Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold290
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: 778129
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.29
Warning! 94969 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:629722 original size:138 final size:137
Alignment explanation
Indices: 629347--629722 Score: 398
Period size: 138 Copynumber: 2.7 Consensus size: 137
629337 TGTACTTGGT
* * * ** **
629347 ATGTCATAAAGGTTTAACGATTTAAGATCGTAACCTCCAAAGCAATTAGTAGACCTACGCTCTTA
1 ATGTCATAAAGGTTTGACGATTTAAGATCGCAACCTCTAAAGCAGCTAGTAGACCTACGCTCCCA
* * * * * *
629412 GTTGATATTATAAGAGCTCGCAGAGTTAAGCTCGC-AGCTCCGACACAGCTAGCGGACCTATGCT
66 GTTGATATTATAAG-GCTCGCAGAATTAAGCTCACAACCTCCGAAACAGCTAACGGACCTACGCT
** *
629476 CCCAGTTT
130 CCCAACTG
* * *
629484 ATGTCATAAAGGTTTGACGATTTAATATCGCAACCTCTAAAGTAGCTAGCAGACCTACGCTCCCA
1 ATGTCATAAAGGTTTGACGATTTAAGATCGCAACCTCTAAAGCAGCTAGTAGACCTACGCTCCCA
** * * * * * * *
629549 ACTGATGTCATAAAGGTTTG-ACAATATAAGATCACAACCTCC-AAAGTAGCTAACGGACCTACG
66 GTTGATATTAT-AAGGCTCGCAGAAT-TAAGCTCACAACCTCCGAAA-CAGCTAACGGACCTACG
*
629612 TTCCCAACTG
128 CTCCCAACTG
*
629622 ATGTCATAAAGGTTTGACGATTTAAGATCGCAACCTCTAAAGCAGCTAGTAGACCTATGCTCCCA
1 ATGTCATAAAGGTTTGACGATTTAAGATCGCAACCTCTAAAGCAGCTAGTAGACCTACGCTCCCA
* *
629687 GTTGACATTATAAGTGCTCGCAGAATTAATCTCACA
66 GTTGATATTATAAG-GCTCGCAGAATTAAGCTCACA
629723 GATGCAACAT
Statistics
Matches: 190, Mismatches: 43, Indels: 11
0.78 0.18 0.05
Matches are distributed among these distances:
136 3 0.02
137 77 0.41
138 106 0.56
139 4 0.02
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (137 bp):
ATGTCATAAAGGTTTGACGATTTAAGATCGCAACCTCTAAAGCAGCTAGTAGACCTACGCTCCCA
GTTGATATTATAAGGCTCGCAGAATTAAGCTCACAACCTCCGAAACAGCTAACGGACCTACGCTC
CCAACTG
Found at i:630685 original size:19 final size:19
Alignment explanation
Indices: 630661--630733 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
630651 TATCTTCAAA
630661 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
630680 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
630699 GATAGGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
630718 GATATGGAATCTTAGA
1 GATATGCAATCTTAGA
630734 AGATATGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:636105 original size:6 final size:6
Alignment explanation
Indices: 636089--636139 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
636079 TGATGATGGA
* * *
636089 AAAAAG GAAAAT AAAAAG -AAAAG AAAAAAG AAAAAG AAAAAT AAAGAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG AAAAAG AAA-AAG
636138 AA
1 AA
636140 GAGGAAAAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
5 5 0.14
6 22 0.61
7 9 0.25
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:636114 original size:24 final size:23
Alignment explanation
Indices: 636087--636148 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
636077 AATGATGATG
*
636087 GAAAAAAGGAAAATAAAAAGAAAA
1 GAAAAAAGGAAAAGAAAAA-AAAA
* *
636111 GAAAAAAGAAAAAGAAAAATAAA
1 GAAAAAAGGAAAAGAAAAAAAAA
*
636134 GAAGAAGAGGAAAAG
1 GAA-AAAAGGAAAAG
636149 GAGAGGCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 6 0.19
24 26 0.81
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (23 bp):
GAAAAAAGGAAAAGAAAAAAAAA
Found at i:636147 original size:18 final size:17
Alignment explanation
Indices: 636091--636147 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 17
636081 ATGATGGAAA
636091 AAAGGAAAATAAA-AAG
1 AAAGGAAAATAAAGAAG
*
636107 AAAAG-AAA-AAAGAA-
1 AAAGGAAAATAAAGAAG
*
636121 AAAGAAAAATAAAGAAG
1 AAAGGAAAATAAAGAAG
636138 AAGAGGAAAA
1 AA-AGGAAAA
636148 GGAGAGGCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 6 0.19
15 8 0.25
16 10 0.31
17 2 0.06
18 6 0.19
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (17 bp):
AAAGGAAAATAAAGAAG
Found at i:637575 original size:44 final size:44
Alignment explanation
Indices: 637507--637715 Score: 276
Period size: 44 Copynumber: 5.0 Consensus size: 44
637497 CGATGACCCT
637507 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTGTA
1 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTGTA
* *
637551 AGTCTTATCTCCCTGGTCAGCAGTGGAATAGTTTGAAAATTGTA
1 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTGTA
* *
637595 AATCCTATCTCCCTAGTCAGCAGTGGAATA-G--G-----TG-A
1 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTGTA
* *
637630 A-TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTG
1 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTGTA
* *
637673 AGTCCTATCTCCCTGGTTAGCAGTGGAATAGGTTGAAGATTGT
1 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTGT
637716 GAATCTTACT
Statistics
Matches: 146, Mismatches: 9, Indels: 20
0.83 0.05 0.11
Matches are distributed among these distances:
34 27 0.18
35 3 0.02
36 2 0.01
37 1 0.01
41 1 0.01
42 2 0.01
43 1 0.01
44 109 0.75
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (44 bp):
AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTGTA
Found at i:637638 original size:34 final size:34
Alignment explanation
Indices: 637595--637661 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
637585 GAAAATTGTA
637595 AATCCTATCTCCCTAGTCAGCAGTGGAATAGGTG
1 AATCCTATCTCCCTAGTCAGCAGTGGAATAGGTG
*
637629 AATCCTATCTCCCTGGTCAGCAGTGGAATAGGT
1 AATCCTATCTCCCTAGTCAGCAGTGGAATAGGT
637662 TGAAGATTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (34 bp):
AATCCTATCTCCCTAGTCAGCAGTGGAATAGGTG
Found at i:637685 original size:78 final size:78
Alignment explanation
Indices: 637556--637705 Score: 246
Period size: 78 Copynumber: 1.9 Consensus size: 78
637546 TTGTAAGTCT
*
637556 TATCTCCCTGGTCAGCAGTGGAATAGTTTGAAAATTGTAAATCCTATCTCCCTAGTCAGCAGTGG
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTGTAAATCCTATCTCCCTAGTCAGCAGTGG
637621 AATAGGTGAATCC
66 AATAGGTGAATCC
* * * * *
637634 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCCTGGTTAGCAGTGG
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTGTAAATCCTATCTCCCTAGTCAGCAGTGG
637699 AATAGGT
66 AATAGGT
637706 TGAAGATTGT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (78 bp):
TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTGTAAATCCTATCTCCCTAGTCAGCAGTGG
AATAGGTGAATCC
Found at i:638013 original size:167 final size:169
Alignment explanation
Indices: 637714--638106 Score: 435
Period size: 167 Copynumber: 2.3 Consensus size: 169
637704 GTTGAAGATT
* * * * * * * * *
637714 GTGAATCTTACTTTCCTGACGTTATAG-CGGAGTAGATTAAAGCTGAGGGCAGCGAATTTTATCT
1 GTGAATCTTACTTCCCTGACGTTGTAGTC-GAGCAGATTGAAGC-CACGACGGCGAATCTTATCT
* *
637778 CTCTGGCGTTAAGACTTGAAATAGCTGAAGCGGAGCGGATTAAAGCTGTGGGCAGCGAATCTTAT
64 CTCTGGCGTTAAGACTTGAAATAGCTGAAGCGGAGCGGATTAAAGATGTGGGCAGCGAATCCTAT
* *
637843 CTCTTTGGCATTACAAT-GAAATAGATTGAAG-C-CAA-AAC
129 CTCTTTGGCATTACAATCG-AACAGATTAAAGTCGCAACAAC
637881 GGTGAATCTTACTTCCCTGACGTTGTAGTCGAGCAGATTGAAGCCACGACGGCGAATCTTATCTC
1 -GTGAATCTTACTTCCCTGACGTTGTAGTCGAGCAGATTGAAGCCACGACGGCGAATCTTATCTC
* * * * * * *
637946 -CTTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGCGGATTGAAGATGTGGGTAGTGAATCCTAT
65 TC-TGGCGTTAAGACTTGAAATAGCTGAAGCGGAGCGGATTAAAGATGTGGGCAGCGAATCCTAT
* *
638010 CTCTTTGGCATTACAGTCGAGCAGATTAAAGTCGCAACAAC
129 CTCTTTGGCATTACAATCGAACAGATTAAAGTCGCAACAAC
* * * *
638051 --GAATCTTACTTCCCTGACAG-TGTAGTGGAACAGATTGAAGCTACGATGGCGAATCT
1 GTGAATCTTACTTCCCTGAC-GTTGTAGTCGAGCAGATTGAAGCCACGACGGCGAATCT
638107 AGTTTCCCCA
Statistics
Matches: 192, Mismatches: 26, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
166 1 0.01
167 144 0.75
168 40 0.21
169 4 0.02
170 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (169 bp):
GTGAATCTTACTTCCCTGACGTTGTAGTCGAGCAGATTGAAGCCACGACGGCGAATCTTATCTCT
CTGGCGTTAAGACTTGAAATAGCTGAAGCGGAGCGGATTAAAGATGTGGGCAGCGAATCCTATCT
CTTTGGCATTACAATCGAACAGATTAAAGTCGCAACAAC
Found at i:638104 original size:50 final size:50
Alignment explanation
Indices: 638050--638398 Score: 153
Period size: 50 Copynumber: 7.2 Consensus size: 50
638040 GTCGCAACAA
* *
638050 CGAATCTTACTTCCCTGACAGTGTAGTGGAACAGATTGAAGCTACGATGG
1 CGAATCTTACTTCCCTGACAGTGTAGTGGAACAGATTGAAGCTACAACGG
* ** * * * ** * * *
638100 CGAATC-TAGTTTCCCCAACATTGCAATTAAAAAGATTGAAGCTGCAATGG
1 CGAATCTTA-CTTCCCTGACAGTGTAGTGGAACAGATTGAAGCTACAACGG
** * * * *
638150 AAAATTTTACTTCCTTGGCGGTGTAGTGGAACAGATTGAAGCTA-AACGG
1 CGAATCTTACTTCCCTGACAGTGTAGTGGAACAGATTGAAGCTACAACGG
*** ** ** * * ** * * **
638199 CGAATCTCGTTTCCCCAACTTTGCAATTAAAAAGATTAAAGCCGCAAACGG
1 CGAATCTTACTTCCCTGACAGTGTAGTGGAACAGATTGAAGCTAC-AACGG
* * * **
638250 CGAATTTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTATGACGG
1 CGAATCTTACTTCCCTGACAGTGTAGTGGAACAGATTGAAGCTACAACGG
** ** ** *
638300 CGAATCTTGTTTCCCCAACA---T--T-G--CA-ATTGAAGCCGCAATGG
1 CGAATCTTACTTCCCTGACAGTGTAGTGGAACAGATTGAAGCTACAACGG
* ** *
638341 CGAATTTTACTTCCCTGGTAGTGTAGTGGAACAGATTGAAGCTACGACGG
1 CGAATCTTACTTCCCTGACAGTGTAGTGGAACAGATTGAAGCTACAACGG
638391 CGAATCTT
1 CGAATCTT
638399 GTTTCCCCAA
Statistics
Matches: 195, Mismatches: 91, Indels: 26
0.62 0.29 0.08
Matches are distributed among these distances:
41 24 0.12
42 2 0.01
44 2 0.01
45 1 0.01
46 1 0.01
47 2 0.01
49 32 0.16
50 97 0.50
51 34 0.17
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (50 bp):
CGAATCTTACTTCCCTGACAGTGTAGTGGAACAGATTGAAGCTACAACGG
Found at i:638176 original size:100 final size:100
Alignment explanation
Indices: 638050--638431 Score: 514
Period size: 100 Copynumber: 3.9 Consensus size: 100
638040 GTCGCAACAA
* * * *
638050 CGAATCTTACTTCCCTGACAGTGTAGTGGAACAGATTGAAGCTACGATGGCGAATCTAGTTTCCC
1 CGAATTTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCC
*
638115 CAACATTGCAATTAAAAAGATTGAAGCTGCAATGG
66 CAACATTGCAATTAAAAAGATTGAAGCCGCAATGG
** * * * *
638150 AAAATTTTACTTCCTTGGCGGTGTAGTGGAACAGATTGAAGCTA-AACGGCGAATCTCGTTTCCC
1 CGAATTTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCC
* * *
638214 CAACTTTGCAATTAAAAAGATTAAAGCCGCAAACGG
66 CAACATTGCAATTAAAAAGATTGAAGCCGC-AATGG
* *
638250 CGAATTTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTATGACGGCGAATCTTGTTTCCC
1 CGAATTTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCC
638315 CAACATTGC--------A-ATTGAAGCCGCAATGG
66 CAACATTGCAATTAAAAAGATTGAAGCCGCAATGG
*
638341 CGAATTTTACTTCCCTGGTAGTGTAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCC
1 CGAATTTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCC
* *
638406 CAACATTGCAATTTAAAAGACTGAAG
66 CAACATTGCAATTAAAAAGATTGAAG
638432 ATGGCAAGTC
Statistics
Matches: 246, Mismatches: 25, Indels: 22
0.84 0.09 0.08
Matches are distributed among these distances:
91 75 0.30
92 10 0.04
93 1 0.00
99 45 0.18
100 89 0.36
101 26 0.11
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (100 bp):
CGAATTTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCC
CAACATTGCAATTAAAAAGATTGAAGCCGCAATGG
Found at i:638403 original size:91 final size:92
Alignment explanation
Indices: 638237--638418 Score: 321
Period size: 91 Copynumber: 2.0 Consensus size: 92
638227 AAAAAGATTA
* *
638237 AAGCCGCAAACGGCGAATTTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTATGACGGCG
1 AAGCCGCAAACGGCGAATTTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACGACGGCG
638302 AATCTTGTTTCCCCAACATTGCAATTG
66 AATCTTGTTTCCCCAACATTGCAATTG
* *
638329 AAGCCGC-AATGGCGAATTTTACTTCCCTGGTAGTGTAGTGGAACAGATTGAAGCTACGACGGCG
1 AAGCCGCAAACGGCGAATTTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACGACGGCG
638393 AATCTTGTTTCCCCAACATTGCAATT
66 AATCTTGTTTCCCCAACATTGCAATT
638419 TAAAAGACTG
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
91 79 0.92
92 7 0.08
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (92 bp):
AAGCCGCAAACGGCGAATTTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACGACGGCG
AATCTTGTTTCCCCAACATTGCAATTG
Found at i:639066 original size:18 final size:17
Alignment explanation
Indices: 639043--639093 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
639033 CTTCAAGGAT
639043 ATGCAATCTTAGATATG
1 ATGCAATCTTAGATATG
639060 AATGCAATCTTAGAAGATATG
1 -ATGCAATCTT---AGATATG
639081 ATGCAATCTTAGA
1 ATGCAATCTTAGA
639094 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.10
18 10 0.33
20 10 0.33
21 7 0.23
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (17 bp):
ATGCAATCTTAGATATG
Found at i:639086 original size:20 final size:21
Alignment explanation
Indices: 639053--639093 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
639043 ATGCAATCTT
639053 AGATATGAATGCAATCTTAGA
1 AGATATGAATGCAATCTTAGA
639074 AGATATG-ATGCAATCTTAGA
1 AGATATGAATGCAATCTTAGA
639094 NNNNNNNNNN
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (21 bp):
AGATATGAATGCAATCTTAGA
Found at i:639340 original size:23 final size:23
Alignment explanation
Indices: 639296--639340 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
639286 TCTTATTTTG
* *
639296 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
639319 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
639341 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:641506 original size:15 final size:15
Alignment explanation
Indices: 641486--641522 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
641476 TTTTGAAAAT
641486 ATTTTTTATTTTACA
1 ATTTTTTATTTTACA
641501 A-TTTTT-TTTTACA
1 ATTTTTTATTTTACA
641514 ATTTGTTTA
1 ATTT-TTTA
641523 ATCGAACTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.42
14 7 0.37
15 4 0.21
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (15 bp):
ATTTTTTATTTTACA
Found at i:641509 original size:12 final size:14
Alignment explanation
Indices: 641488--641517 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
641478 TTGAAAATAT
641488 TTTTTATTTTACAA
1 TTTTTATTTTACAA
641502 TTTTT-TTTTACAA
1 TTTTTATTTTACAA
641515 TTT
1 TTT
641518 GTTTAATCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTATTTTACAA
Found at i:642489 original size:22 final size:22
Alignment explanation
Indices: 642464--642509 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
642454 GCAGCAAGTG
642464 ATTGAGTTCAATAGTTCTTCAT
1 ATTGAGTTCAATAGTTCTTCAT
642486 ATTGAGTTCAATAGTTCTTCAT
1 ATTGAGTTCAATAGTTCTTCAT
642508 AT
1 AT
642510 AAAATGGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (22 bp):
ATTGAGTTCAATAGTTCTTCAT
Found at i:642665 original size:212 final size:212
Alignment explanation
Indices: 642298--642699 Score: 795
Period size: 212 Copynumber: 1.9 Consensus size: 212
642288 AGTTCCTATA
642298 AAAATGGGAAATGCCCTACCTTTGAGTGCAGTTTGAGCTATGATTTACCTAATTAAAAGGAACCA
1 AAAATGGGAAATGCCCTACCTTTGAGTGCAGTTTGAGCTATGATTTACCTAATTAAAAGGAACCA
642363 ATTAGGTTAATGACGAAACCTAAAAATTGATCATTAATCAAATTTGAGTACCTCTACAGGGTAGA
66 ATTAGGTTAATGACGAAACCTAAAAATTGATCATTAATCAAATTTGAGTACCTCTACAGGGTAGA
642428 CCTCAACAGAAAACTGAAGAGTAACAGCAGCAAGTGATTGAGTTCAATAGTTCTTCATATTGAGT
131 CCTCAACAGAAAACTGAAGAGTAACAGCAGCAAGTGATTGAGTTCAATAGTTCTTCATATTGAGT
642493 TCAATAGTTCTTCATAT
196 TCAATAGTTCTTCATAT
642510 AAAATGGGAAATGCCCTACCTTTGAGTGCAGTTTGAGCTATGATTTACCTAATTAAAAGGAACCA
1 AAAATGGGAAATGCCCTACCTTTGAGTGCAGTTTGAGCTATGATTTACCTAATTAAAAGGAACCA
642575 ATTAGGTTAATGACGAAACCTAAAAATTGATCATTAATCAAATTTGAGTACCTCTACAGGGTAGA
66 ATTAGGTTAATGACGAAACCTAAAAATTGATCATTAATCAAATTTGAGTACCTCTACAGGGTAGA
*
642640 CCTCAACAGAAAACTGAAGAGTAACAGTAGCAAGTGATTGAGTTCAATAGTTCTTCATAT
131 CCTCAACAGAAAACTGAAGAGTAACAGCAGCAAGTGATTGAGTTCAATAGTTCTTCATAT
642700 AAAATTATTG
Statistics
Matches: 189, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
212 189 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (212 bp):
AAAATGGGAAATGCCCTACCTTTGAGTGCAGTTTGAGCTATGATTTACCTAATTAAAAGGAACCA
ATTAGGTTAATGACGAAACCTAAAAATTGATCATTAATCAAATTTGAGTACCTCTACAGGGTAGA
CCTCAACAGAAAACTGAAGAGTAACAGCAGCAAGTGATTGAGTTCAATAGTTCTTCATATTGAGT
TCAATAGTTCTTCATAT
Found at i:649041 original size:16 final size:17
Alignment explanation
Indices: 649020--649057 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
649010 ATAAAAAATA
649020 AAAAT-ATATCATTTTT
1 AAAATAATATCATTTTT
649036 AAAATAAATATCATTTTT
1 AAAAT-AATATCATTTTT
649054 AAAA
1 AAAA
649058 CTTAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.25
18 15 0.75
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATAATATCATTTTT
Found at i:649472 original size:209 final size:210
Alignment explanation
Indices: 649094--649519 Score: 836
Period size: 209 Copynumber: 2.0 Consensus size: 210
649084 CTCTTTAAAA
649094 TTTAAAAAATAAAAATGATTTTTAAAACTTATGTACTTTTAAAAGGTAATGACCAAATTAACAAA
1 TTTAAAAAATAAAAAT-ATTTTTAAAACTTATGTACTTTTAAAAGGTAATGACCAAATTAACAAA
649159 AAACTATAAATGTTAAGAGCTAAAAAAGTTATTTTACCTTTGACACCGTTTAACTCTAATAGCAA
65 AAACTATAAATGTTAAGAGCTAAAAAAGTTATTTTACCTTTGACACCGTTTAACTCTAATAGCAA
649224 AATTAGATGGAGGGACCAAGATTTTTAAATAAAAAAAGTATAGGGACTCAATGTCTCAAAATTCA
130 AATTAGATGGAGGGACCAAGATTTTTAAATAAAAAAAGTATAGGGACTCAATGTCTCAAAATTCA
649289 AGTATAAGGACTAGAT
195 AGTATAAGGACTAGAT
649305 TTTAAAAAATAAAAAT-TTTTTAAAACTTATGTACTTTTAAAAGGTAATGACCAAATTAACAAAA
1 TTTAAAAAATAAAAATATTTTTAAAACTTATGTACTTTTAAAAGGTAATGACCAAATTAACAAAA
649369 AACTATAAATGTTAAGAGCTAAAAAAGTTATTTTACCTTTGACACCGTTTAACTCTAATAGCAAA
66 AACTATAAATGTTAAGAGCTAAAAAAGTTATTTTACCTTTGACACCGTTTAACTCTAATAGCAAA
649434 ATTAGATGGAGGGACCAAGATTTTTAAATAAAAAAAGTATAGGGACTCAATGTCTCAAAATTCAA
131 ATTAGATGGAGGGACCAAGATTTTTAAATAAAAAAAGTATAGGGACTCAATGTCTCAAAATTCAA
649499 GTATAAGGACTAGAT
196 GTATAAGGACTAGAT
649514 TTTAAA
1 TTTAAA
649520 TTTTAAAAGA
Statistics
Matches: 215, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
209 199 0.93
211 16 0.07
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.31
Consensus pattern (210 bp):
TTTAAAAAATAAAAATATTTTTAAAACTTATGTACTTTTAAAAGGTAATGACCAAATTAACAAAA
AACTATAAATGTTAAGAGCTAAAAAAGTTATTTTACCTTTGACACCGTTTAACTCTAATAGCAAA
ATTAGATGGAGGGACCAAGATTTTTAAATAAAAAAAGTATAGGGACTCAATGTCTCAAAATTCAA
GTATAAGGACTAGAT
Found at i:652274 original size:114 final size:112
Alignment explanation
Indices: 652141--653080 Score: 1291
Period size: 113 Copynumber: 8.3 Consensus size: 112
652131 AAAATAAGCA
* * * *
652141 TTAGCGGCGTTTTTATAAAAGCGCCGCAAAAAGCCAAAGACAAACGGCACCGTTTTCTGATTTTT
1 TTAGCGGCGTTTTT-TAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* *
652206 TGGGGTC-TTAGCGGCGTTTTCTGTAAAAGCGCCGCTAATGCTCAAGTCT
65 TGGGGTCTTTAGCGGCG-TTTATGT-AAAGCGCCGCTAATGCTCAGGTCT
* *
652255 TTAGCGGCGTTGTTTTAAAAGCGCCGCAAAAAGTCTAAACCCAACGGCACCGTTTTCTGAG-TTT
1 TTAGCGGCGTT-TTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* * * *
652319 TGGGGTCTTTAGTGGCGTTTATGTAAAGTGTCGCTAATGCTCATGTCT
65 TGGGGTCTTTAGCGGCGTTTATGTAAAGCGCCGCTAATGCTCAGGTCT
* * *
652367 TTAGCGGCGTTTTTTTTAAAGCGCCGCAAAAAAGCCTAAGCTCAACGGCACCGTTTTCTAAGTTT
1 TTAGCGGCG-TTTTTTAAAAGCGCCGC-AAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTT
* * * *
652432 TTGGGGTCTTTCGCGGAGTTTATGTAAAGCGCCACTAATGTTCAGGTCT
64 TTGGGGTCTTTAGCGGCGTTTATGTAAAGCGCCGCTAATGCTCAGGTCT
* * *
652481 TTAGTGGCGTTTTTTTTAATGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
1 TTAGCGGCG-TTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
*
652546 TGGGGGTCTTTAGCGGCGCATTTA--TAAAGCGCCGCTAATGCTGAGGTCT
65 T-GGGGTCTTTAGCGGCG--TTTATGTAAAGCGCCGCTAATGCTCAGGTCT
* * *
652595 TTAGCGGCGTTTTCTCAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCATTTTCTGAGTTTT
1 TTAGCGGCGTTTT-TTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
652660 TGGGGTCTTTA-CTGGCGTTTTATGTAAAGCGCCGCTAATGCTCAGGTCT
65 TGGGGTCTTTAGC-GGCG-TTTATGTAAAGCGCCGCTAATGCTCAGGTCT
*
652709 TTAGCGGCGTTTTTTTAAATGCGCCGC-AAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
1 TTAGCGGCG-TTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* * *
652773 TGGGGTCTTTAGTGGCGTTTTATGTAAAGCGTCGCTAATGCTCAGGTCG
65 TGGGGTCTTTAGCGGCG-TTTATGTAAAGCGCCGCTAATGCTCAGGTCT
* *
652822 TTAGCGGCATTTTTTTAAATGCGCCGC-AAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
1 TTAGCGGC-GTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* *
652886 TGGGGTCTTTAGCGGTGTTTCTGTAAAGCGCCGCTAATGCTCAGGTCT
65 TGGGGTCTTTAGCGGCGTTTATGTAAAGCGCCGCTAATGCTCAGGTCT
*
652934 TTAGCGGCGTTTTTCTAAAAGCGCCGCAAAAAGCCTAAGCCCAATGGCACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTT-TAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* * * * *
652999 GGGGGGTTTTTAGCGGCGTTTCTGAATAAGCGCCTCTAATGCTCAGGTCT
65 -TGGGGTCTTTAGCGGCGTTTATGTA-AAGCGCCGCTAATGCTCAGGTCT
653049 TTAGCGGCGTTTTTTAAAAAGCGCCGCAAAAA
1 TTAGCGGCGTTTTTT-AAAAGCGCCGCAAAAA
653081 CATTTTATCT
Statistics
Matches: 744, Mismatches: 62, Indels: 39
0.88 0.07 0.05
Matches are distributed among these distances:
111 5 0.01
112 96 0.13
113 296 0.40
114 284 0.38
115 59 0.08
116 4 0.01
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (112 bp):
TTAGCGGCGTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTTT
GGGGTCTTTAGCGGCGTTTATGTAAAGCGCCGCTAATGCTCAGGTCT
Found at i:652419 original size:113 final size:114
Alignment explanation
Indices: 652141--653080 Score: 1326
Period size: 114 Copynumber: 8.3 Consensus size: 114
652131 AAAATAAGCA
* * * * *
652141 TTAGCGGCGTTTTTATAAAAGCGCCGCAAAAAGCCAAAGACAAACGGCACCGTTTTCTGATTTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* *
652206 TGGGGTC-TTAGCGGCGTTTTCTGTAAAAGCGCCGCTAATGCTCAAGTCT
66 TGGGGTCTTTAGCGGCGTTTTATGT-AAAGCGCCGCTAATGCTCAGGTCT
* * *
652255 TTAGCGGCGTTGTTTTAAAAGCGCCGCAAAAAGTCTAAACCCAACGGCACCGTTTTCTGAG-TTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* * * *
652319 TGGGGTCTTTAGTGGCG-TTTATGTAAAGTGTCGCTAATGCTCATGTCT
66 TGGGGTCTTTAGCGGCGTTTTATGTAAAGCGCCGCTAATGCTCAGGTCT
* * *
652367 TTAGCGGCGTTTTTTTTAAAGCGCCGCAAAAAAGCCTAAGCTCAACGGCACCGTTTTCTAAGTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGC-AAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTT
* * * *
652432 TTGGGGTCTTTCGCGGAG-TTTATGTAAAGCGCCACTAATGTTCAGGTCT
65 TTGGGGTCTTTAGCGGCGTTTTATGTAAAGCGCCGCTAATGCTCAGGTCT
* * *
652481 TTAGTGGCGTTTTTTTTAATGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* *
652546 TGGGGGTCTTTAGCGGCGCATTTA--TAAAGCGCCGCTAATGCTGAGGTCT
66 T-GGGGTCTTTAGCGGCG-TTTTATGTAAAGCGCCGCTAATGCTCAGGTCT
* * * *
652595 TTAGCGGCGTTTTCTCAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCATTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
652660 TGGGGTCTTTA-CTGGCGTTTTATGTAAAGCGCCGCTAATGCTCAGGTCT
66 TGGGGTCTTTAGC-GGCGTTTTATGTAAAGCGCCGCTAATGCTCAGGTCT
*
652709 TTAGCGGCGTTTTTTTAAATGCGCCGC-AAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* * *
652773 TGGGGTCTTTAGTGGCGTTTTATGTAAAGCGTCGCTAATGCTCAGGTCG
66 TGGGGTCTTTAGCGGCGTTTTATGTAAAGCGCCGCTAATGCTCAGGTCT
* *
652822 TTAGCGGCATTTTTTTAAATGCGCCGC-AAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* *
652886 TGGGGTCTTTAGCGGTG-TTTCTGTAAAGCGCCGCTAATGCTCAGGTCT
66 TGGGGTCTTTAGCGGCGTTTTATGTAAAGCGCCGCTAATGCTCAGGTCT
* *
652934 TTAGCGGCGTTTTTCTAAAAGCGCCGCAAAAAGCCTAAGCCCAATGGCACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* * * * *
652999 GGGGGGTTTTTAGCGGCG-TTTCTGAATAAGCGCCTCTAATGCTCAGGTCT
66 -TGGGGTCTTTAGCGGCGTTTTATGTA-AAGCGCCGCTAATGCTCAGGTCT
*
653049 TTAGCGGCGTTTTTTAAAAAGCGCCGCAAAAA
1 TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAA
653081 CATTTTATCT
Statistics
Matches: 743, Mismatches: 70, Indels: 25
0.89 0.08 0.03
Matches are distributed among these distances:
112 103 0.14
113 291 0.39
114 293 0.39
115 52 0.07
116 4 0.01
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (114 bp):
TTAGCGGCGTTTTTTTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
TGGGGTCTTTAGCGGCGTTTTATGTAAAGCGCCGCTAATGCTCAGGTCT
Found at i:652773 original size:340 final size:337
Alignment explanation
Indices: 652141--653079 Score: 1350
Period size: 340 Copynumber: 2.8 Consensus size: 337
652131 AAAATAAGCA
* * * * * *
652141 TTAGCGGCGTTTTTATAAAAGCGCCGCAAAAAGCCAAAGACAAACGGCACCGTTTTCTGATTTTT
1 TTAGCGGCGTTTTTTTAAATGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
*
652206 TGGGGTC-TTAGCGGCGTTTTCTGTAAAAGCGCCGCTAATGCTCAAGTCTTTAGCGGCGTTGTTT
66 TGGGGTCTTTAGCGGCG-TTTCTGT-AAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTT-TTT
* * *
652270 TAAAAGCGCCGCAAAAAGTCTAAACCCAACGGCACCGTTTTCTGAG-TTTTGGGGTCTTTAGTGG
128 CAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTTTGGGGTCTTTACTGG
* * *
652334 CGTTTATGTAAAGTGTCGCTAATGCTCATGTCTTTAGCGGCGTTTTTTTTAAAGCGCCGCAAAAA
193 CGTTTATGTAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCG-TTTTTTTAAAGCGCCGC--AAA
* *
652399 AGCCTAAGCTCAACGGCACCGTTTTCTAAGTTTTTGGGGTCTTTCGCGGAG-TTTATGTAAAGCG
255 AGCCTAAGCCCAACGGCACCGTTTTCTAAGTTTTTGGGGTCTTTAGCGGAGTTTTATGTAAAGCG
* *
652463 CCACTAATGTTCAGGTCT
320 CCACTAATGCTCAGGTCG
* *
652481 TTAGTGGCGTTTTTTTTAATGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAATGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
* * *
652546 TGGGGGTCTTTAGCGGCGCATT-TATAAAGCGCCGCTAATGCTGAGGTCTTTAGCGGCGTTTTCT
66 T-GGGGTCTTTAGCGGCG-TTTCTGTAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTT-T
*
652610 CAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCATTTTCTGAGTTTTTGGGGTCTTTACTGG
128 CAAAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTTTGGGGTCTTTACTGG
652675 CGTTTTATGTAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTTTAAATGCGCCGCAAAA
193 CG-TTTATGTAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTTTAAA-GCGCCGCAAAA
* * * *
652740 GCCTAAGCCCAACGGCACCGTTTTCTGAGTTTTTGGGGTCTTTAGTGGCGTTTTATGTAAAGCGT
256 GCCTAAGCCCAACGGCACCGTTTTCTAAGTTTTTGGGGTCTTTAGCGGAGTTTTATGTAAAGCGC
*
652805 CGCTAATGCTCAGGTCG
321 CACTAATGCTCAGGTCG
*
652822 TTAGCGGCATTTTTTTAAATGCGCCGC-AAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
1 TTAGCGGCGTTTTTTTAAATGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
*
652886 TGGGGTCTTTAGCGGTGTTTCTGTAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTCTA
66 TGGGGTCTTTAGCGGCGTTTCTGTAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTC-A
* * * *
652951 AAAGCGCCGCAAAAAGCCTAAGCCCAATGGCACCGTTTTCTGAGTTTTGGGGGGTTTTTAGC-GG
130 AAAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTT-TGGGGTCTTTA-CTGG
* * * *
653015 CGTTTCTGAATAAGCGCCTCTAATGCTCAGGTCTTTAGCGGCGTTTTTTAAAAAGCGCCGCAAAA
193 CGTTTATGTA-AAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTT-TAAAGCGCCGCAAAA
653080 ACATTTTATC
Statistics
Matches: 541, Mismatches: 45, Indels: 26
0.88 0.07 0.04
Matches are distributed among these distances:
338 4 0.01
339 107 0.20
340 283 0.52
341 92 0.17
342 55 0.10
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (337 bp):
TTAGCGGCGTTTTTTTAAATGCGCCGCAAAAAGCCTAAGCCCAACGGCACCGTTTTCTGAGTTTT
TGGGGTCTTTAGCGGCGTTTCTGTAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTCAA
AAGCGCCGCAAAAAGCCTAAACCCAACGGCACCGTTTTCTGAGTTTTTGGGGTCTTTACTGGCGT
TTATGTAAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTTTAAAGCGCCGCAAAAGCCTA
AGCCCAACGGCACCGTTTTCTAAGTTTTTGGGGTCTTTAGCGGAGTTTTATGTAAAGCGCCACTA
ATGCTCAGGTCG
Found at i:654867 original size:30 final size:32
Alignment explanation
Indices: 654816--654881 Score: 109
Period size: 30 Copynumber: 2.1 Consensus size: 32
654806 CGTTTTTAGA
*
654816 AAAAACGCCGCTAATATATATACAAATTTTCC
1 AAAAACGCCGCTAATATATATACAAATTTCCC
654848 AAAAACGCCGCT-A-ATATATACAAATTTCCC
1 AAAAACGCCGCTAATATATATACAAATTTCCC
654878 AAAA
1 AAAA
654882 CGGCACCGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 20 0.61
31 1 0.03
32 12 0.36
ACGTcount: A:0.47, C:0.23, G:0.06, T:0.24
Consensus pattern (32 bp):
AAAAACGCCGCTAATATATATACAAATTTCCC
Found at i:657360 original size:43 final size:43
Alignment explanation
Indices: 657312--657395 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
657302 ATTAATATTA
* *
657312 TACATAACTTGATTATTTAATATTATACATAAATTACATAAAT
1 TACATAACTTAATTAATTAATATTATACATAAATTACATAAAT
*
657355 TACATAACTTAATTAATTAATATTATACATATATTACATAA
1 TACATAACTTAATTAATTAATATTATACATAAATTACATAA
657396 CTTGCATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.42
Consensus pattern (43 bp):
TACATAACTTAATTAATTAATATTATACATAAATTACATAAAT
Found at i:657431 original size:65 final size:65
Alignment explanation
Indices: 657346--657746 Score: 750
Period size: 65 Copynumber: 6.2 Consensus size: 65
657336 ATACATAAAT
* * *
657346 TACATAAATTACATAACTTAATTAATTAATATTATACA-TATATTACATAACTTGCATTAATATT
1 TACATAAATTATATGACTTAATTAATTAATATTATACATTA-ATTACATAACTTACATTAATATT
657410 A
65 A
657411 TACATAAATTATATGACTTAATTAATTAATATTATACATTAATTACATAACTTACATTAATATTA
1 TACATAAATTATATGACTTAATTAATTAATATTATACATTAATTACATAACTTACATTAATATTA
657476 TACATAAATTATATGACTTAATTAATTAATATTATACATTAATTACATAACTTACATTAATATTA
1 TACATAAATTATATGACTTAATTAATTAATATTATACATTAATTACATAACTTACATTAATATTA
657541 TACATAAATTATATGACTTAATTAATTAATATTATACATTAATTACATAACTTACATTAATATTA
1 TACATAAATTATATGACTTAATTAATTAATATTATACATTAATTACATAACTTACATTAATATTA
657606 TACATAAATTATATGACTTAATTAATTAATATTATACATTAATTACATAACTTACATTAATATTA
1 TACATAAATTATATGACTTAATTAATTAATATTATACATTAATTACATAACTTACATTAATATTA
*
657671 TACATAAATTACATGACTTAATTAATTAATATTATACATTAATTACATAACTTACATTAATATTA
1 TACATAAATTATATGACTTAATTAATTAATATTATACATTAATTACATAACTTACATTAATATTA
657736 TACATAAATTA
1 TACATAAATTA
657747 NNNNNNNNNN
Statistics
Matches: 331, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
65 329 0.99
66 2 0.01
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.42
Consensus pattern (65 bp):
TACATAAATTATATGACTTAATTAATTAATATTATACATTAATTACATAACTTACATTAATATTA
Found at i:665313 original size:43 final size:43
Alignment explanation
Indices: 665261--665405 Score: 172
Period size: 43 Copynumber: 3.4 Consensus size: 43
665251 CGTTTTTGGG
* *
665261 AAAAGCGCCGCTAAAGGCCATGATCTATAGCGGCGCTTATATA
1 AAAAACGCCGCTAAAGACCATGATCTATAGCGGCGCTTATATA
*
665304 AAAAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTT-TCA-A
1 AAAAACGCCGCTAAAGACCATGATCTATAGCGGCGCTTAT-ATA
* * *
665346 CAAAAACGCCGCTAAAGACACCA--ATCTGTAGCGGCGGTTATATT
1 -AAAAACGCCGCTAAAG--ACCATGATCTATAGCGGCGCTTATATA
665390 AAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAG
665406 CTCTTAGTCT
Statistics
Matches: 89, Mismatches: 7, Indels: 12
0.82 0.06 0.11
Matches are distributed among these distances:
42 2 0.02
43 83 0.93
44 1 0.01
45 3 0.03
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACCATGATCTATAGCGGCGCTTATATA
Found at i:667860 original size:18 final size:17
Alignment explanation
Indices: 667837--667890 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 17
667827 ACTCTGCTCA
667837 ATTTTATTTTCTTATAAT
1 ATTTTATTTTCTT-TAAT
* *
667855 ATTTTAAGTTTCATTAAT
1 ATTTT-ATTTTCTTTAAT
667873 ATTCTTTATTTTCTTTAA
1 A-T-TTTATTTTCTTTAA
667891 AAGATTGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 10 0.34
19 16 0.55
20 3 0.10
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (17 bp):
ATTTTATTTTCTTTAAT
Found at i:668506 original size:2 final size:2
Alignment explanation
Indices: 668499--668539 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
668489 TAATGATGCT
* * *
668499 TA TA TA TA TA TA TA GA TA TA TA GA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
668540 TTGTATAAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:671945 original size:45 final size:45
Alignment explanation
Indices: 671804--671949 Score: 112
Period size: 48 Copynumber: 3.0 Consensus size: 45
671794 ATCATTTCTT
* *
671804 CTATAACTTGACTTCTTATACCCTTCATCTTCATCATCCGATTTC
1 CTATAACTAGATTTCTTATACCCTTCATCTTCATCATCCGATTTC
** * ** * * * *
671849 CTCCCACCTCCATATCCTTCTTCTCTTTCATCTGATCTATCATAACTCGATTTC
1 CT-ATAACTAGAT-TTCTTATAC-CCTTCATCT--TC-ATCAT--C-CGATTTC
671903 CTATAACTAGATTTCTTATACCCTTCATCTTCATCATCCGATTTC
1 CTATAACTAGATTTCTTATACCCTTCATCTTCATCATCCGATTTC
671948 CT
1 CT
671950 CCCACTTCCA
Statistics
Matches: 73, Mismatches: 19, Indels: 18
0.66 0.17 0.16
Matches are distributed among these distances:
45 11 0.15
46 5 0.07
47 6 0.08
48 13 0.18
49 2 0.03
50 2 0.03
51 13 0.18
52 6 0.08
53 6 0.08
54 9 0.12
ACGTcount: A:0.21, C:0.33, G:0.04, T:0.42
Consensus pattern (45 bp):
CTATAACTAGATTTCTTATACCCTTCATCTTCATCATCCGATTTC
Found at i:675105 original size:19 final size:19
Alignment explanation
Indices: 675077--675118 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
675067 AAATAACCTA
*
675077 TAAATAATTTAACTAATTT
1 TAAATAATTTAAATAATTT
* *
675096 TAAATTATTTAAATATTTT
1 TAAATAATTTAAATAATTT
675115 TAAA
1 TAAA
675119 AATAATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAATAATTTAAATAATTT
Found at i:676752 original size:37 final size:37
Alignment explanation
Indices: 676702--676774 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
676692 TTCGCCACGT
676702 GTAATCATAGTGTTTTTTTTTTTTTTGAAAAGGGTTG
1 GTAATCATAGTGTTTTTTTTTTTTTTGAAAAGGGTTG
676739 GTAATCATAGTGTTTTTTTTTTTTTTGAAAAGGGTT
1 GTAATCATAGTGTTTTTTTTTTTTTTGAAAAGGGTT
676775 CGAGGTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.22, C:0.03, G:0.21, T:0.55
Consensus pattern (37 bp):
GTAATCATAGTGTTTTTTTTTTTTTTGAAAAGGGTTG
Found at i:679982 original size:12 final size:12
Alignment explanation
Indices: 679959--679997 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 12
679949 GTTTTAATTC
679959 TAAAACAAATATT
1 TAAAA-AAATATT
679972 TAAAAAAATATATT
1 T-AAAAAA-ATATT
679986 TAAAAAAATATT
1 TAAAAAAATATT
679998 CTTTAATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.21
13 9 0.38
14 10 0.42
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAAAAAATATT
Found at i:680003 original size:15 final size:14
Alignment explanation
Indices: 679967--679996 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
679957 TCTAAAACAA
679967 ATATTTAAAAAAAT
1 ATATTTAAAAAAAT
679981 ATATTTAAAAAAAT
1 ATATTTAAAAAAAT
679995 AT
1 AT
679997 TCTTTAATGT
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATTTAAAAAAAT
Found at i:680512 original size:147 final size:147
Alignment explanation
Indices: 680240--680758 Score: 966
Period size: 147 Copynumber: 3.5 Consensus size: 147
680230 AAACAAATCC
*
680240 AAAATTGGAGATGCGGGGGATCGAACCCCGTGCCTCTCGCATGCAAAGCAAGCGCTCTACCATTT
1 AAAA-TGGAGATGCGGGGGATCGAACCCCGTGCCTCTCGCATGCAAAGCGAGCGCTCTACCATTT
* * *
680305 GATCTACATCCCCATTGTGTGTTAGAATCACTGAAAGAAAACATTTCTTATTAGAAAAAAAAAAG
65 GAGCTACATCCCCATTGTGTGTTAGAATCATTGAAAGAAAAAATTTCTTATTAGAAAAAAAAAAG
680370 TGTTGGCAAAAAAGTCTG
130 TGTTGGCAAAAAAGTCTG
680388 AAAATGGAGATGCGGGGGATCGAACCCCGTGCCTCTCGCATGCAAAGCGAGCGCTCTACCATTTG
1 AAAATGGAGATGCGGGGGATCGAACCCCGTGCCTCTCGCATGCAAAGCGAGCGCTCTACCATTTG
680453 AGCTACATCCCCATTGTGTGTTAGAATCATTGAAAGAAAAAATTTCTTATTAGAAAAAAAAAAGT
66 AGCTACATCCCCATTGTGTGTTAGAATCATTGAAAGAAAAAATTTCTTATTAGAAAAAAAAAAGT
680518 GTTGGCAAAAAAGTCTG
131 GTTGGCAAAAAAGTCTG
680535 AAAATGGAGATGCGGGGGATCGAACCCCGTGCCTCTCGCATGCAAAGCGAGCGCTCTACCATTTG
1 AAAATGGAGATGCGGGGGATCGAACCCCGTGCCTCTCGCATGCAAAGCGAGCGCTCTACCATTTG
* *
680600 AGCTACATCCCCATTGTGTGTTAGTATCATTGAAAGAAAAGATTTCTTATTAGAAAAAAAAAAGT
66 AGCTACATCCCCATTGTGTGTTAGAATCATTGAAAGAAAAAATTTCTTATTAGAAAAAAAAAAGT
680665 GTTGGCAAAAAAGTCTG
131 GTTGGCAAAAAAGTCTG
*
680682 GAAATGGAGATGCGGGGGATCGAACCCCGTGCCTCTCGCATGCAAAGCGAGCGCTCTACCATTTG
1 AAAATGGAGATGCGGGGGATCGAACCCCGTGCCTCTCGCATGCAAAGCGAGCGCTCTACCATTTG
680747 AGCTACATCCCC
66 AGCTACATCCCC
680759 CATTCGGGCA
Statistics
Matches: 364, Mismatches: 7, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
147 360 0.99
148 4 0.01
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (147 bp):
AAAATGGAGATGCGGGGGATCGAACCCCGTGCCTCTCGCATGCAAAGCGAGCGCTCTACCATTTG
AGCTACATCCCCATTGTGTGTTAGAATCATTGAAAGAAAAAATTTCTTATTAGAAAAAAAAAAGT
GTTGGCAAAAAAGTCTG
Found at i:689345 original size:6 final size:7
Alignment explanation
Indices: 689326--689350 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
689316 TTTTAAATCA
689326 TATTTTT
1 TATTTTT
689333 TATTTTT
1 TATTTTT
689340 TATTTTT
1 TATTTTT
689347 TATT
1 TATT
689351 ATATGTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TATTTTT
Found at i:689963 original size:21 final size:20
Alignment explanation
Indices: 689934--690006 Score: 53
Period size: 21 Copynumber: 3.6 Consensus size: 20
689924 AAAAGTATAC
*
689934 AATTTTACAAATTCGTAAGAA
1 AATTATACAAATTCGTAA-AA
*
689955 AATTATACAAAAT-GTAAAGA
1 AATTATACAAATTCGTAAA-A
* *
689975 AA-GATA-AATTTCGTAAAAA
1 AATTATACAAATTCGT-AAAA
*
689994 AATTATAAAAATT
1 AATTATACAAATT
690007 ATCATACCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
18 3 0.08
19 9 0.22
20 13 0.32
21 15 0.38
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.30
Consensus pattern (20 bp):
AATTATACAAATTCGTAAAA
Found at i:690246 original size:18 final size:19
Alignment explanation
Indices: 690225--690265 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
690215 TTAATAATTT
690225 TTTAATA-TTTTAT-TAAAA
1 TTTAATACTTTT-TCTAAAA
690243 TTTAATACTTTTTCTAAAA
1 TTTAATACTTTTTCTAAAA
690262 TTTA
1 TTTA
690266 TTTTTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAATACTTTTTCTAAAA
Found at i:690284 original size:13 final size:13
Alignment explanation
Indices: 690251--690293 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 13
690241 AATTTAATAC
690251 TTTTTCTAAAATTT
1 TTTTTCT-AAATTT
*
690265 ATTTTTTTATAATTT
1 -TTTTTCTA-AATTT
690280 TTTTTCTAAATTT
1 TTTTTCTAAATTT
690293 T
1 T
690294 ATTAAGAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 6 0.24
14 8 0.32
15 11 0.44
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTCTAAATTT
Found at i:698765 original size:46 final size:45
Alignment explanation
Indices: 698677--698768 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 45
698667 GTGTGAGCAG
* **
698677 TTTATATGCACCGTTGAGTGGTTTACCCATACCATTTGAGCAACT
1 TTTATATGCACCGTTGAGTGGTTTACCCACACCAACTGAGCAACT
* *
698722 TTTATCTGCACCGTTTGAGTGGTTTATCCACACCACACT-AGCAACT
1 TTTATATGCACCG-TTGAGTGGTTTACCCACACCA-ACTGAGCAACT
698768 T
1 T
698769 CAATTTGCGA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
45 12 0.30
46 27 0.68
47 1 0.03
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (45 bp):
TTTATATGCACCGTTGAGTGGTTTACCCACACCAACTGAGCAACT
Found at i:704600 original size:15 final size:16
Alignment explanation
Indices: 704575--704604 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
704565 AATCACTTAA
704575 TTAACTTAATTAAACT
1 TTAACTTAATTAAACT
704591 TTAA-TTAATTAAAC
1 TTAACTTAATTAAAC
704605 CATAATCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAACTTAATTAAACT
Found at i:712619 original size:23 final size:22
Alignment explanation
Indices: 712576--712633 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
712566 AAAAGGTATC
* *
712576 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
712597 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
712620 TGCATATCATATCT
1 TACAAATCATATCT
712634 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:712636 original size:19 final size:19
Alignment explanation
Indices: 712612--712667 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
712602 AATCATATCT
712612 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
712631 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
712650 TCTAAGATTACATATCAT
1 TCTAAGATTGCATATCAT
712668 TGAAGATTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:716015 original size:18 final size:18
Alignment explanation
Indices: 715962--716015 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
715952 ATTCACCTAA
* *
715962 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAATT
*
715981 ATCCAACCCAACCCAATT
1 ACCCAACCCAACCCAATT
715999 ACCCAACCCAACCCAAT
1 ACCCAACCCAACCCAAT
716016 CATAAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 26 0.84
19 5 0.16
ACGTcount: A:0.41, C:0.46, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAATT
Found at i:718712 original size:19 final size:20
Alignment explanation
Indices: 718688--718728 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
718678 ATTTAATGGT
*
718688 TATATT-TAAATATAGTTTA
1 TATATTCTAAATAAAGTTTA
*
718707 TATATTCTAATTAAAGTTTA
1 TATATTCTAAATAAAGTTTA
718727 TA
1 TA
718729 AATAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (20 bp):
TATATTCTAAATAAAGTTTA
Found at i:728630 original size:20 final size:21
Alignment explanation
Indices: 728607--728653 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
728597 TTTCACATCA
*
728607 ATTTAATAT-TAAAGAATAAT
1 ATTTAATATCAAAAGAATAAT
**
728627 ATTTTCTATCAAAAGAATAAT
1 ATTTAATATCAAAAGAATAAT
728648 ATTTAA
1 ATTTAA
728654 ATAATATTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (21 bp):
ATTTAATATCAAAAGAATAAT
Found at i:730050 original size:16 final size:15
Alignment explanation
Indices: 730023--730052 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
730013 TATTAATGAC
730023 AAACTTATATATAAT
1 AAACTTATATATAAT
730038 AAACTTGATATATAA
1 AAACTT-ATATATAA
730053 CTTTACAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (15 bp):
AAACTTATATATAAT
Found at i:730054 original size:56 final size:56
Alignment explanation
Indices: 729976--730087 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
729966 AATAACTTGT
*
729976 TATAATAAACTTGATATATAACTTTACAACATAGAATTATTAATGACAAACTTATA
1 TATAATAAACTTGATATATAACTTTACAACATAGAATTAATAATGACAAACTTATA
730032 TATAATAAACTTGATATATAACTTTACAACATAGAATTAATAATGACAAACTTATA
1 TATAATAAACTTGATATATAACTTTACAACATAGAATTAATAATGACAAACTTATA
730088 AGGTGTATTC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (56 bp):
TATAATAAACTTGATATATAACTTTACAACATAGAATTAATAATGACAAACTTATA
Found at i:730836 original size:13 final size:13
Alignment explanation
Indices: 730818--730846 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
730808 TCCCAGATGA
730818 ATCACAATGACAG
1 ATCACAATGACAG
730831 ATCACAATGACAG
1 ATCACAATGACAG
730844 ATC
1 ATC
730847 CTTCAATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.24, G:0.14, T:0.17
Consensus pattern (13 bp):
ATCACAATGACAG
Found at i:731037 original size:21 final size:23
Alignment explanation
Indices: 731013--731066 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
731003 TCTCAGCAAT
731013 ATTTATTACAGATC-TAATAGA-
1 ATTTATTACAGATCTTAATAGAC
* *
731034 ATTTATT-CATATCTTACTAGAC
1 ATTTATTACAGATCTTAATAGAC
*
731056 ATTTTTTACAG
1 ATTTATTACAG
731067 TTCACGCCAC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 5 0.19
21 13 0.50
22 6 0.23
23 2 0.08
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.44
Consensus pattern (23 bp):
ATTTATTACAGATCTTAATAGAC
Found at i:765143 original size:25 final size:25
Alignment explanation
Indices: 765091--765153 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
765081 ACCTTAGTTC
** * *
765091 GCTCTCTAATTATTAGCATGTTAGT
1 GCTCTCTAATTATTAGCACATCAAT
*
765116 GCTCTCTGATTATTAGCACATCAAT
1 GCTCTCTAATTATTAGCACATCAAT
*
765141 GCTCTCTATTTAT
1 GCTCTCTAATTAT
765154 CCGCTTTGGC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.43
Consensus pattern (25 bp):
GCTCTCTAATTATTAGCACATCAAT
Found at i:765212 original size:23 final size:23
Alignment explanation
Indices: 765150--765220 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
765140 TGCTCTCTAT
** * *
765150 TTATCCGCTTTGGCGGTGTTTTA
1 TTATCCGCTTCAGTGGTGTTTTG
765173 TTATCCGCTTCAGTGGTGTTTTG
1 TTATCCGCTTCAGTGGTGTTTTG
* *
765196 TTATCTGCTTC-GATGGTGTTCTG
1 TTATCCGCTTCAG-TGGTGTTTTG
765219 TT
1 TT
765221 CTATTCTGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 1 0.02
23 40 0.98
ACGTcount: A:0.08, C:0.17, G:0.25, T:0.49
Consensus pattern (23 bp):
TTATCCGCTTCAGTGGTGTTTTG
Found at i:767564 original size:7 final size:7
Alignment explanation
Indices: 767552--767583 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
767542 ATTAATTTTA
767552 ATTATTT
1 ATTATTT
767559 ATTATTT
1 ATTATTT
767566 ATTATTT
1 ATTATTT
*
767573 ATTATTG
1 ATTATTT
767580 ATTA
1 ATTA
767584 ATAGTATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (7 bp):
ATTATTT
Found at i:770764 original size:64 final size:63
Alignment explanation
Indices: 770648--770826 Score: 231
Period size: 64 Copynumber: 2.8 Consensus size: 63
770638 AAACAAACAT
*
770648 TCGAACCACATATGTA-T-AATTTACA-ACATTAAAATTCAGCTCAAAGAA-TTTGTAACCTATA
1 TCGAACCACATATGTATTAAAATT-CATACATT-AAATTCAGCTC-AAGAACTTTGTAACCTATA
770709 C
63 C
*
770710 TCGAACCACATATGTATGTAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTATAT
1 TCGAACCACATATGTAT-TAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTATAC
* * * *
770774 TTGAACCACATATGTATATAAAATTCATACCTTAAATGCAACTCAAGAACTTT
1 TCGAACCACATATGTAT-TAAAATTCATACATTAAATTCAGCTCAAGAACTTT
770827 AAATATATAT
Statistics
Matches: 105, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
62 16 0.15
63 5 0.05
64 75 0.71
65 9 0.09
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (63 bp):
TCGAACCACATATGTATTAAAATTCATACATTAAATTCAGCTCAAGAACTTTGTAACCTATAC
Found at i:771489 original size:122 final size:122
Alignment explanation
Indices: 771261--771504 Score: 355
Period size: 122 Copynumber: 2.0 Consensus size: 122
771251 AGTCGACTAC
*
771261 TCGACTACTTTTGACTTCCCCCGATCCAACTCCGTTTTCTTCGTTTCTCGATCTAAACATATTAA
1 TCGACTACTTTCGACTTCCCCCGATCCAACTCCGTTTTCTTCGTTTCTCGATCTAAACATATTAA
* * *
771326 AAATTAACTCTTTTATTCAATAATTCATTTAGTTTAGTCCAAAAACACACAAATGGG
66 AAATTAACTCTTTTATTCAATAATTCATTCAATTTAATCCAAAAACACACAAATGGG
** * * *
771383 TCGACTACTTTCGTTTTCCCCCGATCCAATTCCGTTTTCTTCGTTTCTTGATCTAAACATATTCA
1 TCGACTACTTTCGACTTCCCCCGATCCAACTCCGTTTTCTTCGTTTCTCGATCTAAACATATTAA
* * * *
771448 AATTTAGC-CTTTTTATTCATTAATTCATTCAATTTAATCCAAAAACACATAAATGGG
66 AAATTAACTC-TTTTATTCAATAATTCATTCAATTTAATCCAAAAACACACAAATGGG
771505 AAAATTACCA
Statistics
Matches: 108, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
121 1 0.01
122 107 0.99
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (122 bp):
TCGACTACTTTCGACTTCCCCCGATCCAACTCCGTTTTCTTCGTTTCTCGATCTAAACATATTAA
AAATTAACTCTTTTATTCAATAATTCATTCAATTTAATCCAAAAACACACAAATGGG
Found at i:772145 original size:13 final size:13
Alignment explanation
Indices: 772127--772151 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
772117 ACAAACGATA
772127 AAATTTTCACACG
1 AAATTTTCACACG
772140 AAATTTTCACAC
1 AAATTTTCACAC
772152 ATATAAATTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:776115 original size:7 final size:7
Alignment explanation
Indices: 776105--776136 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
776095 CAACCTTTTC
776105 ATTTTAA
1 ATTTTAA
776112 ATTTTAA
1 ATTTTAA
776119 ATTTTAA
1 ATTTTAA
776126 ATTTTAA
1 ATTTTAA
776133 ATTT
1 ATTT
776137 GTTACAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTTTAA
Found at i:777622 original size:40 final size:38
Alignment explanation
Indices: 777527--777662 Score: 139
Period size: 39 Copynumber: 3.5 Consensus size: 38
777517 AGCGATTGGA
* *
777527 CAAAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTTT
1 CAAAAAACGCCGCTAAAAAT-AAGCATTAGCGGCGCTTT
* ** *
777566 TAAAAAACGCCGCTAAAGGTAGCGCATTAGCGGCGCTTAT
1 CAAAAAACGCCGCTAAAAATA-AGCATTAGCGGCGCTT-T
* *
777606 CCAAAAACGCCGCTAAAAATAAGCATTAGCGGCGTTTT
1 CAAAAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTT
* *
777644 CTGAAAAGCGCCG-TAAAAA
1 C-AAAAAACGCCGCTAAAAA
777663 GCCTAAGCCA
Statistics
Matches: 80, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
38 8 0.10
39 54 0.68
40 18 0.22
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.18
Consensus pattern (38 bp):
CAAAAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTT
Found at i:777756 original size:41 final size:41
Alignment explanation
Indices: 777699--777896 Score: 236
Period size: 41 Copynumber: 4.8 Consensus size: 41
777689 GAGTTTTTGG
* *
777699 GGCCTTTAGCGGCGTTTTTGAATAAACGCCGCTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCT
*
777740 GGCCTTTAGCGGCGTTTTTG-AGTAAGCGCCGCTAATGTTCT
1 GGCCTTTAGCGGCGTTTTTGAAG-AAGCGCCGCTAATGCTCT
* * *
777781 GTCTTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
1 GGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCT
** * * * * * *
777822 GATCTTTAGCGGCGTTTTTAAAGAAGCGTCGGTATTACTGT
1 GGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCT
* *
777863 GGCCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTA
1 GGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTA
777897 GTAATAATAA
Statistics
Matches: 133, Mismatches: 22, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
40 1 0.01
41 130 0.98
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (41 bp):
GGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCT
Done.