Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013343.1 Corchorus capsularis cultivar CVL-1 contig13364, 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: 29898
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:1559 original size:12 final size:13
Alignment explanation
Indices: 1518--1562 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1508 AATTATTGTT
*
1518 TGCTTTATTGATC
1 TGCTTTATTAATC
*
1531 TGCTTTATTAATT
1 TGCTTTATTAATC
1544 TGCTTTA-TAATC
1 TGCTTTATTAATC
1556 TGCTTTA
1 TGCTTTA
1563 GATTTAGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.20, C:0.13, G:0.11, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:1570 original size:6 final size:6
Alignment explanation
Indices: 1559--1585 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1549 TATAATCTGC
1559 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1586 GCTTTGCTTT
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:12887 original size:20 final size:20
Alignment explanation
Indices: 12862--12903 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
12852 TGAGCGGCGC
*
12862 TGAAGATGCTTTTGTTGCCG
1 TGAAGATACTTTTGTTGCCG
12882 TGAAGATACTTTTGTTGCCG
1 TGAAGATACTTTTGTTGCCG
12902 TG
1 TG
12904 TGATGGTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40
Consensus pattern (20 bp):
TGAAGATACTTTTGTTGCCG
Found at i:15478 original size:28 final size:28
Alignment explanation
Indices: 15429--15482 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
15419 TTTTGTCTAG
*
15429 TTGCGGCAAATTTTGGACTTTTGGGTAC
1 TTGCGGCAAATTTTGAACTTTTGGGTAC
*
15457 TTGCGGC-AATTTTGCAATTTTTGGGT
1 TTGCGGCAAATTTTG-AACTTTTGGGT
15483 TGCTGCGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.17, C:0.13, G:0.28, T:0.43
Consensus pattern (28 bp):
TTGCGGCAAATTTTGAACTTTTGGGTAC
Found at i:19814 original size:437 final size:439
Alignment explanation
Indices: 19121--20107 Score: 1236
Period size: 437 Copynumber: 2.3 Consensus size: 439
19111 ACAAAAGTCA
* * *
19121 AAGCGTTAAATCGTCCAACCTATAATTGTAAAGGATTCAATAGCATGAAA-CATAAAAGTATGAG
1 AAGCGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCAT-AAAGCATAAAAGTATAAG
* * * * *
19185 GGTTATTAGATAAATAATCCAGCAAAAAAAATATTAGTTTA-TGAAGACAAAACATAAAAATTCC
65 GATCATTTGATAAATAATCCAGCAAAAAATATATTTGTTTATTG-AGACAAAACATAAAAATTCC
* * * * * **
19249 CTCTTGAATCCTCCACGAAAATTATTAATCAAATTCAACTTTCATGCCCTTAATGAAAGTTGTAG
129 CTCTCGAACCCTCCACGAAAATCATTAATCAAATTCAACTTTCAGGCCCTTAACGAAAGTCATAG
* *
19314 ATCACACAATAACCTTTTAACCGACACTTGAACAACTTCAATTGGACAAGTGGGCTAAAAATTAT
194 ATCACACAATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGGCTAAAAATTAT
* * * *
19379 ACGATATTAAATGGACCGGCAATCGAAATCACAAAATTTAAGAAACATATTTTAGAATCAAAACA
259 ACAATATTAAATAGACCGACAATCGAAACCACAAAATTTAAGAAACATATTTTAGAATCAAAACA
* ** * * *
19444 T-TAAATTGG-CTTCAGAGTTTTTCATGAAAGTTGTAGATCATGAGATTACCTTTTAATAGATAC
324 TGAAAATTGGTCTTC--AGTCCTTCATGAAAGTTGTAAATCATGAAATTACCTTTTAATAGACAC
* * *
19507 TTGAATCACCTTGATCGGACAAATAGAAC-AGAAAATACAAA-AATAAAAACCG
387 TTGAATCACATTGATCGGACAAATAAAACAAAAAAATA-AAAGAATAAAAACCG
* ** *
19559 ACGCGTTAAATCGTTGAACCCATAATTGTAAAGGATTAAATATCATAAAGCATAAAA-TATAAGG
1 AAGCGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATAAGG
* * *
19623 ATCATTTGATAAATAATCCAGCAAAAGATATTTTTGTTTATTGAGACCAAACATAAAAATTCCCT
66 ATCATTTGATAAATAATCCAGCAAAAAATATATTTGTTTATTGAGACAAAACATAAAAATTCCCT
* * * * *
19688 CTCGAACCCTCCACGAAACTCATTAATCAAATTTAGCTTTCAGGTCCTTGACGAAAGTCATAGAT
131 CTCGAACCCTCCACGAAAATCATTAATCAAATTCAACTTTCAGGCCCTTAACGAAAGTCATAGAT
* * *
19753 CACACAATAGCCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGT-GGATCGAAAATTATA
196 CACACAATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGGCT-AAAAATTATA
* * * * * * **
19817 CAATATTAGATAGACCGACAATTGAGACCACAAAATTTAAGAAGCATTTTTTAGAGTTGAAACAT
260 CAATATTAAATAGACCGACAATCGAAACCACAAAATTTAAGAAACATATTTTAGAATCAAAACAT
* *
19882 GAAAATTGGTTTTCAGTCCTTCATGAAAGTTGTAAATCATGAAATTATCTTTTAATAGACACTTG
325 GAAAATTGGTCTTCAGTCCTTCATGAAAGTTGTAAATCATGAAATTACCTTTTAATAGACACTTG
* * *
19947 AATCACATTGATCGGACAAGTAAAACAAAAAAATAAAAGAATTAAAGCCG
390 AATCACATTGATCGGACAAATAAAACAAAAAAATAAAAGAATAAAAACCG
* * * * * * * * *
19997 AAACGTTCAATTGTCCAACCCAGAATTTGTGAGGGACTAAATAGCATAAAGTATAAAAGTATAGG
1 AAGCGTTAAATCGTCCAACCCATAA-TTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATAAG
*
20062 GATCATTTGATAAATAATTCAGCAAAAAATA-ATTTGTTTATTGAGA
65 GATCATTTGATAAATAATCCAGCAAAAAATATATTTGTTTATTGAGA
20108 GTGGGGCCAA
Statistics
Matches: 466, Mismatches: 74, Indels: 17
0.84 0.13 0.03
Matches are distributed among these distances:
436 3 0.01
437 295 0.63
438 90 0.19
439 44 0.09
440 34 0.07
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (439 bp):
AAGCGTTAAATCGTCCAACCCATAATTGTAAAGGATTAAATAGCATAAAGCATAAAAGTATAAGG
ATCATTTGATAAATAATCCAGCAAAAAATATATTTGTTTATTGAGACAAAACATAAAAATTCCCT
CTCGAACCCTCCACGAAAATCATTAATCAAATTCAACTTTCAGGCCCTTAACGAAAGTCATAGAT
CACACAATAACCTTTTAACCGACACTTGAACAACCTCAATCGGACAAGTGGGCTAAAAATTATAC
AATATTAAATAGACCGACAATCGAAACCACAAAATTTAAGAAACATATTTTAGAATCAAAACATG
AAAATTGGTCTTCAGTCCTTCATGAAAGTTGTAAATCATGAAATTACCTTTTAATAGACACTTGA
ATCACATTGATCGGACAAATAAAACAAAAAAATAAAAGAATAAAAACCG
Found at i:20985 original size:95 final size:95
Alignment explanation
Indices: 20833--21010 Score: 234
Period size: 95 Copynumber: 1.9 Consensus size: 95
20823 AGATTGGAAT
* * * *
20833 TAAATTGAGAATCCCCAAAGCGATATAATTTGTACCCAAAACATTTCTCAATGTCCCCAAA-AGA
1 TAAATTCAGAATCCCCAAAGAGATATAATTTATACCCAAAACATTTCTCAATATCCCCAAATA-A
* *
20897 TTATATGCACCAACCCCAATTCGCTTTGCTA
65 TCATACGCACCAACCCCAATTCGCTTTGCTA
* * *
20928 TAAATTCAGTATCCCCAAAGAGATATACTTTATACCCAAATCATTTCTC-ATCATCCCCAAATAA
1 TAAATTCAGAATCCCCAAAGAGATATAATTTATACCCAAAACATTTCTCAAT-ATCCCCAAATAA
*
20992 TCATACGCACCATCCCCAA
65 TCATACGCACCAACCCCAA
21011 AATATTTTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
94 2 0.03
95 68 0.96
96 1 0.01
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.27
Consensus pattern (95 bp):
TAAATTCAGAATCCCCAAAGAGATATAATTTATACCCAAAACATTTCTCAATATCCCCAAATAAT
CATACGCACCAACCCCAATTCGCTTTGCTA
Found at i:21380 original size:217 final size:217
Alignment explanation
Indices: 20929--21888 Score: 1349
Period size: 217 Copynumber: 4.5 Consensus size: 217
20919 GCTTTGCTAT
20929 AAATTCAGTATCCCCAAAGAGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATC
1 AAATTCAGTATCCCCAAAGAGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATC
* * * * *
20994 ATACGCACCATCCCCAAAATATTTTTATAGATTGACATTTGTTTATATGCCCAAAATTGCCTTTT
66 ATAAGCACCATCCCC-AAAT-TTTTTAGAGATTGACATTT-TTTATATACCCAAAATTGGC-TTA
* * *
21059 AAACGTGTTTTAATCCATATTTTTATCCTAATTAATTGAA-AAACCCCGTCTATATGAATTTATT
127 AAACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATAAATTTAGT
*
21123 GTCATCTAATAATTAAACAAGAA-GCA
192 GTCATCTAATAACTAAACAA-AATGCA
* * * * *
21149 AAATTCACTATCCCCAAAGAGATGTACTTTATACCCAAATGAGTTCTCATCAACCCCAAATAATC
1 AAATTCAGTATCCCCAAAGAGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATC
*
21214 ATAAGCACCATTCCCAAATTTTTTAGAG-TTGACAATTTTTTATATACCCAAAATTGGCTTAAAA
66 ATAAGCACCATCCCCAAATTTTTTAGAGATTGAC-ATTTTTTATATACCCAAAATTGGCTTAAAA
*
21278 TGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATAAATTTAGTGTC
130 CGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATAAATTTAGTGTC
* *
21343 CTCTAATAATTAAACAAAATGCA
195 ATCTAATAACTAAACAAAATGCA
* * *
21366 AAATTCAGTATCCCCAAAGTGATATACTTTATACCCAAATCATTTCTCATCATCTCAAAATAATC
1 AAATTCAGTATCCCCAAAGAGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATC
* * *
21431 ATATGCACCATCCCCAAATTTTTTAGAAATTGACATTTTTTTTATATATCCAAAATTGGCTTAAA
66 ATAAGCACCATCCCCAAATTTTTTAGAGATTGACA--TTTTTTATATACCCAAAATTGGCTTAAA
*
21496 ACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATAT-AA--TA-T-A
129 ACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATAAATTTAGTGT
* * *
21556 AATTTAATAACTAAACACAATGCA
194 CATCTAATAACTAAACAAAATGCA
* * * * * *
21580 AAATTCAGTATCTCCAAAGGGATAGACATTATGCACAAATCATTTCTCATCATCCCCAAATAATC
1 AAATTCAGTATCCCCAAAGAGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATC
* *
21645 ATAAGCACCATCCCCAAAGTTTTTAGAGATTGACATTTTTCTATATACCCAAAATTGGCTTTAAA
66 ATAAGCACCATCCCCAAATTTTTTAGAGATTGACATTTTT-TATATACCCAAAATTGGCTTAAAA
21710 CGTGTTTTAATCCATA-TTT--T-C--A-TAATTGAATAAA-CCCGTCTATATAAATTTAGTGTC
130 CGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATAAATTTAGTGTC
21767 ATCTAATAACTAAACAAAATGCA
195 ATCTAATAACTAAACAAAATGCA
* * * *
21790 AAATTTAGTATCCCCAAAGGGATATACTTTATACCCAAATCATCTCTCATCATCCCTAAATAATC
1 AAATTCAGTATCCCCAAAGAGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATC
* *
21855 ATATGCACTATCCCCAAATTTTTTAGAGATTGAC
66 ATAAGCACCATCCCCAAATTTTTTAGAGATTGAC
21889 CTGGCAACAG
Statistics
Matches: 665, Mismatches: 63, Indels: 34
0.87 0.08 0.04
Matches are distributed among these distances:
205 11 0.02
206 14 0.02
207 1 0.00
208 2 0.00
209 2 0.00
210 110 0.17
212 8 0.01
213 38 0.06
214 108 0.16
215 1 0.00
216 44 0.07
217 150 0.23
218 19 0.03
219 84 0.13
220 73 0.11
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (217 bp):
AAATTCAGTATCCCCAAAGAGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATC
ATAAGCACCATCCCCAAATTTTTTAGAGATTGACATTTTTTATATACCCAAAATTGGCTTAAAAC
GTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATAAATTTAGTGTCA
TCTAATAACTAAACAAAATGCA
Found at i:21821 original size:424 final size:432
Alignment explanation
Indices: 20929--21888 Score: 1390
Period size: 424 Copynumber: 2.2 Consensus size: 432
20919 GCTTTGCTAT
*
20929 AAATTCAGTATCCCCAAAGAGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATC
1 AAATTCAGTATCCCCAAAGAGATATACTTTATACCCAAATCATTTCTCATCATCCCAAAATAATC
* * * *
20994 ATACGCACCATCCCCAAAATATTTTTATAGATTGACATTTGTTTATATGCCCAAAATTGCCTTTT
66 ATATGCACCATCCCC-AAAT-TTTTTAGAGATTGACATTTGTTTATATACCCAAAATTGCCTTTA
*
21059 AAACGTGTTTTAATCCATATTTTTATCCTAATTAATTGAAAAACCCCGTCTATATGAATTTATTG
129 AAACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAAAAACCCCGTCTATATGAA-TTATTG
** * * *
21124 TCATCTAATAATTAAACAAGAAGCAAAATTCACTATCCCCAAAGAGATGTACTTTATACCCAAAT
193 AAATCTAATAACTAAACAAGAAGCAAAATTCACTATCCCCAAAGAGATGTACATTATACACAAAT
* * *
21189 GAGTTCTCATCAACCCCAAATAATCATAAGCACCATTCCCAAATTTTTTAGAGTTGACAATTTTT
258 CAGTTCTCATCAACCCCAAATAATCATAAGCACCATCCCCAAAGTTTTTAGAGTTGACAATTTTT
*
21254 TATATACCCAAAATTGGCTTAAAATGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAA
323 TATATACCCAAAATTGGCTTAAAACGTGTTTTAATCCATATTTT-ATCC-AATTAATTGAATAAA
* *
21319 CCCCGTCTATATAAATTTAGTGTCCTCTAATAATTAAACAAAATGCA
386 CCCCGTCTATATAAATTTAGTGTCATCTAATAACTAAACAAAATGCA
* *
21366 AAATTCAGTATCCCCAAAGTGATATACTTTATACCCAAATCATTTCTCATCATCTCAAAATAATC
1 AAATTCAGTATCCCCAAAGAGATATACTTTATACCCAAATCATTTCTCATCATCCCAAAATAATC
* * * *
21431 ATATGCACCATCCCCAAATTTTTTAGAAATTGACATTTTTTTTATATATCCAAAATTGGC-TTAA
66 ATATGCACCATCCCCAAATTTTTTAGAGATTGACA-TTTGTTTATATACCCAAAATTGCCTTTAA
21495 AACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATAT-AA-TA-T-A
130 AACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAA-AAACCCCGTCTATATGAATTATTGA
* * * * * *
21556 AATTTAATAACTAAACACA-ATGCAAAATTCAGTATCTCCAAAGGGATAG-ACATTATGCACAAA
194 AATCTAATAACTAAACA-AGAAGCAAAATTCACTATCCCCAAAGAGAT-GTACATTATACACAAA
* *
21619 TCATTTCTCATCATCCCCAAATAATCATAAGCACCATCCCCAAAGTTTTTAGAGATTGAC-ATTT
257 TCAGTTCTCATCAACCCCAAATAATCATAAGCACCATCCCCAAAGTTTTTAGAG-TTGACAATTT
*
21683 TTCTATATACCCAAAATTGGCTTTAAACGTGTTTTAATCCATA-TTT-T-C-A-TAATTGAATAA
321 TT-TATATACCCAAAATTGGCTTAAAACGTGTTTTAATCCATATTTTATCCAATTAATTGAATAA
21743 A-CCCGTCTATATAAATTTAGTGTCATCTAATAACTAAACAAAATGCA
385 ACCCCGTCTATATAAATTTAGTGTCATCTAATAACTAAACAAAATGCA
* * * *
21790 AAATTTAGTATCCCCAAAGGGATATACTTTATACCCAAATCATCTCTCATCATCCCTAAATAATC
1 AAATTCAGTATCCCCAAAGAGATATACTTTATACCCAAATCATTTCTCATCATCCCAAAATAATC
*
21855 ATATGCACTATCCCCAAATTTTTTAGAGATTGAC
66 ATATGCACCATCCCCAAATTTTTTAGAGATTGAC
21889 CTGGCAACAG
Statistics
Matches: 478, Mismatches: 39, Indels: 25
0.88 0.07 0.05
Matches are distributed among these distances:
424 136 0.28
425 12 0.03
426 1 0.00
428 1 0.00
429 1 0.00
431 107 0.22
432 46 0.10
433 2 0.00
435 57 0.12
436 39 0.08
437 76 0.16
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (432 bp):
AAATTCAGTATCCCCAAAGAGATATACTTTATACCCAAATCATTTCTCATCATCCCAAAATAATC
ATATGCACCATCCCCAAATTTTTTAGAGATTGACATTTGTTTATATACCCAAAATTGCCTTTAAA
ACGTGTTTTAATCCATATTTTCATCCTAATTAATTGAAAAACCCCGTCTATATGAATTATTGAAA
TCTAATAACTAAACAAGAAGCAAAATTCACTATCCCCAAAGAGATGTACATTATACACAAATCAG
TTCTCATCAACCCCAAATAATCATAAGCACCATCCCCAAAGTTTTTAGAGTTGACAATTTTTTAT
ATACCCAAAATTGGCTTAAAACGTGTTTTAATCCATATTTTATCCAATTAATTGAATAAACCCCG
TCTATATAAATTTAGTGTCATCTAATAACTAAACAAAATGCA
Found at i:23136 original size:27 final size:28
Alignment explanation
Indices: 23074--23144 Score: 108
Period size: 27 Copynumber: 2.5 Consensus size: 28
23064 ATAAATGTAA
* *
23074 GAAGATGAACCATTCCATAGCATCTATAG
1 GAAGATGAACCATTCAATAACA-CTATAG
23103 GAAGATGAACCATTCAATAACA-TATAG
1 GAAGATGAACCATTCAATAACACTATAG
23130 GAAGATGAACCATTC
1 GAAGATGAACCATTC
23145 TCATTAATCA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 20 0.50
29 20 0.50
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (28 bp):
GAAGATGAACCATTCAATAACACTATAG
Found at i:23620 original size:33 final size:33
Alignment explanation
Indices: 23539--23661 Score: 133
Period size: 33 Copynumber: 3.7 Consensus size: 33
23529 CCGCGCAACA
*
23539 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC
*
23574 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC
* ** *
23607 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC
*
23640 CCGGCCACAACCAGCCACGCGA
1 CCGGCCACAACCGGCCACGCGA
23662 TCCTTTGTCT
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
32 2 0.03
33 65 0.87
35 7 0.09
36 1 0.01
ACGTcount: A:0.24, C:0.41, G:0.27, T:0.07
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGC
Found at i:24578 original size:8 final size:8
Alignment explanation
Indices: 24565--24598 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
24555 ACCTTCTTGA
24565 AAAAATTC
1 AAAAATTC
24573 AAAAATTC
1 AAAAATTC
*
24581 AGAAACTTC
1 A-AAAATTC
24590 AAAAATTC
1 AAAAATTC
24598 A
1 A
24599 TAGCCGATTC
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:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:24689 original size:9 final size:9
Alignment explanation
Indices: 24671--24706 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
24661 AGTTATATCG
*
24671 AAAAATATA
1 AAAAAAATA
24680 AAAAAAATA
1 AAAAAAATA
24689 AAATAAAATA
1 AAA-AAAATA
24699 AAAAAAAT
1 AAAAAAAT
24707 TTCGACCAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAAAAATA
Done.