Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001823.1 Hibiscus syriacus cultivar Beakdansim tig00003690_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: 108896
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:2570 original size:22 final size:21
Alignment explanation
Indices: 2528--2567 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2518 GAGATTATTT
2528 TCTTTTTTCAATTTTGAAATA
1 TCTTTTTTCAATTTTGAAATA
**
2549 TCTTTTTTGTATTTTGAAA
1 TCTTTTTTCAATTTTGAAA
2568 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.60
Consensus pattern (21 bp):
TCTTTTTTCAATTTTGAAATA
Found at i:4428 original size:20 final size:20
Alignment explanation
Indices: 4393--4431 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4383 ATGTTGAGCA
**
4393 TAGGTGTATCGGTACACTTC
1 TAGGTGTATCAATACACTTC
4413 TAGGTGTATCAATACACTT
1 TAGGTGTATCAATACACTT
4432 ATTGTAAAAT
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:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (20 bp):
TAGGTGTATCAATACACTTC
Found at i:8054 original size:27 final size:27
Alignment explanation
Indices: 8023--8077 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
8013 CTGATCCAGG
*
8023 CGGATTTCTCAGTCATGATCAGATATC
1 CGGATTTCTCAGTCATGATCAGAGATC
* *
8050 CGGATTTCTCGGTCATGGTCAGAGATC
1 CGGATTTCTCAGTCATGATCAGAGATC
8077 C
1 C
8078 CGTGAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (27 bp):
CGGATTTCTCAGTCATGATCAGAGATC
Found at i:8344 original size:20 final size:20
Alignment explanation
Indices: 8307--8349 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
8297 ATTCCACCAC
*
8307 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
8327 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
8347 ATG
1 ATG
8350 TGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:14099 original size:45 final size:45
Alignment explanation
Indices: 14035--14138 Score: 140
Period size: 45 Copynumber: 2.3 Consensus size: 45
14025 GATGCACTAA
* * *
14035 GAGTGCATCCATGCATAAAATGCATTTGAAGTTTT-A-AAATAGCTT
1 GAGTGCATCGATGCATAAAATGCATTCGAAGTTTTCATAAA-A-CCT
*
14080 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCT
1 GAGTGCATCGATGCATAAAATGCATTCGAAGTTTTCATAAAACCT
14125 GAGTGCATCGATGC
1 GAGTGCATCGATGC
14139 TTTCATAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
45 48 0.91
46 2 0.04
47 3 0.06
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (45 bp):
GAGTGCATCGATGCATAAAATGCATTCGAAGTTTTCATAAAACCT
Found at i:14142 original size:27 final size:27
Alignment explanation
Indices: 14100--14165 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
14090 ATGCATAAAA
*
14100 TGCATTCGATGTTTTCATAAAACCTGAG
1 TGCA-TCGATGCTTTCATAAAACCTGAG
14128 TGCATCGATGCTTTCATAAAACCTGAG
1 TGCATCGATGCTTTCATAAAACCTGAG
14155 TGCATCGATGC
1 TGCATCGATGC
14166 ATGGTATGTG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 33 0.89
28 4 0.11
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (27 bp):
TGCATCGATGCTTTCATAAAACCTGAG
Found at i:20210 original size:33 final size:33
Alignment explanation
Indices: 20101--20218 Score: 157
Period size: 33 Copynumber: 3.6 Consensus size: 33
20091 TTTTCACCCT
20101 AAACCCGAACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGAATATCACACTTAAAA
* ** *
20135 AAACCCAACCTAACTCGAATATCACACTT-AAA
1 AAACCCGACCCGACCCGAATATCACACTTAAAA
*
20167 AAACCCGACCCGACCCGAATATCAAACTTAAAA
1 AAACCCGACCCGACCCGAATATCACACTTAAAA
* *
20200 AAACCTGACCCGATCCGAA
1 AAACCCGACCCGACCCGAA
20219 CCCGAATTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
32 27 0.38
33 39 0.54
34 6 0.08
ACGTcount: A:0.44, C:0.34, G:0.08, T:0.14
Consensus pattern (33 bp):
AAACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:22644 original size:21 final size:23
Alignment explanation
Indices: 22609--22655 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
22599 ACACCCAAAC
*
22609 TTAACAAAAATAATTCTTCA-CT
1 TTAACAAAAATAATTCTCCACCT
*
22631 TTAACAAATA-AATTCTCCACCT
1 TTAACAAAAATAATTCTCCACCT
22653 TTA
1 TTA
22656 CCATAACACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (23 bp):
TTAACAAAAATAATTCTCCACCT
Found at i:23481 original size:22 final size:21
Alignment explanation
Indices: 23447--23487 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
23437 TGTAGTAAGG
* *
23447 GTATCGGTACCCTGTAGCAGA
1 GTATCGATACCCTGAAGCAGA
23468 GTATCGATACCCCTGAAGCA
1 GTATCGATA-CCCTGAAGCA
23488 ATCTGGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (21 bp):
GTATCGATACCCTGAAGCAGA
Found at i:23543 original size:22 final size:22
Alignment explanation
Indices: 23515--23564 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
23505 CATTCGATAC
23515 TGTTCATTAATGTTCACAG-TAT
1 TGTTCATTAATGTTCAC-GCTAT
*
23537 TGTTCATTACTGTTCACGCTAT
1 TGTTCATTAATGTTCACGCTAT
23559 TGTTCA
1 TGTTCA
23565 AACCGTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.46
Consensus pattern (22 bp):
TGTTCATTAATGTTCACGCTAT
Found at i:25410 original size:6 final size:6
Alignment explanation
Indices: 25401--25426 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
25391 CATCACACCC
25401 ACATAT ACATAT ACATAT ACATAT AC
1 ACATAT ACATAT ACATAT ACATAT AC
25427 TAATTCCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (6 bp):
ACATAT
Found at i:25741 original size:23 final size:23
Alignment explanation
Indices: 25703--25768 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
25693 ATACTAGGGG
*
25703 CTATGAATTTGTCCCGAATGACCA
1 CTATGAA-ATGTCCCGAATGACCA
*
25727 CTATGAAATGTCCCGAAGGACCA
1 CTATGAAATGTCCCGAATGACCA
*
25750 C--TG-TATGTCCCGAATGACC
1 CTATGAAATGTCCCGAATGACC
25769 TATGAACCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.37
21 2 0.05
23 15 0.39
24 7 0.18
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (23 bp):
CTATGAAATGTCCCGAATGACCA
Found at i:26391 original size:20 final size:22
Alignment explanation
Indices: 26366--26423 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
26356 TTCCCCTTGA
26366 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
*
26386 AGTGCATCGATGTATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
26409 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
26424 CTACCCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:28598 original size:7 final size:7
Alignment explanation
Indices: 28586--28652 Score: 62
Period size: 7 Copynumber: 9.6 Consensus size: 7
28576 AATTGGATTA
28586 AGGGTTT
1 AGGGTTT
28593 AGGGTTT
1 AGGGTTT
28600 AGGGTTT
1 AGGGTTT
*
28607 AAGGTTT
1 AGGGTTT
* *
28614 AGTGTAT
1 AGGGTTT
* *
28621 ATGGTAT
1 AGGGTTT
*
28628 ATGGTTT
1 AGGGTTT
28635 AGGGTTT
1 AGGGTTT
* *
28642 AAGATTT
1 AGGGTTT
28649 AGGG
1 AGGG
28653 CTCATTGCAA
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.22, C:0.00, G:0.36, T:0.42
Consensus pattern (7 bp):
AGGGTTT
Found at i:29176 original size:11 final size:11
Alignment explanation
Indices: 29134--29222 Score: 57
Period size: 11 Copynumber: 8.5 Consensus size: 11
29124 CATATTTTTA
*
29134 TTTTATTATAT
1 TTTTAATATAT
29145 TTTTAA-A-A-
1 TTTTAATATAT
*
29153 TTTT-ATAGAAT
1 TTTTAATA-TAT
29164 TTTTAATATAT
1 TTTTAATATAT
29175 TTTTAA-A-AT
1 TTTTAATATAT
29184 TTTATAAT-TAT
1 TTT-TAATATAT
*** *
29195 CAATAATGTAT
1 TTTTAATATAT
29206 TTTTAATATAT
1 TTTTAATATAT
29217 TTTTAA
1 TTTTAA
29223 CAATGTAATT
Statistics
Matches: 60, Mismatches: 9, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
7 1 0.02
8 5 0.08
9 6 0.10
10 10 0.17
11 35 0.58
12 3 0.05
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (11 bp):
TTTTAATATAT
Found at i:29191 original size:21 final size:21
Alignment explanation
Indices: 29132--29191 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 21
29122 ATCATATTTT
* *
29132 TATTTTATTATATTTTTAA-A
1 TATTTTATAAAATTTTTAATA
*
29152 -ATTTTATAGAATTTTTAATA
1 TATTTTATAAAATTTTTAATA
29172 TATTTT-TAAAATTTTATAAT
1 TATTTTATAAAATTTT-TAAT
29192 TATCAATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 15 0.45
20 9 0.27
21 9 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTTTATAAAATTTTTAATA
Found at i:29199 original size:28 final size:29
Alignment explanation
Indices: 29140--29199 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
29130 TTTATTTTAT
* *
29140 TATATTTTTAAAATTTTATAGAATTTTTAA
1 TATATTTTTAAAATTTTATA-AATTATCAA
29170 TATATTTTTAAAATTTTAT-AATTATCAA
1 TATATTTTTAAAATTTTATAAATTATCAA
29198 TA
1 TA
29200 ATGTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 9 0.32
30 19 0.68
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (29 bp):
TATATTTTTAAAATTTTATAAATTATCAA
Found at i:39565 original size:4 final size:4
Alignment explanation
Indices: 39556--39591 Score: 54
Period size: 4 Copynumber: 8.5 Consensus size: 4
39546 TCTATTCATA
39556 TTCT TTCT TTCTT TTCT TTCTT TTCT TTCT TTCT TT
1 TTCT TTCT TTC-T TTCT TTC-T TTCT TTCT TTCT TT
39592 TGTTAAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 22 0.73
5 8 0.27
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTCT
Found at i:39573 original size:9 final size:9
Alignment explanation
Indices: 39559--39591 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
39549 ATTCATATTC
39559 TTTCTTTCT
1 TTTCTTTCT
39568 TTTCTTTCT
1 TTTCTTTCT
39577 TTTCTTTC-
1 TTTCTTTCT
39585 TTTCTTT
1 TTTCTTT
39592 TGTTAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:39574 original size:13 final size:14
Alignment explanation
Indices: 39556--39592 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
39546 TCTATTCATA
39556 TTCTTTC-TTTCTT
1 TTCTTTCTTTTCTT
39569 TTCTTTCTTTTC-T
1 TTCTTTCTTTTCTT
39582 TTCTTTCTTTT
1 TTCTTTCTTTT
39593 GTTAAATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCTTTCTTTTCTT
Found at i:41644 original size:15 final size:15
Alignment explanation
Indices: 41624--41677 Score: 90
Period size: 15 Copynumber: 3.6 Consensus size: 15
41614 TTCGCATCTC
41624 TGAATGATTCAGTGT
1 TGAATGATTCAGTGT
41639 TGAATGATTCAGTGT
1 TGAATGATTCAGTGT
*
41654 TGACTGATTCAGTGT
1 TGAATGATTCAGTGT
*
41669 TGACTGATT
1 TGAATGATT
41678 AAGCAAAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (15 bp):
TGAATGATTCAGTGT
Found at i:51113 original size:12 final size:12
Alignment explanation
Indices: 51088--51180 Score: 64
Period size: 12 Copynumber: 7.8 Consensus size: 12
51078 ACGGAGATAT
* *
51088 CAGAAATCAAAA
1 CAGAATTCAGAA
51100 CAGAATTCAGAA
1 CAGAATTCAGAA
*
51112 CATATATT-AGAA
1 CAGA-ATTCAGAA
* * *
51124 CAGAATCCATAT
1 CAGAATTCAGAA
*
51136 CAGAAATCAGAA
1 CAGAATTCAGAA
**
51148 CAGAATTCAGGT
1 CAGAATTCAGAA
*
51160 CATGTA-TCAGAA
1 CA-GAATTCAGAA
51172 CAGAATTCA
1 CAGAATTCA
51181 AGTCGAAAAT
Statistics
Matches: 59, Mismatches: 18, Indels: 8
0.69 0.21 0.09
Matches are distributed among these distances:
11 4 0.07
12 50 0.85
13 5 0.08
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.20
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:51192 original size:24 final size:24
Alignment explanation
Indices: 51091--51194 Score: 79
Period size: 24 Copynumber: 4.3 Consensus size: 24
51081 GAGATATCAG
* *
51091 AAATCAAAACAGAATTC-AGAACAT
1 AAATCAGAACAGAATTCAAG-TCAT
* * * *
51115 ATATTAGAACAGAATCCATA-TCAG
1 AAATCAGAACAGAATTCA-AGTCAT
*
51139 AAATCAGAACAGAATTCAGGTCAT
1 AAATCAGAACAGAATTCAAGTCAT
**
51163 GTATCAGAACAGAATTCAAGTCGA-
1 AAATCAGAACAGAATTCAAGTC-AT
51187 AAATCAGA
1 AAATCAGA
51195 TAAAATAATT
Statistics
Matches: 60, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
24 58 0.97
25 1 0.02
26 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.20
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAAGTCAT
Found at i:51194 original size:48 final size:48
Alignment explanation
Indices: 51084--51177 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
51074 TTAAACGGAG
* *
51084 ATATCAGAAATCAAAACAGAATTCAGAACATATATTAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTCAGAACATATATCAGAACAGAATCC
** *
51132 ATATCAGAAATCAGAACAGAATTCAGGTCATGTATCAGAACAGAAT
1 ATATCAGAAATCAGAACAGAATTCAGAACATATATCAGAACAGAAT
51178 TCAAGTCGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.21
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATTCAGAACATATATCAGAACAGAATCC
Found at i:53749 original size:24 final size:19
Alignment explanation
Indices: 53700--53771 Score: 126
Period size: 19 Copynumber: 3.8 Consensus size: 19
53690 GGTCAACAGT
53700 AAACGGCTCGGCTCAGCTC
1 AAACGGCTCGGCTCAGCTC
53719 AAACGGCTCGGCTCAGCTC
1 AAACGGCTCGGCTCAGCTC
*
53738 AAATGGCTCGGCTCAGCTC
1 AAACGGCTCGGCTCAGCTC
*
53757 AAGCGGCTCGGCTCA
1 AAACGGCTCGGCTCA
53772 AACGGCTCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.21, C:0.35, G:0.28, T:0.17
Consensus pattern (19 bp):
AAACGGCTCGGCTCAGCTC
Found at i:53763 original size:14 final size:14
Alignment explanation
Indices: 53746--53779 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
53736 TCAAATGGCT
*
53746 CGGCTCAGCTCAAG
1 CGGCTCAGCTCAAA
*
53760 CGGCTCGGCTCAAA
1 CGGCTCAGCTCAAA
53774 CGGCTC
1 CGGCTC
53780 CTCAGGCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.38, G:0.29, T:0.15
Consensus pattern (14 bp):
CGGCTCAGCTCAAA
Found at i:55460 original size:14 final size:15
Alignment explanation
Indices: 55435--55464 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
55425 TGGGGCAGTT
55435 GACCCGGTTTGACCC
1 GACCCGGTTTGACCC
55450 GACCC-GTTTGACCC
1 GACCCGGTTTGACCC
55464 G
1 G
55465 GTCCGACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.13, C:0.40, G:0.27, T:0.20
Consensus pattern (15 bp):
GACCCGGTTTGACCC
Found at i:55478 original size:24 final size:24
Alignment explanation
Indices: 55433--55478 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
55423 GTTGGGGCAG
** **
55433 TTGACCCGGTTTGACCCGACCCGT
1 TTGACCCGGTCCGACCAAACCCGT
55457 TTGACCCGGTCCGACCAAACCC
1 TTGACCCGGTCCGACCAAACCC
55479 AACCTGTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.17, C:0.41, G:0.22, T:0.20
Consensus pattern (24 bp):
TTGACCCGGTCCGACCAAACCCGT
Found at i:57980 original size:21 final size:21
Alignment explanation
Indices: 57938--57980 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
57928 TTTCTGGGTT
* * *
57938 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
57959 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
57980 A
1 A
57981 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:58037 original size:66 final size:67
Alignment explanation
Indices: 57960--58109 Score: 223
Period size: 67 Copynumber: 2.3 Consensus size: 67
57950 ACCCATTCAA
*
57960 GGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATGCTAGAGAGGAATCGATACCCCTA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGAGGAATCGATACCCC-A
58024 -GG
65 GGG
* * * *
58026 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCAG
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGAGGAATCGATACCCCAG
58091 GG
66 GG
*
58093 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
58110 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
66 23 0.30
67 53 0.70
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.17
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGAGGAATCGATACCCCAG
GG
Found at i:58140 original size:17 final size:16
Alignment explanation
Indices: 58113--58148 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
58103 TTCCCCCATG
58113 AGAAAAAAAGAAAGAA
1 AGAAAAAAAGAAAGAA
*
58129 AGAAAGAAAAGAAAGCA
1 AGAAA-AAAAGAAAGAA
58146 AGA
1 AGA
58149 CTAAGCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.75, C:0.03, G:0.22, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAGAAAGAA
Found at i:58455 original size:34 final size:29
Alignment explanation
Indices: 58416--58487 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
58406 CATATTATGA
*
58416 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
58445 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
58474 TACATGACATGAAT
1 TACATGACATGAAT
58488 ATGCAGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:58926 original size:149 final size:149
Alignment explanation
Indices: 58656--58959 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
58646 GGGTAGAGGG
*
58656 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTAAAAGACACAT
58721 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
*
58786 TATGGCACTACGGTGCAAT
131 TATGGCACTAAGGTGCAAT
58805 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTAAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTAAAAGACACAT
58870 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
58935 TATGGCACTAAGGTGCAAT
131 TATGGCACTAAGGTGCAAT
58954 TCTACG
1 TCTACG
58960 GGGCACTTCG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTAAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTAAGGTGCAAT
Found at i:64998 original size:15 final size:15
Alignment explanation
Indices: 64975--65025 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
64965 TTTTCTTTTC
*
64975 TTTTCTTCTTCTATT
1 TTTTTTTCTTCTATT
64990 TTTTTTTCTTCT-TT
1 TTTTTTTCTTCTATT
* *
65004 GTTTTTTTATACTATAT
1 -TTTTTTTCTTCTAT-T
65021 TTTTT
1 TTTTT
65026 AGCTCTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 2 0.07
15 21 0.70
16 6 0.20
17 1 0.03
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTTTTCTTCTATT
Found at i:65009 original size:18 final size:18
Alignment explanation
Indices: 64970--65011 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
64960 TCTATTTTTC
*
64970 TTTTCTTTTCTTCTTCTA
1 TTTTTTTTTCTTCTTCTA
*
64988 TTTTTTTTTCTTCTT-TG
1 TTTTTTTTTCTTCTTCTA
65005 TTTTTTT
1 TTTTTTT
65012 ATACTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTTTTTTCTTCTTCTA
Found at i:67342 original size:7 final size:7
Alignment explanation
Indices: 67330--67371 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
67320 AGATTTTTTA
67330 TGAACAG
1 TGAACAG
67337 TGAACAG
1 TGAACAG
*
67344 TGAATAG
1 TGAACAG
*
67351 T-ACCA-
1 TGAACAG
67356 TGAACAG
1 TGAACAG
67363 TGAACAG
1 TGAACAG
67370 TG
1 TG
67372 TATCGATGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
5 1 0.03
6 5 0.17
7 23 0.79
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.19
Consensus pattern (7 bp):
TGAACAG
Found at i:67891 original size:45 final size:45
Alignment explanation
Indices: 67823--67981 Score: 203
Period size: 45 Copynumber: 3.6 Consensus size: 45
67813 AATATTTTAT
* *
67823 CAATATACTTACCATTTAATCCATAAGCTCGTAAGCTTATAAAAG
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATAAAAC
* ***
67868 CAATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATAAAAC
* ***
67913 CAATATACTTACCATTTATTCCATAAGCTAGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATAAAAC
* *
67958 CAATATACTTGCCA-TTATTACATA
1 CAATATACTTACCATTTATTCCATA
67982 TGCCTATAAG
Statistics
Matches: 104, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
44 9 0.09
45 95 0.91
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (45 bp):
CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATAAAAC
Found at i:70896 original size:15 final size:14
Alignment explanation
Indices: 70866--70892 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
70856 ATCTCTCATT
70866 TTTTTCTATTTTTC
1 TTTTTCTATTTTTC
70880 TTTTTCTATTTTT
1 TTTTTCTATTTTT
70893 TCTTCTTTTT
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:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTCTATTTTTC
Found at i:70901 original size:23 final size:23
Alignment explanation
Indices: 70865--70909 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
70855 AATCTCTCAT
70865 TTTTTTCTATTTTTCTTT-TTCTA
1 TTTTTTCTATTTTT-TTTCTTCTA
70888 TTTTTTCT-TCTTTTTTTCTTCT
1 TTTTTTCTAT-TTTTTTTCTTCT
70910 TTTCTTATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTCTATTTTTTTTCTTCTA
Found at i:70904 original size:11 final size:11
Alignment explanation
Indices: 70864--70912 Score: 57
Period size: 11 Copynumber: 4.4 Consensus size: 11
70854 CAATCTCTCA
70864 TTTTTTTCTAT-
1 TTTTTTTCT-TC
70875 TTTTCTTT-TTC
1 TTTT-TTTCTTC
70886 TATTTTTTCTTC
1 T-TTTTTTCTTC
70898 TTTTTTTCTTC
1 TTTTTTTCTTC
70909 TTTT
1 TTTT
70913 CTTATACTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 23 0.68
12 10 0.29
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTTCTTC
Found at i:73778 original size:45 final size:45
Alignment explanation
Indices: 73719--73903 Score: 264
Period size: 45 Copynumber: 4.1 Consensus size: 45
73709 ACATATCCAA
* * **
73719 TATTTTATCAATATACTTACCATTTAATCCATAAGCTCGTAATAT
1 TATTTTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCT
* *
73764 TATTTTACCAATATACTTACCATTTGTTCCATAAGCTCTTAAGCT
1 TATTTTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCT
73809 TATTTTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCT
* * * * *
73854 TATTTTACTAATATACTTGCCA-TTATTACATATGCTCATAAGCT
1 TATTTTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCT
73898 TATTTT
1 TATTTT
73904 CATGATTACC
Statistics
Matches: 127, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
44 25 0.20
45 102 0.80
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.43
Consensus pattern (45 bp):
TATTTTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCT
Found at i:76797 original size:31 final size:31
Alignment explanation
Indices: 76759--76828 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
76749 CTTTTAAAAC
*
76759 TTGCAATACAGTCCCCCAATATTTAGTCTGT
1 TTGCAATACAGTCCCCCAACATTTAGTCTGT
** * *
76790 TTGCAATATGGTTCCCTAACATTTAGTCTGT
1 TTGCAATACAGTCCCCCAACATTTAGTCTGT
*
76821 TTACAATA
1 TTGCAATA
76829 TGGTCCCCGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (31 bp):
TTGCAATACAGTCCCCCAACATTTAGTCTGT
Found at i:76844 original size:31 final size:31
Alignment explanation
Indices: 76769--76844 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
76759 TTGCAATACA
* * *
76769 GTCCCCCAATATTTAGTCTGTTTGCAATATG
1 GTCCCCGAACATTTAGTCTGTTTACAATATG
* *
76800 GTTCCCTAACATTTAGTCTGTTTACAATATG
1 GTCCCCGAACATTTAGTCTGTTTACAATATG
*
76831 GTCCCCGACCATTT
1 GTCCCCGAACATTT
76845 GACGCTGTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.38
Consensus pattern (31 bp):
GTCCCCGAACATTTAGTCTGTTTACAATATG
Found at i:77568 original size:31 final size:31
Alignment explanation
Indices: 77530--77594 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
77520 TCAAACGGTC
*
77530 GGGGACCATATTGCAAATAGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
* * *
77561 GGGGACCATTTTGCAGACAGACTACATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
77592 GGG
1 GGG
77595 TACTGTATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:81350 original size:24 final size:23
Alignment explanation
Indices: 81319--81363 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
81309 CTTATATTAT
*
81319 ATTTATTACTATTTTTTATTTTG
1 ATTTATTACTAATTTTTATTTTG
*
81342 ATTTAATTATTAATTTTTATTT
1 ATTT-ATTACTAATTTTTATTT
81364 ATTGATCGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (23 bp):
ATTTATTACTAATTTTTATTTTG
Found at i:102634 original size:20 final size:21
Alignment explanation
Indices: 102609--102647 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
102599 ATGGGCATGG
102609 GACCCGAACCGA-CGGGTTCC
1 GACCCGAACCGATCGGGTTCC
*
102629 GACCCGATCCGATCGGGTT
1 GACCCGAACCGATCGGGTT
102648 GGGTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.15
Consensus pattern (21 bp):
GACCCGAACCGATCGGGTTCC
Found at i:103737 original size:22 final size:20
Alignment explanation
Indices: 103695--103748 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 20
103685 GGCCCTTCAA
103695 TATCGATACCCCTACCATGG
1 TATCGATACCCCTACCATGG
**
103715 TATCGATACTACCCTACTTTGG
1 TATCGATAC--CCCTACCATGG
103737 TATCGATACCCC
1 TATCGATACCCC
103749 CATCCATATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.24, C:0.33, G:0.13, T:0.30
Consensus pattern (20 bp):
TATCGATACCCCTACCATGG
Found at i:103837 original size:22 final size:22
Alignment explanation
Indices: 103792--103846 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
103782 GGCCTAGTTT
* *
103792 CGATAC-CCT-TACCATGGTAT
1 CGATACTCCTATACTATGGTAC
*
103812 CGATACTGCTATACTATGGTAC
1 CGATACTCCTATACTATGGTAC
103834 CGATACTCCTATA
1 CGATACTCCTATA
103847 TGGTATCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 6 0.21
21 2 0.07
22 21 0.72
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (22 bp):
CGATACTCCTATACTATGGTAC
Found at i:103893 original size:95 final size:94
Alignment explanation
Indices: 103695--103912 Score: 229
Period size: 95 Copynumber: 2.3 Consensus size: 94
103685 GGCCCTTCAA
* * * *
103695 TATCGATACCCCTACCATGGTATCGATACTACCCTACTTTGGTATCGATACCCCCATCCATATCG
1 TATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACCGATACCCCCATCCATATCG
* * * *
103760 ATACCAAAATTAGATTCGATCTGGCCTAG
66 ATACCAAAATTAGACTCGATATGACCCAG
* * * * * ***
103789 TTTCGATACCCTTACCATGGTATCGATACTGCTATACTATGGTACCGATACTCCTATATGGTATC
1 TATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACCGATACCCCCAT-CCATATC
* * * *
103854 GATACCAAAATTCGGCTCGATATTACCCGG
65 GATACCAAAATTAGACTCGATATGACCCAG
* *
103884 TATCGATACCCTCACCATGGTATTGATAC
1 TATCGATACCCTTACCATGGTATCGATAC
103913 CACTTCGTTA
Statistics
Matches: 100, Mismatches: 23, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
94 48 0.48
95 52 0.52
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (94 bp):
TATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACCGATACCCCCATCCATATCG
ATACCAAAATTAGACTCGATATGACCCAG
Done.