Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009592.1 Hibiscus syriacus cultivar Beakdansim tig00116971_pilon, 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: 7920512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 39
Found at i:3253150 original size:44 final size:42
Alignment explanation
Indices: 3253068--3253164 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 42
3253058 TGCACTACCC
* * * *
3253068 TGCATCGATACACAATTACCTTCGATGTTTTCATTTTAAGGGG
1 TGCATCGATGCACAATTACATTCGATGTTTTCA-TTTAAAGAG
*
3253111 ATGCATCGATGCACCAATTGCATTCGATGTTTTTC-TTTAAAGAG
1 -TGCATCGATGCA-CAATTACATTCGATG-TTTTCATTTAAAGAG
3253155 TGCATCGATG
1 TGCATCGATG
3253165 TACATTGAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
43 10 0.22
44 18 0.39
45 13 0.28
46 5 0.11
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (42 bp):
TGCATCGATGCACAATTACATTCGATGTTTTCATTTAAAGAG
Found at i:3256110 original size:21 final size:21
Alignment explanation
Indices: 3256086--3256126 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3256076 CTGTAAACTA
3256086 GTAATTCCGATAGATATGGTG
1 GTAATTCCGATAGATATGGTG
3256107 GTAATTCCGATAGATATGGT
1 GTAATTCCGATAGATATGGT
3256127 CATGATAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.34
Consensus pattern (21 bp):
GTAATTCCGATAGATATGGTG
Found at i:3256587 original size:21 final size:20
Alignment explanation
Indices: 3256501--3256654 Score: 78
Period size: 21 Copynumber: 7.6 Consensus size: 20
3256491 AAATGACCAA
**
3256501 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
3256520 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
3256540 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
3256560 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
3256581 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3256602 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3256622 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
3256643 GAAAATCGCAAC
1 CAAAATCGCAAC
3256655 ACGAACACAT
Statistics
Matches: 100, Mismatches: 29, Indels: 11
0.71 0.21 0.08
Matches are distributed among these distances:
19 16 0.16
20 38 0.38
21 46 0.46
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3256651 original size:20 final size:20
Alignment explanation
Indices: 3256626--3256695 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
3256616 GATTTTCAAG
* *
3256626 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
*
3256646 AATCGCAACACGAACACATA
1 AATCGCAACGCGAACACATA
* *
3256666 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
3256686 AATCGCAACG
1 AATCGCAACG
3256696 TGTATCCGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
19 1 0.02
20 39 0.93
21 2 0.05
ACGTcount: A:0.41, C:0.27, G:0.17, T:0.14
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:3256689 original size:40 final size:40
Alignment explanation
Indices: 3256626--3256815 Score: 197
Period size: 40 Copynumber: 4.7 Consensus size: 40
3256616 GATTTTCAAG
* ** * *
3256626 AATCGCAACGCGAATATGAAAATCGCAACACG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACACGTAAC-CGTA
** *
3256666 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACACGTAACCGTA
* ** *
3256706 AATCGCAACGTGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACACGTAACCGTA
* *
3256746 TATCGCAACGCGTATCCGTAAATCGCAACGAC--AATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAAC-ACGTAA-CCGT-A
3256787 AATCGCAACGCGTATCCGTAAATCGCAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
3256816 GCGATTTTTA
Statistics
Matches: 128, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
39 1 0.01
40 95 0.74
41 32 0.25
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACACGTAACCGTA
Found at i:3256700 original size:20 final size:20
Alignment explanation
Indices: 3256664--3256818 Score: 231
Period size: 20 Copynumber: 7.7 Consensus size: 20
3256654 CACGAACACA
3256664 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
3256684 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
*
3256704 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
*
3256724 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
3256744 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
3256764 TAAATCGCAACGAC-AATACG
1 TAAATCGCAACG-CGTATCCG
3256784 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
3256805 TAAATCGCAACGCG
1 TAAATCGCAACGCG
3256819 ATTTTTAAAG
Statistics
Matches: 122, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
20 105 0.86
21 17 0.14
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:3256709 original size:60 final size:60
Alignment explanation
Indices: 3256626--3256818 Score: 237
Period size: 60 Copynumber: 3.2 Consensus size: 60
3256616 GATTTTCAAG
* ** * *
3256626 AATCGCAACGCGAATATGAAAATCGCAACACGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACACGAACACGTAAATCGCAACGCGTATCCGTA
* ** * *
3256686 AATCGCAACGTGTATCCGTAAATCGCAACGTGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACACG-AACACGTAAATCGCAACGCGTATCCGTA
* *
3256746 TATCGCAACGCGTATCCGTAAATCGCAACGAC-AATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAAC-ACGAACACGT-AAATCGCAACGCGTATCCGTA
3256807 AATCGCAACGCG
1 AATCGCAACGCG
3256819 ATTTTTAAAG
Statistics
Matches: 111, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
59 1 0.01
60 77 0.69
61 33 0.30
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACACGAACACGTAAATCGCAACGCGTATCCGTA
Found at i:3257237 original size:33 final size:33
Alignment explanation
Indices: 3257198--3257266 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
3257188 TTCACTTAGA
3257198 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
3257231 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
3257264 TTT
1 TTT
3257267 TAAGTTAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.10, C:0.23, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:3257385 original size:20 final size:20
Alignment explanation
Indices: 3257348--3257453 Score: 109
Period size: 21 Copynumber: 5.5 Consensus size: 20
3257338 TGCAGAAGAG
3257348 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
3257369 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
3257389 TCTGCAACGAGAAAATGAAAA
1 TC-GCAACGAGAAAATGAAAA
3257410 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
3257424 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
3257443 TCGCAACGAGA
1 TCGCAACGAGA
3257454 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 17 0.24
21 27 0.39
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:3257427 original size:14 final size:14
Alignment explanation
Indices: 3257408--3257464 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3257398 AGAAAATGAA
3257408 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3257422 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3257441 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3257455 AATCGCAACG
1 AATCGCAACG
3257465 CGAACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3257439 original size:33 final size:33
Alignment explanation
Indices: 3257392--3257468 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
3257382 ATGACTATCT
*
3257392 GCAACGAGAAAATGAAAATCGCAACGAGAGAATC
1 GCAACGCG-AAATGAAAATCGCAACGAGAGAATC
3257426 GCAACGCGAAATGAAAATCGCAACGAGAGAATC
1 GCAACGCGAAATGAAAATCGCAACGAGAGAATC
3257459 GCAACGCGAA
1 GCAACGCGAA
3257469 CCAAAATCGC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 35 0.83
34 7 0.17
ACGTcount: A:0.47, C:0.21, G:0.25, T:0.08
Consensus pattern (33 bp):
GCAACGCGAAATGAAAATCGCAACGAGAGAATC
Found at i:3257516 original size:14 final size:14
Alignment explanation
Indices: 3257497--3257553 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3257487 TTTCATTTCG
3257497 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3257511 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3257530 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3257544 CGTTGCGATT
1 CGTTGCGATT
3257554 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3257522 original size:33 final size:33
Alignment explanation
Indices: 3257480--3257602 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
3257470 CAAAATCGCA
3257480 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3257513 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
3257546 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
3257587 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
3257603 AACCAAAAGG
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3257564 original size:21 final size:21
Alignment explanation
Indices: 3257538--3257602 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
3257528 CGCGTTGCGA
3257538 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
3257559 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
3257579 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
3257600 TTC
1 TTC
3257603 AACCAAAAGG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:3259435 original size:93 final size:93
Alignment explanation
Indices: 3259276--3259591 Score: 596
Period size: 93 Copynumber: 3.4 Consensus size: 93
3259266 TAGATTGCTT
*
3259276 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3259341 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3259369 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3259434 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3259462 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
* *
3259527 TTTGTCTTTTTTTTGCCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
3259555 AGTAAATTTGTTCGGTTGCTGCCAATTCTACTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
3259592 AATACCCTGA
Statistics
Matches: 219, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 219 1.00
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3259726 original size:14 final size:14
Alignment explanation
Indices: 3259707--3259763 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3259697 CGAAACTTAA
3259707 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3259721 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
3259740 AATCGCAACGACAG
1 AATCGCAACGAGAG
3259754 AATCGCAACG
1 AATCGCAACG
3259764 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3259745 original size:19 final size:18
Alignment explanation
Indices: 3259721--3259812 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
3259711 GCAACGAGAG
3259721 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
3259740 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
3259754 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
3259773 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
3259787 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
3259806 AATCGCA
1 AATCGCA
3259813 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:3259747 original size:33 final size:33
Alignment explanation
Indices: 3259689--3259812 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
3259679 TAGTTTACTT
* * *
3259689 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
3259723 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
3259756 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
3259789 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
3259813 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:3259789 original size:14 final size:14
Alignment explanation
Indices: 3259738--3259796 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
3259728 ACGCGAAATG
3259738 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3259752 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
3259771 AAAATCGCAACGAC
1 AAAATCGCAACGAC
3259785 AAAATCGCAACG
1 AAAATCGCAACG
3259797 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3259830 original size:19 final size:19
Alignment explanation
Indices: 3259808--3259980 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
3259798 GAAACCAAAA
*
3259808 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3259827 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3259841 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* * *
3259860 TCGCATTGTGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
3259876 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3259893 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
3259912 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
3259931 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
3259950 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3259970 TCGTGTTGCGA
1 TCGCGTTGCGA
3259981 AAGTAAACTA
Statistics
Matches: 124, Mismatches: 19, Indels: 21
0.76 0.12 0.13
Matches are distributed among these distances:
14 16 0.13
16 8 0.06
17 8 0.06
19 80 0.65
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3259938 original size:38 final size:38
Alignment explanation
Indices: 3259808--3259980 Score: 159
Period size: 33 Copynumber: 4.8 Consensus size: 38
3259798 GAAACCAAAA
*
3259808 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* * *
3259843 T--CGTTGCGATTTTCATTTCGCATTGTGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
3259876 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
3259912 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
3259950 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
3259981 AAGTAAACTA
Statistics
Matches: 113, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 50 0.44
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.39
39 11 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:3261919 original size:13 final size:14
Alignment explanation
Indices: 3261903--3261937 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3261893 ATTGTTTAAT
3261903 TGATTTGT-AAAGA
1 TGATTTGTAAAAGA
*
3261916 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3261930 TGATTTGT
1 TGATTTGT
3261938 GTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3262101 original size:20 final size:19
Alignment explanation
Indices: 3262044--3262123 Score: 98
Period size: 20 Copynumber: 4.4 Consensus size: 19
3262034 AAAAATGACT
3262044 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3262063 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3262077 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3262097 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3262117 ATCGCAA
1 ATCGCAA
3262124 CGAGAGAATC
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 1 0.02
17 3 0.06
19 8 0.15
20 30 0.57
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3262201 original size:53 final size:52
Alignment explanation
Indices: 3262132--3262353 Score: 258
Period size: 53 Copynumber: 4.2 Consensus size: 52
3262122 AACGAGAGAA
* * * *
3262132 TCGCAATGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCCGCA-TTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTACG-ATTTTC-ATT
* *
3262184 CTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTACGATTTTCATT
1 -TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTACGATTTTCATT
*
3262237 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTACGATTTTCATT
* *
3262290 TCGCATTGCGA-TTTCATTTCGCATTGCGATTTTCAT-GTT-GGAATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTC-TCGTTACG-ATTTTCATT
3262341 TCGCATTGCGATT
1 TCGCATTGCGATT
3262354 CTCTCGTTGC
Statistics
Matches: 151, Mismatches: 11, Indels: 15
0.85 0.06 0.08
Matches are distributed among these distances:
50 1 0.01
51 37 0.25
52 28 0.19
53 75 0.50
54 8 0.05
55 2 0.01
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTACGATTTTCATT
Found at i:3262263 original size:86 final size:89
Alignment explanation
Indices: 3262140--3262367 Score: 350
Period size: 86 Copynumber: 2.7 Consensus size: 89
3262130 AATCGCAATG
3262140 CGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
3262205 CGCATTGCGA-TTC-TCTCG-TTA
66 CGCATTGCGATTTCATCTCGATTA
3262226 CGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
* *
3262291 CGCATTGCGATTTCATTTCGCATTG
66 CGCATTGCGATTTCATCTCG-ATTA
3262316 CGATTTTCA--T-G--TTG-GAATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 CGATTTTCATTTCGCATTGCG-ATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
3262368 GTAATTTCCG
Statistics
Matches: 135, Mismatches: 2, Indels: 12
0.91 0.01 0.08
Matches are distributed among these distances:
84 27 0.20
85 13 0.10
86 75 0.56
87 4 0.03
88 5 0.04
90 11 0.08
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (89 bp):
CGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
CGCATTGCGATTTCATCTCGATTA
Found at i:3262375 original size:33 final size:33
Alignment explanation
Indices: 3262156--3262367 Score: 202
Period size: 33 Copynumber: 6.2 Consensus size: 33
3262146 TCATTTCGCA
3262156 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
3262190 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
3262223 TTACGATTTTCATTTCGCATTGCGATTTTCATTTCCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG
* * * * *
3262260 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
*
3262295 TTGCGA-TTTCATTTCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTTCGCATTGCGATTCTC-TCG
3262327 TTG-GAATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCG-ATTTTCATTTCGCATTGCGATTCTCTCG
3262360 TTGCGATT
1 TTGCGATT
3262368 GTAATTTCCG
Statistics
Matches: 146, Mismatches: 15, Indels: 35
0.74 0.08 0.18
Matches are distributed among these distances:
30 9 0.06
31 6 0.04
32 8 0.05
33 77 0.53
34 16 0.11
35 4 0.03
36 3 0.02
37 2 0.01
38 2 0.01
39 7 0.05
40 3 0.02
41 9 0.06
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:3264667 original size:12 final size:12
Alignment explanation
Indices: 3264650--3264674 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3264640 TCTTCGGGGA
3264650 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3264662 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3264674 C
1 C
3264675 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3264883 original size:24 final size:24
Alignment explanation
Indices: 3264849--3264895 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3264839 CTGAAACATC
3264849 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3264873 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3264896 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:3265616 original size:20 final size:20
Alignment explanation
Indices: 3265588--3265756 Score: 171
Period size: 20 Copynumber: 8.4 Consensus size: 20
3265578 AAATTTCAGT
* * * *
3265588 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3265608 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3265628 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3265648 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
3265668 ATTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
3265688 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
3265708 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
3265728 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
3265748 GTTGCGATT
1 GTTGCGATT
3265757 CTTGAAAATC
Statistics
Matches: 127, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.02
20 123 0.97
21 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:3265809 original size:21 final size:20
Alignment explanation
Indices: 3265724--3265821 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
3265714 ATTTATGTGT
* *
3265724 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
3265744 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
3265765 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
3265786 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
3265807 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
3265822 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:3265817 original size:42 final size:43
Alignment explanation
Indices: 3265724--3265822 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
3265714 ATTTATGTGT
* *
3265724 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
3265765 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
3265807 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
3265823 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:3266214 original size:24 final size:25
Alignment explanation
Indices: 3266184--3266239 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
3266174 TAAGGCGTCC
3266184 AAAAAGATTTCTAA-ATTATAAAAA
1 AAAAAGATTTCTAAGATTATAAAAA
* * *
3266208 AAAAAGATTTCTAAGGTTTTGAAAA
1 AAAAAGATTTCTAAGATTATAAAAA
3266233 AAAAAGA
1 AAAAAGA
3266240 AAATTATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.59, C:0.04, G:0.11, T:0.27
Consensus pattern (25 bp):
AAAAAGATTTCTAAGATTATAAAAA
Found at i:3270672 original size:27 final size:27
Alignment explanation
Indices: 3270615--3270672 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
3270605 TAATATAGTC
* *
3270615 ATTTTACACTTCAAGGGTATTTTGGTC
1 ATTTTACACTTCAAGGGAATTTTGGTA
*
3270642 ATTTTACACTTCAGGGGAAATTTT-GTA
1 ATTTTACACTTCAAGGG-AATTTTGGTA
3270669 ATTT
1 ATTT
3270673 CATAATCAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (27 bp):
ATTTTACACTTCAAGGGAATTTTGGTA
Found at i:3275572 original size:57 final size:56
Alignment explanation
Indices: 3275474--3275580 Score: 142
Period size: 57 Copynumber: 1.9 Consensus size: 56
3275464 CCGTAGTGTT
** * **
3275474 AATCCGTATGACACATAAGGTCATGTCCACCATCTGTACTAGGTATCCTTAAGTAC
1 AATCCGTATGACACATAAGGTCATACCCACCATATACACTAGGTATCCTTAAGTAC
* *
3275530 AATCTCGTATGTCACATAAGGTCGTACCCACCATATACACTAGGTATCCTT
1 AATC-CGTATGACACATAAGGTCATACCCACCATATACACTAGGTATCCTT
3275581 TAATGTATCT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
56 4 0.09
57 39 0.91
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (56 bp):
AATCCGTATGACACATAAGGTCATACCCACCATATACACTAGGTATCCTTAAGTAC
Found at i:3277842 original size:27 final size:27
Alignment explanation
Indices: 3277785--3277842 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
3277775 TAATATAATC
* *
3277785 ATTTTACACTTCAAGGGTATTTTGGTT
1 ATTTTACACTTCAAGGGAATTTTGGTA
*
3277812 ATTTTACACTTCAGGGGGAATTTT-GTA
1 ATTTTACACTTCA-AGGGAATTTTGGTA
3277839 ATTT
1 ATTT
3277843 CATAATTAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.47
Consensus pattern (27 bp):
ATTTTACACTTCAAGGGAATTTTGGTA
Found at i:3282682 original size:17 final size:18
Alignment explanation
Indices: 3282644--3282685 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3282634 AATCATAACA
*
3282644 AACTAATAACAAAGTCCT
1 AACTAATAACAAAGTACT
3282662 AACTAATAACAAA-TACT
1 AACTAATAACAAAGTACT
3282679 AACTAAT
1 AACTAAT
3282686 CTTTATTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.55, C:0.19, G:0.02, T:0.24
Consensus pattern (18 bp):
AACTAATAACAAAGTACT
Found at i:3283426 original size:36 final size:36
Alignment explanation
Indices: 3282745--3283413 Score: 921
Period size: 36 Copynumber: 18.6 Consensus size: 36
3282735 AAAGACGAAC
* * * * *
3282745 ACTTGAAACGAAAGTG-CGATACATCTTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
3282780 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* ***
3282816 ACTTGAATAGGAAGTATAGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* * *
3282852 ACTTGAATTGGAAGTACAGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
** *
3282888 ACTTGAATCGGAAGTGTTGATGCTTCCTTTCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* * * *
3282924 ACTTGAATCAGAAGTGTCAATTCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
3282960 ACTTGAATCGGAAGTGCCGATGCTTTCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* *
3282996 ACTTGAATCGGAAGTGCCGATGGTTCCTTCCGTTCA
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
3283032 ACTTGAATCGGAAGTACCGATGCCTT-CTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATG-CTTCCTTCCGTTCG
* *
3283068 ACTTGAATCGGAAGTGCCGATGCTTCCTTCTGTTGG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
3283104 ACTTGAATCGGAAGTACCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
3283140 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCATTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* *
3283176 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCTTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* *
3283212 ACTTGAATCGGAAGTACCGATGGTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* *
3283248 ACTTGAATCAGAAGTACCGATGTCTT-CTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATG-CTTCCTTCCGTTCG
3283284 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
3283320 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* * * ** *
3283356 ACATAAATCGAAAGTATCGATACTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* *
3283392 ACTTAAATCGAAAGTGCCGATG
1 ACTTGAATCGGAAGTGCCGATG
3283414 TTTTATTTCG
Statistics
Matches: 569, Mismatches: 60, Indels: 9
0.89 0.09 0.01
Matches are distributed among these distances:
35 20 0.04
36 545 0.96
37 4 0.01
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (36 bp):
ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
Found at i:3289818 original size:130 final size:130
Alignment explanation
Indices: 3289638--3289913 Score: 473
Period size: 130 Copynumber: 2.1 Consensus size: 130
3289628 CTAAATATCG
* *
3289638 AAATAATATTTATTA-TTATTTTTTTAATAAATTCTATAGTTAATTATAATTTTATTTAGAAGAG
1 AAATAATATTTATTATTTATTTTTTTAATAAATTCTACAGTTAATTATAATTCTATTTAGAAGAG
*
3289702 AGGGGAACGAGGATTCTAAAGGAAAGAAGGAGAGTGCTCCAAATGAGTACCAAATGTGATTGCTC
66 AGGGGAACGAGGATTCTAAAGGAAAGAAAGAGAGTGCTCCAAATGAGTACCAAATGTGATTGCTC
* * *
3289767 AAATAATATTTATTATTTTTTTTTTTTATAAATTCTACAGTTAATTCTAATTCTATTTAGAAGAG
1 AAATAATATTTATTATTTATTTTTTTAATAAATTCTACAGTTAATTATAATTCTATTTAGAAGAG
* *
3289832 AGGGGAATGAGGATTCTAAAGGAAAGAAAGAGAGTGCTCCAAATGAGTACCAAATGTGCTTGCTC
66 AGGGGAACGAGGATTCTAAAGGAAAGAAAGAGAGTGCTCCAAATGAGTACCAAATGTGATTGCTC
3289897 AAATAATATTTATTATT
1 AAATAATATTTATTATT
3289914 GATTAGATGT
Statistics
Matches: 138, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
129 15 0.11
130 123 0.89
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (130 bp):
AAATAATATTTATTATTTATTTTTTTAATAAATTCTACAGTTAATTATAATTCTATTTAGAAGAG
AGGGGAACGAGGATTCTAAAGGAAAGAAAGAGAGTGCTCCAAATGAGTACCAAATGTGATTGCTC
Found at i:3296673 original size:22 final size:22
Alignment explanation
Indices: 3296648--3296689 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
3296638 AATTATGAAG
3296648 TCTAATTTATTAGTAGTTTATT
1 TCTAATTTATTAGTAGTTTATT
3296670 TCTAATTTATTAGTAGTTTA
1 TCTAATTTATTAGTAGTTTA
3296690 CTAATCAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.57
Consensus pattern (22 bp):
TCTAATTTATTAGTAGTTTATT
Found at i:3296693 original size:19 final size:20
Alignment explanation
Indices: 3296648--3296694 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 20
3296638 AATTATGAAG
3296648 TCTAATTTATTAGTAGTTTA
1 TCTAATTTATTAGTAGTTTA
3296668 TTTCTAATTTATTAGTAGTTTA
1 --TCTAATTTATTAGTAGTTTA
3296690 -CTAAT
1 TCTAAT
3296695 CAGCTTAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.20
22 20 0.80
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (20 bp):
TCTAATTTATTAGTAGTTTA
Found at i:3300084 original size:3 final size:3
Alignment explanation
Indices: 3300078--3300125 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
3300068 ATTATTTATT
* *
3300078 TAA TAA TAG TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3300123 TAA
1 TAA
3300126 ATAAAACAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3300115 original size:14 final size:14
Alignment explanation
Indices: 3300055--3300126 Score: 56
Period size: 14 Copynumber: 5.0 Consensus size: 14
3300045 AATTGGGCCT
3300055 ATAATAATAATAAA
1 ATAATAATAATAAA
* * *
3300069 TTATTTATTTAATAATA
1 ATA-ATA-ATAATAA-A
* *
3300086 GTAAT-ATAATATA
1 ATAATAATAATAAA
*
3300099 ATAATAATATTAAA
1 ATAATAATAATAAA
3300113 ATAATAATAATAAA
1 ATAATAATAATAAA
3300127 TAAAACAAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
13 5 0.12
14 26 0.60
15 2 0.05
16 7 0.16
17 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (14 bp):
ATAATAATAATAAA
Found at i:3300514 original size:120 final size:123
Alignment explanation
Indices: 3300339--3300571 Score: 307
Period size: 123 Copynumber: 1.9 Consensus size: 123
3300329 TGACAATTCA
*
3300339 TCTCCTTCTGTGAAGTAATCTAGCAAAAAAGTTGAACAGATTCTTCTCATTATGAACTTATTCTT
1 TCTCCTTCTGTGAAGTAATCTAGCAAAAAAGTTGAACAAATTCTTCTCATTATGAACTTATTCTT
*
3300404 -T-TTCAGATGAGTTCTTCTCATTATGAACTCCTTT-TGGAAATGTTGCTGATGATATG
66 CTCTTCAGATAAGTTCTTCTCATTATGAACT-CTTTCTGGAAATGTTGCTGATGATATG
* * * * *
3300460 TCTCCTTCTGTGATAG-AGTC-ATGC-AAAAGGTTGAACAAATTCTTCTTATTATGAATTTCTTC
1 TCTCCTTCTGTGA-AGTAATCTA-GCAAAAAAGTTGAACAAATTCTTCTCATTATGAACTTATTC
* *
3300522 TTCCTCTTTAGATAAGTTCTTCTCATTATGAACTTTTTCTGGAAATGTTG
64 TT-CTCTTCAGATAAGTTCTTCTCATTATGAACTCTTTCTGGAAATGTTG
3300572 ATCCATCAAG
Statistics
Matches: 97, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
120 36 0.37
121 18 0.19
122 6 0.06
123 37 0.38
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (123 bp):
TCTCCTTCTGTGAAGTAATCTAGCAAAAAAGTTGAACAAATTCTTCTCATTATGAACTTATTCTT
CTCTTCAGATAAGTTCTTCTCATTATGAACTCTTTCTGGAAATGTTGCTGATGATATG
Found at i:3300674 original size:112 final size:113
Alignment explanation
Indices: 3300482--3300786 Score: 465
Period size: 112 Copynumber: 2.7 Consensus size: 113
3300472 ATAGAGTCAT
* * * * *
3300482 GCAAAAGGTTGAACAAATTCTTCTTATTATGAATTTCTTCTTCC-TCTTTAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
3300546 ATTATGAACTTTTTCTGGAAATGTTGATCCATC-AAGTGATGAATTTGAA
66 ATTATGAACTTCTTCTGGAAATGCTGATCCATCGAA-TGATGAA-TTCAA
* *
3300595 -CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
3300659 ATTATGAAC-TCTTCTGGAAATGCTGATCCATCGAATGATGAATTCAA
66 ATTATGAACTTCTTCTGGAAATGCTGATCCATCGAATGATGAATTCAA
*
3300706 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
3300771 ATTATGAACTTCTTCT
66 ATTATGAACTTCTTCT
3300787 TCTTCAGATG
Statistics
Matches: 175, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
111 4 0.02
112 136 0.78
113 35 0.20
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTCTTCTGGAAATGCTGATCCATCGAATGATGAATTCAA
Found at i:3300765 original size:40 final size:39
Alignment explanation
Indices: 3300721--3300817 Score: 164
Period size: 36 Copynumber: 2.5 Consensus size: 39
3300711 AAGTTGAACA
3300721 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
1 AGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATG
3300761 AGTTCTTCTCATTATGAA---CTTCTTCTTCTTCAGATG
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATG
3300797 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
3300818 TACCTGGAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
36 30 0.56
37 6 0.11
40 18 0.33
ACGTcount: A:0.20, C:0.23, G:0.10, T:0.47
Consensus pattern (39 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATG
Found at i:3300766 original size:20 final size:19
Alignment explanation
Indices: 3300743--3300805 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
3300733 TATGAACTTC
3300743 TTCTTCCTTCTTCAGATGAG
1 TTCTT-CTTCTTCAGATGAG
*
3300763 TTCTTC-TCATT---ATGAAC
1 TTCTTCTTC-TTCAGATG-AG
3300780 TTCTTCTTCTTCAGATGAG
1 TTCTTCTTCTTCAGATGAG
3300799 TTCTTCT
1 TTCTTCT
3300806 CATTATGAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 13
0.70 0.04 0.26
Matches are distributed among these distances:
16 3 0.09
17 9 0.26
18 4 0.11
19 11 0.31
20 8 0.23
ACGTcount: A:0.16, C:0.24, G:0.11, T:0.49
Consensus pattern (19 bp):
TTCTTCTTCTTCAGATGAG
Found at i:3300777 original size:16 final size:16
Alignment explanation
Indices: 3300758--3300813 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
3300748 CCTTCTTCAG
3300758 ATGAGTTCTTCTCATT
1 ATGAGTTCTTCTCATT
*
3300774 ATGAACTTCTTCTTC-TT
1 ATG-AGTTCTTC-TCATT
3300791 CAGATGAGTTCTTCTCATT
1 ---ATGAGTTCTTCTCATT
3300810 ATGA
1 ATGA
3300814 ACTTTACCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 7 0.22
17 9 0.28
18 4 0.12
19 9 0.28
20 3 0.09
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.46
Consensus pattern (16 bp):
ATGAGTTCTTCTCATT
Found at i:3300860 original size:149 final size:150
Alignment explanation
Indices: 3300609--3300931 Score: 503
Period size: 149 Copynumber: 2.1 Consensus size: 150
3300599 AGGTTAAACA
3300609 AGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCT
1 AGTTCTTCTCATTATGAAC-T-CTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCT
*
3300674 GGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAA
64 GGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTAAACAAGTTCTTCTCATTATGAA
*
3300739 CTTCTTCTTCCTTCTTCAGATG
129 CTTCCTCTTCCTTCTTCAGATG
3300761 AGTTCTTCTCATTATGAACT-TCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTACCT
1 AGTTCTTCTCATTATGAACTCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTT--CT
* * * *
3300823 GGAAATGTTGATCCATC-AAGTGATGGATTTGAA-CAAAAGGTTAAACAAGTTCTTCTCATTATG
64 GGAAATGCTGATCCATCGAA-TGAT-GAATTCAAGCAAAAAGTTAAACAAGTTCTTCTCATTATG
3300886 AACTTCCTCTTCCTTCTTCAGATG
127 AACTTCCTCTTCCTTCTTCAGATG
3300910 AGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTCT
3300932 ACCTGAAAAT
Statistics
Matches: 160, Mismatches: 6, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
147 2 0.01
148 34 0.21
149 97 0.61
150 7 0.04
151 1 0.01
152 19 0.12
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (150 bp):
AGTTCTTCTCATTATGAACTCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGG
AAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTAAACAAGTTCTTCTCATTATGAACT
TCCTCTTCCTTCTTCAGATG
Found at i:3301119 original size:113 final size:113
Alignment explanation
Indices: 3300761--3301121 Score: 547
Period size: 113 Copynumber: 3.2 Consensus size: 113
3300751 TCTTCAGATG
*
3300761 AGTTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
* * * *
3300822 TGGAAATG-TTGATCCATCAAGTGATGGATTTGAACAAAAGGTTAAACA
66 TGGAAAAGCTT-ATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACA
*
3300870 AGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
* * **
3300935 T-GAAAATGCTGATCCATCGAA-TGATGAATTCAAGCAAAAAGTTGAACA
66 TGGAAAA-GCTTATCCATC-AAGTGATGGATTTGAGCAAAAAGTTGAACA
3300983 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
3301048 TGGAAAAGCTTATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACA
66 TGGAAAAGCTTATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACA
*
3301096 AGCTCTTCTCATTATGAACTTCTTCT
1 AGTTCTTCTCATTATGAACTTCTTCT
3301122 GGAAATGCTG
Statistics
Matches: 227, Mismatches: 16, Indels: 14
0.88 0.06 0.05
Matches are distributed among these distances:
109 18 0.08
112 11 0.05
113 190 0.84
114 8 0.04
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
TGGAAAAGCTTATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACA
Found at i:3301209 original size:309 final size:309
Alignment explanation
Indices: 3300858--3301430 Score: 877
Period size: 309 Copynumber: 1.9 Consensus size: 309
3300848 GATTTGAACA
*
3300858 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGCTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
3300923 ATGAACTCTAC-CT-GAAAATGCTGATCCATCGAA-TGATGAATTCAAGCAAAAAGTTGAACAAG
66 ATGAACT-TACTCTGGAAAA-GCTAATCCATC-AAGTGATGAATTCAAGCAAAAAGTTGAACAAA
*
3300985 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CT
128 TTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACT-TACTCT
* * *
3301049 GGAAAAGCTT-ATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAGCTCTTCTCATTATGA
191 GGAAAAGCTTGATCCATCAAGTGATGAATTCGAGCAAAAAGTTAAACAAGCTCTTCTCATTATGA
3301113 ACTTCTTCTGGAAATGCTGATACTGATCTATTTCCTTCTGTGATAGCATCAAAC
256 ACTTCTTCTGGAAATGCTGATACTGATCTATTTCCTTCTGTGATAGCATCAAAC
* *
3301167 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGCTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
3301232 ATGAACTTTCTTTGGAAAAGTTAATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTC
66 ATGAACTTACTCTGGAAAAGCTAATCCATCAAGTGATGAATTCAAGCAAAAAGTTGAACAAATTC
* *
3301297 TTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA
131 TTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTACTCTGGAAA
* * * * *
3301362 TGTTTGATTCATCAAGTGATGAATTCGAGCAAAAGGTTAAACAAGCTCTTCTCATTATGAACTTT
196 AGCTTGATCCATCAAGTGATGAATTCGAGCAAAAAGTTAAACAAGCTCTTCTCATTATGAACTTC
3301427 TTCT
261 TTCT
3301431 TCCTTCTTCA
Statistics
Matches: 238, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
307 2 0.01
308 43 0.18
309 188 0.79
310 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (309 bp):
AAAGGTTAAACAAGCTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTACTCTGGAAAAGCTAATCCATCAAGTGATGAATTCAAGCAAAAAGTTGAACAAATTC
TTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTACTCTGGAAA
AGCTTGATCCATCAAGTGATGAATTCGAGCAAAAAGTTAAACAAGCTCTTCTCATTATGAACTTC
TTCTGGAAATGCTGATACTGATCTATTTCCTTCTGTGATAGCATCAAAC
Found at i:3301360 original size:112 final size:113
Alignment explanation
Indices: 3301167--3301591 Score: 635
Period size: 112 Copynumber: 3.8 Consensus size: 113
3301157 AGCATCAAAC
3301167 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
3301232 ATGAACTTTCTTTGGAAAAGTTAATCCATCAAGTGATGAATTCAGGCA
66 ATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAGGCA
** * *
3301280 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
3301344 ATGAACTTTCTCTGGAAATGTTTGATTCATCAAGTGATGAATTC-GAGCA
66 ATGAACTTTCTCTGGAAATG-TTGATCCATCAAGTGATGAATTCAG-GCA
* *
3301393 AAAGGTTAAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
3301458 ATGAACTCT-TCTGGAAATGTTGATCCATTGAA-TGATGAATTCAAGCA
66 ATGAACTTTCTCTGGAAATGTTGATCCA-TCAAGTGATGAATTCAGGCA
* *
3301505 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
3301570 ATGAACTCTAC-CTGGAAATGTT
66 ATGAACT-TTCTCTGGAAATGTT
3301592 TTAAGAAAAA
Statistics
Matches: 281, Mismatches: 24, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
112 129 0.46
113 122 0.43
114 30 0.11
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (113 bp):
AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAGGCA
Found at i:3301421 original size:226 final size:226
Alignment explanation
Indices: 3301167--3301592 Score: 689
Period size: 226 Copynumber: 1.9 Consensus size: 226
3301157 AGCATCAAAC
*
3301167 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
3301232 ATGAACT-TTCTTTGGAAAAGTTAATCCA-TCAAGTGATGAATTCAGGCAAAAGGTTGAACAAAT
66 ATGAACTCTTC--TGGAAAAGTTAATCCATTCAA-TGATGAATTCAAGCAAAAAGTTGAACAAAT
* *
3301295 TCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACT-TTCTCTG
128 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTAC-CTG
3301358 GAAATGTTTGATTCATCAAGTGATGAATTCGAGCA
192 GAAATGTTTGATTCATCAAGTGATGAATTCGAGCA
*
3301393 AAAGGTTAAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
3301458 ATGAACTCTTCTGGAAATGTTGATCCATTGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCT
66 ATGAACTCTTCTGGAAAAGTTAATCCATTCAATGATGAATTCAAGCAAAAAGTTGAACAAATTCT
*
3301523 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAA
131 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTACCTGGAAA
3301588 TGTTT
196 TGTTT
3301593 TAAGAAAAAA
Statistics
Matches: 185, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
225 66 0.36
226 114 0.62
227 5 0.03
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (226 bp):
AAAGGTTAAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTTCTGGAAAAGTTAATCCATTCAATGATGAATTCAAGCAAAAAGTTGAACAAATTCT
TCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTACCTGGAAA
TGTTTGATTCATCAAGTGATGAATTCGAGCA
Found at i:3301738 original size:76 final size:76
Alignment explanation
Indices: 3301624--3301785 Score: 243
Period size: 76 Copynumber: 2.1 Consensus size: 76
3301614 CACTGTAAGG
* * * * *
3301624 CTTACAGCTGACTCAAAGGTTTTGAAAACATAAAAAAGCTCCCGAAGGCTTTTTGGACACATCAT
1 CTTACAGATGACCCTAAGGTTTTAAAAACATAAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
3301689 GCACTATAGGA
66 GCACTATAGGA
* * *
3301700 CTTATAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCAT
1 CTTACAGATGACCCTAAGGTTTTAAAAACATAAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
*
3301765 GCACTGTAGGA
66 GCACTATAGGA
3301776 CTTACAGATG
1 CTTACAGATG
3301786 TGGGAAATAG
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (76 bp):
CTTACAGATGACCCTAAGGTTTTAAAAACATAAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
GCACTATAGGA
Found at i:3302488 original size:22 final size:22
Alignment explanation
Indices: 3302463--3302539 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
3302453 AATAAAGCTT
3302463 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
3302485 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
3302507 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
3302529 TCATCTTTGAA
1 TCATCTTTGAA
3302540 GAGTGCAGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:3305080 original size:115 final size:115
Alignment explanation
Indices: 3304961--3305260 Score: 548
Period size: 115 Copynumber: 2.6 Consensus size: 115
3304951 GTTCATAATG
*
3304961 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGGTCTTCTTATTTCTACTAT
* *
3305026 GAGCAAATTCATCTTTCAAATCTAATGATGGGTTTTTGGGGTTCATACCA
66 GAGCAAATTCATCTTTCAAATCTAATGATGGGTTTTTAGGGTTCATACAA
3305076 AACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGGTCTTCTTATTTCTACTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGGTCTTCTTATTTCTACTAT
*
3305141 GAGCAAATTCATCTTTCAAATCTAATGATTGGTTTTTAGGGTTCATACAA
66 GAGCAAATTCATCTTTCAAATCTAATGATGGGTTTTTAGGGTTCATACAA
3305191 AACCAGATCAGATAACTCAAAGAACAAC-TCTAGAAGATGCTATTGGGTCTTCTTATTTCTACTA
1 AACCAGATCAGATAACTCAAAGAAC-ACTTCTAGAAGATGCTATTGGGTCTTCTTATTTCTACTA
3305255 TGAGCA
65 TGAGCA
3305261 CATGGCACTT
Statistics
Matches: 180, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
115 178 0.99
116 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (115 bp):
AACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATTGGGTCTTCTTATTTCTACTAT
GAGCAAATTCATCTTTCAAATCTAATGATGGGTTTTTAGGGTTCATACAA
Found at i:3305302 original size:115 final size:113
Alignment explanation
Indices: 3304919--3305260 Score: 535
Period size: 115 Copynumber: 3.0 Consensus size: 113
3304909 GATCATGTAG
* * * * *
3304919 TTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCATA-ATGAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCTAATGATTGGTTTTG-GGTTCATACA-AAACCAGATCAGATAACTCAAAG
*
3304983 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
64 AACACTTCTAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
* *
3305033 TTCATCTTTCAAATCTAATGATGGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCTAATGATTGG-TTTT-GGGTTCATACAAAACCAGATCAGATAACTCAAAG
3305098 AACACTTCTAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
64 AACACTTCTAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
3305148 TTCATCTTTCAAATCTAATGATTGGTTTTTAGGGTTCATACAAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCTAATGATTGG-TTTT-GGGTTCATACAAAACCAGATCAGATAACTCAAAG
3305213 AACAAC-TCTAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
64 AAC-ACTTCTAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
3305261 CATGGCACTT
Statistics
Matches: 213, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
114 21 0.10
115 189 0.89
116 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (113 bp):
TTCATCTTTCAAATCTAATGATTGGTTTTGGGTTCATACAAAACCAGATCAGATAACTCAAAGAA
CACTTCTAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:3307541 original size:17 final size:16
Alignment explanation
Indices: 3307519--3307565 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
3307509 ATTTTCCTTC
* *
3307519 TTTTTTTTCCTTTTTG
1 TTTTTTTTCCTTCTTA
*
3307535 TTTTTTTTTCTTCTTA
1 TTTTTTTTCCTTCTTA
3307551 TTTTTTTTCCTTCTT
1 TTTTTTTTCCTTCTT
3307566 CTTTCTTTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTTTTTCCTTCTTA
Found at i:3307557 original size:19 final size:19
Alignment explanation
Indices: 3307519--3307569 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
3307509 ATTTTCCTTC
3307519 TTTTTTTTC--CTTTTTGT
1 TTTTTTTTCTTCTTTTTGT
3307536 TTTTTTTTCTTCTTATTT-T
1 TTTTTTTTCTTCTT-TTTGT
**
3307555 TTTTCCTTCTTCTTT
1 TTTTTTTTCTTCTTT
3307570 CTTTGCTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 9 0.31
18 1 0.03
19 16 0.55
20 3 0.10
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTTTTCTTCTTTTTGT
Found at i:3307874 original size:2 final size:2
Alignment explanation
Indices: 3307867--3307908 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3307857 ACAACAAATG
3307867 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3307909 TAAAAGGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3310106 original size:26 final size:26
Alignment explanation
Indices: 3310072--3310122 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
3310062 TTATGGAAAT
*
3310072 ATGCAAATGTAAATACAAACGTAAAA
1 ATGCAAATGCAAATACAAACGTAAAA
* *
3310098 ATGCAAATGCAAATGCAAATGTAAA
1 ATGCAAATGCAAATACAAACGTAAA
3310123 TATATGAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.55, C:0.12, G:0.14, T:0.20
Consensus pattern (26 bp):
ATGCAAATGCAAATACAAACGTAAAA
Found at i:3312387 original size:22 final size:21
Alignment explanation
Indices: 3312340--3312393 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
3312330 AAAATTAATC
*
3312340 AAATAATATATTAATATGATTA
1 AAATAATA-ATTAATATAATTA
* *
3312362 AAATAATAATTATTATTAATTT
1 AAATAATAATTAATA-TAATTA
3312384 AAATATATAA
1 AAATA-ATAA
3312394 CAATAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.22
22 17 0.63
23 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
AAATAATAATTAATATAATTA
Found at i:3313664 original size:3 final size:3
Alignment explanation
Indices: 3313658--3313705 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
3313648 ATTATTTATT
* *
3313658 TAA TAA TAG TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3313703 TAA
1 TAA
3313706 ATAAAACAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3313695 original size:14 final size:14
Alignment explanation
Indices: 3313667--3313706 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3313657 TTAATAATAG
*
3313667 TAAT-ATAATATAA
1 TAATAATAATAAAA
*
3313680 TAATAATATTAAAA
1 TAATAATAATAAAA
3313694 TAATAATAATAAA
1 TAATAATAATAAA
3313707 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:3323501 original size:13 final size:13
Alignment explanation
Indices: 3323457--3323505 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
3323447 TTTAATATTT
*
3323457 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
* *
3323469 ATCGGGACGGATA
1 ATCGGGGCGGGTA
3323482 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
3323495 ATCGGGGCGGG
1 ATCGGGGCGGG
3323506 GATTACCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 10 0.31
13 22 0.69
ACGTcount: A:0.16, C:0.16, G:0.51, T:0.16
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:3327516 original size:28 final size:28
Alignment explanation
Indices: 3327484--3327538 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
3327474 TCTTCGTTTA
* * *
3327484 CATTATGTCATTGAGTCAATGCTTGAAG
1 CATTATATCATCGAGCCAATGCTTGAAG
*
3327512 CATTATATCGTCGAGCCAATGCTTGAA
1 CATTATATCATCGAGCCAATGCTTGAA
3327539 AGTAACGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (28 bp):
CATTATATCATCGAGCCAATGCTTGAAG
Found at i:3327842 original size:19 final size:22
Alignment explanation
Indices: 3327815--3327857 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
3327805 CATATAAATT
3327815 AAATATATT-T-AACTTTTATA
1 AAATATATTCTCAACTTTTATA
3327835 AAAT-TATTCTCAACTTTTATA
1 AAATATATTCTCAACTTTTATA
3327856 AA
1 AA
3327858 GCGAAGGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 5 0.24
21 12 0.57
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATATATTCTCAACTTTTATA
Found at i:3328242 original size:44 final size:44
Alignment explanation
Indices: 3328192--3328282 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
3328182 TAATAAACTC
* *
3328192 CGCTAAAAGTTAGGTTATGTAGAGGCG-TTT-GTATACTAGAACGT
1 CGCTAAAAGTCAGGTTATATAGAGGCGTTTTAGTATAC-A-AACGT
* *
3328236 CGCTAAAGGTCAGGTTATATAGCGGCGTTTTAGTATACAAACGT
1 CGCTAAAAGTCAGGTTATATAGAGGCGTTTTAGTATACAAACGT
3328280 CGC
1 CGC
3328283 AACAGGTTCG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 31 0.76
45 4 0.10
46 6 0.15
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (44 bp):
CGCTAAAAGTCAGGTTATATAGAGGCGTTTTAGTATACAAACGT
Found at i:3332033 original size:41 final size:40
Alignment explanation
Indices: 3331982--3332278 Score: 319
Period size: 40 Copynumber: 7.2 Consensus size: 40
3331972 ATGAACGCTT
3331982 CTAAAGTACGAGTCTATAGCGGCGTTTGTATATAAATGCCA
1 CTAAAGTACGAGTCTATAGCGGCGTTTGTATA-AAATGCCA
* *
3332023 CTAAAGTACGAGTCTTTAGCGGCGTTTGTAAATACAAATACCA
1 CTAAAGTACGAGTCTATAGCGGCGTTTGT--ATA-AAATGCCA
* * * * *
3332066 CAAAAGTACAAGTGTATATCGGCGTTTGTATAAAAAGCCA
1 CTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAATGCCA
* *
3332106 CTAAAGTACAAGTCTATAGCGGCGTTTGTA-AACATAAGCGCAA
1 CTAAAGTACGAGTCTATAGCGGCGTTTGTATAA-A-ATGC-C-A
* *
3332149 CTAAAGTACGAGTGTATAGCGGCGTTTGTATGAAAACGCCA
1 CTAAAGTACGAGTCTATAGCGGCGTTTGTAT-AAAATGCCA
* *
3332190 CTAAAGTACGAGTTTATAGTGGCGTTTGTATAAAATGCCA
1 CTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAATGCCA
* * * * * *
3332230 CTAAAGTACGATTCTTTAG-TGCGTTTTTATACAAACGCCG
1 CTAAAGTACGAGTCTATAGCGGCGTTTGTATA-AAATGCCA
3332270 CTAAAGTAC
1 CTAAAGTAC
3332279 AACTTTGTTG
Statistics
Matches: 221, Mismatches: 26, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
39 12 0.05
40 73 0.33
41 65 0.29
42 2 0.01
43 66 0.30
44 1 0.00
45 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (40 bp):
CTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAATGCCA
Found at i:3332089 original size:43 final size:42
Alignment explanation
Indices: 3331982--3332240 Score: 255
Period size: 41 Copynumber: 6.3 Consensus size: 42
3331972 ATGAACGCTT
*
3331982 CTAAAGTACGAGTCTATAGCGGCGTTTGT-ATATAAATGCCA
1 CTAAAGTACGAGTCTATAGCGGCGTTTGTAATATAAATACCA
* *
3332023 CTAAAGTACGAGTCTTTAGCGGCGTTTGTAAATACAAATACCA
1 CTAAAGTACGAGTCTATAGCGGCGTTTGT-AATATAAATACCA
* * * *
3332066 CAAAAGTACAAGTGTATATCGGCGTTTGT-ATA-AAA-AGCCA
1 CTAAAGTACGAGTCTATAGCGGCGTTTGTAATATAAATA-CCA
* * *** *
3332106 CTAAAGTACAAGTCTATAGCGGCGTTTGTAAACATAAGCGCAA
1 CTAAAGTACGAGTCTATAGCGGCGTTTGT-AATATAAATACCA
* **
3332149 CTAAAGTACGAGTGTATAGCGGCGTTTGT-ATGA-AAACGCCA
1 CTAAAGTACGAGTCTATAGCGGCGTTTGTAAT-ATAAATACCA
* * *
3332190 CTAAAGTACGAGTTTATAGTGGCGTTTGT-ATA-AAATGCCA
1 CTAAAGTACGAGTCTATAGCGGCGTTTGTAATATAAATACCA
3332230 CTAAAGTACGA
1 CTAAAGTACGA
3332241 TTCTTTAGTG
Statistics
Matches: 187, Mismatches: 23, Indels: 17
0.82 0.10 0.07
Matches are distributed among these distances:
39 1 0.01
40 51 0.27
41 67 0.36
42 3 0.02
43 65 0.35
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (42 bp):
CTAAAGTACGAGTCTATAGCGGCGTTTGTAATATAAATACCA
Found at i:3332131 original size:83 final size:83
Alignment explanation
Indices: 3331984--3332219 Score: 310
Period size: 83 Copynumber: 2.8 Consensus size: 83
3331974 GAACGCTTCT
* * *
3331984 AAAGTACGAGTCTATAGCGGCGTTTGTATATAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTT
1 AAAGTACGAGTGTATAGCGGCGTTTGTATA-AAAAGCCACTAAAGTACGAGTCTATAGCGGCGTT
* * *
3332049 TGTAAATACAAATACCACA
65 TGTAAACACAAACACAACA
* * *
3332068 AAAGTACAAGTGTATATCGGCGTTTGTATAAAAAGCCACTAAAGTACAAGTCTATAGCGGCGTTT
1 AAAGTACGAGTGTATAGCGGCGTTTGTATAAAAAGCCACTAAAGTACGAGTCTATAGCGGCGTTT
* * * *
3332133 GTAAACATAAGCGCAACT
66 GTAAACACAAACACAACA
* * *
3332151 AAAGTACGAGTGTATAGCGGCGTTTGTATGAAAACGCCACTAAAGTACGAGTTTATAGTGGCGTT
1 AAAGTACGAGTGTATAGCGGCGTTTGTAT-AAAAAGCCACTAAAGTACGAGTCTATAGCGGCGTT
3332216 TGTA
65 TGTA
3332220 TAAAATGCCA
Statistics
Matches: 132, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
83 70 0.53
84 62 0.47
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (83 bp):
AAAGTACGAGTGTATAGCGGCGTTTGTATAAAAAGCCACTAAAGTACGAGTCTATAGCGGCGTTT
GTAAACACAAACACAACA
Found at i:3332214 original size:124 final size:123
Alignment explanation
Indices: 3331982--3332278 Score: 334
Period size: 124 Copynumber: 2.4 Consensus size: 123
3331972 ATGAACGCTT
* * * *
3331982 CTAAAGTACGAGTCTATAGCGGCGTTTGTATATAAATGCCACTAAAGTACGAGTCTTTAGCGGCG
1 CTAAAGTACAAGTCTATAGCGGCGTTTGTAAACAAATGCCACTAAAGTACGAGTCTATAGCGGCG
*
3332047 TTTGTAAATACAAATACCACAAAAGTACAAGTGTATATCGGCGTTTGTATAAAAAGCCA
66 TTTGT-AATACAAACACCACAAAAGTACAAGTGTATATCGGCGTTTGTATAAAAAGCCA
*
3332106 CTAAAGTACAAGTCTATAGCGGCGTTTGTAAACATAA-GCGCAACTAAAGTACGAGTGTATAGCG
1 CTAAAGTACAAGTCTATAGCGGCGTTTGTAAACA-AATGC-C-ACTAAAGTACGAGTCTATAGCG
* * * * *
3332170 GCGTTTGT-ATGA-AAACGCCACTAAAGTACGAGTTTATAGT-GGCGTTTGTATAAAATGCCA
63 GCGTTTGTAAT-ACAAACACCACAAAAGTACAAGTGTATA-TCGGCGTTTGTATAAAAAGCCA
* * * * * * * *
3332230 CTAAAGTACGATTCTTTAG-TGCGTTTTTATACAAACGCCGCTAAAGTAC
1 CTAAAGTACAAGTCTATAGCGGCGTTTGTAAACAAATGCCACTAAAGTAC
3332279 AACTTTGTTG
Statistics
Matches: 149, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
121 9 0.06
122 3 0.02
123 13 0.09
124 91 0.61
125 5 0.03
126 28 0.19
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (123 bp):
CTAAAGTACAAGTCTATAGCGGCGTTTGTAAACAAATGCCACTAAAGTACGAGTCTATAGCGGCG
TTTGTAATACAAACACCACAAAAGTACAAGTGTATATCGGCGTTTGTATAAAAAGCCA
Found at i:3333022 original size:15 final size:15
Alignment explanation
Indices: 3332987--3333015 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3332977 TAATATCTAT
3332987 TTATAAATAAAATTA
1 TTATAAATAAAATTA
3333002 TTATAAATAAAATT
1 TTATAAATAAAATT
3333016 TATATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTATAAATAAAATTA
Found at i:3334345 original size:130 final size:131
Alignment explanation
Indices: 3334079--3334443 Score: 538
Period size: 130 Copynumber: 2.8 Consensus size: 131
3334069 ATTCTAAGAA
* *
3334079 AGAAAACGATAATATATAATTATTTCCAATC-AATAATAAGTGACCTCTCATGCCTTAAAGCAAT
1 AGAAAACGATAATATCTAATTATTTCCAATCGAA-AATAAATGACCTCTCATGCCTTAAAGCAAT
** * * *
3334143 CATTTATTACTCCGGTCGAAATGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGATTCG
65 CATTTATTACTCCAATCGAAATGAAAAGATATAACTATTTCATCTTAAAAATCAATATTGATTCG
*
3334208 AT
130 AG
* * *
3334210 AGAAAACGATAATATCTAATTATTTCCAACCGAAAATAAATGATCTCTCATGCCTTAAAGCACTC
1 AGAAAACGATAATATCTAATTATTTCCAATCGAAAATAAATGACCTCTCATGCCTTAAAGCAATC
*
3334275 A-TTATTACTCCAATCGAAATGAACAGATATAA-TCATTTCATCTTAAAAATCAATATTGATTCG
66 ATTTATTACTCCAATCGAAATGAAAAGATATAACT-ATTTCATCTTAAAAATCAATATTGATTCG
3334338 AG
130 AG
* *
3334340 AGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATC
1 AGAAAACGATAATATCTAATTATTTCCAATCGAAAATAAATGACCTCTCATGCCTTAAAGCAATC
* * *
3334405 ATTTATTACCCCAACCGAAATGAAAAGATATTACTATTT
66 ATTTATTACTCCAATCGAAATGAAAAGATATAACTATTT
3334444 TCAATATTAA
Statistics
Matches: 210, Mismatches: 20, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
129 1 0.00
130 117 0.56
131 89 0.42
132 3 0.01
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.32
Consensus pattern (131 bp):
AGAAAACGATAATATCTAATTATTTCCAATCGAAAATAAATGACCTCTCATGCCTTAAAGCAATC
ATTTATTACTCCAATCGAAATGAAAAGATATAACTATTTCATCTTAAAAATCAATATTGATTCGA
G
Found at i:3334943 original size:24 final size:23
Alignment explanation
Indices: 3334901--3334950 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
3334891 TGACTATAAT
*
3334901 AAAATAACATAAAAGCAACATGCA
1 AAAATAAAATAAAAGCAACATG-A
3334925 AAAATTAAAATAAAA-CAACATGA
1 AAAA-TAAAATAAAAGCAACATGA
3334948 AAA
1 AAA
3334951 TATGACTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 11 0.46
25 9 0.38
ACGTcount: A:0.68, C:0.12, G:0.06, T:0.14
Consensus pattern (23 bp):
AAAATAAAATAAAAGCAACATGA
Found at i:3336477 original size:3 final size:3
Alignment explanation
Indices: 3336465--3336519 Score: 85
Period size: 3 Copynumber: 18.0 Consensus size: 3
3336455 GTAAAGGCAT
3336465 ATA ATAA ATA ATA ATA ATA A-A TATA ATA ATA ATA ATA ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
3336511 ATA ATA ATA
1 ATA ATA ATA
3336520 GTGTTGGGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.02
3 44 0.90
4 4 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3338131 original size:7 final size:7
Alignment explanation
Indices: 3338119--3338219 Score: 134
Period size: 7 Copynumber: 14.4 Consensus size: 7
3338109 TATTTATTCT
3338119 TTTTTTC
1 TTTTTTC
3338126 TTTTTTC
1 TTTTTTC
3338133 TTTTTTC
1 TTTTTTC
3338140 TTTTTTC
1 TTTTTTC
3338147 TTTTTTC
1 TTTTTTC
3338154 TTTTTTC
1 TTTTTTC
3338161 TTTTTTC
1 TTTTTTC
3338168 TTTTTTC
1 TTTTTTC
3338175 TTTTTTC
1 TTTTTTC
*
3338182 TTTATT-
1 TTTTTTC
**
3338188 TTTCATC
1 TTTTTTC
3338195 ATTTTTTC
1 -TTTTTTC
3338203 TTTTCTT-
1 TTTT-TTC
*
3338210 TATTTTC
1 TTTTTTC
3338217 TTT
1 TTT
3338220 ATTTTCATTT
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
6 6 0.07
7 70 0.84
8 7 0.08
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:3338143 original size:21 final size:21
Alignment explanation
Indices: 3338119--3338237 Score: 134
Period size: 21 Copynumber: 5.6 Consensus size: 21
3338109 TATTTATTCT
3338119 TTTTTTCTTTTTTCTTTTTTC
1 TTTTTTCTTTTTTCTTTTTTC
3338140 TTTTTTCTTTTTTCTTTTTTC
1 TTTTTTCTTTTTTCTTTTTTC
3338161 TTTTTTCTTTTTTCTTTTTTC
1 TTTTTTCTTTTTTCTTTTTTC
* **
3338182 TTTATT-TTTCATCATTTTTTC
1 TTTTTTCTTTTTTC-TTTTTTC
*
3338203 TTTTCTT-TATTTTCTTTATTTTC
1 TTTT-TTCTTTTTTC-TT-TTTTC
* *
3338226 ATTTTCCTTTTT
1 TTTTTTCTTTTT
3338238 CACCATTTCC
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
20 5 0.06
21 57 0.69
22 9 0.11
23 12 0.14
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTTCTTTTTTCTTTTTTC
Found at i:3338201 original size:1 final size:1
Alignment explanation
Indices: 3338118--3338190 Score: 56
Period size: 1 Copynumber: 73.0 Consensus size: 1
3338108 TTATTTATTC
* * * * * * * * *
3338118 TTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
3338183 TTATTTTT
1 TTTTTTTT
3338191 CATCATTTTT
Statistics
Matches: 52, Mismatches: 20, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.01, C:0.12, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:3349395 original size:11 final size:12
Alignment explanation
Indices: 3349374--3349406 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3349364 AATAAATATT
3349374 ATAATAATTTAA
1 ATAATAATTTAA
3349386 ATAA-AATTTAA
1 ATAATAATTTAA
*
3349397 ATTATAATTT
1 ATAATAATTT
3349407 TTTTATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATAATAATTTAA
Found at i:3349661 original size:22 final size:22
Alignment explanation
Indices: 3349633--3349699 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 22
3349623 AATTAAAACA
3349633 TGACTAAAATATTGAAAATTAG
1 TGACTAAAATATTGAAAATTAG
*
3349655 TGACTAAATTA-T-AATAA--A-
1 TGACTAAAATATTGAA-AATTAG
3349673 TG---AAAATATTGAAAATTAG
1 TGACTAAAATATTGAAAATTAG
3349692 TGACTAAA
1 TGACTAAA
3349700 TTATAATCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 18
0.63 0.04 0.33
Matches are distributed among these distances:
15 5 0.15
16 3 0.09
17 2 0.06
18 3 0.09
19 3 0.09
20 2 0.06
21 3 0.09
22 13 0.38
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.31
Consensus pattern (22 bp):
TGACTAAAATATTGAAAATTAG
Found at i:3349716 original size:37 final size:36
Alignment explanation
Indices: 3349637--3349716 Score: 133
Period size: 37 Copynumber: 2.2 Consensus size: 36
3349627 AAAACATGAC
3349637 TAAAATATTGAAAATTAGTGACTAAATTATAATAAA
1 TAAAATATTGAAAATTAGTGACTAAATTATAATAAA
*
3349673 TGAAAATATTGAAAATTAGTGACTAAATTATAATCTAA
1 T-AAAATATTGAAAATTAGTGACTAAATTATAAT-AAA
3349711 TAAAAT
1 TAAAAT
3349717 TAAATACCTA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
36 1 0.02
37 37 0.90
38 3 0.07
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.34
Consensus pattern (36 bp):
TAAAATATTGAAAATTAGTGACTAAATTATAATAAA
Found at i:3350988 original size:3 final size:3
Alignment explanation
Indices: 3350982--3351023 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
3350972 TTATTTTTTT
*
3350982 TAA TAA TAA TAA TAA T-A TATA TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
3351024 AAAAAAATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:3351287 original size:17 final size:17
Alignment explanation
Indices: 3351265--3351323 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
3351255 TTGAACAAGC
3351265 TCTTCTCATTGTGAACT
1 TCTTCTCATTGTGAACT
*
3351282 TCTTCTTC-TTCAGATG-AGT
1 TCTTC-TCATT--G-TGAACT
*
3351301 TCTTCTCATTGCGAACT
1 TCTTCTCATTGTGAACT
3351318 TCTTCT
1 TCTTCT
3351324 GGAAATGCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
16 1 0.03
17 16 0.48
18 4 0.12
19 10 0.30
20 2 0.06
ACGTcount: A:0.15, C:0.25, G:0.12, T:0.47
Consensus pattern (17 bp):
TCTTCTCATTGTGAACT
Found at i:3351514 original size:113 final size:113
Alignment explanation
Indices: 3351367--3352036 Score: 915
Period size: 113 Copynumber: 5.9 Consensus size: 113
3351357 ATAGAGTCAT
* ** *
3351367 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
3351432 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGA
66 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCAAATGATGAATTCGA
* *
3351480 GCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCT
1 GC-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
3351544 CATTATGAACTCTTTCTGGAAAAGTTGATCCATCAAATGATGGATTTGA
65 CATTATGAACTCTCTCTGGAAAAGTTGATCCATCAAATGATGAATTCGA
* * *
3351593 GCAAAAGGTTGAACAAATTCTTCTTATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
3351658 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGA
66 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCAAATGATGAATTCGA
* *
3351706 GCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCT
1 GC-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * *
3351770 CATTATGAACTCTTTCTGGAAAAGTTAATCCATCAAATGATGGATTTGA
65 CATTATGAACTCTCTCTGGAAAAGTTGATCCATCAAATGATGAATTCGA
3351819 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
* * * * *
3351880 CTCATTAGGAACTTTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAA
63 CTCATTATGAACTCT-CTCTGGAAAAGTTGATCCATCAAATGATGAATTCGA
*
3351931 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * ** **
3351996 ATTAAGAACT-TCTACTGGTACTGTTGATCCATTGAATGATG
66 ATTATGAACTCTCT-CTGGAAAAGTTGATCCATCAAATGATG
3352037 GATTTAAATC
Statistics
Matches: 496, Mismatches: 47, Indels: 28
0.87 0.08 0.05
Matches are distributed among these distances:
109 11 0.02
110 5 0.01
111 2 0.00
112 89 0.18
113 364 0.73
114 9 0.02
115 5 0.01
116 11 0.02
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTCTCTGGAAAAGTTGATCCATCAAATGATGAATTCGA
Found at i:3351643 original size:226 final size:226
Alignment explanation
Indices: 3351367--3352041 Score: 1036
Period size: 226 Copynumber: 3.0 Consensus size: 226
3351357 ATAGAGTCAT
* ** *
3351367 GCAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
3351432 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAG
66 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAG
*
3351497 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTTTCTG
131 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCTG
3351562 GAAAAGTTGATCCATCAAATGATGGATTTGA
196 GAAAAGTTGATCCATCAAATGATGGATTTGA
*
3351593 GCAAAAGGTTGAACAAATTCTTCTTATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
3351658 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAG
66 ATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAG
*
3351723 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTCTTTCTG
131 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCTG
*
3351788 GAAAAGTTAATCCATCAAATGATGGATTTGA
196 GAAAAGTTGATCCATCAAATGATGGATTTGA
** *
3351819 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTC-TTC-AGATGACGAGTTCTTCT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCA-GATGAGTTCTTCT
* * * * * * * *
3351882 CATTAGGAACTTTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAAC-AAAAGGTTGAAC
65 CATTATGAACTCT-CTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAA-GTTGAAC
* *
3351945 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAAGAACT-TCT
128 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-T
* * ** **
3352009 ACTGGTACTGTTGATCCATTGAATGATGGATTT
192 TCTGGAAAAGTTGATCCATCAAATGATGGATTT
3352042 AAATCTTTGC
Statistics
Matches: 415, Mismatches: 30, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
224 6 0.01
225 148 0.36
226 261 0.63
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (226 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCGAAAAGTTGAACAAG
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCTG
GAAAAGTTGATCCATCAAATGATGGATTTGA
Found at i:3352892 original size:114 final size:114
Alignment explanation
Indices: 3352729--3353180 Score: 771
Period size: 114 Copynumber: 4.0 Consensus size: 114
3352719 GATCATGCAG
* * * * * * * * *
3352729 TTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATGACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
* *
3352794 AAACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 AAACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCAAA
3352843 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
3352908 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCAAA
66 AAACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCAAA
3352957 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
3353022 ACAA-TTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCAAA
66 A-AACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCAAA
3353071 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
3353136 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAG
66 AAACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAG
3353181 AACGTAGCAC
Statistics
Matches: 322, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
113 1 0.00
114 320 0.99
115 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
AAACTTCCAGAAGATGCTATTGGGTCTTCGTATTCCTACTATGAGCAAA
Found at i:3353502 original size:19 final size:17
Alignment explanation
Indices: 3353474--3353522 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
3353464 AAAATAAAAG
*
3353474 AATAAGTTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
3353493 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
3353509 AATAAATTGAATTT
1 AATAAATTGAATTT
3353523 AGAGAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 3 0.12
19 10 0.38
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:3353889 original size:7 final size:7
Alignment explanation
Indices: 3353877--3353933 Score: 53
Period size: 7 Copynumber: 7.9 Consensus size: 7
3353867 TGACCCCCCT
3353877 TTTTTTC
1 TTTTTTC
3353884 TTTTTTC
1 TTTTTTC
3353891 TTTTTT-
1 TTTTTTC
*
3353897 TTTTCTTT
1 TTTT-TTC
*
3353905 TTTTTTA
1 TTTTTTC
*
3353912 TATTTTATA
1 T-TTTT-TC
3353921 TTTTTTC
1 TTTTTTC
3353928 TTTTTT
1 TTTTTT
3353934 TTCATTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
6 4 0.09
7 25 0.57
8 12 0.27
9 3 0.07
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:3353942 original size:18 final size:17
Alignment explanation
Indices: 3353876--3353947 Score: 74
Period size: 18 Copynumber: 4.1 Consensus size: 17
3353866 TTGACCCCCC
*
3353876 TTTTTTTCTTTTTTCTTT
1 TTTTTTTCTTTTTT-TCT
3353894 TTTTTTTCTTTTTTT-T
1 TTTTTTTCTTTTTTTCT
* *
3353910 TATATTTTATATTTTTTCT
1 T-TTTTTTCT-TTTTTTCT
3353929 TTTTTTTCATTTTTTTCT
1 TTTTTTTC-TTTTTTTCT
3353947 T
1 T
3353948 CAAACATAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.04
17 7 0.15
18 34 0.74
19 3 0.07
ACGTcount: A:0.07, C:0.08, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTCTTTTTTTCT
Found at i:3364968 original size:11 final size:12
Alignment explanation
Indices: 3364947--3364979 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3364937 AATAAATATT
3364947 ATAATAATTTAA
1 ATAATAATTTAA
3364959 ATAA-AATTTAA
1 ATAATAATTTAA
*
3364970 ATTATAATTT
1 ATAATAATTT
3364980 TTTTCATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATAATAATTTAA
Found at i:3366585 original size:3 final size:3
Alignment explanation
Indices: 3366579--3366634 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
3366569 TTATTTTTTT
* *
3366579 TAA TAA TAA TAA TAA -AA TAA TTA TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3366626 TAA TAA TAA
1 TAA TAA TAA
3366635 ATAAATAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3377526 original size:131 final size:131
Alignment explanation
Indices: 3377288--3377648 Score: 503
Period size: 131 Copynumber: 2.8 Consensus size: 131
3377278 ATAATTCTAA
* *
3377288 GAGAGAAAACGATAATATCTAATTATTTTAAATCGAGAATAAATGACCTCTAATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * * * * *
3377353 GT-CATTTATTACTCCGATCGAAATAACGAGATATCACTATTTCGTTTTAAAATTCAATATTGAT
66 -TACATTTATTACTCCAATCGAAATAAAGAGATATCACCATTTCGTCTTAAAAATCAACAATGAT
3377417 TC
130 TC
* * * * *
3377419 GATAGAAAATGATAATATCTAATTATTTCCAATCAATAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
*
3377484 TACATTTATTACTCAAATCGAAATAAAGAGATATCACCATTTCGTCTTAAAAATCAACAATGATT
66 TACATTTATTACTCCAATCGAAATAAAGAGATATCACCATTTCGTCTTAAAAATCAACAATGATT
3377549 C
131 C
**
3377550 GAGAGAAAACGATAATATCTAATTATTTGTAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* *
3377615 -ATCATTTATTACCCCAACCGAAATGAAA-AGATAT
66 TA-CATTTATTACTCCAATCGAAAT-AAAGAGATAT
3377649 TACTATTTTC
Statistics
Matches: 203, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
130 2 0.01
131 198 0.98
132 3 0.01
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTCAAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
TACATTTATTACTCCAATCGAAATAAAGAGATATCACCATTTCGTCTTAAAAATCAACAATGATT
C
Found at i:3378152 original size:24 final size:24
Alignment explanation
Indices: 3378106--3378155 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3378096 TGACTAAAAT
* *
3378106 AAAATAACATAAAAGCAATATGCA
1 AAAATAAAATAAAAGCAACATGCA
3378130 AAAATTAAAATAAAA-CAACATGCA
1 AAAA-TAAAATAAAAGCAACATGCA
3378154 AA
1 AA
3378156 TAGGACTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.66, C:0.12, G:0.06, T:0.16
Consensus pattern (24 bp):
AAAATAAAATAAAAGCAACATGCA
Found at i:3380106 original size:21 final size:21
Alignment explanation
Indices: 3380073--3380250 Score: 213
Period size: 21 Copynumber: 8.6 Consensus size: 21
3380063 GTTTCCAGAT
*
3380073 TCGCAACGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
3380094 TCGTAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
3380115 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
3380136 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* * *
3380156 TCGCATTGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
3380177 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
3380198 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
3380218 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
3380239 TCGCAATGCGAA
1 TCGCAATGCGAA
3380251 TATGTAAATC
Statistics
Matches: 133, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
20 32 0.24
21 101 0.76
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:3380221 original size:41 final size:42
Alignment explanation
Indices: 3380093--3380269 Score: 206
Period size: 41 Copynumber: 4.3 Consensus size: 42
3380083 AACTTGGACT
* * *
3380093 ATCGTAATGCGAACTTGGACTATCGCAATGCGAACT-TGGACT
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAA-TATGTACA
* * * *
3380135 ATCGCAATGCGAA-TATGTA-AATCGCATTGCG-ATA-GTCGACT
1 ATCGCAATGCGAACT-TGGACTATCGCAATGCGAATATGT--ACA
3380176 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTA-A
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTACA
3380217 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTA-A
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTACA
3380258 ATCGCAATGCGA
1 ATCGCAATGCGA
3380270 TAGTCGAAGT
Statistics
Matches: 118, Mismatches: 9, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
39 2 0.02
40 1 0.01
41 83 0.70
42 27 0.23
43 3 0.03
44 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (42 bp):
ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTACA
Found at i:3380284 original size:41 final size:41
Alignment explanation
Indices: 3380198--3380323 Score: 125
Period size: 41 Copynumber: 3.1 Consensus size: 41
3380188 ACTTGGACTA
* * * *
3380198 TCGCAATGCGAATATGTAAATCGCAATGCGA-ACTTGGACT
1 TCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
3380238 ATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
1 -TCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
* * *
3380280 TCGCATTGCG-AT-T-TACATATTCGCATTGCGATAGTCCAAGT
1 TCGCAATGCGAATATGTA-A-A-TCGCAATGCGATAGTCGAAGT
3380321 TCG
1 TCG
3380324 TATTGCGATA
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 3 0.04
41 62 0.84
42 5 0.07
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (41 bp):
TCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGT
Found at i:3380284 original size:62 final size:62
Alignment explanation
Indices: 3380093--3380250 Score: 264
Period size: 62 Copynumber: 2.5 Consensus size: 62
3380083 AACTTGGACT
*
3380093 ATCGTAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
* * *
3380155 ATCGCATTGCGATA-GTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
3380217 ATCGCAATGCGAACTTGGACTATCGCAATGCGAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAA
3380251 TATGTAAATC
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
61 1 0.01
62 85 0.98
63 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (62 bp):
ATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
Found at i:3380289 original size:21 final size:21
Alignment explanation
Indices: 3380259--3380378 Score: 86
Period size: 21 Copynumber: 5.6 Consensus size: 21
3380249 AATATGTAAA
*
3380259 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
3380280 TCGCATTGCGAT-TTAC-ATA-T
1 TCGCATTGCGATAGT-CGA-AGT
*
3380300 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
3380321 TCGTATTGCGATAGATAGTCTAAGT
1 TCGCATTGC----GATAGTCGAAGT
* *
3380346 TCGCATTACGATAGTCG-ACT
1 TCGCATTGCGATAGTCGAAGT
3380366 ATCGCATTGCGAT
1 -TCGCATTGCGAT
3380379 TTATTCCAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 20
0.72 0.09 0.18
Matches are distributed among these distances:
20 19 0.24
21 42 0.53
25 18 0.23
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:3380331 original size:103 final size:103
Alignment explanation
Indices: 3380073--3380276 Score: 338
Period size: 103 Copynumber: 2.0 Consensus size: 103
3380063 GTTTCCAGAT
* * * *
3380073 TCGCAACGCGAACTTGGACTATCGTAATGCGAACT-TGGACTATCGCAATGCGAACTTGGACTAT
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAA-TATGTA-AATCGCAATGCGAACTTGGACTAT
*
3380137 CGCAATGCGAATATGTAAATCGCATTGCGATAGTCGACTA
64 CGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTA
3380177 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGAACTTGGACTATCG
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGAACTTGGACTATCG
3380242 CAATGCGAATATGTAAATCGCAATGCGATAGTCGA
66 CAATGCGAATATGTAAATCGCAATGCGATAGTCGA
3380277 AGTTCGCATT
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
103 60 0.64
104 34 0.36
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (103 bp):
TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGAACTTGGACTATCG
CAATGCGAATATGTAAATCGCAATGCGATAGTCGACTA
Found at i:3380337 original size:25 final size:25
Alignment explanation
Indices: 3380309--3380359 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3380299 TTCGCATTGC
* *
3380309 GATAGTCCAAGTTCGTATTGCGATA
1 GATAGTCCAAGTTCGCATTACGATA
*
3380334 GATAGTCTAAGTTCGCATTACGATA
1 GATAGTCCAAGTTCGCATTACGATA
3380359 G
1 G
3380360 TCGACTATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (25 bp):
GATAGTCCAAGTTCGCATTACGATA
Found at i:3380533 original size:5 final size:5
Alignment explanation
Indices: 3380525--3380556 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
3380515 CCGACCGACC
3380525 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
3380557 GAAGACGACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.22, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:3380680 original size:12 final size:11
Alignment explanation
Indices: 3380663--3380698 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
3380653 GACACGTATT
3380663 ACCACGACCACG
1 ACCACGACC-CG
3380675 ACCACGACCCG
1 ACCACGACCCG
3380686 ACC-CGACCCG
1 ACCACGACCCG
3380696 ACC
1 ACC
3380699 CGAGACGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 5 0.21
12 9 0.38
ACGTcount: A:0.28, C:0.56, G:0.17, T:0.00
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:3380689 original size:5 final size:5
Alignment explanation
Indices: 3380667--3380701 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
3380657 CGTATTACCA
3380667 CGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
3380702 GACGAGACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.26, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:3380707 original size:5 final size:5
Alignment explanation
Indices: 3380699--3380730 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
3380689 CGACCCGACC
3380699 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
3380731 GAAGACGACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.22, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:3380740 original size:15 final size:15
Alignment explanation
Indices: 3380699--3380740 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
3380689 CGACCCGACC
*
3380699 CGAGACGAGACGAGA
1 CGAGAAGAGACGAGA
*
3380714 CGAGACGAGACGAGA
1 CGAGAAGAGACGAGA
3380729 CG-GAAGACGACG
1 CGAGAAGA-GACG
3380741 GCGGCGGCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.38, C:0.21, G:0.40, T:0.00
Consensus pattern (15 bp):
CGAGAAGAGACGAGA
Found at i:3388896 original size:31 final size:30
Alignment explanation
Indices: 3388831--3388912 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
3388821 TTTAAATATA
3388831 TATTTTGATTAAAAAAATATTTTATATACC
1 TATTTTGATTAAAAAAATATTTTATATACC
* *
3388861 TATTTTG-TTCAAAATAATAATTTTA-AGTACT
1 TATTTTGATT-AAAAAAAT-ATTTTATA-TACC
*
3388892 TATTTTGA-CAAAAAAATATTT
1 TATTTTGATTAAAAAAATATTT
3388913 AAAATATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
29 6 0.14
30 22 0.50
31 16 0.36
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (30 bp):
TATTTTGATTAAAAAAATATTTTATATACC
Found at i:3406627 original size:25 final size:24
Alignment explanation
Indices: 3406599--3406652 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
3406589 AATAATCTTC
*
3406599 ATAAACTATATTTATATATGATTTT
1 ATAAAATATATTTATATATGA-TTT
*
3406624 ATAAAATATATTTATATATTATTT
1 ATAAAATATATTTATATATGATTT
3406648 ATAAA
1 ATAAA
3406653 TAATCAAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 8 0.30
25 19 0.70
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
ATAAAATATATTTATATATGATTT
Found at i:3408153 original size:15 final size:14
Alignment explanation
Indices: 3408116--3408158 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 14
3408106 ATAAAAAAGG
3408116 AAAAA-TTAAATAA
1 AAAAAGTTAAATAA
3408129 AAAAAG--AAATAA
1 AAAAAGTTAAATAA
3408141 AAAAATGTTAAATAA
1 AAAAA-GTTAAATAA
3408156 AAA
1 AAA
3408159 CTATAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.42
13 6 0.23
15 9 0.35
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (14 bp):
AAAAAGTTAAATAA
Found at i:3409450 original size:16 final size:15
Alignment explanation
Indices: 3409429--3409496 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 15
3409419 ACTTGGACCT
3409429 AAATAAAAATGAAATA
1 AAATAAAAAT-AAATA
3409445 AAATAAGAAATAAATA
1 AAATAA-AAATAAATA
3409461 AATATATAAAATATAA-A
1 AA-ATA-AAAATA-AATA
3409478 AATAGTAAATAATAAATA
1 AA-A-TAAA-AATAAATA
3409496 A
1 A
3409497 TACTCTATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
16 13 0.29
17 21 0.47
18 11 0.24
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (15 bp):
AAATAAAAATAAATA
Found at i:3409486 original size:24 final size:23
Alignment explanation
Indices: 3409441--3409493 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
3409431 ATAAAAATGA
*
3409441 AATAAAATAAGAAATAAATAAAT
1 AATAAAATAAAAAATAAATAAAT
*
3409464 ATATAAAATATAAAAAT-AGTAAAT
1 A-ATAAAATA-AAAAATAAATAAAT
3409488 AATAAA
1 AATAAA
3409494 TAATACTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 6 0.23
24 15 0.58
25 5 0.19
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (23 bp):
AATAAAATAAAAAATAAATAAAT
Found at i:3409600 original size:43 final size:45
Alignment explanation
Indices: 3409536--3409632 Score: 112
Period size: 43 Copynumber: 2.2 Consensus size: 45
3409526 TTTTCAATAT
* *
3409536 TATATATA-TTATATACGTTTTCAAAAA-CCATTTT-AA-AACTA
1 TATATATATTTATATACATTTTCAAAAATACATTTTCAAGAACTA
* *
3409577 TATATATATTATATATATATTTTCAAAAATATATTTTCAAGAACTA
1 TATATATATT-TATATACATTTTCAAAAATACATTTTCAAGAACTA
3409623 TATTATATAT
1 TA-TATATAT
3409633 GTTTTCAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
41 8 0.17
42 1 0.02
43 16 0.35
44 5 0.11
45 2 0.04
46 7 0.15
47 7 0.15
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.45
Consensus pattern (45 bp):
TATATATATTTATATACATTTTCAAAAATACATTTTCAAGAACTA
Found at i:3409610 original size:14 final size:15
Alignment explanation
Indices: 3409591--3409626 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
3409581 TATATTATAT
3409591 ATATATTTTCAA-AA
1 ATATATTTTCAAGAA
3409605 ATATATTTTCAAGAA
1 ATATATTTTCAAGAA
*
3409620 CTATATT
1 ATATATT
3409627 ATATATGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (15 bp):
ATATATTTTCAAGAA
Found at i:3409638 original size:38 final size:37
Alignment explanation
Indices: 3409588--3409887 Score: 249
Period size: 38 Copynumber: 8.3 Consensus size: 37
3409578 ATATATATTA
* *
3409588 TATATATATTTTCAAAAATATATTTTCAAGAACTATAT
1 TATATATGTTTTCAAAAATATATTTT-AAAAACTATAT
* * *
3409626 TATATATGTTTTCAAAAA-ACAATTT---AA--A-AG
1 TATATATGTTTTCAAAAATATATTTTAAAAACTATAT
* *
3409656 TCTATATGTTTTCAAAAATATGTTTTCAAAAACTATAT
1 TATATATGTTTTCAAAAATATATTTT-AAAAACTATAT
3409694 TATATATGTTTTCAAAAA-ACTATTTTAAAAACTATA-
1 TATATATGTTTTCAAAAATA-TATTTTAAAAACTATAT
* * *
3409730 TATTATATGTTTTCAAAAAAACAATTT-AAAA--A-A-
1 TA-TATATGTTTTCAAAAATATATTTTAAAAACTATAT
*
3409763 -CTATATGTTTTCAAAAATATATTTTCAAAAACTATAT
1 TATATATGTTTTCAAAAATATATTTT-AAAAACTATAT
* *
3409800 TATATAGGTTTTCAAAAA-ACCATTTTAAAAACTATA-
1 TATATATGTTTTCAAAAATA-TATTTTAAAAACTATAT
* *
3409836 TATTATATGTTTTAAAAATATATATTTTCAAAAATATATAT
1 TA-TATATGTTTTCAAAA-ATATATTTT-AAAAA-CTATAT
3409877 TATATAT-TTTT
1 TATATATGTTTT
3409888 GTTATTATAT
Statistics
Matches: 213, Mismatches: 24, Indels: 49
0.74 0.08 0.17
Matches are distributed among these distances:
30 18 0.08
31 26 0.12
33 7 0.03
34 1 0.00
35 3 0.01
36 9 0.04
37 61 0.29
38 67 0.31
39 10 0.05
40 9 0.04
41 2 0.01
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (37 bp):
TATATATGTTTTCAAAAATATATTTTAAAAACTATAT
Found at i:3409662 original size:81 final size:83
Alignment explanation
Indices: 3409540--3409694 Score: 206
Period size: 81 Copynumber: 1.9 Consensus size: 83
3409530 CAATATTATA
* * * *
3409540 TATATTATATACGTTTTCAAAAACCATTTTAAAACTATATATATATT-ATATATATATTTTCAAA
1 TATATTATATACGTTTTCAAAAAACAATTTAAAACTATATATATATTCAAAAATATATTTTCAAA
3409604 AA-TATATTTTCAAGAAC
66 AACTATATTTTCAAGAAC
* * * * * *
3409621 TATATTATATATGTTTTCAAAAAACAATTTAAAAGTCTATATGTTTTCAAAAATATGTTTTCAAA
1 TATATTATATACGTTTTCAAAAAACAATTTAAAACTATATATATATTCAAAAATATATTTTCAAA
3409686 AACTATATT
66 AACTATATT
3409695 ATATATGTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
81 40 0.65
82 16 0.26
83 6 0.10
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (83 bp):
TATATTATATACGTTTTCAAAAAACAATTTAAAACTATATATATATTCAAAAATATATTTTCAAA
AACTATATTTTCAAGAAC
Found at i:3409669 original size:68 final size:69
Alignment explanation
Indices: 3409590--3409733 Score: 229
Period size: 68 Copynumber: 2.1 Consensus size: 69
3409580 ATATATTATA
*
3409590 TATATATTTTCAAAAATATATTTTCAAGAACTATATTATATATGTTTTCAAAAAAC-AATTTAAA
1 TATATATTTTCAAAAATATATTTTCAAAAACTATATTATATATGTTTTCAAAAAACTAATTTAAA
3409654 AGTC
66 AGTC
* * *
3409658 TATATGTTTTCAAAAATATGTTTTCAAAAACTATATTATATATGTTTTCAAAAAACTATTTTAAA
1 TATATATTTTCAAAAATATATTTTCAAAAACTATATTATATATGTTTTCAAAAAACTAATTTAAA
*
3409723 A-AC
66 AGTC
3409726 TATATATT
1 TATATATT
3409734 ATATGTTTTC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
68 61 0.88
69 8 0.12
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.43
Consensus pattern (69 bp):
TATATATTTTCAAAAATATATTTTCAAAAACTATATTATATATGTTTTCAAAAAACTAATTTAAA
AGTC
Found at i:3409678 original size:14 final size:14
Alignment explanation
Indices: 3409659--3409687 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3409649 TTAAAAGTCT
3409659 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
3409673 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
3409687 A
1 A
3409688 CTATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATATGTTTTCAAAA
Found at i:3409749 original size:106 final size:106
Alignment explanation
Indices: 3409588--3409853 Score: 414
Period size: 106 Copynumber: 2.5 Consensus size: 106
3409578 ATATATATTA
* *
3409588 TATATATATTTTCAAAAATA-TATTTTCAAGAACTATAT-TATATATGTTTTC-AAAAAACAATT
1 TATATATGTTTTCAAAAA-ACTATTTT-AAAAACTATATAT-TATATGTTTTCAAAAAAACAATT
** *
3409650 TAAAAGTCTATATGTTTTCAAAAATATGTTTTCAAAAACTATAT
63 TAAAAAACTATATGTTTTCAAAAATATATTTTCAAAAACTATAT
3409694 TATATATGTTTTCAAAAAACTATTTTAAAAACTATATATTATATGTTTTCAAAAAAACAATTTAA
1 TATATATGTTTTCAAAAAACTATTTTAAAAACTATATATTATATGTTTTCAAAAAAACAATTTAA
3409759 AAAACTATATGTTTTCAAAAATATATTTTCAAAAACTATAT
66 AAAACTATATGTTTTCAAAAATATATTTTCAAAAACTATAT
* *
3409800 TATATAGGTTTTCAAAAAACCATTTTAAAAACTATATATTATATGTTTT-AAAAA
1 TATATATGTTTTCAAAAAACTATTTTAAAAACTATATATTATATGTTTTCAAAAA
3409854 TATATATTTT
Statistics
Matches: 150, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
105 27 0.18
106 123 0.82
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.41
Consensus pattern (106 bp):
TATATATGTTTTCAAAAAACTATTTTAAAAACTATATATTATATGTTTTCAAAAAAACAATTTAA
AAAACTATATGTTTTCAAAAATATATTTTCAAAAACTATAT
Found at i:3409768 original size:31 final size:31
Alignment explanation
Indices: 3409733--3409799 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
3409723 AACTATATAT
3409733 TATATGTTTTCAAAAAAACAATTTAAAAAAC
1 TATATGTTTTCAAAAAAACAATTTAAAAAAC
* * * *
3409764 TATATGTTTTCAAAAATATATTTTCAAAAAC
1 TATATGTTTTCAAAAAAACAATTTAAAAAAC
3409795 TATAT
1 TATAT
3409800 TATATAGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (31 bp):
TATATGTTTTCAAAAAAACAATTTAAAAAAC
Found at i:3409768 original size:68 final size:68
Alignment explanation
Indices: 3409696--3409836 Score: 207
Period size: 68 Copynumber: 2.1 Consensus size: 68
3409686 AACTATATTA
*
3409696 TATATGTTTTCAAAAA-ACTATTTT-AAAAACTATA-TATTATATGTTTTCAAAAAAACAATTTA
1 TATATGTTTTCAAAAATA-TATTTTCAAAAACTATATTA-TATAGGTTTTC-AAAAAACAATTTA
3409758 AAAAAC
63 AAAAAC
* *
3409764 TATATGTTTTCAAAAATATATTTTCAAAAACTATATTATATAGGTTTTCAAAAAACCATTTTAAA
1 TATATGTTTTCAAAAATATATTTTCAAAAACTATATTATATAGGTTTTCAAAAAACAATTTAAAA
3409829 AAC
66 AAC
3409832 TATAT
1 TATAT
3409837 ATTATATGTT
Statistics
Matches: 67, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
68 44 0.66
69 21 0.31
70 2 0.03
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.40
Consensus pattern (68 bp):
TATATGTTTTCAAAAATATATTTTCAAAAACTATATTATATAGGTTTTCAAAAAACAATTTAAAA
AAC
Found at i:3409787 original size:14 final size:14
Alignment explanation
Indices: 3409765--3409800 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
3409755 TTAAAAAACT
*
3409765 ATATGTTTTCAAAA
1 ATATATTTTCAAAA
3409779 ATATATTTTCAAAA
1 ATATATTTTCAAAA
3409793 ACTATATT
1 A-TATATT
3409801 ATATAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (14 bp):
ATATATTTTCAAAA
Done.