Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007648.1 Corchorus capsularis cultivar CVL-1 contig07669, 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: 23002
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:2049 original size:26 final size:28
Alignment explanation
Indices: 2010--2082 Score: 91
Period size: 26 Copynumber: 2.7 Consensus size: 28
2000 TTTGAGTCCT
*
2010 AGGGGGATTTTGGTCATTTTTGCAC-TA
1 AGGGGCATTTTGGTCATTTTTGCACGTA
*
2037 A-GGTCATTTTGGTCA--TTTGCACGTTA
1 AGGGGCATTTTGGTCATTTTTGCACG-TA
2063 AGGGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
2083 AAGGTCACTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 7 0.18
26 15 0.39
27 14 0.37
29 2 0.05
ACGTcount: A:0.18, C:0.12, G:0.27, T:0.42
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTTGCACGTA
Found at i:2079 original size:27 final size:25
Alignment explanation
Indices: 2010--2081 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 25
2000 TTTGAGTCCT
*
2010 AGGGGGATTTTGGTCATTTTTGCACTA
1 AGGGGCATTTTGGTCA--TTTGCACTA
*
2037 A-GGTCATTTTGGTCATTTGCACGTTA
1 AGGGGCATTTTGGTCATTTGCAC--TA
2063 AGGGGCATTTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
2082 TAAGGTCACT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
24 7 0.18
26 15 0.38
27 17 0.44
ACGTcount: A:0.18, C:0.12, G:0.28, T:0.42
Consensus pattern (25 bp):
AGGGGCATTTTGGTCATTTGCACTA
Found at i:2253 original size:26 final size:26
Alignment explanation
Indices: 2214--2303 Score: 98
Period size: 26 Copynumber: 3.5 Consensus size: 26
2204 ATCTTCGTTT
2214 TCATTTAGTAATTTGGTTTGTTACAC
1 TCATTTAGTAATTTGGTTTGTTACAC
* * *
2240 TCATTTAGTGATTT-ATCTTCGTT---T
1 TCATTTAGTAATTTGGT-TT-GTTACAC
2264 TCATTTAGTAATTTGGTTTGTTACAC
1 TCATTTAGTAATTTGGTTTGTTACAC
*
2290 TCATTTAGTGATTT
1 TCATTTAGTAATTT
2304 AGCTTTGTGG
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
23 3 0.06
24 15 0.29
25 2 0.04
26 28 0.55
27 3 0.06
ACGTcount: A:0.21, C:0.11, G:0.14, T:0.53
Consensus pattern (26 bp):
TCATTTAGTAATTTGGTTTGTTACAC
Found at i:2262 original size:50 final size:50
Alignment explanation
Indices: 2203--2304 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
2193 TTTGGTATTG
2203 TATCTTCGTTTTCATTTAGTAATTTGGTTTGTTACACTCATTTAGTGATT
1 TATCTTCGTTTTCATTTAGTAATTTGGTTTGTTACACTCATTTAGTGATT
2253 TATCTTCGTTTTCATTTAGTAATTTGGTTTGTTACACTCATTTAGTGATT
1 TATCTTCGTTTTCATTTAGTAATTTGGTTTGTTACACTCATTTAGTGATT
2303 TA
1 TA
2305 GCTTTGTGGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.54
Consensus pattern (50 bp):
TATCTTCGTTTTCATTTAGTAATTTGGTTTGTTACACTCATTTAGTGATT
Found at i:2648 original size:20 final size:20
Alignment explanation
Indices: 2623--2663 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2613 ATAAATACAA
2623 GACATTTGATTTACAAATTG
1 GACATTTGATTTACAAATTG
*
2643 GACATTTGATTTGCAAATTG
1 GACATTTGATTTACAAATTG
2663 G
1 G
2664 TGCTCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.39
Consensus pattern (20 bp):
GACATTTGATTTACAAATTG
Found at i:7143 original size:18 final size:19
Alignment explanation
Indices: 7102--7141 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
7092 ACTCTTTTGG
*
7102 TTTCCTTTTCTTTTTCTTC
1 TTTCCTTTTCTGTTTCTTC
7121 TTTCC-TTTCTGTTTCATTC
1 TTTCCTTTTCTGTTTC-TTC
7140 TT
1 TT
7142 CCCATGCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.03, C:0.25, G:0.03, T:0.70
Consensus pattern (19 bp):
TTTCCTTTTCTGTTTCTTC
Found at i:11471 original size:16 final size:15
Alignment explanation
Indices: 11448--11513 Score: 73
Period size: 15 Copynumber: 4.3 Consensus size: 15
11438 CAAGTGCAAT
11448 AAAA-AAATGAAAAA
1 AAAAGAAATGAAAAA
11462 GAAGAA-AAATGAAAAA
1 -AA-AAGAAATGAAAAA
*
11478 AAAAGAAAGGAAAAA
1 AAAAGAAATGAAAAA
*
11493 AAAAGAAACGAAAAA
1 AAAAGAAATGAAAAA
11508 GAAAAG
1 -AAAAG
11514 CAGCTCTAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
14 2 0.04
15 27 0.59
16 17 0.37
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.03
Consensus pattern (15 bp):
AAAAGAAATGAAAAA
Found at i:11477 original size:17 final size:16
Alignment explanation
Indices: 11450--11500 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
11440 AGTGCAATAA
*
11450 AAAAATGAAAAAGAAG
1 AAAAATGAAAAAAAAG
11466 AAAAATGAAAAAAAA-
1 AAAAATGAAAAAAAAG
* *
11481 AGAAAGGAAAAAAAAAG
1 AAAAATG-AAAAAAAAG
11498 AAA
1 AAA
11501 CGAAAAAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 5 0.17
16 22 0.76
17 2 0.07
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (16 bp):
AAAAATGAAAAAAAAG
Found at i:11485 original size:26 final size:26
Alignment explanation
Indices: 11448--11512 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
11438 CAAGTGCAAT
* * *
11448 AAAAAAATGAAAAAGAAGAAAAATGA
1 AAAAAAAAGAAAAAGAAAAAAAAAGA
*
11474 AAAAAAAAG-AAAGGAAAAAAAAAGA
1 AAAAAAAAGAAAAAGAAAAAAAAAGA
*
11499 AACGAAAAAGAAAA
1 AA-AAAAAAGAAAA
11513 GCAGCTCTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
25 15 0.47
26 14 0.44
27 3 0.09
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.03
Consensus pattern (26 bp):
AAAAAAAAGAAAAAGAAAAAAAAAGA
Found at i:12684 original size:38 final size:38
Alignment explanation
Indices: 12639--12798 Score: 155
Period size: 38 Copynumber: 4.2 Consensus size: 38
12629 GAGAAATGCT
* *
12639 GTCTTTCAGCACTTATCAAGT-TCGACTGGAAACAGATC
1 GTCTTTCATCACTTATCAA-TATCGACTGGAAACAGGTC
* * * **
12677 GTTTTTCATCACTTATCAAGT-TTGACTAGAAGTAGGTC
1 GTCTTTCATCACTTATCAA-TATCGACTGGAAACAGGTC
* *
12715 GTCTTTGATCAGTTATCAATATCGACTGGAAACAGGTC
1 GTCTTTCATCACTTATCAATATCGACTGGAAACAGGTC
* **
12753 GTCTTTCAACAAC-TATCAATATCGACTGGAAATGGGTC
1 GTCTTTCATC-ACTTATCAATATCGACTGGAAACAGGTC
*
12791 ATCTTTCA
1 GTCTTTCA
12799 GCAATTTTCA
Statistics
Matches: 100, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
37 1 0.01
38 98 0.98
39 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (38 bp):
GTCTTTCATCACTTATCAATATCGACTGGAAACAGGTC
Found at i:12796 original size:76 final size:76
Alignment explanation
Indices: 12651--12796 Score: 172
Period size: 76 Copynumber: 1.9 Consensus size: 76
12641 CTTTCAGCAC
* * * * *
12651 TTATCAAGTTCGACTGGAAACAGATCGTTTTTCATCACTTATCAAGTTTGACTAGAAGTAGGTCG
1 TTATCAAGTTCGACTGGAAACAGATCGTCTTTCAACACTTATCAAGTTCGACTAGAAATAGGTCA
12716 TCTTTGATCAG
66 TCTTTGATCAG
* * *
12727 TTATCAA-TATCGACTGGAAACAGGTCGTCTTTCAACAAC-TATCAA-TATCGACTGGAAATGGG
1 TTATCAAGT-TCGACTGGAAACAGATCGTCTTTCAAC-ACTTATCAAGT-TCGACTAGAAATAGG
12789 TCATCTTT
63 TCATCTTT
12797 CAGCAATTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 2 0.03
76 55 0.93
77 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (76 bp):
TTATCAAGTTCGACTGGAAACAGATCGTCTTTCAACACTTATCAAGTTCGACTAGAAATAGGTCA
TCTTTGATCAG
Found at i:12886 original size:19 final size:19
Alignment explanation
Indices: 12851--12932 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 19
12841 TTACGACTTT
* *
12851 TCAACTTTTTAACTTTTCAA
1 TCAACTTTATAGCTTTTC-A
*
12871 T-AACTTTATAGTTTTTCA
1 TCAACTTTATAGCTTTTCA
*
12889 TCAACTTTATTGCTTTTCA
1 TCAACTTTATAGCTTTTCA
* *
12908 TCAACTTTACAGGTTTTCA
1 TCAACTTTATAGCTTTTCA
*
12927 ACAACT
1 TCAACT
12933 GTTCGGCTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
18 2 0.04
19 49 0.94
20 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.48
Consensus pattern (19 bp):
TCAACTTTATAGCTTTTCA
Found at i:12943 original size:19 final size:20
Alignment explanation
Indices: 12863--12953 Score: 75
Period size: 19 Copynumber: 4.8 Consensus size: 20
12853 AACTTTTTAA
* *
12863 CTTTTCAATAACTTTATA-G
1 CTTTTCAACAACTTTACAGG
* * **
12882 TTTTTCATCAACTTTA-TTG
1 CTTTTCAACAACTTTACAGG
*
12901 CTTTTCATCAACTTTACAGG
1 CTTTTCAACAACTTTACAGG
12921 -TTTTCAACAACTGTT-C-GG
1 CTTTTCAACAACT-TTACAGG
12939 CTTTTCAACAACTTT
1 CTTTTCAACAACTTT
12954 TCAATTTACA
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
18 4 0.07
19 53 0.88
20 3 0.05
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (20 bp):
CTTTTCAACAACTTTACAGG
Found at i:13010 original size:19 final size:19
Alignment explanation
Indices: 12986--13058 Score: 91
Period size: 19 Copynumber: 4.1 Consensus size: 19
12976 TTTAGAATTT
12986 ACAACTTTACAGCATTTCA
1 ACAACTTTACAGCATTTCA
*
13005 ACAACTTTTCA--ATTT--
1 ACAACTTTACAGCATTTCA
13020 ACAACTTTACAGCATTTCA
1 ACAACTTTACAGCATTTCA
* *
13039 ACAACTTTTCAGTATTTCA
1 ACAACTTTACAGCATTTCA
13058 A
1 A
13059 TTCACAACTT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
15 10 0.22
17 8 0.17
19 28 0.61
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (19 bp):
ACAACTTTACAGCATTTCA
Found at i:13020 original size:34 final size:34
Alignment explanation
Indices: 12981--13049 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
12971 AGCTTTTTAG
12981 AATTTACAACTTTACAGCATTTCAACAACTTTTC
1 AATTTACAACTTTACAGCATTTCAACAACTTTTC
13015 AATTTACAACTTTACAGCATTTCAACAACTTTTC
1 AATTTACAACTTTACAGCATTTCAACAACTTTTC
13049 A
1 A
13050 GTATTTCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (34 bp):
AATTTACAACTTTACAGCATTTCAACAACTTTTC
Found at i:13057 original size:42 final size:42
Alignment explanation
Indices: 13011--13090 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
13001 TTCAACAACT
* *
13011 TTTCAATTTACAACTTTACAGCATTTCAACAACTTTTCAGTA
1 TTTCAATTCACAACTTTACAGCATTCCAACAACTTTTCAGTA
** *
13053 TTTCAATTCACAACTTTTGAGCATTCCCACAACTTTTC
1 TTTCAATTCACAACTTTACAGCATTCCAACAACTTTTC
13091 GGTTGCTCAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (42 bp):
TTTCAATTCACAACTTTACAGCATTCCAACAACTTTTCAGTA
Found at i:13070 original size:23 final size:22
Alignment explanation
Indices: 13011--13077 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 22
13001 TTCAACAACT
*
13011 TTTCAATTTACAACTTTACAGCA
1 TTTCAA-TTACAACTTTTCAGCA
*
13034 TTTC-A--ACAACTTTTCAGTA
1 TTTCAATTACAACTTTTCAGCA
*
13053 TTTCAATTCACAACTTTTGAGCA
1 TTTCAATT-ACAACTTTTCAGCA
13076 TT
1 TT
13078 CCCACAACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 16 0.44
20 1 0.03
22 1 0.03
23 18 0.50
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (22 bp):
TTTCAATTACAACTTTTCAGCA
Found at i:13551 original size:26 final size:25
Alignment explanation
Indices: 13497--13568 Score: 74
Period size: 27 Copynumber: 2.8 Consensus size: 25
13487 TTTGAGTCCT
*
13497 AGGGGGATTTTGGTCATTTTTGCACTA
1 AGGGGCATTTTGGTCA--TTTGCACTA
*
13524 A-GGTCATTTTGGTCATTTGCACATTA
1 AGGGGCATTTTGGTCATTTGCAC--TA
*
13550 AGGGGCATTTTAGTCATTT
1 AGGGGCATTTTGGTCATTT
13569 TAAGGTCACT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
24 7 0.18
26 15 0.39
27 16 0.42
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.42
Consensus pattern (25 bp):
AGGGGCATTTTGGTCATTTGCACTA
Found at i:19902 original size:28 final size:27
Alignment explanation
Indices: 19833--19903 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 27
19823 AGTACCAAAT
*
19833 AAAATAAAAAATAAAAAATAAAATAAAC
1 AAAAT-AAAAATAAAAAAGAAAATAAAC
* *
19861 AAAACGAAAAATAAAAAGGAAAAT-AAC
1 AAAA-TAAAAATAAAAAAGAAAATAAAC
19888 GAAAATAAAAGATAAA
1 -AAAATAAAA-ATAAA
19904 GAGTAAGGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 7 0.19
28 29 0.81
ACGTcount: A:0.77, C:0.04, G:0.07, T:0.11
Consensus pattern (27 bp):
AAAATAAAAATAAAAAAGAAAATAAAC
Found at i:20972 original size:31 final size:32
Alignment explanation
Indices: 20936--21026 Score: 98
Period size: 31 Copynumber: 2.9 Consensus size: 32
20926 GCTATAAAAT
* *
20936 ATAGCGGCGTCATGGTGCT-AGACGCCGCGAA
1 ATAGCGGCGTCATCGTGCTCAAACGCCGCGAA
* * *
20967 ATAGCGGCGTCTTCTTTCTCAAACGCCGCGAA
1 ATAGCGGCGTCATCGTGCTCAAACGCCGCGAA
*
20999 ATAGCGGCGTCTTTC-TG-TCAAACGCCGC
1 ATAGCGGCGTC-ATCGTGCTCAAACGCCGC
21027 TATATTAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
31 26 0.50
32 23 0.44
33 3 0.06
ACGTcount: A:0.21, C:0.30, G:0.27, T:0.22
Consensus pattern (32 bp):
ATAGCGGCGTCATCGTGCTCAAACGCCGCGAA
Found at i:20985 original size:195 final size:195
Alignment explanation
Indices: 20760--21136 Score: 598
Period size: 195 Copynumber: 1.9 Consensus size: 195
20750 CGTAAGTGTA
* * *
20760 AGACGCCGCGAAATAGCGGGGTCCTCTTTCTCAGACGCCGCGCAATAGCGGCGTCTGTT-TGTCA
1 AGACGCCGCGAAATAGCGGCGTCCTCTTTCTCAAACGCCGCGAAATAGCGGCGTCT-TTCTGTCA
* *
20824 AACGCCGCTATTTTAATATATGGAGGGAGAGATTTTTTTTTTCCTTTTTGTTGGAGGGAAAAATT
65 AACGCCGCTATATTAATATATGGAGGGAGAGATTTTTTTTTACCTTTTTGTTGGAGGGAAAAATT
20889 CCCTCCCCTAAAACAAAG-AAATATTTACAACTACACGGC-TATAAAATATAGCGGCGTCATGGT
130 CCCTCCCCTAAAACAAAGTAAAT-TTTACAACTACAC-GCATATAAAATATAGCGGCGTCATGGT
20952 GCT
193 GCT
*
20955 AGACGCCGCGAAATAGCGGCGTCTTCTTTCTCAAACGCCGCGAAATAGCGGCGTCTTTCTGTCAA
1 AGACGCCGCGAAATAGCGGCGTCCTCTTTCTCAAACGCCGCGAAATAGCGGCGTCTTTCTGTCAA
21020 ACGCCGCTATATTAATATATGGAGGGAGAGATTTTTTTTTACCTTTTTGTTGGAGGGAAAAATTC
66 ACGCCGCTATATTAATATATGGAGGGAGAGATTTTTTTTTACCTTTTTGTTGGAGGGAAAAATTC
* * * * * *
21085 CCTCCTCTGAAGCAAAGTAAATTTTACTATTACACGCATATAATATATAGCG
131 CCTCCCCTAAAACAAAGTAAATTTTACAACTACACGCATATAAAATATAGCG
21137 ACGCCACTAT
Statistics
Matches: 167, Mismatches: 12, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
194 4 0.02
195 159 0.95
196 4 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (195 bp):
AGACGCCGCGAAATAGCGGCGTCCTCTTTCTCAAACGCCGCGAAATAGCGGCGTCTTTCTGTCAA
ACGCCGCTATATTAATATATGGAGGGAGAGATTTTTTTTTACCTTTTTGTTGGAGGGAAAAATTC
CCTCCCCTAAAACAAAGTAAATTTTACAACTACACGCATATAAAATATAGCGGCGTCATGGTGCT
Found at i:20998 original size:32 final size:31
Alignment explanation
Indices: 20957--21026 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 31
20947 ATGGTGCTAG
*
20957 ACGCCGCGAAATAGCGGCGTCTTCTTTCTCAA
1 ACGCCGCGAAATAGCGGCGTCTT-TCTCTCAA
*
20989 ACGCCGCGAAATAGCGGCGTCTTTCTGTCAA
1 ACGCCGCGAAATAGCGGCGTCTTTCTCTCAA
21020 ACGCCGC
1 ACGCCGC
21027 TATATTAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 13 0.36
32 23 0.64
ACGTcount: A:0.21, C:0.33, G:0.24, T:0.21
Consensus pattern (31 bp):
ACGCCGCGAAATAGCGGCGTCTTTCTCTCAA
Found at i:21026 original size:226 final size:225
Alignment explanation
Indices: 20611--21026 Score: 640
Period size: 226 Copynumber: 1.8 Consensus size: 225
20601 CGCCGCCGTA
* *
20611 TTAATATGTGGAGGGAGAGGTTTTTTTTTTCCCTTTTTTGGAGGGAAAAATTCCCTCCCCTAAAA
1 TTAATATATGGAGGGAGAGATTTTTTTTTTCCCTTTTTTGGAGGGAAAAATTCCCTCCCCTAAAA
* *
20676 CAAAGAAAAATTTACAACTACACGGCTATAAAATATAGCGGTGTCTTGGTGCTAGACGCCGCAAA
66 CAAAGAAAAATTTACAACTACACGGCTATAAAATATAGCGGCGTCATGGTGCTAGACGCCGCAAA
* * *
20741 ATAGCGGCGCGTAAGTGTAAGACGCCGCGAAATAGCGGGGTCCTCTTTCTCAGACGCCGCGCAAT
131 ATAGCGGCGCGTAAGTCTAAGACGCCGCGAAATAGCGGCGTCCTCTTTCTCAAACGCCGCGCAAT
20806 AGCGGCGTCTGTTTGTCAAACGCCGCTATT
196 AGCGGCGTCTGTTTGTCAAACGCCGCTATT
*
20836 TTAATATATGGAGGGAGAGATTTTTTTTTTCCTTTTTGTTGGAGGGAAAAATTCCCTCCCCTAAA
1 TTAATATATGGAGGGAGAGATTTTTTTTTTCCCTTTT-TTGGAGGGAAAAATTCCCTCCCCTAAA
* *
20901 ACAAAGAAATATTTACAACTACACGGCTATAAAATATAGCGGCGTCATGGTGCTAGACGCCGCGA
65 ACAAAGAAAAATTTACAACTACACGGCTATAAAATATAGCGGCGTCATGGTGCTAGACGCCGCAA
* *** *
20966 AATAGCGGCGTCTTCTTTCTCAA-ACGCCGCGAAATAGCGGCGT-CT-TTCTGTCAAACGCCGC
130 AATAGCGGCG-CGTAAGTCT-AAGACGCCGCGAAATAGCGGCGTCCTCTT-TCTCAAACGCCGC
21027 TATATTAATA
Statistics
Matches: 172, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
225 36 0.21
226 111 0.65
227 23 0.13
228 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (225 bp):
TTAATATATGGAGGGAGAGATTTTTTTTTTCCCTTTTTTGGAGGGAAAAATTCCCTCCCCTAAAA
CAAAGAAAAATTTACAACTACACGGCTATAAAATATAGCGGCGTCATGGTGCTAGACGCCGCAAA
ATAGCGGCGCGTAAGTCTAAGACGCCGCGAAATAGCGGCGTCCTCTTTCTCAAACGCCGCGCAAT
AGCGGCGTCTGTTTGTCAAACGCCGCTATT
Found at i:21172 original size:32 final size:32
Alignment explanation
Indices: 21136--21210 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
21126 AATATATAGC
* * *
21136 GACGCCACTATTTAGCGGCGTCTGTTTTGTAA
1 GACGCCACTATTTAGCGACATCTGCTTTGTAA
21168 GACGCCACTATTTAGCGACATCTGCTTTGTAA
1 GACGCCACTATTTAGCGACATCTGCTTTGTAA
*
21200 GACGCCGCTAT
1 GACGCCACTAT
21211 CTTCAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (32 bp):
GACGCCACTATTTAGCGACATCTGCTTTGTAA
Found at i:21552 original size:10 final size:10
Alignment explanation
Indices: 21537--21561 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
21527 GTTGTTTGAT
21537 TTTTGTGGAA
1 TTTTGTGGAA
21547 TTTTGTGGAA
1 TTTTGTGGAA
21557 TTTTG
1 TTTTG
21562 GTGTTTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (10 bp):
TTTTGTGGAA
Found at i:22574 original size:22 final size:22
Alignment explanation
Indices: 22520--22576 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
22510 CTAAATGGTG
*
22520 GGAAAATCTTCTTATTTATTTT
1 GGAAAATCTTTTTATTTATTTT
22542 GGAAAATCTTTTTATTTATTTT
1 GGAAAATCTTTTTATTTATTTT
22564 GGAAAATCTTTTT
1 GGAAAATCTTTTT
22577 TCCATCCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.28, C:0.07, G:0.11, T:0.54
Consensus pattern (22 bp):
GGAAAATCTTTTTATTTATTTT
Done.