Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009671.1 Corchorus capsularis cultivar CVL-1 contig09692, 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: 89407
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:7680 original size:88 final size:88
Alignment explanation
Indices: 7567--7739 Score: 310
Period size: 88 Copynumber: 2.0 Consensus size: 88
7557 ATGTTTGTAA
7567 TAAGTAAGAGGCTTAAGGATAGAATCAACCATGGAAAACTTCACAAGAAGTGTCAAATACAACTT
1 TAAGTAAGAGGCTTAAGGATAGAATCAACCATGGAAAACTTCACAAGAAGTGTCAAATACAACTT
7632 TCTACTTCTATTTGATATATCCT
66 TCTACTTCTATTTGATATATCCT
* * **
7655 TAAGTCAGAGGCTTAAGGATAGAATCAGCCATGGAAAACTTCACAAGAAGTGTCAAATACAGTTT
1 TAAGTAAGAGGCTTAAGGATAGAATCAACCATGGAAAACTTCACAAGAAGTGTCAAATACAACTT
7720 TCTACTTCTATTTGATATAT
66 TCTACTTCTATTTGATATAT
7740 TGGGATTCAA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 81 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (88 bp):
TAAGTAAGAGGCTTAAGGATAGAATCAACCATGGAAAACTTCACAAGAAGTGTCAAATACAACTT
TCTACTTCTATTTGATATATCCT
Found at i:9016 original size:28 final size:29
Alignment explanation
Indices: 8962--9027 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
8952 AAAAAATCGC
** *
8962 TTATGTTTTATTTTTGGGTAAAATAATATT
1 TTATG-TTTATTTTTGGACAAAATAATACT
* *
8992 TTATGTTT-TTTTTGGACAAATTAATCCT
1 TTATGTTTATTTTTGGACAAAATAATACT
9020 TTATGTTT
1 TTATGTTT
9028 CAAAAATGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 23 0.74
29 3 0.10
30 5 0.16
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.58
Consensus pattern (29 bp):
TTATGTTTATTTTTGGACAAAATAATACT
Found at i:9219 original size:31 final size:31
Alignment explanation
Indices: 9175--9270 Score: 126
Period size: 31 Copynumber: 3.1 Consensus size: 31
9165 ACGTAAGAGA
*
9175 TTTTT-TTCAAAAGAAAAATATAAGGGATTT
1 TTTTTGTTCCAAAGAAAAATATAAGGGATTT
*
9205 TTTTTGTTCCAAAGAAAAATATAAGGGA-AT
1 TTTTTGTTCCAAAGAAAAATATAAGGGATTT
*
9235 TTTTTG-TCGCAAAAGGAAAATATAAGGGATTT
1 TTTTTGTTC-C-AAAGAAAAATATAAGGGATTT
9267 TTTT
1 TTTT
9271 AGTATTTAGT
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
29 2 0.03
30 13 0.22
31 38 0.66
32 5 0.09
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.39
Consensus pattern (31 bp):
TTTTTGTTCCAAAGAAAAATATAAGGGATTT
Found at i:9489 original size:13 final size:12
Alignment explanation
Indices: 9466--9513 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
9456 AAACAATGGC
9466 ATTTAATAAATAT
1 ATTTAA-AAATAT
9479 ATTTGAAAAATA-
1 ATTT-AAAAATAT
9491 ATGTTAAGAAATAT
1 AT-TTAA-AAATAT
9505 ATTTAAAAA
1 ATTTAAAAA
9514 AATTCTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
12 7 0.23
13 20 0.65
14 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (12 bp):
ATTTAAAAATAT
Found at i:9602 original size:181 final size:176
Alignment explanation
Indices: 9325--9660 Score: 469
Period size: 181 Copynumber: 1.9 Consensus size: 176
9315 TTAAAAAAAT
*
9325 ATATATTTAAAAATTATAATATATCTAATTTTTAATTAAATAGTGAAAAGGTAAAAATAAAATAG
1 ATATATTTAAAAATTATAATATATCTAATTTTTAATAAAATAGTGAAAAGGTAAAAATAAAATAG
* ** * * *
9390 TTATAAAAATATTAGATTTGATTAAATAAAAATAAATTTTTTAATTGAGTAAAA-TCGTAAAAGT
66 TTATAAAAATATTAAATTAAATTAAATAAAAATAAAGTTTTTAATTGAGTAAAACT-ATAAAAAT
*
9454 TTAAACAATGGCATTTAATAAATATATTTGAAAAATAATGTTAAGAA
130 TTAAACAATGACATTTAATAAATATATTTGAAAAATAATGTTAAGAA
*
9501 ATATATTTAAAAAAATTCTAATATATCTAAATTTTTTAACTAAAATAGT-AAAATGGTAAAAATA
1 ATATATTT--AAAAATTATAATATATCT-AA-TTTTTAA-TAAAATAGTGAAAA-GGTAAAAATA
* * * * *
9565 AAATATTTATAAATATATTAAATTAAATTAGATAAAAATATAGTTTTTAGTTGAGTAAAACTATA
60 AAATAGTTATAAAAATATTAAATTAAATTAAATAAAAATAAAGTTTTTAATTGAGTAAAACTATA
9630 AAAATTTAAACAATGACATTTAATAAATATA
125 AAAATTTAAACAATGACATTTAATAAATATA
9661 ATAAAAAATA
Statistics
Matches: 139, Mismatches: 14, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
176 8 0.06
178 17 0.12
179 2 0.01
180 11 0.08
181 100 0.72
182 1 0.01
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.37
Consensus pattern (176 bp):
ATATATTTAAAAATTATAATATATCTAATTTTTAATAAAATAGTGAAAAGGTAAAAATAAAATAG
TTATAAAAATATTAAATTAAATTAAATAAAAATAAAGTTTTTAATTGAGTAAAACTATAAAAATT
TAAACAATGACATTTAATAAATATATTTGAAAAATAATGTTAAGAA
Found at i:10329 original size:30 final size:31
Alignment explanation
Indices: 10279--10347 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
10269 CTCATTTTTG
10279 AAACATAAGGAATTAATTTGTCCCGAAA-AA
1 AAACATAAGGAATTAATTTGTCCCGAAAGAA
* * * *
10309 AAACATAA-GATATTATTTTGTTCCTAAAGTA
1 AAACATAAGGA-ATTAATTTGTCCCGAAAGAA
10340 AAACATAA
1 AAACATAA
10348 TGGATTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 2 0.06
30 22 0.67
31 9 0.27
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (31 bp):
AAACATAAGGAATTAATTTGTCCCGAAAGAA
Found at i:16029 original size:16 final size:16
Alignment explanation
Indices: 16008--16039 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
15998 TTTTCAACTT
16008 CTCCATATGAGCTGCC
1 CTCCATATGAGCTGCC
16024 CTCCATATGAGCTGCC
1 CTCCATATGAGCTGCC
16040 GAGAAGGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.25
Consensus pattern (16 bp):
CTCCATATGAGCTGCC
Found at i:16924 original size:34 final size:35
Alignment explanation
Indices: 16884--16961 Score: 122
Period size: 35 Copynumber: 2.3 Consensus size: 35
16874 CCCAATAAAC
*
16884 CCCAAGAAAGCAGTTA-TTTTCCTGGAGAGAGAAA
1 CCCAAGAAAGCAGTTACTTTTCCTAGAGAGAGAAA
*
16918 CCCAAGAAAGCAGTTACTTTTTCTAGAGAGAGAAA
1 CCCAAGAAAGCAGTTACTTTTCCTAGAGAGAGAAA
*
16953 CACAAGAAA
1 CCCAAGAAA
16962 ATCTTTTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 16 0.40
35 24 0.60
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (35 bp):
CCCAAGAAAGCAGTTACTTTTCCTAGAGAGAGAAA
Found at i:28679 original size:50 final size:50
Alignment explanation
Indices: 28600--28700 Score: 150
Period size: 50 Copynumber: 2.0 Consensus size: 50
28590 ACATTGTTAT
* * *
28600 AATGAGTAAAGAATAAAATGAACTACTGCAAATTAAG-GAACCCTGGATG
1 AATGAGTAAAGAATAAAAGGAACTACTGCAAAGTAAGAAAACCCTGGATG
*
28649 AATGAGTAAAAGAATAAAAGGAACTTCTGCAAAGTAAGAAAACCCTGGATG
1 AATGAGT-AAAGAATAAAAGGAACTACTGCAAAGTAAGAAAACCCTGGATG
28700 A
1 A
28701 CTAGTACATA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 7 0.15
50 27 0.59
51 12 0.26
ACGTcount: A:0.49, C:0.12, G:0.21, T:0.19
Consensus pattern (50 bp):
AATGAGTAAAGAATAAAAGGAACTACTGCAAAGTAAGAAAACCCTGGATG
Found at i:32222 original size:6 final size:6
Alignment explanation
Indices: 32211--32235 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
32201 CTTTTTTAAG
32211 TCCTTT TCCTTT TCCTTT TCCTTT T
1 TCCTTT TCCTTT TCCTTT TCCTTT T
32236 TAGGACATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TCCTTT
Found at i:38341 original size:30 final size:28
Alignment explanation
Indices: 38270--38343 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
38260 GAATTTACAC
*
38270 AAAACGGCCAAATAAGCCCCTGAACTCT
1 AAAAAGGCCAAATAAGCCCCTGAACTCT
**
38298 -AATTGCAGCCAAATAAGCCCCTGAACTCTTT
1 AAAAAG--GCCAAATAAGCCCCTGAACTC--T
38329 AAAAAGGCCAAATAA
1 AAAAAGGCCAAATAA
38344 ACTCTTTTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.08
29 21 0.57
30 9 0.24
31 1 0.03
32 3 0.08
ACGTcount: A:0.42, C:0.27, G:0.14, T:0.18
Consensus pattern (28 bp):
AAAAAGGCCAAATAAGCCCCTGAACTCT
Found at i:39118 original size:18 final size:18
Alignment explanation
Indices: 39097--39131 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39087 TCGATATTTA
* *
39097 TCGATATCTCGATAAATC
1 TCGATATATCCATAAATC
39115 TCGATATATCCATAAAT
1 TCGATATATCCATAAAT
39132 ATCCGTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (18 bp):
TCGATATATCCATAAATC
Found at i:40193 original size:13 final size:12
Alignment explanation
Indices: 40163--40205 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
40153 CATCGATACC
40163 TCGATATATCCG
1 TCGATATATCCG
40175 TCGATATATCCG
1 TCGATATATCCG
40187 TTCGATATATCCG
1 -TCGATATATCCG
40200 TCGATA
1 TCGATA
40206 CTTGTATTTA
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
Found at i:40774 original size:21 final size:22
Alignment explanation
Indices: 40739--40783 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
40729 CACCGAGAAT
*
40739 ATTTTCATCTGTACAGTAACAA
1 ATTTTCATCTATACAGTAACAA
40761 ATTTT-ATCTATACAGTAACAA
1 ATTTTCATCTATACAGTAACAA
40782 AT
1 AT
40784 CTAACACGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.38
Consensus pattern (22 bp):
ATTTTCATCTATACAGTAACAA
Found at i:41234 original size:51 final size:51
Alignment explanation
Indices: 41174--41277 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 51
41164 ATTTAAAGAT
* *
41174 GTGGCAAAATTTCACAATTCATCATTCTCGAATAAGATAAATTGCATCAAA
1 GTGGCAAAATTTCACAATCCATCATTCTCGAATAAGAGAAATTGCATCAAA
* * *
41225 GTGGCAAAATTTCACAATCCATCATTTTCGACTAAGAGAAATTTCATCAAA
1 GTGGCAAAATTTCACAATCCATCATTCTCGAATAAGAGAAATTGCATCAAA
41276 GT
1 GT
41278 TTAAAAGTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (51 bp):
GTGGCAAAATTTCACAATCCATCATTCTCGAATAAGAGAAATTGCATCAAA
Found at i:49797 original size:33 final size:32
Alignment explanation
Indices: 49760--49824 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
49750 GGCGGAGTCT
*
49760 CCCCACTGGGGCGGCTTCACCATGGGCAGGCCG
1 CCCCACTGGGGCGGCTTCACCA-CGGCAGGCCG
* * *
49793 CCCCATTGGGGTGGCTTCGCCACGGCAGGCCG
1 CCCCACTGGGGCGGCTTCACCACGGCAGGCCG
49825 TCCCGGTGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 9 0.32
33 19 0.68
ACGTcount: A:0.11, C:0.38, G:0.37, T:0.14
Consensus pattern (32 bp):
CCCCACTGGGGCGGCTTCACCACGGCAGGCCG
Found at i:49835 original size:32 final size:33
Alignment explanation
Indices: 49760--49836 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 33
49750 GGCGGAGTCT
* *
49760 CCCCACTGGGGCGGCTTCACCATGGGCAGGCCG
1 CCCCAGTGGGGCGGCTTCACCATCGGCAGGCCG
* * *
49793 CCCCATTGGGGTGGCTTCGCCA-CGGCAGGCCG
1 CCCCAGTGGGGCGGCTTCACCATCGGCAGGCCG
* *
49825 TCCCGGTGGGGC
1 CCCCAGTGGGGC
49837 AGCTAGACCA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
32 17 0.47
33 19 0.53
ACGTcount: A:0.09, C:0.38, G:0.39, T:0.14
Consensus pattern (33 bp):
CCCCAGTGGGGCGGCTTCACCATCGGCAGGCCG
Found at i:51370 original size:95 final size:96
Alignment explanation
Indices: 51216--51393 Score: 331
Period size: 95 Copynumber: 1.9 Consensus size: 96
51206 TCCTGTTCTC
* *
51216 TTCTGTTCTGTTCTGTTCATGGTCTTTTTGAAAAGGAGCTTCCTTCTTATGCCTTCGAACTGAAG
1 TTCTGTTCTGTTCTGTTCATGGTCTTTTTGAAAAGGAGCTTCCTTCTCATACCTTCGAACTGAAG
51281 TACTCTGCGCCCATAGTGATTTCAGTTCCTG
66 TACTCTGCGCCCATAGTGATTTCAGTTCCTG
51312 TTCTGTTCTGTTCTGTTCATGGTC-TTTTGAAAAGGAGCTTCCTTCTCATACCTTCGAACTGAAG
1 TTCTGTTCTGTTCTGTTCATGGTCTTTTTGAAAAGGAGCTTCCTTCTCATACCTTCGAACTGAAG
51376 TACTCTGCGCCCATAGTG
66 TACTCTGCGCCCATAGTG
51394 TTGCTGGAGT
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
95 56 0.70
96 24 0.30
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (96 bp):
TTCTGTTCTGTTCTGTTCATGGTCTTTTTGAAAAGGAGCTTCCTTCTCATACCTTCGAACTGAAG
TACTCTGCGCCCATAGTGATTTCAGTTCCTG
Found at i:52374 original size:35 final size:35
Alignment explanation
Indices: 52328--52430 Score: 190
Period size: 35 Copynumber: 2.9 Consensus size: 35
52318 TGTGATTCTA
52328 TATTCTTCCTTATTTC-CTTATATGCTTTGTTGCAC
1 TATTCTTCCTTATTTCTC-TATATGCTTTGTTGCAC
52363 TATTCTTCCTTATTTCTCTATATGCTTTGTTGCAC
1 TATTCTTCCTTATTTCTCTATATGCTTTGTTGCAC
52398 TATTCTTCCTTATTTCTCTATATGCTTTGTTGC
1 TATTCTTCCTTATTTCTCTATATGCTTTGTTGC
52431 GCCAAAAATA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
35 66 0.99
36 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.09, T:0.55
Consensus pattern (35 bp):
TATTCTTCCTTATTTCTCTATATGCTTTGTTGCAC
Found at i:64639 original size:6 final size:6
Alignment explanation
Indices: 64625--64662 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
64615 TCCATATCAA
* *
64625 CACCTC CACCAC CACCTC CACCTC CACCTC CGCCTC CA
1 CACCTC CACCTC CACCTC CACCTC CACCTC CACCTC CA
64663 ATATCTGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.66, G:0.03, T:0.13
Consensus pattern (6 bp):
CACCTC
Found at i:65034 original size:6 final size:6
Alignment explanation
Indices: 64999--65032 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
64989 CCATCTCTAT
*
64999 CACCTC CACCTC CACCTC CACCTC CACCCC CACC
1 CACCTC CACCTC CACCTC CACCTC CACCTC CACC
65033 CCTGCCCCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.71, G:0.00, T:0.12
Consensus pattern (6 bp):
CACCTC
Found at i:65267 original size:99 final size:99
Alignment explanation
Indices: 65163--65362 Score: 346
Period size: 99 Copynumber: 2.0 Consensus size: 99
65153 ACCATCTGCC
* * *
65163 CCTGTTCAACATCATAATGCTAGTGTGCCTCGGCCACCTCCACCTCCGCCTCCGCCTCCCAGAGG
1 CCTGTTCAACATCATAATGCTAGTGCGCCTCGGCCACCTCCACCACCACCTCCGCCTCCCAGAGG
65228 ACCTGCTGGATCAGTTCCTATTCCTCCACCTCCA
66 ACCTGCTGGATCAGTTCCTATTCCTCCACCTCCA
* *
65262 CCTGTTCAACGTCATAATGCTAGTGCGCCTCGGCCACCTCCACCACCACCTCCGCCTCCTAGAGG
1 CCTGTTCAACATCATAATGCTAGTGCGCCTCGGCCACCTCCACCACCACCTCCGCCTCCCAGAGG
*
65327 ACCTGCTGGGTCAGTTCCTATTCCTCCACCTCCA
66 ACCTGCTGGATCAGTTCCTATTCCTCCACCTCCA
65361 CC
1 CC
65363 CCCTGCACCA
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 95 1.00
ACGTcount: A:0.17, C:0.43, G:0.17, T:0.23
Consensus pattern (99 bp):
CCTGTTCAACATCATAATGCTAGTGCGCCTCGGCCACCTCCACCACCACCTCCGCCTCCCAGAGG
ACCTGCTGGATCAGTTCCTATTCCTCCACCTCCA
Found at i:65493 original size:18 final size:18
Alignment explanation
Indices: 65441--65496 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
65431 ACCCGGTGCT
*
65441 CCAAAACTTCCTGCTGCA
1 CCAAAACCTCCTGCTGCA
*** * *
65459 CCCCCACCGCCTCCTGCA
1 CCAAAACCTCCTGCTGCA
65477 CCAAAACCTCCTGCTGCA
1 CCAAAACCTCCTGCTGCA
65495 CC
1 CC
65497 CCCTCCTCCT
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.21, C:0.52, G:0.11, T:0.16
Consensus pattern (18 bp):
CCAAAACCTCCTGCTGCA
Found at i:65504 original size:18 final size:18
Alignment explanation
Indices: 65449--65506 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
65439 CTCCAAAACT
65449 TCCTGCTGCACCCCCACC
1 TCCTGCTGCACCCCCACC
* * ***
65467 GCCTCCTGCACCAAAACC
1 TCCTGCTGCACCCCCACC
*
65485 TCCTGCTGCACCCCCTCC
1 TCCTGCTGCACCCCCACC
65503 TCCT
1 TCCT
65507 CCAGGCCATA
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.14, C:0.57, G:0.10, T:0.19
Consensus pattern (18 bp):
TCCTGCTGCACCCCCACC
Found at i:65508 original size:36 final size:36
Alignment explanation
Indices: 65355--65502 Score: 199
Period size: 36 Copynumber: 4.1 Consensus size: 36
65345 TATTCCTCCA
*
65355 CCTCCACCCCCTGCACCAAAACCTCCTGCTGCGCCC
1 CCTCCACCCCCTGCACCAAAACCTCCTGCTGCACCC
* *
65391 CCTCC-CCCCCTGCTCCAAAACCTCCTGCTGCACTC
1 CCTCCACCCCCTGCACCAAAACCTCCTGCTGCACCC
** * *
65426 CCTCCACCCGGTGCTCCAAAACTTCCTGCTGCACCC
1 CCTCCACCCCCTGCACCAAAACCTCCTGCTGCACCC
* * *
65462 CCACCGCCTCCTGCACCAAAACCTCCTGCTGCACCC
1 CCTCCACCCCCTGCACCAAAACCTCCTGCTGCACCC
65498 CCTCC
1 CCTCC
65503 TCCTCCAGGC
Statistics
Matches: 96, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
35 32 0.33
36 64 0.67
ACGTcount: A:0.16, C:0.56, G:0.11, T:0.17
Consensus pattern (36 bp):
CCTCCACCCCCTGCACCAAAACCTCCTGCTGCACCC
Found at i:69891 original size:11 final size:11
Alignment explanation
Indices: 69875--69901 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
69865 CATCTTTTTT
69875 TTTTTTTAATC
1 TTTTTTTAATC
69886 TTTTTTTAATC
1 TTTTTTTAATC
69897 TTTTT
1 TTTTT
69902 CTTCTTTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTTAATC
Found at i:74593 original size:16 final size:16
Alignment explanation
Indices: 74560--74600 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
74550 TCCTCTTGAA
74560 TTTTCTT-ATTTGGGG
1 TTTTCTTAATTTGGGG
**
74575 TTTTCTTAATTTGTTG
1 TTTTCTTAATTTGGGG
74591 TTTTC-TAATT
1 TTTTCTTAATT
74601 GTTTAATCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.12, C:0.07, G:0.15, T:0.66
Consensus pattern (16 bp):
TTTTCTTAATTTGGGG
Found at i:75972 original size:2 final size:2
Alignment explanation
Indices: 75967--75995 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
75957 AGAAAAAATA
75967 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 A
75996 GTGCTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:83812 original size:29 final size:27
Alignment explanation
Indices: 83734--83812 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 27
83724 GAACTTACAC
*
83734 AAAATGGCCAAATAAGCCTCTGAACTCT
1 AAAAAGGCCAAATAAGCC-CTGAACTCT
*
83762 AATTACA-GCCAAATAAGCCCCTGAACTCTTT
1 AA--AAAGGCCAAATAAG-CCCTGAACTC--T
83793 AAAAAGGCCAAATAAGCCCT
1 AAAAAGGCCAAATAAGCCCT
83813 TTTCTGATGG
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 13 0.31
31 3 0.07
ACGTcount: A:0.41, C:0.27, G:0.13, T:0.20
Consensus pattern (27 bp):
AAAAAGGCCAAATAAGCCCTGAACTCT
Found at i:87468 original size:29 final size:31
Alignment explanation
Indices: 87401--87470 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 31
87391 CAATTAGGGC
*
87401 TCTGAACTTTGGCAAAAGTGTCAAATAAGTG
1 TCTGAACTATGGCAAAAGTGTCAAATAAGTG
* **
87432 T-TCAAACTATGG-AAAA-TGTCAAATCGGTG
1 TCT-GAACTATGGCAAAAGTGTCAAATAAGTG
87461 TCTGAACTAT
1 TCTGAACTAT
87471 TAGATTTCGG
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
29 18 0.56
30 6 0.19
31 8 0.25
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (31 bp):
TCTGAACTATGGCAAAAGTGTCAAATAAGTG
Found at i:88599 original size:7 final size:7
Alignment explanation
Indices: 88581--88610 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
88571 TAAAATTTTA
88581 TTTAAC-
1 TTTAACT
88587 TTTAACT
1 TTTAACT
88594 TTTAACT
1 TTTAACT
88601 TTTAACT
1 TTTAACT
88608 TTT
1 TTT
88611 TATTGGTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTAACT
Done.