Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018058.1 Corchorus olitorius cultivar O-4 contig18091, 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: 67247
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3240 original size:2 final size:2
Alignment explanation
Indices: 3233--3263 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3223 TAATACTATT
3233 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3264 GAAAAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3916 original size:27 final size:29
Alignment explanation
Indices: 3862--3917 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
3852 TCTAAATTGA
* *
3862 TATTATTAAAATATATTTTAATTATGCCAT
1 TATTATTAAAATATA-TTAAAATATGCCAT
3892 TATTATTAAAATATA-TAAAAT-TGCCA
1 TATTATTAAAATATATTAAAATATGCCA
3918 ATATGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 4 0.17
30 15 0.62
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (29 bp):
TATTATTAAAATATATTAAAATATGCCAT
Found at i:3939 original size:46 final size:43
Alignment explanation
Indices: 3871--3956 Score: 127
Period size: 43 Copynumber: 1.9 Consensus size: 43
3861 ATATTATTAA
3871 AATATATTTTAATTATGCCATTATTATTAAAATATATAAAATTGCC
1 AATATATTTTAATTATGCC---ATTATTAAAATATATAAAATTGCC
* *
3917 AATATGTTTTAATTATGTCATTATTAAAATATATAAAATT
1 AATATATTTTAATTATGCCATTATTAAAATATATAAAATT
3957 ACCATTATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
43 21 0.55
46 17 0.45
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (43 bp):
AATATATTTTAATTATGCCATTATTAAAATATATAAAATTGCC
Found at i:4837 original size:22 final size:22
Alignment explanation
Indices: 4749--4974 Score: 124
Period size: 22 Copynumber: 10.2 Consensus size: 22
4739 AATGATATAT
* *
4749 AATTTCATAGAGAGATTATCGA
1 AATTTCATAGAGAGGTTATCAA
* *
4771 AATTTCATACTA-CGG-TATCAAA
1 AATTTCATA-GAGAGGTTATC-AA
* *
4793 AATTT-ATAGGGAGATTAAT-AA
1 AATTTCATAGAGAGGTT-ATCAA
4814 AATTTCATAGAGAGGTTATCAAA
1 AATTTCATAGAGAGGTTATC-AA
**
4837 AAAATCATATG-GAGGTTATCAA
1 AATTTCATA-GAGAGGTTATCAA
* * *
4859 AATTTCATAGAAAAGTTTATTAA
1 AATTTCATAG-AGAGGTTATCAA
**
4882 AATTTCATAGTTAGGTTATCAA
1 AATTTCATAGAGAGGTTATCAA
* * * * *
4904 TATTTCATTGGGAGTTTATCAC
1 AATTTCATAGAGAGGTTATCAA
* * * *
4926 AGTTTCATAGGGTA-ATCATCAA
1 AATTTCATAGAG-AGGTTATCAA
*
4948 AATTTCATAGTGTA-GTTATCAA
1 AATTTCATAGAG-AGGTTATCAA
4970 AATTT
1 AATTT
4975 GGTGGTTATC
Statistics
Matches: 155, Mismatches: 37, Indels: 24
0.72 0.17 0.11
Matches are distributed among these distances:
21 18 0.12
22 96 0.62
23 40 0.26
24 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
AATTTCATAGAGAGGTTATCAA
Found at i:5060 original size:2 final size:2
Alignment explanation
Indices: 5053--5081 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5043 GTTAAAACTA
5053 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
5082 ATAGAGAAAA
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:6430 original size:50 final size:50
Alignment explanation
Indices: 6376--6529 Score: 195
Period size: 50 Copynumber: 3.1 Consensus size: 50
6366 AATGCCTTTC
* * * * *
6376 GAAAAGTGAACTTTGGTCTTGGTCTCACAAATGGAGTGCAATCTTATTTT
1 GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAGTGCAATCTTATTAT
* *
6426 GAAAAGCGAATTTTGATCTTGGACACACAAATGGAATGCAATCTTATTAT
1 GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAGTGCAATCTTATTAT
* *
6476 -AAAAGCGAATTTTGACCTTGGGCTCACAAATGG-GATGCAATCTTATTAT
1 GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAG-TGCAATCTTATTAT
*
6525 AAAAA
1 GAAAA
6530 TACTTGTTCT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
49 44 0.48
50 47 0.52
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (50 bp):
GAAAAGCGAATTTTGATCTTGGACTCACAAATGGAGTGCAATCTTATTAT
Found at i:6504 original size:49 final size:49
Alignment explanation
Indices: 6393--6528 Score: 200
Period size: 49 Copynumber: 2.8 Consensus size: 49
6383 GAACTTTGGT
* * * *
6393 CTTGGTCTCACAAATGGAGTGCAATCTTATTTTGAAAAGCGAATTTTGAT
1 CTTGGACTCACAAATGGAATGCAATCTTATTAT-AAAAGCGAATTTTGAC
*
6443 CTTGGACACACAAATGGAATGCAATCTTATTATAAAAGCGAATTTTGAC
1 CTTGGACTCACAAATGGAATGCAATCTTATTATAAAAGCGAATTTTGAC
* *
6492 CTTGGGCTCACAAATGGGATGCAATCTTATTATAAAA
1 CTTGGACTCACAAATGGAATGCAATCTTATTATAAAA
6529 ATACTTGTTC
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
49 49 0.63
50 29 0.37
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (49 bp):
CTTGGACTCACAAATGGAATGCAATCTTATTATAAAAGCGAATTTTGAC
Found at i:7185 original size:12 final size:12
Alignment explanation
Indices: 7168--7193 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
7158 TTCGATTCAC
7168 TTTTGATTTGAA
1 TTTTGATTTGAA
7180 TTTTGATTTGAA
1 TTTTGATTTGAA
7192 TT
1 TT
7194 ACTCGATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (12 bp):
TTTTGATTTGAA
Found at i:7594 original size:14 final size:13
Alignment explanation
Indices: 7576--7618 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
7566 TTCCAAGTGC
7576 TTTTTTTCA-TTT
1 TTTTTTTCATTTT
*
7588 TCTTTTTCATTTT
1 TTTTTTTCATTTT
*
7601 TTCTTTTCATTTT
1 TTTTTTTCATTTT
7614 TTTTT
1 TTTTT
7619 ATTTTTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTCATTTT
Found at i:7595 original size:12 final size:11
Alignment explanation
Indices: 7576--7625 Score: 66
Period size: 12 Copynumber: 4.4 Consensus size: 11
7566 TTCCAAGTGC
7576 TTTTTTTCATT
1 TTTTTTTCATT
7587 TTCTTTTTCATTT
1 TT-TTTTTCA-TT
7600 TTTCTTTTCATT
1 TTT-TTTTCATT
7612 TTTTTTT-ATT
1 TTTTTTTCATT
7622 TTTT
1 TTTT
7626 ATTATTGGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
10 7 0.19
11 6 0.17
12 13 0.36
13 10 0.28
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTTCATT
Found at i:7601 original size:13 final size:12
Alignment explanation
Indices: 7576--7618 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
7566 TTCCAAGTGC
7576 TTTTTTTCATTT
1 TTTTTTTCATTT
*
7588 TCTTTTTCATTT
1 TTTTTTTCATTT
7600 TTTCTTTTCATTT
1 TTT-TTTTCATTT
7613 TTTTTT
1 TTTTTT
7619 ATTTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 16 0.57
13 12 0.43
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTTCATTT
Found at i:7602 original size:20 final size:20
Alignment explanation
Indices: 7577--7614 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7567 TCCAAGTGCT
7577 TTTTTTCATTTTC-TTTTTCA
1 TTTTTTC-TTTTCATTTTTCA
7597 TTTTTTCTTTTCATTTTT
1 TTTTTTCTTTTCATTTTT
7615 TTTTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTCTTTTCATTTTTCA
Found at i:7608 original size:25 final size:23
Alignment explanation
Indices: 7579--7625 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 23
7569 CAAGTGCTTT
7579 TTTTCATTTTCTTTTTCATTTTTTC
1 TTTTCATTTT-TTTTT-ATTTTTTC
7604 TTTTCATTTTTTTTTATTTTTT
1 TTTTCATTTTTTTTTATTTTTT
7626 ATTATTGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 7 0.32
24 5 0.23
25 10 0.45
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTCATTTTTTTTTATTTTTTC
Found at i:12421 original size:16 final size:16
Alignment explanation
Indices: 12388--12423 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12378 AAAGATTTTG
*
12388 TTTTTGTGTTTTTAAT
1 TTTTTGTGTTTTGAAT
*
12404 TTTTTGTGTTTTGCAT
1 TTTTTGTGTTTTGAAT
12420 TTTT
1 TTTT
12424 ATTTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.08, C:0.03, G:0.14, T:0.75
Consensus pattern (16 bp):
TTTTTGTGTTTTGAAT
Found at i:27116 original size:27 final size:28
Alignment explanation
Indices: 27078--27149 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
27068 TGGACTTAAT
* *
27078 ATGACCGAAATGCCCCTGA-ATATGCGA
1 ATGACCAAAATGCCCCTGAGATATGCAA
* *
27105 ATGACCAAAATGCCCCT-AGGTGTGCAA
1 ATGACCAAAATGCCCCTGAGATATGCAA
27132 ATGACCAAAATGCCCCTG
1 ATGACCAAAATGCCCCTG
27150 GATGACCCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 38 0.97
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (28 bp):
ATGACCAAAATGCCCCTGAGATATGCAA
Found at i:33961 original size:3 final size:3
Alignment explanation
Indices: 33953--33981 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
33943 TTGATGTTGT
33953 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
33982 ACAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:33990 original size:1 final size:1
Alignment explanation
Indices: 33984--34009 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
33974 AACAACAAAC
33984 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
34010 CCTTTGATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:35541 original size:2 final size:2
Alignment explanation
Indices: 35536--35567 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35526 ACACACACAC
35536 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35568 TTGGTATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37440 original size:18 final size:18
Alignment explanation
Indices: 37413--37447 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37403 TTCTCTTGAT
*
37413 TTTCGTTTTAATGCTCTA
1 TTTCGATTTAATGCTCTA
*
37431 TTTCGATTTAATTCTCT
1 TTTCGATTTAATGCTCT
37448 CCTCCCTTTT
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:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (18 bp):
TTTCGATTTAATGCTCTA
Found at i:38446 original size:37 final size:38
Alignment explanation
Indices: 38370--38448 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 38
38360 TTAATTTGGA
**
38370 AATTTAACTAAACTTATTTTGTTATTTTTTTTATAACC
1 AATTTAACTAAACTTATTTTGTTACCTTTTTTATAACC
38408 AATTTAACTAAACTTATTTTGTT-CCTTTTTTATAACC
1 AATTTAACTAAACTTATTTTGTTACCTTTTTTATAACC
38445 AATT
1 AATT
38449 ATAAAATCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 16 0.41
38 23 0.59
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.53
Consensus pattern (38 bp):
AATTTAACTAAACTTATTTTGTTACCTTTTTTATAACC
Found at i:39722 original size:130 final size:126
Alignment explanation
Indices: 39465--39710 Score: 372
Period size: 126 Copynumber: 1.9 Consensus size: 126
39455 TAGTAGGTAT
* *
39465 TATAAATAACCCAAAATCAAAGTCGAAATGACAAAAAAACCAGCTCAAATATTAATCAAACGAAT
1 TATAAATAACCCAAAAGCAAAGTCGAAATG---AAAAAACCAGCTCAAACATTAATCAAACGAAT
39530 GTGGTGATCCGGTTTGGAAAAAAAAATGATAATTTTACATTTTATTTTTATTGTTTAGTATAAAC
63 GTGGTGATCCGGTTTGG-AAAAAAAATGATAATTTTACATTTTATTTTTATTGTTTAGTATAAAC
* * * *
39595 TATAAATAACCCAAAAGCAAAGTCGAAATG-AAAAACTAGCTCAAGCATTGATCAAATGAATGTG
1 TATAAATAACCCAAAAGCAAAGTCGAAATGAAAAAACCAGCTCAAACATTAATCAAACGAATGTG
39659 GTGATCCGGTTTGG-AAAAAAATGGA-AATTTTACATTTTATTTTTATTGTTTA
66 GTGATCCGGTTTGGAAAAAAAAT-GATAATTTTACATTTTATTTTTATTGTTTA
39711 TGTTTAGTAT
Statistics
Matches: 109, Mismatches: 6, Indels: 8
0.89 0.05 0.07
Matches are distributed among these distances:
124 35 0.32
125 2 0.02
126 43 0.39
130 29 0.27
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (126 bp):
TATAAATAACCCAAAAGCAAAGTCGAAATGAAAAAACCAGCTCAAACATTAATCAAACGAATGTG
GTGATCCGGTTTGGAAAAAAAATGATAATTTTACATTTTATTTTTATTGTTTAGTATAAAC
Found at i:42650 original size:18 final size:19
Alignment explanation
Indices: 42616--42653 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
42606 GTCCATCGTT
*
42616 ATCTCCATGGTCTCCATGC
1 ATCTCCATGGCCTCCATGC
42635 ATCTCCAT-GCCTCCATGC
1 ATCTCCATGGCCTCCATGC
42653 A
1 A
42654 ACCCATGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.18, C:0.39, G:0.13, T:0.29
Consensus pattern (19 bp):
ATCTCCATGGCCTCCATGC
Found at i:42933 original size:26 final size:26
Alignment explanation
Indices: 42904--42974 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
42894 AGGGTCATCC
42904 AGGGACATTTTGGTCATTTTTACACTA
1 AGGG-CATTTTGGTCATTTTTACACTA
* * ***
42931 GGGGCATTTTGGTCATCTTTATGTTA
1 AGGGCATTTTGGTCATTTTTACACTA
42957 AGGGCATTTTGGTCATTT
1 AGGGCATTTTGGTCATTT
42975 GTATGTTCAG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 34 0.92
27 3 0.08
ACGTcount: A:0.20, C:0.13, G:0.24, T:0.44
Consensus pattern (26 bp):
AGGGCATTTTGGTCATTTTTACACTA
Found at i:42979 original size:26 final size:26
Alignment explanation
Indices: 42904--43004 Score: 87
Period size: 26 Copynumber: 3.8 Consensus size: 26
42894 AGGGTCATCC
* ***
42904 AGGGACATTTTGGTCATTTTTACACTA
1 AGGG-CATTTTGGTCATTTGTATGTTA
*
42931 GGGGCATTTTGGTCATCTT-TATGTTA
1 AGGGCATTTTGGTCAT-TTGTATGTTA
42957 AGGGCATTTTGGTCATTTGTATGTTCA
1 AGGGCATTTTGGTCATTTGTATGTT-A
* * * *
42984 GGGGTATTCTGGTCAGTTGTA
1 AGGGCATTTTGGTCATTTGTA
43005 GCCCATTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
25 2 0.03
26 37 0.60
27 23 0.37
ACGTcount: A:0.19, C:0.12, G:0.27, T:0.43
Consensus pattern (26 bp):
AGGGCATTTTGGTCATTTGTATGTTA
Found at i:43069 original size:6 final size:6
Alignment explanation
Indices: 43054--43105 Score: 63
Period size: 6 Copynumber: 8.7 Consensus size: 6
43044 CATCATTTGC
*
43054 AAAACAA AAAACA AAAA-A ACAA-A AAAACA AAAACAA AAAACA AAAACA
1 AAAAC-A AAAACA AAAACA AAAACA AAAACA AAAAC-A AAAACA AAAACA
43102 AAAA
1 AAAA
43106 ATCTTAAGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
5 8 0.20
6 22 0.54
7 11 0.27
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:43072 original size:8 final size:7
Alignment explanation
Indices: 43054--43106 Score: 74
Period size: 7 Copynumber: 7.6 Consensus size: 7
43044 CATCATTTGC
43054 AAAACAA
1 AAAACAA
43061 AAAACAAA
1 AAAAC-AA
43069 AAAACAA
1 AAAACAA
43076 AAAA-ACA
1 AAAACA-A
43083 AAAACAA
1 AAAACAA
43090 AAAAC-A
1 AAAACAA
43096 AAAACAA
1 AAAACAA
43103 AAAA
1 AAAA
43107 TCTTAAGGGG
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
6 7 0.17
7 27 0.64
8 8 0.19
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAACAA
Found at i:50436 original size:23 final size:24
Alignment explanation
Indices: 50392--50436 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
50382 ATAATATGGA
50392 GGTTATCAAATATCTCATAGTGTT
1 GGTTATCAAATATCTCATAGTGTT
*
50416 GGTTATCAAA-ATTTCATAGTG
1 GGTTATCAAATATCTCATAGTG
50437 AGGTCTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (24 bp):
GGTTATCAAATATCTCATAGTGTT
Found at i:60389 original size:30 final size:32
Alignment explanation
Indices: 60325--60405 Score: 103
Period size: 30 Copynumber: 2.6 Consensus size: 32
60315 TATTTCTTTT
60325 ACTTTCTAACTTCAAATCCTTTAATACCTTCAA
1 ACTTTCTAACTTCAAATCCTTT-ATACCTTCAA
* **
60358 ACTTTCTAATTTCAAATCCTTT-T-TGTTCAA
1 ACTTTCTAACTTCAAATCCTTTATACCTTCAA
*
60388 ACTTTCTACCTTCAAATC
1 ACTTTCTAACTTCAAATC
60406 TTCTACAACA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 21 0.49
31 1 0.02
33 21 0.49
ACGTcount: A:0.30, C:0.26, G:0.01, T:0.43
Consensus pattern (32 bp):
ACTTTCTAACTTCAAATCCTTTATACCTTCAA
Found at i:60572 original size:33 final size:33
Alignment explanation
Indices: 60516--60591 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
60506 GCTGCCCTCC
* * * * *
60516 GAGGGCTGCATGCCGTGGCTTGTGCCGCCTCAG
1 GAGGGCGGCAAGCCATGGCTTGTGCCACCCCAG
*
60549 GAGGGCGGCAAGCCATGGTTTGTGCCACCCCAG
1 GAGGGCGGCAAGCCATGGCTTGTGCCACCCCAG
60582 GAGGGCGGCA
1 GAGGGCGGCA
60592 TGCCGCCCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.14, C:0.29, G:0.41, T:0.16
Consensus pattern (33 bp):
GAGGGCGGCAAGCCATGGCTTGTGCCACCCCAG
Found at i:60686 original size:17 final size:16
Alignment explanation
Indices: 60660--60696 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
60650 CCATGGCATG
*
60660 TAATTTTTTAATATATT
1 TAATTCTTTAAT-TATT
60677 TAATTCTTTAATTATT
1 TAATTCTTTAATTATT
60693 TAAT
1 TAAT
60697 AATTGTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TAATTCTTTAATTATT
Found at i:60741 original size:19 final size:15
Alignment explanation
Indices: 60701--60729 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
60691 TTTAATAATT
60701 GTTAATTAGTTTATA
1 GTTAATTAGTTTATA
60716 GTTAATTAGTTTAT
1 GTTAATTAGTTTAT
60730 TTACGATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (15 bp):
GTTAATTAGTTTATA
Found at i:60921 original size:30 final size:31
Alignment explanation
Indices: 60845--60925 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
60835 CTCCGCCCGT
60845 AGGGAGAGAGAGGCTCAG-TTGCAGAGGGAG
1 AGGGAGAGAGAGGCTCAGATTGCAGAGGGAG
* * **
60875 AGAGAG-GCTGCTGCTCAGATT-CAGAGGGAG
1 AGGGAGAG-AGAGGCTCAGATTGCAGAGGGAG
60905 AGGGAGAGAGAGGCTCAGATT
1 AGGGAGAGAGAGGCTCAGATT
60926 TTGAGGGATA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
29 1 0.03
30 36 0.90
31 3 0.08
ACGTcount: A:0.30, C:0.12, G:0.44, T:0.14
Consensus pattern (31 bp):
AGGGAGAGAGAGGCTCAGATTGCAGAGGGAG
Found at i:64971 original size:44 final size:44
Alignment explanation
Indices: 64814--64960 Score: 206
Period size: 44 Copynumber: 3.3 Consensus size: 44
64804 AAGACAGGAC
* * *
64814 GGGATCTTTCCCTAGATT-AAAAAACTTTTGAAAGCTGCTTGAA
1 GGGATCTTTCCCTAAATTAAAAAAACTTTTGAAAACTACTTGAA
*
64857 GGGATCTTTCCCTAAATTAAAAAAACTTTTAAAAACTACTTGAA
1 GGGATCTTTCCCTAAATTAAAAAAACTTTTGAAAACTACTTGAA
* **
64901 GGGATCTTTTCCTAAATTAAAAAAACTTTTGAAAACTACTTTGGT
1 GGGATCTTTCCCTAAATTAAAAAAACTTTTGAAAACTAC-TTGAA
*
64946 TGGATCTTTCCCTAA
1 GGGATCTTTCCCTAA
64961 TTCGAAAAAC
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 17 0.18
44 59 0.64
45 16 0.17
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (44 bp):
GGGATCTTTCCCTAAATTAAAAAAACTTTTGAAAACTACTTGAA
Found at i:65570 original size:21 final size:22
Alignment explanation
Indices: 65544--65587 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
65534 AAATAACTAA
* *
65544 AACAAA-CGAAGCCCAAATTAT
1 AACAAAGCCAAGCCCAAAGTAT
65565 AACAAAGCCAAGCCCAAAGTAT
1 AACAAAGCCAAGCCCAAAGTAT
65587 A
1 A
65588 TATGTTAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.52, C:0.25, G:0.11, T:0.11
Consensus pattern (22 bp):
AACAAAGCCAAGCCCAAAGTAT
Found at i:67246 original size:28 final size:30
Alignment explanation
Indices: 67188--67247 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
67178 GCTAAATACC
*
67188 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAAAAATCCCTTATGTTTT-CTTTCGGGA
*
67219 CAAAATAATCCCTTATG-TTT-TTTCGGGA
1 CAAAAAAATCCCTTATGTTTTCTTTCGGGA
67247 C
1 C
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 8 0.30
30 3 0.11
31 16 0.59
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (30 bp):
CAAAAAAATCCCTTATGTTTTCTTTCGGGA
Done.