AGAAAATGAAATGACTTGATCATAGCTGAAGTTG
1 AAAAAATGAAATGACTTGGTTTTAGCCAAAGTCG
* * * * **
5007192 AAAAAAATAAAATGATTTGATCTTAGCTGAAGTC-
1 -AAAAAATGAAATGACTTGGTTTTAGCCAAAGTCG
5007226 AAAAAATGAAATGACTTGG
1 AAAAAATGAAATGACTTGG
5007245 ACTGAGCCAA
Statistics
Matches: 171, Mismatches: 42, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
32 3 0.02
33 91 0.53
34 47 0.27
35 30 0.18
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.27
Consensus pattern (34 bp):
AAAAAATGAAATGACTTGGTTTTAGCCAAAGTCG
Found at i:5007105 original size:67 final size:67
Alignment explanation
Indices: 5006991--5007242 Score: 179
Period size: 67 Copynumber: 3.7 Consensus size: 67
5006981 TCAAAAGTAA
* * * *
5006991 AAAAAATGAAATGACTTGGTTTTACCCAAAGTCAAAAAATAAGATGACTTGGTCTTGGCCAAAGC
1 AAAAAATGAAATGACTTGGTTTTAGCCAAAGTCAAAAAAGAAGATGACTTAGTCTTAGCCAAAGC
5007056 TG
66 TG
* * ** * * **
5007058 GAAAGATGAAATGACTTGGTTTTAGTTAAAGTGAGAAAAGGAA-ATGACTTAGTCTTAGCGGAAG
1 AAAAAATGAAATGACTTGGTTTTAGCCAAAGTCA-AAAAAGAAGATGACTTAGTCTTAGCCAAAG
*
5007122 TTG
65 CTG
* * ** * * **
5007125 AAAAAATAAAATGACTTGATTTTAGCCGGAGTCAGAAAATGAA-ATGACTT-GATCATAGCTGAA
1 AAAAAATGAAATGACTTGGTTTTAGCCAAAGTCA-AAAAAGAAGATGACTTAG-TCTTAGCCAAA
*
5007188 GTTG
64 GCTG
* * * * **
5007192 AAAAAAATAAAATGATTTGATCTTAGCTGAAGTCAAAAAATGAA-ATGACTT
1 -AAAAAATGAAATGACTTGGTTTTAGCCAAAGTCAAAAAA-GAAGATGACTT
5007243 GGACTGAGCC
Statistics
Matches: 151, Mismatches: 30, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
66 1 0.01
67 104 0.69
68 46 0.30
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (67 bp):
AAAAAATGAAATGACTTGGTTTTAGCCAAAGTCAAAAAAGAAGATGACTTAGTCTTAGCCAAAGC
TG
Found at i:5007226 original size:68 final size:68
Alignment explanation
Indices: 5007086--5007243 Score: 212
Period size: 68 Copynumber: 2.3 Consensus size: 68
5007076 GTTTTAGTTA
* * * *
5007086 AAGTGAGAAAAGGAAATGACTT-AGTCTTAGCGGAAGTTGAAAAAATAAAATGACTTGATTTTAG
1 AAGTCAGAAAATGAAATGACTTGAGTCATAGCGGAAGTTGAAAAAATAAAATGACTTGATCTTAG
5007150 CCG
66 CCG
* * *
5007153 GAGTCAGAAAATGAAATGACTTGA-TCATAGCTGAAGTTGAAAAAAATAAAATGATTTGATCTTA
1 AAGTCAGAAAATGAAATGACTTGAGTCATAGCGGAAGTTG-AAAAAATAAAATGACTTGATCTTA
*
5007217 GCTG
65 GCCG
*
5007221 AAGTCAAAAAATGAAATGACTTG
1 AAGTCAGAAAATGAAATGACTTG
5007244 GACTGAGCCA
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
67 32 0.41
68 47 0.59
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.26
Consensus pattern (68 bp):
AAGTCAGAAAATGAAATGACTTGAGTCATAGCGGAAGTTGAAAAAATAAAATGACTTGATCTTAG
CCG
Found at i:5007411 original size:65 final size:65
Alignment explanation
Indices: 5007323--5007708 Score: 217
Period size: 65 Copynumber: 5.9 Consensus size: 65
5007313 GCCCATATAA
* * * *
5007323 AAAAAATGAAGGTGACTAGGACTGAACCCCAAATCAAAAAATTAAATGACCTGGATTGAACTAAG
1 AAAAAATG-A-GTGACTAGGACTGAACCGCAAGTCAAAAAATTAAATGACCTGGACTGAACCAAG
*
5007388 GT
64 AT
* * * * * *
5007390 AAAAAATGAGTGACTGGGACTGAAACGTAAGTCAAAAAATTAAATGATCGGGACTGAACCGAGAT
1 AAAAAATGAGTGACTAGGACTGAACCGCAAGTCAAAAAATTAAATGACCTGGACTGAACCAAGAT
* * * * * * * ***
5007455 AAAAAATAAGTGATTAAGACTGAACTGCAAGTTAAAAAATTAAATGACCTAGACTTAAATGAGAT
1 AAAAAATGAGTGACTAGGACTGAACCGCAAGTCAAAAAATTAAATGACCTGGACTGAACCAAGAT
** * * * * * * *
5007520 CGAAAATGAATGA-TCGAAATTGAACCACAAGTCAAAAAATTAAATGACCTAGATTGAACCAA-A
1 AAAAAATGAGTGACTAG-GACTGAACCGCAAGTCAAAAAATTAAATGACCTGGACTGAACCAAGA
5007583 GT
65 -T
** * * ** * * * *
5007585 CGAAAATAAGTGA-TCGAGACT-AAGTAGCAAGTTAAAAAATTAAATAACCTAGACTGAACCGAT
1 AAAAAATGAGTGACTAG-GACTGAA-CCGCAAGTCAAAAAATTAAATGACCTGGACTGAACC-AA
5007648 G-T
63 GAT
** * * * * * * *
5007650 CGAAAATGAATGA-TCGAAACTGAATCGCAAGTTAGAAAATTAAATGACCTGGATTGAAC
1 AAAAAATGAGTGACTAG-GACTGAACCGCAAGTCAAAAAATTAAATGACCTGGACTGAAC
5007709 TGAAGTTGAA
Statistics
Matches: 253, Mismatches: 60, Indels: 14
0.77 0.18 0.04
Matches are distributed among these distances:
64 4 0.02
65 237 0.94
66 4 0.02
67 8 0.03
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (65 bp):
AAAAAATGAGTGACTAGGACTGAACCGCAAGTCAAAAAATTAAATGACCTGGACTGAACCAAGAT
Found at i:5007443 original size:34 final size:33
Alignment explanation
Indices: 5007356--5007447 Score: 84
Period size: 34 Copynumber: 2.8 Consensus size: 33
5007346 GAACCCCAAA
* *
5007356 TCAAAAAATTAAATGACCTGGATTG-AACTAAGG
1 TCAAAAAATTAAATGA-CGGGACTGAAACTAAGG
* *
5007389 T-AAAAAA-TGAGTGACTGGGACTGAAACGTAA-G
1 TCAAAAAATTAAATGAC-GGGACTGAAAC-TAAGG
5007421 TCAAAAAATTAAATGATCGGGACTGAA
1 TCAAAAAATTAAATGA-CGGGACTGAA
5007448 CCGAGATAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
30 1 0.02
31 10 0.21
32 11 0.23
33 10 0.21
34 14 0.30
35 1 0.02
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.22
Consensus pattern (33 bp):
TCAAAAAATTAAATGACGGGACTGAAACTAAGG
Found at i:5007526 original size:130 final size:130
Alignment explanation
Indices: 5007408--5007698 Score: 336
Period size: 130 Copynumber: 2.2 Consensus size: 130
5007398 AGTGACTGGG
** * * * *
5007408 ACTGAAACGTAAGTCAAAAAATTAAATGATCGGGACTGAACC-GAGATAAAAAATAAGTGATTAA
1 ACTGAAACACAAGTCAAAAAATTAAATGACCGAGACTGAACCAAAG-TAAAAAATAAGTGATCAA
*
5007472 GACTGAACT-GCAAGTTAAAAAATTAAATGACCTAGACTTAAATGAGATCGAAAATGAATGATCG
65 GACT-AACTAGCAAGTTAAAAAATTAAATAACCTAGACTTAAATGAGATCGAAAATGAATGATCG
5007536 AA
129 AA
* * * * ** *
5007538 ATTGAACCACAAGTCAAAAAATTAAATGACCTAGATTGAACCAAAGTCGAAAATAAGTGATCGAG
1 ACTGAAACACAAGTCAAAAAATTAAATGACCGAGACTGAACCAAAGTAAAAAATAAGTGATCAAG
* * **
5007603 ACTAAGTAGCAAGTTAAAAAATTAAATAACCTAGACTGAACCGATG-TCGAAAATGAATGATCGA
66 ACTAACTAGCAAGTTAAAAAATTAAATAACCTAGACTTAAATGA-GATCGAAAATGAATGATCGA
5007667 A
130 A
* * * *
5007668 ACTGAATCGCAAGTTAGAAAATTAAATGACC
1 ACTGAAACACAAGTCAAAAAATTAAATGACC
5007699 TGGATTGAAC
Statistics
Matches: 135, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
129 3 0.02
130 129 0.96
131 3 0.02
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (130 bp):
ACTGAAACACAAGTCAAAAAATTAAATGACCGAGACTGAACCAAAGTAAAAAATAAGTGATCAAG
ACTAACTAGCAAGTTAAAAAATTAAATAACCTAGACTTAAATGAGATCGAAAATGAATGATCGAA
Found at i:5007624 original size:195 final size:195
Alignment explanation
Indices: 5007345--5007699 Score: 427
Period size: 195 Copynumber: 1.8 Consensus size: 195
5007335 TGACTAGGAC
* * * * * *
5007345 TGAACCCCAAATCAAAAAATTAAATGACCTGGATTGAACTAAGGTAAAAAATGAGTGACTGGGAC
1 TGAACCACAAATCAAAAAATTAAATGACCTAGATTGAACCAAAGTAAAAAATAAGTGACTGAGAC
* * * * *
5007410 TGAAACGTAAGTCAAAAAATTAAATGATCGGGACTGAACCGA-GATAAAAAAT-AAGTGAT-TAA
66 TGAAACGCAAGTCAAAAAATTAAATAACCGAGACTGAACCGATG-TAAAAAATGAA-TGATCGAA
5007472 GACTGAA-CTGCAAGTTAAAAAATTAAATGACCTAGACTTAAATGAGATCGAAAATGAATGATCG
129 -ACTGAATC-GCAAGTTAAAAAATTAAATGACCTAGACTTAAATGAGATCGAAAATGAATGATCG
5007536 AAAT
192 AAAT
* **
5007540 TGAACCACAAGTCAAAAAATTAAATGACCTAGATTGAACCAAAGTCGAAAATAAGTGA-TCGAGA
1 TGAACCACAAATCAAAAAATTAAATGACCTAGATTGAACCAAAGTAAAAAATAAGTGACT-GAGA
* * **
5007604 CT-AAGTA-GCAAGTTAAAAAATTAAATAACCTAGACTGAACCGATGTCGAAAATGAATGATCGA
65 CTGAA--ACGCAAGTCAAAAAATTAAATAACCGAGACTGAACCGATGTAAAAAATGAATGATCGA
*
5007667 AACTGAATCGCAAGTTAGAAAATTAAATGACCT
128 AACTGAATCGCAAGTTAAAAAATTAAATGACCT
5007700 GGATTGAACT
Statistics
Matches: 134, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
194 3 0.02
195 124 0.93
196 7 0.05
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.21
Consensus pattern (195 bp):
TGAACCACAAATCAAAAAATTAAATGACCTAGATTGAACCAAAGTAAAAAATAAGTGACTGAGAC
TGAAACGCAAGTCAAAAAATTAAATAACCGAGACTGAACCGATGTAAAAAATGAATGATCGAAAC
TGAATCGCAAGTTAAAAAATTAAATGACCTAGACTTAAATGAGATCGAAAATGAATGATCGAAAT
Found at i:5007720 original size:65 final size:65
Alignment explanation
Indices: 5007473--5007723 Score: 278
Period size: 65 Copynumber: 3.9 Consensus size: 65
5007463 AGTGATTAAG
**
5007473 ACTGAA-CTGCAAGTTAAAAAATTAAATGACCTAGACTT-AAATG-AGATCGAAAATGAATGATC
1 ACTGAATC-GCAAGTTAAAAAATTAAATGACCTAGA-TTGAACCGAAG-TCGAAAATGAATGATC
5007535 GAA
63 GAA
* * * * *
5007538 ATTGAACCACAAGTCAAAAAATTAAATGACCTAGATTGAACCAAAGTCGAAAAT-AAGTGATCGA
1 ACTGAATCGCAAGTTAAAAAATTAAATGACCTAGATTGAACCGAAGTCGAAAATGAA-TGATCGA
*
5007602 G
65 A
* * * *
5007603 ACT-AAGTAGCAAGTTAAAAAATTAAATAACCTAGACTGAACCGATGTCGAAAATGAATGATCGA
1 ACTGAA-TCGCAAGTTAAAAAATTAAATGACCTAGATTGAACCGAAGTCGAAAATGAATGATCGA
5007667 A
65 A
* * * *
5007668 ACTGAATCGCAAGTTAGAAAATTAAATGACCTGGATTGAACTGAAGTTGAAAATGA
1 ACTGAATCGCAAGTTAAAAAATTAAATGACCTAGATTGAACCGAAGTCGAAAATGA
5007724 CTATGTTTGA
Statistics
Matches: 154, Mismatches: 25, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
64 6 0.04
65 141 0.92
66 7 0.05
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (65 bp):
ACTGAATCGCAAGTTAAAAAATTAAATGACCTAGATTGAACCGAAGTCGAAAATGAATGATCGAA
Found at i:5007721 original size:130 final size:130
Alignment explanation
Indices: 5007457--5007708 Score: 355
Period size: 130 Copynumber: 1.9 Consensus size: 130
5007447 ACCGAGATAA
* * * *
5007457 AAAATAAGTGATTAAGACTGAACTGCAAGTTAAAAAATTAAATGACCTAGACTTAAATGAGATCG
1 AAAATAAGTGATCAAGACTGAACTGCAAGTTAAAAAATTAAATAACCTAGACTGAAACGAGATCG
*
5007522 AAAATGAATGATCGAAATTGAACCACAAGTCAAAAAATTAAATGACCTAGATTGAACCAAAGTCG
66 AAAATGAATGATCGAAACTGAACCACAAGTCAAAAAATTAAATGACCTAGATTGAACCAAAGTCG
* * *
5007587 AAAATAAGTGATCGAGACT-AAGTAGCAAGTTAAAAAATTAAATAACCTAGACTGAACCGATG-T
1 AAAATAAGTGATCAAGACTGAACT-GCAAGTTAAAAAATTAAATAACCTAGACTGAAACGA-GAT
* * * * *
5007650 CGAAAATGAATGATCGAAACTGAATCGCAAGTTAGAAAATTAAATGACCTGGATTGAAC
64 CGAAAATGAATGATCGAAACTGAACCACAAGTCAAAAAATTAAATGACCTAGATTGAAC
5007709 TGAAGTTGAA
Statistics
Matches: 107, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
129 3 0.03
130 103 0.96
131 1 0.01
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.22
Consensus pattern (130 bp):
AAAATAAGTGATCAAGACTGAACTGCAAGTTAAAAAATTAAATAACCTAGACTGAAACGAGATCG
AAAATGAATGATCGAAACTGAACCACAAGTCAAAAAATTAAATGACCTAGATTGAACCAAAGTCG
Found at i:5016370 original size:21 final size:22
Alignment explanation
Indices: 5016346--5016387 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
5016336 AAAGTAATAA
5016346 AATAAAAAAT-AAAAAACTATC
1 AATAAAAAATGAAAAAACTATC
*
5016367 AATAAAAAATGAAAAGACTAT
1 AATAAAAAATGAAAAAACTAT
5016388 TGTTGGGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.69, C:0.07, G:0.05, T:0.19
Consensus pattern (22 bp):
AATAAAAAATGAAAAAACTATC
Found at i:5024900 original size:20 final size:21
Alignment explanation
Indices: 5024874--5024930 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
5024864 AATGAAAAAT
*
5024874 GAAAAAAAAGTAAAAAAGTAA
1 GAAAAAAAAGTAAAAAAGAAA
5024895 -AAAAAAAAGTAAGAAAAGAAA
1 GAAAAAAAAGTAA-AAAAGAAA
5024916 GAGAAAAAAAG-AAAA
1 GA-AAAAAAAGTAAAA
5024931 CTTAAACTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 12 0.38
21 9 0.28
22 3 0.09
23 8 0.25
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (21 bp):
GAAAAAAAAGTAAAAAAGAAA
Found at i:5026203 original size:14 final size:14
Alignment explanation
Indices: 5026186--5026218 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5026176 TGTGAATCTT
*
5026186 TGAATAATTGTTTG
1 TGAATAATAGTTTG
5026200 TGAATAATAGTTTG
1 TGAATAATAGTTTG
5026214 TGAAT
1 TGAAT
5026219 TTTTACAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (14 bp):
TGAATAATAGTTTG
Found at i:5026475 original size:35 final size:35
Alignment explanation
Indices: 5026412--5026484 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
5026402 ATATCTTGCG
* ** *
5026412 AACCTAAAACTCTTACTAATCTTTGAATTATTATA
1 AACCTAAAACTCTTACAAAAATTGGAATTATTATA
* *
5026447 AACCTAAAACTCTTACAAAAATTGGAATTTTTGTA
1 AACCTAAAACTCTTACAAAAATTGGAATTATTATA
5026482 AAC
1 AAC
5026485 TTTTGTGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.36
Consensus pattern (35 bp):
AACCTAAAACTCTTACAAAAATTGGAATTATTATA
Found at i:5027078 original size:66 final size:65
Alignment explanation
Indices: 5027008--5027170 Score: 168
Period size: 66 Copynumber: 2.5 Consensus size: 65
5026998 TCAATCCATA
* * * * *
5027008 TCATTTTATTTTTCTAACATGCGTTTCAAT-CTCGGTTACTCATCTTCGACCTTGACTCGGTCTA
1 TCATTTTATTTTTCTAACATACGATTCAATCCT-GATTAATCATCTTCGA-CTTGACTCGATCTA
*
5027072 GG
64 AG
* * * *
5027074 TCATTTTATTTTTTTAACTTACGATTCAATCCTGATTAATCATCTTTGACTTGACTTGATCTAAG
1 TCATTTTATTTTTCTAACATACGATTCAATCCTGATTAATCATCTTCGACTTGACTCGATCTAAG
* * *
5027139 TCA-TTCATTCTTTTTAACCTACGATTCAATCC
1 TCATTTTATT-TTTCTAACATACGATTCAATCC
5027171 CAATCACTTA
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 5 0.06
65 37 0.45
66 39 0.47
67 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.45
Consensus pattern (65 bp):
TCATTTTATTTTTCTAACATACGATTCAATCCTGATTAATCATCTTCGACTTGACTCGATCTAAG
Found at i:5027153 original size:65 final size:66
Alignment explanation
Indices: 5027047--5027170 Score: 171
Period size: 65 Copynumber: 1.9 Consensus size: 66
5027037 TCTCGGTTAC
* * * *
5027047 TCATCTTCGACCTTGACTCGGTCTAGGTCATTTTATTTTTTTAACTTACGATTCAATCCTGATTA
1 TCATCTTCGACCTTGACTCGATCTAAGTCATTTCATTTTTTTAACCTACGATTCAATCCTGATTA
5027112 A
66 A
* *
5027113 TCATCTTTGA-CTTGACTTGATCTAAGTCA-TTCATTCTTTTTAACCTACGATTCAATCC
1 TCATCTTCGACCTTGACTCGATCTAAGTCATTTCATT-TTTTTAACCTACGATTCAATCC
5027171 CAATCACTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 5 0.10
65 37 0.73
66 9 0.18
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (66 bp):
TCATCTTCGACCTTGACTCGATCTAAGTCATTTCATTTTTTTAACCTACGATTCAATCCTGATTA
A
Found at i:5027410 original size:66 final size:65
Alignment explanation
Indices: 5027339--5027484 Score: 168
Period size: 66 Copynumber: 2.2 Consensus size: 65
5027329 CAGTCCGATG
* * ** *
5027339 ATTTATTTTTTTGACTTGCGGTTCAGTCCC-AGTCACTTATTTTTTACCTTGGCTCAATCTAGGT
1 ATTTATTTTTTTGACCTGCGGTTCAATCCCGA-TCACTTATTTTCGACCTTGGCTCAATCTAGAT
5027403 C
65 C
* * * * *
5027404 ATTTTATTTTTTTAACCTGTGGTTCAATCCCGATCACTTATTTTCGATCTTGGTTTAATCTAGAT
1 A-TTTATTTTTTTGACCTGCGGTTCAATCCCGATCACTTATTTTCGACCTTGGCTCAATCTAGAT
5027469 C
65 C
*
5027470 ATTTATTTTTCTGAC
1 ATTTATTTTTTTGAC
5027485 ATATGGTTCA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
65 13 0.19
66 53 0.79
67 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (65 bp):
ATTTATTTTTTTGACCTGCGGTTCAATCCCGATCACTTATTTTCGACCTTGGCTCAATCTAGATC
Found at i:5027498 original size:34 final size:32
Alignment explanation
Indices: 5027339--5027504 Score: 90
Period size: 34 Copynumber: 5.0 Consensus size: 32
5027329 CAGTCCGATG
* * *
5027339 ATTTATTTTTTTGACTTGCGGTTCAGTCCCAG-TC
1 ATTTATTTTTCTGACTT--GGTTCAAT-CTAGATC
* * *
5027373 ACTTATTTTT-T-ACCTTGGCTCAATCTAGGTC
1 ATTTATTTTTCTGA-CTTGGTTCAATCTAGATC
* * **
5027404 ATTTTATTTTTTTAACCTGTGGTTCAATCCCGATC
1 A-TTTATTTTTCTGA-CT-TGGTTCAATCTAGATC
* *
5027439 ACTTA-TTTTC-GATCTTGGTTTAATCTAGATC
1 ATTTATTTTTCTGA-CTTGGTTCAATCTAGATC
*
5027470 ATTTATTTTTCTGACATATGGTTCAATCTTGATC
1 ATTTATTTTTCTGAC-T-TGGTTCAATCTAGATC
5027504 A
1 A
5027505 ACATATTTAA
Statistics
Matches: 103, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
30 3 0.03
31 26 0.25
32 18 0.17
33 12 0.12
34 31 0.30
35 13 0.13
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.48
Consensus pattern (32 bp):
ATTTATTTTTCTGACTTGGTTCAATCTAGATC
Found at i:5030371 original size:18 final size:19
Alignment explanation
Indices: 5030334--5030371 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
5030324 TCAAATCAAC
* *
5030334 TTGATCAAATTCAATTGAT
1 TTGATCAAATTAAATAGAT
5030353 TTGATC-AATTAAATAGAT
1 TTGATCAAATTAAATAGAT
5030371 T
1 T
5030372 AAACTTACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (19 bp):
TTGATCAAATTAAATAGAT
Found at i:5030972 original size:20 final size:21
Alignment explanation
Indices: 5030934--5030974 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
5030924 TTTTATTATG
5030934 ATTTGATATTTTAATTATATT
1 ATTTGATATTTTAATTATATT
5030955 ATTT-ATATTTTACA-TATATT
1 ATTTGATATTTTA-ATTATATT
5030975 TTGAACATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTGATATTTTAATTATATT
Found at i:5040407 original size:14 final size:14
Alignment explanation
Indices: 5040388--5040414 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5040378 CAACTCGAAA
5040388 TTAATTTAATAATT
1 TTAATTTAATAATT
5040402 TTAATTTAATAAT
1 TTAATTTAATAAT
5040415 ATTCATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAATTTAATAATT
Found at i:5049543 original size:57 final size:56
Alignment explanation
Indices: 5049455--5049568 Score: 192
Period size: 57 Copynumber: 2.0 Consensus size: 56
5049445 ATTCTTTGAT
** *
5049455 GGCACTGGGGTTAGCTTTTCTATATATAGGTTTTTCTTGGTTTTGTCAATTTTTTAA
1 GGCACTGAAGTTAGCTTTTCTATATATAGGTTTTT-TTGGTTTTGTCAAATTTTTAA
5049512 GGCACTGAAGTTAGCTTTTCTATATATAGGTTTTTTTGGTTTTGTCAAATTTTTAA
1 GGCACTGAAGTTAGCTTTTCTATATATAGGTTTTTTTGGTTTTGTCAAATTTTTAA
5049568 G
1 G
5049569 AAAAGTTATA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 21 0.39
57 33 0.61
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.50
Consensus pattern (56 bp):
GGCACTGAAGTTAGCTTTTCTATATATAGGTTTTTTTGGTTTTGTCAAATTTTTAA
Found at i:5049997 original size:15 final size:15
Alignment explanation
Indices: 5049977--5050006 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5049967 ATTATCCTAA
*
5049977 GGTCTTAATTTTAAT
1 GGTCTTAAATTTAAT
5049992 GGTCTTAAATTTAAT
1 GGTCTTAAATTTAAT
5050007 ATTGAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (15 bp):
GGTCTTAAATTTAAT
Found at i:5050601 original size:15 final size:15
Alignment explanation
Indices: 5050567--5050607 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
5050557 TTTTTACCTA
*
5050567 AATTTTTAT-GTTTT
1 AATTTTTATATTTTT
5050581 -ATTTTTATATTTTT
1 AATTTTTATATTTTT
*
5050595 AATTTTTTTATTT
1 AATTTTTATATTT
5050608 GAAAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 8 0.35
14 4 0.17
15 11 0.48
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (15 bp):
AATTTTTATATTTTT
Found at i:5056968 original size:25 final size:26
Alignment explanation
Indices: 5056926--5056988 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 26
5056916 TATAGATCAT
*
5056926 TCAAAACATTCATC-AA-ATCATAATG
1 TCAAAACATT-TTCAAACATCATAATG
5056951 TCAAAACATTTTCAAAATCATCATAATG
1 TCAAAACATTTTC-AAA-CATCATAATG
5056979 TC-AAACATTT
1 TCAAAACATTT
5056989 CGTAGATCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 2 0.06
25 10 0.30
26 2 0.06
27 8 0.24
28 11 0.33
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (26 bp):
TCAAAACATTTTCAAACATCATAATG
Found at i:5066603 original size:371 final size:370
Alignment explanation
Indices: 5065919--5066668 Score: 1058
Period size: 371 Copynumber: 2.0 Consensus size: 370
5065909 TAACTACTAG
* * * ** * *
5065919 TGTCACGGGTCGAGACTTAAGCTTCGAACCCGCACGGCTCTGGGATCCGGGCATGCACTCATCCA
1 TGTCACGGATCGAGACTTAAGCTCCGAACCCGCACGGCTCCGAAACCCGGGCATGCACCCATCCA
* * ** ** *
5065984 GTATCTCAGATCAGTCTTACTGTCACGGTTCACACCATTGTGAGGTATTGTCCGCTCTGGCCCCC
66 GCATCCCAGATCAACCTTACTACCACGGTTCACACCATTGTGAGATATTGTCCGCTCTGGCCCCC
* * * *
5066049 TGACCTCACAGTTTTGTCTTACAAAAGGCGCCTCATAAGGCGGAGGTGGTGTGAACCATTTTATA
131 TGACCTCACAGTTTTATCCTACAAAAGGCGCCTCACAAGGCGGAGGTGGTGTGAACCATTATATA
*
5066114 CCTCAGGGACCCTCCTATTATGTTCGATGTGAGATTCAGGACTCTTCCTTAGGTCCGTGACATTC
196 CCTCAGGGACCCTCCTATTATGTTCAATGTGAGATTCAGGACTCTTCCTTAGGTCCGTGACATTC
* * * *
5066179 TCCCGCACCCAACTTCGTGACACCTTCGTCACGAAGGCTGGCCACCTTGCCTACCTCCCTCGAGG
261 TCCCGCACCCAACCTCGTGACACCCTCGTCACGAAGGCTGGCCACCCTGCCTACCTCCATCGAGG
*
5066244 TGCTTGGCGTGGATCAAACGGTATAGGGCTGGCTCTGATACCACT
326 TGCTTGGCGTGGATCAAACGGTATAGGGCTGACTCTGATACCACT
* * *
5066289 TGTCACGGATCGAGACTTAAGCTCCGAACCCGCGCGGCTCCGAAACCCGGGCATTCACCCTTCC-
1 TGTCACGGATCGAGACTTAAGCTCCGAACCCGCACGGCTCCGAAACCCGGGCATGCACCCATCCA
* * *
5066353 GACATCCCAGATCAACCTTCCTACCACGGTTCAGACCCTTGTGAGATATTGTCCGCTCTGGCCCC
66 G-CATCCCAGATCAACCTTACTACCACGGTTCACACCATTGTGAGATATTGTCCGCTCTGGCCCC
* *
5066418 TCT-AGCCTCAC-GATTTTATCCTACAAAAGGTGCCTCACAAGGCGGAGGTGGTGTGAACCCTTA
130 -CTGA-CCTCACAG-TTTTATCCTACAAAAGGCGCCTCACAAGGCGGAGGTGGTGTGAACCATTA
* * *
5066481 TATA-CTCCAGTGACTCTCCTATTATGTTCAATGTGGGATTCAGGACTCTTCCTTAGGTCCGTGA
192 TATACCT-CAGGGACCCTCCTATTATGTTCAATGTGAGATTCAGGACTCTTCCTTAGGTCCGTGA
* * *
5066545 CATTCTCCCGTACCCAACCTCGTGACGCCCTCGTCACGGAGGCTGGCCACCCTGCCTACCTCCAT
256 CATTCTCCCGCACCCAACCTCGTGACACCCTCGTCACGAAGGCTGGCCACCCTGCCTACCTCCAT
* * *
5066610 CGAGGTGTTTGGCGTGGATCGAACGGTATATGGCTGACTCTGATACCACT
321 CGAGGTGCTTGGCGTGGATCAAACGGTATAGGGCTGACTCTGATACCACT
5066660 TGTCACGGA
1 TGTCACGGA
5066669 CCTAAGAAAG
Statistics
Matches: 334, Mismatches: 41, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
369 1 0.00
370 111 0.33
371 222 0.66
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (370 bp):
TGTCACGGATCGAGACTTAAGCTCCGAACCCGCACGGCTCCGAAACCCGGGCATGCACCCATCCA
GCATCCCAGATCAACCTTACTACCACGGTTCACACCATTGTGAGATATTGTCCGCTCTGGCCCCC
TGACCTCACAGTTTTATCCTACAAAAGGCGCCTCACAAGGCGGAGGTGGTGTGAACCATTATATA
CCTCAGGGACCCTCCTATTATGTTCAATGTGAGATTCAGGACTCTTCCTTAGGTCCGTGACATTC
TCCCGCACCCAACCTCGTGACACCCTCGTCACGAAGGCTGGCCACCCTGCCTACCTCCATCGAGG
TGCTTGGCGTGGATCAAACGGTATAGGGCTGACTCTGATACCACT
Found at i:5068300 original size:13 final size:14
Alignment explanation
Indices: 5068284--5068315 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
5068274 AAGATGTTCC
5068284 TAAAAGCATGA-CT
1 TAAAAGCATGACCT
5068297 TAAAAGCATGACCT
1 TAAAAGCATGACCT
5068311 TAAAA
1 TAAAA
5068316 AAGTAGCAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (14 bp):
TAAAAGCATGACCT
Found at i:5076087 original size:16 final size:17
Alignment explanation
Indices: 5076056--5076090 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5076046 AAATATTATT
5076056 TTAAATATAAATATAAAA
1 TTAAATAT-AATATAAAA
5076074 TTAAATAT-ATATAAAA
1 TTAAATATAATATAAAA
5076090 T
1 T
5076091 ATATAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAATATAATATAAAA
Found at i:5081738 original size:56 final size:56
Alignment explanation
Indices: 5081676--5081790 Score: 194
Period size: 56 Copynumber: 2.1 Consensus size: 56
5081666 GACCTATTAA
* *
5081676 ATTAAGCTTTGCTTCAGGTTCAACAGCTTAAGGTTTTTTACGAAGGCCTTGAATTC
1 ATTAAGCTTTACTTCAGGTTCAACAGCTAAAGGTTTTTTACGAAGGCCTTGAATTC
* *
5081732 ATTAAGCTTTACTTCGGGTTCAACCGCTAAAGGTTTTTTACGAAGGCCTTGAATTC
1 ATTAAGCTTTACTTCAGGTTCAACAGCTAAAGGTTTTTTACGAAGGCCTTGAATTC
5081788 ATT
1 ATT
5081791 CTTACCGGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.37
Consensus pattern (56 bp):
ATTAAGCTTTACTTCAGGTTCAACAGCTAAAGGTTTTTTACGAAGGCCTTGAATTC
Found at i:5083625 original size:67 final size:67
Alignment explanation
Indices: 5083531--5083666 Score: 227
Period size: 67 Copynumber: 2.0 Consensus size: 67
5083521 ACCTAATACT
** *
5083531 AAAACAGCAATCAACCACCGGAGATGATGGGTGTCCATCATTAAAATTTTCAATTACATCTGAAG
1 AAAACAGCAATCAACCACCAAAGATGATGGGTGCCCATCATTAAAATTTTCAATTACATCTGAAG
5083596 CA
66 CA
* *
5083598 AAAAGAGCAATCAACTACCAAAGATGATGGGTGCCCATCATTAAAATTTTCAATTACATCTGAAG
1 AAAACAGCAATCAACCACCAAAGATGATGGGTGCCCATCATTAAAATTTTCAATTACATCTGAAG
5083663 CA
66 CA
5083665 AA
1 AA
5083667 TATCATCAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (67 bp):
AAAACAGCAATCAACCACCAAAGATGATGGGTGCCCATCATTAAAATTTTCAATTACATCTGAAG
CA
Found at i:5091853 original size:18 final size:18
Alignment explanation
Indices: 5091830--5091864 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5091820 AGATGGCGCT
5091830 GTAGAAATCTTGGGCACC
1 GTAGAAATCTTGGGCACC
*
5091848 GTAGAAGTCTTGGGCAC
1 GTAGAAATCTTGGGCAC
5091865 TTTTGTTGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (18 bp):
GTAGAAATCTTGGGCACC
Found at i:5095114 original size:18 final size:18
Alignment explanation
Indices: 5095093--5095135 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5095083 ATTAATTTTG
*
5095093 ATAAAATT-AATTATAATA
1 ATAAAATTAAAAT-TAATA
*
5095111 ATAAGATTAAAATTAATA
1 ATAAAATTAAAATTAATA
5095129 ATAAAAT
1 ATAAAAT
5095136 ATATATTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
ATAAAATTAAAATTAATA
Found at i:5096288 original size:21 final size:21
Alignment explanation
Indices: 5096245--5096309 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
5096235 TTAAATGATT
*
5096245 TTAAATTATATTAAATATT-TAA
1 TTAAA-TAT-TTAAATTTTATAA
5096267 -TAAAGTATTTAAATTTTATAA
1 TTAAA-TATTTAAATTTTATAA
*
5096288 TTTAATATTTAAATTTTA-AA
1 TTAAATATTTAAATTTTATAA
5096308 TT
1 TT
5096310 TATTAATTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
20 12 0.32
21 23 0.61
22 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TTAAATATTTAAATTTTATAA
Found at i:5096429 original size:28 final size:28
Alignment explanation
Indices: 5096397--5096458 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
5096387 TATTATATTA
* **
5096397 ATTAATAAA-ATTATAATTTATGTATCAT
1 ATTAA-AAATATTAAAATTTAAATATCAT
*
5096425 ATTAAAAATTTTAAAATTTAAATATCAT
1 ATTAAAAATATTAAAATTTAAATATCAT
5096453 ATTAAA
1 ATTAAA
5096459 TATTTATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 3 0.10
28 26 0.90
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (28 bp):
ATTAAAAATATTAAAATTTAAATATCAT
Found at i:5101688 original size:25 final size:25
Alignment explanation
Indices: 5101659--5101718 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
5101649 TGAGTTAATT
5101659 TTATTTCAATGAATTTTAGTGTTTG
1 TTATTTCAATGAATTTTAGTGTTTG
5101684 TTATTTCAATGAATTTTAGTGTTTG
1 TTATTTCAATGAATTTTAGTGTTTG
*
5101709 -TAATTCAATG
1 TTATTTCAATG
5101719 CTAAGAGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 9 0.26
25 25 0.74
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.53
Consensus pattern (25 bp):
TTATTTCAATGAATTTTAGTGTTTG
Found at i:5110484 original size:15 final size:15
Alignment explanation
Indices: 5110459--5110509 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
5110449 AATAACTTTC
5110459 CTTTAACTTTTTTTTT
1 CTTT-ACTTTTTTTTT
5110475 CTTTACTTTTTCTTTT
1 CTTTACTTTTT-TTTT
* *
5110491 CCTT-CTTTTCGTTTT
1 CTTTACTTTT-TTTTT
5110506 CTTT
1 CTTT
5110510 CCTTCCTACC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 19 0.63
16 11 0.37
ACGTcount: A:0.06, C:0.20, G:0.02, T:0.73
Consensus pattern (15 bp):
CTTTACTTTTTTTTT
Found at i:5110496 original size:20 final size:19
Alignment explanation
Indices: 5110473--5110514 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
5110463 AACTTTTTTT
*
5110473 TTCTTTACTTTTTCTTTTCC
1 TTCTTTACGTTTTC-TTTCC
*
5110493 TTCTTTTCGTTTTCTTTCC
1 TTCTTTACGTTTTCTTTCC
5110512 TTC
1 TTC
5110515 CTACCGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.02, C:0.26, G:0.02, T:0.69
Consensus pattern (19 bp):
TTCTTTACGTTTTCTTTCC
Found at i:5118919 original size:22 final size:21
Alignment explanation
Indices: 5118891--5118977 Score: 70
Period size: 22 Copynumber: 3.9 Consensus size: 21
5118881 TGAGTTTATT
5118891 TATAAATATTAAAAAATATATC
1 TATAAATATTAAAAAATATA-C
5118913 TATAAATATATATAAACGAATATAC
1 TATAAATAT-TA-AAA--AATATAC
* *
5118938 TTATAAATAATAATAAATATAAC
1 -TATAAATATTAAAAAATAT-AC
5118961 TA-AAAT-TTAAATAAATA
1 TATAAATATTAAA-AAATA
5118978 AATATTAATG
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
20 3 0.06
21 9 0.17
22 16 0.30
23 4 0.07
24 5 0.09
25 3 0.06
26 14 0.26
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (21 bp):
TATAAATATTAAAAAATATAC
Found at i:5118925 original size:26 final size:25
Alignment explanation
Indices: 5118890--5118954 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
5118880 ATGAGTTTAT
5118890 TTATAAAT-AT-TAAA-AAATATA-
1 TTATAAATAATATAAACAAATATAC
*
5118911 TCTATAAATATATATAAACGAATATAC
1 T-TATAAATA-ATATAAACAAATATAC
5118938 TTATAAATAATAATAAA
1 TTATAAATAAT-ATAAA
5118955 TATAACTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
21 1 0.03
22 7 0.19
24 2 0.06
25 6 0.17
26 19 0.53
27 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (25 bp):
TTATAAATAATATAAACAAATATAC
Found at i:5119149 original size:23 final size:27
Alignment explanation
Indices: 5119120--5119168 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 27
5119110 AATGAGTTCA
5119120 TTTATAA-ATAT-TAAA-AAA-ATATG
1 TTTATAATATATATAAATAAACATATG
5119143 TTTATAATATATATAAATAAACATAT
1 TTTATAATATATATAAATAAACATAT
5119169 ATAACGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 7 0.32
24 4 0.18
25 4 0.18
26 3 0.14
27 4 0.18
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (27 bp):
TTTATAATATATATAAATAAACATATG
Found at i:5119226 original size:14 final size:14
Alignment explanation
Indices: 5119189--5119239 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
5119179 TATTTATAAA
5119189 TAATAAATAAA-TT
1 TAATAAATAAATTT
*
5119202 TAATTAA-AAATTT
1 TAATAAATAAATTT
*
5119215 TAATAAATAAATAT
1 TAATAAATAAATTT
*
5119229 TAATGAATAAA
1 TAATAAATAAA
5119240 AATAAATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 3 0.09
13 14 0.44
14 15 0.47
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
TAATAAATAAATTT
Found at i:5119313 original size:3 final size:3
Alignment explanation
Indices: 5119305--5119339 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
5119295 AAATATGATT
5119305 TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T
5119340 AAACTAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5119325 original size:16 final size:16
Alignment explanation
Indices: 5119304--5119337 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5119294 AAAATATGAT
5119304 TTTATTATTATTATTA
1 TTTATTATTATTATTA
5119320 TTTATTATTATTATTA
1 TTTATTATTATTATTA
5119336 TT
1 TT
5119338 ATAAACTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTATTATTATTATTA
Found at i:5121331 original size:3 final size:3
Alignment explanation
Indices: 5121323--5121359 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5121313 TTCAGAGTTG
5121323 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
5121360 ATCTTGCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:5130173 original size:339 final size:340
Alignment explanation
Indices: 5129530--5130213 Score: 1253
Period size: 339 Copynumber: 2.0 Consensus size: 340
5129520 TCACTCTAAA
5129530 TGATGAATTTTTGGCTCTAAAAATTTTGAGATTTATTATATTTCATACATCTAAAGAAGTTGAAA
1 TGATGAATTTTTGGCTCTAAAAATTTTGAGATTTATTATATTTCATACATCTAAAGAAGTTGAAA
5129595 ACAAAGGATGTGAAAGTATGTCAACTGTTTTTCATGTTCCATATGCAAAAATATACATTCCATAT
66 ACAAAGGATGTGAAAGTATGTCAACTGTTTTTCATGTTCCATATGCAAAAATATACATTCCATAT
* *
5129660 ATGCCAACATCGGTGTTTGCAATAGGGTATAATATCTACCTTTCCCAAAAAGACATTTCTATTTT
131 ATGCCAACAT--GTGTTTGCAATAGGGTATAATATCTACCATTCCCAAAAAGACATTCCTATTTT
* * *
5129725 ATTTAAGAGGTTTGGATTCGAATGTTAAAATGACAGTTTTAAGATTATGTAAAAATTATTGGTAG
194 ATTTAAGAGATTTGGATTCGAATGTTAAAATGACAGCTTCAAGATTATGTAAAAATTATTGGTAG
* *
5129790 TTTAAAATGTGATGTACCTTATATTGAGTATAAATATTACTTAAAATGATTTTAAAAAAATTATT
259 TTTAAAATGTGATGTACCTTATATTGAGTAGAAATATCACTTAAAATGATTTTAAAAAAATTATT
5129855 TATATTATTTAAGTAAT
324 TATATTATTTAAGTAAT
*
5129872 TGATGATTTTTTGGCTCTAAAAATTTTGAGATTTATTATATTTCATACATCTAAAGAAGTTGAAA
1 TGATGAATTTTTGGCTCTAAAAATTTTGAGATTTATTATATTTCATACATCTAAAGAAGTTGAAA
5129937 ACAAAGGATGTGAAAGTATGTCAACTGTTTTTCATGTTCCATATGCAAAAATATACATTCCATAT
66 ACAAAGGATGTGAAAGTATGTCAACTGTTTTTCATGTTCCATATGCAAAAATATACATTCCATAT
*
5130002 ATGCCAACAT-TGTTTGCAATAGGGTATAATATCTACCATTCTCAAAAAGACATTCCTATTTTAT
131 ATGCCAACATGTGTTTGCAATAGGGTATAATATCTACCATTCCCAAAAAGACATTCCTATTTTAT
5130066 TTAAGAGATTTGGATTCGAATGTTAAAATGACAGCTTCAAGATTATGTAAAAATTATTGGTAGTT
196 TTAAGAGATTTGGATTCGAATGTTAAAATGACAGCTTCAAGATTATGTAAAAATTATTGGTAGTT
*
5130131 TAAAATGTGATGTACCTTATATTGAGTAGAAATATCACTTAAAATGGTTTTAAAAAAATTATTTA
261 TAAAATGTGATGTACCTTATATTGAGTAGAAATATCACTTAAAATGATTTTAAAAAAATTATTTA
5130196 TATTATTTAAGTAAT
326 TATTATTTAAGTAAT
5130211 TGA
1 TGA
5130214 GTTAAGTATT
Statistics
Matches: 332, Mismatches: 10, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
339 193 0.58
342 139 0.42
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (340 bp):
TGATGAATTTTTGGCTCTAAAAATTTTGAGATTTATTATATTTCATACATCTAAAGAAGTTGAAA
ACAAAGGATGTGAAAGTATGTCAACTGTTTTTCATGTTCCATATGCAAAAATATACATTCCATAT
ATGCCAACATGTGTTTGCAATAGGGTATAATATCTACCATTCCCAAAAAGACATTCCTATTTTAT
TTAAGAGATTTGGATTCGAATGTTAAAATGACAGCTTCAAGATTATGTAAAAATTATTGGTAGTT
TAAAATGTGATGTACCTTATATTGAGTAGAAATATCACTTAAAATGATTTTAAAAAAATTATTTA
TATTATTTAAGTAAT
Found at i:5130392 original size:3 final size:3
Alignment explanation
Indices: 5130347--5130375 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5130337 TATTAAATAT
5130347 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5130376 TATTCTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5131635 original size:3 final size:3
Alignment explanation
Indices: 5131627--5131656 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5131617 AGGTATTACA
*
5131627 AAT AAT AAT AAT AAT AAT AAT AAT CAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5131657 TAAATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5133384 original size:2 final size:2
Alignment explanation
Indices: 5133377--5133413 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5133367 ACAACGCTTT
*
5133377 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TC TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5133414 CATAATATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5138520 original size:21 final size:21
Alignment explanation
Indices: 5138496--5138557 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
5138486 ATATTTTCTT
5138496 TTTATTAATAAATAATAATAA
1 TTTATTAATAAATAATAATAA
* *
5138517 TTTATTAATAAATAATATTTA
1 TTTATTAATAAATAATAATAA
5138538 TATT-TTAATAAAT-ATAATAA
1 T-TTATTAATAAATAATAATAA
5138558 ATAATAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 5 0.14
21 29 0.81
22 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTATTAATAAATAATAATAA
Found at i:5138631 original size:29 final size:29
Alignment explanation
Indices: 5138598--5138655 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
5138588 TAATTATAAT
* *
5138598 TTATTATATTTATTAAAATATTATTAAAA
1 TTATTATATTTATTAAAACATTAATAAAA
* *
5138627 TTATTATTTTTATTATAACATTAATAAAA
1 TTATTATATTTATTAAAACATTAATAAAA
5138656 AATAATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
TTATTATATTTATTAAAACATTAATAAAA
Found at i:5141352 original size:29 final size:32
Alignment explanation
Indices: 5141291--5141356 Score: 102
Period size: 29 Copynumber: 2.2 Consensus size: 32
5141281 AAATAAATCC
*
5141291 CAACAAATCAGGAAATAGATCCTGATTGGTGT
1 CAACAAATCAGGAAATAGATCCTGATTGCTGT
5141323 CAACAAATCA-GAAATAG-T-CTGATTGCTGT
1 CAACAAATCAGGAAATAGATCCTGATTGCTGT
5141352 CAACA
1 CAACA
5141357 GTTGGTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 15 0.45
30 1 0.03
31 7 0.21
32 10 0.30
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (32 bp):
CAACAAATCAGGAAATAGATCCTGATTGCTGT
Found at i:5153109 original size:24 final size:24
Alignment explanation
Indices: 5153075--5153131 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
5153065 ATAGATGTAT
*
5153075 ATAAAAGTGTG-GAAAAACTAAAAA
1 ATAAAATTGTGTGAAAAACT-AAAA
* *
5153099 ATAAAATTGTGTGAAAAGCTAAGA
1 ATAAAATTGTGTGAAAAACTAAAA
5153123 ATAAAATTG
1 ATAAAATTG
5153132 AATGTATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 22 0.76
25 7 0.24
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.23
Consensus pattern (24 bp):
ATAAAATTGTGTGAAAAACTAAAA
Found at i:5153302 original size:22 final size:22
Alignment explanation
Indices: 5153274--5153327 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
5153264 ATTTTTTGTC
*
5153274 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGGGACACAAATA
5153296 CTTAATTCTAGGGACACAAATA
1 CTTAATTCTAGGGACACAAATA
5153318 CTTAATTCTA
1 CTTAATTCTA
5153328 AACATATAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (22 bp):
CTTAATTCTAGGGACACAAATA
Found at i:5155812 original size:22 final size:22
Alignment explanation
Indices: 5155784--5155827 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5155774 CTAAATCTTC
*
5155784 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
5155806 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
5155828 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:5159298 original size:18 final size:18
Alignment explanation
Indices: 5159272--5159306 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5159262 TTAATCCATG
*
5159272 GAACCAGAAGCTTTACCT
1 GAACCAGAAACTTTACCT
*
5159290 GAACTAGAAACTTTACC
1 GAACCAGAAACTTTACC
5159307 AAAGAACATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (18 bp):
GAACCAGAAACTTTACCT
Found at i:5159532 original size:23 final size:23
Alignment explanation
Indices: 5159477--5159561 Score: 116
Period size: 23 Copynumber: 3.6 Consensus size: 23
5159467 TTGAAAGGGT
* *
5159477 TCGGCAATGAAGGCCTAAACAGGAT
1 TCGGCAATGAAGGCCTAAA-A-AAG
5159502 TCGGCAATGAAGGCCTAAAAAAG
1 TCGGCAATGAAGGCCTAAAAAAG
*
5159525 TCGGCAATGAAGGCTTAAAAAAG
1 TCGGCAATGAAGGCCTAAAAAAG
*
5159548 TCAGCAATGAAGGC
1 TCGGCAATGAAGGC
5159562 TGAAAATTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
23 36 0.64
24 1 0.02
25 19 0.34
ACGTcount: A:0.40, C:0.18, G:0.27, T:0.15
Consensus pattern (23 bp):
TCGGCAATGAAGGCCTAAAAAAG
Found at i:5159737 original size:22 final size:22
Alignment explanation
Indices: 5159709--5159752 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5159699 CTAAATCTTC
*
5159709 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
5159731 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
5159753 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:5161194 original size:25 final size:25
Alignment explanation
Indices: 5161155--5161212 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
5161145 TAAAATGGCT
*
5161155 ATGAAGGCATTAACAAGGTTCGACA
1 ATGAAGGCATAAACAAGGTTCGACA
* * * *
5161180 ATGAAGGCCTAAACAGGGTTTGGCA
1 ATGAAGGCATAAACAAGGTTCGACA
5161205 ATGAAGGC
1 ATGAAGGC
5161213 TGAAAATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.19
Consensus pattern (25 bp):
ATGAAGGCATAAACAAGGTTCGACA
Found at i:5161283 original size:24 final size:24
Alignment explanation
Indices: 5161256--5161302 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5161246 TCTGATACCA
5161256 TGTG-AAAAAACTAAGAAATAAAAT
1 TGTGTAAAAAACTAAG-AATAAAAT
*
5161280 TGTGTGAAAAACTAAGAATAAAA
1 TGTGTAAAAAACTAAGAATAAAA
5161303 CTAAATGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.60, C:0.04, G:0.15, T:0.21
Consensus pattern (24 bp):
TGTGTAAAAAACTAAGAATAAAAT
Found at i:5161785 original size:22 final size:22
Alignment explanation
Indices: 5161757--5161800 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5161747 CTAAATCTTC
*
5161757 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
5161779 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
5161801 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:5169846 original size:56 final size:56
Alignment explanation
Indices: 5169775--5169894 Score: 190
Period size: 56 Copynumber: 2.2 Consensus size: 56
5169765 AGTTGGCTTG
5169775 ATGT-TTGATAAAAGTAAAAGGAAGGG-TCTGTTTGGGTAAAAAGAGAGTATATAAC
1 ATGTATTGATAAAAGTAAAAGG-AGGGATCTGTTTGGGTAAAAAGAGAGTATATAAC
* * *
5169830 GTGTATTGATAAAAGTAAAAGGAGGGATCTTTTTGGGTAAAAGGAGAGTATATAAC
1 ATGTATTGATAAAAGTAAAAGGAGGGATCTGTTTGGGTAAAAAGAGAGTATATAAC
5169886 ATGTATTGA
1 ATGTATTGA
5169895 AGCACGCATA
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
55 7 0.12
56 52 0.88
ACGTcount: A:0.40, C:0.03, G:0.28, T:0.29
Consensus pattern (56 bp):
ATGTATTGATAAAAGTAAAAGGAGGGATCTGTTTGGGTAAAAAGAGAGTATATAAC
Found at i:5176830 original size:2 final size:2
Alignment explanation
Indices: 5176825--5176861 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5176815 TCTCTCTTTC
5176825 TA TA TA TA TA TA TA 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 TA TA TA TA T
5176862 GCACATGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5184480 original size:39 final size:40
Alignment explanation
Indices: 5184437--5184531 Score: 110
Period size: 40 Copynumber: 2.4 Consensus size: 40
5184427 TCTGTTTCAA
*
5184437 TAAATATTAAAT-TACAAA-AT-TGATATTTTTATAAAAAAT
1 TAAATATTAAATGTACAAATATCT-AT-TTGTTATAAAAAAT
*
5184476 TAAATATATAAATGTA-AAATATCTATTTGTTATAAAATAT
1 TAAATAT-TAAATGTACAAATATCTATTTGTTATAAAAAAT
5184516 TAAATA-TAAATGTACA
1 TAAATATTAAATGTACA
5184532 CTATGCTTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
38 8 0.16
39 8 0.16
40 26 0.53
41 6 0.12
42 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (40 bp):
TAAATATTAAATGTACAAATATCTATTTGTTATAAAAAAT
Found at i:5184609 original size:130 final size:129
Alignment explanation
Indices: 5184469--5184707 Score: 388
Period size: 130 Copynumber: 1.8 Consensus size: 129
5184459 ATATTTTTAT
* * ** *
5184469 AAAAAATTAAATATATAAATGTAAAATATCTATTTGTTATAAAATATTAAATATAAATGTACACT
1 AAAAAATTAAATATATAAATATAAAATATCTATTTGTTATAAAATATTAAATAAAAATCCAAACT
*
5184534 ATGCTTTGAATAAAAAATAAAATTCCTTATAAGTTTGATAGTATATAAATTTGACATCTTTATAA
66 ATGCTTTGAATAAAAAATAAAATTCCTTATAAATTTGATA-TATATAAATTTGACATCTTTATAA
*
5184599 AAAAAATTAAATATATAAATATAAAATATCTATTTGTTATTAAATATTAAATAAAAATCCAAACT
1 AAAAAATTAAATATATAAATATAAAATATCTATTTGTTATAAAATATTAAATAAAAATCCAAACT
* *
5184664 ATGCTTTGAATAAAAAATTAAATTTCTTATAAATTTGATATATA
66 ATGCTTTGAATAAAAAATAAAATTCCTTATAAATTTGATATATA
5184708 AGTTGAATCC
Statistics
Matches: 100, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
129 4 0.04
130 96 0.96
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.38
Consensus pattern (129 bp):
AAAAAATTAAATATATAAATATAAAATATCTATTTGTTATAAAATATTAAATAAAAATCCAAACT
ATGCTTTGAATAAAAAATAAAATTCCTTATAAATTTGATATATATAAATTTGACATCTTTATAA
Found at i:5196782 original size:1 final size:1
Alignment explanation
Indices: 5196776--5196802 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
5196766 ACGGGATAGG
5196776 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
5196803 CTGTTATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5203095 original size:18 final size:18
Alignment explanation
Indices: 5203060--5203095 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5203050 AAAATAAACG
*
5203060 TAATCGATTGGATAAATT
1 TAATCGATTGAATAAATT
*
5203078 TAATCGATTGAATCAATT
1 TAATCGATTGAATAAATT
5203096 AATTATTGAT
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:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (18 bp):
TAATCGATTGAATAAATT
Found at i:5208758 original size:138 final size:138
Alignment explanation
Indices: 5208544--5208800 Score: 363
Period size: 138 Copynumber: 1.9 Consensus size: 138
5208534 GCTCTGCATG
* *
5208544 GCAAATGAAGCAAAGCAACATCTTGAGCCTCAACTCAGTAGCATGGAAACAGATGCAGAGACAAT
1 GCAAATGAAGCAAAGAAACATCTTGAGCCTCAACTCAGTAGCATGGAAACAGAAGCAGAGACAAT
* * *
5208609 GTCAGCTAAGATTGACTCATTAGAAGCAGAAATTGAAAAGGAAAGGGCCTTGTCGGCACAAGTTT
66 GTCAGCAAAGATTGACTCATTAGAAACAGAAATTGAAAAGGAAAGGGCATTGTCGGCACAAGTTT
5208674 CAGTTAAT
131 CAGTTAAT
* * * * * * *
5208682 GCAAATGAATCAAAGAAACTTCTTGAGTCTCAACTCATTAGCATTGAAGCAGAAGCTCGA-ACAA
1 GCAAATGAAGCAAAGAAACATCTTGAGCCTCAACTCAGTAGCATGGAAACAGAAGC-AGAGACAA
* * *
5208746 TGTCTGCAAAGATTGATTCATTAGAAACAGAAGTTGAAAAGGAAAGGGCATTGTC
65 TGTCAGCAAAGATTGACTCATTAGAAACAGAAATTGAAAAGGAAAGGGCATTGTC
5208801 AACACAAATT
Statistics
Matches: 103, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
138 101 0.98
139 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (138 bp):
GCAAATGAAGCAAAGAAACATCTTGAGCCTCAACTCAGTAGCATGGAAACAGAAGCAGAGACAAT
GTCAGCAAAGATTGACTCATTAGAAACAGAAATTGAAAAGGAAAGGGCATTGTCGGCACAAGTTT
CAGTTAAT
Found at i:5212673 original size:2 final size:2
Alignment explanation
Indices: 5212666--5212704 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
5212656 TAAAAAGTGA
*
5212666 AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG -G AA AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5212705 CAATTGACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5217197 original size:11 final size:11
Alignment explanation
Indices: 5217160--5217198 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 11
5217150 AAGAAAATAG
5217160 AATTTATAAAAA
1 AATTTA-AAAAA
5217172 AATTATAAATAAA
1 AATT-TAAA-AAA
5217185 AATTTAAAAAA
1 AATTTAAAAAA
5217196 AAT
1 AAT
5217199 ATGGAAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.24
12 10 0.40
13 9 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AATTTAAAAAA
Found at i:5217259 original size:32 final size:31
Alignment explanation
Indices: 5217223--5217283 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 31
5217213 TTAAAAGATG
*
5217223 TATATGAATTTTTTATAAAAAAATTCAAAACA
1 TATATGAAATTTTTATAAAAAAA-TCAAAACA
5217255 TATATGAAATTTTTATAAAAAAATCAAAA
1 TATATGAAATTTTTATAAAAAAATCAAAA
5217284 TTAAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 6 0.21
32 22 0.79
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (31 bp):
TATATGAAATTTTTATAAAAAAATCAAAACA
Found at i:5218850 original size:19 final size:19
Alignment explanation
Indices: 5218822--5218861 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5218812 TTAGTCAATT
* *
5218822 ATTTTTATAAAAATATTAA
1 ATTTTAATAAAAAAATTAA
5218841 ATTTTAATAAAAAAATTAA
1 ATTTTAATAAAAAAATTAA
5218860 AT
1 AT
5218862 ATAAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTTAATAAAAAAATTAA
Found at i:5224040 original size:36 final size:36
Alignment explanation
Indices: 5223993--5224100 Score: 207
Period size: 36 Copynumber: 3.0 Consensus size: 36
5223983 CAAGTCCTTA
5223993 TTCCAATATCAGAGTCTTGGGAAAATTAGATAGCAG
1 TTCCAATATCAGAGTCTTGGGAAAATTAGATAGCAG
5224029 TTCCAATATCAGAGTCTTGGGAAAATTAGATAGCAG
1 TTCCAATATCAGAGTCTTGGGAAAATTAGATAGCAG
*
5224065 TTCCAATATCAGAGTCTCGGGAAAATTAGATAGCAG
1 TTCCAATATCAGAGTCTTGGGAAAATTAGATAGCAG
5224101 AACCACAAAA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (36 bp):
TTCCAATATCAGAGTCTTGGGAAAATTAGATAGCAG
Found at i:5224618 original size:41 final size:41
Alignment explanation
Indices: 5224556--5224634 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
5224546 GGGCAGTGTA
5224556 AGGTTCTAGAAATGGGAAGTGGTTTGGTGTACATCAATTGC
1 AGGTTCTAGAAATGGGAAGTGGTTTGGTGTACATCAATTGC
*
5224597 AGGTTCTAGAAATGGGTAGTGGTTTGGTGTACATCAAT
1 AGGTTCTAGAAATGGGAAGTGGTTTGGTGTACATCAAT
5224635 GGCTTGGGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.27, C:0.09, G:0.32, T:0.33
Consensus pattern (41 bp):
AGGTTCTAGAAATGGGAAGTGGTTTGGTGTACATCAATTGC
Found at i:5225281 original size:37 final size:37
Alignment explanation
Indices: 5225231--5225307 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
5225221 CTTCTGTGCT
5225231 TGGCATAAAGATTTT-GGACAGTATAAGGTTCTAGAAA
1 TGGCATAAAGATTTTGGGA-AGTATAAGGTTCTAGAAA
*
5225268 TGGCATAAAGATTTTGGGAAGTGTAAGGTTCTAGAAA
1 TGGCATAAAGATTTTGGGAAGTATAAGGTTCTAGAAA
5225305 TGG
1 TGG
5225308 GTAGTGATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
37 35 0.92
38 3 0.08
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.30
Consensus pattern (37 bp):
TGGCATAAAGATTTTGGGAAGTATAAGGTTCTAGAAA
Found at i:5226620 original size:17 final size:16
Alignment explanation
Indices: 5226600--5226635 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
5226590 ATATTTTTAG
5226600 AAAACAAAAAAAAATTA
1 AAAACAAAAAAAAA-TA
*
5226617 AAAAGAAAAAAAAATA
1 AAAACAAAAAAAAATA
5226633 AAA
1 AAA
5226636 TCATGAAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.86, C:0.03, G:0.03, T:0.08
Consensus pattern (16 bp):
AAAACAAAAAAAAATA
Found at i:5231344 original size:2 final size:2
Alignment explanation
Indices: 5231333--5231374 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5231323 TCTTTCAAGA
5231333 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5231374 A
1 A
5231375 AAAGAAGCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5244333 original size:26 final size:28
Alignment explanation
Indices: 5244278--5244333 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 28
5244268 AATTATTATA
* *
5244278 ATTTTTTTAATATATAATAATAATTTTTT
1 ATTTTTTT-ATATATAATAATAAATATTT
5244307 ATTTTTTT-TAT-TAATAATAAATATTT
1 ATTTTTTTATATATAATAATAAATATTT
5244333 A
1 A
5244334 AACTATAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 14 0.56
27 3 0.12
29 8 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
ATTTTTTTATATATAATAATAAATATTT
Found at i:5244515 original size:27 final size:28
Alignment explanation
Indices: 5244484--5244596 Score: 83
Period size: 28 Copynumber: 4.0 Consensus size: 28
5244474 ATATTCTTTT
5244484 AATTTATTTATAAAAAATTATTTAAA-A
1 AATTTATTTATAAAAAATTATTTAAATA
* *
5244511 TATTT-TTGTATAAAAAAATTTTTTAAATA
1 AATTTATT-TAT-AAAAAATTATTTAAATA
* * *
5244540 AATTTTAATTA-AAAAATTTATTTAAA-G
1 AA-TTTATTTATAAAAAATTATTTAAATA
* *
5244567 AGTTTTTTTATATAAAAA-TATCTTAAATA
1 AATTTATTTATA-AAAAATTAT-TTAAATA
5244596 A
1 A
5244597 TCTCTTTATA
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
26 8 0.12
27 12 0.18
28 36 0.55
29 3 0.05
30 5 0.08
31 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.47
Consensus pattern (28 bp):
AATTTATTTATAAAAAATTATTTAAATA
Found at i:5244542 original size:13 final size:12
Alignment explanation
Indices: 5244494--5244565 Score: 54
Period size: 13 Copynumber: 5.3 Consensus size: 12
5244484 AATTTATTTA
*
5244494 TAAAAAATTATT
1 TAAAAAATTTTT
*
5244506 TAAAATATTTTTGT
1 TAAAA-AATTTT-T
5244520 ATAAAAAAATTTTT
1 -T-AAAAAATTTTT
5244534 TAAATAAATTTTAAT
1 TAAA-AAATTTT--T
5244549 TAAAAAATTTATT
1 TAAAAAATTT-TT
5244562 TAAA
1 TAAA
5244566 GAGTTTTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 15
0.73 0.04 0.22
Matches are distributed among these distances:
12 8 0.16
13 17 0.35
14 8 0.16
15 12 0.24
16 4 0.08
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (12 bp):
TAAAAAATTTTT
Found at i:5244941 original size:139 final size:139
Alignment explanation
Indices: 5244759--5245026 Score: 367
Period size: 139 Copynumber: 1.9 Consensus size: 139
5244749 TTTAAGTTCT
* * * * * *
5244759 AAAACTTACAATTGAGTTTCAATTTCTTTCAGATATATTTTTTAAAAGAATAACGATTATTTCAT
1 AAAACTTACAATTGAGTTCCAATCTCTTCCAAACATACTTTTTAAAAGAATAACGATTATTTCAT
*
5244824 CATTTTTTATTTAAATCAAATTTGAAAATAAGATAA-TTTTTCTCTAAAATCCTAAAATACTATA
66 CATTTTTTATTTAAATCAAATTTGAAAATAAAATAATTTTTTCT-TAAAATCCTAAAATACTATA
5244888 AAGAGAGGTA
130 AAGAGAGGTA
* * *
5244898 AAAATTTACAATTGAGTTCCAATCTCTTCCAAACATACTTTTTAAAAGAGTAACGGTTATTTCAT
1 AAAACTTACAATTGAGTTCCAATCTCTTCCAAACATACTTTTTAAAAGAATAACGATTATTTCAT
* * * * * * *
5244963 TATTTTTTATTTGAATTAAATTTGAAAGTAAAATAATTTTTTCTTTAAATCCTAGAATATTATA
66 CATTTTTTATTTAAATCAAATTTGAAAATAAAATAATTTTTTCTTAAAATCCTAAAATACTATA
5245027 GGGAAAGGTG
Statistics
Matches: 111, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
139 104 0.94
140 7 0.06
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (139 bp):
AAAACTTACAATTGAGTTCCAATCTCTTCCAAACATACTTTTTAAAAGAATAACGATTATTTCAT
CATTTTTTATTTAAATCAAATTTGAAAATAAAATAATTTTTTCTTAAAATCCTAAAATACTATAA
AGAGAGGTA
Found at i:5249252 original size:32 final size:32
Alignment explanation
Indices: 5249215--5249282 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
5249205 ACTTAAGTTA
* * *
5249215 AATTTATAGTTAAAATTTAAT-AATTCTAAATT
1 AATTTA-AATTAAAATTTAATAAAATATAAATT
*
5249247 AATTTAAATTAAATTTTAATAAAATATAAATT
1 AATTTAAATTAAAATTTAATAAAATATAAATT
5249279 AATT
1 AATT
5249283 AAAAAATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (32 bp):
AATTTAAATTAAAATTTAATAAAATATAAATT
Found at i:5249303 original size:19 final size:19
Alignment explanation
Indices: 5249259--5249309 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
5249249 TTTAAATTAA
* *
5249259 ATTTTAATAAAATATAAATT
1 ATTTTAA-AAAATAAAAATG
*
5249279 A-ATTAAAAAATAAAAATG
1 ATTTTAAAAAATAAAAATG
*
5249297 ATTTTAACAAATA
1 ATTTTAAAAAATA
5249310 TGTATCCTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 11 0.44
19 13 0.52
20 1 0.04
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
ATTTTAAAAAATAAAAATG
Found at i:5251952 original size:68 final size:69
Alignment explanation
Indices: 5251834--5251973 Score: 264
Period size: 68 Copynumber: 2.0 Consensus size: 69
5251824 ATCCCCATCT
5251834 TCCCATCCCCTTTAGAAATTGAAAAAAACCAGTAGGAAAAGAAAAATCCGCAATCCAATCCAAGA
1 TCCCATCCCCTTTAGAAATTGAAAAAAACCAGTAGGAAAAGAAAAATCCGCAATCCAATCCAAGA
5251899 ATTA
66 ATTA
*
5251903 TCCCATCCCCTTTAGAAATT-AAAAAAACCAGTAGGAAAAGAAAATTCCGCAATCCAATCCAAGA
1 TCCCATCCCCTTTAGAAATTGAAAAAAACCAGTAGGAAAAGAAAAATCCGCAATCCAATCCAAGA
5251967 ATTA
66 ATTA
5251971 TCC
1 TCC
5251974 TATCTCCGCA
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
68 50 0.71
69 20 0.29
ACGTcount: A:0.45, C:0.24, G:0.11, T:0.20
Consensus pattern (69 bp):
TCCCATCCCCTTTAGAAATTGAAAAAAACCAGTAGGAAAAGAAAAATCCGCAATCCAATCCAAGA
ATTA
Found at i:5259062 original size:13 final size:13
Alignment explanation
Indices: 5259046--5259071 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5259036 ATCCCAGACA
5259046 TAGTTCCCAAACC
1 TAGTTCCCAAACC
5259059 TAGTTCCCAAACC
1 TAGTTCCCAAACC
5259072 AACGAATCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.38, G:0.08, T:0.23
Consensus pattern (13 bp):
TAGTTCCCAAACC
Found at i:5266618 original size:23 final size:23
Alignment explanation
Indices: 5266592--5266635 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5266582 GAAACTGTTC
*
5266592 ATTTT-AAATAGACTTATCTATTT
1 ATTTTGAAA-AGACTTAACTATTT
5266615 ATTTTGAAAAGACTTAACTAT
1 ATTTTGAAAAGACTTAACTAT
5266636 CTGTCTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (23 bp):
ATTTTGAAAAGACTTAACTATTT
Found at i:5270745 original size:138 final size:138
Alignment explanation
Indices: 5270588--5270864 Score: 509
Period size: 138 Copynumber: 2.0 Consensus size: 138
5270578 AATCAAACTC
** *
5270588 TTTTAAATTTTTTTTTATTTATAAAATTTGAAATTAAAATTTTATTTAAAAAAAATCAAATAACA
1 TTTTAAAAATTTTTTTATTTATAAAATTTAAAATTAAAATTTTATTTAAAAAAAATCAAATAACA
**
5270653 GACGTTGATTATTTACTTATTTTTATACATACAAGAAAGTTTGGGAGATTTTTTTTTTTTTAATT
66 GACGTTGATTATTTACTTATTTTTATACATACAAGAAAGTTTGGGAGATTTTTTTTTTTAAAATT
5270718 TTGGTATT
131 TTGGTATT
5270726 TTTTAAAAATTTTTTTATTTATAAAATTTAAAATTAAAATTTTATTTAAAAAAAATCAAATAACA
1 TTTTAAAAATTTTTTTATTTATAAAATTTAAAATTAAAATTTTATTTAAAAAAAATCAAATAACA
5270791 GACGTTGATTATTTACTTATTTTTATACATACAAGAAAGTTTGGGAGATTTTTTTTTTTAAAATT
66 GACGTTGATTATTTACTTATTTTTATACATACAAGAAAGTTTGGGAGATTTTTTTTTTTAAAATT
5270856 TTGGTATT
131 TTGGTATT
5270864 T
1 T
5270865 ATTTCTCTCT
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 134 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.49
Consensus pattern (138 bp):
TTTTAAAAATTTTTTTATTTATAAAATTTAAAATTAAAATTTTATTTAAAAAAAATCAAATAACA
GACGTTGATTATTTACTTATTTTTATACATACAAGAAAGTTTGGGAGATTTTTTTTTTTAAAATT
TTGGTATT
Found at i:5272253 original size:22 final size:21
Alignment explanation
Indices: 5272223--5272266 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
5272213 TCTATAGTTC
**
5272223 TGTTTATTATAATCTTAAAAT
1 TGTTTATTATAATAATAAAAT
5272244 TGTTTAATTATAATAATAAAAT
1 TGTTT-ATTATAATAATAAAAT
5272266 T
1 T
5272267 ATATAGAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (21 bp):
TGTTTATTATAATAATAAAAT
Found at i:5274029 original size:24 final size:23
Alignment explanation
Indices: 5273971--5274021 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 23
5273961 ATATGTGGAT
*
5273971 TATATATAAATT---AATTCAAA
1 TATATATAAATTAAAAATTAAAA
5273991 TATATATAAATTAAAAATTAAAA
1 TATATATAAATTAAAAATTAAAA
5274014 TTATATAT
1 -TATATAT
5274022 TTATTAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 12 0.46
23 7 0.27
24 7 0.27
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
TATATATAAATTAAAAATTAAAA
Found at i:5274101 original size:27 final size:28
Alignment explanation
Indices: 5274044--5274101 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
5274034 ATTTTATTTT
*
5274044 TATATAATTTTTATTTTTAATTTTTACA
1 TATATAATTTTTATTTTTAATTTATACA
* *
5274072 TATATAA-TTTTGTTTTTAATTTATATA
1 TATATAATTTTTATTTTTAATTTATACA
5274099 TAT
1 TAT
5274102 GTAAATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (28 bp):
TATATAATTTTTATTTTTAATTTATACA
Found at i:5274963 original size:23 final size:23
Alignment explanation
Indices: 5274901--5274961 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
5274891 AATTATTAAA
*
5274901 TAATATCTAATAA-TTTTAAATTT
1 TAATATGT-ATAATTTTTAAATTT
*
5274924 TAATATGTATAATTTTTTAATTT
1 TAATATGTATAATTTTTAAATTT
5274947 TAA-AT-TATAATTTTT
1 TAATATGTATAATTTTT
5274962 TTATCAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.29
22 6 0.17
23 19 0.54
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TAATATGTATAATTTTTAAATTT
Found at i:5275474 original size:15 final size:17
Alignment explanation
Indices: 5275446--5275478 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
5275436 ATGAATAATT
5275446 ATTTAACTACAAATTCA
1 ATTTAACTACAAATTCA
5275463 ATTTAA-TA-AAATTCA
1 ATTTAACTACAAATTCA
5275478 A
1 A
5275479 ACTTTAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTTAACTACAAATTCA
Found at i:5278246 original size:34 final size:34
Alignment explanation
Indices: 5278190--5278254 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
5278180 AGTTATGTCT
* *
5278190 TTTAAAAACAAAATAATTTTTATTCTTTTTTTTA
1 TTTAAAAACAAAATAATGTTTATTATTTTTTTTA
* * *
5278224 TTTACAAATAAAATTATGTTTATTATTTTTT
1 TTTAAAAACAAAATAATGTTTATTATTTTTT
5278255 ATTCTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (34 bp):
TTTAAAAACAAAATAATGTTTATTATTTTTTTTA
Found at i:5288788 original size:21 final size:22
Alignment explanation
Indices: 5288751--5288797 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
5288741 TTTGTTTAAT
*
5288751 AAAA-AATTGATTGATCAA-AA
1 AAAATAATTGATTAATCAATAA
*
5288771 AAAATAATTTATTAATCAATAA
1 AAAATAATTGATTAATCAATAA
5288793 AAAAT
1 AAAAT
5288798 GAAGCAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 12 0.52
22 7 0.30
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (22 bp):
AAAATAATTGATTAATCAATAA
Found at i:5289492 original size:34 final size:34
Alignment explanation
Indices: 5289451--5289548 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 34
5289441 AGTTTTATTT
5289451 TAAATATTTTTATATTAATATAATTTTTTG-ATA
1 TAAATATTTTTATATTAATATAATTTTTTGAATA
* *
5289484 TCAAATATTATTAT-TAAAATATAATTATTCTTGAATA
1 T-AAATATTTTTATAT-TAATATAATT-TT-TTGAATA
* * *
5289521 TTAATAATTTTAATAATAA-ATAATTTTT
1 TAAAT-ATTTTTATATTAATATAATTTTT
5289549 ATTATTTTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
33 2 0.04
34 21 0.41
35 4 0.08
36 12 0.24
37 12 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (34 bp):
TAAATATTTTTATATTAATATAATTTTTTGAATA
Found at i:5290181 original size:35 final size:37
Alignment explanation
Indices: 5290112--5290197 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 37
5290102 TACCCTCTCT
*
5290112 TAAAATA-TTAAAAAATTATTAATTTAATATTTAATA
1 TAAAATATTTAAATAATTATTAATTTAATATTTAATA
5290148 -AAAATATTTAAATAATATATT-ATATTAA-A-TTAATA
1 TAAAATATTTAAATAAT-TATTAAT-TTAATATTTAATA
* *
5290183 TATAATATTAAAATA
1 TAAAATATTTAAATA
5290198 TTAAATAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
35 12 0.28
36 23 0.53
37 8 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (37 bp):
TAAAATATTTAAATAATTATTAATTTAATATTTAATA
Found at i:5290205 original size:18 final size:18
Alignment explanation
Indices: 5290143--5290205 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
5290133 ATTTAATATT
*
5290143 TAATAAA-AATATTTAAA
1 TAATAAATAATATTAAAA
* * *
5290160 TAATATATTATATTAAAT
1 TAATAAATAATATTAAAA
*
5290178 TAATATATAATATTAAAA
1 TAATAAATAATATTAAAA
*
5290196 TATTAAATAA
1 TAATAAATAA
5290206 AATATTTTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
17 6 0.16
18 31 0.84
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATAAATAATATTAAAA
Found at i:5290270 original size:22 final size:22
Alignment explanation
Indices: 5290216--5290271 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
5290206 AATATTTTTA
* *
5290216 AATACTAAAATATTTTTAAAAAT
1 AATA-TAAAATAGTATTAAAAAT
5290239 AATATGAAAATAGTATT-AAAAT
1 AATAT-AAAATAGTATTAAAAAT
5290261 AATAGTAAAAT
1 AATA-TAAAAT
5290272 CTTTGTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (22 bp):
AATATAAAATAGTATTAAAAAT
Found at i:5290384 original size:21 final size:21
Alignment explanation
Indices: 5290277--5290384 Score: 84
Period size: 21 Copynumber: 5.4 Consensus size: 21
5290267 AAAATCTTTG
*
5290277 TAAACTAATATTTAATATTAT
1 TAAATTAATATTTAATATTAT
** * * *
5290298 TAGTTTGATATGTAAAATTAT
1 TAAATTAATATTTAATATTAT
* * *
5290319 TAAA-CAATATTAAATTTTAT
1 TAAATTAATATTTAATATTAT
5290339 TAAATT--T-TTTAAATATT-T
1 TAAATTAATATTT-AATATTAT
5290357 T-AATTAATATTTAATATTAT
1 TAAATTAATATTTAATATTAT
5290377 TAAATTAA
1 TAAATTAA
5290385 CAATGAATAT
Statistics
Matches: 63, Mismatches: 17, Indels: 14
0.67 0.18 0.15
Matches are distributed among these distances:
17 4 0.06
18 4 0.06
19 13 0.21
20 19 0.30
21 23 0.37
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (21 bp):
TAAATTAATATTTAATATTAT
Found at i:5291407 original size:8 final size:8
Alignment explanation
Indices: 5291394--5291422 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5291384 GTAAAGGGTG
5291394 TTTTTCTT
1 TTTTTCTT
5291402 TTTTTCTT
1 TTTTTCTT
5291410 TTTTT-TT
1 TTTTTCTT
5291417 TTTTTC
1 TTTTTC
5291423 ACTTTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTCTT
Found at i:5292651 original size:2 final size:2
Alignment explanation
Indices: 5292644--5292670 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5292634 TCTAAATCTA
5292644 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5292671 AAGAACTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5294332 original size:21 final size:21
Alignment explanation
Indices: 5294308--5294348 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5294298 ATAATTTTTT
5294308 TAATGTTAAAA-AGTAAAAAAA
1 TAATGTTAAAATA-TAAAAAAA
*
5294329 TAATTTTAAAATATAAAAAA
1 TAATGTTAAAATATAAAAAA
5294349 TAAGAGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (21 bp):
TAATGTTAAAATATAAAAAAA
Found at i:5295610 original size:7 final size:6
Alignment explanation
Indices: 5295567--5295609 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
5295557 AAATGAAAAG
* *
5295567 TTTAAA TTTAAA TTTAAT TTTTAA TTTAAAA TTTAATA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA-A TTTAA
5295610 TTCGAATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
6 20 0.65
7 11 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:5295610 original size:19 final size:18
Alignment explanation
Indices: 5295571--5295611 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
5295561 GAAAAGTTTA
*
5295571 AATTTAAATTTAATTTTT
1 AATTTAAATTTAATATTT
5295589 AATTTAAAATTTAATATTT
1 AATTT-AAATTTAATATTT
5295608 AATT
1 AATT
5295612 CGAATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTAAATTTAATATTT
Found at i:5295750 original size:16 final size:17
Alignment explanation
Indices: 5295719--5295751 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5295709 ATATTTTATT
5295719 AATTAAAATAATAAAAA
1 AATTAAAATAATAAAAA
*
5295736 AATTTAAAT-ATAAAAA
1 AATTAAAATAATAAAAA
5295752 TTCGATTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATTAAAATAATAAAAA
Done.