Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024865.1 Corchorus olitorius cultivar O-4 contig24898, 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: 50682
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4780 original size:110 final size:110
Alignment explanation
Indices: 4587--4808 Score: 444
Period size: 110 Copynumber: 2.0 Consensus size: 110
4577 CTGGACACCC
4587 AAACACTCTTTTAGTGTTTTTCTCTTGTTTCAATCTTGTTTCCGGACATAAAAACATTGTACACG
1 AAACACTCTTTTAGTGTTTTTCTCTTGTTTCAATCTTGTTTCCGGACATAAAAACATTGTACACG
4652 TGTTTCTCTCTCATCAATAACAATCAATTTGTTATTTTTCTTTCA
66 TGTTTCTCTCTCATCAATAACAATCAATTTGTTATTTTTCTTTCA
4697 AAACACTCTTTTAGTGTTTTTCTCTTGTTTCAATCTTGTTTCCGGACATAAAAACATTGTACACG
1 AAACACTCTTTTAGTGTTTTTCTCTTGTTTCAATCTTGTTTCCGGACATAAAAACATTGTACACG
4762 TGTTTCTCTCTCATCAATAACAATCAATTTGTTATTTTTCTTTCA
66 TGTTTCTCTCTCATCAATAACAATCAATTTGTTATTTTTCTTTCA
4807 AA
1 AA
4809 TCCAATTGAA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 112 1.00
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.45
Consensus pattern (110 bp):
AAACACTCTTTTAGTGTTTTTCTCTTGTTTCAATCTTGTTTCCGGACATAAAAACATTGTACACG
TGTTTCTCTCTCATCAATAACAATCAATTTGTTATTTTTCTTTCA
Found at i:5342 original size:10 final size:10
Alignment explanation
Indices: 5316--5347 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5306 CCTTCAAACT
5316 TCAAATT-TC
1 TCAAATTCTC
5325 TC-AATTCTC
1 TCAAATTCTC
5334 TCAAATTCTC
1 TCAAATTCTC
5344 TCAA
1 TCAA
5348 CCTTCAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.19
9 6 0.29
10 11 0.52
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.41
Consensus pattern (10 bp):
TCAAATTCTC
Found at i:5601 original size:19 final size:18
Alignment explanation
Indices: 5579--5622 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
5569 AAATTAAAGG
*
5579 AAAAAAAAATCAGAGATGA
1 AAAAAAAAAACAGAGAT-A
*
5598 AAAAAAAAAAGAGAGATA
1 AAAAAAAAAACAGAGATA
5616 AAAAAAA
1 AAAAAAA
5623 GTCTGGTCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAACAGAGATA
Found at i:5610 original size:17 final size:17
Alignment explanation
Indices: 5578--5622 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
5568 GAAATTAAAG
*
5578 GAAAAAAAAATCAGAGA
1 GAAAAAAAAATAAGAGA
5595 TGAAAAAAAAA-AAGAGA
1 -GAAAAAAAAATAAGAGA
5612 GATAAAAAAAA
1 GA-AAAAAAAA
5623 GTCTGGTCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 2 0.08
17 13 0.52
18 10 0.40
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.07
Consensus pattern (17 bp):
GAAAAAAAAATAAGAGA
Found at i:5689 original size:33 final size:32
Alignment explanation
Indices: 5652--5722 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
5642 GCGACCCGCG
5652 CGCGACCACG-CCATGGTCAAGTCGCGATACGGT
1 CGCGACC-CGACCATGGTCAA-TCGCGATACGGT
* * *
5685 CGCGACCGGACCATGGTCAATTGCGATCCGGT
1 CGCGACCCGACCATGGTCAATCGCGATACGGT
5717 CGCGAC
1 CGCGAC
5723 TGAACGATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 17 0.50
33 17 0.50
ACGTcount: A:0.20, C:0.34, G:0.31, T:0.15
Consensus pattern (32 bp):
CGCGACCCGACCATGGTCAATCGCGATACGGT
Found at i:23709 original size:120 final size:121
Alignment explanation
Indices: 23508--23737 Score: 372
Period size: 120 Copynumber: 1.9 Consensus size: 121
23498 GGTCCAATAT
* * *
23508 TTGCGAAAATGCTCAATTTAAGGCCTATCATTCAAAAAAACTCAAATCGTGGCCCAACATTGCAA
1 TTGCGAAAATGCTCAATTCAAGACCTATCATTCAAAAAAACTCAAATCATGGCCCAACATTGCAA
* * *
23573 AATCGGTTCAATTGAGGGCTCGCGGTCAATTTCTTAGGCTTAATTAAGAGCTCATA
66 AATCGGCTCAATTGAGGGCTCGCAGTCAATTTCATAGGCTTAATTAAGAGCTCATA
* * *
23629 TTGCGAAAATGCTCAATTCAAGACCTTTCATT-AAAAAAACTCAAATCATGGCCCAACGTTGTAA
1 TTGCGAAAATGCTCAATTCAAGACCTATCATTCAAAAAAACTCAAATCATGGCCCAACATTGCAA
23693 AATCGGCTCAATTGAGGGCTCGCAGTCAATTTCATAGGCTTAATT
66 AATCGGCTCAATTGAGGGCTCGCAGTCAATTTCATAGGCTTAATT
23738 GTCACCTTTC
Statistics
Matches: 100, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
120 71 0.71
121 29 0.29
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.28
Consensus pattern (121 bp):
TTGCGAAAATGCTCAATTCAAGACCTATCATTCAAAAAAACTCAAATCATGGCCCAACATTGCAA
AATCGGCTCAATTGAGGGCTCGCAGTCAATTTCATAGGCTTAATTAAGAGCTCATA
Found at i:33829 original size:15 final size:17
Alignment explanation
Indices: 33794--33831 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
33784 AACCGAAAAC
33794 GACCC-AACCCAGAATT
1 GACCCGAACCCAGAATT
33810 GACCCGAACCCA-AA-T
1 GACCCGAACCCAGAATT
33825 GACCCGA
1 GACCCGA
33832 CATTTGAGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.37, C:0.39, G:0.16, T:0.08
Consensus pattern (17 bp):
GACCCGAACCCAGAATT
Found at i:35865 original size:24 final size:24
Alignment explanation
Indices: 35839--36053 Score: 198
Period size: 24 Copynumber: 9.0 Consensus size: 24
35829 ACTTGGTCTT
*
35839 TTCTCACGACCACTATGTGGCCGT
1 TTCTCACGACCACTATGTGGCCGA
* *
35863 TTCTCATGACCACTATGTGGTCGA
1 TTCTCACGACCACTATGTGGCCGA
* * * * *
35887 ATCTCACGACCGCCATGTGGTCAA
1 TTCTCACGACCACTATGTGGCCGA
* *
35911 ATCTCACGACCACTATGTGGCCGT
1 TTCTCACGACCACTATGTGGCCGA
* **
35935 TTCTCACGATCACTATGTGGTTGA
1 TTCTCACGACCACTATGTGGCCGA
* * **
35959 ATCTCACGACCACCATGTGGTCAAA
1 TTCTCACGACCACTATGTGG-CCGA
*
35984 TT-TCACGACCACTATGTGGCCGT
1 TTCTCACGACCACTATGTGGCCGA
* * * *
36007 TTCTCAGGACCACCATGTGGTCAA
1 TTCTCACGACCACTATGTGGCCGA
* *
36031 ATCTCACGACCACCATGTGGCCG
1 TTCTCACGACCACTATGTGGCCG
36054 TGTGATTTTC
Statistics
Matches: 151, Mismatches: 38, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
23 3 0.02
24 146 0.97
25 2 0.01
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (24 bp):
TTCTCACGACCACTATGTGGCCGA
Found at i:35896 original size:48 final size:48
Alignment explanation
Indices: 35840--36054 Score: 232
Period size: 48 Copynumber: 4.5 Consensus size: 48
35830 CTTGGTCTTT
* * * *
35840 TCTCACGACCACTATGTGGCCGTTTCTCATGACCACTATGTGGTCGAA
1 TCTCACGACCACTATGTGGCCGTATCTCACGACCACCATGTGGTCAAA
* * * ** * * ***
35888 TCTCACGACCGCCATGTGGTCAAATCTCACGACCACTATGTGGCCGTT
1 TCTCACGACCACTATGTGGCCGTATCTCACGACCACCATGTGGTCAAA
* ** *
35936 TCTCACGATCACTATGTGGTTGAATCTCACGACCACCATGTGGTCAAA
1 TCTCACGACCACTATGTGGCCGTATCTCACGACCACCATGTGGTCAAA
* * *
35984 TTTCACGACCACTATGTGGCCGTTTCTCAGGACCACCATGTGGTCAAA
1 TCTCACGACCACTATGTGGCCGTATCTCACGACCACCATGTGGTCAAA
*
36032 TCTCACGACCACCATGTGGCCGT
1 TCTCACGACCACTATGTGGCCGT
36055 GTGATTTTCC
Statistics
Matches: 138, Mismatches: 29, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 138 1.00
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (48 bp):
TCTCACGACCACTATGTGGCCGTATCTCACGACCACCATGTGGTCAAA
Found at i:35949 original size:72 final size:72
Alignment explanation
Indices: 35840--36050 Score: 350
Period size: 72 Copynumber: 2.9 Consensus size: 72
35830 CTTGGTCTTT
* *
35840 TCTCACGACCACTATGTGGCCGTTTCTCATGACCACTATGTGGTCGAATCTCACGACCGCCATGT
1 TCTCACGACCACTATGTGGCCGTTTCTCACGACCACTATGTGGTCGAATCTCACGACCACCATGT
35905 GGTCAAA
66 GGTCAAA
* *
35912 TCTCACGACCACTATGTGGCCGTTTCTCACGATCACTATGTGGTTGAATCTCACGACCACCATGT
1 TCTCACGACCACTATGTGGCCGTTTCTCACGACCACTATGTGGTCGAATCTCACGACCACCATGT
35977 GGTCAAA
66 GGTCAAA
* * * *
35984 TTTCACGACCACTATGTGGCCGTTTCTCAGGACCACCATGTGGTCAAATCTCACGACCACCATGT
1 TCTCACGACCACTATGTGGCCGTTTCTCACGACCACTATGTGGTCGAATCTCACGACCACCATGT
36049 GG
66 GG
36051 CCGTGTGATT
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 129 1.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (72 bp):
TCTCACGACCACTATGTGGCCGTTTCTCACGACCACTATGTGGTCGAATCTCACGACCACCATGT
GGTCAAA
Found at i:38618 original size:22 final size:22
Alignment explanation
Indices: 38582--38624 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
38572 TTTTCCGCAA
* *
38582 CAAGTCATGGGCAGGAGTTGTC
1 CAAGTCATGGACAGGACTTGTC
*
38604 CAAGTCCTGGACAGGACTTGT
1 CAAGTCATGGACAGGACTTGT
38625 TCTGAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (22 bp):
CAAGTCATGGACAGGACTTGTC
Found at i:38690 original size:71 final size:71
Alignment explanation
Indices: 38582--38766 Score: 298
Period size: 71 Copynumber: 2.6 Consensus size: 71
38572 TTTTCCGCAA
* * *
38582 CAAGTCATGGGCAGGAGTTGTCCAAGTCCTGGACAGGACTTGTTCTGAATTTTCTTCCGTTTTTC
1 CAAGTCCTGGGCAGGAGTTGT-CAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTC
38647 AACAGAC
65 AACAGAC
* * *
38654 CAATTCCTGGGCAGGAGTTGTCAAGTCTTGGGCAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCA
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTCA
38719 ACAGAC
66 ACAGAC
*
38725 CAGGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT
38767 CCTGTTTTTA
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
71 84 0.82
72 19 0.18
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.31
Consensus pattern (71 bp):
CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTTTCA
ACAGAC
Found at i:38754 original size:21 final size:21
Alignment explanation
Indices: 38728--38767 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38718 AACAGACCAG
*
38728 GTCCTGGGCAGGAGTTGTCAA
1 GTCCTGGGCAGGACTTGTCAA
38749 GTCCTGGGCAGGACTTGTC
1 GTCCTGGGCAGGACTTGTC
38768 CTGTTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25
Consensus pattern (21 bp):
GTCCTGGGCAGGACTTGTCAA
Found at i:41424 original size:24 final size:24
Alignment explanation
Indices: 41391--41561 Score: 173
Period size: 24 Copynumber: 7.1 Consensus size: 24
41381 AATCACTACT
* *
41391 TGGTCTTTTCTCACGATCACTATG
1 TGGTCGTTTCTCACGACCACTATG
* *
41415 TGGCCGTTTCTCATGACCACTATG
1 TGGTCGTTTCTCACGACCACTATG
** * *
41439 TGGTCGAATCTCACAACCACCATG
1 TGGTCGTTTCTCACGACCACTATG
* *
41463 TGGCCGTTTCTCACGACCACCATG
1 TGGTCGTTTCTCACGACCACTATG
** *
41487 TGGTCGAATCTCTCGACCACTATG
1 TGGTCGTTTCTCACGACCACTATG
* *
41511 TGGTCGTTTCTCACGACAACCATG
1 TGGTCGTTTCTCACGACCACTATG
**
41535 TGGTCAAATT-TCACGACCACTATG
1 TGGTC-GTTTCTCACGACCACTATG
41559 TGG
1 TGG
41562 CAGTGTGATT
Statistics
Matches: 118, Mismatches: 28, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
24 116 0.98
25 2 0.02
ACGTcount: A:0.21, C:0.29, G:0.20, T:0.30
Consensus pattern (24 bp):
TGGTCGTTTCTCACGACCACTATG
Found at i:41464 original size:48 final size:48
Alignment explanation
Indices: 41399--41562 Score: 238
Period size: 48 Copynumber: 3.4 Consensus size: 48
41389 CTTGGTCTTT
* * *
41399 TCTCACGATCACTATGTGGCCGTTTCTCATGACCACTATGTGGTCGAA
1 TCTCACGACCACTATGTGGCCGTTTCTCACGACCACCATGTGGTCGAA
* *
41447 TCTCACAACCACCATGTGGCCGTTTCTCACGACCACCATGTGGTCGAA
1 TCTCACGACCACTATGTGGCCGTTTCTCACGACCACCATGTGGTCGAA
* * * *
41495 TCTCTCGACCACTATGTGGTCGTTTCTCACGACAACCATGTGGTCAAA
1 TCTCACGACCACTATGTGGCCGTTTCTCACGACCACCATGTGGTCGAA
*
41543 TTTCACGACCACTATGTGGC
1 TCTCACGACCACTATGTGGC
41563 AGTGTGATTT
Statistics
Matches: 102, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 102 1.00
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (48 bp):
TCTCACGACCACTATGTGGCCGTTTCTCACGACCACCATGTGGTCGAA
Found at i:42516 original size:2 final size:2
Alignment explanation
Indices: 42509--42549 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
42499 ACAGTCAATG
42509 AT AT AT 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 AT AT AT A
42550 ATAGTGTCAA
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42925 original size:52 final size:53
Alignment explanation
Indices: 42839--42958 Score: 131
Period size: 55 Copynumber: 2.3 Consensus size: 53
42829 TAACCCGAAT
* *
42839 ATTATAAATTAAATTTTTTTAATAAAA-TC-CA-TATTGTTATAATTTTAACC
1 ATTATAAATTAAATTTATTCAATAAAATTCACATTATTGTTATAATTTTAACC
* * * *
42889 ATTATAAATTATCAATTTATTCAATAAAATTTATATTATTGTTATGATTTTAACT
1 ATTATAAATTA--AATTTATTCAATAAAATTCACATTATTGTTATAATTTTAACC
*
42944 ATTAT-GATTAAATTT
1 ATTATAAATTAAATTT
42959 GCTAAACTTC
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
50 11 0.19
52 19 0.33
53 1 0.02
54 5 0.09
55 22 0.38
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (53 bp):
ATTATAAATTAAATTTATTCAATAAAATTCACATTATTGTTATAATTTTAACC
Found at i:43001 original size:15 final size:15
Alignment explanation
Indices: 42969--43002 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42959 GCTAAACTTC
*
42969 ATTATATGAACAATT
1 ATTATATGAACAAAT
*
42984 ATTATATGAATAAAT
1 ATTATATGAACAAAT
42999 ATTA
1 ATTA
43003 AACCAGTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (15 bp):
ATTATATGAACAAAT
Found at i:43154 original size:24 final size:24
Alignment explanation
Indices: 43081--43154 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 24
43071 AATTAGAAAA
43081 ATAATTAACAATAGTAATTATTAT
1 ATAATTAACAATAGTAATTATTAT
* * ** **
43105 -TATATTAATAATCA-CAAAGAAAAT
1 ATA-ATTAACAAT-AGTAATTATTAT
43129 ATAATTAACAATAGTAATTATTAT
1 ATAATTAACAATAGTAATTATTAT
43153 AT
1 AT
43155 TAGTAATAAC
Statistics
Matches: 34, Mismatches: 12, Indels: 8
0.63 0.22 0.15
Matches are distributed among these distances:
23 3 0.09
24 28 0.82
25 3 0.09
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (24 bp):
ATAATTAACAATAGTAATTATTAT
Found at i:43167 original size:45 final size:47
Alignment explanation
Indices: 43075--43175 Score: 154
Period size: 45 Copynumber: 2.2 Consensus size: 47
43065 AACAAAAATT
*
43075 AGAAAA-ATAATTAACAATAGTAATTATTATTATATTAATAATCACAA
1 AGAAAATATAATTAACAATAGTAA-TATTATTATATTAATAATAACAA
*
43122 AGAAAATATAATTAACAATAGT-A-ATTATTATATTAGTAATAACAA
1 AGAAAATATAATTAACAATAGTAATATTATTATATTAATAATAACAA
43167 AGAAAATAT
1 AGAAAATAT
43176 GCCGGATAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
45 29 0.57
47 7 0.14
48 15 0.29
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (47 bp):
AGAAAATATAATTAACAATAGTAATATTATTATATTAATAATAACAA
Found at i:43913 original size:178 final size:178
Alignment explanation
Indices: 43623--43960 Score: 450
Period size: 178 Copynumber: 1.9 Consensus size: 178
43613 CCGATTCAGG
* *
43623 TGATTTAAGTGTCTATTAAAAGATTGTTTCATCATCTACAACTTTCATGAAGAACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGAACTCGAAAACTA
* * * * *
43688 AATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAAAATTTGTTGTTTCGTTTAACGGGAATAGA
66 AATTTAATGATTCAAGTATCAAAAATGCTTCCGAAAAATTAGTTGTTTCGGTTAAAGGAAATAGA
* *
43753 CGGTCCACTTAATATTATATAACTTT-TGCTCCAGATGTCTAATTGGGA
131 CGGTCCACGTAATATTACATAA-TTTGTGCTCCAGATGTCTAATTGGGA
* * * * **
43801 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGGCTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGAACTCGAAAACTA
* *
43866 AATTTAAT-ATTCGAGGTAT-AAAAATTGCTTTC-AAAGAATTAGTTGTTTCGGTTAAAGGAAAT
66 AATTTAATGATTC-AAGTATCAAAAA-TGCTTCCGAAA-AATTAGTTGTTTCGGTTAAAGGAAAT
*
43928 AGACGGTCTACGTAATATTACATAATTTGTGCT
128 AGACGGTCCACGTAATATTACATAATTTGTGCT
43961 TATAGTGGAA
Statistics
Matches: 138, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
177 14 0.10
178 124 0.90
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGAACTCGAAAACTA
AATTTAATGATTCAAGTATCAAAAATGCTTCCGAAAAATTAGTTGTTTCGGTTAAAGGAAATAGA
CGGTCCACGTAATATTACATAATTTGTGCTCCAGATGTCTAATTGGGA
Found at i:44727 original size:89 final size:89
Alignment explanation
Indices: 44627--44804 Score: 329
Period size: 89 Copynumber: 2.0 Consensus size: 89
44617 ACTAATAAGA
44627 AATATAATTTGATAAGGATACAAATGATGAAGAGAAGTATAATTTAACAATAATTTTAATTTTAC
1 AATATAATTTGATAAGGATACAAATGATGAAGAGAAGTATAATTTAACAATAATTTTAATTTTAC
*
44692 TAGTATTAGTGTTAAAAGTTGATT
66 TACTATTAGTGTTAAAAGTTGATT
*
44716 AATATAATTTGATAAGGATACAAATGATGAAGAGAAGTATAATTTAACAATAATTTTAATTTTGC
1 AATATAATTTGATAAGGATACAAATGATGAAGAGAAGTATAATTTAACAATAATTTTAATTTTAC
*
44781 TACTATTAGTGTTTAAAGTTGATT
66 TACTATTAGTGTTAAAAGTTGATT
44805 TATAGATTAT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.39
Consensus pattern (89 bp):
AATATAATTTGATAAGGATACAAATGATGAAGAGAAGTATAATTTAACAATAATTTTAATTTTAC
TACTATTAGTGTTAAAAGTTGATT
Found at i:45413 original size:30 final size:31
Alignment explanation
Indices: 45362--45422 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
45352 ATCAATATTA
*
45362 TCTATACTGTATATAAAAGTATGAATAAGGG
1 TCTATACTATATATAAAAGTATGAATAAGGG
45393 TCTATACTATATAT-AAAGTATGAATAAGGG
1 TCTATACTATATATAAAAGTATGAATAAGGG
45423 GAAATTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 16 0.55
31 13 0.45
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.33
Consensus pattern (31 bp):
TCTATACTATATATAAAAGTATGAATAAGGG
Found at i:46154 original size:13 final size:13
Alignment explanation
Indices: 46136--46173 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
46126 CTAAATTGAC
46136 ATTATTAAAATTT
1 ATTATTAAAATTT
46149 ATTATTTAAAAATTT
1 ATTA-TT-AAAATTT
46164 ATTA-TAAAAT
1 ATTATTAAAAT
46174 ACTTATAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 5 0.22
13 5 0.22
14 2 0.09
15 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTATTAAAATTT
Found at i:46666 original size:22 final size:21
Alignment explanation
Indices: 46648--46830 Score: 159
Period size: 22 Copynumber: 8.2 Consensus size: 21
46638 TAATTATTAT
46648 AATTTCATGAGGAGGTTATCAA
1 AATTTCAT-AGGAGGTTATCAA
* * *
46670 AATTCCATAGTGTGGTTACCAA
1 AATTTCATAG-GAGGTTATCAA
*
46692 AATTTCATATGGAAGTTATCAA
1 AATTTCATA-GGAGGTTATCAA
*
46714 AATTTCATTGGAAGGTTATCAA
1 AATTTCATAGG-AGGTTATCAA
*
46736 AATTTCATGGGAAGGTTATCAA
1 AATTTCATAGG-AGGTTATCAA
*
46758 AATTTCATAGGATCAGGTTATTAA
1 AATTTCATAGG---AGGTTATCAA
** **
46782 AATTTTTTAGGAAGGTTATTGA
1 AATTTCATAGG-AGGTTATCAA
* *
46804 AATTTCATAGTGTGGTTATCAC
1 AATTTCATAG-GAGGTTATCAA
46826 AATTT
1 AATTT
46831 TATGTAAAGG
Statistics
Matches: 132, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
21 4 0.03
22 108 0.82
23 2 0.02
24 18 0.14
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (21 bp):
AATTTCATAGGAGGTTATCAA
Found at i:46696 original size:44 final size:44
Alignment explanation
Indices: 46648--46974 Score: 195
Period size: 44 Copynumber: 7.1 Consensus size: 44
46638 TAATTATTAT
* *
46648 AATTTCATGAGGAGGTTATCAAAATTCCATAGTGTGGTTACCAA
1 AATTTCATGAGGAGGTTATCAAAATTTCATAGTGTGGTTATCAA
* * *
46692 AATTTCAT-ATGGAAGTTATCAAAATTTCATTG-GAAGGTTATCAA
1 AATTTCATGA-GGAGGTTATCAAAATTTCATAGTG-TGGTTATCAA
*
46736 AATTTCATG-GGAAGGTTATCAAAATTTCATAG-GATCAGGTTATTAA
1 AATTTCATGAGG-AGGTTATCAAAATTTCATAGTG-T--GGTTATCAA
* * ** *
46782 AATTT-TTTAGGAAGGTTATTGAAATTTCATAGTGTGGTTATCAC
1 AATTTCATGAGG-AGGTTATCAAAATTTCATAGTGTGGTTATCAA
* * *
46826 AATTTTATGTAAAGGTTATCAAAGAGATTATCAAAATGTCATAGTGAGGTTAT-AA
1 AATTTCATG---AGG-------AG-G-TTATCAAAATTTCATAGTGTGGTTATCAA
* * * *
46881 GAATTTCAT-AGTGTGGTTAACAAAATTTCATAAG-GAGGTCA-CTAA
1 -AATTTCATGAG-GAGGTTATCAAAATTTCAT-AGTGTGGTTATC-AA
* * *
46926 TATTTCATGGGGAGGTTATCAAAATTCCATAGTGTGGTTATCAA
1 AATTTCATGAGGAGGTTATCAAAATTTCATAGTGTGGTTATCAA
46970 AATTT
1 AATTT
46975 TTTATTGTGG
Statistics
Matches: 220, Mismatches: 35, Indels: 56
0.71 0.11 0.18
Matches are distributed among these distances:
43 6 0.03
44 128 0.58
45 9 0.04
46 36 0.16
47 1 0.00
48 3 0.01
52 2 0.01
53 1 0.00
54 3 0.01
55 2 0.01
56 29 0.13
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (44 bp):
AATTTCATGAGGAGGTTATCAAAATTTCATAGTGTGGTTATCAA
Found at i:46795 original size:46 final size:45
Alignment explanation
Indices: 46617--46848 Score: 185
Period size: 44 Copynumber: 5.2 Consensus size: 45
46607 GTCTCTGTGT
* * * * * *
46617 GGTTATCAAAATTTTACAAGATA-ATTATTATAATTTCATGAGG-A
1 GGTTATCAAAATTTCATAGGATAGGTTATCAAAATTTCAT-AGGAA
* *
46661 GGTTATCAAAATTCCATAGTG-T-GGTTACCAAAATTTCATATGGAA
1 GGTTATCAAAATTTCATAG-GATAGGTTATCAAAATTTCATA-GGAA
* *
46706 -GTTATCAAAATTTCATTGGA-AGGTTATCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCATAGGATAGGTTATCAAAATTTCATAGGAA
* **
46749 GGTTATCAAAATTTCATAGGATCAGGTTATTAAAATTTTTTAGGAA
1 GGTTATCAAAATTTCATAGGAT-AGGTTATCAAAATTTCATAGGAA
** * * *
46795 GGTTATTGAAATTTCATAGTG-T-GGTTATCACAATTTTAT-GTAAA
1 GGTTATCAAAATTTCATAG-GATAGGTTATCAAAATTTCATAG-GAA
46839 GGTTATCAAA
1 GGTTATCAAA
46849 GAGATTATCA
Statistics
Matches: 152, Mismatches: 25, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
43 7 0.05
44 105 0.69
45 2 0.01
46 37 0.24
47 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38
Consensus pattern (45 bp):
GGTTATCAAAATTTCATAGGATAGGTTATCAAAATTTCATAGGAA
Found at i:46878 original size:22 final size:22
Alignment explanation
Indices: 46853--46974 Score: 115
Period size: 22 Copynumber: 5.5 Consensus size: 22
46843 ATCAAAGAGA
*
46853 TTATCAAAATGTCATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
*
46875 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
46897 TTAACAAAATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* * * *
46919 TCA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* *
46941 TTATCAAAATTCCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
46963 TTATCAAAATTT
1 TTATCAAAATTT
46975 TTTATTGTGG
Statistics
Matches: 80, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
21 4 0.05
22 71 0.89
23 5 0.06
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:49246 original size:20 final size:20
Alignment explanation
Indices: 49208--49249 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
49198 CTTGTTCTTT
* *
49208 TGGCACCTGAATTCTTGATG
1 TGGCACCTGAACTCGTGATG
*
49228 TGGCACCTGAACTGGTGATG
1 TGGCACCTGAACTCGTGATG
49248 TG
1 TG
49250 TACTGAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (20 bp):
TGGCACCTGAACTCGTGATG
Found at i:50580 original size:25 final size:25
Alignment explanation
Indices: 50546--50598 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
50536 TACACTATTA
*
50546 AAAGATAAAGACCTGTCTAAGGTCG
1 AAAGATAAAGACCCGTCTAAGGTCG
*
50571 AAAGATAAAGACCCGTCTGAGGTCG
1 AAAGATAAAGACCCGTCTAAGGTCG
50596 AAA
1 AAA
50599 CTGAAACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.17
Consensus pattern (25 bp):
AAAGATAAAGACCCGTCTAAGGTCG
Found at i:50626 original size:33 final size:32
Alignment explanation
Indices: 50577--50682 Score: 123
Period size: 33 Copynumber: 3.4 Consensus size: 32
50567 GTCGAAAGAT
* *
50577 AAAGACCCGTCTGAGGTCGAAACTGAAACTTAG
1 AAAGACCTGTCCGAGGTCGAAACTGAAA-TTAG
*
50610 AAAGACCTGTCCGAGGTCGAAA-T----TGAG
1 AAAGACCTGTCCGAGGTCGAAACTGAAATTAG
*
50637 AAAGACCTGTCTGAGGTCGAAACTGAAATTTAG
1 AAAGACCTGTCCGAGGTCGAAACTGAAA-TTAG
50670 AAAGACCTGTCCG
1 AAAGACCTGTCCG
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
27 24 0.39
28 1 0.02
32 1 0.02
33 35 0.57
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (32 bp):
AAAGACCTGTCCGAGGTCGAAACTGAAATTAG
Found at i:50657 original size:60 final size:58
Alignment explanation
Indices: 50552--50682 Score: 199
Period size: 60 Copynumber: 2.2 Consensus size: 58
50542 ATTAAAAGAT
** *
50552 AAAGACCTGTCTAAGGTCGAAAGATAAAGACCCGTCTGAGGTCGAAACTGAAACTTAG
1 AAAGACCTGTCCGAGGTCGAAAGAGAAAGACCCGTCTGAGGTCGAAACTGAAACTTAG
* *
50610 AAAGACCTGTCCGAGGTCGAAATTGAGAAAGACCTGTCTGAGGTCGAAACTGAAATTTAG
1 AAAGACCTGTCCGAGGTCGAAA--GAGAAAGACCCGTCTGAGGTCGAAACTGAAACTTAG
50670 AAAGACCTGTCCG
1 AAAGACCTGTCCG
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 20 0.30
60 46 0.70
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (58 bp):
AAAGACCTGTCCGAGGTCGAAAGAGAAAGACCCGTCTGAGGTCGAAACTGAAACTTAG
Done.