Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 372 of 378
Found at i:111142492 original size:30 final size:30
Alignment explanation
Indices: 111142456--111142517 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
111142446 CAACTCATAT
111142456 TGCGAGAGGTGAGTTGAG-CTTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTC-TTTTAATTTC
*
111142486 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
111142516 TG
1 TG
111142518 TTTTTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (30 bp):
TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
Found at i:111142623 original size:252 final size:243
Alignment explanation
Indices: 111141874--111142811 Score: 806
Period size: 252 Copynumber: 3.8 Consensus size: 243
111141864 TTTTTCAAAA
* ** ** * *
111141874 AAAAAATCAACTCATATTGTGAGAAATGAGTTGAGCC-T--CAAGACATGCTGAGGTATTTTCAA
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGC-TCACGTGCTGAGCTATTTTCAA
* * * *
111141936 TTTCTGTT-TTTCAAAAAAAT-AACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--GACACGCT
65 TTT-TTTTCTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACT
* * * * ** * * *
111141997 GAGGTA--ATTTCAATTTCT-GTTGTCAAAAAAATCAACTCGTATTGTGAGAGGCGAGTTGAGCC
128 GAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCACATTGCGAGAGGTGAGTTGAACC
*** ** * * ** *
111142059 TC-AGGTCACACGCCGAGGTATTTTCAATTTCCGTTTTTCA-ATTTTGCCTTTC
192 TCGA-GTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAGATTAAG-TTTTC
*
111142111 AAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTT
1 ----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTT
* *
111142176 CAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACA
62 CAATTTTTTTCTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACA
* * *
111142241 CTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGAGTTGAG
126 CTGAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCACATTGCGAGAGGTGAGTTGAA
* * * **
111142306 CCTCGGGTCACATGTCGAGGTATTTTCAAAATCTGTTTTTCAGATTCTGTTTTC
190 CCTCGAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAGATTAAGTTTTC
*
111142360 -AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAAT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAA-
* * *
111142424 TTTTTTTTTCTCTTCAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTA-ATTTCTG
65 --TTTTTTTCT-TTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC--TTCAGA--TC-A
* * * * * *
111142488 CGAGAGTTGAGTTGAGTCTTTT-AATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTG
122 C-ACA-CTGAGGT-A-TCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGCGAGAGGTG
*
111142551 AGTTGAACCTTC-AGTCATATATCGAGGTATTTTCAAAATCTGCTTTTCA-AGTTAAG-TTTC
183 AGTTGAACC-TCGAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAGA-TTAAGTTTTC
*
111142611 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAA-
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAAT
* * * * * * ***
111142675 TTTCTGCTTTTCAAAAGAATCAACACATATTGTGAGAGGTGAGTTGAGCCTT-TGCTCACGTGCT
66 TTTTTTC-TTTCAAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTCAGATCACACACT
* * ** * * *
111142739 GAGCTA--TTTTCAATTTCTGCTTTTCAAAAGAATCAACTCATATTGCAAGAGGTGAGTTGAGCC
128 GAGGTATCTTTTCAATTTATATTTTTCAAAA-AATCAACTCACATTGCGAGAGGTGAGTTGAACC
*
111142802 TCGGGTCACA
192 TCGAGTCACA
111142812 CGCTGAGGCG
Statistics
Matches: 588, Mismatches: 73, Indels: 71
0.80 0.10 0.10
Matches are distributed among these distances:
239 4 0.01
240 13 0.02
241 39 0.07
242 39 0.07
243 37 0.06
244 94 0.16
245 1 0.00
246 14 0.02
247 42 0.07
248 28 0.05
249 106 0.18
250 8 0.01
251 6 0.01
252 132 0.22
253 7 0.01
254 13 0.02
255 5 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (243 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAAT
TTTTTTCTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAG
GTATCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAACCTCGA
GTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAGATTAAGTTTTC
Found at i:111142826 original size:154 final size:151
Alignment explanation
Indices: 111142607--111142917 Score: 435
Period size: 152 Copynumber: 2.0 Consensus size: 151
111142597 TCAAGTTAAG
* ** **
111142607 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTT
1 TTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACACGCTGAGCTATTTT
* ** *
111142672 CAATTTCTGCTTTTCAAAAGAATCAACACATATTGTGAGAGGTGAGTTGAGCCTTTGCTCACGTG
66 CAATTTCTGCTTTTC-AAA-AATCAACACATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATG
111142737 CTGAGCTATTTTCAATTTCTGCT
129 CTGAGCTATTTTCAATTTCTGCT
* *
111142760 TTTCAAAAGAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGC-GTT
1 TTTCAAAA-AATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACACGCTGA-GCTATT
* *
111142824 TTCAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGCTCACATG
64 TTCAATTTCTGCTTTTCAAAAATCAACACATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATG
* * *
111142889 CTGAGGTCTTTTTAATTTCTGCT
129 CTGAGCTATTTTCAATTTCTGCT
111142912 TTTCAA
1 TTTCAA
111142918 TTTCTGTTTT
Statistics
Matches: 140, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
152 65 0.46
153 11 0.08
154 62 0.44
155 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34
Consensus pattern (151 bp):
TTTCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACACGCTGAGCTATTTT
CAATTTCTGCTTTTCAAAAATCAACACATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGCT
GAGCTATTTTCAATTTCTGCT
Found at i:111142919 original size:14 final size:15
Alignment explanation
Indices: 111142894--111142935 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
111142884 ACATGCTGAG
*
111142894 GTCTTTTTAATTTCT
1 GTCTTTTCAATTTCT
111142909 G-CTTTTCAATTTCT
1 GTCTTTTCAATTTCT
*
111142923 GTTTTTTCAATTT
1 GTCTTTTCAATTT
111142936 ATATTTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (15 bp):
GTCTTTTCAATTTCT
Found at i:111142931 original size:15 final size:14
Alignment explanation
Indices: 111142897--111142946 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
111142887 TGCTGAGGTC
111142897 TTTTT-AATTTCTG
1 TTTTTCAATTTCTG
*
111142910 CTTTTCAATTTCTG
1 TTTTTCAATTTCTG
* *
111142924 TTTTTTCAATTTATA
1 -TTTTTCAATTTCTG
111142939 TTTTTCAA
1 TTTTTCAA
111142947 AAATCAACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 16 0.52
15 11 0.35
ACGTcount: A:0.20, C:0.12, G:0.04, T:0.64
Consensus pattern (14 bp):
TTTTTCAATTTCTG
Found at i:111143727 original size:30 final size:29
Alignment explanation
Indices: 111143691--111143858 Score: 202
Period size: 30 Copynumber: 5.8 Consensus size: 29
111143681 ACTTTTCTCA
*
111143691 ACTAGCCACTCATTTTCCACCACCAACTCC
1 ACTAGCCACAC-TTTTCCACCACCAACTCC
111143721 ACTAGCCACACCTTTTCCACCACCAACT-C
1 ACTAGCCACA-CTTTTCCACCACCAACTCC
*
111143750 -C-A-CCAC-TTTTTCCACCACCAACTCC
1 ACTAGCCACACTTTTCCACCACCAACTCC
* *
111143775 ACTAGCCACACCTTTCCACCATCAACTCC
1 ACTAGCCACACTTTTCCACCACCAACTCC
*
111143804 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACAC-TTTTCCACCACCAACTCC
* *
111143834 ACTAGTCACACCTTCTCCACCACCA
1 ACTAGCCACA-CTTTTCCACCACCA
111143859 CTTGTACCTA
Statistics
Matches: 119, Mismatches: 11, Indels: 16
0.82 0.08 0.11
Matches are distributed among these distances:
24 16 0.13
25 1 0.01
26 5 0.04
27 2 0.02
28 5 0.04
29 27 0.23
30 61 0.51
31 2 0.02
ACGTcount: A:0.26, C:0.48, G:0.03, T:0.23
Consensus pattern (29 bp):
ACTAGCCACACTTTTCCACCACCAACTCC
Found at i:111144416 original size:2 final size:2
Alignment explanation
Indices: 111144409--111144474 Score: 50
Period size: 2 Copynumber: 34.5 Consensus size: 2
111144399 CTATATTACG
* * * *
111144409 TA TA TA TA TA TA CTA T- TT TA TG TA TA TA TC TT TA -A TA T- TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
111144449 TA T- TA TT TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
111144475 TTTTTTACAT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
1 4 0.08
2 45 0.88
3 2 0.04
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (2 bp):
TA
Found at i:111144433 original size:22 final size:22
Alignment explanation
Indices: 111144399--111144463 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
111144389 ATTTTAAATT
* *
111144399 CTATATTACGTATATATATATA
1 CTATTTTATGTATATATATATA
* *
111144421 CTATTTTATGTATATATCTTTA
1 CTATTTTATGTATATATATATA
* * *
111144443 ATATTATAT-TATTTATATATA
1 CTATTTTATGTATATATATATA
111144464 TATATATATA
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
21 9 0.26
22 25 0.74
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (22 bp):
CTATTTTATGTATATATATATA
Found at i:111144460 original size:14 final size:15
Alignment explanation
Indices: 111144409--111144475 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 15
111144399 CTATATTACG
111144409 TATATATATATACTATT
1 TATAT-TATATA-TATT
*
111144426 T-TATGTATATATCTT
1 TATAT-TATATATATT
111144441 TAATATTATAT-TATT
1 T-ATATTATATATATT
*
111144456 TATA-TATATATATA
1 TATATTATATATATT
111144470 TATATT
1 TATATT
111144476 TTTTTACATG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 5 0.12
14 10 0.24
15 9 0.21
16 14 0.33
17 4 0.10
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (15 bp):
TATATTATATATATT
Found at i:111144535 original size:25 final size:25
Alignment explanation
Indices: 111144506--111144554 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
111144496 ATATATCTTA
**
111144506 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
111144531 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
111144555 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:111144732 original size:16 final size:15
Alignment explanation
Indices: 111144708--111144755 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
111144698 TAATTATTAT
*
111144708 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
111144724 TATTTTAATATTTTA
1 TATTTTAATATTTTA
111144739 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
111144755 T
1 T
111144756 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:111144743 original size:7 final size:8
Alignment explanation
Indices: 111144708--111144759 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
111144698 TAATTATTAT
*
111144708 TATTCTAA
1 TATTTTAA
*
111144716 TATTTTGA
1 TATTTTAA
111144724 TATTTTAA
1 TATTTTAA
111144732 TATTTT-A
1 TATTTTAA
111144739 TATTTTATA
1 TATTTTA-A
*
111144748 TATTTTAT
1 TATTTTAA
111144756 TATT
1 TATT
111144760 CACATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:111146919 original size:18 final size:18
Alignment explanation
Indices: 111146896--111146931 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
111146886 AAATAAAGAG
111146896 GAAAAATCTGATTTGTCA
1 GAAAAATCTGATTTGTCA
111146914 GAAAAATCTGATTTGTCA
1 GAAAAATCTGATTTGTCA
111146932 TTCTCCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (18 bp):
GAAAAATCTGATTTGTCA
Found at i:111147455 original size:56 final size:56
Alignment explanation
Indices: 111147355--111147467 Score: 174
Period size: 58 Copynumber: 2.0 Consensus size: 56
111147345 TGAATTTTTG
*
111147355 TTCGCATATTCATGCCATTCAAAGTTGTTAATTTCATTTAAAAAAATAAACTACAA
1 TTCGCAAATTCATGCCATTCAAAGTTGTTAATTTCATTTAAAAAAATAAACTACAA
* *
111147411 TTCGCAAATTCATGCTATATTCAAAGTTGTTAATTTCA-TTAAAAAAATGAACTACAA
1 TTCGCAAATTCATGC--CATTCAAAGTTGTTAATTTCATTTAAAAAAATAAACTACAA
111147468 AAGATGAGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
56 14 0.27
57 18 0.35
58 20 0.38
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (56 bp):
TTCGCAAATTCATGCCATTCAAAGTTGTTAATTTCATTTAAAAAAATAAACTACAA
Found at i:111150804 original size:32 final size:32
Alignment explanation
Indices: 111150738--111150805 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
111150728 AACAATAGTC
* *
111150738 TTCTAAACATAGTTGTTCTTGCAACATAATTA
1 TTCTAAACAGAGTTGTTCTTGCAACATAACTA
*
111150770 TTCTAAACAAGAGTTGTTC-T-CAACATGAGCTA
1 TTCTAAAC-AGAGTTGTTCTTGCAACAT-AACTA
111150802 TTCT
1 TTCT
111150806 CAAATGACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
31 6 0.19
32 16 0.52
33 9 0.29
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (32 bp):
TTCTAAACAGAGTTGTTCTTGCAACATAACTA
Found at i:111150878 original size:15 final size:16
Alignment explanation
Indices: 111150858--111150892 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
111150848 CCTTGATTTG
*
111150858 AACATAGCTATTC-CA
1 AACATAACTATTCTCA
111150873 AACATAACTATTCTCA
1 AACATAACTATTCTCA
111150889 AACA
1 AACA
111150893 AAAGTTGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.46, C:0.26, G:0.03, T:0.26
Consensus pattern (16 bp):
AACATAACTATTCTCA
Found at i:111154623 original size:18 final size:18
Alignment explanation
Indices: 111154592--111154632 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
111154582 AATCTCAATT
* *
111154592 TTTTAGATTATTTTGGAA
1 TTTTAAATTATTTTAGAA
*
111154610 TTTTAAATTTTTTTAGAA
1 TTTTAAATTATTTTAGAA
111154628 TTTTA
1 TTTTA
111154633 TGAATTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (18 bp):
TTTTAAATTATTTTAGAA
Found at i:111154637 original size:27 final size:26
Alignment explanation
Indices: 111154590--111154648 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
111154580 GAAATCTCAA
111154590 TTTTTTAGATTATTTTGGAATTTTAAAT
1 TTTTTTAGA-TATTTTGGAATTTT-AAT
* *
111154618 TTTTTTAGA-ATTTTATGAATTTTTAT
1 TTTTTTAGATATTTT-GGAATTTTAAT
111154644 TTTTT
1 TTTTT
111154649 CTCATAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 12 0.43
27 7 0.25
28 9 0.32
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.66
Consensus pattern (26 bp):
TTTTTTAGATATTTTGGAATTTTAAT
Found at i:111155685 original size:26 final size:27
Alignment explanation
Indices: 111155655--111155705 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
111155645 TATTTAAGGG
111155655 TTTAAAAAGAAATA-TAATTATATTAT
1 TTTAAAAAGAAATATTAATTATATTAT
*
111155681 TTTAAAAATAAATATTAATTATATT
1 TTTAAAAAGAAATATTAATTATATT
111155706 TATTAAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (27 bp):
TTTAAAAAGAAATATTAATTATATTAT
Found at i:111155711 original size:26 final size:26
Alignment explanation
Indices: 111155656--111155718 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
111155646 ATTTAAGGGT
* *
111155656 TTAAAAAGAAATATAATTATATTATT
1 TTAAAAATAAATATAATTATATTATA
111155682 TTAAAAATAAATATTAATTATATT-TA
1 TTAAAAATAAATA-TAATTATATTATA
*
111155708 TTAAACATAAA
1 TTAAAAATAAA
111155719 AAATCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 23 0.70
27 10 0.30
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
TTAAAAATAAATATAATTATATTATA
Found at i:111156942 original size:223 final size:223
Alignment explanation
Indices: 111156550--111156996 Score: 725
Period size: 223 Copynumber: 2.0 Consensus size: 223
111156540 ATGTCGCAAG
**
111156550 TTTAAAACTTGGTATTTCAATAACCATTCATTTTGATATGAAAGAAAAAGCAAAATACTCAGAAC
1 TTTAAAACTTGACATTTCAATAACCATTCATTTTGATATGAAAGAAAAAGCAAAATACTCAGAAC
* *
111156615 ATGTGGCACTGTAAAGTCTGCCATTACTCATTTCAAGAATTTTCGATGAACTGATATGCTATGTA
66 ATGTGGCACTGTAAAGTCTGCCATTACTCATTTCAAGAATTTTCAATGAACTGATATGCCATGTA
* * *
111156680 GCGATGGAGTCAAAAAAAATTTTAAGAAGAGGTCAGAATAAAGTTGCATATTTTATAATAACAAA
131 GCGATAGAGTCAAAAAAAATTTTAAGAAGAGGCCAGAATAAAGTTGCATATATTATAATAACAAA
111156745 AGTGAAATTTTATTATTTTAATAGTCTA
196 AGTGAAATTTTATTATTTTAATAGTCTA
* * * *
111156773 TTTAAAACTTGACATTTCGATAACCATTCATTTTGCTATGAAAGAAAAAGTAAAATACTCAGAGC
1 TTTAAAACTTGACATTTCAATAACCATTCATTTTGATATGAAAGAAAAAGCAAAATACTCAGAAC
* * **
111156838 ATGTGGCATTGTCAAGTCTGTTATTACTCATTTCAAGAATTTTCAATGAACTGATATGCCATGTA
66 ATGTGGCACTGTAAAGTCTGCCATTACTCATTTCAAGAATTTTCAATGAACTGATATGCCATGTA
* *
111156903 GCGGTAGAGT-AAAAAAAACTTTTAAGAGGAGGCCAGAATAAAGTTGCATATATTATAATAACAA
131 GCGATAGAGTCAAAAAAAA-TTTTAAGAAGAGGCCAGAATAAAGTTGCATATATTATAATAACAA
111156967 AAGTGAAATTTTATTATTTTAATAGTCTA
195 AAGTGAAATTTTATTATTTTAATAGTCTA
111156996 T
1 T
111156997 ATCTTTATAA
Statistics
Matches: 206, Mismatches: 17, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
222 8 0.04
223 198 0.96
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (223 bp):
TTTAAAACTTGACATTTCAATAACCATTCATTTTGATATGAAAGAAAAAGCAAAATACTCAGAAC
ATGTGGCACTGTAAAGTCTGCCATTACTCATTTCAAGAATTTTCAATGAACTGATATGCCATGTA
GCGATAGAGTCAAAAAAAATTTTAAGAAGAGGCCAGAATAAAGTTGCATATATTATAATAACAAA
AGTGAAATTTTATTATTTTAATAGTCTA
Found at i:111157850 original size:27 final size:26
Alignment explanation
Indices: 111157797--111157849 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 26
111157787 GATTTTATTA
111157797 ATATTTATAATGTAAAACTTCAAAAAT
1 ATATTTATAATGTAAAACTT-AAAAAT
111157824 ATATTTATAATGTAAAATACTTAAAA
1 ATATTTATAATGT-AAA-ACTTAAAA
111157850 TTAAATAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 13 0.54
28 7 0.29
29 4 0.17
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.38
Consensus pattern (26 bp):
ATATTTATAATGTAAAACTTAAAAAT
Found at i:111161325 original size:28 final size:30
Alignment explanation
Indices: 111161294--111161353 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
111161284 ACGTATATAA
*
111161294 ATAATTT-AC-TAATTTTTAAATA-AAAAAT
1 ATAATTTAACTTAATTCTT-AATACAAAAAT
111161322 ATAATTTAACTTAATTCTTAATACAAAAAT
1 ATAATTTAACTTAATTCTTAATACAAAAAT
111161352 AT
1 AT
111161354 TTATAAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 7 0.25
29 6 0.21
30 15 0.54
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.42
Consensus pattern (30 bp):
ATAATTTAACTTAATTCTTAATACAAAAAT
Found at i:111168496 original size:2 final size:2
Alignment explanation
Indices: 111168489--111168528 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
111168479 GGTTTAACTG
111168489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
111168529 GGTTGTCATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:111169090 original size:38 final size:38
Alignment explanation
Indices: 111168988--111169090 Score: 102
Period size: 38 Copynumber: 2.7 Consensus size: 38
111168978 GTGGAATGGA
** * * *
111168988 TATCTACTGGTTTTTTGGGGTGACACCATGTTAACGAT
1 TATCTACTGGTCCTTCGGAGTGACACCATATTAACGAT
** *
111169026 TATCTACTGGTCCTTCAGGA-CAACACCGTATTAAC-AGT
1 TATCTACTGGTCCTTC-GGAGTGACACCATATTAACGA-T
111169064 TATCTACTGGTCCTTCGGAGTGACACC
1 TATCTACTGGTCCTTCGGAGTGACACC
111169091 TCAAAAAGGG
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
37 4 0.08
38 46 0.88
39 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.33
Consensus pattern (38 bp):
TATCTACTGGTCCTTCGGAGTGACACCATATTAACGAT
Found at i:111172613 original size:2 final size:2
Alignment explanation
Indices: 111172608--111172637 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
111172598 TTATATATGG
111172608 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
111172638 TTGTGTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:111177164 original size:12 final size:13
Alignment explanation
Indices: 111177134--111177164 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
111177124 AAATATGTTA
111177134 GAAAAAGTAATTT
1 GAAAAAGTAATTT
111177147 GAAAAAGTAATTT
1 GAAAAAGTAATTT
*
111177160 CAAAA
1 GAAAA
111177165 CATATAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (13 bp):
GAAAAAGTAATTT
Found at i:111187198 original size:2 final size:2
Alignment explanation
Indices: 111187193--111187233 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
111187183 TTACTTTGTG
*
111187193 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
111187234 GGATAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:111195436 original size:30 final size:30
Alignment explanation
Indices: 111195402--111195459 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
111195392 ATTTATAAGC
* *
111195402 TGTTACTTAGGAATTGGAAGGTTCGTATGA
1 TGTTACGTAGGAATTGGAAAGTTCGTATGA
111195432 TGTTACGTAGGAATTGGAAAGTTCGTAT
1 TGTTACGTAGGAATTGGAAAGTTCGTAT
111195460 CTGTCACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.07, G:0.29, T:0.36
Consensus pattern (30 bp):
TGTTACGTAGGAATTGGAAAGTTCGTATGA
Found at i:111196762 original size:30 final size:30
Alignment explanation
Indices: 111196726--111196793 Score: 118
Period size: 30 Copynumber: 2.2 Consensus size: 30
111196716 TTTAAAATAT
111196726 TATAATTGAATAGTTAAAGTATCGATATTA
1 TATAATTGAATAGTTAAAGTATCGATATTA
*
111196756 TATAATTGAGTAGTTAAAGTATCGATATTA
1 TATAATTGAATAGTTAAAGTATCGATATTA
111196786 TATTAATT
1 TA-TAATT
111196794 ATGCTCTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 31 0.86
31 5 0.14
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.43
Consensus pattern (30 bp):
TATAATTGAATAGTTAAAGTATCGATATTA
Found at i:111199155 original size:6 final size:7
Alignment explanation
Indices: 111199140--111199165 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
111199130 CGCTTTGAAA
111199140 TTTTATT
1 TTTTATT
111199147 TTTTATT
1 TTTTATT
111199154 TTTTATT
1 TTTTATT
111199161 TTTTA
1 TTTTA
111199166 AAAGGGAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:111199265 original size:19 final size:19
Alignment explanation
Indices: 111199241--111199278 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
111199231 GAAATGAATA
111199241 ATTTCAGGCAAATAGGTTG
1 ATTTCAGGCAAATAGGTTG
111199260 ATTTCAGGCAAATAGGTTG
1 ATTTCAGGCAAATAGGTTG
111199279 GCAATCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (19 bp):
ATTTCAGGCAAATAGGTTG
Found at i:111199554 original size:2 final size:2
Alignment explanation
Indices: 111199547--111199592 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
111199537 GTAGGTAAAT
*
111199547 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
111199589 TA TA
1 TA TA
111199593 CATAAACAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:111199656 original size:17 final size:17
Alignment explanation
Indices: 111199634--111199669 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
111199624 AATAGATTGT
111199634 AAAATAAATAATAAATA
1 AAAATAAATAATAAATA
*
111199651 AAAATAAATAATACATA
1 AAAATAAATAATAAATA
111199668 AA
1 AA
111199670 GCATATAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAATAAATAATAAATA
Found at i:111199778 original size:2 final size:2
Alignment explanation
Indices: 111199773--111199802 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
111199763 TTAAAAAATG
111199773 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
111199803 TATGTGCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:111200243 original size:19 final size:20
Alignment explanation
Indices: 111200210--111200249 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
111200200 ATATATGTAT
111200210 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
111200229 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
111200249 A
1 A
111200250 ATGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:111200520 original size:19 final size:18
Alignment explanation
Indices: 111200496--111200538 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
111200486 AGAGGTTAAG
111200496 TTTTTTTTCTTTTTCTTC
1 TTTTTTTTCTTTTTCTTC
*
111200514 ATTTTTTTTCTTTTTTTTC
1 -TTTTTTTTCTTTTTCTTC
111200533 TTTTTT
1 TTTTTT
111200539 ATTTTGGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTTTTTCTTTTTCTTC
Found at i:111200527 original size:9 final size:9
Alignment explanation
Indices: 111200496--111200538 Score: 68
Period size: 9 Copynumber: 4.7 Consensus size: 9
111200486 AGAGGTTAAG
111200496 TTTTTTTTC
1 TTTTTTTTC
*
111200505 TTTTTCTTC
1 TTTTTTTTC
111200514 ATTTTTTTTC
1 -TTTTTTTTC
111200524 TTTTTTTTC
1 TTTTTTTTC
111200533 TTTTTT
1 TTTTTT
111200539 ATTTTGGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:111204788 original size:14 final size:14
Alignment explanation
Indices: 111204769--111204798 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
111204759 AATACCTCCT
111204769 GCAATACCCTATTA
1 GCAATACCCTATTA
111204783 GCAATACCCTATTA
1 GCAATACCCTATTA
111204797 GC
1 GC
111204799 GAGGCACAAT
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:0.33, C:0.30, G:0.10, T:0.27
Consensus pattern (14 bp):
GCAATACCCTATTA
Found at i:111208671 original size:17 final size:17
Alignment explanation
Indices: 111208649--111208682 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
111208639 TTGAAATCAC
*
111208649 AATTTCATATAATTCTT
1 AATTTCATACAATTCTT
111208666 AATTTCATACAATTCTT
1 AATTTCATACAATTCTT
111208683 TCTCTGGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTCATACAATTCTT
Found at i:111208885 original size:32 final size:29
Alignment explanation
Indices: 111208845--111208914 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 29
111208835 GTCCCCTCAT
*
111208845 ATTTTAAAACTTT-TAATTAAGCTCTCTTAAAA
1 ATTTTAAAA-TTTCTAATTAA--TCTC-AAAAA
*
111208877 ATTTTAAAATTTCTCATTAATCTCAAAAA
1 ATTTTAAAATTTCTAATTAATCTCAAAAA
111208906 ATTTTAAAA
1 ATTTTAAAA
111208915 AATATAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 13 0.37
30 4 0.11
31 3 0.09
32 15 0.43
ACGTcount: A:0.44, C:0.11, G:0.01, T:0.43
Consensus pattern (29 bp):
ATTTTAAAATTTCTAATTAATCTCAAAAA
Found at i:111212380 original size:49 final size:49
Alignment explanation
Indices: 111212323--111212420 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
111212313 ATAACAAGTT
111212323 TAAAGAAATGAGAAATTGTAACTGTTTTCGTTAATGGTTAAGCTTTGTG
1 TAAAGAAATGAGAAATTGTAACTGTTTTCGTTAATGGTTAAGCTTTGTG
111212372 TAAAGAAATGAGAAATTGTAACTGTTTTCGTTAATGGTTAAGCTTTGTG
1 TAAAGAAATGAGAAATTGTAACTGTTTTCGTTAATGGTTAAGCTTTGTG
111212421 CAGTAACACC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39
Consensus pattern (49 bp):
TAAAGAAATGAGAAATTGTAACTGTTTTCGTTAATGGTTAAGCTTTGTG
Found at i:111214996 original size:45 final size:47
Alignment explanation
Indices: 111214906--111215000 Score: 133
Period size: 45 Copynumber: 2.1 Consensus size: 47
111214896 TACTGATATA
*
111214906 TCAGCTCGTAAGAGCTTACTGTTTTCAGCTCATTGGAGCTTACCGTT
1 TCAGCTCGTAAGAGCTTACTGTTTTCAGCTCATTAGAGCTTACCGTT
* *
111214953 TCAGGTCGTATGAGCTTACTG-TTT-AGCTCGA-TAGAGCTTACCGTT
1 TCAGCTCGTAAGAGCTTACTGTTTTCAGCTC-ATTAGAGCTTACCGTT
111214998 TCA
1 TCA
111215001 CCTCATTAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
45 21 0.48
46 4 0.09
47 19 0.43
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (47 bp):
TCAGCTCGTAAGAGCTTACTGTTTTCAGCTCATTAGAGCTTACCGTT
Found at i:111218652 original size:11 final size:10
Alignment explanation
Indices: 111218624--111218651 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
111218614 TAATTAAGAT
111218624 AAAAAAAATA
1 AAAAAAAATA
111218634 AAAAAAAATA
1 AAAAAAAATA
111218644 AAAAAAAA
1 AAAAAAAA
111218652 AGAGGATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:111227286 original size:16 final size:18
Alignment explanation
Indices: 111227260--111227293 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
111227250 AATCAAGTTG
111227260 TTTAGAGTTTAGA-TCAT
1 TTTAGAGTTTAGAGTCAT
111227277 TTTA-AGTTTAGAGTCAT
1 TTTAGAGTTTAGAGTCAT
111227294 GTCGTTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (18 bp):
TTTAGAGTTTAGAGTCAT
Found at i:111231960 original size:29 final size:30
Alignment explanation
Indices: 111231920--111231976 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
111231910 TGGTCAAATG
111231920 TGCAATGTTATACAT-AAACTTTGATTTTA
1 TGCAATGTTATACATGAAACTTTGATTTTA
*
111231949 TGCAAT-TCTATACATGAAATTTTGATTT
1 TGCAATGT-TATACATGAAACTTTGATTT
111231977 AATTTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 13 0.52
30 11 0.44
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (30 bp):
TGCAATGTTATACATGAAACTTTGATTTTA
Found at i:111233715 original size:2 final size:2
Alignment explanation
Indices: 111233708--111233739 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
111233698 TGCACCATAA
111233708 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
111233740 TTTTCACACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:111234340 original size:21 final size:20
Alignment explanation
Indices: 111234307--111234345 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
111234297 GACAAATTTA
111234307 ACTCAAAAAATAATAATGGT
1 ACTCAAAAAATAATAATGGT
111234327 ACTCAAATAAATAATAATG
1 ACTCAAA-AAATAATAATG
111234346 TAAACATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (20 bp):
ACTCAAAAAATAATAATGGT
Found at i:111236283 original size:153 final size:153
Alignment explanation
Indices: 111236005--111236312 Score: 589
Period size: 153 Copynumber: 2.0 Consensus size: 153
111235995 GGGACATTGC
*
111236005 GACATGGCGACGTGTTCTCACATAAATCGGGTTTCTTTTCCTAGTTAAACTTTGCTATCTTTTCC
1 GACATGGCGACGTGTTCTCACATAAATCGGGTTTCTTTTCCTAATTAAACTTTGCTATCTTTTCC
*
111236070 CAGTTAATATTTAATTATTCTTCGGATATTTTAATCATATATTCACACGAATTTCAACCTATAAA
66 CAGTTAATATTTAATTATTCTACGGATATTTTAATCATATATTCACACGAATTTCAACCTATAAA
111236135 AGGGCCTTTATAACCTTATAATT
131 AGGGCCTTTATAACCTTATAATT
*
111236158 GACATGGCGACGTGTTCTCACATAAATCGGGTTTCTTTTCCTAATTAAACTTTGGTATCTTTTCC
1 GACATGGCGACGTGTTCTCACATAAATCGGGTTTCTTTTCCTAATTAAACTTTGCTATCTTTTCC
111236223 CAGTTAATATTTAATTATTCTACGGATATTTTAATCATATATTCACACGAATTTCAACCTATAAA
66 CAGTTAATATTTAATTATTCTACGGATATTTTAATCATATATTCACACGAATTTCAACCTATAAA
111236288 AGGGCCTTTATAACCTTATAATT
131 AGGGCCTTTATAACCTTATAATT
111236311 GA
1 GA
111236313 TATCTTCATC
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
153 152 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (153 bp):
GACATGGCGACGTGTTCTCACATAAATCGGGTTTCTTTTCCTAATTAAACTTTGCTATCTTTTCC
CAGTTAATATTTAATTATTCTACGGATATTTTAATCATATATTCACACGAATTTCAACCTATAAA
AGGGCCTTTATAACCTTATAATT
Found at i:111237331 original size:15 final size:15
Alignment explanation
Indices: 111237311--111237340 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
111237301 GATGCTTTAT
*
111237311 ATATATTTTTATATA
1 ATATATATTTATATA
111237326 ATATATATTTATATA
1 ATATATATTTATATA
111237341 TAACTTACCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATATATTTATATA
Found at i:111237331 original size:17 final size:17
Alignment explanation
Indices: 111237309--111237343 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
111237299 TTGATGCTTT
*
111237309 ATATATATTTTTATATA
1 ATATATATTTATATATA
111237326 ATATATATTTATATATA
1 ATATATATTTATATATA
111237343 A
1 A
111237344 CTTACCTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATATATTTATATATA
Found at i:111247695 original size:32 final size:32
Alignment explanation
Indices: 111247659--111247725 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
111247649 TCCTCAACAA
111247659 TTAAATATATTACGATTATCTATAATACTAAT
1 TTAAATATATTACGATTATCTATAATACTAAT
111247691 TTAAATATATTACGATTATCTATAATACTAAT
1 TTAAATATATTACGATTATCTATAATACTAAT
111247723 TTA
1 TTA
111247726 CTAACATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (32 bp):
TTAAATATATTACGATTATCTATAATACTAAT
Found at i:111257273 original size:123 final size:122
Alignment explanation
Indices: 111257053--111257290 Score: 300
Period size: 123 Copynumber: 1.9 Consensus size: 122
111257043 AAAAATCAAT
* ** * *
111257053 ACCTTATTTAAAAGGCATTGAACTACTTACCATTTGACCCCAGAGATGAGCAGGTCTAAGCCCAT
1 ACCTTACTTAAAAGGCATCAAACTACTTACCATTTGACCCCAAAGATGAACAGGTCTAAGCCCAT
* * *
111257118 TTCTTCGTACCGTGCACTATCTTTTTGGGTACATTTATAATTAATTCACATGCATAA
66 TTCTTCATACCATGCACTATCTTTTTGGGTACATTTATAATTAACTCACATGCATAA
* * *
111257175 ACCTTACTTATAAGGCATCAAACTACTTACCATTTGACCCCATAAGATGAATATGTCTAAGCCCA
1 ACCTTACTTAAAAGGCATCAAACTACTTACCATTTGACCCCA-AAGATGAACAGGTCTAAGCCCA
** * *
111257240 TTTC-TCAATATTATGCACTAAT-TTTTTTGGTACATTTATACTTAACTCACA
65 TTTCTTC-ATACCATGCACT-ATCTTTTTGGGTACATTTATAATTAACTCACA
111257291 CACATTGATT
Statistics
Matches: 98, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
122 40 0.41
123 56 0.57
124 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (122 bp):
ACCTTACTTAAAAGGCATCAAACTACTTACCATTTGACCCCAAAGATGAACAGGTCTAAGCCCAT
TTCTTCATACCATGCACTATCTTTTTGGGTACATTTATAATTAACTCACATGCATAA
Found at i:111258417 original size:16 final size:15
Alignment explanation
Indices: 111258396--111258438 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
111258386 AAAATGATAA
111258396 ATAT-TTTAATAATT
1 ATATATTTAATAATT
*
111258410 ATATATTTATTTAATT
1 ATATATTTA-ATAATT
*
111258426 ATAAATTTAATAA
1 ATATATTTAATAA
111258439 AAAATTAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 4 0.17
15 7 0.29
16 13 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATATTTAATAATT
Found at i:111258797 original size:5 final size:6
Alignment explanation
Indices: 111258781--111258805 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
111258771 ACTGAAAATT
111258781 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
111258806 GTATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:111262590 original size:46 final size:44
Alignment explanation
Indices: 111262486--111262593 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
111262476 TGTCTTTGAC
** * * *
111262486 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
111262530 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
111262576 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
111262594 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:111264646 original size:33 final size:33
Alignment explanation
Indices: 111264604--111264670 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
111264594 AAGAATTAAT
111264604 CCTAACCTTTATTAGTTTTAATTTTTAAAGATG
1 CCTAACCTTTATTAGTTTTAATTTTTAAAGATG
111264637 CCTAACCTTTATTAGTTTTAATTTTTAAAGATG
1 CCTAACCTTTATTAGTTTTAATTTTTAAAGATG
111264670 C
1 C
111264671 ATTGTGTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (33 bp):
CCTAACCTTTATTAGTTTTAATTTTTAAAGATG
Found at i:111268686 original size:16 final size:16
Alignment explanation
Indices: 111268667--111268703 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
111268657 TTACTATTGC
*
111268667 TTAAAATTTTAAAAAT
1 TTAAAAGTTTAAAAAT
111268683 TTAAAAGTTTAAAAAT
1 TTAAAAGTTTAAAAAT
*
111268699 ATAAA
1 TTAAA
111268704 TATTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
TTAAAAGTTTAAAAAT
Found at i:111273557 original size:2 final size:2
Alignment explanation
Indices: 111273550--111273582 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
111273540 AAATTAACAA
111273550 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
111273583 AACACTAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:111275799 original size:112 final size:112
Alignment explanation
Indices: 111275659--111275994 Score: 672
Period size: 112 Copynumber: 3.0 Consensus size: 112
111275649 CCTTTTTACG
111275659 AATGGATCCAAAAACAGAACCGAAAACGGTGAGCTTGTCCTCGTCAATGGAACAAAAACAAGGGA
1 AATGGATCCAAAAACAGAACCGAAAACGGTGAGCTTGTCCTCGTCAATGGAACAAAAACAAGGGA
111275724 TTGCCATAACCAGAAATTTTAGTTGTTTTTCTTCGTTTGTATGTTTT
66 TTGCCATAACCAGAAATTTTAGTTGTTTTTCTTCGTTTGTATGTTTT
111275771 AATGGATCCAAAAACAGAACCGAAAACGGTGAGCTTGTCCTCGTCAATGGAACAAAAACAAGGGA
1 AATGGATCCAAAAACAGAACCGAAAACGGTGAGCTTGTCCTCGTCAATGGAACAAAAACAAGGGA
111275836 TTGCCATAACCAGAAATTTTAGTTGTTTTTCTTCGTTTGTATGTTTT
66 TTGCCATAACCAGAAATTTTAGTTGTTTTTCTTCGTTTGTATGTTTT
111275883 AATGGATCCAAAAACAGAACCGAAAACGGTGAGCTTGTCCTCGTCAATGGAACAAAAACAAGGGA
1 AATGGATCCAAAAACAGAACCGAAAACGGTGAGCTTGTCCTCGTCAATGGAACAAAAACAAGGGA
111275948 TTGCCATAACCAGAAATTTTAGTTGTTTTTCTTCGTTTGTATGTTTT
66 TTGCCATAACCAGAAATTTTAGTTGTTTTTCTTCGTTTGTATGTTTT
111275995 TTTATGCTTT
Statistics
Matches: 224, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 224 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (112 bp):
AATGGATCCAAAAACAGAACCGAAAACGGTGAGCTTGTCCTCGTCAATGGAACAAAAACAAGGGA
TTGCCATAACCAGAAATTTTAGTTGTTTTTCTTCGTTTGTATGTTTT
Found at i:111281308 original size:17 final size:17
Alignment explanation
Indices: 111281286--111281328 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
111281276 ACAATTTCTT
*
111281286 TATTAAATGTATATACA
1 TATTAAATATATATACA
* *
111281303 TATTAAAAATATATATA
1 TATTAAATATATATACA
111281320 TATATAAAT
1 TAT-TAAAT
111281329 TCACAAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TATTAAATATATATACA
Found at i:111288371 original size:15 final size:16
Alignment explanation
Indices: 111288351--111288380 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
111288341 TAAAAAAGGT
111288351 GATTTGAAG-CTAATG
1 GATTTGAAGCCTAATG
111288366 GATTTGAAGCCTAAT
1 GATTTGAAGCCTAAT
111288381 CATTCATCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (16 bp):
GATTTGAAGCCTAATG
Found at i:111292267 original size:2 final size:2
Alignment explanation
Indices: 111292260--111292284 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
111292250 ATATAAACTG
111292260 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
111292285 TATATATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:111302867 original size:2 final size:2
Alignment explanation
Indices: 111302818--111302852 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
111302808 TGCAGTTTCC
*
111302818 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
111302853 CACTCTCTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:111304945 original size:2 final size:2
Alignment explanation
Indices: 111304938--111304968 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
111304928 ATGTATTTCC
111304938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
111304969 CACATATACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:111308124 original size:20 final size:20
Alignment explanation
Indices: 111308083--111308120 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
111308073 ATGAGTGAAA
*
111308083 AAAATATGTAATAAATATAT
1 AAAATATGTAATAAAAATAT
111308103 AAAATAT-TAATAAAAATA
1 AAAATATGTAATAAAAATA
111308121 ATAATGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAATATGTAATAAAAATAT
Found at i:111308222 original size:11 final size:9
Alignment explanation
Indices: 111308197--111308222 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
111308187 CGTGAATTTG
111308197 TTTATATAT
1 TTTATATAT
111308206 TTTATATAT
1 TTTATATAT
111308215 TTTATATA
1 TTTATATA
111308223 AAAATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTATATAT
Found at i:111308670 original size:2 final size:2
Alignment explanation
Indices: 111308663--111308707 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
111308653 CCTCCAAGTG
*
111308663 TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
111308704 TA TA
1 TA TA
111308708 AAGTCAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:111308816 original size:27 final size:27
Alignment explanation
Indices: 111308786--111308841 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
111308776 ATATTATAAC
111308786 ATATTACCATATTAATAATCTAAATAT
1 ATATTACCATATTAATAATCTAAATAT
111308813 ATATTACCATATTAATAATCTAAATAT
1 ATATTACCATATTAATAATCTAAATAT
111308840 AT
1 AT
111308842 CTAAACTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (27 bp):
ATATTACCATATTAATAATCTAAATAT
Found at i:111320330 original size:61 final size:61
Alignment explanation
Indices: 111320260--111320381 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
111320250 TTTTGTGATG
111320260 AAATAACCTGATGTCGAAACATTCAGGATGTGAAGTCGTGACTTCACAGGTAGTCCACTAA
1 AAATAACCTGATGTCGAAACATTCAGGATGTGAAGTCGTGACTTCACAGGTAGTCCACTAA
111320321 AAATAACCTGATGTCGAAACATTCAGGATGTGAAGTCGTGACTTCACAGGTAGTCCACTAA
1 AAATAACCTGATGTCGAAACATTCAGGATGTGAAGTCGTGACTTCACAGGTAGTCCACTAA
111320382 CTCCCAAATT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (61 bp):
AAATAACCTGATGTCGAAACATTCAGGATGTGAAGTCGTGACTTCACAGGTAGTCCACTAA
Found at i:111323546 original size:53 final size:53
Alignment explanation
Indices: 111323479--111323629 Score: 198
Period size: 53 Copynumber: 2.8 Consensus size: 53
111323469 ACAAGTGTGC
*
111323479 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGA-AATGTGATAATGCGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGT-ATAATGTGATAATGCGACT
* *
111323532 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGCGACT
* * *
111323585 CCGTATAAGATCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
111323630 ACCGTGTAAG
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
52 2 0.02
53 79 0.90
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGCGACT
Found at i:111331117 original size:53 final size:53
Alignment explanation
Indices: 111330976--111331126 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
111330966 ACAAGTGTGC
* **
111330976 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
111331029 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
111331082 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
111331127 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:111334560 original size:26 final size:26
Alignment explanation
Indices: 111334542--111334664 Score: 86
Period size: 25 Copynumber: 4.9 Consensus size: 26
111334532 ATTTTGTGTA
111334542 TTATATATT-TTATATTATTATTTAC
1 TTATATATTATTATATTATTATTTAC
*
111334567 TTATATTTTATTATATTA-TA-TTAC
1 TTATATATTATTATATTATTATTTAC
* *
111334591 TTCATAT-TT-TTCTATTATCATATTA-
1 TT-ATATATTATTATATTATTAT-TTAC
* *
111334616 ATATATATT-TTAATATATATCA-TTAC
1 TTATATATTATT-ATAT-TATTATTTAC
111334642 TTAT-TATTTATTATATTA-TATTT
1 TTATATA-TTATTATATTATTATTT
111334665 TTATCACATA
Statistics
Matches: 79, Mismatches: 7, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
23 7 0.09
24 14 0.18
25 28 0.35
26 23 0.29
27 7 0.09
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATATATTATTATATTATTATTTAC
Found at i:111334585 original size:8 final size:8
Alignment explanation
Indices: 111334540--111334706 Score: 83
Period size: 8 Copynumber: 21.9 Consensus size: 8
111334530 TTATTTTGTG
111334540 TATTA-TA
1 TATTATTA
111334547 TATT-TTA
1 TATTATTA
111334554 TATTATTA
1 TATTATTA
111334562 T-TTACTTA
1 TATTA-TTA
111334570 TATT-TTA
1 TATTATTA
111334577 T-TATATTA
1 TAT-TATTA
111334585 TATTACTTCA
1 TATTA-TT-A
* *
111334595 TATTTTTC
1 TATTATTA
*
111334603 TATTATCA
1 TATTATTA
*
111334611 TATTAATA
1 TATTATTA
*
111334619 TA-TATTT
1 TATTATTA
*
111334626 TAATA-TA
1 TATTATTA
*
111334633 TATCATTA
1 TATTATTA
*
111334641 -CTTATTA
1 TATTATTA
111334648 T-TTATTA
1 TATTATTA
111334655 TATTA-TA
1 TATTATTA
111334662 T-TT-TTA
1 TATTATTA
* *
111334668 TCA-CATAA
1 T-ATTATTA
111334676 TATT-TATA
1 TATTAT-TA
*
111334684 TATTTTTA
1 TATTATTA
111334692 TATTATTA
1 TATTATTA
111334700 TATTATT
1 TATTATT
111334707 TTACATTTTA
Statistics
Matches: 121, Mismatches: 19, Indels: 39
0.68 0.11 0.22
Matches are distributed among these distances:
6 6 0.05
7 44 0.36
8 58 0.48
9 8 0.07
10 5 0.04
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTATTA
Found at i:111334589 original size:5 final size:5
Alignment explanation
Indices: 111334540--111334589 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
111334530 TTATTTTGTG
* *
111334540 TATTA TA-TA TTTTA TATTA TTATT- TACTTA TATTT TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA -TATTA TA-TTA TATTA TATTA TATTA TATTA
111334590 CTTCATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 5 0.14
5 26 0.70
6 6 0.16
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (5 bp):
TATTA
Found at i:111334702 original size:24 final size:26
Alignment explanation
Indices: 111334540--111334715 Score: 69
Period size: 26 Copynumber: 6.4 Consensus size: 26
111334530 TTATTTTGTG
111334540 TATTATATATTTTATATTATTAT-TTA
1 TATTATAT-TTTTATATTATTATATTA
*
111334566 -CTTATA-TTTTAT-TATATTATATTA
1 TATTATATTTTTATAT-TATTATATTA
* * *
111334590 CT-TCATATTTTTCTATTATCATATTA
1 -TATTATATTTTTATATTATTATATTA
* *
111334616 -ATATATATTTTAATATATATCATTACTTA
1 TAT-TATATTTTTATAT-TATTA-TA-TTA
*
111334645 TTATT-TATTATATTATATTTTTATCACATAATA
1 -TATTATATT-T-TTATATTATTAT---AT--TA
*
111334678 TTTATATATTTTTATATTATTATATTA
1 TAT-TATATTTTTATATTATTATATTA
* *
111334705 TTTTACATTTT
1 TATTATATTTT
111334716 AACAATATAT
Statistics
Matches: 115, Mismatches: 13, Indels: 44
0.67 0.08 0.26
Matches are distributed among these distances:
22 1 0.01
23 12 0.10
24 3 0.03
25 10 0.09
26 31 0.27
27 11 0.10
28 2 0.02
29 10 0.09
30 5 0.04
31 8 0.07
32 14 0.12
33 4 0.03
34 4 0.03
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.61
Consensus pattern (26 bp):
TATTATATTTTTATATTATTATATTA
Found at i:111334730 original size:50 final size:52
Alignment explanation
Indices: 111334643--111334758 Score: 120
Period size: 50 Copynumber: 2.3 Consensus size: 52
111334633 TATCATTACT
* * * *
111334643 TATTATT-TATTATATTATATTTTTATCACATAATATTT-ATA-TATTTTTA
1 TATTATTATATTATTTTACATTTTTAACACATAATATTTCATATTATTATTA
111334692 TATTATTATATTATTTTACA-TTTTAACA-ATATATTATTTCATATTATTATTA
1 TATTATTATATTATTTTACATTTTTAACACATA-A-TATTTCATATTATTATTA
*
111334744 T-CTATTATA-TATTTT
1 TATTATTATATTATTTT
111334759 TCATGTATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
48 3 0.05
49 15 0.26
50 21 0.37
51 10 0.18
52 8 0.14
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60
Consensus pattern (52 bp):
TATTATTATATTATTTTACATTTTTAACACATAATATTTCATATTATTATTA
Found at i:111344483 original size:13 final size:13
Alignment explanation
Indices: 111344465--111344491 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
111344455 TAATAGTTAT
111344465 CTACTTTTATGTA
1 CTACTTTTATGTA
111344478 CTACTTTTATGTA
1 CTACTTTTATGTA
111344491 C
1 C
111344492 ATCAATGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (13 bp):
CTACTTTTATGTA
Found at i:111347531 original size:1 final size:1
Alignment explanation
Indices: 111347525--111347550 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
111347515 AGTAAGGATG
111347525 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
111347551 AAGATTGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:111348927 original size:13 final size:13
Alignment explanation
Indices: 111348909--111348959 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
111348899 TGTTTGGCAA
111348909 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
111348922 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
* *
111348935 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
111348948 TACTTTTGAAAA
1 TGCTTTTGAAAA
111348960 TTTTAGGTGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:111350562 original size:29 final size:28
Alignment explanation
Indices: 111350499--111350563 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
111350489 ATTTAGACTT
* *
111350499 ATTTAATTTTTTTAATATTATAAAAATTA
1 ATTTAATCTATTTAATA-TATAAAAATTA
*
111350528 AATTAATCTATTTAATA-ATAAAAATAATA
1 ATTTAATCTATTTAATATATAAAAAT--TA
111350557 ATTTAAT
1 ATTTAAT
111350564 TTAATTCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 8 0.27
29 22 0.73
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTTAATCTATTTAATATATAAAAATTA
Found at i:111351232 original size:35 final size:35
Alignment explanation
Indices: 111351193--111351298 Score: 176
Period size: 35 Copynumber: 3.0 Consensus size: 35
111351183 CACTTGCCTC
111351193 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
111351228 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
* * * *
111351263 CTCCCATTCTCCCAAGCTGTCTGCCACCAACACCA
1 TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
111351298 T
1 T
111351299 CACACACTCC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.19, C:0.48, G:0.10, T:0.23
Consensus pattern (35 bp):
TTCCCACTCTCCCATGCTGTCTGCCACCAGCACCA
Found at i:111351709 original size:12 final size:12
Alignment explanation
Indices: 111351688--111351736 Score: 89
Period size: 12 Copynumber: 4.1 Consensus size: 12
111351678 TTAAAACATA
111351688 AAAAAAATATAC
1 AAAAAAATATAC
*
111351700 AAAAAGATATAC
1 AAAAAAATATAC
111351712 AAAAAAATATAC
1 AAAAAAATATAC
111351724 AAAAAAATATAC
1 AAAAAAATATAC
111351736 A
1 A
111351737 TTTTTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.73, C:0.08, G:0.02, T:0.16
Consensus pattern (12 bp):
AAAAAAATATAC
Found at i:111351854 original size:11 final size:11
Alignment explanation
Indices: 111351838--111351872 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
111351828 CCGGATTCCC
111351838 CTCCCTTCTCT
1 CTCCCTTCTCT
111351849 CTCCCTTCTCT
1 CTCCCTTCTCT
111351860 CTTCCC-TCTCT
1 C-TCCCTTCTCT
111351871 CT
1 CT
111351873 TCTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:111352359 original size:3 final size:3
Alignment explanation
Indices: 111352351--111352396 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
111352341 TGCATTTCAA
111352351 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
111352397 GAAATACATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:111352508 original size:3 final size:3
Alignment explanation
Indices: 111352500--111352544 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
111352490 TGTGTTTCAA
111352500 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
111352545 ATATCCTTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:111352818 original size:33 final size:30
Alignment explanation
Indices: 111352760--111352829 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 30
111352750 TAATATTATG
*
111352760 TATATATTTTAATATTATCAGTTATATATA
1 TATATATTTTAATACTATCAGTTATATATA
* *
111352790 CTATATGATTTCTAATACTATTATTTATATATA
1 -TATAT-ATTT-TAATACTATCAGTTATATATA
111352823 TATATAT
1 TATATAT
111352830 ATTTTCTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 7 0.21
32 9 0.26
33 18 0.53
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (30 bp):
TATATATTTTAATACTATCAGTTATATATA
Found at i:111354099 original size:20 final size:20
Alignment explanation
Indices: 111354074--111354114 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
111354064 TACTTTTGTG
*
111354074 TGTTATTGTTCAATACAAAT
1 TGTTATTATTCAATACAAAT
111354094 TGTTATTATTCAATACAAAT
1 TGTTATTATTCAATACAAAT
111354114 T
1 T
111354115 TGATCATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (20 bp):
TGTTATTATTCAATACAAAT
Found at i:111354399 original size:55 final size:55
Alignment explanation
Indices: 111354310--111354684 Score: 426
Period size: 55 Copynumber: 6.7 Consensus size: 55
111354300 TGATTTTGGA
* * * * * * *
111354310 TTGAATCGATTATTTTTATGTTTAAATCGATTGTCATGCTAGAATATTGCTTCGT
1 TTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATACTGCTTCTT
* * * *
111354365 TTGAGTCGATTGTTTATATGTTTAAATTGATTGTCATGTTAGAATACTGCTTCTT
1 TTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATACTGCTTCTT
* * *
111354420 TTGAATCGATTGTTTATATGTTTAAATCAATTGTTATGGTGGAATATTGCTTCTTCTTCTT
1 TTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATA------CTGCTTCTT
* * * * *
111354481 TTGAATAGATTATTTATATGTTTAAATCAATTGTTATGTTGGAATATTGTTTCTT
1 TTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATACTGCTTCTT
* * *
111354536 TTGAATCGATTGTTTATATATTTAAGTCGATTGTTATGTTGGAATACTACTTCTT
1 TTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATACTGCTTCTT
* * * * *
111354591 TTAAATTGATTGTTTATATGTTCAAATTGATTGTTATATTGGAATACTGCTTCTT
1 TTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATACTGCTTCTT
* **
111354646 TTGAATCGGTTGTTTATATGTTTAAATAAATTGTTATGT
1 TTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGT
111354685 AGCATGTCTA
Statistics
Matches: 271, Mismatches: 43, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
55 220 0.81
61 51 0.19
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (55 bp):
TTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGGAATACTGCTTCTT
Found at i:111354604 original size:171 final size:165
Alignment explanation
Indices: 111354310--111354684 Score: 462
Period size: 171 Copynumber: 2.2 Consensus size: 165
111354300 TGATTTTGGA
* * * * *
111354310 TTGAATCGATTATTTTTATGTTTAAATCGATTGTCATGCTAGAATATTGCTTCGTTTGAGTCGAT
1 TTGAATCGATTATTTATATGTTTAAATCAATTGTTATGTTAGAATATTGCTTCGTTTGAATCGAT
* * * *
111354375 TGTTTATATGTTTAAATTGATTGTCATGTTAGAATACTGCTTCTTTTGAATCGATTGTTTATATG
66 TGTTTATATATTTAAATCGATTGTCATGTTAGAATACTACTTCTTTTAAATCGATTGTTTATATG
* * *
111354440 TTTAAATCAATTGTTATGGTGGAATATTGCTTCTTCTTCTT
131 TTCAAATCAATTGTTATAGTGGAATA------CTGCTTCTT
* * * *
111354481 TTGAATAGATTATTTATATGTTTAAATCAATTGTTATGTTGGAATATTGTTTCTTTTGAATCGAT
1 TTGAATCGATTATTTATATGTTTAAATCAATTGTTATGTTAGAATATTGCTTCGTTTGAATCGAT
* * * *
111354546 TGTTTATATATTTAAGTCGATTGTTATGTTGGAATACTACTTCTTTTAAATTGATTGTTTATATG
66 TGTTTATATATTTAAATCGATTGTCATGTTAGAATACTACTTCTTTTAAATCGATTGTTTATATG
** *
111354611 TTCAAATTGATTGTTATATTGGAATACTGCTTCTT
131 TTCAAATCAATTGTTATAGTGGAATACTGCTTCTT
* * *
111354646 TTGAATCGGTTGTTTATATGTTTAAATAAATTGTTATGT
1 TTGAATCGATTATTTATATGTTTAAATCAATTGTTATGT
111354685 AGCATGTCTA
Statistics
Matches: 177, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
165 43 0.24
171 134 0.76
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (165 bp):
TTGAATCGATTATTTATATGTTTAAATCAATTGTTATGTTAGAATATTGCTTCGTTTGAATCGAT
TGTTTATATATTTAAATCGATTGTCATGTTAGAATACTACTTCTTTTAAATCGATTGTTTATATG
TTCAAATCAATTGTTATAGTGGAATACTGCTTCTT
Found at i:111356327 original size:66 final size:63
Alignment explanation
Indices: 111356249--111356461 Score: 225
Period size: 66 Copynumber: 3.2 Consensus size: 63
111356239 TAGTACCACT
* *
111356249 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGG-GTCCATC-CTT---AT
*
111356311 CACG
60 CACA
111356315 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGGTCCATCCTTATCAC
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGGTCCATCCTTATCAC
111356380 A
63 A
* *
111356381 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGGATACATCTCGTATC
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGG-TCCATC-CTTATC
111356446 ACA
61 ACA
*
111356449 CATGTGACCTAGC
1 CATGCGACCTAGC
111356462 TACTACAGGG
Statistics
Matches: 133, Mismatches: 6, Indels: 14
0.87 0.04 0.09
Matches are distributed among these distances:
66 69 0.52
67 11 0.08
68 21 0.16
69 4 0.03
70 6 0.05
71 22 0.17
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (63 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGGTCCATCCTTATCACA
Found at i:111356360 original size:71 final size:66
Alignment explanation
Indices: 111356272--111356464 Score: 278
Period size: 66 Copynumber: 2.8 Consensus size: 66
111356262 CGATTTGTCT
* *
111356272 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGG-GTCCATC-CTT---ATCACACATGCGACCTAGCTACATTTAT
111356337 CTTTCA
61 CTTTCA
111356343 CGTAGCTCTCTTGTCTACATGGGTCCATCCTTATCACACATGCGACCTAGCTACATTTATCTTTC
1 CGTAGCTCTCTTGTCTACATGGGTCCATCCTTATCACACATGCGACCTAGCTACATTTATCTTTC
111356408 A
66 A
* * *
111356409 CGTAGCTCTCTTGTCTACATGGGATACATCTCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGG-TCCATC-CTTATCACACATGCGACCTAGCTAC
111356465 TACAGGGTGT
Statistics
Matches: 115, Mismatches: 5, Indels: 7
0.91 0.04 0.06
Matches are distributed among these distances:
66 56 0.49
67 5 0.04
68 23 0.20
69 3 0.03
70 6 0.05
71 22 0.19
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (66 bp):
CGTAGCTCTCTTGTCTACATGGGTCCATCCTTATCACACATGCGACCTAGCTACATTTATCTTTC
A
Found at i:111356361 original size:30 final size:30
Alignment explanation
Indices: 111356327--111356428 Score: 73
Period size: 30 Copynumber: 3.2 Consensus size: 30
111356317 TGCGACCTAG
111356327 CTACATTTATCTTTCACGTAGCTCTCTTGT
1 CTACATTTATCTTTCACGTAGCTCTCTTGT
* ** * *
111356357 CTACATGGGTCCATCCTTATCACACATGCGAC-CTAG-
1 CTACAT---T-TAT-CTT-TCACGTA-GC-TCTCTTGT
111356393 CTACATTTATCTTTCACGTAGCTCTCTTGT
1 CTACATTTATCTTTCACGTAGCTCTCTTGT
111356423 CTACAT
1 CTACAT
111356429 GGGATACATC
Statistics
Matches: 52, Mismatches: 10, Indels: 20
0.63 0.12 0.24
Matches are distributed among these distances:
28 1 0.02
29 5 0.10
30 17 0.33
31 3 0.06
32 2 0.04
33 2 0.04
34 2 0.04
35 3 0.06
36 11 0.21
37 5 0.10
38 1 0.02
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (30 bp):
CTACATTTATCTTTCACGTAGCTCTCTTGT
Found at i:111356483 original size:68 final size:67
Alignment explanation
Indices: 111356267--111356532 Score: 198
Period size: 68 Copynumber: 3.9 Consensus size: 67
111356257 CTAGCCGATT
* * * * * * *
111356267 TGTCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACA
1 TGTCACGTAGCTCTCTTGTCTACATGG-GTACAT--C-TCGTATCACACATGTGACCTAGCTACA
** *
111356332 TTTATC
62 TACAGC
* * * * **
111356338 TTTCACGTAGCTCTCTTGTCTACATGGGTCCATC-CTTATCACACATGCGACCTAGCTACATTTA
1 TGTCACGTAGCTCTCTTGTCTACATGGGTACATCTCGTATCACACATGTGACCTAGCTACATACA
*
111356402 TC
66 GC
*
111356404 TTTCACGTAGCTCTCTTGTCTACATGGGATACATCTCGTATCACACATGTGACCTAGCTAC-TAC
1 TGTCACGTAGCTCTCTTGTCTACATGGG-TACATCTCGTATCACACATGTGACCTAGCTACATAC
*
111356468 AGGG
65 A-GC
* * * * * *
111356472 TGTCTCGTAGCTTTCTTGTAC-ACATGATGTGCA-CTCAGCATCATACATGTGACCTAGCTAC
1 TGTCACGTAGCTCTCTTGT-CTACATG-GGTACATCTC-GTATCACACATGTGACCTAGCTAC
111356533 GCTCCCTCTA
Statistics
Matches: 168, Mismatches: 21, Indels: 15
0.82 0.10 0.07
Matches are distributed among these distances:
66 56 0.33
67 10 0.06
68 70 0.42
69 2 0.01
70 5 0.03
71 25 0.15
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.33
Consensus pattern (67 bp):
TGTCACGTAGCTCTCTTGTCTACATGGGTACATCTCGTATCACACATGTGACCTAGCTACATACA
GC
Found at i:111363925 original size:66 final size:66
Alignment explanation
Indices: 111363807--111363998 Score: 285
Period size: 66 Copynumber: 2.8 Consensus size: 66
111363797 CGATTTGTCT
* * * * *
111363807 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGG-GTACATC-C---GTATCACACATGTGACCTAGCTACATTTAT
111363872 CTTTCA
61 CTTTCA
111363878 CGTAGCTCTCTTGTCTACATGGGTACATCCGTATCACACATGTGACCTAGCTACATTTATCTTTC
1 CGTAGCTCTCTTGTCTACATGGGTACATCCGTATCACACATGTGACCTAGCTACATTTATCTTTC
111363943 A
66 A
111363944 CGTAGCTCTCTTGTCTACATGGGATACATCCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGG-TACATCCGTATCACACATGTGACCTAGCTAC
111363999 TACATGGTGT
Statistics
Matches: 115, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
66 56 0.49
67 31 0.27
69 1 0.01
70 5 0.04
71 22 0.19
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (66 bp):
CGTAGCTCTCTTGTCTACATGGGTACATCCGTATCACACATGTGACCTAGCTACATTTATCTTTC
A
Found at i:111364015 original size:67 final size:66
Alignment explanation
Indices: 111363802--111364066 Score: 246
Period size: 66 Copynumber: 3.9 Consensus size: 66
111363792 CTAGCCGATT
* * * * * *
111363802 TGTCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACA
1 TGTCACGTAGCTCTCTTGTCTACATGG-GTACATC-C---GTATCACACATGTGACCTAGCTACA
**
111363867 TTTATC
61 TACATC
* **
111363873 TTTCACGTAGCTCTCTTGTCTACATGGGTACATCCGTATCACACATGTGACCTAGCTACATTTAT
1 TGTCACGTAGCTCTCTTGTCTACATGGGTACATCCGTATCACACATGTGACCTAGCTACATACAT
111363938 C
66 C
*
111363939 TTTCACGTAGCTCTCTTGTCTACATGGGATACATCCGTATCACACATGTGACCTAGCTAC-TACA
1 TGTCACGTAGCTCTCTTGTCTACATGGG-TACATCCGTATCACACATGTGACCTAGCTACATACA
*
111364003 TGG
65 T-C
* * * * * * *
111364006 TGTCTCGTAGCTTTCTTGTAC-ACATGATGTGCACTCAGCATCATACATGTGACCTAGCTAC
1 TGTCACGTAGCTCTCTTGT-CTACATG-GGTACA-TCCGTATCACACATGTGACCTAGCTAC
111364067 GCTCCCTCTA
Statistics
Matches: 171, Mismatches: 18, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
66 59 0.35
67 55 0.32
68 26 0.15
69 1 0.01
70 5 0.03
71 25 0.15
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (66 bp):
TGTCACGTAGCTCTCTTGTCTACATGGGTACATCCGTATCACACATGTGACCTAGCTACATACAT
C
Found at i:111365778 original size:16 final size:16
Alignment explanation
Indices: 111365759--111365796 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
111365749 ATCATTTTAT
111365759 TTTTCTATCCTTT-CAA
1 TTTTCTAT-CTTTCCAA
*
111365775 TTTTTTATCTTTCCAA
1 TTTTCTATCTTTCCAA
111365791 TTTTCT
1 TTTTCT
111365797 TTTCACTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.16, C:0.21, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTCTATCTTTCCAA
Found at i:111372576 original size:22 final size:22
Alignment explanation
Indices: 111372551--111372592 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
111372541 TTTTTAAATT
* *
111372551 TTTTTACATTTTTGGGTTTGGC
1 TTTTGACATTTTTGGATTTGGC
*
111372573 TTTTGACTTTTTTGGATTTG
1 TTTTGACATTTTTGGATTTG
111372593 AGCCTATTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.10, C:0.07, G:0.21, T:0.62
Consensus pattern (22 bp):
TTTTGACATTTTTGGATTTGGC
Found at i:111372899 original size:17 final size:19
Alignment explanation
Indices: 111372877--111372919 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
111372867 TCTAAATGGG
*
111372877 ATTAAAATAAA-TT-CTTA
1 ATTAAAATAAATTTAATTA
111372894 ATTAAAA-AAATTTAATTA
1 ATTAAAATAAATTTAATTA
111372912 ATTAAAAT
1 ATTAAAAT
111372920 TTTCAAACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 9 0.41
18 10 0.45
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTAAAATAAATTTAATTA
Found at i:111373129 original size:16 final size:17
Alignment explanation
Indices: 111373108--111373140 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
111373098 AGATTTAGGT
111373108 TTAAAA-TTTTAATTAA
1 TTAAAATTTTTAATTAA
111373124 TTAAAATTTTTAATTAA
1 TTAAAATTTTTAATTAA
111373141 AAATCTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAAATTTTTAATTAA
Found at i:111374528 original size:79 final size:78
Alignment explanation
Indices: 111374395--111374601 Score: 218
Period size: 79 Copynumber: 2.6 Consensus size: 78
111374385 TAATCTGTCG
* * * * * * ***
111374395 AAAGAAATGGTTCTTATTTATACTCATTCTCGTAAGATAGAAGTGCCATCGGGATTTTATCCTAT
1 AAAGAAACGGTTCCTATTCATACTCATTCTCGCAAGATAGAAGTGTCGTCGGGATCGGATCCTA-
** *
111374460 CC-ATAATCTTTTTG
65 CCTATAATC-TGGTA
* * * * *
111374474 AGAGAAACGGTTCCTATTCATGCTCGTTCTCGCAAGATAGAAGTGTCGTTGGGATCGGATCTTAC
1 AAAGAAACGGTTCCTATTCATACTCATTCTCGCAAGATAGAAGTGTCGTCGGGATCGGATCCTAC
111374539 CTATAATCTGGTA
66 CTATAATCTGGTA
* *
111374552 AAAGAAACGGTTCCTATTCACACTCATTCTCACAAGATAGAAGTGTCGTC
1 AAAGAAACGGTTCCTATTCATACTCATTCTCGCAAGATAGAAGTGTCGTC
111374602 AGGACTGGAT
Statistics
Matches: 104, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
78 48 0.46
79 56 0.54
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (78 bp):
AAAGAAACGGTTCCTATTCATACTCATTCTCGCAAGATAGAAGTGTCGTCGGGATCGGATCCTAC
CTATAATCTGGTA
Found at i:111374864 original size:153 final size:153
Alignment explanation
Indices: 111374483--111374906 Score: 394
Period size: 153 Copynumber: 2.8 Consensus size: 153
111374473 GAGAGAAACG
** * ** *
111374483 GTTCCTATTCATGCTCGTTCTCGCAAGATAGAAGTGTCGTTGGGATCGGATCTTA-CCTATAA-T
1 GTTCCTATTCACACTCGTTCTCGCAAGATAGAAGTGCCGTCAGGATCGGATCCTATCC-ATAATT
** * * * * *
111374546 CTGGTAAAAGAAACGG-TTCCTATTCACACTCATTCTCACAAGATAGAAGTGTCGTCAGGACTGG
65 CT-CCAAGAGAAA-GGATTCCTATGCACACTCGTTCTCGCAAGATAGAAGTGCCGT-A-GACTGG
*
111374610 ATACTATCCATAATCCGTTGAAAAAATA
126 ATACTATCCATAATCCGTTCAAAAAATA
* * * * * * * * *
111374638 GTTCCTATTCACACTTGTTCTTGTAAGATAGAAGTGCCATCAAGAGT-GAATCCAATCCGTAATC
1 GTTCCTATTCACACTCGTTCTCGCAAGATAGAAGTGCCGTCAGGA-TCGGATCCTATCCATAATT
* * * * * *
111374702 CTTCGAGAGAAAGGATTCCTATGCACACTTGTTCTCGCAAGTTAGATGTGCCGT-GACTGGATTC
65 CTCCAAGAGAAAGGATTCCTATGCACACTCGTTCTCGCAAGATAGAAGTGCCGTAGACTGGATAC
*
111374766 TATCCATGATCC-TTCAAAAGAA-A
130 TATCCATAATCCGTTCAAAA-AATA
* *
111374789 GGTTTCTTATTCACACTCGTTCTCGCAAGATAGAAATGCCGTCAGGATCGGATCCTATCCATAAT
1 -G-TTCCTATTCACACTCGTTCTCGCAAGATAGAAGTGCCGTCAGGATCGGATCCTATCCATAAT
* * * *
111374854 TCTCCAAGAGAAATGATTCCTAAGCACACTCGTTCTCGCAAAATAAAAGTGCC
64 TCTCCAAGAGAAAGGATTCCTATGCACACTCGTTCTCGCAAGATAGAAGTGCC
111374907 TTTAGGACTG
Statistics
Matches: 212, Mismatches: 49, Indels: 18
0.76 0.18 0.06
Matches are distributed among these distances:
151 7 0.03
152 24 0.11
153 93 0.44
154 2 0.01
155 81 0.38
156 5 0.02
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (153 bp):
GTTCCTATTCACACTCGTTCTCGCAAGATAGAAGTGCCGTCAGGATCGGATCCTATCCATAATTC
TCCAAGAGAAAGGATTCCTATGCACACTCGTTCTCGCAAGATAGAAGTGCCGTAGACTGGATACT
ATCCATAATCCGTTCAAAAAATA
Found at i:111374882 original size:78 final size:78
Alignment explanation
Indices: 111374416--111374931 Score: 365
Period size: 78 Copynumber: 6.7 Consensus size: 78
111374406 TCTTATTTAT
* * * * * ** * ** *
111374416 ACTCATTCTCGTAAGATAGAAGTGCCATCGGGATTTTATCCTATCCATAATCTTTTTGAGAGAAA
1 ACTCGTTCTCGCAAGATAGAAGTGCCGTCAGGACTGGATCCTATCCATAATC-CTTCAAAAGAAA
*
111374481 CGG-TTCCTATTCAT
65 -GGATTCCTATTCAC
* * ** *
111374495 GCTCGTTCTCGCAAGATAGAAGTGTCGTTGGGA-TCGGATCTTA-CCTATAAT-CTGGT-AAAAG
1 ACTCGTTCTCGCAAGATAGAAGTGCCGTCAGGACT-GGATCCTATCC-ATAATCCT--TCAAAAG
111374556 AAACGG-TTCCTATTCAC
62 AAA-GGATTCCTATTCAC
* * * * *
111374573 ACTCATTCTCACAAGATAGAAGTGTCGTCAGGACTGGATACTATCCATAATCCGTTGAAAA-AAT
1 ACTCGTTCTCGCAAGATAGAAGTGCCGTCAGGACTGGATCCTATCCATAATCC-TTCAAAAGAA-
111374637 A-G-TTCCTATTCAC
64 AGGATTCCTATTCAC
* * * * * * * * * * *
111374650 ACTTGTTCTTGTAAGATAGAAGTGCCATCAAGAGTGAATCCAATCCGTAATCCTTCGAGAGAAAG
1 ACTCGTTCTCGCAAGATAGAAGTGCCGTCAGGACTGGATCCTATCCATAATCCTTCAAAAGAAAG
*
111374715 GATTCCTATGCAC
66 GATTCCTATTCAC
* * * * *
111374728 ACTTGTTCTCGCAAGTTAGATGTGCCGT---GACTGGATTCTATCCATGATCCTTCAAAAGAAAG
1 ACTCGTTCTCGCAAGATAGAAGTGCCGTCAGGACTGGATCCTATCCATAATCCTTCAAAAGAAAG
* *
111374790 GTTTCTTATTCAC
66 GATTCCTATTCAC
* * * *
111374803 ACTCGTTCTCGCAAGATAGAAATGCCGTCAGGA-TCGGATCCTATCCATAATTCTCCAAGAGAAA
1 ACTCGTTCTCGCAAGATAGAAGTGCCGTCAGGACT-GGATCCTATCCATAATCCTTCAAAAGAAA
* **
111374867 TGATTCCTAAGCAC
65 GGATTCCTATTCAC
* * * * * *
111374881 ACTCGTTCTCGCAAAATAAAAGTGCCTTTAGGACTGAATCCTATTCATAAT
1 ACTCGTTCTCGCAAGATAGAAGTGCCGTCAGGACTGGATCCTATCCATAAT
111374932 TCCTATCTAC
Statistics
Matches: 345, Mismatches: 74, Indels: 37
0.76 0.16 0.08
Matches are distributed among these distances:
75 60 0.17
76 5 0.01
77 57 0.17
78 174 0.50
79 48 0.14
80 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (78 bp):
ACTCGTTCTCGCAAGATAGAAGTGCCGTCAGGACTGGATCCTATCCATAATCCTTCAAAAGAAAG
GATTCCTATTCAC
Found at i:111382653 original size:5 final size:5
Alignment explanation
Indices: 111382643--111382697 Score: 89
Period size: 5 Copynumber: 11.6 Consensus size: 5
111382633 ACAATTGTGA
111382643 AAAAT AAAAT AAAAT -AAAT AAAAT -AAAT AAAAT -AAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
111382690 AAAAT AAA
1 AAAAT AAA
111382698 GAACACACAA
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
4 12 0.26
5 35 0.74
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:111382663 original size:9 final size:9
Alignment explanation
Indices: 111382643--111382697 Score: 92
Period size: 9 Copynumber: 5.9 Consensus size: 9
111382633 ACAATTGTGA
111382643 AAAATAAAAT
1 AAAAT-AAAT
111382653 AAAATAAAT
1 AAAATAAAT
111382662 AAAATAAAT
1 AAAATAAAT
111382671 AAAATAAAT
1 AAAATAAAT
111382680 AAAATAAAAT
1 AAAAT-AAAT
111382690 AAAATAAA
1 AAAATAAA
111382698 GAACACACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
9 30 0.68
10 14 0.32
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAATAAAT
Found at i:111382663 original size:14 final size:14
Alignment explanation
Indices: 111382643--111382697 Score: 78
Period size: 14 Copynumber: 3.9 Consensus size: 14
111382633 ACAATTGTGA
111382643 AAAATAAAATAAA-
1 AAAATAAAATAAAT
111382656 ATAAATAAAATAAAT
1 A-AAATAAAATAAAT
111382671 AAAAT-AAATAAAAT
1 AAAATAAAAT-AAAT
111382685 AAAATAAAATAAA
1 AAAATAAAATAAA
111382698 GAACACACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.13
14 28 0.74
15 5 0.13
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:111384582 original size:22 final size:22
Alignment explanation
Indices: 111384557--111384609 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
111384547 TTTTCTCAAA
111384557 ATTATTAT-TATTTTTCATATGT
1 ATTATTATAT-TTTTTCATATGT
111384579 ATTATTATATTTTTTCATA--T
1 ATTATTATATTTTTTCATATGT
111384599 ATTA-TATATTT
1 ATTATTATATTT
111384610 ATTTATACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.23
20 5 0.17
22 17 0.57
23 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTATTATATTTTTTCATATGT
Found at i:111384608 original size:19 final size:18
Alignment explanation
Indices: 111384559--111384635 Score: 61
Period size: 19 Copynumber: 4.1 Consensus size: 18
111384549 TTCTCAAAAT
111384559 TATTATTA-TTTTTCATA
1 TATTATTATTTTTTCATA
111384576 TGTATTATTATATTTTTTCATA
1 --TATTA-T-TATTTTTTCATA
111384598 TATTATATATTTATTT-ATA
1 TATTAT-TATTT-TTTCATA
* *
111384617 CA-TATTATTTTTACATA
1 TATTATTATTTTTTCATA
111384634 TA
1 TA
111384636 AACTTTCATT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
16 2 0.04
17 9 0.18
18 3 0.06
19 16 0.32
20 9 0.18
21 2 0.04
22 9 0.18
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.61
Consensus pattern (18 bp):
TATTATTATTTTTTCATA
Found at i:111384749 original size:18 final size:18
Alignment explanation
Indices: 111384700--111384746 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
111384690 ATACAATATT
111384700 TATTATGTATTATTTTTA
1 TATTATGTATTATTTTTA
111384718 TATTACT-TATTATTTTTA
1 TATTA-TGTATTATTTTTA
111384736 TATATATGTAT
1 TAT-TATGTAT
111384747 ATTACATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (18 bp):
TATTATGTATTATTTTTA
Found at i:111399851 original size:69 final size:67
Alignment explanation
Indices: 111399769--111399896 Score: 175
Period size: 69 Copynumber: 1.9 Consensus size: 67
111399759 TCCAAATAAG
** *
111399769 AAAAGGCAAAACTACGTCATTTTGATAAATGTTTACCTTTTTAAAGTTAAAAGTCAAAACCATTA
1 AAAAGGCAAAACTACGTCATTTTGATAAATGTTTA-C-TAATAAAGTTAAAAGGCAAAACCATTA
111399834 AGTT
64 AGTT
* * **
111399838 AAAAGGTAAAACTATGTTGTTTTGATAAATGTTTACTAATAAAGTTAAAAGGCAAAACC
1 AAAAGGCAAAACTACGTCATTTTGATAAATGTTTACTAATAAAGTTAAAAGGCAAAACC
111399897 CTTATATTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
67 20 0.38
68 1 0.02
69 31 0.60
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (67 bp):
AAAAGGCAAAACTACGTCATTTTGATAAATGTTTACTAATAAAGTTAAAAGGCAAAACCATTAAG
TT
Found at i:111405211 original size:76 final size:75
Alignment explanation
Indices: 111405070--111405216 Score: 258
Period size: 75 Copynumber: 1.9 Consensus size: 75
111405060 GAAGAACTCG
* *
111405070 ACACCAAAAAATCAATTAATCTGATTGAGTATTAATTCAGCGATTTTTTTATTGTTATAATAACA
1 ACACCAAAAAATCAATTAATCTAATTGAGTATTAATTCAGCGACTTTTTTATTGTTATAATAACA
111405135 AAAAAAGTCA
66 AAAAAAGTCA
*
111405145 ACACCAAAAAATTAATTAATCTAATTGAGTATTAATTCAGGCGACTTTTTTATTGTTATAATAAC
1 ACACCAAAAAATCAATTAATCTAATTGAGTATTAATTCA-GCGACTTTTTTATTGTTATAATAAC
111405210 AAAAAAA
65 AAAAAAA
111405217 TATGACTTAG
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
75 37 0.54
76 31 0.46
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.35
Consensus pattern (75 bp):
ACACCAAAAAATCAATTAATCTAATTGAGTATTAATTCAGCGACTTTTTTATTGTTATAATAACA
AAAAAAGTCA
Found at i:111406048 original size:15 final size:17
Alignment explanation
Indices: 111406021--111406053 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
111406011 TCTAGAAAAT
111406021 TTAAAATAAAATA-TAA
1 TTAAAATAAAATACTAA
111406037 TTAAAA-AAAATACTAA
1 TTAAAATAAAATACTAA
111406053 T
1 T
111406054 AATATTACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
TTAAAATAAAATACTAA
Found at i:111407515 original size:130 final size:133
Alignment explanation
Indices: 111407282--111407616 Score: 448
Period size: 130 Copynumber: 2.6 Consensus size: 133
111407272 GAAAAACCGA
* * * *** * * *
111407282 AACCCAGCACAGTAGGGCATGATTCCTCGAATTTTTAAACATTGAGCATTGCCTT-ATTTT--AG
1 AACCCAGCACAATAGGGCACGATTCCCCGAATTCCCAAACATCGAACATTACCTTCATTTTAAAG
* ** * * *
111407344 GATTTAGAAGACATGAGTGAAATATTTCTAAAGCAATATTCGATTATTTTGAACAAACGGGAGAT
66 AATTTTTAAAACATGAGTGAAATATTTCTAAAGCAATATTCGATTATTTTGAACAAACAGGAAAT
111407409 TGC
131 TGC
* *
111407412 AACCCAGCACGATAGGGCACGATTCCCCGAATTCCCAAACATCGAACATTACTTTCATTTTAAAG
1 AACCCAGCACAATAGGGCACGATTCCCCGAATTCCCAAACATCGAACATTACCTTCATTTTAAAG
*
111407477 AATTTTTAAAACATGAGTG-AA-A-TTCTAAAGGAATATTCGATTATTTTGAACAAACAGGAAAT
66 AATTTTTAAAACATGAGTGAAATATTTCTAAAGCAATATTCGATTATTTTGAACAAACAGGAAAT
111407539 TGC
131 TGC
* *
111407542 AACCCAGCACAATAGGGCACGATTCCCCGAATTCCCAAACATCGAACATTGCCTTCGTTTTAAAG
1 AACCCAGCACAATAGGGCACGATTCCCCGAATTCCCAAACATCGAACATTACCTTCATTTTAAAG
111407607 AATTTTTAAA
66 AATTTTTAAA
111407617 TGAATATTCA
Statistics
Matches: 180, Mismatches: 22, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
130 155 0.86
131 6 0.03
132 2 0.01
133 17 0.09
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (133 bp):
AACCCAGCACAATAGGGCACGATTCCCCGAATTCCCAAACATCGAACATTACCTTCATTTTAAAG
AATTTTTAAAACATGAGTGAAATATTTCTAAAGCAATATTCGATTATTTTGAACAAACAGGAAAT
TGC
Found at i:111425337 original size:3 final size:3
Alignment explanation
Indices: 111425331--111425380 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
111425321 CATCATCATC
111425331 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
111425379 AT
1 AT
111425381 GCAGTTGAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:111426797 original size:19 final size:19
Alignment explanation
Indices: 111426756--111426814 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
111426746 TAATGGTGTT
** *
111426756 TGATTAGTGGAATTGTGTC
1 TGATTAGTGGAATCATGTG
*
111426775 TGATTAGTGGAACCATGTG
1 TGATTAGTGGAATCATGTG
*
111426794 TGATTAGTGAAATCATGTG
1 TGATTAGTGGAATCATGTG
111426813 TG
1 TG
111426815 CATATAAAGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.25, C:0.07, G:0.31, T:0.37
Consensus pattern (19 bp):
TGATTAGTGGAATCATGTG
Found at i:111429347 original size:188 final size:182
Alignment explanation
Indices: 111429030--111429406 Score: 513
Period size: 188 Copynumber: 2.0 Consensus size: 182
111429020 TTTAAAAAAT
* *
111429030 AAAATTTATTATAATTACAAGAAGATATAATTACTACATTAATAGTTAAACTTTCTTACAACTAT
1 AAAATTTATTATAATTACAAGAAGATATAATTACTACATTAATAATTAAACTTTCTTACAACTAC
* * * * **
111429095 TCTATGGTCTTTCAAAACAATAACTCAGAAAAGAAACTCAGTTTTACCTCAATAATTGCAAAGTC
66 TCTATGATCTCTAAAAACAAGAACTCAGAAAAGAAACTCAAATTTACCTCAATAATTGCAAAGTC
* *
111429160 AAGCTTGAACTCAAGTAGCTTGGGCTATCAAATAAGTCAAATT-AAAGTATAGGGATTG
131 AAGCTTAAACTCAAGTAGCTT--G----C-AATAAGTCAAATTAAAAGTACAGGGATTG
* * *
111429218 AAAATTTATTGTAATTACAAGAAGATATAATTACTACCTTAATAATTAAACTTTCTTACAATTAC
1 AAAATTTATTATAATTACAAGAAGATATAATTACTACATTAATAATTAAACTTTCTTACAACTAC
* * * **
111429283 TCTATGATCTCTAAAAACAAGAATTCATAAAAGAAACTCAAATTTATCTTGATAATTGCAAAGTC
66 TCTATGATCTCTAAAAACAAGAACTCAGAAAAGAAACTCAAATTTACCTCAATAATTGCAAAGTC
*
111429348 CAGCTTAAACTCAAGTAGCTTGCAATAAGTCAAATTAAAAGTACAGGGATTG
131 AAGCTTAAACTCAAGTAGCTTGCAATAAGTCAAATTAAAAGTACAGGGATTG
111429400 AAAATTT
1 AAAATTT
111429407 TAAAACTGAA
Statistics
Matches: 169, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
181 13 0.08
182 22 0.13
186 1 0.01
188 133 0.79
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (182 bp):
AAAATTTATTATAATTACAAGAAGATATAATTACTACATTAATAATTAAACTTTCTTACAACTAC
TCTATGATCTCTAAAAACAAGAACTCAGAAAAGAAACTCAAATTTACCTCAATAATTGCAAAGTC
AAGCTTAAACTCAAGTAGCTTGCAATAAGTCAAATTAAAAGTACAGGGATTG
Found at i:111432203 original size:3 final size:3
Alignment explanation
Indices: 111432197--111432234 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
111432187 TAATAATAAT
111432197 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
111432235 TAATAATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:111432239 original size:3 final size:3
Alignment explanation
Indices: 111432233--111432429 Score: 141
Period size: 3 Copynumber: 64.7 Consensus size: 3
111432223 CAACAACAAC
* *
111432233 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT ATT GAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * * * * * *
111432281 AAT AA- AAGG AAT AAA AAT GAT AGT AAT AAT AAG AAT ATT AAC AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
111432326 AGT AAT AAT AGT GAT AAT -AT AAAT ACT AAT ACAT ACAT GAAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT A-AT A-AT -AAT AAT AAT
* * *
111432374 AAT AGT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT GAA- AAT AAG
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
*
111432419 AGT AAT AAT AA
1 AAT AAT AAT AA
111432430 CATCTTATAT
Statistics
Matches: 149, Mismatches: 35, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
2 8 0.05
3 124 0.83
4 16 0.11
5 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:111436403 original size:11 final size:12
Alignment explanation
Indices: 111436383--111436408 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
111436373 GGTAGACAAT
111436383 GGAGGAAAAATG
1 GGAGGAAAAATG
111436395 GGAGGAAAAATG
1 GGAGGAAAAATG
111436407 GG
1 GG
111436409 GCAAGTGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.46, T:0.08
Consensus pattern (12 bp):
GGAGGAAAAATG
Found at i:111436483 original size:32 final size:32
Alignment explanation
Indices: 111436447--111436533 Score: 131
Period size: 35 Copynumber: 2.7 Consensus size: 32
111436437 GTTTTTTTAG
*
111436447 TTTTTTTT-TGTTAGGTTTTTCTTTTTTCTTC
1 TTTTTTTTGGGTTAGGTTTTTCTTTTTTCTTC
111436478 TTTTTTTTGGGGGGTTAGGTTTTTCTTTTTTCTTC
1 TTTTTTTT---GGGTTAGGTTTTTCTTTTTTCTTC
111436513 TTTTTTTTGGGTTAGGTTTTT
1 TTTTTTTTGGGTTAGGTTTTT
111436534 TTTGGGGGGC
Statistics
Matches: 51, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
31 8 0.16
32 13 0.25
35 30 0.59
ACGTcount: A:0.03, C:0.07, G:0.18, T:0.71
Consensus pattern (32 bp):
TTTTTTTTGGGTTAGGTTTTTCTTTTTTCTTC
Done.