Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021134.1 Corchorus olitorius cultivar O-4 contig21167, 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: 197376
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5530 original size:2 final size:2
Alignment explanation
Indices: 5519--5556 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5509 AACTGGTACG
5519 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5557 CTTTATCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5946 original size:25 final size:25
Alignment explanation
Indices: 5881--5934 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
5871 AATGGATGAA
*
5881 TTAAATTCAATACTTTTATTTAACT
1 TTAAATTCAATATTTTTATTTAACT
5906 TTAAATTCAATATTTTTATTTAACT
1 TTAAATTCAATATTTTTATTTAACT
5931 TTAA
1 TTAA
5935 CTTTTAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (25 bp):
TTAAATTCAATATTTTTATTTAACT
Found at i:5947 original size:186 final size:190
Alignment explanation
Indices: 5733--6084 Score: 604
Period size: 186 Copynumber: 1.9 Consensus size: 190
5723 CTTCTTAAAA
*
5733 TTTTATTTAACTTTAACTTTTAAATTTTAATTGGTGGGGAACTTTTATTTAACTTTAATAAAA-T
1 TTTTATTTAACTTTAACTTTTAAATTTTAATTGGTGGGGAACTTTTATTTAACTTTAATAAAAGA
* *
5797 AAAAAAATTGGTAATTCGTAATTCATAAAATTTTTACATATT-A-AA-AAAATTAAATAAAACTT
66 AAAAAAATTGGTAATTCGTAATTCATAAAACTTTTACATATTAAGAATAAAATTAAATAAAAATT
5859 TAGAAGATCATGAATGGATGAATTAAATTCAATACTTTTATTTAACTTTAAATTCAATAT
131 TAGAAGATCATGAATGGATGAATTAAATTCAATACTTTTATTTAACTTTAAATTCAATAT
*
5919 TTTTATTTAACTTTAACTTTTAAATTTTAATTGGTGGGTAACTTTTATTTAACTTTAATAAAAGA
1 TTTTATTTAACTTTAACTTTTAAATTTTAATTGGTGGGGAACTTTTATTTAACTTTAATAAAAGA
5984 AAAAAAATTGGTAATTCGTAATTCATAAAACTTTTACATATTAAAAGAATAAAATTAAATAAAAA
66 AAAAAAATTGGTAATTCGTAATTCATAAAACTTTTACATATT--AAGAATAAAATTAAATAAAAA
* *
6049 TTTAGAAGATCATGAATTGATGAATTAATTTCAATA
129 TTTAGAAGATCATGAATGGATGAATTAAATTCAATA
6085 ATATTCAAAT
Statistics
Matches: 154, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
186 62 0.40
187 41 0.27
190 1 0.01
191 2 0.01
192 48 0.31
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (190 bp):
TTTTATTTAACTTTAACTTTTAAATTTTAATTGGTGGGGAACTTTTATTTAACTTTAATAAAAGA
AAAAAAATTGGTAATTCGTAATTCATAAAACTTTTACATATTAAGAATAAAATTAAATAAAAATT
TAGAAGATCATGAATGGATGAATTAAATTCAATACTTTTATTTAACTTTAAATTCAATAT
Found at i:6480 original size:24 final size:24
Alignment explanation
Indices: 6448--6494 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6438 TTAGTCTTTC
*
6448 TACTTTTTTGCTTC-AGTTTAGTCG
1 TACTTTTTTACTTCTA-TTTAGTCG
6472 TACTTTTTTACTTCTATTTAGTC
1 TACTTTTTTACTTCTATTTAGTC
6495 AATTAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.15, C:0.17, G:0.11, T:0.57
Consensus pattern (24 bp):
TACTTTTTTACTTCTATTTAGTCG
Found at i:8444 original size:135 final size:139
Alignment explanation
Indices: 8215--8486 Score: 417
Period size: 135 Copynumber: 2.0 Consensus size: 139
8205 GAAAATTACA
* *
8215 CAGTAAGTTACCGAATTTGTTAATAACCCCTTATAGTTTTGTTTTTAACCTTTATAACTAATTAT
1 CAGTAAGCTACCGAATTTGTTAATAACCCCTTATAGTTTTGTTTTTAACCTTCATAACT-ATTAT
* * *
8280 ATAGTAACTTTAGATATGAAATTTGATAACCTTCATTATTTATAATAGTTTACTAATGTAATGTT
65 ATAGTAACTTTAGATATGAAAGTTGATAACCTTCATTATTTATAAAAGTTTACTAATGTAAAGTT
8345 ATACAATACT
130 ATACAATACT
* *
8355 CAGTAAGCTACTGAATTTGTTAATAACCTCTTATAG-TTT-TTTTTAACCTTCATAACT-TT-TA
1 CAGTAAGCTACCGAATTTGTTAATAACCCCTTATAGTTTTGTTTTTAACCTTCATAACTATTATA
* * *
8416 TAGTAACTTTAGATATGAGAGTTGATAACCTTTATTATTTATAAAAGTTTCCTAATGTAAAGTTA
66 TAGTAACTTTAGATATGAAAGTTGATAACCTTCATTATTTATAAAAGTTTACTAATGTAAAGTTA
8481 TACAAT
131 TACAAT
8487 TTTCTTGGTA
Statistics
Matches: 122, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
135 67 0.55
136 2 0.02
138 17 0.14
139 3 0.02
140 33 0.27
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (139 bp):
CAGTAAGCTACCGAATTTGTTAATAACCCCTTATAGTTTTGTTTTTAACCTTCATAACTATTATA
TAGTAACTTTAGATATGAAAGTTGATAACCTTCATTATTTATAAAAGTTTACTAATGTAAAGTTA
TACAATACT
Found at i:9382 original size:30 final size:29
Alignment explanation
Indices: 9341--9413 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 29
9331 GTCCTTAAAG
*
9341 GGGCTAAATTGTCCAAAAATTGAGAATCAGA
1 GGGCTTAATTGTCC--AAATTGAGAATCAGA
**
9372 GGGCTT-ATTGTCCCGATTGAGAATCAGA
1 GGGCTTAATTGTCCAAATTGAGAATCAGA
9400 GGGCTTAATTGTCC
1 GGGCTTAATTGTCC
9414 CAACTGAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 19 0.50
29 7 0.18
30 7 0.18
31 5 0.13
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (29 bp):
GGGCTTAATTGTCCAAATTGAGAATCAGA
Found at i:9393 original size:28 final size:29
Alignment explanation
Indices: 9359--9414 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 29
9349 TTGTCCAAAA
9359 ATTGAGAATCAGAGGGCTT-ATTGTCCCG
1 ATTGAGAATCAGAGGGCTTAATTGTCCCG
9387 ATTGAGAATCAGAGGGCTTAATTGTCCC
1 ATTGAGAATCAGAGGGCTTAATTGTCCC
9415 AACTGAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (29 bp):
ATTGAGAATCAGAGGGCTTAATTGTCCCG
Found at i:11319 original size:36 final size:36
Alignment explanation
Indices: 11279--11348 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 36
11269 GAGATTTTGG
11279 AGAAATATGATAA-TCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACT-AAAATTACAAAAAATGTAATA
11315 AGAAATATGATAACTAAAATTACAAAAAATGTAA
1 AGAAATATGATAACTAAAATTACAAAAAATGTAA
11349 GGTTTTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 32 0.97
37 1 0.03
ACGTcount: A:0.61, C:0.06, G:0.09, T:0.24
Consensus pattern (36 bp):
AGAAATATGATAACTAAAATTACAAAAAATGTAATA
Found at i:13814 original size:3 final size:3
Alignment explanation
Indices: 13808--13848 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
13798 AGTAAATTCT
* *
13808 TTC TTC TTC TTC TTT TTC TTC TTC TTT TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
13849 GTATCAGAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:13828 original size:12 final size:12
Alignment explanation
Indices: 13804--13845 Score: 75
Period size: 12 Copynumber: 3.4 Consensus size: 12
13794 TTTTAGTAAA
13804 TTCTTTCTTCTTC
1 TTCTTT-TTCTTC
13817 TTCTTTTTCTTC
1 TTCTTTTTCTTC
13829 TTCTTTTTCTTC
1 TTCTTTTTCTTC
13841 TTCTT
1 TTCTT
13846 CTTGTATCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 23 0.79
13 6 0.21
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTCTTTTTCTTC
Found at i:21724 original size:12 final size:12
Alignment explanation
Indices: 21707--21734 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
21697 ACCTGGCAAT
21707 TCGTGTTTCGTG
1 TCGTGTTTCGTG
21719 TCGTGTTTCGTG
1 TCGTGTTTCGTG
21731 TCGT
1 TCGT
21735 ATAAACGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.32, T:0.50
Consensus pattern (12 bp):
TCGTGTTTCGTG
Found at i:24597 original size:33 final size:33
Alignment explanation
Indices: 24555--24622 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
24545 ATGATACTGC
24555 ATAAAAAAACAAGAATAAAAAACAATGTTAATT
1 ATAAAAAAACAAGAATAAAAAACAATGTTAATT
24588 ATAAAAAAACAAGAATAAAAAACAATGTTAATT
1 ATAAAAAAACAAGAATAAAAAACAATGTTAATT
24621 AT
1 AT
24623 GCACTTTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.22
Consensus pattern (33 bp):
ATAAAAAAACAAGAATAAAAAACAATGTTAATT
Found at i:38384 original size:650 final size:655
Alignment explanation
Indices: 37089--38858 Score: 2098
Period size: 650 Copynumber: 2.7 Consensus size: 655
37079 GTGTTGTTTG
* * * *
37089 ATTTAATTACAAATTAATTC-GAAAAATAAATGGAAAAACGATATTAAAAGCGTGAAAACCCCTT
1 ATTTAATTAGAAATTAATTCAGAAAAA-AAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGT
* * * * *
37153 CAATATTTTTAGTGTTGAATTACATATTTTTTCAGAGTATTGTGGCAAAAAATTGAGAAAAAAAA
65 CAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAA
* * *
37218 TTTTCGTGTCTGTTTTTAGCCGAAATCGTGTACT---AACCATCACTATTTTTGGCTAAAAATGT
130 -TTTCG-GTCAGTTTTTAGCCGAAATCGTGTACTAACAACCATCA-TGTTTTGGGCTAAAAATGT
* * * * * * *
37280 ATTTCA-GGATCTCGACTCAGTTTTGCATGGTTTTCGACATACAGACTCCTTGAAATATTTATAT
192 GTTTCAGGGA-CCCGACTCAGTTTTGCATGATTTTTGGCA-AAAGACTCCTTGAAATATCTATAT
* *
37344 TCATGTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTGTTACGAGCATCTGAATCTTGT
255 TCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
**
37409 TTCGATTTAA-TAGAAATAAATTC-GAAAAAAAAATGGAAAAACGATATTAGAAATGTGAAAAAC
320 TTCGATTTAATTAGAAATAAATTCGGAAAAAAAAA-GGAAAAACGATATTAGAAGCGTG-AAAAC
*
37472 CCTTCAATTTTTTTTGGCATTGAAATATATATATTTTTATTGAGTATTGTGGCAAAAAATTGAGG
383 CCTTCAATTTTTTTTGGCATTG--A-ATATATATTTTTATTGAGTATTGTCGCAAAAAATTGAGG
* * * * *
37537 AAAAACTTTTTGGGTCAGTTTTTACAGAATTTTAGCCGAAATCATGTACTAACCGTCATGGTTTT
445 AAAAACTTTTTGAGTCAGTTTATACAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTT
* *
37602 TGACTAAAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGTCTCCTTG
510 TGACTAAAAACGCGTTCAGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTG
* * * *
37667 AAATATCTATATTCATCGAACTAAATCTCAGCCACATTGGATATAAGGATCTGGTTTTACGAGCA
575 AAATATCTATATACATCGAACCAAATCCCAACCACATTGGATATAAGGATCTGGTTTTACGAGCA
37732 TCTAAATCTTGTTTCA
640 TCTAAATCTTGTTTCA
* * * *
37748 ATTTAGTTAGAAATTAATTCAG-AAAAAAATGGAAAAATGATATTAGAAGTGTGAAAAGCCCGCC
1 ATTTAATTAGAAATTAATTCAGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTC
* * *
37812 AATCTTTTTGGTGTTGAATTATATATTTTTTTTTAGTATTGTGGCAAAAAATTCAGAAGAAAAAT
66 AATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAT
** * ***
37877 TCTCAGGTCAGTTTTTAGCCTTAATCATGTACTAACAACCATCATGGTCTTTGGGCTAAAAACAC
131 T-TC-GGTCAGTTTTTAGCCGAAATCGTGTACTAACAACCATCAT-GT-TTTGGGCTAAAAATGT
* * *
37942 GTTTC-GGGCCCCGATTCAGTTTTACATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATT
192 GTTTCAGGGACCCGACTCAGTTTTGCATGATTTTTGGCA-AAAGACTCCTTGAAATATCTATATT
* * * *
38006 CATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGTATTTAAATCTTCTT
256 CATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
* * *
38071 TCGATTTAATTGGAAACAAATTCGGAAAAGAAAAAGGAAAAACGATATTAGAAGCGTGAAAACTC
321 TCGATTTAATTAGAAATAAATTCGGAAAA-AAAAAGGAAAAACGATATTAGAAGCGTGAAAACCC
* * * *
38136 TTCAATTTTTTTT-G-TTTG-A-AT-T-TTTTT-TTGAGTA-T-TCGCAAAGAATTGATGAAACA
385 TTCAATTTTTTTTGGCATTGAATATATATTTTTATTGAGTATTGTCGCAAAAAATTGAGGAAAAA
* *
38192 TTTTTTGAGTCAGTTTATACAAAATTTTAGCCGAAATCATGTAGTAACCATCACGGTTTTTTG-C
450 CTTTTTGAGTCAGTTTATACAAAATTTTAGCCGAAATCATGTACTAACCATCACGG-TTTTTGAC
* * * * * * * **
38256 TAAAAATGTGTTTAGGGGCCCCGACTCAGTTTTGCATGATTTTTTGCG-TAAGCACTTTTTGAAA
514 TAAAAACGCGTTCAGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAG-ACTCCTTGAAA
* * * * * *
38320 TATCTATATACATTGCACCAAATCCCAACCATATTGGATTTAAGGATTTGTTTTTACGAGCATCT
578 TATCTATATACATCGAACCAAATCCCAACCACATTGGATATAAGGATCTGGTTTTACGAGCATCT
* *
38385 TAATCTTGTTTCG
643 AAATCTTGTTTCA
* *
38398 ACTTAATTAGAAATTAATTCAGAAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAGCCCGTC
1 ATTTAATTAGAAATTAATTCAGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTC
* *
38463 AATCTTTTTGGCT-TTGAATTATATATTTCTTCTGAGTATTGTGGCAAAAAATTCCGAAAAAAAA
66 AATCTTTTTGG-TGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT-C-AGAAAAAA
* * *
38527 AAATTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACAAACATCATTGTTTTGGGGCTAAAAAT
128 AATTTC-GGTCAGTTTTTAGCCGAAATCGTGTACTAACAACCATCA-TGTTTT-GGGCTAAAAAT
* * * *
38592 GTGTTTCGGGGACCTGGCTCAGTTTTGCATGATTTTTGATGCAAAA-ACTCCTTGAAATATCCAT
190 GTGTTTCAGGGACCCGACTCAGTTTTGCATGATTTTTG--GCAAAAGACTCCTTGAAATATCTAT
* * * * *
38656 ATTCATCGAATCAAATCCCAGCCACATTGGATATAAGAATTTGTTTTTACGAGCATCTGAATCTT
253 ATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTT
* * *
38721 GTTTCGATTTAATTAAAAATTAATTCGG--AAAAAATGGAAAAACGATATTAGAAGCGT-AAAAC
318 GTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAC
* * * * * * *
38783 GCCAGTCAA-TCTTTTTGGCGTTGAATTATATATTTTTTTCTAAGTATTGTGGCAAAAAATTCAG
383 -CC-TTCAATTTTTTTTGGCATTGAA-TATATATTTTTAT-TGAGTATTGTCGCAAAAAATTGAG
* *
38847 GAAGAATTTTTT
444 GAAAAACTTTTT
38859 CAGGTCAATT
Statistics
Matches: 941, Mismatches: 134, Indels: 70
0.82 0.12 0.06
Matches are distributed among these distances:
649 8 0.01
650 235 0.25
651 103 0.11
652 65 0.07
653 138 0.15
654 4 0.00
655 7 0.01
656 2 0.00
657 7 0.01
658 114 0.12
659 28 0.03
660 6 0.01
661 145 0.15
662 48 0.05
663 26 0.03
664 5 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (655 bp):
ATTTAATTAGAAATTAATTCAGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTC
AATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAT
TTCGGTCAGTTTTTAGCCGAAATCGTGTACTAACAACCATCATGTTTTGGGCTAAAAATGTGTTT
CAGGGACCCGACTCAGTTTTGCATGATTTTTGGCAAAAGACTCCTTGAAATATCTATATTCATCT
AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
TTAATTAGAAATAAATTCGGAAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAACCCTTCAAT
TTTTTTTGGCATTGAATATATATTTTTATTGAGTATTGTCGCAAAAAATTGAGGAAAAACTTTTT
GAGTCAGTTTATACAAAATTTTAGCCGAAATCATGTACTAACCATCACGGTTTTTGACTAAAAAC
GCGTTCAGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATA
TACATCGAACCAAATCCCAACCACATTGGATATAAGGATCTGGTTTTACGAGCATCTAAATCTTG
TTTCA
Found at i:42579 original size:35 final size:35
Alignment explanation
Indices: 42540--42607 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
42530 TTATATAACC
42540 AATATTTATTTGAACACATATATACCTCACTTCCA
1 AATATTTATTTGAACACATATATACCTCACTTCCA
*
42575 AATATTTATTTGATCACATATATACCTCACTTC
1 AATATTTATTTGAACACATATATACCTCACTTC
42608 ATAGTAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (35 bp):
AATATTTATTTGAACACATATATACCTCACTTCCA
Found at i:42762 original size:17 final size:17
Alignment explanation
Indices: 42732--42764 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42722 AATAAATCGA
42732 AAATAAAGATATTAAAT
1 AAATAAAGATATTAAAT
42749 AAATATAAGA-ATTAAA
1 AAATA-AAGATATTAAA
42765 CATTAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (17 bp):
AAATAAAGATATTAAAT
Found at i:50100 original size:29 final size:31
Alignment explanation
Indices: 50055--50124 Score: 108
Period size: 29 Copynumber: 2.3 Consensus size: 31
50045 GGAAAGGGTC
50055 GAGTACTACTGCTAAAGCCCCCACTACTAAG
1 GAGTACTACTGCTAAAGCCCCCACTACTAAG
50086 GAGTACT-C-GCTAAAGCCCCCACTACTAAGG
1 GAGTACTACTGCTAAAGCCCCCACTACTAA-G
*
50116 GTGTACTAC
1 GAGTACTAC
50125 CTATTTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 20 0.56
30 8 0.22
31 8 0.22
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (31 bp):
GAGTACTACTGCTAAAGCCCCCACTACTAAG
Found at i:69396 original size:17 final size:19
Alignment explanation
Indices: 69374--69410 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
69364 AGAATTCGGG
69374 TAAATA-AAAT-AAGAAAA
1 TAAATATAAATCAAGAAAA
*
69391 TAAATATAATTCAAGAAAA
1 TAAATATAAATCAAGAAAA
69410 T
1 T
69411 CAAGGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
19 8 0.47
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (19 bp):
TAAATATAAATCAAGAAAA
Found at i:70408 original size:17 final size:18
Alignment explanation
Indices: 70386--70426 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
70376 ACACCCTGGG
70386 AAAAAAAT-GA-AAAAGA
1 AAAAAAATAGATAAAAGA
70402 AAAAAAATAGATAAAAGA
1 AAAAAAATAGATAAAAGA
70420 AAAAAAA
1 AAAAAAA
70427 GTACATCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 8 0.35
17 2 0.09
18 13 0.57
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (18 bp):
AAAAAAATAGATAAAAGA
Found at i:75717 original size:204 final size:204
Alignment explanation
Indices: 75360--75764 Score: 657
Period size: 204 Copynumber: 2.0 Consensus size: 204
75350 TTATAAAGAC
* *
75360 AAATTATACAATATACCGTCAGTGGAGTTTAGCAGACTACACAAGCGGCTCCTGAAGGGTGACAT
1 AAATTATACAATACACCGGCAGTGGAGTTTAGCAGACTACACAAGCGGCTCCTGAAGGGTGACAT
* * * * * * *
75425 GTGTCATTTAGGGAGTGGATTGAAATATTTAAAACTTAATTAATTCAAAAAATGGATATGTGTCA
66 GTGTCATCTAAGGACTAGATTGAAATAATTAAAACTTAATTAATTAAAAAAATGGACATGTGTCA
* * *
75490 ACTCCACAACCCGCTTATGGAGTCTAAAATTTACACCGTCGGTGTATCAAATAATTACCCAATTA
131 ACTCCACAACCCGCTTATGGAGTCCAAAATTTACACCGTCGGTATATCAAATAATTACCCAAATA
75555 TAAATTGGT
196 TAAATTGGT
* *
75564 AAATTATACAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCGGGTCCTGAAGGGTGACAT
1 AAATTATACAATACACCGGCAGTGGAGTTTAGCAGACTACACAAGCGGCTCCTGAAGGGTGACAT
*
75629 GTGTCCTCTAAGGACTAGATTGAAATAATTAAAACTTAATTAATTAAAAAAATGGACATGTGTCA
66 GTGTCATCTAAGGACTAGATTGAAATAATTAAAACTTAATTAATTAAAAAAATGGACATGTGTCA
* *
75694 ACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGTCGGTATATCAAATAATTACTCAAATA
131 ACTCCACAACCCGCTTATGGAGTCCAAAATTTACACCGTCGGTATATCAAATAATTACCCAAATA
75759 TAAATT
196 TAAATT
75765 ACTACTCTTG
Statistics
Matches: 184, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
204 184 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (204 bp):
AAATTATACAATACACCGGCAGTGGAGTTTAGCAGACTACACAAGCGGCTCCTGAAGGGTGACAT
GTGTCATCTAAGGACTAGATTGAAATAATTAAAACTTAATTAATTAAAAAAATGGACATGTGTCA
ACTCCACAACCCGCTTATGGAGTCCAAAATTTACACCGTCGGTATATCAAATAATTACCCAAATA
TAAATTGGT
Found at i:80298 original size:3 final size:3
Alignment explanation
Indices: 80290--80314 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
80280 CAACAGACCG
80290 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
80315 CTAATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:82176 original size:1 final size:1
Alignment explanation
Indices: 82172--82201 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
82162 CCACCCCTTC
82172 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
82202 CCCTCTTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:83296 original size:152 final size:150
Alignment explanation
Indices: 82961--83423 Score: 552
Period size: 152 Copynumber: 3.0 Consensus size: 150
82951 GACTTGGTTG
* * *
82961 GCTTAAAATGAATTTGCTGAGGTTAGCTTTGTCGCGAAATACATATGATGTCTTTAAATGCGTCA
1 GCTTAAAATGAATTTGCTGACGTTAGCTTTGTC-C---A-ACATATGATGTCTTTCAATGCGTAA
* *
83026 GATGGTGATGGTAGATAAATAAGATGTCGGTTACGTTCTCATTTTGAATTTATGTGAGTTTTAAT
61 GAGGGTGATGGTAGATAAATAAGATGTCGGAT-CGTTCTCATTTTGAATTTATGTGAGTTTTAAT
* * * *
83091 GAACTAGCTGAATTCCTCTATGTTTG
125 AAACTAACTTAATTCCTCTATGTTTA
* * *
83117 GCTTGAATTGAATTTGCTGACGTTAGCTTTGT-C-ACGTATGATGTCTTTCAATGCGTAAGAGGG
1 GCTTAAAATGAATTTGCTGACGTTAGCTTTGTCCAACATATGATGTCTTTCAATGCGTAAGAGGG
* * *
83180 TGATGGTAGATAAATAAAATGCCGGAATCGTTCTCTTTTTGAATTCTCAATGTGAGTTTTAATAA
66 TGATGGTAGATAAATAAGATGTCGG-ATCGTTCTCATTTTGAATT-T--ATGTGAGTTTTAATAA
83245 ACTAACTTAATTCCTCTATGTTTA
127 ACTAACTTAATTCCTCTATGTTTA
* *
83269 GCTTAAAATGAATTTGCTGACGTTAGCTTTGTCACACAATACATATGATGTCTTTCGATGTGTAA
1 GCTTAAAATGAATTTGCTGACGTTAGCTTTGT--C-C-A-ACATATGATGTCTTTCAATGCGTAA
* * *
83334 GAGGGTGATGGTAGATAAAATAAGATGTTGGTATCATTCTCATTTTGAATATTTTATGTGAGTTC
61 GAGGGTGATGGTAGAT-AAATAAGATGTCGG-ATCGTTCTCATTTTG-A-A-TTTATGTGAGTTT
83399 TAATAAACTAACTTAATTCCTCTAT
121 TAATAAACTAACTTAATTCCTCTAT
83424 ATATTGCTTA
Statistics
Matches: 265, Mismatches: 27, Indels: 26
0.83 0.08 0.08
Matches are distributed among these distances:
149 65 0.25
150 2 0.01
152 66 0.25
154 1 0.00
156 30 0.11
159 38 0.14
160 58 0.22
161 1 0.00
162 2 0.01
163 2 0.01
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.39
Consensus pattern (150 bp):
GCTTAAAATGAATTTGCTGACGTTAGCTTTGTCCAACATATGATGTCTTTCAATGCGTAAGAGGG
TGATGGTAGATAAATAAGATGTCGGATCGTTCTCATTTTGAATTTATGTGAGTTTTAATAAACTA
ACTTAATTCCTCTATGTTTA
Found at i:95315 original size:15 final size:15
Alignment explanation
Indices: 95297--95328 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
95287 TCCTAGTTCA
*
95297 GACAAAGGGAGGTGG
1 GACAAAGGGAGCTGG
95312 GACAAAGGGAGCTGG
1 GACAAAGGGAGCTGG
95327 GA
1 GA
95329 AGAGTTCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.50, T:0.06
Consensus pattern (15 bp):
GACAAAGGGAGCTGG
Found at i:99242 original size:67 final size:67
Alignment explanation
Indices: 99139--99271 Score: 239
Period size: 67 Copynumber: 2.0 Consensus size: 67
99129 CGTTGGTGGC
* * *
99139 TGGTGGTGATTAAGTACCATGTATTGTAAGCCCCTCTTTGAGGCTTTTGGCATTTTCTGACCTTG
1 TGGTGGTGATTAAGTACCATGTACTGTAAGCCCCTCTTTGAGGCCTTTGGCATTTGCTGACCTTG
99204 GT
66 GT
99206 TGGTGGTGATTAAGTACCATGTACTGTAAGCCCCTCTTTGAGGCCTTTGGCATTTGCTGACCTTG
1 TGGTGGTGATTAAGTACCATGTACTGTAAGCCCCTCTTTGAGGCCTTTGGCATTTGCTGACCTTG
99271 G
66 G
99272 ACATTCACCA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.38
Consensus pattern (67 bp):
TGGTGGTGATTAAGTACCATGTACTGTAAGCCCCTCTTTGAGGCCTTTGGCATTTGCTGACCTTG
GT
Found at i:103869 original size:1 final size:1
Alignment explanation
Indices: 103863--103893 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
103853 CTTTCTTCCT
103863 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
103894 GAATAGGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:106449 original size:17 final size:17
Alignment explanation
Indices: 106424--106457 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
106414 TGCGATTGGG
* *
106424 GAGGCAAGGAAGGAGGA
1 GAGGAAAGGAAAGAGGA
106441 GAGGAAAGGAAAGAGGA
1 GAGGAAAGGAAAGAGGA
106458 AAGAGAGGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (17 bp):
GAGGAAAGGAAAGAGGA
Found at i:109191 original size:11 final size:11
Alignment explanation
Indices: 109177--109205 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
109167 CGTTTAGTAG
109177 AGCGGTGTGGT
1 AGCGGTGTGGT
109188 AGCGGTGTGGT
1 AGCGGTGTGGT
109199 AGCGGTG
1 AGCGGTG
109206 CGATTGATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.10, G:0.55, T:0.24
Consensus pattern (11 bp):
AGCGGTGTGGT
Found at i:109357 original size:19 final size:19
Alignment explanation
Indices: 109333--109369 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
109323 TTTGGTCCCA
109333 AAACGGTGATGAAACGATC
1 AAACGGTGATGAAACGATC
*
109352 AAACGGTGGTGAAACGAT
1 AAACGGTGATGAAACGAT
109370 TACAGATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.14, G:0.30, T:0.16
Consensus pattern (19 bp):
AAACGGTGATGAAACGATC
Found at i:117227 original size:2 final size:2
Alignment explanation
Indices: 117220--117249 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
117210 TTTAAGTACT
117220 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
117250 ATAAAATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:144230 original size:19 final size:19
Alignment explanation
Indices: 144206--144253 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
144196 CTCGATACCT
144206 TTCACCACTTATTTAAGCC
1 TTCACCACTTATTTAAGCC
144225 TTCACCACTTATTTAAGCC
1 TTCACCACTTATTTAAGCC
*
144244 TTTACCACTT
1 TTCACCACTT
144254 TTGCCAATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.25, C:0.31, G:0.04, T:0.40
Consensus pattern (19 bp):
TTCACCACTTATTTAAGCC
Found at i:150099 original size:7 final size:7
Alignment explanation
Indices: 150087--150119 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
150077 ATATATGTAT
150087 ATATATA
1 ATATATA
150094 ATATATA
1 ATATATA
150101 ATATAT-
1 ATATATA
150107 ATAATATA
1 AT-ATATA
150115 ATATA
1 ATATA
150120 CTCAAAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 2 0.08
7 20 0.83
8 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATATA
Found at i:162143 original size:35 final size:33
Alignment explanation
Indices: 162092--162173 Score: 123
Period size: 32 Copynumber: 2.5 Consensus size: 33
162082 TATCTCAACG
162092 GGAGAGACCGGTTTTTTTTTTTTTGTTGTTGAAAA
1 GGAGAGACCGG-TTTTTTTTTTTTG-TGTTGAAAA
162127 GGAGAGATCCGG--TTTTTTTTTTGTGTTGAAAA
1 GGAGAGA-CCGGTTTTTTTTTTTTGTGTTGAAAA
162159 GGAGAGACCGGTTTT
1 GGAGAGACCGGTTTT
162174 ACGACTTTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
31 4 0.09
32 16 0.36
33 13 0.30
35 7 0.16
36 4 0.09
ACGTcount: A:0.21, C:0.07, G:0.29, T:0.43
Consensus pattern (33 bp):
GGAGAGACCGGTTTTTTTTTTTTGTGTTGAAAA
Found at i:162146 original size:31 final size:31
Alignment explanation
Indices: 162108--162173 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
162098 ACCGGTTTTT
162108 TTTTTTTTGT-TGTTGAAAAGGAGAGATCCGG
1 TTTTTTTTGTGTGTTGAAAAGGAGAGA-CCGG
*
162139 TTTTTTTTTTGTGTTGAAAAGGAGAGACCGG
1 TTTTTTTTGTGTGTTGAAAAGGAGAGACCGG
162170 TTTT
1 TTTT
162174 ACGACTTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 17 0.52
32 16 0.48
ACGTcount: A:0.21, C:0.06, G:0.27, T:0.45
Consensus pattern (31 bp):
TTTTTTTTGTGTGTTGAAAAGGAGAGACCGG
Found at i:179517 original size:10 final size:9
Alignment explanation
Indices: 179502--179529 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
179492 GGACCTTGAC
179502 TTTTTTTTA
1 TTTTTTTTA
179511 TTTTTTTTA
1 TTTTTTTTA
179520 TTTTTTTTA
1 TTTTTTTTA
179529 T
1 T
179530 CTTATTAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:189641 original size:3 final size:3
Alignment explanation
Indices: 189633--189675 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
189623 ATTTAGCTAT
189633 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
189676 GTATTTGACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:191551 original size:2 final size:2
Alignment explanation
Indices: 191544--191581 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
191534 ATGACGTGTG
191544 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
191582 TAGTTAATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:197001 original size:16 final size:16
Alignment explanation
Indices: 196980--197011 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
196970 TATAATTATT
196980 TATATATTAATAATAA
1 TATATATTAATAATAA
*
196996 TATATATTATTAATAA
1 TATATATTAATAATAA
197012 AAATTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:197006 original size:19 final size:19
Alignment explanation
Indices: 196964--197011 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
196954 GAACGTTCAT
* *
196964 TTATTATATAATTATTTATA
1 TTATTA-ATAATAATATATA
196984 -TATTAATAATAATATATA
1 TTATTAATAATAATATATA
197002 TTATTAATAA
1 TTATTAATAA
197012 AAATTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTAATAATAATATATA
Found at i:197170 original size:18 final size:18
Alignment explanation
Indices: 197143--197177 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
197133 AATTATTACA
197143 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
197161 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
197178 CAATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Done.