Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003201.1 Hibiscus syriacus cultivar Beakdansim tig00006735_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: 96581
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:9328 original size:7 final size:6
Alignment explanation
Indices: 9299--9332 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
9289 ACTAAGTAAT
*
9299 AAAATA AGAATA AAAATA AAAATA ATAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA A-AAATA AAA
9333 CTATCCTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:12089 original size:10 final size:11
Alignment explanation
Indices: 12068--12123 Score: 53
Period size: 10 Copynumber: 5.2 Consensus size: 11
12058 TTATTTATTT
*
12068 AATAATAGTAA
1 AATAATAATAA
12079 AA-AATAATAA
1 AATAATAATAA
*
12089 AATAAT-ATAT
1 AATAATAATAA
* *
12099 TATAATAATAT
1 AATAATAATAA
12110 AATAATAATTAA
1 AATAATAA-TAA
12122 AA
1 AA
12124 ACTGTGACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
10 17 0.46
11 16 0.43
12 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
AATAATAATAA
Found at i:12105 original size:21 final size:20
Alignment explanation
Indices: 12081--12120 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
12071 AATAGTAAAA
12081 AATAATAAAATAATATATTAT
1 AATAATAAAATAATA-ATTAT
*
12102 AATAATATAATAATAATTA
1 AATAATAAAATAATAATTA
12121 AAAACTGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAAAATAATAATTAT
Found at i:12109 original size:11 final size:11
Alignment explanation
Indices: 12067--12118 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
12057 ATTATTTATT
*
12067 TAATAATAGTA
1 TAATAATAATA
*
12078 -AAAAATAATA
1 TAATAATAATA
*
12088 AAATAAT-ATA
1 TAATAATAATA
*
12098 TTATAATAATA
1 TAATAATAATA
12109 TAATAATAAT
1 TAATAATAAT
12119 TAAAAACTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
TAATAATAATA
Found at i:12463 original size:123 final size:123
Alignment explanation
Indices: 12244--12744 Score: 846
Period size: 123 Copynumber: 4.1 Consensus size: 123
12234 TGATTAAGAC
* * * *
12244 GGAAATGTTGATGTTGCTCTATCTCCTTCTGCAATAAAGTCAAACAAAAGGTTGAATAAGTTCTT
1 GGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTT
*
12309 CAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTTT
66 CAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCT
** * *
12367 GGAAATGACGATGCTGCTCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAATAAGTTCAT
1 GGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTT
12432 CAGATTATGAACTTCTTCTTCCTCTTCAGATGAG---TTCTTATTACGAACTCCTTCT
66 CAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCT
12487 GGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTT
1 GGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTT
12552 CAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCT
66 CAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCT
* *
12610 GGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAATCATGCAAAAGGTTGAATAAGTTCTT
1 GGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTT
* * * *
12675 CATATTATAAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTTATTACGAACTCTTTCT
66 CAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCT
12733 GGAAATGTTGAT
1 GGAAATGTTGAT
12745 CCATCGAGTG
Statistics
Matches: 356, Mismatches: 19, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
120 115 0.32
123 241 0.68
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (123 bp):
GGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTT
CAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCT
Found at i:12672 original size:243 final size:244
Alignment explanation
Indices: 12244--12744 Score: 851
Period size: 243 Copynumber: 2.0 Consensus size: 244
12234 TGATTAAGAC
*
12244 GGAAATGTTGATGTTGCTCTATCTCCTTCTGCAATAAAGTCAAACAAAAGGTTGAATAAGTTCTT
1 GGAAATGTTGATGCTGCTCTATCTCCTTCTGCAATAAAGTCAAACAAAAGGTTGAATAAGTTCTT
*
12309 CAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTTTGGAAATG
66 CAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATG
* *
12374 ACGATGCTGCTCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAATAAGTTCATCAGATTA
131 ACGATGCTGCTCTATCTCCTTCTGCGATAGAATCAAGCAAAAGGTTGAATAAGTTCATCAGATTA
*
12439 TGAACTTCTTCTTCCTCTTCAGATGAG-TTCTTATTACGAACTCCTTCT
196 TAAACTTCTTCTTCCTCTTCAGATGAGTTTCTTATTACGAACTCCTTCT
* * *
12487 GGAAATGTTGATGCTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTTCTT
1 GGAAATGTTGATGCTGCTCTATCTCCTTCTGCAATAAAGTCAAACAAAAGGTTGAATAAGTTCTT
12552 CAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATG
66 CAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATG
** * * *
12617 TTGATGCTGCTCTATCTCCTTCTGCGATAGAATCATGCAAAAGGTTGAATAAGTTCTTCATATTA
131 ACGATGCTGCTCTATCTCCTTCTGCGATAGAATCAAGCAAAAGGTTGAATAAGTTCATCAGATTA
*
12682 TAAACTTCTTCTTCCTCTTCAGATGAGTTTTTCTTATTACGAACTCTTTCT
196 TAAACTTCTTCTTCCTCTTCAGATGAG--TTTCTTATTACGAACTCCTTCT
12733 GGAAATGTTGAT
1 GGAAATGTTGAT
12745 CCATCGAGTG
Statistics
Matches: 241, Mismatches: 14, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
243 209 0.87
246 32 0.13
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (244 bp):
GGAAATGTTGATGCTGCTCTATCTCCTTCTGCAATAAAGTCAAACAAAAGGTTGAATAAGTTCTT
CAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATG
ACGATGCTGCTCTATCTCCTTCTGCGATAGAATCAAGCAAAAGGTTGAATAAGTTCATCAGATTA
TAAACTTCTTCTTCCTCTTCAGATGAGTTTCTTATTACGAACTCCTTCT
Found at i:23706 original size:37 final size:37
Alignment explanation
Indices: 23660--23732 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
23650 ATATATATTT
*
23660 TTTATAATAATAATAAT-TAAAATACTTAATTTAAAAAA
1 TTTATAATAAAAATAATATAAAAT-CTTAA-TTAAAAAA
*
23698 TTTA-AATAAAAATAATATAAAATTTTAATTAAAAA
1 TTTATAATAAAAATAATATAAAATCTTAATTAAAAA
23733 GTGATAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 7 0.22
37 15 0.47
38 10 0.31
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (37 bp):
TTTATAATAAAAATAATATAAAATCTTAATTAAAAAA
Found at i:23742 original size:23 final size:22
Alignment explanation
Indices: 23691--23743 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
23681 ATACTTAATT
*
23691 TAAAAAATTTAAATAAAAATAA
1 TAAAAATTTTAAATAAAAATAA
* *
23713 TATAAAATTTTAATTAAAAAGTGA
1 TA-AAAATTTTAAATAAAAA-TAA
23737 TAAAAAT
1 TAAAAAT
23744 AAAAATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 2 0.08
23 20 0.77
24 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (22 bp):
TAAAAATTTTAAATAAAAATAA
Found at i:25709 original size:3 final size:3
Alignment explanation
Indices: 25703--25753 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
25693 CATATTTATT
*
25703 TAA TAA TAA TAA -AA -AA TAA -AA TAA TAA TAT TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25747 TAA TAA T
1 TAA TAA T
25754 TAAAAACCGT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 8 0.19
3 35 0.81
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:25722 original size:7 final size:8
Alignment explanation
Indices: 25707--25758 Score: 52
Period size: 8 Copynumber: 6.2 Consensus size: 8
25697 TTTATTTAAT
25707 AATAATAA
1 AATAATAA
25715 AA-AATAA
1 AATAATAA
25722 AATAATAA
1 AATAATAA
*
25730 TATTAATAA
1 -AATAATAA
*
25739 TATAATAA
1 AATAATAA
25747 TAATAATTAA
1 -AATAA-TAA
25757 AA
1 AA
25759 ACCGTGACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
7 7 0.19
8 13 0.36
9 13 0.36
10 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
AATAATAA
Found at i:25743 original size:17 final size:17
Alignment explanation
Indices: 25704--25758 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
25694 ATATTTATTT
*
25704 AATAATAATAAAAAATAA
1 AATAATAAT-AATAATAA
*
25722 AATAATAATATTAATAA
1 AATAATAATAATAATAA
*
25739 TATAATAATAATAATTAA
1 AATAATAATAATAA-TAA
25757 AA
1 AA
25759 ACCGTGACAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 18 0.58
18 13 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATAATAATAATAATAA
Found at i:25745 original size:14 final size:14
Alignment explanation
Indices: 25703--25753 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
25693 CATATTTATT
25703 TAATAATAATA-AA
1 TAATAATAATATAA
*
25716 AAATAA-AATAATAA
1 TAATAATAAT-ATAA
*
25730 TATTAATAATATAA
1 TAATAATAATATAA
25744 TAATAATAAT
1 TAATAATAAT
25754 TAAAAACCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 3 0.10
13 6 0.19
14 19 0.61
15 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATAATAATATAA
Found at i:32415 original size:132 final size:132
Alignment explanation
Indices: 32066--32482 Score: 450
Period size: 132 Copynumber: 3.2 Consensus size: 132
32056 ATCAAATTTC
* * * * *
32066 TTTAAAAGATCTGGTTTTCCCTAAAGAGTAATGGAGCATATCCTCTTTTTTTTTAGATTTGGTCT
1 TTTACAAGATCT-GATTACCCTAAAGAGTAGTGGAGCATATCCTC-TTTCTTTTAGATTTGGTCT
* * * * *
32131 TGCTGAAGAGCAACGAAGTAAATCAAGTTTGATTCAATCTTCCCTGAAGAG-AAGCAAAGTGAAT
64 TCCTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAAGAGCAA-CGAAGTGAAT
32195 CAATAA
128 CAA-AA
* * ** *
32201 TTTTCAAGATCTGATTACCCGAAA-A--AGTGGAATATATTCT-TTTCCTTTTAGATTTGGTCTT
1 TTTACAAGATCTGATTACCCTAAAGAGTAGTGGAGCATATCCTCTTT-CTTTTAGATTTGGTCTT
* * *
32262 CCTGAAGAGTAGCGAAGCAAATCACGTTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCA
65 CCTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGAATCA
32327 AAA
130 AAA
* * * * * * *
32330 TTTACAA-TTTTGATCTCCCCTAAAGAGTAGTGGAGCAAATCCTCCTTCTTTCAGATTTGGTATT
1 TTTACAAGATCTGAT-TACCCTAAAGAGTAGTGGAGCATATCCTCTTTCTTTTAGATTTGGTCTT
* * **
32394 CCTTAAGAGCAGTGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAAGAGCAGTGAAGTGAATCA
65 CCTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGAATCA
32459 AAA
130 AAA
**
32462 TTTTTAGAGATCTGATTACCC
1 TTTACA-AGATCTGATTACCC
32483 AAAAAAGTGG
Statistics
Matches: 231, Mismatches: 42, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
128 5 0.02
129 18 0.08
130 72 0.31
131 13 0.06
132 91 0.39
133 8 0.03
134 14 0.06
135 10 0.04
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (132 bp):
TTTACAAGATCTGATTACCCTAAAGAGTAGTGGAGCATATCCTCTTTCTTTTAGATTTGGTCTTC
CTGAAGAGCAGCGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGAATCAA
AA
Found at i:32847 original size:22 final size:22
Alignment explanation
Indices: 32822--32864 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
32812 TGAGGGTGTG
32822 TTTA-TATACATATATATTATAT
1 TTTATTATA-ATATATATTATAT
*
32844 TTTATTATATTATATATTATA
1 TTTATTATAATATATATTATA
32865 AATATATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATTATAATATATATTATAT
Found at i:32848 original size:7 final size:7
Alignment explanation
Indices: 32832--32898 Score: 55
Period size: 7 Copynumber: 9.1 Consensus size: 7
32822 TTTATATACA
32832 TATATAT
1 TATATAT
*
32839 TATATTT
1 TATATAT
32846 TATTATAT
1 TA-TATAT
32854 TATATAT
1 TATATAT
*
32861 TATA-AA
1 TATATAT
*
32867 TATATGT
1 TATATAT
*
32874 TATAATGGT
1 TAT-AT-AT
32883 TATATTAT
1 TATA-TAT
32891 TATATAT
1 TATATAT
32898 T
1 T
32899 GTTATACGTA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
6 5 0.10
7 24 0.49
8 14 0.29
9 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (7 bp):
TATATAT
Found at i:32849 original size:10 final size:12
Alignment explanation
Indices: 32832--32864 Score: 52
Period size: 10 Copynumber: 2.9 Consensus size: 12
32822 TTTATATACA
32832 TATATATTATAT
1 TATATATTATAT
32844 T-T-TATTATAT
1 TATATATTATAT
32854 TATATATTATA
1 TATATATTATA
32865 AATATATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.47
11 2 0.11
12 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATATATTATAT
Found at i:32852 original size:15 final size:15
Alignment explanation
Indices: 32834--32863 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
32824 TATATACATA
*
32834 TATATTATATTTTAT
1 TATATTATATATTAT
32849 TATATTATATATTAT
1 TATATTATATATTAT
32864 AAATATATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATATTATATATTAT
Found at i:37014 original size:2 final size:2
Alignment explanation
Indices: 37007--37048 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
36997 AATATTCAGA
37007 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37049 GTGTGTGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38689 original size:16 final size:16
Alignment explanation
Indices: 38668--38725 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 16
38658 ATCATGCTAC
38668 TTCATTTAAGCATG-A
1 TTCATTTAAGCATGCA
*
38683 GTTCATTAAAGCATGCA
1 -TTCATTTAAGCATGCA
*
38700 TTGCATTTAAGCATGTA
1 TT-CATTTAAGCATGCA
38717 TTTCATTTA
1 -TTCATTTA
38726 GGGAAGTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 15 0.42
17 19 0.53
18 2 0.06
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (16 bp):
TTCATTTAAGCATGCA
Found at i:38752 original size:17 final size:17
Alignment explanation
Indices: 38732--38790 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
38722 TTTAGGGAAG
38732 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
38749 TAG-TCATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
38765 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
38782 TAGTTCATT
1 TAGTTCATT
38791 GGATAAAGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:42236 original size:34 final size:33
Alignment explanation
Indices: 42173--42238 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
42163 AGGAAAGTAG
* *
42173 TTCATTTATGCATCTAGTCATTTAATAAACTAC
1 TTCATTCATGCATCTAGTCATTCAATAAACTAC
*
42206 TTCATTCATGCCAT-TAGTTCATTCATTAAACTA
1 TTCATTCATG-CATCTAG-TCATTCAATAAACTA
42239 GTTTATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 12 0.43
34 16 0.57
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (33 bp):
TTCATTCATGCATCTAGTCATTCAATAAACTAC
Found at i:43333 original size:14 final size:14
Alignment explanation
Indices: 43314--43340 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43304 CATTACTTTC
43314 ATATACATATTTAT
1 ATATACATATTTAT
43328 ATATACATATTTA
1 ATATACATATTTA
43341 CCTTCTTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATACATATTTAT
Found at i:45547 original size:17 final size:16
Alignment explanation
Indices: 45507--45561 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
45497 ATGCTACTTG
45507 ATTTAAGCATGAGTTC
1 ATTTAAGCATGAGTTC
* *
45523 ATTAAAGCATGCGTTGC
1 ATTTAAGCATGAGTT-C
* *
45540 ATTTAAGCTTGTATTTC
1 ATTTAAGCATG-AGTTC
45557 ATTTA
1 ATTTA
45562 GGGAAGTAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 13 0.42
17 16 0.52
18 2 0.06
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (16 bp):
ATTTAAGCATGAGTTC
Found at i:48929 original size:16 final size:17
Alignment explanation
Indices: 48908--48965 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
48898 ACCATGCTAC
*
48908 TTCATTTGAGCATG-AT
1 TTCATTTAAGCATGCAT
*
48924 TTCATTAAAGCATGCAT
1 TTCATTTAAGCATGCAT
* * *
48941 TGCATTTAAGCAAGTAT
1 TTCATTTAAGCATGCAT
48958 TTCATTTA
1 TTCATTTA
48966 GGGAAGTAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
16 12 0.35
17 22 0.65
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (17 bp):
TTCATTTAAGCATGCAT
Found at i:48963 original size:17 final size:17
Alignment explanation
Indices: 48908--48982 Score: 62
Period size: 17 Copynumber: 4.5 Consensus size: 17
48898 ACCATGCTAC
* *
48908 TTCATTTGAGCATG-AT
1 TTCATTTAAGCAAGTAT
* * *
48924 TTCATTAAAGCATGCAT
1 TTCATTTAAGCAAGTAT
*
48941 TGCATTTAAGCAAGTAT
1 TTCATTTAAGCAAGTAT
* * *
48958 TTCATTTAGGGAAGTAG
1 TTCATTTAAGCAAGTAT
48975 TTCATTTA
1 TTCATTTA
48983 TGCATCTAGT
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
16 12 0.25
17 36 0.75
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (17 bp):
TTCATTTAAGCAAGTAT
Found at i:49047 original size:18 final size:17
Alignment explanation
Indices: 49021--49082 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
49011 ATTCATGCAT
*
49021 TTAGCTCATTGAAT-AAA
1 TTAGTTCATT-AATCAAA
49038 GTTAGTTCATTAATCAAA
1 -TTAGTTCATTAATCAAA
* * *
49056 TTGGTTCATTCATAAAA
1 TTAGTTCATTAATCAAA
*
49073 CTAGTTCATT
1 TTAGTTCATT
49083 TGTTAAGATA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
17 25 0.68
18 12 0.32
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.40
Consensus pattern (17 bp):
TTAGTTCATTAATCAAA
Found at i:54936 original size:17 final size:18
Alignment explanation
Indices: 54892--54926 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
54882 AAAATTATAA
54892 AAATATAAATAAAGAAAT
1 AAATATAAATAAAGAAAT
54910 AAATATAAATAAA-AAAT
1 AAATATAAATAAAGAAAT
54927 GAAGTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
AAATATAAATAAAGAAAT
Found at i:54946 original size:5 final size:5
Alignment explanation
Indices: 54931--54959 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
54921 AAAAATGAAG
54931 TTAAA TT-AA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
54960 CTATAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TTAAA
Found at i:56315 original size:17 final size:18
Alignment explanation
Indices: 56288--56321 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
56278 CAATTTACTG
56288 ATTACATTTAATATAAAC
1 ATTACATTTAATATAAAC
56306 ATTA-ATTTAATATAAA
1 ATTACATTTAATATAAA
56322 AATAATATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTACATTTAATATAAAC
Found at i:56665 original size:20 final size:20
Alignment explanation
Indices: 56640--56701 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
56630 CTTCTACTTA
56640 TTTCTTTCTCTTTTCTCTTC
1 TTTCTTTCTCTTTTCTCTTC
* *
56660 TTTCTTCCTCGTTTCTCTTC
1 TTTCTTTCTCTTTTCTCTTC
*
56680 TTTC-TTCTCTCTTCT-TTC
1 TTTCTTTCTCTTTTCTCTTC
56698 TTTC
1 TTTC
56702 ACTCCTGGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 7 0.19
19 8 0.22
20 22 0.59
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTCTTTCTCTTTTCTCTTC
Found at i:56693 original size:7 final size:7
Alignment explanation
Indices: 56642--56699 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
56632 TCTACTTATT
56642 TCTT-TC
1 TCTTCTC
*
56648 TCTTTTC
1 TCTTCTC
*
56655 TCTTCTT
1 TCTTCTC
56662 TCTTC-C
1 TCTTCTC
56668 TCGTT-TC
1 TC-TTCTC
*
56675 TCTTCTT
1 TCTTCTC
56682 TCTTCTC
1 TCTTCTC
*
56689 TCTTCTT
1 TCTTCTC
56696 TCTT
1 TCTT
56700 TCACTCCTGG
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
6 8 0.19
7 34 0.81
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.66
Consensus pattern (7 bp):
TCTTCTC
Found at i:56701 original size:27 final size:27
Alignment explanation
Indices: 56626--56701 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
56616 CACGAATTGA
* *
56626 TTCTCTTCT-ACTTATTTCTTTCTCTT
1 TTCTCTTCTCTCTTCTTTCTTTCTCTT
* *
56652 TTCTCTTCTTTCTTC-CTCGTTTCTCTT
1 TTCTCTTCTCTCTTCTTTC-TTTCTCTT
56679 CTT-TCTTCTCTCTTCTTTCTTTC
1 -TTCTCTTCTCTCTTCTTTCTTTC
56702 ACTCCTGGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
26 11 0.27
27 26 0.63
28 4 0.10
ACGTcount: A:0.03, C:0.32, G:0.01, T:0.64
Consensus pattern (27 bp):
TTCTCTTCTCTCTTCTTTCTTTCTCTT
Found at i:57394 original size:17 final size:18
Alignment explanation
Indices: 57368--57412 Score: 83
Period size: 17 Copynumber: 2.6 Consensus size: 18
57358 ATTAAAGTTT
57368 AATCAATTTATTTCTAAC
1 AATCAATTTATTTCTAAC
57386 AAT-AATTTATTTCTAAC
1 AATCAATTTATTTCTAAC
57403 AATCAATTTA
1 AATCAATTTA
57413 AACATTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (18 bp):
AATCAATTTATTTCTAAC
Found at i:63270 original size:26 final size:26
Alignment explanation
Indices: 63240--63313 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 26
63230 TGATCACTCA
*
63240 CACCTTAAAAAACTCTAAACCACTTT
1 CACCTTAAAAAACTCTATACCACTTT
* *
63266 CACC-TACAAAA-TCCTTTACCACTTT
1 CACCTTAAAAAACT-CTATACCACTTT
* * *
63291 TACCTTAATAAACCCTATACCAC
1 CACCTTAAAAAACTCTATACCAC
63314 ATTAACCTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
24 1 0.03
25 19 0.51
26 17 0.46
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (26 bp):
CACCTTAAAAAACTCTATACCACTTT
Found at i:63296 original size:51 final size:51
Alignment explanation
Indices: 63202--63322 Score: 134
Period size: 51 Copynumber: 2.4 Consensus size: 51
63192 CGAACTTTAT
* *
63202 CCTAAACCACTTTAACCTACACAACCCTTGATCACTCACACCTTAAAAAAC
1 CCTAAACCACTTTAACCTACAAAACCCTTGACCACTCACACCTTAAAAAAC
* * * * *** *
63253 TCTAAACCACTTTCACCTACAAAATCCTTTACCACTTTTACCTTAATAAAC
1 CCTAAACCACTTTAACCTACAAAACCCTTGACCACTCACACCTTAAAAAAC
* *
63304 CCTATACCACATTAACCTA
1 CCTAAACCACTTTAACCTA
63323 AAATTACTCT
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.37, C:0.35, G:0.01, T:0.27
Consensus pattern (51 bp):
CCTAAACCACTTTAACCTACAAAACCCTTGACCACTCACACCTTAAAAAAC
Found at i:63668 original size:28 final size:29
Alignment explanation
Indices: 63613--63668 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
63603 CAGCCGAATG
* * * *
63613 GGTGTTACTTTGGGAAATATTGGGAAAAC
1 GGTGTTACATCGGGAAATATTAGAAAAAC
63642 GGTGTTACATCGGG-AATATTAGAAAAA
1 GGTGTTACATCGGGAAATATTAGAAAAA
63669 TAGGGTGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.36, C:0.07, G:0.29, T:0.29
Consensus pattern (29 bp):
GGTGTTACATCGGGAAATATTAGAAAAAC
Found at i:64808 original size:13 final size:13
Alignment explanation
Indices: 64790--64814 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64780 GGTCACGACC
64790 TGACCCGACCCGT
1 TGACCCGACCCGT
64803 TGACCCGACCCG
1 TGACCCGACCCG
64815 ATCGTTGACC
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:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:64812 original size:18 final size:17
Alignment explanation
Indices: 64786--64824 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
64776 GATCGGTCAC
*
64786 GACCTGACCCGACCCGTT
1 GACCCGACCCGA-CCGTT
*
64804 GACCCGACCCGATCGTT
1 GACCCGACCCGACCGTT
64821 GACC
1 GACC
64825 GTTGACCGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.18, C:0.44, G:0.23, T:0.15
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:64874 original size:29 final size:29
Alignment explanation
Indices: 64832--64913 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
64822 ACCGTTGACC
64832 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
*
64861 GGTGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
*
64890 GGTGCTATTCTGGTAATTAATTCA
1 GGTGCTATTCTGGTAAATAATTCA
64914 AAATGAGTGC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.23, C:0.11, G:0.22, T:0.44
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCAGTTTT
Found at i:64923 original size:29 final size:28
Alignment explanation
Indices: 64832--64934 Score: 91
Period size: 29 Copynumber: 3.6 Consensus size: 28
64822 ACCGTTGACC
***
64832 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCA-AAAT
****
64861 GGTGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTC-AAAAT
*
64890 GGTGCTATTCTGGTAATTAATTCAAAAT
1 GGTGCTATTCTGGTAAATAATTCAAAAT
64918 GAGTGCTATAT-TGGTAA
1 G-GTGCTAT-TCTGGTAA
64935 TTATTTTAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
28 2 0.03
29 62 0.95
30 1 0.02
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.42
Consensus pattern (28 bp):
GGTGCTATTCTGGTAAATAATTCAAAAT
Found at i:64935 original size:29 final size:28
Alignment explanation
Indices: 64891--64963 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
64881 TTCGGTTTTG
*
64891 GTGCTATTCTGGTAATTAATTCAAAATGA
1 GTGCTATT-TGGTAATTAATTCAAAAAGA
* * *
64920 GTGCTATATTGGTAATTATTTTAAAAAGG
1 GTGCTAT-TTGGTAATTAATTCAAAAAGA
64949 GTGCTATTTGTGTAA
1 GTGCTATTTG-GTAA
64964 AAAGTTCAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 3 0.08
29 34 0.89
30 1 0.03
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.41
Consensus pattern (28 bp):
GTGCTATTTGGTAATTAATTCAAAAAGA
Found at i:72257 original size:17 final size:18
Alignment explanation
Indices: 72225--72259 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
72215 TGACCGGTCA
72225 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
72243 CGACCCGA-TCGTTGACC
1 CGACCCGACCCGTTGACC
72260 GTTGACCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.14
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:72314 original size:28 final size:29
Alignment explanation
Indices: 72267--72347 Score: 101
Period size: 28 Copynumber: 2.8 Consensus size: 29
72257 ACCGTTGACC
* *
72267 GGTGCTATTTTGGTAAATAATTTGGTTCT
1 GGTGCTATTCTAGTAAATAATTTGGTTCT
* * *
72296 GGTGTTATTCT-GTAAATAATTCGGTTTT
1 GGTGCTATTCTAGTAAATAATTTGGTTCT
*
72324 GGTGCTATTCTAGTATATAATTTG
1 GGTGCTATTCTAGTAAATAATTTG
72348 AAATGAGTGC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 25 0.57
29 19 0.43
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (29 bp):
GGTGCTATTCTAGTAAATAATTTGGTTCT
Found at i:78346 original size:266 final size:265
Alignment explanation
Indices: 77887--78406 Score: 853
Period size: 266 Copynumber: 2.0 Consensus size: 265
77877 CATCGTCGTG
* *
77887 GATTCTTTGTGTACTTATTATAAAGCCTAAAAAGATAAGCTTACAAAACAAGTAATTGTCCATGT
1 GATTCTTTGTGCACTTATTATAAACCCTAAAAAGATAAGCTTACAAAACAAGTAATTGTCCATGT
* * * *
77952 TAGCATAAAAGTGTTATCGTTGGAGAACATTAAGAACCGAGTGGAAGTGGGAGAGATATAAATCA
66 TAGCATAAAAGTGTTATCATTGGAGAACATCAAGAACCAAGTGGAAGTGGGAGAGATAAAAATCA
*
78017 AAAGAAGGTGAGTAGATAAGAATATCATCAAAGTAAACAACATACTTACCTTTGGCATGGTTAGT
131 AAAGAAGATGAGTAGATAAGAATATCATCAAAGTAAACAACATACTTACCTTTGGCATGGTTA--
* *
78082 GCTATTGTTTCATCAATGAGATGGCACAATGACTAAGGCTTTCCTGGATGTAGCCTTTTCAGCAT
194 GCTATTGTTTCATCAATAAGATGGAACAATGACTAAGGCTTTCCTGGATGTAGCCTTTTCAGCAT
78147 CGACAAA
259 CGACAAA
*
78154 GATTCTTTGTGCACTTATTATAAACCCTAAAAAGATAAGCTTACAAAA-AAGTATTTGTCCATGT
1 GATTCTTTGTGCACTTATTATAAACCCTAAAAAGATAAGCTTACAAAACAAGTAATTGTCCATGT
* *
78218 TAGCATAAAAGTGTTCTCATTGGAGAACATCAAGAATCAAGTGGAAGTGGGAGAGATAAAAATCA
66 TAGCATAAAAGTGTTATCATTGGAGAACATCAAGAACCAAGTGGAAGTGGGAGAGATAAAAATCA
* * * * *
78283 AGAGAATATGAGTAGATAAGAATATCATGAAAGTAAACAACATACTTATCTTTGGCTTGGTTAGC
131 AAAGAAGATGAGTAGATAAGAATATCATCAAAGTAAACAACATACTTACCTTTGGCATGGTTAGC
*
78348 TATTGTTTCATCACTAAGATGGAACAATGACTAAGGCTTTCCTGGATGTAGCCTTTTCA
196 TATTGTTTCATCAATAAGATGGAACAATGACTAAGGCTTTCCTGGATGTAGCCTTTTCA
78407 CAGCAAATCT
Statistics
Matches: 235, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
264 58 0.25
266 131 0.56
267 46 0.20
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (265 bp):
GATTCTTTGTGCACTTATTATAAACCCTAAAAAGATAAGCTTACAAAACAAGTAATTGTCCATGT
TAGCATAAAAGTGTTATCATTGGAGAACATCAAGAACCAAGTGGAAGTGGGAGAGATAAAAATCA
AAAGAAGATGAGTAGATAAGAATATCATCAAAGTAAACAACATACTTACCTTTGGCATGGTTAGC
TATTGTTTCATCAATAAGATGGAACAATGACTAAGGCTTTCCTGGATGTAGCCTTTTCAGCATCG
ACAAA
Found at i:78954 original size:19 final size:19
Alignment explanation
Indices: 78926--78965 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
78916 GTATAGTTCG
78926 TAATGGTAT-GTACAAATGA
1 TAATGGTATGGTA-AAATGA
*
78945 TAATGTTATGGTAAAATGA
1 TAATGGTATGGTAAAATGA
78964 TA
1 TA
78966 TGGATGTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (19 bp):
TAATGGTATGGTAAAATGA
Found at i:81160 original size:14 final size:14
Alignment explanation
Indices: 81128--81161 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
81118 TTTATTCACA
81128 ATTTCATTTTTTTC
1 ATTTCATTTTTTTC
81142 A-TTCATTTTTTTC
1 ATTTCATTTTTTTC
81155 ATTTCAT
1 ATTTCAT
81162 GCGGGGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTCATTTTTTTC
Found at i:88907 original size:19 final size:19
Alignment explanation
Indices: 88883--88922 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
88873 TAGCTCGTGA
*
88883 CATCTAGTTCTGGCTGTAG
1 CATCTAGTTCTAGCTGTAG
88902 CATCTAGTTCTAGCTGTAG
1 CATCTAGTTCTAGCTGTAG
88921 CA
1 CA
88923 AAACATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (19 bp):
CATCTAGTTCTAGCTGTAG
Found at i:92556 original size:20 final size:19
Alignment explanation
Indices: 92531--92584 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
92521 GCGAAATAAA
92531 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
92551 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
92571 AATCGCAACGCGAT
1 AATCGCAACGCGAT
92585 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:92595 original size:21 final size:20
Alignment explanation
Indices: 92571--92688 Score: 62
Period size: 20 Copynumber: 5.8 Consensus size: 20
92561 CAGTTCCCAG
92571 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
**
92591 GAATCGCAATACGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
92612 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
* *
92634 AATCTCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
92654 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
92674 AATCGCAACGCGATT
1 AATCGCAACGCGATT
92689 CTGACTATCG
Statistics
Matches: 72, Mismatches: 18, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
19 2 0.03
20 35 0.49
21 31 0.43
22 3 0.04
23 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:92662 original size:20 final size:20
Alignment explanation
Indices: 92634--92884 Score: 183
Period size: 20 Copynumber: 12.5 Consensus size: 20
92624 GATTTTCCAG
* * *
92634 AATCTCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
92654 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
92674 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * * *
92693 CTATCGCAATGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* *
92715 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
92735 AATTGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
92756 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
* *
92776 AATCGCAATGAGAATACGTA
1 AATCGCAACGCGAATACGTA
92796 AATCGCAACGC--ATATCTGTA
1 AATCGCAACGCGAATA-C-GTA
*
92816 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
*
92836 AATCGCAATGCGAATAC-TA
1 AATCGCAACGCGAATACGTA
*
92855 AATCGCAATGCGAAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
92875 AATCGCAACG
1 AATCGCAACG
92885 AGATTCTGAC
Statistics
Matches: 187, Mismatches: 31, Indels: 26
0.77 0.13 0.11
Matches are distributed among these distances:
18 5 0.03
19 20 0.11
20 121 0.65
21 36 0.19
22 5 0.03
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:92726 original size:41 final size:41
Alignment explanation
Indices: 92672--92892 Score: 219
Period size: 41 Copynumber: 5.5 Consensus size: 41
92662 CGCGAACATA
* * *
92672 TAAATCGCAACGCGAT-TCTG-ACTATCGCAATGAGTATCCG
1 TAAATCGCAACGCGATATCTGTA-AATCGCAATGAGAATACG
* * * *
92712 TAAAATCGCAACGCG-TATCCGTAAATTGCAACGACAATACG
1 T-AAATCGCAACGCGATATCTGTAAATCGCAATGAGAATACG
*
92753 TAAAATCGCAACGCG-TATCCGTAAATCGCAATGAGAATACG
1 T-AAATCGCAACGCGATATCTGTAAATCGCAATGAGAATACG
*
92794 TAAATCGCAACGC-ATATCTGTAAATCGCAACGAGAATACG
1 TAAATCGCAACGCGATATCTGTAAATCGCAATGAGAATACG
* *
92834 TAAATCGCAATGCGA-ATAC--TAAATCGCAATGCGAAT-CTG
1 TAAATCGCAACGCGATAT-CTGTAAATCGCAATGAGAATAC-G
*
92873 TAAATCGCAACGAGAT-TCTG
1 TAAATCGCAACGCGATATCTG
92893 ACTATCGCAA
Statistics
Matches: 154, Mismatches: 17, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 52 0.34
41 69 0.45
42 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.22
Consensus pattern (41 bp):
TAAATCGCAACGCGATATCTGTAAATCGCAATGAGAATACG
Found at i:92903 original size:59 final size:60
Alignment explanation
Indices: 92672--92887 Score: 201
Period size: 61 Copynumber: 3.6 Consensus size: 60
92662 CGCGAACATA
* * * * * * * *
92672 TAAATCGCAACGCGAT-TCTG-ACTATCGCAATGAGTATCCGTAAAATCGCAACGCGTATCCG
1 TAAATCGCAACGC-ATATCTGTA-AATCGCAACGAGAATACGT-AAATCGCAATGAGAATACG
* * * *
92733 TAAATTGCAACGACA-ATAC-GTAAAATCGCAACGCGTATCCGTAAATCGCAATGAGAATACG
1 TAAATCGCAACG-CATAT-CTGT-AAATCGCAACGAGAATACGTAAATCGCAATGAGAATACG
*
92794 TAAATCGCAACGCATATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGAATAC-
1 TAAATCGCAACGCATATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGAGAATACG
*
92853 TAAATCGCAATGCGA-ATCTGTAAATCGCAACGAGA
1 TAAATCGCAACGC-ATATCTGTAAATCGCAACGAGA
92888 TTCTGACTAT
Statistics
Matches: 133, Mismatches: 14, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
59 32 0.24
60 38 0.29
61 44 0.33
62 18 0.14
63 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (60 bp):
TAAATCGCAACGCATATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGAGAATACG
Found at i:93752 original size:24 final size:24
Alignment explanation
Indices: 93733--93792 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
93723 TAGTCAGTAT
93733 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * *
93757 CCGGACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
93781 TCGAATTTTGAT
1 TCGAAATTTGAT
93793 GATTTTCAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:95615 original size:19 final size:19
Alignment explanation
Indices: 95591--95662 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 19
95581 TAAAATCATA
95591 TTTAGTTTCGCGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
*
95610 TTTAGTTTCACGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
95629 TTT-G--T--CGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
*
95643 TTTCA-TTTCGCATTGCGAT
1 TTT-AGTTTCGCGTTGCGAT
95662 T
1 T
95663 CTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
14 12 0.27
16 1 0.02
17 1 0.02
18 1 0.02
19 30 0.67
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (19 bp):
TTTAGTTTCGCGTTGCGAT
Found at i:95643 original size:33 final size:33
Alignment explanation
Indices: 95601--95694 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 33
95591 TTTAGTTTCG
* * *
95601 CGTTGCGATTTT-AGTTTCACGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCACATTGCGATTCTCT
*
95634 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCACATTGCGATTCTCT
*
95667 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCACATTGCGAT
95695 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 55 0.98
34 1 0.02
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCACATTGCGATTCTCT
Found at i:95693 original size:19 final size:19
Alignment explanation
Indices: 95636--95694 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
95626 GATTTTGTCG
95636 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
95655 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
95669 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
95688 TTGCGAT
1 TTGCGAT
95695 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:95702 original size:19 final size:17
Alignment explanation
Indices: 95644--95694 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
95634 CGTTGCGATT
95644 TTCATTTCGCATTGCGA
1 TTCATTTCGCATTGCGA
*
95661 TTC-TCTCG--TTGCGA
1 TTCATTTCGCATTGCGA
95675 TTTTCATTTCGCATTGCGA
1 --TTCATTTCGCATTGCGA
95694 T
1 T
95695 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
14 6 0.22
16 7 0.26
17 8 0.30
19 6 0.22
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (17 bp):
TTCATTTCGCATTGCGA
Found at i:96400 original size:94 final size:94
Alignment explanation
Indices: 96254--96581 Score: 595
Period size: 94 Copynumber: 3.5 Consensus size: 94
96244 ATGGATTACA
* * *
96254 TTAC-TTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
96318 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
96347 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCATAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
96412 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
96441 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
96506 TTAGCGGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
96535 TTAATTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAG
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAG
Statistics
Matches: 228, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
93 4 0.02
94 224 0.98
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.20
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Done.