Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009228.1 Hibiscus syriacus cultivar Beakdansim tig00112832_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: 64645
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1473 original size:20 final size:20
Alignment explanation
Indices: 1448--1485 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1438 ACCGATTGCC
1448 CATAGGGTACCGATACCCAT
1 CATAGGGTACCGATACCCAT
1468 CATAGGGTACCGATACCC
1 CATAGGGTACCGATACCC
1486 CTATGCAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.18
Consensus pattern (20 bp):
CATAGGGTACCGATACCCAT
Found at i:9674 original size:54 final size:54
Alignment explanation
Indices: 9559--9677 Score: 143
Period size: 54 Copynumber: 2.2 Consensus size: 54
9549 CATAGGGTGC
* * *
9559 ACCGATACCCCTATGTCAATTTAGGCTCCGAGAAAAACATATTGCCCACAGTGT
1 ACCGATACCCCTATGTCAATTTAGGCTCCGAGAAAAACAGAATGCCCACAGGGT
* * *
9613 ACCGATACCCCTATG-CAAGTTTTGGCTCCGAGAAAAATAGAATGCCCTA-TGGGT
1 ACCGATACCCCTATGTCAA-TTTAGGCTCCGAGAAAAACAGAATGCCC-ACAGGGT
*
9667 ACTGATACCCC
1 ACCGATACCCC
9678 CTGGAGGTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
53 3 0.05
54 52 0.93
55 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (54 bp):
ACCGATACCCCTATGTCAATTTAGGCTCCGAGAAAAACAGAATGCCCACAGGGT
Found at i:11445 original size:48 final size:48
Alignment explanation
Indices: 11391--11494 Score: 118
Period size: 48 Copynumber: 2.2 Consensus size: 48
11381 ATGTTTTATC
* * *
11391 TGATTTCTTATTTGAATTATGTTCGGATACCTGACCTGGATTCTATTT
1 TGATTTCTGATCTGAATTATGTTCGGATACCTGACCTGAATTCTATTT
* * * * * * *
11439 TGATTTCTGATCTGGATTCTGTTCTGATATCTTATCTGAATTCTGTTT
1 TGATTTCTGATCTGAATTATGTTCGGATACCTGACCTGAATTCTATTT
11487 TGATTTCT
1 TGATTTCT
11495 AATATCTCTG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.18, C:0.14, G:0.16, T:0.51
Consensus pattern (48 bp):
TGATTTCTGATCTGAATTATGTTCGGATACCTGACCTGAATTCTATTT
Found at i:11453 original size:24 final size:24
Alignment explanation
Indices: 11421--11494 Score: 94
Period size: 24 Copynumber: 3.1 Consensus size: 24
11411 GTTCGGATAC
* *
11421 CTGACCTGGATTCTATTTTGATTT
1 CTGATCTGGATTCTGTTTTGATTT
* *
11445 CTGATCTGGATTCTGTTCTGATAT
1 CTGATCTGGATTCTGTTTTGATTT
* *
11469 CTTATCTGAATTCTGTTTTGATTT
1 CTGATCTGGATTCTGTTTTGATTT
11493 CT
1 CT
11495 AATATCTCTG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (24 bp):
CTGATCTGGATTCTGTTTTGATTT
Found at i:15586 original size:24 final size:23
Alignment explanation
Indices: 15559--15626 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
15549 GATACCTGAC
15559 CTGGATTCTGTTTTTATTTCAGAT
1 CTGGATTCTGTTTTTATTTC-GAT
*
15583 CTGGATTCTGTTATGATATTT-GAT
1 CTGGATTCTGTT-T-TTATTTCGAT
* *
15607 CTGAATTCTGTTTTGATTTC
1 CTGGATTCTGTTTTTATTTC
15627 TAATATCTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
22 4 0.11
23 1 0.03
24 26 0.70
25 1 0.03
26 5 0.14
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.53
Consensus pattern (23 bp):
CTGGATTCTGTTTTTATTTCGAT
Found at i:18961 original size:31 final size:31
Alignment explanation
Indices: 18887--18954 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
18877 TCAAAATATA
*
18887 TAAGATATGATCACTTTCGTTTTTATTTAAT
1 TAAGATATGGTCACTTTCGTTTTTATTTAAT
* *
18918 TAAGATATGGTCACTTTTGTTTTTATTTATT
1 TAAGATATGGTCACTTTCGTTTTTATTTAAT
18949 TAAGAT
1 TAAGAT
18955 TAGGTCAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.53
Consensus pattern (31 bp):
TAAGATATGGTCACTTTCGTTTTTATTTAAT
Found at i:21152 original size:42 final size:42
Alignment explanation
Indices: 21100--21193 Score: 170
Period size: 42 Copynumber: 2.2 Consensus size: 42
21090 AACTGTTGAC
*
21100 CGTTGACCGGTGTTCACCACTGTTGACCAGAACTCTGACCGG
1 CGTTAACCGGTGTTCACCACTGTTGACCAGAACTCTGACCGG
*
21142 CGTTAACCGGTGTTCATCACTGTTGACCAGAACTCTGACCGG
1 CGTTAACCGGTGTTCACCACTGTTGACCAGAACTCTGACCGG
21184 CGTTAACCGG
1 CGTTAACCGG
21194 GCGTTGAATG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.20, C:0.30, G:0.26, T:0.24
Consensus pattern (42 bp):
CGTTAACCGGTGTTCACCACTGTTGACCAGAACTCTGACCGG
Found at i:23583 original size:26 final size:24
Alignment explanation
Indices: 23549--23605 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
23539 TTTCATCGAA
23549 AAATATG-AATTGTACATGATTTATG
1 AAATATGAAATT-TAC-TGATTTATG
*
23574 AAATCATGAAATTTACTGGTTTATG
1 AAAT-ATGAAATTTACTGATTTATG
*
23599 AAGTATG
1 AAATATG
23606 CTTACCTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 3 0.11
25 15 0.54
26 6 0.21
27 4 0.14
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.39
Consensus pattern (24 bp):
AAATATGAAATTTACTGATTTATG
Found at i:27756 original size:20 final size:19
Alignment explanation
Indices: 27728--27778 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
27718 AGAAATCGAC
* *
27728 TATATTTTTAAATAAATTT
1 TATAATTTTAAATAAATAT
**
27747 ATATAATTTTATTTAAATAT
1 -TATAATTTTAAATAAATAT
27767 TATAATTTTAAA
1 TATAATTTTAAA
27779 ATTATGACAC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATAATTTTAAATAAATAT
Found at i:29527 original size:3 final size:3
Alignment explanation
Indices: 29519--29588 Score: 67
Period size: 3 Copynumber: 24.0 Consensus size: 3
29509 AATGGGCCTG
**
29519 TAA TAA TAA TATA TTT TAA TAA TAA TAA TAA TAA T-A TAA TAA -AA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
29563 GTAA TAA TAC TAA TAA -AA TAA -AA TAA
1 -TAA TAA TAA TAA TAA TAA TAA TAA TAA
29589 AACTGGAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
2 8 0.15
3 43 0.78
4 4 0.07
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:29567 original size:23 final size:23
Alignment explanation
Indices: 29518--29585 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
29508 AAATGGGCCT
**
29518 GTAATAATAAT-ATATTTTAATAA
1 GTAATAATAATAATATAATAA-AA
29541 -TAATAATAATAATATAATAAAA
1 GTAATAATAATAATATAATAAAA
* *
29563 GTAATAATACTAATAAAATAAAA
1 GTAATAATAATAATATAATAAAA
29586 TAAAACTGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.31
23 27 0.69
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (23 bp):
GTAATAATAATAATATAATAAAA
Found at i:30024 original size:25 final size:25
Alignment explanation
Indices: 29990--30045 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
29980 ATCTTACAAT
29990 AATCTTTCTTGTTGTTCTCTACTTG
1 AATCTTTCTTGTTGTTCTCTACTTG
30015 AATCTTTCTTGTTGTTCTCTACTTG
1 AATCTTTCTTGTTGTTCTCTACTTG
30040 AATCTT
1 AATCTT
30046 GGTCCCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.14, C:0.20, G:0.11, T:0.55
Consensus pattern (25 bp):
AATCTTTCTTGTTGTTCTCTACTTG
Found at i:32451 original size:19 final size:19
Alignment explanation
Indices: 32435--32471 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
32425 TATTGATACT
32435 AATATGTAGTATCGATATG
1 AATATGTAGTATCGATATG
32454 AATATGTAGTATCGATAT
1 AATATGTAGTATCGATAT
32472 CGAAAATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (19 bp):
AATATGTAGTATCGATATG
Found at i:37424 original size:13 final size:13
Alignment explanation
Indices: 37392--37438 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
37382 ACCGGTCAAC
37392 GGTCAACGGGTCG
1 GGTCAACGGGTCG
37405 GGT---CGGGTCG
1 GGTCAACGGGTCG
37415 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
37428 GGTAAACGGGT
1 GGTCAACGGGT
37439 AAACGGGTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 10 0.33
13 20 0.67
ACGTcount: A:0.15, C:0.19, G:0.49, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:37471 original size:10 final size:10
Alignment explanation
Indices: 37451--37494 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
37441 ACGGGTCGTG
37451 ACCGGTC-AA
1 ACCGGTCAAA
37460 ACCGGTCAAA
1 ACCGGTCAAA
*
37470 ACCGGT-TAA
1 ACCGGTCAAA
37479 ACCGGTCAAA
1 ACCGGTCAAA
37489 ACCGGT
1 ACCGGT
37495 TTCCAGCGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
9 15 0.48
10 16 0.52
ACGTcount: A:0.34, C:0.30, G:0.23, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:37495 original size:19 final size:19
Alignment explanation
Indices: 37451--37495 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
37441 ACGGGTCGTG
*
37451 ACCGGTCAAACCGGTCAAA
1 ACCGGTTAAACCGGTCAAA
37470 ACCGGTTAAACCGGTCAAA
1 ACCGGTTAAACCGGTCAAA
37489 ACCGGTT
1 ACCGGTT
37496 TCCAGCGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (19 bp):
ACCGGTTAAACCGGTCAAA
Found at i:44670 original size:13 final size:13
Alignment explanation
Indices: 44638--44684 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
44628 ACCGGTCAAC
44638 GGTCAACGGGTCG
1 GGTCAACGGGTCG
44651 GGT---CGGGTCG
1 GGTCAACGGGTCG
44661 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
44674 GGTAAACGGGT
1 GGTCAACGGGT
44685 AAACGGGTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 10 0.33
13 20 0.67
ACGTcount: A:0.15, C:0.19, G:0.49, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:44717 original size:10 final size:10
Alignment explanation
Indices: 44697--44751 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
44687 ACGGGTCGTG
44697 ACCGGTC-AA
1 ACCGGTCAAA
44706 ACCGGTCAAA
1 ACCGGTCAAA
44716 ACCGGTTCAAA
1 ACCGG-TCAAA
*
44727 ACCGGT-TAA
1 ACCGGTCAAA
44736 ACCGGTCAAA
1 ACCGGTCAAA
44746 ACCGGT
1 ACCGGT
44752 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:44752 original size:19 final size:19
Alignment explanation
Indices: 44697--44752 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
44687 ACGGGTCGTG
*
44697 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
44716 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
44736 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
44753 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:46045 original size:25 final size:25
Alignment explanation
Indices: 46011--46065 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
46001 CAACCTTAAT
* *
46011 GATATGTCAGTACCTGAACGTCATG
1 GATATGTCAGTACCTGAACGGCATA
46036 GATATGTCAGTACCTGAACGGCATA
1 GATATGTCAGTACCTGAACGGCATA
46061 GATAT
1 GATAT
46066 TACTTGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (25 bp):
GATATGTCAGTACCTGAACGGCATA
Found at i:46885 original size:24 final size:23
Alignment explanation
Indices: 46858--46925 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
46848 GATACCTGAC
46858 CTGGATTCTGTTTTTATTTCAGAT
1 CTGGATTCTGTTTTTATTTC-GAT
*
46882 CTGGATTCTGTTATGATATTT-GAT
1 CTGGATTCTGTT-T-TTATTTCGAT
* *
46906 CTGAATTCTGTTTTGATTTC
1 CTGGATTCTGTTTTTATTTC
46926 TAATATCTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
22 4 0.11
23 1 0.03
24 26 0.70
25 1 0.03
26 5 0.14
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.53
Consensus pattern (23 bp):
CTGGATTCTGTTTTTATTTCGAT
Found at i:50801 original size:23 final size:23
Alignment explanation
Indices: 50775--50830 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
50765 ACCGGTCATA
50775 ACCCGACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGACCCGTTG
* *
50798 ACCCGACCAGACCTGACCCGTTG
1 ACCCGACCCGACCCGACCCGTTG
50821 ACCCGACCCG
1 ACCCGACCCG
50831 TTGACCGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.50, G:0.21, T:0.09
Consensus pattern (23 bp):
ACCCGACCCGACCCGACCCGTTG
Found at i:50802 original size:13 final size:13
Alignment explanation
Indices: 50784--50836 Score: 67
Period size: 13 Copynumber: 4.3 Consensus size: 13
50774 AACCCGACCC
50784 GACCCGACCCGTT
1 GACCCGACCCGTT
*
50797 GACCCGA-CC--A
1 GACCCGACCCGTT
*
50807 GACCTGACCCGTT
1 GACCCGACCCGTT
50820 GACCCGACCCGTT
1 GACCCGACCCGTT
50833 GACC
1 GACC
50837 GTTGACCGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 6 0.18
11 2 0.06
12 2 0.06
13 23 0.70
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:53141 original size:24 final size:24
Alignment explanation
Indices: 53111--53225 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
53101 TCGATTTGAT
*
53111 TTCTGATATGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
53135 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
* *
53159 TTATGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
*
53183 TTCTGATCTGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
53207 TTTTGATATGATACTTGAC
1 TTCTGATCTGATACTTGAC
53226 GTGAATTATG
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.01
24 80 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:53237 original size:24 final size:24
Alignment explanation
Indices: 53114--53242 Score: 152
Period size: 24 Copynumber: 5.4 Consensus size: 24
53104 ATTTGATTTC
* *
53114 TGATATGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTA
53138 TGATCTGATA-TCTGACATGGATTA
1 TGATCTGATACT-TGACATGGATTA
* *
53162 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTA
* *
53186 TGATCTGATACTTGACCTGGATTT
1 TGATCTGATACTTGACATGGATTA
* * *
53210 TGATATGATACTTGACGTGAATTA
1 TGATCTGATACTTGACATGGATTA
*
53234 TGATTTGAT
1 TGATCTGAT
53243 TTTTGATATA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 90 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.40
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTA
Found at i:53448 original size:2 final size:2
Alignment explanation
Indices: 53441--53483 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
53431 CGGATGGGGG
53441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53483 T
1 T
53484 GTTTTAAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61457 original size:20 final size:19
Alignment explanation
Indices: 61418--61473 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 19
61408 AGCCTTTCTC
* *
61418 TTTTATATAAAAATATTAT
1 TTTTATATAAATATAATAT
*
61437 TATTTATATTAATATAATAT
1 T-TTTATATAAATATAATAT
61457 TTTT-TA-AAATATAATAT
1 TTTTATATAAATATAATAT
61474 AGTATTCTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 10 0.31
18 2 0.06
19 4 0.12
20 16 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTATATAAATATAATAT
Found at i:61578 original size:19 final size:20
Alignment explanation
Indices: 61531--61578 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
61521 AAAGTTATTT
61531 ATTAATAATTTTAATATAACA
1 ATTAAT-ATTTTAATATAACA
* *
61552 A-TATTATTTTAATA-AATA
1 ATTAATATTTTAATATAACA
61570 ATTAATATT
1 ATTAATATT
61579 ATTATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 4 0.17
19 15 0.65
20 3 0.13
21 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTAATATTTTAATATAACA
Found at i:61613 original size:27 final size:25
Alignment explanation
Indices: 61530--61614 Score: 65
Period size: 27 Copynumber: 3.5 Consensus size: 25
61520 TAAAGTTATT
61530 TATTAATAATTTTAAT--ATAAC-AA
1 TATTAAT-ATTTTAATAAATAACTAA
*
61553 TA-T--TATTTTAATAAATAATTAA
1 TATTAATATTTTAATAAATAACTAA
*
61575 TATTATTATTTTAATAAAATATACTAA
1 TATTAATATTTTAAT-AAATA-ACTAA
* *
61602 TCTTAATGTTTTA
1 TATTAATATTTTA
61615 TTTATAAGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
19 8 0.16
20 1 0.02
21 4 0.08
22 5 0.10
23 3 0.06
25 9 0.18
26 5 0.10
27 14 0.29
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (25 bp):
TATTAATATTTTAATAAATAACTAA
Found at i:62563 original size:70 final size:64
Alignment explanation
Indices: 62463--62654 Score: 209
Period size: 70 Copynumber: 2.9 Consensus size: 64
62453 TATTTTAAAC
62463 ATTATA-T-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTTTTAATTAAG-TTTAGGATA
1 ATTATATTATTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTTTTAATTAAGATTTA-GA-A
62525 TT
64 -T
*
62527 ATTTTATATTTATCTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTATTTTAATTAGGATTT
1 A--TTATA-TTAT-TTATCTTTGTATTTTAGTTTAAATAGGTTTTTAG--TTTTAATTAAGATTT
62591 AGAAT
60 AGAAT
* *
62596 ATTATATTATTT-T-TTAGGTATTTTAGTTTAAATA-GTTTTTAGTGTTTAATTAGGATTTA
1 ATTATATTATTTATCTT-TGTATTTTAGTTTAAATAGGTTTTTAGT-TTTAATTAAGATTTA
62655 AGATGTTTTA
Statistics
Matches: 114, Mismatches: 2, Indels: 25
0.81 0.01 0.18
Matches are distributed among these distances:
62 1 0.01
63 18 0.16
64 25 0.22
65 2 0.02
66 9 0.08
67 5 0.04
68 1 0.01
69 9 0.08
70 28 0.25
71 12 0.11
72 4 0.04
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (64 bp):
ATTATATTATTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTTTTAATTAAGATTTAGAAT
Found at i:62586 original size:19 final size:19
Alignment explanation
Indices: 62558--62620 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
62548 TGTATTTTAG
*
62558 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
62577 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
62596 ATTATATTATTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
62617 TTTA
1 TTTA
62621 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 8 0.24
21 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:63273 original size:20 final size:21
Alignment explanation
Indices: 63235--63273 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
63225 TCTTAATTTG
*
63235 TTTATTTAATTATTTTTTTCT
1 TTTATTTAATTATTATTTTCT
*
63256 TTTA-TTAATTCTTATTTT
1 TTTATTTAATTATTATTTT
63274 TTATTTTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTATTTAATTATTATTTTCT
Found at i:63350 original size:16 final size:17
Alignment explanation
Indices: 63313--63351 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
63303 CCCTTTTATA
63313 TTTATTACTATAAATTT
1 TTTATTACTATAAATTT
* *
63330 ATTATTA-TATTAATTT
1 TTTATTACTATAAATTT
63346 TTTATT
1 TTTATT
63352 TTTTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATTACTATAAATTT
Done.