Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1041
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: 1020100
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 3 of 4
Found at i:490209 original size:28 final size:29
Alignment explanation
Indices: 490168--490223 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
490158 TTATTATAAG
** *
490168 ATGATAAATTTTATTTATTATA-TAAATA
1 ATGATAAAACTTATTTATCATATTAAATA
490196 ATGATAAAACTTATTTATCATATTAAAT
1 ATGATAAAACTTATTTATCATATTAAAT
490224 TACCAATGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (29 bp):
ATGATAAAACTTATTTATCATATTAAATA
Found at i:490454 original size:20 final size:22
Alignment explanation
Indices: 490431--490481 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
490421 ATTATTTAAA
490431 ATATTAAAATAT-TAT-TTTTT
1 ATATTAAAATATATATATTTTT
* *
490451 ATATTAATATTTATATATTTTT
1 ATATTAAAATATATATATTTTT
490473 ATAATTAAA
1 AT-ATTAAA
490482 TTTAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 10 0.40
21 3 0.12
22 7 0.28
23 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTAAAATATATATATTTTT
Found at i:501200 original size:7 final size:7
Alignment explanation
Indices: 501182--501210 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
501172 GGCCTTGGCC
501182 TTAGCC-
1 TTAGCCT
501188 TTAGCCT
1 TTAGCCT
501195 TTAGCCT
1 TTAGCCT
501202 TTAGCCT
1 TTAGCCT
501209 TT
1 TT
501211 CAATGGTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (7 bp):
TTAGCCT
Found at i:501207 original size:14 final size:13
Alignment explanation
Indices: 501173--501210 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
501163 CTGTAGCTAG
*
501173 GCCTTGGCC-TTA
1 GCCTTAGCCTTTA
501185 GCCTTAGCCTTTA
1 GCCTTAGCCTTTA
501198 GCCTTTAGCCTTT
1 GCC-TTAGCCTTT
501211 CAATGGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 8 0.35
13 6 0.26
14 9 0.39
ACGTcount: A:0.11, C:0.32, G:0.18, T:0.39
Consensus pattern (13 bp):
GCCTTAGCCTTTA
Found at i:502448 original size:14 final size:14
Alignment explanation
Indices: 502431--502480 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
502421 ATTAGTGAGC
*
502431 ATTAAGTTTTTATT
1 ATTAAATTTTTATT
*
502445 ATTAAATTTATTTTTT
1 ATTAAA-TT-TTTATT
*
502461 ATTAAATTTTTAAT
1 ATTAAATTTTTATT
502475 ATTAAA
1 ATTAAA
502481 AAATTTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 15 0.50
15 4 0.13
16 11 0.37
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTAAATTTTTATT
Found at i:502464 original size:16 final size:17
Alignment explanation
Indices: 502438--502469 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
502428 AGCATTAAGT
502438 TTTTATTATTAAATTTA
1 TTTTATTATTAAATTTA
502455 TTTT-TTATTAAATTT
1 TTTTATTATTAAATTT
502470 TTAATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTATTATTAAATTTA
Found at i:502537 original size:19 final size:19
Alignment explanation
Indices: 502513--502551 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
502503 TAATTAATAT
502513 ATTATGACGCCGACATAAG
1 ATTATGACGCCGACATAAG
*
502532 ATTATGATGCCGACATAAG
1 ATTATGACGCCGACATAAG
502551 A
1 A
502552 ACTAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (19 bp):
ATTATGACGCCGACATAAG
Found at i:502954 original size:6 final size:6
Alignment explanation
Indices: 502939--502973 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
502929 ACCCCCTTTG
* *
502939 CCACCC CCACCA CCACCC CCACCT CCACCC CCACC
1 CCACCC CCACCC CCACCC CCACCC CCACCC CCACC
502974 TCCCCCACCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.20, C:0.77, G:0.00, T:0.03
Consensus pattern (6 bp):
CCACCC
Found at i:502974 original size:12 final size:12
Alignment explanation
Indices: 502939--502986 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
502929 ACCCCCTTTG
*
502939 CCACCCCCACCA
1 CCACCCCCACCT
502951 CCACCCCCACCT
1 CCACCCCCACCT
502963 CCACCCCCACCT
1 CCACCCCCACCT
502975 CC-CCCACCACCT
1 CCACCC-CCACCT
502987 AAACCGCCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
11 3 0.09
12 31 0.91
ACGTcount: A:0.19, C:0.75, G:0.00, T:0.06
Consensus pattern (12 bp):
CCACCCCCACCT
Found at i:503955 original size:2 final size:2
Alignment explanation
Indices: 503948--503976 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
503938 ATCATCGGAC
503948 CA CA CA CA CA CA CA CA CA -A CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
503977 GACAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:505748 original size:21 final size:21
Alignment explanation
Indices: 505694--505750 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
505684 ATATATTTTT
* *
505694 ATAATTAAAATTAAACATATA
1 ATAATTTAAATTAAACAAATA
* ** *
505715 ATATTTTTTATTATACAAATA
1 ATAATTTAAATTAAACAAATA
505736 ATAATTTAAATTAAA
1 ATAATTTAAATTAAA
505751 TTGACTCAAA
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAATTTAAATTAAACAAATA
Found at i:506629 original size:16 final size:18
Alignment explanation
Indices: 506598--506632 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
506588 ATTATTTATA
506598 TTATATAATTTAAAATAT
1 TTATATAATTTAAAATAT
506616 TTATAT-ATTT-AAATAT
1 TTATATAATTTAAAATAT
506632 T
1 T
506633 ATTCATATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATATAATTTAAAATAT
Found at i:506657 original size:5 final size:5
Alignment explanation
Indices: 506647--506714 Score: 56
Period size: 5 Copynumber: 14.4 Consensus size: 5
506637 ATATTGATTT
* * *
506647 TTATA TTATA TTATA TTTTA TTTTAA TTATA TT-TT TTATA TTATA -TA-A
1 TTATA TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA TTATA
*
506695 TTATA TT-TA ATA-A TTATA TT
1 TTATA TTATA TTATA TTATA TT
506715 TACATTATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
3 1 0.02
4 13 0.25
5 33 0.65
6 4 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:506677 original size:16 final size:17
Alignment explanation
Indices: 506632--506692 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
506622 ATTTAAATAT
506632 TATTCATATTGAT-TTTTA
1 TATT-ATATT-ATATTTTA
506650 TATTATATTATATTTTA
1 TATTATATTATATTTTA
*
506667 TTTTA-ATTATATTTTTTA
1 TATTATATTATA--TTTTA
506685 TATTATAT
1 TATTATAT
506693 AATTATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
16 8 0.22
17 14 0.38
18 13 0.35
19 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (17 bp):
TATTATATTATATTTTA
Found at i:506690 original size:35 final size:34
Alignment explanation
Indices: 506644--506715 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 34
506634 TTCATATTGA
*
506644 TTTTTATATTATATTATATTTTATTT-TAATTATAT
1 TTTTTATATTATA-TA-ATTATATTTATAATTATAT
506679 TTTTTATATTATATAATTATATTTAATAATTATAT
1 TTTTTATATTATATAATTATATTT-ATAATTATAT
506714 TT
1 TT
506716 ACATTATGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
33 8 0.24
34 2 0.06
35 24 0.71
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (34 bp):
TTTTTATATTATATAATTATATTTATAATTATAT
Found at i:506698 original size:13 final size:12
Alignment explanation
Indices: 506646--506716 Score: 66
Period size: 13 Copynumber: 6.3 Consensus size: 12
506636 CATATTGATT
506646 TTTAT-ATTATA
1 TTTATAATTATA
*
506657 -TTAT-ATTTTA
1 TTTATAATTATA
506667 TTT-TAATTATA
1 TTTATAATTATA
506678 TTT-T--TTATA
1 TTTATAATTATA
506687 TTATATAATTATA
1 TT-TATAATTATA
506700 TTTAATAATTATA
1 TTT-ATAATTATA
506713 TTTA
1 TTTA
506717 CATTATGTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
9 7 0.14
10 11 0.22
11 12 0.24
12 2 0.04
13 19 0.37
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTATAATTATA
Found at i:508825 original size:25 final size:25
Alignment explanation
Indices: 508791--508840 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
508781 TTTGGCCATG
508791 GCTTATTTTAATTTTCATGTAAAGT
1 GCTTATTTTAATTTTCATGTAAAGT
508816 GCTTATTTTAATTTTCATGTAAAGT
1 GCTTATTTTAATTTTCATGTAAAGT
508841 ATATCTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.12, T:0.52
Consensus pattern (25 bp):
GCTTATTTTAATTTTCATGTAAAGT
Found at i:513251 original size:2 final size:2
Alignment explanation
Indices: 513244--513271 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
513234 TTTGTAATAC
513244 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
513272 ATTATAAGTA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:536861 original size:25 final size:26
Alignment explanation
Indices: 536818--536869 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
536808 ATTTAATATG
* *
536818 ATTTAATTTAAATTATATAATTATTA
1 ATTTAATTAAAATTATATAAATATTA
536844 ATTTAATTAAAATT-TATAAATATTA
1 ATTTAATTAAAATTATATAAATATTA
536869 A
1 A
536870 AAAAATCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTTAATTAAAATTATATAAATATTA
Found at i:537275 original size:29 final size:31
Alignment explanation
Indices: 537215--537282 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 31
537205 TAATGAGTAA
*
537215 TTATTTATAATACAATGATAATATATAATTT
1 TTATTTATAATACAATGATAATATAAAATTT
* *
537246 TTATTTATAATA-TATTA-AATATAAAATTT
1 TTATTTATAATACAATGATAATATAAAATTT
*
537275 TAATTTAT
1 TTATTTAT
537283 TTACGAGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.55
30 3 0.09
31 12 0.36
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
TTATTTATAATACAATGATAATATAAAATTT
Found at i:538496 original size:3 final size:3
Alignment explanation
Indices: 538488--538515 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
538478 AGATGATCAT
538488 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
538516 TGCGTCGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:546216 original size:4 final size:4
Alignment explanation
Indices: 546207--546231 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
546197 TGGTAGTGGT
546207 AGCC AGCC AGCC AGCC AGCC AGCC A
1 AGCC AGCC AGCC AGCC AGCC AGCC A
546232 TGGCACCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.48, G:0.24, T:0.00
Consensus pattern (4 bp):
AGCC
Found at i:546887 original size:2 final size:2
Alignment explanation
Indices: 546880--546920 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
546870 TGTGGCTACT
546880 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
546921 GTGATCAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:550187 original size:20 final size:19
Alignment explanation
Indices: 550170--550209 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
550160 TCAAATATGT
550170 ATTAA-AAATTAAAAATATA
1 ATTAATAAA-TAAAAATATA
550189 ATTAATAAATAAAAAT-TA
1 ATTAATAAATAAAAATATA
550207 ATT
1 ATT
550210 TAATTGATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 12 0.60
20 3 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTAATAAATAAAAATATA
Found at i:550268 original size:16 final size:16
Alignment explanation
Indices: 550247--550278 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
550237 ACAGATAATT
550247 TTTTATTTAATTTTTA
1 TTTTATTTAATTTTTA
*
550263 TTTTATTTTATTTTTA
1 TTTTATTTAATTTTTA
550279 ATTATAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTATTTAATTTTTA
Found at i:550379 original size:16 final size:16
Alignment explanation
Indices: 550355--550406 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
550345 TATATTATTA
550355 TTAATTAATTATTATAT
1 TTAA-TAATTATTATAT
550372 TTAATAATTATT-TAT
1 TTAATAATTATTATAT
550387 ATTAA-AA-TA-TATAT
1 -TTAATAATTATTATAT
550401 TTAATA
1 TTAATA
550407 TATAACTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
13 5 0.16
14 6 0.19
15 5 0.16
16 12 0.38
17 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAATAATTATTATAT
Found at i:550386 original size:17 final size:17
Alignment explanation
Indices: 550355--550389 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
550345 TATATTATTA
550355 TTAATTAATTATTATAT
1 TTAATTAATTATTATAT
550372 TTAA-TAATTATTTATAT
1 TTAATTAATTA-TTATAT
550389 T
1 T
550390 AAAATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTAATTAATTATTATAT
Found at i:562859 original size:40 final size:40
Alignment explanation
Indices: 562804--562885 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
562794 GCCTACGGAG
562804 AAAATAAAATTACCCTTTTTCCCCACACTGATAACAGAAT
1 AAAATAAAATTACCCTTTTTCCCCACACTGATAACAGAAT
562844 AAAATAAAATTACCCTTTTTCCCCACACTGATAACAGAAT
1 AAAATAAAATTACCCTTTTTCCCCACACTGATAACAGAAT
562884 AA
1 AA
562886 TCAAGTCCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.44, C:0.24, G:0.05, T:0.27
Consensus pattern (40 bp):
AAAATAAAATTACCCTTTTTCCCCACACTGATAACAGAAT
Found at i:578992 original size:2 final size:2
Alignment explanation
Indices: 578985--579012 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
578975 TTATAAATTA
578985 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
579013 CTCAGTTCCA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:579486 original size:2 final size:2
Alignment explanation
Indices: 579479--579512 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
579469 AAGCATGGAC
*
579479 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
579513 CAATTATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:585221 original size:13 final size:13
Alignment explanation
Indices: 585203--585228 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
585193 TACACAAAGT
585203 ATGTATCGATACA
1 ATGTATCGATACA
585216 ATGTATCGATACA
1 ATGTATCGATACA
585229 CCAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:585226 original size:32 final size:34
Alignment explanation
Indices: 585185--585249 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
585175 TAGCCAAACT
**
585185 TGTATCGATACA-C-AAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAAATGTATCGATACAA
585217 TGTATCGATACACCAAAAAAATGTATCGATACA
1 TGTATCGATACACCAAAAAAATGTATCGATACA
585250 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 12 0.41
33 1 0.03
34 16 0.55
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (34 bp):
TGTATCGATACACCAAAAAAATGTATCGATACAA
Found at i:585314 original size:20 final size:22
Alignment explanation
Indices: 585283--585326 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
585273 GCTATATTTT
585283 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
585304 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
585325 CA
1 CA
585327 CGGGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:587602 original size:2 final size:2
Alignment explanation
Indices: 587597--587629 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
587587 ATACTGATCC
587597 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
587630 GACATAAGTA
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:588595 original size:318 final size:320
Alignment explanation
Indices: 588004--588649 Score: 1086
Period size: 318 Copynumber: 2.0 Consensus size: 320
587994 GGTCCAGCCA
*
588004 TTTGGCCTTGGCGCCAACCACTCAGCTCCCTCAATTTCTCACATCTACCCCTCAGGCAGGACTGC
1 TTTGGCCTTGACGCCAACCACTCAGCTCCCTCAATTTCTCACATCTACCCCTCAGGCAGGACTGC
588069 TGCAAAGAAAACTGAAGCCCAAAAACAAAAGGGCATTACGGGCAAAATGAAAGGTCCTCCTCTCC
66 TGCAAAGAAAACTGAAGCCCAAAAACAAAAGGGCATTACGGGCAAAATGAAAGGTCCTCCTCTCC
* * * *
588134 ATATTGTTAATACTAAATACTTTGCCGTTACGATAAAGCTAAACCTTTTTGGTTTTGGCCTTTGG
131 ATAGTGTTAATACTAAATACCTAGCCGTTACGATAAAGCTAAACCCTTTTGGTTTTGGCCTTTGG
* *
588199 CTAAAGCCTCGAAACTCTCTTATTATTATATTATTATTTAATTCTAGTGCATTCGAGC-AAAAAA
196 CTAAAGCCTCGAAACTCTCTTATTATTATATTATTATTTAATTCTAGAGCATTCAAGCAAAAAAA
* *
588263 -ATA-ATAATAATAATAATTAATTTCCCTTGTAAAGTAGGTAACGTGAAATTGAGATAGCT
261 CAAATATAATAATAATAATTAATTTCCCTTGCAAAGTAGGT-ACGTGAAATTGAGATAGCT
588322 TTTGGCCTTGACGCCAACCACTCAGCTCCCTCAATTTCTCACATCTACCCCTCAGGCAGGACTGC
1 TTTGGCCTTGACGCCAACCACTCAGCTCCCTCAATTTCTCACATCTACCCCTCAGGCAGGACTGC
*
588387 TGCAAAGGAAACTGAAGCCCAAAAACAAAAGGGCATTACGGGCAAAATGAAAGGTCCTCCTCTCC
66 TGCAAAGAAAACTGAAGCCCAAAAACAAAAGGGCATTACGGGCAAAATGAAAGGTCCTCCTCTCC
588452 ATAGTGTTAATACTAAATACCTAGCCGTTACGATAAAGCTAAACCCTTTTGGTTTTGGCCTTTGG
131 ATAGTGTTAATACTAAATACCTAGCCGTTACGATAAAGCTAAACCCTTTTGGTTTTGGCCTTTGG
*
588517 CTAAAGCCTCGAAACTCTCTTATTATTATATTATTATTTAATTCTAGAGCATTCAATTCAATCGA
196 CTAAAGCCTCGAAACTCTCTTATTATTATATTATTATTTAATTCTAGAGCATTCAA-GCAA---A
* *
588582 GCAAA-AAA-ATAATAATAATAATTAATTTCCCTTGCAAAGTAGGTCCGTGAAATTGAGATAGCT
257 -AAAACAAATATAATAATAATAATTAATTTCCCTTGCAAAGTAGGTACGTGAAATTGAGATAGCT
588645 TTTGG
1 TTTGG
588650 TTTCATTATC
Statistics
Matches: 309, Mismatches: 13, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
318 243 0.79
319 1 0.00
320 1 0.00
323 24 0.08
324 40 0.13
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (320 bp):
TTTGGCCTTGACGCCAACCACTCAGCTCCCTCAATTTCTCACATCTACCCCTCAGGCAGGACTGC
TGCAAAGAAAACTGAAGCCCAAAAACAAAAGGGCATTACGGGCAAAATGAAAGGTCCTCCTCTCC
ATAGTGTTAATACTAAATACCTAGCCGTTACGATAAAGCTAAACCCTTTTGGTTTTGGCCTTTGG
CTAAAGCCTCGAAACTCTCTTATTATTATATTATTATTTAATTCTAGAGCATTCAAGCAAAAAAA
CAAATATAATAATAATAATTAATTTCCCTTGCAAAGTAGGTACGTGAAATTGAGATAGCT
Found at i:594784 original size:3 final size:3
Alignment explanation
Indices: 594776--594808 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
594766 GGACATGTTA
594776 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
594809 GGACAGACTT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:599158 original size:32 final size:31
Alignment explanation
Indices: 599122--599188 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 31
599112 TTTTATATAA
* *
599122 ATATTTTTTTATTTTTTTATATTTAAAATATT
1 ATATTTTTATATTATTTTATATTT-AAATATT
599154 ATATTTTTATATTATTTTATATTTAAATATT
1 ATATTTTTATATTATTTTATATTTAAATATT
599185 -TATT
1 ATATT
599189 AAAAATAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 4 0.12
31 7 0.21
32 22 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (31 bp):
ATATTTTTATATTATTTTATATTTAAATATT
Found at i:599178 original size:16 final size:16
Alignment explanation
Indices: 599131--599178 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
599121 AATATTTTTT
*
599131 TATTTTTTTATATTTA
1 TATTATTTTATATTTA
* * * *
599147 AAATATTATATTTTTA
1 TATTATTTTATATTTA
599163 TATTATTTTATATTTA
1 TATTATTTTATATTTA
599179 AATATTTATT
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTATTTTATATTTA
Found at i:602403 original size:33 final size:34
Alignment explanation
Indices: 602358--602425 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
602348 AGATTCTTAA
* * *
602358 TTAATATCTGACATAGTAGTGTCG-AATGCAGCT
1 TTAATATATGACAAAGTACTGTCGAAATGCAGCT
602391 TTAATATATGACAAAGTACTGTCGAAAATGCAGCT
1 TTAATATATGACAAAGTACTGTCG-AAATGCAGCT
602426 ATCTTCCATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 21 0.70
35 9 0.30
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (34 bp):
TTAATATATGACAAAGTACTGTCGAAATGCAGCT
Found at i:603948 original size:34 final size:34
Alignment explanation
Indices: 603884--604100 Score: 292
Period size: 34 Copynumber: 6.4 Consensus size: 34
603874 ATCAACTCAG
*
603884 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* * *
603917 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
*
603951 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* * *
603985 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* * *
604019 TGTTGACTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
* * * *
604053 TGTTGACTAAATGAGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
604087 TGTTGATTAAATGG
1 TGTTGATTAAATGG
604101 TGGTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 11 0.07
34 153 0.93
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGTTTACCAT
Found at i:604072 original size:102 final size:102
Alignment explanation
Indices: 603886--604100 Score: 333
Period size: 102 Copynumber: 2.1 Consensus size: 102
603876 CAACTCAGTG
603886 TTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACCA
1 TTGATTAAATGGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACCA
* *
603950 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTA
66 TTGTTGACTAAATGAGAGATTTGGTAGCTTACCATTA
* ** * *
603987 TTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGTGATTTGGTGGTTTACCA
1 TTGATTAAATGGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACCA
* * *
604052 TTGTTGACTAAATGAGAGATTTGGTAGGTTGCCATTG
66 TTGTTGACTAAATGAGAGATTTGGTAGCTTACCATTA
604089 TTGATTAAATGG
1 TTGATTAAATGG
604101 TGGTTTTTAC
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 10 0.10
102 93 0.90
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (102 bp):
TTGATTAAATGGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACCA
TTGTTGACTAAATGAGAGATTTGGTAGCTTACCATTA
Found at i:604458 original size:19 final size:19
Alignment explanation
Indices: 604405--604467 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
604395 TGGTTGTCGA
**
604405 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
604424 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
* *
604443 GGTACTATTTAAGTATACG
1 GGTACTATTCACGTATACG
*
604462 GTTACT
1 GGTACT
604468 GTACACGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.37
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:608599 original size:34 final size:34
Alignment explanation
Indices: 608533--608751 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
608523 AAGTGGGAGA
*
608533 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
608566 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
*
608600 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
608634 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
608668 ATTGTTGACTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * * *
608702 ATTGTTGACTAAATGAGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
608736 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
608752 TGGTTTTTAC
Statistics
Matches: 166, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 13 0.08
34 153 0.92
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
Found at i:608723 original size:102 final size:102
Alignment explanation
Indices: 608537--608751 Score: 333
Period size: 102 Copynumber: 2.1 Consensus size: 102
608527 GGGAGAATTG
608537 TTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACCA
1 TTGATTAAATGGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACCA
* *
608601 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCATTA
66 TTGTTGACTAAATGAGAGATTTGGTAGCTTACCATTA
* ** * *
608638 TTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGTGATTTGGTGGTTTACCA
1 TTGATTAAATGGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACCA
* * *
608703 TTGTTGACTAAATGAGAGATTTGGTAGGTTGCCATTG
66 TTGTTGACTAAATGAGAGATTTGGTAGCTTACCATTA
608740 TTGATTAAATGG
1 TTGATTAAATGG
608752 TGGTTTTTAC
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 10 0.10
102 93 0.90
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (102 bp):
TTGATTAAATGGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACCA
TTGTTGACTAAATGAGAGATTTGGTAGCTTACCATTA
Found at i:609920 original size:21 final size:21
Alignment explanation
Indices: 609896--609937 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
609886 TAATTGTAGA
609896 CATGAAAGCACTTTAAGGAGG
1 CATGAAAGCACTTTAAGGAGG
609917 CATGAAAGCACTTTAAGGAGG
1 CATGAAAGCACTTTAAGGAGG
609938 TGGGTCTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.29, T:0.19
Consensus pattern (21 bp):
CATGAAAGCACTTTAAGGAGG
Found at i:610424 original size:18 final size:18
Alignment explanation
Indices: 610401--610435 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
610391 TTACGTGCAG
*
610401 TTTATTTTTTATTATTTA
1 TTTATTATTTATTATTTA
*
610419 TTTATTATTTGTTATTT
1 TTTATTATTTATTATTT
610436 TAATGTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTATTATTTATTATTTA
Found at i:615667 original size:3 final size:3
Alignment explanation
Indices: 615659--615715 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
615649 TCAGCTATAA
*
615659 TAT TAT TAT TAT TAT GAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
615707 TAT TAT TAT
1 TAT TAT TAT
615716 AGCTGTAAGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:616142 original size:2 final size:2
Alignment explanation
Indices: 616135--616160 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
616125 AGCTGATTTA
616135 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
616161 GTGTAGTTTA
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:617725 original size:2 final size:2
Alignment explanation
Indices: 617718--617755 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
617708 AGTGCTTAGG
*
617718 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
617756 TTTGGGACGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:618165 original size:2 final size:2
Alignment explanation
Indices: 618158--618195 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
618148 GAAAAAGGAA
618158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
618196 TGCTGACATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:621276 original size:29 final size:31
Alignment explanation
Indices: 621242--621301 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
621232 AGTAACGAGT
* *
621242 TAAAAAATA-ATAAAAATATTATATTTATAA
1 TAAAAAATATATAAAAATAATATAATTATAA
*
621272 TAAAAAATATATAAATATAATATAATTATA
1 TAAAAAATATATAAAAATAATATAATTATA
621302 TGAATCATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (31 bp):
TAAAAAATATATAAAAATAATATAATTATAA
Found at i:621290 original size:20 final size:21
Alignment explanation
Indices: 621248--621293 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
621238 GAGTTAAAAA
**
621248 ATAAT-AAAAATATTATATTT
1 ATAATAAAAAATATTATAAAT
621268 ATAATAAAAAATA-TATAAAT
1 ATAATAAAAAATATTATAAAT
621288 ATAATA
1 ATAATA
621294 TAATTATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAATAAAAAATATTATAAAT
Found at i:621353 original size:21 final size:20
Alignment explanation
Indices: 621308--621354 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
621298 TATATGAATC
621308 ATTAAA-TTTATAAATTAAT
1 ATTAAATTTTATAAATTAAT
*
621327 AATAAATTTTAATAAATTAAT
1 ATTAAATTTT-ATAAATTAAT
*
621348 TTTAAAT
1 ATTAAAT
621355 GACCAATGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 5 0.22
20 3 0.13
21 15 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTAAATTTTATAAATTAAT
Found at i:621659 original size:12 final size:12
Alignment explanation
Indices: 621638--621684 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
621628 GATCACAGTT
621638 AAAAAA-ATAAA
1 AAAAAATATAAA
621649 AAAAAATAT-AA
1 AAAAAATATAAA
*
621660 AATAAATATAAA
1 AAAAAATATAAA
* *
621672 ATAAAAGATAAA
1 AAAAAATATAAA
621684 A
1 A
621685 GAAATTACGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 16 0.53
12 14 0.47
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (12 bp):
AAAAAATATAAA
Found at i:621671 original size:23 final size:23
Alignment explanation
Indices: 621644--621689 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
621634 AGTTAAAAAA
* *
621644 ATAAAAAAAAATATAAAATAAAT
1 ATAAAAAAAAAGATAAAAGAAAT
*
621667 ATAAAATAAAAGATAAAAGAAAT
1 ATAAAAAAAAAGATAAAAGAAAT
621690 TACGTAGTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (23 bp):
ATAAAAAAAAAGATAAAAGAAAT
Found at i:621970 original size:50 final size:50
Alignment explanation
Indices: 621844--622178 Score: 490
Period size: 50 Copynumber: 6.6 Consensus size: 50
621834 GTGGCCACAT
*
621844 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCCA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
* *
621894 TTTGTCAAAGGTTGGTGAAAAATCGTCAACAATTATGGCCACCTCTCTCTA
1 -TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
** * *
621945 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGTTACCTTTCTCCA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
* *
621995 TTTGTCAAAGGTTGGTGAAGAAATCGTCAACAATTATGGTCACCTCTCTCTA
1 -TTGTCAAAGGTTGGTGAAG-AATCGTCAACAATAATGGCCACCTCTCTCTA
* *
622047 TTGTCAAAAGTTGGTGAAGAATCATCAACAATAATGGCCACCTCTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
* * * *
622097 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTACGACCACCTCTCTTTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
* *
622147 TTGTCAAAGGTTGGTGAAGGATAGTCAACAAT
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAAT
622179 GGCAACAACT
Statistics
Matches: 257, Mismatches: 25, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
50 146 0.57
51 84 0.33
52 27 0.11
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (50 bp):
TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
Found at i:621993 original size:101 final size:101
Alignment explanation
Indices: 621844--622178 Score: 537
Period size: 101 Copynumber: 3.3 Consensus size: 101
621834 GTGGCCACAT
621844 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCCATTTGTCAAAGGTTGG
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCCATTTGTCAAAGGTTGG
621909 TGAAAAATCGTCAACAATTATGGCCACCTCTCTCTA
66 TGAAAAATCGTCAACAATTATGGCCACCTCTCTCTA
** *
621945 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGTTACCTTTCTCCATTTGTCAAAGGTTGG
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCCATTTGTCAAAGGTTGG
*
622010 TGAAGAAATCGTCAACAATTATGGTCACCTCTCTCTA
66 TGAA-AAATCGTCAACAATTATGGCCACCTCTCTCTA
* * *
622047 TTGTCAAAAGTTGGTGAAGAATCATCAACAATAATGGCCACCTCTCTCTA-TTGTCAAAGGTTGG
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCCATTTGTCAAAGGTTGG
* * * *
622111 TGAAGAATCGTCAACAATTACGACCACCTCTCTTTA
66 TGAAAAATCGTCAACAATTATGGCCACCTCTCTCTA
* *
622147 TTGTCAAAGGTTGGTGAAGGATAGTCAACAAT
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAAT
622179 GGCAACAACT
Statistics
Matches: 214, Mismatches: 19, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
100 55 0.26
101 84 0.39
102 75 0.35
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (101 bp):
TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCCATTTGTCAAAGGTTGG
TGAAAAATCGTCAACAATTATGGCCACCTCTCTCTA
Found at i:622117 original size:152 final size:152
Alignment explanation
Indices: 621841--622178 Score: 500
Period size: 152 Copynumber: 2.2 Consensus size: 152
621831 ATTGTGGCCA
*
621841 CATTTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCCATTTGTCAAAGGT
1 CATTTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCCATTTGTCAAAAGT
* *
621906 TGGTGAAAAATCGTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATCGTC
66 TGGTGAAAAATCATCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATCGTC
621971 AACAATAATGGTTACCTTTCTC
131 AACAATAATGGTTACCTTTCTC
* * *
621993 CATTTGTCAAAGGTTGGTGAAGAAATCGTCAACAATTATGGTCACCTCTCTCTA-TTGTCAAAAG
1 CATTTGTCAAAGGTTGGTGAAG-AATCGTCAACAATAATGGCCACCTCTCTCCATTTGTCAAAAG
*
622057 TTGGTGAAGAATCATCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATCGT
65 TTGGTGAAAAATCATCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATCGT
* * *** * *
622122 CAACAATTACGACCACCTCTCTT
130 CAACAATAATGGTTACCTTTCTC
* * *
622145 TA-TTGTCAAAGGTTGGTGAAGGATAGTCAACAAT
1 CATTTGTCAAAGGTTGGTGAAGAATCGTCAACAAT
622179 GGCAACAACT
Statistics
Matches: 168, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
150 11 0.07
151 19 0.11
152 110 0.65
153 28 0.17
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (152 bp):
CATTTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCCATTTGTCAAAAGT
TGGTGAAAAATCATCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATCGTC
AACAATAATGGTTACCTTTCTC
Found at i:625403 original size:303 final size:303
Alignment explanation
Indices: 624856--625462 Score: 1151
Period size: 303 Copynumber: 2.0 Consensus size: 303
624846 AAAGGTAGGC
624856 TTACTGTTTTGAGTCCAGGAAGCAATCCACTATCAGATAGAATCTTTATACCTCGTTCTGACATA
1 TTACTGTTTTGAGTCCAGGAAGCAATCCACTATCAGATAGAATCTTTATACCTCGTTCTGACATA
* *
624921 TGGCCTAATCTACGATGCCACATCATTGTTGATTCTTCATCCGAACTGGTTGTCGCAACAGATGC
66 TGGCCCAATCTACGATGCCACATCATTGTTGATTCTTCATCCGAACTGGTTGTCACAACAGATGC
624986 ATCTGCCTCCTGCAGTGTCTCTCCTTTAAGCATGTATAGATTTGCAGCAACTTTCTCTGCCTTCA
131 ATCTGCCTCCTGCAGTGTCTCTCCTTTAAGCATGTATAGATTTGCAGCAACTTTCTCTGCCTTCA
*
625051 TCACCACCAATGCACCTCTGAGTATTTTCATGACCTCATTCTCTACATGAGTCTTGCATCCGATA
196 TCACCACCAATGCACCTCTGAGTATTTTCATGACCCCATTCTCTACATGAGTCTTGCATCCGATA
*
625116 TCATCTAATTGTCCCAAAGATAATAGATTTTTCTTCAGGCCTT
261 TCATCTAATTGTCCCAAAGACAATAGATTTTTCTTCAGGCCTT
*
625159 TTACTGTTTTGAGTCCAGGAAGCAATCCACTATCAGATAGAATCTTTATACCTCGTTTTGACATA
1 TTACTGTTTTGAGTCCAGGAAGCAATCCACTATCAGATAGAATCTTTATACCTCGTTCTGACATA
*
625224 TGGCCCAATCTACGATGCCACATCATTGTTGATTCTTTATCCGAACTGGTTGTCACAACAGATGC
66 TGGCCCAATCTACGATGCCACATCATTGTTGATTCTTCATCCGAACTGGTTGTCACAACAGATGC
*
625289 GTCTGCCTCCTGCAGTGTCTCTCCTTTAAGCATGTATAGATTTGCAGCAACTTTCTCTGCCTTCA
131 ATCTGCCTCCTGCAGTGTCTCTCCTTTAAGCATGTATAGATTTGCAGCAACTTTCTCTGCCTTCA
625354 TCACCACCAATGCACCTCTGAGTATTTTCATGACCCCATTCTCTACATGAGTCTTGCATCCGATA
196 TCACCACCAATGCACCTCTGAGTATTTTCATGACCCCATTCTCTACATGAGTCTTGCATCCGATA
625419 TCATCTAATTGTCCCAAAGACAATAGATTTTTCTTCAGGCCTT
261 TCATCTAATTGTCCCAAAGACAATAGATTTTTCTTCAGGCCTT
625462 T
1 T
625463 GACATGTCTT
Statistics
Matches: 297, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
303 297 1.00
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.34
Consensus pattern (303 bp):
TTACTGTTTTGAGTCCAGGAAGCAATCCACTATCAGATAGAATCTTTATACCTCGTTCTGACATA
TGGCCCAATCTACGATGCCACATCATTGTTGATTCTTCATCCGAACTGGTTGTCACAACAGATGC
ATCTGCCTCCTGCAGTGTCTCTCCTTTAAGCATGTATAGATTTGCAGCAACTTTCTCTGCCTTCA
TCACCACCAATGCACCTCTGAGTATTTTCATGACCCCATTCTCTACATGAGTCTTGCATCCGATA
TCATCTAATTGTCCCAAAGACAATAGATTTTTCTTCAGGCCTT
Found at i:627006 original size:101 final size:101
Alignment explanation
Indices: 626888--627197 Score: 514
Period size: 101 Copynumber: 3.1 Consensus size: 101
626878 ATGGCCATAT
* *
626888 TTGTCAAAGATTGGTGAAGAATCGTCAACAATAATGATCACCTCTCTCCATTTGTCAAAGGTTGG
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGTCACCTCTCTCCATTTGTCAAAGGTTGG
626953 TGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
66 TGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
* *
626989 TTGTCAAAGGTTGGTGAAGAATCGTTAACAATAATGGCCACCTCTCTCCATTTGTCAAAGGTTGG
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGTCACCTCTCTCCATTTGTCAAAGGTTGG
627054 TGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
66 TGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
* * * *
627090 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGTCACTTCTCTCTA-TTGTCAAAGGTCGA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGTCACCTCTCTCCATTTGTCAAAGGTTGG
* * *
627154 TGAAGAATCGTCAACAATTACGACCACCTCTCTTTA
66 TGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
627190 TTGTCAAA
1 TTGTCAAA
627198 AGTTAATAAA
Statistics
Matches: 196, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
100 53 0.27
101 143 0.73
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (101 bp):
TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGTCACCTCTCTCCATTTGTCAAAGGTTGG
TGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
Found at i:627019 original size:50 final size:50
Alignment explanation
Indices: 626888--627197 Score: 458
Period size: 50 Copynumber: 6.2 Consensus size: 50
626878 ATGGCCATAT
* ** *
626888 TTGTCAAAGATTGGTGAAGAATCGTCAACAATAATGATCACCTCTCTCCA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
*
626938 TTTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
1 -TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
* *
626989 TTGTCAAAGGTTGGTGAAGAATCGTTAACAATAATGGCCACCTCTCTCCA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
*
627039 TTTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
1 -TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
* *
627090 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGTCACTTCTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
* * * * * *
627140 TTGTCAAAGGTCGATGAAGAATCGTCAACAATTACGACCACCTCTCTTTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
627190 TTGTCAAA
1 TTGTCAAA
627198 AGTTAATAAA
Statistics
Matches: 236, Mismatches: 22, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
50 144 0.61
51 92 0.39
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (50 bp):
TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
Found at i:627655 original size:2 final size:2
Alignment explanation
Indices: 627644--627692 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
627634 GCCTCTTCTG
627644 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
627685 AT AT AT AT
1 AT AT AT AT
627693 GGCTGACGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:628903 original size:99 final size:99
Alignment explanation
Indices: 628773--628971 Score: 346
Period size: 99 Copynumber: 2.0 Consensus size: 99
628763 AAGAAAAGTA
628773 CAAGCTTTTATAGTGATAGGTAATGTGTTTATTCTAAATTAATGAAAGAGAGAACCTC-AGTTAA
1 CAAGCTTTTATAGTGATAGGTAATGTGTTTATTCTAAATTAATGAAAGAGAGAACC-CAAGTTAA
* *
628837 TTGCACGATTGGTCCCCAGACATTTGGTTTAATTG
65 TTGCACGATTGGTCCCAAGACATTAGGTTTAATTG
* *
628872 CAAGCTTTTATAGTGATAGGTAATGTTTTTATTCTAAATTAATGAATGAGAGAACCCAAGTTAAT
1 CAAGCTTTTATAGTGATAGGTAATGTGTTTATTCTAAATTAATGAAAGAGAGAACCCAAGTTAAT
628937 TGCACGATTGGTCCCAAGACATTAGGTTTAATTG
66 TGCACGATTGGTCCCAAGACATTAGGTTTAATTG
628971 C
1 C
628972 CCGCTGGCAG
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
98 1 0.01
99 94 0.99
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (99 bp):
CAAGCTTTTATAGTGATAGGTAATGTGTTTATTCTAAATTAATGAAAGAGAGAACCCAAGTTAAT
TGCACGATTGGTCCCAAGACATTAGGTTTAATTG
Found at i:634256 original size:18 final size:18
Alignment explanation
Indices: 634233--634276 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
634223 CGAATAGTAA
* *
634233 TTTTTTATTAATTTTACT
1 TTTTTTATTAAATTTAAT
634251 TTTTTTATTAAATTTAAT
1 TTTTTTATTAAATTTAAT
634269 TTATTTTA
1 TT-TTTTA
634277 AATTTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTTATTAAATTTAAT
Found at i:634345 original size:23 final size:21
Alignment explanation
Indices: 634319--634371 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 21
634309 TTTAATTAAG
634319 TTATTTATTTATAAATTAAAAAT
1 TTATTTA-TT-TAAATTAAAAAT
*
634342 TTATAATTATTTAAATTAAATAT
1 TTAT--TTATTTAAATTAAAAAT
634365 TATATTT
1 T-TATTT
634372 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
22 2 0.08
23 16 0.62
24 5 0.19
25 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATTTATTTAAATTAAAAAT
Found at i:635018 original size:3 final size:3
Alignment explanation
Indices: 635010--635035 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
635000 AGTCCTTGAT
635010 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
635036 AATTCTATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:653928 original size:43 final size:43
Alignment explanation
Indices: 653867--653952 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
653857 AACAATGACA
* *
653867 AAGATCATGTGCGCAGCAGCCTTAGGAAAT-GGGAACCACCAGT
1 AAGATCATATGCGCAGCAGCCATAGGAAATAGGG-ACCACCAGT
*
653910 AAGATCATATGCGCAGCAGCCATAGGAACTAGGGACCACCAGT
1 AAGATCATATGCGCAGCAGCCATAGGAAATAGGGACCACCAGT
653953 CAATCTTTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
43 36 0.92
44 3 0.08
ACGTcount: A:0.34, C:0.24, G:0.27, T:0.15
Consensus pattern (43 bp):
AAGATCATATGCGCAGCAGCCATAGGAAATAGGGACCACCAGT
Found at i:658293 original size:17 final size:18
Alignment explanation
Indices: 658255--658368 Score: 61
Period size: 16 Copynumber: 6.9 Consensus size: 18
658245 TTTATATATC
658255 ATATTTATAATATTTTTT
1 ATATTTATAATATTTTTT
658273 ATATTTA-AAT-TTTTTT
1 ATATTTATAATATTTTTT
**
658289 A-ATATTAT-A-ATTAATT
1 ATAT-TTATAATATTTTTT
* * *
658305 ATATATAGAATA-TTATT
1 ATATTTATAATATTTTTT
*
658322 A-ATTTAT-ATAATTTTT
1 ATATTTATAATATTTTTT
* * *
658338 ATATAT-TAATAATTTAT
1 ATATTTATAATATTTTTT
658355 ATATTT-T-ATATTTT
1 ATATTTATAATATTTT
658369 ATTTATATTA
Statistics
Matches: 75, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
15 5 0.07
16 34 0.45
17 28 0.37
18 8 0.11
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (18 bp):
ATATTTATAATATTTTTT
Found at i:658333 original size:9 final size:9
Alignment explanation
Indices: 658317--658365 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
658307 ATATAGAATA
658317 TTAT-TAAT
1 TTATATAAT
658325 TTATATAAT
1 TTATATAAT
*
658334 TTTTAT-AT
1 TTATATAAT
658342 ATTA-ATAAT
1 -TTATATAAT
*
658351 TTATATATT
1 TTATATAAT
658360 TTATAT
1 TTATAT
658366 TTTATTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
8 11 0.32
9 23 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TTATATAAT
Found at i:658350 original size:26 final size:24
Alignment explanation
Indices: 658314--658365 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 24
658304 TATATATAGA
*
658314 ATATTATTAATTTATATAATTTTTAT
1 ATATTAATAATTTATAT-A-TTTTAT
658340 ATATTAATAATTTATATATTTTAT
1 ATATTAATAATTTATATATTTTAT
658364 AT
1 AT
658366 TTTATTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 8 0.32
25 1 0.04
26 16 0.64
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATATTAATAATTTATATATTTTAT
Found at i:663392 original size:16 final size:16
Alignment explanation
Indices: 663371--663404 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
663361 CGGTCATTGG
663371 ATAAATATTTAATAAA
1 ATAAATATTTAATAAA
663387 ATAAATATTTAATAAA
1 ATAAATATTTAATAAA
663403 AT
1 AT
663405 GAACTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAATATTTAATAAA
Found at i:664786 original size:17 final size:16
Alignment explanation
Indices: 664766--664807 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
664756 TTAATTAATA
664766 TTAAT-TAATAAATATCT
1 TTAATATAAT-AATAT-T
664783 TTAATATAATAATATT
1 TTAATATAATAATATT
*
664799 TTAAAATAA
1 TTAATATAA
664808 ATTAAATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 9 0.39
17 10 0.43
18 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAATATAATAATATT
Found at i:664807 original size:16 final size:18
Alignment explanation
Indices: 664771--664807 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
664761 TAATATTAAT
*
664771 TAATAAATATCTTTAATA
1 TAATAAATATCTTTAAAA
664789 TAAT-AATAT-TTTAAAA
1 TAATAAATATCTTTAAAA
664805 TAA
1 TAA
664808 ATTAAATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 5 0.28
18 4 0.22
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAATATCTTTAAAA
Found at i:665215 original size:13 final size:14
Alignment explanation
Indices: 665198--665234 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
665188 TAATTTTATT
665198 TATTTATATAATAA
1 TATTTATATAATAA
*
665212 -ATTTATAAAATAA
1 TATTTATATAATAA
665225 TATTTA-ATAA
1 TATTTATATAA
665235 ATTTAATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TATTTATATAATAA
Found at i:665255 original size:23 final size:22
Alignment explanation
Indices: 665199--665297 Score: 69
Period size: 23 Copynumber: 4.4 Consensus size: 22
665189 AATTTTATTT
665199 ATTTATATAATAAATTTATAAA
1 ATTTATATAATAAATTTATAAA
* * **
665221 ATAATATTTAATAAATTTAATATG
1 AT-TTATATAATAAATTT-ATAAA
* *
665245 ATTTATATAAT-TATTTTTAAAA
1 ATTTATATAATAAATTTAT-AAA
665267 ATATTATATTTAATAAA-TT-TAAA
1 AT-TTATA--TAATAAATTTATAAA
665290 ATTTATAT
1 ATTTATAT
665298 CACATTTAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 16
0.69 0.13 0.19
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 14 0.24
23 30 0.51
24 6 0.10
25 6 0.10
26 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (22 bp):
ATTTATATAATAAATTTATAAA
Found at i:665288 original size:48 final size:46
Alignment explanation
Indices: 665199--665288 Score: 128
Period size: 46 Copynumber: 1.9 Consensus size: 46
665189 AATTTTATTT
665199 ATTTATATAATAAATTTATAAAATAATATTTAATAAATTTAATATG
1 ATTTATATAATAAATTTATAAAATAATATTTAATAAATTTAATATG
* *
665245 ATTTATATAAT-TATTTTTAAAAATATTATATTTAATAAATTTAA
1 ATTTATATAATAAATTTAT-AAAATA--ATATTTAATAAATTTAA
665289 AATTTATATC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 5 0.13
46 17 0.44
48 17 0.44
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (46 bp):
ATTTATATAATAAATTTATAAAATAATATTTAATAAATTTAATATG
Found at i:682078 original size:27 final size:28
Alignment explanation
Indices: 682046--682116 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 28
682036 GCCACCCATT
*
682046 TGTTTGTAAAAAATGGTGGTTAT-TTTG
1 TGTTTGTCAAAAATGGTGGTTATCTTTG
* *
682073 TGTTTGTCAAAAATTGTGGTTTTCTTTG
1 TGTTTGTCAAAAATGGTGGTTATCTTTG
* *
682101 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
682117 AGGCTTGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 20 0.54
28 17 0.46
ACGTcount: A:0.24, C:0.04, G:0.23, T:0.49
Consensus pattern (28 bp):
TGTTTGTCAAAAATGGTGGTTATCTTTG
Found at i:684720 original size:21 final size:22
Alignment explanation
Indices: 684691--684736 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
684681 TGTTCAGACA
* *
684691 AGTAGTACTCCACAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
684713 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
684734 AGT
1 AGT
684737 TTCAACAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:686643 original size:27 final size:28
Alignment explanation
Indices: 686609--686674 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 28
686599 GCCACCCATT
686609 TGTTTGTCAAAAATGGTGG-TTATTTTG
1 TGTTTGTCAAAAATGGTGGTTTATTTTG
* *
686636 TGTTTGTCAAAAATTGTGGTTTTTTTTG
1 TGTTTGTCAAAAATGGTGGTTTATTTTG
*
686664 TATTTGTCAAA
1 TGTTTGTCAAA
686675 TATGAAAGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 18 0.51
28 17 0.49
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.52
Consensus pattern (28 bp):
TGTTTGTCAAAAATGGTGGTTTATTTTG
Found at i:687691 original size:2 final size:2
Alignment explanation
Indices: 687678--687713 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
687668 TGAGACTTCC
* *
687678 TA TA TA TT TA TA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
687714 ATGTTTTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:694808 original size:2 final size:2
Alignment explanation
Indices: 694801--694828 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
694791 TGTGGAGTCA
694801 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
694829 TAATTTTGAT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:700450 original size:19 final size:17
Alignment explanation
Indices: 700422--700470 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 17
700412 ATTTGTATTT
700422 TTATATTATATTATAAAA
1 TTATATTATATT-TAAAA
700440 TTATAATTATATTTAAAA
1 TTAT-ATTATATTTAAAA
*
700458 -TATTTTATATTTA
1 TTATATTATATTTA
700471 TATAAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 9 0.31
17 3 0.10
18 9 0.31
19 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATATTATATTTAAAA
Found at i:701795 original size:20 final size:20
Alignment explanation
Indices: 701770--701813 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
701760 CAGCCTCACC
701770 CTCCTTATCCCCTCCACCAG
1 CTCCTTATCCCCTCCACCAG
701790 CTCCTTATCCCCTCCACCAG
1 CTCCTTATCCCCTCCACCAG
701810 -TCCT
1 CTCCT
701814 GTCATCCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.14, C:0.55, G:0.05, T:0.27
Consensus pattern (20 bp):
CTCCTTATCCCCTCCACCAG
Found at i:703532 original size:2 final size:2
Alignment explanation
Indices: 703525--703560 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
703515 CCCCTTTCTG
703525 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
703561 CAACTTGAAG
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:704466 original size:2 final size:2
Alignment explanation
Indices: 704459--704504 Score: 58
Period size: 2 Copynumber: 22.5 Consensus size: 2
704449 ACACTTGAAA
*
704459 AT AT AT AT AT AT AT AT AT AT AGT -T GAA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT -AT AT AT AT AT AT AT AT AT
704502 AT A
1 AT A
704505 AATTATTGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 1 0.03
2 37 0.95
3 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:719182 original size:3 final size:3
Alignment explanation
Indices: 719136--719169 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
719126 ATAAAAGCTT
*
719136 TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
719170 TCCAGTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:723095 original size:2 final size:2
Alignment explanation
Indices: 723088--723128 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
723078 AAAGAAACAA
723088 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
723129 TATCGAACGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:724067 original size:2 final size:2
Alignment explanation
Indices: 724060--724091 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
724050 ACAAACACCT
724060 TC TC TC 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
724092 ACAGATGAAC
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):
TC
Found at i:731393 original size:15 final size:15
Alignment explanation
Indices: 731373--731404 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
731363 TTCATGATTT
*
731373 GCCTCGGCGTTCCCG
1 GCCTCGGCGTTACCG
731388 GCCTCGGCGTTACCG
1 GCCTCGGCGTTACCG
731403 GC
1 GC
731405 GGTCGTAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.03, C:0.44, G:0.34, T:0.19
Consensus pattern (15 bp):
GCCTCGGCGTTACCG
Found at i:733637 original size:9 final size:9
Alignment explanation
Indices: 733623--733655 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
733613 TTCAAATCAC
733623 TATTTAAAA
1 TATTTAAAA
733632 TATTTAAAAA
1 TATTT-AAAA
733642 TATTTAAAA
1 TATTTAAAA
733651 -ATTTA
1 TATTTA
733656 TTTTTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 5 0.22
9 9 0.39
10 9 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TATTTAAAA
Found at i:733643 original size:10 final size:10
Alignment explanation
Indices: 733623--733652 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
733613 TTCAAATCAC
733623 TATTT-AAAA
1 TATTTAAAAA
733632 TATTTAAAAA
1 TATTTAAAAA
733642 TATTTAAAAA
1 TATTTAAAAA
733652 T
1 T
733653 TTATTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.25
10 15 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TATTTAAAAA
Found at i:733664 original size:20 final size:20
Alignment explanation
Indices: 733645--733689 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
733635 TTAAAAATAT
733645 TTAA-AAATTTATTTTTATA
1 TTAATAAATTTATTTTTATA
**
733664 TTAATATTTTTATTTTTATAA
1 TTAATAAATTTATTTTTAT-A
733685 TTAAT
1 TTAAT
733690 TTTAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 12 0.55
21 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAATAAATTTATTTTTATA
Found at i:739026 original size:14 final size:15
Alignment explanation
Indices: 739002--739030 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
738992 CATACGAAAG
739002 AAAGTAAAAAAAAAA
1 AAAGTAAAAAAAAAA
739017 AAAG-AAAAAAAAAA
1 AAAGTAAAAAAAAAA
739031 GAAGCCCTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.90, C:0.00, G:0.07, T:0.03
Consensus pattern (15 bp):
AAAGTAAAAAAAAAA
Found at i:744014 original size:40 final size:40
Alignment explanation
Indices: 743959--744038 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
743949 AAAAGATAGT
743959 CTACCAATTTGTGGGATGCTGGGATCATTAATGAATGCCA
1 CTACCAATTTGTGGGATGCTGGGATCATTAATGAATGCCA
*
743999 CTACCAATTTTTGGGATGCTGGGATCATTAATGAATGCCA
1 CTACCAATTTGTGGGATGCTGGGATCATTAATGAATGCCA
744039 AGTCAAGAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (40 bp):
CTACCAATTTGTGGGATGCTGGGATCATTAATGAATGCCA
Found at i:744619 original size:13 final size:14
Alignment explanation
Indices: 744579--744627 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
744569 CTAATCAGGT
*
744579 TATTT-ATAAAAAT
1 TATTTAATAAAAAA
744592 TATTTAAATATAAAAA
1 TATTT-AATA-AAAAA
*
744608 AATTTAATAAAAAA
1 TATTTAATAAAAAA
744622 TATTTA
1 TATTTA
744628 TTTAAATGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 5 0.17
14 10 0.33
15 7 0.23
16 8 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TATTTAATAAAAAA
Found at i:747552 original size:5 final size:5
Alignment explanation
Indices: 747542--747570 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
747532 TTATTATTAT
747542 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
747571 TGGTGCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:748902 original size:2 final size:2
Alignment explanation
Indices: 748897--748927 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
748887 TTTTTTAAGC
748897 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 T
748928 GATGTAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:750995 original size:17 final size:18
Alignment explanation
Indices: 750961--751003 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
750951 TTAAAATTTT
750961 AAATAAAATATTATATTAAA
1 AAAT-AAATATTATATT-AA
750981 AAATAAAT-TTA-ATTAA
1 AAATAAATATTATATTAA
750997 AAATAAA
1 AAATAAA
751004 ATCCATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 9 0.39
17 3 0.13
18 3 0.13
19 4 0.17
20 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAAATATTATATTAA
Found at i:751005 original size:17 final size:19
Alignment explanation
Indices: 750961--751005 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
750951 TTAAAATTTT
750961 AAATAAAATATTATATTAA
1 AAATAAAATATTATATTAA
750980 AAA-ATAAAT-TTA-ATTAA
1 AAATA-AAATATTATATTAA
750997 AAATAAAAT
1 AAATAAAAT
751006 CCATTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 12 0.50
18 5 0.21
19 7 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAAAATATTATATTAA
Found at i:751015 original size:17 final size:17
Alignment explanation
Indices: 750975--751020 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
750965 AAAATATTAT
* *
750975 ATTAAAAAATAAATTTA
1 ATTAAAAAATAAAATCA
*
750992 ATT-AAAAATAAAATCC
1 ATTAAAAAATAAAATCA
751008 ATTAAAAAA-AAAA
1 ATTAAAAAATAAAA
751021 CCTCTTATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (17 bp):
ATTAAAAAATAAAATCA
Found at i:751939 original size:4 final size:4
Alignment explanation
Indices: 751930--751954 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
751920 TCTCTATTCC
751930 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
751955 AAATAGTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:752145 original size:23 final size:23
Alignment explanation
Indices: 752119--752162 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
752109 CATATCTTTC
* *
752119 AAAATATATTATATAAAAATTAA
1 AAAATAAAATATATAAAAATTAA
*
752142 AAAATAAAATATATAAGAATT
1 AAAATAAAATATATAAAAATT
752163 TCGTAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (23 bp):
AAAATAAAATATATAAAAATTAA
Found at i:752659 original size:20 final size:19
Alignment explanation
Indices: 752598--752661 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 19
752588 GAATTATGTT
*
752598 TTTTATACTAAT-ATTATA
1 TTTTATAATAATAATTATA
752616 TTTTATAA-AATAATTATTTA
1 TTTTATAATAATAATTA--TA
752636 TTTTATAATAATAATTATA
1 TTTTATAATAATAATTATA
752655 GTTTTAT
1 -TTTTAT
752662 TTTACTTAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
17 3 0.08
18 11 0.28
19 2 0.05
20 16 0.40
21 8 0.20
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTTATAATAATAATTATA
Found at i:752665 original size:25 final size:20
Alignment explanation
Indices: 752609--752653 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 20
752599 TTTATACTAA
752609 TATTATATTTTATAAAATAAT
1 TATT-TATTTTATAAAATAAT
752630 TATTTATTTTATAATAATAAT
1 TATTTATTTTATAA-AATAAT
752651 TAT
1 TAT
752654 AGTTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTTATTTTATAAAATAAT
Found at i:753078 original size:8 final size:8
Alignment explanation
Indices: 753067--753117 Score: 61
Period size: 8 Copynumber: 6.6 Consensus size: 8
753057 TACATTATTA
753067 GTATATAT
1 GTATATAT
753075 GTATATAT
1 GTATATAT
*
753083 ATATA-AT
1 GTATATAT
753090 -TATATAT
1 GTATATAT
*
753097 ATATATAT
1 GTATATAT
*
753105 GTATACAT
1 GTATATAT
753113 GTATA
1 GTATA
753118 ACCCACGTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 4 0.11
7 4 0.11
8 30 0.79
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (8 bp):
GTATATAT
Found at i:753081 original size:2 final size:2
Alignment explanation
Indices: 753068--753109 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
753058 ACATTATTAG
* *
753068 TA TA TA TG TA TA TA TA TA TA -A T- TA TA TA TA TA TA 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
753108 TA
1 TA
753110 CATGTATAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:757303 original size:9 final size:8
Alignment explanation
Indices: 757289--757331 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 8
757279 ATAAAAAGCT
757289 AAAGAAAA
1 AAAGAAAA
757297 CAAAGAAAA
1 -AAAGAAAA
*
757306 AAAGGAAA
1 AAAGAAAA
757314 AAAGAAAAGA
1 AAAG-AAA-A
757324 AAAGAAAA
1 AAAGAAAA
757332 GGACGTGACG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 12 0.40
9 13 0.43
10 5 0.17
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:757319 original size:16 final size:17
Alignment explanation
Indices: 757298--757331 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
757288 TAAAGAAAAC
*
757298 AAAGAAAA-AAAGGAAA
1 AAAGAAAAGAAAAGAAA
757314 AAAGAAAAGAAAAGAAA
1 AAAGAAAAGAAAAGAAA
757331 A
1 A
757332 GGACGTGACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAGAAAAGAAAAGAAA
Found at i:757949 original size:3 final size:3
Alignment explanation
Indices: 757936--757966 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
757926 AAAGACAAAG
757936 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
757967 AACTCTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:760314 original size:17 final size:17
Alignment explanation
Indices: 760292--760326 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
760282 ATTATATGAA
760292 TAAATTAAATTAAATTT
1 TAAATTAAATTAAATTT
* *
760309 TAAATTAATTTTAATTT
1 TAAATTAAATTAAATTT
760326 T
1 T
760327 TCTTATTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAAATTAAATTAAATTT
Found at i:766014 original size:2 final size:2
Alignment explanation
Indices: 766007--766041 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
765997 CAAAAGCAAC
766007 AT 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 AT A
766042 AACAAATTAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:770950 original size:6 final size:6
Alignment explanation
Indices: 770936--770967 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
770926 ATAAATATAA
*
770936 ATATAT ATATGT ATATGT ATATGT ATATGT AT
1 ATATGT ATATGT ATATGT ATATGT ATATGT AT
770968 TATATTTGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:771486 original size:2 final size:2
Alignment explanation
Indices: 771479--771503 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
771469 GCGTGGGTGC
771479 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
771504 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:771508 original size:2 final size:2
Alignment explanation
Indices: 771503--771536 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
771493 ATATATATAT
771503 AG 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 AG
771537 GATATGCTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:774948 original size:16 final size:18
Alignment explanation
Indices: 774927--774960 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
774917 TTTAAATGAA
774927 TTATTTAT-AA-ATAAAT
1 TTATTTATGAACATAAAT
774943 TTATTTATGAACATAAAT
1 TTATTTATGAACATAAAT
774961 GAACTGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
TTATTTATGAACATAAAT
Found at i:775253 original size:29 final size:30
Alignment explanation
Indices: 775221--775277 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
775211 AAAATAATAT
* *
775221 TAATTTATTTC-AAATTAATATTATTTTAA
1 TAATTTATTTCAAAATTAACAATATTTTAA
775250 TAATTTATTTCAAAATTAACAATATTTT
1 TAATTTATTTCAAAATTAACAATATTTT
775278 GTTTAATGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (30 bp):
TAATTTATTTCAAAATTAACAATATTTTAA
Found at i:776870 original size:22 final size:22
Alignment explanation
Indices: 776842--776883 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
776832 TAGGTTTCAG
776842 ATGATGTGGATATATAAAATAT
1 ATGATGTGGATATATAAAATAT
**
776864 ATGATGTTTATATATAAAAT
1 ATGATGTGGATATATAAAAT
776884 TTAGCAAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.40
Consensus pattern (22 bp):
ATGATGTGGATATATAAAATAT
Found at i:776921 original size:5 final size:5
Alignment explanation
Indices: 776913--776958 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
776903 TAAAATAAAA
*
776913 ATAAT ATAAT AT-AT TTAAAT ATAAT -TAAT ATAAT ATAAT -TAAT ATA
1 ATAAT ATAAT ATAAT AT-AAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
776959 TATTTTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
4 11 0.31
5 21 0.60
6 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
ATAAT
Found at i:776932 original size:24 final size:24
Alignment explanation
Indices: 776899--776954 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
776889 AAGTATGAAA
*
776899 ATATTAAAATAAAAATAATATAAT
1 ATATTTAAATAAAAATAATATAAT
* *
776923 ATATTTAAATATAATTAATATAAT
1 ATATTTAAATAAAAATAATATAAT
*
776947 ATAATTAA
1 ATATTTAA
776955 TATATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATTTAAATAAAAATAATATAAT
Found at i:776952 original size:14 final size:14
Alignment explanation
Indices: 776914--776958 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
776904 AAAATAAAAA
776914 TAATATAATAT-AT
1 TAATATAATATAAT
776927 T--TA-AATATAAT
1 TAATATAATATAAT
776938 TAATATAATATAAT
1 TAATATAATATAAT
776952 TAATATA
1 TAATATA
776959 TATTTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 5 0.18
11 5 0.18
13 3 0.11
14 15 0.54
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATATAATATAAT
Done.