Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009706.1 Corchorus capsularis cultivar CVL-1 contig09727, 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: 100089
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:14835 original size:23 final size:21
Alignment explanation
Indices: 14809--14852 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
14799 GTTGGGCTGT
14809 TAAAAGAGAAAAAAGAAAAAGAA
1 TAAAAGA-AAAAAA-AAAAAGAA
14832 TAAAAGAAAAAAAAAAAAGAA
1 TAAAAGAAAAAAAAAAAAGAA
14853 CAAACGGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.38
22 6 0.29
23 7 0.33
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05
Consensus pattern (21 bp):
TAAAAGAAAAAAAAAAAAGAA
Found at i:16621 original size:463 final size:458
Alignment explanation
Indices: 15746--16648 Score: 1188
Period size: 463 Copynumber: 2.0 Consensus size: 458
15736 GGGACGGGTC
* * * * * *
15746 AAGACCTATTGTTCCATAATCGGAACAATAATTGACAGTTTTGTCCCCCCTGTTGCCAACTTTAT
1 AAGACCTAGTGGTCCATAATCGAAACAATAATTGACAGCTTTATCCCCCATGTTGCCAACTTTAT
* * *
15811 CAAATATTTCGTATACACATTTTACAAGAACCTGTTTGAAGTTGGAGACAATATTCTTTATGGGG
66 CAAATATTCCGTATACAAATTTTACAAGAACCTGGTTGAAGTTGGAGACAATATTCTTTATGGGG
* ** * * * *
15876 AAGATGGAAGAGTATGTGTCGTCAACATACTTTTTCACCATGCGCGATTCAGAAGGAGGTCAGAA
131 AAGATGGAAGAGAATACGTCGTCAACATACATGTTCACCAAGCGCAATTCAGAAGGAGGTCAGAA
* * ** * *
15941 TTTACCGGAGAGTTATATGGTTCACTGATCAAGAAATTGAACCTCTGAGTTTTATGGGAGGGATA
196 ATTACCGGAGAGTTATATGGTCCACAAATCAAGAAATTGAACCTCTAAGTTATATGGGAGGGATA
* * ** * *
16006 TGGAACTAATTGTGAAAAATAAATTGGAAATAATGTCATTGTAATTTTGACAAAATCTCATAGAA
261 TGGAACTAATTGTGAAAAATAAATTGAAAAAAAAATCATTGTAATTTTGACAAAATCCCATAAAA
** * * *
16071 ATAAAATTGTCTAGATCGGCCTCTTTTTTTGATGTCATCGAGATGATAAAATTGGTAATAAATAA
326 ATAAAATTGTCTAGAAAGGCCCCTTTTTTTGATGTCATAGAGATAATAAAATTGGTAATAAATAA
* *
16136 AAATTGACTCTGATACGTATCTTGATTTGAAAACTATTATTTATA-AAAATATAGAGCGAGGCAG
391 AAATTGACTATGATACGTATCTTGATTTGAAAACTATAATTTATACAAAATATAGAGCGAGGCAG
16200 GTT
456 GTT
* * *
16203 AAGACCTAGTGGTCCATAATCGAAACAATATTTGGCAGCTTTATTCCCCATGTTGCCAACTTTAT
1 AAGACCTAGTGGTCCATAATCGAAACAATAATTGACAGCTTTATCCCCCATGTTGCCAACTTTAT
* ** *
16268 CAAATATTCCGTATACAAATTTTCATATTACGAGATTTAGGTTGAGGTTGGAGACAATATTCTTT
66 CAAATATTCCGTATACAAATTTT-ACA--A-GA-ACCT-GGTTGAAGTTGGAGACAATATTCTTT
* * ** *
16333 ATGGGGAAGATGGAAGAGAATACGTTGTCGACATACATGTTCACCAAAG-TTAATTCAGAAGTAG
125 ATGGGGAAGATGGAAGAGAATACGTCGTCAACATACATGTTCACC-AAGCGCAATTCAGAAGGAG
* *
16397 GTCA-ACAATTACTGGAGAGTTATATGGTCCACAAATCAAGAGATTG-ACCTCTAAGTTATATGG
189 GTCAGA-AATTACCGGAGAGTTATATGGTCCACAAATCAAGAAATTGAACCTCTAAGTTATATGG
* *
16460 GAGGGGTATGGAACTAATTGTGTAAAATAAATTGAAAAAAAAAAATCATTGTAATTTTGACAAAA
253 GAGGGATATGGAACTAATTGTGAAAAATAAATTG--AAAAAAAAATCATTGTAATTTTGACAAAA
16525 -CCCATAAAAATAAAATTGTCTAGAAAGGCCCCTTTTTTTGATGTCATTAG-GATAATAAAATTG
316 TCCCATAAAAATAAAATTGTCTAGAAAGGCCCCTTTTTTTGATGTCA-TAGAGATAATAAAATTG
* *
16588 GTAATAAATAAAAATTGGCTATGATATGTATCTTGATTTGAAAACTATAATTTATACAAAA
380 GTAATAAATAAAAATTGACTATGATACGTATCTTGATTTGAAAACTATAATTTATACAAAA
16649 GCATATAACA
Statistics
Matches: 381, Mismatches: 53, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
457 77 0.20
458 2 0.01
460 1 0.00
461 2 0.01
462 50 0.13
463 216 0.57
464 33 0.09
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.32
Consensus pattern (458 bp):
AAGACCTAGTGGTCCATAATCGAAACAATAATTGACAGCTTTATCCCCCATGTTGCCAACTTTAT
CAAATATTCCGTATACAAATTTTACAAGAACCTGGTTGAAGTTGGAGACAATATTCTTTATGGGG
AAGATGGAAGAGAATACGTCGTCAACATACATGTTCACCAAGCGCAATTCAGAAGGAGGTCAGAA
ATTACCGGAGAGTTATATGGTCCACAAATCAAGAAATTGAACCTCTAAGTTATATGGGAGGGATA
TGGAACTAATTGTGAAAAATAAATTGAAAAAAAAATCATTGTAATTTTGACAAAATCCCATAAAA
ATAAAATTGTCTAGAAAGGCCCCTTTTTTTGATGTCATAGAGATAATAAAATTGGTAATAAATAA
AAATTGACTATGATACGTATCTTGATTTGAAAACTATAATTTATACAAAATATAGAGCGAGGCAG
GTT
Found at i:16951 original size:20 final size:20
Alignment explanation
Indices: 16926--16963 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16916 TTCAGTAAGC
*
16926 AAATATACATTGTATATTGA
1 AAATATACATTGAATATTGA
16946 AAATATACATTGAATATT
1 AAATATACATTGAATATT
16964 CAATAAGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (20 bp):
AAATATACATTGAATATTGA
Found at i:17792 original size:26 final size:26
Alignment explanation
Indices: 17762--17814 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
17752 AGTTTACAGT
* *
17762 GAAAACAAATATTGTTTATTCAGTAA
1 GAAAACAAACATTGTATATTCAGTAA
* *
17788 GAAAATATACATTGTATATTCAGTAA
1 GAAAACAAACATTGTATATTCAGTAA
17814 G
1 G
17815 CAAGTGGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (26 bp):
GAAAACAAACATTGTATATTCAGTAA
Found at i:18877 original size:15 final size:15
Alignment explanation
Indices: 18857--18887 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
18847 AATACGTATC
18857 TTGTTTTGAAAACTA
1 TTGTTTTGAAAACTA
18872 TTGTTTTGAAAACTA
1 TTGTTTTGAAAACTA
18887 T
1 T
18888 AATTTATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (15 bp):
TTGTTTTGAAAACTA
Found at i:19671 original size:16 final size:16
Alignment explanation
Indices: 19650--19684 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
19640 GGTTGGAGAC
*
19650 AATATTCTTTATAGGG
1 AATATTCTTTATAGAG
19666 AATATTCTTTATAGAG
1 AATATTCTTTATAGAG
19682 AAT
1 AAT
19685 GCGACGGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (16 bp):
AATATTCTTTATAGAG
Found at i:21056 original size:14 final size:14
Alignment explanation
Indices: 21039--21074 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
21029 AACTTCAAAG
*
21039 ACATGACATGAGTT
1 ACATGACATGAGTC
21053 ACATGACATGAGTC
1 ACATGACATGAGTC
21067 ACATGACA
1 ACATGACA
21075 GAAGCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (14 bp):
ACATGACATGAGTC
Found at i:22128 original size:13 final size:13
Alignment explanation
Indices: 22110--22135 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22100 CATAAGGGGC
22110 AAAAAAAAAACAA
1 AAAAAAAAAACAA
22123 AAAAAAAAAACAA
1 AAAAAAAAAACAA
22136 CAACAACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:24129 original size:31 final size:31
Alignment explanation
Indices: 24092--24156 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
24082 TTGGGTTATC
** *
24092 AGTCTCCAGATCTTTAGATTTTGGATGTTTG
1 AGTCTCCAGATCCCTAGATCTTGGATGTTTG
24123 AGTCTCCAGATCCCTAGATCTTGGATGTTTG
1 AGTCTCCAGATCCCTAGATCTTGGATGTTTG
24154 AGT
1 AGT
24157 TAGTTCAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (31 bp):
AGTCTCCAGATCCCTAGATCTTGGATGTTTG
Found at i:30167 original size:21 final size:21
Alignment explanation
Indices: 30143--30191 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
30133 TAGATTTAGA
* * * *
30143 TTTAATTTACTTTGTTTTGTT
1 TTTAATTTAATTTGCTATCTT
*
30164 TTTAGTTTAATTTGCTATCTT
1 TTTAATTTAATTTGCTATCTT
30185 TTTAATT
1 TTTAATT
30192 AATCTCTTTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.06, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTAATTTAATTTGCTATCTT
Found at i:32518 original size:51 final size:50
Alignment explanation
Indices: 32437--32536 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 50
32427 TCTTGAAAAA
* *
32437 TCAATCGACAGATTGCTTTTTCATCCCCTAATAGAAGTATTTGGAAATTC
1 TCAATCGACAGATTGCTTTTTCATCCCCTAATAGAACTATTTGAAAATTC
* *
32487 TCAATCGACATATTGCCTTTTTCATCTCCTAATAGAACTATTTGAAAATT
1 TCAATCGACAGATTG-CTTTTTCATCCCCTAATAGAACTATTTGAAAATT
32537 GAAAACTCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 14 0.31
51 31 0.69
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (50 bp):
TCAATCGACAGATTGCTTTTTCATCCCCTAATAGAACTATTTGAAAATTC
Found at i:35765 original size:45 final size:45
Alignment explanation
Indices: 35698--35785 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
35688 ATTTTTTAAA
* *
35698 GGAGTTGAATTTTTAAATGTATAATCATACTATAAGAACTAAACC
1 GGAGTTGAACTTTTAAACGTATAATCATACTATAAGAACTAAACC
*
35743 GGAGTTGAACTTTTAAACGTATAATCATACTATAAGAGCTAAA
1 GGAGTTGAACTTTTAAACGTATAATCATACTATAAGAACTAAA
35786 TCATATTAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (45 bp):
GGAGTTGAACTTTTAAACGTATAATCATACTATAAGAACTAAACC
Found at i:36466 original size:43 final size:43
Alignment explanation
Indices: 36405--36494 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
36395 CGGTGTTTGG
36405 AGATACTGAAGTTAGTGGGGTCTTAAGGTGTTTAGAGAGCTTA
1 AGATACTGAAGTTAGTGGGGTCTTAAGGTGTTTAGAGAGCTTA
36448 AGATACTGAAGTTAGTGGGGTCTTAAGGTGTTTAGAGAGCTTA
1 AGATACTGAAGTTAGTGGGGTCTTAAGGTGTTTAGAGAGCTTA
36491 AGAT
1 AGAT
36495 CTAAAGAGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.29, C:0.07, G:0.32, T:0.32
Consensus pattern (43 bp):
AGATACTGAAGTTAGTGGGGTCTTAAGGTGTTTAGAGAGCTTA
Found at i:37459 original size:23 final size:23
Alignment explanation
Indices: 37431--37572 Score: 115
Period size: 21 Copynumber: 6.5 Consensus size: 23
37421 GAAGATTAAC
* *
37431 AAAATCTCATAGGGAGGTTATCA
1 AAAATTTCATAGGAAGGTTATCA
*
37454 AAAA--TCATAGGAAGCTTA-C-
1 AAAATTTCATAGGAAGGTTATCA
*
37473 AAAATTTCATAGGAAGGTTTAT-T
1 AAAATTTCATAGGAAGG-TTATCA
*
37496 AAAATTTCATAGGTAGGTTATC-
1 AAAATTTCATAGGAAGGTTATCA
* *
37518 AAAATTTCATATGAAGTTTATC-
1 AAAATTTCATAGGAAGGTTATCA
* *
37540 ACAATTTCATA-GATA-ATTATC-
1 AAAATTTCATAGGA-AGGTTATCA
37561 AAAATTTCATAG
1 AAAATTTCATAG
37573 CGTGATTATC
Statistics
Matches: 101, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
19 4 0.04
20 1 0.01
21 39 0.39
22 37 0.37
23 20 0.20
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (23 bp):
AAAATTTCATAGGAAGGTTATCA
Found at i:37463 original size:21 final size:22
Alignment explanation
Indices: 37421--37613 Score: 155
Period size: 22 Copynumber: 8.9 Consensus size: 22
37411 AAGATTATAA
* * *
37421 GAAGATTAACAAAATCTCATAG
1 GAAGGTTATCAAAATTTCATAG
* *
37443 GGAGGTTATCAAAA-ATCATAG
1 GAAGGTTATCAAAATTTCATAG
*
37464 GAAGCTTA-CAAAATTTCATAG
1 GAAGGTTATCAAAATTTCATAG
*
37485 GAAGGTTTATTAAAATTTCATAG
1 GAAGG-TTATCAAAATTTCATAG
* *
37508 GTAGGTTATCAAAATTTCATAT
1 GAAGGTTATCAAAATTTCATAG
* *
37530 GAAGTTTATCACAATTTCATA-
1 GAAGGTTATCAAAATTTCATAG
*
37551 GATA-ATTATCAAAATTTCATAG
1 GA-AGGTTATCAAAATTTCATAG
* * *
37573 CG-TGATTATCAAAATTTAATAG
1 -GAAGGTTATCAAAATTTCATAG
* *
37595 AGTA-GTTATTAAAATTTCA
1 -GAAGGTTATCAAAATTTCA
37614 CAAAAAAATT
Statistics
Matches: 139, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
20 5 0.04
21 39 0.28
22 78 0.56
23 17 0.12
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
GAAGGTTATCAAAATTTCATAG
Found at i:37565 original size:65 final size:65
Alignment explanation
Indices: 37421--37594 Score: 185
Period size: 65 Copynumber: 2.7 Consensus size: 65
37411 AAGATTATAA
* * * *
37421 GAAGATTAACAAAATCTCATAGGGAGGTTATCAAAA-ATCATAGGAAGCTTACAAAATTTCATAG
1 GAAGATTATCAAAATTTCATAGGTAGGTTATCAAAATTTCATAGGAAGCTTACAAAATTTCATAG
* * * * *
37485 GAAGGTTTATTAAAATTTCATAGGTAGGTTATCAAAATTTCATATGAAGTTTATCACAATTTCAT
1 GAA-GATTATCAAAATTTCATAGGTAGGTTATCAAAATTTCATAGGAAGCTTA-CAAAATTTCAT
37550 A-
64 AG
* *
37551 GATA-ATTATCAAAATTTCATAGCGT-GATTATCAAAATTTAATAG
1 GA-AGATTATCAAAATTTCATAG-GTAGGTTATCAAAATTTCATAG
37595 AGTAGTTATT
Statistics
Matches: 91, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
64 3 0.03
65 60 0.66
66 16 0.18
67 12 0.13
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.33
Consensus pattern (65 bp):
GAAGATTATCAAAATTTCATAGGTAGGTTATCAAAATTTCATAGGAAGCTTACAAAATTTCATAG
Found at i:41063 original size:3 final size:3
Alignment explanation
Indices: 41055--41106 Score: 68
Period size: 3 Copynumber: 16.3 Consensus size: 3
41045 CCACAAAACA
*
41055 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT ATAC TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TAT -TAT
41103 TAT T
1 TAT T
41107 TTTGTCCCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 36 0.80
4 9 0.20
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:46845 original size:34 final size:34
Alignment explanation
Indices: 46802--46872 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
46792 CTAGTCTCCA
46802 TTATTTTCACAACATGGGTTTCCTTTTTGGGGCT
1 TTATTTTCACAACATGGGTTTCCTTTTTGGGGCT
46836 TTATTTTCACAACATGGGTTTCCTTTTTGGGGCT
1 TTATTTTCACAACATGGGTTTCCTTTTTGGGGCT
46870 TTA
1 TTA
46873 ACTTTATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.48
Consensus pattern (34 bp):
TTATTTTCACAACATGGGTTTCCTTTTTGGGGCT
Found at i:47173 original size:21 final size:22
Alignment explanation
Indices: 47147--47191 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
47137 ACTATCTGGA
47147 TTGCTAAACACCG-CCCCCCTT
1 TTGCTAAACACCGCCCCCCCTT
*
47168 TTGCTAAATACCGCCCCCCCTT
1 TTGCTAAACACCGCCCCCCCTT
47190 TT
1 TT
47192 TACACTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.18, C:0.44, G:0.09, T:0.29
Consensus pattern (22 bp):
TTGCTAAACACCGCCCCCCCTT
Found at i:47298 original size:10 final size:10
Alignment explanation
Indices: 47285--47310 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
47275 CATTTCTAAC
47285 AACTTCTTCA
1 AACTTCTTCA
47295 AACTTCTTCA
1 AACTTCTTCA
47305 AACTTC
1 AACTTC
47311 ATTTCTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (10 bp):
AACTTCTTCA
Found at i:47376 original size:26 final size:26
Alignment explanation
Indices: 47347--47418 Score: 110
Period size: 26 Copynumber: 2.8 Consensus size: 26
47337 TTCCTTCATT
47347 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
47373 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
47399 TTAAACATAAAATAA-TAAAT
1 TTAATCATAAACTAATTAAAT
47419 TAAGTAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 4 0.10
26 38 0.90
ACGTcount: A:0.56, C:0.10, G:0.01, T:0.33
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:47377 original size:15 final size:15
Alignment explanation
Indices: 47347--47390 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
47337 TTCCTTCATT
47347 TTAATCATAAACTAA
1 TTAATCATAAACTAA
47362 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
47373 TTAATCATAAACTAA
1 TTAATCATAAACTAA
47388 TTA
1 TTA
47391 GATACTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 9 0.36
13 4 0.16
15 12 0.48
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:47501 original size:21 final size:22
Alignment explanation
Indices: 47468--47510 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
47458 TAATTAATAT
47468 TTAAAAAATTTTTTTAAAAAAG
1 TTAAAAAATTTTTTTAAAAAAG
*
47490 TTAAAAAATTTTTTAAAAAAA
1 TTAAAAAATTTTTTTAAAAAA
47511 TGGTCGAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TTAAAAAATTTTTTTAAAAAAG
Found at i:56727 original size:14 final size:14
Alignment explanation
Indices: 56708--56734 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
56698 CCGGCACGGT
56708 TTTTTATTCATTGA
1 TTTTTATTCATTGA
56722 TTTTTATTCATTG
1 TTTTTATTCATTG
56735 CTTTCACTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTTATTCATTGA
Found at i:63590 original size:16 final size:18
Alignment explanation
Indices: 63557--63591 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
63547 GACCCGGCCG
63557 GTTGACCCGATAGACCCA
1 GTTGACCCGATAGACCCA
63575 GTTGACCCG-T-GACCCA
1 GTTGACCCGATAGACCCA
63591 G
1 G
63592 CAACCTCGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 1 0.06
18 9 0.53
ACGTcount: A:0.23, C:0.34, G:0.26, T:0.17
Consensus pattern (18 bp):
GTTGACCCGATAGACCCA
Found at i:66044 original size:21 final size:20
Alignment explanation
Indices: 66006--66045 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
65996 AACCATATTT
*
66006 TTTATAAATATAAAATATAA
1 TTTATAAATACAAAATATAA
*
66026 TTTATATAATACAATATATA
1 TTTATA-AATACAAAATATA
66046 TTGTAATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTATAAATACAAAATATAA
Found at i:66065 original size:27 final size:28
Alignment explanation
Indices: 66023--66076 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
66013 ATATAAAATA
66023 TAATTTATATAATACA-A-TATATATTG
1 TAATTTATATAATACATAGTATATATTG
*
66049 TAATGTTATATATTACATAGTATATATT
1 TAAT-TTATATAATACATAGTATATATT
66077 TATATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 11 0.46
28 1 0.04
29 8 0.33
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (28 bp):
TAATTTATATAATACATAGTATATATTG
Found at i:69413 original size:3 final size:3
Alignment explanation
Indices: 69405--69435 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
69395 TTTATATTAG
69405 CTT CTT CTT CTT CTT CTT CTT CTT CATT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT
69436 GCTGTCACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:72156 original size:31 final size:33
Alignment explanation
Indices: 72097--72166 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 33
72087 AAAAAAGTGG
* * *
72097 TTTAAATACTATATAAATCATTTTTATTTGCTGC
1 TTTAAATA-TATAGAAATCATTTTTATTTGATGA
72131 TTTAAAT-TATAGAAATCA-TTTTATTTGATGA
1 TTTAAATATATAGAAATCATTTTTATTTGATGA
72162 TTTAA
1 TTTAA
72167 TTTTAATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 16 0.48
32 10 0.30
34 7 0.21
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (33 bp):
TTTAAATATATAGAAATCATTTTTATTTGATGA
Found at i:76804 original size:26 final size:26
Alignment explanation
Indices: 76768--76822 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
76758 AAACTCACAG
* *
76768 TTGTGCTCCTTAGGGTAGCGGTGGGT
1 TTGTGCTCCTTAGGATAGCAGTGGGT
76794 TTGTGCTCCTTAGGATAGCAGTGGGT
1 TTGTGCTCCTTAGGATAGCAGTGGGT
76820 TTG
1 TTG
76823 ACAAAACCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.11, C:0.15, G:0.38, T:0.36
Consensus pattern (26 bp):
TTGTGCTCCTTAGGATAGCAGTGGGT
Found at i:77871 original size:14 final size:13
Alignment explanation
Indices: 77834--77900 Score: 50
Period size: 13 Copynumber: 5.2 Consensus size: 13
77824 GCATTTCTCG
* *
77834 TGAAAACAAGTTT
1 TGAAAACCATTTT
*
77847 TGAAAATCATTTT
1 TGAAAACCATTTT
*
77860 TGAAAAACCATTTAA
1 TG-AAAACCATTT-T
77875 T-AAAA--ATCTTT
1 TGAAAACCAT-TTT
77886 TGAAAACCATTTT
1 TGAAAACCATTTT
77899 TG
1 TG
77901 TTAGATTCCT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
11 3 0.07
12 6 0.14
13 21 0.50
14 11 0.26
15 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.37
Consensus pattern (13 bp):
TGAAAACCATTTT
Found at i:86731 original size:50 final size:50
Alignment explanation
Indices: 86672--86772 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
86662 ATGCATTCAC
86672 GGCAGCATGACATTAATGATGACAATGACAATGACAACAACAATGAAGAT
1 GGCAGCATGACATTAATGATGACAATGACAATGACAACAACAATGAAGAT
86722 GGCAGCATGACATTAATGATGACAATGACAATGACAACAACAATGAAGAT
1 GGCAGCATGACATTAATGATGACAATGACAATGACAACAACAATGAAGAT
86772 G
1 G
86773 ACGTGGAGAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.18
Consensus pattern (50 bp):
GGCAGCATGACATTAATGATGACAATGACAATGACAACAACAATGAAGAT
Found at i:90031 original size:111 final size:111
Alignment explanation
Indices: 89906--90124 Score: 377
Period size: 111 Copynumber: 2.0 Consensus size: 111
89896 TGGTTGTTTG
**
89906 AACTGGTTCATTACTTTTCTT-AGTTGGCTCCTCAAGTGTAATTTCCTTATTACCATTAGCACTC
1 AACTGGTTCATTACTTTT-TTCAGTTGGCTCCTCAAGTGTAATTTCCTTAACACCATTAGCACTC
*
89970 AAGATCTGTGATTCTTGCCCCATATTGTGTAAATTGGTCATGTTAAC
65 AAGATCTGTGATTCTTGCCCCATATTATGTAAATTGGTCATGTTAAC
*
90017 AACTGGTTCATTACTTTTTTCAGTTGGCTCCTCAAGTTTAATTTCCTTAACACCATTAGCACTCA
1 AACTGGTTCATTACTTTTTTCAGTTGGCTCCTCAAGTGTAATTTCCTTAACACCATTAGCACTCA
*
90082 AGCTCTGTGATTCTTGCCCCATATTATGTAAATTGGTCATGTT
66 AGATCTGTGATTCTTGCCCCATATTATGTAAATTGGTCATGTT
90125 TTCTTCCAAC
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
110 2 0.02
111 100 0.98
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (111 bp):
AACTGGTTCATTACTTTTTTCAGTTGGCTCCTCAAGTGTAATTTCCTTAACACCATTAGCACTCA
AGATCTGTGATTCTTGCCCCATATTATGTAAATTGGTCATGTTAAC
Found at i:91524 original size:27 final size:27
Alignment explanation
Indices: 91494--91547 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
91484 TGCTATCTTC
* *
91494 TAACTACATTAAA-CTTCTACTAATTTG
1 TAACGACATTAAATC-TCGACTAATTTG
91521 TAACGACATTAAATCTCGACTAATTTG
1 TAACGACATTAAATCTCGACTAATTTG
91548 AAATTGAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (27 bp):
TAACGACATTAAATCTCGACTAATTTG
Found at i:97095 original size:1 final size:1
Alignment explanation
Indices: 97089--97129 Score: 73
Period size: 1 Copynumber: 41.0 Consensus size: 1
97079 CTGATTAGAG
*
97089 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
97130 AAATCAGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.02, G:0.00, T:0.98
Consensus pattern (1 bp):
T
Done.