Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold98
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: 1546936
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 25 characters in sequence are not A, C, G, or T
File 5 of 13
Found at i:592307 original size:36 final size:33
Alignment explanation
Indices: 592224--592319 Score: 117
Period size: 36 Copynumber: 2.9 Consensus size: 33
592214 CCTTATAATA
*
592224 CTATC-TTTC-AAGGCTAAGATAGAAAC-CTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTCTCC
**
592254 CTATCTTTTCACGGGCTAAGATAGAACCTTTCTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACC--TCTCC
592289 CTATCTTTTTCAAAGGCTAAGATAGAACCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTC
592320 ACAATCACTT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
30 5 0.09
31 4 0.07
32 14 0.25
34 2 0.04
35 9 0.16
36 21 0.38
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (33 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCC
Found at i:595278 original size:23 final size:24
Alignment explanation
Indices: 595233--595279 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
595223 TAGAGGATTG
*
595233 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
595257 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
595280 TTTTCAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:596212 original size:21 final size:21
Alignment explanation
Indices: 596156--596213 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
596146 TTTATTAGTT
* *
596156 AACTCA-TCATTTTTATTTTGC
1 AACTCATTCA-TTTTCTTTTCC
596177 AACTCATTTC-TTTTCTTTTCC
1 AACTCA-TTCATTTTCTTTTCC
596198 AACTCATTCATTTTCT
1 AACTCATTCATTTTCT
596214 CTTTTAGTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 3 0.09
21 27 0.84
23 2 0.06
ACGTcount: A:0.21, C:0.24, G:0.02, T:0.53
Consensus pattern (21 bp):
AACTCATTCATTTTCTTTTCC
Found at i:598170 original size:25 final size:25
Alignment explanation
Indices: 598139--598191 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
598129 TTCTCTAGCT
598139 GATGGAATGCTGTATTTATAGGCTA
1 GATGGAATGCTGTATTTATAGGCTA
*
598164 GATGGAATGCTGTATTTATAGGTTA
1 GATGGAATGCTGTATTTATAGGCTA
598189 GAT
1 GAT
598192 TAAGGATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.06, G:0.28, T:0.38
Consensus pattern (25 bp):
GATGGAATGCTGTATTTATAGGCTA
Found at i:598565 original size:20 final size:21
Alignment explanation
Indices: 598542--598580 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
598532 TTGAGCAATA
598542 TGTATCGATACA-TCTAGGTG
1 TGTATCGATACATTCTAGGTG
598562 TGTATCGATACATTCTAGG
1 TGTATCGATACATTCTAGG
598581 GTTTTAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTCTAGGTG
Found at i:599824 original size:164 final size:167
Alignment explanation
Indices: 599645--600100 Score: 461
Period size: 166 Copynumber: 2.8 Consensus size: 167
599635 GGAAGTACAA
* * * *
599645 AGTTTTCTTTTCCATAAATTTTTTTAGCAGGATTTTCATC-AAATT-AAAA-TTTGAA-ATTCAT
1 AGTTTTCTTTTCCATAAATGTTTTCAGCAGGGTTTTC-TCTAAATTCAAAATTTTAAATATTCAT
* * * * * ** *
599706 -TAATATTATTA-TCT-AATCACCATTTAATCAG-TTTTGAAAATTTCATTTATTTTTATGAGTT
65 CAAATATCATCAGT-TAAATCA-CAGTAAATCAGCTTTAAAAAATTT--TTTATTTTCATGAGTT
*
599767 TTTCATTTTTTTCCTTGAAA-TTCCCT-TATTTCTGAAAAATCG
126 TTTCATTTTTTTCCTTAAAATTTCCCTGT-TTT-TGAAAAATCG
** * *
599809 AGTTTTCTTTTCCATAAATGTTTTCAGGGGGGTTTT-TCTTAGTTCAAAATTTTAAATATTCATC
1 AGTTTTCTTTTCCATAAATGTTTTCAGCAGGGTTTTCTCTAAATTCAAAATTTTAAATATTCATC
*
599873 AAATATCATCAGTTAAATCATAGTAAATCAGCTTTAAAAAATTTTTTATTTTCATGAGTTTTTCA
66 AAATATCATCAGTTAAATCACAGTAAATCAGCTTTAAAAAATTTTTTATTTTCATGAGTTTTTCA
**
599938 TTTTTTTCCTTAAAATTTTTCTGTTTTTGAAAAATCG
131 TTTTTTTCCTTAAAATTTCCCTGTTTTTGAAAAATCG
* ** * *
599975 AGTTTTCTATTCCATAAATGTTTTCAGCAGGGTTTTCT-T-GGTTCAAAATTTTTAATTTTCATC
1 AGTTTTCTTTTCCATAAATGTTTTCAGCAGGGTTTTCTCTAAATTCAAAATTTTAAATATTCATC
* * * * * * *
600038 AAATATTATCATTTAAATCATAGTAAATCAGTTTTGAAAAATTCATTAATTTTCATGAGTTTT
66 AAATATCATCAGTTAAATCACAGTAAATCAGCTTTAAAAAATT-TTTTATTTTCATGAGTTTT
600101 GAAAATTTTT
Statistics
Matches: 248, Mismatches: 32, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
162 2 0.01
163 3 0.01
164 35 0.14
165 65 0.26
166 101 0.41
167 25 0.10
168 17 0.07
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (167 bp):
AGTTTTCTTTTCCATAAATGTTTTCAGCAGGGTTTTCTCTAAATTCAAAATTTTAAATATTCATC
AAATATCATCAGTTAAATCACAGTAAATCAGCTTTAAAAAATTTTTTATTTTCATGAGTTTTTCA
TTTTTTTCCTTAAAATTTCCCTGTTTTTGAAAAATCG
Found at i:599943 original size:166 final size:165
Alignment explanation
Indices: 599742--600100 Score: 506
Period size: 166 Copynumber: 2.2 Consensus size: 165
599732 ATCAGTTTTG
* *
599742 AAAATTTCATTTATTTTTATGAGTTTTTCATTTTTTTCCTTGAAA-TTCCCT-TATTTCTGAAAA
1 AAAATTT--TTTATTTTCATGAGTTTTTCATTTTTTTCCTTAAAATTTCCCTGT-TTT-TGAAAA
* **
599805 ATCGAGTTTTCTTTTCCATAAATGTTTTCAGGGGGGTTTTTCTTAGTTCAAAATTTTAAATATTC
62 ATCGAGTTTTCTATTCCATAAATGTTTTCAGCAGGG-TTTTCTTAGTTCAAAATTTTAAATATTC
599870 ATCAAATATCATCAGTTAAATCATAGTAAATCAGCTTTAA
126 ATCAAATATCATCAGTTAAATCATAGTAAATCAGCTTTAA
**
599910 AAAATTTTTTATTTTCATGAGTTTTTCATTTTTTTCCTTAAAATTTTTCTGTTTTTGAAAAATCG
1 AAAATTTTTTATTTTCATGAGTTTTTCATTTTTTTCCTTAAAATTTCCCTGTTTTTGAAAAATCG
* * *
599975 AGTTTTCTATTCCATAAATGTTTTCAGCAGGGTTTTCTTGGTTCAAAATTTTTAATTTTCATCAA
66 AGTTTTCTATTCCATAAATGTTTTCAGCAGGGTTTTCTTAGTTCAAAATTTTAAATATTCATCAA
* * * *
600040 ATATTATCATTTAAATCATAGTAAATCAGTTTTGA
131 ATATCATCAGTTAAATCATAGTAAATCAGCTTTAA
* *
600075 AAAATTCATTAATTTTCATGAGTTTT
1 AAAATT-TTTTATTTTCATGAGTTTT
600101 GAAAATTTTT
Statistics
Matches: 172, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
165 67 0.39
166 90 0.52
167 7 0.04
168 8 0.05
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (165 bp):
AAAATTTTTTATTTTCATGAGTTTTTCATTTTTTTCCTTAAAATTTCCCTGTTTTTGAAAAATCG
AGTTTTCTATTCCATAAATGTTTTCAGCAGGGTTTTCTTAGTTCAAAATTTTAAATATTCATCAA
ATATCATCAGTTAAATCATAGTAAATCAGCTTTAA
Found at i:600606 original size:10 final size:9
Alignment explanation
Indices: 600591--600656 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
600581 TGGGAAATAG
600591 AAAGAAAAA
1 AAAGAAAAA
600600 AAGAGAAAAAA
1 AA-AG-AAAAA
600611 AAAGAAAGAA
1 AAAGAAA-AA
600621 AAAGAAAAA
1 AAAGAAAAA
* *
600630 GAA-AAAGA
1 AAAGAAAAA
* *
600638 ATAGAGAAA
1 AAAGAAAAA
*
600647 TAAGAAAAA
1 AAAGAAAAA
600656 A
1 A
600657 CAAGCTAAAC
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
8 5 0.12
9 18 0.42
10 13 0.30
11 7 0.16
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:600614 original size:20 final size:21
Alignment explanation
Indices: 600591--600634 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
600581 TGGGAAATAG
600591 AAAGAAA-AAAAGAGAAAAA-A
1 AAAGAAAGAAAA-AGAAAAAGA
600611 AAAGAAAGAAAAAGAAAAAGA
1 AAAGAAAGAAAAAGAAAAAGA
600632 AAA
1 AAA
600635 AGAATAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAGAAAGAAAAAGAAAAAGA
Found at i:600625 original size:22 final size:23
Alignment explanation
Indices: 600597--600656 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 23
600587 ATAGAAAGAA
600597 AAAAAGAGAAAAAAAAAGAA-AG
1 AAAAAGAGAAAAAAAAAGAATAG
600619 AAAAAGA-AAAAGAAAAAGAATAG
1 AAAAAGAGAAAA-AAAAAGAATAG
600642 AGAAATA-AGAAAAAA
1 A-AAA-AGAGAAAAAA
600657 CAAGCTAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
21 4 0.12
22 15 0.45
23 3 0.09
24 6 0.18
25 5 0.15
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (23 bp):
AAAAAGAGAAAAAAAAAGAATAG
Found at i:600626 original size:6 final size:6
Alignment explanation
Indices: 600584--600655 Score: 62
Period size: 6 Copynumber: 12.0 Consensus size: 6
600574 GGAGCTTTGG
*
600584 GAAATA GAAAGAA -AAAAA GAGAAAA -AAAAA G--AAA GAAAAA GAAAAA
1 GAAAAA GAAA-AA GAAAAA GA-AAAA GAAAAA GAAAAA GAAAAA GAAAAA
*
600630 GAAAAA GAATAGA GAAATAA GAAAAA
1 GAAAAA GAA-AAA GAAA-AA GAAAAA
600656 ACAAGCTAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
4 4 0.07
5 6 0.11
6 30 0.55
7 15 0.27
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (6 bp):
GAAAAA
Found at i:600628 original size:16 final size:17
Alignment explanation
Indices: 600591--600653 Score: 62
Period size: 16 Copynumber: 3.8 Consensus size: 17
600581 TGGGAAATAG
600591 AAAG-AAAA-AAAGAGA
1 AAAGAAAAAGAAAGAGA
600606 AAA-AAAAAGAAAGA-A
1 AAAGAAAAAGAAAGAGA
*
600621 AAAGAAAAAGAAAAAGA
1 AAAGAAAAAGAAAGAGA
600638 ATAGAGAAATAAGAAA
1 A-A-AGAAA-AAGAAA
600654 AAACAAGCTA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
15 11 0.28
16 15 0.38
17 2 0.05
18 1 0.03
19 5 0.12
20 6 0.15
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (17 bp):
AAAGAAAAAGAAAGAGA
Found at i:601515 original size:16 final size:17
Alignment explanation
Indices: 601485--601520 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
601475 ATTTTCGAAC
601485 ATAAAAAAATGAAATAA
1 ATAAAAAAATGAAATAA
*
601502 ATAAAATAAT-AAATAA
1 ATAAAAAAATGAAATAA
601518 ATA
1 ATA
601521 TTATTTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
ATAAAAAAATGAAATAA
Found at i:602449 original size:13 final size:13
Alignment explanation
Indices: 602431--602461 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
602421 ACTTTTCATT
602431 ATGTATTGACACA
1 ATGTATTGACACA
*
602444 ATGTATTGATACA
1 ATGTATTGACACA
602457 ATGTA
1 ATGTA
602462 CTATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATTGACACA
Found at i:602551 original size:19 final size:20
Alignment explanation
Indices: 602506--602555 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
602496 TTGCCAGTTT
*
602506 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAA
*
602526 TATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
602545 CATGTATCGAT
1 CATGTATCGAT
602556 GCAAAACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:607820 original size:29 final size:29
Alignment explanation
Indices: 607732--607832 Score: 114
Period size: 29 Copynumber: 3.5 Consensus size: 29
607722 ATTTTAATTG
* * *
607732 AAAAGTTTAGGGGTCAATGTGTAATTTTG
1 AAAAGTTTAAGGGTCAAAGTGTAATTTTA
* * *
607761 AAAAGTTTTAGGGTCAAAATGTGATTTTA
1 AAAAGTTTAAGGGTCAAAGTGTAATTTTA
* *
607790 AAAAGTTTAAGTGTCAAAGTGTAATTATA
1 AAAAGTTTAAGGGTCAAAGTGTAATTTTA
607819 AAAA-TTTCAAGGGT
1 AAAAGTTT-AAGGGT
607833 TAAAACCTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 3 0.05
29 56 0.95
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.36
Consensus pattern (29 bp):
AAAAGTTTAAGGGTCAAAGTGTAATTTTA
Found at i:613046 original size:18 final size:19
Alignment explanation
Indices: 613023--613063 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
613013 TAACATGAAT
613023 AATAAAAAAATAATAA-AA
1 AATAAAAAAATAATAATAA
**
613041 AATAAAAATGTAATAATAA
1 AATAAAAAAATAATAATAA
613060 AATA
1 AATA
613064 GTAATAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (19 bp):
AATAAAAAAATAATAATAA
Found at i:613254 original size:16 final size:17
Alignment explanation
Indices: 613214--613255 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
613204 AGTGAATAAA
*
613214 CATTGCATGCATATGTT
1 CATTTCATGCATATGTT
*
613231 CATTTCATGCATATTTT
1 CATTTCATGCATATGTT
613248 C-TTTCATG
1 CATTTCATG
613256 TTTCACACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (17 bp):
CATTTCATGCATATGTT
Found at i:621929 original size:13 final size:13
Alignment explanation
Indices: 621911--621935 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
621901 CAGCATTCCC
621911 TGTATCGATACAT
1 TGTATCGATACAT
621924 TGTATCGATACA
1 TGTATCGATACA
621936 AAGGGTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:622403 original size:20 final size:22
Alignment explanation
Indices: 622378--622422 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
622368 GCAGCACTCA
*
622378 CCAGGTCGCGACC-GGCA-CCC
1 CCAGGTCGCAACCGGGCAGCCC
622398 CCAGGTCGCAACCGGGCAGCCC
1 CCAGGTCGCAACCGGGCAGCCC
622420 CCA
1 CCA
622423 CACTCACAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.55
21 4 0.18
22 6 0.27
ACGTcount: A:0.18, C:0.49, G:0.29, T:0.04
Consensus pattern (22 bp):
CCAGGTCGCAACCGGGCAGCCC
Found at i:624410 original size:13 final size:13
Alignment explanation
Indices: 624392--624416 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
624382 AGATTGCACA
624392 GTATCGATACATT
1 GTATCGATACATT
624405 GTATCGATACAT
1 GTATCGATACAT
624417 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:624535 original size:13 final size:13
Alignment explanation
Indices: 624517--624541 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
624507 ACACACAAGT
624517 TGTATCGATACAA
1 TGTATCGATACAA
624530 TGTATCGATACA
1 TGTATCGATACA
624542 TCGCAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:624561 original size:33 final size:32
Alignment explanation
Indices: 624498--624561 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
624488 CTTAACTGTT
** *
624498 TGTATCGATACACACAAGTTGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCAATACAA
*
624530 TGTATCGATACATCGCAAAATGTATCAATACA
1 TGTATCGATACA-CACAAAATGTATCAATACA
624562 TTGGCTTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCAATACAA
Found at i:631421 original size:13 final size:13
Alignment explanation
Indices: 631403--631454 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
631393 AACATTCCTT
631403 GTATCGATACATA
1 GTATCGATACATA
*
631416 GTATCGATACAACA
1 GTATCGATAC-ATA
* *
631430 TTATCGATACATT
1 GTATCGATACATA
631443 GTATCGATACAT
1 GTATCGATACAT
631455 GGGTTACTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
13 22 0.67
14 11 0.33
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
GTATCGATACATA
Found at i:634121 original size:20 final size:20
Alignment explanation
Indices: 634096--634149 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
634086 CTACCACTGT
*
634096 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
634116 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
*
634136 TTGTAACGATACAT
1 TTGTATCGATACAT
634150 TGCTTGTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:640229 original size:20 final size:20
Alignment explanation
Indices: 640204--640241 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
640194 GAAATTTTTC
640204 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
640224 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
640242 TGGAAAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:640292 original size:13 final size:13
Alignment explanation
Indices: 640274--640300 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
640264 ACAACATTCC
640274 TTGTATCGATACA
1 TTGTATCGATACA
640287 TTGTATCGATACA
1 TTGTATCGATACA
640300 T
1 T
640301 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:642860 original size:63 final size:63
Alignment explanation
Indices: 642761--642977 Score: 274
Period size: 63 Copynumber: 3.2 Consensus size: 63
642751 CAGATGTATA
* *
642761 ATTGTATCGATACAAGAAACTGGCAGTAGCTACCCTACCACTGTTTGTATTAACACATGGTAC
1 ATTGTATCGATACATGAAACTGGAAGTAGCTACCCTACCACTGTTTGTATTAACACATGGTAC
642824 ATTGTATCGATACATGAAACTGGAAGTAGCTACCCTACCACTGTTTGTATTAACACATGGTAC
1 ATTGTATCGATACATGAAACTGGAAGTAGCTACCCTACCACTGTTTGTATTAACACATGGTAC
*
642887 ATTGTATCGATACATTGTATCGATACATGAAACTGGTAG-TAGCTACCCTACCACTGTTTGTATT
1 ATTGTATCGATACA-TG-A---A-AC-TGGAA---GTAGCTA-C--CC-TACCACTGTTTGTATT
642951 AACACATGGTAC
52 AACACATGGTAC
642963 ATTGTATCGATACAT
1 ATTGTATCGATACAT
642978 TGTATCGATA
Statistics
Matches: 137, Mismatches: 3, Indels: 16
0.88 0.02 0.10
Matches are distributed among these distances:
63 75 0.55
64 2 0.01
65 1 0.01
68 1 0.01
69 2 0.01
70 4 0.03
72 2 0.01
73 5 0.04
75 3 0.02
76 42 0.31
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (63 bp):
ATTGTATCGATACATGAAACTGGAAGTAGCTACCCTACCACTGTTTGTATTAACACATGGTAC
Found at i:642902 original size:13 final size:13
Alignment explanation
Indices: 642884--642914 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
642874 TAACACATGG
642884 TACATTGTATCGA
1 TACATTGTATCGA
642897 TACATTGTATCGA
1 TACATTGTATCGA
642910 TACAT
1 TACAT
642915 GAAACTGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:642947 original size:76 final size:76
Alignment explanation
Indices: 642821--642992 Score: 335
Period size: 76 Copynumber: 2.3 Consensus size: 76
642811 TAACACATGG
642821 TACATTGTATCGATACATGAAACTGGAAGTAGCTACCCTACCACTGTTTGTATTAACACATGGTA
1 TACATTGTATCGATACATGAAACTGGAAGTAGCTACCCTACCACTGTTTGTATTAACACATGGTA
642886 CATTGTATCGA
66 CATTGTATCGA
*
642897 TACATTGTATCGATACATGAAACTGGTAGTAGCTACCCTACCACTGTTTGTATTAACACATGGTA
1 TACATTGTATCGATACATGAAACTGGAAGTAGCTACCCTACCACTGTTTGTATTAACACATGGTA
642962 CATTGTATCGA
66 CATTGTATCGA
642973 TACATTGTATCGATACATGA
1 TACATTGTATCGATACATGA
642993 TGAATTGTAT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 95 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (76 bp):
TACATTGTATCGATACATGAAACTGGAAGTAGCTACCCTACCACTGTTTGTATTAACACATGGTA
CATTGTATCGA
Found at i:642977 original size:20 final size:20
Alignment explanation
Indices: 642976--643043 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
642966 GTATCGATAC
642976 ATTGTATCGATACATGATGA
1 ATTGTATCGATACATGATGA
642996 ATTGTATCGATAC-------
1 ATTGTATCGATACATGATGA
643009 ATTGTATCGATACATGATGA
1 ATTGTATCGATACATGATGA
*
643029 ATTGTATCGACACAT
1 ATTGTATCGATACAT
643044 TGCTTGTAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
13 13 0.32
20 27 0.68
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (20 bp):
ATTGTATCGATACATGATGA
Found at i:642978 original size:13 final size:13
Alignment explanation
Indices: 642960--643023 Score: 86
Period size: 13 Copynumber: 5.4 Consensus size: 13
642950 TAACACATGG
642960 TACATTGTATCGA
1 TACATTGTATCGA
642973 TACATTGTATCGA
1 TACATTGTATCGA
642986 TACA-TG-AT-G-
1 TACATTGTATCGA
642995 -A-ATTGTATCGA
1 TACATTGTATCGA
643006 TACATTGTATCGA
1 TACATTGTATCGA
643019 TACAT
1 TACAT
643024 GATGAATTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
7 1 0.02
8 3 0.07
9 2 0.04
10 2 0.04
11 2 0.04
12 3 0.07
13 32 0.71
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:642981 original size:33 final size:33
Alignment explanation
Indices: 642944--643045 Score: 125
Period size: 33 Copynumber: 3.1 Consensus size: 33
642934 CTACCACTGT
* *
642944 TTGTATTAACACATGGT-ACATTGTATCGATACA
1 TTGTATCAACACATGATGA-ATTGTATCGATACA
* *
642977 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCAACACATGATGAATTGTATCGATACA
* * *
643010 TTGTATCGATACATGATGAATTGTATCGACACA
1 TTGTATCAACACATGATGAATTGTATCGATACA
643043 TTG
1 TTG
643046 CTTGTAACGG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 62 0.98
34 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (33 bp):
TTGTATCAACACATGATGAATTGTATCGATACA
Found at i:643993 original size:58 final size:56
Alignment explanation
Indices: 643903--644019 Score: 155
Period size: 58 Copynumber: 2.1 Consensus size: 56
643893 ACAACAACTT
* * * *
643903 CTTCTCTAGGTCTCTTTATCCTTTTAGGCTTTGCCTTCGTAATTGGTCTTTGAAAC
1 CTTCTCTAGGTCCCTTTATCCTTTTAGCCTTTGCCCTCGTAATTGATCTTTGAAAC
*
643959 CTTCTCTAGGCCTCCCTTTATCCTCTTT-GCCTTTGCCCTCGTCATTGATCTTTGAAAC
1 CTTCTCTAGG--TCCCTTTATCCT-TTTAGCCTTTGCCCTCGTAATTGATCTTTGAAAC
644017 CTT
1 CTT
644020 TCCAATGCCT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
56 10 0.19
58 40 0.75
59 3 0.06
ACGTcount: A:0.13, C:0.29, G:0.14, T:0.44
Consensus pattern (56 bp):
CTTCTCTAGGTCCCTTTATCCTTTTAGCCTTTGCCCTCGTAATTGATCTTTGAAAC
Found at i:648119 original size:21 final size:21
Alignment explanation
Indices: 648095--648156 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
648085 TCTTCTTCTC
648095 TCTTCCTCCTATCATCCCTCA
1 TCTTCCTCCTATCATCCCTCA
* **
648116 TCTTTCTATTATC-TCTCCT-A
1 TCTTCCTCCTATCATC-CCTCA
648136 TCTTTCCTCCTATCATCCCTC
1 TC-TTCCTCCTATCATCCCTC
648157 CTATCTCTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
20 5 0.16
21 24 0.77
22 2 0.06
ACGTcount: A:0.13, C:0.42, G:0.00, T:0.45
Consensus pattern (21 bp):
TCTTCCTCCTATCATCCCTCA
Found at i:648959 original size:10 final size:10
Alignment explanation
Indices: 648946--648984 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
648936 AGTTTTTCCT
648946 TTTTTTTTGA
1 TTTTTTTTGA
648956 -TTTTTTTGA
1 TTTTTTTTGA
648965 TTTTTTTTGTA
1 TTTTTTTTG-A
648976 TTCTTTTTT
1 TT-TTTTTT
648985 TTCTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.35
10 8 0.31
11 3 0.12
12 6 0.23
ACGTcount: A:0.08, C:0.03, G:0.08, T:0.82
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:650554 original size:20 final size:21
Alignment explanation
Indices: 650529--650580 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
650519 TACCCCGATT
650529 TATCGATACATTG-AAAAATG
1 TATCGATACATTGTAAAAATG
**
650549 TATCGATACA-TGTATGAATG
1 TATCGATACATTGTAAAAATG
650569 TATCGATACATT
1 TATCGATACATT
650581 CTATCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 25 0.89
21 1 0.04
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (21 bp):
TATCGATACATTGTAAAAATG
Found at i:650672 original size:51 final size:51
Alignment explanation
Indices: 650544--650731 Score: 247
Period size: 51 Copynumber: 3.7 Consensus size: 51
650534 ATACATTGAA
*
650544 AAATGTATCGATACATGTATGAATGTATCGATACATTCTATCTTTTTTA-CC
1 AAATGTATCGATACATGTATGAATGTATCGATACATTCTGT-TTTTTTACCC
* * * *
650595 -TATGTATCGATACATTTTTCAATGTATCGATACATTCTGTTTTTTTACCC
1 AAATGTATCGATACATGTATGAATGTATCGATACATTCTGTTTTTTTACCC
* * *
650645 AGATGTATCGATACATGTATGAATGTATCGATACATTCTGTCTTTTTGCCC
1 AAATGTATCGATACATGTATGAATGTATCGATACATTCTGTTTTTTTACCC
* *
650696 AAATGTATTGATACATTGAAT-AATGTATCGATACAT
1 AAATGTATCGATACA-TGTATGAATGTATCGATACAT
650732 CTAGTTAAAA
Statistics
Matches: 120, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
49 7 0.06
50 37 0.31
51 72 0.60
52 4 0.03
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.41
Consensus pattern (51 bp):
AAATGTATCGATACATGTATGAATGTATCGATACATTCTGTTTTTTTACCC
Found at i:654249 original size:24 final size:24
Alignment explanation
Indices: 654222--654296 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
654212 ACATTGTACC
*
654222 GATACATGAACAGTGATGAACACT
1 GATACATGAACAGTGATGAACAAT
654246 GATACATGAACAGTGATGAACAAT
1 GATACATGAACAGTGATGAACAAT
* * *
654270 GATATATGAGCAGTGATGAACAGT
1 GATACATGAACAGTGATGAACAAT
654294 GAT
1 GAT
654297 GTATCAACTA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (24 bp):
GATACATGAACAGTGATGAACAAT
Found at i:657322 original size:20 final size:20
Alignment explanation
Indices: 657297--657372 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
657287 ATAAATAATA
*
657297 AATGTATCGATATATAAGTG
1 AATGTATCGATACATAAGTG
* ***
657317 AATGTATCAATACATGCTTG
1 AATGTATCGATACATAAGTG
*
657337 AAATGTATCGATACATAAGTA
1 -AATGTATCGATACATAAGTG
657358 AATGTATCGATACAT
1 AATGTATCGATACAT
657373 TTGCTATTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATAAGTG
Found at i:658637 original size:19 final size:20
Alignment explanation
Indices: 658609--658663 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
658599 ATATCGATAT
* **
658609 ATTGTGTCGATACATGTTC-
1 ATTGTATCGATACATGGACA
658628 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
658648 ATTGTATCGATACATG
1 ATTGTATCGATACATG
658664 AAGCTGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:662068 original size:19 final size:18
Alignment explanation
Indices: 662043--662107 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
662033 ATTTCAGCGA
662043 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
662061 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
662077 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
662093 TTTTGTATCGATACA
1 -TTTGTATCGATACA
662108 ATGTATCGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:662081 original size:32 final size:32
Alignment explanation
Indices: 662045--662115 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
662035 TTCAGCGATT
662045 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
662077 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
662109 TGTATCG
1 TGTATCG
662116 CTAGGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:662082 original size:13 final size:13
Alignment explanation
Indices: 662064--662088 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
662054 ACATAAGTGT
662064 TGTATCGATACAA
1 TGTATCGATACAA
662077 TGTATCGATACA
1 TGTATCGATACA
662089 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:662177 original size:13 final size:13
Alignment explanation
Indices: 662159--662184 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
662149 CATTTTTCTG
662159 TGTATCGATACAT
1 TGTATCGATACAT
662172 TGTATCGATACAT
1 TGTATCGATACAT
662185 CTATTCTTTG
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:662202 original size:34 final size:33
Alignment explanation
Indices: 662141--662205 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
662131 CAAGGAAATC
*
662141 TATCGATACATTTTTCTGTGTATCGATACATTG
1 TATCGATACATTATTCTGTGTATCGATACATTG
*
662174 TATCGATACATCTATTCTTTGTATCGATACAT
1 TATCGATACAT-TATTCTGTGTATCGATACAT
662206 CTAGGAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (33 bp):
TATCGATACATTATTCTGTGTATCGATACATTG
Found at i:664573 original size:51 final size:51
Alignment explanation
Indices: 664512--664618 Score: 146
Period size: 51 Copynumber: 2.1 Consensus size: 51
664502 CCGCAATCAA
* * *
664512 GGATATCCAACTCCGATTTTATTTTC-AAAACACTAA-TTTTCTATAATCGG
1 GGATATCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-ACAATCGG
664562 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCACAATCGG
1 GGATA-TCCAACTCCGATTTTATTTCC-AAAAACACCAATTTTTCACAATCGG
664615 GGAT
1 GGAT
664619 GCTGCAACCC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
50 5 0.10
51 20 0.40
53 20 0.40
54 5 0.10
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34
Consensus pattern (51 bp):
GGATATCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGG
Found at i:664618 original size:53 final size:50
Alignment explanation
Indices: 664512--664618 Score: 144
Period size: 53 Copynumber: 2.1 Consensus size: 50
664502 CCGCAATCAA
* * *
664512 GGATATCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGG
1 GGATATCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTACAATCGG
664562 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTT-TCACAATCGG
1 GGATA-TCCAACTCCGATTTTATTTCC--AAAACACCAATTTTCT-ACAATCGG
664615 GGAT
1 GGAT
664619 GCTGCAACCC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
50 5 0.10
51 20 0.40
52 1 0.02
53 24 0.48
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34
Consensus pattern (50 bp):
GGATATCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTACAATCGG
Found at i:664744 original size:103 final size:106
Alignment explanation
Indices: 664560--664803 Score: 325
Period size: 103 Copynumber: 2.3 Consensus size: 106
664550 TTCTATAATC
* * *
664560 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCACAATCGGGGATGCTGCA
1 GGGGATACTCCAAC-CCGGTTTTATTTCCAAAAAACACCAATTTTT-ACAATCGGGGATACTCCA
* *
664625 ACCCCGTTAATCATCGGGGATACTCCAACCCCATTATTTCTGA
64 ACCCCGTTAATCATCGGGGATACTCCAACCCCATTATCTCCGA
* * *
664668 GGGGACACTCCAACCCTGGTTTTATTT-C-TAAAACATCAATTTTT-C-ATCGGGGATACTCCAA
1 GGGGATACTCCAACCC-GGTTTTATTTCCAAAAAACACCAATTTTTACAATCGGGGATACTCCAA
*
664729 CCCCGTTAATCATCGGGGATACTCCAACCCCGTTATCTCCGA
65 CCCCGTTAATCATCGGGGATACTCCAACCCCATTATCTCCGA
* *
664771 GGGGATACTCCAACCCCGGCTTTATTCCCAAAA
1 GGGGATACTCCAA-CCCGGTTTTATTTCCAAAA
664804 TATTGATTTC
Statistics
Matches: 119, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
103 73 0.61
104 5 0.04
105 2 0.02
106 14 0.12
107 3 0.03
108 22 0.18
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (106 bp):
GGGGATACTCCAACCCGGTTTTATTTCCAAAAAACACCAATTTTTACAATCGGGGATACTCCAAC
CCCGTTAATCATCGGGGATACTCCAACCCCATTATCTCCGA
Found at i:664783 original size:28 final size:27
Alignment explanation
Indices: 664711--664788 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 27
664701 CATCAATTTT
664711 TCATCGGGGATACTCCAACCCCGTTAA
1 TCATCGGGGATACTCCAACCCCGTTAA
664738 TCATCGGGGATACTCCAACCCCGTT-A
1 TCATCGGGGATACTCCAACCCCGTTAA
664764 TC-TCCGAGGGGATACTCCAACCCCG
1 TCAT-C--GGGGATACTCCAACCCCG
664789 GCTTTATTCC
Statistics
Matches: 48, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
25 1 0.02
26 4 0.08
27 25 0.52
28 18 0.38
ACGTcount: A:0.23, C:0.36, G:0.21, T:0.21
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCGTTAA
Found at i:664920 original size:77 final size:78
Alignment explanation
Indices: 664744--664942 Score: 197
Period size: 77 Copynumber: 2.5 Consensus size: 78
664734 TTAATCATCG
* * * *
664744 GGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTG
1 GGGATACTCC-ACCCTGTTATTTCCGAGGGGATACTCCAACCCCGGATTTATTCCCAAAATATCG
* **
664809 ATTTCTCATAATTG
65 ATTTCTCACAATCA
* * ** *
664823 GGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAATCCC-GATTT-TTTTC-TAATCATC
1 GGGATACTCCACCCT-GTTATTTCCGAGGGGATACTCCAACCCCGGATTTATTCCCAAAAT-ATC
664885 GATTTCTCACAATCA
64 GATTTCTCACAATCA
* * * *
664900 GGGATACTCCAGCCCTGTTATTTTCAAAGGGACACTCCAACCC
1 GGGATACTCCA-CCCTGTTATTTCCGAGGGGATACTCCAACCC
664943 TGTTATTATC
Statistics
Matches: 99, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
76 3 0.03
77 50 0.51
78 10 0.10
79 36 0.36
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (78 bp):
GGGATACTCCACCCTGTTATTTCCGAGGGGATACTCCAACCCCGGATTTATTCCCAAAATATCGA
TTTCTCACAATCA
Found at i:671556 original size:13 final size:13
Alignment explanation
Indices: 671538--671564 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
671528 ACATTATGCT
671538 TTGTATCGATACA
1 TTGTATCGATACA
671551 TTGTATCGATACA
1 TTGTATCGATACA
671564 T
1 T
671565 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:671594 original size:20 final size:19
Alignment explanation
Indices: 671548--671604 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
671538 TTGTATCGAT
*
671548 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
671567 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
671586 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
671605 AAACTGGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:671667 original size:13 final size:13
Alignment explanation
Indices: 671649--671679 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
671639 CGATACATGG
*
671649 TACATTGTATTGA
1 TACATTGTATCGA
671662 TACATTGTATCGA
1 TACATTGTATCGA
671675 TACAT
1 TACAT
671680 GATGAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:671697 original size:33 final size:33
Alignment explanation
Indices: 671633--671700 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
671623 CTACCATTGT
* * *
671633 TTGTATCGATACATGGTACATTGTATTGATACA
1 TTGTATCGATACATGATACATTATATCGATACA
671666 TTGTATCGATACATGATGA-ATTATATCGATACA
1 TTGTATCGATACATGAT-ACATTATATCGATACA
671699 TT
1 TT
671701 ACTTCTAACG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (33 bp):
TTGTATCGATACATGATACATTATATCGATACA
Found at i:675118 original size:4 final size:4
Alignment explanation
Indices: 675099--675132 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
675089 ATTTATGAAG
*
675099 ATAA AAAA AT-A ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
675133 TTGTTGTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:675658 original size:22 final size:20
Alignment explanation
Indices: 675606--675681 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 20
675596 ACCAAGGGAA
* *
675606 TGTATCGATATATTAT-TAAA
1 TGTATCGATACATT-TCTAAT
*
675626 TGTATCAATACATGCTTAC-AAT
1 TGTATCGATACAT--TT-CTAAT
*
675648 TGTATCGATACATTTCTCAT
1 TGTATCGATACATTTCTAAT
675668 TGTATCGATACATT
1 TGTATCGATACATT
675682 CTGGTTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
19 1 0.02
20 29 0.63
21 1 0.02
22 15 0.33
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTTCTAAT
Found at i:686403 original size:52 final size:51
Alignment explanation
Indices: 686325--686473 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
686315 CGAAATATGA
*
686325 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTCGGC
* *
686377 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTCGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTCGGC
**
686429 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
686474 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTCGGC
Found at i:686480 original size:13 final size:13
Alignment explanation
Indices: 686462--686486 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
686452 CAAAGATCAG
686462 TGTATCGATACAA
1 TGTATCGATACAA
686475 TGTATCGATACA
1 TGTATCGATACA
686487 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:686564 original size:33 final size:33
Alignment explanation
Indices: 686527--686593 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
686517 AGTAGCTTAA
686527 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
686560 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
686593 A
1 A
686594 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:686567 original size:13 final size:13
Alignment explanation
Indices: 686549--686573 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
686539 CAAAAAAATA
686549 TGTATCGATACAT
1 TGTATCGATACAT
686562 TGTATCGATACA
1 TGTATCGATACA
686574 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:687513 original size:52 final size:52
Alignment explanation
Indices: 687381--687592 Score: 208
Period size: 52 Copynumber: 4.2 Consensus size: 52
687371 GAAAAGTGAT
* * * * * * * *
687381 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-G-A
* * *
687435 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
687488 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T--A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* *
687532 AAA-GTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
687583 AAAGGTGCCA
1 AAAGGTGCCA
687593 CCGACTTGTG
Statistics
Matches: 130, Mismatches: 18, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
43 34 0.26
44 5 0.04
46 1 0.01
49 1 0.01
51 5 0.04
52 38 0.29
53 6 0.05
54 5 0.04
55 35 0.27
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
Found at i:687549 original size:43 final size:44
Alignment explanation
Indices: 687487--687576 Score: 146
Period size: 43 Copynumber: 2.1 Consensus size: 44
687477 TTAAAGATGG
*
687487 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
687531 AAAA-GTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
687574 AAA
1 AAA
687577 GATGGAAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
43 39 0.91
44 4 0.09
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (44 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:687622 original size:30 final size:29
Alignment explanation
Indices: 687579--687662 Score: 102
Period size: 27 Copynumber: 3.0 Consensus size: 29
687569 GACTTAAAGA
*
687579 TGGAAAA-GGTGCCACCGACTTGTGGGCT
1 TGGAAAAGGGTGCCACTGACTTGTGGGCT
*
687607 TCGGAAAAGGGTGCCACTGATTTGTGGGCT
1 T-GGAAAAGGGTGCCACTGACTTGTGGGCT
* *
687637 TTG--AAGGTTGCCACTGACTTGTGGGC
1 TGGAAAAGGGTGCCACTGACTTGTGGGC
687663 CCACTGACTT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
27 21 0.43
28 1 0.02
29 7 0.14
30 20 0.41
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.26
Consensus pattern (29 bp):
TGGAAAAGGGTGCCACTGACTTGTGGGCT
Found at i:687668 original size:16 final size:16
Alignment explanation
Indices: 687647--687678 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
687637 TTGAAGGTTG
687647 CCACTGACTTGTGGGC
1 CCACTGACTTGTGGGC
687663 CCACTGACTTGTGGGC
1 CCACTGACTTGTGGGC
687679 TTTTGAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.31, G:0.31, T:0.25
Consensus pattern (16 bp):
CCACTGACTTGTGGGC
Found at i:687681 original size:43 final size:45
Alignment explanation
Indices: 687620--687708 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 45
687610 GAAAAGGGTG
* * *
687620 CCACTGATTTGTGGGC-TTTG-AAGGTTGCCACTGACTTGTGGGC
1 CCACTGACTTGTGGGCTTTTGAAAGGGTGCCACTAACTTGTGGGC
687663 CCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGC
1 CCACTGACTTGTGGGCTTTTG-AAAGGGTGCCACTAACTTGTGGGC
687709 TGAAAAAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 15 0.38
44 4 0.10
46 21 0.52
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.30
Consensus pattern (45 bp):
CCACTGACTTGTGGGCTTTTGAAAGGGTGCCACTAACTTGTGGGC
Found at i:687703 original size:30 final size:30
Alignment explanation
Indices: 687663--687886 Score: 136
Period size: 30 Copynumber: 7.3 Consensus size: 30
687653 ACTTGTGGGC
687663 CCACTGACTTGTGGGCTTTTGAAAAGGGTG
1 CCACTGACTTGTGGGCTTTTGAAAAGGGTG
* *** *
687693 CCACTAACTTGTGGGCTGAAAAAGAAAAAGAGTG
1 CCACTGACTTGTGGGCT---TTTG-AAAAGGGTG
* * * * *
687727 CTACGGAGTTGTGGTGTGGACTTTGGAAAA-GATG
1 CCACTGA-CT-T-GTG-GG-CTTTTGAAAAGGGTG
* *
687761 CCACCGACTTGTGGGC-TTCGAAAAAGGGTG
1 CCACTGACTTGTGGGCTTTTG-AAAAGGGTG
* *
687791 CCACTGATTTGTGGGC-TTTG--AAGGTTG
1 CCACTGACTTGTGGGCTTTTGAAAAGGGTG
***
687818 CCACTGACTTGTGGGCTTTTGAAAAAAATG
1 CCACTGACTTGTGGGCTTTTGAAAAGGGTG
***
687848 CCACTGACTTGTGGGC-TTTGAAAAAAATG
1 CCACTGACTTGTGGGCTTTTGAAAAGGGTG
687877 CCACTGACTT
1 CCACTGACTT
687887 CGTCCCCACA
Statistics
Matches: 153, Mismatches: 27, Indels: 29
0.73 0.13 0.14
Matches are distributed among these distances:
27 21 0.14
28 7 0.05
29 28 0.18
30 58 0.38
31 3 0.02
32 1 0.01
33 2 0.01
34 19 0.12
35 5 0.03
36 2 0.01
37 3 0.02
38 2 0.01
39 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.27
Consensus pattern (30 bp):
CCACTGACTTGTGGGCTTTTGAAAAGGGTG
Found at i:687785 original size:29 final size:29
Alignment explanation
Indices: 687741--687886 Score: 170
Period size: 30 Copynumber: 5.0 Consensus size: 29
687731 GGAGTTGTGG
* * *
687741 TGTGGACTTTGGAAAAGATGCCACCGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* * *
687770 TGTGGGCTTCGAAAAAGGGTGCCACTGATT
1 TGTGGGCTTTGAAAAA-GATGCCACTGACT
* *
687800 TGTGGGCTTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
*
687827 TGTGGGCTTTTGAAAAAAATGCCACTGACT
1 TGTGGGC-TTTGAAAAAGATGCCACTGACT
*
687857 TGTGGGCTTTGAAAAAAATGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
687886 T
1 T
687887 CGTCCCCACA
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
27 18 0.18
28 6 0.06
29 36 0.36
30 40 0.40
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAAGATGCCACTGACT
Found at i:687831 original size:57 final size:57
Alignment explanation
Indices: 687759--687869 Score: 161
Period size: 57 Copynumber: 1.9 Consensus size: 57
687749 TTGGAAAAGA
** *
687759 TGCCACCGACTTGTGGGC-TTCGAAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGT
1 TGCCACCGACTTGTGGGCTTTCGAAAAA-AATGCCACTGACTTGTGGGCTTTGAAGGT
* *
687816 TGCCACTGACTTGTGGGCTTTTGAAAAAAATGCCACTGACTTGTGGGCTTTGAA
1 TGCCACCGACTTGTGGGCTTTCGAAAAAAATGCCACTGACTTGTGGGCTTTGAA
687870 AAAAATGCCA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
57 40 0.83
58 8 0.17
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (57 bp):
TGCCACCGACTTGTGGGCTTTCGAAAAAAATGCCACTGACTTGTGGGCTTTGAAGGT
Found at i:689445 original size:20 final size:21
Alignment explanation
Indices: 689409--689448 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
689399 TTACAAATTT
*
689409 CTTCATTTTTACTTCAAAATA
1 CTTCATTTTTACATCAAAATA
689430 CTTCATTTTT-CATCAAAAT
1 CTTCATTTTTACATCAAAAT
689449 CACCAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (21 bp):
CTTCATTTTTACATCAAAATA
Found at i:691819 original size:13 final size:13
Alignment explanation
Indices: 691801--691827 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
691791 ACATTATGCT
691801 TTGTATCGATACA
1 TTGTATCGATACA
691814 TTGTATCGATACA
1 TTGTATCGATACA
691827 T
1 T
691828 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:691857 original size:20 final size:19
Alignment explanation
Indices: 691811--691867 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
691801 TTGTATCGAT
*
691811 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
691830 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
*
691849 ACAATTGTATGGATACATG
1 AC-ATTGTATCGATACATG
691868 AAACTGGCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:691930 original size:13 final size:13
Alignment explanation
Indices: 691912--691942 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
691902 CGATACATGG
*
691912 TACATTGTATTGA
1 TACATTGTATCGA
691925 TACATTGTATCGA
1 TACATTGTATCGA
691938 TACAT
1 TACAT
691943 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:691934 original size:33 final size:33
Alignment explanation
Indices: 691896--691963 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
691886 CTACCATTGT
* *
691896 TTGTATCGATACATGGT-ACATTGTATTGATACA
1 TTGTATCGATACATGATGA-ATTGTATCGATACA
691929 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTGTATCGATACA
691962 TT
1 TT
691964 ACTTCTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.40
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTGTATCGATACA
Found at i:695786 original size:21 final size:19
Alignment explanation
Indices: 695760--695814 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
695750 TTCTACAATT
695760 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAA-AGT-AA
* **
695781 TGTATCGATACATAAGTTT
1 TGTATCGATACAAAAGTAA
695800 TGTATCGATACAAAA
1 TGTATCGATACAAAA
695815 TTACCCTGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:695805 original size:19 final size:21
Alignment explanation
Indices: 695757--695813 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
695747 AATTTCTACA
695757 ATTTGTATCGATACAAACAGT
1 ATTTGTATCGATACAAACAGT
** *
695778 AAATGTATCGATACATA-AGT
1 ATTTGTATCGATACAAACAGT
695798 -TTTGTATCGATACAAA
1 ATTTGTATCGATACAAA
695814 ATTACCCTGC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (21 bp):
ATTTGTATCGATACAAACAGT
Found at i:702677 original size:60 final size:60
Alignment explanation
Indices: 702613--702728 Score: 180
Period size: 60 Copynumber: 1.9 Consensus size: 60
702603 TCGCTTCCTA
* * *
702613 AAGTCTACGACTT-AGTGGCATTTCTTCTCCAAGTCCATGACTTAGTGGCAACCTTTCCCG
1 AAGTCCACGA-TTCAGTGGCATCTCTTCTCCAAGTCCATGACTTAGTAGCAACCTTTCCCG
*
702673 AAGTCCACGATTCAGTGGCATCTCTTCTCCAAGTCCATGACTTAGTAGCATCCTTT
1 AAGTCCACGATTCAGTGGCATCTCTTCTCCAAGTCCATGACTTAGTAGCAACCTTT
702729 TTCTTGCAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 2 0.04
60 49 0.96
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.32
Consensus pattern (60 bp):
AAGTCCACGATTCAGTGGCATCTCTTCTCCAAGTCCATGACTTAGTAGCAACCTTTCCCG
Found at i:702724 original size:30 final size:30
Alignment explanation
Indices: 702593--702757 Score: 131
Period size: 30 Copynumber: 5.4 Consensus size: 30
702583 TTTCCAAAAG
* * * *
702593 CTTAGTGGCATCGCTTC-CTAAAGTCTACGA
1 CTTAGTGGCATCTCTTCTC-CAAGTCCATGA
*
702623 CTTAGTGGCATTTCTTCTCCAAGTCCATGA
1 CTTAGTGGCATCTCTTCTCCAAGTCCATGA
* *
702653 CTTAGTGGCAAC-CTT-TCCCGAAGTCCACGA
1 CTTAGTGGCATCTCTTCT-CC-AAGTCCATGA
702683 -TTCAGTGGCATCTCTTCTCCAAGTCCATGA
1 CTT-AGTGGCATCTCTTCTCCAAGTCCATGA
* * * *
702713 CTTAGTAGCATCCTTTTTCTTGCAAGTCCATAA
1 CTTAGTGGCAT-C-TCTTC-TCCAAGTCCATGA
*
702746 CTTAGTGCCATC
1 CTTAGTGGCATC
702758 CTTTTTCTTC
Statistics
Matches: 109, Mismatches: 16, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
28 1 0.01
29 7 0.06
30 66 0.61
31 9 0.08
32 6 0.06
33 20 0.18
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (30 bp):
CTTAGTGGCATCTCTTCTCCAAGTCCATGA
Found at i:702739 original size:33 final size:33
Alignment explanation
Indices: 702702--702766 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
702692 ATCTCTTCTC
*
702702 CAAGTCCATGACTTAGTAG-CATCCTTTTTCTTG
1 CAAGTCCATAACTTAGT-GCCATCCTTTTTCTTG
702735 CAAGTCCATAACTTAGTGCCATCCTTTTTCTT
1 CAAGTCCATAACTTAGTGCCATCCTTTTTCTT
702767 CAAAGTACAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (33 bp):
CAAGTCCATAACTTAGTGCCATCCTTTTTCTTG
Found at i:702814 original size:33 final size:33
Alignment explanation
Indices: 702769--702906 Score: 112
Period size: 33 Copynumber: 4.4 Consensus size: 33
702759 TTTTTCTTCA
*
702769 AAGTACACAACTCTGTGGCACCTTTTTCCCTTT
1 AAGTCCACAACTCTGTGGCACCTTTTTCCCTTT
* * * *
702802 AAGTCCACAACTCCGTCGCACCTTTTTCTCTTA
1 AAGTCCACAACTCTGTGGCACCTTTTTCCCTTT
* *
702835 AAGCCCACAACT-TCGTGGCA-C-----CCTTTT
1 AAGTCCACAACTCT-GTGGCACCTTTTTCCCTTT
* * *
702862 AAGTCCACAACTCTGTGGTATCTTTTT-CTTTT
1 AAGTCCACAACTCTGTGGCACCTTTTTCCCTTT
*
702894 AAGTCAACAACTC
1 AAGTCCACAACTC
702907 CATAGCACCC
Statistics
Matches: 83, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
27 19 0.23
28 2 0.02
32 18 0.22
33 44 0.53
ACGTcount: A:0.23, C:0.31, G:0.12, T:0.34
Consensus pattern (33 bp):
AAGTCCACAACTCTGTGGCACCTTTTTCCCTTT
Found at i:702871 original size:27 final size:27
Alignment explanation
Indices: 702839--703346 Score: 208
Period size: 27 Copynumber: 17.9 Consensus size: 27
702829 CTCTTAAAGC
702839 CCACAACTTCGTGGCACCCTTTTAAGT
1 CCACAACTTCGTGGCACCCTTTTAAGT
* *
702866 CCACAAC-TCTGTGGTATCTTTTTCTTTTAAGT
1 CCACAACTTC-GTGGCA-C----CCTTTTAAGT
* * * *
702898 CAACAACTCCATAGCACCCTTTTAAGT
1 CCACAACTTCGTGGCACCCTTTTAAGT
* * *
702925 CCATAACTTCGTGGCCCCCTTTTCAGT
1 CCACAACTTCGTGGCACCCTTTTAAGT
* *
702952 CTACAACTCCGTGGCACCCTTTTAAGT
1 CCACAACTTCGTGGCACCCTTTTAAGT
** *
702979 TTATAAC-TCTGTGGCACCCTTTTAAGT
1 CCACAACTTC-GTGGCACCCTTTTAAGT
* * * *
703006 CTATAACTCCATGGCATCTTTTCCTTTTAAGT
1 CCACAACTTCGTGGCA-C----CCTTTTAAGT
*
703038 CCACAACTCCGTGGCACCCTTTTAAGT
1 CCACAACTTCGTGGCACCCTTTTAAGT
* *
703065 CCACAA-TTCCGTGGCGTCTATTCCTTTAAAGT
1 CCACAACTT-CGT-G-G-C-A-CCCTTTTAAGT
* *
703097 CCACAACTT-ATGGCACTCTTTTAAGT
1 CCACAACTTCGTGGCACCCTTTTAAGT
* * *
703123 CCATAAC-TCTGTAGCACCTTTTTCTTTTCAAAGC
1 CCACAACTTC-GTGGCACC-----CTTTT--AAGT
* * *
703157 CCATAACTTCATGGCA-CCATTTAAGT
1 CCACAACTTCGTGGCACCCTTTTAAGT
* *
703183 CCACAACTCCGTGGCACCATTTTTCATTTTAAAGG
1 CCACAACTTCGTGGCACC------C-TTTT-AAGT
* *
703218 CCACAACTCCGTGGCACCCTTTTAAAT
1 CCACAACTTCGTGGCACCCTTTTAAGT
* ***
703245 CCACAACTTCGTGACACCCTTTTTTTT
1 CCACAACTTCGTGGCACCCTTTTAAGT
* ***
703272 CCA-AAGC-CCACAGCA-CCTTTTAAG-
1 CCACAA-CTTCGTGGCACCCTTTTAAGT
* *
703296 CTTACAATTTCGTGGCACCCTTTTAAGT
1 C-CACAACTTCGTGGCACCCTTTTAAGT
* * *
703324 CCACAACTCCATGGCACCTTTTT
1 CCACAACTTCGTGGCACCCTTTT
703347 CTTTTAAAGC
Statistics
Matches: 359, Mismatches: 76, Indels: 92
0.68 0.14 0.17
Matches are distributed among these distances:
24 1 0.00
25 8 0.02
26 45 0.13
27 176 0.49
28 14 0.04
29 3 0.01
30 2 0.01
31 4 0.01
32 61 0.17
33 5 0.01
34 17 0.05
35 23 0.06
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.34
Consensus pattern (27 bp):
CCACAACTTCGTGGCACCCTTTTAAGT
Found at i:702894 original size:32 final size:32
Alignment explanation
Indices: 702724--703240 Score: 145
Period size: 27 Copynumber: 17.2 Consensus size: 32
702714 TTAGTAGCAT
** * *
702724 CCTTTTTCTTGCAAGTCCATAACT-TAGTGCCA
1 CCTTTTTCTTTTAAGTCCACAACTCT-GTGGCA
** *
702756 TCCTTTTTCTTCAAAGTACACAACTCTGTGGCA
1 -CCTTTTTCTTTTAAGTCCACAACTCTGTGGCA
* * *
702789 CCTTTTTCCCTTTAAGTCCACAACTCCGTCGCA
1 CCTTTTT-CTTTTAAGTCCACAACTCTGTGGCA
* *
702822 CCTTTTTCTCTTAAAGCCCACAACT-TCGTGGCA
1 CCTTTTTCT-TTTAAGTCCACAACTCT-GTGGCA
*
702855 CC-----CTTTTAAGTCCACAACTCTGTGGTA
1 CCTTTTTCTTTTAAGTCCACAACTCTGTGGCA
* * ** *
702882 TCTTTTTCTTTTAAGTCAACAACTCCATAGCA
1 CCTTTTTCTTTTAAGTCCACAACTCTGTGGCA
*
702914 CC-----CTTTTAAGTCCATAACT-TCGTGGC-
1 CCTTTTTCTTTTAAGTCCACAACTCT-GTGGCA
* * * *
702940 CC----CCTTTTCAGTCTACAACTCCGTGGCA
1 CCTTTTTCTTTTAAGTCCACAACTCTGTGGCA
** *
702968 CC-----CTTTTAAGTTTATAACTCTGTGGCA
1 CCTTTTTCTTTTAAGTCCACAACTCTGTGGCA
* * **
702995 CC-----CTTTTAAGTCTATAACTCCATGGCA
1 CCTTTTTCTTTTAAGTCCACAACTCTGTGGCA
* * *
703022 TCTTTTCCTTTTAAGTCCACAACTCCGTGGCA
1 CCTTTTTCTTTTAAGTCCACAACTCTGTGGCA
* * *
703054 CC-----CTTTTAAGTCCACAATTCCGTGGCG
1 CCTTTTTCTTTTAAGTCCACAACTCTGTGGCA
* * * * *
703081 TCTATTCCTTTAAAGTCCACAACT-TATGGCA
1 CCTTTTTCTTTTAAGTCCACAACTCTGTGGCA
* *
703112 -C----TCTTTTAAGTCCATAACTCTGTAGCA
1 CCTTTTTCTTTTAAGTCCACAACTCTGTGGCA
* * *
703139 CCTTTTTCTTTTCAAAGCCCATAACT-TCATGGCA
1 CCTTTTTCTTTT--AAGTCCACAACTCT-GTGGCA
* *
703173 -C-----CATTTAAGTCCACAACTCCGTGGCA
1 CCTTTTTCTTTTAAGTCCACAACTCTGTGGCA
* *
703199 CCATTTTTCATTTTAAAGGCCACAACTCCGTGGCA
1 CC-TTTTTC-TTTT-AAGTCCACAACTCTGTGGCA
*
703234 CCCTTTT
1 CCTTTTT
703241 AAATCCACAA
Statistics
Matches: 370, Mismatches: 71, Indels: 85
0.70 0.13 0.16
Matches are distributed among these distances:
26 32 0.09
27 132 0.36
28 10 0.03
30 1 0.00
31 4 0.01
32 73 0.20
33 74 0.20
34 23 0.06
35 21 0.06
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.35
Consensus pattern (32 bp):
CCTTTTTCTTTTAAGTCCACAACTCTGTGGCA
Found at i:702917 original size:59 final size:60
Alignment explanation
Indices: 702799--702932 Score: 162
Period size: 59 Copynumber: 2.2 Consensus size: 60
702789 CCTTTTTCCC
* * * *
702799 TTTAAGTCCACAACTCCGTCGCACCTTTTTCTCTTAAAGCCCACAACTTCGTGGCACCCT
1 TTTAAGTCCACAACTCCGTCGCACCTTTTTCTCTTAAAGCCAACAACTCCATAGCACCCT
* * * * * *
702859 TTTAAGTCCACAACTCTGTGGTATCTTTTTCT-TTTAAGTCAACAACTCCATAGCACCCT
1 TTTAAGTCCACAACTCCGTCGCACCTTTTTCTCTTAAAGCCAACAACTCCATAGCACCCT
*
702918 TTTAAGTCCATAACT
1 TTTAAGTCCACAACT
702933 TCGTGGCCCC
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
59 35 0.56
60 28 0.44
ACGTcount: A:0.25, C:0.31, G:0.10, T:0.34
Consensus pattern (60 bp):
TTTAAGTCCACAACTCCGTCGCACCTTTTTCTCTTAAAGCCAACAACTCCATAGCACCCT
Found at i:703055 original size:59 final size:59
Alignment explanation
Indices: 702915--703267 Score: 288
Period size: 59 Copynumber: 6.0 Consensus size: 59
702905 TCCATAGCAC
* * * * *
702915 CCTTTTAAGTCCATAACTTCGTGGCCCCCTTTTCAGTCTACAACTCCGTGGCA-C----
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTT
** * * * * * *
702969 CCTTTTAAGTTTATAACTCTGTGGCACCCTTTTAAGTCTATAACTCCATGGCATCTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTT
* ** *
703028 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAATTCCGTGGCGTCTATT
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTT
* ** * * * *
703087 CCTTTAAAGTCCACAACT-TATGGCACTCTTTTAAGTCCATAACTCTGTAGCACCTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTT
* * * * * *
703145 TCTTTTCAAAGCCCATAACTTCATGGCA-CCATTTAAGTCCACAACTCCGTGGCACCATTTTT
1 CCTTTT--AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC--TTTT
* * * * *
703207 CATTTTAAAGGCCACAACTCCGTGGCACCCTTTTAAATCCACAACTTCGTGACACCCTTTT
1 CCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCTTTT
703268 TTTTCCAAAG
Statistics
Matches: 238, Mismatches: 49, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
54 45 0.19
55 1 0.00
58 34 0.14
59 66 0.28
60 33 0.14
61 27 0.11
62 30 0.13
63 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.34
Consensus pattern (59 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTT
Found at i:703143 original size:26 final size:25
Alignment explanation
Indices: 703087--703144 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
703077 GGCGTCTATT
* *
703087 CCTTTAAAGTCCACAACTTATGGCA
1 CCTTTTAAGTCCACAACTTATAGCA
* *
703112 CTCTTTTAAGTCCATAACTCTGTAGCA
1 C-CTTTTAAGTCCACAACT-TATAGCA
703139 CCTTTT
1 CCTTTT
703145 TCTTTTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 1 0.04
26 20 0.74
27 6 0.22
ACGTcount: A:0.26, C:0.28, G:0.10, T:0.36
Consensus pattern (25 bp):
CCTTTTAAGTCCACAACTTATAGCA
Found at i:703182 original size:60 final size:61
Alignment explanation
Indices: 703089--703252 Score: 181
Period size: 60 Copynumber: 2.7 Consensus size: 61
703079 CGTCTATTCC
* * * *
703089 TTTAAAGTCCACAACTT-ATGGCACTCTTTTAAGTCCATAACTCTGTAGCACC-TTTTTC-T
1 TTTAAAGCCCACAACTTCATGGCAC-CATTTAAGTCCACAACTCCGTAGCACCATTTTTCAT
* *
703148 TTTCAAAGCCCATAACTTCATGGCACCATTTAAGTCCACAACTCCGTGGCACCATTTTTCAT
1 TTT-AAAGCCCACAACTTCATGGCACCATTTAAGTCCACAACTCCGTAGCACCATTTTTCAT
* * * * *
703210 TTTAAAGGCCACAACTCCGTGGCACCCTTTTAAATCCACAACT
1 TTTAAAGCCCACAACTTCATGGCA-CCATTTAAGTCCACAACT
703253 TCGTGACACC
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
59 3 0.03
60 35 0.40
61 30 0.34
62 20 0.23
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.32
Consensus pattern (61 bp):
TTTAAAGCCCACAACTTCATGGCACCATTTAAGTCCACAACTCCGTAGCACCATTTTTCAT
Found at i:703407 original size:35 final size:33
Alignment explanation
Indices: 703320--703413 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
703310 GCACCCTTTT
*
703320 AAGTCCACAACTCCATGGCACCTTTTTCTTTTA
1 AAGTCCACAACTCCATGGCACCTTTTTCTTTCA
* * *
703353 AAG-CCTATAACTCCGTGGCACCTTTTTCCTTCTCC
1 AAGTCC-ACAACTCCATGGCACCTTTTT-CTT-TCA
703388 AAGTCCACAACTCCATGGCACCTTTT
1 AAGTCCACAACTCCATGGCACCTTTT
703414 CAGTTTAAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
32 2 0.04
33 22 0.43
34 3 0.06
35 22 0.43
36 2 0.04
ACGTcount: A:0.22, C:0.34, G:0.11, T:0.33
Consensus pattern (33 bp):
AAGTCCACAACTCCATGGCACCTTTTTCTTTCA
Found at i:703552 original size:49 final size:49
Alignment explanation
Indices: 703479--703784 Score: 434
Period size: 49 Copynumber: 6.2 Consensus size: 49
703469 GGTGGTAACC
* *
703479 CATCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCGCGTTGGCACCTT
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACGTTGGCACCTT
* *
703528 CATCTTTAAGTCCAATGTCACTGGCCTTGAATCAGCATGTTGGCACCTT
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACGTTGGCACCTT
* *
703577 CATCTTTAAGTACAATGTCGCTAGCCTTGAATCAGCACGTTGGCACCTT
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACGTTGGCACCTT
* * *
703626 CATCTTTATGTCCAATGTCGTTGGCCTTGAATCAGCACGTTGGGACCTT
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACGTTGGCACCTT
* * * * *
703675 CATCTTTAAATCAAATGTCACTGGCCTTGAATCAGCACATTGGTACCTT
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACGTTGGCACCTT
* * **
703724 CATCTTTAAGTCCAATGTCGTTGGCCTTGAATCAACAAATTGGCA-CTAT
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACGTTGGCACCT-T
703773 CATCTTTAAGTC
1 CATCTTTAAGTC
703785 TAGTGTTGCA
Statistics
Matches: 229, Mismatches: 27, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
48 2 0.01
49 227 0.99
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (49 bp):
CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACGTTGGCACCTT
Found at i:704779 original size:13 final size:13
Alignment explanation
Indices: 704761--704785 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
704751 CATATTGCTT
704761 TGTATCGATACAC
1 TGTATCGATACAC
704774 TGTATCGATACA
1 TGTATCGATACA
704786 TGATCTTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:705184 original size:31 final size:32
Alignment explanation
Indices: 705143--705206 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
705133 AATTCAAGTT
*
705143 TTATTATTTCAAAGAGCTTTTGTATT-CTTTG
1 TTATTATTTCAAAGAGCATTTGTATTCCTTTG
* **
705174 TTATTCTTTCAAAGCTCATTTGTATTCCTTTG
1 TTATTATTTCAAAGAGCATTTGTATTCCTTTG
705206 T
1 T
705207 GCTTATTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 22 0.79
32 6 0.21
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.55
Consensus pattern (32 bp):
TTATTATTTCAAAGAGCATTTGTATTCCTTTG
Found at i:706901 original size:13 final size:13
Alignment explanation
Indices: 706883--706909 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
706873 ACATATTACT
706883 TTGTATCGATACA
1 TTGTATCGATACA
706896 TTGTATCGATACA
1 TTGTATCGATACA
706909 T
1 T
706910 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:708365 original size:13 final size:13
Alignment explanation
Indices: 708347--708372 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
708337 CAATTTTTTG
708347 TGTATCGATACAT
1 TGTATCGATACAT
708360 TGTATCGATACAT
1 TGTATCGATACAT
708373 ACTTTGTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:708384 original size:32 final size:33
Alignment explanation
Indices: 708327--708390 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
708317 TACAAGCCAA
**
708327 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
708360 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
708391 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:710243 original size:21 final size:20
Alignment explanation
Indices: 710214--710256 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
710204 GACTAGTGTA
* *
710214 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
710235 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
710255 GG
1 GG
710257 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:716930 original size:32 final size:33
Alignment explanation
Indices: 716871--716934 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
716861 TACAAGCCAA
**
716871 TGTATCGATACAATTTTTTGTGCATCGATACAT
1 TGTATCGATACAATACTTTGTGCATCGATACAT
*
716904 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGCATCGATACA
716935 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGCATCGATACAT
Found at i:719844 original size:108 final size:108
Alignment explanation
Indices: 719655--719872 Score: 418
Period size: 108 Copynumber: 2.0 Consensus size: 108
719645 CACAAAATTG
*
719655 TCATGTAATTGATACTAGTAATAATAAAACAATTTTTTTAGGCCATAGAGAAGGGAATATTTACA
1 TCATGTAATTGATACTAGAAATAATAAAACAATTTTTTTAGGCCATAGAGAAGGGAATATTTACA
*
719720 TTGCTTGTGTTGGTATATTTTCTAGACTTTGACATTTTCACTT
66 TTGCTTGTGTTGGTATATTTTCTAGACTTTGACACTTTCACTT
719763 TCATGTAATTGATACTAGAAATAATAAAACAATTTTTTTAGGCCATAGAGAAGGGAATATTTACA
1 TCATGTAATTGATACTAGAAATAATAAAACAATTTTTTTAGGCCATAGAGAAGGGAATATTTACA
719828 TTGCTTGTGTTGGTATATTTTCTAGACTTTGACACTTTCACTT
66 TTGCTTGTGTTGGTATATTTTCTAGACTTTGACACTTTCACTT
719871 TC
1 TC
719873 TAGTTTTTGT
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.41
Consensus pattern (108 bp):
TCATGTAATTGATACTAGAAATAATAAAACAATTTTTTTAGGCCATAGAGAAGGGAATATTTACA
TTGCTTGTGTTGGTATATTTTCTAGACTTTGACACTTTCACTT
Found at i:727308 original size:20 final size:21
Alignment explanation
Indices: 727272--727310 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
727262 GTATAACATT
*
727272 CTTTTCATAATTTCTTTGACA
1 CTTTTCATAAATTCTTTGACA
727293 CTTTTC-TAAATTCTTTGA
1 CTTTTCATAAATTCTTTGA
727311 TCCAAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.54
Consensus pattern (21 bp):
CTTTTCATAAATTCTTTGACA
Found at i:729352 original size:13 final size:13
Alignment explanation
Indices: 729334--729358 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
729324 AGATTGCATA
729334 GTATCGATACATT
1 GTATCGATACATT
729347 GTATCGATACAT
1 GTATCGATACAT
729359 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:729371 original size:20 final size:21
Alignment explanation
Indices: 729346--729398 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
729336 ATCGATACAT
*
729346 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
* *
729366 TGTATCAATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
729387 TGTATCGATACA
1 TGTATCGATACA
729399 GGTCATTGGC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:734073 original size:13 final size:13
Alignment explanation
Indices: 734055--734079 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
734045 AGATTGCATA
734055 GTATCGATACATT
1 GTATCGATACATT
734068 GTATCGATACAT
1 GTATCGATACAT
734080 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:739084 original size:15 final size:15
Alignment explanation
Indices: 739064--739094 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
739054 TAAAAATGTC
*
739064 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
739079 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
739094 C
1 C
739095 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:741191 original size:13 final size:13
Alignment explanation
Indices: 741173--741197 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
741163 CATTTTTCTT
741173 TGTATCGATACAC
1 TGTATCGATACAC
741186 TGTATCGATACA
1 TGTATCGATACA
741198 GGGGGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:741349 original size:20 final size:20
Alignment explanation
Indices: 741306--741351 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
741296 AAATCTTTTG
741306 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
741327 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
741347 CAAAA
1 CAAAA
741352 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:743767 original size:20 final size:20
Alignment explanation
Indices: 743722--743773 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
743712 GTAGCCAAAC
**
743722 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
743742 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
743761 TTGTATCGATACA
1 TTGTATCGATACA
743774 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:745096 original size:19 final size:20
Alignment explanation
Indices: 745048--745096 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
745038 AAATGAGATG
745048 AAGAAAGAAAATGGAAAAAGC
1 AAGAAA-AAAATGGAAAAAGC
* *
745069 AAAAGAAAAAAT-GAAAAATC
1 AAGA-AAAAAATGGAAAAAGC
745089 AAGAAAAA
1 AAGAAAAA
745097 GACAAAGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 4 0.17
20 10 0.42
21 8 0.33
22 2 0.08
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.06
Consensus pattern (20 bp):
AAGAAAAAAATGGAAAAAGC
Found at i:746691 original size:11 final size:11
Alignment explanation
Indices: 746675--746704 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
746665 GCCATTATAA
746675 GCTTGTTTGGT
1 GCTTGTTTGGT
746686 GCTTGTTTGGT
1 GCTTGTTTGGT
746697 GCTTGTTT
1 GCTTGTTT
746705 TCATGCTTTC
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:0.00, C:0.10, G:0.33, T:0.57
Consensus pattern (11 bp):
GCTTGTTTGGT
Found at i:746928 original size:13 final size:13
Alignment explanation
Indices: 746910--746936 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
746900 TACAATGAAC
746910 ATGTATCGATACA
1 ATGTATCGATACA
746923 ATGTATCGATACA
1 ATGTATCGATACA
746936 A
1 A
746937 AGTAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:746951 original size:33 final size:32
Alignment explanation
Indices: 746891--746955 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
746881 CAATTTGGCC
* *
746891 ATGTATTGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
746923 ATGTATCGATACAAAGTAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
746956 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:747838 original size:19 final size:20
Alignment explanation
Indices: 747806--747843 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
747796 ATCACTAGAG
*
747806 CTAGTCGAGGAATT-GTGCT
1 CTAGTCGAGAAATTCGTGCT
*
747825 CTAGTCTAGAAATTCGTGC
1 CTAGTCGAGAAATTCGTGC
747844 GTTCATCGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
CTAGTCGAGAAATTCGTGCT
Found at i:753784 original size:20 final size:19
Alignment explanation
Indices: 753754--753791 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
753744 TCCAATTTGC
753754 TTGTATGTATCGATACATT
1 TTGTATGTATCGATACATT
753773 TTGTAGTGTATCGATACAT
1 TTGTA-TGTATCGATACAT
753792 CTGGGCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGTATGTATCGATACATT
Found at i:753849 original size:13 final size:13
Alignment explanation
Indices: 753831--753855 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
753821 CAAAGATCAG
753831 TGTATCGATACAA
1 TGTATCGATACAA
753844 TGTATCGATACA
1 TGTATCGATACA
753856 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:753932 original size:19 final size:19
Alignment explanation
Indices: 753908--753955 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
753898 AGCGATACAT
753908 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
753927 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
753946 TGTATCGATA
1 TGTATCGATA
753956 TAAATCGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:756671 original size:19 final size:20
Alignment explanation
Indices: 756647--756699 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
756637 ACGATTTGGC
*
756647 CATGTATCGATACAATG-AA
1 CATGTATCGATACAAAGTAA
*
756666 CATGTATCGATACAAAGTAG
1 CATGTATCGATACAAAGTAA
*
756686 CATTTATCGATACA
1 CATGTATCGATACA
756700 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (20 bp):
CATGTATCGATACAAAGTAA
Found at i:757425 original size:60 final size:60
Alignment explanation
Indices: 757353--757818 Score: 303
Period size: 60 Copynumber: 7.8 Consensus size: 60
757343 TAAGTCTTTT
* * * ** *
757353 CTCATTTGATTGTACTTGGTCAAATCTTACCCCTCTTGACTATATTTGGACAAGACCTTC
1 CTCATTTGACTATACTTAGTCAAATCTTACCCCTCTTGACTATATTCAGTCAAGACCTTC
* * * * * * * ** *
757413 CTTATTTAATTGTA-TTCAATCAAAT-TT-CACCCTCATTTTACTATATTTAGTCAACTCTTTC
1 CTCATTTGACTATACTT-AGTCAAATCTTAC-CCCTC--TTGACTATATTCAGTCAAGACCTTC
* ** * * *
757474 CTTATTTGACTATACTCGGTCAAATCTTAACCCTCTTGACTATATTCGGTCAAAACCTTC
1 CTCATTTGACTATACTTAGTCAAATCTTACCCCTCTTGACTATATTCAGTCAAGACCTTC
* * * * *
757534 CTCATTTGACTATATTTGGTCAAAT-TT-CACCT-TTG-CTTGATATTCAGTCAAGTCTTTC
1 CTCATTTGACTATACTTAGTCAAATCTTACCCCTCTTGAC-T-ATATTCAGTCAAGACCTTC
* * * * *
757592 CTCATTTAACTATACTCAGTCAAA-CTTTACCCTTCTTGACTGTATTC-GATCAAGACTTTC
1 CTCATTTGACTATACTTAGTCAAATC-TTACCCCTCTTGACTATATTCAG-TCAAGACCTTC
* * * * * *
757652 CTCATTTAACTGT-TTTCAGTCAAATTTTACCCTCACTTGACTGTATTCAGTCAAGA-CTATC
1 CTCATTTGACTATACTT-AGTCAAATCTTACCC-CTCTTGACTATATTCAGTCAAGACCT-TC
* * *
757713 CTCATTTGACTGTACTCAATCAAAT-TGTACCCCTCTTGACTATATTCAGTCAAGA-CTATC
1 CTCATTTGACTATACTTAGTCAAATCT-TACCCCTCTTGACTATATTCAGTCAAGACCT-TC
* * * *
757773 TTTATTTGACTATACTTGGTCAAATCTTA-CCCTGTTCGACTATATT
1 CTCATTTGACTATACTTAGTCAAATCTTACCCCTCTT-GACTATATT
757819 TGTCAAGTCT
Statistics
Matches: 322, Mismatches: 60, Indels: 48
0.75 0.14 0.11
Matches are distributed among these distances:
56 1 0.00
57 4 0.01
58 39 0.12
59 21 0.07
60 160 0.50
61 86 0.27
62 11 0.03
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.41
Consensus pattern (60 bp):
CTCATTTGACTATACTTAGTCAAATCTTACCCCTCTTGACTATATTCAGTCAAGACCTTC
Found at i:757496 original size:30 final size:30
Alignment explanation
Indices: 757447--757558 Score: 100
Period size: 30 Copynumber: 3.7 Consensus size: 30
757437 TTTCACCCTC
* ** *
757447 ATTTTACTATATTTAGTCAACTCTTTCCTT
1 ATTTGACTATATTCGGTCAAATCTTTCCTT
* * *
757477 ATTTGACTATACTCGGTCAAATCTTAACCCT
1 ATTTGACTATATTCGGTCAAATCTT-TCCTT
* * * *
757508 -CTTGACTATATTCGGTCAAAACCTTCCTC
1 ATTTGACTATATTCGGTCAAATCTTTCCTT
*
757537 ATTTGACTATATTTGGTCAAAT
1 ATTTGACTATATTCGGTCAAAT
757559 TTCACCTTTG
Statistics
Matches: 63, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
29 2 0.03
30 58 0.92
31 3 0.05
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (30 bp):
ATTTGACTATATTCGGTCAAATCTTTCCTT
Found at i:757664 original size:30 final size:30
Alignment explanation
Indices: 757509--757783 Score: 151
Period size: 30 Copynumber: 9.2 Consensus size: 30
757499 CTTAACCCTC
* * * *
757509 TTGACTATATTCGGTCAAAACCTTCCTCAT
1 TTGACTGTATTCAGTCAAGACTTTCCTCAT
* **
757539 TTGACTATATTTGGTCAA-A-TTTCAC-C-T
1 TTGACTGTATTCAGTCAAGACTTTC-CTCAT
*
757566 TTG-CTTGATATTCAGTCAAGTCTTTCCTCAT
1 TTGAC-TG-TATTCAGTCAAGACTTTCCTCAT
* * * *
757597 TTAACTATACTCAGTCAA-ACTTTACC-CTT
1 TTGACTGTATTCAGTCAAGACTTT-CCTCAT
757626 CTTGACTGTATTC-GATCAAGACTTTCCTCAT
1 -TTGACTGTATTCAG-TCAAGACTTTCCTCAT
* * * *
757657 TTAACTGTTTTCAGTCAA-ATTTTACCCTCAC
1 TTGACTGTATTCAGTCAAGACTTT--CCTCAT
*
757688 TTGACTGTATTCAGTCAAGACTATCCTCAT
1 TTGACTGTATTCAGTCAAGACTTTCCTCAT
* * *
757718 TTGACTGTACTCAATCAA-A-TTGTACC-CCT
1 TTGACTGTATTCAGTCAAGACTT-T-CCTCAT
* * * *
757747 CTTGACTATATTCAGTCAAGACTATCTTTAT
1 -TTGACTGTATTCAGTCAAGACTTTCCTCAT
757778 TTGACT
1 TTGACT
757784 ATACTTGGTC
Statistics
Matches: 187, Mismatches: 35, Indels: 46
0.70 0.13 0.17
Matches are distributed among these distances:
26 1 0.01
27 5 0.03
28 14 0.07
29 18 0.10
30 108 0.58
31 36 0.19
32 5 0.03
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (30 bp):
TTGACTGTATTCAGTCAAGACTTTCCTCAT
Found at i:757782 original size:239 final size:239
Alignment explanation
Indices: 757344--757797 Score: 556
Period size: 239 Copynumber: 1.9 Consensus size: 239
757334 GTATTTGGTT
* * * * ** *
757344 AAGTCTTTTCTCATTTGATTGTACTTGGTCAAATCTTACCCCTCTTGACTATATTTGGACAAGAC
1 AAGTCTTTCCTCATTTAACTATACTCAGTCAAATCTTACCCCTCTTGACTATATTTCGACAAGAC
* * * * * * *
757409 CTTCCTTATTTAATTGTATTCAATCAAATTTCACCCTCATTTTACTATATTTAGTCAACTCTTTC
66 CTTCCTCATTTAACTGTATTCAATCAAATTTCACCCTCACTTGACTATATTCAGTCAACACTATC
* ** *
757474 CTTATTTGACTATACTCGGTCAAATCTTAACCCTCTTGACTATATTCGGTCAAAACCTTCCTCAT
131 CTCATTTGACTATACTCAATCAAATCTTAACCCTCTTGACTATATTCAGTCAAAACCTTCCTCAT
*
757539 TTGACTATATTTGGTCAAATTTCACCTTTGCTTGATATTCAGTC
196 TTGACTATACTTGGTCAAATTTCACCTTTGCTTGATATTCAGTC
* *
757583 AAGTCTTTCCTCATTTAACTATACTCAGTCAAA-CTTTACCCTTCTTGACTGTA-TTCGATCAAG
1 AAGTCTTTCCTCATTTAACTATACTCAGTCAAATC-TTACCCCTCTTGACTATATTTCGA-CAAG
* * * * * *
757646 ACTTTCCTCATTTAACTGTTTTCAGTCAAATTTTACCCTCACTTGACTGTATTCAGTCAAGACTA
64 ACCTTCCTCATTTAACTGTATTCAATCAAATTTCACCCTCACTTGACTATATTCAGTCAACACTA
* * * *
757711 TCCTCATTTGACTGTACTCAATCAAAT-TGTACCCCTCTTGACTATATTCAGTCAAGA-CTATCT
129 TCCTCATTTGACTATACTCAATCAAATCT-TAACCCTCTTGACTATATTCAGTCAAAACCT-TCC
*
757774 TTATTTGACTATACTTGGTCAAAT
192 TCATTTGACTATACTTGGTCAAAT
757798 CTTACCCTGT
Statistics
Matches: 179, Mismatches: 32, Indels: 8
0.82 0.15 0.04
Matches are distributed among these distances:
238 8 0.04
239 171 0.96
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.41
Consensus pattern (239 bp):
AAGTCTTTCCTCATTTAACTATACTCAGTCAAATCTTACCCCTCTTGACTATATTTCGACAAGAC
CTTCCTCATTTAACTGTATTCAATCAAATTTCACCCTCACTTGACTATATTCAGTCAACACTATC
CTCATTTGACTATACTCAATCAAATCTTAACCCTCTTGACTATATTCAGTCAAAACCTTCCTCAT
TTGACTATACTTGGTCAAATTTCACCTTTGCTTGATATTCAGTC
Found at i:757990 original size:60 final size:60
Alignment explanation
Indices: 757845--757993 Score: 192
Period size: 60 Copynumber: 2.5 Consensus size: 60
757835 TTTTGATTGT
* * *
757845 ATCTTACCCTGCTCGATTGTATTCGATCAACTCTTTCTTCATTTAACTGTACTTAATCAA
1 ATCTTACCCTGCTTGATTGTATTCGGTCAACTCTTTCTTCATTTAACTATACTTAATCAA
* * * * * * *
757905 ATCTTGCCCTGCTTGACTGTATTCGGTCAAGTCTTTCTTTATTTGACTATATTTGATCAA
1 ATCTTACCCTGCTTGATTGTATTCGGTCAACTCTTTCTTCATTTAACTATACTTAATCAA
757965 ATCTTA-CCTCGCTTGATTGTATTCGGTCA
1 ATCTTACCCT-GCTTGATTGTATTCGGTCA
757994 TGCCTTTCCT
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
59 3 0.04
60 73 0.96
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (60 bp):
ATCTTACCCTGCTTGATTGTATTCGGTCAACTCTTTCTTCATTTAACTATACTTAATCAA
Found at i:759299 original size:165 final size:164
Alignment explanation
Indices: 759054--759520 Score: 480
Period size: 165 Copynumber: 2.8 Consensus size: 164
759044 TCAAATTACG
* * *
759054 GAATTTTCTTCTCCGTAATTTTTTTTGGGAGGA-TTTTCATGAGTTTAAAATTTTTAAAATTCAT
1 GAATTTTCTACTCCATAATTTTTTTT-GGAGGATTTTTCTTG-GTTTAAAATTTTTAAAATTCAT
* * *
759118 CAAATATTATTATTTAATTCATATTAACTCAGTTTTCAAAAATTCATTCATTTTCATAGATTTTT
64 CAAATATTAGTATTTAATTCATATTAAATCAGTTTTGAAAAATTCATTCATTTTCAT-GATTTTT
* * * * *
759183 GAATTTTTCCTT-GAAATTTCATTATTTTCGAAAAATA
128 GAATTTTTCCTTAAAAATCTCACT-TTTCCCAAAAATA
* * **
759220 GAATTTTCTACTCTATAATTTTTTTTGGATGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCA
1 GAATTTTCTACTCCATAATTTTTTTTGGAGGATTTTTCTTGGTTTAAAATTTTTAAAATTCATCA
* * * *
759285 AATATTAGTATTTAATTCACATTAAATTAGTTTTGAAAAATTCGTTCACTTTCATGAGTTTTCT-
66 AATATTAGTATTTAATTCATATTAAATCAGTTTTGAAAAATTCATTCATTTTCATGA-TTTT-TG
* * * *
759349 ATTTTTTTCTTAAAAATCTCCCTTTTCCCAAAAATT
129 AATTTTTCCTTAAAAATCTCACTTTTCCCAAAAATA
* * * * * * *
759385 GAGTTTTCTAATCCATAAATTTTTTTGGGGGGCATTTCT-TTGGTTTAAAATTTTGAGAATTCAT
1 GAATTTTCTACTCCAT-AATTTTTTTTGGAGG-ATTTTTCTTGGTTTAAAATTTTTAAAATTCAT
* * *
759449 CTAATATT-GTCATTTAATTCCTATTAAATCAGTTTTTGAAAAA-TCATTTCATTTT-ATGAGTT
64 CAAATATTAGT-ATTTAATTCATATTAAATCAG-TTTTGAAAAATTCA-TTCATTTTCATGATTT
*
759511 TTGAGTTTTT
126 TTGAATTTTT
759521 TTTTTTGTAT
Statistics
Matches: 249, Mismatches: 42, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
164 3 0.01
165 122 0.49
166 102 0.41
167 22 0.09
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.50
Consensus pattern (164 bp):
GAATTTTCTACTCCATAATTTTTTTTGGAGGATTTTTCTTGGTTTAAAATTTTTAAAATTCATCA
AATATTAGTATTTAATTCATATTAAATCAGTTTTGAAAAATTCATTCATTTTCATGATTTTTGAA
TTTTTCCTTAAAAATCTCACTTTTCCCAAAAATA
Found at i:759522 original size:166 final size:162
Alignment explanation
Indices: 758943--759522 Score: 467
Period size: 166 Copynumber: 3.5 Consensus size: 162
758933 TTCAAGCATC
* * * * * * * *
758943 AAAATTCCTCAAATATTATCATTTAAATCCCATTAAATTAGTTTTGAAAAATTCCTTTTATTTTT
1 AAAATTCATCAAATATTGT-ATTTAATTCCTATTAAATCAGTTTTGAAAAATT-CATTCATTTTA
* * * * * ** *
759008 TGAGTTATTTATTTTCTT-TTAGAATTCCTCA-TATTT-TC-AAATTACGGAATTTTCTTCTCCG
64 TGAGTT-TTGATTTTTTTCTTA-AAAT-CTCACTATTTCCCAAAAATA--GAATTTTCTAATCCA
*
759069 TAATTTTTTTTGGGAGGATTT-TCATGAGTTTAAAATTTTT
124 TAA-TTTTTTTGGGAGGATTTCTCTTG-GTTTAAAATTTTT
* * * *
759109 AAAATTCATCAAATATTATTATTTAATTCATATTAACTCAGTTTTCAAAAATTCATTCATTTTCA
1 AAAATTCATCAAATATT-GTATTTAATTCCTATTAAATCAGTTTTGAAAAATTCATTCATTTT-A
* * * * * * * * * *
759174 TAGATTTTTGAATTTTTCCTTGAAATTTCATTATTTTCGAAAAATAGAATTTTCTACTCTATAAT
64 T-GAGTTTTGATTTTTTTCTTAAAATCTCACTATTTCCCAAAAATAGAATTTTCTAATCCATAAT
* * * **
759239 TTTTTTTGGATGATTTTTCTTGGTTTTTAATTTTT
128 TTTTTTGGGAGGATTTCTCTTGGTTTAAAATTTTT
* * *
759274 AAAATTCATCAAATATTAGTATTTAATTCAC-ATTAAATTAGTTTTGAAAAATTCGTTCACTTTC
1 AAAATTCATCAAATATT-GTATTTAATTC-CTATTAAATCAGTTTTGAAAAATTCATTCA-TTTT
* * * *
759338 ATGAGTTTTCTATTTTTTTCTTAAAAATCTCCCT-TTTCCCAAAAATTGAGTTTTCTAATCCATA
63 ATGAGTTTT-GATTTTTTTCTT-AAAATCTCACTATTTCCCAAAAATAGAATTTTCTAATCCAT-
* *
759402 AATTTTTTTGGGGGGCATTTCT-TTGGTTTAAAATTTTG
125 AATTTTTTTGGGAGG-ATTTCTCTTGGTTTAAAATTTTT
* *
759440 AGAATTCATCTAATATTGTCATTTAATTCCTATTAAATCAGTTTTTGAAAAA-TCATTTCATTTT
1 AAAATTCATCAAATATTGT-ATTTAATTCCTATTAAATCAG-TTTTGAAAAATTCA-TTCATTTT
759504 ATGAGTTTTGAGTTTTTTT
63 ATGAGTTTTGA-TTTTTTT
759523 TTTTGTATTT
Statistics
Matches: 331, Mismatches: 64, Indels: 38
0.76 0.15 0.09
Matches are distributed among these distances:
164 6 0.02
165 127 0.38
166 167 0.50
167 26 0.08
168 5 0.02
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.50
Consensus pattern (162 bp):
AAAATTCATCAAATATTGTATTTAATTCCTATTAAATCAGTTTTGAAAAATTCATTCATTTTATG
AGTTTTGATTTTTTTCTTAAAATCTCACTATTTCCCAAAAATAGAATTTTCTAATCCATAATTTT
TTTGGGAGGATTTCTCTTGGTTTAAAATTTTT
Done.