Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007316.1 Hibiscus syriacus cultivar Beakdansim tig00019513_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: 47269
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:688 original size:32 final size:32
Alignment explanation
Indices: 650--726 Score: 122
Period size: 31 Copynumber: 2.4 Consensus size: 32
640 TGGATATTGT
*
650 TGTTTTAGTTTGTTGGATATTGAAATTG-AAA
1 TGTTTTAGATTGTTGGATATTGAAATTGAAAA
681 TGTTTTTAGATTG-TGGATATTGAAATTGAAAA
1 TG-TTTTAGATTGTTGGATATTGAAATTGAAAA
713 TGTTTTAGATTGTT
1 TGTTTTAGATTGTT
727 AGACAATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
31 27 0.64
32 15 0.36
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (32 bp):
TGTTTTAGATTGTTGGATATTGAAATTGAAAA
Found at i:7454 original size:14 final size:14
Alignment explanation
Indices: 7435--7467 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
7425 CGCTGGGCAT
7435 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
7449 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
7463 ACGAG
1 CCGAG
7468 CTATGCGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:7545 original size:14 final size:14
Alignment explanation
Indices: 7523--7589 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
7513 CCTCGCATAG
*
7523 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
7537 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
7551 CTCGGATGCTTTCGGATGGC
1 CTC-G--G---TCGGATGGC
7571 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
7585 CTCGG
1 CTCGG
7590 ATGCCCAGCG
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
14 30 0.65
15 1 0.02
17 2 0.04
19 1 0.02
20 12 0.26
ACGTcount: A:0.07, C:0.28, G:0.39, T:0.25
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:7570 original size:34 final size:34
Alignment explanation
Indices: 7527--7593 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
7517 GCATAGCTCG
7527 TTCGGATGGCCTCGGTCGGATGGCCTCGGATGCT
1 TTCGGATGGCCTCGGTCGGATGGCCTCGGATGCT
7561 TTCGGATGGCCTCGGTCGGATGGCCTCGGATGC
1 TTCGGATGGCCTCGGTCGGATGGCCTCGGATGC
7594 CCAGCGTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.09, C:0.27, G:0.39, T:0.25
Consensus pattern (34 bp):
TTCGGATGGCCTCGGTCGGATGGCCTCGGATGCT
Found at i:10560 original size:3 final size:3
Alignment explanation
Indices: 10552--10589 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
10542 TTTTGATCCC
* *
10552 TCT TCT TCT TCT TCT TCT TCA TCT TCT TCA TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
10590 AAGCTCTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:13177 original size:2 final size:2
Alignment explanation
Indices: 13170--13198 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13160 ATAATACAAT
13170 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13199 CGTACATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13463 original size:12 final size:12
Alignment explanation
Indices: 13440--13480 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
13430 TTTAAGGTTA
13440 TAAAAGTTTATAT
1 TAAAA-TTTATAT
13453 TAAAATTTATAT
1 TAAAATTTATAT
*
13465 TTAAATTT-T-T
1 TAAAATTTATAT
13475 TAAAAT
1 TAAAAT
13481 ATAATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 6 0.23
11 1 0.04
12 14 0.54
13 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
TAAAATTTATAT
Found at i:17122 original size:22 final size:22
Alignment explanation
Indices: 17097--17144 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
17087 CGAATGGTGA
17097 CAAACAATGCATCTAATTATGT
1 CAAACAATGCATCTAATTATGT
17119 CAAACAATGCATCTAATTATGT
1 CAAACAATGCATCTAATTATGT
17141 CAAA
1 CAAA
17145 GCCAATAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (22 bp):
CAAACAATGCATCTAATTATGT
Found at i:23779 original size:19 final size:19
Alignment explanation
Indices: 23743--23785 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
23733 TCAAGTTTGG
* *
23743 AGATATACATCGAGTTTTA
1 AGATATACATCAAATTTTA
*
23762 AGATATATATCAAATTTTA
1 AGATATACATCAAATTTTA
*
23781 GGATA
1 AGATA
23786 CATCACAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (19 bp):
AGATATACATCAAATTTTA
Found at i:24181 original size:40 final size:40
Alignment explanation
Indices: 24132--24238 Score: 196
Period size: 40 Copynumber: 2.7 Consensus size: 40
24122 ATACTTAAAG
*
24132 TTTAGTTTTTGTTTCATTTTAATACTCTGCATTTAAAAAC
1 TTTAGTTTTTGTTTCATTTTAGTACTCTGCATTTAAAAAC
*
24172 TTTAGTTTTTGTTTCATTTTAGTACTCTGCCTTTAAAAAC
1 TTTAGTTTTTGTTTCATTTTAGTACTCTGCATTTAAAAAC
24212 TTTAGTTTTTGTTTCATTTTAGTACTC
1 TTTAGTTTTTGTTTCATTTTAGTACTC
24239 ATTCAAAATT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.55
Consensus pattern (40 bp):
TTTAGTTTTTGTTTCATTTTAGTACTCTGCATTTAAAAAC
Found at i:25307 original size:21 final size:21
Alignment explanation
Indices: 25192--25307 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
25182 GCGAAATAAA
**
25192 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
25212 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
25232 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
25253 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
25273 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
25295 AATCGCAACGCGA
1 AATCGCAACGCGA
25308 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:25320 original size:20 final size:20
Alignment explanation
Indices: 25295--25487 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
25285 GATTTTCCAG
* ** *
25295 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
25315 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
25335 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
25355 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
25375 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
25395 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
25415 TATCGCAACGCGTATCTGTA
1 AATCGCAACGCGTATCCGTA
* *
25435 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
25456 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
25476 AATCGCAACGCG
1 AATCGCAACGCG
25488 ATTTTTAAAG
Statistics
Matches: 149, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
19 1 0.01
20 129 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:25905 original size:33 final size:33
Alignment explanation
Indices: 25866--25936 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
25856 TTCACTTAGA
25866 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
25899 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
25932 TTTCA
1 TTTCA
25937 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:26043 original size:21 final size:20
Alignment explanation
Indices: 26017--26089 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
26007 GCAGAAGAGT
26017 CGCAACGAGATAAATGAAAAC
1 CGCAACGAGA-AAATGAAAAC
* * *
26038 CGCAACGTGAAAATGACTATC
1 CGCAACGAGAAAATGA-AAAC
* *
26059 TGCAACGAGAAAAATGAAAAT
1 CGCAACGAG-AAAATGAAAAC
26080 CGCAACGAGA
1 CGCAACGAGA
26090 GAATCGCAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
20 7 0.17
21 27 0.66
22 7 0.17
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.12
Consensus pattern (20 bp):
CGCAACGAGAAAATGAAAAC
Found at i:26096 original size:14 final size:14
Alignment explanation
Indices: 26077--26132 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
26067 GAAAAATGAA
26077 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
26091 AATCGCAACGCGAAATG
1 AATCGCAA--CGAGA-G
26108 AAATCGCAACGAGAG
1 -AATCGCAACGAGAG
26123 AATCGCAACG
1 AATCGCAACG
26133 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 18 0.50
15 1 0.03
16 8 0.22
17 1 0.03
18 8 0.22
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:26115 original size:32 final size:33
Alignment explanation
Indices: 26070--26148 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
26060 GCAACGAGAA
26070 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
26103 AAATG-AAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
26135 AAACCAAAATCGCA
1 AAATGAAAATCGCA
26149 TTGCGATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 30 0.70
33 13 0.30
ACGTcount: A:0.47, C:0.23, G:0.22, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:26166 original size:19 final size:19
Alignment explanation
Indices: 26144--26271 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
26134 GAAACCAAAA
*
26144 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
26163 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
26177 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
26196 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
26210 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
26230 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
26250 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
26270 TC
1 TC
26272 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:26185 original size:14 final size:14
Alignment explanation
Indices: 26166--26222 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
26156 TTTCATTTCG
26166 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
26180 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
26199 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
26213 CGTTGCGATT
1 CGTTGCGATT
26223 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:26191 original size:33 final size:33
Alignment explanation
Indices: 26149--26271 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
26139 CAAAATCGCA
26149 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
26182 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
26215 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
26256 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
26272 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:26233 original size:21 final size:21
Alignment explanation
Indices: 26207--26271 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
26197 CGCGTTGCGA
26207 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
26228 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
26248 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
26269 TTC
1 TTC
26272 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:28112 original size:93 final size:93
Alignment explanation
Indices: 27953--28268 Score: 623
Period size: 93 Copynumber: 3.4 Consensus size: 93
27943 TAGATTGCTT
*
27953 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
28018 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
28046 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
28111 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
28139 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
28204 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
28232 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
28269 AATATCCTGA
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 222 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:28403 original size:14 final size:14
Alignment explanation
Indices: 28384--28440 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
28374 CGAAACTTAA
28384 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
28398 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
28417 AATCGCAACGACAG
1 AATCGCAACGAGAG
28431 AATCGCAACG
1 AATCGCAACG
28441 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:28424 original size:33 final size:33
Alignment explanation
Indices: 28366--28456 Score: 128
Period size: 33 Copynumber: 2.7 Consensus size: 33
28356 TAGTTTACTT
* * *
28366 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAA-TCAAAATCGCAACGACAGAA
*
28400 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAATCAAAATCGCAACGACAGAA
*
28433 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAATCAAAATCGCA
28457 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
33 40 0.77
34 12 0.23
ACGTcount: A:0.45, C:0.26, G:0.19, T:0.10
Consensus pattern (33 bp):
TCGCAACGCGAAATCAAAATCGCAACGACAGAA
Found at i:28455 original size:19 final size:18
Alignment explanation
Indices: 28398--28456 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
28388 GCAACGAGAG
*
28398 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-CAA
*
28417 AATCGCAA--CG--ACAG
1 AATCGCAACGCGAAACAA
28431 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-CAA
28450 AATCGCA
1 AATCGCA
28457 TTGCGATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 9 0.28
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.53
ACGTcount: A:0.46, C:0.27, G:0.19, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAACAA
Found at i:28474 original size:19 final size:19
Alignment explanation
Indices: 28452--28624 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
28442 GAAACCAAAA
*
28452 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
28471 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
28485 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
28504 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
28520 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
28537 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
28556 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
28575 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
28594 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
28614 TCGTGTTGCGA
1 TCGCGTTGCGA
28625 AAGTAAACTA
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 17 0.13
16 8 0.06
17 8 0.06
19 81 0.64
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:28493 original size:14 final size:14
Alignment explanation
Indices: 28474--28530 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
28464 TTTCATTTCG
28474 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
28488 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
28505 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
28521 CGTTGCGATT
1 CGTTGCGATT
28531 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:28582 original size:38 final size:38
Alignment explanation
Indices: 28452--28624 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
28442 GAAACCAAAA
*
28452 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
28487 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
28520 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
28556 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
28594 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
28625 AAGTAAACTA
Statistics
Matches: 115, Mismatches: 15, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 52 0.45
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:30559 original size:14 final size:14
Alignment explanation
Indices: 30540--30573 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
30530 ATTGTTTAAT
30540 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
30554 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
30568 TGATTT
1 TGATTT
30574 ATGTAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:30758 original size:20 final size:19
Alignment explanation
Indices: 30682--30780 Score: 127
Period size: 20 Copynumber: 5.4 Consensus size: 19
30672 AAAAATGACT
30682 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
30701 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
30720 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
30734 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
30754 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
30774 ATCGCAA
1 ATCGCAA
30781 CGAGAGAATC
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 1 0.01
17 3 0.04
19 26 0.37
20 30 0.43
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:30785 original size:54 final size:53
Alignment explanation
Indices: 30682--30798 Score: 209
Period size: 54 Copynumber: 2.2 Consensus size: 53
30672 AAAAATGACT
30682 ATCGCAATGC-GAAATGAAAATCGCAATGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATAAAAATCGCAACGAGAGA
*
30734 ATCGCAATGCGGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATAAAAATCGCAACGAGAGA
30788 ATCGCAATGCG
1 ATCGCAATGCG
30799 ATTTTCATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 10 0.16
53 19 0.31
54 33 0.53
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATAAAAATCGCAACGAGAGA
Found at i:30817 original size:19 final size:19
Alignment explanation
Indices: 30789--31021 Score: 298
Period size: 19 Copynumber: 12.9 Consensus size: 19
30779 AACGAGAGAA
*
30789 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
30808 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
30827 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
30843 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
30860 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
30876 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
30893 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
30912 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
30929 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
30946 TCGCATTGTGATTTTCATT
1 TCGCATTGCGATTTTCATT
30965 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
30984 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
31003 TCCGCATTGCGATTTTCAT
1 T-CGCATTGCGATTTTCAT
31022 GTTGGGATTT
Statistics
Matches: 188, Mismatches: 9, Indels: 33
0.82 0.04 0.14
Matches are distributed among these distances:
14 18 0.10
16 19 0.10
17 20 0.11
18 3 0.02
19 101 0.54
20 27 0.14
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:30851 original size:14 final size:14
Alignment explanation
Indices: 30832--30886 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
30822 TCATTTCGCA
30832 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
30846 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
30863 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
30879 TTGCGATT
1 TTGCGATT
30887 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:30855 original size:33 final size:33
Alignment explanation
Indices: 30813--31063 Score: 222
Period size: 33 Copynumber: 7.2 Consensus size: 33
30803 TCATTTCGCA
30813 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
30846 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
30879 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG
* * * * *
30916 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
* *
30951 TTGTGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
30987 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* * *
31023 TTGGGATTTTTATTTTGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
31056 TTGCGATT
1 TTGCGATT
31064 GTAATTTCCG
Statistics
Matches: 176, Mismatches: 22, Indels: 40
0.74 0.09 0.17
Matches are distributed among these distances:
31 9 0.05
32 4 0.02
33 86 0.49
34 15 0.09
35 4 0.02
36 7 0.04
37 5 0.03
38 16 0.09
39 18 0.10
40 3 0.02
41 9 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:31009 original size:91 final size:90
Alignment explanation
Indices: 30789--31054 Score: 400
Period size: 91 Copynumber: 3.0 Consensus size: 90
30779 AACGAGAGAA
*
30789 TCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGAT
30853 TTTCATTTCGCATTGCGA--TTCTC
66 TTTCATTTCGCATTGCGATTTTCTC
30876 TCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGAT
* *
30939 TTTCATTTCGCATTGTGATTTTCATT
66 TTTCATTTCGCATTGCGATTTTC-TC
* *
30965 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGA
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGA
* * *
31029 TTTTTATTTTGCATTGCGATTCTCTC
65 TTTTCATTTCGCATTGCGATTTTCTC
31055 GTTGCGATTG
Statistics
Matches: 162, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
85 33 0.20
86 42 0.26
87 3 0.02
88 3 0.02
89 4 0.02
90 1 0.01
91 75 0.46
92 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (90 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGAT
TTTCATTTCGCATTGCGATTTTCTC
Found at i:33363 original size:12 final size:12
Alignment explanation
Indices: 33346--33370 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33336 TCTTCGGGGA
33346 CTTTTTCTTCTT
1 CTTTTTCTTCTT
33358 CTTTTTCTTCTT
1 CTTTTTCTTCTT
33370 C
1 C
33371 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:34308 original size:20 final size:20
Alignment explanation
Indices: 34280--34508 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
34270 AAATTTCAGT
* * *
34280 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
34300 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
34320 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
34340 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
34360 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
34380 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
34400 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
34420 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
34440 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
34460 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
34480 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
34500 GTTGCGATT
1 GTTGCGATT
34509 CTTGAAAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:34561 original size:21 final size:20
Alignment explanation
Indices: 34476--34573 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
34466 ATTTATGTGT
* *
34476 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
34496 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
34517 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
34538 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
34559 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
34574 GGAAATGATT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:34569 original size:42 final size:43
Alignment explanation
Indices: 34476--34574 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
34466 ATTTATGTGT
* *
34476 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
34517 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
34559 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
34575 GAAATGATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:42481 original size:25 final size:27
Alignment explanation
Indices: 42426--42490 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 27
42416 GAATTTTTGG
*
42426 TCCACCCGACCCGAAAATTATAAACCC
1 TCCACCCGACCCGAAAATTATAAACAC
* *
42453 TCCACCCGACCCG-AAA-TATATACAT
1 TCCACCCGACCCGAAAATTATAAACAC
*
42478 TCCACACGACCCG
1 TCCACCCGACCCG
42491 GTCCACACAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 18 0.53
26 3 0.09
27 13 0.38
ACGTcount: A:0.34, C:0.42, G:0.09, T:0.15
Consensus pattern (27 bp):
TCCACCCGACCCGAAAATTATAAACAC
Done.