Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, whole genome shotgun sequence
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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 5 of 138
Found at i:1029386 original size:48 final size:48
Alignment explanation
Indices: 1029281--1029386 Score: 133
Period size: 47 Copynumber: 2.2 Consensus size: 48
1029271 TTCCAAAGAT
* * *
1029281 AAAAAAAAATTTCTAAATAGATCCAAATGCTGAAAAATTTAGAAATTA
1 AAAAAAAAATTTCTAAATAGACCCAAATGCTAAAAAATTTAGAAATAA
* * * *
1029329 AAAAGAAAATTTCT-AATTGGCCCAAATGGTAAAAAATTTAGAAATAA
1 AAAAAAAAATTTCTAAATAGACCCAAATGCTAAAAAATTTAGAAATAA
1029376 AAATAAAAAAT
1 AAA-AAAAAAT
1029387 AAAAATAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
47 30 0.61
48 19 0.39
ACGTcount: A:0.58, C:0.08, G:0.09, T:0.25
Consensus pattern (48 bp):
AAAAAAAAATTTCTAAATAGACCCAAATGCTAAAAAATTTAGAAATAA
Found at i:1036409 original size:12 final size:12
Alignment explanation
Indices: 1036389--1036419 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1036379 TCTCAAATCT
1036389 TACTATATATAA
1 TACTATATATAA
*
1036401 TAGTATATATAA
1 TACTATATATAA
1036413 TACTATA
1 TACTATA
1036420 CGTTAAACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (12 bp):
TACTATATATAA
Found at i:1048671 original size:25 final size:25
Alignment explanation
Indices: 1048643--1048701 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
1048633 ATTAATTAAA
*
1048643 ATTAATATAT-TTTATTAAAATATAT
1 ATTAATATATATTTATAAAAAT-TAT
1048668 ATTAATATATATTTATAAAAATTAT
1 ATTAATATATATTTATAAAAATTAT
1048693 -TTAA-ATATA
1 ATTAATATATA
1048702 CAAGATAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 5 0.16
24 4 0.12
25 13 0.41
26 10 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTAATATATATTTATAAAAATTAT
Found at i:1050893 original size:22 final size:23
Alignment explanation
Indices: 1050843--1050893 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1050833 TAAATTTTTT
1050843 TTATTTTATATACTATTTAATAA
1 TTATTTTATATACTATTTAATAA
**
1050866 AAATTTTA-ATA-TATTTAAATAA
1 TTATTTTATATACTATTT-AATAA
1050888 TTATTT
1 TTATTT
1050894 ACATTTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 5 0.22
22 12 0.52
23 6 0.26
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TTATTTTATATACTATTTAATAA
Found at i:1051843 original size:23 final size:23
Alignment explanation
Indices: 1051780--1051844 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
1051770 TTTTATTAAA
*
1051780 TTTATTTATGATTTTTATTAAAATT
1 TTTATTTAT-ATTATT-TTAAAATT
** * * *
1051805 TAAAATTGTATCATTTTAAAATT
1 TTTATTTATATTATTTTAAAATT
1051828 TTTATTTATATTATTTT
1 TTTATTTATATTATTTT
1051845 TATATCATAT
Statistics
Matches: 29, Mismatches: 11, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
23 20 0.69
24 4 0.14
25 5 0.17
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.62
Consensus pattern (23 bp):
TTTATTTATATTATTTTAAAATT
Found at i:1051845 original size:16 final size:16
Alignment explanation
Indices: 1051825--1051858 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1051815 TCATTTTAAA
*
1051825 ATTTTTAT-TTATATT
1 ATTTTTATATCATATT
1051840 ATTTTTATATCATATT
1 ATTTTTATATCATATT
1051856 ATT
1 ATT
1051859 ATATCATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTATATCATATT
Found at i:1051860 original size:13 final size:13
Alignment explanation
Indices: 1051839--1051868 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1051829 TTATTTATAT
*
1051839 TATTTTTATATCA
1 TATTATTATATCA
1051852 TATTATTATATCA
1 TATTATTATATCA
1051865 TATT
1 TATT
1051869 TAAATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTATTATATCA
Found at i:1057543 original size:26 final size:25
Alignment explanation
Indices: 1057501--1057549 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
1057491 TTTATTAAAA
* *
1057501 TTTTTTTAATTATAATTATAATATT
1 TTTTTTTAATCACAATTATAATATT
1057526 TTTTTTTCAATCACAATTATAATA
1 TTTTTTT-AATCACAATTATAATA
1057550 ATAATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTTTTTAATCACAATTATAATATT
Found at i:1066412 original size:4 final size:4
Alignment explanation
Indices: 1066398--1066428 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1066388 AATAAAAATA
*
1066398 AATT AAAT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AATT AAT
1066429 ATTTATTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (4 bp):
AATT
Found at i:1066415 original size:12 final size:12
Alignment explanation
Indices: 1066381--1066427 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
1066371 TTTAACTCTG
1066381 ATAAGTTAA-TAA
1 ATAA-TTAATTAA
*
1066393 A-AATAAATTAA
1 ATAATTAATTAA
1066404 ATAATTAATTAA
1 ATAATTAATTAA
*
1066416 TTAATTAATTAA
1 ATAATTAATTAA
1066428 TATTTATTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 3 0.10
11 6 0.20
12 21 0.70
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (12 bp):
ATAATTAATTAA
Found at i:1070732 original size:12 final size:12
Alignment explanation
Indices: 1070715--1070757 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
1070705 TTTTTTATCG
*
1070715 ATATAAATTTTT
1 ATATAAATTATT
*
1070727 ATATAAAATATT
1 ATATAAATTATT
*
1070739 ATATAAATTAAT
1 ATATAAATTATT
1070751 ATATAAA
1 ATATAAA
1070758 ATTTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATATAAATTATT
Found at i:1070742 original size:24 final size:24
Alignment explanation
Indices: 1070715--1070784 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
1070705 TTTTTTATCG
*
1070715 ATATAAATTTTTATATAAAATATT
1 ATATAAATTTATATATAAAATATT
*
1070739 ATATAAATTAATATATAAAAT-TT
1 ATATAAATTTATATATAAAATATT
1070762 A-AT-AATTTATATGATATAAATAT
1 ATATAAATTTATAT-ATA-AAATAT
1070785 ATGGATATCG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 8 0.20
22 5 0.12
23 7 0.17
24 20 0.50
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (24 bp):
ATATAAATTTATATATAAAATATT
Found at i:1071995 original size:14 final size:13
Alignment explanation
Indices: 1071971--1072007 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1071961 TTTATATAGT
*
1071971 AAAAAATAAATTA
1 AAAAAATAAAATA
1071984 AAAAAATAAAATA
1 AAAAAATAAAATA
*
1071997 TAAAAATAAAA
1 AAAAAATAAAA
1072008 ATATACATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAAAATAAAATA
Found at i:1072008 original size:14 final size:13
Alignment explanation
Indices: 1071972--1072012 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1071962 TTATATAGTA
* *
1071972 AAAAATAAATTAA
1 AAAAATAAAATAT
1071985 AAAAATAAAATAT
1 AAAAATAAAATAT
1071998 AAAAATAAAAATAT
1 AAAAAT-AAAATAT
1072012 A
1 A
1072013 CATTTATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAAATAAAATAT
Found at i:1081899 original size:3 final size:3
Alignment explanation
Indices: 1081891--1081921 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1081881 TCACGGTTGC
1081891 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1081922 ATGCATGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1087908 original size:2 final size:2
Alignment explanation
Indices: 1087901--1087938 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1087891 ATATACAAGA
*
1087901 AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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
1087939 TCCCTTGCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1091582 original size:39 final size:39
Alignment explanation
Indices: 1091528--1091709 Score: 249
Period size: 39 Copynumber: 4.7 Consensus size: 39
1091518 CTGGGATCAA
*
1091528 CAACTGAGATTTTTCTTCAGTGTATTCTGTTGGTGTCAG
1 CAACTGAGATTTTTCTTCAGTGTATTCTTTTGGTGTCAG
*
1091567 CAACTGAGATTTTTCTTCAGTGTATTCTATTGGTGTCAG
1 CAACTGAGATTTTTCTTCAGTGTATTCTTTTGGTGTCAG
* * *
1091606 CAACTGAGATTTTTCTTCAATGTACTCTTTTGGTG-CTAC
1 CAACTGAGATTTTTCTTCAGTGTATTCTTTTGGTGTC-AG
* * * *
1091645 CAACTGAGAATTTTCTTCAATGTACTCTTTTGGTGACAG
1 CAACTGAGATTTTTCTTCAGTGTATTCTTTTGGTGTCAG
* *
1091684 CAACTGAGGTTTCTCTTCAGTGTATT
1 CAACTGAGATTTTTCTTCAGTGTATT
1091710 GAATGGTGGA
Statistics
Matches: 129, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
38 1 0.01
39 127 0.98
40 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (39 bp):
CAACTGAGATTTTTCTTCAGTGTATTCTTTTGGTGTCAG
Found at i:1104908 original size:20 final size:20
Alignment explanation
Indices: 1104879--1104917 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1104869 TTTATTATTA
1104879 AAAATAAATAAATCAAAAAT
1 AAAATAAATAAATCAAAAAT
* *
1104899 AAAATCAATAAATTAAAAA
1 AAAATAAATAAATCAAAAA
1104918 ATTTTATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATAAATAAATCAAAAAT
Found at i:1109323 original size:14 final size:15
Alignment explanation
Indices: 1109294--1109335 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1109284 ATAAAATAAT
1109294 ATAATTCAATTTTAA
1 ATAATTCAATTTTAA
*
1109309 ATAATTCAATTTAAA
1 ATAATTCAATTTTAA
*
1109324 ATTAATTGAATT
1 A-TAATTCAATT
1109336 GATCGAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (15 bp):
ATAATTCAATTTTAA
Found at i:1109390 original size:2 final size:2
Alignment explanation
Indices: 1109383--1109412 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1109373 ATCTTGTCTT
1109383 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
1109413 ATGAAAGAAA
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):
TA
Found at i:1111303 original size:3 final size:3
Alignment explanation
Indices: 1111295--1111322 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1111285 TATTATACCG
1111295 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1111323 TATATTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1111328 original size:6 final size:6
Alignment explanation
Indices: 1111319--1111364 Score: 74
Period size: 6 Copynumber: 7.5 Consensus size: 6
1111309 TTATTATTAT
*
1111319 TATTTA TATTTA TATTTA TATTTTT TATTTA TATTTA TATTTA TAT
1 TATTTA TATTTA TATTTA TA-TTTA TATTTA TATTTA TATTTA TAT
1111365 ATTTTTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 32 0.86
7 5 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TATTTA
Found at i:1111369 original size:25 final size:25
Alignment explanation
Indices: 1111309--1111375 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 25
1111299 ATTATTATTA
1111309 TTAT-TATTATTATTTATATTTATAT
1 TTATATATT-TTATTTATATTTATAT
*
1111334 TTATATTTTTTATTTATATTTATAT
1 TTATATATTTTATTTATATTTATAT
*
1111359 TTATATATTTTTTTTAT
1 TTATATATTTTATTTAT
1111376 TTTTTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 35 0.92
26 3 0.08
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (25 bp):
TTATATATTTTATTTATATTTATAT
Found at i:1111374 original size:19 final size:19
Alignment explanation
Indices: 1111319--1111375 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
1111309 TTATTATTAT
*
1111319 TATTTATAT-TTATATTTA
1 TATTTATATATTTTATTTA
*
1111337 TATTT-TTTATTTATATTTA
1 TATTTATATATTT-TATTTA
*
1111356 TATTTATATATTTTTTTTA
1 TATTTATATATTTTATTTA
1111375 T
1 T
1111376 TTTTTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 2 0.06
18 7 0.22
19 17 0.53
20 6 0.19
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTTATATATTTTATTTA
Found at i:1111378 original size:6 final size:6
Alignment explanation
Indices: 1111295--1111386 Score: 60
Period size: 6 Copynumber: 15.3 Consensus size: 6
1111285 TATTATACCG
* * * * * * *
1111295 TATTAT TATTAT TATTAT TATTAT TATTTA TATTTA TATTTA TATTTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TA-TTTT
* * * * *
1111344 TATTTA TATTTA TATTTA TATATT T-TTTT TATTTT TTTTTT TA
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TA
1111387 CTACTTTCTT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
5 4 0.05
6 66 0.88
7 5 0.07
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (6 bp):
TATTTT
Found at i:1111786 original size:11 final size:10
Alignment explanation
Indices: 1111769--1111827 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
1111759 CTATCTAGAA
*
1111769 ATTTTTTTGG
1 ATTTTTTTAG
1111779 ATTTTTTTAG
1 ATTTTTTTAG
*
1111789 ATTTTTTTGAA
1 ATTTTTTT-AG
1111800 AGTTTTTTT--
1 A-TTTTTTTAG
*
1111809 ATTTTTCTAG
1 ATTTTTTTAG
*
1111819 GTTTTTTTA
1 ATTTTTTTA
1111828 AGAACACTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
8 6 0.15
9 1 0.03
10 24 0.60
11 2 0.05
12 7 0.17
ACGTcount: A:0.17, C:0.02, G:0.12, T:0.69
Consensus pattern (10 bp):
ATTTTTTTAG
Found at i:1111813 original size:30 final size:30
Alignment explanation
Indices: 1111766--1111826 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
1111756 GAGCTATCTA
*
1111766 GAAATTTTTTTGGATTTTTTTAGATTTTTTT
1 GAAATTTTTTT-GATTTTTCTAGATTTTTTT
*
1111797 GAAAGTTTTTTT-ATTTTTCTAGGTTTTTTT
1 GAAA-TTTTTTTGATTTTTCTAGATTTTTTT
1111827 AAGAACACTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 16 0.59
31 4 0.15
32 7 0.26
ACGTcount: A:0.18, C:0.02, G:0.13, T:0.67
Consensus pattern (30 bp):
GAAATTTTTTTGATTTTTCTAGATTTTTTT
Found at i:1112219 original size:5 final size:5
Alignment explanation
Indices: 1112198--1112255 Score: 59
Period size: 5 Copynumber: 12.0 Consensus size: 5
1112188 CGATCACATG
* * *
1112198 TTTTC TTTT- TTTCA TTTTA TTTT- TATT- TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1112245 TTTTA GTTTTA
1 TTTTA -TTTTA
1112256 AACTATTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
4 9 0.20
5 32 0.70
6 5 0.11
ACGTcount: A:0.16, C:0.03, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:1123096 original size:89 final size:89
Alignment explanation
Indices: 1122861--1123111 Score: 297
Period size: 89 Copynumber: 2.8 Consensus size: 89
1122851 TTATGATTCG
* * * * *
1122861 TGGTTTCATCCTAATCATTTATTTTTTATCTTGACTCAATCTTAGTCACTTTATTTTAACTTGTG
1 TGGTTTCATCCTGATCATTTATTTTTAATCTTGACTCAGTCTTAGTCACTTTATTTTGACTTATG
* * * * *
1122926 ATTTCATTCCGATCACATGATTTG
66 GTTTTATCCCAATCACATGATTTA
* * *
1122950 TGGTTTCATCTTGATCATTTATTTTTGATCTTGACTC-GATCTTGGTCACTTTATTTTGACTTAT
1 TGGTTTCATCCTGATCATTTATTTTTAATCTTGACTCAG-TCTTAGTCACTTTATTTTGACTTAT
* *
1123014 GGTTTTATCCCAATGACATGGTTTA
65 GGTTTTATCCCAATCACATGATTTA
* * * * * *
1123039 TGGTTTTATCCTGATCATTTATTTTCAACCTCGACTCAGTCTTTGTCACTTTATTTTGACTCATG
1 TGGTTTCATCCTGATCATTTATTTTTAATCTTGACTCAGTCTTAGTCACTTTATTTTGACTTATG
1123104 GTTTTATC
66 GTTTTATC
1123112 TCGATCACGT
Statistics
Matches: 138, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
89 137 0.99
90 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.49
Consensus pattern (89 bp):
TGGTTTCATCCTGATCATTTATTTTTAATCTTGACTCAGTCTTAGTCACTTTATTTTGACTTATG
GTTTTATCCCAATCACATGATTTA
Found at i:1123177 original size:208 final size:208
Alignment explanation
Indices: 1122963--1123415 Score: 489
Period size: 208 Copynumber: 2.2 Consensus size: 208
1122953 TTTCATCTTG
* * *
1122963 ATCATTTATTTTTGATCTTGACTCGATCTTGGTCACTTTATTTTGACTTATGGTTTTATCCCAAT
1 ATCATTTATTTTTGACCTCGACTCGATCTTGGTCACTTTATTTTGACTTATGATTTTATCCCAAT
* * * * * *
1123028 GACATGGTTTATGGTTTTATC-CTGATCATTTATTTTCAACCTCGACTCAGTCTTTGTCACTTTA
66 CACATGATTCATAGTTTTATCTC-GATCATTTATTTTCAACCTCGACTCAGTCCTCGTCACTTTA
* * * * **
1123092 TTTTGACTCATGGTTTTATCTCGATCACGTGATCTTAGCTTAATTTAGATCACTTCTTACAATTC
130 TTTTGACTCATGGTTTCATCCCGATCACATGATCTTAGCTCAATCCAGATCACTTCTTACAATTC
*
1123157 GTGATTTCATCCCA
195 ATGATTTCATCCCA
* * * * *** *
1123171 ATCATTTATTTTCT-ACCTCAACTCGATCCTGGTCACTTTATTTTGACTTGTGATTTTGTTTTAG
1 ATCATTTATTTT-TGACCTCGACTCGATCTTGGTCACTTTATTTTGACTTATGATTTTATCCCAA
* * * * * *
1123235 TCATATGATTCGTAGTTTTATTTCGATCATTTATTTTTAACCTCGACTTAGTCCTCGTTACTTTA
65 TCACATGATTCATAGTTTTATCTCGATCATTTATTTTCAACCTCGACTCAGTCCTCGTCACTTTA
* * * * * **
1123300 TTTTGACTCGTGGTTTCATCCCGGTCACATGATGTTGGCTCAATCCAGATCATTTCTTATGATTC
130 TTTTGACTCATGGTTTCATCCCGATCACATGATCTTAGCTCAATCCAGATCACTTCTTACAATTC
* * *
1123365 ATGGTTTCATCTCG
195 ATGATTTCATCCCA
*
1123379 ATCATTTATTTTTGACCTCGA-TCCGATCTTAGTCACT
1 ATCATTTATTTTTGACCTCGACT-CGATCTTGGTCACT
1123416 CTATCTCAAC
Statistics
Matches: 198, Mismatches: 43, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
207 2 0.01
208 194 0.98
209 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.46
Consensus pattern (208 bp):
ATCATTTATTTTTGACCTCGACTCGATCTTGGTCACTTTATTTTGACTTATGATTTTATCCCAAT
CACATGATTCATAGTTTTATCTCGATCATTTATTTTCAACCTCGACTCAGTCCTCGTCACTTTAT
TTTGACTCATGGTTTCATCCCGATCACATGATCTTAGCTCAATCCAGATCACTTCTTACAATTCA
TGATTTCATCCCA
Found at i:1123300 original size:297 final size:297
Alignment explanation
Indices: 1122755--1123321 Score: 654
Period size: 297 Copynumber: 1.9 Consensus size: 297
1122745 AGAAGATCTA
** * *
1122755 ATCATTTATTTTTGATCTCAACTCAGTCCTGGTCACTTTATTCTGACTCGTGATTTCATCTCAAT
1 ATCATTTATTTTCAACCTCAACTCAGTCCTGGTCACTTTATTCTGACTCATGATTTCATCTCAAT
* * * * ** * *
1122820 CATGTGCTCTTGGCTCAATCCAGATCACTTTTTATGATTCGTGGTTTCATCCTAATCATTTATTT
66 CACGTGATCTTAGCTCAATCCAGATCACTTCTTACAATTCGTGATTTCATCCCAATCATTTATTT
* * ** * * *
1122885 TTTATCTTGACTCAATCTTAGTCACTTTATTTTAACTTGTGATTTCATTCCGATCACATGATTTG
131 TCTACCTCAACTCAATCCTAGTCACTTTATTTTAACTTGTGATTTCATTCAGATCACATGATTCG
* * * * * * * *
1122950 TGGTTTCATCTTGATCATTTATTTTTGATCTTGACTCGATCTTGGTCACTTTATTTTGACTTATG
196 TAGTTTCATCTTGATCATTTATTTTTAACCTCGACTAGATCCTCGTCACTTTATTTTGACTCATG
*
1123015 GTTTTATCCCAATGACATGGTTTATGGTTTTATCCTG
261 GTTTCATCCCAATGACATGGTTTATGGTTTTATCCTG
* * * * * * *
1123052 ATCATTTATTTTCAACCTCGACTCAGTCTTTGTCACTTTATTTTGACTCATGGTTTTATCTCGAT
1 ATCATTTATTTTCAACCTCAACTCAGTCCTGGTCACTTTATTCTGACTCATGATTTCATCTCAAT
* **
1123117 CACGTGATCTTAGCTTAATTTAGATCACTTCTTACAATTCGTGATTTCATCCCAATCATTTATTT
66 CACGTGATCTTAGCTCAATCCAGATCACTTCTTACAATTCGTGATTTCATCCCAATCATTTATTT
* * * ** * *
1123182 TCTACCTCAACTCGATCCTGGTCACTTTATTTTGACTTGTGATTTTGTTTTAG-TCATATGATTC
131 TCTACCTCAACTCAATCCTAGTCACTTTATTTTAACTTGTGA-TTTCATTCAGATCACATGATTC
* *
1123246 GTAGTTTTAT-TTCGATCATTTATTTTTAACCTCGACTTAG-TCCTCGTTACTTTATTTTGACTC
195 GTAGTTTCATCTT-GATCATTTATTTTTAACCTCGAC-TAGATCCTCGTCACTTTATTTTGACTC
*
1123309 GTGGTTTCATCCC
258 ATGGTTTCATCCC
1123322 GGTCACATGA
Statistics
Matches: 219, Mismatches: 48, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
296 2 0.01
297 209 0.95
298 8 0.04
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (297 bp):
ATCATTTATTTTCAACCTCAACTCAGTCCTGGTCACTTTATTCTGACTCATGATTTCATCTCAAT
CACGTGATCTTAGCTCAATCCAGATCACTTCTTACAATTCGTGATTTCATCCCAATCATTTATTT
TCTACCTCAACTCAATCCTAGTCACTTTATTTTAACTTGTGATTTCATTCAGATCACATGATTCG
TAGTTTCATCTTGATCATTTATTTTTAACCTCGACTAGATCCTCGTCACTTTATTTTGACTCATG
GTTTCATCCCAATGACATGGTTTATGGTTTTATCCTG
Found at i:1123875 original size:3 final size:3
Alignment explanation
Indices: 1123867--1123909 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
1123857 TATTATATCA
* *
1123867 TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1123910 TTTCATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1124769 original size:5 final size:5
Alignment explanation
Indices: 1124761--1124797 Score: 56
Period size: 5 Copynumber: 7.0 Consensus size: 5
1124751 ATTTTTCTTT
1124761 TTTTA TTTTA TTTTTA TTTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA -TTTTA -TTTTA TTTTA TTTTA TTTTA
1124798 ACCTATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 20 0.65
6 11 0.35
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1124776 original size:11 final size:11
Alignment explanation
Indices: 1124760--1124796 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
1124750 GATTTTTCTT
1124760 TTTTTATTTTA
1 TTTTTATTTTA
1124771 TTTTTATTTT-
1 TTTTTATTTTA
1124781 TATTTTATTTTA
1 T-TTTTATTTTA
1124793 TTTT
1 TTTT
1124797 AACCTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.04
11 22 0.92
12 1 0.04
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:1124824 original size:32 final size:32
Alignment explanation
Indices: 1124769--1124830 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1124759 TTTTTTATTT
* * *
1124769 TATTTTTATTTTTATTTTATTTTATTTTAACC
1 TATTTTTATTATTATTCTATTTTACTTTAACC
1124801 TATTTTTATTATT-TTCTAGTTTTACTTTAA
1 TATTTTTATTATTATTCTA-TTTTACTTTAA
1124831 AAAAAAGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 4 0.15
32 22 0.85
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (32 bp):
TATTTTTATTATTATTCTATTTTACTTTAACC
Found at i:1126399 original size:7 final size:7
Alignment explanation
Indices: 1126367--1126409 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
1126357 TTGTTAATAT
1126367 ATTTTTA
1 ATTTTTA
1126374 A-TTTTA
1 ATTTTTA
*
1126380 ATTATTA
1 ATTTTTA
*
1126387 AATTTTA
1 ATTTTTA
1126394 ATTTTTA
1 ATTTTTA
1126401 TATTTTTA
1 -ATTTTTA
1126409 A
1 A
1126410 AAAATATGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
ATTTTTA
Found at i:1149199 original size:23 final size:22
Alignment explanation
Indices: 1149164--1149207 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
1149154 ACGACATAAA
*
1149164 TAAAATATAAATATAATATTATT
1 TAAAATATAAATAAAAT-TTATT
* *
1149187 TAAAATTTTAATAAAATTTAT
1 TAAAATATAAATAAAATTTAT
1149208 AAATAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAAATATAAATAAAATTTATT
Found at i:1151023 original size:2 final size:2
Alignment explanation
Indices: 1151016--1151040 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1151006 TGTACTTATT
1151016 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1151041 TTCTCCCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1153849 original size:31 final size:31
Alignment explanation
Indices: 1153811--1153872 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1153801 AGGTTTTCAA
1153811 ACCCTGTACCTTCCTCTTTTTTAATTTTGTT
1 ACCCTGTACCTTCCTCTTTTTTAATTTTGTT
1153842 ACCCTGTACCTTCCTCTTTTTTAATTTTGTT
1 ACCCTGTACCTTCCTCTTTTTTAATTTTGTT
1153873 CTCGTTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.13, C:0.26, G:0.06, T:0.55
Consensus pattern (31 bp):
ACCCTGTACCTTCCTCTTTTTTAATTTTGTT
Found at i:1161435 original size:15 final size:15
Alignment explanation
Indices: 1161390--1161443 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
1161380 TATTGAACAT
*
1161390 ATTTTTATTTTTATAA
1 ATTTTTATATTTAT-A
*
1161406 AATTTTAT-TTT-TA
1 ATTTTTATATTTATA
1161419 ATTTTTATATTTATA
1 ATTTTTATATTTATA
*
1161434 ATTTATATAT
1 ATTTTTATAT
1161444 ATAAATTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
13 8 0.24
14 4 0.12
15 14 0.42
16 7 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTATATTTATA
Found at i:1161466 original size:15 final size:13
Alignment explanation
Indices: 1161423--1161457 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1161413 TTTTTAATTT
* *
1161423 TTATATTTATAAT
1 TTATATATATAAA
1161436 TTATATATATAAA
1 TTATATATATAAA
1161449 TTATATATA
1 TTATATATA
1161458 ATTATATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTATATATATAAA
Found at i:1161616 original size:19 final size:22
Alignment explanation
Indices: 1161592--1161632 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 22
1161582 TTCAAACCAA
1161592 ATAAATT-TTAA-A-TAAATAT
1 ATAAATTATTAATACTAAATAT
1161611 ATAAATTATTAATACTAAATAT
1 ATAAATTATTAATACTAAATAT
1161633 GAGTATGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 1 0.05
22 7 0.37
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAAATTATTAATACTAAATAT
Found at i:1162498 original size:17 final size:15
Alignment explanation
Indices: 1162473--1162520 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 15
1162463 TTGCTTACTC
*
1162473 TATAATATATATATATA
1 TATATTATATA-AT-TA
*
1162490 TATATTATATAATTG
1 TATATTATATAATTA
1162505 TATATTAT-TAATTA
1 TATATTATATAATTA
1162519 TA
1 TA
1162521 GTTGACAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 7 0.25
15 9 0.32
16 2 0.07
17 10 0.36
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
TATATTATATAATTA
Found at i:1162620 original size:8 final size:8
Alignment explanation
Indices: 1162594--1162645 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
1162584 TTAATAAAAG
1162594 ATTTATAA
1 ATTTATAA
*
1162602 ATTTAAAAA
1 ATTT-ATAA
1162611 ATTTATAA
1 ATTTATAA
*
1162619 A--TAAAA
1 ATTTATAA
1162625 ATTTAATAA
1 ATTT-ATAA
1162634 ATTTATAA
1 ATTTATAA
1162642 ATTT
1 ATTT
1162646 TAATTGAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
6 5 0.14
8 17 0.47
9 14 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
ATTTATAA
Found at i:1162622 original size:32 final size:32
Alignment explanation
Indices: 1162580--1162647 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
1162570 TTTCAAATTT
*
1162580 TTTATTAATAAAAGATTT-ATAAATTTAAAAAA
1 TTTATAAATAAAA-ATTTAATAAATTTAAAAAA
* *
1162612 TTTATAAATAAAAATTTAATAAATTTATAAAT
1 TTTATAAATAAAAATTTAATAAATTTAAAAAA
1162644 TTTA
1 TTTA
1162648 ATTGAATTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 4 0.12
32 28 0.88
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (32 bp):
TTTATAAATAAAAATTTAATAAATTTAAAAAA
Found at i:1162625 original size:15 final size:15
Alignment explanation
Indices: 1162580--1162635 Score: 60
Period size: 15 Copynumber: 3.6 Consensus size: 15
1162570 TTTCAAATTT
* *
1162580 TTTATTAATAAAAGA
1 TTTATAAATAAAAAA
1162595 TTTATAAATTTAAAAAA
1 TTTATAAA--TAAAAAA
1162612 TTTATAAAT-AAAAA
1 TTTATAAATAAAAAA
1162626 TTTAATAAAT
1 TTT-ATAAAT
1162636 TTATAAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
14 8 0.22
15 14 0.39
17 14 0.39
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
TTTATAAATAAAAAA
Found at i:1162645 original size:17 final size:16
Alignment explanation
Indices: 1162588--1162645 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
1162578 TTTTTATTAA
1162588 TAAAAGATTTATAAATT
1 TAAAA-ATTTATAAATT
1162605 TAAAAAATTTATAAA--
1 T-AAAAATTTATAAATT
1162620 TAAAAATTTAATAAATT
1 TAAAAATTT-ATAAATT
*
1162637 TATAAATTT
1 TAAAAATTT
1162646 TAATTGAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 8 0.22
15 6 0.17
17 18 0.50
18 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
TAAAAATTTATAAATT
Found at i:1162650 original size:23 final size:23
Alignment explanation
Indices: 1162600--1162643 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1162590 AAAGATTTAT
1162600 AAATTTAAAAAATTTATAAATAA
1 AAATTTAAAAAATTTATAAATAA
*
1162623 AAATTTAATAAATTTATAAAT
1 AAATTTAAAAAATTTATAAAT
1162644 TTTAATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATTTAAAAAATTTATAAATAA
Found at i:1162990 original size:13 final size:13
Alignment explanation
Indices: 1162972--1162997 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1162962 TGAGTTATTG
1162972 TACTTTTTTTTTT
1 TACTTTTTTTTTT
1162985 TACTTTTTTTTTT
1 TACTTTTTTTTTT
1162998 GTTAGGGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (13 bp):
TACTTTTTTTTTT
Found at i:1169597 original size:2 final size:2
Alignment explanation
Indices: 1169590--1169624 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1169580 AGTCAAGATG
1169590 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 A
1169625 CCAAACATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1177312 original size:14 final size:14
Alignment explanation
Indices: 1177262--1177304 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
1177252 ATAACAATAG
*
1177262 GAAAGTAATGAAAT
1 GAAAGAAATGAAAT
1177276 GAAA-AAAT-AAAT
1 GAAAGAAATGAAAT
1177288 GAAAGAAATGAAAT
1 GAAAGAAATGAAAT
1177302 GAA
1 GAA
1177305 GGAGATGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 8 0.31
13 7 0.27
14 11 0.42
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (14 bp):
GAAAGAAATGAAAT
Found at i:1188483 original size:34 final size:34
Alignment explanation
Indices: 1188440--1188506 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
1188430 GAACAAGGAA
1188440 TTGTAGATGTTCGAATCTGCTGATTCTTCATGAT
1 TTGTAGATGTTCGAATCTGCTGATTCTTCATGAT
1188474 TTGTAGATGTTCGAATCTGCTGATTCTTCATGA
1 TTGTAGATGTTCGAATCTGCTGATTCTTCATGA
1188507 CCAAGAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.43
Consensus pattern (34 bp):
TTGTAGATGTTCGAATCTGCTGATTCTTCATGAT
Found at i:1188716 original size:21 final size:21
Alignment explanation
Indices: 1188692--1188732 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1188682 CCCAGAAGCA
* *
1188692 TCATTTTTTTTCCTTACATCT
1 TCATTATTTTCCCTTACATCT
*
1188713 TCATTATTTTCCCTTCCATC
1 TCATTATTTTCCCTTACATC
1188733 CCCATTTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.29, G:0.00, T:0.56
Consensus pattern (21 bp):
TCATTATTTTCCCTTACATCT
Found at i:1191858 original size:24 final size:22
Alignment explanation
Indices: 1191814--1191864 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
1191804 ATCGATTGAG
1191814 TTTGAGTCGATATAATATTAAA
1 TTTGAGTCGATATAATATTAAA
* *
1191836 TTTGAGTTCGAGTTTAATTTTAAA
1 TTTGAG-TCGA-TATAATATTAAA
1191860 TTTGA
1 TTTGA
1191865 TACTTGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.24
23 4 0.16
24 15 0.60
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (22 bp):
TTTGAGTCGATATAATATTAAA
Found at i:1192049 original size:10 final size:10
Alignment explanation
Indices: 1192025--1192054 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1192015 TATTTTATCA
1192025 ATTAAAATA-
1 ATTAAAATAT
1192034 ATTAAAATAT
1 ATTAAAATAT
1192044 ATTAAAATAT
1 ATTAAAATAT
1192054 A
1 A
1192055 AAAATTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:1193981 original size:4 final size:4
Alignment explanation
Indices: 1193962--1193994 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
1193952 ATTATAAACG
1193962 GAAA GAAA -AAA GGAAA GAAA GAAA GAAA GAAA G
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA G
1193995 GCAGAAACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 3 0.11
4 21 0.78
5 3 0.11
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:1195159 original size:20 final size:21
Alignment explanation
Indices: 1195122--1195163 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1195112 TATTTCCAGG
1195122 TAATAGGCTTATCACCTTTCT
1 TAATAGGCTTATCACCTTTCT
1195143 TAATAGGCTTA-CACCTTTCT
1 TAATAGGCTTATCACCTTTCT
1195163 T
1 T
1195164 TGTAACTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.43
Consensus pattern (21 bp):
TAATAGGCTTATCACCTTTCT
Found at i:1196287 original size:22 final size:22
Alignment explanation
Indices: 1196262--1196303 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1196252 TTTTTCTCCT
* *
1196262 TAATTCTAGGGATACAAATACG
1 TAATTATAGAGATACAAATACG
1196284 TAATTATAGAGATACAAATA
1 TAATTATAGAGATACAAATA
1196304 TAAATATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (22 bp):
TAATTATAGAGATACAAATACG
Found at i:1198157 original size:20 final size:20
Alignment explanation
Indices: 1198132--1198174 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1198122 ATTATAAGAT
1198132 AAGGGAAGATAAAGAGAATG
1 AAGGGAAGATAAAGAGAATG
*
1198152 AAGGGAAGATGAAGAGAATG
1 AAGGGAAGATAAAGAGAATG
1198172 AAG
1 AAG
1198175 CGGAGAAGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.37, T:0.09
Consensus pattern (20 bp):
AAGGGAAGATAAAGAGAATG
Found at i:1200529 original size:22 final size:22
Alignment explanation
Indices: 1200504--1200547 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1200494 ATTTTTTGCC
*
1200504 CTTAATTATAGGGATACAAATA
1 CTTAATTATAGAGATACAAATA
*
1200526 CTTAATTATAGATATACAAATA
1 CTTAATTATAGAGATACAAATA
1200548 TAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (22 bp):
CTTAATTATAGAGATACAAATA
Found at i:1200557 original size:22 final size:22
Alignment explanation
Indices: 1200507--1200560 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1200497 TTTTGCCCTT
** *
1200507 AATTATAGGGATACAAATACTT
1 AATTATAGATATACAAATACTA
1200529 AATTATAGATATACAAATA-TA
1 AATTATAGATATACAAATACTA
1200550 AATATATAGAT
1 AAT-TATAGAT
1200561 TATAATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 4 0.14
22 24 0.86
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (22 bp):
AATTATAGATATACAAATACTA
Found at i:1205121 original size:15 final size:17
Alignment explanation
Indices: 1205085--1205121 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1205075 TGTAAAAATA
1205085 TAAAAATAAAAACATG-
1 TAAAAATAAAAACATGT
*
1205101 TAAAAAAAAAAACA-GT
1 TAAAAATAAAAACATGT
1205117 TAAAA
1 TAAAA
1205122 TTTTAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.16
Consensus pattern (17 bp):
TAAAAATAAAAACATGT
Found at i:1210723 original size:2 final size:2
Alignment explanation
Indices: 1210716--1210750 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1210706 CTAAGTAGAT
1210716 TA TA 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 TA TA T
1210751 TAGTCTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1213041 original size:22 final size:21
Alignment explanation
Indices: 1212998--1213051 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
1212988 AATAATCTTC
**
1212998 TCTTTTC-TTTTCTCTCGTTT
1 TCTTTTCATTTTCTCTCACTT
1213018 TCTTTTCAATTTTCTCTCACTT
1 TCTTTTC-ATTTTCTCTCACTT
*
1213040 TCTATTCATTTT
1 TCTTTTCATTTT
1213052 GTAGCAGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.24
21 5 0.17
22 17 0.59
ACGTcount: A:0.09, C:0.24, G:0.02, T:0.65
Consensus pattern (21 bp):
TCTTTTCATTTTCTCTCACTT
Found at i:1225457 original size:22 final size:21
Alignment explanation
Indices: 1225426--1225479 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
1225416 GTACAAAAGT
*
1225426 TCATTATTATGGTATAG-TGAC
1 TCATCATTATGGTA-AGATGAC
*
1225447 TCATCACTTATGGTACGATGAC
1 TCATCA-TTATGGTAAGATGAC
1225469 TCATCATTATG
1 TCATCATTATG
1225480 ACTCATACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (21 bp):
TCATCATTATGGTAAGATGAC
Found at i:1230933 original size:12 final size:12
Alignment explanation
Indices: 1230916--1230940 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1230906 GGAGATATGT
1230916 GGTAAAGGTTTG
1 GGTAAAGGTTTG
1230928 GGTAAAGGTTTG
1 GGTAAAGGTTTG
1230940 G
1 G
1230941 TGGAATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (12 bp):
GGTAAAGGTTTG
Found at i:1234639 original size:18 final size:18
Alignment explanation
Indices: 1234616--1234661 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1234606 CTCACCTTGA
1234616 TGATGAATTTGATCTACC
1 TGATGAATTTGATCTACC
* *
1234634 TGATGAATTCGATCTACT
1 TGATGAATTTGATCTACC
1234652 TGATGAATTT
1 TGATGAATTT
1234662 CTTAACCTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41
Consensus pattern (18 bp):
TGATGAATTTGATCTACC
Found at i:1235834 original size:22 final size:22
Alignment explanation
Indices: 1235809--1235853 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1235799 ATCAAGTCAT
*
1235809 AGTGATGAGTCACCGTACCATA
1 AGTGATGAGTCACCATACCATA
*
1235831 AGTGATGAGTCACTATACCATA
1 AGTGATGAGTCACCATACCATA
1235853 A
1 A
1235854 TAATAAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (22 bp):
AGTGATGAGTCACCATACCATA
Found at i:1242101 original size:12 final size:12
Alignment explanation
Indices: 1242084--1242117 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1242074 TCACAAGACT
*
1242084 TCCTTCGAAATC
1 TCCTTCGAAACC
1242096 TCCTTCGAAACC
1 TCCTTCGAAACC
1242108 TCCTTC-AAAC
1 TCCTTCGAAAC
1242118 ACCTTGCAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.26, C:0.38, G:0.06, T:0.29
Consensus pattern (12 bp):
TCCTTCGAAACC
Found at i:1243480 original size:21 final size:21
Alignment explanation
Indices: 1243405--1243498 Score: 71
Period size: 21 Copynumber: 4.4 Consensus size: 21
1243395 TCAAGTCATA
*
1243405 ATGAGTCACTGTACCATAAGTG
1 ATGAGTCACTGTACCAT-AGTT
* * *
1243427 ATGAGTCACTATACCATAATA
1 ATGAGTCACTGTACCATAGTT
* ** **
1243448 ATAAACCTTTGTACCATAGTT
1 ATGAGTCACTGTACCATAGTT
* *
1243469 ATGAGTCATTGTACCTTAGTT
1 ATGAGTCACTGTACCATAGTT
*
1243490 ATGACTCAC
1 ATGAGTCAC
1243499 CATCCTTTAG
Statistics
Matches: 54, Mismatches: 18, Indels: 1
0.74 0.25 0.01
Matches are distributed among these distances:
21 38 0.70
22 16 0.30
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (21 bp):
ATGAGTCACTGTACCATAGTT
Found at i:1244573 original size:22 final size:22
Alignment explanation
Indices: 1244548--1244592 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1244538 TATGAGTCAT
*
1244548 AGTGATGAGTCATCGTACCATA
1 AGTGATGAGTCATCATACCATA
*
1244570 AGTGATGAGTCATTATACCATA
1 AGTGATGAGTCATCATACCATA
1244592 A
1 A
1244593 TAATGAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (22 bp):
AGTGATGAGTCATCATACCATA
Found at i:1244627 original size:21 final size:21
Alignment explanation
Indices: 1244545--1244640 Score: 93
Period size: 21 Copynumber: 4.5 Consensus size: 21
1244535 TAGTATGAGT
* *
1244545 CATAGTGATGAGTCATCGTAC
1 CATAGTAATGAGTCATTGTAC
* *
1244566 CATAAGTGATGAGTCATTATAC
1 CAT-AGTAATGAGTCATTGTAC
* ** *
1244588 CATAATAATGAACCTTTGTAC
1 CATAGTAATGAGTCATTGTAC
1244609 CATAGTAATGAGTCATTGTAC
1 CATAGTAATGAGTCATTGTAC
* *
1244630 CTTAGTTATGA
1 CATAGTAATGA
1244641 CTCACAATCC
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
21 41 0.68
22 19 0.32
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (21 bp):
CATAGTAATGAGTCATTGTAC
Found at i:1250194 original size:13 final size:12
Alignment explanation
Indices: 1250176--1250259 Score: 53
Period size: 13 Copynumber: 6.5 Consensus size: 12
1250166 ATATAATTAT
1250176 AATTATAATTTTA
1 AATTAT-ATTTTA
1250189 AATTATATTATTTA
1 AATTATA-T-TTTA
* *
1250203 TATATATTTTTTTA
1 AAT-TA-TATTTTA
1250217 ATATTATA-TTTA
1 A-ATTATATTTTA
* *
1250229 TATCATATTATTA
1 AATTATATT-TTA
*
1250242 TATTATATTTTA
1 AATTATATTTTA
1250254 AATTAT
1 AATTAT
1250260 CATATCAACT
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
11 5 0.09
12 14 0.25
13 19 0.34
14 12 0.21
15 5 0.09
16 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (12 bp):
AATTATATTTTA
Found at i:1250244 original size:24 final size:23
Alignment explanation
Indices: 1250190--1250251 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 23
1250180 ATAATTTTAA
*
1250190 ATTATATTAT-TTATATATATTTT
1 ATTATATTATATT-TATATATATT
*
1250213 TTTAATATTATATTTATATCATATT
1 ATT-ATATTATATTTATAT-ATATT
1250238 ATTATATTATATTT
1 ATTATATTATATTT
1250252 TAAATTATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 2 0.06
24 23 0.70
25 8 0.24
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
ATTATATTATATTTATATATATT
Found at i:1252045 original size:192 final size:193
Alignment explanation
Indices: 1251714--1252095 Score: 676
Period size: 192 Copynumber: 2.0 Consensus size: 193
1251704 GATGATCACG
* *
1251714 AGATCCTGGCTGATTCTAAACAAGAATGATTCATTTCTTTAAAGCAACATTGTTGAAACAATATT
1 AGATCCTGGCTGATTCTAAACAAGAATGATTCATTTCTTTAAAGCAACAGTGTTGAAACAACATT
*
1251779 GGTTCTTGCTTTGTTTTTTGAGAATGATTCTGGGGCTCCATCTCATTAGAAAGAGAACGGCCAAA
66 GGTTCTTGCTTTGCTTTTTGAGAATGATTCTGGGGCTCCATCTCATTAGAAAGAGAACGGCCAAA
1251844 AAATGGGACTTCAAACTCATATAAACCTGCTGGCCTTTCATCACCCATTATTTTACAGAGAGC
131 AAATGGGACTTCAAACTCATATAAACCTGCTGGCCTTTCATCACCCATTATTTTACAGAGAGC
*
1251907 AGATCCTGGCTGATTCTAAACAAGAATGATTCATTTCTTTAAAGCAACAGTGTTG-AGCAACATT
1 AGATCCTGGCTGATTCTAAACAAGAATGATTCATTTCTTTAAAGCAACAGTGTTGAAACAACATT
* * *
1251971 GTTTCTTGCTTTGCTTTTTGAGAATGATTCTGGTGCTCCCTCTCATTAGAAAGAGAACGGCCAAA
66 GGTTCTTGCTTTGCTTTTTGAGAATGATTCTGGGGCTCCATCTCATTAGAAAGAGAACGGCCAAA
* *
1252036 AACTGGGACTTCAAACTCATATAAACCTGCTGGTCTTTCATCACCCATTATTTTACAGAG
131 AAATGGGACTTCAAACTCATATAAACCTGCTGGCCTTTCATCACCCATTATTTTACAGAG
1252096 CATTCATCCA
Statistics
Matches: 180, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
192 126 0.70
193 54 0.30
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (193 bp):
AGATCCTGGCTGATTCTAAACAAGAATGATTCATTTCTTTAAAGCAACAGTGTTGAAACAACATT
GGTTCTTGCTTTGCTTTTTGAGAATGATTCTGGGGCTCCATCTCATTAGAAAGAGAACGGCCAAA
AAATGGGACTTCAAACTCATATAAACCTGCTGGCCTTTCATCACCCATTATTTTACAGAGAGC
Found at i:1252429 original size:2 final size:2
Alignment explanation
Indices: 1252422--1252459 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1252412 GGCCAAACCA
1252422 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
1252460 TAACAAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1253382 original size:14 final size:15
Alignment explanation
Indices: 1253363--1253391 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1253353 GTTAATGTTG
1253363 AATTAAATT-ATTAA
1 AATTAAATTAATTAA
1253377 AATTAAATTAATTAA
1 AATTAAATTAATTAA
1253392 TTAATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTAAATTAATTAA
Found at i:1253526 original size:16 final size:16
Alignment explanation
Indices: 1253501--1253533 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1253491 AATTGAATAA
1253501 TAAATATA-TTTAAAT
1 TAAATATATTTTAAAT
1253516 TAAATTATATTTTAAAT
1 TAAA-TATATTTTAAAT
1253533 T
1 T
1253534 TCTAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 4 0.25
17 8 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAATATATTTTAAAT
Found at i:1253672 original size:16 final size:16
Alignment explanation
Indices: 1253651--1253685 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1253641 TTATGTATTT
1253651 TTATTTTATATTTAGA
1 TTATTTTATATTTAGA
*
1253667 TTATTTTATATTTTGA
1 TTATTTTATATTTAGA
1253683 TTA
1 TTA
1253686 AAATTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (16 bp):
TTATTTTATATTTAGA
Found at i:1253826 original size:18 final size:19
Alignment explanation
Indices: 1253798--1253833 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1253788 TCAATTGATT
1253798 AATCAAATTAAATCAATTC
1 AATCAAATTAAATCAATTC
*
1253817 AATC-AATTAATTCAATT
1 AATCAAATTAAATCAATT
1253834 GATTTCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (19 bp):
AATCAAATTAAATCAATTC
Found at i:1255787 original size:25 final size:23
Alignment explanation
Indices: 1255759--1255806 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
1255749 CATATTAAAT
1255759 AAAAATTTATTTATATATAGTTTAA
1 AAAAATTTATTTATAT-TA-TTTAA
*
1255784 AAAATTTTATTTATATTATTTAA
1 AAAAATTTATTTATATTATTTAA
1255807 GTAAATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.23
24 2 0.09
25 15 0.68
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
AAAAATTTATTTATATTATTTAA
Found at i:1260378 original size:21 final size:21
Alignment explanation
Indices: 1260352--1260393 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1260342 GTATTATATT
*
1260352 ATATAAGTATA-TATATTTTAA
1 ATATAAATATATTA-ATTTTAA
1260373 ATATAAATATATTAATTTTAA
1 ATATAAATATATTAATTTTAA
1260394 TTAATCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATATAAATATATTAATTTTAA
Found at i:1260429 original size:20 final size:20
Alignment explanation
Indices: 1260406--1260445 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1260396 AATCTAAAAT
*
1260406 AAAATTTATATTATTAAATAA
1 AAAATTAAT-TTATTAAATAA
1260427 AAAATTAATTTATTAAATA
1 AAAATTAATTTATTAAATA
1260446 TATAAAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATTAATTTATTAAATAA
Found at i:1272336 original size:12 final size:12
Alignment explanation
Indices: 1272319--1272344 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1272309 TCTATGGTTG
1272319 TTGTTATTATTA
1 TTGTTATTATTA
1272331 TTGTTATTATTA
1 TTGTTATTATTA
1272343 TT
1 TT
1272345 AACAAAATTA
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:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTATTATTA
Found at i:1273779 original size:121 final size:122
Alignment explanation
Indices: 1273543--1273766 Score: 328
Period size: 121 Copynumber: 1.8 Consensus size: 122
1273533 ACACGTGATC
*
1273543 TGTTAAAATAATATTATCTTATATTTAATAAATATTTAATTTTTTATAATTTTATATTCAAATTA
1 TGTTAAAATAATATTATCTTATATTTAATAAATATATAATTTTTTATAATTTTATATTCAAATTA
* * * * *
1273608 GACTCTTTTACTTATAATAAATTAGTTTTAAGTTACATGCTACACGTGATAGAATCG
66 AACTCTTTCACTTATAATAAATTAGTTTTAAGATAAATGCTACACATGATAGAATCG
* *
1273665 TGTTAAAATAGTATTAT-TTTTATTTAATAAATATATAATTTTTTATAATTTTATATTCAAATTA
1 TGTTAAAATAATATTATCTTATATTTAATAAATATATAATTTTTTATAATTTTATATTCAAATTA
*
1273729 AA-TCTCTTCACTTATAATTAATT-GATTTTAAGATAAAT
66 AACTCT-TTCACTTATAATAAATTAG-TTTTAAGATAAAT
1273767 ATTTAATATG
Statistics
Matches: 92, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
120 4 0.04
121 72 0.78
122 16 0.17
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.49
Consensus pattern (122 bp):
TGTTAAAATAATATTATCTTATATTTAATAAATATATAATTTTTTATAATTTTATATTCAAATTA
AACTCTTTCACTTATAATAAATTAGTTTTAAGATAAATGCTACACATGATAGAATCG
Found at i:1276736 original size:22 final size:22
Alignment explanation
Indices: 1276706--1276751 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1276696 AAAAATATTT
*
1276706 AAATATTAAAAAATTAAATTAA
1 AAATATTAAAAAATTAAAATAA
* * *
1276728 AAATTTTAATAACTTAAAATAA
1 AAATATTAAAAAATTAAAATAA
1276750 AA
1 AA
1276752 TAATAATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATATTAAAAAATTAAAATAA
Found at i:1276892 original size:4 final size:4
Alignment explanation
Indices: 1276885--1276939 Score: 58
Period size: 4 Copynumber: 13.0 Consensus size: 4
1276875 AATCAATCAA
*
1276885 AATT AATTT AA-T AATT AATT AATT AATAA AATTT AATTT AATT AATT
1 AATT AA-TT AATT AATT AATT AATT AAT-T AA-TT AA-TT AATT AATT
1276932 AATT AATT
1 AATT AATT
1276940 CAAATAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
3 3 0.07
4 28 0.62
5 13 0.29
6 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
AATT
Found at i:1276932 original size:27 final size:25
Alignment explanation
Indices: 1276889--1276938 Score: 82
Period size: 27 Copynumber: 1.9 Consensus size: 25
1276879 AATCAAAATT
1276889 AATTTAATAATTAATTAATTAATAA
1 AATTTAATAATTAATTAATTAATAA
1276914 AATTTAATTTAATTAATTAATTAAT
1 AATTTAA--TAATTAATTAATTAAT
1276939 TCAAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 7 0.30
27 16 0.70
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AATTTAATAATTAATTAATTAATAA
Found at i:1282309 original size:2 final size:2
Alignment explanation
Indices: 1282302--1282342 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1282292 AGTCTATTTG
1282302 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1282343 GCTTTGAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1288552 original size:21 final size:23
Alignment explanation
Indices: 1288528--1288573 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
1288518 TTAAATTTAA
1288528 TTTTAAATTATT-AT-ATAAAGT
1 TTTTAAATTATTCATAATAAAGT
* *
1288549 TTTTGAGTTATTCATAATAAAGT
1 TTTTAAATTATTCATAATAAAGT
1288572 TT
1 TT
1288574 ATACTTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 2 0.10
23 9 0.43
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (23 bp):
TTTTAAATTATTCATAATAAAGT
Found at i:1289086 original size:15 final size:15
Alignment explanation
Indices: 1289066--1289096 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1289056 TGATAACGGT
1289066 TCGAATTTGATTTAA
1 TCGAATTTGATTTAA
1289081 TCGAATTTGATTTAA
1 TCGAATTTGATTTAA
1289096 T
1 T
1289097 TTTTTCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (15 bp):
TCGAATTTGATTTAA
Found at i:1294455 original size:2 final size:2
Alignment explanation
Indices: 1294442--1294483 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
1294432 AGAGGAAAGA
1294442 AG AG ACG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG A-G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1294484 AAGCGGGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1296969 original size:20 final size:20
Alignment explanation
Indices: 1296944--1296982 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1296934 AGACATTGAG
1296944 ATTCTAGAAGTAACTCCCAC
1 ATTCTAGAAGTAACTCCCAC
* *
1296964 ATTCTAGAGGTGACTCCCA
1 ATTCTAGAAGTAACTCCCA
1296983 TTATGCAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTCTAGAAGTAACTCCCAC
Found at i:1305730 original size:62 final size:63
Alignment explanation
Indices: 1305664--1305787 Score: 137
Period size: 64 Copynumber: 2.0 Consensus size: 63
1305654 ATCTGCTCAT
* * *
1305664 AAAAAAT-AAAAGTGATTATTGAAGGCG-TTTTCTGTCAGAAAA-GCCTTCAATAATTCTCCTAA
1 AAAAAATGAAAAG-GATTATTGAAGGAGTTTTTCTATCA-AAAACGCCTTCAATAAATCTCCTAA
* * * *
1305726 AAAAATTGCAGAGGATTATTGAAGGAGTTTTTTTTATCAAAAACGCCTTCAATAAATCTCCT
1 AAAAAATGAAAAGGATTATTGAAGGAG-TTTTTCTATCAAAAACGCCTTCAATAAATCTCCT
1305788 TGTCAAATAA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
62 19 0.37
63 7 0.14
64 25 0.49
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (63 bp):
AAAAAATGAAAAGGATTATTGAAGGAGTTTTTCTATCAAAAACGCCTTCAATAAATCTCCTAA
Found at i:1305937 original size:82 final size:82
Alignment explanation
Indices: 1305799--1305964 Score: 260
Period size: 82 Copynumber: 2.0 Consensus size: 82
1305789 GTCAAATAAT
* * *
1305799 TTGTGAAAAATGAAGTAGCATTGATGATTAGAGTATACGGTTGTTAATTATAAGGTCCTATGTTC
1 TTGTGAAAAATGAAGTAGCATTGATGATTAGAGTATACAGTTGTTAATTATAAGGTCATAGGTTC
* *
1305864 GATCATTTCCTTCAGCA
66 AATCATTTCCTTAAGCA
* * *
1305881 TTGTGAAAAATGGAGTAGCATTGATGATTAGAGTATACAGTTGTTAATTATGAGGTCATAGGTTT
1 TTGTGAAAAATGAAGTAGCATTGATGATTAGAGTATACAGTTGTTAATTATAAGGTCATAGGTTC
1305946 AATCATTTCCTTAAGCA
66 AATCATTTCCTTAAGCA
1305963 TT
1 TT
1305965 TTTTAAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.37
Consensus pattern (82 bp):
TTGTGAAAAATGAAGTAGCATTGATGATTAGAGTATACAGTTGTTAATTATAAGGTCATAGGTTC
AATCATTTCCTTAAGCA
Found at i:1306330 original size:65 final size:64
Alignment explanation
Indices: 1306226--1306365 Score: 203
Period size: 66 Copynumber: 2.2 Consensus size: 64
1306216 TTATGAGCAA
* **
1306226 ATTATTCAAGGTATTTTTTTACTTAAAACGCCTTCAATAAT-CCTT-TATAAAAAATTGAAAGAG
1 ATTATTGAAGGTATTTTTTTACAGAAAACGCCTTCAATAATCCCTTCTA-AAAAAATTGAAAGAG
*
1306289 ATTATTGAAGGTATTTTTTTTTACAGAAAACGCCTTCAATAATCCCTTCTAAAAAAATTGAAAGG
1 ATTATTGAAGGTA--TTTTTTTACAGAAAACGCCTTCAATAATCCCTTCTAAAAAAATTGAAAGA
1306354 G
64 G
1306355 ATTATTGAAGG
1 ATTATTGAAGG
1306366 CGTTTTTGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
63 12 0.17
65 26 0.38
66 29 0.42
67 2 0.03
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (64 bp):
ATTATTGAAGGTATTTTTTTACAGAAAACGCCTTCAATAATCCCTTCTAAAAAAATTGAAAGAG
Found at i:1309271 original size:34 final size:34
Alignment explanation
Indices: 1309224--1309317 Score: 136
Period size: 34 Copynumber: 2.8 Consensus size: 34
1309214 ATTTAGTTAC
* *
1309224 GTTTGTATCAAAAAATATCGTTAAATTT-ATGAT
1 GTTTGTATTAAAAAATATCGTTAAATTTAATAAT
1309257 GTTTGTATTAAAAAATATCGTTAAATTTAATAAT
1 GTTTGTATTAAAAAATATCGTTAAATTTAATAAT
* * *
1309291 TTTTTTATTAGAAAATATCGTTAAATT
1 GTTTGTATTAAAAAATATCGTTAAATT
1309318 AAATGACGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 27 0.49
34 28 0.51
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (34 bp):
GTTTGTATTAAAAAATATCGTTAAATTTAATAAT
Found at i:1325001 original size:20 final size:20
Alignment explanation
Indices: 1324978--1325015 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1324968 GATATTATTA
1324978 AATA-CTATTATTTATTTTCT
1 AATATCTATTA-TTATTTTCT
*
1324998 AATATTTATTATTATTTT
1 AATATCTATTATTATTTT
1325016 TTCTGTCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
AATATCTATTATTATTTTCT
Found at i:1332786 original size:14 final size:12
Alignment explanation
Indices: 1332761--1332811 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
1332751 TTTAAAAAAT
1332761 AATTTAATGAAA
1 AATTTAATGAAA
1332773 AATTTAAATCGAAA
1 AATTT-AAT-GAAA
1332787 AA-TTAAT--AA
1 AATTTAATGAAA
1332796 AATTTAATGTAAA
1 AATTTAATG-AAA
1332809 AAT
1 AAT
1332812 AAATAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
9 4 0.12
10 5 0.15
12 8 0.24
13 10 0.30
14 6 0.18
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (12 bp):
AATTTAATGAAA
Found at i:1332815 original size:26 final size:24
Alignment explanation
Indices: 1332790--1332836 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
1332780 ATCGAAAAAT
1332790 TAAT-AAAATTTAATGTAAAAATAAA
1 TAATAAAAATTT-AT-TAAAAATAAA
1332815 TAATAAAAATTTATTAAAAATA
1 TAATAAAAATTTATTAAAAATA
1332837 TTTTTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 6 0.29
26 7 0.33
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
TAATAAAAATTTATTAAAAATAAA
Found at i:1332816 original size:22 final size:23
Alignment explanation
Indices: 1332771--1332817 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1332761 AATTTAATGA
*
1332771 AAAATTTAAATCGAAAAATTAAT
1 AAAATTTAAATCGAAAAATAAAT
1332794 AAAATTT-AAT-GTAAAAATAAAT
1 AAAATTTAAATCG-AAAAATAAAT
1332816 AA
1 AA
1332818 TAAAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 14 0.64
23 7 0.32
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
AAAATTTAAATCGAAAAATAAAT
Found at i:1333681 original size:2 final size:2
Alignment explanation
Indices: 1333674--1333715 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1333664 ACGTCAAAGG
*
1333674 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1333716 GATCAAATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1334371 original size:2 final size:2
Alignment explanation
Indices: 1334364--1334398 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1334354 GATAGATGAT
1334364 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1334399 TTTTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1340743 original size:12 final size:12
Alignment explanation
Indices: 1340728--1340775 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
1340718 ATCTTATTTT
*
1340728 TTATACATAAAA
1 TTATAAATAAAA
1340740 TTAT-AATAAAA
1 TTATAAATAAAA
1340751 -TA-AAATAAAA
1 TTATAAATAAAA
1340761 TTATAAATAAAA
1 TTATAAATAAAA
1340773 TTA
1 TTA
1340776 AATTAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 9 0.28
11 8 0.25
12 15 0.47
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
TTATAAATAAAA
Found at i:1340754 original size:5 final size:5
Alignment explanation
Indices: 1340734--1340785 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
1340724 TTTTTTATAC
* * *
1340734 ATAAA ATTATA ATAAA ATAAA ATAAA ATTATAA ATAAA ATTAA ATTAA
1 ATAAA A-TAAA ATAAA ATAAA ATAAA A-TA-AA ATAAA ATAAA ATAAA
1340782 ATAA
1 ATAA
1340786 TATTATTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 29 0.73
6 8 0.20
7 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (5 bp):
ATAAA
Found at i:1340758 original size:21 final size:22
Alignment explanation
Indices: 1340734--1340783 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1340724 TTTTTTATAC
1340734 ATAAAATTAT-AATAAAATAAA
1 ATAAAATTATAAATAAAATAAA
*
1340755 ATAAAATTATAAATAAAATTAA
1 ATAAAATTATAAATAAAATAAA
*
1340777 ATTAAAT
1 ATAAAAT
1340784 AATATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
ATAAAATTATAAATAAAATAAA
Found at i:1340770 original size:17 final size:17
Alignment explanation
Indices: 1340748--1340780 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1340738 AATTATAATA
1340748 AAATAAAATAAAATTAT
1 AAATAAAATAAAATTAT
*
1340765 AAATAAAATTAAATTA
1 AAATAAAATAAAATTA
1340781 AATAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATAAAATAAAATTAT
Found at i:1341275 original size:20 final size:19
Alignment explanation
Indices: 1341235--1341282 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
1341225 ATGTATATAT
*
1341235 TTATATATTTAATAAATAAA
1 TTAT-TATTAAATAAATAAA
*
1341255 TTTTTATTAAATAATATAAA
1 TTATTATTAAATAA-ATAAA
1341275 TTATTATT
1 TTATTATT
1341283 TTAGACTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTATTAAATAAATAAA
Found at i:1341376 original size:7 final size:7
Alignment explanation
Indices: 1341366--1341390 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1341356 TAAAAAATAA
1341366 TTTTAAT
1 TTTTAAT
1341373 TTTTAAT
1 TTTTAAT
1341380 TTTTAAT
1 TTTTAAT
1341387 TTTT
1 TTTT
1341391 TTAAATGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTAAT
Found at i:1351403 original size:11 final size:11
Alignment explanation
Indices: 1351387--1351412 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1351377 TTTCACTTTT
1351387 TCATATTATAA
1 TCATATTATAA
1351398 TCATATTATAA
1 TCATATTATAA
1351409 TCAT
1 TCAT
1351413 GTATTACTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (11 bp):
TCATATTATAA
Found at i:1352171 original size:18 final size:18
Alignment explanation
Indices: 1352148--1352186 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1352138 ACGTATAAAT
1352148 ACAAAATA-AAAGTACCCC
1 ACAAAATAGAAA-TACCCC
1352166 ACAAAATAGAAATACCCC
1 ACAAAATAGAAATACCCC
1352184 ACA
1 ACA
1352187 TCCCACAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.56, C:0.28, G:0.05, T:0.10
Consensus pattern (18 bp):
ACAAAATAGAAATACCCC
Found at i:1360236 original size:2 final size:2
Alignment explanation
Indices: 1360229--1360264 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1360219 TCATCAAATC
1360229 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
1360265 TTGGAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1364852 original size:16 final size:18
Alignment explanation
Indices: 1364821--1364854 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1364811 AAATTCAAAA
1364821 AGTCATGATATTTTATAT
1 AGTCATGATATTTTATAT
1364839 AGTCAT-AT-TTTTATAT
1 AGTCATGATATTTTATAT
1364855 TTAAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (18 bp):
AGTCATGATATTTTATAT
Found at i:1368364 original size:22 final size:24
Alignment explanation
Indices: 1368324--1368373 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
1368314 ATATATTTAG
*
1368324 TAAATATATTTTTATTAAA-TAAT
1 TAAATATATTATTATTAAATTAAT
1368347 ATAAAT-TATTATT-TTAAATTAAT
1 -TAAATATATTATTATTAAATTAAT
1368370 TAAA
1 TAAA
1368374 ATTAATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 9 0.38
23 10 0.42
24 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAATATATTATTATTAAATTAAT
Found at i:1370420 original size:15 final size:15
Alignment explanation
Indices: 1370400--1370431 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1370390 ATTAAGAGAA
1370400 TAGTTTATGAAATAT
1 TAGTTTATGAAATAT
*
1370415 TAGTTTATGATATAT
1 TAGTTTATGAAATAT
1370430 TA
1 TA
1370432 TCCTTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (15 bp):
TAGTTTATGAAATAT
Found at i:1380090 original size:32 final size:34
Alignment explanation
Indices: 1380054--1380122 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 34
1380044 AAGTGATCAA
* *
1380054 ATTATATCCAAACAATAAA-AATAA-AAAATTAT
1 ATTATATCAAAACAATAAATAAAAATAAAATTAT
* *
1380086 ATTATATTAAAATAATAAATAAAAATAAAATTAT
1 ATTATATCAAAACAATAAATAAAAATAAAATTAT
1380120 ATT
1 ATT
1380123 CAAATAATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 16 0.52
33 4 0.13
34 11 0.35
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (34 bp):
ATTATATCAAAACAATAAATAAAAATAAAATTAT
Found at i:1380109 original size:29 final size:30
Alignment explanation
Indices: 1380068--1380144 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
1380058 TATCCAAACA
* *
1380068 ATAA-AAATAAAAAATTATATTATATTAAA
1 ATAATAAATAAAAAATAAAATTATATTAAA
*
1380097 ATAATAAAT-AAAAATAAAATTATATTCAA
1 ATAATAAATAAAAAATAAAATTATATTAAA
*
1380126 ATAATGAAA-AAATAATAAA
1 ATAAT-AAATAAAAAATAAA
1380145 GTAATATTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 26 0.63
30 15 0.37
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (30 bp):
ATAATAAATAAAAAATAAAATTATATTAAA
Found at i:1380152 original size:30 final size:29
Alignment explanation
Indices: 1380067--1380154 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
1380057 ATATCCAAAC
* * * *
1380067 AATAA-AAATAAAAAATTATATTATATTAA
1 AATAATAAAT-AAAAATAAAATAATATTCA
*
1380096 AATAATAAATAAAAATAAAATTATATTCA
1 AATAATAAATAAAAATAAAATAATATTCA
*
1380125 AATAATGAAA-AAATAATAAAGTAATATTCA
1 AATAAT-AAATAAA-AATAAAATAATATTCA
1380155 CACAATTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
29 30 0.59
30 21 0.41
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (29 bp):
AATAATAAATAAAAATAAAATAATATTCA
Found at i:1380922 original size:21 final size:21
Alignment explanation
Indices: 1380896--1380940 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1380886 AAAAAGAAAC
1380896 CTGCTGAAGGAAACCAGCAGT
1 CTGCTGAAGGAAACCAGCAGT
* *
1380917 CTGCTGCAGGAAACCAGTAGT
1 CTGCTGAAGGAAACCAGCAGT
1380938 CTG
1 CTG
1380941 TTGTTGTCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.18
Consensus pattern (21 bp):
CTGCTGAAGGAAACCAGCAGT
Found at i:1383566 original size:15 final size:14
Alignment explanation
Indices: 1383546--1383578 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
1383536 TAATTTTAAG
1383546 TTTAATTTGATTTGA
1 TTTAATTTGA-TTGA
1383561 TTTAATTTGATTGA
1 TTTAATTTGATTGA
1383575 TTTA
1 TTTA
1383579 TTTATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (14 bp):
TTTAATTTGATTGA
Done.