Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009461.1 Hibiscus syriacus cultivar Beakdansim tig00113724_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: 2346588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 12
Found at i:1616424 original size:39 final size:40
Alignment explanation
Indices: 1616379--1616469 Score: 116
Period size: 39 Copynumber: 2.3 Consensus size: 40
1616369 TCAATCAGAA
*
1616379 CAAAAAGAAAAAAACAAAA-AAGAAAAG-AAGCA-AAAAAG
1 CAAAAAGAAAAAAACAAAAGAA-AAAAGAAAGAACAAAAAG
* *
1616417 CAAAAAAGAAGAAAACAAAAGAAAAAAGAAAGAACAAAAAT
1 C-AAAAAGAAAAAAACAAAAGAAAAAAGAAAGAACAAAAAG
1616458 CAAAAAGAAAAA
1 CAAAAAGAAAAA
1616470 GGGACAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
38 1 0.02
39 22 0.49
40 16 0.36
41 6 0.13
ACGTcount: A:0.79, C:0.08, G:0.12, T:0.01
Consensus pattern (40 bp):
CAAAAAGAAAAAAACAAAAGAAAAAAGAAAGAACAAAAAG
Found at i:1616425 original size:19 final size:20
Alignment explanation
Indices: 1616380--1616455 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
1616370 CAATCAGAAC
*
1616380 AAAAAGAAAAAAACAAAA-A
1 AAAAAGAAGAAAACAAAAGA
*
1616399 AGAAAAGAAG-CAA-AAAAGCA
1 A-AAAAGAAGAAAACAAAAG-A
1616419 AAAAAGAAGAAAACAAAAGA
1 AAAAAGAAGAAAACAAAAGA
*
1616439 AAAAAGAA-AGAACAAAA
1 AAAAAGAAGAAAACAAAA
1616456 ATCAAAAAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
18 4 0.08
19 19 0.40
20 20 0.42
21 5 0.10
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAAAGAAGAAAACAAAAGA
Found at i:1616437 original size:32 final size:31
Alignment explanation
Indices: 1616380--1616463 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 31
1616370 CAATCAGAAC
*
1616380 AAAAAGAAAAAAACAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAAACAAAAAACAAAAGAAGCA
* * *
1616411 AAAAAGCAAAAAAGAAGAAAACAAAAGAA-AA
1 AAAAAGAAAAAAACAA-AAAACAAAAGAAGCA
1616442 AAGAAAGAACAAAAATCAAAAA
1 AA-AAAGAA-AAAAA-CAAAAA
1616464 GAAAAAGGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
31 17 0.40
32 16 0.37
33 8 0.19
34 2 0.05
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.01
Consensus pattern (31 bp):
AAAAAGAAAAAAACAAAAAACAAAAGAAGCA
Found at i:1616468 original size:13 final size:13
Alignment explanation
Indices: 1616377--1616469 Score: 59
Period size: 13 Copynumber: 7.1 Consensus size: 13
1616367 ATTCAATCAG
1616377 AACAAAAAGAAAA
1 AACAAAAAGAAAA
* *
1616390 AA-ACAAA-AAAG
1 AACAAAAAGAAAA
*
1616401 AA-AAGAAGCAAAA
1 AACAAAAAG-AAAA
1616414 AAGCAAAAAAGAAGAA
1 AA-C-AAAAAGAA-AA
1616430 AAC-AAAAGAAAA
1 AACAAAAAGAAAA
* *
1616442 AAGAAAGAACAAAA
1 AACAAA-AAGAAAA
*
1616456 ATCAAAAAGAAAA
1 AACAAAAAGAAAA
1616469 A
1 A
1616470 GGGACAAAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 16
0.69 0.12 0.18
Matches are distributed among these distances:
11 8 0.13
12 8 0.13
13 23 0.38
14 10 0.16
15 3 0.05
16 9 0.15
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.01
Consensus pattern (13 bp):
AACAAAAAGAAAA
Found at i:1616469 original size:7 final size:7
Alignment explanation
Indices: 1616380--1616469 Score: 67
Period size: 7 Copynumber: 12.6 Consensus size: 7
1616370 CAATCAGAAC
1616380 AAAAAGAA
1 AAAAAG-A
*
1616388 AAAAACA
1 AAAAAGA
1616395 AAAAAGA
1 AAAAAGA
1616402 AAAGAAGCA
1 AAA-AAG-A
1616411 AAAAAGCA
1 AAAAAG-A
1616419 AAAAAGA
1 AAAAAGA
*
1616426 AGAAA-A
1 AAAAAGA
*
1616432 CAAAAGA
1 AAAAAGA
1616439 AAAAAGA
1 AAAAAGA
* *
1616446 AAGAA-C
1 AAAAAGA
**
1616452 AAAAATC
1 AAAAAGA
1616459 AAAAAGA
1 AAAAAGA
1616466 AAAA
1 AAAA
1616470 GGGACAAAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
6 8 0.12
7 36 0.54
8 19 0.28
9 4 0.06
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.01
Consensus pattern (7 bp):
AAAAAGA
Found at i:1617109 original size:22 final size:22
Alignment explanation
Indices: 1617077--1617153 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
1617067 GCTACCCCAT
*
1617077 CAAACCATTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
1617099 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
1617121 CAAACCTTTGAGCATCAAATGT
1 CAAACCTTTGAGCATCAAATGC
1617143 CAAACCTTTGA
1 CAAACCTTTGA
1617154 CCAAACATAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:1617373 original size:24 final size:24
Alignment explanation
Indices: 1617345--1617407 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
1617335 GGGACAATAT
1617345 TTTCAAAACTTTTAATTAAACATC
1 TTTCAAAACTTTTAATTAAACATC
* *
1617369 TTTCAAAACTCTTGATTAAACATC
1 TTTCAAAACTTTTAATTAAACATC
*
1617393 TTTCGAAACTCTTTA
1 TTTCAAAACT-TTTA
1617408 TTGATATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.37, C:0.19, G:0.03, T:0.41
Consensus pattern (24 bp):
TTTCAAAACTTTTAATTAAACATC
Found at i:1618137 original size:106 final size:106
Alignment explanation
Indices: 1617987--1619570 Score: 2237
Period size: 106 Copynumber: 15.0 Consensus size: 106
1617977 GCCACTCAAG
* * * * * *
1617987 ACAACACAAGTTCAACTTCACAACGAAGGGACCACTTGTTGTCAACAAACAACTTCTCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
1618052 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA
66 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA
*
1618093 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
* * *
1618158 GAGCCAATTTCAACTTCATAGCGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA
* * *
1618199 ACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTTTCAATAAACAACTTCTCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
*
1618264 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA
*
1618305 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
* *
1618370 GACCCAATTTCAACTTCACAGCGAAGGATATTGGACT-CAA
66 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA
* ** * *
1618410 GACAACGCAAGTTCAACTTCACTATTAAAGGGAGACCGCTGGTTGTCAACAAACAACTTCTCAAT
1 -ACAACGCAAGTTCAACTTCACGA-CGAA-GG-GACCGCTGGTTGTCAATAAACAACTTCCCAAT
*
1618475 TTCAGAGCCAATTTCAACTTTACAACGAAGGATATTGGACTCCAA
62 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA
* *
1618520 ACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAATTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
*
1618585 GAGCCAATTTCAACTTCACAGA-GTAGGATATTGGACT-CAA
66 GAGCCAATTTCAACTTCACA-ACGAAGGATATTGGACTCCAA
* * *
1618625 GACAATGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAATAACTTCCCAATTTC
1 -ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC
*
1618690 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
65 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA
*
1618732 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAAC-TCCTCAATTTC
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCC-CAATTTC
*
1618796 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG
65 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA
* * *
1618838 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTTTCAACAAACAATTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
* *
1618903 TAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT-CAA
66 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA
*
1618943 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTT
1 -ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC
* *
1619008 AGAGCCAATTTCAACTTCACAGA-AAAGGATATTGGACTCCAG
65 AGAGCCAATTTCAACTTCACA-ACGAAGGATATTGGACTCCAA
* * * * *
1619050 ACAATGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
* *
1619115 GAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA
* *
1619156 ACAACGCAAGTTCAACTTCACTACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
*
1619221 GAGCCAATTTCAACTTCACAACGTAA-GATATTAGACT-CAA
66 GAGCCAATTTCAACTTCACAACG-AAGGATATTGGACTCCAA
*
1619261 GACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAACTTCCCAATTTC
1 -ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC
* * * *
1619326 AAAGCCAATTTCAACTTCTCAGCGAAGGATCTTGGAC-CCAA
65 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA
* * * * * * * *
1619367 GACAACACAAGCTCAACTTCACAATGAAGGG-GCGACTGATTGTCAA-CAA-AA-TT-TC-A-TT
1 -ACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAACTTCCCAATTT
* * * *
1619425 CAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAG
64 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA
* * * * * * * *
1619468 ACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAGTTCCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
* * *
1619533 GAGCCAATTTTAACTTCACGACGGAGGATATTGGACTC
66 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1619571 AGAACAATGC
Statistics
Matches: 1332, Mismatches: 118, Indels: 56
0.88 0.08 0.04
Matches are distributed among these distances:
100 74 0.06
101 6 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 19 0.01
106 1113 0.84
107 14 0.01
108 4 0.00
109 89 0.07
110 3 0.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (106 bp):
ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA
Found at i:1620389 original size:37 final size:37
Alignment explanation
Indices: 1620299--1620404 Score: 140
Period size: 37 Copynumber: 2.9 Consensus size: 37
1620289 CATTTTCGTC
* *
1620299 CTACTAGGATTCAAACTCTTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
1620336 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
1620373 CTACTATGATTTAAACTCCTAAAGATAGGATA
1 CTACTAGGATTCAAACTCCTAAAAATAGGATA
1620405 CACAAGCACT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:1620947 original size:21 final size:22
Alignment explanation
Indices: 1620923--1620967 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1620913 TATTCATTGG
*
1620923 TTATTTTTTA-ATACTATA-TTT
1 TTATTTTATATATA-TATAGTTT
1620944 TTATTTTATATATATATAGTTT
1 TTATTTTATATATATATAGTTT
1620966 TT
1 TT
1620968 TTTAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTTTATATATATATAGTTT
Found at i:1620976 original size:20 final size:18
Alignment explanation
Indices: 1620926--1620976 Score: 50
Period size: 21 Copynumber: 2.7 Consensus size: 18
1620916 TCATTGGTTA
1620926 TTTTTT-AATACTATATTT
1 TTTTTTAAATA-TATATTT
*
1620944 TTATTTTATATATATATAGTT
1 TT-TTTTA-A-ATATATATTT
1620965 TTTTTTAAATAT
1 TTTTTTAAATAT
1620977 TTTACTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 6 0.21
19 5 0.18
20 5 0.18
21 9 0.32
22 3 0.11
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTTTAAATATATATTT
Found at i:1621004 original size:2 final size:2
Alignment explanation
Indices: 1620997--1621062 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
1620987 AGCGTATTAT
1620997 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1621038 TA TA TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1621063 GTAATTATCT
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 60 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1621215 original size:5 final size:5
Alignment explanation
Indices: 1621205--1621239 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
1621195 TTGGTTTTTT
*
1621205 TTATA TTATA TTATA TTATT TTCATA TTATA TTAT
1 TTATA TTATA TTATA TTATA TT-ATA TTATA TTAT
1621240 TATCGTATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:1621233 original size:16 final size:16
Alignment explanation
Indices: 1621212--1621259 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1621202 TTTTTATATT
1621212 ATATTATATTATTTTC
1 ATATTATATTATTTTC
*
1621228 ATATTATATTATTATC
1 ATATTATATTATTTTC
* *
1621244 GTATGATTATTATTTT
1 ATATTA-TATTATTTT
1621260 TTCTATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 19 0.70
17 8 0.30
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (16 bp):
ATATTATATTATTTTC
Found at i:1624496 original size:81 final size:81
Alignment explanation
Indices: 1624371--1624797 Score: 656
Period size: 81 Copynumber: 5.3 Consensus size: 81
1624361 TTCTTTAGTG
* * * * * * * *
1624371 TTTTACCCAAAGGCATTTAGCCTTTCATCTAACTTGCATGATTGACATCTTTCTGCCAAATGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCAC
* *
1624436 AGCTAGACCATTAATA
66 AGCTAGGCCATTAATC
* * * * *
1624452 TTTTACTCAATGGTATTCAACCATTCATCTAACTGGCATAATTGACATCTTTTTGCCAAATGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCAC
1624517 AGCTAGGCCATTAATC
66 AGCTAGGCCATTAATC
* *
1624533 TTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCAT
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCAC
1624598 AGCTAGGCCATTAATC
66 AGCTAGGCCATTAATC
*
1624614 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGACATAATTGACACCTTTCTGCCAAATGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCAC
* *
1624679 AACTAGGCTATTAATC
66 AGCTAGGCCATTAATC
*
1624695 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCATTCTGCCAAATGCAC
1 TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCAC
1624760 AGCTAGGCCATTAATC
66 AGCTAGGCCATTAATC
*
1624776 TTTTACTCAACAGTATTTAACC
1 TTTTACTCAACGGTATTTAACC
1624798 TATAACACCC
Statistics
Matches: 318, Mismatches: 28, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 318 1.00
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (81 bp):
TTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCAC
AGCTAGGCCATTAATC
Found at i:1625065 original size:21 final size:22
Alignment explanation
Indices: 1625039--1625083 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1625029 GAATGCAAAT
1625039 AGGGAATC-AGTACCCTGCTAC
1 AGGGAATCGAGTACCCTGCTAC
* *
1625060 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGAGTACCCTGCTAC
1625082 AG
1 AG
1625084 TATTTTCGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (22 bp):
AGGGAATCGAGTACCCTGCTAC
Found at i:1625701 original size:23 final size:23
Alignment explanation
Indices: 1625635--1625720 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
1625625 TCATATATAT
1625635 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
1625658 TTTGTC-CTGAAG-GACCGCGTAGAGA
1 -TTG-CACCGAAGTG-CCACGTAGA-A
1625683 -TGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
1625705 TTGTACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
1625721 TATAATATGT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
22 2 0.04
23 29 0.58
24 17 0.34
25 2 0.04
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:1627242 original size:81 final size:81
Alignment explanation
Indices: 1627137--1627473 Score: 516
Period size: 81 Copynumber: 4.2 Consensus size: 81
1627127 GGATGTTACA
* * *
1627137 TAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAACTAGACCATTAATAT
1 TAACCGTTCATCTAACTGGCATAATTGACACCTTTATGCCAAATGCACAACTAGGCCATTAATCT
*
1627202 TTTACTCAACAGTATT
66 TTTACTCAACGGTATT
* * * * *
1627218 TAACCGTTCTTCTAACTGGCATAA-TGACACCTTTCTACCGAATGCACAGCTAGGCCATTAATCT
1 TAACCGTTCATCTAACTGGCATAATTGACACCTTTATGCCAAATGCACAACTAGGCCATTAATCT
*
1627282 TTTACTCAACGATATT
66 TTTACTCAACGGTATT
* * *
1627298 TAACCATTCATCTAACTGGCATAATTGACACATTTATGCCAAATGCACATCTCA-GCCATTAATC
1 TAACCGTTCATCTAACTGGCATAATTGACACCTTTATGCCAAATGCACAACT-AGGCCATTAATC
1627362 TTTTACTCAACGGTATT
65 TTTTACTCAACGGTATT
*
1627379 TAACCGTTCATCTAACTGGCATAATTGACACATTTTATGCCAAATGCACAACTAGGCCATTAATC
1 TAACCGTTCATCTAACTGGCATAATTGACAC-CTTTATGCCAAATGCACAACTAGGCCATTAATC
1627444 TTTTACTCAACGGTATT
65 TTTTACTCAACGGTATT
1627461 TAACCGTTCATCT
1 TAACCGTTCATCT
1627474 TTATGCCAAA
Statistics
Matches: 233, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
80 71 0.30
81 102 0.44
82 60 0.26
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (81 bp):
TAACCGTTCATCTAACTGGCATAATTGACACCTTTATGCCAAATGCACAACTAGGCCATTAATCT
TTTACTCAACGGTATT
Found at i:1627508 original size:61 final size:61
Alignment explanation
Indices: 1627412--1627534 Score: 210
Period size: 61 Copynumber: 2.0 Consensus size: 61
1627402 ATTGACACAT
* *
1627412 TTTATGCCAAATGCACAACTAGGCCATTAATCTTTTACTCAACGGTATTTAACCGTTCATC
1 TTTATGCCAAATGCACAACTAGGCCATTAACCTTTTACTCAACGGTATTTAACCATTCATC
* *
1627473 TTTATGCCAAATGCATAGCTAGGCCATTAACCTTTTACTCAACGGTATTTAACCATTCATC
1 TTTATGCCAAATGCACAACTAGGCCATTAACCTTTTACTCAACGGTATTTAACCATTCATC
1627534 T
1 T
1627535 AACTGGCATA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (61 bp):
TTTATGCCAAATGCACAACTAGGCCATTAACCTTTTACTCAACGGTATTTAACCATTCATC
Found at i:1627614 original size:81 final size:81
Alignment explanation
Indices: 1627472--1627833 Score: 548
Period size: 81 Copynumber: 4.5 Consensus size: 81
1627462 AACCGTTCAT
* * *
1627472 CTTTATGCCAAATGCATAGCTAGGCCATTAACCTTTTACTCAACGGTATTTAACCATTCATCTAA
1 CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCATTCATCTAA
1627537 CTGGCATAATTGACAC
66 CTGGCATAATTGACAC
* * * **
1627553 CTTTCTTCCAAATACACAGCTAGGCCATTAATCTTTTACTCAATGGTATTTAACTGTTCATCTAA
1 CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCATTCATCTAA
*
1627618 TTGGCATAATTGACAC
66 CTGGCATAATTGACAC
* * *
1627634 CTTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACT--ACGGTATTTAATCGTTCATCTAA
1 CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCATTCATCTAA
* *
1627697 CTAGAATAATTGACAC
66 CTGGCATAATTGACAC
*
1627713 CTTTCTGCCAAATGCAGAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCATTCATCTAA
1 CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCATTCATCTAA
* *
1627778 CTGACATAAGTGACAC
66 CTGGCATAATTGACAC
*
1627794 CTTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACT
1 CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
1627834 TTAGAATTGT
Statistics
Matches: 251, Mismatches: 28, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
79 71 0.28
81 180 0.72
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (81 bp):
CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCATTCATCTAA
CTGGCATAATTGACAC
Found at i:1627743 original size:160 final size:161
Alignment explanation
Indices: 1627472--1627833 Score: 555
Period size: 160 Copynumber: 2.2 Consensus size: 161
1627462 AACCGTTCAT
* * * *
1627472 CTTTATGCCAAATGCATAGCTAGGCCATTAACCTTTTACTCAACGGTATTTAACCATTCATCTAA
1 CTTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACT-AACGGTATTTAACCATTCATCTAA
* * * *
1627537 CTGGCATAATTGACACCTTTCTTCCAAATACACAGCTAGGCCATTAATCTTTTACTCAATGGTAT
65 CTAGAATAATTGACACCTTTCTGCCAAATACACAGCTAGGCCATTAATCTTTTACTCAACGGTAT
** * * *
1627602 TTAACTGTTCATCTAATTGGCATAATTGACAC
130 TTAACCATTCATCTAACTGACATAAGTGACAC
* *
1627634 CTTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACT-ACGGTATTTAATCGTTCATCTAAC
1 CTTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACTAACGGTATTTAACCATTCATCTAAC
* *
1627698 TAGAATAATTGACACCTTTCTGCCAAATGCAGAGCTAGGCCATTAATCTTTTACTCAACGGTATT
66 TAGAATAATTGACACCTTTCTGCCAAATACACAGCTAGGCCATTAATCTTTTACTCAACGGTATT
1627763 TAACCATTCATCTAACTGACATAAGTGACAC
131 TAACCATTCATCTAACTGACATAAGTGACAC
1627794 CTTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACT
1 CTTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACT
1627834 TTAGAATTGT
Statistics
Matches: 183, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
160 147 0.80
162 36 0.20
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (161 bp):
CTTTCTGCCAAATGCACAACTAGGCCATTAATCTTTTACTAACGGTATTTAACCATTCATCTAAC
TAGAATAATTGACACCTTTCTGCCAAATACACAGCTAGGCCATTAATCTTTTACTCAACGGTATT
TAACCATTCATCTAACTGACATAAGTGACAC
Found at i:1628471 original size:19 final size:19
Alignment explanation
Indices: 1628447--1628494 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1628437 TATACTATAG
*
1628447 TACCGATACCCTATTACGA
1 TACCGATACCCTAGTACGA
* *
1628466 TACCGATACCTTAGTACGG
1 TACCGATACCCTAGTACGA
1628485 TACCGATACC
1 TACCGATACC
1628495 ATTTCTGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (19 bp):
TACCGATACCCTAGTACGA
Found at i:1632931 original size:31 final size:31
Alignment explanation
Indices: 1632893--1632956 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
1632883 TTGTACATGT
*
1632893 AAGTAATATTTGTAACGTTATTCAATAAATC
1 AAGTAATATTTGTAACGTTATTAAATAAATC
*
1632924 AAGTAATATTTGTAATGTTATTAAATAAATC
1 AAGTAATATTTGTAACGTTATTAAATAAATC
1632955 AA
1 AA
1632957 ATAACATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (31 bp):
AAGTAATATTTGTAACGTTATTAAATAAATC
Found at i:1640473 original size:19 final size:19
Alignment explanation
Indices: 1640434--1640474 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1640424 ATTTATATTT
** *
1640434 AAATAACACAAAATTTTTG
1 AAATAACACAAAAACTATG
1640453 AAATAACACAAAAACTATG
1 AAATAACACAAAAACTATG
1640472 AAA
1 AAA
1640475 ACCTTCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.61, C:0.12, G:0.05, T:0.22
Consensus pattern (19 bp):
AAATAACACAAAAACTATG
Found at i:1641367 original size:24 final size:24
Alignment explanation
Indices: 1641340--1641446 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
1641330 AAACGGAGAT
*
1641340 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
1641364 ATCAGATATCAGAACAGAATCCGG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
1641388 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
1641412 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
1641436 ATCAGAAATCA
1 ATCAGAAATCA
1641447 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1641446 original size:48 final size:48
Alignment explanation
Indices: 1641340--1641448 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
1641330 AAACGGAGAT
* * * **
1641340 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCGG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
1641388 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1641436 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1641449 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1642610 original size:18 final size:18
Alignment explanation
Indices: 1642583--1642618 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1642573 CGATCTTATT
1642583 ATTTAATTCAGTCATTTC
1 ATTTAATTCAGTCATTTC
* *
1642601 ATTTACTTCAGTCCTTTC
1 ATTTAATTCAGTCATTTC
1642619 GAACAATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTTAATTCAGTCATTTC
Found at i:1643967 original size:18 final size:18
Alignment explanation
Indices: 1643944--1644020 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
1643934 CAACGGTCAA
1643944 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1643962 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
*
1643975 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
1643993 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1644011 CGGGTCGGGT
1 CGGGTCGGGT
1644021 TGTGACCGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 12 0.23
18 40 0.77
ACGTcount: A:0.12, C:0.21, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1643976 original size:31 final size:31
Alignment explanation
Indices: 1643938--1644016 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
1643928 ACGGGTCAAC
1643938 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
*
1643969 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1644000 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
1644017 GGGTTGTGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.14, C:0.22, G:0.48, T:0.16
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:1643980 original size:8 final size:8
Alignment explanation
Indices: 1643923--1643962 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
1643913 GGTCAACTCC
1643923 GGTCAACG
1 GGTCAACG
1643931 GGTCAAC-
1 GGTCAACG
1643938 GGTCAACG
1 GGTCAACG
1643946 GGT---CG
1 GGTCAACG
1643951 GGTCAACG
1 GGTCAACG
1643959 GGTC
1 GGTC
1643963 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.20, C:0.25, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1644016 original size:13 final size:13
Alignment explanation
Indices: 1643923--1643998 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 13
1643913 GGTCAACTCC
*
1643923 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1643938 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1643951 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
1643969 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1643982 GGTAAACGGGTCG
1 GGTCAACGGGTCG
1643995 GGTC
1 GGTC
1643999 GGGTCAACGG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 28 0.53
15 12 0.23
18 13 0.25
ACGTcount: A:0.17, C:0.22, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1646175 original size:24 final size:24
Alignment explanation
Indices: 1646148--1646254 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
1646138 AAACGGAGAT
*
1646148 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
1646172 ATCAGATATCAGAACAGAATCCGG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
1646196 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
1646220 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
1646244 ATCAGAAATCA
1 ATCAGAAATCA
1646255 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1646254 original size:48 final size:48
Alignment explanation
Indices: 1646148--1646256 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
1646138 AAACGGAGAT
* * * **
1646148 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCGG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
1646196 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1646244 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1646257 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1647418 original size:18 final size:18
Alignment explanation
Indices: 1647391--1647426 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1647381 CGATCTTATT
1647391 ATTTAATTCAGTCATTTC
1 ATTTAATTCAGTCATTTC
* *
1647409 ATTTACTTCAGTCCTTTC
1 ATTTAATTCAGTCATTTC
1647427 GAACAATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTTAATTCAGTCATTTC
Found at i:1648773 original size:18 final size:18
Alignment explanation
Indices: 1648750--1648826 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
1648740 CAACGGTCAA
1648750 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1648768 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
*
1648781 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
1648799 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1648817 CGGGTCGGGT
1 CGGGTCGGGT
1648827 TGTGACCGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 12 0.23
18 40 0.77
ACGTcount: A:0.12, C:0.21, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1648782 original size:31 final size:31
Alignment explanation
Indices: 1648744--1648822 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
1648734 ACGGGTCAAC
1648744 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
*
1648775 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1648806 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
1648823 GGGTTGTGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.14, C:0.22, G:0.48, T:0.16
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:1648786 original size:8 final size:8
Alignment explanation
Indices: 1648729--1648768 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
1648719 GGTCAACTCC
1648729 GGTCAACG
1 GGTCAACG
1648737 GGTCAAC-
1 GGTCAACG
1648744 GGTCAACG
1 GGTCAACG
1648752 GGT---CG
1 GGTCAACG
1648757 GGTCAACG
1 GGTCAACG
1648765 GGTC
1 GGTC
1648769 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.20, C:0.25, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1648822 original size:13 final size:13
Alignment explanation
Indices: 1648729--1648804 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 13
1648719 GGTCAACTCC
*
1648729 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1648744 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1648757 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
1648775 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1648788 GGTAAACGGGTCG
1 GGTCAACGGGTCG
1648801 GGTC
1 GGTC
1648805 GGGTCAACGG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 28 0.53
15 12 0.23
18 13 0.25
ACGTcount: A:0.17, C:0.22, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1652869 original size:18 final size:18
Alignment explanation
Indices: 1652846--1652912 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 18
1652836 ATTTTGGTAC
1652846 CGATACTCAAGTGAGTAT
1 CGATACTCAAGTGAGTAT
*
1652864 CGATACCCAAGTGGGAGAGTAT
1 CGATACTCAAGT----GAGTAT
1652886 CGATACTCTAAG-GAGAATAT
1 CGATACTC-AAGTGAG--TAT
1652906 CGATACT
1 CGATACT
1652913 GAGATAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
18 14 0.35
20 10 0.25
22 13 0.32
23 3 0.08
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (18 bp):
CGATACTCAAGTGAGTAT
Found at i:1662906 original size:21 final size:21
Alignment explanation
Indices: 1662880--1662919 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1662870 GAGAAATTGT
1662880 TTTTAAAATAT-AAAAATGATG
1 TTTTAAAAT-TGAAAAATGATG
1662901 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
1662920 AAATAAGCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATG
Found at i:1671351 original size:25 final size:25
Alignment explanation
Indices: 1671323--1671380 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
1671313 TAAAATTATT
1671323 AAAACAACTTTTATGACTACGTTCC
1 AAAACAACTTTTATGACTACGTTCC
* *
1671348 AAAACAACTTTTATGTCTACGTTTC
1 AAAACAACTTTTATGACTACGTTCC
1671373 AAAACAAC
1 AAAACAAC
1671381 AAGTTCCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (25 bp):
AAAACAACTTTTATGACTACGTTCC
Found at i:1673847 original size:20 final size:19
Alignment explanation
Indices: 1673810--1673860 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1673800 CTCAAAATCA
*
1673810 TTTTTCAAAATCTCATTTTG
1 TTTTTCAAAA-CCCATTTTG
1673830 TTTTTCAAAACCCAATTTTG
1 TTTTTCAAAACCC-ATTTTG
*
1673850 -CTTTCAAAACC
1 TTTTTCAAAACC
1673861 AAATCATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (19 bp):
TTTTTCAAAACCCATTTTG
Found at i:1676622 original size:24 final size:23
Alignment explanation
Indices: 1676569--1676717 Score: 74
Period size: 23 Copynumber: 6.4 Consensus size: 23
1676559 GTCGAAACTT
*
1676569 CCACATAGAATTGCACCGAAGTA
1 CCACGTAGAATTGCACCGAAGTA
* * * *
1676592 CCGCGTAGAATATGCACTGAGGTG
1 CCACGTAGAAT-TGCACCGAAGTA
*
1676616 CCACGTAGAAATAT-C-CCGAAGGA
1 CCACGTAG-AAT-TGCACCGAAGTA
* ** *
1676639 CCACATAGAATTGTC-CTAAAGGA
1 CCACGTAGAATTG-CACCGAAGTA
* *
1676662 TCACGTAGAATTGTC-CCGAAGGA
1 CCACGTAGAATTG-CACCGAAGTA
* *
1676685 CCACATAGAATTGTC-CCGAAGGA
1 CCACGTAGAATTG-CACCGAAGTA
*
1676708 CCGCGTAGAA
1 CCACGTAGAA
1676718 CCCTCGACTC
Statistics
Matches: 101, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
21 1 0.01
22 3 0.03
23 75 0.74
24 17 0.17
25 5 0.05
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.18
Consensus pattern (23 bp):
CCACGTAGAATTGCACCGAAGTA
Found at i:1676707 original size:46 final size:46
Alignment explanation
Indices: 1676616--1676717 Score: 150
Period size: 46 Copynumber: 2.2 Consensus size: 46
1676606 CACTGAGGTG
*
1676616 CCACGTAGAAATATCCCGAAGGACCACATAGAATTGTCCTAAAGGA
1 CCACGTAGAAATATCCCGAAGGACCACATAGAATTGTCCCAAAGGA
* * * *
1676662 TCACGTAGAATTGTCCCGAAGGACCACATAGAATTGTCCCGAAGGA
1 CCACGTAGAAATATCCCGAAGGACCACATAGAATTGTCCCAAAGGA
*
1676708 CCGCGTAGAA
1 CCACGTAGAA
1676718 CCCTCGACTC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.18
Consensus pattern (46 bp):
CCACGTAGAAATATCCCGAAGGACCACATAGAATTGTCCCAAAGGA
Found at i:1676716 original size:23 final size:23
Alignment explanation
Indices: 1676616--1676717 Score: 132
Period size: 23 Copynumber: 4.4 Consensus size: 23
1676606 CACTGAGGTG
* *
1676616 CCACGTAGAAATATCCCGAAGGA
1 CCACGTAGAATTGTCCCGAAGGA
* **
1676639 CCACATAGAATTGTCCTAAAGGA
1 CCACGTAGAATTGTCCCGAAGGA
*
1676662 TCACGTAGAATTGTCCCGAAGGA
1 CCACGTAGAATTGTCCCGAAGGA
*
1676685 CCACATAGAATTGTCCCGAAGGA
1 CCACGTAGAATTGTCCCGAAGGA
*
1676708 CCGCGTAGAA
1 CCACGTAGAA
1676718 CCCTCGACTC
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.18
Consensus pattern (23 bp):
CCACGTAGAATTGTCCCGAAGGA
Found at i:1678254 original size:29 final size:29
Alignment explanation
Indices: 1678220--1678316 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 29
1678210 AAAAAAATTG
* * *
1678220 AATACTTTTGGTACTTATTTTGAAGAAAA
1 AATACTTTAGATACTTATTTTGAACAAAA
* *
1678249 AATACTTTAGATACATATTTTGACCAAAA
1 AATACTTTAGATACTTATTTTGAACAAAA
* *
1678278 AGATAACTTTAAATA-TTATTTTGATCAAAA
1 A-AT-ACTTTAGATACTTATTTTGAACAAAA
1678308 AATACTTTA
1 AATACTTTA
1678317 AATATTTAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 6 0.10
29 27 0.47
30 16 0.28
31 9 0.16
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.39
Consensus pattern (29 bp):
AATACTTTAGATACTTATTTTGAACAAAA
Found at i:1678300 original size:30 final size:28
Alignment explanation
Indices: 1678234--1678322 Score: 106
Period size: 30 Copynumber: 3.1 Consensus size: 28
1678224 CTTTTGGTAC
* *
1678234 TTATTTTGAAGAAAAAATACTTTAGATA
1 TTATTTTGAACAAAAAATACTTTAAATA
* *
1678262 CATATTTTGACCAAAAAGATAACTTTAAATA
1 -TTATTTTGAACAAAAA-AT-ACTTTAAATA
*
1678293 TTATTTTGATCAAAAAATACTTTAAATA
1 TTATTTTGAACAAAAAATACTTTAAATA
1678321 TT
1 TT
1678323 TAAATAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
28 12 0.23
29 15 0.29
30 16 0.31
31 9 0.17
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (28 bp):
TTATTTTGAACAAAAAATACTTTAAATA
Found at i:1678411 original size:2 final size:2
Alignment explanation
Indices: 1678406--1678431 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1678396 AAAAATGACT
1678406 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
1678432 ATTCCTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1680258 original size:9 final size:9
Alignment explanation
Indices: 1680237--1680305 Score: 51
Period size: 9 Copynumber: 8.1 Consensus size: 9
1680227 AAATAACAAT
1680237 TAAATAA-A
1 TAAATAATA
1680245 TAAATAATA
1 TAAATAATA
1680254 TAAAT-ATA
1 TAAATAATA
*
1680262 -ATAATATTA
1 TA-AATAATA
*
1680271 T-AAT-GTA
1 TAAATAATA
1680278 TATAATAA-A
1 TA-AATAATA
*
1680287 TATATAATA
1 TAAATAATA
1680296 TAAATAATA
1 TAAATAATA
1680305 T
1 T
1680306 TATATACTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
7 4 0.08
8 20 0.42
9 24 0.50
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (9 bp):
TAAATAATA
Found at i:1680280 original size:26 final size:27
Alignment explanation
Indices: 1680251--1680427 Score: 104
Period size: 26 Copynumber: 6.5 Consensus size: 27
1680241 TAAATAAATA
1680251 ATATAAATATAATAATATTATAATGTA-T
1 ATATAAATATAATAATATTATAA--TACT
* *
1680279 ATAATAAATAT-ATAATATAAATAATATT
1 AT-ATAAATATAATAATAT-TATAATACT
* *
1680307 ATAT-ACTATAAT-ATA-TATGATACT
1 ATATAAATATAATAATATTATAATACT
1680331 ATATAAA-ATAATATATATTAT-ATACT
1 ATATAAATATAATA-ATATTATAATACT
* *
1680357 ATATAAATATATGTAATACAATATACCATACT
1 ATATAAATATA-ATAAT--ATTATA--ATACT
* * *
1680389 ATAT-AATAT-ATTATA-TAAAATAAT
1 ATATAAATATAATAATATTATAATACT
1680413 ATATAACATATAATA
1 ATATAA-ATATAATA
1680428 TAAAATATAA
Statistics
Matches: 118, Mismatches: 13, Indels: 37
0.70 0.08 0.22
Matches are distributed among these distances:
24 23 0.19
25 2 0.02
26 29 0.25
27 17 0.14
28 14 0.12
29 19 0.16
31 5 0.04
32 9 0.08
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.40
Consensus pattern (27 bp):
ATATAAATATAATAATATTATAATACT
Found at i:1680282 original size:20 final size:18
Alignment explanation
Indices: 1680247--1680345 Score: 82
Period size: 17 Copynumber: 5.5 Consensus size: 18
1680237 TAAATAAATA
*
1680247 AATAATATAA-ATATAAT
1 AATATTATAATATATAAT
1680264 AATATTATAATGTATATAAT
1 AATATTATAA--TATATAAT
1680284 AA-ATATATAATATA-AAT
1 AATAT-TATAATATATAAT
1680301 AATATTAT-ATACTATAAT
1 AATATTATAATA-TATAAT
* *
1680319 ATATATGATACTATATAA-
1 A-ATATTATAATATATAAT
*
1680337 AATAATATA
1 AATATTATA
1680346 TATTATATAC
Statistics
Matches: 68, Mismatches: 5, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
16 3 0.04
17 25 0.37
18 11 0.16
19 13 0.19
20 16 0.24
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
AATATTATAATATATAAT
Found at i:1680298 original size:42 final size:43
Alignment explanation
Indices: 1680239--1680460 Score: 155
Period size: 43 Copynumber: 4.9 Consensus size: 43
1680229 ATAACAATTA
* * *
1680239 AATAAATAAATAATATAAATATAATA-ATATTATAATGTATAT
1 AATAAATATATAATATAAATATAATATATACTATAATATATAT
*
1680281 AATAAATATATAATATAAATAATATTATATACTATAATATATAT
1 AATAAATATATAATATAAAT-ATAATATATACTATAATATATAT
* * * * *
1680325 GAT-ACTATATAAAATAATATATATTATATACTATATAAATATATGT
1 AATAAATATATAATATAA-ATATAATATATAC--TAT-AATATATAT
* * **
1680371 AATACAATATACCATACTATATAATATATTATATAAAATAATATATA-
1 AATA-AATAT---ATAATATA-AATATAATATATACTATAATATATAT
* *
1680418 ACATATAATATAAAATATAAA-ATAACATATAACATATAATATA
1 A-ATA-AATATATAATATAAATATAATATAT-AC-TATAATATA
1680461 GTGTATATTA
Statistics
Matches: 143, Mismatches: 22, Indels: 27
0.74 0.11 0.14
Matches are distributed among these distances:
42 19 0.13
43 35 0.24
44 21 0.15
45 17 0.12
46 10 0.07
47 1 0.01
48 19 0.13
49 2 0.01
51 18 0.13
52 1 0.01
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (43 bp):
AATAAATATATAATATAAATATAATATATACTATAATATATAT
Found at i:1680309 original size:17 final size:17
Alignment explanation
Indices: 1680240--1680354 Score: 71
Period size: 18 Copynumber: 6.5 Consensus size: 17
1680230 TAACAATTAA
1680240 ATAA-ATAAATAATA-T
1 ATAATATAAATAATATT
1680255 A-AATAT-AATAATATT
1 ATAATATAAATAATATT
1680270 ATAATGTATATAATAA-ATAT
1 ATAA--TATA-AATAATAT-T
1680290 ATAATATAAATAATATT
1 ATAATATAAATAATATT
*
1680307 AT-ATACTATAATATATATG
1 ATAATA-TA-AATA-ATATT
1680326 ATACTATATAAAATAATATAT
1 ATA--ATAT-AAATAATAT-T
*
1680347 ATTATATA
1 ATAATATA
1680355 CTATATAAAT
Statistics
Matches: 80, Mismatches: 3, Indels: 31
0.70 0.03 0.27
Matches are distributed among these distances:
14 9 0.11
15 5 0.06
16 5 0.06
17 10 0.12
18 14 0.17
19 12 0.15
20 14 0.17
21 7 0.09
22 4 0.05
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
ATAATATAAATAATATT
Found at i:1680321 original size:12 final size:12
Alignment explanation
Indices: 1680239--1680460 Score: 123
Period size: 12 Copynumber: 19.1 Consensus size: 12
1680229 ATAACAATTA
*
1680239 AATAAATAA-AT
1 AATATATAATAT
1680250 AATATA-AATAT
1 AATATATAATAT
*
1680261 AATA-ATATTAT
1 AATATATAATAT
1680272 AATGTATATAATA-
1 AA--TATATAATAT
1680285 AATATATAATAT
1 AATATATAATAT
1680297 -A-A-ATAATAT
1 AATATATAATAT
*
1680306 --TATATACTAT
1 AATATATAATAT
1680316 AATATAT-ATGAT
1 AATATATAAT-AT
* *
1680328 ACTATATAAAAT
1 AATATATAATAT
1680340 AATATATATTATAT
1 AATATATA--ATAT
*
1680354 ACTATATAA-AT
1 AATATATAATAT
*
1680365 -ATATGTAATA-
1 AATATATAATAT
* **
1680375 CA-ATATACCAT
1 AATATATAATAT
*
1680386 ACTATATAATAT
1 AATATATAATAT
* *
1680398 ATTATATAAAAT
1 AATATATAATAT
1680410 AATATATAACATAT
1 AATATAT-A-ATAT
*
1680424 AATATAAAATAT
1 AATATATAATAT
*
1680436 AAAATA-ACATAT
1 AATATATA-ATAT
*
1680448 AACATATAATAT
1 AATATATAATAT
1680460 A
1 A
1680461 GTGTATATTA
Statistics
Matches: 163, Mismatches: 26, Indels: 43
0.70 0.11 0.19
Matches are distributed among these distances:
9 8 0.05
10 21 0.13
11 33 0.20
12 69 0.42
13 8 0.05
14 24 0.15
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (12 bp):
AATATATAATAT
Found at i:1680416 original size:19 final size:19
Alignment explanation
Indices: 1680401--1680437 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1680391 ATAATATATT
*
1680401 ATATAAAATAATATATAAC
1 ATATAAAATAAAATATAAC
*
1680420 ATATAATATAAAATATAA
1 ATATAAAATAAAATATAA
1680438 AATAACATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
ATATAAAATAAAATATAAC
Found at i:1680428 original size:31 final size:31
Alignment explanation
Indices: 1680389--1680460 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
1680379 ATACCATACT
** *
1680389 ATATAATATATTATATAAAATAATATATAAC
1 ATATAATATAAAATATAAAATAACATATAAC
1680420 ATATAATATAAAATATAAAATAACATATAAC
1 ATATAATATAAAATATAAAATAACATATAAC
1680451 ATATAATATA
1 ATATAATATA
1680461 GTGTATATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (31 bp):
ATATAATATAAAATATAAAATAACATATAAC
Found at i:1680990 original size:21 final size:22
Alignment explanation
Indices: 1680964--1681026 Score: 83
Period size: 23 Copynumber: 2.9 Consensus size: 22
1680954 AATATTTATC
1680964 CTTGTGACAC-ATTTTTCTGCT
1 CTTGTGACACGATTTTTCTGCT
*
1680985 CTTGTGACACGTTTTTTTCTGCT
1 CTTGTGACACG-ATTTTTCTGCT
* *
1681008 CTTGTGGCACGCTTTTTCT
1 CTTGTGACACGATTTTTCT
1681027 CTGCTTTTGG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.27
22 7 0.19
23 20 0.54
ACGTcount: A:0.10, C:0.24, G:0.17, T:0.49
Consensus pattern (22 bp):
CTTGTGACACGATTTTTCTGCT
Found at i:1681005 original size:23 final size:24
Alignment explanation
Indices: 1680975--1681031 Score: 89
Period size: 23 Copynumber: 2.4 Consensus size: 24
1680965 TTGTGACACA
1680975 TTTTTCTGCTCTTGTGACACG-TT
1 TTTTTCTGCTCTTGTGACACGCTT
*
1680998 TTTTTCTGCTCTTGTGGCACGCTT
1 TTTTTCTGCTCTTGTGACACGCTT
*
1681022 TTTCTCTGCT
1 TTTTTCTGCT
1681032 TTTGGGGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 20 0.65
24 11 0.35
ACGTcount: A:0.05, C:0.25, G:0.18, T:0.53
Consensus pattern (24 bp):
TTTTTCTGCTCTTGTGACACGCTT
Found at i:1681043 original size:24 final size:24
Alignment explanation
Indices: 1680975--1681044 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
1680965 TTGTGACACA
*
1680975 TTTT-TCTGCTCTT-GTGACACG-T
1 TTTTCTCTGCTCTTGGGGA-ACGCT
* * *
1680997 TTTTTTCTGCTCTTGTGGCACGCT
1 TTTTCTCTGCTCTTGGGGAACGCT
*
1681021 TTTTCTCTGCTTTTGGGGAACGCT
1 TTTTCTCTGCTCTTGGGGAACGCT
1681045 CCTTATGATT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 22 0.58
ACGTcount: A:0.07, C:0.23, G:0.21, T:0.49
Consensus pattern (24 bp):
TTTTCTCTGCTCTTGGGGAACGCT
Found at i:1685168 original size:21 final size:21
Alignment explanation
Indices: 1685139--1685185 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1685129 AATATGTAAA
*
1685139 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCAAAAT
*
1685160 TCGCGTTGCGATTTTCAAAAT
1 TCGCATTGCGATTTTCAAAAT
1685181 TCGCA
1 TCGCA
1685186 ACGCGAATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCAAAAT
Found at i:1685191 original size:21 final size:21
Alignment explanation
Indices: 1685146--1685191 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1685136 AAATCGCATT
* ***
1685146 GCGATTTTCCAAATTCGCGTT
1 GCGATTTTCAAAATTCGCAAC
1685167 GCGATTTTCAAAATTCGCAAC
1 GCGATTTTCAAAATTCGCAAC
1685188 GCGA
1 GCGA
1685192 ATCTGTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (21 bp):
GCGATTTTCAAAATTCGCAAC
Found at i:1685208 original size:20 final size:20
Alignment explanation
Indices: 1685183--1685227 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1685173 TTCAAAATTC
1685183 GCAACGCGAATCTGTAAATA
1 GCAACGCGAATCTGTAAATA
* *
1685203 GCAACGCGAATTTGTAAATC
1 GCAACGCGAATCTGTAAATA
1685223 GCAAC
1 GCAAC
1685228 ACATAAGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (20 bp):
GCAACGCGAATCTGTAAATA
Found at i:1685244 original size:20 final size:20
Alignment explanation
Indices: 1685221--1685267 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1685211 AATTTGTAAA
1685221 TCGCAACAC-ATAAGTCAAAT
1 TCGCAACACGAT-AGTCAAAT
**
1685241 TCGCAATGCGATAGTCAAAT
1 TCGCAACACGATAGTCAAAT
1685261 TCGCAAC
1 TCGCAAC
1685268 GCGGAATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (20 bp):
TCGCAACACGATAGTCAAAT
Found at i:1685281 original size:21 final size:20
Alignment explanation
Indices: 1685255--1685307 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
1685245 AATGCGATAG
1685255 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAAC-CGGAATT
* *
1685276 TCAAATTCACAA-CTGAATT
1 TCAAATTCGCAACCGGAATT
1685295 TCAAATTCGCAAC
1 TCAAATTCGCAAC
1685308 TAGATTTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.61
21 11 0.39
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.26
Consensus pattern (20 bp):
TCAAATTCGCAACCGGAATT
Found at i:1685527 original size:16 final size:16
Alignment explanation
Indices: 1685506--1685540 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1685496 CCATCTCTAA
*
1685506 TTTATTTTTACATAAT
1 TTTATTTCTACATAAT
*
1685522 TTTATTTCTATATAAT
1 TTTATTTCTACATAAT
1685538 TTT
1 TTT
1685541 TCAATGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATTTCTACATAAT
Found at i:1686295 original size:23 final size:24
Alignment explanation
Indices: 1686253--1686305 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
1686243 GTATTCAAAA
*
1686253 TTTGATCTTGGTCAAAACTCGGAC
1 TTTGATCTTGGTCAAAACTCAGAC
* *
1686277 TTTGATCTT-GTCAATACTCAGAT
1 TTTGATCTTGGTCAAAACTCAGAC
1686300 TTTGAT
1 TTTGAT
1686306 GATGTGATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (24 bp):
TTTGATCTTGGTCAAAACTCAGAC
Found at i:1688973 original size:20 final size:20
Alignment explanation
Indices: 1688950--1689043 Score: 67
Period size: 20 Copynumber: 5.0 Consensus size: 20
1688940 AATCGCAAAC
1688950 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
* **
1688970 CGAATTTGACTATCGC--AA
1 CGAATTTGACTTTCGCGTTG
*
1688988 CG--CTT-A-TTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
*
1689004 CAAATTT-ACCTTTCGCGTTG
1 CGAATTTGA-CTTTCGCGTTG
* *
1689024 CGAATTTGAATATCGCGTTG
1 CGAATTTGACTTTCGCGTTG
1689044 TACATTATTT
Statistics
Matches: 55, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
14 5 0.09
15 1 0.02
16 3 0.05
18 5 0.09
20 40 0.73
21 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
CGAATTTGACTTTCGCGTTG
Found at i:1689486 original size:18 final size:18
Alignment explanation
Indices: 1689465--1689500 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1689455 GTAATTGGAG
1689465 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1689483 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1689501 AATAAATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1689508 original size:24 final size:24
Alignment explanation
Indices: 1689457--1689509 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1689447 TTTCATAGGT
* * *
1689457 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
1689481 AATTTGAGTTTGAATTTCAAA-ATA
1 AATTTGAGTTTGAATTT-AAATATA
1689505 AATTT
1 AATTT
1689510 CAGCTCCACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1689859 original size:39 final size:39
Alignment explanation
Indices: 1689812--1689898 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
1689802 TCCGATGCTC
** *
1689812 ATCAAAATCCAAAGCTCGTATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCACATGGTGACAAGCAAAAGGAA
* *
1689851 ATCCAAATCCAAATCTCACATGGTGACAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCACATGGTGACAAGCAAAAGGAA
1689890 ATCAAAATC
1 ATCAAAATC
1689899 TACAACTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.46, C:0.22, G:0.16, T:0.16
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCACATGGTGACAAGCAAAAGGAA
Found at i:1690133 original size:20 final size:20
Alignment explanation
Indices: 1690110--1690168 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
1690100 AATAAGCGTT
*
1690110 GCGATAGCCAAATTCGCAAC
1 GCGAAAGCCAAATTCGCAAC
* *
1690130 GCGAAAGCCAAATGCACAAC
1 GCGAAAGCCAAATTCGCAAC
*
1690150 GCGAAAGTCAAATTCGCAA
1 GCGAAAGCCAAATTCGCAA
1690169 ACCGAAAATC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.41, C:0.27, G:0.20, T:0.12
Consensus pattern (20 bp):
GCGAAAGCCAAATTCGCAAC
Found at i:1690174 original size:20 final size:21
Alignment explanation
Indices: 1690110--1690175 Score: 77
Period size: 20 Copynumber: 3.3 Consensus size: 21
1690100 AATAAGCGTT
*
1690110 GCGATAGCCAAATTCGC-AAC
1 GCGAAAGCCAAATTCGCAAAC
1690130 GCGAAAGCCAAA-T-GCACAAC
1 GCGAAAGCCAAATTCGCA-AAC
*
1690150 GCGAAAGTCAAATTCGCAAAC
1 GCGAAAGCCAAATTCGCAAAC
1690171 -CGAAA
1 GCGAAA
1690176 ATCGCGTTGC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 2 0.05
19 1 0.03
20 30 0.75
21 4 0.10
22 3 0.08
ACGTcount: A:0.42, C:0.27, G:0.20, T:0.11
Consensus pattern (21 bp):
GCGAAAGCCAAATTCGCAAAC
Found at i:1690333 original size:28 final size:28
Alignment explanation
Indices: 1690301--1690354 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1690291 ATAATTCTTA
*
1690301 TTTACACATCAAATTAAACAAATCAACT
1 TTTACAAATCAAATTAAACAAATCAACT
* **
1690329 TTTACAAATCAACTTTTACAAATCAA
1 TTTACAAATCAAATTAAACAAATCAA
1690355 TTAATCAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (28 bp):
TTTACAAATCAAATTAAACAAATCAACT
Found at i:1690335 original size:14 final size:14
Alignment explanation
Indices: 1690318--1690354 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1690308 ATCAAATTAA
1690318 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1690332 ACAAATCAACTTTT
1 ACAAATCAACTTTT
1690346 ACAAATCAA
1 ACAAATCAA
1690355 TTAATCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1691826 original size:21 final size:21
Alignment explanation
Indices: 1691766--1691860 Score: 93
Period size: 21 Copynumber: 4.5 Consensus size: 21
1691756 TGAATCGGGA
* * * *
1691766 TCTTGAACGGTGGGTGGGACC
1 TCTTGAACGATGAGAGGGGCC
*
1691787 TCTTGAACGATGACAGGGGCC
1 TCTTGAACGATGAGAGGGGCC
* * *
1691808 TCTTGAACGGTGGGAGGGGCT
1 TCTTGAACGATGAGAGGGGCC
*
1691829 TCTTCG-ATGATGAGAGGGGCC
1 TCTT-GAACGATGAGAGGGGCC
1691850 TCTTGAACGAT
1 TCTTGAACGAT
1691861 AGGAGGCATC
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
20 1 0.02
21 56 0.97
22 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.24
Consensus pattern (21 bp):
TCTTGAACGATGAGAGGGGCC
Found at i:1691841 original size:42 final size:42
Alignment explanation
Indices: 1691766--1691883 Score: 130
Period size: 42 Copynumber: 2.8 Consensus size: 42
1691756 TGAATCGGGA
*
1691766 TCTTGAACGGTGGGTGGGACCTCTTGAACGATGACAGGGGCC
1 TCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGCC
* * * *
1691808 TCTTGAACGGTGGGAGGGGCTTCTTCG-ATGATGAGAGGGGCC
1 TCTTGAACGGTGGGAGGGACCTCTT-GAACGATGACAGGGGCC
* * * * *
1691850 TCTTGAACGATAGGAGGCATCTCTTGAATGATGA
1 TCTTGAACGGTGGGAGGGACCTCTTGAACGATGA
1691884 TAGGTGCATC
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.02
42 61 0.97
43 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.25
Consensus pattern (42 bp):
TCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGCC
Found at i:1694078 original size:19 final size:20
Alignment explanation
Indices: 1694018--1694070 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1694008 AAACTTAAAT
* *
1694018 TCGCAATGCAAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
1694038 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
1694058 TCGCAACGCGAAA
1 TCGCAACGCGAAA
1694071 CTAAAATCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:1694602 original size:20 final size:20
Alignment explanation
Indices: 1694577--1694745 Score: 202
Period size: 20 Copynumber: 8.5 Consensus size: 20
1694567 GCGTAAAAAC
*
1694577 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGTGTTGCGA
1694597 ATTTGACTATCGTGTTGCGA
1 ATTTGACTATCGTGTTGCGA
1694617 ATTTGACT-TCCGTGTTGCG-
1 ATTTGACTAT-CGTGTTGCGA
*
1694636 ATTT-ACAAATTCGTGTTGCGA
1 ATTTGAC-TA-TCGTGTTGCGA
* *
1694657 ATTTGACTTTTGTGTTGCGA
1 ATTTGACTATCGTGTTGCGA
**
1694677 ATTTGACTATCACGTTGCGA
1 ATTTGACTATCGTGTTGCGA
* *
1694697 ATTTGACT-TTGTGTTGCAA
1 ATTTGACTATCGTGTTGCGA
*
1694716 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGTGTTGCGA
1694736 ATTTGACTAT
1 ATTTGACTAT
1694746 ACGTTGCGAT
Statistics
Matches: 126, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
18 2 0.02
19 20 0.16
20 97 0.77
21 5 0.04
22 2 0.02
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTGACTATCGTGTTGCGA
Found at i:1694792 original size:59 final size:59
Alignment explanation
Indices: 1694590--1694799 Score: 209
Period size: 59 Copynumber: 3.5 Consensus size: 59
1694580 TGACTATCGC
* *
1694590 GTTGCG-AATTTGACTATCGTGTTGCGAATTTGACT-TCCGTGTTGCGATTTACAAATTCGT
1 GTTGCGAAATTTGACT-TCGTGTTGCGAATTTGACTATAC--GTTGCGATTTACAGATTCGT
* *
1694650 GTTGCG-AATTTGACTTTTGTGTTGCGAATTTGACTATCACGTTGCGAATTT---GACTTTGT
1 GTTGCGAAATTTGAC-TTCGTGTTGCGAATTTGACTAT-ACGTTGCG-ATTTACAGA-TTCGT
* *
1694709 GTTGC-AAATTTGACTATCGCGTTGCGAATTTGACTATACGTTGCGATTTACAGATTCGC
1 GTTGCGAAATTTGACT-TCGTGTTGCGAATTTGACTATACGTTGCGATTTACAGATTCGT
* * * *
1694768 ATTACGAAATTGGAGTTCGTGTTGCGAATTTG
1 GTTGCGAAATTTGACTTCGTGTTGCGAATTTG
1694800 TTGGTCATTT
Statistics
Matches: 126, Mismatches: 13, Indels: 23
0.78 0.08 0.14
Matches are distributed among these distances:
57 4 0.03
58 10 0.08
59 57 0.45
60 48 0.38
61 6 0.05
62 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (59 bp):
GTTGCGAAATTTGACTTCGTGTTGCGAATTTGACTATACGTTGCGATTTACAGATTCGT
Found at i:1695767 original size:30 final size:30
Alignment explanation
Indices: 1695655--1696006 Score: 239
Period size: 29 Copynumber: 11.8 Consensus size: 30
1695645 ACTTAAATCA
* *
1695655 TATCCTAACTTTACAAAAATATATATTATTTT
1 TATCTTAACTTT--AAAAATATATTTTATTTT
* * * * *
1695687 CAT-TCAA-TTTATTAAATATATTTTACTCT
1 TATCTTAACTTTA-AAAATATATTTTATTTT
* * *
1695716 TATTTTGAC-TT-AAAATTTATTTTATTTT
1 TATCTTAACTTTAAAAATATATTTTATTTT
1695744 TATCTTAACTTTAAAAATATATTTTATTTT
1 TATCTTAACTTTAAAAATATATTTTATTTT
* * *
1695774 TAT-TCAA-TTTATTAAATATATTTTACTTT
1 TATCTTAACTTTA-AAAATATATTTTATTTT
* * *
1695803 CATTTTAAC-TTAAAAGT-TAATTTTATTTT
1 TATCTTAACTTTAAAAATAT-ATTTTATTTT
* *
1695832 TATCTTAAATTT-AAAACATATTTTATTCTT
1 TATCTTAACTTTAAAAATATATTTTATT-TT
* * *
1695862 T-TATTAACTTTAAAAATATATTGTATTAT
1 TATCTTAACTTTAAAAATATATTTTATTTT
1695891 TATCTTAACTTTAAAAA-ATATTTT-TTTT
1 TATCTTAACTTTAAAAATATATTTTATTTT
* ** *
1695919 CTTTCATTAA-TTTAGAAAATATATTTGGTTAT
1 -TATC-TTAACTTTA-AAAATATATTTTATTTT
* *
1695951 TATCTTAACTTCAAATAATATATTTTTTCTTT
1 TATCTTAACTTTAAA-AATATATTTTAT-TTT
1695983 TAT-TTAGA-TTTAAAAAATATATTT
1 TATCTTA-ACTTT-AAAAATATATTT
1696007 GAATTTAAGA
Statistics
Matches: 249, Mismatches: 47, Indels: 49
0.72 0.14 0.14
Matches are distributed among these distances:
28 29 0.12
29 89 0.36
30 79 0.32
31 38 0.15
32 14 0.06
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (30 bp):
TATCTTAACTTTAAAAATATATTTTATTTT
Found at i:1695771 original size:87 final size:88
Alignment explanation
Indices: 1695655--1695858 Score: 297
Period size: 87 Copynumber: 2.3 Consensus size: 88
1695645 ACTTAAATCA
* *
1695655 TATCCTAACTTTACAAAAATATATATTATTTTCATTCAATTTATTAAATATATTTTACTCTT-AT
1 TATCTTAACTTT--AAAAATATATTTTATTTTCATTCAATTTATTAAATATATTTTACT-TTCAT
* *
1695719 TTTGACTTAAAA-TTTATTTTATTTT
63 TTTAACTTAAAAGTTAATTTTATTTT
*
1695744 TATCTTAACTTTAAAAATATATTTTATTTTTATTCAATTTATTAAATATATTTTACTTTCATTTT
1 TATCTTAACTTTAAAAATATATTTTATTTTCATTCAATTTATTAAATATATTTTACTTTCATTTT
1695809 AACTTAAAAGTTAATTTTATTTT
66 AACTTAAAAGTTAATTTTATTTT
* *
1695832 TATCTTAAATTT-AAAACATATTTTATT
1 TATCTTAACTTTAAAAATATATTTTATT
1695859 CTTTTATTAA
Statistics
Matches: 106, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
86 2 0.02
87 70 0.66
88 23 0.22
89 11 0.10
ACGTcount: A:0.36, C:0.08, G:0.01, T:0.55
Consensus pattern (88 bp):
TATCTTAACTTTAAAAATATATTTTATTTTCATTCAATTTATTAAATATATTTTACTTTCATTTT
AACTTAAAAGTTAATTTTATTTT
Found at i:1695951 original size:60 final size:60
Alignment explanation
Indices: 1695822--1696007 Score: 218
Period size: 60 Copynumber: 3.1 Consensus size: 60
1695812 TTAAAAGTTA
* * * *
1695822 ATTT-TATTTTTATCTTAAATTTAAAACATA-TTTTATTCTTTTATTAACTTTAAAAATAT
1 ATTTGTATTATTATCTTAACTTTAAAAAATATTTTTTTTCTTTTATTAA-TTTAAAAATAT
*
1695881 A-TTGTATTATTATCTTAACTTTAAAAAATATTTTTTTTCTTTCATTAATTTAGAAAATAT
1 ATTTGTATTATTATCTTAACTTTAAAAAATATTTTTTTTCTTTTATTAATTTA-AAAATAT
* * * *
1695941 ATTTG-GTTATTATCTTAACTTCAAATAATATATTTTTTCTTTTATTTAGATTTAAAAAATAT
1 ATTTGTATTATTATCTTAACTTTAAAAAATATTTTTTTTCTTTTA-TTA-ATTT-AAAAATAT
1696003 ATTTG
1 ATTTG
1696008 AATTTAAGAT
Statistics
Matches: 110, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
58 2 0.02
59 28 0.25
60 57 0.52
61 6 0.05
62 16 0.15
63 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.54
Consensus pattern (60 bp):
ATTTGTATTATTATCTTAACTTTAAAAAATATTTTTTTTCTTTTATTAATTTAAAAATAT
Found at i:1696110 original size:29 final size:28
Alignment explanation
Indices: 1696078--1696208 Score: 106
Period size: 29 Copynumber: 4.6 Consensus size: 28
1696068 TTAAGAGAAT
1696078 AATAAAATACATTTTTAAGTTAATAAAAG
1 AATAAAATA-ATTTTTAAGTTAATAAAAG
* *
1696107 AATAAAA-AA-TTTAAAGTTAA-AATAAT
1 AATAAAATAATTTTTAAGTTAATAA-AAG
* * *
1696133 AACAAAAATGCATATTTAAGTTAATAAAAG
1 AA-TAAAAT-AATTTTTAAGTTAATAAAAG
* * * *
1696163 AATAAAATATTTTTTAAAATTAAGATAAG
1 AATAAAATAATTTTT-AAGTTAATAAAAG
*
1696192 AATAAAATATTTTTTAA
1 AATAAAATAATTTTTAA
1696209 AATTCAAATA
Statistics
Matches: 81, Mismatches: 14, Indels: 15
0.74 0.13 0.14
Matches are distributed among these distances:
25 2 0.02
26 14 0.17
27 5 0.06
28 7 0.09
29 38 0.47
30 13 0.16
31 2 0.02
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.34
Consensus pattern (28 bp):
AATAAAATAATTTTTAAGTTAATAAAAG
Found at i:1696116 original size:31 final size:31
Alignment explanation
Indices: 1696073--1696169 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 31
1696063 TATAGTTAAG
1696073 AGAATAATAAAATACATTTTTAAGTTAATAAA
1 AGAATAA-AAAATACATTTTTAAGTTAATAAA
*
1696105 AGAAT--AAAA-A-A-TTTAAAGTTAA-AATA
1 AGAATAAAAAATACATTTTTAAGTTAATAA-A
* * * *
1696131 ATAA-CAAAAATGCATATTTAAGTTAATAAA
1 AGAATAAAAAATACATTTTTAAGTTAATAAA
1696161 AGAATAAAA
1 AGAATAAAA
1696170 TATTTTTTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 17
0.68 0.09 0.23
Matches are distributed among these distances:
25 2 0.04
26 14 0.28
27 5 0.10
28 1 0.02
29 5 0.10
30 13 0.26
31 5 0.10
32 5 0.10
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (31 bp):
AGAATAAAAAATACATTTTTAAGTTAATAAA
Found at i:1696172 original size:25 final size:25
Alignment explanation
Indices: 1696091--1696174 Score: 80
Period size: 28 Copynumber: 3.1 Consensus size: 25
1696081 AAAATACATT
*
1696091 TTTAAGTTAATAAAAGAATAAAAAA
1 TTTAAGTTAATAAAAGAATAAAATA
*
1696116 TTTAAAGTTAAAATAATAACAA-AAATGCATA
1 TTT-AAGTT--AATAA-AAGAATAAA---ATA
1696147 TTTAAGTTAATAAAAGAATAAAATA
1 TTTAAGTTAATAAAAGAATAAAATA
1696172 TTT
1 TTT
1696175 TTTAAAATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
25 9 0.19
26 5 0.10
27 4 0.08
28 16 0.33
29 4 0.08
30 5 0.10
31 5 0.10
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.32
Consensus pattern (25 bp):
TTTAAGTTAATAAAAGAATAAAATA
Found at i:1696209 original size:29 final size:29
Alignment explanation
Indices: 1696160--1696230 Score: 117
Period size: 29 Copynumber: 2.4 Consensus size: 29
1696150 AAGTTAATAA
1696160 AAGAATAAAATATTTTTTAAAATT-AAGAT
1 AAGAATAAAATATTTTTTAAAATTCAA-AT
1696189 AAGAATAAAATATTTTTTAAAATTCAAAT
1 AAGAATAAAATATTTTTTAAAATTCAAAT
*
1696218 AAAAATAAAATAT
1 AAGAATAAAATAT
1696231 ATTTAATAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 38 0.95
30 2 0.05
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.35
Consensus pattern (29 bp):
AAGAATAAAATATTTTTTAAAATTCAAAT
Found at i:1702882 original size:2 final size:2
Alignment explanation
Indices: 1702875--1702910 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1702865 CGTATAAAAC
1702875 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
1702911 CAAAATATCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1703343 original size:39 final size:39
Alignment explanation
Indices: 1703282--1703378 Score: 149
Period size: 39 Copynumber: 2.5 Consensus size: 39
1703272 TCGCATAAGG
* *
1703282 ACCTGCGGTAAGGACTTACCCTGAGCACAAAGTAGAGGA
1 ACCTGCAGTAAGGACTTACCCTGAGCACAAAGCAGAGGA
**
1703321 GTCTGCAGTAAGGACTTACCCTGAGCACAAAGCAGAGGA
1 ACCTGCAGTAAGGACTTACCCTGAGCACAAAGCAGAGGA
*
1703360 ACCTGCAGTAAGGTCTTAC
1 ACCTGCAGTAAGGACTTAC
1703379 AAGTCATAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.32, C:0.24, G:0.27, T:0.18
Consensus pattern (39 bp):
ACCTGCAGTAAGGACTTACCCTGAGCACAAAGCAGAGGA
Found at i:1706221 original size:32 final size:32
Alignment explanation
Indices: 1706147--1706225 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 32
1706137 ACGATTGTGA
* *
1706147 CTACAATGCATCATCTGAATGCAACACTAAAC
1 CTACTATGCATCATATGAATGCAACACTAAAC
* **
1706179 CTACTATGCATTATATGAATGCAACACTCGAC
1 CTACTATGCATCATATGAATGCAACACTAAAC
* *
1706211 CTATTGTGCATCATA
1 CTACTATGCATCATA
1706226 CACTAGCTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.28
Consensus pattern (32 bp):
CTACTATGCATCATATGAATGCAACACTAAAC
Found at i:1712113 original size:86 final size:87
Alignment explanation
Indices: 1711961--1712135 Score: 253
Period size: 86 Copynumber: 2.0 Consensus size: 87
1711951 CGAATAATTT
* ****
1711961 GGTCTTTGCCTCATTTAATGTGGTTAATTGAAACTTTGAGTTATCCAAAAATTTAAGA-TTTTCC
1 GGTCTTTGCCTCATTTAATGTGCTTAATTGAAACTTTGAGTTATCCAAAAATTTAAGACCCCCCC
1712025 CCCAAAATAAGTAATGATTTTA
66 CCCAAAATAAGTAATGATTTTA
* *
1712047 GGTCTTTGTCTCTTTTAATGTGCTTAATTGAAACTTTGAGTTATCCAAAAATTTAAGACCCCCCC
1 GGTCTTTGCCTCATTTAATGTGCTTAATTGAAACTTTGAGTTATCCAAAAATTTAAGA--CCCCC
*
1712112 CCCCCAAAGTAAGTAATGATTTTA
64 CCCCCAAAATAAGTAATGATTTTA
1712136 TGTATTTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
86 55 0.71
89 23 0.29
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (87 bp):
GGTCTTTGCCTCATTTAATGTGCTTAATTGAAACTTTGAGTTATCCAAAAATTTAAGACCCCCCC
CCCAAAATAAGTAATGATTTTA
Found at i:1713217 original size:12 final size:12
Alignment explanation
Indices: 1713200--1713261 Score: 54
Period size: 12 Copynumber: 5.0 Consensus size: 12
1713190 TATTATATAG
1713200 TTTTGAAAATAT
1 TTTTGAAAATAT
1713212 TTTTGAAAATAT
1 TTTTGAAAATAT
* * *
1713224 ATAT-AATATATAG
1 TTTTGAA-A-ATAT
*
1713237 TTTTGAAAACGAT
1 TTTTGAAAA-TAT
1713250 TTTTGAAAATAT
1 TTTTGAAAATAT
1713262 ATATATTATA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
11 2 0.05
12 18 0.47
13 16 0.42
14 2 0.05
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.45
Consensus pattern (12 bp):
TTTTGAAAATAT
Found at i:1713261 original size:38 final size:38
Alignment explanation
Indices: 1713174--1713648 Score: 488
Period size: 37 Copynumber: 12.7 Consensus size: 38
1713164 TTAAAAAATT
* * * * *
1713174 ATTTTTG-AAATATTTATATTATATAG-TTTTGAAAAT
1 ATTTTTGAAAATATATATAATATATGGTTTTTAAAAAC
* *
1713210 ATTTTTGAAAATATATATAATATATAG-TTTTGAAAAC
1 ATTTTTGAAAATATATATAATATATGGTTTTTAAAAAC
* * *
1713247 GATTTTTGAAAATATATATATTATATAGTTTTTTGAAAAC
1 -ATTTTTGAAAATATATATAATATAT-GGTTTTTAAAAAC
* **
1713287 A-TTTTGAAAACATATATAATATATGGTTTGTTGTGAAAC
1 ATTTTTGAAAATATATATAATATATGGTTT-TT-AAAAAC
1713326 A-TTTTGAAAACT-TATATAATATATGGTTTTTAAAAAC
1 ATTTTTGAAAA-TATATATAATATATGGTTTTTAAAAAC
*
1713363 A-TTTTGAAAACT-TATATAATATATGGCTTTTAAAAAC
1 ATTTTTGAAAA-TATATATAATATATGGTTTTTAAAAAC
1713400 A-TTTTGAAAATATATATAATATAT-GTTTTTAAAAAC
1 ATTTTTGAAAATATATATAATATATGGTTTTTAAAAAC
*
1713436 ATTTTTGAAAACT-TATGTAATATATGGTTTTTAAAAAAC
1 ATTTTTGAAAA-TATATATAATATATGGTTTTT-AAAAAC
*
1713475 ATTTTTGAAAACT-TATATAATATATGGTTTTAAAAAAC
1 ATTTTTGAAAA-TATATATAATATATGGTTTTTAAAAAC
*
1713513 ATTTTTGAAAACT-TATATAATATATGGTCTTTAAAAAAAC
1 ATTTTTGAAAA-TATATATAATATATGGT-TTT-TAAAAAC
*
1713553 A-TTTTGAAAATATATATAATATATGATTTTT-AAAAC
1 ATTTTTGAAAATATATATAATATATGGTTTTTAAAAAC
* *
1713589 A-TTTTGAAAA-CTATATAATATATAG-TTTT-AAAA-
1 ATTTTTGAAAATATATATAATATATGGTTTTTAAAAAC
1713622 ATGTTTT-AAGAATATATATATATATAT
1 AT-TTTTGAA-AATATATATA-ATATAT
1713649 ATATATATAT
Statistics
Matches: 394, Mismatches: 25, Indels: 39
0.86 0.05 0.09
Matches are distributed among these distances:
33 1 0.00
34 10 0.03
35 18 0.05
36 41 0.10
37 118 0.30
38 94 0.24
39 94 0.24
40 18 0.05
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (38 bp):
ATTTTTGAAAATATATATAATATATGGTTTTTAAAAAC
Found at i:1713326 original size:39 final size:37
Alignment explanation
Indices: 1713212--1713648 Score: 490
Period size: 39 Copynumber: 11.6 Consensus size: 37
1713202 TTGAAAATAT
* * *
1713212 TTTTGAAAATATATATAATATATAG-TTTTGAAAACGA
1 TTTTGAAAACATATATAATATATGGTTTTTAAAAAC-A
* * * *
1713249 TTTTTGAAAATATATATATTATATAGTTTTTTGAAAACA
1 -TTTTGAAAACATATATAATATAT-GGTTTTTAAAAACA
**
1713288 TTTTGAAAACATATATAATATATGGTTTGTTGTGAAACA
1 TTTTGAAAACATATATAATATATGGTTT-TT-AAAAACA
*
1713327 TTTTGAAAACTTATATAATATATGGTTTTTAAAAACA
1 TTTTGAAAACATATATAATATATGGTTTTTAAAAACA
* *
1713364 TTTTGAAAACTTATATAATATATGGCTTTTAAAAACA
1 TTTTGAAAACATATATAATATATGGTTTTTAAAAACA
*
1713401 TTTTGAAAATATATATAATATAT-GTTTTTAAAAACA
1 TTTTGAAAACATATATAATATATGGTTTTTAAAAACA
* *
1713437 TTTTTGAAAACTTATGTAATATATGGTTTTTAAAAAACA
1 -TTTTGAAAACATATATAATATATGGTTTTT-AAAAACA
* *
1713476 TTTTTGAAAACTTATATAATATATGGTTTTAAAAAACA
1 -TTTTGAAAACATATATAATATATGGTTTTTAAAAACA
* *
1713514 TTTTTGAAAACTTATATAATATATGGTCTTTAAAAAAACA
1 -TTTTGAAAACATATATAATATATGGT-TTT-TAAAAACA
* *
1713554 TTTTGAAAATATATATAATATATGATTTTT-AAAACA
1 TTTTGAAAACATATATAATATATGGTTTTTAAAAACA
* **
1713590 TTTTGAAAAC-TATATAATATATAG-TTTTAAAAATG
1 TTTTGAAAACATATATAATATATGGTTTTTAAAAACA
*
1713625 TTTT-AAGAATATATATATATATAT
1 TTTTGAA-AACATATATA-ATATAT
1713649 ATATATATAT
Statistics
Matches: 356, Mismatches: 30, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
34 6 0.02
35 22 0.06
36 33 0.09
37 92 0.26
38 90 0.25
39 95 0.27
40 18 0.05
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.43
Consensus pattern (37 bp):
TTTTGAAAACATATATAATATATGGTTTTTAAAAACA
Found at i:1713640 original size:2 final size:2
Alignment explanation
Indices: 1713633--1713668 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1713623 TGTTTTAAGA
1713633 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
1713669 TTTTATTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1714863 original size:17 final size:16
Alignment explanation
Indices: 1714840--1714967 Score: 68
Period size: 17 Copynumber: 7.8 Consensus size: 16
1714830 TTTATTATTA
* *
1714840 TTTTTATTTCATTTTT
1 TTTTTATTTTATTTAT
1714856 TATTTTATTTTATTTCAT
1 T-TTTTATTTTATTT-AT
*
1714874 TTTTTGTTTTA-TT-T
1 TTTTTATTTTATTTAT
*
1714888 TCTTTATTTT-TATTAT
1 TTTTTATTTTAT-TTAT
* *
1714904 TTTTCT-TTTTACTCA-
1 TTTT-TATTTTATTTAT
* *
1714919 ATTTTATTTATCTTTAT
1 TTTTTATTT-TATTTAT
*
1714936 TTATTTGTTTTATTTAT
1 TT-TTTATTTTATTTAT
1714953 TTTATTATTATTATT
1 TTT-TTATT-TTATT
1714968 ATTATTATAT
Statistics
Matches: 83, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
14 10 0.12
15 8 0.10
16 17 0.20
17 35 0.42
18 13 0.16
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTTTATTTTATTTAT
Found at i:1714866 original size:22 final size:22
Alignment explanation
Indices: 1714827--1714898 Score: 101
Period size: 22 Copynumber: 3.2 Consensus size: 22
1714817 AATTTAACCC
1714827 TTTTTTATTATTATTTTTATTTCA
1 TTTTTTATT-TTA-TTTTATTTCA
1714851 TTTTTTATTTTATTTTATTTCA
1 TTTTTTATTTTATTTTATTTCA
* *
1714873 TTTTTTGTTTTATTTTCTTT-A
1 TTTTTTATTTTATTTTATTTCA
1714894 TTTTT
1 TTTTT
1714899 ATTATTTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
21 6 0.13
22 28 0.61
23 3 0.07
24 9 0.20
ACGTcount: A:0.15, C:0.04, G:0.01, T:0.79
Consensus pattern (22 bp):
TTTTTTATTTTATTTTATTTCA
Found at i:1714895 original size:57 final size:59
Alignment explanation
Indices: 1714834--1714967 Score: 136
Period size: 63 Copynumber: 2.2 Consensus size: 59
1714824 CCCTTTTTTA
1714834 TTATTATTTTTATTTCATTTTT-T-ATTTTATTTTAT-TTCATTT-TTTGTTTTATTT-TCT
1 TTATTATTTTTATTTC-TTTTTATAATTTTA-TTTATCTTCATTTATTTGTTTTATTTAT-T
*
1714891 TTATT-TTTATTATTTTTCTTTTTACTCAATTTTATTTATCTTTATTTATTTGTTTTATTTATT
1 TTATTATTT-TTA--TTTCTTTTTA-T-AATTTTATTTATCTTCATTTATTTGTTTTATTTATT
*
1714954 TTATTATTATTATT
1 TTATTATTTTTATT
1714968 ATTATTATAT
Statistics
Matches: 64, Mismatches: 2, Indels: 18
0.76 0.02 0.21
Matches are distributed among these distances:
56 3 0.05
57 8 0.12
58 5 0.08
59 4 0.06
60 1 0.02
61 7 0.11
62 12 0.19
63 21 0.33
64 3 0.05
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.75
Consensus pattern (59 bp):
TTATTATTTTTATTTCTTTTTATAATTTTATTTATCTTCATTTATTTGTTTTATTTATT
Found at i:1714900 original size:15 final size:15
Alignment explanation
Indices: 1714834--1714973 Score: 60
Period size: 16 Copynumber: 8.9 Consensus size: 15
1714824 CCCTTTTTTA
1714834 TTATTATTTTTATTT
1 TTATTATTTTTATTT
*
1714849 CATT-TTTTATTTTA-TT
1 --TTATTAT-TTTTATTT
1714865 TTATTTCATTTTT-TGTT
1 TTA-TT-ATTTTTAT-TT
1714882 TTATT-TTCTTTATTT
1 TTATTATT-TTTATTT
*
1714897 TTATTATTTTTCTTT
1 TTATTATTTTTATTT
* *
1714912 TTACTCAATTTTATTT
1 TTA-TTATTTTTATTT
1714928 ATCT-TTATTTATT-TGTT
1 -T-TATTATTT-TTAT-TT
*
1714945 TTATT-TATTTTATTA
1 TTATTAT-TTTTATTT
*
1714960 TTATTATTATTATT
1 TTATTATTTTTATT
1714974 ATATTAATAT
Statistics
Matches: 95, Mismatches: 10, Indels: 38
0.66 0.07 0.27
Matches are distributed among these distances:
14 4 0.04
15 35 0.37
16 37 0.39
17 18 0.19
18 1 0.01
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.74
Consensus pattern (15 bp):
TTATTATTTTTATTT
Found at i:1714949 original size:9 final size:9
Alignment explanation
Indices: 1714841--1714978 Score: 62
Period size: 9 Copynumber: 15.2 Consensus size: 9
1714831 TTATTATTAT
1714841 TTTTATTTCA
1 TTTTATTT-A
1714851 -TTT-TTTA
1 TTTTATTTA
1714858 TTTTATTTTA
1 TTTTA-TTTA
*
1714868 TTTCATTT-
1 TTTTATTTA
1714876 TTTGT-TTTA
1 TTT-TATTTA
*
1714885 TTTTCTTTA
1 TTTTATTTA
1714894 TTTT-TATTA
1 TTTTAT-TTA
*
1714903 TTTT-TCT-
1 TTTTATTTA
**
1714910 TTTTACTCAA
1 TTTTA-TTTA
1714920 TTTTATTTA
1 TTTTATTTA
1714929 TCTTTATTTA
1 T-TTTATTTA
1714939 TTTGT-TTTA
1 TTT-TATTTA
1714948 -TTTATTTTA
1 TTTTA-TTTA
1714957 TTATTA-TTA
1 TT-TTATTTA
1714966 TTATTATTATA
1 TT-TTATT-TA
1714977 TT
1 TT
1714979 AATATTATTT
Statistics
Matches: 104, Mismatches: 6, Indels: 35
0.72 0.04 0.24
Matches are distributed among these distances:
7 6 0.06
8 17 0.16
9 49 0.47
10 25 0.24
11 7 0.07
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (9 bp):
TTTTATTTA
Found at i:1714949 original size:13 final size:14
Alignment explanation
Indices: 1714921--1714954 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1714911 TTTACTCAAT
1714921 TTTATTTATCTTTA
1 TTTATTTATCTTTA
*
1714935 TTTATTTGT-TTTA
1 TTTATTTATCTTTA
1714948 TTTATTT
1 TTTATTT
1714955 TATTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTATTTATCTTTA
Found at i:1714962 original size:3 final size:3
Alignment explanation
Indices: 1714949--1714987 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
1714939 TTTGTTTTAT
*
1714949 TTA TT- TTA TTA TTA TTA TTA TTA TTA -TA TTA ATA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1714988 TTCCTTCTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1714978 original size:20 final size:20
Alignment explanation
Indices: 1714949--1714987 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1714939 TTTGTTTTAT
* *
1714949 TTATTTTATTATTATTATTA
1 TTATTATATTAATATTATTA
1714969 TTATTATATTAATATTATT
1 TTATTATATTAATATTATT
1714988 TTCCTTCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTATATTAATATTATTA
Found at i:1719076 original size:99 final size:99
Alignment explanation
Indices: 1718962--1719163 Score: 314
Period size: 99 Copynumber: 2.0 Consensus size: 99
1718952 ATATAATATT
* ** *
1718962 ATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGTAATTGGTTAAACTCCCCGACTTTATGG
1 ATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAACAATTGGTTAAACGCCCCGACTTTATGG
1719027 ATAAGATTCAGCTAGCATGATAAAGGTGATTATA
66 ATAAGATTCAGCTAGCATGATAAAGGTGATTATA
* *
1719061 ATATCTATACAATAAAGCTTGAGTTGTCCCTCTAAAACAATTGGTTAAACGCCCCGGCTTTATGG
1 ATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAACAATTGGTTAAACGCCCCGACTTTATGG
* * * *
1719126 ATAAGATTTAGTTAGCCTGATAAATGTGATTATA
66 ATAAGATTCAGCTAGCATGATAAAGGTGATTATA
1719160 ATAT
1 ATAT
1719164 TCAATTGTCC
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 93 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (99 bp):
ATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAACAATTGGTTAAACGCCCCGACTTTATGG
ATAAGATTCAGCTAGCATGATAAAGGTGATTATA
Found at i:1720890 original size:86 final size:86
Alignment explanation
Indices: 1720760--1721089 Score: 450
Period size: 86 Copynumber: 3.8 Consensus size: 86
1720750 TACAATATAG
* *
1720760 CTCAAAGCGAGAAGGGTTATCTGTCAAC-CAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGA
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGA
1720824 CATATCAAATTTACAGCATAA
66 CATATCAAATTTACAGCATAA
* * * * *
1720845 ATCAAGGTGATAAGGGTTATCTATCAGCAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGA
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGA
1720910 CATATCAAATTTACAGCATAA
66 CATATCAAATTTACAGCATAA
* *
1720931 CTCAAGGCAAGAAGGGTTATCTGTCAGCAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGG
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAAAACCTTCGAGTTCGATTACATTCAGCTCAA-GG
* *
1720996 A-ATATCAAATTTACAACATAG
65 ACATATCAAATTTACAGCATAA
** * * * * * *
1721017 CTCAAAACGAGAAGGGTTATATGTCAACAAAAAA-ATGTCAAGTTCGATTCCATTCAGCTCGATG
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAAAACCT-TCGAGTTCGATTACATTCAGCTCAAGG
1721081 ACATATCAA
65 ACATATCAA
1721090 CCGCATGGTA
Statistics
Matches: 217, Mismatches: 24, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
85 25 0.12
86 189 0.87
87 3 0.01
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (86 bp):
CTCAAGGCGAGAAGGGTTATCTGTCAACAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGA
CATATCAAATTTACAGCATAA
Found at i:1722028 original size:38 final size:38
Alignment explanation
Indices: 1721946--1722354 Score: 318
Period size: 38 Copynumber: 10.8 Consensus size: 38
1721936 TTTGTTAAAA
*
1721946 AAAATCATTTTTG-AAATATATAT--TATATA--ATTTG
1 AAAA-CATTTTTGAAAATATATATAATATATAGTTTTTG
1721980 AAAACATTTTTGAAAATATATATAATATATAG-TTTTG
1 AAAACATTTTTGAAAATATATATAATATATAGTTTTTG
* *
1722017 AAAACATTTTTTGAAAATGTATATATTATATAGTTTTTTG
1 AAAACA-TTTTTGAAAATATATATAATATATAG-TTTTTG
* * * *
1722057 AAAGCATTTTTGAAAACATATATAATATATGGTTTTTTTCAAAAAA
1 AAAACATTTTTGAAAATATATATAATATATAG--TTTTT------G
* *
1722103 AAAACA-TTTTGAAAATATATATAATATAT-GCTTTTA
1 AAAACATTTTTGAAAATATATATAATATATAGTTTTTG
* *
1722139 AAAACA-TTTTGAAAACT-TATATAATATATGGTTTTTAA
1 AAAACATTTTTGAAAA-TATATATAATATATAGTTTTT-G
* * *
1722177 AAAACA-TTTTGAAAACT-TATAAAATATATGGTTTTTA
1 AAAACATTTTTGAAAA-TATATATAATATATAGTTTTTG
*
1722214 AAAAAATATTTTGAAAATATATATAATATAT-GATTTTT-
1 AAAACAT-TTTTGAAAATATATATAATATATAG-TTTTTG
*
1722252 AAAACA-TTTTGAAAA-CTATATAATATATAG-TTTTG
1 AAAACATTTTTGAAAATATATATAATATATAGTTTTTG
* * *
1722287 AAAACTTTTTTAAAAATATGTATATAATATAT-GGTTTT-
1 AAAACATTTTTGAAAATA--TATATAATATATAGTTTTTG
* * *
1722325 ATAATATTTTTGAATATATATA-AATATATA
1 AAAACATTTTTGAAAATATATATAATATATA
1722355 TATATATATA
Statistics
Matches: 320, Mismatches: 26, Indels: 56
0.80 0.06 0.14
Matches are distributed among these distances:
33 8 0.03
34 18 0.06
35 24 0.08
36 56 0.17
37 22 0.07
38 81 0.25
39 63 0.20
40 16 0.05
42 4 0.01
44 1 0.00
45 22 0.07
46 5 0.02
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (38 bp):
AAAACATTTTTGAAAATATATATAATATATAGTTTTTG
Found at i:1722153 original size:158 final size:156
Alignment explanation
Indices: 1721942--1722251 Score: 369
Period size: 158 Copynumber: 2.0 Consensus size: 156
1721932 AGTTTTTGTT
* *
1721942 AAAAAAAATCATTTTTGAAATATATATTATATAATTTGAAAACATTTTTGAAAA-TATATATAAT
1 AAAAAAAAACATTTTTGAAATATATATTATATAATTTAAAAACATTTTTGAAAACT-TATATAAT
* ** * * * * **
1722006 ATATAGTTTTGAAAACATTTTTTGAAAA-TGTATATATTATATAGTTTTTTGAAAGCAT-TTTTG
65 ATATAGTTTTGAAAAAACATTTTGAAAACT-TATAAAATATAT-GGTTTTTAAAAAAATATTTTG
*
1722069 AAAACATATATAATATATGGTTTTTTTCA
128 AAAACATATATAATATATGATTTTTTTCA
**
1722098 AAAAAAAAACA-TTTTGAAAATATATATAATATATGCTTTTAAAAACA-TTTTGAAAACTTATAT
1 AAAAAAAAACATTTTTG-AAATATATAT--TATAT-AATTTAAAAACATTTTTGAAAACTTATAT
* *
1722161 AATATATGGTTTTTAAAAAACATTTTGAAAACTTATAAAATATATGGTTTTTAAAAAAATATTTT
62 AATATATAGTTTTGAAAAAACATTTTGAAAACTTATAAAATATATGGTTTTTAAAAAAATATTTT
*
1722226 GAAAATATATATAATATATGATTTTT
127 GAAAACATATATAATATATGATTTTT
1722252 AAAACATTTT
Statistics
Matches: 130, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
155 5 0.04
156 20 0.15
157 11 0.08
158 83 0.64
159 11 0.08
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (156 bp):
AAAAAAAAACATTTTTGAAATATATATTATATAATTTAAAAACATTTTTGAAAACTTATATAATA
TATAGTTTTGAAAAAACATTTTGAAAACTTATAAAATATATGGTTTTTAAAAAAATATTTTGAAA
ACATATATAATATATGATTTTTTTCA
Found at i:1722345 original size:2 final size:2
Alignment explanation
Indices: 1722338--1722379 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1722328 ATATTTTTGA
*
1722338 AT AT AT AT AA 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
1722380 TATTTATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1722354 original size:74 final size:76
Alignment explanation
Indices: 1722103--1722354 Score: 274
Period size: 74 Copynumber: 3.4 Consensus size: 76
1722093 TTTCAAAAAA
*
1722103 AAAACATTTTGAAAA-TATATATAATATAT-GCTTTTAAAAAC-ATTTTGAAAA-CTTATATAAT
1 AAAACATTTTGAAAACTATATA-AATATATAGCTTTTAAAAACTATTTTGAAAATATTATATAAT
*
1722164 ATATGGTTTTTAA
65 ATATGG-TTTTAT
* * *
1722177 AAAACATTTTGAAAACT-TATAAAATATATGGTTTTTAAAAAAATATTTTGAAAATA-TATATAA
1 AAAACATTTTGAAAACTATAT-AAATATATAGCTTTT-AAAAACTATTTTGAAAATATTATATAA
*
1722240 TATATGATTTT-T
64 TATATGGTTTTAT
* * *
1722252 AAAACATTTTGAAAACTATAT-AATATATAG-TTTTGAAAACTTTTTTAAAAATATGTATATAAT
1 AAAACATTTTGAAAACTATATAAATATATAGCTTTTAAAAACTATTTTGAAAATAT-TATATAAT
1722315 ATATGGTTTTAT
65 ATATGGTTTTAT
* * *
1722327 AATA-TTTTTGAATA-TATATAAATATATA
1 AAAACATTTTGAAAACTATATAAATATATA
1722355 TATATATATA
Statistics
Matches: 153, Mismatches: 14, Indels: 22
0.81 0.07 0.12
Matches are distributed among these distances:
72 15 0.10
73 9 0.06
74 66 0.43
75 28 0.18
76 12 0.08
77 23 0.15
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (76 bp):
AAAACATTTTGAAAACTATATAAATATATAGCTTTTAAAAACTATTTTGAAAATATTATATAATA
TATGGTTTTAT
Found at i:1722386 original size:4 final size:4
Alignment explanation
Indices: 1722379--1722404 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1722369 TATATATATA
1722379 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
1722405 TATTGTGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:1723653 original size:22 final size:22
Alignment explanation
Indices: 1723628--1723690 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
1723618 AAAATTTAAC
1723628 CATTTTTTATTATTATTTATTT
1 CATTTTTTATTATTATTTATTT
* *
1723650 CATTTTTCATT-TCATTTCATTT
1 CATTTTTTATTATTATTT-ATTT
*
1723672 CATTTTCT-TTATT-TTTATT
1 CATTTTTTATTATTATTTATT
1723691 ATTTTTCTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 3 0.09
21 10 0.29
22 21 0.62
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (22 bp):
CATTTTTTATTATTATTTATTT
Found at i:1724937 original size:7 final size:6
Alignment explanation
Indices: 1724893--1724922 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1724883 TATTTAATTA
1724893 TCTTTT T-TTTT TCTTTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT T
1724923 TAGTTATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TCTTTT
Found at i:1725030 original size:2 final size:2
Alignment explanation
Indices: 1724958--1725019 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1724948 TATTTTAATT
1724958 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1725000 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
1725020 CACTTTATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1736327 original size:14 final size:14
Alignment explanation
Indices: 1736308--1736334 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1736298 GATCAAAACT
1736308 TCAAGATTCCAGAA
1 TCAAGATTCCAGAA
1736322 TCAAGATTCCAGA
1 TCAAGATTCCAGA
1736335 CAGGCAACCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAA
Found at i:1736965 original size:94 final size:93
Alignment explanation
Indices: 1736806--1736976 Score: 247
Period size: 94 Copynumber: 1.8 Consensus size: 93
1736796 TCAACATCAC
* **
1736806 AGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCAAAACGAAGGGATGGCTGGTTGTC
1 AGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCAAAACGAAGGGA-GGCTGACTGTC
*
1736871 AACAAACCATTTCCCAGTTTCAGAACCAA
65 AACAAACAATTTCCCAGTTTCAGAACCAA
*
1736900 AGCGAAGGATATTGGACTC-ATGACAACACAAGCTCAACTTCACAACGAATGGGCA-GCTGACTG
1 AGCGAAGGATATTGGACTCGA-GACAACACAAGCTCAACTTCAAAACGAA-GGG-AGGCTGACTG
1736963 TCAACAAACAATTT
63 TCAACAAACAATTT
1736977 AACAGTTCCA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
93 1 0.01
94 64 0.93
95 3 0.04
96 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (93 bp):
AGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCAAAACGAAGGGAGGCTGACTGTCA
ACAAACAATTTCCCAGTTTCAGAACCAA
Found at i:1747766 original size:19 final size:21
Alignment explanation
Indices: 1747722--1747766 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
1747712 ATTTACAGTA
1747722 AATTATTACATAAAACATTATT
1 AATT-TTACATAAAACATTATT
1747744 --TTTTAC-TAAAA-ATTATT
1 AATTTTACATAAAACATTATT
1747761 AATTTT
1 AATTTT
1747767 GATATCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
17 6 0.29
18 5 0.24
19 8 0.38
20 2 0.10
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTTTACATAAAACATTATT
Found at i:1749353 original size:8 final size:8
Alignment explanation
Indices: 1749340--1749384 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
1749330 TTTAAATTTT
*
1749340 AAATATAG
1 AAATATAA
**
1749348 AAATATTC
1 AAATATAA
1749356 AAATATAA
1 AAATATAA
1749364 AAATATAA
1 AAATATAA
*
1749372 AAATAAAA
1 AAATATAA
1749380 AAATA
1 AAATA
1749385 AATTACTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (8 bp):
AAATATAA
Found at i:1749626 original size:25 final size:25
Alignment explanation
Indices: 1749570--1749629 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
1749560 GTATTCTTAC
*
1749570 TAGATTAATCGAGACTTAGAAAATT
1 TAGATTAATCGAGACTTACAAAATT
* * *
1749595 TAAATTAGTCGAGACTTACAAATTT
1 TAGATTAATCGAGACTTACAAAATT
*
1749620 TGGATTAATC
1 TAGATTAATC
1749630 AAAACTTATT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (25 bp):
TAGATTAATCGAGACTTACAAAATT
Found at i:1749947 original size:44 final size:41
Alignment explanation
Indices: 1749899--1750061 Score: 165
Period size: 38 Copynumber: 4.0 Consensus size: 41
1749889 TTTAGAAGTA
1749899 ATTATTTTATAATCTATTATATATATTTATTTTTATAATATTTT
1 ATTATTTT-TAAT-TA-TATATATATTTATTTTTATAATATTTT
1749943 ATTATTTTT-A--ATATATATATTTATTTTTATAATATTTT
1 ATTATTTTTAATTATATATATATTTATTTTTATAATATTTT
* * *
1749981 ATTATTTTTAATATATATATATATATAATTTT-TAATAATTT
1 ATTATTTTTAAT-TATATATATATTTATTTTTATAATATTTT
* * ** * *
1750022 AATAATTTTAAAAAAATTTATATTTATTTTT-TAAATATTT
1 ATTATTTTTAATTATATATATATTTATTTTTAT-AATATTT
1750062 AAATAATTTA
Statistics
Matches: 102, Mismatches: 12, Indels: 13
0.80 0.09 0.10
Matches are distributed among these distances:
38 36 0.35
39 2 0.02
40 15 0.15
41 23 0.23
42 17 0.17
43 1 0.01
44 8 0.08
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.61
Consensus pattern (41 bp):
ATTATTTTTAATTATATATATATTTATTTTTATAATATTTT
Found at i:1749954 original size:17 final size:18
Alignment explanation
Indices: 1749919--1749996 Score: 90
Period size: 19 Copynumber: 4.3 Consensus size: 18
1749909 AATCTATTAT
*
1749919 ATATATTTATT-TTTATA
1 ATATATTTATTATTTTTA
1749936 ATAT-TTTATTATTTTTA
1 ATATATTTATTATTTTTA
*
1749953 ATATATATATTTATTTTT-
1 ATATATTTA-TTATTTTTA
1749971 ATAATATTTTATTATTTTTA
1 AT-ATA-TTTATTATTTTTA
1749991 ATATAT
1 ATATAT
1749997 ATATATATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
16 6 0.12
17 13 0.25
18 6 0.12
19 22 0.42
20 5 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATATTTATTATTTTTA
Found at i:1749967 original size:38 final size:38
Alignment explanation
Indices: 1749916--1750000 Score: 170
Period size: 38 Copynumber: 2.2 Consensus size: 38
1749906 TATAATCTAT
1749916 TATATATATTTATTTTTATAATATTTTATTATTTTTAA
1 TATATATATTTATTTTTATAATATTTTATTATTTTTAA
1749954 TATATATATTTATTTTTATAATATTTTATTATTTTTAA
1 TATATATATTTATTTTTATAATATTTTATTATTTTTAA
1749992 TATATATAT
1 TATATATAT
1750001 ATATATAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (38 bp):
TATATATATTTATTTTTATAATATTTTATTATTTTTAA
Done.