Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001699.1 Hibiscus syriacus cultivar Beakdansim tig00003394_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: 104537
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:794 original size:16 final size:17
Alignment explanation
Indices: 773--807 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
763 AATATCAATA
*
773 AAGCTCAA-ACACATCT
1 AAGCTCAACACAAATCT
789 AAGCTCAACACAAATCT
1 AAGCTCAACACAAATCT
806 AA
1 AA
808 ACAAACAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.49, C:0.29, G:0.06, T:0.17
Consensus pattern (17 bp):
AAGCTCAACACAAATCT
Found at i:6173 original size:23 final size:25
Alignment explanation
Indices: 6142--6193 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
6132 ACACTTATTA
6142 TAAATAAGTTTT-AT-ATCAAA-CT
1 TAAATAAGTTTTAATAATCAAACCT
6164 TAAATTAAGTTTTAATAATCAAACCT
1 TAAA-TAAGTTTTAATAATCAAACCT
6190 TAAA
1 TAAA
6194 ATATATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.15
23 8 0.31
24 2 0.08
25 6 0.23
26 6 0.23
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (25 bp):
TAAATAAGTTTTAATAATCAAACCT
Found at i:18446 original size:60 final size:60
Alignment explanation
Indices: 18376--18491 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 60
18366 ACAAACGTCC
* *
18376 TTCGAATATAG-GATGTTGTTTTGTTGAGTATC-CAGACTATTAAAAATTATAAAATGATCT
1 TTCGAATATAGAG-TGTTGCTTTGTTGAGTATCTC-GACTATTAAAAATTACAAAATGATCT
* *
18436 TTCGACTATAGAGTGTTGCTTTGTTGAGTATCTCGACTATTAAAAGTTACAAAATG
1 TTCGAATATAGAGTGTTGCTTTGTTGAGTATCTCGACTATTAAAAATTACAAAATG
18492 GTCACACAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 48 0.96
61 2 0.04
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (60 bp):
TTCGAATATAGAGTGTTGCTTTGTTGAGTATCTCGACTATTAAAAATTACAAAATGATCT
Found at i:18504 original size:60 final size:60
Alignment explanation
Indices: 18389--18504 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
18379 GAATATAGGA
* * *** *
18389 TGTTGTTTTGTTGAGTATCCAGACTATTAAAAATTATAAAATGATCTTTCGACTATAGAG
1 TGTTGCTTTGTTGAGTATCCAGACTATTAAAAATTACAAAATGATCACACAACTATAGAG
* *
18449 TGTTGCTTTGTTGAGTATCTC-GACTATTAAAAGTTACAAAATGGTCACACAACTAT
1 TGTTGCTTTGTTGAGTATC-CAGACTATTAAAAATTACAAAATGATCACACAACTAT
18505 TTATATAGTC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 46 0.98
61 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (60 bp):
TGTTGCTTTGTTGAGTATCCAGACTATTAAAAATTACAAAATGATCACACAACTATAGAG
Found at i:19206 original size:19 final size:19
Alignment explanation
Indices: 19154--19206 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
19144 ACTTTTAAAT
*
19154 TTTTACAACTCGAGTTATA
1 TTTTACAATTCGAGTTATA
19173 TTTTA-AGTTATTCGAGTTATA
1 TTTTACA---ATTCGAGTTATA
19194 TTTTACAATTCGA
1 TTTTACAATTCGA
19207 TTTAAACTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 1 0.03
19 11 0.38
21 16 0.55
22 1 0.03
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.47
Consensus pattern (19 bp):
TTTTACAATTCGAGTTATA
Found at i:21389 original size:2 final size:2
Alignment explanation
Indices: 21382--21406 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21372 TATCTTAAAT
21382 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
21407 GCGCTAAAAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21631 original size:21 final size:20
Alignment explanation
Indices: 21545--21702 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
21535 AAATGACCAA
**
21545 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
21564 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
21584 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
21604 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
21625 GAAAATCGTAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
21646 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
21666 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
21687 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
21703 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 41 0.40
21 45 0.44
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:21731 original size:20 final size:20
Alignment explanation
Indices: 21669--21862 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
21659 CGATTTTCCA
* ** *
21669 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
21689 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
21709 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
21729 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
21749 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
21769 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
21789 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
21809 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
*
21829 AAAATCGCAATGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
21850 AAATCGCAACGCG
1 AAATCGCAACGCG
21863 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 16 0.11
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:21753 original size:60 final size:60
Alignment explanation
Indices: 21669--21862 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
21659 CGATTTTCCA
* ** * * *
21669 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ***
21729 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* **
21789 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGT
21850 AAATCGCAACGCG
1 AAATCGCAACGCG
21863 ATATTTAAAG
Statistics
Matches: 113, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 81 0.72
61 32 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
Found at i:22284 original size:33 final size:33
Alignment explanation
Indices: 22245--22315 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
22235 TTCACTTAGA
*
22245 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
22278 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
22311 TTTCA
1 TTTCA
22316 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:22439 original size:20 final size:20
Alignment explanation
Indices: 22395--22504 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
22385 TGCAGAAGAG
*
22395 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
22416 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
22436 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
22457 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
22471 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
22490 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
22505 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:22452 original size:41 final size:38
Alignment explanation
Indices: 22388--22504 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
22378 TTCAATTTGC
* *
22388 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
22426 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
22467 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
22500 AGAAT
1 AGAAT
22505 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:22474 original size:14 final size:14
Alignment explanation
Indices: 22455--22511 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
22445 GAGAAATGAA
22455 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
22469 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
22488 AATCGCAACGAGAG
1 AATCGCAACGAGAG
22502 AATCGCAACG
1 AATCGCAACG
22512 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:22487 original size:33 final size:33
Alignment explanation
Indices: 22447--22527 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
22437 CGCAACGAGA
22447 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
22480 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
22513 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
22528 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:22545 original size:19 final size:19
Alignment explanation
Indices: 22523--22650 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
22513 GAAACCAAAA
*
22523 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
22542 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
22556 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
22575 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
22589 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
22609 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
22629 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
22649 TC
1 TC
22651 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:22564 original size:14 final size:14
Alignment explanation
Indices: 22545--22601 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
22535 TTTCATTTCG
22545 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
22559 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
22578 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
22592 CGTTGCGATT
1 CGTTGCGATT
22602 TTCATTTCTC
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:22570 original size:33 final size:33
Alignment explanation
Indices: 22528--22650 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
22518 CAAAATCGCA
22528 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
22561 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
22594 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
22635 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
22651 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:22612 original size:21 final size:21
Alignment explanation
Indices: 22586--22650 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
22576 CGCGTTGCGA
22586 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
22607 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
22627 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
22648 TTC
1 TTC
22651 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:24506 original size:93 final size:93
Alignment explanation
Indices: 24347--24815 Score: 922
Period size: 93 Copynumber: 5.1 Consensus size: 93
24337 TAGATTGCTT
*
24347 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24412 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24440 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24505 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24533 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24598 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24626 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24691 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24719 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24784 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24811 AGTAA
1 AGTAA
24816 TGCAATCCAT
Statistics
Matches: 375, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 6 0.02
93 369 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:24903 original size:19 final size:19
Alignment explanation
Indices: 24863--24991 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
24853 TAGTTTACTT
* *
24863 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
24883 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
24902 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
24921 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
24935 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
24954 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
24968 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
24987 TCGCA
1 TCGCA
24992 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:24942 original size:33 final size:32
Alignment explanation
Indices: 24899--24991 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
24889 CGCGAAACCA
**
24899 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
24931 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
24964 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
24992 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:24989 original size:52 final size:52
Alignment explanation
Indices: 24863--24991 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
24853 TAGTTTACTT
**
24863 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
24915 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
24968 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
24992 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:25009 original size:19 final size:19
Alignment explanation
Indices: 24987--25159 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
24977 GAAACCAAAA
*
24987 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
25006 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
25022 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
25039 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
25055 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
25072 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
25091 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
25110 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
*
25129 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
25149 TCGTGTTGCGA
1 TCGCGTTGCGA
25160 AAGTAAACTA
Statistics
Matches: 128, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
14 15 0.12
16 11 0.09
17 11 0.09
19 79 0.62
20 12 0.09
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:25028 original size:14 final size:14
Alignment explanation
Indices: 25009--25065 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
24999 TTTCATTTCG
25009 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
25023 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
25040 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
25056 CGTTGCGATT
1 CGTTGCGATT
25066 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:25117 original size:38 final size:38
Alignment explanation
Indices: 24987--25159 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
24977 GAAACCAAAA
*
24987 TCGCATTGCGATTTTCATTTCGCGTTGCGA-T-TC-TT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
25022 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* **
25055 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
** *
25091 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
25129 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
25160 AAGTAAACTA
Statistics
Matches: 116, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
33 56 0.48
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.09
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
Found at i:27104 original size:14 final size:14
Alignment explanation
Indices: 27085--27120 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
27075 ATTGTTTAAT
27085 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
27099 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
27113 TGATTTGT
1 TGATTTGT
27121 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:27243 original size:19 final size:19
Alignment explanation
Indices: 27227--27324 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
27217 AAAAATGACT
27227 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27246 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
27265 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
27279 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27298 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
27318 ATCGCAA
1 ATCGCAA
27325 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:27356 original size:53 final size:53
Alignment explanation
Indices: 27227--27343 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
27217 AAAAATGACT
27227 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
27279 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
27332 ATCGCAATGCGA
1 ATCGCAATGCGA
27344 TTTTAATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:27361 original size:19 final size:19
Alignment explanation
Indices: 27333--27483 Score: 143
Period size: 19 Copynumber: 8.7 Consensus size: 19
27323 AACGAGAGAA
* *
27333 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
27352 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
27368 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
27385 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
27404 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
27420 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
27437 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
27455 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
27471 TCGCATTGCGATT
1 TCGCATTGCGATT
27484 CTCTCGTTGC
Statistics
Matches: 108, Mismatches: 8, Indels: 32
0.73 0.05 0.22
Matches are distributed among these distances:
14 23 0.21
16 16 0.15
17 12 0.11
18 3 0.03
19 42 0.39
20 12 0.11
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:27396 original size:52 final size:52
Alignment explanation
Indices: 27333--27452 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
27323 AACGAGAGAA
*
27333 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
27385 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
27437 TCCGCATTGCGATTTT
1 T-CGCATTGCGATTTT
27453 CATGTTGGGA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 51 0.78
53 14 0.22
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:27505 original size:33 final size:33
Alignment explanation
Indices: 27390--27497 Score: 173
Period size: 33 Copynumber: 3.2 Consensus size: 33
27380 TCATTTCGCA
27390 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
27423 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
27457 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
27490 TTGCGATT
1 TTGCGATT
27498 GTAATTTCCG
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
32 1 0.01
33 37 0.54
34 29 0.43
35 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:29795 original size:12 final size:12
Alignment explanation
Indices: 29778--29802 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29768 TCTTCGGGGA
29778 CTTTTTCTTCTT
1 CTTTTTCTTCTT
29790 CTTTTTCTTCTT
1 CTTTTTCTTCTT
29802 C
1 C
29803 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:30011 original size:24 final size:24
Alignment explanation
Indices: 29977--30023 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
29967 CTGAAACATC
29977 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
30001 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
30024 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:30766 original size:40 final size:39
Alignment explanation
Indices: 30706--30935 Score: 210
Period size: 40 Copynumber: 5.8 Consensus size: 39
30696 AAATTTCAGT
* * * *
30706 GTTGTGATTTACAGATTCTCGATGCGATTTACGGATTATC
1 GTTGCGATTTACAGATACGCGTTGCGATTTACGGA-TATC
* *
30746 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATACGCGTTGCGATTTACGGA-TATC
* *
30786 GTTGCGATTTACGGATACGCGTTGCGATATACGGATA-C
1 GTTGCGATTTACAGATACGCGTTGCGATTTACGGATATC
** *
30824 GCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACAC
1 G--TTGCGATTTACAGATACGCGTTGCGATTTACGGATA-TC
* * * * * **
30866 ATTGCGATTTACGGATGCGCGTTGCGATTTATGTGTTCGC
1 GTTGCGATTTACAGATACGCGTTGCGATTTACG-GATATC
* * *
30906 GTTGCGATTTTCATATTCGCGTTGCGATTT
1 GTTGCGATTTACAGATACGCGTTGCGATTT
30936 TGGAAAATCG
Statistics
Matches: 163, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 156 0.96
41 2 0.01
42 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (39 bp):
GTTGCGATTTACAGATACGCGTTGCGATTTACGGATATC
Found at i:30798 original size:20 final size:20
Alignment explanation
Indices: 30706--30896 Score: 158
Period size: 20 Copynumber: 9.6 Consensus size: 20
30696 AAATTTCAGT
* * *
30706 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTATC
*
30726 GATGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTATC
* *
30746 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTATC
30766 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTATC
*
30786 GTTGCGATTTACGGA-TACGC
1 GTTGCGATTTACGGATTA-TC
*
30806 GTTGCGATATACGGA-TA-C
1 GTTGCGATTTACGGATTATC
** *
30824 GCATTGCGATTTACCCA-TACGC
1 G--TTGCGATTTACGGATTA-TC
*
30846 GTTGCGATTTACGGA-TACAC
1 GTTGCGATTTACGGATTA-TC
* ***
30866 ATTGCGATTTACGGATGCGC
1 GTTGCGATTTACGGATTATC
30886 GTTGCGATTTA
1 GTTGCGATTTA
30897 TGTGTTCGCG
Statistics
Matches: 143, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
18 2 0.01
19 2 0.01
20 137 0.96
22 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATTATC
Found at i:30809 original size:60 final size:60
Alignment explanation
Indices: 30706--30896 Score: 206
Period size: 60 Copynumber: 3.2 Consensus size: 60
30696 AAATTTCAGT
* * * * * * *
30706 GTTGTGATTTACAGATTCTCGATGCGATTTACGGATTA-TCGTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTATCGTTGCGATTTACGGA-TACACGTTGCGATTTACGGATACGC
* * *
30766 GTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGC
1 GTTGCGATTTACAGATTATCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGC
* ** * * *
30826 ATTGCGATTTACCCA-TACGCGTTGCGATTTACGGATACACATTGCGATTTACGGATGCGC
1 GTTGCGATTTACAGATTA-TCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGC
30886 GTTGCGATTTA
1 GTTGCGATTTA
30897 TGTGTTCGCG
Statistics
Matches: 111, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
59 4 0.04
60 107 0.96
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (60 bp):
GTTGCGATTTACAGATTATCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGC
Found at i:30906 original size:20 final size:20
Alignment explanation
Indices: 30883--30936 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
30873 TTTACGGATG
* *
30883 CGCGTTGCGATTTAT-GTGTT
1 CGCGTTGCGATTT-TCATATT
30903 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
30923 CGCGTTGCGATTTT
1 CGCGTTGCGATTTT
30937 GGAAAATCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.11, C:0.19, G:0.26, T:0.44
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:30931 original size:60 final size:59
Alignment explanation
Indices: 30728--30935 Score: 202
Period size: 60 Copynumber: 3.5 Consensus size: 59
30718 AGATTCTCGA
* * * * **
30728 TGCGATTTACGGATTA-TCGTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGT
1 TGCGATTTACGGA-TACGCGTTGCGATTTACGGATACGCGTTGCGATTTACGG-TTCGCGT
* * ** *
30788 TGCGATTTACGGATACGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGT
1 TGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTA-CGGTTCGCGT
* * * *
30848 TGCGATTTACGGATACACATTGCGATTTACGGATGCGCGTTGCGATTTATGTGTTCGCGT
1 TGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACG-GTTCGCGT
* ** *
30908 TGCGATTTTCATATTCGCGTTGCGATTT
1 TGCGATTTACGGATACGCGTTGCGATTT
30936 TGGAAAATCG
Statistics
Matches: 119, Mismatches: 26, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
59 2 0.02
60 116 0.97
61 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (59 bp):
TGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGTTCGCGT
Found at i:30952 original size:21 final size:21
Alignment explanation
Indices: 30922--31004 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
30912 ATTTTCATAT
*
30922 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
30943 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
30964 TCGCATTGCGATTTT-TAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
30985 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
31005 CTGATTTGCG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:30995 original size:42 final size:43
Alignment explanation
Indices: 30902--31000 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
30892 ATTTATGTGT
*
30902 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGGAAAA
** *
30943 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-TAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGGAA-AA
*
30985 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
31001 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGGAAAA
Found at i:31395 original size:16 final size:16
Alignment explanation
Indices: 31374--31407 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
31364 AGTGTAGCTG
*
31374 ATGTGTATGAGCAGTT
1 ATGTGTATGACCAGTT
31390 ATGTGTATGACCAGTT
1 ATGTGTATGACCAGTT
31406 AT
1 AT
31408 AATACTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.38
Consensus pattern (16 bp):
ATGTGTATGACCAGTT
Found at i:37784 original size:16 final size:17
Alignment explanation
Indices: 37750--37801 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
37740 ATTAATTCTA
37750 TTTATATTAAATATTAT
1 TTTATATTAAATATTAT
37767 TTTATA-TAAA-ATTGAT
1 TTTATATTAAATATT-AT
* * *
37783 TTGAAATTAAATATAAT
1 TTTATATTAAATATTAT
37800 TT
1 TT
37802 ATCACAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 3 0.10
16 10 0.34
17 14 0.48
18 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
TTTATATTAAATATTAT
Found at i:44492 original size:2 final size:2
Alignment explanation
Indices: 44487--44515 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44477 ACACCTTCAA
44487 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 A
44516 AAATTATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48772 original size:45 final size:45
Alignment explanation
Indices: 48661--48775 Score: 176
Period size: 45 Copynumber: 2.6 Consensus size: 45
48651 CACCTATATG
* * * * *
48661 CATTTCAATTATGTCATCCTTACATGTCTTTTATACACTATTATA
1 CATTTCATTTATGGCATCCTTTCATGCCTTTGATACACTATTATA
*
48706 CCTTTCATTTATGGCATCCTTTCATGCCTTTGATACACTATTATA
1 CATTTCATTTATGGCATCCTTTCATGCCTTTGATACACTATTATA
48751 CATTTCATTTATGGCATCCTTTCAT
1 CATTTCATTTATGGCATCCTTTCAT
48776 ACAATTATGC
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.24, C:0.23, G:0.07, T:0.46
Consensus pattern (45 bp):
CATTTCATTTATGGCATCCTTTCATGCCTTTGATACACTATTATA
Found at i:49044 original size:68 final size:68
Alignment explanation
Indices: 48944--49073 Score: 206
Period size: 68 Copynumber: 1.9 Consensus size: 68
48934 ACTCAACGGT
* * *
48944 ACTTAATCGTTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCCCAGCTAGGCCTCAAA
1 ACTTAATCGTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGCTAGGCCTCAAA
49009 GAC
66 GAC
* * *
49012 ACTTAATCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTC
1 ACTTAATCGTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGCTAGGCCTC
49074 TTGATCTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (68 bp):
ACTTAATCGTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGCTAGGCCTCAAA
GAC
Found at i:49593 original size:57 final size:57
Alignment explanation
Indices: 49475--50129 Score: 988
Period size: 57 Copynumber: 11.5 Consensus size: 57
49465 GTCCTATATG
* *
49475 GAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCGTACGAAACACCCTATCT
1 GAAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCGTACGAAACGCCCTATCT
** *
49533 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAATACCATATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * * * *
49590 GAAATTCATACGCTTAGTATGATTTCTTAACATTTTAGCATACGTAATGCCCAATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
** * *
49647 GAAATTTGTACACTTAGTATGACTTCTTAACATTTTAGCATACGAAACGCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
*
49704 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATAT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * *
49761 GAAATTCATACACTTAGTACGATTTCTTAACATTTTAGCATACGAAACACCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * * *
49818 GAAATTTATACACTTAGTACGATTTCTTAACATTTTAGCGTACAAAAAGCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * *
49875 GAAATTTATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCCATAT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* *
49932 GAAATTCATACACTTAGTATGATTTCTTAAAATTTTAGCGTACGAAACGCCTTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * * *
49989 GAAATTCATACACTTAGTATGATTTCTTAAAATTTTAGCGTACAAAACGCCTTATCC
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
*
50046 GAAATTCATACACTTAGTATGATTTCTTAA-ATTTTAGCGTACGAAACGTCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* *
50102 AAAATTCATACACTTATTATGATTTCTT
1 GAAATTCATACACTTAGTATGATTTCTT
50130 GTATTTTGCA
Statistics
Matches: 549, Mismatches: 48, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
56 48 0.09
57 476 0.87
58 25 0.05
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.36
Consensus pattern (57 bp):
GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
Found at i:50517 original size:22 final size:22
Alignment explanation
Indices: 50489--50544 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
50479 TACCCTTATC
*
50489 ATGGTATCGATATTACTATACT
1 ATGGTATCGATAGTACTATACT
*
50511 ATGGTATCGATAGTATTATACT
1 ATGGTATCGATAGTACTATACT
*
50533 ATGGTACCGATA
1 ATGGTATCGATA
50545 CCCCCTTCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (22 bp):
ATGGTATCGATAGTACTATACT
Found at i:57573 original size:10 final size:10
Alignment explanation
Indices: 57558--57582 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
57548 ATCGAAAAGC
57558 GTTTTGATCT
1 GTTTTGATCT
57568 GTTTTGATCT
1 GTTTTGATCT
57578 GTTTT
1 GTTTT
57583 AGTATCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.20, T:0.64
Consensus pattern (10 bp):
GTTTTGATCT
Found at i:60066 original size:23 final size:23
Alignment explanation
Indices: 60036--60079 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
60026 GCAGCTCCCG
60036 CTTCTATATTCGGACACCTACCA
1 CTTCTATATTCGGACACCTACCA
* *
60059 CTTCTATATTTGGGCACCTAC
1 CTTCTATATTCGGACACCTAC
60080 AAACTCCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.32, G:0.11, T:0.34
Consensus pattern (23 bp):
CTTCTATATTCGGACACCTACCA
Found at i:60875 original size:39 final size:39
Alignment explanation
Indices: 60832--60915 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
60822 TAATGTATGC
*
60832 TCTTTTTGAAATTCCCAGGAGCTGCAATTCAATCTATTT
1 TCTTTTTGAAATTCCCAGGAGCTGCAATTCAATCCATTT
* *
60871 TCTTTTTTAAATTCCCAGGAGTTGCAATTCAATCCATTT
1 TCTTTTTGAAATTCCCAGGAGCTGCAATTCAATCCATTT
60910 TCTTTT
1 TCTTTT
60916 CATGTTGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.45
Consensus pattern (39 bp):
TCTTTTTGAAATTCCCAGGAGCTGCAATTCAATCCATTT
Found at i:65232 original size:20 final size:20
Alignment explanation
Indices: 65144--65233 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
65134 ATGACCAACA
* *
65144 AATTCGCAACGCGATTTCCA
1 AATTCGCAACGCGATTTTCG
*
65164 AATTCGCAACTCGA-TTTCTG
1 AATTCGCAACGCGATTTTC-G
65184 AATTCGCAACGCGAATTTT-G
1 AATTCGCAACGCG-ATTTTCG
** * *
65204 TTTTTGCAACTCGATTTTCG
1 AATTCGCAACGCGATTTTCG
65224 AATTCGCAAC
1 AATTCGCAAC
65234 ACGAATTTTA
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
19 8 0.15
20 43 0.78
21 1 0.02
22 3 0.05
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (20 bp):
AATTCGCAACGCGATTTTCG
Found at i:65249 original size:20 final size:20
Alignment explanation
Indices: 65186--65251 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
65176 GATTTCTGAA
* **
65186 TTCGCAACGCGAATTTTGTT
1 TTCGCAACACGAATTTTAAT
* *
65206 TTTGCAACTCG-ATTTTCGAA-
1 TTCGCAACACGAATTTT--AAT
65226 TTCGCAACACGAATTTTAAT
1 TTCGCAACACGAATTTTAAT
65246 TTCGCA
1 TTCGCA
65252 CCAGGTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
19 7 0.19
20 24 0.67
21 5 0.14
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (20 bp):
TTCGCAACACGAATTTTAAT
Found at i:65266 original size:18 final size:18
Alignment explanation
Indices: 65239--65287 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
65229 GCAACACGAA
*
65239 TTTTAATTTCGCACCAGG
1 TTTTATTTTCGCACCAGG
65257 TTTTATTTTCGCACCAGG
1 TTTTATTTTCGCACCAGG
65275 TTTTATTTTCGCA
1 TTTTATTTTCGCA
65288 ACACAAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.47
Consensus pattern (18 bp):
TTTTATTTTCGCACCAGG
Found at i:65456 original size:16 final size:16
Alignment explanation
Indices: 65435--65465 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
65425 TCTCTAATTT
65435 TTTTTACATAATTTTA
1 TTTTTACATAATTTTA
*
65451 TTTTTATATAATTTT
1 TTTTTACATAATTTT
65466 TCAATGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTACATAATTTTA
Found at i:66251 original size:24 final size:24
Alignment explanation
Indices: 66224--66301 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 24
66214 GTATTCGAAA
66224 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
66248 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
66272 TTTGATCTTAGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
66296 TTTGAT
1 TTTGAT
66302 GATGTTTCAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:67413 original size:14 final size:14
Alignment explanation
Indices: 67394--67424 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
67384 AGTAGCCATG
67394 GATGCTAACAATGA
1 GATGCTAACAATGA
67408 GATGCTAACAATGA
1 GATGCTAACAATGA
67422 GAT
1 GAT
67425 ACTGCCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.23
Consensus pattern (14 bp):
GATGCTAACAATGA
Found at i:68911 original size:20 final size:20
Alignment explanation
Indices: 68886--68939 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
68876 GATTGTTGCG
68886 AAAGTCAAATTCGCAACT-CA
1 AAAGTCAAATTCGCAA-TGCA
*
68906 AAAGTCAAATTCGCAATGCG
1 AAAGTCAAATTCGCAATGCA
68926 AAAGTCAAATTCGC
1 AAAGTCAAATTCGC
68940 GTTGCGATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (20 bp):
AAAGTCAAATTCGCAATGCA
Found at i:68945 original size:20 final size:20
Alignment explanation
Indices: 68881--68946 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
68871 GTTGCGATTG
68881 TTGCGAAAGTCAAATTCGCAA
1 TTGCGAAAGTCAAATTCGC-A
* *
68902 CT-CAAAAGTCAAATTCGCA
1 TTGCGAAAGTCAAATTCGCA
* *
68921 ATGCGAAAGTCAAATTCGCG
1 TTGCGAAAGTCAAATTCGCA
68941 TTGCGA
1 TTGCGA
68947 TTGTTACGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.05
20 35 0.92
21 1 0.03
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (20 bp):
TTGCGAAAGTCAAATTCGCA
Found at i:70560 original size:20 final size:20
Alignment explanation
Indices: 70531--70647 Score: 81
Period size: 21 Copynumber: 5.7 Consensus size: 20
70521 CATGTGAATC
70531 GGACTCTTGAACGGTGGGAG
1 GGACTCTTGAACGGTGGGAG
* * **
70551 GGATTCTTGAACGATGACAGG
1 GGACTCTTGAACGGTGGGA-G
*
70572 GGCCTCTTGAACGGTGGGAGG
1 GGACTCTTGAACGGTGGGA-G
* * * *
70593 GGCCTCTTGAATGATGAGAGG
1 GGACTCTTGAACGGTGGGA-G
* * *
70614 GGCCTCTTGAACGATAGGAGG
1 GGACTCTTGAACGGTGGGA-G
*
70635 GGCCTCTTGAACG
1 GGACTCTTGAACG
70648 ATGACAGGTG
Statistics
Matches: 81, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
20 15 0.19
21 66 0.81
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.21
Consensus pattern (20 bp):
GGACTCTTGAACGGTGGGAG
Found at i:70581 original size:21 final size:21
Alignment explanation
Indices: 70555--70651 Score: 142
Period size: 21 Copynumber: 4.6 Consensus size: 21
70545 TGGGAGGGAT
*
70555 TCTTGAACGATGACAGGGGCC
1 TCTTGAACGATGAGAGGGGCC
* *
70576 TCTTGAACGGTGGGAGGGGCC
1 TCTTGAACGATGAGAGGGGCC
*
70597 TCTTGAATGATGAGAGGGGCC
1 TCTTGAACGATGAGAGGGGCC
70618 TCTTGAACGAT-AGGAGGGGCC
1 TCTTGAACGATGA-GAGGGGCC
70639 TCTTGAACGATGA
1 TCTTGAACGATGA
70652 CAGGTGAATC
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
20 1 0.01
21 65 0.97
22 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (21 bp):
TCTTGAACGATGAGAGGGGCC
Found at i:70615 original size:42 final size:42
Alignment explanation
Indices: 70534--70655 Score: 183
Period size: 42 Copynumber: 2.9 Consensus size: 42
70524 GTGAATCGGA
**
70534 CTCTTGAACGGTGGGA-GGGATTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGC
* *
70575 CTCTTGAACGGTGGGAGGGGCCTCTTGAATGATGAGAGGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGC
* *
70617 CTCTTGAACGATAGGAGGGGCCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGG
70656 TGAATCGGGC
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 16 0.22
42 56 0.78
ACGTcount: A:0.22, C:0.18, G:0.39, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGC
Found at i:70816 original size:4 final size:4
Alignment explanation
Indices: 70795--70832 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
70785 GGGTCACTAA
* *
70795 AAAT AAAT TAAT ACAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
70833 TGTCGAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:72667 original size:20 final size:20
Alignment explanation
Indices: 72644--72686 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
72634 TCTGAAACTT
72644 AAAATCGCAACGCGAAAATA
1 AAAATCGCAACGCGAAAATA
* *
72664 AAAATTGCAACGCGAAACTA
1 AAAATCGCAACGCGAAAATA
72684 AAA
1 AAA
72687 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.19, G:0.14, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATA
Found at i:72740 original size:20 final size:20
Alignment explanation
Indices: 72717--72755 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
72707 TCGCGTTACG
72717 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
72737 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
72756 AAGTTTCAAA
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:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:72762 original size:20 final size:20
Alignment explanation
Indices: 72719--72762 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
72709 GCGTTACGAT
* *
72719 TTTCGTGTTGCGAATTTCAT
1 TTTCGTGTTGCGAATTTAAG
72739 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
72759 TTTC
1 TTTC
72763 AAAAACTATT
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:0.14, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:73254 original size:19 final size:20
Alignment explanation
Indices: 73232--73269 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
73222 AATATTGTGT
73232 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
73251 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
73270 CTCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:73279 original size:19 final size:20
Alignment explanation
Indices: 73240--73282 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
73230 GTTTCGAATT
*
73240 CGAAAATAAAATTCGCGTTG
1 CGAAAATAAAACTCGCGTTG
*
73260 CGAAAAT-AAACTCGCTTTG
1 CGAAAATAAAACTCGCGTTG
73279 CGAA
1 CGAA
73283 TTTGACTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (20 bp):
CGAAAATAAAACTCGCGTTG
Found at i:76833 original size:2 final size:2
Alignment explanation
Indices: 76826--76871 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
76816 CATTGTTCAA
76826 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
76868 AT AT
1 AT AT
76872 TTTTCGAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77567 original size:34 final size:34
Alignment explanation
Indices: 77524--77594 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
77514 CTTGTTTTGA
77524 TCGGGTCTCGGGTGGAGGCTTCCTTGTTCTCGGG
1 TCGGGTCTCGGGTGGAGGCTTCCTTGTTCTCGGG
*
77558 TCGGGTCTCGGGTGGAGGCTTCCTTGTTCTCTGG
1 TCGGGTCTCGGGTGGAGGCTTCCTTGTTCTCGGG
77592 TCG
1 TCG
77595 AATCGAGTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.03, C:0.24, G:0.39, T:0.34
Consensus pattern (34 bp):
TCGGGTCTCGGGTGGAGGCTTCCTTGTTCTCGGG
Found at i:95257 original size:11 final size:11
Alignment explanation
Indices: 95241--95272 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
95231 ATTACATGAC
95241 ATTTAGTTTAT
1 ATTTAGTTTAT
95252 ATTTAGTTTAT
1 ATTTAGTTTAT
95263 ATTTAGTTTA
1 ATTTAGTTTA
95273 GTTCTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (11 bp):
ATTTAGTTTAT
Found at i:97863 original size:65 final size:65
Alignment explanation
Indices: 97725--97885 Score: 175
Period size: 65 Copynumber: 2.5 Consensus size: 65
97715 GTGCACTAAG
* * *
97725 AGTGCGTCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
* * * * * *
97789 GGTGCATCGATACATCAAATGCATTTGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGC
97852 T
65 T
* * *
97853 AAGTGTATCGATGCATGAAATGCAGTCGATGTT
1 -AGTGCATCGATGCATCAAATGCATTCGATGTT
97886 CAATTTAATT
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
64 26 0.33
65 50 0.63
66 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
Found at i:100012 original size:13 final size:13
Alignment explanation
Indices: 99984--100022 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
99974 TGGGCAATGT
*
99984 TTTGAAAA-ACTA
1 TTTGAAAATAATA
99996 TTTGAAAATAATA
1 TTTGAAAATAATA
*
100009 TTTGTAAATAATA
1 TTTGAAAATAATA
100022 T
1 T
100023 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Done.