Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005577.1 Hibiscus syriacus cultivar Beakdansim tig00012938_pilon, 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: 57480
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Found at i:7587 original size:21 final size:21
Alignment explanation
Indices: 7561--7634 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
7551 GTTTCCAGAT
*
7561 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTGGACTA
7582 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTGGACTA
* *
7603 TCGCAATGCAAACTTGGACTA
1 TCGCAACGCGAACTTGGACTA
*
7624 TCGCAATGCGA
1 TCGCAACGCGA
7635 TTTACATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (21 bp):
TCGCAACGCGAACTTGGACTA
Found at i:7673 original size:21 final size:21
Alignment explanation
Indices: 7643--7737 Score: 122
Period size: 21 Copynumber: 4.6 Consensus size: 21
7633 GATTTACATA
*
7643 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
7664 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
7685 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
7706 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
7725 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
7738 TTATTCCAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
19 15 0.24
21 47 0.76
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:7723 original size:40 final size:42
Alignment explanation
Indices: 7668--7762 Score: 167
Period size: 40 Copynumber: 2.3 Consensus size: 42
7658 TCCAAGTTCG
7668 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
7708 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
7750 CGTTGTGATAGTC
1 CGTTGCGATAGTC
7763 CAAAATCGTA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
40 29 0.56
41 2 0.04
42 21 0.40
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:7753 original size:21 final size:20
Alignment explanation
Indices: 7689--7754 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 20
7679 TCGAAGTTCG
7689 CGTTGCGATT-TTCCAAATT
1 CGTTGCGATTATTCCAAATT
* * *
7708 CGTTGCGA-TAGTCGAAGTT
1 CGTTGCGATTATTCCAAATT
7727 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TTATTCCAAATT
7750 CGTTG
1 CGTTG
7755 TGATAGTCCA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 14 0.39
21 13 0.36
23 8 0.22
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTATTCCAAATT
Found at i:7765 original size:61 final size:60
Alignment explanation
Indices: 7649--7771 Score: 140
Period size: 61 Copynumber: 2.0 Consensus size: 60
7639 CATATTCGCA
* * ** *
7649 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAATTC-CGTTGCGATAGTCCAAAATCG
* * *
7710 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT-CGTTGTGATAGTCCAAAATCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCCAAATTCCGTTGCGATAGTCCAAAATCG
7771 T
1 T
7772 AACGACTGGT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
61 44 0.85
63 8 0.15
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (60 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAATTCCGTTGCGATAGTCCAAAATCG
Found at i:7766 original size:19 final size:19
Alignment explanation
Indices: 7649--7771 Score: 84
Period size: 21 Copynumber: 6.1 Consensus size: 19
7639 CATATTCGCA
*
7649 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAATT--CG
* *
7670 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAATT--CG
**
7691 TTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAATTCG
* *
7710 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAATT--CG
*
7731 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAATTCG
* *
7752 TTGTGATAGTCCAAAATCG
1 TTGCGATAGTCCAAATTCG
7771 T
1 T
7772 AACGACTGGT
Statistics
Matches: 83, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
19 27 0.33
21 48 0.58
23 8 0.10
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (19 bp):
TTGCGATAGTCCAAATTCG
Found at i:8340 original size:6 final size:6
Alignment explanation
Indices: 8329--8367 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
8319 GTCTCGTCTG
8329 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
8368 AATACGTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:8515 original size:42 final size:42
Alignment explanation
Indices: 8456--8673 Score: 379
Period size: 42 Copynumber: 5.3 Consensus size: 42
8446 TGCGACTTTG
8456 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
8498 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACCTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
8540 GACTATCGCAACAAATTTGGAATAAATCGCAATGCAAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
8582 GACTATCGCAACGAATTT-GAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
8623 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
8663 GACTATCGCAA
1 GACTATCGCAA
8674 TGCGAACTTG
Statistics
Matches: 167, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
40 30 0.18
41 40 0.24
42 97 0.58
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:8670 original size:21 final size:20
Alignment explanation
Indices: 8481--8700 Score: 144
Period size: 21 Copynumber: 10.6 Consensus size: 20
8471 TTTGGAATAA
8481 ATCGCAACGCGAACTTCGACT
1 ATCGCAA-GCGAACTTCGACT
* * *
8502 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTCGACT
*
8521 AAATCGCAACGCGAACCTCGACT
1 --ATCGCAA-GCGAACTTCGACT
* * * *
8544 ATCGCAA-CAAATTTGGAAT
1 ATCGCAAGCGAACTTCGACT
*
8563 AAATCGCAATGCAAACTTCGACT
1 --ATCGCAA-GCGAACTTCGACT
* *
8586 ATCGCAA-CGAA-TTTGAAT
1 ATCGCAAGCGAACTTCGACT
8604 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAA-GCGAACTTCGACT
* * **
8627 ATCGCAA-CGAATTTGGAAA
1 ATCGCAAGCGAACTTCGACT
8646 ATCGCAACGCGAACTTCGACT
1 ATCGCAA-GCGAACTTCGACT
*
8667 ATCGCAATGCGAACTTGGACT
1 ATCGCAA-GCGAACTTCGACT
8688 ATCGCAATGCGAA
1 ATCGCAA-GCGAA
8701 TATGTAAATT
Statistics
Matches: 154, Mismatches: 30, Indels: 30
0.72 0.14 0.14
Matches are distributed among these distances:
18 5 0.03
19 34 0.22
20 7 0.05
21 82 0.53
22 4 0.03
23 22 0.14
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAAGCGAACTTCGACT
Found at i:8700 original size:42 final size:41
Alignment explanation
Indices: 8456--8700 Score: 352
Period size: 42 Copynumber: 5.9 Consensus size: 41
8446 TGCGACTTTG
8456 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAAT-AATCGCAACGCGAACTTC
*
8498 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACCTC
1 GACTATCGCAACGAATTTGGAAT-AATCGCAACGCGAACTTC
* * *
8540 GACTATCGCAACAAATTTGGAATAAATCGCAATGCAAACTTC
1 GACTATCGCAACGAATTTGGAAT-AATCGCAACGCGAACTTC
8582 GACTATCGCAACGAATTT-GAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAAT-AATCGCAACGCGAACTTC
8623 GACTATCGCAACGAATTTGGAA-AATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAATCGCAACGCGAACTTC
* * *
8663 GACTATCGCAATGCGAACTTGGACT-ATCGCAATGCGAA
1 GACTATCGCAA--CGAATTTGGAATAATCGCAACGCGAA
8701 TATGTAAATT
Statistics
Matches: 188, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
40 29 0.15
41 39 0.21
42 120 0.64
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (41 bp):
GACTATCGCAACGAATTTGGAATAATCGCAACGCGAACTTC
Found at i:8920 original size:31 final size:31
Alignment explanation
Indices: 8885--8966 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
8875 GTTATTTTCT
*
8885 CTAAATTTTAAATTAAATATTAACTTGACCA
1 CTAAATTTTAAATAAAATATTAACTTGACCA
* * * *
8916 CTAAATTTTGAATAAAATAATAATTTGATCA
1 CTAAATTTTAAATAAAATATTAACTTGACCA
*
8947 CTAAATTTTAGATAAAATAT
1 CTAAATTTTAAATAAAATAT
8967 CAATTTAACT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.39
Consensus pattern (31 bp):
CTAAATTTTAAATAAAATATTAACTTGACCA
Found at i:13408 original size:24 final size:24
Alignment explanation
Indices: 13381--13427 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
13371 AAACTTATAT
* *
13381 TAAAATTTTAGGGGTTTAAAATTG
1 TAAAATTTTAGAGGTGTAAAATTG
13405 TAAAATTTTAGAGGTGTAAAATT
1 TAAAATTTTAGAGGTGTAAAATT
13428 AAACTATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (24 bp):
TAAAATTTTAGAGGTGTAAAATTG
Found at i:15061 original size:82 final size:82
Alignment explanation
Indices: 14924--15083 Score: 275
Period size: 82 Copynumber: 2.0 Consensus size: 82
14914 TATCAATGGA
* * *
14924 CTGCAGATTCCATGCATTTCGATCCCAGGTTCCTCCATTGCAATAATGGATGCCATTACTGTGAA
1 CTGCAGATTCCATGCATTTCAATACCAGGTTCCTCCATTGCAATAATGGATGCCATTACTCTGAA
14989 GTTCTTTCTGCTTCGCG
66 GTTCTTTCTGCTTCGCG
* *
15006 CTGCAGATTCCATGCATTTCAATATCAGGTTCCTCCATTGCAATAATGGATGCCATTACTCTGAG
1 CTGCAGATTCCATGCATTTCAATACCAGGTTCCTCCATTGCAATAATGGATGCCATTACTCTGAA
15071 GTTCTTTCTGCTT
66 GTTCTTTCTGCTT
15084 TGTGCTTGTG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (82 bp):
CTGCAGATTCCATGCATTTCAATACCAGGTTCCTCCATTGCAATAATGGATGCCATTACTCTGAA
GTTCTTTCTGCTTCGCG
Found at i:18681 original size:17 final size:18
Alignment explanation
Indices: 18659--18696 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
18649 CCCAAACATG
18659 CCTCTCCC-AATTACCCT
1 CCTCTCCCTAATTACCCT
*
18676 CCTCTCCCTCATTACCCT
1 CCTCTCCCTAATTACCCT
18694 CCT
1 CCT
18697 GATCATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.13, C:0.55, G:0.00, T:0.32
Consensus pattern (18 bp):
CCTCTCCCTAATTACCCT
Found at i:27145 original size:13 final size:13
Alignment explanation
Indices: 27127--27188 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 13
27117 TGCGTCATAA
*
27127 ATTTATGACGCGC
1 ATTTATGACGCAC
**
27140 ATTTATGACATAC
1 ATTTATGACGCAC
* *
27153 ATTTATGGCACAC
1 ATTTATGACGCAC
27166 ATTTATGACGCAC
1 ATTTATGACGCAC
*
27179 ATTCATGACG
1 ATTTATGACG
27189 TTCATTGAGC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:40748 original size:18 final size:17
Alignment explanation
Indices: 40725--40759 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
40715 CGAACCGGTT
40725 CGACCCGACCCGTTGACC
1 CGACCCGA-CCGTTGACC
40743 CGACCCGACCGTTGACC
1 CGACCCGACCGTTGACC
40760 GTTAACCGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.17, C:0.49, G:0.23, T:0.11
Consensus pattern (17 bp):
CGACCCGACCGTTGACC
Found at i:40887 original size:24 final size:26
Alignment explanation
Indices: 40850--40908 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
40840 AAAAAAAAAA
*
40850 TTAAAAAA-GGTATTTT-GTAATT-T
1 TTAAAAAATGATATTTTAGTAATTAT
40873 TTAAAAAATGATATTTTAGTAATTAT
1 TTAAAAAATGATATTTTAGTAATTAT
*
40899 TTTAAAAATG
1 TTAAAAAATG
40909 GTGCTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 8 0.26
24 7 0.23
25 6 0.19
26 10 0.32
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (26 bp):
TTAAAAAATGATATTTTAGTAATTAT
Found at i:40961 original size:30 final size:29
Alignment explanation
Indices: 40884--40965 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
40874 TAAAAAATGA
40884 TATTTTAGTAATTATTTTAAAAATGGTGC
1 TATTTTAGTAATTATTTTAAAAATGGTGC
* *
40913 TATTTTGGTAATTCTTTTAAAAATGGTGC
1 TATTTTAGTAATTATTTTAAAAATGGTGC
* *
40942 TATTTTTGTAATTTTTTTTAAAAA
1 TATTTTAGTAA-TTATTTTAAAAA
40966 AAGGTGTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 37 0.77
30 11 0.23
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (29 bp):
TATTTTAGTAATTATTTTAAAAATGGTGC
Found at i:45154 original size:17 final size:18
Alignment explanation
Indices: 45132--45165 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
45122 TAGTTTTTTT
45132 GGATTTTT-GGGAATTTA
1 GGATTTTTAGGGAATTTA
45149 GGATTTTTAGGGAATTT
1 GGATTTTTAGGGAATTT
45166 TGGGTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (18 bp):
GGATTTTTAGGGAATTTA
Found at i:45173 original size:18 final size:17
Alignment explanation
Indices: 45128--45174 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
45118 TTTCTAGTTT
45128 TTTTGGATTTTTGGGAA
1 TTTTGGATTTTTGGGAA
*
45145 TTTAGGATTTTTAGGGAA
1 TTTTGGATTTTT-GGGAA
*
45163 TTTTGGGTTTTT
1 TTTTGGATTTTT
45175 CAAAAATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.55
Consensus pattern (17 bp):
TTTTGGATTTTTGGGAA
Found at i:52207 original size:65 final size:65
Alignment explanation
Indices: 52104--52260 Score: 208
Period size: 65 Copynumber: 2.4 Consensus size: 65
52094 ATGCTAAGAT
* * *
52104 TCGATGCAATTTCCATGTTCATGGCCTCAAGCTGAGATACCAGAACAGACTACAAATGCGACCAC
1 TCGATGCAATTTCCATGTTCATGGCCTCAAGCTAAGATACAAGAACAGACAACAAATGCGACCAC
* * * * * *
52169 TCGATGCAACTTCCATGTTCATGGCTTCAA-CATAAGATACAATAACAGACAACAGATGCTACGA
1 TCGATGCAATTTCCATGTTCATGGCCTCAAGC-TAAGATACAAGAACAGACAACAAATGCGACCA
*
52233 T
65 C
52234 TCGATGCAATTTCCATGTTCATGGCCT
1 TCGATGCAATTTCCATGTTCATGGCCT
52261 TGACTTGATG
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 1 0.01
65 78 0.99
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (65 bp):
TCGATGCAATTTCCATGTTCATGGCCTCAAGCTAAGATACAAGAACAGACAACAAATGCGACCAC
Found at i:53609 original size:19 final size:19
Alignment explanation
Indices: 53574--53612 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53564 TATTAAAAAG
*
53574 TTATAAAATAATCTTTTAT
1 TTATAAAATAATATTTTAT
53593 TTAT-AAATAATTATTTTAT
1 TTATAAAATAA-TATTTTAT
53612 T
1 T
53613 AAATTTTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATAAAATAATATTTTAT
Found at i:54294 original size:58 final size:60
Alignment explanation
Indices: 54186--54303 Score: 145
Period size: 63 Copynumber: 2.0 Consensus size: 60
54176 GTTGTCAATA
*
54186 ATTAATAAAATTTATATATATTCATAGTTAATAAAGTAAGACTTAACTAAAATAAATAAATTG
1 ATTAATAAAATTTATATATATTCATAGTTAAT-AAG-AAGACTAAACTAAAA-AAATAAATTG
* *
54249 ATTAATAAGATTT-TATATATTTC-TAGTTAAT-A-AAGACTAAACTAAAAAAGTAAAT
1 ATTAATAAAATTTATATATA-TTCATAGTTAATAAGAAGACTAAACTAAAAAAATAAAT
54304 ATTTAAATTA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
57 7 0.14
58 14 0.27
60 1 0.02
62 14 0.27
63 15 0.29
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (60 bp):
ATTAATAAAATTTATATATATTCATAGTTAATAAGAAGACTAAACTAAAAAAATAAATTG
Found at i:56065 original size:24 final size:24
Alignment explanation
Indices: 56037--56131 Score: 100
Period size: 24 Copynumber: 4.0 Consensus size: 24
56027 AAACGGAGAT
*
56037 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCATAACAGAATTCAG
* * *
56061 ATCAGATATCATAACAGAATCCCG
1 ATCAGAAATCATAACAGAATTCAG
* * *
56085 ATCAGAAATCAGAACATAATTCTG
1 ATCAGAAATCATAACAGAATTCAG
* * *
56109 ATAAAAAATCATAACATAATTCA
1 ATCAGAAATCATAACAGAATTCA
56132 AATAAAAAAT
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.51, C:0.18, G:0.09, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCATAACAGAATTCAG
Found at i:56136 original size:24 final size:24
Alignment explanation
Indices: 56090--56145 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
56080 TCCCGATCAG
**
56090 AAATCAGAACATAATTCTGATAAA
1 AAATCAGAACATAATTCAAATAAA
*
56114 AAATCATAACATAATTCAAATAAA
1 AAATCAGAACATAATTCAAATAAA
56138 AAATCAGA
1 AAATCAGA
56146 TAAAACATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.59, C:0.12, G:0.05, T:0.23
Consensus pattern (24 bp):
AAATCAGAACATAATTCAAATAAA
Found at i:56518 original size:27 final size:25
Alignment explanation
Indices: 56480--56530 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
56470 TTATCCATAG
*
56480 ATCATCTTCGGAATCATCACTGAATAT
1 ATCATATTCGGAATCA-CA-TGAATAT
56507 ATCATATTCGGAATCACATGAATA
1 ATCATATTCGGAATCACATGAATA
56531 AATCTTAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.26
26 2 0.09
27 15 0.65
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (25 bp):
ATCATATTCGGAATCACATGAATAT
Done.