Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005262.1 Hibiscus syriacus cultivar Beakdansim tig00011900_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: 133646
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:869 original size:20 final size:20
Alignment explanation
Indices: 844--882 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
834 CTACCTAATA
844 TTATTGTACTTGATAATATG
1 TTATTGTACTTGATAATATG
864 TTATTGTACTTGATAATAT
1 TTATTGTACTTGATAATAT
883 TTCCGGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (20 bp):
TTATTGTACTTGATAATATG
Found at i:3915 original size:19 final size:20
Alignment explanation
Indices: 3885--3922 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
3875 TTTCTCTCTG
3885 GAGAGAAAAGAACAAACCTA
1 GAGAGAAAAGAACAAACCTA
3905 GAGAG-AAAGAACAAACCT
1 GAGAGAAAAGAACAAACCT
3923 TTTATTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.58, C:0.16, G:0.21, T:0.05
Consensus pattern (20 bp):
GAGAGAAAAGAACAAACCTA
Found at i:10144 original size:26 final size:26
Alignment explanation
Indices: 10105--10184 Score: 142
Period size: 26 Copynumber: 3.1 Consensus size: 26
10095 CCAATGACGG
* *
10105 CCCTCCTACGTCACAATCAACGAAGA
1 CCCTCCAACATCACAATCAACGAAGA
10131 CCCTCCAACATCACAATCAACGAAGA
1 CCCTCCAACATCACAATCAACGAAGA
10157 CCCTCCAACATCACAATCAACGAAGA
1 CCCTCCAACATCACAATCAACGAAGA
10183 CC
1 CC
10185 ATCACATCCC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.39, C:0.40, G:0.09, T:0.12
Consensus pattern (26 bp):
CCCTCCAACATCACAATCAACGAAGA
Found at i:10281 original size:69 final size:69
Alignment explanation
Indices: 10202--10339 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
10192 CCCCCCAAAT
*
10202 TTCCATCTCCACTAGCTTACCAACGAAGTGGGAATTGGCCCAAAGTTTCCTTTGCTTTTCCGGAA
1 TTCCATCTCCACTAGCTTACCAACGAAGTGGGAATTGACCCAAAGTTTCCTTTGCTTTTCCGGAA
10267 GAGG
66 GAGG
10271 TTCCATCTCCACTAGCTTACCAACGAAGTGGGAATTGACCCAAAGTTTCCTTTGCTTTTCCGGAA
1 TTCCATCTCCACTAGCTTACCAACGAAGTGGGAATTGACCCAAAGTTTCCTTTGCTTTTCCGGAA
10336 GAGG
66 GAGG
10340 GTTCACATAG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (69 bp):
TTCCATCTCCACTAGCTTACCAACGAAGTGGGAATTGACCCAAAGTTTCCTTTGCTTTTCCGGAA
GAGG
Found at i:16377 original size:31 final size:30
Alignment explanation
Indices: 16342--16399 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
16332 TATTTTTTAC
*
16342 ATAGTTATTATATTTATATTAATATAATTAT
1 ATAGTTATTAT-TTTATATTAAAATAATTAT
*
16373 ATAGTTATTATTTTTTATTAAAATAAT
1 ATAGTTATTATTTTATATTAAAATAAT
16400 ATTTATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (30 bp):
ATAGTTATTATTTTATATTAAAATAATTAT
Found at i:16418 original size:16 final size:15
Alignment explanation
Indices: 16379--16433 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
16369 TTATATAGTT
*
16379 ATTATTTTTTATTAA
1 ATTATTATTTATTAA
* *
16394 AATAATATTTATATAA
1 ATTATTATTTAT-TAA
16410 ATTATTATTTATTTAA
1 ATTATTATTTA-TTAA
16426 ATTTATTA
1 A-TTATTA
16434 ATTAATTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 9 0.28
16 16 0.50
17 7 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATTATTTATTAA
Found at i:17838 original size:2 final size:2
Alignment explanation
Indices: 17831--17879 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
17821 TTGTCTAAAC
17831 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
17873 TA TA TA T
1 TA TA TA T
17880 TTATTTATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19030 original size:3 final size:3
Alignment explanation
Indices: 19022--19059 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
19012 GACAGTTACC
* *
19022 CTT CTT CTT CTT CTT C-T CCT CTT CTT CTT CTT TTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
19060 TTTTTTCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:51954 original size:14 final size:13
Alignment explanation
Indices: 51935--52039 Score: 50
Period size: 15 Copynumber: 7.5 Consensus size: 13
51925 ATTTCGCTTG
51935 AAAAAGAAATAAAA
1 AAAAAGAAA-AAAA
51949 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
**
51962 ATGAAAATG-ATGAAA
1 A--AAAA-GAAAAAAA
*
51977 AAAAAGAGAGAAAA
1 AAAAAGA-AAAAAA
* * * *
51991 ATAGAGAAGAAGA
1 AAAAAGAAAAAAA
*
52004 AAAATGAAAAAATGA
1 AAAAAGAAAAAA--A
52019 AAAAAGAAAAATAA
1 AAAAAGAAAAA-AA
52033 ATAAAAG
1 A-AAAAG
52040 GGGGTTCAAG
Statistics
Matches: 69, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
12 1 0.01
13 21 0.30
14 20 0.29
15 25 0.36
16 2 0.03
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:53377 original size:37 final size:36
Alignment explanation
Indices: 53318--53387 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
53308 AAACAAGTCA
*
53318 ATCTTAAGCCTTCACGAAAGAGTAATGAAGCAAATC
1 ATCTTAAGACTTCACGAAAGAGTAATGAAGCAAATC
*
53354 ATCTATAAGACTTCAC-AGAAGAGTAGTGAAGCAA
1 ATCT-TAAGACTTCACGA-AAGAGTAATGAAGCAA
53388 GCTCATTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 5 0.17
37 25 0.83
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (36 bp):
ATCTTAAGACTTCACGAAAGAGTAATGAAGCAAATC
Found at i:53658 original size:109 final size:110
Alignment explanation
Indices: 53404--53810 Score: 448
Period size: 109 Copynumber: 3.8 Consensus size: 110
53394 TTTATGAAGA
* * *
53404 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACACGTTTGT-TGAAGA----TCGAGTCTT
1 TCGAGTCCTATACTCCCTGAAAGAATAGAGAGCAGACACGTTT-TATGAAGATTGTTCGAGTCTT
*
53464 ATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGA----
65 ATACTCCCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* * *
53506 TCGAGTTCTATACTCCCTGAACGAATAGAGAGCAGAC-CTGTTTTATGAAGATTGTTTGAGT-TC
1 TCGAGTCCTATACTCCCTGAAAGAATAGAGAGCAGACAC-GTTTTATGAAGATTGTTCGAGTCT-
* * * *
53569 TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTT-AAGATTGT
64 TATACTCCCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* * * *
53615 TCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTTATGAAGATTGTTCGAGT-TCT
1 TCGAGTCCTATACTCCCTGAAAGAATAGAGAGCAGACACGTTTTATGAAGATTGTTCGAGTCT-T
* *
53679 -TACTCCCTGAACGG-ATAGGGAGCAGACATGTTTATTGAAGATTGT
65 ATACTCCCTGAA-GGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* * * ***
53724 TCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGCCGAAGATTGTTCGAGTCTTA
1 TCGAGTCCTATACTCCCTGAAAGAATAGAGAGCAGACACGTTTTATGAAGATTGTTCGAGTCTTA
*
53789 TACTCCCTGAAAGAATAGGGAG
66 TACTCCCTGAAGGAATAGGGAG
53811 TGGACCCTTC
Statistics
Matches: 258, Mismatches: 30, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
101 2 0.01
102 42 0.16
105 5 0.02
106 40 0.16
108 27 0.10
109 121 0.47
110 21 0.08
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (110 bp):
TCGAGTCCTATACTCCCTGAAAGAATAGAGAGCAGACACGTTTTATGAAGATTGTTCGAGTCTTA
TACTCCCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
Found at i:53831 original size:55 final size:55
Alignment explanation
Indices: 53404--53810 Score: 425
Period size: 55 Copynumber: 7.6 Consensus size: 55
53394 TTTATGAAGA
* * * *
53404 TCGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACACGTTTGTTGAAGA----
1 TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
*
53455 TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGA----
1 TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* *
53506 TCGAGT-TCTATACTCCCTGAACGAATAGAGAGCAGAC-CTGTTT-TATGAAGATTGT
1 TCGAGTCT-TATACTCCCTGAAGGAATAGGGAGCAGACAC-GTTTGT-TGAAGATTGT
* * * * *
53561 TTGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTT-AAGATTGT
1 TCGAGTCT-TATACTCCCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* * * * *
53615 TCGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTT-TATGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACACGTTTGT-TGAAGATTGT
* *
53670 TCGAGT-TCT-TACTCCCTGAACGG-ATAGGGAGCAGACATGTTTATTGAAGATTGT
1 TCGAGTCT-TATACTCCCTGAA-GGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
* **
53724 TCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTGCCGAAGATTGT
1 TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
*
53779 TCGAGTCTTATACTCCCTGAAAGAATAGGGAG
1 TCGAGTCTTATACTCCCTGAAGGAATAGGGAG
53811 TGGACCCTTC
Statistics
Matches: 313, Mismatches: 25, Indels: 32
0.85 0.07 0.09
Matches are distributed among these distances:
50 3 0.01
51 90 0.29
53 1 0.00
54 91 0.29
55 126 0.40
56 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (55 bp):
TCGAGTCTTATACTCCCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
Found at i:60947 original size:30 final size:30
Alignment explanation
Indices: 60913--60971 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
60903 TATTAAAAAA
60913 TGCTAAATCGAAATACACAATAAGAAATGG
1 TGCTAAATCGAAATACACAATAAGAAATGG
*
60943 TGCTAAATCGAAATACACAATATGAAATG
1 TGCTAAATCGAAATACACAATAAGAAATG
60972 ATAGTTATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.49, C:0.14, G:0.15, T:0.22
Consensus pattern (30 bp):
TGCTAAATCGAAATACACAATAAGAAATGG
Found at i:66930 original size:21 final size:21
Alignment explanation
Indices: 66904--66948 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
66894 GATTTCTGGG
* *
66904 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
66925 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
66946 CAA
1 CAA
66949 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:67850 original size:31 final size:31
Alignment explanation
Indices: 67812--67965 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
67802 GGGTCGAGGG
67812 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
67843 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
67874 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
67905 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
67936 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
67966 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:70943 original size:21 final size:21
Alignment explanation
Indices: 70917--70961 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
70907 GATTTCTGGG
* *
70917 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
70938 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
70959 CAA
1 CAA
70962 ACGACAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:71863 original size:31 final size:31
Alignment explanation
Indices: 71825--71975 Score: 241
Period size: 31 Copynumber: 4.9 Consensus size: 31
71815 GGGTCGAGGG
71825 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
71856 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
71887 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
71918 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* *
71949 TTATCTAGGTTCTTCGGAATC-TATGGA
1 TTACCTATGTTCTTCGGAA-CATATGGA
71976 TTGGTCCTTC
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 111 0.99
32 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:78700 original size:19 final size:20
Alignment explanation
Indices: 78658--78716 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
78648 ATAATTCAAC
* *
78658 ATTTAAATAGTTATTATCAT
1 ATTTAAATAGTAATTATAAT
78678 ATTTAAATAGTAATT-TAAT
1 ATTTAAATAGTAATTATAAT
*
78697 ATTTAATATATTATATTATA
1 ATTTAA-ATAGTA-ATTATA
78717 TTAATATTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 9 0.27
20 19 0.58
21 3 0.09
22 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (20 bp):
ATTTAAATAGTAATTATAAT
Found at i:84015 original size:29 final size:29
Alignment explanation
Indices: 83981--84039 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
83971 CCTAAATTAA
83981 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
84010 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
84039 T
1 T
84040 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:88679 original size:29 final size:29
Alignment explanation
Indices: 88645--88703 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
88635 CCTAAATTAA
88645 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
88674 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
88703 T
1 T
88704 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:91736 original size:96 final size:96
Alignment explanation
Indices: 91568--91759 Score: 339
Period size: 96 Copynumber: 2.0 Consensus size: 96
91558 ACAAGATCAT
*
91568 CGGTGACATATTCAATATATTCAGTAGGAAGAATGAGGTCAACATGGGTGACGATTGTTTCAAGT
1 CGGTGACATATTCAATATATTCAGTAGGAAGAATGAGGTCAACATGGGAGACGATTGTTTCAAGT
*
91633 TTTGTCTCCAAAGGTGGTTATCAGCCGACGG
66 TTCGTCTCCAAAGGTGGTTATCAGCCGACGG
* *
91664 CGGTGACATATTCAATATATTCAGTAGGAAGAATGAGGTCAACATGGGAGATGATTGTTTCGAGT
1 CGGTGACATATTCAATATATTCAGTAGGAAGAATGAGGTCAACATGGGAGACGATTGTTTCAAGT
*
91729 TTCGTCTCCAAAGGTGGTTATCAGTCGACGG
66 TTCGTCTCCAAAGGTGGTTATCAGCCGACGG
91760 GAAGGAGTTC
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 91 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (96 bp):
CGGTGACATATTCAATATATTCAGTAGGAAGAATGAGGTCAACATGGGAGACGATTGTTTCAAGT
TTCGTCTCCAAAGGTGGTTATCAGCCGACGG
Found at i:100675 original size:21 final size:21
Alignment explanation
Indices: 100632--100675 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
100622 ATTATCAATA
* *
100632 ATAAATATTTTAATTTAATAT
1 ATAAATATTTTAATATAAAAT
100653 ATAAATACTTTT-ATATAAAAT
1 ATAAATA-TTTTAATATAAAAT
100674 AT
1 AT
100676 TATTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAAATATTTTAATATAAAAT
Found at i:102359 original size:14 final size:15
Alignment explanation
Indices: 102340--102372 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
102330 ACATAAATGA
102340 TATAAAAA-ATTATG
1 TATAAAAATATTATG
*
102354 TATAAAAATATTATT
1 TATAAAAATATTATG
102369 TATA
1 TATA
102373 TAATGAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TATAAAAATATTATG
Found at i:104960 original size:96 final size:96
Alignment explanation
Indices: 104796--104990 Score: 354
Period size: 96 Copynumber: 2.0 Consensus size: 96
104786 GGCTGATGGC
* * *
104796 CCAAATGGCTTTGGACTTGATTTCGAAAGCATTTATTTGGAGAATTTATGAGCAACCTTATGCTG
1 CCAAATGGCTTAGGACTTGATTTCAAAAGCATTTATTTGGAGAATTTATGAGAAACCTTATGCTG
*
104861 AGTTACGACTGTCGAAATGGGTAGGCAGCAA
66 AGTTACGACGGTCGAAATGGGTAGGCAGCAA
104892 CCAAATGGCTTAGGACTTGATTTCAAAAGCATTTATTTGGAGAATTTATGAGAAACCTTATGCTG
1 CCAAATGGCTTAGGACTTGATTTCAAAAGCATTTATTTGGAGAATTTATGAGAAACCTTATGCTG
104957 AGTTACGACGGTCGAAATGGGTAGGCAGCAA
66 AGTTACGACGGTCGAAATGGGTAGGCAGCAA
104988 CCA
1 CCA
104991 CCCACGCTAG
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (96 bp):
CCAAATGGCTTAGGACTTGATTTCAAAAGCATTTATTTGGAGAATTTATGAGAAACCTTATGCTG
AGTTACGACGGTCGAAATGGGTAGGCAGCAA
Found at i:107371 original size:15 final size:15
Alignment explanation
Indices: 107351--107379 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
107341 TGGCCGACCG
107351 AACCGAATTAACCAT
1 AACCGAATTAACCAT
107366 AACCGAATTAACCA
1 AACCGAATTAACCA
107380 AACTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (15 bp):
AACCGAATTAACCAT
Found at i:107812 original size:184 final size:184
Alignment explanation
Indices: 107504--107892 Score: 633
Period size: 184 Copynumber: 2.1 Consensus size: 184
107494 AAATTTCTAA
* *
107504 TATATATAAAAT-TA-AATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATAAATA
1 TATATATAATATATATAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATAAATA
*
107567 ATTATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
66 ATTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
* * * *
107632 TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTTAGCCCATATGT
131 TTCGATCTTAAAGTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGT
*
107686 TATATATAATATATATAATATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATAT
1 TATATATAATATATATAATATTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATAAAT
*
107750 AATTATAAAATAAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGT
65 AATTATAAAAT-AAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGT
*
107814 TATTCGATCTTAAAGTATTAATTGGGTTTTTAATGATTTGGGTTGAGCCCATATGT
129 TATTCGATCTTAAAGTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGT
*
107870 TATATATAATATATTTAATATTT
1 TATATATAATATATATAATATTT
107893 AAAATTTAAT
Statistics
Matches: 192, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
182 11 0.06
183 8 0.04
184 162 0.84
185 11 0.06
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATATAATATATATAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATAAATA
ATTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
TTCGATCTTAAAGTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGT
Found at i:114361 original size:18 final size:18
Alignment explanation
Indices: 114335--114373 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
114325 GATTGTATGC
*
114335 AAAAAAGAGGAAGGAACT
1 AAAAAAGAGGAAGAAACT
* *
114353 AAAAGAGAGGCAGAAACT
1 AAAAAAGAGGAAGAAACT
114371 AAA
1 AAA
114374 GGTAACTGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.08, G:0.26, T:0.05
Consensus pattern (18 bp):
AAAAAAGAGGAAGAAACT
Found at i:132953 original size:43 final size:44
Alignment explanation
Indices: 132889--132981 Score: 143
Period size: 43 Copynumber: 2.1 Consensus size: 44
132879 TACAGCAATA
* * * *
132889 ACAGTACATAAAACTTAAAAACATCCCCTGGCATAAAAGCCTTT
1 ACAGTACATAAAACTTAAAAACACCCCCTGCCATAAAAACCTTC
132933 ACAGTACAT-AAACTTAAAAACACCCCCTGCCATAAAAACCTTC
1 ACAGTACATAAAACTTAAAAACACCCCCTGCCATAAAAACCTTC
132976 ACAGTA
1 ACAGTA
132982 GAATAGAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
43 36 0.80
44 9 0.20
ACGTcount: A:0.44, C:0.28, G:0.08, T:0.20
Consensus pattern (44 bp):
ACAGTACATAAAACTTAAAAACACCCCCTGCCATAAAAACCTTC
Done.