Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006101.1 Hibiscus syriacus cultivar Beakdansim tig00014460_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: 70759
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:8801 original size:13 final size:13
Alignment explanation
Indices: 8783--8810 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
8773 TGATATAAGC
8783 AATGGTTGCGATT
1 AATGGTTGCGATT
8796 AATGGTTGCGATT
1 AATGGTTGCGATT
8809 AA
1 AA
8811 GATGATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (13 bp):
AATGGTTGCGATT
Found at i:9127 original size:2 final size:2
Alignment explanation
Indices: 9120--9179 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
9110 GGTGTTGTAA
9120 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9162 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
9180 GCGATTGCAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9669 original size:2 final size:2
Alignment explanation
Indices: 9662--9686 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9652 TAAGAGCTAA
9662 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
9687 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9720 original size:23 final size:23
Alignment explanation
Indices: 9686--9773 Score: 108
Period size: 23 Copynumber: 3.9 Consensus size: 23
9676 ATATATATAT
9686 AAAAAAAA-AAAAAAAAAAAAAG
1 AAAAAAAAGAAAAAAAAAAAAAG
*
9708 AAAAAAAAGAAAAAAAAAGAAAG
1 AAAAAAAAGAAAAAAAAAAAAAG
* * **
9731 AATAAAAAGAAAAGAAAACGAAG
1 AAAAAAAAGAAAAAAAAAAAAAG
*
9754 -AAAAATAGAAAAAAAAAAAA
1 AAAAAAAAGAAAAAAAAAAAA
9774 TGAGAGATGA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
22 23 0.42
23 32 0.58
ACGTcount: A:0.86, C:0.01, G:0.10, T:0.02
Consensus pattern (23 bp):
AAAAAAAAGAAAAAAAAAAAAAG
Found at i:9791 original size:1 final size:1
Alignment explanation
Indices: 9686--9773 Score: 68
Period size: 1 Copynumber: 88.0 Consensus size: 1
9676 ATATATATAT
* * * * * * * **
9686 AAAAAAAAAAAAAAAAAAAAAGAAAAAAAAGAAAAAAAAAGAAAGAATAAAAAGAAAAGAAAACG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
9751 AAGAAAAATAGAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAA
9774 TGAGAGATGA
Statistics
Matches: 64, Mismatches: 23, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.86, C:0.01, G:0.10, T:0.02
Consensus pattern (1 bp):
A
Found at i:12120 original size:284 final size:283
Alignment explanation
Indices: 11610--12177 Score: 1037
Period size: 284 Copynumber: 2.0 Consensus size: 283
11600 TTAATGGTTT
* *
11610 AATTTCATGTGTAATTTGAATTATTTTATTAAAGTGACTGAATTGTAACTTTTGGAAATTACAAG
1 AATTTCATGTGTAATTTGAATTATTTTATTAAAGTGACTAAATTATAACTTTTGGAAATTACAAG
*
11675 GGCAAAACGGTAAAGTGAAAAACAAATTTGTTCATCTTTGACTATTAAAAGATGACAAGGCTGAT
66 GGCAAAACGGTAAAGTGAAAAACAAATTTGTTCACCTTTGACTATTAAAAGATGACAAGGCTGAT
*
11740 ATTTAATTGATTTTGAAGATGATAAGGATATGTGTCTTGGTTTTATGGTAATTATGAAGTTATAT
131 ATTTAATTGATTTTGAAGATGATAAGGATATGTATCTTGGTTTTATGGTAATTATGAAGTTATAT
*
11805 TAAGGGTATATTGCTATTTTCTCAAGTTAATGATTAAATATTATATTAAAAGATGATAAGCATGA
196 TAAGGGTATATTGCTATTTTATCAAGTTAATGATTAAATA-TATATTAAAAGATGATAAGCATGA
11870 CATGAATCTAAAAGATCATGCTAA
260 CATGAATCTAAAAGATCATGCTAA
*
11894 AATTTCATGTGTAATTTGAATTATTTTATTAAAGTGACTAAATTATAATTTTTGGAAATTACAAG
1 AATTTCATGTGTAATTTGAATTATTTTATTAAAGTGACTAAATTATAACTTTTGGAAATTACAAG
11959 GGCAAAACGGTAAAGTGAAAAACAAATTTGTTCACCTTTGACTATTAAAAGATGACAAGGCTGAT
66 GGCAAAACGGTAAAGTGAAAAACAAATTTGTTCACCTTTGACTATTAAAAGATGACAAGGCTGAT
*
12024 ATTTAATTGATTTTGAAGATGATAAGGATATGTATCTTTGTTTTATGGTAATTATGAAGTTATAT
131 ATTTAATTGATTTTGAAGATGATAAGGATATGTATCTTGGTTTTATGGTAATTATGAAGTTATAT
* *
12089 TAAGGGTATATTGGTATTTTATCAAGTTAATGATTAAATATATATTAAAAGATGATAAGCATGAT
196 TAAGGGTATATTGCTATTTTATCAAGTTAATGATTAAATATATATTAAAAGATGATAAGCATGAC
*
12154 ATGAATCTAAAATATCATGCTAA
261 ATGAATCTAAAAGATCATGCTAA
12177 A
1 A
12178 TGTTCATCTT
Statistics
Matches: 274, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
283 47 0.17
284 227 0.83
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.38
Consensus pattern (283 bp):
AATTTCATGTGTAATTTGAATTATTTTATTAAAGTGACTAAATTATAACTTTTGGAAATTACAAG
GGCAAAACGGTAAAGTGAAAAACAAATTTGTTCACCTTTGACTATTAAAAGATGACAAGGCTGAT
ATTTAATTGATTTTGAAGATGATAAGGATATGTATCTTGGTTTTATGGTAATTATGAAGTTATAT
TAAGGGTATATTGCTATTTTATCAAGTTAATGATTAAATATATATTAAAAGATGATAAGCATGAC
ATGAATCTAAAAGATCATGCTAA
Found at i:13540 original size:40 final size:40
Alignment explanation
Indices: 13485--13646 Score: 288
Period size: 40 Copynumber: 4.0 Consensus size: 40
13475 TGCAAGTTTA
13485 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
13525 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATTTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
13565 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
13605 TAATACACTTCGGTGTATATGGTGGACACGACCTTATATG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
13645 TA
1 TA
13647 GCACTACGGT
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 116 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:13844 original size:45 final size:46
Alignment explanation
Indices: 13754--13862 Score: 143
Period size: 45 Copynumber: 2.4 Consensus size: 46
13744 AGCATGCAAG
* *
13754 TAAGCTTACGAGCTTAT-GGAATATTGGCAAGTATATGGGTAAAAA
1 TAAGCTTACGAGCTTATGGGAATAATGACAAGTATATGGGTAAAAA
* * *
13799 TAAGCTTACGAGCTTATGGGACA-AATGATAAGTATTTTGGT-AAAA
1 TAAGCTTACGAGCTTATGGGA-ATAATGACAAGTATATGGGTAAAAA
13844 TAAGCTTACGAGCTTATGG
1 TAAGCTTACGAGCTTATGG
13863 TTAATAAATG
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
45 40 0.70
46 16 0.28
47 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (46 bp):
TAAGCTTACGAGCTTATGGGAATAATGACAAGTATATGGGTAAAAA
Found at i:14607 original size:39 final size:39
Alignment explanation
Indices: 14564--14655 Score: 125
Period size: 39 Copynumber: 2.4 Consensus size: 39
14554 GGTGTTAAAC
14564 TAACATTCTAAATTCCTAATTTCTTAAAATT-TTTCACCA-
1 TAACATTCTAAATTCCTAATTTCTT-AAATTATTTCA-CAT
* *
14603 TAACATTCTAAATTCTTAATTTGTTAAATTATTTCACAT
1 TAACATTCTAAATTCCTAATTTCTTAAATTATTTCACAT
*
14642 TAACATTATAAATT
1 TAACATTCTAAATT
14656 ATTTTTTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
38 7 0.15
39 41 0.85
ACGTcount: A:0.38, C:0.15, G:0.01, T:0.46
Consensus pattern (39 bp):
TAACATTCTAAATTCCTAATTTCTTAAATTATTTCACAT
Found at i:14978 original size:30 final size:30
Alignment explanation
Indices: 14921--14980 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
14911 ACACGGGCTG
***
14921 AAATTTTGATACCCGAAAATTTTGGGTACC
1 AAATTTTGATACCCGAAAATCACGGGTACC
14951 AAATTTTGGATACCCGAAAA-CACGGGTACC
1 AAATTTT-GATACCCGAAAATCACGGGTACC
14981 TGGTTTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (30 bp):
AAATTTTGATACCCGAAAATCACGGGTACC
Found at i:20392 original size:3 final size:3
Alignment explanation
Indices: 20384--20426 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
20374 TCGGGTCTTG
*
20384 TAA TAA TAA TAA TAA TAA TAA TATA TTA TAAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA TA
20427 TATTATATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 32 0.89
4 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:20418 original size:23 final size:25
Alignment explanation
Indices: 20388--20438 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
20378 GTCTTGTAAT
*
20388 AATAATAATAATAATAATATATTATA
1 AATAATAATAAT-ATATTATATTATA
20414 AATAATAATAATATATTATATTATA
1 AATAATAATAATATATTATATTATA
20439 TATGTATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATAATAATAATATATTATATTATA
Found at i:20419 original size:20 final size:20
Alignment explanation
Indices: 20394--20433 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
20384 TAATAATAAT
20394 AATAATAATAATATATTATA
1 AATAATAATAATATATTATA
20414 AATAATAATAATATATTATA
1 AATAATAATAATATATTATA
20434 TTATATATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAATAATAATATATTATA
Found at i:20669 original size:36 final size:36
Alignment explanation
Indices: 20622--20713 Score: 175
Period size: 36 Copynumber: 2.6 Consensus size: 36
20612 TCTAATCTTG
20622 CTTCACTACTCTTCCGTGAAGGTTGAAAATGACTAA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATGACTAA
*
20658 CTTCACTACTCTTCCGTGAAGGTTGAAAATGACTGA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATGACTAA
20694 CTTCACTACTCTTCCGTGAA
1 CTTCACTACTCTTCCGTGAA
20714 ACTCAGATTC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (36 bp):
CTTCACTACTCTTCCGTGAAGGTTGAAAATGACTAA
Found at i:20844 original size:20 final size:20
Alignment explanation
Indices: 20821--20893 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
20811 ACCCAAATAA
*
20821 TTTACAAATTACCCAGAGGT
1 TTTACAAATGACCCAGAGGT
* **
20841 TTTACAAATGGCCTGGAGGT
1 TTTACAAATGACCCAGAGGT
20861 TTTACAAATGACCCAGAGGT
1 TTTACAAATGACCCAGAGGT
20881 TTTACAAATGACC
1 TTTACAAATGACC
20894 GGAGGTCTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (20 bp):
TTTACAAATGACCCAGAGGT
Found at i:20876 original size:40 final size:39
Alignment explanation
Indices: 20821--20899 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 39
20811 ACCCAAATAA
* *
20821 TTTACAAATTACCCAGAGGTTTTACAAATGGCCTGGAGGT
1 TTTACAAATGACCCAGAGGTTTTACAAATGACC-GGAGGT
20861 TTTACAAATGACCCAGAGGTTTTACAAATGACCGGAGGT
1 TTTACAAATGACCCAGAGGTTTTACAAATGACCGGAGGT
20900 CTAAAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
39 6 0.16
40 31 0.84
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (39 bp):
TTTACAAATGACCCAGAGGTTTTACAAATGACCGGAGGT
Found at i:27673 original size:19 final size:20
Alignment explanation
Indices: 27649--27688 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
27639 TATCCCATCC
27649 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
27668 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
27688 T
1 T
27689 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:28581 original size:90 final size:90
Alignment explanation
Indices: 28461--28638 Score: 311
Period size: 90 Copynumber: 2.0 Consensus size: 90
28451 TAATCTCGAA
* *
28461 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
28526 TAGGGAAACTTGGATATAAAAGGAT
66 TAGGGAAACTTGGATATAAAAGGAT
*
28551 TATTAAATTTCAATTAATTAAATATTGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
* *
28616 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGAAACTTGGATATAAAAGG
28639 GTGTGTTAGG
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGAAACTTGGATATAAAAGGAT
Found at i:35254 original size:90 final size:89
Alignment explanation
Indices: 35145--35319 Score: 287
Period size: 90 Copynumber: 2.0 Consensus size: 89
35135 TCCCGAATAT
* * * *
35145 TTAATTTCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAAATTTAATTAATTTAAAATAAGAAAAACCCTAATATGATTAG
35210 GGTAACTTGGATATAAAAGGATTA
66 GGTAACTTGGATATAAAAGGATTA
*
35234 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTAAAATAAGAAAAACCCTAATATGATTA
1 TTAAATTC-AATTAATTAAATATAAATTTAATTAATTTAAAATAAGAAAAACCCTAATATGATTA
*
35299 GGGTAACTTGGCTATAAAAGG
65 GGGTAACTTGGATATAAAAGG
35320 GTATGTTAGG
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 7 0.09
90 72 0.91
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAAATTTAATTAATTTAAAATAAGAAAAACCCTAATATGATTAG
GGTAACTTGGATATAAAAGGATTA
Found at i:43582 original size:3 final size:3
Alignment explanation
Indices: 43574--43645 Score: 90
Period size: 3 Copynumber: 22.7 Consensus size: 3
43564 TCGGGTCTTG
*
43574 TAA TAA TAA TAA TAA TAA TAA TAA TATA TAT TATA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA-A TAA TAA TAA TAA
*
43621 TATA TAT TATA TAA TAA TAA TAA TA
1 TA-A TAA TA-A TAA TAA TAA TAA TA
43646 TATTATATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
3 51 0.84
4 10 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:43612 original size:23 final size:23
Alignment explanation
Indices: 43585--43666 Score: 128
Period size: 23 Copynumber: 3.4 Consensus size: 23
43575 AATAATAATA
43585 ATAATAATAATAATATATATTAT
1 ATAATAATAATAATATATATTAT
43608 ATAATAATAATAATATATATTAT
1 ATAATAATAATAATATATATTAT
43631 ATAATAATAATAATATATTATATTAT
1 ATAATAATAAT-A-ATA-TATATTAT
43657 ATATATAATA
1 ATA-ATAATA
43667 GAAATGTCAC
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
23 34 0.62
24 1 0.02
25 3 0.05
26 11 0.20
27 6 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATAATAATAATAATATATATTAT
Found at i:43618 original size:26 final size:26
Alignment explanation
Indices: 43582--43666 Score: 124
Period size: 26 Copynumber: 3.3 Consensus size: 26
43572 TGTAATAATA
43582 ATAATAATAATAATAATATATA-T-T
1 ATAATAATAATAATAATATATATTAT
43606 AT-ATAATAATAATAATATATATTAT
1 ATAATAATAATAATAATATATATTAT
43631 ATAATAATAATAAT-ATATTATATTAT
1 ATAATAATAATAATAATA-TATATTAT
43657 ATATATAATA
1 ATA-ATAATA
43667 GAAATGTCAC
Statistics
Matches: 56, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
23 19 0.34
24 3 0.05
25 6 0.11
26 22 0.39
27 6 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAATAATAATAATAATATATATTAT
Found at i:46357 original size:29 final size:31
Alignment explanation
Indices: 46308--46366 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 31
46298 AAATAAATTT
*
46308 AAAAATTATAATTTAGACCCATAAAATTTTC
1 AAAAATTATAATTTAGACCCACAAAATTTTC
*
46339 AAAAACTT-TAATTT-G-CCCACAAATTTTT
1 AAAAA-TTATAATTTAGACCCACAAAATTTT
46367 AATAATTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
29 11 0.44
30 1 0.04
31 11 0.44
32 2 0.08
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.37
Consensus pattern (31 bp):
AAAAATTATAATTTAGACCCACAAAATTTTC
Found at i:58049 original size:13 final size:14
Alignment explanation
Indices: 58026--58056 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
58016 ACTATCGATA
58026 TATTCGTTTATTTG
1 TATTCGTTTATTTG
58040 TATT-GTTTATTTG
1 TATTCGTTTATTTG
58053 TATT
1 TATT
58057 ATTTTAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.16, C:0.03, G:0.13, T:0.68
Consensus pattern (14 bp):
TATTCGTTTATTTG
Found at i:58585 original size:20 final size:20
Alignment explanation
Indices: 58560--58597 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
58550 AAATAAATCA
*
58560 CAAAAGGAGATCAAGTATAC
1 CAAAAGAAGATCAAGTATAC
58580 CAAAAGAAGATCAAGTAT
1 CAAAAGAAGATCAAGTAT
58598 CAAAAACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.13, G:0.18, T:0.16
Consensus pattern (20 bp):
CAAAAGAAGATCAAGTATAC
Found at i:59139 original size:27 final size:26
Alignment explanation
Indices: 59109--59159 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
59099 TCGTTAAAAT
*
59109 ATCAAGTCAAACTCAAATTTAAATCGA
1 ATCAACTCAAA-TCAAATTTAAATCGA
* *
59136 ATCAACTCAAATTAAATTTTAATC
1 ATCAACTCAAATCAAATTTAAATC
59160 ATTTTTTCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (26 bp):
ATCAACTCAAATCAAATTTAAATCGA
Found at i:59464 original size:60 final size:60
Alignment explanation
Indices: 59349--59466 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
59339 AGGGTAATAT
* ***
59349 TTTGTTGAGTCACTCGATTATTAAAAGTTATAAAATGATTTTTCGACTATAATATGTTGC
1 TTTGTTGAGTCACTCGATTATTAAAAGTTACAAAATGATTCACCGACTATAATATGTTGC
* * *
59409 TTTGTTGAGTCCCTCTATTATTAAAAGTTACAAAATGA-TCACCGACTATTCATATGTT
1 TTTGTTGAGTCACTCGATTATTAAAAGTTACAAAATGATTCACCGACTA-TAATATGTT
59467 CCAAACTCAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 7 0.14
60 43 0.86
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (60 bp):
TTTGTTGAGTCACTCGATTATTAAAAGTTACAAAATGATTCACCGACTATAATATGTTGC
Found at i:60722 original size:35 final size:35
Alignment explanation
Indices: 60676--60787 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
60666 AAAATAGTCC
* * *
60676 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
*
60711 TCAATTTCATTCTAAACCCTAAATTCTAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
** * *
60746 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
60781 TCAATTT
1 TCAATTT
60788 AAGGTTTAGA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
Found at i:60851 original size:35 final size:35
Alignment explanation
Indices: 60783--60857 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
60773 AAAATACTTC
* * *
60783 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
* *
60818 AATTTAGGGTTTAGAATGAAATT-AAGGTGTTTTGA
1 AATTTAAGGTTTAGAATGAAATTGAA-GTATTTTGA
60853 AATTT
1 AATTT
60858 TGAACATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
Found at i:64315 original size:20 final size:20
Alignment explanation
Indices: 64286--64323 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
64276 CCTAAATCCG
* *
64286 TCGAGTAGTATCGGTACTCC
1 TCGAGGAGTATCGATACTCC
64306 TCGAGGAGTATCGATACT
1 TCGAGGAGTATCGATACT
64324 TCATGGAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (20 bp):
TCGAGGAGTATCGATACTCC
Found at i:64421 original size:21 final size:20
Alignment explanation
Indices: 64357--64443 Score: 68
Period size: 20 Copynumber: 4.2 Consensus size: 20
64347 CGATACCTGG
*
64357 GTATCGATACCCATTCAAGTA
1 GTATCGATA-CTATTCAAGTA
* * * * *
64378 GTATTGGTAATATATGAA-CA
1 GTATCGATACTAT-TCAAGTA
64398 GTATCGATACTCATTCAAGTA
1 GTATCGATACT-ATTCAAGTA
* *
64419 GTATCGATACTATGCTAGTA
1 GTATCGATACTATTCAAGTA
64439 GTATC
1 GTATC
64444 CATAACTAGT
Statistics
Matches: 50, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
20 26 0.52
21 24 0.48
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (20 bp):
GTATCGATACTATTCAAGTA
Found at i:64440 original size:20 final size:21
Alignment explanation
Indices: 64397--64443 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
64387 ATATATGAAC
*
64397 AGTATCGATACTCATTCAAGT
1 AGTATCGATACTCATGCAAGT
*
64418 AGTATCGATACT-ATGCTAGT
1 AGTATCGATACTCATGCAAGT
64438 AGTATC
1 AGTATC
64444 CATAACTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (21 bp):
AGTATCGATACTCATGCAAGT
Found at i:70236 original size:24 final size:24
Alignment explanation
Indices: 70206--70285 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
70196 TGCAACTCAA
*
70206 TAGTATCGATACTACTATGTGCAG
1 TAGTATCGATACTACTATGTACAG
*
70230 TAGTATCGATAC--C---GTCCAG
1 TAGTATCGATACTACTATGTACAG
* *
70249 TGAGTATCGATACTACTATATAAAG
1 T-AGTATCGATACTACTATGTACAG
70274 TAGTATCGATAC
1 TAGTATCGATAC
70286 CAAACATGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
19 6 0.13
20 11 0.24
22 2 0.04
24 23 0.50
25 4 0.09
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (24 bp):
TAGTATCGATACTACTATGTACAG
Found at i:70511 original size:14 final size:14
Alignment explanation
Indices: 70492--70521 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
70482 TTGACTCTCA
70492 ATTTTGACTCGATT
1 ATTTTGACTCGATT
70506 ATTTTGACTCGATT
1 ATTTTGACTCGATT
70520 AT
1 AT
70522 GGTTCGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (14 bp):
ATTTTGACTCGATT
Found at i:70680 original size:20 final size:18
Alignment explanation
Indices: 70645--70685 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
70635 TGAATAATTG
*
70645 AATCGAATATAATATTTA
1 AATCGAATATAATATTAA
70663 AATCGAATATAAAATATTAA
1 AATCGAATAT--AATATTAA
70683 AAT
1 AAT
70686 TAATTAACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
20 10 0.50
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (18 bp):
AATCGAATATAATATTAA
Done.