Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003574.1 Hibiscus syriacus cultivar Beakdansim tig00007543_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: 65737
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Found at i:930 original size:90 final size:91
Alignment explanation
Indices: 792--956 Score: 269
Period size: 90 Copynumber: 1.8 Consensus size: 91
782 AAACTTTACA
* * * *
792 TCTCTTTTCTTTTTTTCAGAATTGTCACTAACAACCAAAACTATATTTTGAGTAAACAAACAAAG
1 TCTCTTTTCTTTTTTTCAGAAATGACACTAAAAACCAAAACTACATTTTGAGTAAACAAACAAAG
*
857 CGAGGAGCAAATAAACTTCAAAAAAT
66 CAAGGAGCAAATAAACTTCAAAAAAT
*
883 TCTCTTTTC-TTTTTTCATAAATGACACTAAAAACCAAAACTACATTTTGAGTAAACAAACAAAG
1 TCTCTTTTCTTTTTTTCAGAAATGACACTAAAAACCAAAACTACATTTTGAGTAAACAAACAAAG
947 CAAGGAGCAA
66 CAAGGAGCAA
957 TATAGTATGG
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 59 0.87
91 9 0.13
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (91 bp):
TCTCTTTTCTTTTTTTCAGAAATGACACTAAAAACCAAAACTACATTTTGAGTAAACAAACAAAG
CAAGGAGCAAATAAACTTCAAAAAAT
Found at i:1710 original size:31 final size:31
Alignment explanation
Indices: 1675--1733 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1665 AGCTTAAAAG
*
1675 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
1706 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
1734 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1784 original size:22 final size:22
Alignment explanation
Indices: 1757--1989 Score: 305
Period size: 22 Copynumber: 10.6 Consensus size: 22
1747 ATAATAAATT
*
1757 TTTTAAAATAAATCTATTCATA
1 TTTTAAAATAAATCAATTCATA
*
1779 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
1801 TTTTAAAATAAGTCAATTCATA
1 TTTTAAAATAAATCAATTCATA
***
1823 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
1845 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
1867 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
**
1889 TTTTAAAATAAAT-TTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
1911 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
1933 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
1955 TTTTAAAATAAATCAATAT-ATA
1 TTTTAAAATAAATCAAT-TCATA
1977 TTTTAAAATAAAT
1 TTTTAAAATAAAT
1990 TTTAAAAAAG
Statistics
Matches: 187, Mismatches: 17, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
21 3 0.02
22 182 0.97
23 2 0.01
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTCATA
Found at i:1827 original size:66 final size:66
Alignment explanation
Indices: 1757--1989 Score: 355
Period size: 66 Copynumber: 3.5 Consensus size: 66
1747 ATAATAAATT
* *
1757 TTTTAAAATAAATCTATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAGTCAATTCAT
1 TTTTAAAATAAATCTATTCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATTCAT
1822 A
66 A
* *
1823 TTTTAAAATAAATTTTTTCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAA-TCTA
1 TTTTAAAATAAATCTATTCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATTC-A
1887 TA
65 TA
* *
1889 TTTTAAAATAAAT-TTTTCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCA
1 TTTTAAAATAAATCTATT-CATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATTCA
1953 TA
65 TA
*
1955 TTTTAAAATAAATCAATAT-ATATTTTAAAATAAAT
1 TTTTAAAATAAATCTAT-TCATATTTTAAAATAAAT
1990 TTTAAAAAAG
Statistics
Matches: 155, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
65 6 0.04
66 146 0.94
67 2 0.01
68 1 0.01
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (66 bp):
TTTTAAAATAAATCTATTCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATTCAT
A
Found at i:3636 original size:2 final size:2
Alignment explanation
Indices: 3629--3662 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3619 ATTTAAGATA
3629 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
3663 TTATTATGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4791 original size:32 final size:32
Alignment explanation
Indices: 4749--4827 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 32
4739 AAAGTACTTT
* * * * *
4749 TTTATTAAATGAATTTATTTATCACTGAAAAG
1 TTTATGAAATGAAGTGATATATCAATGAAAAG
*
4781 TTTATGAAATGAAGTGGTATATCAATGAAAAG
1 TTTATGAAATGAAGTGATATATCAATGAAAAG
* *
4813 TTTCTGAAGTGAAGT
1 TTTATGAAATGAAGT
4828 AATTGGCGAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.38
Consensus pattern (32 bp):
TTTATGAAATGAAGTGATATATCAATGAAAAG
Found at i:6542 original size:17 final size:17
Alignment explanation
Indices: 6492--6544 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
6482 ATCAAAGAGT
6492 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
* **
6509 TAGTTAAACGAATGAAC
1 TAGTTTAATTAATGAAC
*
6526 TAGTTTAATTAAAGAAC
1 TAGTTTAATTAATGAAC
6543 TA
1 TA
6545 ACTTTATTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:9628 original size:15 final size:15
Alignment explanation
Indices: 9610--9644 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
9600 CTACCATAAG
*
9610 AGTACTAATAACATT
1 AGTACTAACAACATT
9625 AGTACTAACAACATT
1 AGTACTAACAACATT
9640 AGTAC
1 AGTAC
9645 AACTACCCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.29
Consensus pattern (15 bp):
AGTACTAACAACATT
Found at i:12669 original size:17 final size:17
Alignment explanation
Indices: 12639--12674 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12629 ATCAAAGAGT
* *
12639 TAGTTTAATTAATGAAC
1 TAGTTAAATGAATGAAC
12656 TAGTTAAATGAATGAAC
1 TAGTTAAATGAATGAAC
12673 TA
1 TA
12675 ATTTAGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (17 bp):
TAGTTAAATGAATGAAC
Found at i:21483 original size:21 final size:21
Alignment explanation
Indices: 21366--21483 Score: 80
Period size: 21 Copynumber: 5.7 Consensus size: 21
21356 ACGCGAAATA
**
21366 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
21386 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
21406 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
21427 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
21448 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
21469 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
21484 ACACATAAAT
Statistics
Matches: 72, Mismatches: 22, Indels: 7
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.01
20 24 0.33
21 45 0.62
22 2 0.03
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:21495 original size:20 final size:20
Alignment explanation
Indices: 21470--21643 Score: 208
Period size: 20 Copynumber: 8.7 Consensus size: 20
21460 CGATTTTCCA
* *
21470 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
21490 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
21510 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
21530 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
**
21550 AAATCGCAATACGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
21570 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
21590 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
21610 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
21631 AAATCGCAACGCG
1 AAATCGCAACGCG
21644 ATATTTAAAG
Statistics
Matches: 130, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
19 1 0.01
20 111 0.85
21 17 0.13
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:22064 original size:33 final size:33
Alignment explanation
Indices: 22025--22095 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
22015 TTCACTTAGA
* *
22025 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
22058 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
22091 TTTCA
1 TTTCA
22096 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:22232 original size:41 final size:41
Alignment explanation
Indices: 22174--22251 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
22164 TTGCAGAAGA
*
22174 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
22215 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
22252 CGCAACGAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:22248 original size:21 final size:21
Alignment explanation
Indices: 22175--22250 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
22165 TGCAGAAGAG
*
22175 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
22196 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
22216 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
22237 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
22251 TCGCAACGAG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:22254 original size:14 final size:14
Alignment explanation
Indices: 22235--22272 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
22225 GAGAAATGAA
22235 AATCGCAACGAGAG
1 AATCGCAACGAGAG
22249 AATCGCAACGAGAG
1 AATCGCAACGAGAG
22263 AATCGCAACG
1 AATCGCAACG
22273 CGAAACCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.42, C:0.24, G:0.26, T:0.08
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:22306 original size:19 final size:19
Alignment explanation
Indices: 22284--22381 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
22274 GAAACCAAAA
*
22284 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
22303 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
22317 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
22336 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
22350 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
22369 TCGCGTTGCGATT
1 TCGCGTTGCGATT
22382 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:22325 original size:14 final size:14
Alignment explanation
Indices: 22306--22395 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
22296 TTTCATTTCG
22306 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
22320 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
22339 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
22353 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
22370 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
22386 CGTTGCGATT
1 CGTTGCGATT
22396 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:22331 original size:33 final size:33
Alignment explanation
Indices: 22289--22403 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
22279 CAAAATCGCA
22289 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
22322 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
22355 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
22388 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
22404 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:24258 original size:93 final size:93
Alignment explanation
Indices: 24099--24572 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
24089 TAGATTGCTT
*
24099 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24164 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24192 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24257 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
24285 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24350 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
24378 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24443 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24471 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24536 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24564 AGTAAATTT
1 AGTAAATTT
24573 ATCCATTCAA
Statistics
Matches: 378, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 378 1.00
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:24656 original size:19 final size:19
Alignment explanation
Indices: 24616--24744 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
24606 TAGTTTACTT
* *
24616 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
24636 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
24655 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
24674 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
24688 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
24707 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
24721 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
24740 TCGCA
1 TCGCA
24745 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:24695 original size:33 final size:32
Alignment explanation
Indices: 24652--24744 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
24642 CGCGAAACCA
**
24652 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
24684 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
24717 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
24745 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:24742 original size:52 final size:52
Alignment explanation
Indices: 24616--24744 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
24606 TAGTTTACTT
**
24616 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
24668 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
24721 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
24745 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:24762 original size:19 final size:19
Alignment explanation
Indices: 24740--24874 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
24730 GAAACCAAAA
*
24740 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
24759 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
24775 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
24792 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
24808 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
24825 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
24844 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
24864 TCGTGTTGCGA
1 TCGCGTTGCGA
24875 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:24781 original size:14 final size:14
Alignment explanation
Indices: 24762--24818 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
24752 TTTCATTTCG
24762 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
24776 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
24793 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
24809 CGTTGCGATT
1 CGTTGCGATT
24819 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:24787 original size:33 final size:33
Alignment explanation
Indices: 24745--24837 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
24735 CAAAATCGCA
*
24745 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
24778 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
24811 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
24838 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:26818 original size:13 final size:14
Alignment explanation
Indices: 26793--26827 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
26783 ATTGTTTAAT
26793 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
26807 TGATTTGT-AAAGT
1 TGATTTGTAAAAGA
26820 TGATTTGT
1 TGATTTGT
26828 GTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:26962 original size:19 final size:19
Alignment explanation
Indices: 26934--27033 Score: 129
Period size: 19 Copynumber: 5.5 Consensus size: 19
26924 AAAATTGACT
26934 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
26953 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
26972 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
26986 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27005 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
*
27025 ATTGCAATG
1 ATCGCAATG
27034 GGAGAATCGC
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 37 0.53
20 17 0.24
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:27063 original size:53 final size:53
Alignment explanation
Indices: 26934--27050 Score: 191
Period size: 53 Copynumber: 2.2 Consensus size: 53
26924 AAAATTGACT
*
26934 ATCGCAATGCGAAATGAAAATCACAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* * *
26986 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATTGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
27039 ATCGCAATGCGA
1 ATCGCAATGCGA
27051 TTTTAATTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 28 0.47
53 32 0.53
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:27068 original size:19 final size:19
Alignment explanation
Indices: 27040--27207 Score: 177
Period size: 19 Copynumber: 9.6 Consensus size: 19
27030 AATGGGAGAA
* *
27040 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
27059 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
27075 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
27092 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
27111 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
27127 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
27144 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
27163 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
27179 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
27196 TCCGCATTGCGA
1 T-CGCATTGCGA
27208 AATGTAATGG
Statistics
Matches: 125, Mismatches: 8, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
14 18 0.14
16 21 0.17
17 18 0.14
18 2 0.02
19 60 0.48
20 6 0.05
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:27093 original size:33 final size:33
Alignment explanation
Indices: 27046--27207 Score: 159
Period size: 33 Copynumber: 4.7 Consensus size: 33
27036 AGAATCGCAA
*
27046 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
27079 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
27117 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
27150 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
27183 TGCGATTTTCATTTCCGCATTGCGA
1 TGCGATTTTCATTT-CGCATTGCGA
27208 AATGTAATGG
Statistics
Matches: 104, Mismatches: 13, Indels: 23
0.74 0.09 0.16
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 49 0.47
34 10 0.10
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:27103 original size:52 final size:52
Alignment explanation
Indices: 27040--27207 Score: 309
Period size: 52 Copynumber: 3.2 Consensus size: 52
27030 AATGGGAGAA
* *
27040 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
27092 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
27144 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
27196 TCCGCATTGCGA
1 T-CGCATTGCGA
27208 AATGTAATGG
Statistics
Matches: 113, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 103 0.91
53 10 0.09
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:27289 original size:19 final size:19
Alignment explanation
Indices: 27265--27362 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
27255 AAAATTGACT
27265 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27284 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
27303 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
27317 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27336 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
27356 ATCGCAA
1 ATCGCAA
27363 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:27343 original size:52 final size:53
Alignment explanation
Indices: 27265--27381 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
27255 AAAATTGACT
27265 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
27317 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
27370 ATCGCAATGCGA
1 ATCGCAATGCGA
27382 TTTCATTTCG
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:29701 original size:12 final size:12
Alignment explanation
Indices: 29684--29708 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29674 TCTTCGGGGA
29684 CTTTTTCTTCTT
1 CTTTTTCTTCTT
29696 CTTTTTCTTCTT
1 CTTTTTCTTCTT
29708 C
1 C
29709 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:29915 original size:24 final size:24
Alignment explanation
Indices: 29881--29927 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
29871 CTGAAACATC
29881 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
29905 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
29928 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:30635 original size:20 final size:20
Alignment explanation
Indices: 30607--30836 Score: 246
Period size: 20 Copynumber: 11.5 Consensus size: 20
30597 AAATTTCAGT
* * *
30607 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
30627 GTTGCGATTTACGGATTCTC
1 GTTGCGATTTACGGATTCGC
**
30647 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
30667 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
30687 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
30707 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
30727 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
30747 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
30767 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
30787 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
30807 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
30827 GTTGCGATTT
1 GTTGCGATTT
30837 TGGAAAATCG
Statistics
Matches: 184, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 183 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:31416 original size:188 final size:188
Alignment explanation
Indices: 31091--31437 Score: 534
Period size: 188 Copynumber: 1.8 Consensus size: 188
31081 TCGAAAAATA
* * *
31091 AAACTCCTTTTATTATTCAAACTTAAATAGATATTATTTTAATATGAAATATACAAAAGTGTATA
1 AAACTCCTTTTACTATTCAAACTTAAACAGATATTATTTTAATATGAAATATACAAAAGTATATA
* * * *
31156 ATTATCTTTAATATTCAAAGTTAAAAAAAGTAACAAATACATTTTTAAGTTGACATATTCAAAGA
66 ATTATCTTTAATACTCAAAATTAAAAAAAGTAACAAATACATTTTTAAATTGACATATTAAAAGA
31221 ATAATTATCCTAATAATATTCAAATTAAATAATATATTTAATTTGCAATAGACAAGGT
131 ATAATTATCCTAATAATATTCAAATTAAATAATATATTTAATTTGCAATAGACAAGGT
* *
31279 AAACTCCTTTTACTATTCAAACTTAAACATATATTATTTTAATTTGAAATATACAAAAGTATATA
1 AAACTCCTTTTACTATTCAAACTTAAACAGATATTATTTTAATATGAAATATACAAAAGTATATA
* * * *
31344 ATTATCTTTTAATACTCAAAATTAAAAAGA-TAACAAATGCCTTTTTAAATTGACTTATTAAAAG
66 ATTATC-TTTAATACTCAAAATTAAAAAAAGTAACAAATACATTTTTAAATTGACATATTAAAAG
* * *
31408 AGTAATTATCCTACTATTATTCAAATTAAA
130 AATAATTATCCTAATAATATTCAAATTAAA
31438 AATCATCTTT
Statistics
Matches: 142, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
188 122 0.86
189 20 0.14
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (188 bp):
AAACTCCTTTTACTATTCAAACTTAAACAGATATTATTTTAATATGAAATATACAAAAGTATATA
ATTATCTTTAATACTCAAAATTAAAAAAAGTAACAAATACATTTTTAAATTGACATATTAAAAGA
ATAATTATCCTAATAATATTCAAATTAAATAATATATTTAATTTGCAATAGACAAGGT
Found at i:32054 original size:26 final size:26
Alignment explanation
Indices: 32018--32070 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
32008 ATGCAATTAT
32018 GTTGTCCCTTTGAACCTAAATCTTGG
1 GTTGTCCCTTTGAACCTAAATCTTGG
*
32044 GTTGTCCCTTTGAACCTAGATCTTGG
1 GTTGTCCCTTTGAACCTAAATCTTGG
32070 G
1 G
32071 ATCTCCAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
GTTGTCCCTTTGAACCTAAATCTTGG
Found at i:34148 original size:130 final size:131
Alignment explanation
Indices: 33946--34185 Score: 419
Period size: 130 Copynumber: 1.8 Consensus size: 131
33936 CTTCACTATA
* * *
33946 GTTAATTAAAACTCAAACCATCAAGATTCAAGGTGTGCCCCACAAAGTGTGCAACAACAGAGATC
1 GTTAATCAAAACCCAAACCATCAAGATTCAAGGTGTGCCCAACAAAGTGTGCAACAACAGAGATC
* *
34011 TTGCAAAGATATTCGAATCTAATTTGAAATCATAAATTCAAAAATTGAAGGATTAAACTCACCAT
66 TTGCAAAGATATTCAAATCCAATTTGAAATCATAAATTCAAAAATTGAAGGATTAAACTCACCAT
34076 T
131 T
*
34077 GTTAATCAAAACCCAAACCATCAAGATTC-AGGTGTGCCCAACAAAGTGTGCAACAAGAGAGATC
1 GTTAATCAAAACCCAAACCATCAAGATTCAAGGTGTGCCCAACAAAGTGTGCAACAACAGAGATC
34141 TTGCAAAGATATTCAAATCCAATTTGAAATCATAAATTCAAAAAT
66 TTGCAAAGATATTCAAATCCAATTTGAAATCATAAATTCAAAAAT
34186 AAAAATCATT
Statistics
Matches: 103, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
130 76 0.74
131 27 0.26
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.25
Consensus pattern (131 bp):
GTTAATCAAAACCCAAACCATCAAGATTCAAGGTGTGCCCAACAAAGTGTGCAACAACAGAGATC
TTGCAAAGATATTCAAATCCAATTTGAAATCATAAATTCAAAAATTGAAGGATTAAACTCACCAT
T
Found at i:34439 original size:34 final size:35
Alignment explanation
Indices: 34388--34456 Score: 131
Period size: 34 Copynumber: 2.0 Consensus size: 35
34378 TATTAATCGG
34388 AATCACTTAAGGCTTGTCACTACACAATTTTCTTA
1 AATCACTTAAGGCTTGTCACTACACAATTTTCTTA
34423 AATCACTT-AGGCTTGTCACTACACAATTTTCTTA
1 AATCACTTAAGGCTTGTCACTACACAATTTTCTTA
34457 GCCAGATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 26 0.76
35 8 0.24
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (35 bp):
AATCACTTAAGGCTTGTCACTACACAATTTTCTTA
Found at i:36879 original size:2 final size:2
Alignment explanation
Indices: 36872--36908 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
36862 AAATTATCCT
36872 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36909 TAAAAAGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38002 original size:540 final size:543
Alignment explanation
Indices: 36979--38063 Score: 2106
Period size: 540 Copynumber: 2.0 Consensus size: 543
36969 TTTAAATTCA
36979 TAAAATTTATATAATTTTTTTTATAAAATTTAAAAGATAAATAGATTTAATGAAAGGGTAAAATT
1 TAAAATTTATATAATTTTTTTTATAAAATTTAAAAGATAAATAGATTTAATGAAAGGGTAAAATT
37044 TTATTTTAACCCATGAACTTCATATAAAATTCTAATTATTGATTTTTTTTTTTGTAATTTAAGGG
66 TTATTTTAACCCATGAACTTCATATAAAATTCTAATTATTGA-TTTTTTTTTTGTAATTTAAGGG
37109 CATTTTAGTCCAAAACGCCGGTAATCCAACAATACCTAAGGGAAGGGGTAATCACATTCCCGATA
130 CATTTTAGTCCAAAACGCCGGTAATCCAACAATACCTAAGGGAAGGGGTAAT-ACATTCCCGATA
37174 ATATACCCAAAAATACCACTGTTGGGAATAAAAGATTACCGGAAATAGGATTACTGACTAACCAA
194 ATATACCCAAAAATACCACTGTTGGGAATAAAAGATTACCGGAAATAGGATTACTGACTAACCAA
*
37239 ACGGGGGAATGCCATTCTATTCTCCGATAATTCCATATTACCTGAACCAAACACCCATGAAGGTT
259 ACGGGGGAATGCCATTCTATTCCCCGATAATTCCATATTACCTGAACCAAACACCCATGAAGGTT
37304 CTTAAAAAAAAAGAAAGAAAGAAAAGCTTACTGATTCAATACCGTCTTCAGCGTAGGAGTCAATG
324 CTTAAAAAAAAAGAAAGAAAGAAAAGCTTACTGATTCAATACCGTCTTCAGCGTAGGAGTCAATG
37369 GAATCAAATTCAGCGGTGTCTCTCTGAGGCTCAGATTCAACGAAGGTACCATCGTTAGTAGTCAT
389 GAATCAAATTCAGCGGTGTCTCTCTGAGGCTCAGATTCAACGAAGGTACCATCGTTAGTAGTCAT
37434 TGACAACGTATTGAAGTTCGTCGTTTTGAAATCGTTCCATTATGCTACAATAAAGAAACAGGTTA
454 TGACAACGTATTGAAGTTCGTCGTTTTGAAATCGTTCCATTATGCTACAATAAAGAAACAGGTTA
37499 AACAAGATTTTGATTAGAAATACAT
519 AACAAGATTTTGATTAGAAATACAT
37524 TAAAATTTATATAATTTTTTTTATAAAATTTAAAAGATAAATAGATTTAATGAAAGGGTAAAATT
1 TAAAATTTATATAATTTTTTTTATAAAATTTAAAAGATAAATAGATTTAATGAAAGGGTAAAATT
37589 TTATTTTAACCCATGAACTTCATATAAAATTCTAATTATTGA-TTTTTTTTTGTAATTTAAGGGC
66 TTATTTTAACCCATGAACTTCATATAAAATTCTAATTATTGATTTTTTTTTTGTAATTTAAGGGC
37653 ATTTTAGTCCAAAACGCCGGTAATCCAACAATACCTAAGGGAA-GGGTAAT-CATTCCCGATAAT
131 ATTTTAGTCCAAAACGCCGGTAATCCAACAATACCTAAGGGAAGGGGTAATACATTCCCGATAAT
37716 A-ACCCAAAAATACCACTGTTGGGAATAAAAGATTACCGGAAATAGGATTACTGACTAACCAAAC
196 ATACCCAAAAATACCACTGTTGGGAATAAAAGATTACCGGAAATAGGATTACTGACTAACCAAAC
37780 GGGGGAATGCCATTCTATTCCCCGATAATTCCATATTACCTGAACCAAACACCCATGAAGGTTCT
261 GGGGGAATGCCATTCTATTCCCCGATAATTCCATATTACCTGAACCAAACACCCATGAAGGTTCT
37845 TAAAAAAAAAAGAAAGAAAGAAAAGCTTACTGATTCAATACCGTCTTCAGCGTAGGAGTCAATGG
326 T-AAAAAAAAAGAAAGAAAGAAAAGCTTACTGATTCAATACCGTCTTCAGCGTAGGAGTCAATGG
37910 AATCAAATTCAGCGGTGTCTCTCTGAGGCTCAGATTCAACGAAGGTACCATCGTTAGTAGTCATT
390 AATCAAATTCAGCGGTGTCTCTCTGAGGCTCAGATTCAACGAAGGTACCATCGTTAGTAGTCATT
37975 GACAACGTATTGAAGTTCGTCGTTTTGAAATCGTTCCATTATGCTACAATAAAGAAACAGGTTAA
455 GACAACGTATTGAAGTTCGTCGTTTTGAAATCGTTCCATTATGCTACAATAAAGAAACAGGTTAA
38040 ACAAGATTTTGATTAGAAATACAT
520 ACAAGATTTTGATTAGAAATACAT
38064 AGCTTTCAAC
Statistics
Matches: 538, Mismatches: 1, Indels: 7
0.99 0.00 0.01
Matches are distributed among these distances:
539 128 0.24
540 231 0.43
542 7 0.01
543 65 0.12
545 107 0.20
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (543 bp):
TAAAATTTATATAATTTTTTTTATAAAATTTAAAAGATAAATAGATTTAATGAAAGGGTAAAATT
TTATTTTAACCCATGAACTTCATATAAAATTCTAATTATTGATTTTTTTTTTGTAATTTAAGGGC
ATTTTAGTCCAAAACGCCGGTAATCCAACAATACCTAAGGGAAGGGGTAATACATTCCCGATAAT
ATACCCAAAAATACCACTGTTGGGAATAAAAGATTACCGGAAATAGGATTACTGACTAACCAAAC
GGGGGAATGCCATTCTATTCCCCGATAATTCCATATTACCTGAACCAAACACCCATGAAGGTTCT
TAAAAAAAAAGAAAGAAAGAAAAGCTTACTGATTCAATACCGTCTTCAGCGTAGGAGTCAATGGA
ATCAAATTCAGCGGTGTCTCTCTGAGGCTCAGATTCAACGAAGGTACCATCGTTAGTAGTCATTG
ACAACGTATTGAAGTTCGTCGTTTTGAAATCGTTCCATTATGCTACAATAAAGAAACAGGTTAAA
CAAGATTTTGATTAGAAATACAT
Found at i:40156 original size:31 final size:31
Alignment explanation
Indices: 40113--40171 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
40103 CATTATTTCC
*
40113 AAGTGACTAAAACTTAATAAAACGATAACGT
1 AAGTGACCAAAACTTAATAAAACGATAACGT
40144 AAGTGACCAAAACTTAATAAAACGATAA
1 AAGTGACCAAAACTTAATAAAACGATAA
40172 AATAAGTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.54, C:0.14, G:0.12, T:0.20
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACGATAACGT
Found at i:40178 original size:31 final size:31
Alignment explanation
Indices: 40113--40178 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
40103 CATTATTTCC
* **
40113 AAGTGACTAAAACTTAATAAAACGATAACGT
1 AAGTGACCAAAACTTAATAAAACGATAAAAT
40144 AAGTGACCAAAACTTAATAAAACGATAAAAT
1 AAGTGACCAAAACTTAATAAAACGATAAAAT
40175 AAGT
1 AAGT
40179 TACTAGAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACGATAAAAT
Found at i:43296 original size:22 final size:22
Alignment explanation
Indices: 43271--43312 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
43261 GACTGACCAC
43271 TATGCCCCGAAGGACCACTGTA
1 TATGCCCCGAAGGACCACTGTA
* *
43293 TATGTCCCGAAGGACTACTG
1 TATGCCCCGAAGGACCACTG
43313 ATAATCCCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (22 bp):
TATGCCCCGAAGGACCACTGTA
Found at i:44306 original size:12 final size:12
Alignment explanation
Indices: 44289--44313 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44279 TGATGACAAG
44289 TCAAATTTAACT
1 TCAAATTTAACT
44301 TCAAATTTAACT
1 TCAAATTTAACT
44313 T
1 T
44314 ATCAACTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TCAAATTTAACT
Found at i:47414 original size:18 final size:18
Alignment explanation
Indices: 47391--47463 Score: 94
Period size: 18 Copynumber: 3.9 Consensus size: 18
47381 ACTGTATATT
47391 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
47409 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
*
47428 TTTATCCCGAAGGACCACTA
1 --TGTCCCGAAGGACCACTA
*
47448 TGT-CCTAAGGACCACT
1 TGTCCCGAAGGACCACT
47464 CCTTAAGAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
17 12 0.24
18 19 0.39
19 1 0.02
20 1 0.02
21 16 0.33
ACGTcount: A:0.27, C:0.32, G:0.21, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:47437 original size:39 final size:38
Alignment explanation
Indices: 47388--47463 Score: 125
Period size: 39 Copynumber: 2.0 Consensus size: 38
47378 GGCACTGTAT
*
47388 ATTTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTG
1 ATTTATCCCGAAGGACCACTATGT-CCGAAGGACCACTG
*
47427 ATTTATCCCGAAGGACCACTATGTCCTAAGGACCACT
1 ATTTATCCCGAAGGACCACTATGTCCGAAGGACCACT
47464 CCTTAAGAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 12 0.34
39 23 0.66
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (38 bp):
ATTTATCCCGAAGGACCACTATGTCCGAAGGACCACTG
Found at i:58105 original size:19 final size:19
Alignment explanation
Indices: 58081--58120 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
58071 AATAAATTTA
58081 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
58100 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
58119 AT
1 AT
58121 ACCCGGCCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:58154 original size:12 final size:12
Alignment explanation
Indices: 58139--58172 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
58129 CGATTCCCGG
58139 CCCAATACCCAA
1 CCCAATACCCAA
*
58151 CCCAATACCCAG
1 CCCAATACCCAA
58163 CCCAATACCC
1 CCCAATACCC
58173 GTTTAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.35, C:0.53, G:0.03, T:0.09
Consensus pattern (12 bp):
CCCAATACCCAA
Found at i:63193 original size:31 final size:28
Alignment explanation
Indices: 63158--63214 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
63148 TAACCTTTTG
*
63158 AAATTATCGAATTGGTCCCCTAACTTTTCAA
1 AAATTA-CGAAATGGTCCCC-AA-TTTTCAA
*
63189 AAATTACTAAATGGTCCCCAATTTTC
1 AAATTACGAAATGGTCCCCAATTTTC
63215 TAAGGCTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.21
29 2 0.08
30 11 0.46
31 6 0.25
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (28 bp):
AAATTACGAAATGGTCCCCAATTTTCAA
Done.