Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007281.1 Corchorus capsularis cultivar CVL-1 contig07302, 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: 22247
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Found at i:1350 original size:20 final size:20
Alignment explanation
Indices: 1321--1374 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1311 AAATGGGATA
*
1321 TTTGGCTAAAAGATGTAACC
1 TTTGGATAAAAGATGTAACC
* *
1341 TTTGGTTAAAAGATTTAACC
1 TTTGGATAAAAGATGTAACC
*
1361 TTTGAATAAAAGAT
1 TTTGGATAAAAGAT
1375 TGAATTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (20 bp):
TTTGGATAAAAGATGTAACC
Found at i:1415 original size:50 final size:50
Alignment explanation
Indices: 1356--1686 Score: 348
Period size: 51 Copynumber: 6.6 Consensus size: 50
1346 TTAAAAGATT
* *
1356 TAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAAGAAAAATG
1 TAACCTTTGAGTAAAAGATTGAATTTTTAAGTAATTAGTAAAGAAAAATG
* * *
1406 TCATCTTTGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAA-AAAAGATT
1 TAACCTTTGAGTAAAAGATTGAATTTTTA-AGTAATTAGTAAAGAAAA-ATG
* *
1457 TAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAAGAAAAATG
1 TAACCTTTGAGTAAAAGATTGAATTTTTAAGTAATTAGTAAAGAAAAATG
* ** * * * ** *
1507 TCATATTTGAGTAAAAGATTGAATTTTTTTAGAATAATTAGTGAATAAAGGTT
1 TAACCTTTGAGTAAAAGATTGAA--TTTTTA-AGTAATTAGTAAAGAAAAATG
* *
1560 TAACCTTTGAATAAAAGATTG---TTTTAAGTAATTGGTAAAGAAAAATG
1 TAACCTTTGAGTAAAAGATTGAATTTTTAAGTAATTAGTAAAGAAAAATG
* * * * ** *
1607 TCATCTTTGAGTAAAAGATTGAATTTTTAGAATAATTAGTAAATAAAGGTT
1 TAACCTTTGAGTAAAAGATTGAATTTTTA-AGTAATTAGTAAAGAAAAATG
1658 TAACCTTTGAGTAAAAGATTG-ATTTTTAA
1 TAACCTTTGAGTAAAAGATTGAATTTTTAA
1687 AAAAAAAAAT
Statistics
Matches: 228, Mismatches: 43, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
47 32 0.14
48 5 0.02
49 1 0.00
50 75 0.33
51 78 0.34
52 6 0.03
53 31 0.14
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (50 bp):
TAACCTTTGAGTAAAAGATTGAATTTTTAAGTAATTAGTAAAGAAAAATG
Found at i:1523 original size:101 final size:100
Alignment explanation
Indices: 1348--1686 Score: 556
Period size: 101 Copynumber: 3.4 Consensus size: 100
1338 ACCTTTGGTT
1348 AAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAAGAAAAATGTCATCTT
1 AAAAGATTTAACCTTTGAATAAAAGATTG-ATTTTTAAGTAATTGGTAAAGAAAAATGTCATCTT
*
1413 TGAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAA
65 TGAGTAAAAGATTGAATTTTTAGAATAATTAGTAAA
*
1449 AAAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAAGAAAAATGTCATATT
1 AAAAGATTTAACCTTTGAATAAAAGATTG-ATTTTTAAGTAATTGGTAAAGAAAAATGTCATCTT
*
1514 TGAGTAAAAGATTGAATTTTTTTAGAATAATTAGTGAA
65 TGAGTAAAAGATTGAA--TTTTTAGAATAATTAGTAAA
* *
1552 TAAAGGTTTAACCTTTGAATAAAAGATTG--TTTTAAGTAATTGGTAAAGAAAAATGTCATCTTT
1 AAAAGATTTAACCTTTGAATAAAAGATTGATTTTTAAGTAATTGGTAAAGAAAAATGTCATCTTT
1615 GAGTAAAAGATTGAATTTTTAGAATAATTAGTAAA
66 GAGTAAAAGATTGAATTTTTAGAATAATTAGTAAA
* * *
1650 TAAAGGTTTAACCTTTGAGTAAAAGATTGATTTTTAA
1 AAAAGATTTAACCTTTGAATAAAAGATTGATTTTTAA
1687 AAAAAAAAAT
Statistics
Matches: 226, Mismatches: 8, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
98 47 0.21
100 54 0.24
101 80 0.35
103 45 0.20
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (100 bp):
AAAAGATTTAACCTTTGAATAAAAGATTGATTTTTAAGTAATTGGTAAAGAAAAATGTCATCTTT
GAGTAAAAGATTGAATTTTTAGAATAATTAGTAAA
Found at i:2461 original size:54 final size:54
Alignment explanation
Indices: 2367--2507 Score: 203
Period size: 54 Copynumber: 2.6 Consensus size: 54
2357 GAAAGGGGGC
* * *
2367 AATCAGTAATTAAGTAAAAAGGGATTAATTAGAGTTAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGT-AAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
2422 AATCAGTAATTAAGTAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
* *
2476 AATCAGTAATCAGGTAAAA-AGATAGTAATCAG
1 AATCAGTAATTAAGTAAAAGAGAT--TAATCAG
2508 TAAATTGATT
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
53 4 0.05
54 53 0.67
55 22 0.28
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.26
Consensus pattern (54 bp):
AATCAGTAATTAAGTAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
Found at i:2814 original size:21 final size:21
Alignment explanation
Indices: 2789--2999 Score: 117
Period size: 21 Copynumber: 9.9 Consensus size: 21
2779 ATCTGAAAGG
* *
2789 GTAAAATGGTAATTAGTAATA
1 GTAAAATAGTAATCAGTAATA
*
2810 GTAAAATAGTAATCAGTAAAAA
1 GTAAAATAGTAATCAGT-AATA
* ** *
2832 GTAAGAA-GGTAATCAACAAGA
1 GTAA-AATAGTAATCAGTAATA
* *
2853 GTAAAATAGTAGTCAGTAAAAA
1 GTAAAATAGTAATCAGT-AATA
*
2875 GT-AAATAGTAATCAGTAAGA
1 GTAAAATAGTAATCAGTAATA
* * *
2895 GTAAAACAGTAATCACTAAGAA
1 GTAAAATAGTAATCAGTAA-TA
* *
2917 GTAAAA-GGCTAATCAGTAAGAA
1 GTAAAATAG-TAATCAGTAA-TA
* *
2939 GTAAAA-GGTAATCAGTAAAAA
1 GTAAAATAGTAATCAGT-AATA
* * * *
2960 GCAAAA-GGCAATCAGTAAAA
1 GTAAAATAGTAATCAGTAATA
*
2980 GGTAAAACAGTAATCAGTAA
1 -GTAAAATAGTAATCAGTAA
3000 AAAAGGAGCA
Statistics
Matches: 156, Mismatches: 24, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
20 11 0.07
21 85 0.54
22 58 0.37
23 2 0.01
ACGTcount: A:0.53, C:0.08, G:0.19, T:0.20
Consensus pattern (21 bp):
GTAAAATAGTAATCAGTAATA
Found at i:2821 original size:14 final size:15
Alignment explanation
Indices: 2802--2835 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2792 AAATGGTAAT
2802 TAGTAAT-AGTAAAA
1 TAGTAATCAGTAAAA
2816 TAGTAATCAGTAAAA
1 TAGTAATCAGTAAAA
2831 -AGTAA
1 TAGTAA
2836 GAAGGTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (15 bp):
TAGTAATCAGTAAAA
Found at i:2857 original size:43 final size:42
Alignment explanation
Indices: 2809--3101 Score: 243
Period size: 43 Copynumber: 6.7 Consensus size: 42
2799 AATTAGTAAT
2809 AGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAACAAG
1 AGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAACAAG
* **
2852 AGTAAAATAGTAGTCAGTAAAAAGTAAATA-GTAATCAGTAAG
1 AGTAAAATAGTAATCAGTAAAAAGTAAA-AGGTAATCAACAAG
* * * **
2894 AGTAAAACAGTAATCACTAAGAAGTAAAAGGCTAATCAGTAAG
1 AGTAAAATAGTAATCAGTAAAAAGTAAAAGG-TAATCAACAAG
* * * *
2937 AAGTAAAA-GGTAATCAGTAAAAAGCAAAAGGCAATCAGTAAAAG
1 -AGTAAAATAGTAATCAGTAAAAAGTAAAAGGTAATCA--ACAAG
* * *
2981 -GTAAAACAGTAATCAGTAAAAAAGGAGCAGAAAATAGTAATCGATTA-AAG
1 AGTAAAATAGTAATCAGT--AAAA--AG--TAAAA-GGTAATC-A--ACAAG
**
3031 AGTAAAAGGGTAATCAGTAAAAAGTAAGAAGGTAATCAACAAG
1 AGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAACAAG
*
3074 AGTAAAATAGTAATCAGTACAAAGTAAA
1 AGTAAAATAGTAATCAGTAAAAAGTAAA
3102 GAATAATCAG
Statistics
Matches: 206, Mismatches: 26, Indels: 37
0.77 0.10 0.14
Matches are distributed among these distances:
41 1 0.00
42 49 0.24
43 93 0.45
44 11 0.05
45 12 0.06
46 2 0.01
47 4 0.02
49 8 0.04
50 8 0.04
51 18 0.09
ACGTcount: A:0.54, C:0.08, G:0.19, T:0.18
Consensus pattern (42 bp):
AGTAAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAACAAG
Found at i:2886 original size:64 final size:63
Alignment explanation
Indices: 2757--3002 Score: 211
Period size: 64 Copynumber: 3.9 Consensus size: 63
2747 AATAGCATGC
* * * * *
2757 AATCAGTAAAAAGTAAAAAGGT-ATCTGA-AAGGGTAAAATGGTAATTAGT-AATAGTAAAATAG
1 AATCAGTAAAAAGT-AAAAGGTAATC-AACAAGAGTAAAATAGTAATCAGTAAAAAGT-AAATAG
2819 T
63 T
*
2820 AATCAGTAAAAAGTAAGAAGGTAATCAACAAGAGTAAAATAGTAGTCAGTAAAAAGTAAATAGT
1 AATCAGTAAAAAGTAA-AAGGTAATCAACAAGAGTAAAATAGTAATCAGTAAAAAGTAAATAGT
* * * *
2884 AATCAGT-AAGAGTAAAACAGTAATC-ACTAAGAAGTAAAA-GGCTAATCAGTAAGAAGTAAA-A
1 AATCAGTAAAAAGTAAAA-GGTAATCAAC-AAG-AGTAAAATAG-TAATCAGTAAAAAGTAAATA
2945 GGT
62 -GT
* * * *
2948 AATCAGTAAAAAGCAAAAGGCAATCAGTAAAAG-GTAAAACAGTAATCAGTAAAAA
1 AATCAGTAAAAAGTAAAAGGTAATCA--ACAAGAGTAAAATAGTAATCAGTAAAAA
3003 AGGAGCAGAA
Statistics
Matches: 151, Mismatches: 18, Indels: 27
0.77 0.09 0.14
Matches are distributed among these distances:
62 6 0.04
63 38 0.25
64 89 0.59
65 14 0.09
66 3 0.02
67 1 0.01
ACGTcount: A:0.54, C:0.07, G:0.19, T:0.20
Consensus pattern (63 bp):
AATCAGTAAAAAGTAAAAGGTAATCAACAAGAGTAAAATAGTAATCAGTAAAAAGTAAATAGT
Found at i:3108 original size:21 final size:22
Alignment explanation
Indices: 2809--3113 Score: 96
Period size: 21 Copynumber: 13.9 Consensus size: 22
2799 AATTAGTAAT
*
2809 AGTAAA-ATAGTAATCAGTAAAA
1 AGTAAAGA-AGTAATCAGTACAA
2831 AGT-AAGAAGGTAATCA--ACAA
1 AGTAAAGAA-GTAATCAGTACAA
* *
2851 GAGTAAA-ATAGTAGTCAGTAAAA
1 -AGTAAAGA-AGTAATCAGTACAA
* *
2874 AGTAAA-TAGTAATCAGTA-AG
1 AGTAAAGAAGTAATCAGTACAA
*
2894 AGTAAA-ACAGTAATCACTA-AGA
1 AGTAAAGA-AGTAATCAGTACA-A
*
2916 AGTAAA-AGGCTAATCAGTA-AGA
1 AGTAAAGAAG-TAATCAGTACA-A
* *
2938 AGTAAA-AGGTAATCAGTAAAA
1 AGTAAAGAAGTAATCAGTACAA
* * *
2959 AGCAAA-AGGCAATCAGTA-AA
1 AGTAAAGAAGTAATCAGTACAA
*
2979 AGGTAAA-ACAGTAATCAGTAAAAAA
1 A-GTAAAGA-AGTAATCAGT--ACAA
* * *
3004 GGAGCAGAAAATAGTAATCGATTA-AA
1 --AGTA-AAGA-AGTAATC-AGTACAA
* *
3030 GAGTAAA-AGGGTAATCAGTAAAA
1 -AGTAAAGA-AGTAATCAGTACAA
3053 AGT-AAGAAGGTAATCA--ACAA
1 AGTAAAGAA-GTAATCAGTACAA
3073 GAGTAAA-ATAGTAATCAGTACAA
1 -AGTAAAGA-AGTAATCAGTACAA
3096 AGTAAAGAA-TAATCAGTA
1 AGTAAAGAAGTAATCAGTA
3114 AAATAGTGAT
Statistics
Matches: 228, Mismatches: 25, Indels: 61
0.73 0.08 0.19
Matches are distributed among these distances:
20 16 0.07
21 88 0.39
22 80 0.35
23 17 0.07
24 3 0.01
25 6 0.03
26 4 0.02
27 4 0.02
28 8 0.04
29 2 0.01
ACGTcount: A:0.54, C:0.08, G:0.19, T:0.19
Consensus pattern (22 bp):
AGTAAAGAAGTAATCAGTACAA
Found at i:13980 original size:3 final size:3
Alignment explanation
Indices: 13964--14034 Score: 115
Period size: 3 Copynumber: 23.0 Consensus size: 3
13954 TCAAAAATTG
*
13964 TTA TTA TTGC TTA TTA TTA CTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
14011 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
14035 AATGCAGTGA
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
3 59 0.92
4 5 0.08
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:17937 original size:25 final size:25
Alignment explanation
Indices: 17907--17988 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
17897 TACCTTCTTC
17907 TTTTACTAATTACCTTTCTTACTCT
1 TTTTACTAATTACCTTTCTTACTCT
*
17932 TTTTACTGATTA-CTATAT-TTACTCTT
1 TTTTACTAATTACCT-T-TCTTACTC-T
* *
17958 TTTTACTTATTACCATTTTCTTCCTCT
1 TTTTACTAATTACC--TTTCTTACTCT
17985 TTTT
1 TTTT
17989 TTTTTACTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
24 2 0.04
25 18 0.38
26 13 0.28
27 7 0.15
28 6 0.13
29 1 0.02
ACGTcount: A:0.18, C:0.21, G:0.01, T:0.60
Consensus pattern (25 bp):
TTTTACTAATTACCTTTCTTACTCT
Found at i:17987 original size:26 final size:26
Alignment explanation
Indices: 17900--17987 Score: 67
Period size: 26 Copynumber: 3.4 Consensus size: 26
17890 CATTTTCTAC
*
17900 CTTCTTCTTTTACTAATTACC--TTT
1 CTTCCTCTTTTACTAATTACCATTTT
* * *
17924 CTTACTCTTTTTACTGATTACTATATTT
1 CTTCCTC-TTTTACTAATTACCAT-TTT
* *
17952 AC-T-CTTTTTTACTTATTACCATTTT
1 -CTTCCTCTTTTACTAATTACCATTTT
17977 CTTCCTCTTTT
1 CTTCCTCTTTT
17988 TTTTTTACTG
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
24 6 0.12
25 16 0.33
26 20 0.41
27 2 0.04
28 4 0.08
29 1 0.02
ACGTcount: A:0.17, C:0.23, G:0.01, T:0.59
Consensus pattern (26 bp):
CTTCCTCTTTTACTAATTACCATTTT
Found at i:17996 original size:32 final size:31
Alignment explanation
Indices: 17956--18019 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
17946 ATATTTACTC
* *
17956 TTTTTTACTTATTA-CCATTTTCTTCCTCTTTT
1 TTTTTTACTGATTATCC-TTTTCTTACT-TTTT
17988 TTTTTTACTGATTATCCTTTTCTTACTTTTT
1 TTTTTTACTGATTATCCTTTTCTTACTTTTT
18019 T
1 T
18020 ACTGAATACC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 5 0.17
32 22 0.76
33 2 0.07
ACGTcount: A:0.12, C:0.19, G:0.02, T:0.67
Consensus pattern (31 bp):
TTTTTTACTGATTATCCTTTTCTTACTTTTT
Found at i:18034 original size:26 final size:26
Alignment explanation
Indices: 17988--18040 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
17978 TTCCTCTTTT
*
17988 TTTTTTACTGATTATCCTTTTCTTAC
1 TTTTTTACTGAATATCCTTTTCTTAC
*
18014 TTTTTTACTGAATA-CCATTTTTTTAC
1 TTTTTTACTGAATATCC-TTTTCTTAC
18040 T
1 T
18041 GATTATCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.19, C:0.17, G:0.04, T:0.60
Consensus pattern (26 bp):
TTTTTTACTGAATATCCTTTTCTTAC
Found at i:18095 original size:26 final size:25
Alignment explanation
Indices: 18066--18162 Score: 104
Period size: 32 Copynumber: 3.5 Consensus size: 25
18056 TTTCTTACTG
18066 ATTACTATTTTACTCTCTTGAATTTA
1 ATTACTATTTTACTCT-TTGAATTTA
18092 ATTACTATTTTTACTCTTTGAATTTA
1 ATTACTA-TTTTACTCTTTGAATTTA
18118 ATTACCAATTGTCATTTTACTCTTTGAATTTA
1 ATTA-C-----T-ATTTTACTCTTTGAATTTA
*
18150 ATTACCATTTTAC
1 ATTACTATTTTAC
18163 CATTTTACTC
Statistics
Matches: 62, Mismatches: 1, Indels: 17
0.77 0.01 0.21
Matches are distributed among these distances:
25 7 0.11
26 20 0.32
27 10 0.16
31 1 0.02
32 23 0.37
33 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
ATTACTATTTTACTCTTTGAATTTA
Found at i:18167 original size:33 final size:32
Alignment explanation
Indices: 18100--18175 Score: 118
Period size: 32 Copynumber: 2.3 Consensus size: 32
18090 TAATTACTAT
18100 TTTTACTCTTTGAATTTAATTACCAATTGTCA
1 TTTTACTCTTTGAATTTAATTACCAATTGTCA
*
18132 TTTTACTCTTTGAATTTAATTACC-ATTTTACCA
1 TTTTACTCTTTGAATTTAATTACCAATTGT--CA
18165 TTTTACTCTTT
1 TTTTACTCTTT
18176 ACTGATTACT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
31 4 0.10
32 24 0.59
33 13 0.32
ACGTcount: A:0.25, C:0.17, G:0.04, T:0.54
Consensus pattern (32 bp):
TTTTACTCTTTGAATTTAATTACCAATTGTCA
Found at i:18255 original size:40 final size:39
Alignment explanation
Indices: 18211--18358 Score: 175
Period size: 40 Copynumber: 3.9 Consensus size: 39
18201 TTTTTACTCT
18211 TTACCGATTTACTGATTACTTCTTTTACTTTTACTCTTAA
1 TTACC-ATTTACTGATTACTTCTTTTACTTTTACTCTTAA
18251 TTACCATTTTACTGATTACTTCTTTTACTTTTACTCTTAA
1 TTACCA-TTTACTGATTACTTCTTTTACTTTTACTCTTAA
* * * *
18291 TTACCAACTTACTAATTACTTATTTTACTTTCACTC-T-A
1 TTACC-ATTTACTGATTACTTCTTTTACTTTTACTCTTAA
*
18329 -T----TTTACTGATTACTTCTTTTACTTTCACTC
1 TTACCATTTACTGATTACTTCTTTTACTTTTACTC
18359 CATTCTACTA
Statistics
Matches: 99, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
32 26 0.26
37 1 0.01
38 1 0.01
39 2 0.02
40 68 0.69
41 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.03, T:0.53
Consensus pattern (39 bp):
TTACCATTTACTGATTACTTCTTTTACTTTTACTCTTAA
Found at i:18330 original size:16 final size:16
Alignment explanation
Indices: 18311--18358 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
18301 ACTAATTACT
18311 TATTTTACTTTCACTC
1 TATTTTACTTTCACTC
18327 TATTTTACTGATT-ACT-
1 TATTTTACT--TTCACTC
*
18343 TCTTTTACTTTCACTC
1 TATTTTACTTTCACTC
18359 CATTCTACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
14 2 0.07
15 3 0.11
16 17 0.63
17 3 0.11
18 2 0.07
ACGTcount: A:0.19, C:0.23, G:0.02, T:0.56
Consensus pattern (16 bp):
TATTTTACTTTCACTC
Found at i:18376 original size:32 final size:32
Alignment explanation
Indices: 18300--18376 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
18290 ATTACCAACT
* * *
18300 TACTAATTACTTATTTTACTTTCACTCTATTT
1 TACTAATTACTTCTTTTACTTTCACTCCATTC
*
18332 TACTGATTACTTCTTTTACTTTCACTCCATTC
1 TACTAATTACTTCTTTTACTTTCACTCCATTC
*
18364 TACTAATCACTTC
1 TACTAATTACTTC
18377 CTCTTTTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.23, C:0.25, G:0.01, T:0.51
Consensus pattern (32 bp):
TACTAATTACTTCTTTTACTTTCACTCCATTC
Found at i:18396 original size:29 final size:31
Alignment explanation
Indices: 18364--18428 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 31
18354 CACTCCATTC
18364 TACTAATCACTTCCTCTTTTA-TT-TCTTTT
1 TACTAATCACTTCCTCTTTTACTTATCTTTT
* * * *
18393 TACTGATTACTTCTTTTTTTACTTTATCTTTT
1 TACTAATCACTTCCTCTTTTAC-TTATCTTTT
18425 TACT
1 TACT
18429 TTTGCTGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 17 0.59
31 2 0.07
32 10 0.34
ACGTcount: A:0.17, C:0.20, G:0.02, T:0.62
Consensus pattern (31 bp):
TACTAATCACTTCCTCTTTTACTTATCTTTT
Found at i:18559 original size:32 final size:32
Alignment explanation
Indices: 18491--18563 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
18481 CTGATTAATC
* *
18491 CTTTTACCTTGACTCTTAATTACTAACTTACT
1 CTTTTACTTTGACCCTTAATTACTAACTTACT
* *
18523 CTTTTACTTTGACCCTTAATTACTGA-TTGCT
1 CTTTTACTTTGACCCTTAATTACTAACTTACT
18554 ACTTTTACTT
1 -CTTTTACTT
18564 CATCTCTTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.22, C:0.23, G:0.05, T:0.49
Consensus pattern (32 bp):
CTTTTACTTTGACCCTTAATTACTAACTTACT
Found at i:18660 original size:60 final size:63
Alignment explanation
Indices: 18541--18660 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 63
18531 TTGACCCTTA
* * * *
18541 ATTACTGATTGCTACTTTTACTTCATCTCTTAGTTATCAGTTTACTAATTAATCCTTTTATTTG
1 ATTACTGATTACTACTTTTACTT-ATCTCTTAATTATCAATCTACTAATTAATCCTTTTATTTG
*
18605 ATTACTGATTACTACTTTTAC-T-TC-CTTAATTATCAATCTACTAATTAATCTTTTTA
1 ATTACTGATTACTACTTTTACTTATCTCTTAATTATCAATCTACTAATTAATCCTTTTA
18661 CTTCCTCTCT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
60 28 0.55
61 2 0.04
63 1 0.02
64 20 0.39
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (63 bp):
ATTACTGATTACTACTTTTACTTATCTCTTAATTATCAATCTACTAATTAATCCTTTTATTTG
Found at i:20397 original size:18 final size:18
Alignment explanation
Indices: 20374--20438 Score: 51
Period size: 18 Copynumber: 3.3 Consensus size: 18
20364 CATCGCACAA
20374 GCCATCCGGCCACAACCG
1 GCCATCCGGCCACAACCG
*
20392 GCCATCGAACGGGC-CAACGCATG
1 GCCATC---CGGCCACAAC-C--G
20415 CGCCATCCGGCCACAACCG
1 -GCCATCCGGCCACAACCG
20434 GCCAT
1 GCCAT
20439 TCGATCCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
18 11 0.30
19 1 0.03
20 4 0.11
21 10 0.27
22 4 0.11
23 1 0.03
24 6 0.16
ACGTcount: A:0.23, C:0.45, G:0.25, T:0.08
Consensus pattern (18 bp):
GCCATCCGGCCACAACCG
Done.