Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008134.1 Corchorus capsularis cultivar CVL-1 contig08155, 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: 22675
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:476 original size:116 final size:116
Alignment explanation
Indices: 272--504 Score: 441
Period size: 116 Copynumber: 2.0 Consensus size: 116
262 TAAGCTTTGA
272 TTAATTCAGAGCTGAGCAACGTCAAATCCTAATTGGAAAAGTCATATGATATGAACTTCTCAACA
1 TTAATTCAGAGCTGAGCAACGTCAAATCCTAATTGGAAAAGTCATATGATATGAACTTCTCAACA
*
337 TCCAATAGTCATATTAAGCCTTGACGCATTGGACTCTAATGGGGTAGATTC
66 TCCAATAGTCATACTAAGCCTTGACGCATTGGACTCTAATGGGGTAGATTC
388 TTAATTCAGAGCTGAGCAACGTCAAA-CGCTAATTGGAAAAGTCATATGATATGAACTTCTCAAC
1 TTAATTCAGAGCTGAGCAACGTCAAATC-CTAATTGGAAAAGTCATATGATATGAACTTCTCAAC
452 ATCCAATAGTCATACTAAGCCTTGACGCATTGGACTCTAATGGGGTAGATTC
65 ATCCAATAGTCATACTAAGCCTTGACGCATTGGACTCTAATGGGGTAGATTC
504 T
1 T
505 GTAGACACCC
Statistics
Matches: 115, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
115 1 0.01
116 114 0.99
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (116 bp):
TTAATTCAGAGCTGAGCAACGTCAAATCCTAATTGGAAAAGTCATATGATATGAACTTCTCAACA
TCCAATAGTCATACTAAGCCTTGACGCATTGGACTCTAATGGGGTAGATTC
Found at i:2245 original size:36 final size:38
Alignment explanation
Indices: 2199--2281 Score: 134
Period size: 39 Copynumber: 2.2 Consensus size: 38
2189 GCAATCGAGG
*
2199 GGGGAAAATTTC-AAAAAAAA-GGGAGATCAATTTCGA
1 GGGGAGAATTTCAAAAAAAAAGGGGAGATCAATTTCGA
2235 GGGGAGAATTTCAAAAAAAAAAGGGGAGATCAATTTCGA
1 GGGGAGAATTTC-AAAAAAAAAGGGGAGATCAATTTCGA
2274 GGGGAGAA
1 GGGGAGAA
2282 AAATTAAGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
36 11 0.26
38 8 0.19
39 24 0.56
ACGTcount: A:0.46, C:0.07, G:0.30, T:0.17
Consensus pattern (38 bp):
GGGGAGAATTTCAAAAAAAAAGGGGAGATCAATTTCGA
Found at i:5110 original size:97 final size:97
Alignment explanation
Indices: 4941--5557 Score: 851
Period size: 97 Copynumber: 6.4 Consensus size: 97
4931 AGTTTTCACT
* * *
4941 TGCTATTTCCCAAAATGTCCTTCCCGAACGGAAGGCATTTATTTTTAACTGTTTTTCCCAAAACG
1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGTTTTTCCCAAAACG
* *
5006 CCATTCCCGGATGGAAGGCACTGATTTTTACC
66 CCCTTCCCGGACGGAAGGCACTGATTTTTACC
* * *
5038 TGCTATTTCCCAAAATACCCTTCCCGGCCGGAAGACATTTATTTTTACCTGTTTTTCCCAAAACG
1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGTTTTTCCCAAAACG
* *
5103 CCCTTCCCGGACAGAAGGCACTGATTCTTACC
66 CCCTTCCCGGACGGAAGGCACTGATTTTTACC
* * * * * * * *
5135 TGTTTTTTACCAAAACGCCCTTCCCGGACGGAAGGCACTAATTTGTACCTGTTTTTCCTAAAACG
1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGTTTTTCCCAAAACG
5200 CCCTTCCCGGACGGAAGGCACTGATTTTTACC
66 CCCTTCCCGGACGGAAGGCACTGATTTTTACC
*
5232 TGCTATTTCCCAAAATGCCTTTCCCGGACGGAAGGCATTTATTTTTACCTGTTTTTCCCAAAACG
1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGTTTTTCCCAAAACG
* *
5297 CTCTTCCCGAACGGAAGGCACTGATTTTTACC
66 CCCTTCCCGGACGGAAGGCACTGATTTTTACC
*
5329 TACTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGTTTTTCCCAAAACG
1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGTTTTTCCCAAAACG
* * *
5394 TCCTTCCCGGACGGAAGGCACT--TATTTACT
66 CCCTTCCCGGACGGAAGGCACTGATTTTTACC
* * ** * *
5424 TGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGACGCTTATTTTTACCTATTTTTTCCCAAAG
1 TGCTA-TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCT-GTTTTTCCCAAAA
* * * *
5489 TGCCCTTCCCAGACGGAAGGCACTAATTTTTACT
64 CGCCCTTCCCGGACGGAAGGCACTGATTTTTACC
* * * *
5523 TGCTTTTTCCTAAAACGCCCTTCCCGGATGGAAGG
1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGG
5558 TGTTAGTTTT
Statistics
Matches: 459, Mismatches: 57, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
95 10 0.02
96 41 0.09
97 371 0.81
98 26 0.06
99 11 0.02
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (97 bp):
TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGTTTTTCCCAAAACG
CCCTTCCCGGACGGAAGGCACTGATTTTTACC
Found at i:5579 original size:48 final size:49
Alignment explanation
Indices: 4941--5557 Score: 726
Period size: 49 Copynumber: 12.7 Consensus size: 49
4931 AGTTTTCACT
* * * * * *
4941 TGCTATTTCCCAAAATGTCCTTCCCGAACGGAAGGCATTTATTTTTAAC
1 TGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACC
* * *
4990 TG-TTTTTCCCAAAACGCCATTCCCGGATGGAAGGCACTGATTTTTACC
1 TGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACC
* ** * * *
5038 TGCTATTTCCCAAAATACCCTTCCCGGCCGGAAGACATTTATTTTTACC
1 TGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACC
* * *
5087 TG-TTTTTCCCAAAACGCCCTTCCCGGACAGAAGGCACTGATTCTTACC
1 TGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACC
* * * *
5135 TGTTTTTTACCAAAACGCCCTTCCCGGACGGAAGGCACTAATTTGTACC
1 TGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACC
* *
5184 TG-TTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACC
1 TGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACC
* * * *
5232 TGCTATTTCCCAAAATGCCTTTCCCGGACGGAAGGCATTTATTTTTACC
1 TGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACC
* * *
5281 TG-TTTTTCCCAAAACGCTCTTCCCGAACGGAAGGCACTGATTTTTACC
1 TGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACC
* * * *
5329 TACTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACC
1 TGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACC
* *
5378 TG-TTTTTCCCAAAACGTCCTTCCCGGACGGAAGGCACTTA--TTTACT
1 TGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACC
* * * *
5424 TGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGACGCTTATTTTTACC
1 TGCT-TTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACC
** ** * * *
5474 TATTTTTTCCCAAAGTGCCCTTCCCAGACGGAAGGCACTAATTTTTACT
1 TGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACC
* *
5523 TGCTTTTTCCTAAAACGCCCTTCCCGGATGGAAGG
1 TGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGG
5558 TGTTAGTTTT
Statistics
Matches: 476, Mismatches: 84, Indels: 16
0.83 0.15 0.03
Matches are distributed among these distances:
46 7 0.01
47 1 0.00
48 228 0.48
49 233 0.49
50 7 0.01
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (49 bp):
TGCTTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACC
Found at i:10020 original size:14 final size:13
Alignment explanation
Indices: 9996--10032 Score: 65
Period size: 14 Copynumber: 2.8 Consensus size: 13
9986 TGAGATATTT
9996 TTTTCAAAAAATG
1 TTTTCAAAAAATG
10009 TTTTCAAGAAAATG
1 TTTTCAA-AAAATG
10023 TTTTCAAAAA
1 TTTTCAAAAA
10033 TGAGTTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
TTTTCAAAAAATG
Found at i:11652 original size:37 final size:37
Alignment explanation
Indices: 11560--11671 Score: 106
Period size: 37 Copynumber: 3.1 Consensus size: 37
11550 AGAAAATTCA
*
11560 CAAAGATCAAC--AATCGACCACGGATTGGTCTCTCCT
1 CAAAGATCAACAAAAT-GACCACGGATTGGTCTCTTCT
* ** *
11596 C-ATGTATCAA-ACAGCTGACCACGGATTGGTCGCTTCT
1 CAAAG-ATCAACA-AAATGACCACGGATTGGTCTCTTCT
* *
11633 CAAAGATCAACAAAATGACCATGGACTGGTCTCTTCT
1 CAAAGATCAACAAAATGACCACGGATTGGTCTCTTCT
11670 CA
1 CA
11672 GGCTCCAACA
Statistics
Matches: 59, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
35 2 0.03
36 6 0.10
37 47 0.80
38 4 0.07
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (37 bp):
CAAAGATCAACAAAATGACCACGGATTGGTCTCTTCT
Found at i:11840 original size:38 final size:39
Alignment explanation
Indices: 11765--11855 Score: 130
Period size: 38 Copynumber: 2.4 Consensus size: 39
11755 TGGTCCCTTT
* * * * *
11765 CAGGTCACCTTTCGGCAGTCATCAAAAGTTGGCTGGAAA
1 CAGGTCATCTTTCAGCAATAATCAAAAGTTGACTGGAAA
11804 CAGGTCATCTTTCAGCAATAATC-AAAGTTGACTGGAAA
1 CAGGTCATCTTTCAGCAATAATCAAAAGTTGACTGGAAA
11842 CAGGTCATCTTTCA
1 CAGGTCATCTTTCA
11856 AGTTATCAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 28 0.60
39 19 0.40
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (39 bp):
CAGGTCATCTTTCAGCAATAATCAAAAGTTGACTGGAAA
Found at i:11930 original size:38 final size:36
Alignment explanation
Indices: 11868--11948 Score: 135
Period size: 38 Copynumber: 2.2 Consensus size: 36
11858 TTATCAGAGA
*
11868 TCATCTTCCAAATTATCAAAGTTGACTGGAAACAGG
1 TCATCTTCCAAATAATCAAAGTTGACTGGAAACAGG
11904 TCATCTTCCAACAGTAATCAAAGTTGACTGGAAACAGG
1 TCATCTTCCAA-A-TAATCAAAGTTGACTGGAAACAGG
11942 TCATCTT
1 TCATCTT
11949 TCAAGTTATC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
36 11 0.26
37 1 0.02
38 30 0.71
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (36 bp):
TCATCTTCCAAATAATCAAAGTTGACTGGAAACAGG
Found at i:11953 original size:96 final size:99
Alignment explanation
Indices: 11789--12049 Score: 361
Period size: 96 Copynumber: 2.7 Consensus size: 99
11779 GCAGTCATCA
* * *
11789 AAAGTTGGCTGGAAACAGGTCATCTTTCAGCAATAATCAAAGTTGACTGGAAACAGGTCATCTTT
1 AAAGTTGACTGGAAACAGGTCATCTTCCAACAATAATCAAAGTTGACTGGAAACAGGTCATCTTT
*
11854 CAAGTTATCAGAGATCATC-TTCCA-AA-TTATC
66 CAAGTTATCAGAGATCATCTTTCAATAAGTTATC
*
11885 AAAGTTGACTGGAAACAGGTCATCTTCCAACAGTAATCAAAGTTGACTGGAAACAGGTCATCTTT
1 AAAGTTGACTGGAAACAGGTCATCTTCCAACAATAATCAAAGTTGACTGGAAACAGGTCATCTTT
11950 CAAGTTATCAGAGATCATCTTTTCAATAAGTTATC
66 CAAGTTATCAGAGATCATC-TTTCAATAAGTTATC
* * * * ** * *
11985 AAAGTTGACTGGAAACAAGTCATCTTTCAGCAATTATCTTA--CGACTGGAAACAGGTCATTTTT
1 AAAGTTGACTGGAAACAGGTCATCTTCCAACAATAATCAAAGTTGACTGGAAACAGGTCATCTTT
12048 CA
66 CA
12050 GTAGTTATTA
Statistics
Matches: 147, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
96 80 0.54
98 26 0.18
99 2 0.01
100 39 0.27
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (99 bp):
AAAGTTGACTGGAAACAGGTCATCTTCCAACAATAATCAAAGTTGACTGGAAACAGGTCATCTTT
CAAGTTATCAGAGATCATCTTTCAATAAGTTATC
Found at i:12071 original size:74 final size:73
Alignment explanation
Indices: 11987--12241 Score: 223
Period size: 74 Copynumber: 3.4 Consensus size: 73
11977 AAGTTATCAA
*
11987 AGTT-GACTGGAAACAAGTCATCTTTCAGCAATTATCTTACGACTGGAAACAGGTCATTTTTCAG
1 AGTTCGACTGGAAACAAGTCATCTTTCAGCAATTATCTTACGACTGGAAACAGGTCATCTTTCAG
*
12051 TAGTTATT
66 CAGTTATT
* ** **
12059 AGGTTTGACTGGAAAC-AGATCATCTTTCAATAAGTTATCAAAGCTGACTGGAAACAGGTCATCT
1 A-GTTCGACTGGAAACAAG-TCATCTTTCAGCAA-TTATCTTA-C-GACTGGAAACAGGTCATCT
*
12123 TTCAGCAATTATCT
61 TTCAGCAGTTAT-T
* * * ** *
12137 --TACGACTGGAAACAGGTCGTCTTTCAGCGCTTGTCAAGTT-CGACTGGAAACAGGTCATCTTT
1 AGTTCGACTGGAAACAAGTCATCTTTCAGCAATTATC---TTACGACTGGAAACAGGTCATCTTT
* *
12199 CAACAGTTATCA
63 CAGCAGTTAT-T
* *
12211 AGATCGACTGGAAACATGTCATCTTTCAGCA
1 AGTTCGACTGGAAACAAGTCATCTTTCAGCA
12242 GTTTTCGGTT
Statistics
Matches: 144, Mismatches: 26, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
72 1 0.01
73 5 0.03
74 56 0.39
75 27 0.19
76 26 0.18
77 28 0.19
78 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (73 bp):
AGTTCGACTGGAAACAAGTCATCTTTCAGCAATTATCTTACGACTGGAAACAGGTCATCTTTCAG
CAGTTATT
Found at i:12112 original size:113 final size:113
Alignment explanation
Indices: 11961--12241 Score: 397
Period size: 113 Copynumber: 2.5 Consensus size: 113
11951 AAGTTATCAG
*
11961 AGATCATCTTTTCAATAAGTTATCAAAGTTGACTGGAAACAAGTCATCTTTCAGCAATTATCTTA
1 AGATCATC-TTTCAATAAGTTATCAAAGATGACTGGAAACAAGTCATCTTTCAGCAATTATCTTA
* * * *
12026 CGACTGGAAACAGGTCATTTTTCAGTAG-TTATTAGGTTTGACTGGAAAC
65 CGACTGGAAACAGGTCATCTTTCAG-AGCTTATCAAGTTCGACTGGAAAC
* *
12075 AGATCATCTTTCAATAAGTTATCAAAGCTGACTGGAAACAGGTCATCTTTCAGCAATTATCTTAC
1 AGATCATCTTTCAATAAGTTATCAAAGATGACTGGAAACAAGTCATCTTTCAGCAATTATCTTAC
* * *
12140 GACTGGAAACAGGTCGTCTTTCAGCGCTTGTCAAGTTCGACTGGAAAC
66 GACTGGAAACAGGTCATCTTTCAGAGCTTATCAAGTTCGACTGGAAAC
* * *
12188 AGGTCATCTTTCAA-CAGTTATC-AAGATCGACTGGAAACATGTCATCTTTCAGCA
1 AGATCATCTTTCAATAAGTTATCAAAGAT-GACTGGAAACAAGTCATCTTTCAGCA
12242 GTTTTCGGTT
Statistics
Matches: 152, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
111 4 0.03
112 33 0.22
113 107 0.70
114 8 0.05
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (113 bp):
AGATCATCTTTCAATAAGTTATCAAAGATGACTGGAAACAAGTCATCTTTCAGCAATTATCTTAC
GACTGGAAACAGGTCATCTTTCAGAGCTTATCAAGTTCGACTGGAAAC
Found at i:12244 original size:38 final size:38
Alignment explanation
Indices: 11978--12244 Score: 242
Period size: 38 Copynumber: 7.1 Consensus size: 38
11968 CTTTTCAATA
* *
11978 AGTTATCAA-AGTTGACTGGAAACAAGTCATCTTTCAGC
1 AGTTATCAAGA-TCGACTGGAAACAGGTCATCTTTCAGC
* ** * *
12016 AATTATC-TTA-CGACTGGAAACAGGTCATTTTTCAGT
1 AGTTATCAAGATCGACTGGAAACAGGTCATCTTTCAGC
* * * * * **
12052 AGTTATTAGGTTTGACTGGAAACAGATCATCTTTCAATA
1 AGTTATCAAGATCGACTGGAAACAGGTCATCTTTC-AGC
*
12091 AGTTATCAA-AGCTGACTGGAAACAGGTCATCTTTCAGC
1 AGTTATCAAGATC-GACTGGAAACAGGTCATCTTTCAGC
* ** *
12129 AATTATC-TTA-CGACTGGAAACAGGTCGTCTTTCAGC
1 AGTTATCAAGATCGACTGGAAACAGGTCATCTTTCAGC
* * *
12165 -GCTTGTCAAGTTCGACTGGAAACAGGTCATCTTTCAAC
1 AG-TTATCAAGATCGACTGGAAACAGGTCATCTTTCAGC
*
12203 AGTTATCAAGATCGACTGGAAACATGTCATCTTTCAGC
1 AGTTATCAAGATCGACTGGAAACAGGTCATCTTTCAGC
12241 AGTT
1 AGTT
12245 TTCGGTTGCT
Statistics
Matches: 181, Mismatches: 38, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
36 55 0.30
37 1 0.01
38 95 0.52
39 30 0.17
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (38 bp):
AGTTATCAAGATCGACTGGAAACAGGTCATCTTTCAGC
Found at i:12338 original size:17 final size:15
Alignment explanation
Indices: 12274--12332 Score: 73
Period size: 15 Copynumber: 3.7 Consensus size: 15
12264 GGGCACTCCA
12274 ACAACTTTTCAATTT
1 ACAACTTTTCAATTT
*
12289 ACAACTTTTCAGCTTTT
1 ACAACTTTTCA--ATTT
12306 ACAACTTTTTCAATTT
1 ACAAC-TTTTCAATTT
*
12322 TCAACTTTTCA
1 ACAACTTTTCA
12333 GTATTTCAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
15 17 0.45
16 7 0.18
17 8 0.21
18 6 0.16
ACGTcount: A:0.29, C:0.22, G:0.02, T:0.47
Consensus pattern (15 bp):
ACAACTTTTCAATTT
Found at i:12356 original size:15 final size:15
Alignment explanation
Indices: 12336--12366 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12326 CTTTTCAGTA
12336 TTTCAATTCACAACT
1 TTTCAATTCACAACT
*
12351 TTTCAATTGACAACT
1 TTTCAATTCACAACT
12366 T
1 T
12367 CCATGTGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.23, G:0.03, T:0.42
Consensus pattern (15 bp):
TTTCAATTCACAACT
Found at i:12452 original size:48 final size:47
Alignment explanation
Indices: 12363--12509 Score: 240
Period size: 47 Copynumber: 3.1 Consensus size: 47
12353 TCAATTGACA
*
12363 ACTTCCATGTGAGTCAGCAATCCTTCGACCCAAGTTGGTCTTTCCTC
1 ACTTCCATGTGAGTCAGAAATCCTTCGACCCAAGTTGGTCTTTCCTC
*
12410 ACTTCCATGTGAGTCAGAAATCATTCCGACCCAAGTTGGTCTTTCCTC
1 ACTTCCATGTGAGTCAGAAATCCTT-CGACCCAAGTTGGTCTTTCCTC
* * *
12458 ATTTCCATGTGAGTCAGAAATCCTTCGACCAAAGTTGGTCTTTTCTC
1 ACTTCCATGTGAGTCAGAAATCCTTCGACCCAAGTTGGTCTTTCCTC
12505 ACTTC
1 ACTTC
12510 TATGCAAAGT
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
47 47 0.51
48 45 0.49
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (47 bp):
ACTTCCATGTGAGTCAGAAATCCTTCGACCCAAGTTGGTCTTTCCTC
Found at i:12582 original size:47 final size:48
Alignment explanation
Indices: 12482--12584 Score: 115
Period size: 47 Copynumber: 2.2 Consensus size: 48
12472 CAGAAATCCT
* * *
12482 TCGACCAAAGTTGGTCTTTTCTCACTTCTATGCAAAGTTACAATTTGG
1 TCGACCACAGTTGGTCTTTGCTCACTTCTATGCAAAGTTACAATTTGA
* *
12530 T-GACCACAGTTGGTCTTTGCTCGCTT-TCATGC-GAGTATACAATTT-A
1 TCGACCACAGTTGGTCTTTGCTCACTTCT-ATGCAAAGT-TACAATTTGA
12576 TCGACCACA
1 TCGACCACA
12585 AACTGTTCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
46 5 0.11
47 41 0.87
48 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.35
Consensus pattern (48 bp):
TCGACCACAGTTGGTCTTTGCTCACTTCTATGCAAAGTTACAATTTGA
Found at i:16343 original size:49 final size:48
Alignment explanation
Indices: 16223--16786 Score: 641
Period size: 48 Copynumber: 11.7 Consensus size: 48
16213 TCACTTGCTA
* * *
16223 TTTCCCAAAATGTCCTTCCCGGACGGAAGGCATTTATTTTTACCTGTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGTT
* * * *
16271 TTTCCCAAAACGCCATTCCCGGACGGAAGGCAATGATTTTTACCTGCTA
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTG-TT
* *
16320 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGTT
* * * *
16368 TCTCCCAAAACGCCCTTCCCGGACAGAAGGCACTGATTCTTACCTGTTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTG-TT
* * *
16417 TTTACCAAAACGCCCTTCCCGGACGGAAGGCACTAATCTTTACCTGTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGTT
*
16465 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACCTGTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGTT
* * * *
16513 TTTCCTAAAACACCCTTCCCGGACGGAAGGCACTAATCTTTACCTGTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGTT
* *
16561 TTTCCC-AAATGCCCTTCCCGGACGGAAGGCACTTA-TTTTACTTGCTAT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTG-T-T
* * * * *
16609 TTTCCAAAAATGCCCTTCCCGGACGGAAGACGCTTATTTTTACCTACTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCT-GTT
** * *
16658 TTTCCCAAAGTGCCCTTCCCGGACGGAAGGCACTAATTTTTACTTGTTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTG-TT
* * * * * *
16707 TTTCCTAAAACGTCCTTCCCTGATGGAAGGC-GTTAGTTTTA-CTCGCTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCT-G-TT
** * * *
16755 TTTCTTAAAATGCCCTTTCCGGACGAAAGGCA
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCA
16787 AGTTCACTTT
Statistics
Matches: 440, Mismatches: 66, Indels: 19
0.84 0.13 0.04
Matches are distributed among these distances:
46 7 0.02
47 28 0.06
48 218 0.50
49 179 0.41
50 8 0.02
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.32
Consensus pattern (48 bp):
TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGTT
Found at i:16387 original size:97 final size:97
Alignment explanation
Indices: 16218--16786 Score: 662
Period size: 97 Copynumber: 5.9 Consensus size: 97
16208 AGTTTTCACT
* * *
16218 TGCTATTTCCCAAAATGTCCTTCCCGGACGGAAGGCATTTATTTTTACCTGTTTTTCCCAAAACG
1 TGCTATTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGTTTTTCCCAAAACG
* *
16283 CCATTCCCGGACGGAAGGCAATGATTTTTACC
66 CCCTTCCCGGACGGAAGGCACTGATTTTTACC
* * *
16315 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGTTTCTCCCAAAACG
1 TGCTATTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGTTTTTCCCAAAACG
* *
16380 CCCTTCCCGGACAGAAGGCACTGATTCTTACC
66 CCCTTCCCGGACGGAAGGCACTGATTTTTACC
* * * * *
16412 TGTTTTTTACCAAAACGCCCTTCCCGGACGGAAGGCACTAATCTTTACCTGTTTTTCCCAAAACG
1 TGCTATTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGTTTTTCCCAAAACG
16477 CCCTTCCCGGACGGAAGGCACTGATTTTTACC
66 CCCTTCCCGGACGGAAGGCACTGATTTTTACC
* * * * * *
16509 TG-TTTTTCCTAAAACACCCTTCCCGGACGGAAGGCACTAATCTTTACCTGTTTTTCCC-AAATG
1 TGCTATTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGTTTTTCCCAAAACG
* *
16572 CCCTTCCCGGACGGAAGGCACTTA-TTTTACT
66 CCCTTCCCGGACGGAAGGCACTGATTTTTACC
* * * * * *
16603 TGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGACGCTTATTTTTACCTACTTTTTCCCAAAG
1 TGCTA-TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCT-GTTTTTCCCAAAA
* * *
16668 TGCCCTTCCCGGACGGAAGGCACTAATTTTTACT
64 CGCCCTTCCCGGACGGAAGGCACTGATTTTTACC
* * * * * * * * **
16702 TGTTTTTTCCTAAAACGTCCTTCCCTGATGGAAGGC-GTTAGTTTTA-CTCGCTTTTTCTTAAAA
1 TGCTATTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCT-G-TTTTTCCCAAAA
* * *
16765 TGCCCTTTCCGGACGAAAGGCA
64 CGCCCTTCCCGGACGGAAGGCA
16787 AGTTCACTTT
Statistics
Matches: 416, Mismatches: 50, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
94 8 0.02
95 28 0.07
96 93 0.22
97 225 0.54
98 52 0.12
99 10 0.02
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.32
Consensus pattern (97 bp):
TGCTATTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACCTGTTTTTCCCAAAACG
CCCTTCCCGGACGGAAGGCACTGATTTTTACC
Done.