Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000489.1 Hibiscus syriacus cultivar Beakdansim tig00000933_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: 167646
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2818 original size:2 final size:2
Alignment explanation
Indices: 2811--2838 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2801 TCTCTAATCC
2811 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
2839 GCATAACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10880 original size:23 final size:23
Alignment explanation
Indices: 10835--10880 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
10825 TTATACCTAT
* *
10835 AGATACTTATTTCATATGTTATA
1 AGATAATTATTTCATATGATATA
10858 AGATAATTATTTTCATAT-ATATA
1 AGATAATTA-TTTCATATGATATA
10881 TATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (23 bp):
AGATAATTATTTCATATGATATA
Found at i:12530 original size:21 final size:21
Alignment explanation
Indices: 12488--12538 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
12478 ATTGGAGTGC
12488 AAAAAGAAAGAAAACACAAAAA
1 AAAAAG-AAGAAAACACAAAAA
* *
12510 GAAAAGAAGAAAAGA-AGAAAA
1 AAAAAGAAGAAAACACA-AAAA
12531 AAAAAGAA
1 AAAAAGAA
12539 AAAGATTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 19 0.76
22 5 0.20
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAAAGAAGAAAACACAAAAA
Found at i:12540 original size:8 final size:8
Alignment explanation
Indices: 12488--12543 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
12478 ATTGGAGTGC
12488 AAAAAGAA
1 AAAAAGAA
* *
12496 AGAAAACAC
1 A-AAAAGAA
12505 AAAAAGAA
1 AAAAAGAA
*
12513 AAGAAGAA
1 AAAAAGAA
*
12521 AAGAAGAA
1 AAAAAGAA
12529 AAAAA-AA
1 AAAAAGAA
12536 GAAAAAGA
1 -AAAAAGA
12544 TTTCAAAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
7 2 0.05
8 30 0.77
9 7 0.18
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:15383 original size:23 final size:23
Alignment explanation
Indices: 15329--15385 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
15319 TTTCTATCTT
*
15329 TATATCTATAGATACTTATTTCA
1 TATATATATAGATACTTATTTCA
* *
15352 TATGT-TATAAGATAGTTATTTTCA
1 TATATATAT-AGATACTTA-TTTCA
15376 TATATATATA
1 TATATATATA
15386 TTAGACCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 3 0.11
23 12 0.43
24 10 0.36
25 3 0.11
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (23 bp):
TATATATATAGATACTTATTTCA
Found at i:17383 original size:27 final size:26
Alignment explanation
Indices: 17330--17386 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
17320 TCCCATCCTT
* * *
17330 ATTTCATTTCATTTCTTATCTTTATC
1 ATTTCATTTAATTTCTTATATTAATC
*
17356 ATTTCATTTAATCTTCTTTTATTAATC
1 ATTTCATTTAAT-TTCTTATATTAATC
17383 ATTT
1 ATTT
17387 TCCTTTCTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTTCATTTAATTTCTTATATTAATC
Found at i:17646 original size:18 final size:18
Alignment explanation
Indices: 17622--17669 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
17612 AGAAAAGACA
* *
17622 AAAAGAATAAAAATTCAG
1 AAAAGAAGAAAAATTAAG
*
17640 AATAGAAGAAAAATTAAG
1 AAAAGAAGAAAAATTAAG
17658 AAAAGAAGAAAA
1 AAAAGAAGAAAA
17670 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.71, C:0.02, G:0.15, T:0.12
Consensus pattern (18 bp):
AAAAGAAGAAAAATTAAG
Found at i:22309 original size:24 final size:24
Alignment explanation
Indices: 22282--22336 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
22272 AGAATCATGG
22282 CTTTTGGAGAACTAAA-AGATGTAA
1 CTTTTGGAGAAC-AAATAGATGTAA
** * *
22306 CTTTTAAAGAACAAATAGTTGTTA
1 CTTTTGGAGAACAAATAGATGTAA
22330 CTTTTGG
1 CTTTTGG
22337 TGATCAACGA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (24 bp):
CTTTTGGAGAACAAATAGATGTAA
Found at i:25036 original size:6 final size:6
Alignment explanation
Indices: 24995--25038 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
24985 AAAACCAACA
*
24995 AAAAGAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAAAG A
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
25039 CTCCTACATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:26312 original size:24 final size:24
Alignment explanation
Indices: 26284--26338 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
26274 AGATTCATGG
26284 CTTTTGGAGAACTAAA-AGATGTGA
1 CTTTTGGAGAAC-AAATAGATGTGA
** * *
26308 CTTTTAAAGAACAAATAGTTGTTA
1 CTTTTGGAGAACAAATAGATGTGA
26332 CTTTTGG
1 CTTTTGG
26339 TGATTAACGA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (24 bp):
CTTTTGGAGAACAAATAGATGTGA
Found at i:33701 original size:32 final size:32
Alignment explanation
Indices: 33651--33741 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 32
33641 CATATACTAC
* * *
33651 TCAGGTTTGTATTAAGATAATGCACAGTATAG
1 TCAGGTTTGCATTCAGATAATGCACAATATAG
*
33683 TCAGGTTTGCATTCAGATAATGCGCAATATAG
1 TCAGGTTTGCATTCAGATAATGCACAATATAG
*
33715 TAAGGTATT-CATTC--ATAATGCACAATA
1 TCAGGT-TTGCATTCAGATAATGCACAATA
33742 GTATTAGTGT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
30 12 0.23
32 38 0.73
33 2 0.04
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (32 bp):
TCAGGTTTGCATTCAGATAATGCACAATATAG
Found at i:35132 original size:19 final size:19
Alignment explanation
Indices: 35102--35146 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
35092 TTATGAAAAA
*
35102 TCCTTGAGGTGAAAGAGGT
1 TCCTTGAAGTGAAAGAGGT
*
35121 TTCTTGAAGTGAAAGAGGT
1 TCCTTGAAGTGAAAGAGGT
35140 TCCTTGA
1 TCCTTGA
35147 GGGACTTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.27, C:0.11, G:0.31, T:0.31
Consensus pattern (19 bp):
TCCTTGAAGTGAAAGAGGT
Found at i:41183 original size:22 final size:21
Alignment explanation
Indices: 41144--41184 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
41134 CATCTCCATT
41144 TCATCATCAACACCATCAACA
1 TCATCATCAACACCATCAACA
* *
41165 TCATCCATCAAGACTATCAA
1 TCAT-CATCAACACCATCAA
41185 TTCCACAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.41, C:0.34, G:0.02, T:0.22
Consensus pattern (21 bp):
TCATCATCAACACCATCAACA
Found at i:41345 original size:8 final size:8
Alignment explanation
Indices: 41317--41357 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
41307 AGGAAAGAAA
41317 AAGAAAAG
1 AAGAAAAG
*
41325 ACA-AAAGG
1 A-AGAAAAG
41333 AAGAAAAG
1 AAGAAAAG
41341 AAGAAAAG
1 AAGAAAAG
41349 AA-AAAAG
1 AAGAAAAG
41356 AA
1 AA
41358 TAGAATTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
7 8 0.28
8 20 0.69
9 1 0.03
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (8 bp):
AAGAAAAG
Found at i:47094 original size:19 final size:19
Alignment explanation
Indices: 47070--47114 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
47060 TATGACAAAG
47070 TCCTTGAGGTGAAAGAGGT
1 TCCTTGAGGTGAAAGAGGT
47089 TCCTTGAGGTGAAAGAGGT
1 TCCTTGAGGTGAAAGAGGT
47108 TCCTTGA
1 TCCTTGA
47115 TGGACTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.13, G:0.33, T:0.29
Consensus pattern (19 bp):
TCCTTGAGGTGAAAGAGGT
Found at i:53199 original size:22 final size:21
Alignment explanation
Indices: 53163--53203 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
53153 CATCTCCATT
53163 TCATCATCAACACCATCAACA
1 TCATCATCAACACCATCAACA
*
53184 TCATCCATCAAGACCATCAA
1 TCAT-CATCAACACCATCAA
53204 TTCCATAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.41, C:0.37, G:0.02, T:0.20
Consensus pattern (21 bp):
TCATCATCAACACCATCAACA
Found at i:55510 original size:3 final size:3
Alignment explanation
Indices: 55502--55566 Score: 85
Period size: 3 Copynumber: 21.3 Consensus size: 3
55492 CCATTTTAAA
* * * *
55502 ATT ATT ATT ATT ATT ATA ATT ATT ACT ATT ATT ATT AAT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
55550 ATTT ATT ATT ATT ATT A
1 A-TT ATT ATT ATT ATT A
55567 AATAAATATA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:57176 original size:131 final size:131
Alignment explanation
Indices: 56937--57274 Score: 339
Period size: 128 Copynumber: 2.6 Consensus size: 131
56927 TAAAAGTATT
* *
56937 TATTTATTTTTAATATTAAGAAAGGGGTTGTCTTAAAATAACTAGTTGTCCTTTTCTGATATTTT
1 TATTTATTTTTAATATTAAGAAAGGGGTTGTCTTAAAATAACTAGATGTCATTTTCTGATATTTT
* *
57002 AAAATAAATAAAATGCTATATTTAATTTAATAATATTTATATATATTAAGGTAAATATCATATTT
66 --AATAAATAAAATACTATATTTAAATTAATAATATTTATATATATTAAGGTAAATATCATATTT
57067 TTA
129 TTA
* *
57070 TATTTATTTTTTAATATT-A-AAAGGGG-TGTCTTAAAATAACTGGATGTCATTTTTTGATATTT
1 TATTTA-TTTTTAATATTAAGAAAGGGGTTGTCTTAAAATAACTAGATGTCATTTTCTGATATTT
* * * ** * ****
57132 T-TTAAATAAAATATTATATTTAAATTAGTTTTATTTAAATTATATTTTTTTAGAA-AT--TATC
65 TAATAAATAAAATACTATATTTAAATTAATAATATTTATA-TATATTAAGGTA-AATATCATAT-
* *
57193 ATTAA
127 TTTTA
* * * *
57198 TATTTATTTATTTATATTAAGGAAATGGGTTGTCTTAAAGTAACTATATGTCATTTTCTGATATT
1 TATTTATTT-TTAATATTAA-GAAAGGGGTTGTCTTAAAATAACTAGATGTCATTTTCTGATATT
57263 TCTAAATAAATA
64 T-T-AATAAATA
57275 TCCTATTTAT
Statistics
Matches: 168, Mismatches: 25, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
127 6 0.04
128 46 0.27
129 11 0.07
130 2 0.01
131 39 0.23
132 39 0.23
133 8 0.05
134 11 0.07
135 6 0.04
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (131 bp):
TATTTATTTTTAATATTAAGAAAGGGGTTGTCTTAAAATAACTAGATGTCATTTTCTGATATTTT
AATAAATAAAATACTATATTTAAATTAATAATATTTATATATATTAAGGTAAATATCATATTTTT
A
Found at i:59923 original size:42 final size:43
Alignment explanation
Indices: 59845--59929 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 43
59835 TGTCTTTGGA
* *
59845 GAAGTTATGAATGAAAGTTATCCCCTATATGTAAAGTTTTGTT
1 GAAGTTAGGAATGAAAGCTATCCCCTATATGTAAAGTTTTGTT
* *
59888 GAAGTTAGGAGTGAAAGCTAT-CTCTATATGTAAAGTTTTGTT
1 GAAGTTAGGAATGAAAGCTATCCCCTATATGTAAAGTTTTGTT
59930 TGATGTACCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
42 20 0.53
43 18 0.47
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (43 bp):
GAAGTTAGGAATGAAAGCTATCCCCTATATGTAAAGTTTTGTT
Found at i:61606 original size:15 final size:15
Alignment explanation
Indices: 61588--61618 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
61578 GAGAAATGAA
61588 GAAAAGAAAGGAAAG
1 GAAAAGAAAGGAAAG
*
61603 GAAATGAAAGGAAAG
1 GAAAAGAAAGGAAAG
61618 G
1 G
61619 TAATTCGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.35, T:0.03
Consensus pattern (15 bp):
GAAAAGAAAGGAAAG
Found at i:63053 original size:14 final size:16
Alignment explanation
Indices: 63029--63060 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
63019 GAAAAGAAAA
63029 AAGAGATG-AAAACAG
1 AAGAGATGAAAAACAG
63044 AAGA-ATGAAAAACAG
1 AAGAGATGAAAAACAG
63059 AA
1 AA
63061 AAAAAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.19
15 13 0.81
ACGTcount: A:0.66, C:0.06, G:0.22, T:0.06
Consensus pattern (16 bp):
AAGAGATGAAAAACAG
Found at i:63093 original size:16 final size:16
Alignment explanation
Indices: 63034--63095 Score: 60
Period size: 15 Copynumber: 4.1 Consensus size: 16
63024 GAAAAAAGAG
*
63034 ATGAAAACAGAAG--A
1 ATGAAAAAAGAAGAAA
63048 ATGAAAAACAGAA-AAA
1 ATGAAAAA-AGAAGAAA
*
63064 AAGAAAAAAG-AGAAA
1 ATGAAAAAAGAAGAAA
*
63079 ATGAAAGAAGAAGAAA
1 ATGAAAAAAGAAGAAA
63095 A
1 A
63096 ATTGAATCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 8 0.21
15 17 0.44
16 14 0.36
ACGTcount: A:0.73, C:0.03, G:0.19, T:0.05
Consensus pattern (16 bp):
ATGAAAAAAGAAGAAA
Found at i:64683 original size:74 final size:75
Alignment explanation
Indices: 64585--64757 Score: 224
Period size: 75 Copynumber: 2.3 Consensus size: 75
64575 ATCAAACAAG
* *
64585 AAGCAAATGTTAGGGCATGCTGAAAGCCCATTT-AATCAAAAAT-AGGAATGTTTACGCATTTTG
1 AAGCAAATGTTAGGGCATGATGAAAGCCCATTTCAAT-AAAAATCAGGAATGTTGACGCATTTTG
*
64648 AATGTTTGTAT
65 AACGTTTGTAT
* * * *
64659 AAGCAAATGTTAGGGTATGATGAAAGCCCATTTCAATAAGAATCAGGAATGTTGATGCGTTTTGA
1 AAGCAAATGTTAGGGCATGATGAAAGCCCATTTCAATAAAAATCAGGAATGTTGACGCATTTTGA
64724 ACGTTTGTAT
66 ACGTTTGTAT
* * * *
64734 CAGCAAATGCTGGGGCATGCTGAA
1 AAGCAAATGTTAGGGCATGATGAA
64758 GGCTAATATC
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
74 36 0.42
75 49 0.58
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.30
Consensus pattern (75 bp):
AAGCAAATGTTAGGGCATGATGAAAGCCCATTTCAATAAAAATCAGGAATGTTGACGCATTTTGA
ACGTTTGTAT
Found at i:65778 original size:53 final size:53
Alignment explanation
Indices: 65631--65783 Score: 189
Period size: 54 Copynumber: 2.8 Consensus size: 53
65621 AAATCTAGGA
* * * *
65631 AGAAGCCACAAGAAAGAATAAATATGTTGTCAAATATTTTACGAATATCTGTGC
1 AGAAACCACAAGAAAG-ATGAATGTGTTGTCAAATATTTTACGAACATCTGTGC
* * * * *
65685 AGAAACCATAGGAAATGATGAATGTGTTGTCAAAAATTTTACGAACATCTTTGT
1 AGAAACCACAAGAAA-GATGAATGTGTTGTCAAATATTTTACGAACATCTGTGC
* *
65739 AGAAACCACAAGAAAGATGATTGTGTTGTCAAATGTTTTACGAAC
1 AGAAACCACAAGAAAGATGAATGTGTTGTCAAATATTTTACGAAC
65784 CAGTAATTAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
53 27 0.32
54 56 0.67
55 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (53 bp):
AGAAACCACAAGAAAGATGAATGTGTTGTCAAATATTTTACGAACATCTGTGC
Found at i:66151 original size:22 final size:23
Alignment explanation
Indices: 66123--66203 Score: 114
Period size: 22 Copynumber: 3.7 Consensus size: 23
66113 CTGCATCTAC
*
66123 ATTCTTCAAAGATAATAGATT-T
1 ATTCTTCAAAGATGATAGATTCT
66145 ATTCTTCAAAGATGATAGATTCT
1 ATTCTTCAAAGATGATAGATTCT
*
66168 -CTCTTCAAAGATGATAGATTCT
1 ATTCTTCAAAGATGATAGATTCT
*
66190 CTT-TTCAAAGATGA
1 ATTCTTCAAAGATGA
66204 AAGTTTTATT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
22 52 0.96
23 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (23 bp):
ATTCTTCAAAGATGATAGATTCT
Found at i:69750 original size:25 final size:22
Alignment explanation
Indices: 69721--69766 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
69711 TTTTTAACCC
69721 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
69746 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
69767 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:74262 original size:25 final size:22
Alignment explanation
Indices: 74233--74278 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
74223 TTTTTAACCC
74233 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
74258 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
74279 GCATCATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:77813 original size:43 final size:47
Alignment explanation
Indices: 77738--77840 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 47
77728 ATAACTAATG
77738 AATAAAATAATAATAAACTAAACATGTCTTAA-C-T-C-TAATTCCT
1 AATAAAATAATAATAAACTAAACATGTCTTAACCATCCTTAATTCCT
*
77781 AATAAAATAATAAT-AACTAAAATATTGT-TTAACTCATCCTTAATTCCT
1 AATAAAATAATAATAAACT-AAACA-TGTCTTAAC-CATCCTTAATTCCT
77829 AATAAAATAATA
1 AATAAAATAATA
77841 TATCTAATCC
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
42 4 0.08
43 22 0.42
44 3 0.06
45 1 0.02
46 1 0.02
47 1 0.02
48 20 0.38
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (47 bp):
AATAAAATAATAATAAACTAAACATGTCTTAACCATCCTTAATTCCT
Found at i:79515 original size:14 final size:14
Alignment explanation
Indices: 79496--79525 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
79486 TTTCCTCTTT
79496 TTAGTGGTAATTCG
1 TTAGTGGTAATTCG
79510 TTAGTGGTAATTCG
1 TTAGTGGTAATTCG
79524 TT
1 TT
79526 TGGTAGATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.07, G:0.27, T:0.47
Consensus pattern (14 bp):
TTAGTGGTAATTCG
Found at i:81904 original size:11 final size:11
Alignment explanation
Indices: 81888--81929 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
81878 ACAAGGTAGG
81888 AAACAAGATTA
1 AAACAAGATTA
81899 AAACAAGATTA
1 AAACAAGATTA
*
81910 AAATAAGATTA
1 AAACAAGATTA
*
81921 AAAAAAGAT
1 AAACAAGAT
81930 AAACAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (11 bp):
AAACAAGATTA
Found at i:81937 original size:11 final size:10
Alignment explanation
Indices: 81892--81943 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 10
81882 GGTAGGAAAC
*
81892 AAGATTAAAAC
1 AAGA-TAAAAA
*
81903 AAGATTAAAAT
1 AAGA-TAAAAA
81914 AAGATTAAAAA
1 AAGA-TAAAAA
81925 AAGATAAACAA
1 AAGATAAA-AA
81936 AAGATAAA
1 AAGATAAA
81944 GAAATTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
10 4 0.11
11 34 0.89
ACGTcount: A:0.69, C:0.04, G:0.10, T:0.17
Consensus pattern (10 bp):
AAGATAAAAA
Found at i:81939 original size:22 final size:22
Alignment explanation
Indices: 81892--81940 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
81882 GGTAGGAAAC
* *
81892 AAGATTAAAACAAGATTAAAAT
1 AAGATTAAAAAAAGATTAAAAA
81914 AAGATTAAAAAAAGA-TAAACAA
1 AAGATTAAAAAAAGATTAAA-AA
81936 AAGAT
1 AAGAT
81941 AAAGAAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.67, C:0.04, G:0.10, T:0.18
Consensus pattern (22 bp):
AAGATTAAAAAAAGATTAAAAA
Found at i:82456 original size:47 final size:47
Alignment explanation
Indices: 82372--82492 Score: 215
Period size: 47 Copynumber: 2.5 Consensus size: 47
82362 GTCTTAACTG
82372 TAATTCCTAATAAAATAATAATAACTAAAAATAATGTTTTAACTCATCCT
1 TAATTCCTAATAAAATAAT-A-AA-TAAAAATAATGTTTTAACTCATCCT
82422 TAATTCCTAATAAAATAATAAATAAAAATAATGTTTTAACTCATCCT
1 TAATTCCTAATAAAATAATAAATAAAAATAATGTTTTAACTCATCCT
82469 TAATTCCTAATAAAATAATAAATA
1 TAATTCCTAATAAAATAATAAATA
82493 TAATCCTAAA
Statistics
Matches: 71, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
47 49 0.69
48 2 0.03
49 1 0.01
50 19 0.27
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (47 bp):
TAATTCCTAATAAAATAATAAATAAAAATAATGTTTTAACTCATCCT
Found at i:91628 original size:21 final size:23
Alignment explanation
Indices: 91602--91652 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
91592 AGGGAATCAA
91602 TCCCCCCTTG-A-GGGAACCGAT
1 TCCCCCCTTGAAGGGGAACCGAT
*
91623 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCTTGAAGGGGAACCGAT
91646 TCCCCCC
1 TCCCCCC
91653 ACAGGGGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 1 0.04
23 16 0.62
ACGTcount: A:0.18, C:0.41, G:0.22, T:0.20
Consensus pattern (23 bp):
TCCCCCCTTGAAGGGGAACCGAT
Found at i:109851 original size:22 final size:23
Alignment explanation
Indices: 109823--109866 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
109813 ATTTTTTTTT
*
109823 CAAAAAAAAAA-AGGCAAAAAAA
1 CAAAAAAAAAAGAGCCAAAAAAA
109845 CAAAAAAAAAAGAGCCAAAAAA
1 CAAAAAAAAAAGAGCCAAAAAA
109867 GCCAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (23 bp):
CAAAAAAAAAAGAGCCAAAAAAA
Found at i:109873 original size:23 final size:23
Alignment explanation
Indices: 109823--109873 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
109813 ATTTTTTTTT
*
109823 CAAAAAAAAAAAGGCAAAAAAA-
1 CAAAAAAAAAAAGCCAAAAAAAC
*
109845 CAAAAAAAAAAGAGCCAAAAAAGC
1 CAAAAAAAAAA-AGCCAAAAAAAC
109869 CAAAA
1 CAAAA
109874 TTTCAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.44
23 9 0.36
24 5 0.20
ACGTcount: A:0.76, C:0.14, G:0.10, T:0.00
Consensus pattern (23 bp):
CAAAAAAAAAAAGCCAAAAAAAC
Found at i:117414 original size:23 final size:24
Alignment explanation
Indices: 117365--117417 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
117355 TTCTTTGCCT
* *
117365 TTTC-TTCTTTTGAGTGCTGGATT
1 TTTCTTTCTTTTGAGTGCTGCATC
*
117388 TTTCTTTCTTTTGAGTGCTTCA-C
1 TTTCTTTCTTTTGAGTGCTGCATC
117411 TTTCTTT
1 TTTCTTT
117418 TCTGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTGCATC
Found at i:124754 original size:20 final size:19
Alignment explanation
Indices: 124697--124765 Score: 102
Period size: 19 Copynumber: 3.6 Consensus size: 19
124687 AACCAAGAGA
* *
124697 ATGTATCTTCATTTAAATC
1 ATGTATTTTCATTAAAATC
124716 ATGTATTTTCATTAAAATC
1 ATGTATTTTCATTAAAATC
*
124735 ATTTATTTTCATTAAAAATC
1 ATGTATTTTCATT-AAAATC
124755 ATGTATTTTCA
1 ATGTATTTTCA
124766 AAAAGGGTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 29 0.64
20 16 0.36
ACGTcount: A:0.35, C:0.12, G:0.04, T:0.49
Consensus pattern (19 bp):
ATGTATTTTCATTAAAATC
Found at i:129922 original size:17 final size:17
Alignment explanation
Indices: 129900--129973 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 17
129890 AATTTTAATA
129900 AATGAACTAGTTTTATG
1 AATGAACTAGTTTTATG
* *
129917 AATGAACTAGTTTAATT
1 AATGAACTAGTTTTATG
* *
129934 AATGACCTA-TTTTATTC
1 AATGAACTAGTTTTA-TG
* *
129951 AATGAACTAGATGTATG
1 AATGAACTAGTTTTATG
129968 AATGAA
1 AATGAA
129974 GTAGCTTACT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
16 4 0.09
17 39 0.85
18 3 0.07
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (17 bp):
AATGAACTAGTTTTATG
Found at i:129932 original size:34 final size:34
Alignment explanation
Indices: 129893--129960 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
129883 TAAGATTAAT
*
129893 TTTAATAAATGAACTAGTTTTA-TGAATGAACTAG
1 TTTAATAAATGAACTA-TTTTATTCAATGAACTAG
* *
129927 TTTAATTAATGACCTATTTTATTCAATGAACTAG
1 TTTAATAAATGAACTATTTTATTCAATGAACTAG
129961 ATGTATGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 25 0.83
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (34 bp):
TTTAATAAATGAACTATTTTATTCAATGAACTAG
Found at i:129989 original size:51 final size:51
Alignment explanation
Indices: 129891--129989 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
129881 ATTAAGATTA
* * * *
129891 ATTTTAATAAATGAACTAGTTTTATGAATGAACTAGTTTAATTAATGACCT
1 ATTTTAATAAATGAACTAGATGTATGAATGAACTAGCTTAATAAATGACCT
* * * *
129942 ATTTTATTCAATGAACTAGATGTATGAATGAAGTAGCTTACTAAATGA
1 ATTTTAATAAATGAACTAGATGTATGAATGAACTAGCTTAATAAATGA
129990 TCTAAATATG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.38
Consensus pattern (51 bp):
ATTTTAATAAATGAACTAGATGTATGAATGAACTAGCTTAATAAATGACCT
Found at i:134727 original size:13 final size:11
Alignment explanation
Indices: 134707--134863 Score: 115
Period size: 11 Copynumber: 13.2 Consensus size: 11
134697 AATATAGGCG
134707 TGATATGGTGA
1 TGATATGGTGA
134718 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
134731 TGATATAGGCG-
1 TGATAT-GGTGA
134742 TGATAATGGTGA
1 TGAT-ATGGTGA
134754 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
134767 TGATATAGG-CA
1 TGATAT-GGTGA
134778 TGATAATGGTGA
1 TGAT-ATGGTGA
134790 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
134803 TGATATAGG-CA
1 TGATAT-GGTGA
134814 TGATAATGGTGA
1 TGAT-ATGGTGA
134826 TGGACTATGGTGA
1 T-GA-TATGGTGA
134839 TGATATAGGTG-
1 TGATAT-GGTGA
134850 TGATAATGGTGA
1 TGAT-ATGGTGA
134862 TG
1 TG
134864 GACAGATTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 39
0.73 0.04 0.24
Matches are distributed among these distances:
11 44 0.37
12 33 0.28
13 39 0.32
14 4 0.03
ACGTcount: A:0.30, C:0.03, G:0.35, T:0.32
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:134763 original size:36 final size:36
Alignment explanation
Indices: 134690--134866 Score: 293
Period size: 36 Copynumber: 4.9 Consensus size: 36
134680 ATTTATAAGT
* *
134690 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
134725 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
* *
134761 TGGTGATGATATAGGCATGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
134797 TGGTGATGATATAGGCATGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
134833 TGGTGATGATATAGGTGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
134867 AGATTGTATC
Statistics
Matches: 134, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 20 0.15
36 114 0.85
ACGTcount: A:0.30, C:0.04, G:0.35, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:134862 original size:23 final size:24
Alignment explanation
Indices: 134690--134863 Score: 129
Period size: 23 Copynumber: 7.3 Consensus size: 24
134680 ATTTATAAGT
* *
134690 TGGTGATAATATA-GGCG-TGATA
1 TGGTGATGATATATGGTGATGATA
134712 TGGTGATGGA-ATATGGTGATGATA
1 TGGTGAT-GATATATGGTGATGATA
*
134736 TAGGCG-TGATA-ATGGTGATGGACTA
1 T-GGTGATGATATATGGTGAT-GA-TA
*
134761 TGGTGATGATATA-GG-CATGATAA
1 TGGTGATGATATATGGTGATGAT-A
134784 TGGTGATGGA-ATATGGTGATGATA
1 TGGTGAT-GATATATGGTGATGATA
*
134808 TAGG-CATGATA-ATGGTGATGGACTA
1 T-GGTGATGATATATGGTGAT-GA-TA
134833 TGGTGATGATATA-GGTG-TGATAA
1 TGGTGATGATATATGGTGATGAT-A
134856 TGGTGATG
1 TGGTGATG
134864 GACAGATTGT
Statistics
Matches: 124, Mismatches: 8, Indels: 39
0.73 0.05 0.23
Matches are distributed among these distances:
22 12 0.10
23 48 0.39
24 29 0.23
25 33 0.27
26 2 0.02
ACGTcount: A:0.30, C:0.03, G:0.35, T:0.32
Consensus pattern (24 bp):
TGGTGATGATATATGGTGATGATA
Found at i:141336 original size:19 final size:19
Alignment explanation
Indices: 141312--141350 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
141302 ATCGAGACCT
141312 CCTAGTC-GGAATGAAAAGG
1 CCTAGTCAGG-ATGAAAAGG
*
141331 CCTAGTCATGATGAAAAGG
1 CCTAGTCAGGATGAAAAGG
141350 C
1 C
141351 AAATTGGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (19 bp):
CCTAGTCAGGATGAAAAGG
Found at i:144706 original size:12 final size:13
Alignment explanation
Indices: 144679--144711 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
144669 GTGCAAAAAG
144679 AAAAGAAAAGACA
1 AAAAGAAAAGACA
144692 AAAAGAAAAGTA-A
1 AAAAGAAAAG-ACA
144705 AAAAGAA
1 AAAAGAA
144712 CTCAAGCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 18 0.95
14 1 0.05
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (13 bp):
AAAAGAAAAGACA
Found at i:145839 original size:18 final size:16
Alignment explanation
Indices: 145793--145833 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
145783 AAGACGTTGC
145793 AGTTGAAAAATGAGAG
1 AGTTGAAAAATGAGAG
145809 AGTTGAAAAATGAGAG
1 AGTTGAAAAATGAGAG
145825 AGTTGAAAA
1 AGTTGAAAA
145834 GAATGAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.29, T:0.20
Consensus pattern (16 bp):
AGTTGAAAAATGAGAG
Found at i:149430 original size:48 final size:48
Alignment explanation
Indices: 149338--149430 Score: 116
Period size: 49 Copynumber: 1.9 Consensus size: 48
149328 CACACTCCAA
* * * * *
149338 TTTGCCTTTCATCGCGACTAGGAGGGTTGGCTAGAGCCATTTATCGAG
1 TTTGCCTTTCATCACGACTAGGAGGGTTCGATAGAGACACTTATCGAG
*
149386 TTTGCCTTTTCATTACGACTAGGAGGGTTCGATAG-GACACTTATC
1 TTTGCC-TTTCATCACGACTAGGAGGGTTCGATAGAGACACTTATC
149431 CATCTATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 14 0.37
49 24 0.63
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.33
Consensus pattern (48 bp):
TTTGCCTTTCATCACGACTAGGAGGGTTCGATAGAGACACTTATCGAG
Found at i:155072 original size:24 final size:21
Alignment explanation
Indices: 155038--155080 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
155028 TCCACAAGAC
*
155038 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
155060 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
155081 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:157756 original size:26 final size:25
Alignment explanation
Indices: 157727--157783 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
157717 AAAAAATCAG
*
157727 GAAAAAAGT-GAAGCACTCAAAAGAAA
1 GAAAAAAGTCCAA-CACTCAAAAG-AA
* *
157753 GAAACAATTCCAACACTCAAAAGAA
1 GAAAAAAGTCCAACACTCAAAAGAA
157778 GAAAAA
1 GAAAAA
157784 GCAAAGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 7 0.27
26 17 0.65
27 2 0.08
ACGTcount: A:0.61, C:0.16, G:0.14, T:0.09
Consensus pattern (25 bp):
GAAAAAAGTCCAACACTCAAAAGAA
Done.