Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007213.1 Hibiscus syriacus cultivar Beakdansim tig00019067_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: 66378
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:301 original size:20 final size:20
Alignment explanation
Indices: 276--329 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
266 GATTTTGTAT
276 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
296 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
316 TATCGCATTGCGAT
1 TATCGCATTGCGAT
330 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:348 original size:61 final size:61
Alignment explanation
Indices: 236--350 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 61
226 CGCTATGTAA
* * * ** *
236 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
* *
297 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATCGCATTGCGAT
351 TTACTTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
61 43 0.96
62 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTAAGT
Found at i:1684 original size:2 final size:2
Alignment explanation
Indices: 1677--1731 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1667 GAATTAAGGT
1677 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
1719 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1732 CTTTATAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6731 original size:17 final size:18
Alignment explanation
Indices: 6706--6747 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
6696 CGATCCAGTT
*
6706 CGACTCGACCCGTTGA-C
1 CGACCCGACCCGTTGACC
6723 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
6741 CGACCCG
1 CGACCCG
6748 GTGACATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.17, C:0.48, G:0.24, T:0.12
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:6791 original size:29 final size:29
Alignment explanation
Indices: 6761--6935 Score: 171
Period size: 29 Copynumber: 6.1 Consensus size: 29
6751 ACATTTTAGA
* * *
6761 AATTATTTTGAAAAAGGTGATATTCTGGA
1 AATTATTTTGAAAAAAGTGACATTCTGGG
* * *
6790 AATTATTTTGGAAAATGTGACATTTTGGG
1 AATTATTTTGAAAAAAGTGACATTCTGGG
* *
6819 AA-T-TTTT-AAAAAAATGACATTATGGG
1 AATTATTTTGAAAAAAGTGACATTCTGGG
* *
6845 AATTATTTTG-AAAAAGTAACATTTTTGGG
1 AATTATTTTGAAAAAAGTGACA-TTCTGGG
* * *
6874 ATTTTTTTTGAAAAAAGTGACATTCTTGG
1 AATTATTTTGAAAAAAGTGACATTCTGGG
*
6903 AATTATTTTG-AAAAAGATGACATTTTGGG
1 AATTATTTTGAAAAAAG-TGACATTCTGGG
6932 AATT
1 AATT
6936 TTCAAATATG
Statistics
Matches: 119, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
26 17 0.14
27 5 0.04
28 20 0.17
29 67 0.56
30 10 0.08
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.40
Consensus pattern (29 bp):
AATTATTTTGAAAAAAGTGACATTCTGGG
Found at i:6909 original size:58 final size:56
Alignment explanation
Indices: 6748--6937 Score: 197
Period size: 58 Copynumber: 3.3 Consensus size: 56
6738 ACCCGACCCG
** * * * *
6748 GTGACATTTTAGAAATTATTTTGAAAAAGGTGATATTC-TGGAAATTATTTTGGAAAAT
1 GTGACATTTT-GGGATTTTTTTGAAAAAAGTGACATTCTTGG-AATTATTTT-GAAAAA
* * * *
6806 GTGACATTTTGGGA-ATTTTT-AAAAAAATGACATTATGGGAATTATTTTGAAAAA
1 GTGACATTTTGGGATTTTTTTGAAAAAAGTGACATTCTTGGAATTATTTTGAAAAA
*
6860 GTAACATTTTTGGGATTTTTTTTGAAAAAAGTGACATTCTTGGAATTATTTTGAAAAA
1 GTGACA-TTTTGGGA-TTTTTTTGAAAAAAGTGACATTCTTGGAATTATTTTGAAAAA
*
6918 GATGACATTTTGGGAATTTT
1 G-TGACATTTTGGGATTTTT
6938 CAAATATGAC
Statistics
Matches: 109, Mismatches: 17, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
54 10 0.09
55 28 0.26
56 6 0.06
57 11 0.10
58 50 0.46
59 4 0.04
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (56 bp):
GTGACATTTTGGGATTTTTTTGAAAAAAGTGACATTCTTGGAATTATTTTGAAAAA
Found at i:10248 original size:28 final size:29
Alignment explanation
Indices: 10211--10270 Score: 104
Period size: 28 Copynumber: 2.1 Consensus size: 29
10201 AAATTATTTT
10211 ATATAGTATTCTTAATAAAAAATTCATTA
1 ATATAGTATTCTTAATAAAAAATTCATTA
*
10240 ATAT-GTATTCTTAATAACAAATTCATTA
1 ATATAGTATTCTTAATAAAAAATTCATTA
10268 ATA
1 ATA
10271 ACAGTTGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (29 bp):
ATATAGTATTCTTAATAAAAAATTCATTA
Found at i:10272 original size:15 final size:14
Alignment explanation
Indices: 10218--10273 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
10208 TTTATATAGT
*
10218 ATTCTTAATAAAAA
1 ATTCTTAATAACAA
***
10232 ATTCATTAAT-ATGT
1 ATTC-TTAATAACAA
10246 ATTCTTAATAACAA
1 ATTCTTAATAACAA
10260 ATTCATTAATAACA
1 ATTC-TTAATAACA
10274 GTTGTATATG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
13 5 0.15
14 14 0.42
15 14 0.42
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (14 bp):
ATTCTTAATAACAA
Found at i:14754 original size:20 final size:21
Alignment explanation
Indices: 14699--14755 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
14689 ATACCCCCCC
*
14699 AATGGTATCGATACCCCTATG
1 AATGGTATCGATACCACTATG
*
14720 CAATGATATCGATACCACTATG
1 -AATGGTATCGATACCACTATG
*
14742 -ATGGTACCGATACC
1 AATGGTATCGATACC
14756 CTAAGGCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.39
22 19 0.61
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (21 bp):
AATGGTATCGATACCACTATG
Found at i:20568 original size:22 final size:23
Alignment explanation
Indices: 20524--20628 Score: 139
Period size: 22 Copynumber: 4.8 Consensus size: 23
20514 TTTTGTGCAT
**
20524 TAGGTATCGATA-CCCCTGAGAA
1 TAGGTATCGATACCCCCTTTGAA
20546 T-GGTATCGATACCCCCTTTGAA
1 TAGGTATCGATACCCCCTTTGAA
*
20568 TAGGTATCGATA-CCCCTAT-AA
1 TAGGTATCGATACCCCCTTTGAA
20589 TAGGTATCGATACCCCC-TTGAA
1 TAGGTATCGATACCCCCTTTGAA
*
20611 TGGGTATCGATACCCCCT
1 TAGGTATCGATACCCCCT
20629 GATGGTACCG
Statistics
Matches: 73, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
21 25 0.34
22 38 0.52
23 10 0.14
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (23 bp):
TAGGTATCGATACCCCCTTTGAA
Found at i:20628 original size:44 final size:44
Alignment explanation
Indices: 20524--20626 Score: 165
Period size: 44 Copynumber: 2.4 Consensus size: 44
20514 TTTTGTGCAT
20524 TAGGTATCGATACCCCTGAGAATGGTATCGATACCCCCTTTGAA
1 TAGGTATCGATACCCCTGAGAATGGTATCGATACCCCCTTTGAA
*
20568 TAGGTATCGATACCCCT-ATAATAGGTATCGATACCCCC-TTGAA
1 TAGGTATCGATACCCCTGAGAAT-GGTATCGATACCCCCTTTGAA
*
20611 TGGGTATCGATACCCC
1 TAGGTATCGATACCCC
20627 CTGATGGTAC
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
43 24 0.43
44 32 0.57
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (44 bp):
TAGGTATCGATACCCCTGAGAATGGTATCGATACCCCCTTTGAA
Found at i:22632 original size:21 final size:21
Alignment explanation
Indices: 22594--22642 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
22584 TTGAATGCTT
22594 TTGGATTGTTTAACTTTGTTTG
1 TTGGA-TGTTTAACTTTGTTTG
22616 TTGGATGTTTGAA-TTTGTTTG
1 TTGGATGTTT-AACTTTGTTTG
*
22637 ATGGAT
1 TTGGAT
22643 TATGAATGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.16, C:0.02, G:0.27, T:0.55
Consensus pattern (21 bp):
TTGGATGTTTAACTTTGTTTG
Found at i:22982 original size:12 final size:12
Alignment explanation
Indices: 22965--23013 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
22955 GTAATTTCAA
22965 TTCAAAATTGAT
1 TTCAAAATTGAT
22977 TTCAAAATTGAT
1 TTCAAAATTGAT
**
22989 TTC-ATTTTGAT
1 TTCAAAATTGAT
*
23000 TTCAAAAATGAT
1 TTCAAAATTGAT
23012 TT
1 TT
23014 TCAATAATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 9 0.29
12 22 0.71
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (12 bp):
TTCAAAATTGAT
Found at i:23436 original size:22 final size:21
Alignment explanation
Indices: 23388--23467 Score: 76
Period size: 22 Copynumber: 3.8 Consensus size: 21
23378 CAGAATGCTA
*
23388 GAATGGTATCGATACCCC-CT
1 GAATGGTATCGATACCCCTAT
23408 -AATGGTATCGATACCCCTAT
1 GAATGGTATCGATACCCCTAT
* *
23428 GCAATGGTATTGAAACCCCCCTAT
1 G-AATGGTATCGATA--CCCCTAT
*
23452 G-ATGGTACCGATACCC
1 GAATGGTATCGATACCC
23468 TAAGGCGTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
19 17 0.35
20 4 0.08
22 20 0.41
24 8 0.16
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.25
Consensus pattern (21 bp):
GAATGGTATCGATACCCCTAT
Found at i:26959 original size:14 final size:14
Alignment explanation
Indices: 26937--26975 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
26927 TGGTGGCGTC
26937 GAGGAAGGAGAAAG
1 GAGGAAGGAGAAAG
*
26951 GAGGTAGGAGAAAGG
1 GAGGAAGGAGAAA-G
*
26966 GAGAAAGGAG
1 GAGGAAGGAG
26976 GTAGGGGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.51, T:0.03
Consensus pattern (14 bp):
GAGGAAGGAGAAAG
Found at i:27010 original size:22 final size:22
Alignment explanation
Indices: 26943--26998 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
26933 CGTCGAGGAA
*
26943 GGAGAAAGGAGGTAGGAGAAAG
1 GGAGAAAGGAGGTAGGGGAAAG
26965 GGAGAAAGGAGGTAGGGGAAAG
1 GGAGAAAGGAGGTAGGGGAAAG
*
26987 GGAGAAGGGAGG
1 GGAGAAAGGAGG
26999 GGGAGGAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.55, T:0.04
Consensus pattern (22 bp):
GGAGAAAGGAGGTAGGGGAAAG
Found at i:27088 original size:21 final size:21
Alignment explanation
Indices: 27040--27089 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
27030 TTAAAAAATC
27040 TTTTTTAAAAATATATATTAA
1 TTTTTTAAAAATATATATTAA
* * *
27061 TTATTTAAATAA-ATATTTTAT
1 TTTTTTAAA-AATATATATTAA
27082 TTTTTTAA
1 TTTTTTAA
27090 CTTTTTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTTTAAAAATATATATTAA
Found at i:40166 original size:17 final size:17
Alignment explanation
Indices: 40141--40174 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40131 CCGGTTTCGG
40141 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
* *
40158 TTTTTAAAAAATCGGTT
1 TTTTAAAAAAACCGGTT
40175 ATAAAAAACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:40610 original size:13 final size:13
Alignment explanation
Indices: 40589--40643 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
40579 AAGTTCGATA
*
40589 AATTCAAATACTT
1 AATTGAAATACTT
40602 AATTGAAATACTT
1 AATTGAAATACTT
* *
40615 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
40629 AATTGAAATACTT
1 AATTGAAATACTT
40642 AA
1 AA
40644 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:40725 original size:32 final size:33
Alignment explanation
Indices: 40629--40727 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
40619 AACTCAACAT
* * *
40629 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
40662 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
40695 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
40727 A
1 A
40728 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:40746 original size:21 final size:21
Alignment explanation
Indices: 40722--40761 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40712 ACTTCAAGTT
40722 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
40743 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
40762 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:49909 original size:19 final size:19
Alignment explanation
Indices: 49885--49935 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
49875 CTTTAACGTG
* *
49885 TGCATCGATGCATTAGCTA
1 TGCATCGATACACTAGCTA
49904 TGCATCGATACACTAGCTA
1 TGCATCGATACACTAGCTA
*
49923 TGCATCGGTACAC
1 TGCATCGATACAC
49936 AAATCTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (19 bp):
TGCATCGATACACTAGCTA
Found at i:50286 original size:22 final size:23
Alignment explanation
Indices: 50243--50291 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
50233 ATCTCACTCA
*
50243 AATTCTAACATGTTCTAAATC-T
1 AATTCTAACATCTTCTAAATCTT
*
50265 AATTCTAACA-CTTCATATATCTT
1 AATTCTAACATCTTC-TAAATCTT
50288 AATT
1 AATT
50292 AAGTCGATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.43
Consensus pattern (23 bp):
AATTCTAACATCTTCTAAATCTT
Found at i:56142 original size:18 final size:18
Alignment explanation
Indices: 56119--56190 Score: 99
Period size: 18 Copynumber: 3.8 Consensus size: 18
56109 ATTGAATATT
56119 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
56137 TCCCGAATGACCACTGATATG
1 TCCCGAAGGACCAC---TATG
*
56158 TCCCGAATGACCACTATG
1 TCCCGAAGGACCACTATG
56176 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
56191 GATATCCCTC
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
18 31 0.63
21 18 0.37
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.19
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:56159 original size:21 final size:21
Alignment explanation
Indices: 56133--56195 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
56123 GAAGGACCAC
56133 TATGTCCCGAATGACCACTGA
1 TATGTCCCGAATGACCACTGA
56154 TATGTCCCGAATGACCAC---
1 TATGTCCCGAATGACCACTGA
*
56172 TATGTCCCGAAGGACCACTGA
1 TATGTCCCGAATGACCACTGA
56193 TAT
1 TAT
56196 CCCTCGACTC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
18 17 0.45
21 21 0.55
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (21 bp):
TATGTCCCGAATGACCACTGA
Found at i:56173 original size:39 final size:39
Alignment explanation
Indices: 56114--56195 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
56104 GGGGCATTGA
* *
56114 ATATTTCCCGAAGGACCACTATGTCCCGAATGACCACTG
1 ATATGTCCCGAAGGACCACTATGTCCCGAAGGACCACTG
*
56153 ATATGTCCCGAATGACCACTATGTCCCGAAGGACCACTG
1 ATATGTCCCGAAGGACCACTATGTCCCGAAGGACCACTG
56192 ATAT
1 ATAT
56196 CCCTCGACTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.23
Consensus pattern (39 bp):
ATATGTCCCGAAGGACCACTATGTCCCGAAGGACCACTG
Found at i:60113 original size:43 final size:43
Alignment explanation
Indices: 60065--60187 Score: 174
Period size: 43 Copynumber: 2.9 Consensus size: 43
60055 TCTAGAATGC
* *
60065 TTTTAATATGTTAGTTTGATGTACTTGTGGATTGTTACTTTAG
1 TTTTAATATGTTAGTTTGGTGTATTTGTGGATTGTTACTTTAG
* *
60108 TTTTAATATGTTAGTTTGGTGAATTTGTGGATTGCTACTTTAG
1 TTTTAATATGTTAGTTTGGTGTATTTGTGGATTGTTACTTTAG
* * * *
60151 TTTAAATATGCTAGTTTGGTGTATTTATGGTTTGTTA
1 TTTTAATATGTTAGTTTGGTGTATTTGTGGATTGTTA
60188 GTTTGGAATT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.21, C:0.04, G:0.22, T:0.53
Consensus pattern (43 bp):
TTTTAATATGTTAGTTTGGTGTATTTGTGGATTGTTACTTTAG
Found at i:60355 original size:21 final size:21
Alignment explanation
Indices: 60329--60373 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
60319 ATTTTTTAGT
*
60329 GAGCTTAACGAGCAACGAATC
1 GAGCTTAACGAGAAACGAATC
*
60350 GAGCTTAACGAGAAACGAGTC
1 GAGCTTAACGAGAAACGAATC
60371 GAG
1 GAG
60374 TTGAGCAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.20, G:0.29, T:0.13
Consensus pattern (21 bp):
GAGCTTAACGAGAAACGAATC
Found at i:60431 original size:34 final size:36
Alignment explanation
Indices: 60354--60439 Score: 113
Period size: 34 Copynumber: 2.4 Consensus size: 36
60344 CGAATCGAGC
* * *
60354 TTAACGAGAAACGAGTCGAGTTGAGCAGCAAAATTTT
1 TTAACGAG-CACGAGTCGAGTCGAACAGCAAAATTTT
*
60391 TTAACGAGCACGAGTCGAGTCGAACATC-AAA-TTT
1 TTAACGAGCACGAGTCGAGTCGAACAGCAAAATTTT
60425 TTAACGAGCACGAGT
1 TTAACGAGCACGAGT
60440 TGAGCACTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
34 18 0.40
35 3 0.07
36 16 0.36
37 8 0.18
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (36 bp):
TTAACGAGCACGAGTCGAGTCGAACAGCAAAATTTT
Found at i:62567 original size:16 final size:16
Alignment explanation
Indices: 62546--62584 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
62536 GTTTATGGTG
62546 AAATAAATTAAATAAA
1 AAATAAATTAAATAAA
**
62562 AAATAAATTAGGTAAA
1 AAATAAATTAAATAAA
62578 AAATAAA
1 AAATAAA
62585 GACTCGTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (16 bp):
AAATAAATTAAATAAA
Found at i:62908 original size:16 final size:17
Alignment explanation
Indices: 62873--62919 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
62863 CTGATAATTT
* *
62873 TAAAATTTTTAAAATAA
1 TAAAATTATAAAAATAA
*
62890 TAAAATTA-AAAAATTA
1 TAAAATTATAAAAATAA
*
62906 TAATATTATAAAAA
1 TAAAATTATAAAAA
62920 AACTTTACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATTATAAAAATAA
Found at i:64221 original size:2 final size:2
Alignment explanation
Indices: 64151--64208 Score: 68
Period size: 2 Copynumber: 30.5 Consensus size: 2
64141 CAGTTTTCTG
* *
64151 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT CT AT CT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
64191 AT AT -T TT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
64209 CGTATGAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
1 3 0.06
2 45 0.94
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:65570 original size:21 final size:22
Alignment explanation
Indices: 65546--65590 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
65536 CAATACACTT
65546 GCAGAAGAAACGTC-ACTGGAA
1 GCAGAAGAAACGTCAACTGGAA
65567 GCAGAAGAAACGTCAACTGGAA
1 GCAGAAGAAACGTCAACTGGAA
65589 GC
1 GC
65591 CCCCTCCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.42, C:0.20, G:0.29, T:0.09
Consensus pattern (22 bp):
GCAGAAGAAACGTCAACTGGAA
Done.