Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014931.1 Kokia drynarioides strain JFW-HI SEQ_129974, 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: 102131
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 234 characters in sequence are not A, C, G, or T
Found at i:4098 original size:17 final size:17
Alignment explanation
Indices: 4072--4108 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4062 AATAATTATT
* *
4072 TTTTTGAAAATATAAAA
1 TTTTTAAAAAAATAAAA
4089 TTTTTAAAAAAATAAAA
1 TTTTTAAAAAAATAAAA
4106 TTT
1 TTT
4109 GCATATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
TTTTTAAAAAAATAAAA
Found at i:4899 original size:21 final size:21
Alignment explanation
Indices: 4874--4914 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4864 CAGAACGATG
*
4874 TAATTTTGTCTTTTAATTTAA
1 TAATTTTGACTTTTAATTTAA
4895 TAATTTTGACTTTTAATTTA
1 TAATTTTGACTTTTAATTTA
4915 CAAAAAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (21 bp):
TAATTTTGACTTTTAATTTAA
Found at i:8503 original size:34 final size:34
Alignment explanation
Indices: 8464--8532 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
8454 ACAAATTAGA
8464 TGAGTAGCAACATTTTTAGACAAAAAATGAAAAT
1 TGAGTAGCAACATTTTTAGACAAAAAATGAAAAT
*
8498 TGAGTAGCAACATTTTTAGACAAACAATGAAAAT
1 TGAGTAGCAACATTTTTAGACAAAAAATGAAAAT
8532 T
1 T
8533 CTTACTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (34 bp):
TGAGTAGCAACATTTTTAGACAAAAAATGAAAAT
Found at i:16282 original size:52 final size:52
Alignment explanation
Indices: 16215--16541 Score: 405
Period size: 52 Copynumber: 6.3 Consensus size: 52
16205 TCTGATGACA
* *
16215 ATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGGTAACT
1 ATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATAACT
* * *
16267 ATG-GTTCATCGTGAGTATATGAAACATTTACAAATTATGAGGTCCGATAACT
1 ATGTG-TCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATAACT
**
16319 ATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGAGGTCCG---ACT
1 ATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATAACT
* * * *
16368 ATATGTCATCGTGAGTATATGAACCCTTTAC-GAATTATGAGGTTCGATGACT
1 ATGTGTCATCGTGAGTATATGAATCCTTTACAG-ATTATGAGGTCCGATAACT
* * *
16420 ATGTGTTATCGTGAATATATGAATCTTTTACAGATTATGAGGTCCGATAACT
1 ATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATAACT
* * * *
16472 ATGTGTCATCGTGAGTATTTGGATCCTATTACAGATT-TAAGGTCCGATGACT
1 ATGTGTCATCGTGAGTATATGAATCCT-TTACAGATTATGAGGTCCGATAACT
* *
16524 TTGTGTCATCATGAGTAT
1 ATGTGTCATCGTGAGTAT
16542 GAAATGGGAA
Statistics
Matches: 237, Mismatches: 30, Indels: 16
0.84 0.11 0.06
Matches are distributed among these distances:
48 1 0.00
49 43 0.18
51 1 0.00
52 181 0.76
53 11 0.05
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (52 bp):
ATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATAACT
Found at i:16498 original size:153 final size:153
Alignment explanation
Indices: 16218--16498 Score: 447
Period size: 153 Copynumber: 1.8 Consensus size: 153
16208 GATGACAATG
* * * *
16218 TGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGGTAACTATGGTTCATCGTGAGT
1 TGTCATCGTGAGTATATGAACCCTTTACGAATTATGAGGTCCGATAACTATGGTTCATCGTGAAT
16283 ATATGAAACATTTACAAATTATGAGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCCTTT
66 ATATGAAACATTTACAAATTATGAGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCCTTT
16348 ATGGATTATGAGGTCCGACTATA
131 ATGGATTATGAGGTCCGACTATA
* *
16371 TGTCATCGTGAGTATATGAACCCTTTACGAATTATGAGGTTCGATGACTATGTGTT-ATCGTGAA
1 TGTCATCGTGAGTATATGAACCCTTTACGAATTATGAGGTCCGATAACTATG-GTTCATCGTGAA
* * * * *
16435 TATATGAATCTTTTACAGATTATGAGGTCCGATAACTATGTGTCATCGTGAGTATTTGGATCCT
65 TATATGAAACATTTACAAATTATGAGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCCT
16499 ATTACAGATT
Statistics
Matches: 116, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
153 113 0.97
154 3 0.03
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (153 bp):
TGTCATCGTGAGTATATGAACCCTTTACGAATTATGAGGTCCGATAACTATGGTTCATCGTGAAT
ATATGAAACATTTACAAATTATGAGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCCTTT
ATGGATTATGAGGTCCGACTATA
Found at i:19659 original size:20 final size:20
Alignment explanation
Indices: 19610--19660 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
19600 ACTGTTGACC
19610 TGATCGTTGACCGTTGACTT
1 TGATCGTTGACCGTTGACTT
* * * * *
19630 TTAACTTTGACCTTTTACTT
1 TGATCGTTGACCGTTGACTT
19650 TGATCGTTGAC
1 TGATCGTTGAC
19661 TCATATTTTT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.45
Consensus pattern (20 bp):
TGATCGTTGACCGTTGACTT
Found at i:21136 original size:19 final size:19
Alignment explanation
Indices: 21112--21150 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
21102 TGCTATAAGG
21112 AAAGAAGGACCATGAATGA
1 AAAGAAGGACCATGAATGA
21131 AAAGAAGGACCATGAATGA
1 AAAGAAGGACCATGAATGA
21150 A
1 A
21151 TTTGGTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.10, G:0.26, T:0.10
Consensus pattern (19 bp):
AAAGAAGGACCATGAATGA
Found at i:23649 original size:1 final size:1
Alignment explanation
Indices: 23643--23731 Score: 88
Period size: 1 Copynumber: 89.0 Consensus size: 1
23633 GCCCTTAACC
**********
23643 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
23708 TTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTT
23732 CTGATTTCAA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
1 86 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:40028 original size:12 final size:12
Alignment explanation
Indices: 39997--40031 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
39987 ATCATTAATA
* *
39997 AATAAACAAGTC
1 AATAAACGAGCC
40009 AATAAACGAGCC
1 AATAAACGAGCC
40021 AATAAACGAGC
1 AATAAACGAGC
40032 TTTTAAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.54, C:0.20, G:0.14, T:0.11
Consensus pattern (12 bp):
AATAAACGAGCC
Found at i:43133 original size:22 final size:22
Alignment explanation
Indices: 43103--43153 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
43093 GTAAAATTAG
*
43103 TATA-ATATACAA-AATAATATA
1 TATATATATA-AACAATAAGATA
*
43124 TATATATATAAACAATAAGCTA
1 TATATATATAAACAATAAGATA
43146 TATATATA
1 TATATATA
43154 CATATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (22 bp):
TATATATATAAACAATAAGATA
Found at i:50539 original size:18 final size:17
Alignment explanation
Indices: 50516--50635 Score: 62
Period size: 18 Copynumber: 7.3 Consensus size: 17
50506 TTGCTTTCCA
50516 ATTTATTACTTTAATTT
1 ATTTATTACTTTAATTT
*
50533 CATTTA-TCCTTTAA-TT
1 -ATTTATTACTTTAATTT
** *
50549 A-AAATCA-TTTAACTTT
1 ATTTATTACTTTAA-TTT
50565 ATTTATTACTTTTAA---
1 ATTTATTAC-TTTAATTT
50580 ATTTATTA-TTTGAATTT
1 ATTTATTACTTT-AATTT
* *
50597 CATTTATTCCTTTAAATTA
1 -ATTTATTACTTT-AATTT
50616 ATTTATT-CTTTAA-TT
1 ATTTATTACTTTAATTT
50631 ATTTA
1 ATTTA
50636 ATTTTTAATT
Statistics
Matches: 78, Mismatches: 12, Indels: 27
0.67 0.10 0.23
Matches are distributed among these distances:
13 3 0.04
14 8 0.10
15 15 0.19
16 7 0.09
17 14 0.18
18 19 0.24
19 12 0.15
ACGTcount: A:0.32, C:0.09, G:0.01, T:0.58
Consensus pattern (17 bp):
ATTTATTACTTTAATTT
Found at i:50613 original size:32 final size:31
Alignment explanation
Indices: 50515--50614 Score: 98
Period size: 32 Copynumber: 3.1 Consensus size: 31
50505 TTTGCTTTCC
50515 AATTTATTACTTTAATTTCATTTA-TCCTTT-
1 AATTTATTA-TTTAATTTCATTTATTCCTTTA
* * *
50545 AATTAAAATCATTTAACTTT-ATTTATTACTTTTA
1 AATT--TATTATTTAA-TTTCATTTATT-CCTTTA
50579 AATTTATTATTTGAATTTCATTTATTCCTTTA
1 AATTTATTATTT-AATTTCATTTATTCCTTTA
50611 AATT
1 AATT
50615 AATTTATTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
30 4 0.07
31 10 0.18
32 25 0.45
33 13 0.23
34 4 0.07
ACGTcount: A:0.32, C:0.10, G:0.01, T:0.57
Consensus pattern (31 bp):
AATTTATTATTTAATTTCATTTATTCCTTTA
Found at i:50642 original size:15 final size:15
Alignment explanation
Indices: 50563--50646 Score: 57
Period size: 15 Copynumber: 5.2 Consensus size: 15
50553 TCATTTAACT
50563 TTATTTATTACTTTTAA
1 TTATTTATT-C-TTTAA
*
50580 --ATTTATTATTTGAA
1 TTATTTATTCTTT-AA
50594 TTTCATTTATTCCTTTAAA
1 -TT-ATTTATT-CTTT-AA
50613 TTAATTTATTCTTTAA
1 TT-ATTTATTCTTTAA
50629 TTATTTAATT-TTTAA
1 TTATTT-ATTCTTTAA
50644 TTA
1 TTA
50647 AAATTGTATT
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
13 3 0.05
14 2 0.04
15 19 0.34
16 7 0.12
17 4 0.07
18 16 0.29
19 5 0.09
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (15 bp):
TTATTTATTCTTTAA
Found at i:61673 original size:22 final size:22
Alignment explanation
Indices: 61634--61675 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
61624 TATTTAAAAA
*
61634 TATTTTTAATTATTATTTTATG
1 TATTTTTAATTATAATTTTATG
61656 TATTTTATAATTA-AATTTTA
1 TATTTT-TAATTATAATTTTA
61676 ATTTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TATTTTTAATTATAATTTTATG
Found at i:62417 original size:23 final size:23
Alignment explanation
Indices: 62387--62433 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
62377 CGATGGTTAG
62387 ATGAGATAGTAAAAATCATTCCT
1 ATGAGATAGTAAAAATCATTCCT
62410 ATGAGATAGTAAAAATCATTCCT
1 ATGAGATAGTAAAAATCATTCCT
62433 A
1 A
62434 CCTTAATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30
Consensus pattern (23 bp):
ATGAGATAGTAAAAATCATTCCT
Found at i:74621 original size:2 final size:2
Alignment explanation
Indices: 74614--74638 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
74604 AAAGCAGAAC
74614 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
74639 AGACAGGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:74993 original size:2 final size:2
Alignment explanation
Indices: 74988--75026 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
74978 GGAAAAAATA
74988 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
75027 AAATGATATT
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:75251 original size:27 final size:26
Alignment explanation
Indices: 75221--75282 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
75211 ATAGTGATTT
*
75221 ATTTGGTTT-TTCTTATTTTGATAAAAA
1 ATTTAGTTTATTCTTATTTT-A-AAAAA
* *
75248 ATTTATTTTATTTTTATTTTAAAAAA
1 ATTTAGTTTATTCTTATTTTAAAAAA
75274 ATTTTAGTT
1 A-TTTAGTT
75283 CTTGAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 6 0.21
27 14 0.48
28 9 0.31
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (26 bp):
ATTTAGTTTATTCTTATTTTAAAAAA
Found at i:75419 original size:20 final size:17
Alignment explanation
Indices: 75394--75437 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 17
75384 ATCTCGAGAA
75394 ATTTAAAATATATAAAAATT
1 ATTTAAAAT-T-T-AAAATT
75414 ATTTAAAATTTAAAATT
1 ATTTAAAATTTAAAATT
75431 A-TTAAAA
1 ATTTAAAA
75438 AAGCATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.25
17 7 0.29
18 1 0.04
19 1 0.04
20 9 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTAAAATTTAAAATT
Found at i:75779 original size:6 final size:6
Alignment explanation
Indices: 75757--75823 Score: 55
Period size: 6 Copynumber: 11.0 Consensus size: 6
75747 GTTTAAATGG
* * * * *
75757 ATTTAA ATTTAT TTTTAA ATTTAA ATTTATCT TTTTAA ATTTAA ATTT-G
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTA--A ATTTAA ATTTAA ATTTAA
*
75806 CTTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA
75824 TAAAATTTGA
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
5 3 0.07
6 39 0.85
8 4 0.09
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (6 bp):
ATTTAA
Found at i:77551 original size:30 final size:30
Alignment explanation
Indices: 77486--77926 Score: 392
Period size: 30 Copynumber: 14.9 Consensus size: 30
77476 CTAAACTGTT
*
77486 CAAAAATT-CAATTTT-ACCCTCG-AACTTC
1 CAAAAATTCCATTTTTGACCC-CGAAACTTC
*
77514 CAAAAATTCCATTTTTGACCCCAAAAC-TC
1 CAAAAATTCCATTTTTGACCCCGAAACTTC
*
77543 TTAAAAATTCCATTTTT-ACCCTCG-AACTTC
1 -CAAAAATTCCATTTTTGACCC-CGAAACTTC
* *
77573 CAAAAATTCCATTTTTGACCTCGAAACTTT
1 CAAAAATTCCATTTTTGACCCCGAAACTTC
*
77603 CAAAAATTCAATTTTT-ACCCACG-AACTTC
1 CAAAAATTCCATTTTTGACCC-CGAAACTTC
* *
77632 CAAAAATTCCATTTTTCACCTCGAAACTTC
1 CAAAAATTCCATTTTTGACCCCGAAACTTC
*
77662 CAAAAATTCCATTTTT-ACCCTC-TAACTTC
1 CAAAAATTCCATTTTTGACCC-CGAAACTTC
* ** *
77691 CAAAAATTCCATGTTCAAACCCGAAACTTC
1 CAAAAATTCCATTTTTGACCCCGAAACTTC
**
77721 CAAAAATTCCATTTTTGACCTTGAAACTTC
1 CAAAAATTCCATTTTTGACCCCGAAACTTC
* *
77751 CAAAAGTTCCATTTTTGACCTCGAAACTTC
1 CAAAAATTCCATTTTTGACCCCGAAACTTC
* *
77781 CAAAAGTTCCATTTTTGACCTCGAAACTTC
1 CAAAAATTCCATTTTTGACCCCGAAACTTC
* *
77811 CAAAAGTTCCATTTTT-ACCCCCG-AACCTC
1 CAAAAATTCCATTTTTGA-CCCCGAAACTTC
* ** * * ** *
77840 TAAACTTTTCATTTTTAACCCTAAAACTTT
1 CAAAAATTCCATTTTTGACCCCGAAACTTC
*
77870 CAAAAATTACC-CTTTTG-CCCTCG-AA-TGTC
1 CAAAAATT-CCATTTTTGACCC-CGAAACT-TC
* * *
77899 CAAAAACTCTATTTTTGACCTCGAAACT
1 CAAAAATTCCATTTTTGACCCCGAAACT
77927 CTCAAAATTA
Statistics
Matches: 340, Mismatches: 49, Indels: 45
0.78 0.11 0.10
Matches are distributed among these distances:
28 10 0.03
29 123 0.36
30 205 0.60
31 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (30 bp):
CAAAAATTCCATTTTTGACCCCGAAACTTC
Found at i:77570 original size:59 final size:59
Alignment explanation
Indices: 77486--77831 Score: 441
Period size: 59 Copynumber: 5.9 Consensus size: 59
77476 CTAAACTGTT
* *
77486 CAAAAATT-CAATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCAAAAC-TC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTC
* * *
77543 TTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTT
1 -CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTC
* * * *
77603 CAAAAATTCAATTTTTACCCACGAACTTCCAAAAATTCCATTTTTCACCTCGAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTC
* * ** *
77662 CAAAAATTCCATTTTTACCCTCTAACTTCCAAAAATTCCATGTTCAAACCCGAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTC
* * *
77721 CAAAAATTCCATTTTTGA-CCTTGAAACTTCCAAAAGTTCCATTTTTGACCTCGAAACTTC
1 CAAAAATTCCATTTTT-ACCCTCG-AACTTCCAAAAATTCCATTTTTGACCCCGAAACTTC
* *
77781 CAAAAGTTCCATTTTTGA-CCTCGAAACTTCCAAAAGTTCCATTTTT-ACCCC
1 CAAAAATTCCATTTTT-ACCCTCG-AACTTCCAAAAATTCCATTTTTGACCCC
77832 CGAACCTCTA
Statistics
Matches: 255, Mismatches: 29, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
58 7 0.03
59 172 0.67
60 76 0.30
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (59 bp):
CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTC
Found at i:77664 original size:89 final size:89
Alignment explanation
Indices: 77486--77829 Score: 427
Period size: 89 Copynumber: 3.9 Consensus size: 89
77476 CTAAACTGTT
* * *
77486 CAAAAATT-CAATTTTACCCTCG-AACTTCCAAAAATTCCATTTTTGACCCCAAAAC-TCTTAAA
1 CAAAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTC-CAAA
77548 AATTCCATTTTTACCCTCG-AACTTC
65 AATTCCATTTTTA-CCTCGAAACTTC
* *
77573 CAAAAATTCCATTTTTGA-CCTCGAAACTTTCAAAAATTCAATTTTT-ACCCACG-AACTTCCAA
1 CAAAAATTCCATTTTT-ACCCTCGAAACTTCCAAAAATTCCATTTTTGACCC-CGAAACTTCCAA
77635 AAATTCCATTTTTCACCTCGAAACTTC
64 AAATTCCATTTTT-ACCTCGAAACTTC
* * ** *
77662 CAAAAATTCCATTTTTACCCTC-TAACTTCCAAAAATTCCATGTTCAAACCCGAAACTTCCAAAA
1 CAAAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAA
*
77726 ATTCCATTTTTGACCTTGAAACTTC
66 ATTCCATTTTT-ACCTCGAAACTTC
* * *
77751 CAAAAGTTCCATTTTTGA-CCTCGAAACTTCCAAAAGTTCCATTTTTGACCTCGAAACTTCCAAA
1 CAAAAATTCCATTTTT-ACCCTCGAAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAA
*
77815 AGTTCCATTTTTACC
65 AATTCCATTTTTACC
77830 CCCGAACCTC
Statistics
Matches: 223, Mismatches: 22, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
87 8 0.04
88 59 0.26
89 110 0.49
90 46 0.21
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (89 bp):
CAAAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAA
ATTCCATTTTTACCTCGAAACTTC
Found at i:77913 original size:59 final size:58
Alignment explanation
Indices: 77849--78009 Score: 152
Period size: 58 Copynumber: 2.8 Consensus size: 58
77839 CTAAACTTTT
77849 CATTTTTAACCCTAAAACTTTCAAAAATTACCCTTTTGCCCTCGAATGTCCAAAAACTC
1 CATTTTTAACCCTAAAACTTTC-AAAATTACCCTTTTGCCCTCGAATGTCCAAAAACTC
* * * * * *
77908 TATTTTTGA-CCTCGAAACTCTCAAAATTACCCTTCTAT-CCC-CGAATGTCTAAAAATTC
1 CATTTTTAACCCT-AAAACTTTCAAAATTACCCTT-T-TGCCCTCGAATGTCCAAAAACTC
* * *
77966 CATTTTTAACCC-CAAATTTTCCCAAAATTACCATTTTG-CCTCGA
1 CATTTTTAACCCTAAAACTTT--CAAAATTACCCTTTTGCCCTCGA
78010 GAATTCAAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
57 8 0.10
58 41 0.50
59 32 0.39
60 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.34
Consensus pattern (58 bp):
CATTTTTAACCCTAAAACTTTCAAAATTACCCTTTTGCCCTCGAATGTCCAAAAACTC
Found at i:82320 original size:22 final size:21
Alignment explanation
Indices: 82279--82321 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
82269 CCTAGACAAA
*
82279 TAGAGGAAAAATACAGGCGAT
1 TAGAGGAAAAATACACGCGAT
82300 TAGAGGAGAAAAT-CGACGCGAT
1 TAGAGGA-AAAATAC-ACGCGAT
82322 GCAAGGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14
Consensus pattern (21 bp):
TAGAGGAAAAATACACGCGAT
Found at i:90205 original size:205 final size:204
Alignment explanation
Indices: 89847--90425 Score: 874
Period size: 205 Copynumber: 2.8 Consensus size: 204
89837 ACGATTATCC
* *
89847 ACAAACGACGCGGCCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAA-TCCACGCTCG
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCCA--CTCG
**
89911 ATGTGAGCAAATCTTCGAACCCCAGCTTTTTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAA
64 ATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAA
* * *
89976 AGGTTAGCTTCCTGATGGGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATCAGATACAGAGA
129 AGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATCAGATACAAAAA
90041 AGCGAATTGAA
194 AGCGAATTGAA
* * *
90052 GCAAACGACACGGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACTCGCACTCGA
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTC-CACTCGA
* *
90117 TGTGAGTAAATCTTCGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTTGAAGCAATAAAA
65 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAAA
*
90182 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAAAA
130 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATCAGATACAAAAAA
90247 GCGAATTGAA
195 GCGAATTGAA
* *
90257 ACAAACGACGCGGTCATCTCCCTGATGAGATACTGAGAAGAAGACCAAATCAATC-CCACGCTCG
1 ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCCA--CTCG
** * *
90321 ATAAGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGACAAGCAGGTCGAAGCAATAAA
64 ATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAA
* * * * **
90386 CGGTCATCTTCCTGATGAGATGCTGAGAAGAAGACCAAAT
129 AGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAAT
90426 CAAACCCACG
Statistics
Matches: 340, Mismatches: 30, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
203 2 0.01
204 1 0.00
205 333 0.98
206 2 0.01
207 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (204 bp):
ACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCCACTCGAT
GTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAAAG
GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATCAGATACAAAAAAG
CGAATTGAA
Found at i:90483 original size:119 final size:120
Alignment explanation
Indices: 90267--90528 Score: 391
Period size: 119 Copynumber: 2.2 Consensus size: 120
90257 ACAAACGACG
* *
90267 CGGTCATCTCCCTGATGAGATACTGAGAAGAAGACCAAATCAATCCCACGCTCGATAAGAGCAAA
1 CGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATAAGAGCAAA
* *
90332 TCTTCGAACCCCAGCTTCCTGATGAGACACTGACAAGCAGGTCGAAGCAAT-AAA
66 TCTTCGAACCCCAGCTTCCTGATGAGACACTGACAAGCAAGTCAAAGCAATAAAA
* **
90386 CGGTCATCTTCCTGATGAGATGCTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAA
1 CGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATAAGAGCAAA
* * *
90451 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCAAAGTAATAAAA
66 TCTTCGAACCCCAGCTTCCTGATGAGACACTGACAAGCAAGTCAAAGCAATAAAA
* * * *
90506 TGGTTAGCTTCCTGATGAAATAC
1 CGGTCATCTTCCTGATGAGATAC
90529 GGGGAAGTGA
Statistics
Matches: 127, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
119 106 0.83
120 21 0.17
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (120 bp):
CGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATAAGAGCAAA
TCTTCGAACCCCAGCTTCCTGATGAGACACTGACAAGCAAGTCAAAGCAATAAAA
Found at i:90574 original size:37 final size:37
Alignment explanation
Indices: 90513--90583 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
90503 AAATGGTTAG
* * **
90513 CTTCCTGATGAAATACGGGGAAGTGAACCAAAACCAT
1 CTTCCTGATGAAACACAGAAAAGTGAACCAAAACCAT
* *
90550 CTTCCTGATGAAACACAGAAAAGTGGATCAAAAC
1 CTTCCTGATGAAACACAGAAAAGTGAACCAAAAC
90584 AAGTGATATG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (37 bp):
CTTCCTGATGAAACACAGAAAAGTGAACCAAAACCAT
Found at i:91002 original size:6 final size:6
Alignment explanation
Indices: 90981--91063 Score: 64
Period size: 6 Copynumber: 13.8 Consensus size: 6
90971 TTTAAATTGG
** **
90981 TTTAAA TTTATT TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTATCTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA--AA
**
91030 TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
91064 TCAAATTTGA
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
4 2 0.03
5 5 0.08
6 46 0.78
7 2 0.03
8 4 0.07
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:91016 original size:17 final size:18
Alignment explanation
Indices: 90981--91062 Score: 114
Period size: 17 Copynumber: 4.6 Consensus size: 18
90971 TTTAAATTGG
*
90981 TTTAAATTTATTTTTAAA
1 TTTAAATTTATCTTTAAA
90999 TTTAAATTTATC-TTAAA
1 TTTAAATTTATCTTTAAA
91016 TTTAAATTTATCTTTTTAAA
1 TTTAAATTTATC--TTTAAA
*
91036 TTTAAATTT-GCTTTAAA
1 TTTAAATTTATCTTTAAA
91053 TTTAAATTTA
1 TTTAAATTTA
91063 ATCAAATTTG
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
17 32 0.55
18 11 0.19
19 1 0.02
20 14 0.24
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (18 bp):
TTTAAATTTATCTTTAAA
Found at i:91039 original size:37 final size:35
Alignment explanation
Indices: 90981--91062 Score: 121
Period size: 37 Copynumber: 2.3 Consensus size: 35
90971 TTTAAATTGG
*
90981 TTTAAATTTATTTTTAAATTTAAATTT-ATCTTAAA
1 TTTAAATTTATTTTTAAATTTAAATTTGCT-TTAAA
91016 TTTAAATTTATCTTTTTAAATTTAAATTTGCTTTAAA
1 TTTAAATTTA--TTTTTAAATTTAAATTTGCTTTAAA
91053 TTTAAATTTA
1 TTTAAATTTA
91063 ATCAAATTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 10 0.23
37 32 0.74
38 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (35 bp):
TTTAAATTTATTTTTAAATTTAAATTTGCTTTAAA
Found at i:92095 original size:30 final size:30
Alignment explanation
Indices: 92060--92155 Score: 138
Period size: 30 Copynumber: 3.2 Consensus size: 30
92050 GAAGCAGTGG
* * *
92060 CGCGTGCACCGTAGGACTGTGGGACGGCAG
1 CGCGTGCACCGGAGGACTGCGGGACGGCAA
*
92090 CGCGTGCACCGGAGGACTGCGGGACGACAA
1 CGCGTGCACCGGAGGACTGCGGGACGGCAA
* *
92120 CGCTTGCACCGGAGGACTGCAGGACGGCAA
1 CGCGTGCACCGGAGGACTGCGGGACGGCAA
92150 CGCGTG
1 CGCGTG
92156 GTGCGCGTGG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.20, C:0.29, G:0.41, T:0.10
Consensus pattern (30 bp):
CGCGTGCACCGGAGGACTGCGGGACGGCAA
Found at i:92807 original size:29 final size:29
Alignment explanation
Indices: 92770--93181 Score: 312
Period size: 29 Copynumber: 14.0 Consensus size: 29
92760 TATTGCCCTA
92770 AACTGTCCAAAAATTCCATTTTTACCCTCG
1 AACT-TCCAAAAATTCCATTTTTACCCTCG
92800 AACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
** *
92829 AACTTTTAAAAATTCCAATTTTGACCC-CG
1 AACTTCCAAAAATTCC-ATTTTTACCCTCG
*
92858 AAACTTCCAAAAATTCCATTTTTGA-CCTTG
1 -AACTTCCAAAAATTCCATTTTT-ACCCTCG
*
92888 AAACTTCCAAAAAATCCA-TTTTACCGC-CG
1 -AACTTCCAAAAATTCCATTTTTACC-CTCG
* **
92917 AACTTCCAAAAATTCAATTTTTAACCC-AA
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* * *
92946 AACTTCCAAAAATTTCATTGTTGACTC-CG
1 AACTTCCAAAAATTCCATT-TTTACCCTCG
* *
92975 AAACTTCCAAAAGTTCCATTTTTACCCCCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* * *
93005 AACCTCTAAAATTTCCATTTTTGACCC-CG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
** *
93034 AAACTTTTAAAAATTTCCCTTTTT-CCCTCG
1 -AACTTCCAAAAA-TTCCATTTTTACCCTCG
* *
93064 AA-TGTCCAAAAACTCCATTTTCGA-CCTCG
1 AACT-TCCAAAAATTCCATTTT-TACCCTCG
* *
93093 AAATTCTC-AAAATTACC-GTTTTACCCTCG
1 AACTTC-CAAAAATT-CCATTTTTACCCTCG
* *
93122 AA-TGTCTAAAAATTCCATTTTTAACCTCG
1 AACT-TCCAAAAATTCCATTTTTACCCTCG
* *
93151 AATTTTCCCAAAATTACCA-TTTTACCCTCG
1 AA-CTTCCAAAAATT-CCATTTTTACCCTCG
93181 A
1 A
93182 GAATCCAAAA
Statistics
Matches: 310, Mismatches: 44, Indels: 56
0.76 0.11 0.14
Matches are distributed among these distances:
28 28 0.09
29 160 0.52
30 109 0.35
31 13 0.04
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:92863 original size:30 final size:29
Alignment explanation
Indices: 92769--93207 Score: 275
Period size: 30 Copynumber: 15.0 Consensus size: 29
92759 TTATTGCCCT
*
92769 AAACTGTCCAAAAATTCCATTTTTACCCTCG
1 AAACT-TCCAAAAATTCCATTTTGACCC-CG
*
92800 -AACTTCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTGACCC-CG
**
92829 -AACTTTTAAAAATTCCAATTTTGACCCCG
1 AAACTTCCAAAAATTCC-ATTTTGACCCCG
**
92858 AAACTTCCAAAAATTCCATTTTTGACCTTG
1 AAACTTCCAAAAATTCCA-TTTTGACCCCG
*
92888 AAACTTCCAAAAAATCCATTTT-ACCGCCG
1 AAACTTCCAAAAATTCCATTTTGACC-CCG
* * * *
92917 -AACTTCCAAAAATTCAATTTTTAACCCA
1 AAACTTCCAAAAATTCCATTTTGACCCCG
* *
92945 AAACTTCCAAAAATTTCATTGTTGACTCCG
1 AAACTTCCAAAAATTCCATT-TTGACCCCG
* *
92975 AAACTTCCAAAAGTTCCATTTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTGA-CCCCG
* * *
93005 -AACCTCTAAAATTTCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCA-TTTTGACCCCG
** * *
93034 AAACTTTTAAAAATTTCCCTTTT-TCCCTCG
1 AAACTTCCAAAAA-TTCCATTTTGACCC-CG
* *
93064 -AA-TGTCCAAAAACTCCATTTTCGACCTCG
1 AAACT-TCCAAAAATTCCATTTT-GACCCCG
*
93093 AAA-TTCTC-AAAATTACCGTTTT-ACCCTCG
1 AAACTTC-CAAAAATT-CCATTTTGACCC-CG
* * *
93122 -AA-TGTCTAAAAATTCCATTTTTAACCTCG
1 AAACT-TCCAAAAATTCCA-TTTTGACCCCG
** *
93151 AATTTTCCCAAAATTACCATTTT-ACCCTCG
1 AAACTTCCAAAAATT-CCATTTTGACCC-CG
93181 AGAA--TCC-AAAATTACCATTTTG-CCCCG
1 A-AACTTCCAAAAATT-CCATTTTGACCCCG
93208 TTGAGTATCC
Statistics
Matches: 329, Mismatches: 50, Indels: 62
0.75 0.11 0.14
Matches are distributed among these distances:
27 2 0.01
28 57 0.17
29 130 0.40
30 131 0.40
31 9 0.03
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTGACCCCG
Found at i:92863 original size:59 final size:58
Alignment explanation
Indices: 92770--93207 Score: 348
Period size: 59 Copynumber: 7.5 Consensus size: 58
92760 TATTGCCCTA
*
92770 AACTGTCCAAAAATTCCATTTTTACCCTCG-AACTTCCAAAAATTCCATTTTTACCCTCG
1 AACT-TCCAAAAATTCCATTTTGACCC-CGAAACTTCCAAAAATTCCATTTTTACCCTCG
** *
92829 AACTTTTAAAAATTCCAATTTTGACCCCGAAACTTCCAAAAATTCCATTTTTGA-CCTTG
1 AACTTCCAAAAATTCC-ATTTTGACCCCGAAACTTCCAAAAATTCCATTTTT-ACCCTCG
* * **
92888 AAACTTCCAAAAAATCCATTTT-ACCGCCG-AACTTCCAAAAATTCAATTTTTAACCC-AA
1 -AACTTCCAAAAATTCCATTTTGACC-CCGAAACTTCCAAAAATTCCATTTTT-ACCCTCG
* * * *
92946 AACTTCCAAAAATTTCATTGTTGACTCCGAAACTTCCAAAAGTTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATT-TTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCG
* * * ** *
93005 AACCTCTAAAATTTCCATTTTTGACCCCGAAACTTTTAAAAATTTCCCTTTTT-CCCTCG
1 AACTTCCAAAAATTCCA-TTTTGACCCCGAAACTTCCAAAAA-TTCCATTTTTACCCTCG
* * *
93064 AA-TGTCCAAAAACTCCATTTTCGACCTCGAAA-TTCTC-AAAATTACC-GTTTTACCCTCG
1 AACT-TCCAAAAATTCCATTTT-GACCCCGAAACTTC-CAAAAATT-CCATTTTTACCCTCG
* * * ** *
93122 AA-TGTCTAAAAATTCCATTTTTAACCTCGAATTTTCCCAAAATTACCA-TTTTACCCTCG
1 AACT-TCCAAAAATTCCA-TTTTGACCCCGAAACTTCCAAAAATT-CCATTTTTACCCTCG
*
93181 AGA-ATCC-AAAATTACCATTTTG-CCCCG
1 A-ACTTCCAAAAATT-CCATTTTGACCCCG
93208 TTGAGTATCC
Statistics
Matches: 312, Mismatches: 44, Indels: 48
0.77 0.11 0.12
Matches are distributed among these distances:
57 27 0.09
58 98 0.31
59 161 0.52
60 26 0.08
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.33
Consensus pattern (58 bp):
AACTTCCAAAAATTCCATTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:96121 original size:52 final size:53
Alignment explanation
Indices: 96059--96166 Score: 209
Period size: 53 Copynumber: 2.1 Consensus size: 53
96049 CGAGGCATCG
96059 TAAGAGAATCAAATCAGGT-AAAAAAAAACAATAACTCTTAATCTCATTCCTA
1 TAAGAGAATCAAATCAGGTAAAAAAAAAACAATAACTCTTAATCTCATTCCTA
96111 TAAGAGAATCAAATCAGGTAAAAAAAAAACAATAACTCTTAATCTCATTCCTA
1 TAAGAGAATCAAATCAGGTAAAAAAAAAACAATAACTCTTAATCTCATTCCTA
96164 TAA
1 TAA
96167 ATTTGGTACT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 19 0.35
53 36 0.65
ACGTcount: A:0.51, C:0.17, G:0.07, T:0.25
Consensus pattern (53 bp):
TAAGAGAATCAAATCAGGTAAAAAAAAAACAATAACTCTTAATCTCATTCCTA
Found at i:98224 original size:30 final size:31
Alignment explanation
Indices: 98157--98228 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
98147 AAGCCAAGAG
* *
98157 GACTGTTTTGTCACTTTTCCATAACTTTAGT
1 GACTGTTTTGTCACTTTTCCATAACTTGAGC
*
98188 GACTGTTTTGTCACATTTT-CA-AAGTTGAGC
1 GACTGTTTTGTCAC-TTTTCCATAACTTGAGC
98218 GACTGTTTTGT
1 GACTGTTTTGT
98229 TAAATGTAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 17 0.46
31 16 0.43
32 4 0.11
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.46
Consensus pattern (31 bp):
GACTGTTTTGTCACTTTTCCATAACTTGAGC
Found at i:98491 original size:8 final size:7
Alignment explanation
Indices: 98463--98488 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
98453 AAATTACATT
98463 AAAAATA
1 AAAAATA
98470 AAAAATA
1 AAAAATA
98477 AAAAATA
1 AAAAATA
98484 AAAAA
1 AAAAA
98489 ATACGCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:98870 original size:30 final size:30
Alignment explanation
Indices: 98836--98897 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
98826 ATTCATTACA
* *
98836 AAAATTTTGGGTAATTTACCAAAATAACCC
1 AAAATTTTGGATAATTTACAAAAATAACCC
* * *
98866 AAAATTTTTGATTATTTACAAAAATGACCC
1 AAAATTTTGGATAATTTACAAAAATAACCC
98896 AA
1 AA
98898 GTTCAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (30 bp):
AAAATTTTGGATAATTTACAAAAATAACCC
Found at i:99314 original size:17 final size:17
Alignment explanation
Indices: 99294--99348 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
99284 AAAAAATAAT
99294 AATTAGAATATACAGGA
1 AATTAGAATATACAGGA
*
99311 AATTAGAA-A-A-A-AA
1 AATTAGAATATACAGGA
*
99324 AATTAAAATATACAGGA
1 AATTAGAATATACAGGA
99341 AATTAGAA
1 AATTAGAA
99349 ATTAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
13 8 0.27
14 2 0.07
15 2 0.07
16 2 0.07
17 16 0.53
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.22
Consensus pattern (17 bp):
AATTAGAATATACAGGA
Found at i:99334 original size:30 final size:30
Alignment explanation
Indices: 99285--99363 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
99275 TAAATTTTAA
*
99285 AAAAATAATAATTAGAATATACAGGAAATTAG
1 AAAAA-AA-AATTAAAATATACAGGAAATTAG
99317 AAAAAAAAATTAAAATATACAGGAAATTAG
1 AAAAAAAAATTAAAATATACAGGAAATTAG
** *
99347 AAATTAAATTTAAAATA
1 AAAAAAAAATTAAAATA
99364 AAAACGAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 36 0.84
31 2 0.05
32 5 0.12
ACGTcount: A:0.63, C:0.03, G:0.09, T:0.25
Consensus pattern (30 bp):
AAAAAAAAATTAAAATATACAGGAAATTAG
Found at i:99373 original size:30 final size:30
Alignment explanation
Indices: 99309--99391 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 30
99299 GAATATACAG
** * * * *
99309 GAAATTAGAAAAAAAAATTAAAATATACAG
1 GAAATTAGAAATTAAATTTAAAATAAAAAC
99339 GAAATTAGAAATTAAATTTAAAATAAAAAC
1 GAAATTAGAAATTAAATTTAAAATAAAAAC
*
99369 GAAATTACAAATTAAATTTAAAA
1 GAAATTAGAAATTAAATTTAAAA
99392 AGTAAACGGA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.25
Consensus pattern (30 bp):
GAAATTAGAAATTAAATTTAAAATAAAAAC
Found at i:99896 original size:24 final size:24
Alignment explanation
Indices: 99869--99927 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
99859 TTGGTCCTGA
**
99869 GGCTCGTAATCGGGCTCGTCCGCG
1 GGCTCGTAATCGGGCTAATCCGCG
* * *
99893 GGCTCGTCATTGGGCTAATCCTCG
1 GGCTCGTAATCGGGCTAATCCGCG
*
99917 GGCTCGAAATC
1 GGCTCGTAATC
99928 TGAACCGGGG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.14, C:0.31, G:0.32, T:0.24
Consensus pattern (24 bp):
GGCTCGTAATCGGGCTAATCCGCG
Found at i:101135 original size:26 final size:26
Alignment explanation
Indices: 101099--101150 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
101089 GGATTTTACG
101099 AGAGATTTCTAAAGTTTTCGTATAGC
1 AGAGATTTCTAAAGTTTTCGTATAGC
101125 AGAGATTTCTAAAGTTTTCGTATAGC
1 AGAGATTTCTAAAGTTTTCGTATAGC
101151 CATGTAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (26 bp):
AGAGATTTCTAAAGTTTTCGTATAGC
Found at i:101685 original size:22 final size:21
Alignment explanation
Indices: 101637--101696 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
101627 CGAGGTGTTG
*
101637 GTGAGCTGGAAT-TTCGGTTTT
1 GTGAGCTGGAATATT-GGTTTA
101658 GCTGAGCTGGAATATTGGTTTAA
1 G-TGAGCTGGAATATTGGTTT-A
*
101681 GTGAGGTGGAA-ATTGG
1 GTGAGCTGGAATATTGG
101697 GTGGTCCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 6 0.18
22 25 0.74
23 3 0.09
ACGTcount: A:0.22, C:0.07, G:0.37, T:0.35
Consensus pattern (21 bp):
GTGAGCTGGAATATTGGTTTA
Found at i:101891 original size:86 final size:86
Alignment explanation
Indices: 101789--102131 Score: 532
Period size: 86 Copynumber: 4.0 Consensus size: 86
101779 ATTTAAAATA
101789 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGTA
* *
101854 TTGTTAAATCAACACTTTATT
66 TTGTCAAATCAACACATTATT
* * * *
101875 TGATAAAAATTAT-A-AT-ATAATAATAATTTATACTTTAAATA-TGAAAATTTGATAAATAATG
1 TGATAAAAATTGTAATATAATAATAATAATTTTTA-TTTAAATATTTAAAA-TTAATAAATAATG
* *
101936 TATTGTCAAATTAACACAATATTT
64 TATTGTCAAATCAACACATTA-TT
*
101960 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATATA
1 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGTA
*
102025 TTGTCAAATCAACATATTATT
66 TTGTCAAATCAACACATTATT
*
102046 TAATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGTA
102111 TTGTCAAATCAACACATTATT
66 TTGTCAAATCAACACATTATT
Statistics
Matches: 231, Mismatches: 19, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
83 20 0.09
84 39 0.17
85 15 0.06
86 98 0.42
87 39 0.17
88 20 0.09
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (86 bp):
TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGTA
TTGTCAAATCAACACATTATT
Done.