Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009571.1 Hibiscus syriacus cultivar Beakdansim tig00116934_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: 592744
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:6761 original size:31 final size:31
Alignment explanation
Indices: 6723--6794 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
6713 TTGATCCACT
6723 TTGGTCCATGTTGGGACAACTTGCACCAGCC
1 TTGGTCCATGTTGGGACAACTTGCACCAGCC
6754 TTGGTCCATGTTGGGACAACTTGCACCAGCC
1 TTGGTCCATGTTGGGACAACTTGCACCAGCC
6785 TTGGTCCATG
1 TTGGTCCATG
6795 CTCAATTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (31 bp):
TTGGTCCATGTTGGGACAACTTGCACCAGCC
Found at i:7264 original size:23 final size:22
Alignment explanation
Indices: 7221--7264 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
7211 TGAAATAATA
* **
7221 TATTTATTAAAAATATTATTTT
1 TATTTAATAAAAATAGGATTTT
7243 TATTTAATAAAAATAAGGATTT
1 TATTTAATAAAAAT-AGGATTT
7265 AATTGAACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
TATTTAATAAAAATAGGATTTT
Found at i:8100 original size:85 final size:84
Alignment explanation
Indices: 7957--8125 Score: 329
Period size: 85 Copynumber: 2.0 Consensus size: 84
7947 TACCAAAAGA
7957 TGGCCAAATGACATCAACATCAAATCTTACAAATGCATGGTCAAAGAAGTTGATTTCCCCCCCCC
1 TGGCCAAATGACATCAACATCAAATCTTACAAATGCATGGTCAAAGAAGTTGATTT-CCCCCCCC
8022 CCCCAATAACTCACAATCAT
65 CCCCAATAACTCACAATCAT
8042 TGGCCAAATGACATCAACATCAAATCTTACAAATGCATGGTCAAAGAAGTTGATTTCCCCCCCCC
1 TGGCCAAATGACATCAACATCAAATCTTACAAATGCATGGTCAAAGAAGTTGATTTCCCCCCCCC
8107 CCCAATAACTCACAATCAT
66 CCCAATAACTCACAATCAT
8126 ATATCGACCT
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 28 0.33
85 56 0.67
ACGTcount: A:0.36, C:0.31, G:0.11, T:0.22
Consensus pattern (84 bp):
TGGCCAAATGACATCAACATCAAATCTTACAAATGCATGGTCAAAGAAGTTGATTTCCCCCCCCC
CCCAATAACTCACAATCAT
Found at i:9721 original size:127 final size:127
Alignment explanation
Indices: 9495--9734 Score: 462
Period size: 127 Copynumber: 1.9 Consensus size: 127
9485 AAATTATTTA
9495 ATTTTACATCCCTTTGAGATTTTATAATCTCGTACCTCAAAGATTTTAATATAAATTTTTATATT
1 ATTTTACATCCCTTTGAGATTTTATAATCTCGTACCTCAAAGATTTTAATATAAATTTTTATATT
*
9560 CATACCTCTTGACATAACTTTTTACGTCTGTTTCTGATTCAGTTGATAGATAGATGATTATT
66 CATACCTCTTGACATAACTTTTTACGTCTGTTTCTGATTCAATTGATAGATAGATGATTATT
*
9622 ATTTTACATCCCTTTGAGATTTTATAATCTTGTACCTCAAAGATTTTAATATAAATTTTTATATT
1 ATTTTACATCCCTTTGAGATTTTATAATCTCGTACCTCAAAGATTTTAATATAAATTTTTATATT
9687 CATACCTCTTGACATAACTTTTTACGTCTGTTTCTGATTCAATTGATA
66 CATACCTCTTGACATAACTTTTTACGTCTGTTTCTGATTCAATTGATA
9735 TAAATTTATA
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 111 1.00
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.46
Consensus pattern (127 bp):
ATTTTACATCCCTTTGAGATTTTATAATCTCGTACCTCAAAGATTTTAATATAAATTTTTATATT
CATACCTCTTGACATAACTTTTTACGTCTGTTTCTGATTCAATTGATAGATAGATGATTATT
Found at i:10338 original size:2 final size:2
Alignment explanation
Indices: 10331--10362 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10321 AATTATAAAA
10331 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
10363 TCTGGTTACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12082 original size:16 final size:17
Alignment explanation
Indices: 12061--12116 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 17
12051 ATATTTTATT
12061 ATATTTTTAA-TATTTA
1 ATATTTTTAATTATTTA
12077 ATA--TTTAATTTATTTA
1 ATATTTTTAA-TTATTTA
* *
12093 ATA-TTTTACTTAATTA
1 ATATTTTTAATTATTTA
12109 AT-TTTTTA
1 ATATTTTTA
12117 CAGATATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 5 0.15
16 25 0.74
17 4 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTTTTAATTATTTA
Found at i:12105 original size:21 final size:20
Alignment explanation
Indices: 12051--12112 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
12041 TGTCTAATGT
12051 ATATTTTATT-ATATT-TTTA
1 ATATTTTATTAAT-TTATTTA
12070 ATATTTAATATTTAATTTATTTA
1 ATATTT--TA-TTAATTTATTTA
*
12093 ATATTTTACTTAATTAATTT
1 ATATTTTA-TTAATTTATTT
12113 TTTACAGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
19 6 0.17
21 14 0.39
22 4 0.11
23 12 0.33
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATTTTATTAATTTATTTA
Found at i:13877 original size:33 final size:30
Alignment explanation
Indices: 13829--13893 Score: 78
Period size: 33 Copynumber: 2.1 Consensus size: 30
13819 CCAGATGTCG
*
13829 CCGCCGTCGCCTTCACCTG-GTTTTATGACC
1 CCGCCGTCGCCTTCA-CAGAGTTTTATGACC
13859 CCGCCGTCGCCACATTCACAGAGTTTTATGACC
1 CCGCCGTCG-C-C-TTCACAGAGTTTTATGACC
13892 CC
1 CC
13894 TCCTGGAGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 9 0.30
31 1 0.03
32 3 0.10
33 17 0.57
ACGTcount: A:0.15, C:0.40, G:0.18, T:0.26
Consensus pattern (30 bp):
CCGCCGTCGCCTTCACAGAGTTTTATGACC
Found at i:14423 original size:23 final size:23
Alignment explanation
Indices: 14392--14447 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
14382 CGTTAATATG
14392 GTTAGATTTATTTTAATTTATTTT
1 GTTA-ATTTATTTTAATTTATTTT
* *
14416 GTTAATTTTTTTTAATTTTTTTT
1 GTTAATTTATTTTAATTTATTTT
14439 GCTTAATTT
1 G-TTAATTT
14448 TGTTTATTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.70
Consensus pattern (23 bp):
GTTAATTTATTTTAATTTATTTT
Found at i:14453 original size:24 final size:23
Alignment explanation
Indices: 14403--14453 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
14393 TTAGATTTAT
*
14403 TTTAATTTATTTTGTTAATTTTT
1 TTTAATTTATTTTGTTAATTTTG
*
14426 TTTAATTTTTTTTGCTTAATTTTG
1 TTTAATTTATTTTG-TTAATTTTG
14450 TTTA
1 TTTA
14454 TTACCATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.73
Consensus pattern (23 bp):
TTTAATTTATTTTGTTAATTTTG
Found at i:18844 original size:18 final size:18
Alignment explanation
Indices: 18817--18851 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18807 TATTTTGGAG
*
18817 CTTAATTGTTTATTAACT
1 CTTAACTGTTTATTAACT
18835 CTTAACTGTTTATTAAC
1 CTTAACTGTTTATTAAC
18852 AAACAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (18 bp):
CTTAACTGTTTATTAACT
Found at i:23628 original size:21 final size:21
Alignment explanation
Indices: 23513--23628 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
23503 GCGAAATAAA
**
23513 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
23533 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
23553 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
23574 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
23594 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
23616 AATCGCAACGCGA
1 AATCGCAACGCGA
23629 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:23641 original size:20 final size:20
Alignment explanation
Indices: 23616--23808 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
23606 GATTTTCCAG
* ** *
23616 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
23636 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
23656 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
23676 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
23696 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
23716 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
23736 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
23756 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
23777 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
23797 AATCGCAACGCG
1 AATCGCAACGCG
23809 ATTTTTAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 131 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:24227 original size:33 final size:33
Alignment explanation
Indices: 24188--24258 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
24178 TTCACTTAGA
24188 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
24221 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
24254 TTTCA
1 TTTCA
24259 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:24364 original size:21 final size:20
Alignment explanation
Indices: 24338--24444 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
24328 TGCAGAAGAG
24338 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
24359 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
24379 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
24401 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
24415 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
24434 TCGCAACGAGA
1 TCGCAACGAGA
24445 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:24418 original size:14 final size:14
Alignment explanation
Indices: 24399--24455 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
24389 GAAAAATGAA
24399 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
24413 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
24432 AATCGCAACGAGAG
1 AATCGCAACGAGAG
24446 AATCGCAACG
1 AATCGCAACG
24456 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:24430 original size:33 final size:33
Alignment explanation
Indices: 24392--24471 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
24382 GCAACGAGAA
24392 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
24425 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
24458 AAACCAAAATCGCA
1 AAATGAAAATCGCA
24472 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:24489 original size:19 final size:19
Alignment explanation
Indices: 24467--24580 Score: 94
Period size: 19 Copynumber: 6.1 Consensus size: 19
24457 GAAACCAAAA
*
24467 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
24486 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
24500 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
24519 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
24539 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
24559 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
24579 TC
1 TC
24581 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
17 3 0.04
19 29 0.36
20 21 0.26
21 14 0.17
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:24576 original size:41 final size:40
Alignment explanation
Indices: 24497--24580 Score: 132
Period size: 41 Copynumber: 2.1 Consensus size: 40
24487 CGCGTTGCGA
***
24497 TTCTCTCGTTGCGATTTTCATTTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAGTCATTTCTCGTTGCGATTTTCAT
24537 TTCTCTCGTTGCGACAGTCATTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAGTCATT-TCTCGTTGCGATTTTCAT
24578 TTC
1 TTC
24581 AACCAAAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 19 0.47
41 21 0.52
ACGTcount: A:0.11, C:0.25, G:0.15, T:0.49
Consensus pattern (40 bp):
TTCTCTCGTTGCGACAGTCATTTCTCGTTGCGATTTTCAT
Found at i:24577 original size:20 final size:20
Alignment explanation
Indices: 24496--24578 Score: 123
Period size: 20 Copynumber: 4.2 Consensus size: 20
24486 TCGCGTTGCG
24496 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
24516 ATT-TCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
24535 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
24556 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
24576 ATT
1 ATT
24579 TCAACCAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.31
20 24 0.44
21 14 0.25
ACGTcount: A:0.12, C:0.24, G:0.16, T:0.48
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:26424 original size:93 final size:93
Alignment explanation
Indices: 26265--26580 Score: 614
Period size: 93 Copynumber: 3.4 Consensus size: 93
26255 TAGATTGCTT
*
26265 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26330 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
26358 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26423 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
26451 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTAAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26516 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
26544 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
26581 AATACCCTGA
Statistics
Matches: 221, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 221 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:26736 original size:33 final size:33
Alignment explanation
Indices: 26678--26801 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
26668 TAGTTTACTT
* * *
26678 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
* **
26712 TTGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
26745 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
26778 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
26802 TTACGATTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 70 0.86
34 11 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.10
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:26738 original size:19 final size:18
Alignment explanation
Indices: 26714--26801 Score: 57
Period size: 19 Copynumber: 5.2 Consensus size: 18
26704 CGAGAGAATT
26714 GCAACGCGAAATGAAAATC
1 GCAACGCGAAA-GAAAATC
*
26733 GCAA--CGACAG--AATC
1 GCAACGCGAAAGAAAATC
*
26747 GCAACGCGAAACCAAAATC
1 GCAACGCGAAA-GAAAATC
*
26766 GCAA--CG--ACAAAATC
1 GCAACGCGAAAGAAAATC
*
26780 GCAACGCGAAACCAAAATC
1 GCAACGCGAAA-GAAAATC
26799 GCA
1 GCA
26802 TTACGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
14 19 0.34
15 1 0.02
16 7 0.12
17 6 0.11
18 1 0.02
19 22 0.39
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (18 bp):
GCAACGCGAAAGAAAATC
Found at i:26748 original size:14 final size:14
Alignment explanation
Indices: 26727--26785 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
26717 ACGCGAAATG
26727 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
26741 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
26760 AAAATCGCAACGAC
1 AAAATCGCAACGAC
26774 AAAATCGCAACG
1 AAAATCGCAACG
26786 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:26819 original size:19 final size:19
Alignment explanation
Indices: 26805--26950 Score: 132
Period size: 19 Copynumber: 8.2 Consensus size: 19
26795 AATCGCATTA
26805 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
*
26824 CGA--TTC---TCTCGTTG
1 CGATTTTCATTTCGCGTTG
*
26838 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCGTTG
*
26857 CGA--TTC-TGT--CGTTG
1 CGATTTTCATTTCGCGTTG
26871 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
** *
26890 CGATTTTGGTTTCTCGTTG
1 CGATTTTCATTTCGCGTTG
*
26909 CGATTCTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
* *
26928 CGATTTTAAGTTTCGTGTTG
1 CGATTTTCA-TTTCGCGTTG
26948 CGA
1 CGA
26951 AAGTAAACTA
Statistics
Matches: 100, Mismatches: 16, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
14 17 0.17
16 8 0.08
17 8 0.08
19 55 0.55
20 12 0.12
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (19 bp):
CGATTTTCATTTCGCGTTG
Found at i:26838 original size:14 final size:14
Alignment explanation
Indices: 26819--26875 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
26809 TTTCATTTCG
26819 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
26833 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
26850 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
26866 CGTTGCGATT
1 CGTTGCGATT
26876 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:26847 original size:33 final size:33
Alignment explanation
Indices: 26805--26932 Score: 175
Period size: 33 Copynumber: 3.7 Consensus size: 33
26795 AATCGCATTA
26805 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
* *
26838 CGATTTTCATTTCGCATTGCGATTCTGTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
*
26871 CGATTTTCATTTCGCGTTGCGATTTTGGTTTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGA---T--TCTCTCGTTG
*
26909 CGATTCTCATTTCGCGTTGCGATT
1 CGATTTTCATTTCGCGTTGCGATT
26933 TTAAGTTTCG
Statistics
Matches: 84, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
33 53 0.63
35 1 0.01
36 1 0.01
38 29 0.35
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.46
Consensus pattern (33 bp):
CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
Found at i:28894 original size:14 final size:14
Alignment explanation
Indices: 28875--28910 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
28865 ATTGTTTAAT
28875 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
28889 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
28903 TGATTTGT
1 TGATTTGT
28911 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:29097 original size:20 final size:19
Alignment explanation
Indices: 29017--29115 Score: 127
Period size: 20 Copynumber: 5.4 Consensus size: 19
29007 AAAAATGACT
29017 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
29036 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
29055 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
29069 ATCGTAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
29089 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
29109 ATCGCAA
1 ATCGCAA
29116 CGAGAGAATC
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 1 0.01
17 3 0.04
19 27 0.39
20 29 0.41
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:29119 original size:54 final size:53
Alignment explanation
Indices: 29017--29133 Score: 209
Period size: 54 Copynumber: 2.2 Consensus size: 53
29007 AAAAATGACT
29017 ATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
29069 ATCGTAATGCGGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
29123 ATCGCAATGCG
1 ATCGCAATGCG
29134 ATTTTCATTT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
52 9 0.15
53 19 0.31
54 33 0.54
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:29152 original size:19 final size:19
Alignment explanation
Indices: 29124--29338 Score: 262
Period size: 19 Copynumber: 11.9 Consensus size: 19
29114 AACGAGAGAA
*
29124 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29143 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
29162 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
29179 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29196 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
29215 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
29231 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29248 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
29267 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
29284 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29301 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29320 TCCGCATTGCGATTTTCAT
1 T-CGCATTGCGATTTTCAT
29339 GTTGGGATTT
Statistics
Matches: 171, Mismatches: 7, Indels: 35
0.80 0.03 0.16
Matches are distributed among these distances:
14 18 0.11
16 17 0.10
17 19 0.11
18 6 0.04
19 74 0.43
20 37 0.22
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:29193 original size:53 final size:53
Alignment explanation
Indices: 29130--29366 Score: 415
Period size: 53 Copynumber: 4.5 Consensus size: 53
29120 AGAATCGCAA
29130 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
29183 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
29235 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
29288 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGT
* * *
29341 TGGGATTTTCATTTCGCGTTGTGATT
1 TGCGATTTTCATTTCGCATTGCGATT
29367 CTCTCGTTGC
Statistics
Matches: 178, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
52 52 0.29
53 125 0.70
54 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:29206 original size:33 final size:33
Alignment explanation
Indices: 29148--29313 Score: 167
Period size: 33 Copynumber: 4.8 Consensus size: 33
29138 TCATTTCGCA
29148 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
29182 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
29218 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
29253 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
29287 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
29314 TTCATTTCCG
Statistics
Matches: 108, Mismatches: 12, Indels: 25
0.74 0.08 0.17
Matches are distributed among these distances:
31 4 0.04
32 6 0.06
33 34 0.31
34 33 0.31
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.07
39 3 0.03
40 9 0.08
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:29291 original size:86 final size:84
Alignment explanation
Indices: 29201--29380 Score: 224
Period size: 86 Copynumber: 2.1 Consensus size: 84
29191 TCATTTCGCA
29201 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-TTGCGATTTTCATTTCGCATTGCGATTT
1 TTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTCA--T-G--TTGCGATTT
29262 TCATTTCCGCATTGCGATTCTCTCG
61 TCATTT-CGCATTGCGATTCTCTCG
* *
29287 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-ATTGCGATTTTCATGTTGCGATTTTCA
* *
29352 TTTCGCGTTGTGATTCTCTCG
64 TTTCGCATTGCGATTCTCTCG
29373 TTGCGATT
1 TTGCGATT
29381 GTAATTTCCG
Statistics
Matches: 84, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
86 49 0.58
87 14 0.17
88 3 0.04
89 3 0.04
90 3 0.04
92 12 0.14
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.47
Consensus pattern (84 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTCATGTTGCGATTTTCATT
TCGCATTGCGATTCTCTCG
Found at i:29292 original size:105 final size:106
Alignment explanation
Indices: 29130--29366 Score: 415
Period size: 105 Copynumber: 2.2 Consensus size: 106
29120 AGAATCGCAA
29130 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
29195 TTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
66 TTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCAT-GT
29235 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
29300 TTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGT
66 TTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCATGT
* * *
29341 TGGGATTTTCATTTCGCGTTGTGATT
1 TGCGATTTTCATTTCGCATTGCGATT
29367 CTCTCGTTGC
Statistics
Matches: 126, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
105 86 0.68
106 39 0.31
107 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (106 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCATGT
Found at i:31682 original size:12 final size:12
Alignment explanation
Indices: 31665--31689 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31655 TCTTCGGGGA
31665 CTTTTTCTTCTT
1 CTTTTTCTTCTT
31677 CTTTTTCTTCTT
1 CTTTTTCTTCTT
31689 C
1 C
31690 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:31898 original size:24 final size:24
Alignment explanation
Indices: 31864--31910 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
31854 CTGAAACATC
31864 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
31888 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
31911 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:32631 original size:20 final size:20
Alignment explanation
Indices: 32603--32831 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
32593 AAATTTCAGT
* * *
32603 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
32623 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
32643 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
32663 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
32683 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
32703 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
32723 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
32743 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
32763 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
32783 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
32803 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
32823 GTTGCGATT
1 GTTGCGATT
32832 CTTGAAAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:32884 original size:21 final size:20
Alignment explanation
Indices: 32799--32896 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
32789 ATTTATGTGT
* *
32799 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
32819 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
32840 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
32861 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
32882 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
32897 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:32892 original size:42 final size:43
Alignment explanation
Indices: 32799--32897 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
32789 ATTTATGTGT
* *
32799 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
32840 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
32882 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
32898 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:34908 original size:14 final size:14
Alignment explanation
Indices: 34889--34918 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
34879 TTTAGATTTT
*
34889 TTAAAATTACATTA
1 TTAAAAATACATTA
34903 TTAAAAATACATTA
1 TTAAAAATACATTA
34917 TT
1 TT
34919 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:35011 original size:7 final size:7
Alignment explanation
Indices: 34996--35047 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
34986 AATTATATAA
34996 TAGGGTT
1 TAGGGTT
*
35003 TATGGTT
1 TAGGGTT
**
35010 TAGTATT
1 TAGGGTT
35017 TAGGGTT
1 TAGGGTT
35024 TAGGGTT
1 TAGGGTT
*
35031 TAAGGTT
1 TAGGGTT
35038 T-GTGGTT
1 TAG-GGTT
35045 TAG
1 TAG
35048 TTAGGGGTGT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
7 34 0.97
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.48
Consensus pattern (7 bp):
TAGGGTT
Found at i:35293 original size:17 final size:17
Alignment explanation
Indices: 35271--35303 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35261 CAATTAATTC
35271 AAATAATATCTAATTAT
1 AAATAATATCTAATTAT
35288 AAATAATATCTAATTA
1 AAATAATATCTAATTA
35304 ATTTGATTCA
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:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATAATATCTAATTAT
Found at i:35606 original size:7 final size:6
Alignment explanation
Indices: 35586--35648 Score: 63
Period size: 7 Copynumber: 9.3 Consensus size: 6
35576 TGAACACCCC
35586 TAGGTT TAGTGTT TATGGTT TAGGGTT TAGGTT TAAGGTT TAAGGTT TAGGATT
1 TAGGTT TAG-GTT TA-GGTT TA-GGTT TAGGTT T-AGGTT T-AGGTT TAGG-TT
35640 TAGGGTT TA
1 TA-GGTT TA
35649 AGTTATGCAC
Statistics
Matches: 51, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
6 11 0.22
7 37 0.73
8 3 0.06
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.48
Consensus pattern (6 bp):
TAGGTT
Found at i:35616 original size:27 final size:26
Alignment explanation
Indices: 35586--35648 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
35576 TGAACACCCC
* *
35586 TAGGTTTAGTGTTTATGGTTTAGGGTT
1 TAGGTTTAG-GTTTAAGGTTTAGGATT
35613 TAGGTTTAAGGTTTAAGGTTTAGGATT
1 TAGGTTT-AGGTTTAAGGTTTAGGATT
35640 TAGGGTTTA
1 TA-GGTTTA
35649 AGTTATGCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 25 0.78
28 7 0.22
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.48
Consensus pattern (26 bp):
TAGGTTTAGGTTTAAGGTTTAGGATT
Found at i:37813 original size:11 final size:11
Alignment explanation
Indices: 37797--37845 Score: 71
Period size: 11 Copynumber: 4.5 Consensus size: 11
37787 TTAACCTGTC
37797 GAGCTTGAATT
1 GAGCTTGAATT
37808 GAGCTTGAATT
1 GAGCTTGAATT
* * *
37819 GAGTTTTAAAT
1 GAGCTTGAATT
37830 GAGCTTGAATT
1 GAGCTTGAATT
37841 GAGCT
1 GAGCT
37846 CAGTCTCGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.37
Consensus pattern (11 bp):
GAGCTTGAATT
Found at i:39657 original size:21 final size:21
Alignment explanation
Indices: 39631--39672 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
39621 AGAATTCCTG
*
39631 GAATGTATCATTACCTAACAT
1 GAATGTAGCATTACCTAACAT
39652 GAATGTAGCATTACCTAACAT
1 GAATGTAGCATTACCTAACAT
39673 ATGATTGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (21 bp):
GAATGTAGCATTACCTAACAT
Found at i:42782 original size:18 final size:18
Alignment explanation
Indices: 42759--42795 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42749 TTCGAATTGA
42759 TCAA-TTTTATTTTAAAAT
1 TCAATTTTTA-TTTAAAAT
42777 TCAATTTTTATTTAAAAT
1 TCAATTTTTATTTAAAAT
42795 T
1 T
42796 TTTAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTTTATTTAAAAT
Found at i:63239 original size:12 final size:12
Alignment explanation
Indices: 63222--63248 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
63212 TATTAAGGAT
63222 ATTTAGTCTTTA
1 ATTTAGTCTTTA
63234 ATTTAGTCTTTA
1 ATTTAGTCTTTA
63246 ATT
1 ATT
63249 AAGAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (12 bp):
ATTTAGTCTTTA
Found at i:64306 original size:17 final size:17
Alignment explanation
Indices: 64284--64322 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
64274 ATTATCAATA
64284 TAAAATA-AAAAAATTCT
1 TAAAATATAAAAAATT-T
*
64301 TAAAATATAGAAAATTT
1 TAAAATATAAAAAATTT
64318 TAAAA
1 TAAAA
64323 ATTTTAGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (17 bp):
TAAAATATAAAAAATTT
Found at i:67630 original size:2 final size:2
Alignment explanation
Indices: 67625--67662 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
67615 ACACACACAC
67625 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
67663 GGTGCTTGAT
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):
AT
Found at i:71067 original size:36 final size:36
Alignment explanation
Indices: 71020--71115 Score: 183
Period size: 36 Copynumber: 2.6 Consensus size: 36
71010 TTTGAATGCA
71020 GTACTAAAATGAAACAAAACTAATGTTTTTAACAAG
1 GTACTAAAATGAAACAAAACTAATGTTTTTAACAAG
71056 GTACTAAAATGAAACAAAACTAATGTTTTTAACAAG
1 GTACTAAAATGAAACAAAACTAATGTTTTTAACAAG
71092 GTACTAAAATGAAACAAAAACTAA
1 GTACTAAAATGAAAC-AAAACTAA
71116 ACTTTAGGTA
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 51 0.86
37 8 0.14
ACGTcount: A:0.53, C:0.11, G:0.10, T:0.25
Consensus pattern (36 bp):
GTACTAAAATGAAACAAAACTAATGTTTTTAACAAG
Found at i:75328 original size:2 final size:2
Alignment explanation
Indices: 75321--75366 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
75311 CACATACTCT
75321 TA TA 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 TA TA
75363 TA TA
1 TA TA
75367 ATAAAATGCA
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):
TA
Found at i:83574 original size:7 final size:7
Alignment explanation
Indices: 83562--83586 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
83552 CACAAGTACA
83562 CAAAGAC
1 CAAAGAC
83569 CAAAGAC
1 CAAAGAC
83576 CAAAGAC
1 CAAAGAC
83583 CAAA
1 CAAA
83587 AATAAAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.28, G:0.12, T:0.00
Consensus pattern (7 bp):
CAAAGAC
Found at i:88946 original size:17 final size:16
Alignment explanation
Indices: 88898--88956 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
88888 TCGTCACGAG
*
88898 TTTTAATAAAATATAT
1 TTTTAATAAAATAAAT
* *
88914 TTTTATTAAAAAAAAT
1 TTTTAATAAAATAAAT
*
88930 ATTTTAATATAATAAA-
1 -TTTTAATAAAATAAAT
88946 TTTTAATAAAA
1 TTTTAATAAAA
88957 GTTATTTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
15 10 0.29
16 13 0.37
17 12 0.34
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTTAATAAAATAAAT
Found at i:92206 original size:3 final size:3
Alignment explanation
Indices: 92193--92346 Score: 55
Period size: 3 Copynumber: 51.3 Consensus size: 3
92183 TTATCGTAAC
*
92193 TAT TTT TAT TAT TAT T-T T-T TAT ATAT TACGT T-T TAT TA- TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA--T TAT TAT TAT TAT -TAT
92238 TAT TAT TAT TA- TAT GTAT ATAT GT-T T-T TA- TAT ATAT ATAT TACT
1 TAT TAT TAT TAT TAT -TAT -TAT -TAT TAT TAT TAT -TAT -TAT TA-T
* * *
92282 TAT T-T T-T TA- TACT CAT TAT TAT T-T CTAT TAT TCT TAC TAT T-T
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
*
92324 TCAT TAT TAC TAT TAT TAT TAT T
1 T-AT TAT TAT TAT TAT TAT TAT T
92347 TCGTTTTTAC
Statistics
Matches: 119, Mismatches: 12, Indels: 40
0.70 0.07 0.23
Matches are distributed among these distances:
2 24 0.20
3 66 0.55
4 27 0.23
5 2 0.02
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:92210 original size:12 final size:12
Alignment explanation
Indices: 92193--92249 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 12
92183 TTATCGTAAC
92193 TATTTTTATTAT
1 TATTTTTATTAT
92205 TATTTTTTATATAT
1 TA-TTTTTAT-TAT
*
92219 TACGTTTTATTAT
1 TA-TTTTTATTAT
92232 ATATATTATTATTAT
1 -TAT-TT-TTATTAT
92247 TAT
1 TAT
92250 ATGTATATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
12 2 0.05
13 10 0.27
14 18 0.49
15 7 0.19
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (12 bp):
TATTTTTATTAT
Found at i:92240 original size:36 final size:39
Alignment explanation
Indices: 92199--92292 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 39
92189 TAACTATTTT
92199 TATTATTATTTTTTATATAT-TACG-TTTTAT-TATATA
1 TATTATTATTTTTTATATATATACGTTTTTATATATATA
* * *
92235 TATTATTATTATTATATGTATATATGTTTTTATATATATA
1 TATTATTATT-TTTTATATATATACGTTTTTATATATATA
92275 TATTACTTATTTTTTATA
1 TATTA-TTATTTTTTATA
92293 CTCATTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
36 10 0.21
37 8 0.17
38 3 0.06
39 6 0.12
40 16 0.33
41 5 0.10
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (39 bp):
TATTATTATTTTTTATATATATACGTTTTTATATATATA
Found at i:92369 original size:2 final size:2
Alignment explanation
Indices: 92362--92396 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
92352 TTTACTTATT
*
92362 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
92397 TTTTACGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:92491 original size:14 final size:14
Alignment explanation
Indices: 92474--92556 Score: 53
Period size: 14 Copynumber: 5.8 Consensus size: 14
92464 TTCTTTTTTC
92474 TTTATTTATTATTT
1 TTTATTTATTATTT
* *
92488 TTTATATATT-GTT
1 TTTATTTATTATTT
* *
92501 TTTATTTCTCATATT
1 TTTATTTATTAT-TT
**
92516 TTTAGGTATT-TTAT
1 TTTATTTATTATT-T
92530 TTTATTTATTTATTT
1 TTTATTTA-TTATTT
*
92545 TTGTGTTTATTA
1 TT-TATTTATTA
92557 ACTCCATATT
Statistics
Matches: 50, Mismatches: 13, Indels: 11
0.68 0.18 0.15
Matches are distributed among these distances:
13 10 0.20
14 17 0.34
15 16 0.32
16 7 0.14
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.71
Consensus pattern (14 bp):
TTTATTTATTATTT
Found at i:94396 original size:64 final size:64
Alignment explanation
Indices: 94341--94503 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
94331 CGGTGCACCA
*
94341 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTACATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTACATCGATGCATGG
** * ** *
94405 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTACATCGATGCATGG
* *
94470 AGAGTGCATCGATGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
94504 CAATTAATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 39 0.46
65 46 0.54
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTACATCGATGCATGG
Found at i:94475 original size:19 final size:19
Alignment explanation
Indices: 94451--94501 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
94441 GAAAATATTC
94451 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
94470 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
94489 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
94502 TTCAATTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.13
18 7 0.23
19 20 0.65
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:94543 original size:65 final size:65
Alignment explanation
Indices: 94345--94552 Score: 207
Period size: 65 Copynumber: 3.2 Consensus size: 65
94335 GCACCAAGTG
* ** * *
94345 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTACATCGATGCATGG-CTT
1 TGCATCGATGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-T
94408 G-
64 GA
* *
94409 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGATGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
94472 A
65 A
* *
94473 GTGCATCGATGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGA
1 -TGCATCGATGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGA
94535 CTGA
62 CTGA
*
94539 TGCATCGGTGCATG
1 TGCATCGATGCATG
94553 CCTTTGAATA
Statistics
Matches: 123, Mismatches: 11, Indels: 19
0.80 0.07 0.12
Matches are distributed among these distances:
62 3 0.02
63 8 0.07
64 51 0.41
65 59 0.48
66 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (65 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA
Found at i:95674 original size:21 final size:21
Alignment explanation
Indices: 95618--95681 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
95608 TCAATAAACC
* *
95618 ATTAGGA-GCTTGAGGATCAGG
1 ATTAGGATG-TTGAGGAACGGG
* **
95639 ATTAGGTTGAGGAGGAACGGG
1 ATTAGGATGTTGAGGAACGGG
95660 ATTAGGATGTTGAGGAACGGG
1 ATTAGGATGTTGAGGAACGGG
95681 A
1 A
95682 GGATGGTTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.42, T:0.22
Consensus pattern (21 bp):
ATTAGGATGTTGAGGAACGGG
Found at i:100297 original size:22 final size:21
Alignment explanation
Indices: 100255--100294 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
100245 GAGTTTGTTT
*
100255 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
100276 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
100295 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:102371 original size:19 final size:19
Alignment explanation
Indices: 102347--102397 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
102337 GAAAATATTC
102347 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
* *
102366 AGAGTGCAACGGTGCATGG
1 AGAGTGCATCGATGCATGG
102385 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
102398 TTCAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.15
18 5 0.19
19 18 0.67
ACGTcount: A:0.27, C:0.16, G:0.35, T:0.22
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:102373 original size:65 final size:65
Alignment explanation
Indices: 102222--102399 Score: 216
Period size: 64 Copynumber: 2.8 Consensus size: 65
102212 GAACACTTGA
*** *
102222 TGCATCGATGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGG
1 TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGG
** * **
102286 TGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGA
1 TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAG-
102350 G
65 G
* * * *
102351 TGCATCGATGCATGGAGAGTGCAACGGTGCATGGAATGCATTCGATGTT
1 TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
102400 CAATTAATTC
Statistics
Matches: 96, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 49 0.51
65 47 0.49
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (65 bp):
TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGG
Found at i:102444 original size:65 final size:65
Alignment explanation
Indices: 102241--102448 Score: 198
Period size: 65 Copynumber: 3.2 Consensus size: 65
102231 GCACCAAGTG
* * ** *
102241 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTT
1 TGCATCGGTGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-T
102304 G-
64 GA
* * *
102305 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
102368 A
65 A
* * *
102369 GTGCAACGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGA
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGA
102431 CTGA
62 CTGA
102435 TGCATCGGTGCATG
1 TGCATCGGTGCATG
102449 CCTTTGAATA
Statistics
Matches: 122, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 8 0.07
64 51 0.42
65 58 0.48
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (65 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA
Found at i:107171 original size:72 final size:72
Alignment explanation
Indices: 107081--107508 Score: 631
Period size: 72 Copynumber: 5.9 Consensus size: 72
107071 TACAGATGAT
* * * * * **
107081 TTGTCTTACTTGAGACTGTTTTACTTGAAAGAAGAGTTATTTTCTTTGAGATTGTCATTCTTAAA
1 TTGTCTCACTTGAGACTGTTCTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
107146 ACAGACC
66 ACAGACC
* * * **
107153 TTGTCTCACTTGAGACTGTTTTACTTGAAATATGATTTATTTCCCTCAAGATTGTGTTTCTTAAA
1 TTGTCTCACTTGAGACTGTTCTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
* *
107218 ATAGACA
66 ACAGACC
* **
107225 TTGTCTCACTTGAGACTGTTCTACTTGAAAGAAGATTTATTTCCCTCAAGATTATTTTTCTTAAA
1 TTGTCTCACTTGAGACTGTTCTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
*
107290 ACAGACA
66 ACAGACC
*
107297 TTGTCTCACTTGAGATTGTTCTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
1 TTGTCTCACTTGAGACTGTTCTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
107362 ACAGACC
66 ACAGACC
*
107369 TTGTCTCACTTAAGACTGTTCTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
1 TTGTCTCACTTGAGACTGTTCTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
107434 ACAGACC
66 ACAGACC
* * * **
107441 TTGTCTCACTTGAGACTATTTTACTCGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAAA
1 TTGTCTCACTTGAGACTGTTCTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
107506 ACA
66 ACA
107509 AGATTTTATC
Statistics
Matches: 325, Mismatches: 31, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 325 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (72 bp):
TTGTCTCACTTGAGACTGTTCTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAAA
ACAGACC
Found at i:107647 original size:36 final size:36
Alignment explanation
Indices: 107595--107686 Score: 105
Period size: 37 Copynumber: 2.6 Consensus size: 36
107585 TAAACATTGA
* * *
107595 AAACA-TTTCCCTTGAAATGAATTTTGTCTCTCTTG
1 AAACAGTTTCCCTTGAAATAAATTGTGTCTCCCTTG
* * *
107630 AGATAGTTTCCCTTGAAACAAAATTGTGTCTCCCTTG
1 AAACAGTTTCCCTTGAAA-TAAATTGTGTCTCCCTTG
*
107667 AAACAGTTTCTCTTGAAATA
1 AAACAGTTTCCCTTGAAATA
107687 TAAACATTGA
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
35 3 0.07
36 13 0.29
37 29 0.64
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (36 bp):
AAACAGTTTCCCTTGAAATAAATTGTGTCTCCCTTG
Found at i:107690 original size:102 final size:102
Alignment explanation
Indices: 107511--108226 Score: 1085
Period size: 104 Copynumber: 7.0 Consensus size: 102
107501 TTAAAACAAG
* * * * * *
107511 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAGAAAATTTTATCTCCCTTGAGACAATTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTG-AA-ACAAAATTTTGTCTCCCTTGAGACAGTTTCT
107576 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
64 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* *
107615 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTGTGTCTCCCTTGAAACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
* *
107680 TGAAATATAAACATTGAAAATATTTCCCTTGAAATGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* * * * *
107717 ATTTTGTATTTCTTGAGATAGTTTCCCTCGAAGCAGAAAATTTTGTCCCCCTTGAGACAGTTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAA--ACAAAATTTTGTCTCCCTTGAGACAGTTTCT
107782 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
64 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
*
107821 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAAACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
* *
107886 TGAAATATAAACATTGAAAATATTTCCCTTGAAATGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* * * * *
107923 ATTTTGTATTTCTTGAGATAGTTTCCCTCGAAGCAGAAAATTTTGTCCCCCTTGAGACAGTTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAA--ACAAAATTTTGTCTCCCTTGAGACAGTTTCT
107988 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
64 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* *
108027 ATTTTGTCTCTCTTGATATAGTTTCCCTTGAAAC-AAATTTCGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
* *
108091 TAAAATATAAACATTGAAAACATTTCCCTTGAAATGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
*
108128 ATTTTGTCTCTCTTGAGATTGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
* *
108192 TGAAACATAAACTTTAAAAACAGTTTCCCTTGAAA
66 TGAAACATAAACATTGAAAACA-TTTCCCTTGAAA
108227 CAAAATCTTT
Statistics
Matches: 556, Mismatches: 51, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
101 142 0.26
102 199 0.36
103 2 0.00
104 213 0.38
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (102 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
Found at i:107853 original size:36 final size:36
Alignment explanation
Indices: 107801--107892 Score: 114
Period size: 37 Copynumber: 2.6 Consensus size: 36
107791 TAAACATTGA
* *
107801 AAACA-TTTCCCTTGAAATGAATTTTGTCTCTCTTG
1 AAACAGTTTCCCTTGAAATAAATTTTGTCTCCCTTG
* * *
107836 AGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTG
1 AAACAGTTTCCCTTGAAA-TAAATTTTGTCTCCCTTG
*
107873 AAACAGTTTCTCTTGAAATA
1 AAACAGTTTCCCTTGAAATA
107893 TAAACATTGA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
35 3 0.07
36 13 0.28
37 30 0.65
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (36 bp):
AAACAGTTTCCCTTGAAATAAATTTTGTCTCCCTTG
Found at i:107876 original size:206 final size:206
Alignment explanation
Indices: 107522--108226 Score: 1202
Period size: 206 Copynumber: 3.4 Consensus size: 206
107512 TTTTATCTCG
** * * *
107522 CTTGAGATAGTTTCCCTCGAAATAGAAAATTTTATCTCCCTTGAGACAATTTCTCTTGAAACATA
1 CTTGAGATAGTTTCCCTCGAAGCAGAAAATTTTGTCCCCCTTGAGACAGTTTCTCTTGAAACATA
107587 AACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA
66 AACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA
*
107652 ATTGTGTCTCCCTTGAAACAGTTTCTCTTGAAATATAAACATTGAAAATATTTCCCTTGAAATGA
131 ATTTTGTCTCCCTTGAAACAGTTTCTCTTGAAATATAAACATTGAAAATATTTCCCTTGAAATGA
107717 ATTTTGTATTT
196 ATTTTGTATTT
107728 CTTGAGATAGTTTCCCTCGAAGCAGAAAATTTTGTCCCCCTTGAGACAGTTTCTCTTGAAACATA
1 CTTGAGATAGTTTCCCTCGAAGCAGAAAATTTTGTCCCCCTTGAGACAGTTTCTCTTGAAACATA
107793 AACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA
66 AACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA
107858 ATTTTGTCTCCCTTGAAACAGTTTCTCTTGAAATATAAACATTGAAAATATTTCCCTTGAAATGA
131 ATTTTGTCTCCCTTGAAACAGTTTCTCTTGAAATATAAACATTGAAAATATTTCCCTTGAAATGA
107923 ATTTTGTATTT
196 ATTTTGTATTT
107934 CTTGAGATAGTTTCCCTCGAAGCAGAAAATTTTGTCCCCCTTGAGACAGTTTCTCTTGAAACATA
1 CTTGAGATAGTTTCCCTCGAAGCAGAAAATTTTGTCCCCCTTGAGACAGTTTCTCTTGAAACATA
*
107999 AACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGATATAGTTTCCCTTGAAAC-AA
66 AACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA
* * * *
108063 ATTTCGTCTCCCTTGAGACAGTTTCTCTTAAAATATAAACATTGAAAACATTTCCCTTGAAATGA
131 ATTTTGTCTCCCTTGAAACAGTTTCTCTTGAAATATAAACATTGAAAATATTTCCCTTGAAATGA
* *
108128 ATTTTGTCTCT
196 ATTTTGTATTT
* * * *
108139 CTTGAGATTGTTTCCCTTGAA--A-CAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATA
1 CTTGAGATAGTTTCCCTCGAAGCAGAAAATTTTGTCCCCCTTGAGACAGTTTCTCTTGAAACATA
* *
108201 AACTTTAAAAACAGTTTCCCTTGAAA
66 AACATTGAAAACA-TTTCCCTTGAAA
108227 CAAAATCTTT
Statistics
Matches: 479, Mismatches: 19, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
202 49 0.10
203 13 0.03
205 91 0.19
206 326 0.68
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (206 bp):
CTTGAGATAGTTTCCCTCGAAGCAGAAAATTTTGTCCCCCTTGAGACAGTTTCTCTTGAAACATA
AACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA
ATTTTGTCTCCCTTGAAACAGTTTCTCTTGAAATATAAACATTGAAAATATTTCCCTTGAAATGA
ATTTTGTATTT
Found at i:108059 original size:36 final size:36
Alignment explanation
Indices: 108012--108097 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 36
108002 ATTGAAAACA
* * * * *
108012 TTTCCCTTGAAATGAATTTTGTCTCTCTTGATATAG
1 TTTCCCTTGAAATAAATTTCGTCTCCCTTGAGACAG
*
108048 TTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAATAAATTTCGTCTCCCTTGAGACAG
* *
108084 TTTCTCTTAAAATA
1 TTTCCCTTGAAATA
108098 TAAACATTGA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAATAAATTTCGTCTCCCTTGAGACAG
Found at i:108160 original size:36 final size:36
Alignment explanation
Indices: 108113--108198 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
108103 ATTGAAAACA
** * **
108113 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATTG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
108149 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
108185 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
108199 TAAACTTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
Found at i:108387 original size:33 final size:35
Alignment explanation
Indices: 108331--108408 Score: 117
Period size: 33 Copynumber: 2.3 Consensus size: 35
108321 TGAAACAAAT
*
108331 ACCTTTGAAATCGTTTTCTCTTGAAACAT-AGAAA
1 ACCTTTGAAATCGATTTCTCTTGAAACATAAGAAA
108365 ACCTTTGAAATC-ATTTCTCTTGAAACATAAGAAA
1 ACCTTTGAAATCGATTTCTCTTGAAACATAAGAAA
*
108399 ATC-TTGAAAT
1 ACCTTTGAAAT
108409 TTTTTAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
33 22 0.54
34 19 0.46
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (35 bp):
ACCTTTGAAATCGATTTCTCTTGAAACATAAGAAA
Found at i:110143 original size:3 final size:3
Alignment explanation
Indices: 110135--110289 Score: 65
Period size: 3 Copynumber: 50.3 Consensus size: 3
110125 TTATCGTAAC
* * * *
110135 TAT TAT TAT TAT TAA TAT TTT TTT TA- TAT TACG T-T TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT -TAT
*
110180 TAT TAT TAT TAT TA- TAT GTAT ATAT GTGT ATAT ATAT ATAT TACT TAT
1 TAT TAT TAT TAT TAT TAT -TAT -TAT -TAT -TAT -TAT -TAT TA-T TAT
* * *
110228 T-T T-T TA- TACT CAT TAT TAT T-T CTAT TAT TCT TAC TAT T-T TCAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT T-AT
*
110271 TAT TAC TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
110290 TCGTTTTTAC
Statistics
Matches: 119, Mismatches: 19, Indels: 28
0.72 0.11 0.17
Matches are distributed among these distances:
2 14 0.12
3 76 0.64
4 29 0.24
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:110202 original size:39 final size:37
Alignment explanation
Indices: 110138--110228 Score: 92
Period size: 39 Copynumber: 2.4 Consensus size: 37
110128 TCGTAACTAT
* * * * *
110138 TATTATTATTAATATTTTTTTTATATTACGTTTATTATA
1 TATTATTATTATTATTATATGTATA-TACGTGTA-TATA
*
110177 TATTATTATTATTATTATATGTATATATGTGTATATA
1 TATTATTATTATTATTATATGTATATACGTGTATATA
110214 TATATATTACTTATT
1 TAT-TATTA-TTATT
110229 TTTTATACTC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
37 7 0.16
38 11 0.25
39 26 0.59
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (37 bp):
TATTATTATTATTATTATATGTATATACGTGTATATA
Found at i:111921 original size:19 final size:19
Alignment explanation
Indices: 111883--111921 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
111873 AGGATTTAGG
** *
111883 TTTATTTTAATTTAATATA
1 TTTATTTTAACATAAAATA
111902 TTTATTTTAACATAAAATA
1 TTTATTTTAACATAAAATA
111921 T
1 T
111922 ATTAAATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTATTTTAACATAAAATA
Found at i:111934 original size:21 final size:21
Alignment explanation
Indices: 111896--111936 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
111886 ATTTTAATTT
* * *
111896 AATATATTTATTTTAACATAA
1 AATATATTAAATTAAACATAA
111917 AATATATTAAATTAAACATA
1 AATATATTAAATTAAACATA
111937 TTAAATCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
AATATATTAAATTAAACATAA
Found at i:115121 original size:91 final size:91
Alignment explanation
Indices: 115010--115189 Score: 290
Period size: 91 Copynumber: 2.0 Consensus size: 91
115000 CAGATCGCTC
*
115010 AGTTTTTTGTTGAGTCAATATCAAAGCAACCAA-TTTTGGATCATGTCAATATCATATCAATTAT
1 AGTTTTTTGTTGAGTCAATATCAAAGCAACCAATTTTTGGATCAGGTCAATATCATATCAATTA-
115074 TTTTTTGATTTGGCTCAATCTTTGATT
65 TTTTTTGATTTGGCTCAATCTTTGATT
* ** * *
115101 AGTTTTTTGTTGGGTCAATATTGAAGCAATCAATTTTTGGATCAGGTCAATATCATATCGATTAT
1 AGTTTTTTGTTGAGTCAATATCAAAGCAACCAATTTTTGGATCAGGTCAATATCATATCAATTAT
115166 TTTTTGATTTGGCTCAATCTTTGA
66 TTTTTGATTTGGCTCAATCTTTGA
115190 ATCTTCGAGT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
91 54 0.66
92 28 0.34
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (91 bp):
AGTTTTTTGTTGAGTCAATATCAAAGCAACCAATTTTTGGATCAGGTCAATATCATATCAATTAT
TTTTTGATTTGGCTCAATCTTTGATT
Found at i:115183 original size:32 final size:33
Alignment explanation
Indices: 115055--115183 Score: 78
Period size: 31 Copynumber: 4.2 Consensus size: 33
115045 TTGGATCATG
*
115055 TCAATATCATATCAATTATTTTTTTGATTTGGC
1 TCAATATCATATCAATTAGTTTTTTGATTTGGC
** *
115088 TC-A-ATC-T-TTGATTAGTTTTTTG--TTGGG
1 TCAATATCATATCAATTAGTTTTTTGATTTGGC
* * * * * **
115115 TCAATATTGA-AGCAATCAATTTTTGGATCAGG-
1 TCAATA-TCATATCAATTAGTTTTTTGATTTGGC
*
115147 TCAATATCATATCGATTA-TTTTTTGATTTGGC
1 TCAATATCATATCAATTAGTTTTTTGATTTGGC
115179 TCAAT
1 TCAAT
115184 CTTTGAATCT
Statistics
Matches: 67, Mismatches: 20, Indels: 19
0.63 0.19 0.18
Matches are distributed among these distances:
27 6 0.09
28 1 0.01
29 13 0.19
30 2 0.03
31 24 0.36
32 17 0.25
33 4 0.06
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (33 bp):
TCAATATCATATCAATTAGTTTTTTGATTTGGC
Found at i:115672 original size:21 final size:21
Alignment explanation
Indices: 115646--115689 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
115636 TCAATTCGAG
115646 TTAGTTTCAGTTAGGGTCAAA
1 TTAGTTTCAGTTAGGGTCAAA
115667 TTAGTTTCAGTTAGGGTCAAA
1 TTAGTTTCAGTTAGGGTCAAA
115688 TT
1 TT
115690 GAATATCGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (21 bp):
TTAGTTTCAGTTAGGGTCAAA
Found at i:121433 original size:18 final size:18
Alignment explanation
Indices: 121393--121453 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
121383 TTCTCTTGAC
*
121393 ATTTT-AAAATTA-TTAT
1 ATTTTAAAAAATATTTAT
121409 ATATTTAAAAAATATTTAT
1 AT-TTTAAAAAATATTTAT
*
121428 ATTTTATTAAAAATAATTTTT
1 ATTTTA--AAAAAT-ATTTAT
121449 ATTTT
1 ATTTT
121454 TCTTAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
16 2 0.05
17 3 0.08
18 10 0.27
19 6 0.16
20 6 0.16
21 10 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTAAAAAATATTTAT
Found at i:121435 original size:22 final size:23
Alignment explanation
Indices: 121410--121461 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 23
121400 AATTATTATA
121410 TATTTAAAAAAT-ATTTATATTT
1 TATTTAAAAAATAATTTATATTT
*
121432 TA-TT-AAAAATAATTTTTATTT
1 TATTTAAAAAATAATTTATATTT
121453 T-TCTTAAAA
1 TAT-TTAAAA
121462 TTTTATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 6 0.24
21 12 0.48
22 4 0.16
23 3 0.12
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTTAAAAAATAATTTATATTT
Found at i:121461 original size:21 final size:22
Alignment explanation
Indices: 121413--121462 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
121403 TATTATATAT
121413 TTAAAA-AATATTTATATTTTA
1 TTAAAATAATATTTATATTTTA
* *
121434 TTAAAAATAATTTTTAT-TTTTC
1 TT-AAAATAATATTTATATTTTA
121456 TTAAAAT
1 TTAAAAT
121463 TTTATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 7 0.28
22 10 0.40
23 8 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAAAATAATATTTATATTTTA
Found at i:125189 original size:2 final size:2
Alignment explanation
Indices: 125182--125207 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
125172 TATCTACACC
125182 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
125208 AGCTGAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:130537 original size:21 final size:21
Alignment explanation
Indices: 130504--130596 Score: 138
Period size: 21 Copynumber: 4.5 Consensus size: 21
130494 CATATTCGCA
130504 TTGCGATAG--TCCAAGTTCG
1 TTGCGATAGTCTCCAAGTTCG
*
130523 TTACGATAGTCTCCAAGTTCG
1 TTGCGATAGTCTCCAAGTTCG
130544 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAGTCTCCAAGTTCG
*
130565 TTGC-ATTAGTCTCCAAATTCG
1 TTGCGA-TAGTCTCCAAGTTCG
130586 TTGCGATAGTC
1 TTGCGATAGTC
130597 CAAAATCGCA
Statistics
Matches: 67, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.12
20 1 0.01
21 57 0.85
22 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (21 bp):
TTGCGATAGTCTCCAAGTTCG
Found at i:131734 original size:30 final size:30
Alignment explanation
Indices: 131710--131773 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
131700 ATTTATTTTC
*
131710 GTCTTTTTAAAATTTTATGAATTTAAGTTA
1 GTCTTCTTAAAATTTTATGAATTTAAGTTA
* *
131740 TTCTTCTTAAAATTTTAT-AAGTTTAAGTTG
1 GTCTTCTTAAAATTTTATGAA-TTTAAGTTA
131770 GTCT
1 GTCT
131774 CATAACATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.53
Consensus pattern (30 bp):
GTCTTCTTAAAATTTTATGAATTTAAGTTA
Found at i:134837 original size:60 final size:59
Alignment explanation
Indices: 134666--134834 Score: 196
Period size: 60 Copynumber: 2.8 Consensus size: 59
134656 TATAACCTTT
* * * * *
134666 ATTTTAAATCGGTCCTTAAACTTCTGAATATTTCAATTTTACCCCAAAATTATTACTCTC
1 ATTTTAAATTGGTCCTTAAACTTTTGAATATTT-AATTTTATCCCAAAATTATGACCCTC
* ** * *
134726 ATTTTAAATTAGTCCTTAAACTTTTGAGCATTCTAATTTCATCCCTAAATTATGACCCTC
1 ATTTTAAATTGGTCCTTAAACTTTTGAATATT-TAATTTTATCCCAAAATTATGACCCTC
134786 -TTTCTAAATTGGTCCTTAAACTTTTGAATATTATAATTTTATCCACAAA
1 ATTT-TAAATTGGTCCTTAAACTTTTGAATATT-TAATTTTATCC-CAAA
134835 TTAATCCGTA
Statistics
Matches: 90, Mismatches: 16, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
59 3 0.03
60 83 0.92
61 4 0.04
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.43
Consensus pattern (59 bp):
ATTTTAAATTGGTCCTTAAACTTTTGAATATTTAATTTTATCCCAAAATTATGACCCTC
Found at i:135507 original size:31 final size:29
Alignment explanation
Indices: 135469--135539 Score: 97
Period size: 31 Copynumber: 2.4 Consensus size: 29
135459 ATGATTTAAC
*
135469 AGTTCAATGGTATAATTGACATGAAAATCAA
1 AGTTCAATGGTATAATTGACA--AAAATAAA
* *
135500 AGTTCAATGCTATAATTGACAAAATTAAA
1 AGTTCAATGGTATAATTGACAAAAATAAA
135529 AGTTCAATGGT
1 AGTTCAATGGT
135540 TAGATTATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 16 0.44
31 20 0.56
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (29 bp):
AGTTCAATGGTATAATTGACAAAAATAAA
Found at i:135826 original size:2 final size:2
Alignment explanation
Indices: 135819--135857 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
135809 AAGCATAACA
135819 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
135858 ATACTTATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:137704 original size:44 final size:44
Alignment explanation
Indices: 137641--137728 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
137631 CAGTAAAGAC
137641 TTTGCATATCCTTCAAAGTCATGCACATCACAAAAAGCTCCTAA
1 TTTGCATATCCTTCAAAGTCATGCACATCACAAAAAGCTCCTAA
*
137685 TTTGCATATCCTTCAAAGTCTTGCACATCACAAAAAGCTCCTAA
1 TTTGCATATCCTTCAAAGTCATGCACATCACAAAAAGCTCCTAA
137729 AAGAATCTCC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.35, C:0.27, G:0.09, T:0.28
Consensus pattern (44 bp):
TTTGCATATCCTTCAAAGTCATGCACATCACAAAAAGCTCCTAA
Found at i:139148 original size:17 final size:15
Alignment explanation
Indices: 139126--139169 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
139116 GTTTTTTCGG
139126 TTCGGTTCGGTTTTT
1 TTCGGTTCGGTTTTT
*
139141 TTAACGGTTCGG-ATTT
1 TT--CGGTTCGGTTTTT
139157 TTCGGTTCGGTTT
1 TTCGGTTCGGTTT
139170 ATCGGTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 8 0.33
15 3 0.12
16 5 0.21
17 8 0.33
ACGTcount: A:0.07, C:0.14, G:0.27, T:0.52
Consensus pattern (15 bp):
TTCGGTTCGGTTTTT
Found at i:150436 original size:37 final size:36
Alignment explanation
Indices: 150394--150502 Score: 184
Period size: 35 Copynumber: 3.0 Consensus size: 36
150384 ATATTTCAAC
*
150394 AAACATCTACCAAACTTTGAAAAACCATTTTTCAAAG
1 AAACATTTACCAAACTTTG-AAAACCATTTTTCAAAG
150431 AAACATTTACCAAACTTTGAAAACCA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
150466 AAACATTTACCAAACTTTGAAAACCATTTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCA-TTTTTCAAAG
150503 TTGGTTGCCA
Statistics
Matches: 69, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
35 35 0.51
36 7 0.10
37 27 0.39
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
Found at i:150458 original size:21 final size:21
Alignment explanation
Indices: 150434--150494 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
150424 TTCAAAGAAA
150434 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
150455 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
150469 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
150490 CATTT
1 CATTT
150495 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:155073 original size:37 final size:37
Alignment explanation
Indices: 155031--155104 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
155021 ATATTTCAAC
*
155031 AAACATCTATCAAACTTTGAAAATCAATTTTTCAAAG
1 AAACATCTACCAAACTTTGAAAATCAATTTTTCAAAG
* *
155068 AAACATTTACCAAACTTTGAAAATCATTTTTTCAAAG
1 AAACATCTACCAAACTTTGAAAATCAATTTTTCAAAG
155105 TTGATTGCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (37 bp):
AAACATCTACCAAACTTTGAAAATCAATTTTTCAAAG
Found at i:155263 original size:21 final size:21
Alignment explanation
Indices: 155237--155278 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
155227 GTGGTGTCTG
155237 GGGTTTTTACGTTGCGAATTC
1 GGGTTTTTACGTTGCGAATTC
155258 GGGTTTTTACGTTGCGAATTC
1 GGGTTTTTACGTTGCGAATTC
155279 TGATAAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (21 bp):
GGGTTTTTACGTTGCGAATTC
Found at i:167088 original size:31 final size:32
Alignment explanation
Indices: 167053--167127 Score: 80
Period size: 37 Copynumber: 2.2 Consensus size: 32
167043 CAGTATTGAT
*
167053 CAAGATGCAC-AGATATTAATTAACATTACCG
1 CAAGATGAACGAGATATTAATTAACATTACCG
*
167084 CAAGATGTATAGAACGATATATTAATTAACATTACCG
1 C-A-A-G-AT-GAACGAGATATTAATTAACATTACCG
167121 CAAGATG
1 CAAGATG
167128 TAATAAGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
31 1 0.03
32 2 0.06
33 3 0.08
34 2 0.06
35 3 0.08
36 4 0.11
37 21 0.58
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.27
Consensus pattern (32 bp):
CAAGATGAACGAGATATTAATTAACATTACCG
Found at i:167106 original size:37 final size:39
Alignment explanation
Indices: 167065--167140 Score: 138
Period size: 37 Copynumber: 2.0 Consensus size: 39
167055 AGATGCACAG
167065 ATATTAATTAACATTACCGCAAGATGT-AT-AGAACGAT
1 ATATTAATTAACATTACCGCAAGATGTAATAAGAACGAT
167102 ATATTAATTAACATTACCGCAAGATGTAATAAGAACGAT
1 ATATTAATTAACATTACCGCAAGATGTAATAAGAACGAT
167141 TTCATTGTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 27 0.73
38 2 0.05
39 8 0.22
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (39 bp):
ATATTAATTAACATTACCGCAAGATGTAATAAGAACGAT
Found at i:168471 original size:34 final size:35
Alignment explanation
Indices: 168433--168507 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 35
168423 TATAGCTAAA
* *
168433 AAAATCGTCTTTATTCGAATTTTG-CAAAAATAGC
1 AAAATCATATTTATTCGAATTTTGCCAAAAATAGC
168467 AAAATCATATTTATTCGAATTTTGCCAAAAATAGC
1 AAAATCATATTTATTCGAATTTTGCCAAAAATAGC
168502 AAAATC
1 AAAATC
168508 CCGAAATCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 22 0.58
35 16 0.42
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATCATATTTATTCGAATTTTGCCAAAAATAGC
Found at i:169593 original size:19 final size:20
Alignment explanation
Indices: 169566--169609 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
169556 ACAGACGCGC
*
169566 ATATGAATGACTGCATATG-
1 ATATTAATGACTGCATATGA
169585 ATATTAATGACTGCATATGA
1 ATATTAATGACTGCATATGA
169605 ATATT
1 ATATT
169610 GTTCACTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (20 bp):
ATATTAATGACTGCATATGA
Found at i:170685 original size:31 final size:31
Alignment explanation
Indices: 170621--170733 Score: 199
Period size: 31 Copynumber: 3.6 Consensus size: 31
170611 TATTATATAT
170621 TACAGTGACCATTTTGTAACAATTTAAAAAGA
1 TACAGTGACCATTTTGTAACAATTT-AAAAGA
170653 TACAGTGACCATTTTGTAACAATTTAAAAGA
1 TACAGTGACCATTTTGTAACAATTTAAAAGA
170684 TACAGTGACCATTTTGTAACAATTTAAAAGA
1 TACAGTGACCATTTTGTAACAATTTAAAAGA
* *
170715 TACAATGATCATTTTGTAA
1 TACAGTGACCATTTTGTAA
170734 ACTTTAGAAT
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
31 54 0.68
32 25 0.32
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (31 bp):
TACAGTGACCATTTTGTAACAATTTAAAAGA
Found at i:178330 original size:40 final size:42
Alignment explanation
Indices: 178284--178392 Score: 127
Period size: 40 Copynumber: 2.6 Consensus size: 42
178274 TTTATATTGT
178284 TAAAATATTTTATTTAATTA-TTAAAATATAA-AAAT-GATAA
1 TAAAATATTTTATTTAATTATTTAAAATATAATAAATAG-TAA
* ** *
178324 TAAAATA-TTAATTTAACCATTTAAAATATAATAAATAGTTA
1 TAAAATATTTTATTTAATTATTTAAAATATAATAAATAGTAA
*
178365 TAAAATATATTATTTTAATTATTTAAAA
1 TAAAATATTTTA-TTTAATTATTTAAAA
178393 AATTAATATA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
39 9 0.16
40 18 0.32
41 13 0.23
42 3 0.05
43 13 0.23
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (42 bp):
TAAAATATTTTATTTAATTATTTAAAATATAATAAATAGTAA
Found at i:178389 original size:43 final size:38
Alignment explanation
Indices: 178284--178392 Score: 112
Period size: 43 Copynumber: 2.7 Consensus size: 38
178274 TTTATATTGT
*
178284 TAAAATATTTTATTTAATTA-TTAAAATATAAAAATGA
1 TAAAATATATTATTTAATTATTTAAAATATAAAAATGA
* **
178321 TAATAAAATATTAATTTAACCATTTAAAATATAATAAATAGTTA
1 TAA-AATATATT-ATTTAATTATTTAAAATATAA-AAAT-G--A
178365 TAAAATATATTATTTTAATTATTTAAAA
1 TAAAATATATTA-TTTAATTATTTAAAA
178393 AATTAATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
37 3 0.05
38 6 0.11
39 7 0.12
40 11 0.19
41 4 0.07
42 2 0.04
43 20 0.35
44 4 0.07
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (38 bp):
TAAAATATATTATTTAATTATTTAAAATATAAAAATGA
Found at i:183449 original size:2 final size:2
Alignment explanation
Indices: 183442--183486 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
183432 TTACACCAAC
183442 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
183484 AT A
1 AT A
183487 ACTGCAATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:183748 original size:39 final size:35
Alignment explanation
Indices: 183694--183765 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 35
183684 AACCTGACCT
*
183694 GATTAAAAAATTATACATCCTTCACTCAATTCGAATC
1 GATTAAAAAATTATAC-T-CTTCACTCAACTCGAATC
183731 GATTCAAAAAATATATACTCTTCACTCAACTCGAA
1 GATT-AAAAAAT-TATACTCTTCACTCAACTCGAA
183766 CACGATCCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 19 0.59
38 8 0.25
39 5 0.16
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31
Consensus pattern (35 bp):
GATTAAAAAATTATACTCTTCACTCAACTCGAATC
Found at i:183863 original size:21 final size:18
Alignment explanation
Indices: 183811--183863 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 18
183801 ACCTGACCCG
183811 AAATAATATATTTATTAAA
1 AAAT-ATATATTTATTAAA
183830 AAATAT-TATTTTATTCAATAA
1 AAATATATA-TTTATT--A-AA
183851 AAATATATATTTA
1 AAATATATATTTA
183864 ATGGAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 2 0.07
18 8 0.28
19 4 0.14
20 1 0.03
21 12 0.41
22 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATATATATTTATTAAA
Found at i:183873 original size:21 final size:22
Alignment explanation
Indices: 183827--183882 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
183817 TATATTTATT
* *
183827 AAAAAATAT-TATTTTATTCAA
1 AAAAAATATATATTTAATGCAA
* *
183848 TAAAAATATATATTTAATGGAA
1 AAAAAATATATATTTAATGCAA
183870 AAAATAATATATA
1 AAAA-AATATATA
183883 CATGGATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 8 0.29
22 12 0.43
23 8 0.29
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (22 bp):
AAAAAATATATATTTAATGCAA
Found at i:183887 original size:20 final size:20
Alignment explanation
Indices: 183849--183888 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
183839 TTTATTCAAT
*
183849 AAAAATATATATTTAATGGA
1 AAAAATATATATATAATGGA
183869 AAAAATA-ATATATACATGGA
1 AAAAATATATATATA-ATGGA
183889 TATTATGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (20 bp):
AAAAATATATATATAATGGA
Found at i:184506 original size:3 final size:3
Alignment explanation
Indices: 184493--184553 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
184483 TTCGTCCCAC
*
184493 TAT TA- TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
184540 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
184554 CTTTTTATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:184910 original size:15 final size:12
Alignment explanation
Indices: 184880--184912 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
184870 CAAACCCCCG
184880 ACCACCAACGCT
1 ACCACCAACGCT
184892 ACCACCAACGCT
1 ACCACCAACGCT
*
184904 GCCACCAAC
1 ACCACCAAC
184913 CACGAGCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.33, C:0.52, G:0.09, T:0.06
Consensus pattern (12 bp):
ACCACCAACGCT
Found at i:186132 original size:5 final size:6
Alignment explanation
Indices: 186115--186139 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
186105 GTTTTAGTCC
186115 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
186140 GCATGTTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:186869 original size:128 final size:123
Alignment explanation
Indices: 186639--186955 Score: 275
Period size: 128 Copynumber: 2.5 Consensus size: 123
186629 TCGAAGTAAT
* * * * * * * *
186639 AAATGAATGTTTTAAGGCATGATAGGTCATTTATTCTCGATTGGAATAATTCGATATTACTGTTT
1 AAATG-ATGCTTTAAGGTATGAGAGGTCATTTATTATCAAATGGAATAATTAGATATTACCGTTT
* * * *
186704 TTCTCAAATCAATATTGTTTTTAAGATAGAATGATGATATCTCTTCATTTCAATTGGAGCA
65 TCCTCAAATCAATATTGATTTTAAGAGAGAATAATG--ATCTCTTCATTTCAATTGGAGCA
*
186765 ATTAATGACTGCTTTAAGGTATGAGAGGTCATTTATTATCAAATGG-A-AATTATATATTACCGT
1 A--AATGA-TGCTTTAAGGTATGAGAGGTCATTTATTATCAAATGGAATAATTAGATATTACCGT
* * * * * *
186828 TTTCCCTCGAATCGATATTGAATTTTAAGACGA-AATAATGATCTCTTTATTTCGATTGGGGTA
63 TTT-CCTCAAATCAATATTG-ATTTTAAGA-GAGAATAATGATCTCTTCATTTCAATTGGAGCA
* * * ** * *
186891 AAATGAT-C-TTAAGGTACGAGAGATCATTTATTCTTGATTGGAAATAATTAGATATTATCGTTT
1 AAATGATGCTTTAAGGTATGAGAGGTCATTTATTATCAAATGG-AATAATTAGATATTACCGTTT
186954 TC
65 TC
186956 ACTCTTAAAA
Statistics
Matches: 155, Mismatches: 27, Indels: 21
0.76 0.13 0.10
Matches are distributed among these distances:
121 27 0.17
122 1 0.01
123 3 0.02
124 22 0.14
126 37 0.24
127 15 0.10
128 49 0.32
129 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (123 bp):
AAATGATGCTTTAAGGTATGAGAGGTCATTTATTATCAAATGGAATAATTAGATATTACCGTTTT
CCTCAAATCAATATTGATTTTAAGAGAGAATAATGATCTCTTCATTTCAATTGGAGCA
Found at i:190340 original size:14 final size:14
Alignment explanation
Indices: 190318--190350 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
190308 CATCCGAGAG
*
190318 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
190332 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
190346 CTCGG
1 CTCGG
190351 ATGCTCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:190350 original size:10 final size:10
Alignment explanation
Indices: 190337--190373 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
190327 ATGGCCTCGG
190337 TCGGATGGCC
1 TCGGATGGCC
190347 TCGGAT-GCTC
1 TCGGATGGC-C
190357 TCGGATGGCC
1 TCGGATGGCC
190367 TCGGATG
1 TCGGATG
190374 CCCAGCGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.11, C:0.27, G:0.38, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:190362 original size:20 final size:20
Alignment explanation
Indices: 190337--190374 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
190327 ATGGCCTCGG
190337 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
190357 TCGGATGGCCTCGGATGC
1 TCGGATGGCCTCGGATGC
190375 CCAGCGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.29, G:0.37, T:0.24
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:201313 original size:71 final size:70
Alignment explanation
Indices: 201198--201337 Score: 235
Period size: 71 Copynumber: 2.0 Consensus size: 70
201188 CCTTAGATAT
*
201198 GTAAGGAATTACCAGTTCGATCGTCTGAACCTATATAAGGAATTACCAGTTTAATCGAGCTGAAC
1 GTAAGGAATTACCAGTTCGATCGTCTGAACCTATATAAGGAATTACCAATTTAATCGAGCTGAAC
201263 CTGTC
66 CTGTC
* * *
201268 GTAAGTAATTACCAGTTCGATCAGTCTGAACCTATATAAGGAATTACTAATTTGATCGAGCTGAA
1 GTAAGGAATTACCAGTTCGATC-GTCTGAACCTATATAAGGAATTACCAATTTAATCGAGCTGAA
201333 CCTGT
65 CCTGT
201338 AGAGATTGCA
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 21 0.32
71 44 0.68
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (70 bp):
GTAAGGAATTACCAGTTCGATCGTCTGAACCTATATAAGGAATTACCAATTTAATCGAGCTGAAC
CTGTC
Found at i:201332 original size:35 final size:35
Alignment explanation
Indices: 201199--201335 Score: 161
Period size: 35 Copynumber: 3.9 Consensus size: 35
201189 CTTAGATATG
*
201199 TAAGGAATTACCAGTTCGATCG-TCTGAACCTATA
1 TAAGGAATTACCAGTTCGATCGAGCTGAACCTATA
** * *
201233 TAAGGAATTACCAGTTTAATCGAGCTGAACCTGTCG
1 TAAGGAATTACCAGTTCGATCGAGCTGAACCTAT-A
*
201269 TAAGTAATTACCAGTTCGATC-AGTCTGAACCTATA
1 TAAGGAATTACCAGTTCGATCGAG-CTGAACCTATA
* * *
201304 TAAGGAATTACTAATTTGATCGAGCTGAACCT
1 TAAGGAATTACCAGTTCGATCGAGCTGAACCT
201336 GTAGAGATTG
Statistics
Matches: 85, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
34 20 0.24
35 36 0.42
36 29 0.34
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (35 bp):
TAAGGAATTACCAGTTCGATCGAGCTGAACCTATA
Found at i:204154 original size:26 final size:28
Alignment explanation
Indices: 204105--204166 Score: 101
Period size: 26 Copynumber: 2.3 Consensus size: 28
204095 TAGTATATGT
*
204105 ATTTTATCTATTTACTATTTATTATAAA
1 ATTTTATCTATATACTATTTATTATAAA
204133 ATTTTATCTA-AT-CTATTTATTATAAA
1 ATTTTATCTATATACTATTTATTATAAA
204159 ATTTTATC
1 ATTTTATC
204167 ATACAACATG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
26 22 0.67
27 1 0.03
28 10 0.30
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTTATCTATATACTATTTATTATAAA
Done.