Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003825.1 Hibiscus syriacus cultivar Beakdansim tig00008201_pilon, whole genome shotgun sequence
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: 105745
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:187 original size:79 final size:81
Alignment explanation
Indices: 101--303 Score: 265
Period size: 81 Copynumber: 2.5 Consensus size: 81
91 GATATGTTCA
* * *
101 TGAGCTGAATATAATCGAACTCGAAGGTTTGCTGACAGATAGCTTTTCTCG-CT-ATG-TATGCT
1 TGAGCTGAATGTAATCGAACTCGAAGGTTTGCTGATAGATAG-TTTTCTCGACTGA-GCTATACT
*
163 GTAAA-TTGATGTGCCTT
64 GTAAATTTAATGTGCCTT
*
180 TGAGCTGAATGTAATCGAACTCGAAGTTCTTGCTAGATAGATAGTTTTCTCGACTGAGCTATACT
1 TGAGCTGAATGTAATCGAACTCGAAGGT-TTGCT-GATAGATAGTTTTCTCGACTGAGCTATACT
245 GTAAATTTAATGTGCCTT
64 GTAAATTTAATGTGCCTT
263 TGAG--GAATGTAATCGAACTCGAAGGTCTTTGCTGATAGATA
1 TGAGCTGAATGTAATCGAACTCGAAGG--TTTGCTGATAGATA
304 ACCCTTCTCG
Statistics
Matches: 110, Mismatches: 6, Indels: 14
0.85 0.05 0.11
Matches are distributed among these distances:
79 26 0.24
80 13 0.12
81 39 0.35
82 16 0.15
83 16 0.15
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (81 bp):
TGAGCTGAATGTAATCGAACTCGAAGGTTTGCTGATAGATAGTTTTCTCGACTGAGCTATACTGT
AAATTTAATGTGCCTT
Found at i:604 original size:65 final size:60
Alignment explanation
Indices: 457--623 Score: 199
Period size: 65 Copynumber: 2.7 Consensus size: 60
447 CGTGAAGTTA
* * * *
457 GCTTTGAGTTGGATATTCTTCGTTGTGAAGTTGAAATCCAAGAATTGTTTTACCAAATTT
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAAGAATAGTTTCACCAAATTG
* * * * *
517 GTTTTGAGCTGGATATCATTCGTCGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAA----GAAT-AGTTTCACCAAATTG
*
582 GCTTTGAGTTTGATATCCTTCGTTGTGAAGTTGAAATCCAAG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAAG
624 GGTTGAATTG
Statistics
Matches: 88, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
60 36 0.41
61 1 0.01
64 3 0.03
65 48 0.55
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (60 bp):
GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAAGAATAGTTTCACCAAATTG
Found at i:735 original size:121 final size:120
Alignment explanation
Indices: 591--983 Score: 549
Period size: 121 Copynumber: 3.3 Consensus size: 120
581 GGCTTTGAGT
** *
591 TTGATATCCTTCGTTGTGAAGTTGAAATCCAAGGGTTGAATTGCTGCTTGTGGGCACAATATCCT
1 TTGATATCCTTCGTCATGAAGTTGAAATCCAAGGGTTGAATTGCTGCTTGTGGGCACGATATCCT
* * * * * *
656 TAGTCGTGAAATTGAAATCATGGATGGCTCATTCATTATGAAGTTGAGCTTTGAA
66 TCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAACTTTGAA
* * *
711 TTAGATATCCTTCATCATGAAGTTGAAATCCAAGGGTTGTACTGCTGCTTGTGGGCACGATATCC
1 TT-GATATCCTTCGTCATGAAGTTGAAATCCAAGGGTTGAATTGCTGCTTGTGGGCACGATATCC
* *
776 TTCGTTGTGAAGTTTAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAACTTTGAA
65 TTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAACTTTGAA
*
832 TTGAATATCCTTCGTCATGAAGTTGAAATCCAAGGGGT-ACATTGCTGCTTGT-GGCACGATATC
1 TTG-ATATCCTTCGTCATGAAGTTGAAATCCAAGGGTTGA-ATTGCTGCTTGTGGGCACGATATC
* *
895 CTTCGTCGTGAAGTTGAAATTGTGGATGG-TCATTCGTTGTGAAGTTAAACTTTGAA
64 CTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAACTTTGAA
* **
951 TTGGATATCATTCGTTGTGAAGTTGAAATCCAA
1 TT-GATATCCTTCGTCATGAAGTTGAAATCCAA
984 ATTGGTTTGA
Statistics
Matches: 244, Mismatches: 25, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
119 54 0.22
120 41 0.17
121 149 0.61
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (120 bp):
TTGATATCCTTCGTCATGAAGTTGAAATCCAAGGGTTGAATTGCTGCTTGTGGGCACGATATCCT
TCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAACTTTGAA
Found at i:937 original size:31 final size:31
Alignment explanation
Indices: 889--979 Score: 96
Period size: 34 Copynumber: 2.8 Consensus size: 31
879 CTTGTGGCAC
* *
889 GATATCCTTCGTCGTGAAGTTGAAATTG-TG
1 GATATCATTCGTTGTGAAGTTGAAATTGATG
*
919 GATGGTCATTCGTTGTGAAGTT-AAACTTTGAATTG
1 GAT-ATCATTCGTTGTGAAGTTGAAA--TTG-A-TG
954 GATATCATTCGTTGTGAAGTTGAAAT
1 GATATCATTCGTTGTGAAGTTGAAAT
980 CCAAATTGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
30 6 0.12
31 15 0.30
32 3 0.06
33 1 0.02
34 17 0.34
35 8 0.16
ACGTcount: A:0.26, C:0.10, G:0.25, T:0.38
Consensus pattern (31 bp):
GATATCATTCGTTGTGAAGTTGAAATTGATG
Found at i:987 original size:34 final size:34
Alignment explanation
Indices: 924--988 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
914 TTGTGGATGG
***
924 TCATTCGTTGTGAAGTTAAACTTTGAATTGGATA
1 TCATTCGTTGTGAAGTTAAACTCCAAATTGGATA
958 TCATTCGTTGTGAAGTTGAAA-TCCAAATTGG
1 TCATTCGTTGTGAAGTT-AAACTCCAAATTGG
989 TTTGAGTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 24 0.89
35 3 0.11
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (34 bp):
TCATTCGTTGTGAAGTTAAACTCCAAATTGGATA
Found at i:1467 original size:31 final size:31
Alignment explanation
Indices: 1395--1469 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 31
1385 GTTAAATCCC
* *
1395 CAAAGATGCCCCAAAATTCGATGTTGAATCT
1 CAAAAATGCCCCAAAATTCGATGGTGAATCT
* *
1426 CTAAAAATGCCCCAACATTTGA-GGTGAATCTT
1 C-AAAAATGCCCCAAAATTCGATGGTGAATC-T
*
1458 CAAATATGCCCC
1 CAAAAATGCCCC
1470 CATTGTTCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 18 0.49
32 19 0.51
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (31 bp):
CAAAAATGCCCCAAAATTCGATGGTGAATCT
Found at i:2556 original size:14 final size:12
Alignment explanation
Indices: 2534--2577 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
2524 TTTTCCTTTG
2534 TTTTTCTCTCTGT
1 TTTTTCTCTCT-T
2547 TTTTTGCTCTCTT
1 TTTTT-CTCTCTT
2560 TTTTTCTCT-TT
1 TTTTTCTCTCTT
*
2571 TTGTTCT
1 TTTTTCT
2578 GATTGGATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 8 0.28
12 4 0.14
13 11 0.38
14 6 0.21
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.73
Consensus pattern (12 bp):
TTTTTCTCTCTT
Found at i:6455 original size:103 final size:103
Alignment explanation
Indices: 6329--6536 Score: 416
Period size: 103 Copynumber: 2.0 Consensus size: 103
6319 ACCATTTTGT
6329 TATCTTTCGATAATGTTAGTGATTCTTTTATTATTTTTGAAACTTCATAGGAAAAAGATAAATTT
1 TATCTTTCGATAATGTTAGTGATTCTTTTATTATTTTTGAAACTTCATAGGAAAAAGATAAATTT
6394 AATCATACTACAATGACCCATTTGTATAACTTACCCTA
66 AATCATACTACAATGACCCATTTGTATAACTTACCCTA
6432 TATCTTTCGATAATGTTAGTGATTCTTTTATTATTTTTGAAACTTCATAGGAAAAAGATAAATTT
1 TATCTTTCGATAATGTTAGTGATTCTTTTATTATTTTTGAAACTTCATAGGAAAAAGATAAATTT
6497 AATCATACTACAATGACCCATTTGTATAACTTACCCTA
66 AATCATACTACAATGACCCATTTGTATAACTTACCCTA
6535 TA
1 TA
6537 AAACTAGATA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (103 bp):
TATCTTTCGATAATGTTAGTGATTCTTTTATTATTTTTGAAACTTCATAGGAAAAAGATAAATTT
AATCATACTACAATGACCCATTTGTATAACTTACCCTA
Found at i:11153 original size:15 final size:15
Alignment explanation
Indices: 11133--11247 Score: 57
Period size: 15 Copynumber: 8.1 Consensus size: 15
11123 GAATTCTAAA
11133 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
11148 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
** *
11163 TCA--TCGAT-AATA-
1 T-ATTTAAATAAAAAT
11175 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
**
11190 TATTTCTATAAAAAT
1 TATTTAAATAAAAAT
** *
11205 TCA--TCGAT-AATA-
1 T-ATTTAAATAAAAAT
11217 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
**
11232 TATTTCTATAAAAAT
1 TATTTAAATAAAAAT
11247 T
1 T
11248 CATCGATAAT
Statistics
Matches: 74, Mismatches: 16, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
11 2 0.03
12 2 0.03
13 12 0.16
14 13 0.18
15 43 0.58
16 2 0.03
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:11183 original size:42 final size:42
Alignment explanation
Indices: 11132--11262 Score: 253
Period size: 42 Copynumber: 3.1 Consensus size: 42
11122 TGAATTCTAA
*
11132 ATATTTAAATAAAAATTATTTATATAAAAATTCATCGATAAT
1 ATATTTAAATAAAAATTATTTCTATAAAAATTCATCGATAAT
11174 ATATTTAAATAAAAATTATTTCTATAAAAATTCATCGATAAT
1 ATATTTAAATAAAAATTATTTCTATAAAAATTCATCGATAAT
11216 ATATTTAAATAAAAATTATTTCTATAAAAATTCATCGATAAT
1 ATATTTAAATAAAAATTATTTCTATAAAAATTCATCGATAAT
11258 ATATT
1 ATATT
11263 ACTTTATTAT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.41
Consensus pattern (42 bp):
ATATTTAAATAAAAATTATTTCTATAAAAATTCATCGATAAT
Found at i:11369 original size:35 final size:31
Alignment explanation
Indices: 11307--11369 Score: 81
Period size: 35 Copynumber: 1.9 Consensus size: 31
11297 ATTTTAATTA
*
11307 ATATTAAATTTTACATAATTTATCTAAAAAT
1 ATATTAAATTTTACATAATTTAACTAAAAAT
11338 ATATTAACATTTTACATCAACATTTAACTAAA
1 ATATTAA-ATTTTACAT--A-ATTTAACTAAA
11370 TGCTCAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 7 0.26
32 9 0.33
34 1 0.04
35 10 0.37
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (31 bp):
ATATTAAATTTTACATAATTTAACTAAAAAT
Found at i:15958 original size:23 final size:22
Alignment explanation
Indices: 15914--15958 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
15904 TAATATAATT
15914 AAAATTAAATTATCAAATTATAA
1 AAAATTAAATTA-CAAATTATAA
15937 AAAATATAAATTA-AAATCTATA
1 AAAAT-TAAATTACAAAT-TATA
15959 TTTGTGAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 9 0.45
24 7 0.35
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAATTAAATTACAAATTATAA
Found at i:16799 original size:62 final size:63
Alignment explanation
Indices: 16730--16853 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 63
16720 TTTAACGATT
* * *
16730 AAAATTTTGTTAATTTTTAGAATTTATG-AGCAGAATTAAATAAAACGATGTAACATTTATTA
1 AAAATTTTGTTAATCTTTAGAATTTATGAAACAGAATTAAATAAAACGATCTAACATTTATTA
* * *
16792 AAAATTTTGTTAATCTTTAGAATTTATGAAATATAATTAAATAAAATGATCTAACATTTATT
1 AAAATTTTGTTAATCTTTAGAATTTATGAAACAGAATTAAATAAAACGATCTAACATTTATT
16854 TAAATATATG
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
62 27 0.49
63 28 0.51
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (63 bp):
AAAATTTTGTTAATCTTTAGAATTTATGAAACAGAATTAAATAAAACGATCTAACATTTATTA
Found at i:18380 original size:21 final size:21
Alignment explanation
Indices: 18355--18396 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18345 AACATTTAAT
*
18355 ATTATTTATTATAAAAAATTA
1 ATTATTAATTATAAAAAATTA
* *
18376 ATTATTAATTTTAAAATATTA
1 ATTATTAATTATAAAAAATTA
18397 TAATAATTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATTATAAAAAATTA
Found at i:19404 original size:17 final size:19
Alignment explanation
Indices: 19382--19416 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19372 ATTTTTTAGT
19382 TGAG-TTTAAAA-ATTAAC
1 TGAGTTTTAAAATATTAAC
19399 TGAGTTTTAAAATATTAA
1 TGAGTTTTAAAATATTAA
19417 TGGATCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (19 bp):
TGAGTTTTAAAATATTAAC
Found at i:19510 original size:14 final size:14
Alignment explanation
Indices: 19476--19514 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
19466 GAGATTGAGT
* *
19476 TGAATATAAACAAC
1 TGAACATAAACAAA
19490 T-AACATAAACAAA
1 TGAACATAAACAAA
19503 TGAACATAAACA
1 TGAACATAAACA
19515 GACATAGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.62, C:0.15, G:0.05, T:0.18
Consensus pattern (14 bp):
TGAACATAAACAAA
Found at i:19959 original size:21 final size:21
Alignment explanation
Indices: 19925--19964 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19915 GTAAAAAAAT
19925 TACCTAAAAGATTATTATTTC
1 TACCTAAAAGATTATTATTTC
* *
19946 TACCTCAAATATTATTATT
1 TACCTAAAAGATTATTATT
19965 GGACACTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.45
Consensus pattern (21 bp):
TACCTAAAAGATTATTATTTC
Found at i:20475 original size:27 final size:27
Alignment explanation
Indices: 20445--20514 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
20435 TATTAATAAC
*
20445 TAAAAGTGATTTTGAAAATGTTACAGT
1 TAAAAGTGATTTTGAAAATGTTACAAT
*
20472 TAAAAGTAATTTTGAAAATGTTACAAT
1 TAAAAGTGATTTTGAAAATGTTACAAT
20499 TAAAAGTGATTTTGAA
1 TAAAAGTGATTTTGAA
20515 CATATACTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.37
Consensus pattern (27 bp):
TAAAAGTGATTTTGAAAATGTTACAAT
Found at i:21785 original size:29 final size:29
Alignment explanation
Indices: 21704--21772 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
21694 TAGGGTGACG
21704 TAAGTCGTCATGTCATCCGGGCGACCTAC
1 TAAGTCGTCATGTCATCCGGGCGACCTAC
*
21733 TAGGTCGTCATGTCATCCGGGCGACCTAC
1 TAAGTCGTCATGTCATCCGGGCGACCTAC
21762 TAAGTCGTCAT
1 TAAGTCGTCAT
21773 TTCTTCCCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.26
Consensus pattern (29 bp):
TAAGTCGTCATGTCATCCGGGCGACCTAC
Found at i:26648 original size:183 final size:184
Alignment explanation
Indices: 26276--26661 Score: 613
Period size: 183 Copynumber: 2.1 Consensus size: 184
26266 TTTTCTAATT
* *
26276 TATATAA-A-ATTAAATATTTTTTAATTCAAAAAAGTTTATAATTAATTTAAATAATAAATAATT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAGTTTACAATTAATTTAAATAATAAATAATT
26339 ATAAAATAAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 ATAAAATAAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* * *
26404 AGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTTAGCCCATATGTTA
131 AGATCTTAAATTATTAATTGGATTTTAAATGATTTGGGCTTAACCCATATGTTA
*
26458 TATATAATATATTTAATATTTTTTAATT-AAAAACAGTTTACAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAA-AGTTTACAATTAATTTAAATAATAAATAAT
*
26522 TATAAAATAAAAAA-TTTATAT-AATTTTTTAATTAATTAATATTGATTTAAAGTTTAAAAGTTA
65 TATAAAATAAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTT-AAGTTTAAAAGTTA
* * *
26585 TTGGATCTTAAATTATTAATTGGATTTTTAATGATTTGGG-TTGAACTCATATGTTA
129 TTAGATCTTAAATTATTAATTGGATTTTAAATGATTTGGGCTT-AACCCATATGTTA
26641 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
26662 AAAATTTAAT
Statistics
Matches: 189, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
182 36 0.19
183 94 0.50
184 59 0.31
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAGTTTACAATTAATTTAAATAATAAATAATT
ATAAAATAAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
AGATCTTAAATTATTAATTGGATTTTAAATGATTTGGGCTTAACCCATATGTTA
Found at i:31617 original size:22 final size:22
Alignment explanation
Indices: 31587--31634 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
31577 ATACGGTATA
*
31587 AACAGTACCGTGAACAGTAATG
1 AACAATACCGTGAACAGTAATG
*
31609 AACAATACCTTGAACAGTAATG
1 AACAATACCGTGAACAGTAATG
31631 AACA
1 AACA
31635 GTGATGCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.19
Consensus pattern (22 bp):
AACAATACCGTGAACAGTAATG
Found at i:31635 original size:32 final size:32
Alignment explanation
Indices: 31597--31659 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
31587 AACAGTACCG
*
31597 TGAACAGTAATGAACAATACCTTGAACAGTAA
1 TGAACAGTAATGAACAATACCGTGAACAGTAA
* * *
31629 TGAACAGTGATGCACAGTACCGTGAACAGTA
1 TGAACAGTAATGAACAATACCGTGAACAGTA
31660 CCGAATCCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (32 bp):
TGAACAGTAATGAACAATACCGTGAACAGTAA
Found at i:31729 original size:20 final size:21
Alignment explanation
Indices: 31694--31733 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
31684 TGCTTCAGGG
31694 GTATCGATACCCCTGCTACAA
1 GTATCGATACCCCTGCTACAA
31715 GTATCGATA-CCCTGCTACA
1 GTATCGATACCCCTGCTACA
31734 GTGTTGCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (21 bp):
GTATCGATACCCCTGCTACAA
Found at i:32187 original size:21 final size:21
Alignment explanation
Indices: 32162--32216 Score: 92
Period size: 21 Copynumber: 2.5 Consensus size: 21
32152 AATACACTTA
32162 ACATCATATAATTCATGTAAT
1 ACATCATATAATTCATGTAAT
32183 ACATCATATAATTCATGTAAT
1 ACATCATATAATTCATGTAAT
32204 ACAGTTCATATAA
1 ACA--TCATATAA
32217 CTAAAAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 24 0.75
23 8 0.25
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATCATATAATTCATGTAAT
Found at i:32640 original size:23 final size:23
Alignment explanation
Indices: 32598--32641 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
32588 ATTACATATA
*
32598 TGTCCCGAAGGACCATGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
*
32621 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
32642 CCCTCGACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:36309 original size:111 final size:111
Alignment explanation
Indices: 36087--36756 Score: 1049
Period size: 111 Copynumber: 6.0 Consensus size: 111
36077 GGTAAAATTA
* ** * * **
36087 AATCAGGGTAGACTTGTTCCATTATCACTTATGGAATATCAAATCTTGAAAGAGATTTGATCTGT
1 AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGAAAGAGA-GGGATCTGT
* * *
36152 TCCGCTT-CTCCTGAGGGAATATCAGATCTAGGAAAGTTGATCCATTG
65 TCCACTTCCT-CTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
* * * *
36199 AATCAGGGTAGACTTGTTCCACTATCGCTCAGGGAATATCAAATCTTTAAAGAGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
*
36264 CTACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
* *
36310 AATCAAGGTAGACTTGTTTCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
36375 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
*
36421 AATCAAGGTAGACTTGTTCCGCTATCACTTAGGGAATATCAAATCTTG-AA-AGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* *
36484 CTACTTCCTCTGAGGGAATATCAGATCTGTGAAAGTTGATTCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
*
36530 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* *
36595 CCACTTCTTCTAAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
*
36641 AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTATT
1 AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* * * *
36706 CCACTTCTTCTAAGGGAATATCAGATATGGGAAAGTTGATCCATTG
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
36752 AATCA
1 AATCA
36757 GGGTCGAACC
Statistics
Matches: 522, Mismatches: 33, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
109 103 0.20
110 4 0.01
111 363 0.70
112 52 0.10
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (111 bp):
AATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
Found at i:36555 original size:220 final size:221
Alignment explanation
Indices: 36087--36756 Score: 1056
Period size: 220 Copynumber: 3.0 Consensus size: 221
36077 GGTAAAATTA
* ** * * * **
36087 AATCAGGGTAGACTTGTTCCATTATCACTTATGGAATATCAAATCTTGAAAGAGATTTGATCTGT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGA-GGGATCTGT
* * * *
36152 TCCGCTT-CTCCTGAGGGAATATCAGATCTAGGAAAGTTGATCCATTGAATCAGGGTAGACTTGT
65 TCCACTTCCT-CTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTGAATCAAGGTAGACTTGT
* * *
36216 TCCACTATCGCTCAGGGAATATCAAATCTTTAAAGAGAGGGATCTGTTCTACTTCCTCTGAGGGA
129 TCCGCTATCACTCAGGGAATATCAAATC-TTGAAGAGAGGGATCTGTTCTACTTCCTCTGAGGGA
36281 ATATCAGATCTGGGAAAGTTGATTCATTG
193 ATATCAGATCTGGGAAAGTTGATTCATTG
*
36310 AATCAAGGTAGACTTGTTTCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
36375 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTGAATCAAGGTAGACTTGTTC
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTGAATCAAGGTAGACTTGTTC
*
36440 CGCTATCACTTAGGGAATATCAAATCTTGAA-AGAGGGATCTGTTCTACTTCCTCTGAGGGAATA
131 CGCTATCACTCAGGGAATATCAAATCTTGAAGAGAGGGATCTGTTCTACTTCCTCTGAGGGAATA
*
36504 TCAGATCTGTGAAAGTTGATTCATTG
196 TCAGATCTGGGAAAGTTGATTCATTG
36530 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
1 AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
* *
36595 CCACTTCTTCTAAGGGAATATCAGATCTGGGAAAGTTGATTCATTGAATCAAGGTAGACTTGTTC
66 CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTGAATCAAGGTAGACTTGTTC
* * * *
36660 CGCTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTATTCCACTTCTTCTAAGGGAAT
131 CGCTATCACTCAGGGAATATCAAATCTTG-AAGAGAGGGATCTGTTCTACTTCCTCTGAGGGAAT
* *
36725 ATCAGATATGGGAAAGTTGATCCATTG
195 ATCAGATCTGGGAAAGTTGATTCATTG
36752 AATCA
1 AATCA
36757 GGGTCGAACC
Statistics
Matches: 415, Mismatches: 29, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
220 213 0.51
221 6 0.01
222 146 0.35
223 50 0.12
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (221 bp):
AATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTT
CCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTGAATCAAGGTAGACTTGTTC
CGCTATCACTCAGGGAATATCAAATCTTGAAGAGAGGGATCTGTTCTACTTCCTCTGAGGGAATA
TCAGATCTGGGAAAGTTGATTCATTG
Found at i:36698 original size:331 final size:332
Alignment explanation
Indices: 36087--36756 Score: 1076
Period size: 331 Copynumber: 2.0 Consensus size: 332
36077 GGTAAAATTA
* * * *
36087 AATCAGGGTAGACTTGTTCCATTATCACTTATGGAATATCAAATCTTGAAAGAGATTTGATCTGT
1 AATCAAGGTAGACTTGTTCCACTATCACTTAGGGAATATCAAATCTTGAAAGAG--TGGATCTGT
* *
36152 TCCGCTTCTCCTGAGGGAATATCAGATCTAGGAAAGTTGATCCATTGAATCAGGGTAGACTTGTT
64 TCCACTTCTCCTGAGGGAATATCAGATCTAGGAAAGTTGATCCATTGAATCAAGGTAGACTTGTT
* * * *
36217 CCACTATCGCTCAGGGAATATCAAATCTTTAAAGAGAGGGATCTGTTCTACTTCCTCTGAGGGAA
129 CCACTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACTTCCTCTAAGGGAA
* *
36282 TATCAGATCTGGGAAAGTTGATTCATTGAATCAAGGTAGACTTGTTTCGCTGTCACTCAGGGAAT
194 TATCAGATCTGGGAAAGTTGATTCATTGAATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAAT
* * *
36347 ATCAAATCTTGAAAGAGAGGGATCTGTTCCACTTCCTCTGAGGGAATATCAGATCTGGGAAAGTT
259 ATCAAATCTTGAAAGAGAGGGATCTATTCCACTTCCTCTAAGGGAATATCAGATATGGGAAAGTT
*
36412 GATTCATTG
324 GATCCATTG
*
36421 AATCAAGGTAGACTTGTTCCGCTATCACTTAGGGAATATCAAATCTTGAAAGAG-GGATCTGTTC
1 AATCAAGGTAGACTTGTTCCACTATCACTTAGGGAATATCAAATCTTGAAAGAGTGGATCTGTTC
* *
36485 TACTTC-CTCTGAGGGAATATCAGATCT-GTGAAAGTTGATTCATTGAATCAAGGTAGACTTGTT
66 CACTTCTC-CTGAGGGAATATCAGATCTAG-GAAAGTTGATCCATTGAATCAAGGTAGACTTGTT
* * *
36548 CCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACTTCTTCTAAGGGAA
129 CCACTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACTTCCTCTAAGGGAA
36613 TATCAGATCTGGGAAAGTTGATTCATTGAATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAAT
194 TATCAGATCTGGGAAAGTTGATTCATTGAATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAAT
*
36678 ATCAAATCTTGAAAGAGAGGGATCTATTCCACTTCTTCTAAGGGAATATCAGATATGGGAAAGTT
259 ATCAAATCTTGAAAGAGAGGGATCTATTCCACTTCCTCTAAGGGAATATCAGATATGGGAAAGTT
36743 GATCCATTG
324 GATCCATTG
36752 AATCA
1 AATCA
36757 GGGTCGAACC
Statistics
Matches: 311, Mismatches: 23, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
330 2 0.01
331 259 0.83
334 50 0.16
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (332 bp):
AATCAAGGTAGACTTGTTCCACTATCACTTAGGGAATATCAAATCTTGAAAGAGTGGATCTGTTC
CACTTCTCCTGAGGGAATATCAGATCTAGGAAAGTTGATCCATTGAATCAAGGTAGACTTGTTCC
ACTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACTTCCTCTAAGGGAATA
TCAGATCTGGGAAAGTTGATTCATTGAATCAAGGTAGACTTGTTCCGCTATCACTCAGGGAATAT
CAAATCTTGAAAGAGAGGGATCTATTCCACTTCCTCTAAGGGAATATCAGATATGGGAAAGTTGA
TCCATTG
Found at i:37953 original size:23 final size:23
Alignment explanation
Indices: 37924--37999 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
37914 CCTTCTTTTA
37924 TTTTTCTTTTTATTTTTCCTCAT
1 TTTTTCTTTTTATTTTTCCTCAT
37947 TTTTTCTTTCTT-TTTTT--TCATT
1 TTTTTCTTT-TTATTTTTCCTCA-T
** *
37969 TTTTTCCATTCATTTTTCCATTCAT
1 TTTTTCTTTTTATTTTTCC--TCAT
37994 TTTTTC
1 TTTTTC
38000 AGGCGAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
21 4 0.09
22 13 0.30
23 14 0.33
24 2 0.05
25 7 0.16
26 3 0.07
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTTTCTTTTTATTTTTCCTCAT
Found at i:37980 original size:14 final size:14
Alignment explanation
Indices: 37963--37998 Score: 58
Period size: 12 Copynumber: 2.7 Consensus size: 14
37953 TTTCTTTTTT
37963 TTCATTTTTTTCCA
1 TTCATTTTTTTCCA
37977 TTCA--TTTTTCCA
1 TTCATTTTTTTCCA
37989 TTCATTTTTT
1 TTCATTTTTT
37999 CAGGCGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 12 0.60
14 8 0.40
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (14 bp):
TTCATTTTTTTCCA
Found at i:56158 original size:23 final size:23
Alignment explanation
Indices: 56128--56192 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
56118 ATTACATATA
56128 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
*
56151 TGTCCCGAATGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
*
56174 TGTCCCGAAGGACCGCGTA
1 TGTCCCGAAGGACCACGTA
56193 AACCCTCGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:57139 original size:51 final size:51
Alignment explanation
Indices: 57075--57176 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
57065 CTTCAAATTC
57075 AACTCATCAACTCTATTTCAAGATTTCACTCAAGAACTCCAAATCTTTAAT
1 AACTCATCAACTCTATTTCAAGATTTCACTCAAGAACTCCAAATCTTTAAT
57126 AACTCATCAACTCTATTTCAAGATTTCACTCAAGAACTCCAAATCTTTAAT
1 AACTCATCAACTCTATTTCAAGATTTCACTCAAGAACTCCAAATCTTTAAT
57177 CTTCCTAACT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.33
Consensus pattern (51 bp):
AACTCATCAACTCTATTTCAAGATTTCACTCAAGAACTCCAAATCTTTAAT
Found at i:68910 original size:18 final size:18
Alignment explanation
Indices: 68887--68946 Score: 81
Period size: 18 Copynumber: 3.5 Consensus size: 18
68877 CTTACTCTCT
68887 TCATCATCGCCATCATCA
1 TCATCATCGCCATCATCA
68905 TCATCA---CCATCATCA
1 TCATCATCGCCATCATCA
* *
68920 TCATCATCACCATCAACA
1 TCATCATCGCCATCATCA
68938 TCATCATCG
1 TCATCATCG
68947 TTGTCATCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
15 15 0.41
18 22 0.59
ACGTcount: A:0.32, C:0.38, G:0.03, T:0.27
Consensus pattern (18 bp):
TCATCATCGCCATCATCA
Found at i:68958 original size:3 final size:3
Alignment explanation
Indices: 68887--68945 Score: 73
Period size: 3 Copynumber: 19.7 Consensus size: 3
68877 CTTACTCTCT
* * * *
68887 TCA TCA TCG CCA TCA TCA TCA TCA CCA TCA TCA TCA TCA TCA CCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
*
68935 ACA TCA TCA TC
1 TCA TCA TCA TC
68946 GTTGTCATCA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.32, C:0.39, G:0.02, T:0.27
Consensus pattern (3 bp):
TCA
Found at i:70509 original size:2 final size:2
Alignment explanation
Indices: 70502--70593 Score: 177
Period size: 2 Copynumber: 46.5 Consensus size: 2
70492 ATTCTAACCC
70502 AT AT 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 AT AT
70544 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70585 AT AT AT AT A
1 AT AT AT AT A
70594 GTAATCAAAT
Statistics
Matches: 89, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 88 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:80097 original size:2 final size:2
Alignment explanation
Indices: 80090--80148 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
80080 TGTTATGCAT
80090 TA TA TA TA TA 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 TA TA TA TA TA
80132 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
80149 TGTAGAGATG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:81250 original size:18 final size:19
Alignment explanation
Indices: 81216--81251 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
81206 AATGTAAATA
*
81216 AGAAAATAATGAATAAAAC
1 AGAAAAGAATGAATAAAAC
81235 AGAAAAGAAT-AATAAAA
1 AGAAAAGAATGAATAAAA
81252 TAACTAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.72, C:0.03, G:0.11, T:0.14
Consensus pattern (19 bp):
AGAAAAGAATGAATAAAAC
Found at i:81460 original size:20 final size:20
Alignment explanation
Indices: 81435--81476 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
81425 ATTTAATGGT
81435 TAATAAAACAAGTAA-AAATA
1 TAATAAAACAA-TAATAAATA
*
81455 TAATAAAAGAATAATAAATA
1 TAATAAAACAATAATAAATA
81475 TA
1 TA
81477 TATTAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (20 bp):
TAATAAAACAATAATAAATA
Found at i:81569 original size:15 final size:15
Alignment explanation
Indices: 81532--81577 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
81522 AAATAGGAAT
*
81532 AAAATA-AACAATAA
1 AAAATATAATAATAA
81546 AAAATATAATAATAA
1 AAAATATAATAATAA
*
81561 TAAAA-ATAATCATAA
1 -AAAATATAATAATAA
81576 AA
1 AA
81578 GGACCAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 8 0.29
15 16 0.57
16 4 0.14
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAATATAATAATAA
Found at i:81570 original size:12 final size:11
Alignment explanation
Indices: 81492--81569 Score: 50
Period size: 12 Copynumber: 6.6 Consensus size: 11
81482 AATACTTGGT
81492 AAAATAAAATA
1 AAAATAAAATA
* *
81503 AAATTAATGATA
1 AAAATAA-AATA
*
81515 AGAAATTAAATA
1 A-AAATAAAATA
**
81527 GGAATAAAATA
1 AAAATAAAATA
81538 AACAATAAAA-A
1 AA-AATAAAATA
81549 ATATAATAATAATA
1 A-A-AATAA-AATA
81563 AAAATAA
1 AAAATAA
81570 TCATAAAAGG
Statistics
Matches: 50, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
11 16 0.32
12 25 0.50
13 7 0.14
14 2 0.04
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:81576 original size:30 final size:29
Alignment explanation
Indices: 81493--81577 Score: 75
Period size: 30 Copynumber: 2.9 Consensus size: 29
81483 ATACTTGGTA
* * *
81493 AAATAAAATAAAATTAATGATAAGAAATT
1 AAATAAAATAAAAATAATCATAAAAAATT
* *
81522 AAATAGGAAT-AAAATAAACAATAAAAAA-T
1 AAATA-AAATAAAAATAATC-ATAAAAAATT
81551 ATAATAATAATAAAAATAATCATAAAA
1 A-AATAA-AATAAAAATAATCATAAAA
81578 GGACCAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
29 13 0.30
30 23 0.52
31 8 0.18
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (29 bp):
AAATAAAATAAAAATAATCATAAAAAATT
Found at i:83645 original size:65 final size:63
Alignment explanation
Indices: 83510--83682 Score: 228
Period size: 65 Copynumber: 2.8 Consensus size: 63
83500 AAGTTGAGCC
* * *
83510 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGTATT--GT--TTCACCAATTTGGCT
1 TTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAA-TCTTGAGTAATTCACCAAATTGGCT
* *
83570 TTGATTTGGATATACTTCGTTGTGAAGTTGAAATCCAATCTTGAGTAAGTCTCACCAAATTGGCT
1 TTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAGTAA-T-TCACCAAATTGGCT
* *
83635 TTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTCGAGTAA
1 TTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAGTAA
83683 ATGGTGTTGC
Statistics
Matches: 99, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
59 3 0.03
60 35 0.35
61 2 0.02
64 1 0.01
65 58 0.59
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (63 bp):
TTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGAGTAATTCACCAAATTGGCT
Found at i:84468 original size:13 final size:13
Alignment explanation
Indices: 84435--84481 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
84425 ACCCACCTCA
84435 TTTTTCTTTTCCT
1 TTTTTCTTTTCCT
*
84448 TTTCTCTTTT-CT
1 TTTTTCTTTTCCT
84460 TTTGTTCTTTTTCTCT
1 TTT-TTC-TTTTC-CT
84476 TTTTTC
1 TTTTTC
84482 AATTTAGGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 5 0.18
13 11 0.39
14 4 0.14
15 3 0.11
16 5 0.18
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTTCTTTTCCT
Found at i:95210 original size:14 final size:14
Alignment explanation
Indices: 95191--95222 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
95181 AATACTTGGT
95191 AAAATAAAATAAAA
1 AAAATAAAATAAAA
*
95205 AAAATAAAGTAAAA
1 AAAATAAAATAAAA
95219 AAAA
1 AAAA
95223 AGGATATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.12
Consensus pattern (14 bp):
AAAATAAAATAAAA
Found at i:96057 original size:14 final size:16
Alignment explanation
Indices: 96029--96060 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
96019 CGTAACCCCT
96029 TGTGTAATATGCGTAG
1 TGTGTAATATGCGTAG
96045 TGTGTAA-AT-CGTAG
1 TGTGTAATATGCGTAG
96059 TG
1 TG
96061 ATATTACATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.38
Consensus pattern (16 bp):
TGTGTAATATGCGTAG
Found at i:96459 original size:20 final size:20
Alignment explanation
Indices: 96434--96482 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
96424 TCGACTATCG
96434 CATTGCGATTTACATATTCT
1 CATTGCGATTTACATATTCT
96454 CATTGCGATTTACATATTCT
1 CATTGCGATTTACATATTCT
96474 CATTGCGAT
1 CATTGCGAT
96483 AGTGAAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.43
Consensus pattern (20 bp):
CATTGCGATTTACATATTCT
Found at i:96519 original size:21 final size:21
Alignment explanation
Indices: 96495--96651 Score: 189
Period size: 21 Copynumber: 7.5 Consensus size: 21
96485 TGAAAGTTCG
96495 CGTTGCGATTTATTCCAAGTT
1 CGTTGCGATTTATTCCAAGTT
*
96516 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAGTT
96537 CGTTGCGA--TATTCCAAGTT
1 CGTTGCGATTTATTCCAAGTT
96556 CGCGTTGCGATTTATTCCAAGTT
1 --CGTTGCGATTTATTCCAAGTT
* * *
96579 CATTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAGTT
*
96598 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAGTT
*
96621 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAGTT
96642 CGTTGC-ATTT
1 CGTTGCGATTT
96652 GTTTCTTAAG
Statistics
Matches: 119, Mismatches: 9, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
19 19 0.16
20 4 0.03
21 77 0.65
23 19 0.16
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAGTT
Found at i:97400 original size:21 final size:21
Alignment explanation
Indices: 97337--97580 Score: 111
Period size: 21 Copynumber: 11.2 Consensus size: 21
97327 CACCAGTCGT
*
97337 TGCGATTTTGGACTATCGCAA
1 TGCGAATTTGGACTATCGCAA
* *
97358 --CGAATTTGGAATAAATCACAA
1 TGCGAATTTGGACT--ATCGCAA
* *
97379 CGCGAATTTCGACTATCGCAA
1 TGCGAATTTGGACTATCGCAA
*
97400 --CGAATTTGGAATAAATCGCAA
1 TGCGAATTTGGACT--ATCGCAA
*
97421 TGCGAACTTGGACTATCGCAA
1 TGCGAATTTGGACTATCGCAA
* * *
97442 TGCGAATATGTA-AATCGCAA
1 TGCGAATTTGGACTATCGCAA
* * * * * *
97462 TGCGATAATCGAAGTTTGCGTTGCGA
1 TGCGA-ATTTGGACTAT-C---GCAA
*
97488 TAGTCGAATTTGGAATAAATCGCAA
1 T-G-CGAATTTGGACT--ATCGCAA
* * * *
97513 CGTGAACTTCGACTATCGCAA
1 TGCGAATTTGGACTATCGCAA
*
97534 TGCGAACTTGGACTATCGCAA
1 TGCGAATTTGGACTATCGCAA
* * *
97555 TGCGAACTTCGACTATCGCAT
1 TGCGAATTTGGACTATCGCAA
97576 TGCGA
1 TGCGA
97581 TAGTCGAAGT
Statistics
Matches: 168, Mismatches: 37, Indels: 36
0.70 0.15 0.15
Matches are distributed among these distances:
19 20 0.12
20 12 0.07
21 87 0.52
22 1 0.01
23 29 0.17
24 1 0.01
25 3 0.02
26 4 0.02
27 6 0.04
28 4 0.02
29 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (21 bp):
TGCGAATTTGGACTATCGCAA
Found at i:97406 original size:42 final size:42
Alignment explanation
Indices: 97338--97441 Score: 163
Period size: 42 Copynumber: 2.5 Consensus size: 42
97328 ACCAGTCGTT
*
97338 GCGATTTTGGACTATCGCAACGAATTTGGAATAAATCACAAC
1 GCGAATTTGGACTATCGCAACGAATTTGGAATAAATCACAAC
* * *
97380 GCGAATTTCGACTATCGCAACGAATTTGGAATAAATCGCAAT
1 GCGAATTTGGACTATCGCAACGAATTTGGAATAAATCACAAC
*
97422 GCGAACTTGGACTATCGCAA
1 GCGAATTTGGACTATCGCAA
97442 TGCGAATATG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (42 bp):
GCGAATTTGGACTATCGCAACGAATTTGGAATAAATCACAAC
Found at i:97587 original size:21 final size:21
Alignment explanation
Indices: 97506--97580 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
97496 TTTGGAATAA
* *
97506 ATCGCAACGTGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
97527 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
97548 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
97569 ATCGCATTGCGA
1 ATCGCAATGCGA
97581 TAGTCGAAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:98115 original size:21 final size:21
Alignment explanation
Indices: 98089--98140 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
98079 GTTGCATTTC
98089 GCGTTGCGATAATTGAAAATA
1 GCGTTGCGATAATTGAAAATA
* *
98110 GCGTTGCGATAGTTGAAAATC
1 GCGTTGCGATAATTGAAAATA
98131 GCGTTGCGAT
1 GCGTTGCGAT
98141 TTTCCATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (21 bp):
GCGTTGCGATAATTGAAAATA
Found at i:98154 original size:20 final size:20
Alignment explanation
Indices: 98129--98318 Score: 188
Period size: 20 Copynumber: 9.3 Consensus size: 20
98119 TAGTTGAAAA
*
98129 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
*
98149 TCGCGTTGCGATTTACCAGT
1 TCGCGTTGCGATTTTCCAGT
*
98169 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
98189 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
*** *
98209 TCGCGTTGCGATAGTTGAAAAT
1 TCGCGTTGCGAT--TTTCCAGT
* *
98231 T-GCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
*
98252 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
* *
98273 TCG-TTGTGCGATTTTCCATT
1 TCGCGT-TGCGATTTTCCAGT
98293 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
98313 TCGCGT
1 TCGCGT
98319 CGGGTCGGGT
Statistics
Matches: 143, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
20 95 0.66
21 33 0.23
22 15 0.10
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:98342 original size:6 final size:6
Alignment explanation
Indices: 98317--98363 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
98307 TCCAGTTCGC
98317 GTCG-G GTCG-G GTCG-G GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
98362 GT
1 GT
98364 AATACGTGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 14 0.34
6 27 0.66
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GTCGTG
Found at i:98488 original size:21 final size:19
Alignment explanation
Indices: 98436--98491 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 19
98426 AAATCTTTTT
98436 TTTA-ACTATCGCAACGAA
1 TTTAGACTATCGCAACGAA
* **
98454 TTTGGAAAATCGCAACGACA
1 TTTAGACTATCGCAACGA-A
98474 TTGTAGACTATCGCAACG
1 TT-TAGACTATCGCAACG
98492 CGAAATGGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 3 0.10
19 11 0.38
20 3 0.10
21 12 0.41
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (19 bp):
TTTAGACTATCGCAACGAA
Found at i:98508 original size:20 final size:20
Alignment explanation
Indices: 98483--98637 Score: 139
Period size: 20 Copynumber: 7.6 Consensus size: 20
98473 ATTGTAGACT
98483 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
98503 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
98524 ATCGGAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
98544 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
98565 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
98585 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
98606 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
98626 ATCGCAACGCGA
1 ATCGCAACGCGA
98638 TTTTCAATTA
Statistics
Matches: 100, Mismatches: 32, Indels: 6
0.72 0.23 0.04
Matches are distributed among these distances:
20 56 0.56
21 44 0.44
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:98508 original size:41 final size:41
Alignment explanation
Indices: 98434--98662 Score: 340
Period size: 41 Copynumber: 5.6 Consensus size: 41
98424 CAAAATCTTT
* *
98434 TTTTTAACTATCGCAA--CGAATTTGGAAAATCGCAACGAC-A
1 TTTTCAACTATCGCAACGCGAA-ATGGAAAATCGCAACG-CGA
*
98474 TTGT-AGACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 TTTTCA-ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
*
98515 TTTTCAACTATCGGAACGCGAAATGGAAAATCGCAACGCGA
1 TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
98556 TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
98597 TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
* * *
98638 TTTTCAATTATCGCAATGTGAAATG
1 TTTTCAACTATCGCAACGCGAAATG
98663 CAACGCGAAT
Statistics
Matches: 176, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
39 1 0.01
40 14 0.08
41 156 0.89
42 5 0.03
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (41 bp):
TTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
Found at i:98532 original size:21 final size:21
Alignment explanation
Indices: 98503--98653 Score: 128
Period size: 21 Copynumber: 7.3 Consensus size: 21
98493 GAAATGGAAA
98503 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* ** ** *
98524 ATCGGAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
98544 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
98565 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
98585 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
98606 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
*
98626 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
98647 ATCGCAA
1 ATCGCAA
98654 TGTGAAATGC
Statistics
Matches: 95, Mismatches: 32, Indels: 6
0.71 0.24 0.05
Matches are distributed among these distances:
20 44 0.46
21 51 0.54
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:100016 original size:25 final size:25
Alignment explanation
Indices: 99959--100007 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
99949 ATGAATATCC
*
99959 AAATAAATTTTTATAGTTTTTTAAA
1 AAATAAATTTTTATAGATTTTTAAA
99984 AAATAAATATTTTATA-ATTTTTAA
1 AAATAAAT-TTTTATAGATTTTTAA
100008 TAATCAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
AAATAAATTTTTATAGATTTTTAAA
Done.