Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021536.1 Corchorus olitorius cultivar O-4 contig21569, 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: 17379
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Found at i:645 original size:2 final size:2
Alignment explanation
Indices: 640--704 Score: 59
Period size: 2 Copynumber: 34.5 Consensus size: 2
630 TATATATGGT
* * *
640 TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA -A CCA -A AA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
680 TA TA TA TA TA TA T- TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
705 TTTGCCCCTA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
1 5 0.09
2 48 0.89
3 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3756 original size:28 final size:28
Alignment explanation
Indices: 3724--3779 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
3714 CTTCATTAGA
3724 GAAGTCACATTGCCTTCACAATTATATT
1 GAAGTCACATTGCCTTCACAATTATATT
3752 GAAGTCACATTGCCTTCACAATTATATT
1 GAAGTCACATTGCCTTCACAATTATATT
3780 TGAGATTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (28 bp):
GAAGTCACATTGCCTTCACAATTATATT
Found at i:6254 original size:22 final size:22
Alignment explanation
Indices: 6226--6268 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
6216 CAATTTTCTT
6226 TTCGAATTAAATTGTTTGATAC
1 TTCGAATTAAATTGTTTGATAC
6248 TTCGAATTAAATTGTTTGATA
1 TTCGAATTAAATTGTTTGATA
6269 AGTAGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.47
Consensus pattern (22 bp):
TTCGAATTAAATTGTTTGATAC
Found at i:7286 original size:3 final size:3
Alignment explanation
Indices: 7278--7313 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
7268 GGAGAGAGTG
7278 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
7314 ATATATCTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9638 original size:116 final size:116
Alignment explanation
Indices: 9433--9661 Score: 433
Period size: 116 Copynumber: 2.0 Consensus size: 116
9423 TCACTCTCTT
9433 AACTAATACTGCTACTTGCAAGGTTAGTTTTGGGAAATAACTAATAAATATGCATTGGTTTTGCT
1 AACTAATACTGCTACTTGCAAGGTTAGTTTTGGGAAATAACTAATAAATATGCATTGGTTTTGCT
*
9498 AAAGAGACTTATAAATTGAGACAAAAAAAAACCTTCTAAAAGGAGATTTGGA
66 AAAAAGACTTATAAATTGAGAC-AAAAAAAACCTTCTAAAAGGAGATTTGGA
9550 AACTAATACTGCTACTTGCAAGGTTAGTTTT-GGAAATAACTAATAAATATGCATTGGTTTTGCT
1 AACTAATACTGCTACTTGCAAGGTTAGTTTTGGGAAATAACTAATAAATATGCATTGGTTTTGCT
9614 AAAAAGACTTATAAATTGAGACAAAAAAAACCTTCTAAAAGGAGATTT
66 AAAAAGACTTATAAATTGAGACAAAAAAAACCTTCTAAAAGGAGATTT
9662 ATAATTAGGG
Statistics
Matches: 111, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
115 26 0.23
116 54 0.49
117 31 0.28
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (116 bp):
AACTAATACTGCTACTTGCAAGGTTAGTTTTGGGAAATAACTAATAAATATGCATTGGTTTTGCT
AAAAAGACTTATAAATTGAGACAAAAAAAACCTTCTAAAAGGAGATTTGGA
Found at i:11322 original size:2 final size:2
Alignment explanation
Indices: 11315--11342 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11305 AAGTGTATGG
11315 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
11343 TGTTGCAGTA
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:13815 original size:27 final size:26
Alignment explanation
Indices: 13760--13821 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
13750 TCTAAATTTC
13760 TATTATTTTAATAATGGAATAATTAAAA
1 TATTA-TTTAATAATGGAAT-ATTAAAA
13788 TATTATTTAATAATGGTAAT-TTAGAAA
1 TATTATTTAATAATGG-AATATTA-AAA
13815 TA-TATTT
1 TATTATTT
13822 GAAAAAAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.25
27 16 0.50
28 8 0.25
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (26 bp):
TATTATTTAATAATGGAATATTAAAA
Found at i:13878 original size:2 final size:2
Alignment explanation
Indices: 13871--13897 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13861 ATTCGTACTT
13871 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
13898 TCCAAGACAA
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:14414 original size:22 final size:22
Alignment explanation
Indices: 14352--14807 Score: 207
Period size: 22 Copynumber: 21.0 Consensus size: 22
14342 AAATTTTTTT
14352 TAACCTC-CGTATGAAATTTTTGA
1 TAACCTCAC-TATGAAA-TTTTGA
* * *
14375 TGACCT-ACCTAAGGAATTTTGA
1 TAACCTCA-CTATGAAATTTTGA
*
14397 AAACCTCACTATGAAATTTTGA
1 TAACCTCACTATGAAATTTTGA
* *
14419 TAACTTC-CGAATGAAATTTTGA
1 TAACCTCAC-TATGAAATTTTGA
* * *
14441 TAACCAACACTATGAGATGTTGA
1 TAACC-TCACTATGAAATTTTGA
** *
14464 TAACCTC-CATATGGTATATTGA
1 TAACCTCAC-TATGAAATTTTGA
* ** * *
14486 TAACCACGTTATGAAAATTTAA
1 TAACCTCACTATGAAATTTTGA
* *
14508 GAACCTCCAGT-TG-AATTGTT-A
1 TAACCT-CACTATGAAATT-TTGA
* * * *
14529 GTAATCACACTCTGAAATTTTAA
1 -TAACCTCACTATGAAATTTTGA
* * * *
14552 TAATCACATTATGAAATTGTGA
1 TAACCTCACTATGAAATTTTGA
** *
14574 TAA-CTTGCTATAAAATTTTGA
1 TAACCTCACTATGAAATTTTGA
*
14595 TAACCTC-CTTATGAAATCTTGA
1 TAACCTCAC-TATGAAATTTTGA
14617 TAA-CT-AC----AAATTTTGA
1 TAACCTCACTATGAAATTTTGA
* ** *
14633 TAACCTCCCTATGATTTTTTTA
1 TAACCTCACTATGAAATTTTGA
* *
14655 TAACCTCATTATGAAATTTTGT
1 TAACCTCACTATGAAATTTTGA
* *
14677 TAATCTCCCTATGAAATTTTGA
1 TAACCTCACTATGAAATTTTGA
* * *
14699 TCTACAT-AGTATGAAATTTTGA
1 T-AACCTCACTATGAAATTTTGA
*
14721 TAACCCTC-TTATGAAATTTTGA
1 TAA-CCTCACTATGAAATTTTGA
* * *
14743 -AAACTAAACTATGAAATTTTAA
1 TAACCT-CACTATGAAATTTTGA
14765 TAACCTTCA-TATGAAATTTTGA
1 TAACC-TCACTATGAAATTTTGA
* *
14787 TATCCTC-C-CTGAAATTTTGA
1 TAACCTCACTATGAAATTTTGA
14807 T
1 T
14808 TATTCCATAG
Statistics
Matches: 322, Mismatches: 80, Indels: 65
0.69 0.17 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 14 0.04
21 33 0.10
22 218 0.68
23 40 0.12
24 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
TAACCTCACTATGAAATTTTGA
Found at i:14595 original size:21 final size:22
Alignment explanation
Indices: 14560--14621 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 22
14550 AATAATCACA
* * *
14560 TTATGAAATTGTGATAACTTGC
1 TTATAAAATTTTGATAACTTCC
*
14582 -TATAAAATTTTGATAACCTCC
1 TTATAAAATTTTGATAACTTCC
* *
14603 TTATGAAATCTTGATAACT
1 TTATAAAATTTTGATAACT
14622 ACAAATTTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.40
Consensus pattern (22 bp):
TTATAAAATTTTGATAACTTCC
Found at i:14937 original size:22 final size:22
Alignment explanation
Indices: 14912--15332 Score: 155
Period size: 22 Copynumber: 19.0 Consensus size: 22
14902 AATCACATGT
*
14912 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
*
14934 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
14956 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
*** *
14978 TGAAATTTTGATATTTTCATTA
1 TGAAATTTTGATAACCTCTTTA
* *
15000 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
15022 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
*
15044 TGAAATTTTGCTAA--TCTTCCTA
1 TGAAATTTTGATAACCTCTT--TA
*
15066 T-AAATTTCGATAATCCAATCTTTA
1 TGAAATTTTGATAA-CC--TCTTTA
* * * *
15090 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* *
15112 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
15132 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
* *
15152 TGAAATTAAGACTTTTATAACCT-TCATA
1 TGAAA-T-----TTTGATAACCTCT-TTA
* * **
15180 TGAAATTTTGATAAGCACACTA
1 TGAAATTTTGATAACCTCTTTA
** * * **
15202 AAAAATTTTAATAACCACACTA
1 TGAAATTTTGATAACCTCTTTA
**
15224 TGAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCTCTTTA
* *
15246 TGAAATATT-AGTAACCTCCTTA
1 TGAAATTTTGA-TAACCTCTTTA
* * **
15268 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCTTTA
*
15290 TGAAATTCTT-ATAACCT-TGCTA
1 TGAAATT-TTGATAACCTCT-TTA
* *
15312 TGACATTTTGATAATCTCTTT
1 TGAAATTTTGATAACCTCTTT
15333 GATAACCTAA
Statistics
Matches: 296, Mismatches: 75, Indels: 56
0.69 0.18 0.13
Matches are distributed among these distances:
19 2 0.01
20 15 0.05
21 28 0.09
22 211 0.71
23 5 0.02
24 4 0.01
25 12 0.04
26 8 0.03
27 2 0.01
28 9 0.03
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:15248 original size:66 final size:65
Alignment explanation
Indices: 15164--15325 Score: 175
Period size: 66 Copynumber: 2.5 Consensus size: 65
15154 AAATTAAGAC
* *
15164 TTTTATAACCTTCATATGAAATTTTGATAAGCACAC-TAAAAAATTTTAATAACCACACTATGAA
1 TTTTATAACCTTCCTATGAAATTTTGATAACCAC-CTTAAAAAATTTTAATAACCACACTATGAA
15228 A
65 A
* * * ** **
15229 TTTTGATAACCTCCCTATGAAATATT-AGTAACCTCCTTATGAAATTTTGTTAACCACACTATGA
1 TTTT-ATAACCTTCCTATGAAATTTTGA-TAACCACCTTAAAAAATTTTAATAACCACACTATGA
15293 AA
64 AA
* *
15295 TTCTTATAACCTTGCTATGACATTTTGATAA
1 TT-TTATAACCTTCCTATGAAATTTTGATAA
15326 TCTCTTTGAT
Statistics
Matches: 79, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
65 6 0.08
66 70 0.89
67 3 0.04
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (65 bp):
TTTTATAACCTTCCTATGAAATTTTGATAACCACCTTAAAAAATTTTAATAACCACACTATGAAA
Found at i:15442 original size:22 final size:21
Alignment explanation
Indices: 15395--15544 Score: 129
Period size: 22 Copynumber: 6.8 Consensus size: 21
15385 CTTTCCTAAA
*
15395 AAATTTTAATAACCTGATCCTATG
1 AAATTTTGATAACC--A-CCTATG
*
15419 AAATTTTGGTAACCACACTATG
1 AAATTTTGATAACCAC-CTATG
* *
15441 AAATTTTGATAACCTTCCCATG
1 AAATTTTGATAACC-ACCTATG
**
15463 AAATTTTGATAACTTCCATATG
1 AAATTTTGATAACCACC-TATG
*
15485 AAATTTTGGTAACCACCTCATG
1 AAATTTTGATAACCACCT-ATG
* * *
15507 AAATTATAATAACCATCTTATG
1 AAATTTTGATAACCA-CCTATG
*
15529 AAATTTTAATAACCAC
1 AAATTTTGATAACCAC
15545 ACAGAGACAA
Statistics
Matches: 106, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
21 6 0.06
22 85 0.80
23 3 0.03
24 12 0.11
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (21 bp):
AAATTTTGATAACCACCTATG
Found at i:15510 original size:66 final size:66
Alignment explanation
Indices: 15395--15541 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 66
15385 CTTTCCTAAA
* * *
15395 AAATTTTAATAACCTGATCC-TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCC
1 AAATTTTAATAA-CT--TCCATATGAAATTTTGGTAACCACACTATGAAATTATAATAACCATCC
15459 CATG
63 CATG
* **
15463 AAATTTTGATAACTTCCATATGAAATTTTGGTAACCAC-CTCATGAAATTATAATAACCATCTTA
1 AAATTTTAATAACTTCCATATGAAATTTTGGTAACCACACT-ATGAAATTATAATAACCATCCCA
15527 TG
65 TG
15529 AAATTTTAATAAC
1 AAATTTTAATAAC
15542 CACACAGAGA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
65 5 0.07
66 52 0.74
67 2 0.03
68 11 0.16
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (66 bp):
AAATTTTAATAACTTCCATATGAAATTTTGGTAACCACACTATGAAATTATAATAACCATCCCAT
G
Found at i:16237 original size:22 final size:22
Alignment explanation
Indices: 16205--16251 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
16195 ATAATTACAC
16205 TTTGATGACC-TCCTTATGAAAT
1 TTTGATGACCTTCC-TATGAAAT
*
16227 TTTGATTACCTTCCTATGAAAT
1 TTTGATGACCTTCCTATGAAAT
16249 TTT
1 TTT
16252 AACAACGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.47
Consensus pattern (22 bp):
TTTGATGACCTTCCTATGAAAT
Found at i:16439 original size:22 final size:22
Alignment explanation
Indices: 16391--16440 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
16381 ATGATCAACA
* *
16391 TTATGAGATGTTGATAACCTCC
1 TTATGAGATATTGATAACCACC
* * *
16413 ATATGATATATTGATAACCACG
1 TTATGAGATATTGATAACCACC
16435 TTATGA
1 TTATGA
16441 AAATTTCAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (22 bp):
TTATGAGATATTGATAACCACC
Found at i:16496 original size:22 final size:22
Alignment explanation
Indices: 16471--16539 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
16461 GAATTGTTAG
*
16471 TAATTACACTCTGAAATTTTGA
1 TAATTACACTATGAAATTTTGA
* * *
16493 TAATCATACTATGAAATTGTGA
1 TAATTACACTATGAAATTTTGA
* *
16515 TAACCT-CGCTATGAAATTTTGA
1 TAA-TTACACTATGAAATTTTGA
16537 TAA
1 TAA
16540 ACCTTCCTAT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.38
Consensus pattern (22 bp):
TAATTACACTATGAAATTTTGA
Found at i:16769 original size:22 final size:22
Alignment explanation
Indices: 16482--16782 Score: 158
Period size: 22 Copynumber: 13.9 Consensus size: 22
16472 AATTACACTC
* *
16482 TGAAATTTTGATAATCAT-ACTA
1 TGAAATTTTGATAACCTTCA-TA
* *
16504 TGAAATTGTGATAACC-TCGCTA
1 TGAAATTTTGATAACCTTC-ATA
*
16526 TGAAATTTTGATAAACCTTCCTA
1 TGAAATTTTGAT-AACCTTCATA
* * *
16549 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AACCTTCATA
** * *
16572 CAAAATTTTGATAACCTCCTTA
1 TGAAATTTTGATAACCTTCATA
* *
16594 TGAAATCTTGAT-A---GC-TA
1 TGAAATTTTGATAACCTTCATA
* * *
16611 -CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCTTCATA
*
16632 TG-AATGTTTGATAACC-TAATTA
1 TGAAAT-TTTGATAACCTTCA-TA
* * *
16654 TGAAATTTTGTTAATCTCCATA
1 TGAAATTTTGATAACCTTCATA
* * *
16676 TGAAATTTTGATCTACATAC-TA
1 TGAAATTTTGAT-AACCTTCATA
* *
16698 TGAAATTTTGATAACCCTCTTA
1 TGAAATTTTGATAACCTTCATA
* **
16720 TGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCTTCA-TA
*
16742 TTAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAACCTTCATA
* *
16764 AGAAATTTTGATATCCTTC
1 TGAAATTTTGATAACCTTC
16783 CTGAAATTTT
Statistics
Matches: 217, Mismatches: 44, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
16 9 0.04
17 3 0.01
18 1 0.00
20 1 0.00
21 13 0.06
22 137 0.63
23 51 0.24
24 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:16946 original size:22 final size:22
Alignment explanation
Indices: 16897--17314 Score: 178
Period size: 22 Copynumber: 18.9 Consensus size: 22
16887 AATCACATTT
* ** *
16897 TGAAAATTTGATAATTTCTTTA
1 TGAAATTTTGATAACCTCTCTA
16919 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
16941 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
16963 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* ** *
16985 TGTAATTTTGATAACCTCGATT
1 TGAAATTTTGATAACCTCTCTA
** *
17007 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTCTA
*
17029 TGAAATTTTGATAATCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
*
17051 T-AAATTTTGATAATCCAATTTCTA
1 TGAAATTTTGATAA-CC--TCTCTA
* * *
17075 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTCTA
* * *
17097 TGAGA-TTTGATAA-TTTTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
17117 TCAAATTTTGGT-A-CTC-CTTA
1 TGAAATTTTGATAACCTCTC-TA
* *
17137 TGAAATTGAGACTTTTATAATCT-TCATA
1 TGAAA-T-----TTTGATAACCTCTC-TA
* * * *
17165 TGGAATTTTGATAATCACAC-A
1 TGAAATTTTGATAACCTCTCTA
** * * *
17186 AAAAAATTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
* *
17208 TGAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTCTCTA
*
17230 TGAAATATT-AGTAACCT-TCATA
1 TGAAATTTTGA-TAACCTCTC-TA
* * * *
17252 TGAGATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
17274 TGAAATTCTT-ATAACCTCTCTA
1 TGAAATT-TTGATAACCTCTCTA
* *
17296 TGACATTTTGATAATCTCT
1 TGAAATTTTGATAACCTCT
17315 TTGATAACCT
Statistics
Matches: 293, Mismatches: 76, Indels: 54
0.69 0.18 0.13
Matches are distributed among these distances:
19 1 0.00
20 15 0.05
21 45 0.15
22 194 0.66
23 5 0.02
24 6 0.02
25 12 0.04
26 4 0.01
27 2 0.01
28 9 0.03
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:16992 original size:44 final size:44
Alignment explanation
Indices: 16872--17110 Score: 175
Period size: 44 Copynumber: 5.4 Consensus size: 44
16862 AGAAATTCCA
* * * **
16872 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAATTTCT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
* * * * * * *
16916 TTATGAAATTTTGATAACCTC-TCTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACAT-TATGAAATTTTGATAACCTCT
* *
16960 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
* * * *
17004 ATTTGAAATTTTGATAA-CAACACTATGAAATTTTGATAATCT-T
1 CTATGAAATTTTGATAATC-ACATTATGAAATTTTGATAACCTCT
* * *
17047 CCTAT-AAATTTTGATAATC-CAATTTCTATGAAATTTCGATAATCACT
1 -CTATGAAATTTTGATAATCAC-A--T-TATGAAATTTTGATAACCTCT
*
17094 CTATGAGA-TTTGATAAT
1 CTATGAAATTTTGATAAT
17111 TTTCTATCAA
Statistics
Matches: 151, Mismatches: 33, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
42 1 0.01
43 15 0.10
44 101 0.67
45 1 0.01
46 30 0.20
47 3 0.02
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
Done.