Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005607.1 Hibiscus syriacus cultivar Beakdansim tig00013041_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: 63578
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2183 original size:40 final size:39
Alignment explanation
Indices: 2117--2204 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 39
2107 AACCATAAGC
* *
2117 ATATCGATACTGCTATGAGGTATCGATACTACAAGAACA
1 ATATCGATAATGCTATGAGGTATCGATACTACAAGAAAA
* * *
2156 ATATCGATAATGTTCATGTGGTATCGATACTATAAGAAAA
1 ATATCGATAATGCT-ATGAGGTATCGATACTACAAGAAAA
2196 ATATCGATA
1 ATATCGATA
2205 CTTCTTTCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 12 0.28
40 31 0.72
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.30
Consensus pattern (39 bp):
ATATCGATAATGCTATGAGGTATCGATACTACAAGAAAA
Found at i:6582 original size:82 final size:81
Alignment explanation
Indices: 6489--6766 Score: 375
Period size: 82 Copynumber: 3.4 Consensus size: 81
6479 CCAAATAATG
*
6489 GTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACTTTTC
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACTTTTT
*
6554 AAAAAATGGGTCAAATA
66 AAAAAAT-GGTGAAATA
* *
6571 GTGGTGCATTATCATCTTCTGCAACTTTTCAAAGGTCATTCAATGCATAATTTAAACAAATTTTT
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACTTTTT
*
6636 AGAAAATTGGTGAAATA
66 A-AAAAATGGTGAAATA
* * *
6653 GTAGTGCATTATCATCTTCTACAACTTGTT-AGAGATCATTCAATGCATAATTTAAACAACTTTT
1 GTGGTGCATTATCATCTTCTGCAACTT-TTCAGAGGTCATTCAATGCATAATTTAAACAACTTTT
*
6717 TAGACAACAT-GTGAAATA
65 TA-A-AAAATGGTGAAATA
*
6735 GTGGTGTC-TTGTCATCTT-TAGCAACTTTTCAG
1 GTGGTG-CATTATCATCTTCT-GCAACTTTTCAG
6767 TGATGTATCA
Statistics
Matches: 175, Mismatches: 15, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
81 3 0.02
82 161 0.92
83 11 0.06
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (81 bp):
GTGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATTTAAACAACTTTTT
AAAAAATGGTGAAATA
Found at i:11615 original size:2 final size:2
Alignment explanation
Indices: 11608--11642 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11598 AAAATAAAAG
11608 TA TA TA TA TA 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 TA TA T
11643 GAATTTAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11969 original size:30 final size:32
Alignment explanation
Indices: 11917--11975 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 32
11907 ATCTAAAATT
*
11917 AAATAAAAAATGAAAGTGATCATATATTAATA
1 AAATAAAAAATGAAAATGATCATATATTAATA
11949 AAAT-AAAAAT-AAAATGATCATATATTA
1 AAATAAAAAATGAAAATGATCATATATTA
11976 TATTTTTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 16 0.62
31 6 0.23
32 4 0.15
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (32 bp):
AAATAAAAAATGAAAATGATCATATATTAATA
Found at i:13462 original size:49 final size:48
Alignment explanation
Indices: 13403--13708 Score: 233
Period size: 49 Copynumber: 6.2 Consensus size: 48
13393 ACTGCTCTAA
* * * *
13403 AATGAAAGTTAAATGCCTAACTATGCATTTTTGGTAGAAA-GTTACCACT
1 AATGCAAGTTAAATG-CTAACTGTGCATTTTTGGCAGAAATG-TGCCACT
* ** * *
13452 AATGCAAGTTAGATGAAAAATGGTACA-TTTTGGCAGAAATGTGCCACT
1 AATGCAAGTTAAATGCTAACT-GTGCATTTTTGGCAGAAATGTGCCACT
* * *
13500 AATACAAGTTAAATGCCTAACTGTGCATTTTTTGTAGAAATGTGCCACT
1 AATGCAAGTTAAATG-CTAACTGTGCATTTTTGGCAGAAATGTGCCACT
* * ** * * *
13549 AATGCCAGTTAGATGAAAAATGGTGCATTTTTTGCAGAAATGTGTCACT
1 AATGCAAGTTAAATGCTAACT-GTGCATTTTTGGCAGAAATGTGCCACT
***
13598 AATGCAAGTTAAATGTCTAAC-GATGCATTTTTTTTTATAGAAATGTGCCACT
1 AATGCAAGTTAAATG-CTAACTG-TGCA---TTTTTGGCAGAAATGTGCCACT
* ** * *
13650 AATGCAAGTTAGATGAAAAATGGTGCATCTTTGGCAGAAA-GATGCCACT
1 AATGCAAGTTAAATGCTAACT-GTGCATTTTTGGCAGAAATG-TGCCACT
13699 AATGCAAGTT
1 AATGCAAGTT
13709 TTAACTAAAA
Statistics
Matches: 203, Mismatches: 41, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
48 42 0.21
49 119 0.59
50 2 0.01
51 2 0.01
52 37 0.18
53 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (48 bp):
AATGCAAGTTAAATGCTAACTGTGCATTTTTGGCAGAAATGTGCCACT
Found at i:13578 original size:97 final size:97
Alignment explanation
Indices: 13403--13708 Score: 420
Period size: 101 Copynumber: 3.1 Consensus size: 97
13393 ACTGCTCTAA
* * * *
13403 AATGAAAGTTAAATGCCTAACTATGCATTTTTGGTAGAAA-GTTACCACTAATGCAAGTTAGATG
1 AATGCAAGTTAAATGCCTAACTGTGCATTTTTTGTAGAAATG-TGCCACTAATGCAAGTTAGATG
*
13467 AAAAATGGTACATTTTGGCAGAAATGTGCCACT
65 AAAAATGGTGCATTTTGGCAGAAATGTGCCACT
* *
13500 AATACAAGTTAAATGCCTAACTGTGCATTTTTTGTAGAAATGTGCCACTAATGCCAGTTAGATGA
1 AATGCAAGTTAAATGCCTAACTGTGCATTTTTTGTAGAAATGTGCCACTAATGCAAGTTAGATGA
* *
13565 AAAATGGTGCATTTTTTGCAGAAATGTGTCACT
66 AAAATGGTGCA-TTTTGGCAGAAATGTGCCACT
* *
13598 AATGCAAGTTAAATGTCTAAC-GATGCATTTTTTTTTATAGAAATGTGCCACTAATGCAAGTTAG
1 AATGCAAGTTAAATGCCTAACTG-TGCA---TTTTTTGTAGAAATGTGCCACTAATGCAAGTTAG
13662 ATGAAAAATGGTGCATCTTTGGCAGAAA-GATGCCACT
62 ATGAAAAATGGTGCAT-TTTGGCAGAAATG-TGCCACT
13699 AATGCAAGTT
1 AATGCAAGTT
13709 TTAACTAAAA
Statistics
Matches: 186, Mismatches: 15, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
97 68 0.37
98 43 0.23
100 2 0.01
101 73 0.39
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (97 bp):
AATGCAAGTTAAATGCCTAACTGTGCATTTTTTGTAGAAATGTGCCACTAATGCAAGTTAGATGA
AAAATGGTGCATTTTGGCAGAAATGTGCCACT
Found at i:18197 original size:35 final size:35
Alignment explanation
Indices: 18124--18199 Score: 84
Period size: 39 Copynumber: 2.1 Consensus size: 35
18114 AATCTTACCT
**
18124 GACCCAAAAATTATATATCCTCCATCTGATCCGATCC
1 GACCCAAAAATTATATATCCTCCATC-GAAAC-ATCC
18161 GACCCGAAAAATATATATATCCTCCATC-AAAC-TCC
1 GACCC-AAAAAT-TATATATCCTCCATCGAAACATCC
18196 GACC
1 GACC
18200 TGACCTGACT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
35 7 0.20
37 7 0.20
38 6 0.17
39 15 0.43
ACGTcount: A:0.36, C:0.33, G:0.08, T:0.24
Consensus pattern (35 bp):
GACCCAAAAATTATATATCCTCCATCGAAACATCC
Found at i:21464 original size:23 final size:23
Alignment explanation
Indices: 21416--21470 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
21406 TTTCTTTAAT
* * *
21416 TATATA-ATTTAATATTATATATA
1 TATATATA-TTAATATAATACAAA
21439 TATATATATTAATATAATACAAA
1 TATATATATTAATATAATACAAA
21462 TATA-ATATT
1 TATATATATT
21471 TTATATTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.18
23 22 0.79
24 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TATATATATTAATATAATACAAA
Found at i:21535 original size:34 final size:34
Alignment explanation
Indices: 21497--21603 Score: 91
Period size: 34 Copynumber: 3.3 Consensus size: 34
21487 ATATGAATAT
*
21497 AATATTTTATATATCTTAATTCTTAAA-TTTTAAA
1 AATATTTTATATATCTTAA-TCTTAAACTATTAAA
* * * *
21531 AATATTTTTTTTATTTTTATCTTAAACTATTAAA
1 AATATTTTATATATCTTAATCTTAAACTATTAAA
* *
21565 TATATTTTAT-T-T-TT--TCTTAACCTATTAAA
1 AATATTTTATATATCTTAATCTTAAACTATTAAA
*
21594 TATATTTTAT
1 AATATTTTAT
21604 TTTTATTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
29 24 0.38
31 2 0.03
32 1 0.02
33 8 0.12
34 29 0.45
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (34 bp):
AATATTTTATATATCTTAATCTTAAACTATTAAA
Found at i:21584 original size:29 final size:30
Alignment explanation
Indices: 21539--21642 Score: 133
Period size: 29 Copynumber: 3.5 Consensus size: 30
21529 AAAATATTTT
21539 TTTTATTTTTATCTTAAACTATTAAATATA
1 TTTTATTTTTATCTTAAACTATTAAATATA
*
21569 TTTTATTTTT-TCTTAACCTATTAAATATA
1 TTTTATTTTTATCTTAAACTATTAAATATA
* *
21598 TTTTATTTTTAT-TTTAA-TATAAAATATATA
1 TTTTATTTTTATCTTAAACTAT-TAA-ATATA
*
21628 TTTTATCTTTATCTT
1 TTTTATTTTTATCTT
21643 CACTTAAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
28 3 0.05
29 33 0.51
30 27 0.42
31 2 0.03
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTTATTTTTATCTTAAACTATTAAATATA
Found at i:21605 original size:34 final size:34
Alignment explanation
Indices: 21529--21612 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 34
21519 TTAAATTTTA
21529 AAAATATTTT-TTTTATTTTTATCTTAAACTATT
1 AAAATATTTTATTTTATTTTTATCTTAAACTATT
*
21562 -AAATA---TATTTTATTTTT-TCTTAACCTATT
1 AAAATATTTTATTTTATTTTTATCTTAAACTATT
21591 AAATATATTTTATTTTTATTTT
1 AAA-ATATTTTA-TTTTATTTT
21613 AATATAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
29 12 0.28
30 12 0.28
31 3 0.07
32 5 0.12
34 2 0.05
35 9 0.21
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (34 bp):
AAAATATTTTATTTTATTTTTATCTTAAACTATT
Found at i:21654 original size:59 final size:59
Alignment explanation
Indices: 21539--21682 Score: 138
Period size: 59 Copynumber: 2.5 Consensus size: 59
21529 AAAATATTTT
* * * *
21539 TTTTATTTTTATCTTAA-ACTATTAA-ATATATTTTATTTTTTCTTAACCTATTAAATATA
1 TTTTATTTTTATTTTAATA-TA-AAATATATATTTTATTTTATCTTAACCTATAAAATATA
* * *
21598 TTTTATTTTTATTTTAATATAAAATATATATTTTATCTTTATCTTCACTTA-AAAATATT
1 TTTTATTTTTATTTTAATATAAAATATATATTTTAT-TTTATCTTAACCTATAAAATATA
* *
21657 TTTTATCTTAATTTT--TA-AAAATATAT
1 TTTTATTTTTATTTTAATATAAAATATAT
21683 TAACTTAAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
56 9 0.12
57 2 0.03
58 2 0.03
59 48 0.66
60 12 0.16
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (59 bp):
TTTTATTTTTATTTTAATATAAAATATATATTTTATTTTATCTTAACCTATAAAATATA
Found at i:21663 original size:29 final size:29
Alignment explanation
Indices: 21591--21670 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 29
21581 TTAACCTATT
* *
21591 AAATATATTTTATTTTTATTTTAATATAA
1 AAATATATTTTATCTTTATTTCAATATAA
*
21620 AATATATATTTTATCTTTATCTTCACT-TAA
1 AA-ATATATTTTATCTTTAT-TTCAATATAA
* *
21650 AAATATTTTTTATCTTAATTT
1 AAATATATTTTATCTTTATTT
21671 TTAAAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 2 0.05
29 17 0.39
30 21 0.48
31 4 0.09
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (29 bp):
AAATATATTTTATCTTTATTTCAATATAA
Found at i:21701 original size:9 final size:9
Alignment explanation
Indices: 21687--21734 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
21677 ATATATTAAC
21687 TTAAATATT
1 TTAAATATT
21696 TTAAATATT
1 TTAAATATT
*
21705 TTATTATTATT
1 TTA--AATATT
21716 TTAATATATT
1 TTAA-ATATT
*
21726 TTATATATT
1 TTAAATATT
21735 CTTATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 18 0.55
10 7 0.21
11 8 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTAAATATT
Found at i:21731 original size:28 final size:27
Alignment explanation
Indices: 21687--21744 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
21677 ATATATTAAC
*
21687 TTAAATATTTTAAATATTTTATTATTATT
1 TTAAATATTTT-AATATATTATTATT-TT
*
21716 TTAATATATTTT-ATATATTCTTATTTT
1 TTAA-ATATTTTAATATATTATTATTTT
21743 TT
1 TT
21745 GTTTATGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 4 0.15
28 11 0.42
29 4 0.15
30 7 0.27
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (27 bp):
TTAAATATTTTAATATATTATTATTTT
Found at i:26465 original size:20 final size:20
Alignment explanation
Indices: 26442--26482 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
26432 ATGAACCGTC
* *
26442 TGAAAACCGGTAGAACCGGT
1 TGAAAACCGGCAAAACCGGT
*
26462 TGAAAATCGGCAAAACCGGT
1 TGAAAACCGGCAAAACCGGT
26482 T
1 T
26483 TGAACCGCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.17
Consensus pattern (20 bp):
TGAAAACCGGCAAAACCGGT
Found at i:27616 original size:19 final size:20
Alignment explanation
Indices: 27588--27629 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
27578 TTATCTTAAT
27588 AAATAAAAATATATTAA-ATA
1 AAATAAAAATATA-TAATATA
*
27608 AAAT-AAAATTTATAATATA
1 AAATAAAAATATATAATATA
27627 AAA
1 AAA
27630 AATAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 3 0.15
19 13 0.65
20 4 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATAAAAATATATAATATA
Found at i:27634 original size:12 final size:12
Alignment explanation
Indices: 27603--27645 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
27593 AAAATATATT
27603 AAATAAAATAAA
1 AAATAAAATAAA
* *
27615 ATTTATAATATAAA
1 A--AATAAAATAAA
27629 AAATAAAATAAA
1 AAATAAAATAAA
27641 AAATA
1 AAATA
27646 TGTCACCCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 15 0.60
14 10 0.40
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:27645 original size:21 final size:23
Alignment explanation
Indices: 27588--27646 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 23
27578 TTATCTTAAT
27588 AAATAAAAATATATTAAATAAAATA
1 AAATAAAAA-ATA-TAAATAAAATA
** *
27613 AAATTTATAATAT-AA-AAAATA
1 AAATAAAAAATATAAATAAAATA
27634 AAATAAAAAATAT
1 AAATAAAAAATAT
27647 GTCACCCCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
21 16 0.57
22 2 0.07
23 1 0.04
24 3 0.11
25 6 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATAAAAAATATAAATAAAATA
Found at i:32824 original size:19 final size:19
Alignment explanation
Indices: 32796--32837 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
32786 TTCAGATGAG
*
32796 ATACCGAAATGTGAACCAA
1 ATACCAAAATGTGAACCAA
32815 ATACCAAAATGTGAACCAA
1 ATACCAAAATGTGAACCAA
32834 ATAC
1 ATAC
32838 AAAGTGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.50, C:0.21, G:0.12, T:0.17
Consensus pattern (19 bp):
ATACCAAAATGTGAACCAA
Found at i:32927 original size:22 final size:22
Alignment explanation
Indices: 32919--32981 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
32909 AGGAGTAAAA
32919 AAAAGAAAAAAAAGAAAAAAAG
1 AAAAGAAAAAAAAGAAAAAAAG
*
32941 AAAAG--AAAAAAGAACAAAGAAC
1 AAAAGAAAAAAAAGAA-AAA-AAG
*
32963 AAAAG-AAAGAAAGAAAAAA
1 AAAAGAAAAAAAAGAAAAAA
32982 CAAGAAGCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
20 9 0.25
21 4 0.11
22 15 0.42
23 8 0.22
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAAAAAGAAAAAAAG
Found at i:32929 original size:7 final size:7
Alignment explanation
Indices: 32926--32981 Score: 69
Period size: 7 Copynumber: 7.9 Consensus size: 7
32916 AAAAAAAGAA
32926 AAAAAAG
1 AAAAAAG
32933 AAAAAA-
1 AAAAAAG
*
32939 AGAAAAG
1 AAAAAAG
32946 AAAAAAG
1 AAAAAAG
*
32953 AACAAAG
1 AAAAAAG
32960 AACAAAAG
1 AA-AAAAG
32968 AAAGAAAG
1 AAA-AAAG
32976 AAAAAA
1 AAAAAA
32982 CAAGAAGCAC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
6 5 0.12
7 24 0.57
8 13 0.31
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:32929 original size:8 final size:8
Alignment explanation
Indices: 32916--32981 Score: 69
Period size: 8 Copynumber: 7.8 Consensus size: 8
32906 ATAAGGAGTA
32916 AAAAAAAG
1 AAAAAAAG
32924 AAAAAAAAG
1 -AAAAAAAG
32933 AAAAAAAG
1 AAAAAAAG
*
32941 AAAAGAAAA
1 AAAA-AAAG
32950 AAGAACAAAG
1 AA-AA-AAAG
*
32960 AACAAAAG
1 AAAAAAAG
*
32968 AAAGAAAG
1 AAAAAAAG
32976 AAAAAA
1 AAAAAA
32982 CAAGAAGCAC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
8 27 0.56
9 14 0.29
10 7 0.15
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:32949 original size:27 final size:27
Alignment explanation
Indices: 32915--32987 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 27
32905 AATAAGGAGT
32915 AAAA-AAAAGAAAAAAAAGAAAAAAAG
1 AAAAGAAAAGAAAAAAAAGAAAAAAAG
* *
32941 AAAAGAAAA-AAGAACAAAGAACAAAAG
1 AAAAGAAAAGAA-AAAAAAGAAAAAAAG
32968 -AAAG-AAAGAAAAAACAAGAA
1 AAAAGAAAAGAAAAAA-AAGAA
32988 GCACATACAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
25 6 0.15
26 17 0.43
27 17 0.43
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (27 bp):
AAAAGAAAAGAAAAAAAAGAAAAAAAG
Found at i:33876 original size:74 final size:76
Alignment explanation
Indices: 33706--33911 Score: 249
Period size: 75 Copynumber: 2.7 Consensus size: 76
33696 CCGTTGTACA
* * * * *
33706 AGGGGGGAATCGGTACC-CC-ATTGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTTGGA
1 AGGGGGGAATCGGTTCCTCCTA-TGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
*** *
33769 ACAAAATTGTTT
65 ACAAAACCATTC
*
33781 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAA
*
33845 CCAAACCATTC
66 CAAAACCATTC
* *
33856 A-GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAA
33912 TTTTTGGCTT
Statistics
Matches: 114, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
74 21 0.18
75 59 0.52
76 33 0.29
77 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAA
CAAAACCATTC
Found at i:34542 original size:17 final size:17
Alignment explanation
Indices: 34520--34563 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
34510 TTCATAAATC
34520 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
34537 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
34554 -AAATATCCAA
1 CAAA-ATCCAA
34564 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:34555 original size:9 final size:8
Alignment explanation
Indices: 34515--34565 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
34505 CACCATTCAT
34515 AAATCC-A
1 AAATCCAA
34522 AAATCCAA
1 AAATCCAA
*
34530 CAATCCACA
1 AAATCCA-A
34539 AAAT-CAA
1 AAATCCAA
34546 ACAATCCAA
1 A-AATCCAA
34555 AATATCCAA
1 AA-ATCCAA
34564 AA
1 AA
34566 TGTTGAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATCCAA
Found at i:42056 original size:76 final size:76
Alignment explanation
Indices: 41968--42176 Score: 246
Period size: 76 Copynumber: 2.8 Consensus size: 76
41958 CCGTTGTACA
* *
41968 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
** *
42032 CAAAAACTGTTT
66 C-AAAACCATTC
* * * * *
42044 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGTTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
*
42108 CCAAACCATTC
66 CAAAACCATTC
* *
42119 A-GGGGGAATCAGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGG-ATCGGTTCCCTCCGAGCATA-CTGGAATT
42177 TTTGGCTTTG
Statistics
Matches: 112, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
74 20 0.18
75 12 0.11
76 79 0.71
77 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.24
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
CAAAACCATTC
Found at i:43766 original size:61 final size:62
Alignment explanation
Indices: 43557--43771 Score: 267
Period size: 61 Copynumber: 3.4 Consensus size: 62
43547 TATCAGTATC
* *
43557 CTTTGAGT-TGTTTCTCTCGAAACAAATTTTGTCTCTCGAGACAGTTTCTTTT-ACAAAAAT
1 CTTTGAGTCTGTTTCTCTTGAAACAAATTTTGTCTCTCGAGACAGTTTCTTTTGAGAAAAAT
* * * *
43617 CTTTGAGTCTGTTTCTCTGGAAACAAACTTTCGTCTCTCTTGAGACAATTTATTTTGAGAAATAA
1 CTTTGAGTCTGTTTCTCTTGAAACAAA-TTTTGTCTCTC--GAGACAGTTTCTTTTGAGAAA-AA
43682 GT
62 -T
* *
43684 CTTTGAGTTTGTTTC-CTTGAAACAAATTTTGTCTCTCGAGATAGTTTCTTTTGAGAAAAAT
1 CTTTGAGTCTGTTTCTCTTGAAACAAATTTTGTCTCTCGAGACAGTTTCTTTTGAGAAAAAT
*
43745 CTTTGAGTCTGTGTCT-TTGAAAGCAAA
1 CTTTGAGTCTGTTTCTCTTGAAA-CAAA
43772 ATTTACTATC
Statistics
Matches: 133, Mismatches: 13, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
60 8 0.06
61 37 0.28
62 16 0.12
63 18 0.14
64 13 0.10
65 14 0.11
66 12 0.09
67 15 0.11
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (62 bp):
CTTTGAGTCTGTTTCTCTTGAAACAAATTTTGTCTCTCGAGACAGTTTCTTTTGAGAAAAAT
Found at i:44134 original size:134 final size:131
Alignment explanation
Indices: 43873--44230 Score: 400
Period size: 134 Copynumber: 2.7 Consensus size: 131
43863 TGAAACCATT
* * * * **
43873 ATCCCTAAAGATGGTCA-GCCGTCCTGATCACGTAGGAACCGTGTCATCCCCCGAAAAGATCTCC
1 ATCCCTAAAGATGGT-ATGTCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCC
** * * * * * *
43937 TCATCACGTAGGAGCTATTTCACCCC-TAGATAACCAGCCATCCTCATCGCGTAGGAACTGTGTT
65 TCATCACGTAGGAGCCGTGTCACCCCTTA-ATAACCAGCCATCCCCATCACATAAGAACCGTGTT
*
44001 TTC
129 ATC
* * * *
44004 ACCCTCCCTAAAGATGGTATGTCATCCTCATCTCATAGGAACCGTGTAATCCACCGACCAGATAT
1 A---TCCCTAAAGATGGTATGTCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
* *
44069 CCTCATCACGTAGGAGCCGTGTCACCCCTTAATAACCAGCCGTCCCCATCATATAAGAACCGTGT
63 CCTCATCACGTAGGAGCCGTGTCACCCCTTAATAACCAGCCATCCCCATCACATAAGAACCGTGT
44134 TATC
128 TATC
* ** *
44138 ATCCCTAAAAATGGCCT-TCCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCATATCTCC
1 ATCCCTAAAGATGGTATGT-CATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCC
*
44202 TCATCACGTAGGAGTCGTGTCA-CCCTTAA
65 TCATCACGTAGGAGCCGTGTCACCCCTTAA
44231 CTGACCATAA
Statistics
Matches: 191, Mismatches: 30, Indels: 13
0.82 0.13 0.06
Matches are distributed among these distances:
130 8 0.04
131 75 0.39
133 1 0.01
134 105 0.55
135 2 0.01
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (131 bp):
ATCCCTAAAGATGGTATGTCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCT
CATCACGTAGGAGCCGTGTCACCCCTTAATAACCAGCCATCCCCATCACATAAGAACCGTGTTAT
C
Found at i:45860 original size:15 final size:15
Alignment explanation
Indices: 45829--45868 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
45819 ACCACTAAAT
45829 TTTTTA-TT-TTTTA
1 TTTTTATTTATTTTA
45842 -TTTTATTTATTTTA
1 TTTTTATTTATTTTA
*
45856 TTTTTATATATTT
1 TTTTTATTTATTT
45869 GTTTGTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 5 0.22
13 2 0.09
14 5 0.22
15 11 0.48
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTATTTATTTTA
Found at i:46011 original size:32 final size:33
Alignment explanation
Indices: 45972--46067 Score: 90
Period size: 35 Copynumber: 2.9 Consensus size: 33
45962 TTTTCTAACT
45972 TACTAACATTCTAAC-TTTTATTTTATTGTTCA
1 TACTAACATTCTAACTTTTTATTTTATTGTTCA
* * * *
46004 TATTAACATACTGACTTTTTTATTTTTATTGTTCT
1 TACTAACATTCTAAC-TTTTTA-TTTTATTGTTCA
*
46039 TACTAAC--TCATTAACATTTTATTTTATTG
1 TACTAACATTC--TAACTTTTTATTTTATTG
46068 CACAAACTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
32 12 0.24
33 9 0.18
34 10 0.20
35 20 0.39
ACGTcount: A:0.27, C:0.14, G:0.04, T:0.55
Consensus pattern (33 bp):
TACTAACATTCTAACTTTTTATTTTATTGTTCA
Found at i:48198 original size:34 final size:35
Alignment explanation
Indices: 48151--48239 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 35
48141 TGCATTGCAT
* * *
48151 TTAATTCATCTAGTTCATTTAGGGAAA-TAGTTCA
1 TTAATTAAACTAGTTCATTTAAGGAAACTAGTTCA
**
48185 TTAATTAAACTAGTTCA-TTAATTAAACTAGTTCA
1 TTAATTAAACTAGTTCATTTAAGGAAACTAGTTCA
* * *
48219 TTCATCAAACTAGTTCGTTTA
1 TTAATTAAACTAGTTCATTTA
48240 TTAAATTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
33 6 0.13
34 36 0.80
35 3 0.07
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (35 bp):
TTAATTAAACTAGTTCATTTAAGGAAACTAGTTCA
Found at i:48222 original size:21 final size:17
Alignment explanation
Indices: 48178--48244 Score: 98
Period size: 17 Copynumber: 3.9 Consensus size: 17
48168 TTTAGGGAAA
48178 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
48195 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
48212 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
* *
48229 TAGTTCGTTTATTAAA
1 TAGTTCATTAATTAAA
48245 TTAAATCTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:50903 original size:26 final size:26
Alignment explanation
Indices: 50874--50923 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
50864 AAACTATGTA
50874 ATTTATATATATA-TATATAATATAAG
1 ATTTATATATATAGTATAT-ATATAAG
*
50900 ATTTATGTATATAGTATATATATA
1 ATTTATATATATAGTATATATATA
50924 GTATATTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (26 bp):
ATTTATATATATAGTATATATATAAG
Found at i:50935 original size:9 final size:11
Alignment explanation
Indices: 50877--50953 Score: 56
Period size: 11 Copynumber: 7.4 Consensus size: 11
50867 CTATGTAATT
50877 TATATA-TATA
1 TATATAGTATA
*
50887 TATATAATATA
1 TATATAGTATA
* * *
50898 -AGAT-TTATG
1 TATATAGTATA
50907 TATATAGTATA
1 TATATAGTATA
50918 TATATAGTATA
1 TATATAGTATA
*
50929 T-TA-AGTACA
1 TATATAGTATA
*
50938 TATATATTACTA
1 TATATAGTA-TA
50950 TATA
1 TATA
50954 AATAGTTTAC
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
9 9 0.17
10 16 0.31
11 22 0.42
12 5 0.10
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (11 bp):
TATATAGTATA
Found at i:51039 original size:9 final size:9
Alignment explanation
Indices: 51025--51057 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
51015 ATGTAAACAA
*
51025 TATATAAAC
1 TATATAAAG
51034 TATATAAAG
1 TATATAAAG
51043 TAT-TAAAG
1 TATATAAAG
51051 TATATAA
1 TATATAA
51058 TTTATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (9 bp):
TATATAAAG
Found at i:51132 original size:15 final size:14
Alignment explanation
Indices: 51111--51187 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 14
51101 ATACTATATT
51111 TATATTATAAACTA
1 TATATTATAAACTA
51125 TATAATTATTACAAGCTA
1 TAT-ATTA-TA-AA-CTA
*
51143 TATA-TATAAATTA
1 TATATTATAAACTA
* *
51156 TGTTTATATAAACTA
1 TATAT-TATAAACTA
51171 TATATGTATAAACTA
1 TATAT-TATAAACTA
51186 TA
1 TA
51188 AAAGGTATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
13 4 0.08
14 5 0.10
15 28 0.56
16 4 0.08
17 3 0.06
18 6 0.12
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (14 bp):
TATATTATAAACTA
Found at i:51283 original size:25 final size:25
Alignment explanation
Indices: 51160--51290 Score: 72
Period size: 25 Copynumber: 5.2 Consensus size: 25
51150 AAATTATGTT
*
51160 TATATAAACTATATA-TGTATAAAC
1 TATATAAAGTATATAGTGTATAAAC
* *
51184 TATA-AAAGGTATATAATTTATAAAC
1 TATATAAA-GTATATAGTGTATAAAC
* * * *
51209 TATAATTTATATTAATATAGTGTACATA-
1 TAT-A--TAAAGT-ATATAGTGTATAAAC
* * *
51237 TATAT-ATGTATGTATGTATATAAAC
1 TATATAAAGTATATA-GTGTATAAAC
* *
51262 TATATAAAGTATATAGTTTATAAAT
1 TATATAAAGTATATAGTGTATAAAC
51287 TATA
1 TATA
51291 ATTTATATTA
Statistics
Matches: 78, Mismatches: 19, Indels: 19
0.67 0.16 0.16
Matches are distributed among these distances:
23 7 0.09
24 17 0.22
25 29 0.37
26 8 0.10
27 1 0.01
28 4 0.05
29 12 0.15
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.42
Consensus pattern (25 bp):
TATATAAAGTATATAGTGTATAAAC
Found at i:51603 original size:83 final size:83
Alignment explanation
Indices: 51516--51710 Score: 190
Period size: 77 Copynumber: 2.3 Consensus size: 83
51506 TTTATAAACA
* *
51516 ATAGTTAATATATGTAACATATAGTATATGTTTACATGTAAAC-TATATATGTAACTTATAGTAC
1 ATAGTTAATATATGTAAC-TATAGTATATG--TACATGTAAACATATATATATAACCTATAGTAC
*
51580 ATGTATGTATA-AA-CTATTT
63 ATGTATATATACAATCTATTT
* * *
51599 ATAG-T-ATATAT-AAACTAT-GTATA-GTATATGTAAACTATATATATATAACCTATAGTATAT
1 ATAGTTAATATATGTAACTATAGTATATGTACATGTAAAC-ATATATATATAACCTATAGTACAT
51659 GTATATATACAATCTATTT
65 GTATATATACAATCTATTT
*
51678 ATATGTAAACTATATATGTAACCTATAGTATAT
1 ATA-GT-TA--ATATATGTAA-CTATAGTATAT
51711 ATATTATGTA
Statistics
Matches: 90, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
75 10 0.11
77 29 0.32
78 7 0.08
79 12 0.13
80 4 0.04
81 6 0.07
82 1 0.01
83 4 0.04
85 6 0.07
86 2 0.02
87 4 0.04
88 5 0.06
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.42
Consensus pattern (83 bp):
ATAGTTAATATATGTAACTATAGTATATGTACATGTAAACATATATATATAACCTATAGTACATG
TATATATACAATCTATTT
Found at i:51605 original size:20 final size:20
Alignment explanation
Indices: 51582--51758 Score: 99
Period size: 20 Copynumber: 8.9 Consensus size: 20
51572 TATAGTACAT
* *
51582 GTATGTATAAACTATTTATA
1 GTATATATAAACTATATATA
*
51602 GTATATATAAACTATGTATA
1 GTATATATAAACTATATATA
*
51622 GTATATGTAAAC----TATA
1 GTATATATAAACTATATATA
*
51638 -TATATATAACCTATAGTATA
1 GTATATATAAACTATA-TATA
*
51658 TGTATATATACAA-TCTAT-T-
1 -GTATATATA-AACTATATATA
*
51677 -TATATGTAAACTATATAT-
1 GTATATATAAACTATATATA
*
51695 GTA-ACCTATAGTA-TATATATTA
1 GTATA--TATA-AACTATATA-TA
51717 TGTATATATACAATCTATATATA
1 -GTATATATA-AA-CTATATATA
*
51740 GTTTATATAAACTATATAT
1 GTATATATAAACTATATAT
51759 GTAACTTATA
Statistics
Matches: 123, Mismatches: 14, Indels: 40
0.69 0.08 0.23
Matches are distributed among these distances:
15 9 0.07
16 6 0.05
17 11 0.09
18 2 0.02
19 2 0.02
20 51 0.41
21 5 0.04
22 24 0.20
23 6 0.05
24 7 0.06
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.43
Consensus pattern (20 bp):
GTATATATAAACTATATATA
Found at i:51663 original size:37 final size:37
Alignment explanation
Indices: 51523--51691 Score: 121
Period size: 37 Copynumber: 4.4 Consensus size: 37
51513 ACAATAGTTA
* * *
51523 ATATATGTAACATATAGTATATGTTTACATGTAAAC--T
1 ATATATGTAACCTATAGTATATG--TATATATAAACTAT
* * *
51560 ATATATGTAACTTATAGTACATGTATGTATAAACTATTTAT
1 ATATATGTAACCTATAGTATATGTATATATAAAC----TAT
* * *
51601 AGTATATATAAACTAT-GTATA-GTATATGTAAACTAT
1 A-TATATGTAACCTATAGTATATGTATATATAAACTAT
*
51637 ATATATATAACCTATAGTATATGTATATATACAATCTAT
1 ATATATGTAACCTATAGTATATGTATATATA-AA-CTAT
* *
51676 TTATATGTAAACTATA
1 ATATATGTAACCTATA
51692 TATGTAACCT
Statistics
Matches: 105, Mismatches: 16, Indels: 20
0.74 0.11 0.14
Matches are distributed among these distances:
35 21 0.20
36 9 0.09
37 29 0.28
38 2 0.02
39 17 0.16
40 10 0.10
41 6 0.06
42 11 0.10
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (37 bp):
ATATATGTAACCTATAGTATATGTATATATAAACTAT
Found at i:51825 original size:21 final size:21
Alignment explanation
Indices: 51799--51846 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
51789 ATTAGTGTAC
* *
51799 TATATAGTTTATAACCTATAG
1 TATATAATTTATAAACTATAG
51820 TATATAATTTATAAACTATAG
1 TATATAATTTATAAACTATAG
*
51841 TTTATA
1 TATATA
51847 TTAATGTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (21 bp):
TATATAATTTATAAACTATAG
Found at i:51907 original size:15 final size:15
Alignment explanation
Indices: 51857--51907 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
51847 TTAATGTACT
*
51857 ATATAGTTTATATTA
1 ATATAATTTATATTA
* *
51872 TTATTAA-TTATCTTA
1 ATA-TAATTTATATTA
51887 ACTATAATTTATATTA
1 A-TATAATTTATATTA
51903 ATATA
1 ATATA
51908 GTATATAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (15 bp):
ATATAATTTATATTA
Found at i:51926 original size:36 final size:36
Alignment explanation
Indices: 51886--52018 Score: 152
Period size: 36 Copynumber: 3.9 Consensus size: 36
51876 TAATTATCTT
51886 AACTATAATTTATATTAATATAGTATATAGTTTATA
1 AACTATAATTTATATTAATATAGTATATAGTTTATA
* * *
51922 AACTATAATTTGTATTAATGTAGTAGATAGTTTATA
1 AACTATAATTTATATTAATATAGTATATAGTTTATA
* * *
51958 AACTATAATTTACATTAATAT--TA-A-A--ATATT
1 AACTATAATTTATATTAATATAGTATATAGTTTATA
* *
51988 AACTATAGTTTATATTAAAATAGTATATAGT
1 AACTATAATTTATATTAATATAGTATATAGT
52019 ATTAATATTA
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
30 21 0.26
32 3 0.04
33 2 0.03
34 3 0.04
36 51 0.64
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (36 bp):
AACTATAATTTATATTAATATAGTATATAGTTTATA
Found at i:52002 original size:89 final size:88
Alignment explanation
Indices: 51815--52001 Score: 213
Period size: 89 Copynumber: 2.1 Consensus size: 88
51805 GTTTATAACC
* * * *
51815 TATAGTATATAATTTATAAACTATAGTTTATATTAATGTACTATATAGTTTATATTATTATTAAT
1 TATAGTATATAATTTATAAACTATAATTTATATTAATGTACTAGATAGTTTATATAACTATTAAT
*
51880 TATCTTAACTATAATTTATATTAA
66 TATCTTAACTATAA-TAATATTAA
* * *
51904 TATAGTATATAGTTTATAAACTATAATTTGTATTAATGTAGTAGATAGTTTATA-AACTA-TAAT
1 TATAGTATATAATTTATAAACTATAATTTATATTAATGTACTAGATAGTTTATATAACTATTAAT
51967 T-TACATTAA-TATTAA-AATATTAA
66 TAT-C-TTAACTA-TAATAATATTAA
*
51990 CTATAGTTTATA
1 -TATAGTATATA
52002 TTAAAATAGT
Statistics
Matches: 85, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
86 8 0.09
87 18 0.21
88 10 0.12
89 49 0.58
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (88 bp):
TATAGTATATAATTTATAAACTATAATTTATATTAATGTACTAGATAGTTTATATAACTATTAAT
TATCTTAACTATAATAATATTAA
Found at i:52026 original size:24 final size:26
Alignment explanation
Indices: 51971--52029 Score: 81
Period size: 24 Copynumber: 2.4 Consensus size: 26
51961 TATAATTTAC
*
51971 ATTAATATTAAAATATTAACTATAGT
1 ATTAATATTAAAATAGTAACTATAGT
51997 -TT-ATATTAAAATAGT-A-TATAGT
1 ATTAATATTAAAATAGTAACTATAGT
52019 ATTAATATTAA
1 ATTAATATTAA
52030 TTATAGTCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 6 0.20
23 3 0.10
24 19 0.63
25 2 0.07
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (26 bp):
ATTAATATTAAAATAGTAACTATAGT
Found at i:52035 original size:40 final size:36
Alignment explanation
Indices: 51982--52070 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 36
51972 TTAATATTAA
* *
51982 AATATTAACTATAGTTTATATTAA-AATAGTATATAGTATT
1 AATATTAATTATAGTCTATA--AACAATA-TAT-TA-TATT
*
52022 AATATTAATTATAGTCTATAAACCATATATTATATT
1 AATATTAATTATAGTCTATAAACAATATATTATATT
52058 AATATTAATTATA
1 AATATTAATTATA
52071 TTAACTATAG
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
36 17 0.38
37 2 0.04
38 5 0.11
39 3 0.07
40 18 0.40
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (36 bp):
AATATTAATTATAGTCTATAAACAATATATTATATT
Found at i:52219 original size:15 final size:15
Alignment explanation
Indices: 52199--52227 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52189 ACAAGTTAAT
52199 ATTAATATTAATTAC
1 ATTAATATTAATTAC
52214 ATTAATATTAATTA
1 ATTAATATTAATTA
52228 TAATATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTAATATTAATTAC
Found at i:52231 original size:21 final size:20
Alignment explanation
Indices: 52194--52254 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
52184 TTAATACAAG
52194 TTAATATTAA-TATTAATTACA
1 TTAATATTAATTA-TAATTA-A
*
52215 TTAATATTAATTATAATATAT
1 TTAATATTAATTATAAT-TAA
* *
52236 TTTATATTAATAATAATTA
1 TTAATATTAATTATAATTA
52255 TAAATAGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 2 0.06
21 29 0.83
22 4 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAATATTAATTATAATTAA
Found at i:52244 original size:27 final size:24
Alignment explanation
Indices: 52214--52279 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 24
52204 TATTAATTAC
*
52214 ATTAATATTAATTATAATATATTTTAT
1 ATTAATATTAATTATAA-ATA-GTT-T
*
52241 ATTAATAATAATTATAAATAGTTT
1 ATTAATATTAATTATAAATAGTTT
*
52265 ATTAATATAAATTAT
1 ATTAATATTAATTAT
52280 TTAGGGATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.40
25 2 0.06
26 3 0.09
27 16 0.46
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTAATATTAATTATAAATAGTTT
Found at i:52255 original size:15 final size:15
Alignment explanation
Indices: 52197--52256 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 15
52187 ATACAAGTTA
*
52197 ATATTAATATTAATT
1 ATATTAATAATAATT
* *
52212 ACATTAATATTAATT
1 ATATTAATAATAATT
* *
52227 ATAAT-AT-AT-TTT
1 ATATTAATAATAATT
52239 ATATTAATAATAATT
1 ATATTAATAATAATT
52254 ATA
1 ATA
52257 AATAGTTTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
12 6 0.17
13 3 0.09
14 4 0.11
15 22 0.63
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTAATAATAATT
Found at i:52786 original size:18 final size:18
Alignment explanation
Indices: 52749--52883 Score: 96
Period size: 18 Copynumber: 7.6 Consensus size: 18
52739 CATCTTTTGT
52749 AACCTAAA-CC-AACCCTG
1 AACCTAAACCCAAACCC-G
52766 AACCTAAACCCAAACCCG
1 AACCTAAACCCAAACCCG
*
52784 AACCTAAACCCGAACCC-
1 AACCTAAACCCAAACCCG
* * * * *
52801 AAACTCGAATCTAAACCCA
1 AACCT-AAACCCAAACCCG
* *
52820 AACCCAAACCCAAACTCG
1 AACCTAAACCCAAACCCG
* *
52838 AATCTGAACCCAAACCCG
1 AACCTAAACCCAAACCCG
** * *
52856 AACCCGAACCCAAATCCA
1 AACCTAAACCCAAACCCG
*
52874 AACCCAAACC
1 AACCTAAACC
52884 TAAAAAAACC
Statistics
Matches: 92, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
17 12 0.13
18 72 0.78
19 8 0.09
ACGTcount: A:0.44, C:0.42, G:0.06, T:0.08
Consensus pattern (18 bp):
AACCTAAACCCAAACCCG
Found at i:52799 original size:6 final size:6
Alignment explanation
Indices: 52766--52883 Score: 92
Period size: 6 Copynumber: 19.7 Consensus size: 6
52756 ACCAACCCTG
* * * * * * * *
52766 AACCTA AACCCA AACCCG AACCTA AACCCG AACCCA AACTCG AATCTA
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* * * ** * *
52814 AACCCA AACCCA AACCCA AACTCG AATCTG AACCCA AACCCG AACCCG
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
*
52862 AACCCA AATCCA AACCCA AACC
1 AACCCA AACCCA AACCCA AACC
52884 TAAAAAAACC
Statistics
Matches: 85, Mismatches: 27, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
6 85 1.00
ACGTcount: A:0.44, C:0.42, G:0.06, T:0.08
Consensus pattern (6 bp):
AACCCA
Found at i:52799 original size:24 final size:24
Alignment explanation
Indices: 52766--52887 Score: 111
Period size: 24 Copynumber: 5.1 Consensus size: 24
52756 ACCAACCCTG
*
52766 AACCTAAACCCAAACCCGAACCTA
1 AACCCAAACCCAAACCCGAACCTA
* * *
52790 AACCCGAACCCAAACTCGAATCTA
1 AACCCAAACCCAAACCCGAACCTA
* *
52814 AACCCAAACCCAAACCC-AAACTCG
1 AACCCAAACCCAAACCCGAACCT-A
* ** **
52838 AATCTGAACCCAAACCCGAACCCG
1 AACCCAAACCCAAACCCGAACCTA
* *
52862 AACCCAAATCCAAACCCAAACCTA
1 AACCCAAACCCAAACCCGAACCTA
52886 AA
1 AA
52888 AAAACCCTAA
Statistics
Matches: 76, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
23 4 0.05
24 69 0.91
25 3 0.04
ACGTcount: A:0.45, C:0.41, G:0.06, T:0.08
Consensus pattern (24 bp):
AACCCAAACCCAAACCCGAACCTA
Found at i:52823 original size:30 final size:30
Alignment explanation
Indices: 52784--52883 Score: 137
Period size: 30 Copynumber: 3.3 Consensus size: 30
52774 CCCAAACCCG
*
52784 AACCTAAACCCGAACCCAAACTCGAATCTA
1 AACCCAAACCCGAACCCAAACTCGAATCTA
* *
52814 AACCCAAACCCAAACCCAAACTCGAATCTG
1 AACCCAAACCCGAACCCAAACTCGAATCTA
* * * *
52844 AACCCAAACCCGAACCCGAACCCAAATCCA
1 AACCCAAACCCGAACCCAAACTCGAATCTA
52874 AACCCAAACC
1 AACCCAAACC
52884 TAAAAAAACC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.44, C:0.42, G:0.06, T:0.08
Consensus pattern (30 bp):
AACCCAAACCCGAACCCAAACTCGAATCTA
Found at i:56370 original size:24 final size:24
Alignment explanation
Indices: 56318--56395 Score: 149
Period size: 24 Copynumber: 3.3 Consensus size: 24
56308 TTATTTTTTC
56318 TTTACATAAATTAAACTATA-TAA
1 TTTACATAAATTAAACTATATTAA
56341 TTTACATAAATTAAACTATATTAA
1 TTTACATAAATTAAACTATATTAA
56365 TTTACATAAATTAAACTATATTAA
1 TTTACATAAATTAAACTATATTAA
56389 TTTACAT
1 TTTACAT
56396 TTAATCATTG
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 20 0.37
24 34 0.63
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (24 bp):
TTTACATAAATTAAACTATATTAA
Found at i:56390 original size:14 final size:13
Alignment explanation
Indices: 56326--56390 Score: 52
Period size: 12 Copynumber: 5.3 Consensus size: 13
56316 TCTTTACATA
56326 AATTAAACTATAT
1 AATTAAACTATAT
*
56339 AATT-TAC-ATA-
1 AATTAAACTATAT
56349 AATTAAACTATATT
1 AATTAAACTATA-T
*
56363 AATT-TAC-ATA-
1 AATTAAACTATAT
56373 AATTAAACTATATT
1 AATTAAACTATA-T
56387 AATT
1 AATT
56391 TACATTTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 15
0.68 0.07 0.25
Matches are distributed among these distances:
10 8 0.20
11 7 0.17
12 11 0.28
13 6 0.15
14 8 0.20
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (13 bp):
AATTAAACTATAT
Found at i:56643 original size:16 final size:16
Alignment explanation
Indices: 56622--56652 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
56612 ATGGTAATAT
56622 AAGTCAGGTAAATGTC
1 AAGTCAGGTAAATGTC
56638 AAGTCAGGTAAATGT
1 AAGTCAGGTAAATGT
56653 AGATCAGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.10, G:0.26, T:0.26
Consensus pattern (16 bp):
AAGTCAGGTAAATGTC
Found at i:57449 original size:90 final size:91
Alignment explanation
Indices: 57295--57476 Score: 339
Period size: 90 Copynumber: 2.0 Consensus size: 91
57285 TTTGAATAAT
57295 TTGAATGTAATCAATCACTTGTAGTTAAAAAACAAATGGTATAATTGATGGGGTTATTATTGATT
1 TTGAATGTAATCAATCACTTGTAGTTAAAAAACAAATGGTATAATTGATGGGGTTATTATTGATT
*
57360 AGCGTGAGTCAAAAGTCGACATCAAC
66 AGCGTGAGTCAAAAGTCCACATCAAC
*
57386 TTGAATGTAATCAATCACTTGTA-TTTAAAAACAAATGGTATAATTGATGGGGTTATTATTGATT
1 TTGAATGTAATCAATCACTTGTAGTTAAAAAACAAATGGTATAATTGATGGGGTTATTATTGATT
57450 AGCGTGAGTCAAAAGTCCACATCAAC
66 AGCGTGAGTCAAAAGTCCACATCAAC
57476 T
1 T
57477 ACACCATTTG
Statistics
Matches: 89, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
90 66 0.74
91 23 0.26
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (91 bp):
TTGAATGTAATCAATCACTTGTAGTTAAAAAACAAATGGTATAATTGATGGGGTTATTATTGATT
AGCGTGAGTCAAAAGTCCACATCAAC
Found at i:62497 original size:23 final size:22
Alignment explanation
Indices: 62463--62505 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
62453 CGAAATATCA
62463 TTCATGATACAT-ATCATATATG
1 TTCATGATACATCAT-ATATATG
62485 TTCATGATAACATCATATATA
1 TTCATGAT-ACATCATATATA
62506 AAATCAGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 9 0.47
24 2 0.11
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (22 bp):
TTCATGATACATCATATATATG
Found at i:62504 original size:21 final size:22
Alignment explanation
Indices: 62463--62504 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
62453 CGAAATATCA
*
62463 TTCATGATACATATCATATATG
1 TTCATGATACACATCATATATG
62485 TTCATGATA-ACATCATATAT
1 TTCATGATACACATCATATAT
62505 AAAATCAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (22 bp):
TTCATGATACACATCATATATG
Done.