Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001865.1 Hibiscus syriacus cultivar Beakdansim tig00003776_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: 85564
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:3719 original size:2 final size:2
Alignment explanation
Indices: 3712--3745 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3702 TCTCCACATG
3712 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
3746 AGCCAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12518 original size:24 final size:21
Alignment explanation
Indices: 12480--12534 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
12470 CGTCGTCATC
*
12480 ATCATCATCCCCATCATCTGCCAT
1 ATCATCATCTCCATCA-C--CCAT
* *
12504 GTCATCATCTTCATCACCCAT
1 ATCATCATCTCCATCACCCAT
12525 ATCATCATCT
1 ATCATCATCT
12535 GCCCTATTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 13 0.48
23 1 0.04
24 13 0.48
ACGTcount: A:0.25, C:0.38, G:0.04, T:0.33
Consensus pattern (21 bp):
ATCATCATCTCCATCACCCAT
Found at i:24004 original size:120 final size:119
Alignment explanation
Indices: 23845--24088 Score: 461
Period size: 119 Copynumber: 2.0 Consensus size: 119
23835 GTAAGATCTC
*
23845 GCGTGTGCGATGTGGGTCGGTCTAGATTAATCAAGACGAAATCTTGTAAACGGGAGTAAAACAAA
1 GCGTGTGCGATGTGGGTCGGTCAAGATTAATCAAGACGAAATCTTGTAAACGGGAGTAAAAC-AA
*
23910 AAATAGTATAAAATTCCATATTTGATAGATTTAACTATGTTTATTTAGTTAATTA
65 AAATAGTATAAAATTCCATATTTGATAGATTTAACTATGTTTATTTAATTAATTA
23965 GCGTGTGCGATGTGGGTCGGTCAAGATTAATCAAGACGAAATCTTGTAAACGGGAGTAAAACAAA
1 GCGTGTGCGATGTGGGTCGGTCAAGATTAATCAAGACGAAATCTTGTAAACGGGAGTAAAACAAA
24030 AATAGTATAAAATTCCATATTTGATAGATTTAACTATGTTTATTTAATTAATTA
66 AATAGTATAAAATTCCATATTTGATAGATTTAACTATGTTTATTTAATTAATTA
24084 GCGTG
1 GCGTG
24089 AGATTAAAAG
Statistics
Matches: 122, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
119 61 0.50
120 61 0.50
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.33
Consensus pattern (119 bp):
GCGTGTGCGATGTGGGTCGGTCAAGATTAATCAAGACGAAATCTTGTAAACGGGAGTAAAACAAA
AATAGTATAAAATTCCATATTTGATAGATTTAACTATGTTTATTTAATTAATTA
Found at i:24573 original size:22 final size:22
Alignment explanation
Indices: 24548--24589 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
24538 TATTTATTTA
24548 ATATTTCTAATAATATAATATT
1 ATATTTCTAATAATATAATATT
* *
24570 ATATTTTTAATATTATAATA
1 ATATTTCTAATAATATAATA
24590 AAATAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATTTCTAATAATATAATATT
Found at i:24880 original size:14 final size:14
Alignment explanation
Indices: 24863--24949 Score: 59
Period size: 14 Copynumber: 6.1 Consensus size: 14
24853 AAAATATACC
*
24863 AATATTAATATTTT
1 AATAATAATATTTT
* *
24877 AATAATAAAATTAT
1 AATAATAATATTTT
*
24891 AAAAATAATATTTT
1 AATAATAATATTTT
* **
24905 ATTAATAAATAAATT
1 AATAAT-AATATTTT
**
24920 -ATTTTAATATTTT
1 AATAATAATATTTT
*
24933 AAAAATAATATTATT
1 AATAATAATATT-TT
24948 AA
1 AA
24950 GTTTTATGAT
Statistics
Matches: 52, Mismatches: 18, Indels: 5
0.69 0.24 0.07
Matches are distributed among these distances:
13 6 0.12
14 36 0.69
15 10 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AATAATAATATTTT
Found at i:24912 original size:20 final size:22
Alignment explanation
Indices: 24889--24949 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 22
24879 TAATAAAATT
24889 ATAAAAATAATATTTT-AT-TA
1 ATAAAAATAATATTTTAATATA
* *
24909 ATAAATAA-ATTATTTTAATATT
1 ATAAA-AATAATATTTTAATATA
*
24931 TTAAAAATAATATTATTAA
1 ATAAAAATAATATT-TTAA
24950 GTTTTATGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 12 0.38
21 6 0.19
22 10 0.31
23 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATAAAAATAATATTTTAATATA
Found at i:24928 original size:17 final size:17
Alignment explanation
Indices: 24871--24928 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
24861 CCAATATTAA
24871 TATTTTAAT-AATAAA-
1 TATTTTAATAAATAAAT
*
24886 -ATTATAA-AAATAATAT
1 TATTTTAATAAATAA-AT
24902 T-TTATTAATAAATAAAT
1 TATT-TTAATAAATAAAT
24919 TATTTTAATA
1 TATTTTAATA
24929 TTTTAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
14 11 0.32
15 1 0.03
16 2 0.06
17 12 0.35
18 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTTTAATAAATAAAT
Found at i:24948 original size:28 final size:27
Alignment explanation
Indices: 24866--24949 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 27
24856 ATATACCAAT
*
24866 ATTAATATTTTAATAATAAAATTATAAA
1 ATTAATATTTTAATAAT-AAATTATTAA
* * * *
24894 AATAATATTTTATTAATAAATAAATTAT
1 ATTAATATTTTAATAATAAAT-TATTAA
* *
24922 TTTAATATTTTAAAAATAATATTATTAA
1 ATTAATATTTTAATAATAA-ATTATTAA
24950 GTTTTATGAT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
27 4 0.09
28 37 0.86
29 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTAATATTTTAATAATAAATTATTAA
Found at i:25202 original size:13 final size:13
Alignment explanation
Indices: 25157--25208 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
25147 AAGTTTTGGA
*
25157 AATTTTTAATTTTT
1 AATTATTAA-TTTT
* *
25171 AATTACTGATTTT
1 AATTATTAATTTT
*
25184 AATTATTTATTTT
1 AATTATTAATTTT
25197 AATTATTAATTT
1 AATTATTAATTT
25209 ATTTGTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 26 0.81
14 6 0.19
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (13 bp):
AATTATTAATTTT
Found at i:25210 original size:21 final size:20
Alignment explanation
Indices: 25182--25222 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
25172 ATTACTGATT
25182 TTAATTATTTATTTTAATTA
1 TTAATTATTTATTTTAATTA
* *
25202 TTAATTTATTTGTTTTTATTA
1 TTAA-TTATTTATTTTAATTA
25223 AAAAAATAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
TTAATTATTTATTTTAATTA
Found at i:27394 original size:20 final size:20
Alignment explanation
Indices: 27369--27406 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27359 CTGAAAATTT
27369 AAAATTACCATATATTTTAA
1 AAAATTACCATATATTTTAA
* *
27389 AAAATTTCTATATATTTT
1 AAAATTACCATATATTTT
27407 TATTGAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATTACCATATATTTTAA
Found at i:27751 original size:36 final size:36
Alignment explanation
Indices: 27711--27816 Score: 194
Period size: 36 Copynumber: 2.9 Consensus size: 36
27701 AGCCAATGCC
27711 ACCTTTAGATTTCTGTTAGACAACCTTTAGATAGGA
1 ACCTTTAGATTTCTGTTAGACAACCTTTAGATAGGA
*
27747 ACCTTTAGATTTCTGTTATACAACCTTTAGATAGGA
1 ACCTTTAGATTTCTGTTAGACAACCTTTAGATAGGA
*
27783 ACCTTTAGATTTCTGTTAGATAACCTTTAGATAG
1 ACCTTTAGATTTCTGTTAGACAACCTTTAGATAG
27817 ATTCGCCTCA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (36 bp):
ACCTTTAGATTTCTGTTAGACAACCTTTAGATAGGA
Found at i:29705 original size:17 final size:17
Alignment explanation
Indices: 29683--29720 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
29673 TATAGGATGC
29683 CAATGGGGGAACGAAAT
1 CAATGGGGGAACGAAAT
29700 CAATGGGGGAACGAAAT
1 CAATGGGGGAACGAAAT
29717 CAAT
1 CAAT
29721 AGGCGAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.13, G:0.32, T:0.13
Consensus pattern (17 bp):
CAATGGGGGAACGAAAT
Found at i:34558 original size:7 final size:7
Alignment explanation
Indices: 34546--34579 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
34536 TGTAGGGTAG
34546 TGGCTAC
1 TGGCTAC
34553 TGGCTAC
1 TGGCTAC
34560 TGGCTAC
1 TGGCTAC
34567 TGGCTAC
1 TGGCTAC
34574 TGGCTA
1 TGGCTA
34580 AAGCTAAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.26, G:0.29, T:0.29
Consensus pattern (7 bp):
TGGCTAC
Found at i:43451 original size:21 final size:21
Alignment explanation
Indices: 43425--43503 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 21
43415 TTTCCAAATT
43425 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
43446 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * *
43467 CATTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
43488 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
43504 AATCGCAACG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
19 7 0.14
21 34 0.69
23 8 0.16
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.32
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:43613 original size:12 final size:12
Alignment explanation
Indices: 43593--43629 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
43583 GACACGTATT
*
43593 ACCACGACCACG
1 ACCATGACCACG
*
43605 ACCATGACCATG
1 ACCATGACCACG
43617 ACCATGACCACG
1 ACCATGACCACG
43629 A
1 A
43630 GACGAGAGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.35, C:0.41, G:0.16, T:0.08
Consensus pattern (12 bp):
ACCATGACCACG
Found at i:44167 original size:21 final size:20
Alignment explanation
Indices: 44090--44183 Score: 84
Period size: 21 Copynumber: 4.6 Consensus size: 20
44080 ATTTTGGACT
*
44090 ATCGCAA-CGAATTTGGAATAA
1 ATCGCAAGCGAACTTGG-A-AA
**
44111 ATCGCAAGCGAACTTGGACT
1 ATCGCAAGCGAACTTGGAAA
*
44131 ATCGCAA-CGAATTTGGAAA
1 ATCGCAAGCGAACTTGGAAA
**
44150 ATCGCAACGCGAACTTGGACT
1 ATCGCAA-GCGAACTTGGAAA
44171 ATCGCAATGCGAA
1 ATCGCAA-GCGAA
44184 TATGTAAATC
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 16 0.27
20 7 0.12
21 29 0.48
22 8 0.13
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.20
Consensus pattern (20 bp):
ATCGCAAGCGAACTTGGAAA
Found at i:44173 original size:40 final size:41
Alignment explanation
Indices: 44083--44177 Score: 167
Period size: 41 Copynumber: 2.3 Consensus size: 41
44073 GTGCATGATT
44083 TTGGACTATCGCAACGAATTTGGAATAAATCGCAAGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAAGCGAAC
44124 TTGGACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAA-GCGAAC
44164 TTGGACTATCGCAA
1 TTGGACTATCGCAA
44178 TGCGAATATG
Statistics
Matches: 53, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
39 9 0.17
40 21 0.40
41 23 0.43
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (41 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAAGCGAAC
Found at i:44507 original size:11 final size:11
Alignment explanation
Indices: 44488--44534 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
44478 TTAAAATATT
44488 ATTTTATAATA
1 ATTTTATAATA
*
44499 ATTTGAT-A-A
1 ATTTTATAATA
**
44508 ATTCAATAATA
1 ATTTTATAATA
44519 ATTTTATAATA
1 ATTTTATAATA
44530 ATTTT
1 ATTTT
44535 GAAAAAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
9 6 0.21
10 2 0.07
11 21 0.72
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (11 bp):
ATTTTATAATA
Found at i:44526 original size:31 final size:31
Alignment explanation
Indices: 44482--44559 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 31
44472 GATCATTTAA
* *
44482 AATAT-TATTTTATAATAA-TTTGATAAATT
1 AATATATATTTTATAATAATTTTGAAAAAAT
44511 CAATA-ATAATTTTATAATAATTTTGAAAAAAT
1 -AATATAT-ATTTTATAATAATTTTGAAAAAAT
44543 AATATATATTTTATAAT
1 AATATATATTTTATAAT
44560 TTTTAATTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 5 0.12
31 26 0.62
32 11 0.26
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (31 bp):
AATATATATTTTATAATAATTTTGAAAAAAT
Found at i:52498 original size:72 final size:73
Alignment explanation
Indices: 52419--52565 Score: 206
Period size: 72 Copynumber: 2.0 Consensus size: 73
52409 GATCATTTTT
* * * *
52419 AGTCGTTCTACTCAAATCATTCTTACGGATGATAAAA-AACCTAAAATTTAAAGACATTATAATT
1 AGTCGTTCCACTCAAATCATTCCTACCGATAATAAAATAACCTAAAATTTAAAGACATTATAATT
*
52483 AAGATTTA
66 AAGACTTA
** **
52491 AGTCGTTCCACTCAAATCATTCCTACCGATAATAAAATAAGTTAAAATTTAAAGACATTATGGTT
1 AGTCGTTCCACTCAAATCATTCCTACCGATAATAAAATAACCTAAAATTTAAAGACATTATAATT
52556 AAGACTTA
66 AAGACTTA
52564 AG
1 AG
52566 AAAATAATTT
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
72 33 0.51
73 32 0.49
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (73 bp):
AGTCGTTCCACTCAAATCATTCCTACCGATAATAAAATAACCTAAAATTTAAAGACATTATAATT
AAGACTTA
Found at i:53345 original size:63 final size:63
Alignment explanation
Indices: 53269--53388 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 63
53259 CTAAATCCTA
* *
53269 ACCCGACCTGACCCGAATATCA-CACTTAAAAAAACCGACCCAACCCGACCA-AAATAAAGTTTC
1 ACCCGACCCGACCCGAATAT-ATCAATT-AAAAAACCGACCCAACCCGACCATAAATAAAGTTTC
* * *
53332 ACCCGACCCGACCCGAATATATGAATTAGAAACCCGACCCAACCCGACCATAAATAA
1 ACCCGACCCGACCCGAATATATCAATTAAAAAACCGACCCAACCCGACCATAAATAA
53389 TAAAAAAATT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
62 22 0.44
63 28 0.56
ACGTcount: A:0.41, C:0.35, G:0.11, T:0.13
Consensus pattern (63 bp):
ACCCGACCCGACCCGAATATATCAATTAAAAAACCGACCCAACCCGACCATAAATAAAGTTTC
Found at i:54723 original size:23 final size:23
Alignment explanation
Indices: 54690--54733 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
54680 TCATGTACAA
*
54690 TTTGTTCTAGACATTTAACTGTT
1 TTTGTTCTAGACATATAACTGTT
*
54713 TTTGTTTTAGACATATAACTG
1 TTTGTTCTAGACATATAACTG
54734 GTTTAGGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (23 bp):
TTTGTTCTAGACATATAACTGTT
Found at i:57685 original size:40 final size:40
Alignment explanation
Indices: 57640--57719 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
57630 TCTTCCACTC
57640 TTTTTTACCTCCAACTTGTTAATCATCATTTTATATATAT
1 TTTTTTACCTCCAACTTGTTAATCATCATTTTATATATAT
57680 TTTTTTACCTCCAACTTGTTAATCATCATTTTATATATAT
1 TTTTTTACCTCCAACTTGTTAATCATCATTTTATATATAT
57720 ATATATATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.17, G:0.03, T:0.53
Consensus pattern (40 bp):
TTTTTTACCTCCAACTTGTTAATCATCATTTTATATATAT
Found at i:58252 original size:22 final size:22
Alignment explanation
Indices: 58226--58279 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
58216 TTCCATTTCG
58226 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
58248 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
58270 CGTTGCGATA
1 CGTTGCGATA
58280 ATTAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.37
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:58369 original size:6 final size:6
Alignment explanation
Indices: 58358--58390 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
58348 GACACGTATT
58358 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
58391 CGAGACGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:59047 original size:41 final size:42
Alignment explanation
Indices: 58990--59073 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 42
58980 CAAGAATTTT
** *
58990 GACAACTGTAGACTATCGCAACGA-ATTTGGAAAATCGCAAC
1 GACAACTGTAGACTATCGCAACGAGAAATGAAAAATCGCAAC
*
59031 GACAACTGTATACTATCGCAACGAGAAATGAAAAATCGCAAC
1 GACAACTGTAGACTATCGCAACGAGAAATGAAAAATCGCAAC
59073 G
1 G
59074 CGAAATGGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
41 23 0.61
42 15 0.39
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (42 bp):
GACAACTGTAGACTATCGCAACGAGAAATGAAAAATCGCAAC
Found at i:59051 original size:22 final size:21
Alignment explanation
Indices: 58990--59054 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 21
58980 CAAGAATTTT
58990 GACAACTGTAGACTATCGCAAC
1 GACAACTGTA-ACTATCGCAAC
** * *
59012 GA-ATTTGGAA-AATCGCAAC
1 GACAACTGTAACTATCGCAAC
59031 GACAACTGTATACTATCGCAAC
1 GACAACTGTA-ACTATCGCAAC
59053 GA
1 GA
59055 GAAATGAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 10 0.31
20 5 0.16
21 5 0.16
22 12 0.38
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (21 bp):
GACAACTGTAACTATCGCAAC
Found at i:59070 original size:20 final size:20
Alignment explanation
Indices: 59045--59140 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
59035 ACTGTATACT
*
59045 ATCGCAACGAGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
*
59065 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
* *
59085 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGAAAA
*
59105 ATCGCAACGCAAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
59125 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
59141 CAACGCGAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:59126 original size:60 final size:62
Alignment explanation
Indices: 59017--59140 Score: 184
Period size: 60 Copynumber: 2.0 Consensus size: 62
59007 GCAACGAATT
* *
59017 TGGAAAATCGCAACGACAACTGTATACTATCGCAACGAGAAATGAAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTGGATACAATCGCAACGAGAAATGAAAAATCGCAACGCGAAA
59079 TGGAAAATCGCAACG-CGAACTGGA-A-AATCGCAACGCA-AAATGAAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGAC-AACTGGATACAATCGCAACG-AGAAATGAAAAATCGCAACGCGAAA
59139 TG
1 TG
59141 CAACGCGAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
60 34 0.59
61 3 0.05
62 21 0.36
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (62 bp):
TGGAAAATCGCAACGACAACTGGATACAATCGCAACGAGAAATGAAAAATCGCAACGCGAAA
Found at i:59175 original size:20 final size:19
Alignment explanation
Indices: 59152--59189 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
59142 AACGCGAATT
59152 TGCGATAGTAGAGATCGCAA
1 TGCGA-AGTAGAGATCGCAA
*
59172 TGCGAATTAGAGATCGCA
1 TGCGAAGTAGAGATCGCA
59190 TTGTGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (19 bp):
TGCGAAGTAGAGATCGCAA
Found at i:63871 original size:43 final size:43
Alignment explanation
Indices: 63801--63962 Score: 207
Period size: 43 Copynumber: 3.8 Consensus size: 43
63791 GTAATCGAAG
* * *
63801 CCGAAATTCGAAACCATTGAAACCGTTCTAAGATATGCCTAAC
1 CCGAAATTCGAAACCATCGAAACCGTTCTAACATATGCCTAAT
* * * *
63844 CCGAAATCCAAAACCATCGAAATCGTTCTAACATATACCTAAT
1 CCGAAATTCGAAACCATCGAAACCGTTCTAACATATGCCTAAT
* *
63887 CCAAAATTCGAAACCATTGAAACCGTTCTAACATATGCCTAAT
1 CCGAAATTCGAAACCATCGAAACCGTTCTAACATATGCCTAAT
* * **
63930 CCGAAATTCGAAACTATCAAAATGGTTCTAACA
1 CCGAAATTCGAAACCATCGAAACCGTTCTAACA
63963 CAAACCCAAT
Statistics
Matches: 100, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 100 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.24
Consensus pattern (43 bp):
CCGAAATTCGAAACCATCGAAACCGTTCTAACATATGCCTAAT
Found at i:63958 original size:86 final size:86
Alignment explanation
Indices: 63804--63962 Score: 255
Period size: 86 Copynumber: 1.8 Consensus size: 86
63794 ATCGAAGCCG
* *
63804 AAATTCGAAACCATTGAAACCGTTCTAAGATATGCCTAACCCGAAATCCAAAACCATCGAAATCG
1 AAATTCGAAACCATTGAAACCGTTCTAACATATGCCTAACCCGAAATCCAAAACCATCAAAATCG
63869 TTCTAACATATACCTAATCCA
66 TTCTAACATATACCTAATCCA
* * * * *
63890 AAATTCGAAACCATTGAAACCGTTCTAACATATGCCTAATCCGAAATTCGAAACTATCAAAATGG
1 AAATTCGAAACCATTGAAACCGTTCTAACATATGCCTAACCCGAAATCCAAAACCATCAAAATCG
63955 TTCTAACA
66 TTCTAACA
63963 CAAACCCAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 66 1.00
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.25
Consensus pattern (86 bp):
AAATTCGAAACCATTGAAACCGTTCTAACATATGCCTAACCCGAAATCCAAAACCATCAAAATCG
TTCTAACATATACCTAATCCA
Found at i:78130 original size:13 final size:13
Alignment explanation
Indices: 78112--78137 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
78102 CAATCTTTTT
78112 TTTTGAAGGTTTG
1 TTTTGAAGGTTTG
78125 TTTTGAAGGTTTG
1 TTTTGAAGGTTTG
78138 GAATTTAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
TTTTGAAGGTTTG
Found at i:85283 original size:27 final size:27
Alignment explanation
Indices: 85225--85305 Score: 101
Period size: 27 Copynumber: 2.9 Consensus size: 27
85215 CTCACCTAAC
85225 TAAATTGATGTAAGCAAATGACATCATTAT
1 TAAA-TGATGTAAGC--ATGACATCATTAT
85255 TAAATGATGTAAGCATGACATC-TTAAT
1 TAAATGATGTAAGCATGACATCATT-AT
*
85282 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAG-CATGACATCA
85306 ATTTAGTTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
26 2 0.04
27 23 0.49
28 8 0.17
29 10 0.21
30 4 0.09
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (27 bp):
TAAATGATGTAAGCATGACATCATTAT
Done.