Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 180 of 198
Found at i:56244298 original size:13 final size:13
Alignment explanation
Indices: 56244277--56244308 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
56244267 GCTTGGATCA
*
56244277 TCATCAAATAAAT
1 TCATAAAATAAAT
56244290 TCATAAAATAAAT
1 TCATAAAATAAAT
56244303 TCATAA
1 TCATAA
56244309 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:56244579 original size:29 final size:30
Alignment explanation
Indices: 56244520--56244577 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
56244510 CCTCGACTCT
*
56244520 AACTTTTTCAAAATTACAATTTTGCCCCCA
1 AACTTTTACAAAATTACAATTTTGCCCCCA
* * *
56244550 AACTTTTACATAATTACATTTTTTCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
56244578 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.26, G:0.02, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCCA
Found at i:56247163 original size:18 final size:18
Alignment explanation
Indices: 56247131--56247219 Score: 101
Period size: 18 Copynumber: 4.8 Consensus size: 18
56247121 TATATATTAC
*
56247131 ATTAC-TTACTAAAATAT
1 ATTACATTACTTAAATAT
*
56247148 GTTACATTACTTAAATAT
1 ATTACATTACTTAAATAT
*
56247166 ATTAC-TTACTAAAATTTAT
1 ATTACATTACTTAAA--TAT
56247185 AATTTACATTACTTAAATAT
1 -A-TTACATTACTTAAATAT
56247205 ATTACATTACTTAAA
1 ATTACATTACTTAAA
56247220 ATTTATATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
17 12 0.20
18 29 0.48
19 4 0.07
20 4 0.07
21 4 0.07
22 8 0.13
ACGTcount: A:0.44, C:0.11, G:0.01, T:0.44
Consensus pattern (18 bp):
ATTACATTACTTAAATAT
Found at i:56247174 original size:22 final size:20
Alignment explanation
Indices: 56247122--56247217 Score: 60
Period size: 17 Copynumber: 4.8 Consensus size: 20
56247112 ATTTTTAAGT
56247122 ATATATTACATTACTTACTAA
1 ATATATTAC-TTACTTACTAA
*
56247143 A-ATA-T-GTTACATTACTTAA
1 ATATATTACTTAC-TTAC-TAA
56247162 ATATATTACTTAC-TA--AA
1 ATATATTACTTACTTACTAA
* * *
56247179 ATTTATAATTTACATTACTTAA
1 ATATATTACTTAC-TTAC-TAA
56247201 ATATATTACATTACTTA
1 ATATATTAC-TTACTTA
56247218 AAATTTATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 21
0.66 0.09 0.25
Matches are distributed among these distances:
17 16 0.29
18 4 0.07
19 7 0.12
20 8 0.14
21 2 0.04
22 15 0.27
23 4 0.07
ACGTcount: A:0.43, C:0.11, G:0.01, T:0.45
Consensus pattern (20 bp):
ATATATTACTTACTTACTAA
Found at i:56247192 original size:39 final size:41
Alignment explanation
Indices: 56247149--56247226 Score: 142
Period size: 39 Copynumber: 2.0 Consensus size: 41
56247139 CTAAAATATG
56247149 TTACATTACTTAAATATATTAC-TTAC-TAAAATTTATAAT
1 TTACATTACTTAAATATATTACATTACTTAAAATTTATAAT
56247188 TTACATTACTTAAATATATTACATTACTTAAAATTTATA
1 TTACATTACTTAAATATATTACATTACTTAAAATTTATA
56247227 TATATATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 22 0.59
40 4 0.11
41 11 0.30
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (41 bp):
TTACATTACTTAAATATATTACATTACTTAAAATTTATAAT
Found at i:56247315 original size:12 final size:12
Alignment explanation
Indices: 56247298--56247334 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
56247288 AATAAATTTT
56247298 ATAATTTTAAAA
1 ATAATTTTAAAA
56247310 ATAATTTTAAAA
1 ATAATTTTAAAA
*
56247322 ATAATTATAAAA
1 ATAATTTTAAAA
56247334 A
1 A
56247335 ATATACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAATTTTAAAA
Found at i:56247379 original size:12 final size:12
Alignment explanation
Indices: 56247362--56247390 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
56247352 ATACTTACAT
56247362 AACTTATATATA
1 AACTTATATATA
56247374 AACTTATATATA
1 AACTTATATATA
56247386 AACTT
1 AACTT
56247391 GCATAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (12 bp):
AACTTATATATA
Found at i:56247404 original size:9 final size:9
Alignment explanation
Indices: 56247386--56247748 Score: 150
Period size: 9 Copynumber: 41.8 Consensus size: 9
56247376 CTTATATATA
*
56247386 AACTTGCAT
1 AACTTACAT
56247395 AACTTACAT
1 AACTTACAT
*
56247404 AA-TAACATAAT
1 AACTTAC---AT
56247415 AACTTACAT
1 AACTTACAT
*
56247424 AA--TACAC
1 AACTTACAT
56247431 AACTTACAT
1 AACTTACAT
*
56247440 AACTTAAAT
1 AACTTACAT
56247449 AACTTACAT
1 AACTTACAT
*
56247458 -A-GTACAT
1 AACTTACAT
**
56247465 AACTTTGAT
1 AACTTACAT
*
56247474 AACTAACAT
1 AACTTACAT
* *
56247483 TA--TACAC
1 AACTTACAT
56247490 AACTTACAT
1 AACTTACAT
**
56247499 AACACACACTT
1 AACTTACA--T
*
56247510 AA-ATACAT
1 AACTTACAT
56247518 AACTTACAT
1 AACTTACAT
56247527 AACTTACAT
1 AACTTACAT
*
56247536 AA--TACAC
1 AACTTACAT
56247543 AACTTA-ATT
1 AACTTACA-T
*
56247552 AATATTATACAT
1 -A-ACT-TACAT
*
56247564 AACATACAT
1 AACTTACAT
56247573 AA--TACAT
1 AACTTACAT
*
56247580 AA--TACAC
1 AACTTACAT
56247587 AACTTA-ATT
1 AACTTACA-T
*
56247596 AATATTATACAT
1 -A-ACT-TACAT
*
56247608 AACATACAT
1 AACTTACAT
56247617 AA--TACAT
1 AACTTACAT
*
56247624 AA-TACACAT
1 AACT-TACAT
56247633 AACTTACAT
1 AACTTACAT
56247642 AA--TACAT
1 AACTTACAT
*
56247649 AACTAACAT
1 AACTTACAT
* *
56247658 AA--TAAAC
1 AACTTACAT
*
56247665 AACTTACGT
1 AACTTACAT
*
56247674 AACTTAAAT
1 AACTTACAT
56247683 AACTTACAT
1 AACTTACAT
*
56247692 AGCTTACAT
1 AACTTACAT
56247701 AA--TACAT
1 AACTTACAT
56247708 AACTTACAT
1 AACTTACAT
* *
56247717 TACTTATAT
1 AACTTACAT
56247726 AA--TACAT
1 AACTTACAT
56247733 AACTTACAT
1 AACTTACAT
*
56247742 AATTTAC
1 AACTTAC
56247749 CTAATACATA
Statistics
Matches: 264, Mismatches: 52, Indels: 76
0.67 0.13 0.19
Matches are distributed among these distances:
7 65 0.25
8 10 0.04
9 156 0.59
10 9 0.03
11 13 0.05
12 9 0.03
13 2 0.01
ACGTcount: A:0.49, C:0.19, G:0.01, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:56247455 original size:34 final size:35
Alignment explanation
Indices: 56247412--56247547 Score: 123
Period size: 34 Copynumber: 3.7 Consensus size: 35
56247402 ATAATAACAT
56247412 AATAACTTACATAATACACAAC-TTACATAACTTA
1 AATAACTTACATAATACACAACTTTACATAACTTA
* * *
56247446 AATAACTTACATAGTACATAACTTTGATAACTAACATTA
1 AATAACTTACATAATACACAACTTT-A-CA-TAAC-TTA
* *
56247485 TACACAACTTACATAACACAC-ACTTAAATACATAACTTA
1 -A-ATAACTTACATAATACACAACTT---TACATAACTTA
*
56247524 CATAACTTACATAATACACAACTT
1 AATAACTTACATAATACACAACTT
56247548 AATTAATATT
Statistics
Matches: 80, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
34 20 0.25
35 2 0.03
36 1 0.01
37 17 0.21
38 8 0.10
39 6 0.08
40 9 0.11
41 15 0.19
42 1 0.01
43 1 0.01
ACGTcount: A:0.48, C:0.21, G:0.01, T:0.29
Consensus pattern (35 bp):
AATAACTTACATAATACACAACTTTACATAACTTA
Found at i:56247463 original size:25 final size:26
Alignment explanation
Indices: 56247435--56247759 Score: 121
Period size: 25 Copynumber: 13.3 Consensus size: 26
56247425 ATACACAACT
*
56247435 TACATAACTTAAATAACTTACA-TAG
1 TACATAACTTAAATAACTTACATTAA
** *
56247460 TACATAACTTTGATAACTAACATT-A
1 TACATAACTTAAATAACTTACATTAA
* * **
56247485 TACACAACTTACATAACACACACTTAAA
1 TACATAACTTAAATAACTTACA-TT-AA
*
56247513 TACATAACTTACATAACTTACA-TAA
1 TACATAACTTAAATAACTTACATTAA
* *
56247538 TACACAACTTAATTAA--T--ATT-A
1 TACATAACTTAAATAACTTACATTAA
* *
56247559 TACATAACATACATAA--TACA-TAA
1 TACATAACTTAAATAACTTACATTAA
* *
56247582 TACACAACTTAATTAA--T--ATT-A
1 TACATAACTTAAATAACTTACATTAA
* *
56247603 TACATAACATACATAA--TACA-TAA
1 TACATAACTTAAATAACTTACATTAA
*
56247626 TACACATAACTTACATAA--TACA-TAA
1 T--ACATAACTTAAATAACTTACATTAA
* *
56247651 CTAACATAA--TAAACAACTTAC-GTAA
1 -T-ACATAACTTAAATAACTTACATTAA
* * *
56247676 CTTAAATAACTTACATAGCTTACA-TAA
1 --TACATAACTTAAATAACTTACATTAA
* * *
56247703 TACATAACTTACATTACTTATA-TAA
1 TACATAACTTAAATAACTTACATTAA
* * *
56247728 TACATAACTTACATAATTTAC-CTAA
1 TACATAACTTAAATAACTTACATTAA
56247753 TACATAA
1 TACATAA
56247760 ATATATATCA
Statistics
Matches: 234, Mismatches: 43, Indels: 46
0.72 0.13 0.14
Matches are distributed among these distances:
21 30 0.13
22 4 0.02
23 24 0.10
25 138 0.59
26 6 0.03
27 12 0.05
28 20 0.09
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.31
Consensus pattern (26 bp):
TACATAACTTAAATAACTTACATTAA
Found at i:56247536 original size:37 final size:37
Alignment explanation
Indices: 56247395--56247574 Score: 120
Period size: 37 Copynumber: 4.9 Consensus size: 37
56247385 AAACTTGCAT
* ** *
56247395 AACTTACATAATAACATA-ATAACTTACATAATACAC
1 AACTTAAATAATACTATACATAACTTACATAACACAC
* * ** *
56247431 AACTTACAT-A-ACT-TAAATAACTTACATAGTACAT
1 AACTTAAATAATACTATACATAACTTACATAACACAC
* * *
56247465 AACTTTGATAACTAACATTATACACAACTTACATAACACAC
1 AAC-TT-A-AA-TAATACTATACATAACTTACATAACACAC
*
56247506 -ACTTAAATACATAACT-TACATAACTTACATAATACAC
1 AACTTAAATA-AT-ACTATACATAACTTACATAACACAC
* * *
56247543 AACTTAATTAATATTATACATAACATACATAA
1 AACTTAAATAATACTATACATAACTTACATAA
56247575 TACATAATAC
Statistics
Matches: 114, Mismatches: 18, Indels: 23
0.74 0.12 0.15
Matches are distributed among these distances:
33 2 0.02
34 20 0.18
35 3 0.03
36 14 0.12
37 40 0.35
38 12 0.11
39 3 0.03
40 4 0.04
41 16 0.14
ACGTcount: A:0.49, C:0.19, G:0.01, T:0.30
Consensus pattern (37 bp):
AACTTAAATAATACTATACATAACTTACATAACACAC
Found at i:56247579 original size:7 final size:7
Alignment explanation
Indices: 56247567--56247661 Score: 52
Period size: 7 Copynumber: 12.4 Consensus size: 7
56247557 TATACATAAC
56247567 ATACATA
1 ATACATA
56247574 ATACATA
1 ATACATA
*
56247581 ATACACA
1 ATACATA
56247588 ACTTA-ATTA
1 A--TACA-TA
*
56247597 AT--ATT
1 ATACATA
56247602 ATACATAA
1 ATACAT-A
56247610 CATACATA
1 -ATACATA
56247618 ATACATA
1 ATACATA
56247625 ATACACATA
1 AT--ACATA
56247634 ACTTACATA
1 A--TACATA
56247643 ATACATA
1 ATACATA
56247650 ACTAACATA
1 A-T-ACATA
56247659 ATA
1 ATA
56247662 AACAACTTAC
Statistics
Matches: 71, Mismatches: 4, Indels: 26
0.70 0.04 0.26
Matches are distributed among these distances:
5 3 0.04
6 1 0.01
7 34 0.48
8 4 0.06
9 28 0.39
11 1 0.01
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (7 bp):
ATACATA
Found at i:56247590 original size:44 final size:44
Alignment explanation
Indices: 56247512--56247631 Score: 213
Period size: 44 Copynumber: 2.7 Consensus size: 44
56247502 ACACACTTAA
*
56247512 ATACATAACTTACATAACTTACATAATACACAACTTAATTAATATT
1 ATACATAACATACATAA--TACATAATACACAACTTAATTAATATT
56247558 ATACATAACATACATAATACATAATACACAACTTAATTAATATT
1 ATACATAACATACATAATACATAATACACAACTTAATTAATATT
56247602 ATACATAACATACATAATACATAATACACA
1 ATACATAACATACATAATACATAATACACA
56247632 TAACTTACAT
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
44 57 0.78
46 16 0.22
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (44 bp):
ATACATAACATACATAATACATAATACACAACTTAATTAATATT
Found at i:56247731 original size:16 final size:16
Alignment explanation
Indices: 56247392--56247744 Score: 115
Period size: 16 Copynumber: 21.9 Consensus size: 16
56247382 TATAAACTTG
56247392 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
56247409 CATAATAACTTACATAATA
1 C---ATAACTTACATAATA
*
56247428 CACAACTTACATAACTTA
1 CATAACTTACATAA--TA
* *
56247446 AATAACTTACATAGTA
1 CATAACTTACATAATA
56247462 CATAAC-T---T--T-
1 CATAACTTACATAATA
* * *
56247471 GATAACTAACATTATA
1 CATAACTTACATAATA
* *
56247487 CACAACTTACATAACACA
1 CATAACTTACAT-A-ATA
*
56247505 CACTTAA-ATACATAACTTA
1 CA--TAACTTACATAA--TA
56247524 CATAACTTACATAATA
1 CATAACTTACATAATA
*
56247540 CACAACTTA-AT--TA
1 CATAACTTACATAATA
*
56247553 -AT-ATTATACATAACATA
1 CATAACT-TACAT-A-ATA
56247570 CATAA--TACATAATA
1 CATAACTTACATAATA
*
56247584 CACAACTTA-AT--TA
1 CATAACTTACATAATA
*
56247597 -AT-ATTATACATAACATA
1 CATAACT-TACAT-A-ATA
56247614 CATAA--TACATAATACA
1 CATAACTTACATAAT--A
56247630 CATAACTTACATAATA
1 CATAACTTACATAATA
*
56247646 CATAACTAACATAATA
1 CATAACTTACATAATA
* * *
56247662 AACAACTTACGTAACTTA
1 CATAACTTACATAA--TA
* *
56247680 AATAACTTACATAGCTTA
1 CATAACTTACATA--ATA
56247698 CATAA--TACATAACTTA
1 CATAACTTACATAA--TA
* *
56247714 CATTACTTATATAATA
1 CATAACTTACATAATA
56247730 CATAACTTACATAAT
1 CATAACTTACATAAT
56247745 TTACCTAATA
Statistics
Matches: 251, Mismatches: 36, Indels: 99
0.65 0.09 0.26
Matches are distributed among these distances:
9 5 0.02
10 1 0.00
11 4 0.02
12 7 0.03
13 9 0.04
14 9 0.04
15 8 0.03
16 109 0.43
17 9 0.04
18 62 0.25
19 12 0.05
20 16 0.06
ACGTcount: A:0.49, C:0.19, G:0.01, T:0.31
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:56249589 original size:21 final size:21
Alignment explanation
Indices: 56249563--56249612 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
56249553 CTACAACTTA
*
56249563 AAGCAGAGGTGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGGG
*
56249584 AAGCAGAGGCGGTAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGGG
56249605 AAGCAGAG
1 AAGCAGAG
56249613 CAGAGTAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.50, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGGG
Found at i:56250026 original size:43 final size:43
Alignment explanation
Indices: 56249979--56250189 Score: 280
Period size: 43 Copynumber: 4.9 Consensus size: 43
56249969 GTTTGTGAGG
56249979 GAAGCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTTATA
1 GAAGCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTTATA
* * * * *
56250022 GAAGCACCACTAAAGAACATGACCTTTAGTGACGTTTGTTATA
1 GAAGCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTTATA
56250065 GAAGCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTTATA
1 GAAGCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTTATA
* * * * * * *
56250108 AAAGTGCTGCTACAGAACATGACCTTTAGCGGCGTTTGTGACA
1 GAAGCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTTATA
**
56250151 GCGGCGCCGCTAAAGAACATGACCA-TTAGCGGCGTTTGT
1 GAAGCGCCGCTAAAGAACATGA-CATTTAGCGGCGTTTGT
56250190 GGGAAAAATG
Statistics
Matches: 143, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
43 142 0.99
44 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (43 bp):
GAAGCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTTATA
Found at i:56250214 original size:43 final size:43
Alignment explanation
Indices: 56249984--56250214 Score: 196
Period size: 43 Copynumber: 5.4 Consensus size: 43
56249974 TGAGGGAAGC
* * * *
56249984 GCCGCTAAAGAACATGA-CATTTAGCGGCGTTTGTTATAGAAGC
1 GCCGCTAAAGAACATGACCA-TTAGCGGCGTTTGTGACAAAAGT
* * * * * * * * *
56250027 ACCACTAAAGAACATGACCTTTAGTGACGTTTGTTATAGAAGC
1 GCCGCTAAAGAACATGACCATTAGCGGCGTTTGTGACAAAAGT
* *
56250070 GCCGCTAAAGAACATGA-CATTTAGCGGCGTTTGTTATAAAAGT
1 GCCGCTAAAGAACATGACCA-TTAGCGGCGTTTGTGACAAAAGT
* * * *** *
56250113 GCTGCTACAGAACATGACCTTTAGCGGCGTTTGTGACAGCGGC
1 GCCGCTAAAGAACATGACCATTAGCGGCGTTTGTGACAAAAGT
** *
56250156 GCCGCTAAAGAACATGACCATTAGCGGCGTTTGTGGGAAAAAT
1 GCCGCTAAAGAACATGACCATTAGCGGCGTTTGTGACAAAAGT
*
56250199 GCCGCTAAAGTACATG
1 GCCGCTAAAGAACATG
56250215 GTCTTTAGCA
Statistics
Matches: 153, Mismatches: 32, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
42 1 0.01
43 150 0.98
44 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (43 bp):
GCCGCTAAAGAACATGACCATTAGCGGCGTTTGTGACAAAAGT
Found at i:56250214 original size:86 final size:86
Alignment explanation
Indices: 56249962--56250230 Score: 315
Period size: 86 Copynumber: 3.1 Consensus size: 86
56249952 CATCAAACAA
* ** * *
56249962 TAGCGGTGTTTGTGAGGGAAGCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTTATAGAAGC
1 TAGCGGCGTTTGTGACAGAAGCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTTATAAAAGT
* *
56250027 ACCACTAAAGAACATGACCTT
66 GCCGCTAAAGAACATGACCTT
* * * *
56250048 TAGTGACGTTTGTTATAGAAGCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTTATAAAAGT
1 TAGCGGCGTTTGTGACAGAAGCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTTATAAAAGT
* *
56250113 GCTGCTACAGAACATGACCTT
66 GCCGCTAAAGAACATGACCTT
** *** *
56250134 TAGCGGCGTTTGTGACAGCGGCGCCGCTAAAGAACATGACCA-TTAGCGGCGTTTGTGGGAAAAA
1 TAGCGGCGTTTGTGACAGAAGCGCCGCTAAAGAACATGA-CATTTAGCGGCGTTTGTTATAAAAG
* **
56250198 TGCCGCTAAAGTACATGGTCTT
65 TGCCGCTAAAGAACATGACCTT
*
56250220 TAGCAGCGTTT
1 TAGCGGCGTTT
56250231 ATAAAAATAA
Statistics
Matches: 154, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
86 152 0.99
87 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (86 bp):
TAGCGGCGTTTGTGACAGAAGCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTTATAAAAGT
GCCGCTAAAGAACATGACCTT
Found at i:56250222 original size:129 final size:129
Alignment explanation
Indices: 56249987--56250230 Score: 292
Period size: 129 Copynumber: 1.9 Consensus size: 129
56249977 GGGAAGCGCC
* * * *
56249987 GCTAAAGAACATGACATTTAGCGGCGTTTGTTATAGAAGCACCACTAAAGAACATGACCTTTAGT
1 GCTAAAGAACATGACATTTAGCGGCGTTTGTGACAGAAGCACCACTAAAGAACATGACCATTAGC
* * * * *
56250052 GACGTTTGTTATAGAAGCGCCGCTAAAGAACATGACATTTAGCGGCGTTTGTTATAAAAGTGCT
66 GACGTTTGTGAGAAAAACGCCGCTAAAGAACATGACATTTAGCAGCGTTTGTTATAAAAGTGCT
* * ** * *
56250116 GCTACAGAACATGACCTTTAGCGGCGTTTGTGACAGCGGCGCCGCTAAAGAACATGACCATTAGC
1 GCTAAAGAACATGACATTTAGCGGCGTTTGTGACAGAAGCACCACTAAAGAACATGACCATTAGC
* * * * *
56250181 GGCGTTTGTGGGAAAAATGCCGCTAAAGTACATGGTC-TTTAGCAGCGTTT
66 GACGTTTGTGAGAAAAACGCCGCTAAAGAACAT-GACATTTAGCAGCGTTT
56250231 ATAAAAATAA
Statistics
Matches: 94, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
129 92 0.98
130 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (129 bp):
GCTAAAGAACATGACATTTAGCGGCGTTTGTGACAGAAGCACCACTAAAGAACATGACCATTAGC
GACGTTTGTGAGAAAAACGCCGCTAAAGAACATGACATTTAGCAGCGTTTGTTATAAAAGTGCT
Found at i:56262081 original size:16 final size:16
Alignment explanation
Indices: 56262054--56262097 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
56262044 CTATTCCTTA
56262054 TCTTCCTTCAAAGCGG
1 TCTTCCTTCAAAGCGG
* *
56262070 TTTTCGTTCAAAGCGG
1 TCTTCCTTCAAAGCGG
56262086 TCTTCCTTCAAA
1 TCTTCCTTCAAA
56262098 ATGATTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.36
Consensus pattern (16 bp):
TCTTCCTTCAAAGCGG
Found at i:56271664 original size:12 final size:12
Alignment explanation
Indices: 56271649--56271714 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 12
56271639 TCATCGTCGT
*
56271649 CTTCTTCTTCAA
1 CTTCCTCTTCAA
*
56271661 CTTCCTCTTCTA
1 CTTCCTCTTCAA
** **
56271673 CTTCAACTTCTT
1 CTTCCTCTTCAA
* *
56271685 CTTCCACTTCTA
1 CTTCCTCTTCAA
*
56271697 CTTCCTCTTCCA
1 CTTCCTCTTCAA
56271709 CTTCCT
1 CTTCCT
56271715 GTAGTTGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 45 1.00
ACGTcount: A:0.12, C:0.41, G:0.00, T:0.47
Consensus pattern (12 bp):
CTTCCTCTTCAA
Found at i:56271671 original size:18 final size:18
Alignment explanation
Indices: 56271648--56271712 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
56271638 GTCATCGTCG
*
56271648 TCTTCTTCTTCAACTTCC
1 TCTTCTACTTCAACTTCC
*
56271666 TCTTCTACTTCAACTTCT
1 TCTTCTACTTCAACTTCC
* *
56271684 TCTTCCACTTCTACTTCC
1 TCTTCTACTTCAACTTCC
*
56271702 TCTTCCACTTC
1 TCTTCTACTTC
56271713 CTGTAGTTGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.12, C:0.40, G:0.00, T:0.48
Consensus pattern (18 bp):
TCTTCTACTTCAACTTCC
Found at i:56272428 original size:20 final size:21
Alignment explanation
Indices: 56272403--56272456 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
56272393 TGAACTTATA
56272403 AAAATTATTATAAA-AC-ATTT
1 AAAATT-TTATAAACACTATTT
*
56272423 AAAATTTTATAAACACTCTTT
1 AAAATTTTATAAACACTATTT
*
56272444 AAAATTCTATAAA
1 AAAATTTTATAAA
56272457 AATAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 7 0.23
20 8 0.27
21 15 0.50
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAATTTTATAAACACTATTT
Found at i:56272973 original size:9 final size:9
Alignment explanation
Indices: 56272961--56273130 Score: 67
Period size: 9 Copynumber: 18.0 Consensus size: 9
56272951 TTTTAAATAT
56272961 TTTTTATAA
1 TTTTTATAA
*
56272970 TTTTCTACAA
1 TTTT-TATAA
*
56272980 TTTTTATGAT
1 TTTTTAT-AA
*
56272990 TTTTTAAGAA
1 TTTTT-ATAA
* * *
56273000 TTCTAATTCA
1 TTTTTA-TAA
56273010 TTTTT-TAA
1 TTTTTATAA
* *
56273018 TTTTAATTA
1 TTTTTATAA
**
56273027 TTTAAAATAA
1 TTT-TTATAA
*
56273037 GTTTTATTAA
1 TTTTTA-TAA
56273047 -TTTTATGATA
1 TTTTTAT-A-A
56273057 TTTTTATAA
1 TTTTTATAA
*
56273066 TTTATTAGAA
1 TTT-TTATAA
*
56273076 TTATTAT-A
1 TTTTTATAA
56273084 TTTTTATAA
1 TTTTTATAA
*
56273093 TATTTATAA
1 TTTTTATAA
**
56273102 GCTTTATAA
1 TTTTTATAA
56273111 TTTTTTTATAA
1 --TTTTTATAA
*
56273122 TTTTAATAA
1 TTTTTATAA
56273131 GTTTATATCA
Statistics
Matches: 118, Mismatches: 29, Indels: 28
0.67 0.17 0.16
Matches are distributed among these distances:
8 14 0.12
9 50 0.42
10 40 0.34
11 14 0.12
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.59
Consensus pattern (9 bp):
TTTTTATAA
Found at i:56273065 original size:29 final size:27
Alignment explanation
Indices: 56273033--56273137 Score: 88
Period size: 29 Copynumber: 3.7 Consensus size: 27
56273023 ATTATTTAAA
*
56273033 ATAAGTTTTATTAATTTTATGATATTTTT
1 ATAA-TTTTATTAA-TTTATAATATTTTT
* *
56273062 ATAA-TTTATTAGAATTATTATATTTTT
1 ATAATTTTATTA-ATTTATAATATTTTT
*
56273089 ATAATATTTA-TAAGCTTTATAATTTTTTT
1 ATAAT-TTTATTAA--TTTATAATATTTTT
*
56273118 ATAATTTTAATAAGTTTATA
1 ATAATTTTATTAA-TTTATA
56273138 TCAAATTTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
27 24 0.38
28 13 0.20
29 27 0.42
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (27 bp):
ATAATTTTATTAATTTATAATATTTTT
Found at i:56283529 original size:41 final size:41
Alignment explanation
Indices: 56283484--56283562 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
56283474 CAGGGCTGGT
* * *
56283484 TGTTGTTAACTGAAAACTTTCACCTATAGTTCAGTCAGAGC
1 TGTTGTCAACTGAAAACTATCACCTAGAGTTCAGTCAGAGC
*
56283525 TGTTGTCAACTGACAACTATCACCTAGAGTTCAGTCAG
1 TGTTGTCAACTGAAAACTATCACCTAGAGTTCAGTCAG
56283563 TCGGCTGAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (41 bp):
TGTTGTCAACTGAAAACTATCACCTAGAGTTCAGTCAGAGC
Found at i:56284152 original size:21 final size:20
Alignment explanation
Indices: 56284127--56284175 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
56284117 TCTCTCTCAA
56284127 CAAAAATTACAAAAAAAAATT
1 CAAAAATT-CAAAAAAAAATT
* *
56284148 CAAAATATTTATAAAAAAATT
1 CAAAA-ATTCAAAAAAAAATT
*
56284169 AAAAAAT
1 CAAAAAT
56284176 ATATTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 19 0.79
22 3 0.12
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.24
Consensus pattern (20 bp):
CAAAAATTCAAAAAAAAATT
Found at i:56284185 original size:23 final size:23
Alignment explanation
Indices: 56284139--56284202 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
56284129 AAAATTACAA
*
56284139 AAAAAAATT-CAAAATAT-TTAT
1 AAAAAAATTAAAAAATATATTAT
*
56284160 AAAAAAATTAAAAAATATATTTT
1 AAAAAAATTAAAAAATATATTAT
56284183 AAAAAAATTAAAAAATATAT
1 AAAAAAATTAAAAAATATAT
56284203 AAAGAAAGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.23
22 7 0.18
23 23 0.59
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAAAATTAAAAAATATATTAT
Found at i:56289064 original size:20 final size:20
Alignment explanation
Indices: 56289041--56289078 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56289031 GATAAAATCA
*
56289041 AGTTAAAATAGTTTCAATTG
1 AGTTAAAACAGTTTCAATTG
*
56289061 AGTTAAAACATTTTCAAT
1 AGTTAAAACAGTTTCAAT
56289079 CATGTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (20 bp):
AGTTAAAACAGTTTCAATTG
Found at i:56291791 original size:49 final size:49
Alignment explanation
Indices: 56291700--56291839 Score: 167
Period size: 49 Copynumber: 2.9 Consensus size: 49
56291690 ATGAAACATT
**
56291700 AACCCGTGACCACATAACCACTACCAACTAGGGGCCTGAGTTATAGTTG
1 AACCCGTGACCACATAACCACTGTCAACTAGGGGCCTGAGTTATAGTTG
*
56291749 AACCCGTGACCACATAACCACTGTCAA-TCGGGGCC-GCTAGTTATAGTTG
1 AACCCGTGACCACATAACCACTGTCAACTAGGGGCCTG--AGTTATAGTTG
** * * * *
56291798 AACCTATGACCGCATAACCACCGTCAACTAAGAGCCTGAGTT
1 AACCCGTGACCACATAACCACTGTCAACTAGGGGCCTGAGTT
56291840 GCAATTCCAT
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
47 1 0.01
48 7 0.09
49 63 0.82
50 5 0.06
51 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (49 bp):
AACCCGTGACCACATAACCACTGTCAACTAGGGGCCTGAGTTATAGTTG
Found at i:56295824 original size:32 final size:30
Alignment explanation
Indices: 56295783--56295850 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
56295773 AGAGTTTTAC
*
56295783 GTATATAATTGCACCA-AATATTCAAAGTTCAT
1 GTATATAATTACA-CATAA-ATT-AAAGTTCAT
56295815 GTATATAATTACACATTAAATTAAAGTTCAT
1 GTATATAATTACACA-TAAATTAAAGTTCAT
56295846 GTATA
1 GTATA
56295851 ATTTTGAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
31 16 0.48
32 15 0.45
33 2 0.06
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.37
Consensus pattern (30 bp):
GTATATAATTACACATAAATTAAAGTTCAT
Found at i:56296976 original size:49 final size:49
Alignment explanation
Indices: 56296897--56297000 Score: 138
Period size: 49 Copynumber: 2.1 Consensus size: 49
56296887 GCATGAAACA
* * *
56296897 TGAACCCGTGACCACATAACCATTGCCAATTGGGGT-CCCGAGTTATAGT
1 TGAACCCGTGAACACATAACCACTACCAATT-GGGTCCCCGAGTTATAGT
* * *
56296946 TGAACCCGTGAACGCATAACCACTATCAATTGGGTCCCCTAGTTATAGT
1 TGAACCCGTGAACACATAACCACTACCAATTGGGTCCCCGAGTTATAGT
56296995 TGAACC
1 TGAACC
56297001 TATGGCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
48 4 0.08
49 44 0.92
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (49 bp):
TGAACCCGTGAACACATAACCACTACCAATTGGGTCCCCGAGTTATAGT
Found at i:56297029 original size:49 final size:48
Alignment explanation
Indices: 56296929--56297038 Score: 123
Period size: 49 Copynumber: 2.2 Consensus size: 48
56296919 TTGCCAATTG
* * *
56296929 GGGTCCCGAGTTATAGTTGAACCCGTGAACGCATAACCACTATCAATT
1 GGGTCCCGAGTTATAGTTGAACCCATGAACGCATAACCACCATCAACT
* * * *
56296977 GGGTCCCCTAGTTATAGTTGAACCTATG-GCTGCATAACCACCGTCAACT
1 GGGT-CCCGAGTTATAGTTGAACCCATGAAC-GCATAACCACCATCAACT
56297026 GGGTGCCCGAGTT
1 GGGT-CCCGAGTT
56297039 GCAATTCCAC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
48 5 0.10
49 46 0.90
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (48 bp):
GGGTCCCGAGTTATAGTTGAACCCATGAACGCATAACCACCATCAACT
Found at i:56300914 original size:29 final size:30
Alignment explanation
Indices: 56300872--56300930 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
56300862 TATGATTTAA
* *
56300872 TGTGTAATTGTATACATGAAA-TTTGATTT
1 TGTGCAATTGTATACATAAAATTTTGATTT
*
56300901 TGTGCAATTTTATACATAAAATTTTGATTT
1 TGTGCAATTGTATACATAAAATTTTGATTT
56300931 GATCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATAAAATTTTGATTT
Found at i:56300939 original size:30 final size:29
Alignment explanation
Indices: 56300877--56300939 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
56300867 TTTAATGTGT
* *
56300877 AATTGTATACATGAAATTTGATTTTGTGC
1 AATTGTATACATAAAATTTGATTTTGTCC
*
56300906 AATTTTATACATAAAATTTTGA-TTTGATCC
1 AATTGTATACATAAAA-TTTGATTTTG-TCC
56300936 AATT
1 AATT
56300940 CTTGTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (29 bp):
AATTGTATACATAAAATTTGATTTTGTCC
Found at i:56313084 original size:23 final size:23
Alignment explanation
Indices: 56313049--56313092 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
56313039 TCTTCTTAAA
*
56313049 AAAAATTATATATATCAAATAAG
1 AAAAATTACATATATCAAATAAG
* *
56313072 AAAATTTACATATATTAAATA
1 AAAAATTACATATATCAAATA
56313093 TTTGAAATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (23 bp):
AAAAATTACATATATCAAATAAG
Found at i:56316322 original size:21 final size:20
Alignment explanation
Indices: 56316297--56316339 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
56316287 CCAATTTACG
56316297 TTAAAAATTAAATTATAGAAA
1 TTAAAAATTAAATT-TAGAAA
**
56316318 TTAAATCTTAAATTTAGAAA
1 TTAAAAATTAAATTTAGAAA
56316338 TT
1 TT
56316340 TTAAAGGGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (20 bp):
TTAAAAATTAAATTTAGAAA
Found at i:56320601 original size:13 final size:14
Alignment explanation
Indices: 56320580--56320608 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
56320570 GGTAAATCGG
56320580 ATTAGTAAATATTT
1 ATTAGTAAATATTT
56320594 ATTA-TAAATATTT
1 ATTAGTAAATATTT
56320607 AT
1 AT
56320609 GAAGTTAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (14 bp):
ATTAGTAAATATTT
Found at i:56327066 original size:29 final size:30
Alignment explanation
Indices: 56327010--56327089 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 30
56327000 ATACCAAAAT
* * *
56327010 TATACATGACATATGATTTAATTTGCAATTG
1 TATACATGAAATTTGATTT-ATGTGCAATTG
*
56327041 TATACATGAAATTTGATTT-TGTGCAATTT
1 TATACATGAAATTTGATTTATGTGCAATTG
56327070 TATACATGAAATTTTGATTT
1 TATACATGAAA-TTTGATTT
56327090 GATCCAATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 19 0.43
30 8 0.18
31 17 0.39
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.46
Consensus pattern (30 bp):
TATACATGAAATTTGATTTATGTGCAATTG
Found at i:56327098 original size:30 final size:29
Alignment explanation
Indices: 56327035--56327098 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
56327025 ATTTAATTTG
*
56327035 CAATTGTATACATGAAATTTGATTTTGTG
1 CAATTGTATACATGAAATTTGATTTTGTC
*
56327064 CAATTTTATACATGAAATTTTGA-TTTGATC
1 CAATTGTATACATGAAA-TTTGATTTTG-TC
56327094 CAATT
1 CAATT
56327099 CTTGTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (29 bp):
CAATTGTATACATGAAATTTGATTTTGTC
Found at i:56327314 original size:29 final size:30
Alignment explanation
Indices: 56327277--56327343 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
56327267 TTAGAGTTTT
* *
56327277 ATGTGTATAATTG-CATCAAATTAAAGTTC
1 ATGTATATAATTGACATCAAATCAAAGTTC
*
56327306 ATGTATATAATTGCACATTAAATCAAAGTTC
1 ATGTATATAATTG-ACATCAAATCAAAGTTC
56327337 ATGTATA
1 ATGTATA
56327344 ATTTTGAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 12 0.36
31 21 0.64
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (30 bp):
ATGTATATAATTGACATCAAATCAAAGTTC
Found at i:56328268 original size:24 final size:24
Alignment explanation
Indices: 56328236--56328283 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
56328226 AGAAGAGAAT
56328236 GGAAAAT-AAAGAAAAAAAGTTAAA
1 GGAAAATAAAAGAAAAAAA-TTAAA
*
56328260 GGAATATAAAAGAAAAAAATTAAA
1 GGAAAATAAAAGAAAAAAATTAAA
56328284 TTGCTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (24 bp):
GGAAAATAAAAGAAAAAAATTAAA
Found at i:56335491 original size:2 final size:2
Alignment explanation
Indices: 56335486--56335518 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
56335476 AAAAAAAAAA
56335486 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56335519 AAGTATTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56336976 original size:29 final size:29
Alignment explanation
Indices: 56336927--56336982 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
56336917 ATTATTAAAT
**
56336927 TTAATTTAATACTTATTTGATAATATTTA
1 TTAATTTAATACTTAAGTGATAATATTTA
*
56336956 TTAATTTAATA-TTAAAGTGATTATATT
1 TTAATTTAATACTT-AAGTGATAATATT
56336983 AATATTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (29 bp):
TTAATTTAATACTTAAGTGATAATATTTA
Found at i:56337057 original size:12 final size:12
Alignment explanation
Indices: 56337040--56337085 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
56337030 AATTTAATAG
56337040 ATTTAATATTAA
1 ATTTAATATTAA
56337052 ATTTAATATAATAA
1 ATTTAATAT--TAA
56337066 ATATT-ATATT-A
1 AT-TTAATATTAA
56337077 ATTTAATAT
1 ATTTAATAT
56337086 CTTTTCGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
10 2 0.07
11 7 0.23
12 10 0.33
14 9 0.30
15 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:56337058 original size:26 final size:25
Alignment explanation
Indices: 56337028--56337085 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
56337018 AAATAATCTA
* *
56337028 TTAATTTAATAGAT-TTAATATTAAAT
1 TTAATATAATAAATATT-ATATT-AAT
56337054 TTAATATAATAAATATTATATTAAT
1 TTAATATAATAAATATTATATTAAT
56337079 TTAATAT
1 TTAATAT
56337086 CTTTTCGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 10 0.34
26 17 0.59
27 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TTAATATAATAAATATTATATTAAT
Found at i:56337083 original size:20 final size:21
Alignment explanation
Indices: 56337026--56337084 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
56337016 ATAAATAATC
* * *
56337026 TATT-AATTTAATAGATTTAA
1 TATTAAATTTAATATAATAAA
56337046 TATTAAATTTAATATAATAAA
1 TATTAAATTTAATATAATAAA
* *
56337067 TATTATA-TTAATTTAATA
1 TATTAAATTTAATATAATA
56337085 TCTTTTCGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TATTAAATTTAATATAATAAA
Found at i:56338597 original size:39 final size:39
Alignment explanation
Indices: 56338554--56338715 Score: 288
Period size: 39 Copynumber: 4.2 Consensus size: 39
56338544 CGACGCCGGA
*
56338554 GCGGGCGACTGTGTACCGGGTGAAGGGGCTGGGGGTGGC
1 GCGGGCGACTGTGTACCGGGTGAAGGGGCTGGGGCTGGC
* *
56338593 GCGGGCGACTGTGTACCAGGTGAAGGGGCTGGGGGTGGC
1 GCGGGCGACTGTGTACCGGGTGAAGGGGCTGGGGCTGGC
*
56338632 GCGGGCGACTGTGTTCCGGGTGAAGGGGCTGGGGCTGGC
1 GCGGGCGACTGTGTACCGGGTGAAGGGGCTGGGGCTGGC
56338671 GCGGGCGACTGTGTACCGGGTGAAGGGGCTGGGGCTGGC
1 GCGGGCGACTGTGTACCGGGTGAAGGGGCTGGGGCTGGC
56338710 GCGGGC
1 GCGGGC
56338716 TGGGGCAAAA
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 118 1.00
ACGTcount: A:0.10, C:0.20, G:0.55, T:0.15
Consensus pattern (39 bp):
GCGGGCGACTGTGTACCGGGTGAAGGGGCTGGGGCTGGC
Found at i:56342116 original size:20 final size:21
Alignment explanation
Indices: 56342076--56342117 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
56342066 AGCAAAAGAG
*
56342076 AAGAAAAAAAAATAAAGTTAA
1 AAGAAAAAAAAAGAAAGTTAA
*
56342097 AAGAACAAAAAAGAAA-TTAA
1 AAGAAAAAAAAAGAAAGTTAA
56342117 A
1 A
56342118 TTGCCCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (21 bp):
AAGAAAAAAAAAGAAAGTTAA
Found at i:56343019 original size:29 final size:30
Alignment explanation
Indices: 56342966--56343024 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
56342956 GAATTAGATT
* * *
56342966 AAATCAAAATTTTATGTATAAAATTGCACA
1 AAATCAAAATTTCATGTACAAAATTACACA
*
56342996 AAATC-AAATTTCATGTACACAATTACACA
1 AAATCAAAATTTCATGTACAAAATTACACA
56343025 TTAAATCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATGTACAAAATTACACA
Found at i:56344964 original size:23 final size:23
Alignment explanation
Indices: 56344938--56344981 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
56344928 GCATTTCAAA
*
56344938 TATTTAATATATGTAAATTTTCT
1 TATTTAATATATATAAATTTTCT
* *
56344961 TATTTGATATATATAATTTTT
1 TATTTAATATATATAAATTTT
56344982 TTTAAGAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (23 bp):
TATTTAATATATATAAATTTTCT
Found at i:56347151 original size:29 final size:30
Alignment explanation
Indices: 56347098--56347156 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
56347088 TAATTATGTC
* *
56347098 AAATCAAAATTTCAAGTGTAAAATTGCACA
1 AAATCAAAATTTCAAGTATAAAATTACACA
* *
56347128 AAATC-AAATTTCATGTATACAATTACACA
1 AAATCAAAATTTCAAGTATAAAATTACACA
56347157 TTAAATCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (30 bp):
AAATCAAAATTTCAAGTATAAAATTACACA
Found at i:56349255 original size:51 final size:51
Alignment explanation
Indices: 56349179--56349282 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
56349169 TTTTAAGAAG
56349179 AAAGAATAAGAGACGACGAGAAGCTGAAAGCCTTTAAATTCCATTTCAACT
1 AAAGAATAAGAGACGACGAGAAGCTGAAAGCCTTTAAATTCCATTTCAACT
56349230 AAAGAATAAGAGACGACGAGAAGCTGAAAGCCTTTAAATTCCATTTCAACT
1 AAAGAATAAGAGACGACGAGAAGCTGAAAGCCTTTAAATTCCATTTCAACT
56349281 AA
1 AA
56349283 CTTTTTATAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.21
Consensus pattern (51 bp):
AAAGAATAAGAGACGACGAGAAGCTGAAAGCCTTTAAATTCCATTTCAACT
Found at i:56352799 original size:11 final size:11
Alignment explanation
Indices: 56352785--56352914 Score: 98
Period size: 11 Copynumber: 12.4 Consensus size: 11
56352775 AATTTTTTAA
56352785 TTTTAAAATAT
1 TTTTAAAATAT
56352796 TTTTAAAATACT
1 TTTTAAAATA-T
** *
56352808 TTTTTTATTAT
1 TTTTAAAATAT
* *
56352819 TTTT---TTAA
1 TTTTAAAATAT
56352827 TTTTAAAATAT
1 TTTTAAAATAT
56352838 TTTTAAAATACT
1 TTTTAAAATA-T
56352850 TTTT-AAAT-T
1 TTTTAAAATAT
*
56352859 TTTT-TAA-A-
1 TTTTAAAATAT
56352867 TTTTAAAATA-
1 TTTTAAAATAT
56352877 TTTTAAAATAT
1 TTTTAAAATAT
*
56352888 TTTAAAAATAT
1 TTTTAAAATAT
*
56352899 TTTAAAAATACT
1 TTTTAAAATA-T
56352911 TTTT
1 TTTT
56352915 TTAATTTTTA
Statistics
Matches: 99, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
8 11 0.11
9 9 0.09
10 11 0.11
11 51 0.52
12 17 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:56352830 original size:42 final size:42
Alignment explanation
Indices: 56352768--56352890 Score: 177
Period size: 42 Copynumber: 3.0 Consensus size: 42
56352758 AATATATTTA
*
56352768 TTTTT-TTAATTTTTTAATTTTAAAATATTTTTAAAATACTT
1 TTTTTATTATTTTTTTAATTTTAAAATATTTTTAAAATACTT
56352809 TTTTTATTATTTTTTTAATTTTAAAATATTTTTAAAATAC--
1 TTTTTATTATTTTTTTAATTTTAAAATATTTTTAAAATACTT
*
56352849 TTTTTA-AATTTTTTTAAATTTTAAAATA-TTTTAAAATA-TT
1 TTTTTATTATTTTTTT-AATTTTAAAATATTTTTAAAATACTT
56352889 TT
1 TT
56352891 AAAAATATTT
Statistics
Matches: 76, Mismatches: 2, Indels: 9
0.87 0.02 0.10
Matches are distributed among these distances:
39 18 0.24
40 20 0.26
41 5 0.07
42 33 0.43
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (42 bp):
TTTTTATTATTTTTTTAATTTTAAAATATTTTTAAAATACTT
Found at i:56358235 original size:15 final size:15
Alignment explanation
Indices: 56358215--56358245 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
56358205 AAATGATGAG
56358215 AATGATTCTTTCTAA
1 AATGATTCTTTCTAA
56358230 AATGATTCTTTCTAA
1 AATGATTCTTTCTAA
56358245 A
1 A
56358246 TTGTTTGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (15 bp):
AATGATTCTTTCTAA
Found at i:56362154 original size:2 final size:2
Alignment explanation
Indices: 56362147--56362171 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56362137 ACCAATACAA
56362147 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
56362172 ACCAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56368980 original size:49 final size:49
Alignment explanation
Indices: 56368926--56369042 Score: 216
Period size: 49 Copynumber: 2.4 Consensus size: 49
56368916 TGATAAAACT
56368926 TGCATTTCCCATTCATTTCCGACTTACCAAACAGGGCACTACCAAGACC
1 TGCATTTCCCATTCATTTCCGACTTACCAAACAGGGCACTACCAAGACC
56368975 TGCATTTCCCATTCATTTCCGACTTACCAAACAGGGCACTACCAAGACC
1 TGCATTTCCCATTCATTTCCGACTTACCAAACAGGGCACTACCAAGACC
* *
56369024 TGCATTTTCCACTCATTTC
1 TGCATTTCCCATTCATTTC
56369043 TTACCATCCA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 66 1.00
ACGTcount: A:0.26, C:0.34, G:0.11, T:0.28
Consensus pattern (49 bp):
TGCATTTCCCATTCATTTCCGACTTACCAAACAGGGCACTACCAAGACC
Found at i:56369069 original size:50 final size:49
Alignment explanation
Indices: 56368926--56369071 Score: 177
Period size: 49 Copynumber: 3.0 Consensus size: 49
56368916 TGATAAAACT
* * *
56368926 TGCATTTCCCATTCATTTCCGACTTACCAAACAGGGCACTACCAAGACC
1 TGCATTTCCCACTCATTTCCGACATACCAAACAGAGCACTACCAAGACC
* * *
56368975 TGCATTTCCCATTCATTTCCGACTTACCAAACAGGGCACTACCAAGACC
1 TGCATTTCCCACTCATTTCCGACATACCAAACAGAGCACTACCAAGACC
* ** *
56369024 TGCATTTTCCACTCATTTCTTACCAT-CCAAGCAGAAGCACTACCAAGA
1 TGCATTTCCCACTCATTTCCGA-CATACCAAACAG-AGCACTACCAAGA
56369072 TTTTCATTTA
Statistics
Matches: 88, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
49 74 0.84
50 14 0.16
ACGTcount: A:0.29, C:0.34, G:0.12, T:0.25
Consensus pattern (49 bp):
TGCATTTCCCACTCATTTCCGACATACCAAACAGAGCACTACCAAGACC
Found at i:56372262 original size:23 final size:23
Alignment explanation
Indices: 56372236--56372279 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
56372226 TTGAAGTGCA
*
56372236 AAAATGAATTGCATCAATGTGTC
1 AAAATAAATTGCATCAATGTGTC
* *
56372259 AAAATAAATTGCGTCGATGTG
1 AAAATAAATTGCATCAATGTG
56372280 CCAGAATGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (23 bp):
AAAATAAATTGCATCAATGTGTC
Found at i:56383138 original size:23 final size:27
Alignment explanation
Indices: 56383092--56383148 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
56383082 TGACCCCAGC
56383092 AATTAAAGAGCAATATAATAAATAAAT
1 AATTAAAGAGCAATATAATAAATAAAT
*
56383119 AATTAAAGAGCAATATAATAAATACAT
1 AATTAAAGAGCAATATAATAAATAAAT
56383146 AAT
1 AAT
56383149 ATCCCATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.26
Consensus pattern (27 bp):
AATTAAAGAGCAATATAATAAATAAAT
Found at i:56385035 original size:79 final size:78
Alignment explanation
Indices: 56384904--56385061 Score: 253
Period size: 79 Copynumber: 2.0 Consensus size: 78
56384894 GTGTCCAGTC
* * * *
56384904 CGTGGATGAACTTGGATATTGGTAAATTGTTGTCATCTCATTCAGTTTGTAGAGGTTAATACCTT
1 CGTGGATGAACTTGGACATTGGTAAATTGTTGTCACCTCATTCAATTCGTAGAGGTTAATACC-T
*
56384969 TTTTTATAAGAAAA
65 TTTCTATAAGAAAA
*
56384983 CGTGGATGAACTTGGACATTGGTAATTTGTTGTCACCTCATTCAATTCGTAGAGGTTAATACCTT
1 CGTGGATGAACTTGGACATTGGTAAATTGTTGTCACCTCATTCAATTCGTAGAGGTTAATACCTT
56385048 TTCTATAAGAAAA
66 TTCTATAAGAAAA
56385061 C
1 C
56385062 TTTCAAATTT
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
78 15 0.21
79 58 0.79
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (78 bp):
CGTGGATGAACTTGGACATTGGTAAATTGTTGTCACCTCATTCAATTCGTAGAGGTTAATACCTT
TTCTATAAGAAAA
Found at i:56389717 original size:18 final size:17
Alignment explanation
Indices: 56389696--56389733 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
56389686 ATTTTGGGGG
56389696 TTTTAAGGGTTTAAGGTT
1 TTTTAA-GGTTTAAGGTT
*
56389714 TTTTAAGGTTTAGGGTT
1 TTTTAAGGTTTAAGGTT
56389731 TTT
1 TTT
56389734 AGCCATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.55
Consensus pattern (17 bp):
TTTTAAGGTTTAAGGTT
Found at i:56389732 original size:16 final size:18
Alignment explanation
Indices: 56389696--56389734 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
56389686 ATTTTGGGGG
*
56389696 TTTTAAGGGTTTAAGGTT
1 TTTTAAGGGTTTAAGGGT
56389714 TTTTAA-GGTTT-AGGGT
1 TTTTAAGGGTTTAAGGGT
56389730 TTTTA
1 TTTTA
56389735 GCCATTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 5 0.25
18 6 0.30
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.54
Consensus pattern (18 bp):
TTTTAAGGGTTTAAGGGT
Found at i:56391102 original size:9 final size:9
Alignment explanation
Indices: 56391088--56391156 Score: 86
Period size: 9 Copynumber: 7.7 Consensus size: 9
56391078 TTTGGTTAAA
*
56391088 AATTAACTG
1 AATTAACCG
56391097 AATTAACCG
1 AATTAACCG
*
56391106 AATTACCCG
1 AATTAACCG
*
56391115 AATTACCCG
1 AATTAACCG
56391124 AATTAACC-
1 AATTAACCG
*
56391132 AGATTACCCG
1 A-ATTAACCG
56391142 AATTAACCG
1 AATTAACCG
56391151 AATTAA
1 AATTAA
56391157 TCAAATTGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
8 1 0.02
9 51 0.96
10 1 0.02
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:56391126 original size:27 final size:27
Alignment explanation
Indices: 56391088--56391156 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
56391078 TTTGGTTAAA
*
56391088 AATTAACTGAATTAACC-GAATTACCCG
1 AATTAACCGAATTAACCAG-ATTACCCG
*
56391115 AATTACCCGAATTAACCAGATTACCCG
1 AATTAACCGAATTAACCAGATTACCCG
56391142 AATTAACCGAATTAA
1 AATTAACCGAATTAA
56391157 TCAAATTGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 37 0.97
28 1 0.03
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (27 bp):
AATTAACCGAATTAACCAGATTACCCG
Found at i:56392681 original size:3 final size:3
Alignment explanation
Indices: 56392673--56392732 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
56392663 TTTCAAAAAT
56392673 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
56392721 ATA ATA ATA ATA
1 ATA ATA ATA ATA
56392733 TGATAACTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:56393487 original size:37 final size:39
Alignment explanation
Indices: 56393432--56393509 Score: 133
Period size: 37 Copynumber: 2.1 Consensus size: 39
56393422 AAAATCCGAT
*
56393432 ATTCGGCCTGAATATAAAAAAAAA-T-ATAAATTTAATA
1 ATTCAGCCTGAATATAAAAAAAAATTAATAAATTTAATA
56393469 ATTCAGCCTGAATATAAAAAAAAATTAATAAATTTAATA
1 ATTCAGCCTGAATATAAAAAAAAATTAATAAATTTAATA
56393508 AT
1 AT
56393510 GCTAACAACT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
37 23 0.61
38 1 0.03
39 14 0.37
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (39 bp):
ATTCAGCCTGAATATAAAAAAAAATTAATAAATTTAATA
Found at i:56394756 original size:10 final size:10
Alignment explanation
Indices: 56394743--56394769 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
56394733 ATGAATTATA
56394743 TTAAATTGAG
1 TTAAATTGAG
56394753 TTAAATTGAG
1 TTAAATTGAG
56394763 TTAAATT
1 TTAAATT
56394770 CATTTGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (10 bp):
TTAAATTGAG
Found at i:56395127 original size:25 final size:25
Alignment explanation
Indices: 56395099--56395173 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
56395089 ATCCCAATAC
* *
56395099 TTGGCTCTCATGAGCTTTTA-GATAT
1 TTGGCTCTCATAAGC-TTCACGATAT
56395124 TTGGCTCTCATAAGCTTCACGATAT
1 TTGGCTCTCATAAGCTTCACGATAT
* * *
56395149 TTGGCTCGCAAAAGCTTCTCGATAT
1 TTGGCTCTCATAAGCTTCACGATAT
56395174 ACAACTCACA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
24 3 0.07
25 41 0.93
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (25 bp):
TTGGCTCTCATAAGCTTCACGATAT
Found at i:56397641 original size:18 final size:19
Alignment explanation
Indices: 56397618--56397657 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
56397608 AATGGATTAA
*
56397618 TAATAA-AATTTGAAATTT
1 TAATAATAATTTGAAATAT
*
56397636 TAATAATATTTTGAAATAT
1 TAATAATAATTTGAAATAT
56397655 TAA
1 TAA
56397658 ATATTAATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
TAATAATAATTTGAAATAT
Found at i:56399772 original size:21 final size:21
Alignment explanation
Indices: 56399743--56399782 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
56399733 AACGGAACCA
56399743 TTGACGTGGCCAGTTAACTAG
1 TTGACGTGGCCAGTTAACTAG
*
56399764 TTGATGTGGCCAGTTAACT
1 TTGACGTGGCCAGTTAACT
56399783 TGCCACGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGACGTGGCCAGTTAACTAG
Found at i:56399865 original size:28 final size:29
Alignment explanation
Indices: 56399826--56399892 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
56399816 TTTTCGTCCT
56399826 TTTTTA-TTTTTA-ATAAATGACCCAATA
1 TTTTTACTTTTTACATAAATGACCCAATA
* *
56399853 TTTTTACTTTTTACGTAAATGGCCCAATA
1 TTTTTACTTTTTACATAAATGACCCAATA
56399882 TGTTTATACTT
1 T-TTT-TACTT
56399893 ATTTTTCTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 6 0.18
28 6 0.18
29 14 0.41
30 3 0.09
31 5 0.15
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.49
Consensus pattern (29 bp):
TTTTTACTTTTTACATAAATGACCCAATA
Found at i:56400917 original size:139 final size:139
Alignment explanation
Indices: 56400667--56400917 Score: 468
Period size: 139 Copynumber: 1.8 Consensus size: 139
56400657 ACTGATTTAT
56400667 TATTTTTTAAAAATTATTTAACTAAATTAAAATTAAAGTGATTATTTTATCAACTGCATAAAAAA
1 TATTTTTTAAAAATTATTTAACTAAATTAAAATTAAAGTGATTATTTTATCAACTGCATAAAAAA
**
56400732 TGAGTGATTGATGTAATTTACCTAAAAATTATAAAAATTTATAAAAAAATAAAAAATTGGGGGCA
66 TGAGTGATTGATGTAATTTACCTAAAAATTATAAAAAAATATAAAAAAATAAAAAATTGGGGGCA
56400797 TCATTAGTC
131 TCATTAGTC
56400806 TATTTTTTAAAAATTATTTAACTAAATTAAAATTAAAGTGATTATTTTATCAACTGCATAAAAAA
1 TATTTTTTAAAAATTATTTAACTAAATTAAAATTAAAGTGATTATTTTATCAACTGCATAAAAAA
56400871 TGAGTGATTGATGTAATTTACCTAAAAATTTATAAAAAAATA-AAAAA
66 TGAGTGATTGATGTAATTTACCTAAAAA-TTATAAAAAAATATAAAAA
56400918 TTGGGGGCAT
Statistics
Matches: 109, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
139 98 0.90
140 11 0.10
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (139 bp):
TATTTTTTAAAAATTATTTAACTAAATTAAAATTAAAGTGATTATTTTATCAACTGCATAAAAAA
TGAGTGATTGATGTAATTTACCTAAAAATTATAAAAAAATATAAAAAAATAAAAAATTGGGGGCA
TCATTAGTC
Found at i:56407168 original size:19 final size:19
Alignment explanation
Indices: 56407144--56407182 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
56407134 CCCTGAAGTA
*
56407144 TACCTATTTTCTTTCTTTG
1 TACCTAATTTCTTTCTTTG
*
56407163 TACCTAATTTCTTTTTTTG
1 TACCTAATTTCTTTCTTTG
56407182 T
1 T
56407183 CTCAATTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.18, G:0.05, T:0.64
Consensus pattern (19 bp):
TACCTAATTTCTTTCTTTG
Found at i:56407395 original size:16 final size:17
Alignment explanation
Indices: 56407349--56407396 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
56407339 TAAATACATA
56407349 AAAATTCATAAAAAATAT
1 AAAATT-ATAAAAAATAT
*
56407367 AAAATTTAGAAAAAATAT
1 AAAA-TTATAAAAAATAT
56407385 -AAATTATAAAAA
1 AAAATTATAAAAA
56407397 TTAAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 8 0.30
17 3 0.11
18 14 0.52
19 2 0.07
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAATTATAAAAAATAT
Found at i:56407406 original size:23 final size:23
Alignment explanation
Indices: 56407376--56407419 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
56407366 TAAAATTTAG
*
56407376 AAAAAATATAAA-TTATAAAAATT
1 AAAAAATA-AAACTTACAAAAATT
56407399 AAAAAATAAAACTTACAAAAA
1 AAAAAATAAAACTTACAAAAA
56407420 ATATGATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (23 bp):
AAAAAATAAAACTTACAAAAATT
Found at i:56407542 original size:8 final size:8
Alignment explanation
Indices: 56407529--56407567 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
56407519 CCTTTTTTTT
56407529 TTATAAAA
1 TTATAAAA
56407537 TTATAAAA
1 TTATAAAA
*
56407545 -TATATAA
1 TTATAAAA
56407552 TTATAAAA
1 TTATAAAA
*
56407560 TTCTAAAA
1 TTATAAAA
56407568 AGAATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (8 bp):
TTATAAAA
Found at i:56407553 original size:15 final size:15
Alignment explanation
Indices: 56407530--56407560 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56407520 CTTTTTTTTT
56407530 TATAAAATTATAAAA
1 TATAAAATTATAAAA
*
56407545 TATATAATTATAAAA
1 TATAAAATTATAAAA
56407560 T
1 T
56407561 TCTAAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATAAAATTATAAAA
Found at i:56407997 original size:19 final size:17
Alignment explanation
Indices: 56407947--56408004 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
56407937 AATACATGCG
*
56407947 TTTTTTTATT-TTTTAA
1 TTTTTATATTATTTTAA
*
56407963 TTTTTATAATATTTTTAA
1 TTTTTATATTA-TTTTAA
*
56407981 TTTTTATGTATTATTTTGA
1 TTTTTA--TATTATTTTAA
56408000 TTTTT
1 TTTTT
56408005 TAAAACTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
16 8 0.24
18 12 0.35
19 10 0.29
20 4 0.12
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTATATTATTTTAA
Found at i:56409068 original size:60 final size:60
Alignment explanation
Indices: 56408995--56409111 Score: 198
Period size: 60 Copynumber: 1.9 Consensus size: 60
56408985 ATACTAAACT
* * *
56408995 AAACACAATAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAACAATTTACAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
*
56409055 AAACACAACAATTTACAACATAATCCTAAATTACTAACAAATTACTTTTAAAATAAT
1 AAACACAACAATTTACAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAAT
56409112 GATAAAAAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (60 bp):
AAACACAACAATTTACAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:56413091 original size:18 final size:17
Alignment explanation
Indices: 56413068--56413106 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
56413058 TCTTTAGATT
*
56413068 TTTTTAAAAATATATAAA
1 TTTTTAAAAA-ACATAAA
56413086 TTTTTAAAAAACATAAA
1 TTTTTAAAAAACATAAA
56413103 TTTT
1 TTTT
56413107 ATTATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTTTAAAAAACATAAA
Found at i:56415237 original size:34 final size:34
Alignment explanation
Indices: 56415198--56415266 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
56415188 TTGAAAACGA
56415198 TGGTGTAATTGATTATTGGATGGTTAATTAGGTT
1 TGGTGTAATTGATTATTGGATGGTTAATTAGGTT
56415232 TGGTGTAATTGATTATTGGATGGTTAATTAGGTT
1 TGGTGTAATTGATTATTGGATGGTTAATTAGGTT
56415266 T
1 T
56415267 CGGGTAGTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (34 bp):
TGGTGTAATTGATTATTGGATGGTTAATTAGGTT
Found at i:56415259 original size:19 final size:19
Alignment explanation
Indices: 56415196--56415260 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
56415186 TATTGAAAAC
56415196 GATGGTGTAATTGATTATTG
1 GATGGT-TAATTGATTATTG
*
56415216 GATGGTTAATT-AGGT-TTG
1 GATGGTTAATTGA-TTATTG
56415234 G-T-G-TAATTGATTATTG
1 GATGGTTAATTGATTATTG
56415250 GATGGTTAATT
1 GATGGTTAATT
56415261 AGGTTTCGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
15 6 0.16
16 6 0.16
17 2 0.05
18 6 0.16
19 11 0.30
20 6 0.16
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (19 bp):
GATGGTTAATTGATTATTG
Found at i:56417591 original size:63 final size:63
Alignment explanation
Indices: 56417493--56417623 Score: 255
Period size: 63 Copynumber: 2.1 Consensus size: 63
56417483 TCATCAAAAC
56417493 CTTC-TTTCTTTTCTTGTAGGCGGCTTTCCTCGTTGAATCATTGGTGATATAAGCAAATTAAT
1 CTTCTTTTCTTTTCTTGTAGGCGGCTTTCCTCGTTGAATCATTGGTGATATAAGCAAATTAAT
56417555 CTTCTTTTCTTTTCTTGTAGGCGGCTTTCCTCGTTGAATCATTGGTGATATAAGCAAATTAAT
1 CTTCTTTTCTTTTCTTGTAGGCGGCTTTCCTCGTTGAATCATTGGTGATATAAGCAAATTAAT
56417618 CTTCTT
1 CTTCTT
56417624 CCTCGTCATG
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
62 4 0.06
63 64 0.94
ACGTcount: A:0.20, C:0.18, G:0.17, T:0.45
Consensus pattern (63 bp):
CTTCTTTTCTTTTCTTGTAGGCGGCTTTCCTCGTTGAATCATTGGTGATATAAGCAAATTAAT
Found at i:56420050 original size:25 final size:24
Alignment explanation
Indices: 56419938--56420050 Score: 79
Period size: 25 Copynumber: 4.5 Consensus size: 24
56419928 CGTAACCAGA
*
56419938 AAGCTCATGCGAGCCAA-TATCG-GG
1 AAGCTCAT-AGAGCCAATTAT-GAGG
* * *
56419962 AAGCTCCAGAGAGCC-ATTAATCAAG
1 AAGCT-CATAGAGCCAATT-ATGAGG
*
56419987 AAGCTCATGAGAGCCAATTATTAGG
1 AAGCTCAT-AGAGCCAATTATGAGG
**
56420012 AAGCTCCGGAGAGCCAATTATGAGG
1 AAGCT-CATAGAGCCAATTATGAGG
56420037 AAGCTCATATGAGC
1 AAGCTCATA-GAGC
56420051 AATAAACGGG
Statistics
Matches: 69, Mismatches: 12, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
23 1 0.01
24 15 0.22
25 49 0.71
26 4 0.06
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.19
Consensus pattern (24 bp):
AAGCTCATAGAGCCAATTATGAGG
Found at i:56420098 original size:74 final size:74
Alignment explanation
Indices: 56419986--56420124 Score: 167
Period size: 74 Copynumber: 1.9 Consensus size: 74
56419976 CATTAATCAA
* * * *
56419986 GAAGCTCATGAGAGCCAATTATTAGGAAGCTCCGGAGAGCCA-ATTATGAGGAAGCTCATATGAG
1 GAAGCTCAAGAGAGCCAATTATCAGGAAGCTCCGGAGAGCCATATAAT-AGGAAGCTCATAAGAG
56420050 CAATAAACGG
65 CAATAAACGG
* * *
56420060 GAAGCTCAAGAGAGCC-ATTAATCGGGATGCT-CGTGAGAGCCATATAATAGGATGCTCATAAGA
1 GAAGCTCAAGAGAGCCAATT-ATCAGGAAGCTCCG-GAGAGCCATATAATAGGAAGCTCATAAGA
56420123 GC
64 GC
56420125 TAAATAACAG
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
73 5 0.09
74 46 0.84
75 4 0.07
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.19
Consensus pattern (74 bp):
GAAGCTCAAGAGAGCCAATTATCAGGAAGCTCCGGAGAGCCATATAATAGGAAGCTCATAAGAGC
AATAAACGG
Found at i:56420123 original size:25 final size:25
Alignment explanation
Indices: 56419971--56420124 Score: 75
Period size: 25 Copynumber: 6.2 Consensus size: 25
56419961 GAAGCTCCAG
* * *
56419971 AGAGCCATTAATCAAGAAGCTCATG
1 AGAGCCATTAATCAGGATGCTCATA
* * ***
56419996 AGAGCCAATT-ATTAGGAAGCTCCGG
1 AGAGCC-ATTAATCAGGATGCTCATA
* *
56420021 AGAGCCAATT-ATGAGGAAGCTCATA
1 AGAGCC-ATTAATCAGGATGCTCATA
* * * * *
56420046 TGAG-CAATAAACGGGAAGCTCA-A
1 AGAGCCATTAATCAGGATGCTCATA
* * *
56420069 GAGAGCCATTAATCGGGATGCTCGTG
1 -AGAGCCATTAATCAGGATGCTCATA
56420095 AGAGCCATATAAT-AGGATGCTCATA
1 AGAGCCAT-TAATCAGGATGCTCATA
56420120 AGAGC
1 AGAGC
56420125 TAAATAACAG
Statistics
Matches: 101, Mismatches: 22, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
23 3 0.03
24 14 0.14
25 77 0.76
26 7 0.07
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.19
Consensus pattern (25 bp):
AGAGCCATTAATCAGGATGCTCATA
Found at i:56420131 original size:25 final size:25
Alignment explanation
Indices: 56420084--56420141 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
56420074 CCATTAATCG
* * * *
56420084 GGATGCTCGTGAGAGCCATATAATA
1 GGATGCTCATAAGAGCCAAATAACA
*
56420109 GGATGCTCATAAGAGCTAAATAACA
1 GGATGCTCATAAGAGCCAAATAACA
*
56420134 GGACGCTC
1 GGATGCTC
56420142 TTGCGAGCTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (25 bp):
GGATGCTCATAAGAGCCAAATAACA
Found at i:56420943 original size:4 final size:4
Alignment explanation
Indices: 56420930--56420964 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
56420920 AAAATCTTAT
56420930 TTTA -TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
56420965 ATTTTATGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:56424492 original size:14 final size:14
Alignment explanation
Indices: 56424473--56424503 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
56424463 GACGTTATGC
56424473 CTAGATTGAAAAGG
1 CTAGATTGAAAAGG
56424487 CTAGATTGAAAAGG
1 CTAGATTGAAAAGG
56424501 CTA
1 CTA
56424504 CATTAGCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.23
Consensus pattern (14 bp):
CTAGATTGAAAAGG
Found at i:56438972 original size:15 final size:14
Alignment explanation
Indices: 56438951--56438986 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
56438941 ATAATCCGTA
*
56438951 ATAATTATCTTAAT
1 ATAATTATCCTAAT
56438965 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
56438980 ATAATTA
1 ATAATTA
56438987 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:56439549 original size:4 final size:4
Alignment explanation
Indices: 56439535--56439589 Score: 58
Period size: 4 Copynumber: 13.0 Consensus size: 4
56439525 AGTCTCCAAA
*
56439535 TTAT ATAT TTAT TTAT TTAT TTAT TTATT TTGATT TTGAT TTAT TTA-
1 TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TT-A-T TT-AT TTAT TTAT
56439582 TTAT TTAT
1 TTAT TTAT
56439590 ATTTTTTATG
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 3 0.07
4 30 0.65
5 6 0.13
6 7 0.15
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:56439597 original size:16 final size:15
Alignment explanation
Indices: 56439534--56439598 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 15
56439524 TAGTCTCCAA
* *
56439534 ATTATATATTTATTT
1 ATTATTTATTTTTTT
56439549 ATTTATTTATTTATTTT
1 A-TTATTTATTT-TTTT
* *
56439566 GATT-TTGATTTATTT
1 -ATTATTTATTTTTTT
56439581 ATTATTTATATTTTTT
1 ATTATTTAT-TTTTTT
56439597 AT
1 AT
56439599 GCTTTAGGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
14 3 0.08
15 8 0.21
16 22 0.56
17 5 0.13
18 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
ATTATTTATTTTTTT
Found at i:56447070 original size:15 final size:14
Alignment explanation
Indices: 56447049--56447084 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
56447039 ATAATCCTTA
*
56447049 ATAATTATCTTAAT
1 ATAATTATCCTAAT
56447063 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
56447078 ATAATTA
1 ATAATTA
56447085 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:56447217 original size:30 final size:30
Alignment explanation
Indices: 56447181--56447241 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
56447171 TTGTGTCGCA
56447181 CATTTTATCTCTAAATTCACGCTTTTGGCC
1 CATTTTATCTCTAAATTCACGCTTTTGGCC
56447211 CATTTTATCTCTAAATTCACGCTTTTGGCC
1 CATTTTATCTCTAAATTCACGCTTTTGGCC
56447241 C
1 C
56447242 TTAATTTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.20, C:0.28, G:0.10, T:0.43
Consensus pattern (30 bp):
CATTTTATCTCTAAATTCACGCTTTTGGCC
Found at i:56448443 original size:49 final size:48
Alignment explanation
Indices: 56448322--56448446 Score: 137
Period size: 49 Copynumber: 2.6 Consensus size: 48
56448312 ATACACATTT
* *
56448322 TACCAT-CTCGGATGGCTCGACAATGATGGTTTACACTATTCAATATTT
1 TACCATCCT-GGATGGCTCGAAAATGATGGTTTACACTATTCAATATTC
** * * * *
56448370 TATTATCCTGGATGGC-CTGGAAATGGTGTTTTGCACTATTTCAATATTC
1 TACCATCCTGGATGGCTC-GAAAATGATGGTTTACACTA-TTCAATATTC
56448419 TACCATCCTGGATGGCTCGAAAATGATG
1 TACCATCCTGGATGGCTCGAAAATGATG
56448447 ACTTTCATTA
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
47 1 0.02
48 26 0.43
49 33 0.54
50 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (48 bp):
TACCATCCTGGATGGCTCGAAAATGATGGTTTACACTATTCAATATTC
Found at i:56449201 original size:40 final size:44
Alignment explanation
Indices: 56449139--56449227 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 44
56449129 CTTTCTCTAC
* **
56449139 TTAATTTCACTTATATAGCATGATTAATTTATTATTAAGCT-TAA
1 TTAATTTCACTTATATA-CATGATTAATTAAGCATTAAGCTATAA
56449183 TTAATTT-ACTTA-AT-CATGATTAATTAAGCATTAAGCTATAA
1 TTAATTTCACTTATATACATGATTAATTAAGCATTAAGCTATAA
56449224 TTAA
1 TTAA
56449228 CTTAATCCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
40 20 0.49
41 7 0.17
42 2 0.05
43 5 0.12
44 7 0.17
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (44 bp):
TTAATTTCACTTATATACATGATTAATTAAGCATTAAGCTATAA
Found at i:56452891 original size:21 final size:22
Alignment explanation
Indices: 56452852--56452898 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
56452842 TATAAAAACA
*
56452852 AAAAAAAAAAACTTAATTTTTG
1 AAAAAAAAAAACTTAATTTTGG
* *
56452874 AAAAAAAAATAGTT-ATTTTGG
1 AAAAAAAAAAACTTAATTTTGG
56452895 AAAA
1 AAAA
56452899 TTAAGAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (22 bp):
AAAAAAAAAAACTTAATTTTGG
Found at i:56461332 original size:15 final size:16
Alignment explanation
Indices: 56461314--56461343 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56461304 ATTTGATCAT
56461314 TTTTTA-TTTAATAAG
1 TTTTTATTTTAATAAG
56461329 TTTTTATTTTAATAA
1 TTTTTATTTTAATAA
56461344 ATTAATAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
TTTTTATTTTAATAAG
Found at i:56463638 original size:17 final size:17
Alignment explanation
Indices: 56463616--56463648 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
56463606 TTTGAATTTT
56463616 TGAATTATGTGATTTAG
1 TGAATTATGTGATTTAG
*
56463633 TGAATTTTGTGATTTA
1 TGAATTATGTGATTTA
56463649 AAAAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (17 bp):
TGAATTATGTGATTTAG
Found at i:56464901 original size:24 final size:24
Alignment explanation
Indices: 56464874--56464948 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 24
56464864 ATGGAAAATT
56464874 GTGAAAAGTAGGTATGGTGTTTCA
1 GTGAAAAGTAGGTATGGTGTTTCA
** ** *
56464898 GTGAAGAA--AGCCATACTGAGTT--
1 GTGAA-AAGTAGGTATGGTG-TTTCA
56464920 GTGAAAAGTAGGTATGGTGTTTCA
1 GTGAAAAGTAGGTATGGTGTTTCA
56464944 GTGAA
1 GTGAA
56464949 GAAAACCATA
Statistics
Matches: 35, Mismatches: 10, Indels: 12
0.61 0.18 0.21
Matches are distributed among these distances:
21 2 0.06
22 7 0.20
23 12 0.34
24 12 0.34
25 2 0.06
ACGTcount: A:0.32, C:0.07, G:0.32, T:0.29
Consensus pattern (24 bp):
GTGAAAAGTAGGTATGGTGTTTCA
Found at i:56464925 original size:46 final size:45
Alignment explanation
Indices: 56464872--56465011 Score: 244
Period size: 46 Copynumber: 3.0 Consensus size: 45
56464862 CCATGGAAAA
56464872 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAGCCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAA-CCATACTGAG
56464918 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAG-AAACCATACTGAG
*
56464964 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGGAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAA-GAAACCATACTGAG
56465010 TT
1 TT
56465012 ATAGCATTGT
Statistics
Matches: 91, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
46 87 0.96
47 4 0.04
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.29
Consensus pattern (45 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAACCATACTGAG
Found at i:56468702 original size:25 final size:25
Alignment explanation
Indices: 56468657--56468707 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
56468647 ACTCTTCTCA
* *
56468657 TCTCTTCACTTCTCTATCATTTTTC
1 TCTCTTCACTTCCCTATCATTGTTC
*
56468682 TCTCTTCATTTCCCT-TACATTGTTC
1 TCTCTTCACTTCCCTAT-CATTGTTC
56468707 T
1 T
56468708 TCATTCCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.12, C:0.31, G:0.02, T:0.55
Consensus pattern (25 bp):
TCTCTTCACTTCCCTATCATTGTTC
Found at i:56476495 original size:28 final size:27
Alignment explanation
Indices: 56476423--56476498 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 27
56476413 GAAGCATAAA
56476423 AAATTTAAAAGATAAA-ATAAAAAACTCC
1 AAATTTAAAA-ATAAACAT-AAAAACTCC
* * *
56476451 AAATTATGAGAAT-AACATAAAAACTCT
1 AAATT-TAAAAATAAACATAAAAACTCC
56476478 AAATTTAAATAATAAACATAA
1 AAATTTAAA-AATAAACATAA
56476499 TTTTTTAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
26 2 0.05
27 18 0.46
28 16 0.41
29 3 0.08
ACGTcount: A:0.62, C:0.09, G:0.04, T:0.25
Consensus pattern (27 bp):
AAATTTAAAAATAAACATAAAAACTCC
Found at i:56478981 original size:22 final size:22
Alignment explanation
Indices: 56478956--56478998 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
56478946 CCAAGCTTCA
*
56478956 ATATTGTCAAGCTCGAGCTTGT
1 ATATTGCCAAGCTCGAGCTTGT
56478978 ATATTGCCAAGCTCGAGCTTG
1 ATATTGCCAAGCTCGAGCTTG
56478999 AGTTCAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (22 bp):
ATATTGCCAAGCTCGAGCTTGT
Found at i:56482408 original size:19 final size:20
Alignment explanation
Indices: 56482370--56482416 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
56482360 TATTTTATGG
**
56482370 TACTATTACTTGTTTATTAT
1 TACTATTACTTGCCTATTAT
56482390 TACTATTA-TTGCCTATTAT
1 TACTATTACTTGCCTATTAT
*
56482409 TATTATTA
1 TACTATTA
56482417 ATATTATTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.57
Consensus pattern (20 bp):
TACTATTACTTGCCTATTAT
Found at i:56482699 original size:33 final size:32
Alignment explanation
Indices: 56482624--56482699 Score: 77
Period size: 33 Copynumber: 2.4 Consensus size: 32
56482614 CTTTTATATA
* **
56482624 CTTTATATTTT-ATATATATATTTATACATTT
1 CTTTATATTTTAATATATACATAAATACATTT
56482655 CTATTAT-TTTTAAATATATACATAAATACATATT
1 CT-TTATATTTT-AATATATACATAAATACAT-TT
56482689 -TTTATATTTTA
1 CTTTATATTTTA
56482700 TTTTACAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
31 6 0.16
32 9 0.24
33 20 0.54
34 2 0.05
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (32 bp):
CTTTATATTTTAATATATACATAAATACATTT
Found at i:56487538 original size:7 final size:7
Alignment explanation
Indices: 56487513--56487554 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
56487503 AGTGATGTGA
56487513 AAAAATG
1 AAAAATG
56487520 AAAAGATG
1 AAAA-ATG
56487528 -AAAATG
1 AAAAATG
56487534 AAAAATG
1 AAAAATG
56487541 AAAAA-G
1 AAAAATG
56487547 TAAAAATG
1 -AAAAATG
56487555 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 4 0.13
7 23 0.74
8 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:56487552 original size:21 final size:21
Alignment explanation
Indices: 56487513--56487554 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
56487503 AGTGATGTGA
*
56487513 AAAAATGAAAAGATGAAAATG
1 AAAAATGAAAAGATAAAAATG
56487534 AAAAATGAAAA-AGTAAAAATG
1 AAAAATGAAAAGA-TAAAAATG
56487555 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAGATAAAAATG
Found at i:56489063 original size:89 final size:89
Alignment explanation
Indices: 56488838--56489785 Score: 1221
Period size: 89 Copynumber: 10.7 Consensus size: 89
56488828 GTGAAGTAGC
* *
56488838 AGCAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATATTGTCTTCCCATA
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
** *
56488903 CTGGTGGCAAAACAGATCAAAGAA
66 CTGGTGGTGAAACAGATCGAAGAA
* * *
56488927 A-CAGATCTTGTTTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTATCTTCCCATA
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
*
56488991 CTGGTGGCGAAACAGATCGAAGAA
66 CTGGTGGTGAAACAGATCGAAGAA
*
56489015 AGCAGATCCTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
*
56489080 CTAGTGGTGAAACAGATCGAAGAA
66 CTGGTGGTGAAACAGATCGAAGAA
56489104 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
*
56489169 CTGGT-GTCGAAACAGATCAAAGAA
66 CTGGTGGT-GAAACAGATCGAAGAA
* *
56489193 AGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
*
56489258 CTGGTGGTGAAACAGATCAAAGAA
66 CTGGTGGTGAAACAGATCGAAGAA
*
56489282 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGGTAACAGATCTTGTCTTCCCATA
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
*
56489347 CTGGTGGTGAAACAAATCGAAGAA
66 CTGGTGGTGAAACAGATCGAAGAA
* *
56489371 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTATCTTCCCATA
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
* **
56489436 CTGGTGGCGAAGTAGATCGAAGAA
66 CTGGTGGTGAAACAGATCGAAGAA
* * * ***
56489460 AGCAGATTTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAA-A-AAGAAGATCTTGTCTTCATG
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC-AAAGATAA-CAGATCTTGTCTTCCCA
* * ** *
56489523 TATTGG-CGTGAAGTAGATCGAAGAT
64 TACTGGTGGTGAAACAGATCGAAGAA
* * * * * *
56489548 AGCAGATCTTATCTTC-TCATACTGGTGGCGAAGTAGGTCGAAA-A-AAGCAGATCTTGTCTTCA
1 AGCAGATCTTGTCTTCAT-GTACTGG-CGTGAAGTAGATC-AAAGATAA-CAGATCTTGTCTTCC
** * * ***
56489610 TGTATTGG-CGTGAAGTTGATCGAAGAA
62 CATACTGGTGGTGAAACAGATCGAAGAA
* * * * * * *
56489637 AACAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAATATAGCAGATCTTGTCTTCCCATT
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
* **
56489702 CTGGTGGTGGAGTAGATCGAAGAA
66 CTGGTGGTGAAACAGATCGAAGAA
* * * * *
56489726 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGATAGCATATCTTGTCTTC
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTC
56489786 ATGTATTGGC
Statistics
Matches: 773, Mismatches: 75, Indels: 22
0.89 0.09 0.03
Matches are distributed among these distances:
87 3 0.00
88 148 0.19
89 616 0.80
90 6 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (89 bp):
AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
CTGGTGGTGAAACAGATCGAAGAA
Found at i:56489337 original size:133 final size:132
Alignment explanation
Indices: 56488840--56489806 Score: 941
Period size: 133 Copynumber: 7.3 Consensus size: 132
56488830 GAAGTAGCAG
* * **
56488840 CAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAA-CAGATATTGTCTTCCCATAC
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA-AAGCAGATCTTGTCTTCATATAC
** ** * * *
56488904 TGGTGGCAAAACAGATCAAAGAAA-CAGATCTTGTTTTCATGTACTGGCGTGAAGTAGATCAAAG
65 TGGTGGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAA-
*
56488968 GTAA
129 GAAA
* *** * * ** * * *
56488972 CAGATCTTATCTTCCCATACTGGTGGCGAAACAGATCGAAGAAAGCAGATCCTGTCTTCATGTAC
1 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATATAC
* * * **
56489037 TGG-CGTGAAGTAGATCAAAGATAA-CAGATCTTGTCTTCCCATACTAGT-G-GTGAAACAGATC
65 TGGTGGTGAAGTAGATCAAAGA-AAGCAGATCTTGTCTT--CAT-GTATTGGCGTGAAGTAGATC
56489098 GAAGAAA
126 GAAGAAA
**
56489105 GCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAA-CAGATCTTGTCTTCCCATA
1 -CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGA-AAGCAGATCTTGTCTTCATATA
** * *
56489169 CTGGT-GTCGAAACAGATCAAAGAAAGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAA
64 CTGGTGGT-GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGA
56489233 AGATAA
128 AGA-AA
*** * ** *
56489239 CAGATCTTGTCTTCCCATACTGGTGGTGAAACAGATCAAAGAAAGCAGATCTTGTCTTCATGTAC
1 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATATAC
* * *** * * ** *
56489304 TGG-CGTGAAGTAGATCAAAGGTAA-CAGATCTTGTCTTCCCATACTGGTGGTGAAACAAATCGA
65 TGGTGGTGAAGTAGATCAAA-GAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGA
56489367 AGAAA
128 AGAAA
* * **
56489372 GCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTATCTTCCCATAC
1 -CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATATAC
* * * *
56489437 TGGTGGCGAAGTAGATCGAAGAAAGCAGATTTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAA
65 TGGTGGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG
56489502 AAA
130 AAA
* * * * *
56489505 GAAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTATCTTC-TCATA
1 -CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCAT-ATA
* * *
56489569 CTGGTGGCGAAGTAGGTCGAAA-AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTTGATCGA
64 CTGGTGGTGAAGTAGATC-AAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGA
56489633 AGAAAA
128 AG-AAA
* * * * * ** *
56489639 CAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAATATAGCAGATCTTGTCTTCCCATTCT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATATACT
* * *
56489704 GGTGGTGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAGA
66 GGTGGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGA
*
56489769 TAG
131 -AA
* *
56489772 CATATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
1 CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGAT
56489807 TGAAGATTAC
Statistics
Matches: 690, Mismatches: 117, Indels: 55
0.80 0.14 0.06
Matches are distributed among these distances:
131 3 0.00
132 42 0.06
133 469 0.68
134 169 0.24
135 4 0.01
136 3 0.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (132 bp):
CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATATACT
GGTGGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGA
AA
Found at i:56489959 original size:44 final size:44
Alignment explanation
Indices: 56489800--56490234 Score: 194
Period size: 44 Copynumber: 9.9 Consensus size: 44
56489790 ATTGGCGTGA
** *
56489800 AGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTGGGCAGCAGTGG
* ** **** * * *
56489844 AGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTA-CAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTG-GG-CAGCAGTGG
* * *
56489889 AGTACATTG-A-A-TCCAGAAAT-TCTATCTCCCTGGGCAACAGTGG
1 AGTAGATTGAAGATTACAG--ATCT-TATCTCCCTGGGCAGCAGTGG
* *** *
56489932 AATAGATTGAAGATTACAGATCTTATCTCCCTAAACAGTAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTGGGCAGCAGTGG
* * *** * * *
56489976 AGCAGATCGAAGATGGTAGATTTTACCTCCCTGAGGTTA-CAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTG-GG-CAGCAGTGG
* * *
56490021 AGTACATTGAAGCCAGTA-A-TTC-TATCTCCCTGGGCAGCAGTGG
1 AGTAGATTGAAG--ATTACAGATCTTATCTCCCTGGGCAGCAGTGG
* * ** *
56490064 AATAGATTGAAGACTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTGGGCAGCAGTGG
* ** ** * * *
56490108 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTA-CAGTGG
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTG-GG-CAGCAGTGG
* * *
56490153 AGTACATTGAAGCCAGTA-A-TTC-TATCTCCCTGGGCAGCAGTGG
1 AGTAGATTGAAG--ATTACAGATCTTATCTCCCTGGGCAGCAGTGG
* * * *
56490196 AATAAATTGAAGATTACAGATCTTATCTCTCTAGGCAGC
1 AGTAGATTGAAGATTACAGATCTTATCTCCCTGGGCAGC
56490235 GAAGTAGATC
Statistics
Matches: 274, Mismatches: 91, Indels: 52
0.66 0.22 0.12
Matches are distributed among these distances:
41 6 0.02
42 6 0.02
43 57 0.21
44 151 0.55
45 43 0.16
46 9 0.03
47 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (44 bp):
AGTAGATTGAAGATTACAGATCTTATCTCCCTGGGCAGCAGTGG
Found at i:56489971 original size:132 final size:132
Alignment explanation
Indices: 56489802--56490233 Score: 765
Period size: 132 Copynumber: 3.3 Consensus size: 132
56489792 TGGCGTGAAG
*
56489802 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTAGATTT
* * *
56489867 TACCTCCCTGAGGTTACAGTGGAGTACATTGAATCCAGAAATTCTATCTCCCTGGGCAACAGTGG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
56489932 AA
131 AA
* *
56489934 TAGATTGAAGATTACAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAGATGGTAGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTAGATTT
56489999 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
56490064 AA
131 AA
* *
56490066 TAGATTGAAGACTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTAGATTT
56490131 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
56490196 AA
131 AA
* * *
56490198 TAAATTGAAGATTACAGATCTTATCTCTCTAGGCAG
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAG
56490234 CGAAGTAGAT
Statistics
Matches: 286, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 286 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (132 bp):
TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTAGATTT
TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
AA
Found at i:56491927 original size:3 final size:3
Alignment explanation
Indices: 56491919--56491970 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
56491909 CTATTACTTG
* * *
56491919 TTA TTA TTA CTA TTA TTG TCTA TTA TTA TTA TTA TTA ATA TTA TTCA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT-A
56491966 TTA TT
1 TTA TT
56491971 TTCATGTACA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 36 0.88
4 5 0.12
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:56491931 original size:19 final size:19
Alignment explanation
Indices: 56491907--56491954 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
56491897 TATTTTATGG
56491907 TACTATTACTTGT-TATTAT
1 TACTATTA-TTGTCTATTAT
56491926 TACTATTATTGTCTATTAT
1 TACTATTATTGTCTATTAT
*
56491945 TATTATTATT
1 TACTATTATT
56491955 AATATTATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.60
Consensus pattern (19 bp):
TACTATTATTGTCTATTAT
Found at i:56491970 original size:25 final size:28
Alignment explanation
Indices: 56491909--56491963 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
56491899 TTTTATGGTA
* *
56491909 CTATTACTTGTTATTATTACTATTATTGT
1 CTATTA-TTATTATTATTAATATTATTGT
56491938 CTATTATTATTATTATTAATATTATT
1 CTATTATTATTATTATTAATATTATT
56491964 CATTATTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (28 bp):
CTATTATTATTATTATTAATATTATTGT
Found at i:56492213 original size:27 final size:26
Alignment explanation
Indices: 56492162--56492213 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
56492152 TAAACTTTTA
*
56492162 TATACTTTATATTTTTTATATATATT
1 TATACTTTATATTTTTTATAAATATT
*
56492188 TATACATTTCTATTATTTT-TAAATAT
1 TATAC-TTTATATT-TTTTATAAATAT
56492214 ATACATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 5 0.23
27 13 0.59
28 4 0.18
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.62
Consensus pattern (26 bp):
TATACTTTATATTTTTTATAAATATT
Found at i:56499764 original size:24 final size:24
Alignment explanation
Indices: 56499737--56499798 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
56499727 AAATACCATA
* * *
56499737 CCAACCCTGCACTCTATTTACTGT
1 CCAACCCTACACTCCATCTACTGT
*
56499761 CCAACCCTACACTCCATCTCCTGT
1 CCAACCCTACACTCCATCTACTGT
56499785 CCAACCCTACACTC
1 CCAACCCTACACTC
56499799 ATGTGGGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.23, C:0.47, G:0.05, T:0.26
Consensus pattern (24 bp):
CCAACCCTACACTCCATCTACTGT
Found at i:56502501 original size:3 final size:3
Alignment explanation
Indices: 56502493--56502574 Score: 155
Period size: 3 Copynumber: 27.3 Consensus size: 3
56502483 AGTTTAAGGA
56502493 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
*
56502541 TTG TTG TTG TTG TTG TTG TTG TTA TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
56502575 AAATCATCTC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.01, C:0.00, G:0.32, T:0.67
Consensus pattern (3 bp):
TTG
Done.