Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_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: 6287495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 33
Found at i:3567997 original size:19 final size:19
Alignment explanation
Indices: 3567969--3568018 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
3567959 TTTTATATCT
3567969 AGTTTCGAAACTTTATGGG
1 AGTTTCGAAACTTTATGGG
* *
3567988 AGTTTTGAAACTTTCTGGG
1 AGTTTCGAAACTTTATGGG
3568007 AGTTTCGAAACT
1 AGTTTCGAAACT
3568019 ATGACCCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (19 bp):
AGTTTCGAAACTTTATGGG
Found at i:3569534 original size:20 final size:20
Alignment explanation
Indices: 3569497--3569548 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3569487 ACTGTGCCAG
3569497 AAGTATCGATAC-CGACCCTT
1 AAGTATCGATACTCGACCC-T
*
3569517 GAGTATCGATACTC-ACCCT
1 AAGTATCGATACTCGACCCT
*
3569536 AAATATCGATACT
1 AAGTATCGATACT
3569549 AAAAATAGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.43
20 15 0.54
21 1 0.04
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (20 bp):
AAGTATCGATACTCGACCCT
Found at i:3571844 original size:52 final size:52
Alignment explanation
Indices: 3571761--3571859 Score: 171
Period size: 52 Copynumber: 1.9 Consensus size: 52
3571751 AATATCCACT
* *
3571761 TGTCTTCTTTACCGATATATTTATGAGCCATACCTAACAAATCTCCATCCCC
1 TGTCCTCTTTACCGATATATTTATAAGCCATACCTAACAAATCTCCATCCCC
*
3571813 TGTCCTCTTTACCGGTATATTTATAAGCCATACCTAACAAATCTCCA
1 TGTCCTCTTTACCGATATATTTATAAGCCATACCTAACAAATCTCCA
3571860 CCTTGGCGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.28, C:0.29, G:0.08, T:0.34
Consensus pattern (52 bp):
TGTCCTCTTTACCGATATATTTATAAGCCATACCTAACAAATCTCCATCCCC
Found at i:3575718 original size:14 final size:14
Alignment explanation
Indices: 3575701--3575743 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
3575691 TTTTATTTAA
3575701 ATTTAATTATAAAT
1 ATTTAATTATAAAT
3575715 ATTT-ATT-T-AA-
1 ATTTAATTATAAAT
3575725 ATTTAATTATAAAT
1 ATTTAATTATAAAT
3575739 ATTTA
1 ATTTA
3575744 TAATATTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 4 0.16
11 5 0.20
12 2 0.08
13 5 0.20
14 9 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTAATTATAAAT
Found at i:3575719 original size:24 final size:24
Alignment explanation
Indices: 3575692--3575744 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
3575682 TTTTTGAGTT
3575692 TTTATTTAAATTTAATTATAAATA
1 TTTATTTAAATTTAATTATAAATA
3575716 TTTATTTAAATTTAATTATAAATA
1 TTTATTTAAATTTAATTATAAATA
3575740 TTTAT
1 TTTAT
3575745 AATATTATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTATTTAAATTTAATTATAAATA
Found at i:3581346 original size:2 final size:2
Alignment explanation
Indices: 3581339--3581382 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3581329 ATCCTAACCC
3581339 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3581381 TA
1 TA
3581383 AAGTATACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3583398 original size:20 final size:20
Alignment explanation
Indices: 3583381--3583419 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3583371 TTAGTACTGT
*
3583381 ATGAACAGTATCGATACTAG
1 ATGAACAATATCGATACTAG
3583401 ATGAACAATATCGATACTA
1 ATGAACAATATCGATACTA
3583420 AGTGCACAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (20 bp):
ATGAACAATATCGATACTAG
Found at i:3585555 original size:7 final size:7
Alignment explanation
Indices: 3585545--3585693 Score: 59
Period size: 7 Copynumber: 21.7 Consensus size: 7
3585535 ACATATAGTA
3585545 TATATAG
1 TATATAG
3585552 TATATAG
1 TATATAG
**
3585559 TATATTT
1 TATATAG
3585566 TATATAG
1 TATATAG
3585573 TATATTACGG
1 TATA-TA--G
* *
3585583 TACATTAT
1 TATA-TAG
*
3585591 TATATGG
1 TATATAG
3585598 TATAT--
1 TATATAG
*
3585603 TATATAT
1 TATATAG
3585610 TATATTA-
1 TATA-TAG
3585617 TATTATA-
1 TA-TATAG
3585624 TATATA-
1 TATATAG
*
3585630 TATATAT
1 TATATAG
3585637 TATATACG
1 TATATA-G
*
3585645 -ATATAT
1 TATATAG
*
3585651 TATATTAT
1 TATA-TAG
3585659 TAT-TA-
1 TATATAG
3585664 TATATAG
1 TATATAG
3585671 TATAT--
1 TATATAG
3585676 TATATAG
1 TATATAG
*
3585683 TACATA-
1 TATATAG
3585689 TATAT
1 TATAT
3585694 TATAACATAT
Statistics
Matches: 114, Mismatches: 13, Indels: 31
0.72 0.08 0.20
Matches are distributed among these distances:
5 13 0.11
6 18 0.16
7 61 0.54
8 15 0.13
10 7 0.06
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (7 bp):
TATATAG
Found at i:3585616 original size:27 final size:24
Alignment explanation
Indices: 3585586--3585783 Score: 146
Period size: 23 Copynumber: 8.2 Consensus size: 24
3585576 ATTACGGTAC
3585586 ATTATTATATGGTATATTATATATTAT
1 ATTA-TATAT-GTATA-TATATATTAT
*
3585613 ATTATAT-TATATATATATA-TAT
1 ATTATATATGTATATATATATTAT
*
3585635 ATTATATACG-ATATATTATATTATT
1 ATTATATATGTATATA-TATATTA-T
* *
3585660 ATTATATATAGTATATTATATAGTAC
1 ATTATATAT-GTATA-TATATATTAT
*
3585686 A-TATATAT-TATAACATATATTAT
1 ATTATATATGTAT-ATATATATTAT
* *
3585709 ATATATAAAATCTATAT-TATA-TAT
1 AT-TAT-ATATGTATATATATATTAT
3585733 ATTATATATGTATAT-TATATTAT
1 ATTATATATGTATATATATATTAT
* *
3585756 ATTATAT-T-TATTTATTTATTATT
1 ATTATATATGTATATATATATTA-T
3585779 ATTAT
1 ATTAT
3585784 TTTGGTTTTC
Statistics
Matches: 141, Mismatches: 15, Indels: 34
0.74 0.08 0.18
Matches are distributed among these distances:
21 4 0.03
22 34 0.24
23 40 0.28
24 12 0.09
25 24 0.17
26 9 0.06
27 16 0.11
28 2 0.01
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (24 bp):
ATTATATATGTATATATATATTAT
Found at i:3585625 original size:2 final size:2
Alignment explanation
Indices: 3585598--3585762 Score: 116
Period size: 2 Copynumber: 90.5 Consensus size: 2
3585588 TATTATATGG
3585598 TA TA T- TA TA TA T- TA TA T- TA TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3585636 T- TA TA TA CGA TA TA T- TA TA T- TA T- TA T- TA TA TA TA GTA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
3585675 T- TA TA TA GTA CA TA TA TA T- TA TA -A CA TA TA T- TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
3585714 TA -A AA TC TA TA T- TA TA TA TA T- TA TA TA TG TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3585752 T- TA TA T- TA TA T
1 TA TA TA TA TA TA T
3585763 TTATTTATTT
Statistics
Matches: 131, Mismatches: 10, Indels: 44
0.71 0.05 0.24
Matches are distributed among these distances:
1 19 0.15
2 107 0.82
3 5 0.04
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3585773 original size:8 final size:9
Alignment explanation
Indices: 3585745--3585777 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
3585735 TATATATGTA
3585745 TATTATATT
1 TATTATATT
3585754 ATATTATATT
1 -TATTATATT
3585764 TATT-TATT
1 TATTATATT
3585772 TATTAT
1 TATTAT
3585778 TATTATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 5 0.23
10 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTATATT
Found at i:3585778 original size:25 final size:24
Alignment explanation
Indices: 3585586--3585783 Score: 123
Period size: 25 Copynumber: 8.2 Consensus size: 24
3585576 ATTACGGTAC
3585586 ATTATTATATGGTATATTATATATTAT
1 ATTA-TATAT-GTATATTAT-TATTAT
*
3585613 ATTATAT-TATATA-TA-TATATAT
1 ATTATATATGTATATTATTAT-TAT
*
3585635 ATTATATACGATATATTA-TATTATT
1 ATTATATATG-TATATTATTATTA-T
* *
3585660 ATTATATATAGTATATTATATAGTAC
1 ATTATATAT-GTATATTAT-TATTAT
**
3585686 A-TATATAT-TATAACATATATTAT
1 ATTATATATGTATATTAT-TATTAT
* *
3585709 ATATATAAAATCTATATTA-TA-TAT
1 AT-TAT-ATATGTATATTATTATTAT
3585733 ATTATATATGTATATTA-TATTAT
1 ATTATATATGTATATTATTATTAT
3585756 ATTATAT-T-TAT-TTATTTATTATT
1 ATTATATATGTATATTA-TTATTA-T
3585779 ATTAT
1 ATTAT
3585784 TTTGGTTTTC
Statistics
Matches: 140, Mismatches: 15, Indels: 36
0.73 0.08 0.19
Matches are distributed among these distances:
20 3 0.02
21 6 0.04
22 28 0.20
23 33 0.24
24 15 0.11
25 34 0.24
26 8 0.06
27 13 0.09
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (24 bp):
ATTATATATGTATATTATTATTAT
Found at i:3587918 original size:6 final size:6
Alignment explanation
Indices: 3587880--3587925 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
3587870 TGGGGTAGGA
* * *
3587880 ATTTTT A-TTTT ATTTTC ATTATT ATTTTG ATTTTT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
3587926 ACTAATAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (6 bp):
ATTTTT
Found at i:3594992 original size:14 final size:14
Alignment explanation
Indices: 3594973--3595006 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3594963 CACATTTAGT
3594973 ATATATAGTATATA
1 ATATATAGTATATA
*
3594987 ATATATATTATATA
1 ATATATAGTATATA
*
3595001 GTATAT
1 ATATAT
3595007 TATGGTACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (14 bp):
ATATATAGTATATA
Found at i:3595248 original size:21 final size:21
Alignment explanation
Indices: 3595133--3595248 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
3595123 GCGAAATAAA
**
3595133 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
3595153 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
3595173 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
3595194 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
3595214 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
3595236 AATCGCAACGCGA
1 AATCGCAACGCGA
3595249 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:3595278 original size:20 final size:20
Alignment explanation
Indices: 3595255--3595428 Score: 120
Period size: 20 Copynumber: 8.7 Consensus size: 20
3595245 GCGAATATGA
3595255 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
3595275 AAATCGTAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
3595295 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
* *
3595315 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
3595335 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
3595355 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
3595375 AAATCACAACGAC--AATACGT
1 AAATCGCAACG-CGTAA-CCAT
* *
3595395 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTAACCAT
3595416 AAATCGCAACGCG
1 AAATCGCAACGCG
3595429 ATTTTAAAGC
Statistics
Matches: 132, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.01
20 114 0.86
21 16 0.12
22 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:3595318 original size:40 final size:40
Alignment explanation
Indices: 3595274--3595426 Score: 216
Period size: 40 Copynumber: 3.8 Consensus size: 40
3595264 CGCGAACACA
* *
3595274 TAAATCGTAACGCGTATCCGTAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGAGTATCCG
* *
3595314 TAAATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGAGTATCCG
* * ** *
3595354 TATATCGCAACGCGTATCCGTAAATCACAACGACAATACG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGAGTATCCG
3595394 TAAAATCGCAACGCGTATCCGTAAATCGCAACG
1 T-AAATCGCAACGCGTATCCGTAAATCGCAACG
3595427 CGATTTTAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 71 0.71
41 29 0.29
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (40 bp):
TAAATCGCAACGCGTATCCGTAAATCGCAACGAGTATCCG
Found at i:3595319 original size:60 final size:60
Alignment explanation
Indices: 3595236--3595428 Score: 237
Period size: 60 Copynumber: 3.2 Consensus size: 60
3595226 GATTTTCCAG
* ** * * *
3595236 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGTAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACGTAAATCGCAACGCGTATCCGTA
* * *
3595296 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACGTAAATCGCAACGCGTATCCGTA
* * *
3595356 TATCGCAACGCGTATCCGTAAATCACAACGAC-AATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGAACACGT-AAATCGCAACGCGTATCCGTA
3595417 AATCGCAACGCG
1 AATCGCAACGCG
3595429 ATTTTAAAGC
Statistics
Matches: 113, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
59 1 0.01
60 78 0.69
61 34 0.30
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACGTAAATCGCAACGCGTATCCGTA
Found at i:3595842 original size:32 final size:33
Alignment explanation
Indices: 3595804--3595871 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 33
3595794 TTCACTTAGA
3595804 TTTCATTTCGCGTTACGATTC-CTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
3595836 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
3595869 TTT
1 TTT
3595872 TCAAGTTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 19 0.58
33 14 0.42
ACGTcount: A:0.10, C:0.24, G:0.18, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:3596016 original size:21 final size:21
Alignment explanation
Indices: 3595949--3596021 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
3595939 TTTGCAGAAG
*
3595949 TCGCAACGAGATAAATG-AAA
1 TCGCAACGAGAAAAATGAAAA
* **
3595969 TCGCAACGTG-AAAATGACTA
1 TCGCAACGAGAAAAATGAAAA
3595989 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAAAAATGAAAA
3596011 TCGCAACGAGA
1 TCGCAACGAGA
3596022 TAATCGCAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 5 0.12
20 12 0.28
21 16 0.37
22 10 0.23
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (21 bp):
TCGCAACGAGAAAAATGAAAA
Found at i:3596028 original size:14 final size:14
Alignment explanation
Indices: 3596006--3596070 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
3595996 CGAGAAAAAT
3596006 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
3596020 GATAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
3596038 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
3596053 GAGAATCGCAACGC
1 GAAAATCGCAACGA
3596067 GAAA
1 GAAA
3596071 CCAAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.46, C:0.22, G:0.23, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:3596040 original size:33 final size:33
Alignment explanation
Indices: 3596002--3596081 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
3595992 GCAACGAGAA
*
3596002 AAATGAAAATCGCAACGAGATAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
3596035 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
3596068 AAACCAAAATCGCA
1 AAATGAAAATCGCA
3596082 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:3596099 original size:19 final size:19
Alignment explanation
Indices: 3596077--3596205 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
3596067 GAAACCAAAA
*
3596077 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3596096 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3596110 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3596129 TCGCGTTGCGA--TTC-TC
1 TCGCGTTGCGATTTTCATT
*
3596145 TCG-TTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
3596164 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
3596184 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
3596204 TC
1 TC
3596206 AACCAAAGAC
Statistics
Matches: 85, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
14 10 0.12
15 6 0.07
16 7 0.08
17 9 0.11
19 23 0.27
20 21 0.25
21 9 0.11
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3596118 original size:14 final size:14
Alignment explanation
Indices: 3596099--3596156 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 14
3596089 TTTCATTTCG
3596099 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3596113 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3596132 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3596146 CGTTTGCGATT
1 CG-TTGCGATT
3596157 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
14 12 0.33
15 8 0.22
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3596124 original size:33 final size:33
Alignment explanation
Indices: 3596082--3596205 Score: 158
Period size: 33 Copynumber: 3.5 Consensus size: 33
3596072 CAAAATCGCA
3596082 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3596115 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
3596148 TTTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 -TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
3596190 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
3596206 AACCAAAGAC
Statistics
Matches: 81, Mismatches: 1, Indels: 12
0.86 0.01 0.13
Matches are distributed among these distances:
33 33 0.41
34 12 0.15
35 2 0.02
36 6 0.07
38 1 0.01
39 3 0.04
40 3 0.04
41 12 0.15
42 9 0.11
ACGTcount: A:0.10, C:0.24, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3596202 original size:20 final size:20
Alignment explanation
Indices: 3596106--3596203 Score: 93
Period size: 20 Copynumber: 5.2 Consensus size: 20
3596096 TCGCGTTGCG
3596106 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
3596126 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
3596139 ATTCTCTCGTTTGCGATTTTC
1 ATTCTCTCG-TTGCGATTTTC
***
3596160 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
3596181 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
3596201 ATT
1 ATT
3596204 TCAACCAAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
13 3 0.05
14 4 0.07
15 5 0.08
19 9 0.15
20 22 0.36
21 10 0.16
22 8 0.13
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:3597790 original size:92 final size:91
Alignment explanation
Indices: 3597623--3597842 Score: 406
Period size: 92 Copynumber: 2.4 Consensus size: 91
3597613 TAGATTGCTT
*
3597623 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3597688 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTG-TTT-TCTTTTGGTTGAA
3597716 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3597780 TTTGTCTTTGTTTTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTCTTTTGGTTGAA
3597806 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
3597843 AATACCTGAA
Statistics
Matches: 125, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
90 19 0.15
91 33 0.26
92 67 0.54
93 6 0.05
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.45
Consensus pattern (91 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTCTTTTGGTTGAA
Found at i:3597976 original size:14 final size:14
Alignment explanation
Indices: 3597957--3598013 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3597947 CGAAACTTAA
3597957 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3597971 AATCGCAACACGAAATGAA
1 AATCGC-A-ACG--A-GAG
*
3597990 AATCGCAACGACAG
1 AATCGCAACGAGAG
3598004 AATCGCAACG
1 AATCGCAACG
3598014 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 8 0.23
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3597996 original size:33 final size:33
Alignment explanation
Indices: 3597943--3598062 Score: 150
Period size: 33 Copynumber: 3.6 Consensus size: 33
3597933 TTACTTTCGA
* *
3597943 AACACGAAACTTAAAATCGCAACGAGAGAATCGC
1 AACACGAAA-TCAAAATCGCAACGACAGAATCGC
*
3597977 AACACGAAATGAAAATCGCAACGACAGAATCGC
1 AACACGAAATCAAAATCGCAACGACAGAATCGC
* * *
3598010 AACGCGAAACCAAAATCGCAACGACAAAATCGC
1 AACACGAAATCAAAATCGCAACGACAGAATCGC
* * *
3598043 AACGCAAAACCAAAATCGCA
1 AACACGAAATCAAAATCGCA
3598063 TTGCGATTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 70 0.89
34 9 0.11
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.08
Consensus pattern (33 bp):
AACACGAAATCAAAATCGCAACGACAGAATCGC
Found at i:3598028 original size:19 final size:19
Alignment explanation
Indices: 3598004--3598062 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
3597994 GCAACGACAG
3598004 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
3598023 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
*
3598037 AATCGCAACGCAAAACCAA
1 AATCGCAACGCGAAACCAA
3598056 AATCGCA
1 AATCGCA
3598063 TTGCGATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 11 0.32
15 1 0.03
16 1 0.03
17 2 0.06
18 1 0.03
19 18 0.53
ACGTcount: A:0.49, C:0.31, G:0.14, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:3598039 original size:14 final size:14
Alignment explanation
Indices: 3597988--3598051 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 14
3597978 ACACGAAATG
3597988 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3598002 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
3598021 AAAATCGCAACGAC
1 AAAATCGCAACGAC
3598035 AAAATCGCAACG-C
1 AAAATCGCAACGAC
3598048 AAAA
1 AAAA
3598052 CCAAAATCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
13 5 0.12
14 22 0.51
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.23
ACGTcount: A:0.50, C:0.28, G:0.16, T:0.06
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3598080 original size:19 final size:19
Alignment explanation
Indices: 3598058--3598229 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
3598048 AAAACCAAAA
*
3598058 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3598077 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3598091 TCTCGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
* *
3598109 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
3598125 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3598142 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
3598161 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
3598180 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
3598199 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3598219 TCGTGTTGCGA
1 TCGCGTTGCGA
3598230 AAGTAAACTA
Statistics
Matches: 126, Mismatches: 17, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
14 17 0.13
15 3 0.02
16 5 0.04
17 8 0.06
18 9 0.07
19 72 0.57
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3598099 original size:14 final size:14
Alignment explanation
Indices: 3598080--3598135 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
3598070 TTTCATTTCG
3598080 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3598094 CGTTGCGATTTCATTT
1 CGTTGCGA-TTC-TCT
*
3598110 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
3598126 CGTTGCGATT
1 CGTTGCGATT
3598136 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 16 0.44
15 3 0.08
16 8 0.22
17 3 0.08
18 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3598144 original size:33 final size:33
Alignment explanation
Indices: 3598063--3598154 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
3598053 CAAAATCGCA
3598063 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
3598096 TTGCGA-TTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3598128 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
3598155 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3598741 original size:20 final size:20
Alignment explanation
Indices: 3598683--3598742 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
3598673 CTCGAGAGTC
*
3598683 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCATTCAAGAGG
** * *
3598703 CCACTGTCATCATTGAAGAGG
1 CC-CTCCCACCATTCAAGAGG
*
3598724 TCCTCCCACCATTCAAGAG
1 CCCTCCCACCATTCAAGAG
3598743 CCCGATTCAC
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.25, C:0.37, G:0.18, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCATTCAAGAGG
Found at i:3600157 original size:13 final size:14
Alignment explanation
Indices: 3600141--3600175 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3600131 ATTGTTTAAT
3600141 TGATTTGT-AAAGA
1 TGATTTGTAAAAGA
*
3600154 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3600168 TGATTTGT
1 TGATTTGT
3600176 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:3600290 original size:19 final size:19
Alignment explanation
Indices: 3600266--3600352 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
3600256 GCATTATGTT
3600266 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
3600285 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
3600302 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
3600318 GAAATG-AAATCGCAATGC
1 GAAATGAAAATCGCAATGC
3600336 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
3600353 CGAGAGAATC
Statistics
Matches: 59, Mismatches: 2, Indels: 13
0.80 0.03 0.18
Matches are distributed among these distances:
14 10 0.17
15 1 0.02
16 2 0.03
17 2 0.03
18 12 0.20
19 23 0.39
20 9 0.15
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:3600344 original size:52 final size:52
Alignment explanation
Indices: 3600266--3600371 Score: 196
Period size: 52 Copynumber: 2.0 Consensus size: 52
3600256 GCATTATGTT
3600266 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
3600318 GAAATG-AAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
3600370 GA
1 GA
3600372 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 12 0.23
52 41 0.77
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (52 bp):
GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:3600389 original size:19 final size:19
Alignment explanation
Indices: 3600361--3600621 Score: 285
Period size: 19 Copynumber: 14.7 Consensus size: 19
3600351 AACGAGAGAA
*
3600361 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3600380 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
3600399 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
3600416 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3600433 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
3600452 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
3600468 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
3600484 TCGCATTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
*
3600503 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
3600520 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3600537 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
3600556 TCGCACTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3600575 TCCGCATTGCGATTTTC--T
1 T-CGCATTGCGATTTTCATT
*
3600593 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
3600609 TCGCATTGCGATT
1 TCGCATTGCGATT
3600622 CTCTTGTTGC
Statistics
Matches: 206, Mismatches: 13, Indels: 46
0.78 0.05 0.17
Matches are distributed among these distances:
14 28 0.14
15 3 0.01
16 21 0.10
17 16 0.08
18 13 0.06
19 92 0.45
20 33 0.16
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:3600448 original size:72 final size:69
Alignment explanation
Indices: 3600362--3600654 Score: 260
Period size: 72 Copynumber: 4.2 Consensus size: 69
3600352 ACGAGAGAAT
*
3600362 CGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
1 CGCATTGCGATTTTC-TTTCG--TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
3600427 TTCATTT-
62 TTCATTTC
* * * * * *
3600434 CGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG-ATTTC-ATT-TCGCATTGCAAT
1 CGCATTGCGATTTTC-TTTCG--TTGCGATT-T-TCATTTCGCATTGCGATTCTCTCGTTGCGAT
3600496 TTTCATTTC
61 TTTCATTTC
* * *
3600505 CGCATTGCGA--TTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCACTGCGAT
1 CGCATTGCGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGAT
3600568 TTTCATTTC
61 TTTCATTTC
* * * *
3600577 CGCATTGCGATTTTC-TT-GTTGGGATTTTCATTTCGCATTGCGATTCTCTTGTTGCGATTGTAA
1 CGCATTGCGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
3600640 TTTC
66 TTTC
**
3600644 CGTGTTGCGAT
1 CGCATTGCGAT
3600655 AGTCAAATGC
Statistics
Matches: 183, Mismatches: 25, Indels: 31
0.77 0.10 0.13
Matches are distributed among these distances:
64 6 0.03
65 5 0.03
66 9 0.05
67 22 0.12
68 6 0.03
69 6 0.03
70 22 0.12
71 13 0.07
72 83 0.45
73 4 0.02
74 7 0.04
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (69 bp):
CGCATTGCGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
TTTC
Found at i:3600484 original size:104 final size:103
Alignment explanation
Indices: 3600367--3600635 Score: 380
Period size: 104 Copynumber: 2.6 Consensus size: 103
3600357 AGAATCGCAA
3600367 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGA-TTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
3600432 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC-GT
65 TTCGCATTGCGATTTTCATTTCGCACTGCGATT-T-TCAGT
*
3600472 TGCGATTTCATTTCGCATTGCAATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TGCGATTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
3600537 TCGCATTGCGATTTTCATTTCGCACTGCGATTTTCATT
66 TCGCATTGCGATTTTCATTTCGCACTGCGATTTTCAGT
* * *** * *
3600575 TCCGCATTGCGATTTTCTTGTTGGGATTTTCATTT-CGCATTGCGATTCTCTTGTTGCGATT
1 TGCG-ATTTC-A-TTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
3600636 GTAATTTCCG
Statistics
Matches: 149, Mismatches: 11, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
102 2 0.01
103 5 0.03
104 94 0.63
105 31 0.21
106 17 0.11
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (103 bp):
TGCGATTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
TCGCATTGCGATTTTCATTTCGCACTGCGATTTTCAGT
Found at i:3603125 original size:24 final size:24
Alignment explanation
Indices: 3603091--3603137 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3603081 CTGAAACATC
3603091 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3603115 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3603138 GAACAAATTT
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:3603859 original size:20 final size:19
Alignment explanation
Indices: 3603818--3604003 Score: 178
Period size: 20 Copynumber: 9.5 Consensus size: 19
3603808 AAATTTCAGT
* *
3603818 GTTGTGATTTACAGAT-TC
1 GTTGCGATTTACGGATATC
3603836 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGA-TATC
* *
3603856 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGA-TATC
3603876 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGA-TATC
*
3603896 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATA-TC
* *
3603916 GTTGCGATATACGAATA-C
1 GTTGCGATTTACGGATATC
*
3603934 GCATTGCGATTTACGGATAGC
1 G--TTGCGATTTACGGATATC
* *
3603955 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATA-TC
* *
3603975 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATA-TC
3603995 GTTGCGATT
1 GTTGCGATT
3604004 ATGTGTTCGC
Statistics
Matches: 144, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.10
19 18 0.12
20 109 0.76
21 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (19 bp):
GTTGCGATTTACGGATATC
Found at i:3603886 original size:40 final size:40
Alignment explanation
Indices: 3603818--3604042 Score: 196
Period size: 40 Copynumber: 5.7 Consensus size: 40
3603808 AAATTTCAGT
*
3603818 GTTGTGATTTACAGATT--CGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
*
3603856 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
* * * *
3603896 GTTGCGATTTACGGATACGCGTTGCGATATAC-GAATA-C
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
* * * *
3603934 GCATTGCGATTTACGGA-TAGCGTTGCTATTTACGGA-TACAC
1 G--TTGCGATTTACAGATTCGCGTTGCGATTTACGGATTA-TC
* * * * **
3603975 GTTGCGGTTTACGGATACGCGTTGCGA-TTATGTG-TTCGC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACG-GATTATC
* *
3604014 GTTGCGATTTTCATATTCGCGTTGCGATT
1 GTTGCGATTTACAGATTCGCGTTGCGATT
3604043 CTTGAAAATC
Statistics
Matches: 154, Mismatches: 22, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
38 18 0.12
39 58 0.38
40 76 0.49
41 2 0.01
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (40 bp):
GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
Found at i:3603979 original size:59 final size:60
Alignment explanation
Indices: 3603823--3604003 Score: 192
Period size: 59 Copynumber: 3.1 Consensus size: 60
3603813 TCAGTGTTGT
* * * * * *
3603823 GATTTACAGATT--CGTTGCGATTTACGGATTA-TCGTTGCGATTTAC-AGATTCTCGTTGC
1 GATTTACGGATTAGCGTTGCGATTTACGGA-TACACGTTGCGATATACGA-ATACGCATTGC
* *
3603881 GATTTACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGAATACGCATTGC
1 GATTTACGGATTAGCGTTGCGATTTACGGATACACGTTGCGATATACGAATACGCATTGC
* * * * *
3603941 GATTTACGGA-TAGCGTTGCTATTTACGGATACACGTTGCGGTTTACGGATACGCGTTGC
1 GATTTACGGATTAGCGTTGCGATTTACGGATACACGTTGCGATATACGAATACGCATTGC
3604000 GATT
1 GATT
3604004 ATGTGTTCGC
Statistics
Matches: 106, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
58 11 0.10
59 48 0.45
60 46 0.43
61 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (60 bp):
GATTTACGGATTAGCGTTGCGATTTACGGATACACGTTGCGATATACGAATACGCATTGC
Found at i:3604016 original size:19 final size:20
Alignment explanation
Indices: 3603992--3604042 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
3603982 TTTACGGATA
* *
3603992 CGCGTTGCGATTAT-GTGTT
1 CGCGTTGCGATTATCATATT
*
3604011 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTATCATATT
3604031 CGCGTTGCGATT
1 CGCGTTGCGATT
3604043 CTTGAAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.12, C:0.20, G:0.27, T:0.41
Consensus pattern (20 bp):
CGCGTTGCGATTATCATATT
Found at i:3604017 original size:39 final size:38
Alignment explanation
Indices: 3603855--3604042 Score: 155
Period size: 39 Copynumber: 4.8 Consensus size: 38
3603845 TACGGATTAT
* * * *
3603855 CGTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTACGG--TACG
*
3603895 CGTTGCGATTTACGGATACGCGTTGCGATATACGAATACG
1 CGTTGCGATTTACGGATACGCGTTGCGAT-TACG-GTACG
* * *
3603935 CATTGCGATTTACGGATA-GCGTTGCTATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTACGG-TACG
* * *
3603974 CGTTGCGGTTTACGGATACGCGTTGCGATTATGTGTTCG
1 CGTTGCGATTTACGGATACGCGTTGCGATTACG-GTACG
* ** *
3604013 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACGGATACGCGTTGCGATT
3604043 CTTGAAAATC
Statistics
Matches: 121, Mismatches: 20, Indels: 15
0.78 0.13 0.10
Matches are distributed among these distances:
39 65 0.54
40 56 0.46
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (38 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTACGGTACG
Found at i:3604095 original size:21 final size:20
Alignment explanation
Indices: 3604010--3604107 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
3604000 GATTATGTGT
* *
3604010 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
3604030 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
3604051 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
3604072 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
3604093 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
3604108 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:3604103 original size:42 final size:43
Alignment explanation
Indices: 3604010--3604108 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
3604000 GATTATGTGT
* *
3604010 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
3604051 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
3604093 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
3604109 GAAACTGATA
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:3604266 original size:7 final size:7
Alignment explanation
Indices: 3604254--3604487 Score: 162
Period size: 7 Copynumber: 32.1 Consensus size: 7
3604244 TTCTCTAACG
3604254 TATATTA
1 TATATTA
3604261 TATATTA
1 TATATTA
3604268 TATA-TA
1 TATATTA
3604274 TTATATTA
1 -TATATTA
3604282 TATAGTATA
1 TATA-T-TA
3604291 CTATATTA
1 -TATATTA
3604299 TATATTA
1 TATATTA
*
3604306 TACGA-TA
1 TA-TATTA
3604313 TAGTA-TA
1 TA-TATTA
3604320 T-TATTA
1 TATATTA
*
3604326 TATATAA
1 TATATTA
3604333 TATATTA
1 TATATTA
3604340 TATATTA
1 TATATTA
*
3604347 TATAGTA
1 TATATTA
*
3604354 TATATAA
1 TATATTA
*
3604361 CATATTA
1 TATATTA
3604368 TATAGTATA
1 TATA-T-TA
3604377 TATTATTA
1 TA-TATTA
3604385 TATATTA
1 TATATTA
3604392 TAT-TATA
1 TATAT-TA
3604399 TATATTA
1 TATATTA
3604406 GTATTATTA
1 -TA-TATTA
3604415 TAAATATTA
1 T--ATATTA
3604424 TATTATT-
1 TA-TATTA
*
3604431 T-TAGTA
1 TATATTA
3604437 TATATTA
1 TATATTA
*
3604444 TTTATTA
1 TATATTA
*
3604451 TATTAATA
1 TA-TATTA
3604459 TTATATTA
1 -TATATTA
3604467 TATTATTA
1 TA-TATTA
*
3604475 T-TAATA
1 TATATTA
3604481 T-TATTA
1 TATATTA
3604487 T
1 T
3604488 TTTTTATTTT
Statistics
Matches: 185, Mismatches: 19, Indels: 47
0.74 0.08 0.19
Matches are distributed among these distances:
5 5 0.03
6 17 0.09
7 102 0.55
8 33 0.18
9 21 0.11
10 7 0.04
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (7 bp):
TATATTA
Found at i:3604269 original size:5 final size:5
Alignment explanation
Indices: 3604261--3604484 Score: 124
Period size: 5 Copynumber: 42.6 Consensus size: 5
3604251 ACGTATATTA
* *
3604261 TATAT TATA- TATAT TATAT TATAT AGTATAC TATATT ATATAT TATACGA
1 TATAT TATAT TATAT TATAT TATAT --TATAT TATA-T -TATAT TATA--T
* * *
3604311 TATAG TATAT TATTAT ATATAA TATAT TATA- TAT-T ATATAG TATA-
1 TATAT TATAT TA-TAT -TATAT TATAT TATAT TATAT -TATAT TATAT
* *
3604356 TATAA CATAT TATA- TAGTA- TATAT TAT-T ATATAT TATAT TATA- TATAT
1 TATAT TATAT TATAT TA-TAT TATAT TATAT -TATAT TATAT TATAT TATAT
* *
3604404 TAGTAT TATTAT AAATAT TATAT TATTT TAGTA- TATAT TATTTAT TATAT
1 TA-TAT TA-TAT -TATAT TATAT TATAT TA-TAT TATAT TA--TAT TATAT
3604454 TAATAT TATAT TATAT TATTAT TAATAT TAT
1 T-ATAT TATAT TATAT TA-TAT T-ATAT TAT
3604485 TATTTTTTAT
Statistics
Matches: 176, Mismatches: 16, Indels: 54
0.72 0.07 0.22
Matches are distributed among these distances:
4 22 0.12
5 101 0.57
6 32 0.18
7 21 0.12
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (5 bp):
TATAT
Found at i:3604283 original size:12 final size:12
Alignment explanation
Indices: 3604254--3604475 Score: 151
Period size: 12 Copynumber: 18.2 Consensus size: 12
3604244 TTCTCTAACG
3604254 TATATTATATAT
1 TATATTATATAT
3604266 TATATATATTATAT
1 TATAT-TA-TATAT
*
3604280 TATA-TAGTATAC
1 TATATTA-TATAT
3604292 TATATTATATAT
1 TATATTATATAT
** *
3604304 TATACGATATAG
1 TATATTATATAT
3604316 TATATTAT-TA-
1 TATATTATATAT
*
3604326 TATATAATATATT
1 TATATTATATA-T
3604339 ATATATTATATAGT
1 -TATATTATATA-T
* *
3604353 ATATATAACATAT
1 -TATATTATATAT
3604366 TATA-TAGTATA-
1 TATATTA-TATAT
3604377 TATTATTATATAT
1 TA-TATTATATAT
3604390 TATATTATATA-
1 TATATTATATAT
*
3604401 TATTAGTAT-TAT
1 TA-TATTATATAT
3604413 TATA--A-ATAT
1 TATATTATATAT
*
3604422 TATATTATTTTAGT
1 TATATTA-TATA-T
*
3604436 ATATATTATTTAT
1 -TATATTATATAT
3604449 TATATTA-ATAT
1 TATATTATATAT
3604460 TATATTATATTAT
1 TATATTATA-TAT
3604473 TAT
1 TAT
3604476 TAATATTATT
Statistics
Matches: 170, Mismatches: 18, Indels: 43
0.74 0.08 0.19
Matches are distributed among these distances:
9 8 0.05
10 7 0.04
11 24 0.14
12 71 0.42
13 18 0.11
14 35 0.21
15 7 0.04
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (12 bp):
TATATTATATAT
Found at i:3604385 original size:3 final size:3
Alignment explanation
Indices: 3604363--3604488 Score: 86
Period size: 3 Copynumber: 42.3 Consensus size: 3
3604353 ATATATAACA
* *
3604363 TAT TAT ATAG TAT ATAT TAT TAT ATAT TA- TAT TA- TAT ATAT TAG TAT
1 TAT TAT -TAT TAT -TAT TAT TAT -TAT TAT TAT TAT TAT -TAT TAT TAT
* * *
3604410 TAT TAT AAA TAT TA- TAT TAT T-T TAG TAT ATAT TATT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT TAT
* *
3604454 TAA TAT TA- TAT TA- TAT TAT TAT TAA TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3604489 TTTTATTTTC
Statistics
Matches: 96, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
2 14 0.15
3 65 0.68
4 17 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:3604494 original size:27 final size:28
Alignment explanation
Indices: 3604261--3604484 Score: 127
Period size: 27 Copynumber: 8.1 Consensus size: 28
3604251 ACGTATATTA
*
3604261 TATATTATA-TA-TATTA-TATTATATAG
1 TATATTATATTAGTATTATTATTA-ATAT
* **
3604287 TATACTATATTA-TA-TATTA-TACGA-
1 TATATTATATTAGTATTATTATTAATAT
* * * *
3604311 TATAGTATATTATTATATATAATATATTA-
1 TATATTATATTAGTAT-TATTAT-TAATAT
*
3604340 TATATTATA-TAGTA-TA-TATAACATAT
1 TATATTATATTAGTATTATTATTA-ATAT
*
3604366 TATA-TAGTATATATTATTATATATT-ATAT
1 TATATTA-TAT-TAGTATTAT-TATTAATAT
*
3604395 TATA-TATATTAGTATTATTATAAATAT
1 TATATTATATTAGTATTATTATTAATAT
*
3604422 TATATTATTTTAGTATATATTATTTATTATAT
1 TATATTATATTAGTAT-TATTA-TTA--ATAT
3604454 TAATATTATATTA-TATTATTATTAATAT
1 T-ATATTATATTAGTATTATTATTAATAT
3604482 TAT
1 TAT
3604485 TATTTTTTAT
Statistics
Matches: 157, Mismatches: 19, Indels: 43
0.72 0.09 0.20
Matches are distributed among these distances:
24 12 0.08
25 9 0.06
26 23 0.15
27 28 0.18
28 26 0.17
29 28 0.18
30 5 0.03
31 8 0.05
32 8 0.05
33 10 0.06
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (28 bp):
TATATTATATTAGTATTATTATTAATAT
Found at i:3608757 original size:96 final size:95
Alignment explanation
Indices: 3608562--3608793 Score: 274
Period size: 96 Copynumber: 2.4 Consensus size: 95
3608552 AAACTTATAC
*
3608562 GCCTTCAATGACTCCCGTTCAGCTCAATACAACCTGAAACTCAAATGCAACAAATACTGCAAACA
1 GCCTTCAATGACTCCCATTCAGCTCAATACAACCTGAAACTCAAATGCAACAAATACTGCAAACA
*
3608627 TACTGAAATATTTTCCCAGGTAAACACTTGT
66 TACTGAAATATTTTCACA-GTAAACACTTGT
* * *
3608658 GCCTTCAATTACTCCCCTTCAGCTCAATACAACCTGAAAC-CAAAATGCAACAAATACTGCAAAT
1 GCCTTCAATGACTCCCATTCAGCTCAATACAACCTGAAACTC-AAATGCAACAAATACTGCAAAC
* * * * *
3608722 ATAGTGAGATCTTTTTTACA-TATA-ACTCTGTT
65 ATACTGAAAT-ATTTTCACAGTAAACACT-TG-T
* * *
3608754 GCCTTCAATGA-TTCCATTCAACTCAATACAACCTAAAACT
1 GCCTTCAATGACTCCCATTCAGCTCAATACAACCTGAAACT
3608794 AGAATGCTGT
Statistics
Matches: 117, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
94 3 0.03
95 30 0.26
96 78 0.67
97 6 0.05
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.28
Consensus pattern (95 bp):
GCCTTCAATGACTCCCATTCAGCTCAATACAACCTGAAACTCAAATGCAACAAATACTGCAAACA
TACTGAAATATTTTCACAGTAAACACTTGT
Found at i:3609889 original size:36 final size:36
Alignment explanation
Indices: 3609842--3609913 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
3609832 GGCTCAATGT
3609842 CAATCCAGCTCAATCCATCAACTATAGTTGTTCATG
1 CAATCCAGCTCAATCCATCAACTATAGTTGTTCATG
3609878 CAATCCAGCTCAATCCATCAACTATAGTTGTTCATG
1 CAATCCAGCTCAATCCATCAACTATAGTTGTTCATG
3609914 GTTCAGTGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (36 bp):
CAATCCAGCTCAATCCATCAACTATAGTTGTTCATG
Found at i:3610417 original size:29 final size:29
Alignment explanation
Indices: 3610375--3610444 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
3610365 ATGTCGGGGT
*
3610375 AGGTCGCCATGCACGACCAACGACCTACA
1 AGGTCGCCATGCACGACCAACAACCTACA
* ** *
3610404 AGGTCGCCATGCACGCCCCGCAACCTATA
1 AGGTCGCCATGCACGACCAACAACCTACA
3610433 A-GTCGCCATGCA
1 AGGTCGCCATGCA
3610445 GTCCTGGCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 11 0.31
29 25 0.69
ACGTcount: A:0.27, C:0.39, G:0.21, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGACCAACAACCTACA
Found at i:3610728 original size:19 final size:19
Alignment explanation
Indices: 3610686--3610729 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3610676 GAATCATAAC
*
3610686 AGAAAGAAAGGGAGAAGAG
1 AGAAAGAAAGGAAGAAGAG
*
3610705 TGAAAGAAAAGGAAGAAGA-
1 AGAAAG-AAAGGAAGAAGAG
3610724 AGAAAG
1 AGAAAG
3610730 GGAGATAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.02
Consensus pattern (19 bp):
AGAAAGAAAGGAAGAAGAG
Found at i:3610870 original size:21 final size:21
Alignment explanation
Indices: 3610845--3610884 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3610835 GTTAATTAGT
3610845 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
3610866 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
3610885 CATACATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:3610961 original size:43 final size:42
Alignment explanation
Indices: 3610900--3611000 Score: 107
Period size: 43 Copynumber: 2.4 Consensus size: 42
3610890 ATAAATATAA
* *
3610900 AATTATTTAATTAGTTTGTT-T-GATAGTTATATATTAAAAAAAT
1 AATTAATTAATTTGTTTGTTATCGATAGTTATATA-T--AAAAAT
*
3610943 AATTAATTAATTTGTTTGTTAGTCGTTAGTTATATATAAAAAT
1 AATTAATTAATTTGTTTGTTA-TCGATAGTTATATATAAAAAT
* *
3610986 ATTTAATTAGTTTGT
1 AATTAATTAATTTGT
3611001 AGTTAGTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
43 37 0.74
45 2 0.04
46 11 0.22
ACGTcount: A:0.38, C:0.01, G:0.11, T:0.50
Consensus pattern (42 bp):
AATTAATTAATTTGTTTGTTATCGATAGTTATATATAAAAAT
Found at i:3611113 original size:36 final size:37
Alignment explanation
Indices: 3611039--3611118 Score: 103
Period size: 39 Copynumber: 2.2 Consensus size: 37
3611029 TTTGTTGAAT
3611039 TTATATTATATAAAAAATTAGTTAATTAGTAGTGTAAG
1 TTATATTATATAAAAAATTAGTTAATTAGTA-TGTAAG
*
3611077 TTATATTATAATTAAAAAA-TAGTTTATTAGT-T-TAAG
1 TTATATTAT-A-TAAAAAATTAGTTAATTAGTATGTAAG
3611113 TTATAT
1 TTATAT
3611119 AAAAGAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
36 10 0.26
37 1 0.03
38 9 0.23
39 12 0.31
40 7 0.18
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (37 bp):
TTATATTATATAAAAAATTAGTTAATTAGTATGTAAG
Found at i:3613785 original size:24 final size:25
Alignment explanation
Indices: 3613679--3613787 Score: 93
Period size: 24 Copynumber: 4.5 Consensus size: 25
3613669 AAACGGAGAT
* *
3613679 ATCATAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
3613703 ATCAGATATCATAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
3613727 ATCAGAAATCAGAATAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
3613752 -TAATG-TATCAGAACATAATTCAAG
1 ATCA-GAAATCAGAACAGAATTCAAG
3613776 -TCAGAAATCAGA
1 ATCAGAAATCAGA
3613788 TAAAATATTT
Statistics
Matches: 68, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
23 3 0.04
24 60 0.88
25 5 0.07
ACGTcount: A:0.50, C:0.16, G:0.13, T:0.22
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:3618547 original size:24 final size:24
Alignment explanation
Indices: 3618520--3618607 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 24
3618510 GATATCATAA
* *
3618520 ATCAAAACAGAATTCAGATTAGAT
1 ATCATAACAGAATTCAGATAAGAT
* * * *
3618544 ATCATAACATAATCCAGATCAGAA
1 ATCATAACAGAATTCAGATAAGAT
* *
3618568 ATCAGAACAGAATTCAGGTAATG-T
1 ATCATAACAGAATTCAGATAA-GAT
3618592 ATCATAACAGAATTCA
1 ATCATAACAGAATTCA
3618608 AGTCAGAAAT
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
24 50 0.98
25 1 0.02
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCATAACAGAATTCAGATAAGAT
Found at i:3618595 original size:48 final size:47
Alignment explanation
Indices: 3618513--3618621 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 47
3618503 AAATGGAGAT
* * * *
3618513 ATCATAAATCAAAACAGAATTCAGATTAGATATCATAACATAATCCA
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCATAACAGAATCCA
* *
3618560 GATCAGAAATCAGAACAGAATTCAGGTAATG-TATCATAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGATAA-GATATCATAACAGAATCCA
3618608 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
3618622 TAAAATATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 1 0.02
48 51 0.96
49 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.23
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCATAACAGAATCCA
Found at i:3618619 original size:24 final size:25
Alignment explanation
Indices: 3618513--3618619 Score: 80
Period size: 24 Copynumber: 4.4 Consensus size: 25
3618503 AAATGGAGAT
* *
3618513 ATCATAAATCAAAACAGAATTC-AG
1 ATCAGAAATCATAACAGAATTCAAG
* * * *
3618537 ATTAGATATCATAACATAA-TCCAG
1 ATCAGAAATCATAACAGAATTCAAG
*
3618561 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCATAACAGAATTCAAG
* * *
3618585 GTAATG-TATCATAACAGAATTCAAG
1 ATCA-GAAATCATAACAGAATTCAAG
3618610 -TCAGAAATCA
1 ATCAGAAATCA
3618620 GATAAAATAT
Statistics
Matches: 63, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
23 3 0.05
24 55 0.87
25 5 0.08
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (25 bp):
ATCAGAAATCATAACAGAATTCAAG
Found at i:3623382 original size:24 final size:24
Alignment explanation
Indices: 3623355--3623442 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 24
3623345 GATATCATAA
* *
3623355 ATCAAAACAGAATTCAGATTAGAT
1 ATCATAACAGAATTCAGATAAGAT
* * * *
3623379 ATCATAACATAATCCAGATCAGAA
1 ATCATAACAGAATTCAGATAAGAT
* *
3623403 ATCAGAACAGAATTCAGGTAATG-T
1 ATCATAACAGAATTCAGATAA-GAT
3623427 ATCATAACAGAATTCA
1 ATCATAACAGAATTCA
3623443 AGTCAGAAAT
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
24 50 0.98
25 1 0.02
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCATAACAGAATTCAGATAAGAT
Found at i:3623430 original size:48 final size:47
Alignment explanation
Indices: 3623348--3623456 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 47
3623338 AAATGGAGAT
* * * *
3623348 ATCATAAATCAAAACAGAATTCAGATTAGATATCATAACATAATCCA
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCATAACAGAATCCA
* *
3623395 GATCAGAAATCAGAACAGAATTCAGGTAATG-TATCATAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGATAA-GATATCATAACAGAATCCA
3623443 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
3623457 TAAAATATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 1 0.02
48 51 0.96
49 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.23
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCATAACAGAATCCA
Found at i:3623454 original size:24 final size:25
Alignment explanation
Indices: 3623348--3623454 Score: 80
Period size: 24 Copynumber: 4.4 Consensus size: 25
3623338 AAATGGAGAT
* *
3623348 ATCATAAATCAAAACAGAATTC-AG
1 ATCAGAAATCATAACAGAATTCAAG
* * * *
3623372 ATTAGATATCATAACATAA-TCCAG
1 ATCAGAAATCATAACAGAATTCAAG
*
3623396 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCATAACAGAATTCAAG
* * *
3623420 GTAATG-TATCATAACAGAATTCAAG
1 ATCA-GAAATCATAACAGAATTCAAG
3623445 -TCAGAAATCA
1 ATCAGAAATCA
3623455 GATAAAATAT
Statistics
Matches: 63, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
23 3 0.05
24 55 0.87
25 5 0.08
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (25 bp):
ATCAGAAATCATAACAGAATTCAAG
Found at i:3625702 original size:20 final size:19
Alignment explanation
Indices: 3625669--3625707 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3625659 AAATATTACT
3625669 CTTGAATTCCAGCTCACCAA
1 CTTGAATTCCAGCTC-CCAA
* *
3625689 CTTGATTTCTAGCTCCCAA
1 CTTGAATTCCAGCTCCCAA
3625708 TCTTTTTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.33, G:0.10, T:0.31
Consensus pattern (19 bp):
CTTGAATTCCAGCTCCCAA
Found at i:3627829 original size:16 final size:16
Alignment explanation
Indices: 3627830--3627872 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
3627820 TATTTATAAA
*
3627830 TATAAATTCGACTAGT
1 TATAAATTCAACTAGT
*
3627846 TATAAATTCAACTATT
1 TATAAATTCAACTAGT
3627862 TATAAATTCAA
1 TATAAATTCAA
3627873 TTTAAATTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (16 bp):
TATAAATTCAACTAGT
Found at i:3627832 original size:22 final size:22
Alignment explanation
Indices: 3627805--3627852 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
3627795 GAAATGTAAA
*
3627805 AAATATAAATTCGACTATTTAT
1 AAATATAAATTCGACTAGTTAT
3627827 AAATATAAATTCGACTAGTTAT
1 AAATATAAATTCGACTAGTTAT
3627849 AAAT
1 AAAT
3627853 TCAACTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (22 bp):
AAATATAAATTCGACTAGTTAT
Found at i:3627913 original size:11 final size:11
Alignment explanation
Indices: 3627899--3627960 Score: 52
Period size: 11 Copynumber: 5.2 Consensus size: 11
3627889 TATATTAAAA
3627899 TATTTAATCAT
1 TATTTAATCAT
* *
3627910 TATTAAATAAT
1 TATTTAATCAT
3627921 TATTAGTAATCAT
1 TATT--TAATCAT
*
3627934 TATTAAATCAT
1 TATTTAATCAT
3627945 TAGTTTCAAATCAT
1 TA-TTT--AATCAT
3627959 TA
1 TA
3627961 AATATTAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
11 21 0.52
12 2 0.05
13 9 0.22
14 8 0.20
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (11 bp):
TATTTAATCAT
Found at i:3627930 original size:24 final size:23
Alignment explanation
Indices: 3627899--3628130 Score: 102
Period size: 24 Copynumber: 9.6 Consensus size: 23
3627889 TATATTAAAA
3627899 TATT-TAATCATTATTAAATAAT
1 TATTATAATCATTATTAAATAAT
*
3627921 TATTAGTAATCATTATTAAATCAT
1 TATTA-TAATCATTATTAAATAAT
*
3627945 TAGTT-TCAA--ATCATTAAAT-AT
1 TA-TTAT-AATCATTATTAAATAAT
* * *
3627966 TAATAATAAATAATTATT-AGTAAT
1 T-ATTAT-AATCATTATTAAATAAT
*
3627990 TATTACTAAATCATTAGTATCAAATCAT
1 TATTA-T-AATCATTA-T-T-AAATAAT
* * **
3628018 TA-AAT-ATTATTATTCCATAAT
1 TATTATAATCATTATTAAATAAT
* *
3628039 TATTAGTAATAATTATTAAATCAT
1 TATTA-TAATCATTATTAAATAAT
*
3628063 TAGTATCAAATCATTATTATAATATCAT
1 TATTAT--AATCATTATTA-AATA--AT
*
3628091 TATTACTAATCATTATTAAATCAT
1 TATTA-TAATCATTATTAAATAAT
*
3628115 TACTATCAAATCATTA
1 TATTAT--AATCATTA
3628131 AATATTAGTA
Statistics
Matches: 159, Mismatches: 26, Indels: 47
0.69 0.11 0.20
Matches are distributed among these distances:
21 10 0.06
22 19 0.12
23 10 0.06
24 66 0.42
25 21 0.13
26 8 0.05
27 12 0.08
28 12 0.08
29 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (23 bp):
TATTATAATCATTATTAAATAAT
Found at i:3627946 original size:21 final size:21
Alignment explanation
Indices: 3627903--3628067 Score: 57
Period size: 21 Copynumber: 8.1 Consensus size: 21
3627893 TTAAAATATT
*
3627903 TAATCATTATTAAATAATTATTAG
1 TAATCATTATT--A-AATCATTAG
3627927 TAATCATTATTAAATCATTAG
1 TAATCATTATTAAATCATTAG
* * *
3627948 T-TTCAAATCATTAAAT-ATTAA
1 TAATC--ATTATTAAATCATTAG
* *
3627969 TAAT-A--AAT-AATTATTAG
1 TAATCATTATTAAATCATTAG
* *
3627986 TAATTATTACTAAATCATTAG
1 TAATCATTATTAAATCATTAG
* *
3628007 T-ATCAAATCATTAAAT-ATTAT
1 TAATC--ATTATTAAATCATTAG
* * *
3628028 TATTC--CA-T-AATTATTAG
1 TAATCATTATTAAATCATTAG
*
3628045 TAATAATTATTAAATCATTAG
1 TAATCATTATTAAATCATTAG
3628066 TA
1 TA
3628068 TCAAATCATT
Statistics
Matches: 106, Mismatches: 19, Indels: 35
0.66 0.12 0.22
Matches are distributed among these distances:
16 6 0.06
17 18 0.17
18 3 0.03
19 2 0.02
20 7 0.07
21 38 0.36
22 21 0.20
24 11 0.10
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (21 bp):
TAATCATTATTAAATCATTAG
Found at i:3627978 original size:59 final size:59
Alignment explanation
Indices: 3627913--3628177 Score: 330
Period size: 59 Copynumber: 4.6 Consensus size: 59
3627903 TAATCATTAT
*
3627913 TAAATAATTATTAGTAATCATTATTAAATCATTAGTTTCAAATCATTAAATATTAATAA
1 TAAATAATTATTAGTAATCATTATTAAATCATTAGTATCAAATCATTAAATATTAATAA
* * * *
3627972 TAAATAATTATTAGTAATTATTACTAAATCATTAGTATCAAATCATTAAATATTATTAT
1 TAAATAATTATTAGTAATCATTATTAAATCATTAGTATCAAATCATTAAATATTAATAA
** *
3628031 TCCATAATTATTAGTAATAATTATTAAATCATTAGTATCAAATCA-T---TATT-ATAA
1 TAAATAATTATTAGTAATCATTATTAAATCATTAGTATCAAATCATTAAATATTAATAA
* * * *
3628085 T--ATCATTATTACTAATCATTATTAAATCATTACTATCAAATCATTAAATATTAGTAA
1 TAAATAATTATTAGTAATCATTATTAAATCATTAGTATCAAATCATTAAATATTAATAA
*
3628142 TAAAT-ATTATTACTAATCATTACTATCAAATCATTA
1 TAAATAATTATTAGTAATCATTA-T-T-AAATCATTA
3628178 AATATTAATA
Statistics
Matches: 180, Mismatches: 16, Indels: 18
0.84 0.07 0.08
Matches are distributed among these distances:
52 38 0.21
53 1 0.01
54 3 0.02
55 4 0.02
56 4 0.02
57 4 0.02
58 18 0.10
59 98 0.54
60 1 0.01
61 9 0.05
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (59 bp):
TAAATAATTATTAGTAATCATTATTAAATCATTAGTATCAAATCATTAAATATTAATAA
Found at i:3628075 original size:14 final size:14
Alignment explanation
Indices: 3628050--3628130 Score: 82
Period size: 14 Copynumber: 6.1 Consensus size: 14
3628040 ATTAGTAATA
*
3628050 ATTATTAAATCATT
1 ATTATCAAATCATT
*
3628064 AGTATCAAATCATT
1 ATTATCAAATCATT
3628078 ATTAT-AATATCATT
1 ATTATCAA-ATCATT
*
3628092 ATTA-CTAATCATT
1 ATTATCAAATCATT
3628105 A-T-T-AAATCATT
1 ATTATCAAATCATT
*
3628116 ACTATCAAATCATT
1 ATTATCAAATCATT
3628130 A
1 A
3628131 AATATTAGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
11 8 0.14
12 2 0.04
13 10 0.18
14 36 0.64
ACGTcount: A:0.43, C:0.12, G:0.01, T:0.43
Consensus pattern (14 bp):
ATTATCAAATCATT
Found at i:3628137 original size:21 final size:23
Alignment explanation
Indices: 3628092--3628198 Score: 93
Period size: 21 Copynumber: 4.8 Consensus size: 23
3628082 TAATATCATT
*
3628092 ATTACTAATC--ATTATTAAATC
1 ATTACTAATCAAATCATTAAATC
3628113 ATTACT-ATCAAATCATTAAAT-
1 ATTACTAATCAAATCATTAAATC
* * *
3628134 ATTAGTAATAAATATTATTACTAATC
1 ATTACTAATCAA-ATCATTA--AATC
3628160 ATTACT-ATCAAATCATTAAAT-
1 ATTACTAATCAAATCATTAAATC
*
3628181 ATTAATAAT-AAATCATTA
1 ATTACTAATCAAATCATTA
3628199 TTAGTAATCA
Statistics
Matches: 70, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
20 3 0.04
21 25 0.36
22 18 0.26
23 6 0.09
24 6 0.09
25 7 0.10
26 5 0.07
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.40
Consensus pattern (23 bp):
ATTACTAATCAAATCATTAAATC
Found at i:3628162 original size:47 final size:47
Alignment explanation
Indices: 3628098--3628214 Score: 193
Period size: 47 Copynumber: 2.5 Consensus size: 47
3628088 CATTATTACT
*
3628098 AATCATTATTA-AATCATTACTATCAAATCATTAAATATTAGTAATA
1 AATCATTATTATAATCATTACTATCAAATCATTAAATATTAATAATA
3628144 AAT-ATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
1 AATCATTATTA-TAATCATTACTATCAAATCATTAAATATTAATAATA
3628191 AATCATTATTAGTAATCATTACTA
1 AATCATTATTA-TAATCATTACTA
3628215 AATCATTAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
45 7 0.11
46 3 0.05
47 37 0.56
48 19 0.29
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (47 bp):
AATCATTATTATAATCATTACTATCAAATCATTAAATATTAATAATA
Found at i:3641068 original size:17 final size:17
Alignment explanation
Indices: 3641046--3641103 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 17
3641036 TAATATAAAC
3641046 TAAACAAAATATTTTTT
1 TAAACAAAATATTTTTT
*
3641063 TAAACAACAATAAATATTTT
1 TAAACAA-AAT--ATTTTTT
*
3641083 TAAACACAATA-TTTTT
1 TAAACAAAATATTTTTT
3641099 TAAAC
1 TAAAC
3641104 GAGAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 9 0.26
17 8 0.23
18 3 0.09
19 3 0.09
20 12 0.34
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAACAAAATATTTTTT
Found at i:3641236 original size:10 final size:10
Alignment explanation
Indices: 3641216--3641262 Score: 69
Period size: 10 Copynumber: 4.7 Consensus size: 10
3641206 TTTATGCCTT
3641216 CTTTC-TTTC
1 CTTTCTTTTC
3641225 CTTTCTTTTC
1 CTTTCTTTTC
3641235 CTTTCTTTTC
1 CTTTCTTTTC
*
3641245 CTTTCTTGTTT
1 CTTTCTT-TTC
3641256 CTTTCTT
1 CTTTCTT
3641263 CGAATCAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
9 5 0.14
10 21 0.60
11 9 0.26
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (10 bp):
CTTTCTTTTC
Found at i:3641597 original size:28 final size:30
Alignment explanation
Indices: 3641549--3641611 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
3641539 TTTTTTTATA
3641549 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
3641579 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
3641607 TAATA
1 TAATA
3641612 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:3641618 original size:28 final size:28
Alignment explanation
Indices: 3641553--3641618 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
3641543 TTTATATAAT
3641553 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
3641581 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
3641609 ATAATTTATA
1 ATAATATATA
3641619 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:3641621 original size:21 final size:21
Alignment explanation
Indices: 3641588--3641636 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3641578 CTAATATAAT
3641588 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
3641609 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
3641630 ATTAACT
1 A-TAACT
3641637 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:3641762 original size:19 final size:19
Alignment explanation
Indices: 3641738--3641790 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
3641728 GCAACTTATC
*
3641738 TTCCTTTCTTCTTTTTCCT
1 TTCCTTTCTTCTTTTCCCT
*
3641757 TTCCTTTCTCTCTTCTCCCT
1 TTCCTTTCT-TCTTTTCCCT
3641777 TT-CTTTCTTTCTTT
1 TTCCTTTC-TTCTTT
3641791 CTTATGCTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (19 bp):
TTCCTTTCTTCTTTTCCCT
Found at i:3651117 original size:23 final size:23
Alignment explanation
Indices: 3651087--3651135 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3651077 TGGTGGTTGG
*
3651087 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
3651110 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
3651133 TTT
1 TTT
3651136 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:3657698 original size:36 final size:35
Alignment explanation
Indices: 3657618--3657753 Score: 161
Period size: 35 Copynumber: 3.9 Consensus size: 35
3657608 AGATGATTAA
* * * * *
3657618 TTGAATCGAAAATATTGATGATTCCTTCCATTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
*
3657653 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTC-AC
* *
3657689 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
*
3657724 TTGAATCGAAA--GT-GATGCTTCCTTTCGTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTC
3657754 TTCTTATTCA
Statistics
Matches: 90, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
32 17 0.19
33 1 0.01
35 40 0.44
36 32 0.36
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.38
Consensus pattern (35 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
Found at i:3658835 original size:21 final size:21
Alignment explanation
Indices: 3658809--3658848 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3658799 GCTCACCAAC
3658809 TTCTATTAACAGACTAACCTA
1 TTCTATTAACAGACTAACCTA
3658830 TTCTATTAACAGACTAACC
1 TTCTATTAACAGACTAACC
3658849 ACCTAGCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.33
Consensus pattern (21 bp):
TTCTATTAACAGACTAACCTA
Found at i:3660529 original size:16 final size:17
Alignment explanation
Indices: 3660510--3660549 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3660500 TATTATTATT
3660510 TTTATATTTTA-TTTCA
1 TTTATATTTTATTTTCA
* *
3660526 TTTATACTTTATTTTTA
1 TTTATATTTTATTTTCA
3660543 TTTATAT
1 TTTATAT
3660550 ATATATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATATTTTATTTTCA
Found at i:3660530 original size:28 final size:28
Alignment explanation
Indices: 3660472--3660549 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 28
3660462 CCCCTACTAA
*
3660472 TATTATATATGTTTA-ATTATATTTCCAT
1 TATTAT-TATTTTTATATTATATTTCCAT
*
3660500 TATTATTATTTTTATATTTTATTT-CAT
1 TATTATTATTTTTATATTATATTTCCAT
3660527 T-TATACTTTATTTTTAT-TTATAT
1 TAT-TA--TTATTTTTATATTATAT
3660550 ATATATATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
26 1 0.02
27 13 0.30
28 19 0.44
29 10 0.23
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.65
Consensus pattern (28 bp):
TATTATTATTTTTATATTATATTTCCAT
Found at i:3660552 original size:21 final size:23
Alignment explanation
Indices: 3660510--3660560 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
3660500 TATTATTATT
*
3660510 TTTATATTTTATTTCATTTATAC
1 TTTATATTTTATTTCATATATAC
3660533 TTTAT-TTTTATTT-ATATATA-
1 TTTATATTTTATTTCATATATAC
*
3660553 TATATATT
1 TTTATATT
3660561 ACTTATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 4 0.16
21 8 0.32
22 8 0.32
23 5 0.20
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTATATTTTATTTCATATATAC
Found at i:3660649 original size:29 final size:29
Alignment explanation
Indices: 3660617--3660679 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
3660607 TTTCTGTTTC
*
3660617 TTTTTTATTTATTAC-TATTATTACTATT-
1 TTTTTT-TTTAATACTTATTATTACTATTA
3660645 TTTTTATTTTAATACTTATTATTACTATTA
1 TTTTT-TTTTAATACTTATTATTACTATTA
3660675 TTTTT
1 TTTTT
3660680 ATACCTTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 12 0.39
29 14 0.45
30 5 0.16
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.68
Consensus pattern (29 bp):
TTTTTTTTTAATACTTATTATTACTATTA
Found at i:3660706 original size:2 final size:2
Alignment explanation
Indices: 3660699--3660738 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3660689 TTATAAGTTA
*
3660699 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3660739 GACTATTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3663035 original size:3 final size:3
Alignment explanation
Indices: 3663027--3663093 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
3663017 ATTATTTATT
* * * **
3663027 TAA TAA TAA TAA TAA TATA TAA TAT TAA TAA TAA TAA CAA TAT TTT
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3663073 TAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
3663094 AATGAAAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3663101 original size:12 final size:12
Alignment explanation
Indices: 3663028--3663102 Score: 53
Period size: 12 Copynumber: 6.2 Consensus size: 12
3663018 TTATTTATTT
*
3663028 AATAATAATAAT
1 AATAATAATAAA
**
3663040 AATATATAATATT
1 AATA-ATAATAAA
*
3663053 AATAATAATAAC
1 AATAATAATAAA
* ** *
3663065 AATATTTTTAAT
1 AATAATAATAAA
3663077 AATAATAATAAA
1 AATAATAATAAA
3663089 AATAA-AATGAAA
1 AATAATAAT-AAA
3663101 AA
1 AA
3663103 ATTATTGTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
11 3 0.06
12 36 0.72
13 11 0.22
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:3663283 original size:25 final size:26
Alignment explanation
Indices: 3663250--3663300 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
3663240 TTTATTTAAC
*
3663250 ATAAGTTTT-ATTTTCTTTGTTTTTAT
1 ATAAGTTTTCA-TTTCTTTGATTTTAT
3663276 ATAA-TTTTCATTTCTTTGATTTTAT
1 ATAAGTTTTCATTTCTTTGATTTTAT
3663301 GTTTGCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.67
Consensus pattern (26 bp):
ATAAGTTTTCATTTCTTTGATTTTAT
Found at i:3663412 original size:15 final size:14
Alignment explanation
Indices: 3663388--3663421 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3663378 TTTTATTTTA
*
3663388 TTTATTT-TTTCCC
1 TTTATTTCTTTTCC
3663401 TTTATTTCTTTTCC
1 TTTATTTCTTTTCC
3663415 TTTATTT
1 TTTATTT
3663422 ATCATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTCTTTTCC
Found at i:3666692 original size:7 final size:7
Alignment explanation
Indices: 3666681--3666721 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
3666671 CATACATTGA
3666681 ATATTTT
1 ATATTTT
*
3666688 GTATTTT
1 ATATTTT
3666695 ATA-TTT
1 ATATTTT
3666701 ATATTTT
1 ATATTTT
*
3666708 ATTTTTT
1 ATATTTT
3666715 ATATTTT
1 ATATTTT
3666722 CCATGTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (7 bp):
ATATTTT
Found at i:3666706 original size:20 final size:20
Alignment explanation
Indices: 3666681--3666720 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3666671 CATACATTGA
*
3666681 ATATTTTGTATTTTATATTT
1 ATATTTTATATTTTATATTT
*
3666701 ATATTTTATTTTTTATATTT
1 ATATTTTATATTTTATATTT
3666721 TCCATGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
ATATTTTATATTTTATATTT
Found at i:3668590 original size:21 final size:21
Alignment explanation
Indices: 3668546--3668590 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3668536 GAATTTTATT
* *
3668546 AAGAAATTCATGATTCCCCTG
1 AAGAAATTCAGGATTCCCCAG
*
3668567 AAGAAATTCAGGATTCCTCAG
1 AAGAAATTCAGGATTCCCCAG
3668588 AAG
1 AAG
3668591 CAGACATTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (21 bp):
AAGAAATTCAGGATTCCCCAG
Found at i:3673903 original size:10 final size:10
Alignment explanation
Indices: 3673888--3673940 Score: 63
Period size: 10 Copynumber: 5.4 Consensus size: 10
3673878 GCTCTAAATT
3673888 AAAAAAAAAG
1 AAAAAAAAAG
3673898 AAAAAAAAAG
1 AAAAAAAAAG
*
3673908 AAAAAAAAAC
1 AAAAAAAAAG
*
3673918 AAAAGAAAA-
1 AAAAAAAAAG
* *
3673927 AAGAGAAAAG
1 AAAAAAAAAG
3673937 AAAA
1 AAAA
3673941 TAAGATGGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
9 8 0.21
10 30 0.79
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:3673915 original size:14 final size:14
Alignment explanation
Indices: 3673888--3673940 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
3673878 GCTCTAAATT
*
3673888 AAAAAA-AAAGAAA
1 AAAAAAGAAAAAAA
3673901 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
*
3673915 AACAAAAGAAAAAAG
1 AA-AAAAGAAAAAAA
*
3673930 AGAAAAGAAAA
1 AAAAAAGAAAA
3673941 TAAGATGGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
13 6 0.17
14 17 0.49
15 12 0.34
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAAA
Found at i:3673945 original size:15 final size:14
Alignment explanation
Indices: 3673893--3673945 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 14
3673883 AAATTAAAAA
3673893 AAAAGAAAAAA-A-
1 AAAAGAAAAAAGAC
3673905 AAGAA-AAAAAA-AC
1 AA-AAGAAAAAAGAC
*
3673918 AAAAGAAAAAAGAG
1 AAAAGAAAAAAGAC
3673932 AAAAGAAAATAAGA
1 AAAAGAAAA-AAGA
3673946 TGGGTTCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
12 11 0.31
13 10 0.29
14 10 0.29
15 4 0.11
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (14 bp):
AAAAGAAAAAAGAC
Found at i:3677104 original size:2 final size:2
Alignment explanation
Indices: 3677099--3677141 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3677089 TTTATTTTTT
3677099 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3677141 T
1 T
3677142 TACTTATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3677157 original size:17 final size:16
Alignment explanation
Indices: 3677137--3677174 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3677127 TATATATATA
3677137 TATATTACTTATATTTT
1 TATATT-CTTATATTTT
*
3677154 TATATTTTTATATTTT
1 TATATTCTTATATTTT
3677170 T-TATT
1 TATATT
3677175 TTTTTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 10 0.50
17 6 0.30
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TATATTCTTATATTTT
Found at i:3677178 original size:16 final size:16
Alignment explanation
Indices: 3677145--3677232 Score: 54
Period size: 18 Copynumber: 5.0 Consensus size: 16
3677135 TATATATTAC
3677145 TTATA-TTTTTATATTT
1 TTATATTTTTTAT-TTT
3677161 TTATATTTTTTATTTTTT
1 TTATATTTTTTA--TTTT
3677179 TTATAATTCCTTTTATTTCT
1 TTAT-ATT--TTTTATTT-T
* *
3677199 GTT-TCTTTTTTATTTA
1 -TTATATTTTTTATTTT
3677215 TTACTATTTTTTTATTTT
1 TTA-TA-TTTTTTATTTT
3677233 AATACTTATT
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
15 2 0.04
16 5 0.09
17 15 0.26
18 17 0.30
19 9 0.16
20 2 0.04
21 7 0.12
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (16 bp):
TTATATTTTTTATTTT
Found at i:3677179 original size:8 final size:8
Alignment explanation
Indices: 3677145--3677177 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
3677135 TATATATTAC
3677145 TTATATTT
1 TTATATTT
3677153 TTATATTT
1 TTATATTT
3677161 TTATATTT
1 TTATATTT
3677169 TT-TATTT
1 TTATATTT
3677176 TT
1 TT
3677178 TTTATAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTATATTT
Found at i:3677488 original size:25 final size:26
Alignment explanation
Indices: 3677455--3677505 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
3677445 TTTATTTAAC
*
3677455 ATAAGTTTT-ATTTTCTTTGTTTTTAT
1 ATAAGTTTTCA-TTTCTTTGATTTTAT
3677481 ATAA-TTTTCATTTCTTTGATTTTAT
1 ATAAGTTTTCATTTCTTTGATTTTAT
3677506 GTTTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.67
Consensus pattern (26 bp):
ATAAGTTTTCATTTCTTTGATTTTAT
Found at i:3677598 original size:14 final size:14
Alignment explanation
Indices: 3677579--3677610 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3677569 ATATGCTTTA
3677579 TTTTTTATTTTATT
1 TTTTTTATTTTATT
3677593 TTTTTTATTTTATT
1 TTTTTTATTTTATT
3677607 TTTT
1 TTTT
3677611 CCTTTATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTATTTTATT
Found at i:3677605 original size:26 final size:26
Alignment explanation
Indices: 3677574--3677633 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
3677564 TTAATATATG
* *
3677574 CTTTATTTTTTATTTTATTTTTTTTA
1 CTTTATTTTTTACTTTATTTCTTTTA
* * *
3677600 TTTTATTTTTTCCTTTATTTCTTTTC
1 CTTTATTTTTTACTTTATTTCTTTTA
3677626 CTTTATTT
1 CTTTATTT
3677634 ATCATATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (26 bp):
CTTTATTTTTTACTTTATTTCTTTTA
Found at i:3677624 original size:14 final size:14
Alignment explanation
Indices: 3677607--3677633 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3677597 TTATTTTATT
3677607 TTTTCCTTTATTTC
1 TTTTCCTTTATTTC
3677621 TTTTCCTTTATTT
1 TTTTCCTTTATTT
3677634 ATCATATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTCCTTTATTTC
Found at i:3684203 original size:21 final size:22
Alignment explanation
Indices: 3684173--3684221 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
3684163 AGGGAATTGA
3684173 TCCCCCTTG-A-GGGAACCAAT
1 TCCCCCTTGAAGGGGAACCAAT
*
3684193 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCC-TTGAAGGGGAACCAAT
3684216 TCCCCC
1 TCCCCC
3684222 CACAGGGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 6 0.24
21 3 0.12
22 1 0.04
23 15 0.60
ACGTcount: A:0.20, C:0.39, G:0.20, T:0.20
Consensus pattern (22 bp):
TCCCCCTTGAAGGGGAACCAAT
Found at i:3684248 original size:20 final size:21
Alignment explanation
Indices: 3684204--3684243 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3684194 CCCCCTTTGA
*
3684204 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
3684225 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
3684244 TAGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:3691175 original size:27 final size:28
Alignment explanation
Indices: 3691145--3691199 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
3691135 TACCTCGTAC
3691145 TTCGA-AAGGATGCTATTTTAATATATA
1 TTCGACAAGGATGCTATTTTAATATATA
* *
3691172 TTCGACTAAGGGTGCTATTTTTATATAT
1 TTCGAC-AAGGATGCTATTTTAATATAT
3691200 TATAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
29 19 0.79
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (28 bp):
TTCGACAAGGATGCTATTTTAATATATA
Found at i:3691752 original size:16 final size:16
Alignment explanation
Indices: 3691731--3691765 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3691721 TTACCCGACC
3691731 TGTTTTCAACCTCACA
1 TGTTTTCAACCTCACA
* *
3691747 TGTTTTTAACCTGACA
1 TGTTTTCAACCTCACA
3691763 TGT
1 TGT
3691766 AAATGATCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (16 bp):
TGTTTTCAACCTCACA
Found at i:3691975 original size:9 final size:9
Alignment explanation
Indices: 3691961--3691986 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3691951 AATTATTTAC
3691961 TAAAATTAA
1 TAAAATTAA
3691970 TAAAATTAA
1 TAAAATTAA
3691979 TAAAATTA
1 TAAAATTA
3691987 TTTAAATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TAAAATTAA
Found at i:3692054 original size:14 final size:14
Alignment explanation
Indices: 3692032--3692078 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
3692022 TGCAAAGGAA
*
3692032 AATTAATATAGTTT
1 AATTTATATAGTTT
3692046 AATTTATATA----
1 AATTTATATAGTTT
3692056 AA-TTATATAGTTT
1 AATTTATATAGTTT
3692069 AATTTATATA
1 AATTTATATA
3692079 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:3692065 original size:23 final size:24
Alignment explanation
Indices: 3692031--3692080 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
3692021 ATGCAAAGGA
3692031 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
3692055 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
3692078 AAA
1 AAA
3692081 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:3692712 original size:2 final size:2
Alignment explanation
Indices: 3692705--3692766 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
3692695 ACTTTGAATA
3692705 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
3692747 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
3692767 TAAACATAAG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3693214 original size:2 final size:2
Alignment explanation
Indices: 3693207--3693261 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
3693197 TATGTTTAAT
3693207 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3693249 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
3693262 TATTCAAAGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3693356 original size:19 final size:20
Alignment explanation
Indices: 3693331--3693414 Score: 73
Period size: 20 Copynumber: 4.0 Consensus size: 20
3693321 TTGATTTTAT
3693331 TTGGG-AATTTAGAGGGAAA
1 TTGGGAAATTTAGAGGGAAA
*
3693350 TTAGGAAAATTTGAGAATATAGGGAAA
1 TT-GGGAAATTT-AG---A--GGGAAA
*
3693377 TTGGG-AATTTAGAGGAAAA
1 TTGGGAAATTTAGAGGGAAA
3693396 TTGGGAAATTTAGAGGGAA
1 TTGGGAAATTTAGAGGGAA
3693415 TAGAAAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 17
0.71 0.05 0.23
Matches are distributed among these distances:
19 12 0.23
20 14 0.27
21 6 0.12
22 2 0.04
24 2 0.04
25 6 0.12
26 2 0.04
27 8 0.15
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (20 bp):
TTGGGAAATTTAGAGGGAAA
Done.