Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008788.1 Hibiscus syriacus cultivar Beakdansim tig00111930_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: 62185
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4510 original size:32 final size:32
Alignment explanation
Indices: 4474--4570 Score: 106
Period size: 32 Copynumber: 3.0 Consensus size: 32
4464 TTGACCAAAA
* *
4474 CCAAAAATCAACCGATCCAATATTGACCCGAC
1 CCAAAAATCAACAGATCCGATATTGACCCGAC
* * *
4506 CC-AAAATCTAACATATCCGATATTAACCCGGC
1 CCAAAAATC-AACAGATCCGATATTGACCCGAC
* * *
4538 CCAAAAATCAACTGATTCGATATTGATCCGAC
1 CCAAAAATCAACAGATCCGATATTGACCCGAC
4570 C
1 C
4571 TGATATTAAC
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
31 6 0.12
32 40 0.77
33 6 0.12
ACGTcount: A:0.38, C:0.31, G:0.10, T:0.21
Consensus pattern (32 bp):
CCAAAAATCAACAGATCCGATATTGACCCGAC
Found at i:4656 original size:16 final size:16
Alignment explanation
Indices: 4631--4664 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4621 AAAAACAATC
*
4631 GATCTGATAATCACCT
1 GATCTAATAATCACCT
4647 GATCTAATAATCACCT
1 GATCTAATAATCACCT
4663 GA
1 GA
4665 CCCGATACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (16 bp):
GATCTAATAATCACCT
Found at i:6607 original size:21 final size:20
Alignment explanation
Indices: 6583--6631 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
6573 TAGTTCTATA
6583 AAGTTCTTTTCT-TTTATTTT
1 AAGTT-TTTTCTATTTATTTT
*
6603 CAAGTTTTTTTTACTTTATTTT
1 -AAGTTTTTTCTA-TTTATTTT
6625 AAGTTTT
1 AAGTTTT
6632 ATTTTTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 5 0.20
21 12 0.48
22 8 0.32
ACGTcount: A:0.18, C:0.08, G:0.06, T:0.67
Consensus pattern (20 bp):
AAGTTTTTTCTATTTATTTT
Found at i:6620 original size:22 final size:22
Alignment explanation
Indices: 6595--6636 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
6585 GTTCTTTTCT
6595 TTTATTTTCAAGTTTT-TTTTAC
1 TTTATTTT-AAGTTTTATTTTAC
6617 TTTATTTTAAGTTTTATTTT
1 TTTATTTTAAGTTTTATTTT
6637 TAAACATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (22 bp):
TTTATTTTAAGTTTTATTTTAC
Found at i:10857 original size:20 final size:21
Alignment explanation
Indices: 10817--10858 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
10807 ATGTATGAGA
10817 ATGTTGTGGCAAAATGAAATGG
1 ATGTTGTGG-AAAATGAAATGG
*
10839 ATGTTGTGG-AAATGGAATGG
1 ATGTTGTGGAAAATGAAATGG
10859 TGGTATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.33, C:0.02, G:0.36, T:0.29
Consensus pattern (21 bp):
ATGTTGTGGAAAATGAAATGG
Found at i:16198 original size:12 final size:12
Alignment explanation
Indices: 16183--16232 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
16173 TCTAAAAAAG
*
16183 ACAAGGAAAATA
1 ACAAGTAAAATA
16195 ACAAGTAAAACTA
1 ACAAGTAAAA-TA
16208 TACAA--AAAATGA
1 -ACAAGTAAAAT-A
16220 ACAAGTAAAATA
1 ACAAGTAAAATA
16232 A
1 A
16233 AAATGCTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
11 5 0.16
12 16 0.50
13 7 0.22
14 4 0.12
ACGTcount: A:0.66, C:0.10, G:0.10, T:0.14
Consensus pattern (12 bp):
ACAAGTAAAATA
Found at i:16505 original size:20 final size:21
Alignment explanation
Indices: 16465--16506 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
16455 ACAAATGAGA
16465 ATGTTGTGGCAAAATGAAATGG
1 ATGTTGTGG-AAAATGAAATGG
*
16487 ATGTTGTGG-AAATGGAATGG
1 ATGTTGTGGAAAATGAAATGG
16507 TGGTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.33, C:0.02, G:0.36, T:0.29
Consensus pattern (21 bp):
ATGTTGTGGAAAATGAAATGG
Found at i:17676 original size:36 final size:37
Alignment explanation
Indices: 17620--17694 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 37
17610 TTCGTCCTAT
*
17620 TAGGATTCAAACTCTCAAAAATATGATAGAATTCTGC
1 TAGGATTCAAACTCTCAAAAATAGGATAGAATTCTGC
*
17657 TAGGATTC-AACTC-CTAAAAATAGGATAGAATTTTGC
1 TAGGATTCAAACTCTC-AAAAATAGGATAGAATTCTGC
17693 TA
1 TA
17695 TGTTTTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
35 1 0.03
36 26 0.74
37 8 0.23
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (37 bp):
TAGGATTCAAACTCTCAAAAATAGGATAGAATTCTGC
Found at i:18237 original size:19 final size:21
Alignment explanation
Indices: 18194--18256 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
18184 TTTTTAAAGT
18194 TATTATATATATATATATTTA
1 TATTATATATATATATATTTA
18215 TATTATAT-TAT-TAT-TTTA
1 TATTATATATATATATATTTA
*
18233 CTATTAACGTATATAAATATATTT
1 -TATT-A--TATATATATATATTT
18257 TTCTCTTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
18 4 0.12
19 7 0.21
20 4 0.12
21 8 0.24
22 3 0.09
23 2 0.06
24 3 0.09
25 3 0.09
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (21 bp):
TATTATATATATATATATTTA
Found at i:18430 original size:16 final size:16
Alignment explanation
Indices: 18409--18442 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18399 CATGTATTTA
18409 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
18425 TATTATTTTACTTTAT
1 TATTATATTACATTAT
18441 TA
1 TA
18443 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:18761 original size:14 final size:14
Alignment explanation
Indices: 18744--18782 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
18734 TTTCCCTTCT
18744 ATTTTCTTTATTTC
1 ATTTTCTTTATTTC
*
18758 ATTTACTTTATTTC
1 ATTTTCTTTATTTC
*
18772 CTTTTCCTTTA
1 ATTTT-CTTTA
18783 ACGCGTTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTTCTTTATTTC
Found at i:21823 original size:20 final size:20
Alignment explanation
Indices: 21771--21840 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
21761 CAAAAAGGGT
*
21771 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAG-AAAAA-ACAAGAA-CA
21794 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
21815 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
21835 AAAAAG
1 AAAAAG
21841 GGAACAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 18 0.43
21 7 0.17
22 6 0.14
23 10 0.24
24 1 0.02
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:22476 original size:22 final size:22
Alignment explanation
Indices: 22448--22498 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
22438 CCCCATCAAT
22448 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
* *
22470 CCTTTGAGCATCAAATGCGAAA
1 CCTTTGAGCATCAAATACCAAA
22492 CCTTTGA
1 CCTTTGA
22499 CCAAACACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:23452 original size:37 final size:37
Alignment explanation
Indices: 23358--23467 Score: 159
Period size: 37 Copynumber: 3.0 Consensus size: 37
23348 GTGCTCACCA
23358 TTTTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* *
23394 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* * *
23431 TTTTCTCCCTTGAGATAGTTTCTCTTGAAACATAAAC
1 TTTTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
23468 ATTGAAAACA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 30 0.46
37 32 0.49
38 3 0.05
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (37 bp):
TTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:23553 original size:37 final size:37
Alignment explanation
Indices: 23478--23569 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
23468 ATTGAAAACA
* * * *
23478 TTTCCCTTGAAA-TAAGTTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
23514 TTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
23551 TTTCTCTTGAAACATAAAT
1 TTTCCCTTGAAACA-AAAT
23570 ATTGGAAACA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
36 12 0.25
37 32 0.67
38 4 0.08
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:23553 original size:102 final size:102
Alignment explanation
Indices: 23376--23767 Score: 644
Period size: 102 Copynumber: 3.9 Consensus size: 102
23366 CTTGAGACAG
** * * *
23376 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
23441 TGAGATAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
23478 TTTCCCTTGAAAT-AAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCC
1 TTTCCCTTGAAATGAA-TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCC
* *
23542 TTGAGACAGTTTCTCTTGAAACATAAATATTGGAAACA
65 TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
23580 TTTCCCTTGAAATGAATTTTATCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
23645 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
23682 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
23746 TGAGACAGTTTCTCTTGAAACA
66 TGAGACAGTTTCTCTTGAAACA
23768 CAAAACCTTT
Statistics
Matches: 273, Mismatches: 15, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
101 38 0.14
102 233 0.85
103 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:23647 original size:37 final size:37
Alignment explanation
Indices: 23580--23666 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
23570 ATTGGAAACA
** * *
23580 TTTCCCTTGAAA-TGAATTTTATCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAG
*
23616 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAG
23653 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
23667 TAAACATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
36 12 0.27
37 30 0.68
38 2 0.05
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAG
Found at i:23728 original size:36 final size:36
Alignment explanation
Indices: 23681--23767 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
23671 CATTGAAAAC
** * *
23681 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
*
23717 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* *
23753 GTTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
23768 CAAAACCTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
Found at i:23858 original size:67 final size:67
Alignment explanation
Indices: 23709--23867 Score: 214
Period size: 67 Copynumber: 2.4 Consensus size: 67
23699 TTCGTCTCTC
** * *
23709 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAAC
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGAAAGTTTCTCTTGAAACACAAAAC
23774 CT
66 CT
* * *
23776 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCATGAGAAAGTTTCTCTTGAAACATAAAAT
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGAAAGTTTCTCTTGAAACACAAAAC
23841 CT
66 CT
*
23843 TTGA-ATT-TATCTCCCTTAAAACAAA
1 TTGAGATTGT-T-TCCCTTGAAACAAA
23868 ATTTCGTTTC
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 76 0.94
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGAAAGTTTCTCTTGAAACACAAAAC
CT
Found at i:24761 original size:100 final size:102
Alignment explanation
Indices: 24447--24856 Score: 389
Period size: 106 Copynumber: 3.9 Consensus size: 102
24437 TAGCTAGAAT
* * * * ** *
24447 CAAGTTCAATTTCACAACGAAGGGACGGCTGGTTGCCAACAACAATTTCAGTTTCA-TCCGCGAT
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAATTTCAG-TTCAGAGC-CAAT
* ** *
24511 TTCAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACA
64 TTCAACTTCACAG-CAAAGGATAT--TG-GACTCGAGACAACA
* * * * *
24553 CAAGTTCAACTTCACAATGAAGGGACTGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAA-A-ATTTC--AGTTCAGAGCCA
* *
24618 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACAACA
62 ATTTCAACTTCACAGCAAAGGATATTGGACTCGAGACAACA
* * *
24659 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTTTCAAC-AAGATTTC-GTTCAGAGTCAATTT
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAATTTCAGTTCAGAGCCAATTT
* *
24722 CAACTTCACAGCAAAGGATATTAGACTCGAGACAGCA
66 CAACTTCACAGCAAAGGATATTGGACTCGAGACAACA
* * * * * *
24759 CAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCGGTTCCAGAACCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAA-AATTT--CAGTT-CAGAGCCA
24824 ATTTCAACTTCACAG-AAGAGGATATTGGACTCG
62 ATTTCAACTTCACAGCAA-AGGATATTGGACTCG
24857 GAACAATATT
Statistics
Matches: 256, Mismatches: 35, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
100 81 0.32
101 2 0.01
102 4 0.02
103 4 0.02
104 1 0.00
105 7 0.03
106 121 0.47
107 3 0.01
108 4 0.02
109 26 0.10
110 3 0.01
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (102 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAATTTCAGTTCAGAGCCAATTT
CAACTTCACAGCAAAGGATATTGGACTCGAGACAACA
Found at i:25374 original size:36 final size:37
Alignment explanation
Indices: 25317--25392 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 37
25307 TTTCGTCCTA
25317 CTAGGATTCAAACTCTCAAAAATAGGATAAAATTCTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAAAATTCTG
* *
25354 CTAGGATTC-AACTC-CTAAAAATAGGATAGAATTTTG
1 CTAGGATTCAAACTCTC-AAAAATAGGATAAAATTCTG
25390 CTA
1 CTA
25393 TGTTTTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 1 0.03
36 26 0.72
37 9 0.25
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAAAATTCTG
Found at i:25882 original size:11 final size:11
Alignment explanation
Indices: 25862--25947 Score: 50
Period size: 11 Copynumber: 7.3 Consensus size: 11
25852 TTGATTATTT
*
25862 TTATTCTAATA
1 TTATTTTAATA
*
25873 TTATTTTAATG
1 TTATTTTAATA
25884 TT-TTTTAA-A
1 TTATTTTAATA
25893 GTTATTATATATATA
1 -TTATT-T-TA-ATA
25908 TATATTTATAATTA
1 T-TATTT-TAA-TA
*
25922 TTATATTTATTA
1 TTAT-TTTAATA
*
25934 TTATTTTACTA
1 TTATTTTAATA
25945 TTA
1 TTA
25948 ACGTATATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
10 8 0.13
11 22 0.36
12 7 0.11
13 8 0.13
14 11 0.18
15 5 0.08
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:25926 original size:15 final size:15
Alignment explanation
Indices: 25908--25938 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25898 TATATATATA
25908 TATATTTATAATTAT
1 TATATTTATAATTAT
*
25923 TATATTTATTATTAT
1 TATATTTATAATTAT
25938 T
1 T
25939 TTACTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATTTATAATTAT
Found at i:29982 original size:17 final size:19
Alignment explanation
Indices: 29956--29999 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
29946 ATTTTTATTT
*
29956 TCTTTATTTT-CT-TTAAA
1 TCTTTTTTTTACTATTAAA
*
29973 TCTTTTTTTTATTATTAAA
1 TCTTTTTTTTACTATTAAA
29992 TCTTTTTT
1 TCTTTTTT
30000 ACGAAGACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
19 13 0.57
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTTTTTACTATTAAA
Found at i:31813 original size:20 final size:19
Alignment explanation
Indices: 31788--31826 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
31778 CACAGACAAG
*
31788 GAGTATAGGTACTGACCCTT
1 GAGTATAGATACT-ACCCTT
*
31808 GAGTATCGATACTACCCTT
1 GAGTATAGATACTACCCTT
31827 TACATTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (19 bp):
GAGTATAGATACTACCCTT
Found at i:33849 original size:10 final size:10
Alignment explanation
Indices: 33820--33907 Score: 94
Period size: 10 Copynumber: 9.1 Consensus size: 10
33810 GCTGCTGGAA
33820 AACCGGTTTG
1 AACCGGTTTG
*
33830 -ACCAGTTTTG
1 AACC-GGTTTG
33840 AACCGGTTTG
1 AACCGGTTTG
*
33850 -ACCGGTTCG
1 AACCGGTTTG
33859 AACCGGTTTG
1 AACCGGTTTG
*
33869 -ACCGGTCTG
1 AACCGGTTTG
33878 AACCGGTTTG
1 AACCGGTTTG
*
33888 -ACCGGTCTG
1 AACCGGTTTG
*
33897 AACCGGGTTG
1 AACCGGTTTG
33907 A
1 A
33908 CCCGACCCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
9 27 0.42
10 34 0.53
11 3 0.05
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:33863 original size:19 final size:19
Alignment explanation
Indices: 33820--33909 Score: 128
Period size: 19 Copynumber: 4.7 Consensus size: 19
33810 GCTGCTGGAA
* *
33820 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
33840 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
33859 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
33878 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
33897 AACCGGGTTGACC
1 AACCGGTTTGACC
33910 CGACCCGACT
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
18 1 0.02
19 51 0.77
20 14 0.21
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:33925 original size:17 final size:17
Alignment explanation
Indices: 33903--33960 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
33893 TCTGAACCGG
*
33903 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
33920 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
33937 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
33954 GTTGACC
1 GTTGACC
33961 GTGACCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:33967 original size:6 final size:7
Alignment explanation
Indices: 33950--33979 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
33940 GACCCGACCC
33950 GACCGTT
1 GACCGTT
33957 GACCG-T
1 GACCGTT
33963 GACCGTT
1 GACCGTT
33970 GACCGTT
1 GACCGTT
33977 GAC
1 GAC
33980 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:33968 original size:13 final size:13
Alignment explanation
Indices: 33950--33975 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33940 GACCCGACCC
33950 GACCGTTGACCGT
1 GACCGTTGACCGT
33963 GACCGTTGACCGT
1 GACCGTTGACCGT
33976 TGACTTTCTT
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:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:34932 original size:32 final size:31
Alignment explanation
Indices: 34885--34972 Score: 79
Period size: 32 Copynumber: 2.8 Consensus size: 31
34875 ATCATTCTCG
** *
34885 GGTAGGCCCTGCGGCCCTAAGATGTGTTCTTA
1 GGTAGGCCCCACGGCCCTAAGATGT-ATCTTA
* * * *
34917 GGTAGGCCCCACGGCCCCAAAATCTATCTTG
1 GGTAGGCCCCACGGCCCTAAGATGTATCTTA
*
34948 GGTAGGCTCTCA-GGCCCTAAGATGT
1 GGTAGGC-CCCACGGCCCTAAGATGT
34973 TCCCTTAGGG
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
31 21 0.48
32 23 0.52
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.24
Consensus pattern (31 bp):
GGTAGGCCCCACGGCCCTAAGATGTATCTTA
Found at i:41195 original size:10 final size:10
Alignment explanation
Indices: 41166--41253 Score: 94
Period size: 10 Copynumber: 9.1 Consensus size: 10
41156 GCTGCTGGAA
41166 AACCGGTTTG
1 AACCGGTTTG
*
41176 -ACCAGTTTTG
1 AACC-GGTTTG
41186 AACCGGTTTG
1 AACCGGTTTG
*
41196 -ACCGGTTCG
1 AACCGGTTTG
41205 AACCGGTTTG
1 AACCGGTTTG
*
41215 -ACCGGTCTG
1 AACCGGTTTG
41224 AACCGGTTTG
1 AACCGGTTTG
*
41234 -ACCGGTCTG
1 AACCGGTTTG
*
41243 AACCGGGTTG
1 AACCGGTTTG
41253 A
1 A
41254 CCCGACCCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
9 27 0.42
10 34 0.53
11 3 0.05
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:41209 original size:19 final size:19
Alignment explanation
Indices: 41166--41255 Score: 128
Period size: 19 Copynumber: 4.7 Consensus size: 19
41156 GCTGCTGGAA
* *
41166 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
41186 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
41205 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
41224 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
41243 AACCGGGTTGACC
1 AACCGGTTTGACC
41256 CGACCCGACT
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
18 1 0.02
19 51 0.77
20 14 0.21
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:41271 original size:17 final size:17
Alignment explanation
Indices: 41249--41306 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
41239 TCTGAACCGG
*
41249 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
*
41266 GTTGACCCGACCGGACC
1 GTTGACCCGACCCGACC
41283 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
41300 GTTGACC
1 GTTGACC
41307 GTGACCGTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.17, C:0.41, G:0.26, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:41288 original size:34 final size:36
Alignment explanation
Indices: 41249--41325 Score: 113
Period size: 34 Copynumber: 2.2 Consensus size: 36
41239 TCTGAACCGG
*
41249 GTTGACCCGACCCGACTGTTGACC-CGACCG-GACC
1 GTTGACCCGACCCGACCGTTGACCGCGACCGTGACC
*
41283 GTTGACCCGACCCGACCGTTGACCGTGACCGTTGACC
1 GTTGACCCGACCCGACCGTTGACCGCGACCG-TGACC
41320 GTTGAC
1 GTTGAC
41326 TTTCTTTGAC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
34 23 0.61
35 5 0.13
37 10 0.26
ACGTcount: A:0.17, C:0.38, G:0.27, T:0.18
Consensus pattern (36 bp):
GTTGACCCGACCCGACCGTTGACCGCGACCGTGACC
Found at i:41313 original size:6 final size:7
Alignment explanation
Indices: 41296--41325 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
41286 GACCCGACCC
41296 GACCGTT
1 GACCGTT
41303 GACCG-T
1 GACCGTT
41309 GACCGTT
1 GACCGTT
41316 GACCGTT
1 GACCGTT
41323 GAC
1 GAC
41326 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:41314 original size:13 final size:13
Alignment explanation
Indices: 41296--41321 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41286 GACCCGACCC
41296 GACCGTTGACCGT
1 GACCGTTGACCGT
41309 GACCGTTGACCGT
1 GACCGTTGACCGT
41322 TGACTTTCTT
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:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:42263 original size:63 final size:63
Alignment explanation
Indices: 42195--42318 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
42185 CTAATGTGAC
* ** * *
42195 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
42258 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
42319 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 50 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:45953 original size:3 final size:3
Alignment explanation
Indices: 45945--46000 Score: 89
Period size: 3 Copynumber: 19.0 Consensus size: 3
45935 TTACCAAATG
45945 ATA ATA AT- ATGA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
45989 ATA ATA ATA ATA
1 ATA ATA ATA ATA
46001 TATGCATTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.08
3 44 0.88
4 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:46896 original size:15 final size:14
Alignment explanation
Indices: 46876--46931 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
46866 AAAAATAAAT
46876 ACTGAAAATTAAAGG
1 ACTG-AAATTAAAGG
*
46891 ACTGAAATGTAAA-T
1 ACTGAAAT-TAAAGG
*
46905 ACTATAAATTAAAGG
1 ACT-GAAATTAAAGG
*
46920 ATTGAAATTAAA
1 ACTGAAATTAAA
46932 ATAATAGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
14 19 0.58
15 14 0.42
ACGTcount: A:0.54, C:0.05, G:0.14, T:0.27
Consensus pattern (14 bp):
ACTGAAATTAAAGG
Found at i:46934 original size:29 final size:29
Alignment explanation
Indices: 46871--46931 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
46861 GAAGGAAAAA
46871 TAAATACTGAAAATTAAAGGACTGAAATG
1 TAAATACTGAAAATTAAAGGACTGAAATG
*
46900 TAAATACT-ATAAATTAAAGGATTGAAAT-
1 TAAATACTGA-AAATTAAAGGACTGAAATG
46928 TAAA
1 TAAA
46932 ATAATAGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 5 0.17
29 25 0.83
ACGTcount: A:0.54, C:0.05, G:0.13, T:0.28
Consensus pattern (29 bp):
TAAATACTGAAAATTAAAGGACTGAAATG
Found at i:53928 original size:11 final size:11
Alignment explanation
Indices: 53912--53974 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
53902 AAAATTACAT
53912 TATTAAAAATA
1 TATTAAAAATA
53923 TATTAAAAATA
1 TATTAAAAATA
* ***
53934 TACTATTTATA
1 TATTAAAAATA
53945 -ATTATAAAAT-
1 TATTA-AAAATA
53955 T-TTAAAAATA
1 TATTAAAAATA
53965 TATTAAAAAT
1 TATTAAAAAT
53975 TCTATAATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
9 5 0.12
10 7 0.17
11 28 0.70
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:54482 original size:7 final size:7
Alignment explanation
Indices: 54470--54499 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
54460 ATTTGCAATG
54470 AACCCTA
1 AACCCTA
54477 AACCCTA
1 AACCCTA
*
54484 AACTCTA
1 AACCCTA
54491 AACCCTA
1 AACCCTA
54498 AA
1 AA
54500 TCATAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (7 bp):
AACCCTA
Found at i:54493 original size:14 final size:14
Alignment explanation
Indices: 54474--54517 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
54464 GCAATGAACC
54474 CTAAACCCTAAACT
1 CTAAACCCTAAACT
54488 CTAAACCCTAAA-T
1 CTAAACCCTAAACT
**
54501 CATAAACTATAAACT
1 C-TAAACCCTAAACT
54516 CT
1 CT
54518 TAATCCGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (14 bp):
CTAAACCCTAAACT
Found at i:54522 original size:21 final size:21
Alignment explanation
Indices: 54470--54514 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
54460 ATTTGCAATG
* * *
54470 AACCCTAAACCCTAAACTCTA
1 AACCCTAAATCATAAACTATA
54491 AACCCTAAATCATAAACTATA
1 AACCCTAAATCATAAACTATA
54512 AAC
1 AAC
54515 TCTTAATCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (21 bp):
AACCCTAAATCATAAACTATA
Found at i:55926 original size:12 final size:12
Alignment explanation
Indices: 55909--55953 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
55899 TTCAATCTTG
55909 AATCGAGCTTAA
1 AATCGAGCTTAA
*
55921 AATCGAGCTT-G
1 AATCGAGCTTAA
*
55932 AATCGAGCTAAA
1 AATCGAGCTTAA
*
55944 AATTGAGCTT
1 AATCGAGCTT
55954 CAATCGAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (12 bp):
AATCGAGCTTAA
Found at i:55931 original size:23 final size:23
Alignment explanation
Indices: 55905--55961 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
55895 AGGCTTCAAT
*
55905 CTTGAATCGAGCTTAAAATCGAG
1 CTTGAATCGAGCTAAAAATCGAG
*
55928 CTTGAATCGAGCTAAAAATTGAG
1 CTTGAATCGAGCTAAAAATCGAG
*
55951 CTTCAATCGAG
1 CTTGAATCGAG
55962 TTTGAGTCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (23 bp):
CTTGAATCGAGCTAAAAATCGAG
Found at i:55937 original size:11 final size:11
Alignment explanation
Indices: 55905--55987 Score: 58
Period size: 11 Copynumber: 7.2 Consensus size: 11
55895 AGGCTTCAAT
55905 CTTGAATCGAG
1 CTTGAATCGAG
*
55916 CTTAAAATCGAG
1 CTT-GAATCGAG
55928 CTTGAATCGAG
1 CTTGAATCGAG
** *
55939 CTAAAAATTGAG
1 CT-TGAATCGAG
*
55951 CTTCAATCGAG
1 CTTGAATCGAG
* *
55962 TTTGAGTCTCGAG
1 CTTGA--ATCGAG
*
55975 CTTTAATCGAG
1 CTTGAATCGAG
55986 CT
1 CT
55988 ATTGATTTTT
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
11 28 0.52
12 18 0.33
13 8 0.15
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (11 bp):
CTTGAATCGAG
Done.