Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004541.1 Hibiscus syriacus cultivar Beakdansim tig00010051_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: 115183
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1751 original size:19 final size:20
Alignment explanation
Indices: 1709--1755 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1699 CATAATTTTT
1709 TAATAATAATTATCGTAGAA
1 TAATAATAATTATCGTAGAA
**
1729 -AATAATAATT-TTTTAGAA
1 TAATAATAATTATCGTAGAA
1747 TAATAATAA
1 TAATAATAA
1756 CGATCGTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.38
Consensus pattern (20 bp):
TAATAATAATTATCGTAGAA
Found at i:2299 original size:18 final size:18
Alignment explanation
Indices: 2270--2322 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
2260 ATAATAATTA
* *
2270 ATTTAAATAAAATTGATA-
1 ATTTATATAAAAAT-ATAG
2288 ATTTAT-TAAAAATATAG
1 ATTTATATAAAAATATAG
2305 ATTTATATAAAAA-ATAG
1 ATTTATATAAAAATATAG
2322 A
1 A
2323 AAGTTTAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 3 0.10
17 17 0.55
18 11 0.35
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
ATTTATATAAAAATATAG
Found at i:3034 original size:16 final size:16
Alignment explanation
Indices: 2951--3046 Score: 52
Period size: 16 Copynumber: 6.0 Consensus size: 16
2941 CCGACCCAAA
*
2951 AATCAACCGATTCGAT
1 AATCAACCGATCCGAT
* * * *
2967 -ATTAATCCGAACCCAA
1 AATCAA-CCGATCCGAT
*
2983 AATCAACCGATTCGAT
1 AATCAACCGATCCGAT
* * * *
2999 -ATTAATCCGAACCCAA
1 AATCAA-CCGATCCGAT
3015 AATCAACCGATCCGAT
1 AATCAACCGATCCGAT
* *
3031 AATCATCCGACCCGAT
1 AATCAACCGATCCGAT
3047 CTGATTTACC
Statistics
Matches: 55, Mismatches: 21, Indels: 8
0.65 0.25 0.10
Matches are distributed among these distances:
15 8 0.15
16 39 0.71
17 8 0.15
ACGTcount: A:0.39, C:0.30, G:0.10, T:0.21
Consensus pattern (16 bp):
AATCAACCGATCCGAT
Found at i:3039 original size:32 final size:32
Alignment explanation
Indices: 2880--3040 Score: 182
Period size: 32 Copynumber: 5.0 Consensus size: 32
2870 GGTTGACATA
* ** *
2880 AACCGAAAATCAACCGATATGATATTAACCCG
1 AACCCAAAATCAACCGATCCGATATTAATCCG
* * * *
2912 AA-TCGAAATCTAACCGATCCGTTATTAACCCG
1 AACCCAAAATC-AACCGATCCGATATTAATCCG
*
2944 -ACCCAAAAATCAACCGATTCGATATTAATCCG
1 AACCC-AAAATCAACCGATCCGATATTAATCCG
*
2976 AACCCAAAATCAACCGATTCGATATTAATCCG
1 AACCCAAAATCAACCGATCCGATATTAATCCG
* *
3008 AACCCAAAATCAACCGATCCGATAATCATCCG
1 AACCCAAAATCAACCGATCCGATATTAATCCG
3040 A
1 A
3041 CCCGATCTGA
Statistics
Matches: 111, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
31 6 0.05
32 96 0.86
33 9 0.08
ACGTcount: A:0.40, C:0.29, G:0.11, T:0.20
Consensus pattern (32 bp):
AACCCAAAATCAACCGATCCGATATTAATCCG
Found at i:6555 original size:2 final size:2
Alignment explanation
Indices: 6465--6535 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
6455 AATAAACACT
6465 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6536 GAGAGAAATA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6663 original size:2 final size:2
Alignment explanation
Indices: 6599--6650 Score: 52
Period size: 2 Copynumber: 26.0 Consensus size: 2
6589 AAACTATGTA
* * * *
6599 AT AT AT AT AT AA AT AT A- AT AT AT AG AT TT AT GT AT AT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
6641 AT AT AT AT AT
1 AT AT AT AT AT
6651 TAAGTACATA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6814 original size:13 final size:11
Alignment explanation
Indices: 6798--6843 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
6788 AATATAAGTT
6798 TATATATAAAC
1 TATATATAAAC
6809 TATATATAAAC
1 TATATATAAAC
*
6820 TATAT-T-TA-
1 TATATATAAAC
6828 TAT-TATAAAC
1 TATATATAAAC
6838 TATATA
1 TATATA
6844 ATTATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
7 1 0.03
8 4 0.14
9 2 0.07
10 4 0.14
11 18 0.62
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (11 bp):
TATATATAAAC
Found at i:6849 original size:18 final size:19
Alignment explanation
Indices: 6800--6862 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 19
6790 TATAAGTTTA
6800 TATATAA-ACTATATATAAAC
1 TATATAATA-TAT-TATAAAC
*
6820 TATAT-TTATATTATAAAC
1 TATATAATATATTATAAAC
**
6838 TATATAAT-TATTATATGC
1 TATATAATATATTATAAAC
6856 TATATAA
1 TATATAA
6863 AAACTATGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
18 27 0.73
19 4 0.11
20 6 0.16
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (19 bp):
TATATAATATATTATAAAC
Found at i:6934 original size:2 final size:2
Alignment explanation
Indices: 6927--7004 Score: 90
Period size: 2 Copynumber: 40.0 Consensus size: 2
6917 ATTAATTTAG
* * *
6927 TA TA TA TA TA TA TA TA TA TG TA TA -A CTA -A TA TA TG TA -A TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
*
6967 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7005 GTAATAAAGT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
1 3 0.05
2 60 0.94
3 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:7052 original size:2 final size:2
Alignment explanation
Indices: 7045--7118 Score: 50
Period size: 2 Copynumber: 38.0 Consensus size: 2
7035 ATGCATAAAC
* *
7045 TA TA TA TA TA TA -A TA TA AA T- TA TA TA GT- TA T- TA TA AA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
* *
7085 TA TA TG TA TA AA CTA TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
7119 AGCTACATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
1 5 0.09
2 48 0.86
3 3 0.05
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:7070 original size:18 final size:17
Alignment explanation
Indices: 7046--7118 Score: 62
Period size: 16 Copynumber: 4.3 Consensus size: 17
7036 TGCATAAACT
7046 ATATATATATAATATAA
1 ATATATATATAATATAA
*
7063 AT-TATATAGTTATTATAA
1 ATATATATA--TAATATAA
*
7081 ACTATATATGT-ATA-AA
1 A-TATATATATAATATAA
* *
7097 CTATATATATAATATAT
1 ATATATATATAATATAA
7114 ATATA
1 ATATA
7119 AGCTACATAT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
15 8 0.19
16 11 0.26
17 9 0.21
18 9 0.21
19 1 0.02
20 5 0.12
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
ATATATATATAATATAA
Found at i:7096 original size:15 final size:15
Alignment explanation
Indices: 7076--7146 Score: 73
Period size: 15 Copynumber: 5.1 Consensus size: 15
7066 ATATAGTTAT
7076 TATAAACTATATATG
1 TATAAACTATATATG
7091 TATAAACTATATA--
1 TATAAACTATATATG
7104 TAT-AA-TATATA--
1 TATAAACTATATATG
* *
7115 TATAAGCTACATATG
1 TATAAACTATATATG
*
7130 TATAAATTATATATG
1 TATAAACTATATATG
7145 TA
1 TA
7147 ATCTATATAG
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
11 9 0.19
12 3 0.06
13 8 0.17
15 27 0.57
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.41
Consensus pattern (15 bp):
TATAAACTATATATG
Found at i:7129 original size:39 final size:39
Alignment explanation
Indices: 7076--7155 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 39
7066 ATATAGTTAT
*
7076 TATAAACTATATATGTATAAACTATATATATAATATATA
1 TATAAACTACATATGTATAAACTATATATATAATATATA
* * * *
7115 TATAAGCTACATATGTATAAATTATATATGTAATCTATA
1 TATAAACTACATATGTATAAACTATATATATAATATATA
7154 TA
1 TA
7156 GTTTATATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.41
Consensus pattern (39 bp):
TATAAACTACATATGTATAAACTATATATATAATATATA
Found at i:7187 original size:31 final size:31
Alignment explanation
Indices: 7130--7193 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
7120 GCTACATATG
7130 TATAAATTATATATGTAATCTATATAGTTTA
1 TATAAATTATATATGTAATCTATATAGTTTA
*
7161 TATAAACTATATATATGTAA-C-CTATAGTTTA
1 TATAAA-T-TATATATGTAATCTATATAGTTTA
7192 TA
1 TA
7194 AAGAATAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 17 0.57
32 2 0.07
33 11 0.37
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (31 bp):
TATAAATTATATATGTAATCTATATAGTTTA
Found at i:7241 original size:54 final size:55
Alignment explanation
Indices: 7150--7284 Score: 209
Period size: 54 Copynumber: 2.5 Consensus size: 55
7140 ATATGTAATC
* * * *
7150 TATATAGTTTATATAAACTATATATATGTAACCTATAGTTTATAAAGAATAGTTTA
1 TATATAATTTATATAAACTATATATA-GTAACCTATAGTCTATAAACAATAGTTGA
*
7206 TATATAATTTATATAAACTATATATA-TAACGTATAGTCTATAAACAATAGTTGA
1 TATATAATTTATATAAACTATATATAGTAACCTATAGTCTATAAACAATAGTTGA
7260 TATATAATTTATATAAACTATATAT
1 TATATAATTTATATAAACTATATAT
7285 GTATAAACAC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
54 49 0.66
56 25 0.34
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (55 bp):
TATATAATTTATATAAACTATATATAGTAACCTATAGTCTATAAACAATAGTTGA
Found at i:7274 original size:27 final size:26
Alignment explanation
Indices: 7190--7277 Score: 67
Period size: 27 Copynumber: 3.3 Consensus size: 26
7180 ACCTATAGTT
*
7190 TATAAAGAATAGTTTATATATAATTTA
1 TATAAACAATAG-TTATATATAATTTA
*
7217 TATAAAC--TA--TATATATAACGTATAGTC
1 TATAAACAATAGTTATATATAA--T-T--TA
7244 TATAAACAATAGTTGATATATAATTTA
1 TATAAACAATAGTT-ATATATAATTTA
7271 TATAAAC
1 TATAAAC
7278 TATATATGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 20
0.68 0.04 0.28
Matches are distributed among these distances:
22 9 0.19
24 1 0.02
25 3 0.06
27 22 0.46
29 3 0.06
30 1 0.02
31 1 0.02
32 8 0.17
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.40
Consensus pattern (26 bp):
TATAAACAATAGTTATATATAATTTA
Found at i:8143 original size:20 final size:20
Alignment explanation
Indices: 8118--8188 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
8108 ATTTAATCGA
* *
8118 TATCGATATCGAAAGGGGA-G
1 TATCGATA-CCAAAGGGAAGG
*
8138 TATCGATACCAATGGGAAGG
1 TATCGATACCAAAGGGAAGG
8158 TATCGATACCAAAGGGAAGG
1 TATCGATACCAAAGGGAAGG
8178 TATCGATACCA
1 TATCGATACCA
8189 TAGCATAGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.15
20 39 0.85
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (20 bp):
TATCGATACCAAAGGGAAGG
Found at i:9064 original size:54 final size:54
Alignment explanation
Indices: 8570--9022 Score: 771
Period size: 54 Copynumber: 8.4 Consensus size: 54
8560 GATTTCCAAA
*
8570 TCGGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
* *
8624 TTGGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
*
8678 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
8732 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
* *
8786 TCGGCACTAAGTGTGCATTTCACTGAATTCATCCTAGGTGGATGAATAACCGTT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
8840 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
* * **
8894 TCGGCACTAAGTGTGTATTTCACGGAATTCATCCTATGTAGATGAATAATTGTT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
* * * * *
8948 TCGGCACTAAGTGTGTATTTCACAGAATTCATCCTATATGAATGAATAACTGTT
1 TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
9002 TCGGCACTAAGTGTGCATTTC
1 TCGGCACTAAGTGTGCATTTC
9023 GCAGAATTTA
Statistics
Matches: 378, Mismatches: 21, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 378 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (54 bp):
TCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTT
Found at i:16748 original size:32 final size:33
Alignment explanation
Indices: 16697--16768 Score: 128
Period size: 32 Copynumber: 2.2 Consensus size: 33
16687 TACAAACCAG
16697 ATTACGTTAAAAGTCATTTTTTACAACAAAATGA
1 ATTACGTT-AAAGTCATTTTTTACAACAAAATGA
16731 ATTACGTT-AAGTCATTTTTTACAACAAAATGA
1 ATTACGTTAAAGTCATTTTTTACAACAAAATGA
16763 ATTACG
1 ATTACG
16769 ATATGTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 30 0.79
34 8 0.21
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (33 bp):
ATTACGTTAAAGTCATTTTTTACAACAAAATGA
Found at i:27551 original size:14 final size:15
Alignment explanation
Indices: 27516--27559 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 15
27506 AACTCTATCC
27516 CTTTCATTTCTTATT
1 CTTTCATTTCTTATT
* *
27531 ATTTCATTT-TTTTT
1 CTTTCATTTCTTATT
27545 CTTTCATTTCTTATT
1 CTTTCATTTCTTATT
27560 TCATTAATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (15 bp):
CTTTCATTTCTTATT
Found at i:27758 original size:12 final size:13
Alignment explanation
Indices: 27741--27778 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
27731 AAAGTGTTGC
27741 AATAAAGAA-AAA
1 AATAAAGAAGAAA
27753 AATAAAGAAGAAA
1 AATAAAGAAGAAA
*
27766 AAGAAA-AAGAAA
1 AATAAAGAAGAAA
27778 A
1 A
27779 GAACTCCTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (13 bp):
AATAAAGAAGAAA
Found at i:32172 original size:13 final size:13
Alignment explanation
Indices: 32156--32194 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
32146 AAAGTGTTGC
32156 AATAAAGAAAAAA
1 AATAAAGAAAAAA
32169 AATAAAGAAGAAAA
1 AATAAAGAA-AAAA
*
32183 AGAAAAAGAAAA
1 A-ATAAAGAAAA
32195 GAACTCCTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 9 0.39
14 7 0.30
15 7 0.30
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (13 bp):
AATAAAGAAAAAA
Found at i:36368 original size:10 final size:10
Alignment explanation
Indices: 36353--36391 Score: 55
Period size: 9 Copynumber: 4.1 Consensus size: 10
36343 TATATCCCTT
36353 TCATTTCTTA
1 TCATTTCTTA
*
36363 TCATTTCTTT
1 TCATTTCTTA
36373 TC-TTTCTT-
1 TCATTTCTTA
36381 TCATTTCTTA
1 TCATTTCTTA
36391 T
1 T
36392 TTCATTAGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
8 2 0.08
9 12 0.46
10 12 0.46
ACGTcount: A:0.13, C:0.21, G:0.00, T:0.67
Consensus pattern (10 bp):
TCATTTCTTA
Found at i:40577 original size:4 final size:4
Alignment explanation
Indices: 40570--40608 Score: 69
Period size: 4 Copynumber: 9.5 Consensus size: 4
40560 GATGTCAATT
40570 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AATAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA-AG AA
40609 TTGCATGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 30 0.88
5 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:44177 original size:91 final size:91
Alignment explanation
Indices: 44022--44388 Score: 653
Period size: 91 Copynumber: 4.0 Consensus size: 91
44012 CTACAATACG
44022 TCACAAAAGACATCCATAATATTTGACGATTTTTAGAAGATATCGAGATTACATAATATCTTTAA
1 TCACAAAAGACATCCATAATATTTGACGATTTTTAGAAGATATCGAGATTACATAATATCTTTAA
*
44087 AATGATATGATTTAAATATAATCTTA
66 AATGATATGATTCAAATATAATCTTA
* * *
44113 TCACAAAAGACATCCATAATATTTGACGATTTTTAGAATATATCGAGATTATATTATATCTTTAA
1 TCACAAAAGACATCCATAATATTTGACGATTTTTAGAAGATATCGAGATTACATAATATCTTTAA
44178 AATGATATGATTCAAATATAATCTTA
66 AATGATATGATTCAAATATAATCTTA
* * *
44204 TCACAAAAGACATCCATAATATTTGATGATTTTTAGAAGATATCGAGATTACATTATATTTTTAA
1 TCACAAAAGACATCCATAATATTTGACGATTTTTAGAAGATATCGAGATTACATAATATCTTTAA
44269 AATGATATGATTCAAATATAATCTTA
66 AATGATATGATTCAAATATAATCTTA
*
44295 TCACAAAAGACATCCATAATATTTGACGATTTTTAAAAGATATCGAGATTACATAATATCTTTAA
1 TCACAAAAGACATCCATAATATTTGACGATTTTTAGAAGATATCGAGATTACATAATATCTTTAA
*
44360 AATGATATGATTCGAATATAATCTTA
66 AATGATATGATTCAAATATAATCTTA
44386 TCA
1 TCA
44389 TTTTACGAGC
Statistics
Matches: 263, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 263 1.00
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (91 bp):
TCACAAAAGACATCCATAATATTTGACGATTTTTAGAAGATATCGAGATTACATAATATCTTTAA
AATGATATGATTCAAATATAATCTTA
Found at i:48598 original size:21 final size:20
Alignment explanation
Indices: 48574--48613 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
48564 CAATAAAAAA
*
48574 ATAAATAATATATATATATTC
1 ATAAATAAAATA-ATATATTC
48595 ATAAATAAAATAATATATT
1 ATAAATAAAATAATATATT
48614 ATGCTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAATAAAATAATATATTC
Found at i:48627 original size:18 final size:20
Alignment explanation
Indices: 48606--48649 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
48596 TAAATAAAAT
48606 AATATATTAT-GCT-ATTTA
1 AATATATTATGGCTAATTTA
*
48624 AATATA-TATGGTTAATTTA
1 AATATATTATGGCTAATTTA
48643 AATATAT
1 AATATAT
48650 CTATACATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 3 0.14
18 8 0.36
19 11 0.50
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (20 bp):
AATATATTATGGCTAATTTA
Found at i:48763 original size:2 final size:2
Alignment explanation
Indices: 48758--48802 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
48748 AAGTAAAAAC
48758 AT AT AT AT AT AT AT AT 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
48800 AT A
1 AT A
48803 CACACATTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:63084 original size:10 final size:10
Alignment explanation
Indices: 63071--63123 Score: 56
Period size: 11 Copynumber: 5.3 Consensus size: 10
63061 AGTGAAAATG
63071 AAAAATG-AA
1 AAAAATGAAA
*
63080 AAAAATAAAA
1 AAAAATGAAA
*
63090 AAATAATAAAA
1 AAA-AATGAAA
63101 AAAAATG-AA
1 AAAAATGAAA
63110 AAAAATGGAAA
1 AAAAAT-GAAA
63121 AAA
1 AAA
63124 GGAAGGGTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
9 14 0.37
10 9 0.24
11 15 0.39
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:63085 original size:9 final size:10
Alignment explanation
Indices: 63071--63123 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
63061 AGTGAAAATG
63071 AAAAAT-GAA
1 AAAAATAGAA
*
63080 AAAAATAAAA
1 AAAAATAGAA
*
63090 AAATAATAAAA
1 AAA-AATAGAA
63101 AAAAAT-GAA
1 AAAAATAGAA
*
63110 AAAAATGGAA
1 AAAAATAGAA
63120 AAAA
1 AAAA
63124 GGAAGGGTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
9 14 0.36
10 15 0.38
11 10 0.26
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (10 bp):
AAAAATAGAA
Found at i:64312 original size:110 final size:110
Alignment explanation
Indices: 64123--64508 Score: 596
Period size: 111 Copynumber: 3.5 Consensus size: 110
64113 CCAACGATAA
* * *
64123 TTGAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGTTGAAGATTG
1 TTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTG
*
64188 TTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
66 TTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
*
64233 TTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGTTGAAGATTG
1 TTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTG
64298 TTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTG
66 TTCGAGTCTCATACTCTCTGAAG-AAATAGGGAGCAGACACGATTG
* * * *
64344 TTGAAGATTGTTCGAGTCTCATTCTCTCTGAAGAAAATAGGGAGCATG-CACGATTATTGAAGAT
1 TTGAAAATTGTTCGAGTCTTATACTCTCTGAAG-AAATAGGGAGCA-GACACGATTGTTGAAGAT
* * *
64408 TGTTCGAGTCTCATACTCTCTGGAGAAATAGGGAGCAGGCACGATTA
64 TGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* * *
64455 TCGAGAATCGTTCGAGTCTTATACTCTCTGAA-AAATAGGGAGCAGACACGATTG
1 TTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
64509 ACGAAGATAT
Statistics
Matches: 254, Mismatches: 18, Indels: 9
0.90 0.06 0.03
Matches are distributed among these distances:
108 1 0.00
109 19 0.07
110 85 0.33
111 98 0.39
112 50 0.20
113 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (110 bp):
TTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTG
TTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
Found at i:64351 original size:56 final size:55
Alignment explanation
Indices: 64123--64546 Score: 592
Period size: 55 Copynumber: 7.7 Consensus size: 55
64113 CCAACGATAA
* *
64123 TTGAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
64178 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* *
64233 TTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
*
64288 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAG-AAATAGGGAGCAGACACGATTG
* * *
64344 TTGAAGATTGTTCGAGTCTCATTCTCTCTGAAGAAAATAGGGAGCATG-CACGATTA
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAG-AAATAGGGAGCA-GACACGATTG
* * * *
64400 TTGAAGATTGTTCGAGTCTCATACTCTCTGGAGAAATAGGGAGCAGGCACGATTA
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* *
64455 TCG-AGAATCGTTCGAGTCTTATACTCTCTGAA-AAATAGGGAGCAGACACGATTG
1 TTGAAG-ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
** * *
64509 ACGAAGATAT-TT-GAGT-TT-TACTCCCTGAAGCAATAGGG
1 TTGAAGAT-TGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
64547 GGTAAAACCA
Statistics
Matches: 341, Mismatches: 21, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
51 10 0.03
52 9 0.03
53 4 0.01
54 29 0.09
55 184 0.54
56 104 0.30
57 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (55 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
Found at i:70782 original size:26 final size:26
Alignment explanation
Indices: 70732--70782 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
70722 CACTTTAAGA
* *
70732 TAAAAATTATATACATATTTTATAAC
1 TAAAAATTACATACATATTTCATAAC
70758 TAAAAATTACATAC-TATATTCATAA
1 TAAAAATTACATACATAT-TTCATAA
70783 TAATATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (26 bp):
TAAAAATTACATACATATTTCATAAC
Found at i:73093 original size:54 final size:53
Alignment explanation
Indices: 73031--73696 Score: 1018
Period size: 54 Copynumber: 12.5 Consensus size: 53
73021 CTGCTCCCTA
*
73031 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTATGGG-CTCGCTCTCTCT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC-CGCTCTCT-T
* * *
73085 TTTCTTCAGGGAGTAGAACTCGAACAATCATCTTCCTACGGGTCTGCTCTCTC
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
* * * * * *
73138 TTCCTTCAAGGAGTAGAACTTGAACAATCATCTTCCTACGGGTCCGCTGTCTC
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
73191 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
* *
73244 TTTCTTCAGGGAGTAAGAACTCAAACAATAATCTTCCTATGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
* *
73298 TTTCTTCAGGGAGTAAGAACTTGAACAATAATCTTCCTACGGGTCCGCTCTCTA
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
*
73352 TTTATTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
* *
73405 TTTCTTCAGGGAGTAATAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTA
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
* *
73459 TTTCTTCATGGATTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
73512 TTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
1 TTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
* * *
73566 TTTCTTCAGGGAGTAGAACTCGATCAATAATCTTCCTACGGGTCCAC-C-CTA
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
* *
73617 TTTATTCAGGGAATAGAACTCGAACAATAATCTTCCTACGGGTCCGC-C-CTAT
1 TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCT-T
73669 TTTCTTCAGGGAGTAGAACTCGAACAAT
1 TTTCTTCAGGGAGTAGAACTCGAACAAT
73697 CTTCTGTTGC
Statistics
Matches: 564, Mismatches: 43, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
51 48 0.09
52 27 0.05
53 239 0.42
54 249 0.44
55 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (53 bp):
TTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTT
Found at i:73145 original size:107 final size:107
Alignment explanation
Indices: 73023--73696 Score: 1031
Period size: 107 Copynumber: 6.3 Consensus size: 107
73013 AATCGTGTCT
* *
73023 GCTCCCTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTATGGG-CTCGCTCTCTCTTT
1 GCTCTCTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC-CGCTCTCT-TTT
* *
73087 TCTTCAGGGAGT-AGAACTCGAACAATCATCTTCCTACGGGTCT
64 TCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCC
* * * * * * *
73130 GCTCTCTCTTCCTTCAAGGAGTAGAACTTGAACAATCATCTTCCTACGGGTCCGCTGTCTCTTTC
1 GCTCTCTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTC
73195 TTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCC
66 TTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCC
* * *
73236 GCTCTCTTTTTCTTCAGGGAGTAAGAACTCAAACAATAATCTTCCTATGGGTCCGCTCTCTTTTT
1 GCTCTCTATTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTT
*
73301 CTTCAGGGAGTAAGAACTTGAACAATAATCTTCCTACGGGTCC
65 CTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCC
*
73344 GCTCTCTATTTATTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTC
1 GCTCTCTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTC
*
73409 TTCAGGGAGTAATAACTCGAACAATAATCTTCCTACGGGTCC
66 TTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCC
* *
73451 GCTCTCTATTTCTTCATGGATTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTC
1 GCTCTCTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTC
73516 TTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCC
66 TTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCC
* * * * *
73558 GCTCTCTTTTTCTTCAGGGAGTAGAACTCGATCAATAATCTTCCTACGGGTCCAC-C-CTATTTA
1 GCTCTCTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTC
*
73621 TTCAGGGAAT-AGAACTCGAACAATAATCTTCCTACGGGTCC
66 TTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCC
73662 GC-C-CTATTTTCTTCAGGGAGTAGAACTCGAACAAT
1 GCTCTCTA-TTTCTTCAGGGAGTAGAACTCGAACAAT
73697 CTTCTGTTGC
Statistics
Matches: 522, Mismatches: 41, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
102 2 0.00
103 28 0.05
104 33 0.06
105 14 0.03
106 63 0.12
107 331 0.63
108 51 0.10
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (107 bp):
GCTCTCTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTC
TTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCC
Found at i:75051 original size:11 final size:11
Alignment explanation
Indices: 75035--75061 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
75025 ATTTTATTTG
75035 TTTTTGTTTTA
1 TTTTTGTTTTA
75046 TTTTTGTTTTA
1 TTTTTGTTTTA
75057 TTTTT
1 TTTTT
75062 TTCATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (11 bp):
TTTTTGTTTTA
Found at i:75069 original size:8 final size:8
Alignment explanation
Indices: 75058--75142 Score: 100
Period size: 8 Copynumber: 10.1 Consensus size: 8
75048 TTTGTTTTAT
75058 TTTTTTCA
1 TTTTTTCA
75066 TTTTTTTCA
1 -TTTTTTCA
75075 TTTTTTTCA
1 -TTTTTTCA
75084 TTTTTTCA
1 TTTTTTCA
*
75092 TTTTTTTTA
1 -TTTTTTCA
*
75101 TTTTTTTA
1 TTTTTTCA
75109 TTTTTTCA
1 TTTTTTCA
75117 -TTTTTCA
1 TTTTTTCA
75124 TTTTTTTTCA
1 --TTTTTTCA
75134 TTTTTTCA
1 TTTTTTCA
75142 T
1 T
75143 CTTCAAGCAA
Statistics
Matches: 70, Mismatches: 2, Indels: 9
0.86 0.02 0.11
Matches are distributed among these distances:
7 7 0.10
8 32 0.46
9 24 0.34
10 7 0.10
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCA
Found at i:75070 original size:9 final size:9
Alignment explanation
Indices: 75052--75139 Score: 116
Period size: 9 Copynumber: 10.3 Consensus size: 9
75042 TTTATTTTTG
75052 TTTT-ATTT
1 TTTTCATTT
75060 TTTTCATTT
1 TTTTCATTT
75069 TTTTCATTT
1 TTTTCATTT
75078 TTTTCA-TT
1 TTTTCATTT
75086 TTTTCATTT
1 TTTTCATTT
*
75095 TTTTTATTT
1 TTTTCATTT
75104 TTTT-A-TT
1 TTTTCATTT
75111 TTTTCA--T
1 TTTTCATTT
75118 TTTTCATTTT
1 TTTTCA-TTT
75128 TTTTCATTT
1 TTTTCATTT
75137 TTT
1 TTT
75140 CATCTTCAAG
Statistics
Matches: 73, Mismatches: 1, Indels: 11
0.86 0.01 0.13
Matches are distributed among these distances:
7 13 0.18
8 14 0.19
9 39 0.53
10 7 0.10
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTCATTT
Found at i:75072 original size:17 final size:17
Alignment explanation
Indices: 75052--75139 Score: 117
Period size: 17 Copynumber: 5.2 Consensus size: 17
75042 TTTATTTTTG
75052 TTTTATTTTTTTCATTT
1 TTTTATTTTTTTCATTT
75069 TTTTCATTTTTTTCATTT
1 TTTT-ATTTTTTTCATTT
* *
75087 TTTCATTTTTTTTATTT
1 TTTTATTTTTTTCATTT
75104 TTTTA-TTTTTTCA-TT
1 TTTTATTTTTTTCATTT
*
75119 TTTCATTTTTTTTCATTT
1 TTTTA-TTTTTTTCATTT
75137 TTT
1 TTT
75140 CATCTTCAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
15 6 0.10
16 7 0.11
17 28 0.45
18 21 0.34
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTATTTTTTTCATTT
Found at i:75140 original size:25 final size:25
Alignment explanation
Indices: 75041--75142 Score: 111
Period size: 25 Copynumber: 4.0 Consensus size: 25
75031 TTTGTTTTTG
*
75041 TTTTATT-TTTGTTTTATTTTTTTCAT
1 TTTTATTATTT-TTTCA-TTTTTTCAT
75067 TTTT-TTCATTTTTTTCATTTTTTCAT
1 TTTTATT-A-TTTTTTCATTTTTTCAT
* *
75093 TTTTTTTATTTTTTTATTTTTTCAT
1 TTTTATTATTTTTTCATTTTTTCAT
75118 TTTTCATT-TTTTTTCATTTTTTCAT
1 TTTT-ATTATTTTTTCATTTTTTCAT
75143 CTTCAAGCAA
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
25 38 0.57
26 20 0.30
27 6 0.09
28 3 0.04
ACGTcount: A:0.12, C:0.08, G:0.01, T:0.79
Consensus pattern (25 bp):
TTTTATTATTTTTTCATTTTTTCAT
Found at i:79841 original size:26 final size:26
Alignment explanation
Indices: 79791--79841 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
79781 CACTTTAATA
* *
79791 TAAAAATTATATACATATTTTATAAC
1 TAAAAATTACATACATATTTCATAAC
79817 TAAAAATTACATAC-TATATTCATAA
1 TAAAAATTACATACATAT-TTCATAA
79842 TAATATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (26 bp):
TAAAAATTACATACATATTTCATAAC
Found at i:81766 original size:2 final size:2
Alignment explanation
Indices: 81759--81800 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
81749 AATTGTTTGC
81759 AT AT AT AT AT AT AT AT 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
81801 TAATACCTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82774 original size:21 final size:21
Alignment explanation
Indices: 82748--82788 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
82738 TATGTGTTAG
82748 GTATCTAAATTATTT-ATTTTA
1 GTATCTAAATT-TTTAATTTTA
82769 GTATCTAAATTTTTAATTTT
1 GTATCTAAATTTTTAATTTT
82789 TTTAAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
GTATCTAAATTTTTAATTTTA
Found at i:84124 original size:17 final size:19
Alignment explanation
Indices: 84093--84136 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
84083 CTTAAATTTA
84093 ATTT-TTTTATGATAAT-T
1 ATTTATTTTATGATAATGT
84110 ATTTATTTTAT-ATAATGT
1 ATTTATTTTATGATAATGT
84128 ATTTATTTT
1 ATTTATTTT
84137 GAAATTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATGATAATGT
Found at i:84749 original size:17 final size:17
Alignment explanation
Indices: 84727--84761 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
84717 TGTGATATTT
*
84727 GGGTTAGGTCAGGTTCG
1 GGGTTAGGCCAGGTTCG
84744 GGGTTAGGCCAGGTTCG
1 GGGTTAGGCCAGGTTCG
84761 G
1 G
84762 TTTAGGGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.14, G:0.49, T:0.26
Consensus pattern (17 bp):
GGGTTAGGCCAGGTTCG
Found at i:90932 original size:14 final size:14
Alignment explanation
Indices: 90910--90939 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
90900 TTTTTATTTA
90910 ATTAAGATATAATT
1 ATTAAGATATAATT
*
90924 ATTACGATATAATT
1 ATTAAGATATAATT
90938 AT
1 AT
90940 CGTTAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (14 bp):
ATTAAGATATAATT
Found at i:91279 original size:19 final size:20
Alignment explanation
Indices: 91233--91283 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
91223 TATTATTAAC
*
91233 TTAAT-TTAAAA-ATATTTT
1 TTAATGTTAAAATATATATT
*
91251 TTAATTTTAAAATATATATT
1 TTAATGTTAAAATATATATT
91271 TT-ATGTTAAAATA
1 TTAATGTTAAAATA
91284 CTTTGAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 5 0.17
19 16 0.55
20 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TTAATGTTAAAATATATATT
Found at i:91781 original size:29 final size:29
Alignment explanation
Indices: 91749--91804 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
91739 GTAACATTCT
* *
91749 ATAGTCGAAGGACCATTT-TGTAACTTTTG
1 ATAGTCAAAGAACCATTTATGT-ACTTTTG
91778 ATAGTCAAAGAACCATTTATGTACTTT
1 ATAGTCAAAGAACCATTTATGTACTTT
91805 ACCCTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (29 bp):
ATAGTCAAAGAACCATTTATGTACTTTTG
Found at i:91884 original size:31 final size:30
Alignment explanation
Indices: 91832--91935 Score: 104
Period size: 31 Copynumber: 3.3 Consensus size: 30
91822 GTAAATTAAG
*
91832 ATAAAATATATACTTTAAAAAGTTAAAACAATA
1 ATAAAATATATA-TTTTAAAAGTTAAAA-AA-A
*
91865 ATAAAATATAT-TTTTAAAAGTATAGATAAAA
1 ATAAAATATATATTTTAAAAGT-TA-AAAAAA
*
91896 ATAAAATATATATTTTTAAA-TTAAAATTAAA
1 ATAAAATATATATTTTAAAAGTTAAAA--AAA
91927 ATAAAATAT
1 ATAAAATAT
91936 TTTTAAATTA
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
29 2 0.03
30 2 0.03
31 34 0.55
32 11 0.18
33 13 0.21
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.36
Consensus pattern (30 bp):
ATAAAATATATATTTTAAAAGTTAAAAAAA
Found at i:91951 original size:26 final size:27
Alignment explanation
Indices: 91891--91968 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
91881 AAAGTATAGA
* *
91891 TAAAAATAAAAT-ATATATTTTTAAAT
1 TAAAATTAAAATAAAATATTTTTAAAT
91917 TAAAATTAAAATAAAATATTTTTAAAT
1 TAAAATTAAAATAAAATATTTTTAAAT
* * *
91944 T-AATTTAATAATAAAACATATTTAA
1 TAAAATTAA-AATAAAATATTTTTAA
91969 TAAGTTAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
26 17 0.38
27 28 0.62
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
TAAAATTAAAATAAAATATTTTTAAAT
Found at i:92066 original size:2 final size:2
Alignment explanation
Indices: 92061--92088 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
92051 TTTATTAATG
92061 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
92089 GATTTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:92101 original size:68 final size:68
Alignment explanation
Indices: 92001--92128 Score: 231
Period size: 68 Copynumber: 1.9 Consensus size: 68
91991 CTTAAAGCTA
*
92001 ATATATATATATATATTATAGATTTAAGTTAAGTATTTATTCACTATTT-TTTTATTAATGTATA
1 ATATATATATATATATTATAGATTTAAATTAAGTATTTATTCACTATTTCTTTTATTAATGTATA
92065 TAT
66 TAT
92068 ATATATATATATATATATATAGATTTAAATTAAGTATTTATTCACTATTTCTTTTATTAAT
1 ATATATATATATATAT-TATAGATTTAAATTAAGTATTTATTCACTATTTCTTTTATTAAT
92129 ATACGGTAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
67 16 0.28
68 32 0.55
69 10 0.17
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (68 bp):
ATATATATATATATATTATAGATTTAAATTAAGTATTTATTCACTATTTCTTTTATTAATGTATA
TAT
Found at i:92142 original size:68 final size:68
Alignment explanation
Indices: 92000--92142 Score: 209
Period size: 68 Copynumber: 2.1 Consensus size: 68
91990 TCTTAAAGCT
*
92000 AATATATATATATATATTATAGATTTAAGTTAAGTATTTATTCACTATTTTTTTATTAATGTATA
1 AATATATATATATATATTATAGATTTAAATTAAGTATTTATTCACTATTTTTTTATTAA-GTATA
*
92065 TATA
65 GATA
*
92069 TATATATATATATATA-TATAGATTTAAATTAAGTATTTATTCACTATTTCTTTTATTAA-TATA
1 AATATATATATATATATTATAGATTTAAATTAAGTATTTATTCACTATTT-TTTTATTAAGTATA
*
92132 CGGTA
65 -GATA
92137 AATATA
1 AATATA
92143 ATGTAATATC
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
67 4 0.06
68 39 0.58
69 24 0.36
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (68 bp):
AATATATATATATATATTATAGATTTAAATTAAGTATTTATTCACTATTTTTTTATTAAGTATAG
ATA
Found at i:95825 original size:19 final size:19
Alignment explanation
Indices: 95766--95848 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 19
95756 CAACGGCCGA
**
95766 GTCAAAGTTAATGGGTCGG
1 GTCAAAGTTAACAGGTCGG
* * *
95785 GTCAAAGTCAACATGTTGG
1 GTCAAAGTTAACAGGTCGG
*
95804 GTCAAAGTTAACAGGTCAG
1 GTCAAAGTTAACAGGTCGG
* *
95823 GTC-ATGTTAACTCGGTTCGG
1 GTCAAAGTTAAC-AGG-TCGG
95843 GTCAAA
1 GTCAAA
95849 TAGATATGGT
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
18 7 0.15
19 34 0.71
20 6 0.12
21 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (19 bp):
GTCAAAGTTAACAGGTCGG
Found at i:100187 original size:19 final size:19
Alignment explanation
Indices: 100147--100187 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
100137 TTTGGTTAAA
* *
100147 GTCAAAGTCAATGGGTCGG
1 GTCAAAGTCAATGAGTCAG
100166 GTCAAAGTCAATGAGTCAG
1 GTCAAAGTCAATGAGTCAG
100185 GTC
1 GTC
100188 GTGTTAACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.32, T:0.22
Consensus pattern (19 bp):
GTCAAAGTCAATGAGTCAG
Found at i:102929 original size:18 final size:18
Alignment explanation
Indices: 102885--102930 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
102875 GTATTCTATT
102885 TAAAATTAAA-TAATTGA
1 TAAAATTAAATTAATTGA
* *
102902 TATAATTAAATTACTTGA
1 TAAAATTAAATTAATTGA
*
102920 TAAAAATAAAT
1 TAAAATTAAAT
102931 GTTAAAGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (18 bp):
TAAAATTAAATTAATTGA
Found at i:107987 original size:4 final size:4
Alignment explanation
Indices: 107980--108012 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
107970 TATATATATA
107980 TATT TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT T
108013 GATCATATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:113361 original size:37 final size:38
Alignment explanation
Indices: 113307--113380 Score: 105
Period size: 37 Copynumber: 1.9 Consensus size: 38
113297 TTATCGTGAT
* *
113307 GATAAGAAAACGGAATCA-AACTGAATCATCACTCACA
1 GATAAGAAAAAGCAATCACAACTGAATCATCACTCACA
*
113344 GATAAGAAAAAGCAATCACTCACTGAATCATCACTCA
1 GATAAGAAAAAGCAATCAC-AACTGAATCATCACTCA
113381 AAAAGAACAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 16 0.50
39 16 0.50
ACGTcount: A:0.47, C:0.23, G:0.12, T:0.18
Consensus pattern (38 bp):
GATAAGAAAAAGCAATCACAACTGAATCATCACTCACA
Found at i:114570 original size:18 final size:17
Alignment explanation
Indices: 114539--114577 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
114529 TTTGTTTTAT
*
114539 TTTTTATTTTTTATGTA
1 TTTTTATTTCTTATGTA
*
114556 TTTTTATTTACTTATTTA
1 TTTTTATTT-CTTATGTA
114574 TTTT
1 TTTT
114578 GTTCTGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTTTATTTCTTATGTA
Done.