Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold117
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: 3231771
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 68836 characters in sequence are not A, C, G, or T
File 9 of 18
Found at i:1434547 original size:8 final size:8
Alignment explanation
Indices: 1434532--1434568 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
1434522 ATTTAACCCC
1434532 AAAAAGAA
1 AAAAAGAA
*
1434540 AGAAAGAA
1 AAAAAGAA
1434548 AAAAAGAAA
1 AAAAAG-AA
1434557 AAAAAGAA
1 AAAAAGAA
1434565 AAAA
1 AAAA
1434569 GGAGTTCGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 18 0.69
9 8 0.31
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:1434553 original size:16 final size:17
Alignment explanation
Indices: 1434532--1434568 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1434522 ATTTAACCCC
*
1434532 AAAAAG-AAAGAAAGAA
1 AAAAAGAAAAAAAAGAA
1434548 AAAAAGAAAAAAAAGAA
1 AAAAAGAAAAAAAAGAA
1434565 AAAA
1 AAAA
1434569 GGAGTTCGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAAAGAA
Found at i:1440896 original size:20 final size:21
Alignment explanation
Indices: 1440856--1440896 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1440846 AGATAACAAT
* *
1440856 TTTTTTAAATAATTATTTAAA
1 TTTTTTAAATAAATATATAAA
1440877 TTTTTTAAA-AAATATATAAA
1 TTTTTTAAATAAATATATAAA
1440897 AAATTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTTTAAATAAATATATAAA
Found at i:1443674 original size:48 final size:48
Alignment explanation
Indices: 1443598--1443741 Score: 234
Period size: 48 Copynumber: 3.0 Consensus size: 48
1443588 AGCCTAACTC
* ** *
1443598 TAGTACTTCTTCAGTTCTTGTAGAAGATGCCAATGTCCTAGTTGGAGA
1 TAGTGCTTCTTCAGTTCTTGTAGAAGATGCTGATGTCCTTGTTGGAGA
1443646 TAGTGCTTCTTCAGTTCTTGTAGAAGATGCTGATGTCCTTGTTGGAGA
1 TAGTGCTTCTTCAGTTCTTGTAGAAGATGCTGATGTCCTTGTTGGAGA
* *
1443694 TGGTGCTTCTTCAGTTCTTGTAGAAGATGCTGATGTTCTTGTTGGAGA
1 TAGTGCTTCTTCAGTTCTTGTAGAAGATGCTGATGTCCTTGTTGGAGA
1443742 AGGCGAAGAA
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 90 1.00
ACGTcount: A:0.20, C:0.15, G:0.26, T:0.39
Consensus pattern (48 bp):
TAGTGCTTCTTCAGTTCTTGTAGAAGATGCTGATGTCCTTGTTGGAGA
Found at i:1443676 original size:24 final size:24
Alignment explanation
Indices: 1443649--1443724 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
1443639 TTGGAGATAG
1443649 TGCTTCTTCAGTTCTTGTAGAAGA
1 TGCTTCTTCAGTTCTTGTAGAAGA
** * * * * *
1443673 TGCTGATGTC-CTTGTTGGAGATGG
1 TGCTTCT-TCAGTTCTTGTAGAAGA
1443697 TGCTTCTTCAGTTCTTGTAGAAGA
1 TGCTTCTTCAGTTCTTGTAGAAGA
1443721 TGCT
1 TGCT
1443725 GATGTTCTTG
Statistics
Matches: 36, Mismatches: 14, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
23 2 0.06
24 32 0.89
25 2 0.06
ACGTcount: A:0.17, C:0.16, G:0.26, T:0.41
Consensus pattern (24 bp):
TGCTTCTTCAGTTCTTGTAGAAGA
Found at i:1443721 original size:27 final size:27
Alignment explanation
Indices: 1443643--1443722 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
1443633 TCCTAGTTGG
*
1443643 AGATAGTGCTTCTTCAGTTCTTGTAGA
1 AGATGGTGCTTCTTCAGTTCTTGTAGA
* * *
1443670 AGATGCTGATGTC--C--TTGTTG--G-
1 AGATGGTGCT-TCTTCAGTTCTTGTAGA
1443691 AGATGGTGCTTCTTCAGTTCTTGTAGA
1 AGATGGTGCTTCTTCAGTTCTTGTAGA
1443718 AGATG
1 AGATG
1443723 CTGATGTTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 16
0.62 0.11 0.26
Matches are distributed among these distances:
20 2 0.05
21 8 0.21
22 2 0.05
24 10 0.26
26 2 0.05
27 12 0.32
28 2 0.05
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.39
Consensus pattern (27 bp):
AGATGGTGCTTCTTCAGTTCTTGTAGA
Found at i:1443742 original size:24 final size:24
Alignment explanation
Indices: 1443667--1443743 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
1443657 CAGTTCTTGT
*
1443667 AGAAGATGCTGATGTCCTTGTTGG
1 AGAAGATGCTGATGTTCTTGTTGG
* * * * *
1443691 AGATGGTGCT--TCTTCAGTTCTTGT
1 AGAAGATGCTGATGTTC--TTGTTGG
1443715 AGAAGATGCTGATGTTCTTGTTGG
1 AGAAGATGCTGATGTTCTTGTTGG
1443739 AGAAG
1 AGAAG
1443744 GCGAAGAAGT
Statistics
Matches: 38, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
22 3 0.08
24 31 0.82
26 4 0.11
ACGTcount: A:0.21, C:0.12, G:0.31, T:0.36
Consensus pattern (24 bp):
AGAAGATGCTGATGTTCTTGTTGG
Found at i:1443882 original size:48 final size:48
Alignment explanation
Indices: 1443811--1443906 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
1443801 AGCCTAAGTC
* *
1443811 TAGTGCTTCTTCAGTTCTTGTAGAAGATGCTGATGTCCTTGCTGGAGA
1 TAGTGCTTCTTCAGTTCCTGTAGAAGATGCTGATGTCCTGGCTGGAGA
*
1443859 TAGTGCTTCTTCAGTTCCTGTAGAAGATGCTGATGTCCTGGTTGGAGA
1 TAGTGCTTCTTCAGTTCCTGTAGAAGATGCTGATGTCCTGGCTGGAGA
1443907 AGGCGAAGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.36
Consensus pattern (48 bp):
TAGTGCTTCTTCAGTTCCTGTAGAAGATGCTGATGTCCTGGCTGGAGA
Found at i:1447950 original size:64 final size:64
Alignment explanation
Indices: 1447870--1447989 Score: 195
Period size: 64 Copynumber: 1.9 Consensus size: 64
1447860 CATCACTTTT
* *
1447870 ATAGGATATTTGTGAAGAGGGAGATGGCTTAATGTGGTCGTGTCATATATATTTGAAGTTGTGC
1 ATAGGATATTTCTGAAGAGGGAGATGGCTTAATGTGGTCATGTCATATATATTTGAAGTTGTGC
* * *
1447934 ATAGGATATTTCTGAAGATGGAGATGGCTTTATGTGGTCATGTCATATATGTTTGA
1 ATAGGATATTTCTGAAGAGGGAGATGGCTTAATGTGGTCATGTCATATATATTTGA
1447990 CGTTCAAAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.38
Consensus pattern (64 bp):
ATAGGATATTTCTGAAGAGGGAGATGGCTTAATGTGGTCATGTCATATATATTTGAAGTTGTGC
Found at i:1460541 original size:14 final size:15
Alignment explanation
Indices: 1460523--1460574 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
1460513 AAAATATAAA
1460523 ATTAAAAATAATTTT
1 ATTAAAAATAATTTT
1460538 -TTAAAAA-AACTTTT
1 ATTAAAAATAA-TTTT
* *
1460552 ATAAAAAATAATTCAT
1 ATTAAAAATAATT-TT
1460568 ATTAAAA
1 ATTAAAA
1460575 TTTAAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
13 2 0.07
14 11 0.37
15 8 0.27
16 9 0.30
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAAAAATAATTTT
Found at i:1463990 original size:2 final size:2
Alignment explanation
Indices: 1463985--1464012 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1463975 CATTTTTTAC
1463985 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
1464013 TTTCAAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1466794 original size:273 final size:275
Alignment explanation
Indices: 1466299--1466847 Score: 922
Period size: 273 Copynumber: 2.0 Consensus size: 275
1466289 TTTCTTTTGA
*
1466299 AGAAGGGAAAATTTATTGCAAGTCTAATCATCAATTTAATAATCGGTAGTTCTCTTCTTGAAACC
1 AGAAGGGAAAATTTATTGCAAGTCTAATCATAAATTTAATAATCGGTAGTTCTCTTCTTGAAACC
* * * *
1466364 GTAATCAGCCACTAAATATGCCAATAGTTATGGAAAGCTCAATGTGTCTATCAATTAAAATATTA
66 ATAATCAGCCACCAAATATGCCAATAGTTATGAAAAGCCCAATGTGTCTATCAATTAAAATATTA
* * * *
1466429 GAATCTATTAGTACCAATCACTGAAATATGCAGACATATAAAAGGAGTCTCTACCAAAGTCATGG
131 GAATCTATTAGTACCAACCACTGAAATATGCAGACATATAAAAAGAGGCTCTACCAAAGCCATGG
* *
1466494 CTTGTAAGCTTTGGGAGTATAAACGTTGATATCTAGTTGGTCGTCTTTCATCGATCCAATTTGCT
196 CTTGTAAGCTTTGGCAGTATAAACGTTGATATCTAGTTGGTCGTCTTTAATCGATCCAATTTGCT
* *
1466559 TCCAATATGCGTTAC
261 TCCAAGATGCATTAC
* *
1466574 AGAAGGGAAAATTTATTGCAAGTCTAATGATAAATTTACTAATCGGTAGTTCTCTTCTTGAAACC
1 AGAAGGGAAAATTTATTGCAAGTCTAATCATAAATTTAATAATCGGTAGTTCTCTTCTTGAAACC
1466639 ATAATCAGCCACCAAATATGCCAATAGTTAT-AAAAGCCCAATGTGTCTATCAATT-AAATATTA
66 ATAATCAGCCACCAAATATGCCAATAGTTATGAAAAGCCCAATGTGTCTATCAATTAAAATATTA
1466702 GAATCTATTAGTACCAACCACTGAAATATGCAGACATATAAAAAGAGGCTCTACCAAAGCCATGG
131 GAATCTATTAGTACCAACCACTGAAATATGCAGACATATAAAAAGAGGCTCTACCAAAGCCATGG
* * *
1466767 CTTGTAAGCTTTGGCAGTATTAACGTTGATATCTAGTTGGTCGTTTTTAATCTATCCAATTTGCT
196 CTTGTAAGCTTTGGCAGTATAAACGTTGATATCTAGTTGGTCGTCTTTAATCGATCCAATTTGCT
1466832 TCCAAGATGCATTAC
261 TCCAAGATGCATTAC
1466847 A
1 A
1466848 ATCAGAAAAC
Statistics
Matches: 256, Mismatches: 18, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
273 143 0.56
274 22 0.09
275 91 0.36
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (275 bp):
AGAAGGGAAAATTTATTGCAAGTCTAATCATAAATTTAATAATCGGTAGTTCTCTTCTTGAAACC
ATAATCAGCCACCAAATATGCCAATAGTTATGAAAAGCCCAATGTGTCTATCAATTAAAATATTA
GAATCTATTAGTACCAACCACTGAAATATGCAGACATATAAAAAGAGGCTCTACCAAAGCCATGG
CTTGTAAGCTTTGGCAGTATAAACGTTGATATCTAGTTGGTCGTCTTTAATCGATCCAATTTGCT
TCCAAGATGCATTAC
Found at i:1466909 original size:31 final size:30
Alignment explanation
Indices: 1466874--1466977 Score: 90
Period size: 31 Copynumber: 3.3 Consensus size: 30
1466864 GCAACTATAT
1466874 TTTTACATGCCATTTAGCAAATAATGAATAA
1 TTTTAC-TGCCATTTAGCAAATAATGAATAA
*
1466905 TTTTATCTG-CA--TATC-AATACATGCAACTACA
1 TTTTA-CTGCCATTTAGCAAATA-ATG-AA-TA-A
1466936 TATTTACTTGCCATTTAGCAAATAATGAATAA
1 T-TTTAC-TGCCATTTAGCAAATAATGAATAA
1466968 TTTTATCTGC
1 TTTTA-CTGC
1466978 ATATATTGTA
Statistics
Matches: 59, Mismatches: 2, Indels: 24
0.69 0.02 0.28
Matches are distributed among these distances:
27 4 0.07
28 6 0.10
29 2 0.03
30 4 0.07
31 17 0.29
32 10 0.17
33 4 0.07
34 2 0.03
35 6 0.10
36 4 0.07
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (30 bp):
TTTTACTGCCATTTAGCAAATAATGAATAA
Found at i:1466957 original size:63 final size:63
Alignment explanation
Indices: 1466858--1466981 Score: 221
Period size: 63 Copynumber: 2.0 Consensus size: 63
1466848 ATCAGAAAAC
* *
1466858 ATACATGCAACTATATTTTTACATGCCATTTAGCAAATAATGAATAATTTTATCTGCATATCA
1 ATACATGCAACTACATATTTACATGCCATTTAGCAAATAATGAATAATTTTATCTGCATATCA
*
1466921 ATACATGCAACTACATATTTACTTGCCATTTAGCAAATAATGAATAATTTTATCTGCATAT
1 ATACATGCAACTACATATTTACATGCCATTTAGCAAATAATGAATAATTTTATCTGCATAT
1466982 ATTGTAGCGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (63 bp):
ATACATGCAACTACATATTTACATGCCATTTAGCAAATAATGAATAATTTTATCTGCATATCA
Found at i:1470269 original size:21 final size:21
Alignment explanation
Indices: 1470245--1470285 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1470235 TTTGTGTTTG
1470245 TAAAAAATGATAATTTTTTTA
1 TAAAAAATGATAATTTTTTTA
*
1470266 TAAAAAATGATGATTTTTTT
1 TAAAAAATGATAATTTTTTT
1470286 TGTTTGTAAA
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:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (21 bp):
TAAAAAATGATAATTTTTTTA
Found at i:1470304 original size:26 final size:25
Alignment explanation
Indices: 1470258--1470306 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
1470248 AAAATGATAA
*
1470258 TTTTTTTATAAAAAATGATGATTTT
1 TTTTTTTATAAAAAATAATGATTTT
* *
1470283 TTTTGTTTGTAAAAATTAATGATT
1 TTTT-TTTATAAAAAATAATGATT
1470307 AATTTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (25 bp):
TTTTTTTATAAAAAATAATGATTTT
Found at i:1474817 original size:28 final size:29
Alignment explanation
Indices: 1474777--1474855 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 29
1474767 ACAAAAGCCA
* *
1474777 CCTTTTGTGTTTGTAAAAAATAGTGA-TT
1 CCTTTTTTGTTTGTCAAAAATAGTGAGTT
1474805 CCTTTTTTGTTTGTCAAAAATAGT-AGTT
1 CCTTTTTTGTTTGTCAAAAATAGTGAGTT
*
1474833 --TTTTTTGTTTGTCAAAATTAGTG
1 CCTTTTTTGTTTGTCAAAAATAGTG
1474856 GCTAATTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
26 21 0.46
27 1 0.02
28 24 0.52
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.51
Consensus pattern (29 bp):
CCTTTTTTGTTTGTCAAAAATAGTGAGTT
Found at i:1474864 original size:26 final size:26
Alignment explanation
Indices: 1474809--1474864 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
1474799 GTGATTCCTT
* **
1474809 TTTTGTTTGTCAAAAATAGTAGTTTT
1 TTTTGTTTGTCAAAAATAGTAGCTAA
* *
1474835 TTTTGTTTGTCAAAATTAGTGGCTAA
1 TTTTGTTTGTCAAAAATAGTAGCTAA
1474861 TTTT
1 TTTT
1474865 TATTATAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.54
Consensus pattern (26 bp):
TTTTGTTTGTCAAAAATAGTAGCTAA
Found at i:1475080 original size:22 final size:22
Alignment explanation
Indices: 1475052--1475097 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1475042 TAATAACTTA
*
1475052 CAAATAAAATATCTGTTGATTC
1 CAAATAAAATATCTGTTAATTC
1475074 CAAATAAAATATCTGTTAATTC
1 CAAATAAAATATCTGTTAATTC
1475096 CA
1 CA
1475098 TCGTACCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (22 bp):
CAAATAAAATATCTGTTAATTC
Found at i:1477104 original size:15 final size:15
Alignment explanation
Indices: 1477062--1477104 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1477052 ACATGATTAA
*
1477062 ACATGTGTTAGTGAT
1 ACATGTGTTAGTTAT
* *
1477077 ACATATGTTAGTTCT
1 ACATGTGTTAGTTAT
1477092 ACATGTGTTAGTT
1 ACATGTGTTAGTT
1477105 GTTAGTTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (15 bp):
ACATGTGTTAGTTAT
Found at i:1481320 original size:12 final size:14
Alignment explanation
Indices: 1481302--1481336 Score: 56
Period size: 12 Copynumber: 2.6 Consensus size: 14
1481292 GTTCTTAAAA
1481302 AATTATTTAT-ATT
1 AATTATTTATAATT
1481315 -ATTATTTATAATT
1 AATTATTTATAATT
1481328 AATTATTTA
1 AATTATTTA
1481337 ATATCTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 9 0.45
13 3 0.15
14 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AATTATTTATAATT
Found at i:1501856 original size:2 final size:2
Alignment explanation
Indices: 1501849--1501880 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1501839 CACTACAACA
*
1501849 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1501881 CAGCTTATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1504004 original size:14 final size:15
Alignment explanation
Indices: 1503967--1504005 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1503957 ACATATGCCT
1503967 TACACATGTACAAGG
1 TACACATGTACAAGG
* *
1503982 TACATATGTAGAA-G
1 TACACATGTACAAGG
1503996 TACACATGTA
1 TACACATGTA
1504006 TAAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (15 bp):
TACACATGTACAAGG
Found at i:1504177 original size:20 final size:20
Alignment explanation
Indices: 1504123--1504177 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 20
1504113 TAAAATAATA
* *
1504123 TTTTATTTAAATTAAATTAT
1 TTTTAATTAAATTTAATTAT
**
1504143 TAAT-ATT-AATATTAATTAT
1 TTTTAATTAAAT-TTAATTAT
1504162 TTTTAATTAAATTTAA
1 TTTTAATTAAATTTAA
1504178 ATTTAAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
18 3 0.12
19 11 0.42
20 9 0.35
21 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTAATTAAATTTAATTAT
Found at i:1504307 original size:17 final size:17
Alignment explanation
Indices: 1504280--1504320 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1504270 AAAATATTAT
1504280 ATATTTA-AATTTTTTAA
1 ATATTTATAA-TTTTTAA
1504297 A-ATTTATAATTTTTAA
1 ATATTTATAATTTTTAA
1504313 ATATTTAT
1 ATATTTAT
1504321 TACTAACGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATTTATAATTTTTAA
Found at i:1506676 original size:33 final size:33
Alignment explanation
Indices: 1506636--1506702 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1506626 TTAGTTGACA
*
1506636 TTTTCTTTCCCAATTTTTTTGTTACTATCTTAG
1 TTTTCTTTCCCAATTTTTTTGTTACAATCTTAG
1506669 TTTTCTTTCCCAATTTTTTTGTTACAATCTTAG
1 TTTTCTTTCCCAATTTTTTTGTTACAATCTTAG
1506702 T
1 T
1506703 CTAACCAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.16, C:0.18, G:0.06, T:0.60
Consensus pattern (33 bp):
TTTTCTTTCCCAATTTTTTTGTTACAATCTTAG
Found at i:1510575 original size:19 final size:19
Alignment explanation
Indices: 1510543--1510581 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1510533 AAGATTATAC
1510543 ATCATTTATAATATTAATA
1 ATCATTTATAATATTAATA
1510562 ATCATTTA-ATATATTAATA
1 ATCATTTATA-ATATTAATA
1510581 A
1 A
1510582 AATATTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
ATCATTTATAATATTAATA
Found at i:1511572 original size:17 final size:19
Alignment explanation
Indices: 1511528--1511572 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1511518 TATTTATACA
1511528 TATATTTAAAAAATAATAT
1 TATATTTAAAAAATAATAT
*
1511547 TAT-TATTAAAATA-AAT-T
1 TATAT-TTAAAAAATAATAT
1511564 TATATTTAA
1 TATATTTAA
1511573 TATATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 8 0.35
18 5 0.22
19 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATTTAAAAAATAATAT
Found at i:1511655 original size:21 final size:21
Alignment explanation
Indices: 1511608--1511656 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1511598 TTAATAAAAT
* *
1511608 ATATAATATTATTTTTATTTA
1 ATATAAAATTATTTATATTTA
*
1511629 AAATAAAATTATTTATATTTA
1 ATATAAAATTATTTATATTTA
*
1511650 TTATAAA
1 ATATAAA
1511657 TTTTTTAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATAAAATTATTTATATTTA
Found at i:1511657 original size:25 final size:26
Alignment explanation
Indices: 1511561--1511656 Score: 76
Period size: 25 Copynumber: 3.7 Consensus size: 26
1511551 ATTAAAATAA
* **
1511561 ATTTATATTTAATAT-ATTTAAAATGT
1 ATTTATATTTATTATAAAATAAAAT-T
1511587 ATGTTATA-TTATTAATAAAATATATAA-T
1 AT-TTATATTTATT-ATAAAATA-A-AATT
*
1511615 A-TTATTTTTATT-TAAAATAAAATT
1 ATTTATATTTATTATAAAATAAAATT
1511639 ATTTATATTTATTATAAA
1 ATTTATATTTATTATAAA
1511657 TTTTTTAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
23 2 0.04
24 3 0.05
25 17 0.30
26 14 0.25
27 12 0.21
28 5 0.09
29 1 0.02
30 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
ATTTATATTTATTATAAAATAAAATT
Found at i:1515242 original size:19 final size:19
Alignment explanation
Indices: 1515220--1515310 Score: 51
Period size: 21 Copynumber: 4.6 Consensus size: 19
1515210 ACCCACCATT
1515220 AAAAAATAAAATATTATTA
1 AAAAAATAAAATATTATTA
* * *
1515239 AAAATTATTATAATATTTTTA
1 AAAA--AATAAAATATTATTA
* *
1515260 AATTTAATTAAAATA--ATTA
1 AA--AAAATAAAATATTATTA
* *
1515279 ATTAAAAATATAATATTTTTA
1 A--AAAAATAAAATATTATTA
1515300 AAAAAATAAAA
1 AAAAAATAAAA
1515311 ATAAAACATT
Statistics
Matches: 53, Mismatches: 11, Indels: 16
0.66 0.14 0.20
Matches are distributed among these distances:
19 25 0.47
21 27 0.51
23 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAAATAAAATATTATTA
Found at i:1515247 original size:10 final size:11
Alignment explanation
Indices: 1515226--1515285 Score: 54
Period size: 10 Copynumber: 5.5 Consensus size: 11
1515216 CATTAAAAAA
1515226 TAAAATATTAT
1 TAAAATATTAT
1515237 TAAAA-ATTAT
1 TAAAATATTAT
*
1515247 TATAATATT-T
1 TAAAATATTAT
*
1515257 TTAAAT-TTAAT
1 TAAAATATT-AT
1515268 TAAAATAATTAAT
1 TAAAAT-ATT-AT
1515281 TAAAA
1 TAAAA
1515286 ATATAATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 2 0.05
10 14 0.35
11 14 0.35
13 10 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TAAAATATTAT
Found at i:1515255 original size:21 final size:22
Alignment explanation
Indices: 1515226--1515292 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 22
1515216 CATTAAAAAA
1515226 TAAAATATTATTAAAAATT-AT
1 TAAAATATTATTAAAAATTAAT
* * *
1515247 TATAATATT-TTTAAATTTAAT
1 TAAAATATTATTAAAAATTAAT
1515268 TAAAATAATTAATTAAAAATATAAT
1 TAAAAT-ATT-ATTAAAAAT-TAAT
1515293 ATTTTTAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 7 0.20
21 15 0.43
22 3 0.09
24 6 0.17
25 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAAATATTATTAAAAATTAAT
Found at i:1516564 original size:3 final size:3
Alignment explanation
Indices: 1516556--1516585 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1516546 GCGCCTGTCC
1516556 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
1516586 ATTGGCCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
GTT
Found at i:1518997 original size:2 final size:2
Alignment explanation
Indices: 1518990--1519020 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1518980 TCACCATAAT
1518990 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1519021 CAGTTCCAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1519524 original size:2 final size:2
Alignment explanation
Indices: 1519517--1519553 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1519507 AACGTAAAGG
1519517 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1519554 GTTTAAGGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1519828 original size:2 final size:2
Alignment explanation
Indices: 1519821--1519854 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1519811 GATTGAGAAT
1519821 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1519855 AATTTTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1520128 original size:18 final size:18
Alignment explanation
Indices: 1520105--1520140 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1520095 CATTTCATGA
1520105 CCATGCTTGATTAGATAT
1 CCATGCTTGATTAGATAT
1520123 CCATGCTTGATTAGATAT
1 CCATGCTTGATTAGATAT
1520141 TCTTTCTTAA
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:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (18 bp):
CCATGCTTGATTAGATAT
Found at i:1524669 original size:2 final size:2
Alignment explanation
Indices: 1524662--1524708 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1524652 TTTAACATCT
1524662 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1524704 TA TA T
1 TA TA T
1524709 TATGTCCATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1526238 original size:16 final size:16
Alignment explanation
Indices: 1526180--1526445 Score: 110
Period size: 16 Copynumber: 15.8 Consensus size: 16
1526170 ATCAATCAAA
* *
1526180 TTAAATTTGAAATTAAC
1 TTAAATTT-AAAATAAT
* * *
1526197 TCAAATTTGAAATAAG
1 TTAAATTTAAAATAAT
* *
1526213 TTAGAGTTAAAATAAT
1 TTAAATTTAAAATAAT
* *
1526229 TTAAATTTAAATTGAT
1 TTAAATTTAAAATAAT
* *
1526245 TTGAATTCGTTAAATTAGTAT
1 TT-AAAT--TTAAAATA--AT
* *
1526266 GTTAAATTT-TATTAAT
1 -TTAAATTTAAAATAAT
* *
1526282 TTAAAAATTAAATTTAA-
1 TT-AAATTTAAA-ATAAT
* *
1526299 TT-AACTTAAAATCGAT
1 TTAAATTTAAAAT-AAT
*
1526315 TCAAATTTAAAATAAT
1 TTAAATTTAAAATAAT
*
1526331 ATAAATTTAATTAACTCAAAT
1 TTAAATTTAA--AA-T--AAT
*
1526352 ATTAAATTT-AATTAAT
1 -TTAAATTTAAAATAAT
*
1526368 TAAAATTTAAAATAAT
1 TTAAATTTAAAATAAT
*
1526384 TTAAAATTAAAATAAT
1 TTAAATTTAAAATAAT
*
1526400 TTAACA-TAAAAATAAT
1 TTAA-ATTTAAAATAAT
*
1526416 TTAAATTTAAAAATTAT
1 TTAAATTT-AAAATAAT
1526433 TTAAATTTTAAAA
1 TTAAA-TTTAAAA
1526446 ATGACCGAGT
Statistics
Matches: 190, Mismatches: 36, Indels: 46
0.70 0.13 0.17
Matches are distributed among these distances:
14 1 0.01
15 18 0.09
16 89 0.47
17 39 0.21
18 14 0.07
19 11 0.06
21 9 0.05
22 9 0.05
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (16 bp):
TTAAATTTAAAATAAT
Found at i:1526380 original size:22 final size:22
Alignment explanation
Indices: 1526267--1526378 Score: 87
Period size: 22 Copynumber: 5.2 Consensus size: 22
1526257 AATTAGTATG
* *
1526267 TTAAATTTTATTAATTTAAAA-A
1 TTAAATTTAATTAA-CTAAAATA
1526289 TTAAATTTAATTAACTTAAAATCGA
1 TTAAATTTAATTAAC-TAAAAT--A
1526314 TTCAAATTTAA--AA-T--AATA
1 TT-AAATTTAATTAACTAAAATA
*
1526332 -TAAATTTAATTAACTCAAATA
1 TTAAATTTAATTAACTAAAATA
*
1526353 TTAAATTTAATTAATTAAAAT-
1 TTAAATTTAATTAACTAAAATA
1526374 TTAAA
1 TTAAA
1526379 ATAATTTAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 23
0.74 0.04 0.23
Matches are distributed among these distances:
16 8 0.11
17 1 0.01
18 3 0.04
19 1 0.01
20 3 0.04
21 9 0.12
22 37 0.49
24 2 0.03
25 3 0.04
26 8 0.11
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (22 bp):
TTAAATTTAATTAACTAAAATA
Found at i:1529756 original size:37 final size:37
Alignment explanation
Indices: 1529701--1529781 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
1529691 TGGATTGACC
* *
1529701 AATCCACTATGATTGTTAGTATTTGGGTGACTTGGTT
1 AATCCACTATAATTGTTAGTATTTGAGTGACTTGGTT
* * **
1529738 AATCTACTATAATTGTTAGTATTTGAGTGGCTTGGCC
1 AATCCACTATAATTGTTAGTATTTGAGTGACTTGGTT
1529775 AATCCAC
1 AATCCAC
1529782 GAAAATTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (37 bp):
AATCCACTATAATTGTTAGTATTTGAGTGACTTGGTT
Found at i:1536309 original size:3 final size:3
Alignment explanation
Indices: 1536303--1536335 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1536293 TTTTTTTTTA
1536303 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1536336 TGTTTGTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1536681 original size:16 final size:15
Alignment explanation
Indices: 1536641--1536687 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
1536631 GACTCGAAAG
1536641 ATTAATTTAAAATTATT
1 ATTAATTT-AAATT-TT
*
1536658 ATTTATTTAAATTTT
1 ATTAATTTAAATTTT
1536673 ATATAATTTAAATTT
1 AT-TAATTTAAATTT
1536688 AAATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 16 0.59
17 7 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTAATTTAAATTTT
Found at i:1536722 original size:20 final size:18
Alignment explanation
Indices: 1536662--1536722 Score: 50
Period size: 22 Copynumber: 3.1 Consensus size: 18
1536652 ATTATTATTT
1536662 ATTTAAATTTTATATAATTTAA
1 ATTTAAATTTTA-AT-A--TAA
**
1536684 ATTTAAATTTTTTTATAA
1 ATTTAAATTTTAATATAA
1536702 ATATTAAATATTTAATATAA
1 AT-TTAAAT-TTTAATATAA
1536722 A
1 A
1536723 GTGTAAGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 5 0.15
19 6 0.18
20 10 0.30
21 1 0.03
22 11 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTAAATTTTAATATAA
Found at i:1537571 original size:7 final size:7
Alignment explanation
Indices: 1537559--1537591 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
1537549 GCTCTAATAT
1537559 TTTTAAA
1 TTTTAAA
1537566 TTTTAAA
1 TTTTAAA
1537573 TTTTAAA
1 TTTTAAA
1537580 TTTTAATA
1 TTTTAA-A
1537588 TTTT
1 TTTT
1537592 CTAATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.80
8 5 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:1537578 original size:14 final size:15
Alignment explanation
Indices: 1537553--1537623 Score: 65
Period size: 15 Copynumber: 4.6 Consensus size: 15
1537543 ATCATCGCTC
1537553 TAATATTTTTAAATTT
1 TAATA-TTTTAAATTT
1537569 TAA-ATTTTAAATTT
1 TAATATTTTAAATTT
*
1537583 TAATATTTTCTAATTT
1 TAATATTTT-AAATTT
*
1537599 T-TTATTTTAAAATTAT
1 TAATATTTT-AAATT-T
*
1537615 TATTATTTT
1 TAATATTTT
1537624 TATATAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
14 13 0.28
15 16 0.34
16 11 0.23
17 7 0.15
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (15 bp):
TAATATTTTAAATTT
Found at i:1537589 original size:30 final size:32
Alignment explanation
Indices: 1537553--1537625 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 32
1537543 ATCATCGCTC
1537553 TAATATTTTTAAATTTTAAATTTT-AAATT-T
1 TAATATTTTTAAATTTTAAATTTTAAAATTAT
**
1537583 TAATATTTTCT-AATTTTTTATTTTAAAATTAT
1 TAATATTTT-TAAATTTTAAATTTTAAAATTAT
*
1537615 TATTATTTTTA
1 TAATATTTTTA
1537626 TATAAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 20 0.56
31 7 0.19
32 9 0.25
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (32 bp):
TAATATTTTTAAATTTTAAATTTTAAAATTAT
Found at i:1538592 original size:2 final size:2
Alignment explanation
Indices: 1538585--1538625 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
1538575 ATATTCATGC
* *
1538585 AT AT AT AT AT AT AT AT AT AT -T AT AG AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1538626 GAAAAGTCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1539824 original size:22 final size:21
Alignment explanation
Indices: 1539799--1539864 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
1539789 AAAATGTTTT
*
1539799 ATTTTATTATTGTTAATATTAA
1 ATTTTATAATT-TTAATATTAA
* *
1539821 ATTTTA-CATTTATAAAATTAA
1 ATTTTATAATTT-TAATATTAA
1539842 TATTTTATAATTTTAATATTAA
1 -ATTTTATAATTTTAATATTAA
1539864 A
1 A
1539865 AATAAAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.03
21 12 0.32
22 20 0.54
23 4 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTTTATAATTTTAATATTAA
Found at i:1545586 original size:12 final size:13
Alignment explanation
Indices: 1545558--1545590 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
1545548 GGGAAGAGAT
1545558 TTGAAACTTGAAAA
1 TTGAAA-TTGAAAA
1545572 TTGAAATTG-AAA
1 TTGAAATTGAAAA
1545584 TTGAAAT
1 TTGAAAT
1545591 AATGATTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 3 0.16
14 6 0.32
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.33
Consensus pattern (13 bp):
TTGAAATTGAAAA
Found at i:1545750 original size:4 final size:4
Alignment explanation
Indices: 1545741--1545781 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
1545731 AGTTCACGTG
* * *
1545741 ATAT ATAT ATAT ATAT ATAT ATAT ACAT ACAT ATAC ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
1545782 ATCAATGCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (4 bp):
ATAT
Found at i:1545752 original size:6 final size:6
Alignment explanation
Indices: 1545741--1545781 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
1545731 AGTTCACGTG
* * *
1545741 ATATAT ATATAT ATATAT ATATAT ACATAC ATATAC ATATA
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATA
1545782 ATCAATGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (6 bp):
ATATAT
Found at i:1545756 original size:10 final size:10
Alignment explanation
Indices: 1545741--1545781 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
1545731 AGTTCACGTG
*
1545741 ATATATATAT
1 ATATACATAT
*
1545751 ATATATATAT
1 ATATACATAT
*
1545761 ATATACATAC
1 ATATACATAT
1545771 ATATACATAT
1 ATATACATAT
1545781 A
1 A
1545782 ATCAATGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATACATAT
Found at i:1547606 original size:13 final size:13
Alignment explanation
Indices: 1547588--1547634 Score: 67
Period size: 13 Copynumber: 3.4 Consensus size: 13
1547578 TGTTGATTTT
1547588 AAATAAATTATTA
1 AAATAAATTATTA
1547601 AAATAATATTAATTAA
1 AAATAA-ATT-ATT-A
1547617 AAATAAATTATTA
1 AAATAAATTATTA
1547630 AAATA
1 AAATA
1547635 TTATTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 12 0.39
14 6 0.19
15 6 0.19
16 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATAAATTATTA
Found at i:1547629 original size:14 final size:14
Alignment explanation
Indices: 1547588--1547632 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
1547578 TGTTGATTTT
1547588 AAATAAATTATT-A
1 AAATAAATTATTAA
1547601 AAATAATATTAATTAA
1 AAATAA-ATT-ATTAA
1547617 AAATAAATTATTAA
1 AAATAAATTATTAA
1547631 AA
1 AA
1547633 TATTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.21
14 10 0.34
15 6 0.21
16 7 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATAAATTATTAA
Found at i:1547640 original size:14 final size:14
Alignment explanation
Indices: 1547594--1547642 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1547584 TTTTAAATAA
*
1547594 ATTATTAAAATAAT
1 ATTATTAAAATATT
*
1547608 ATTAATTAAAA-ATAA
1 ATT-ATTAAAATAT-T
1547623 ATTATTAAAATATT
1 ATTATTAAAATATT
1547637 ATTATT
1 ATTATT
1547643 TTGATTTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTATTAAAATATT
Found at i:1547768 original size:26 final size:29
Alignment explanation
Indices: 1547739--1547796 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
1547729 AGCTTTAGTG
1547739 ATTTTTAT-ATAA-ATTAATT-GA-TTATT
1 ATTTTTATAATAATATT-ATTAGAGTTATT
*
1547765 ATTTTTTTAATAATATTATTAGAGTTATT
1 ATTTTTATAATAATATTATTAGAGTTATT
1547794 ATT
1 ATT
1547797 ATATTGATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 7 0.26
27 7 0.26
28 5 0.19
29 8 0.30
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (29 bp):
ATTTTTATAATAATATTATTAGAGTTATT
Found at i:1547793 original size:29 final size:28
Alignment explanation
Indices: 1547740--1547796 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
1547730 GCTTTAGTGA
1547740 TTTTTATATAAATTAATTGATTATTATT
1 TTTTTATATAAATTAATTGATTATTATT
1547768 TTTTTA-ATAATATT-ATTAGAGTTATTATT
1 TTTTTATATAA-ATTAATT-GA-TTATTATT
1547797 ATATTGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 7 0.27
28 11 0.42
29 8 0.31
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (28 bp):
TTTTTATATAAATTAATTGATTATTATT
Found at i:1547882 original size:19 final size:19
Alignment explanation
Indices: 1547842--1547887 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
1547832 TTTTTTAAAA
* *
1547842 ATTAATAAAAGATTATACT
1 ATTAATAAAAAATCATACT
*
1547861 ATTAATAAAAAATCATATT
1 ATTAATAAAAAATCATACT
1547880 ATT-ATAAA
1 ATTAATAAA
1547888 TAGTTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (19 bp):
ATTAATAAAAAATCATACT
Found at i:1548317 original size:38 final size:36
Alignment explanation
Indices: 1548228--1548319 Score: 94
Period size: 40 Copynumber: 2.4 Consensus size: 36
1548218 GTAATTAGAT
* *
1548228 AATTATAATTTAAATTTTAACATAATTAGATGATTATA
1 AATTA-AA-TTAAATTTTAAAATAATTAAATGATTATA
* *
1548266 ATTCTTAATTTAAATTTTAAAAAATAATTAAATGATTATA
1 A--ATTAAATTAAATTTT--AAAATAATTAAATGATTATA
1548306 AATTAAATTAAATT
1 AATTAAATTAAATT
1548320 AAATATTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
38 21 0.48
39 1 0.02
40 22 0.50
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (36 bp):
AATTAAATTAAATTTTAAAATAATTAAATGATTATA
Found at i:1548335 original size:43 final size:42
Alignment explanation
Indices: 1548227--1548349 Score: 119
Period size: 43 Copynumber: 3.0 Consensus size: 42
1548217 CGTAATTAGA
* * *
1548227 TAATTATAATTTAA-ATTTTAACATAATTAGATGATTAT-AAT
1 TAATTA-AATTAAATATTTTAAAATAATTAAATGATTATAAAT
* * *
1548268 T-CTTAATTTAAAT-TTTAAAAAATAATTAAATGATTATAAAT
1 TAATTAAATTAAATATTT-TAAAATAATTAAATGATTATAAAT
* *
1548309 TAAATTAAATTAAATATTTTAAAATAATTATATAATTATAA
1 T-AATTAAATTAAATATTTTAAAATAATTAAATGATTATAA
1548350 TCTAAAAAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
39 8 0.12
40 20 0.31
41 5 0.08
43 29 0.45
44 3 0.05
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (42 bp):
TAATTAAATTAAATATTTTAAAATAATTAAATGATTATAAAT
Found at i:1548714 original size:18 final size:18
Alignment explanation
Indices: 1548691--1548744 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
1548681 ATTAAATTAA
*
1548691 TTTTAA-ATATTTTATAAT
1 TTTTAATATAATTTA-AAT
1548709 TTTTAATATAATTTAAA-
1 TTTTAATATAATTTAAAT
1548726 -TTT-ATATAA-TTAAAT
1 TTTTAATATAATTTAAAT
1548741 TTTT
1 TTTT
1548745 TATTTTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 5 0.16
15 6 0.19
16 6 0.19
18 8 0.25
19 7 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTAATATAATTTAAAT
Found at i:1548740 original size:14 final size:15
Alignment explanation
Indices: 1548714--1548742 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1548704 ATAATTTTTA
1548714 ATATAATTTAAATTT
1 ATATAATTTAAATTT
1548729 ATATAA-TTAAATTT
1 ATATAATTTAAATTT
1548743 TTTATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATAATTTAAATTT
Found at i:1548955 original size:16 final size:18
Alignment explanation
Indices: 1548919--1548960 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
1548909 TAAATATAAT
1548919 TATATT-ATTTAATTTAA
1 TATATTAATTTAATTTAA
1548936 -ATATTAATTT-A-TTAA
1 TATATTAATTTAATTTAA
1548951 TATATTAATT
1 TATATTAATT
1548961 ATATAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 4 0.17
16 15 0.65
17 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATTAATTTAATTTAA
Found at i:1549512 original size:30 final size:30
Alignment explanation
Indices: 1549477--1549540 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 30
1549467 AAGAACAATA
1549477 TTTTGCAACATTTTTCAAACACG-ATTTGGT
1 TTTTGCAACATTTTTCAAACACGAATTT-GT
*
1549507 TTTTGCAATATTTTTCAAACACGAATTTGT
1 TTTTGCAACATTTTTCAAACACGAATTTGT
1549537 TTTT
1 TTTT
1549541 AAGTTGAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.88
31 4 0.12
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (30 bp):
TTTTGCAACATTTTTCAAACACGAATTTGT
Found at i:1549666 original size:24 final size:23
Alignment explanation
Indices: 1549639--1549717 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 23
1549629 TCGAATTAAA
1549639 AAAATTATAAAATAATAAATTTTT
1 AAAA-TATAAAATAATAAATTTTT
*
1549663 AAAAATATAAATTAAT--ATTTTT
1 -AAAATATAAAATAATAAATTTTT
*
1549685 -ATAT-TAAAAT-ATAATATTTTT
1 AAAATATAAAATAATAA-ATTTTT
*
1549706 TAAATATAAAAT
1 AAAATATAAAAT
1549718 TTTATTTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
18 2 0.04
19 5 0.11
20 3 0.07
21 6 0.13
22 9 0.20
23 6 0.13
24 10 0.22
25 4 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATATAAAATAATAAATTTTT
Found at i:1549724 original size:42 final size:44
Alignment explanation
Indices: 1549646--1549730 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 44
1549636 AAAAAAATTA
1549646 TAAAATAATAAATTTTTAAAAATATAAATTAATATTTT-TATAT
1 TAAAATAATAAATTTTTAAAAATATAAATTAATATTTTATATAT
* *
1549689 TAAAAT-ATAATATTTTT-TAAATATAAAATT-TTATTTTATATA
1 TAAAATAATAA-ATTTTTAAAAATAT-AAATTAATATTTTATATA
1549731 ACTTTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
42 16 0.43
43 21 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (44 bp):
TAAAATAATAAATTTTTAAAAATATAAATTAATATTTTATATAT
Found at i:1549789 original size:21 final size:21
Alignment explanation
Indices: 1549748--1549789 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1549738 ATTTTTAAAT
*
1549748 TTTTAAATATTTACATGATAA
1 TTTTAAATATTTACATAATAA
1549769 TTTTAAATATTTTA-ATAATAA
1 TTTTAAATA-TTTACATAATAA
1549790 AATATACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTTAAATATTTACATAATAA
Found at i:1552576 original size:2 final size:2
Alignment explanation
Indices: 1552569--1552599 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1552559 GACTACCCGC
1552569 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
1552600 ATTGTAAATT
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:1553130 original size:21 final size:20
Alignment explanation
Indices: 1553090--1553141 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
1553080 TATTTAATCA
*
1553090 TATAATATA-ATATTTATTT
1 TATAATAAATATATTTATTT
* *
1553109 TTTATTAAATATATTATATTT
1 TATAATAAATATATT-TATTT
1553130 TATAATAAATAT
1 TATAATAAATAT
1553142 TATCAAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 6 0.23
20 5 0.19
21 15 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATAATAAATATATTTATTT
Found at i:1555172 original size:96 final size:96
Alignment explanation
Indices: 1555008--1555204 Score: 306
Period size: 96 Copynumber: 2.1 Consensus size: 96
1554998 CATGGCTGCT
1555008 TTATGTCTTTGTGGAGTTGACTAGCATCTTTGCCCTCTCCATATTTGGTTTAAGATCTATGCTGC
1 TTATGTCTTTGTGGAGTTGACTAGCATCTTTGCCCTCTCCATATTTGGTTTAAGATCTATGCTGC
* *
1555073 CCCCAACTCTAGACATGGGCTCTTACCACAA
66 CCCCAACTCTAGACATGGCCGCTTACCACAA
* * *
1555104 TTATGTCTTTGTGGAGTTTACTAGCATGTTGTGGCCTCTCCATATTTGGTTTAA-ATCTATGCTG
1 TTATGTCTTTGTGGAGTTGACTAGCATCTT-TGCCCTCTCCATATTTGGTTTAAGATCTATGCTG
* *
1555168 CCCCCATCTCTAGACGTGGCCGCTTACCACAA
65 CCCCCAACTCTAGACATGGCCGCTTACCACAA
*
1555200 CTATG
1 TTATG
1555205 CAGTTCTGGT
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
96 70 0.76
97 22 0.24
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (96 bp):
TTATGTCTTTGTGGAGTTGACTAGCATCTTTGCCCTCTCCATATTTGGTTTAAGATCTATGCTGC
CCCCAACTCTAGACATGGCCGCTTACCACAA
Found at i:1556295 original size:3 final size:3
Alignment explanation
Indices: 1556287--1556324 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1556277 TTGCAGTATG
1556287 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GT
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GT
1556325 CTGTTGCTTT
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:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
GTA
Found at i:1556755 original size:31 final size:32
Alignment explanation
Indices: 1556714--1556788 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 32
1556704 TATTTAAATA
*
1556714 AATTATTATTTTTATCATAATTA-TAGTTATT-T
1 AATT-TTATTTTTAT-ATAATAATTAGTTATTAT
* *
1556746 TATTTTATTTTTATATAATAATTATTTATTAT
1 AATTTTATTTTTATATAATAATTAGTTATTAT
1556778 AATTTTATTTT
1 AATTTTATTTT
1556789 ATTTGAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 6 0.16
31 17 0.46
32 14 0.38
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (32 bp):
AATTTTATTTTTATATAATAATTAGTTATTAT
Found at i:1561050 original size:3 final size:3
Alignment explanation
Indices: 1561042--1561075 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1561032 TATAAACTTT
1561042 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1561076 CTAATTTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1561943 original size:17 final size:15
Alignment explanation
Indices: 1561918--1562090 Score: 67
Period size: 17 Copynumber: 11.2 Consensus size: 15
1561908 ATTATAATCG
1561918 TATTTA-TATA-TTA
1 TATTTATTATATTTA
1561931 TATTGTATTATATTTTA
1 TATT-TATTATA-TTTA
*
1561948 TATTTTTTATATTTA
1 TATTTATTATATTTA
* *
1561963 TA--TA-AATTTTTA
1 TATTTATTATATTTA
*
1561975 TATTTTTTATATTTA
1 TATTTATTATATTTA
*
1561990 TATTATGATTAAAATATT-
1 TATT-T-ATT-ATAT-TTA
1562008 T-TTTATT-TATATTA
1 TATTTATTATAT-TTA
*
1562022 TATTTTAATTATTTTTA
1 TA-TTT-ATTATATTTA
*
1562039 TATTTATATCATATGTA
1 TATTTAT-T-ATATTTA
*
1562056 TAATTA-TATCATATTA
1 TATTTATTAT-AT-TTA
* *
1562072 AATATTATTAGATTTA
1 TAT-TTATTATATTTA
1562088 TAT
1 TAT
1562091 GCCTCTCCAA
Statistics
Matches: 119, Mismatches: 19, Indels: 41
0.66 0.11 0.23
Matches are distributed among these distances:
12 8 0.07
13 10 0.08
14 6 0.05
15 28 0.24
16 23 0.19
17 34 0.29
18 8 0.07
19 2 0.02
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.61
Consensus pattern (15 bp):
TATTTATTATATTTA
Found at i:1561957 original size:9 final size:9
Alignment explanation
Indices: 1561943--1561988 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
1561933 TTGTATTATA
1561943 TTTTATATT
1 TTTTATATT
1561952 TTTTATA-T
1 TTTTATATT
* *
1561960 TTATATAAAT
1 TTTTAT-ATT
1561970 TTTTATATT
1 TTTTATATT
1561979 TTTTATATT
1 TTTTATATT
1561988 T
1 T
1561989 ATATTATGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 6 0.19
9 20 0.62
10 6 0.19
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTATATT
Found at i:1562009 original size:27 final size:28
Alignment explanation
Indices: 1561928--1562052 Score: 109
Period size: 27 Copynumber: 4.6 Consensus size: 28
1561918 TATTTATATA
* * *
1561928 TTATA-TTGTATTATATTTTATAT-TTT
1 TTATATTTATATTATATTTAAAATATTT
* **
1561954 TTATATTTATA-TAAATTT-TTATATTTT
1 TTATATTTATATTATATTTAAAATA-TTT
1561981 TTATATTTATATTATGA-TTAAAATATTT
1 TTATATTTATATTAT-ATTTAAAATATTT
* *
1562009 TT-TATTTATATTATATTTTAATTATTT
1 TTATATTTATATTATATTTAAAATATTT
*
1562036 TTATATTTATATCATAT
1 TTATATTTATATTATAT
1562053 GTATAATTAT
Statistics
Matches: 82, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
25 3 0.04
26 12 0.15
27 41 0.50
28 22 0.27
29 4 0.05
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.65
Consensus pattern (28 bp):
TTATATTTATATTATATTTAAAATATTT
Found at i:1562069 original size:28 final size:28
Alignment explanation
Indices: 1562011--1562070 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1562001 AAATATTTTT
* * * *
1562011 TATTTATATTATATTTTAATTATTTTTA
1 TATTTATATCATATTATAATTATTATCA
1562039 TATTTATATCATATGTATAATTA-TATCA
1 TATTTATATCATAT-TATAATTATTATCA
1562067 TATT
1 TATT
1562071 AAATATTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 20 0.74
29 7 0.26
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (28 bp):
TATTTATATCATATTATAATTATTATCA
Found at i:1563027 original size:25 final size:24
Alignment explanation
Indices: 1562999--1563071 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
1562989 TTATATAAAT
1562999 TTTAATATATTAATA-ATTTATATTA
1 TTTAATAT-TTAATATATTTAT-TTA
*
1563024 TTTAA-ATTTTAAAATATTTATTTA
1 TTTAATA-TTTAATATATTTATTTA
*
1563048 TATT-ATATTTAATATTATTAATTT
1 T-TTAATATTTAATA-TATTTATTT
1563072 TAAATTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
24 17 0.43
25 23 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTAATATTTAATATATTTATTTA
Found at i:1563030 original size:32 final size:29
Alignment explanation
Indices: 1562989--1563055 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 29
1562979 TTAAAATATT
*
1562989 TTATATAAATTTTAATATATTAATAATTTATA
1 TTATATAAATTTTAAAATATT--T-ATTTATA
*
1563021 TTATTTAAATTTTAAAATATTTATTTATA
1 TTATATAAATTTTAAAATATTTATTTATA
1563050 TTATAT
1 TTATAT
1563056 TTAATATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 12 0.38
30 1 0.03
32 19 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TTATATAAATTTTAAAATATTTATTTATA
Found at i:1563073 original size:26 final size:27
Alignment explanation
Indices: 1562999--1563118 Score: 72
Period size: 29 Copynumber: 4.5 Consensus size: 27
1562989 TTATATAAAT
1562999 TTTAATA-TATTAATAATTTATATTAT-
1 TTTAATATTATTAAT-ATTTATATTATA
* * * *
1563025 TTAAATTTTAAAATATTTATTTATATTATA
1 TTTAATATT--ATTA-ATATTTATATTATA
*
1563055 TTTAATATTATTAAT-TTTAAATT-T-
1 TTTAATATTATTAATATTTATATTATA
* * *
1563079 TTTTAT-TTATATTATATTTATATGATA
1 TTTAATATTAT-TAATATTTATATTATA
*
1563106 TTTAATAATATTA
1 TTTAATATTATTA
1563119 TTAAATTTAA
Statistics
Matches: 68, Mismatches: 16, Indels: 19
0.66 0.16 0.18
Matches are distributed among these distances:
23 4 0.06
24 8 0.12
25 7 0.10
26 13 0.19
27 8 0.12
28 6 0.09
29 14 0.21
30 8 0.12
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (27 bp):
TTTAATATTATTAATATTTATATTATA
Found at i:1563098 original size:15 final size:15
Alignment explanation
Indices: 1563037--1563119 Score: 51
Period size: 15 Copynumber: 5.1 Consensus size: 15
1563027 AAATTTTAAA
1563037 ATATTTATTTATATT
1 ATATTTATTTATATT
1563052 ATATTTAATATTATTAATTTT
1 ATATTT-AT-TTA-T-A--TT
* *
1563073 AAATTTTTTTAT-TT
1 ATATTTATTTATATT
*
1563087 ATATTATATTTATATG
1 ATATT-TATTTATATT
* *
1563103 ATATTTAATAATATT
1 ATATTTATTTATATT
1563118 AT
1 AT
1563120 TAAATTTAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
14 6 0.12
15 21 0.40
16 8 0.15
17 3 0.06
18 2 0.04
19 4 0.08
20 1 0.02
21 7 0.13
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (15 bp):
ATATTTATTTATATT
Found at i:1564516 original size:14 final size:14
Alignment explanation
Indices: 1564480--1564527 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1564470 TAAATATGAT
1564480 ATAAATATATAATATA
1 ATAAA-ATATAAT-TA
* *
1564496 AT-TAATATATTTA
1 ATAAAATATAATTA
1564509 ATAAAATATAATTA
1 ATAAAATATAATTA
1564523 ATAAA
1 ATAAA
1564528 GGTAATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 4 0.15
14 20 0.74
15 1 0.04
16 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAAAATATAATTA
Found at i:1564533 original size:23 final size:23
Alignment explanation
Indices: 1564490--1564534 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1564480 ATAAATATAT
* **
1564490 AATATAATTAATATATTTAATAA
1 AATATAATTAATAAAGGTAATAA
1564513 AATATAATTAATAAAGGTAATA
1 AATATAATTAATAAAGGTAATA
1564535 TATTTATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
AATATAATTAATAAAGGTAATAA
Found at i:1566471 original size:24 final size:26
Alignment explanation
Indices: 1566443--1566494 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
1566433 GATATGAATT
1566443 AAAATAATATA-TAAA-AATTTAATA
1 AAAATAATATATTAAATAATTTAATA
* *
1566467 AAAATAATCTATTAAATAATTTATTA
1 AAAATAATATATTAAATAATTTAATA
1566493 AA
1 AA
1566495 TGATAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.42
25 4 0.17
26 10 0.42
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
AAAATAATATATTAAATAATTTAATA
Found at i:1571829 original size:3 final size:3
Alignment explanation
Indices: 1571817--1571889 Score: 55
Period size: 3 Copynumber: 25.0 Consensus size: 3
1571807 AGTTTGATCA
*
1571817 TAT T-T TAT TAT TAT TAT TAT TAAT TAT TA- TAT T-T AAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT -TAT TAT
* * * *
1571861 TAT TAT AAA TA- AAA TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1571890 AAATAATATA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
2 6 0.11
3 45 0.80
4 5 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:1571864 original size:20 final size:20
Alignment explanation
Indices: 1571834--1571886 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1571824 TTATTATTAT
** *
1571834 TATTAATTATTATATTTAATA
1 TATT-ATTATTATAAATAAAA
1571855 TATTATTATTATAAATAAAA
1 TATTATTATTATAAATAAAA
1571875 TATTATTATTAT
1 TATTATTATTAT
1571887 TATAAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTATTATTATAAATAAAA
Found at i:1571871 original size:17 final size:16
Alignment explanation
Indices: 1571825--1571883 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 16
1571815 CATATTTTAT
1571825 TATTATTATTATTAAT-
1 TATTATTATTA-TAATA
1571841 TATTA-TATT-TAATA
1 TATTATTATTATAATA
1571855 TATTATTATTATAAATA
1 TATTATTATTAT-AATA
* *
1571872 AAATATTATTAT
1 TATTATTATTAT
1571884 TATTATAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
13 4 0.11
14 5 0.14
15 8 0.22
16 6 0.16
17 14 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTATTATTATAATA
Found at i:1571881 original size:23 final size:23
Alignment explanation
Indices: 1571828--1571902 Score: 89
Period size: 23 Copynumber: 3.2 Consensus size: 23
1571818 ATTTTATTAT
* **
1571828 TATTATTATTAATTATTATATTTAA
1 TATTATTATT-ATTA-TAAATAAAA
1571853 TA-TATTATTATTATAAATAAAA
1 TATTATTATTATTATAAATAAAA
*
1571875 TATTATTATTATTATAAATAATA
1 TATTATTATTATTATAAATAAAA
1571898 TATTA
1 TATTA
1571903 GTTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.18
23 28 0.62
24 7 0.16
25 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTATTATTATTATAAATAAAA
Found at i:1572230 original size:3 final size:3
Alignment explanation
Indices: 1572222--1572248 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1572212 CGATATCAGG
1572222 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1572249 CTTTCATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1577911 original size:2 final size:2
Alignment explanation
Indices: 1577906--1577931 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1577896 TATATATGCC
1577906 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
1577932 CATACAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1582737 original size:77 final size:77
Alignment explanation
Indices: 1582610--1582762 Score: 306
Period size: 77 Copynumber: 2.0 Consensus size: 77
1582600 ATTTAGCAAC
1582610 TAAACTTTTAAGAAAAGTGTTGCCAACCTATGTTACCCAGACTCGAGGGGGTGATTGTTAGATAT
1 TAAACTTTTAAGAAAAGTGTTGCCAACCTATGTTACCCAGACTCGAGGGGGTGATTGTTAGATAT
1582675 AAGTATGTGTCA
66 AAGTATGTGTCA
1582687 TAAACTTTTAAGAAAAGTGTTGCCAACCTATGTTACCCAGACTCGAGGGGGTGATTGTTAGATAT
1 TAAACTTTTAAGAAAAGTGTTGCCAACCTATGTTACCCAGACTCGAGGGGGTGATTGTTAGATAT
1582752 AAGTATGTGTC
66 AAGTATGTGTC
1582763 CGACATTAGG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (77 bp):
TAAACTTTTAAGAAAAGTGTTGCCAACCTATGTTACCCAGACTCGAGGGGGTGATTGTTAGATAT
AAGTATGTGTCA
Found at i:1593929 original size:3 final size:3
Alignment explanation
Indices: 1593921--1593952 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1593911 TCAATAATCA
1593921 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1593953 ATGTTTCACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1594299 original size:29 final size:32
Alignment explanation
Indices: 1594258--1594326 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 32
1594248 TACTTTTGAA
* * *
1594258 ATAATTGT-ATTATGTTAATA-T-ATTTTTAT
1 ATAATTATAATTATATTAATATTAATTATTAT
*
1594287 AT-ATTATAATTATATTTATATTAATTATTAT
1 ATAATTATAATTATATTAATATTAATTATTAT
1594318 ATAATTATA
1 ATAATTATA
1594327 TAAATTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
28 4 0.12
29 12 0.38
30 1 0.03
31 9 0.28
32 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (32 bp):
ATAATTATAATTATATTAATATTAATTATTAT
Found at i:1594341 original size:40 final size:41
Alignment explanation
Indices: 1594297--1594375 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
1594287 ATATTATAAT
*
1594297 TATATTTAT-ATTAATTATTATAT-AATTATATAAATTTAAA
1 TATATTAATAATTAA-TATTATATAAATTATATAAATTTAAA
* * *
1594337 TATATTAATAATTTATATTATATAAATTTTATATATTTA
1 TATATTAATAATTAATATTATATAAATTATATAAATTTA
1594376 TATTATAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 16 0.48
41 17 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (41 bp):
TATATTAATAATTAATATTATATAAATTATATAAATTTAAA
Found at i:1594357 original size:32 final size:33
Alignment explanation
Indices: 1594303--1594382 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 33
1594293 TAATTATATT
*
1594303 TATATTAATTATTATATAATTATATAAATTTAAA
1 TATATTAATAATTATATAATTATATAAATTT-AA
*
1594337 TATATTAATAATT-TAT-ATTATATAAATTTTA
1 TATATTAATAATTATATAATTATATAAATTTAA
*
1594368 TATATTTAT-ATTATA
1 TATATTAATAATTATA
1594383 ATCGAATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 3 0.07
31 11 0.26
32 13 0.31
33 3 0.07
34 12 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TATATTAATAATTATATAATTATATAAATTTAA
Found at i:1594399 original size:30 final size:32
Alignment explanation
Indices: 1594358--1594416 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
1594348 TTTATATTAT
1594358 ATAAATTTTATAT-AT-TTATATTATAATCGA
1 ATAAATTTTATATAATATTATATTATAATCGA
* *
1594388 ATAATTTTTATATAATATTATATTTTAAT
1 ATAAATTTTATATAATATTATATTATAAT
1594417 TATTTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 12 0.48
31 2 0.08
32 11 0.44
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (32 bp):
ATAAATTTTATATAATATTATATTATAATCGA
Found at i:1594449 original size:30 final size:30
Alignment explanation
Indices: 1594337--1594455 Score: 90
Period size: 27 Copynumber: 4.1 Consensus size: 30
1594327 TAAATTTAAA
*
1594337 TATATTAATAATTTATATTATATAA--ATTTT
1 TATATT-AT-ATTTATATAATATAATTATTTT
* ** *
1594367 ATATATT-TATAT-TATAATCGAATAATTTT
1 -TATATTATATTTATATAATATAATTATTTT
* *
1594396 TATATAATA-TTATAT--TTTAATTATTTT
1 TATATTATATTTATATAATATAATTATTTT
*
1594423 TATATTATATTTATATAATATAATTATATT
1 TATATTATATTTATATAATATAATTATTTT
1594453 TAT
1 TAT
1594456 CAAAATTTAA
Statistics
Matches: 69, Mismatches: 12, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
27 24 0.35
28 15 0.22
29 11 0.16
30 13 0.19
31 6 0.09
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (30 bp):
TATATTATATTTATATAATATAATTATTTT
Found at i:1595312 original size:19 final size:19
Alignment explanation
Indices: 1595282--1595350 Score: 63
Period size: 18 Copynumber: 3.6 Consensus size: 19
1595272 ATTGATAAAT
*
1595282 TTTAAAT-TAAATTATTTA
1 TTTAAATATAAAATATTTA
1595300 TTTAAATA-AAAATATTTTAA
1 TTTAAATATAAAATA-TTT-A
*
1595320 TTTAAAATATAAAAATAATT-
1 TTT-AAATAT-AAAATATTTA
1595340 TTTAAATATAA
1 TTTAAATATAA
1595351 TTAAATAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
18 14 0.33
19 9 0.21
20 7 0.16
21 5 0.12
22 2 0.05
23 6 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTAAATATAAAATATTTA
Found at i:1595360 original size:24 final size:26
Alignment explanation
Indices: 1595301--1595361 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 26
1595291 AATTATTTAT
* *
1595301 TTAAATAAAAATATTTTAATTTAAAA
1 TTAAATAATAATATTTTAATATAAAA
*
1595327 TATAAA-AATAAT-TTTTAA-ATATAA
1 T-TAAATAATAATATTTTAATATAAAA
1595351 TTAAATAATAA
1 TTAAATAATAA
1595362 AATGAATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 4 0.13
24 10 0.33
25 6 0.20
26 6 0.20
27 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TTAAATAATAATATTTTAATATAAAA
Found at i:1595444 original size:23 final size:23
Alignment explanation
Indices: 1595418--1595461 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1595408 GAAAAGGAAG
*
1595418 AAAAGGAAATCTTTAACAAAAAA
1 AAAAAGAAATCTTTAACAAAAAA
*
1595441 AAAAAGAAATCTTTAATAAAA
1 AAAAAGAAATCTTTAACAAAA
1595462 TAATAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.20
Consensus pattern (23 bp):
AAAAAGAAATCTTTAACAAAAAA
Found at i:1596125 original size:18 final size:17
Alignment explanation
Indices: 1596098--1596131 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1596088 TTTATTTTTA
*
1596098 AATTTTTTTATCAAATC
1 AATTTTTTTATAAAATC
1596115 AATTATTTTTATAAAAT
1 AATT-TTTTTATAAAAT
1596132 TTTAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTTTTTATAAAATC
Found at i:1596768 original size:16 final size:15
Alignment explanation
Indices: 1596731--1596777 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
1596721 AATTTAAAAT
1596731 TAAATTAATT-TTATA
1 TAAATTAATTATTA-A
*
1596746 AATAATTAATATATTAA
1 TA-AATTAAT-TATTAA
1596763 TAAATTAATTATTAA
1 TAAATTAATTATTAA
1596778 ATTAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 7 0.26
16 14 0.52
17 3 0.11
18 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAATTAATTATTAA
Found at i:1596781 original size:20 final size:19
Alignment explanation
Indices: 1596743--1596795 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
1596733 AATTAATTTT
* *
1596743 ATAAATAATTAATATATTA
1 ATAAATAATTATTAAATTA
1596762 ATAAATTAATTATTAAATTA
1 ATAAA-TAATTATTAAATTA
*
1596782 A-AAAAATATTATTA
1 ATAAATA-ATTATTA
1596796 TATTTATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 1 0.03
19 15 0.52
20 13 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAAATAATTATTAAATTA
Found at i:1597773 original size:21 final size:22
Alignment explanation
Indices: 1597743--1597784 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1597733 AAATTAATTT
*
1597743 ATAAAATTTT-ATACAATAAAG
1 ATAAAATTTTAATAAAATAAAG
*
1597764 ATAAATTTTTAATAAAATAAA
1 ATAAAATTTTAATAAAATAAA
1597785 TTTTAGAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAAAATTTTAATAAAATAAAG
Found at i:1597785 original size:16 final size:17
Alignment explanation
Indices: 1597757--1597788 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1597747 AATTTTATAC
1597757 AATAAAGATAAATTTTT
1 AATAAAGATAAATTTTT
1597774 AATAAA-ATAAATTTT
1 AATAAAGATAAATTTT
1597789 AGAGTAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
AATAAAGATAAATTTTT
Found at i:1609704 original size:22 final size:23
Alignment explanation
Indices: 1609659--1609705 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1609649 GAACTGGTAG
*
1609659 ATTTTTTTTTTTGAAATATTTAA
1 ATTTTTTTTTTTGAAATATATAA
1609682 ATTTTGTTTTTTT-AAA-ATATAA
1 ATTTT-TTTTTTTGAAATATATAA
1609704 AT
1 AT
1609706 AAAAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 8 0.36
24 7 0.32
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
ATTTTTTTTTTTGAAATATATAA
Found at i:1609857 original size:21 final size:24
Alignment explanation
Indices: 1609805--1609858 Score: 60
Period size: 26 Copynumber: 2.3 Consensus size: 24
1609795 TTTATAAATT
*
1609805 TTAATTAAATTATCAATTACATAA
1 TTAATTAAATTATCAATTAAATAA
1609829 TTTAAATTAAATTAT-AA-TAAATAA
1 -TT-AATTAAATTATCAATTAAATAA
1609853 -TAATTA
1 TTAATTA
1609859 TTTAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.19
22 1 0.04
24 6 0.22
25 4 0.15
26 11 0.41
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAATTAAATTATCAATTAAATAA
Found at i:1609989 original size:169 final size:169
Alignment explanation
Indices: 1609710--1610031 Score: 558
Period size: 169 Copynumber: 1.9 Consensus size: 169
1609700 ATAAATAAAA
*
1609710 ATAAAAATTATAATGATAAATTTTGTTATTTGTATTAATAAATAAAGTAGAATTATTTTCACATT
1 ATAAAAATTATAATGATAAATTTTATTATTTGTATTAATAAATAAAGTAGAATTATTTTCACATT
*
1609775 TTGTATGGAGATTTTTAATATTTATAAATTTTAATTAAATTATCAATTACATAATTTAAATTAAA
66 TTGTATGGAGATTTTTAATATTTATAAATTTTAAGTAAATTATCAATTACATAATTTAAATTAAA
1609840 TTATAATAAATAATAATTATTTAAAGTTTGTTATTTTTT
131 TTATAATAAATAATAATTATTTAAAGTTTGTTATTTTTT
*
1609879 ATAAAAATTATAATGATAAATTTTATTATTTGTATTAATAAA-AAAGCTAGAATTCTTTTCACAT
1 ATAAAAATTATAATGATAAATTTTATTATTTGTATTAATAAATAAAG-TAGAATTATTTTCACAT
*
1609943 TTTGT-TGGGAGATTTTTAATATTTATAAGTTTTAAGTAAATTATCAATTACATAATTTAAATTA
65 TTTGTAT-GGAGATTTTTAATATTTATAAATTTTAAGTAAATTATCAATTACATAATTTAAATTA
* *
1610007 TATTATATTAAATAATAATTATTTA
129 AATTATAATAAATAATAATTATTTA
1610032 TTTAAATAAT
Statistics
Matches: 145, Mismatches: 6, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
168 5 0.03
169 140 0.97
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.48
Consensus pattern (169 bp):
ATAAAAATTATAATGATAAATTTTATTATTTGTATTAATAAATAAAGTAGAATTATTTTCACATT
TTGTATGGAGATTTTTAATATTTATAAATTTTAAGTAAATTATCAATTACATAATTTAAATTAAA
TTATAATAAATAATAATTATTTAAAGTTTGTTATTTTTT
Found at i:1610047 original size:19 final size:21
Alignment explanation
Indices: 1610002--1610041 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
1609992 ACATAATTTA
1610002 AATTATATTATATTAAATAAT
1 AATTATATTATATTAAATAAT
1610023 AATTAT-TTAT-TTAAATAAT
1 AATTATATTATATTAAATAAT
1610042 TTTTATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
20 4 0.21
21 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTATATTATATTAAATAAT
Found at i:1612320 original size:20 final size:20
Alignment explanation
Indices: 1612294--1612339 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1612284 TTTATTTAAA
* *
1612294 TATATATTTATATTA-ATTT
1 TATATATTCATAATATATTT
1612313 TGATATATTCATAATATATTT
1 T-ATATATTCATAATATATTT
1612334 TATATA
1 TATATA
1612340 AATTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 17 0.74
21 5 0.22
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TATATATTCATAATATATTT
Found at i:1612353 original size:32 final size:33
Alignment explanation
Indices: 1612292--1612353 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
1612282 AATTTATTTA
* * *
1612292 AATATATATTTATATTAATTTTGATATATTCAT
1 AATATATATTTATATAAATTTTAAAATATTCAT
1612325 AATATAT-TTTATATAAATTTTAAAATATT
1 AATATATATTTATATAAATTTTAAAATATT
1612354 TATTTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 19 0.73
33 7 0.27
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (33 bp):
AATATATATTTATATAAATTTTAAAATATTCAT
Found at i:1616825 original size:2 final size:2
Alignment explanation
Indices: 1616818--1616844 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1616808 ATAGTTTATA
1616818 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1616845 AGAAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1619543 original size:12 final size:12
Alignment explanation
Indices: 1619506--1619544 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1619496 GAGTTCAGAC
*
1619506 AGCAGGAGCCGA
1 AGCAGGAGCCGG
*
1619518 AGCAGGAGCAGG
1 AGCAGGAGCCGG
1619530 AGCAGGAGCCGG
1 AGCAGGAGCCGG
1619542 AGC
1 AGC
1619545 CCCATGGATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.31, C:0.23, G:0.46, T:0.00
Consensus pattern (12 bp):
AGCAGGAGCCGG
Found at i:1619545 original size:6 final size:6
Alignment explanation
Indices: 1619506--1619544 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1619496 GAGTTCAGAC
* * *
1619506 AGCAGG AGCCGA AGCAGG AGCAGG AGCAGG AGCCGG AGC
1 AGCAGG AGCAGG AGCAGG AGCAGG AGCAGG AGCAGG AGC
1619545 CCCATGGATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.31, C:0.23, G:0.46, T:0.00
Consensus pattern (6 bp):
AGCAGG
Found at i:1621348 original size:3 final size:3
Alignment explanation
Indices: 1621340--1621368 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1621330 GGAGATCGAA
1621340 GTG GTG GTG GTG GTG GTG GTG GTG GTG GT
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GT
1621369 TACCGAGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (3 bp):
GTG
Found at i:1623837 original size:18 final size:18
Alignment explanation
Indices: 1623805--1623839 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1623795 ATGGATGCAG
*
1623805 CAGAGGAGACGGAGGATA
1 CAGAGGAGACAGAGGATA
*
1623823 CAGAGGAGGCAGAGGAT
1 CAGAGGAGACAGAGGAT
1623840 GTTGGTAGAG
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:0.37, C:0.11, G:0.46, T:0.06
Consensus pattern (18 bp):
CAGAGGAGACAGAGGATA
Found at i:1628403 original size:8 final size:8
Alignment explanation
Indices: 1628390--1628421 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1628380 GGTTATCACA
1628390 TGCGTGTG
1 TGCGTGTG
1628398 TGCGTGTG
1 TGCGTGTG
1628406 T--GTGTG
1 TGCGTGTG
1628412 TGCGTGTG
1 TGCGTGTG
1628420 TG
1 TG
1628422 TGTACAGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.27
8 16 0.73
ACGTcount: A:0.00, C:0.09, G:0.50, T:0.41
Consensus pattern (8 bp):
TGCGTGTG
Found at i:1628412 original size:14 final size:14
Alignment explanation
Indices: 1628393--1628424 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1628383 TATCACATGC
1628393 GTGTGTGCGTGTGT
1 GTGTGTGCGTGTGT
1628407 GTGTGTGCGTGTGT
1 GTGTGTGCGTGTGT
1628421 GTGT
1 GTGT
1628425 ACAGACACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.06, G:0.50, T:0.44
Consensus pattern (14 bp):
GTGTGTGCGTGTGT
Done.