Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013459.1 Corchorus olitorius cultivar O-4 contig13492, 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: 16185
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:41 original size:15 final size:15
Alignment explanation
Indices: 4--51 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1 ATT
* *
4 TTTAAAACTTATTAA
1 TTTAAAATTTATTTA
*
19 GTTAAAAATTTATTTA
1 -TTTAAAATTTATTTA
*
35 TTTAAAATTTAATTA
1 TTTAAAATTTATTTA
50 TT
1 TT
52 GTGATTAACC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTAAAATTTATTTA
Found at i:769 original size:24 final size:25
Alignment explanation
Indices: 740--789 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
730 TAGAGTGACG
740 ATAAAA-TAAATAAGCAAGA-AAATA
1 ATAAAATTAAATAA-CAAGATAAATA
*
764 ATAAAATTAAGTAACAAGATAAATA
1 ATAAAATTAAATAACAAGATAAATA
789 A
1 A
790 ATACTCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.68, C:0.04, G:0.08, T:0.20
Consensus pattern (25 bp):
ATAAAATTAAATAACAAGATAAATA
Found at i:2642 original size:17 final size:17
Alignment explanation
Indices: 2620--2663 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
2610 TTGTGGCAGT
* *
2620 TTTTTTTAGATGGGTAG
1 TTTTTTTAAATAGGTAG
2637 -TTTTTTAAATAGGTAG
1 TTTTTTTAAATAGGTAG
2653 TTTTTTTAAAT
1 TTTTTTTAAAT
2664 GATATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.25, C:0.00, G:0.18, T:0.57
Consensus pattern (17 bp):
TTTTTTTAAATAGGTAG
Found at i:4400 original size:25 final size:25
Alignment explanation
Indices: 4372--4430 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
4362 AGCAATCTAG
* *
4372 CAGCGGACTTCAACGAGCTTCCTGA
1 CAGCGGACTTCAACAAGCTTCATGA
* *
4397 CAGC-GAGCTTCAATAAGCTTCATGG
1 CAGCGGA-CTTCAACAAGCTTCATGA
4422 CAGCGGACT
1 CAGCGGACT
4431 CCACTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 2 0.07
25 24 0.86
26 2 0.07
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.20
Consensus pattern (25 bp):
CAGCGGACTTCAACAAGCTTCATGA
Found at i:7961 original size:336 final size:334
Alignment explanation
Indices: 7337--8658 Score: 1684
Period size: 336 Copynumber: 3.9 Consensus size: 334
7327 CCCCCCAAAT
* *
7337 TTCTTTCTTTTCTTTAATTCTCATATCTTTTCCATTAAAGAGAAAAAACATTTTGTAATTTAATT
1 TTCTTT-TTTTCTTTAATTCTCATATCTTTTTCATTTAAGAGAAAAAACATTTTGTAA--T--TT
*
7402 TGTTGAAAGAGAAAGCAGCAAGAATTAACAACCACGTAATCCAACAGTTAACTTTAACTGAAAAT
61 TGTTGAAAGAGAAAGCAGCAAGAATTAACAACCACGTAATCCAACAATTAACTTTAACTGAAAAT
* *
7467 ATTAGTTTTCTAATTGAGTGTCCTACTGATAGATCCTGATAATCCAATGCTAAAATGAATAAATG
126 ATTAGTTTTCTAATTGAGTGTCCTA--GATAGATCCTGATAATCCAATACTAAAATGAATACATG
* * *
7532 TGTTCTTACCTCAAACTCGAGGTTCCTTTCCCTTTCCTCAAGGACTTTCCTTTCCTTTTCAAC-C
189 TGTGCTTACCTCAAACCCGAGGTTCCTTTCCCTTTCCTCAAGGACTTTCCTTTCCTTTTCAGCTC
*
7596 CAAGCAACTTGGATAGATGGAGATTAGAGATTAGAATCATAGATGTTCATACAACAAAAAATGAA
254 C-AGCAACCTGGATAGATGGAGATTAGAGATTAGAATCATAGATGTTCATACAACAAAAAATGAA
7661 ATAAAATGTTTCTTTTC
318 ATAAAATGTTTCTTTTC
*
7678 TTCTTTTTTTCTTTAATTCTCATATCTGTTTCATTTAAGAGAAAAAACATTTTGTAATTTTGTTG
1 TTCTTTTTTTCTTTAATTCTCATATCTTTTTCATTTAAGAGAAAAAACATTTTGTAATTTTGTTG
* *
7743 AAAGAGAAAGTAGCAAGAATTAACAACCACGTAATCCAACAATTAACTTTAACTGAAAATCTTAG
66 AAAGAGAAAGCAGCAAGAATTAACAACCACGTAATCCAACAATTAACTTTAACTGAAAATATTAG
* *
7808 TTTTCTAATTGAGTGCCCTAATGATAGATCCTGATAATCCAATGCTAAAATGAATACATGTGTGC
131 TTTTCTAATTGAGTGTCCT-A-GATAGATCCTGATAATCCAATACTAAAATGAATACATGTGTGC
* * * *
7873 TTACCTCAAACCCGAGGTTCCTTTACCTTTCCTTAAGGACATTCCTTTTCTTTTCAGCTCCAGCA
194 TTACCTCAAACCCGAGGTTCCTTTCCCTTTCCTCAAGGACTTTCCTTTCCTTTTCAGCTCCAGCA
7938 ACCTGGATAGATGGAGATTAGAGATTAGAATCATAGATGTTCATACAACAAAAAATGAAATAAAA
259 ACCTGGATAGATGGAGATTAGAGATTAGAATCATAGATGTTCATACAACAAAAAATGAAATAAAA
*
8003 TG-----ATTC
324 TGTTTCTTTTC
* *
8009 TT-TTTTTTCCTTTAATTCTTATATCTTTTTCATTTAAGAGAAAAAACATTTTGTAATTTTGTTG
1 TTCTTTTTTTCTTTAATTCTCATATCTTTTTCATTTAAGAGAAAAAACATTTTGTAATTTTGTTG
* ** * ** * *
8073 AAAGAGAAAGCAGCAACTTTG-GTTCCCGTCAACCACCGAATACGATGCTTAACAA-CCACATCA
66 AAAGAGAAAGCAGCAA----GAATT---AACAACCA-CG--TA--AT-C-CAACAATTAACTTTA
* * * * * * * * *
8136 TC-CAACAGT-TTACTTTGACTGAAAATATTAGTATTCTAGATGGATCCTGATAATCCAATACTA
117 ACTGAA-AATATTAGTTT-TCT---AAT-TGAGTGTCCTAGATAGATCCTGATAATCCAATACTA
*
8199 AAATGAATACATGTGTGCTTACCTCAAACCTGAGGTTCCTTTCCCTTTCCTCAAGGACTTTCCTT
176 AAATGAATACATGTGTGCTTACCTCAAACCCGAGGTTCCTTTCCCTTTCCTCAAGGACTTTCCTT
* *
8264 TCCTTTTCAGCTCAAGCAACCTGGATAGATGCAGATTAGAGATTAGAATCATAGATGTTCATACA
241 TCCTTTTCAGCTCCAGCAACCTGGATAGATGGAGATTAGAGATTAGAATCATAGATGTTCATACA
**
8329 ACAAAAAATGAAATTTAATGTTTCTTTTC
306 ACAAAAAATGAAATAAAATGTTTCTTTTC
8358 TTCTTTTTTTATTCTTTAATTCTCATATCTTTTTCATTTAAGAGAAAAAACATTTTGTAATTTTG
1 TTC--TTTTT-TTCTTTAATTCTCATATCTTTTTCATTTAAGAGAAAAAACATTTTGTAATTTTG
* * * *
8423 TTGAAAGAGAAAGCAGCAAGAATTAACAACCACGTCATCCAACAGTTTACTTTGACTGAAAATAT
63 TTGAAAGAGAAAGCAGCAAGAATTAACAACCACGTAATCCAACAATTAACTTTAACTGAAAATAT
*
8488 TAG---------T-A-T-T-CTAGATTGATCCTGATAATCCAATACTAAAATGAATACATGTGTG
128 TAGTTTTCTAATTGAGTGTCCTAGATAGATCCTGATAATCCAATACTAAAATGAATACATGTGTG
* * * * *
8540 CTTACCTCAAACCCGAGGTTCTTTTCCCTTTCCTTAAGGACCTTCCTTTCATTTTCAGCTCGAGC
193 CTTACCTCAAACCCGAGGTTCCTTTCCCTTTCCTCAAGGACTTTCCTTTCCTTTTCAGCTCCAGC
* *
8605 AACCTGGATAGATGGAGATTAGAGATTAGAATCATAGATATTCATACAATAAAA
258 AACCTGGATAGATGGAGATTAGAGATTAGAATCATAGATGTTCATACAACAAAA
8659 TGTTTCTTTT
Statistics
Matches: 869, Mismatches: 77, Indels: 87
0.84 0.07 0.08
Matches are distributed among these distances:
324 154 0.18
325 1 0.00
326 1 0.00
327 1 0.00
328 1 0.00
330 74 0.09
331 5 0.01
333 2 0.00
334 1 0.00
336 257 0.30
337 5 0.01
338 1 0.00
339 2 0.00
340 52 0.06
341 23 0.03
342 17 0.02
343 5 0.01
344 165 0.19
345 4 0.00
346 8 0.01
347 6 0.01
349 6 0.01
350 2 0.00
352 5 0.01
353 71 0.08
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (334 bp):
TTCTTTTTTTCTTTAATTCTCATATCTTTTTCATTTAAGAGAAAAAACATTTTGTAATTTTGTTG
AAAGAGAAAGCAGCAAGAATTAACAACCACGTAATCCAACAATTAACTTTAACTGAAAATATTAG
TTTTCTAATTGAGTGTCCTAGATAGATCCTGATAATCCAATACTAAAATGAATACATGTGTGCTT
ACCTCAAACCCGAGGTTCCTTTCCCTTTCCTCAAGGACTTTCCTTTCCTTTTCAGCTCCAGCAAC
CTGGATAGATGGAGATTAGAGATTAGAATCATAGATGTTCATACAACAAAAAATGAAATAAAATG
TTTCTTTTC
Found at i:10169 original size:146 final size:145
Alignment explanation
Indices: 9783--10467 Score: 667
Period size: 146 Copynumber: 4.9 Consensus size: 145
9773 CCCATTTCTT
* * * * *
9783 GATCCCTGTAGCTGCCGTTCCGGCCT-TCAACCCTAAATTCTCTCTCATCGACTGTTTTAGGGTT
1 GATCCCCGTAGCTGCCATTTCGGCCTCT-AACCCTAAATTCTCTCTCCTCGACCGTTTTAGGGTT
** * ** * *
9847 AC-T---GTTTAGG-GTTTTAACGTTAG-GGTATACAGTTTTAAGAACTATAGTGGTCTCTAACC
65 ACTTAGGGTTT-GGTGTTTTAGGGTCAGTGGTGCACGGTTTTAAGGACTATAGTGGTCTCTAACC
9906 CTAGG--CTCTCT-CTC
129 CTAGGCTCTCTCTCCTC
* * * * * *
9920 GATCCCCGTAGCTGACGTTTCGGCCTCTAATCCTAAATTCCCTCT-CTGTGATCGTTTTAGGGGT
1 GATCCCCGTAGCTGCCATTTCGGCCTCTAACCCTAAATTCTCTCTCCT-CGACCGTTTTA-GGGT
** * * *
9984 ATTGTCTAGGGTTTGGTGTTTTAGGGTCAG-GGTGTACGGTTTTAAGGAGTATATTGGTCTCTAA
64 -TACT-TAGGGTTTGGTGTTTTAGGGTCAGTGGTGCACGGTTTTAAGGACTATAGTGGTCTCTAA
*
10048 CCCTAGGCTCTCTCTTCTC
127 CCCTAGGCTCTCTCTCCTC
* * * * * * * *
10067 GATCCCCGTAGCTGCCGTTCCAGCCTTTAACCCTAAACTCTTTCTCATCGACCGTTTTA-GCTTA
1 GATCCCCGTAGCTGCCATTTCGGCCTCTAACCCTAAATTCTCTCTCCTCGACCGTTTTAGGGTTA
10131 CAATTTAGGGTTTGGTGTTTTAGGGTC-GTGGTGCACGGTTTTAAGGACTATAGTGGTCTCTAAC
66 C---TTAGGGTTTGGTGTTTTAGGGTCAGTGGTGCACGGTTTTAAGGACTATAGTGGTCTCTAAC
* *
10195 CTTAGGATCTCTCTCCTC
128 CCTAGGCTCTCTCTCCTC
* * * *
10213 GATCCCCATAGCTACCATTTCGGCCTCTAACCTTAAATTCTCTCTCCTCGACCATTTTAGGGTTA
1 GATCCCCGTAGCTGCCATTTCGGCCTCTAACCCTAAATTCTCTCTCCTCGACCGTTTTAGGGTTA
* *
10278 C----GGTTTAGG-GTTTTAGGGTCAGT-GTGCACGATTTTAAGGACTATAGTGGTCTCTAATCC
66 CTTAGGGTTT-GGTGTTTTAGGGTCAGTGGTGCACGGTTTTAAGGACTATAGTGGTCTCTAACCC
10337 TAGGCTCTCTCTCCTC
130 TAGGCTCTCTCTCCTC
* *
10353 GATCCCCGTAGCTTCCATTTCGGCCTCTAACCCTAAATTATCTCTCCTCGACCGTTTTA--G---
1 GATCCCCGTAGCTGCCATTTCGGCCTCTAACCCTAAATTCTCTCTCCTCGACCGTTTTAGGGTTA
* *
10413 ----GGG-TTGGTGTTTTAGGGTCA-TGGTGTACGGTTTTAAGTACTATAGTGGTCTCTAA
66 CTTAGGGTTTGGTGTTTTAGGGTCAGTGGTGCACGGTTTTAAGGACTATAGTGGTCTCTAA
10468 AATCAGCAGT
Statistics
Matches: 461, Mismatches: 63, Indels: 51
0.80 0.11 0.09
Matches are distributed among these distances:
133 3 0.01
134 44 0.10
135 2 0.00
136 1 0.00
137 46 0.10
138 6 0.01
139 1 0.00
140 118 0.26
141 5 0.01
143 2 0.00
144 51 0.11
145 3 0.01
146 123 0.27
147 55 0.12
148 1 0.00
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (145 bp):
GATCCCCGTAGCTGCCATTTCGGCCTCTAACCCTAAATTCTCTCTCCTCGACCGTTTTAGGGTTA
CTTAGGGTTTGGTGTTTTAGGGTCAGTGGTGCACGGTTTTAAGGACTATAGTGGTCTCTAACCCT
AGGCTCTCTCTCCTC
Found at i:10346 original size:140 final size:140
Alignment explanation
Indices: 9783--10467 Score: 657
Period size: 140 Copynumber: 4.9 Consensus size: 140
9773 CCCATTTCTT
* * * * * *
9783 GATCCCTGTAGCTGCCGTTCCGGCCT-TCAACCCTAAATTCTCTCTCATCGACTGTTTTAGGGTT
1 GATCCCCGTAGCTACCATTTCGGCCTCT-AACCCTAAATTCTCTCTCCTCGACCGTTTTAGGGTT
* ** * * * * *
9847 ACTGTTTAGG-GTTTTAACGTTAGGGTATACAGTTTTAAGAACTATAGTGGTCTCTAACCCTAGG
65 ACGGTTT-GGTGTTTTAGGGTCAGTGTGTACGGTTTTAAGGACTATAGTGGTCTCTAACCCTAGG
9911 --CTCTCT-CTC
129 CTCTCTCTCCTC
* * * * *
9920 GATCCCCGTAGCTGA-CGTTTCGGCCTCTAATCCTAAATTCCCTCT-CTGTGATCGTTTTAGGGG
1 GATCCCCGTAGCT-ACCATTTCGGCCTCTAACCCTAAATTCTCTCTCCT-CGACCGTTTTA--GG
* * * *
9983 TATTGTCTAGGGTTTGGTGTTTTAGGGTCAGGGTGTACGGTTTTAAGGAGTATATTGGTCTCTAA
62 ----GT-TACGGTTTGGTGTTTTAGGGTCAGTGTGTACGGTTTTAAGGACTATAGTGGTCTCTAA
*
10048 CCCTAGGCTCTCTCTTCTC
122 CCCTAGGCTCTCTCTCCTC
* * * * * * * * *
10067 GATCCCCGTAGCTGCCGTTCCAGCCTTTAACCCTAAACTCTTTCTCATCGACCGTTTTA-GCTTA
1 GATCCCCGTAGCTACCATTTCGGCCTCTAACCCTAAATTCTCTCTCCTCGACCGTTTTAGGGTTA
*
10131 CAATTTAGGGTTTGGTGTTTTAGGGTC-GTGGTGCACGGTTTTAAGGACTATAGTGGTCTCTAAC
66 C-------GGTTTGGTGTTTTAGGGTCAGT-GTGTACGGTTTTAAGGACTATAGTGGTCTCTAAC
* *
10195 CTTAGGATCTCTCTCCTC
123 CCTAGGCTCTCTCTCCTC
* * *
10213 GATCCCCATAGCTACCATTTCGGCCTCTAACCTTAAATTCTCTCTCCTCGACCATTTTAGGGTTA
1 GATCCCCGTAGCTACCATTTCGGCCTCTAACCCTAAATTCTCTCTCCTCGACCGTTTTAGGGTTA
* * *
10278 CGGTTTAGG-GTTTTAGGGTCAGTGTGCACGATTTTAAGGACTATAGTGGTCTCTAATCCTAGGC
66 CGGTTT-GGTGTTTTAGGGTCAGTGTGTACGGTTTTAAGGACTATAGTGGTCTCTAACCCTAGGC
10342 TCTCTCTCCTC
130 TCTCTCTCCTC
* *
10353 GATCCCCGTAGCTTCCATTTCGGCCTCTAACCCTAAATTATCTCTCCTCGACCGTTTTA-GG---
1 GATCCCCGTAGCTACCATTTCGGCCTCTAACCCTAAATTCTCTCTCCTCGACCGTTTTAGGGTTA
*
10414 -GG-TTGGTGTTTTAGGGTCA-TGGTGTACGGTTTTAAGTACTATAGTGGTCTCTAA
66 CGGTTTGGTGTTTTAGGGTCAGT-GTGTACGGTTTTAAGGACTATAGTGGTCTCTAA
10468 AATCAGCAGT
Statistics
Matches: 456, Mismatches: 63, Indels: 61
0.79 0.11 0.11
Matches are distributed among these distances:
133 3 0.01
134 44 0.10
135 2 0.00
136 1 0.00
137 45 0.10
138 1 0.00
139 6 0.01
140 119 0.26
141 4 0.01
143 4 0.01
144 53 0.12
145 1 0.00
146 119 0.26
147 53 0.12
148 1 0.00
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (140 bp):
GATCCCCGTAGCTACCATTTCGGCCTCTAACCCTAAATTCTCTCTCCTCGACCGTTTTAGGGTTA
CGGTTTGGTGTTTTAGGGTCAGTGTGTACGGTTTTAAGGACTATAGTGGTCTCTAACCCTAGGCT
CTCTCTCCTC
Found at i:10356 original size:286 final size:286
Alignment explanation
Indices: 9878--10412 Score: 697
Period size: 286 Copynumber: 1.9 Consensus size: 286
9868 AGGGTATACA
* *
9878 GTTTTAAGAACTATAGTGGTCTCTAACCCTAGGCTCTCTCTCGATCCCCGTAGCTGACGTTTCGG
1 GTTTTAAGAACTATAGTGGTCTCTAACCCTAGGCTCTCTCTCGATCCCCATAGCTGACATTTCGG
* * * *
9943 CCTCTAATCCTAAATTCCCTCTCTGTGATCGTTTTAGGGGTATTGTCTAGGGTTTGGTGTTTTAG
66 CCTCTAATCCTAAATTCCCTCTCTGCGACCATTTTA-GGG---TGTCTACGGTTTGGTGTTTTAG
* * * * *
10008 GGTCAGGGTGTACGGTTTTAAGGAGTATATTGGTCTCTAACCCTAGGCTCTCTCTTCTCGATCCC
127 GGTCAGGGTGCACGATTTTAAGGACTATAGTGGTCTCTAACCCTAGGCTCTCTCTCCTCGATCCC
* * * *
10073 CGTAGCTGCCGTTCCAGCCTTTAACCCTAAACTCTTTCTCATCGACCGTTTTAGCTTACAATTTA
192 CGTAGCTGCCATTCCAGCCTCTAACCCTAAACTATCTCTCATCGACCGTTTTAGCTTACAATTTA
10138 GGGTTTGGTGTTTTAGGGTCGTGGTGCACG
257 GGGTTTGGTGTTTTAGGGTCGTGGTGCACG
* *
10168 GTTTTAAGGACTATAGTGGTCTCTAACCTTAGGATCTCTCTCCTCGATCCCCATAGCT-ACCATT
1 GTTTTAAGAACTATAGTGGTCTCTAACCCTAGG--CTCTCT-CTCGATCCCCATAGCTGA-CATT
*
10232 TCGGCCTCTAA-CCTTAAATTCTCTCTCCT-CGACCATTTTA-GG-GT-TACGGTTTAGG-GTTT
62 TCGGCCTCTAATCC-TAAATTCCCTCT-CTGCGACCATTTTAGGGTGTCTACGGTTT-GGTGTTT
* *
10291 TAGGGTCAGTGTGCACGATTTTAAGGACTATAGTGGTCTCTAATCCTAGGCTCTCTCTCCTCGAT
124 TAGGGTCAGGGTGCACGATTTTAAGGACTATAGTGGTCTCTAACCCTAGGCTCTCTCTCCTCGAT
* * * * *
10356 CCCCGTAGCTTCCATTTCGGCCTCTAACCCTAAATTATCTCTCCTCGACCGTTTTAG
189 CCCCGTAGCTGCCATTCCAGCCTCTAACCCTAAACTATCTCTCATCGACCGTTTTAG
10413 GGGTTGGTGT
Statistics
Matches: 213, Mismatches: 25, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
286 117 0.55
287 4 0.02
290 31 0.15
291 2 0.01
292 9 0.04
293 48 0.23
294 2 0.01
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.36
Consensus pattern (286 bp):
GTTTTAAGAACTATAGTGGTCTCTAACCCTAGGCTCTCTCTCGATCCCCATAGCTGACATTTCGG
CCTCTAATCCTAAATTCCCTCTCTGCGACCATTTTAGGGTGTCTACGGTTTGGTGTTTTAGGGTC
AGGGTGCACGATTTTAAGGACTATAGTGGTCTCTAACCCTAGGCTCTCTCTCCTCGATCCCCGTA
GCTGCCATTCCAGCCTCTAACCCTAAACTATCTCTCATCGACCGTTTTAGCTTACAATTTAGGGT
TTGGTGTTTTAGGGTCGTGGTGCACG
Found at i:10535 original size:32 final size:32
Alignment explanation
Indices: 10494--10559 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
10484 TTTTGACTTC
**
10494 TGAGAGGTTGTAAGGTGGCTGAAAATCAAACT
1 TGAGAGGTTGTAAGGCAGCTGAAAATCAAACT
10526 TGAGAGGTTGTAAGGCAGCTGAAAATCAAACT
1 TGAGAGGTTGTAAGGCAGCTGAAAATCAAACT
10558 TG
1 TG
10560 TGCAAGGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.35, C:0.11, G:0.30, T:0.24
Consensus pattern (32 bp):
TGAGAGGTTGTAAGGCAGCTGAAAATCAAACT
Found at i:11864 original size:332 final size:331
Alignment explanation
Indices: 10922--12158 Score: 1646
Period size: 332 Copynumber: 3.7 Consensus size: 331
10912 GAACGAATAT
* * * **
10922 ATTAATTCGGAAACATATAGGAAAACCGATATTAGAAGCGTGAAAAACCCTTTAATCTTTTTGAA
1 ATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGC
* * *
10987 GTTGAATTAAATATATTCTATAACTGTTTTGGCCAAAGATTGTGGAAAAAACTTTCGGGTCAATT
66 GTTGAATTATACATATTCTATAACTGTTTTGGCCAAAGATTGTGAAAAAAACTTTCGGGTCAATT
* **
11052 TTTGCAAAATTTTAGCCGAATTCGTGTACTAACCATCATAGTTTTGGCTAAAAACGCGTTCCTGG
131 TTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATC-TTTTTTTGGCTAAAAACGCGTT-CTGG
* *** * * *
11117 GTCCTTAGCTCAGTTTTCAATGATTTTTGG-CCCGGGACTGCTTGATATATCTATATTCATCTAA
194 GGCCCCGGCTCAGTTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAA
** * *
11181 CCAAATCTCAGATAAATTGGATTTAAGGATTTGATTTTACGAGCATCATAATCATGTTTCGATTT
259 CCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACAAGCATCAAAATCATGTTTCGATTT
11246 AATCAGAA
324 AATCAGAA
* * *
11254 ACTAATTCGGGAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGC
1 ATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGC
* * * * * * * * * *
11319 GTTGAATTATACATATTCTATTAGTGTTTTGGTCAAAAATTATGGAAAAAATCTTTTGTGTTAGT
66 GTTGAATTATACATATTCTATAACTGTTTTGGCCAAAGATTGT-GAAAAAAACTTTCGGGTCAAT
* * *
11384 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAGCCATCACGTTTTTTTGGCTAAAAATGTGTTCT
130 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCAT--C-TTTTTTTGGCTAAAAACGCGTTCT
* * * *
11449 GGGACCCCGACTCAG-TTTCTAATGATTTTTGGCCCTGAGACTCCTTGACATATCTGTATTCATC
192 GGGGCCCCGGCTCAGTTTTC-AATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATC
* * *
11513 TAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGAATTTACAAGCATCAAAATTATTTTTCGA
256 TAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACAAGCATCAAAATCATGTTTCGA
*
11578 TTTAATCA-TA
321 TTTAATCAGAA
* * *
11588 ATTAATTCAGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAATCCTTCAATCTTTTTTGC
1 ATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGC
* *
11653 GTTGAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGAAAAAAAAAACTTTCGGGTCT
66 GTTGAATTATACATATTCTATAACTGTTTTGGCCAAAGATTGTG---AAAAAAACTTTCGGGTCA
* * *
11718 ATTTTTCCAAAATTTTAGCCGAAATCGTGTATTAACCAT-TTTTTTTAGCTAAAAACGCGTTCTG
128 ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCTTTTTTTGGCTAAAAACGCGTTCTG
* * *
11782 GGGCCCCGGCACA-ATTTCTAATGATTTTTGGCCCCGAGACTCCTTAACATATCTATATTCATCT
193 GGGCCCCGGCTCAGTTTTC-AATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCT
* * *
11846 AACCAAATCTCGGCCAAATTGGATTTAAGGATTTGATTTTACAGGCATCAGAATCATGTTTCGAT
257 AACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACAAGCATCAAAATCATGTTTCGAT
11911 TTAA-CTAGAA
322 TTAATC-AGAA
* * *
11921 ATTAATTCGGAAAGATATAAGAAAATCGATATTAGAAGCGTGAAAAATCCTTCAACCTTTTTGGC
1 ATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGC
** *
11986 GTTGAATTATTTATATTCTATAACTGTTTTGGCCAAAGATTGTGGAAAAAACTTTCGGGTCAATT
66 GTTGAATTATACATATTCTATAACTGTTTTGGCCAAAGATTGTGAAAAAAACTTTCGGGTCAATT
* * ** *
12051 TTTGCAAAATTTTAGCCGAAATCGTGTAC-CATCAT-GGTTTTTGGCTAAAAACGCGTTC-CGGG
131 TTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCTTTTTTTGGCTAAAAACGCGTTCTGGGG
*
12113 CTCCCGGTTCAGTTTTCAATGATTTTTGGCCCCGAGACTCCTTGAC
196 C-CCCGGCTCAGTTTTCAATGATTTTTGGCCCCGAGACTCCTTGAC
12159 CCAAATTGTA
Statistics
Matches: 790, Mismatches: 102, Indels: 29
0.86 0.11 0.03
Matches are distributed among these distances:
328 4 0.01
329 59 0.07
330 50 0.06
331 1 0.00
332 236 0.30
333 158 0.20
334 123 0.16
335 111 0.14
336 48 0.06
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (331 bp):
ATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGC
GTTGAATTATACATATTCTATAACTGTTTTGGCCAAAGATTGTGAAAAAAACTTTCGGGTCAATT
TTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCTTTTTTTGGCTAAAAACGCGTTCTGGGG
CCCCGGCTCAGTTTTCAATGATTTTTGGCCCCGAGACTCCTTGACATATCTATATTCATCTAACC
AAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACAAGCATCAAAATCATGTTTCGATTTAA
TCAGAA
Found at i:13082 original size:331 final size:331
Alignment explanation
Indices: 12349--13247 Score: 1205
Period size: 331 Copynumber: 2.7 Consensus size: 331
12339 TTCGGGTCAG
* * * *
12349 CTAACCAAATCTCAGCGAAATTGGATTTAAGGATTTGATTTTATGAGCGTTAGAATCATGTTTCG
1 CTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGAGCATTAGATTCATGTTTCG
* * * *
12414 ATTTAATTAGAAATTAATTTGGGAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACTCTTT
66 ATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAAC-CTTC
** * * *
12479 AATCTTTTTGGCGTTGAATTATACATATTCTATTTGTGTTTTCGTCAAAAATTATGGAAAAAACC
130 AATCTTTTTGGCGTTGAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTATGGAAAAAA-C
* * *
12544 TTTTGTGT-TAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAGCCATCACGTTTTTTTTGGC
194 TTTTGGGTCTA--TTTTGCAAAATTTTAGCCGAAATCCTGTACTAACCATCACG--TTTTTTGGC
* * * * * * *
12608 TAAAAATGCGTTATGGGGTCCCGGCTCAGTTTCTAATGATTTTTGGCCTCGAGACTCCTTGACAT
255 TAAAAACGCGTTATGGGGCCCCGACTCAGTTTCTAATGATTTTTGGCCCCAAAACTCCTTGACAC
*
12673 ATCTGTATTAAT
320 ATCTATATTAAT
* * * * *
12685 CTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGAATTTACGGGCATCAAAATT-ATATTTC
1 CTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGAGCAT-TAGATTCATGTTTC
* *
12749 GATTTAATCA-TAATTAATTCAGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAATCCTT
65 GATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAA-CCTT
* * *
12813 CAATATTTTTTGCGTTGAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTGTGAGAAAAAA
129 CAATCTTTTTGGCGTTGAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTATG-GAAAAAA
* * *
12878 CTTTTGGGTCTATTTTCCAAAATTTTAGTCGAAATCCTGTATTAACCATCACG-TTTTTGGCTAA
193 CTTTTGGGTCTATTTTGCAAAATTTTAGCCGAAATCCTGTACTAACCATCACGTTTTTTGGCTAA
* *
12942 AAACGCGTTCTGGGGCCCCGACTTAGTTT-TCAATGATTTTTGGCCCCAAAACTCCTTGACACAT
258 AAACGCGTTATGGGGCCCCGACTCAGTTTCT-AATGATTTTTGGCCCCAAAACTCCTTGACACAT
*
13006 CTATATTCAT
322 CTATATTAAT
* * *
13016 TTAACCAAATCTCAGCCAAATTGGATTTAAGAATTTGATTTTACGTGCATTAGATTCATGTTTCG
1 CTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGAGCATTAGATTCATGTTTCG
*
13081 ATTTAATCAGAAATTAATTCGGAAAGATTTAGGAAAATCGATATTAGAAGCGTGAAAAACCCTTC
66 ATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAA-CCTTC
*
13146 AATCTTTTTGGCGTTGAATTATATATGTATTCTATAAGTGTTTTGGCCAAAGATTATGGAAAAAA
130 AATCTTTTTGGCGTTGAATTATACA--TATTCTATAAGTGTTTTGGCCAAAGATTATGGAAAAAA
* * *
13211 CTTTCGGGTCATTTTTTGCAAAATTTTAACCGAAATC
193 CTTTTGGGTC-TATTTTGCAAAATTTTAGCCGAAATC
13248 GTATATATAT
Statistics
Matches: 493, Mismatches: 60, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
330 5 0.01
331 134 0.27
332 73 0.15
333 16 0.03
334 88 0.18
335 104 0.21
336 70 0.14
337 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (331 bp):
CTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTGATTTTACGAGCATTAGATTCATGTTTCG
ATTTAATCAGAAATTAATTCGGAAAGATATAGGAAAATCGATATTAGAAGCGTGAAAAACCTTCA
ATCTTTTTGGCGTTGAATTATACATATTCTATAAGTGTTTTGGCCAAAGATTATGGAAAAAACTT
TTGGGTCTATTTTGCAAAATTTTAGCCGAAATCCTGTACTAACCATCACGTTTTTTGGCTAAAAA
CGCGTTATGGGGCCCCGACTCAGTTTCTAATGATTTTTGGCCCCAAAACTCCTTGACACATCTAT
ATTAAT
Found at i:14689 original size:2 final size:2
Alignment explanation
Indices: 14684--14762 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
14674 AGAAGAAGAC
14684 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
14726 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
14763 GTAGGAAAGG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.