Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 13 of 24
Found at i:2639041 original size:11 final size:10
Alignment explanation
Indices: 2639017--2639086 Score: 51
Period size: 10 Copynumber: 7.1 Consensus size: 10
2639007 TTTAAAATAT
2639017 TATATTTTTA
1 TATATTTTTA
2639027 TATATTTTGTA
1 TATATTTT-TA
*
2639038 TATA--TTAA
1 TATATTTTTA
2639046 TA-ATTTATT-
1 TATATTT-TTA
2639055 T-TATTTTATA
1 TATATTTT-TA
2639065 TATATTTTTA
1 TATATTTTTA
*
2639075 TAAATTTGTTA
1 TATATTT-TTA
2639086 T
1 T
2639087 TTTATGTATG
Statistics
Matches: 48, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
7 1 0.02
8 4 0.08
9 9 0.19
10 18 0.38
11 16 0.33
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (10 bp):
TATATTTTTA
Found at i:2639065 original size:34 final size:34
Alignment explanation
Indices: 2638991--2639081 Score: 85
Period size: 37 Copynumber: 2.6 Consensus size: 34
2638981 TATGTTTGTA
*
2638991 TTTATATTTTTTTATATTTAAAATATTATATTTT
1 TTTATATTTTTATATATTTAAAATATTATATTTT
* *
2639025 TATATATTTTGTATATA-TTAATAATTTATTTTATTTT
1 TTTATATTTT-TATATATTTAA-AA--TATTATATTTT
* *
2639062 ATATATATTTTTATAAATTT
1 -TTTATATTTTTATATATTT
2639082 GTTATTTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
34 13 0.28
35 7 0.15
37 15 0.32
38 12 0.26
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (34 bp):
TTTATATTTTTATATATTTAAAATATTATATTTT
Found at i:2639226 original size:23 final size:24
Alignment explanation
Indices: 2639175--2639228 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
2639165 ATATTTTTAT
* *
2639175 ATTTGTATATTCATGTTATATTTA
1 ATTTTTATATTCATGTTATAATTA
* *
2639199 TTTTTTATATT-ATGTTTTAATTA
1 ATTTTTATATTCATGTTATAATTA
2639222 ATTTTTA
1 ATTTTTA
2639229 ATTTTGTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.65
Consensus pattern (24 bp):
ATTTTTATATTCATGTTATAATTA
Found at i:2642832 original size:15 final size:15
Alignment explanation
Indices: 2642812--2642842 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2642802 CAACATCTTA
*
2642812 TATTATAAAATTATT
1 TATTATAAAATAATT
2642827 TATTATAAAATAATT
1 TATTATAAAATAATT
2642842 T
1 T
2642843 TAATTTATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTATAAAATAATT
Found at i:2646812 original size:16 final size:16
Alignment explanation
Indices: 2646791--2646822 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2646781 TTATTGAATT
*
2646791 TTATTTTTTAAAAAAA
1 TTATTTTTCAAAAAAA
2646807 TTATTTTTCAAAAAAA
1 TTATTTTTCAAAAAAA
2646823 AAAAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTATTTTTCAAAAAAA
Found at i:2646825 original size:22 final size:22
Alignment explanation
Indices: 2646800--2646849 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2646790 TTTATTTTTT
*
2646800 AAAAAAATT-ATTTTTCAAAAAA
1 AAAAAAATTAACTTTT-AAAAAA
* *
2646822 AAAAAATTTAACTTTTAGAAAA
1 AAAAAAATTAACTTTTAAAAAA
2646844 AAAAAA
1 AAAAAA
2646850 GCATTTGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAAAAATTAACTTTTAAAAAA
Found at i:2647310 original size:22 final size:22
Alignment explanation
Indices: 2647280--2647327 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2647270 GGGTCTTAAT
2647280 AAAAAGACAAAATAAG-GGGAA
1 AAAAAGACAAAATAAGTGGGAA
* *
2647301 AAAAAGGACAGATTAAGTGGGAA
1 AAAAA-GACAAAATAAGTGGGAA
2647324 AAAA
1 AAAA
2647328 GGGATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 9 0.39
23 9 0.39
ACGTcount: A:0.62, C:0.04, G:0.25, T:0.08
Consensus pattern (22 bp):
AAAAAGACAAAATAAGTGGGAA
Found at i:2655617 original size:2 final size:2
Alignment explanation
Indices: 2655610--2655645 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2655600 TACCCATTTC
*
2655610 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2655646 TAGGTTGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:2657167 original size:2 final size:2
Alignment explanation
Indices: 2657160--2657197 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2657150 GATTCTGCAC
2657160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2657198 TTCACTATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2663316 original size:12 final size:12
Alignment explanation
Indices: 2663299--2663324 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2663289 CAGAGCGCCC
2663299 CAAAACATACAA
1 CAAAACATACAA
2663311 CAAAACATACAA
1 CAAAACATACAA
2663323 CA
1 CA
2663325 TAATGGCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.27, G:0.00, T:0.08
Consensus pattern (12 bp):
CAAAACATACAA
Found at i:2663951 original size:27 final size:27
Alignment explanation
Indices: 2663921--2663974 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2663911 CGGATATTAA
2663921 TTCCTCACCAATTTCACCATTATAAGT
1 TTCCTCACCAATTTCACCATTATAAGT
2663948 TTCCTCACCAATTTCACCATTATAAGT
1 TTCCTCACCAATTTCACCATTATAAGT
2663975 ACTGGTCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.30, G:0.04, T:0.37
Consensus pattern (27 bp):
TTCCTCACCAATTTCACCATTATAAGT
Found at i:2665454 original size:22 final size:24
Alignment explanation
Indices: 2665426--2665486 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 24
2665416 ATTATACTTG
2665426 ATTTATAATATAA-ATAAAA-TAT
1 ATTTATAATATAATATAAAATTAT
* *
2665448 ATTTATATTATAATTTAAAATTAT
1 ATTTATAATATAATATAAAATTAT
*
2665472 ATAATATAATATAAT
1 AT-TTATAATATAAT
2665487 TTATCACTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 12 0.38
23 5 0.16
24 5 0.16
25 10 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTTATAATATAATATAAAATTAT
Found at i:2665487 original size:18 final size:18
Alignment explanation
Indices: 2665429--2665539 Score: 51
Period size: 16 Copynumber: 6.4 Consensus size: 18
2665419 ATACTTGATT
*
2665429 TATAA-TATA-AATAAAA
1 TATAATTATATAATATAA
*
2665445 TAT-ATT-TATATTATAA
1 TATAATTATATAATATAA
*
2665461 TTTAAAATTATATAATATAA
1 --TATAATTATATAATATAA
*
2665481 TATAATT-TATCACT-T-A
1 TATAATTATAT-AATATAA
* * *
2665497 TATATTTTATATTATACAA
1 TATA-ATTATATAATATAA
*
2665516 TATATTTATAT-A-ATAA
1 TATAATTATATAATATAA
2665532 TATAATTA
1 TATAATTA
2665540 ATTTATTTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 22
0.68 0.11 0.21
Matches are distributed among these distances:
15 3 0.04
16 24 0.33
17 8 0.11
18 20 0.28
19 8 0.11
20 9 0.12
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.48
Consensus pattern (18 bp):
TATAATTATATAATATAA
Found at i:2665839 original size:18 final size:17
Alignment explanation
Indices: 2665816--2665849 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2665806 AATATTTGTT
*
2665816 ATATTATAATAGATTAAA
1 ATATTAAAATAG-TTAAA
2665834 ATATTAAAATAGTTAA
1 ATATTAAAATAGTTAA
2665850 TGAACTACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
ATATTAAAATAGTTAAA
Found at i:2667263 original size:2 final size:2
Alignment explanation
Indices: 2667250--2667292 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2667240 TACATGGATC
*
2667250 TA TA TA TT 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
2667292 T
1 T
2667293 TATGCACACG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2669302 original size:31 final size:32
Alignment explanation
Indices: 2669267--2669328 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
2669257 ACTTAAATTA
2669267 TAATT-TAATAATA-ATAAATAATT-ATATAAAC
1 TAATTATAA-AATACATAAAT-ATTAATATAAAC
*
2669298 TAATTATAAAATACGTAAATATTAATATAAA
1 TAATTATAAAATACATAAATATTAATATAAA
2669329 AATAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 12 0.44
32 15 0.56
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (32 bp):
TAATTATAAAATACATAAATATTAATATAAAC
Found at i:2669479 original size:20 final size:19
Alignment explanation
Indices: 2669445--2669501 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
2669435 ATCATAAATT
2669445 ATTTTAT-TAAAATATAAA
1 ATTTTATATAAAATATAAA
*
2669463 ATTTTATATAAATATATAAT
1 ATTTTATATAAA-ATATAAA
*
2669483 ATTTTAAATAAAATTATAA
1 ATTTTATATAAAA-TATAA
2669502 GACGTGCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.21
19 5 0.15
20 22 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTTATATAAAATATAAA
Found at i:2678894 original size:14 final size:17
Alignment explanation
Indices: 2678875--2678910 Score: 51
Period size: 14 Copynumber: 2.3 Consensus size: 17
2678865 AAAAATTAAA
2678875 TATTTTTA-AA-AAAT-
1 TATTTTTATAATAAATC
2678889 TATTTTTATAATAAATC
1 TATTTTTATAATAAATC
2678906 TATTT
1 TATTT
2678911 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.42
15 2 0.11
16 4 0.21
17 5 0.26
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTTTATAATAAATC
Found at i:2679112 original size:29 final size:29
Alignment explanation
Indices: 2679070--2679127 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
2679060 TATCACTTTC
2679070 CTTTTATTAAAAAAAAAGAATAATTACAA
1 CTTTTATTAAAAAAAAAGAATAATTACAA
2679099 CTTTTATTAAAAAAAAAGAATAATTACAA
1 CTTTTATTAAAAAAAAAGAATAATTACAA
2679128 ACCTCAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (29 bp):
CTTTTATTAAAAAAAAAGAATAATTACAA
Found at i:2691543 original size:101 final size:101
Alignment explanation
Indices: 2691368--2691570 Score: 406
Period size: 101 Copynumber: 2.0 Consensus size: 101
2691358 CTTGCCTCAG
2691368 TAGGCAAGCTAGTGTTTGCTGCATCTACATCTCATTTTAGGTATGAAATTGATGCACTTCATCCA
1 TAGGCAAGCTAGTGTTTGCTGCATCTACATCTCATTTTAGGTATGAAATTGATGCACTTCATCCA
2691433 GAAACTAAAATAATATGAAAAATGTATTGTATTTAA
66 GAAACTAAAATAATATGAAAAATGTATTGTATTTAA
2691469 TAGGCAAGCTAGTGTTTGCTGCATCTACATCTCATTTTAGGTATGAAATTGATGCACTTCATCCA
1 TAGGCAAGCTAGTGTTTGCTGCATCTACATCTCATTTTAGGTATGAAATTGATGCACTTCATCCA
2691534 GAAACTAAAATAATATGAAAAATGTATTGTATTTAA
66 GAAACTAAAATAATATGAAAAATGTATTGTATTTAA
2691570 T
1 T
2691571 GGTTTAAAGC
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (101 bp):
TAGGCAAGCTAGTGTTTGCTGCATCTACATCTCATTTTAGGTATGAAATTGATGCACTTCATCCA
GAAACTAAAATAATATGAAAAATGTATTGTATTTAA
Found at i:2693380 original size:4 final size:4
Alignment explanation
Indices: 2693371--2693412 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
2693361 TAGATGCCAA
2693371 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
2693413 GTGTGCATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:2694388 original size:179 final size:179
Alignment explanation
Indices: 2694109--2694447 Score: 563
Period size: 179 Copynumber: 1.9 Consensus size: 179
2694099 GTTTATGATA
* *
2694109 TCATAGATGCCCTACCTTTGAGAAAGTAAGAGATGCTCGGATTAATTGGTAAACATGTTAAGTTG
1 TCATAGATGCCCTACCTGTGAGAAAGTAAGAGATGCTCAGATTAATTGGTAAACATGTTAAGTTG
* ** * *
2694174 TAGTTTCTCATTCGGTCAGATTATTATATCAAATCAGATATCAACTTAATTAGGCTGTTTA-TCT
66 TACTTTCTCATTCAATCAGATTATGATATCAAATCAAATATCAACTTAATTAGGCTG-TTACTCT
*
2694238 TTTGACTACTTTTGAGTACCAGTAAGATATAGCAATGGTCATTTTTTACT
130 TTTGACTACTTTTGAGTACCAATAAGATATAGCAATGGTCATTTTTTACT
*
2694288 TCATAGATGCCCTACCTGTGAGAAAGTAAGAGATGCTCAGATTAATTGGTAAACATGTTTAGTTG
1 TCATAGATGCCCTACCTGTGAGAAAGTAAGAGATGCTCAGATTAATTGGTAAACATGTTAAGTTG
* *
2694353 TTCTTTCTCATTTAATCAGATTATGATATCAAATCAAATATCAACTTAATTAGGCTGTTACTCTT
66 TACTTTCTCATTCAATCAGATTATGATATCAAATCAAATATCAACTTAATTAGGCTGTTACTCTT
2694418 TTGACTACTTTTGAGTACCAATAAGATATA
131 TTGACTACTTTTGAGTACCAATAAGATATA
2694448 CTTTTCATTC
Statistics
Matches: 148, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
178 3 0.02
179 145 0.98
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (179 bp):
TCATAGATGCCCTACCTGTGAGAAAGTAAGAGATGCTCAGATTAATTGGTAAACATGTTAAGTTG
TACTTTCTCATTCAATCAGATTATGATATCAAATCAAATATCAACTTAATTAGGCTGTTACTCTT
TTGACTACTTTTGAGTACCAATAAGATATAGCAATGGTCATTTTTTACT
Found at i:2696864 original size:3 final size:3
Alignment explanation
Indices: 2696856--2696896 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2696846 TATACACGTG
2696856 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2696897 TTTATAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2699185 original size:37 final size:36
Alignment explanation
Indices: 2699082--2699186 Score: 92
Period size: 37 Copynumber: 2.8 Consensus size: 36
2699072 AAAAAGTAAT
2699082 AATATA-ATATTAAAAAATAATAAAAATATAATTTTATG
1 AATATATATATTAAAAAAT-AT--AAATATAATTTTATG
* *
2699120 AATATATATGATTAAAATAT-TAGTATATAATATTT-T-
1 AATATATAT-ATTAAAAAATATA-AATATAAT-TTTATG
2699156 AATATAATTATATTAAAAAATATAAATATAA
1 AATAT-A-TATATTAAAAAATATAAATATAA
2699187 ATATAAATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
36 6 0.11
37 24 0.43
38 15 0.27
39 2 0.04
40 9 0.16
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (36 bp):
AATATATATATTAAAAAATATAAATATAATTTTATG
Found at i:2700182 original size:21 final size:21
Alignment explanation
Indices: 2700157--2700196 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2700147 TAAATATATT
2700157 TAATTTTTATAATT-TTTTATA
1 TAATTTTTAT-ATTATTTTATA
2700178 TAATTTTTATATTATTTTA
1 TAATTTTTATATTATTTTA
2700197 AATATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TAATTTTTATATTATTTTATA
Found at i:2700184 original size:11 final size:11
Alignment explanation
Indices: 2700157--2700195 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2700147 TAAATATATT
2700157 TAATTTTTATA
1 TAATTTTTATA
*
2700168 -ATTTTTTATA
1 TAATTTTTATA
2700178 TAATTTTTATA
1 TAATTTTTATA
*
2700189 TTATTTT
1 TAATTTT
2700196 AAATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:2700349 original size:2 final size:2
Alignment explanation
Indices: 2700342--2700366 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2700332 TACCATAAAC
2700342 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 A
2700367 AACACTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2704173 original size:357 final size:357
Alignment explanation
Indices: 2703518--2704233 Score: 1414
Period size: 357 Copynumber: 2.0 Consensus size: 357
2703508 AGCATACCAG
2703518 CTTGGGAAAGCCACCAGTTATCATCATATGGAACTTGCCACACAAAGTAGCCCAGCAACTTCTTT
1 CTTGGGAAAGCCACCAGTTATCATCATATGGAACTTGCCACACAAAGTAGCCCAGCAACTTCTTT
2703583 TCCTTGGCATACGTAACTTTGACAACCTCAACATCATCGAAACCAATCCAGGTCGTTCCTACAGC
66 TCCTTGGCATACGTAACTTTGACAACCTCAACATCATCGAAACCAATCCAGGTCGTTCCTACAGC
2703648 GCAGTAATTCACTACGTAAATAGCATTATACACTGTTTTGGCTCGATATATTTGAATATAATTCC
131 GCAGTAATTCACTACGTAAATAGCATTATACACTGTTTTGGCTCGATATATTTGAATATAATTCC
*
2703713 TGATGTCCTTGTAGGTCACCTTCCCGGTTTCTGAAATAACCGGCCCTGATTCTGGTGCGCCAATG
196 TGATGTCCTTGTAGGTCACCTTCCCGGTTTCTGAAATAACCGGCCCTGATGCTGGTGCGCCAATG
2703778 ACGTTATACTTGAGGTCCACAAGTGTCCACGTGTATCCATAGAAAGGCAACCCCAAAACCAACTT
261 ACGTTATACTTGAGGTCCACAAGTGTCCACGTGTATCCATAGAAAGGCAACCCCAAAACCAACTT
2703843 ATTGGCTGGTAATCCTCCATCAATCCATGATT
326 ATTGGCTGGTAATCCTCCATCAATCCATGATT
2703875 CTTGGGAAAGCCACCAGTTATCATCATATGGAACTTGCCACACAAAGTAGCCCAGCAACTTCTTT
1 CTTGGGAAAGCCACCAGTTATCATCATATGGAACTTGCCACACAAAGTAGCCCAGCAACTTCTTT
*
2703940 TCCTTGGCATACGTAACTTTGACAACCTCAACATCATCGAAACCAATCCAGGTCGTTCCTACAGG
66 TCCTTGGCATACGTAACTTTGACAACCTCAACATCATCGAAACCAATCCAGGTCGTTCCTACAGC
2704005 GCAGTAATTCACTACGTAAATAGCATTATACACTGTTTTGGCTCGATATATTTGAATATAATTCC
131 GCAGTAATTCACTACGTAAATAGCATTATACACTGTTTTGGCTCGATATATTTGAATATAATTCC
2704070 TGATGTCCTTGTAGGTCACCTTCCCGGTTTCTGAAATAACCGGCCCTGATGCTGGTGCGCCAATG
196 TGATGTCCTTGTAGGTCACCTTCCCGGTTTCTGAAATAACCGGCCCTGATGCTGGTGCGCCAATG
2704135 ACGTTATACTTGAGGTCCACAAGTGTCCACGTGTATCCATAGAAAGGCAACCCCAAAACCAACTT
261 ACGTTATACTTGAGGTCCACAAGTGTCCACGTGTATCCATAGAAAGGCAACCCCAAAACCAACTT
2704200 ATTGGCTGGTAATCCTCCATCAATCCATGATT
326 ATTGGCTGGTAATCCTCCATCAATCCATGATT
2704232 CT
1 CT
2704234 ATACCATAAT
Statistics
Matches: 357, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
357 357 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (357 bp):
CTTGGGAAAGCCACCAGTTATCATCATATGGAACTTGCCACACAAAGTAGCCCAGCAACTTCTTT
TCCTTGGCATACGTAACTTTGACAACCTCAACATCATCGAAACCAATCCAGGTCGTTCCTACAGC
GCAGTAATTCACTACGTAAATAGCATTATACACTGTTTTGGCTCGATATATTTGAATATAATTCC
TGATGTCCTTGTAGGTCACCTTCCCGGTTTCTGAAATAACCGGCCCTGATGCTGGTGCGCCAATG
ACGTTATACTTGAGGTCCACAAGTGTCCACGTGTATCCATAGAAAGGCAACCCCAAAACCAACTT
ATTGGCTGGTAATCCTCCATCAATCCATGATT
Found at i:2707426 original size:23 final size:23
Alignment explanation
Indices: 2707373--2707426 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
2707363 TTTTAAAAAA
2707373 TATTATTTAATAAATATAATATTT
1 TATT-TTTAATAAATATAATATTT
* * *
2707397 AAATTTTAA-AAATTATAATCTTT
1 TATTTTTAATAAA-TATAATATTT
2707420 TATTTTT
1 TATTTTT
2707427 TAAGCTGTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 3 0.12
23 19 0.79
24 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTTTTAATAAATATAATATTT
Found at i:2707637 original size:21 final size:22
Alignment explanation
Indices: 2707613--2707653 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2707603 ATATTTTGTA
2707613 AAATTACAAGTAT-ATAAATAG
1 AAATTACAAGTATCATAAATAG
*
2707634 AAATTACAATTATCATAAAT
1 AAATTACAAGTATCATAAAT
2707654 TTTTAGATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (22 bp):
AAATTACAAGTATCATAAATAG
Found at i:2708579 original size:21 final size:22
Alignment explanation
Indices: 2708547--2708590 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
2708537 CTGTTACATT
2708547 AAAGATTTCATTT-GAACTTTG
1 AAAGATTTCATTTAGAACTTTG
*
2708568 AAAG-TTTGCATTTAGATCTTTG
1 AAAGATTT-CATTTAGAACTTTG
2708590 A
1 A
2708591 TACCTATCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 3 0.15
21 9 0.45
22 8 0.40
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (22 bp):
AAAGATTTCATTTAGAACTTTG
Found at i:2711575 original size:24 final size:24
Alignment explanation
Indices: 2711534--2711582 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2711524 ATTATAATAT
*
2711534 AATATAATATAAAAAAATAAGACA
1 AATATAATATAAAAAAATAAAACA
*
2711558 AATATAA-ATATAATAAATAAAACA
1 AATATAATATA-AAAAAATAAAACA
2711582 A
1 A
2711583 TTTAGTGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (24 bp):
AATATAATATAAAAAAATAAAACA
Found at i:2712167 original size:21 final size:21
Alignment explanation
Indices: 2712141--2712181 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2712131 TTAATTTTAT
*
2712141 AAATTTAATTTATATTAAATA
1 AAATTTAATTAATATTAAATA
* *
2712162 AAATTTGATTAATTTTAAAT
1 AAATTTAATTAATATTAAAT
2712182 TATTATTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATTTAATTAATATTAAATA
Found at i:2712202 original size:36 final size:39
Alignment explanation
Indices: 2712131--2712203 Score: 100
Period size: 36 Copynumber: 1.9 Consensus size: 39
2712121 ATAGTTTATT
2712131 TTAATTTTATAAATTTAATTTATATTAAATAAAATTTGA
1 TTAATTTTATAAATTTAATTTATATTAAATAAAATTTGA
*
2712170 TTAA-TTT-TAAATTATTATTTAT-TT-AATAAAATTT
1 TTAATTTTATAAATT-TAATTTATATTAAATAAAATTT
2712204 TTATGTAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 10 0.31
37 8 0.25
38 10 0.31
39 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (39 bp):
TTAATTTTATAAATTTAATTTATATTAAATAAAATTTGA
Found at i:2712484 original size:21 final size:20
Alignment explanation
Indices: 2712443--2712484 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
2712433 TATTTAAAAA
*
2712443 ATATTTTTATATTAATTTTT
1 ATATTTTTATATTAATATTT
2712463 ATATATTTTATAATTAA-ATTT
1 ATAT-TTTTAT-ATTAATATTT
2712484 A
1 A
2712485 AATAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATTTTTATATTAATATTT
Found at i:2712521 original size:18 final size:19
Alignment explanation
Indices: 2712481--2712521 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2712471 TATAATTAAA
2712481 TTTAAATAAAAATATAATAT
1 TTTAAATAAAAATAT-ATAT
*
2712501 TTTAATTAAAAATAT-TAT
1 TTTAAATAAAAATATATAT
2712519 TTT
1 TTT
2712522 GAGTGGATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
20 14 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAAATAAAAATATATAT
Found at i:2712717 original size:24 final size:25
Alignment explanation
Indices: 2712668--2712717 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
2712658 TAAAAAATAT
* *
2712668 AATTTAAAATTATTATTTATATTAA
1 AATTTAAAATTATAATATATATTAA
2712693 AATTTAAAA-TATAATATATATTAA
1 AATTTAAAATTATAATATATATTAA
2712717 A
1 A
2712718 TATAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AATTTAAAATTATAATATATATTAA
Found at i:2712755 original size:19 final size:19
Alignment explanation
Indices: 2712700--2712755 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 19
2712690 TAAAATTTAA
*
2712700 AATATAATATATATTAAATAT
1 AATATAA-AT-TATTAAAAAT
2712721 AATATAAATT-TCTAAAAAT
1 AATATAAATTAT-TAAAAAT
2712740 AAT-TAAAATTATTAAA
1 AATAT-AAATTATTAAA
2712756 CATCATAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 2 0.06
19 19 0.61
20 3 0.10
21 7 0.23
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AATATAAATTATTAAAAAT
Found at i:2714244 original size:20 final size:20
Alignment explanation
Indices: 2714204--2714260 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
2714194 TTAACAGTAA
2714204 TTAA-TATTATATTA-A-TT
1 TTAATTATTATATTATATTT
*
2714221 TTAATTTTTATATTATATTT
1 TTAATTATTATATTATATTT
*
2714241 TTAATTATTAAATTTATATT
1 TTAATTATTATA-TTATATT
2714261 AATCTATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 4 0.12
18 9 0.27
19 1 0.03
20 12 0.36
21 7 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTAATTATTATATTATATTT
Found at i:2714461 original size:19 final size:19
Alignment explanation
Indices: 2714423--2714474 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2714413 GCTTGGGCGA
*
2714423 AATTTCTTTATTAGTTAAT
1 AATTTCTTTATTAGTAAAT
*
2714442 AATTTCTTTATTATGAAATAT
1 AATTTCTTTATTA-GTAA-AT
*
2714463 AATTTTTTTATT
1 AATTTCTTTATT
2714475 GTATAACGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 13 0.46
20 2 0.07
21 13 0.46
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (19 bp):
AATTTCTTTATTAGTAAAT
Found at i:2714614 original size:19 final size:17
Alignment explanation
Indices: 2714580--2714616 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
2714570 TGATTTAATA
2714580 ATTTTAATTTTTATATT
1 ATTTTAATTTTTATATT
2714597 ATTTTATATTTATTATATT
1 ATTTTA-ATTT-TTATATT
2714616 A
1 A
2714617 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 4 0.22
19 8 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTAATTTTTATATT
Found at i:2714848 original size:11 final size:12
Alignment explanation
Indices: 2714826--2714855 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
2714816 TTAGATCAAG
2714826 TTAAAATCAAAT
1 TTAAAATCAAAT
2714838 TTAAAAT-AAAT
1 TTAAAATCAAAT
2714849 TTAAAAT
1 TTAAAAT
2714856 TTAATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (12 bp):
TTAAAATCAAAT
Found at i:2716167 original size:11 final size:11
Alignment explanation
Indices: 2716124--2716175 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
2716114 GTCATATGGA
2716124 TTTTTTTTTTC
1 TTTTTTTTTTC
**
2716135 AATTTATTTTCCTC
1 --TTT-TTTTTTTC
2716149 TTTTTTTTTTC
1 TTTTTTTTTTC
2716160 TTTTTTTTTT-
1 TTTTTTTTTTC
2716170 TTTTTT
1 TTTTTT
2716176 GGCCTTCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
10 6 0.18
11 16 0.47
12 3 0.09
13 3 0.09
14 6 0.18
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:2719591 original size:2 final size:2
Alignment explanation
Indices: 2719584--2719631 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
2719574 GTTGCATGAA
* * *
2719584 AT AT AT AT AA AT AT AT AT AT AT AG AT AT AG 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
2719626 AT AT AT
1 AT AT AT
2719632 GATTAATTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2721193 original size:22 final size:22
Alignment explanation
Indices: 2721135--2721193 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
2721125 TTGATATAAT
* *
2721135 TATTTTTAAAATATATATTTAA
1 TATTTTTAAATTAAATATTTAA
*
2721157 TATATTTAAAAATTAAAT-TTTAA
1 TAT-TTT-TAAATTAAATATTTAA
2721180 TATTTTTAATATTA
1 TATTTTTAA-ATTA
2721194 TCTTTATGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 2 0.07
22 10 0.33
23 11 0.37
24 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTTTTAAATTAAATATTTAA
Found at i:2722867 original size:15 final size:16
Alignment explanation
Indices: 2722847--2722876 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2722837 TCTTAATAAG
2722847 TATTTTT-TAAAATTA
1 TATTTTTATAAAATTA
2722862 TATTTTTATAAAATT
1 TATTTTTATAAAATT
2722877 TTGAAATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTTATAAAATTA
Found at i:2726228 original size:19 final size:20
Alignment explanation
Indices: 2726204--2726242 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2726194 ATAAAAAATA
*
2726204 ATTTAAT-TATTTTTTTTAT
1 ATTTAATATATTATTTTTAT
2726223 ATTTAATATATTATTTTTAT
1 ATTTAATATATTATTTTTAT
2726243 TAATTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTAATATATTATTTTTAT
Found at i:2726250 original size:18 final size:19
Alignment explanation
Indices: 2726204--2726257 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
2726194 ATAAAAAATA
*
2726204 ATTTAATTATTTTTTTTAT
1 ATTTAATTATATTTTTTAT
2726223 ATTTAA-TATATTATTTT-T
1 ATTTAATTATATT-TTTTAT
2726241 A-TTAATTATATTTTTTA
1 ATTTAATTATATTTTTTA
2726258 AAATATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 8 0.26
18 13 0.42
19 10 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTAATTATATTTTTTAT
Found at i:2733643 original size:11 final size:11
Alignment explanation
Indices: 2733629--2733663 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2733619 GCAAAAGAAT
2733629 AACAAAAAAAA
1 AACAAAAAAAA
2733640 AACAAAAAAAA
1 AACAAAAAAAA
*
2733651 AAGAAAAGAAAA
1 AACAAAA-AAAA
2733663 A
1 A
2733664 TATAAGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.89, C:0.06, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAAAAA
Found at i:2735210 original size:2 final size:2
Alignment explanation
Indices: 2735203--2735228 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2735193 CCTTGACATG
2735203 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
2735229 CCTCCTTTAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2742566 original size:2 final size:2
Alignment explanation
Indices: 2742529--2742555 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2742519 GCAATGAAGG
2742529 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 A
2742556 CACAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2751811 original size:9 final size:9
Alignment explanation
Indices: 2751797--2751830 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
2751787 CCCAGATCTC
2751797 TCTTTTTTT
1 TCTTTTTTT
2751806 TCTTTTTTT
1 TCTTTTTTT
2751815 T-TTTTTTT
1 TCTTTTTTT
2751823 TCTTTTTT
1 TCTTTTTT
2751831 CCCCTTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:2752683 original size:2 final size:2
Alignment explanation
Indices: 2752676--2752718 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2752666 ACTTGAAAGA
2752676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2752718 A
1 A
2752719 GTGTTTACCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2761656 original size:109 final size:108
Alignment explanation
Indices: 2761465--2761682 Score: 400
Period size: 109 Copynumber: 2.0 Consensus size: 108
2761455 TGCACCCAAA
*
2761465 AAAGGTATATACCTTAATGACAAATCATATTTGCAAAAAGATTCATGAATTGTGTAGTTTTAAAT
1 AAAGGTATATACCTTAATGACAAATCATATTTGCAAAAAGATTCATGAATTGTGTAGTTTAAAAT
*
2761530 TACTCTCGATCTAAAAGTAAATGTCTGGGACATGAGAATTGTGC
66 TACTCTCAATCTAAAAGTAAAT-TCTGGGACATGAGAATTGTGC
*
2761574 AAAGGTATCTACCTTAATGACAAATCATATTTGCAAAAAGATTCATGAATTGTGTAGTTTAAAAT
1 AAAGGTATATACCTTAATGACAAATCATATTTGCAAAAAGATTCATGAATTGTGTAGTTTAAAAT
2761639 TACTCTCAATCTAAAAGTAAATTCTGGGACATGAGAATTGTGC
66 TACTCTCAATCTAAAAGTAAATTCTGGGACATGAGAATTGTGC
2761682 A
1 A
2761683 GGAAACAACA
Statistics
Matches: 106, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
108 22 0.21
109 84 0.79
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.33
Consensus pattern (108 bp):
AAAGGTATATACCTTAATGACAAATCATATTTGCAAAAAGATTCATGAATTGTGTAGTTTAAAAT
TACTCTCAATCTAAAAGTAAATTCTGGGACATGAGAATTGTGC
Found at i:2768277 original size:2 final size:2
Alignment explanation
Indices: 2768270--2768295 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2768260 TGCCATTTGA
2768270 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
2768296 TCTTTATTAT
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):
AT
Found at i:2768424 original size:3 final size:3
Alignment explanation
Indices: 2768416--2768447 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2768406 AAATTCAGAT
2768416 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2768448 TTAACCTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2772075 original size:31 final size:31
Alignment explanation
Indices: 2772038--2772098 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
2772028 CAAGAGGATA
2772038 AAAATCACAAAGTAAGAGAATAGAGAAAGAT
1 AAAATCACAAAGTAAGAGAATAGAGAAAGAT
2772069 AAAATCACAAAGTAAGAGAATAGAGAAAGA
1 AAAATCACAAAGTAAGAGAATAGAGAAAGA
2772099 CCAGGCGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.62, C:0.07, G:0.20, T:0.11
Consensus pattern (31 bp):
AAAATCACAAAGTAAGAGAATAGAGAAAGAT
Found at i:2772341 original size:38 final size:39
Alignment explanation
Indices: 2772288--2772362 Score: 109
Period size: 38 Copynumber: 1.9 Consensus size: 39
2772278 TGTAATAAAT
*
2772288 ATATATATAATTTTATAATATATTTTTTATAATAATTTAA
1 ATATATATAATTTTATAATATATATTTTAT-ATAATTTAA
*
2772328 ATATATAT-A-TTTATAATATGTATTTTATATAATTT
1 ATATATATAATTTTATAATATATATTTTATATAATTT
2772363 TATTAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 7 0.21
38 17 0.52
39 1 0.03
40 8 0.24
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (39 bp):
ATATATATAATTTTATAATATATATTTTATATAATTTAA
Found at i:2772352 original size:27 final size:24
Alignment explanation
Indices: 2772289--2772345 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
2772279 GTAATAAATA
*
2772289 TATATATAATTTTATAATATATTTTT
1 TATA-ATAA-TTTATAATATATTATT
2772315 TATAATAATTTA-AATATATATATT
1 TATAATAATTTATAATATAT-TATT
2772339 TATAATA
1 TATAATA
2772346 TGTATTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 7 0.24
24 14 0.48
25 4 0.14
26 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATAATAATTTATAATATATTATT
Found at i:2772354 original size:14 final size:14
Alignment explanation
Indices: 2772290--2772356 Score: 63
Period size: 15 Copynumber: 5.0 Consensus size: 14
2772280 TAATAAATAT
2772290 ATATATAATTTTATA
1 ATATAT-ATTTTATA
2772305 ATATAT-TTTT-T-
1 ATATATATTTTATA
*
2772316 ATA-ATAATTTA-A
1 ATATATATTTTATA
2772328 ATATATATATTTATA
1 ATATATAT-TTTATA
*
2772343 ATATGTATTTTATA
1 ATATATATTTTATA
2772357 TAATTTTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
10 2 0.05
11 6 0.14
12 4 0.09
13 7 0.16
14 10 0.23
15 14 0.33
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (14 bp):
ATATATATTTTATA
Found at i:2772604 original size:36 final size:38
Alignment explanation
Indices: 2772550--2772625 Score: 113
Period size: 38 Copynumber: 2.0 Consensus size: 38
2772540 TTGTATGTAA
2772550 TAAATATATATAATTTTATAATA-TATTTTATAATAATT
1 TAAATATATATAATTTTATAATAGTATTTTAT-ATAATT
2772588 TAAATATATAT-A-TTTATAATATGTATTTTATATAATT
1 TAAATATATATAATTTTATAATA-GTATTTTATATAATT
2772625 T
1 T
2772626 TATTAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
36 9 0.25
37 8 0.22
38 19 0.53
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (38 bp):
TAAATATATATAATTTTATAATAGTATTTTATATAATT
Found at i:2772627 original size:24 final size:22
Alignment explanation
Indices: 2772554--2772628 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 22
2772544 ATGTAATAAA
2772554 TATATATAATTTTATAATATATTT
1 TATA-ATAATTTTAT-ATATATTT
*
2772578 TATAATAATTTAAATATATATATT
1 TATAATAATTT-TATATATAT-TT
2772602 TATAATATGTATTTTATATA-ATTT
1 TATAATA---ATTTTATATATATTT
2772626 TAT
1 TAT
2772629 TAAAAAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
23 13 0.30
24 20 0.45
25 2 0.05
26 5 0.11
27 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (22 bp):
TATAATAATTTTATATATATTT
Found at i:2772639 original size:36 final size:36
Alignment explanation
Indices: 2772550--2772639 Score: 85
Period size: 36 Copynumber: 2.4 Consensus size: 36
2772540 TTGTATGTAA
*
2772550 TAAATATATATAATTTTATAATATATTTTATAATAATT
1 TAAATATA-A-AAATTTATAATATATTTTATAATAATT
* *
2772588 TAAATATATATATTTATAATATGTATTTTAT-ATAATT
1 TAAATATAAAAATTTATAATA--TATTTTATAATAATT
* *
2772625 TTATTA-AAAAATTTA
1 TAAATATAAAAATTTA
2772640 AAAAATATGT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
36 17 0.40
37 10 0.23
38 16 0.37
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (36 bp):
TAAATATAAAAATTTATAATATATTTTATAATAATT
Found at i:2775900 original size:15 final size:14
Alignment explanation
Indices: 2775865--2775919 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
2775855 AAAAATATTT
2775865 TAAATATAATTATAA
1 TAAATATAATTA-AA
*
2775880 T-TATATCAATTAAA
1 TAAATAT-AATTAAA
*
2775894 TAAATATTATATAAA
1 TAAATATAAT-TAAA
2775909 TAAAT-TAATTA
1 TAAATATAATTA
2775920 TCGAGTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 2 0.06
14 12 0.36
15 19 0.58
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAATATAATTAAA
Found at i:2785329 original size:2 final size:2
Alignment explanation
Indices: 2785322--2785358 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2785312 TCCGAGATAA
2785322 AT AT AT 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 AT AT AT A
2785359 ATGTGTGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2787246 original size:33 final size:33
Alignment explanation
Indices: 2787178--2787251 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
2787168 ATTAAATATT
* * *
2787178 ATATTAATATTTATTTAATAATATTAATGTAAA
1 ATATTTATATGTATTTAATAATATTAATATAAA
2787211 ATATTTATATGTATTTAATAA-ATT-ATAATATAA
1 ATATTTATATGTATTTAATAATATTAAT-ATA-AA
2787244 ATATTTAT
1 ATATTTAT
2787252 TAAAATATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 2 0.06
32 5 0.14
33 29 0.81
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (33 bp):
ATATTTATATGTATTTAATAATATTAATATAAA
Found at i:2790680 original size:32 final size:32
Alignment explanation
Indices: 2790614--2790682 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
2790604 TTGCTAAAGA
*
2790614 AATTTTTTGAGTTATTATATTAAATAAATTAT
1 AATTTTTTGAGTTATTATATTAAATAAATAAT
2790646 AATTTTTAATGAGTTATTATATT-AA-AAATAAT
1 AATTTTT--TGAGTTATTATATTAAATAAATAAT
2790678 AATTT
1 AATTT
2790683 AATTATATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
32 18 0.53
33 2 0.06
34 14 0.41
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (32 bp):
AATTTTTTGAGTTATTATATTAAATAAATAAT
Found at i:2793487 original size:15 final size:15
Alignment explanation
Indices: 2793467--2793508 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
2793457 AATTTAAATC
2793467 TAATTTTTTTAATTA
1 TAATTTTTTTAATTA
* *
2793482 TTATTTTTTTCATTA
1 TAATTTTTTTAATTA
2793497 TAATTTATTTTA
1 TAATTT-TTTTA
2793509 CCATCATCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (15 bp):
TAATTTTTTTAATTA
Found at i:2794213 original size:2 final size:2
Alignment explanation
Indices: 2794206--2794232 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2794196 ATGTGTTGTG
2794206 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2794233 GTATGTACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2795222 original size:2 final size:2
Alignment explanation
Indices: 2795215--2795241 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2795205 TTCATGCAGT
2795215 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2795242 GTTCTATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2797154 original size:36 final size:35
Alignment explanation
Indices: 2797075--2797154 Score: 81
Period size: 36 Copynumber: 2.2 Consensus size: 35
2797065 TTTAATATTT
* *
2797075 ATAAATAAATATATATTTAATAAATTATTTTTTAA
1 ATAAATAAAAATATATTTAATAAATAATTTTTTAA
* * *
2797110 ATTTAATAAAAATATTCTATTAA-AAATAATTTTTTTA
1 A-TAAATAAAAATA-TAT-TTAATAAATAATTTTTTAA
2797147 ATAAATAA
1 ATAAATAA
2797155 TTAAATAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
35 1 0.03
36 16 0.44
37 15 0.42
38 4 0.11
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (35 bp):
ATAAATAAAAATATATTTAATAAATAATTTTTTAA
Found at i:2797736 original size:5 final size:5
Alignment explanation
Indices: 2797726--2797759 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
2797716 ATTACAAATA
2797726 TATAT TATAT TATAT TATAT TATA- TATTAT TATA
1 TATAT TATAT TATAT TATAT TATAT TA-TAT TATA
2797760 GCTGACTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 2 0.07
5 23 0.85
6 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:2798014 original size:20 final size:19
Alignment explanation
Indices: 2797993--2798046 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
2797983 ATATTAAGAT
2797993 TTTATATAAAAATATAATA
1 TTTATATAAAAATATAATA
* *
2798012 TTTATATTAAATATGTAATA
1 TTTATA-TAAAAATATAATA
* *
2798032 ATTATATTAAAATAT
1 TTTATATAAAAATAT
2798047 TTTATATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TTTATATAAAAATATAATA
Found at i:2798257 original size:2 final size:2
Alignment explanation
Indices: 2798250--2798274 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2798240 ACAATCCCAT
2798250 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2798275 GTTTTCGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2798452 original size:15 final size:15
Alignment explanation
Indices: 2798434--2798477 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2798424 TACATAATCA
*
2798434 TAAAATTAATAAAAT
1 TAAAAATAATAAAAT
*
2798449 TAAAAATAATAATAT
1 TAAAAATAATAAAAT
*
2798464 TAAATATATATAAA
1 TAAAAATA-ATAAA
2798478 TTATTAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAAAATAATAAAAT
Found at i:2798499 original size:24 final size:28
Alignment explanation
Indices: 2798455--2798506 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 28
2798445 AAATTAAAAA
2798455 TAATAATATTAAATATATAT-AAATTAT
1 TAATAATATTAAATATATATAAAATTAT
2798482 TAATAA-ATTAAAT-T-TATAAAATTAT
1 TAATAATATTAAATATATATAAAATTAT
2798507 AAAACATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 3 0.12
25 8 0.33
26 7 0.29
27 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TAATAATATTAAATATATATAAAATTAT
Found at i:2799760 original size:2 final size:2
Alignment explanation
Indices: 2799755--2799782 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2799745 ATGTCACACA
2799755 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2799783 GCAACTCTGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2803638 original size:38 final size:39
Alignment explanation
Indices: 2803595--2803687 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 39
2803585 AGTTTGTACT
*
2803595 GTCACCTTTGCCTCCCTTGATGT-AACTTGCAAGTTT-AA
1 GTCACCTTTGCCTCCCTTCATGTGAA-TTGCAAGTTTAAA
** * *
2803633 GTCACCTTTGCCTCTTTTTCTTGTGAATTGTAAGTTTAAA
1 GTCACCTTTGCCTC-CCTTCATGTGAATTGCAAGTTTAAA
2803673 GTCACCTTTGCCTCC
1 GTCACCTTTGCCTCC
2803688 TTTCGCCATT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
38 14 0.30
39 14 0.30
40 18 0.39
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.41
Consensus pattern (39 bp):
GTCACCTTTGCCTCCCTTCATGTGAATTGCAAGTTTAAA
Found at i:2804557 original size:2 final size:2
Alignment explanation
Indices: 2804550--2804581 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2804540 ATTGTTTTCA
2804550 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
2804582 TAAACATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2805806 original size:2 final size:2
Alignment explanation
Indices: 2805799--2805832 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2805789 GTCTATTGAA
2805799 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
2805833 TTAGCAGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2810980 original size:22 final size:21
Alignment explanation
Indices: 2810940--2810980 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
2810930 TTAATATATA
2810940 ATAAATATATAATATTTTATT
1 ATAAATATATAATATTTTATT
2810961 ATAAATGATAATAA-ATTTTA
1 ATAAAT-AT-ATAATATTTTA
2810981 ATTTTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATAAATATATAATATTTTATT
Found at i:2811015 original size:18 final size:18
Alignment explanation
Indices: 2810968--2811019 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
2810958 ATTATAAATG
2810968 ATAATAA-ATT-TTAATTT
1 ATAATAATATTATT-ATTT
2810985 -TAATTAATA-TATTATTT
1 ATAA-TAATATTATTATTT
2811002 ATAATAATATTATTATTT
1 ATAATAATATTATTATTT
2811020 TTAAGTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.10
17 13 0.43
18 14 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATAATAATATTATTATTT
Found at i:2811028 original size:24 final size:23
Alignment explanation
Indices: 2811001--2811045 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2810991 ATATATTATT
* *
2811001 TATAATAATATTATTATTTTTAAG
1 TATAATAA-ATAATAATTTTTAAG
2811025 TATAATAAATAATAATTTTTA
1 TATAATAAATAATAATTTTTA
2811046 TTATTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TATAATAAATAATAATTTTTAAG
Found at i:2811107 original size:10 final size:11
Alignment explanation
Indices: 2811081--2811106 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2811071 ATATATAATA
2811081 ATTTTAAAAAT
1 ATTTTAAAAAT
2811092 ATTTTAAAAAT
1 ATTTTAAAAAT
2811103 ATTT
1 ATTT
2811107 ATTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:2811135 original size:25 final size:23
Alignment explanation
Indices: 2811096--2811151 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
2811086 AAAAATATTT
2811096 TAAAAATATTTATTAATTAAATA
1 TAAAAATATTTATTAATTAAATA
**
2811119 TAAAAATA--TATTAATTATTTA
1 TAAAAATATTTATTAATTAAATA
*
2811140 AAAAAATATTTA
1 TAAAAATATTTA
2811152 CCTTAACTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 18 0.64
23 10 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAAAATATTTATTAATTAAATA
Found at i:2812358 original size:2 final size:2
Alignment explanation
Indices: 2812340--2812432 Score: 56
Period size: 2 Copynumber: 49.5 Consensus size: 2
2812330 TTTAATAATT
* * * * *
2812340 TA TA TA TT TA TA T- TA TA TA TA AA T- TA TT TA TA TA TT TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
2812380 TA -A TT TA TA -A TA TA TA AA T- TT TA -A TA TA T- TCA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
2812418 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
2812433 TAATTTTTAT
Statistics
Matches: 70, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
1 7 0.10
2 62 0.89
3 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:2812366 original size:24 final size:23
Alignment explanation
Indices: 2812342--2812454 Score: 63
Period size: 24 Copynumber: 4.7 Consensus size: 23
2812332 TAATAATTTA
2812342 TATATT-TATATTATATATAAAT
1 TATATTATATATTATATATAAAT
* *
2812364 TAT-TTATATATT-TTTATAATT
1 TATATTATATATTATATATAAAT
* * *
2812385 TATAATATATAAATTTTA-ATATAT
1 TAT-AT-TATATATTATATATAAAT
2812409 TCATATATATATATATATATATATTAATT
1 T-ATAT-TATATAT-TATATATA--AA-T
* *
2812438 TTTATTATTTATTATAT
1 TATATTATATATTATAT
2812455 TTTATTTTAT
Statistics
Matches: 69, Mismatches: 11, Indels: 18
0.70 0.11 0.18
Matches are distributed among these distances:
21 12 0.17
22 9 0.13
23 1 0.01
24 21 0.30
25 6 0.09
26 8 0.12
27 6 0.09
28 4 0.06
29 2 0.03
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.58
Consensus pattern (23 bp):
TATATTATATATTATATATAAAT
Found at i:2812467 original size:17 final size:18
Alignment explanation
Indices: 2812428--2812467 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
2812418 TATATATATA
2812428 TATATTAATTTTTATTAT
1 TATATTAATTTTTATTAT
2812446 T-TATT-ATATTTTATT-T
1 TATATTAAT-TTTTATTAT
2812462 TATATT
1 TATATT
2812468 TTAATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 4 0.20
17 15 0.75
18 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TATATTAATTTTTATTAT
Found at i:2812645 original size:18 final size:18
Alignment explanation
Indices: 2812619--2812692 Score: 50
Period size: 18 Copynumber: 4.1 Consensus size: 18
2812609 GTTTATTATC
*
2812619 TTTATATTAATATTTAAA
1 TTTAAATTAATATTTAAA
2812637 TTTAAATTAAATAATATT--A
1 TTTAAATT-AAT-AT-TTAAA
2812656 TTT--ATTAGATATTTAAA
1 TTTAAATTA-ATATTTAAA
*
2812673 TTTATAA-AAATATTTAAA
1 TTTA-AATTAATATTTAAA
2812691 TT
1 TT
2812693 CAATAAGTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
15 2 0.04
16 3 0.07
17 9 0.20
18 18 0.40
19 8 0.18
20 3 0.07
21 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (18 bp):
TTTAAATTAATATTTAAA
Found at i:2812778 original size:14 final size:13
Alignment explanation
Indices: 2812761--2812831 Score: 54
Period size: 14 Copynumber: 5.2 Consensus size: 13
2812751 ATTTGAATAA
2812761 TAAAATTACATATT
1 TAAAATTA-ATATT
* *
2812775 TAAATTTATTATT
1 TAAAATTAATATT
*
2812788 TATAATATAA-ATT
1 TAAAAT-TAATATT
2812801 TAAATATTAAATATT
1 TAAA-ATT-AATATT
*
2812816 TAATGATTAATATT
1 TAA-AATTAATATT
2812830 TA
1 TA
2812832 TATTTTTTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 15 0.33
14 21 0.47
15 9 0.20
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (13 bp):
TAAAATTAATATT
Found at i:2812894 original size:30 final size:28
Alignment explanation
Indices: 2812770--2812885 Score: 80
Period size: 28 Copynumber: 4.1 Consensus size: 28
2812760 ATAAAATTAC
* * *
2812770 ATATTTAAATTTATTATTTATAA-TATA
1 ATATTTAAATTTATAAATAATAATTATA
* * *
2812797 A-ATTTAAATAT-TAAATATTTAATGATTA
1 ATATTTAAATTTATAAATA-ATAATTA-TA
*
2812825 ATATTTATATTTTTTATAAATAATAATTATA
1 ATATTTA-A--ATTTATAAATAATAATTATA
2812856 ATATTTAAATTTATAAA-AATAAATTA-A
1 ATATTTAAATTTATAAATAAT-AATTATA
2812883 ATA
1 ATA
2812886 ATTTTTAAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 18
0.70 0.11 0.18
Matches are distributed among these distances:
25 3 0.04
26 12 0.17
27 9 0.13
28 16 0.23
29 5 0.07
30 2 0.03
31 9 0.13
32 7 0.10
33 6 0.09
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
ATATTTAAATTTATAAATAATAATTATA
Found at i:2813296 original size:2 final size:2
Alignment explanation
Indices: 2813253--2813278 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2813243 ACACTTATCC
2813253 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
2813279 CAGCACAAAA
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):
AT
Found at i:2814024 original size:22 final size:20
Alignment explanation
Indices: 2814002--2814064 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
2813992 TAAAAATTAT
2814002 TTTTATATTAATATTCAAATA
1 TTTTATATTAATATT-AAATA
*
2814023 TTTTATAGTTAAAATTAAA-A
1 TTTTATA-TTAATATTAAATA
2814043 TTTTAT-TTAATTATTAAATA
1 TTTTATATTAA-TATTAAATA
2814063 TT
1 TT
2814065 CAAATATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
18 4 0.11
19 6 0.16
20 10 0.27
21 10 0.27
22 7 0.19
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTATATTAATATTAAATA
Found at i:2814392 original size:23 final size:25
Alignment explanation
Indices: 2814364--2814414 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
2814354 CAAAGCAATA
2814364 ATATATGTATA-A-ATTACGTTTAT
1 ATATATGTATAGATATTACGTTTAT
* *
2814387 ATATATTTATAGATATTATGTTTAT
1 ATATATGTATAGATATTACGTTTAT
2814412 ATA
1 ATA
2814415 ATATTAGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.42
24 1 0.04
25 13 0.54
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (25 bp):
ATATATGTATAGATATTACGTTTAT
Found at i:2816178 original size:18 final size:19
Alignment explanation
Indices: 2816157--2816199 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
2816147 TTTTTAATAT
2816157 AAATATAAAATTAT-TAAA
1 AAATATAAAATTATATAAA
* **
2816175 AAATTTTTAATTATATAAA
1 AAATATAAAATTATATAAA
2816194 AAATAT
1 AAATAT
2816200 TTTAAAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATATAAAATTATATAAA
Found at i:2816185 original size:31 final size:31
Alignment explanation
Indices: 2816147--2816207 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2816137 TTTAATATAT
*
2816147 TTTTTAATATAAATATAAAAT-TATTAAAAAA
1 TTTTTAAT-TAAATAAAAAATATATTAAAAAA
* *
2816178 TTTTTAATTATATAAAAAATATTTTAAAAA
1 TTTTTAATTAAATAAAAAATATATTAAAAA
2816208 TAAATATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TTTTTAATTAAATAAAAAATATATTAAAAAA
Found at i:2816202 original size:20 final size:18
Alignment explanation
Indices: 2816165--2816204 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 18
2816155 ATAAATATAA
2816165 AATTATTAAAAAATTTTT
1 AATTATTAAAAAATTTTT
2816183 AATTATATAAAAAATATTTT
1 AATTAT-TAAAAAAT-TTTT
2816203 AA
1 AA
2816205 AAATAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.30
19 8 0.40
20 6 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTATTAAAAAATTTTT
Found at i:2817359 original size:11 final size:11
Alignment explanation
Indices: 2817345--2817373 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2817335 ATCCATCTCT
2817345 TTCCTTTACCC
1 TTCCTTTACCC
2817356 TTCCTTTACCC
1 TTCCTTTACCC
2817367 TTCCTTT
1 TTCCTTT
2817374 CCAGTAATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.41, G:0.00, T:0.52
Consensus pattern (11 bp):
TTCCTTTACCC
Found at i:2824157 original size:5 final size:5
Alignment explanation
Indices: 2824147--2824171 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2824137 GAAAGCCTTT
2824147 GAGTC GAGTC GAGTC GAGTC GAGTC
1 GAGTC GAGTC GAGTC GAGTC GAGTC
2824172 TGGTCTGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (5 bp):
GAGTC
Found at i:2824780 original size:15 final size:15
Alignment explanation
Indices: 2824739--2824789 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
2824729 GACCATAAAT
2824739 AAATAAAATATTAATA
1 AAATAAAATA-TAATA
** * *
2824755 ATTTTAGATATAATA
1 AAATAAAATATAATA
2824770 AAATAAAATATAA-A
1 AAATAAAATATAATA
2824784 AAATAA
1 AAATAA
2824790 TTAAAATTTA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 7 0.26
15 14 0.52
16 6 0.22
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (15 bp):
AAATAAAATATAATA
Found at i:2824796 original size:18 final size:19
Alignment explanation
Indices: 2824766--2824819 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 19
2824756 TTTTAGATAT
*
2824766 AATAAAATAAAATATAAAA
1 AATAATATAAAATATAAAA
*
2824785 AATAAT-TAAAAT-T-TAA
1 AATAATATAAAATATAAAA
2824801 AATAATATAAATATATAAA
1 AATAATATAAA-ATATAAA
2824820 TATATCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 8 0.29
17 5 0.18
18 8 0.29
19 6 0.21
20 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AATAATATAAAATATAAAA
Found at i:2824804 original size:16 final size:16
Alignment explanation
Indices: 2824783--2824833 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
2824773 TAAAATATAA
2824783 AAAATAATTAAAATTT
1 AAAATAATTAAAATTT
*
2824799 AAAATAA-TATAAATAT
1 AAAATAATTA-AAATTT
*
2824815 ATAAATATATCAAAATTT
1 A-AAATA-ATTAAAATTT
2824833 A
1 A
2824834 TATAAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 2 0.07
16 13 0.46
17 5 0.18
18 7 0.25
19 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATAATTAAAATTT
Found at i:2824837 original size:20 final size:19
Alignment explanation
Indices: 2824812--2824852 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
2824802 ATAATATAAA
2824812 TATATAAATATATCAAAATT
1 TATATAAATATA-CAAAATT
*
2824832 TATATAAATATACAATATT
1 TATATAAATATACAAAATT
2824851 TA
1 TA
2824853 AAATAAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TATATAAATATACAAAATT
Found at i:2824842 original size:34 final size:34
Alignment explanation
Indices: 2824769--2824855 Score: 90
Period size: 34 Copynumber: 2.6 Consensus size: 34
2824759 TAGATATAAT
*
2824769 AAAATA-AAATATA-AAAAATAATTAAAATTTAA
1 AAAATATAAATATATAAAAATAATCAAAATTTAA
*
2824801 AATAATATAAATATATAAATAT-ATCAAAATTTATA
1 AA-AATATAAATATATAAAAATAATCAAAATTTA-A
* *
2824836 TAAATATACAATATTTAAAA
1 AAAATATA-AATATATAAAA
2824856 TAAAACTACT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
32 2 0.04
33 4 0.09
34 23 0.51
35 16 0.36
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (34 bp):
AAAATATAAATATATAAAAATAATCAAAATTTAA
Found at i:2824858 original size:20 final size:20
Alignment explanation
Indices: 2824815--2824859 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2824805 ATATAAATAT
*
2824815 ATAAATATATCAAAATTTAT
1 ATAAATATATCAAAATTTAA
*
2824835 ATAAATATA-CAATATTTAAA
1 ATAAATATATCAAAATTT-AA
2824855 ATAAA
1 ATAAA
2824860 ACTACTAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAATATATCAAAATTTAA
Found at i:2825196 original size:2 final size:2
Alignment explanation
Indices: 2825189--2825229 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2825179 CAGCTTAATA
2825189 AT AT AT AT AT 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 AT AT AT AT AT A
2825230 GAAAAGATGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2826594 original size:2 final size:2
Alignment explanation
Indices: 2826587--2826618 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2826577 ATTTATACCC
2826587 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2826619 ATTTCTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2826952 original size:3 final size:3
Alignment explanation
Indices: 2826937--2826975 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2826927 ATTTAGAGGG
*
2826937 AGA AGA GGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
2826976 CGAGTTGGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2827396 original size:10 final size:10
Alignment explanation
Indices: 2827367--2827397 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2827357 TTTGATCTGT
*
2827367 TTGCTTGAAT
1 TTGCTTGAAC
2827377 TTGCTTGAAC
1 TTGCTTGAAC
2827387 TTGCTTGAAC
1 TTGCTTGAAC
2827397 T
1 T
2827398 CCACACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45
Consensus pattern (10 bp):
TTGCTTGAAC
Found at i:2837329 original size:17 final size:18
Alignment explanation
Indices: 2837309--2837342 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2837299 TTAAAATTTA
2837309 ATTTGTATT-AATTTAAT
1 ATTTGTATTAAATTTAAT
*
2837326 ATTTTTATTAAATTTAA
1 ATTTGTATTAAATTTAA
2837343 AAATATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
ATTTGTATTAAATTTAAT
Found at i:2837358 original size:34 final size:34
Alignment explanation
Indices: 2837320--2837389 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
2837310 TTTGTATTAA
* *
2837320 TTTAATATTTTTATTAAAT-TTAAAAATATAATTT
1 TTTAATATTTATACTAAATATTAAAAATAT-ATTT
* *
2837354 TTTAATATTTATACTATATATTAAATATATATTT
1 TTTAATATTTATACTAAATATTAAAAATATATTT
2837388 TT
1 TT
2837390 ATAAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 22 0.71
35 9 0.29
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (34 bp):
TTTAATATTTATACTAAATATTAAAAATATATTT
Found at i:2837556 original size:29 final size:32
Alignment explanation
Indices: 2837523--2837587 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 32
2837513 TTTTTTATTA
*
2837523 AAATTTATTTTTTAAAT-T-TAATAAA-TTTT
1 AAATTTATTTTTTAAATATCGAATAAATTTTT
2837552 AAA--T-TTTTTTAAATATCGAATAAATTTTT
1 AAATTTATTTTTTAAATATCGAATAAATTTTT
2837581 AAATTTA
1 AAATTTA
2837588 AAAATAACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
26 10 0.34
27 2 0.07
28 6 0.21
29 10 0.34
31 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (32 bp):
AAATTTATTTTTTAAATATCGAATAAATTTTT
Found at i:2837574 original size:28 final size:27
Alignment explanation
Indices: 2837530--2837586 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
2837520 TTAAAATTTA
*
2837530 TTTTTTAAATTTAATAAA-TTTTAAAT
1 TTTTTTAAATTGAATAAATTTTTAAAT
2837556 TTTTTTAAATATCGAATAAATTTTTAAAT
1 TTTTTTAAAT-T-GAATAAATTTTTAAAT
2837585 TT
1 TT
2837587 AAAAATAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 10 0.37
27 1 0.04
28 6 0.22
29 10 0.37
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (27 bp):
TTTTTTAAATTGAATAAATTTTTAAAT
Found at i:2837911 original size:24 final size:23
Alignment explanation
Indices: 2837878--2838021 Score: 81
Period size: 24 Copynumber: 6.5 Consensus size: 23
2837868 ATGGTATAGA
*
2837878 AAATAAATAAAATAAATATAATAT
1 AAATATATAAAATAAATAT-ATAT
2837902 AAATATAT-AAAT--ATAT-TA-
1 AAATATATAAAATAAATATATAT
* *
2837920 AAATTTATAAAATAAA-ATTTAT
1 AAATATATAAAATAAATATATAT
* **
2837942 TAATATATCAAAATTTATATATAT
1 AAATATAT-AAAATAAATATATAT
* * * *
2837966 ATATATATAACAT-ATTAAATAT
1 AAATATATAAAATAAATATATAT
* *
2837988 -AAT-TATAAAAAAAAGCATAATAT
1 AAATATATAAAATAAA-TAT-ATAT
2838011 AAATATATAAA
1 AAATATATAAA
2838022 TTATTAATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 23
0.68 0.15 0.18
Matches are distributed among these distances:
18 7 0.08
19 6 0.07
20 8 0.09
21 10 0.11
22 13 0.15
23 18 0.20
24 21 0.24
25 6 0.07
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (23 bp):
AAATATATAAAATAAATATATAT
Found at i:2837928 original size:18 final size:18
Alignment explanation
Indices: 2837889--2837967 Score: 76
Period size: 18 Copynumber: 4.6 Consensus size: 18
2837879 AATAAATAAA
* *
2837889 ATAAATATAATATAAATAT
1 ATAAATATATTA-AAATTT
2837908 ATAAATATATTAAAATTT
1 ATAAATATATTAAAATTT
2837926 AT-AA-A-A-TAAAATTT
1 ATAAATATATTAAAATTT
* *
2837940 ATTAATATATCAAAATTT
1 ATAAATATATTAAAATTT
*
2837958 ATATATATAT
1 ATAAATATAT
2837968 ATATATAACA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.20
15 3 0.06
16 2 0.04
17 3 0.06
18 22 0.43
19 11 0.22
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAAATATATTAAAATTT
Found at i:2837955 original size:32 final size:33
Alignment explanation
Indices: 2837897--2837980 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 33
2837887 AAATAAATAT
*
2837897 AATATAAATATATAAATATATTAAAATTTATAA
1 AATATAAATATATAAATATATCAAAATTTATAA
* *
2837930 AATA-AAATTTATTAATATATCAAAATTTAT-A
1 AATATAAATATATAAATATATCAAAATTTATAA
* *
2837961 TATATATATATATAACATAT
1 AATATAAATATATAA-ATAT
2837981 TAAATATAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
31 4 0.10
32 30 0.71
33 8 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (33 bp):
AATATAAATATATAAATATATCAAAATTTATAA
Found at i:2838698 original size:25 final size:26
Alignment explanation
Indices: 2838656--2838725 Score: 65
Period size: 25 Copynumber: 2.7 Consensus size: 26
2838646 ATTTTTTATT
*
2838656 AAATATTTT-TAATTTATTATT-ATAA
1 AAATATTTTATAATATATT-TTCATAA
2838681 AAATATTTTATAA-ATATTTTCATAA
1 AAATATTTTATAATATATTTTCATAA
*
2838706 ATATAATTTTAATACATATA
1 AAAT-ATTTT-ATA-ATATA
2838726 AATTTTTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
24 2 0.05
25 20 0.54
26 8 0.22
27 3 0.08
28 1 0.03
29 3 0.08
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (26 bp):
AAATATTTTATAATATATTTTCATAA
Found at i:2838707 original size:12 final size:11
Alignment explanation
Indices: 2838649--2838709 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 11
2838639 CATCTCAATT
2838649 TTTTATTAAATA
1 TTTTA-TAAATA
*
2838661 TTTT-TAATTTA
1 TTTTATAA-ATA
2838672 TTATTATAAAAATA
1 TT-TTAT--AAATA
2838686 TTTTATAAATA
1 TTTTATAAATA
2838697 TTTTCATAAATA
1 TTTT-ATAAATA
2838709 T
1 T
2838710 AATTTTAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
10 3 0.07
11 13 0.32
12 14 0.34
13 5 0.12
14 4 0.10
15 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTATAAATA
Found at i:2839050 original size:3 final size:3
Alignment explanation
Indices: 2839042--2839085 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
2839032 TTAATGCTAT
*
2839042 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2839086 TCTTTCAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2842349 original size:32 final size:32
Alignment explanation
Indices: 2842312--2842396 Score: 145
Period size: 31 Copynumber: 2.7 Consensus size: 32
2842302 AATTATAGTC
*
2842312 ACCTTAAGATGGGAAAACAGAAAGGCTGTAAA
1 ACCTTAAGATGCGAAAACAGAAAGGCTGTAAA
2842344 ACCTTAAGATGCG-AAACAGAAAGGCTGTAAA
1 ACCTTAAGATGCGAAAACAGAAAGGCTGTAAA
*
2842375 ACCTTAAGATGCAAAAACAGAA
1 ACCTTAAGATGCGAAAACAGAA
2842397 TGTACAACTC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
31 30 0.60
32 20 0.40
ACGTcount: A:0.48, C:0.15, G:0.21, T:0.15
Consensus pattern (32 bp):
ACCTTAAGATGCGAAAACAGAAAGGCTGTAAA
Done.