Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168200.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_436, 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: 26926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:83 original size:18 final size:18
Alignment explanation
Indices: 56--289 Score: 388
Period size: 18 Copynumber: 13.1 Consensus size: 18
46 TAGTCTCCAT
*
56 TTTTTTATTCACTATAGG
1 TTTTTCATTCACTATAGG
74 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
92 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
110 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
128 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
146 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
164 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
182 -TTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
199 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
217 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
235 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
253 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
271 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
289 T
1 T
290 CTCGATTCTG
Statistics
Matches: 211, Mismatches: 0, Indels: 10
0.95 0.00 0.05
Matches are distributed among these distances:
17 21 0.10
18 186 0.88
19 4 0.02
ACGTcount: A:0.22, C:0.15, G:0.13, T:0.50
Consensus pattern (18 bp):
TTTTTCATTCACTATAGG
Found at i:630 original size:18 final size:18
Alignment explanation
Indices: 607--644 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
597 TTTTTTGCGC
607 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
625 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
643 AT
1 AT
645 GGAATTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (18 bp):
ATTGCATACGGCTTTACA
Found at i:2580 original size:78 final size:78
Alignment explanation
Indices: 2451--2619 Score: 320
Period size: 78 Copynumber: 2.2 Consensus size: 78
2441 AGTAAAAAGA
* *
2451 ATGTAAAATTATATTTCGCTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
2516 TTATCTTAATAAT
66 TTATCTTAATAAT
2529 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
2594 TTATCTTAATAAT
66 TTATCTTAATAAT
2607 ATGTAATATTATA
1 ATGTAATATTATA
2620 ATATGTAATA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 89 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (78 bp):
ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
TTATCTTAATAAT
Found at i:2622 original size:15 final size:15
Alignment explanation
Indices: 2602--2634 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2592 TCTTATCTTA
2602 ATAATATGTAATATT
1 ATAATATGTAATATT
2617 ATAATATGTAATATT
1 ATAATATGTAATATT
2632 ATA
1 ATA
2635 TTTCACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAATATGTAATATT
Found at i:2715 original size:15 final size:15
Alignment explanation
Indices: 2695--2727 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2685 TCTTATCTTA
2695 ATAATATGTAATATT
1 ATAATATGTAATATT
2710 ATAATATGTAATATT
1 ATAATATGTAATATT
2725 ATA
1 ATA
2728 TTTCACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAATATGTAATATT
Found at i:2816 original size:93 final size:93
Alignment explanation
Indices: 2524--2800 Score: 554
Period size: 93 Copynumber: 3.0 Consensus size: 93
2514 TCTTATCTTA
2524 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
2589 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
2617 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
2682 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
2710 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
2775 TGGTCTTATCTTAATAATATGTAATA
66 TGGTCTTATCTTAATAATATGTAATA
2801 ATGGTCTTAA
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 184 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.42
Consensus pattern (93 bp):
ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
TGGTCTTATCTTAATAATATGTAATATT
Found at i:5206 original size:21 final size:20
Alignment explanation
Indices: 5181--5248 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
5171 TTCCATTATT
*
5181 ATATAATTATATAAATAATAT
1 ATATAATTATATAAAT-ATAA
5202 ATATAA--ATATAAATATAA
1 ATATAATTATATAAATATAA
*
5220 ATATAAATAATATAAATATAA
1 ATAT-AATTATATAAATATAA
5241 ATATAATT
1 ATATAATT
5249 TCAAGATCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.17
19 10 0.24
20 3 0.07
21 22 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATAATTATATAAATATAA
Found at i:5213 original size:6 final size:6
Alignment explanation
Indices: 5189--5246 Score: 77
Period size: 6 Copynumber: 10.0 Consensus size: 6
5179 TTATATAATT
*
5189 ATATAA ATAATAT ATATAA ATATAA ATATAA ATAT-A A-AT-A ATATAA
1 ATATAA AT-ATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
5235 ATATAA ATATAA
1 ATATAA ATATAA
5247 TTTCAAGATC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
4 4 0.09
5 4 0.09
6 34 0.72
7 5 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:5225 original size:27 final size:26
Alignment explanation
Indices: 5181--5246 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
5171 TTCCATTATT
*
5181 ATATAATTATATAAAT-AATATATATAA
1 ATATAAATATA-AAATAAATA-ATATAA
5208 ATATAAATATAAATATAAATAATATAA
1 ATATAAATATAAA-ATAAATAATATAA
5235 ATATAAATATAA
1 ATATAAATATAA
5247 TTTCAAGATC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 2 0.06
27 30 0.83
28 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATAAATATAAAATAAATAATATAA
Found at i:7217 original size:23 final size:23
Alignment explanation
Indices: 7191--7236 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
7181 TATATTGTAA
7191 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
7214 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
7237 GGGGAGGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.04, T:0.48
Consensus pattern (23 bp):
CCAATCATTTATCTTATTACTTG
Found at i:12746 original size:21 final size:21
Alignment explanation
Indices: 12722--12765 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
12712 GATTCTTTGC
12722 TTTGAGATTTTATCTGATCTA
1 TTTGAGATTTTATCTGATCTA
12743 TTTGAGATTTTATCTGATCTA
1 TTTGAGATTTTATCTGATCTA
12764 TT
1 TT
12766 ATAAATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.55
Consensus pattern (21 bp):
TTTGAGATTTTATCTGATCTA
Found at i:12773 original size:21 final size:21
Alignment explanation
Indices: 12722--12773 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
12712 GATTCTTTGC
*
12722 TTTGAGATTTTATCTGATCTA
1 TTTGAAATTTTATCTGATCTA
*
12743 TTTGAGATTTTATCTGATCTA
1 TTTGAAATTTTATCTGATCTA
12764 TTAT-AAATTT
1 TT-TGAAATTT
12774 GTATATCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.54
Consensus pattern (21 bp):
TTTGAAATTTTATCTGATCTA
Found at i:12986 original size:37 final size:38
Alignment explanation
Indices: 12945--13016 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
12935 ACAATCAAAT
12945 AAAATGAAAATAAAA-TTTTAAAATGAAAATAAAAAAA
1 AAAATGAAAATAAAATTTTTAAAATGAAAATAAAAAAA
12982 AAAATGAAAATAAAATTTTTAAAATGAAAATAAAA
1 AAAATGAAAATAAAATTTTTAAAATGAAAATAAAA
13017 TTTTCGCGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 15 0.44
38 19 0.56
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (38 bp):
AAAATGAAAATAAAATTTTTAAAATGAAAATAAAAAAA
Found at i:12987 original size:18 final size:19
Alignment explanation
Indices: 12945--13017 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
12935 ACAATCAAAT
***
12945 AAAATGAAAATAAAATTTT
1 AAAATGAAAATAAAATAAA
12964 AAAATGAAAATAAAA-AAA
1 AAAATGAAAATAAAATAAA
***
12982 AAAATGAAAATAAAATTTTT
1 AAAATGAAAATAAAA-TAAA
13002 AAAATGAAAATAAAAT
1 AAAATGAAAATAAAAT
13018 TTTCGCGGGC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 15 0.33
19 16 0.35
20 15 0.33
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (19 bp):
AAAATGAAAATAAAATAAA
Found at i:13295 original size:24 final size:25
Alignment explanation
Indices: 13252--13315 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
13242 TGGAGCCTTA
**
13252 ATTTAATATTTAATAAAAATTTAAT
1 ATTTAATAAATAATAAAAATTTAAT
13277 ATTTAATAAA-AATAAAAATTTAAT
1 ATTTAATAAATAATAAAAATTTAAT
13301 ATTTAATAAATAATA
1 ATTTAATAAATAATA
13316 TTTAATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 24 0.67
25 12 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAATAAATAATAAAAATTTAAT
Found at i:13310 original size:18 final size:18
Alignment explanation
Indices: 13251--13289 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
13241 ATGGAGCCTT
13251 AATTTAATATTTAATAAA
1 AATTTAATATTTAATAAA
13269 AATTTAATATTTAATAAA
1 AATTTAATATTTAATAAA
13287 AAT
1 AAT
13290 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTAATATTTAATAAA
Found at i:13316 original size:14 final size:14
Alignment explanation
Indices: 13297--13324 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13287 AATAAAAATT
13297 TAATATTTAATAAA
1 TAATATTTAATAAA
13311 TAATATTTAATAAA
1 TAATATTTAATAAA
13325 AAAATTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATATTTAATAAA
Found at i:13329 original size:18 final size:18
Alignment explanation
Indices: 13255--13329 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
13245 AGCCTTAATT
**
13255 TAATATTTAATAAAAATT
1 TAATATTTAATAAAAAAA
13273 TAATATTTAATAAAAATAA
1 TAATATTTAATAAAAA-AA
*
13292 -AA-ATTTAATATTTAATAAA
1 TAATATTTAATA---AAAAAA
13311 TAATATTTAATAAAAAAA
1 TAATATTTAATAAAAAAA
13329 T
1 T
13330 TTGTTAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
17 8 0.17
18 24 0.51
19 2 0.04
20 5 0.11
21 8 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATATTTAATAAAAAAA
Found at i:14705 original size:14 final size:14
Alignment explanation
Indices: 14686--14713 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
14676 AACAAATTTT
14686 TTTATTAAATATTA
1 TTTATTAAATATTA
14700 TTTATTAAATATTA
1 TTTATTAAATATTA
14714 AATTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATTAAATATTA
Found at i:14731 original size:17 final size:18
Alignment explanation
Indices: 14721--14759 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
14711 TTAAATTTTT
14721 ATTTTTATTAAATATTAA
1 ATTTTTATTAAATATTAA
14739 ATTTTTATTAAATATTAA
1 ATTTTTATTAAATATTAA
14757 ATT
1 ATT
14760 AAGGCTCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTATTAAATATTAA
Found at i:14731 original size:24 final size:25
Alignment explanation
Indices: 14695--14758 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
14685 TTTTATTAAA
14695 TATTATTTATTAAATATTAAATTTT
1 TATTATTTATTAAATATTAAATTTT
14720 TATT-TTTATTAAATATTAAATTTT
1 TATTATTTATTAAATATTAAATTTT
**
14744 TATTAAATATTAAAT
1 TATTATTTATTAAAT
14759 TAAGGCTCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 24 0.67
25 12 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTATTTATTAAATATTAAATTTT
Found at i:15015 original size:20 final size:20
Alignment explanation
Indices: 14990--15067 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
14980 TTCGCCCGCG
14990 AAAATTTTATTTTCATTTTA
1 AAAATTTTATTTTCATTTTA
15010 AAAATTTTATTTTCATTTT-
1 AAAATTTTATTTTCATTTTA
***
15029 -TTTTTTTATTTTCATTTTA
1 AAAATTTTATTTTCATTTTA
15048 AAAATTTTATTTTCATTTTA
1 AAAATTTTATTTTCATTTTA
15068 TTTGATTGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.30
20 35 0.70
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (20 bp):
AAAATTTTATTTTCATTTTA
Found at i:15045 original size:38 final size:38
Alignment explanation
Indices: 14994--15066 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
14984 CCCGCGAAAA
14994 TTTTATTTTCATTTTAAAAATTTTATTTTCATTTTTTT
1 TTTTATTTTCATTTTAAAAATTTTATTTTCATTTTTTT
15032 TTTTATTTTCATTTTAAAAATTTTATTTTCATTTT
1 TTTTATTTTCATTTTAAAAATTTTATTTTCATTTT
15067 ATTTGATTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (38 bp):
TTTTATTTTCATTTTAAAAATTTTATTTTCATTTTTTT
Found at i:15084 original size:38 final size:37
Alignment explanation
Indices: 14993--15084 Score: 105
Period size: 38 Copynumber: 2.4 Consensus size: 37
14983 GCCCGCGAAA
* *
14993 ATTTTATTTTCATTTTAAAAATTTTATTTTCATTTTTT
1 ATTTGATTTTAATTTTAAAAATTTTATTTTCA-TTTTT
* * *
15031 TTTTTATTTTCATTTTAAAAATTTTATTTTCA-TTTT
1 ATTTGATTTTAATTTTAAAAATTTTATTTTCATTTTT
15067 ATTTGATTGTTAAATTTT
1 ATTTGATT-TT-AATTTT
15085 TGTCGATCCG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
36 10 0.21
37 2 0.04
38 36 0.75
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (37 bp):
ATTTGATTTTAATTTTAAAAATTTTATTTTCATTTTT
Found at i:15283 original size:20 final size:21
Alignment explanation
Indices: 15245--15287 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
15235 ACAAATTTAT
15245 AATAGATCAGATAAAATCTCA
1 AATAGATCAGATAAAATCTCA
15266 AATAGATCAGAT-AAATCTCA
1 AATAGATCAGATAAAATCTCA
15286 AA
1 AA
15288 GCAAAGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.53, C:0.14, G:0.09, T:0.23
Consensus pattern (21 bp):
AATAGATCAGATAAAATCTCA
Found at i:20797 original size:23 final size:23
Alignment explanation
Indices: 20771--20816 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
20761 GTTCCTCCCC
20771 CAAGTAATAAGATAAATGATTGG
1 CAAGTAATAAGATAAATGATTGG
20794 CAAGTAATAAGATAAATGATTGG
1 CAAGTAATAAGATAAATGATTGG
20817 TTACAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.22, T:0.26
Consensus pattern (23 bp):
CAAGTAATAAGATAAATGATTGG
Found at i:22770 original size:6 final size:6
Alignment explanation
Indices: 22759--22816 Score: 77
Period size: 6 Copynumber: 10.0 Consensus size: 6
22749 GATCTTGAAA
22759 TTATAT TTATAT TTATA- -T-TAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
*
22804 ATATTAT TTATAT
1 TTA-TAT TTATAT
22817 AATTATATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 1 0.02
6 37 0.80
7 5 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTATAT
Found at i:22785 original size:21 final size:21
Alignment explanation
Indices: 22759--22825 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
22749 GATCTTGAAA
22759 TTATATTTATATTTATATTAT
1 TTATATTTATATTTATATTAT
22780 TTATATTTATATTTATATT-T
1 TTATATTTATATTTATATTAT
* * *
22800 ATATATAT-TATTTATATAAT
1 TTATATTTATATTTATATTAT
22820 TATATA
1 T-TATA
22826 ATAATGGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.22
20 8 0.20
21 23 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATATTTATATTTATATTAT
Found at i:22817 original size:27 final size:27
Alignment explanation
Indices: 22759--22816 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
22749 GATCTTGAAA
22759 TTATATTTATATTTATATTATTTATAT
1 TTATATTTATATTTATATTATTTATAT
*
22786 TTATATTTATATTTATA-TATAT-TAT
1 TTATATTTATATTTATATTATTTATAT
22811 TTATAT
1 TTATAT
22817 AATTATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 9 0.30
26 4 0.13
27 17 0.57
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TTATATTTATATTTATATTATTTATAT
Found at i:22822 original size:27 final size:29
Alignment explanation
Indices: 22757--22824 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 29
22747 GTGATCTTGA
22757 AATTATATTTATATTTATATTATTTATATTT
1 AATTATATTTATA-TTATATTATTTATA-TT
22788 ATATTTATATTTATA-TATATTATTTATA-T
1 A-A-TTATATTTATATTATATTATTTATATT
22817 AATTATAT
1 AATTATAT
22825 AATAATGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
27 6 0.17
28 1 0.03
29 2 0.06
31 14 0.40
32 1 0.03
33 11 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
AATTATATTTATATTATATTATTTATATT
Found at i:25298 original size:15 final size:15
Alignment explanation
Indices: 25278--25310 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
25268 CAAAGTGAAA
25278 TATAATATTACATAT
1 TATAATATTACATAT
25293 TATAATATTACATAT
1 TATAATATTACATAT
25308 TAT
1 TAT
25311 TAAGATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAATATTACATAT
Found at i:25377 original size:78 final size:78
Alignment explanation
Indices: 25293--25554 Score: 301
Period size: 78 Copynumber: 3.2 Consensus size: 78
25283 TATTACATAT
25293 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
1 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
25358 AATCAAAGTGAAA
66 AATCAAAGTGAAA
* * ** * *
25371 TATAATATTACATATTA-TAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTA
1 TATAATATTACATATTATTAAGA-TA-AGACCATT---AT--TA-C-GTATTAC--A-----TTA
25435 CGTATTACGCTTCCACAATCAAAGTGAAA
50 CGTATTACGCTTCCACAATCAAAGTGAAA
25464 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
1 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
*
25529 AATCAAAGCGAAA
66 AATCAAAGTGAAA
*
25542 TATAATTTTACAT
1 TATAATATTACAT
25555 TCTTTTTACT
Statistics
Matches: 153, Mismatches: 14, Indels: 34
0.76 0.07 0.17
Matches are distributed among these distances:
77 4 0.03
78 62 0.41
79 5 0.03
82 2 0.01
83 1 0.01
84 1 0.01
85 7 0.05
86 7 0.05
87 1 0.01
88 1 0.01
89 2 0.01
92 5 0.03
93 51 0.33
94 4 0.03
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (78 bp):
TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
AATCAAAGTGAAA
Found at i:25391 original size:15 final size:15
Alignment explanation
Indices: 25371--25403 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
25361 CAAAGTGAAA
25371 TATAATATTACATAT
1 TATAATATTACATAT
25386 TATAATATTACATAT
1 TATAATATTACATAT
25401 TAT
1 TAT
25404 TAAGATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAATATTACATAT
Found at i:25512 original size:93 final size:93
Alignment explanation
Indices: 25205--25481 Score: 554
Period size: 93 Copynumber: 3.0 Consensus size: 93
25195 TTAAGACCAT
25205 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
1 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
25270 AAGTGAAATATAATATTACATATTATAA
66 AAGTGAAATATAATATTACATATTATAA
25298 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
1 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
25363 AAGTGAAATATAATATTACATATTATAA
66 AAGTGAAATATAATATTACATATTATAA
25391 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
1 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
25456 AAGTGAAATATAATATTACATATTAT
66 AAGTGAAATATAATATTACATATTAT
25482 TAAGATAAGA
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 184 1.00
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.37
Consensus pattern (93 bp):
TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
AAGTGAAATATAATATTACATATTATAA
Done.