Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000183.1 Hibiscus syriacus cultivar Beakdansim tig00000324_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: 109555
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:203 original size:2 final size:2
Alignment explanation
Indices: 196--239 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
186 TTGTGCTTGG
196 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT A- 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
236 AT AT
1 AT AT
240 TGATTGATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:220 original size:19 final size:19
Alignment explanation
Indices: 196--239 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
186 TTGTGCTTGG
196 ATATATATATATAATATAT
1 ATATATATATATAATATAT
215 ATATATATATATAATATAT
1 ATATATATATATAATATAT
234 ATATAT
1 ATATAT
240 TGATTGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATATATATATAATATAT
Found at i:1649 original size:18 final size:18
Alignment explanation
Indices: 1626--1662 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1616 AAGGAGGGGC
1626 ACCCCTCAAGAGGATCAG
1 ACCCCTCAAGAGGATCAG
1644 ACCCCTCAAGAGGATCAG
1 ACCCCTCAAGAGGATCAG
1662 A
1 A
1663 GGCTCCCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.32, G:0.22, T:0.11
Consensus pattern (18 bp):
ACCCCTCAAGAGGATCAG
Found at i:6887 original size:21 final size:21
Alignment explanation
Indices: 6836--6888 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
6826 ATTATGACTA
**
6836 TCGCAATGCGATTTTTTAATT
1 TCGCAATGCGATTTTCCAATT
**
6857 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
6878 TCGCAATGCGA
1 TCGCAATGCGA
6889 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:6943 original size:20 final size:20
Alignment explanation
Indices: 6918--7032 Score: 133
Period size: 20 Copynumber: 5.7 Consensus size: 20
6908 AATTGGGAAA
*
6918 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
6938 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
6959 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
6979 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
6999 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
7019 TTCGCAACGAGATA
1 ATCGCAACGCGATA
7033 ATACATAATC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.77
21 15 0.18
22 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:7015 original size:40 final size:40
Alignment explanation
Indices: 6916--7052 Score: 177
Period size: 41 Copynumber: 3.4 Consensus size: 40
6906 CAAATTGGGA
* *
6916 AAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
6956 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTTAC
1 -AAATCGCAACGCGATACTGACTTTCGCAACGCGATA-ATAC
** *
6998 -TTTCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
7037 ATAATCGCAATGCGAT
1 A-AATCGCAACGCGAT
7053 TTTCAAAGCG
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
39 3 0.04
40 32 0.39
41 45 0.54
42 3 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (40 bp):
AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:7257 original size:28 final size:28
Alignment explanation
Indices: 7217--7291 Score: 141
Period size: 28 Copynumber: 2.7 Consensus size: 28
7207 CACTCTCTCA
7217 CCCATCTCCGACGAAATCCATCCCCATC
1 CCCATCTCCGACGAAATCCATCCCCATC
7245 CCCATCTCCGACGAAATCCATCCCCATC
1 CCCATCTCCGACGAAATCCATCCCCATC
*
7273 CCCATCTCCGGCGAAATCC
1 CCCATCTCCGACGAAATCC
7292 GTCTATCTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.24, C:0.49, G:0.09, T:0.17
Consensus pattern (28 bp):
CCCATCTCCGACGAAATCCATCCCCATC
Found at i:7606 original size:20 final size:20
Alignment explanation
Indices: 7557--7615 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
7547 TTTATTCTCT
* **
7557 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
7577 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
7597 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
7616 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:7806 original size:25 final size:24
Alignment explanation
Indices: 7752--7806 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
7742 TGTTTATTAT
* *
7752 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
7776 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
7802 TGTTT
1 TGTTT
7807 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:8958 original size:18 final size:18
Alignment explanation
Indices: 8931--8974 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
8921 CTTCGGGAGT
8931 CATCACCTCACCCAGAGC
1 CATCACCTCACCCAGAGC
* *
8949 TATCATCTCACCCAGAGC
1 CATCACCTCACCCAGAGC
8967 CATCACCT
1 CATCACCT
8975 ATTCTGTCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.45, G:0.09, T:0.18
Consensus pattern (18 bp):
CATCACCTCACCCAGAGC
Found at i:9527 original size:19 final size:20
Alignment explanation
Indices: 9484--9539 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
9474 CGTAACACGA
9484 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
9504 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
9523 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
9540 TCAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:9547 original size:14 final size:14
Alignment explanation
Indices: 9528--9586 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
9518 ATGCGAAATG
9528 AAAATCGCAACGTC
1 AAAATCGCAACGTC
*
9542 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG---TC
*
9561 AAAATCGCAACGAC
1 AAAATCGCAACGTC
9575 AAAATCGCAACG
1 AAAATCGCAACG
9587 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 22 0.59
16 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.47, C:0.24, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGTC
Found at i:9554 original size:33 final size:33
Alignment explanation
Indices: 9512--9591 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
9502 GGAAATGGCT
*
9512 ATCGCAATGCGAAATGAAAATCGCAACGTCAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
9545 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
9578 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
9592 CACAAATTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:9566 original size:19 final size:19
Alignment explanation
Indices: 9512--9570 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
9502 GGAAATGGCT
9512 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
9531 ATCGCAA--CG---TCAAA
1 ATCGCAATGCGAAATGAAA
9545 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
9564 ATCGCAA
1 ATCGCAA
9571 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 11 0.33
16 2 0.06
17 2 0.06
19 18 0.55
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:9688 original size:20 final size:20
Alignment explanation
Indices: 9634--9720 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
9624 GCGATTTTGT
**
9634 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
* * *
9653 CATTGTGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
9673 CGTTGCGATAGTCATTTCCT
1 CGTTGCGATAGTCATTTCCG
*
9693 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
9713 CGTTGCGA
1 CGTTGCGA
9721 AAGTAAGTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
19 12 0.21
20 44 0.79
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:9731 original size:20 final size:19
Alignment explanation
Indices: 9666--9746 Score: 72
Period size: 20 Copynumber: 4.1 Consensus size: 19
9656 TGTGATAGCC
* *
9666 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGAAAGTA
* *
9686 ATTTCCTCGTTGCGATAGTCA
1 ATTT-CGCGTTGCGAAAGT-A
*
9707 TTTTCGCGTTGCGAAAGTA
1 ATTTCGCGTTGCGAAAGTA
*
9726 AGTTTCGTGTTGCGAAAGTA
1 A-TTTCGCGTTGCGAAAGTA
9746 A
1 A
9747 ACTATTCTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.02
20 48 0.92
21 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (19 bp):
ATTTCGCGTTGCGAAAGTA
Found at i:9738 original size:40 final size:40
Alignment explanation
Indices: 9659--9740 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
9649 TTCGCATTGT
* *
9659 GATAGCCATTTCCGCGTTGCGATAGTCATTTCCTCGTTGC
1 GATAGCCATTTCCGCGTTGCGAAAGTAATTTCCTCGTTGC
* * *
9699 GATAGTCATTTTCGCGTTGCGAAAGTAAGTTTCGT-GTTGC
1 GATAGCCATTTCCGCGTTGCGAAAGTAA-TTTCCTCGTTGC
9739 GA
1 GA
9741 AAGTAAACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
40 31 0.86
41 5 0.14
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (40 bp):
GATAGCCATTTCCGCGTTGCGAAAGTAATTTCCTCGTTGC
Found at i:10052 original size:21 final size:20
Alignment explanation
Indices: 10028--10095 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
10018 CTGTCATCCC
10028 TCAAGAGTCCCCTCCAATCAT
1 TCAAGAGTCCCCTCC-ATCAT
* * **
10049 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCAT
*
10070 TCAAGAGTCCCC-CCACCAT
1 TCAAGAGTCCCCTCCATCAT
10089 TCAAGAG
1 TCAAGAG
10096 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
19 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.28, C:0.40, G:0.13, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCAT
Found at i:10080 original size:42 final size:40
Alignment explanation
Indices: 10021--10098 Score: 129
Period size: 42 Copynumber: 1.9 Consensus size: 40
10011 GACTCACCTG
*
10021 TCATCCCTCAAGAGTCCCCTCCAATCATTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CC-ACCATTCAAGAGGCCCCTA
10063 TCATCCCTCAAGAGTCCCCCCACCATTCAAGAGGCC
1 TCATCCCTCAAGAGTCCCCCCACCATTCAAGAGGCC
10099 ACTGTCATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 14 0.40
41 2 0.06
42 19 0.54
ACGTcount: A:0.26, C:0.42, G:0.13, T:0.19
Consensus pattern (40 bp):
TCATCCCTCAAGAGTCCCCCCACCATTCAAGAGGCCCCTA
Found at i:10116 original size:40 final size:40
Alignment explanation
Indices: 10021--10106 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
10011 GACTCACCTG
* *
10021 TCATCCCTCAAGAGTCCCCTCCAATCATTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CC-ACCATTCAAGAGGCCACTA
*
10063 TCATCCCTCAAGAGTCCCCCCACCATTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCACCATTCAAGAGGCCACTA
10103 TCAT
1 TCAT
10107 TGTTGAAGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 20 0.49
41 2 0.05
42 19 0.46
ACGTcount: A:0.26, C:0.41, G:0.13, T:0.21
Consensus pattern (40 bp):
TCATCCCTCAAGAGTCCCCCCACCATTCAAGAGGCCACTA
Found at i:11498 original size:14 final size:14
Alignment explanation
Indices: 11464--11502 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
11454 TTGATTGTTT
11464 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
11478 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
11492 TGTTGATTTGT
1 AATTGATTTGT
11503 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:11648 original size:14 final size:14
Alignment explanation
Indices: 11629--11682 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
11619 GAAACTAACT
*
11629 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
11643 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
11662 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
11676 ATCGCAA
1 ATCGCAA
11683 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:11666 original size:19 final size:17
Alignment explanation
Indices: 11642--11687 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 17
11632 GCAACGAGAG
11642 AATCGCAATGCGAAATGAA
1 AATCGCAATGCG-AA-GAA
11661 AATCGCAA--CG-AGAA
1 AATCGCAATGCGAAGAA
11675 AATCGCAATGCGA
1 AATCGCAATGCGA
11688 TTTTCATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
14 11 0.46
15 1 0.04
16 2 0.08
17 2 0.08
19 8 0.33
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (17 bp):
AATCGCAATGCGAAGAA
Found at i:11731 original size:20 final size:20
Alignment explanation
Indices: 11706--11763 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
11696 TCGCATTGCG
*
11706 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
* *
11726 ATTTTCGCGTTGCGGTTGCC
1 ATTTTCGCGTTGCGATAGCC
11746 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
11764 TCAAATGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.12, C:0.22, G:0.26, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:12142 original size:20 final size:20
Alignment explanation
Indices: 12117--12184 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
12107 ATGTTGATCT
12117 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
12137 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
12157 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
*
12177 CATTGCGA
1 CGTTGCGA
12185 TTTTGTATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:12226 original size:20 final size:20
Alignment explanation
Indices: 12117--12216 Score: 112
Period size: 20 Copynumber: 5.0 Consensus size: 20
12107 ATGTTGATCT
*
12117 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGTATCG
*
12137 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGTATCG
12157 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
* ** *
12177 CATTGCGATTTTGT-ATTATCG
1 CGTTGCGA--AAGTCAGTATCG
*
12198 CGTTGCGATAGTCAGTATC
1 CGTTGCGAAAGTCAGTATC
12217 ACATTGCGAT
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.04
20 51 0.74
21 13 0.19
22 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGTATCG
Found at i:12280 original size:21 final size:20
Alignment explanation
Indices: 12256--12317 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
12246 ATTTACTTAT
*
12256 TCGCATTGTGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
*
12277 TCGCATCGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
*
12298 TCGCGTTGCGAATCTGGAAA
1 TCGCATTGCGAAT-TGGAAA
12318 CTGATTTGCG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 3 0.09
21 28 0.80
22 4 0.11
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:13425 original size:15 final size:16
Alignment explanation
Indices: 13396--13429 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
13386 AAATTAAGAA
*
13396 TTTAGATATTGGGGAT
1 TTTAGATATTAGGGAT
13412 TTTAGAT-TTAGGGAT
1 TTTAGATATTAGGGAT
13427 TTT
1 TTT
13430 GGGTGACAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (16 bp):
TTTAGATATTAGGGAT
Found at i:13646 original size:22 final size:21
Alignment explanation
Indices: 13619--13661 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
13609 AAAGTAATTT
13619 TATTTTTTA--ATTAAAAACAA
1 TATTTTTTATTATTAAAAA-AA
13639 TATTTTTTATTATTAAAAAAA
1 TATTTTTTATTATTAAAAAAA
13660 TA
1 TA
13662 AATGGCAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TATTTTTTATTATTAAAAAAA
Found at i:23449 original size:19 final size:18
Alignment explanation
Indices: 23426--23483 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
23416 AACCAATAAT
23426 AATAAACATAAAATAATTG
1 AATAAA-ATAAAATAATTG
*
23445 GATAAAA-AAAATGAAATTG
1 AATAAAATAAAAT--AATTG
*
23464 AATAAAATAAAATAAATG
1 AATAAAATAAAATAATTG
23482 AA
1 AA
23484 GATAAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 5 0.15
18 7 0.21
19 16 0.48
20 5 0.15
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.22
Consensus pattern (18 bp):
AATAAAATAAAATAATTG
Found at i:23617 original size:12 final size:13
Alignment explanation
Indices: 23589--23627 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
23579 GAAAATAAAT
*
23589 AAATAGTATAAATA
1 AAATA-TATAAAAA
23603 AAATA-ATAAAAA
1 AAATATATAAAAA
23615 AAATATATAAAAA
1 AAATATATAAAAA
23628 TATAAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 11 0.48
13 7 0.30
14 5 0.22
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
AAATATATAAAAA
Found at i:23618 original size:17 final size:17
Alignment explanation
Indices: 23542--23619 Score: 50
Period size: 17 Copynumber: 4.4 Consensus size: 17
23532 TTAAAAAAAG
*
23542 AAAAATAATAATAAGAACA
1 AAAAATAA-AATAATAA-A
* *
23561 AAAAATTAAAATTATAAT
1 AAAAA-TAAAATAATAAA
* **
23579 GAAAAT-AAATAAATAGT
1 AAAAATAAAAT-AATAAA
*
23596 ATAAATAAAATAATAAA
1 AAAAATAAAATAATAAA
23613 AAAAATA
1 AAAAATA
23620 TATAAAAATA
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
16 4 0.09
17 19 0.42
18 8 0.18
19 11 0.24
20 3 0.07
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (17 bp):
AAAAATAAAATAATAAA
Found at i:23802 original size:13 final size:13
Alignment explanation
Indices: 23784--23809 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23774 TAACGTTAGG
23784 AAAATATAGTAAA
1 AAAATATAGTAAA
23797 AAAATATAGTAAA
1 AAAATATAGTAAA
23810 TAAGTAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
AAAATATAGTAAA
Found at i:23921 original size:23 final size:23
Alignment explanation
Indices: 23895--23938 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
23885 AATGAAAAAA
23895 AAAAT-TATAACAAATAAATAAAT
1 AAAATATAT-ACAAATAAATAAAT
*
23918 AAAATATATACATATAAATAA
1 AAAATATATACAAATAAATAA
23939 TAAGGGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAATATATACAAATAAATAAAT
Found at i:24425 original size:37 final size:37
Alignment explanation
Indices: 24332--24435 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
24322 ATGTTTGTGG
* * ** *
24332 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
* * *
24369 ATCATATTTTTAGGAGTTTGAATCCTAGTAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
24406 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
24436 GGACGAAAAG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:25370 original size:106 final size:106
Alignment explanation
Indices: 25186--26460 Score: 1971
Period size: 106 Copynumber: 12.0 Consensus size: 106
25176 GCATTGTTCC
* * * *
25186 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
25251 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTATC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
25292 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTTTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
25357 CCAGCGGTCCCTTCGTCCTGAAGTTCAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
25398 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
25463 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
25504 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
25569 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
25610 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
25675 CCAGCGGTCCCTTCATCGTGAAGCTGAGCTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
25716 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTTTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
25781 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
25822 GAGTCCAATATTCTTCGCTT-TGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCG-TTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
25886 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
25928 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
**
25993 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTAACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
26034 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
26098 CCAGCTGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
26139 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
26204 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
26245 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
26310 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
26351 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAACTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
26416 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
26457 GAGT
1 GAGT
26461 GGCACGATAT
Statistics
Matches: 1084, Mismatches: 81, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
105 100 0.09
106 983 0.91
107 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:28082 original size:17 final size:16
Alignment explanation
Indices: 28056--28116 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
28046 TTTTTGTCCC
28056 TTTTTC-TTTTTGATT
1 TTTTTCTTTTTTGATT
28071 TTTGTTCTTTTTTTTG-TT
1 TTT-TTC--TTTTTTGATT
* *
28089 TTCTTCTTTTTTGCTT
1 TTTTTCTTTTTTGATT
*
28105 CTTTTCTTTTTT
1 TTTTTCTTTTTT
28117 TTTTTGCCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
15 10 0.26
16 15 0.39
17 3 0.08
18 4 0.11
19 6 0.16
ACGTcount: A:0.02, C:0.11, G:0.07, T:0.80
Consensus pattern (16 bp):
TTTTTCTTTTTTGATT
Found at i:32551 original size:22 final size:20
Alignment explanation
Indices: 32521--32568 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
32511 GCAAAGAAAC
32521 TAAAAATAT-AATGAAAATAAA
1 TAAAAATATAAAT-AAAAT-AA
32542 TAAATAATATAAATAAAATAA
1 TAAA-AATATAAATAAAATAA
32563 TAAAAA
1 TAAAAA
32569 AATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.08
21 10 0.40
22 10 0.40
23 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (20 bp):
TAAAAATATAAATAAAATAA
Found at i:32572 original size:22 final size:23
Alignment explanation
Indices: 32522--32574 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
32512 CAAAGAAACT
32522 AAAAATAT-AATGAAAATAAATA
1 AAAAATATAAATGAAAATAAATA
*
32544 AATAATATAAAT-AAAAT-AATAA
1 AAAAATATAAATGAAAATAAAT-A
32566 AAAAATATA
1 AAAAATATA
32575 TATATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 3 0.11
22 21 0.78
23 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAAATATAAATGAAAATAAATA
Found at i:32591 original size:26 final size:25
Alignment explanation
Indices: 32536--32594 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
32526 ATATAATGAA
*
32536 AATAAATAAATAATATAAATAAAAT
1 AATAAAAAAATAATATAAATAAAAT
*
32561 AATAAAAAAATATATATATATATAAAT
1 AATAAAAAAATA-ATATAAATA-AAAT
32588 -ATAAAAA
1 AATAAAAA
32595 TGTATGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 11 0.37
26 15 0.50
27 4 0.13
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (25 bp):
AATAAAAAAATAATATAAATAAAAT
Found at i:32682 original size:30 final size:30
Alignment explanation
Indices: 32648--32726 Score: 74
Period size: 30 Copynumber: 2.6 Consensus size: 30
32638 TAAATAAATG
*
32648 AAAAATAA-ATATACATAT-AATATTAACTAA
1 AAAAATAATA-AT-CATATAAATATAAACTAA
*
32678 AAAAATAGTAATCATATAAATATAAACTAA
1 AAAAATAATAATCATATAAATATAAACTAA
*
32708 AATAAAGTAAGAAT-ATATA
1 AA-AAA-TAATAATCATATA
32727 TGTATAACAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
29 5 0.12
30 22 0.54
31 9 0.22
32 5 0.12
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (30 bp):
AAAAATAATAATCATATAAATATAAACTAA
Found at i:32693 original size:29 final size:29
Alignment explanation
Indices: 32661--32717 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
32651 AATAAATATA
*
32661 CATAT-AATATTAACTAAAAAAATAGTAAT
1 CATATAAATATAAACTAAAAAAA-AGTAAT
*
32690 CATATAAATATAAACTAAAATAAAGTAA
1 CATATAAATATAAACTAAAAAAAAGTAA
32718 GAATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (29 bp):
CATATAAATATAAACTAAAAAAAAGTAAT
Found at i:32723 original size:29 final size:30
Alignment explanation
Indices: 32662--32724 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
32652 ATAAATATAC
* **
32662 ATAT-AATATTAACTAAAAAAATAGTAATC
1 ATATAAATATAAACTAAAAAAATAGTAAGA
*
32691 ATATAAATATAAACTAAAATAA-AGTAAGA
1 ATATAAATATAAACTAAAAAAATAGTAAGA
32720 ATATA
1 ATATA
32725 TATGTATAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (30 bp):
ATATAAATATAAACTAAAAAAATAGTAAGA
Found at i:32813 original size:3 final size:3
Alignment explanation
Indices: 32780--32850 Score: 67
Period size: 3 Copynumber: 23.0 Consensus size: 3
32770 GTAAACATAG
*
32780 ATA AAA ATA ATA TATA TATA TATA TATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA -ATA -ATA -ATA -ATA ATA ATA ATA ATA ATA ATA ATA
32829 ATA ATA GA-A A-A ATA AT- ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA
32851 TAACGCAAGG
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 5 0.08
3 41 0.66
4 16 0.26
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:33420 original size:37 final size:37
Alignment explanation
Indices: 33327--33428 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
33317 ATGCTTGTGG
* * ** * *
33327 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* *
33364 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
33401 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
33429 TATGATGAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:47283 original size:40 final size:41
Alignment explanation
Indices: 47200--47284 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 41
47190 CATAGTCGCT
47200 GTTTTCATTTACATTTCATGTCCTATTTCTTTCACCTCGGATA
1 GTTTTCATTTACATTTCATGTCCTA--TCTTTCACCTCGGATA
47243 GTTTTCATTTACATTTCATGTCCTA-CTTTCACCTCGGATA
1 GTTTTCATTTACATTTCATGTCCTATCTTTCACCTCGGATA
47283 GT
1 GT
47285 GGCAATCTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
40 17 0.40
43 25 0.60
ACGTcount: A:0.19, C:0.24, G:0.11, T:0.47
Consensus pattern (41 bp):
GTTTTCATTTACATTTCATGTCCTATCTTTCACCTCGGATA
Found at i:47959 original size:14 final size:14
Alignment explanation
Indices: 47940--47971 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
47930 CGTTCGTGAA
47940 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
47954 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
47968 CGTT
1 CGTT
47972 TATGTTCATT
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:0.06, C:0.16, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:49088 original size:16 final size:16
Alignment explanation
Indices: 49067--49133 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
49057 GTCTCCAACG
49067 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
49083 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
* **
49099 TTTATGTTCATGTTTG
1 TTTATGTTCGTGTTCA
49115 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
49129 TTTAT
1 TTTAT
49134 TAAATGAACG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 39 0.85
ACGTcount: A:0.12, C:0.09, G:0.18, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:49106 original size:32 final size:32
Alignment explanation
Indices: 49065--49125 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
49055 AGGTCTCCAA
*
49065 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCATGTTCATTTATGTTCGTGTT
**
49097 CGTTTATGTTCATGTTTGTTTATGTTCGT
1 CGTTTATGTTCATGTTCATTTATGTTCGT
49126 TTATTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.10, C:0.11, G:0.21, T:0.57
Consensus pattern (32 bp):
CGTTTATGTTCATGTTCATTTATGTTCGTGTT
Found at i:49116 original size:26 final size:26
Alignment explanation
Indices: 49077--49129 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
49067 TTTATGTTCG
*
49077 TGTTCATTTATGTTCGTGTTCGTTTA
1 TGTTCATTTATGTTCATGTTCGTTTA
*
49103 TGTTCATGTT-TGTTTATGTTCGTTTA
1 TGTTCAT-TTATGTTCATGTTCGTTTA
49129 T
1 T
49130 TTATTAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.11, C:0.09, G:0.19, T:0.60
Consensus pattern (26 bp):
TGTTCATTTATGTTCATGTTCGTTTA
Found at i:49243 original size:14 final size:14
Alignment explanation
Indices: 49224--49255 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
49214 CGTTCGTGAA
49224 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
49238 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
49252 CGTT
1 CGTT
49256 TATGTTCATT
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:0.06, C:0.16, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:50373 original size:16 final size:16
Alignment explanation
Indices: 50352--50418 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
50342 GCCTCCAACG
50352 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
50368 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
* **
50384 TTTATGTTCATGTTTG
1 TTTATGTTCGTGTTCA
50400 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
50414 TTTAT
1 TTTAT
50419 TAAATGAACG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 39 0.85
ACGTcount: A:0.12, C:0.09, G:0.18, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:50391 original size:32 final size:32
Alignment explanation
Indices: 50350--50410 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
50340 AGGCCTCCAA
*
50350 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCATGTTCATTTATGTTCGTGTT
**
50382 CGTTTATGTTCATGTTTGTTTATGTTCGT
1 CGTTTATGTTCATGTTCATTTATGTTCGT
50411 TTATTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.10, C:0.11, G:0.21, T:0.57
Consensus pattern (32 bp):
CGTTTATGTTCATGTTCATTTATGTTCGTGTT
Found at i:50401 original size:26 final size:26
Alignment explanation
Indices: 50362--50414 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
50352 TTTATGTTCG
*
50362 TGTTCATTTATGTTCGTGTTCGTTTA
1 TGTTCATTTATGTTCATGTTCGTTTA
*
50388 TGTTCATGTT-TGTTTATGTTCGTTTA
1 TGTTCAT-TTATGTTCATGTTCGTTTA
50414 T
1 T
50415 TTATTAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.11, C:0.09, G:0.19, T:0.60
Consensus pattern (26 bp):
TGTTCATTTATGTTCATGTTCGTTTA
Found at i:50508 original size:16 final size:14
Alignment explanation
Indices: 50487--50521 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
50477 ATTTTGTTCG
50487 TTTATGTTCGTATTCA
1 TTTATGTTCGT-TT-A
50503 TTTATGTTCGTTTA
1 TTTATGTTCGTTTA
50517 TTTAT
1 TTTAT
50522 TAAATGAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 2 0.11
16 11 0.58
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.63
Consensus pattern (14 bp):
TTTATGTTCGTTTA
Found at i:50915 original size:22 final size:22
Alignment explanation
Indices: 50859--50915 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
50849 TGCAGCTAAA
*
50859 ACCCAACCATCACACAAAATCC
1 ACCCAACCCTCACACAAAATCC
* * *
50881 ACCGGAACACTCACA-AATATCCC
1 ACC-CAACCCTCACACAAAAT-CC
50904 ACCCAACCCTCA
1 ACCCAACCCTCA
50916 AAAGAAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.40, C:0.46, G:0.04, T:0.11
Consensus pattern (22 bp):
ACCCAACCCTCACACAAAATCC
Found at i:53831 original size:45 final size:48
Alignment explanation
Indices: 53749--53877 Score: 126
Period size: 45 Copynumber: 2.8 Consensus size: 48
53739 TATTCACGTG
* * * * *
53749 ATAAATTTTAA-TAAAATTATTTTTTATTTAAATTTTTATCT-TGGTATA
1 ATAAAATTTAATTAAAAATA-TATTTATTTAAAATTTTAT-TATGATATA
* *
53797 ATAAAATTTAA-TAAAAA-A-ATTTATTTAAAATTTTATTATGATGTG
1 ATAAAATTTAATTAAAAATATATTTATTTAAAATTTTATTATGATATA
53842 ATAAAATTTAATTAAAAATATATTT-TATTAAAATTT
1 ATAAAATTTAATTAAAAATATATTTAT-TTAAAATTT
53878 ATCACTTTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
44 1 0.01
45 31 0.45
46 6 0.09
47 3 0.04
48 28 0.41
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.50
Consensus pattern (48 bp):
ATAAAATTTAATTAAAAATATATTTATTTAAAATTTTATTATGATATA
Found at i:55649 original size:23 final size:23
Alignment explanation
Indices: 55623--55682 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
55613 ATCAAGCACA
* *
55623 ATAATATATTAGGTA-CTGCTTAT
1 ATAATATAATAGGTATC-ACTTAT
*
55646 ATAATGTAATAGGTATCACTTAT
1 ATAATATAATAGGTATCACTTAT
*
55669 ATAATAAAATAGGT
1 ATAATATAATAGGT
55683 TAATTACTGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTATCACTTAT
Found at i:55736 original size:23 final size:23
Alignment explanation
Indices: 55722--55792 Score: 106
Period size: 23 Copynumber: 3.1 Consensus size: 23
55712 AACATATTAA
*
55722 GTAGCGCTTATATAATGTAATAG
1 GTAGCGCTTATATAATATAATAG
*
55745 GTAGCGCTTATATAATAAAATAG
1 GTAGCGCTTATATAATATAATAG
* *
55768 GTAGCGATTATATAATAAAATAG
1 GTAGCGCTTATATAATATAATAG
55791 GT
1 GT
55793 TAATTACTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (23 bp):
GTAGCGCTTATATAATATAATAG
Found at i:55746 original size:110 final size:109
Alignment explanation
Indices: 55623--55876 Score: 357
Period size: 110 Copynumber: 2.3 Consensus size: 109
55613 ATCAAGCACA
* * ** *
55623 ATAATATATTAGGTACTGCTTATATAATGTAATAGGTATC-ACTTATATAATAAAATAGGTTAAT
1 ATAATGTAATAGGTAC-GCTTATATAATAAAATAGGTAGCGA-TTATATAATAAAATAGGTTAAT
* *
55687 TACTGGAAACATTATCAAACACAATAACATATTAAGTAGCGCTTAT
64 TACTAGAAACATTATCAAACACAATAACATATTAAGTAGCACTTAT
55733 ATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTAGCGATTATATAATAAAATAGGTTAATT
1 ATAATGTAATAGGTA-CGCTTATATAATAAAATAGGTAGCGATTATATAATAAAATAGGTTAATT
* * * *
55798 ACTATAAACATTATCAAGCACAATAACATATTAGGTATCACTTAT
65 ACTAGAAACATTATCAAACACAATAACATATTAAGTAGCACTTAT
*
55843 ATAATGTAATAGGTAACACTTATATAATAAAATA
1 ATAATGTAATAGGT-ACGCTTATATAATAAAATA
55877 AGTTAATTAC
Statistics
Matches: 129, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
110 126 0.98
111 3 0.02
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (109 bp):
ATAATGTAATAGGTACGCTTATATAATAAAATAGGTAGCGATTATATAATAAAATAGGTTAATTA
CTAGAAACATTATCAAACACAATAACATATTAAGTAGCACTTAT
Found at i:55767 original size:87 final size:86
Alignment explanation
Indices: 55533--55769 Score: 357
Period size: 87 Copynumber: 2.7 Consensus size: 86
55523 ATTACAAAGT
* * * * *
55533 ACAATAACATATTAGGTATCACTTATATAATATAATAGATAGCTCTTATATAATAAAATAAGTTA
1 ACAATAACATATTAGGTA-CGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTA
*
55598 ATTACTGGAAACATTATCAAGC
65 ATTACTGGAAACATTATCAAAC
* *
55620 ACAATAATATATTAGGTACTGCTTATATAATGTAATAGGTATCACTTATATAATAAAATAGGTTA
1 ACAATAACATATTAGGTAC-GCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTA
55685 ATTACTGGAAACATTATCAAAC
65 ATTACTGGAAACATTATCAAAC
* *
55707 ACAATAACATATTAAGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGT
1 ACAATAACATATTAGGTA-CGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGT
55770 AGCGATTATA
Statistics
Matches: 136, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
86 1 0.01
87 134 0.99
88 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (86 bp):
ACAATAACATATTAGGTACGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAA
TTACTGGAAACATTATCAAAC
Found at i:55833 original size:87 final size:87
Alignment explanation
Indices: 55742--55974 Score: 351
Period size: 87 Copynumber: 2.7 Consensus size: 87
55732 TATAATGTAA
** *
55742 TAGGTAGCGCTTATATAATAAAATAGGTAGCGATTATATAATAAAATAGGTTAATTACTATAAAC
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGATTATATAATAAAATAGGTTAATTACTAGAAAC
55807 ATTATCAAGCACAATAACATAT
66 ATTATCAAGCACAATAACATAT
* * * * *
55829 TAGGTATCACTTATATAATGTAATAGGTAAC-ACTTATATAATAAAATAAGTTAATTACTGGAAA
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGA-TTATATAATAAAATAGGTTAATTACTAGAAA
*
55893 CATTATCAAGCACAATCACATAT
65 CATTATCAAGCACAATAACATAT
* *
55916 TAGGTAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACT
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGATTATATAATAAAATAGGTTAATTACT
55975 TAATTTGTTA
Statistics
Matches: 129, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
86 1 0.01
87 128 0.99
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.32
Consensus pattern (87 bp):
TAGGTAGCGCTTATATAATGTAATAGGTAGCGATTATATAATAAAATAGGTTAATTACTAGAAAC
ATTATCAAGCACAATAACATAT
Found at i:55876 original size:23 final size:23
Alignment explanation
Indices: 55829--55876 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
55819 AATAACATAT
* **
55829 TAGGTATCACTTATATAATGTAA
1 TAGGTAACACTTATATAATAAAA
55852 TAGGTAACACTTATATAATAAAA
1 TAGGTAACACTTATATAATAAAA
55875 TA
1 TA
55877 AGTTAATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.35
Consensus pattern (23 bp):
TAGGTAACACTTATATAATAAAA
Found at i:55889 original size:197 final size:197
Alignment explanation
Indices: 55536--55966 Score: 675
Period size: 197 Copynumber: 2.2 Consensus size: 197
55526 ACAAAGTACA
* * * * * * **
55536 ATAACATATTAGGTATCACTTATATAATATAATAGATAGCTCTTATATAATAAAATAAGTTAATT
1 ATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTAGCGATTATATAATAAAATAAGTTAATT
* * * *
55601 ACTGGAAACATTATCAAGCACAATAATATATTAGGTACTGCTTATATAATGTAATAGGTATCACT
66 ACTAGAAACATTATCAAGCACAATAACATATTAGGTACTACTTATATAATGTAATAGGTAACACT
*
55666 TATATAATAAAATAGGTTAATTACTGGAAACATTATCAAACACAATAACATATTAAGTAGCGCTT
131 TATATAATAAAATAAGTTAATTACTGGAAACATTATCAAACACAATAACATATTAAGTAGCGCTT
55731 AT
196 AT
* *
55733 ATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTAGCGATTATATAATAAAATAGGTTAATT
1 ATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTAGCGATTATATAATAAAATAAGTTAATT
*
55798 ACTATAAACATTATCAAGCACAATAACATATTAGGTA-TCACTTATATAATGTAATAGGTAACAC
66 ACTAGAAACATTATCAAGCACAATAACATATTAGGTACT-ACTTATATAATGTAATAGGTAACAC
* * *
55862 TTATATAATAAAATAAGTTAATTACTGGAAACATTATCAAGCACAATCACATATTAGGTAGCGCT
130 TTATATAATAAAATAAGTTAATTACTGGAAACATTATCAAACACAATAACATATTAAGTAGCGCT
55927 TAT
195 TAT
55930 ATAACGTAATAGGTAGCGCTTATATAATAAAATAGGT
1 ATAACGTAATAGGTAGCGCTTATATAATAAAATAGGT
55967 TAATTACTTA
Statistics
Matches: 213, Mismatches: 20, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
196 1 0.00
197 212 1.00
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (197 bp):
ATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTAGCGATTATATAATAAAATAAGTTAATT
ACTAGAAACATTATCAAGCACAATAACATATTAGGTACTACTTATATAATGTAATAGGTAACACT
TATATAATAAAATAAGTTAATTACTGGAAACATTATCAAACACAATAACATATTAAGTAGCGCTT
AT
Found at i:55963 original size:23 final size:23
Alignment explanation
Indices: 55916--55966 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
55906 AATCACATAT
**
55916 TAGGTAGCGCTTATATAACGTAA
1 TAGGTAGCGCTTATATAACAAAA
*
55939 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAACAAAA
55962 TAGGT
1 TAGGT
55967 TAATTACTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAACAAAA
Found at i:56517 original size:24 final size:23
Alignment explanation
Indices: 56490--56545 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 23
56480 TTACCAAGGA
56490 TAACAATAAAATAATATTATTTAT
1 TAACAATAAAATAATATTATTT-T
56514 TAACAA-AATAATAATATTATTTT
1 TAACAATAA-AATAATATTATTTT
56537 TAA-AATAAA
1 TAACAATAAA
56546 CATTGCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 3 0.10
23 8 0.27
24 19 0.63
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (23 bp):
TAACAATAAAATAATATTATTTT
Found at i:56951 original size:200 final size:197
Alignment explanation
Indices: 56545--56987 Score: 552
Period size: 200 Copynumber: 2.2 Consensus size: 197
56535 TTTAAAATAA
* * * *
56545 ACATTGCAAATGTATCTATTACATTATAATTATCGGTTACGATGTTTTTGGGATCGATATAATTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATAT-ATTT
* * *
56610 TAAATGTATCGACACTTTATGCGTGCACCTCATTGGTTATTCATTCTGGAAAAAAGTATTAACAC
65 TAAATGTATCGACACTTTATGCGTGCACCTCATTGGTCATTCATTATGGAAAAAAGTATCAACAC
* * ** *
56675 AAACTTAAAATGTGTCGATACATTATGTAGACTTATTTTCTCATAAAATCGGTATATTTATATAG
130 AAACTTAAAATGTGTCGATACATTATGTAGACCTATTCTCTCATAAAATCAATATATTTATACAG
56740 AGT
195 AGT
*
56743 ACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATACT-TTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATA-TATTT
* * * *
56807 AATAAATGTATCGACACTTTATGTGTGCACCTCGTTTGG-CATTCATTATGGACAAAATGTATCG
65 --TAAATGTATCGACACTTTATGCGTGCACCTC-ATTGGTCATTCATTATGGA-AAAAAGTATCA
*** * * *
56871 ACAC-TTTTTAAATTTGTGTCGATATATTATGTTGACCTATTCTCTCATAAAATCAATATATTTA
126 ACACAAACTTAAA-ATGTGTCGATACATTATGTAGACCTATTCTCTCATAAAATCAATATATTTA
*
56935 TACCG-GTT
190 TACAGAG-T
* *
56943 ATATTGTAAATTTACCTATTACATTATAATTATCGGTTTTGATGT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
56988 AACATATGTG
Statistics
Matches: 211, Mismatches: 27, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
197 3 0.01
198 54 0.26
199 48 0.23
200 106 0.50
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (197 bp):
ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATATATTTT
AAATGTATCGACACTTTATGCGTGCACCTCATTGGTCATTCATTATGGAAAAAAGTATCAACACA
AACTTAAAATGTGTCGATACATTATGTAGACCTATTCTCTCATAAAATCAATATATTTATACAGA
GT
Found at i:57116 original size:13 final size:14
Alignment explanation
Indices: 57088--57120 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
57078 TTATAATAAA
57088 TAATAATATAATTT
1 TAATAATATAATTT
*
57102 TAATAAT-TTATTT
1 TAATAATATAATTT
57115 TAATAA
1 TAATAA
57121 AATATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATAATATAATTT
Found at i:57221 original size:24 final size:25
Alignment explanation
Indices: 57192--57256 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 25
57182 TAAATAATAT
57192 TAAATAAATTATTTTAATATTTTAA
1 TAAATAAATTATTTTAATATTTTAA
*
57217 -AAAT-AA-TATTATTATTATTTTAA
1 TAAATAAATTATT-TTAATATTTTAA
*
57240 TAAATATTATTATTTTA
1 TAAATA-AATTATTTTA
57257 TTGTATTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
22 4 0.12
23 13 0.39
24 8 0.24
26 4 0.12
27 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TAAATAAATTATTTTAATATTTTAA
Found at i:57239 original size:23 final size:24
Alignment explanation
Indices: 57192--57258 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 24
57182 TAAATAATAT
*
57192 TAAATAA-ATTATTTTAATATTTTAA
1 TAAATAATATTA--TTATTATTTTAA
57217 -AAATAATATTATTATTATTTTAA
1 TAAATAATATTATTATTATTTTAA
*
57240 TAAATATTATTATT-TTATT
1 TAAATAATATTATTATTATT
57259 GTATTTGATG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
23 16 0.42
24 18 0.47
25 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TAAATAATATTATTATTATTTTAA
Found at i:57247 original size:21 final size:22
Alignment explanation
Indices: 57191--57253 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
57181 ATAAATAATA
*
57191 TTAAATAAATTATT-TTAATATT
1 TTAAATAAA-TATTATTATTATT
*
57213 TTAAAAATAATATTATTATTATT
1 TTAAATA-AATATTATTATTATT
57236 TT-AATAAATATTATTATT
1 TTAAATAAATATTATTATT
57254 TTATTGTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 12 0.33
22 13 0.36
23 11 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAAATAAATATTATTATTATT
Found at i:57697 original size:31 final size:31
Alignment explanation
Indices: 57661--57720 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
57651 TATGCACAAT
* *
57661 AATAACAAAACCGGTATCACTTTTTTTTATC
1 AATAACAAAACCGATACCACTTTTTTTTATC
*
57692 AATAACAAAATCGATACCACTTTTTTTTA
1 AATAACAAAACCGATACCACTTTTTTTTA
57721 GCAGTATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (31 bp):
AATAACAAAACCGATACCACTTTTTTTTATC
Found at i:61416 original size:60 final size:60
Alignment explanation
Indices: 61352--61468 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
61342 CTGCCTCTGC
* * * *
61352 CTTTGCCACTGTCT-TGGCTTCTGCCTTTACCTCCGTCTTTTGTTCTTCCTTTATCACTAT
1 CTTTGCCACTGTCTCTGCCTT-TGCCTTTACCTCCGTCTTTGGCTCTGCCTTTATCACTAT
* * * *
61412 CTTTGCCTCTGTGTCTGCCTTTGCCTTTATCTCTGTCTTTGGCTCTGCCTTTATCAC
1 CTTTGCCACTGTCTCTGCCTTTGCCTTTACCTCCGTCTTTGGCTCTGCCTTTATCAC
61469 CTTCTTTACT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 43 0.90
61 5 0.10
ACGTcount: A:0.07, C:0.32, G:0.14, T:0.48
Consensus pattern (60 bp):
CTTTGCCACTGTCTCTGCCTTTGCCTTTACCTCCGTCTTTGGCTCTGCCTTTATCACTAT
Found at i:61445 original size:24 final size:24
Alignment explanation
Indices: 61418--61466 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
61408 CTATCTTTGC
* *
61418 CTCTGTGTCTGCCTTTGCCTTTAT
1 CTCTGTCTCTGCCTCTGCCTTTAT
* *
61442 CTCTGTCTTTGGCTCTGCCTTTAT
1 CTCTGTCTCTGCCTCTGCCTTTAT
61466 C
1 C
61467 ACCTTCTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.04, C:0.31, G:0.16, T:0.49
Consensus pattern (24 bp):
CTCTGTCTCTGCCTCTGCCTTTAT
Found at i:61499 original size:84 final size:84
Alignment explanation
Indices: 61323--61499 Score: 187
Period size: 84 Copynumber: 2.1 Consensus size: 84
61313 TGCCTTTACT
* *
61323 ACTGTCTTTCCCTCTGTGTCTGCCTCTGCCTTTGCCACTGTCTTGGCTTCTGCCTTTACCTCCGT
1 ACTGTCTTTCCCTCTGTGTCTGCCTCTGCCTTTACCACTGTCTTGGCTTCTGCCTTTACCACCGT
** * *
61388 CTTTTGTTCTTCCTTTATC
66 CTTTACTTCTTCATTTAGC
* * * * * * *
61407 ACTATCTTTGCCTCTGTGTCTGCCTTTGCCTTTATCTCTGTCTTTGGC-TCTGCCTTTATCACCT
1 ACTGTCTTTCCCTCTGTGTCTGCCTCTGCCTTTACCACTGTC-TTGGCTTCTGCCTTTACCACCG
*
61471 TCTTTACTTCTAT-ATTTGGC
65 TCTTTACTTCT-TCATTTAGC
*
61491 TCTGTCTTT
1 ACTGTCTTT
61500 ACTTCTGACG
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
84 69 0.92
85 6 0.08
ACGTcount: A:0.07, C:0.31, G:0.14, T:0.49
Consensus pattern (84 bp):
ACTGTCTTTCCCTCTGTGTCTGCCTCTGCCTTTACCACTGTCTTGGCTTCTGCCTTTACCACCGT
CTTTACTTCTTCATTTAGC
Found at i:61975 original size:39 final size:39
Alignment explanation
Indices: 61912--62144 Score: 277
Period size: 39 Copynumber: 6.0 Consensus size: 39
61902 ATAGGCTCAT
* * * * *
61912 GTTCCTTTTGTCGTTCCAAAACTGCACTAGAACTATCAA
1 GTTCGTTTTGTTGTTCCGAAACTGCACTAGAAATATCAC
* * *
61951 GTTCGTTTTGTTGTTCCGACACTGCGCTAGAATTATCAC
1 GTTCGTTTTGTTGTTCCGAAACTGCACTAGAAATATCAC
* * * *
61990 GTTCGTTTTGTTGTTTCGAAACTGCATTAGAACTATCAA
1 GTTCGTTTTGTTGTTCCGAAACTGCACTAGAAATATCAC
* * * *
62029 GTTCGTTTTGTCGTTCCGACACTGCGCTAGAATTATCAC
1 GTTCGTTTTGTTGTTCCGAAACTGCACTAGAAATATCAC
* *
62068 GTTTGTTTTGTTGTTTCGAAACTGCACTAGAAATATCAC
1 GTTCGTTTTGTTGTTCCGAAACTGCACTAGAAATATCAC
* * *
62107 GTCCGCTTTGTTGTTCCGAAATTGCACTAGAAATATCA
1 GTTCGTTTTGTTGTTCCGAAACTGCACTAGAAATATCA
62145 TCGGTATATG
Statistics
Matches: 163, Mismatches: 31, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 163 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (39 bp):
GTTCGTTTTGTTGTTCCGAAACTGCACTAGAAATATCAC
Found at i:62046 original size:78 final size:78
Alignment explanation
Indices: 61912--62144 Score: 331
Period size: 78 Copynumber: 3.0 Consensus size: 78
61902 ATAGGCTCAT
* * * *
61912 GTTCCTTTTGTCGTTCCAAAACTGCACTAGAACTATCAAGTTCGTTTTGTTGTTCCGACACTGCG
1 GTTCGTTTTGTTGTTTCGAAACTGCACTAGAACTATCAAGTTCGTTTTGTTGTTCCGACACTGCG
61977 CTAGAATTATCAC
66 CTAGAATTATCAC
* *
61990 GTTCGTTTTGTTGTTTCGAAACTGCATTAGAACTATCAAGTTCGTTTTGTCGTTCCGACACTGCG
1 GTTCGTTTTGTTGTTTCGAAACTGCACTAGAACTATCAAGTTCGTTTTGTTGTTCCGACACTGCG
62055 CTAGAATTATCAC
66 CTAGAATTATCAC
* * * * * * * *
62068 GTTTGTTTTGTTGTTTCGAAACTGCACTAGAAATATCACGTCCGCTTTGTTGTTCCGAAATTGCA
1 GTTCGTTTTGTTGTTTCGAAACTGCACTAGAACTATCAAGTTCGTTTTGTTGTTCCGACACTGCG
*
62133 CTAGAAATATCA
66 CTAGAATTATCA
62145 TCGGTATATG
Statistics
Matches: 138, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 138 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (78 bp):
GTTCGTTTTGTTGTTTCGAAACTGCACTAGAACTATCAAGTTCGTTTTGTTGTTCCGACACTGCG
CTAGAATTATCAC
Found at i:62127 original size:117 final size:117
Alignment explanation
Indices: 61912--62144 Score: 313
Period size: 117 Copynumber: 2.0 Consensus size: 117
61902 ATAGGCTCAT
* *
61912 GTTCCTTTTGTCGTTCCAAAACTGCACTAGAACTATCAAGTTCGTTTTGTTGTTCCGACACTGCG
1 GTTCCTTTTGTCGTTCCAAAACTGCACTAGAACTATCAAGTTCGTTTTGTTGTTCCGAAACTGCA
* * * * * *
61977 CTAGAATTATCACGTTCGTTTTGTTGTTTCGAAACTGCATTAGAACTATCAA
66 CTAGAAATATCACGTCCGCTTTGTTGTTCCGAAACTGCACTAGAAATATCAA
* * * * * * * *
62029 GTTCGTTTTGTCGTTCCGACACTGCGCTAGAATTATCACGTTTGTTTTGTTGTTTCGAAACTGCA
1 GTTCCTTTTGTCGTTCCAAAACTGCACTAGAACTATCAAGTTCGTTTTGTTGTTCCGAAACTGCA
*
62094 CTAGAAATATCACGTCCGCTTTGTTGTTCCGAAATTGCACTAGAAATATCA
66 CTAGAAATATCACGTCCGCTTTGTTGTTCCGAAACTGCACTAGAAATATCA
62145 TCGGTATATG
Statistics
Matches: 99, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
117 99 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (117 bp):
GTTCCTTTTGTCGTTCCAAAACTGCACTAGAACTATCAAGTTCGTTTTGTTGTTCCGAAACTGCA
CTAGAAATATCACGTCCGCTTTGTTGTTCCGAAACTGCACTAGAAATATCAA
Found at i:62380 original size:39 final size:39
Alignment explanation
Indices: 62262--62477 Score: 177
Period size: 39 Copynumber: 5.5 Consensus size: 39
62252 ATTGGTATCG
* * * *
62262 TCCGCTTCACCTTGATCAGCAGCGTTTGGTGCTATGGCGTCA
1 TCCGCTCCACCTTGATCAGCA---TTTGGTGTTCTGGCATCA
* * * * *
62304 TACGCTCCACCTTGATCAGCATTGGGTGCTATGGCATCG
1 TCCGCTCCACCTTGATCAGCATTTGGTGTTCTGGCATCA
* *
62343 TTCGCTCCACCTTGATCAGCATTTGGTGTTCTAGCATCA
1 TCCGCTCCACCTTGATCAGCATTTGGTGTTCTGGCATCA
* * *
62382 TCCGCTTCATCC-TGATCA-TATTTTGGTGTTCTGGTATCA
1 TCCGCTCCA-CCTTGATCAGCA-TTTGGTGTTCTGGCATCA
* * * *
62421 TCCGCTTCACCCTGATCAGCTTTTGGTGTTTCT-GTATCA
1 TCCGCTCCACCTTGATCAGCATTTGGTG-TTCTGGCATCA
* *
62460 TCCACTTCACCTTGATCA
1 TCCGCTCCACCTTGATCA
62478 TCTTTCACAA
Statistics
Matches: 149, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
38 3 0.02
39 121 0.81
40 6 0.04
42 19 0.13
ACGTcount: A:0.16, C:0.28, G:0.20, T:0.36
Consensus pattern (39 bp):
TCCGCTCCACCTTGATCAGCATTTGGTGTTCTGGCATCA
Found at i:62947 original size:216 final size:216
Alignment explanation
Indices: 62573--63006 Score: 868
Period size: 216 Copynumber: 2.0 Consensus size: 216
62563 CCTTTCTGTC
62573 AGGACTGCTAGGAGGTTTCTTTGAAGCCGAAGCAGGAGTCGATCGTCCCCTCCTAGTCTTAGTGC
1 AGGACTGCTAGGAGGTTTCTTTGAAGCCGAAGCAGGAGTCGATCGTCCCCTCCTAGTCTTAGTGC
62638 TAATAGTACTAGTAGTAGTAGGAGACTTGTGCGAGCTCCTAGACGAAGACACCGTCGATGTCTGT
66 TAATAGTACTAGTAGTAGTAGGAGACTTGTGCGAGCTCCTAGACGAAGACACCGTCGATGTCTGT
62703 GATTTCGTCGGAGCATTCGGCTTTTTGGCAACCCTCTCCAAGGGCGCCTTGGGTGCAACAGCACC
131 GATTTCGTCGGAGCATTCGGCTTTTTGGCAACCCTCTCCAAGGGCGCCTTGGGTGCAACAGCACC
62768 AGGTTTCGAAGTCAAAGAACG
196 AGGTTTCGAAGTCAAAGAACG
62789 AGGACTGCTAGGAGGTTTCTTTGAAGCCGAAGCAGGAGTCGATCGTCCCCTCCTAGTCTTAGTGC
1 AGGACTGCTAGGAGGTTTCTTTGAAGCCGAAGCAGGAGTCGATCGTCCCCTCCTAGTCTTAGTGC
62854 TAATAGTACTAGTAGTAGTAGGAGACTTGTGCGAGCTCCTAGACGAAGACACCGTCGATGTCTGT
66 TAATAGTACTAGTAGTAGTAGGAGACTTGTGCGAGCTCCTAGACGAAGACACCGTCGATGTCTGT
62919 GATTTCGTCGGAGCATTCGGCTTTTTGGCAACCCTCTCCAAGGGCGCCTTGGGTGCAACAGCACC
131 GATTTCGTCGGAGCATTCGGCTTTTTGGCAACCCTCTCCAAGGGCGCCTTGGGTGCAACAGCACC
62984 AGGTTTCGAAGTCAAAGAACG
196 AGGTTTCGAAGTCAAAGAACG
63005 AG
1 AG
63007 ACGAGGATGT
Statistics
Matches: 218, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
216 218 1.00
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (216 bp):
AGGACTGCTAGGAGGTTTCTTTGAAGCCGAAGCAGGAGTCGATCGTCCCCTCCTAGTCTTAGTGC
TAATAGTACTAGTAGTAGTAGGAGACTTGTGCGAGCTCCTAGACGAAGACACCGTCGATGTCTGT
GATTTCGTCGGAGCATTCGGCTTTTTGGCAACCCTCTCCAAGGGCGCCTTGGGTGCAACAGCACC
AGGTTTCGAAGTCAAAGAACG
Found at i:64721 original size:2 final size:2
Alignment explanation
Indices: 64716--64768 Score: 67
Period size: 2 Copynumber: 27.5 Consensus size: 2
64706 TTGAGATTAT
64716 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA CTA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
*
64757 TA -A TA TA AA TA T
1 TA TA TA TA TA TA T
64769 TGTAATAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
1 3 0.07
2 40 0.89
3 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:65203 original size:16 final size:17
Alignment explanation
Indices: 65182--65220 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
65172 AACTATTGAT
65182 AATATTTT-TTTA-ATAA
1 AATATTTTATTTATA-AA
65198 AATATTTTATTTATAAA
1 AATATTTTATTTATAAA
65215 AATATT
1 AATATT
65221 ATTAATTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 12 0.57
18 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATATTTTATTTATAAA
Found at i:68680 original size:55 final size:55
Alignment explanation
Indices: 68609--68718 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
68599 ATGGAATTGC
68609 TGAGGTATACAAACAGGATATTCCAACCTGGAATTCTTATGCATGGATTTACAAA
1 TGAGGTATACAAACAGGATATTCCAACCTGGAATTCTTATGCATGGATTTACAAA
68664 TGAGGTATACAAACAGGATATTCCAACCTGGAATTCTTATGCATGGATTTACAAA
1 TGAGGTATACAAACAGGATATTCCAACCTGGAATTCTTATGCATGGATTTACAAA
68719 ATTTCTTCTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (55 bp):
TGAGGTATACAAACAGGATATTCCAACCTGGAATTCTTATGCATGGATTTACAAA
Found at i:68732 original size:2 final size:2
Alignment explanation
Indices: 68725--68752 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
68715 CAAAATTTCT
68725 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
68753 CCCTTGTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:73664 original size:21 final size:21
Alignment explanation
Indices: 73640--73680 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
73630 AGTTTTATTG
73640 TACTAACATAATAATCTACAC
1 TACTAACATAATAATCTACAC
* *
73661 TACTATCATATTAATCTACA
1 TACTAACATAATAATCTACA
73681 TATAAACGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (21 bp):
TACTAACATAATAATCTACAC
Found at i:86451 original size:20 final size:20
Alignment explanation
Indices: 86428--86585 Score: 190
Period size: 20 Copynumber: 7.8 Consensus size: 20
86418 ATTCGCGTTG
*
86428 CATTTCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTTTC
* *
86448 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* ** *
86469 AAAATCACGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* *
86489 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* **
86510 AAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
86530 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
86550 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
86570 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
86586 AGTCTATAGT
Statistics
Matches: 114, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
20 85 0.75
21 29 0.25
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:86481 original size:21 final size:21
Alignment explanation
Indices: 86452--86525 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
86442 ATTTTTCATT
86452 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
86473 TCACGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
86493 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
86514 TCGCGTTGCGAT
1 TCGCGTTGCGAT
86526 TTTCCATTTC
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:86482 original size:41 final size:41
Alignment explanation
Indices: 86432--86588 Score: 244
Period size: 41 Copynumber: 3.9 Consensus size: 41
86422 GCGTTGCATT
*
86432 TCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
86473 TCACGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
* ** **
86514 TCGCGTTGCGATTTTCCATTTCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
86554 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
86589 CTATAGTTGT
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
40 35 0.33
41 71 0.67
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:86500 original size:61 final size:61
Alignment explanation
Indices: 86428--86588 Score: 198
Period size: 61 Copynumber: 2.6 Consensus size: 61
86418 ATTCGCGTTG
* *
86428 CATTTCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTCAAAATCACGTTGCGATTTTC
* ** ** * * ** *
86489 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTTCAAAATCACGTTGCGATTTTC
86550 CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
86589 CTATAGTTGT
Statistics
Matches: 81, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
60 15 0.19
61 51 0.63
62 15 0.19
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.40
Consensus pattern (61 bp):
CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTCAAAATCACGTTGCGATTTTC
Found at i:86605 original size:22 final size:21
Alignment explanation
Indices: 86577--86648 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
86567 TTCCATTTCG
86577 CGTTGCGATAGTCTATAGTTGT
1 CGTTGCGATAGTCTA-AGTTGT
** * *
86599 CGTTGCGATTTTCCAA-AT-T
1 CGTTGCGATAGTCTAAGTTGT
86618 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTA-AGTTGT
86640 CGTTGCGAT
1 CGTTGCGAT
86649 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.33
20 2 0.05
21 2 0.05
22 22 0.56
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (21 bp):
CGTTGCGATAGTCTAAGTTGT
Found at i:86613 original size:82 final size:82
Alignment explanation
Indices: 86432--86588 Score: 244
Period size: 81 Copynumber: 1.9 Consensus size: 82
86422 GCGTTGCATT
* *
86432 TCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCATTTCGC
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTCAAAATCACGTTGCGATTTTCCATTTCGC
86497 GTTGCGATAGTTGAAAA
66 GTTGCGATAGTTGAAAA
* * ** *
86514 TCGCGTTGCGATTTTCCATTTCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATTTTCCATTTCGC
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTCAAAATCACGTTGCGATTTTCCATTTCGC
86578 GTTGCGATAGT
66 GTTGCGATAGT
86589 CTATAGTTGT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
81 37 0.54
82 31 0.46
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (82 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTCAAAATCACGTTGCGATTTTCCATTTCGC
GTTGCGATAGTTGAAAA
Found at i:86622 original size:19 final size:19
Alignment explanation
Indices: 86598--86663 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
86588 TCTATAGTTG
86598 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
86617 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
86638 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
86658 TCGTTG
1 TCGTTG
86664 TGATAGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:86622 original size:81 final size:80
Alignment explanation
Indices: 86476--86626 Score: 216
Period size: 81 Copynumber: 1.9 Consensus size: 80
86466 TTGAAAATCA
*
86476 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC-CGTT
86541 GCGATTTTCCATTTCG
65 GCGATTTTCCATTTCG
* * *
86557 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ATAGTTGTCGTTGCGATTTTCCAAATT-CG
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATTCCG
86620 TTGCGAT
63 TTGCGAT
86627 AGTCTACAGT
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
81 45 0.71
82 15 0.24
83 3 0.05
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.41
Consensus pattern (80 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTCCGTTG
CGATTTTCCATTTCG
Found at i:86632 original size:41 final size:41
Alignment explanation
Indices: 86557--86670 Score: 176
Period size: 41 Copynumber: 2.8 Consensus size: 41
86547 TTCCATTTCG
* *
86557 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTATAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
86599 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
*
86640 CGTTGCGATTTTCCAAATTCGTTGTGATAGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGT
86671 TAAAAAAAGA
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
41 51 0.75
42 14 0.21
43 3 0.04
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:86663 original size:122 final size:120
Alignment explanation
Indices: 86428--86663 Score: 282
Period size: 122 Copynumber: 1.9 Consensus size: 120
86418 ATTCGCGTTG
* *
86428 CATTTCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCATT
1 CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCAAT
*
86493 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
66 TC-CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC-CGTTGCGATTTTC
** **
86550 CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ATAGTTGTCGTTGCGATTTTCCA
1 CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGA-AAATCACGTTGCGATTTTCC-
* * *
86614 AATT-CGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT-CGTTG
63 AATTCCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATTCCGTTG
86664 TGATAGTTAA
Statistics
Matches: 98, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
122 60 0.61
123 32 0.33
124 6 0.06
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (120 bp):
CATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCAAT
TCCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTCCGTTGCGATTTTC
Found at i:87402 original size:42 final size:41
Alignment explanation
Indices: 87351--87562 Score: 128
Period size: 41 Copynumber: 5.0 Consensus size: 41
87341 ACGAATTTGG
87351 AAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAATGA
1 AAAATCGCAACG-CAACTGTCA-ACTATCGCAACGCGAAATGA
* * *
87393 AAAATCGCAACGCGATTTTCAACTATCGCAACGCGAATTTGCGATGA
1 AAAATCGCAACGCAACTGTCAACTATCGCAACGCGAA------ATGA
* * *** * * *
87440 TGGAGATCGCGTTGCGA-TTTCAACTATCGCAACGCGAAATGG
1 --AAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAATGA
* *
87482 AAAATCGCAACGCGATCT-CCAACTATCGCAACGCGAAATGTA
1 AAAATCGCAACGC-AACTGTCAACTATCGCAACGCGAAATG-A
* **
87524 AAAA-CGCAACGCGAA-TTTCAACTATCGCAATACGAAATG
1 AAAATCGCAACGC-AACTGTCAACTATCGCAACGCGAAATG
87563 CAACGTGAAT
Statistics
Matches: 135, Mismatches: 22, Indels: 27
0.73 0.12 0.15
Matches are distributed among these distances:
40 9 0.07
41 70 0.52
42 21 0.16
47 4 0.03
48 21 0.16
49 10 0.07
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAATGA
Found at i:87476 original size:20 final size:21
Alignment explanation
Indices: 87456--87553 Score: 78
Period size: 20 Copynumber: 4.8 Consensus size: 21
87446 TCGCGTTGCG
87456 ATTTCAACTATCGCAACGCGA
1 ATTTCAACTATCGCAACGCGA
* ** *
87477 AATGGAA-AATCGCAACGCG-
1 ATTTCAACTATCGCAACGCGA
*
87496 ATCTCCAACTATCGCAACGCGAA
1 AT-TTCAACTATCGCAACGCG-A
* * *
87519 ATGT-AA-AAACGCAACGCGA
1 ATTTCAACTATCGCAACGCGA
87538 ATTTCAACTATCGCAA
1 ATTTCAACTATCGCAA
87554 TACGAAATGC
Statistics
Matches: 56, Mismatches: 15, Indels: 12
0.67 0.18 0.14
Matches are distributed among these distances:
19 5 0.09
20 26 0.46
21 23 0.41
23 2 0.04
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (21 bp):
ATTTCAACTATCGCAACGCGA
Found at i:97385 original size:24 final size:24
Alignment explanation
Indices: 97351--97418 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
97341 GAGTCAAGGG
*
97351 TCTACGCGGTCCTTCGGGACAAAT
1 TCTACGTGGTCCTTCGGGACAAAT
*
97375 TCTACGTGGTCATTCGGGACAAAT
1 TCTACGTGGTCCTTCGGGACAAAT
*
97399 TTTACGTGGTCCTTCGGGAC
1 TCTACGTGGTCCTTCGGGAC
97419 GTATATGTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.29
Consensus pattern (24 bp):
TCTACGTGGTCCTTCGGGACAAAT
Found at i:97583 original size:24 final size:24
Alignment explanation
Indices: 97532--97597 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
97522 CAATATTATA
*
97532 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTACGGTGCAAATTCTACG
* *
97555 CGGCACTTCGGTGCAAATTCTACG
1 TGGCACTACGGTGCAAATTCTACG
97579 TGGCACTACGGTGCAAATT
1 TGGCACTACGGTGCAAATT
97598 TATATGAGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 12 0.32
24 25 0.68
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (24 bp):
TGGCACTACGGTGCAAATTCTACG
Found at i:99957 original size:19 final size:20
Alignment explanation
Indices: 99920--99957 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
99910 CTTTTTTTTA
*
99920 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
99940 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
99958 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:100008 original size:21 final size:21
Alignment explanation
Indices: 99984--100025 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
99974 TTCATATTCG
* *
99984 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
100005 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
100026 CAGCCCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:108354 original size:12 final size:12
Alignment explanation
Indices: 108317--108356 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
108307 GTGATCAGAT
108317 GGAAGAAGATGA
1 GGAAGAAGATGA
* *
108329 AGAAGAAGAGGA
1 GGAAGAAGATGA
*
108341 GGAGGAAGATGA
1 GGAAGAAGATGA
108353 GGAA
1 GGAA
108357 CTAGATCCGC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.45, T:0.05
Consensus pattern (12 bp):
GGAAGAAGATGA
Done.