Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004700.1 Hibiscus syriacus cultivar Beakdansim tig00010560_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: 119539
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:22045 original size:12 final size:13
Alignment explanation
Indices: 22025--22053 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
22015 TTCGTGCGAT
22025 TTTTCGTTATAAA
1 TTTTCGTTATAAA
22038 TTTT-GTTATAAA
1 TTTTCGTTATAAA
22050 TTTT
1 TTTT
22054 TTTTATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (13 bp):
TTTTCGTTATAAA
Found at i:25441 original size:35 final size:34
Alignment explanation
Indices: 25356--25442 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
25346 AATATAATTT
*
25356 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
25390 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
25428 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
25443 AATGAAATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:27790 original size:10 final size:10
Alignment explanation
Indices: 27771--27808 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
27761 CTTAAATAGA
*
27771 GAGAGTATTT
1 GAGAGAATTT
27781 GAGAGAATTT
1 GAGAGAATTT
27791 GAGAGAATTT
1 GAGAGAATTT
27801 GAGAGAAT
1 GAGAGAAT
27809 ATGGTGTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:29639 original size:24 final size:24
Alignment explanation
Indices: 29607--29655 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
29597 GTGTACTATG
29607 TATGTCTAAAAATTTATATAAGTC
1 TATGTCTAAAAATTTATATAAGTC
*
29631 TATGTCTAAAAATTTATGTAAGTC
1 TATGTCTAAAAATTTATATAAGTC
29655 T
1 T
29656 TACATTTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (24 bp):
TATGTCTAAAAATTTATATAAGTC
Found at i:33441 original size:24 final size:24
Alignment explanation
Indices: 33391--33459 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
33381 TTTATTATAA
* * * *
33391 GTATCAATTTCAAT-AAAAATTAT
1 GTATTAATTTAAATAAAAAAATAG
33414 GTATTAATTTAAATAAAAAAATAG
1 GTATTAATTTAAATAAAAAAATAG
**
33438 GTATTGGTTTAAATAAAGAAAA
1 GTATTAATTTAAATAAA-AAAA
33460 AACTCATACG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.32
24 22 0.58
25 4 0.11
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.35
Consensus pattern (24 bp):
GTATTAATTTAAATAAAAAAATAG
Found at i:33515 original size:2 final size:2
Alignment explanation
Indices: 33508--33533 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33498 AAGTTACATC
33508 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
33534 GTTGTCACAT
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:34595 original size:31 final size:31
Alignment explanation
Indices: 34526--34595 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 31
34516 TTTAATATGG
* *
34526 ATTTCTAAAAATTTTGAAGGAGTTAAATTAA
1 ATTTTTAAAAATTTTGAAAGAGTTAAATTAA
34557 ATGTTTTAAAAATTTT-AAAGA-TCTAAATTATA
1 AT-TTTTAAAAATTTTGAAAGAGT-TAAATTA-A
34589 ATTTTTA
1 ATTTTTA
34596 TATTTTCGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
30 1 0.03
31 18 0.53
32 15 0.44
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (31 bp):
ATTTTTAAAAATTTTGAAAGAGTTAAATTAA
Found at i:35477 original size:22 final size:22
Alignment explanation
Indices: 35438--35483 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
35428 AGATAAAATT
* *
35438 AATATACTTAAAAGAATTTAAA
1 AATATAATTAAAAGAATTAAAA
* *
35460 AATATAATTAATATAATTAAAA
1 AATATAATTAAAAGAATTAAAA
35482 AA
1 AA
35484 ATTGATTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AATATAATTAAAAGAATTAAAA
Found at i:36897 original size:78 final size:78
Alignment explanation
Indices: 36768--36925 Score: 307
Period size: 78 Copynumber: 2.0 Consensus size: 78
36758 ACCGTCCAGC
36768 TCAGTTGGTAGAACGCAAGGTTCTTAACATTGAGGTTGTGGGATCGAGTTTTATAAAGGGCATTT
1 TCAGTTGGTAGAACGCAAGGTTCTTAACATTGAGGTTGTGGGATCGAGTTTTATAAAGGGCATTT
36833 TATAATTCGGATG
66 TATAATTCGGATG
*
36846 TCAGTTGGTAGAACGCAAGGTTCTTAACCTTGAGGTTGTGGGATCGAGTTTTATAAAGGGCATTT
1 TCAGTTGGTAGAACGCAAGGTTCTTAACATTGAGGTTGTGGGATCGAGTTTTATAAAGGGCATTT
36911 TATAATTCGGATG
66 TATAATTCGGATG
36924 TC
1 TC
36926 TTCCACGTAA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.35
Consensus pattern (78 bp):
TCAGTTGGTAGAACGCAAGGTTCTTAACATTGAGGTTGTGGGATCGAGTTTTATAAAGGGCATTT
TATAATTCGGATG
Found at i:38263 original size:20 final size:20
Alignment explanation
Indices: 38238--38278 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
38228 GACCGACAAC
*
38238 GATTAACCTGAAAATCTAAA
1 GATTAACCCGAAAATCTAAA
38258 GATTAACCCGAAAATCTAAA
1 GATTAACCCGAAAATCTAAA
38278 G
1 G
38279 GTTGATCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (20 bp):
GATTAACCCGAAAATCTAAA
Found at i:38388 original size:32 final size:32
Alignment explanation
Indices: 38338--38426 Score: 142
Period size: 32 Copynumber: 2.8 Consensus size: 32
38328 GACCAAAATC
*
38338 AAAACCAACCAATCCAATATTAACCTAACCCG
1 AAAACCAACTAATCCAATATTAACCTAACCCG
* *
38370 AAAATCAACTAATTCAATATTAACCTAACCCG
1 AAAACCAACTAATCCAATATTAACCTAACCCG
*
38402 AAAACCAACTAATCCAATTTTAACC
1 AAAACCAACTAATCCAATATTAACC
38427 CGAACTAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.21
Consensus pattern (32 bp):
AAAACCAACTAATCCAATATTAACCTAACCCG
Found at i:42120 original size:15 final size:16
Alignment explanation
Indices: 42094--42124 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
42084 AATAGCTCCA
42094 TATTATTAGAAGTTCC
1 TATTATTAGAAGTTCC
42110 TATTA-TAGAAGTTCC
1 TATTATTAGAAGTTCC
42125 CTCGATCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (16 bp):
TATTATTAGAAGTTCC
Found at i:50935 original size:4 final size:4
Alignment explanation
Indices: 50926--50952 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
50916 CAATGCATGT
50926 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
50953 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:52197 original size:9 final size:9
Alignment explanation
Indices: 52183--52208 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
52173 TCCTGTCCTC
52183 GCTTACTCT
1 GCTTACTCT
52192 GCTTACTCT
1 GCTTACTCT
52201 GCTTACTC
1 GCTTACTC
52209 CTTGTATACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.12, T:0.42
Consensus pattern (9 bp):
GCTTACTCT
Found at i:52690 original size:24 final size:24
Alignment explanation
Indices: 52663--52708 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
52653 ACATATATTA
*
52663 CACCAAAGTGCCGCATAGAAATTG
1 CACCAAAGTGCCACATAGAAATTG
*
52687 CACCGAAGTGCCACATAGAAAT
1 CACCAAAGTGCCACATAGAAAT
52709 GTCCCGAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (24 bp):
CACCAAAGTGCCACATAGAAATTG
Found at i:52723 original size:23 final size:23
Alignment explanation
Indices: 52676--52798 Score: 124
Period size: 23 Copynumber: 5.3 Consensus size: 23
52666 CAAAGTGCCG
52676 CATAGAAAT-TGCACCGAAGTG-CCA
1 CATAGAAATGT-C-CCGAAG-GACCA
52700 CATAGAAATGTCCCGAAGGACCA
1 CATAGAAATGTCCCGAAGGACCA
* *
52723 CATAGATATGTCCCGAAGGACCG
1 CATAGAAATGTCCCGAAGGACCA
* * *
52746 CGTAGAATTGTCCCTAAGGACCA
1 CATAGAAATGTCCCGAAGGACCA
* * * *
52769 CGTAGAATTGTCCCAAAGGACCG
1 CATAGAAATGTCCCGAAGGACCA
52792 CATAGAA
1 CATAGAA
52799 CCCTCGACTC
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
22 1 0.01
23 75 0.86
24 10 0.11
25 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (23 bp):
CATAGAAATGTCCCGAAGGACCA
Found at i:54060 original size:15 final size:15
Alignment explanation
Indices: 54040--54113 Score: 53
Period size: 15 Copynumber: 4.9 Consensus size: 15
54030 TTCACGTTGG
54040 ACATTTTCACTTAAC
1 ACATTTTCACTTAAC
* * *
54055 ATATTTTCACATAAA
1 ACATTTTCACTTAAC
* *
54070 ACA-GTTCACATATATC
1 ACATTTTCAC-T-TAAC
54086 ACATTTTCACTATAAC
1 ACATTTTCACT-TAAC
*
54102 A-TTTTTCACTTA
1 ACATTTTCACTTA
54114 TCATTTTTGT
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
14 7 0.16
15 22 0.49
16 11 0.24
17 5 0.11
ACGTcount: A:0.36, C:0.22, G:0.01, T:0.41
Consensus pattern (15 bp):
ACATTTTCACTTAAC
Found at i:54121 original size:15 final size:15
Alignment explanation
Indices: 54043--54121 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 15
54033 ACGTTGGACA
54043 TTTTCACT-TAACAT
1 TTTTCACTATAACAT
*
54057 ATTTTCACATAAAACA-
1 -TTTTCAC-TATAACAT
*
54073 -GTTCACATATATCACA-
1 TTTTCAC-TATA--ACAT
54089 TTTTCACTATAACAT
1 TTTTCACTATAACAT
*
54104 TTTTCACT-TATCAT
1 TTTTCACTATAACAT
54118 TTTT
1 TTTT
54122 GTTCCGTAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
14 21 0.40
15 15 0.28
16 8 0.15
17 9 0.17
ACGTcount: A:0.33, C:0.20, G:0.01, T:0.46
Consensus pattern (15 bp):
TTTTCACTATAACAT
Found at i:55702 original size:31 final size:31
Alignment explanation
Indices: 55653--55775 Score: 88
Period size: 31 Copynumber: 3.8 Consensus size: 31
55643 GTAGTTTACC
*
55653 CTAAATAATA-ATCGAGTGAACAAAACATAAA
1 CTAAATAATATAT-AAGTGAACAAAACATAAA
* * * **
55684 GTAGATAATATATAAGTGACCAAATACGTAGTTTACC
1 CTAAATAATATATAAGTGAACAAA-AC--A---TAAA
55721 CTAAATAATA-ATCAAGTGAACAAAACATAAA
1 CTAAATAATATAT-AAGTGAACAAAACATAAA
* *
55752 TTAAATAATATATAAGTGACCAAA
1 CTAAATAATATATAAGTGAACAAA
55776 TAGGTAGTTT
Statistics
Matches: 70, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
31 38 0.54
32 6 0.09
34 2 0.03
36 4 0.06
37 20 0.29
ACGTcount: A:0.53, C:0.12, G:0.11, T:0.24
Consensus pattern (31 bp):
CTAAATAATATATAAGTGAACAAAACATAAA
Found at i:55739 original size:68 final size:68
Alignment explanation
Indices: 55629--55793 Score: 294
Period size: 68 Copynumber: 2.4 Consensus size: 68
55619 GTTACAATAC
* *
55629 AAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGTGAACAAAACATAAAGTAGATAATA
1 AAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCAAGTGAACAAAACATAAAGTAAATAATA
55694 TAT
66 TAT
* *
55697 AAGTGACCAAATACGTAGTTTACCCTAAATAATAATCAAGTGAACAAAACATAAATTAAATAATA
1 AAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCAAGTGAACAAAACATAAAGTAAATAATA
55762 TAT
66 TAT
55765 AAGTGACCAAATAGGTAGTTTACCCTAAA
1 AAGTGACCAAATAGGTAGTTTACCCTAAA
55794 AAAATCCCTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 92 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.25
Consensus pattern (68 bp):
AAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCAAGTGAACAAAACATAAAGTAAATAATA
TAT
Found at i:58291 original size:29 final size:29
Alignment explanation
Indices: 58233--58310 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
58223 GGATCCCAAA
* * *
58233 CAGAAACAACACAAGAATATGATCTCATG
1 CAGAAACAAGACAGGGATATGATCTCATG
* * *
58262 CATAAATAAGACGGGGATATGATC-CTATG
1 CAGAAACAAGACAGGGATATGATCTC-ATG
*
58291 CAGAAACAGGACAGGGATAT
1 CAGAAACAAGACAGGGATAT
58311 TGTCCTCCGT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
28 1 0.03
29 37 0.97
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.18
Consensus pattern (29 bp):
CAGAAACAAGACAGGGATATGATCTCATG
Found at i:59653 original size:10 final size:10
Alignment explanation
Indices: 59638--59708 Score: 52
Period size: 10 Copynumber: 6.7 Consensus size: 10
59628 ACACGCTGGG
59638 CATCCGAGAC
1 CATCCGAGAC
59648 CATCCGACCGAGGC
1 CATCCGA--GA--C
* *
59662 CATTCGAGAG
1 CATCCGAGAC
**
59672 CATCCGAGGT
1 CATCCGAGAC
*
59682 CATCCGAGAG
1 CATCCGAGAC
*
59692 CATCCGAGGC
1 CATCCGAGAC
59702 CATCCGA
1 CATCCGA
59709 TCGAGGCCAT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
10 37 0.77
12 4 0.08
14 7 0.15
ACGTcount: A:0.25, C:0.35, G:0.27, T:0.13
Consensus pattern (10 bp):
CATCCGAGAC
Found at i:59680 original size:20 final size:20
Alignment explanation
Indices: 59655--59708 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
59645 GACCATCCGA
*
59655 CCGAGGCCATTCGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
*
59675 CCGAGGTCATCCGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
59695 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
59709 TCGAGGCCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.24, C:0.33, G:0.30, T:0.13
Consensus pattern (20 bp):
CCGAGGCCATCCGAGAGCAT
Found at i:59737 original size:23 final size:23
Alignment explanation
Indices: 59710--59760 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
59700 GCCATCCGAT
*
59710 CGAGGCCATCCAAACGAGCTATG
1 CGAGGCCAACCAAACGAGCTATG
* * *
59733 CGAGGGCAACCGAGCGAGCTATG
1 CGAGGCCAACCAAACGAGCTATG
59756 CGAGG
1 CGAGG
59761 GAATCCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.27, G:0.35, T:0.10
Consensus pattern (23 bp):
CGAGGCCAACCAAACGAGCTATG
Found at i:59761 original size:23 final size:23
Alignment explanation
Indices: 59724--59769 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
59714 GCCATCCAAA
59724 CGAGCTATGCGAGGGCAA-CCGAG
1 CGAGCTATGCGAGGG-AATCCGAG
59747 CGAGCTATGCGAGGGAATCCGAG
1 CGAGCTATGCGAGGGAATCCGAG
59770 GGAAGCCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.26, C:0.24, G:0.39, T:0.11
Consensus pattern (23 bp):
CGAGCTATGCGAGGGAATCCGAG
Found at i:59820 original size:29 final size:29
Alignment explanation
Indices: 59787--59842 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
59777 GAGCGAGGGC
*
59787 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
*
59816 AGGTCGCCCGGAGGGCATGGTGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
59843 TGTGTTGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.20, C:0.29, G:0.38, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:59943 original size:29 final size:29
Alignment explanation
Indices: 59901--59957 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
59891 GAGCAAGGGT
*
59901 AGGTCGCCCGGAGTGTATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
* *
59930 AGGTCGCCTGGAGTGCATGGTGACCTAC
1 AGGTCGCCCGGAGTGCATGGCGACCTAC
59958 GGCAAACACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.19, C:0.26, G:0.35, T:0.19
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:60480 original size:33 final size:32
Alignment explanation
Indices: 60419--60479 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
60409 ATTCATTTTT
*
60419 TTAAAATTAATAAAATTGCAATAAAAAAAGAA
1 TTAAAATGAATAAAATTGCAATAAAAAAAGAA
60451 TTAAAAGTGAATAAAATT-CAATAAAAAAA
1 TTAAAA-TGAATAAAATTGCAATAAAAAAA
60480 ATATCACCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.25
Consensus pattern (32 bp):
TTAAAATGAATAAAATTGCAATAAAAAAAGAA
Found at i:61116 original size:282 final size:276
Alignment explanation
Indices: 60787--61352 Score: 942
Period size: 282 Copynumber: 2.0 Consensus size: 276
60777 AGAATTTTGG
60787 TTATAAAACTTTTATAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGA
1 TTATAAAACTTTTATAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGA
* *
60852 TTATACGTATTGTGTAATTTCATACAAAAATC-AAATAATTTTAT-TAAAATGAATAAACATTAT
66 TTATACGTATTATGTAATTTCATACAAAAATCAAAATAATTTTATGAAAAATGAA-AAACATTAT
*
60915 TAACTGTTGTTAAAAATAATAATT-ATGAATAATAATTCATTTGATCTCTCAATTGTAATTAAAA
130 TAACTGTTGTTAAAAATAATAATTAATGAATAATAATTCATTTGATCCCTCAATTGTAATTAAAA
*
60979 GTTTATTTTAATATTTTAATATTTTTAAACAATTAATTTTAAAAGTCAATAA-TTTTTTCAAAAA
195 ----A-ATT-AT-TTTT-ATATTTTTAAACAATTAATTTTAAAAGTCAATAATTTTTTTCAAAAA
* * *
61043 TATATGAAATTTATATTTTTTTAAA
252 TATATGAAATTCAAAATTTTTTAAA
61068 TTATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAG
1 TTATAAAACTTTTAT-AAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAG
*
61133 ATTATACGTATTATGTAATTTCATGCAAAAATCAAAATAATTTTATGAAAAATGAAAAACATTAT
65 ATTATACGTATTATGTAATTTCATACAAAAATCAAAATAATTTTATGAAAAATGAAAAACATTAT
61198 TAACTGTTGTTAAAAATAATAATTAATGAATAATAATTCATTTGATCCCTCAATTGTAATTAAAA
130 TAACTGTTGTTAAAAATAATAATTAATGAATAATAATTCATTTGATCCCTCAATTGTAATTAAAA
61263 AATTATTTTTATATTTTTAAACAATTAATTTTAAAAGTCAATAATTTTTTTCAAAAATATATGAA
195 AATTATTTTTATATTTTTAAACAATTAATTTTAAAAGTCAATAATTTTTTTCAAAAATATATGAA
61328 ATTCAAAATTTTTTAAA
260 ATTCAAAATTTTTTAAA
61345 TTATAAAA
1 TTATAAAA
61353 TATTTATTAT
Statistics
Matches: 272, Mismatches: 8, Indels: 14
0.93 0.03 0.05
Matches are distributed among these distances:
276 34 0.12
277 46 0.17
278 2 0.01
279 2 0.01
280 1 0.00
281 15 0.06
282 80 0.29
283 45 0.17
284 47 0.17
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (276 bp):
TTATAAAACTTTTATAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGA
TTATACGTATTATGTAATTTCATACAAAAATCAAAATAATTTTATGAAAAATGAAAAACATTATT
AACTGTTGTTAAAAATAATAATTAATGAATAATAATTCATTTGATCCCTCAATTGTAATTAAAAA
ATTATTTTTATATTTTTAAACAATTAATTTTAAAAGTCAATAATTTTTTTCAAAAATATATGAAA
TTCAAAATTTTTTAAA
Found at i:61185 original size:21 final size:22
Alignment explanation
Indices: 61148--61190 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
61138 ACGTATTATG
61148 TAATTTCATGCAAAAATCAAAA
1 TAATTTCATGCAAAAATCAAAA
* *
61170 TAATTTTATG-AAAAATGAAAA
1 TAATTTCATGCAAAAATCAAAA
61191 ACATTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (22 bp):
TAATTTCATGCAAAAATCAAAA
Found at i:61191 original size:22 final size:22
Alignment explanation
Indices: 61148--61191 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
61138 ACGTATTATG
*
61148 TAATTTCATGCAAAAATCAAAA
1 TAATTTCATGCAAAAATAAAAA
*
61170 TAATTTTATG-AAAAATGAAAAA
1 TAATTTCATGCAAAAAT-AAAAA
61192 CATTATTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (22 bp):
TAATTTCATGCAAAAATAAAAA
Found at i:61966 original size:65 final size:63
Alignment explanation
Indices: 61897--62056 Score: 196
Period size: 65 Copynumber: 2.5 Consensus size: 63
61887 AATTAAATTG
* * *
61897 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATACACTCAGGATATTT-TG-
61961 A
63 A
** * *
61962 AACATCGAATGCATTTGATGCATCGATGCACCAACCATGCATTGATACACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATACACTCAGGATATTTTGA
* *
62026 AACATCAAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
62057 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 1 0.01
64 29 0.35
65 49 0.58
66 5 0.06
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATACACTCAGGATATTTTGA
Found at i:63397 original size:19 final size:20
Alignment explanation
Indices: 63373--63420 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
63363 AACGATTTTC
*
63373 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
*
63392 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
63412 TTTTGAAAA
1 TTTTGAAAA
63421 AGGATTTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:64749 original size:29 final size:30
Alignment explanation
Indices: 64679--64738 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
64669 CAATTTAAGG
*
64679 CAAAATGATTTTTGGACTTGAATTGAATTTA
1 CAAAATG-TTTTTGGACTTGAATTAAATTTA
64710 CAAAATGTTTTTGGACTT-AATTAAATTTA
1 CAAAATGTTTTTGGACTTGAATTAAATTTA
64739 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 11 0.39
31 7 0.25
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTAAATTTA
Found at i:64942 original size:21 final size:21
Alignment explanation
Indices: 64916--64979 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
64906 AATTCAATTA
64916 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
* **
64937 GTGCATTGATGCATC-CTGCT
1 GTGCATCGATGCATCAAGGCT
*
64957 GTGCATCCATGCA-CGAAGGCT
1 GTGCATCGATGCATC-AAGGCT
64978 GT
1 GT
64980 AACGGCTAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
19 1 0.03
20 14 0.41
21 19 0.56
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (21 bp):
GTGCATCGATGCATCAAGGCT
Found at i:65040 original size:20 final size:20
Alignment explanation
Indices: 65015--65065 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
65005 GAAGGGGTAT
65015 CGATGCACCATATAGTGCAC
1 CGATGCACCATATAGTGCAC
65035 CGATGCACCATATAGTGCAC
1 CGATGCACCATATAGTGCAC
65055 CGATGCACCAT
1 CGATGCACCAT
65066 GTTATGGGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (20 bp):
CGATGCACCATATAGTGCAC
Found at i:66806 original size:21 final size:21
Alignment explanation
Indices: 66780--66819 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
66770 GAGAAATTAT
66780 TTTTAAAATAT-AAAAATGATA
1 TTTTAAAAT-TGAAAAATGATA
66801 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
66820 AAATAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATA
Found at i:71425 original size:21 final size:21
Alignment explanation
Indices: 71399--71443 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
71389 GATTTCTGGG
* *
71399 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
71420 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
71441 CAA
1 CAA
71444 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:72159 original size:31 final size:31
Alignment explanation
Indices: 72121--72274 Score: 247
Period size: 31 Copynumber: 5.0 Consensus size: 31
72111 GGGTCGAGGG
*
72121 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
72152 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
72183 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
72214 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
72245 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
72275 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:75305 original size:21 final size:21
Alignment explanation
Indices: 75272--75312 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
75262 TTCTGGGCAA
* *
75272 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
75293 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
75313 ACGAACAAGA
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:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:76027 original size:31 final size:31
Alignment explanation
Indices: 75989--76142 Score: 247
Period size: 31 Copynumber: 5.0 Consensus size: 31
75979 GGGTCGAGGG
*
75989 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
76020 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
76051 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
76082 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
76113 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
76143 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:79017 original size:2 final size:2
Alignment explanation
Indices: 79012--79037 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
79002 ACACACACAC
79012 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
79038 TTAATCAATT
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):
AT
Found at i:79714 original size:64 final size:66
Alignment explanation
Indices: 79558--79717 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 66
79548 AATTAAATTG
* * *
79558 AACATCGAATGCATTTCATGCATTGATGCA-CATACCATGCACCGATGCACTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGATTTTATGA
79622 A
66 A
* * * *
79623 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGAT-TTTATG
79686 -A
65 AA
*
79687 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
79718 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 31 0.36
65 49 0.58
66 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (66 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGATTTTATGA
A
Found at i:84061 original size:16 final size:16
Alignment explanation
Indices: 84040--84071 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
84030 AAGTTTTCTC
84040 TTCTCTTATGAATGTT
1 TTCTCTTATGAATGTT
*
84056 TTCTCTTATGTATGTT
1 TTCTCTTATGAATGTT
84072 GCATGTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.59
Consensus pattern (16 bp):
TTCTCTTATGAATGTT
Found at i:84671 original size:5 final size:5
Alignment explanation
Indices: 84657--84857 Score: 58
Period size: 5 Copynumber: 40.8 Consensus size: 5
84647 TAAAATAAAG
* *
84657 AAATG AAATA AAATA AAA-A ACATA AAACCCTA AAA-A ATAACTA -AATA
1 AAATA AAATA AAATA AAATA AAATA AAA---TA AAATA A-AA-TA AAATA
** *
84704 AAA-A AAATA AAAT- AAATA AAA-A ATAATA AAAGGCTA ATGTCA AAACA
1 AAATA AAATA AAATA AAATA AAATA A-AATA AAA---TA AAAT-A AAATA
* * * *
84751 AGAAGA AAAGA A-ATA A-ATA -AATA AAATA AAATA AAAT- -AATA GAATT
1 A-AATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
* *
84797 AAATA AAATA AAA-A ATAAGA TAAA-A ACATA AACA-A AAAT- AAA-A
1 AAATA AAATA AAATA A-AATA -AAATA AAATA AA-ATA AAATA AAATA
84840 AAATA AAA-A AAATA AAAT
1 AAATA AAATA AAATA AAAT
84858 GTATATATAT
Statistics
Matches: 151, Mismatches: 15, Indels: 60
0.67 0.07 0.27
Matches are distributed among these distances:
3 3 0.02
4 41 0.27
5 85 0.56
6 12 0.08
7 2 0.01
8 8 0.05
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:84709 original size:18 final size:17
Alignment explanation
Indices: 84688--84733 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
84678 ATAAAACCCT
*
84688 AAAAAATAACTAAATAA
1 AAAAAATAAATAAATAA
84705 AAAAAATAAAATAAATAA
1 AAAAAAT-AAATAAATAA
84723 AAAATAATAAA
1 AAAA-AATAAA
84734 AGGCTAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 7 0.27
18 16 0.62
19 3 0.12
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAAAATAAATAAATAA
Found at i:84715 original size:8 final size:8
Alignment explanation
Indices: 84648--84856 Score: 53
Period size: 8 Copynumber: 24.1 Consensus size: 8
84638 AACAATTACT
84648 AAAATAAA
1 AAAATAAA
*
84656 GAAATGAAA
1 AAAAT-AAA
84665 TAAAATAAA
1 -AAAATAAA
84674 AAACATAAA
1 AAA-ATAAA
***
84683 ACCCT-AA
1 AAAATAAA
*
84690 AAAATAAC
1 AAAATAAA
*
84698 TAAATAAAA
1 AAAAT-AAA
84707 AAAATAAA
1 AAAATAAA
84715 ATAAAT-AA
1 A-AAATAAA
*
84723 AAAATAAT
1 AAAATAAA
****
84731 AAAAGGCT
1 AAAATAAA
**
84739 AATGTCAAA
1 AAAAT-AAA
* * *
84748 ACAAGAAG
1 AAAATAAA
*
84756 AAAAGAAA
1 AAAATAAA
*
84764 TAAATAAA
1 AAAATAAA
84772 TAAAATAAAA
1 -AAAAT-AAA
84782 TAAAATAATA
1 -AAAATAA-A
* *
84792 GAATTAAA
1 AAAATAAA
84800 TAAAATAAAAA
1 -AAAAT--AAA
84811 ATAAGATAAA
1 A-AA-ATAAA
*
84821 AACATAAACA
1 AAAAT-AA-A
84831 AAAATAAA
1 AAAATAAA
84839 AAAATAAAA
1 AAAAT-AAA
84848 AAAATAAA
1 AAAATAAA
84856 A
1 A
84857 TGTATATATA
Statistics
Matches: 144, Mismatches: 38, Indels: 38
0.65 0.17 0.17
Matches are distributed among these distances:
7 8 0.06
8 55 0.38
9 50 0.35
10 24 0.17
11 5 0.03
12 2 0.01
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (8 bp):
AAAATAAA
Found at i:84784 original size:18 final size:18
Alignment explanation
Indices: 84761--84857 Score: 87
Period size: 18 Copynumber: 5.5 Consensus size: 18
84751 AGAAGAAAAG
84761 AAAT-AAATAAATAAAATA
1 AAATAAAATAAAT-AAATA
*
84779 AAATAAAAT-AATAGAATT
1 AAATAAAATAAATA-AATA
84797 AAATAAAATAAA-AAATA
1 AAATAAAATAAATAAATA
* * *
84814 AGATAAAA-ACATAAACAA
1 AAATAAAATAAATAAA-TA
*
84832 AAATAAAA-AAATAAAAA
1 AAATAAAATAAATAAATA
84849 AAATAAAAT
1 AAATAAAAT
84858 GTATATATAT
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
16 2 0.03
17 24 0.36
18 34 0.52
19 6 0.09
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (18 bp):
AAATAAAATAAATAAATA
Found at i:84787 original size:23 final size:23
Alignment explanation
Indices: 84761--84875 Score: 94
Period size: 23 Copynumber: 5.0 Consensus size: 23
84751 AGAAGAAAAG
84761 AAATAAATAAATAAAATAAAATA
1 AAATAAATAAATAAAATAAAATA
*
84784 AAAT-AATAGAATTAAATAAAATAAA
1 AAATAAATA-AATAAAATAAAAT--A
*
84809 AAATAAGATAAA-AACATAAACA-A
1 AAATAA-ATAAATAAAATAAA-ATA
*
84832 AAATAAAAAAATAAAA-AAAATA
1 AAATAAATAAATAAAATAAAATA
** * *
84854 AAATGTATATATATAATAAAAT
1 AAATAAATAAATAAAATAAAAT
84876 GTAGTATTAA
Statistics
Matches: 73, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
21 1 0.01
22 23 0.32
23 31 0.42
25 11 0.15
26 4 0.05
27 3 0.04
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.22
Consensus pattern (23 bp):
AAATAAATAAATAAAATAAAATA
Found at i:84873 original size:18 final size:17
Alignment explanation
Indices: 84849--84890 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
84839 AAAATAAAAA
84849 AAATAAAATGTA-TATAT
1 AAATAAAATGTAGTAT-T
84866 ATAATAAAATGTAGTATT
1 A-AATAAAATGTAGTATT
84884 AAATAAA
1 AAATAAA
84891 TATAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.30
18 13 0.57
19 3 0.13
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (17 bp):
AAATAAAATGTAGTATT
Found at i:88456 original size:145 final size:145
Alignment explanation
Indices: 88251--88604 Score: 381
Period size: 145 Copynumber: 2.4 Consensus size: 145
88241 TCTGGATTTG
* * * * * *
88251 TTTTCTCCGATTCACCACCGTCTACCGTCCGATCGTCATG-ATATTTCAGTATGCTGTTCGTGTT
1 TTTTCTCCGATCCACCGCCGTCCACCGTCTGATCGTCATGAAT-TTTCAGTATGTTGTTCGTG-A
* * * * * *
88315 TACATT-ACACAACTTTTCACTGTT-TGAAGTATTGATCGGAGATCCCGATTGCCGACAAAAGGC
64 TACATTCACACAACTCTTCACCGTTCAGAA-TATTAATCGGAGATCCCGATCGCAGACAAAAGGC
*
88378 TAAAAACCGTTCAACTTA
128 CAAAAACCGTTCAACTTA
* ** ** * *
88396 TTTTCTCTGATCTGCCGTTGTCCACCGTCTGATCGTCTTGAATTTTCAGTATGTTGTTCGTGATG
1 TTTTCTCCGATCCACCGCCGTCCACCGTCTGATCGTCATGAATTTTCAGTATGTTGTTCGTGATA
** * * * * * *
88461 GTTTCGCGCAACTCTTGACCGTTCAGAATGTTAATCGGAGATCCCGATCGCAGGCAAGAGGCCAA
66 CATTCACACAACTCTTCACCGTTCAGAATATTAATCGGAGATCCCGATCGCAGACAAAAGGCCAA
**
88526 AAACCGTTCGGCTTA
131 AAACCGTTCAACTTA
*
88541 TTTTCTCCGATCCACCGCCGTCCACCGTCTGATCGTCCTGAATTTTCAGTATGTTGTTCGTGAT
1 TTTTCTCCGATCCACCGCCGTCCACCGTCTGATCGTCATGAATTTTCAGTATGTTGTTCGTGAT
88605 GGTCTTGCGC
Statistics
Matches: 170, Mismatches: 36, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
144 3 0.02
145 162 0.95
146 5 0.03
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (145 bp):
TTTTCTCCGATCCACCGCCGTCCACCGTCTGATCGTCATGAATTTTCAGTATGTTGTTCGTGATA
CATTCACACAACTCTTCACCGTTCAGAATATTAATCGGAGATCCCGATCGCAGACAAAAGGCCAA
AAACCGTTCAACTTA
Found at i:88605 original size:145 final size:145
Alignment explanation
Indices: 88349--88654 Score: 436
Period size: 145 Copynumber: 2.1 Consensus size: 145
88339 TGAAGTATTG
* * * * ** *
88349 ATCGGAGATCCCGATTGCCGACAAAAGGCTAAAAACCGTTCAACTTATTTTCTCTGATCTGCCGT
1 ATCGGAGATCCCGATCGCAGACAAAAGGCCAAAAACCGTTCAACTTATTTTCTCCGATCCACCGC
* *
88414 TGTCCACCGTCTGATCGTCTTGAATTTTCAGTATGTTGTTCGTGATGGT-TTCGCGCAACTCTTG
66 CGTCCACCGTCTGATCGTCCTGAATTTTCAGTATGTTGTTCGTGATGGTCTT-GCGCAACTCTTG
*
88478 ACCGTTC-AGAATGTTA
130 ACCGTTCGA-AATGGTA
* * **
88494 ATCGGAGATCCCGATCGCAGGCAAGAGGCCAAAAACCGTTCGGCTTATTTTCTCCGATCCACCGC
1 ATCGGAGATCCCGATCGCAGACAAAAGGCCAAAAACCGTTCAACTTATTTTCTCCGATCCACCGC
*
88559 CGTCCACCGTCTGATCGTCCTGAATTTTCAGTATGTTGTTCGTGATGGTCTTGCGCAACTTTTGA
66 CGTCCACCGTCTGATCGTCCTGAATTTTCAGTATGTTGTTCGTGATGGTCTTGCGCAACTCTTGA
*
88624 CCGTTCGAAATGGTG
131 CCGTTCGAAATGGTA
88639 ATCGGAGATCCCGATC
1 ATCGGAGATCCCGATC
88655 AACGACGAGA
Statistics
Matches: 143, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
145 140 0.98
146 3 0.02
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (145 bp):
ATCGGAGATCCCGATCGCAGACAAAAGGCCAAAAACCGTTCAACTTATTTTCTCCGATCCACCGC
CGTCCACCGTCTGATCGTCCTGAATTTTCAGTATGTTGTTCGTGATGGTCTTGCGCAACTCTTGA
CCGTTCGAAATGGTA
Found at i:88977 original size:3 final size:3
Alignment explanation
Indices: 88964--89046 Score: 67
Period size: 3 Copynumber: 26.7 Consensus size: 3
88954 TGTGGTATAG
* * * * *
88964 TAA TAA TTAA TAA TAA TAT TAT TAG TAA TAA TTAA TAA TAA TAT TAT
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
* * *
89011 TAT TAA TAA TAA TAG TAA TAA TAA TATT TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA
89047 TTTTTTCGAC
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
3 60 0.88
4 8 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:88995 original size:25 final size:25
Alignment explanation
Indices: 88961--89030 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
88951 TTTTGTGGTA
88961 TAGTAATAATTAATAATAATATTAT
1 TAGTAATAATTAATAATAATATTAT
88986 TAGTAATAATTAATAATAATATTAT
1 TAGTAATAATTAATAATAATATTAT
* *
89011 TATTAATAA-TAATAGTAATA
1 TAGTAATAATTAATAATAATA
89031 ATAATATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
24 10 0.23
25 33 0.77
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
TAGTAATAATTAATAATAATATTAT
Found at i:89033 original size:40 final size:40
Alignment explanation
Indices: 88969--89048 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
88959 TATAGTAATA
* * *
88969 ATTAATAATAATATTATTAGTAATAAT-TAATAATAATATT
1 ATTAATAATAATAATAGTAATAATAATAT-ATAATAATATT
* *
89009 ATTATTAATAATAATAGTAATAATAATATTTAATAATATT
1 ATTAATAATAATAATAGTAATAATAATATATAATAATATT
89049 TTTTCGACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (40 bp):
ATTAATAATAATAATAGTAATAATAATATATAATAATATT
Found at i:89041 original size:25 final size:26
Alignment explanation
Indices: 88964--89046 Score: 100
Period size: 28 Copynumber: 3.2 Consensus size: 26
88954 TGTGGTATAG
*
88964 TAATAAT-TAATAATAATATTATTAG
1 TAATAATATAATAATAATATTATTAA
*
88989 TAATAATTAATAATAATATTATTATTAA
1 TAATAA-T-ATAATAATAATATTATTAA
89017 TAATAATAGTAATAATAATA-T-TTAA
1 TAATAATA-TAATAATAATATTATTAA
89042 TAATA
1 TAATA
89047 TTTTTTCGAC
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
25 15 0.29
26 3 0.06
27 11 0.22
28 22 0.43
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
TAATAATATAATAATAATATTATTAA
Found at i:92876 original size:19 final size:21
Alignment explanation
Indices: 92848--92894 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
92838 ATTATATAAA
*
92848 ATTTAGTTT-ATA-CAATCAT
1 ATTTATTTTAATATCAATCAT
*
92867 ATTTATTTTAATATCATTCAT
1 ATTTATTTTAATATCAATCAT
92888 -TTTATTT
1 ATTTATTT
92895 AGAATTTAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 8 0.33
20 10 0.42
21 6 0.25
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTTATTTTAATATCAATCAT
Found at i:94759 original size:22 final size:21
Alignment explanation
Indices: 94728--94778 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
94718 AAATATAAAA
* *
94728 TATAATAAATAATATTATTTAT
1 TATAAAAAATAATAATA-TTAT
94750 TATAAAAAATAATAATATTAT
1 TATAAAAAATAATAATATTAT
*
94771 TTTAAAAA
1 TATAAAAA
94779 TATTAGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATAAAAAATAATAATATTAT
Found at i:95073 original size:31 final size:28
Alignment explanation
Indices: 95035--95093 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
95025 AGTATTCACT
* *
95035 ATTAATAATTCAATAATATTATTTTTAATAA
1 ATTAATAAAT-AATAAT-TT-TTATTAATAA
95066 ATTAATAAATAATAATTTTTATTAATAA
1 ATTAATAAATAATAATTTTTATTAATAA
95094 TTTATTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 9 0.35
29 2 0.08
30 6 0.23
31 9 0.35
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTAATAAATAATAATTTTTATTAATAA
Found at i:95093 original size:13 final size:14
Alignment explanation
Indices: 95046--95101 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
95036 TTAATAATTC
*
95046 AATAATATTATTTTT
1 AATAAT-TTATTATT
* * *
95061 AATAAATTAATAAAT
1 AAT-AATTTATTATT
95076 AATAATTT-TTATT
1 AATAATTTATTATT
95089 AATAATTTATTAT
1 AATAATTTATTAT
95102 ATATTATTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
13 11 0.34
14 8 0.25
15 10 0.31
16 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATAATTTATTATT
Found at i:98122 original size:50 final size:50
Alignment explanation
Indices: 98068--98193 Score: 153
Period size: 50 Copynumber: 2.5 Consensus size: 50
98058 AGATATCCAG
* * *
98068 GTATAGCGCGGATCATGGGGCGCGCTATACCCACGTGACGCCAGATCACC
1 GTATAGCGCGGATCAGGGGGCGCGCTATACACACGTGACGCCAAATCACC
** ** * *
98118 GTATATTGCGGGGCAGGGGGCACGCTATACACACGTGACGCCAAATCAGC
1 GTATAGCGCGGATCAGGGGGCGCGCTATACACACGTGACGCCAAATCACC
* *
98168 GTATAGCACGGTTCAGGGGGCGCGCT
1 GTATAGCGCGGATCAGGGGGCGCGCT
98194 TTACTGCTAC
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.22, C:0.28, G:0.33, T:0.17
Consensus pattern (50 bp):
GTATAGCGCGGATCAGGGGGCGCGCTATACACACGTGACGCCAAATCACC
Found at i:101533 original size:23 final size:23
Alignment explanation
Indices: 101496--101555 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
101486 ATTTTGTTAG
*
101496 ATTTAAGGATTAAATTAATATTTT
1 ATTTAAAG-TTAAATTAATATTTT
*
101520 ATTTAAAGTTAAATTGATATTTT
1 ATTTAAAGTTAAATTAATATTTT
* *
101543 ATCTAAAATTAAA
1 ATTTAAAGTTAAA
101556 GATCAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 25 0.78
24 7 0.22
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (23 bp):
ATTTAAAGTTAAATTAATATTTT
Found at i:107924 original size:30 final size:31
Alignment explanation
Indices: 107869--107926 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
107859 TATTAAATGG
107869 TAAATGATAATCAAATTACAATAACTGATAT
1 TAAATGATAATCAAATTACAATAACTGATAT
107900 TAAATGATAAT-AAATTA-AATTAACTGA
1 TAAATGATAATCAAATTACAA-TAACTGA
107927 AATACATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 2 0.08
30 13 0.50
31 11 0.42
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATGATAATCAAATTACAATAACTGATAT
Found at i:107935 original size:19 final size:20
Alignment explanation
Indices: 107898--107937 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
107888 AATAACTGAT
107898 ATTAAATGATAATAAATTAA
1 ATTAAATGATAATAAATTAA
* *
107918 ATTAACTGA-AATACATTAA
1 ATTAAATGATAATAAATTAA
107937 A
1 A
107938 AAAGTCCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
ATTAAATGATAATAAATTAA
Found at i:108158 original size:3 final size:3
Alignment explanation
Indices: 108152--108177 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
108142 ATCACCATCA
108152 TCG TCG TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TC
108178 CTGAGTAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.31, T:0.35
Consensus pattern (3 bp):
TCG
Found at i:113491 original size:24 final size:24
Alignment explanation
Indices: 113392--113491 Score: 78
Period size: 24 Copynumber: 4.2 Consensus size: 24
113382 ATATTTTATC
* *
113392 TGATTTCTGATTTGAATTATGTTT
1 TGATATCTGATCTGAATTATGTTT
* * * *
113416 TGACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTATGTTT
* * * *
113440 TGAT-TCCT-AACTTGGATTCTGTTA
1 TGATAT-CTGATC-TGAATTATGTTT
113464 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTATGTTT
113488 TGAT
1 TGAT
113492 TTTTGATATC
Statistics
Matches: 57, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
23 3 0.05
24 51 0.89
25 3 0.05
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.48
Consensus pattern (24 bp):
TGATATCTGATCTGAATTATGTTT
Found at i:114514 original size:19 final size:19
Alignment explanation
Indices: 114490--114540 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
114480 TAATTAAATC
114490 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
114509 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
114528 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
114541 TTTCAACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:117091 original size:24 final size:23
Alignment explanation
Indices: 117023--117100 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 23
117013 TGATCTTGTA
*
117023 CATCGATGCACATTCAAGGCATG
1 CATCGATGCACATTCAAGGGATG
*
117046 CATC-AGTG--CA-TCATGCGGATG
1 CATCGA-TGCACATTCAAG-GGATG
117067 CATCGATGCACATTCAAAGGGATG
1 CATCGATGCACATTC-AAGGGATG
117091 CATCGATGCA
1 CATCGATGCA
117101 TTGTTAAGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
20 4 0.09
21 12 0.27
22 2 0.04
23 8 0.18
24 17 0.38
25 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22
Consensus pattern (23 bp):
CATCGATGCACATTCAAGGGATG
Done.