Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015405.1 Corchorus capsularis cultivar CVL-1 contig15426, 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: 41908
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1149 original size:32 final size:31
Alignment explanation
Indices: 1113--1186 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 31
1103 AGACCTGAAT
* *
1113 GACCCAAAACCCGTATGATCCGAGACCCAAAG
1 GACCCAAAACCCGAATAATCCGA-ACCCAAAG
* * * *
1145 GACCCGAAACCCGAATAATCCGAACCTAGAT
1 GACCCAAAACCCGAATAATCCGAACCCAAAG
1176 GACCCAAAACC
1 GACCCAAAACC
1187 AAAATGACCC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
31 15 0.43
32 20 0.57
ACGTcount: A:0.39, C:0.35, G:0.16, T:0.09
Consensus pattern (31 bp):
GACCCAAAACCCGAATAATCCGAACCCAAAG
Found at i:1824 original size:166 final size:166
Alignment explanation
Indices: 1385--1868 Score: 634
Period size: 166 Copynumber: 2.9 Consensus size: 166
1375 AAAGATGTGA
* ** * * **
1385 AATTACTAAAAGATCCCCACCCCGGATTAAGGA-GGAGCGAGAGAACTAATTTTTTTCGTCTTTT
1 AATTAATAAAAGATCCCCACCAAGGATTGATGATGGAGTTAGAGAACTAATTTTTTTCGTC-TTT
* * * * * *
1449 TCC-ACTTGGCAAATTATTTAAATGTCCTAATTTTTTATTCTTAAGGGGATTAAATAACTAGACT
65 TCCTACTTGGTAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTA-ACT
* *
1513 TTTTGGTCATTTCTCAATTGACATTAATAGAGTAGTGG
129 TTTTGGTCATTTCTCAATGGACATTAATAGAGTAGTAG
* * * * ** * * *
1551 AATTACTAAAAGATCCCTACCAAGGCTTGTTTTTGGAGTTAGAGAACTTATTTTTTTAGTATTTT
1 AATTAATAAAAGATCCCCACCAAGGATTGATGATGGAGTTAGAGAACTAATTTTTTTCGTCTTTT
*
1616 CCTACTTGGTAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAAGTAATCTT
66 CCTACTTGGTAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAA-CTT
1681 TTTGGTCATTTCTCAATGGAC-TTGAATAGAGTAGTAG
130 TTTGGTCATTTCTCAATGGACATT-AATAGAGTAGTAG
* * *
1718 AATTAATAAAAGATCCCCATCAAGGATTGATGAT-GAGTTAGAGAACTAATCTTTTTCGTCTTTA
1 AATTAATAAAAGATCCCCACCAAGGATTGATGATGGAGTTAGAGAACTAATTTTTTTCGTCTTTT
1782 CCTACTTGGTAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTT
66 CCTACTTGGTAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACT-AACTT
*
1847 TTTGGTCATTTCTCAATTGACA
130 TTTGGTCATTTCTCAATGGACA
1869 AAATGACTCA
Statistics
Matches: 275, Mismatches: 37, Indels: 11
0.85 0.11 0.03
Matches are distributed among these distances:
166 139 0.51
167 136 0.49
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (166 bp):
AATTAATAAAAGATCCCCACCAAGGATTGATGATGGAGTTAGAGAACTAATTTTTTTCGTCTTTT
CCTACTTGGTAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAACTTT
TTGGTCATTTCTCAATGGACATTAATAGAGTAGTAG
Found at i:2806 original size:2 final size:2
Alignment explanation
Indices: 2799--2825 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2789 GATTTGGCAT
2799 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 T
2826 GATGGAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7648 original size:2 final size:2
Alignment explanation
Indices: 7633--7671 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
7623 TCAATGTTCA
* *
7633 AT AT AT CT AA 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 A
7672 AAAGTATGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:7794 original size:31 final size:32
Alignment explanation
Indices: 7759--7819 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
7749 ATGTTTTCTG
7759 ATTGTACCCTTATTT-TTAAAACATATTTCCA
1 ATTGTACCCTTATTTCTTAAAACATATTTCCA
*
7790 ATTGTACCCTTTTTTCTTAAAACATATTTC
1 ATTGTACCCTTATTTCTTAAAACATATTTC
7820 TAAATTACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.48
Consensus pattern (32 bp):
ATTGTACCCTTATTTCTTAAAACATATTTCCA
Found at i:8314 original size:202 final size:201
Alignment explanation
Indices: 7944--8349 Score: 638
Period size: 204 Copynumber: 2.0 Consensus size: 201
7934 TATAATACGT
* * *
7944 ATATTAAATGGAAAATTATACAATACACTGGCGGTGGAGTTTAGAAAACTACACAAGCGGGTCCT
1 ATATTAAATAGAAAATTATACAATACACCGGCAGTGGAGTTTAGAAAACTACACAAGCGGGTCCT
*
8009 GAAGGGTGACATGTGTCCCTTAGGGACTAGATTGAAATATTTAAAACTTGATTAATTCAAAAAAT
66 GAAGGGTGACATGTGTCCCGTAGGGACTAGATTGAAATATTTAAAACTTGA-TAATTCAAAAAAT
* * * *
8074 GGACATGTGTCAACTCCACAAGCCGCTTGTGGAGTCCAAAATTTACACCGCCTG-TGTATCATAT
130 GGACATGTATCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACAACGAC-GATGTATCATAT
8138 AATCACCC
194 AATCACCC
* *
8146 ATATTAAATTAGACAAATTATACAATACACCGTCAGTGGAGTTTA-ACAGACTACACAAGCGGGT
1 ATATTAAA-TAGA-AAATTATACAATACACCGGCAGTGGAGTTTAGA-AAACTACACAAGCGGGT
*
8210 CCTGAAGGGTGACATGTGTCCCGTAGGGACTAGATTGAAATTTTTAAAACTTG-TAATTCAAAAA
63 CCTGAAGGGTGACATGTGTCCCGTAGGGACTAGATTGAAATATTTAAAACTTGATAATTCAAAAA
*
8274 ATTGACATGTATCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACAACGACGATGTATCATA
128 ATGGACATGTATCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACAACGACGATGTATCATA
8339 TAATCACCC
193 TAATCACCC
8348 AT
1 AT
8350 TAAAGTATTA
Statistics
Matches: 188, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
201 1 0.01
202 88 0.47
203 4 0.02
204 95 0.51
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (201 bp):
ATATTAAATAGAAAATTATACAATACACCGGCAGTGGAGTTTAGAAAACTACACAAGCGGGTCCT
GAAGGGTGACATGTGTCCCGTAGGGACTAGATTGAAATATTTAAAACTTGATAATTCAAAAAATG
GACATGTATCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACAACGACGATGTATCATATAA
TCACCC
Found at i:8450 original size:20 final size:19
Alignment explanation
Indices: 8425--8462 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
8415 TACTATTATT
8425 TTTTAAATTT-AATATTTTAC
1 TTTT-AATTTCAAT-TTTTAC
8445 TTTTAATTTCAATTTTTA
1 TTTTAATTTCAATTTTTA
8463 AATGTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTAATTTCAATTTTTAC
Found at i:8799 original size:19 final size:20
Alignment explanation
Indices: 8772--8809 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
8762 TACTATTATT
8772 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
8792 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
8810 AATGCTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:9079 original size:22 final size:22
Alignment explanation
Indices: 8972--9135 Score: 147
Period size: 22 Copynumber: 7.4 Consensus size: 22
8962 CTTGTCACTA
*
8972 TGTGGTTATCAAAATTTCAAAAG
1 TGTGGTTATCAAAATTTC-ATAG
* *
8995 T-TGGTTATTATAATTTCATGAG
1 TGTGGTTATCAAAATTTCAT-AG
* *
9017 -GAGGTTATCAAAATTCCATAG
1 TGTGGTTATCAAAATTTCATAG
*
9038 TGTGGTTACCAAAATTTCATAG
1 TGTGGTTATCAAAATTTCATAG
*
9060 TGTGGTTACCAAAATTTCATAG
1 TGTGGTTATCAAAATTTCATAG
* *
9082 -GATCAGGTTATTAAAATTTCTTAG
1 TG-T--GGTTATCAAAATTTCATAG
*
9106 -GTTGGTTATTAAAATTTCATAG
1 TG-TGGTTATCAAAATTTCATAG
*
9128 GGTGGTTA
1 TGTGGTTA
9136 ATTATCACAG
Statistics
Matches: 119, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
21 4 0.03
22 95 0.80
23 2 0.02
24 18 0.15
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (22 bp):
TGTGGTTATCAAAATTTCATAG
Found at i:9227 original size:22 final size:22
Alignment explanation
Indices: 9175--9304 Score: 97
Period size: 22 Copynumber: 6.0 Consensus size: 22
9165 AAGAGATTAT
* * *
9175 CAAAATGTCATAGCGAGGTTTA
1 CAAAATTTCATAGTGAGGTTAA
* *
9197 -AGAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAGTGAGGTTAA
9218 CAAAATTTCATTAG-GAGGTT-A
1 CAAAATTTCA-TAGTGAGGTTAA
* * * *
9239 CTAATATTTCATGGGGAGGTTAT
1 C-AAAATTTCATAGTGAGGTTAA
* * *
9262 CAAAATTTTATAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAA
9284 CAAAATTTCATA-TGAAGGTTA
1 CAAAATTTCATAGTG-AGGTTA
9305 TAAAAGTCTC
Statistics
Matches: 85, Mismatches: 17, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
21 22 0.26
22 59 0.69
23 4 0.05
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAA
Found at i:9305 original size:22 final size:22
Alignment explanation
Indices: 9199--9561 Score: 87
Period size: 22 Copynumber: 16.3 Consensus size: 22
9189 GAGGTTTAAG
* *
9199 AATTTCATAGTG-TGGTTAACAA
1 AATTTCATA-TGAAGGTTATCAA
*
9221 AATTTCAT-TAGGAGGTTA-CTAA
1 AATTTCATAT-GAAGGTTATC-AA
* ** *
9243 TATTTCATGGGGAGGTTATCAA
1 AATTTCATATGAAGGTTATCAA
* *
9265 AATTTTATAGTG-TGGTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
9287 AATTTCATATGAAGGTTAT-AA
1 AATTTCATATGAAGGTTATCAA
* * *
9308 AAGTCTCAATTTCAT-AAGGAGTACCAA
1 AA-TTTC-A--T-ATGAAGG-TTATCAA
* *
9335 AATTTGATA-GAATGTTATC-A
1 AATTTCATATGAAGGTTATCAA
* *
9355 AATCTCATA-G-AGTGATTATCGA
1 AATTTCATATGAAG-G-TTATCAA
9377 AATTTCATA-GAGATCGGATTATCAA
1 AATTTCATATGA-A--GG-TTATCAA
*
9402 AATTT-ATATGAAGATTATCAA
1 AATTTCATATGAAGGTTATCAA
**
9423 AATTTCATAGTG-TTGTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
* * *
9445 AATTTTA-AAGCGAGGTTATCAA
1 AATTTCATATG-AAGGTTATCAA
* * * *
9467 AATTACATAATG-TGATTATCAG
1 AATTTCAT-ATGAAGGTTATCAA
* * * *
9489 AATTTAATA-GAGGGGTCAACAA
1 AATTTCATATGA-AGGTTATCAA
** *
9511 AATTTTGTA-AAGAGGTTATCAA
1 AATTTCATATGA-AGGTTATCAA
*
9533 AATTTCATA-AAGAGGTTATCAA
1 AATTTCATATGA-AGGTTATCAA
*
9555 ATTTTCA
1 AATTTCA
9562 AAATGTGATT
Statistics
Matches: 257, Mismatches: 53, Indels: 62
0.69 0.14 0.17
Matches are distributed among these distances:
19 1 0.00
20 13 0.05
21 30 0.12
22 168 0.65
23 6 0.02
24 7 0.03
25 21 0.08
26 7 0.03
27 4 0.02
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
AATTTCATATGAAGGTTATCAA
Found at i:9357 original size:20 final size:22
Alignment explanation
Indices: 9334--9432 Score: 89
Period size: 21 Copynumber: 4.5 Consensus size: 22
9324 AGGAGTACCA
*
9334 AAATTTGATAGAATG-TTATC-
1 AAATTTCATAGAATGATTATCG
* *
9354 AAATCTCATAGAGTGATTATCG
1 AAATTTCATAGAATGATTATCG
*
9376 AAATTTCATAGAGATCGGATTATCA
1 AAATTTCATAGA-AT--GATTATCG
*
9401 AAATTT-ATATGAA-GATTATCA
1 AAATTTCATA-GAATGATTATCG
9422 AAATTTCATAG
1 AAATTTCATAG
9433 TGTTGTTATC
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
20 12 0.18
21 20 0.30
22 14 0.21
23 1 0.02
24 4 0.06
25 15 0.23
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
AAATTTCATAGAATGATTATCG
Found at i:9558 original size:21 final size:22
Alignment explanation
Indices: 9315--9561 Score: 116
Period size: 22 Copynumber: 11.3 Consensus size: 22
9305 TAAAAGTCTC
* *
9315 AATTTCATAAGGA-G-TACCAA
1 AATTTCATAAAGAGGTTATCAA
* * *
9335 AATTTGATAGA-ATGTTATC-A
1 AATTTCATAAAGAGGTTATCAA
* * * * *
9355 AATCTCATAGAGTGATTATCGA
1 AATTTCATAAAGAGGTTATCAA
*
9377 AATTTCATAGAGATCGGATTATCAA
1 AATTTCATAAAGA--GG-TTATCAA
9402 AATTT-ATATGAAGA--TTATCAA
1 AATTTCATA--AAGAGGTTATCAA
** **
9423 AATTTCATAGTGTTGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
9445 AATTT--TAAAGCGAGGTTATCAA
1 AATTTCATAAA--GAGGTTATCAA
* * * * *
9467 AATTACATAATGTGATTATCAG
1 AATTTCATAAAGAGGTTATCAA
* * * * *
9489 AATTTAATAGAGGGGTCAACAA
1 AATTTCATAAAGAGGTTATCAA
**
9511 AATTTTGTAAAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
9533 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
*
9555 ATTTTCA
1 AATTTCA
9562 AAATGTGATT
Statistics
Matches: 167, Mismatches: 44, Indels: 30
0.69 0.18 0.12
Matches are distributed among these distances:
19 1 0.01
20 22 0.13
21 20 0.12
22 103 0.62
24 7 0.04
25 11 0.07
26 3 0.02
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.34
Consensus pattern (22 bp):
AATTTCATAAAGAGGTTATCAA
Found at i:9714 original size:22 final size:22
Alignment explanation
Indices: 9686--9850 Score: 108
Period size: 22 Copynumber: 7.5 Consensus size: 22
9676 TCAGGGAGGA
9686 TATCAAAATTTCATATGAAGAT
1 TATCAAAATTTCATATGAAGAT
**
9708 TATCAAAATTTCATAGTTTAG-T
1 TATCAAAATTTCATA-TGAAGAT
* * * *
9730 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGAT
* *
9752 TATGAAAATTTCATAGTTTGTAG--
1 TATCAAAATTTCATA---TGAAGAT
* *
9775 -ATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATATGAAGAT
*
9796 TAACAAAATTTCATAATG-AGAT
1 TATCAAAATTTCAT-ATGAAGAT
** *
9818 TATCAAAAAATCATAGGAA-ACT
1 TATCAAAATTTCATATGAAGA-T
9840 TATCAAAATTT
1 TATCAAAATTT
9851 TTAGTTATCA
Statistics
Matches: 109, Mismatches: 23, Indels: 22
0.71 0.15 0.14
Matches are distributed among these distances:
19 3 0.03
21 4 0.04
22 95 0.87
23 5 0.05
25 2 0.02
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGAT
Found at i:9823 original size:44 final size:43
Alignment explanation
Indices: 9686--10247 Score: 154
Period size: 44 Copynumber: 12.9 Consensus size: 43
9676 TCAGGGAGGA
* * *
9686 TATCAAAATTTCATATGAAGATTATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAGGGAGATTATCAAAATTTCATA-ATTAGT
* * * *
9730 TTTCAAAATTTCATAAGAGG-G-TTATGAAAATTTCATAGTTTGT
1 TATCAAAATTTCAT-AG-GGAGATTATCAAAATTTCATAATTAGT
* * *
9773 AGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGAT
1 -TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATTAG-T
** *
9818 TATCAAAAAATCATA-GGAAACTTATCAAAA-TT--T--TTAGT
1 TATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAATTAGT
* * * * * * *
9856 TATCAAGATTTCGTA-AGAAAGTTATCAAATTTTTATAGA-GAGGTT
1 TATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATA-ATTA-G-T
* * ***
9901 TATC-AAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAATTA-GT
* * * * * *
9945 TATCACAATTTCATAGTGTGATTATCAAAACTTCAGAGTGT-GAT
1 TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAAT-TAG-T
* * * * * * * *
9989 TACCAACAA-TTCATATGGAGGTTTTTAAATTTTCATAACATGGT
1 TATCAA-AATTTCATAGGGAGATTATCAAAATTTCATAA-TTAGT
* * * * * * *
10033 TATCAATATATCATATGGAGGTTATCAACATCTT-ATAGTGTTGGT
1 TATCAAAATTTCATAGGGAGATTATCAAAAT-TTCATA--ATTAGT
* *
10078 TATCAAAATTTCATTGGTA-AGTTATCAAAATTTCAT-ATTGAGGT
1 TATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAATT-A-GT
* * * * **
10122 CT-TC-AAATTTCCTTAGAGAGGTTAACAAAATTTCATAAGAAGGT
1 -TATCAAAATTT-CATAGGGAGATTATCAAAATTTCATAATTA-GT
** *** * * * *
10166 TAAAAAAATTT-ATAAAAAGATTCTCGAAATTTCATAGTATCGT
1 TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAAT-TAGT
* * * *
10209 TATTAAAATTTTATAGGAAGGTTATCAAAATTTCATAAT
1 TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAAT
10248 GAGATCATAA
Statistics
Matches: 373, Mismatches: 106, Indels: 78
0.67 0.19 0.14
Matches are distributed among these distances:
38 24 0.06
39 5 0.01
41 2 0.01
42 4 0.01
43 52 0.14
44 204 0.55
45 81 0.22
46 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (43 bp):
TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAATTAGT
Found at i:9905 original size:23 final size:22
Alignment explanation
Indices: 9877--9955 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
9867 CGTAAGAAAG
9877 TTATCAAATTTTTATAGAGAGGT
1 TTATCAAATTTTTATAG-GAGGT
*
9900 TTATCAAA-TTTTATAGGAAGAT
1 TTATCAAATTTTTATAGG-AGGT
* *
9922 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAATTTTTATAG-GAGGT
9944 TTATCACAATTT
1 TTATCA-AATTT
9956 CATAGTGTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.02
22 25 0.52
23 21 0.44
24 1 0.02
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.41
Consensus pattern (22 bp):
TTATCAAATTTTTATAGGAGGT
Found at i:9969 original size:22 final size:22
Alignment explanation
Indices: 9922--10114 Score: 85
Period size: 22 Copynumber: 8.7 Consensus size: 22
9912 ATAGGAAGAT
* * *
9922 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCATAGTGTGA
*
9944 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
* *
9966 TTATCAAAACTTCAGAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
*
9988 TTACCAACAA-TTCATA-TG-GA
1 TTATCAA-AATTTCATAGTGTGA
* * * *** *
10008 GGTTTTTAAATTTTCATAACATGG
1 --TTATCAAAATTTCATAGTGTGA
* *
10032 TTATCAATATATCATA-TG-GA
1 TTATCAAAATTTCATAGTGTGA
* *
10052 GGTTATCAACATCTT-ATAGTGTTGG
1 --TTATCAAAAT-TTCATAGTG-TGA
* *
10077 TTATCAAAATTTCATTG-GTAA
1 TTATCAAAATTTCATAGTGTGA
10098 GTTATCAAAATTTCATA
1 -TTATCAAAATTTCATA
10115 TTGAGGTCTT
Statistics
Matches: 125, Mismatches: 32, Indels: 28
0.68 0.17 0.15
Matches are distributed among these distances:
20 3 0.02
21 4 0.03
22 99 0.79
23 17 0.14
24 1 0.01
25 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Found at i:10150 original size:22 final size:22
Alignment explanation
Indices: 10126--10246 Score: 75
Period size: 22 Copynumber: 5.5 Consensus size: 22
10116 TGAGGTCTTC
* *
10126 AAATTTCCTTAGAGAGGTTAACA
1 AAATTTCATAAGA-AGGTTAACA
*
10149 AAATTTCATAAGAAGGTTAAAA
1 AAATTTCATAAGAAGGTTAACA
* * ** *
10171 AAATTT-ATAAAAAGATTCTCG
1 AAATTTCATAAGAAGGTTAACA
** **
10192 AAATTTCAT-AGTATCGTTATTA
1 AAATTTCATAAG-AAGGTTAACA
* * *
10214 AAATTTTATAGGAAGGTTATCA
1 AAATTTCATAAGAAGGTTAACA
10236 AAATTTCATAA
1 AAATTTCATAA
10247 TGAGATCATA
Statistics
Matches: 72, Mismatches: 23, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
21 16 0.22
22 44 0.61
23 12 0.17
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (22 bp):
AAATTTCATAAGAAGGTTAACA
Found at i:10350 original size:2 final size:2
Alignment explanation
Indices: 10343--10381 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
10333 TTAAAACTAG
*
10343 TA TA TA TA TA TA TA TA TA TG 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
10382 CTTTTCTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12661 original size:35 final size:35
Alignment explanation
Indices: 12614--12685 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
12604 GATCCTCTTT
* *
12614 GATACTGTAGTTAGTAGGA-TATTAAGGTGTTTGGA
1 GATACTGAAGTTAGT-GGAGTATTAAGGTGTTTAGA
*
12649 GATACTGAAGTTAGTGGAGTCTTAAGGTGTTTAGA
1 GATACTGAAGTTAGTGGAGTATTAAGGTGTTTAGA
12684 GA
1 GA
12686 GTTTAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 3 0.09
35 30 0.91
ACGTcount: A:0.29, C:0.04, G:0.32, T:0.35
Consensus pattern (35 bp):
GATACTGAAGTTAGTGGAGTATTAAGGTGTTTAGA
Found at i:12766 original size:2 final size:2
Alignment explanation
Indices: 12759--12783 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12749 AAATACATAC
12759 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12784 CAGGGTGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14244 original size:22 final size:21
Alignment explanation
Indices: 14153--14277 Score: 88
Period size: 22 Copynumber: 5.8 Consensus size: 21
14143 ATAGGAAAGT
* *
14153 TTATTAAAATTTCATAGTTAGG
1 TTATCAAAATTTCATAGGT-GG
* * * *
14175 TTATCAAAATCTCTTATGGAGT
1 TTATCAAAATTTCATA-GGTGG
* * **
14197 TTATCACAATTTTATAGGTAA
1 TTATCAAAATTTCATAGGTGG
*
14218 TTATCAAAATTTCATATGTTGG
1 TTATCAAAATTTCATA-GGTGG
* *
14240 TTATCAAAATTTGATAGGGTAG
1 TTATCAAAATTTCATA-GGTGG
*
14262 TTACCAAAATTTCATA
1 TTATCAAAATTTCATA
14278 AAAGTATTCA
Statistics
Matches: 77, Mismatches: 24, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
21 16 0.21
22 60 0.78
23 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.42
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGTGG
Found at i:14546 original size:2 final size:2
Alignment explanation
Indices: 14539--14566 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
14529 TTGCAAGTAG
14539 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
14567 TTAAGTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15350 original size:2 final size:2
Alignment explanation
Indices: 15343--15373 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15333 CATAGAGTAG
15343 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15374 GGTAATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16551 original size:28 final size:28
Alignment explanation
Indices: 16510--16565 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
16500 TTAACTATCC
**
16510 ATTTTGGGGTAAATTGACCCCTTAACTT
1 ATTTTGGGACAAATTGACCCCTTAACTT
**
16538 ATTTTGGGACAAATTGACCTTTTAACTT
1 ATTTTGGGACAAATTGACCCCTTAACTT
16566 TTAAAAACGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (28 bp):
ATTTTGGGACAAATTGACCCCTTAACTT
Found at i:22815 original size:19 final size:18
Alignment explanation
Indices: 22782--22818 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
22772 TTGAAATAAT
22782 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
22800 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
22819 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:24562 original size:15 final size:15
Alignment explanation
Indices: 24518--24562 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
24508 TGTTTAAGTG
*
24518 ACCCGAACCCGAATTA
1 ACCCGAACTC-AATTA
* *
24534 ACCCGAATTGAATTA
1 ACCCGAACTCAATTA
24549 ACCCGAACTCAATT
1 ACCCGAACTCAATT
24563 TATGGTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.38, C:0.31, G:0.11, T:0.20
Consensus pattern (15 bp):
ACCCGAACTCAATTA
Found at i:26569 original size:13 final size:14
Alignment explanation
Indices: 26551--26583 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
26541 ACTAGGAACA
26551 AGAAAAG-TAGAAG
1 AGAAAAGATAGAAG
26564 AGAAAAGAATAGAAG
1 AGAAAAG-ATAGAAG
26579 AGAAA
1 AGAAA
26584 GATTGTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
15 11 0.61
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.06
Consensus pattern (14 bp):
AGAAAAGATAGAAG
Found at i:29101 original size:19 final size:18
Alignment explanation
Indices: 29068--29104 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
29058 TTGAAATAAT
29068 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
29086 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
29105 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:30738 original size:19 final size:18
Alignment explanation
Indices: 30705--30741 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
30695 TTGAAATAAT
30705 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
30723 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
30742 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:33426 original size:17 final size:17
Alignment explanation
Indices: 33406--33438 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
33396 GGACCCGTGG
33406 CCGAACCCGAACCCGAT
1 CCGAACCCGAACCCGAT
*
33423 CCGAATCCGAACCCGA
1 CCGAACCCGAACCCGA
33439 AAATACCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.45, G:0.18, T:0.06
Consensus pattern (17 bp):
CCGAACCCGAACCCGAT
Found at i:33459 original size:15 final size:15
Alignment explanation
Indices: 33429--33476 Score: 78
Period size: 16 Copynumber: 3.1 Consensus size: 15
33419 CGATCCGAAT
33429 CCGAACCCGAAAATAC
1 CCGAACCCG-AAATAC
33445 CCGAACCCGAAATAC
1 CCGAACCCGAAATAC
33460 CCGAACCCGGAAATAC
1 CCGAACCC-GAAATAC
33476 C
1 C
33477 TGAAGTACCC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 14 0.45
16 17 0.55
ACGTcount: A:0.40, C:0.40, G:0.15, T:0.06
Consensus pattern (15 bp):
CCGAACCCGAAATAC
Found at i:38530 original size:25 final size:25
Alignment explanation
Indices: 38481--38531 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
38471 TTAGTAGAAT
*
38481 AATTGTAAAAGTTTATTTCTAAAAA
1 AATTGTAAAAGTATATTTCTAAAAA
38506 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGTAAAAG--TATATTTCTAAAAA
38532 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 6 0.26
27 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
AATTGTAAAAGTATATTTCTAAAAA
Found at i:41632 original size:60 final size:60
Alignment explanation
Indices: 41539--41699 Score: 270
Period size: 60 Copynumber: 2.7 Consensus size: 60
41529 GCTAATTACT
* *
41539 CAAATAAGGGCATAACGTT-TACCAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
* *
41599 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTTGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
41659 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGG
41700 CCTGGTGTCA
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
60 95 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
Found at i:41637 original size:31 final size:31
Alignment explanation
Indices: 41599--41702 Score: 117
Period size: 31 Copynumber: 3.4 Consensus size: 31
41589 TTAATTTGGC
41599 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * * **
41630 CAAATAAGGGTCTGATC-TT-T-TAATTTTGC-
1 CAAATAAGGGCCT-AACGTTATCGAA-AATGCT
41659 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
41690 CAAATAAGGGCCT
1 CAAATAAGGGCCT
41703 GGTGTCAGTT
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 2 0.04
29 16 0.28
30 8 0.14
31 29 0.51
32 2 0.04
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:41668 original size:29 final size:29
Alignment explanation
Indices: 41570--41668 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 29
41560 CCAAAATGCT
* *
41570 CAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGTCTGATCTTTTAATTTTGC
* * * **
41599 CAAATAAGGGCCT-AACGTTATCGAA-AATGC
1 CAAATAAGGGTCTGATC-TT-T-TAATTTTGC
41629 TCAAATAAGGGTCTGATCTTTTAATTTTGC
1 -CAAATAAGGGTCTGATCTTTTAATTTTGC
41659 CAAATAAGGG
1 CAAATAAGGG
41669 CCTAACGTTA
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
28 2 0.04
29 25 0.48
30 7 0.13
31 16 0.31
32 2 0.04
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (29 bp):
CAAATAAGGGTCTGATCTTTTAATTTTGC
Found at i:41875 original size:59 final size:60
Alignment explanation
Indices: 41733--41892 Score: 268
Period size: 60 Copynumber: 2.7 Consensus size: 60
41723 GTGAGACAGT
* ** *
41733 CCCTTATTTGAGCATTTTGGCAAACTTTAGGCCCTTATTTGGCCAAATTCAAAGATGGGC
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATCAGA
41793 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATT-AAAGATCAGA
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATCAGA
*
41852 CCCTTATTTGAGTATTTTGGCAAACGTTAGGCCCTTATTTG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
41893 AGCAATTAGC
Statistics
Matches: 95, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
59 47 0.49
60 48 0.51
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGATCAGA
Done.