Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010394.1 Corchorus capsularis cultivar CVL-1 contig10415, 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: 70430
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:616 original size:115 final size:114
Alignment explanation
Indices: 392--627 Score: 357
Period size: 115 Copynumber: 2.1 Consensus size: 114
382 CATGTATAGA
* * * *
392 GATATTACCAAAGCTCTGACATGACATAATTACAAAATATGTAACGTAAATTTGCTAAGAACCCT
1 GATATTACCAAAGCTCTGACAGGACATAATTACAAAATATGTAACGTAAACTTACCAAGAACCCT
* *
457 TCATATATATAGAGAAAATTTATGCCAACTACCTTTTCACATATATGGC
66 TCACATATATAGAGAAAATTTATGCCAACAACCTTTTCACATATATGGC
*
506 GATATTGCCGAAA-CTCTGACAGGACATAATTACAAAATATGTAACGTAAACTTACCAACGAACC
1 GATATTACC-AAAGCTCTGACAGGACATAATTACAAAATATGTAACGTAAACTTACCAA-GAACC
* * *
570 CTTCACATATGTTGAGAAAATTTATGCCAACAACCTTTTTACATATATGGC
64 CTTCACATATATAGAGAAAATTTATGCCAACAACCTTTTCACATATATGGC
621 GATATTA
1 GATATTA
628 GCGAAGTTCT
Statistics
Matches: 109, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
114 49 0.45
115 60 0.55
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (114 bp):
GATATTACCAAAGCTCTGACAGGACATAATTACAAAATATGTAACGTAAACTTACCAAGAACCCT
TCACATATATAGAGAAAATTTATGCCAACAACCTTTTCACATATATGGC
Found at i:781 original size:307 final size:307
Alignment explanation
Indices: 197--1447 Score: 2180
Period size: 307 Copynumber: 4.1 Consensus size: 307
187 CATGTATAGA
** * * *
197 GATATTACCAAAGCTCTTTCAAGACATGATTACAAAATATGTAACGTAAATTTGCCAACGAACCC
1 GATATTACCAAAGCTCTGACAGGACATAATTACAAAATATGTAACGTAAATTTACCAACGAACCC
262 TTCACATATGTATAGAGAAAATTTATGCCAACAACCTTTTTACATATATGGCGATATTAGCGAAG
66 TTCACATATG--TAGAGAAAATTTATGCCAACAACCTTTTTACATATATGGCGATATTAGCGAAG
* *
327 TTCTGATGTGGTACAATTCTATCCATGTAACGTAAAATTGTCAGCGAATCACTCACATGTATAGA
129 TTCTGACGTGGTACAATTCTATCCATGTAACGTAAAATTGCCAGCGAATCACTCACATGTATAGA
*
392 GATATTACCAAAGCTCTGACATGACATAATTACAAAATATGTAACGTAAATTTGCTAAGAACCCT
194 GATATTACCAAAGCTCTGACACGACATAATTACAAAATATGTAACGTAAATTTGCTAAGAACCCT
*
457 TCATATATATAGAGAAAATTTATGCCAACTACCTTTTCACATATATGGC
259 TCACATATATAGAGAAAATTTATGCCAACTACCTTTTCACATATATGGC
* *
506 GATATTGCCGAAA-CTCTGACAGGACATAATTACAAAATATGTAACGTAAACTTACCAACGAACC
1 GATATTACC-AAAGCTCTGACAGGACATAATTACAAAATATGTAACGTAAATTTACCAACGAACC
*
570 CTTCACATATGTTGAGAAAATTTATGCCAACAACCTTTTTACATATATGGCGATATTAGCGAAGT
65 CTTCACATATGTAGAGAAAATTTATGCCAACAACCTTTTTACATATATGGCGATATTAGCGAAGT
*
635 TCTGACGTGGTACAATTCTATCCATGTAATGTAAAATTGCCAGCGAATCACTCACATGTATAGAG
130 TCTGACGTGGTACAATTCTATCCATGTAACGTAAAATTGCCAGCGAATCACTCACATGTATAGAG
* *
700 ATATTACCAAAGCTCTGACACGACATAATTACAAAATATGTAACATAAATTTGCTAAGAATCCTT
195 ATATTACCAAAGCTCTGACACGACATAATTACAAAATATGTAACGTAAATTTGCTAAGAACCCTT
*
765 CACATATATAGAGAAAATTTATACCAACTACCTTTTCACATATATGGC
260 CACATATATAGAGAAAATTTATGCCAACTACCTTTTCACATATATGGC
* *
813 GATATTACCAAAGCTCTGACAGGACATAATTACAAAGTATGTAACGTAAATTTACCAACAAACCC
1 GATATTACCAAAGCTCTGACAGGACATAATTACAAAATATGTAACGTAAATTTACCAACGAACCC
*
878 TTCACATATGTAGAGAAAATTTATGCCAACAACCTTTTTACATATATGGCGATATTACCGAAGTT
66 TTCACATATGTAGAGAAAATTTATGCCAACAACCTTTTTACATATATGGCGATATTAGCGAAGTT
*
943 CTGATGTGGTACAATTCTATCCATGTAACGTAAAATTGCCAGCGAATCACTCACATGTATAGAGA
131 CTGACGTGGTACAATTCTATCCATGTAACGTAAAATTGCCAGCGAATCACTCACATGTATAGAGA
*
1008 TATTACCAAAGCTCTGACATGACATAATTACAAAATATGTAACGTAAATTTGCTAAGAACCCTTC
196 TATTACCAAAGCTCTGACACGACATAATTACAAAATATGTAACGTAAATTTGCTAAGAACCCTTC
1073 ACATATATAGAGAAAATTTATGCCAACTACCTTTTCACATATATGGC
261 ACATATATAGAGAAAATTTATGCCAACTACCTTTTCACATATATGGC
*
1120 GATATTACCAAAGCTCTGACAGGACATAATTACAAAATATGTAACATAAATTTACCAACGAACCC
1 GATATTACCAAAGCTCTGACAGGACATAATTACAAAATATGTAACGTAAATTTACCAACGAACCC
1185 TTCACATATGTAGAGAAAATTTATGCCAACAACCTTTTTACATATATGGCGATATTAGCGAAGTT
66 TTCACATATGTAGAGAAAATTTATGCCAACAACCTTTTTACATATATGGCGATATTAGCGAAGTT
* *
1250 CTGACGTGGTACAATTCTATCCATGTAACGTAAAATTGCCAGCGAATCACTCACATATATTGAGA
131 CTGACGTGGTACAATTCTATCCATGTAACGTAAAATTGCCAGCGAATCACTCACATGTATAGAGA
** *
1315 TATTGTCAAAGCTCTAACACGACATAATTACAAAATATGTAACGTAAATTTGCTAAGAACCCTTC
196 TATTACCAAAGCTCTGACACGACATAATTACAAAATATGTAACGTAAATTTGCTAAGAACCCTTC
* * *
1380 ACATGTATAGAGAAAGTTTATGCCAACTACATTTTCACATATATGGC
261 ACATATATAGAGAAAATTTATGCCAACTACCTTTTCACATATATGGC
* *
1427 GATATTAGCAAAGTTCTGACA
1 GATATTACCAAAGCTCTGACA
1448 TGGTACAATT
Statistics
Matches: 896, Mismatches: 44, Indels: 6
0.95 0.05 0.01
Matches are distributed among these distances:
306 3 0.00
307 826 0.92
309 64 0.07
310 3 0.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (307 bp):
GATATTACCAAAGCTCTGACAGGACATAATTACAAAATATGTAACGTAAATTTACCAACGAACCC
TTCACATATGTAGAGAAAATTTATGCCAACAACCTTTTTACATATATGGCGATATTAGCGAAGTT
CTGACGTGGTACAATTCTATCCATGTAACGTAAAATTGCCAGCGAATCACTCACATGTATAGAGA
TATTACCAAAGCTCTGACACGACATAATTACAAAATATGTAACGTAAATTTGCTAAGAACCCTTC
ACATATATAGAGAAAATTTATGCCAACTACCTTTTCACATATATGGC
Found at i:929 original size:115 final size:114
Alignment explanation
Indices: 699--946 Score: 370
Period size: 115 Copynumber: 2.2 Consensus size: 114
689 CATGTATAGA
* * * *
699 GATATTACCAAAGCTCTGACACGACATAATTACAAAATATGTAACATAAATTTGCTAAGAATCCT
1 GATATTACCAAAGCTCTGACACGACATAATTACAAAATATGTAACATAAATTTACCAAAAACCCT
*
764 TCACATATATAGAGAAAATTTATACCAACTACCTTTTCACATATATGGC
66 TCACATATATAGAGAAAATTTATACCAACAACCTTTTCACATATATGGC
* * *
813 GATATTACCAAAGCTCTGACAGGACATAATTACAAAGTATGTAACGTAAATTTACCAACAAACCC
1 GATATTACCAAAGCTCTGACACGACATAATTACAAAATATGTAACATAAATTTACCAA-AAACCC
* * *
878 TTCACATATGTAGAGAAAATTTATGCCAACAACCTTTTTACATATATGGC
65 TTCACATATATAGAGAAAATTTATACCAACAACCTTTTCACATATATGGC
* *
928 GATATTACCGAAGTTCTGA
1 GATATTACCAAAGCTCTGA
947 TGTGGTACAA
Statistics
Matches: 120, Mismatches: 13, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
114 53 0.44
115 67 0.56
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (114 bp):
GATATTACCAAAGCTCTGACACGACATAATTACAAAATATGTAACATAAATTTACCAAAAACCCT
TCACATATATAGAGAAAATTTATACCAACAACCTTTTCACATATATGGC
Found at i:1164 original size:193 final size:193
Alignment explanation
Indices: 813--1169 Score: 513
Period size: 192 Copynumber: 1.8 Consensus size: 193
803 CATATATGGC
*
813 GATATTACCAAAGCTCTGACAGGACATAATTACAAAGTATGTAACGTAAATTTACCAACAAACCC
1 GATATTACCAAAGCTCTGACAGGACATAATTACAAAATATGTAACGTAAATTTACCAACAAACCC
* * * *
878 TTCACATATGTAGAGAAAATTTATGCCAACAACCTTTTTACATATATGGCGATATTACCGAAGTT
66 TTCACATATATAGAGAAAATTTATGCCAACAACCTTTTCACATATATGGCGATATTACCAAAGCT
** * ** *
943 CTGATGTGGTACAATTCTATCCATGTAACGTAAAATTGCCAGCGAATCACTCACATGTATAGA
131 CTGATCAGGTACAATTCAAAACATGTAACATAAAATTGCCAGCGAATCACTCACATGTATAGA
* * * *
1006 GATATTACCAAAGCTCTGACATGACATAATTACAAAATATGTAACGTAAATTTGCTAA-GAACCC
1 GATATTACCAAAGCTCTGACAGGACATAATTACAAAATATGTAACGTAAATTTACCAACAAACCC
*
1070 TTCACATATATAGAGAAAATTTATGCCAACTACCTTTTCACATATATGGCGATATTACCAAAGCT
66 TTCACATATATAGAGAAAATTTATGCCAACAACCTTTTCACATATATGGCGATATTACCAAAGCT
*
1135 CTGA-CAGG-ACATAATTACAAAATATGTAACATAAA
131 CTGATCAGGTAC--AATT-CAAAACATGTAACATAAA
1170 TTTACCAACG
Statistics
Matches: 144, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
190 2 0.01
191 2 0.01
192 73 0.51
193 67 0.47
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.28
Consensus pattern (193 bp):
GATATTACCAAAGCTCTGACAGGACATAATTACAAAATATGTAACGTAAATTTACCAACAAACCC
TTCACATATATAGAGAAAATTTATGCCAACAACCTTTTCACATATATGGCGATATTACCAAAGCT
CTGATCAGGTACAATTCAAAACATGTAACATAAAATTGCCAGCGAATCACTCACATGTATAGA
Found at i:1254 original size:115 final size:114
Alignment explanation
Indices: 1006--1241 Score: 400
Period size: 115 Copynumber: 2.1 Consensus size: 114
996 CATGTATAGA
* * * *
1006 GATATTACCAAAGCTCTGACATGACATAATTACAAAATATGTAACGTAAATTTGCTAAGAACCCT
1 GATATTACCAAAGCTCTGACAGGACATAATTACAAAATATGTAACATAAATTTACCAAGAACCCT
*
1071 TCACATATATAGAGAAAATTTATGCCAACTACCTTTTCACATATATGGC
66 TCACATATATAGAGAAAATTTATGCCAACAACCTTTTCACATATATGGC
1120 GATATTACCAAAGCTCTGACAGGACATAATTACAAAATATGTAACATAAATTTACCAACGAACCC
1 GATATTACCAAAGCTCTGACAGGACATAATTACAAAATATGTAACATAAATTTACCAA-GAACCC
* *
1185 TTCACATATGTAGAGAAAATTTATGCCAACAACCTTTTTACATATATGGC
65 TTCACATATATAGAGAAAATTTATGCCAACAACCTTTTCACATATATGGC
1235 GATATTA
1 GATATTA
1242 GCGAAGTTCT
Statistics
Matches: 114, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
114 54 0.47
115 60 0.53
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.29
Consensus pattern (114 bp):
GATATTACCAAAGCTCTGACAGGACATAATTACAAAATATGTAACATAAATTTACCAAGAACCCT
TCACATATATAGAGAAAATTTATGCCAACAACCTTTTCACATATATGGC
Found at i:1435 original size:192 final size:193
Alignment explanation
Indices: 1107--1507 Score: 590
Period size: 192 Copynumber: 2.1 Consensus size: 193
1097 AACTACCTTT
* * *
1107 TCACATATATGGCGATATTACCAAAGCTCTGACAGGACATAATTACAAAATATGTAACATAAATT
1 TCACATATATGGAGATATTACCAAAGCTCTAACACGACATAATTACAAAATATGTAACATAAATT
* * *
1172 TACCAACGAACCCTTCACATATGTAGAGAAAATTTATGCCAACAACCTTTTTACATATATGGCGA
66 TACCAACGAACCCTTCACATATATAGAGAAAATTTATGCCAACAACATTTTCACATATATGGCGA
* *
1237 TATTAGCGAAGTTCTGACGTGGTACAATTCTATCCATGTAACGTAAAA-TTGCCAGCGAATCAC
131 TATTAGCAAAGTTCTGACATGGTACAATTCTATCCATGTAACGTAAAATTTGCCAGCGAATC-C
* ** *
1300 TCACATATATTGAGATATTGTCAAAGCTCTAACACGACATAATTACAAAATATGTAACGTAAATT
1 TCACATATATGGAGATATTACCAAAGCTCTAACACGACATAATTACAAAATATGTAACATAAATT
* * * * *
1365 TGCTAA-GAACCCTTCACATGTATAGAGAAAGTTTATGCCAACTACATTTTCACATATATGGCGA
66 TACCAACGAACCCTTCACATATATAGAGAAAATTTATGCCAACAACATTTTCACATATATGGCGA
*
1429 TATTAGCAAAGTTCTGACATGGTACAATTCTATCCATGTAACGTAAAATTTGCCAGTGAATCC
131 TATTAGCAAAGTTCTGACATGGTACAATTCTATCCATGTAACGTAAAATTTGCCAGCGAATCC
**
1492 TCTACATGGATGGAGA
1 TC-ACATATATGGAGA
1508 GGTTACCTTT
Statistics
Matches: 185, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
192 101 0.55
193 84 0.45
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (193 bp):
TCACATATATGGAGATATTACCAAAGCTCTAACACGACATAATTACAAAATATGTAACATAAATT
TACCAACGAACCCTTCACATATATAGAGAAAATTTATGCCAACAACATTTTCACATATATGGCGA
TATTAGCAAAGTTCTGACATGGTACAATTCTATCCATGTAACGTAAAATTTGCCAGCGAATCC
Found at i:4228 original size:30 final size:30
Alignment explanation
Indices: 4155--4230 Score: 111
Period size: 29 Copynumber: 2.6 Consensus size: 30
4145 ACTTGTAGCG
* *
4155 TTTA-GACGTTTTGCCCCCTGGACTTCAAT
1 TTTAGGACGTTTTGCCCCATGAACTTCAAT
*
4184 TTT-GGACATTTTGCCCCATGAACTTCAAT
1 TTTAGGACGTTTTGCCCCATGAACTTCAAT
4213 TTTAGGACGTTTTGCCCC
1 TTTAGGACGTTTTGCCCC
4231 TTCAACCTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 28 0.68
30 13 0.32
ACGTcount: A:0.18, C:0.26, G:0.17, T:0.38
Consensus pattern (30 bp):
TTTAGGACGTTTTGCCCCATGAACTTCAAT
Found at i:4485 original size:29 final size:29
Alignment explanation
Indices: 4413--4486 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
4403 TAGGTTGAGG
4413 GGGTAAAATGTCCCAAAATTGAAGTTAAGA
1 GGGTAAAATGT-CCAAAATTGAAGTTAAGA
* *
4443 GGGTAAAATATCCAAAATTGAAGTTCATGA
1 GGGTAAAATGTCCAAAATTGAAGTT-AAGA
*
4473 -GGTAAAACGTCCAA
1 GGGTAAAATGTCCAA
4487 CCGCTACAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
29 26 0.67
30 13 0.33
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (29 bp):
GGGTAAAATGTCCAAAATTGAAGTTAAGA
Found at i:10219 original size:17 final size:16
Alignment explanation
Indices: 10180--10225 Score: 67
Period size: 17 Copynumber: 2.9 Consensus size: 16
10170 TTTGGTAGGG
10180 AGGAAA-GAAATAGAA
1 AGGAAAGGAAATAGAA
*
10195 ATGAAAGGAAATAGTAA
1 AGGAAAGGAAATAG-AA
10212 AGGAAAGGAAATAG
1 AGGAAAGGAAATAG
10226 GGAGGAAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 5 0.19
16 7 0.26
17 15 0.56
ACGTcount: A:0.61, C:0.00, G:0.28, T:0.11
Consensus pattern (16 bp):
AGGAAAGGAAATAGAA
Found at i:11015 original size:1 final size:1
Alignment explanation
Indices: 11011--11040 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
11001 GATGATTGCG
11011 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11041 CTGGTGAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:14074 original size:16 final size:16
Alignment explanation
Indices: 14050--14086 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
14040 TATAAATCAT
*
14050 TTACGTAAAAGTTAAA
1 TTACTTAAAAGTTAAA
*
14066 TTACTTAAAAGTTAGA
1 TTACTTAAAAGTTAAA
14082 TTACT
1 TTACT
14087 ATTCACTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (16 bp):
TTACTTAAAAGTTAAA
Found at i:14183 original size:2 final size:2
Alignment explanation
Indices: 14176--14214 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
14166 TCCGTGGGAC
14176 TA TA TA 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 TA TA TA T
14215 CGAAATTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14511 original size:15 final size:15
Alignment explanation
Indices: 14487--14528 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
14477 TCTTTTTTCC
*
14487 TTATACTATATACTA
1 TTATATTATATACTA
* *
14502 TTATATTATATATTT
1 TTATATTATATACTA
14517 TTATATTA-ATAC
1 TTATATTATATAC
14529 ATCCATCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 3 0.13
15 20 0.87
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATATTATATACTA
Found at i:20577 original size:20 final size:20
Alignment explanation
Indices: 20552--20594 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
20542 CTAATTGGAA
20552 AATGATTAATCTCAAACCTC
1 AATGATTAATCTCAAACCTC
20572 AATGATTAATCTCAAACCTC
1 AATGATTAATCTCAAACCTC
20592 AAT
1 AAT
20595 CTAAAAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (20 bp):
AATGATTAATCTCAAACCTC
Found at i:27794 original size:17 final size:15
Alignment explanation
Indices: 27772--27806 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
27762 CTGAATCATG
27772 TTTTTCTTTCTTTTCTT
1 TTTTTCTTT-TTTT-TT
27789 TTTTTCTTTTTTTTT
1 TTTTTCTTTTTTTTT
27804 TTT
1 TTT
27807 CATGAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 4 0.22
17 9 0.50
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTCTTTTTTTTT
Found at i:27796 original size:13 final size:13
Alignment explanation
Indices: 27773--27807 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
27763 TGAATCATGT
27773 TTTTCTTTCTTTTC
1 TTTT-TTTCTTTTC
*
27787 TTTTTTTCTTTTT
1 TTTTTTTCTTTTC
27800 TTTTTTTC
1 TTTTTTTC
27808 ATGAAATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:37694 original size:17 final size:17
Alignment explanation
Indices: 37674--37710 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
37664 GGAATGTGGA
*
37674 GATAGATGGATGACGAT
1 GATAAATGGATGACGAT
*
37691 GATAAATTGATGACGAT
1 GATAAATGGATGACGAT
37708 GAT
1 GAT
37711 GAAACTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (17 bp):
GATAAATGGATGACGAT
Found at i:58920 original size:14 final size:14
Alignment explanation
Indices: 58901--58928 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58891 AATGAATGGG
58901 AAAAAAAATGAAAA
1 AAAAAAAATGAAAA
58915 AAAAAAAATGAAAA
1 AAAAAAAATGAAAA
58929 CCAACCAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (14 bp):
AAAAAAAATGAAAA
Found at i:59669 original size:4 final size:4
Alignment explanation
Indices: 59660--59693 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
59650 AGGCGTATCT
*
59660 TTAA TTAA TTAA TTAA CTAA TTAA -TAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
59694 GTACTGCTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (4 bp):
TTAA
Found at i:67338 original size:2 final size:2
Alignment explanation
Indices: 67331--67371 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
67321 TCAAGGAGAC
67331 AT AT AT AT 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 AT AT AT AT A
67372 GTGCAATGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.