Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005312.1 Hibiscus syriacus cultivar Beakdansim tig00012020_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: 99293
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:1601 original size:17 final size:18
Alignment explanation
Indices: 1579--1627 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
1569 ATGTAAAATG
*
1579 GTATCGATACCGTATA-A
1 GTATCGATACCATATAGA
**
1596 GTATCGGCACCATATAGTA
1 GTATCGATACCATATAG-A
1615 GTATCGATACCAT
1 GTATCGATACCAT
1628 GGTGGGGGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 13 0.52
19 12 0.48
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (18 bp):
GTATCGATACCATATAGA
Found at i:2025 original size:54 final size:54
Alignment explanation
Indices: 1961--2265 Score: 358
Period size: 54 Copynumber: 5.6 Consensus size: 54
1951 TTGCCAAATA
* * * * *
1961 GGCACAAAGTGTGCAAATCACGGAACTCATCATATGTTGATGAATCATTGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACTGTTTC
* * *
2015 GGCACTAAGTGTGCAATTCACGGAATTCATCATTTATTGATGAATAACTATTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACTGTTTC
***** * * *
2069 TATGTTAAGTTTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACTGTTTC
* * *
2123 GGCACTATGTGTACAATTCACGGAATTCATCATATGTTGATGAATTACTGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACTGTTTC
* * * * *
2177 GGCACTAAGTGTGAAATTCACAGAATTCATCACATGTTGATGAATCACCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACTGTTTC
* * * *
2231 GACACTAAGTGTGCAATTCATGAAATTTATCATAT
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATAT
2266 CGATGAAAAC
Statistics
Matches: 207, Mismatches: 44, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 207 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACTGTTTC
Found at i:2433 original size:54 final size:54
Alignment explanation
Indices: 2291--2434 Score: 190
Period size: 54 Copynumber: 2.7 Consensus size: 54
2281 GTACTCATGA
* *
2291 AATTCATCATATG-T--TGAATCACCGTTTCTG-CACTAAGTGTGCAATTCACGG
1 AATTCATCATATGTTGATGAATCATCGTTTC-GACACTAAGTGTGCAATTCACAG
* *
2342 AATTCATCGTATGTTGATGAATCATCGTTT-TATCACTAAGTGTGCAATTCACAG
1 AATTCATCATATGTTGATGAATCATCGTTTCGA-CACTAAGTGTGCAATTCACAG
*
2396 AATTCATCATATGTTGATGAATAATCGTTTCGACACTAA
1 AATTCATCATATGTTGATGAATCATCGTTTCGACACTAA
2435 ATTGTTTCGG
Statistics
Matches: 80, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
51 12 0.15
52 1 0.01
54 66 0.82
55 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (54 bp):
AATTCATCATATGTTGATGAATCATCGTTTCGACACTAAGTGTGCAATTCACAG
Found at i:2535 original size:124 final size:124
Alignment explanation
Indices: 2314--2541 Score: 291
Period size: 124 Copynumber: 1.8 Consensus size: 124
2304 TTGAATCACC
* * * * * *** *
2314 GTTTCTGCACTAAGTGTGCAATTCACGGAATTCATCGTATGTTGATGAATCATCGTTTTATCACT
1 GTTTCGGCACTAAGTGTGCAATTCACGGAATTCATCATATGTAGATGAATCACCCTACAAACACT
*
2379 AAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAATCGTTTCGACACTAAATT
66 AAGTGTGCAACTCACAGAATTCATCATATGTTGATGAATAATCGTTTCGACACTAAATT
*
2438 GTTTCGGCACTAAGTGTGCAATTCACGGAATTCATCATTTGTAGATGAA-CAACCCTACAAACAC
1 GTTTCGGCACTAAGTGTGCAATTCACGGAATTCATCATATGTAGATGAATC-ACCCTACAAACAC
* *
2502 TATA-TGTGCAACTCACA-ACATTTATCATGTGTTGATGAAT
65 TA-AGTGTGCAACTCACAGA-ATTCATCATATGTTGATGAAT
2542 GACTGTGTAG
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
123 2 0.02
124 85 0.97
125 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (124 bp):
GTTTCGGCACTAAGTGTGCAATTCACGGAATTCATCATATGTAGATGAATCACCCTACAAACACT
AAGTGTGCAACTCACAGAATTCATCATATGTTGATGAATAATCGTTTCGACACTAAATT
Found at i:2670 original size:44 final size:45
Alignment explanation
Indices: 2571--2719 Score: 193
Period size: 44 Copynumber: 3.4 Consensus size: 45
2561 GTGCATATTA
* *
2571 ATGAAAGG-TGCCAT-AA-GAAATGTATAATAATGTAT-AAAGGC
1 ATGAAAGGATGTCATAAATGAAATGTATAATAATGTATAAAAGAC
* * *
2612 ATGAAAGGATGTCATAAATG-AATGTATAACAGTATATAAAAGAC
1 ATGAAAGGATGTCATAAATGAAATGTATAATAATGTATAAAAGAC
* *
2656 ATGAAATGATGTCATAAATGAAATGAATAATAATGTATAAAAGAC
1 ATGAAAGGATGTCATAAATGAAATGTATAATAATGTATAAAAGAC
2701 ATGAAAGGATGT-ATAAATG
1 ATGAAAGGATGTCATAAATG
2720 TAATTAATAA
Statistics
Matches: 92, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
41 8 0.09
42 5 0.05
43 16 0.17
44 32 0.35
45 31 0.34
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.26
Consensus pattern (45 bp):
ATGAAAGGATGTCATAAATGAAATGTATAATAATGTATAAAAGAC
Found at i:2714 original size:21 final size:21
Alignment explanation
Indices: 2646--2717 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
2636 TATAACAGTA
2646 TATAAAAGACATGAAATGATG
1 TATAAAAGACATGAAATGATG
* * *
2667 TCATAAATGAAATGAATAATAATG
1 T-ATAAAAGACATG-A-AATGATG
*
2691 TATAAAAGACATGAAAGGATG
1 TATAAAAGACATGAAATGATG
2712 TATAAA
1 TATAAA
2718 TGTAATTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
21 12 0.29
22 11 0.27
23 11 0.27
24 7 0.17
ACGTcount: A:0.54, C:0.04, G:0.17, T:0.25
Consensus pattern (21 bp):
TATAAAAGACATGAAATGATG
Found at i:2743 original size:44 final size:45
Alignment explanation
Indices: 2596--2734 Score: 162
Period size: 44 Copynumber: 3.1 Consensus size: 45
2586 AGAAATGTAT
*
2596 AATAATGTAT-AAAGGCATGAAAGGATGTCATAAATGAATGT-AT-
1 AATAATGTATAAAAGACATGAAAGGATGTCATAAATGAAT-TAATA
* * * * *
2639 AACAGTATATAAAAGACATGAAATGATGTCATAAATGAAATGAAT-
1 AATAATGTATAAAAGACATGAAAGGATGTCATAAATG-AATTAATA
2684 AATAATGTATAAAAGACATGAAAGGATGT-ATAAATGTAATTAATA
1 AATAATGTATAAAAGACATGAAAGGATGTCATAAATG-AATTAATA
2729 AATAAT
1 AATAAT
2735 TACTAAAGAA
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
43 7 0.09
44 37 0.46
45 36 0.45
ACGTcount: A:0.52, C:0.04, G:0.17, T:0.27
Consensus pattern (45 bp):
AATAATGTATAAAAGACATGAAAGGATGTCATAAATGAATTAATA
Found at i:7515 original size:20 final size:21
Alignment explanation
Indices: 7484--7523 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
7474 GCAAGGCTTG
7484 ACAAGAAGTTTCAAAACTTTT
1 ACAAGAAGTTTCAAAACTTTT
*
7505 ACAAG-AGTTTCGAAACTTT
1 ACAAGAAGTTTCAAAACTTT
7524 CTAGTACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (21 bp):
ACAAGAAGTTTCAAAACTTTT
Found at i:14769 original size:22 final size:20
Alignment explanation
Indices: 14714--14777 Score: 71
Period size: 17 Copynumber: 3.2 Consensus size: 20
14704 TTTGACCAGT
*
14714 TTGACCCGACCGACCCGAACG
1 TTGACCCGACCG-CCCGACCG
14735 TTGACCCGA---CCCGACCG
1 TTGACCCGACCGCCCGACCG
14752 TTGACCCGACTCGTCCCGACCG
1 TTGACCCGAC-CG-CCCGACCG
14774 TTGA
1 TTGA
14778 TCGTTGACTT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 16 0.43
21 9 0.24
22 12 0.32
ACGTcount: A:0.19, C:0.42, G:0.23, T:0.16
Consensus pattern (20 bp):
TTGACCCGACCGCCCGACCG
Found at i:18215 original size:20 final size:20
Alignment explanation
Indices: 18168--18220 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
18158 ATGCTTTAAT
18168 GTTTTGAAACTTT-ACAAGA
1 GTTTTGAAACTTTCACAAGA
* *
18187 GTTTTGAAACTTTCGCAATA
1 GTTTTGAAACTTTCACAAGA
*
18207 GTTTCGAAACTTTC
1 GTTTTGAAACTTTC
18221 CTTAAAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
GTTTTGAAACTTTCACAAGA
Found at i:29868 original size:2 final size:2
Alignment explanation
Indices: 29857--29886 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
29847 TAATAAAATG
29857 TA TA -A 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 T
29887 GTGCATGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39427 original size:20 final size:20
Alignment explanation
Indices: 39384--39449 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
39374 TTTCGATATG
39384 GATACTCAAT-CTTC-GTATA
1 GATAC-CAATCCTTCGGTATA
39403 GATACCAATCCTTCGGTATA
1 GATACCAATCCTTCGGTATA
*
39423 TATACCAATCCTTCGGTATA
1 GATACCAATCCTTCGGTATA
*
39443 GAGACCA
1 GATACCA
39450 TTCAGTCTCG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
18 4 0.10
19 9 0.21
20 29 0.69
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (20 bp):
GATACCAATCCTTCGGTATA
Found at i:58793 original size:20 final size:20
Alignment explanation
Indices: 58768--58841 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
58758 CCCTTCAACT
58768 AAAGGATCGATCCCCTTCCC
1 AAAGGATCGATCCCCTTCCC
* * *
58788 AAAGGATCAAT-CCCATCAGC
1 AAAGGATCGATCCCCTTC-CC
* *
58808 AAAGGATTGATCCCTTTCCC
1 AAAGGATCGATCCCCTTCCC
*
58828 AAATGATCGATCCC
1 AAAGGATCGATCCC
58842 AAACTCACTG
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 5 0.12
20 33 0.79
21 4 0.10
ACGTcount: A:0.31, C:0.32, G:0.15, T:0.22
Consensus pattern (20 bp):
AAAGGATCGATCCCCTTCCC
Found at i:58821 original size:40 final size:41
Alignment explanation
Indices: 58747--58842 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 41
58737 ATTTTCATAA
* *
58747 AAAGGATTAATCCCTTCAACTAAAGGATCGATCCCCTTCCC
1 AAAGGATCAATCCCATCAACTAAAGGATCGATCCCCTTCCC
* * *
58788 AAAGGATCAATCCCATCAGC-AAAGGATTGATCCCTTTCCC
1 AAAGGATCAATCCCATCAACTAAAGGATCGATCCCCTTCCC
* *
58828 AAATGATCGATCCCA
1 AAAGGATCAATCCCA
58843 AACTCACTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 31 0.65
41 17 0.35
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.23
Consensus pattern (41 bp):
AAAGGATCAATCCCATCAACTAAAGGATCGATCCCCTTCCC
Found at i:60110 original size:58 final size:58
Alignment explanation
Indices: 59977--60525 Score: 746
Period size: 58 Copynumber: 9.5 Consensus size: 58
59967 ACCGTTACGA
* * * *
59977 AAATTTATACACTTAGTATGAATTTCCT-AGTTTTGCACAT--AAA-GTGCCCATACAG
1 AAATTCATCCACTTAGTATGAATTTCTTAAG-TTTACACATAAAAATGTGCCCATACAG
** * * ** *
60032 AAATTCATCCACACATTATGAATTTCTTAAGTTTACACATAAAATTGTGCTTATACAA
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACAG
* * * * * *
60090 AAATTCATCCACTTAATATGAATTTCTAAAGTTTACAAATTAAAATGTGCACATACGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACAG
* * * * *
60148 AAATTCATCTACTTAGTATGAATTTCTTAAATTTACACATAAAAATGCGCACATACGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACAG
* * *
60206 AAATTCATTCACTTAATATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACAA
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACAG
* * * *
60264 AAATTCATCCACTTAGTATGAATTTCTTAAATTTACACATAAAATTGTGCACATACGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACAG
* *
60322 AAATTCATCCACTTAATATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACAA
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACAG
*
60380 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACAG
* * *
60438 AAATTCATACACTTACTATGAATTTCTTAAGTTTACGCATAAAAATGTGCCCATACAG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACAG
60496 AAATTCATCCACTTAGTATGAATTTCTTAA
1 AAATTCATCCACTTAGTATGAATTTCTTAA
60526 CATTTTTGCA
Statistics
Matches: 431, Mismatches: 59, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
55 30 0.07
56 2 0.00
57 2 0.00
58 397 0.92
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (58 bp):
AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACAG
Found at i:61042 original size:95 final size:95
Alignment explanation
Indices: 60869--61087 Score: 246
Period size: 95 Copynumber: 2.3 Consensus size: 95
60859 AGTATGGATA
* * * * *
60869 CCCT-ACCATAGTATCGATACTACTATACTATGGTACCAAAACCCCCTTTCGGTATCGATATCAA
1 CCCTAACCATGGTATCGATACTACCATATTATAGTACCAAAACCCCCTTTCGGTATCGATACCAA
* *
60933 TATTAGATTTGATGTTTCATGGTCTCGATA-
66 TATTAGATTTGATGTTGCATGGTATCGA-AG
* ** ** *
60963 CCCTTATTATGGTATCGATACTACCATATTATAGTACTGATACCCCCTTTCGGTATCGATACCAA
1 CCCTAACCATGGTATCGATACTACCATATTATAGTACCAAAACCCCCTTTCGGTATCGATACCAA
* *
61028 -ATTTAGGTTTGATGTTGCCTGGTATCGAAG
66 TA-TTAGATTTGATGTTGCATGGTATCGAAG
* *
61058 CCCTAACCATGGCATCGATACTACCTTATT
1 CCCTAACCATGGTATCGATACTACCATATT
61088 GGTATTGATA
Statistics
Matches: 103, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
94 6 0.06
95 97 0.94
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (95 bp):
CCCTAACCATGGTATCGATACTACCATATTATAGTACCAAAACCCCCTTTCGGTATCGATACCAA
TATTAGATTTGATGTTGCATGGTATCGAAG
Found at i:62444 original size:2 final size:2
Alignment explanation
Indices: 62437--62502 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
62427 TATGATTTGT
62437 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
62479 TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG
62503 ATATAGAAGT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:63682 original size:24 final size:24
Alignment explanation
Indices: 63655--63726 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
63645 TATATTTACC
63655 ATTTATCCATAAACTCGTAAGCTT
1 ATTTATCCATAAACTCGTAAGCTT
* * *
63679 ATTT-TACCA-ATAC-AGTTAGC--
1 ATTTAT-CCATAAACTCGTAAGCTT
*
63699 ATTTATCCATAAGCTCGTAAGCTT
1 ATTTATCCATAAACTCGTAAGCTT
63723 ATTT
1 ATTT
63727 TTACCAATAC
Statistics
Matches: 35, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
20 7 0.20
21 3 0.09
22 10 0.29
23 4 0.11
24 11 0.31
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (24 bp):
ATTTATCCATAAACTCGTAAGCTT
Found at i:63747 original size:45 final size:44
Alignment explanation
Indices: 63604--63755 Score: 241
Period size: 44 Copynumber: 3.4 Consensus size: 44
63594 AATAAAATTT
*
63604 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAT-CCATAAGCTCGTAAGCTTATTTTACCAATACA
* *
63649 TTTACCATTTATCCATAAACTCGTAAGCTTATTTTACCAATACA
1 CTTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACA
* *
63693 GTTAGCATTTATCCATAAGCTCGTAAGCTTATTTTTACCAATACA
1 CTTACCATTTATCCATAAGCTCGTAAGCTTA-TTTTACCAATACA
63738 CTTACCATTTATCCATAA
1 CTTACCATTTATCCATAA
63756 CCATATATCA
Statistics
Matches: 98, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
44 58 0.59
45 40 0.41
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (44 bp):
CTTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACA
Found at i:72644 original size:20 final size:20
Alignment explanation
Indices: 72619--72658 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
72609 AACATTCGAT
72619 CGACGA-TTCACGACAAACGA
1 CGACGAGTT-ACGACAAACGA
*
72639 CGACGAGTTTCGACAAACGA
1 CGACGAGTTACGACAAACGA
72659 TCACTGAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.38, C:0.28, G:0.23, T:0.12
Consensus pattern (20 bp):
CGACGAGTTACGACAAACGA
Found at i:77566 original size:40 final size:42
Alignment explanation
Indices: 77470--77577 Score: 139
Period size: 40 Copynumber: 2.6 Consensus size: 42
77460 ATAAAAAATG
**
77470 TCGCAATAGGTTAGGACATTTAGCGATGTTTTGTTTACAAACA
1 TCGCAATAGGTTAGGACATTTAGCGA-GCATTGTTTACAAACA
* *
77513 TCACAATAGGTTAGGACATTTAGCGA-CATT-TTTCCAAACA
1 TCGCAATAGGTTAGGACATTTAGCGAGCATTGTTTACAAACA
* *
77553 TTGCAATATGTTAGGACATTTAGCG
1 TCGCAATAGGTTAGGACATTTAGCG
77578 GCACTTTTGA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
40 31 0.53
41 2 0.03
43 25 0.43
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (42 bp):
TCGCAATAGGTTAGGACATTTAGCGAGCATTGTTTACAAACA
Found at i:78083 original size:21 final size:21
Alignment explanation
Indices: 78057--78110 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
78047 CCCTCTCTGT
* * *
78057 TTCTCTCGTTTTTCTTTCTAC
1 TTCTCTCGCTTCTCATTCTAC
*
78078 TTCTCTTGCTTCTCATTCTAC
1 TTCTCTCGCTTCTCATTCTAC
*
78099 TTCTCTCACTTC
1 TTCTCTCGCTTC
78111 AACTTCGGCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.07, C:0.33, G:0.04, T:0.56
Consensus pattern (21 bp):
TTCTCTCGCTTCTCATTCTAC
Found at i:81260 original size:47 final size:49
Alignment explanation
Indices: 81207--81304 Score: 130
Period size: 47 Copynumber: 2.0 Consensus size: 49
81197 TTCCCGAATT
*
81207 ATATACTAGTCTTGCGAACA-AGATTTCTAAAC-T-ATCACAAGTGTTTG
1 ATATACTAGTCTTGCGAACAGA-ATTTCTAAACATAATCAAAAGTGTTTG
* * *
81254 ATATACTGGTGTTGCGAACAGAATTTGTAAACATAATCAAAAGTGTTTG
1 ATATACTAGTCTTGCGAACAGAATTTCTAAACATAATCAAAAGTGTTTG
81303 AT
1 AT
81305 GCTAAAAGTG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
47 27 0.61
48 2 0.05
49 15 0.34
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (49 bp):
ATATACTAGTCTTGCGAACAGAATTTCTAAACATAATCAAAAGTGTTTG
Found at i:82537 original size:16 final size:16
Alignment explanation
Indices: 82518--82551 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
82508 TTAAAATATC
*
82518 AAAAATTTATAATAAA
1 AAAAAGTTATAATAAA
*
82534 AAAAAGTTATACTAAA
1 AAAAAGTTATAATAAA
82550 AA
1 AA
82552 TTTAAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAAAGTTATAATAAA
Found at i:83511 original size:26 final size:27
Alignment explanation
Indices: 83456--83512 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
83446 AAGTTTTCTA
*
83456 ATTTTCAAAAAACTAAAAATGAAAATT
1 ATTTTCAAAAAACTAAAAAAGAAAATT
*
83483 ATTTTCTAAAAA-TAAAAACAGAAAA-T
1 ATTTTCAAAAAACTAAAAA-AGAAAATT
83509 ATTT
1 ATTT
83513 CATAGAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.32
Consensus pattern (27 bp):
ATTTTCAAAAAACTAAAAAAGAAAATT
Found at i:84017 original size:10 final size:9
Alignment explanation
Indices: 83971--84025 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
83961 AATGACAAGG
*
83971 TAATTTTTT
1 TAATTATTT
83980 TAATTATTT
1 TAATTATTT
83989 T-ATTATTT
1 TAATTATTT
* *
83997 AAATTAGTT
1 TAATTATTT
84006 TAGATTATTT
1 TA-ATTATTT
84016 T-A-TATTT
1 TAATTATTT
84023 TAA
1 TAA
84026 GATTAAATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
7 6 0.16
8 9 0.24
9 16 0.42
10 7 0.18
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (9 bp):
TAATTATTT
Found at i:84024 original size:27 final size:27
Alignment explanation
Indices: 83978--84030 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
83968 AGGTAATTTT
83978 TTTAATTATTTTATTATTTAA-ATTAG
1 TTTAATTATTTTATTATTTAAGATTAG
84004 TTTAGATTATTTTA-TATTTTAAGATTA
1 TTTA-ATTATTTTATTA-TTTAAGATTA
84031 AATTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 6 0.25
27 14 0.58
28 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (27 bp):
TTTAATTATTTTATTATTTAAGATTAG
Found at i:95305 original size:12 final size:12
Alignment explanation
Indices: 95288--95313 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
95278 GAGTGATTCG
95288 GATGAAGATGAC
1 GATGAAGATGAC
95300 GATGAAGATGAC
1 GATGAAGATGAC
95312 GA
1 GA
95314 GAAAATGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.35, T:0.15
Consensus pattern (12 bp):
GATGAAGATGAC
Done.