Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004016.1 Hibiscus syriacus cultivar Beakdansim tig00008768_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: 67341
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:12862 original size:21 final size:21
Alignment explanation
Indices: 12836--12878 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
12826 CCTTGAGCTA
12836 TCGAGTCAAAAAGTAAAAAAC
1 TCGAGTCAAAAAGTAAAAAAC
12857 TCGAGTCAAAAAGTAAAAAAC
1 TCGAGTCAAAAAGTAAAAAAC
12878 T
1 T
12879 AAAAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.16
Consensus pattern (21 bp):
TCGAGTCAAAAAGTAAAAAAC
Found at i:17360 original size:14 final size:15
Alignment explanation
Indices: 17341--17370 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
17331 AATACTTCAT
17341 ACATATTTTA-TAAA
1 ACATATTTTATTAAA
17355 ACATATTTTATTAAA
1 ACATATTTTATTAAA
17370 A
1 A
17371 GGGACATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (15 bp):
ACATATTTTATTAAA
Found at i:18807 original size:15 final size:15
Alignment explanation
Indices: 18787--18820 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
18777 CCCCGAACAA
18787 TACTATAAGAATCAG
1 TACTATAAGAATCAG
18802 TACTATAAGAATCAG
1 TACTATAAGAATCAG
18817 TACT
1 TACT
18821 GAACATCCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (15 bp):
TACTATAAGAATCAG
Found at i:19987 original size:22 final size:22
Alignment explanation
Indices: 19959--20011 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
19949 TCTAAATACT
* *
19959 AATACTAAATAAAAGGAATTTG
1 AATACTAAATAAAAGAAATTCG
19981 AATACTAAATAAAAGAAATTCG
1 AATACTAAATAAAAGAAATTCG
20003 AATATCTAA
1 AATA-CTAA
20012 CTAATATCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.57, C:0.08, G:0.09, T:0.26
Consensus pattern (22 bp):
AATACTAAATAAAAGAAATTCG
Found at i:20132 original size:2 final size:2
Alignment explanation
Indices: 20096--20121 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20086 AATCTAAATA
20096 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
20122 TGAATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20819 original size:22 final size:22
Alignment explanation
Indices: 20791--20832 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
20781 TATAATTTTT
20791 TATAAAATTAAAGAATTAAATA
1 TATAAAATTAAAGAATTAAATA
20813 TATAAAATTAAAGAATTAAA
1 TATAAAATTAAAGAATTAAA
20833 GAAAAAGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (22 bp):
TATAAAATTAAAGAATTAAATA
Found at i:24065 original size:21 final size:21
Alignment explanation
Indices: 24003--24072 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
23993 CCACTTCGTT
* *
24003 TCTTTTTCTCCAAGCTACTTC
1 TCTTTTTTTCCAAGTTACTTC
* *
24024 TCTTTTTGTCCAAGTTGCTTC
1 TCTTTTTTTCCAAGTTACTTC
*
24045 TCTTTTTTTCTAA-TTCACTTC
1 TCTTTTTTTCCAAGTT-ACTTC
24066 -CTTTTTT
1 TCTTTTTT
24073 CTTTGTGAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
20 9 0.21
21 33 0.79
ACGTcount: A:0.11, C:0.26, G:0.06, T:0.57
Consensus pattern (21 bp):
TCTTTTTTTCCAAGTTACTTC
Found at i:24597 original size:22 final size:22
Alignment explanation
Indices: 24572--24615 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
24562 TTATTTTACA
* *
24572 TTTTGACTTTTTTTTTGTTTGG
1 TTTTGACTTTTATCTTGTTTGG
**
24594 TTTTTTCTTTTATCTTGTTTGG
1 TTTTGACTTTTATCTTGTTTGG
24616 AAAAACTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.05, C:0.07, G:0.16, T:0.73
Consensus pattern (22 bp):
TTTTGACTTTTATCTTGTTTGG
Found at i:25165 original size:13 final size:13
Alignment explanation
Indices: 25147--25173 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25137 TTTTCTATTT
25147 TCTCTTTTATTAA
1 TCTCTTTTATTAA
25160 TCTCTTTTATTAA
1 TCTCTTTTATTAA
25173 T
1 T
25174 TTTAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (13 bp):
TCTCTTTTATTAA
Found at i:25298 original size:13 final size:13
Alignment explanation
Indices: 25280--25306 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25270 TTTTCTATTT
25280 TCTCTTTTATTAA
1 TCTCTTTTATTAA
25293 TCTCTTTTATTAA
1 TCTCTTTTATTAA
25306 T
1 T
25307 TTTAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.15, G:0.00, T:0.63
Consensus pattern (13 bp):
TCTCTTTTATTAA
Found at i:25333 original size:133 final size:134
Alignment explanation
Indices: 25095--25361 Score: 491
Period size: 133 Copynumber: 2.0 Consensus size: 134
25085 TTCGATATGT
* *
25095 TTTACCGAGAAGGTCTATGGTTCGAGTCTGTATAGCCCTATATTTTCTATTTTCTCTTTTATTAA
1 TTTACCGAGAAGGTCTATGGTTCGAGCCCGTATAGCCCTATATTTTCTATTTTCTCTTTTATTAA
*
25160 TCTCTTTTATTAATTTTAAATATTCGTTAAAATAATAAAAATGAAAATAA-ATTCTTAAAACTAA
66 TCTCTTTTATTAATTTTAAATATTCATTAAAATAATAAAAATGAAAATAATATTCTTAAAACTAA
25224 AAAA
131 AAAA
25228 TTTACCGAGAAGGTCTATGGTTCGAGCCCGTATAGCCCTATATTTTCTATTTTCTCTTTTATTAA
1 TTTACCGAGAAGGTCTATGGTTCGAGCCCGTATAGCCCTATATTTTCTATTTTCTCTTTTATTAA
*
25293 TCTCTTTTATTAATTTTAAATATTCATTAAATTAATAAAAATGAAAATAATATTCTTAAAACTAA
66 TCTCTTTTATTAATTTTAAATATTCATTAAAATAATAAAAATGAAAATAATATTCTTAAAACTAA
25358 AAAA
131 AAAA
25362 ACTAAAGCAA
Statistics
Matches: 129, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
133 111 0.86
134 18 0.14
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.42
Consensus pattern (134 bp):
TTTACCGAGAAGGTCTATGGTTCGAGCCCGTATAGCCCTATATTTTCTATTTTCTCTTTTATTAA
TCTCTTTTATTAATTTTAAATATTCATTAAAATAATAAAAATGAAAATAATATTCTTAAAACTAA
AAAA
Found at i:28090 original size:22 final size:21
Alignment explanation
Indices: 28056--28096 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
28046 ATAATTATTT
28056 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
28077 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
28097 TTTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:29285 original size:21 final size:21
Alignment explanation
Indices: 29256--29308 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
29246 ATTCTGACTA
29256 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
29277 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
29298 TCGCAATGCGA
1 TCGCATTGCGA
29309 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:29323 original size:20 final size:20
Alignment explanation
Indices: 29298--29343 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
29288 TTTTCCTAAT
29298 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTA-GTAAA
29318 TCGCAATGCGAATTAGTAAA
1 TCGCAATGCGAATTAGTAAA
29338 TCGCAA
1 TCGCAA
29344 CGAGATTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATTAGTAAA
Found at i:29421 original size:18 final size:18
Alignment explanation
Indices: 29398--29442 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
29388 GATTTCTGAA
29398 TTCGCAACAGGTTTTAAT
1 TTCGCAACAGGTTTTAAT
29416 TTCGCAACAGGTTTTAAT
1 TTCGCAACAGGTTTTAAT
29434 TTCGCAACA
1 TTCGCAACA
29443 CAAATGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (18 bp):
TTCGCAACAGGTTTTAAT
Found at i:30251 original size:24 final size:24
Alignment explanation
Indices: 30224--30277 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
30214 GTATTCGAAA
30224 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
30248 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
30272 TTTGAT
1 TTTGAT
30278 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:32799 original size:33 final size:33
Alignment explanation
Indices: 32757--32881 Score: 214
Period size: 33 Copynumber: 3.8 Consensus size: 33
32747 AAATGACTAA
*
32757 CGCAATGCGAAATGAAAATCACAACGAGAGAAT
1 CGCAATGCGAAATGAAAATCGCAACGAGAGAAT
32790 CGCAATGCGAAATGAAAATCGCAACGAGAGAAT
1 CGCAATGCGAAATGAAAATCGCAACGAGAGAAT
* *
32823 CGCAATGCGAAATGAAAATCGCAACAAGGGAAT
1 CGCAATGCGAAATGAAAATCGCAACGAGAGAAT
*
32856 CGCAAAGCGAAATGAAAATCGCAACG
1 CGCAATGCGAAATGAAAATCGCAACG
32882 CGAATTTAGT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
CGCAATGCGAAATGAAAATCGCAACGAGAGAAT
Found at i:32811 original size:19 final size:18
Alignment explanation
Indices: 32735--32885 Score: 85
Period size: 19 Copynumber: 8.7 Consensus size: 18
32725 CTTAATGTCT
*
32735 ATCGCAACGCAGAAATGACTA
1 ATCGCAA-GC-GAAATGA-AA
32756 A-CGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* *
32774 ATCACAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
32788 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
32807 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
32821 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
32840 ATCGCAA-C--AA-GGGA
1 ATCGCAAGCGAAATGAAA
32854 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
32873 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
32886 TTTAGTTTCG
Statistics
Matches: 101, Mismatches: 12, Indels: 36
0.68 0.08 0.24
Matches are distributed among these distances:
14 26 0.26
15 6 0.06
16 5 0.05
17 5 0.05
18 8 0.08
19 43 0.43
20 7 0.07
21 1 0.01
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:32916 original size:19 final size:19
Alignment explanation
Indices: 32881--32943 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
32871 AAATCGCAAC
*
32881 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
32900 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
32919 ACGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
32938 GCGATT
1 GCGATT
32944 CTCTCGTTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 39 0.98
20 1 0.03
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.44
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:32974 original size:19 final size:19
Alignment explanation
Indices: 32891--32975 Score: 92
Period size: 19 Copynumber: 4.7 Consensus size: 19
32881 GCGAATTTAG
32891 TTTCGCGTTGCGATTTT-A
1 TTTCGCGTTGCGATTTTCA
*
32909 GTTTCGCGTTACGATTTTCA
1 -TTTCGCGTTGCGATTTTCA
32929 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
32945 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
32962 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
32976 AGTCATTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
14 10 0.18
16 3 0.05
17 3 0.05
19 38 0.69
20 1 0.02
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:33101 original size:14 final size:14
Alignment explanation
Indices: 33082--33118 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
33072 CATCAATTAA
33082 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
33096 ACAAATCATCTTTT
1 ACAAATCAACTTTT
33110 ACAAATCAA
1 ACAAATCAA
33119 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:34533 original size:21 final size:21
Alignment explanation
Indices: 34467--34533 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
34457 GTGAATCGGG
34467 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAATGGTGGGAGGGGA
* * * ** * *
34487 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAATGGTGGGAGGGGA
34509 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
34530 CTCT
1 CTCT
34534 CGAGGAATGA
Statistics
Matches: 31, Mismatches: 14, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGGA
Found at i:35018 original size:19 final size:19
Alignment explanation
Indices: 34978--35091 Score: 102
Period size: 19 Copynumber: 5.8 Consensus size: 19
34968 TCTGGAACTT
*
34978 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
** *
34999 ACTATCGTAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
35018 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGCGA-AATG
* *
35038 AAAATCGCATCGCGAAACG
1 AAAATCGCAACGCGAAATG
* **
35057 AAAATCGTAACGCGAAACCA
1 AAAATCGCAACGCGAAA-TG
35077 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
35092 TTATAGTTTC
Statistics
Matches: 76, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
19 34 0.45
20 32 0.42
21 10 0.13
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:35082 original size:20 final size:19
Alignment explanation
Indices: 35002--35091 Score: 81
Period size: 20 Copynumber: 4.6 Consensus size: 19
34992 AAAAATGACT
* **
35002 ATCGTAACGCGAAATGAAA
1 ATCGCAACGCGAAACAAAA
* **
35021 ATCGCAACGAGAGAATGAAA
1 ATCGCAACGCGA-AACAAAA
* *
35041 ATCGCATCGCGAAACGAAA
1 ATCGCAACGCGAAACAAAA
*
35060 ATCGTAACGCGAAACCAAAA
1 ATCGCAACGCGAAA-CAAAA
35080 ATCGCAACGCGA
1 ATCGCAACGCGA
35092 TTATAGTTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
19 28 0.47
20 32 0.53
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAACAAAA
Found at i:35122 original size:20 final size:19
Alignment explanation
Indices: 35097--35198 Score: 132
Period size: 19 Copynumber: 5.3 Consensus size: 19
35087 CGCGATTATA
*
35097 GTTTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGA-TTTTC
35117 GTTTCGCGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
*
35136 GTTTCACGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
*
35155 GTTTCGCGTTACGATTTTC
1 GTTTCGCGTTGCGATTTTC
* *
35174 ATTCTCTCGTTGCGATTTTC
1 GTT-TCGCGTTGCGATTTTC
*
35194 ATTTC
1 GTTTC
35199 AACCAAATGA
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
19 43 0.58
20 31 0.42
ACGTcount: A:0.09, C:0.21, G:0.22, T:0.49
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTC
Found at i:35146 original size:39 final size:39
Alignment explanation
Indices: 35088--35192 Score: 131
Period size: 39 Copynumber: 2.7 Consensus size: 39
35078 AAATCGCAAC
* * * *
35088 GCGATTATAGTTTCGCGTTGCGATTTTTGGTTTCGCGTT
1 GCGATTTTCGTTTCACGTTGCGATTTTTCGTTTCGCGTT
35127 GCGATTTTCGTTTCACGTTGCGA-TTTTCGTTTCGCGTT
1 GCGATTTTCGTTTCACGTTGCGATTTTTCGTTTCGCGTT
* * *
35165 ACGATTTTCATTCTCTCGTTGCGATTTT
1 GCGATTTTCGTT-TCACGTTGCGATTTT
35193 CATTTCAACC
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
38 24 0.42
39 30 0.53
40 3 0.05
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (39 bp):
GCGATTTTCGTTTCACGTTGCGATTTTTCGTTTCGCGTT
Found at i:35185 original size:58 final size:58
Alignment explanation
Indices: 35088--35199 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
35078 AAATCGCAAC
* ** *
35088 GCGATTATAGTTTCGCGTTGCGATTTTTGGTTTCGCGTTGCGATTTTCGTTTCACGTT
1 GCGATTATAGTTTCGCGTTACGATTTTTCATTTCGCGTTGCGATTTTCATTTCACGTT
* * *
35146 GCGATTTTCGTTTCGCGTTACGA-TTTTCATTCTCTCGTTGCGATTTTCATTTCA
1 GCGATTATAGTTTCGCGTTACGATTTTTCATT-TCGCGTTGCGATTTTCATTTCA
35200 ACCAAATGAC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
57 6 0.13
58 40 0.87
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.47
Consensus pattern (58 bp):
GCGATTATAGTTTCGCGTTACGATTTTTCATTTCGCGTTGCGATTTTCATTTCACGTT
Found at i:35397 original size:94 final size:94
Alignment explanation
Indices: 35289--35664 Score: 595
Period size: 94 Copynumber: 4.1 Consensus size: 94
35279 ATGGATTGCA
*
35289 TTAC-TTCAACCAAAAGAAAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
35353 TTAGTAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
35382 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
35447 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
35476 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
** *
35541 TTAGCAGAATTGGTTGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
35570 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAATA-AAT----A
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAA-AGAATACACA
* * * *
35629 GTTTAGTAGTATTGGTAGCAACCGAATAAAT
64 GTTTAGCAGAATTGGCAGCAACCGAACAAAT
35660 TTACT
1 TTACT
35665 AAGCAATCTA
Statistics
Matches: 270, Mismatches: 9, Indels: 10
0.93 0.03 0.03
Matches are distributed among these distances:
90 33 0.12
93 23 0.09
94 213 0.79
95 1 0.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:37447 original size:19 final size:20
Alignment explanation
Indices: 37423--37477 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
37413 GCGATTATCT
37423 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATTTTCATTTCCG
37442 CGTTGCGATTTTCATTTCCG
1 CGTTGCGATTTTCATTTCCG
37462 CGTTGCGATTTTCATT
1 CGTTGCGATTTTCATT
37478 CTCAAAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCG
Found at i:38043 original size:20 final size:20
Alignment explanation
Indices: 38020--38113 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
38010 CGATAGTCAG
38020 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
38040 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
38060 AATTCGCATTGCGAATTACGT
1 -ATTCGCATTGCGATTTACGT
* *
38081 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
38101 ATTCGCATTGCGA
1 ATTCGCATTGCGA
38114 ATTAAGAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 46 0.73
21 17 0.27
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.37
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:38127 original size:41 final size:41
Alignment explanation
Indices: 38020--38117 Score: 144
Period size: 41 Copynumber: 2.4 Consensus size: 41
38010 CGATAGTCAG
* * *
38020 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGAATTACGTAATCGCATTGCGATTTACCTA
* *
38061 ATTCGCATTGCGAATTACGTAATCGCGTTGCGATTTACGT-
1 ATTCGCATTGCGAATTACGTAATCGCATTGCGATTTACCTA
38101 ATTCGCATTGCGAATTA
1 ATTCGCATTGCGAATTA
38118 AGAAAATCGC
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
40 17 0.33
41 35 0.67
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.38
Consensus pattern (41 bp):
ATTCGCATTGCGAATTACGTAATCGCATTGCGATTTACCTA
Found at i:38128 original size:61 final size:61
Alignment explanation
Indices: 38022--38137 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 61
38012 ATAGTCAGAT
* ** * * **
38022 TCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGAATTACGTAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGAATTAACAAAATCGCAACGCGAATTACGTAA
* *
38083 TCGCGTTGCGATTTACGTATTCGCATTGCGAATTAAGAAAATCGCAACGCGAATT
1 TCGCATTGCGATTTACGTATTCGCATTGCGAATTAACAAAATCGCAACGCGAATT
38138 TGGGAAATCG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 46 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (61 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGAATTAACAAAATCGCAACGCGAATTACGTAA
Found at i:38134 original size:21 final size:21
Alignment explanation
Indices: 38110--38155 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
38100 TATTCGCATT
38110 GCGAATTAAGAAAATCGCAAC
1 GCGAATTAAGAAAATCGCAAC
** * *
38131 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAAGAAAATCGCAAC
38152 GCGA
1 GCGA
38156 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAAGAAAATCGCAAC
Found at i:51667 original size:35 final size:35
Alignment explanation
Indices: 51628--51697 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
51618 AAAAATTTTA
51628 TAAACATTTTAAAGGTGAACACATATATATTATTG
1 TAAACATTTTAAAGGTGAACACATATATATTATTG
51663 TAAACATTTTAAAGGTGAACACATATATATTATTG
1 TAAACATTTTAAAGGTGAACACATATATATTATTG
51698 ATATAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (35 bp):
TAAACATTTTAAAGGTGAACACATATATATTATTG
Found at i:53381 original size:184 final size:186
Alignment explanation
Indices: 53163--53551 Score: 653
Period size: 185 Copynumber: 2.1 Consensus size: 186
53153 TTTTCTAATT
* * * *
53163 TATATAA-AAATTAAATGTTTTTTAATTCAAAAAAA-AGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAATAGTTTACAATTAATTTAAATAATATATA
53226 ATTATAAAATAAAAAATTCAAATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAAATTCAAATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
*
53291 TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
131 TTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGG-TTGAGCCCATATGTTA
53347 TATATAATATATTTAATATTTTTTAATT-AAAAAAATAGTTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAATAGTTTACAATTAATTTAAATAATATATA
* * * *
53411 ATTATAAAATAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAAATTCAAATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
53476 TTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGTTGAGCCCATATGTTA
131 TTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGTTGAGCCCATATGTTA
53532 TATAT-ATATATTTAATATTT
1 TATATAATATATTTAATATTT
53552 AAAATTTAAT
Statistics
Matches: 193, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
184 31 0.16
185 162 0.84
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAATAGTTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAAATTCAAATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
TTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGTTGAGCCCATATGTTA
Found at i:60750 original size:24 final size:24
Alignment explanation
Indices: 60723--60875 Score: 297
Period size: 24 Copynumber: 6.4 Consensus size: 24
60713 ATTTTATTAC
*
60723 TTTATATCAACCAGTTATCTGTCA
1 TTTACATCAACCAGTTATCTGTCA
60747 TTTACATCAACCAGTTATCTGTCA
1 TTTACATCAACCAGTTATCTGTCA
60771 TTTACATCAACCAGTTATCTGTCA
1 TTTACATCAACCAGTTATCTGTCA
60795 TTTACATCAACCAGTTATCTGTCA
1 TTTACATCAACCAGTTATCTGTCA
60819 TTTACATCAACCAGTTATCTGTCA
1 TTTACATCAACCAGTTATCTGTCA
60843 TTTACATCAACCAGTTATCTGTCA
1 TTTACATCAACCAGTTATCTGTCA
60867 TTTACATCA
1 TTTACATCA
60876 GCACTCGTAA
Statistics
Matches: 128, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
24 128 1.00
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (24 bp):
TTTACATCAACCAGTTATCTGTCA
Done.