Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006581.1 Hibiscus syriacus cultivar Beakdansim tig00016130_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: 69761
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:15125 original size:20 final size:20
Alignment explanation
Indices: 15100--15139 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
15090 TTTTGGTGCA
*
15100 GAGGGAATCGATCCCCCCTT
1 GAGGGAACCGATCCCCCCTT
*
15120 GAGGGAACCGATTCCCCCTT
1 GAGGGAACCGATCCCCCCTT
15140 TGAAAAGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCTT
Found at i:15462 original size:36 final size:36
Alignment explanation
Indices: 15415--15487 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
15405 TTCTAAACTC
*
15415 ACTATTTTATTGATTTTGATCATAGGACTAGTTTTA
1 ACTATTTTATTGATTTTGAACATAGGACTAGTTTTA
15451 ACTATTTTATTGATTTTGAACATAGGACTAGTTTTA
1 ACTATTTTATTGATTTTGAACATAGGACTAGTTTTA
15487 A
1 A
15488 TTAGTTCTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (36 bp):
ACTATTTTATTGATTTTGAACATAGGACTAGTTTTA
Found at i:15948 original size:19 final size:19
Alignment explanation
Indices: 15924--15962 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
15914 AAATCCTCCT
15924 CCTATTCCAATTTCTAATC
1 CCTATTCCAATTTCTAATC
15943 CCTATTCCAATTTCTAATC
1 CCTATTCCAATTTCTAATC
15962 C
1 C
15963 TAATCCCATT
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:0.26, C:0.33, G:0.00, T:0.41
Consensus pattern (19 bp):
CCTATTCCAATTTCTAATC
Found at i:23760 original size:53 final size:53
Alignment explanation
Indices: 23702--24122 Score: 556
Period size: 53 Copynumber: 7.9 Consensus size: 53
23692 TTCGACCAGT
* * * * *
23702 GGGTTCTCTCCTTCTTGCTTCAAGGAGTATAACTCGAATAATCTTCTGCCTAC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
* *
23755 AGGTTCGCTCCCTCTTGTTTCAAGGG-GTAGAACTCGAACAATCTTCTGCCTAC
1 GGGTTCGCTCCCTCTTGCTTC-AGGGAGTAGAACTCGAACAATCTTCTGCCTAC
* * * * * *
23808 GAGTTCACTCCCTCTTGCTTTAGGGAGTATAACTCGAATAATCTTCTGCCTAT
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
**
23861 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGTTTAC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
** *
23914 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATGATCTTCTGCTTAC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
* * * * *
23967 GGGTTCGCTCCCACTTGCTTAATGGAGCGTAGAACTCGAACAATCTTCTGCTTAT
1 GGGTTCGCTCCCTCTTGCTTCA-GG-GAGTAGAACTCGAACAATCTTCTGCCTAC
* * *
24022 GGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACGATATTCTGCCTAC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
* *
24075 GGGTTCGCTCCCTCTTGTTTCAGGGAGTAGAACTCGAACAATTTTCTG
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
24123 GTGTAATTCT
Statistics
Matches: 320, Mismatches: 44, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
52 4 0.01
53 265 0.83
54 7 0.02
55 44 0.14
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.32
Consensus pattern (53 bp):
GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
Found at i:24058 original size:214 final size:212
Alignment explanation
Indices: 23702--24122 Score: 628
Period size: 214 Copynumber: 2.0 Consensus size: 212
23692 TTCGACCAGT
* * *
23702 GGGTTCTCTCCTTCTTGCTTCAAGGAGTATAACTCGAATAATCTTCTGCCTACAGGTTCGCTCCC
1 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAATAATCTTCTGCCTACAGGTTCGCTCCC
* * *
23767 TCTTGTTTCAAGGGGTAGAACTCGAACAATCTTCTGCCTACGAGTTCACTCCCTCTTGCTTTAGG
66 ACTTGCTTCAAGGGGTAGAACTCGAACAATCTTCTGCCTACGAGTTCACTCCCTCTTGCTTCAGG
* * * *
23832 GAGTATAACTCGAATAATCTTCTGCCTATGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCG
131 GAGTAGAACTCGAACAATATTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCG
23897 AACAATCTTCTGTTTAC
196 AACAATCTTCTGTTTAC
* * * *
23914 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATGATCTTCTGCTTACGGGTTCGCTCCC
1 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAATAATCTTCTGCCTACAGGTTCGCTCCC
* * *
23979 ACTTGCTT-AATGGAGCGTAGAACTCGAACAATCTTCTGCTTATGGGTTCACTCCCTCTTGCTTC
66 ACTTGCTTCAA-GG-G-GTAGAACTCGAACAATCTTCTGCCTACGAGTTCACTCCCTCTTGCTTC
* *
24043 AGGGAGTAGAACTCGAACGATATTCTGCCTACGGGTTCGCTCCCTCTTGTTTCAGGGAGTAGAAC
128 AGGGAGTAGAACTCGAACAATATTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAAC
*
24108 TCGAACAATTTTCTG
193 TCGAACAATCTTCTG
24123 GTGTAATTCT
Statistics
Matches: 186, Mismatches: 20, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
211 2 0.01
212 66 0.35
213 1 0.01
214 117 0.63
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.32
Consensus pattern (212 bp):
GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAATAATCTTCTGCCTACAGGTTCGCTCCC
ACTTGCTTCAAGGGGTAGAACTCGAACAATCTTCTGCCTACGAGTTCACTCCCTCTTGCTTCAGG
GAGTAGAACTCGAACAATATTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCG
AACAATCTTCTGTTTAC
Found at i:24628 original size:42 final size:42
Alignment explanation
Indices: 24544--24727 Score: 201
Period size: 42 Copynumber: 4.4 Consensus size: 42
24534 ACATCCTACC
* * * * *
24544 CGAAGGACTT-ATGGATGACCCGAAGGA-TTCATTATCTTGCT
1 CGAAAGACTTAAT-GATGACCCGAATGATTTAATCATCATGCT
* ** * * *
24585 CGAAAGACTCAAAAATGACTCAAATGATTTAATCAGCATGCT
1 CGAAAGACTTAATGATGACCCGAATGATTTAATCATCATGCT
*
24627 CGAAAGACTTAATGATGGCCCGAATGATTTAATCATCATGCT
1 CGAAAGACTTAATGATGACCCGAATGATTTAATCATCATGCT
* * *
24669 CGAAATACTTACTGATGACCCGAAGGATTTAATCATCATGCT
1 CGAAAGACTTAATGATGACCCGAATGATTTAATCATCATGCT
*
24711 CGAAAGACTTACTGATG
1 CGAAAGACTTAATGATG
24728 GCACTTACTG
Statistics
Matches: 118, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
41 18 0.15
42 100 0.85
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (42 bp):
CGAAAGACTTAATGATGACCCGAATGATTTAATCATCATGCT
Found at i:24735 original size:13 final size:13
Alignment explanation
Indices: 24717--24741 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24707 TGCTCGAAAG
24717 ACTTACTGATGGC
1 ACTTACTGATGGC
24730 ACTTACTGATGG
1 ACTTACTGATGG
24742 GTTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:24841 original size:42 final size:42
Alignment explanation
Indices: 24779--24876 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
24769 CTTAAAAATT
* *
24779 ACCCTAAGGATTTAATCATCATGCTCAAAATACTTACTGATG
1 ACCCTAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATG
* * *
24821 GCCCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATG
1 ACCCTAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATG
* *
24863 ACTCGAAGGATTTA
1 ACCCTAAGGATTTA
24877 CTAAGTGCGA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (42 bp):
ACCCTAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATG
Found at i:38141 original size:65 final size:65
Alignment explanation
Indices: 38037--38163 Score: 227
Period size: 65 Copynumber: 2.0 Consensus size: 65
38027 TGTTGTGAGT
*
38037 CATGAGAGGAATACTTTGAAGATGAAACCTCAATGAGTTGAGGGAGTCATCGATAGATTTGGAGC
1 CATGACAGGAATACTTTGAAGATGAAACCTCAATGAGTTGAGGGAGTCATCGATAGATTTGGAGC
* *
38102 CATGACAGGAATACTTTGAAGATGAAGCCTCAATGAGTTGAGGGAGTCATTGATAGATTTGG
1 CATGACAGGAATACTTTGAAGATGAAACCTCAATGAGTTGAGGGAGTCATCGATAGATTTGG
38164 TTATCGAATC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (65 bp):
CATGACAGGAATACTTTGAAGATGAAACCTCAATGAGTTGAGGGAGTCATCGATAGATTTGGAGC
Found at i:40878 original size:37 final size:37
Alignment explanation
Indices: 40805--40879 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
40795 GTTGGAAAAT
* *
40805 ATTTATATATTTTATTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTATTTAAAAAATTGAAAATCATAAA
*
40842 ATTTATATATATATT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATAT-T-TTATTTAAAAAATTGAAAATCATAAA
40879 A
1 A
40880 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 16 0.48
38 15 0.45
39 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTATTTAAAAAATTGAAAATCATAAA
Found at i:49560 original size:28 final size:28
Alignment explanation
Indices: 49506--49559 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
49496 AAGTTAGATT
* * *
49506 AAAAAACATAATAAATAATGGATAAAAG
1 AAAAAAAAAAATAAATAATGAATAAAAG
49534 AAAAAAAAAAATAAATAAT-AATAAAA
1 AAAAAAAAAAATAAATAATGAATAAAA
49560 ATTTAAGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.17
Consensus pattern (28 bp):
AAAAAAAAAAATAAATAATGAATAAAAG
Found at i:49572 original size:23 final size:22
Alignment explanation
Indices: 49541--49603 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
49531 AAGAAAAAAA
49541 AAAATAAATAATAATAAAAATTT
1 AAAA-AAATAATAATAAAAATTT
* ** *
49564 AAGGAAAATAAGGAGAAAAATTT
1 AA-AAAAATAATAATAAAAATTT
49587 AAAAATAATAATAATAA
1 AAAAA-AATAATAATAA
49604 TAATAAATGA
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
22 2 0.07
23 27 0.90
24 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (22 bp):
AAAAAAATAATAATAAAAATTT
Found at i:49711 original size:21 final size:22
Alignment explanation
Indices: 49687--49727 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
49677 GCACCTATAT
49687 ATATCTAAAAA-AAAATAAATA
1 ATATCTAAAAATAAAATAAATA
*
49708 ATATTTAAAAATAAAATAAA
1 ATATCTAAAAATAAAATAAA
49728 GAAGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
ATATCTAAAAATAAAATAAATA
Found at i:50623 original size:7 final size:7
Alignment explanation
Indices: 50613--50678 Score: 51
Period size: 7 Copynumber: 8.9 Consensus size: 7
50603 ACCTGGACAG
50613 AAAAAAT
1 AAAAAAT
50620 AAAAAAT
1 AAAAAAT
50627 AAAAAAT
1 AAAAAAT
**
50634 AAGGAAT
1 AAAAAAT
50641 AAAAAAAT
1 -AAAAAAT
* *
50649 AATAATAG
1 AA-AAAAT
50657 AATAATAAT
1 AA-AA-AAT
*
50666 AAATAAT
1 AAAAAAT
50673 AAAAAA
1 AAAAAA
50679 ATATTTTCAA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
7 29 0.63
8 14 0.30
9 3 0.07
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (7 bp):
AAAAAAT
Found at i:50660 original size:11 final size:10
Alignment explanation
Indices: 50624--50674 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
50614 AAAAATAAAA
*
50624 AATAAAAAAT
1 AATAAATAAT
**
50634 AAGGAATAA-
1 AATAAATAAT
50643 AA-AAATAAT
1 AATAAATAAT
50652 AATAGAATAAT
1 AATA-AATAAT
50663 AATAAATAAT
1 AATAAATAAT
50673 AA
1 AA
50675 AAAAATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 5 0.15
9 4 0.12
10 15 0.44
11 10 0.29
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.22
Consensus pattern (10 bp):
AATAAATAAT
Found at i:50663 original size:29 final size:28
Alignment explanation
Indices: 50613--50681 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
50603 ACCTGGACAG
* *
50613 AAAAAATAAAAAATAAAAAATAAGGAATA
1 AAAAAAT-AATAATAAAAAATAAGAAATA
* *
50642 AAAAAATAATAATAGAATAATAATAAATA
1 AAAAAATAATAATA-AAAAATAAGAAATA
50671 ATAAAAA-AATA
1 A-AAAAATAATA
50682 TTTTCAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 6 0.18
29 23 0.68
30 5 0.15
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (28 bp):
AAAAAATAATAATAAAAAATAAGAAATA
Found at i:50680 original size:11 final size:11
Alignment explanation
Indices: 50620--50681 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
50610 CAGAAAAAAT
50620 AAAAAATAA-A
1 AAAAAATAATA
**
50630 AAATAAGGAATA
1 AAA-AAATAATA
50642 AAAAAATAATA
1 AAAAAATAATA
* *
50653 ATAGAATAAT-
1 AAAAAATAATA
*
50663 AATAAATAATA
1 AAAAAATAATA
50674 AAAAAATA
1 AAAAAATA
50682 TTTTCAAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
10 10 0.26
11 25 0.64
12 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (11 bp):
AAAAAATAATA
Found at i:50776 original size:36 final size:35
Alignment explanation
Indices: 50676--51098 Score: 256
Period size: 36 Copynumber: 11.8 Consensus size: 35
50666 AAATAATAAA
* * **
50676 AAAATATTTTCAAAAAA-CATATAATATATAAATTTC
1 AAAATGTTTT-AAAAAATTATATAATATAT-GTTTTC
* * *
50712 CAAATGTTTTAAAACATTTATATCATATATGTTTTC
1 AAAATGTTTTAAAA-AATTATATAATATATGTTTTC
* *
50748 AAAAATGTTTTAAAAAATTATATAATATATATATTTGTA
1 -AAAATGTTTTAAAAAATTATAT-A-ATATATGTTT-TC
* *
50787 AAAATGTTTTAAAAAAATATAT-AT-TAT-ATTTC
1 AAAATGTTTTAAAAAATTATATAATATATGTTTTC
* *
50819 AAAATGTTTTTTAAAAACTATATAATATATAAAGGTTTTC
1 AAAATG-TTTTAAAAAATTATATAATATAT----GTTTTC
* *
50859 AAAATGTTTT-TAAAATCTATATAATATAAAGGTTTTC
1 AAAATGTTTTAAAAAAT-TATATAATAT--ATGTTTTC
* * * *
50896 AAAATGTTTTCAAAACTATATATTATATAAG-TTTC
1 AAAATGTTTTAAAAAAT-TATATAATATATGTTTTC
* * *
50931 AAAATATTTTTAAAAACTT-TAT-ATATAAGTTTTC
1 AAAAT-GTTTTAAAAAATTATATAATATATGTTTTC
* * * *
50965 AAAATGATTTAAAAAACTATATATTATATATTTTC
1 AAAATGTTTTAAAAAATTATATAATATATGTTTTC
* * * *
51000 TAAAAT-ATTTAAAAACTATATATTATATAAGTTTTC
1 -AAAATGTTTTAAAAAAT-TATATAATATATGTTTTC
* * *
51036 AAAAATGTTTT-AAAACTATATATTATATAT-ATTTC
1 -AAAATGTTTTAAAAAAT-TATATAATATATGTTTTC
* * *
51071 AAAATGTTTTTAAAAACTATATATTATA
1 AAAATGTTTTAAAAAATTATATAATATA
51099 CGTATTTTCA
Statistics
Matches: 312, Mismatches: 49, Indels: 54
0.75 0.12 0.13
Matches are distributed among these distances:
32 7 0.02
33 32 0.10
34 39 0.12
35 45 0.14
36 74 0.24
37 42 0.13
38 47 0.15
39 15 0.05
40 10 0.03
41 1 0.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (35 bp):
AAAATGTTTTAAAAAATTATATAATATATGTTTTC
Found at i:50809 original size:31 final size:33
Alignment explanation
Indices: 50748--50848 Score: 98
Period size: 33 Copynumber: 2.9 Consensus size: 33
50738 ATATGTTTTC
50748 AAAAATG-TTTTAAAAAATTATATAATATATATATTTGT
1 AAAAATGTTTTTAAAAAA--ATAT-ATAT-TATA-TT-T
50786 AAAAATG-TTTTAAAAAAATATATATTATATTT
1 AAAAATGTTTTTAAAAAAATATATATTATATTT
* * * *
50818 CAAAATGTTTTTTAAAAACTATATAATATAT
1 AAAAATGTTTTTAAAAAAATATATATTATAT
50849 AAAGGTTTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
32 7 0.12
33 22 0.38
34 4 0.07
35 4 0.07
36 4 0.07
38 17 0.29
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (33 bp):
AAAAATGTTTTTAAAAAAATATATATTATATTT
Found at i:50881 original size:72 final size:70
Alignment explanation
Indices: 50688--51098 Score: 364
Period size: 72 Copynumber: 5.8 Consensus size: 70
50678 AATATTTTCA
* * *
50688 AAAAAC-ATATAATATATAAATTTCCAAATG-TTTT-AAAACATTTATATCATATATGTTTTCAA
1 AAAAACTATATAATATATAAATTTCAAAATGTTTTTAAAAAC-TATATAT-ATATAAG-TTTC-A
50750 AAATGTTTT
62 AAATGTTTT
* * * * *
50759 AAAAAATTATATAATATATATATTTGTAAAAATGTTTTAAAAAAATATATAT-TAT-A-TTTCAA
1 -AAAAACTATATAATATATA-AATT-TCAAAATGTTTTTAAAAACTATATATATATAAGTTTCAA
50821 AATGTTTTTT
63 AATG--TTTT
*
50831 AAAAACTATATAATATATAAAGGTTTTCAAAATGTTTTTAAAATCTATATA-ATATAAAGGTTTT
1 AAAAACTATATAATATATAAA---TTTCAAAATGTTTTTAAAAACTATATATATAT-AA-G-TTT
50895 CAAAATGTTTT
60 CAAAATGTTTT
* * * *
50906 CAAAACTATATATTATATAAGTTTCAAAATATTTTTAAAAACT-T-TATATATAAGTTTTCAAAA
1 AAAAACTATATAATATATAAATTTCAAAATGTTTTTAAAAACTATATATATATAAG-TTTCAAAA
*
50969 TGATTTA
65 TG-TTTT
* * *
50976 AAAAACTATATATTATAT-ATTTTCTAAAA--TATTTAAAAACTATATATTATATAAGTTTTCAA
1 AAAAACTATATAATATATAAATTTC-AAAATGTTTTTAAAAACTATATA-TATATAAG-TTTC-A
51038 AAATGTTTT
62 AAATGTTTT
* *
51047 -AAAACTATATATTATATATATTTCAAAATGTTTTTAAAAACTATATAT-TATA
1 AAAAACTATATAATATATAAATTTCAAAATGTTTTTAAAAACTATATATATATA
51099 CGTATTTTCA
Statistics
Matches: 286, Mismatches: 27, Indels: 54
0.78 0.07 0.15
Matches are distributed among these distances:
68 11 0.04
69 18 0.06
70 62 0.22
71 48 0.17
72 75 0.26
73 14 0.05
74 7 0.02
75 28 0.10
76 9 0.03
77 14 0.05
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (70 bp):
AAAAACTATATAATATATAAATTTCAAAATGTTTTTAAAAACTATATATATATAAGTTTCAAAAT
GTTTT
Found at i:51105 original size:36 final size:35
Alignment explanation
Indices: 50744--51111 Score: 264
Period size: 36 Copynumber: 10.2 Consensus size: 35
50734 TCATATATGT
* *
50744 TTTCAAAAATGTTTTAAAAAATTATATAATATATA-TA
1 TTTC-AAAATGTTTTTAAAAACTATAT-AT-TATAGTA
* * *
50781 TTTGTAAAAATGTTTTAAAAAAATATATA-T-TA-TA
1 -TT-TCAAAATGTTTTTAAAAACTATATATTATAGTA
50815 TTTCAAAATGTTTTTTAAAAACTATATAATATATAAAGGT-
1 TTTCAAAATG-TTTTTAAAAACTATAT-AT-TAT--A-GTA
* *
50855 TTTCAAAATGTTTTTAAAATCTATATAATATAAAGGT-
1 TTTCAAAATGTTTTTAAAAACTATAT-AT-TATA-GTA
*
50892 TTTCAAAATG-TTTTCAAAACTATATATTATA-TAA
1 TTTCAAAATGTTTTTAAAAACTATATATTATAGT-A
* *
50926 GTTTCAAAATATTTTTAAAAACTTTATA-TATAAGT-
1 -TTTCAAAATGTTTTTAAAAACTATATATTAT-AGTA
* *
50961 TTTCAAAATGATTTAAAAAACTATATATTATA-TA
1 TTTCAAAATGTTTTTAAAAACTATATATTATAGTA
*
50995 TTTTCTAAAA--TATTTAAAAACTATATATTATA-TAA
1 -TTTC-AAAATGTTTTTAAAAACTATATATTATAGT-A
*
51030 GTTTTCAAAAATG-TTTT-AAAACTATATATTATATATA
1 --TTTC-AAAATGTTTTTAAAAACTATATATTATA-GTA
51067 TTTCAAAATGTTTTTAAAAACTATATATTATACGTA
1 TTTCAAAATGTTTTTAAAAACTATATATTATA-GTA
51103 TTTTCAAAA
1 -TTTCAAAA
51112 ACCATTTGCA
Statistics
Matches: 277, Mismatches: 24, Indels: 59
0.77 0.07 0.16
Matches are distributed among these distances:
32 8 0.03
33 17 0.06
34 58 0.21
35 31 0.11
36 76 0.27
37 29 0.10
38 24 0.09
39 23 0.08
40 10 0.04
41 1 0.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (35 bp):
TTTCAAAATGTTTTTAAAAACTATATATTATAGTA
Found at i:51873 original size:84 final size:84
Alignment explanation
Indices: 51477--53137 Score: 1831
Period size: 84 Copynumber: 19.8 Consensus size: 84
51467 ATGTGGTTGA
* * * * * * * **
51477 TTGAGCTGAACGAAATCGAACTCGAAGGT-ATTTGTTGACAGATAGCCCTTCTTGCCTTTAACTA
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
*
51541 TGCTGTAAATGATGTGCCT
66 TGCTGCAAATGATGTGCCT
* * * * *
51560 TGGAGCTGAGTGTAATCGAACCCGAAGGTC---T-TTGGCAGATAACCCTTCTAGCCTTGAGTTA
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
51621 TGCTGCAAATGATGTGCCT
66 TGCTGCAAATGATGTGCCT
* * * * * ** *
51640 CTGAGCTGAGTGTAATCGAACTCGAAGG-C--CT-TTGGCAGATAGCTGTTCTTACCTTGAGTTA
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
* *
51701 TGTTGCAAATAATGTGCCT
66 TGCTGCAAATGATGTGCCT
** * * *
51720 TTGAGCAAAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTAGCCTTGAGTTA
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
* * **
51781 TGTTGTAAATGATGCACCT
66 TGCTGCAAATGATGTGCCT
* * * *
51800 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTTCCTTGAGCTA
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
** *
51865 TATTGTAAATGATGTGCCT
66 TGCTGCAAATGATGTGCCT
* * * * * *
51884 TGGAGATGAGCGTAGTTGAACTCGAAGGTCTTTTATTGGCAGATAACTCTTCTAGCCTTGAGTTA
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
*
51949 TACTGCAAATGATGTGCCT
66 TGCTGCAAATGATGTGCCT
* * * ** * *
51968 TGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTTGTTAGCAGATAGTCCTTCTCGCCTTGAGCTA
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
*
52033 TGCTGCAAATGTTGTGCCT
66 TGCTGCAAATGATGTGCCT
* * * * * *
52052 TTGAGCTGAGTGTAATCAAACTCGAAGGTTTTTTGCTGGCAGATAACCCTTCTAGCCTTGAGTTA
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
**
52117 TATTGCAAATGATGTGCCT
66 TGCTGCAAATGATGTGCCT
* * * * *
52136 TAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGAAGAATAACCCTTTTTTCCTTGAGCT
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAG-ATAACCCTTCTTGCCTTGAGTT
* *
52201 ATGTTACAAATGATGTGCCT
65 ATGCTGCAAATGATGTGCCT
* * * *
52221 TGGAGCTGAGCGTAGTTGAACTCGAAGGTCATTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTA
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
*
52286 TACTGCAAATGATGTGCCT
66 TGCTGCAAATGATGTGCCT
* *
52305 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTA
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
*
52370 TGCTGTAAATGATGTG-CT
66 TGCTGCAAATGATGTGCCT
* * * * * * * *
52388 TTGGAACTGAGCGGAGTCGAACTCGAAGATCTTTTATTGGCAAATAGCACTTCTTGCCTTGAGCT
1 TT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTT
*
52453 ATGTTGCAAATGATGTGCCT
65 ATGCTGCAAATGATGTGCCT
* * * * * * * *
52473 TGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTTATTAGCAGATAAGCCTTCTAGACTTGAGTTG
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
* * * *
52538 TGCTGTAAAAGTTATGCCT
66 TGCTGCAAATGATGTGCCT
* * * *
52557 TTGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTA
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
*
52622 TACTGCAAATGATGTGCCT
66 TGCTGCAAATGATGTGCCT
* * * *
52641 TGGAGCTGAGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTGGCC
1 T-----T---GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCC
* * *
52706 TTGTGTTATGCTACAAATGATATGCCT
58 TTGAGTTATGCTGCAAATGATGTGCCT
** * * * * * *
52733 TTGAGCTGTTCGTATTTGAACTCGAAGGTCTTTTATTGGCAAATAGCCCTTCTTGCCTTGAGCTA
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
52798 TGCTGCAAATGATGTGCCT
66 TGCTGCAAATGATGTGCCT
* * * * * * *
52817 TGGAGATGAGCATATTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCATTCTAGCCTTGAGTTA
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
*
52882 TGCTGCAAATGATATGCCT
66 TGCTGCAAATGATGTGCCT
* * * * * * * *
52901 TGGAGCTGAGTGTAATCGAACTCGAATGTCTTTTGGTGGCAAATAGCCCTTCTTGCCTTGAGCTA
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
52966 TGCTGCAAATGATGTGCCT
66 TGCTGCAAATGATGTGCCT
* *
52985 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGAAGATAACCCTTCTTGCCTTGAGTTA
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
53050 TGCTGCAAATGATGTGCCT
66 TGCTGCAAATGATGTGCCT
* * * * * *
53069 TTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGCTGACAGATAACCCTTCTCGCCTTGAGTTA
1 TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
53133 TGCTG
66 TGCTG
53138 ATGATAGTTT
Statistics
Matches: 1332, Mismatches: 228, Indels: 36
0.83 0.14 0.02
Matches are distributed among these distances:
79 1 0.00
80 202 0.15
81 2 0.00
83 62 0.05
84 913 0.69
85 77 0.06
87 1 0.00
89 1 0.00
92 73 0.05
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (84 bp):
TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTA
TGCTGCAAATGATGTGCCT
Found at i:54571 original size:14 final size:14
Alignment explanation
Indices: 54552--54584 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
54542 TTAATCTTAA
*
54552 TTTAAATTTAATTT
1 TTTAAATTTAATCT
54566 TTTAAATTTAATCT
1 TTTAAATTTAATCT
54580 TTTAA
1 TTTAA
54585 CCATATTATG
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:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTAAATTTAATCT
Found at i:57258 original size:20 final size:20
Alignment explanation
Indices: 57221--57259 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
57211 CTTAAAATAA
* *
57221 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCTAATTTTG
57241 TTTTTCAAAATCTAATTTT
1 TTTTTCAAAATCTAATTTT
57260 ACTTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:57265 original size:21 final size:20
Alignment explanation
Indices: 57221--57265 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
57211 CTTAAAATAA
* * *
57221 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCTAATTTTC
57241 TTTTTCAAAATCTAATTTTAC
1 TTTTTCAAAATCTAATTTT-C
57262 TTTT
1 TTTT
57266 AAAAGAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.27, C:0.11, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTC
Found at i:59583 original size:16 final size:18
Alignment explanation
Indices: 59551--59585 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
59541 TAAATTATTA
59551 TTAATTTTATAAAATAAT
1 TTAATTTTATAAAATAAT
59569 TTAATTTT-T-AAATAAT
1 TTAATTTTATAAAATAAT
59585 T
1 T
59586 ATATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 1 0.06
18 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAATTTTATAAAATAAT
Found at i:59592 original size:2 final size:2
Alignment explanation
Indices: 59585--59655 Score: 74
Period size: 2 Copynumber: 36.0 Consensus size: 2
59575 TTTAAATAAT
* * * * *
59585 TA TA TA TA TA TA TA TA TC TA -A TA AA AA TA TA T- TGA TT TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
59626 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
59656 ATTATTAGTA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
1 2 0.03
2 55 0.95
3 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:64484 original size:21 final size:21
Alignment explanation
Indices: 64460--64533 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
64450 GCGTTGCATT
64460 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * * ** **
64481 TCGCATTACGAT-TTTTTATT
1 TCGCGTTGCGATAGTTGAAAA
64501 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
64522 TCGCGTTGCGAT
1 TCGCGTTGCGAT
64534 TTTTCATTTC
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 13 0.34
21 25 0.66
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:64504 original size:41 final size:41
Alignment explanation
Indices: 64456--64549 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
64446 ATTCGCGTTG
64456 CATTTCGCGTTGCGATAGTTGAAAATCGCATTACGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCATTACGATTTTT
* * *
64497 TATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCATTACGATTTTT
64538 CATTTCGCGTTG
1 CATTTCGCGTTG
64550 TGATTTTTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCATTACGATTTTT
Found at i:64512 original size:20 final size:20
Alignment explanation
Indices: 64489--64573 Score: 98
Period size: 20 Copynumber: 4.2 Consensus size: 20
64479 AATCGCATTA
*
64489 CGATTTTTTATTTCGCGTTG
1 CGATTTTTCATTTCGCGTTG
* ** **
64509 CGATAGTTGAAAATCGCGTTG
1 CGAT-TTTTCATTTCGCGTTG
64530 CGATTTTTCATTTCGCGTTG
1 CGATTTTTCATTTCGCGTTG
*
64550 TGATTTTTCATTTCGCGTTG
1 CGATTTTTCATTTCGCGTTG
64570 CGAT
1 CGAT
64574 AGTCTACAGT
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 37 0.71
21 15 0.29
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.46
Consensus pattern (20 bp):
CGATTTTTCATTTCGCGTTG
Found at i:64610 original size:19 final size:19
Alignment explanation
Indices: 64586--64689 Score: 127
Period size: 19 Copynumber: 5.3 Consensus size: 19
64576 TCTACAGTTG
64586 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
*
64605 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTCCAAAT
64624 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * * **
64643 TCGTTGCAATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
64664 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
64684 TCGTTG
1 TCGTTG
64690 TGAAAATTCG
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
19 51 0.73
20 5 0.07
21 5 0.07
22 9 0.13
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:64610 original size:61 final size:60
Alignment explanation
Indices: 64489--64620 Score: 151
Period size: 61 Copynumber: 2.2 Consensus size: 60
64479 AATCGCATTA
* * *
64489 CGATTTTTTATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTCATTTCGCGTTG
1 CGATTTTTCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC-CGTTG
* * * *
64550 TGATTTTTCATTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT-CGTTG
1 CGATTTTTCATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATTCCGTTG
64611 CGATTTTTCA
1 CGATTTTTCA
64621 AATTCGTTGC
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
61 43 0.72
62 14 0.23
63 3 0.05
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.45
Consensus pattern (60 bp):
CGATTTTTCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTCCGTTG
Found at i:64637 original size:38 final size:40
Alignment explanation
Indices: 64565--64689 Score: 146
Period size: 41 Copynumber: 3.1 Consensus size: 40
64555 TTTCATTTCG
* **
64565 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCAATA-TCTACAAATGTCGTTGCGATTTTCCAAATT
* * *
64606 CGTTGCGAT-TTTTCAAAT-TCGTTGCGATTTTCCAAATT
1 CGTTGCAATATCTACAAATGTCGTTGCGATTTTCCAAATT
**
64644 CGTTGCAATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCAATA-TCTACAAATGTCGTTGCGATTTTCCAAATT
64685 CGTTG
1 CGTTG
64690 TGAAAATTCG
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
38 28 0.39
39 5 0.07
40 5 0.07
41 34 0.47
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (40 bp):
CGTTGCAATATCTACAAATGTCGTTGCGATTTTCCAAATT
Found at i:64798 original size:6 final size:6
Alignment explanation
Indices: 64787--64823 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
64777 GACACGTATT
64787 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
64824 GACGAGACGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:64830 original size:5 final size:5
Alignment explanation
Indices: 64820--64851 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
64810 GACCACGACC
64820 ACGAG ACGAG ACGAG ACGAG ACGAG ACG-G ACG
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACG
64852 GCGGCGGCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.38, C:0.22, G:0.41, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:65540 original size:20 final size:20
Alignment explanation
Indices: 65515--65566 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
65505 ATTTTCAACT
65515 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATAGAAA
65535 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATAGAAA
65555 ATCGCAACGCGA
1 ATCGCAACGCGA
65567 TTTTCAACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATAGAAA
Found at i:65540 original size:61 final size:61
Alignment explanation
Indices: 65474--65590 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 61
65464 ACTGTAGACT
* ***
65474 ATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCAACTATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATAGAAA
*
65535 ATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACTATCGGAACGCGAAAT
1 ATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAAT
65591 GCAACGCGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (61 bp):
ATCGCAACGCGAAATAGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATAGAAA
Found at i:66608 original size:21 final size:21
Alignment explanation
Indices: 66582--66628 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
66572 GTTTCTAGAT
66582 TCGCAACGAAAACTTCGACTA
1 TCGCAACGAAAACTTCGACTA
*
66603 TCGCAACGCAAACTTCGACTA
1 TCGCAACGAAAACTTCGACTA
66624 TCGCA
1 TCGCA
66629 TTGCGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.32, G:0.15, T:0.19
Consensus pattern (21 bp):
TCGCAACGAAAACTTCGACTA
Found at i:66734 original size:21 final size:21
Alignment explanation
Indices: 66643--66807 Score: 90
Period size: 21 Copynumber: 8.0 Consensus size: 21
66633 GATTTACGTA
*
66643 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
66664 TTCGATTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* ** ** *
66685 TTGGCGTTGTAATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
66706 TT--TGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * * *
66725 TTCGCGTTGCAATTTATTACAAA
1 TTCGCGTTGCGA--TAGTCCAAG
66748 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
66767 TTCGCATTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
66790 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
66808 AATTGTAACG
Statistics
Matches: 104, Mismatches: 32, Indels: 18
0.68 0.21 0.12
Matches are distributed among these distances:
19 28 0.27
21 59 0.57
23 17 0.16
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:66760 original size:42 final size:42
Alignment explanation
Indices: 66670--66807 Score: 199
Period size: 42 Copynumber: 3.3 Consensus size: 42
66660 CAAGTTCGAT
* * * *
66670 TTGCGATAGTCGAAGTTGGCGTTGTAA-TT-TTCCAAATTTG
1 TTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATTCG
*
66710 TTGCGATAGTCCAAGTTCGCGTTGCAATTTATTACAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATTCG
* *
66752 TTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATTCG
66794 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
66808 AATTGTAACG
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 24 0.27
41 2 0.02
42 62 0.70
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATTCG
Found at i:67732 original size:19 final size:19
Alignment explanation
Indices: 67673--67872 Score: 168
Period size: 19 Copynumber: 9.8 Consensus size: 19
67663 TGCGATTTTG
67673 GACTATCGCAACGAA-TTC
1 GACTATCGCAACGAACTTC
*
67691 AGAATAAATCGCAACGCGAACTTC
1 -GACT--ATCGCAA--CGAACTTC
* *
67715 GACTATCGCAATGAACTTA
1 GACTATCGCAACGAACTTC
*
67734 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAA--CGAACTTC
* *
67757 GACTATCGCAACGAATTTG
1 GACTATCGCAACGAACTTC
*
67776 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAA--CGAACTTC
*
67799 GACTATCGCAACGAACTTG
1 GACTATCGCAACGAACTTC
*
67818 GACTATCGCAACGAACTTG
1 GACTATCGCAACGAACTTC
*
67837 GACTATCGCAACGCGAACTTA
1 GACTATCGCAA--CGAACTTC
67858 GACTATCGCAACGAA
1 GACTATCGCAACGAA
67873 TTTGGAAAAT
Statistics
Matches: 150, Mismatches: 16, Indels: 30
0.77 0.08 0.15
Matches are distributed among these distances:
19 62 0.41
21 60 0.40
23 25 0.17
24 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (19 bp):
GACTATCGCAACGAACTTC
Found at i:67737 original size:42 final size:42
Alignment explanation
Indices: 67673--67859 Score: 258
Period size: 42 Copynumber: 4.5 Consensus size: 42
67663 TGCGATTTTG
67673 GACTATCGCAACGAA-TTCAGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTT-AGAATAAATCGCAACGCGAACTTC
*
67715 GACTATCGCAATGAACTTAGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTAGAATAAATCGCAACGCGAACTTC
* *
67757 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTAGAATAAATCGCAACGCGAACTTC
* * *
67799 GACTATCGCAACGAACTTGGACT--ATCGCAA--CGAACTTG
1 GACTATCGCAACGAACTTAGAATAAATCGCAACGCGAACTTC
67837 GACTATCGCAACGCGAACTTAGA
1 GACTATCGCAA--CGAACTTAGA
67860 CTATCGCAAC
Statistics
Matches: 134, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
38 18 0.13
40 16 0.12
42 98 0.73
43 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTAGAATAAATCGCAACGCGAACTTC
Found at i:67855 original size:21 final size:21
Alignment explanation
Indices: 67698--67870 Score: 173
Period size: 19 Copynumber: 8.4 Consensus size: 21
67688 TTCAGAATAA
67698 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * *
67719 ATCGCAA--TGAACTTAGAAT
1 ATCGCAACGCGAACTTCGACT
67738 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* * *
67761 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
67780 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
*
67803 ATCGCAA--CGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
67822 ATCGCAA--CGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
67841 ATCGCAACGCGAACTTAGACT
1 ATCGCAACGCGAACTTCGACT
67862 ATCGCAACG
1 ATCGCAACG
67871 AATTTGGAAA
Statistics
Matches: 128, Mismatches: 14, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
19 55 0.43
21 55 0.43
23 18 0.14
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:67885 original size:40 final size:38
Alignment explanation
Indices: 67803--67886 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 38
67793 AACTTCGACT
* **
67803 ATCGCAACGAACTTGGACTATCGCAACGAACTTGGACT
1 ATCGCAACGAACTTAGACTATCGCAACGAACTTGGAAA
*
67841 ATCGCAACGCGAACTTAGACTATCGCAACGAATTTGGAAA
1 ATCGCAA--CGAACTTAGACTATCGCAACGAACTTGGAAA
67881 ATCGCA
1 ATCGCA
67887 TTGCGATAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 7 0.17
40 33 0.82
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (38 bp):
ATCGCAACGAACTTAGACTATCGCAACGAACTTGGAAA
Found at i:67908 original size:21 final size:21
Alignment explanation
Indices: 67882--67955 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
67872 ATTTGGAAAA
67882 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
67903 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
67924 TCGCGTTGCGATAGTCGATGT
1 TCGCATTGCGATAGTCGAAGT
* *
67945 TCTCGTTGCGA
1 TCGCATTGCGA
67956 ATCTGGAAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Done.