Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008111.1 Corchorus capsularis cultivar CVL-1 contig08132, 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: 29458
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Found at i:4606 original size:12 final size:13
Alignment explanation
Indices: 4565--4609 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
4555 AATTATTGTT
*
4565 TGCTTCATTAATC
1 TGCTTTATTAATC
*
4578 TGCTTTATTAATT
1 TGCTTTATTAATC
4591 TGCTTTA-TAATC
1 TGCTTTATTAATC
4603 TGCTTTA
1 TGCTTTA
4610 GATTTAGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.22, C:0.16, G:0.09, T:0.53
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:4617 original size:6 final size:6
Alignment explanation
Indices: 4606--4638 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
4596 TATAATCTGC
*
4606 TTTAGA TTTAGA TTTAGA TTTAGA TTTTGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
4639 GCTTTGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (6 bp):
TTTAGA
Found at i:8741 original size:30 final size:30
Alignment explanation
Indices: 8705--8764 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
8695 AAAGGATCGA
*
8705 ATGGCCGGTTGTGGCCGGATGGCCCATGCG
1 ATGGCCGGTTCTGGCCGGATGGCCCATGCG
8735 ATGGCCGGTTCTGGCCGGATGGCCCATGCG
1 ATGGCCGGTTCTGGCCGGATGGCCCATGCG
8765 TCGGCCCGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.10, C:0.28, G:0.42, T:0.20
Consensus pattern (30 bp):
ATGGCCGGTTCTGGCCGGATGGCCCATGCG
Found at i:9436 original size:21 final size:21
Alignment explanation
Indices: 9410--9458 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
9400 GCATAAGTGA
*
9410 CCGGCCATGCGACTTGGAGAT
1 CCGGCCATGCGACCTGGAGAT
*
9431 CCGGCCATGTGACCTGGAGAT
1 CCGGCCATGCGACCTGGAGAT
*
9452 CTGGCCA
1 CCGGCCA
9459 CACAACTCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.18, C:0.31, G:0.33, T:0.18
Consensus pattern (21 bp):
CCGGCCATGCGACCTGGAGAT
Found at i:9508 original size:33 final size:33
Alignment explanation
Indices: 9465--9558 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
9455 GCCACACAAC
* *
9465 TCGGAGATGCCCGGACATC-ACCGGCCACGCGACA
1 TCGGACATGCCCGGCCA-CAACCGGCCACGCGA-A
9499 T-GGACATGCCCGGCCACAACCGGCCACGCGAA
1 TCGGACATGCCCGGCCACAACCGGCCACGCGAA
*
9531 TCGGCCATGCCCGGCCACAACCGGCCAC
1 TCGGACATGCCCGGCCACAACCGGCCAC
9559 ATGATCCTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
32 3 0.05
33 51 0.93
34 1 0.02
ACGTcount: A:0.22, C:0.43, G:0.28, T:0.07
Consensus pattern (33 bp):
TCGGACATGCCCGGCCACAACCGGCCACGCGAA
Found at i:16592 original size:33 final size:33
Alignment explanation
Indices: 16550--16621 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
16540 TTCTTTTCAC
16550 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
16583 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
16616 CCAAAA
1 CCAAAA
16622 TAGATTTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.25
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:16688 original size:33 final size:33
Alignment explanation
Indices: 16651--16755 Score: 131
Period size: 33 Copynumber: 3.2 Consensus size: 33
16641 ATTAGCATCC
*
16651 AAAACAGATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
* * *
16684 AAAACAGATTTAGTGTCATTGCAAACAACACTC
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
** *
16717 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCGCAAACAACACT-T
16750 AAAACA
1 AAAACA
16756 CTCTTTTCAA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 1 0.02
33 58 0.98
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.25
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACACTT
Found at i:20851 original size:15 final size:15
Alignment explanation
Indices: 20831--20880 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
20821 TGTTATGTTA
20831 TATGTTATAATATTG
1 TATGTTATAATATTG
* *
20846 TATG-T-T-ATGTTA
1 TATGTTATAATATTG
*
20858 TATGTTACAATATTG
1 TATGTTATAATATTG
20873 TATGTTAT
1 TATGTTAT
20881 GTTATGTGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
12 8 0.31
13 2 0.08
14 1 0.04
15 15 0.58
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.54
Consensus pattern (15 bp):
TATGTTATAATATTG
Found at i:20852 original size:27 final size:27
Alignment explanation
Indices: 20819--20893 Score: 132
Period size: 27 Copynumber: 2.8 Consensus size: 27
20809 TGACTATTAT
20819 TATGTTATGTTATATGTTATAATATTG
1 TATGTTATGTTATATGTTATAATATTG
*
20846 TATGTTATGTTATATGTTACAATATTG
1 TATGTTATGTTATATGTTATAATATTG
*
20873 TATGTTATGTTATGTGTTATA
1 TATGTTATGTTATATGTTATA
20894 TATCTATAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.28, C:0.01, G:0.16, T:0.55
Consensus pattern (27 bp):
TATGTTATGTTATATGTTATAATATTG
Found at i:21936 original size:437 final size:439
Alignment explanation
Indices: 21095--21937 Score: 1056
Period size: 437 Copynumber: 1.9 Consensus size: 439
21085 ATGGACCCGT
* *
21095 TCTCAATAAACAAATATTTTTTTGTTGGTTTATTTATCAAATGATCCCTATACTTTTATGCTTTA
1 TCTCAATAAACAAATATTTTTTTGCTGGATTATTTATCAAATGATCCCTATACTTTTATGCTTTA
* * * *
21160 TGCCATTTAGTCCCTTAGAATTTCTGGGTTGGACGATTGAACGTTTCGACTTTAATTCTTTTATT
66 TGCCATTTAATCCCTTACAATTTATAGGTTGGACGATTGAACGTTTCGACTTTAATTCTTTTATT
* * * * *
21225 TTTTGTTTTGCTTGTCCAGTCAAGGTGATTCAAGTGTCTATTAAAAGGTGATTTCATGATCTACA
131 TTCTGTTCTACTTGTCCAGTCAAGGTGATTCAAGTGTCTATGAAAAGGTAATTTCATGATCTACA
* * * *
21290 ATTTCCATGAAGGACTCAAAAGCCAATTTTAATATTTTGATTCTAAAAAATGCTTCTGAAATTTT
196 ATTTCCATGAAGAACTCAAAAGCCAATTTTAATATTTTAATTCTAAAAAATGCTTCTAAAATCTT
* * ** * *
21355 GTCGTCTCGATCGCCGGTCTATTTGATATCGTATAATTTTCGGTCTGCTTGTCCGATTGAGGCTG
261 GTCGTCTCAATCGCCGGTCTATTTAATATCGTATAATTTTCGGTCCACTTGTACGATTGAAGCTG
* * *
21420 TTCAAGTGTCGGTTAAAAGGTTATTCTGTGATCTACGACTTTCGTTATGGGCCTCAAACCTGAAT
326 TTCAAGTGTCGGTTAAAAGGTTATTCTGTGATCTACGACTTTCATTAAGGGCCTAAAACCTGAAT
21485 TTGATTAATGAGTTTCGTGGAGGGTTCAAGAGGGAATTTTTATGTTTTG
391 TTGATTAATGAGTTTCGTGGAGGGTTCAAGAGGGAATTTTTATGTTTTG
* * * *
21534 TCTCCATAAAGAAATATTTTTTTTGCTGGATTATTTATTAAATGAT-CCTCATACTTTTATGTTT
1 TCTCAATAAACAAATA-TTTTTTTGCTGGATTATTTATCAAATGATCCCT-ATACTTTTATGCTT
* * * * * *
21598 TATGCTATTTAATCCTTTACAA-TTATAGGTTGGATGATTTAAC-TCTTCG-GTTTTATT-TTTG
64 TATGCCATTTAATCCCTTACAATTTATAGGTTGGACGATTGAACGT-TTCGACTTTAATTCTTT-
* * *
21659 TATTTTCTGTTCTATTTGTCC-GATCAAGGTGATTCAAGTGTTTATGAAAAGGTAATTTTATGAT
127 TATTTTCTGTTCTACTTGTCCAG-TCAAGGTGATTCAAGTGTCTATGAAAAGGTAATTTCATGAT
* * *
21723 CTACAACTTT-CATGAAGAACTCAGAAGTCAATTTTAATGTTTTAATTCT-AAAAATGCTTCTAA
191 CTACAA-TTTCCATGAAGAACTCAAAAGCCAATTTTAATATTTTAATTCTAAAAAATGCTTCTAA
* * * ** * * *
21786 AATCTTGTGGTTTCAATTGTTGGTCTATTTAATGTTGTATAATTTTTGGTCCACTTGTACGATTG
255 AATCTTGTCGTCTCAATCGCCGGTCTATTTAATATCGTATAATTTTCGGTCCACTTGTACGATTG
* * * * *
21851 AAGTTGTTCAGGTGTCGGTTAGATGGTTATTGTGTGATCTACGACTTTCATTAAGTGG-CTAAAA
320 AAGCTGTTCAAGTGTCGGTTAAAAGGTTATTCTGTGATCTACGACTTTCATTAAG-GGCCTAAAA
* **
21915 GCTGAATTTGATTTGTGAGTTTC
384 CCTGAATTTGATTAATGAGTTTC
21938 ATGAATGATT
Statistics
Matches: 341, Mismatches: 56, Indels: 16
0.83 0.14 0.04
Matches are distributed among these distances:
437 140 0.41
438 103 0.30
439 41 0.12
440 57 0.17
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.43
Consensus pattern (439 bp):
TCTCAATAAACAAATATTTTTTTGCTGGATTATTTATCAAATGATCCCTATACTTTTATGCTTTA
TGCCATTTAATCCCTTACAATTTATAGGTTGGACGATTGAACGTTTCGACTTTAATTCTTTTATT
TTCTGTTCTACTTGTCCAGTCAAGGTGATTCAAGTGTCTATGAAAAGGTAATTTCATGATCTACA
ATTTCCATGAAGAACTCAAAAGCCAATTTTAATATTTTAATTCTAAAAAATGCTTCTAAAATCTT
GTCGTCTCAATCGCCGGTCTATTTAATATCGTATAATTTTCGGTCCACTTGTACGATTGAAGCTG
TTCAAGTGTCGGTTAAAAGGTTATTCTGTGATCTACGACTTTCATTAAGGGCCTAAAACCTGAAT
TTGATTAATGAGTTTCGTGGAGGGTTCAAGAGGGAATTTTTATGTTTTG
Found at i:22328 original size:69 final size:69
Alignment explanation
Indices: 22250--22379 Score: 197
Period size: 69 Copynumber: 1.9 Consensus size: 69
22240 ATATTATTAA
* * * * *
22250 TTAATCTAATCATTATTCGTATTTATTCTTGCTCAGATTGATTGTGAATTATTGGTTTTTTTCCT
1 TTAATCTAATCATTAATCATATTTATTCTTGCTCAAATTGATTATGAATTATTGATTTTTTTCCT
22315 TGGT
66 TGGT
* *
22319 TTAATCTAATTATTAATCATATTTATTCTTGCTCAAATTGATTATGGATTATTGATTTTTT
1 TTAATCTAATCATTAATCATATTTATTCTTGCTCAAATTGATTATGAATTATTGATTTTTT
22380 AGTTTTAACC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 54 1.00
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.54
Consensus pattern (69 bp):
TTAATCTAATCATTAATCATATTTATTCTTGCTCAAATTGATTATGAATTATTGATTTTTTTCCT
TGGT
Found at i:26293 original size:9 final size:8
Alignment explanation
Indices: 26241--26292 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 8
26231 GTTTAGTTTA
26241 ATAATATAT
1 ATAA-ATAT
26250 ATAAAT-T
1 ATAAATAT
*
26257 ATATATAT
1 ATAAATAT
26265 ATAAATAAT
1 ATAAAT-AT
26274 ACTAAATAT
1 A-TAAATAT
26283 AT-AATAT
1 ATAAATAT
26290 ATA
1 ATA
26293 TTTTAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 13 0.35
8 9 0.24
9 10 0.27
10 5 0.14
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAAATAT
Found at i:28350 original size:13 final size:13
Alignment explanation
Indices: 28305--28351 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
28295 ATCATTTTTA
28305 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
28318 CT-TTTTACTAATT
1 CTCTTTT-CTTACT
28331 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
28345 CTCTTTT
1 CTCTTTT
28352 ATTTATTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:28366 original size:29 final size:28
Alignment explanation
Indices: 28302--28379 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 28
28292 TTTATCATTT
*
28302 TTACTCTTTTCTTACTCT-TTTTACTAA
1 TTACACTTTTCTTACTCTCTTTTACTAA
* * *
28329 TTACTCTTTTCTTACTCTCTTTTATTTA
1 TTACACTTTTCTTACTCTCTTTTACTAA
28357 TTACCAC-TTT-TTACTCTTCTTTT
1 TTA-CACTTTTCTTACTC-TCTTTT
28380 TTTCTTATAC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
27 24 0.53
28 19 0.42
29 2 0.04
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (28 bp):
TTACACTTTTCTTACTCTCTTTTACTAA
Found at i:28458 original size:21 final size:21
Alignment explanation
Indices: 28413--28705 Score: 113
Period size: 21 Copynumber: 14.8 Consensus size: 21
28403 ACTCTTTGAA
*
28413 TTACTGATCACCT-TTT-ACTC
1 TTACTGATTA-CTATTTGACTC
28433 TTTACTGATTACTATTTGACTC
1 -TTACTGATTACTATTTGACTC
* *
28455 TTACTAATTACCACTTTG-CTC
1 TTACTGATTACTA-TTTGACTC
* * *
28476 TTACTGGTTACTGTTTTACTC
1 TTACTGATTACTATTTGACTC
*
28497 TTACTGA-T--TA--T--CTT
1 TTACTGATTACTATTTGACTC
*
28511 TTACTGATTACTATTTTACTC
1 TTACTGATTACTATTTGACTC
*
28532 TTTACTGATTAC---CT---TC
1 -TTACTGATTACTATTTGACTC
*
28548 -TACTGATTACTATTTTACTC
1 TTACTGATTACTATTTGACTC
28568 TTACTGATTACCT-TTTG----
1 TTACTGATTA-CTATTTGACTC
*
28585 ---CTGATTACTATTTTACTC
1 TTACTGATTACTATTTGACTC
* *
28603 TTTACTGATTACCT-TCTT-TCTTT
1 -TTACTGATTA-CTAT-TTGAC-TC
* *
28626 TTAATGATTACTATTTTACTC
1 TTACTGATTACTATTTGACTC
*
28647 TTTACTGATTACCATTTTG-CTC
1 -TTACTGATTACTA-TTTGACTC
* *
28669 TCATTGATTACTATTTTG-CTC
1 TTACTGATTACTA-TTTGACTC
28690 TTACTGATTACTATTT
1 TTACTGATTACTATTT
28706 TACCTTTTAC
Statistics
Matches: 207, Mismatches: 29, Indels: 73
0.67 0.09 0.24
Matches are distributed among these distances:
13 2 0.01
14 29 0.14
15 1 0.00
16 3 0.01
17 3 0.01
18 1 0.00
19 2 0.01
20 11 0.05
21 92 0.44
22 55 0.27
23 8 0.04
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.52
Consensus pattern (21 bp):
TTACTGATTACTATTTGACTC
Found at i:28514 original size:14 final size:15
Alignment explanation
Indices: 28497--28530 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
28487 TGTTTTACTC
*
28497 TTACTGATTA-TCTT
1 TTACTGATTACTATT
28511 TTACTGATTACTATT
1 TTACTGATTACTATT
28526 TTACT
1 TTACT
28531 CTTTACTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.56
Consensus pattern (15 bp):
TTACTGATTACTATT
Found at i:28515 original size:35 final size:36
Alignment explanation
Indices: 28476--28664 Score: 229
Period size: 35 Copynumber: 5.1 Consensus size: 36
28466 CACTTTGCTC
* * *
28476 TTACTGGTTACTGTTTTACTC-TTACTGATTATCTT
1 TTACTGATTACTATTTTACTCTTTACTGATTACCTT
28511 TTACTGATTACTATTTTACTCTTTACTGATTACCTT
1 TTACTGATTACTATTTTACTCTTTACTGATTACCTT
*
28547 CTACTGATTACTATTTTACTC-TTACTGATTACCTT
1 TTACTGATTACTATTTTACTCTTTACTGATTACCTT
*
28582 TTGCTGATTACTATTTTACTCTTTACTGATTACCTTCTTTCTTT
1 TTACTGATTACTATTTTACTCTTTACTGATTA----C---C-TT
*
28626 TTAATGATTACTATTTTACTCTTTACTGATTACCATT
1 TTACTGATTACTATTTTACTCTTTACTGATTACC-TT
28663 TT
1 TT
28665 GCTCTCATTG
Statistics
Matches: 135, Mismatches: 9, Indels: 18
0.83 0.06 0.11
Matches are distributed among these distances:
35 52 0.39
36 43 0.32
37 5 0.04
40 2 0.01
43 1 0.01
44 32 0.24
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.53
Consensus pattern (36 bp):
TTACTGATTACTATTTTACTCTTTACTGATTACCTT
Found at i:28536 original size:22 final size:22
Alignment explanation
Indices: 28510--28721 Score: 145
Period size: 22 Copynumber: 9.5 Consensus size: 22
28500 CTGATTATCT
28510 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
* *
28532 TTTACTGATTACCTTCTACTGATTACTAT
1 TTTACTGATTA----CTA-T-TTTACT-C
*
28561 TTTACT-CTTACTGA--TTAC-C
1 TTTACTGATTACT-ATTTTACTC
*
28580 TTTTGCTGATTACTATTTTACTC
1 -TTTACTGATTACTATTTTACTC
*
28603 TTTACTGATTACCT-TCTTT-CTT
1 TTTACTGATTA-CTAT-TTTACTC
*
28625 TTTAATGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
* *
28647 TTTACTGATTACCATTTTGCTC
1 TTTACTGATTACTATTTTACTC
* * *
28669 -TCATTGATTACTATTTTGCTC
1 TTTACTGATTACTATTTTACTC
28690 -TTACTGATTACTATTTTAC-C
1 TTTACTGATTACTATTTTACTC
*
28710 TTTTACAGATTA
1 -TTTACTGATTA
28722 TCATTACTTT
Statistics
Matches: 151, Mismatches: 20, Indels: 38
0.72 0.10 0.18
Matches are distributed among these distances:
20 7 0.05
21 48 0.32
22 69 0.46
23 6 0.04
24 2 0.01
25 1 0.01
26 3 0.02
27 1 0.01
28 8 0.05
29 6 0.04
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (22 bp):
TTTACTGATTACTATTTTACTC
Found at i:28567 original size:71 final size:71
Alignment explanation
Indices: 28477--28619 Score: 250
Period size: 71 Copynumber: 2.0 Consensus size: 71
28467 ACTTTGCTCT
* * *
28477 TACTGGTTACTGTTTTACTCTTACTGATTATCTTTTACTGATTACTATTTTACTCTTTACTGATT
1 TACTGATTACTATTTTACTCTTACTGATTACCTTTTACTGATTACTATTTTACTCTTTACTGATT
28542 ACCTTC
66 ACCTTC
*
28548 TACTGATTACTATTTTACTCTTACTGATTACCTTTTGCTGATTACTATTTTACTCTTTACTGATT
1 TACTGATTACTATTTTACTCTTACTGATTACCTTTTACTGATTACTATTTTACTCTTTACTGATT
28613 ACCTTC
66 ACCTTC
28619 T
1 T
28620 TTCTTTTTAA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.20, C:0.20, G:0.08, T:0.52
Consensus pattern (71 bp):
TACTGATTACTATTTTACTCTTACTGATTACCTTTTACTGATTACTATTTTACTCTTTACTGATT
ACCTTC
Found at i:28706 original size:21 final size:21
Alignment explanation
Indices: 28585--28708 Score: 126
Period size: 21 Copynumber: 5.8 Consensus size: 21
28575 TTACCTTTTG
28585 CTGATTACTATTTTACTCTTTA
1 CTGATTACTATTTTACTC-TTA
*
28607 CTGATTACCT-TCTTT-CTTTTTA
1 CTGATTA-CTAT-TTTAC-TCTTA
*
28629 ATGATTACTATTTTACTCTTTA
1 CTGATTACTATTTTACTC-TTA
* * *
28651 CTGATTACCATTTTGCTCTCA
1 CTGATTACTATTTTACTCTTA
* *
28672 TTGATTACTATTTTGCTCTTA
1 CTGATTACTATTTTACTCTTA
28693 CTGATTACTATTTTAC
1 CTGATTACTATTTTAC
28709 CTTTTACAGA
Statistics
Matches: 84, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
21 40 0.48
22 38 0.45
23 6 0.07
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.53
Consensus pattern (21 bp):
CTGATTACTATTTTACTCTTA
Found at i:28779 original size:15 final size:14
Alignment explanation
Indices: 28724--28787 Score: 58
Period size: 15 Copynumber: 4.4 Consensus size: 14
28714 ACAGATTATC
*
28724 ATTACTTTATTATTG
1 ATTACTTT-TTACTG
*
28739 ATTACCTTTTACT-
1 ATTACTTTTTACTG
*
28752 ATTTCATTCTTTACTG
1 ATTAC-TT-TTTACTG
28768 ATTATCTTTTTACTG
1 ATTA-CTTTTTACTG
28783 ATTAC
1 ATTAC
28788 CCTTTACTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
13 4 0.10
14 6 0.15
15 24 0.60
16 5 0.12
17 1 0.03
ACGTcount: A:0.23, C:0.16, G:0.05, T:0.56
Consensus pattern (14 bp):
ATTACTTTTTACTG
Found at i:28817 original size:35 final size:35
Alignment explanation
Indices: 28776--28899 Score: 149
Period size: 35 Copynumber: 3.5 Consensus size: 35
28766 TGATTATCTT
*
28776 TTTACTGATTACCCTTTACTCTTTACCATTCTTCC
1 TTTACTGATTACCCTTTACTTTTTACCATTCTTCC
* * *
28811 TTTACTGATTACTCTTTACTTTTTACCAATCTTCT
1 TTTACTGATTACCCTTTACTTTTTACCATTCTTCC
* * *
28846 TTTACTGATTACTCTTTACTTTTTTATCATTTTTCCC
1 TTTACTGATTACCCTTTAC-TTTTTACCATTCTT-CC
*
28883 TTTACTAATTACTCCTT
1 TTTACTGATTAC-CCTT
28900 ACTAATTATT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
35 50 0.66
36 11 0.14
37 12 0.16
38 3 0.04
ACGTcount: A:0.19, C:0.25, G:0.02, T:0.54
Consensus pattern (35 bp):
TTTACTGATTACCCTTTACTTTTTACCATTCTTCC
Found at i:28915 original size:14 final size:14
Alignment explanation
Indices: 28882--28916 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28872 TCATTTTTCC
28882 CTTTACTAATTACT
1 CTTTACTAATTACT
* *
28896 CCTTACTAATTATT
1 CTTTACTAATTACT
28910 CTTTACT
1 CTTTACT
28917 CTTTACCATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (14 bp):
CTTTACTAATTACT
Found at i:29129 original size:71 final size:71
Alignment explanation
Indices: 29035--29191 Score: 178
Period size: 71 Copynumber: 2.2 Consensus size: 71
29025 CGATTTAATC
* ** * *
29035 CATTGACTTTTAATTATTGATTTACTTATTACTA--TTTTTATCTTGACT-CTTAATTACTGATT
1 CATTGACTCTTAATTATCAATTTACTGATTACTATCTTTTTA-CTTGACTACTGAATTACTGATT
*
29097 AATCTCTTA
65 -A-CTATTA
* * *
29106 CCTTGACTCTTAATTATCAATTTACTGATTACTATCTTTTTACTTGATTACTGATTTACTGATTA
1 CATTGACTCTTAATTATCAATTTACTGATTACTATCTTTTTACTTGACTACTGAATTACTGATTA
29171 CTATTA
66 CTATTA
29177 CATTGACTC-TAATTA
1 CATTGACTCTTAATTA
29192 ATCTCTTTTA
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
70 6 0.08
71 42 0.58
72 7 0.10
73 18 0.25
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.50
Consensus pattern (71 bp):
CATTGACTCTTAATTATCAATTTACTGATTACTATCTTTTTACTTGACTACTGAATTACTGATTA
CTATTA
Found at i:29200 original size:55 final size:55
Alignment explanation
Indices: 29140--29336 Score: 225
Period size: 55 Copynumber: 3.4 Consensus size: 55
29130 CTGATTACTA
*
29140 TCTTTTTACTTGATTACTGATTTACTGATTACTATTACATTGACTCTAATTAATC
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTACATTGACTCTAATTAATC
*
29195 TC-TTTTACTTAATTACTGATTTACTGATTACTATTACTTTAATATTACCTTGACTCTAACTAAT
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTAC---------A--TTGACTCTAATTAAT
29259 C
55 C
* * * * *
29260 TCTTCTTACTTAACTACTGATTTACTGATTACTATTACCTTAACTCTGATTAATC
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTACATTGACTCTAATTAATC
29315 TCTTTTTACTTAATTACTGATT
1 TCTTTTTACTTAATTACTGATT
29337 GCCCCTTTTT
Statistics
Matches: 120, Mismatches: 10, Indels: 24
0.78 0.06 0.16
Matches are distributed among these distances:
54 34 0.28
55 35 0.29
63 1 0.01
65 17 0.14
66 33 0.28
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (55 bp):
TCTTTTTACTTAATTACTGATTTACTGATTACTATTACATTGACTCTAATTAATC
Found at i:29202 original size:54 final size:54
Alignment explanation
Indices: 29139--29336 Score: 218
Period size: 54 Copynumber: 3.4 Consensus size: 54
29129 ACTGATTACT
*
29139 ATCT-TTTTACTTGATTACTGATTTACTGATTACTATTACATTGACTCTAATTA
1 ATCTCTTTTACTTAATTACTGATTTACTGATTACTATTACATTGACTCTAATTA
*
29192 ATCTCTTTTACTTAATTACTGATTTACTGATTACTATTACTTTAATATTACCTTGACTCTAACTA
1 ATCTCTTTTACTTAATTACTGATTTACTGATTACTATTAC---------A--TTGACTCTAATTA
* * * *
29257 ATCTCTTCTTACTTAACTACTGATTTACTGATTACTATTACCTTAACTCTGATTA
1 ATCTCTT-TTACTTAATTACTGATTTACTGATTACTATTACATTGACTCTAATTA
29312 ATCTCTTTTTACTTAATTACTGATT
1 ATCTC-TTTTACTTAATTACTGATT
29337 GCCCCTTTTT
Statistics
Matches: 123, Mismatches: 8, Indels: 26
0.78 0.05 0.17
Matches are distributed among these distances:
53 4 0.03
54 34 0.28
55 31 0.25
56 2 0.02
63 1 0.01
65 19 0.15
66 32 0.26
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (54 bp):
ATCTCTTTTACTTAATTACTGATTTACTGATTACTATTACATTGACTCTAATTA
Found at i:29290 original size:66 final size:65
Alignment explanation
Indices: 29144--29302 Score: 219
Period size: 66 Copynumber: 2.4 Consensus size: 65
29134 TTACTATCTT
* * *
29144 TTTACTTGATTACTGATTTACTGATTACTATTACATTGACTCTAATTAATCTCTTTTACTTAATT
1 TTTAC-TGATTACT-A-TTACT--TTAATATTACATTGACTCTAACTAATCTCTTTTACTTAACT
29209 ACTGA
61 ACTGA
*
29214 TTTACTGATTACTATTACTTTAATATTACCTTGACTCTAACTAATCTCTTCTTACTTAACTACTG
1 TTTACTGATTACTATTACTTTAATATTACATTGACTCTAACTAATCTCTT-TTACTTAACTACTG
29279 A
65 A
*
29280 TTTACTGATTACTATTACCTTAA
1 TTTACTGATTACTATTACTTTAA
29303 CTCTGATTAA
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
65 28 0.34
66 36 0.43
67 5 0.06
68 1 0.01
69 8 0.10
70 5 0.06
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (65 bp):
TTTACTGATTACTATTACTTTAATATTACATTGACTCTAACTAATCTCTTTTACTTAACTACTGA
Done.