Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 125 of 222
Found at i:40562397 original size:6 final size:6
Alignment explanation
Indices: 40562365--40562418 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
40562355 AAAGAAATTG
* * ** *
40562365 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
40562412 AAAGAA A
1 AAAGAA A
40562419 TCAAAATAGT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
5 3 0.08
6 35 0.92
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:40562478 original size:18 final size:18
Alignment explanation
Indices: 40562457--40562491 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40562447 AGAAAAGAAA
40562457 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
40562475 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
40562492 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:40567192 original size:30 final size:30
Alignment explanation
Indices: 40567107--40567203 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
40567097 TAAACTAAAA
* *
40567107 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
40567137 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
*
40567167 TGAGCTAAGGTTTAGCTTGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
40567196 ATGAGCTA
1 -TGAGCTA
40567204 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:40570511 original size:30 final size:30
Alignment explanation
Indices: 40570475--40570601 Score: 103
Period size: 30 Copynumber: 4.2 Consensus size: 30
40570465 AGCTCACTCC
40570475 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
40570505 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * * * * * *
40570535 CAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
40570565 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
40570595 TAGCTCA
1 TAGCTCA
40570602 TTTTAGTTTA
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
29 1 0.01
30 80 0.99
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:40573716 original size:12 final size:13
Alignment explanation
Indices: 40573694--40573722 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40573684 AAGTTTTATT
40573694 TTTATTTTATTTA
1 TTTATTTTATTTA
40573707 TTTA-TTTATTTA
1 TTTATTTTATTTA
40573719 TTTA
1 TTTA
40573723 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:40576108 original size:30 final size:30
Alignment explanation
Indices: 40576072--40576198 Score: 103
Period size: 30 Copynumber: 4.2 Consensus size: 30
40576062 AGCTCTCTCC
40576072 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
40576102 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * * * * * *
40576132 CAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
40576162 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
40576192 TAGCTCA
1 TAGCTCA
40576199 TTTTAGTTTA
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
29 1 0.01
30 80 0.99
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:40586743 original size:21 final size:20
Alignment explanation
Indices: 40586714--40586752 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
40586704 ACCAATAAAA
40586714 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCG-ATTGTAGC
40586734 TAAATTGAGCTCGATTGTA
1 TAAA-TGAGCTCGATTGTA
40586753 ACACCCCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAAATGAGCTCGATTGTAGC
Found at i:40588529 original size:48 final size:47
Alignment explanation
Indices: 40588387--40588922 Score: 635
Period size: 48 Copynumber: 11.3 Consensus size: 47
40588377 ACTGGGCCTG
* *
40588387 TCACATATATGCACTTTCAGCATTCCATCACAT--GCCATTTAGG-CTTA
1 TCACATATATACACTTTCA-CATT-CATCACATCGGCTA-TTAGGCCTTA
*
40588434 TAACATATATACACTTTCACATT-ATCACA----C-ATTAGG-CTTAA
1 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTT-A
*
40588475 TTACATATA-ACA-TTGTCACATTCATGCACATCGGCTATTAGGCCTTA
1 TCACATATATACACTT-TCACATTCAT-CACATCGGCTATTAGGCCTTA
40588522 TTCACATATATATACACTTTCACATTCATCACATC-GCTATTAGGCCTTA
1 -TCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
*
40588571 TAAGCACA-ATATAACAC-TTCACATTCATCACATTGGCTATTAAGGCCTTA
1 T---CACATATAT-ACACTTTCACATTCATCACATCGGCTATT-AGGCCTTA
*
40588621 TCACACATATACACTTTCACATTCATTCA-ATCGGC-ATTAGGCCTTA
1 TCACATATATACACTTTCACATTCA-TCACATCGGCTATTAGGCCTTA
* *
40588667 TCACATCATATATCACTTTCACATTCATTTACATCGGCCATTAGGCCTTA
1 TCACAT-ATATA-CACTTTCACATTCA-TCACATCGGCTATTAGGCCTTA
40588717 TCACATATATACACTTTCACATTCATCACATCGGC-ATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
40588763 TCACATATATACACCTTTCACATTCATCACATCGGCTATTAAGGCCTTAA
1 TCACATATATACA-CTTTCACATTCATCACATCGGCTATT-AGGCCTT-A
*
40588813 ACACATATATA-ACTTTCACATTCATCACATCGGCTATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
40588859 TCAACATATA-ACAACTTTCACATTCATCACATCGGCTCATTAGGCCTTA
1 TC-ACATATATAC-ACTTTCACATTCATCACATCGGCT-ATTAGGCCTTA
40588908 TCACATATATACACT
1 TCACATATATACACT
40588923 GTCTTTGGCT
Statistics
Matches: 441, Mismatches: 11, Indels: 73
0.84 0.02 0.14
Matches are distributed among these distances:
39 2 0.00
40 18 0.04
41 12 0.03
42 5 0.01
44 6 0.01
46 45 0.10
47 85 0.19
48 140 0.32
49 62 0.14
50 48 0.11
51 16 0.04
52 2 0.00
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.33
Consensus pattern (47 bp):
TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
Found at i:40588880 original size:191 final size:188
Alignment explanation
Indices: 40588387--40588922 Score: 642
Period size: 191 Copynumber: 2.8 Consensus size: 188
40588377 ACTGGGCCTG
* * * *
40588387 TCACATATATGCA-CTTTCAGCATTCCATCACAT-GCCATTTAGG-CTTATA-ACATATATACAC
1 TCACATATATACACCTTTCA-CATT-CATCACATGGCTATTAAGGCCTTAAACACATATATA-AC
* *
40588448 TTTCACATT-ATCACA----CATTAGG-CTTAAT-TACATATAACA-TTGTCACATTCATGCACA
63 TTTCACATTCATCACATCGGCATTAGGCCTT-ATCAACATATAACACTT-TCACATTCATTCACA
*
40588505 TCGGCTATTAGGCCTTATTCACATATATATACACTTTCACATTCATCACATCGCTATTAGGCCTT
126 TCGGCCATTAGGCCTTA-TCAC--ATATATACACTTTCACATTCATCACATCGCTATTAGGCCTT
40588570 A
188 A
*
40588571 TAAGCACA-ATATA-ACAC-TTCACATTCATCACATTGGCTATTAAGGCCTTATCACACATATA-
1 T---CACATATATACAC-CTTTCACATTCATCACA-TGGCTATTAAGGCCTTA-AACACATATAT
* *
40588632 CACTTTCACATTCATTCA-ATCGGCATTAGGCCTTATCACATCATATATCACTTTCACATTCATT
60 AACTTTCACATTCA-TCACATCGGCATTAGGCCTTATCA-A-CATATAACACTTTCACATTCATT
*
40588696 TACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGC-ATTAGGCC
122 CACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC-GCTATTAGGCC
40588760 TTA
186 TTA
40588763 TCACATATATACACCTTTCACATTCATCACATCGGCTATTAAGGCCTTAAACACATATATAACTT
1 TCACATATATACACCTTTCACATTCATCACAT-GGCTATTAAGGCCTTAAACACATATATAACTT
40588828 TCACATTCATCACATCGGCTATTAGGCCTTATCAACATATAACAACTTTCACATTCA-TCACATC
65 TCACATTCATCACATCGGC-ATTAGGCCTTATCAACATATAAC-ACTTTCACATTCATTCACATC
40588892 GGCTCATTAGGCCTTATCACATATATACACT
128 GGC-CATTAGGCCTTATCACATATATACACT
40588923 GTCTTTGGCT
Statistics
Matches: 307, Mismatches: 14, Indels: 55
0.82 0.04 0.15
Matches are distributed among these distances:
184 8 0.03
185 6 0.02
186 16 0.05
187 20 0.07
188 3 0.01
189 14 0.05
190 35 0.11
191 93 0.30
192 63 0.21
193 5 0.02
194 5 0.02
195 37 0.12
196 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.33
Consensus pattern (188 bp):
TCACATATATACACCTTTCACATTCATCACATGGCTATTAAGGCCTTAAACACATATATAACTTT
CACATTCATCACATCGGCATTAGGCCTTATCAACATATAACACTTTCACATTCATTCACATCGGC
CATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGCTATTAGGCCTTA
Found at i:40595341 original size:12 final size:11
Alignment explanation
Indices: 40595318--40595367 Score: 54
Period size: 9 Copynumber: 4.7 Consensus size: 11
40595308 TGTAGATTCC
40595318 AAAAAAAT--A
1 AAAAAAATGAA
40595327 AAAAAAATCGAA
1 AAAAAAAT-GAA
40595339 AAAAAAA--AA
1 AAAAAAATGAA
40595348 AAAAAAATTGAA
1 AAAAAAA-TGAA
40595360 AAAAAAAT
1 AAAAAAAT
40595368 TGCTACGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 17 0.49
11 1 0.03
12 17 0.49
ACGTcount: A:0.84, C:0.02, G:0.04, T:0.10
Consensus pattern (11 bp):
AAAAAAATGAA
Found at i:40595344 original size:21 final size:21
Alignment explanation
Indices: 40595318--40595367 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
40595308 TGTAGATTCC
40595318 AAAAAAATAAAAAAAATCGAA
1 AAAAAAATAAAAAAAATCGAA
* *
40595339 AAAAAAAAAAAAAAAATTGAA
1 AAAAAAATAAAAAAAATCGAA
40595360 AAAAAAAT
1 AAAAAAAT
40595368 TGCTACGGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.84, C:0.02, G:0.04, T:0.10
Consensus pattern (21 bp):
AAAAAAATAAAAAAAATCGAA
Found at i:40595368 original size:12 final size:12
Alignment explanation
Indices: 40595326--40595369 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
40595316 CCAAAAAAAT
*
40595326 AAAAAAAATCGA
1 AAAAAAAATTGA
40595338 AAAAAAAA---A
1 AAAAAAAATTGA
40595347 AAAAAAAATTGA
1 AAAAAAAATTGA
40595359 AAAAAAAATTG
1 AAAAAAAATTG
40595370 CTACGGTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.31
12 20 0.69
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.11
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:40613317 original size:39 final size:40
Alignment explanation
Indices: 40613222--40613444 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
40613212 TTGAATGATG
*
40613222 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
40613260 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
40613301 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
40613340 TCCGGGCTAAG-CCCGAAGGCATTTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
40613379 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
40613418 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
40613445 AACGAGGAGC
Statistics
Matches: 162, Mismatches: 13, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
39 92 0.57
40 58 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:40613407 original size:79 final size:81
Alignment explanation
Indices: 40613222--40613444 Score: 273
Period size: 79 Copynumber: 2.8 Consensus size: 81
40613212 TTGAATGATG
* * *
40613222 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
*
40613284 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
40613301 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
* *
40613362 TTGTGTGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * * *
40613379 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
40613443 TG
66 TG
40613445 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 45 0.36
79 56 0.44
80 25 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:40613466 original size:79 final size:79
Alignment explanation
Indices: 40613222--40613477 Score: 208
Period size: 79 Copynumber: 3.3 Consensus size: 79
40613212 TTGAATGATG
* * * *
40613222 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
40613283 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
40613301 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
*** *
40613365 TGTGAGTTACTAAA
66 AACGAGTGACTAAA
*
40613379 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
40613442 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
40613459 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
40613478 TACGTGATTT
Statistics
Matches: 151, Mismatches: 16, Indels: 20
0.81 0.09 0.11
Matches are distributed among these distances:
77 1 0.01
78 45 0.30
79 69 0.46
80 35 0.23
81 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:40621426 original size:30 final size:30
Alignment explanation
Indices: 40621369--40621427 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
40621359 GCCTTTTGAA
* * *
40621369 AATATTTACAAAAAGAGACATCTAATTTTT
1 AATACTTACAAAAAGAGACACCAAATTTTT
40621399 AATACTTACAAAAAGAG-CAACCAAATTTT
1 AATACTTACAAAAAGAGAC-ACCAAATTTT
40621428 GAAAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.31
Consensus pattern (30 bp):
AATACTTACAAAAAGAGACACCAAATTTTT
Found at i:40641410 original size:34 final size:34
Alignment explanation
Indices: 40641367--40641435 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
40641357 TAACAAGAGA
*
40641367 TAGAAAATGATATTTTATCACTTTTATAGATGAC
1 TAGAAAATGATATTTTATCACTTTTATAAATGAC
40641401 TAGAAAATGATATTTTATCACTTTTATAAATGAC
1 TAGAAAATGATATTTTATCACTTTTATAAATGAC
40641435 T
1 T
40641436 TCTCTATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (34 bp):
TAGAAAATGATATTTTATCACTTTTATAAATGAC
Found at i:40644985 original size:25 final size:21
Alignment explanation
Indices: 40644936--40644976 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
40644926 ATGTAGTGAT
40644936 GTTAGTTATTAAATATAGTTG
1 GTTAGTTATTAAATATAGTTG
*
40644957 GTTAGTTGTTAAATATAGTT
1 GTTAGTTATTAAATATAGTT
40644977 AGGAGGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.49
Consensus pattern (21 bp):
GTTAGTTATTAAATATAGTTG
Found at i:40654128 original size:14 final size:13
Alignment explanation
Indices: 40654109--40654143 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
40654099 ACCGTATACA
40654109 ATTTTTTTTTCTCG
1 ATTTTTTTTT-TCG
40654123 A-TTTTTTTTTCG
1 ATTTTTTTTTTCG
40654135 ATTTTTTTT
1 ATTTTTTTT
40654144 GAATCTACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 15 0.75
14 1 0.05
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.77
Consensus pattern (13 bp):
ATTTTTTTTTTCG
Found at i:40654143 original size:12 final size:13
Alignment explanation
Indices: 40654111--40654143 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
40654101 CGTATACAAT
40654111 TTTTTTTTCTCGA
1 TTTTTTTTCTCGA
40654124 TTTTTTTT-TCGA
1 TTTTTTTTCTCGA
40654136 TTTTTTTT
1 TTTTTTTT
40654144 GAATCTACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (13 bp):
TTTTTTTTCTCGA
Found at i:40662685 original size:29 final size:31
Alignment explanation
Indices: 40662647--40662707 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
40662637 TTGATAATTA
*
40662647 ATGTACCACATTAGACATCTT-C-AAAGTAC
1 ATGTAACACATTAGACATCTTACGAAAGTAC
* *
40662676 ATGTAACACATTGGACATTTTACGAAAGTAC
1 ATGTAACACATTAGACATCTTACGAAAGTAC
40662707 A
1 A
40662708 AGTACTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 18 0.67
30 1 0.04
31 8 0.30
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (31 bp):
ATGTAACACATTAGACATCTTACGAAAGTAC
Found at i:40662778 original size:92 final size:92
Alignment explanation
Indices: 40662615--40662803 Score: 229
Period size: 92 Copynumber: 2.1 Consensus size: 92
40662605 CGTTGTTAAT
* * **
40662615 AAGTACCATAATGAAACATATATTGATAATTAATGTACCACATTAGACATCTTCAAAGTACATGT
1 AAGTACCATAATAAAACATATATTGATAATTAATGTACCACATTAGACATCTTAAAAGTACAAAT
**
40662680 AACACATTGGACATTTTACGAAAGTAC
66 AACACATTAAACATTTTACGAAAGTAC
* * *
40662707 AAGTACTATAATAAAACATATATTGATAGTTTAA-GTACCACA-TATACATCTTTAAAAGTACAA
1 AAGTACCATAATAAAACATATATTGATA-ATTAATGTACCACATTAGACATC-TTAAAAGTACAA
* * **
40662770 ATATCACATTAAATATTTTGTGAAAGTAC
64 ATAACACATTAAACATTTTACGAAAGTAC
40662799 AAGTA
1 AAGTA
40662804 TCAAAAGTGA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
91 7 0.09
92 71 0.87
93 4 0.05
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (92 bp):
AAGTACCATAATAAAACATATATTGATAATTAATGTACCACATTAGACATCTTAAAAGTACAAAT
AACACATTAAACATTTTACGAAAGTAC
Found at i:40667846 original size:19 final size:18
Alignment explanation
Indices: 40667823--40667880 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
40667813 AATTCTACCA
40667823 TTTCTTTTCTTTTCTTTT
1 TTTCTTTTCTTTTCTTTT
*
40667841 TGTTCTTTCCTTGTTCTTTAT
1 T-TTCTTTTCTT-TTCTTT-T
*
40667862 TTCCTTTGT-TTTTCTTTT
1 TTTCTTT-TCTTTTCTTTT
40667880 T
1 T
40667881 ATATTTTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 3 0.09
19 15 0.45
20 13 0.39
21 2 0.06
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTCTTTTCTTTTCTTTT
Found at i:40673188 original size:32 final size:32
Alignment explanation
Indices: 40673138--40673199 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
40673128 ATTCTGAGAC
*
40673138 ACTAGGGTTTGCTAGCCCCCTCTCCTAGTTAA
1 ACTAGGGTCTGCTAGCCCCCTCTCCTAGTTAA
* *
40673170 ACTAGGGTCTGCTGGCCCCCTCTCGTAGTT
1 ACTAGGGTCTGCTAGCCCCCTCTCCTAGTT
40673200 TTCCTATATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.15, C:0.32, G:0.23, T:0.31
Consensus pattern (32 bp):
ACTAGGGTCTGCTAGCCCCCTCTCCTAGTTAA
Found at i:40674401 original size:18 final size:18
Alignment explanation
Indices: 40674378--40674417 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
40674368 TTTTTACGTA
40674378 AATAAAAATGTTACAAAG
1 AATAAAAATGTTACAAAG
* *
40674396 AATAAAGATGTTGCAAAG
1 AATAAAAATGTTACAAAG
40674414 AATA
1 AATA
40674418 CTATACTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.15, T:0.23
Consensus pattern (18 bp):
AATAAAAATGTTACAAAG
Found at i:40683332 original size:6 final size:6
Alignment explanation
Indices: 40683323--40683352 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
40683313 CACCGATCTT
*
40683323 CCCTTT CCCTTC CCCTTC CCCTTC CCCTTC
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC
40683353 GCTTGACACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
CCCTTC
Found at i:40686394 original size:22 final size:24
Alignment explanation
Indices: 40686344--40686394 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
40686334 TTGCAATGCT
40686344 TTTATATTTTAATAATTGAGTATTA
1 TTTATATTTTAAT-ATTGAGTATTA
40686369 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATAT-TTTAATATTGAGTATTA
40686390 TTTAT
1 TTTAT
40686395 TTATAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 4 0.17
24 6 0.25
25 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTATATTTTAATATTGAGTATTA
Found at i:40686544 original size:14 final size:15
Alignment explanation
Indices: 40686522--40686598 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
40686512 CAATCAAACA
40686522 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
40686536 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
40686551 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
40686571 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
40686585 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
40686599 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:40686563 original size:20 final size:20
Alignment explanation
Indices: 40686538--40686577 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40686528 AATATTTTCC
*
40686538 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
40686558 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
40686578 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:40686583 original size:34 final size:35
Alignment explanation
Indices: 40686526--40686592 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
40686516 CAAACACCAG
*
40686526 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
40686561 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
40686593 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:40686599 original size:14 final size:14
Alignment explanation
Indices: 40686561--40686600 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
40686551 ACAGAAAAGT
*
40686561 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
40686575 AAATCATTTTACGG
1 AAAACATTTTACAG
40686589 AAAACATTTTAC
1 AAAACATTTTAC
40686601 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:40687699 original size:6 final size:6
Alignment explanation
Indices: 40687669--40687723 Score: 74
Period size: 6 Copynumber: 8.5 Consensus size: 6
40687659 GTGGTGGACC
40687669 GGAGGT GGAATGGT GGATTGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT
1 GGAGGT GG-A-GGT GGA--GGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT
40687721 GGA
1 GGA
40687724 TTTTCGATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
6 32 0.70
7 2 0.04
8 12 0.26
ACGTcount: A:0.18, C:0.00, G:0.62, T:0.20
Consensus pattern (6 bp):
GGAGGT
Found at i:40693348 original size:29 final size:29
Alignment explanation
Indices: 40693294--40693355 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
40693284 ACAACCCTAT
* *
40693294 GCTCACATGCATTGCTCGTCTACAT-GGA
1 GCTCACATGCATAGCTCGTATACATGGGA
* *
40693322 GCTCACAGTTCATAGCTCGTATGCATGGGA
1 GCTCACA-TGCATAGCTCGTATACATGGGA
40693352 GCTC
1 GCTC
40693356 GCAGAACACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 7 0.25
29 14 0.50
30 7 0.25
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.27
Consensus pattern (29 bp):
GCTCACATGCATAGCTCGTATACATGGGA
Found at i:40693841 original size:17 final size:16
Alignment explanation
Indices: 40693810--40693843 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
40693800 ATTCAACTGA
40693810 TATCCTTTATTTCTCT
1 TATCCTTTATTTCTCT
*
40693826 TATCCATTTCTTTCTCT
1 TATCC-TTTATTTCTCT
40693843 T
1 T
40693844 TTGTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (16 bp):
TATCCTTTATTTCTCT
Found at i:40697632 original size:41 final size:41
Alignment explanation
Indices: 40697571--40697797 Score: 260
Period size: 41 Copynumber: 5.6 Consensus size: 41
40697561 CTTTCGGGAT
* *
40697571 TTTAGCGGCGTTTTTCAAAAAGCATCGCTAATGCTTGGGGC
1 TTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTTGGGGC
* * * *
40697612 TTTAGCGGCGGTTTTGAAAAAGCGCTGCTAATGATTGGGGC
1 TTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTTGGGGC
* * * *
40697653 TTTAGCGGCATTTTTG-AAAAGCGCCACTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTTGGGGC
* * *
40697693 TTTAGCGGCGTTTTTGAAAAAACACCACTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTTGGGGC
* * * * **
40697734 TTTAACGGCATTTTTGAAAAAGCGCCGCTAATGC-TCGATC
1 TTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTTGGGGC
*
40697774 TTTAGCGGCGTTTTTAAAAAAGCA
1 TTTAGCGGCGTTTTTGAAAAAGCA
40697798 ACACAAAAAA
Statistics
Matches: 157, Mismatches: 28, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
40 57 0.36
41 100 0.64
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTTGGGGC
Found at i:40697708 original size:81 final size:81
Alignment explanation
Indices: 40697571--40697797 Score: 276
Period size: 81 Copynumber: 2.8 Consensus size: 81
40697561 CTTTCGGGAT
* * ** * * *
40697571 TTTAGCGGCGTTTTTCAAAAAGCATCGCTAATGCTTGGGGCTTTAGCGGCGGTTTTGAAAAAGCG
1 TTTAGCGGCATTTTT-GAAAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTTTTGAAAAAGCA
** *
40697636 CTGCTAATGATTGGGGC
65 CCACTAATGATCGGGGC
* *
40697653 TTTAGCGGCATTTTTGAAAAGCGCCACTAATGCTCGGGGCTTTAGCGGCGTTTTTGAAAAAACAC
1 TTTAGCGGCATTTTTGAAAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTTTTGAAAAAGCAC
*
40697718 CACTAATGCTCGGGGC
66 CACTAATGATCGGGGC
* ** *
40697734 TTTAACGGCATTTTTGAAAAAGCGCCGCTAATGCTC-GATCTTTAGCGGCGTTTTTAAAAAAGCA
1 TTTAGCGGCATTTTTG-AAAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTTTTGAAAAAGCA
40697798 ACACAAAAAA
Statistics
Matches: 125, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
81 93 0.74
82 32 0.26
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (81 bp):
TTTAGCGGCATTTTTGAAAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTTTTGAAAAAGCAC
CACTAATGATCGGGGC
Found at i:40698205 original size:7 final size:7
Alignment explanation
Indices: 40698105--40698216 Score: 57
Period size: 7 Copynumber: 15.7 Consensus size: 7
40698095 TATCACTATA
*
40698105 GTTTAAG
1 GTTTATG
*
40698112 GTTTTTG
1 GTTTATG
*
40698119 GTTTAGG
1 GTTTATG
*
40698126 GTATATG
1 GTTTATG
**
40698133 GTTTACA
1 GTTTATG
*
40698140 GTTTAAG
1 GTTTATG
*
40698147 GTTTAGG
1 GTTTATG
40698154 AGTTACTAT-
1 -GTT--TATG
*
40698163 -TTTAAG
1 GTTTATG
40698169 GTTTATG
1 GTTTATG
**
40698176 GAATATGG
1 GTTTAT-G
*
40698184 GTTTAGG
1 GTTTATG
*
40698191 GATTATG
1 GTTTATG
40698198 GTTTATG
1 GTTTATG
40698205 GTTTATG
1 GTTTATG
40698212 GTTTA
1 GTTTA
40698217 AAGGCTAGGG
Statistics
Matches: 76, Mismatches: 23, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
5 2 0.03
7 65 0.86
8 7 0.09
10 2 0.03
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (7 bp):
GTTTATG
Found at i:40698264 original size:7 final size:7
Alignment explanation
Indices: 40698182--40698285 Score: 63
Period size: 7 Copynumber: 15.0 Consensus size: 7
40698172 TATGGAATAT
40698182 GGGTTTA
1 GGGTTTA
*
40698189 GGGATTA
1 GGGTTTA
*
40698196 TGGTTTA
1 GGGTTTA
*
40698203 TGGTTTA
1 GGGTTTA
*
40698210 TGGTTTAA
1 GGGTTT-A
* *
40698218 AGG-CTA
1 GGGTTTA
40698224 GGGTTTA
1 GGGTTTA
*
40698231 AGGTTTA
1 GGGTTTA
40698238 GAGGTTGT-
1 G-GGTT-TA
* *
40698246 GTGTTAA
1 GGGTTTA
40698253 GGGTTTA
1 GGGTTTA
40698260 GGG-TTA
1 GGGTTTA
40698266 -GGTTTA
1 GGGTTTA
*
40698272 TGGTTTA
1 GGGTTTA
40698279 GGGTTTA
1 GGGTTTA
40698286 AATTAACTAG
Statistics
Matches: 76, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
5 2 0.03
6 9 0.12
7 56 0.74
8 8 0.11
9 1 0.01
ACGTcount: A:0.19, C:0.01, G:0.37, T:0.43
Consensus pattern (7 bp):
GGGTTTA
Found at i:40701149 original size:16 final size:16
Alignment explanation
Indices: 40701125--40701158 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40701115 TAATACTATT
*
40701125 TAATTTTTGATATTAA
1 TAATGTTTGATATTAA
*
40701141 TAATGTTTGATTTTAA
1 TAATGTTTGATATTAA
40701157 TA
1 TA
40701159 TTTAATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (16 bp):
TAATGTTTGATATTAA
Found at i:40701163 original size:23 final size:24
Alignment explanation
Indices: 40701110--40701172 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 24
40701100 TTATATTAAT
* *
40701110 ATATTTAATACTATTTAATTTTTG
1 ATATTTAATAATATTTAATTTTTA
* *
40701134 ATA-TTAATAATGTTTGA-TTTTA
1 ATATTTAATAATATTTAATTTTTA
40701156 ATATTTAAT-ATATTTAA
1 ATATTTAATAATATTTAA
40701173 ATGTTTTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
22 13 0.41
23 16 0.50
24 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (24 bp):
ATATTTAATAATATTTAATTTTTA
Found at i:40706477 original size:22 final size:22
Alignment explanation
Indices: 40706428--40706477 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
40706418 ACTAATGCAG
* * * *
40706428 CTGACTCTGCTAACCAGAGTAG
1 CTGACCCTACTAACCAGAGCAA
*
40706450 CCGACCCTACTAACCAGAGCAA
1 CTGACCCTACTAACCAGAGCAA
40706472 CTGACC
1 CTGACC
40706478 ACTATGAACC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.30, C:0.36, G:0.18, T:0.16
Consensus pattern (22 bp):
CTGACCCTACTAACCAGAGCAA
Found at i:40711373 original size:27 final size:27
Alignment explanation
Indices: 40711307--40711373 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
40711297 GTAGTGATTC
40711307 AATTTGGTTAATTCGGGTAATTCGGTT
1 AATTTGGTTAATTCGGGTAATTCGGTT
* ** *
40711334 AATTCGGAAAATTCTGGTAATTCGGTT
1 AATTTGGTTAATTCGGGTAATTCGGTT
40711361 AATTTGGTTAATT
1 AATTTGGTTAATT
40711374 TTTAACCAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.43
Consensus pattern (27 bp):
AATTTGGTTAATTCGGGTAATTCGGTT
Found at i:40711374 original size:9 final size:9
Alignment explanation
Indices: 40711307--40711373 Score: 73
Period size: 9 Copynumber: 7.4 Consensus size: 9
40711297 GTAGTGATTC
*
40711307 AATTTGGTT
1 AATTCGGTT
*
40711316 AATTCGGGT
1 AATTCGGTT
40711325 AATTCGGTT
1 AATTCGGTT
**
40711334 AATTCGGAA
1 AATTCGGTT
40711343 AATTCTGG-T
1 AATTC-GGTT
40711352 AATTCGGTT
1 AATTCGGTT
*
40711361 AATTTGGTT
1 AATTCGGTT
40711370 AATT
1 AATT
40711374 TTTAACCAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
8 2 0.04
9 45 0.92
10 2 0.04
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:40711783 original size:29 final size:28
Alignment explanation
Indices: 40711741--40711798 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
40711731 AAACATATTA
40711741 AATTTTAATAAAAAAATTA-ATAAAAATTT
1 AATTTTAAT-AAAAAATTAGA-AAAAATTT
* *
40711770 AATTTTTATTAAAAATTAGAAAAAATTT
1 AATTTTAATAAAAAATTAGAAAAAATTT
40711798 A
1 A
40711799 TAAAAATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (28 bp):
AATTTTAATAAAAAATTAGAAAAAATTT
Found at i:40711812 original size:19 final size:19
Alignment explanation
Indices: 40711790--40711878 Score: 67
Period size: 19 Copynumber: 4.7 Consensus size: 19
40711780 AAAAATTAGA
40711790 AAAAATTTATAAAAATCAT
1 AAAAATTTATAAAAATCAT
** **
40711809 AAAAGA-AAATAAAAATTGT
1 AAAA-ATTTATAAAAATCAT
*
40711828 AAAATTTTATAAAAATCAT
1 AAAAATTTATAAAAATCAT
* *
40711847 AAAAA-ATACAAAAAT-AT
1 AAAAATTTATAAAAATCAT
40711864 AAAAAAATTTATAAA
1 --AAAAATTTATAAA
40711879 GTCGTAAGAA
Statistics
Matches: 51, Mismatches: 14, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
17 2 0.04
18 8 0.16
19 35 0.69
20 6 0.12
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAATTTATAAAAATCAT
Found at i:40711875 original size:38 final size:38
Alignment explanation
Indices: 40711780--40711878 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 38
40711770 AATTTTTATT
*
40711780 AAAAATTAGAAAAAATTTATAAAAATCATAAAAGAAAAT
1 AAAAATTA-AAAAAATTTATAAAAATCATAAAAGAAAAC
** * *
40711819 AAAAATTGTAAAATTTTATAAAAATCATAAAA-AATAC
1 AAAAATTAAAAAAATTTATAAAAATCATAAAAGAAAAC
40711856 AAAAATATAAAAAAATTTATAAA
1 AAAAAT-TAAAAAAATTTATAAA
40711879 GTCGTAAGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
37 9 0.18
38 35 0.69
39 7 0.14
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (38 bp):
AAAAATTAAAAAAATTTATAAAAATCATAAAAGAAAAC
Found at i:40711914 original size:30 final size:29
Alignment explanation
Indices: 40711856--40711928 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 29
40711846 TAAAAAATAC
*
40711856 AAAAATATAAAAAAATTTATAAAGTCGTA
1 AAAAATATAAAAAAATATATAAAGTCGTA
*
40711885 AGAAAATAATAAAAAAATATA-AAATTCGTA
1 A-AAAAT-ATAAAAAAATATATAAAGTCGTA
40711915 AAAGAATTATAAAA
1 AAA-AA-TATAAAA
40711929 TTATCATATC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 3 0.08
30 22 0.58
31 13 0.34
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.25
Consensus pattern (29 bp):
AAAAATATAAAAAAATATATAAAGTCGTA
Found at i:40713598 original size:37 final size:37
Alignment explanation
Indices: 40713546--40713616 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
40713536 AATGAAATAC
* * * *
40713546 GAATGCTTTATATATTTATAGAACAGATGTCTAATTT
1 GAATGCTTTAAATATTCACAGAAAAGATGTCTAATTT
40713583 GAATGCTTTAAATATTCACAGAAAAGATGTCTAA
1 GAATGCTTTAAATATTCACAGAAAAGATGTCTAA
40713617 GCCGGAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (37 bp):
GAATGCTTTAAATATTCACAGAAAAGATGTCTAATTT
Found at i:40716428 original size:91 final size:91
Alignment explanation
Indices: 40716290--40716493 Score: 372
Period size: 91 Copynumber: 2.2 Consensus size: 91
40716280 ATCACTTGTC
*
40716290 CTAGGTTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 CTAGGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
40716355 TTTGTCACTTGATCAGATAAGTGTAG
66 TTTGTCACTTGATCAGATAAGTGTAG
40716381 CTAGGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 CTAGGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
40716446 TTTGTCACTTGATCAGATAAGTGTAG
66 TTTGTCACTTGATCAGATAAGTGTAG
* *
40716472 CTAAAGCTATCACTTATCACTT
1 CT-AGGCTACCACTTATCACTT
40716494 ATCAGAAGTA
Statistics
Matches: 109, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
91 92 0.84
92 17 0.16
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (91 bp):
CTAGGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
TTTGTCACTTGATCAGATAAGTGTAG
Found at i:40716497 original size:53 final size:46
Alignment explanation
Indices: 40716296--40716493 Score: 371
Period size: 46 Copynumber: 4.3 Consensus size: 46
40716286 TGTCCTAGGT
40716296 TACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
1 TACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
*
40716342 TACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGC
1 TACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
40716387 TACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
1 TACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
40716433 TACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
1 TACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
*
40716479 TATCACTTATCACTT
1 TACCACTTATCACTT
40716494 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
45 44 0.30
46 104 0.70
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (46 bp):
TACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
Found at i:40720519 original size:188 final size:177
Alignment explanation
Indices: 40720183--40720535 Score: 449
Period size: 176 Copynumber: 1.9 Consensus size: 177
40720173 TATTATCATA
* * *
40720183 TATTAAATAATTTATATAAAATTAAATTAAATATATAATATTGCAATTTATATATAAAAAAGATG
1 TATTAAATAATTTATATAAAATTAAATTAAATATATAATAGTGCAATATAGATATAAAAAAGATG
* ** * *
40720248 TGTTATCTATGGTTAAAATTTTCATAAAAGGAATATAAAAATTTTTAACATTAAATTAAAAATAA
66 CGTTATCTATGGTTAAAATTTTCATAAAAAAAATATAAAAAATTTAAACATTAAATTAAAAATAA
* *
40720313 TATACTTTTTTAAAGAATTAAAAAAGAAT-ATATATTTTATTTTATG
131 TATAATTTTTAAAAGAATTAAAAAAGAATAATATATTTTATTTTATG
*
40720359 TATTATATAATTTATATAAAATTAAATTAAATATATAATAGTGCAATATAGATATAAAAAA-ATT
1 TATTAAATAATTTATATAAAATTAAATTAAATATATAATAGTGCAATATAGATATAAAAAAGA-T
*
40720423 GCGTTAAATTGTTTATGGTTAAAATTTTCATAAAACAAAAAAACATATAAAAAAATTTAAACATT
65 GCGTT--A---TCTATGGTTAAAATTTTCAT-----AAAAAAA-ATAT-AAAAAATTTAAACATT
* *
40720488 AAATTAAAAATAATATAATTTTTAAAAGAATTTAAAAATAATAATATA
118 AAATTAAAAATAATATAATTTTTAAAAGAATTAAAAAAGAATAATATA
40720536 GGTGAGCTTA
Statistics
Matches: 149, Mismatches: 14, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
175 1 0.01
176 62 0.42
178 1 0.01
181 19 0.13
186 5 0.03
187 4 0.03
188 52 0.35
189 5 0.03
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (177 bp):
TATTAAATAATTTATATAAAATTAAATTAAATATATAATAGTGCAATATAGATATAAAAAAGATG
CGTTATCTATGGTTAAAATTTTCATAAAAAAAATATAAAAAATTTAAACATTAAATTAAAAATAA
TATAATTTTTAAAAGAATTAAAAAAGAATAATATATTTTATTTTATG
Found at i:40729937 original size:40 final size:40
Alignment explanation
Indices: 40729882--40730101 Score: 339
Period size: 40 Copynumber: 5.7 Consensus size: 40
40729872 GAGCATTGGA
*
40729882 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
*
40729922 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
*
40729962 ATATATCC-GGCTATGA-CCGAA-GC-ATTATGC-A---G
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
40729994 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
40730034 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
* *
40730074 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
40730102 ATGTGTTTGC
Statistics
Matches: 168, Mismatches: 4, Indels: 16
0.89 0.02 0.09
Matches are distributed among these distances:
32 9 0.05
33 7 0.04
34 5 0.03
35 3 0.02
36 14 0.08
37 3 0.02
38 5 0.03
39 7 0.04
40 115 0.68
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
Found at i:40730038 original size:72 final size:78
Alignment explanation
Indices: 40729882--40730101 Score: 317
Period size: 72 Copynumber: 2.8 Consensus size: 78
40729872 GAGCATTGGA
*
40729882 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGC-A-ATGATATATCCGGGCTAAGACCCGAAGG
*
40729947 CAATTATGCGAGTTG
64 CAATTATGCAAGTTG
*
40729962 ATATATCC-GGCTATGA-CCGAA-GC-ATTATGC-A-GATATATCCGGGCTAAGACCCGAAGGCA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAATGATATATCCGGGCTAAGACCCGAAGGCA
40730021 ATTATGCAAGTTG
66 ATTATGCAAGTTG
* *
40730034 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTGATATGTCCGGGTTAAGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAA--TGATATATCCGGGCTAAGACCCGAAGG
40730099 CAA
64 CAA
40730102 ATGTGTTTGC
Statistics
Matches: 126, Mismatches: 6, Indels: 16
0.85 0.04 0.11
Matches are distributed among these distances:
72 48 0.38
73 7 0.06
74 5 0.04
75 2 0.02
76 14 0.11
77 3 0.02
78 5 0.04
79 7 0.06
80 35 0.28
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.22
Consensus pattern (78 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAATGATATATCCGGGCTAAGACCCGAAGGCA
ATTATGCAAGTTG
Found at i:40730083 original size:112 final size:112
Alignment explanation
Indices: 40729882--40730083 Score: 377
Period size: 112 Copynumber: 1.8 Consensus size: 112
40729872 GAGCATTGGA
*
40729882 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTGATATATCCGGGCTAAGACCCGAAGG
*
40729947 CAATTATGCGAGTTGATATATCCGGCTATGACCGAAGCATTATGCAG
66 CAATTATGCAAGTTGATATATCCGGCTATGACCGAAGCATTATGCAG
40729994 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTGATATATCCGGGCTAAGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTGATATATCCGGGCTAAGACCCGAAGG
*
40730059 CAATTATGCAAGTTGATATGTCCGG
66 CAATTATGCAAGTTGATATATCCGG
40730084 GTTAAGACCC
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 87 1.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (112 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTGATATATCCGGGCTAAGACCCGAAGG
CAATTATGCAAGTTGATATATCCGGCTATGACCGAAGCATTATGCAG
Found at i:40735349 original size:22 final size:22
Alignment explanation
Indices: 40735324--40735376 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
40735314 ACTTATTGCC
40735324 ATTGATGTATTATGCCAATATA
1 ATTGATGTATTATGCCAATATA
*
40735346 ATTGAT-TGATTGTGCCAATATA
1 ATTGATGT-ATTATGCCAATATA
*
40735368 ATTTATGTA
1 ATTGATGTA
40735377 AGATGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (22 bp):
ATTGATGTATTATGCCAATATA
Found at i:40737823 original size:16 final size:17
Alignment explanation
Indices: 40737804--40737839 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
40737794 TTGTTTTATG
*
40737804 TTTCTT-TCTTTTTCTT
1 TTTCTTCTCTTTTACTT
40737820 TTTCTTCTCTTTTACTT
1 TTTCTTCTCTTTTACTT
40737837 TTT
1 TTT
40737840 GCTCTACTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTCTTCTCTTTTACTT
Found at i:40737832 original size:17 final size:16
Alignment explanation
Indices: 40737791--40737839 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
40737781 TCTTTACTTC
* *
40737791 TCTTTGTTTTA-TGTT
1 TCTTTCTTTTACTTTT
*
40737806 TCTTTCTTTTTCTTTT
1 TCTTTCTTTTACTTTT
40737822 TCTTCTCTTTTACTTTT
1 TCTT-TCTTTTACTTTT
40737839 T
1 T
40737840 GCTCTACTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 9 0.32
16 7 0.25
17 12 0.43
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (16 bp):
TCTTTCTTTTACTTTT
Found at i:40740333 original size:22 final size:23
Alignment explanation
Indices: 40740303--40740346 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
40740293 CAACCAATTT
40740303 ATTTCAACATATTT-TCAAGATAG
1 ATTTCAACATATTTAT-AAGATAG
40740326 ATTT-AACATATTTATAAGATA
1 ATTTCAACATATTTATAAGATA
40740347 ACCTCATCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (23 bp):
ATTTCAACATATTTATAAGATAG
Found at i:40744604 original size:18 final size:18
Alignment explanation
Indices: 40744559--40744605 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
40744549 GTACATACAT
*
40744559 TTTGTTATCTGTTATTCTA
1 TTTG-TATCTGGTATTCTA
*
40744578 -TTATATCTGGTATTCTA
1 TTTGTATCTGGTATTCTA
40744595 TTTGTATCTGG
1 TTTGTATCTGG
40744606 CTATGGGGCG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.17, C:0.11, G:0.15, T:0.57
Consensus pattern (18 bp):
TTTGTATCTGGTATTCTA
Found at i:40759406 original size:54 final size:54
Alignment explanation
Indices: 40759334--40759444 Score: 168
Period size: 54 Copynumber: 2.1 Consensus size: 54
40759324 CACACGACCA
* *
40759334 GTCCCCTAATCTTATGCGAGAGATAAGCCCGTGTGAGGTGGGTCACACGGTCGT
1 GTCCCCTAATCGTATGCGAGAGATAAGCCCGTGTGAGGTGGGTCACACGGCCGT
* * * *
40759388 GTCCCCTAATCGTGTGCGAGAGCTAAGCTCGTTTGAGGTGGGTCACACGGCCGT
1 GTCCCCTAATCGTATGCGAGAGATAAGCCCGTGTGAGGTGGGTCACACGGCCGT
40759442 GTC
1 GTC
40759445 ACTGGGTCAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.18, C:0.25, G:0.32, T:0.24
Consensus pattern (54 bp):
GTCCCCTAATCGTATGCGAGAGATAAGCCCGTGTGAGGTGGGTCACACGGCCGT
Found at i:40761855 original size:18 final size:18
Alignment explanation
Indices: 40761832--40761871 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
40761822 CTTCCAGGTC
40761832 GTTACAATAACTAACTTG
1 GTTACAATAACTAACTTG
*
40761850 GTTACAATAGCTAACTTG
1 GTTACAATAACTAACTTG
40761868 GTTA
1 GTTA
40761872 GTATATTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (18 bp):
GTTACAATAACTAACTTG
Found at i:40762384 original size:24 final size:24
Alignment explanation
Indices: 40762352--40762400 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
40762342 AAATAAATTA
40762352 TGATACGACCATTCTGAAGACAAG
1 TGATACGACCATTCTGAAGACAAG
*
40762376 TGATACGACCATTTTGAAGACAAG
1 TGATACGACCATTCTGAAGACAAG
40762400 T
1 T
40762401 CTATGGCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.24
Consensus pattern (24 bp):
TGATACGACCATTCTGAAGACAAG
Found at i:40763408 original size:31 final size:31
Alignment explanation
Indices: 40763322--40763419 Score: 115
Period size: 31 Copynumber: 3.2 Consensus size: 31
40763312 ACACCGGTAA
* * *
40763322 ATAGTACCTAATAAAATATAAACACCAACAC
1 ATAGTACCTGATAAAATATAAACATCAGCAC
* * * * *
40763353 ATTGTGCCTGATACAATAAAAACATCAGTAC
1 ATAGTACCTGATAAAATATAAACATCAGCAC
*
40763384 ATAGTACCTGCTAAAATATAAACATCAGCAC
1 ATAGTACCTGATAAAATATAAACATCAGCAC
40763415 ATAGT
1 ATAGT
40763420 GCCTACTATA
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.23
Consensus pattern (31 bp):
ATAGTACCTGATAAAATATAAACATCAGCAC
Found at i:40767261 original size:31 final size:31
Alignment explanation
Indices: 40767225--40767359 Score: 136
Period size: 31 Copynumber: 4.4 Consensus size: 31
40767215 ATATGGCTGA
40767225 ACATTGCTGAAAATAATTTTTATATGGTTAT
1 ACATTGCTGAAAATAATTTTTATATGGTTAT
* * *
40767256 TCATTGCTGAAATTGAA-TTATATA-GGTATAT
1 ACATTGCTGAAAAT-AATTTTTATATGGT-TAT
* **
40767287 A-AGTTGCTG-AAATGATTCGTATATGGTTGA-
1 ACA-TTGCTGAAAATAATTTTTATATGGTT-AT
40767317 ACATTGCTGAAAATAATTTTTATATGGTTAT
1 ACATTGCTGAAAATAATTTTTATATGGTTAT
*
40767348 ACATTGTTGAAA
1 ACATTGCTGAAA
40767360 TTAAATTGTT
Statistics
Matches: 83, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
29 1 0.01
30 21 0.25
31 59 0.71
32 2 0.02
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (31 bp):
ACATTGCTGAAAATAATTTTTATATGGTTAT
Found at i:40767304 original size:92 final size:92
Alignment explanation
Indices: 40767152--40767366 Score: 296
Period size: 92 Copynumber: 2.4 Consensus size: 92
40767142 GCCGAATTCG
* * * * *
40767152 AATTTTT-TTTGGTTATACATTGCTG--A-TATATTGTATA-TTACATAAGTTGCCGAAATGATT
1 AATTTTTATATGGTTATACATTGCTGAAATTAAATTATATAGGTATATAAGTTGCCGAAATGATT
40767212 CATATATGGCTGAACATTGCTGAAAAT
66 CATATATGGCTGAACATTGCTGAAAAT
* * *
40767239 AATTTTTATATGGTTATTCATTGCTGAAATTGAATTATATAGGTATATAAGTTGCTGAAATGATT
1 AATTTTTATATGGTTATACATTGCTGAAATTAAATTATATAGGTATATAAGTTGCCGAAATGATT
* *
40767304 CGTATATGGTTGAACATTGCTGAAAAT
66 CATATATGGCTGAACATTGCTGAAAAT
*
40767331 AATTTTTATATGGTTATACATTGTTGAAATTAAATT
1 AATTTTTATATGGTTATACATTGCTGAAATTAAATT
40767367 GTTTATGAAT
Statistics
Matches: 110, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
87 7 0.06
88 16 0.15
90 1 0.01
91 8 0.07
92 78 0.71
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.43
Consensus pattern (92 bp):
AATTTTTATATGGTTATACATTGCTGAAATTAAATTATATAGGTATATAAGTTGCCGAAATGATT
CATATATGGCTGAACATTGCTGAAAAT
Found at i:40767379 original size:92 final size:92
Alignment explanation
Indices: 40767193--40767389 Score: 286
Period size: 92 Copynumber: 2.1 Consensus size: 92
40767183 TGTATATTAC
*
40767193 ATAAGTTGCCGAAATGATTCATATATGGCTGAACATTGCTGAAAATAATTTTTATATGGTTATTC
1 ATAAGTTGCCGAAATGATTCATATATGGCTGAACATTGCTGAAAATAATTTTTATATGGTTATAC
* *
40767258 ATTGCTGAAATTGAATTATATAGGTAT
66 ATTGCTGAAATTAAATTATATAGGAAT
* * *
40767285 ATAAGTTGCTGAAATGATTCGTATATGGTTGAACATTGCTGAAAATAATTTTTATATGGTTATAC
1 ATAAGTTGCCGAAATGATTCATATATGGCTGAACATTGCTGAAAATAATTTTTATATGGTTATAC
* * * *
40767350 ATTGTTGAAATTAAATTGTTTATGAAT
66 ATTGCTGAAATTAAATTATATAGGAAT
* *
40767377 ATAGGATGCCGAA
1 ATAAGTTGCCGAA
40767390 TTTGATTTGT
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (92 bp):
ATAAGTTGCCGAAATGATTCATATATGGCTGAACATTGCTGAAAATAATTTTTATATGGTTATAC
ATTGCTGAAATTAAATTATATAGGAAT
Found at i:40767423 original size:31 final size:31
Alignment explanation
Indices: 40767365--40767518 Score: 118
Period size: 31 Copynumber: 5.0 Consensus size: 31
40767355 TGAAATTAAA
* *
40767365 TTGTTTATGAATATAGGA-TGCCGAATTTGAT
1 TTGTATATGAATATA-CATTGCCGAATTTGAT
* *
40767396 TTGTATATGATTATACATTGCCAAATTTGAT
1 TTGTATATGAATATACATTGCCGAATTTGAT
** * *
40767427 TCT-TATATGGTTATATATTGCCGAA-TTGCT
1 T-TGTATATGAATATACATTGCCGAATTTGAT
* * * **
40767457 TGGTATATCAATATTCATTGTTGAATTTGAT
1 TTGTATATGAATATACATTGCCGAATTTGAT
* * *
40767488 TCGTATATGAATATATATTGCTGAA-TTGAT
1 TTGTATATGAATATACATTGCCGAATTTGAT
40767518 T
1 T
40767519 AGAGCATTAG
Statistics
Matches: 97, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
30 27 0.28
31 69 0.71
32 1 0.01
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.45
Consensus pattern (31 bp):
TTGTATATGAATATACATTGCCGAATTTGAT
Found at i:40773981 original size:26 final size:26
Alignment explanation
Indices: 40773945--40773998 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
40773935 TATGTATAAC
40773945 CATGTACTCAATTTGGTCAAAATGAT
1 CATGTACTCAATTTGGTCAAAATGAT
40773971 CATGTACTCAATTTGGTCAAAATGAT
1 CATGTACTCAATTTGGTCAAAATGAT
40773997 CA
1 CA
40773999 ACTAACTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (26 bp):
CATGTACTCAATTTGGTCAAAATGAT
Found at i:40784168 original size:50 final size:50
Alignment explanation
Indices: 40784044--40784340 Score: 312
Period size: 50 Copynumber: 5.8 Consensus size: 50
40784034 GATAATAACA
* ** * *
40784044 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * **
40784093 TACCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
40784143 TGCCCATGCCATGTCCCAAACATGGTCTTACA-GAGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATATCGG
* * * *
40784193 TGCCAACGCCATGTCCCAGACATGGCCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
40784243 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC--GG
* *
40784298 ATGCCAATGCCATGTCCCAGACATAGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
40784341 TTACCCAAAT
Statistics
Matches: 209, Mismatches: 29, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
48 1 0.00
49 40 0.19
50 125 0.60
51 1 0.00
53 2 0.01
55 2 0.01
56 38 0.18
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:40787259 original size:44 final size:46
Alignment explanation
Indices: 40787177--40787270 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 46
40787167 AAAAAATTGG
* *
40787177 GTTTGGGGGGAAGTAAAAGTTTTGGAGAGAAAGTAAAAGGAAAAAA
1 GTTTGGGGGAAAGTAAAAGTTTTGGAGAGAAAATAAAAGGAAAAAA
* *
40787223 GTTT-GGGGAAAGTAAAGGTTTT-GAGGGAAAATAAAAGGAAAAAA
1 GTTTGGGGGAAAGTAAAAGTTTTGGAGAGAAAATAAAAGGAAAAAA
40787267 GTTT
1 GTTT
40787271 TGGAGGGTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 24 0.55
45 16 0.36
46 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.33, T:0.22
Consensus pattern (46 bp):
GTTTGGGGGAAAGTAAAAGTTTTGGAGAGAAAATAAAAGGAAAAAA
Found at i:40787273 original size:45 final size:46
Alignment explanation
Indices: 40787177--40787273 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 46
40787167 AAAAAATTGG
* * *
40787177 GTTTGGGGGGAAGTAAAAGTTTTGGAGAGAAAGTAAAAGGAAAAAA
1 GTTTTGGGGAAAGTAAAAGTTTTGGAGAGAAAATAAAAGGAAAAAA
* *
40787223 G-TTTGGGGAAAGTAAAGGTTTT-GAGGGAAAATAAAAGGAAAAAA
1 GTTTTGGGGAAAGTAAAAGTTTTGGAGAGAAAATAAAAGGAAAAAA
40787267 GTTTTGG
1 GTTTTGG
40787274 AGGGTTTGGG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 21 0.47
45 23 0.51
46 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.34, T:0.23
Consensus pattern (46 bp):
GTTTTGGGGAAAGTAAAAGTTTTGGAGAGAAAATAAAAGGAAAAAA
Found at i:40790466 original size:21 final size:22
Alignment explanation
Indices: 40790440--40790483 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
40790430 GTAATTATTA
* *
40790440 TTTTTATTTTTATATGTA-ATT
1 TTTTTATCTATATATGTACATT
40790461 TTTTTATCTATATATGTACATT
1 TTTTTATCTATATATGTACATT
40790483 T
1 T
40790484 GTTGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTTTATCTATATATGTACATT
Found at i:40795610 original size:14 final size:15
Alignment explanation
Indices: 40795586--40795618 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
40795576 TCCCAAGCTG
40795586 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
40795601 GGAA-GACCTTATTT
1 GGAAGGACCTTATGT
40795615 GGAA
1 GGAA
40795619 AAGCGTCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Found at i:40795709 original size:5 final size:5
Alignment explanation
Indices: 40795694--40795722 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
40795684 AGAAATATTT
40795694 CAAAA -AAAA CAAAA CAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA
40795723 AAAGGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:40797051 original size:43 final size:43
Alignment explanation
Indices: 40797002--40797139 Score: 105
Period size: 44 Copynumber: 3.2 Consensus size: 43
40796992 CACTGATAGT
40797002 GAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGC
1 GAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGC
* ** * * * * * ** **
40797045 GAAGCAGGTTAAAAATAACAGATCTTGCCTTCCTGCATCAACAGC
1 GAAGCAGATCGAAGACACCAG-CCTTGCCTCCCTGGGT-TGCAGC
* * * *
40797090 GAAACAAATCGAAGACACCAGCCTTGCCTCCCTAGGTTGTAGC
1 GAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGC
*
40797133 GGAGCAG
1 GAAGCAG
40797140 GCTAAAAATA
Statistics
Matches: 62, Mismatches: 31, Indels: 4
0.64 0.32 0.04
Matches are distributed among these distances:
43 22 0.35
44 23 0.37
45 17 0.27
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.18
Consensus pattern (43 bp):
GAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGC
Found at i:40797128 original size:88 final size:88
Alignment explanation
Indices: 40796976--40797199 Score: 295
Period size: 88 Copynumber: 2.5 Consensus size: 88
40796966 TGAAGAGAGT
** * * * * *
40796976 AGATCTTGCCTTCCTACACTGATAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
1 AGATCTTGCCTTCCTACACCAACAGCGAAACAAATCGAAGACACCAGCCTTGCCTCCCTAGGTTG
*
40797041 CAGCGAAGCAGGTTAAAAATAAC
66 CAGCGAAGCAGGCTAAAAATAAC
* *
40797064 AGATCTTGCCTTCCTGCATCAACAGCGAAACAAATCGAAGACACCAGCCTTGCCTCCCTAGGTTG
1 AGATCTTGCCTTCCTACACCAACAGCGAAACAAATCGAAGACACCAGCCTTGCCTCCCTAGGTTG
* * *
40797129 TAGCGGAGCAGGCTAAAAATAGC
66 CAGCGAAGCAGGCTAAAAATAAC
* * *
40797152 AGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACATCCAG
1 AGATCTTGCCTTCCTACACCAACAGCGAAACAAATCGAAGACA-CCAG
40797200 TCTTATCTCC
Statistics
Matches: 117, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
88 113 0.97
89 4 0.03
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (88 bp):
AGATCTTGCCTTCCTACACCAACAGCGAAACAAATCGAAGACACCAGCCTTGCCTCCCTAGGTTG
CAGCGAAGCAGGCTAAAAATAAC
Found at i:40797455 original size:217 final size:217
Alignment explanation
Indices: 40797192--40797658 Score: 792
Period size: 217 Copynumber: 2.2 Consensus size: 217
40797182 CAGATCGAAG
*
40797192 ACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAATAAGCAGGTCTTATCCCCCTG
1 ACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAATAAGCAGGTCTTATCCCCCTG
* * * *
40797257 AAGTTGCAGTGGGGCAGACCCAAAATGGCGAATCTTATCTCCC-AAAAGTTGCAATGGAACATAT
66 AAGTTGCAGTGGGGCAGACCCAAAATGGCAAATATTATCTCCCTAAAA-TTGCAATAGAACAGAT
* *
40797321 TTAAGCCTATAATCCTATCTCCTTAAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTC
130 TTAAGCCTATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGAATTAAAATCACAGATCTTATCTC
40797386 TCTGAAGTTGCAAAGAGCAGATC
195 TCTGAAGTTGCAAAGAGCAGATC
40797409 ACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAATAAGCAGGTCTTATCCCCCTG
1 ACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAATAAGCAGGTCTTATCCCCCTG
* * * *
40797474 AAGTTGCAGTGGGGCAGACCTAAAATGGCAAATATTATCTCCCTAGAATTGCAGTAGAGCAGATT
66 AAGTTGCAGTGGGGCAGACCCAAAATGGCAAATATTATCTCCCTAAAATTGCAATAGAACAGATT
*
40797539 TAAGCCTATAATCCTATCTCCCTAAAGTTGCAGTGGAGTGAATTAAAATCACAGATCTTATCTCT
131 TAAGCCTATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGAATTAAAATCACAGATCTTATCTCT
*
40797604 CTGAAGTTGCAGAGAGCAGATC
196 CTGAAGTTGCAAAGAGCAGATC
*
40797626 ATATCTAGTCTTATCTCCCTGAAGTTGCAGTGG
1 ACATCTAGTCTTATCTCCCTGAAGTTGCAGTGG
40797659 GGCGGACCCA
Statistics
Matches: 235, Mismatches: 14, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
217 232 0.99
218 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (217 bp):
ACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAATAAGCAGGTCTTATCCCCCTG
AAGTTGCAGTGGGGCAGACCCAAAATGGCAAATATTATCTCCCTAAAATTGCAATAGAACAGATT
TAAGCCTATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGAATTAAAATCACAGATCTTATCTCT
CTGAAGTTGCAAAGAGCAGATC
Found at i:40797515 original size:173 final size:173
Alignment explanation
Indices: 40797336--40797711 Score: 376
Period size: 173 Copynumber: 2.2 Consensus size: 173
40797326 CCTATAATCC
* * * * *
40797336 TATCTCCTTAAAGTTGCAGTGGAGCGGATTAAAATC-ACAGATCTTATCTCTCTGAAGTTGCA-A
1 TATCTCCTTAAAGTTGCAGTGGAGCAGATTAAAACCTACA-ATCCTATCTCCCTAAAGTTGCAGA
* * * *
40797399 AGAGCAG-A-TCACATC-TAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAATAAGC-A
65 AGAG-AGAATTAAAATCACAGATCTTATCTCCCTGAAGTTGCAG-AGAGCAGA-T-AAT-AGCTA
*
40797459 GGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACCTAAAATGGC-AAATAT
125 -GTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACCCAAAATGGCGAAA-AT
* * * * * *
40797509 TATCTCCCTAGAA-TTGCAGTAGAGCAGATTTAAGCCTATAATCCTATCTCCCTAAAGTTGCAGT
1 TATCTCCTTA-AAGTTGCAGTGGAGCAGATTAAAACCTACAATCCTATCTCCCTAAAGTTGCAGA
* * * * *
40797573 GGAGTGAATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCATATCTAGTCTT
65 AGAGAGAATTAAAATCACAGATCTTATCTCCCTGAAGTTGCAGAGAGCAGATAATAGCTAGTCTT
* * *
40797638 ATCTCCCTGAAGTTGCAGTGGGGCGGACCCAAAATGGCGAAACT
130 ATCCCCCTGAAGTTGCAGTGGGGCAGACCCAAAATGGCGAAAAT
40797682 TATCT-CTCTAAAGTTGCAGTGGAGCAGATT
1 TATCTCCT-TAAAGTTGCAGTGGAGCAGATT
40797712 TAAGCTTATA
Statistics
Matches: 166, Mismatches: 26, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
172 3 0.02
173 113 0.68
174 14 0.08
175 6 0.04
176 9 0.05
177 21 0.13
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (173 bp):
TATCTCCTTAAAGTTGCAGTGGAGCAGATTAAAACCTACAATCCTATCTCCCTAAAGTTGCAGAA
GAGAGAATTAAAATCACAGATCTTATCTCCCTGAAGTTGCAGAGAGCAGATAATAGCTAGTCTTA
TCCCCCTGAAGTTGCAGTGGGGCAGACCCAAAATGGCGAAAAT
Found at i:40797796 original size:173 final size:174
Alignment explanation
Indices: 40797417--40797840 Score: 441
Period size: 173 Copynumber: 2.4 Consensus size: 174
40797407 TCACATCTAG
* *
40797417 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAATAAGC-AGGTCTTATCCCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-AAT-ATCTA-GTCTTATCTCCCTGAAGTTGC
* *
40797481 AGTGGGGCAGACCTAAAATGGCAAATATTATCTCCCTAGAATTGCAGTAGAGCAGATTTAAGCCT
62 AGTGGGGCGGACCCAAAATGGCAAATATTATCTCCCTAGAATTGCAGTAGAGCAGATTTAAGCCT
* * *
40797546 ATAATCCTATCTCCCTAAAGTTGCAGTGGAGTGAATTAAAATCACAGA
127 ATAATCCTATCCCCCTAAAGTTGCAGTGGAGTGAATGAAAAGCACAGA
* * *
40797594 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCATATCTAGTCTTATCTCCCTGAAGTTGCAGTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAATATCTAGTCTTATCTCCCTGAAGTTGCAGTG
* * * *
40797658 GGGCGGACCCAAAATGGCGAAA-CTTATCTCTCTA-AAGTTGCAGTGGAGCAGATTTAAGCTTAT
66 GGGCGGACCCAAAATGGC-AAATATTATCTCCCTAGAA-TTGCAGTAGAGCAGATTTAAGCCTAT
* * * * * ** *
40797721 AATCTTATCCCCCTGAGGTTTCCGT-GAG-GCAGACTGAAGGGC-GA-A
129 AATCCTATCCCCCTAAAGTTGCAGTGGAGTG-A-A-TGAAAAGCACAGA
** * *
40797766 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGGTCAATAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAATATC--TAGTCTTATCTCCCTGAAGTTGCA
*
40797831 GTGGAGCGGA
63 GTGGGGCGGA
40797841 TTAAAATCAT
Statistics
Matches: 207, Mismatches: 30, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
171 1 0.00
172 28 0.14
173 104 0.50
174 14 0.07
175 1 0.00
176 38 0.18
177 21 0.10
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (174 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAATATCTAGTCTTATCTCCCTGAAGTTGCAGTG
GGGCGGACCCAAAATGGCAAATATTATCTCCCTAGAATTGCAGTAGAGCAGATTTAAGCCTATAA
TCCTATCCCCCTAAAGTTGCAGTGGAGTGAATGAAAAGCACAGA
Found at i:40797822 original size:44 final size:44
Alignment explanation
Indices: 40797200--40797868 Score: 268
Period size: 44 Copynumber: 15.3 Consensus size: 44
40797190 AGACATCCAG
**
40797200 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAATAA-G-CA-GG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT---TAAGGTCATAA
* * ** *
40797244 TCTTATCCCCCTGAAGTTGCAGTGGGGCAGACCCAAAATGG-C-GAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA--CTTAA-GGTCATAA
** * * * * *
40797289 TCTTATCTCCCAAAAGTTGCAATGGAACATATTTAA-GCCTATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTTAAGGTC-ATAA
* * * * ** *
40797333 TCCTATCTCCTTAAAGTTGCAGTGGAGCGGA-TTAAAATCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTTAAGGTCATA-A
* ** * *
40797377 TCTTATCTCTCTGAAGTTGCA-AAGAGCAGA-TCACA--TC-TAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTTA-AGGTCATAA
**
40797417 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAATAA-G-CA-GG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT---TAAGGTCATAA
* * *
40797461 TCTTATCCCCCTGAAGTTGCAGTGGGGCAGACCTAAAATGG-CA-AA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CT-TAA-GGTCATAA
* * * *
40797506 TATTATCTCCCTAGAA-TTGCAGTAGAGCAGATTTAA-GCCTATAA
1 TCTTATCTCCCT-GAAGTTGCAGTGGAGCAGACTTAAGGTC-ATAA
* * * * ** *
40797550 TCCTATCTCCCTAAAGTTGCAGTGGAG-TGAATTAAAATCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTTAAGGTCATA-A
* * * *
40797594 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCATA--TC-TAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTTA-AGGTCATAA
* * **
40797634 TCTTATCTCCCTGAAGTTGCAGTGGGGCGGACCCAAAATGG-CGA-AA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA--CTTAA-GGTC-ATAA
* * * * *
40797680 -CTTATCTCTCTAAAGTTGCAGTGGAGCAGATTTAAGCTTATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTTAAGGTCATAA
* * * * * * *
40797723 TCTTATCCCCCTGAGGTTTCCGT-GAGGCAGACTGAAGGGC-GAA
1 TCTTATCTCCCTGAAGTTGCAGTGGA-GCAGACTTAAGGTCATAA
40797766 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAGGTCAATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTTAAGGTC-ATAA
* * ** *
40797810 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGA-TTAAAATCATGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTTAAGGTCAT-AA
*
40797854 TCTTATCTCGCTGAA
1 TCTTATCTCCCTGAA
40797869 ATCACAGTAG
Statistics
Matches: 466, Mismatches: 112, Indels: 94
0.69 0.17 0.14
Matches are distributed among these distances:
40 41 0.09
41 16 0.03
42 15 0.03
43 74 0.16
44 233 0.50
45 82 0.18
46 5 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTTAAGGTCATAA
Found at i:40798305 original size:18 final size:18
Alignment explanation
Indices: 40798282--40798316 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40798272 ACAAAACACA
* *
40798282 TGGCCCGATTTCAAACGG
1 TGGCCCAATTACAAACGG
40798300 TGGCCCAATTACAAACG
1 TGGCCCAATTACAAACG
40798317 CGGCCCAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (18 bp):
TGGCCCAATTACAAACGG
Found at i:40799491 original size:20 final size:21
Alignment explanation
Indices: 40799466--40799508 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
40799456 GTAATTATTA
* *
40799466 TTTTTATTTTTATATGTA-AT
1 TTTTTATCTATATATGTACAT
40799486 TTTTTATCTATATATGTACAT
1 TTTTTATCTATATATGTACAT
40799507 TT
1 TT
40799509 GTTGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTTTATCTATATATGTACAT
Found at i:40801869 original size:24 final size:23
Alignment explanation
Indices: 40801825--40801869 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
40801815 GTTTTATGGC
*
40801825 TTTTAGGGTTTAGGGTGCAGGCT
1 TTTTAGGGTTTAGGGTCCAGGCT
40801848 TTTTAGGAG-TTAGGGGTCCAGG
1 TTTTAGG-GTTTA-GGGTCCAGG
40801870 AAAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.16, C:0.09, G:0.40, T:0.36
Consensus pattern (23 bp):
TTTTAGGGTTTAGGGTCCAGGCT
Found at i:40802040 original size:125 final size:123
Alignment explanation
Indices: 40801911--40802165 Score: 352
Period size: 125 Copynumber: 2.1 Consensus size: 123
40801901 AAATAGTGGG
** * * * **
40801911 AAATCGCTTCTACTAGGATGCTATTTAAGAAGAAATTGTGAAATAGTGGTCTCGTGGACGCGATT
1 AAATCGCTAATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
*
40801976 TCGCTACAG-TGGTCATGT-GAGAAATAATTTTTTTTTGACGTTTTCTGAGGAAATAGTATA
66 TCGCTACAGTTGGTCATGTAG-GAAATAA--TTTTTTTGACG-TTTCTGAGCAAATAGTATA
* *
40802036 AAATCGCTAATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
1 AAATCGCTAATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
* *
40802101 TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTGACGTTTCTGAGCAAATAGTGTC
66 TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTGACGTTTCTGAGCAAATAGTATA
40802159 AAATCGC
1 AAATCGC
40802166 GCCCTCGTGG
Statistics
Matches: 116, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
123 23 0.20
124 11 0.09
125 65 0.56
126 16 0.14
127 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (123 bp):
AAATCGCTAATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTGACGTTTCTGAGCAAATAGTATA
Found at i:40802215 original size:83 final size:83
Alignment explanation
Indices: 40802076--40802276 Score: 384
Period size: 83 Copynumber: 2.4 Consensus size: 83
40802066 AGAAATTGTG
*
40802076 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTGACGT
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTTTGACGT
40802141 TTCTGAGCAAATAGTGTC
66 TTCTGAGCAAATAGTGTC
40802159 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTTTGACGT
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTTTGACGT
40802224 TTCTGAGCAAATAGTGTC
66 TTCTGAGCAAATAGTGTC
*
40802242 AAATCGCGCCCTTGTGGACGCGATTTCGCTACAGT
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGT
40802277 AGCAAGTTTG
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 116 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (83 bp):
AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTTTGACGT
TTCTGAGCAAATAGTGTC
Found at i:40805443 original size:23 final size:23
Alignment explanation
Indices: 40805413--40805636 Score: 155
Period size: 23 Copynumber: 8.8 Consensus size: 23
40805403 TACAATTTAA
40805413 TTAGGGTTTTTAATTAAATAGGG
1 TTAGGGTTTTTAATTAAATAGGG
*
40805436 TTAGGGTTTTTAATTTAATTAGGTTAGG
1 TTAGGGTTTTTAA-TTAAATA-G---GG
* *
40805464 TTAGGGTTTTTAATTAATTAGGT
1 TTAGGGTTTTTAATTAAATAGGG
*
40805487 TTAGGGTTTTTAATTTAATTAAATAAGG
1 TTAGGG---TT--TTTAATTAAATAGGG
40805515 TTAGGGTTTTTAATTAAATTA-GG
1 TTAGGGTTTTTAATTAAA-TAGGG
*
40805538 TTAGGATTTTTAATTTAATTAGGTTAGGG
1 TTAGGGTTTTTAA-TTAA--A---TAGGG
*
40805567 TTAGGGTTTTTAATTTAATTAAATAAGG
1 TTAGGG-TT----TTTAATTAAATAGGG
* *
40805595 TTAGGATTTTTAATTTAAGTA-GG
1 TTAGGGTTTTTAA-TTAAATAGGG
40805618 TTAGGGTTTTTAATTAAAT
1 TTAGGGTTTTTAATTAAAT
40805637 TAAATAAGGT
Statistics
Matches: 166, Mismatches: 12, Indels: 47
0.74 0.05 0.21
Matches are distributed among these distances:
22 5 0.03
23 63 0.38
24 18 0.11
25 3 0.02
26 4 0.02
27 9 0.05
28 45 0.27
29 7 0.04
30 2 0.01
31 1 0.01
33 4 0.02
34 5 0.03
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (23 bp):
TTAGGGTTTTTAATTAAATAGGG
Found at i:40805465 original size:28 final size:28
Alignment explanation
Indices: 40805421--40806036 Score: 519
Period size: 28 Copynumber: 22.5 Consensus size: 28
40805411 AATTAGGGTT
*
40805421 TTTAATTAA-ATAGGGTTAGGGTTTTTAA
1 TTTAATTAAGTTA-GGTTAGGGTTTTTAA
*
40805449 TTTAATTAGGTTAGGTTAGGGTTTTTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA
*
40805477 -TTAATT-AG---GTTTAGGGTTTTTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA
* *
40805500 TTTAATTAAATAAGGTTAGGGTTTTTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA
*
40805528 -TT-A--AA-TTAGGTTAGGATTTTTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA
*
40805551 TTTAATTAGGTTAGGGTTAGGGTTTTTAA
1 TTTAATTAAGTTA-GGTTAGGGTTTTTAA
* * *
40805580 TTTAATTAAATAAGGTTAGGATTTTTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA
40805608 --T--TTAAG-TAGGTTAGGGTTTTTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA
* * *
40805631 TTAAATTAAATAAGGTTAGGGTTTTTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA
*
40805659 TTTAAGTAGGTTAGGTTAGGGTTAGGGTTTTTAA
1 TTT-A--A--TTAAGTTA-GGTTAGGGTTTTTAA
*
40805693 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA
40805721 -TT-A--AA-TTAGGTTAGGGTTTTTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA
* * *
40805744 TTTAATTAAATAAGGTTAGGGTTTTTTA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA
*
40805772 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA
40805800 --T--TTAAG-TAGGTTAGGG-TTTTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA
40805822 -TT-A--AA-TTAGGTTAGGGTTTTTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA
* *
40805845 TTTAATTAGGTTAGGTTAGGGTTAGGGTT--
1 TTTAATTAAGTTAGGTTAGGGTT---TTTAA
*
40805874 TTTAATTAAATTAGGTTAGGGTTTTTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA
40805902 TTTAATTAGGTTAGGTTAGGGTTAGGGTTTTTAA
1 TTTAATTA----A-GTTA-GGTTAGGGTTTTTAA
* *
40805936 TTTAATTAAATAAGGTTAGGGTTTTTAA
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA
* * *****
40805964 TTTAATTAGGTTATGTTAGGGTTAGGGT
1 TTTAATTAAGTTAGGTTAGGGTTTTTAA
40805992 TTCTAATTAAG-TAGGGTTTAGGGTTTTTAA
1 TT-TAATTAAGTTA-GG-TTAGGGTTTTTAA
*
40806022 TTTAATTAAATTAGG
1 TTTAATTAAGTTAGG
40806037 GTTTTTAATT
Statistics
Matches: 480, Mismatches: 56, Indels: 103
0.75 0.09 0.16
Matches are distributed among these distances:
22 18 0.04
23 80 0.17
24 24 0.05
25 4 0.01
26 7 0.01
27 18 0.04
28 188 0.39
29 73 0.15
30 13 0.03
31 4 0.01
32 1 0.00
33 9 0.02
34 41 0.09
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (28 bp):
TTTAATTAAGTTAGGTTAGGGTTTTTAA
Found at i:40805869 original size:34 final size:33
Alignment explanation
Indices: 40805830--40805999 Score: 181
Period size: 34 Copynumber: 5.5 Consensus size: 33
40805820 AATTAAATTA
40805830 GGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAG
1 GGTTAGGGTTTTTAATTTAATTAGGTTA-GTTAG
40805864 GGTTAGGGTTTTTAA-TT-A--A----A-TTA-
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGTTAG
40805887 GGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAG
1 GGTTAGGGTTTTTAATTTAATTAGGTTA-GTTAG
* *
40805921 GGTTAGGGTTTTTAATTTAATTA----A-ATAA
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGTTAG
40805949 GGTTAGGGTTTTTAATTTAATTAGGTTATGTTAG
1 GGTTAGGGTTTTTAATTTAATTAGGTTA-GTTAG
*
40805983 GGTTAGGGTTTCTAATT
1 GGTTAGGGTTTTTAATT
40806000 AAGTAGGGTT
Statistics
Matches: 114, Mismatches: 5, Indels: 34
0.75 0.03 0.22
Matches are distributed among these distances:
23 15 0.13
24 5 0.04
25 1 0.01
26 1 0.01
27 1 0.01
28 25 0.22
30 2 0.02
31 1 0.01
32 2 0.02
33 5 0.04
34 56 0.49
ACGTcount: A:0.26, C:0.01, G:0.26, T:0.48
Consensus pattern (33 bp):
GGTTAGGGTTTTTAATTTAATTAGGTTAGTTAG
Found at i:40805891 original size:23 final size:23
Alignment explanation
Indices: 40805864--40805916 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
40805854 GTTAGGTTAG
40805864 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
40805887 GGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAATTAAATTA
40805910 GGTTAGG
1 GGTTAGG
40805917 TTAGGGTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (23 bp):
GGTTAGGGTTTTTAATTAAATTA
Found at i:40805906 original size:62 final size:57
Alignment explanation
Indices: 40805678--40806029 Score: 395
Period size: 57 Copynumber: 6.4 Consensus size: 57
40805668 GTTAGGTTAG
*
40805678 GGTTAGGGTTTTTAATTTAATTA----A-ATTA-GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
** * **
40805729 GGTTAGGGTTTTTAATTTAATTAAATAAGGTTAGGGTT--TTTTATTTAATTAAATTA
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTAGGGTT-TTTAATTAAATTA
40805785 GGTTAGGGTTTTTAA--T--TTA----A-G-TA-GGTTAGGG-TTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
40805830 GGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
*
40805887 GGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTAGGGTTTTTAATTTAATTAAATAA
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTAGGG---TT--TTTAATTAAATTA
* * *
40805949 GGTTAGGGTTTTTAATTTAATTAGGTTATGTTAGGGTTAGGGTTTCTAATT-AAGTA
1 GGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
40806005 GGGTTTAGGGTTTTTAATTTAATTA
1 -GG-TTAGGGTTTTTAATTTAATTA
40806030 AATTAGGGTT
Statistics
Matches: 263, Mismatches: 10, Indels: 49
0.82 0.03 0.15
Matches are distributed among these distances:
45 32 0.12
46 3 0.01
47 2 0.01
48 1 0.00
49 3 0.01
51 23 0.09
52 3 0.01
53 1 0.00
54 2 0.01
55 5 0.02
56 42 0.16
57 68 0.26
58 21 0.08
59 2 0.01
60 2 0.01
62 53 0.20
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.48
Consensus pattern (57 bp):
GGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
Found at i:40805973 original size:57 final size:54
Alignment explanation
Indices: 40805434--40806029 Score: 396
Period size: 51 Copynumber: 10.9 Consensus size: 54
40805424 AATTAAATAG
* ** *
40805434 GGTTAGGGTTTTTAATTTAATTAGGTTAGGTTAGGGTTTTTAA-TTAATTAGG-T-
1 GGTTAGGGTTATT--TTTAATTAAATAAGGTTAGGGTTTTTAATTTAATTAGGTTA
* *
40805487 --TTAGGGTTTTTAATTTAATTAAATAAGGTTAGGGTTTTTAATTAAATTAGGTTA
1 GGTTAGGGTTATT--TTTAATTAAATAAGGTTAGGGTTTTTAATTTAATTAGGTTA
* * ** * ** *
40805541 GGATT---TTTA-ATTTAATTAGGTTAGGGTTAGGGTTTTTAATTTAATTAAATAA
1 GG-TTAGGGTTATTTTTAATTA-AATAAGGTTAGGGTTTTTAATTTAATTAGGTTA
* * ** *
40805593 GGTTA-GG--ATTTTTAATTTAAGT-AGGTTAGGGTTTTTAATTAAATTAAATAA
1 GGTTAGGGTTATTTTTAA-TTAAATAAGGTTAGGGTTTTTAATTTAATTAGGTTA
* ** * **
40805644 GGTTAGGGTTTTTAATTTAAGTAGGTTAGGTTAGGGTTAGGGTTTTTAATTTAATTAAATTA
1 GGTTAGGGTTATT--TTT-A--A--TTA-AATAAGGTTAGGGTTTTTAATTTAATTAGGTTA
* ** *
40805706 GGTTAGGG---TTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAAATAA
1 GGTTAGGGTTATTTTTAATTAAATAAGGTTAGGGTTTTTAATTTAATTAGGTTA
* *
40805757 GGTTAGGGTTTTTTATTTAATTAAATTAGGTTAGGGTTTTTAATTT-A--A-G-TA
1 GGTTAGGG-TTATT-TTTAATTAAATAAGGTTAGGGTTTTTAATTTAATTAGGTTA
*
40805808 GGTTAGGG----TTTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTA
1 GGTTAGGGTTATTTTTAATTAAATAAGGTTAGGGTTTTTAATTTAATTAGGTTA
*
40805858 GGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTA
1 GGTTAGGGTTA---TTTTTAATTAAATAAGGTTAGGGTTTTTAATTTAATTAGGTTA
40805915 GGTTAGGGTTAGGGTTTTTAATTTAATTAAATAAGGTTAGGGTTTTTAATTTAATTAGGTTA
1 GGTTAGGGTTA------TT--TTTAATTAAATAAGGTTAGGGTTTTTAATTTAATTAGGTTA
* * * *
40805977 TGTTAGGGTTAGGGTTTCTAATTAAGTAGGGTTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTA---TTTTTAATTAAATAAGG-TTAGGGTTTTTAATTTAATTA
40806030 AATTAGGGTT
Statistics
Matches: 453, Mismatches: 45, Indels: 85
0.78 0.08 0.15
Matches are distributed among these distances:
45 31 0.07
46 2 0.00
48 1 0.00
49 1 0.00
50 10 0.02
51 126 0.28
52 47 0.10
53 5 0.01
54 5 0.01
55 3 0.01
56 35 0.08
57 71 0.16
58 21 0.05
59 5 0.01
60 5 0.01
61 1 0.00
62 84 0.19
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (54 bp):
GGTTAGGGTTATTTTTAATTAAATAAGGTTAGGGTTTTTAATTTAATTAGGTTA
Found at i:40806015 original size:24 final size:24
Alignment explanation
Indices: 40805980--40806069 Score: 105
Period size: 24 Copynumber: 3.8 Consensus size: 24
40805970 TAGGTTATGT
*
40805980 TAGGG-TTAGGGTTTCTAATTAAG
1 TAGGGTTTAGGGTTTTTAATTAAG
*
40806003 TAGGGTTTAGGGTTTTTAATTTAAT
1 TAGGGTTTAGGGTTTTTAA-TTAAG
**
40806028 TA--AATTAGGGTTTTTAATTAAG
1 TAGGGTTTAGGGTTTTTAATTAAG
*
40806050 TAGGGTTTAGGGATTTTAAT
1 TAGGGTTTAGGGTTTTTAAT
40806070 CAAATAATGT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
22 6 0.11
23 18 0.33
24 25 0.45
25 6 0.11
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.46
Consensus pattern (24 bp):
TAGGGTTTAGGGTTTTTAATTAAG
Found at i:40806055 original size:17 final size:18
Alignment explanation
Indices: 40806022--40806057 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40806012 GGGTTTTTAA
*
40806022 TTTAATTAAATTAGGGTT
1 TTTAATTAAAGTAGGGTT
40806040 TTTAATT-AAGTAGGGTT
1 TTTAATTAAAGTAGGGTT
40806057 T
1 T
40806058 AGGGATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (18 bp):
TTTAATTAAAGTAGGGTT
Found at i:40808374 original size:29 final size:29
Alignment explanation
Indices: 40808340--40808396 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
40808330 TGAAAATATT
40808340 AAAAATATTAAAATTATT-TTAAAAAAATA
1 AAAAATATTAAAATT-TTCTTAAAAAAATA
*
40808369 AAAAATTTTAAAATTTTCTTAAAAAAAT
1 AAAAATATTAAAATTTTCTTAAAAAAAT
40808397 GAAATTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (29 bp):
AAAAATATTAAAATTTTCTTAAAAAAATA
Found at i:40808468 original size:22 final size:22
Alignment explanation
Indices: 40808438--40808479 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40808428 ATTTGGAGAT
*
40808438 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
40808460 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
40808480 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:40808500 original size:52 final size:51
Alignment explanation
Indices: 40808429--40808531 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
40808419 TTAATATGGA
* * *
40808429 TTTGGAGATTTTTTGAAGGAAATTGAGAG-GATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTT-GAAGGGAA-TTGAGAG
*
40808480 TTTGAGAGAATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
40808532 AAATTTTGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.33
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
Found at i:40808506 original size:22 final size:23
Alignment explanation
Indices: 40808481--40808572 Score: 111
Period size: 22 Copynumber: 4.2 Consensus size: 23
40808471 ATTTGAGAGT
40808481 TTGAGAG-AATTTTGGAAGGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
40808503 TTGATAGAAATTTT-GAAGGGAA
1 TTGAGAGAAATTTTGGAAGGAAA
*
40808525 TTGAGAGAAATTTTGAAAGG-AA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
40808547 TTGAGAG-AATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
40808569 TTGA
1 TTGA
40808573 TATTGAATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
21 9 0.15
22 41 0.68
23 10 0.17
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (23 bp):
TTGAGAGAAATTTTGGAAGGAAA
Found at i:40808530 original size:44 final size:44
Alignment explanation
Indices: 40808481--40808572 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
40808471 ATTTGAGAGT
* * * *
40808481 TTGAGAG-AATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAA
1 TTGAGAGAAATTTTGAAAGG-AATTGAGAGAAATTTTGAAAGAAA
*
40808525 TTGAGAGAAATTTTGAAAGGAATTGAGAGAATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
40808569 TTGA
1 TTGA
40808573 TATTGAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 31 0.74
45 11 0.26
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (44 bp):
TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
Found at i:40810654 original size:44 final size:44
Alignment explanation
Indices: 40810605--40810694 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
40810595 AATTTCATTA
40810605 TATTTTTACTTATTTCTTGCGTTCACTACCTCATTAGAATTTCT
1 TATTTTTACTTATTTCTTGCGTTCACTACCTCATTAGAATTTCT
40810649 TATTTTTACTTATTTCTTGCGTTCACTACCTCATTAGAATTTCT
1 TATTTTTACTTATTTCTTGCGTTCACTACCTCATTAGAATTTCT
40810693 TA
1 TA
40810695 CTCTGATCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.52
Consensus pattern (44 bp):
TATTTTTACTTATTTCTTGCGTTCACTACCTCATTAGAATTTCT
Found at i:40823747 original size:57 final size:54
Alignment explanation
Indices: 40823622--40823793 Score: 144
Period size: 48 Copynumber: 3.3 Consensus size: 54
40823612 TTCCAAAAAT
* * * *
40823622 AATATTATTTTAAT-AGATGTAATATTAAATTAAAT-TAAATACTTATC-T--T-
1 AATATTATATTAATAAGATTTAATATTAAATTTAATCT-AATATTTATCTTGATA
* * * * * *
40823671 AATAGTAT-TTTATTA-ATTTAATATTAAGTTTAATTTAATGTTTATCTTGTAGATA
1 AATATTATATTAATAAGATTTAATATTAAATTTAATCTAATATTTATC-T-T-GATA
* *
40823726 AATATTCTATTAATAAGATTTAATGTTAAATTTAATCTAATATTTATCTTGATA
1 AATATTATATTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTGATA
40823780 AATATTATATTAAT
1 AATATTATATTAAT
40823794 TTAATATTAA
Statistics
Matches: 96, Mismatches: 16, Indels: 17
0.74 0.12 0.13
Matches are distributed among these distances:
48 28 0.29
49 9 0.09
51 1 0.01
54 18 0.19
55 7 0.07
56 6 0.06
57 27 0.28
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.49
Consensus pattern (54 bp):
AATATTATATTAATAAGATTTAATATTAAATTTAATCTAATATTTATCTTGATA
Found at i:40831304 original size:21 final size:21
Alignment explanation
Indices: 40831278--40831320 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40831268 TCTGCAACCA
40831278 CTTAGTTGTATGAACCTTGTT
1 CTTAGTTGTATGAACCTTGTT
40831299 CTTAGTTGTATGAACCTTGTT
1 CTTAGTTGTATGAACCTTGTT
40831320 C
1 C
40831321 CGGATTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.47
Consensus pattern (21 bp):
CTTAGTTGTATGAACCTTGTT
Found at i:40831836 original size:14 final size:14
Alignment explanation
Indices: 40831817--40831846 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
40831807 TGAAACGAAT
40831817 TCTTTAAGGTATTC
1 TCTTTAAGGTATTC
40831831 TCTTTAAGGTATTC
1 TCTTTAAGGTATTC
40831845 TC
1 TC
40831847 ATGTACCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (14 bp):
TCTTTAAGGTATTC
Found at i:40838285 original size:51 final size:50
Alignment explanation
Indices: 40838160--40838354 Score: 205
Period size: 51 Copynumber: 3.9 Consensus size: 50
40838150 GAAAGTGATT
* * *
40838160 GTCACATGTGTAGTACTATGTGCAGTCTACTACGTGTACCGGAATAATA-G
1 GTCACATGTGTAGTACTATGTGCAGGCTACTACGCGTACC-GAATAGTATG
** * * *
40838210 GTCGTATGTGTAGTACTATATGCAGGCTACTATGCGTACCGAATAGTTTCG
1 GTCACATGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAATAGTAT-G
* * * *
40838261 ATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT-GATAATG
1 GTCACATGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAATAG-T-ATG
* * *
40838312 GTCACATGTGTAGTACTATGTGCAGACTACTATGCGAACCGAA
1 GTCACATGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAA
40838355 CATCATTGAT
Statistics
Matches: 117, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
49 6 0.05
50 35 0.30
51 75 0.64
52 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (50 bp):
GTCACATGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAATAGTATG
Found at i:40838420 original size:45 final size:45
Alignment explanation
Indices: 40838356--40838441 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
40838346 CGAACCGAAC
* * *
40838356 ATCATTGATTAGTAAGGTGGTTGCTATGTGATGATTCCACCAGAA
1 ATCATTAATTAATAAGGTGGTTGCTATGTGATGAATCCACCAGAA
*
40838401 ATCATTAATTAATAAGGTGGTTGCTATGTGCTGAATCCACC
1 ATCATTAATTAATAAGGTGGTTGCTATGTGATGAATCCACC
40838442 GAGTATCTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (45 bp):
ATCATTAATTAATAAGGTGGTTGCTATGTGATGAATCCACCAGAA
Found at i:40838561 original size:38 final size:37
Alignment explanation
Indices: 40838518--40838590 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 37
40838508 AGGTGTGGAA
40838518 TTGAATTGAATAT-CGACTTAGAAA-TGAAAAAGTGAATT
1 TTGAATTGAAT-TGCGA-TT-GAAAGTGAAAAAGTGAATT
*
40838556 TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATTGCGATTGAAAGTGAAAAAGTGAA
40838591 ATTATAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 4 0.12
37 15 0.47
38 13 0.41
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATTGCGATTGAAAGTGAAAAAGTGAATT
Found at i:40841650 original size:41 final size:41
Alignment explanation
Indices: 40841618--40841699 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
40841608 ATATTTCATT
* *
40841618 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTCC
1 TTATCTTTTAGTAGTTTACTAAAATAAGGGAATTATTTTCC
**
40841659 TTATCTTTTAGTAGTTTACTAAAATAAAAGAATTATTTTCC
1 TTATCTTTTAGTAGTTTACTAAAATAAGGGAATTATTTTCC
40841700 CAATTAGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.48
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTACTAAAATAAGGGAATTATTTTCC
Found at i:40844120 original size:19 final size:19
Alignment explanation
Indices: 40844096--40844136 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
40844086 TATTTTAAGG
40844096 TTATTTAGATAGATAAATC
1 TTATTTAGATAGATAAATC
*
40844115 TTATTTAGGTAGATAAATC
1 TTATTTAGATAGATAAATC
40844134 TTA
1 TTA
40844137 GAATAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (19 bp):
TTATTTAGATAGATAAATC
Found at i:40844215 original size:37 final size:37
Alignment explanation
Indices: 40844174--40844244 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
40844164 ATATCTTATT
40844174 TTATCCTTTAGTAGTTTATTAGAATAAGGGAATTTCC
1 TTATCCTTTAGTAGTTTATTAGAATAAGGGAATTTCC
*
40844211 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATT
1 TTATCCTTTAGTAGTTTATTAGAATAAGGGAATT
40844245 ATTTTCCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (37 bp):
TTATCCTTTAGTAGTTTATTAGAATAAGGGAATTTCC
Found at i:40847707 original size:29 final size:30
Alignment explanation
Indices: 40847644--40847723 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 30
40847634 ATCCCAAAAC
*
40847644 TATACATGAACTTTGGTTTAATGTGCAATTG
1 TATACATGAACTTTGATTT-ATGTGCAATTG
*
40847675 TATACATGAACTTTGATTT-TGTGCAATTT
1 TATACATGAACTTTGATTTATGTGCAATTG
*
40847704 TATACATGAAATTTTGATTT
1 TATACATG-AACTTTGATTT
40847724 GATTCAATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.38
30 10 0.22
31 18 0.40
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATGTGCAATTG
Found at i:40852360 original size:16 final size:16
Alignment explanation
Indices: 40852339--40852372 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
40852329 CCTTGGATGG
40852339 TAAAAATTTTAGCTGC
1 TAAAAATTTTAGCTGC
40852355 TAAAAATTTTAGCTGC
1 TAAAAATTTTAGCTGC
40852371 TA
1 TA
40852373 CCATCTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
TAAAAATTTTAGCTGC
Found at i:40860338 original size:17 final size:17
Alignment explanation
Indices: 40860316--40860367 Score: 104
Period size: 17 Copynumber: 3.1 Consensus size: 17
40860306 TTTCAAATGC
40860316 ACCACACGAGAACATAA
1 ACCACACGAGAACATAA
40860333 ACCACACGAGAACATAA
1 ACCACACGAGAACATAA
40860350 ACCACACGAGAACATAA
1 ACCACACGAGAACATAA
40860367 A
1 A
40860368 GGCTACGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.54, C:0.29, G:0.12, T:0.06
Consensus pattern (17 bp):
ACCACACGAGAACATAA
Found at i:40880459 original size:47 final size:47
Alignment explanation
Indices: 40880406--40880500 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
40880396 TGAGAACCAC
40880406 TACTTTCTTATTGATGATGGTGTTTGATTAATGAAATTTAATGGCTT
1 TACTTTCTTATTGATGATGGTGTTTGATTAATGAAATTTAATGGCTT
40880453 TACTTTCTTATTGATGATGGTGTTTGATTAATGAAATTTAATGGCTT
1 TACTTTCTTATTGATGATGGTGTTTGATTAATGAAATTTAATGGCTT
40880500 T
1 T
40880501 CTGAGCCTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.49
Consensus pattern (47 bp):
TACTTTCTTATTGATGATGGTGTTTGATTAATGAAATTTAATGGCTT
Found at i:40880877 original size:13 final size:13
Alignment explanation
Indices: 40880859--40880894 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
40880849 AAAAAAGAGA
40880859 TTGTTTTAAATTC
1 TTGTTTTAAATTC
40880872 TTGTTTTAAATTC
1 TTGTTTTAAATTC
40880885 TAT-TTTTAAA
1 T-TGTTTTAAA
40880895 ATATTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 21 0.95
14 1 0.05
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.61
Consensus pattern (13 bp):
TTGTTTTAAATTC
Found at i:40881319 original size:28 final size:28
Alignment explanation
Indices: 40881266--40881320 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
40881256 TGAAAAGTGG
*
40881266 AGGGACTAAATTTATAAAATTAAAATAT
1 AGGGACTAAATTTAGAAAATTAAAATAT
* *
40881294 AGGGAC-AAATTTCGAAATTTATAAATA
1 AGGGACTAAATTTAGAAAATTA-AAATA
40881321 GTACAAGAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.31
Consensus pattern (28 bp):
AGGGACTAAATTTAGAAAATTAAAATAT
Found at i:40884956 original size:13 final size:13
Alignment explanation
Indices: 40884938--40884970 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
40884928 GAGTGTTAGA
40884938 ATATTATTATAGG
1 ATATTATTATAGG
*
40884951 ATATTATTATGGG
1 ATATTATTATAGG
40884964 ATATTAT
1 ATATTAT
40884971 CTCTTAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
ATATTATTATAGG
Found at i:40885279 original size:9 final size:9
Alignment explanation
Indices: 40885249--40885341 Score: 98
Period size: 9 Copynumber: 10.4 Consensus size: 9
40885239 TTTGGTTAAA
40885249 AATTAACCG
1 AATTAACCG
* * *
40885258 AATTGAGCA
1 AATTAACCG
40885267 AATTAACCG
1 AATTAACCG
*
40885276 AATTACCCG
1 AATTAACCG
*
40885285 AATTACCCG
1 AATTAACCG
40885294 AATTAACCG
1 AATTAACCG
*
40885303 AA-TACCCG
1 AATTAACCG
*
40885311 AATTACCCG
1 AATTAACCG
40885320 AATTAACCG
1 AATTAACCG
* *
40885329 GATTAACCT
1 AATTAACCG
40885338 AATT
1 AATT
40885342 GAATCATACA
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
8 7 0.10
9 63 0.90
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:40885315 original size:26 final size:27
Alignment explanation
Indices: 40885267--40885333 Score: 118
Period size: 26 Copynumber: 2.5 Consensus size: 27
40885257 GAATTGAGCA
40885267 AATTAACCGAATTACCCGAATTACCCG
1 AATTAACCGAATTACCCGAATTACCCG
40885294 AATTAACCGAA-TACCCGAATTACCCG
1 AATTAACCGAATTACCCGAATTACCCG
*
40885320 AATTAACCGGATTA
1 AATTAACCGAATTA
40885334 ACCTAATTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 25 0.66
27 13 0.34
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (27 bp):
AATTAACCGAATTACCCGAATTACCCG
Found at i:40885396 original size:13 final size:14
Alignment explanation
Indices: 40885380--40885416 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
40885370 ACTTTTATAC
40885380 TTTAGTTTTAG-GT
1 TTTAGTTTTAGAGT
40885393 TTTAGTTTTAGAGT
1 TTTAGTTTTAGAGT
*
40885407 TTTATTTTTA
1 TTTAGTTTTA
40885417 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.65
Consensus pattern (14 bp):
TTTAGTTTTAGAGT
Found at i:40895534 original size:21 final size:21
Alignment explanation
Indices: 40895495--40895537 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
40895485 CTTTGACTTG
40895495 TTTAACTTTGAATTAAAAAAA
1 TTTAACTTTGAATTAAAAAAA
*
40895516 TTTAA-TTTTAATTATAAAAAA
1 TTTAACTTTGAATTA-AAAAAA
40895537 T
1 T
40895538 CATGCCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TTTAACTTTGAATTAAAAAAA
Found at i:40898325 original size:23 final size:23
Alignment explanation
Indices: 40898296--40898417 Score: 172
Period size: 23 Copynumber: 5.3 Consensus size: 23
40898286 AGTGTTATTG
40898296 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
40898319 TTTAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
40898342 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
40898365 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
40898388 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
40898411 ATCAGTG
1 ATCAGTG
40898418 TGGCACTTAT
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 84 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Done.