Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015341.1 Corchorus capsularis cultivar CVL-1 contig15362, 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: 83160
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1991 original size:20 final size:21
Alignment explanation
Indices: 1966--2007 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1956 TCTTGGGTTC
1966 TACTCTCACGGAA-TGTGAGT
1 TACTCTCACGGAATTGTGAGT
*
1986 TACTCTCATGGAATTGTGAGT
1 TACTCTCACGGAATTGTGAGT
2007 T
1 T
2008 TTCTCTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (21 bp):
TACTCTCACGGAATTGTGAGT
Found at i:3013 original size:23 final size:20
Alignment explanation
Indices: 2962--3018 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 20
2952 ATTAAAATAA
2962 ATATAATATATATTTATATT
1 ATATAATATATATTTATATT
* *
2982 ATATGATATATCAGTTTTTATAT
1 ATATAATATAT-A-TTTATAT-T
3005 ATATAATATATATT
1 ATATAATATATATT
3019 AAAAATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 10 0.32
21 3 0.10
22 7 0.23
23 11 0.35
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (20 bp):
ATATAATATATATTTATATT
Found at i:8360 original size:28 final size:28
Alignment explanation
Indices: 8320--8376 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
8310 ATCAAATACA
8320 ACTTTCAGACCCTTGACGAAAGTCGTAG
1 ACTTTCAGACCCTTGACGAAAGTCGTAG
8348 ACTTTCAGACCCTTGACGAAAGTCGTAG
1 ACTTTCAGACCCTTGACGAAAGTCGTAG
8376 A
1 A
8377 TAACACAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (28 bp):
ACTTTCAGACCCTTGACGAAAGTCGTAG
Found at i:10664 original size:28 final size:28
Alignment explanation
Indices: 10617--10685 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 28
10607 ACCGACTGAT
** ** *
10617 TATATATAAATATATAATATAGTTTTTA
1 TATATATATTTATATAATATAGTAATAA
* *
10645 TATTTATATTTATATTATATAGTAATAA
1 TATATATATTTATATAATATAGTAATAA
10673 TATATATATTTAT
1 TATATATATTTAT
10686 CAGAAATTAG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (28 bp):
TATATATATTTATATAATATAGTAATAA
Found at i:27607 original size:16 final size:16
Alignment explanation
Indices: 27583--27622 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
27573 TTCTGAATTG
*
27583 AATTCTGAATTCTGAA
1 AATTGTGAATTCTGAA
27599 AATTGTGAATTCTGAA
1 AATTGTGAATTCTGAA
*
27615 ATTTGTGA
1 AATTGTGA
27623 TTTGCGAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.40
Consensus pattern (16 bp):
AATTGTGAATTCTGAA
Found at i:27860 original size:12 final size:12
Alignment explanation
Indices: 27839--27868 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
27829 ACTGAATATT
27839 CAGA-TTGGAAA
1 CAGATTTGGAAA
27850 CAGATTTGGAAA
1 CAGATTTGGAAA
27862 CAGATTT
1 CAGATTT
27869 TGATGTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (12 bp):
CAGATTTGGAAA
Found at i:29443 original size:2 final size:2
Alignment explanation
Indices: 29436--29467 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29426 TACCTTTTAC
29436 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
29468 GATTTATTTT
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:32635 original size:26 final size:26
Alignment explanation
Indices: 32604--32664 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
32594 ACATTGATAT
*
32604 ATAATTTTAACCTTAGTTAAAATTGA
1 ATAATTTTAACCTTAATTAAAATTGA
32630 ATAATTTTAACCTTAATTAAAATTGA
1 ATAATTTTAACCTTAATTAAAATTGA
32656 ATAATTTTA
1 ATAATTTTA
32665 TTAATAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (26 bp):
ATAATTTTAACCTTAATTAAAATTGA
Found at i:35895 original size:13 final size:13
Alignment explanation
Indices: 35879--35903 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35869 TGGAATCAAG
35879 GCTTGAAATCGAC
1 GCTTGAAATCGAC
35892 GCTTGAAATCGA
1 GCTTGAAATCGA
35904 GGGTTTCGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (13 bp):
GCTTGAAATCGAC
Found at i:38147 original size:22 final size:22
Alignment explanation
Indices: 38116--38181 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
38106 AAAGATGAGA
*
38116 AAAATCAAATTGAAAATAAAAAT
1 AAAAT-AAATTAAAAATAAAAAT
*
38139 ATAAA-AAATTAAAAATTAAAAT
1 A-AAATAAATTAAAAATAAAAAT
*
38161 AAAATATATTAAAAATAAAAA
1 AAAATAAATTAAAAATAAAAA
38182 AATGCCACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 3 0.08
22 30 0.81
23 1 0.03
24 3 0.08
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAATAAATTAAAAATAAAAAT
Found at i:38169 original size:29 final size:29
Alignment explanation
Indices: 38122--38182 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
38112 GAGAAAAATC
*
38122 AAATTGAAAATAAAAATATAAAAAATTAA
1 AAATTGAAAATAAAAATATAAAAAATAAA
*
38151 AAATT-AAAATAAAATATATTAAAAATAAA
1 AAATTGAAAATAAAA-ATATAAAAAATAAA
38180 AAA
1 AAA
38183 ATGCCACATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 9 0.31
29 20 0.69
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (29 bp):
AAATTGAAAATAAAAATATAAAAAATAAA
Found at i:38177 original size:16 final size:15
Alignment explanation
Indices: 38128--38181 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
38118 AATCAAATTG
*
38128 AAAATAAAAATATAA
1 AAAATAAAAATATTA
*
38143 AAAATTAAAA-ATT-
1 AAAATAAAAATATTA
38156 AAAATAAAATATATTA
1 AAAATAAAA-ATATTA
38172 AAAATAAAAA
1 AAAATAAAAA
38182 AATGCCACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 8 0.24
14 3 0.09
15 13 0.39
16 9 0.27
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAATAAAAATATTA
Found at i:38180 original size:27 final size:27
Alignment explanation
Indices: 38115--38180 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 27
38105 GAAAGATGAG
*
38115 AAAAATCAAATTGAAAATAAAAATATA
1 AAAAATAAAATTGAAAATAAAAATATA
*
38142 AAAAATTAAAAATT-AAAATAAAATATATT
1 AAAAA-T-AAAATTGAAAATAAAA-ATATA
38171 AAAAATAAAA
1 AAAAATAAAA
38181 AAATGCCACA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 9 0.26
28 11 0.32
29 14 0.41
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (27 bp):
AAAAATAAAATTGAAAATAAAAATATA
Found at i:38475 original size:28 final size:28
Alignment explanation
Indices: 38444--38500 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
38434 TATGTTTTTG
*
38444 TTTTAGAACAAAATAATCCGTTATATTT
1 TTTTAGAACAAAATAATCCCTTATATTT
* * * *
38472 TTTTGGGACAAATTAATCCCTTATGTTT
1 TTTTAGAACAAAATAATCCCTTATATTT
38500 T
1 T
38501 AAAAGTGAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.46
Consensus pattern (28 bp):
TTTTAGAACAAAATAATCCCTTATATTT
Found at i:41105 original size:37 final size:40
Alignment explanation
Indices: 41064--41138 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
41054 AAGGAAGGCC
41064 AGTTGAAGT-G-G-AGAAGAAGAAATAAGGGAAAGAAAAG
1 AGTTGAAGTGGAGAAGAAGAAGAAATAAGGGAAAGAAAAG
41101 AGTTGAAGTGGAGAAGAAGAAGAAATAAGGGAAAGAAA
1 AGTTGAAGTGGAGAAGAAGAAGAAATAAGGGAAAGAAA
41139 GGAGAAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
37 9 0.26
38 1 0.03
39 1 0.03
40 24 0.69
ACGTcount: A:0.55, C:0.00, G:0.35, T:0.11
Consensus pattern (40 bp):
AGTTGAAGTGGAGAAGAAGAAGAAATAAGGGAAAGAAAAG
Found at i:41392 original size:29 final size:32
Alignment explanation
Indices: 41344--41424 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
41334 CTCACTTTTG
* *
41344 AAACGTAAGGGATTAATTTG-TCCC-AAA-AA
1 AAACATAAGGGATTATTTTGCTCCCAAAACAA
**
41373 AAGTATAAGGGATTATTTTGCTCCCAAAACAA
1 AAACATAAGGGATTATTTTGCTCCCAAAACAA
*
41405 AAACATAAGGGATTTTTTTG
1 AAACATAAGGGATTATTTTG
41425 GGTATTTAGT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 16 0.38
30 4 0.10
31 3 0.07
32 19 0.45
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (32 bp):
AAACATAAGGGATTATTTTGCTCCCAAAACAA
Found at i:41617 original size:30 final size:30
Alignment explanation
Indices: 41581--41639 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
41571 TCTCACGGAA
41581 TGTGAGTTTTCTTTGTAATTTATTTGTTTC
1 TGTGAGTTTTCTTTGTAATTTATTTGTTTC
41611 TGTGAGTTTTCTTTGTAATTTATTTGTTT
1 TGTGAGTTTTCTTTGTAATTTATTTGTTT
41640 GTAATTTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.14, C:0.05, G:0.17, T:0.64
Consensus pattern (30 bp):
TGTGAGTTTTCTTTGTAATTTATTTGTTTC
Found at i:41642 original size:15 final size:15
Alignment explanation
Indices: 41592--41646 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
41582 GTGAGTTTTC
41592 TTTGTAATTTATTTG
1 TTTGTAATTTATTTG
* * *
41607 TTTCTGTGA-GT-TTTC
1 -TT-TGTAATTTATTTG
41622 TTTGTAATTTATTTG
1 TTTGTAATTTATTTG
41637 TTTGTAATTT
1 TTTGTAATTT
41647 GTAAATAGGG
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
13 4 0.13
14 3 0.10
15 16 0.53
16 3 0.10
17 4 0.13
ACGTcount: A:0.16, C:0.04, G:0.15, T:0.65
Consensus pattern (15 bp):
TTTGTAATTTATTTG
Found at i:44043 original size:22 final size:22
Alignment explanation
Indices: 44015--44207 Score: 96
Period size: 22 Copynumber: 8.7 Consensus size: 22
44005 TTAAAATCAC
44015 TATAAAATTTTGATAACATCCA
1 TATAAAATTTTGATAACATCCA
* *
44037 TATAAAATTTTGATAA-TTACAA
1 TATAAAATTTTGATAACAT-CCA
* * ** *
44059 TATAAAGTTTTTATGATGATAC-
1 TATAAAATTTTGAT-AACATCCA
* * *
44081 TATAAAATTTCGAGAACTTCCA
1 TATAAAATTTTGATAACATCCA
* * * *
44103 TATGAAATTTTGTTAACTTCCC
1 TATAAAATTTTGATAACATCCA
*
44125 TATAAAATTTTG-TTACACTCCCA
1 TATAAAATTTTGATAACA-T-CCA
*
44148 -ATAAAAATTTTAATAACCA-CC-
1 TAT-AAAATTTTGATAA-CATCCA
44169 TAATAAAATTTTGATAAC--CACA
1 T-ATAAAATTTTGATAACATC-CA
*
44191 CTATGAAATTTTGATAA
1 -TATAAAATTTTGATAA
44208 TGTCCCAATG
Statistics
Matches: 128, Mismatches: 29, Indels: 28
0.69 0.16 0.15
Matches are distributed among these distances:
20 1 0.01
21 9 0.07
22 99 0.77
23 14 0.11
24 3 0.02
25 2 0.02
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (22 bp):
TATAAAATTTTGATAACATCCA
Found at i:45976 original size:59 final size:59
Alignment explanation
Indices: 45911--46028 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 59
45901 GGAAATTCTC
* * * *
45911 AGCTCCATTAAGTTGACAAAATCCATTTAAAAAAACAAAAGGGTAAAACTTACAATTAG
1 AGCTCCATCAAATTGACAAAATCCATTCAAAAAAACAAAAGGGAAAAACTTACAATTAG
* *
45970 AGCTCCATCAAATTGACAAAATCCATTCAAAAGAACAAAAGGGAAAAACTTATAATTAG
1 AGCTCCATCAAATTGACAAAATCCATTCAAAAAAACAAAAGGGAAAAACTTACAATTAG
46029 GGTCATCAGG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (59 bp):
AGCTCCATCAAATTGACAAAATCCATTCAAAAAAACAAAAGGGAAAAACTTACAATTAG
Found at i:46399 original size:16 final size:15
Alignment explanation
Indices: 46378--46407 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
46368 AAATGAGAAA
46378 GCGAGAGAAGAAAATG
1 GCGAGAGAA-AAAATG
46394 GCGAGAGAAAAAAT
1 GCGAGAGAAAAAAT
46408 TGAGGATCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.07, G:0.33, T:0.07
Consensus pattern (15 bp):
GCGAGAGAAAAAATG
Found at i:46461 original size:2 final size:2
Alignment explanation
Indices: 46454--46482 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
46444 TAATATTTAA
46454 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46483 TAATTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58245 original size:51 final size:48
Alignment explanation
Indices: 58187--58287 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 48
58177 AAGAATCCGC
58187 CAATTGGTTGCAATCTCTCGGGACTTTCTAATAATAGACTAATACTACAGG
1 CAATTGGTTGCAATCTCTCGGGACTTTC---TAATAGACTAATACTACAGG
58238 CAATTGGTTGCAATCTCTCGGGACTTTCTAATAGACTAATACTACAGG
1 CAATTGGTTGCAATCTCTCGGGACTTTCTAATAGACTAATACTACAGG
58286 CA
1 CA
58288 GGATTTTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
48 22 0.44
51 28 0.56
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (48 bp):
CAATTGGTTGCAATCTCTCGGGACTTTCTAATAGACTAATACTACAGG
Found at i:63739 original size:11 final size:10
Alignment explanation
Indices: 63721--63754 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
63711 GAAGTTCGTG
63721 TTTTGAAGAT
1 TTTTGAAGAT
63731 TTCTTGAAGAT
1 TT-TTGAAGAT
63742 ATTTTGAAGAT
1 -TTTTGAAGAT
63753 TT
1 TT
63755 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:66909 original size:84 final size:84
Alignment explanation
Indices: 66813--66967 Score: 276
Period size: 84 Copynumber: 1.8 Consensus size: 84
66803 AAATATATTT
66813 AAAATTCTAATATATCTAA-TTTTTGCAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATA
1 AAAATTCTAATATATCTAAGTTTTT-CAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATA
66877 AAGAGATTAGATTTAATTAA
65 AAGAGATTAGATTTAATTAA
* *
66897 AAAATTCTAATATATCTAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATATTTATAA
1 AAAATTCTAATATATCTAAGTTTTTCAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAA
66962 AGAGAT
66 AGAGAT
66968 AAAAAAAAGT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
84 63 0.93
85 5 0.07
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (84 bp):
AAAATTCTAATATATCTAAGTTTTTCAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAA
AGAGATTAGATTTAATTAA
Found at i:67202 original size:76 final size:80
Alignment explanation
Indices: 67111--67271 Score: 222
Period size: 86 Copynumber: 2.0 Consensus size: 80
67101 AGAAATAAAT
67111 TTAAAAAATTCTAATACATCTAAGTTTTGT-AATTAAAATAGT-A-AAA-ATAAAATAGTTATAA
1 TTAAAAAATTCTAATACATCTAAGTTTTGTAAATTAAAATAGTAATAAAGATAAAATAGTTATAA
67172 AGAGATTAGATTTAG
66 AGAGATTAGATTTAG
* *
67187 TTAAAAAATTCTAATATATCTAAGTTTTTTAAAATTAAAATAGTAAAATGTTAAAGATAAAATAG
1 TTAAAAAATTCTAATACATCTAAGTTTTGT-AAATTAAAATAGT--AA---TAAAGATAAAATAG
67252 TTATAAAGAGATTAGATTTA
60 TTATAAAGAGATTAGATTTA
67272 ATTAGATAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
76 28 0.38
78 12 0.16
81 1 0.01
85 3 0.04
86 29 0.40
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.37
Consensus pattern (80 bp):
TTAAAAAATTCTAATACATCTAAGTTTTGTAAATTAAAATAGTAATAAAGATAAAATAGTTATAA
AGAGATTAGATTTAG
Found at i:73634 original size:15 final size:16
Alignment explanation
Indices: 73614--73659 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
73604 TACAATTGTC
73614 ATAGTAGTATTAATT-
1 ATAGTAGTATTAATTA
73629 ATAGTAGTATTAATTA
1 ATAGTAGTATTAATTA
* *
73645 ATATTAATATTAATT
1 ATAGTAGTATTAATT
73660 GATCTTTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 15 0.54
16 13 0.46
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (16 bp):
ATAGTAGTATTAATTA
Found at i:73794 original size:71 final size:69
Alignment explanation
Indices: 73678--73809 Score: 246
Period size: 71 Copynumber: 1.9 Consensus size: 69
73668 CTACCTTTAG
73678 CATGCAAGAAAAGTAATGAATTTATTGCTTAATAGATTTTATATGGAAAGACACACTGTTCAAAA
1 CATGCAAGAAAAGTAATGAATTTATTGCTTAATAGATTTTATATGGAAAG--ACACTGTTCAAAA
73743 AAAAAA
64 AAAAAA
73749 CATGCAAGAAAAGTAATGAATTTATTGCTTAATAGATTTTATATGGAAAGACACTGTTCAA
1 CATGCAAGAAAAGTAATGAATTTATTGCTTAATAGATTTTATATGGAAAGACACTGTTCAA
73810 TCTATAAATG
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
69 11 0.18
71 50 0.82
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (69 bp):
CATGCAAGAAAAGTAATGAATTTATTGCTTAATAGATTTTATATGGAAAGACACTGTTCAAAAAA
AAAA
Found at i:75242 original size:14 final size:14
Alignment explanation
Indices: 75223--75255 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
75213 ATATTGGCAC
75223 TATTATTATAATTA
1 TATTATTATAATTA
75237 TATTATTATAATTA
1 TATTATTATAATTA
*
75251 AATTA
1 TATTA
75256 AATATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATTATTATAATTA
Found at i:80955 original size:72 final size:73
Alignment explanation
Indices: 80704--80966 Score: 343
Period size: 72 Copynumber: 3.6 Consensus size: 73
80694 TGTCCGTCCT
** * * *
80704 GGTCATGCACATGA-CTTGTGTTGGTCATGTGCATGACTTACTCAGGTGCAAGAAGGTTAAAACG
1 GGTCATGGGCATGACCTTCTGTTGGTCATGTGCATGACTTGCTCAGGTGCAAGAAGGCTAAAACG
* *
80768 CCTTTAGA
66 CATATAGA
*
80776 GGTCATGGGCATGACCTTCTGTTGGTCATGTGCATGACTTGCTCAGGTGCAAGAAGGCTAAAACT
1 GGTCATGGGCATGACCTTCTGTTGGTCATGTGCATGACTTGCTCAGGTGCAAGAAGGCTAAAACG
*
80841 CA-ACAGA
66 CATATAGA
* * *
80848 AGTCATGGGCATGACCTTCTGTTGATCATGTGCATGACTTCCTCAGGTGCAAGAAGGCTAAAACG
1 GGTCATGGGCATGACCTTCTGTTGGTCATGTGCATGACTTGCTCAGGTGCAAGAAGGCTAAAACG
*
80913 CATATGGA
66 CATATAGA
* * * * *
80921 GGTCATGGGCATGACCTGCT-CTGGTCACGCGCATGATTTGCTCAGG
1 GGTCATGGGCATGACCTTCTGTTGGTCATGTGCATGACTTGCTCAGG
80967 GTCCTTTTCT
Statistics
Matches: 166, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
72 98 0.59
73 68 0.41
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (73 bp):
GGTCATGGGCATGACCTTCTGTTGGTCATGTGCATGACTTGCTCAGGTGCAAGAAGGCTAAAACG
CATATAGA
Found at i:81143 original size:27 final size:27
Alignment explanation
Indices: 81113--81241 Score: 84
Period size: 23 Copynumber: 5.1 Consensus size: 27
81103 TACATTATTA
81113 TCACTAAATACAATGATTGTTAAGAGT
1 TCACTAAATACAATGATTGTTAAGAGT
* * **
81140 TCAC-AAA-A-TA-GATTCTATACCA--
1 TCACTAAATACAATGATTGT-TAAGAGT
81162 TCACTAAATACAATGATTGTTAAGAGT
1 TCACTAAATACAATGATTGTTAAGAGT
* ** *
81189 TCAC-AAA-A-GA-GATTCCATAACA--
1 TCACTAAATACAATGATT-GTTAAGAGT
81211 TCACTAAATACAATGATTGTTAAGAGT
1 TCACTAAATACAATGATTGTTAAGAGT
81238 TCAC
1 TCAC
81242 AAAAAAGATT
Statistics
Matches: 72, Mismatches: 16, Indels: 28
0.62 0.14 0.24
Matches are distributed among these distances:
22 8 0.11
23 15 0.21
24 11 0.15
25 11 0.15
26 15 0.21
27 12 0.17
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (27 bp):
TCACTAAATACAATGATTGTTAAGAGT
Found at i:81184 original size:49 final size:48
Alignment explanation
Indices: 81072--81255 Score: 287
Period size: 49 Copynumber: 3.8 Consensus size: 48
81062 GAACACAATA
**
81072 ACAATGATTGTTAAGAGTTCACAAAAGAGATTACATTATTATCACTAAAT
1 ACAATGATTGTTAAGAGTTCACAAAAGAGATT-CA-TAACATCACTAAAT
* *
81122 ACAATGATTGTTAAGAGTTCACAAAATAGATTCTATACCATCACTAAAT
1 ACAATGATTGTTAAGAGTTCACAAAAGAGATTC-ATAACATCACTAAAT
81171 ACAATGATTGTTAAGAGTTCACAAAAGAGATTCCATAACATCACTAAAT
1 ACAATGATTGTTAAGAGTTCACAAAAGAGATT-CATAACATCACTAAAT
*
81220 ACAATGATTGTTAAGAGTTCACAAAAAAGATTCATA
1 ACAATGATTGTTAAGAGTTCACAAAAGAGATTCATA
81256 TTATTGAGAA
Statistics
Matches: 126, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
48 4 0.03
49 89 0.71
50 33 0.26
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (48 bp):
ACAATGATTGTTAAGAGTTCACAAAAGAGATTCATAACATCACTAAAT
Found at i:81242 original size:98 final size:99
Alignment explanation
Indices: 81072--81252 Score: 319
Period size: 98 Copynumber: 1.8 Consensus size: 99
81062 GAACACAATA
**
81072 ACAATGATTGTTAAGAGTTCACAAAAGAGATTACATTATTATCACTAAATACAATGATTGTTAAG
1 ACAATGATTGTTAAGAGTTCACAAAAGAGATTACATTAACATCACTAAATACAATGATTGTTAAG
*
81137 AGTTCACAAAATAGATTCTATACCATCACTAAAT
66 AGTTCACAAAAAAGATTCTATACCATCACTAAAT
*
81171 ACAATGATTGTTAAGAGTTCACAAAAGAGATTCCA-TAACATCACTAAATACAATGATTGTTAAG
1 ACAATGATTGTTAAGAGTTCACAAAAGAGATTACATTAACATCACTAAATACAATGATTGTTAAG
81235 AGTTCACAAAAAAGATTC
66 AGTTCACAAAAAAGATTC
81253 ATATTATTGA
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
98 44 0.56
99 34 0.44
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.29
Consensus pattern (99 bp):
ACAATGATTGTTAAGAGTTCACAAAAGAGATTACATTAACATCACTAAATACAATGATTGTTAAG
AGTTCACAAAAAAGATTCTATACCATCACTAAAT
Done.