Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013036.1 Corchorus olitorius cultivar O-4 contig13069, 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: 161580
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:11992 original size:14 final size:14
Alignment explanation
Indices: 11973--11999 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11963 AACTAACCAG
11973 TATAACCAGTATTA
1 TATAACCAGTATTA
11987 TATAACCAGTATT
1 TATAACCAGTATT
12000 TATTTTAACA
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:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (14 bp):
TATAACCAGTATTA
Found at i:13135 original size:40 final size:41
Alignment explanation
Indices: 13069--13146 Score: 124
Period size: 41 Copynumber: 1.9 Consensus size: 41
13059 ACTCAATTTT
*
13069 AAAAAATTGGATGGGATCTTTCCCCT-AATTGAAAACTTTG
1 AAAAAATTGGATAGGATCTTTCCCCTAAATTGAAAACTTTG
13109 AAAAAGATTGGATAGGATCTTT-CCCTAAATTGAAAACT
1 AAAAA-ATTGGATAGGATCTTTCCCCTAAATTGAAAACT
13147 GAATGTGATC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 9 0.26
41 26 0.74
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (41 bp):
AAAAAATTGGATAGGATCTTTCCCCTAAATTGAAAACTTTG
Found at i:13290 original size:40 final size:37
Alignment explanation
Indices: 13181--13351 Score: 234
Period size: 40 Copynumber: 4.4 Consensus size: 37
13171 AAGACCTAAA
* *
13181 TTGAATACTTTGAAAACTTGATGGGATCTTTCCCTAAA
1 TTGAAAACTTTGAAAACTTGATGGGATCTTTCCC-AAT
*
13219 TTGAAAACTTTGAAGACTTGATGGGATCTTTCCCAAT
1 TTGAAAACTTTGAAAACTTGATGGGATCTTTCCCAAT
*
13256 TTGAAATACTTTTGAAAAGCTAGATGGGATCTTTCCCAAT
1 TTGAAA-AC-TTTGAAAA-CTTGATGGGATCTTTCCCAAT
13296 TTGAAGAACTTTTGAAAAACTTGATGGGATCTTTCCCAAT
1 TTGAA-AAC-TTTG-AAAACTTGATGGGATCTTTCCCAAT
13336 TTGAAAAACTTTGAAA
1 TTG-AAAACTTTGAAA
13352 GAAATTCCTT
Statistics
Matches: 121, Mismatches: 6, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
37 8 0.07
38 37 0.31
39 11 0.09
40 58 0.48
41 7 0.06
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (37 bp):
TTGAAAACTTTGAAAACTTGATGGGATCTTTCCCAAT
Found at i:14127 original size:17 final size:17
Alignment explanation
Indices: 14094--14164 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
14084 ATGCATAAAT
* *
14094 AAAAGCCCAAGTAATAA
1 AAAAGCCCAAATTATAA
14111 AAAAGCCCAAATTATAA
1 AAAAGCCCAAATTATAA
* *
14128 ATAATG-CCAAATTAAAA
1 A-AAAGCCCAAATTATAA
* *
14145 TAAAAACCCAAATCATAA
1 -AAAAGCCCAAATTATAA
14163 AA
1 AA
14165 GGTACCCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
17 30 0.70
18 13 0.30
ACGTcount: A:0.61, C:0.17, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAAGCCCAAATTATAA
Found at i:14163 original size:35 final size:35
Alignment explanation
Indices: 14069--14163 Score: 102
Period size: 35 Copynumber: 2.6 Consensus size: 35
14059 AACTAGACTC
*
14069 AAAACAAAAACCCAAATGCATAAATAAAAGCCCAAGT
1 AAAA-AAAAACCCAAAT-CATAAATAAAAGCCAAAGT
* * * *
14106 AATAAAAAAGCCCAAATTATAAAT-AATGCCAAATT
1 AA-AAAAAAACCCAAATCATAAATAAAAGCCAAAGT
14141 AAAATAAAAACCCAAATCATAAA
1 AAAA-AAAAACCCAAATCATAAA
14164 AGGTACCCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
34 2 0.04
35 26 0.53
36 6 0.12
37 13 0.27
38 2 0.04
ACGTcount: A:0.61, C:0.18, G:0.05, T:0.16
Consensus pattern (35 bp):
AAAAAAAAACCCAAATCATAAATAAAAGCCAAAGT
Found at i:22823 original size:9 final size:9
Alignment explanation
Indices: 22809--22839 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
22799 ATCGACCCAA
22809 TCAAGCAAT
1 TCAAGCAAT
22818 TCAAGCAAT
1 TCAAGCAAT
22827 TCAAGCAAT
1 TCAAGCAAT
22836 TCAA
1 TCAA
22840 AGCATTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.23
Consensus pattern (9 bp):
TCAAGCAAT
Found at i:26575 original size:11 final size:11
Alignment explanation
Indices: 26559--26584 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
26549 TCCTTGCCTA
26559 AAAACTAGAAG
1 AAAACTAGAAG
26570 AAAACTAGAAG
1 AAAACTAGAAG
26581 AAAA
1 AAAA
26585 GAAATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:29095 original size:93 final size:93
Alignment explanation
Indices: 28997--29168 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
28987 TAGTAATATG
28997 GTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAAT
1 GTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAAT
29062 AAAACTATAAAAGTAAAATAGTATAATA
66 AAAACTATAAAAGTAAAATAGTATAATA
** *
29090 GTAAAAATAAAATATTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGATT
1 GTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAAT
*
29155 AAATCTATAAAAGT
66 AAAACTATAAAAGT
29169 TTAAACAATG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.52, C:0.01, G:0.12, T:0.35
Consensus pattern (93 bp):
GTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAAT
AAAACTATAAAAGTAAAATAGTATAATA
Found at i:30160 original size:16 final size:16
Alignment explanation
Indices: 30112--30160 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
30102 AAGATTTTTG
30112 TTAGTTTATATTATAA
1 TTAGTTTATATTATAA
* *
30128 TT-GTTTTTGTTCA-AA
1 TTAGTTTATATT-ATAA
30143 TTAGTTTATATTATAA
1 TTAGTTTATATTATAA
30159 TT
1 TT
30161 GAAAAAAGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (16 bp):
TTAGTTTATATTATAA
Found at i:30719 original size:6 final size:6
Alignment explanation
Indices: 30690--30736 Score: 67
Period size: 6 Copynumber: 7.5 Consensus size: 6
30680 GTACTTTTTA
*
30690 ATATAG TATATAG AGTATAA ATATAG ATATAG ATATAG ATATAG ATA
1 ATATAG -ATATAG A-TATAG ATATAG ATATAG ATATAG ATATAG ATA
30737 GATTAATTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
6 26 0.70
7 11 0.30
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:35655 original size:114 final size:114
Alignment explanation
Indices: 35534--35752 Score: 359
Period size: 114 Copynumber: 1.9 Consensus size: 114
35524 TGAAAAAAAG
35534 TTTGCAGGGTTGTTGCAGAAAGTGGCGCAGGACCAGAGAGAAAAT-AGTAACGGAGCTTAATTTT
1 TTTGCAGGGTTGTTGCAGAAAGTGGCGCAGGACCAGAGAGAAAATAAG-AACGGAGCTTAATTTT
* *
35598 TTGCACAGAGCAAATTTGTAGCTGCATGAGCGTGTTGAAAAAAGATAGAT
65 TTGCACAGAGCAAATTTGTAGCTGCAGGAGCGTCTTGAAAAAAGATAGAT
* *
35648 TTTGCAGGGTTGTTGCAGAAAGTGGCGCAGGACCAGAGAGAAAATAAGCACGGAGCTTAGTTTTT
1 TTTGCAGGGTTGTTGCAGAAAGTGGCGCAGGACCAGAGAGAAAATAAGAACGGAGCTTAATTTTT
* * *
35713 TGCGCGGAGCAAATTTGTAGCTGCAGGAGGGTCTTGAAAA
66 TGCACAGAGCAAATTTGTAGCTGCAGGAGCGTCTTGAAAA
35753 CTGAAGGGGG
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
114 95 0.98
115 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (114 bp):
TTTGCAGGGTTGTTGCAGAAAGTGGCGCAGGACCAGAGAGAAAATAAGAACGGAGCTTAATTTTT
TGCACAGAGCAAATTTGTAGCTGCAGGAGCGTCTTGAAAAAAGATAGAT
Found at i:50071 original size:114 final size:115
Alignment explanation
Indices: 49937--50176 Score: 403
Period size: 114 Copynumber: 2.1 Consensus size: 115
49927 GAGGCTGGCT
*
49937 CGTGTTTAAAAAAGATAGATTTTGCAGGGTTGCTGCAGAAAATGGCGCAGGG-TCAGAGAGAAAA
1 CGTGTTGAAAAAAGATAGATTTTGCAGGGTTGCTGCAGAAAATGGCGCAGGGCT-AGAGAGAAAA
*
50001 TAAGCACGGAGCTTAG-TTTTTTGCACTGAGCAAATTTGTAGCTGCAGGAG
65 TAAGCACGGAGCTTAGTTTTTTTGCACAGAGCAAATTTGTAGCTGCAGGAG
* *
50051 CGTGTTGAAAAAAGATAGATTTTGCAGGGTTGTTGCAGAAAGTGGCGCAGGGCTAGAGAGAAAAT
1 CGTGTTGAAAAAAGATAGATTTTGCAGGGTTGCTGCAGAAAATGGCGCAGGGCTAGAGAGAAAAT
50116 AAGCACGGAGCTTAGTTTTTTTGCACAGAGCAAATTTGTAGCTGCAGGAG
66 AAGCACGGAGCTTAGTTTTTTTGCACAGAGCAAATTTGTAGCTGCAGGAG
* *
50166 CATCTTGAAAA
1 CGTGTTGAAAA
50177 CTGAAGGGGG
Statistics
Matches: 118, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
114 75 0.64
115 43 0.36
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (115 bp):
CGTGTTGAAAAAAGATAGATTTTGCAGGGTTGCTGCAGAAAATGGCGCAGGGCTAGAGAGAAAAT
AAGCACGGAGCTTAGTTTTTTTGCACAGAGCAAATTTGTAGCTGCAGGAG
Found at i:56203 original size:235 final size:235
Alignment explanation
Indices: 55787--56248 Score: 789
Period size: 235 Copynumber: 2.0 Consensus size: 235
55777 TAATATGTAG
*
55787 TATATATATTTAGTCACTTAACTTTAAATGAATTTCTATTTTGGTCACTTAACTAAGAAAAGTTA
1 TATAAATATTTAGTCACTTAACTTTAAATGAATTTCTATTTTGGTCACTTAACTAAGAAAAGTTA
* *
55852 CAATTTGATCACTTAACTTTGTAAAATTGAATATTTTAATCACTAAACCCTTAATGTGCTTATGT
66 CAATTTGATCACTTAACTTTGTAAAACTGAATATTTTAATCACTAAAACCTTAATGTGCTTATGT
* *
55917 GACATGTCAAGTGGCATAGTCACATCATTCTAATAGTGATTTGGTGACCAAAAGATTCAATTTTA
131 GACATGTCAAGTGGCATAGTCACATCATTCCAATAGTGATTTGCTGACCAAAAGATTCAATTTTA
*
55982 CAAATATAAATGACCAAAACGTTATTTTTTATGGAACTAA
196 CAAATATAAATAACCAAAACGTTATTTTTTATGGAACTAA
* * *
56022 TATAAATATTTAGTCACTTAACTTTAAGTGAGTTTCTATTTTGGTCACTTAACTATGAAAAGTTA
1 TATAAATATTTAGTCACTTAACTTTAAATGAATTTCTATTTTGGTCACTTAACTAAGAAAAGTTA
* *
56087 CAATTTGATCACTTAACTTTGTAAAACTGAATATTTTAGTCACTAAAACCTTAATTTGCTTATGT
66 CAATTTGATCACTTAACTTTGTAAAACTGAATATTTTAATCACTAAAACCTTAATGTGCTTATGT
* *
56152 GGCATGTCACGTGGCATAGTCACATCATTCCAATAGTGATTTGCTGACCAAAAGATTCAATTTTA
131 GACATGTCAAGTGGCATAGTCACATCATTCCAATAGTGATTTGCTGACCAAAAGATTCAATTTTA
* *
56217 CAAATATAAGTAATCAAAACGTTATTTTTTAT
196 CAAATATAAATAACCAAAACGTTATTTTTTAT
56249 AGTTTAATGA
Statistics
Matches: 212, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
235 212 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (235 bp):
TATAAATATTTAGTCACTTAACTTTAAATGAATTTCTATTTTGGTCACTTAACTAAGAAAAGTTA
CAATTTGATCACTTAACTTTGTAAAACTGAATATTTTAATCACTAAAACCTTAATGTGCTTATGT
GACATGTCAAGTGGCATAGTCACATCATTCCAATAGTGATTTGCTGACCAAAAGATTCAATTTTA
CAAATATAAATAACCAAAACGTTATTTTTTATGGAACTAA
Found at i:60616 original size:21 final size:22
Alignment explanation
Indices: 60571--60613 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
60561 AAAGATTATA
*
60571 TTATTTAAAAATCTTATAAGAG
1 TTATTAAAAAATCTTATAAGAG
60593 TTATTAAATAAATCTTATAAG
1 TTATTAAA-AAATCTTATAAG
60614 TTACTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (22 bp):
TTATTAAAAAATCTTATAAGAG
Found at i:60621 original size:21 final size:23
Alignment explanation
Indices: 60579--60621 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
60569 TATTATTTAA
*
60579 AAATCTTATAAGAGTTATTAAAT
1 AAATCTTATAAGAGTTACTAAAT
60602 AAATCTTAT-A-AGTTACTAAA
1 AAATCTTATAAGAGTTACTAAA
60622 AATACACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 1 0.05
23 9 0.47
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (23 bp):
AAATCTTATAAGAGTTACTAAAT
Found at i:63049 original size:99 final size:101
Alignment explanation
Indices: 62877--63111 Score: 278
Period size: 100 Copynumber: 2.3 Consensus size: 101
62867 AGTTTTAGAG
* * * * *
62877 TTAAAATATTTATTTATAGAGTTTTAGATATAAAAAAAATTAGTCCTAAGTTAATAAGGTTTGAC
1 TTAAAATATTTATTTCTAGGGTTTTAG--A-AAAAAAAATTAGCCCCAAATTAATAAGGTTTGAC
* **
62942 ACTAAATT-AAAAAATGATTTTAAGGGTATGTCCTAAAC
63 ACTAAATTAAAAAAATGAATTTAAGGGTATAACCTAAAC
*
62980 TTAAAATATTTATTTCTAGGGTTTTAGAAAAAAAAA-TAGCCCCAAATTAATAAGGTTT-ACCCC
1 TTAAAATATTTATTTCTAGGGTTTTAGAAAAAAAAATTAGCCCCAAATTAATAAGGTTTGA-CAC
*
63043 TAAATTAAAAAAATTAATTTAAGGGTATAACCTAAAC
65 TAAATTAAAAAAATGAATTTAAGGGTATAACCTAAAC
* * * *
63080 TTAAAATGTTTGTTCCCTAGGATTTTAGAAAA
1 TTAAAATATTTATT-TCTAGGGTTTTAGAAAA
63112 CATATTAAAT
Statistics
Matches: 115, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
98 1 0.01
99 27 0.23
100 46 0.40
101 16 0.14
103 25 0.22
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.35
Consensus pattern (101 bp):
TTAAAATATTTATTTCTAGGGTTTTAGAAAAAAAAATTAGCCCCAAATTAATAAGGTTTGACACT
AAATTAAAAAAATGAATTTAAGGGTATAACCTAAAC
Found at i:64029 original size:31 final size:31
Alignment explanation
Indices: 63986--64046 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
63976 CAAAAATATC
* * *
63986 AGTCCTTGTACTCATAAGATTGGGTTAATTT
1 AGTCCTTATACTCACAAGATTGGGTCAATTT
*
64017 AGTCCTTATACTCACAATATTGGGTCAATT
1 AGTCCTTATACTCACAAGATTGGGTCAATT
64047 GAGTATGTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (31 bp):
AGTCCTTATACTCACAAGATTGGGTCAATTT
Found at i:65826 original size:17 final size:16
Alignment explanation
Indices: 65800--65833 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
65790 GTGATTATTT
65800 TAATCCAAAAATAATTA
1 TAATCC-AAAATAATTA
*
65817 TAATCTAAAATAATTA
1 TAATCCAAAATAATTA
65833 T
1 T
65834 GAAAAGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATCCAAAATAATTA
Found at i:66549 original size:18 final size:18
Alignment explanation
Indices: 66526--66561 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
66516 GATGGCTTTT
*
66526 GGCAGTTTTTTTTAAATG
1 GGCAGTTTTTTTAAAATG
66544 GGCAGTTTTTTTAAAATG
1 GGCAGTTTTTTTAAAATG
66562 ATATAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (18 bp):
GGCAGTTTTTTTAAAATG
Found at i:94982 original size:22 final size:23
Alignment explanation
Indices: 94957--95000 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
94947 ATATCCACAT
94957 ACAATTAAT-ATATAAT-TAAAAC
1 ACAATTAATCATA-AATATAAAAC
94979 ACAATTAATCATAAATATAAAA
1 ACAATTAATCATAAATATAAAA
95001 TAGTAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (23 bp):
ACAATTAATCATAAATATAAAAC
Found at i:96262 original size:53 final size:53
Alignment explanation
Indices: 96195--96302 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
96185 GAGCAATAAT
*
96195 ATATATATACTATATATTATTTTTAGTGATTATAGAAATTACTTAAAGGCCAA
1 ATATATATACTATATATTATTTTTAGTGACTATAGAAATTACTTAAAGGCCAA
* *
96248 ATATATATATTATATATTATTTTTAGTGACTATGGAAATTACTTAAAGGCCAA
1 ATATATATACTATATATTATTTTTAGTGACTATAGAAATTACTTAAAGGCCAA
96301 AT
1 AT
96303 TGAGGATTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (53 bp):
ATATATATACTATATATTATTTTTAGTGACTATAGAAATTACTTAAAGGCCAA
Found at i:109056 original size:33 final size:33
Alignment explanation
Indices: 109009--109071 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
108999 TTGCTTCCTG
109009 TCAAAAGAAAACAAGAAACTTTAGCAACTTCAC
1 TCAAAAGAAAACAAGAAACTTTAGCAACTTCAC
*
109042 TCAAGAGAAAACAAGAAACTTTAGCAACTT
1 TCAAAAGAAAACAAGAAACTTTAGCAACTT
109072 TTCAACTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.51, C:0.19, G:0.11, T:0.19
Consensus pattern (33 bp):
TCAAAAGAAAACAAGAAACTTTAGCAACTTCAC
Found at i:110030 original size:2 final size:2
Alignment explanation
Indices: 110023--110050 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
110013 CAATGCCCTA
110023 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
110051 TCTTGTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115238 original size:2 final size:2
Alignment explanation
Indices: 115231--115258 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
115221 GACAAATGCG
115231 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
115259 CGTACTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:117527 original size:6 final size:6
Alignment explanation
Indices: 117516--117543 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
117506 TTTAAGAGAT
117516 TAAAGA TAAAGA TAAAGA TAAAGA TAAA
1 TAAAGA TAAAGA TAAAGA TAAAGA TAAA
117544 AAAAAAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (6 bp):
TAAAGA
Found at i:117550 original size:18 final size:18
Alignment explanation
Indices: 117516--117551 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
117506 TTTAAGAGAT
* *
117516 TAAAGATAAAGATAAAGA
1 TAAAGATAAAAAAAAAGA
117534 TAAAGATAAAAAAAAAGA
1 TAAAGATAAAAAAAAAGA
117552 AGTACCGCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (18 bp):
TAAAGATAAAAAAAAAGA
Found at i:124965 original size:29 final size:30
Alignment explanation
Indices: 124914--124970 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
124904 CTTACACAAA
* *
124914 ACAGTCAAATAAACTCTTAAACT-TTAATT
1 ACAGCCAAATAAACCCTTAAACTCTTAATT
* *
124943 ACAGCCAAATAAGCCCTTGAACTCTTAA
1 ACAGCCAAATAAACCCTTAAACTCTTAA
124971 AAAATATCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (30 bp):
ACAGCCAAATAAACCCTTAAACTCTTAATT
Found at i:141888 original size:15 final size:17
Alignment explanation
Indices: 141858--141889 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
141848 TGCGAAATCA
141858 TTTTCCTCTATTTATCT
1 TTTTCCTCTATTTATCT
141875 TTTTCCT-T-TTTATCT
1 TTTTCCTCTATTTATCT
141890 CACGCAGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.09, C:0.22, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTCCTCTATTTATCT
Found at i:143031 original size:22 final size:22
Alignment explanation
Indices: 143006--143109 Score: 115
Period size: 22 Copynumber: 4.8 Consensus size: 22
142996 TTGAATATTT
143006 TTATGAAATTTTGATAATTACC
1 TTATGAAATTTTGATAATTACC
* *
143028 TTATTAAATTTTGATAACTACC
1 TTATGAAATTTTGATAATTACC
*
143050 CTATGAAATTTTGATAATTA-C
1 TTATGAAATTTTGATAATTACC
* *
143071 GTATGAAATTATGATAA--ACTC
1 TTATGAAATTTTGATAATTAC-C
*
143092 TATATGAAACTTTGATAA
1 T-TATGAAATTTTGATAA
143110 CCTAACTATA
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.01
21 17 0.25
22 51 0.74
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (22 bp):
TTATGAAATTTTGATAATTACC
Found at i:143098 original size:43 final size:44
Alignment explanation
Indices: 143007--143109 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 44
142997 TGAATATTTT
* * * *
143007 TATGAAATTTTGATAATTACCTTATTAAATTTTGATAACTACCC
1 TATGAAATTTTGATAATTACCGTATGAAATTATGATAACTACCA
*
143051 TATGAAATTTTGATAATTA-CGTATGAAATTATGATAAACT-CTA
1 TATGAAATTTTGATAATTACCGTATGAAATTATGAT-AACTACCA
*
143094 TATGAAACTTTGATAA
1 TATGAAATTTTGATAA
143110 CCTAACTATA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
43 29 0.56
44 23 0.44
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.41
Consensus pattern (44 bp):
TATGAAATTTTGATAATTACCGTATGAAATTATGATAACTACCA
Found at i:143124 original size:65 final size:64
Alignment explanation
Indices: 143007--143131 Score: 146
Period size: 65 Copynumber: 1.9 Consensus size: 64
142997 TGAATATTTT
* * * * * *
143007 TATGAAATTTTGATAATTACCTTATTAAATTTTGATAACTACCCTATGAAATTTTGATAATTACG
1 TATGAAATTATGATAA-TACCTTATGAAACTTTGATAACTACACTATAAAATTTTAATAATTACG
143072 TATGAAATTATGATAA-ACTCTATATGAAACTTTGATAACCTA-ACTATAAAATTTTAATAA
1 TATGAAATTATGATAATAC-CT-TATGAAACTTTGATAA-CTACACTATAAAATTTTAATAA
143132 ACCTTCCTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
63 2 0.04
64 2 0.04
65 44 0.86
66 3 0.06
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (64 bp):
TATGAAATTATGATAATACCTTATGAAACTTTGATAACTACACTATAAAATTTTAATAATTACG
Found at i:144145 original size:35 final size:35
Alignment explanation
Indices: 144099--144165 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
144089 TAAGCTTTGT
* *
144099 AAACATCTTAAGACCCCACTAACCTCAGTATCTCC
1 AAACACCTTAAGACCCCACTAACCTCAATATCTCC
* * *
144134 AAACACCTTAAGATCCTACTAACTTCAATATC
1 AAACACCTTAAGACCCCACTAACCTCAATATC
144166 AAAGAGGATC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.25
Consensus pattern (35 bp):
AAACACCTTAAGACCCCACTAACCTCAATATCTCC
Found at i:146621 original size:21 final size:21
Alignment explanation
Indices: 146596--146678 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
146586 TATCTTAGAT
146596 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
146617 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
146638 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
146660 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
146679 TTACTAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:146629 original size:25 final size:25
Alignment explanation
Indices: 146598--146646 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
146588 TCTTAGATAT
*
146598 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
146623 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
146647 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:147386 original size:24 final size:24
Alignment explanation
Indices: 147354--147408 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
147344 TCTTTGTTTT
*
147354 TTAAAATGTTTTGTCTAAATAAAA
1 TTAAAATGTTTTATCTAAATAAAA
147378 TTAAAATGTTTTATCTAAATAAAA
1 TTAAAATGTTTTATCTAAATAAAA
147402 TTAAAAT
1 TTAAAAT
147409 TTTAATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (24 bp):
TTAAAATGTTTTATCTAAATAAAA
Found at i:150002 original size:30 final size:31
Alignment explanation
Indices: 149938--150013 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
149928 ACTAAATATC
* *
149938 CAAAAAAATCCCTTATGTTTTTCTTATAGGA
1 CAAAATAATCCCTTATATTTTTCTTATAGGA
* *
149969 CAAAATAATCCCTTATATTTTT-TTTTGGGA
1 CAAAATAATCCCTTATATTTTTCTTATAGGA
*
149999 CAAATTAATCCCTTA
1 CAAAATAATCCCTTA
150014 CGTTTCAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 20 0.50
31 20 0.50
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (31 bp):
CAAAATAATCCCTTATATTTTTCTTATAGGA
Found at i:150962 original size:25 final size:25
Alignment explanation
Indices: 150928--150977 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
150918 TGAGATTTAT
150928 TTGGAGGAAGAAGACGAGCCAAAGG
1 TTGGAGGAAGAAGACGAGCCAAAGG
150953 TTGGAGGAAGAAGACGAGCCAAAGG
1 TTGGAGGAAGAAGACGAGCCAAAGG
150978 GGAGTTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.40, T:0.08
Consensus pattern (25 bp):
TTGGAGGAAGAAGACGAGCCAAAGG
Found at i:151169 original size:22 final size:22
Alignment explanation
Indices: 151127--151175 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
151117 TTTACTTTTT
* *
151127 TTTTTTTCCTTTGTCCATTTCG
1 TTTTATTCCTTTGTCCATTTCA
*
151149 TTTTATTCCTTT-TCCCTTTTCA
1 TTTTATTCCTTTGT-CCATTTCA
151171 TTTTA
1 TTTTA
151176 ATTTTCCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.08, C:0.22, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTTATTCCTTTGTCCATTTCA
Found at i:151428 original size:29 final size:31
Alignment explanation
Indices: 151386--151459 Score: 116
Period size: 29 Copynumber: 2.5 Consensus size: 31
151376 CTCACTTTTG
*
151386 AAACGTAAGGGATTAATTTGTCCC-AAA-AA
1 AAACATAAGGGATTAATTTGTCCCGAAAGAA
*
151415 AAACATAAGGGATTATTTTGTCCCGAAAGAA
1 AAACATAAGGGATTAATTTGTCCCGAAAGAA
151446 AAACATAAGGGATT
1 AAACATAAGGGATT
151460 TTTTTGGGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
29 22 0.54
30 3 0.07
31 16 0.39
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (31 bp):
AAACATAAGGGATTAATTTGTCCCGAAAGAA
Found at i:159458 original size:331 final size:322
Alignment explanation
Indices: 158830--159473 Score: 691
Period size: 331 Copynumber: 1.9 Consensus size: 322
158820 ATTACCAAAA
* *
158830 AATGTAAGGTTATTGAATTAATTGATACTATTATACCTCTTTTATGATCATTATAGGTTTTTCAA
1 AATGTAAGGTCATTGAATTAATTGATACTAATATACCTCTTTTATGATCATTATAGGTTTTTCAA
*
158895 TAACTTTTGTTAAAAAAAAAAAGGTAAATATTCACCATTGATGAAAGTTTACTAATGTTATTAAG
66 TAAC-TTTGTCAAAAAAAAAAAGGTAAATATTCACCATTGATGAAAGTTTACTAATG-T-TT---
*
158960 AATTTAAGGATTAGTAAATACATTTTTAATAACTTTTATAGCTTTATTAGTAAACTTAAGTAATA
125 AATTTAAGGATTAGTAAATACATTTTTAATAACTTTTATAGCTTTATTAGTAAACTGAAGTAATA
* * * *
159025 AAATTGGTAACTTTTATTAATGATAAAAAGTTAATAAGGATGTAAGGTTATTTCCATCTCGATAG
190 AAATTGGTAACTTTTATTAATGATAAAAAGTTAATAAGGATGTAAGATTACTTCAATCTAGATAG
* *
159090 TACTATAATGTTTTCCATAATCTTTATAACCTAAGTAATCTTAAATAAGAAAATTAGTATTATAC
255 TAATATAATGTTTTCCATAATCCTTAT-A--TAAGTAATCTTAAATAAGAAAATTAGTATTATAC
159155 CTTTAT
317 CTTTAT
* * * * * *
159161 AATGTAAGGTCATTGAATTAGTTGATAGTAATATATCTTTTTTATGATTATTATAGGTTTTTCAG
1 AATGTAAGGTCATTGAATTAATTGATACTAATATACCTCTTTTATGATCATTATAGGTTTTTCAA
* * * *
159226 TAAC-TT-TCAAGGAAAAAAATGGTAAATCTTCATCATTGATGAAAGTTTGTACTAATG-TT-A-
66 TAACTTTGTCAA-AAAAAAAAAGGTAAATATTCACCATTGATGAAAG-TT-TACTAATGTTTAAT
* * *
159286 TTAAGGATTGGTAAATACAATTTTT-ATAAGTTTTATAGCTTGT-TTAGTAGATTGCTGAAGTAA
128 TTAAGGATTAGTAAATAC-ATTTTTAATAACTTTTATAGCTT-TATTAGTA-A--ACTGAAGTAA
*
159349 TAAAATTGGAAATTAACTTTCATTTGATTAGAAGTTGCT-AAAA-TTAATAAGGATGTAAGATTA
188 TAAAATTGG----TAAC--T--TTT-ATT--AA--TGATAAAAAGTTAATAAGGATGTAAGATTA
* * *
159412 CTTGAATCTAGATAGTAATATAATGTTTTTCATAA-CCTT-T-TAAGTAATCTTAGATAAGAAAA
240 CTTCAATCTAGATAGTAATATAATGTTTTCCATAATCCTTATATAAGTAATCTTAAATAAGAAAA
159474 CCTTTATAAC
Statistics
Matches: 265, Mismatches: 27, Indels: 42
0.79 0.08 0.13
Matches are distributed among these distances:
323 38 0.14
324 9 0.03
326 17 0.06
328 5 0.02
329 32 0.12
330 6 0.02
331 90 0.34
332 1 0.00
334 3 0.01
335 4 0.02
336 3 0.01
337 50 0.19
338 4 0.02
339 3 0.01
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (322 bp):
AATGTAAGGTCATTGAATTAATTGATACTAATATACCTCTTTTATGATCATTATAGGTTTTTCAA
TAACTTTGTCAAAAAAAAAAAGGTAAATATTCACCATTGATGAAAGTTTACTAATGTTTAATTTA
AGGATTAGTAAATACATTTTTAATAACTTTTATAGCTTTATTAGTAAACTGAAGTAATAAAATTG
GTAACTTTTATTAATGATAAAAAGTTAATAAGGATGTAAGATTACTTCAATCTAGATAGTAATAT
AATGTTTTCCATAATCCTTATATAAGTAATCTTAAATAAGAAAATTAGTATTATACCTTTAT
Found at i:161553 original size:2 final size:2
Alignment explanation
Indices: 161548--161580 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
161538 TTTGTTCGAT
161548 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.