Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004851.1 Hibiscus syriacus cultivar Beakdansim tig00010934_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: 102917
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:6705 original size:22 final size:21
Alignment explanation
Indices: 6663--6702 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6653 GAGTTTATTT
*
6663 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
6684 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
6703 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:16156 original size:15 final size:15
Alignment explanation
Indices: 16133--16162 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16123 ATGTAGGTTC
16133 TAATATTAATCTAAT
1 TAATATTAATCTAAT
*
16148 TAATTTTAATCTAAT
1 TAATATTAATCTAAT
16163 ATTAAACCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATATTAATCTAAT
Found at i:24217 original size:14 final size:14
Alignment explanation
Indices: 24194--24245 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
24184 CGTTCGTGAA
24194 CGTTCAGTTATGTT
1 CGTTCAGTTATGTT
*
24208 CGTTCGGTTATGTT
1 CGTTCAGTTATGTT
24222 CG-T---TTATGTT
1 CGTTCAGTTATGTT
*
24232 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
24246 TAATTCAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 9 0.27
11 1 0.03
13 1 0.03
14 22 0.67
ACGTcount: A:0.12, C:0.13, G:0.21, T:0.54
Consensus pattern (14 bp):
CGTTCAGTTATGTT
Found at i:25347 original size:16 final size:16
Alignment explanation
Indices: 25326--25403 Score: 117
Period size: 16 Copynumber: 5.0 Consensus size: 16
25316 GGTCTCCAAC
25326 GTTCGTGTTCATTTAT
1 GTTCGTGTTCATTTAT
25342 GTTCGTGTTCATTTAT
1 GTTCGTGTTCATTTAT
*
25358 GTTCGTGTTCGTTTAT
1 GTTCGTGTTCATTTAT
25374 GTTCGTGTT-AGTTTAT
1 GTTCGTGTTCA-TTTAT
25390 GTTCGT-TT-ATTTAT
1 GTTCGTGTTCATTTAT
25404 TAAATGAACG
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
14 5 0.08
15 3 0.05
16 51 0.86
ACGTcount: A:0.12, C:0.10, G:0.21, T:0.58
Consensus pattern (16 bp):
GTTCGTGTTCATTTAT
Found at i:25376 original size:26 final size:26
Alignment explanation
Indices: 25347--25399 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
25337 TTTATGTTCG
*
25347 TGTTCAT-TTATGTTCGTGTTCGTTTA
1 TGTTCATGTTA-GTTCATGTTCGTTTA
* *
25373 TGTTCGTGTTAGTTTATGTTCGTTTA
1 TGTTCATGTTAGTTCATGTTCGTTTA
25399 T
1 T
25400 TTATTAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.11, C:0.09, G:0.21, T:0.58
Consensus pattern (26 bp):
TGTTCATGTTAGTTCATGTTCGTTTA
Found at i:38406 original size:14 final size:14
Alignment explanation
Indices: 38387--38434 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
38377 TATATGTTTG
38387 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
38401 TTTA---T-GTTCA
1 TTTATGTTCGTTCA
38411 TTTATGTTCGTTCA
1 TTTATGTTCGTTCA
*
38425 TTTATATTCG
1 TTTATGTTCG
38435 AACAGAGGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
10 9 0.31
11 1 0.03
13 1 0.03
14 18 0.62
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.58
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:38711 original size:10 final size:10
Alignment explanation
Indices: 38696--38800 Score: 84
Period size: 10 Copynumber: 10.1 Consensus size: 10
38686 GTGTTTGTGT
38696 TGTTCGTTTA
1 TGTTCGTTTA
**
38706 TGTTCGTTCG
1 TGTTCGTTTA
*
38716 TATTCGTTTA
1 TGTTCGTTTA
**
38726 TGTTCGTTCG
1 TGTTCGTTTA
*
38736 TATTCGTTTA
1 TGTTCGTTTA
**
38746 TGTTCGTTCG
1 TGTTCGTTTA
*
38756 TATTCGTTTA
1 TGTTCGTTTA
*
38766 TGTTCGTTCGTTCT
1 TGTTCG-T--TT-A
38780 TGTTCGTTTA
1 TGTTCGTTTA
38790 TGTTCGTTTA
1 TGTTCGTTTA
38800 T
1 T
38801 TTATTAAATG
Statistics
Matches: 71, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
10 59 0.83
11 3 0.04
13 3 0.04
14 6 0.08
ACGTcount: A:0.09, C:0.14, G:0.20, T:0.57
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:38797 original size:20 final size:20
Alignment explanation
Indices: 38698--38776 Score: 158
Period size: 20 Copynumber: 4.0 Consensus size: 20
38688 GTTTGTGTTG
38698 TTCGTTTATGTTCGTTCGTA
1 TTCGTTTATGTTCGTTCGTA
38718 TTCGTTTATGTTCGTTCGTA
1 TTCGTTTATGTTCGTTCGTA
38738 TTCGTTTATGTTCGTTCGTA
1 TTCGTTTATGTTCGTTCGTA
38758 TTCGTTTATGTTCGTTCGT
1 TTCGTTTATGTTCGTTCGT
38777 TCTTGTTCGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.09, C:0.15, G:0.20, T:0.56
Consensus pattern (20 bp):
TTCGTTTATGTTCGTTCGTA
Found at i:41048 original size:35 final size:35
Alignment explanation
Indices: 41008--41144 Score: 132
Period size: 35 Copynumber: 3.9 Consensus size: 35
40998 AGTTTATGCG
**
41008 GGTTCAGTTCAATCAAACTGGTAATTCCTTATATA
1 GGTTCAGACCAATCAAACTGGTAATTCCTTATATA
* * **
41043 GGTTCAGACCGATCGAACTGGTAATTCCTTACGGTA
1 GGTTCAGACCAATCAAACTGGTAATTCCTTA-TATA
*** *
41079 GGTTCAG-CTTGGTCAAATTGGTAATTCCTTATATA
1 GGTTCAGAC-CAATCAAACTGGTAATTCCTTATATA
* * *
41114 GGTTTAGACCAATCGAGCTGGTAATTCCTTA
1 GGTTCAGACCAATCAAACTGGTAATTCCTTA
41145 CGGATCTAAG
Statistics
Matches: 80, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
35 52 0.65
36 28 0.35
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (35 bp):
GGTTCAGACCAATCAAACTGGTAATTCCTTATATA
Found at i:44917 original size:20 final size:21
Alignment explanation
Indices: 44863--44925 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
44853 GATTCCCCTG
44863 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
44887 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
44907 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
44926 TGTACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:51376 original size:30 final size:29
Alignment explanation
Indices: 51322--51382 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
51312 ACCGGTAAAG
* *
51322 AACCGGAAGAACCGACTGAGAACCGACAA
1 AACCGGAAGAACCGACTAAAAACCGACAA
* *
51351 AACCGGAATGAACCGGCTAAAAACCGGCAA
1 AACCGGAA-GAACCGACTAAAAACCGACAA
51381 AA
1 AA
51383 TCAGTGTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.46, C:0.26, G:0.23, T:0.05
Consensus pattern (29 bp):
AACCGGAAGAACCGACTAAAAACCGACAA
Found at i:52094 original size:2 final size:2
Alignment explanation
Indices: 52089--52134 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
52079 AAAAAAATGT
52089 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
52131 -A TA T
1 TA TA T
52135 TGCTTTGAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60923 original size:20 final size:20
Alignment explanation
Indices: 60898--60936 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
60888 AAACAAATAA
60898 AATAATAAAATAAAATATAT
1 AATAATAAAATAAAATATAT
* *
60918 AATAATATAATATAATATA
1 AATAATAAAATAAAATATA
60937 ATACTTAAAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAATAAAATAAAATATAT
Found at i:61611 original size:19 final size:20
Alignment explanation
Indices: 61587--61631 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
61577 GAGCGTTCAG
*
61587 TTGAGTCGAGTAAAAATA-T
1 TTGAGTCGAGTAAAAAAATT
61606 TTGAGTCGAGTAAAAAAATT
1 TTGAGTCGAGTAAAAAAATT
61626 TTGAGT
1 TTGAGT
61632 TATTTGAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.33
Consensus pattern (20 bp):
TTGAGTCGAGTAAAAAAATT
Found at i:61841 original size:2 final size:2
Alignment explanation
Indices: 61836--61862 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61826 ATATGTGATG
61836 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 T
61863 CATTCAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:71396 original size:24 final size:24
Alignment explanation
Indices: 71369--71420 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
71359 AACGGATATA
*
71369 TCAAAAATCAAAACATAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
** * *
71393 TCAAGTATCAGATCAAAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
71417 TCAA
1 TCAA
71421 GTATTCAATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.19
Consensus pattern (24 bp):
TCAAAAATCAAAACAAAATCCAGG
Found at i:71449 original size:24 final size:25
Alignment explanation
Indices: 71385--71449 Score: 98
Period size: 24 Copynumber: 2.7 Consensus size: 25
71375 ATCAAAACAT
71385 AATCCAGGTCAAGTA-TCAGATCAA
1 AATCCAGGTCAAGTATTCAGATCAA
*
71409 AATCCAGGTCAAGTATTCA-ATCAG
1 AATCCAGGTCAAGTATTCAGATCAA
*
71433 AATCCAGGTCAGGTATT
1 AATCCAGGTCAAGTATT
71450 ATAATAGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 35 0.92
25 3 0.08
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (25 bp):
AATCCAGGTCAAGTATTCAGATCAA
Found at i:74259 original size:91 final size:90
Alignment explanation
Indices: 74097--74268 Score: 224
Period size: 91 Copynumber: 1.9 Consensus size: 90
74087 GGTGCACTAC
* *
74097 GAGTGAATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATGGTC
1 GAGTGAATCGATGCATAAAATGCATTCGATGTTTAGAAAAA-CCTGAGTGCATCGATACATGGTC
*
74162 TTGTGCATCGATGCATCAAATGCACT
65 TGGTGCATCGATGCATCAAATGCACT
* *
74188 GAGTGCATCGATGCATAAAATGCATTCGATGTTTAAGAAATTAA-TTGA-TGCATCGATACATGG
1 GAGTGAATCGATGCATAAAATGCATTCGATGTTT-AGAAA--AACCTGAGTGCATCGATACATGG
*
74251 AT-TGGTGCATCGGTGCAT
63 -TCTGGTGCATCGATGCAT
74269 GCCTTTGAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
91 61 0.86
92 8 0.11
94 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (90 bp):
GAGTGAATCGATGCATAAAATGCATTCGATGTTTAGAAAAACCTGAGTGCATCGATACATGGTCT
GGTGCATCGATGCATCAAATGCACT
Found at i:76912 original size:23 final size:22
Alignment explanation
Indices: 76883--76962 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
76873 GCATGACCCC
76883 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * * *
76905 CGTGCATCGGTGTACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
76927 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
76949 ATGCATCGATGCAC
1 GTGCATCGATGCAC
76963 TGTTAGGTGT
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
21 14 0.31
22 16 0.36
23 15 0.33
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:76937 original size:44 final size:42
Alignment explanation
Indices: 76861--76981 Score: 120
Period size: 43 Copynumber: 2.8 Consensus size: 42
76851 AAAACCCGAC
* ** *
76861 GGATGCATCGATGCA-TGACCCCGTGCATCGATGCACATTCAA
1 GGATGCATCGATGCACTG-TCAGGTGTATCGATGCACATTCAA
* * *
76903 GGCGTGCATCGGTGTACCT-TCATGGTGTATCGATGCACATTCAA
1 GG-ATGCATCGATGCA-CTGTCA-GGTGTATCGATGCACATTCAA
*
76947 GGATGCATCGATGCACTGTTAGGTGTATCGATGCA
1 GGATGCATCGATGCACTGTCAGGTGTATCGATGCA
76982 TGAAGCACAA
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
42 18 0.29
43 23 0.37
44 21 0.33
45 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (42 bp):
GGATGCATCGATGCACTGTCAGGTGTATCGATGCACATTCAA
Found at i:76978 original size:20 final size:21
Alignment explanation
Indices: 76887--76981 Score: 77
Period size: 21 Copynumber: 4.4 Consensus size: 21
76877 GACCCCGTGC
*
76887 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* * * *
76910 ATCGGTGTACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
*
76931 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
76953 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
76973 ATCGATGCA
1 ATCGATGCA
76982 TGAAGCACAA
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 11 0.19
21 21 0.36
22 14 0.24
23 12 0.21
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:82481 original size:26 final size:26
Alignment explanation
Indices: 82450--82519 Score: 131
Period size: 26 Copynumber: 2.7 Consensus size: 26
82440 TTGAAAAAGC
82450 CTGAGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATCAAATGCA
82476 CTGAGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATCAAATGCA
*
82502 CTGAGTCCATCGATGCAT
1 CTGAGTGCATCGATGCAT
82520 GGCATGTGCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (26 bp):
CTGAGTGCATCGATGCATCAAATGCA
Found at i:82594 original size:20 final size:20
Alignment explanation
Indices: 82566--82604 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
82556 CAAGAAATTA
82566 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
82586 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
82605 CCTTTGAAAA
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:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:86406 original size:140 final size:141
Alignment explanation
Indices: 86239--86548 Score: 453
Period size: 140 Copynumber: 2.2 Consensus size: 141
86229 ACAATGACAA
* *
86239 AACAACAATGTTGTGAGCCCGGGACACTTCGACAAGGAAATTGGAAGACTCTTGGTAGGATTTCT
1 AACAACAATGTTGTGAGCCCGGGACACTTCGACAAAGAAATTGGAAGACTCTTGATAGGATTTCT
* ** * * *
86304 GGAAAGATCAAGAA-CCTTGAGTGCATCCATATGCTTGAA-AATCGTTCTGGAATACTCGCTATA
66 GGAAAGATCAAGAATCC-TAAGCCCATCCATATGCTTGAAGAACCCTTCCGGAATACTCGCTATA
** * *
86367 TTGCATTGAGAC
130 TCACAATCAGAC
86379 AACAACAATGTTGTGAGCCCGGGACACTTCGACAAAGAAATTGGAAGACTCTTGATAGGATTTCT
1 AACAACAATGTTGTGAGCCCGGGACACTTCGACAAAGAAATTGGAAGACTCTTGATAGGATTTCT
*
86444 GGAAAGATCAAGAATCCTAAGCCCATGCATATGCTTGAAGAACCCTTCCGGAATACTCGCTATAT
66 GGAAAGATCAAGAATCCTAAGCCCATCCATATGCTTGAAGAACCCTTCCGGAATACTCGCTATAT
86509 CACAATCAGAC
131 CACAATCAGAC
* * *
86520 AACAGCAATGTTGTGAGCCTGGGGCACTT
1 AACAACAATGTTGTGAGCCCGGGACACTT
86549 TGGGGGTGAC
Statistics
Matches: 152, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
140 95 0.62
141 57 0.38
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (141 bp):
AACAACAATGTTGTGAGCCCGGGACACTTCGACAAAGAAATTGGAAGACTCTTGATAGGATTTCT
GGAAAGATCAAGAATCCTAAGCCCATCCATATGCTTGAAGAACCCTTCCGGAATACTCGCTATAT
CACAATCAGAC
Found at i:87352 original size:36 final size:36
Alignment explanation
Indices: 87302--87373 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
87292 CCATTTGACG
87302 GCTCAGGATATCCTATTCTCTCAAGTGAAACCTTCT
1 GCTCAGGATATCCTATTCTCTCAAGTGAAACCTTCT
*
87338 GCTCAGGA-ATTCCTATTTTCTCAAGTGAAACCTTCT
1 GCTCAGGATA-TCCTATTCTCTCAAGTGAAACCTTCT
87374 CCCATAGGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 1 0.03
36 33 0.97
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (36 bp):
GCTCAGGATATCCTATTCTCTCAAGTGAAACCTTCT
Found at i:92357 original size:24 final size:24
Alignment explanation
Indices: 92325--92380 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
92315 CTATTCTTTC
92325 GCTTCAATTGAGCTAAAATTTTAG
1 GCTTCAATTGAGCTAAAATTTTAG
*
92349 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTAAAATTTTAG
92373 GCTTCAAT
1 GCTTCAAT
92381 CGAACTTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTAAAATTTTAG
Found at i:92638 original size:20 final size:20
Alignment explanation
Indices: 92612--92657 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
92602 GCGGTTCAAA
92612 CCGGTTTTGC-CGGTTTTCAG
1 CCGGTTTT-CTCGGTTTTCAG
*
92632 TCGGTTTTCTCGGTTTTCAG
1 CCGGTTTTCTCGGTTTTCAG
92652 CCGGTT
1 CCGGTT
92658 CTTTCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.04, C:0.24, G:0.28, T:0.43
Consensus pattern (20 bp):
CCGGTTTTCTCGGTTTTCAG
Found at i:98177 original size:13 final size:13
Alignment explanation
Indices: 98156--98186 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
98146 TATTGAGTGA
98156 TGTTGAACATACT
1 TGTTGAACATACT
*
98169 TGTTTAACATACT
1 TGTTGAACATACT
98182 TGTTG
1 TGTTG
98187 CATCCCATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (13 bp):
TGTTGAACATACT
Done.