Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013524.1 Corchorus capsularis cultivar CVL-1 contig13545, 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: 47939
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:59 original size:33 final size:33
Alignment explanation
Indices: 16--121 Score: 158
Period size: 33 Copynumber: 3.2 Consensus size: 33
6 TGTCGTCCCA
* * *
16 GAGGATGGCACACCACGGTGGGTGCCGTCCCCG
1 GAGGACGGCACACCACGGTTGGTGCCGTCCTCG
* *
49 GAGGACGGCACACCACGGTTGGTGCCATCCTAG
1 GAGGACGGCACACCACGGTTGGTGCCGTCCTCG
*
82 GAGGGCGGCACACCACGGTTGGTGCCGTCCTCG
1 GAGGACGGCACACCACGGTTGGTGCCGTCCTCG
115 GAGGACG
1 GAGGACG
122 ACACCGCGCC
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.17, C:0.31, G:0.39, T:0.13
Consensus pattern (33 bp):
GAGGACGGCACACCACGGTTGGTGCCGTCCTCG
Found at i:1450 original size:77 final size:78
Alignment explanation
Indices: 1322--1472 Score: 277
Period size: 77 Copynumber: 1.9 Consensus size: 78
1312 ATCATCTAAT
*
1322 ATTTTATTTAAAATGGTAAAAAAAAACAAAAGTTAGAAATAATAAGAGTTGCCTAGTAGTCACAC
1 ATTTTATTTAAAATGGTAAAAAAAAACAAAAGTTAGAAATAATAAGAGTTGCCTAGTAGACACAC
1387 ACACACACAAAAA
66 ACACACACAAAAA
*
1400 ATTTTATTTAAAATGGT-AAAGAAAACAAAAGTTAGAAATAATAAGAGTTGCCTAGTAGACACAC
1 ATTTTATTTAAAATGGTAAAAAAAAACAAAAGTTAGAAATAATAAGAGTTGCCTAGTAGACACAC
1464 ACACACACA
66 ACACACACA
1473 CAAATAGTTG
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
77 54 0.76
78 17 0.24
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (78 bp):
ATTTTATTTAAAATGGTAAAAAAAAACAAAAGTTAGAAATAATAAGAGTTGCCTAGTAGACACAC
ACACACACAAAAA
Found at i:4697 original size:5 final size:5
Alignment explanation
Indices: 4687--4714 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
4677 TTATTCTTTC
4687 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
4715 TCTTTACCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:4720 original size:15 final size:15
Alignment explanation
Indices: 4676--4720 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
4666 TTTTTAAAGA
4676 TTTATTCTTTCTTTAT
1 TTTATT-TTTCTTTAT
4692 TTTATTTTAT-TTTAT
1 TTTATTTT-TCTTTAT
4707 TTTATTTTTCTTTA
1 TTTATTTTTCTTTA
4721 CCGATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.04
15 19 0.70
16 7 0.26
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTATTTTTCTTTAT
Found at i:7619 original size:13 final size:15
Alignment explanation
Indices: 7601--7633 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
7591 AACTTTATTA
7601 TTATTATTA-CA-AT
1 TTATTATTACCAGAT
7614 TTATTATTACCAGAT
1 TTATTATTACCAGAT
7629 TTATT
1 TTATT
7634 TTTTGCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 2 0.11
15 7 0.39
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATTATTACCAGAT
Found at i:24845 original size:32 final size:33
Alignment explanation
Indices: 24775--24855 Score: 101
Period size: 36 Copynumber: 2.4 Consensus size: 33
24765 AGGAGTCTTT
24775 CCACTAGGACGGCTCTGCCACGGCGGAGCAGCCGCC
1 CCACTAGGACGGCTCTGCCACGGC---GCAGCCGCC
* *
24811 CCACTAGGACGGCTCTGTCACGGC-TAGCCGCC
1 CCACTAGGACGGCTCTGCCACGGCGCAGCCGCC
*
24843 CCACTAGGGCGGC
1 CCACTAGGACGGC
24856 AAGACTATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 19 0.45
36 23 0.55
ACGTcount: A:0.16, C:0.41, G:0.32, T:0.11
Consensus pattern (33 bp):
CCACTAGGACGGCTCTGCCACGGCGCAGCCGCC
Found at i:24951 original size:32 final size:31
Alignment explanation
Indices: 24894--24953 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
24884 TAGTACCGGT
* *
24894 GCCGCCCCGGGGGCGGTCTGTCCATGGCAAA
1 GCCGCCCCGGGGGCGGCCTGACCATGGCAAA
24925 GCCGCCCCAGGGGGCGGCCCT-ACCATGGC
1 GCCGCCCC-GGGGGCGG-CCTGACCATGGC
24954 TCAGCTACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 8 0.32
32 15 0.60
33 2 0.08
ACGTcount: A:0.12, C:0.40, G:0.38, T:0.10
Consensus pattern (31 bp):
GCCGCCCCGGGGGCGGCCTGACCATGGCAAA
Found at i:36603 original size:21 final size:19
Alignment explanation
Indices: 36577--36628 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
36567 CAATAATTTT
36577 TAAAAATCTTAATAAAGTCAC
1 TAAAAA-CTTAA-AAAGTCAC
* *
36598 TAAAAACCTTGAAAAGTTAC
1 TAAAAA-CTTAAAAAGTCAC
36618 TATAAAACTTA
1 TA-AAAACTTA
36629 TTGAGGTCGC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (19 bp):
TAAAAACTTAAAAAGTCAC
Found at i:36716 original size:21 final size:21
Alignment explanation
Indices: 36692--36790 Score: 76
Period size: 20 Copynumber: 4.8 Consensus size: 21
36682 ATAAACTCAA
** *
36692 TAATAAGGTTATTGGAAACCT
1 TAATAAGGTTATTAAAAAACT
* **
36713 TAATATGGTTCCTAAAAAACT
1 TAATAAGGTTATTAAAAAACT
36734 TAATAAGGTTA-TAAAAAACT
1 TAATAAGGTTATTAAAAAACT
* * * *
36754 TTATAATGTTAGT-AAAAATT
1 TAATAAGGTTATTAAAAAACT
* *
36774 TTATAAGATTATTAAAA
1 TAATAAGGTTATTAAAA
36791 TAAATTGATA
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
20 34 0.55
21 28 0.45
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.36
Consensus pattern (21 bp):
TAATAAGGTTATTAAAAAACT
Found at i:36750 original size:20 final size:21
Alignment explanation
Indices: 36692--36771 Score: 72
Period size: 21 Copynumber: 3.9 Consensus size: 21
36682 ATAAACTCAA
* ** *
36692 TAATAAGGTTATTGGAAACCT
1 TAATAAGGTTAGTAAAAAACT
* **
36713 TAATATGGTTCCTAAAAAACT
1 TAATAAGGTTAGTAAAAAACT
36734 TAATAAGGTTA-TAAAAAACT
1 TAATAAGGTTAGTAAAAAACT
* *
36754 TTATAATGTTAGTAAAAA
1 TAATAAGGTTAGTAAAAA
36772 TTTTATAAGA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 18 0.38
21 30 0.62
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (21 bp):
TAATAAGGTTAGTAAAAAACT
Found at i:37406 original size:198 final size:198
Alignment explanation
Indices: 36989--39021 Score: 1937
Period size: 199 Copynumber: 10.4 Consensus size: 198
36979 CTATATACTA
* * * *
36989 TAAAT-TTTTATTAATAATGAAATAAGGTATGTGTCAACTTTTTAACCCGCTTATGGAGTCCAAA
1 TAAATATTTAATTAATTATGAAAT-GGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAA
* * *
37053 ATTTTTACACTGACAGTGTATTGTATAATAATCCAATAAGAAAAATTATATTATACACCGTCAGT
65 A--TTTACACTGACAGTTTATTGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCAGT
* * * * * * * ***
37118 CGAGTTTAGAAGACTCCAAGTGC-GAGGTTTAAGGATTGAGATGTGTCCCCTTAAGGAATAAACA
128 GGAGTTTAGCAGACTGCACGTGCAG-GGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTA
*
37182 TTAAAAT
192 TTAATAT
* *
37189 TAAATATTTAATT-ATTATGATATAGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTGCAAA
1 TAAATATTTAATTAATTATGAAAT-GGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAA
*** * **
37253 ATTTATTTTGACAGTTTATTGTATAATAATCCTATAAGAACAATTATAAAATACACCGTCAGTGG
65 ATTTACACTGACAGTTTATTGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCAGTGG
* * *
37318 AGTTTAG-AGACTGCACGTGCATGGTTTAACGGTTGACATGTGTCCCCTTAGGGAATATGCATTA
130 AGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTA
37382 ATAT
195 ATAT
* * * * *
37386 TAAATATTTTATTAATTATGAAATGGAGTATGTATCAACTTCTTAACTCACTTATGAAGTCCAAA
1 TAAATATTTAATTAATTATGAAATGG-GTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAA
* * * * *
37451 ATTTACACCGA-ATGTGTATTGTATAATAATCTTATAAGAAAAATTATACTATACACAGTCAGTT
65 ATTTACACTGACA-GTTTATTGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCAGTG
* * * * * *
37515 GAGTTTAGCATACTGCACGTGCGGGGTTTTAGGGTTGACACGTATCCCCTTAAGGAATATGTATT
129 GAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATT
37580 AATAT
194 AATAT
* * * * * * * * *
37585 TAAATATCTAATTTATTAAGAAATGAGGTGTATGTCAACTTCTTAATCCGCTTATGAAATTCAAA
1 TAAATATTTAATTAATTATGAAATG-GGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAA
* *
37650 ATTTACACTAACAATTTATTGTATAATAATCCTATAAGAAAAATTATACTATACACCGT-AGGTG
65 ATTTACACTGACAGTTTATTGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCA-GTG
* * * * * * *
37714 GAGTTTAGTAGACTGCACATGCAAGGTTTAAGGGTTAATATGTGT-CCATTAAGGAATATGTATT
129 GAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATT
37778 AATA-
194 AATAT
* *
37782 -ATATATTT-TTTAATTATGAAATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAA
1 TAAATATTTAATTAATTATGAAATG-GGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAA
* * * *
37845 ATTTA-ACTGACAGTTTATTGTATAATATTCCTATAAGAAATATTATACTATACACCGTAAGTAG
65 ATTTACACTGACAGTTTATTGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCAGTGG
* * *
37909 AGTTTAGCAGACTGCATGTGCAGGGTTTAAGGGTAGACATGTGTGCCCTTAGGGAATATGTATTA
130 AGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTA
*
37974 ATGT
195 ATAT
* *
37978 TAAATATTTAATTAATTATGAAATGAGGTATGCGTCAACTTCTTAACCCGCTTTTGGAGTCC-AA
1 TAAATATTTAATTAATTATGAAATG-GGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAA
* * * *
38042 ATTTACATTGACAGTTTATTATATAATAATCCTATAAGAACAATTATA-TAATATACCGTCAGTG
65 ATTTACACTGACAGTTTATTGTATAATAATCCTATAAGAAAAATTATACT-ATACACCGTCAGTG
* *
38106 GAGTTTAGCAGACTGCGCGTGCATGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATT
129 GAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATT
38171 AATAT
194 AATAT
* * * ** * * *
38176 TAAATATTTGATTAATTATGAAATAAGATACATTTCAACTTCTTAACCCGCTTATGAAATCCAAA
1 TAAATATTTAATTAATTATGAAAT-GGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAA
* * ** * * * *** * * *
38241 ATTTATA-AGA-A--AAATTGTACT-ATCAT-C-GTCAGTCGAGTT-TAGC---AGACTG-CA-T
65 ATTTACACTGACAGTTTATTGTA-TAATAATCCTATAAGAAAAATTATA-CTATACACCGTCAGT
** ** * * *** * ** ***** **
38293 ---G--T-GCAGGACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAAGGAAAATGTA-TTAA
128 GGAGTTTAGCA-GAC-TGC-ACG-TGCAGGGTTTA-A-GGGTTGACATGTGTCCCCT-TAGGGAA
38351 TAT-TA--AATAT
186 TATGTATTAATAT
* * * * * *
38361 T--TTAATT-ATGAA--ATG--A--GGTATGTGTCAACTTCATAACCTGCTTTTGGAGTCCAAAA
1 TAAATATTTAATTAATTATGAAATGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAA
* ** * * * *
38417 TTTCCAGAGACAGTTCATTGTATAATAATCCTATAAGAAAAATTATACTCTACACTGTAAGTGGA
66 TTTACACTGACAGTTTATTGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCAGTGGA
* * * * *
38482 GTTTAGCAAACTGCACGTGCAAGGTTTATGGATTGACATGTGTCCCTTTAGGGAATATGTATTAA
131 GTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAA
38547 TAT
196 TAT
* * * * * * * *
38550 TACATATTCAATTGATGATAAAATGAGGTATGTGTCAACTTCTTAACCCGCTTCTAGAGTCTAAA
1 TAAATATTTAATTAATTATGAAATG-GGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAA
** * *
38615 ATTTACACTGACAGCGTGTTGTATGATAATCCTATAAGAAAAATTATA-TAATACACCGTCAGTG
65 ATTTACACTGACAGTTTATTGTATAATAATCCTATAAGAAAAATTATACT-ATACACCGTCAGTG
* *
38679 GATTTTAGCAGACTGCACGCGC-GGGATTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTAT
129 GAGTTTAGCAGACTGCACGTGCAGGG-TTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTAT
38743 TAATAT
193 TAATAT
* * * *
38749 CAAATATTTAATTAATTATGAAATGGGGTATATTTCAACTTCTTAACCCGCTTATGAAGTCCAAA
1 TAAATATTTAATTAATTATGAAAT-GGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAA
* ** * * *
38814 ATTTACAATGACAGTGGATTGTATAATAATCCTATAAGAAATATTATACCATACACCGTCAGTCG
65 ATTTACACTGACAGTTTATTGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCAGTGG
* * * *
38879 AATTTAGCAGACTGCACTTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAAGGAATATGTTTTA
130 AGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTA
38944 ATAT
195 ATAT
* * * * **
38948 TAAATATTTAATTGATTATGAAATGAGGTACGTGTCAACTTCTTAACCCGTTTAGGGAGTGTAAA
1 TAAATATTTAATTAATTATGAAATG-GGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAA
39013 ATTTACACT
65 ATTTACACT
39022 AAAAAGTGTA
Statistics
Matches: 1484, Mismatches: 282, Indels: 135
0.78 0.15 0.07
Matches are distributed among these distances:
175 35 0.02
176 3 0.00
177 1 0.00
178 2 0.00
179 10 0.01
180 4 0.00
181 7 0.00
182 9 0.01
183 8 0.01
184 8 0.01
185 12 0.01
186 19 0.01
187 5 0.00
188 20 0.01
189 12 0.01
190 7 0.00
191 6 0.00
192 8 0.01
193 6 0.00
194 92 0.06
195 81 0.05
196 8 0.01
197 81 0.05
198 404 0.27
199 572 0.39
200 58 0.04
201 6 0.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (198 bp):
TAAATATTTAATTAATTATGAAATGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAA
TTTACACTGACAGTTTATTGTATAATAATCCTATAAGAAAAATTATACTATACACCGTCAGTGGA
GTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAA
TAT
Found at i:39403 original size:15 final size:15
Alignment explanation
Indices: 39378--39428 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
39368 TTAATTTGAT
39378 GGAATAATTAATTAAA
1 GGAA-AATTAATTAAA
39394 GGAAAATTAATT-AA
1 GGAAAATTAATTAAA
39408 --AAAATTAATTAAA
1 GGAAAATTAATTAAA
*
39421 GAAAAATT
1 GGAAAATT
39429 TTAAAAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 10 0.31
13 2 0.06
14 2 0.06
15 14 0.44
16 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (15 bp):
GGAAAATTAATTAAA
Found at i:39413 original size:12 final size:12
Alignment explanation
Indices: 39396--39420 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39386 TAATTAAAGG
39396 AAAATTAATTAA
1 AAAATTAATTAA
39408 AAAATTAATTAA
1 AAAATTAATTAA
39420 A
1 A
39421 GAAAAATTTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTAATTAA
Found at i:39415 original size:27 final size:25
Alignment explanation
Indices: 39383--39435 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 25
39373 TTGATGGAAT
*
39383 AATTAATTAAAGGAAAATTAATTAAAA
1 AATTAATTAAAGAAAAATT--TTAAAA
39410 AATTAATTAAAGAAAAATTTTAAAA
1 AATTAATTAAAGAAAAATTTTAAAA
39435 A
1 A
39436 TTAGATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 7 0.28
27 18 0.72
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (25 bp):
AATTAATTAAAGAAAAATTTTAAAA
Found at i:40487 original size:21 final size:21
Alignment explanation
Indices: 40461--40508 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
40451 GATTAAATAC
* *
40461 TCAATT-CTTTTTTTTGATAAT
1 TCAATTGCTTTTATATG-TAAT
40482 TCAATTGCTTTTATATGTAAT
1 TCAATTGCTTTTATATGTAAT
40503 TCAATT
1 TCAATT
40509 ATCCCTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.56
Consensus pattern (21 bp):
TCAATTGCTTTTATATGTAAT
Found at i:40635 original size:17 final size:17
Alignment explanation
Indices: 40613--40646 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40603 AATATATATA
40613 TATATATATATGTACAT
1 TATATATATATGTACAT
40630 TATATATATATGTACAT
1 TATATATATATGTACAT
40647 GTCCCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (17 bp):
TATATATATATGTACAT
Found at i:40656 original size:23 final size:22
Alignment explanation
Indices: 40606--40657 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
40596 TCGGCCAAAT
*
40606 ATATATATATATATATATGTAC
1 ATATATATATATATACATGTAC
* *
40628 ATTATATATATATGTACATGTCCC
1 A-TATATATATATATACATGT-AC
40652 ATATAT
1 ATATAT
40658 GAAATAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 22 0.88
24 2 0.08
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (22 bp):
ATATATATATATATACATGTAC
Found at i:41342 original size:37 final size:36
Alignment explanation
Indices: 41300--41370 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 36
41290 CTAATTTTAT
41300 TATTTCAAATAATTGATTGATTAACCGTGCTAAATAG
1 TATTTCAAATAATTGATTGATTAACCGTG-TAAATAG
41337 TATTTCAAATAATTGATTGATTAACCGTGTAAAT
1 TATTTCAAATAATTGATTGATTAACCGTGTAAAT
41371 GAATTTGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 5 0.15
37 29 0.85
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (36 bp):
TATTTCAAATAATTGATTGATTAACCGTGTAAATAG
Found at i:42953 original size:74 final size:74
Alignment explanation
Indices: 42863--43019 Score: 269
Period size: 74 Copynumber: 2.1 Consensus size: 74
42853 TTGTCTTTTC
* * * *
42863 ACACTTTTCGGGTGACTAAAAAGTCCCTTTATGAGTTTCCTCTATTCCTTTTCCTTCTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCTCAATTCCTTTTCCTTCTACCCTTT
42928 TTCGTAATT
66 TTCGTAATT
42937 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCTCAATTCCTTTTCCTTCTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCTCAATTCCTTTTCCTTCTACCCTTT
43002 TTCGTAATT
66 TTCGTAATT
*
43011 ACACATTTC
1 ACACTTTTC
43020 CCTTCCTTAA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.21, C:0.27, G:0.10, T:0.42
Consensus pattern (74 bp):
ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCTCAATTCCTTTTCCTTCTACCCTTT
TTCGTAATT
Found at i:44190 original size:10 final size:10
Alignment explanation
Indices: 44177--44202 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
44167 AAATCTCGAT
44177 ATATCCGTAA
1 ATATCCGTAA
44187 ATATCCGTAA
1 ATATCCGTAA
44197 ATATCC
1 ATATCC
44203 ATATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:45226 original size:13 final size:12
Alignment explanation
Indices: 45196--45238 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
45186 CATCGATACC
45196 TCGATATATCCG
1 TCGATATATCCG
45208 TCGATATATCCG
1 TCGATATATCCG
45220 TTCGATATATCCG
1 -TCGATATATCCG
45233 TCGATA
1 TCGATA
45239 CCTGTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Done.