Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold43
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: 2559314
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 13088 characters in sequence are not A, C, G, or T
File 5 of 19
Found at i:553031 original size:24 final size:24
Alignment explanation
Indices: 552959--553032 Score: 60
Period size: 25 Copynumber: 3.0 Consensus size: 24
552949 ACCTAATGAT
*
552959 ATTAATTAAAATAATATTT-TAAAA
1 ATTAATTAAAATTATATTTAT-AAA
* * * *
552983 AATAATGTTAATTTATGTTTAATAAA
1 ATTAAT-TAAAATTATATTT-ATAAA
*
553009 ATTAATTAAAGTTATATTTATAAA
1 ATTAATTAAAATTATATTTATAAA
553033 GAAAATATAT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
24 10 0.26
25 19 0.50
26 8 0.21
27 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (24 bp):
ATTAATTAAAATTATATTTATAAA
Found at i:553232 original size:15 final size:15
Alignment explanation
Indices: 553192--553236 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
553182 AATTAATTAA
553192 TTAATTACATATTATT
1 TTAATTA-ATATTATT
*
553208 TTCA-TAATATTATT
1 TTAATTAATATTATT
553222 TTAATTAATATTATT
1 TTAATTAATATTATT
553237 AGATACTCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 11 0.42
15 12 0.46
16 3 0.12
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATTAATATTATT
Found at i:553403 original size:21 final size:22
Alignment explanation
Indices: 553370--553414 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
553360 ATAATTAATG
**
553370 TTTTTAATTTAATAA-AAATAA
1 TTTTTAAAATAATAATAAATAA
553391 TTTTTAAAATAATAATTAAATAA
1 TTTTTAAAATAATAA-TAAATAA
553414 T
1 T
553415 GTGTATAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
23 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTTTAAAATAATAATAAATAA
Found at i:555718 original size:2 final size:2
Alignment explanation
Indices: 555711--555742 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
555701 TTCTTTCTTG
555711 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
555743 TGGAAACTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:557911 original size:2 final size:2
Alignment explanation
Indices: 557904--557936 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
557894 TTAGTCCTTA
557904 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
557937 AATGTATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:558145 original size:2 final size:2
Alignment explanation
Indices: 558138--558170 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
558128 ATTCGAAGTA
558138 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
558171 GACACACGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:559516 original size:2 final size:2
Alignment explanation
Indices: 559509--559540 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
559499 TTTCTTCAAC
559509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
559541 CAATCAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:559593 original size:2 final size:2
Alignment explanation
Indices: 559588--559615 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
559578 ATATATATAT
559588 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
559616 GGAAGGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:560058 original size:2 final size:2
Alignment explanation
Indices: 560051--560095 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
560041 ATTGAACATC
* * *
560051 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
560093 TA T
1 TA T
560096 GCAGCCGAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
TA
Found at i:560301 original size:2 final size:2
Alignment explanation
Indices: 560289--560321 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
560279 TCATGCCCAA
560289 TC TC ATC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC -TC TC TC TC TC TC TC TC TC TC TC TC TC TC
560322 ACATAAAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:579512 original size:208 final size:206
Alignment explanation
Indices: 578977--579759 Score: 1100
Period size: 208 Copynumber: 3.8 Consensus size: 206
578967 ATAGATAAAT
* * *
578977 AAATAAAGACATAGCTTAAAACTCCGTTTGGAAGCTGAGAAAACGAATGAAAATAAACGGAAAAC
1 AAATAAAGACACAGCTTAAAACTCCATTTGGAAGCTGAGAAAACGAAGGAAAATAAACGGAAAAC
* *
579042 CTCTCAGCG--TA---T-ATGTTCCATTCTA-TTTCTCGCCAACCAAACAGAACAATCAAAAAGA
66 CTCTCAACGTATAGGTTCATGTTCCATTCCATTTTCTCGCCAACCAAACAGAACAATCAAAAAGA
*
579100 TCAATCAGAAGTTAATCAATAAAAGAAAGTTGAAATTTCTCACTATGAATCCGCTATAGAACAAC
131 TAAATCAGAAGTTAATCAATAAAAGAAAGTTGAAATTTCTCACTATGAATCCGCTATAGAACAAC
*
579165 ATTTTCACAAA
196 ATTTTCAAAAA
* * * * * *
579176 AAATAAAGAGACGGCTCAAAACTCCATTAGGAAGTTGAGAAAACGAAGGAAAATAAATGGAAAAC
1 AAATAAAGACACAGCTTAAAACTCCATTTGGAAGCTGAGAAAACGAAGGAAAATAAACGGAAAAC
* * * *
579241 TTCTCAATGTATAGGTTCATGTTCCATTCCATTTTCTCGTCAACCAAACAGAACGATCAAAAAGA
66 CTCTCAACGTATAGGTTCATGTTCCATTCCATTTTCTCGCCAACCAAACAGAACAATCAAAAAGA
*
579306 TAAATCAGAAGTTAATCAGTAAAAGAAAGTTGAAATTTCTCACTATGAATCCGCTATAGAACAAC
131 TAAATCAGAAGTTAATCAATAAAAGAAAGTTGAAATTTCTCACTATGAATCCGCTATAGAACAAC
579371 ATTTTTCAGAAAA
196 A-TTTTCA-AAAA
* * *
579384 AAATAAAGACACAGCTTAACACTCCATCTGGAAGCTGAGAAAACGAAGGAAAAATAAACGGGAAA
1 AAATAAAGACACAGCTTAAAACTCCATTTGGAAGCTGAGAAAACGAAGG-AAAATAAACGGAAAA
* *
579449 CCTCTAAACGTATCGGTTCATGTTCCATTCC-TTTTCTCGCCAACCAAACAGAACAATCAAAAAG
65 CCTCTCAACGTATAGGTTCATGTTCCATTCCATTTTCTCGCCAACCAAACAGAACAATCAAAAAG
* * *
579513 ATCAATCAGAAGTTAATCAATAAAAGGAAGTTGAAATTTCTCACTATGAATCCACTATAGAACAA
130 ATAAATCAGAAGTTAATCAATAAAAGAAAGTTGAAATTTCTCACTATGAATCCGCTATAGAACAA
579578 CATTTTCACAAAAA
195 CATTTT--CAAAAA
579592 AAATAAAAGACACAGCTTAAAACTCCATTTGGAAGCTGAGAAAACGAAGGAAAATAAACGGAAAA
1 AAAT-AAAGACACAGCTTAAAACTCCATTTGGAAGCTGAGAAAACGAAGGAAAATAAACGGAAAA
* * * * *
579657 CCTCTCAAC--ATAGATTCACGTTCCATTCCTTTTTCTCGCCAACCAAACAAAACAATCAAAATG
65 CCTCTCAACGTATAGGTTCATGTTCCATTCCATTTTCTCGCCAACCAAACAGAACAATCAAAAAG
* *
579720 ATCAATCATATCAGAAGTTACTCATTAAAAGAAAGTTGAA
130 AT--A--A-ATCAGAAGTTAATCAATAAAAGAAAGTTGAA
579760 TCTTACGTTT
Statistics
Matches: 515, Mismatches: 50, Indels: 25
0.87 0.08 0.04
Matches are distributed among these distances:
199 62 0.12
201 2 0.00
204 1 0.00
205 12 0.02
206 112 0.22
207 43 0.08
208 169 0.33
209 85 0.17
211 1 0.00
212 28 0.05
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (206 bp):
AAATAAAGACACAGCTTAAAACTCCATTTGGAAGCTGAGAAAACGAAGGAAAATAAACGGAAAAC
CTCTCAACGTATAGGTTCATGTTCCATTCCATTTTCTCGCCAACCAAACAGAACAATCAAAAAGA
TAAATCAGAAGTTAATCAATAAAAGAAAGTTGAAATTTCTCACTATGAATCCGCTATAGAACAAC
ATTTTCAAAAA
Found at i:580431 original size:20 final size:19
Alignment explanation
Indices: 580408--580446 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
580398 ATTTTGGGTT
*
580408 ATTTGATATATTTAAATAAA
1 ATTTGAAATATTT-AATAAA
*
580428 ATTTTAAATATTTAATAAA
1 ATTTGAAATATTTAATAAA
580447 TATTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTTGAAATATTTAATAAA
Found at i:581739 original size:19 final size:19
Alignment explanation
Indices: 581706--581744 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
581696 ATAAAGTAAA
581706 ATTTTTAAAAGTTGATAATT
1 ATTTTTAAAAGTTGA-AATT
581726 ATTTTTAAAA-TTGAAATT
1 ATTTTTAAAAGTTGAAATT
581744 A
1 A
581745 AATGGACCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 4 0.21
20 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (19 bp):
ATTTTTAAAAGTTGAAATT
Found at i:583455 original size:19 final size:19
Alignment explanation
Indices: 583413--583455 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
583403 ATCAATTAAT
**
583413 TTAAATTATTTATTAAAAA
1 TTAAATTAAATATTAAAAA
* *
583432 ATAAATTAAATATTAAATA
1 TTAAATTAAATATTAAAAA
583451 TTAAA
1 TTAAA
583456 AAATAATTAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAATTAAATATTAAAAA
Found at i:583467 original size:29 final size:28
Alignment explanation
Indices: 583406--583471 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 28
583396 TGATTTAATC
* **
583406 AATTAATTTAAATTATTTATTAAAAAAT
1 AATTAATTAAAATTAAATATTAAAAAAT
583434 -A--AATTAAATATTAAATATTAAAAAAT
1 AATTAATTAAA-ATTAAATATTAAAAAAT
583460 AATTAATTAAAA
1 AATTAATTAAAA
583472 AATCAGATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
25 6 0.19
26 15 0.48
27 2 0.06
28 1 0.03
29 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
AATTAATTAAAATTAAATATTAAAAAAT
Found at i:583852 original size:122 final size:124
Alignment explanation
Indices: 583695--583938 Score: 348
Period size: 122 Copynumber: 2.0 Consensus size: 124
583685 ATTACCAATT
* * * * * * *
583695 TTTTACCTATTTAAATAAGTATTGAATATAGTAATTGATTAAAATATGAATTTAGTTTATTAGTA
1 TTTTACCTATTTAAATAAATATTAAATATAATAATTAATTAAAATATGAATTTAATTTAATAGCA
* * * **
583760 TAATCTTTAATATATAACTAAATAGTTAAAAATTTAAATCTTGTTACTTTTAAAAATAA
66 TAACCTTTAACATATAACTAAATAATTAAAAATTTAAATCTCATTACTTTTAAAAATAA
*
583819 TTTTA-CTA-TTAAATAAATATTAAATATAATAATTAATTAAAATATGTATTTAATTTAATAGCA
1 TTTTACCTATTTAAATAAATATTAAATATAATAATTAATTAAAATATGAATTTAATTTAATAGCA
*
583882 TAACCTTTAACATATAACTAAATAATTAAAGATTTAAATCTCATTACTTTTAAAAAT
66 TAACCTTTAACATATAACTAAATAATTAAAAATTTAAATCTCATTACTTTTAAAAAT
583939 TTTAATTTTT
Statistics
Matches: 106, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
122 98 0.92
123 3 0.03
124 5 0.05
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (124 bp):
TTTTACCTATTTAAATAAATATTAAATATAATAATTAATTAAAATATGAATTTAATTTAATAGCA
TAACCTTTAACATATAACTAAATAATTAAAAATTTAAATCTCATTACTTTTAAAAATAA
Found at i:587914 original size:14 final size:15
Alignment explanation
Indices: 587875--587931 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
587865 TGCATATCAA
*
587875 AAATATAAAATTTAGT
1 AAATATAAAATATA-T
587891 AAAT-TAAAATATAT
1 AAATATAAAATATAT
*
587905 AAATAT-AAATAAAT
1 AAATATAAAATATAT
*
587919 AATTAT-AAATATA
1 AAATATAAAATATA
587932 ATTATCGAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 23 0.64
15 9 0.25
16 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
AAATATAAAATATAT
Found at i:588122 original size:17 final size:18
Alignment explanation
Indices: 588098--588139 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
588088 TATTAAGTTT
588098 AAAA-AAAAATTATA-AA
1 AAAATAAAAATTATATAA
* *
588114 AAATTAAAATTTATATAA
1 AAAATAAAAATTATATAA
588132 AAAATAAA
1 AAAATAAA
588140 TCAGACTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 9 0.43
18 9 0.43
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATAAAAATTATATAA
Found at i:588216 original size:20 final size:19
Alignment explanation
Indices: 588191--588240 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
588181 CCCAAATAAG
588191 ATATTTTATTATAAAAATTT
1 ATATTTTATTATAAAAA-TT
** *
588211 ATATTTTAAAATAATAATT
1 ATATTTTATTATAAAAATT
588230 ATAATTTTATT
1 AT-ATTTTATT
588241 TTATTAATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTTTATTATAAAAATT
Found at i:588748 original size:19 final size:20
Alignment explanation
Indices: 588706--588748 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
588696 ATATCATATT
* *
588706 TTAAAAACTTTTTAAATACA
1 TTAAAAACTTTTTAAAAAAA
588726 -TAAAAA-TTTTTAAAAAAA
1 TTAAAAACTTTTTAAAAAAA
588744 TTAAA
1 TTAAA
588749 TATATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAAAACTTTTTAAAAAAA
Found at i:589886 original size:22 final size:21
Alignment explanation
Indices: 589848--589891 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
589838 AAATTTTTAT
*
589848 TTTTATATTATTATTAATATA
1 TTTTATATTATTATTAAAATA
589869 TTTTATAATTAATT-TTAAAATA
1 TTTTAT-ATT-ATTATTAAAATA
589891 T
1 T
589892 ATATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 11 0.55
23 3 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTATATTATTATTAAAATA
Found at i:592600 original size:23 final size:23
Alignment explanation
Indices: 592551--592601 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
592541 AATATTTTTT
* * *
592551 ATTTTTTAAAACAAATAAAGATC
1 ATTTTTTAAAACAAAAAAACATA
592574 ATTTTTTAAAA-AAAAAAACATA
1 ATTTTTTAAAACAAAAAAACATA
*
592596 AATTTT
1 ATTTTT
592602 GAACTTTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (23 bp):
ATTTTTTAAAACAAAAAAACATA
Found at i:593157 original size:17 final size:17
Alignment explanation
Indices: 593135--593170 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
593125 CATTTCATAT
* *
593135 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTCTTTCTTC
593152 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
593169 TT
1 TT
593171 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:594462 original size:32 final size:32
Alignment explanation
Indices: 594413--594854 Score: 699
Period size: 32 Copynumber: 13.8 Consensus size: 32
594403 AAAATGGTGA
* * *
594413 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
594445 TTTTAAATGGGTTGCCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * * *
594477 TTTTAAATGGGTTGCCACCAACTTCTGGGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
594509 TTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
594541 TTTGAAATGGGTTGCCACCTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
594573 TTT-AGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
594605 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
594637 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
594669 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
594701 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
594733 TTTGGAATGGGTTGTCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
594765 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
594797 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
594829 TTTGAAATGGG-TGCCACAGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
594855 CATTTAAAAG
Statistics
Matches: 385, Mismatches: 23, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
31 14 0.04
32 370 0.96
33 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.34, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:594870 original size:27 final size:27
Alignment explanation
Indices: 594837--596040 Score: 1895
Period size: 27 Copynumber: 44.0 Consensus size: 27
594827 GCTTTGAAAT
* * *
594837 GGGTGCCACAGAGTTGTGCATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
594864 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
594891 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
594918 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
594946 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
594974 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
595001 GGGTGCCACGAAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
595028 AGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
** * *
595055 GAATGCCACGAAGTTATGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
595082 GGGTGCCACGGAGTTGTGGTCTTAAACA
1 GGGTGCCACGGAGTTGTGGACTTAAA-A
*
595110 GGGATGCCACAGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
595138 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
595165 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
595192 AGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
595219 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
595246 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
595273 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
595301 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
595328 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
595355 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
595382 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
595409 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
595436 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
595463 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* *
595491 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
595518 GGGTGCCACGGAATTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
595546 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
595573 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
595600 GGGTGCCACGGAGTTGTGGTCTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
595628 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
595655 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
595682 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
595709 GGGTGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
595736 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
595764 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
595791 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
* *
595819 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
595846 GGGTACCACGGAGTTGTGGATTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-CTTAAAA
*
595874 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
595901 GGGGTGCCACGGAGTTGTGGATTTTAAAA
1 -GGGTGCCACGGAGTTGTGGA-CTTAAAA
*
595930 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
595957 GGGTACCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
595985 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
596012 GGATGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
596040 G
1 G
596041 AAAATGCCAC
Statistics
Matches: 1088, Mismatches: 75, Indels: 27
0.91 0.06 0.02
Matches are distributed among these distances:
27 758 0.70
28 303 0.28
29 27 0.02
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:597099 original size:1 final size:1
Alignment explanation
Indices: 597093--597127 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
597083 GGTGAAAAGG
**
597093 TTTTTTTTTTTTTTGGTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
597128 AGGATTAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (1 bp):
T
Found at i:597112 original size:16 final size:16
Alignment explanation
Indices: 597091--597122 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
597081 AGGGTGAAAA
597091 GGTTTTTTTTTTTTTT
1 GGTTTTTTTTTTTTTT
597107 GGTTTTTTTTTTTTTT
1 GGTTTTTTTTTTTTTT
597123 TTTTTAGGAT
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:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (16 bp):
GGTTTTTTTTTTTTTT
Found at i:603882 original size:17 final size:17
Alignment explanation
Indices: 603860--603895 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
603850 CATTTCATAT
* *
603860 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTCTTTCTTC
603877 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
603894 TT
1 TT
603896 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:612515 original size:3 final size:3
Alignment explanation
Indices: 612507--612539 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
612497 TTTGATGCCA
612507 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
612540 CTTTTTATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TGT
Found at i:617459 original size:18 final size:19
Alignment explanation
Indices: 617436--617478 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
617426 ATCAGTTTGA
*
617436 GTTAAAATAAT-TTTAAAT
1 GTTAAAAAAATGTTTAAAT
*
617454 GTTAAAAAAATGTTTTAAT
1 GTTAAAAAAATGTTTAAAT
617473 GTTAAA
1 GTTAAA
617479 TAAGTAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (19 bp):
GTTAAAAAAATGTTTAAAT
Found at i:619424 original size:2 final size:2
Alignment explanation
Indices: 619411--619442 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
619401 GCCTTTTATC
*
619411 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
619443 TTAAATTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:623317 original size:22 final size:22
Alignment explanation
Indices: 623291--623338 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
623281 TTTCATTTAA
623291 TAAAAATAAATTTT-TATAAAT
1 TAAAAATAAATTTTATATAAAT
* *
623312 TAAAAATTAATTTTATATATAT
1 TAAAAATAAATTTTATATAAAT
623334 TAAAA
1 TAAAA
623339 TATTAACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAAAATAAATTTTATATAAAT
Found at i:624687 original size:68 final size:70
Alignment explanation
Indices: 624599--624728 Score: 201
Period size: 68 Copynumber: 1.9 Consensus size: 70
624589 AAGATAAGAG
* * * *
624599 CATAATTAATTGAAATTTAAAAAAAATTAAATGTTAAAATTTAAACTTTAAATTTATTAAAAAGT
1 CATAATCAATTGAAATTTAAAAAAAATTAAATATTAAAATTTAAACTTGAAATCTATTAAAAAGT
624664 GATTA
66 GATTA
*
624669 CATAATCAATT-AAA-TTAAAAAAAATTAAATATTAAAATTTAATCTTGAAATCTATTAAAA
1 CATAATCAATTGAAATTTAAAAAAAATTAAATATTAAAATTTAAACTTGAAATCTATTAAAA
624729 TCATTTCTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 42 0.76
69 3 0.05
70 10 0.18
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.37
Consensus pattern (70 bp):
CATAATCAATTGAAATTTAAAAAAAATTAAATATTAAAATTTAAACTTGAAATCTATTAAAAAGT
GATTA
Found at i:627036 original size:29 final size:29
Alignment explanation
Indices: 627000--627059 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
626990 TTTTTATTTA
627000 AATTTAAT--TATAAAAAAT-ATAAAAAT
1 AATTTAATAATATAAAAAATAATAAAAAT
* *
627026 AATTTAATAATATAATAAATAATAAAATT
1 AATTTAATAATATAAAAAATAATAAAAAT
627055 AATTT
1 AATTT
627060 TTAAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 8 0.28
28 9 0.31
29 12 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
AATTTAATAATATAAAAAATAATAAAAAT
Found at i:627634 original size:15 final size:15
Alignment explanation
Indices: 627616--627662 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
627606 TTTAAAAAGT
627616 TTTAATTTTTATATA
1 TTTAATTTTTATATA
* *
627631 TTTAA-TGTTATAAA
1 TTTAATTTTTATATA
*
627645 TTTATTTTTTATAATA
1 TTTAATTTTTAT-ATA
627661 TT
1 TT
627663 AACATACCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 11 0.44
15 10 0.40
16 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTAATTTTTATATA
Found at i:627954 original size:6 final size:6
Alignment explanation
Indices: 627943--627984 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
627933 TTGTATTTGA
* * *
627943 AAATTT AAATTT AAATTT AAATTT AGATTT AGATTT GAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
627985 CAAAATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:628308 original size:7 final size:7
Alignment explanation
Indices: 628294--628324 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
628284 AAAATAGTTA
628294 AAAATTT
1 AAAATTT
*
628301 AAATTTT
1 AAAATTT
628308 AAAATTT
1 AAAATTT
628315 AAAATTT
1 AAAATTT
628322 AAA
1 AAA
628325 CTTAAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAAATTT
Found at i:629263 original size:16 final size:16
Alignment explanation
Indices: 629244--629290 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
629234 AATTATTTTT
629244 AATTATTATTAAATTA
1 AATTATTATTAAATTA
*
629260 AATTATAATTAAATTA
1 AATTATTATTAAATTA
* *
629276 TATTCTTATTTAAAT
1 AATTATTA-TTAAAT
629291 AGATACGTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTATTATTAAATTA
Found at i:629658 original size:32 final size:32
Alignment explanation
Indices: 629600--629664 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
629590 ATAATAATTT
***
629600 ATAAAATATTATTATTTATGTCAAATAATAAA
1 ATAAAATATTATTATTTATAAAAAATAATAAA
*
629632 ATAATAAT-TTATTATTTATAAAAAATATTAAA
1 ATAA-AATATTATTATTTATAAAAAATAATAAA
629664 A
1 A
629665 ATTTTATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (32 bp):
ATAAAATATTATTATTTATAAAAAATAATAAA
Found at i:631852 original size:16 final size:17
Alignment explanation
Indices: 631833--631874 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
631823 TTTATTTTTT
*
631833 TATTTTTTACT-CAAAA
1 TATTTTTAACTACAAAA
*
631849 TATTTTTAACTACAAAT
1 TATTTTTAACTACAAAA
631866 TATTTTTAA
1 TATTTTTAA
631875 TTACTATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTTTTAACTACAAAA
Found at i:632127 original size:498 final size:499
Alignment explanation
Indices: 631313--632294 Score: 1528
Period size: 498 Copynumber: 2.0 Consensus size: 499
631303 CATTTATTAA
* * * *
631313 TTATTTATTTTTGTTTTTCTTTTATTTTTTATTCAAAATATTTTTAATTATAAATTATTTTAATT
1 TTATTTATTTTTGTATTTCTTTTATTTTTTACTCAAAATATTTTTAACTACAAATTATTTTAATT
* *
631378 ACTATCAAATTAAATTATATCCTTATTTAATTTAGATACATTAAATATTTTTTTCAAAGTTTGTG
66 ACTATCAAATTAAATTATATCCTTATTTAATTTAGACACATTAAATATTTTTTTCAAAGTTTGTA
** * * *
631443 TCTTACAAATAATTTCACTTGACTAGTAAATTGTAAGTACCGTGGGCATGTCCTAACTCTGGATT
131 TCTTACAAATAATCCCACTTGACTAGTAAATTGTAAGTACCATGAGCATATCCTAACTCTGGATT
* *
631508 TTGATAACTTTCCTTTACTTAAATTTTTCTGTACAAAAAATATTTTAAACTTATCTTTAATTCAA
196 TTAATAACTTTCCTTTACTGAAATTTTTCTGTACAAAAAATATTTTAAACTTATCTTTAATTCAA
*
631573 TTATTTATATTAACTTTGATATTACTATGTTATATTATTTTTATTTAAAAATAAATCAATTGTCA
261 TTATTTATATTAACTTTGATATTAATATGTTATATTATTTTTATTTAAAAATAAATCAATTGTCA
631638 TTATTTTAAAAAGTTTAAATATAAAGAAATTGATTAAAGCAAAAAAATCATATTTTTAATATTTA
326 TTATTTTAAAAAGTTTAAATATAAAGAAATTGATTAAAG-AAAAAAATCATATTTTTAATATTTA
* * *
631703 AAGTAAAATTTAAATAAATATTAGTTTGATTAAT-AATGTTACATAGTTACTTTTTCAAGAGATA
390 AAGTAAAACTTAAATAAATATTAGTTTGATTAATAAATGCTACATAATTACTTTTT-AAGAGATA
631767 AAATATATTTTTCTATATATTTTTAATTCTTTTACATAGTTACATAG
454 AAATATATTTTTCTATATA-TTTTAATTCTTTTACATAGTTACATAG
631814 TTATTTA-TTTT-TATTT-TTTTATTTTTTACTCAAAATATTTTTAACTACAAATTATTTTTAAT
1 TTATTTATTTTTGTATTTCTTTTATTTTTTACTCAAAATATTTTTAACTACAAATTA-TTTTAAT
* * *
631876 TACTATCAAATTAAATTATATTCTTATTTAATTTAGACACTTTAAATA-TTTTTTCAAGGTTTGT
65 TACTATCAAATTAAATTATATCCTTATTTAATTTAGACACATTAAATATTTTTTTCAAAGTTTGT
* *
631940 ATCTTACAAGTAATCCCACTTGACTAGTAAATTGTAAGTATCATGAGCATATCCTAACTCTGGAT
130 ATCTTACAAATAATCCCACTTGACTAGTAAATTGTAAGTACCATGAGCATATCCTAACTCTGGAT
** * * * *
632005 TTTAATAACTTTTTTTTA-TCGAATTTTTTTTGTACAAAAAATATTTTAAATTTATTTTTAATTC
195 TTTAATAACTTTCCTTTACT-GAAATTTTTCTGTACAAAAAATATTTTAAACTTATCTTTAATTC
*
632069 AATTATTTATATTAACTGTT-ATATTAATATGTTATGTTATTTTTATTTAAAAATAAATCAATTG
259 AATTATTTATATTAACT-TTGATATTAATATGTTATATTATTTTTATTTAAAAATAAATCAATTG
* *
632133 TCATTATTTTAAAATGTTTAAATATAAAGAAATTGATTAAAGTAAAAAATCATATTTTTAATATT
323 TCATTATTTTAAAAAGTTTAAATATAAAGAAATTGATTAAAGAAAAAAATCATATTTTTAATATT
* * *
632198 TAAAGTAAAACTTGAATAAATATTAGTTTGATTAATAAAATGCTACATAATTAGTTTTTAAGGGA
388 TAAAGTAAAACTTAAATAAATATTAGTTTGATTAAT-AAATGCTACATAATTACTTTTTAAGAGA
* *
632263 TAAAATGTATTTTTTTATATATTTTAATTCTT
452 TAAAATATATTTTTCTATATATTTTAATTCTT
632295 CTTTTTTTCC
Statistics
Matches: 440, Mismatches: 36, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
497 68 0.15
498 285 0.65
499 76 0.17
500 4 0.01
501 7 0.02
ACGTcount: A:0.37, C:0.08, G:0.07, T:0.48
Consensus pattern (499 bp):
TTATTTATTTTTGTATTTCTTTTATTTTTTACTCAAAATATTTTTAACTACAAATTATTTTAATT
ACTATCAAATTAAATTATATCCTTATTTAATTTAGACACATTAAATATTTTTTTCAAAGTTTGTA
TCTTACAAATAATCCCACTTGACTAGTAAATTGTAAGTACCATGAGCATATCCTAACTCTGGATT
TTAATAACTTTCCTTTACTGAAATTTTTCTGTACAAAAAATATTTTAAACTTATCTTTAATTCAA
TTATTTATATTAACTTTGATATTAATATGTTATATTATTTTTATTTAAAAATAAATCAATTGTCA
TTATTTTAAAAAGTTTAAATATAAAGAAATTGATTAAAGAAAAAAATCATATTTTTAATATTTAA
AGTAAAACTTAAATAAATATTAGTTTGATTAATAAATGCTACATAATTACTTTTTAAGAGATAAA
ATATATTTTTCTATATATTTTAATTCTTTTACATAGTTACATAG
Found at i:635494 original size:19 final size:18
Alignment explanation
Indices: 635465--635507 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
635455 TAATATAAAT
635465 TTTTAAAAAT-ATTTTAA
1 TTTTAAAAATAATTTTAA
635482 CTTTTAAATAATAATTTTAA
1 -TTTTAAA-AATAATTTTAA
635502 TTTTAA
1 TTTTAA
635508 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.30
19 9 0.39
20 7 0.30
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTAAAAATAATTTTAA
Found at i:635877 original size:12 final size:14
Alignment explanation
Indices: 635847--635878 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
635837 ATTTAAAAAT
635847 TATTTATATATTAA
1 TATTTATATATTAA
635861 TATTTATA-ATTAA
1 TATTTATATATTAA
635874 -ATTTA
1 TATTTA
635879 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.28
13 5 0.28
14 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTTATATATTAA
Found at i:636285 original size:12 final size:12
Alignment explanation
Indices: 636268--636293 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
636258 AATACGTAAA
636268 TATATTAAAATT
1 TATATTAAAATT
636280 TATATTAAAATT
1 TATATTAAAATT
636292 TA
1 TA
636294 AAAAATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATTAAAATT
Found at i:636321 original size:12 final size:13
Alignment explanation
Indices: 636297--636330 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
636287 AAATTTAAAA
*
636297 AATATAAAATTAT
1 AATATATAATTAT
636310 AA-ATATAATTAT
1 AATATATAATTAT
636322 AATATATAA
1 AATATATAA
636331 AAATATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATATAATTAT
Found at i:637226 original size:23 final size:22
Alignment explanation
Indices: 637191--637233 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
637181 ATAAATCTAA
*
637191 ATTTTTTTTTTATATTTTATGT
1 ATTTTTTTTTTATAATTTATGT
637213 ATTTTATTTTTTATAATTTAT
1 ATTTT-TTTTTTATAATTTAT
637234 ATAATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (22 bp):
ATTTTTTTTTTATAATTTATGT
Found at i:638887 original size:14 final size:14
Alignment explanation
Indices: 638868--638911 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
638858 TATATTAACT
638868 TTAAAATTAATTTA
1 TTAAAATTAATTTA
*
638882 TTAAAA-TATTTTA
1 TTAAAATTAATTTA
* *
638895 TTTAAATTAATTAA
1 TTAAAATTAATTTA
638909 TTA
1 TTA
638912 CTATTATTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAAAATTAATTTA
Found at i:639662 original size:24 final size:25
Alignment explanation
Indices: 639617--639676 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
639607 TAATTTATTT
*
639617 TTAAAT-AAAAATAATATAATAT-A
1 TTAAATCAAAATTAATATAATATAA
639640 TTAACATCAAAATTAATAT-ATATAA
1 TTAA-ATCAAAATTAATATAATATAA
*
639665 TTAAATTAAAAT
1 TTAAATCAAAAT
639677 AAATTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 4 0.12
24 13 0.41
25 15 0.47
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (25 bp):
TTAAATCAAAATTAATATAATATAA
Found at i:641265 original size:98 final size:98
Alignment explanation
Indices: 641096--641273 Score: 347
Period size: 98 Copynumber: 1.8 Consensus size: 98
641086 CGTATGATGT
641096 TTTCCTGGCTGACTTAAGCAAAATTTTCTGTAGGATGAAATTTTTTTAATGAAAATGCCATAGTT
1 TTTCCTGGCTGACTTAAGCAAAATTTTCTGTAGGATGAAATTTTTTTAATGAAAATGCCATAGTT
*
641161 CATCCAAATTGAAAGTTGTGCTATATTTAGTGC
66 CATCCAAAGTGAAAGTTGTGCTATATTTAGTGC
641194 TTTCCTGGCTGACTTAAGCAAAATTTTCTGTAGGATGAAATTTTTTTAATGAAAATGCCATAGTT
1 TTTCCTGGCTGACTTAAGCAAAATTTTCTGTAGGATGAAATTTTTTTAATGAAAATGCCATAGTT
641259 CATCCAAAGTGAAAG
66 CATCCAAAGTGAAAG
641274 AATGTTTGAG
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 79 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.37
Consensus pattern (98 bp):
TTTCCTGGCTGACTTAAGCAAAATTTTCTGTAGGATGAAATTTTTTTAATGAAAATGCCATAGTT
CATCCAAAGTGAAAGTTGTGCTATATTTAGTGC
Found at i:644609 original size:23 final size:23
Alignment explanation
Indices: 644583--644628 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
644573 AAAAACATTT
*
644583 TATATAAATTTTAATTATAAAAA
1 TATATAAATATTAATTATAAAAA
*
644606 TATATAAATATTAATTTTAAAAA
1 TATATAAATATTAATTATAAAAA
644629 ATTTTTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATATAAATATTAATTATAAAAA
Found at i:646326 original size:76 final size:76
Alignment explanation
Indices: 646228--646503 Score: 254
Period size: 76 Copynumber: 3.6 Consensus size: 76
646218 GAGATAACAT
* *
646228 CACTTAACACT-TCC-CCCTGTGTAGCTCACAGAGCTTACATGTGGACATCCAATATTTAACAGA
1 CACTTAACACTCTCCTCAC-GTGTAGCTCACAGAGCTTACATGTGGACATCCAATATTAAACAGA
*
646291 TAAGGATAATAC
65 TAGGGATAATAC
* * * * *
646303 CACTTAACACTCTCATTACGTGTAGCTCAGAGAGCTTACATGTGGAAATCCAATACTTAAACAGG
1 CACTTAACACTCTCCTCACGTGTAGCTCACAGAGCTTACATGTGGACATCCAATA-TTAAACAGA
*
646368 TGTGGGATAATAC
65 T-AGGGATAATAC
* * ** * * * * * *
646381 CACTCAATACTC-CCTCACACGTAACTCACAAAGCTTACATGTGGACATCAAAAACTCAACAGAC
1 CACTTAACACTCTCCTCACGTGTAGCTCACAGAGCTTACATGTGGACATCCAATATTAAACAGA-
** *
646445 GCGGGATAACAC
65 TAGGGATAATAC
* * * *
646457 CACTTAACACT-TCCCCATGTGTAGCTGATAGAGCTTACATGTGGACA
1 CACTTAACACTCTCCTCACGTGTAGCTCACAGAGCTTACATGTGGACA
646504 ACCTCACCAG
Statistics
Matches: 158, Mismatches: 37, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
75 11 0.07
76 87 0.55
77 41 0.26
78 19 0.12
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (76 bp):
CACTTAACACTCTCCTCACGTGTAGCTCACAGAGCTTACATGTGGACATCCAATATTAAACAGAT
AGGGATAATAC
Found at i:646424 original size:77 final size:76
Alignment explanation
Indices: 646252--646425 Score: 197
Period size: 77 Copynumber: 2.3 Consensus size: 76
646242 CCCTGTGTAG
* * *
646252 CTCACAGAGCTTACATGTGGACATCCAATATTTAACAGATAAGGATAATACCACTTAACACTCTC
1 CTCACAGAGCTTACATGTGGAAATCCAATATTAAACAGATAAGGATAATACCACTCAACACTCTC
* ** *
646317 ATTACGTGTAG
66 ATCACACGTAA
* * ** *
646328 CTCAGAGAGCTTACATGTGGAAATCCAATACTTAAACAGGTGTGGGATAATACCACTCAATACTC
1 CTCACAGAGCTTACATGTGGAAATCCAATA-TTAAACAGAT-AAGGATAATACCACTCAACACTC
*
646393 -CCTCACACGTAA
64 TCATCACACGTAA
*
646405 CTCACAAAGCTTACATGTGGA
1 CTCACAGAGCTTACATGTGGA
646426 CATCAAAAAC
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
76 28 0.35
77 34 0.42
78 19 0.23
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (76 bp):
CTCACAGAGCTTACATGTGGAAATCCAATATTAAACAGATAAGGATAATACCACTCAACACTCTC
ATCACACGTAA
Found at i:648031 original size:2 final size:2
Alignment explanation
Indices: 648024--648049 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
648014 CAAGTCATAG
648024 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
648050 ATGCACTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:650658 original size:14 final size:14
Alignment explanation
Indices: 650619--650656 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
650609 TTTTTCCTCC
650619 ATTTATAATTTAAT
1 ATTTATAATTTAAT
650633 ATTTATAATTTAAT
1 ATTTATAATTTAAT
650647 ATTTA-AATTT
1 ATTTATAATTT
650657 TATTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTATAATTTAAT
Found at i:652377 original size:17 final size:19
Alignment explanation
Indices: 652355--652389 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
652345 ATTAAAAAGT
652355 TTTAACT-T-TTATTAATA
1 TTTAACTATATTATTAATA
652372 TTTAACTATATTATTAAT
1 TTTAACTATATTATTAAT
652390 TAAATGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAACTATATTATTAATA
Found at i:652622 original size:19 final size:19
Alignment explanation
Indices: 652600--652639 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
652590 CATTTAATAA
652600 AAATATTTTAATTA-AAATT
1 AAAT-TTTTAATTATAAATT
*
652619 AAATTTTTATTTATAAATT
1 AAATTTTTAATTATAAATT
652638 AA
1 AA
652640 TTAAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATTTTTAATTATAAATT
Found at i:652989 original size:32 final size:32
Alignment explanation
Indices: 652924--652989 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
652914 TATAATTTTT
*
652924 TATTTAAATTTAATTAAAAATATAAAGATAAA
1 TATTTAAATTTAATTAAAAATATAAAGAAAAA
*
652956 TATTTAATGTTTAATATAAAAA-ATAAA-AAAAA
1 TATTTAA-ATTTAAT-TAAAAATATAAAGAAAAA
652988 TA
1 TA
652990 CTCCCACCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 13 0.43
33 11 0.37
34 6 0.20
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (32 bp):
TATTTAAATTTAATTAAAAATATAAAGAAAAA
Found at i:666916 original size:15 final size:15
Alignment explanation
Indices: 666898--666928 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
666888 TTAGAAAGAA
666898 AATAACCCCTACCCC
1 AATAACCCCTACCCC
666913 AATAACCCCTACCCC
1 AATAACCCCTACCCC
666928 A
1 A
666929 CTGTTCCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.52, G:0.00, T:0.13
Consensus pattern (15 bp):
AATAACCCCTACCCC
Found at i:669144 original size:16 final size:16
Alignment explanation
Indices: 669120--669177 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
669110 ATTTTCCTTC
669120 TATTATTATTTAATAA
1 TATTATTATTTAATAA
* * **
669136 TATTTTTATTT-CTTC
1 TATTATTATTTAATAA
669151 TATTATTATTTAATAA
1 TATTATTATTTAATAA
*
669167 TATTTTTATTT
1 TATTATTATTT
669178 TAATTATAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 11 0.34
16 21 0.66
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTATTATTTAATAA
Found at i:669154 original size:31 final size:31
Alignment explanation
Indices: 669116--669177 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
669106 CAACATTTTC
669116 CTTCTATTATTATTTAATAATATTTTTATTT
1 CTTCTATTATTATTTAATAATATTTTTATTT
669147 CTTCTATTATTATTTAATAATATTTTTATTT
1 CTTCTATTATTATTTAATAATATTTTTATTT
669178 TAATTATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (31 bp):
CTTCTATTATTATTTAATAATATTTTTATTT
Found at i:670610 original size:26 final size:25
Alignment explanation
Indices: 670570--670633 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
670560 TTAATTAAAA
* *
670570 TTTTAAGTATATATAATTTATTATATT
1 TTTTAA-TATTTATAA-TTATAATATT
670597 TTTTAATATTTAT-ATTATAATATT
1 TTTTAATATTTATAATTATAATATT
*
670621 ATTT-AT-TTTATAA
1 TTTTAATATTTATAA
670634 AATATAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 5 0.15
23 3 0.09
24 12 0.36
25 1 0.03
26 6 0.18
27 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTTAATATTTATAATTATAATATT
Found at i:670833 original size:3 final size:3
Alignment explanation
Indices: 670825--670855 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
670815 TTTATTTCTG
670825 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
670856 AAACACTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:671166 original size:24 final size:24
Alignment explanation
Indices: 671125--671183 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
671115 TTAATTAATT
*
671125 TATATATAATATTAATTTGTACATGA
1 TATATATAATATTAATTT-T-CATAA
671151 TATATATAAT-TT-ATTTTCATAA
1 TATATATAATATTAATTTTCATAA
*
671173 TTTATATAATA
1 TATATATAATA
671184 AAAAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 13 0.43
23 1 0.03
24 4 0.13
25 2 0.07
26 10 0.33
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.51
Consensus pattern (24 bp):
TATATATAATATTAATTTTCATAA
Found at i:680549 original size:22 final size:22
Alignment explanation
Indices: 680523--680567 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
680513 GTTAAGATAA
680523 AATTTTGTCGGCAAATTGGAAT
1 AATTTTGTCGGCAAATTGGAAT
*
680545 AATTTTGTTGGCAAATTGGAAT
1 AATTTTGTCGGCAAATTGGAAT
680567 A
1 A
680568 GATATCCGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (22 bp):
AATTTTGTCGGCAAATTGGAAT
Found at i:685760 original size:157 final size:158
Alignment explanation
Indices: 685441--686015 Score: 748
Period size: 157 Copynumber: 3.7 Consensus size: 158
685431 GTATACCTTT
**
685441 AATATTTCAACATCAGTAGTTACCCATAAGAGTGAACTCTTGTGATG-TCTGTTGGGTGACCATT
1 AATATTTCAACATTGGTAGTTACCCATAAGAGTGAACTCTTGTGATGCT-TGTTGGGTGACCATT
* * * *
685505 CTCATTTGGGATCAAGTATTTCTTTTG-CCGATATTTGCTTTTGACAGACGGTGGATGAGAGACC
65 CTCATTTAGGATCAAGTATTTCTTGTGTCGGA-ATTTGCTTTTGACAGACGATGGATGAGAGACC
*
685569 TAGCAATTCGCGTATCCGTGTCATACATTG
129 TAGCAATTCGTGTATCCGTGTCATACATTG
* * *
685599 AATATTTCAACATTGGTAGTTACTCGTAAGAGTGATCTCTTGTGATGCTTGTTGGGTGACCATTC
1 AATATTTCAACATTGGTAGTTACCCATAAGAGTGAACTCTTGTGATGCTTGTTGGGTGACCATTC
* * *
685664 TCATTT-GGATCAAGTATTTCTTGTGTCGGAATTTGCTTTTGAGAGACAATGAATGAGAGACCTA
66 TCATTTAGGATCAAGTATTTCTTGTGTCGGAATTTGCTTTTGACAGACGATGGATGAGAGACCTA
* * *
685728 GCAATTCATTTATCTGTGTCATACATTG
131 GCAATTCGTGTATCCGTGTCATACATTG
* * *
685756 AATATTTCAACATTGGTAGTTACCCATAAGAATGATCTCTTGTGATGCTTGTTGGGTG-TCATTC
1 AATATTTCAACATTGGTAGTTACCCATAAGAGTGAACTCTTGTGATGCTTGTTGGGTGACCATTC
* * * * * * *
685820 TTATTTAGAATCAAGTACTTGTTGTGTTGGAATTTGCTTCTGACAGACGATGGATAAGAGACCTA
66 TCATTTAGGATCAAGTATTTCTTGTGTCGGAATTTGCTTTTGACAGACGATGGATGAGAGACCTA
* * * *
685885 GCTATTTGTGTA-CCATCTCATACATTG
131 GCAATTCGTGTATCCGTGTCATACATTG
* * * * **
685912 AATAATTCAACAGTGGTAGTTACCCATGAGAGTGAACTCTTGTGATTCTTGTTGGGCAACCATTC
1 AATATTTCAACATTGGTAGTTACCCATAAGAGTGAACTCTTGTGATGCTTGTTGGGTGACCATTC
*
685977 TCATTT-GAGATCAAGTATTTCTTGTGCCGGAATTTGCTT
66 TCATTTAG-GATCAAGTATTTCTTGTGTCGGAATTTGCTT
686016 GCAACAAACG
Statistics
Matches: 361, Mismatches: 51, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
156 73 0.20
157 220 0.61
158 67 0.19
159 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.37
Consensus pattern (158 bp):
AATATTTCAACATTGGTAGTTACCCATAAGAGTGAACTCTTGTGATGCTTGTTGGGTGACCATTC
TCATTTAGGATCAAGTATTTCTTGTGTCGGAATTTGCTTTTGACAGACGATGGATGAGAGACCTA
GCAATTCGTGTATCCGTGTCATACATTG
Found at i:687084 original size:29 final size:29
Alignment explanation
Indices: 687025--687090 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
687015 TGTTGTTCTC
*
687025 TTTTAGTTT-ATTGAATTTTACTATTAAA
1 TTTTAATTTGATTGAATTTTACTATTAAA
* **
687053 TTTTGATTTGATTGAATTTTA-TCATTTGA
1 TTTTAATTTGATTGAATTTTACT-ATTAAA
687082 TTTTAATTT
1 TTTTAATTT
687091 TTGATGATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 8 0.26
29 23 0.74
ACGTcount: A:0.27, C:0.03, G:0.09, T:0.61
Consensus pattern (29 bp):
TTTTAATTTGATTGAATTTTACTATTAAA
Found at i:689462 original size:34 final size:34
Alignment explanation
Indices: 689419--689483 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
689409 AAAGAATTGG
689419 ATAAAACTTTCTTCAATGGATGCACGATCATATC
1 ATAAAACTTTCTTCAATGGATGCACGATCATATC
* *
689453 ATAAAACTTTCTTCGATGGATGCATGATCAT
1 ATAAAACTTTCTTCAATGGATGCACGATCAT
689484 TCTTGATTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (34 bp):
ATAAAACTTTCTTCAATGGATGCACGATCATATC
Found at i:689792 original size:2 final size:2
Alignment explanation
Indices: 689787--689813 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
689777 TATATGTATA
689787 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
689814 TTTCCTTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:690428 original size:2 final size:2
Alignment explanation
Indices: 690406--690448 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
690396 ACTCTCTTTT
* * *
690406 TA TA AA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
690448 T
1 T
690449 TAAGAAGCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:691773 original size:2 final size:2
Alignment explanation
Indices: 691766--691801 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
691756 TTACTTAGAC
691766 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
691802 GGATTTGGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:692934 original size:16 final size:16
Alignment explanation
Indices: 692899--692957 Score: 70
Period size: 15 Copynumber: 3.8 Consensus size: 16
692889 CTTAATAGAA
692899 AAAATAATTAAA-TTTT
1 AAAA-AATTAAATTTTT
692915 -AAAAATTAAATTTTT
1 AAAAAATTAAATTTTT
*
692930 AAAAAA-TATATTTTT
1 AAAAAATTAAATTTTT
*
692945 AAAAAAATAAATT
1 AAAAAATTAAATT
692958 AAAAATACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
14 7 0.18
15 21 0.55
16 10 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAAAATTAAATTTTT
Found at i:695773 original size:13 final size:12
Alignment explanation
Indices: 695701--695774 Score: 57
Period size: 12 Copynumber: 6.2 Consensus size: 12
695691 AGATAATAAC
*
695701 TATTTTAT-TTT
1 TATTTTATATTA
*
695712 TATTTTTATTTTA
1 TA-TTTTATATTA
695725 TATTTTATA-TA
1 TATTTTATATTA
*
695736 TAATTTA-ATTA
1 TATTTTATATTA
*
695747 TA-TTTATGAATA
1 TATTTTAT-ATTA
695759 TATTTTATATTTA
1 TATTTTATA-TTA
695772 TAT
1 TAT
695775 CTTAAAAAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
10 5 0.10
11 14 0.27
12 18 0.35
13 14 0.27
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (12 bp):
TATTTTATATTA
Found at i:696018 original size:16 final size:18
Alignment explanation
Indices: 695999--696032 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
695989 AATTTTTTAA
695999 ATTTTT-AA-TTAAAAAT
1 ATTTTTAAAGTTAAAAAT
696015 ATTTTTAAAGTTAAAAAT
1 ATTTTTAAAGTTAAAAAT
696033 TATATTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTTTTAAAGTTAAAAAT
Found at i:696961 original size:42 final size:41
Alignment explanation
Indices: 696902--696984 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 41
696892 CAAATCAAAA
* *
696902 AATAAAGTAATATATATTAACATTTAAAAATTTTAAAATTT
1 AATAAAATAATATATATTAACATTCAAAAATTTTAAAATTT
* *
696943 AATAAAATATATATATATTAACATTCGAAAATTTTAATATTT
1 AATAAAATA-ATATATATTAACATTCAAAAATTTTAAAATTT
696985 TAAAAGTACT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 8 0.22
42 29 0.78
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (41 bp):
AATAAAATAATATATATTAACATTCAAAAATTTTAAAATTT
Found at i:697376 original size:33 final size:34
Alignment explanation
Indices: 697334--697399 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
697324 CCTTCAAATT
*
697334 TCATCTAATTTTTAAAAAA-TCAATATATCTCTC
1 TCATCTAATTTTCAAAAAACTCAATATATCTCTC
* *
697367 TCATTTAATTTTCAAAAAACTGAATATATCTCT
1 TCATCTAATTTTCAAAAAACTCAATATATCTCT
697400 AGATAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.42
Consensus pattern (34 bp):
TCATCTAATTTTCAAAAAACTCAATATATCTCTC
Found at i:697618 original size:32 final size:34
Alignment explanation
Indices: 697570--697634 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
697560 AAGAAATTTT
*
697570 TTATTTTTGAATTTAATAATATT-TAGATAAATA
1 TTATTTTTGAATTTAATAATATTAGAGATAAATA
697603 TTATTTTT-AATTTAATAATATTAGAGATAAAT
1 TTATTTTTGAATTTAATAATATTAGAGATAAAT
697635 CGTCCTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (34 bp):
TTATTTTTGAATTTAATAATATTAGAGATAAATA
Found at i:698571 original size:2 final size:2
Alignment explanation
Indices: 698564--698596 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
698554 CATATGAGAA
*
698564 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
698597 CATAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:701305 original size:25 final size:25
Alignment explanation
Indices: 701258--701310 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
701248 TATCTTTAAA
* *
701258 ATTTTAAAATAATAATAATTAATTT
1 ATTTTAAAATAATAATAAATAATAT
*
701283 ATTTTTAAATAA-AATAACATAATAT
1 ATTTTAAAATAATAATAA-ATAATAT
701308 ATT
1 ATT
701311 AATATGGAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTTTAAAATAATAATAAATAATAT
Found at i:701959 original size:22 final size:21
Alignment explanation
Indices: 701905--701972 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
701895 CTTTTTATTT
* **
701905 ATAAATTAAATAAATATTATTT
1 ATAAATTAAA-AAATTTTATAA
701927 AT-AATT-AAAAATATTTATAA
1 ATAAATTAAAAAAT-TTTATAA
*
701947 CATAAATTTAAAAATTTTATAA
1 -ATAAATTAAAAAATTTTATAA
701969 ATAA
1 ATAA
701973 TAATTATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 4 0.10
20 6 0.15
21 10 0.26
22 13 0.33
23 6 0.15
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAAATTAAAAAATTTTATAA
Found at i:701977 original size:23 final size:24
Alignment explanation
Indices: 701926--701977 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
701916 AAATATTATT
701926 TATAA-TTAAAAATATTTATAACA
1 TATAATTTAAAAATATTTATAACA
701949 TA-AATTTAAAAAT-TTTATAA-A
1 TATAATTTAAAAATATTTATAACA
701970 TAATAATT
1 T-ATAATT
701978 ATTTTTATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 2 0.08
22 10 0.38
23 14 0.54
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
TATAATTTAAAAATATTTATAACA
Found at i:702645 original size:23 final size:24
Alignment explanation
Indices: 702619--702676 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
702609 TTATTAATAC
* *
702619 TAATTTAATTCATTTTTTATTG-T
1 TAATTTAATTAAATTTTTATTGAT
*
702642 TAATTTAATTAAATTTTTGTTGAT
1 TAATTTAATTAAATTTTTATTGAT
702666 TCAATTTAATT
1 T-AATTTAATT
702677 TTTTATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 19 0.63
24 2 0.07
25 9 0.30
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.60
Consensus pattern (24 bp):
TAATTTAATTAAATTTTTATTGAT
Found at i:702671 original size:20 final size:20
Alignment explanation
Indices: 702638--702679 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
702628 TCATTTTTTA
*
702638 TTGTTAATTTAATTAAATTT
1 TTGTTAATTCAATTAAATTT
* *
702658 TTGTTGATTCAATTTAATTT
1 TTGTTAATTCAATTAAATTT
702678 TT
1 TT
702680 TATATAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (20 bp):
TTGTTAATTCAATTAAATTT
Found at i:704251 original size:2 final size:2
Alignment explanation
Indices: 704244--704270 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
704234 GAATACATAC
704244 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
704271 AATTATGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:704477 original size:2 final size:2
Alignment explanation
Indices: 704470--704495 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
704460 AAATTTTGTC
704470 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
704496 CTGATTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:704703 original size:21 final size:23
Alignment explanation
Indices: 704677--704727 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
704667 ATTATATATT
704677 AATATTTATATT-A-TAAATAAA
1 AATATTTATATTAATTAAATAAA
* *
704698 AATATTTTTATTAATTAAATAAT
1 AATATTTATATTAATTAAATAAA
704721 AAT-TTTA
1 AATATTTA
704728 ATCAAATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 11 0.44
22 4 0.16
23 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATATTTATATTAATTAAATAAA
Found at i:706601 original size:35 final size:35
Alignment explanation
Indices: 706562--706629 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
706552 ATACGATGAA
706562 GCTTGATTTAATCATTTATAGTTTCATATTCAAAG
1 GCTTGATTTAATCATTTATAGTTTCATATTCAAAG
* *
706597 GCTTGGTTTAATCATTTATAGTTTCGTATTCAA
1 GCTTGATTTAATCATTTATAGTTTCATATTCAA
706630 GTTGAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (35 bp):
GCTTGATTTAATCATTTATAGTTTCATATTCAAAG
Found at i:706742 original size:24 final size:23
Alignment explanation
Indices: 706710--706768 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 23
706700 TTTTTTATCA
706710 ATTTTTTAAGATGAGAATCGAAT
1 ATTTTTTAAGATGAGAATCGAAT
* *
706733 CATTTCTTAAAATGAGAATCGAAT
1 -ATTTTTTAAGATGAGAATCGAAT
706757 ATTTTTTAAGAT
1 ATTTTTTAAGAT
706769 AATGGTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 10 0.32
24 21 0.68
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.41
Consensus pattern (23 bp):
ATTTTTTAAGATGAGAATCGAAT
Found at i:707045 original size:8 final size:8
Alignment explanation
Indices: 706982--707068 Score: 67
Period size: 8 Copynumber: 11.0 Consensus size: 8
706972 AAGAACATAT
706982 AATT-TAA
1 AATTATAA
706989 AATTAATAA
1 AATT-ATAA
706998 AA-TAT-A
1 AATTATAA
*
707004 AATTAT-T
1 AATTATAA
707011 AATATATCAA
1 AAT-TAT-AA
707021 AATTAATAA
1 AATT-ATAA
**
707030 AAAAATAA
1 AATTATAA
707038 AATTATAA
1 AATTATAA
707046 AATTATAA
1 AATTATAA
*
707054 AA-TATAT
1 AATTATAA
707061 AATTATAA
1 AATTATAA
707069 TATAAATATA
Statistics
Matches: 64, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
6 3 0.05
7 18 0.28
8 28 0.44
9 10 0.16
10 5 0.08
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (8 bp):
AATTATAA
Found at i:707056 original size:33 final size:30
Alignment explanation
Indices: 706982--707056 Score: 80
Period size: 33 Copynumber: 2.4 Consensus size: 30
706972 AAGAACATAT
* *
706982 AATT-TAAAATTAATAAAATATAAATTATT
1 AATTATAAAATTAATAAAAAATAAATTATA
707011 AATATATCAAAATTAATAAAAAAATAAAATTATAA
1 AAT-TAT-AAAATTAAT-AAAAAAT-AAATTAT-A
707046 AATTATAAAAT
1 AATTATAAAAT
707057 ATATAATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
29 3 0.08
30 1 0.03
31 1 0.03
32 9 0.24
33 11 0.29
34 10 0.26
35 3 0.08
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (30 bp):
AATTATAAAATTAATAAAAAATAAATTATA
Found at i:707064 original size:15 final size:16
Alignment explanation
Indices: 706982--707068 Score: 67
Period size: 15 Copynumber: 5.5 Consensus size: 16
706972 AAGAACATAT
706982 AATT-TAAAATTAATAA
1 AATTATAAAATT-ATAA
*
706998 AA-TAT-AAATTAT-T
1 AATTATAAAATTATAA
707011 AATATATCAAAATTAATAA
1 AAT-TAT-AAAATT-ATAA
**
707030 AAAAATAAAATTATAA
1 AATTATAAAATTATAA
*
707046 AATTATAAAA-TATAT
1 AATTATAAAATTATAA
707061 AATTATAA
1 AATTATAA
707069 TATAAATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
13 2 0.04
14 2 0.04
15 21 0.37
16 15 0.26
17 11 0.19
18 4 0.07
19 2 0.04
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTATAAAATTATAA
Found at i:708782 original size:23 final size:23
Alignment explanation
Indices: 708746--708792 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
708736 ACAAGTGGTC
* *
708746 TATATATGTGTATATACATACTA
1 TATATATATATATATACATACTA
708769 TATATATATATATATACATACTA
1 TATATATATATATATACATACTA
708792 T
1 T
708793 TAAGTTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (23 bp):
TATATATATATATATACATACTA
Found at i:711134 original size:2 final size:2
Alignment explanation
Indices: 711127--711161 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
711117 ATGAGGATTT
711127 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
711162 GTATGTATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:713109 original size:18 final size:20
Alignment explanation
Indices: 713076--713132 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 20
713066 AAATTAATAA
*
713076 TTTTTATGTAAAAAATGAGC
1 TTTTTATGTAAAAAATAAGC
*
713096 TTTTTA-GT-AAAAATAAGT
1 TTTTTATGTAAAAAATAAGC
*
713114 TTTTTAAAGTAAAAAATAA
1 TTTTT-ATGTAAAAAATAA
713133 ATATTAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 13 0.41
19 3 0.09
20 8 0.25
21 8 0.25
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (20 bp):
TTTTTATGTAAAAAATAAGC
Found at i:713513 original size:24 final size:24
Alignment explanation
Indices: 713462--713515 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
713452 AATGTGCATA
*
713462 TTTTT-AATTTATTTTATTATTAT
1 TTTTTAAATTTATTTTATTATAAT
*
713485 ATTTTAAATTTATCTTTA-TATAAT
1 TTTTTAAATTTAT-TTTATTATAAT
713509 TTTTTAA
1 TTTTTAA
713516 CATAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 18 0.69
25 4 0.15
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTTAAATTTATTTTATTATAAT
Found at i:713668 original size:5 final size:5
Alignment explanation
Indices: 713658--713692 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
713648 GGAATTACCT
*
713658 TTTTA TTTTA TTTTA ATTTA TTTTA TTTTA GTTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTT
713693 TAATTTGTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:713679 original size:15 final size:15
Alignment explanation
Indices: 713659--713687 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
713649 GAATTACCTT
713659 TTTATTTTATTTTAA
1 TTTATTTTATTTTAA
713674 TTTATTTTATTTTA
1 TTTATTTTATTTTA
713688 GTTTTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTTATTTTAA
Found at i:714229 original size:44 final size:45
Alignment explanation
Indices: 714180--714265 Score: 104
Period size: 44 Copynumber: 1.9 Consensus size: 45
714170 AATATTTATA
* *
714180 ATTAAAACAAATTAAT-ATCTTTTTGATTTT-TTAAATAAATTTTT
1 ATTAAAA-AAATTAATGATCTTTTTAATTTTATGAAATAAATTTTT
** *
714224 ATTAAAAATTTTAATGATTTTTTTAATTTTATGAAATAAATT
1 ATTAAAAAAATTAATGATCTTTTTAATTTTATGAAATAAATT
714266 AAAAAATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
43 6 0.17
44 19 0.54
45 10 0.29
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.52
Consensus pattern (45 bp):
ATTAAAAAAATTAATGATCTTTTTAATTTTATGAAATAAATTTTT
Found at i:714512 original size:19 final size:18
Alignment explanation
Indices: 714478--714526 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
714468 AATGAATATA
714478 TAAATTTTAATAATAATT
1 TAAATTTTAATAATAATT
*
714496 TAAATTATTATTAATAA-T
1 TAAATT-TTAATAATAATT
*
714514 GAAATTTT-ATAAT
1 TAAATTTTAATAAT
714527 TTTATAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 4 0.15
17 2 0.07
18 12 0.44
19 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TAAATTTTAATAATAATT
Found at i:714787 original size:2 final size:2
Alignment explanation
Indices: 714782--714813 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
714772 GCAAAAAAAC
714782 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
714814 CGCACTGGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:719421 original size:14 final size:14
Alignment explanation
Indices: 719388--719429 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
719378 AAAAATATTT
*
719388 ATAATATT-AAAAT
1 ATAATATTAAAAAA
719401 ATAAATATTAAAAAA
1 AT-AATATTAAAAAA
719416 ATAATATTTAAAAA
1 ATAATA-TTAAAAA
719430 GCAAGCTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 2 0.08
14 10 0.40
15 13 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATATTAAAAAA
Found at i:719561 original size:132 final size:131
Alignment explanation
Indices: 719284--719545 Score: 366
Period size: 132 Copynumber: 2.0 Consensus size: 131
719274 ATCTTAATTC
*
719284 TAATATTTAAAAAGCAAGCTTCATTTGATTCAACTTATTTTTTAAATTATATAATACATTTTATT
1 TAATATTTAAAAAGCAAGCTTCATTCGATTCAACTTATTTTTTAAATTATATAATACATTTTATT
* * * *
719349 TTTATTTTTATTTATATTATATGAAGAATAAAAATATTTATAATATTAAAATATAAATATTAAAA
66 TTTATTTTTATTTATATTATAT--AGAATAAAAATATATAAAAAATAAAAATATAAATATTAAAA
719414 AAA
129 AAA
*
719417 TAATATTTAAAAAGCAAGCTTCATTCGATTTAACTTATTTTTT-AATTATATAATACATTTTATT
1 TAATATTTAAAAAGCAAGCTTCATTCGATTCAACTTATTTTTTAAATTATATAATACATTTTATT
* * * * *
719481 TTTATTTTTATTTATATTATAT-GATTTATATTGTATAAAAAATAAAAATATTTATAATATTAAA
66 TTTATTTTTATTTATATTATATAGAATAAAAATATATAAAAAATAAAAATA--TA-AATATTAAA
719545 A
128 A
719546 TGTAAATATT
Statistics
Matches: 115, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
129 19 0.17
131 2 0.02
132 53 0.46
133 41 0.36
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.48
Consensus pattern (131 bp):
TAATATTTAAAAAGCAAGCTTCATTCGATTCAACTTATTTTTTAAATTATATAATACATTTTATT
TTTATTTTTATTTATATTATATAGAATAAAAATATATAAAAAATAAAAATATAAATATTAAAAAA
A
Found at i:720024 original size:21 final size:21
Alignment explanation
Indices: 719998--720102 Score: 70
Period size: 21 Copynumber: 4.7 Consensus size: 21
719988 ATTTATATAA
719998 ATTTTTATATATTAATTATTT
1 ATTTTTATATATTAATTATTT
* *
720019 ATTTTTATATTTTGATATATTT
1 ATTTTTATATATTAAT-TATTT
720041 AAATATTTATATTATATTAATATTATTT
1 --AT-TTT-TA-TATATT-A-ATTATTT
* *
720069 -TATGTTATATTTTAATTATTT
1 AT-TTTTATATATTAATTATTT
*
720090 -TTTATATATATTA
1 ATTTTTATATATTA
720103 TGTTTATGTT
Statistics
Matches: 67, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
20 9 0.13
21 22 0.33
22 6 0.09
23 5 0.07
24 4 0.06
25 7 0.10
26 2 0.03
27 5 0.07
28 5 0.07
29 2 0.03
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
ATTTTTATATATTAATTATTT
Found at i:720037 original size:29 final size:29
Alignment explanation
Indices: 719988--720058 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
719978 AAAAATATAA
* * *
719988 ATTTATA-TAAATTTTTATATA-TTAATT
1 ATTTATATTATATTTTGATATATTTAAAT
*
720015 ATTTATTTTTATATTTTGATATATTTAAAT
1 ATTTA-TATTATATTTTGATATATTTAAAT
720045 ATTTATATTATATT
1 ATTTATATTATATT
720059 AATATTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 5 0.14
28 1 0.03
29 20 0.56
30 10 0.28
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (29 bp):
ATTTATATTATATTTTGATATATTTAAAT
Found at i:720063 original size:11 final size:11
Alignment explanation
Indices: 720043--720101 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
720033 ATATATTTAA
720043 ATATTTATATT
1 ATATTTATATT
*
720054 ATATTAATATT
1 ATATTTATATT
*
720065 AT-TTTATGTT
1 ATATTTATATT
720075 ATATTT-TAATT
1 ATATTTAT-ATT
*
720086 AT-TTTTTATAT
1 ATATTTATAT-T
720097 ATATT
1 ATATT
720102 ATGTTTATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
10 14 0.36
11 23 0.59
12 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
ATATTTATATT
Found at i:720144 original size:48 final size:48
Alignment explanation
Indices: 720043--720144 Score: 107
Period size: 48 Copynumber: 2.1 Consensus size: 48
720033 ATATATTTAA
* * *
720043 ATATTTATATTATATTAATATTATTTTATGTTATATTTTAATTATTTT
1 ATATATATATTATATTAATATTATTTTATGTTATATTTAAATTAGTTT
* * * * * *
720091 TTATATATATTATGTTTATGTTATTTTGT-TTATAATTTAAATTCGTTT
1 ATATATATATTATATTAATATTATTTTATGTTAT-ATTTAAATTAGTTT
720139 ATATAT
1 ATATAT
720145 TTTAACATGT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
47 4 0.09
48 39 0.91
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (48 bp):
ATATATATATTATATTAATATTATTTTATGTTATATTTAAATTAGTTT
Found at i:720190 original size:12 final size:12
Alignment explanation
Indices: 720173--720212 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
720163 ACGTGTCGTA
720173 TTTATATTATTT
1 TTTATATTATTT
**
720185 TTTATATTATAA
1 TTTATATTATTT
720197 TTTA-ATTATTT
1 TTTATATTATTT
720208 TTTAT
1 TTTAT
720213 TTTTTGTGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:720307 original size:25 final size:23
Alignment explanation
Indices: 720279--720326 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
720269 GTATACTTAA
720279 AATTTTATAAATTTATATAAATTTT
1 AATTTT-T-AATTTATATAAATTTT
* *
720304 AATTTTTCATTTATATATATTTT
1 AATTTTTAATTTATATAAATTTT
720327 GATGTGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
24 1 0.05
25 6 0.29
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
AATTTTTAATTTATATAAATTTT
Found at i:720496 original size:20 final size:22
Alignment explanation
Indices: 720449--720496 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
720439 TATGCATATC
*
720449 ATGTTCATATTATTTTTCTTTTT
1 ATGTTCATATTA-TTTTCTTTAT
*
720472 GTGTTCATATTA-TTT-TTTAT
1 ATGTTCATATTATTTTCTTTAT
720492 ATGTT
1 ATGTT
720497 TAAAATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 8 0.36
21 3 0.14
23 11 0.50
ACGTcount: A:0.19, C:0.06, G:0.08, T:0.67
Consensus pattern (22 bp):
ATGTTCATATTATTTTCTTTAT
Found at i:720652 original size:17 final size:18
Alignment explanation
Indices: 720607--720663 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 18
720597 ATGTTATGTT
720607 TTTTATTATTTATAT-ATA
1 TTTTA-TATTTATATCATA
* *
720625 TATTATGTTTATATCATA
1 TTTTATATTTATATCATA
*
720643 TTTTA-ATTTATCTCATA
1 TTTTATATTTATATCATA
720660 TTTT
1 TTTT
720664 CGACACATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
17 22 0.67
18 11 0.33
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTATATTTATATCATA
Found at i:732353 original size:2 final size:2
Alignment explanation
Indices: 732346--732377 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
732336 AATTTACAAG
732346 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
732378 CACACATGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:733253 original size:17 final size:17
Alignment explanation
Indices: 733230--733263 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
733220 ATAGACAATT
*
733230 TTTTTTTCATATTTTTTA
1 TTTTTTACA-ATTTTTTA
733248 TTTTTTACAATTTTTT
1 TTTTTTACAATTTTTT
733264 TTACATGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTACAATTTTTTA
Found at i:734237 original size:12 final size:13
Alignment explanation
Indices: 734220--734248 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
734210 TAAATTATTT
734220 ATTTAAAT-TAAA
1 ATTTAAATATAAA
734232 ATTTAAATATAAA
1 ATTTAAATATAAA
734245 ATTT
1 ATTT
734249 TTAATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTTAAATATAAA
Found at i:734269 original size:5 final size:5
Alignment explanation
Indices: 734248--734291 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
734238 ATATAAAATT
* *
734248 TTTAA TTTAA ATAAA TTTAA TTTAA TTTAA TTTATTA TTTAA TT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTA--A TTTAA TT
734292 ATAAATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 28 0.85
7 5 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTTAA
Found at i:734289 original size:17 final size:17
Alignment explanation
Indices: 734267--734313 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
734257 AATAAATTTA
734267 ATTTAATTTAATTTATT
1 ATTTAATTTAATTTATT
*
734284 ATTTAATTATAA-ATATT
1 ATTTAATT-TAATTTATT
*
734301 ATTT-TTTTAATTT
1 ATTTAATTTAATTT
734314 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.12
16 3 0.12
17 16 0.64
18 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTAATTTAATTTATT
Found at i:734453 original size:5 final size:5
Alignment explanation
Indices: 734427--734488 Score: 53
Period size: 5 Copynumber: 13.0 Consensus size: 5
734417 ACATTTTAAT
* *
734427 TATAA TTTAGA TATGA TA-AA TATAA TATAAA TATAA TATAA TA-AA -ATAA
1 TATAA TATA-A TATAA TATAA TATAA TAT-AA TATAA TATAA TATAA TATAA
734476 TATAA -A-AA TATAA
1 TATAA TATAA TATAA
734489 ATATTTTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
3 3 0.07
4 9 0.20
5 26 0.57
6 8 0.17
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (5 bp):
TATAA
Found at i:734458 original size:11 final size:11
Alignment explanation
Indices: 734442--734492 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
734432 TTTAGATATG
734442 ATAAATATAAT
1 ATAAATATAAT
734453 ATAAATATAAT
1 ATAAATATAAT
734464 AT-AATA-AA-
1 ATAAATATAAT
*
734472 ATAATATAAAAAT
1 ATAA-AT-ATAAT
734485 ATAAATAT
1 ATAAATAT
734493 TTTAAATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
8 2 0.06
9 3 0.09
10 6 0.18
11 15 0.44
12 4 0.12
13 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:734488 original size:13 final size:13
Alignment explanation
Indices: 734444--734488 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
734434 TAGATATGAT
734444 AAATATAATAT--
1 AAATATAATATAA
734455 AAATATAATATAA
1 AAATATAATATAA
734468 TAAA-ATAATATAA
1 -AAATATAATATAA
734481 AAATATAA
1 AAATATAA
734489 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.37
12 3 0.10
13 13 0.43
14 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:734551 original size:32 final size:31
Alignment explanation
Indices: 734472--734551 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
734462 ATATAATAAA
** *
734472 ATAATATAAAAATATAAATATTTTAAATTTAT
1 ATAATAT-AAAATATTTATATTTTAAAATTAT
** * *
734504 ATAATACGAATTATTTATGTTTTAAAATTAT
1 ATAATATAAAATATTTATATTTTAAAATTAT
734535 ATAAATATAAAATATTT
1 AT-AATATAAAATATTT
734552 TAAATATTAT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
31 20 0.54
32 17 0.46
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (31 bp):
ATAATATAAAATATTTATATTTTAAAATTAT
Found at i:734571 original size:26 final size:27
Alignment explanation
Indices: 734443--734606 Score: 97
Period size: 26 Copynumber: 5.9 Consensus size: 27
734433 TTAGATATGA
* * *
734443 TAAATATAATATAAATATAATATA-AT
1 TAAATATTATATAAATATAAAATATTT
* * *
734469 AAAATAATATAAAAATAT-AAATATTT
1 TAAATATTATATAAATATAAAATATTT
* *
734495 TAAAT-TTATAT-AATACGAATTATTTATGTTT
1 TAAATATTATATAAATA-TAA--A---ATATTT
734526 TAAA-ATTATATAAATATAAAATATTT
1 TAAATATTATATAAATATAAAATATTT
* *
734552 TAAATATTAT-TATATGTAAAATATTAT
1 TAAATATTATATAAATATAAAATATT-T
*
734579 TATAATATTAAATAAATTATATAAATAT
1 TA-AATATTATATAAA-TATA-AAATAT
734607 GATATAAAAA
Statistics
Matches: 104, Mismatches: 18, Indels: 27
0.70 0.12 0.18
Matches are distributed among these distances:
24 4 0.04
25 8 0.08
26 42 0.40
27 8 0.08
28 8 0.08
29 4 0.04
30 3 0.03
31 23 0.22
32 4 0.04
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (27 bp):
TAAATATTATATAAATATAAAATATTT
Found at i:734597 original size:20 final size:21
Alignment explanation
Indices: 734552--734607 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
734542 TAAAATATTT
*
734552 TAAA-TATTATTATATGTAAA
1 TAAATTATTATAATATGTAAA
*
734572 -ATATTATTATAATAT-TAAA
1 TAAATTATTATAATATGTAAA
734591 TAAATTA-TATAAATATG
1 TAAATTATTAT-AATATG
734608 ATATAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 9 0.31
20 20 0.69
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
TAAATTATTATAATATGTAAA
Done.