Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009978.1 Corchorus capsularis cultivar CVL-1 contig09999, 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: 56583
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:23 original size:13 final size:13
Alignment explanation
Indices: 7--41 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1 TTTTTT
*
7 AATTTTTTTTTAA
1 AATTTTTTTTAAA
20 AATTTTTTTTAAA
1 AATTTTTTTTAAA
33 AGATTTTTT
1 A-ATTTTTT
42 ACCTCAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (13 bp):
AATTTTTTTTAAA
Found at i:30 original size:12 final size:12
Alignment explanation
Indices: 1--33 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
*
1 TTTTTT-AATTT
1 TTTTTTAAAATT
12 TTTTTTAAAATT
1 TTTTTTAAAATT
24 TTTTTTAAAA
1 TTTTTTAAAA
34 GATTTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTTAAAATT
Found at i:204 original size:21 final size:21
Alignment explanation
Indices: 171--215 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
161 AAAAATTATA
*
171 AAAAGGGGAGCGGTGTTTAGC
1 AAAAGGGGAGCGGTGTTTAAC
192 AAAAGAGGG-GCGGTGTTTAAC
1 AAAAG-GGGAGCGGTGTTTAAC
213 AAA
1 AAA
216 CCCCATATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.36, C:0.09, G:0.38, T:0.18
Consensus pattern (21 bp):
AAAAGGGGAGCGGTGTTTAAC
Found at i:8691 original size:31 final size:30
Alignment explanation
Indices: 8653--8857 Score: 203
Period size: 31 Copynumber: 6.6 Consensus size: 30
8643 ACGGTGTCCG
*
8653 ACATGGCATGCCACGTGTATCAAAAAGTGAC
1 ACATGGCACGCCACGTGTA-CAAAAAGTGAC
** * *
8684 ATGTGGCACGCCACATGTACAAAAAAGTTAAC
1 ACATGGCACGCCACGTGTAC-AAAAAG-TGAC
* *
8716 ACATGTCACGTCACGTGTACCAAAAAGTGAC
1 ACATGGCACGCCACGTGTA-CAAAAAGTGAC
*
8747 ACATGTCACGCCACGTGTACCAAAAAGTGAC
1 ACATGGCACGCCACGTGTA-CAAAAAGTGAC
* *
8778 ACATGTCACGCCATGTGTACGAAAAAGTGAC
1 ACATGGCACGCCACGTGTAC-AAAAAGTGAC
* * *
8809 ACATGGCATGCCACATGTTTTCAAAAAGTGAC
1 ACATGGCACGCCAC--GTGTACAAAAAGTGAC
* *
8841 ACGTGGCATGCCACGTG
1 ACATGGCACGCCACGTG
8858 CATAAAAGGA
Statistics
Matches: 148, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
30 4 0.03
31 93 0.63
32 46 0.31
33 5 0.03
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (30 bp):
ACATGGCACGCCACGTGTACAAAAAGTGAC
Found at i:8810 original size:62 final size:62
Alignment explanation
Indices: 8653--8857 Score: 230
Period size: 63 Copynumber: 3.3 Consensus size: 62
8643 ACGGTGTCCG
* * * ** * *
8653 ACATGGCATGCCACGTGTATCAAAAAGTGACATGTGGCACGCCACATGTACAAAAAAGTTAAC
1 ACATGTCACGCCACGTGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAG-TGAC
* * *
8716 ACATGTCACGTCACGTGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGTGAC
1 ACATGTCACGCCACGTGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTGAC
* * * **
8778 ACATGTCACGCCATGTGTACGAAAAAGTGACACATGGCATGCCACATGTTTTCAAAAAGTGAC
1 ACATGTCACGCCACGTGTACCAAAAAGTGACACATGGCACGCCACATG-TACCAAAAAGTGAC
* * *
8841 ACGTGGCATGCCACGTG
1 ACATGTCACGCCACGTG
8858 CATAAAAGGA
Statistics
Matches: 119, Mismatches: 22, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
62 45 0.38
63 74 0.62
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (62 bp):
ACATGTCACGCCACGTGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTGAC
Found at i:8834 original size:94 final size:94
Alignment explanation
Indices: 8653--8857 Score: 241
Period size: 94 Copynumber: 2.2 Consensus size: 94
8643 ACGGTGTCCG
* **
8653 ACATGGCATGCCACGTGTATCAAAAAGTGACATGTGGCACGCCACATGTACAAAAAAGTTAACAC
1 ACATGGCATGCCACGTGTACCAAAAAGTGACACATGGCACGCCACATGTACAAAAAAGTTAACAC
* * *
8718 ATGTCACGTCACGTGTACCAAAAAGTGAC
66 ATGGCACGCCACATGTACCAAAAAGTGAC
* * * ** * *
8747 ACATGTCACGCCACGTGTACCAAAAAGTGACACATGTCACGCCATGTGTACGAAAAAG-TGACAC
1 ACATGGCATGCCACGTGTACCAAAAAGTGACACATGGCACGCCACATGTACAAAAAAGTTAACAC
* **
8811 ATGGCATGCCACATGTTTTCAAAAAGTGAC
66 ATGGCACGCCACATG-TACCAAAAAGTGAC
*
8841 ACGTGGCATGCCACGTG
1 ACATGGCATGCCACGTG
8858 CATAAAAGGA
Statistics
Matches: 91, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
93 16 0.18
94 75 0.82
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (94 bp):
ACATGGCATGCCACGTGTACCAAAAAGTGACACATGGCACGCCACATGTACAAAAAAGTTAACAC
ATGGCACGCCACATGTACCAAAAAGTGAC
Found at i:12944 original size:14 final size:14
Alignment explanation
Indices: 12933--12959 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12923 AAGTCAGCTT
12933 GGACACGTCAGCAA
1 GGACACGTCAGCAA
12947 GGACACGTCAGCA
1 GGACACGTCAGCA
12960 TTCTTGTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.30, G:0.30, T:0.07
Consensus pattern (14 bp):
GGACACGTCAGCAA
Found at i:17333 original size:20 final size:21
Alignment explanation
Indices: 17308--17346 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
17298 TATCTTGGTA
17308 TTTTATGGTTTTA-GATTTAT
1 TTTTATGGTTTTATGATTTAT
*
17328 TTTTATGTTTTTATGATTT
1 TTTTATGGTTTTATGATTT
17347 CTAATTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (21 bp):
TTTTATGGTTTTATGATTTAT
Found at i:18692 original size:15 final size:16
Alignment explanation
Indices: 18651--18693 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
18641 GAAGAGTAAT
*
18651 TATTAAAAATATATAA
1 TATTTAAAATATATAA
*
18667 TATTTAAAATATATTA
1 TATTTAAAATATATAA
*
18683 -ATTTATAATAT
1 TATTTAAAATAT
18694 CATATCAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTTAAAATATATAA
Found at i:19265 original size:68 final size:67
Alignment explanation
Indices: 19114--19272 Score: 173
Period size: 68 Copynumber: 2.4 Consensus size: 67
19104 AGAAAAAAAC
* * * * *
19114 TATAATTTTATTTC-A-ATATATATACACATATATATCAAATTTTTGAGCTACGTCGATTTCGTT
1 TATAATTTTATTCCAATATATATATACACATATATATAAAACTTTTAAGCTACGCCGATTTCGTT
19177 AA
66 AA
* * *
19179 TATAATTTTATTCCAATATATATATATATATATATATAAAAACTTTTAAGCTACGCC-AGTTTCT
1 TATAATTTTATTCCAATATATATATACACATATATAT-AAAACTTTTAAGCTACGCCGA-TTTCG
19243 TTAA
64 TTAA
**
19247 TATAATGTTT-TTGTAATATATATATA
1 TATAAT-TTTATTCCAATATATATATA
19273 GATGAGATAA
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
65 13 0.16
66 1 0.01
67 19 0.24
68 43 0.54
69 3 0.04
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (67 bp):
TATAATTTTATTCCAATATATATATACACATATATATAAAACTTTTAAGCTACGCCGATTTCGTT
AA
Found at i:20850 original size:15 final size:15
Alignment explanation
Indices: 20830--20882 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
20820 GCTTTCCCCG
20830 GCAGCGAGCTTCCTA
1 GCAGCGAGCTTCCTA
*
20845 GCAGCGAACATT-CTA
1 GCAGCGAGC-TTCCTA
* *
20860 GCGGCGAGTTTCCTA
1 GCAGCGAGCTTCCTA
20875 GCAGCGAG
1 GCAGCGAG
20883 TTACTCTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 2 0.06
15 27 0.87
16 2 0.06
ACGTcount: A:0.23, C:0.28, G:0.30, T:0.19
Consensus pattern (15 bp):
GCAGCGAGCTTCCTA
Found at i:21073 original size:3 final size:3
Alignment explanation
Indices: 21065--21095 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
21055 AACACGATTA
*
21065 TCT TCT TCT TCT TCT TGT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
21096 GCGGCTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:21087 original size:15 final size:15
Alignment explanation
Indices: 21067--21096 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21057 CACGATTATC
21067 TTCTTCTTCTTCTTG
1 TTCTTCTTCTTCTTG
21082 TTCTTCTTCTTCTTG
1 TTCTTCTTCTTCTTG
21097 CGGCTTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.27, G:0.07, T:0.67
Consensus pattern (15 bp):
TTCTTCTTCTTCTTG
Found at i:23005 original size:2 final size:2
Alignment explanation
Indices: 22998--23023 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22988 TTTTGAAATA
22998 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
23024 GTATTGTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49826 original size:30 final size:30
Alignment explanation
Indices: 49792--49849 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
49782 TCTGCGGCTA
* * * *
49792 CTCCATGCAATGGTCGGTCTTGTGCGATGG
1 CTCCATCCAATGGGCGGTCATATGCGATGG
49822 CTCCATCCAATGGGCGGTCATATGCGAT
1 CTCCATCCAATGGGCGGTCATATGCGAT
49850 CCCATCATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.28
Consensus pattern (30 bp):
CTCCATCCAATGGGCGGTCATATGCGATGG
Found at i:54192 original size:37 final size:37
Alignment explanation
Indices: 54150--54250 Score: 116
Period size: 37 Copynumber: 2.7 Consensus size: 37
54140 AAAGATCTCA
* *
54150 AAGTTTTCAATTTAGGGAAAGATCCCATCTAGTCTTTT
1 AAGTTTTAAATTTAGGGAAAGATCCCATCCAGT-TTTT
*
54188 -AG-TTTAAGATTTAGGGAAAGATACCATCCAGTTTTT
1 AAGTTTTAA-ATTTAGGGAAAGATCCCATCCAGTTTTT
*
54224 CAAAATTTTAAATTTAGGGAAAGATCC
1 --AAGTTTTAAATTTAGGGAAAGATCC
54251 TGTCAAAAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
36 8 0.15
37 24 0.45
39 16 0.30
40 5 0.09
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.36
Consensus pattern (37 bp):
AAGTTTTAAATTTAGGGAAAGATCCCATCCAGTTTTT
Found at i:55859 original size:21 final size:21
Alignment explanation
Indices: 55801--55859 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
55791 TTTACTGAAT
* *
55801 TACTGATTACCATTACTATTT
1 TACTGATTACTATTACTATTG
55822 TACTGATTATTCT-TTACT-TTG
1 TACTGATTA--CTATTACTATTG
55843 TACTGATTACTAGTTAC
1 TACTGATTACTA-TTAC
55860 CATTTTATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.06
21 24 0.75
22 5 0.16
23 1 0.03
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.49
Consensus pattern (21 bp):
TACTGATTACTATTACTATTG
Found at i:55945 original size:35 final size:33
Alignment explanation
Indices: 55906--56001 Score: 97
Period size: 34 Copynumber: 2.8 Consensus size: 33
55896 GATTAATATT
*
55906 TTACTCTTTACCATTTTTTTTTACTGGA-TTACTCC
1 TTACTCTTTACCATTTTTCTTTACT-GACTT-CT-C
*
55941 TTACTCTTCT-CCATTCTTCTTTACTGACTTCTC
1 TTACTCTT-TACCATTTTTCTTTACTGACTTCTC
* *
55974 TTCACTCTTTACCATTTTCCTTTGCTGA
1 TT-ACTCTTTACCATTTTTCTTTACTGA
56002 TTACCATTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
33 4 0.08
34 24 0.46
35 23 0.44
36 1 0.02
ACGTcount: A:0.15, C:0.28, G:0.05, T:0.52
Consensus pattern (33 bp):
TTACTCTTTACCATTTTTCTTTACTGACTTCTC
Found at i:56013 original size:19 final size:20
Alignment explanation
Indices: 55982--56024 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
55972 TCTTCACTCT
55982 TTACCATTTTCCTTTGCTGA
1 TTACCATTTTCCTTTGCTGA
56002 TTACCA-TTTCCTTTGCTGA
1 TTACCATTTTCCTTTGCTGA
56021 TTAC
1 TTAC
56025 TCTTTACTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.16, C:0.26, G:0.09, T:0.49
Consensus pattern (20 bp):
TTACCATTTTCCTTTGCTGA
Found at i:56033 original size:7 final size:7
Alignment explanation
Indices: 56021--56072 Score: 70
Period size: 7 Copynumber: 7.6 Consensus size: 7
56011 CCTTTGCTGA
56021 TTACTCT
1 TTACTCT
56028 TTACTCT
1 TTACTCT
56035 TTACTCT
1 TTACTCT
56042 TT-CTCT
1 TTACTCT
**
56048 TTACTGA
1 TTACTCT
*
56055 TTACTTT
1 TTACTCT
56062 TTACTCT
1 TTACTCT
56069 TTAC
1 TTAC
56073 GATTTTTCTC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
6 6 0.15
7 33 0.85
ACGTcount: A:0.15, C:0.25, G:0.02, T:0.58
Consensus pattern (7 bp):
TTACTCT
Found at i:56049 original size:20 final size:21
Alignment explanation
Indices: 56022--56072 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 21
56012 CTTTGCTGAT
56022 TACTCTTTACTCTTTACTC-T
1 TACTCTTTACTCTTTACTCAT
* ** **
56042 TTCTCTTTACTGATTACTTTT
1 TACTCTTTACTCTTTACTCAT
56063 TACTCTTTAC
1 TACTCTTTAC
56073 GATTTTTCTC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.16, C:0.25, G:0.02, T:0.57
Consensus pattern (21 bp):
TACTCTTTACTCTTTACTCAT
Found at i:56083 original size:15 final size:17
Alignment explanation
Indices: 56059--56092 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
56049 TACTGATTAC
56059 TTTTTACTCTTTAC-GA
1 TTTTTACTCTTTACTGA
56075 TTTTT-CTCTTTACTGA
1 TTTTTACTCTTTACTGA
56091 TT
1 TT
56093 ACCATTTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTTTACTCTTTACTGA
Found at i:56094 original size:22 final size:22
Alignment explanation
Indices: 56055--56320 Score: 202
Period size: 22 Copynumber: 12.5 Consensus size: 22
56045 TCTTTACTGA
* ** *
56055 TTACTTTTTACTCTTTACGATT
1 TTACTCTTTACTGATTACCATT
*
56077 TTTCTCTTTACTGATTACCA-T
1 TTACTCTTTACTGATTACCATT
**
56098 TT-C-CTTTGTTGATTA-C-TCT
1 TTACTCTTTACTGATTACCAT-T
56117 TTACTCTTTACTGATTACCATT
1 TTACTCTTTACTGATTACCATT
* * *
56139 TTACTCTTTTCTAATTACTATT
1 TTACTCTTTACTGATTACCATT
*
56161 TTACTTTTTACTGATTA-CATTT
1 TTACTCTTTACTGATTACCA-TT
*
56183 TTACTTTTTACTGATTACCA--
1 TTACTCTTTACTGATTACCATT
* *
56203 TTGCT-TCTTACTGATTA-C-TA
1 TTACTCT-TTACTGATTACCATT
56223 TTACT-TTCTACTGATTACTC-TT
1 TTACTCTT-TACTGATTAC-CATT
* *
56245 TTAATTTTTACTGATTACCATT
1 TTACTCTTTACTGATTACCATT
*
56267 TTACAT-TTTACTAATTACCATT
1 TTAC-TCTTTACTGATTACCATT
*
56289 TTACCCTTTACTGATTACC-TT
1 TTACTCTTTACTGATTACCATT
*
56310 TTACTTTTTAC
1 TTACTCTTTAC
56321 CATTTTACCT
Statistics
Matches: 200, Mismatches: 26, Indels: 37
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.00
19 16 0.08
20 30 0.15
21 26 0.13
22 121 0.61
23 6 0.03
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.54
Consensus pattern (22 bp):
TTACTCTTTACTGATTACCATT
Found at i:56119 original size:89 final size:89
Alignment explanation
Indices: 55932--56128 Score: 269
Period size: 89 Copynumber: 2.2 Consensus size: 89
55922 TTTTTTACTG
*
55932 GATTACTCCTTACTC-TT-CTCCATTCTTCTTTACTGACTTCTCTTCACTCTTTACCATTTTCCT
1 GATTACTCTTTACTCTTTACTCCATTCTTCTTTACTGACTTCTCTTCACTCTTTACCATTTTCCT
*
55995 TTGCTGATTACCATTTCCTTTGCT
66 TTACTGATTACCATTTCCTTTGCT
* * * *
56019 GATTACTCTTTACTCTTTACT-CTTTC-TCTTTACTGA-TTACTTTTTACTCTTTACGATTTTTC
1 GATTACTCTTTACTCTTTACTCCATTCTTCTTTACTGACTT-CTCTTCACTCTTTACCA-TTTTC
*
56081 TCTTTACTGATTACCATTTCCTTTGTT
64 -CTTTACTGATTACCATTTCCTTTGCT
56108 GATTACTCTTTACTCTTTACT
1 GATTACTCTTTACTCTTTACT
56129 GATTACCATT
Statistics
Matches: 98, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
86 2 0.02
87 38 0.39
88 11 0.11
89 47 0.48
ACGTcount: A:0.15, C:0.26, G:0.06, T:0.53
Consensus pattern (89 bp):
GATTACTCTTTACTCTTTACTCCATTCTTCTTTACTGACTTCTCTTCACTCTTTACCATTTTCCT
TTACTGATTACCATTTCCTTTGCT
Found at i:56194 original size:106 final size:105
Alignment explanation
Indices: 56055--56316 Score: 282
Period size: 106 Copynumber: 2.5 Consensus size: 105
56045 TCTTTACTGA
** ** *
56055 TTACTTTTTACTCTTTACGATTTTT-CTCTTTACTGATTACCATTTCCTTTGTTGATTACTCTTT
1 TTACTTTTTACTAATTAC-ATTTTTACTCTTTACTGATTACCATTTCCTTTACTGATTACT-ATT
* *
56119 ACTCTT-TACTGATTAC-CATTTTACTCTTTT-CTAATTACTATT
64 ACT-TTCTACTGATTACTC-TTTTAAT-TTTTACTAATTACCATT
* * * *
56161 TTACTTTTTACTGATTACATTTTTACTTTTTACTGATTACCATTGCTTCTTACTGATTACTATTA
1 TTACTTTTTACTAATTACATTTTTACTCTTTACTGATTACCATTTCCT-TTACTGATTACTATTA
*
56226 CTTTCTACTGATTACTCTTTTAATTTTTACTGATTACCATT
65 CTTTCTACTGATTACTCTTTTAATTTTTACTAATTACCATT
* * * *
56267 TTACATTTTACTAATTACCA-TTTTACCCTTTACTGATTACCTTTTACTTT
1 TTACTTTTTACTAATTA-CATTTTTACTCTTTACTGATTACCATTTCCTTT
56317 TTACCATTTT
Statistics
Matches: 131, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
105 14 0.11
106 104 0.79
107 13 0.10
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.54
Consensus pattern (105 bp):
TTACTTTTTACTAATTACATTTTTACTCTTTACTGATTACCATTTCCTTTACTGATTACTATTAC
TTTCTACTGATTACTCTTTTAATTTTTACTAATTACCATT
Found at i:56227 original size:84 final size:86
Alignment explanation
Indices: 56124--56288 Score: 221
Period size: 84 Copynumber: 1.9 Consensus size: 86
56114 TCTTTACTCT
* * *
56124 TTACTGATTACCATTTTACTCTT-TTCTAATTACTATTTTACTTTTTACTGATTA-CATTTTTAC
1 TTACTGATTACCATATTACT-TTCTACTAATTACTATTTTAATTTTTACTGATTACCA-TTTTAC
* *
56187 TTTTTACTGATTACCATTGCTTC
64 ATTTTACTAATTACCATTGCTTC
* *
56210 TTACTGATTA-C-TATTACTTTCTACTGATTACTCTTTTAATTTTTACTGATTACCATTTTACAT
1 TTACTGATTACCATATTACTTTCTACTAATTACTATTTTAATTTTTACTGATTACCATTTTACAT
56273 TTTACTAATTACCATT
66 TTTACTAATTACCATT
56289 TTACCCTTTA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
83 2 0.03
84 55 0.79
85 3 0.04
86 10 0.14
ACGTcount: A:0.24, C:0.18, G:0.04, T:0.53
Consensus pattern (86 bp):
TTACTGATTACCATATTACTTTCTACTAATTACTATTTTAATTTTTACTGATTACCATTTTACAT
TTTACTAATTACCATTGCTTC
Found at i:56247 original size:62 final size:64
Alignment explanation
Indices: 56081--56320 Score: 221
Period size: 62 Copynumber: 3.8 Consensus size: 64
56071 ACGATTTTTC
* * * * * *
56081 TCTTTACTGATTACCATTTCCTTTGT--TGATTACTC-TTTACTCTTTACTGATTACCATTTTA
1 TCTTTACTAATTACTATTTACTTTCTACTGATTACTCTTTTACTTTTTACTGATTACCATTCTA
* *
56142 CTCTTTTCTAATTACTATTTTACTTTTTACTGATTACAT-TTTTACTTTTTACTGATTACCATTG
1 -TCTTTACTAATTACTA-TTTACTTTCTACTGATTAC-TCTTTTACTTTTTACTGATTACCATT-
56206 CT-
62 CTA
* * *
56208 TC-TTACTGATTACTA-TTACTTTCTACTGATTACTCTTTTAATTTTTACTGATTACCATTTTA
1 TCTTTACTAATTACTATTTACTTTCTACTGATTACTCTTTTACTTTTTACTGATTACCATTCTA
* *
56270 -CATTTTACTAATTACCATTTTACCCTT-TACTGATTAC-CTTTTACTTTTTAC
1 TC--TTTACTAATTACTA-TTTA-CTTTCTACTGATTACTCTTTTACTTTTTAC
56321 CATTTTACCT
Statistics
Matches: 148, Mismatches: 16, Indels: 25
0.78 0.08 0.13
Matches are distributed among these distances:
61 3 0.02
62 53 0.36
63 8 0.05
64 22 0.15
65 22 0.15
66 36 0.24
67 4 0.03
ACGTcount: A:0.22, C:0.20, G:0.05, T:0.53
Consensus pattern (64 bp):
TCTTTACTAATTACTATTTACTTTCTACTGATTACTCTTTTACTTTTTACTGATTACCATTCTA
Found at i:56390 original size:15 final size:14
Alignment explanation
Indices: 56368--56404 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
56358 ATCATTTTTG
56368 TCTTTACTGATTAC
1 TCTTTACTGATTAC
56382 TCTTCTACTGATTAC
1 TCTT-TACTGATTAC
56397 TCTTTACT
1 TCTTTACT
56405 CTTTACCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.19, C:0.24, G:0.05, T:0.51
Consensus pattern (14 bp):
TCTTTACTGATTAC
Found at i:56418 original size:22 final size:22
Alignment explanation
Indices: 56393--56544 Score: 98
Period size: 22 Copynumber: 7.1 Consensus size: 22
56383 CTTCTACTGA
* **
56393 TTACTCTTTACTCTTTACCATT
1 TTACTTTTTACTAATTACCATT
* *
56415 TTACTTTTTTCTAATTACTATT
1 TTACTTTTTACTAATTACCATT
* *
56437 TTACTTTTTACTGATTACCTTT
1 TTACTTTTTACTAATTACCATT
* *
56459 TTACTTTTTACTGATTAGCA--
1 TTACTTTTTACTAATTACCATT
* * * *
56479 TTGCTTCTTACTGACTT--C-TA
1 TTACTTTTTACT-AATTACCATT
* *
56499 TTACTCTTTACTGATTACCATT
1 TTACTTTTTACTAATTACCATT
* * *
56521 TTACCTTTTACTGATTACTATT
1 TTACTTTTTACTAATTACCATT
56543 TT
1 TT
56545 CTGCTCCTTT
Statistics
Matches: 100, Mismatches: 24, Indels: 12
0.74 0.18 0.09
Matches are distributed among these distances:
19 3 0.03
20 19 0.19
21 3 0.03
22 75 0.75
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.55
Consensus pattern (22 bp):
TTACTTTTTACTAATTACCATT
Found at i:56423 original size:7 final size:7
Alignment explanation
Indices: 56393--56470 Score: 57
Period size: 7 Copynumber: 10.7 Consensus size: 7
56383 CTTCTACTGA
*
56393 TTACTCT
1 TTACTTT
*
56400 TTACTCT
1 TTACTTT
*
56407 TTACCATT
1 TTA-CTTT
56415 TTACTTT
1 TTACTTT
* **
56422 TTTCTAA
1 TTACTTT
56429 TTACTATT
1 TTACT-TT
56437 TTACTTT
1 TTACTTT
**
56444 TTACTGA
1 TTACTTT
56451 TTACCTTT
1 TTA-CTTT
56459 TTACTTT
1 TTACTTT
56466 TTACT
1 TTACT
56471 GATTAGCATT
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
7 40 0.73
8 15 0.27
ACGTcount: A:0.19, C:0.19, G:0.01, T:0.60
Consensus pattern (7 bp):
TTACTTT
Found at i:56447 original size:15 final size:14
Alignment explanation
Indices: 56393--56470 Score: 57
Period size: 15 Copynumber: 5.4 Consensus size: 14
56383 CTTCTACTGA
* *
56393 TTACTCTTTACTCT
1 TTACTTTTTACTTT
*
56407 TTACCATTTTACTTT
1 TTA-CTTTTTACTTT
* **
56422 TTTCTAATTACTATT
1 TTACTTTTTACT-TT
**
56437 TTACTTTTTACTGA
1 TTACTTTTTACTTT
56451 TTACCTTTTTACTTT
1 TTA-CTTTTTACTTT
56466 TTACT
1 TTACT
56471 GATTAGCATT
Statistics
Matches: 47, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
14 14 0.30
15 33 0.70
ACGTcount: A:0.19, C:0.19, G:0.01, T:0.60
Consensus pattern (14 bp):
TTACTTTTTACTTT
Done.