Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005458.1 Hibiscus syriacus cultivar Beakdansim tig00012499_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: 63917
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:7176 original size:39 final size:39
Alignment explanation
Indices: 7087--7178 Score: 114
Period size: 39 Copynumber: 2.4 Consensus size: 39
7077 GGGATTCTCT
* * * * *
7087 ATTTGTCTGAAAACGTCATGCAGTCGTGGGGTCTTCTTC
1 ATTTGCCTGAAGACGCCATGCAGTCGTGGAGTCTTCATC
7126 ATTTGCCTGAAGACGCCATGCAGTCGTGGAGTCTTCAT-
1 ATTTGCCTGAAGACGCCATGCAGTCGTGGAGTCTTCATC
*
7164 ATTTAGCTTGAAGAC
1 ATTT-GCCTGAAGAC
7179 ACGTTGAGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 4 0.09
39 42 0.91
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.33
Consensus pattern (39 bp):
ATTTGCCTGAAGACGCCATGCAGTCGTGGAGTCTTCATC
Found at i:12294 original size:24 final size:25
Alignment explanation
Indices: 12247--12294 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
12237 ATCGTCAGAG
*
12247 TTGGCATCGTCTTTAATCTGAGAAA
1 TTGGCATCGTCTTTAATCTAAGAAA
* *
12272 TTGGCAT-TTCTTTAATGTAAGAA
1 TTGGCATCGTCTTTAATCTAAGAA
12295 TTTTATTGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (25 bp):
TTGGCATCGTCTTTAATCTAAGAAA
Found at i:14230 original size:31 final size:29
Alignment explanation
Indices: 14164--14222 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 29
14154 GTGTATAAGG
14164 AAAAGAATATTTAATATTTTTATTTCAAA
1 AAAAGAATATTTAATATTTTTATTTCAAA
14193 AAAAGAATATTTAATATTTTT-TTCTCAAA
1 AAAAGAATATTTAATATTTTTATT-TCAAA
14222 A
1 A
14223 TAAAAGAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (29 bp):
AAAAGAATATTTAATATTTTTATTTCAAA
Found at i:15731 original size:33 final size:33
Alignment explanation
Indices: 15694--15762 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
15684 ATGCCTCAGA
*
15694 CATTAATTATCTCGGATCTACTCACATTGTTGT
1 CATTAATTATCTCGGATCTACTCACATTGTCGT
* *
15727 CATTAATTATCTCGGATTTATTCACATTGTCGT
1 CATTAATTATCTCGGATCTACTCACATTGTCGT
15760 CAT
1 CAT
15763 CCCCTCTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (33 bp):
CATTAATTATCTCGGATCTACTCACATTGTCGT
Found at i:18037 original size:27 final size:27
Alignment explanation
Indices: 18007--18058 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
17997 GTGGGATGCT
**
18007 TGTCATGATGACATTTAAAATATTAAA
1 TGTCATGACCACATTTAAAATATTAAA
18034 TGTCATGACCACATTTAAAATATTA
1 TGTCATGACCACATTTAAAATATTA
18059 TTTATTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.37
Consensus pattern (27 bp):
TGTCATGACCACATTTAAAATATTAAA
Found at i:19308 original size:48 final size:48
Alignment explanation
Indices: 19233--19329 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
19223 AATTGTCCTT
19233 CATCCGTTCATCGATCCATCCTAATTGCATCCCAAGAGTGGGAAGTTG
1 CATCCGTTCATCGATCCATCCTAATTGCATCCCAAGAGTGGGAAGTTG
* * *
19281 CATCCGTTCCTCGATCCATCTTGATTGCATCCCAAGAGTGGGAAGTTG
1 CATCCGTTCATCGATCCATCCTAATTGCATCCCAAGAGTGGGAAGTTG
19329 C
1 C
19330 TCTATATTGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (48 bp):
CATCCGTTCATCGATCCATCCTAATTGCATCCCAAGAGTGGGAAGTTG
Found at i:20738 original size:2 final size:2
Alignment explanation
Indices: 20731--20758 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20721 TCCATACTTT
20731 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20759 AAAGTGTGTA
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):
TA
Found at i:30909 original size:15 final size:15
Alignment explanation
Indices: 30889--30923 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
30879 CTTCTTTTCC
30889 CTATCAACTGAAACA
1 CTATCAACTGAAACA
*
30904 CTATCAACTGAAACC
1 CTATCAACTGAAACA
30919 CTATC
1 CTATC
30924 TTCCTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.40, C:0.31, G:0.06, T:0.23
Consensus pattern (15 bp):
CTATCAACTGAAACA
Found at i:32377 original size:21 final size:21
Alignment explanation
Indices: 32353--32508 Score: 129
Period size: 21 Copynumber: 7.6 Consensus size: 21
32343 GCGTTGCATT
32353 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
32374 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
32395 TCGCGTTGCAAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
32415 TCGCGTTGCGATAGTTGACAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
32436 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
* ** **
32456 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
32476 TCGCGTTGCGATAGTTGACAA
1 TCGCGTTGCGATAGTTGAAAA
32497 TCGCGTTGCGAT
1 TCGCGTTGCGAT
32509 TTTCCATTTC
Statistics
Matches: 108, Mismatches: 25, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
20 48 0.44
21 60 0.56
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:32423 original size:41 final size:41
Alignment explanation
Indices: 32374--32467 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
32364 TAGTTGAAAA
32374 TCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATT
* *
32415 TCGCGTTGCGATAGTTGACAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATT
32456 TCGCGTTGCGAT
1 TCGCGTTGCGAT
32468 TTTCCATTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.36
Consensus pattern (41 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATT
Found at i:32490 original size:61 final size:61
Alignment explanation
Indices: 32349--32528 Score: 288
Period size: 61 Copynumber: 2.9 Consensus size: 61
32339 ATTCGCGTTG
* * ** ** *
32349 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTC
1 CATTTCGCGTTGCGATAGTTGACAATCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATTTTC
32411 CATTTCGCGTTGCGATAGTTGACAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGACAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
32472 CATTTCGCGTTGCGATAGTTGACAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTGACAATCGCGTTGCGATTTTCCATTTCGCGTTGCGAT
32529 AGTCTACAGT
Statistics
Matches: 111, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
61 75 0.68
62 36 0.32
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (61 bp):
CATTTCGCGTTGCGATAGTTGACAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
Found at i:32501 original size:41 final size:42
Alignment explanation
Indices: 32500--32639 Score: 241
Period size: 42 Copynumber: 3.4 Consensus size: 42
32490 TTGACAATCG
32500 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
32542 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
32584 CGTTGCGATTTTCCAAATTT---GTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCC--ATTTCGCGTTGCGATAGTCTACAGTTGT
32625 CGTTGCGATTTTCCA
1 CGTTGCGATTTTCCA
32640 AATTCGTTAA
Statistics
Matches: 96, Mismatches: 0, Indels: 7
0.93 0.00 0.07
Matches are distributed among these distances:
39 1 0.01
41 35 0.36
42 56 0.58
44 4 0.04
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.41
Consensus pattern (42 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
Found at i:32559 original size:42 final size:42
Alignment explanation
Indices: 32459--32639 Score: 282
Period size: 41 Copynumber: 4.4 Consensus size: 42
32449 TTCCATTTCG
* *
32459 CGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGACAATCG-
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAGTTGT
32500 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
32542 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
32584 CGTTGCGATTTTCCAAATTT---GTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCC--ATTTCGCGTTGCGATAGTCTACAGTTGT
32625 CGTTGCGATTTTCCA
1 CGTTGCGATTTTCCA
32640 AATTCGTTAA
Statistics
Matches: 134, Mismatches: 2, Indels: 10
0.92 0.01 0.07
Matches are distributed among these distances:
39 1 0.01
41 72 0.54
42 57 0.43
44 4 0.03
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (42 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
Found at i:32562 original size:83 final size:82
Alignment explanation
Indices: 32459--32639 Score: 278
Period size: 83 Copynumber: 2.2 Consensus size: 82
32449 TTCCATTTCG
32459 CGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGACAATCG-CGTTGCGATTTTCC-ATTTCGC
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAATCGTCGTTGCGATTTTCCAATTT---
32521 GTTGCGATAGTCTACAGTTGT
62 GTTGCGATAGTCTACAGTTGT
* *
32542 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTTGTT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAATCGTCGTTGCGATTTTCC-AATTTGTT
32607 GCGATAGTCTACAGTTGT
65 GCGATAGTCTACAGTTGT
32625 CGTTGCGATTTTCCA
1 CGTTGCGATTTTCCA
32640 AATTCGTTAA
Statistics
Matches: 92, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
83 73 0.79
84 15 0.16
86 4 0.04
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (82 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAATCGTCGTTGCGATTTTCCAATTTGTTG
CGATAGTCTACAGTTGT
Found at i:32568 original size:20 final size:20
Alignment explanation
Indices: 32395--32570 Score: 178
Period size: 20 Copynumber: 8.6 Consensus size: 20
32385 TAGTTGAAAA
*
32395 TCGCGTTGCAATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
** *
32415 TCGCGTTGCGATAGTTGACA-A
1 TCGCGTTGCGAT--TTTCCATT
32436 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
32456 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
** *
32476 TCGCGTTGCGATAGTTGACA-A
1 TCGCGTTGCGAT--TTTCCATT
32497 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
32517 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCATT
32539 T-GTCGTTGCGATTTTCCATT
1 TCG-CGTTGCGATTTTCCATT
32559 TCGCGTTGCGAT
1 TCGCGTTGCGAT
32571 AGTCTACAGT
Statistics
Matches: 127, Mismatches: 19, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
19 8 0.06
20 70 0.55
21 26 0.20
22 23 0.18
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:32609 original size:19 final size:21
Alignment explanation
Indices: 32538--32643 Score: 76
Period size: 22 Copynumber: 5.1 Consensus size: 21
32528 TAGTCTACAG
*
32538 TTGTCGTTGCGATTTTCC-AT
1 TTGTCGTTGCGATTTTCCAAA
** * *
32558 TTCG-CGTTGCGATAGTCTACAG
1 TT-GTCGTTGCGATTTTCCA-AA
32580 TTGTCGTTGCGATTTTCCAAA
1 TTGTCGTTGCGATTTTCCAAA
** * *
32601 TT-T-GTTGCGATAGTCTACAG
1 TTGTCGTTGCGATTTTCCA-AA
32621 TTGTCGTTGCGATTTTCCAAA
1 TTGTCGTTGCGATTTTCCAAA
32642 TT
1 TT
32644 CGTTAAAAAA
Statistics
Matches: 63, Mismatches: 16, Indels: 13
0.68 0.17 0.14
Matches are distributed among these distances:
19 11 0.17
20 17 0.27
21 9 0.14
22 26 0.41
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (21 bp):
TTGTCGTTGCGATTTTCCAAA
Found at i:32731 original size:6 final size:6
Alignment explanation
Indices: 32720--32770 Score: 95
Period size: 6 Copynumber: 8.7 Consensus size: 6
32710 AGACACGTAT
32720 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC-C
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
32767 GACC
1 GACC
32771 CGAGACGAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.11
6 40 0.89
ACGTcount: A:0.31, C:0.51, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:33326 original size:6 final size:6
Alignment explanation
Indices: 33315--33341 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
33305 TCTCGTCTCG
33315 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
33342 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:33471 original size:22 final size:22
Alignment explanation
Indices: 33446--33509 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 22
33436 GTAGATTACA
33446 ACAAATTTAGAAAATCGCAACG
1 ACAAATTTAGAAAATCGCAACG
* * **
33468 ACAACTGTAGACTATCGCAACG
1 ACAAATTTAGAAAATCGCAACG
*
33490 -CGAAA-TGA-AAAATCGCAACG
1 AC-AAATTTAGAAAATCGCAACG
33510 CGATTTTCAA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
20 10 0.31
21 2 0.06
22 20 0.62
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.16
Consensus pattern (22 bp):
ACAAATTTAGAAAATCGCAACG
Found at i:39052 original size:22 final size:20
Alignment explanation
Indices: 39022--39129 Score: 103
Period size: 21 Copynumber: 5.2 Consensus size: 20
39012 TAAATATATA
39022 AATATTTTAAATAATTAGAAT
1 AATATTTTAAATAATTA-AAT
* *
39043 AATATATTTATAATCATT-TAT
1 AATAT-TTTA-AATAATTAAAT
*
39064 TATATTTTAAATAATTAAAT
1 AATATTTTAAATAATTAAAT
* *
39084 AATATATTTATAATCATT-TAT
1 AATAT-TTTA-AATAATTAAAT
*
39105 TATATTTTAAATAATTAAAT
1 AATATTTTAAATAATTAAAT
39125 AATAT
1 AATAT
39130 ATTTTAACAT
Statistics
Matches: 69, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
19 12 0.17
20 20 0.29
21 21 0.30
22 10 0.14
23 6 0.09
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (20 bp):
AATATTTTAAATAATTAAAT
Found at i:39069 original size:19 final size:19
Alignment explanation
Indices: 39045--39111 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 19
39035 ATTAGAATAA
39045 TATATTTATAATCATTTAT
1 TATATTTATAATCATTTAT
* *
39064 TATATTT-TAAATAATTAAATAA
1 TATATTTAT-AATCATT---TAT
39086 TATATTTATAATCATTTAT
1 TATATTTATAATCATTTAT
39105 TATATTT
1 TATATTT
39112 TAAATAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
18 1 0.03
19 22 0.56
22 15 0.38
23 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
TATATTTATAATCATTTAT
Found at i:39096 original size:41 final size:41
Alignment explanation
Indices: 39023--39140 Score: 213
Period size: 41 Copynumber: 2.9 Consensus size: 41
39013 AAATATATAA
39023 ATATTTTAAATAATTAGAATAATATATTTATAATCATTTATT
1 ATATTTTAAATAATTA-AATAATATATTTATAATCATTTATT
39065 ATATTTTAAATAATTAAATAATATATTTATAATCATTTATT
1 ATATTTTAAATAATTAAATAATATATTTATAATCATTTATT
39106 ATATTTTAAATAATTAAATAATATATTT-TAA-CATT
1 ATATTTTAAATAATTAAATAATATATTTATAATCATT
39141 ATAAAAATAA
Statistics
Matches: 76, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
39 4 0.05
40 3 0.04
41 53 0.70
42 16 0.21
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.50
Consensus pattern (41 bp):
ATATTTTAAATAATTAAATAATATATTTATAATCATTTATT
Found at i:39145 original size:22 final size:22
Alignment explanation
Indices: 39019--39136 Score: 110
Period size: 22 Copynumber: 5.6 Consensus size: 22
39009 ACCTAAATAT
39019 ATAA-ATATTTTAAATAATTAGA
1 ATAATATATTTTAAATAATTA-A
*
39041 ATAATATA-TTTATAATCATT--
1 ATAATATATTTTA-AATAATTAA
*
39061 -TATTATATTTTAAATAATTAA
1 ATAATATATTTTAAATAATTAA
*
39082 ATAATATA-TTTATAATCATT--
1 ATAATATATTTTA-AATAATTAA
*
39102 -TATTATATTTTAAATAATTAA
1 ATAATATATTTTAAATAATTAA
39123 ATAATATATTTTAA
1 ATAATATATTTTAA
39137 CATTATAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
19 24 0.31
20 8 0.10
21 4 0.05
22 32 0.42
23 9 0.12
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (22 bp):
ATAATATATTTTAAATAATTAA
Found at i:43064 original size:131 final size:131
Alignment explanation
Indices: 42701--43065 Score: 453
Period size: 132 Copynumber: 2.8 Consensus size: 131
42691 CGATATTGCG
* * * * * *
42701 AATAGTAATATATTTTCATTTCGGTTGGAGTAATAAATTACTGTTTTAAGGCATGAGAGGTCATT
1 AATAGTAATATCTATTCATTTCGATTGGAGTAATAAATGATTGTTTTAAGGTATGAGAGGTCATT
* * ** * ** * * *
42766 TATTCTCCATTGGAAATAATTCGATATTGCCTTTTTTTCTCGAATTAATATTGATTTTTAAAATG
66 TATTCTCAATTGGAAATAATTAGATATTATCATTTTCACTCGAATCAATATTGAATTTTAAAACG
*
42831 G
131 A
* * *
42832 AAT-GATTATATCTATTCATTTCGATTGGAGCAATAAATGATTGCTTTTAAGATATGAGAGGTCA
1 AATAG-TAATATCTATTCATTTCGATTGGAGTAATAAATGATTG-TTTTAAGGTATGAGAGGTCA
* * *
42896 TTTATTCTCAATTGGAAATCATTAGATATTATCATTTTCACTCGAATCGATATTGAATTTTAAGA
64 TTTATTCTCAATTGGAAATAATTAGATATTATCATTTTCACTCGAATCAATATTGAATTTTAAAA
42961 CGA
129 CGA
* * *
42964 AATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGATTGTTTTAAGGTATGAGAGATCATT
1 AATAGTAATATCTATTCATTTCGATTGGAGTAATAAATGATTGTTTTAAGGTATGAGAGGTCATT
* *
43029 TATTCTCGATTGGAAATGATTAGATATTATCATTTTC
66 TATTCTCAATTGGAAATAATTAGATATTATCATTTTC
43066 GCTCTTAAAA
Statistics
Matches: 201, Mismatches: 30, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
130 1 0.00
131 89 0.44
132 110 0.55
133 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (131 bp):
AATAGTAATATCTATTCATTTCGATTGGAGTAATAAATGATTGTTTTAAGGTATGAGAGGTCATT
TATTCTCAATTGGAAATAATTAGATATTATCATTTTCACTCGAATCAATATTGAATTTTAAAACG
A
Found at i:45570 original size:14 final size:14
Alignment explanation
Indices: 45551--45579 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
45541 TAAATCACCA
45551 AAGTCAACATTCAT
1 AAGTCAACATTCAT
45565 AAGTCAACATTCAT
1 AAGTCAACATTCAT
45579 A
1 A
45580 TTGAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.28
Consensus pattern (14 bp):
AAGTCAACATTCAT
Found at i:51174 original size:15 final size:15
Alignment explanation
Indices: 51151--51213 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 15
51141 AACAAATCAT
* *
51151 CTGCCATTGAGTCCA
1 CTGCAATTGACTCCA
51166 CTGCAATTGACTCCA
1 CTGCAATTGACTCCA
* * *
51181 TTACCATTGACTCCA
1 CTGCAATTGACTCCA
* * *
51196 TTACCATTGACTCCA
1 CTGCAATTGACTCCA
51211 CTG
1 CTG
51214 GAAAACAAGC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.24, C:0.33, G:0.13, T:0.30
Consensus pattern (15 bp):
CTGCAATTGACTCCA
Found at i:51188 original size:30 final size:30
Alignment explanation
Indices: 51154--51210 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
51144 AAATCATCTG
* *
51154 CCATTGAGTCCACTGCAATTGACTCCATTA
1 CCATTGACTCCACTACAATTGACTCCATTA
* *
51184 CCATTGACTCCATTACCATTGACTCCA
1 CCATTGACTCCACTACAATTGACTCCA
51211 CTGGAAAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.26, C:0.33, G:0.11, T:0.30
Consensus pattern (30 bp):
CCATTGACTCCACTACAATTGACTCCATTA
Done.