Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 50 of 135
Found at i:20285457 original size:21 final size:21
Alignment explanation
Indices: 20285433--20285478 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
20285423 AAACCTTAAA
*
20285433 TTAAAATATTA-AGTTTAGAAT
1 TTAAAAT-TTAGAGTTCAGAAT
*
20285454 TTAAGATTTAGAGTTCAGAAT
1 TTAAAATTTAGAGTTCAGAAT
20285475 TTAA
1 TTAA
20285479 GTGTTTGGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.41
Consensus pattern (21 bp):
TTAAAATTTAGAGTTCAGAAT
Found at i:20286142 original size:34 final size:38
Alignment explanation
Indices: 20286099--20286168 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 38
20286089 TAAAATATAA
20286099 TAAAAATAAAATC-C-TAA-ATG-CATT-AACTCAATT
1 TAAAAATAAAATCGCATAAGATGCCATTAAACTCAATT
20286132 TAAATAATAAAATCGCATAAGATGCCATTAAACTCAA
1 TAAA-AATAAAATCGCATAAGATGCCATTAAACTCAA
20286169 GCAAAAACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
33 4 0.13
34 9 0.29
35 1 0.03
36 3 0.10
37 3 0.10
38 4 0.13
39 7 0.23
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.27
Consensus pattern (38 bp):
TAAAAATAAAATCGCATAAGATGCCATTAAACTCAATT
Found at i:20290553 original size:17 final size:17
Alignment explanation
Indices: 20290531--20290566 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20290521 AAAGATATTA
20290531 TTCTTTAATTTGCACTT
1 TTCTTTAATTTGCACTT
**
20290548 TTCTTTTGTTTGCACTT
1 TTCTTTAATTTGCACTT
20290565 TT
1 TT
20290567 ATAAATCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TTCTTTAATTTGCACTT
Found at i:20313396 original size:21 final size:21
Alignment explanation
Indices: 20313372--20313412 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20313362 TTTTAATAGT
*
20313372 TTTTTAATAT-TTTTTAGAAAA
1 TTTTTAA-ATCTTTTGAGAAAA
20313393 TTTTTAAATCTTTTGAGAAA
1 TTTTTAAATCTTTTGAGAAA
20313413 TATTCTAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTTTAAATCTTTTGAGAAAA
Found at i:20329263 original size:27 final size:28
Alignment explanation
Indices: 20329211--20329266 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
20329201 AACTTGATCA
* *
20329211 AATCAAAATTTTATGTATAAAGTTACAC
1 AATCAAAATATTACGTATAAAGTTACAC
20329239 AATCAAAA-ATTACGTATACAA-TTACAC
1 AATCAAAATATTACGTATA-AAGTTACAC
20329266 A
1 A
20329267 TTAAATCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.30
Consensus pattern (28 bp):
AATCAAAATATTACGTATAAAGTTACAC
Found at i:20331717 original size:2 final size:2
Alignment explanation
Indices: 20331710--20331739 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20331700 ACATTATACA
20331710 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
20331740 CTTCTAACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20342997 original size:13 final size:13
Alignment explanation
Indices: 20342976--20343013 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
20342966 ACACTCAAAT
*
20342976 TTCTGAAAAGCAC
1 TTCTCAAAAGCAC
20342989 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
20343002 TTCTCAAAAGCA
1 TTCTCAAAAGCA
20343014 ATGAAGAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:20345527 original size:20 final size:21
Alignment explanation
Indices: 20345490--20345547 Score: 91
Period size: 20 Copynumber: 2.8 Consensus size: 21
20345480 CGTGTTTTAC
20345490 TTTTTGTTCAGCTCTTATGAG
1 TTTTTGTTCAGCTCTTATGAG
20345511 TTTTTGTTCAGCT-TTATGAG
1 TTTTTGTTCAGCTCTTATGAG
* *
20345531 CTTCTGTTCAGCTCTTA
1 TTTTTGTTCAGCTCTTA
20345548 CAAGCTTCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.14, C:0.17, G:0.17, T:0.52
Consensus pattern (21 bp):
TTTTTGTTCAGCTCTTATGAG
Found at i:20345555 original size:21 final size:21
Alignment explanation
Indices: 20345494--20345559 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
20345484 TTTTACTTTT
* *
20345494 TGTTCAGCTCTTATGAGTTTT
1 TGTTCAGCTCTTATGAGCTTC
20345515 TGTTCAGCT-TTATGAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
**
20345535 TGTTCAGCTCTTACAAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
20345556 TGTT
1 TGTT
20345560 GGTGTATTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 18 0.45
21 22 0.55
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TGTTCAGCTCTTATGAGCTTC
Found at i:20345779 original size:20 final size:21
Alignment explanation
Indices: 20345736--20345781 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
20345726 GAATTTATGG
*
20345736 ATGATAGGAAATTGTCAGTGA
1 ATGATAGGAAATTGACAGTGA
*
20345757 ATGATAGGGAATTGACA-TGA
1 ATGATAGGAAATTGACAGTGA
20345777 ATGAT
1 ATGAT
20345782 TTTATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.39, C:0.04, G:0.28, T:0.28
Consensus pattern (21 bp):
ATGATAGGAAATTGACAGTGA
Found at i:20353924 original size:12 final size:12
Alignment explanation
Indices: 20353907--20353934 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
20353897 ATTTTTTAAA
20353907 AAATATAATAAT
1 AAATATAATAAT
20353919 AAATATAATAAT
1 AAATATAATAAT
20353931 AAAT
1 AAAT
20353935 TTAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATATAATAAT
Found at i:20358428 original size:26 final size:26
Alignment explanation
Indices: 20358370--20358422 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
20358360 CAGTAACGGA
*
20358370 AAGCTCACAAAGAACCTTTAATCGAG
1 AAGCTCACAAAGAACCTATAATCGAG
*
20358396 AAGCTCACAAAGAGCCATATAA-CGAG
1 AAGCTCACAAAGAACC-TATAATCGAG
20358422 A
1 A
20358423 CACTCATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (26 bp):
AAGCTCACAAAGAACCTATAATCGAG
Found at i:20359587 original size:41 final size:40
Alignment explanation
Indices: 20359455--20359588 Score: 109
Period size: 37 Copynumber: 3.4 Consensus size: 40
20359445 ACCAGTTTGG
* *
20359455 CACCCAATGCCTCATC-AGA-TAATTCGAAATAATAATTTGA
1 CACCCAATGCCTCATCGA-ATTAATTCG-AATAGTAAATTGA
* * * *
20359495 CACCCAGTGTCTCATCG-ATTAA-ACTG-A-AGTAAATTGG
1 CACCCAATGCCTCATCGAATTAATTC-GAATAGTAAATTGA
* *
20359532 CACCCAGTACCTCATCGAATTAATTCGAAGTAGTAAATTGA
1 CACCCAATGCCTCATCGAATTAATTCGAA-TAGTAAATTGA
*
20359573 CACCCAATGTCTCATC
1 CACCCAATGCCTCATC
20359589 AACTCGAAGT
Statistics
Matches: 73, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
37 22 0.30
38 7 0.10
39 4 0.05
40 18 0.25
41 22 0.30
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (40 bp):
CACCCAATGCCTCATCGAATTAATTCGAATAGTAAATTGA
Found at i:20360940 original size:21 final size:22
Alignment explanation
Indices: 20360905--20360945 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
20360895 GCTTTGCGTC
20360905 TTTCTTTCTCTTTCTCTTTTTT
1 TTTCTTTCTCTTTCTCTTTTTT
*
20360927 TTTCTTTC-CTTTCTGTTTT
1 TTTCTTTCTCTTTCTCTTTT
20360946 CGTTTGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTCTTTCTCTTTCTCTTTTTT
Found at i:20360945 original size:16 final size:16
Alignment explanation
Indices: 20360903--20360946 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
20360893 TAGCTTTGCG
*
20360903 TCTTTCTTTCTCTTTC
1 TCTTTCTTTTTCTTTC
*
20360919 TCTTTTTTTTTCTTTC
1 TCTTTCTTTTTCTTTC
20360935 -CTTTCTGTTTTC
1 TCTTTCT-TTTTC
20360947 GTTTGGCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (16 bp):
TCTTTCTTTTTCTTTC
Found at i:20365290 original size:25 final size:26
Alignment explanation
Indices: 20365256--20365327 Score: 94
Period size: 25 Copynumber: 2.8 Consensus size: 26
20365246 CACACCACAA
* *
20365256 CTCTTATGAGCATCCCGATAT-TTGG
1 CTCTTATGAGCTTCCCGATATAATGG
* *
20365281 CTCTCATGAGCTTCTCGAT-TAATGG
1 CTCTTATGAGCTTCCCGATATAATGG
20365306 CTCTTATGAGCTTCCCGATATA
1 CTCTTATGAGCTTCCCGATATA
20365328 CAGCTCGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
24 1 0.03
25 36 0.92
26 2 0.05
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (26 bp):
CTCTTATGAGCTTCCCGATATAATGG
Found at i:20365333 original size:25 final size:25
Alignment explanation
Indices: 20365256--20365372 Score: 87
Period size: 25 Copynumber: 4.7 Consensus size: 25
20365246 CACACCACAA
* * ***
20365256 CTCTTATGAGCATCCCGATATTTGG
1 CTCTCATGAGCTTCCCGATATACAG
*
20365281 CTCTCATGAGCTTCTCGAT-TA-ATGG
1 CTCTCATGAGCTTCCCGATATACA--G
*
20365306 CTCTTATGAGCTTCCCGATATACAG
1 CTCTCATGAGCTTCCCGATATACAG
* * *
20365331 CTC-GATTGAGCTTCCTGTTATACAG
1 CTCTCA-TGAGCTTCCCGATATACAG
*
20365356 CTCACATGAGCTTCCCG
1 CTCTCATGAGCTTCCCG
20365373 TTACATGGCT
Statistics
Matches: 74, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
24 2 0.03
25 68 0.92
26 3 0.04
27 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (25 bp):
CTCTCATGAGCTTCCCGATATACAG
Found at i:20365383 original size:25 final size:26
Alignment explanation
Indices: 20365261--20365405 Score: 81
Period size: 25 Copynumber: 5.8 Consensus size: 26
20365251 CACAACTCTT
* ** *
20365261 ATGAGCATCCCGA-TATTTGGCTCTC
1 ATGAGCTTCCCGATTACATGGCTCAC
* **
20365286 ATGAGCTTCTCGATTA-ATGGCTCTT
1 ATGAGCTTCCCGATTACATGGCTCAC
20365311 ATGAGCTTCCCGATATACA--GCTCGA-
1 ATGAGCTTCCCGAT-TACATGGCTC-AC
* * *
20365336 TTGAGCTTCCTGTTATACA--GCTCAC
1 ATGAGCTTCCCGAT-TACATGGCTCAC
*
20365361 ATGAGCTTCCCG-TTACATGGCTCAA
1 ATGAGCTTCCCGATTACATGGCTCAC
* * *
20365386 AAGAGTTTCCCGTTTACATG
1 ATGAGCTTCCCGATTACATG
20365406 CTCGTATAAG
Statistics
Matches: 98, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
23 4 0.04
24 2 0.02
25 80 0.82
26 11 0.11
27 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (26 bp):
ATGAGCTTCCCGATTACATGGCTCAC
Found at i:20367509 original size:20 final size:21
Alignment explanation
Indices: 20367465--20367509 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
20367455 GAAAACAGGG
20367465 GAAAAAGGAAAGAAAAAGAAA
1 GAAAAAGGAAAGAAAAAGAAA
* *
20367486 -AAAAAGGGAAG-GAAAGAAA
1 GAAAAAGGAAAGAAAAAGAAA
20367505 GAAAA
1 GAAAA
20367510 TTTGGGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (21 bp):
GAAAAAGGAAAGAAAAAGAAA
Found at i:20368309 original size:25 final size:25
Alignment explanation
Indices: 20368258--20368313 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
20368248 AGTTTAGCGC
* * ***
20368258 GCTCTCTTATTATTAGCACGTTGGT
1 GCTCTCTGATTACTAGCACGACAGT
20368283 GCTCTCTGATTACTAGCACGACAGT
1 GCTCTCTGATTACTAGCACGACAGT
20368308 GCTCTC
1 GCTCTC
20368314 CGTTTAGCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.36
Consensus pattern (25 bp):
GCTCTCTGATTACTAGCACGACAGT
Found at i:20369525 original size:13 final size:13
Alignment explanation
Indices: 20369502--20369535 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
20369492 TTTATTTTCT
20369502 AATAT-AATATTA
1 AATATAAATATTA
20369514 AATATAAATATTA
1 AATATAAATATTA
20369527 AATATAAAT
1 AATATAAAT
20369536 GCAATATCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATAAATATTA
Found at i:20378943 original size:3 final size:3
Alignment explanation
Indices: 20378935--20378966 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
20378925 TTTCAGTTTT
*
20378935 TTC TTC TTC CTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
20378967 GTCACTCACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:20379546 original size:40 final size:40
Alignment explanation
Indices: 20379491--20379569 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
20379481 GTTCCAAAAA
20379491 TACATAGCATATTGACATGTGATTTTGCAATTTCTAAATG
1 TACATAGCATATTGACATGTGATTTTGCAATTTCTAAATG
*
20379531 TACATAGCATATTGACATGTTATTTTGCAATTTCTAAAT
1 TACATAGCATATTGACATGTGATTTTGCAATTTCTAAAT
20379570 TGTAGGATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (40 bp):
TACATAGCATATTGACATGTGATTTTGCAATTTCTAAATG
Found at i:20382820 original size:20 final size:20
Alignment explanation
Indices: 20382795--20382835 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20382785 ATTCATTGAC
20382795 CCAAATGTTGATTTTTGAGG
1 CCAAATGTTGATTTTTGAGG
20382815 CCAAATGTTGATTTTTGAGG
1 CCAAATGTTGATTTTTGAGG
20382835 C
1 C
20382836 TTATGATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (20 bp):
CCAAATGTTGATTTTTGAGG
Found at i:20384020 original size:3 final size:3
Alignment explanation
Indices: 20384012--20384046 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
20384002 TTTTATAGAA
20384012 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
20384047 AAAGGGGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:20386464 original size:10 final size:10
Alignment explanation
Indices: 20386428--20386456 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
20386418 GTATAATTAA
20386428 AATA-TTTTT
1 AATATTTTTT
20386437 AATATTTTTT
1 AATATTTTTT
20386447 AATATTTTTT
1 AATATTTTTT
20386457 GAATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
AATATTTTTT
Found at i:20395919 original size:5 final size:5
Alignment explanation
Indices: 20395909--20395942 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
20395899 TTGACAAAAC
20395909 CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT CTCT
1 CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT CTCT
20395943 GCTTTTCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (5 bp):
CTCTT
Found at i:20395950 original size:15 final size:15
Alignment explanation
Indices: 20395909--20395950 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
20395899 TTGACAAAAC
*
20395909 CTCTTCTCTTCTCTT
1 CTCTGCTCTTCTCTT
*
20395924 CTCTTCTCTTCTCTT
1 CTCTGCTCTTCTCTT
*
20395939 CTCTGCTTTTCT
1 CTCTGCTCTTCT
20395951 TACTTTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.00, C:0.38, G:0.02, T:0.60
Consensus pattern (15 bp):
CTCTGCTCTTCTCTT
Found at i:20406106 original size:15 final size:16
Alignment explanation
Indices: 20406088--20406125 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
20406078 ATTCCCAGCC
20406088 ATCATATTCCA-TCGA
1 ATCATATTCCATTCGA
* *
20406103 ATCACATTCCATTGGA
1 ATCATATTCCATTCGA
20406119 ATCATAT
1 ATCATAT
20406126 CATGGAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (16 bp):
ATCATATTCCATTCGA
Found at i:20407319 original size:6 final size:6
Alignment explanation
Indices: 20407278--20407319 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
20407268 ATGTTGATTA
* * *
20407278 GGTTTG GGTTTG GGTTTG GGTTTT GGTTTT GGTTTT GGTTTT
1 GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT
20407320 ATCACAGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.40, T:0.60
Consensus pattern (6 bp):
GGTTTT
Found at i:20407319 original size:12 final size:12
Alignment explanation
Indices: 20407278--20407318 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
20407268 ATGTTGATTA
*
20407278 GGTTTGGGTTTG
1 GGTTTGGGTTTT
20407290 GGTTTGGGTTTT
1 GGTTTGGGTTTT
*
20407302 GGTTTTGGTTTT
1 GGTTTGGGTTTT
20407314 GGTTT
1 GGTTT
20407319 TATCACAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.41, T:0.59
Consensus pattern (12 bp):
GGTTTGGGTTTT
Found at i:20426989 original size:45 final size:45
Alignment explanation
Indices: 20426935--20427068 Score: 213
Period size: 44 Copynumber: 3.0 Consensus size: 45
20426925 ATCCCGTCTT
*
20426935 TGTAA-CTTAACCATGA-TTACGTAACAACTAACGGAGCCCATTAC
1 TGTAATCTTAACCGT-ATTTACGTAACAACTAACGGAGCCCATTAC
20426979 TGTAATCTTAACCGTATTTACGT-ACAACTAACGGAGCCCATTAC
1 TGTAATCTTAACCGTATTTACGTAACAACTAACGGAGCCCATTAC
*
20427023 TGTAATCTCAACCGTATTTACGTAA-AACTAACGGAGCCCATTAC
1 TGTAATCTTAACCGTATTTACGTAACAACTAACGGAGCCCATTAC
20427067 TG
1 TG
20427069 ATTTTAACAG
Statistics
Matches: 85, Mismatches: 2, Indels: 6
0.91 0.02 0.06
Matches are distributed among these distances:
44 70 0.82
45 15 0.18
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.28
Consensus pattern (45 bp):
TGTAATCTTAACCGTATTTACGTAACAACTAACGGAGCCCATTAC
Found at i:20438971 original size:31 final size:31
Alignment explanation
Indices: 20438936--20439010 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
20438926 AACAAAATTA
** *
20438936 AATAGTTGAATGATCAAAGTAGAAATTTACT
1 AATAGTTGAATGATCAAAAAAGAAACTTACT
*
20438967 AATAGTT-AGATAATCAAAAAAGAAACTTACT
1 AATAGTTGA-ATGATCAAAAAAGAAACTTACT
* *
20438998 AATAATTGGATGA
1 AATAGTTGAATGA
20439011 CTACTAATGC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (31 bp):
AATAGTTGAATGATCAAAAAAGAAACTTACT
Found at i:20449894 original size:29 final size:30
Alignment explanation
Indices: 20449841--20449899 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
20449831 TACGTTGACA
*
20449841 TAATATAGAAACAAATAATTATA-TTATTT
1 TAATATAAAAACAAATAATTATATTTATTT
*
20449870 TAATATAAAAATAAATAAATT-TATTTATTT
1 TAATATAAAAACAAAT-AATTATATTTATTT
20449900 AAACATGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (30 bp):
TAATATAAAAACAAATAATTATATTTATTT
Found at i:20460112 original size:66 final size:66
Alignment explanation
Indices: 20460006--20460146 Score: 282
Period size: 66 Copynumber: 2.1 Consensus size: 66
20459996 AATAATATAG
20460006 AGTAAGCATATTATGCTTAGTAAGTTCGTATAATGGGAAAGTAACTTACCATTCATTTATATTTA
1 AGTAAGCATATTATGCTTAGTAAGTTCGTATAATGGGAAAGTAACTTACCATTCATTTATATTTA
20460071 A
66 A
20460072 AGTAAGCATATTATGCTTAGTAAGTTCGTATAATGGGAAAGTAACTTACCATTCATTTATATTTA
1 AGTAAGCATATTATGCTTAGTAAGTTCGTATAATGGGAAAGTAACTTACCATTCATTTATATTTA
20460137 A
66 A
20460138 AGTAAGCAT
1 AGTAAGCAT
20460147 GCAAAATTCA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 75 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (66 bp):
AGTAAGCATATTATGCTTAGTAAGTTCGTATAATGGGAAAGTAACTTACCATTCATTTATATTTA
A
Found at i:20460716 original size:26 final size:26
Alignment explanation
Indices: 20460687--20460736 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
20460677 TGAGAGCCAC
*
20460687 TAATTAGGAAGCTCACAAAGAGCCTT
1 TAATCAGGAAGCTCACAAAGAGCCTT
* * *
20460713 TAATCGGGAAGTTCACGAAGAGCC
1 TAATCAGGAAGCTCACAAAGAGCC
20460737 ATATAACGGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (26 bp):
TAATCAGGAAGCTCACAAAGAGCCTT
Found at i:20460746 original size:26 final size:26
Alignment explanation
Indices: 20460693--20460753 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
20460683 CCACTAATTA
*
20460693 GGAAGCTCACAAAGAGCCTTTAATCG
1 GGAAGCTCACAAAGAGCCTATAATCG
* *
20460719 GGAAGTTCACGAAGAGCCATATAA-CG
1 GGAAGCTCACAAAGAGCC-TATAATCG
*
20460745 GGATGCTCA
1 GGAAGCTCA
20460754 TAAGAGCTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.18
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCTATAATCG
Found at i:20471098 original size:13 final size:13
Alignment explanation
Indices: 20471065--20471091 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20471055 CCAGTCAATC
20471065 ATTCAAAGCATAA
1 ATTCAAAGCATAA
20471078 ATTCAAAGCATAA
1 ATTCAAAGCATAA
20471091 A
1 A
20471092 GTTAAAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (13 bp):
ATTCAAAGCATAA
Found at i:20481867 original size:13 final size:13
Alignment explanation
Indices: 20481849--20481900 Score: 59
Period size: 13 Copynumber: 3.7 Consensus size: 13
20481839 AATGACTCGC
20481849 GACCGTGTGGCAT
1 GACCGTGTGGCAT
*
20481862 GACCGTGTGTGTCACGC
1 GACCGTGTG-G-CA--T
20481879 GACCGTGTGGCAT
1 GACCGTGTGGCAT
20481892 GACCGTGTG
1 GACCGTGTG
20481901 TGTCACACGA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 18 0.55
14 1 0.03
15 4 0.12
16 1 0.03
17 9 0.27
ACGTcount: A:0.13, C:0.25, G:0.38, T:0.23
Consensus pattern (13 bp):
GACCGTGTGGCAT
Found at i:20481882 original size:17 final size:16
Alignment explanation
Indices: 20481862--20481917 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
20481852 CGTGTGGCAT
20481862 GACCGTGTGTGTCACGC
1 GACCGTGTGTGTCAC-C
*
20481879 GACCGTGTG-G-CA-T
1 GACCGTGTGTGTCACC
20481892 GACCGTGTGTGTCACAC
1 GACCGTGTGTGTCAC-C
20481909 GACCGTGTG
1 GACCGTGTG
20481918 ACAGCCCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 9 0.27
14 1 0.03
15 4 0.12
16 1 0.03
17 18 0.55
ACGTcount: A:0.14, C:0.27, G:0.36, T:0.23
Consensus pattern (16 bp):
GACCGTGTGTGTCACC
Found at i:20481882 original size:30 final size:30
Alignment explanation
Indices: 20481846--20481917 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
20481836 CAAAATGACT
20481846 CGCGACCGTGTGGCATGACCGTGTGTGTCA
1 CGCGACCGTGTGGCATGACCGTGTGTGTCA
20481876 CGCGACCGTGTGGCATGACCGTGTGTGTCA
1 CGCGACCGTGTGGCATGACCGTGTGTGTCA
*
20481906 CACGACCGTGTG
1 CGCGACCGTGTG
20481918 ACAGCCCATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.14, C:0.28, G:0.36, T:0.22
Consensus pattern (30 bp):
CGCGACCGTGTGGCATGACCGTGTGTGTCA
Found at i:20487338 original size:2 final size:2
Alignment explanation
Indices: 20487331--20487378 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
20487321 CTCCCCACTT
20487331 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
20487373 TC TC TC
1 TC TC TC
20487379 GCTGCGTGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:20512623 original size:2 final size:2
Alignment explanation
Indices: 20512616--20512643 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20512606 TACGAATGAA
20512616 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
20512644 CTCATATCAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20518613 original size:11 final size:11
Alignment explanation
Indices: 20518583--20518616 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
20518573 AAACTAATCA
20518583 TCTCTCAATTAT
1 TCTCTCAATT-T
*
20518595 TTTCTCAATTT
1 TCTCTCAATTT
20518606 TCTCTCAATTT
1 TCTCTCAATTT
20518617 CATCTGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.56
Consensus pattern (11 bp):
TCTCTCAATTT
Found at i:20518692 original size:51 final size:51
Alignment explanation
Indices: 20518613--20518718 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 51
20518603 TTTTCTCTCA
* * *
20518613 ATTTCATCTGAATTTACTTTCAAATTCCT-TCCAAATTTCTCTCAAATCCAT
1 ATTTAATCTCAATTTACTCTCAAATTCCTCT-CAAATTTCTCTCAAATCCAT
* * * * *
20518664 ATTTAATCTCAATTTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCT
1 ATTTAATCTCAATTTACTCTCAAATTCCTCTCAAATTTCTCTCAAATCCAT
20518715 ATTT
1 ATTT
20518719 TTAAATAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 45 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.02, T:0.46
Consensus pattern (51 bp):
ATTTAATCTCAATTTACTCTCAAATTCCTCTCAAATTTCTCTCAAATCCAT
Found at i:20521009 original size:522 final size:522
Alignment explanation
Indices: 20520025--20521068 Score: 2088
Period size: 522 Copynumber: 2.0 Consensus size: 522
20520015 AAATTCTAAC
20520025 GCACCATCTGCAGACAGATCGACATTATGCATGTGGGCTGGAGGTGAGTATGCTCTAAATCGTAG
1 GCACCATCTGCAGACAGATCGACATTATGCATGTGGGCTGGAGGTGAGTATGCTCTAAATCGTAG
20520090 ATTTTCTTCTTCATCTGAACTCCTTTCAGCATCATCAAGTTCTGTTGGAATAGGCTCCGGTTCAG
66 ATTTTCTTCTTCATCTGAACTCCTTTCAGCATCATCAAGTTCTGTTGGAATAGGCTCCGGTTCAG
20520155 AAAATAAGCCAACTTCTGCACCATCGGGCCCGGGCTCTCGAGGTGGATCCACATCGGAGTCATCT
131 AAAATAAGCCAACTTCTGCACCATCGGGCCCGGGCTCTCGAGGTGGATCCACATCGGAGTCATCT
20520220 TCTAACCCACAATCATCTACAGCGTACGAGGTCCTCTTGCCGGTGGATGTCGTAAGGAGTACATC
196 TCTAACCCACAATCATCTACAGCGTACGAGGTCCTCTTGCCGGTGGATGTCGTAAGGAGTACATC
20520285 ATCCCTTCTTCTGGACATTTCATAACGTCCCCAATTGGATGTAGATTGCCAACCACTAGAACTTG
261 ATCCCTTCTTCTGGACATTTCATAACGTCCCCAATTGGATGTAGATTGCCAACCACTAGAACTTG
20520350 ATGTCGTTCTCCAGTACGTATTTCCAGCATCAAACATCGAGCCACCGACGTACATGTCCCATCCA
326 ATGTCGTTCTCCAGTACGTATTTCCAGCATCAAACATCGAGCCACCGACGTACATGTCCCATCCA
20520415 CTGATAGAATGTTTTGCAGGGGATGTGCATTCCACACCGCTACCAAACATGGGTTGTTCCGTGTT
391 CTGATAGAATGTTTTGCAGGGGATGTGCATTCCACACCGCTACCAAACATGGGTTGTTCCGTGTT
20520480 TTGTAACCCGCTAACCGAGTGTCGGTCAGGGGTCGTGTATACATCTCGAACACTGGTCACAAGTA
456 TTGTAACCCGCTAACCGAGTGTCGGTCAGGGGTCGTGTATACATCTCGAACACTGGTCACAAGTA
20520545 CA
521 CA
20520547 GCACCATCTGCAGACAGATCGACATTATGCATGTGGGCTGGAGGTGAGTATGCTCTAAATCGTAG
1 GCACCATCTGCAGACAGATCGACATTATGCATGTGGGCTGGAGGTGAGTATGCTCTAAATCGTAG
20520612 ATTTTCTTCTTCATCTGAACTCCTTTCAGCATCATCAAGTTCTGTTGGAATAGGCTCCGGTTCAG
66 ATTTTCTTCTTCATCTGAACTCCTTTCAGCATCATCAAGTTCTGTTGGAATAGGCTCCGGTTCAG
20520677 AAAATAAGCCAACTTCTGCACCATCGGGCCCGGGCTCTCGAGGTGGATCCACATCGGAGTCATCT
131 AAAATAAGCCAACTTCTGCACCATCGGGCCCGGGCTCTCGAGGTGGATCCACATCGGAGTCATCT
20520742 TCTAACCCACAATCATCTACAGCGTACGAGGTCCTCTTGCCGGTGGATGTCGTAAGGAGTACATC
196 TCTAACCCACAATCATCTACAGCGTACGAGGTCCTCTTGCCGGTGGATGTCGTAAGGAGTACATC
20520807 ATCCCTTCTTCTGGACATTTCATAACGTCCCCAATTGGATGTAGATTGCCAACCACTAGAACTTG
261 ATCCCTTCTTCTGGACATTTCATAACGTCCCCAATTGGATGTAGATTGCCAACCACTAGAACTTG
20520872 ATGTCGTTCTCCAGTACGTATTTCCAGCATCAAACATCGAGCCACCGACGTACATGTCCCATCCA
326 ATGTCGTTCTCCAGTACGTATTTCCAGCATCAAACATCGAGCCACCGACGTACATGTCCCATCCA
20520937 CTGATAGAATGTTTTGCAGGGGATGTGCATTCCACACCGCTACCAAACATGGGTTGTTCCGTGTT
391 CTGATAGAATGTTTTGCAGGGGATGTGCATTCCACACCGCTACCAAACATGGGTTGTTCCGTGTT
20521002 TTGTAACCCGCTAACCGAGTGTCGGTCAGGGGTCGTGTATACATCTCGAACACTGGTCACAAGTA
456 TTGTAACCCGCTAACCGAGTGTCGGTCAGGGGTCGTGTATACATCTCGAACACTGGTCACAAGTA
20521067 CA
521 CA
20521069 TCATTTGGCG
Statistics
Matches: 522, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
522 522 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.27
Consensus pattern (522 bp):
GCACCATCTGCAGACAGATCGACATTATGCATGTGGGCTGGAGGTGAGTATGCTCTAAATCGTAG
ATTTTCTTCTTCATCTGAACTCCTTTCAGCATCATCAAGTTCTGTTGGAATAGGCTCCGGTTCAG
AAAATAAGCCAACTTCTGCACCATCGGGCCCGGGCTCTCGAGGTGGATCCACATCGGAGTCATCT
TCTAACCCACAATCATCTACAGCGTACGAGGTCCTCTTGCCGGTGGATGTCGTAAGGAGTACATC
ATCCCTTCTTCTGGACATTTCATAACGTCCCCAATTGGATGTAGATTGCCAACCACTAGAACTTG
ATGTCGTTCTCCAGTACGTATTTCCAGCATCAAACATCGAGCCACCGACGTACATGTCCCATCCA
CTGATAGAATGTTTTGCAGGGGATGTGCATTCCACACCGCTACCAAACATGGGTTGTTCCGTGTT
TTGTAACCCGCTAACCGAGTGTCGGTCAGGGGTCGTGTATACATCTCGAACACTGGTCACAAGTA
CA
Found at i:20523177 original size:45 final size:46
Alignment explanation
Indices: 20523075--20523179 Score: 140
Period size: 46 Copynumber: 2.3 Consensus size: 46
20523065 ATGTGCCGAC
* ** * *
20523075 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAAATACTGT
1 TACTGTTACTGTTACAGATTCAACACTTTGCGTGTCGAAATACAGT
* *
20523121 TACCGTTACTGTTACAGATTCAACACTTTGCGTGTTG-AATACAGT
1 TACTGTTACTGTTACAGATTCAACACTTTGCGTGTCGAAATACAGT
20523166 TACTGTTACTGTTA
1 TACTGTTACTGTTA
20523180 TTGCTACCGT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 20 0.39
46 31 0.61
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (46 bp):
TACTGTTACTGTTACAGATTCAACACTTTGCGTGTCGAAATACAGT
Found at i:20523294 original size:19 final size:19
Alignment explanation
Indices: 20523266--20523306 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
20523256 ATAGGGGCAA
20523266 ATAAAATAAATTGACTGAT
1 ATAAAATAAATTGACTGAT
* *
20523285 ATAAATTAAATTGAGTGAT
1 ATAAAATAAATTGACTGAT
20523304 ATA
1 ATA
20523307 GTATATGTGA
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:0.51, C:0.02, G:0.12, T:0.34
Consensus pattern (19 bp):
ATAAAATAAATTGACTGAT
Found at i:20524422 original size:125 final size:126
Alignment explanation
Indices: 20524224--20524692 Score: 685
Period size: 125 Copynumber: 3.7 Consensus size: 126
20524214 TACTATTTGC
* * * *
20524224 TCAACTTGAAATTATTTTTTTCAGGACCTACTGTAGCAAAAGCGCGTCCACGACGGCGCGATTTC
1 TCAACTCGAAATTATTTTTTGCAGGACCTACTGTAGCAAAAGCGCGTACACGAGGGCGCGATTTC
* * *
20524289 ACAAATTCTTCTCATAAAGTATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACA
66 ACAAATTCTTCTAATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACG
* * *
20524350 TCAACTCGAGATTA-TTTTTGCATGACCTACTGTAGCAAAAGTGCGTACAC-ATGGGCGCGATTT
1 TCAACTCGAAATTATTTTTTGCAGGACCTACTGTAGCAAAAGCGCGTACACGA-GGGCGCGATTT
*
20524413 CACAAATTCTTCTAATAAAGCATCCTGCTTGAAGC-ATTTTTATACTATTTGCTCAGAAACG
65 CACAAATTCTTCTAATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACG
* * * *
20524474 TCAACTCGAAATTATTTTTTCCAGGACCTACTGTAGCAAAAGTGCGTCCACGAGCGCGCGATTTC
1 TCAACTCGAAATTATTTTTTGCAGGACCTACTGTAGCAAAAGCGCGTACACGAGGGCGCGATTTC
* * * *
20524539 ACAAATTCTTTTTATAAAGTATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAAAAACG
66 ACAAATTCTTCTAATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACG
* *
20524600 TCAACTCGAAATTA-TTTTTGCAGGACCTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTC
1 TCAACTCGAAATTATTTTTTGCAGGACCTACTGTAGCAAAAGCGCGTACACGAGGGCGCGATTTC
* * *
20524664 AGAAATTCTTCTGATAAACCATCCTGCTT
66 ACAAATTCTTCTAATAAAGCATCCTGCTT
20524693 TGATTTTATC
Statistics
Matches: 307, Mismatches: 32, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
124 38 0.12
125 218 0.71
126 51 0.17
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (126 bp):
TCAACTCGAAATTATTTTTTGCAGGACCTACTGTAGCAAAAGCGCGTACACGAGGGCGCGATTTC
ACAAATTCTTCTAATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACG
Found at i:20524567 original size:250 final size:241
Alignment explanation
Indices: 20524135--20524692 Score: 857
Period size: 250 Copynumber: 2.3 Consensus size: 241
20524125 GGGTGTTACA
* * *
20524135 CTACTGTAGCAAAAGCGCGTTCACGTGGGCACGATTTTACAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
* *
20524200 TTGAAGCGTTTTTATACTATTTGCTCAACTTGAAATTATTTTTTTCAGGACCTACTGTAGCAAAA
66 TTGAAGCATTTTTATACTATTTGCTCAACTTGAAATTATTTTTTCCAGGACCTACTGTAGCAAAA
20524265 GCGCGTCCACGACGGCGCGATTTCACAAATTCTTCTCATAAAGTATCCTGCTTGAAGCGTTTTTT
131 GCGCGTCCACGACGGCGCGATTTCACAAATTCTTCTCATAAAGTATCCTGCTTGAAGCGTTTTTT
* * *
20524330 ATACTATTTGCTCAGAAACATCAACTCGAGATTATTTTTGCATGAC
196 ATACTATTTGCTCAAAAACATCAACTCGAAATTATTTTTGCAGGAC
* * *
20524376 CTACTGTAGCAAAAGTGCGTACACATGGGCGCGATTTCACAAATTCTTCTAATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
20524441 TTGAAGCATTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCCAGGACCTACT
66 TTGAAGCATTTTTATACTATTTGCTC---AAC-T----T-GAAATTATTTTTTCCAGGACCTACT
* * *
20524506 GTAGCAAAAGTGCGTCCACGA-GCGCGCGATTTCACAAATTCTTTTTATAAAGTATCCTGCTTGA
122 GTAGCAAAAGCGCGTCCACGACG-GCGCGATTTCACAAATTCTTCTCATAAAGTATCCTGCTTGA
*
20524570 AGCGTTTTTTATACTATTTGCTCAAAAACGTCAACTCGAAATTATTTTTGCAGGAC
186 AGCGTTTTTTATACTATTTGCTCAAAAACATCAACTCGAAATTATTTTTGCAGGAC
* * *
20524626 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCAGAAATTCTTCTGATAAACCATCCTGC
1 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
20524691 TT
66 TT
20524693 TGATTTTATC
Statistics
Matches: 286, Mismatches: 21, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
241 84 0.29
244 3 0.01
245 1 0.00
249 2 0.01
250 196 0.69
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (241 bp):
CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCATTTTTATACTATTTGCTCAACTTGAAATTATTTTTTCCAGGACCTACTGTAGCAAAA
GCGCGTCCACGACGGCGCGATTTCACAAATTCTTCTCATAAAGTATCCTGCTTGAAGCGTTTTTT
ATACTATTTGCTCAAAAACATCAACTCGAAATTATTTTTGCAGGAC
Found at i:20525233 original size:6 final size:6
Alignment explanation
Indices: 20525222--20525249 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20525212 ATATTGGGTT
20525222 CAATCA CAATCA CAATCA CAATCA CAAT
1 CAATCA CAATCA CAATCA CAATCA CAAT
20525250 ATTGTCTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (6 bp):
CAATCA
Found at i:20540371 original size:21 final size:21
Alignment explanation
Indices: 20540345--20540502 Score: 77
Period size: 21 Copynumber: 7.5 Consensus size: 21
20540335 TGTGTTTACT
*
20540345 TTCTGTTTAGCTCTCATGAGC
1 TTCTGTTCAGCTCTCATGAGC
* *
20540366 TTCTGTTCAACTCAT-ATGAGT
1 TTCTGTTCAGCTC-TCATGAGC
** * **
20540387 TTCCATTCAGCTATTTTGAGC
1 TTCTGTTCAGCTCTCATGAGC
* * * * *
20540408 TTCTGTTTAACCCTCGTGAGT
1 TTCTGTTCAGCTCTCATGAGC
* * *
20540429 TTCCGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTCATGAGC
* * * * *
20540450 TTCAGTTCAACCCTTATTG-GT
1 TTCTGTTCAGCTCTCA-TGAGC
* *
20540471 TTCTGTTTAGCTCACATGAGC
1 TTCTGTTCAGCTCTCATGAGC
20540492 TTCTGTTCAGC
1 TTCTGTTCAGC
20540503 CTTTGGGCTT
Statistics
Matches: 94, Mismatches: 39, Indels: 8
0.67 0.28 0.06
Matches are distributed among these distances:
20 3 0.03
21 89 0.95
22 2 0.02
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (21 bp):
TTCTGTTCAGCTCTCATGAGC
Found at i:20540428 original size:42 final size:42
Alignment explanation
Indices: 20540382--20540463 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
20540372 TCAACTCATA
** * *
20540382 TGAGTTTCCATTCAGCTATTTTGAGCTTCTGTTTAACCCTCG
1 TGAGTTTCCATTCAGCTATTACGAGCTTCAGTTCAACCCTCG
* *
20540424 TGAGTTTCCGTTCAGCTCTTACGAGCTTCAGTTCAACCCT
1 TGAGTTTCCATTCAGCTATTACGAGCTTCAGTTCAACCCT
20540464 TATTGGTTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.39
Consensus pattern (42 bp):
TGAGTTTCCATTCAGCTATTACGAGCTTCAGTTCAACCCTCG
Found at i:20540502 original size:63 final size:63
Alignment explanation
Indices: 20540344--20540502 Score: 160
Period size: 63 Copynumber: 2.5 Consensus size: 63
20540334 TTGTGTTTAC
* * * * *
20540344 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCAACTCATATGAGTTTCCATTCAGCTATTTTGAG
1 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCAGCTCATACGAGCTTCCATTCAACCATTTTGAG
* * * * * * * *
20540407 CTTCTGTTTAACCCTCGTGAGTTTCCGTTCAGCTCTTACGAGCTT-CAGTTCAACCCTTATTG-G
1 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCAGCTCATACGAGCTTCCA-TTCAACCATT-TTGAG
*
20540470 TTTCTGTTTAGCTCACATGAGCTTCTGTTCAGC
1 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCAGC
20540503 CTTTGGGCTT
Statistics
Matches: 74, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
62 2 0.03
63 69 0.93
64 3 0.04
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.42
Consensus pattern (63 bp):
TTTCTGTTTAGCTCTCATGAGCTTCTGTTCAGCTCATACGAGCTTCCATTCAACCATTTTGAG
Found at i:20541406 original size:42 final size:42
Alignment explanation
Indices: 20541347--20541428 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
20541337 TCAAAATTGT
* *
20541347 TCACACGACCTGTCACAC-AGGCGTGTGGTTTGGCCGTGTGTC
1 TCACACGACCTGTCACACGA-GCGTGTGGCTTGGCAGTGTGTC
* *
20541389 TCACACGGCCTAG-CACACGAGCTTGTGGCTTGGCAGTGTG
1 TCACACGACCT-GTCACACGAGCGTGTGGCTTGGCAGTGTG
20541429 ACCTAAGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.16, C:0.28, G:0.32, T:0.24
Consensus pattern (42 bp):
TCACACGACCTGTCACACGAGCGTGTGGCTTGGCAGTGTGTC
Found at i:20542239 original size:21 final size:21
Alignment explanation
Indices: 20542196--20542305 Score: 116
Period size: 21 Copynumber: 5.3 Consensus size: 21
20542186 TGAATACGCC
*
20542196 AACAGAAGCTC--AAAAGCTG
1 AACAGAAGCTCATAAAAGCTA
* *
20542215 AATAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCATAAAAGCTA
* *
20542236 AATAGAAGCTCGTAAAAGCTA
1 AACAGAAGCTCATAAAAGCTA
* * * *
20542257 AACAGAAGTTCATAAGAGTTG
1 AACAGAAGCTCATAAAAGCTA
*
20542278 AACAGAAGCTCGTAAAAGCTA
1 AACAGAAGCTCATAAAAGCTA
20542299 AACAGAA
1 AACAGAA
20542306 AGTAAAATAC
Statistics
Matches: 73, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
19 10 0.14
21 63 0.86
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCATAAAAGCTA
Found at i:20542264 original size:42 final size:42
Alignment explanation
Indices: 20542196--20542305 Score: 152
Period size: 42 Copynumber: 2.7 Consensus size: 42
20542186 TGAATACGCC
* *
20542196 AACAGAAGCTC--AAAAGCTGAATAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCGTAAAAGCTAAACAGAAGCTCATAAGAGCTA
* * * *
20542236 AATAGAAGCTCGTAAAAGCTAAACAGAAGTTCATAAGAGTTG
1 AACAGAAGCTCGTAAAAGCTAAACAGAAGCTCATAAGAGCTA
20542278 AACAGAAGCTCGTAAAAGCTAAACAGAA
1 AACAGAAGCTCGTAAAAGCTAAACAGAA
20542306 AGTAAAATAC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 10 0.16
42 51 0.84
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.16
Consensus pattern (42 bp):
AACAGAAGCTCGTAAAAGCTAAACAGAAGCTCATAAGAGCTA
Found at i:20547266 original size:24 final size:24
Alignment explanation
Indices: 20547211--20547288 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
20547201 GAGGATGAGA
* * *
20547211 TGGTGGGTGTGTTGGTGGCTTGGT
1 TGGTGGCTGAGTTGGAGGCTTGGT
* *
20547235 CGGGGGCTGAGTTGGAGGCTTGGT
1 TGGTGGCTGAGTTGGAGGCTTGGT
* * *
20547259 TGGTGGCTTAGTCGGGGGC-TGAGT
1 TGGTGGCTGAGTTGGAGGCTTG-GT
20547283 TGGTGG
1 TGGTGG
20547289 TTTAGGCGGG
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.05, C:0.09, G:0.54, T:0.32
Consensus pattern (24 bp):
TGGTGGCTGAGTTGGAGGCTTGGT
Found at i:20547293 original size:24 final size:24
Alignment explanation
Indices: 20547257--20547338 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
20547247 TGGAGGCTTG
* *
20547257 GTTGGTGGCTTAGTCGGGGGCTGA
1 GTTGGAGGTTTAGTCGGGGGCTGA
* * *
20547281 GTTGGTGGTTTAGGCGGGGGTTGA
1 GTTGGAGGTTTAGTCGGGGGCTGA
* * * *
20547305 GTTGGAGGTTTGGTTGGTGGCTTA
1 GTTGGAGGTTTAGTCGGGGGCTGA
20547329 GTTGGAGGTT
1 GTTGGAGGTT
20547339 GAACTGGTGG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.09, C:0.06, G:0.50, T:0.35
Consensus pattern (24 bp):
GTTGGAGGTTTAGTCGGGGGCTGA
Found at i:20547347 original size:60 final size:60
Alignment explanation
Indices: 20547235--20547384 Score: 169
Period size: 60 Copynumber: 2.5 Consensus size: 60
20547225 GTGGCTTGGT
* **
20547235 CGGGGGCTGAGTTGGAGGCTTGGTTGGTGGCTTAGTCGGGGGCTGAGTTGGTGGTTTAGG
1 CGGGGGCTGAGTTGGAGGCTTGGTTGGTGGCTTAGTCGGAGGCTGAACTGGTGGTTTAGG
* * * * *
20547295 CGGGGGTTGAGTTGGAGGTTTGGTTGGTGGCTTAGTTGGAGGTTGAACTGGTGGCTT-GG
1 CGGGGGCTGAGTTGGAGGCTTGGTTGGTGGCTTAGTCGGAGGCTGAACTGGTGGTTTAGG
* * *
20547354 -GTGGAGCAGAAGTTGGGGGCTTGGTTGGTGG
1 CG-GGGGCTG-AGTTGGAGGCTTGGTTGGTGG
20547385 TTGCACTGGC
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
58 1 0.01
59 6 0.08
60 68 0.91
ACGTcount: A:0.10, C:0.08, G:0.51, T:0.31
Consensus pattern (60 bp):
CGGGGGCTGAGTTGGAGGCTTGGTTGGTGGCTTAGTCGGAGGCTGAACTGGTGGTTTAGG
Found at i:20547358 original size:24 final size:24
Alignment explanation
Indices: 20547319--20547417 Score: 65
Period size: 24 Copynumber: 4.1 Consensus size: 24
20547309 GAGGTTTGGT
* *
20547319 TGGTGGCTTAGTTGGAGGTTGAAC
1 TGGTGGCTTGGGTGGAGGTTGAAC
** *
20547343 TGGTGGCTTGGGTGGA-GCAGAAGT
1 TGGTGGCTTGGGTGGAGGTTGAA-C
* * * *
20547367 TGGGGGCTTGGTTGGTGGTTGCAC
1 TGGTGGCTTGGGTGGAGGTTGAAC
* * * *
20547391 TGGCGCCTTGGGTGGTGGATGAAC
1 TGGTGGCTTGGGTGGAGGTTGAAC
20547415 TGG
1 TGG
20547418 AGGAGGAGTG
Statistics
Matches: 56, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
23 4 0.07
24 49 0.88
25 3 0.05
ACGTcount: A:0.12, C:0.11, G:0.47, T:0.29
Consensus pattern (24 bp):
TGGTGGCTTGGGTGGAGGTTGAAC
Found at i:20547489 original size:12 final size:12
Alignment explanation
Indices: 20547446--20547499 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
20547436 GGGCTTAGTG
*
20547446 GGTGGATGAGGAT
1 GGTGG-TGAGGGT
*
20547459 GGGGGTGAGGGT
1 GGTGGTGAGGGT
20547471 GAG-GGTGAGGGT
1 G-GTGGTGAGGGT
*
20547483 GGTGGTGATGGT
1 GGTGGTGAGGGT
20547495 GGTGG
1 GGTGG
20547500 GTTGGTGGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 1 0.03
12 30 0.83
13 5 0.14
ACGTcount: A:0.13, C:0.00, G:0.65, T:0.22
Consensus pattern (12 bp):
GGTGGTGAGGGT
Found at i:20550456 original size:30 final size:30
Alignment explanation
Indices: 20550420--20550481 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
20550410 CCAAACACTT
20550420 AAGCCCATATAATATATAGTAAAGAATATC
1 AAGCCCATATAATATATAGTAAAGAATATC
20550450 AAGCCCATATAATATATAGTAAAGAATATC
1 AAGCCCATATAATATATAGTAAAGAATATC
20550480 AA
1 AA
20550482 AAAATAGTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.26
Consensus pattern (30 bp):
AAGCCCATATAATATATAGTAAAGAATATC
Found at i:20555674 original size:18 final size:19
Alignment explanation
Indices: 20555632--20555680 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
20555622 TCAAGATCTT
20555632 AAATTAATGTAGTCCAAAG
1 AAATTAATGTAGTCCAAAG
*
20555651 AAATTAATGTGGTCCAAA-
1 AAATTAATGTAGTCCAAAG
20555669 AAATTAAT-TAGT
1 AAATTAATGTAGT
20555681 AAATTTTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 3 0.11
18 8 0.29
19 17 0.61
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (19 bp):
AAATTAATGTAGTCCAAAG
Found at i:20559482 original size:46 final size:46
Alignment explanation
Indices: 20559399--20559628 Score: 372
Period size: 46 Copynumber: 5.0 Consensus size: 46
20559389 ACATAGCTAT
* *
20559399 AACTCAGTATGGTTTTCTTCGCGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
20559445 AACTCAGTATGGTTTTCTTCACTGAAACACCAAACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
*
20559491 AACTCAGTATGGTTTTCTTCACTG-AACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* * *
20559536 AACTCAGTATGGTTTTCTTCGCGGCAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
*
20559582 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
20559628 A
1 A
20559629 CTTTTCCATG
Statistics
Matches: 171, Mismatches: 12, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
45 42 0.25
46 129 0.75
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:20559555 original size:91 final size:92
Alignment explanation
Indices: 20559399--20559628 Score: 372
Period size: 91 Copynumber: 2.5 Consensus size: 92
20559389 ACATAGCTAT
* *
20559399 AACTCAGTATGGTTTTCTTCGCGGAAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTT
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTT
*
20559464 CACTGAAACACCAAACCTACTTTTCAC
66 CACGGAAACACCAAACCTACTTTTCAC
*
20559491 AACTCAGTATGGTTTTCTTCACTG-AACACCATACCTACTTTTCACAACTCAGTATGGTTTTCTT
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTT
* * * *
20559555 CGCGGCAATACCATACCTACTTTTCAC
66 CACGGAAACACCAAACCTACTTTTCAC
*
20559582 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCACA
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACA
20559629 CTTTTCCATG
Statistics
Matches: 127, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
91 85 0.67
92 42 0.33
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.34
Consensus pattern (92 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCACAACTCAGTATGGTTTTCTT
CACGGAAACACCAAACCTACTTTTCAC
Found at i:20560890 original size:16 final size:17
Alignment explanation
Indices: 20560844--20560891 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
20560834 TTATTCTTTT
20560844 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
20560861 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
20560878 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
20560892 TTATAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:20565488 original size:29 final size:29
Alignment explanation
Indices: 20565454--20565511 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
20565444 CGATATTCCC
* *
20565454 TACTCATCATAGCTATATTATTATTCGAT
1 TACTCACCATAGCTATACTATTATTCGAT
20565483 TACTCACCATAGCTATACTATTATTCGAT
1 TACTCACCATAGCTATACTATTATTCGAT
20565512 AGATGTGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (29 bp):
TACTCACCATAGCTATACTATTATTCGAT
Found at i:20574407 original size:2 final size:2
Alignment explanation
Indices: 20574400--20574430 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20574390 AAAACAAAGA
20574400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20574431 CATACTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20583482 original size:31 final size:29
Alignment explanation
Indices: 20583447--20583506 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
20583437 GTGATCACTT
20583447 CGTAACACAATAATAACATAAGTGACTAAAA
1 CGTAACA-AATAA-AACATAAGTGACTAAAA
** *
20583478 CGTAACATTTCAAACATAAGTGACTAAAA
1 CGTAACAAATAAAACATAAGTGACTAAAA
20583507 TATGACCTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 17 0.65
30 2 0.08
31 7 0.27
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.22
Consensus pattern (29 bp):
CGTAACAAATAAAACATAAGTGACTAAAA
Found at i:20585735 original size:13 final size:13
Alignment explanation
Indices: 20585717--20585741 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20585707 GAATTTACTT
20585717 GTGTGAAAATTTC
1 GTGTGAAAATTTC
20585730 GTGTGAAAATTT
1 GTGTGAAAATTT
20585742 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:20586920 original size:41 final size:41
Alignment explanation
Indices: 20586810--20586921 Score: 154
Period size: 41 Copynumber: 2.7 Consensus size: 41
20586800 TTTTGTAAGT
* * *
20586810 TCAGGCTTTATGCCTAACAGAATTTATGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGATTTGTGCCGGTGAATTATA
*
20586851 TCAGGCTTTATGCCTAGCA-GACTCTGTGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGA-TTTGTGCCGGTGAATTATA
* *
20586892 TCAGACTTTATGTCTAGCAGGATTTGTGCC
1 TCAGGCTTTATGCCTAGCAGGATTTGTGCC
20586922 TAGCAGGCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
40 1 0.02
41 59 0.95
42 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGATTTGTGCCGGTGAATTATA
Found at i:20586937 original size:16 final size:16
Alignment explanation
Indices: 20586897--20586937 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
20586887 TTATATCAGA
*
20586897 CTTTATGTCTAGCAGG
1 CTTTATGCCTAGCAGG
* *
20586913 ATTTGTGCCTAGCAGG
1 CTTTATGCCTAGCAGG
20586929 CTTTATGCC
1 CTTTATGCC
20586938 AGTGTTTTAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (16 bp):
CTTTATGCCTAGCAGG
Found at i:20589576 original size:25 final size:26
Alignment explanation
Indices: 20589515--20589596 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 26
20589505 ACTTTAACGC
* ** *
20589515 GCTCTCTAATTATTATTACATC-AGT
1 GCTCTCTAATTACTAGCACGTCTAGT
* * * *
20589540 GCTCTTTGATTATTAGCATGT-TAGT
1 GCTCTCTAATTACTAGCACGTCTAGT
20589565 GCTCTCTAATTACTAGCACGTCT-GT
1 GCTCTCTAATTACTAGCACGTCTAGT
20589590 GCTCTCT
1 GCTCTCT
20589597 GTATAGCACT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
25 44 0.98
26 1 0.02
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.43
Consensus pattern (26 bp):
GCTCTCTAATTACTAGCACGTCTAGT
Found at i:20589613 original size:22 final size:22
Alignment explanation
Indices: 20589578--20589620 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20589568 CTCTAATTAC
*
20589578 TAGCACGTCTGTGCTCTCTGTA
1 TAGCACGTCAGTGCTCTCTGTA
*
20589600 TAGCACTTCAGTGCTCTCTGT
1 TAGCACGTCAGTGCTCTCTGT
20589621 TCATTAGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.28, G:0.21, T:0.37
Consensus pattern (22 bp):
TAGCACGTCAGTGCTCTCTGTA
Found at i:20590401 original size:57 final size:58
Alignment explanation
Indices: 20590313--20590424 Score: 145
Period size: 57 Copynumber: 1.9 Consensus size: 58
20590303 TGGATCGTCA
** * **
20590313 ACAAATATTAAAGCCATCATTGTCAGGCAA-CCGAGATGGTAGAATAAAATAGTTTGG
1 ACAAATACCAAAGCCATCATTGCCAGGCAACCCGAGATGACAGAATAAAATAGTTTGG
** *
20590370 ACAAATACCAAAGCCATTGTTGCCAGGCAACCCGGGATGACAGAATAAAATAGTT
1 ACAAATACCAAAGCCATCATTGCCAGGCAACCCGAGATGACAGAATAAAATAGTT
20590425 CAAATTCCTA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
57 25 0.54
58 21 0.46
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (58 bp):
ACAAATACCAAAGCCATCATTGCCAGGCAACCCGAGATGACAGAATAAAATAGTTTGG
Found at i:20600133 original size:326 final size:326
Alignment explanation
Indices: 20599540--20600197 Score: 1127
Period size: 326 Copynumber: 2.0 Consensus size: 326
20599530 ATGTAGTAGT
* *
20599540 CATACCCAATCATTTTAACAACCCATTATTGTTGGGATAGGGTGATAGCTTGCCGATTCGCTAAG
1 CATACCCAATCATTTTAACAACCCATTATTGTTGGAATAGGGTGATAGCTTGCCGATTCGCTAAA
* *
20599605 AACTTCAGGCTTTGGTGATCGGTCCTGATTTGAAACCTCTTCCCAACCAAGTACGTGTGCCATTT
66 AACTTCAGGCTTTGGCGATCGATCCTGATTTGAAACCTCTTCCCAACCAAGTACGTGTGCCATTT
* * * *
20599670 CTTGACTGCTATGAGAACCGTGAACATTTCTTTATTGTAGATGGAAAGTGCCTCATGTTTCACTC
131 CTTGACTACCATGAGAACCGTGAACATTTCCTTATCGTAGATGGAAAGTGCCTCATGTTTCACTC
* *
20599735 TTAGCCCTTTGCTGAAAAATGCCACGGGTCTTCTTTTCTGGTGTAACACAACCCCGACCCCTTGA
196 CTAGCCCTTTGCTGAAAAATGCCACGGGTCTTCCTTTCTGGTGTAACACAACCCCGACCCCTTGA
* **
20599800 CCACATGCATCAGTGTCGATGCAAAACTTTTCATTAAAATTGAGAAGACATAGTATTGGTGCTTG
261 CCACATGCATCAGTGTCGATGCAAAACTCTTCATTAAAATTGAGAAGACATAGTACCGGTGCTTG
20599865 G
326 G
* *
20599866 CATACCCAATCATTTTAACAACCTATTATTGTTGGAATGGGGTGATAGCTTGCCGATTCGCTAAA
1 CATACCCAATCATTTTAACAACCCATTATTGTTGGAATAGGGTGATAGCTTGCCGATTCGCTAAA
20599931 AACTTCAGGCTTTGGCGATCGATCCTGATTTGAAACCTCTTCCCAACCAAGTACGTGTGCCATTT
66 AACTTCAGGCTTTGGCGATCGATCCTGATTTGAAACCTCTTCCCAACCAAGTACGTGTGCCATTT
* * *
20599996 CTTGACTACCATGAGAACTGTGAACATTTCCTTATCGTATATGTAAAGTGCCTCATGTTTCACTC
131 CTTGACTACCATGAGAACCGTGAACATTTCCTTATCGTAGATGGAAAGTGCCTCATGTTTCACTC
*
20600061 CTAGCCCTTTGCTGAAAAATGCCACGGGTCTTCCTTTCTGGTTTAACACAACCCCGACCCCTTGA
196 CTAGCCCTTTGCTGAAAAATGCCACGGGTCTTCCTTTCTGGTGTAACACAACCCCGACCCCTTGA
* *
20600126 CCACATGCGTCAGTGTCGATGCAAAACTCTTCATTAAAATTGGGAAGACATAGTACCGGTGCTTG
261 CCACATGCATCAGTGTCGATGCAAAACTCTTCATTAAAATTGAGAAGACATAGTACCGGTGCTTG
20600191 G
326 G
20600192 CATACC
1 CATACC
20600198 GCTTGCTTTA
Statistics
Matches: 311, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
326 311 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (326 bp):
CATACCCAATCATTTTAACAACCCATTATTGTTGGAATAGGGTGATAGCTTGCCGATTCGCTAAA
AACTTCAGGCTTTGGCGATCGATCCTGATTTGAAACCTCTTCCCAACCAAGTACGTGTGCCATTT
CTTGACTACCATGAGAACCGTGAACATTTCCTTATCGTAGATGGAAAGTGCCTCATGTTTCACTC
CTAGCCCTTTGCTGAAAAATGCCACGGGTCTTCCTTTCTGGTGTAACACAACCCCGACCCCTTGA
CCACATGCATCAGTGTCGATGCAAAACTCTTCATTAAAATTGAGAAGACATAGTACCGGTGCTTG
G
Found at i:20600926 original size:84 final size:84
Alignment explanation
Indices: 20600785--20601049 Score: 458
Period size: 84 Copynumber: 3.2 Consensus size: 84
20600775 GAGAAAAAGA
* *
20600785 GAGCTTTTCCCAGGTCATCCAACAATTTTTCTATGATAGGTATGGGGAACCTATCTGTAACACCC
1 GAGCTTGTCCCAGGTCATCCAACAATTCTTCTATGATAGGTATGGGGAACCTATCTGTAACACCC
* *
20600850 CTATCTTGTATTCGTCACG
66 CTATCTCGTATTCGTCACC
* *
20600869 GAGCTTGTCCCAGGTCATCCAACAATTCTTCTATGATAGGTATGGGGAATCTATCTGTAATACCC
1 GAGCTTGTCCCAGGTCATCCAACAATTCTTCTATGATAGGTATGGGGAACCTATCTGTAACACCC
20600934 CTATCTCGTATTCGTCACC
66 CTATCTCGTATTCGTCACC
*
20600953 GAGCTTGTCCCAGGTCATCCAACAATTCTTCTATGATAGGTATGGGGAACCTATCTGTAACACTC
1 GAGCTTGTCCCAGGTCATCCAACAATTCTTCTATGATAGGTATGGGGAACCTATCTGTAACACCC
*
20601018 TTATCTCGTATTCGTCACC
66 CTATCTCGTATTCGTCACC
20601037 GAGCTTGTCCCAG
1 GAGCTTGTCCCAG
20601050 AGCACTACCG
Statistics
Matches: 171, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 171 1.00
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.32
Consensus pattern (84 bp):
GAGCTTGTCCCAGGTCATCCAACAATTCTTCTATGATAGGTATGGGGAACCTATCTGTAACACCC
CTATCTCGTATTCGTCACC
Found at i:20601796 original size:17 final size:17
Alignment explanation
Indices: 20601774--20601834 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
20601764 ATTGAATCAC
20601774 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
20601791 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
20601811 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
20601828 TACATAA
1 TACATAA
20601835 GTCTTGAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 20 0.61
20 13 0.39
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:20601811 original size:37 final size:36
Alignment explanation
Indices: 20601765--20601860 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 36
20601755 ATTACCCGAA
20601765 TTGAATCACTACATAATTAAAAACATTACATAAGTC
1 TTGAATCACTACATAATTAAAAACATTACATAAGTC
20601801 TTTGAATCACTACATAATTAAAAACATTACATAAGTC
1 -TTGAATCACTACATAATTAAAAACATTACATAAGTC
*
20601838 TTGAAATTAAC-ACATAATTAAAA
1 TTG-AA-TCACTACATAATTAAAA
20601861 TGTAAGTATT
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
36 3 0.05
37 50 0.89
38 3 0.05
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (36 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTC
Found at i:20602026 original size:6 final size:6
Alignment explanation
Indices: 20602015--20602042 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20602005 TTGGGTAGAC
20602015 TTTAGT TTTAGT TTTAGT TTTAGT TTTA
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTA
20602043 TTGGGTTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.14, T:0.68
Consensus pattern (6 bp):
TTTAGT
Found at i:20602053 original size:5 final size:5
Alignment explanation
Indices: 20602043--20602084 Score: 57
Period size: 5 Copynumber: 7.8 Consensus size: 5
20602033 TTTAGTTTTA
20602043 TTGGG TTGGG TAATTGGG TTGGG TTGGG TTGGG TTGGG TTGG
1 TTGGG TTGGG T---TGGG TTGGG TTGGG TTGGG TTGGG TTGG
20602085 ATAATTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 29 0.85
8 5 0.15
ACGTcount: A:0.05, C:0.00, G:0.55, T:0.40
Consensus pattern (5 bp):
TTGGG
Found at i:20602060 original size:13 final size:13
Alignment explanation
Indices: 20602042--20602066 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20602032 TTTTAGTTTT
20602042 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
20602055 ATTGGGTTGGGT
1 ATTGGGTTGGGT
20602067 TGGGTTGGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:20604537 original size:46 final size:45
Alignment explanation
Indices: 20604431--20604627 Score: 243
Period size: 46 Copynumber: 4.6 Consensus size: 45
20604421 CATATGACCT
*
20604431 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
20604474 CTTATCACTTTACCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
20604520 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
** *
20604557 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAACTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
20604603 CTTATCACTTTGTCACTTGATCAGA
1 CTTATCACTTTGTCACTTGATCAGA
20604628 AGTACTCAAA
Statistics
Matches: 132, Mismatches: 10, Indels: 21
0.81 0.06 0.13
Matches are distributed among these distances:
37 28 0.21
39 2 0.02
40 3 0.02
41 1 0.01
42 1 0.01
43 10 0.08
44 5 0.04
45 21 0.16
46 61 0.46
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:20604558 original size:37 final size:37
Alignment explanation
Indices: 20604517--20604591 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
20604507 GCTGAAGCTA
20604517 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
* **
20604554 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
20604591 C
1 C
20604592 TAAAACTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (37 bp):
CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
Found at i:20604577 original size:83 final size:83
Alignment explanation
Indices: 20604471--20604627 Score: 251
Period size: 83 Copynumber: 1.9 Consensus size: 83
20604461 AGCTAGGCTA
* *
20604471 CCACTTATCACTTTACCACTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTATCAC
1 CCACTTATCACTTTACCACTTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTATCAC
20604536 TTGATCAGATAAGTGTAG
66 TTGATCAGATAAGTGTAG
**** *
20604554 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTCAC
1 CCACTTATCACTTTACCACTTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTATCAC
20604619 TTGATCAGA
66 TTGATCAGA
20604628 AGTACTCAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 67 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.34
Consensus pattern (83 bp):
CCACTTATCACTTTACCACTTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTATCAC
TTGATCAGATAAGTGTAG
Found at i:20605094 original size:30 final size:30
Alignment explanation
Indices: 20605060--20605271 Score: 424
Period size: 30 Copynumber: 7.1 Consensus size: 30
20605050 TAGACTACTA
20605060 CATAGCCTTTCATACTCAAAACCGCAACAC
1 CATAGCCTTTCATACTCAAAACCGCAACAC
20605090 CATAGCCTTTCATACTCAAAACCGCAACAC
1 CATAGCCTTTCATACTCAAAACCGCAACAC
20605120 CATAGCCTTTCATACTCAAAACCGCAACAC
1 CATAGCCTTTCATACTCAAAACCGCAACAC
20605150 CATAGCCTTTCATACTCAAAACCGCAACAC
1 CATAGCCTTTCATACTCAAAACCGCAACAC
20605180 CATAGCCTTTCATACTCAAAACCGCAACAC
1 CATAGCCTTTCATACTCAAAACCGCAACAC
20605210 CATAGCCTTTCATACTCAAAACCGCAACAC
1 CATAGCCTTTCATACTCAAAACCGCAACAC
20605240 CATAGCCTTTCATACTCAAAACCGCAACAC
1 CATAGCCTTTCATACTCAAAACCGCAACAC
20605270 CA
1 CA
20605272 AACCTTAATT
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 182 1.00
ACGTcount: A:0.37, C:0.37, G:0.07, T:0.20
Consensus pattern (30 bp):
CATAGCCTTTCATACTCAAAACCGCAACAC
Found at i:20609190 original size:51 final size:51
Alignment explanation
Indices: 20609117--20609218 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
20609107 ATCACATTTA
20609117 TCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACGACTTATCACTTG
1 TCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACGACTTATCACTTG
* * *
20609168 TCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTTATCACTTG
1 TCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACGACTTATCACTTG
20609219 CTACTGATCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (51 bp):
TCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACGACTTATCACTTG
Found at i:20611606 original size:21 final size:21
Alignment explanation
Indices: 20611546--20611607 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
20611536 GAGTTCTTGT
* * *
20611546 TGCATCACCCCCATATCATTC
1 TGCATGACTCCCATATCTTTC
* *
20611567 TGCATGACTCCCGTGTCTTTC
1 TGCATGACTCCCATATCTTTC
20611588 TGCATGACTCCCATATCTTT
1 TGCATGACTCCCATATCTTT
20611608 TTGTAATCTC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.18, C:0.35, G:0.11, T:0.35
Consensus pattern (21 bp):
TGCATGACTCCCATATCTTTC
Found at i:20614377 original size:153 final size:154
Alignment explanation
Indices: 20614195--20614502 Score: 609
Period size: 153 Copynumber: 2.0 Consensus size: 154
20614185 ATTTTAAGGG
20614195 TGAAATGATCTAGAAACTAAGGAAATGGATGAATTAGGACCAAATTGAATAAGTGAATAATTATA
1 TGAAATGATCTAGAAACTAAGGAAATGGATGAATTAGGACCAAATTGAATAAGTGAATAATTATA
20614260 AGGGATTAAATCACAATTTTACCAAATTAAGTGATGACTCAATGATATAATTTTAAAAGATCATA
66 AGGGATTAAATCACAATTTTACCAAATTAAGTGATGACTCAATGATATAATTTTAAAAGATCATA
20614325 AAGGGCAAAATGGTCAATTAGAAA
131 AAGGGCAAAATGGTCAATTAGAAA
20614349 TGAAATGATCT-GAAACTAAGGAAATGGATGAATTAGGACCAAATTGAATAAGTGAATAATTATA
1 TGAAATGATCTAGAAACTAAGGAAATGGATGAATTAGGACCAAATTGAATAAGTGAATAATTATA
20614413 AGGGATTAAATCACAATTTTACCAAATTAAGTGATGACTCAATGATATAATTTTAAAAGATCATA
66 AGGGATTAAATCACAATTTTACCAAATTAAGTGATGACTCAATGATATAATTTTAAAAGATCATA
20614478 AAGGGCAAAATGGTCAATTAGAAA
131 AAGGGCAAAATGGTCAATTAGAAA
20614502 T
1 T
20614503 AGAGAGAACT
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
153 143 0.93
154 11 0.07
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (154 bp):
TGAAATGATCTAGAAACTAAGGAAATGGATGAATTAGGACCAAATTGAATAAGTGAATAATTATA
AGGGATTAAATCACAATTTTACCAAATTAAGTGATGACTCAATGATATAATTTTAAAAGATCATA
AAGGGCAAAATGGTCAATTAGAAA
Found at i:20628279 original size:42 final size:42
Alignment explanation
Indices: 20628214--20628335 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 42
20628204 TTAACTCATA
* * * *
20628214 TGAGTTTCCGTTTCACCCTAATGGGTTTCTGTTCAGCTCTTT
1 TGAGCTTCAGTTTAACCTTAATGGGTTTCTGTTCAGCTCTTT
**
20628256 TGAGCTTCAGTTTAACCTTAATGGGTTTCCATTCAGCTCTTT
1 TGAGCTTCAGTTTAACCTTAATGGGTTTCTGTTCAGCTCTTT
* * *
20628298 TGAGCTTCAATTTAACTTTTATGGGTTT-TCGTTCAGCT
1 TGAGCTTCAGTTTAACCTTAATGGGTTTCT-GTTCAGCT
20628336 TTTACGAGCT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (42 bp):
TGAGCTTCAGTTTAACCTTAATGGGTTTCTGTTCAGCTCTTT
Found at i:20628339 original size:21 final size:21
Alignment explanation
Indices: 20628327--20628374 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
20628317 TATGGGTTTT
20628327 CGTTCAGCTTTTACGAGCTTC
1 CGTTCAGCTTTTACGAGCTTC
20628348 CGTTCAGCTTTTACGAGCTTC
1 CGTTCAGCTTTTACGAGCTTC
20628369 CGTTCA
1 CGTTCA
20628375 ACCCTTATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.15, C:0.29, G:0.19, T:0.38
Consensus pattern (21 bp):
CGTTCAGCTTTTACGAGCTTC
Found at i:20629434 original size:17 final size:17
Alignment explanation
Indices: 20629412--20629474 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
20629402 ATTAAATCAC
20629412 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
20629429 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
*
20629449 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
20629466 TACATAATT
1 TACATAATT
20629475 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 21 0.62
20 13 0.38
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.35
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:20629452 original size:37 final size:37
Alignment explanation
Indices: 20629406--20629477 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
20629396 ACCAGAATTA
20629406 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
* *
20629443 AATCACTACATAATTAAAAATATTACATAATTCTT
1 AATCACTACATAATTAAAAACATTACATAAGTCTT
20629478 GAAATTAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (37 bp):
AATCACTACATAATTAAAAACATTACATAAGTCTTTG
Found at i:20629658 original size:38 final size:39
Alignment explanation
Indices: 20629607--20629703 Score: 151
Period size: 39 Copynumber: 2.5 Consensus size: 39
20629597 ACTTAGAATT
* *
20629607 AGACTTTAGTTTTATTTTTATCGGGTT-GGTAATTGGGC
1 AGACTTTAGTTTTAGTTTTATCGGGTTGGGTAATTGGAC
* *
20629645 AGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGAT
1 AGACTTTAGTTTTAGTTTTATCGGGTTGGGTAATTGGAC
20629684 AGACTTTAGTTTTAGTTTTA
1 AGACTTTAGTTTTAGTTTTA
20629704 GTTTTAGTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
38 25 0.46
39 29 0.54
ACGTcount: A:0.21, C:0.05, G:0.25, T:0.49
Consensus pattern (39 bp):
AGACTTTAGTTTTAGTTTTATCGGGTTGGGTAATTGGAC
Found at i:20629699 original size:6 final size:6
Alignment explanation
Indices: 20629688--20629721 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
20629678 TTGGATAGAC
20629688 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTA
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTA
20629722 TTGGGTTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.68
Consensus pattern (6 bp):
TTTAGT
Found at i:20629739 original size:13 final size:13
Alignment explanation
Indices: 20629721--20629745 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20629711 TTTTAGTTTT
20629721 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
20629734 ATTGGGTTGGGT
1 ATTGGGTTGGGT
20629746 TGGATAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:20630820 original size:21 final size:21
Alignment explanation
Indices: 20630790--20630846 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
20630780 GCTTCAGATT
20630790 AACCCTTATGGGTTTCCATTC
1 AACCCTTATGGGTTTCCATTC
* * *
20630811 AGCTCTTATGAGTTTCCATTC
1 AACCCTTATGGGTTTCCATTC
*
20630832 AACCCTTACGGGTTT
1 AACCCTTATGGGTTT
20630847 TCGTTTAGCA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.39
Consensus pattern (21 bp):
AACCCTTATGGGTTTCCATTC
Found at i:20647014 original size:176 final size:175
Alignment explanation
Indices: 20646712--20647064 Score: 476
Period size: 176 Copynumber: 2.0 Consensus size: 175
20646702 ATCTTCCCCC
* * * * * *
20646712 TACCATCTCCCCTCTTCTCTCCCTCGTCTCTGCAAATCAGTTTTTTTTTTCTTTTCATCTCAGTT
1 TACCATCGCCCCTCTTCTCTCCCTCGTATCTACAAATCAGTTTTTATTCTCTTCTCATCTCAGTT
* * * *
20646777 CTCGCCCACCGCCGTGTCCGCTGATTTTTTCCTGATCTGACCCGTATTCCGTGTTGGATCGTGTT
66 CTCGCCCACCGCC--GTCCGCTGATTTTTTCCGGATCTGACCCGTATCCCGTGTCGGATCGTGTC
* *
20646842 GACACAGGTACTGCACCCCAAACTG-CCGAGTCAGGGTAACGAAGCT
129 GACACAAGTACTGCACCCCAAACTGCCCGAGCCAGGGTAACGAAGCT
**
20646888 TACCATCGCCCCTCTTCTCTTTCTCGTATCTACAAATCAGGTTTCTTCATTCTCTTCTCATCTCA
1 TACCATCGCCCCTCTTCTCTCCCTCGTATCTACAAATCA-GTTT-TT-ATTCTCTTCTCATCTCA
*
20646953 GTTCTCGCCCACCGCC-TCCGCTGTTTTTTTCCGGATCTGACCCGTATCCCGTGTCGGATCGTGT
63 GTTCTCGCCCACCGCCGTCCGCTGATTTTTTCCGGATCTGACCCGTATCCCGTGTCGGATCGTGT
* * *
20647017 CGACACAAGTACTGCATCCCAAATTGCTCCGAGCCCGGGTAACGAAGC
128 CGACACAAGTACTGCACCCCAAACTGC-CCGAGCCAGGGTAACGAAGC
20647065 CTATAATTAT
Statistics
Matches: 154, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
176 100 0.65
177 4 0.03
178 20 0.13
179 30 0.19
ACGTcount: A:0.16, C:0.34, G:0.17, T:0.33
Consensus pattern (175 bp):
TACCATCGCCCCTCTTCTCTCCCTCGTATCTACAAATCAGTTTTTATTCTCTTCTCATCTCAGTT
CTCGCCCACCGCCGTCCGCTGATTTTTTCCGGATCTGACCCGTATCCCGTGTCGGATCGTGTCGA
CACAAGTACTGCACCCCAAACTGCCCGAGCCAGGGTAACGAAGCT
Found at i:20651776 original size:11 final size:11
Alignment explanation
Indices: 20651760--20651797 Score: 76
Period size: 11 Copynumber: 3.5 Consensus size: 11
20651750 AAATAAAAAA
20651760 TAAAAATATTT
1 TAAAAATATTT
20651771 TAAAAATATTT
1 TAAAAATATTT
20651782 TAAAAATATTT
1 TAAAAATATTT
20651793 TAAAA
1 TAAAA
20651798 TTAAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:20652251 original size:3 final size:3
Alignment explanation
Indices: 20652245--20652272 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
20652235 CGTCTATTTC
20652245 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
20652273 TTTGGGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:20668482 original size:9 final size:9
Alignment explanation
Indices: 20668468--20668495 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20668458 TGAGTTTTCG
20668468 AATTCGAAT
1 AATTCGAAT
20668477 AATTCGAAT
1 AATTCGAAT
20668486 AATTCGAAT
1 AATTCGAAT
20668495 A
1 A
20668496 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:20668709 original size:30 final size:31
Alignment explanation
Indices: 20668675--20668735 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
20668665 AAACCTTTTA
*
20668675 TTTTCTCCC-AAAATTTTTACTCTC-TCCCAC
1 TTTTC-CCCTAAAACTTTTACTCTCTTCCCAC
*
20668705 TTTTCCCCTAAAACTTTTATTCTCTTCCCAC
1 TTTTCCCCTAAAACTTTTACTCTCTTCCCAC
20668736 CCCACCTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 3 0.11
30 18 0.67
31 6 0.22
ACGTcount: A:0.20, C:0.36, G:0.00, T:0.44
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCTCTTCCCAC
Found at i:20668843 original size:17 final size:17
Alignment explanation
Indices: 20668816--20668873 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
20668806 CTCCCCCCTA
*
20668816 TTTATTTCCCCTCAAACT
1 TTTATTTCCCC-AAAACT
20668834 TTTA-TTCCCCAAAACTT
1 TTTATTTCCCCAAAAC-T
*
20668851 TTTATTTTCCACCTAAACT
1 TTTA-TTTCC-CCAAAACT
20668870 TTTA
1 TTTA
20668874 CTTCTCACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 4 0.12
17 11 0.32
18 4 0.12
19 9 0.26
20 6 0.18
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTATTTCCCCAAAACT
Found at i:20669215 original size:5 final size:5
Alignment explanation
Indices: 20669205--20669230 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20669195 GAACAAATAT
20669205 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
20669231 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:20669330 original size:5 final size:5
Alignment explanation
Indices: 20669320--20669350 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
20669310 CTCGAAAATT
*
20669320 TTCGA TTCGA TTCGA TTCAA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
20669351 CGAATACTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:20679395 original size:1 final size:1
Alignment explanation
Indices: 20679389--20679425 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
20679379 AAACACGACC
20679389 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20679426 CAGAGTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20681000 original size:18 final size:18
Alignment explanation
Indices: 20680973--20681008 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20680963 AATTCTAATA
*
20680973 CCTTTTCCTTTTACAAAC
1 CCTTTACCTTTTACAAAC
20680991 CCTTTACCTTTTACAAAC
1 CCTTTACCTTTTACAAAC
20681009 TCGTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.33, G:0.00, T:0.42
Consensus pattern (18 bp):
CCTTTACCTTTTACAAAC
Found at i:20695960 original size:108 final size:108
Alignment explanation
Indices: 20695771--20695976 Score: 297
Period size: 108 Copynumber: 1.9 Consensus size: 108
20695761 TGGAAATCAT
** *
20695771 GTATTTAAAACACAGAGGTATATTTAAAAATAACATATGATAAATAATGAAATATTTGGTTTGAA
1 GTATTTAAAACACAGAGGTATATTTAAAAATAACATACAATAAATAATAAAATATTTGGTTTGAA
* *
20695836 ACTAATTAATATTAATAACACATGAAATATGTACAATTTTCAC
66 ACTAATTAATAATAATAACACATAAAATATGTACAATTTTCAC
** * * *
20695879 GTATTTAAAACATGGATGTGTATTTAAAAATAACATACAATAAATAATAAAATGTATT-GTTTGA
1 GTATTTAAAACACAGAGGTATATTTAAAAATAACATACAATAAATAATAAAATAT-TTGGTTTGA
*
20695943 AATTAATTAATAATAATAACACATAAAATATGTA
65 AACTAATTAATAATAATAACACATAAAATATGTA
20695977 TAATATTAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
108 84 0.98
109 2 0.02
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (108 bp):
GTATTTAAAACACAGAGGTATATTTAAAAATAACATACAATAAATAATAAAATATTTGGTTTGAA
ACTAATTAATAATAATAACACATAAAATATGTACAATTTTCAC
Found at i:20699629 original size:33 final size:33
Alignment explanation
Indices: 20699587--20699737 Score: 126
Period size: 33 Copynumber: 4.4 Consensus size: 33
20699577 ACAATGTTTA
* *
20699587 AATG-TAAGACCATAGCTGGGTTATGGCATTTT
1 AATGATAAGACCATAACTGGGTTATGGCATTAT
*
20699619 AATGAAAAGACCATAACTGGGTTATGGCAGTATAGAT
1 AATGATAAGACCATAACTGGGTTATGGCA-T-T--AT
* * * *
20699656 ACATGTGTAAGACCATAGCTGGGCTATGGCATTCT
1 A-ATG-ATAAGACCATAACTGGGTTATGGCATTAT
* * * *
20699691 GATGATAAGACCATAACTGAGTTATGGCACTACA
1 AATGATAAGACCATAACTGGGTTATGGCATTA-T
20699725 AATG-TAAGACCAT
1 AATGATAAGACCAT
20699738 GGCAGGGTCA
Statistics
Matches: 94, Mismatches: 17, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
32 4 0.04
33 53 0.56
34 7 0.07
35 2 0.02
37 3 0.03
38 4 0.04
39 21 0.22
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.27
Consensus pattern (33 bp):
AATGATAAGACCATAACTGGGTTATGGCATTAT
Found at i:20701511 original size:22 final size:22
Alignment explanation
Indices: 20701486--20701529 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
20701476 TTGTTTTACC
*
20701486 TATGCATAAAATAAAATAAATA
1 TATGCATAAAATAAAAAAAATA
* *
20701508 TATGTATAAATTAAAAAAAATA
1 TATGCATAAAATAAAAAAAATA
20701530 GATGAGGTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (22 bp):
TATGCATAAAATAAAAAAAATA
Found at i:20705879 original size:7 final size:6
Alignment explanation
Indices: 20705863--20705920 Score: 63
Period size: 5 Copynumber: 10.2 Consensus size: 6
20705853 AAGCCAGCCA
20705863 CTCCCC CTCCACC CTCCCC C-CCCC C-CCCC C-CCCC C-CCCC C-CCCC
1 CTCCCC CTCC-CC CTCCCC CTCCCC CTCCCC CTCCCC CTCCCC CTCCCC
20705907 CTCCCCC CTCCCC C
1 CT-CCCC CTCCCC C
20705921 CTTATAACAT
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
5 25 0.51
6 12 0.24
7 12 0.24
ACGTcount: A:0.02, C:0.90, G:0.00, T:0.09
Consensus pattern (6 bp):
CTCCCC
Found at i:20705881 original size:13 final size:13
Alignment explanation
Indices: 20705863--20705920 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
20705853 AAGCCAGCCA
*
20705863 CTCCCCCTCCACC
1 CTCCCCCTCCCCC
20705876 CTCCCCC-CCCCC
1 CTCCCCCTCCCCC
* *
20705888 CCCCCCCCCCCCC
1 CTCCCCCTCCCCC
*
20705901 CCCCCCCTCCCCC
1 CTCCCCCTCCCCC
20705914 CTCCCCC
1 CTCCCCC
20705921 CTTATAACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.25
13 30 0.75
ACGTcount: A:0.02, C:0.90, G:0.00, T:0.09
Consensus pattern (13 bp):
CTCCCCCTCCCCC
Found at i:20705882 original size:1 final size:1
Alignment explanation
Indices: 20705878--20705921 Score: 70
Period size: 1 Copynumber: 44.0 Consensus size: 1
20705868 CCTCCACCCT
* *
20705878 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTCCCCCCTCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
20705922 TTATAACATC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.95, G:0.00, T:0.05
Consensus pattern (1 bp):
C
Found at i:20705921 original size:7 final size:7
Alignment explanation
Indices: 20705865--20705922 Score: 79
Period size: 6 Copynumber: 8.9 Consensus size: 7
20705855 GCCAGCCACT
20705865 CCCCCTC
1 CCCCCTC
*
20705872 CACCCTC
1 CCCCCTC
20705879 CCCCC-C
1 CCCCCTC
20705885 CCCCC-C
1 CCCCCTC
20705891 CCCCC-C
1 CCCCCTC
20705897 CCCCC-C
1 CCCCCTC
20705903 CCCCCTC
1 CCCCCTC
20705910 CCCCCTC
1 CCCCCTC
20705917 CCCCCT
1 CCCCCT
20705923 TATAACATCA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
6 24 0.50
7 24 0.50
ACGTcount: A:0.02, C:0.90, G:0.00, T:0.09
Consensus pattern (7 bp):
CCCCCTC
Found at i:20708244 original size:110 final size:111
Alignment explanation
Indices: 20708041--20708260 Score: 433
Period size: 110 Copynumber: 2.0 Consensus size: 111
20708031 ACTTCTTCCG
20708041 TTTTGGAAATTCCTTTCAGTTTCTTAGTTAGAATGGGTGACGATATTCTGCCTAAATAGTAAACA
1 TTTTGGAAATTCCTTTCAGTTTCTTAGTTAGAATGGGTGACGATATTCTGCCTAAATAGTAAACA
20708106 CAGGTAATAAATAACAGAATACTAAAGATTCGAGCCATAGAATTTT
66 CAGGTAATAAATAACAGAATACTAAAGATTCGAGCCATAGAATTTT
20708152 TTTTGGAAA-TCCTTTCAGTTTCTTAGTTAGAATGGGTGACGATATTCTGCCTAAATAGTAAACA
1 TTTTGGAAATTCCTTTCAGTTTCTTAGTTAGAATGGGTGACGATATTCTGCCTAAATAGTAAACA
20708216 CAGGTAATAAATAACAGAATACTAAAGATTCGAGCCATAGAATTT
66 CAGGTAATAAATAACAGAATACTAAAGATTCGAGCCATAGAATTT
20708261 CGAACCTGTA
Statistics
Matches: 109, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
110 100 0.92
111 9 0.08
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (111 bp):
TTTTGGAAATTCCTTTCAGTTTCTTAGTTAGAATGGGTGACGATATTCTGCCTAAATAGTAAACA
CAGGTAATAAATAACAGAATACTAAAGATTCGAGCCATAGAATTTT
Found at i:20708801 original size:17 final size:17
Alignment explanation
Indices: 20708779--20708813 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20708769 AATAAAAGAA
20708779 TAGGCACAATTAAATAT
1 TAGGCACAATTAAATAT
*
20708796 TAGGCACAATTGAATAT
1 TAGGCACAATTAAATAT
20708813 T
1 T
20708814 TAAAATTCAC
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:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (17 bp):
TAGGCACAATTAAATAT
Found at i:20709205 original size:40 final size:40
Alignment explanation
Indices: 20709146--20709247 Score: 132
Period size: 40 Copynumber: 2.5 Consensus size: 40
20709136 AACACACTAG
* * * ***
20709146 TTTGGCACCTAGTGCCTCATCGGATAATTTGAAGTAATAA
1 TTTGACACCCAGTGTCTCATCGGATAAACCGAAGTAATAA
* *
20709186 TTTGACATCCAGTGTCTCATCGGCTAAACCGAAGTAATAA
1 TTTGACACCCAGTGTCTCATCGGATAAACCGAAGTAATAA
20709226 TTTGACACCCAGTGTCTCATCG
1 TTTGACACCCAGTGTCTCATCG
20709248 ACTCGAAGTC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (40 bp):
TTTGACACCCAGTGTCTCATCGGATAAACCGAAGTAATAA
Found at i:20712280 original size:18 final size:18
Alignment explanation
Indices: 20712257--20712301 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
20712247 CCGTATCTTC
20712257 GATTTTGAAACTATTAAA
1 GATTTTGAAACTATTAAA
20712275 GATTTTGAAACTATTAAA
1 GATTTTGAAACTATTAAA
20712293 GATTTTGAA
1 GATTTTGAA
20712302 TGTTTCTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.40
Consensus pattern (18 bp):
GATTTTGAAACTATTAAA
Found at i:20720022 original size:5 final size:5
Alignment explanation
Indices: 20720014--20720068 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
20720004 TATTTAATTT
* *
20720014 ATATA ATATA ATACA ATATA ATATA TTATATT ATATA ATA-A A-ATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA --ATATA ATATA ATATA ATATA ATATA
20720063 ATATA A
1 ATATA A
20720069 AACATAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.20
5 28 0.68
7 4 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Done.