Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010187.1 Corchorus capsularis cultivar CVL-1 contig10208, 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: 76111
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:186 original size:20 final size:20
Alignment explanation
Indices: 161--200 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
151 AAAAAGGAGT
161 AAAAATAATGGTCTGCAAAG
1 AAAAATAATGGTCTGCAAAG
181 AAAAATAATGGTCTGCAAAG
1 AAAAATAATGGTCTGCAAAG
201 TTATCATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.20, T:0.20
Consensus pattern (20 bp):
AAAAATAATGGTCTGCAAAG
Found at i:347 original size:92 final size:92
Alignment explanation
Indices: 190--428 Score: 451
Period size: 92 Copynumber: 2.6 Consensus size: 92
180 GAAAAATAAT
*
190 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGATATTGTCTCCAATAATGCAAAGCTGACTCAT
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
255 TGAATGAAGAGAAAGCCAAATTATGAA
66 TGAATGAAGAGAAAGCCAAATTATGAA
282 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
*
347 TGGATGAAGAGAAAGCCAAATTATGAA
66 TGAATGAAGAGAAAGCCAAATTATGAA
*
374 GGTCTGCAAAGTTATCGTGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAA
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAA
429 TAGTACAAAG
Statistics
Matches: 144, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 144 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (92 bp):
GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
TGAATGAAGAGAAAGCCAAATTATGAA
Found at i:3463 original size:30 final size:30
Alignment explanation
Indices: 3427--3487 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
3417 CAATTCTTGC
*
3427 TTCTTGAAATAATTCTTCAAT-AGTCTTCAA
1 TTCTTGAAATAA-TCTTCAATAAATCTTCAA
*
3457 TTCTTGAAATTATCTTCAATAAATCTTCAA
1 TTCTTGAAATAATCTTCAATAAATCTTCAA
3487 T
1 T
3488 CACGAACTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.44
Consensus pattern (30 bp):
TTCTTGAAATAATCTTCAATAAATCTTCAA
Found at i:7233 original size:26 final size:28
Alignment explanation
Indices: 7187--7338 Score: 80
Period size: 26 Copynumber: 5.8 Consensus size: 28
7177 ATAATAAAAC
* * *
7187 ATATATGATATATATATAATATCTTT-TA
1 ATATAT-ATTTATATAAAATATATTTATA
7215 A-ATATATTTATATAAAATATATTTATA
1 ATATATATTTATATAAAATATATTTATA
* * * *
7242 ATATATAATATATTTTAAATTTTATTTAT-
1 ATATAT-ATTTA-TATAAAATATATTTATA
* * *
7271 -T-TATATATA-ATAAAA-ACATATATA
1 ATATATATTTATATAAAATATATTTATA
*
7295 ATATA-A--TATATATAATATATTT-TA
1 ATATATATTTATATAAAATATATTTATA
7319 A-ATATA-TTATATAAAA-ATAT
1 ATATATATTTATATAAAATATAT
7339 CTATTCGGTT
Statistics
Matches: 97, Mismatches: 16, Indels: 26
0.70 0.12 0.19
Matches are distributed among these distances:
23 10 0.10
24 17 0.18
25 14 0.14
26 23 0.24
27 10 0.10
28 6 0.06
29 4 0.04
30 13 0.13
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
ATATATATTTATATAAAATATATTTATA
Found at i:7234 original size:15 final size:17
Alignment explanation
Indices: 7213--7332 Score: 68
Period size: 18 Copynumber: 6.9 Consensus size: 17
7203 TAATATCTTT
7213 TAAATATATTTAT-ATA
1 TAAATATATTTATAATA
7229 -AAATATATTTATAATA
1 TAAATATATTTATAATA
7245 TATAATATATTT-TAA-A
1 TA-AATATATTTATAATA
** *
7261 TTTTATTTATTTATATATAA
1 -TAAATATATTTATA-AT-A
* * *
7281 TAAAAACATATATAATA
1 TAAATATATTTATAATA
* * *
7298 TAATATATATAATATATTT
1 TAA-ATATAT-TTATAATA
7317 TAAATATATTATATAA
1 TAAATATATT-TATAA
7333 AAATATCTAT
Statistics
Matches: 78, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
15 12 0.15
16 11 0.14
17 11 0.14
18 26 0.33
19 17 0.22
20 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATATATTTATAATA
Found at i:7246 original size:55 final size:52
Alignment explanation
Indices: 7170--7338 Score: 131
Period size: 51 Copynumber: 3.3 Consensus size: 52
7160 AATTTTATTT
* * *
7170 TTTATATATAATA-AAACATATAT-GATATATATATAATATCTTTTAAATATA
1 TTTATATAAAATATATACATATATATATATATATATAATAT-TTTTAAATATA
** * *
7221 TTTATATAAAATATATTTATA-ATATATAATATATTTTAA-A-TTTT--ATTTA
1 TTTATATAAAATATATACATATATATAT-ATATA-TATAATATTTTTAAATATA
* * *
7270 TTTATATATAATAAAAACATATATAATATAATATATATAATATATTTTAAATATA
1 TTTATATAAAATATATACATATAT-ATAT-ATATATATAATAT-TTTTAAATATA
7325 -TTATATAAAA-ATAT
1 TTTATATAAAATATAT
7339 CTATTCGGTT
Statistics
Matches: 90, Mismatches: 17, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
49 20 0.22
50 6 0.07
51 29 0.32
52 6 0.07
53 12 0.13
54 13 0.14
55 4 0.04
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (52 bp):
TTTATATAAAATATATACATATATATATATATATATAATATTTTTAAATATA
Found at i:7251 original size:18 final size:15
Alignment explanation
Indices: 7214--7256 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
7204 AATATCTTTT
7214 AAATATATTTATATA
1 AAATATATTTATATA
7229 AAATATATTTATAATA
1 AAATATATTTAT-ATA
7245 TATAATATATTT
1 -A-AATATATTT
7257 TAAATTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.48
16 3 0.12
17 1 0.04
18 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATATATTTATATA
Found at i:7292 original size:44 final size:44
Alignment explanation
Indices: 7200--7292 Score: 98
Period size: 44 Copynumber: 2.1 Consensus size: 44
7190 TATGATATAT
* * * * *
7200 ATATAATATCTTTTAAATATATTTATATAAAATATATTTATAAT
1 ATATAATATATTTTAAATATATTTATATAAAATATAATAAAAAC
* * *
7244 ATATAATATATTTTAAATTTTATTTAT-TTATATATAATAAAAAC
1 ATATAATATATTTTAAA-TATATTTATATAAAATATAATAAAAAC
7288 ATATA
1 ATATA
7293 TAATATAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
44 32 0.80
45 8 0.20
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (44 bp):
ATATAATATATTTTAAATATATTTATATAAAATATAATAAAAAC
Found at i:7317 original size:53 final size:52
Alignment explanation
Indices: 7161--7318 Score: 150
Period size: 53 Copynumber: 3.1 Consensus size: 52
7151 TATATTTTAA
*
7161 ATTTTATTT-TTTATATATAAT-AAAACATATAT--GATATATATATAATAT
1 ATTTTATTTATTTATATATAATAAAAACATATATAATATATATATATAATAT
* ** * * * ** *
7209 CTTTTAAATATATT-TATAT-A-AAATATATTTATAATATATAATATATTTTAA
1 ATTTTATTTAT-TTATATATAATAAAAACATATATAATATAT-ATATATAATAT
7260 ATTTTATTTATTTATATATAATAAAAACATATATAATATAATATATATAATAT
1 ATTTTATTTATTTATATATAATAAAAACATATATAATAT-ATATATATAATAT
7313 ATTTTA
1 ATTTTA
7319 AATATATTAT
Statistics
Matches: 81, Mismatches: 19, Indels: 15
0.70 0.17 0.13
Matches are distributed among these distances:
48 15 0.19
49 6 0.07
50 8 0.10
51 21 0.26
52 1 0.01
53 28 0.35
54 2 0.02
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (52 bp):
ATTTTATTTATTTATATATAATAAAAACATATATAATATATATATATAATAT
Found at i:13369 original size:9 final size:9
Alignment explanation
Indices: 13355--13393 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
13345 TTAATTTCTT
*
13355 TTAATTTAA
1 TTAATTAAA
13364 TTAATTAAA
1 TTAATTAAA
**
13373 TTAAAGAAA
1 TTAATTAAA
13382 TTAATTAAA
1 TTAATTAAA
13391 TTA
1 TTA
13394 TGTTCAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (9 bp):
TTAATTAAA
Found at i:15593 original size:15 final size:15
Alignment explanation
Indices: 15569--15612 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
15559 TGCTAGGGTG
*
15569 AATGGCGCAAACAAC
1 AATGGTGCAAACAAC
15584 AATGGTGCAAACAAC
1 AATGGTGCAAACAAC
* *
15599 CATGGTGCGAACAA
1 AATGGTGCAAACAA
15613 TCATGTTGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (15 bp):
AATGGTGCAAACAAC
Found at i:15617 original size:15 final size:15
Alignment explanation
Indices: 15570--15617 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
15560 GCTAGGGTGA
* *
15570 ATGGCGCAAACAACA
1 ATGGTGCAAACAACC
15585 ATGGTGCAAACAACC
1 ATGGTGCAAACAACC
* *
15600 ATGGTGCGAACAATC
1 ATGGTGCAAACAACC
15615 ATG
1 ATG
15618 TTGTGCAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.15
Consensus pattern (15 bp):
ATGGTGCAAACAACC
Found at i:31420 original size:6 final size:6
Alignment explanation
Indices: 31409--31453 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
31399 TATATTCTGC
31409 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
31454 GCTTTGTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (6 bp):
TTTAGA
Found at i:34149 original size:10 final size:10
Alignment explanation
Indices: 34134--34158 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
34124 ATTCATGCAC
34134 AATTCCAGAA
1 AATTCCAGAA
34144 AATTCCAGAA
1 AATTCCAGAA
34154 AATTC
1 AATTC
34159 TAGAGTCGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:35097 original size:6 final size:6
Alignment explanation
Indices: 35086--35112 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
35076 TATATTCTGC
35086 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
35113 GCTTTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:36729 original size:15 final size:15
Alignment explanation
Indices: 36694--36733 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
36684 GGAACCAAGG
*
36694 TAATTTTC-AAGGCC
1 TAATTTTCAAAGACC
*
36708 GAATTTTCAAAGACC
1 TAATTTTCAAAGACC
36723 TAATTTTCAAA
1 TAATTTTCAAA
36734 CTTCACAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (15 bp):
TAATTTTCAAAGACC
Found at i:38042 original size:21 final size:21
Alignment explanation
Indices: 37981--38043 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
37971 CCAGCCTCTG
*
37981 CCGTGCCGCCTGCCCGGCCAAG
1 CCGTGCCGCCTGCCCGGCC-AT
*
38003 CCAG-GCC-ACTG-CCGCGCCAT
1 CC-GTGCCGCCTGCCCG-GCCAT
38023 CCGTGCCGCCTGCCCGGCCAT
1 CCGTGCCGCCTGCCCGGCCAT
38044 GCTCGGACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
19 1 0.03
20 9 0.27
21 14 0.42
22 8 0.24
23 1 0.03
ACGTcount: A:0.10, C:0.51, G:0.29, T:0.11
Consensus pattern (21 bp):
CCGTGCCGCCTGCCCGGCCAT
Found at i:40513 original size:10 final size:10
Alignment explanation
Indices: 40498--40522 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40488 GTTCCTGCAC
40498 AATTCCAGAA
1 AATTCCAGAA
40508 AATTCCAGAA
1 AATTCCAGAA
40518 AATTC
1 AATTC
40523 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:41460 original size:6 final size:6
Alignment explanation
Indices: 41449--41487 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
41439 TATATTCTGC
41449 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
41488 TCTTTGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (6 bp):
TTTAGA
Found at i:53264 original size:32 final size:32
Alignment explanation
Indices: 53228--53350 Score: 201
Period size: 32 Copynumber: 3.8 Consensus size: 32
53218 ATTTGAACCT
53228 AAACCCGAAAAAACCCGAACCCGAAAAAGCTC
1 AAACCCGAAAAAACCCGAACCCGAAAAAGCTC
* *
53260 AAACCCGAAAAAACACGAAGCCGAAAAAGCTC
1 AAACCCGAAAAAACCCGAACCCGAAAAAGCTC
*
53292 AAACCCGAAAAAATCCGAACCCGAAAAAGCTC
1 AAACCCGAAAAAACCCGAACCCGAAAAAGCTC
* *
53324 AAATCCGAAAAAACCCGAATCCGAAAA
1 AAACCCGAAAAAACCCGAACCCGAAAA
53351 TCTATGAAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 83 1.00
ACGTcount: A:0.52, C:0.30, G:0.13, T:0.05
Consensus pattern (32 bp):
AAACCCGAAAAAACCCGAACCCGAAAAAGCTC
Found at i:53344 original size:16 final size:16
Alignment explanation
Indices: 53229--53350 Score: 118
Period size: 16 Copynumber: 7.6 Consensus size: 16
53219 TTTGAACCTA
53229 AACCCGAAAAAACCCG
1 AACCCGAAAAAACCCG
* * *
53245 AACCCGAAAAAGCTCA
1 AACCCGAAAAAACCCG
*
53261 AACCCGAAAAAACACG
1 AACCCGAAAAAACCCG
* * * *
53277 AAGCCGAAAAAGCTCA
1 AACCCGAAAAAACCCG
*
53293 AACCCGAAAAAATCCG
1 AACCCGAAAAAACCCG
* * *
53309 AACCCGAAAAAGCTCA
1 AACCCGAAAAAACCCG
*
53325 AATCCGAAAAAACCCG
1 AACCCGAAAAAACCCG
*
53341 AATCCGAAAA
1 AACCCGAAAA
53351 TCTATGAAAA
Statistics
Matches: 83, Mismatches: 23, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 83 1.00
ACGTcount: A:0.52, C:0.30, G:0.13, T:0.05
Consensus pattern (16 bp):
AACCCGAAAAAACCCG
Found at i:53526 original size:32 final size:31
Alignment explanation
Indices: 53498--53605 Score: 153
Period size: 32 Copynumber: 3.4 Consensus size: 31
53488 ACCCAAACAG
*
53498 AACCCGAACTCGAATTAACCTGATCCAAATTC
1 AACCCGAACCCGAATTAACCTGATCCAAA-TC
* * *
53530 AACCCAAACCCGAATTAATCTGATCCAAATT
1 AACCCGAACCCGAATTAACCTGATCCAAATC
*
53561 AACCCGAACCCAAATTAACCTGATCCAAATCC
1 AACCCGAACCCGAATTAACCTGATCCAAAT-C
53593 AACCCGAACCCGA
1 AACCCGAACCCGA
53606 CTCAAACCCG
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
31 28 0.42
32 38 0.58
ACGTcount: A:0.40, C:0.34, G:0.08, T:0.18
Consensus pattern (31 bp):
AACCCGAACCCGAATTAACCTGATCCAAATC
Found at i:53562 original size:15 final size:15
Alignment explanation
Indices: 53510--53590 Score: 72
Period size: 15 Copynumber: 5.2 Consensus size: 15
53500 CCCGAACTCG
53510 AATTAACCTGATCCA
1 AATTAACCTGATCCA
** * *
53525 AATTCAACCCAAACCCG
1 AATT-AA-CCTGATCCA
*
53542 AATTAATCTGATCCA
1 AATTAACCTGATCCA
* *
53557 AATTAACCCGAACCCA
1 AATTAACCTG-ATCCA
53573 AATTAACCTGATCCA
1 AATTAACCTGATCCA
53588 AAT
1 AAT
53591 CCAACCCGAA
Statistics
Matches: 49, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
15 23 0.47
16 17 0.35
17 9 0.18
ACGTcount: A:0.42, C:0.30, G:0.06, T:0.22
Consensus pattern (15 bp):
AATTAACCTGATCCA
Found at i:53631 original size:63 final size:63
Alignment explanation
Indices: 53498--53637 Score: 156
Period size: 63 Copynumber: 2.2 Consensus size: 63
53488 ACCCAAACAG
* * * * * * *
53498 AACCCGAACTCGAATTAACCTGATCCAAATTCAACCCAAACCCGAATTAATCTGATCCAAATT
1 AACCCGAACCCAAATTAACCTGATCCAAATCCAACCCAAACCCGAATAAACCCGAACCAAATT
* * **
53561 AACCCGAACCCAAATTAACCTGATCCAAATCCAACCCGAACCCGACTCAAACCCGAACCCGA-T
1 AACCCGAACCCAAATTAACCTGATCCAAATCCAACCCAAACCCGAAT-AAACCCGAACCAAATT
*
53624 AATCCGAACCCAAA
1 AACCCGAACCCAAA
53638 CCCAACATGA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
63 56 0.88
64 8 0.12
ACGTcount: A:0.40, C:0.36, G:0.09, T:0.16
Consensus pattern (63 bp):
AACCCGAACCCAAATTAACCTGATCCAAATCCAACCCAAACCCGAATAAACCCGAACCAAATT
Found at i:54081 original size:225 final size:225
Alignment explanation
Indices: 53690--54140 Score: 902
Period size: 225 Copynumber: 2.0 Consensus size: 225
53680 ACAAACCGTC
53690 GTTACCCTGTGCTCTCCTTCTAAGCTTCGGAAAGTAACTACCGTCTTGGCAATAGGAATAGGCAA
1 GTTACCCTGTGCTCTCCTTCTAAGCTTCGGAAAGTAACTACCGTCTTGGCAATAGGAATAGGCAA
53755 TAGCAAAAATAACCAAATTTCTCTTCCGAAAAGGCTAGAAAATCTAGTAAATTATTTATTCTCCT
66 TAGCAAAAATAACCAAATTTCTCTTCCGAAAAGGCTAGAAAATCTAGTAAATTATTTATTCTCCT
53820 TTTTTTTCAATTTCCAATTAAAAAAAAGAAAAAGAAAAAGAAAGGAGAAGAGAAACAAAAGGTTG
131 TTTTTTTCAATTTCCAATTAAAAAAAAGAAAAAGAAAAAGAAAGGAGAAGAGAAACAAAAGGTTG
53885 AGAGTGGAGAGCTTAAACAATTTGTTTATA
196 AGAGTGGAGAGCTTAAACAATTTGTTTATA
53915 GTTACCCTGTGCTCTCCTTCTAAGCTTCGGAAAGTAACTACCGTCTTGGCAATAGGAATAGGCAA
1 GTTACCCTGTGCTCTCCTTCTAAGCTTCGGAAAGTAACTACCGTCTTGGCAATAGGAATAGGCAA
53980 TAGCAAAAATAACCAAATTTCTCTTCCGAAAAGGCTAGAAAATCTAGTAAATTATTTATTCTCCT
66 TAGCAAAAATAACCAAATTTCTCTTCCGAAAAGGCTAGAAAATCTAGTAAATTATTTATTCTCCT
54045 TTTTTTTCAATTTCCAATTAAAAAAAAGAAAAAGAAAAAGAAAGGAGAAGAGAAACAAAAGGTTG
131 TTTTTTTCAATTTCCAATTAAAAAAAAGAAAAAGAAAAAGAAAGGAGAAGAGAAACAAAAGGTTG
54110 AGAGTGGAGAGCTTAAACAATTTGTTTATA
196 AGAGTGGAGAGCTTAAACAATTTGTTTATA
54140 G
1 G
54141 GGTTTTAGTT
Statistics
Matches: 226, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
225 226 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (225 bp):
GTTACCCTGTGCTCTCCTTCTAAGCTTCGGAAAGTAACTACCGTCTTGGCAATAGGAATAGGCAA
TAGCAAAAATAACCAAATTTCTCTTCCGAAAAGGCTAGAAAATCTAGTAAATTATTTATTCTCCT
TTTTTTTCAATTTCCAATTAAAAAAAAGAAAAAGAAAAAGAAAGGAGAAGAGAAACAAAAGGTTG
AGAGTGGAGAGCTTAAACAATTTGTTTATA
Found at i:61409 original size:30 final size:30
Alignment explanation
Indices: 61373--61435 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
61363 GTGGCCGAGA
*
61373 TTTGAAGCGTTGTCGTCGTTTCCTCTGCCG
1 TTTGAAGCGTTGCCGTCGTTTCCTCTGCCG
*
61403 TTTGAAGCGTTGCCGTCGTTTCCTCTGTCG
1 TTTGAAGCGTTGCCGTCGTTTCCTCTGCCG
61433 TTT
1 TTT
61436 TTCTTACCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.06, C:0.25, G:0.25, T:0.43
Consensus pattern (30 bp):
TTTGAAGCGTTGCCGTCGTTTCCTCTGCCG
Found at i:63153 original size:29 final size:29
Alignment explanation
Indices: 63117--63185 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
63107 CTTGGCAACA
****
63117 GGGCTTATTTGGCCTTTTTAAGAGTTCAG
1 GGGCTTATTTGGCCGAAATAAGAGTTCAG
* *
63146 GGGCTTATTTTGCCGAAATAATAGTTCAG
1 GGGCTTATTTGGCCGAAATAAGAGTTCAG
63175 GGGCTTATTTG
1 GGGCTTATTTG
63186 ACGGTTCGGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.39
Consensus pattern (29 bp):
GGGCTTATTTGGCCGAAATAAGAGTTCAG
Found at i:64415 original size:22 final size:22
Alignment explanation
Indices: 64389--64436 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
64379 ATTGAATGTA
64389 TAATCTTTTCTATAACACCTTG
1 TAATCTTTTCTATAACACCTTG
64411 TAATCTTTTCTATAACACCTTG
1 TAATCTTTTCTATAACACCTTG
64433 TAAT
1 TAAT
64437 GGTGCAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (22 bp):
TAATCTTTTCTATAACACCTTG
Found at i:70121 original size:33 final size:32
Alignment explanation
Indices: 70034--70174 Score: 113
Period size: 33 Copynumber: 4.3 Consensus size: 32
70024 CAAAGGATCA
* *
70034 TGTGGCCGGTTGTGGCCGGGCATGGCCGA-GTCA
1 TGTGGCCGG-TGTGGCCGGGCATCGCC-ATGTCG
* * * * *
70067 AGTGTCCGGGTGTAGCTGGGCATGGCCATGTCG
1 TGTGGCC-GGTGTGGCCGGGCATCGCCATGTCG
* *
70100 TGTGGCCGGTGATGGCCGGGCATCTCCATGTTG
1 TGTGGCCGGTG-TGGCCGGGCATCGCCATGTCG
** * *
70133 CATGGCCGGTGTTGCGCGGGCATCTCCATGTCG
1 TGTGGCCGGTGTGGC-CGGGCATCGCCATGTCG
70166 TGTGGCCGG
1 TGTGGCCGG
70175 ATCTCCAAGT
Statistics
Matches: 86, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
32 8 0.09
33 76 0.88
34 2 0.02
ACGTcount: A:0.09, C:0.25, G:0.42, T:0.24
Consensus pattern (32 bp):
TGTGGCCGGTGTGGCCGGGCATCGCCATGTCG
Found at i:70178 original size:21 final size:21
Alignment explanation
Indices: 70154--70195 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
70144 TTGCGCGGGC
* **
70154 ATCTCCATGTCGTGTGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
70175 ATCTCCAAGTCGCATGGCCGG
1 ATCTCCAAGTCGCATGGCCGG
70196 TCACTTGTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.24
Consensus pattern (21 bp):
ATCTCCAAGTCGCATGGCCGG
Found at i:75560 original size:9 final size:9
Alignment explanation
Indices: 75546--75580 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
75536 TGGTCGAAAT
75546 TTTTTTTTA
1 TTTTTTTTA
75555 TTTTTTTTA
1 TTTTTTTTA
75564 TTTTTTTATA
1 TTTTTTT-TA
*
75574 TATTTTT
1 TTTTTTT
75581 CGATATAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:75687 original size:9 final size:8
Alignment explanation
Indices: 75653--75686 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
75643 GAATCGGCTA
75653 TGAATTTT
1 TGAATTTT
*
75661 TGAAGTTTC
1 TGAA-TTTT
75670 TGAATTTT
1 TGAATTTT
75678 TGAATTTT
1 TGAATTTT
75686 T
1 T
75687 TCAAGAAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Done.