Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 135 of 135
Found at i:48292508 original size:27 final size:27
Alignment explanation
Indices: 48292468--48292523 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
48292458 TACTACTCAA
48292468 AATCTTGAGAAAGAAAAGTAATGGAGT
1 AATCTTGAGAAAGAAAAGTAATGGAGT
*
48292495 AATCTTGAGTAAGAAAAGTAATGGAGT
1 AATCTTGAGAAAGAAAAGTAATGGAGT
48292522 AA
1 AA
48292524 GTTCAATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.48, C:0.04, G:0.25, T:0.23
Consensus pattern (27 bp):
AATCTTGAGAAAGAAAAGTAATGGAGT
Found at i:48296774 original size:39 final size:41
Alignment explanation
Indices: 48296711--48296800 Score: 112
Period size: 39 Copynumber: 2.2 Consensus size: 41
48296701 AAAAATTATA
* * * * *
48296711 TTTAATACAATAAAATATTTATTATATTTAT-TTA-TGTTC
1 TTTAATATAATAAAACATTCATTATACTTATGGTAGTGTTC
*
48296750 TTTAATATAATAAAACATTCATTATACTTATGGTAGTGTTT
1 TTTAATATAATAAAACATTCATTATACTTATGGTAGTGTTC
48296791 TTTAATATAA
1 TTTAATATAA
48296801 ATAATTTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 27 0.63
40 2 0.05
41 14 0.33
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (41 bp):
TTTAATATAATAAAACATTCATTATACTTATGGTAGTGTTC
Found at i:48298832 original size:16 final size:16
Alignment explanation
Indices: 48298811--48298843 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48298801 TATAATCATT
48298811 TTAAATTACTAG-TATA
1 TTAAATTA-TAGATATA
48298827 TTAAATTATAGATATA
1 TTAAATTATAGATATA
48298843 T
1 T
48298844 ATTAGTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (16 bp):
TTAAATTATAGATATA
Found at i:48299214 original size:11 final size:11
Alignment explanation
Indices: 48299200--48299229 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
48299190 CTCAACTTTC
48299200 TCTCAATTTAT
1 TCTCAATTTAT
48299211 TCTCAATTTAT
1 TCTCAATTTAT
48299222 TCTCAATT
1 TCTCAATT
48299230 CTCTCTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (11 bp):
TCTCAATTTAT
Found at i:48312692 original size:16 final size:16
Alignment explanation
Indices: 48312671--48312704 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48312661 CCAATATCCA
* *
48312671 ATTATCATATTTGCAC
1 ATTATCACATTTACAC
48312687 ATTATCACATTTACAC
1 ATTATCACATTTACAC
48312703 AT
1 AT
48312705 ATATATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTATCACATTTACAC
Found at i:48318482 original size:20 final size:20
Alignment explanation
Indices: 48318466--48318513 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
48318456 ATATAAATAT
*
48318466 TATAAAAAAATTTTAAAGAA
1 TATAAAAAAATGTTAAAGAA
*
48318486 TATATAAAAATGTTAAA-AA
1 TATAAAAAAATGTTAAAGAA
48318505 TA-AAAAAAA
1 TATAAAAAAA
48318514 GTTTCCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 6 0.24
19 4 0.16
20 15 0.60
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (20 bp):
TATAAAAAAATGTTAAAGAA
Found at i:48321158 original size:28 final size:26
Alignment explanation
Indices: 48321117--48321170 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 26
48321107 TTTCACATTT
*
48321117 AATATTTATATTTACATAAAATGTTTAA
1 AATATTTATATTTA-A-AAAATATTTAA
* *
48321145 AATATTTGTGTTTAAAAAATATTTAA
1 AATATTTATATTTAAAAAATATTTAA
48321171 TGTGTACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 10 0.43
27 1 0.04
28 12 0.52
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (26 bp):
AATATTTATATTTAAAAAATATTTAA
Found at i:48322396 original size:95 final size:95
Alignment explanation
Indices: 48322060--48322389 Score: 619
Period size: 95 Copynumber: 3.5 Consensus size: 95
48322050 TTTAGGGTTT
* *
48322060 CTTAATTAAATTAATTATAAATTTTT--CAAAATTAGATTAGGGTTTCATGTTTATGGTTTTTAA
1 CTTAAGTAAATTAATTAT-AATTTTTAAAAAAATTAGATTAGGGTTTCATGTTTATGGTTTTTAA
48322123 GAAAAAACCAATTAAATTAGGGTTAAGGGTA
65 GAAAAAACCAATTAAATTAGGGTTAAGGGTA
48322154 CTTAAGTAAATTAATTATAATTTTTAAAAAAATTAGATTAGGGTTTCATGTTTATGGTTTTTAAG
1 CTTAAGTAAATTAATTATAATTTTTAAAAAAATTAGATTAGGGTTTCATGTTTATGGTTTTTAAG
48322219 AAAAAACCAATTAAATTAGGGTTAAGGGTA
66 AAAAAACCAATTAAATTAGGGTTAAGGGTA
48322249 CTTAAGTAAATTAATTATAATTTTTAAAAAAATTAGATTAGGGTTTCATGTTTATGGTTTTTAAG
1 CTTAAGTAAATTAATTATAATTTTTAAAAAAATTAGATTAGGGTTTCATGTTTATGGTTTTTAAG
48322314 AAAAAACCAATTAAATTAGGGTTAAGGGTA
66 AAAAAACCAATTAAATTAGGGTTAAGGGTA
48322344 CTTAAGTAAATTAATTATAATTTTTAAAAAAATTAGATTAGGGTTT
1 CTTAAGTAAATTAATTATAATTTTTAAAAAAATTAGATTAGGGTTT
48322390 AGTGTTTGTT
Statistics
Matches: 232, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
93 7 0.03
94 17 0.07
95 208 0.90
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.40
Consensus pattern (95 bp):
CTTAAGTAAATTAATTATAATTTTTAAAAAAATTAGATTAGGGTTTCATGTTTATGGTTTTTAAG
AAAAAACCAATTAAATTAGGGTTAAGGGTA
Found at i:48322665 original size:126 final size:125
Alignment explanation
Indices: 48322409--48322698 Score: 454
Period size: 126 Copynumber: 2.3 Consensus size: 125
48322399 TAATTTAAAA
* * * *
48322409 AAGCTCCCACGTGGACACTTTTTTGCTACAGTAGTTACTGAAAAAATAATTTTGAGAAGACGTTT
1 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTCGAGAAGACGTTT
* * *
48322474 CTGAGGAAAAGTGGCAAAAACGCTTTAAGTAAGATGCATTGTCAGCAAAAGTACTGAAAG
66 CTGAGCAAAAGTGGCAAAAACGCTTTAAGCAAGATGCATTGTCAGCAAAAGCACTGAAAG
*
48322534 AAGCTCCTACGTGGACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTCGAGAAGACGTTT
1 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTCGAGAAGACGTTT
* * * *
48322599 TTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGCACTGAAAG
66 CTGAGCAAA-AGTGGCAAAAACGCTTTAAGCAAGATGCATTGTCAGCAAAAGCACTGAAAG
*
48322660 AAGCTCCCACGTGGAAGCTCTTTTGCTACAGTAGTTCCT
1 AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCCT
48322699 ATTTGGCATG
Statistics
Matches: 150, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
125 67 0.45
126 83 0.55
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (125 bp):
AAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTCGAGAAGACGTTT
CTGAGCAAAAGTGGCAAAAACGCTTTAAGCAAGATGCATTGTCAGCAAAAGCACTGAAAG
Found at i:48323492 original size:60 final size:59
Alignment explanation
Indices: 48323313--48323526 Score: 205
Period size: 59 Copynumber: 3.7 Consensus size: 59
48323303 ATTATTTATA
48323313 TATTTT-TTAAATGAAATAATATAGAAATATTCAAAATATTGCCTTATTTAAAAGAATTTC
1 TATTTTATTAAA-GAAA-AATATAGAAATATTCAAAATATTGCCTTATTTAAAAGAATTTC
* * * * * * * * *
48323373 TATTTTATTAAA-AATATTAAAGTAA-ATT--ACA-ATTACTTTATTCAAAACAACGTTT-
1 TATTTTATTAAAGAAAAATATAGAAATATTCAAAATATTGCCTTATTTAAAAGAA--TTTC
48323428 TATTTTATTAAACGAAAAATATAGAAATATTCAAAATATTGCCTTATTTAAAAGAATTTC
1 TATTTTATTAAA-GAAAAATATAGAAATATTCAAAATATTGCCTTATTTAAAAGAATTTC
48323488 TATTTTATTAAA-AATATAA-A-AGTAAATATTCAAAATATT
1 TATTTTATTAAAGAA-A-AATATAG-AAATATTCAAAATATT
48323527 TGTACAAATA
Statistics
Matches: 123, Mismatches: 18, Indels: 27
0.73 0.11 0.16
Matches are distributed among these distances:
54 15 0.12
55 14 0.11
56 3 0.02
57 12 0.10
58 14 0.11
59 23 0.19
60 22 0.18
61 20 0.16
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (59 bp):
TATTTTATTAAAGAAAAATATAGAAATATTCAAAATATTGCCTTATTTAAAAGAATTTC
Found at i:48323944 original size:18 final size:18
Alignment explanation
Indices: 48323918--48323960 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
48323908 GACTAGAAAA
* * *
48323918 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
48323936 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
48323954 AGGATAC
1 AGGATAC
48323961 TTACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:48324061 original size:30 final size:30
Alignment explanation
Indices: 48324022--48324081 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
48324012 GTTGGGCAGA
* *
48324022 GTGACTGTGTCGGTGCTGTTGCTGGGCCTG
1 GTGACTGTGTCGGCGCTGTTGATGGGCCTG
* *
48324052 GTGATTGTGTGGGCGCTGTTGATGGGCCTG
1 GTGACTGTGTCGGCGCTGTTGATGGGCCTG
48324082 CGTCATCGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.05, C:0.17, G:0.45, T:0.33
Consensus pattern (30 bp):
GTGACTGTGTCGGCGCTGTTGATGGGCCTG
Found at i:48325776 original size:11 final size:11
Alignment explanation
Indices: 48325762--48325834 Score: 85
Period size: 11 Copynumber: 6.6 Consensus size: 11
48325752 GAGAGCTTTA
48325762 AGAGAAATTTG
1 AGAGAAATTTG
*
48325773 AGAGGAATTTG
1 AGAGAAATTTG
*
48325784 AGAGAAATATG
1 AGAGAAATTTG
*
48325795 AGAGAATATTGG
1 AGAGAA-ATTTG
*
48325807 AGAGAAATATG
1 AGAGAAATTTG
*
48325818 AAAG-AATTTG
1 AGAGAAATTTG
48325828 AGAGAAA
1 AGAGAAA
48325835 GGATTTAAGT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
10 8 0.16
11 33 0.66
12 9 0.18
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (11 bp):
AGAGAAATTTG
Found at i:48325813 original size:23 final size:21
Alignment explanation
Indices: 48325762--48325834 Score: 101
Period size: 23 Copynumber: 3.3 Consensus size: 21
48325752 GAGAGCTTTA
*
48325762 AGAGAAATTTGAGAGGAATTTG
1 AGAGAAATATGAGA-GAATTTG
48325784 AGAGAAATATGAGAGAATATTGG
1 AGAGAAATATGAGAGAAT-TT-G
*
48325807 AGAGAAATATGAAAGAATTTG
1 AGAGAAATATGAGAGAATTTG
48325828 AGAGAAA
1 AGAGAAA
48325835 GGATTTAAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.26
22 17 0.36
23 18 0.38
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (21 bp):
AGAGAAATATGAGAGAATTTG
Found at i:48326625 original size:20 final size:18
Alignment explanation
Indices: 48326596--48326638 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
48326586 TTTTCTCGAT
*
48326596 TCTTTTGTTCTCCTTTCTC
1 TCTTTCGTTCTCC-TTCTC
*
48326615 ATCTTTCGTTCTTCTTCTC
1 -TCTTTCGTTCTCCTTCTC
48326634 TCTTT
1 TCTTT
48326639 AGCAAACCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 5 0.24
20 11 0.52
ACGTcount: A:0.02, C:0.30, G:0.05, T:0.63
Consensus pattern (18 bp):
TCTTTCGTTCTCCTTCTC
Found at i:48345939 original size:3 final size:3
Alignment explanation
Indices: 48345931--48345999 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
48345921 TTGTCAACTT
48345931 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
48345979 ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
48346000 GGGGAATGAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:48351434 original size:38 final size:38
Alignment explanation
Indices: 48351383--48351460 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
48351373 ATACAAAGTA
48351383 AGGTTTAAATACCAAAGTGCAAATAATAGAAAAGCTAT
1 AGGTTTAAATACCAAAGTGCAAATAATAGAAAAGCTAT
*
48351421 AGGTTTAAATACCAAAGTGCAGATAATAGAAAAGCTAT
1 AGGTTTAAATACCAAAGTGCAAATAATAGAAAAGCTAT
48351459 AG
1 AG
48351461 TAAAAACTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.23
Consensus pattern (38 bp):
AGGTTTAAATACCAAAGTGCAAATAATAGAAAAGCTAT
Found at i:48352654 original size:43 final size:43
Alignment explanation
Indices: 48352607--48352697 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
48352597 AAAAAAATAA
* * *
48352607 GGTAATAAAACATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATCTT
* *
48352650 GGTAATAAAAGATGCAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATCTT
48352693 -GTAAT
1 GGTAAT
48352698 GAACTCAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (43 bp):
GGTAATAAAACATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:48355330 original size:24 final size:23
Alignment explanation
Indices: 48355277--48355323 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
48355267 ATTAAGTTTT
*
48355277 AACATGTTAGTCATATTCTATAC
1 AACATGTTAGTCATATTATATAC
48355300 AAGCATGTTAGTCTTATATTATAT
1 AA-CATGTTAGTC--ATATTATAT
48355324 GCACATGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 10 0.50
26 8 0.40
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (23 bp):
AACATGTTAGTCATATTATATAC
Found at i:48359037 original size:41 final size:41
Alignment explanation
Indices: 48358984--48359167 Score: 194
Period size: 41 Copynumber: 4.5 Consensus size: 41
48358974 GCCCTTTCAA
* * * *
48358984 AAAAACGTCGCTAAAAACCTGAGCATTAGCGACGCCTTTTC
1 AAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCCTTTTC
* *
48359025 AAAAACGCCGCTAAAACCCCGAGCATTAGCGGTG-CTTAATC
1 AAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCCTT-TTC
* *
48359066 AAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTTTA
1 AAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCCTTTTC
** * *
48359107 AAAAACGTTGCTAAAACCCAC-AGCATTAGCGGCG-CTACTCC
1 AAAAACGCCGCTAAAACCC-CGAGCATTAGCGGCGCCT-TTTC
* *
48359148 AAAAACGCCACTAAAGCCCC
1 AAAAACGCCGCTAAAACCCC
48359168 TGATAGGTCA
Statistics
Matches: 119, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
40 5 0.04
41 111 0.93
42 3 0.03
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.17
Consensus pattern (41 bp):
AAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCCTTTTC
Found at i:48359121 original size:82 final size:82
Alignment explanation
Indices: 48358984--48359167 Score: 228
Period size: 82 Copynumber: 2.2 Consensus size: 82
48358974 GCCCTTTCAA
* * * *
48358984 AAAAACGTCGCTAAAAACCTGAGCATTAGCGACGCCTTTTCAAAAACGCCGCTAAAACCC-CGAG
1 AAAAACGCCGCTAAAACCCCGAGCATTAGCGACGCCTTTTAAAAAACGCCGCTAAAACCCAC-AG
*
48359048 CATTAGCGGTGCTTAAT-C
65 CATTAGCGGCGC-TAATCC
* * **
48359066 AAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTTTAAAAAACGTTGCTAAAACCCACAGC
1 AAAAACGCCGCTAAAACCCCGAGCATTAGCGACGCCTTTTAAAAAACGCCGCTAAAACCCACAGC
*
48359131 ATTAGCGGCGCTACTCC
66 ATTAGCGGCGCTAATCC
* *
48359148 AAAAACGCCACTAAAGCCCC
1 AAAAACGCCGCTAAAACCCC
48359168 TGATAGGTCA
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
81 3 0.03
82 84 0.95
83 1 0.01
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.17
Consensus pattern (82 bp):
AAAAACGCCGCTAAAACCCCGAGCATTAGCGACGCCTTTTAAAAAACGCCGCTAAAACCCACAGC
ATTAGCGGCGCTAATCC
Found at i:48365620 original size:16 final size:16
Alignment explanation
Indices: 48365583--48365613 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48365573 AGACATAAAG
*
48365583 GAAAAAACCCAACAAC
1 GAAACAACCCAACAAC
48365599 GAAACAACCCAACAA
1 GAAACAACCCAACAA
48365614 GCTAACAGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.32, G:0.06, T:0.00
Consensus pattern (16 bp):
GAAACAACCCAACAAC
Found at i:48366498 original size:21 final size:21
Alignment explanation
Indices: 48366469--48366511 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
48366459 CATCCATTTC
*
48366469 AAATTTATTGATT-TTTCAAAT
1 AAATATATT-ATTCTTTCAAAT
*
48366490 AAATATATTATTCTTTTAAAT
1 AAATATATTATTCTTTCAAAT
48366511 A
1 A
48366512 TTCAATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (21 bp):
AAATATATTATTCTTTCAAAT
Found at i:48379760 original size:11 final size:11
Alignment explanation
Indices: 48379722--48379764 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
48379712 AGATGTGAGA
48379722 AAAAATTATAT
1 AAAAATTATAT
*
48379733 AATAAATTTATAA
1 AA-AAA-TTATAT
*
48379746 AAAAATGATAT
1 AAAAATTATAT
48379757 AAAAATTA
1 AAAAATTA
48379765 AATGTGATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 13 0.50
12 6 0.23
13 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AAAAATTATAT
Found at i:48387811 original size:21 final size:20
Alignment explanation
Indices: 48387785--48387839 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
48387775 AAGAACAAAT
48387785 GAAAAAAGAAAGGAAAGAAAA
1 GAAAAAAGAAAGGAAAG-AAA
* *
48387806 GAAAAACGGAAGGAAAGAAA
1 GAAAAAAGAAAGGAAAGAAA
*
48387826 GAATAAAGACAAGG
1 GAAAAAAGA-AAGG
48387840 CTAGGGTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.67, C:0.04, G:0.27, T:0.02
Consensus pattern (20 bp):
GAAAAAAGAAAGGAAAGAAA
Found at i:48388648 original size:41 final size:40
Alignment explanation
Indices: 48388600--48388708 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 40
48388590 TCGACTTCGA
*
48388600 GTCGATGAGACACTGGGTGTCAATTTATTACTTCGGATTAATT
1 GTCGATGAGGCACTGGGTGTCAATTTATTACTTC-GATT--TT
*
48388643 -T-GATGAGGCACTGGGTGCCAA--T-TTACTTCGATTTT
1 GTCGATGAGGCACTGGGTGTCAATTTATTACTTCGATTTT
48388678 GTCGATGAGGCACTGGGTGTCAATTTATTAC
1 GTCGATGAGGCACTGGGTGTCAATTTATTAC
48388709 CTTAAATTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
35 2 0.03
36 1 0.02
37 23 0.40
38 7 0.12
39 2 0.03
40 4 0.07
41 18 0.31
42 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.36
Consensus pattern (40 bp):
GTCGATGAGGCACTGGGTGTCAATTTATTACTTCGATTTT
Found at i:48403476 original size:22 final size:21
Alignment explanation
Indices: 48403440--48403480 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
48403430 AAAATAAGGT
48403440 GAATTTTTTTAATTTCATTTTA
1 GAATTTTTTTAATTT-ATTTTA
48403462 GAATTTTTCTT-ATTTATTT
1 GAATTTTT-TTAATTTATTT
48403481 AATTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 12 0.67
23 2 0.11
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (21 bp):
GAATTTTTTTAATTTATTTTA
Found at i:48405163 original size:18 final size:18
Alignment explanation
Indices: 48405136--48405193 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
48405126 TTACTTGAAA
48405136 TTTA-AATATTTTTTATT
1 TTTATAATATTTTTTATT
*
48405153 TTTATAATATTTTTCAATT
1 TTTATAATATTTTT-TATT
48405172 TTTAT-ATATTATTTTGATT
1 TTTATAATATT-TTTT-ATT
48405191 TTT
1 TTT
48405194 TAAATTTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 4 0.11
18 14 0.40
19 17 0.49
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTATAATATTTTTTATT
Found at i:48405172 original size:19 final size:18
Alignment explanation
Indices: 48405136--48405225 Score: 61
Period size: 19 Copynumber: 5.3 Consensus size: 18
48405126 TTACTTGAAA
*
48405136 TTTA-AATATTTTTTATT
1 TTTATAATATTTTTAATT
48405153 TTTATAATATTTTTCAATT
1 TTTATAATATTTTT-AATT
*
48405172 TTTAT-ATATTATTTTGATT
1 TTTATAATA-T-TTTTAATT
*
48405191 TTT-TAA-ATTTATAA--
1 TTTATAATATTTTTAATT
*
48405205 -TTAT-ATATTTTTAAAT
1 TTTATAATATTTTTAATT
48405221 TTTAT
1 TTTAT
48405226 TAAAAATATT
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
13 3 0.05
14 8 0.14
16 4 0.07
17 9 0.16
18 14 0.24
19 16 0.28
20 4 0.07
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (18 bp):
TTTATAATATTTTTAATT
Found at i:48405216 original size:22 final size:22
Alignment explanation
Indices: 48405190--48405257 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
48405180 TTATTTTGAT
48405190 TTTTTAAATTTATAATTATATA
1 TTTTTAAATTTATAATTATATA
*
48405212 TTTTTAAATTT-T-ATTAAAAATA
1 TTTTTAAATTTATAATT--ATATA
*
48405234 TTTTTAAAATTATATATTATATA
1 TTTTTAAATTTATA-ATTATATA
48405257 T
1 T
48405258 GATTTTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 3 0.08
21 1 0.03
22 25 0.66
23 6 0.16
25 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTTAAATTTATAATTATATA
Found at i:48407696 original size:25 final size:25
Alignment explanation
Indices: 48407663--48407775 Score: 140
Period size: 25 Copynumber: 4.5 Consensus size: 25
48407653 ATACATGTAT
*
48407663 GCTCATACGAGCTATGAATCGGTAT
1 GCTCATACGAGCTATGAATCGGTAA
* *
48407688 GCTCTTACGAGCTGTGAATCGGTAA
1 GCTCATACGAGCTATGAATCGGTAA
*
48407713 GCTCATACGAGCTGA-GAATCAGTAA
1 GCTCATACGAGCT-ATGAATCGGTAA
**
48407738 GCTC-TCACGAGCTACAAATCGGTAA
1 GCTCAT-ACGAGCTATGAATCGGTAA
48407763 GCTCATACGAGCT
1 GCTCATACGAGCT
48407776 GTGTGTGTCC
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
24 2 0.03
25 73 0.96
26 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTATGAATCGGTAA
Found at i:48407722 original size:50 final size:50
Alignment explanation
Indices: 48407663--48407776 Score: 158
Period size: 50 Copynumber: 2.3 Consensus size: 50
48407653 ATACATGTAT
* * * ***
48407663 GCTCATACGAGCT-ATGAATCGGTATGCTCTTACGAGCTGTGAATCGGTAA
1 GCTCATACGAGCTGA-GAATCAGTAAGCTCTCACGAGCTACAAATCGGTAA
48407713 GCTCATACGAGCTGAGAATCAGTAAGCTCTCACGAGCTACAAATCGGTAA
1 GCTCATACGAGCTGAGAATCAGTAAGCTCTCACGAGCTACAAATCGGTAA
48407763 GCTCATACGAGCTG
1 GCTCATACGAGCTG
48407777 TGTGTGTCCA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 56 0.98
51 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.24
Consensus pattern (50 bp):
GCTCATACGAGCTGAGAATCAGTAAGCTCTCACGAGCTACAAATCGGTAA
Found at i:48415061 original size:25 final size:25
Alignment explanation
Indices: 48415025--48415115 Score: 112
Period size: 25 Copynumber: 3.6 Consensus size: 25
48415015 ATACATGTAT
48415025 GCTCATACGAGCTGTGAATCGGTAA
1 GCTCATACGAGCTGTGAATCGGTAA
* *
48415050 GTTCATACGAGCTGAGAATCGGTAA
1 GCTCATACGAGCTGTGAATCGGTAA
** *
48415075 GCTC-TCACGAGCTGCAAATTGGTAA
1 GCTCAT-ACGAGCTGTGAATCGGTAA
*
48415100 GCTCATACTAGCTGTG
1 GCTCATACGAGCTGTG
48415116 GTATGTCCAC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
24 1 0.02
25 53 0.96
26 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (25 bp):
GCTCATACGAGCTGTGAATCGGTAA
Found at i:48431748 original size:21 final size:21
Alignment explanation
Indices: 48431724--48431763 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
48431714 CGTATAAGAA
* *
48431724 ATTAATTTATTAGAGAAATGC
1 ATTAATTTATCAGAAAAATGC
48431745 ATTAATTTATCAGAAAAAT
1 ATTAATTTATCAGAAAAAT
48431764 AAAATACCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (21 bp):
ATTAATTTATCAGAAAAATGC
Found at i:48434798 original size:344 final size:344
Alignment explanation
Indices: 48434157--48434852 Score: 1284
Period size: 344 Copynumber: 2.0 Consensus size: 344
48434147 TTCATTGTCA
*
48434157 GTATACTAGTCAAGGAATGAAGTAAAGTGTCTTAATCATTACTATTTATGCAAGCCTAAACATTG
1 GTATACCAGTCAAGGAATGAAGTAAAGTGTCTTAATCATTACTATTTATGCAAGCCTAAACATTG
48434222 TGAAACGAAGAACTTTGTGGAACCATCTTACTTTGTTGGCTTTCGAAGAGGAGGTACCATGACTT
66 TGAAACGAAGAACTTTGTGGAACCATCTTACTTTGTTGGCTTTCGAAGAGGAGGTACCATGACTT
* * *
48434287 TTTGGGGGTGACTTCAATGCTATTGTCTCTTGTGAATAAAGAAAAGGAGGTATAGGGAATCGAAT
131 TTTGGGGGTAACTTCAATGCTATTGTCTCTTGTGAAGAAAGAAAAGGAGGTACAGGGAATCGAAT
* *
48434352 TGGTATTGATCATTTATTCTGAGACTTCTTATTTGATAATGGACTGCAAGACATGTGTAACACCC
196 TGGTATTGATAATTTATTCTAAGACTTCTTATTTGATAATGGACTGCAAGACATGTGTAACACCC
48434417 CGAGCCTAGCCTAGACGTTATGGTCGAATCTGAGAATGTTACAAAGAAAAGTTATAAAACCAACC
261 CGAGCCTAGCCTAGACGTTATGGTCGAATCTGAGAATGTTACAAAGAAAAGTTATAAAACCAACC
48434482 TTATCATTTTGAAAACACC
326 TTATCATTTTGAAAACACC
*
48434501 GTATACCAGTCAATGAATGAAGTAAAGTGTCTTAATCATTACTATTTATGCAAGCCTAAACATTG
1 GTATACCAGTCAAGGAATGAAGTAAAGTGTCTTAATCATTACTATTTATGCAAGCCTAAACATTG
*
48434566 TGAAACGAAGAACTTTGTGGAACCATCTTGCTTTGTTGGCTTTCGAAGAGGAGGTACCATGACTT
66 TGAAACGAAGAACTTTGTGGAACCATCTTACTTTGTTGGCTTTCGAAGAGGAGGTACCATGACTT
* *
48434631 TTTGGGGGTAACTTTAATGCTATTGTCTCTTGTGAAGAAAGAAAAGGAGGTGCAGGGAATCGAAT
131 TTTGGGGGTAACTTCAATGCTATTGTCTCTTGTGAAGAAAGAAAAGGAGGTACAGGGAATCGAAT
48434696 TGGTATTGATAATTTATTCTAAGACTTCTTATTTGATAATGGACTGCAAGACATGTGTAACACCC
196 TGGTATTGATAATTTATTCTAAGACTTCTTATTTGATAATGGACTGCAAGACATGTGTAACACCC
*
48434761 CGAGCTTAGCCTAGACGTTATGGTCGAATCTGAGAATGTTACAAAGAAAAGTTATAAAACCAACC
261 CGAGCCTAGCCTAGACGTTATGGTCGAATCTGAGAATGTTACAAAGAAAAGTTATAAAACCAACC
*
48434826 TTATCATTTTGAAAACATC
326 TTATCATTTTGAAAACACC
48434845 GTATACCA
1 GTATACCA
48434853 TTGTTAATAA
Statistics
Matches: 340, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
344 340 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (344 bp):
GTATACCAGTCAAGGAATGAAGTAAAGTGTCTTAATCATTACTATTTATGCAAGCCTAAACATTG
TGAAACGAAGAACTTTGTGGAACCATCTTACTTTGTTGGCTTTCGAAGAGGAGGTACCATGACTT
TTTGGGGGTAACTTCAATGCTATTGTCTCTTGTGAAGAAAGAAAAGGAGGTACAGGGAATCGAAT
TGGTATTGATAATTTATTCTAAGACTTCTTATTTGATAATGGACTGCAAGACATGTGTAACACCC
CGAGCCTAGCCTAGACGTTATGGTCGAATCTGAGAATGTTACAAAGAAAAGTTATAAAACCAACC
TTATCATTTTGAAAACACC
Found at i:48447719 original size:164 final size:164
Alignment explanation
Indices: 48447448--48447850 Score: 716
Period size: 164 Copynumber: 2.5 Consensus size: 164
48447438 TTTATTTTGG
48447448 TTGCTCTTGTTGAGAGTCGAACTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAG
1 TTGCTCTTGTTGAGAGTCGAACTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAG
* * *
48447513 CTACAAGAGCCTTGTTGATAGCTCAATCGAAAGTAATTTAAAGATTCATAACTAAAGTAGATTAC
66 CTACAAGAGCCTTGGTGAGAGCCCAATCGAAAGTAATTTAAAGATTCATAACTAAAGTAGATTAC
* **
48447578 ATGTCTGAACTCAAAATAGAAAATAAAACACAGT
131 ATGTCAGAACTCAAAATAGAAAATAAAACACAAA
*
48447612 TTGCTCTCGTTGAGAGTCGAACTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAG
1 TTGCTCTTGTTGAGAGTCGAACTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAG
* *
48447677 CTACAAGAGCCTTGGTGAGAGCCCAATCGAAAGTATTTTAAAGATTCATAACTTAAGTAGATTAC
66 CTACAAGAGCCTTGGTGAGAGCCCAATCGAAAGTAATTTAAAGATTCATAACTAAAGTAGATTAC
*
48447742 ATGTCAGAACTCAAAATAGAAAATAAAGCACAAA
131 ATGTCAGAACTCAAAATAGAAAATAAAACACAAA
48447776 TTGCTCTTGTTGAGAGTCGAACTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAG
1 TTGCTCTTGTTGAGAGTCGAACTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAG
48447841 CTACAAGAGC
66 CTACAAGAGC
48447851 TGCCTGATAA
Statistics
Matches: 228, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
164 228 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (164 bp):
TTGCTCTTGTTGAGAGTCGAACTCAAGACCTCCCGCTTACTAAACGGGTGCTCTAACCAACTGAG
CTACAAGAGCCTTGGTGAGAGCCCAATCGAAAGTAATTTAAAGATTCATAACTAAAGTAGATTAC
ATGTCAGAACTCAAAATAGAAAATAAAACACAAA
Found at i:48454436 original size:27 final size:26
Alignment explanation
Indices: 48454381--48454443 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
48454371 TTTAAAGCAC
* *
48454381 AAAAGTATATATACATAAATATTTAA
1 AAAAGTATATAAAAATAAATATTTAA
*
48454407 AAAAGTATCATAAAAATAAA-ATTATTA
1 AAAAGTAT-ATAAAAATAAATATT-TAA
48454434 AAAA-TATATA
1 AAAAGTATATA
48454444 GATAATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 3 0.09
26 14 0.44
27 15 0.47
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (26 bp):
AAAAGTATATAAAAATAAATATTTAA
Found at i:48459520 original size:6 final size:6
Alignment explanation
Indices: 48459509--48459552 Score: 79
Period size: 6 Copynumber: 7.2 Consensus size: 6
48459499 AAGCATGTTA
48459509 TATCTG TATCTG TATCTG TATCTG TATCTG TATTCTG TATCTG T
1 TATCTG TATCTG TATCTG TATCTG TATCTG TA-TCTG TATCTG T
48459553 TTTTGGGGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 31 0.84
7 6 0.16
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TATCTG
Found at i:48468133 original size:123 final size:124
Alignment explanation
Indices: 48467903--48468150 Score: 480
Period size: 123 Copynumber: 2.0 Consensus size: 124
48467893 CAATAATTTA
48467903 ACCTAGGGTTCATATTTGGAAAAATACCCATAGGTGAAATGTGTTTATTTTGATGTTTTATGATA
1 ACCTAGGGTTCATATTTGGAAAAATACCCATAGGTGAAATGTGTTTATTTTGATGTTTTATGATA
48467968 GAATATGAAGTCTTAATTTATGTTAAACAACTTTTGCTAAGTGATTTTAAGTGAAAACG
66 GAATATGAAGTCTTAATTTATGTTAAACAACTTTTGCTAAGTGATTTTAAGTGAAAACG
48468027 ACCTAGGGTT-ATATTTGGAAAAATACCCATAGGTGAAATGTGTTTATTTTGATGTTTTATGATA
1 ACCTAGGGTTCATATTTGGAAAAATACCCATAGGTGAAATGTGTTTATTTTGATGTTTTATGATA
*
48468091 GAATATGAAGTCTTAATTTATGTTAAACCACTTTTGCTAAGTGATTTTAAGTGAAAACG
66 GAATATGAAGTCTTAATTTATGTTAAACAACTTTTGCTAAGTGATTTTAAGTGAAAACG
48468150 A
1 A
48468151 GTAAAACGAC
Statistics
Matches: 123, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
123 113 0.92
124 10 0.08
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.39
Consensus pattern (124 bp):
ACCTAGGGTTCATATTTGGAAAAATACCCATAGGTGAAATGTGTTTATTTTGATGTTTTATGATA
GAATATGAAGTCTTAATTTATGTTAAACAACTTTTGCTAAGTGATTTTAAGTGAAAACG
Found at i:48473115 original size:33 final size:31
Alignment explanation
Indices: 48473073--48473158 Score: 95
Period size: 31 Copynumber: 2.7 Consensus size: 31
48473063 CTTGTGGTGA
* *
48473073 TGGG-CCACACGGGCTAGGCCA-AGTTGGGCTTG
1 TGGGCCCACACGGGC-AGGCCACA--CGGGCGTG
*
48473105 TGGGCCCACACGGGCATGCCACACGGGCGTG
1 TGGGCCCACACGGGCAGGCCACACGGGCGTG
*
48473136 TGGGCCCACACGGGCAAGCCACA
1 TGGGCCCACACGGGCAGGCCACA
48473159 TGGCTATGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
31 28 0.58
32 9 0.19
33 11 0.23
ACGTcount: A:0.19, C:0.33, G:0.37, T:0.12
Consensus pattern (31 bp):
TGGGCCCACACGGGCAGGCCACACGGGCGTG
Found at i:48473119 original size:18 final size:17
Alignment explanation
Indices: 48473098--48473150 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
48473088 AGGCCAAGTT
48473098 GGGCTTGTGGGCCCACAC
1 GGGC-TGTGGGCCCACAC
*
48473116 GGGC-AT--G-CCACAC
1 GGGCTGTGGGCCCACAC
48473129 GGGCGTGTGGGCCCACAC
1 GGGC-TGTGGGCCCACAC
48473147 GGGC
1 GGGC
48473151 AAGCCACATG
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
13 10 0.36
14 1 0.04
15 1 0.04
16 1 0.04
17 1 0.04
18 14 0.50
ACGTcount: A:0.13, C:0.34, G:0.42, T:0.11
Consensus pattern (17 bp):
GGGCTGTGGGCCCACAC
Found at i:48473169 original size:31 final size:31
Alignment explanation
Indices: 48473098--48473174 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
48473088 AGGCCAAGTT
*
48473098 GGGCTTGTGGGCCCACACGGGCATGCCACAC
1 GGGCTTGTGGGCCCACACGGGCAAGCCACAC
*
48473129 GGGCGTGTGGGCCCACACGGGCAAGCCACA-
1 GGGCTTGTGGGCCCACACGGGCAAGCCACAC
*
48473159 TGGCTATGTGGGCCCA
1 GGGCT-TGTGGGCCCA
48473175 TATTTTTGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 3 0.07
31 38 0.93
ACGTcount: A:0.17, C:0.32, G:0.38, T:0.13
Consensus pattern (31 bp):
GGGCTTGTGGGCCCACACGGGCAAGCCACAC
Found at i:48474779 original size:37 final size:37
Alignment explanation
Indices: 48474724--48474796 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
48474714 CTTTGAGAGG
*
48474724 GTTGAATCTTAAGGTTTTGG-TAGAAACCTTAAGGGA
1 GTTGAATCTTAAGATTTTGGTTAGAAACCTTAAGGGA
*
48474760 GTTGCAATCTTAAGATTTTGGTTAGAAATCTTAAGGG
1 GTTG-AATCTTAAGATTTTGGTTAGAAACCTTAAGGG
48474797 GGATTGTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 4 0.12
37 15 0.45
38 14 0.42
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (37 bp):
GTTGAATCTTAAGATTTTGGTTAGAAACCTTAAGGGA
Found at i:48476496 original size:20 final size:19
Alignment explanation
Indices: 48476460--48476512 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
48476450 TAATTATTTT
*
48476460 TAATTAATTTAATTAAACA
1 TAATTAATTAAATTAAACA
*
48476479 TAATTAATTAATATTAAACT
1 TAATTAATTAA-ATTAAACA
48476499 TAATTTAA-TAAATT
1 TAA-TTAATTAAATT
48476513 TAATGGATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 13 0.43
20 13 0.43
21 4 0.13
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (19 bp):
TAATTAATTAAATTAAACA
Found at i:48476515 original size:20 final size:20
Alignment explanation
Indices: 48476471--48476515 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
48476461 AATTAATTTA
*
48476471 ATTAAACATAATTAATTAAT
1 ATTAAACATAATTAATAAAT
*
48476491 ATTAAACTTAATTTAATAAAT
1 ATTAAACATAA-TTAATAAAT
48476512 -TTAA
1 ATTAA
48476516 TGGATGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTAAACATAATTAATAAAT
Found at i:48478809 original size:16 final size:15
Alignment explanation
Indices: 48478776--48478830 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 15
48478766 TAATTGGGTT
*
48478776 ATTATTT-ATATT-A
1 ATTATTTAAAATTGA
48478789 ATTATTTAAAATTGA
1 ATTATTTAAAATTGA
**
48478804 ACTTATTTCTAATTGA
1 A-TTATTTAAAATTGA
48478820 A-TATTTAAAAT
1 ATTATTTAAAAT
48478831 CTTCAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
13 7 0.21
14 12 0.35
15 2 0.06
16 13 0.38
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (15 bp):
ATTATTTAAAATTGA
Found at i:48479158 original size:14 final size:15
Alignment explanation
Indices: 48479132--48479169 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
48479122 GGAGTATATA
48479132 TATGGATTTAGGGAT
1 TATGGATTTAGGGAT
48479147 TATGGA-TTAGGGAT
1 TATGGATTTAGGGAT
48479161 TATGG-TTTA
1 TATGGATTTA
48479170 ATTAAGGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (15 bp):
TATGGATTTAGGGAT
Found at i:48479479 original size:14 final size:14
Alignment explanation
Indices: 48479460--48479486 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48479450 ATATATGGAT
48479460 TTAGGGATTATAGA
1 TTAGGGATTATAGA
48479474 TTAGGGATTATAG
1 TTAGGGATTATAG
48479487 TTTAATTAAG
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:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (14 bp):
TTAGGGATTATAGA
Found at i:48479548 original size:22 final size:23
Alignment explanation
Indices: 48479523--48479580 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
48479513 AGGTTTACGG
48479523 GTTAGCGGTTTAGAGGTT-A-GAT
1 GTTAG-GGTTTAGAGGTTAAGGAT
*
48479545 GTTAGTGGTTAAGA-GTTAAGGAT
1 GTTAG-GGTTTAGAGGTTAAGGAT
48479568 -TTAGGGTTTAGAG
1 GTTAGGGTTTAGAG
48479581 TTTTAGGGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 10 0.33
22 17 0.57
23 3 0.10
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (23 bp):
GTTAGGGTTTAGAGGTTAAGGAT
Found at i:48479857 original size:47 final size:49
Alignment explanation
Indices: 48479799--48479903 Score: 146
Period size: 47 Copynumber: 2.1 Consensus size: 49
48479789 AAACGAAATA
48479799 AAAAAACTAAAATTT-TGAA-TTTTATCTA-AT-TTTTATAAATATTACTT
1 AAAAAACTAAAATTTAT-AATTTTTA-CTACATATTTTATAAATATTACTT
48479846 AAAAAACTAAAATTTATAATTTTTACTACTATATTTTATAAATATTACTT
1 AAAAAACTAAAATTTATAATTTTTACTAC-ATATTTTATAAATATTACTT
48479896 AAACAAAC
1 AAA-AAAC
48479904 CTATGGAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
47 20 0.38
48 6 0.12
49 2 0.04
50 20 0.38
51 4 0.08
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.43
Consensus pattern (49 bp):
AAAAAACTAAAATTTATAATTTTTACTACATATTTTATAAATATTACTT
Found at i:48480479 original size:21 final size:22
Alignment explanation
Indices: 48480444--48480485 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
48480434 TAAATATTAC
48480444 TTAAACAAAACTAATAAATAAG
1 TTAAACAAAACTAATAAATAAG
* *
48480466 TTAAA-AAAATTAATATATAA
1 TTAAACAAAACTAATAAATAA
48480486 CATTTGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (22 bp):
TTAAACAAAACTAATAAATAAG
Found at i:48480607 original size:153 final size:153
Alignment explanation
Indices: 48480302--48480610 Score: 484
Period size: 153 Copynumber: 2.0 Consensus size: 153
48480292 TAAATAGAGT
48480302 TAATAAATAAGTTAAAAAATGTAATAGATAACATTTGATAATTTAGGAGAGGACCAAATTATAAG
1 TAATAAATAAGTTAAAAAATGTAATAGATAACATTTGATAATTTAGGAGAGGACCAAATTATAAG
* *
48480367 AAATAAAATTAAAATAGAAAAAAATGAAATAAAAACACTAAAATTGTTAATTTTATCTAATTTAT
66 AAATAAAATTAAAATAAAAAAAAATGAAATAAAAACACTAAAATTGTTAATTTTATCTAATATAT
48480432 TATAAATATTACTTAAACAAAAC
131 TATAAATATTACTTAAACAAAAC
* *
48480455 TAATAAATAAGTTAAAAAAAT-TAATATATAACATTTGATAATTTAGGAGAGGACCAACTTATAA
1 TAATAAATAAGTT-AAAAAATGTAATAGATAACATTTGATAATTTAGGAGAGGACCAAATTATAA
*
48480519 GAAATAAAATTAAAATAAAAAGAAAAAATGAAATAAAAACACTAGAATT-TTGAATTTTATCTAA
65 GAAATAAAATTAAAAT--AAA-AAAAAATGAAATAAAAACACTAAAATTGTT-AATTTTATCTAA
*
48480583 TAT-TTATAACTATTACTT-AA-AAAAC
126 TATATTATAAATATTACTTAAACAAAAC
48480608 TAA
1 TAA
48480611 AATTTATAAT
Statistics
Matches: 145, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
153 78 0.54
154 9 0.06
155 18 0.12
156 40 0.28
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.31
Consensus pattern (153 bp):
TAATAAATAAGTTAAAAAATGTAATAGATAACATTTGATAATTTAGGAGAGGACCAAATTATAAG
AAATAAAATTAAAATAAAAAAAAATGAAATAAAAACACTAAAATTGTTAATTTTATCTAATATAT
TATAAATATTACTTAAACAAAAC
Found at i:48480622 original size:47 final size:50
Alignment explanation
Indices: 48480552--48480653 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 50
48480542 AAAAATGAAA
* *
48480552 TAAAAACACTAGAATTTTGAA-TTTTATCTA-ATA-TTTATAACTATTACT
1 TAAAAACACTAAAATTTTGAATTTTTA-CTACATATTTTATAAATATTACT
48480600 TAAAAA-ACTAAAATTTAT-AATTTTTACTACTATATTTTATAAATATTACT
1 TAAAAACACTAAAATTT-TGAATTTTTACTAC-ATATTTTATAAATATTACT
48480650 TAAA
1 TAAA
48480654 CAAAACTATG
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
47 14 0.30
48 12 0.26
49 3 0.06
50 18 0.38
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (50 bp):
TAAAAACACTAAAATTTTGAATTTTTACTACATATTTTATAAATATTACT
Found at i:48481247 original size:16 final size:16
Alignment explanation
Indices: 48481198--48481248 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
48481188 CCGGTGCTCG
*
48481198 TCTACCGTCGCACTCG
1 TCTACCGTCGCACTCC
** **
48481214 TGGACCGTCGCAGGCC
1 TCTACCGTCGCACTCC
48481230 TCTACCGTCGCACTCC
1 TCTACCGTCGCACTCC
48481246 TCT
1 TCT
48481249 GCTGTCGGAG
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.12, C:0.43, G:0.22, T:0.24
Consensus pattern (16 bp):
TCTACCGTCGCACTCC
Found at i:48481767 original size:14 final size:14
Alignment explanation
Indices: 48481748--48481777 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
48481738 TAAAAGGTTT
48481748 TTTAGTTAATCATC
1 TTTAGTTAATCATC
48481762 TTTAGTTAATCATC
1 TTTAGTTAATCATC
48481776 TT
1 TT
48481778 GCTGTTCGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (14 bp):
TTTAGTTAATCATC
Found at i:48482025 original size:22 final size:22
Alignment explanation
Indices: 48481993--48482036 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
48481983 CATTTGATCA
48481993 ATTGTTGTAGCCAATGCAAATT
1 ATTGTTGTAGCCAATGCAAATT
*
48482015 ATTGTTTTAGCCAATGCAAATT
1 ATTGTTGTAGCCAATGCAAATT
48482037 TTATTATTTA
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:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (22 bp):
ATTGTTGTAGCCAATGCAAATT
Found at i:48482626 original size:12 final size:12
Alignment explanation
Indices: 48482586--48482633 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
48482576 AAACTTATAT
48482586 ATAATAACTTAC
1 ATAATAACTTAC
48482598 AT-AT-A--TA-
1 ATAATAACTTAC
48482605 ATACATAACTTAC
1 ATA-ATAACTTAC
48482618 ATAATAACTTAC
1 ATAATAACTTAC
48482630 ATAA
1 ATAA
48482634 CTTATATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
7 2 0.07
8 2 0.07
9 2 0.07
10 2 0.07
11 2 0.07
12 17 0.57
13 3 0.10
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAATAACTTAC
Found at i:48482632 original size:21 final size:20
Alignment explanation
Indices: 48482581--48482637 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
48482571 TATTGAAACT
48482581 TATAT-ATA-ATAACTTACA
1 TATATAATACATAACTTACA
48482599 TATATAATACATAACTTACA
1 TATATAATACATAACTTACA
48482619 TA-ATAACTTACATAACTTA
1 TATATAA--TACATAACTTA
48482638 TATAGAAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.14
19 7 0.20
20 12 0.34
21 11 0.31
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (20 bp):
TATATAATACATAACTTACA
Found at i:48482636 original size:55 final size:54
Alignment explanation
Indices: 48482543--48482731 Score: 151
Period size: 54 Copynumber: 3.5 Consensus size: 54
48482533 ATATATATAT
*
48482543 ATATATAATACATAACTTACATAACTTATA-TTGA-AACTTATATATAATAACTTAC
1 ATATATAATACATAACTTACATAA--TA-ACTTAATAACTTATATATAATAACTTAC
* * *
48482598 ATATATAATACATAACTTACATAATAACTTACATAACTTATATA-GA-AAGTTAT
1 ATATATAATACATAACTTACATAATAACTTA-ATAACTTATATATAATAACTTAC
* * * * * *
48482651 ATATA-AACTTGCATAACTTACATAATAACATAACAACTTAGATAATACATAGCCTAC
1 ATATATAA--TACATAACTTACATAATAACTTAATAACTTATAT-ATA-ATAACTTAC
48482708 ATA-ACT--TACATAACTTACATAATA
1 ATATA-TAATACATAACTTACATAATA
48482732 CACCACTTAC
Statistics
Matches: 109, Mismatches: 14, Indels: 23
0.75 0.10 0.16
Matches are distributed among these distances:
52 3 0.03
53 23 0.21
54 41 0.38
55 34 0.31
56 2 0.02
57 6 0.06
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34
Consensus pattern (54 bp):
ATATATAATACATAACTTACATAATAACTTAATAACTTATATATAATAACTTAC
Found at i:48482674 original size:9 final size:9
Alignment explanation
Indices: 48482656--48482853 Score: 99
Period size: 9 Copynumber: 23.7 Consensus size: 9
48482646 GTTATATATA
*
48482656 AACTTGCAT
1 AACTTACAT
48482665 AACTTACAT
1 AACTTACAT
*
48482674 AA-TAACAT
1 AACTTACAT
*
48482682 AACAACTTAGAT
1 ---AACTTACAT
48482694 AA--TACAT
1 AACTTACAT
* *
48482701 AGCCTACAT
1 AACTTACAT
48482710 AACTTACAT
1 AACTTACAT
48482719 AACTTACAT
1 AACTTACAT
*
48482728 AA--TACAC
1 AACTTACAT
*
48482735 CACTTACAT
1 AACTTACAT
48482744 -A---A-AT
1 AACTTACAT
*
48482748 AACTTGCAT
1 AACTTACAT
48482757 AA--TACAT
1 AACTTACAT
* *
48482764 AGCCTACAT
1 AACTTACAT
*
48482773 AACTTATAT
1 AACTTACAT
48482782 AACTTACAT
1 AACTTACAT
*
48482791 AA--TACAC
1 AACTTACAT
*
48482798 CACTTACAT
1 AACTTACAT
48482807 AA--TACAT
1 AACTTACAT
*
48482814 TACTTACAT
1 AACTTACAT
48482823 AACTTACAT
1 AACTTACAT
* *
48482832 TA--TACAC
1 AACTTACAT
48482839 AACTTACAT
1 AACTTACAT
48482848 AACTTA
1 AACTTA
48482854 ATTAATATTA
Statistics
Matches: 140, Mismatches: 28, Indels: 42
0.67 0.13 0.20
Matches are distributed among these distances:
4 2 0.01
5 2 0.01
7 31 0.22
8 6 0.04
9 93 0.66
11 2 0.01
12 4 0.03
ACGTcount: A:0.45, C:0.22, G:0.03, T:0.30
Consensus pattern (9 bp):
AACTTACAT
Found at i:48482714 original size:54 final size:56
Alignment explanation
Indices: 48482656--48482794 Score: 158
Period size: 63 Copynumber: 2.4 Consensus size: 56
48482646 GTTATATATA
*
48482656 AACTTGCATAACTTACATAATA-ACAT-AACAACTTAG-ATAATACATAGCCTACAT
1 AACTTACATAACTTACATAATATACATAAACAACTT-GCATAATACATAGCCTACAT
*
48482710 AACTTACATAACTTACATAATACACCACTTACATAAATAACTTGCATAATACATAGCCTACAT
1 AACTTACATAACTTACATAAT-----A--TACATAAACAACTTGCATAATACATAGCCTACAT
*
48482773 AACTTATATAACTTACATAATA
1 AACTTACATAACTTACATAATA
48482795 CACCACTTAC
Statistics
Matches: 72, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
54 20 0.28
58 1 0.01
59 1 0.01
62 5 0.07
63 45 0.62
ACGTcount: A:0.46, C:0.21, G:0.04, T:0.29
Consensus pattern (56 bp):
AACTTACATAACTTACATAATATACATAAACAACTTGCATAATACATAGCCTACAT
Found at i:48482723 original size:63 final size:63
Alignment explanation
Indices: 48482674--48482808 Score: 193
Period size: 63 Copynumber: 2.2 Consensus size: 63
48482664 TAACTTACAT
48482674 AATAACAT-AACAACTTAG-ATAATACATAGCCTACATAACTTACATAACTTACATAATACACC
1 AATAACATAAACAACTT-GCATAATACATAGCCTACATAACTTACATAACTTACATAATACACC
* * * *
48482736 ACTTACATAAATAACTTGCATAATACATAGCCTACATAACTTATATAACTTACATAATACACC
1 AATAACATAAACAACTTGCATAATACATAGCCTACATAACTTACATAACTTACATAATACACC
* *
48482799 ACTTACATAA
1 AATAACATAA
48482809 TACATTACTT
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
62 7 0.10
63 60 0.90
ACGTcount: A:0.47, C:0.22, G:0.03, T:0.28
Consensus pattern (63 bp):
AATAACATAAACAACTTGCATAATACATAGCCTACATAACTTACATAACTTACATAATACACC
Found at i:48482733 original size:25 final size:25
Alignment explanation
Indices: 48482685--48482831 Score: 78
Period size: 25 Copynumber: 6.0 Consensus size: 25
48482675 ATAACATAAC
* * *
48482685 AACTTAGATAATACATAGCCTACAT
1 AACTTACATAATACATAACTTACAT
*
48482710 AACTTACATAACTTACATAA--TACAC
1 AACTTACATAA--TACATAACTTACAT
* *
48482735 CACTTACAT-A-A-ATAACTTGCAT
1 AACTTACATAATACATAACTTACAT
* *
48482757 AA--TACATAGCCTACATAACTTATAT
1 AACTTACATA--ATACATAACTTACAT
**
48482782 AACTTACATAATACACCACTTACAT
1 AACTTACATAATACATAACTTACAT
*
48482807 AA--TACATTACTTACATAACTTACAT
1 AACTTACA-TA-ATACATAACTTACAT
48482832 TATACACAAC
Statistics
Matches: 92, Mismatches: 17, Indels: 26
0.68 0.13 0.19
Matches are distributed among these distances:
20 9 0.10
21 1 0.01
22 4 0.04
23 4 0.04
24 4 0.04
25 58 0.63
27 12 0.13
ACGTcount: A:0.44, C:0.22, G:0.03, T:0.31
Consensus pattern (25 bp):
AACTTACATAATACATAACTTACAT
Found at i:48482819 original size:41 final size:41
Alignment explanation
Indices: 48482768--48482849 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
48482758 ATACATAGCC
* *
48482768 TACATAACTTATATAACTTACATAATACACCACTTACATAA
1 TACATAACTTACATAACTTACATAATACACAACTTACATAA
* *
48482809 TACATTACTTACATAACTTACATTATACACAACTTACATAA
1 TACATAACTTACATAACTTACATAATACACAACTTACATAA
48482850 CTTAATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (41 bp):
TACATAACTTACATAACTTACATAATACACAACTTACATAA
Found at i:48482836 original size:25 final size:25
Alignment explanation
Indices: 48482799--48482876 Score: 92
Period size: 25 Copynumber: 3.3 Consensus size: 25
48482789 ATAATACACC
*
48482799 ACTTACATAATACATTACTTACATA
1 ACTTACATTATACATTACTTACATA
**
48482824 ACTTACATTATACACAACTTACATA
1 ACTTACATTATACATTACTTACATA
*
48482849 ACTTA-ATTA-ATATTA--TACATA
1 ACTTACATTATACATTACTTACATA
48482870 ACTTACA
1 ACTTACA
48482877 GCCAAGATAC
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
21 11 0.24
22 1 0.02
23 3 0.07
24 4 0.09
25 27 0.59
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (25 bp):
ACTTACATTATACATTACTTACATA
Found at i:48482837 original size:16 final size:16
Alignment explanation
Indices: 48482662--48482824 Score: 125
Period size: 16 Copynumber: 9.9 Consensus size: 16
48482652 TATAAACTTG
48482662 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
*
48482679 CATAACAACTTAGATAATA
1 CAT---AACTTACATAATA
* *
48482698 CATAGCCTACATAACTTA
1 CATAACTTACATAA--TA
48482716 CATAACTTACATAATA
1 CATAACTTACATAATA
**
48482732 CACCACTTACAT-A-A
1 CATAACTTACATAATA
*
48482746 -ATAACTTGCATAATA
1 CATAACTTACATAATA
* *
48482761 CATAGCCTACATAACTTA
1 CATAACTTACATAA--TA
*
48482779 TATAACTTACATAATA
1 CATAACTTACATAATA
**
48482795 CACCACTTACATAATA
1 CATAACTTACATAATA
*
48482811 CATTACTTACATAA
1 CATAACTTACATAA
48482825 CTTACATTAT
Statistics
Matches: 114, Mismatches: 22, Indels: 21
0.73 0.14 0.13
Matches are distributed among these distances:
13 8 0.07
14 2 0.02
15 2 0.02
16 57 0.50
17 3 0.03
18 27 0.24
19 4 0.04
20 11 0.10
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.29
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:48484686 original size:21 final size:21
Alignment explanation
Indices: 48484616--48484673 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
48484606 CAGCAACTTA
48484616 AAGCAGAGGCTGCAGCAAAAG
1 AAGCAGAGGCTGCAGCAAAAG
48484637 AAGCAGAGGCTGCAGCAAAAG
1 AAGCAGAGGCTGCAGCAAAAG
48484658 AAGCAGAGGCTGCAGC
1 AAGCAGAGGCTGCAGC
48484674 GAGGGAAGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.40, C:0.21, G:0.34, T:0.05
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCAAAAG
Found at i:48485140 original size:42 final size:42
Alignment explanation
Indices: 48485013--48485148 Score: 166
Period size: 43 Copynumber: 3.2 Consensus size: 42
48485003 GTCATAACAA
* *
48485013 TAGCGGCGCTTGT-GGTAGAAGCGCCGCTAAAGAACATGGCCTT
1 TAGCGGCGTTTGTAGG-A-AAGCGCCGCTAAAGAACATGACCTT
* *
48485056 TAGCTGCGTTTGTGGGAAATGCGCCGCTAAAGAACATGACCTT
1 TAGCGGCGTTTGTAGGAAA-GCGCCGCTAAAGAACATGACCTT
* * * *
48485099 TAGCGGCGTTTTTATGAAAGCGTCGCTAAAGAACATCACCTT
1 TAGCGGCGTTTGTAGGAAAGCGCCGCTAAAGAACATGACCTT
48485141 TAGCGGCG
1 TAGCGGCG
48485149 ATGACAACAG
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
42 31 0.38
43 49 0.60
44 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (42 bp):
TAGCGGCGTTTGTAGGAAAGCGCCGCTAAAGAACATGACCTT
Found at i:48486420 original size:24 final size:24
Alignment explanation
Indices: 48486389--48486436 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
48486379 AAAAATTATA
48486389 AAAATATTAAAAATTTCA-AAAAAT
1 AAAATATTAAAAATTT-ATAAAAAT
*
48486413 AAAATATTAATAATTTATAAAAAT
1 AAAATATTAAAAATTTATAAAAAT
48486437 TATACATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAATATTAAAAATTTATAAAAAT
Found at i:48487576 original size:22 final size:22
Alignment explanation
Indices: 48487551--48487603 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
48487541 ATATTTTTAT
*
48487551 ATTTTTTAAAATGATATAAATA
1 ATTTTTTAAAATGATAAAAATA
* **
48487573 ATTTTTT-AATTTTTAAAAATA
1 ATTTTTTAAAATGATAAAAATA
48487594 ATTTTTTAAA
1 ATTTTTTAAA
48487604 TTTTTAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTTTTAAAATGATAAAAATA
Found at i:48487577 original size:29 final size:27
Alignment explanation
Indices: 48487525--48487590 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 27
48487515 TTAATTGATT
*
48487525 TTTTTTAAAATTAAATATATTTTTATA
1 TTTTTTAAAATTAAATATAATTTTATA
*
48487552 TTTTTTAAAATGATATAA-ATAATTTTTTA
1 TTTTTTAAAAT--TA-AATATAATTTTATA
*
48487581 ATTTTTAAAA
1 TTTTTTAAAA
48487591 ATAATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 11 0.33
29 20 0.61
30 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TTTTTTAAAATTAAATATAATTTTATA
Found at i:48487592 original size:21 final size:22
Alignment explanation
Indices: 48487568--48487610 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
48487558 AAAATGATAT
48487568 AAATAATTTTTT-AATTTTTAA
1 AAATAATTTTTTAAATTTTTAA
48487589 AAATAATTTTTTAAATTTTTAA
1 AAATAATTTTTTAAATTTTTAA
48487611 TTTCAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATAATTTTTTAAATTTTTAA
Found at i:48487704 original size:157 final size:158
Alignment explanation
Indices: 48487455--48487770 Score: 625
Period size: 157 Copynumber: 2.0 Consensus size: 158
48487445 GCATTGTTTG
48487455 TCAAATAACCCCAAAATATTGTGGAAAAGGGTGGCATCCACATTTATGTCATGTAAGTAATTAAT
1 TCAAATAACCCCAAAATATTGTGGAAAAGGGTGGCATCCACATTTATGTCATGTAAGTAATTAAT
48487520 TGATTTTTTTTAAAATTAAATATATTTTTATATTTTTTAAAATGATATAAATAATTTTTTAATTT
66 TGATTTTTTTTAAAATTAAATATATTTTTATATTTTTTAAAATGATATAAATAATTTTTTAATTT
48487585 TTAAAAATAATTTTTTAAATTTTTAATT
131 TTAAAAATAATTTTTTAAATTTTTAATT
48487613 TCAAATAA-CCCAAAATATTGTGGAAAAGGGTGGCATCCACATTTATGTCATGTAAGTAATTAAT
1 TCAAATAACCCCAAAATATTGTGGAAAAGGGTGGCATCCACATTTATGTCATGTAAGTAATTAAT
48487677 TGATTTTTTTTAAAATTAAATATATTTTTATATTTTTTAAAATGATATAAATAATTTTTTAATTT
66 TGATTTTTTTTAAAATTAAATATATTTTTATATTTTTTAAAATGATATAAATAATTTTTTAATTT
48487742 TTAAAAATAATTTTTTAAATTTTTAATT
131 TTAAAAATAATTTTTTAAATTTTTAATT
48487770 T
1 T
48487771 TTAAATTTTA
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
157 150 0.95
158 8 0.05
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (158 bp):
TCAAATAACCCCAAAATATTGTGGAAAAGGGTGGCATCCACATTTATGTCATGTAAGTAATTAAT
TGATTTTTTTTAAAATTAAATATATTTTTATATTTTTTAAAATGATATAAATAATTTTTTAATTT
TTAAAAATAATTTTTTAAATTTTTAATT
Found at i:48487733 original size:22 final size:22
Alignment explanation
Indices: 48487708--48487760 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
48487698 ATATTTTTAT
*
48487708 ATTTTTTAAAATGATATAAATA
1 ATTTTTTAAAATGATAAAAATA
* **
48487730 ATTTTTT-AATTTTTAAAAATA
1 ATTTTTTAAAATGATAAAAATA
48487751 ATTTTTTAAA
1 ATTTTTTAAA
48487761 TTTTTAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTTTTAAAATGATAAAAATA
Found at i:48487734 original size:29 final size:27
Alignment explanation
Indices: 48487682--48487747 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 27
48487672 TTAATTGATT
*
48487682 TTTTTTAAAATTAAATATATTTTTATA
1 TTTTTTAAAATTAAATATAATTTTATA
*
48487709 TTTTTTAAAATGATATAA-ATAATTTTTTA
1 TTTTTTAAAAT--TA-AATATAATTTTATA
*
48487738 ATTTTTAAAA
1 TTTTTTAAAA
48487748 ATAATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 11 0.33
29 20 0.61
30 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TTTTTTAAAATTAAATATAATTTTATA
Found at i:48487749 original size:21 final size:22
Alignment explanation
Indices: 48487725--48487767 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
48487715 AAAATGATAT
48487725 AAATAATTTTTT-AATTTTTAA
1 AAATAATTTTTTAAATTTTTAA
48487746 AAATAATTTTTTAAATTTTTAA
1 AAATAATTTTTTAAATTTTTAA
48487768 TTTTTAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATAATTTTTTAAATTTTTAA
Found at i:48487749 original size:30 final size:29
Alignment explanation
Indices: 48487690--48487775 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
48487680 TTTTTTTTAA
*
48487690 AATTAAAT-ATATTTTTATATTTTTTAAAAT
1 AATTAAATAAT-TTTTTA-ATTTTTAAAAAT
*
48487720 GATATAAATAATTTTTTAATTTTTAAAAAT
1 AAT-TAAATAATTTTTTAATTTTTAAAAAT
*** *
48487750 AATTTTTTAAATTTTTAATTTTTAAA
1 AATTAAATAATTTTTTAATTTTTAAA
48487776 TTTTAAAAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
29 19 0.40
30 15 0.32
31 11 0.23
32 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
AATTAAATAATTTTTTAATTTTTAAAAAT
Found at i:48494192 original size:31 final size:32
Alignment explanation
Indices: 48494157--48494219 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 32
48494147 CTTTTCAGAC
* * *
48494157 TTTGAGCAAATTTTTCTTTGCT-TTTTATTCT
1 TTTGAACAAACTTATCTTTGCTCTTTTATTCT
* *
48494188 TTTGAACGAACTTATCTTTGTTCTTTTATTCT
1 TTTGAACAAACTTATCTTTGCTCTTTTATTCT
48494220 CTCTCTCTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.17, C:0.14, G:0.10, T:0.59
Consensus pattern (32 bp):
TTTGAACAAACTTATCTTTGCTCTTTTATTCT
Found at i:48494975 original size:22 final size:22
Alignment explanation
Indices: 48494925--48494968 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
48494915 AATTATTAAC
* *
48494925 ATATTGAATTTTAATTAATTTT
1 ATATTAAATTTTAATAAATTTT
*
48494947 ATATTAAATTTTCATAAATTTT
1 ATATTAAATTTTAATAAATTTT
48494969 GATTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
ATATTAAATTTTAATAAATTTT
Found at i:48510958 original size:22 final size:22
Alignment explanation
Indices: 48510912--48510975 Score: 119
Period size: 22 Copynumber: 2.9 Consensus size: 22
48510902 CACTCTTGGG
48510912 TCTTTGGACATCTTGTTGGGACA
1 TCTTTGGACATCTTGTT-GGACA
48510935 TCTTTGGACATCTTGTTGGACA
1 TCTTTGGACATCTTGTTGGACA
48510957 TCTTTGGACATCTTGTTGG
1 TCTTTGGACATCTTGTTGG
48510976 GTCTTTGGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 24 0.59
23 17 0.41
ACGTcount: A:0.16, C:0.17, G:0.25, T:0.42
Consensus pattern (22 bp):
TCTTTGGACATCTTGTTGGACA
Found at i:48510990 original size:10 final size:10
Alignment explanation
Indices: 48510912--48510970 Score: 73
Period size: 10 Copynumber: 5.4 Consensus size: 10
48510902 CACTCTTGGG
48510912 TCTTTGGACA
1 TCTTTGGACA
48510922 TCTTGTTGGGACA
1 TC-T-TT-GGACA
48510935 TCTTTGGACA
1 TCTTTGGACA
48510945 TCTTGTTGGACA
1 TC-T-TTGGACA
48510957 TCTTTGGACA
1 TCTTTGGACA
48510967 TCTT
1 TCTT
48510971 GTTGGGTCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
10 20 0.45
11 5 0.11
12 12 0.27
13 7 0.16
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (10 bp):
TCTTTGGACA
Found at i:48516736 original size:17 final size:17
Alignment explanation
Indices: 48516704--48516737 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
48516694 TATCCTTGAA
*
48516704 AAAATAAAAATAAAAAC
1 AAAATAAAAAGAAAAAC
48516721 AAAATAAAAAGGAAAAA
1 AAAATAAAAA-GAAAAA
48516738 GGAAAGAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (17 bp):
AAAATAAAAAGAAAAAC
Found at i:48524386 original size:43 final size:43
Alignment explanation
Indices: 48524321--48524440 Score: 222
Period size: 43 Copynumber: 2.8 Consensus size: 43
48524311 ATCGACCGCA
*
48524321 GCATGAATACTTAGTTCAATGGAAGGGACTTCCTAACAGCGCG
1 GCATGAATACTTAGTTCGATGGAAGGGACTTCCTAACAGCGCG
*
48524364 GCATGAATACTTAGTTCGATGGAAGGGACTTCCTAACAGTGCG
1 GCATGAATACTTAGTTCGATGGAAGGGACTTCCTAACAGCGCG
48524407 GCATGAATACTTAGTTCGATGGAAGGGACTTCCT
1 GCATGAATACTTAGTTCGATGGAAGGGACTTCCT
48524441 GACATCGAAG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (43 bp):
GCATGAATACTTAGTTCGATGGAAGGGACTTCCTAACAGCGCG
Found at i:48531371 original size:45 final size:45
Alignment explanation
Indices: 48531298--48531464 Score: 153
Period size: 45 Copynumber: 3.7 Consensus size: 45
48531288 GCTATGCGCC
* *
48531298 TAAAATGAGTAAGACCATAACTGAAAGATGTTATGATATTAT-GA
1 TAAAATGAGTAAGACCATAACTGAAAGATGCTATGATATCATGGA
** * *
48531342 TAAAGATGAGTAAGACCATAGTTGTAAGATGCTATGGTATCATGGA
1 TAAA-ATGAGTAAGACCATAACTGAAAGATGCTATGATATCATGGA
** * * * *
48531388 -ATAAATGAGTAAGACCATGGCTAAAACATACTATGACATCATGG-
1 TA-AAATGAGTAAGACCATAACTGAAAGATGCTATGATATCATGGA
* *
48531432 TAAACATGACT-AGACCATAACTGAAAGACGCTA
1 TAAA-ATGAGTAAGACCATAACTGAAAGATGCTA
48531465 CAGAATCATA
Statistics
Matches: 97, Mismatches: 21, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
44 22 0.23
45 71 0.73
46 4 0.04
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.25
Consensus pattern (45 bp):
TAAAATGAGTAAGACCATAACTGAAAGATGCTATGATATCATGGA
Found at i:48531628 original size:27 final size:27
Alignment explanation
Indices: 48531549--48531629 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
48531539 CATCATAAAA
* *
48531549 AGTCCAACGAGACATTAAATATA-GGAT
1 AGTCTAACGGGACATTAAATA-AGGGAT
* * * *
48531576 AGCCTAATGGGACATTAAACATGGGAT
1 AGTCTAACGGGACATTAAATAAGGGAT
*
48531603 AGTCTAACGGGACACTAAATAAGGGAT
1 AGTCTAACGGGACATTAAATAAGGGAT
48531630 GGTTCGTCAA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (27 bp):
AGTCTAACGGGACATTAAATAAGGGAT
Found at i:48560555 original size:24 final size:25
Alignment explanation
Indices: 48560523--48560574 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
48560513 CATATTTTTA
48560523 GAGAAATAAGGAAGGTGAGA-G-AAG
1 GAGAAATAAGG-AGGTGAGATGTAAG
*
48560547 GAGAAATAAGGCGGTGAGATGTAAG
1 GAGAAATAAGGAGGTGAGATGTAAG
48560572 GAG
1 GAG
48560575 GGAATTGGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 7 0.28
24 12 0.48
25 6 0.24
ACGTcount: A:0.44, C:0.02, G:0.42, T:0.12
Consensus pattern (25 bp):
GAGAAATAAGGAGGTGAGATGTAAG
Found at i:48565016 original size:19 final size:19
Alignment explanation
Indices: 48564992--48565030 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
48564982 CCCTCTTGTT
48564992 AGGGACTGACAATGTACTA
1 AGGGACTGACAATGTACTA
48565011 AGGGACTGACAATGTACTA
1 AGGGACTGACAATGTACTA
48565030 A
1 A
48565031 CCTTGTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (19 bp):
AGGGACTGACAATGTACTA
Found at i:48566669 original size:30 final size:31
Alignment explanation
Indices: 48566633--48566693 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
48566623 GGTATCAAAT
48566633 AAAGTCAAAGATAAGGGTATC-AAATATTGG
1 AAAGTCAAAGATAAGGGTATCGAAATATTGG
** *
48566663 AAAGTCAAAGATTTGGGTATCGAGATATTGG
1 AAAGTCAAAGATAAGGGTATCGAAATATTGG
48566694 CATAAGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.41, C:0.07, G:0.26, T:0.26
Consensus pattern (31 bp):
AAAGTCAAAGATAAGGGTATCGAAATATTGG
Found at i:48571251 original size:15 final size:15
Alignment explanation
Indices: 48571231--48571302 Score: 58
Period size: 15 Copynumber: 4.8 Consensus size: 15
48571221 TGATGGAAAG
*
48571231 TCAAATATATGGTTA
1 TCAAATATATGGATA
*
48571246 TCAAATA-ATGGAAA
1 TCAAATATATGGATA
* *
48571260 GTCAAAGATATGGGTA
1 -TCAAATATATGGATA
*
48571276 TCAAATAT-TGGAAAA
1 TCAAATATATGG-ATA
*
48571291 TCAAAGATATGG
1 TCAAATATATGG
48571303 GTATTGAGAT
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
14 8 0.18
15 28 0.64
16 8 0.18
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (15 bp):
TCAAATATATGGATA
Found at i:48571259 original size:30 final size:30
Alignment explanation
Indices: 48571223--48571306 Score: 132
Period size: 30 Copynumber: 2.8 Consensus size: 30
48571213 GAGATTATTG
* *
48571223 ATGGAAAGTCAAATATATGGTTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
48571253 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
* *
48571283 TTGGAAAATCAAAGATATGGGTAT
1 ATGGAAAGTCAAAGATATGGGTAT
48571307 TGAGATATTG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:48571469 original size:2 final size:2
Alignment explanation
Indices: 48571462--48571488 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48571452 AAGGCATTGT
48571462 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
48571489 TTGTAAATTC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:48574162 original size:170 final size:169
Alignment explanation
Indices: 48573874--48574212 Score: 669
Period size: 170 Copynumber: 2.0 Consensus size: 169
48573864 ACATTTTGCC
48573874 CCCTTTAAAAAAAATCTTTTTCTAGGTGTTACAATACAACTCAAATTCTTTGACTATAATGAAAA
1 CCCTTTAAAAAAAATCTTTTTCTAGGTGTTACAATACAACTCAAATTCTTTGACTATAATGAAAA
48573939 TGACTTAAGAAGATCAAAGCTCAACCAGCACCACCACTCTTATTGAAACAATCATATGACAGTTT
66 TGACTTAAGAAGATCAAAGCTCAACCAGCACCACCACTCTTATTGAAACAATCATATGACAGTTT
48574004 AGGCTTTAAGATGAAAAAGAAAATATCAGAAGCACAACA
131 AGGCTTTAAGATGAAAAAGAAAATATCAGAAGCACAACA
48574043 CCCTTTAAAAAAAATTCTTTTTCTAGGTGTTACAATACAACTCAAATTCTTTGACTATAATGAAA
1 CCCTTTAAAAAAAA-TCTTTTTCTAGGTGTTACAATACAACTCAAATTCTTTGACTATAATGAAA
48574108 ATGACTTAAGAAGATCAAAGCTCAACCAGCACCACCACTCTTATTGAAACAATCATATGACAGTT
65 ATGACTTAAGAAGATCAAAGCTCAACCAGCACCACCACTCTTATTGAAACAATCATATGACAGTT
48574173 TAGGCTTTAAGATGAAAAAGAAAATATCAGAAGCACAACA
130 TAGGCTTTAAGATGAAAAAGAAAATATCAGAAGCACAACA
48574213 TTAAAATCTG
Statistics
Matches: 169, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
169 14 0.08
170 155 0.92
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (169 bp):
CCCTTTAAAAAAAATCTTTTTCTAGGTGTTACAATACAACTCAAATTCTTTGACTATAATGAAAA
TGACTTAAGAAGATCAAAGCTCAACCAGCACCACCACTCTTATTGAAACAATCATATGACAGTTT
AGGCTTTAAGATGAAAAAGAAAATATCAGAAGCACAACA
Done.