Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023952.1 Corchorus olitorius cultivar O-4 contig23985, 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: 14493
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:1482 original size:16 final size:15
Alignment explanation
Indices: 1439--1490 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
1429 TTCCATTTTC
*
1439 ATATGTTATGTTATT
1 ATATATTATGTTATT
*
1454 AT-TATTAT-ATATT
1 ATATATTATGTTATT
1467 ATATATATATGTTATT
1 ATATAT-TATGTTATT
*
1483 GTATATTA
1 ATATATTA
1491 ATTAGTAGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 6 0.20
14 8 0.27
15 7 0.23
16 9 0.30
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (15 bp):
ATATATTATGTTATT
Found at i:4263 original size:105 final size:107
Alignment explanation
Indices: 4154--4453 Score: 315
Period size: 107 Copynumber: 2.8 Consensus size: 107
4144 CTAGTAAAGA
* * *
4154 ATTTTGATTTCTAAGAGTAAATTAT-GAAATTAA-AGATTT-TAATTATAGATTTTTAGAAATAA
1 ATTTTTATTT-TAAGAGTAAATT-TCAAAATTAATA-ATTTATAATTATAGAGTTTTAGAAATAA
* * * **
4216 AATATAAAATTAATTTTACTATGTTTAGT-CCAAATTAAA-ATTT
63 AATACAAAACTAATTTCACTAAATTTAGTCCCAAATTAAAGATTT
* ** * *
4259 ATTTTTATTTTAAGGGTAAATTTCAAAATTAATAATTTATTGTTATAGGGTTTTAGAATTAAAAT
1 ATTTTTATTTTAAGAGTAAATTTCAAAATTAATAATTTATAATTATAGAGTTTTAGAAATAAAAT
*
4324 ACAAAACTAATTTCACTAAATTTAGTCCCAAATTAAAGTTTT
66 ACAAAACTAATTTCACTAAATTTAGTCCCAAATTAAAGATTT
* * * ** * *
4366 ATTTTTATTTTAACAGTAAATTCCATAATTAATAATTTATTGTTATAGGGTTTTAAAAATAAAAT
1 ATTTTTATTTTAAGAGTAAATTTCAAAATTAATAATTTATAATTATAGAGTTTTAGAAATAAAAT
* * *
4431 ATATAACTAA-TTCACTAAGTTTA
66 ACAAAACTAATTTCACTAAATTTA
4454 AGCCGAATTA
Statistics
Matches: 167, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
103 1 0.01
104 22 0.13
105 52 0.31
106 22 0.13
107 70 0.42
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (107 bp):
ATTTTTATTTTAAGAGTAAATTTCAAAATTAATAATTTATAATTATAGAGTTTTAGAAATAAAAT
ACAAAACTAATTTCACTAAATTTAGTCCCAAATTAAAGATTT
Found at i:4403 original size:107 final size:105
Alignment explanation
Indices: 4204--4483 Score: 366
Period size: 107 Copynumber: 2.6 Consensus size: 105
4194 AATTATAGAT
* * *
4204 TTTTAGAAATAAAATATAAAATTAATTTTACTATGTTTAGTCCAAATTAAAATTTATTTTTATTT
1 TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGTCCAAATTAAAATTTATTTTTATTT
** *
4269 TAAGGGTAAATTTCAAAATTAATAATTTATTGTTATAGGG
66 TAACAGTAAATTCCAAAATTAATAATTTATTGTTATAGGG
* * * *
4309 TTTTAGAATTAAAATACAAAACTAATTTCACTAAATTTAGTCCCAAATTAAAGTTTTATTTTTAT
1 TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGT-CCAAATTAAA-ATTTATTTTTAT
*
4374 TTTAACAGTAAATTCCATAATTAATAATTTATTGTTATAGGG
64 TTTAACAGTAAATTCCAAAATTAATAATTTATTGTTATAGGG
* * * * *
4416 TTTTAAAAATAAAATATATAACTAA-TTCACTAAGTTTAAG-CCGAATTAAAATTAAAATTTTAT
1 TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTT-AGTCCAAATTAAAATT-TATTTTTAT
4479 TTTAA
64 TTTAA
4484 GGGTCAGTTA
Statistics
Matches: 151, Mismatches: 20, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
104 2 0.01
105 56 0.37
106 21 0.14
107 72 0.48
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.43
Consensus pattern (105 bp):
TTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGTCCAAATTAAAATTTATTTTTATTT
TAACAGTAAATTCCAAAATTAATAATTTATTGTTATAGGG
Found at i:5156 original size:15 final size:16
Alignment explanation
Indices: 5109--5171 Score: 69
Period size: 16 Copynumber: 4.1 Consensus size: 16
5099 CATGCAGTTT
*
5109 TTTCGGGTCATTCGGG
1 TTTCGGATCATTCGGG
*
5125 TTTCGCG-TCA-TCTGG
1 TTTCG-GATCATTCGGG
*
5140 TTT-GGATTATTCGGG
1 TTTCGGATCATTCGGG
5155 TTTCGGATCATTCGGG
1 TTTCGGATCATTCGGG
5171 T
1 T
5172 CTCGAGTTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 1 0.03
14 3 0.08
15 14 0.36
16 20 0.51
17 1 0.03
ACGTcount: A:0.10, C:0.17, G:0.32, T:0.41
Consensus pattern (16 bp):
TTTCGGATCATTCGGG
Found at i:5450 original size:42 final size:42
Alignment explanation
Indices: 5403--5484 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
5393 TAGATATTAA
*
5403 TTTTGAATATTAAATACATAATTGATTATCAGGTGAGGTAGG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
*
5445 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTA
5485 TGTGTCAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
Found at i:6477 original size:166 final size:165
Alignment explanation
Indices: 6190--6521 Score: 472
Period size: 166 Copynumber: 2.0 Consensus size: 165
6180 TATATAAAAG
*
6190 TACGAAGAATGGAAAACTTTATGTTTTCCGATTGTACCCCTTTTTCAAATATATTTCTAAATCAA
1 TACGAAGAATGGAAAACTTTATGTTTTCCGATTGCACCCCTTTTTCAAATATATTTCTAAATCAA
* *
6255 TATTATTAAAATTTATTATTTAAAAATTAATTGTAAAATTTCAATTTATACCGAATTATAAGTTT
66 TATTATTAAAATTTAGTA-TTAAAAATTAATTGTAAAATTTCAATTTAGACCGAATTATAAGTTT
6320 GTAAAATTGATTTCCGTTAATAAACATGCAAATTTC
130 GTAAAATTGATTTCCGTTAATAAACATGCAAATTTC
* * * **
6356 TACGAATAATGGGAAACTTTATGTTTTCCGATTGCACCCTTTTTTTCAAATATATTTCTAAATTG
1 TACGAAGAATGGAAAACTTTATGTTTTCCGATTGCACCC-CTTTTTCAAATATATTTCTAAATCA
* **
6421 CTATTATTAAAATTTAGTA-T-AATTTTATCATT-TAAAAATTTCAATTTAGACCGAATTATAAG
65 ATATTATTAAAATTTAGTATTAAAAATTA--ATTGT-AAAATTTCAATTTAGACCGAATTATAAG
* * *
6483 TTTGTGAAATTGATTTTCGTTGATAAACATGCAAATTTC
127 TTTGTAAAATTGATTTCCGTTAATAAACATGCAAATTTC
6522 CTTTACTATT
Statistics
Matches: 148, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
164 5 0.03
165 2 0.01
166 102 0.69
167 39 0.26
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.42
Consensus pattern (165 bp):
TACGAAGAATGGAAAACTTTATGTTTTCCGATTGCACCCCTTTTTCAAATATATTTCTAAATCAA
TATTATTAAAATTTAGTATTAAAAATTAATTGTAAAATTTCAATTTAGACCGAATTATAAGTTTG
TAAAATTGATTTCCGTTAATAAACATGCAAATTTC
Found at i:6966 original size:22 final size:23
Alignment explanation
Indices: 6927--6969 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
6917 AATCCTAATC
6927 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
6950 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
6970 ACTCCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:9313 original size:26 final size:25
Alignment explanation
Indices: 9261--9313 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
9251 GAAACACAAC
*
9261 TTCAAATTGCATAAAGCTGCACTTT
1 TTCAAATTGCATAAAGCTGCACCTT
* *
9286 TTCAGATTGACATAAAGCTGCTCCTT
1 TTCAAATTG-CATAAAGCTGCACCTT
9312 TT
1 TT
9314 GGAGCACTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (25 bp):
TTCAAATTGCATAAAGCTGCACCTT
Found at i:11990 original size:22 final size:23
Alignment explanation
Indices: 11951--11993 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
11941 AATCCTAATC
11951 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
11974 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
11994 ACTCCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:12186 original size:44 final size:44
Alignment explanation
Indices: 12131--12822 Score: 171
Period size: 44 Copynumber: 15.3 Consensus size: 44
12121 GTCTCTGGGT
* **
12131 GGTTATTAAAATTTCATAAGATGGTTATTTTAATTTCATGAGG-A
1 GGTTATCAAAATTTCATAAGATGGTTATTAAAATTTCAT-AGGAA
* * **
12175 GGTTATCAAAATTCCAT-AGTGTGGTTACCAAAATTTCATATGGAA
1 GGTTATCAAAATTTCATAAG-ATGGTTATTAAAATTTCATA-GGAA
* * * * *
12220 -ATTATCAAAATTTTATGAGAAGGTTATTAAAATTTCATAGTGTA
1 GGTTATCAAAATTTCATAAGATGGTTATTAAAATTTCATAG-GAA
* * * *
12264 -GTTACCAAAATTTCATAGGATCAGGTTATTATAATTTCTTAGGAA
1 GGTTATCAAAATTTCATAAGAT--GGTTATTAAAATTTCATAGGAA
* * * * * * *
12309 GGTTATTAAAATTTCAT-GGTGTGGTTATCACAATTTTATAGAAA
1 GGTTATCAAAATTTCATAAG-ATGGTTATTAAAATTTCATAGGAA
* *
12353 GGTTATCAAAGAGATTATCAAAATGCCATAGCGAGGTTA-TAAGAATTTCATAGTG-T
1 GGTTATC-AA-A-ATT-TCATAA-G--AT-----GGTTATTAA-AATTTCATAG-GAA
* * * * *
12409 GGTTAACAAAATTTCATAAGGA-GGTTACTAATATTTCATGGGGA
1 GGTTATCAAAATTTCATAA-GATGGTTATTAAAATTTCATAGGAA
* * * *
12453 GGTTATCAAAATTTCAT-AGTGTGGTTATCAAAAGTTT-TTAGTG-T
1 GGTTATCAAAATTTCATAAG-ATGGTTATTAAAA-TTTCATAG-GAA
* ** * *
12497 GGTTATCAAAATTTCAT-AGTGTGGTTAGCAAAAGTTT-TTAGTG-T
1 GGTTATCAAAATTTCATAAG-ATGGTTATTAAAA-TTTCATAG-GAA
* * *
12541 GGTTATCAAAATTTCATATGAAGGTTATAAAAGTCTCAATTTCATAAGG-A
1 GGTTATCAAAATTTCATAAGATGGTTAT-TAA-----AATTTCAT-AGGAA
* * * * *
12591 -G-TACCAAAATTTGAT-AGAAGGTTA-TCAAATCTCATA-G-A
1 GGTTATCAAAATTTCATAAGATGGTTATTAAAATTTCATAGGAA
* * *
12629 GTGATTATCAAAATTTAATAGAGACCGGATTATCAAAA-TTCATAGGAA
1 G-G-TTATCAAAATTTCATA-AGA-TGG-TTATTAAAATTTCATAGGAA
* * * * * * *
12677 GATTATTAAAATTGCAT--GGTGGTGTTATCAAAATTTCAAAGTAA
1 GGTTATCAAAATTTCATAAGAT-G-GTTATTAAAATTTCATAGGAA
* * * *
12721 GGTTATCAAAATTACATAATG-TGATTATCAAAATTTCATA-GAGG
1 GGTTATCAAAATTTCATAA-GATGGTTATTAAAATTTCATAGGA-A
* * * * *
12765 GGTCAACAAAATTTTATAGAGA-GGTTATCAAAATTTCATA-AAA
1 GGTTATCAAAATTTCATA-AGATGGTTATTAAAATTTCATAGGAA
* *
12808 AGTTATCAAATTTTC
1 GGTTATCAAAATTTC
12823 TAAATGTGAT
Statistics
Matches: 487, Mismatches: 103, Indels: 117
0.69 0.15 0.17
Matches are distributed among these distances:
38 2 0.00
39 1 0.00
40 8 0.02
42 13 0.03
43 28 0.06
44 278 0.57
45 24 0.05
46 54 0.11
47 16 0.03
48 17 0.03
49 4 0.01
50 6 0.01
51 3 0.01
52 6 0.01
53 3 0.01
54 1 0.00
55 3 0.01
56 20 0.04
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAAGATGGTTATTAAAATTTCATAGGAA
Found at i:12212 original size:66 final size:66
Alignment explanation
Indices: 12129--12358 Score: 230
Period size: 66 Copynumber: 3.5 Consensus size: 66
12119 TTGTCTCTGG
** * * * *
12129 GTGGTTATTAAAATTTCATAAGATGGTTATTTTAATTTCATGAGGAGGTTATCAAAATTCCATAG
1 GTGGTTACCAAAATTTCATAGGATGGTTATTATAATTTCATGAGGAGGTTATTAAAATTTCATAG
12194 T
66 T
** * * * *
12195 GTGGTTACCAAAATTTCATATGGA-AATTATCAAAATTTTATGAGAAGGTTATTAAAATTTCATA
1 GTGGTTACCAAAATTTCATA-GGATGGTTATTATAATTTCATGAGGAGGTTATTAAAATTTCATA
12259 GT
65 GT
* *
12261 GTAGTTACCAAAATTTCATAGGATCAGGTTATTATAATTTC-TTAGGAAGGTTATTAAAATTTCA
1 GTGGTTACCAAAATTTCATAGGAT--GGTTATTATAATTTCATGAGG-AGGTTATTAAAATTTCA
*
12325 TGGT
63 TAGT
* * * * *
12329 GTGGTTATCACAATTTTATAGAAAGGTTAT
1 GTGGTTACCAAAATTTCATAGGATGGTTAT
12359 CAAAGAGATT
Statistics
Matches: 132, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
65 3 0.02
66 76 0.58
67 5 0.04
68 48 0.36
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (66 bp):
GTGGTTACCAAAATTTCATAGGATGGTTATTATAATTTCATGAGGAGGTTATTAAAATTTCATAG
T
Found at i:12299 original size:24 final size:22
Alignment explanation
Indices: 12131--12325 Score: 139
Period size: 22 Copynumber: 8.8 Consensus size: 22
12121 GTCTCTGGGT
* *
12131 GGTTATTAAAATTTCATAAGAT
1 GGTTATTAAAATTTCATAGGAA
**
12153 GGTTATTTTAATTTCATGAGG-A
1 GGTTATTAAAATTTCAT-AGGAA
* * *
12175 GGTTATCAAAATTCCATAGTG-T
1 GGTTATTAAAATTTCATAG-GAA
**
12197 GGTTACCAAAATTTCATATGGAA
1 GGTTATTAAAATTTCATA-GGAA
* * *
12220 -ATTATCAAAATTTTAT-GAGAA
1 GGTTATTAAAATTTCATAG-GAA
*
12241 GGTTATTAAAATTTCATAGTGTA
1 GGTTATTAAAATTTCATAG-GAA
**
12264 -GTTACCAAAATTTCATAGGATCA
1 GGTTATTAAAATTTCATAGGA--A
* *
12287 GGTTATTATAATTTCTTAGGAA
1 GGTTATTAAAATTTCATAGGAA
12309 GGTTATTAAAATTTCAT
1 GGTTATTAAAATTTCAT
12326 GGTGTGGTTA
Statistics
Matches: 134, Mismatches: 29, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
20 1 0.01
21 6 0.04
22 104 0.78
23 7 0.05
24 16 0.12
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.39
Consensus pattern (22 bp):
GGTTATTAAAATTTCATAGGAA
Found at i:12404 original size:22 final size:21
Alignment explanation
Indices: 12379--12572 Score: 135
Period size: 22 Copynumber: 8.9 Consensus size: 21
12369 ATCAAAATGC
*
12379 CATAGCGAGGTTATAAGAATTT
1 CATAGTGAGGTTATAA-AATTT
* *
12401 CATAGTGTGGTTAACAAAATTT
1 CATAGTGAGGTT-ATAAAATTT
*
12423 CATAAG-GAGGTTACTAATATTT
1 CAT-AGTGAGGTTA-TAAAATTT
* *
12445 CATGGGGAGGTTATCAAAATTT
1 CATAGTGAGGTTAT-AAAATTT
*
12467 CATAGTGTGGTTATCAAAAGTTT
1 CATAGTGAGGTTAT-AAAA-TTT
* *
12490 -TTAGTGTGGTTATCAAAATTT
1 CATAGTGAGGTTAT-AAAATTT
* *
12511 CATAGTGTGGTTAGCAAAAGTTT
1 CATAGTGAGGTTA-TAAAA-TTT
* *
12534 -TTAGTGTGGTTATCAAAATTT
1 CATAGTGAGGTTAT-AAAATTT
12555 CATA-TGAAGGTTATAAAA
1 CATAGTG-AGGTTATAAAA
12573 GTCTCAATTT
Statistics
Matches: 142, Mismatches: 18, Indels: 25
0.77 0.10 0.14
Matches are distributed among these distances:
21 15 0.11
22 116 0.82
23 11 0.08
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (21 bp):
CATAGTGAGGTTATAAAATTT
Found at i:12501 original size:66 final size:65
Alignment explanation
Indices: 12367--12804 Score: 204
Period size: 66 Copynumber: 6.6 Consensus size: 65
12357 ATCAAAGAGA
** * *
12367 TTATCAAAATGCCATAGCGAGGTTAT-AAGAATTTCATAGTGTGGTTAACAAAATTTCATAAGGA
1 TTATCAAAATTTCATAGGGAGGTTATCAA-AATTTCATAGTGTGGTTATCAAAATTT-ATAAGGA
12431 GG
64 GG
* * *
12433 TTA-CTAATATTTCATGGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAAGTTT-TTAGTG
1 TTATC-AAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAA-TTTATAAG-G
*
12496 TGG
63 AGG
* * * * * *
12499 TTATCAAAATTTCATAGTGTGGTTAGCAAAAGTTT-TTAGTGTGGTTATCAAAATTTCATATGAA
1 TTATCAAAATTTCATAGGGAGGTTATCAAAA-TTTCATAGTGTGGTTATCAAAATTT-ATAAGGA
12563 GG
64 GG
* * * * ** *
12565 TTATAAAAGTCTCAATTTCATAAGGA-G-TACCAAAATTTGATAG-AAGGTTATC-AAATCTCAT
1 TTAT-CAA-----AATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAAT-TTAT
12626 -A-GAGTG
59 AAGGAG-G
* * * * * *
12632 ATTATCAAAATTTAATAGAGACCGGATTATCAAAA-TTCATAG-GAAGATTATTAAAATTGCAT-
1 -TTATCAAAATTTCATAGGGA--GG-TTATCAAAATTTCATAGTG-TGGTTATCAAAATT-TATA
*
12694 -GGTGGTG
60 AGG-AG-G
* ** * * *
12701 TTATCAAAATTTCAAAGTAAGGTTATCAAAATTACATAATGTGATTATCAAAATTTCATAGAGG-
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTT-ATA-AGGA
12765 GG
64 GG
* * * *
12767 TCAACAAAATTTTATAGAGAGGTTATCAAAATTTCATA
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATA
12805 AAAAGTTATC
Statistics
Matches: 283, Mismatches: 55, Indels: 68
0.70 0.14 0.17
Matches are distributed among these distances:
62 10 0.04
65 17 0.06
66 153 0.54
67 32 0.11
68 34 0.12
69 16 0.06
70 10 0.04
71 1 0.00
72 10 0.04
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.34
Consensus pattern (65 bp):
TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTATAAGGAGG
Found at i:12649 original size:22 final size:22
Alignment explanation
Indices: 12455--12804 Score: 141
Period size: 22 Copynumber: 15.7 Consensus size: 22
12445 CATGGGGAGG
* *
12455 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGAGTGA
* * *
12477 TTATCAAAAGTTT-TTAGTGTGG
1 TTATCAAAA-TTTCATAGAGTGA
* *
12499 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGAGTGA
* * * *
12521 TTAGCAAAAGTTT-TTAGTGTGG
1 TTATCAAAA-TTTCATAGAGTGA
*
12543 TTATCAAAATTTCATATGAAGGTTA
1 TTATCAAAATTTCATA-G-A-GTGA
* **
12568 TAAAAGTCTCAATTTCATA-AG-GA
1 T--TA-TCAAAATTTCATAGAGTGA
* * *
12591 GTACCAAAATTTGATAGAAG-G-
1 TTATCAAAATTTCATAG-AGTGA
*
12612 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGAGTGA
* *
12633 TTATCAAAATTTAATAGAGACCGGA
1 TTATCAAAATTTCATAGAG---TGA
*
12658 TTATCAAAA-TTCATAG-GAAGA
1 TTATCAAAATTTCATAGAG-TGA
* * * *
12679 TTATTAAAATTGCATGGTGGTG-
1 TTATCAAAATTTCATAG-AGTGA
*
12701 TTATCAAAATTTCA-A-AGTAAGG
1 TTATCAAAATTTCATAGAGT--GA
*
12723 TTATCAAAATTACATA-ATGTGA
1 TTATCAAAATTTCATAGA-GTGA
* *
12745 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGAGTGA
* * * * *
12767 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGAGTGA
12789 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
12805 AAAAGTTATC
Statistics
Matches: 252, Mismatches: 49, Indels: 54
0.71 0.14 0.15
Matches are distributed among these distances:
19 4 0.02
20 19 0.08
21 26 0.10
22 153 0.61
23 13 0.05
24 10 0.04
25 15 0.06
27 1 0.00
28 11 0.04
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAGTGA
Found at i:12826 original size:20 final size:21
Alignment explanation
Indices: 12700--12826 Score: 69
Period size: 22 Copynumber: 5.9 Consensus size: 21
12690 GCATGGTGGT
*
12700 GTTATCAAAATTTCA-AAGTAAG
1 GTTATCAAAATTTCATAA--AAA
* ***
12722 GTTATCAAAATTACATAATGT
1 GTTATCAAAATTTCATAAAAA
***
12743 GATTATCAAAATTTCATAGAGGG
1 G-TTATCAAAATTTCATA-AAAA
* * * * *
12766 GTCAACAAAATTTTATAGAGAG
1 GTTATCAAAATTTCATA-AAAA
12788 GTTATCAAAATTTCATAAAAA
1 GTTATCAAAATTTCATAAAAA
*
12809 GTTATCAAATTTTC-TAAA
1 GTTATCAAAATTTCATAAA
12827 TGTGATTACT
Statistics
Matches: 85, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
20 4 0.05
21 16 0.19
22 60 0.71
23 5 0.06
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (21 bp):
GTTATCAAAATTTCATAAAAA
Found at i:13357 original size:22 final size:22
Alignment explanation
Indices: 13307--13620 Score: 186
Period size: 22 Copynumber: 14.5 Consensus size: 22
13297 TTATGGAATA
*
13307 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* * *
13327 AACAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
13349 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* * *
13371 TTCAAATTTTCATA-AGAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
* * *
13393 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
* *
13415 ATTAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* * **
13437 AACAGAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
13459 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
13481 ATCAAAA-TT--T--GTA-GCT
1 ATCAAAATTTCATAGGGAGGTT
* * *
13497 ATCAAGATTTCATAAGGACGTT
1 ATCAAAATTTCATAGGGAGGTT
13519 ATCAAAATGTT-ATAGGGAGGTTT
1 ATCAAAAT-TTCATAGGGAGG-TT
* *
13542 ATCAAAATTTTATAGGAAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
13565 ATCAAAATTTCATAGCGGA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* * * *
13587 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
*
13609 ATCAAAACTTCA
1 ATCAAAATTTCA
13621 AAGTGTGATT
Statistics
Matches: 223, Mismatches: 53, Indels: 34
0.72 0.17 0.11
Matches are distributed among these distances:
16 8 0.04
17 4 0.02
19 2 0.01
20 11 0.05
21 6 0.03
22 148 0.66
23 42 0.19
24 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:13573 original size:23 final size:23
Alignment explanation
Indices: 13517--13579 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
13507 CATAAGGACG
* *
13517 TTATCAAAATGTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGGT
13540 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGAAGGT
*
13563 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
13580 CGGAGTTATC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGGT
Found at i:13625 original size:22 final size:22
Alignment explanation
Indices: 13563--13631 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
13553 ATAGGAAGGT
*
13563 TTATCAAAATTTCATAGCG-GA
1 TTATCAAAATTTCATAGTGTGA
*
13584 GTTATCACAATTTCATAGTGTGA
1 -TTATCAAAATTTCATAGTGTGA
* *
13607 TTATCAAAACTTCAAAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
13629 TTA
1 TTA
13632 CTAACAATTC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
22 39 0.95
23 2 0.05
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Done.