Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001749.1 Hibiscus syriacus cultivar Beakdansim tig00003540_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: 174337
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:7062 original size:20 final size:21
Alignment explanation
Indices: 7022--7061 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
7012 AATTTTGGGG
7022 CTAAATTAAATATTTTAAAAT
1 CTAAATTAAATATTTTAAAAT
7043 CTAAATTATAAT-TTTTAAA
1 CTAAATTA-AATATTTTAAA
7062 TTTTAGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
CTAAATTAAATATTTTAAAAT
Found at i:30652 original size:21 final size:20
Alignment explanation
Indices: 30566--30722 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
30556 AAATGACCAA
**
30566 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
30585 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
30605 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
30625 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
30646 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
30666 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
30686 ACAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
30707 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
30723 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:30675 original size:41 final size:41
Alignment explanation
Indices: 30625--30722 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
30615 AATCAGTTTC
* *
30625 CAAAATCGCAACGCGATTCTT-GAAAATCGCAATGCG-ATAGT
1 CAAAATCGCAACGCGATT-TTACAAAATCGCAACGCGAATA-T
* **
30666 CAAATTCGCATTGCGATTTTACAAAATCGCAACGCGAATAT
1 CAAAATCGCAACGCGATTTTACAAAATCGCAACGCGAATAT
*
30707 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
30723 ACACATAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.04
41 41 0.89
42 3 0.07
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (41 bp):
CAAAATCGCAACGCGATTTTACAAAATCGCAACGCGAATAT
Found at i:30736 original size:61 final size:61
Alignment explanation
Indices: 30565--30741 Score: 182
Period size: 61 Copynumber: 2.9 Consensus size: 61
30555 AAAATGACCA
* * * *
30565 ACAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGATCCCCAGAATCGCAAAT-C-AGTTT
1 ACAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACAAAATCGC-AATGCGAGTTT
* * * * ** * * *
30624 CCAAAATCGCAACGCGATTCTTGAAAATCGCAATGCGATAGTCAAATTCGCATTGCGATTTT
1 ACAAAATCGCAACGCGAAT-ATGAAAATCGCAACGCGATACACAAAATCGCAATGCGAGTTT
30686 ACAAAATCGCAACGCGAATATGAAAATCGCAACGCGA-ACACATAAATCGCAATGCG
1 ACAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACA-AAATCGCAATGCG
30742 TATCCGTAAA
Statistics
Matches: 93, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
59 16 0.17
60 5 0.05
61 51 0.55
62 21 0.23
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (61 bp):
ACAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACAAAATCGCAATGCGAGTTT
Found at i:30751 original size:20 final size:20
Alignment explanation
Indices: 30689--30882 Score: 194
Period size: 20 Copynumber: 9.7 Consensus size: 20
30679 CGATTTTACA
* ** *
30689 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
30709 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
30729 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
30749 AAATCACAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
30769 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
30789 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
30809 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTATCCGT
* * *
30829 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
30849 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
30870 AAATCGCAACGCG
1 AAATCGCAACGCG
30883 ATATTTAAAG
Statistics
Matches: 140, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
19 2 0.01
20 120 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:30775 original size:60 final size:60
Alignment explanation
Indices: 30689--30882 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 60
30679 CGATTTTACA
* ** * *
30689 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * * ***
30749 AAATCACAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ** *
30809 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGT
30870 AAATCGCAACGCG
1 AAATCGCAACGCG
30883 ATATTTAAAG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 79 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
Found at i:31299 original size:33 final size:33
Alignment explanation
Indices: 31260--31330 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
31250 TTCACTTAGA
31260 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
31293 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
31326 TTTCA
1 TTTCA
31331 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:31466 original size:41 final size:41
Alignment explanation
Indices: 31408--31485 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
31398 TTGCAGAAGA
*
31408 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
31449 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
31486 CGCAAAGCGA
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:31482 original size:21 final size:21
Alignment explanation
Indices: 31409--31484 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
31399 TGCAGAAGAG
*
31409 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
31430 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
31450 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
31471 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
31485 TCGCAAAGCG
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:31488 original size:14 final size:14
Alignment explanation
Indices: 31469--31558 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
31459 GAGAAATGAA
31469 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
31483 AATCGCAAAGCGATATGAA
1 AATCGC-AA-CG--A-GAG
31502 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
31516 AATCGCAAAGCGATATGAA
1 AATCGC-AA-CG--A-GAG
31535 AATCGCAACGAGAG
1 AATCGCAACGAGAG
31549 AATCGCAACG
1 AATCGCAACG
31559 CGAAACCAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 26 0.42
15 6 0.10
16 4 0.06
17 4 0.06
18 6 0.10
19 16 0.26
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:31507 original size:19 final size:19
Alignment explanation
Indices: 31483--31542 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
31473 GCAACGAGAG
31483 AATCGCAAAGCGATATGAA
1 AATCGCAAAGCGATATGAA
*
31502 AATCGC-AA-CG--A-GAG
1 AATCGCAAAGCGATATGAA
31516 AATCGCAAAGCGATATGAA
1 AATCGCAAAGCGATATGAA
31535 AATCGCAA
1 AATCGCAA
31543 CGAGAGAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 8 0.24
15 3 0.09
16 2 0.06
17 2 0.06
18 3 0.09
19 16 0.47
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAAAGCGATATGAA
Found at i:31574 original size:33 final size:33
Alignment explanation
Indices: 31464--31561 Score: 187
Period size: 33 Copynumber: 3.0 Consensus size: 33
31454 AACGAGAGAA
31464 ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
1 ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
31497 ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
1 ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
*
31530 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 ATGAAAATCGCAACGAGAGAATCGCAAAGCGA
31562 AACCAAAATC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
Found at i:31592 original size:19 final size:19
Alignment explanation
Indices: 31570--31653 Score: 115
Period size: 19 Copynumber: 4.7 Consensus size: 19
31560 GAAACCAAAA
*
31570 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
31589 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
31608 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
31622 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
31641 TCGCGTTGCGATT
1 TCGCGTTGCGATT
31654 CTCTCGTTGC
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 10 0.18
16 3 0.05
17 3 0.05
19 41 0.72
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:31630 original size:14 final size:14
Alignment explanation
Indices: 31611--31667 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
31601 TTTCATTTCG
31611 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
31625 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
31644 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
31658 CGTTGCGATT
1 CGTTGCGATT
31668 TTCATTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:31634 original size:33 final size:33
Alignment explanation
Indices: 31592--31675 Score: 168
Period size: 33 Copynumber: 2.5 Consensus size: 33
31582 TTTCATTTCG
31592 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
31625 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
31658 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
31676 AACCAAAAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:33202 original size:37 final size:37
Alignment explanation
Indices: 33152--33227 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
33142 ATGCCTTGCG
33152 TGAGGAGATCGGTACTCTACGCGATAACGATGGTGCA
1 TGAGGAGATCGGTACTCTACGCGATAACGATGGTGCA
*
33189 TGAGGAGATCGGTACTCTACGTGATAACGATGGTGCA
1 TGAGGAGATCGGTACTCTACGCGATAACGATGGTGCA
33226 TG
1 TG
33228 GCGTGTGGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (37 bp):
TGAGGAGATCGGTACTCTACGCGATAACGATGGTGCA
Found at i:33565 original size:93 final size:93
Alignment explanation
Indices: 33406--33781 Score: 736
Period size: 93 Copynumber: 4.1 Consensus size: 93
33396 TAGATTGCTT
*
33406 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
33471 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
33499 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
33564 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
33592 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
33657 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
33685 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
33750 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
33777 AGTAA
1 AGTAA
33782 TGCAATCCAT
Statistics
Matches: 282, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 6 0.02
93 276 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:33869 original size:19 final size:19
Alignment explanation
Indices: 33829--33957 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
33819 TAGTTTACTT
* *
33829 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
33849 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
33868 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
33887 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
33901 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* *
33920 TCGCAA--CG--A-TAAGA
1 TCGCAACGCGAAACCAAAA
33934 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
33953 TCGCA
1 TCGCA
33958 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:33908 original size:33 final size:32
Alignment explanation
Indices: 33865--33957 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
33855 CGCGAAACCA
**
33865 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
33897 AGAATCGCAACGCGAAACCAAAATCGCAACGAT
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
33930 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
33958 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:33955 original size:52 final size:52
Alignment explanation
Indices: 33829--33957 Score: 138
Period size: 52 Copynumber: 2.5 Consensus size: 52
33819 TAGTTTACTT
** *
33829 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAA
* * * *
33881 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGATAAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAA-A
*
33934 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
33958 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.69
53 2 0.03
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAA
Found at i:33975 original size:19 final size:19
Alignment explanation
Indices: 33953--34087 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
33943 GAAACCAAAA
*
33953 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
33972 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
33988 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
34005 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
34021 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
34038 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
34057 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
34077 TCGTGTTGCGA
1 TCGCGTTGCGA
34088 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:33994 original size:14 final size:14
Alignment explanation
Indices: 33975--34031 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
33965 TTTCATTTCG
33975 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
33989 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
34006 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
34022 CGTTGCGATT
1 CGTTGCGATT
34032 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:34000 original size:33 final size:33
Alignment explanation
Indices: 33958--34050 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
33948 CAAAATCGCA
*
33958 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
33991 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
34024 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
34051 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:36029 original size:14 final size:14
Alignment explanation
Indices: 36010--36045 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
36000 ATTGTTTAAT
36010 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
36024 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
36038 TGATTTGT
1 TGATTTGT
36046 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:36167 original size:19 final size:19
Alignment explanation
Indices: 36151--36248 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
36141 AAAAATGACT
36151 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
36170 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
36189 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
36203 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
36222 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
36242 ATCGCAA
1 ATCGCAA
36249 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:36280 original size:53 final size:53
Alignment explanation
Indices: 36151--36266 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
36141 AAAAATGACT
36151 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
36203 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
36256 ATCGCAATGCG
1 ATCGCAATGCG
36267 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:36310 original size:33 final size:33
Alignment explanation
Indices: 36273--36425 Score: 159
Period size: 33 Copynumber: 4.5 Consensus size: 33
36263 TGCGTTTATA
36273 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
36306 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
36346 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
36377 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
36410 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
36426 TTCATTTCGC
Statistics
Matches: 97, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 52 0.54
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:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:36319 original size:19 final size:19
Alignment explanation
Indices: 36295--36511 Score: 240
Period size: 19 Copynumber: 12.4 Consensus size: 19
36285 GATTCTCTCG
36295 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
36314 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
36333 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
36347 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
36366 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
36385 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
36399 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
36418 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
36437 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
36451 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
36471 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
36485 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
36504 TTGCGATT
1 TTGCGATT
36512 GTAATTTCCG
Statistics
Matches: 169, Mismatches: 8, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 29 0.17
16 23 0.14
17 20 0.12
18 3 0.02
19 82 0.49
20 12 0.07
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:36330 original size:52 final size:52
Alignment explanation
Indices: 36273--36483 Score: 413
Period size: 52 Copynumber: 4.0 Consensus size: 52
36263 TGCGTTTATA
36273 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
36325 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
36377 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
36429 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
36482 AT
1 AT
36484 GTTGGGATTT
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 141 0.89
53 17 0.11
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:36455 original size:33 final size:33
Alignment explanation
Indices: 36314--36511 Score: 197
Period size: 33 Copynumber: 5.8 Consensus size: 33
36304 TCATTTCGCA
36314 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
36347 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
36383 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
36418 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
36451 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
36485 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
36512 GTAATTTCCG
Statistics
Matches: 137, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
31 9 0.07
32 5 0.04
33 62 0.45
34 29 0.21
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.06
39 3 0.02
40 9 0.07
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:38809 original size:12 final size:12
Alignment explanation
Indices: 38792--38816 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38782 TCTTCGGGGA
38792 CTTTTTCTTCTT
1 CTTTTTCTTCTT
38804 CTTTTTCTTCTT
1 CTTTTTCTTCTT
38816 C
1 C
38817 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:39747 original size:20 final size:20
Alignment explanation
Indices: 39719--39928 Score: 206
Period size: 20 Copynumber: 10.5 Consensus size: 20
39709 AAATTTCAGT
* * *
39719 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
39739 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
39759 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
39779 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
39799 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
39819 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
** *
39839 GTTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
39859 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
39879 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
39899 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
39919 GTTGCGATTT
1 GTTGCGATTT
39929 TGGAAAATCG
Statistics
Matches: 162, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 161 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:39945 original size:21 final size:20
Alignment explanation
Indices: 39895--39992 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
39885 ATTTATGTGT
* * * *
39895 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
39915 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
39936 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
39956 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
39977 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
39993 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:39968 original size:61 final size:60
Alignment explanation
Indices: 39895--40051 Score: 176
Period size: 61 Copynumber: 2.6 Consensus size: 60
39885 ATTTATGTGT
*
39895 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCA-ATGCGAATT-TGACTA
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAAT-G-ATATGCG-ATTCTGACGA
* * * * * **
39956 TCGCATTGCGATTTTCAAGAATCGCGTTGCGATTTTGGAAACTGATTTGCGATTCTGGGGA
1 TCGCGTTGCGATTTTC-ATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
*
40017 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTG
40052 TTGGTCATTT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
59 16 0.20
60 5 0.06
61 37 0.46
62 23 0.28
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (60 bp):
TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
Found at i:39987 original size:41 final size:41
Alignment explanation
Indices: 39895--40051 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
39885 ATTTATGTGT
* * *
39895 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
39936 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
39977 TCGCGTTGCGATTTTGGAAACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
40017 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
40052 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:40841 original size:28 final size:28
Alignment explanation
Indices: 40804--40864 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
40794 TATTACAAAT
*
40804 ATATAGATTATTTTATAAATATTTT-TAG
1 ATATAGATTATTTTAT-AATATTTTCGAG
*
40832 ATATATATTATTTTATAATATTTTCGAG
1 ATATAGATTATTTTATAATATTTTCGAG
40860 ATATA
1 ATATA
40865 CCTCATTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (28 bp):
ATATAGATTATTTTATAATATTTTCGAG
Found at i:46424 original size:2 final size:2
Alignment explanation
Indices: 46417--46457 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
46407 TATTGATTAA
46417 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46458 CATGAATCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48850 original size:2 final size:2
Alignment explanation
Indices: 48841--48871 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
48831 ATATTTTATG
48841 AT AT -T 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
48872 GTATTGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:51937 original size:2 final size:2
Alignment explanation
Indices: 51930--51956 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
51920 TGATGAATAA
51930 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
51957 CCTTCGATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53336 original size:21 final size:21
Alignment explanation
Indices: 53310--53358 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
53300 AATATCATAA
53310 ACTGCCATGTAAGCACTATAG
1 ACTGCCATGTAAGCACTATAG
53331 ACTGCCATGTAAGCACTATAG
1 ACTGCCATGTAAGCACTATAG
53352 ACTGCCA
1 ACTGCCA
53359 CATCAACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (21 bp):
ACTGCCATGTAAGCACTATAG
Found at i:54152 original size:3 final size:3
Alignment explanation
Indices: 54144--54179 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
54134 TGATTGCTCC
54144 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
54180 TAATTCTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:58234 original size:22 final size:24
Alignment explanation
Indices: 58208--58253 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
58198 CTCGGATTTC
* *
58208 TTCTCTTCATTCT-CATG-TTCTT
1 TTCTCATCAATCTCCATGATTCTT
58230 TTCTCATCAATCTCCATGATTCTT
1 TTCTCATCAATCTCCATGATTCTT
58254 GCTGATATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 4 0.20
24 5 0.25
ACGTcount: A:0.15, C:0.28, G:0.04, T:0.52
Consensus pattern (24 bp):
TTCTCATCAATCTCCATGATTCTT
Found at i:60352 original size:12 final size:12
Alignment explanation
Indices: 60321--60353 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
60311 AAATACCGGA
60321 AATAAAATAAAT
1 AATAAAATAAAT
60333 AA-ATAAATAAAT
1 AATA-AAATAAAT
60345 AATAAAATA
1 AATAAAATA
60354 GAAGAGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.05
12 17 0.89
13 1 0.05
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAAAATAAAT
Found at i:68945 original size:15 final size:15
Alignment explanation
Indices: 68925--68955 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
68915 GGATTTAGTA
68925 TGTGTTAGAAAAGGG
1 TGTGTTAGAAAAGGG
68940 TGTGTTAGAAAAGGG
1 TGTGTTAGAAAAGGG
68955 T
1 T
68956 ACGAGTCCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.39, T:0.29
Consensus pattern (15 bp):
TGTGTTAGAAAAGGG
Found at i:71161 original size:18 final size:18
Alignment explanation
Indices: 71135--71171 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
71125 TTGGGGTGAA
71135 TGTTATATACCAATCTTT
1 TGTTATATACCAATCTTT
*
71153 TGTTTTATACCAATCTTT
1 TGTTATATACCAATCTTT
71171 T
1 T
71172 AAAGTTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.54
Consensus pattern (18 bp):
TGTTATATACCAATCTTT
Found at i:72897 original size:22 final size:22
Alignment explanation
Indices: 72872--72915 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
72862 TCGTCACTGT
*
72872 TGGTTTTAGTTCTTATATTAAA
1 TGGTTTTAGTTCCTATATTAAA
72894 TGGTTTTAGTTCCTATATTAAA
1 TGGTTTTAGTTCCTATATTAAA
72916 AAAACTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.52
Consensus pattern (22 bp):
TGGTTTTAGTTCCTATATTAAA
Found at i:76441 original size:13 final size:14
Alignment explanation
Indices: 76418--76447 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
76408 TTCCCATTAC
76418 AGACGTGCATATGA
1 AGACGTGCATATGA
76432 AGAC-TGCATATGA
1 AGACGTGCATATGA
76445 AGA
1 AGA
76448 TTGTCCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:86847 original size:28 final size:29
Alignment explanation
Indices: 86816--86872 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
86806 AATAGTAGGG
86816 TGACCA-TTTATAACTTTTAATAGTCAGA
1 TGACCATTTTATAACTTTTAATAGTCAGA
86844 TGACCATTTTATAACTTTTAATAGTCAGA
1 TGACCATTTTATAACTTTTAATAGTCAGA
86873 GGACTCAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (29 bp):
TGACCATTTTATAACTTTTAATAGTCAGA
Found at i:88917 original size:2 final size:2
Alignment explanation
Indices: 88910--88934 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
88900 TGTTTGATTC
88910 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
88935 AAACACATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:90045 original size:14 final size:14
Alignment explanation
Indices: 90026--90054 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
90016 AACCATTGAC
90026 TTGATATGCCTCTA
1 TTGATATGCCTCTA
90040 TTGATATGCCTCTA
1 TTGATATGCCTCTA
90054 T
1 T
90055 AGGGTAAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.45
Consensus pattern (14 bp):
TTGATATGCCTCTA
Found at i:94794 original size:11 final size:11
Alignment explanation
Indices: 94778--94802 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
94768 ATAATATTAT
94778 TAAAAATAAAA
1 TAAAAATAAAA
94789 TAAAAATAAAA
1 TAAAAATAAAA
94800 TAA
1 TAA
94803 CCCTAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:100421 original size:15 final size:16
Alignment explanation
Indices: 100396--100428 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
100386 ACATGATTGA
*
100396 GGGACTAAAATCGAAC
1 GGGACTAAAATCAAAC
100412 GGGA-TAAAATCAAAC
1 GGGACTAAAATCAAAC
100427 GG
1 GG
100429 ATTGATAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.45, C:0.15, G:0.27, T:0.12
Consensus pattern (16 bp):
GGGACTAAAATCAAAC
Found at i:100454 original size:31 final size:31
Alignment explanation
Indices: 100412--100479 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
100402 AAAATCGAAC
**
100412 GGGA-TAAAATCAAACGGATTGATAACGTTA
1 GGGACTAAAATCAAACGGATCAATAACGTTA
* *
100442 GGGACTAAAATCAGACGGATCAATAATGTTA
1 GGGACTAAAATCAAACGGATCAATAACGTTA
100473 GGGACTA
1 GGGACTA
100480 TTCCCCCATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (31 bp):
GGGACTAAAATCAAACGGATCAATAACGTTA
Found at i:104447 original size:16 final size:16
Alignment explanation
Indices: 104428--104477 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 16
104418 AAACATTTTT
104428 TATTAAAATAATAAAA
1 TATTAAAATAATAAAA
104444 TATTAAAATACAT--AA
1 TATTAAAATA-ATAAAA
*
104459 TATT-CAATAA-AAAA
1 TATTAAAATAATAAAA
104473 TATTA
1 TATTA
104478 TATTTTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
13 1 0.03
14 10 0.34
15 6 0.21
16 10 0.34
17 2 0.07
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (16 bp):
TATTAAAATAATAAAA
Found at i:105289 original size:33 final size:32
Alignment explanation
Indices: 105251--105334 Score: 80
Period size: 33 Copynumber: 2.6 Consensus size: 32
105241 TATTAAAATA
*
105251 AAAATTTATAATCATTAAATCTCTAAA-AATTAT
1 AAAATTTATAATCA--AAATCTATAAATAATTAT
* * * *
105284 AAAATTGATCATCAGAATTTATAAATAATTAT
1 AAAATTTATAATCAAAATCTATAAATAATTAT
*
105316 AAAATTTACTAATAAAAAT
1 AAAATTTA-TAATCAAAAT
105335 AATCATTAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
31 8 0.20
32 13 0.32
33 19 0.47
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (32 bp):
AAAATTTATAATCAAAATCTATAAATAATTAT
Found at i:105367 original size:31 final size:30
Alignment explanation
Indices: 105320--105382 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
105310 AATTATAAAA
105320 TTTACTAATAAAAATAATCA-TTAAATTTAT
1 TTTACTAATAAAAATAATCATTTAAA-TTAT
* *
105350 TTTACTATTATAAAATAATTATTTAAATTAT
1 TTTACTAATA-AAAATAATCATTTAAATTAT
105381 TT
1 TT
105383 AATTTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 9 0.31
31 15 0.52
32 5 0.17
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (30 bp):
TTTACTAATAAAAATAATCATTTAAATTAT
Found at i:107399 original size:18 final size:18
Alignment explanation
Indices: 107376--107442 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 18
107366 TGTGTAAAAC
107376 TATAATATAATAAAATTA
1 TATAATATAATAAAATTA
* *
107394 TATAATATATTTAAATTA
1 TATAATATAATAAAATTA
* *
107412 TATAATATATTTAAATTA
1 TATAATATAATAAAATTA
107430 T-TAA-A-AATAAAAT
1 TATAATATAATAAAAT
107443 GATAAAAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
15 6 0.13
16 1 0.02
17 3 0.07
18 35 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATAATATAATAAAATTA
Found at i:112787 original size:15 final size:15
Alignment explanation
Indices: 112769--112884 Score: 52
Period size: 15 Copynumber: 7.5 Consensus size: 15
112759 TGCAAGTGCC
112769 GCTCATGTAAATGCA
1 GCTCATGTAAATGCA
* ** *
112784 GCTCTTGCGACTGCA
1 GCTCATGTAAATGCA
* *
112799 GTTCAAGTAAATGCA
1 GCTCATGTAAATGCA
* ** *
112814 GCTCCTGCGACTGCA
1 GCTCATGTAAATGCA
* * *
112829 GTTCTTGTAAGTGCA
1 GCTCATGTAAATGCA
112844 GCAGTTCATGTAAATGCA
1 GC---TCATGTAAATGCA
* * * *
112862 GCTCGTGTGACTGCT
1 GCTCATGTAAATGCA
112877 GCTCATGT
1 GCTCATGT
112885 TCAAGCTGCT
Statistics
Matches: 69, Mismatches: 29, Indels: 6
0.66 0.28 0.06
Matches are distributed among these distances:
15 56 0.81
18 13 0.19
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.29
Consensus pattern (15 bp):
GCTCATGTAAATGCA
Found at i:112844 original size:30 final size:30
Alignment explanation
Indices: 112771--112845 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
112761 CAAGTGCCGC
*
112771 TCATGTAAATGCAGCTCTTGCGACTGCAGT
1 TCATGTAAATGCAGCTCCTGCGACTGCAGT
*
112801 TCAAGTAAATGCAGCTCCTGCGACTGCAGT
1 TCATGTAAATGCAGCTCCTGCGACTGCAGT
* *
112831 TCTTGTAAGTGCAGC
1 TCATGTAAATGCAGC
112846 AGTTCATGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (30 bp):
TCATGTAAATGCAGCTCCTGCGACTGCAGT
Found at i:112849 original size:18 final size:18
Alignment explanation
Indices: 112826--112863 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
112816 TCCTGCGACT
* *
112826 GCAGTTCTTGTAAGTGCA
1 GCAGTTCATGTAAATGCA
112844 GCAGTTCATGTAAATGCA
1 GCAGTTCATGTAAATGCA
112862 GC
1 GC
112864 TCGTGTGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (18 bp):
GCAGTTCATGTAAATGCA
Found at i:112955 original size:63 final size:63
Alignment explanation
Indices: 112855--113041 Score: 214
Period size: 63 Copynumber: 2.9 Consensus size: 63
112845 CAGTTCATGT
* * * *
112855 AAATGCAGCTCGTGTGACTGCTGCTCATGTTCAAGCTGCTGCACAATCTCAAAATGGCGATGC
1 AAATGCAGCTCGTGCGACTGCTGTTCGTGTTCAAGCTGCTGCACAATCCCAAAATGGCGATGC
*
112918 AAATGCAGCTCGTGCGACTGCTGTTCGTGTTTC-AGCTGCTGCACAATCCCGAAATGGCGATGC
1 AAATGCAGCTCGTGCGACTGCTGTTCGTG-TTCAAGCTGCTGCACAATCCCAAAATGGCGATGC
* * * * * ***
112981 AAGTGCGGCTCATCATGCGACTACTGTTCGTGTTCGAGCTGCTGCGTGATCCCAAAATGGC
1 AAATGCAG--C-TCGTGCGACTGCTGTTCGTGTTCAAGCTGCTGCACAATCCCAAAATGGC
113042 AATGTTTCTC
Statistics
Matches: 106, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
63 60 0.57
64 3 0.03
65 4 0.04
66 39 0.37
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.26
Consensus pattern (63 bp):
AAATGCAGCTCGTGCGACTGCTGTTCGTGTTCAAGCTGCTGCACAATCCCAAAATGGCGATGC
Found at i:115992 original size:89 final size:89
Alignment explanation
Indices: 115836--116013 Score: 302
Period size: 89 Copynumber: 2.0 Consensus size: 89
115826 ATTCTAATAA
* * **
115836 ACATTTGGAATTCTTCCAAGTTACACACATGTTTGTATTAGTATATGTATAATTATACAGATGGA
1 ACATTTAGAATTCTTCCAAGTTACACACATGTTCGTATTAGTATATGTATAATTATACAGAAAGA
*
115901 TAGAGAAGATTACAGAAATTAGGG
66 TAGAGAAGATTAAAGAAATTAGGG
115925 ACATTTAGAATTCTTCCAAGTTACACACATGTTCGTATTAGTATATGTATAATTATACAGAAAGA
1 ACATTTAGAATTCTTCCAAGTTACACACATGTTCGTATTAGTATATGTATAATTATACAGAAAGA
*
115990 TAGAGAAGATTAAAGATATTAGGG
66 TAGAGAAGATTAAAGAAATTAGGG
116014 TAAATTATGT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (89 bp):
ACATTTAGAATTCTTCCAAGTTACACACATGTTCGTATTAGTATATGTATAATTATACAGAAAGA
TAGAGAAGATTAAAGAAATTAGGG
Found at i:116924 original size:22 final size:22
Alignment explanation
Indices: 116899--116942 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
116889 ATACCAGATG
116899 AAGTCTGCATCAATCCAGCTTT
1 AAGTCTGCATCAATCCAGCTTT
116921 AAGTCTGCATCAATCCAGCTTT
1 AAGTCTGCATCAATCCAGCTTT
116943 CTTTCACTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (22 bp):
AAGTCTGCATCAATCCAGCTTT
Found at i:127194 original size:31 final size:31
Alignment explanation
Indices: 127151--127209 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
127141 CGAATTGAGT
* *
127151 ATTAAAATTGAACAAATTGATAATATTATGG
1 ATTAAAAGTGAACAAATAGATAATATTATGG
*
127182 ATTAAAAGTGAACGAATAGATAATATTA
1 ATTAAAAGTGAACAAATAGATAATATTA
127210 GGGAGGAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (31 bp):
ATTAAAAGTGAACAAATAGATAATATTATGG
Found at i:134398 original size:15 final size:16
Alignment explanation
Indices: 134371--134402 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
134361 TGAACTATAC
134371 TGATCACTCTTCTTCT
1 TGATCACTCTTCTTCT
134387 TGATCA-TCTTCTTCT
1 TGATCACTCTTCTTCT
134402 T
1 T
134403 CTTTTTGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.12, C:0.28, G:0.06, T:0.53
Consensus pattern (16 bp):
TGATCACTCTTCTTCT
Found at i:136860 original size:25 final size:25
Alignment explanation
Indices: 136832--136881 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
136822 GCATGTACCG
136832 ATTTCTAGCT-GATAGATAGGGTTTC
1 ATTTCTAG-TGGATAGATAGGGTTTC
136857 ATTTCTAGTGGATAGATAGGGTTTC
1 ATTTCTAGTGGATAGATAGGGTTTC
136882 GGTATTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (25 bp):
ATTTCTAGTGGATAGATAGGGTTTC
Found at i:146642 original size:21 final size:21
Alignment explanation
Indices: 146618--146659 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
146608 TACGCGTGAC
*
146618 CTGCTTCAACGCTGTTGTTGA
1 CTGCTTCAACGCTGTTATTGA
* *
146639 CTGCTTCTACTCTGTTATTGA
1 CTGCTTCAACGCTGTTATTGA
146660 AGTTGGTAAA
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:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (21 bp):
CTGCTTCAACGCTGTTATTGA
Found at i:149907 original size:23 final size:25
Alignment explanation
Indices: 149862--149907 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
149852 GACGTGGCAT
149862 AAATAATAAATATTAATTTTAAATA
1 AAATAATAAATATTAATTTTAAATA
*
149887 AAATAAT-AAT-TTGATTTTAAA
1 AAATAATAAATATTAATTTTAAA
149908 AGTAGAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
AAATAATAAATATTAATTTTAAATA
Found at i:170103 original size:15 final size:15
Alignment explanation
Indices: 170076--170123 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
170066 TGACCTTTTT
170076 AAATA-AATAAAAATA
1 AAATATAAT-AAAATA
170091 AAATATAATAAAATA
1 AAATATAATAAAATA
*
170106 ACAATCTAA-AAAATA
1 A-AATATAATAAAATA
170121 AAA
1 AAA
170124 GGAAGCTCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 2 0.07
15 19 0.63
16 9 0.30
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATATAATAAAATA
Found at i:173384 original size:15 final size:15
Alignment explanation
Indices: 173359--173394 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
173349 GGACAACCGG
173359 TATTG-TTCCATACC
1 TATTGTTTCCATACC
173373 TATTGTTTCCATACC
1 TATTGTTTCCATACC
*
173388 TTTTGTT
1 TATTGTT
173395 CTTTATTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.17, C:0.22, G:0.08, T:0.53
Consensus pattern (15 bp):
TATTGTTTCCATACC
Done.