Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 121 of 290
Found at i:41127566 original size:25 final size:25
Alignment explanation
Indices: 41127538--41127589 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
41127528 TGCCTTATAA
41127538 AATGTTTAAATAGCTAGGTCTTGAG
1 AATGTTTAAATAGCTAGGTCTTGAG
41127563 AATGTTTAAATAGCTAGGTCTTGAG
1 AATGTTTAAATAGCTAGGTCTTGAG
41127588 AA
1 AA
41127590 ACCCAAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (25 bp):
AATGTTTAAATAGCTAGGTCTTGAG
Found at i:41134068 original size:55 final size:55
Alignment explanation
Indices: 41133984--41134101 Score: 139
Period size: 55 Copynumber: 2.1 Consensus size: 55
41133974 AAGTCTCACA
* * * *
41133984 CCCGTGTTAATCTAATAGGTTCAGCCACGGTTGC-TTGGCACAGGCGTGTCGCATG
1 CCCGTGTTAATCTAACAGGTTCAGCCACGGTTACAAT-GCACAGGCGTGTCACATG
* * ** *
41134039 CCCGTGTTAATTTGACAGGTTTGGCCACGGTTACAATGCACGGGCGTGTCACATG
1 CCCGTGTTAATCTAACAGGTTCAGCCACGGTTACAATGCACAGGCGTGTCACATG
41134094 CCCGTGTT
1 CCCGTGTT
41134102 GTTTTGGCAG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
55 52 0.98
56 1 0.02
ACGTcount: A:0.18, C:0.25, G:0.29, T:0.28
Consensus pattern (55 bp):
CCCGTGTTAATCTAACAGGTTCAGCCACGGTTACAATGCACAGGCGTGTCACATG
Found at i:41141546 original size:13 final size:13
Alignment explanation
Indices: 41141530--41141561 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
41141520 CTCACACGGG
41141530 CGTGTCACATGGC
1 CGTGTCACATGGC
41141543 CGTGTCACATGGC
1 CGTGTCACATGGC
41141556 CGTGTC
1 CGTGTC
41141562 CCTGTGGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.31, G:0.31, T:0.25
Consensus pattern (13 bp):
CGTGTCACATGGC
Found at i:41150210 original size:30 final size:30
Alignment explanation
Indices: 41150175--41150232 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
41150165 CACGACCATT
41150175 ACACACGGGCGTGTGG-TCTACCCGTGTGTC
1 ACACACGGGCGTGTGGATC-ACCCGTGTGTC
41150205 ACACACGGGCGTGTGGATCACCCGTGTG
1 ACACACGGGCGTGTGGATCACCCGTGTG
41150233 GAAGTGCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.16, C:0.29, G:0.34, T:0.21
Consensus pattern (30 bp):
ACACACGGGCGTGTGGATCACCCGTGTGTC
Found at i:41152095 original size:6 final size:6
Alignment explanation
Indices: 41152084--41152119 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
41152074 AAATAAAGGG
41152084 AAATAA AAATAA AAATAA AAATAA AAAT-A AAATAA A
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A
41152120 TAGACTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:41170121 original size:22 final size:21
Alignment explanation
Indices: 41170091--41170156 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
41170081 TACAAATTAA
41170091 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
41170113 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
41170134 ATCT--AAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
41170153 ATCT
1 ATCT
41170157 AAGATTGTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 19 0.46
21 10 0.24
22 12 0.29
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:41170143 original size:19 final size:19
Alignment explanation
Indices: 41170108--41170186 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
41170098 AGATTACAAG
41170108 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
41170129 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
41170148 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
41170165 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
41170184 ATC
1 ATC
41170187 CTTAAAGATT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
20 1 0.02
21 8 0.14
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:41170150 original size:14 final size:15
Alignment explanation
Indices: 41170130--41170186 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
41170120 AGATTGCATA
41170130 TCATATCTAAGATTG
1 TCATATCTAAGATTG
41170145 CATATCATATCTAAGATTG
1 ----TCATATCTAAGATTG
41170164 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
41170181 -CATATC
1 TCATATC
41170187 CTTAAAGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.16
17 17 0.45
19 15 0.39
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:41170172 original size:36 final size:39
Alignment explanation
Indices: 41170108--41170186 Score: 128
Period size: 36 Copynumber: 2.1 Consensus size: 39
41170098 AGATTACAAG
41170108 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGCAT
1 ATCATATCTTCAAGATTG-ATATCATATCTAAGATTGCAT
41170148 ATCATATC-T-AAGATTG-TATCATATCTAAGATTGCAT
1 ATCATATCTTCAAGATTGATATCATATCTAAGATTGCAT
41170184 ATC
1 ATC
41170187 CTTAAAGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
36 23 0.59
38 7 0.18
39 1 0.03
40 8 0.21
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (39 bp):
ATCATATCTTCAAGATTGATATCATATCTAAGATTGCAT
Found at i:41171168 original size:47 final size:47
Alignment explanation
Indices: 41171114--41171243 Score: 188
Period size: 47 Copynumber: 2.8 Consensus size: 47
41171104 ATGTGAATAA
*
41171114 TACCTTGATTTGGCTATAGGCCATGGTATAGGTATTCAGAGAGAAGT
1 TACCTTGATTTGGCTATAGGCCATGGTATAGGTACTCAGAGAGAAGT
* * * * *
41171161 TACCTTGATTTGGCTACAAGCCATGGTATAGGTACTCCGGGATAAGT
1 TACCTTGATTTGGCTATAGGCCATGGTATAGGTACTCAGAGAGAAGT
* *
41171208 TACCTTGATTTGGCTATGGGTCATGGTATAGGTACT
1 TACCTTGATTTGGCTATAGGCCATGGTATAGGTACT
41171244 TATTGATTAA
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 73 1.00
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (47 bp):
TACCTTGATTTGGCTATAGGCCATGGTATAGGTACTCAGAGAGAAGT
Found at i:41171345 original size:20 final size:20
Alignment explanation
Indices: 41171320--41171364 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
41171310 TTTGAGAAAG
*
41171320 AGGTACGTACGAGACGGTAC
1 AGGTACGTACGAGACGATAC
41171340 AGGTACGTACGAGACGATAC
1 AGGTACGTACGAGACGATAC
41171360 AGGTA
1 AGGTA
41171365 TGTATGGAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.33, T:0.16
Consensus pattern (20 bp):
AGGTACGTACGAGACGATAC
Found at i:41172676 original size:30 final size:30
Alignment explanation
Indices: 41172640--41172699 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
41172630 TGTGAAATGT
41172640 TAGTTAACTGTTGTGTTTGGTCGGTAATAC
1 TAGTTAACTGTTGTGTTTGGTCGGTAATAC
41172670 TAGTTAACTGTTGTGTTTGGTCGGTAATAC
1 TAGTTAACTGTTGTGTTTGGTCGGTAATAC
41172700 CTCTCAACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (30 bp):
TAGTTAACTGTTGTGTTTGGTCGGTAATAC
Found at i:41181165 original size:11 final size:11
Alignment explanation
Indices: 41181151--41181200 Score: 64
Period size: 11 Copynumber: 4.4 Consensus size: 11
41181141 AATATTTTAA
41181151 AAATTCTTGAC
1 AAATTCTTGAC
* *
41181162 AAATTATTTTGTC
1 AAA-T-TCTTGAC
41181175 AAATTCTTGAC
1 AAATTCTTGAC
41181186 AAATTCTTGAC
1 AAATTCTTGAC
41181197 AAAT
1 AAAT
41181201 ATACAAGTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 23 0.70
12 2 0.06
13 8 0.24
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATTCTTGAC
Found at i:41181600 original size:18 final size:19
Alignment explanation
Indices: 41181579--41181614 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
41181569 TTTGAAATTC
41181579 TTCATCTCT-CAATTCTAT
1 TTCATCTCTGCAATTCTAT
*
41181597 TTCATCTTTGCAATTCTA
1 TTCATCTCTGCAATTCTA
41181615 CAAAAAGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.22, C:0.25, G:0.03, T:0.50
Consensus pattern (19 bp):
TTCATCTCTGCAATTCTAT
Found at i:41195948 original size:20 final size:20
Alignment explanation
Indices: 41195912--41195949 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41195902 AAAAGACCAT
**
41195912 TTAACCGTTAACTTTAACAA
1 TTAACCGTTAAAGTTAACAA
41195932 TTAACCGTTAAAGTTAAC
1 TTAACCGTTAAAGTTAAC
41195950 TGCCTCTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (20 bp):
TTAACCGTTAAAGTTAACAA
Found at i:41196054 original size:18 final size:17
Alignment explanation
Indices: 41196008--41196057 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
41195998 ACATGTAGCA
*
41196008 AAAAAATTATAAAA-AT
1 AAAAAATTATAAAATTT
*
41196024 -AAAAATCAATAAAATTT
1 AAAAAAT-TATAAAATTT
*
41196041 AAAAAATTATTAAATTT
1 AAAAAATTATAAAATTT
41196058 TAATGAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
15 6 0.22
16 6 0.22
17 9 0.33
18 6 0.22
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAAAATTATAAAATTT
Found at i:41196298 original size:29 final size:27
Alignment explanation
Indices: 41196259--41196419 Score: 90
Period size: 29 Copynumber: 5.5 Consensus size: 27
41196249 TTCTTTACAG
41196259 TTTTCATAATTTTCTTATGACTTTATAAAA
1 TTTT-ATAATTTT-TTATGA-TTTATAAAA
* *
41196289 TTTTATAATTTTTCTAT-ATTTCTATATA
1 TTTTATAATTTTT-TATGATTTATA-AAA
41196317 TTTTATATATTTTTTATGATTTTTATAAAA
1 TTTTATA-ATTTTTTATGA--TTTATAAAA
* * * *
41196347 TTTTAAAACCTTTTTTATAATTTTTTACAA
1 TTTTATAA--TTTTTTATGA-TTTATAAAA
* * * * *
41196377 TTTTTTAAATTCTTTCTAATTTTTAATAA
1 TTTTAT-AATTTTTTATGATTTATAA-AA
41196406 TTTTTATAATTTTT
1 -TTTTATAATTTTT
41196420 ATAAATTTTA
Statistics
Matches: 105, Mismatches: 15, Indels: 23
0.73 0.10 0.16
Matches are distributed among these distances:
27 5 0.05
28 20 0.19
29 35 0.33
30 29 0.28
31 16 0.15
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.61
Consensus pattern (27 bp):
TTTTATAATTTTTTATGATTTATAAAA
Found at i:41196325 original size:9 final size:9
Alignment explanation
Indices: 41196288--41196343 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
41196278 ACTTTATAAA
41196288 ATTTTATA-
1 ATTTTATAT
*
41196296 ATTTTTCTAT
1 A-TTTTATAT
41196306 ATTTCTATAT
1 ATTT-TATAT
41196316 ATTTTATAT
1 ATTTTATAT
*
41196325 ATTTTTTAT
1 ATTTTATAT
41196334 GATTTT-TAT
1 -ATTTTATAT
41196343 A
1 A
41196344 AAATTTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
8 2 0.05
9 25 0.61
10 14 0.34
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (9 bp):
ATTTTATAT
Found at i:41196380 original size:9 final size:9
Alignment explanation
Indices: 41196289--41196453 Score: 113
Period size: 10 Copynumber: 17.4 Consensus size: 9
41196279 CTTTATAAAA
41196289 TTTTATAAT
1 TTTTATAAT
*
41196298 TTTTCTATAT
1 TTTTATA-AT
*
41196308 TTCTATATAT
1 TTTTATA-AT
*
41196318 TTTATATATT
1 TTT-TATAAT
*
41196328 TTTTATGAT
1 TTTTATAAT
*
41196337 TTTTATAAAA
1 TTTTAT-AAT
*
41196347 TTTTAAAACCTT
1 TTTTATAA---T
41196359 TTTTATAATT
1 TTTTATAA-T
*
41196369 TTTTACAAT
1 TTTTATAAT
41196378 TTTT-TAAAT
1 TTTTAT-AAT
*
41196387 TCTTTCTAAT
1 T-TTTATAAT
41196397 TTTTAATAAT
1 TTTT-ATAAT
41196407 TTTTATAAT
1 TTTTATAAT
41196416 TTTTATAAAT
1 TTTTAT-AAT
*
41196426 TTTAATAAT
1 TTTTATAAT
41196435 TTTT-T-AT
1 TTTTATAAT
41196442 TTTTAT-AT
1 TTTTATAAT
41196450 TTTT
1 TTTT
41196454 TTACCACATG
Statistics
Matches: 127, Mismatches: 17, Indels: 25
0.75 0.10 0.15
Matches are distributed among these distances:
7 6 0.05
8 8 0.06
9 47 0.37
10 54 0.43
11 5 0.04
12 7 0.06
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:41196433 original size:19 final size:19
Alignment explanation
Indices: 41196280--41196453 Score: 128
Period size: 19 Copynumber: 9.2 Consensus size: 19
41196270 TTCTTATGAC
*
41196280 TTTATAAAATTTTATAATT
1 TTTATAAATTTTTATAATT
* * *
41196299 TTTCTATATTTCTAT-ATAT
1 TTTATAAATTTTTATAAT-T
* *
41196318 TTTATATATTTTTTATGATT
1 TTTATA-AATTTTTATAATT
* *
41196338 TTTATAAAATTTTAAAACCTTT
1 TTTATAAATTTTTATAA---TT
* *
41196360 TTTATAATTTTTTACAATT
1 TTTATAAATTTTTATAATT
*
41196379 TTT-TAAATTCTTTCTAATT
1 TTTATAAATT-TTTATAATT
41196398 TTTA-ATAATTTTTATAATT
1 TTTATA-AATTTTTATAATT
*
41196417 TTTATAAATTTTAATAATT
1 TTTATAAATTTTTATAATT
41196436 TTT-T--ATTTTTAT-ATT
1 TTTATAAATTTTTATAATT
41196451 TTT
1 TTT
41196454 TTACCACATG
Statistics
Matches: 124, Mismatches: 21, Indels: 24
0.73 0.12 0.14
Matches are distributed among these distances:
15 6 0.05
16 7 0.06
18 8 0.06
19 67 0.54
20 18 0.15
21 2 0.02
22 16 0.13
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (19 bp):
TTTATAAATTTTTATAATT
Found at i:41196702 original size:85 final size:85
Alignment explanation
Indices: 41196613--41196779 Score: 207
Period size: 85 Copynumber: 2.0 Consensus size: 85
41196603 AAGTACGAGA
* *
41196613 TTAATTG-TATTTTTTGAAAAAATTTGA-AAGCCTTTTT-ATGC-ATTTTGAAAGTTTAAGTACC
1 TTAATTGCT-TTTTTTAAAAAAATTT-ACAAGCCTTTTTGAT-CTATTTTAAAAGTTTAAGTACC
* *
41196674 GAATTGAGTGTAAAAAAAAAGGGC
63 AAATTGAATG-AAAAAAAAAGGGC
* *
41196698 TTAATTGCTTTTTTTAAAAAAATTTACAGGCCTTTTTGATCTATTTTAAAAGTTTAAGTATCAAA
1 TTAATTGCTTTTTTTAAAAAAATTTACAAGCCTTTTTGATCTATTTTAAAAGTTTAAGTACCAAA
*
41196763 TTGAATGAAAAAGAAAG
66 TTGAATGAAAAAAAAAG
41196780 CAATAGCTTA
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
84 1 0.01
85 41 0.58
86 29 0.41
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (85 bp):
TTAATTGCTTTTTTTAAAAAAATTTACAAGCCTTTTTGATCTATTTTAAAAGTTTAAGTACCAAA
TTGAATGAAAAAAAAAGGGC
Found at i:41196756 original size:86 final size:87
Alignment explanation
Indices: 41196613--41196807 Score: 220
Period size: 86 Copynumber: 2.2 Consensus size: 87
41196603 AAGTACGAGA
* *
41196613 TTAATTG-TATTTTTTGAAAAAATTTGAAAGCCTTTTTATGCATTTTGAAAGTTTAAGTACCGAA
1 TTAATTGCT-TTTTTTGAAAAAATTTGAAAGCCTTTTTATGCATTTTAAAAGTTTAAGTACCAAA
* * *
41196677 TTGAGTGTAAAA-AAA-AAGGGC
65 TTGAATGAAAAAGAAACAAGAGC
* * *
41196698 TTAATTGCTTTTTTTAAAAAAATTT-ACAGGCCTTTTTGAT-CTATTTTAAAAGTTTAAGTATCA
1 TTAATTGCTTTTTTTGAAAAAATTTGA-AAGCCTTTTT-ATGC-ATTTTAAAAGTTTAAGTACCA
*
41196761 AATTGAATGAAAAAGAAAGCAATAGC
63 AATTGAATGAAAAAGAAA-CAAGAGC
*
41196787 TTAATTGCTTCTTTTGAAAAA
1 TTAATTGCTTTTTTTGAAAAA
41196808 GTTCGAGGAC
Statistics
Matches: 92, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
84 1 0.01
85 32 0.35
86 33 0.36
87 3 0.03
89 23 0.25
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.39
Consensus pattern (87 bp):
TTAATTGCTTTTTTTGAAAAAATTTGAAAGCCTTTTTATGCATTTTAAAAGTTTAAGTACCAAAT
TGAATGAAAAAGAAACAAGAGC
Found at i:41198567 original size:48 final size:48
Alignment explanation
Indices: 41198486--41198594 Score: 200
Period size: 48 Copynumber: 2.2 Consensus size: 48
41198476 TTCTTTCATC
41198486 TTTTCTATTGTAACACTGTTCATTACGATAACACCTTTAAATCCAATGAA
1 TTTT-TATT-TAACACTGTTCATTACGATAACACCTTTAAATCCAATGAA
41198536 TTTTTATTTAACACTGTTCATTACGATAACACCTTTAAATCCAATGAA
1 TTTTTATTTAACACTGTTCATTACGATAACACCTTTAAATCCAATGAA
41198584 TTTTTATTTAA
1 TTTTTATTTAA
41198595 GTTATAACTG
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
48 51 0.86
49 4 0.07
50 4 0.07
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.42
Consensus pattern (48 bp):
TTTTTATTTAACACTGTTCATTACGATAACACCTTTAAATCCAATGAA
Found at i:41199454 original size:18 final size:17
Alignment explanation
Indices: 41199431--41199465 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41199421 TTGCCGGTAG
41199431 ATACATGCATATGGATGC
1 ATACATGCATA-GGATGC
*
41199449 ATACATGCTTAGGATGC
1 ATACATGCATAGGATGC
41199466 CATTTCCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (17 bp):
ATACATGCATAGGATGC
Found at i:41205252 original size:29 final size:30
Alignment explanation
Indices: 41205218--41205274 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
41205208 ATATAATAAC
*
41205218 TCTTAATGTTT-A-ACATTCTATTAATTTTA
1 TCTTAAT-TTTGACACATTCAATTAATTTTA
41205247 TCTTAATTTTGACACATTCAATTAATTT
1 TCTTAATTTTGACACATTCAATTAATTT
41205275 GGTCTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 3 0.12
29 8 0.32
30 14 0.56
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.53
Consensus pattern (30 bp):
TCTTAATTTTGACACATTCAATTAATTTTA
Found at i:41218257 original size:51 final size:51
Alignment explanation
Indices: 41218186--41218299 Score: 192
Period size: 51 Copynumber: 2.2 Consensus size: 51
41218176 CTGATCACAT
*
41218186 TTATAACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
41218237 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* *
41218288 TTGTCCCTTGTC
1 TTATCACTTGTC
41218300 GCTTGTCACT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:41219838 original size:60 final size:60
Alignment explanation
Indices: 41219745--41219863 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
41219735 TTAGTCCTAG
*
41219745 TTTATTAAGTAAATTTTGCAATATTCCAATTTTGGCCTTAATACATCAATTTTCCTGCTT
1 TTTATTAAGTAAATTTTGCAATATTCCAATTTTGGCCTTAATACATCAATTGTCCTGCTT
* * *
41219805 TTTATTAAGTAAATTTTGCAATATTCCAATTTTGGTCTTCATACTTCAATTGTCCTGCT
1 TTTATTAAGTAAATTTTGCAATATTCCAATTTTGGCCTTAATACATCAATTGTCCTGCT
41219864 GATTTCATGC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.27, C:0.17, G:0.09, T:0.47
Consensus pattern (60 bp):
TTTATTAAGTAAATTTTGCAATATTCCAATTTTGGCCTTAATACATCAATTGTCCTGCTT
Found at i:41225886 original size:51 final size:51
Alignment explanation
Indices: 41225815--41226642 Score: 1629
Period size: 51 Copynumber: 16.2 Consensus size: 51
41225805 CTGATCACAT
41225815 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
41225866 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
41225917 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
41225968 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
41226019 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
41226070 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
41226121 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
41226172 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
41226223 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
41226274 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
41226325 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
41226376 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
41226427 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
41226478 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
41226529 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
41226580 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* *
41226631 TTGTCCCTTGTC
1 TTATCACTTGTC
41226643 GCTTGTCACT
Statistics
Matches: 774, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 774 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.32
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:41233424 original size:154 final size:154
Alignment explanation
Indices: 41233193--41233499 Score: 569
Period size: 154 Copynumber: 2.0 Consensus size: 154
41233183 TCTCGCTCTT
41233193 GCATCATAGAAATTGGAATATCACTACTTGTTCCTTGTTCAGAAGTCTGCACTCTACTGTTAGCT
1 GCATCATAGAAATTGGAATATCACTACTTGTTCCTTGTTCAGAAGTCTGCACTCTACTGTTAGCT
* *
41233258 TCCTCCTGTTCAGTGCGTTCATGTCTATCTGACATCTTTATAATCAAAGAATATCTATAAAAATG
66 TCCTCCTATTCAGTGCGTTCAGGTCTATCTGACATCTTTATAATCAAAGAATATCTATAAAAATG
41233323 ACAAAGATTAGATCGGATCATACC
131 ACAAAGATTAGATCGGATCATACC
* *
41233347 GCATCATAGAAATTGGAATATCCCTACTTGTTCCTTGTTCAGAAGTCTGCACTCTACTGTTTGCT
1 GCATCATAGAAATTGGAATATCACTACTTGTTCCTTGTTCAGAAGTCTGCACTCTACTGTTAGCT
*
41233412 TCCTCCTATTCAGTGCGTTCAGGTCTATCTGACATCTTTATAATCGAAGAATATCTATAAAAATG
66 TCCTCCTATTCAGTGCGTTCAGGTCTATCTGACATCTTTATAATCAAAGAATATCTATAAAAATG
41233477 ACAAAGATTAGATCGGATCATAC
131 ACAAAGATTAGATCGGATCATAC
41233500 ACATCACACT
Statistics
Matches: 148, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 148 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (154 bp):
GCATCATAGAAATTGGAATATCACTACTTGTTCCTTGTTCAGAAGTCTGCACTCTACTGTTAGCT
TCCTCCTATTCAGTGCGTTCAGGTCTATCTGACATCTTTATAATCAAAGAATATCTATAAAAATG
ACAAAGATTAGATCGGATCATACC
Found at i:41233949 original size:196 final size:196
Alignment explanation
Indices: 41233615--41233994 Score: 715
Period size: 196 Copynumber: 1.9 Consensus size: 196
41233605 CACTCCTTAC
*
41233615 CCGTATTCGTCACCAGAATAGGGTAGGAGGCATTACCGGAGTTTACCGAATTAATTTTCCATTAA
1 CCGTATTCGTCACCAGAATAGGGTAGGAGGCATTACCGAAGTTTACCGAATTAATTTTCCATTAA
*
41233680 TACGAGTTAAATACTATTCGTTTACTAAAACATGTCATGGCGTCCTTTAGATGGGCCTCCAGAGC
66 TACGAGTTAAATACTATTCATTTACTAAAACATGTCATGGCGTCCTTTAGATGGGCCTCCAGAGC
41233745 CCAAAACATACTTCGAGACCAAACCAAAATTAAATCGAAACCATAGGGAATTTTATCATTTAAGT
131 CCAAAACATACTTCGAGACCAAACCAAAATTAAATCGAAACCATAGGGAATTTTATCATTTAAGT
41233810 A
196 A
*
41233811 CCGTATTCGTCACCAGAATAGGGTAGGAGGCATTACCGAAGTTTACCTAATTAATTTTCCATTAA
1 CCGTATTCGTCACCAGAATAGGGTAGGAGGCATTACCGAAGTTTACCGAATTAATTTTCCATTAA
*
41233876 TACGAGTTAAATACTATTCATTTACTAAAACATGTCATGGCGTCCTTTAGATGGGCCTCTAGAGC
66 TACGAGTTAAATACTATTCATTTACTAAAACATGTCATGGCGTCCTTTAGATGGGCCTCCAGAGC
*
41233941 CCAAAACATACTTCGAGACCAAACCAGAATTAAATCGAAACCATAGGGAATTTT
131 CCAAAACATACTTCGAGACCAAACCAAAATTAAATCGAAACCATAGGGAATTTT
41233995 TCGCAAAATC
Statistics
Matches: 179, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
196 179 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (196 bp):
CCGTATTCGTCACCAGAATAGGGTAGGAGGCATTACCGAAGTTTACCGAATTAATTTTCCATTAA
TACGAGTTAAATACTATTCATTTACTAAAACATGTCATGGCGTCCTTTAGATGGGCCTCCAGAGC
CCAAAACATACTTCGAGACCAAACCAAAATTAAATCGAAACCATAGGGAATTTTATCATTTAAGT
A
Found at i:41238322 original size:27 final size:27
Alignment explanation
Indices: 41238286--41238339 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
41238276 TTCTCATAAA
*
41238286 AAATTATTAACAAATCATA-AAAATTAT
1 AAATTATTAA-AAATAATATAAAATTAT
41238313 AAATTATTAAAAATAATATAAAATTAT
1 AAATTATTAAAAATAATATAAAATTAT
41238340 TAAAAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (27 bp):
AAATTATTAAAAATAATATAAAATTAT
Found at i:41238323 original size:17 final size:17
Alignment explanation
Indices: 41238303--41238352 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 17
41238293 TAACAAATCA
41238303 TAAAAATTATAAATTAT
1 TAAAAATTATAAATTAT
41238320 TAAAAATAATATAAAATTAT
1 TAAAAAT--TAT-AAATTAT
41238340 TAAAAA-TATAAAT
1 TAAAAATTATAAAT
41238353 ATTGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.13
17 10 0.33
19 3 0.10
20 13 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAATTATAAATTAT
Found at i:41238326 original size:10 final size:10
Alignment explanation
Indices: 41238284--41238346 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
41238274 TTTTCTCATA
41238284 AAAAATTATT
1 AAAAATTATT
*
41238294 AACAAATCA-T
1 AA-AAATTATT
41238304 AAAAATTA-T
1 AAAAATTATT
41238313 --AAATTATT
1 AAAAATTATT
*
41238321 AAAAA-TAAT
1 AAAAATTATT
41238330 ATAAAATTATT
1 A-AAAATTATT
41238341 AAAAAT
1 AAAAAT
41238347 ATAAATATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
7 6 0.14
8 1 0.02
9 10 0.23
10 17 0.40
11 9 0.21
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAAATTATT
Found at i:41238360 original size:17 final size:17
Alignment explanation
Indices: 41238302--41238367 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
41238292 TTAACAAATC
41238302 ATAAAAATTATAAATTATT
1 ATAAAAA-TATAAA-TATT
*
41238321 AAAAATAATATAAA-ATT
1 ATAAA-AATATAAATATT
41238338 ATTAAAAATATAAATATT
1 A-TAAAAATATAAATATT
*
41238356 GT-AAAATATAAA
1 ATAAAAATATAAA
41238368 AAATATAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
16 10 0.24
17 13 0.32
18 6 0.15
19 10 0.24
20 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
ATAAAAATATAAATATT
Found at i:41238375 original size:25 final size:25
Alignment explanation
Indices: 41238285--41238394 Score: 95
Period size: 25 Copynumber: 4.5 Consensus size: 25
41238275 TTTCTCATAA
*
41238285 AAAATTATTAACAAATCATAAAAATTAT
1 AAAA-TATTAA-AAAT-ATAAATATTAT
*
41238313 AAATTATT-AAAA-AT-AATA-TA-
1 AAAATATTAAAAATATAAATATTAT
* *
41238333 AAATTATTAAAAATATAAATATTGT
1 AAAATATTAAAAATATAAATATTAT
* * *
41238358 AAAATATAAAAAATATAATTATTAA
1 AAAATATTAAAAATATAAATATTAT
41238383 AAAATATTAAAA
1 AAAATATTAAAA
41238395 CCCATTTGAA
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
20 8 0.12
21 6 0.09
22 5 0.07
23 6 0.09
24 1 0.01
25 34 0.50
26 1 0.01
27 4 0.06
28 3 0.04
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.34
Consensus pattern (25 bp):
AAAATATTAAAAATATAAATATTAT
Found at i:41238917 original size:11 final size:9
Alignment explanation
Indices: 41238887--41239048 Score: 77
Period size: 9 Copynumber: 17.7 Consensus size: 9
41238877 CTTACAATTT
41238887 TTTTTATAA
1 TTTTTATAA
41238896 TTTTTATAA
1 TTTTTATAA
41238905 TTATTTATCAA
1 TT-TTTAT-AA
*
41238916 TTTTAAT-A
1 TTTTTATAA
*
41238924 TTTTATATTA
1 TTTT-TATAA
**
41238934 TTTTTACGA
1 TTTTTATAA
*
41238943 TTTTTATAC
1 TTTTTATAA
*
41238952 GTTTTATAAA
1 TTTTTAT-AA
* *
41238962 ATTTTAAATA
1 TTTTTATA-A
41238972 TGTTTTATTAA
1 T-TTTTA-TAA
*
41238983 TATTATATATA
1 T-TTTTATA-A
*
41238994 TTTCT-TAA
1 TTTTTATAA
*
41239002 TTTCT-TAA
1 TTTTTATAA
41239010 TTTTTAT--
1 TTTTTATAA
41239017 TTTTTGA-AA
1 TTTTT-ATAA
*
41239026 TATTTATAA
1 TTTTTATAA
41239035 TTTTTAT-A
1 TTTTTATAA
41239043 TTTTTA
1 TTTTTA
41239049 AAAATTTTTT
Statistics
Matches: 120, Mismatches: 19, Indels: 29
0.71 0.11 0.17
Matches are distributed among these distances:
7 5 0.04
8 27 0.22
9 44 0.37
10 26 0.22
11 17 0.14
12 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:41239036 original size:25 final size:25
Alignment explanation
Indices: 41239007--41239055 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
41238997 CTTAATTTCT
*
41239007 TAATTTTTAT-TTTTTGAAATATTTA
1 TAATTTTTATATTTTT-AAAAATTTA
41239032 TAATTTTTATATTTTTAAAAATTT
1 TAATTTTTATATTTTTAAAAATTT
41239056 TTTATGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
TAATTTTTATATTTTTAAAAATTTA
Found at i:41253019 original size:27 final size:27
Alignment explanation
Indices: 41252980--41253094 Score: 178
Period size: 27 Copynumber: 4.2 Consensus size: 27
41252970 GTGACAAAGT
41252980 CACCAGATACAGATAATCGTGGCATAGC
1 CACCAGAT-CAGATAATCGTGGCATAGC
41253008 CACCAGATCAGATAATCGTGGCATAGC
1 CACCAGATCAGATAATCGTGGCATAGC
* *
41253035 CACCAGAACAGATATAT-GTGGCAGAGC
1 CACCAGATCAGATA-ATCGTGGCATAGC
*
41253062 CACCAGATCAGATAATTGTGGCATAGC
1 CACCAGATCAGATAATCGTGGCATAGC
41253089 CACCAG
1 CACCAG
41253095 GACGTTTCCT
Statistics
Matches: 81, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
26 2 0.02
27 69 0.85
28 10 0.12
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (27 bp):
CACCAGATCAGATAATCGTGGCATAGC
Found at i:41254746 original size:26 final size:26
Alignment explanation
Indices: 41254715--41254822 Score: 155
Period size: 26 Copynumber: 4.2 Consensus size: 26
41254705 TGAAATGCCC
41254715 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
41254741 ATCATGGAACATTTACCT-AACCTATT
1 ATCATGGAACATTTACCTAAACC-ATT
* *
41254767 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
* * *
41254793 ATCATGAAACATTTACCCAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
41254819 ATCA
1 ATCA
41254823 ATTTGTACCA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
25 4 0.05
26 67 0.91
27 3 0.04
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:41254793 original size:52 final size:52
Alignment explanation
Indices: 41254715--41254822 Score: 171
Period size: 52 Copynumber: 2.1 Consensus size: 52
41254705 TGAAATGCCC
* * *
41254715 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAAACCATTATCATGAAACATTTACCCAACCCATT
* *
41254767 ATCATGGAATATTTACCTAATCCATTATCATGAAACATTTACCCAACCCATT
1 ATCATGGAACATTTACCTAAACCATTATCATGAAACATTTACCCAACCCATT
41254819 ATCA
1 ATCA
41254823 ATTTGTACCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (52 bp):
ATCATGGAACATTTACCTAAACCATTATCATGAAACATTTACCCAACCCATT
Found at i:41274763 original size:26 final size:26
Alignment explanation
Indices: 41274706--41274763 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
41274696 TTAAAATGAC
* *
41274706 TTCCAAAACAATGCCTATTCCTTAGG
1 TTCCAAAACAATGCCCATTCCTTAGA
* * *
41274732 TGCCAAAATAATGCCCATTCTTTAGA
1 TTCCAAAACAATGCCCATTCCTTAGA
41274758 TTCCAA
1 TTCCAA
41274764 GCCAAACCAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (26 bp):
TTCCAAAACAATGCCCATTCCTTAGA
Found at i:41275722 original size:45 final size:45
Alignment explanation
Indices: 41275650--41275775 Score: 171
Period size: 45 Copynumber: 2.8 Consensus size: 45
41275640 TCTGCCATGT
* * * * * *
41275650 TGCCAAAGTGTCTTTCAACCATAGTCTTACACATTTGAATCGTGA
1 TGCCATAGCGTCTTTCAGCTATGGTCTTACTCATTTGAATCGTGA
* *
41275695 TGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTTTGTATCGTGA
1 TGCCATAGCGTCTTTCAGCTATGGTCTTACTCATTTGAATCGTGA
*
41275740 TGCCATAGCATCTTTCAGCTATGGTCTTACTCATTT
1 TGCCATAGCGTCTTTCAGCTATGGTCTTACTCATTT
41275776 TTCAACCAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (45 bp):
TGCCATAGCGTCTTTCAGCTATGGTCTTACTCATTTGAATCGTGA
Found at i:41280784 original size:47 final size:47
Alignment explanation
Indices: 41280667--41280932 Score: 224
Period size: 47 Copynumber: 5.7 Consensus size: 47
41280657 GATTTGTGCA
* **
41280667 CCAGTGTAAGACATGTCTGGGACATGCTTCGGCTACATTG-TGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCTACAGAGATGAGAG
** * *
41280713 CCAGTGTAAGACCATACCTAGGACATGGCATCGGC-ACAGAGATGAGTG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACAGAGATGAGAG
* *
41280761 CTAGAGTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGAT---AG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGG-CT--ACAGAGATGAGAG
* * * * *
41280808 CCAGTGTAAGACGTGTCTGGGACACGCATCGACTA-AGAG-T-TGTG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCTACAGAGATGAGAG
* * * * * *
41280852 CAAGTGTAAGACATGTCTAGGACATGCATCAGCATGCATATATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGC-TACAGAGATGAGAG
41280900 CCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCG
41280933 ACAATTTATC
Statistics
Matches: 172, Mismatches: 33, Indels: 26
0.74 0.14 0.11
Matches are distributed among these distances:
42 1 0.01
43 4 0.02
44 29 0.17
45 1 0.01
46 22 0.13
47 56 0.33
48 33 0.19
49 13 0.08
50 13 0.08
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (47 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCGGCTACAGAGATGAGAG
Found at i:41280881 original size:91 final size:94
Alignment explanation
Indices: 41280660--41280934 Score: 249
Period size: 94 Copynumber: 2.9 Consensus size: 94
41280650 ATTGGGTGAT
* * * * **
41280660 TTGTGCACCAGTGTAAGACATGTCTGGGACATGCTTCGGC-TACATTG-TGAGAGCCAGTGTAAG
1 TTGTGCA--AGTGTAAGACATGTCTAGGACATGCATCAGCATGCACAGATGAGAGCCAGTGTAAG
** * * *
41280723 ACCATACCTAGGACATGGCATCGGC-ACAGAG
64 ACCATGTCTGGGACATCGCATCGACTA-AGAG
* * * * * * *
41280754 ATGAGTGCTAGAGTAAGACATGTCTGGGACATGCATCGGCCT-CGACAGA-GATAGCCAGTGTAA
1 -T-TGTGCAAGTGTAAGACATGTCTAGGACATGCATCAGCATGC-ACAGATGAGAGCCAGTGTAA
*
41280817 GA-CGTGTCTGGGACA-CGCATCGACTAAGAG
63 GACCATGTCTGGGACATCGCATCGACTAAGAG
* *
41280847 TTGTGCAAGTGTAAGACATGTCTAGGACATGCATCAGCATGCATATATGAGAGCCAGTGTAAGAC
1 TTGTGCAAGTGTAAGACATGTCTAGGACATGCATCAGCATGCACAGATGAGAGCCAGTGTAAGAC
*
41280912 CATGTCTGGGACATGGCATCGAC
66 CATGTCTGGGACATCGCATCGAC
41280935 AATTTATCCC
Statistics
Matches: 147, Mismatches: 24, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
91 36 0.24
92 17 0.12
93 23 0.16
94 48 0.33
95 19 0.13
96 4 0.03
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (94 bp):
TTGTGCAAGTGTAAGACATGTCTAGGACATGCATCAGCATGCACAGATGAGAGCCAGTGTAAGAC
CATGTCTGGGACATCGCATCGACTAAGAG
Found at i:41288277 original size:47 final size:45
Alignment explanation
Indices: 41288162--41288426 Score: 212
Period size: 47 Copynumber: 5.7 Consensus size: 45
41288152 GATTTGTGCA
* * * * *
41288162 CCAGTGTAAGACATGTCTAGGACATGCTTCGGCTACATTATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCTAGA-GATGAGTG
**
41288208 CCAGTGTAAGACCATACCTGGGACATGGCATCGGCATAGAGATGAGTG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TAGAGATGAGTG
** * *
41288256 CCAAAGTAAGACATGTCTGGGACATGCATCGGCCTCGACA-GAGATAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGG-CTAGAGATGAG-T-G
* *
41288303 CCAGTGTAAGACATGTCTGGGACACGCATCGGCTA-AGA-GTTGTG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCTAGAGATG-AGTG
* * * * * *
41288347 CAAGTGTAAGACATGTCTGGGACATGAATCAGCATGCATATATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGC-T--AGAGATGAGTG
*
41288395 CTAGTGTAAGACCATGTCTGGGACATGGCATC
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATC
41288427 AACAATTTAT
Statistics
Matches: 177, Mismatches: 28, Indels: 24
0.77 0.12 0.10
Matches are distributed among these distances:
44 30 0.17
45 8 0.05
46 26 0.15
47 55 0.31
48 36 0.20
49 18 0.10
50 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (45 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCGGCTAGAGATGAGTG
Found at i:41295258 original size:17 final size:17
Alignment explanation
Indices: 41295235--41295268 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41295225 CTTTTAGAAC
*
41295235 AAAAAAAGAGAAGAAAAG
1 AAAAAAA-AGAACAAAAG
41295253 AAAAAAAAGAACAAAA
1 AAAAAAAAGAACAAAA
41295269 ACTGCTTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAACAAAAG
Found at i:41300097 original size:18 final size:19
Alignment explanation
Indices: 41300074--41300115 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
41300064 TGTATAAGAA
*
41300074 TGAAATT-AAGATCAATTT
1 TGAAATTGAAGATCAAATT
*
41300092 TGAAATTGAAGCTCAAATT
1 TGAAATTGAAGATCAAATT
41300111 TGAAA
1 TGAAA
41300116 GTTATGGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.33
Consensus pattern (19 bp):
TGAAATTGAAGATCAAATT
Found at i:41302049 original size:3 final size:3
Alignment explanation
Indices: 41302041--41302072 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41302031 TTCAAATCAC
41302041 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41302073 AATTCCTATA
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:41302821 original size:33 final size:33
Alignment explanation
Indices: 41302779--41302863 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
41302769 TAGAAAAACT
*
41302779 AATATTTTCTGGTGTTTGGATGAATCTTTGTAA
1 AATATTTTCTGGTGTTTGGATAAATCTTTGTAA
41302812 AATATTTTCTGGTGTTTGGATAAATCTTTGTAA
1 AATATTTTCTGGTGTTTGGATAAATCTTTGTAA
**
41302845 AATATTTTCTATTGTTTGG
1 AATATTTTCTGGTGTTTGG
41302864 CAGATTTTCT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.51
Consensus pattern (33 bp):
AATATTTTCTGGTGTTTGGATAAATCTTTGTAA
Found at i:41308304 original size:79 final size:78
Alignment explanation
Indices: 41308170--41308403 Score: 326
Period size: 79 Copynumber: 3.0 Consensus size: 78
41308160 CTTGAGTCAC
* * * * *
41308170 ATATCATCTAACTGTAGTGAATCAGGATGACCTTTTCAGGTCAAATCCTACCCACCTTAAGTTAT
1 ATATCATGTAACTGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTAC
41308235 CATAAGGAATCAT
66 CATAAGGAATCAT
* * * * *
41308248 ATATCGTGTAACCGTAGCGAATTAGGATTACCCTTTTTAGGTCAAATCCTATCCACCTTAGGTTA
1 ATATCATGTAACTGTAGCGAATCAGGATTA-CCTTTTCAGGTCAAATCCTATCCACCTTAAGTTA
*
41308313 CCATAATGAATCAT
65 CCATAAGGAATCAT
* *
41308327 ATATCATGTAACTGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCTCCTTTAGTTAC
1 ATATCATGTAACTGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTAC
41308392 CAT-AGTGAATCA
66 CATAAG-GAATCA
41308404 GGAATAAATC
Statistics
Matches: 135, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
77 1 0.01
78 64 0.47
79 70 0.52
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (78 bp):
ATATCATGTAACTGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTAC
CATAAGGAATCAT
Found at i:41308500 original size:40 final size:40
Alignment explanation
Indices: 41308368--41308505 Score: 154
Period size: 40 Copynumber: 3.5 Consensus size: 40
41308358 CTTTTCAGGT
*
41308368 CAAATCCTATCCTCCTTT--AGTTACCATAGTGAATCAGGAA
1 CAAATCCTATCC-ACTTTAAAG-TACCATAGTGAATCAGGAA
* * * *
41308408 TAAATCCTATTCACTTTAAATTACCATAGTGAATTAGGAA
1 CAAATCCTATCCACTTTAAAGTACCATAGTGAATCAGGAA
* * ** *
41308448 CAAATCCTATCCACTTTGAGGTATTATAGTGAATGAGGAA
1 CAAATCCTATCCACTTTAAAGTACCATAGTGAATCAGGAA
41308488 CAAATCCTATCCACTTTA
1 CAAATCCTATCCACTTTA
41308506 TATTCTCGAG
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 4 0.05
40 77 0.94
41 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAAGTACCATAGTGAATCAGGAA
Found at i:41313977 original size:79 final size:78
Alignment explanation
Indices: 41313843--41314076 Score: 353
Period size: 79 Copynumber: 3.0 Consensus size: 78
41313833 CTCGAGTCAC
* * * * *
41313843 ATATCATGTAACTGTAGTGAATCAAGATTACCTTTTCAGGTCAAATCCTACCCACCTTAAGTTAT
1 ATATCATGTAACCGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTAC
41313908 CATAAGGAATCAT
66 CATAAGGAATCAT
* *
41313921 ATATCGTGTAACCGTAGCGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAGGTTA
1 ATATCATGTAACCGTAGCGAATCAGGATTA-CCTTTTCAGGTCAAATCCTATCCACCTTAAGTTA
*
41313986 CCATAATGAATCAT
65 CCATAAGGAATCAT
* *
41314000 ATATCATGTAACGGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCTCCTTAAGTTAC
1 ATATCATGTAACCGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTAC
41314065 CAT-AGTGAATCA
66 CATAAG-GAATCA
41314077 GGAATAAATC
Statistics
Matches: 141, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
77 1 0.01
78 68 0.48
79 72 0.51
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (78 bp):
ATATCATGTAACCGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTAC
CATAAGGAATCAT
Found at i:41314074 original size:78 final size:78
Alignment explanation
Indices: 41313843--41314076 Score: 353
Period size: 78 Copynumber: 3.0 Consensus size: 78
41313833 CTCGAGTCAC
* * * * *
41313843 ATATCATGTAACTGTAGTGAATCAAGATTACCTTTTCAGGTCAAATCCTACCCACCTTAAGTTAT
1 ATATCATGTAACCGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTAC
41313908 CATAAG-GAATCAT
66 CAT-AGTGAATCAT
* *
41313921 ATATCGTGTAACCGTAGCGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAGGTTA
1 ATATCATGTAACCGTAGCGAATCAGGATTA-CCTTTTCAGGTCAAATCCTATCCACCTTAAGTTA
*
41313986 CCATAATGAATCAT
65 CCATAGTGAATCAT
* *
41314000 ATATCATGTAACGGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCTCCTTAAGTTAC
1 ATATCATGTAACCGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTAC
41314065 CATAGTGAATCA
66 CATAGTGAATCA
41314077 GGAATAAATC
Statistics
Matches: 141, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
78 71 0.50
79 70 0.50
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (78 bp):
ATATCATGTAACCGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTAC
CATAGTGAATCAT
Found at i:41314089 original size:40 final size:40
Alignment explanation
Indices: 41314041--41314178 Score: 177
Period size: 40 Copynumber: 3.5 Consensus size: 40
41314031 CTTTTCAGGT
* *
41314041 CAAATCCTATCCTCCTTAAGTTACCATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
* * *
41314081 TAAATCCTATTCACTTTAAATTACCATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
* * **
41314121 CAAATCCTATCCACTTTGAGGTATTATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
* *
41314161 CGAATCATATCCACTTTA
1 CAAATCCTATCCACTTTA
41314179 TATTCTCGAG
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
Found at i:41315851 original size:23 final size:22
Alignment explanation
Indices: 41315817--41315859 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
41315807 CCTTACATGT
41315817 ATATATTAAATAAAATAATAAA
1 ATATATTAAATAAAATAATAAA
* *
41315839 ATATCATTTAATAAACTAATA
1 ATAT-ATTAAATAAAATAATA
41315860 TTTATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (22 bp):
ATATATTAAATAAAATAATAAA
Found at i:41319248 original size:26 final size:24
Alignment explanation
Indices: 41319203--41319250 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
41319193 GTATCATTTT
*
41319203 TATTTGTTTTTATGTTTTTAAATA
1 TATTTGTTTTTATATTTTTAAATA
41319227 TATTTGATTTATTATATTTTTAAA
1 TATTTG-TTT-TTATATTTTTAAA
41319251 ATTTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (24 bp):
TATTTGTTTTTATATTTTTAAATA
Found at i:41325872 original size:21 final size:21
Alignment explanation
Indices: 41325826--41325865 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41325816 TATAGGCAAC
*
41325826 CAAAACATGCCAATTCATATA
1 CAAATCATGCCAATTCATATA
*
41325847 CAAATCATGCCATTTCATA
1 CAAATCATGCCAATTCATA
41325866 AGTAAATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.25, G:0.05, T:0.28
Consensus pattern (21 bp):
CAAATCATGCCAATTCATATA
Found at i:41326984 original size:43 final size:43
Alignment explanation
Indices: 41326899--41327014 Score: 171
Period size: 43 Copynumber: 2.7 Consensus size: 43
41326889 TCTATGCCAC
* * * *
41326899 TGTCCCAGACAGGGTCTTACACG-AATCATAATACGATACCAA
1 TGTCTCAGACATGGTCTTACACGTAATCACAATACAATACCAA
*
41326941 TGTCTCAGACATGGTCTTACACGTAATCACAATACAATTCCAA
1 TGTCTCAGACATGGTCTTACACGTAATCACAATACAATACCAA
*
41326984 TGTCTCAGACATGGTCTTACATGTAATCACA
1 TGTCTCAGACATGGTCTTACACGTAATCACA
41327015 TCTCAATAAC
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
42 21 0.31
43 46 0.69
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.27
Consensus pattern (43 bp):
TGTCTCAGACATGGTCTTACACGTAATCACAATACAATACCAA
Found at i:41329754 original size:7 final size:7
Alignment explanation
Indices: 41329730--41329761 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
41329720 GGTTTTCTCA
41329730 AAATG-G
1 AAATGAG
41329736 AAATGA-
1 AAATGAG
41329742 AAATGAG
1 AAATGAG
41329749 AAATGAG
1 AAATGAG
41329756 AAATGA
1 AAATGA
41329762 TTCATTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 11 0.46
7 13 0.54
ACGTcount: A:0.59, C:0.00, G:0.25, T:0.16
Consensus pattern (7 bp):
AAATGAG
Found at i:41330869 original size:27 final size:27
Alignment explanation
Indices: 41330821--41330979 Score: 191
Period size: 27 Copynumber: 5.9 Consensus size: 27
41330811 GCGAGGCTGC
* * *
41330821 CAGATATTGTGACAAAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGATA
41330848 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
41330874 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
** *
41330901 CAGATAATCATGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
41330928 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
41330955 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
41330980 GACGCTTCCT
Statistics
Matches: 115, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.09
27 101 0.88
28 4 0.03
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:41330915 original size:54 final size:54
Alignment explanation
Indices: 41330821--41330979 Score: 241
Period size: 54 Copynumber: 3.0 Consensus size: 54
41330811 GCGAGGCTGC
* * * *
41330821 CAGATAT-TGTGACAAAGTCACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAA
1 CAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCACCAGAA
**
41330874 CAGATATATGTGGCAGAGCCACCAGATCAGATAATCATGGCATAGCCACCAGAA
1 CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGAA
41330928 CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAG
41330980 GACGCTTCCT
Statistics
Matches: 96, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
53 12 0.12
54 84 0.88
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (54 bp):
CAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGAA
Found at i:41331119 original size:26 final size:27
Alignment explanation
Indices: 41331083--41331157 Score: 98
Period size: 26 Copynumber: 2.8 Consensus size: 27
41331073 CAAAAGTAAC
* *
41331083 CCTAGGGGTATAATGGTAATTTTGC-A
1 CCTAGGGGTATAATAGTAATTTTCCTA
*
41331109 CCTAGGGGTATAACAGTAATTTTCCTA
1 CCTAGGGGTATAATAGTAATTTTCCTA
* *
41331136 CATAGGGGTATTATAGTAATTT
1 CCTAGGGGTATAATAGTAATTT
41331158 AGCTGCTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 22 0.52
27 20 0.48
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (27 bp):
CCTAGGGGTATAATAGTAATTTTCCTA
Found at i:41332622 original size:26 final size:26
Alignment explanation
Indices: 41332591--41332698 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
41332581 TGAAATGCCC
41332591 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
41332617 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
41332643 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
41332669 ATCATGGAACATTTACCT-AACTCATT
1 ATCATGGAACATTTACCTAAAC-CATT
41332695 ATCA
1 ATCA
41332699 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 2 0.03
26 74 0.97
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:41342913 original size:31 final size:30
Alignment explanation
Indices: 41342848--41342914 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
41342838 AAATTATCCT
* *
41342848 TATTAATTTTTATACTACCAAAAATAGCCC
1 TATTAATTTTTATACCACCAAAAATAGCCA
*
41342878 TATTAATTTTTTATACCACCTAAAATA-CCTA
1 TATTAA-TTTTTATACCACCAAAAATAGCC-A
41342909 TATTAA
1 TATTAA
41342915 CTCTTCATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.40, C:0.18, G:0.01, T:0.40
Consensus pattern (30 bp):
TATTAATTTTTATACCACCAAAAATAGCCA
Found at i:41345537 original size:15 final size:14
Alignment explanation
Indices: 41345492--41345550 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 14
41345482 TAATTTTCCC
*
41345492 TTTTCCTTTCTTTT
1 TTTTCCTTTATTTT
41345506 TCTTTCC--TA-TTT
1 T-TTTCCTTTATTTT
41345518 TTTTCCTTTATTTT
1 TTTTCCTTTATTTT
*
41345532 TATTTCTTTTATTTAT
1 T-TTTCCTTTATTT-T
41345548 TTT
1 TTT
41345551 ATGTTTCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
11 5 0.14
12 4 0.11
13 3 0.08
14 5 0.14
15 18 0.49
16 2 0.05
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCCTTTATTTT
Found at i:41345602 original size:18 final size:17
Alignment explanation
Indices: 41345572--41345614 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
41345562 AATTAATAAT
41345572 TAATATAATAATATATTA
1 TAAT-TAATAATATATTA
*
41345590 TAATTAATAAATATCTTA
1 TAATTAAT-AATATATTA
*
41345608 TACTTAA
1 TAATTAA
41345615 AGTATAAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTAATAATATATTA
Found at i:41349440 original size:28 final size:27
Alignment explanation
Indices: 41349415--41349469 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
41349405 CAACATAAAT
41349415 AATAAAATAA-AATGAAAATAATATAATG
1 AATAAAATAATAA-G-AAATAATATAATG
*
41349443 AATACAATAATAAGAAATAATAATAAT
1 AATAAAATAATAAGAAATAAT-ATAAT
41349470 TCAGTTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.29
28 15 0.62
29 2 0.08
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (27 bp):
AATAAAATAATAAGAAATAATATAATG
Found at i:41353709 original size:30 final size:30
Alignment explanation
Indices: 41353675--41353825 Score: 302
Period size: 30 Copynumber: 5.0 Consensus size: 30
41353665 TTGCAAAAAT
41353675 TTTAAAGGTTTAGGTTTTTAAATTGATTAA
1 TTTAAAGGTTTAGGTTTTTAAATTGATTAA
41353705 TTTAAAGGTTTAGGTTTTTAAATTGATTAA
1 TTTAAAGGTTTAGGTTTTTAAATTGATTAA
41353735 TTTAAAGGTTTAGGTTTTTAAATTGATTAA
1 TTTAAAGGTTTAGGTTTTTAAATTGATTAA
41353765 TTTAAAGGTTTAGGTTTTTAAATTGATTAA
1 TTTAAAGGTTTAGGTTTTTAAATTGATTAA
41353795 TTTAAAGGTTTAGGTTTTTAAATTGATTAA
1 TTTAAAGGTTTAGGTTTTTAAATTGATTAA
41353825 T
1 T
41353826 ATAGGTGTAT
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 121 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (30 bp):
TTTAAAGGTTTAGGTTTTTAAATTGATTAA
Found at i:41356285 original size:18 final size:18
Alignment explanation
Indices: 41356262--41356298 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
41356252 TAATGAAGTG
41356262 TGTATAATAAA-ATTAAAA
1 TGTATAA-AAATATTAAAA
41356280 TGTATAAAAATATTAAAA
1 TGTATAAAAATATTAAAA
41356298 T
1 T
41356299 AGAATTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
TGTATAAAAATATTAAAA
Found at i:41356876 original size:9 final size:9
Alignment explanation
Indices: 41356862--41356939 Score: 77
Period size: 9 Copynumber: 8.7 Consensus size: 9
41356852 ATAAGTATAA
*
41356862 AATTAACAG
1 AATTAACCG
41356871 AATTAACCG
1 AATTAACCG
**
41356880 AATTAGTCG
1 AATTAACCG
41356889 AATTAACCG
1 AATTAACCG
41356898 AATT-ACTCG
1 AATTAAC-CG
* *
41356907 AATTACCCA
1 AATTAACCG
* *
41356916 AATTACCCA
1 AATTAACCG
41356925 AATTAACCG
1 AATTAACCG
41356934 AATTAA
1 AATTAA
41356940 ACAAATTATT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
8 2 0.03
9 55 0.95
10 1 0.02
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:41356891 original size:18 final size:18
Alignment explanation
Indices: 41356870--41356938 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
41356860 AAAATTAACA
*
41356870 GAATTAACCGAATTAGTC
1 GAATTAACCGAATTACTC
41356888 GAATTAACCGAATTACTC
1 GAATTAACCGAATTACTC
* * *
41356906 GAATTACCCAAATTACCC
1 GAATTAACCGAATTACTC
*
41356924 AAATTAACCGAATTA
1 GAATTAACCGAATTA
41356939 AACAAATTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.26
Consensus pattern (18 bp):
GAATTAACCGAATTACTC
Found at i:41356892 original size:27 final size:27
Alignment explanation
Indices: 41356861--41356947 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
41356851 AATAAGTATA
**
41356861 AAATTAACAGAATTAACCGAATTAGTC
1 AAATTAACAGAATTAACCGAATTACCC
* *
41356888 GAATTAACCGAATT-ACTCGAATTACCC
1 AAATTAACAGAATTAAC-CGAATTACCC
* **
41356915 AAATTACCCA-AATTAACCGAATTAAAC
1 AAATTA-ACAGAATTAACCGAATTACCC
41356942 AAATTA
1 AAATTA
41356948 TTTGTATAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
26 2 0.04
27 43 0.90
28 3 0.06
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (27 bp):
AAATTAACAGAATTAACCGAATTACCC
Found at i:41356982 original size:5 final size:6
Alignment explanation
Indices: 41356967--41357007 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
41356957 AATTATATGT
*
41356967 TTTTTA TTTTTA TTTTTA GTTTTAA CTTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTTTA -TTTTTA TTTTTA TTT
41357008 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
6 21 0.68
7 10 0.32
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:41358561 original size:31 final size:28
Alignment explanation
Indices: 41358520--41358578 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 28
41358510 TTGCGTTGAG
*
41358520 AAATTTATTTAATTAGAAAAATAATTTATTT
1 AAATTAATTTAA-TA-AAAAAT-ATTTATTT
*
41358551 AAATTAATTTAATAAATAATATTTATTT
1 AAATTAATTTAATAAAAAATATTTATTT
41358579 TGAGAAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 8 0.31
29 5 0.19
30 2 0.08
31 11 0.42
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
AAATTAATTTAATAAAAAATATTTATTT
Found at i:41365777 original size:14 final size:14
Alignment explanation
Indices: 41365760--41365803 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
41365750 TCATTTAAGA
41365760 TTTAATTTTTATAT
1 TTTAATTTTTATAT
*
41365774 TTTAATTTTTA-AC
1 TTTAATTTTTATAT
* *
41365787 TTTGATTTCTATAT
1 TTTAATTTTTATAT
41365801 TTT
1 TTT
41365804 TATAATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:41367378 original size:24 final size:22
Alignment explanation
Indices: 41367317--41367378 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
41367307 TTGGAAGTGA
41367317 AAAAAAACATAGTTAAGAGAAG
1 AAAAAAACATAGTTAAGAGAAG
* *
41367339 AAAGAAACAGTGAGTTAAGAGAGTTG
1 AAAAAAACA-T-AGTTAAGAGA--AG
*
41367365 AAAAAAATATAGTT
1 AAAAAAACATAGTT
41367379 GTCAAACAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
22 8 0.25
23 1 0.03
24 14 0.44
25 1 0.03
26 8 0.25
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.19
Consensus pattern (22 bp):
AAAAAAACATAGTTAAGAGAAG
Found at i:41377229 original size:14 final size:14
Alignment explanation
Indices: 41377210--41377236 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41377200 AAGGACAATT
41377210 CTCTTGGGAAAATA
1 CTCTTGGGAAAATA
41377224 CTCTTGGGAAAAT
1 CTCTTGGGAAAAT
41377237 TCGATTGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (14 bp):
CTCTTGGGAAAATA
Found at i:41379300 original size:47 final size:47
Alignment explanation
Indices: 41379247--41379340 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
41379237 TTACAAGCTC
*
41379247 TGCATGAAAAATAGTTGTATGCTAAATTCAGTAAATGTGAATTCTGA
1 TGCATGAAAAATAGTTGTATACTAAATTCAGTAAATGTGAATTCTGA
*
41379294 TGCATGAAAAATAGTTGTATACTAAATTCAGTGAATGTGAATTCTGA
1 TGCATGAAAAATAGTTGTATACTAAATTCAGTAAATGTGAATTCTGA
41379341 CTTTAGGAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (47 bp):
TGCATGAAAAATAGTTGTATACTAAATTCAGTAAATGTGAATTCTGA
Found at i:41380433 original size:34 final size:34
Alignment explanation
Indices: 41380381--41380447 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
41380371 TTATTATAGT
** *
41380381 CAGTGACGATACTGGAATGGAAATGGGAAAGAGC
1 CAGTGACGATACCAGAATGGAAATAGGAAAGAGC
*
41380415 CAGTTACGATACCAGAATGGAAATAGGAAAGAG
1 CAGTGACGATACCAGAATGGAAATAGGAAAGAG
41380448 TTACTATGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.42, C:0.12, G:0.31, T:0.15
Consensus pattern (34 bp):
CAGTGACGATACCAGAATGGAAATAGGAAAGAGC
Found at i:41387398 original size:15 final size:14
Alignment explanation
Indices: 41387377--41387423 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
41387367 AATTAATATA
41387377 TAATTAATCAAAT-T
1 TAATTAAT-AAATCT
41387391 TAACTTAATAAATCT
1 TAA-TTAATAAATCT
*
41387406 TAATTAAGTTAATCT
1 TAATTAA-TAAATCT
41387421 TAA
1 TAA
41387424 CTTTAATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (14 bp):
TAATTAATAAATCT
Found at i:41389425 original size:19 final size:19
Alignment explanation
Indices: 41389403--41389439 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41389393 ACCACTGTCA
41389403 CCCACCGTAATAAAATTTG
1 CCCACCGTAATAAAATTTG
*
41389422 CCCACCGTAATCAAATTT
1 CCCACCGTAATAAAATTT
41389440 TTTATTAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.30, G:0.08, T:0.27
Consensus pattern (19 bp):
CCCACCGTAATAAAATTTG
Found at i:41390219 original size:30 final size:30
Alignment explanation
Indices: 41390162--41390219 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
41390152 GGGAGGGGAA
* * **
41390162 TAAAAGTTTTGGGGGCAAAGTGGAAAGGAG
1 TAAAAGTTTTGAGGGAAAAGTAAAAAGGAG
41390192 TAAAAGTTTTGAGGGAAAAGTAAAAAGG
1 TAAAAGTTTTGAGGGAAAAGTAAAAAGG
41390220 TTTGTGAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.34, T:0.21
Consensus pattern (30 bp):
TAAAAGTTTTGAGGGAAAAGTAAAAAGGAG
Found at i:41398446 original size:31 final size:33
Alignment explanation
Indices: 41398381--41398447 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 33
41398371 GCCGTGTGAT
* *
41398381 CCACACGGGCAAAGCCAATCTGAGCGTGTGGGC
1 CCACACGGGCAAAGCCAATATGAGCGTGTAGGC
* *
41398414 CCACACGGGC-AA-CCCATATGGGCGTGTAGGC
1 CCACACGGGCAAAGCCAATATGAGCGTGTAGGC
41398445 CCA
1 CCA
41398448 TCTATCTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 18 0.60
32 2 0.07
33 10 0.33
ACGTcount: A:0.24, C:0.33, G:0.31, T:0.12
Consensus pattern (33 bp):
CCACACGGGCAAAGCCAATATGAGCGTGTAGGC
Found at i:41398968 original size:35 final size:35
Alignment explanation
Indices: 41398904--41398970 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
41398894 TGATTTGCAC
* *
41398904 ATCTGTATCTGTATCTGAGATGGATTTAGGCCCGA
1 ATCTGCATCTGTATCTGAGATGGACTTAGGCCCGA
*
41398939 ATCTGCATCTGTATCTGTA-ATGGGCTTAGGCC
1 ATCTGCATCTGTATCTG-AGATGGACTTAGGCC
41398971 TAATTTGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 27 0.96
36 1 0.04
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (35 bp):
ATCTGCATCTGTATCTGAGATGGACTTAGGCCCGA
Found at i:41399982 original size:31 final size:31
Alignment explanation
Indices: 41399947--41400009 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
41399937 TTTTATCATG
41399947 TTTGGTTTGTATCTGATATTTAAGGATTTTC
1 TTTGGTTTGTATCTGATATTTAAGGATTTTC
41399978 TTTGGTTTGTATCTGATATTTAAGGATTTTC
1 TTTGGTTTGTATCTGATATTTAAGGATTTTC
41400009 T
1 T
41400010 ACTACTATCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.56
Consensus pattern (31 bp):
TTTGGTTTGTATCTGATATTTAAGGATTTTC
Found at i:41408130 original size:37 final size:35
Alignment explanation
Indices: 41408087--41408170 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 35
41408077 AACATCATAC
41408087 ATATTTTATTTGTTATTAT-TAATTAATTTTAAATTAT
1 ATATTTTATTT-TTATTATAT-ATTAATTTTAAA-TAT
*
41408124 ATATTTTATTATTTATTATATGTTAATTTTAAATAT
1 ATATTTTATT-TTTATTATATATTAATTTTAAATAT
*
41408160 ACA-TTTATTTT
1 ATATTTTATTTT
41408171 CTAAATTCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
34 2 0.05
35 6 0.14
36 5 0.12
37 28 0.65
38 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (35 bp):
ATATTTTATTTTTATTATATATTAATTTTAAATAT
Found at i:41408815 original size:16 final size:17
Alignment explanation
Indices: 41408794--41408825 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
41408784 ATAAATCATT
41408794 AAAAATTT-TAAAAATA
1 AAAAATTTATAAAAATA
41408810 AAAAATTTATAAAAAT
1 AAAAATTTATAAAAAT
41408826 TAATTATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAATTTATAAAAATA
Found at i:41413083 original size:32 final size:33
Alignment explanation
Indices: 41413023--41413088 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
41413013 ATTAATCAAT
* * * *
41413023 ATGAGTTATTAAATTAAATTAATTAA-TTTATA
1 ATGAATTACTAAATTAAAGTAATCAATTTTATA
*
41413055 ATGAATTACTAAATTCAAGTAATCAATTTTATA
1 ATGAATTACTAAATTAAAGTAATCAATTTTATA
41413088 A
1 A
41413089 GTTCATGATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 21 0.75
33 7 0.25
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (33 bp):
ATGAATTACTAAATTAAAGTAATCAATTTTATA
Found at i:41413278 original size:31 final size:30
Alignment explanation
Indices: 41413230--41413291 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
41413220 CTGAAATTTA
**
41413230 ATCATTTTATTGAAATAATATTTTAATTAAT
1 ATCATTTTATTGAAATAA-ATGATAATTAAT
*
41413261 ATCATTTTGATT-TAATAAATGATAATTAAT
1 ATCATTTT-ATTGAAATAAATGATAATTAAT
41413291 A
1 A
41413292 GATTTGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 11 0.41
31 13 0.48
32 3 0.11
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (30 bp):
ATCATTTTATTGAAATAAATGATAATTAAT
Found at i:41415619 original size:5 final size:5
Alignment explanation
Indices: 41415609--41415633 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
41415599 TAGCGATGGA
41415609 TGGTC TGGTC TGGTC TGGTC TGGTC
1 TGGTC TGGTC TGGTC TGGTC TGGTC
41415634 ATCCCCCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.40, T:0.40
Consensus pattern (5 bp):
TGGTC
Found at i:41430280 original size:23 final size:24
Alignment explanation
Indices: 41430254--41430301 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
41430244 AGAACAGAAC
41430254 AAACTGAAAC-AAAAAATTGTCCA
1 AAACTGAAACAAAAAAATTGTCCA
41430277 AAACTGAAACAAAAAAATTGTCCA
1 AAACTGAAACAAAAAAATTGTCCA
41430301 A
1 A
41430302 CTGAGATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.58, C:0.17, G:0.08, T:0.17
Consensus pattern (24 bp):
AAACTGAAACAAAAAAATTGTCCA
Found at i:41432521 original size:17 final size:18
Alignment explanation
Indices: 41432493--41432526 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41432483 CATATATGTA
*
41432493 ACATAAACATATTTATTC
1 ACATAAACATATATATTC
41432511 ACATAAA-ATATATATT
1 ACATAAACATATATATT
41432527 TAATGATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (18 bp):
ACATAAACATATATATTC
Found at i:41432800 original size:31 final size:31
Alignment explanation
Indices: 41432742--41432800 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
41432732 AGTGGGACTG
* *
41432742 AAACTAGCAGGAAGCGAAGCTAGCGAGATCA
1 AAACTAGCAGGAAGCAAAGCTAACGAGATCA
*
41432773 AAACTAGCTGGAAGCAAAAG-TAACGAGA
1 AAACTAGCAGGAAGC-AAAGCTAACGAGA
41432801 GGTGAAGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.88
32 3 0.12
ACGTcount: A:0.46, C:0.17, G:0.27, T:0.10
Consensus pattern (31 bp):
AAACTAGCAGGAAGCAAAGCTAACGAGATCA
Found at i:41437021 original size:16 final size:15
Alignment explanation
Indices: 41436996--41437029 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
41436986 CATAGGAAAC
*
41436996 AGAAATGGGAAAATAA
1 AGAAAAGGGAAAA-AA
41437012 AGAAAAGGGAAAAAA
1 AGAAAAGGGAAAAAA
41437027 AGA
1 AGA
41437030 GAGAGATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.06
Consensus pattern (15 bp):
AGAAAAGGGAAAAAA
Found at i:41437918 original size:27 final size:28
Alignment explanation
Indices: 41437885--41437978 Score: 90
Period size: 27 Copynumber: 3.5 Consensus size: 28
41437875 AAACAAACAA
*
41437885 CAAAATTCAAAACAAAGGAAAACAGCAG
1 CAAAATTCAAAACAAAGGAAAACACCAG
* * *
41437913 C-AAATTCAAAATAAATGATAACACCAG
1 CAAAATTCAAAACAAAGGAAAACACCAG
*
41437940 CAAAATTC-AAATAAA-GAATAACACCAG
1 CAAAATTCAAAACAAAGGAA-AACACCAG
*
41437967 -AAAGTT-AAAACA
1 CAAAATTCAAAACA
41437979 CATGATTAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
26 11 0.20
27 38 0.68
28 7 0.12
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.14
Consensus pattern (28 bp):
CAAAATTCAAAACAAAGGAAAACACCAG
Found at i:41438716 original size:27 final size:28
Alignment explanation
Indices: 41438686--41438755 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 28
41438676 AAAAAAAAAA
*
41438686 TCAAAACAAAGGA-AAACAGCAGCAAA-T
1 TCAAAACAAAGGATAAA-AACAGCAAATT
*
41438713 TCAAAACAAATGATAAAAACAGCAAATT
1 TCAAAACAAAGGATAAAAACAGCAAATT
*
41438741 TC-AAATAAAGGATAA
1 TCAAAACAAAGGATAA
41438756 CCCCAGAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 31 0.84
28 6 0.16
ACGTcount: A:0.60, C:0.14, G:0.11, T:0.14
Consensus pattern (28 bp):
TCAAAACAAAGGATAAAAACAGCAAATT
Found at i:41439355 original size:2 final size:2
Alignment explanation
Indices: 41439348--41439376 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41439338 GAATATTGGA
41439348 AG 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 AG A
41439377 ATGAAGCAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41441645 original size:24 final size:27
Alignment explanation
Indices: 41441612--41441673 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 27
41441602 AACAAACAAA
*
41441612 AAAATTCAAAACAAA-G-GACAGCAGC
1 AAAATTCAAAACAAATGAAACAGCAGC
*
41441637 -AAATTCAAAAGAAATGATAACAGCAGC
1 AAAATTCAAAACAAATGA-AACAGCAGC
41441664 AAAATTCAAA
1 AAAATTCAAA
41441674 TAAAGAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 13 0.42
25 1 0.03
27 8 0.26
28 9 0.29
ACGTcount: A:0.58, C:0.16, G:0.13, T:0.13
Consensus pattern (27 bp):
AAAATTCAAAACAAATGAAACAGCAGC
Found at i:41445023 original size:15 final size:15
Alignment explanation
Indices: 41445005--41445042 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
41444995 CAGTTTCCAT
41445005 GTCATCATCATCGTC
1 GTCATCATCATCGTC
41445020 GTCATCATCATCGTC
1 GTCATCATCATCGTC
*
41445035 ATCATCAT
1 GTCATCAT
41445043 GCCGTTGCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.32, G:0.11, T:0.34
Consensus pattern (15 bp):
GTCATCATCATCGTC
Found at i:41445026 original size:12 final size:12
Alignment explanation
Indices: 41445009--41445042 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
41444999 TTCCATGTCA
*
41445009 TCATCATCGTCG
1 TCATCATCATCG
41445021 TCATCATCATCG
1 TCATCATCATCG
41445033 TCATCATCAT
1 TCATCATCAT
41445043 GCCGTTGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.32, G:0.09, T:0.35
Consensus pattern (12 bp):
TCATCATCATCG
Found at i:41451281 original size:77 final size:77
Alignment explanation
Indices: 41450958--41451265 Score: 607
Period size: 77 Copynumber: 4.0 Consensus size: 77
41450948 TATAATAGTA
41450958 TAAAATCTCTTCAAATTTGCACTAGTACCTTGAATCAGAAAGATTCCTACAGAGGATCTTCTGGT
1 TAAAATCTCTTCAAATTTGCACTAGTACCTTGAATCAGAAAGATTCCTACAGAGGATCTTCTGGT
41451023 TATATGTCATGG
66 TATATGTCATGG
41451035 TAAAATCTCTTCAAATTTGCACTAGTACCTTGAATCAGAAAGATTCCTACAGAGGATCTTCTGGT
1 TAAAATCTCTTCAAATTTGCACTAGTACCTTGAATCAGAAAGATTCCTACAGAGGATCTTCTGGT
41451100 TATATGTCATGG
66 TATATGTCATGG
41451112 TAAAATCTCTTCAAATTTGCACTAGTACCTTGAATCAGAAAGATTCCTACAGAGGATCTTCTGGT
1 TAAAATCTCTTCAAATTTGCACTAGTACCTTGAATCAGAAAGATTCCTACAGAGGATCTTCTGGT
41451177 TATATGTCATGG
66 TATATGTCATGG
41451189 TAAAATCTCTTCAAATTTGCACTAGTACCTTGAATCAGAAAGATTCCTACAGAGGATCTTCTGGT
1 TAAAATCTCTTCAAATTTGCACTAGTACCTTGAATCAGAAAGATTCCTACAGAGGATCTTCTGGT
*
41451254 TATATATCATGG
66 TATATGTCATGG
41451266 CACATCAGTA
Statistics
Matches: 230, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 230 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (77 bp):
TAAAATCTCTTCAAATTTGCACTAGTACCTTGAATCAGAAAGATTCCTACAGAGGATCTTCTGGT
TATATGTCATGG
Found at i:41454738 original size:42 final size:43
Alignment explanation
Indices: 41454691--41454772 Score: 130
Period size: 42 Copynumber: 1.9 Consensus size: 43
41454681 AAGTCACTTG
*
41454691 ACTAGCAATTTGACTCAAA-TATTTGTTTAGAAGCACTCGAGA
1 ACTAGCAATTTGACTCAAACGATTTGTTTAGAAGCACTCGAGA
*
41454733 ACTAGCAATTTGATTCAAACCGATTTGTTTAGAAGCACTC
1 ACTAGCAATTTGACTCAAA-CGATTTGTTTAGAAGCACTC
41454773 AAGAGCTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 18 0.50
44 18 0.50
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (43 bp):
ACTAGCAATTTGACTCAAACGATTTGTTTAGAAGCACTCGAGA
Found at i:41459645 original size:25 final size:24
Alignment explanation
Indices: 41459599--41459646 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
41459589 TTGTGAATGT
41459599 AGTCCTATACTTTTAATCAATTTTG
1 AGTCCTATACTTTTAA-CAATTTTG
41459624 AGTCCTTATACTTTTCAA-AATTT
1 AGTCC-TATACTTTT-AACAATTT
41459647 AAAATTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
25 10 0.48
26 9 0.43
27 2 0.10
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (24 bp):
AGTCCTATACTTTTAACAATTTTG
Found at i:41459824 original size:31 final size:29
Alignment explanation
Indices: 41459741--41459834 Score: 80
Period size: 31 Copynumber: 3.0 Consensus size: 29
41459731 TTAGGTCCTA
* *
41459741 AACTTAGCAATTCTTCCCACATTAGGGCGTG
1 AACTTAGCAATT-TTTCCACATTA-GGCTTG
* * * *
41459772 GACTTGGTAACTTTTTACACATTAGGACTTG
1 AACTTAGCAA-TTTTTCCACATTAGG-CTTG
41459803 AACTTAGCAATTGTTTCCACATTAAGGCTTG
1 AACTTAGCAATT-TTTCCACATT-AGGCTTG
41459834 A
1 A
41459835 GCTTTAGGGT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
30 4 0.08
31 40 0.82
32 5 0.10
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (29 bp):
AACTTAGCAATTTTTCCACATTAGGCTTG
Found at i:41462148 original size:58 final size:56
Alignment explanation
Indices: 41462064--41462231 Score: 201
Period size: 56 Copynumber: 2.9 Consensus size: 56
41462054 ACAAGCTTAG
* * * *
41462064 GTACCAAATTAGAAAAAAAGTTTCAAGTTTAGGTACCACATTGGATCAAAAAAACTAAT
1 GTACCAAATTAG-AAAAAAGTGTCAAGTTCAGGTACCAAATTGGA-CAAAAAAAAT-AT
* * * *
41462123 GTACTAAATTAGGAAAAAGTGTCAAGTTCAGGTATCAAATTTGACAAAAAAAATAT
1 GTACCAAATTAGAAAAAAGTGTCAAGTTCAGGTACCAAATTGGACAAAAAAAATAT
* * * *
41462179 GTACCAAATTAGAAAAAAATGTCAAGTTCATGTGCCAATTTGGACAAAAAAAA
1 GTACCAAATTAGAAAAAAGTGTCAAGTTCAGGTACCAAATTGGACAAAAAAAA
41462232 ACTTAGATAT
Statistics
Matches: 93, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
56 47 0.51
57 9 0.10
58 26 0.28
59 11 0.12
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (56 bp):
GTACCAAATTAGAAAAAAGTGTCAAGTTCAGGTACCAAATTGGACAAAAAAAATAT
Found at i:41462230 original size:115 final size:115
Alignment explanation
Indices: 41462064--41462277 Score: 267
Period size: 115 Copynumber: 1.9 Consensus size: 115
41462054 ACAAGCTTAG
* *
41462064 GTACCAAATTAGAAAAAAAGTTTCAAGTTTAGGTACCACATTGGATCAAAAAAACTAATG-TA-C
1 GTACCAAATTAGAAAAAAAGTGTCAAGTTCAGGTACCACATTGGATCAAAAAAACTAA-GATATC
* * *
41462127 TAAATTAGGAAAAAGTGTCAAGTTCAGGTATCAAATTTGACAAAAAAAATAT
65 TAAA-TAAGAAAAAGTGTCAAATTCAGGTACCAAATTTGACAAAAAAAATAT
* * *
41462179 GTACCAAATTAGAAAAAAA-TGTCAAGTTCATGTGCCA-ATTTGGA-CAAAAAAAAACTTAGATA
1 GTACCAAATTAGAAAAAAAGTGTCAAGTTCAGGTACCACA-TTGGATC--AAAAAAACTAAGATA
*
41462241 TCTAAATAAGAAAAAGTGTCAAATTCATGTACCAAAT
63 TCTAAATAAGAAAAAGTGTCAAATTCAGGTACCAAAT
41462278 AATATATTAA
Statistics
Matches: 85, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
113 2 0.02
114 20 0.24
115 58 0.68
116 5 0.06
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (115 bp):
GTACCAAATTAGAAAAAAAGTGTCAAGTTCAGGTACCACATTGGATCAAAAAAACTAAGATATCT
AAATAAGAAAAAGTGTCAAATTCAGGTACCAAATTTGACAAAAAAAATAT
Found at i:41465809 original size:28 final size:28
Alignment explanation
Indices: 41465732--41465839 Score: 108
Period size: 29 Copynumber: 3.8 Consensus size: 28
41465722 ACGAGACTAT
* * * *
41465732 TTTGCTCACACAAGTTGACAGTTATCAGG
1 TTTGCTCACACAAGCTGACATTTATGA-A
* * *
41465761 GTTGCTCACACAAGTTAACATTTATGAA
1 TTTGCTCACACAAGCTGACATTTATGAA
*
41465789 TTTGCTCACACAAACTGACATTTTATGAA
1 TTTGCTCACACAAGCTGACA-TTTATGAA
* *
41465818 TTTGCTCATACAAGCGGACATT
1 TTTGCTCACACAAGCTGACATT
41465840 GTATCGAGGT
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
28 18 0.27
29 48 0.73
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (28 bp):
TTTGCTCACACAAGCTGACATTTATGAA
Found at i:41473070 original size:4 final size:4
Alignment explanation
Indices: 41473063--41473108 Score: 83
Period size: 4 Copynumber: 11.2 Consensus size: 4
41473053 TTATATTAAT
41473063 TAAA TAAA GTAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA -TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
41473109 TAAAAGTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 37 0.90
5 4 0.10
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:41474606 original size:47 final size:47
Alignment explanation
Indices: 41474527--41474628 Score: 125
Period size: 47 Copynumber: 2.2 Consensus size: 47
41474517 CCTTGTATGT
** * * *
41474527 CGTACTGTTACTGTTACTTCGGATTATTCCGATGGGGTACTCTGTAC
1 CGTACTGTTACTGTTACTTCGGATTAGGCCGATGAGGCACTATGTAC
* *
41474574 CGTACTGTTACTGTTTACTTCGGCTT-GGCCGATGAGGCACTATGTGC
1 CGTACTGTTACTG-TTACTTCGGATTAGGCCGATGAGGCACTATGTAC
41474621 CGTACTGT
1 CGTACTGT
41474629 ACTAGTGTGA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
47 36 0.77
48 11 0.23
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (47 bp):
CGTACTGTTACTGTTACTTCGGATTAGGCCGATGAGGCACTATGTAC
Found at i:41474734 original size:18 final size:18
Alignment explanation
Indices: 41474697--41474805 Score: 92
Period size: 18 Copynumber: 6.1 Consensus size: 18
41474687 TAAATAAAAG
* *
41474697 TACTGAATGATTGACTGT
1 TACTGAATAATTGATTGT
*
41474715 TACTGAATAATTGATCGT
1 TACTGAATAATTGATTGT
* * *
41474733 TACTAAATAACTGATTGC
1 TACTGAATAATTGATTGT
** * *
41474751 TACTGAGCAAATAATTGT
1 TACTGAATAATTGATTGT
* * *
41474769 TACTGAATAACTAATTGC
1 TACTGAATAATTGATTGT
*
41474787 TACTGAATAATTGAATGT
1 TACTGAATAATTGATTGT
41474805 T
1 T
41474806 GCTAAATGAA
Statistics
Matches: 70, Mismatches: 21, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TACTGAATAATTGATTGT
Found at i:41474756 original size:36 final size:36
Alignment explanation
Indices: 41474715--41474800 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
41474705 GATTGACTGT
*
41474715 TACTGAATAATTGATCGTTACTAAATAACTGATTGC
1 TACTGAATAATTGATCGTTACTAAATAACTAATTGC
** * * * *
41474751 TACTGAGCAAATAATTGTTACTGAATAACTAATTGC
1 TACTGAATAATTGATCGTTACTAAATAACTAATTGC
41474787 TACTGAATAATTGA
1 TACTGAATAATTGA
41474801 ATGTTGCTAA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (36 bp):
TACTGAATAATTGATCGTTACTAAATAACTAATTGC
Found at i:41476805 original size:137 final size:138
Alignment explanation
Indices: 41476568--41476883 Score: 377
Period size: 137 Copynumber: 2.3 Consensus size: 138
41476558 TTATCTTCGA
* * * * * **
41476568 CATGATGCCATAGTGTCTTTCAACTATAGTCTTACTCATTTTCTGTCAGGTTGCCATGGTATCTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCACATTGCCATGGTATCTT
* ** * * **
41476633 TCAACCATGGTCTTGTTCATTTCATGTTACATTGCCATGGTATCTTTCAACCATGGTCTTATTCA
66 TCAACCATAGTCTTCATCATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTACACA
* *
41476698 -TTCCCGT
131 TTTCACAT
* *
41476705 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACATTGCCATGGTGTCT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTC-TGTCACATTGCCATGGTATCT
* ** *
41476769 TTTAACCATAGTCTTACAT-ATTTCATATCATGTTGCCATGGTGTCTTTCAACCATGGTCTTACA
65 TTCAACCATAGTCTT-CATCATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTACA
*
41476833 CATTTCATAT
129 CATTTCACAT
*
41476843 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTT
41476884 CATTTCAGAA
Statistics
Matches: 150, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
136 5 0.03
137 102 0.68
138 40 0.27
139 3 0.02
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (138 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCACATTGCCATGGTATCTT
TCAACCATAGTCTTCATCATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTACACA
TTTCACAT
Found at i:41476884 original size:46 final size:46
Alignment explanation
Indices: 41476568--41476886 Score: 365
Period size: 46 Copynumber: 7.0 Consensus size: 46
41476558 TTATCTTCGA
* * * * *
41476568 CATGATGCCATAGTGTCTTTCAACTATAGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGT
* **
41476614 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* ** * **
41476660 TACATTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
41476705 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
** * * * *
41476751 CACATTGCCATGGTGTCTTTTAACCATAGTCTTACAT-ATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTAC-TCATTTCATGT
* * *
41476797 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
*
41476843 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
41476887 TTCAGAAAAC
Statistics
Matches: 235, Mismatches: 34, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
45 43 0.18
46 191 0.81
47 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Found at i:41480456 original size:26 final size:26
Alignment explanation
Indices: 41480427--41480551 Score: 93
Period size: 26 Copynumber: 5.0 Consensus size: 26
41480417 TCCTCTCTCA
41480427 AGCCATATAACAGGAAGCTCACAAAG
1 AGCCATATAACAGGAAGCTCACAAAG
* *
41480453 AGCCAT-TAATCGGGAAGCTCACAAAT
1 AGCCATATAA-CAGGAAGCTCACAAAG
* ***
41480479 AGCC-TAT--TAGGAAGCTC-CTCCG
1 AGCCATATAACAGGAAGCTCACAAAG
* * *
41480501 GGCTATATAACAGGAAGCTCA-TAAG
1 AGCCATATAACAGGAAGCTCACAAAG
* *
41480526 AGCCATA-ATCAGGAAGTTCACAAAG
1 AGCCATATAACAGGAAGCTCACAAAG
41480551 A
1 A
41480552 ACTTTTAATC
Statistics
Matches: 74, Mismatches: 18, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
22 3 0.04
23 11 0.15
24 11 0.15
25 24 0.32
26 25 0.34
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (26 bp):
AGCCATATAACAGGAAGCTCACAAAG
Found at i:41480584 original size:26 final size:26
Alignment explanation
Indices: 41480511--41480588 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 26
41480501 GGCTATATAA
* *
41480511 CAGGAAGCTCAT-AAGAGCC-ATAAT
1 CAGGAAGCTCATAAAAAGCCTTTAAT
* * *
41480535 CAGGAAGTTCACAAAGAA-CTTTTAAT
1 CAGGAAGCTCATAAA-AAGCCTTTAAT
41480561 CAGGAAGCTCATAAAAAGCCTTTAAT
1 CAGGAAGCTCATAAAAAGCCTTTAAT
41480587 CA
1 CA
41480589 AGAGCTTCAG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
24 10 0.24
25 5 0.12
26 27 0.64
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (26 bp):
CAGGAAGCTCATAAAAAGCCTTTAAT
Found at i:41483902 original size:18 final size:17
Alignment explanation
Indices: 41483861--41483904 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
41483851 AATCTGGGCT
**
41483861 GTGTGAGCCACATGGGC
1 GTGTGAGCCACACAGGC
*
41483878 CTGTGAGCCTACACAGGC
1 GTGTGAGCC-ACACAGGC
41483896 GTGTGAGCC
1 GTGTGAGCC
41483905 CGATTTGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.18, C:0.27, G:0.36, T:0.18
Consensus pattern (17 bp):
GTGTGAGCCACACAGGC
Found at i:41485361 original size:21 final size:21
Alignment explanation
Indices: 41485323--41485362 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41485313 GAATTTCCAA
*
41485323 AAATTTTAAGAAAGATTAATT
1 AAATTTTAAGAAAAATTAATT
41485344 AAATTTTCAA-AAAAATTAA
1 AAATTTT-AAGAAAAATTAA
41485363 AAAGTACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (21 bp):
AAATTTTAAGAAAAATTAATT
Found at i:41489844 original size:44 final size:41
Alignment explanation
Indices: 41489745--41489863 Score: 141
Period size: 44 Copynumber: 2.8 Consensus size: 41
41489735 ACAAATATCA
* *
41489745 ATGCCACTGTCCCAGATAGGGTCTTACACGAAATCTAATATG
1 ATGCCAC-GTCCCAGACATGGTCTTACACGAAATCTAATATG
*
41489787 ATGCCGATGTCCCAGACATGGTCTTACACGTAAATCATAAGT-TG
1 ATGCC-ACGTCCCAGACATGGTCTTACACG-AAATC-TAA-TATG
*
41489831 ATGCCAACGTCCCAGACGTGGTCTTACACGAAA
1 ATGCC-ACGTCCCAGACATGGTCTTACACGAAA
41489864 ACACATATTG
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
42 25 0.37
43 9 0.13
44 32 0.48
45 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (41 bp):
ATGCCACGTCCCAGACATGGTCTTACACGAAATCTAATATG
Found at i:41490454 original size:23 final size:23
Alignment explanation
Indices: 41490428--41490473 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
41490418 TTCATCAAAA
*
41490428 TTTCAAAGGCAAAACATGTTAAC
1 TTTCAAAGACAAAACATGTTAAC
*
41490451 TTTCAAAGATAAAACATGTTAAC
1 TTTCAAAGACAAAACATGTTAAC
41490474 CCAACATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (23 bp):
TTTCAAAGACAAAACATGTTAAC
Found at i:41492089 original size:20 final size:22
Alignment explanation
Indices: 41492054--41492094 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
41492044 GGGACTAAAC
41492054 TGAAATCTTATAAAATTTTTCG
1 TGAAATCTTATAAAATTTTTCG
41492076 TGAAAT-TT-TAAAATTTTTC
1 TGAAATCTTATAAAATTTTTC
41492095 TTAAATACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 2 0.11
22 6 0.32
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (22 bp):
TGAAATCTTATAAAATTTTTCG
Done.