Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007806.1 Corchorus capsularis cultivar CVL-1 contig07827, 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: 27416
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:114 original size:66 final size:66
Alignment explanation
Indices: 8--131 Score: 203
Period size: 66 Copynumber: 1.9 Consensus size: 66
1 ATCACAA
* *
8 ATTTAATTGTTATTTATTTTTAACATTATGCAAATTAAATTCTAACGTTATATATTAATGTTATA
1 ATTTAATTATTATTTATTTTTAACATTATGCAAATTAAATTCTAACGTTATAAATTAATGTTATA
73 T
66 T
* * *
74 ATTTAATTATTATTTATTTTTAACGTTATGTAAATTAAATTTTAACGTTATAAATTAA
1 ATTTAATTATTATTTATTTTTAACATTATGCAAATTAAATTCTAACGTTATAAATTAA
132 ATTCTAACGT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.52
Consensus pattern (66 bp):
ATTTAATTATTATTTATTTTTAACATTATGCAAATTAAATTCTAACGTTATAAATTAATGTTATA
T
Found at i:129 original size:20 final size:20
Alignment explanation
Indices: 91--145 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 20
81 TATTATTTAT
91 TTTTAACGTTATGTAAATTAAA
1 TTTTAACGTTA--TAAATTAAA
113 TTTTAACGTTATAAATTAAA
1 TTTTAACGTTATAAATTAAA
*
133 TTCTAACGTTATA
1 TTTTAACGTTATA
146 TATATATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 21 0.66
22 11 0.34
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (20 bp):
TTTTAACGTTATAAATTAAA
Found at i:208 original size:19 final size:21
Alignment explanation
Indices: 184--232 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
174 TTATATAACA
*
184 TTATATTT-AATTCTTAAGGT
1 TTATATTTAAATTCTTAACGT
204 TATATATATTAAATTCTTAACG-
1 T-TATAT-TTAAATTCTTAACGT
226 TTATATT
1 TTATATT
233 CAATATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 2 0.08
21 10 0.40
22 3 0.12
23 10 0.40
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (21 bp):
TTATATTTAAATTCTTAACGT
Found at i:230 original size:21 final size:23
Alignment explanation
Indices: 152--231 Score: 79
Period size: 23 Copynumber: 3.2 Consensus size: 23
142 TATATATATA
*
152 TATATATATTAAATTCTTAATGTT
1 TATATATATTAAATTCTTAACG-T
* *
176 ATATAACATTATATTTAATTCTTAAGGT
1 -TAT---A-TATATTAAATTCTTAACGT
204 TATATATATTAAATTCTTAACGT
1 TATATATATTAAATTCTTAACGT
227 TATAT
1 TATAT
232 TCAATATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
23 22 0.47
24 1 0.02
25 3 0.06
27 3 0.06
28 2 0.04
29 16 0.34
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50
Consensus pattern (23 bp):
TATATATATTAAATTCTTAACGT
Found at i:1629 original size:2 final size:2
Alignment explanation
Indices: 1622--1654 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1612 TGCTAGTATG
1622 TA 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 TA T
1655 GATCATTAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5085 original size:75 final size:76
Alignment explanation
Indices: 4939--5086 Score: 192
Period size: 76 Copynumber: 2.0 Consensus size: 76
4929 TCAACGCCAT
* * *
4939 AAATTGACAGATTTGAAGGATTTGGAATTGATGAAGAATATGATCGTTGGAGGCAAATATAAGTA
1 AAATTGACAGATTTGAAGGATTTGCAATTAATGAAGAATATGACCGTTGGAGGCAAATATAAGTA
*
5004 TTTAAGGAAAC
66 TATAAGGAAAC
* ** * *
5015 AAATTGACAGATTTGATA-GATTTGCATTTAATGTGGAA-ATGACCGTTGGAGGCAAATGTGAGT
1 AAATTGACAGATTTGA-AGGATTTGCAATTAATGAAGAATATGACCGTTGGAGGCAAATATAAGT
5078 ATATAAGGA
65 ATATAAGGA
5087 CTCGAGAAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
75 30 0.48
76 31 0.50
77 1 0.02
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.30
Consensus pattern (76 bp):
AAATTGACAGATTTGAAGGATTTGCAATTAATGAAGAATATGACCGTTGGAGGCAAATATAAGTA
TATAAGGAAAC
Found at i:5470 original size:16 final size:16
Alignment explanation
Indices: 5438--5497 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
5428 ACCCGCCTGA
*
5438 ACCCGAACCTG-AAAT
1 ACCCGAACCCGAAAAT
5453 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
* *
5469 ACCTGAACCCGAGACA-
1 ACCCGAACCCGA-AAAT
5485 ACCCGAACCCGAA
1 ACCCGAACCCGAA
5498 CCCGCCCGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
15 11 0.28
16 26 0.67
17 2 0.05
ACGTcount: A:0.40, C:0.38, G:0.15, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:5505 original size:16 final size:16
Alignment explanation
Indices: 5486--5517 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5476 CCCGAGACAA
5486 CCCGAACCCGAACCCG
1 CCCGAACCCGAACCCG
*
5502 CCCGAACGCGAACCCG
1 CCCGAACCCGAACCCG
5518 ACCCCAGCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.53, G:0.22, T:0.00
Consensus pattern (16 bp):
CCCGAACCCGAACCCG
Found at i:6077 original size:47 final size:47
Alignment explanation
Indices: 6022--6115 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
6012 TTAGTTTTTT
6022 TAACAATTACTCAATCTTTATATATGCTTCCTCCTTTCTCCGTTCCA
1 TAACAATTACTCAATCTTTATATATGCTTCCTCCTTTCTCCGTTCCA
6069 TAACAATTACTCAATCTTTATATATGCTTCCTCCTTTCTCCGTTCCA
1 TAACAATTACTCAATCTTTATATATGCTTCCTCCTTTCTCCGTTCCA
6116 AAATAACTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.23, C:0.30, G:0.04, T:0.43
Consensus pattern (47 bp):
TAACAATTACTCAATCTTTATATATGCTTCCTCCTTTCTCCGTTCCA
Found at i:6382 original size:16 final size:16
Alignment explanation
Indices: 6358--6430 Score: 114
Period size: 15 Copynumber: 4.7 Consensus size: 16
6348 CGAACCCGAT
6358 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
6374 CCAAACCCG-AAATAC
1 CCGAACCCGAAAATAC
6389 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
6405 CCGAACCCG-AAGTAC
1 CCGAACCCGAAAATAC
6420 CCGAACCCGAA
1 CCGAACCCGAA
6431 CCCGAACCCG
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
15 28 0.54
16 24 0.46
ACGTcount: A:0.41, C:0.40, G:0.14, T:0.05
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:6395 original size:31 final size:31
Alignment explanation
Indices: 6358--6430 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
6348 CGAACCCGAT
6358 CCGAACCCGAAAATACCCAAACCCGAAATAC
1 CCGAACCCGAAAATACCCAAACCCGAAATAC
* *
6389 CCGAACCCGAAAATACCCGAACCCGAAGTAC
1 CCGAACCCGAAAATACCCAAACCCGAAATAC
6420 CCGAACCCGAA
1 CCGAACCCGAA
6431 CCCGAACCCG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.41, C:0.40, G:0.14, T:0.05
Consensus pattern (31 bp):
CCGAACCCGAAAATACCCAAACCCGAAATAC
Found at i:6412 original size:6 final size:6
Alignment explanation
Indices: 6403--6450 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
6393 ACCCGAAAAT
6403 ACCCGA ACCCGAA GTACCCGA ACCCGA ACCCGA ACCCG- -CCCGA ACCCG
1 ACCCGA ACCCG-A --ACCCGA ACCCGA ACCCGA ACCCGA ACCCGA ACCCG
6451 CCCAATTGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
4 4 0.11
6 26 0.70
7 1 0.03
8 1 0.03
9 5 0.14
ACGTcount: A:0.29, C:0.50, G:0.19, T:0.02
Consensus pattern (6 bp):
ACCCGA
Found at i:6446 original size:10 final size:10
Alignment explanation
Indices: 6419--6453 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
6409 ACCCGAAGTA
6419 CCCGAACCCG
1 CCCGAACCCG
6429 AACCCGAACCCG
1 --CCCGAACCCG
6441 CCCGAACCCG
1 CCCGAACCCG
6451 CCC
1 CCC
6454 AATTGCCAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
12 10 0.43
ACGTcount: A:0.23, C:0.60, G:0.17, T:0.00
Consensus pattern (10 bp):
CCCGAACCCG
Found at i:6502 original size:28 final size:28
Alignment explanation
Indices: 6462--6523 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
6452 CCAATTGCCA
6462 GTTCTAGTAATTAGTGCGGGGAGCACTT
1 GTTCTAGTAATTAGTGCGGGGAGCACTT
6490 GTTCTAGTAATTAGTGCGGGGAGCACTT
1 GTTCTAGTAATTAGTGCGGGGAGCACTT
6518 GTTCTA
1 GTTCTA
6524 AGCTTGGGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.34
Consensus pattern (28 bp):
GTTCTAGTAATTAGTGCGGGGAGCACTT
Found at i:9364 original size:7 final size:7
Alignment explanation
Indices: 9352--9383 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
9342 AGCAGTTGGA
9352 AATTTTC
1 AATTTTC
9359 AATTTTC
1 AATTTTC
*
9366 AATCTTC
1 AATTTTC
9373 AATTTTC
1 AATTTTC
9380 AATT
1 AATT
9384 CTGTTTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (7 bp):
AATTTTC
Found at i:12314 original size:3 final size:3
Alignment explanation
Indices: 12308--12355 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
12298 CTACTAGTAC
12308 TAT TAT TAT ATAT TAT TA- TAT TAT TAT TAT TA- TAT ATAT TA- TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
12352 TAT T
1 TAT T
12356 TTTAGTGACT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 6 0.15
3 28 0.70
4 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:12331 original size:18 final size:18
Alignment explanation
Indices: 12308--12355 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
12298 CTACTAGTAC
12308 TATTATTATATATTAT-TA
1 TATTATTAT-TATTATATA
12326 TATTATTATTATTATATA
1 TATTATTATTATTATATA
12344 TATTA-TATTATT
1 TATTATTATTATT
12356 TTTAGTGACT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 13 0.45
18 16 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTATTATTATTATATA
Found at i:12337 original size:14 final size:14
Alignment explanation
Indices: 12311--12354 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
12301 CTAGTACTAT
12311 TATTATATATTATTA
1 TATTAT-TATTATTA
12326 TATTATTATTATTA
1 TATTATTATTATTA
12340 TATATATTA-TATTA
1 TAT-TATTATTATTA
12354 T
1 T
12355 TTTTAGTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:12439 original size:16 final size:17
Alignment explanation
Indices: 12413--12444 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12403 GGTGCCTCCT
12413 TTTTGTTTTGTTTTTTG
1 TTTTGTTTTGTTTTTTG
12430 TTTT-TTTTGTTTTTT
1 TTTTGTTTTGTTTTTT
12445 CTCACTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (17 bp):
TTTTGTTTTGTTTTTTG
Found at i:17846 original size:17 final size:16
Alignment explanation
Indices: 17824--17863 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
17814 GAATGAGGAT
17824 AAGAGGAAGTAGCTGGC
1 AAGAGG-AGTAGCTGGC
*
17841 AAGAGGTGTAGCTGGC
1 AAGAGGAGTAGCTGGC
17857 AAG-GGAG
1 AAGAGGAG
17864 CAGGTGAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 3 0.14
16 12 0.57
17 6 0.29
ACGTcount: A:0.33, C:0.10, G:0.45, T:0.12
Consensus pattern (16 bp):
AAGAGGAGTAGCTGGC
Found at i:19160 original size:40 final size:40
Alignment explanation
Indices: 19109--19255 Score: 217
Period size: 40 Copynumber: 3.7 Consensus size: 40
19099 CATAGTTAAG
19109 GACTTAATTCATAGAAATTAAGTAAAAACAGCAGTCGAAA
1 GACTTAATTCATAGAAATTAAGTAAAAACAGCAGTCGAAA
*
19149 GACTTAATTCATAGAAATTAAGTAAAAACAGTAGTC-AGAA
1 GACTTAATTCATAGAAATTAAGTAAAAACAGCAGTCGA-AA
* * * *
19189 GACTTAATTCATAGAAATCAAGTAAAAACAACAATCTG-AG
1 GACTTAATTCATAGAAATTAAGTAAAAACAGCAGTC-GAAA
19229 GACTTAATTCATAGAAATTAAGTAAAA
1 GACTTAATTCATAGAAATTAAGTAAAA
19256 GTAAAAAAAA
Statistics
Matches: 97, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
39 1 0.01
40 96 0.99
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (40 bp):
GACTTAATTCATAGAAATTAAGTAAAAACAGCAGTCGAAA
Found at i:19345 original size:73 final size:75
Alignment explanation
Indices: 19260--19415 Score: 235
Period size: 78 Copynumber: 2.1 Consensus size: 75
19250 GTAAAAGTAA
*
19260 AAAAAAAAGAGACTGGCTTAGTTTC-AAGGAAACTAGGTAAAGAAAAGACTG-CTTAATTTCAAG
1 AAAAAAAAGAGACTGGCTTAATTTCAAAGGAAACTAGGTAAAGAAAAGACTGACTTAATTTCAAG
19323 GAAATTAAGT
66 GAAATTAAGT
* * *
19333 AAAAAAAGGAGACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAGATTGACTTAATTTC
1 AAAAAAAAGAGACTGGCTTAATTTC---AAAGGAAACTAGGTAAAGAAAAGACTGACTTAATTTC
19398 AAGGAAATTAAGT
63 AAGGAAATTAAGT
19411 AAAAA
1 AAAAA
19416 GACTGGCTCA
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
73 23 0.31
77 24 0.32
78 27 0.36
ACGTcount: A:0.49, C:0.08, G:0.20, T:0.23
Consensus pattern (75 bp):
AAAAAAAAGAGACTGGCTTAATTTCAAAGGAAACTAGGTAAAGAAAAGACTGACTTAATTTCAAG
GAAATTAAGT
Found at i:19420 original size:73 final size:75
Alignment explanation
Indices: 19285--19478 Score: 259
Period size: 73 Copynumber: 2.6 Consensus size: 75
19275 GCTTAGTTTC
*
19285 AAGGAAACTAGGTAAAGAAAAGACTG-CTTAATTTCAAGGAAATTAAGTAAAAAAAGGAGACTGG
1 AAGGAAATTAGGTAAAGAAAAGACTGACTTAATTTCAAGGAAATTAAGT--AAAAA-GAGACTGG
*
19349 CTTAATTTCAAGA
63 CTCAATTTCAAGA
*
19362 AAGGAAATTAGGTAAAGAAAAGATTGACTTAATTTCAAGGAAATTAAGT-AAAA-AGACTGGCTC
1 AAGGAAATTAGGTAAAGAAAAGACTGACTTAATTTCAAGGAAATTAAGTAAAAAGAGACTGGCTC
* *
19425 AGTTTTAAGA
66 AATTTCAAGA
* * *
19435 AAGGAAATTAGGTAAGGATAAGAACAGACTTAATTTCAAGGAAA
1 AAGGAAATTAGGTAAAGAAAAG-ACTGACTTAATTTCAAGGAAA
19479 GAAATTAGGT
Statistics
Matches: 106, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
73 37 0.35
74 19 0.18
75 4 0.04
77 24 0.23
78 22 0.21
ACGTcount: A:0.48, C:0.08, G:0.21, T:0.23
Consensus pattern (75 bp):
AAGGAAATTAGGTAAAGAAAAGACTGACTTAATTTCAAGGAAATTAAGTAAAAAGAGACTGGCTC
AATTTCAAGA
Found at i:19485 original size:41 final size:42
Alignment explanation
Indices: 19433--19511 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 42
19423 TCAGTTTTAA
*
19433 GAAAGGAAATTAGGTAAGGATAAGAACAGACTTAATTTCAAG
1 GAAAGGAAATTAGGTAAGGACAAGAACAGACTTAATTTCAAG
* *
19475 GAAA-GAAATTAGGTAAGGACCAGCACAGACTTAATTT
1 GAAAGGAAATTAGGTAAGGACAAGAACAGACTTAATTT
19512 AGGGTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 30 0.88
42 4 0.12
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.22
Consensus pattern (42 bp):
GAAAGGAAATTAGGTAAGGACAAGAACAGACTTAATTTCAAG
Found at i:19703 original size:36 final size:35
Alignment explanation
Indices: 19517--19685 Score: 293
Period size: 35 Copynumber: 4.8 Consensus size: 35
19507 AATTTAGGGT
19517 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
19552 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
*
19587 AATTAAGTAAATTAACAAAGACTTAATTTCACAAG
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
19622 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGT-AAATTAGCAAAGACTTAATTTCACAAG
* *
19658 AATTAAGTAAAGTCAGCAAAGATTTAAT
1 AATTAAGTAAA-TTAGCAAAGACTTAAT
19686 CCAAAGATGA
Statistics
Matches: 128, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
35 80 0.62
36 48 0.38
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (35 bp):
AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
Found at i:19760 original size:11 final size:11
Alignment explanation
Indices: 19744--19869 Score: 162
Period size: 11 Copynumber: 11.2 Consensus size: 11
19734 TTAGGCAAAA
19744 GAAAGAAGACT
1 GAAAGAAGACT
19755 GAAAGAAGACT
1 GAAAGAAGACT
*
19766 GAAAGAAAACT
1 GAAAGAAGACT
19777 GAAAGAAGACT
1 GAAAGAAGACT
* *
19788 AAAAAAAGACT
1 GAAAGAAGACT
19799 GAAAGAAGACT
1 GAAAGAAGACT
*
19810 GAAAAAAGGACT
1 GAAAGAA-GACT
19822 GAAAGAAGACT
1 GAAAGAAGACT
* *
19833 GAAAAAAGACAA
1 GAAAGAAGAC-T
*
19845 AAAAGAAGGACT
1 GAAAGAA-GACT
19857 GAAAGAAGACT
1 GAAAGAAGACT
19868 GA
1 GA
19870 CTTAATTTCA
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
11 74 0.76
12 21 0.21
13 3 0.03
ACGTcount: A:0.60, C:0.09, G:0.24, T:0.08
Consensus pattern (11 bp):
GAAAGAAGACT
Found at i:20003 original size:39 final size:35
Alignment explanation
Indices: 19858--20132 Score: 290
Period size: 35 Copynumber: 7.8 Consensus size: 35
19848 AGAAGGACTG
* *
19858 AAAGA-AGACTGACTTAATTTCAAAGAAATTAGGT
1 AAAGATAGACTGGCTTAATTTCAAGGAAATTAGGT
*
19892 AAAAGA-AGACTGGCTTAGTTTCAAGGAAATTAGGT
1 -AAAGATAGACTGGCTTAATTTCAAGGAAATTAGGT
19927 AAAGATAGACTGGCTTAATTTCAAGGAAATTAGGT
1 AAAGATAGACTGGCTTAATTTCAAGGAAATTAGGT
* *
19962 AAAGATATACTGGCTTAATTTCAAGAAAGGAAATTGGGT
1 AAAGATAGACTGGCTTAATTTC----AAGGAAATTAGGT
* * *
20001 AAAGATAGACTGGCTTAATTTGAAGGAAATTAAGC
1 AAAGATAGACTGGCTTAATTTCAAGGAAATTAGGT
* * * *
20036 AAAGAAAAGACTGGC-TAGTTTCAGGGAAACTAGGT
1 AAAG-ATAGACTGGCTTAATTTCAAGGAAATTAGGT
* * * *
20071 AAAGAAAGACTGGCTTAATTTTAAGAAAATTAAGT
1 AAAGATAGACTGGCTTAATTTCAAGGAAATTAGGT
* * *
20106 AAA-AGACACAGGCTTAATTTC-AGGAAA
1 AAAGATAGACTGGCTTAATTTCAAGGAAA
20133 GGAAATTAAG
Statistics
Matches: 204, Mismatches: 29, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
33 5 0.02
34 29 0.14
35 129 0.63
36 9 0.04
39 32 0.16
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.25
Consensus pattern (35 bp):
AAAGATAGACTGGCTTAATTTCAAGGAAATTAGGT
Found at i:20011 original size:109 final size:109
Alignment explanation
Indices: 19858--20098 Score: 298
Period size: 109 Copynumber: 2.3 Consensus size: 109
19848 AGAAGGACTG
* *
19858 AAAG-AAGACTGACTTAATTTC---AAA-GAAATTAGGTAAAAGAAGACTGGCTTAGTTTCAAGG
1 AAAGAAAGACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAAGAAGACTGGCTTAATTTCAAGG
* * * *
19918 AAATTAGGTAAAG-ATAGACTGGCTTAATTTCAAGGAAATTAGGT
66 AAATTAAGCAAAGAAAAGACTGGC-TAATTTCAAGGAAACTAGGT
* * * *
19962 AAAGATATACTGGCTTAATTTCAAGAAAGGAAATTGGGT-AAAGATAGACTGGCTTAATTTGAAG
1 AAAGAAAGACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAAGA-AGACTGGCTTAATTTCAAG
* *
20026 GAAATTAAGCAAAGAAAAGACTGGCTAGTTTCAGGGAAACTAGGT
65 GAAATTAAGCAAAGAAAAGACTGGCTAATTTCAAGGAAACTAGGT
*
20071 AAAGAAAGACTGGCTTAATTTTAAGAAA
1 AAAGAAAGACTGGCTTAATTTCAAGAAA
20099 ATTAAGTAAA
Statistics
Matches: 115, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
104 4 0.03
105 14 0.12
108 8 0.07
109 80 0.70
110 9 0.08
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.26
Consensus pattern (109 bp):
AAAGAAAGACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAAGAAGACTGGCTTAATTTCAAGG
AAATTAAGCAAAGAAAAGACTGGCTAATTTCAAGGAAACTAGGT
Done.