Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023975.1 Corchorus olitorius cultivar O-4 contig24008, 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: 53036
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--33 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34 AGAGAAAAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3239 original size:19 final size:19
Alignment explanation
Indices: 3217--3267 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
3207 TGGCTGAAAT
3217 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
3236 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
3255 TAATT-ATTATTAA
1 TAATTAATTATTAA
3268 AAACAACACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:8749 original size:83 final size:83
Alignment explanation
Indices: 8610--8776 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
8600 CTTAGAATTG
8610 TTAGGCAATGAAACATATGCATTATAAACAGGATAAAAATGAATGAAAGAATGCAAATTACAAGC
1 TTAGGCAATGAAACATATGCATTATAAACAGGATAAAAATGAATGAAAGAATGCAAATTACAAGC
8675 TATGTAATCAGTAGCACC
66 TATGTAATCAGTAGCACC
8693 TTAGGCAATGAAACATATGCATTATAAACAGGATAAAAATGAATGAAAGAATGCAAATTACAAGC
1 TTAGGCAATGAAACATATGCATTATAAACAGGATAAAAATGAATGAAAGAATGCAAATTACAAGC
8758 TATGTAATCAGTAGCACC
66 TATGTAATCAGTAGCACC
8776 T
1 T
8777 GTATCAACAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.23
Consensus pattern (83 bp):
TTAGGCAATGAAACATATGCATTATAAACAGGATAAAAATGAATGAAAGAATGCAAATTACAAGC
TATGTAATCAGTAGCACC
Found at i:9429 original size:34 final size:34
Alignment explanation
Indices: 9391--9458 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
9381 CTCAACTTGC
*
9391 AAAGGCGTGATGAAGGCCCGTTTAACTTCATTGG
1 AAAGGCGTGATGAAGGCCCGTGTAACTTCATTGG
9425 AAAGGCGTGATGAAGGCCCGTGTAACTTCATTGG
1 AAAGGCGTGATGAAGGCCCGTGTAACTTCATTGG
9459 TGTAAGAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (34 bp):
AAAGGCGTGATGAAGGCCCGTGTAACTTCATTGG
Found at i:12568 original size:16 final size:16
Alignment explanation
Indices: 12547--12577 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12537 ATTAGCCTCA
12547 AAAGAAAAATAAAAAT
1 AAAGAAAAATAAAAAT
12563 AAAGAAAAATAAAAA
1 AAAGAAAAATAAAAA
12578 GATAAGGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAGAAAAATAAAAAT
Found at i:14201 original size:21 final size:21
Alignment explanation
Indices: 14168--14210 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
14158 CTCCACCTGG
14168 GCGCCCACATGG-TTGCCTTGA
1 GCGCCCACATGGTTTG-CTTGA
**
14189 GCGCCCATGTGGTTTGCTTGA
1 GCGCCCACATGGTTTGCTTGA
14210 G
1 G
14211 AACCCAGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.12, C:0.28, G:0.33, T:0.28
Consensus pattern (21 bp):
GCGCCCACATGGTTTGCTTGA
Found at i:14292 original size:76 final size:76
Alignment explanation
Indices: 14155--14304 Score: 169
Period size: 76 Copynumber: 2.0 Consensus size: 76
14145 GAAAGGACCC
** * * *
14155 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCGCCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTAAAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
14220 GGGCGGTGTGA
66 GGGCGGTGTGA
* * * **
14231 CGACTCCAGCTGGGTGCCCACATGGTTTGTCTAAAG-ACCCATGT-GTTTCGCCTGATCACCCAG
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTAAAGCACCCATGTGGTTT-GCCTGAGAACCCAG
*
14294 ATGGGCTGTGT
64 ATGGGCGGTGT
14305 CATAGCTCAT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
75 4 0.07
76 50 0.82
77 7 0.11
ACGTcount: A:0.16, C:0.29, G:0.31, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTAAAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCGGTGTGA
Found at i:15294 original size:29 final size:27
Alignment explanation
Indices: 15237--15288 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
15227 GTGATTTAGG
*
15237 GGTTACTAACTCCCTTTTTTCTTTTGA
1 GGTTACTAACACCCTTTTTTCTTTTGA
* *
15264 GGTTACTAACACTCTTTTTTTTTTT
1 GGTTACTAACACCCTTTTTTCTTTT
15289 CAGAGGGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.15, C:0.19, G:0.10, T:0.56
Consensus pattern (27 bp):
GGTTACTAACACCCTTTTTTCTTTTGA
Found at i:20157 original size:21 final size:21
Alignment explanation
Indices: 20124--20172 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
20114 AAGAATTGTA
**
20124 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
20144 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
20165 GCGTTCCT
1 GC-TTCCT
20173 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.12, C:0.29, G:0.18, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:21343 original size:10 final size:9
Alignment explanation
Indices: 21300--21357 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
21290 TAAAAGTAAC
21300 TAAGAAAAA
1 TAAGAAAAA
*
21309 TAAACAAAAA
1 T-AAGAAAAA
21319 TAA-AAGAAA
1 TAAGAA-AAA
21328 -AAGAAAAA
1 TAAGAAAAA
21336 TAACGAAAAA
1 TAA-GAAAAA
*
21346 TAA-AAAGA
1 TAAGAAAAA
21354 TAAG
1 TAAG
21358 GGTAAGAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 14 0.34
9 10 0.24
10 17 0.41
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10
Consensus pattern (9 bp):
TAAGAAAAA
Found at i:21343 original size:16 final size:17
Alignment explanation
Indices: 21314--21351 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
21304 AAAAATAAAC
21314 AAAAATAAAAGAAAAAG
1 AAAAATAAAAGAAAAAG
* *
21331 AAAAAT-AACGAAAAAT
1 AAAAATAAAAGAAAAAG
21347 AAAAA
1 AAAAA
21352 GATAAGGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAAATAAAAGAAAAAG
Found at i:23090 original size:76 final size:76
Alignment explanation
Indices: 22940--23083 Score: 168
Period size: 76 Copynumber: 1.9 Consensus size: 76
22930 ACAAGGACCC
* * * *
22940 CGACTCTACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
23005 GGGCAGTGTCA
66 GGGCAGTGTCA
* * **
23016 CGACTCCAGCTGGGCGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
23078 GATGGG
63 GATGGG
23084 TTGTGTCTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
75 4 0.07
76 47 0.82
77 6 0.11
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:26185 original size:34 final size:34
Alignment explanation
Indices: 26142--26243 Score: 186
Period size: 34 Copynumber: 3.0 Consensus size: 34
26132 CTCAACTTGT
*
26142 AAAGGCGTGATGAAGGCCCGTTTAACATCATTGG
1 AAAGGCGTGATGAAGGCCCGTTTAACTTCATTGG
26176 AAAGGCGTGATGAAGGCCCGTTTAACTTCATTGG
1 AAAGGCGTGATGAAGGCCCGTTTAACTTCATTGG
*
26210 AAAGGCGTGATGAAGGCCCGTGTAACTTCATTGG
1 AAAGGCGTGATGAAGGCCCGTTTAACTTCATTGG
26244 TGTAAGAGCT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (34 bp):
AAAGGCGTGATGAAGGCCCGTTTAACTTCATTGG
Found at i:29430 original size:12 final size:12
Alignment explanation
Indices: 29413--29437 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29403 ATCCCATTTA
29413 CTTTCGTTTGGG
1 CTTTCGTTTGGG
29425 CTTTCGTTTGGG
1 CTTTCGTTTGGG
29437 C
1 C
29438 CATCCTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.20, G:0.32, T:0.48
Consensus pattern (12 bp):
CTTTCGTTTGGG
Found at i:35232 original size:30 final size:30
Alignment explanation
Indices: 35196--35257 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
35186 TCAGCAGCCT
35196 TCTTCGCAAATCC-TAAATCTTCTTTACCTC
1 TCTTCGCAAA-CCTTAAATCTTCTTTACCTC
35226 TCTTCGCAAACCTTAAATCTTCTTTACCTC
1 TCTTCGCAAACCTTAAATCTTCTTTACCTC
35256 TC
1 TC
35258 GACAGCGCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.23, C:0.34, G:0.03, T:0.40
Consensus pattern (30 bp):
TCTTCGCAAACCTTAAATCTTCTTTACCTC
Found at i:38740 original size:27 final size:26
Alignment explanation
Indices: 38710--38783 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 26
38700 CCTTTGTTGC
38710 AAAATGATCAAAATGCCCCTGAATGTA
1 AAAATGA-CAAAATGCCCCTGAATGTA
* *
38737 AAAATGACTAAAATACCCCTGAATGTG
1 AAAATGAC-AAAATGCCCCTGAATGTA
*
38764 CAAATGACCAAAATGCCCCT
1 AAAATGA-CAAAATGCCCCT
38784 AGATTTTGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 1 0.02
27 39 0.95
28 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (26 bp):
AAAATGACAAAATGCCCCTGAATGTA
Found at i:39394 original size:69 final size:69
Alignment explanation
Indices: 39297--39566 Score: 387
Period size: 69 Copynumber: 3.9 Consensus size: 69
39287 CACTGCTGTA
* * * * * * * *** *
39297 TGGATGGAACCGATGTTTAAACTGACTCGAATGGAAACGAGTTTGACTTATGTTGAAGTCTATAT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATAT
39362 GGCT
66 GGCT
* * *
39366 TGGATGAAACCAAGGCTTGAAATGACTCGTATGGAAATGAGTTTGGCTTGTGGAAAAGCCTATAT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATAT
39431 GGCT
66 GGCT
* *
39435 TGGATGGAACCAAGGCTTGAACTGACTCGGACGGAAACGAGTTTGGCTTGTGGAAAAGCCTATAT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATAT
39500 GGCT
66 GGCT
*
39504 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAATGAGTTTGGCTTGTGGAAAAGCCTAT
1 TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTAT
39567 GTGGATAATT
Statistics
Matches: 179, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 179 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.27
Consensus pattern (69 bp):
TGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATAT
GGCT
Found at i:39580 original size:50 final size:50
Alignment explanation
Indices: 39526--39713 Score: 340
Period size: 50 Copynumber: 3.8 Consensus size: 50
39516 AGGCTTGAAC
*
39526 TGACTCGTATGGAAATGAGTTTGGCTTGTGGAAAAGCCTATGTGGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGATAAT
39576 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGATAAT
*
39626 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAAT
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGATAAT
* *
39676 TGACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCC
1 TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
39714 AAAGCATTCG
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 134 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.30
Consensus pattern (50 bp):
TGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTGGATAAT
Found at i:40519 original size:50 final size:50
Alignment explanation
Indices: 40375--40522 Score: 242
Period size: 50 Copynumber: 3.0 Consensus size: 50
40365 TCAATGTCCT
* * *
40375 TTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTACT
1 TTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTACA
* * *
40425 TTGAAAAGCAAATTTTGATCTTGAACTCAAAAATGGAAAGCAATTTTACA
1 TTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTACA
40475 TTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
1 TTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTA
40523 TTGTAAAACT
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 89 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (50 bp):
TTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATTTTACA
Found at i:41173 original size:15 final size:15
Alignment explanation
Indices: 41150--41212 Score: 67
Period size: 15 Copynumber: 4.2 Consensus size: 15
41140 TTTGATTTGA
* *
41150 TTTGATTTTTTTGTT
1 TTTGTTTTTTTTATT
*
41165 TTTG-TTTTTTGATT
1 TTTGTTTTTTTTATT
41179 TTTGATTTTTTTTATT
1 TTTG-TTTTTTTTATT
41195 TTT-TATTTTTTTATT
1 TTTGT-TTTTTTTATT
41210 TTT
1 TTT
41213 TGATTGATTG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
14 13 0.31
15 17 0.40
16 12 0.29
ACGTcount: A:0.10, C:0.00, G:0.08, T:0.83
Consensus pattern (15 bp):
TTTGTTTTTTTTATT
Found at i:41198 original size:39 final size:39
Alignment explanation
Indices: 41133--41254 Score: 133
Period size: 39 Copynumber: 3.1 Consensus size: 39
41123 ATCCATTCTC
* * * *
41133 TTTTGA-TTTTGATTTGATTTGATTTTTT-TGTTTTTGTT
1 TTTTGATTTTTGATTT-TTTTTATTTTTTATTTTTTTATT
41171 TTTTGATTTTTGATTTTTTTTATTTTTTATTTTTTTATT
1 TTTTGATTTTTGATTTTTTTTATTTTTTATTTTTTTATT
* *
41210 TTTTGATTGATTGA-TTTTTTTATTTATTATTTTTTTGAATT
1 TTTTGATT-TTTGATTTTTTTTATTTTTTATTTTTTT--ATT
41251 TTTT
1 TTTT
41255 TTTTAAATTT
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
38 16 0.22
39 46 0.63
40 4 0.05
41 7 0.10
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (39 bp):
TTTTGATTTTTGATTTTTTTTATTTTTTATTTTTTTATT
Found at i:41234 original size:8 final size:8
Alignment explanation
Indices: 41163--41255 Score: 66
Period size: 8 Copynumber: 11.6 Consensus size: 8
41153 GATTTTTTTG
*
41163 TTTTTGTT
1 TTTTTATT
*
41171 TTTTGA-T
1 TTTTTATT
*
41178 TTTTGATT
1 TTTTTATT
41186 TTTTT-TAT
1 TTTTTAT-T
41194 TTTTTATT
1 TTTTTATT
41202 TTTTTATT
1 TTTTTATT
*
41210 TTTTGATT
1 TTTTTATT
** *
41218 GATTGATT
1 TTTTTATT
41226 TTTTTA-T
1 TTTTTATT
*
41233 TTATTATT
1 TTTTTATT
41241 TTTTTGAATT
1 TTTTT--ATT
41251 TTTTT
1 TTTTT
41256 TTTAAATTTC
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
7 14 0.21
8 45 0.66
9 1 0.01
10 8 0.12
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (8 bp):
TTTTTATT
Found at i:41667 original size:16 final size:18
Alignment explanation
Indices: 41646--41679 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41636 TTTATTTTCC
41646 TTTTTTC-A-TTTTCATT
1 TTTTTTCAATTTTTCATT
41662 TTTTTTCAATTTTTCATT
1 TTTTTTCAATTTTTCATT
41680 CATTTTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTCAATTTTTCATT
Found at i:51909 original size:39 final size:39
Alignment explanation
Indices: 51797--51964 Score: 103
Period size: 39 Copynumber: 4.3 Consensus size: 39
51787 TATCATAGCA
* * * * *
51797 AACCTGCTTAGGTCCTTGTTTAGAACTTTC-GTTCAA-TCA
1 AACCTGCTTAGGTCCTCGTGTA-AAATTTCTGTTTAAGT-G
* * * * **
51836 AACCTGTTTAGGTTCTTGTGTAGAATGCCTGTTTAAGTG
1 AACCTGCTTAGGTCCTCGTGTAAAATTTCTGTTTAAGTG
* * *
51875 AACCTGCTTAGGT-CTACGTTTAGGAGTTTC-GTTTAA-TCG
1 AACCTGCTTAGGTCCT-CGTGTA-AAATTTCTGTTTAAGT-G
* * *
51914 AACCTACATAGGTCCTTGTGTAAAATTTCTGTTTAAGTG
1 AACCTGCTTAGGTCCTCGTGTAAAATTTCTGTTTAAGTG
51953 AACCTGCTTAGG
1 AACCTGCTTAGG
51965 ATCTCTGCCT
Statistics
Matches: 98, Mismatches: 23, Indels: 16
0.72 0.17 0.12
Matches are distributed among these distances:
38 11 0.11
39 79 0.81
40 8 0.08
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (39 bp):
AACCTGCTTAGGTCCTCGTGTAAAATTTCTGTTTAAGTG
Found at i:51926 original size:78 final size:78
Alignment explanation
Indices: 51797--51964 Score: 212
Period size: 78 Copynumber: 2.2 Consensus size: 78
51787 TATCATAGCA
* *** * *
51797 AACCTGCTTAGGTCCTTGTTTAGAACTTTCGTTCAATCAAACCTGTTTAGGTTCTTGTGTAGAAT
1 AACCTGCTTAGGTCCTCGTTTAGAACTTTCGTTCAATCAAACCTACATAGGTCCTTGTGTAAAAT
51862 GCCTGTTTAAGTG
66 GCCTGTTTAAGTG
* * * *
51875 AACCTGCTTAGGT-CTACGTTTAGGAGTTTCGTTTAATCGAACCTACATAGGTCCTTGTGTAAAA
1 AACCTGCTTAGGTCCT-CGTTTAGAACTTTCGTTCAATCAAACCTACATAGGTCCTTGTGTAAAA
**
51939 TTTCTGTTTAAGTG
65 TGCCTGTTTAAGTG
51953 AACCTGCTTAGG
1 AACCTGCTTAGG
51965 ATCTCTGCCT
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
77 2 0.03
78 75 0.97
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (78 bp):
AACCTGCTTAGGTCCTCGTTTAGAACTTTCGTTCAATCAAACCTACATAGGTCCTTGTGTAAAAT
GCCTGTTTAAGTG
Found at i:52254 original size:39 final size:39
Alignment explanation
Indices: 52022--52254 Score: 172
Period size: 38 Copynumber: 6.0 Consensus size: 39
52012 TAGAATCTCA
* * *
52022 TTAGAATTTCTGTTTAAG-AGAACCTGCTTAGGTCCTCGT
1 TTAGAATTTCCGTTTAAGCA-AACCTGCTCAGGTCCTTGT
* * * * * *
52061 TCAGAATCT-CATGTAAGCAAACCTGCTTAGGTCCTTAT
1 TTAGAATTTCCGTTTAAGCAAACCTGCTCAGGTCCTTGT
* * * *
52099 TCAGAA-TTCTCGTTCAAGTAAAACCTGCTCAGGTCCCTGT
1 TTAGAATTTC-CGTTTAAG-CAAACCTGCTCAGGTCCTTGT
* ** * **
52139 TTAGGATTTCCGTTTAAGTGAACCTGCT-AAGT-CTACAT
1 TTAGAATTTCCGTTTAAGCAAACCTGCTCAGGTCCT-TGT
* * *
52177 TTAGAATCT-CGTTTAAGCAAAACTGCTTAGGTCCTTGT
1 TTAGAATTTCCGTTTAAGCAAACCTGCTCAGGTCCTTGT
* *
52215 TTAAAATTTCCGTTTAAGCAAACCTGCTCAGGTCTTTGT
1 TTAGAATTTCCGTTTAAGCAAACCTGCTCAGGTCCTTGT
52254 T
1 T
52255 CCATTTAAGT
Statistics
Matches: 148, Mismatches: 37, Indels: 18
0.73 0.18 0.09
Matches are distributed among these distances:
37 17 0.11
38 50 0.34
39 50 0.34
40 28 0.19
41 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (39 bp):
TTAGAATTTCCGTTTAAGCAAACCTGCTCAGGTCCTTGT
Found at i:52324 original size:37 final size:37
Alignment explanation
Indices: 52269--52354 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 37
52259 TTAAGTGAAT
*
52269 CTGCTTAGGATCTCTGCTT-TGAGTTCATTCGAAT-AAAC
1 CTGCTTAGG-TCTATGCTTATG-GTTCATTC-AATCAAAC
* *
52307 CTGCTTAGGTCTATGCTTAATGTTTCGTTCAATCAAAC
1 CTGCTTAGGTCTATGCTT-ATGGTTCATTCAATCAAAC
52345 CTGCTTAGGT
1 CTGCTTAGGT
52355 TCCTCTTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
37 11 0.26
38 29 0.69
39 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (37 bp):
CTGCTTAGGTCTATGCTTATGGTTCATTCAATCAAAC
Done.