Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000782.1 Hibiscus syriacus cultivar Beakdansim tig00001518_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: 159937
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:112 original size:17 final size:17
Alignment explanation
Indices: 90--125 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
80 ATGATTTTGG
90 TAATATAATAATAATAA
1 TAATATAATAATAATAA
**
107 TAATATTGTAATAATAA
1 TAATATAATAATAATAA
124 TA
1 TA
126 TTTTTTGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
TAATATAATAATAATAA
Found at i:118 original size:14 final size:14
Alignment explanation
Indices: 101--127 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
91 AATATAATAA
101 TAATAATAATATTG
1 TAATAATAATATTG
115 TAATAATAATATT
1 TAATAATAATATT
128 TTTTGGGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
TAATAATAATATTG
Found at i:2593 original size:16 final size:18
Alignment explanation
Indices: 2572--2604 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2562 TTGAGAAAGA
2572 TTATAAT-A-TATATATC
1 TTATAATCATTATATATC
2588 TTATAATCATTATATAT
1 TTATAATCATTATATAT
2605 TATTCGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (18 bp):
TTATAATCATTATATATC
Found at i:5559 original size:20 final size:20
Alignment explanation
Indices: 5534--5571 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5524 AACAAAAATC
5534 CCGGTTTTTCCCGATTTTTT
1 CCGGTTTTTCCCGATTTTTT
*
5554 CCGGTTTTTTCCGATTTT
1 CCGGTTTTTCCCGATTTT
5572 CAGCCTGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.24, G:0.16, T:0.55
Consensus pattern (20 bp):
CCGGTTTTTCCCGATTTTTT
Found at i:5563 original size:10 final size:10
Alignment explanation
Indices: 5538--5571 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5528 AAAATCCCGG
*
5538 TTTTTCCCGA
1 TTTTTTCCGA
*
5548 TTTTTTCCGG
1 TTTTTTCCGA
5558 TTTTTTCCGA
1 TTTTTTCCGA
5568 TTTT
1 TTTT
5572 CAGCCTGTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.06, C:0.21, G:0.12, T:0.62
Consensus pattern (10 bp):
TTTTTTCCGA
Found at i:7726 original size:31 final size:31
Alignment explanation
Indices: 7683--7742 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
7673 ATGTATCTAG
* * *
7683 ACCTTCAAATTTTGGTTTATTTTGATTTTAC
1 ACCTCCAAATTTTAGTTTATTTTAATTTTAC
7714 ACCTCCAAATTTTAGTTTATTTTAATTTT
1 ACCTCCAAATTTTAGTTTATTTTAATTTT
7743 GTCCCTCTCA
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:0.25, C:0.13, G:0.07, T:0.55
Consensus pattern (31 bp):
ACCTCCAAATTTTAGTTTATTTTAATTTTAC
Found at i:8925 original size:31 final size:31
Alignment explanation
Indices: 8890--8952 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
8880 AACACAAAAT
8890 ATATGGTCACTTTCGTTTTTATTTAATTAAG
1 ATATGGTCACTTTCGTTTTTATTTAATTAAG
8921 ATATGGTCACTTTCGTTTTTATTTAATTAAG
1 ATATGGTCACTTTCGTTTTTATTTAATTAAG
8952 A
1 A
8953 AGTGATCACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.51
Consensus pattern (31 bp):
ATATGGTCACTTTCGTTTTTATTTAATTAAG
Found at i:9334 original size:48 final size:48
Alignment explanation
Indices: 9260--9359 Score: 155
Period size: 48 Copynumber: 2.1 Consensus size: 48
9250 CAAAAGCTTA
* * * * *
9260 CAAACGTCAGTATAAATCCATGTTCATTAGTAGTTTTCTCTAACCACT
1 CAAACGTCAGTACAAATCCATATTCATAAATAGCTTTCTCTAACCACT
9308 CAAACGTCAGTACAAATCCATATTCATAAATAGCTTTCTCTAACCACT
1 CAAACGTCAGTACAAATCCATATTCATAAATAGCTTTCTCTAACCACT
9356 CAAA
1 CAAA
9360 GCCAGTTGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.31
Consensus pattern (48 bp):
CAAACGTCAGTACAAATCCATATTCATAAATAGCTTTCTCTAACCACT
Found at i:10675 original size:3 final size:3
Alignment explanation
Indices: 10667--10695 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
10657 ACCTTATATT
10667 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
10696 TATATTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:16475 original size:25 final size:24
Alignment explanation
Indices: 16438--16484 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
16428 CAAATTAATA
* *
16438 AAAAAAATTGAATATTATTATTTTT
1 AAAAAAATAGAATAAT-TTATTTTT
*
16463 AAAATAATAGAATAATTTATTT
1 AAAAAAATAGAATAATTTATTT
16485 AATATTAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 6 0.32
25 13 0.68
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (24 bp):
AAAAAAATAGAATAATTTATTTTT
Found at i:16649 original size:22 final size:21
Alignment explanation
Indices: 16609--16649 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
16599 ATTATTAAAA
**
16609 TAAAAATATTAATTTATATTT
1 TAAAAATATTAATAAATATTT
16630 TAAAAAGTATTAATAAATAT
1 TAAAAA-TATTAATAAATAT
16650 ATTTTAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TAAAAATATTAATAAATATTT
Found at i:16737 original size:22 final size:21
Alignment explanation
Indices: 16694--16797 Score: 65
Period size: 20 Copynumber: 4.9 Consensus size: 21
16684 TTGAGTATAT
16694 TATTATAATATTAAAAATATTA
1 TATTAT-ATATTAAAAATATTA
*
16716 TATTATATATTAAAACTAATTA
1 TATTATATATTAAAAAT-ATTA
* * *
16738 -A-TATATTTTAAATATTTTA
1 TATTATATATTAAAAATATTA
*
16757 -ATTAAAACGATATT-AAAATATTA
1 TATT---A-TATATTAAAAATATTA
*
16780 TATTA-ATATTAAATATAT
1 TATTATATATTAAAAATAT
16798 AAAATGATAT
Statistics
Matches: 64, Mismatches: 10, Indels: 18
0.70 0.11 0.20
Matches are distributed among these distances:
19 9 0.14
20 18 0.28
21 12 0.19
22 10 0.16
23 8 0.12
24 7 0.11
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (21 bp):
TATTATATATTAAAAATATTA
Found at i:17629 original size:43 final size:44
Alignment explanation
Indices: 17565--17666 Score: 118
Period size: 43 Copynumber: 2.3 Consensus size: 44
17555 TAGATTTGGA
* * * * *
17565 ATCCTCAAATTCGAATGAGCAAGATTATCCTCATATTTT-CAGT
1 ATCCTCAAGTACGAAGGAGCAAGATCATCCTCACATTTTCCAGT
* *
17608 CATCC-CAAGTACGAAGGAGCAAGATCATCCTCGCATTTTCCGGT
1 -ATCCTCAAGTACGAAGGAGCAAGATCATCCTCACATTTTCCAGT
17652 ATCCTCAAGTACGAA
1 ATCCTCAAGTACGAA
17667 TGAGTGTAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
43 32 0.65
44 17 0.35
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (44 bp):
ATCCTCAAGTACGAAGGAGCAAGATCATCCTCACATTTTCCAGT
Found at i:19732 original size:30 final size:30
Alignment explanation
Indices: 19696--19795 Score: 146
Period size: 30 Copynumber: 3.3 Consensus size: 30
19686 AAACGCAAAG
* *
19696 AAGAAGAAGAGGTAGAAACGATAGAAGAAA
1 AAGAAGAAGAGGTAGAAACGACAGAAGCAA
*
19726 AAGAAGAAAAGGTAGAAACGACAGAAGCAA
1 AAGAAGAAGAGGTAGAAACGACAGAAGCAA
* * *
19756 AAGAAGAAGAGGGAGAAGCGGCAGAAGCAA
1 AAGAAGAAGAGGTAGAAACGACAGAAGCAA
19786 AAGAAGAAGA
1 AAGAAGAAGA
19796 ATAGAAGTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.58, C:0.07, G:0.32, T:0.03
Consensus pattern (30 bp):
AAGAAGAAGAGGTAGAAACGACAGAAGCAA
Found at i:23709 original size:15 final size:15
Alignment explanation
Indices: 23685--23715 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
23675 TTCTTCTTCA
23685 ACTTGCTCATCCTCT
1 ACTTGCTCATCCTCT
*
23700 ACTTGTTCATCCTCT
1 ACTTGCTCATCCTCT
23715 A
1 A
23716 TAGTAACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.35, G:0.06, T:0.42
Consensus pattern (15 bp):
ACTTGCTCATCCTCT
Found at i:25468 original size:20 final size:20
Alignment explanation
Indices: 25414--25461 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
25404 TTCCATATTC
* * *
25414 TTCCATACTCTTCCATAAGG
1 TTCCACACTCGTCCATAAGA
25434 TTCCACACTCGTCCATAAGA
1 TTCCACACTCGTCCATAAGA
25454 TTCCACAC
1 TTCCACAC
25462 ATCTCCAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.35, G:0.08, T:0.29
Consensus pattern (20 bp):
TTCCACACTCGTCCATAAGA
Found at i:25476 original size:20 final size:20
Alignment explanation
Indices: 25414--25478 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
25404 TTCCATATTC
* * * *
25414 TTCCATACTCTTCCATAAGG
1 TTCCACACTCGTCCAGAAGA
*
25434 TTCCACACTCGTCCATAAGA
1 TTCCACACTCGTCCAGAAGA
*
25454 TTCCACACATC-TCCAGAATA
1 TTCCACAC-TCGTCCAGAAGA
25474 TTCCA
1 TTCCA
25479 GAGGATTCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 37 0.95
21 2 0.05
ACGTcount: A:0.29, C:0.34, G:0.08, T:0.29
Consensus pattern (20 bp):
TTCCACACTCGTCCAGAAGA
Found at i:28785 original size:17 final size:17
Alignment explanation
Indices: 28763--28795 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28753 GCAAAAATAG
28763 AATTTCTTATTGAATGA
1 AATTTCTTATTGAATGA
28780 AATTTCTTATTGAATG
1 AATTTCTTATTGAATG
28796 GAATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (17 bp):
AATTTCTTATTGAATGA
Found at i:30592 original size:13 final size:13
Alignment explanation
Indices: 30574--30599 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30564 GGCTATTGTC
30574 TATTGTTTATGGT
1 TATTGTTTATGGT
30587 TATTGTTTATGGT
1 TATTGTTTATGGT
30600 ATATGGTTAT
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:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (13 bp):
TATTGTTTATGGT
Found at i:30592 original size:20 final size:20
Alignment explanation
Indices: 30567--30609 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
30557 TATATTAGGC
* *
30567 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
*
30587 TATTGTTTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
30607 TAT
1 TAT
30610 AGAATAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.02, G:0.21, T:0.58
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:30695 original size:45 final size:46
Alignment explanation
Indices: 30621--30746 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
30611 GAATAATGGC
*
30621 AAGTGTATTGGTAAAATAAGCTTACGAGCTTATGG-AACAAATAGT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGTAACAAATAGT
* ** *
30666 AAGTATATTGGTAAAATAAGCTTATGAGCTTATGGTATTAAATGGT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGTAACAAATAGT
30712 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
30747 GATAAATGGT
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
45 33 0.45
46 41 0.55
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (46 bp):
AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGTAACAAATAGT
Found at i:30731 original size:46 final size:44
Alignment explanation
Indices: 30615--30759 Score: 209
Period size: 45 Copynumber: 3.2 Consensus size: 44
30605 GTTATAGAAT
* * *
30615 AATGGCAAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGAACA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG-ATA
* *
30660 AATAGTAAGTATATTGGTAAAATAAGCTTATGAGCTTATGGTATTA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG-A-TA
30706 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGATA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT-GGATA
30751 AATGGTAAG
1 AATGGTAAG
30760 AGATTTTTTT
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
45 49 0.54
46 39 0.43
47 2 0.02
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (44 bp):
AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGATA
Found at i:31135 original size:20 final size:20
Alignment explanation
Indices: 31110--31148 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
31100 CAATTAGTGT
31110 ATCGATACATCCTGCTGTGG
1 ATCGATACATCCTGCTGTGG
*
31130 ATCGATGCATCCTGCTGTG
1 ATCGATACATCCTGCTGTG
31149 CATCCATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.31
Consensus pattern (20 bp):
ATCGATACATCCTGCTGTGG
Found at i:31157 original size:20 final size:20
Alignment explanation
Indices: 31117--31160 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
31107 TGTATCGATA
* *
31117 CATCCTGCTGTGGATCGATG
1 CATCCTGCTGTGCATCCATG
31137 CATCCTGCTGTGCATCCATG
1 CATCCTGCTGTGCATCCATG
31157 CATC
1 CATC
31161 AAGGCTGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.32, G:0.23, T:0.30
Consensus pattern (20 bp):
CATCCTGCTGTGCATCCATG
Found at i:34279 original size:21 final size:21
Alignment explanation
Indices: 34253--34292 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
34243 AAAAAATTGG
34253 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
34274 TAACAATTGATATCTTTTT
1 TAACAATTGATATCATTTT
34293 CATTAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:34581 original size:20 final size:19
Alignment explanation
Indices: 34513--34725 Score: 79
Period size: 20 Copynumber: 10.8 Consensus size: 19
34503 AGGGTGTCAA
* *
34513 AGTGCATCCATGCACCCCTGC
1 AGTGCATCGATGCA--CCTGT
*
34534 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCGATGCACCTG----T
34557 AGTGCATCGATGCACCATGT
1 AGTGCATCGATGCACC-TGT
* **
34577 AGTGCATCCATGCA-CTCC
1 AGTGCATCGATGCACCTGT
* *
34595 A-T--TTCGAATGCA-AT-T
1 AGTGCATCG-ATGCACCTGT
34610 AGTGCATCGATGCATCCTGCT
1 AGTGCATCGATGCA-CCTG-T
*
34631 -GTGCATCGATGCATCATGCT
1 AGTGCATCGATGCA-CCTG-T
*
34651 -GTGTATCGATGCATCCTG-
1 AGTGCATCGATGCA-CCTGT
34669 ATGTGCATCGATGCATCCTGCT
1 A-GTGCATCGATGCA-CCTG-T
*
34691 A-TGCATCGATGCTTCCT-T
1 AGTGCATCGATGC-ACCTGT
*
34709 CTGTGCATCGATGCACC
1 -AGTGCATCGATGCACC
34726 AAGGCTGTAA
Statistics
Matches: 154, Mismatches: 18, Indels: 42
0.72 0.08 0.20
Matches are distributed among these distances:
15 3 0.02
16 7 0.05
17 6 0.04
18 6 0.04
19 8 0.05
20 91 0.59
21 15 0.10
22 1 0.01
23 15 0.10
24 2 0.01
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (19 bp):
AGTGCATCGATGCACCTGT
Found at i:34661 original size:40 final size:40
Alignment explanation
Indices: 34612--34723 Score: 170
Period size: 40 Copynumber: 2.8 Consensus size: 40
34602 ATGCAATTAG
*
34612 TGCATCGATGCATCCTGCTGTGCATCGATGCATCATGCTG
1 TGCATCGATGCATCCTGCTGTGCATCGATGCATCATGCTA
* * *
34652 TGTATCGATGCATCCTGATGTGCATCGATGCATCCTGCTA
1 TGCATCGATGCATCCTGCTGTGCATCGATGCATCATGCTA
* *
34692 TGCATCGATGCTTCCTTCTGTGCATCGATGCA
1 TGCATCGATGCATCCTGCTGTGCATCGATGCA
34724 CCAAGGCTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.32
Consensus pattern (40 bp):
TGCATCGATGCATCCTGCTGTGCATCGATGCATCATGCTA
Found at i:34677 original size:60 final size:60
Alignment explanation
Indices: 34611--34723 Score: 181
Period size: 60 Copynumber: 1.9 Consensus size: 60
34601 AATGCAATTA
* *
34611 GTGCATCGATGCATCCTGCTGTGCATCGATGCATCATGCTGTGTATCGATGCATCCTGAT
1 GTGCATCGATGCATCCTGCTATGCATCGATGCATCATGCTGTGCATCGATGCATCCTGAT
* * *
34671 GTGCATCGATGCATCCTGCTATGCATCGATGCTTCCTTCTGTGCATCGATGCA
1 GTGCATCGATGCATCCTGCTATGCATCGATGCATCATGCTGTGCATCGATGCA
34724 CCAAGGCTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.32
Consensus pattern (60 bp):
GTGCATCGATGCATCCTGCTATGCATCGATGCATCATGCTGTGCATCGATGCATCCTGAT
Found at i:37192 original size:19 final size:20
Alignment explanation
Indices: 37168--37215 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
37158 AACGATTTTC
*
37168 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
37187 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
37207 TTTTGAAAA
1 TTTTGAAAA
37216 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:39519 original size:7 final size:7
Alignment explanation
Indices: 39498--39535 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
39488 ACGTGTACCG
*
39498 TTCACTG
1 TTCACTA
39505 TT-ACTA
1 TTCACTA
39511 TTCACTA
1 TTCACTA
39518 TTCACTA
1 TTCACTA
39525 TTCACTA
1 TTCACTA
39532 TTCA
1 TTCA
39536 TAAAAAATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.45
Consensus pattern (7 bp):
TTCACTA
Found at i:40558 original size:10 final size:10
Alignment explanation
Indices: 40532--40592 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
40522 GAAGCTCTAC
40532 ACTCTTCCACT
1 ACTCTTCCA-T
*
40543 -CCCTTCCAT
1 ACTCTTCCAT
*
40552 ATTCTTCCAT
1 ACTCTTCCAT
40562 ACTCTTCCAT
1 ACTCTTCCAT
*** *
40572 AAGGTTCCAC
1 ACTCTTCCAT
40582 ACTCTTCCAT
1 ACTCTTCCAT
40592 A
1 A
40593 AGGTTCCACA
Statistics
Matches: 37, Mismatches: 12, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
9 1 0.03
10 36 0.97
ACGTcount: A:0.21, C:0.39, G:0.03, T:0.36
Consensus pattern (10 bp):
ACTCTTCCAT
Found at i:40568 original size:20 final size:20
Alignment explanation
Indices: 40535--40604 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
40525 GCTCTACACT
* * **
40535 CTTCCACTCCCTTCCATATT
1 CTTCCACACTCTTCCATAAG
*
40555 CTTCCATACTCTTCCATAAG
1 CTTCCACACTCTTCCATAAG
*
40575 GTTCCACACTCTTCCATAAG
1 CTTCCACACTCTTCCATAAG
*
40595 GTTCCACACT
1 CTTCCACACT
40605 TCTCCAGAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.21, C:0.39, G:0.06, T:0.34
Consensus pattern (20 bp):
CTTCCACACTCTTCCATAAG
Found at i:40610 original size:20 final size:20
Alignment explanation
Indices: 40556--40604 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
40546 TTCCATATTC
*
40556 TTCCATACTCTTCCATAAGG
1 TTCCACACTCTTCCATAAGG
40576 TTCCACACTCTTCCATAAGG
1 TTCCACACTCTTCCATAAGG
40596 TTCCACACT
1 TTCCACACT
40605 TCTCCAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.35, G:0.08, T:0.33
Consensus pattern (20 bp):
TTCCACACTCTTCCATAAGG
Found at i:42080 original size:82 final size:82
Alignment explanation
Indices: 41993--42194 Score: 341
Period size: 82 Copynumber: 2.5 Consensus size: 82
41983 ACGTCGCTAT
* * *
41993 AGAGTAGTACTTTAGCGGCATTTTTATACAAACGCCGCAATAGGTTCATCCATAGTGTCGCTTTT
1 AGAGTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCAATAGGTTCATCCATAGTGGCGCTTTT
*
42058 TCAACAAACACCGCAAC
66 TCAACAAACACCACAAC
* *
42075 AGAGTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCAATTGGTTCATCCATAGTGGCGTTTTT
1 AGAGTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCAATAGGTTCATCCATAGTGGCGCTTTT
*
42140 TCAACAAACGCCACAAC
66 TCAACAAACACCACAAC
42157 AGAGTAGTACTTTAGTGGCGTTTTTATACAAACGCCGC
1 AGAGTAGTACTTTAGTGGCGTTTTTATACAAACGCCGC
42195 TATACACTCA
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 113 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (82 bp):
AGAGTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCAATAGGTTCATCCATAGTGGCGCTTTT
TCAACAAACACCACAAC
Found at i:42323 original size:41 final size:41
Alignment explanation
Indices: 41972--42324 Score: 237
Period size: 41 Copynumber: 8.6 Consensus size: 41
41962 TTAGCGTCGT
* * * * * *
41972 TTTTTATAAAAACGTCGCTATAGAGTAGTACTTTAGCGGCA
1 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCG
* ** * ** *
42013 TTTTTATACAAACGCCGCAATAGGTTCAT-CCATAGTGTCG
1 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCG
* * * * *
42053 CTTTTTCA-ACAAACACCGCAACAGAGTAGTACTTTAGTGGCG
1 -TTTTT-ATACAAACGCCGCTATAGACTCGTACTTTAGTGGCG
* * ** * **
42095 TTTTTATACAAACGCCGCAATTGGTTCAT-CCATAGTGGCG
1 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCG
* * * * *
42135 TTTTT-TCAACAAACGCCACAACAGAGTAGTACTTTAGTGGCG
1 TTTTTAT--ACAAACGCCGCTATAGACTCGTACTTTAGTGGCG
* * * *
42177 TTTTTATACAAACGCCGCTATACACTCATATTTTAGTGGCA
1 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCG
* * * * *
42218 TTTGTGTTTACAAATGTCGTTAAAGACTCGTACTTTAGTGGCG
1 TTT-T-TATACAAACGCCGCTATAGACTCGTACTTTAGTGGCG
* *
42261 TTTTTATACAAACGCCGCTATAGAATTGTACTTTAGTGGCG
1 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCG
* *
42302 TTTTTGTACAAACGCCACTATAG
1 TTTTTATACAAACGCCGCTATAG
42325 CCTAACGTGT
Statistics
Matches: 236, Mismatches: 66, Indels: 20
0.73 0.20 0.06
Matches are distributed among these distances:
39 1 0.00
40 21 0.09
41 157 0.67
42 25 0.11
43 32 0.14
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (41 bp):
TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCG
Found at i:45106 original size:42 final size:42
Alignment explanation
Indices: 45048--45307 Score: 219
Period size: 43 Copynumber: 6.2 Consensus size: 42
45038 ATTGTATCAA
* * *
45048 AAAAATGCCGCTATAGATATGATCTTTTGCGACATTTGTTCC
1 AAAAACGCCGCTATAGATATGACCTTTTGCGACGTTTGTTCC
* * * *
45090 CAAAACACCGCTATAGATCTGACCTTTTGCGACGTTTATT--
1 AAAAACGCCGCTATAGATATGACCTTTTGCGACGTTTGTTCC
* * * * * * *
45130 ATGAAACACTGCTATAGATCTGATCTTTTGCTG-TGTTTTTTCC
1 A-AAAACGCCGCTATAGATATGACCTTTTGC-GACGTTTGTTCC
* * *
45173 AAAAACGCTGCTATAGATCTCGACCTTTTAC-AGCGTTTGTTCC
1 AAAAACGCCGCTATAGATAT-GACCTTTTGCGA-CGTTTGTTCC
* * *
45216 AAAAACGCCACTATAGATATCGACTTTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATAT-GACCTTTTGCGACGTTTGTTCC
* *
45259 AAAAACGTCGCTATAGATATCGACC---TACGACGTTTGTTCC
1 AAAAACGCCGCTATAGATAT-GACCTTTTGCGACGTTTGTTCC
45299 AAAAACGCC
1 AAAAACGCC
45308 ACGATATATC
Statistics
Matches: 179, Mismatches: 31, Indels: 18
0.79 0.14 0.08
Matches are distributed among these distances:
40 21 0.12
41 32 0.18
42 51 0.28
43 75 0.42
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (42 bp):
AAAAACGCCGCTATAGATATGACCTTTTGCGACGTTTGTTCC
Found at i:45332 original size:83 final size:84
Alignment explanation
Indices: 45164--45332 Score: 209
Period size: 83 Copynumber: 2.0 Consensus size: 84
45154 CTTTTGCTGT
* * *
45164 GTTTTTTCCAAAAACGCTGCTATAGATCTCGACCTTTTACAGCGTTTGTTCCAAAAACGCCACTA
1 GTTTGTTCCAAAAACGCTGCTATAGATATCGACC--TTACAGCGTTTGTTCCAAAAACGCCACGA
* *
45229 TAGATATCGACTTTTTGCGGC
64 TAGATATCGACCTATTGCGGC
45250 GTTTGTTCCAAAAACG-TCGCTATAGATATCGACC-TAC-GACGTTTGTTCCAAAAACGCCACGA
1 GTTTGTTCCAAAAACGCT-GCTATAGATATCGACCTTACAG-CGTTTGTTCCAAAAACGCCACGA
* * *
45312 TATATCTTGACCTATTGCGGC
64 TAGATATCGACCTATTGCGGC
45333 ATTTTTTTGA
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
82 1 0.01
83 41 0.56
85 1 0.01
86 30 0.41
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (84 bp):
GTTTGTTCCAAAAACGCTGCTATAGATATCGACCTTACAGCGTTTGTTCCAAAAACGCCACGATA
GATATCGACCTATTGCGGC
Found at i:46687 original size:2 final size:2
Alignment explanation
Indices: 46680--46717 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
46670 GAGAACAGAT
46680 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46718 CGGCAATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47853 original size:20 final size:20
Alignment explanation
Indices: 47828--47881 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
47818 CGATCTCAAA
*
47828 TTCGCAACGCGAATTCCAAT
1 TTCGCAACACGAATTCCAAT
* *
47848 TTCGCAACTC-AGTTTCCAAT
1 TTCGCAACACGA-ATTCCAAT
47868 TTCGCAACACGAAT
1 TTCGCAACACGAAT
47882 ATGTAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.28
Consensus pattern (20 bp):
TTCGCAACACGAATTCCAAT
Found at i:47928 original size:20 final size:20
Alignment explanation
Indices: 47905--47988 Score: 118
Period size: 20 Copynumber: 4.2 Consensus size: 20
47895 TGCGATTTTC
47905 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
47925 CAAATTCGC-ACAC-AGAAGT
1 CAAATTCGCAACGCGA-AAGT
* *
47944 CAAATTCGTAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
47964 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
47984 CAAAT
1 CAAAT
47989 GTTTTTACGC
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
18 1 0.02
19 15 0.27
20 38 0.69
21 1 0.02
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:48141 original size:22 final size:22
Alignment explanation
Indices: 48116--48165 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
48106 CTACGGCGAC
48116 ATCCGTACCCATCTCCGACGAA
1 ATCCGTACCCATCTCCGACGAA
* * *
48138 ATCCGTCCCCATTTTCGACGAA
1 ATCCGTACCCATCTCCGACGAA
48160 ATCCGT
1 ATCCGT
48166 TTATCTCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.38, G:0.14, T:0.24
Consensus pattern (22 bp):
ATCCGTACCCATCTCCGACGAA
Found at i:48398 original size:13 final size:13
Alignment explanation
Indices: 48380--48424 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
48370 AGTATTTGTC
48380 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
48393 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
* *
48406 TTCGTTTTATCTT
1 TTTGTTTTGTCTT
48419 TTTGTT
1 TTTGTT
48425 GAAGAAACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.02, C:0.09, G:0.13, T:0.76
Consensus pattern (13 bp):
TTTGTTTTGTCTT
Found at i:48418 original size:26 final size:24
Alignment explanation
Indices: 48374--48424 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 24
48364 GAAGTTAGTA
*
48374 TTTGTCTTTGTTTTGTCTTTTTGT
1 TTTGTCTTTGTTTTATCTTTTTGT
48398 TTTGTCTTTTCGTTTTATCTTTTTGT
1 TTTGTC-TTT-GTTTTATCTTTTTGT
48424 T
1 T
48425 GAAGAAACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 6 0.25
25 3 0.12
26 15 0.62
ACGTcount: A:0.02, C:0.10, G:0.14, T:0.75
Consensus pattern (24 bp):
TTTGTCTTTGTTTTATCTTTTTGT
Found at i:48493 original size:19 final size:20
Alignment explanation
Indices: 48448--48485 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
48438 ATCACAACAC
*
48448 GAAAATCGCAACGCGAAAAT
1 GAAAATCGCAACACGAAAAT
48468 GAAAATCGCAACAC-AAAA
1 GAAAATCGCAACACGAAAA
48486 CTAAAATCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.55, C:0.21, G:0.16, T:0.08
Consensus pattern (20 bp):
GAAAATCGCAACACGAAAAT
Found at i:50710 original size:42 final size:42
Alignment explanation
Indices: 50663--50782 Score: 109
Period size: 42 Copynumber: 2.9 Consensus size: 42
50653 GATGCACCTA
* *
50663 TCATCATTCAAGAGGCGCCTCCTATCGTTCAAGAGGCCTCTC
1 TCATCATTCAAGAGGCCCCTCCTATCGTTCAAGAGGCCCCTC
* * * * * *
50705 TCATCA-TCGAATAAGCCCCTCCCACCGTTCAAGAGTCCCCTT
1 TCATCATTC-AAGAGGCCCCTCCTATCGTTCAAGAGGCCCCTC
* * *
50747 TCATCGTTCAAGAGTCCCCT-TTCATCGTTCAAGAGG
1 TCATCATTCAAGAGGCCCCTCCT-ATCGTTCAAGAGG
50783 TCTTGTCTGC
Statistics
Matches: 59, Mismatches: 16, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
41 2 0.03
42 55 0.93
43 2 0.03
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.27
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCTCCTATCGTTCAAGAGGCCCCTC
Found at i:50744 original size:21 final size:21
Alignment explanation
Indices: 50730--50781 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
50720 CCCCTCCCAC
50730 CGTTCAAGAGTCCCCTTTCAT
1 CGTTCAAGAGTCCCCTTTCAT
50751 CGTTCAAGAGTCCCCTTTCAT
1 CGTTCAAGAGTCCCCTTTCAT
50772 CGTTCAAGAG
1 CGTTCAAGAG
50782 GTCTTGTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (21 bp):
CGTTCAAGAGTCCCCTTTCAT
Found at i:52382 original size:20 final size:20
Alignment explanation
Indices: 52356--52429 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
52346 GTTGAAGGTA
52356 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* *
52376 TAAATTCGCAATGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* *
52396 CAAATTTGCAACGTGAAAGT
1 CAAATTCGCAACGCGAAAGT
52416 CAAATTCGCAACGC
1 CAAATTCGCAACGC
52430 TTATTTCGCG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:52724 original size:39 final size:39
Alignment explanation
Indices: 52670--52756 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
52660 TCAAGTTGTA
52670 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
52709 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
52748 GATTTTGAT
1 GATTTTGAT
52757 GAGCATCGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:53167 original size:25 final size:25
Alignment explanation
Indices: 53133--53182 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
53123 ATTATTTTTC
*
53133 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
53158 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
53183 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:53268 original size:20 final size:20
Alignment explanation
Indices: 53245--53283 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
53235 ACCTGTTGAA
53245 GGTAAATTCACAACGCGAAT
1 GGTAAATTCACAACGCGAAT
53265 GGTAAATTCACAACGCGAA
1 GGTAAATTCACAACGCGAA
53284 ATAAGCGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (20 bp):
GGTAAATTCACAACGCGAAT
Found at i:53431 original size:34 final size:34
Alignment explanation
Indices: 53336--53434 Score: 144
Period size: 34 Copynumber: 2.9 Consensus size: 34
53326 TCGGTTTGCG
* ***
53336 ATTTCGCGTTGCGAATTTGACTATCGCAACGCTT
1 ATTTCGCGTTGCGAATTTGACTTTCGCGTTGCTT
*
53370 ATTTCGCGTTGTGAATTTGACTTTCGCGTTGCTT
1 ATTTCGCGTTGCGAATTTGACTTTCGCGTTGCTT
*
53404 ATTTCGTGTTGCGAATTTGACTTTCGCGTTG
1 ATTTCGCGTTGCGAATTTGACTTTCGCGTTG
53435 ATCGCAACAT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.42
Consensus pattern (34 bp):
ATTTCGCGTTGCGAATTTGACTTTCGCGTTGCTT
Found at i:53434 original size:20 final size:20
Alignment explanation
Indices: 53371--53434 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
53361 GCAACGCTTA
*
53371 TTTCGCGTTGTGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
53391 TTTCGCGTTGC----TT-A-
1 TTTCGCGTTGCGAATTTGAC
*
53405 TTTCGTGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
53425 TTTCGCGTTG
1 TTTCGCGTTG
53435 ATCGCAACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
18 2 0.06
19 1 0.03
20 19 0.54
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:56037 original size:24 final size:24
Alignment explanation
Indices: 56010--56056 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
56000 ATCATCGAAA
56010 TCCGAGTATTGACCAAGATCAAAG
1 TCCGAGTATTGACCAAGATCAAAG
* *
56034 TCCGGGTATTGACCAATATCAAA
1 TCCGAGTATTGACCAAGATCAAA
56057 TTTTGAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAAAG
Found at i:56203 original size:12 final size:12
Alignment explanation
Indices: 56182--56215 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
56172 GGTTGTGGGT
*
56182 TTTGAGATTGTG
1 TTTGATATTGTG
56194 TTTGATATTGTG
1 TTTGATATTGTG
*
56206 TTTGGTATTG
1 TTTGATATTG
56216 GAAATGCGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:57084 original size:20 final size:19
Alignment explanation
Indices: 57039--57103 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
57029 TTACATATTT
*
57039 GCGTTGCGAAATTGGAAAC
1 GCGTTGCGAAATTGGAATC
*
57058 TGGGTTGCGAAATTGGAATTC
1 -GCGTTGCGAAATTGGAA-TC
*
57079 GCGTTGC-AAATTTGAGATC
1 GCGTTGCGAAATTGGA-ATC
57098 GCGTTG
1 GCGTTG
57104 TGAATTTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
19 15 0.38
20 23 0.59
21 1 0.03
ACGTcount: A:0.25, C:0.14, G:0.32, T:0.29
Consensus pattern (19 bp):
GCGTTGCGAAATTGGAATC
Found at i:57593 original size:18 final size:18
Alignment explanation
Indices: 57570--57623 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 18
57560 TCAACAATAA
57570 ATTAATTTAAATAAAATT
1 ATTAATTTAAATAAAATT
*
57588 GA-TAATTT-ATTAAAATT
1 -ATTAATTTAAATAAAATT
57605 ATTAGATTTATAATAAAAT
1 ATTA-ATTTA-AATAAAAT
57624 AATAAAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 1 0.03
17 10 0.34
18 10 0.34
19 1 0.03
20 7 0.24
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
ATTAATTTAAATAAAATT
Found at i:63897 original size:17 final size:17
Alignment explanation
Indices: 63875--63907 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
63865 ATAATTTAAT
63875 AAAAAC-ACAATGATTTG
1 AAAAACAACAAT-ATTTG
63892 AAAAACAACAATATTT
1 AAAAACAACAATATTT
63908 TTTTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAAACAACAATATTTG
Found at i:68208 original size:22 final size:21
Alignment explanation
Indices: 68166--68205 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
68156 GAGTTTGTTT
*
68166 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
68187 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
68206 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:70880 original size:27 final size:27
Alignment explanation
Indices: 70842--70903 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
70832 GTCCTCTGTT
70842 AAGGGTCTTTCCATGAGTACACCACTA
1 AAGGGTCTTTCCATGAGTACACCACTA
70869 AAGGGTCTTTCCATGAGTACACCACTA
1 AAGGGTCTTTCCATGAGTACACCACTA
70896 AAGGGTCT
1 AAGGGTCT
70904 CTAACCCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (27 bp):
AAGGGTCTTTCCATGAGTACACCACTA
Found at i:74190 original size:20 final size:20
Alignment explanation
Indices: 74153--74190 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
74143 TCAACGTATG
*
74153 TATATATCTTGTAGTATTTT
1 TATATATCTTGTAATATTTT
74173 TATATA-CTTGTAAATATT
1 TATATATCTTGT-AATATT
74191 ATATATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (20 bp):
TATATATCTTGTAATATTTT
Found at i:77197 original size:31 final size:31
Alignment explanation
Indices: 77159--77221 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
77149 AGTTACATCG
77159 GGGACCATATTACAAACGGACTAAATGTTGA
1 GGGACCATATTACAAACGGACTAAATGTTGA
77190 GGGACCATATTACAAACGGACTAAATGTTGA
1 GGGACCATATTACAAACGGACTAAATGTTGA
77221 G
1 G
77222 AGATTATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (31 bp):
GGGACCATATTACAAACGGACTAAATGTTGA
Found at i:81769 original size:30 final size:31
Alignment explanation
Indices: 81730--81794 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
81720 GGGGACCAAC
*
81730 TTAACATTTT-AAAATATTTGGAA-GTTTAAT
1 TTAAAATTTTCAAAA-ATTTGGAAGGTTTAAT
*
81760 TTAAAATTTTCAAAAATTTTGAAGGGTTTAAT
1 TTAAAATTTTCAAAAATTTGGAA-GGTTTAAT
81792 TTA
1 TTA
81795 TATTATTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 16 0.53
31 4 0.13
32 10 0.33
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (31 bp):
TTAAAATTTTCAAAAATTTGGAAGGTTTAAT
Found at i:81776 original size:32 final size:36
Alignment explanation
Indices: 81740--81817 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 36
81730 TTAACATTTT
81740 AAAATATTTGGAA-GTTTAATTTA-A-AATTTT-CA
1 AAAATATTTGGAAGGTTTAATTTATATAATTTTCCA
*
81772 AAAAT-TTT-GAAGGGTTTAATTTATATTATTTTCCA
1 AAAATATTTGGAA-GGTTTAATTTATATAATTTTCCA
*
81807 AAAGTATTTGG
1 AAAATATTTGG
81818 TTCTAACTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
30 3 0.08
31 3 0.08
32 15 0.41
33 1 0.03
34 5 0.14
35 6 0.16
36 3 0.08
37 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (36 bp):
AAAATATTTGGAAGGTTTAATTTATATAATTTTCCA
Found at i:81961 original size:32 final size:31
Alignment explanation
Indices: 81924--82005 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 31
81914 TTTAATGTGC
*
81924 ATTTTTAAAAATTTAGAGGGACCAAATTAATT
1 ATTTTTAAAAATTTAGAGGGACCAAATT-ATA
* * * * *
81956 TTTTTTGAAAATTTAAAGGGTCTAAATTATA
1 ATTTTTAAAAATTTAGAGGGACCAAATTATA
*
81987 ATTTTTAAAATTTTAGAGG
1 ATTTTTAAAAATTTAGAGG
82006 CCATGGCCCT
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 17 0.43
32 23 0.57
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.43
Consensus pattern (31 bp):
ATTTTTAAAAATTTAGAGGGACCAAATTATA
Found at i:82955 original size:30 final size:30
Alignment explanation
Indices: 82914--82989 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
82904 AAAATCGAAT
*
82914 TAAATGGGGATGGGGAAAAATCGTTTATGC
1 TAAATGGGGATGGGGAAAAACCGTTTATGC
* *
82944 TAAACGGGGATGGGGAAAAACCGTTTATGT
1 TAAATGGGGATGGGGAAAAACCGTTTATGC
*
82974 TAAATAGGGATGGGGA
1 TAAATGGGGATGGGGA
82990 CGAGTTTAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.34, C:0.07, G:0.36, T:0.24
Consensus pattern (30 bp):
TAAATGGGGATGGGGAAAAACCGTTTATGC
Found at i:88873 original size:18 final size:18
Alignment explanation
Indices: 88846--88885 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
88836 ATGCATTCAT
88846 TAATTAAAAACACCAAAA
1 TAATTAAAAACACCAAAA
*
88864 TAATTGAAAACACCAAAA
1 TAATTAAAAACACCAAAA
88882 TAAT
1 TAAT
88886 ACGATAAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.62, C:0.15, G:0.03, T:0.20
Consensus pattern (18 bp):
TAATTAAAAACACCAAAA
Found at i:92570 original size:21 final size:21
Alignment explanation
Indices: 92528--92570 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
92518 TTTCTGGGCT
* *
92528 AGGGGAATTGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
92549 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
92570 A
1 A
92571 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:93445 original size:103 final size:103
Alignment explanation
Indices: 93117--93437 Score: 615
Period size: 103 Copynumber: 3.1 Consensus size: 103
93107 GTAGAGGGTC
93117 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
93182 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
93220 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
93285 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
93323 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
93388 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
93426 TATGTGGTCCTT
1 TATGTGGTCCTT
93438 ATGGACATTA
Statistics
Matches: 212, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:93487 original size:23 final size:23
Alignment explanation
Indices: 93454--93519 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
93444 ATTATTATAT
*
93454 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
93477 GGCACTCCGGTGCAATTATACGT
1 GGCACTACGGTGCAATTATACGC
*
93500 GGAACTTA-GGTGCAATTATA
1 GGCAC-TACGGTGCAATTATA
93520 TGAGCTGTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 36 0.97
24 1 0.03
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:99604 original size:21 final size:21
Alignment explanation
Indices: 99562--99604 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
99552 TTTCTGGGCT
* *
99562 AGGGGAATTGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
99583 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
99604 A
1 A
99605 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:99657 original size:20 final size:20
Alignment explanation
Indices: 99632--99669 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
99622 GAACGCTAGA
*
99632 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
99652 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
99670 TAATAAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:100477 original size:103 final size:103
Alignment explanation
Indices: 100149--100469 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 103
100139 GTAGAGGGTC
* *
100149 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
100214 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
100252 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
100317 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
**
100355 TATGTGGTTATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
100420 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
100458 TATATGGTCCTT
1 TATGTGGTCCTT
100470 ATGGACATTA
Statistics
Matches: 207, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 207 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:100521 original size:23 final size:23
Alignment explanation
Indices: 100495--100548 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 23
100485 TGGCACTACA
100495 GTGCAATTCTACGTGGCACTCT-G
1 GTGCAATTCTACGTGGCACT-TAG
100518 GTGCAATTCTACGTGGCACTTAG
1 GTGCAATTCTACGTGGCACTTAG
100541 GTGCAATT
1 GTGCAATT
100549 ATATGAGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 1 0.03
23 29 0.97
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.31
Consensus pattern (23 bp):
GTGCAATTCTACGTGGCACTTAG
Found at i:101837 original size:28 final size:26
Alignment explanation
Indices: 101790--101842 Score: 61
Period size: 28 Copynumber: 2.0 Consensus size: 26
101780 TGATTTTGCT
*
101790 TTATTATTTTATTTTAATTTAATTTC
1 TTATTATTTTATTATAATTTAATTTC
* *
101816 TTATATATTATTATTATCATTTCATTT
1 TTAT-TATT-TTATTATAATTTAATTT
101843 AATTATTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 4 0.18
27 4 0.18
28 14 0.64
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (26 bp):
TTATTATTTTATTATAATTTAATTTC
Found at i:113653 original size:2 final size:2
Alignment explanation
Indices: 113648--113691 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
113638 TTATAAAAAA
113648 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
113688 AT AT
1 AT AT
113692 TTTCTTAAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114226 original size:26 final size:27
Alignment explanation
Indices: 114174--114231 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
114164 TAATTCTTTC
*
114174 TTTTCAAAATTTTTATATATACGTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
114202 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
114228 TTTT
1 TTTT
114232 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:123703 original size:22 final size:22
Alignment explanation
Indices: 123678--123754 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
123668 ATCTACACTT
123678 TTCAAAGATGATAGATTCTTTC
1 TTCAAAGATGATAGATTCTTTC
*
123700 TTCAAAGATGATAACATATC--TC
1 TTCAAAGATGAT-AGAT-TCTTTC
* *
123722 TTTAAAGATGATATG-TTCTTTT
1 TTCAAAGATGATA-GATTCTTTC
123744 TTCAAAGATGA
1 TTCAAAGATGA
123755 AAGCTTTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
20 2 0.04
21 2 0.04
22 36 0.80
23 3 0.07
24 2 0.04
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTTTC
Found at i:124308 original size:124 final size:122
Alignment explanation
Indices: 124128--124836 Score: 828
Period size: 124 Copynumber: 5.9 Consensus size: 122
124118 CACTTGATGG
*
124128 ATCAAATTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCAT
124193 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
65 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAA-GAGATAGATCAGC
124252 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCAT
* * *
124317 AATGAGAAGAACTTGTTCAACCTTTTGCATGGCTCTATCATAGAAGGAGATAGATCAAC
65 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAA-GAGATAGATCAGC
*
124376 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGA-GGAAGAAGAAGTTCAT
* * * * * *
124441 AATGAGAAGAGCTTGTTCAACCTTTTGCTTCAAT-TCATCAC--------TCGAT--GG
65 AATGAGAAGAACTTGTTCAACCTTTTGCATGACTCT-ATCACAGAAGAGATAGATCAGC
* * * *
124489 ATCAACATTGCCAG-GTAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCA
1 ATCAACTTTTCCAGAG-A-AAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCA
* * * * *
124553 TAATGAGAAGAATTTGTTCAACCTTTTGCTTGAAT-TCATCAC--------TCGAT--GG
64 TAATGAGAAGAACTTGTTCAACCTTTTGCATGACTCT-ATCACAGAAGAGATAGATCAGC
* *
124602 ATCAACTTTTCCAGAG--AGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
124665 ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATTACGGAAAGAGATAGATCAAC
66 ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAG-AAGAGATAGATCAGC
*
124723 ATCAACTTTTCCAGAGAAAGTTCATAATGAA-AAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAAT-AAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
** * *
124787 -CCGAGAAGAACTTGTTCAGCC-TTTGCATGATTAC-ATCACAGAATGAGATA
65 AATGAGAAGAACTTGTTCAACCTTTTGCATGACT-CTATCACAGAA-GAGATA
124837 AATTATCATC
Statistics
Matches: 523, Mismatches: 40, Indels: 47
0.86 0.07 0.08
Matches are distributed among these distances:
110 79 0.15
111 1 0.00
112 1 0.00
113 85 0.16
114 32 0.06
115 4 0.01
119 4 0.01
120 2 0.00
121 37 0.07
122 19 0.04
123 43 0.08
124 216 0.41
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (122 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGAGATAGATCAGC
Found at i:124680 original size:110 final size:111
Alignment explanation
Indices: 124376--124810 Score: 541
Period size: 113 Copynumber: 3.8 Consensus size: 111
124366 ATAGATCAAC
124376 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA-GGAAGAAGAAGTTCAT
*
124441 AATGAGAAGAGCTTGTTCAACCTTTTGCTTCAATTCATCACTCGATGG
64 AATGAGAAGAACTTGTTCAACCTTTTGCTTCAATTCATCACTCGATGG
* * *
124489 ATCAACATTGCCAGGTAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCAT
1 ATCAACTTTTCCA-G-AGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
* *
124554 AATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTCGATGG
64 AATGAGAAGAACTTGTTCAACCTTTTGCTTCAATTCATCACTCGATGG
*
124602 ATCAACTTTTCCAGAG-AGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATAA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
* ** * * **
124666 TGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATTACGGAAAGAGATAGATCAAC
66 TGAGAAGAACTTGTTCAACCTTTTGC-T---TCAATT-C---ATCA-CTCGAT--GG
* *
124723 ATCAACTTTTCCAGAGAAAGTTCATAATGAAAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT-
1 ATCAACTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
** *
124787 CCGAGAAGAACTTGTTCAGCCTTT
65 ATGAGAAGAACTTGTTCAACCTTT
124811 GCATGATTAC
Statistics
Matches: 282, Mismatches: 25, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
110 71 0.25
111 3 0.01
112 1 0.00
113 82 0.29
114 36 0.13
115 3 0.01
118 2 0.01
119 4 0.01
121 16 0.06
122 21 0.07
123 43 0.15
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (111 bp):
ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCTTCAATTCATCACTCGATGG
Found at i:124878 original size:117 final size:122
Alignment explanation
Indices: 124618--124880 Score: 313
Period size: 123 Copynumber: 2.2 Consensus size: 122
124608 TTTTCCAGAG
* *
124618 AGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTTATCTAAAGAGGAAGAAGAAGTTCATAACGAGAAGAACTTGTTCA
* * * **
124683 ACCTTTTGCATGACTCTATTACGGAAAGAGATAGATCAACATCAACTTTTCCAGAGAA
66 ACCTTTTGCATGACTCTATCACAGAAAGAGATAAATCAACATCAACTAGT-CAGAGAA
* * *
124741 AGTTCATAATGAAAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT-CCGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTTATCTAAAGAGGAAGAAGAAGTTCATAACGAGAAGAACTTGTTCA
* * * * * * *
124805 GCC-TTTGCATGATTAC-ATCACAGAATGAGATAAATTATCATC-CCTAGT-GGA-AA
66 ACCTTTTGCATGACT-CTATCACAGAAAGAGATAAATCAACATCAACTAGTCAGAGAA
124858 AGTTCATAATGAGAAGAACTTAT
1 AGTTCATAATGAGAAGAACTTAT
124881 AGCTCAGAAG
Statistics
Matches: 121, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
117 24 0.20
118 2 0.02
120 3 0.02
121 30 0.25
122 19 0.16
123 43 0.36
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (122 bp):
AGTTCATAATGAGAAGAACTTATCTAAAGAGGAAGAAGAAGTTCATAACGAGAAGAACTTGTTCA
ACCTTTTGCATGACTCTATCACAGAAAGAGATAAATCAACATCAACTAGTCAGAGAA
Found at i:125989 original size:4 final size:4
Alignment explanation
Indices: 125982--126020 Score: 69
Period size: 4 Copynumber: 9.5 Consensus size: 4
125972 ATAATAAATA
125982 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTATT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTAT TT
126021 TTATAATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 30 0.88
5 4 0.12
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:126252 original size:17 final size:16
Alignment explanation
Indices: 126232--126272 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
126222 ATAAATATCC
126232 TATTTTTATATATATAT
1 TATTTTTATATATA-AT
*
126249 TA-TTTTAT-TTTAAT
1 TATTTTTATATATAAT
126263 TATTTTTATA
1 TATTTTTATA
126273 GAAATGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
14 4 0.19
15 9 0.43
16 6 0.29
17 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTTTATATATAAT
Found at i:128616 original size:210 final size:204
Alignment explanation
Indices: 128057--128646 Score: 656
Period size: 204 Copynumber: 2.9 Consensus size: 204
128047 ATATCACGAT
* ** * *
128057 TTCTCCTTCTGTCGTCGATAATTCGGTCCTCGACACCGGAGATACAGACAGTCA-CTCTCGAGAG
1 TTCTCCTTCTGTGGTCGATAATTCGGTCCTCGACACCGGAGATATGGACAGT-ATCTCCCAAGAG
* * * * * * *
128121 AATACGTCGGTCGCTCTATGGAATGCCGATCCTCCAGCTGCTGAAACCAATGGGAATGGCATTGG
65 AATACATCGGTCCCTCTATCGAATGCCGATCCTCCAGTTGCTGAAACCAAAGAGAGTGGCATTGG
* *
128186 AGTTAC-TGTCCAAGAAAACACCTCTCTTCCTGCTACTGTTGAAACCACAGGTGATAACGATAGC
130 AGTT-CTTGTCCAAGAAAACACCTCTCTTCCTCCAACTGTTGAAACCACAGGTGATAACGATAGC
128250 CTTACTTCACC
194 CTTACTTCACC
* * * *
128261 TTCTCCTTCTGTTGTCGATAATTCGGTCCTCGACACCGGAGATATGGATAGTCTCT-CAAGAGAG
1 TTCTCCTTCTGTGGTCGATAATTCGGTCCTCGACACCGGAGATATGGACAGTATCTCCCA-AGAG
* *
128325 AATACATCGGTCTCTCGATCGAATGCCGATCCTCCA-TCTGCTGAAACCAAA-AGGAGTGGCATT
65 AATACATCGGTCCCTCTATCGAATGCCGATCCTCCAGT-TGCTGAAACCAAAGA-GAGTGGCATT
* ** *
128388 GGAGTTATTGAACAAGAAAACACCTCTGTTCCTCCAACTGTTGAAACCA-ATGGTGATAAC-AGT
128 GGAGTTCTTGTCCAAGAAAACACCTCTCTTCCTCCAACTGTTGAAACCACA-GGTGATAACGA-T
*
128451 AGCCTTACTTCTCC
191 AGCCTTACTTCACC
* *
128465 TTCTCCTTCAACTTCGATGGAT-GATAATTCGGTCCTCGACACCGGAGACATGGAGAGTATCTCC
1 TTCTCCTT---C-T-G-TGG-TCGATAATTCGGTCCTCGACACCGGAGATATGGACAGTATCTCC
* * * * **
128529 CAAGAGAATACATCAGTCCCTCTTTCGAAAGCTGATCCTCCAGTTGCTGAAACCAAAGAGAGCAG
59 CAAGAGAATACATCGGTCCCTCTATCGAATGCCGATCCTCCAGTTGCTGAAACCAAAGAGAGTGG
* * * * *
128594 CAATGAAGATCTTGTCCAAGAAAACACATCCCTTCCTCCAACTGTTGAAACCA
124 CATTGGAGTTCTTGTCCAAGAAAACACCTCTCTTCCTCCAACTGTTGAAACCA
128647 GAGAGGAAGG
Statistics
Matches: 324, Mismatches: 45, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
203 2 0.01
204 180 0.56
207 1 0.00
208 1 0.00
209 1 0.00
210 134 0.41
211 5 0.02
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (204 bp):
TTCTCCTTCTGTGGTCGATAATTCGGTCCTCGACACCGGAGATATGGACAGTATCTCCCAAGAGA
ATACATCGGTCCCTCTATCGAATGCCGATCCTCCAGTTGCTGAAACCAAAGAGAGTGGCATTGGA
GTTCTTGTCCAAGAAAACACCTCTCTTCCTCCAACTGTTGAAACCACAGGTGATAACGATAGCCT
TACTTCACC
Found at i:130404 original size:15 final size:15
Alignment explanation
Indices: 130384--130420 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
130374 ATATTTAGCT
*
130384 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
130399 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
130414 GGGCGGG
1 GGGCGGG
130421 TAATGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:131114 original size:22 final size:22
Alignment explanation
Indices: 131086--131139 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
131076 AGCAAGCTTG
131086 TAACAAACTCTTAACAGCTGCT
1 TAACAAACTCTTAACAGCTGCT
* *
131108 TAACAAACTCTTAATAGTTGCT
1 TAACAAACTCTTAACAGCTGCT
131130 TAACAAACTC
1 TAACAAACTC
131140 ATGCACAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30
Consensus pattern (22 bp):
TAACAAACTCTTAACAGCTGCT
Found at i:136339 original size:20 final size:22
Alignment explanation
Indices: 136314--136353 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
136304 AGTCATATCT
136314 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
136334 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
136354 TCTATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:136511 original size:36 final size:36
Alignment explanation
Indices: 136464--136536 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
136454 TTGCAGCCAG
*
136464 AGTGTATGGATACACTACA-GGGTGTATCGATACACT
1 AGTGTATGGATACACT-CATAGGTGTATCGATACACT
* *
136500 AGTGTATGGATATACTCATAGGTGTATCGGTACACT
1 AGTGTATGGATACACTCATAGGTGTATCGATACACT
136536 A
1 A
136537 TTTACATTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 2 0.06
36 31 0.94
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (36 bp):
AGTGTATGGATACACTCATAGGTGTATCGATACACT
Found at i:136881 original size:21 final size:20
Alignment explanation
Indices: 136857--136920 Score: 78
Period size: 21 Copynumber: 3.2 Consensus size: 20
136847 AATGTTTAAT
136857 GAAAAAGATACCAATTGTTAA
1 GAAAAAGATACCAATTGTT-A
* *
136878 GAAAAGGATATCAATTGTT-
1 GAAAAAGATACCAATTGTTA
*
136897 -AAAAAGATACAAATTGTTA
1 GAAAAAGATACCAATTGTTA
136916 GAAAA
1 GAAAA
136921 TATATGAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 15 0.42
20 4 0.11
21 17 0.47
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (20 bp):
GAAAAAGATACCAATTGTTA
Found at i:136905 original size:18 final size:19
Alignment explanation
Indices: 136859--136925 Score: 75
Period size: 18 Copynumber: 3.5 Consensus size: 19
136849 TGTTTAATGA
*
136859 AAAAGATACCAATTGTTAAG
1 AAAAGATATCAATTGTT-AG
136879 AAAAGGATATCAATTGTTA-
1 AAAA-GATATCAATTGTTAG
136898 AAAAGATA-CAAATTGTTAG
1 AAAAGATATC-AATTGTTAG
*
136917 AAAATATAT
1 AAAAGATAT
136926 GAAAATGTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 1 0.02
18 12 0.29
19 11 0.27
20 5 0.12
21 12 0.29
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.28
Consensus pattern (19 bp):
AAAAGATATCAATTGTTAG
Found at i:139001 original size:9 final size:9
Alignment explanation
Indices: 138989--139072 Score: 88
Period size: 9 Copynumber: 9.6 Consensus size: 9
138979 CTTGAAGAGG
138989 AAAAA-GAA
1 AAAAATGAA
138997 AAAAATGAA
1 AAAAATGAA
139006 AAAAATGAA
1 AAAAATGAA
139015 AAAAATG-A
1 AAAAATGAA
139023 AAAAA-G-A
1 AAAAATGAA
*
139030 AAAGA-GAA
1 AAAAATGAA
139038 AAAAATGAA
1 AAAAATGAA
*
139047 TAAAAATGGAG
1 -AAAAAT-GAA
139058 AAAAATGAA
1 AAAAATGAA
139067 ACAAAA
1 A-AAAA
139073 AGGAGGGTTC
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
7 7 0.11
8 16 0.24
9 25 0.38
10 16 0.24
11 2 0.03
ACGTcount: A:0.76, C:0.01, G:0.14, T:0.08
Consensus pattern (9 bp):
AAAAATGAA
Found at i:139044 original size:32 final size:35
Alignment explanation
Indices: 138989--139072 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 35
138979 CTTGAAGAGG
138989 AAAAAGAAAAAAATGAAAAAAATGAA-AAAAATGA
1 AAAAAGAAAAAAATGAAAAAAATGAATAAAAATGA
*
139023 AAAAAG-AAAAGA-GAAAAAAATGAATAAAAATGGA
1 AAAAAGAAAAAAATGAAAAAAATGAATAAAAAT-GA
139057 GAAAAATGAAACAAAA
1 -AAAAA-GAAA-AAAA
139073 AGGAGGGTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
32 12 0.29
33 11 0.26
34 8 0.19
35 5 0.12
36 1 0.02
37 2 0.05
38 3 0.07
ACGTcount: A:0.76, C:0.01, G:0.14, T:0.08
Consensus pattern (35 bp):
AAAAAGAAAAAAATGAAAAAAATGAATAAAAATGA
Found at i:139044 original size:41 final size:42
Alignment explanation
Indices: 138988--139067 Score: 128
Period size: 41 Copynumber: 1.9 Consensus size: 42
138978 GCTTGAAGAG
138988 GAAAAAGAAAAAAATGAA-AAAAAT-GAAAAAAATGAAAAAA
1 GAAAAAGAAAAAAATGAATAAAAATGGAAAAAAATGAAAAAA
*
139028 GAAAAGAGAAAAAAATGAATAAAAATGGAGAAAAATGAAA
1 GAAAA-AGAAAAAAATGAATAAAAATGGAAAAAAATGAAA
139068 CAAAAAGGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 5 0.14
41 13 0.36
42 6 0.17
43 12 0.33
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (42 bp):
GAAAAAGAAAAAAATGAATAAAAATGGAAAAAAATGAAAAAA
Found at i:139077 original size:20 final size:19
Alignment explanation
Indices: 138989--139076 Score: 81
Period size: 20 Copynumber: 4.4 Consensus size: 19
138979 CTTGAAGAGG
138989 AAAAA-GAAAAAAATG-AA
1 AAAAAGGAAAAAAATGAAA
*
139006 AAAAATGAAAAAAATGAAAAA
1 AAAAAGGAAAAAAATG--AAA
139027 AGAAAAGAGAAAAAAATGAATA
1 A-AAAAG-GAAAAAAATGAA-A
* *
139049 AAAATGGAGAAAAATGAAA
1 AAAAAGGAAAAAAATGAAA
139068 CAAAAAGGA
1 -AAAAAGGA
139077 GGGTTCAAGA
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
17 5 0.08
18 10 0.17
19 1 0.02
20 18 0.31
21 9 0.15
22 6 0.10
23 10 0.17
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.08
Consensus pattern (19 bp):
AAAAAGGAAAAAAATGAAA
Found at i:140171 original size:55 final size:55
Alignment explanation
Indices: 140102--140730 Score: 831
Period size: 55 Copynumber: 11.4 Consensus size: 55
140092 TTGAAGCATC
* * * *
140102 AAGATTGTTTGAGTCTTATACTCTCTGAAGGAATATGGAGCGGACATGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* * *
140157 AAGATTGTTCGAGTCTTATACTTTCTGAAGGAATAAGGAGCAGACACGATTATTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
*
140212 AAGATTGTTCTAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* *
140267 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATACGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* * * * *
140322 AAGATTGTTCGAGTCATATACTCTCTAAAGTAATAGAGAACAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
*
140377 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTA
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
*
140432 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGAAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* * *
140487 AAGATTGTTCAAATCTTATACTCTCTGAAGGAATAGGGAGCAGAAACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
140542 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* * * * * * **
140597 AAGA-TGTTCAAGT-TCTATACTCCCTGAAAGAAAGAGGGAGC-GAACCCGTTTGCAG
1 AAGATTGTTCGAGTCT-TATACTCTCTG-AAGGAATAGGGAGCAG-ACACGATTGTTG
* * * * *
140652 AAGATTGTTCGAGT-TCTATACTCCCTAAAGTG-ATAGAGAGCAAACCCG-TTGTTCAG
1 AAGATTGTTCGAGTCT-TATACTCTCTGAAG-GAATAGGGAGCAGACACGATTGTT--G
*
140708 AAGATTGTGCGAGT-TCTATACTC
1 AAGATTGTTCGAGTCT-TATACTC
140731 GTGAAGCGAT
Statistics
Matches: 515, Mismatches: 51, Indels: 15
0.89 0.09 0.03
Matches are distributed among these distances:
53 1 0.00
54 22 0.04
55 449 0.87
56 43 0.08
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.29
Consensus pattern (55 bp):
AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
Found at i:140670 original size:56 final size:56
Alignment explanation
Indices: 140211--140840 Score: 263
Period size: 55 Copynumber: 11.4 Consensus size: 56
140201 CACGATTATT
* * * * * **
140211 GAAGATTGTTCTAG-TCTTATACTCTCTG-AAGGAATAGGGAGC-AGACACGATTGTT
1 GAAGATTGTTCGAGTTC-TATACTCCCTGAAAGAAATAGGGAGCGA-ACCCGTTTGCA
* * * * **
140266 GAAGATTGTTCGAG-TCTTATACTCTCTG-AAGAAATACGGAGC-AGACACGATTGTT
1 GAAGATTGTTCGAGTTC-TATACTCCCTGAAAGAAATAGGGAGCGA-ACCCGTTTGCA
* * * * * * **
140321 GAAGATTGTTCGAG-TCATATACTCTCT-AAAGTAATAGAGAAC-AGACACGATTGTT
1 GAAGATTGTTCGAGTTC-TATACTCCCTGAAAGAAATAGGGAGCGA-ACCCGTTTGCA
* * * * *
140376 GAAGATTGTTCGAG-TCTTATACTCTCTG-AAGGAATAGGGAGC-AGACACGATTGTTA
1 GAAGATTGTTCGAGTTC-TATACTCCCTGAAAGAAATAGGGAGCGA-ACCCGTTTG-CA
* * * * * **
140432 -AAGATTGTTCGAG-TCTTATACTCTCTG-AAGGAATAGGAAGC-AGACACGATTGTT
1 GAAGATTGTTCGAGTTC-TATACTCCCTGAAAGAAATAGGGAGCGA-ACCCGTTTGCA
** * * * * **
140486 GAAGATTGTTC-AAATCTTATACTCTCTG-AAGGAATAGGGAGCAGAA-ACGATTGTT
1 GAAGATTGTTCGAGTTC-TATACTCCCTGAAAGAAATAGGGAGC-GAACCCGTTTGCA
* * * * **
140541 GAAGATTGTTCGAG-TCTTATACTCTCTG-AAGGAATAGGGAGC-AGACACGATTGTT
1 GAAGATTGTTCGAGTTC-TATACTCCCTGAAAGAAATAGGGAGCGA-ACCCGTTTGCA
* *
140596 GAAGA-TGTTCAAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCA
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAATAGGGAGCGAACCCGTTTGCA
** * * *
140651 GAAGATTGTTCGAGTTCTATACTCCCT-AAAGTGATAGAGAGCAAACCCGTTGTTCA
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAATAGGGAGCGAACCCGTT-TGCA
* * ** * * * *
140707 GAAGATTGTGCGAGTTCTATACT-CGTG-AAGCGATATGAAGTGAACTCGTTTGCA
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAATAGGGAGCGAACCCGTTTGCA
* * * ** *
140761 GAAGATTCTTCGAGATCTATACTCCCTG-AAGCAATAATGAGCGAACGCGTGTT-CA
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAATAGGGAGCGAACCCGT-TTGCA
* * *
140816 GAAGATTTTTTTGAGTCCTATACTC
1 GAAGA-TTGTTCGAGTTCTATACTC
140841 TCTAAAATAA
Statistics
Matches: 499, Mismatches: 57, Indels: 37
0.84 0.10 0.06
Matches are distributed among these distances:
53 1 0.00
54 43 0.09
55 388 0.78
56 66 0.13
57 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (56 bp):
GAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAATAGGGAGCGAACCCGTTTGCA
Found at i:144468 original size:21 final size:20
Alignment explanation
Indices: 144442--144511 Score: 94
Period size: 16 Copynumber: 3.6 Consensus size: 20
144432 AGCAGTCATA
144442 GGTGTATGGATACACCTACAG
1 GGTGTATGGATACA-CTACAG
*
144463 GGTGTATCGATACAC--CA-
1 GGTGTATGGATACACTACAG
144480 -GTGTATGGATACACTACAG
1 GGTGTATGGATACACTACAG
144499 GGTGTATGGATAC
1 GGTGTATGGATAC
144512 CCTTTGACAC
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
16 13 0.30
18 4 0.09
20 13 0.30
21 13 0.30
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (20 bp):
GGTGTATGGATACACTACAG
Found at i:149787 original size:20 final size:21
Alignment explanation
Indices: 149747--149789 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
149737 CAAAAACTAG
149747 CAAATTGGAGAATCATGGAAC
1 CAAATTGGAGAATCATGGAAC
*
149768 CAAATTGGAGAAT-TTGGAAC
1 CAAATTGGAGAATCATGGAAC
149788 CA
1 CA
149790 TATTCCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (21 bp):
CAAATTGGAGAATCATGGAAC
Found at i:150365 original size:83 final size:80
Alignment explanation
Indices: 150222--150551 Score: 491
Period size: 83 Copynumber: 4.0 Consensus size: 80
150212 ATCTTCACTG
* * * * *
150222 TCATACACACCATGATTCAAGCATCATTATCATCGTTCAGTTTTGGGCCTTGACATATATGTTTT
1 TCATACACACCATTATTCAAGCATCATCATCATCATTCAGTTTTGGGCCTTAACATATATGTTAT
*
150287 GCACCTACTCATATA
66 GCATCTACTCATATA
150302 TCATACACACCATTATTCAAGCATCATCATCATTTTCATTCAGTTTTGGGCCTTAACATATATGT
1 TCATACACACCATTATTCAAGCATCATCATCA---TCATTCAGTTTTGGGCCTTAACATATATGT
150367 TATGCATCTACTCATATA
63 TATGCATCTACTCATATA
* *
150385 TCATACACACCATTATTCAAGCATCATCATCATCGTTCAATTTTGGGCCTTAACATATATGTTAT
1 TCATACACACCATTATTCAAGCATCATCATCATCATTCAGTTTTGGGCCTTAACATATATGTTAT
* *
150450 GCATCTATTCGTATA
66 GCATCTACTCATATA
*
150465 TCATGA-ACACCATTATTCTAGCATCATCATCATCTTCATTCAGTTTTGGGCCTTAACATATATG
1 TCAT-ACACACCATTATTCAAGCATCATCATCA---TCATTCAGTTTTGGGCCTTAACATATATG
150529 TTATGCATCTACTCATATA
62 TTATGCATCTACTCATATA
150548 TCAT
1 TCAT
150552 CATGCTTGCA
Statistics
Matches: 228, Mismatches: 15, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
80 103 0.45
81 1 0.00
83 124 0.54
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (80 bp):
TCATACACACCATTATTCAAGCATCATCATCATCATTCAGTTTTGGGCCTTAACATATATGTTAT
GCATCTACTCATATA
Found at i:150492 original size:163 final size:163
Alignment explanation
Indices: 150222--150551 Score: 554
Period size: 163 Copynumber: 2.0 Consensus size: 163
150212 ATCTTCACTG
* * * *
150222 TCATACACACCATGATTCAAGCATCATTATCATCGTTCAGTTTTGGGCCTTGACATATATGTTTT
1 TCATACACACCATGATTCAAGCATCATCATCATCGTTCAATTTTGGGCCTTAACATATATGTTAT
*
150287 GCACCTACTCATATATCATACACACCATTATTCAAGCATCATCATCATTTTCATTCAGTTTTGGG
66 GCACCTACTCATATATCATACACACCATTATTCAAGCATCATCATCATCTTCATTCAGTTTTGGG
150352 CCTTAACATATATGTTATGCATCTACTCATATA
131 CCTTAACATATATGTTATGCATCTACTCATATA
*
150385 TCATACACACCATTATTCAAGCATCATCATCATCGTTCAATTTTGGGCCTTAACATATATGTTAT
1 TCATACACACCATGATTCAAGCATCATCATCATCGTTCAATTTTGGGCCTTAACATATATGTTAT
* * * *
150450 GCATCTATTCGTATATCATGA-ACACCATTATTCTAGCATCATCATCATCTTCATTCAGTTTTGG
66 GCACCTACTCATATATCAT-ACACACCATTATTCAAGCATCATCATCATCTTCATTCAGTTTTGG
150514 GCCTTAACATATATGTTATGCATCTACTCATATA
130 GCCTTAACATATATGTTATGCATCTACTCATATA
150548 TCAT
1 TCAT
150552 CATGCTTGCA
Statistics
Matches: 156, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
163 155 0.99
164 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (163 bp):
TCATACACACCATGATTCAAGCATCATCATCATCGTTCAATTTTGGGCCTTAACATATATGTTAT
GCACCTACTCATATATCATACACACCATTATTCAAGCATCATCATCATCTTCATTCAGTTTTGGG
CCTTAACATATATGTTATGCATCTACTCATATA
Found at i:158069 original size:29 final size:29
Alignment explanation
Indices: 158036--158107 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
158026 ATTAATTTTT
* *
158036 TTCGTTCCCTAAAATTTTATAAGTTCAAG
1 TTCGTCCCCTAAAATTTTATAAATTCAAG
* *
158065 TTCGTCCCCTGAAATTTTATAAATTTAAG
1 TTCGTCCCCTAAAATTTTATAAATTCAAG
158094 TTCGCTCCACCTAA
1 TTCG-TCC-CCTAA
158108 CTTAAAAACA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 29 0.81
30 3 0.08
31 4 0.11
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (29 bp):
TTCGTCCCCTAAAATTTTATAAATTCAAG
Done.