Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000654.1 Hibiscus syriacus cultivar Beakdansim tig00001264_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: 88668
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:11 original size:2 final size:2
Alignment explanation
Indices: 1--44 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1 AT AT -T AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41 AT AT
1 AT AT
45 TAAGTGTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4519 original size:32 final size:30
Alignment explanation
Indices: 4465--4534 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 30
4455 TTGAAGTTTG
* *
4465 TTCGAGTTCGAATTGAGCTTCATATTTTTTAT
1 TTCGAGTTCCAATCGAGCTTC--ATTTTTTAT
* *
4497 TTTGAGTTCCAATCGAGTTTCATTTTTTAT
1 TTCGAGTTCCAATCGAGCTTCATTTTTTAT
4527 TTCGAGTT
1 TTCGAGTT
4535 TGAGTCGAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 16 0.48
32 17 0.52
ACGTcount: A:0.20, C:0.13, G:0.16, T:0.51
Consensus pattern (30 bp):
TTCGAGTTCCAATCGAGCTTCATTTTTTAT
Found at i:4837 original size:39 final size:40
Alignment explanation
Indices: 4790--4868 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
4780 TTTAAATTAG
* * *
4790 TATTTATTT-AAAAGAGTTTTTAA-TAAGTAATAATTAATT
1 TATTTATTTAAAAAGAATTTTAAATTAA-TAACAATTAATT
4829 TATTTATTTAAAAAGAATTTTAAATTAATAACAATTAATT
1 TATTTATTTAAAAAGAATTTTAAATTAATAACAATTAATT
4869 AATCTAAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
39 9 0.26
40 23 0.66
41 3 0.09
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (40 bp):
TATTTATTTAAAAAGAATTTTAAATTAATAACAATTAATT
Found at i:5276 original size:42 final size:41
Alignment explanation
Indices: 5148--5298 Score: 144
Period size: 42 Copynumber: 3.6 Consensus size: 41
5138 TTTAACGGCG
* * * * *
5148 TTTTTATACAAACTCCGCAATAGGGTTCATATATAGTGACAT
1 TTTTTA-ACAAACGCCGTAATAGAGTTCATCTATAGTGGCAT
* * * *
5190 TTTTCAACAAACGCCGAAATAGAG-T-AGTACGATAGCGGCAT
1 TTTTTAACAAACGCCGTAATAGAGTTCA-T-CTATAGTGGCAT
*
5231 TTTTTATACAAACGCCGTAATAGAGTTCATCTATAGTGGCTT
1 TTTTTA-ACAAACGCCGTAATAGAGTTCATCTATAGTGGCAT
*
5273 TTTTTCAACAAACGCCGTAACAGAGT
1 TTTTT-AACAAACGCCGTAATAGAGT
5299 AATACTTTAG
Statistics
Matches: 89, Mismatches: 14, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
39 1 0.01
40 2 0.02
41 28 0.31
42 54 0.61
43 3 0.03
44 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (41 bp):
TTTTTAACAAACGCCGTAATAGAGTTCATCTATAGTGGCAT
Found at i:5318 original size:42 final size:41
Alignment explanation
Indices: 5189--5318 Score: 120
Period size: 42 Copynumber: 3.1 Consensus size: 41
5179 TATAGTGACA
* * * * *
5189 TTTTTCAACAAACGCCGAAATAGAGTAGTACGATAGCGGCAT
1 TTTTTCAACAAACGCCGTAATAGAGTAATACTATAGTGG-TT
*
5231 TTTTT-ATACAAACGCCGTAATAGAGTTCAT-CTATAGTGGCTT
1 TTTTTCA-ACAAACGCCGTAATAGAG-TAATACTATAGTGG-TT
* * * *
5273 TTTTTCAACAAACGCCGTAACAGAGTAATACTTTAGTTGTG
1 TTTTTCAACAAACGCCGTAATAGAGTAATACTATAGTGGTT
5314 TTTTT
1 TTTTT
5319 ATATAAATGT
Statistics
Matches: 73, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
41 10 0.14
42 60 0.82
43 3 0.04
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (41 bp):
TTTTTCAACAAACGCCGTAATAGAGTAATACTATAGTGGTT
Found at i:5318 original size:83 final size:82
Alignment explanation
Indices: 5138--5581 Score: 374
Period size: 82 Copynumber: 5.4 Consensus size: 82
5128 AAATGGTAAT
* * * * *
5138 TTTAACGGCGTTTTTATACAAACT-CCGCAATAGGGTTCATATATAGTGACATTTTTCAACAAAC
1 TTTAGCGGTGTTTTTATACAAA-TGCCGTAATAGGGTTCATCTATAGTGGCATTTTTCAACAAAC
*
5202 GCCGAAATAGAGTAGTAC
65 GCCGCAATAGAGTAGTAC
** * * *
5220 GATAGCGGCAT-TTTTTATACAAACGCCGTAATAGAGTTCATCTATAGTGGCTTTTTTTCAACAA
1 TTTAGCGG--TGTTTTTATACAAATGCCGTAATAGGGTTCATCTATAGTGGC-ATTTTTCAACAA
* * *
5284 ACGCCGTAACAGAGTAATAC
63 ACGCCGCAATAGAGTAGTAC
** * *** *
5304 TTTAGTTGTGTTTTTATATAAATGTTATAATAGGGTTCATCTATGGTGGCATTTTTTCAACAAAC
1 TTTAGCGGTGTTTTTATACAAATGCCGTAATAGGGTTCATCTATAGTGGCA-TTTTTCAACAAAC
** *
5369 GTTGCAATATAGTAGTAC
65 GCCGCAATAGAGTAGTAC
* * * * * ** * * *
5387 -TTAGCGGTGTTTTTATTCAAATGCCATAATAGGGTTCATATTTGGTGGTGTTTATCAATAAACA
1 TTTAGCGGTGTTTTTATACAAATGCCGTAATAGGGTTCATCTATAGTGGCATTTTTCAACAAACG
*
5451 CCGCAATATAGTAGTAC
66 CCGCAATAGAGTAGTAC
** * * * *** *
5468 TTTAGCGGCATTTTTATACAAATGCCGCAATAGGGTTAATCTATATTGGCATTTAAAAAAAAACG
1 TTTAGCGGTGTTTTTATACAAATGCCGTAATAGGGTTCATCTATAGTGGCATTTTTCAACAAACG
*
5533 CCGCAACAGAGTAGTAC
66 CCGCAATAGAGTAGTAC
* * * *
5550 TTTAGTGGCGTTTTT-TACAAATGTCGCAATAG
1 TTTAGCGGTGTTTTTATACAAATGCCGTAATAG
5582 TTTGTTATAT
Statistics
Matches: 288, Mismatches: 67, Indels: 15
0.78 0.18 0.04
Matches are distributed among these distances:
81 42 0.15
82 122 0.42
83 92 0.32
84 32 0.11
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (82 bp):
TTTAGCGGTGTTTTTATACAAATGCCGTAATAGGGTTCATCTATAGTGGCATTTTTCAACAAACG
CCGCAATAGAGTAGTAC
Found at i:8093 original size:20 final size:23
Alignment explanation
Indices: 8041--8087 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
8031 AAGACATCCT
8041 ACAAATAGACCCTTTCATTGTTA
1 ACAAATAGACCCTTTCATTGTTA
**
8064 ACAAATAGACCCTTTTGTTGTTA
1 ACAAATAGACCCTTTCATTGTTA
8087 A
1 A
8088 AAAGACATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (23 bp):
ACAAATAGACCCTTTCATTGTTA
Found at i:8455 original size:19 final size:21
Alignment explanation
Indices: 8410--8460 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
8400 CCCCTACCAT
8410 GGTATCGATACTACTATACTA
1 GGTATCGATACTACTATACTA
8431 TGGTATCGATACT-CTATTAC-A
1 -GGTATCGATACTACTA-TACTA
8452 -GTATCGATA
1 GGTATCGATA
8461 GCATTTTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.32
21 4 0.14
22 15 0.54
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (21 bp):
GGTATCGATACTACTATACTA
Found at i:8512 original size:20 final size:19
Alignment explanation
Indices: 8487--8552 Score: 64
Period size: 18 Copynumber: 3.5 Consensus size: 19
8477 TTATCAATGA
8487 TATCGATACTTTCCTCATAG
1 TATCGATACTTTCCTCA-AG
** *
8507 TATCGATACCCTCCTC-GG
1 TATCGATACTTTCCTCAAG
* *
8525 TATCGATACTTGCAT-AAG
1 TATCGATACTTTCCTCAAG
8543 TATCGATACT
1 TATCGATACT
8553 GCTCAGCTGA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
18 23 0.62
20 14 0.38
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.35
Consensus pattern (19 bp):
TATCGATACTTTCCTCAAG
Found at i:11478 original size:21 final size:21
Alignment explanation
Indices: 11453--11496 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
11443 ATTTACTATA
* *
11453 ATGGATTTTAAGTTGGTTGTT
1 ATGGAATTAAAGTTGGTTGTT
*
11474 ATGGAATTAAAGTTTGTTGTT
1 ATGGAATTAAAGTTGGTTGTT
11495 AT
1 AT
11497 AGATGTCATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (21 bp):
ATGGAATTAAAGTTGGTTGTT
Found at i:11730 original size:43 final size:42
Alignment explanation
Indices: 11682--11808 Score: 137
Period size: 43 Copynumber: 2.9 Consensus size: 42
11672 ATAATTTGCG
11682 GCGTTTATGACAAAAAACGCCGCTATAGATCTAACCTTTGGCA
1 GCGTTTAT-ACAAAAAACGCCGCTATAGATCTAACCTTTGGCA
* * * * *
11725 GCGTTTATTCAGAAAACGCCGCTATAGATCTTGACCTTTTGCG
1 GCGTTTATACAAAAAACGCCGCTATAGATC-TAACCTTTGGCA
* * *
11768 GCGTTTGTATCTAAAAAATGCCGCTATAGATCCCAACCTTT
1 GCGTTTATA-C-AAAAAACGCCGCTATAGAT-CTAACCTTT
11809 TGCGGCCGTT
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
42 20 0.29
43 24 0.35
44 1 0.01
45 23 0.33
46 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (42 bp):
GCGTTTATACAAAAAACGCCGCTATAGATCTAACCTTTGGCA
Found at i:11831 original size:88 final size:86
Alignment explanation
Indices: 11676--11861 Score: 232
Period size: 88 Copynumber: 2.1 Consensus size: 86
11666 TTTTAGATAA
* *
11676 TTTGCGGCGTTTATGACAAAAAACGCCGCTATAGATCTAACCTTTGGCAGCGTTTATTCAGAAAA
1 TTTGCGGCGTTTATGACAAAAAACGCCGCTATAGATCCAACCTTTGGCAGCGTTTATTCACAAAA
* * *
11741 CGCCGCTATAGATCTTGACCT
66 CGCCACTATAGATATCGACCT
* * * * *
11762 TTTGCGGCGTTTGT-ATCTAAAAAATGCCGCTATAGATCCCAACCTTTTGCGGCCGTTTGTTC-C
1 TTTGCGGCGTTTATGA-C-AAAAAACGCCGCTATAGAT-CCAACCTTTGGCAG-CGTTTATTCAC
11825 AAAACGCCACTATAGATATCGACCT
62 AAAACGCCACTATAGATATCGACCT
11850 TTTGCGGCGTTT
1 TTTGCGGCGTTT
11862 TTTCCAACAA
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
85 1 0.01
86 14 0.16
87 18 0.21
88 45 0.52
89 8 0.09
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (86 bp):
TTTGCGGCGTTTATGACAAAAAACGCCGCTATAGATCCAACCTTTGGCAGCGTTTATTCACAAAA
CGCCACTATAGATATCGACCT
Found at i:11850 original size:43 final size:42
Alignment explanation
Indices: 11695--11892 Score: 200
Period size: 43 Copynumber: 4.6 Consensus size: 42
11685 TTTATGACAA
* * * * *
11695 AAAACGCCGCTATAGATCT-AACCTTTGGCAGCGTTTATTCAG
1 AAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTC-C
* *
11737 AAAACGCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTATCTAA
1 AAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGT-TC--C
* * *
11782 AAAATGCCGCTATAGATCCCAACCTTTTGCGGCCGTTTGTTCC
1 AAAACGCCGCTATAGATCTCGACCTTTTGCGG-CGTTTGTTCC
* * *
11825 AAAACGCCACTATAGATATCGACCTTTTGCGGCGTTTTTTCC
1 AAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
* *
11867 AACAACGCTGCTATAGATCTTGACCT
1 AA-AACGCCGCTATAGATCTCGACCT
11893 ATTACGGCAT
Statistics
Matches: 131, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
42 30 0.23
43 61 0.47
44 2 0.02
45 31 0.24
46 7 0.05
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (42 bp):
AAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCC
Found at i:11906 original size:43 final size:42
Alignment explanation
Indices: 11821--11907 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 42
11811 CGGCCGTTTG
* * *
11821 TTCCAAAACGCCACTATAGATATCGACCTTTTGCGGCGTTTT
1 TTCCAAAACGCCACTATAGATATCGACCTATTACGGCATTTT
** * *
11863 TTCCAACAACGCTGCTATAGATCTTGACCTATTACGGCATTTT
1 TTCCAA-AACGCCACTATAGATATCGACCTATTACGGCATTTT
11906 TT
1 TT
11908 GTTCTCAAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 6 0.16
43 31 0.84
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (42 bp):
TTCCAAAACGCCACTATAGATATCGACCTATTACGGCATTTT
Found at i:13019 original size:32 final size:32
Alignment explanation
Indices: 12949--13009 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
12939 AACTGGTATT
* * *
12949 ACCCGACCTGTTTTCAACCTGACCTGTGATGA
1 ACCCGACATGTTTTCAAACTGACCTGTAATGA
*
12981 ACCCGACATGTTTTTAAACTGACCTGTAA
1 ACCCGACATGTTTTCAAACTGACCTGTAA
13010 ATGATCCGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (32 bp):
ACCCGACATGTTTTCAAACTGACCTGTAATGA
Found at i:13240 original size:23 final size:23
Alignment explanation
Indices: 13197--13268 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 23
13187 AAATAGACCT
13197 ATTATATAAAATTATTTAATAAA
1 ATTATATAAAATTATTTAATAAA
13220 ATTA-ATAAAATTATTTAAATATAA
1 ATTATATAAAATTATTT-AATA-AA
13244 ATTATATAAAA-TATTATTAATAAA
1 ATTATATAAAATTA-T-TTAATAAA
13268 A
1 A
13269 ATATTGGCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
22 12 0.27
23 8 0.18
24 11 0.25
25 11 0.25
26 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTATATAAAATTATTTAATAAA
Found at i:13333 original size:23 final size:24
Alignment explanation
Indices: 13296--13346 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
13286 TGATTAAATT
13296 TAAATTAATATAGTTTAATTTATA
1 TAAATTAATATAGTTTAATTTATA
*
13320 TAAATT-ATATAGTTTAATTTATG
1 TAAATTAATATAGTTTAATTTATA
13343 TAAA
1 TAAA
13347 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (24 bp):
TAAATTAATATAGTTTAATTTATA
Found at i:14193 original size:13 final size:14
Alignment explanation
Indices: 14144--14193 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 14
14134 TATTAAATAA
14144 TAATTGCATGTTAT
1 TAATTGCATGTTAT
**
14158 TAATT-CATG-TGG
1 TAATTGCATGTTAT
14170 T-ATTGCATGTTAT
1 TAATTGCATGTTAT
14183 TAATT-CATGTT
1 TAATTGCATGTT
14194 GCATTAGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
11 3 0.10
12 6 0.21
13 12 0.41
14 8 0.28
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (14 bp):
TAATTGCATGTTAT
Found at i:14206 original size:25 final size:25
Alignment explanation
Indices: 14146--14198 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
14136 TTAAATAATA
*
14146 ATTGCATGTTATTAATTCATGTGGT
1 ATTGCATGTTATTAATTCATGTGGC
*
14171 ATTGCATGTTATTAATTCATGTTGC
1 ATTGCATGTTATTAATTCATGTGGC
14196 ATT
1 ATT
14199 AGTTGTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.09, G:0.17, T:0.49
Consensus pattern (25 bp):
ATTGCATGTTATTAATTCATGTGGC
Found at i:14626 original size:5 final size:5
Alignment explanation
Indices: 14616--14668 Score: 65
Period size: 5 Copynumber: 11.0 Consensus size: 5
14606 AGGAACAAAT
* * *
14616 TAAAA TAAAA TAAAA T--AA GAAAA TAAAA TAAAA TAAAA TAAAA CAACA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
14664 TAAAA
1 TAAAA
14669 AATATATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 2 0.05
5 38 0.95
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:14638 original size:18 final size:18
Alignment explanation
Indices: 14617--14651 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
14607 GGAACAAATT
14617 AAAATAAAATAAAATAAG
1 AAAATAAAATAAAATAAG
14635 AAAATAAAATAAAATAA
1 AAAATAAAATAAAATAA
14652 AATAAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAATAAAATAAAATAAG
Found at i:14640 original size:13 final size:13
Alignment explanation
Indices: 14622--14646 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14612 AAATTAAAAT
14622 AAAATAAAATAAG
1 AAAATAAAATAAG
14635 AAAATAAAATAA
1 AAAATAAAATAA
14647 AATAAAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAATAAAATAAG
Found at i:16060 original size:21 final size:21
Alignment explanation
Indices: 16029--16089 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
16019 TACAAAAATA
*
16029 AAAAATAAAAAATATTAATAAT
1 AAAAAT-AAAAATAATAATAAT
*
16051 AAAAATAAAAATAATAGTAAT
1 AAAAATAAAAATAATAATAAT
*
16072 AATAAATAAATA-AATAAT
1 AA-AAATAAAAATAATAAT
16090 TTTTTTAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAAATAAAAATAATAATAAT
Found at i:16086 original size:24 final size:23
Alignment explanation
Indices: 16025--16089 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 23
16015 AGCCTACAAA
* *
16025 AATAAAAAATAAAAAATATTAAT
1 AATAAAAAATAAATAATAGTAAT
*
16048 AATAAAAATAAAAATAATAGTAAT
1 AATAAAAA-ATAAATAATAGTAAT
16072 AATAAATAAATAAATAAT
1 AATAAA-AAATAAATAAT
16090 TTTTTTAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 8 0.22
24 26 0.72
25 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (23 bp):
AATAAAAAATAAATAATAGTAAT
Found at i:16460 original size:84 final size:84
Alignment explanation
Indices: 16319--16576 Score: 374
Period size: 84 Copynumber: 3.1 Consensus size: 84
16309 GAATGAAATA
* * * * *
16319 GAAGGTCTTTGGTTGGCAGATAACCCTTC-TCGACTTAAGCAATACTGCAAATGATGTGCCTTGG
1 GAAGGTCTTTGGTTGGCAAATAGCCCTTCGT-GCCTTAAGCTATATTGCAAATGATGTGCCTTGG
16383 AGCTGAGCGTAGTCGAACTC
65 AGCTGAGCGTAGTCGAACTC
* * *
16403 GAAGGTATTTGGTTGGAAAATAGCCCTTCGTGCCTTGAGCTATATTGCAAATGATGTGCCTTGGA
1 GAAGGTCTTTGGTTGGCAAATAGCCCTTCGTGCCTTAAGCTATATTGCAAATGATGTGCCTTGGA
* *
16468 GATGAGCGTAGTTGAACTC
66 GCTGAGCGTAGTCGAACTC
* *
16487 GAAGGTCTTTGGTTGGCAAATAGCCCTTCGTGCCTTAAGCTATGTTGCAAATGATGTGTCTTGGA
1 GAAGGTCTTTGGTTGGCAAATAGCCCTTCGTGCCTTAAGCTATATTGCAAATGATGTGCCTTGGA
* *
16552 GCTGAGTGTAATCGAACTC
66 GCTGAGCGTAGTCGAACTC
16571 GAAGGT
1 GAAGGT
16577 TTGGTGTTTC
Statistics
Matches: 154, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
84 153 0.99
85 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (84 bp):
GAAGGTCTTTGGTTGGCAAATAGCCCTTCGTGCCTTAAGCTATATTGCAAATGATGTGCCTTGGA
GCTGAGCGTAGTCGAACTC
Found at i:16960 original size:124 final size:124
Alignment explanation
Indices: 16740--17114 Score: 572
Period size: 124 Copynumber: 3.0 Consensus size: 124
16730 CTGCTTGTTC
** * * * *
16740 CTGAAGATGAATGTTGCTGGTGGGTACGATTCCCTTCTTCGTGAAGTTGAAACCGTGGATGACCC
1 CTGAAGATGAATGTTAATGGTGAGCACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGGCCC
*
16805 CTTCGTTGTGAAGTTGAGCCTCT-ACTTGAATATCCTTCGTCATGAAGTTGAAATCCAAG
66 CTTCGTTGTGAAGTTGAGCCT-TAACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAG
*
16864 CTGAAGATGAATGTTAATGGTGAGCACGATTTCCTTCATCGTGAAGTTGAAACCGTGGATGGCCC
1 CTGAAGATGAATGTTAATGGTGAGCACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGGCCC
*
16929 CTTCGTTGTGAAGTTGATCCTTAACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAG
66 CTTCGTTGTGAAGTTGAGCCTTAACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAG
* * * * * *
16988 CTGAAGATGAATGTTAGTGATGAGCACGATTCCCTTCGTCATGAAGTTGAAACCGCGGATGGCTC
1 CTGAAGATGAATGTTAATGGTGAGCACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGGCCC
* *
17053 CTTCGTTGTGAAGTTGAGCCTTTAACTTGAATATCATTTGTCGTGAAGTTGAAATCCAAG
66 CTTCGTTGTGAAGTTGAGCC-TTAACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAG
17113 CT
1 CT
17115 TGTATTGTTT
Statistics
Matches: 230, Mismatches: 19, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
123 1 0.00
124 190 0.83
125 39 0.17
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (124 bp):
CTGAAGATGAATGTTAATGGTGAGCACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGGCCC
CTTCGTTGTGAAGTTGAGCCTTAACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAG
Found at i:17329 original size:110 final size:110
Alignment explanation
Indices: 17111--17383 Score: 349
Period size: 110 Copynumber: 2.5 Consensus size: 110
17101 TTGAAATCCA
* * * *
17111 AGCTTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTC----TGAAACTG
1 AGCTTGTGTTGTTTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAACTG
** * * * *
17172 GGAAATTGTTTGTTGACAGCCAGTCGCTCCTTCGCTGTGAAGTTG
66 AAAAATTGTTTGTTGACAACCAGTCGCCCCTTCACTGTGAAGCTG
** *
17217 AGCTTGTGTTGTTTTGAGTTTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACT-
1 AGCTTGTGTTGTTTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAACTG
* *
17281 AAAAAGTTGTTTGTTGACAATCAGTCGCCCCTTCATTGTGAAGCTG
66 AAAAA-TTGTTTGTTGACAACCAGTCGCCCCTTCACTGTGAAGCTG
* *
17327 AGCTTGTGTTGTCTTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAA
1 AGCTTGTGTTGTTTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
17384 ACTGGGAAGC
Statistics
Matches: 142, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
106 46 0.32
109 3 0.02
110 93 0.65
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.36
Consensus pattern (110 bp):
AGCTTGTGTTGTTTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAACTG
AAAAATTGTTTGTTGACAACCAGTCGCCCCTTCACTGTGAAGCTG
Found at i:18067 original size:32 final size:32
Alignment explanation
Indices: 18017--18093 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 32
18007 CATCAGGATG
** * *
18017 TTGAATCCCCAAAGATGCCCCGATATTCAATA
1 TTGAATCTTCAAAAATGCCCCAATATTCAATA
** *
18049 TTGAATCTTCAAAAATGCCCCAATATTTGATG
1 TTGAATCTTCAAAAATGCCCCAATATTCAATA
*
18081 TTAAATCTTCAAA
1 TTGAATCTTCAAA
18094 GGTGCCCCCG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.31
Consensus pattern (32 bp):
TTGAATCTTCAAAAATGCCCCAATATTCAATA
Found at i:22084 original size:11 final size:11
Alignment explanation
Indices: 22068--22093 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
22058 GTGAGATAAG
22068 AAATAATAAAT
1 AAATAATAAAT
22079 AAATAATAAAT
1 AAATAATAAAT
22090 AAAT
1 AAAT
22094 CAAAGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:22122 original size:18 final size:18
Alignment explanation
Indices: 22109--22149 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
22099 AAAAAAAATT
*
22109 AAAATAAAATAAAATAAG
1 AAAATAAAACAAAATAAG
22127 AAAATAAAACAAAATAA-
1 AAAATAAAACAAAATAAG
22144 AAAATA
1 AAAATA
22150 TATTAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.15
Consensus pattern (18 bp):
AAAATAAAACAAAATAAG
Found at i:23536 original size:3 final size:3
Alignment explanation
Indices: 23505--23585 Score: 78
Period size: 3 Copynumber: 27.0 Consensus size: 3
23495 TATGGGGCCT
* * *
23505 ATA AAA ATA A-A AAA ATA A-A A-A ATA TTA ATA ATA ATA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
*
23548 ATA ATA ATA ATA ATA ATA GTA ATA ATAA ATAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A AT-A ATA ATA
23586 TTTTTAAATC
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
2 6 0.09
3 51 0.76
4 10 0.15
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:24112 original size:6 final size:6
Alignment explanation
Indices: 24064--24139 Score: 70
Period size: 6 Copynumber: 13.0 Consensus size: 6
24054 TGATGAGAAC
* * * *
24064 ATTAAT ATAAACT ATTTAT ATTAAT A-AAAT ATTTAT AATTAAT ATT-A-
1 ATTAAT ATTAA-T ATTAAT ATTAAT ATTAAT ATTAAT -ATTAAT ATTAAT
24111 ATT-AT ATTAAT ATTAAT ATTAAT ATTAAT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT
24140 CTTTATCTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
4 4 0.07
5 8 0.14
6 36 0.63
7 9 0.16
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (6 bp):
ATTAAT
Found at i:24131 original size:21 final size:22
Alignment explanation
Indices: 24092--24133 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
24082 TATTAATAAA
*
24092 ATATTTATAATTAATATTAATT
1 ATATTAATAATTAATATTAATT
24114 ATATTAAT-ATTAATATTAAT
1 ATATTAATAATTAATATTAAT
24134 ATTAATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATTAATAATTAATATTAATT
Found at i:24213 original size:6 final size:6
Alignment explanation
Indices: 24202--24286 Score: 87
Period size: 6 Copynumber: 15.3 Consensus size: 6
24192 ACTATTTATA
*
24202 ATTAAT ATTAAT A-TAA- ATTATAA ATTAAT ATTAAT ATTAAT ATTAAT
1 ATTAAT ATTAAT ATTAAT ATTA-AT ATTAAT ATTAAT ATTAAT ATTAAT
*
24249 A-TAAT -TT-AT ATTAAT ATTAA- CTT-AT ATTAAT A-TAAT AT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT AT
24287 AGTTTATAAT
Statistics
Matches: 67, Mismatches: 3, Indels: 18
0.76 0.03 0.20
Matches are distributed among these distances:
4 4 0.06
5 21 0.31
6 38 0.57
7 4 0.06
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTAAT
Found at i:24231 original size:23 final size:23
Alignment explanation
Indices: 24197--24312 Score: 96
Period size: 23 Copynumber: 5.0 Consensus size: 23
24187 AATAAACTAT
24197 TTATAATTAATATTAATA-TAAA
1 TTATAATTAATATTAATATTAAA
24219 TTATAAATTAATATTAATATTAATA
1 TTAT-AATTAATATTAATATTAA-A
* *
24244 TTAATATAATTTATATTAATATTAAC
1 -T--TATAATTAATATTAATATTAAA
**
24270 TTAT-ATTAATA-TAATA-TAGT
1 TTATAATTAATATTAATATTAAA
**
24290 TTATAATTTGTAATTAATATTAA
1 TTATAATTAAT-ATTAATATTAA
24313 CATAAAATAT
Statistics
Matches: 76, Mismatches: 8, Indels: 18
0.75 0.08 0.18
Matches are distributed among these distances:
20 6 0.08
21 9 0.12
22 11 0.14
23 22 0.29
24 5 0.07
25 2 0.03
26 1 0.01
27 17 0.22
28 3 0.04
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (23 bp):
TTATAATTAATATTAATATTAAA
Found at i:24247 original size:35 final size:33
Alignment explanation
Indices: 24201--24283 Score: 116
Period size: 35 Copynumber: 2.5 Consensus size: 33
24191 AACTATTTAT
24201 AATTAATATTAATATAAATTATAAATTAATATTA
1 AATTAATATTAATATAAATT-TAAATTAATATTA
*
24235 ATATTAATATTAATAT-AATTTATATTAATATTA
1 A-ATTAATATTAATATAAATTTAAATTAATATTA
*
24268 ACTT-ATATTAATATAA
1 AATTAATATTAATATAA
24284 TATAGTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
31 10 0.22
32 3 0.07
33 13 0.29
34 5 0.11
35 14 0.31
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (33 bp):
AATTAATATTAATATAAATTTAAATTAATATTA
Found at i:24338 original size:31 final size:31
Alignment explanation
Indices: 24301--24363 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
24291 TATAATTTGT
24301 AATTAATATTAACATAAAATATAGTCTATAA
1 AATTAATATTAACATAAAATATAGTCTATAA
* * * *
24332 AATTAATATTAATATAAACTATATTTTATAA
1 AATTAATATTAACATAAAATATAGTCTATAA
24363 A
1 A
24364 TTTTATAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.40
Consensus pattern (31 bp):
AATTAATATTAACATAAAATATAGTCTATAA
Found at i:24391 original size:21 final size:21
Alignment explanation
Indices: 24344--24396 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
24334 TTAATATTAA
* * *
24344 TATAAACTATATTTTATAAAT
1 TATATACTATAATTTATAAAC
* *
24365 TTTATAGTATAATTTATAAAC
1 TATATACTATAATTTATAAAC
24386 TATATACTATA
1 TATATACTATA
24397 TTAATATAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (21 bp):
TATATACTATAATTTATAAAC
Found at i:24453 original size:22 final size:22
Alignment explanation
Indices: 24425--24527 Score: 88
Period size: 22 Copynumber: 4.8 Consensus size: 22
24415 AAGATAATTA
24425 ACATTAATATAAACTATATAGT
1 ACATTAATATAAACTATATAGT
*
24447 ACATTAATATAAACTATAGA-T
1 ACATTAATATAAACTATATAGT
* * * *
24468 -TATAAATTATATACTATA-GGT
1 ACATTAA-TATAAACTATATAGT
* *
24489 -TATAAAGTATAAACTATATAGT
1 ACATTAA-TATAAACTATATAGT
*
24511 ACACTAATATAAACTAT
1 ACATTAATATAAACTAT
24528 TGTTTATAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
20 4 0.06
21 28 0.42
22 31 0.47
23 3 0.05
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.36
Consensus pattern (22 bp):
ACATTAATATAAACTATATAGT
Found at i:24483 original size:21 final size:21
Alignment explanation
Indices: 24454--24506 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
24444 AGTACATTAA
*
24454 TATAAACTATAGATTATAAAT
1 TATAAACTATAGATTATAAAG
* *
24475 TATATACTATAGGTTATAAAG
1 TATAAACTATAGATTATAAAG
24496 TATAAACTATA
1 TATAAACTATA
24507 TAGTACACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.38
Consensus pattern (21 bp):
TATAAACTATAGATTATAAAG
Found at i:24542 original size:21 final size:20
Alignment explanation
Indices: 24452--24542 Score: 67
Period size: 21 Copynumber: 4.3 Consensus size: 20
24442 ATAGTACATT
*
24452 AATATAAACTATAGATTATA
1 AATATAAACTATAGTTTATA
* *
24472 AATTATATACTATAGGTTATA
1 AA-TATAAACTATAGTTTATA
* *
24493 AAGTATAAACTATA-TAGTACA
1 AA-TATAAACTATAGT-TTATA
*
24514 CTAATATAAACTATTGTTTATA
1 --AATATAAACTATAGTTTATA
24536 AACTATA
1 AA-TATA
24543 CATTACATAT
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
20 4 0.07
21 35 0.64
22 13 0.24
23 3 0.05
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.37
Consensus pattern (20 bp):
AATATAAACTATAGTTTATA
Found at i:24629 original size:20 final size:20
Alignment explanation
Indices: 24549--24645 Score: 85
Period size: 20 Copynumber: 5.0 Consensus size: 20
24539 TATACATTAC
24549 ATATATAGTTTATATA-ACAT
1 ATATATAGTTTATATATAC-T
* **
24569 ATAAATAAATTATATATACT
1 ATATATAGTTTATATATACT
* *
24589 ATATACTA-TATGT-TATA-T
1 ATATA-TAGTTTATATATACT
24607 ATATATAGTTTATATATACT
1 ATATATAGTTTATATATACT
* *
24627 ATACATAGTTTATACATAC
1 ATATATAGTTTATATATAC
24646 ATGTACTATA
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
17 2 0.03
18 9 0.15
19 8 0.13
20 38 0.62
21 4 0.07
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (20 bp):
ATATATAGTTTATATATACT
Found at i:24674 original size:35 final size:36
Alignment explanation
Indices: 24635--24704 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
24625 CTATACATAG
*
24635 TTTATA-CATACATGTACTATAAGTTACATATATAA
1 TTTATAGCATACATATACTATAAGTTACATATATAA
* *
24670 TTTATATGTATACATATACTATAGGTTACATATAT
1 TTTATA-GCATACATATACTATAAGTTACATATAT
24705 TAACTATTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 6 0.20
37 24 0.80
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (36 bp):
TTTATAGCATACATATACTATAAGTTACATATATAA
Found at i:24700 original size:57 final size:57
Alignment explanation
Indices: 24549--24701 Score: 138
Period size: 58 Copynumber: 2.7 Consensus size: 57
24539 TATACATTAC
* * * * * *
24549 ATATATAGTTTATATA-ACATATAAATAAAT-TATATATACTATATACTATATGTTATAT
1 ATATATAGTTTATATATAC-TATACAT-AGTGTATACATAC-ATGTACTATAAGTTACAT
*
24607 ATATATAGTTTATATATACTATACATAGTTTATACATACATGTACTATAAGTTACAT
1 ATATATAGTTTATATATACTATACATAGTGTATACATACATGTACTATAAGTTACAT
24664 ATATA-A-TTTATATGTATACATATACTATAG-GT-TACATA
1 ATATATAGTTTATA--TATAC-TATAC-ATAGTGTATACATA
24702 TATTAACTAT
Statistics
Matches: 82, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
55 6 0.07
56 1 0.01
57 33 0.40
58 36 0.44
59 6 0.07
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (57 bp):
ATATATAGTTTATATATACTATACATAGTGTATACATACATGTACTATAAGTTACAT
Found at i:24791 original size:13 final size:15
Alignment explanation
Indices: 24741--24793 Score: 70
Period size: 15 Copynumber: 3.4 Consensus size: 15
24731 AATGTTACAT
24741 ATATAATTTATATAAA
1 ATAT-ATTTATATAAA
* *
24757 CTATTGTTTATATAAA
1 ATA-TATTTATATAAA
24773 ATATATTTATATAAA
1 ATATATTTATATAAA
24788 ATATAT
1 ATATAT
24794 ATGAATTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 17 0.53
16 14 0.44
17 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
ATATATTTATATAAA
Found at i:24792 original size:49 final size:49
Alignment explanation
Indices: 24700--24794 Score: 113
Period size: 49 Copynumber: 1.9 Consensus size: 49
24690 ATAGGTTACA
* * * * *
24700 TATATTAACTATTGTTTATAAACTATATGTTAATGTTACATATATAATT
1 TATATAAACTATTGTTTATAAAATATATGTTAATATAAAATATATAATT
24749 TATATAAACTATTGTTTATATAAAATATAT-TT-ATATAAAATATATA
1 TATATAAACTATTG-TT-TATAAAATATATGTTAATATAAAATATATA
24795 TGAATTATCA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
49 24 0.62
50 4 0.10
51 11 0.28
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (49 bp):
TATATAAACTATTGTTTATAAAATATATGTTAATATAAAATATATAATT
Found at i:24836 original size:7 final size:7
Alignment explanation
Indices: 24824--24862 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
24814 ACATATATAA
24824 TTTAGGG
1 TTTAGGG
24831 TTTAGGG
1 TTTAGGG
24838 TTTAGGG
1 TTTAGGG
24845 TTTAGGG
1 TTTAGGG
24852 TTTAGGG
1 TTTAGGG
24859 TTTA
1 TTTA
24863 AGATTTCTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:24959 original size:2 final size:2
Alignment explanation
Indices: 24954--25006 Score: 54
Period size: 2 Copynumber: 26.0 Consensus size: 2
24944 ATATAGTTTT
** *
24954 TA TA TA TA TA TA TA TA GG T- TA TA TA TA TA TA TA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
24996 TA TA TA CTA TA
1 TA TA TA -TA TA
25007 AATAGCTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
1 1 0.02
2 39 0.91
3 3 0.07
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (2 bp):
TA
Found at i:24967 original size:19 final size:19
Alignment explanation
Indices: 24952--25017 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 19
24942 TTATATAGTT
24952 TTTATATATATATATATAGG
1 TTTATATATATATATATA-G
24972 TTATATATATATATATATAG
1 TT-TATATATATATATATAG
*
24992 TTTATATATACTATAAATAG
1 TTTATATATA-TATATATAG
*
25012 CTTATA
1 TTTATA
25018 CATACATGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.19
20 18 0.43
21 16 0.38
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (19 bp):
TTTATATATATATATATAG
Found at i:24969 original size:21 final size:21
Alignment explanation
Indices: 24943--25006 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
24933 TAATTTACTT
*
24943 TATATAGTTTTTATATATATA
1 TATATAGTTTATATATATATA
*
24964 TATATAGGTTATATATATATA
1 TATATAGTTTATATATATATA
24985 TATATAGTTTATATATACTATA
1 TATATAGTTTATATATA-TATA
25007 AATAGCTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 35 0.90
22 4 0.10
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (21 bp):
TATATAGTTTATATATATATA
Found at i:25099 original size:2 final size:2
Alignment explanation
Indices: 25086--25252 Score: 109
Period size: 2 Copynumber: 85.5 Consensus size: 2
25076 TTAGGATTCC
* * * *
25086 AT AT AA AT AT AT AT AT AT A- AT CT AT AG AT -T AT TT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
25125 AGT -T AT AT AT AC AT AT AT AT AT AT AT AT ACT AT AT -T A- AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * * * * *
25166 AA AT -T AT A- AT TT AT AA ACT AT AT AT -T TT AT AT AGT TT AT AC
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT
* *
25207 AT AT AT AGT TT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25250 AT A
1 AT A
25253 GAAAAATAAA
Statistics
Matches: 126, Mismatches: 25, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
1 9 0.07
2 111 0.88
3 6 0.05
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25192 original size:15 final size:15
Alignment explanation
Indices: 25086--25252 Score: 60
Period size: 15 Copynumber: 11.2 Consensus size: 15
25076 TTAGGATTCC
25086 ATATAAA-TATATAT
1 ATATAAACTATATAT
* *
25100 ATATAATCTATAGATT
1 ATATAAACTATATA-T
* * *
25116 ATTTATATTAGT-TAT
1 ATATAAACTA-TATAT
25131 ATATACATA-TATATAT
1 ATATA-A-ACTATATAT
*
25147 ATATATACTATAT-T
1 ATATAAACTATATAT
*
25161 AATATAAATTATA-AT
1 -ATATAAACTATATAT
*
25176 TTATAAACTATATATT
1 ATATAAACTATATA-T
* * * * *
25192 TTATATAGTTTATAC
1 ATATAAACTATATAT
* * *
25207 ATATATAGTTTATAT
1 ATATAAACTATATAT
* *
25222 ACATATA-TATATAT
1 ATATAAACTATATAT
*
25236 ATATATA-TATATAT
1 ATATAAACTATATAT
25250 ATA
1 ATA
25253 GAAAAATAAA
Statistics
Matches: 119, Mismatches: 23, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
14 40 0.34
15 47 0.39
16 30 0.25
17 2 0.02
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (15 bp):
ATATAAACTATATAT
Found at i:25503 original size:19 final size:20
Alignment explanation
Indices: 25463--25507 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
25453 CAAATTTCTA
*
25463 TTCCCTCTAAATTTTTCAAT
1 TTCCCTCTAAATTTTACAAT
*
25483 TTCCTTCTAAA-TTTACAAT
1 TTCCCTCTAAATTTTACAAT
25502 TTCCCT
1 TTCCCT
25508 ATATTCTCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (20 bp):
TTCCCTCTAAATTTTACAAT
Found at i:25692 original size:15 final size:15
Alignment explanation
Indices: 25669--25707 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
25659 TATACTTTTT
25669 TATAGTTTATACATA
1 TATAGTTTATACATA
*
25684 TATA-ATT-TACATA
1 TATAGTTTATACATA
25697 TATAGTTTATA
1 TATAGTTTATA
25708 TATAGTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
13 10 0.50
14 4 0.20
15 6 0.30
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (15 bp):
TATAGTTTATACATA
Found at i:25694 original size:13 final size:13
Alignment explanation
Indices: 25678--25711 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
25668 TTATAGTTTA
25678 TACATATATAATT
1 TACATATATAATT
*
25691 TACATATATAGTT
1 TACATATATAATT
*
25704 TATATATA
1 TACATATA
25712 GTTAATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (13 bp):
TACATATATAATT
Found at i:25698 original size:26 final size:27
Alignment explanation
Indices: 25643--25707 Score: 62
Period size: 26 Copynumber: 2.4 Consensus size: 27
25633 ATATATAAAT
* **
25643 TATAGTTTATAAACTATATACTTT-TT
1 TATAGTTTATAAACTATATAATTTCAA
*
25669 TATAGTTTATACA-TATATAATTTACATA
1 TATAGTTTATAAACTATATAATTT-CA-A
25697 TATAGTTTATA
1 TATAGTTTATA
25708 TATAGTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 9 0.28
26 12 0.38
28 11 0.34
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.51
Consensus pattern (27 bp):
TATAGTTTATAAACTATATAATTTCAA
Found at i:25774 original size:18 final size:18
Alignment explanation
Indices: 25730--25782 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
25720 AAACACAATT
*
25730 TATATATATAGCTTATAA
1 TATATATATAGTTTATAA
25748 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
*
25766 TATAAATATAGTTTATA
1 TATATATATAGTTTATA
25783 TATTTAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 1 0.03
18 29 0.94
19 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:25790 original size:13 final size:13
Alignment explanation
Indices: 25774--25798 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25764 AATATAAATA
25774 TAGTTTATATATT
1 TAGTTTATATATT
25787 TAGTTTATATAT
1 TAGTTTATATAT
25799 AAACTTTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
TAGTTTATATATT
Found at i:27282 original size:22 final size:22
Alignment explanation
Indices: 27257--27322 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 22
27247 AACCTTTTAG
27257 ATTTATGATTTTTAGTTTGATT
1 ATTTATGATTTTTAGTTTGATT
* *
27279 ATTT-T-ATTATTACTTT--TT
1 ATTTATGATTTTTAGTTTGATT
* *
27297 AATTATGATCTTTAGTTTGATT
1 ATTTATGATTTTTAGTTTGATT
27319 ATTT
1 ATTT
27323 TATTGGTAGG
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
18 5 0.15
19 1 0.03
20 17 0.52
21 1 0.03
22 9 0.27
ACGTcount: A:0.24, C:0.03, G:0.09, T:0.64
Consensus pattern (22 bp):
ATTTATGATTTTTAGTTTGATT
Found at i:30897 original size:18 final size:18
Alignment explanation
Indices: 30871--30908 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
30861 TCCAAAGTTT
30871 AACAATCCACAAA-ATTCA
1 AACAATCCA-AAATATTCA
*
30889 AACATTCCAAAATATTCA
1 AACAATCCAAAATATTCA
30907 AA
1 AA
30909 ATGTTGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (18 bp):
AACAATCCAAAATATTCA
Found at i:32904 original size:19 final size:19
Alignment explanation
Indices: 32877--32940 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
32867 AAATCCAGAA
* *
32877 CCCCAAGGGGGTATCGATT
1 CCCCTAGGGGGAATCGATT
*
32896 CCCCTAGGGGGAATCGGTT
1 CCCCTAGGGGGAATCGATT
32915 CCCCTTCAAAGGGGGAATCGATT
1 CCCC-T---AGGGGGAATCGATT
32938 CCC
1 CCC
32941 TCATGAGGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 20 0.54
20 1 0.03
23 16 0.43
ACGTcount: A:0.20, C:0.30, G:0.30, T:0.20
Consensus pattern (19 bp):
CCCCTAGGGGGAATCGATT
Found at i:39808 original size:21 final size:18
Alignment explanation
Indices: 39749--39813 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 18
39739 ATTTTTATTA
*
39749 TTTTTTTTATCAATTTAT
1 TTTTTTTTATCTATTTAT
39767 TTTTTTTTA-CTATTT-T
1 TTTTTTTTATCTATTTAT
39783 CTTTTTCTAGTTATCTATTTAT
1 -TTTTT-T--TTATCTATTTAT
39805 TTTTGTTTT
1 TTTT-TTTT
39814 TATTTTTAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
16 1 0.03
17 10 0.26
18 10 0.26
19 2 0.05
20 3 0.08
21 11 0.28
22 2 0.05
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTTTTTATCTATTTAT
Found at i:39816 original size:20 final size:19
Alignment explanation
Indices: 39742--39816 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 19
39732 GCAACCCATT
*
39742 TTTATTATTTTTTTTATCAA
1 TTTATT-TTTTTTTTATCTA
39762 TTTA-TTTTTTTTTA-CTA
1 TTTATTTTTTTTTTATCTA
*
39779 TTT-TCTTTTTCTAGTTATCTA
1 TTTAT-TTTTT-T-TTTATCTA
39800 TTTATTTTTGTTTTTAT
1 TTTATTTTT-TTTTTAT
39817 TTTTAGGTAC
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
17 5 0.11
18 14 0.31
19 2 0.04
20 11 0.24
21 11 0.24
22 2 0.04
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (19 bp):
TTTATTTTTTTTTTATCTA
Found at i:41793 original size:20 final size:19
Alignment explanation
Indices: 41768--41813 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
41758 TATATTTTTC
*
41768 TTATTTTTATTTATTTCAAT
1 TTATTTTAATTTA-TTCAAT
*
41788 TTATTTCAATTTATTCAAT
1 TTATTTTAATTTATTCAAT
*
41807 TTCTTTT
1 TTATTTT
41814 GCTAAACCCC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTTAATTTATTCAAT
Found at i:41806 original size:9 final size:10
Alignment explanation
Indices: 41776--41808 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
41766 TCTTATTTTT
41776 ATTTATTTCA
1 ATTTATTTCA
41786 ATTTATTTCA
1 ATTTATTTCA
41796 ATTTA-TTCA
1 ATTTATTTCA
41805 ATTT
1 ATTT
41809 CTTTTGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (10 bp):
ATTTATTTCA
Found at i:48984 original size:16 final size:16
Alignment explanation
Indices: 48954--48984 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48944 TAATATTAAA
*
48954 ACTTGAACTCGAAAAG
1 ACTTGAACTCAAAAAG
48970 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
48985 AAATTTAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:51537 original size:14 final size:14
Alignment explanation
Indices: 51518--51551 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
51508 ATTCGAATGG
*
51518 TTTTTCTCTTGATA
1 TTTTTCTCTCGATA
*
51532 TTTTTCTCTCGATC
1 TTTTTCTCTCGATA
51546 TTTTTC
1 TTTTTC
51552 GTTCGAGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.21, G:0.06, T:0.65
Consensus pattern (14 bp):
TTTTTCTCTCGATA
Found at i:52696 original size:121 final size:121
Alignment explanation
Indices: 52482--52832 Score: 551
Period size: 121 Copynumber: 2.9 Consensus size: 121
52472 GTCGATCCAT
* * *
52482 TGGGCACAATATCCTTTGTCGTGAAGTTAAAATCGTGGATGGCTCATTCGTTGTGAACTTGAGCT
1 TGGGCACGATATCCTTTGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCT
* * * *
52547 TGGAATTAGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTG
66 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTACTGCTTG
52603 TGGGCACGATATCCTTTGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCT
1 TGGGCACGATATCCTTTGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCT
* * **
52668 TTGAATTGGATATCCTTCGTCGAGAAGTTAAAATCCAAGGGTTATATTACTGCTTG
66 TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTACTGCTTG
* * * *
52724 TGGCCATGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTC-TTCGTAAAGTTGAGC
1 TGGGCACGATATCCTTTGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTT-GTGAAGTTGAGC
52788 TTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTG
65 TTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTG
52833 TTTCACCAAA
Statistics
Matches: 211, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
120 2 0.01
121 209 0.99
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (121 bp):
TGGGCACGATATCCTTTGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCT
TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTACTGCTTG
Found at i:52881 original size:60 final size:58
Alignment explanation
Indices: 52782--52947 Score: 190
Period size: 58 Copynumber: 2.8 Consensus size: 58
52772 CTTCGTAAAG
* *
52782 TTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGT-TGTTTCACCAAA
1 TTGA-CTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAA---TCTGCTTCACCAAA
** * * * *
52843 TTGGTTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATTCAATCTGCTTCATCGAA
1 TTGACTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTGCTTCACCAAA
* * *
52901 TTGACTTTAAGTTGGATATCATTCGTCCTGAAGTTGAAATCCAATCT
1 TTGACTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
52948 TGTGTTGTGT
Statistics
Matches: 89, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
57 1 0.01
58 49 0.55
60 36 0.40
61 3 0.03
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (58 bp):
TTGACTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTGCTTCACCAAA
Found at i:53350 original size:15 final size:15
Alignment explanation
Indices: 53330--53362 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
53320 ATTTATTTTC
53330 TTGCCCCATCAAATT
1 TTGCCCCATCAAATT
*
53345 TTGCCCTATCAAATT
1 TTGCCCCATCAAATT
53360 TTG
1 TTG
53363 AATTTTCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.39
Consensus pattern (15 bp):
TTGCCCCATCAAATT
Found at i:56155 original size:15 final size:15
Alignment explanation
Indices: 56135--56163 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
56125 ATAAGAGGTA
56135 TCTTATTCTTTTTAT
1 TCTTATTCTTTTTAT
56150 TCTTATTCTTTTTA
1 TCTTATTCTTTTTA
56164 GCCTTCTTGA
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:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (15 bp):
TCTTATTCTTTTTAT
Found at i:61815 original size:28 final size:28
Alignment explanation
Indices: 61783--61839 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
61773 ATGTCGTTGT
* * * *
61783 TTTCAAGCATTGACTTTACAACATAATG
1 TTTCAAGCACTAACTTGAAAACATAATG
61811 TTTCAAGCACTAACTTGAAAACATAATG
1 TTTCAAGCACTAACTTGAAAACATAATG
61839 T
1 T
61840 AAACGGAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.33
Consensus pattern (28 bp):
TTTCAAGCACTAACTTGAAAACATAATG
Found at i:62027 original size:19 final size:19
Alignment explanation
Indices: 62003--62040 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
61993 TTTGTAATTT
*
62003 TTAATAATCCTAATCGAAA
1 TTAATAATCATAATCGAAA
62022 TTAATAATCATAATCGAAA
1 TTAATAATCATAATCGAAA
62041 GACTCAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.32
Consensus pattern (19 bp):
TTAATAATCATAATCGAAA
Found at i:73913 original size:16 final size:16
Alignment explanation
Indices: 73889--73919 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
73879 AATAACATTT
*
73889 TTGTCTCATGTCTGAA
1 TTGTATCATGTCTGAA
73905 TTGTATCATGTCTGA
1 TTGTATCATGTCTGA
73920 CCAACAACAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45
Consensus pattern (16 bp):
TTGTATCATGTCTGAA
Found at i:82401 original size:20 final size:20
Alignment explanation
Indices: 82354--82410 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
82344 TGGTTTCTCG
* *
82354 TTGAATTTATTTTCTTTTTC
1 TTGATTTTATTTTCCTTTTC
*
82374 TTGTTTTTATATTTCCTTTT-
1 TTGATTTTAT-TTTCCTTTTC
82394 TTGATTTT-TTTT-CTTTT
1 TTGATTTTATTTTCCTTTT
82411 TATTATTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 5 0.16
18 3 0.09
19 1 0.03
20 15 0.47
21 8 0.25
ACGTcount: A:0.11, C:0.09, G:0.05, T:0.75
Consensus pattern (20 bp):
TTGATTTTATTTTCCTTTTC
Found at i:84879 original size:31 final size:31
Alignment explanation
Indices: 84844--84926 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 31
84834 TAGATTTTGA
* *
84844 GGCCGTGGGGCCTACCTAAGAACAATCTTAG
1 GGCCGTAGGGCCTACCTAAGAACAATCTCAG
* ** **
84875 GGCCGCAGGGCCTACCCGAGAATGATCTCAG
1 GGCCGTAGGGCCTACCTAAGAACAATCTCAG
*
84906 GGCCGTAGAGCCTACCTAAGA
1 GGCCGTAGGGCCTACCTAAGA
84927 GTCACATTAG
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.25, C:0.29, G:0.30, T:0.16
Consensus pattern (31 bp):
GGCCGTAGGGCCTACCTAAGAACAATCTCAG
Done.