Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014640.1 Corchorus capsularis cultivar CVL-1 contig14661, 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: 65494
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:6588 original size:2 final size:2
Alignment explanation
Indices: 6581--6606 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6571 TACTCACTCA
6581 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
6607 TTACGAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7176 original size:33 final size:30
Alignment explanation
Indices: 7134--7218 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 30
7124 AGAGCTCATT
7134 AAAGGAGTTAACACACTTTT-GTGCCCAAGTAAA
1 AAAGGAGTTAACACACTTTTAGTG-CCAAG---A
* *
7167 AAAGGAGTTAACGCACTTATTTATTGCCAAGA
1 AAAGGAGTTAACACAC-T-TTTAGTGCCAAGA
7199 AAAGGAGTTAACACACTTTT
1 AAAGGAGTTAACACACTTTT
7219 TGTCGTGACC
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
30 3 0.07
31 1 0.02
32 16 0.35
33 15 0.33
34 1 0.02
35 8 0.17
36 2 0.04
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (30 bp):
AAAGGAGTTAACACACTTTTAGTGCCAAGA
Found at i:7610 original size:2 final size:2
Alignment explanation
Indices: 7558--7591 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
7548 CAAAGCAAAG
7558 AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
7592 CTTTTGTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7616 original size:3 final size:3
Alignment explanation
Indices: 7608--7639 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
7598 TGCTTGATAT
7608 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
7640 GTAAGAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:11233 original size:22 final size:22
Alignment explanation
Indices: 11207--11253 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
11197 ATTTATTCAT
11207 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
**
11229 TATTAATTAGTTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
11251 TAT
1 TAT
11254 AGTATAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:11412 original size:11 final size:11
Alignment explanation
Indices: 11396--11431 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
11386 TAATATATAG
11396 TATTAATTA-A
1 TATTAATTAGA
11406 CTATTAATTAGA
1 -TATTAATTAGA
11418 TATTAATTAGA
1 TATTAATTAGA
11429 TAT
1 TAT
11432 AGTATAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 23 0.96
12 1 0.04
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (11 bp):
TATTAATTAGA
Found at i:11517 original size:178 final size:178
Alignment explanation
Indices: 11218--11772 Score: 772
Period size: 178 Copynumber: 3.0 Consensus size: 178
11208 ATTAATTAAC
* *
11218 TATTAATTAGATATTAATTAGTTATTAATTAGATATAGTATAATGGATGATTAAGGAGGGGCTTT
1 TATTAATTATATATTAATTAGATATTAATTAGATATAGTATAATGGATGATTAAGGA-GGGCTTT
11283 AAATTAATATGTTAGATGTGAGAAATTACCAAAATGGGGCGATAAGGTGGCACCATGTTAAAAGT
65 AAATTAATATGTTAGATGTGAGAAATTACCAAAATGGGGCGATAAGGTGGCACCATGTTAAAAGT
*
11348 TGAAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAAATAATAT-ATAG
130 TGAAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAAATAATATAATAA
11396 TATTAATTA-ACTATTAATTAGATATTAATTAGATATAGTATAATGGATGATTAAGGAGGGACTT
1 TATTAATTATA-TATTAATTAGATATTAATTAGATATAGTATAATGGATGATTAAGGAGGG-CTT
*
11460 TAAATTAATATGTTAGATGTGAGAAATTACCAAAATGGGGTGATAAGGTGGCACCATGTTAAAAG
64 TAAATTAATATGTTAGATGTGAGAAATTACCAAAATGGGGCGATAAGGTGGCACCATGTTAAAAG
*
11525 TTGAAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAAATATTCCCTTTTAATAATATTGAA
129 TTGAAAGGGCTTGTTAGTAATTTCCATAGGGGAC-AAAA-A--------TAAT-ATAAT-AA
11587 TTTATTCATTATTAATTAACTATTAATTAGATATTAATTAGATATAGTATAATGGATGATTAAGG
1 --TATT-A--ATT-A-T-A-TATTAATTAGATATTAATTAGATATAGTATAATGGATGATTAAGG
* *
11652 AGATGCTTTAAAAATTAATATGTTAGATGTGAGAAATTACCAAAATGGGACGATAAGGTGGCACC
57 AG-GGCTTT--AAATTAATATGTTAGATGTGAGAAATTACCAAAATGGGGCGATAAGGTGGCACC
*
11717 AGGTTAAAAGTTGAAAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAAATAATAT
119 ATGTTAAAAGTTG-AAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAAATAATAT
11773 GTAAAATAAT
Statistics
Matches: 341, Mismatches: 8, Indels: 42
0.87 0.02 0.11
Matches are distributed among these distances:
177 4 0.01
178 155 0.45
179 4 0.01
180 1 0.00
188 4 0.01
189 2 0.01
190 1 0.00
191 1 0.00
192 2 0.01
193 8 0.02
194 1 0.00
196 3 0.01
197 1 0.00
200 53 0.16
201 2 0.01
202 68 0.20
203 31 0.09
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (178 bp):
TATTAATTATATATTAATTAGATATTAATTAGATATAGTATAATGGATGATTAAGGAGGGCTTTA
AATTAATATGTTAGATGTGAGAAATTACCAAAATGGGGCGATAAGGTGGCACCATGTTAAAAGTT
GAAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAAATAATATAATAA
Found at i:11612 original size:11 final size:11
Alignment explanation
Indices: 11596--11631 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
11586 ATTTATTCAT
11596 TATTAATTA-A
1 TATTAATTAGA
11606 CTATTAATTAGA
1 -TATTAATTAGA
11618 TATTAATTAGA
1 TATTAATTAGA
11629 TAT
1 TAT
11632 AGTATAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 23 0.96
12 1 0.04
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (11 bp):
TATTAATTAGA
Found at i:11783 original size:202 final size:199
Alignment explanation
Indices: 11396--11783 Score: 636
Period size: 202 Copynumber: 1.9 Consensus size: 199
11386 TAATATATAG
11396 TATTAATTAACTATTAATTAGATATTAATTAGATATAGTATAATGGATGATTAAGGAGGGACTTT
1 TATTAATTAACTATTAATTAGATATTAATTAGATATAGTATAATGGATGATTAAGGAGGGACTTT
** *
11461 AAATTAATATGTTAGATGTGAGAAATTACCAAAATGGGGTGATAAGGTGGCACCATGTTAAAAGT
66 AAATTAATATGTTAGATGTGAGAAATTACCAAAATGGGACGATAAGGTGGCACCAGGTTAAAAGT
* * **
11526 TGAAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAAATATTCCCTTTTAATAATATTGAATTTA
131 TGAAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAAATAAT-CATTAAAATAATATTGAATTTA
11591 TTCAT
195 TTCAT
*
11596 TATTAATTAACTATTAATTAGATATTAATTAGATATAGTATAATGGATGATTAAGGAGATG-CTT
1 TATTAATTAACTATTAATTAGATATTAATTAGATATAGTATAATGGATGATTAAGGAG-GGACTT
11660 TAAAAATTAATATGTTAGATGTGAGAAATTACCAAAATGGGACGATAAGGTGGCACCAGGTTAAA
65 T--AAATTAATATGTTAGATGTGAGAAATTACCAAAATGGGACGATAAGGTGGCACCAGGTTAAA
11725 AGTTGAAAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAAATAAT-ATGTAAAATAATA
128 AGTTG-AAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAAATAATCAT-TAAAATAATA
11784 GCCCACACTG
Statistics
Matches: 175, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
200 62 0.35
201 2 0.01
202 72 0.41
203 39 0.22
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (199 bp):
TATTAATTAACTATTAATTAGATATTAATTAGATATAGTATAATGGATGATTAAGGAGGGACTTT
AAATTAATATGTTAGATGTGAGAAATTACCAAAATGGGACGATAAGGTGGCACCAGGTTAAAAGT
TGAAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAAATAATCATTAAAATAATATTGAATTTAT
TCAT
Found at i:13848 original size:437 final size:439
Alignment explanation
Indices: 13018--13946 Score: 1574
Period size: 437 Copynumber: 2.1 Consensus size: 439
13008 TAAACTAATA
* * * *
13018 TTTTTTGTTGGATTATTTATCTAATGATCCTTATACTTTTATGCTTTATGATATTTAGTCATTTA
1 TTTTTTATT-GATTATTTATCTAATGATCCTCATACTTTTATACTTTATGCTATTTAGTCATTTA
* * * * *
13083 TAATTATAGGTTGGACAATTTAACGCGTTCTCATTTATTATTGTATTTTTTTTCCTATTTGTCTG
65 CAATTATAGGTTGGACAATTTAACGCATTCGCATTTATTATTGTATTTTTTTTCCTATTTATCCG
13148 ATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCAAGATCTACAATTTTCATGAAGAACTCA
130 ATTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCAAGATCTACAATTTTCATGAAGAACTCA
13213 AAAGTCAATTTTAATGTTTTGATTTTAAAAAATGCTTCCGAAATTTTGTGGATTTGATTGCCAGT
195 AAAGTCAATTTTAATGTTTTGATTTTAAAAAATGCTTCCGAAATTTTGTGGATTTGATTGCCAGT
13278 CAATTTAATATCGTATAATTTTTTGTCCACATGTCCGATTGAAGTTATTGAAGTGTCGGTTAGAA
260 CAATTTAATATCGTATAATTTTTTGTCCACATGTCCGATTGAAGTTATTGAAGTGTCGGTTAGAA
* ** *
13343 GGTTATTGCATGATTTATGACTTTCATGAAAGACCCGAAAGTTAAATTTGATCTACGAGTTTCAT
325 GGTTATTGCATGATTTACGACTTTCATGAAAGACCCGAAAACTAAATTTGATCTACGAGTTCCAT
*
13408 GAAGGTTTCAAAAGGGAGTTTTTATGTTCAAGATCTCCATTAACAAACAT
390 GAAGGGTTCAAAAGGGAGTTTTTATGTTCAAGATCTCCATTAACAAACAT
*
13458 TTTTTTATT-ATTATTTATCTAATGATCCTCATACTTTTATACTTTATGCTATTTAGTCCTTTAC
1 TTTTTTATTGATTATTTATCTAATGATCCTCATACTTTTATACTTTATGCTATTTAGTCATTTAC
* *
13522 AATTATAGGTTGGACTATTTAACGCATTCGCATTTATTTTTGTA-TTTTTTTCCTATTTATCCGA
66 AATTATAGGTTGGACAATTTAACGCATTCGCATTTATTATTGTATTTTTTTTCCTATTTATCCGA
* *
13586 TTAAGGTGATTCAAGTGTCTATTAAAAGGTTATTTCATGATCTACAATTTTCATGAAGAACTCAA
131 TTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCAAGATCTACAATTTTCATGAAGAACTCAA
* * * * *
13651 AAGTCAATTTTAATGTTTTGATTTTAAAAAATGCTTCTGCAATTTTGTGGTTTTGATTGTCGGTC
196 AAGTCAATTTTAATGTTTTGATTTTAAAAAATGCTTCCGAAATTTTGTGGATTTGATTGCCAGTC
13716 AATTTAATATCGTATAATTTTTTGTCCACATGTCCGATTGAAGTTATTGAAGTGTCGGTTAGAAG
261 AATTTAATATCGTATAATTTTTTGTCCACATGTCCGATTGAAGTTATTGAAGTGTCGGTTAGAAG
* *
13781 GTTATTGCATGATTTACGACTTTCATGAAGGACCCGAAAACTAAATTTGATCTCCGAGTTCCATG
326 GTTATTGCATGATTTACGACTTTCATGAAAGACCCGAAAACTAAATTTGATCTACGAGTTCCATG
13846 AAGGGTTCAAAAGGGAGTTTTTATGTTCAAGATCTCCATTAACAAACAT
391 AAGGGTTCAAAAGGGAGTTTTTATGTTCAAGATCTCCATTAACAAACAT
* *
13895 TTTTTTGTTGGATTATTTATCTAATGATCCTCATACTTTCATACTTTATGCT
1 TTTTTTATT-GATTATTTATCTAATGATCCTCATACTTTTATACTTTATGCT
13947 GTTCATGATC
Statistics
Matches: 459, Mismatches: 28, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
437 321 0.70
438 90 0.20
439 40 0.09
440 8 0.02
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (439 bp):
TTTTTTATTGATTATTTATCTAATGATCCTCATACTTTTATACTTTATGCTATTTAGTCATTTAC
AATTATAGGTTGGACAATTTAACGCATTCGCATTTATTATTGTATTTTTTTTCCTATTTATCCGA
TTAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCAAGATCTACAATTTTCATGAAGAACTCAA
AAGTCAATTTTAATGTTTTGATTTTAAAAAATGCTTCCGAAATTTTGTGGATTTGATTGCCAGTC
AATTTAATATCGTATAATTTTTTGTCCACATGTCCGATTGAAGTTATTGAAGTGTCGGTTAGAAG
GTTATTGCATGATTTACGACTTTCATGAAAGACCCGAAAACTAAATTTGATCTACGAGTTCCATG
AAGGGTTCAAAAGGGAGTTTTTATGTTCAAGATCTCCATTAACAAACAT
Found at i:17564 original size:10 final size:10
Alignment explanation
Indices: 17549--17587 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
17539 ACCGAATGAG
17549 AAACAAAAAA
1 AAACAAAAAA
*
17559 AAACAAAAGA
1 AAACAAAAAA
17569 AAACAAAAGAA
1 AAACAAAA-AA
17580 AAA-AAAAA
1 AAACAAAAA
17588 CTTAAGTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 1 0.04
10 21 0.81
11 4 0.15
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (10 bp):
AAACAAAAAA
Found at i:17574 original size:20 final size:20
Alignment explanation
Indices: 17549--17586 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17539 ACCGAATGAG
17549 AAACAAAA-AAAAACAAAAGA
1 AAACAAAAGAAAAA-AAAAGA
17569 AAACAAAAGAAAAAAAAA
1 AAACAAAAGAAAAAAAAA
17587 ACTTAAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (20 bp):
AAACAAAAGAAAAAAAAAGA
Found at i:19387 original size:30 final size:29
Alignment explanation
Indices: 19324--19393 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
19314 ACCGAACCGT
***
19324 CAAATAAGCCCCTGAACTATTATTTCAGC
1 CAAATAAGCCCCTGAACTATTATAAAAGC
* *
19353 CAAATAAGCTCCTGAACTCTTATAAAAGGC
1 CAAATAAGCCCCTGAACTATTATAAAA-GC
19383 CAAATAAGCCC
1 CAAATAAGCCC
19394 TATTGCCAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 22 0.65
30 12 0.35
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTATAAAAGC
Found at i:21225 original size:12 final size:12
Alignment explanation
Indices: 21197--21238 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
21187 AAAAACATTT
*
21197 AAAGAAGAAGAAG
1 AAAGAA-AAAAAG
21210 -AAGAAAAAAAG
1 AAAGAAAAAAAG
*
21221 AAAGAAAGAAAG
1 AAAGAAAAAAAG
21233 AAAGAA
1 AAAGAA
21239 GCTGGTCGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 5 0.19
12 21 0.81
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAG
Found at i:21316 original size:16 final size:14
Alignment explanation
Indices: 21288--21325 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
21278 CGGCAACTAG
21288 CTTTTTTCTTTCTT
1 CTTTTTTCTTTCTT
21302 CTTTTTTC-TTCTT
1 CTTTTTTCTTTCTT
*
21315 CTTCTTTCTTT
1 CTTTTTTCTTT
21326 AAAATGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
CTTTTTTCTTTCTT
Found at i:27381 original size:15 final size:14
Alignment explanation
Indices: 27356--27385 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
27346 ATAAAAAATA
27356 AATATTTTTATTTT
1 AATATTTTTATTTT
27370 AATATATTTTATTTT
1 AATAT-TTTTATTTT
27385 A
1 A
27386 TTGAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATATTTTTATTTT
Found at i:28617 original size:33 final size:32
Alignment explanation
Indices: 28579--28640 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
28569 TGGTTAACTC
*
28579 ATTTTCTGTTGTTTGGATGTTTTTATGAAAGAT
1 ATTTTCTGTTGTTTGGATGGTTTT-TGAAAGAT
* *
28612 ATTTTCTTTTGTTTGGTTGGTTTTTGAAA
1 ATTTTCTGTTGTTTGGATGGTTTTTGAAA
28641 ATTTTCATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 5 0.19
33 21 0.81
ACGTcount: A:0.18, C:0.03, G:0.21, T:0.58
Consensus pattern (32 bp):
ATTTTCTGTTGTTTGGATGGTTTTTGAAAGAT
Found at i:28914 original size:33 final size:33
Alignment explanation
Indices: 28872--28937 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
28862 TATTGTTTAA
28872 GGCCCTATATATACGGTCTGTAGCCCATATATG
1 GGCCCTATATATACGGTCTGTAGCCCATATATG
**
28905 GGCCCTATATATTTGGTCTGTAGCCCATATATG
1 GGCCCTATATATACGGTCTGTAGCCCATATATG
28938 CCTCTATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (33 bp):
GGCCCTATATATACGGTCTGTAGCCCATATATG
Found at i:29122 original size:2 final size:2
Alignment explanation
Indices: 29115--29141 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29105 AAATTTGCAG
29115 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
29142 GATAATAGAA
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:30165 original size:31 final size:31
Alignment explanation
Indices: 30123--30181 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
30113 AAACAGGAGT
30123 CTTAACTAATTACACCATAGCGAAGTTCAAG
1 CTTAACTAATTACACCATAGCGAAGTTCAAG
* *
30154 CTTAGCTAATTACACCATAGCTAAGTTC
1 CTTAACTAATTACACCATAGCGAAGTTC
30182 CAATCACTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.29
Consensus pattern (31 bp):
CTTAACTAATTACACCATAGCGAAGTTCAAG
Found at i:30726 original size:61 final size:61
Alignment explanation
Indices: 30652--30773 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
30642 CTTTTTCTCT
*
30652 CTTCATTTGTAGGCATGTTAAGCGCCCTCCATACTGCTATAGCCAATCCCACTACAAGAAC
1 CTTCATTTGTAGGCATGCTAAGCGCCCTCCATACTGCTATAGCCAATCCCACTACAAGAAC
30713 CTTCATTTGTAGGCATGCTAAGCGCCCTCCATACTGCTATAGCCAATCCCACTACAAGAAC
1 CTTCATTTGTAGGCATGCTAAGCGCCCTCCATACTGCTATAGCCAATCCCACTACAAGAAC
30774 AATGATAACG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (61 bp):
CTTCATTTGTAGGCATGCTAAGCGCCCTCCATACTGCTATAGCCAATCCCACTACAAGAAC
Found at i:36987 original size:72 final size:71
Alignment explanation
Indices: 36855--36994 Score: 244
Period size: 72 Copynumber: 2.0 Consensus size: 71
36845 TTATAACATC
*
36855 TGTGAATGTTTGTTGGAGTCCCCCAATCATCGCTTTTTCAAATTGAACACAGATGAGTCATCTAC
1 TGTGAATGTTTGTTGGAGTCCCCCAATCATCGCTTTTTCAAATTAAACACAGATGAGTCATCTAC
36920 GGGTAG
66 GGGTAG
* *
36926 TGTGAATGTTTGTTGGAGTCCCCCAATCCATGGCTTTTTCAAATTAAACACAGATGGGTCATCTA
1 TGTGAATGTTTGTTGGAGTCCCCCAAT-CATCGCTTTTTCAAATTAAACACAGATGAGTCATCTA
36991 CGGG
65 CGGG
36995 CAGTCCGAGT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
71 27 0.42
72 38 0.58
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (71 bp):
TGTGAATGTTTGTTGGAGTCCCCCAATCATCGCTTTTTCAAATTAAACACAGATGAGTCATCTAC
GGGTAG
Found at i:37478 original size:1 final size:1
Alignment explanation
Indices: 37472--37506 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
37462 CCTTTTCACC
* *
37472 AAAAAAAAAAAAAAAAAAAAAAGAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
37507 CCAAACTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:45916 original size:12 final size:12
Alignment explanation
Indices: 45895--45938 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
45885 AAGCGATAGC
45895 AGTGGGAGTGGT
1 AGTGGGAGTGGT
*
45907 AGTGGTAGTGGT
1 AGTGGGAGTGGT
* *
45919 AGTGGGAGCGGG
1 AGTGGGAGTGGT
45931 AGTGGGAG
1 AGTGGGAG
45939 CAGTAGTAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.18, C:0.02, G:0.59, T:0.20
Consensus pattern (12 bp):
AGTGGGAGTGGT
Found at i:45939 original size:12 final size:12
Alignment explanation
Indices: 45895--45945 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
45885 AAGCGATAGC
*
45895 AGTGGGAGTGGT
1 AGTGGGAGCGGT
* *
45907 AGTGGTAGTGGT
1 AGTGGGAGCGGT
*
45919 AGTGGGAGCGGG
1 AGTGGGAGCGGT
*
45931 AGTGGGAGCAGT
1 AGTGGGAGCGGT
45943 AGT
1 AGT
45946 AGTGATAGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.20, C:0.04, G:0.55, T:0.22
Consensus pattern (12 bp):
AGTGGGAGCGGT
Found at i:46734 original size:42 final size:42
Alignment explanation
Indices: 46675--46760 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
46665 AATATGATGG
46675 TCAGGGAGGTGAGAAAACTAAGCAATCGAAAAATTTCAAATC
1 TCAGGGAGGTGAGAAAACTAAGCAATCGAAAAATTTCAAATC
*
46717 TCAGGGAGGTGAGAAAACTAAGCAATCGAAAAATTTCAGATC
1 TCAGGGAGGTGAGAAAACTAAGCAATCGAAAAATTTCAAATC
46759 TC
1 TC
46761 GGATCAAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (42 bp):
TCAGGGAGGTGAGAAAACTAAGCAATCGAAAAATTTCAAATC
Found at i:51758 original size:12 final size:12
Alignment explanation
Indices: 51741--51831 Score: 64
Period size: 12 Copynumber: 7.7 Consensus size: 12
51731 ACGTAGACAT
*
51741 AGAAGGAGTAGA
1 AGAAGGAGAAGA
51753 AGAAGGAGAAGA
1 AGAAGGAGAAGA
*
51765 AGAAGAAGAAGA
1 AGAAGGAGAAGA
*
51777 AG-AGGAAGAAGG
1 AGAAGG-AGAAGA
* * *
51789 GGAAGGGGAGGA
1 AGAAGGAGAAGA
*
51801 GGAA-GACGAAGA
1 AGAAGGA-GAAGA
51813 AG-AGGAAGAAGA
1 AGAAGG-AGAAGA
51825 AG-AGGAG
1 AGAAGGAG
51832 GAGTACGACG
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
11 6 0.10
12 53 0.84
13 4 0.06
ACGTcount: A:0.52, C:0.01, G:0.46, T:0.01
Consensus pattern (12 bp):
AGAAGGAGAAGA
Found at i:51806 original size:36 final size:36
Alignment explanation
Indices: 51766--51855 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 36
51756 AGGAGAAGAA
** *
51766 GAAGAAGAAGAAGAGGAAGAAGGGGAAGG-GGAGGAG
1 GAAGAAGAAGAAGAGGAAGAAGAAG-AGGAGGAGGAC
* *
51802 GAAGACGAAGAAGAGGAAGAAGAAGAGGAGGAGTAC
1 GAAGAAGAAGAAGAGGAAGAAGAAGAGGAGGAGGAC
*
51838 GACGAAGAAGAAGAGGAA
1 GAAGAAGAAGAAGAGGAA
51856 AGTGAAGCTG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
35 3 0.07
36 43 0.93
ACGTcount: A:0.50, C:0.03, G:0.46, T:0.01
Consensus pattern (36 bp):
GAAGAAGAAGAAGAGGAAGAAGAAGAGGAGGAGGAC
Found at i:51847 original size:3 final size:3
Alignment explanation
Indices: 51750--51827 Score: 66
Period size: 3 Copynumber: 26.0 Consensus size: 3
51740 TAGAAGGAGT
* * * * * *
51750 AGA AGA AGG AGA AGA AGA AGA AGA AGA AGA GGA AGA AGG GGA AGG GGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * *
51798 GGA GGA AGA CGA AGA AGA GGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
51828 GGAGGAGTAC
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.54, C:0.01, G:0.45, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:59706 original size:19 final size:19
Alignment explanation
Indices: 59682--59718 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
59672 ATGCATACAT
59682 ATTCATTTGCTCTT-CTAAC
1 ATTCATTTG-TCTTGCTAAC
59701 ATTCATTTGTCTTGCTAA
1 ATTCATTTGTCTTGCTAA
59719 GTAGATGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.49
Consensus pattern (19 bp):
ATTCATTTGTCTTGCTAAC
Found at i:63708 original size:15 final size:14
Alignment explanation
Indices: 63684--63714 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
63674 AAACTAACAC
63684 AAAAAAAAAAAATA
1 AAAAAAAAAAAATA
63698 AAAAAATAAAAAATA
1 AAAAAA-AAAAAATA
63713 AA
1 AA
63715 GATTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAAAAAAAAAATA
Done.