Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 211 of 211
Found at i:62617964 original size:288 final size:287
Alignment explanation
Indices: 62617364--62618261 Score: 1327
Period size: 288 Copynumber: 3.1 Consensus size: 287
62617354 CCCTACTTTC
* * * * * *
62617364 AAAA-CAAATGAATACGAAAACATAGCATCAAACTACAA-TTATACTTACCATATACCATAATAA
1 AAAAGCAAAAGAATAGGACAACATAGCATCAAACTACAAGCTATACTTAACATATACCATAATCA
* * ** * * * *
62617427 AAAAGATGCCATCCAAATCATCATCAAACTAAGCTGAAAA-CCGAAACTATGAATGCTTAAATGA
66 AAAAGATGCCATCCAAATCATCATCAAACTATGTTGAAAATAGGAAATTACGAATGCTTATACGA
*
62617491 TACCAAAAGAACAGGAAAGTCGACTGTTCTTAAACCACTTGAAAGCATAATTAAATGACTTCACA
131 TACCAAAAGAACAGGAAAGTC-A-TGTTCTTAAACCACTTGAAAGCATAA-TCAATGACTTCACA
62617556 TTTTTAAGTTAAAAAATGTAGTAATATCACTTCCGAAGCACGTTATTATATCGGCTTTTCAGTAC
193 TTTTTAAGTTAAAAAATGTAGTAATATCACTTCCGAAGCACGTTATTATATCGGCTTTTCAGTAC
*
62617621 CAATCACTACTTCCAAACAACTTCAAAGTT
258 CAATCACTACTTACAAACAACTTCAAAGTT
* * *
62617651 AAAAGTAAAAGAATAGGACAACATAGCATCAAACTACAAGCTATACTTATCATATACCATAATCG
1 AAAAGCAAAAGAATAGGACAACATAGCATCAAACTACAAGCTATACTTAACATATACCATAATCA
* * * *
62617716 AAAAGATGTCACCCAAACCATCATCAAACTATGTTGAAAATAGGAAATTACGAATGTTTATACGA
66 AAAAGATGCCATCCAAATCATCATCAAACTATGTTGAAAATAGGAAATTACGAATGCTTATACGA
* *
62617781 TACCAAAAGAACAGGAAAGTTATGTTCTTAAACCACTTGAAAGCATAATCAATGACTTTACATTT
131 TACCAAAAGAACAGGAAAGTCATGTTCTTAAACCACTTGAAAGCATAATCAATGACTTCACATTT
62617846 TTAAGTTAAAAAATGTAGTAATATCACTTCCGAAGCACGTTATTATATCGGCTTTTCAGTACCAA
196 TTAAGTTAAAAAATGTAGTAATATCACTTCCGAAGCACGTTATTATATCGGCTTTTCAGTACCAA
62617911 TCACTACTTAACAAACAACTTCAAAGTT
261 TCACTACTT-ACAAACAACTTCAAAGTT
* *
62617939 AAAAGCAAAAGAATGGGACAACATAGCATCAAACTACAAGCTATACTTAACATATTCCATAATCA
1 AAAAGCAAAAGAATAGGACAACATAGCATCAAACTACAAGCTATACTTAACATATACCATAATCA
* *
62618004 AAAAGATGCCTTCCAAATCATCATCAAACTATGTTGAAAATAGGAAATTAC-AAGTGCTGATACG
66 AAAAGATGCCATCCAAATCATCATCAAACTATGTTGAAAATAGGAAATTACGAA-TGCTTATACG
* * *
62618068 ATACCAAAAGAACAGGAAAGTCGTGTTCTTAAACCACTTGAAAGCATAATCAATGACTTCAGACT
130 ATACCAAAAGAACAGGAAAGTCATGTTCTTAAACCACTTGAAAGCATAATCAATGACTTCACATT
* * * * *
62618133 TTTAAGTTCAAAAATGTACTAATATCACTTCCGAAGCACGTTATCATATCCGCTTTTCACTACCA
195 TTTAAGTTAAAAAATGTAGTAATATCACTTCCGAAGCACGTTATTATATCGGCTTTTCAGTACCA
* * *
62618198 ATCACTACTCACAAACTACTTCAAAGAT
260 ATCACTACTTACAAACAACTTCAAAGTT
* * *
62618226 AAAAACAAAAGAATAGGACAAACCTAGCATAAAACT
1 AAAAGCAAAAGAATAGGAC-AACATAGCATCAAACT
62618262 GCAACAAATA
Statistics
Matches: 553, Mismatches: 52, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
287 128 0.23
288 331 0.60
289 57 0.10
290 37 0.07
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (287 bp):
AAAAGCAAAAGAATAGGACAACATAGCATCAAACTACAAGCTATACTTAACATATACCATAATCA
AAAAGATGCCATCCAAATCATCATCAAACTATGTTGAAAATAGGAAATTACGAATGCTTATACGA
TACCAAAAGAACAGGAAAGTCATGTTCTTAAACCACTTGAAAGCATAATCAATGACTTCACATTT
TTAAGTTAAAAAATGTAGTAATATCACTTCCGAAGCACGTTATTATATCGGCTTTTCAGTACCAA
TCACTACTTACAAACAACTTCAAAGTT
Found at i:62628592 original size:22 final size:23
Alignment explanation
Indices: 62628556--62628615 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
62628546 ATAATATCTA
*
62628556 AATAATAACATC-AAATTAGTAGC
1 AATAATAACAGCAAAATT-GTAGC
62628579 AATAA-AACAGCAAAATTGTAGC
1 AATAATAACAGCAAAATTGTAGC
*
62628601 AA-AATAACAACAAAA
1 AATAATAACAGCAAAA
62628616 AAAAAGAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 2 0.06
22 21 0.64
23 10 0.30
ACGTcount: A:0.60, C:0.13, G:0.08, T:0.18
Consensus pattern (23 bp):
AATAATAACAGCAAAATTGTAGC
Found at i:62629671 original size:21 final size:20
Alignment explanation
Indices: 62629642--62629680 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
62629632 TATTTTTAAG
62629642 TTTAGTTTTGTACTAATTATTC
1 TTTAGTTTTGT-CT-ATTATTC
62629664 TTTA-TTTTGTCTATTAT
1 TTTAGTTTTGTCTATTAT
62629681 AATACATACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 6 0.35
22 4 0.24
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTAGTTTTGTCTATTATTC
Found at i:62630165 original size:31 final size:31
Alignment explanation
Indices: 62630106--62630240 Score: 109
Period size: 31 Copynumber: 4.2 Consensus size: 31
62630096 AATAAATACC
*
62630106 AAAAATATATTTT--AAAAATTTAAAAAAATTA
1 AAAAATATATTTTAAAAAAATTT--TAAAATTA
62630137 AAAAATATATTTTAAAAAAATTTTAAAATTTTAAA
1 AAAAATATATTTTAAAAAAATTTTAAAA--TT--A
* * *
62630172 AAAAAAAGTATTTTAAAAATATTTTAAAAATA
1 AAAAATA-TATTTTAAAAAAATTTTAAAATTA
*
62630204 AAAAA-AT-TTTAAAAAAAGTATTTTAAAA-TA
1 AAAAATATATTTTAAAAAA--ATTTTAAAATTA
62630234 AAAAATA
1 AAAAATA
62630241 AAAAATAAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
29 8 0.09
30 8 0.09
31 28 0.32
32 6 0.07
33 10 0.11
34 1 0.01
35 7 0.08
36 20 0.23
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (31 bp):
AAAAATATATTTTAAAAAAATTTTAAAATTA
Found at i:62630189 original size:12 final size:11
Alignment explanation
Indices: 62630106--62630203 Score: 54
Period size: 11 Copynumber: 9.6 Consensus size: 11
62630096 AATAAATACC
62630106 AAAAATATATTT
1 AAAAATAT-TTT
*
62630118 TAAAA-A-TTT
1 AAAAATATTTT
* **
62630127 AAAAAAATTAA
1 AAAAATATTTT
62630138 AAAATATATTTT
1 AAAA-ATATTTT
*
62630150 AAAAAAATTTT
1 AAAAATATTTT
62630161 --AAA-ATTTT
1 AAAAATATTTT
62630169 AAAAA-A----
1 AAAAATATTTT
*
62630175 AAAAGTATTTT
1 AAAAATATTTT
62630186 AAAAATATTTT
1 AAAAATATTTT
62630197 AAAAATA
1 AAAAATA
62630204 AAAAAATTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 21
0.68 0.10 0.22
Matches are distributed among these distances:
6 4 0.06
7 1 0.02
8 5 0.08
9 10 0.15
10 5 0.08
11 29 0.44
12 12 0.18
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:62630206 original size:28 final size:30
Alignment explanation
Indices: 62630164--62630238 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
62630154 AAATTTTAAA
*
62630164 ATTTTAAAAA-AAAAAGTATTTT-AAAAA-T
1 ATTTTAAAAATAAAAA-AATTTTAAAAAAGT
62630192 ATTTTAAAAATAAAAAAATTTTAAAAAAAGT
1 ATTTTAAAAATAAAAAAATTTT-AAAAAAGT
62630223 ATTTT-AAAATAAAAAA
1 ATTTTAAAAATAAAAAA
62630239 TAAAAAATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
28 15 0.36
29 5 0.12
30 16 0.38
31 6 0.14
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (30 bp):
ATTTTAAAAATAAAAAAATTTTAAAAAAGT
Found at i:62630232 original size:30 final size:28
Alignment explanation
Indices: 62630149--62630238 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 28
62630139 AAATATATTT
62630149 TAAAAAA-ATTTT--AAA-ATTTTAAAA
1 TAAAAAAGATTTTAAAAATATTTTAAAA
62630173 -AAAAAAGTATTTTAAAAATATTTTAAAAA
1 TAAAAAAG-ATTTTAAAAATATTTT-AAAA
62630202 TAAAAAA-ATTTTAAAAAAAGTATTTTAAAA
1 TAAAAAAGATTTT--AAAAA-TATTTTAAAA
62630232 TAAAAAA
1 TAAAAAA
62630239 TAAAAAATAA
Statistics
Matches: 56, Mismatches: 0, Indels: 14
0.80 0.00 0.20
Matches are distributed among these distances:
23 6 0.11
25 5 0.09
27 3 0.05
28 10 0.18
29 4 0.07
30 22 0.39
31 6 0.11
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (28 bp):
TAAAAAAGATTTTAAAAATATTTTAAAA
Found at i:62630243 original size:6 final size:7
Alignment explanation
Indices: 62630228--62630252 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
62630218 AAAGTATTTT
62630228 AAAATAA
1 AAAATAA
62630235 AAAATAA
1 AAAATAA
62630242 AAAATAA
1 AAAATAA
62630249 AAAA
1 AAAA
62630253 CAAATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:62630244 original size:67 final size:67
Alignment explanation
Indices: 62630113--62630245 Score: 157
Period size: 67 Copynumber: 2.0 Consensus size: 67
62630103 ACCAAAAATA
* **
62630113 TATTTTAAAAATTTAAAAAAATTAAAAAATATATTTTAAAAAAATTTTAAAATTTTAAAAAAAAA
1 TATTTTAAAAATTTAAAAAAATTAAAAAATATATTTAAAAAAAATTTTAAAATTAAAAAAAAAAA
62630178 AG
66 AG
**
62630180 TATTTTAAAAATATTTTAAAAA-TAAAAAA-AT-TTTAAAAAAAGTATTTTAAAA-TAAAAAATA
1 TATTTTAAAAAT-TTAAAAAAATTAAAAAATATATTTAAAAAAA--ATTTTAAAATTAAAAAA-A
62630241 AAAAA
62 AAAAA
62630246 TAAAAAACAA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
65 9 0.16
66 7 0.12
67 34 0.60
68 7 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (67 bp):
TATTTTAAAAATTTAAAAAAATTAAAAAATATATTTAAAAAAAATTTTAAAATTAAAAAAAAAAA
AG
Found at i:62630250 original size:78 final size:78
Alignment explanation
Indices: 62630107--62630252 Score: 174
Period size: 78 Copynumber: 1.9 Consensus size: 78
62630097 ATAAATACCA
*** **
62630107 AAAATATATTTTAAAAATTTAAAAAAATTAAAAAATATATTTTAAAAAAATTTTAAAATTTTAAA
1 AAAATATATTTTAAAAA-TTAAAAAAATTAAAAAATATATTTTAAAAAAAAAATAAAATAATAAA
62630172 AAAAAAAGTATTTT
65 AAAAAAAGTATTTT
62630186 AAAA-ATATTTTAAAAA-TAAAAAAATTTTAAAAAA-AGTATTTTAAAATAAAAAATAAAA-AAT
1 AAAATATATTTTAAAAATTAAAAAAA--TTAAAAAATA-TATTTTAAAA-AAAAAATAAAATAAT
62630247 AAAAAA
62 AAAAAA
62630253 CAAATATATT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
76 8 0.14
77 1 0.02
78 37 0.64
79 12 0.21
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (78 bp):
AAAATATATTTTAAAAATTAAAAAAATTAAAAAATATATTTTAAAAAAAAAATAAAATAATAAAA
AAAAAAGTATTTT
Found at i:62633172 original size:22 final size:23
Alignment explanation
Indices: 62633138--62633181 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
62633128 GACTCTTCTA
*
62633138 AAATGAAAAAAATTATAAAATTC
1 AAATGAAAAAAATAATAAAATTC
*
62633161 AAAT-AAATAAATAATAAAATT
1 AAATGAAAAAAATAATAAAATT
62633182 ATAATTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (23 bp):
AAATGAAAAAAATAATAAAATTC
Found at i:62635385 original size:50 final size:49
Alignment explanation
Indices: 62635303--62635404 Score: 159
Period size: 50 Copynumber: 2.1 Consensus size: 49
62635293 CCTATATATT
*
62635303 TTTCATTCGGTTGTTTTTGTCACCACCTTCACTATTCTTCTTCTTCTTC
1 TTTCATTCGGTTGTTTTTGTCACCACCTTCACTACTCTTCTTCTTCTTC
* * *
62635352 TTTCATTTGGTTGTTTTTTGTCACTATCTTCACTACTCTTCTTCTTCTTC
1 TTTCATTCGGTTG-TTTTTGTCACCACCTTCACTACTCTTCTTCTTCTTC
62635402 TTT
1 TTT
62635405 TTAACGTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
49 12 0.25
50 36 0.75
ACGTcount: A:0.10, C:0.25, G:0.08, T:0.57
Consensus pattern (49 bp):
TTTCATTCGGTTGTTTTTGTCACCACCTTCACTACTCTTCTTCTTCTTC
Found at i:62638407 original size:29 final size:29
Alignment explanation
Indices: 62638352--62638407 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
62638342 ATAGGCCCGG
* * * *
62638352 ATCTTTCTATTATTAAATACATTAATTTA
1 ATCTTTATATTATTAAAAAAATAAATTTA
62638381 ATCTTTATATTATTAAAAAAATAAATT
1 ATCTTTATATTATTAAAAAAATAAATT
62638408 AACATTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (29 bp):
ATCTTTATATTATTAAAAAAATAAATTTA
Found at i:62638872 original size:11 final size:11
Alignment explanation
Indices: 62638856--62638881 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
62638846 TATTTTTTTA
62638856 TTTTAAAATAC
1 TTTTAAAATAC
62638867 TTTTAAAATAC
1 TTTTAAAATAC
62638878 TTTT
1 TTTT
62638882 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:62638900 original size:41 final size:40
Alignment explanation
Indices: 62638847--62638933 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 40
62638837 AAATATTTTT
62638847 ATTTTTTTATTTTAAAATACTTTTAAAATACT-TTTTTTAA
1 ATTTTTTTATTTTAAAATACTTTTAAAATA-TATTTTTTAA
* *
62638887 ATTTTTTTAATTTTAAAATATTTTTAAAATATATTTTTTTA
1 ATTTTTTT-ATTTTAAAATACTTTTAAAATATATTTTTTAA
62638928 ATTTTT
1 ATTTTT
62638934 AAAATAAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
40 9 0.21
41 34 0.79
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (40 bp):
ATTTTTTTATTTTAAAATACTTTTAAAATATATTTTTTAA
Found at i:62638905 original size:17 final size:17
Alignment explanation
Indices: 62638880--62638913 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
62638870 TAAAATACTT
* *
62638880 TTTTTAAATTTTTTTAA
1 TTTTAAAATATTTTTAA
62638897 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
62638914 AATATATTTT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:62638953 original size:22 final size:21
Alignment explanation
Indices: 62638905--62638953 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
62638895 AATTTTAAAA
* *
62638905 TATTTTTAAAATATATTTTTT
1 TATTTTTAAAATAAATTTTTG
62638926 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
62638949 TATTT
1 TATTT
62638954 ATTTAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 22 0.92
23 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:62657406 original size:20 final size:20
Alignment explanation
Indices: 62657381--62657451 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
62657371 CTTGAACCTT
*
62657381 GAACCTCGAA-CCCAAACATC
1 GAACCTCAAATCCCAAAC-TC
62657401 GAACCTCAAATCCCAAACTC
1 GAACCTCAAATCCCAAACTC
* * *
62657421 GAATCTTAAA-CCCTAAACTT
1 GAACCTCAAATCCC-AAACTC
62657441 GCAACCTCAAA
1 G-AACCTCAAA
62657452 CTCCGAACCT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
19 3 0.07
20 25 0.60
21 14 0.33
ACGTcount: A:0.41, C:0.35, G:0.07, T:0.17
Consensus pattern (20 bp):
GAACCTCAAATCCCAAACTC
Found at i:62658883 original size:10 final size:10
Alignment explanation
Indices: 62658868--62658924 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
62658858 AAAAATTTAT
62658868 TTTTAAAATA
1 TTTTAAAATA
62658878 TTTT-AAA-A
1 TTTTAAAATA
* *
62658886 -TTAAAAAAA
1 TTTTAAAATA
*
62658895 TTTAAAAATA
1 TTTTAAAATA
62658905 TTTTAAAAATA
1 TTTT-AAAATA
62658916 TTTTAAAAT
1 TTTTAAAAT
62658925 TAAAAAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
7 2 0.05
8 4 0.10
9 4 0.10
10 20 0.50
11 10 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTTAAAATA
Found at i:62658946 original size:39 final size:40
Alignment explanation
Indices: 62658858--62658981 Score: 191
Period size: 39 Copynumber: 3.1 Consensus size: 40
62658848 AATAAATACC
* **
62658858 AAAAATTTATTTTTAAAATATTTTAAAATTAAAAAAATTT
1 AAAAATTTATTTTAAAAATATTTTAAAATTAAAAAAATAA
62658898 AAAAA--TATTTTAAAAATATTTTAAAATT-AAAAAATAA
1 AAAAATTTATTTTAAAAATATTTTAAAATTAAAAAAATAA
62658935 AAAAATTTATTTTAAAAATATTTTAAAATTAAAAAAATTAA
1 AAAAATTTATTTTAAAAATATTTTAAAATTAAAAAAA-TAA
62658976 AAAAAT
1 AAAAAT
62658982 AAATATTTAT
Statistics
Matches: 77, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
37 12 0.16
38 22 0.29
39 23 0.30
40 11 0.14
41 9 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (40 bp):
AAAAATTTATTTTAAAAATATTTTAAAATTAAAAAAATAA
Found at i:62661711 original size:4 final size:4
Alignment explanation
Indices: 62661702--62661756 Score: 92
Period size: 4 Copynumber: 13.8 Consensus size: 4
62661692 TATGATTGCA
* *
62661702 TATG TATG TATG TGTG TGTG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
62661750 TATG TAT
1 TATG TAT
62661757 ATGTGTTACG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:62669252 original size:11 final size:11
Alignment explanation
Indices: 62669236--62669260 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
62669226 GAACTTGACA
62669236 ACTCTTCTAAT
1 ACTCTTCTAAT
62669247 ACTCTTCTAAT
1 ACTCTTCTAAT
62669258 ACT
1 ACT
62669261 AGGGCATGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (11 bp):
ACTCTTCTAAT
Found at i:62669743 original size:23 final size:23
Alignment explanation
Indices: 62669707--62669758 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
62669697 AAAACAAAAA
* * *
62669707 AAAAAAAACCCAAAGGGGGAGAG
1 AAAAAAAACACAAAGAGAGAGAG
*
62669730 AAAAAAAATACAAAGAGAGAGAG
1 AAAAAAAACACAAAGAGAGAGAG
*
62669753 GAAAAA
1 AAAAAA
62669759 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.65, C:0.08, G:0.25, T:0.02
Consensus pattern (23 bp):
AAAAAAAACACAAAGAGAGAGAG
Found at i:62698492 original size:17 final size:19
Alignment explanation
Indices: 62698465--62698499 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
62698455 TAAAACATTT
62698465 ATTGTTAATATAT-TTATA
1 ATTGTTAATATATATTATA
62698483 ATTG-TAATATATATTAT
1 ATTGTTAATATATATTAT
62698500 TAAAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (19 bp):
ATTGTTAATATATATTATA
Found at i:62722408 original size:3 final size:3
Alignment explanation
Indices: 62722402--62722434 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
62722392 ACTGTCACCT
62722402 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
62722435 AGATTACTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:62722614 original size:6 final size:6
Alignment explanation
Indices: 62722603--62722630 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
62722593 AAAGTTGAAC
62722603 TATACA TATACA TATACA TATACA TATA
1 TATACA TATACA TATACA TATACA TATA
62722631 TATACCTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (6 bp):
TATACA
Found at i:62727905 original size:18 final size:19
Alignment explanation
Indices: 62727868--62727906 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
62727858 AATTATTTAA
62727868 AAAATCTAAAAAATATAAT
1 AAAATCTAAAAAATATAAT
* *
62727887 AAAATTTAATAAA-ATAAT
1 AAAATCTAAAAAATATAAT
62727905 AA
1 AA
62727907 TTTTGGAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAATCTAAAAAATATAAT
Found at i:62750396 original size:13 final size:13
Alignment explanation
Indices: 62750378--62750402 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62750368 AAATATATAA
62750378 TTTTGAAAAGCAC
1 TTTTGAAAAGCAC
62750391 TTTTGAAAAGCA
1 TTTTGAAAAGCA
62750403 ATAAGAAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (13 bp):
TTTTGAAAAGCAC
Found at i:62762160 original size:16 final size:16
Alignment explanation
Indices: 62762141--62762172 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
62762131 ATACGTATAT
62762141 AACCAAATAATTACAC
1 AACCAAATAATTACAC
62762157 AACCAAATAATTACAC
1 AACCAAATAATTACAC
62762173 GTGACATGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (16 bp):
AACCAAATAATTACAC
Found at i:62766679 original size:4 final size:4
Alignment explanation
Indices: 62766672--62766702 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
62766662 TCCATATATA
62766672 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
62766703 TGAAGTGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:62773944 original size:31 final size:29
Alignment explanation
Indices: 62773909--62773971 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 29
62773899 ATATTAAAAC
*
62773909 TATACATGAACTTTGATTCAATGTGTAATTT
1 TATACATGAACTTTAATTC--TGTGTAATTT
62773940 TATACATGAACTTTAATTCTGTGTAATTT
1 TATACATGAACTTTAATTCTGTGTAATTT
62773969 TAT
1 TAT
62773972 GCATACAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 13 0.42
31 18 0.58
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.48
Consensus pattern (29 bp):
TATACATGAACTTTAATTCTGTGTAATTT
Found at i:62791072 original size:6 final size:6
Alignment explanation
Indices: 62791061--62791091 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
62791051 CAATGAGTAT
62791061 CTTAGC CTTAGC CTTAGC CTTAGC CTTAGC C
1 CTTAGC CTTAGC CTTAGC CTTAGC CTTAGC C
62791092 CATTTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.35, G:0.16, T:0.32
Consensus pattern (6 bp):
CTTAGC
Found at i:62810236 original size:6 final size:6
Alignment explanation
Indices: 62810227--62810256 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
62810217 AAATATAAAT
62810227 GGCTAA GGCTAA GGCTAA -GCTAA GGCTAA G
1 GGCTAA GGCTAA GGCTAA GGCTAA GGCTAA G
62810257 ATACTCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (6 bp):
GGCTAA
Found at i:62810250 original size:11 final size:11
Alignment explanation
Indices: 62810227--62810256 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
62810217 AAATATAAAT
62810227 GGCTAAGGCTAA
1 GGCTAA-GCTAA
62810239 GGCTAAGCTAA
1 GGCTAAGCTAA
62810250 GGCTAAG
1 GGCTAAG
62810257 ATACTCATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (11 bp):
GGCTAAGCTAA
Done.