Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014386.1 Kokia drynarioides strain JFW-HI SEQ_129424, 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: 33400
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Found at i:205 original size:29 final size:29
Alignment explanation
Indices: 168--433 Score: 268
Period size: 29 Copynumber: 9.1 Consensus size: 29
158 TTAGACATCC
* *
168 GGGGGAAAAATGGAATTTTTGGAAGTTTG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
197 GGGGTAAAAATGGAATTTTTGGAAGTTTTA
1 GGGGTAAAAATGGAATTTTTGGAAG-TTTA
*
227 -GGGTCAAAAATGGAATTTTTGGAAG-TTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTA
* *
255 GAGTGTAAAAATGGAATTTTTTGAAGTTTA
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTA
* *
285 GAGGTAAAAATGGAA-TTTTGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
* * * *
313 GAGGTAAAAAATGAAATTTTTTGAAGTTCA
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTA
***
343 GGGGTAAAAATGGAATTTTCAAAAGTTTTA
1 GGGGTAAAAATGGAATTTTTGGAAG-TTTA
* * *
373 GGGTTAAAAATGGAATATTTGGAAGTTCA
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
* ** *
402 AGGGTAAAAATTAAATTTTCGGACAGTTTA
1 GGGGTAAAAATGGAATTTTTGGA-AGTTTA
432 GG
1 GG
434 AACCTCCAGG
Statistics
Matches: 194, Mismatches: 34, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
28 18 0.09
29 104 0.54
30 72 0.37
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTA
Found at i:314 original size:58 final size:57
Alignment explanation
Indices: 173--430 Score: 270
Period size: 59 Copynumber: 4.4 Consensus size: 57
163 CATCCGGGGG
* * *
173 AAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTTGAAG-TTTAGGGT
231 CAAAAATGGAATTTTTGGAAG-TTCGAGTGTAAAAATGGAATTTTTTGAAGTTTAGAGGT
1 -AAAAATGGAATTTTTGGAAGTTTCGAG-GTAAAAATGGAATTTTTTGAAGTTTAG-GGT
* *
290 AAAAATGGAA-TTTTGGAAGTTTCGAGGTAAAAAATGAAATTTTTTGAAGTTCAGGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT-AAAAATGGAATTTTTTGAAGTTTA-GGGT
*** * * * *
348 AAAAATGGAATTTTCAAAAGTTT-TAGGGTTAAAAATGGAATATTTGGAAGTTCAAGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGA-GG-TAAAAATGGAATTTTTTGAAGTT-TAGGGT
** *
407 AAAAATTAAATTTTCGGACAGTTT
1 AAAAATGGAATTTTTGGA-AGTTT
431 AGGAACCTCC
Statistics
Matches: 172, Mismatches: 17, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
57 11 0.06
58 61 0.35
59 93 0.54
60 7 0.04
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.34
Consensus pattern (57 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTTGAAGTTTAGGGT
Found at i:1302 original size:10 final size:10
Alignment explanation
Indices: 1287--1311 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1277 TTCTATTTTT
1287 TTATTTATTA
1 TTATTTATTA
1297 TTATTTATTA
1 TTATTTATTA
1307 TTATT
1 TTATT
1312 AATAAACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTATTTATTA
Found at i:2137 original size:7 final size:6
Alignment explanation
Indices: 2124--2206 Score: 52
Period size: 6 Copynumber: 14.3 Consensus size: 6
2114 ATTTAAATAG
*
2124 ATTTAA ACTTTAA ATTTATA A--TAA ATTTAAA ATTT-A A-GTAA ATTTAA
1 ATTTAA A-TTTAA ATTTA-A ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA
* * * *
2171 ACTTAA A-ATAA ATTTAA TTTTAA A-ATAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
2207 CCTGTTGGGT
Statistics
Matches: 59, Mismatches: 9, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
4 3 0.05
5 14 0.24
6 28 0.47
7 14 0.24
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:2151 original size:24 final size:23
Alignment explanation
Indices: 2114--2160 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
2104 ATTGGACTTG
* *
2114 ATTTAAATAGATTTAAACTTTAA
1 ATTTAAATAAATTTAAAATTTAA
2137 ATTTATAATAAATTTAAAATTTAA
1 ATTTA-AATAAATTTAAAATTTAA
2161 GTAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTTAAATAAATTTAAAATTTAA
Found at i:2152 original size:17 final size:17
Alignment explanation
Indices: 2127--2206 Score: 99
Period size: 17 Copynumber: 4.6 Consensus size: 17
2117 TAAATAGATT
*
2127 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTAAAA
*
2145 TAAATTTAAAATTT-AAG
1 TAAATTT-AAATTTAAAA
*
2162 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
2179 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
2196 TAAATTTAAAT
1 TAAATTTAAAT
2207 CCTGTTGGGT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
16 5 0.09
17 38 0.72
18 10 0.19
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:14920 original size:28 final size:28
Alignment explanation
Indices: 14877--14939 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
14867 AAAATGAGAC
14877 TTTTCGGATACTCGGGAGCAAAATGGTAA
1 TTTT-GGATACTCGGGAGCAAAATGGTAA
* * **
14906 TTTTGGATTCTCGGGGGTGAAATGGTAA
1 TTTTGGATACTCGGGAGCAAAATGGTAA
14934 TTTTGG
1 TTTTGG
14940 GAAAATTCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.24, C:0.10, G:0.32, T:0.35
Consensus pattern (28 bp):
TTTTGGATACTCGGGAGCAAAATGGTAA
Found at i:15104 original size:29 final size:29
Alignment explanation
Indices: 15040--15406 Score: 341
Period size: 29 Copynumber: 12.5 Consensus size: 29
15030 CATCTGGGGG
**
15040 AAAAATGGTAATTTTTTAAAGTTTC-AGGGT
1 AAAAATGG-AATTTTTGGAAG-TTCGAGGGT
*
15070 CAAAAATGGAATTTTGGGAAGTTCGAGGGT
1 -AAAAATGGAATTTTTGGAAGTTCGAGGGT
* *
15100 AAAAATGGAATTTTTAGAAGTTTTGA-GGT
1 AAAAATGGAATTTTTGGAAG-TTCGAGGGT
*
15129 CAAAATGGAATTTTTGGAAGTTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGT
* * *
15158 AAAAATGGAA-TTTTGTATGTTTTG-GGGTT
1 AAAAATGGAATTTTTGGAAG-TTCGAGGG-T
* * *
15187 AAAATTGGAATTTTTTGAAGTT-TAGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGA-GGGT
* * ** *
15216 AAAAATGGATTTTTTAGAAGTTTTATGGT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGT
* * *
15245 CAAAAATGGATTTTTTTGAAGTTCAAGGGT
1 -AAAAATGGAATTTTTGGAAGTTCGAGGGT
*** *
15275 AAAAATGGAATTTTCAAAAGTTTTG-GGGT
1 AAAAATGGAATTTTTGGAAG-TTCGAGGGT
*
15304 CAAAAATGGAATTTTTGGAAGTTTGAGGGT
1 -AAAAATGGAATTTTTGGAAGTTCGAGGGT
*
15334 AAAAATGGAATTTTTGGAAGTTTCGAGGTT
1 AAAAATGGAATTTTTGGAAG-TTCGAGGGT
*
15364 AAAAATGGAATTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGT
*
15393 AAATATGGAATTTT
1 AAAAATGGAATTTT
15407 CTGATAGTTT
Statistics
Matches: 282, Mismatches: 40, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
28 14 0.05
29 156 0.55
30 104 0.37
31 8 0.03
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGGT
Found at i:15112 original size:59 final size:59
Alignment explanation
Indices: 15000--15406 Score: 429
Period size: 59 Copynumber: 6.9 Consensus size: 59
14990 TAATTTTGAG
* * * *
15000 AGTTTTAAGGTCGAAAATGGAGTTTTTGGACA--TCTG-GGGGAAAAATGGTAATTTTTTAA
1 AGTTTTAGGGTCAAAAATGGAATTTTTGGA-AGTTC-GAGGGTAAAAATGG-AATTTTTTAA
* *
15059 AGTTTCAGGGTCAAAAATGGAATTTTGGGAAGTTCGAGGGTAAAAATGGAA-TTTTTAGA
1 AGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTTA-A
*
15118 AGTTTT-GAGGTC-AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTGT-A
1 AGTTTTAG-GGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTTAA
* * * * * *
15175 TGTTTTGGGGTTAAAATTGGAATTTTTTGAAGTT-TAGGGGTAAAAATGG-ATTTTTTAGA
1 AGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTCGA-GGGTAAAAATGGAATTTTTTA-A
* * * * **
15234 AGTTTTATGGTCAAAAATGGATTTTTTTGAAGTTCAAGGGTAAAAATGGAATTTTCAAA
1 AGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTTAA
* * **
15293 AGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGA
1 AGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTTAA
* * * *
15352 AG-TTTCGAGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAATATGGAATTTT
1 AGTTTTAG-GGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTT
15407 CTGATAGTTT
Statistics
Matches: 296, Mismatches: 38, Indels: 28
0.82 0.10 0.08
Matches are distributed among these distances:
57 16 0.05
58 81 0.27
59 179 0.60
60 20 0.07
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.36
Consensus pattern (59 bp):
AGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTTAA
Found at i:16134 original size:77 final size:77
Alignment explanation
Indices: 16039--16182 Score: 225
Period size: 77 Copynumber: 1.9 Consensus size: 77
16029 GTCACGAGTT
* * *
16039 CGTAGCCACGCGCCGTTGCGCTTCTCTGCCATGGCACCGTCCGATCATCCACGCGCCCCCATCTC
1 CGTAGCCACGCGCCGTTGCGCGTCTCCGCCATAGCACCGTCCGATCATCCACGCGCCCCCATCTC
16104 CGGTCATCGGTC
66 CGGTCATCGGTC
* * **
16116 CGTAGCCACGCTCCGTTGCGCGTCTCCGCCATAGCACCGTCCGATCGTCCACGCTTCCCCATCTC
1 CGTAGCCACGCGCCGTTGCGCGTCTCCGCCATAGCACCGTCCGATCATCCACGCGCCCCCATCTC
16181 CG
66 CG
16183 ATCACTGGTA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 60 1.00
ACGTcount: A:0.12, C:0.45, G:0.22, T:0.21
Consensus pattern (77 bp):
CGTAGCCACGCGCCGTTGCGCGTCTCCGCCATAGCACCGTCCGATCATCCACGCGCCCCCATCTC
CGGTCATCGGTC
Found at i:16426 original size:10 final size:10
Alignment explanation
Indices: 16411--16435 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16401 TTTCTATTTT
16411 TTATTTATTA
1 TTATTTATTA
16421 TTATTTATTA
1 TTATTTATTA
16431 TTATT
1 TTATT
16436 AATAAACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTATTTATTA
Found at i:17265 original size:17 final size:17
Alignment explanation
Indices: 17243--17292 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
17233 TTGGACTTGA
17243 TTTAAATAAATTTAAAC
1 TTTAAATAAATTTAAAC
*
17260 TTTAAATAAATTT-AAT
1 TTTAAATAAATTTAAAC
*
17276 TTTAAAATAAAATTAAA
1 TTT-AAATAAATTTAAA
17293 TCTTATTGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 5 0.17
17 22 0.76
18 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATAAATTTAAAC
Found at i:18532 original size:41 final size:40
Alignment explanation
Indices: 18466--18545 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 40
18456 TCAGACATTT
18466 TTTTTAAAGGATCGAAATTAAATTTTTATTATATCTTTAAAG
1 TTTTTAAAGGATCGAAATTAAATTTTTATTAT-T-TTTAAAG
*
18508 TTTTTAAAGGAT-TAAATTAAATTTTTATTATTTTTAAA
1 TTTTTAAAGGATCGAAATTAAATTTTTATTATTTTTAAA
18546 AAGAATTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
39 6 0.16
40 1 0.03
41 18 0.49
42 12 0.32
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (40 bp):
TTTTTAAAGGATCGAAATTAAATTTTTATTATTTTTAAAG
Found at i:19471 original size:6 final size:6
Alignment explanation
Indices: 19462--19486 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19452 TTTTATACAT
19462 ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA A
19487 CAATTGCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:23725 original size:31 final size:30
Alignment explanation
Indices: 23689--23751 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
23679 TTATAATGGT
* * *
23689 AAAATTGCACTTTGATCTTTTAAAAATAATA
1 AAAATT-CAATTTAATCATTTAAAAATAATA
* *
23720 AAAATTTAATTTAATCATTTAAAAATTATA
1 AAAATTCAATTTAATCATTTAAAAATAATA
23750 AA
1 AA
23752 GATATAAGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (30 bp):
AAAATTCAATTTAATCATTTAAAAATAATA
Found at i:25230 original size:5 final size:5
Alignment explanation
Indices: 25220--25246 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
25210 ACCTCAAAAT
25220 ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
25247 TAGGATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:27026 original size:3 final size:3
Alignment explanation
Indices: 27018--27043 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
27008 AGAAATTGAA
27018 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
27044 CATCAAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:27568 original size:23 final size:23
Alignment explanation
Indices: 27540--27583 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
27530 GCCTGAATTT
27540 TTAAATTTTAAAAAATAAAAAAA
1 TTAAATTTTAAAAAATAAAAAAA
*
27563 TTAAATTTTTAAAAATAAAAA
1 TTAAATTTTAAAAAATAAAAA
27584 TACAGTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
TTAAATTTTAAAAAATAAAAAAA
Found at i:29191 original size:23 final size:23
Alignment explanation
Indices: 29165--29225 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
29155 ATTTAAAATT
*
29165 TTAAAAAATAAAAATTATATAAA
1 TTAAAAAATAAAAATTATAAAAA
* * *
29188 TTAAGAAATTATAATTATAAAAA
1 TTAAAAAATAAAAATTATAAAAA
* *
29211 TGATAAAATACAAAA
1 TTAAAAAATA-AAAA
29226 AAAAAAAAAA
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 25 0.89
24 3 0.11
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.30
Consensus pattern (23 bp):
TTAAAAAATAAAAATTATAAAAA
Found at i:30314 original size:41 final size:39
Alignment explanation
Indices: 30251--30327 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 39
30241 TTTATGTGTT
* *
30251 TTTTTTTTTTTTTTTAAATTTCTGGAAATTTT-CTATACA
1 TTTTTATTTTTTTTTAAATTTCT-AAAATTTTGCTATACA
30290 TTTTTATTTTTTTTTAGAATTTTCTAAAATTTTGCTAT
1 TTTTTATTTTTTTTTA-AA-TTTCTAAAATTTTGCTAT
30328 TTTTATGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 15 0.45
40 9 0.27
41 9 0.27
ACGTcount: A:0.23, C:0.06, G:0.05, T:0.65
Consensus pattern (39 bp):
TTTTTATTTTTTTTTAAATTTCTAAAATTTTGCTATACA
Found at i:32547 original size:437 final size:437
Alignment explanation
Indices: 30927--32582 Score: 2664
Period size: 437 Copynumber: 3.8 Consensus size: 437
30917 AAAAAAAAAT
* * * * **
30927 ACTTTTTATAATTTATAAAATTTTAAATTAATAATAATAAAATTGCACTTTGGGC-TTCAAAAAT
1 ACTTTTTATAATTTATAAAATTTTAAAATAGTAATAGTAAAATTGCATTTTGATCATTCAAAAAT
* * *
30991 -ATAAAAATTTGATTTAAACCTTTAAAAATTATAAAGATATAAGCTATTAAAATGATTAAATTAA
66 AATAAAAATTTGATTTAACCCTTTAAAAATTATAAAGATATAAGCTATTAAAATGATGAAATTAC
* *
31055 ATTTTTACTATTATAAAAATATATAATTTAGTTTCGACCTCTCAAAACAAATTTTTTAA-CCC--
131 ATTTTAACTATTATAAAAATATATAATTTAGTTCCGACCTCTCAAAACAAATTTTTTAACCCCGT
* * * *
31117 CAC------CA-CTG-TTAATTAGGCATGGTTCCAACCAAGTAGGAAACTAAATTTATTATGTAT
196 CACTGTTATTAGCAGTTTAATTAGGCATGGTTCTAACCACGTAGGAAACTAAATTTATTATGTAT
* * * * * *
31174 GTCTAGCCCGAAAGGACCATTAGTATGTATAAAAGCAACTGTGAAACTTGAAAAAGTTATTGTGA
261 GTGTAGCCTGAAAGGACCATCAATATGTATAAAAGCAACTGTAAAACTTGAAAAAGTTACTGTGA
* * * *
31239 AGG-CAATAGACTAAAGCCTTTTCCAAAAAGTTAGACTTAGTAGTTAGTGACGGAGCGTAGTGGA
326 AGGCCAATAGACTAAAGCCTTTTCCAAAAAGTTAGACTTAGTAATCAATGACGGAGCATAGTGGA
* * * *
31303 GATCCGAGAGTCATGGTTCATTCTAAAATGGAAAAATTTTAATTTAG
391 GATCTGGGAGTCATGATTCATTCTAAAATGGTAAAATTTTAATTTAG
*
31350 A-TTCTTTATAATTTATAAAATTTTAAAATAGTAATAGTAAAATTACATTTTGATCATTCAAAAA
1 ACTT-TTTATAATTTATAAAATTTTAAAATAGTAATAGTAAAATTGCATTTTGATCATTCAAAAA
* * * * *
31414 TGAGAAAAATTTGATTTAACTCTTTAAAAATTATAAATATATAATCTATTAAAATGATGAAATTA
65 TAATAAAAATTTGATTTAACCCTTTAAAAATTATAAAGATATAAGCTATTAAAATGATGAAATTA
* *
31479 CATTTTAACTATTATAAAAAATATATAATTTAGTTCCGACCTCTCAAAATAGATTTTTTAACCCC
130 CATTTTAACTATTAT-AAAAATATATAATTTAGTTCCGACCTCTCAAAACAAATTTTTTAACCCC
*
31544 GTCACTGTTATTAACAGTTTAATTAGGCATGGTTCTAACCACGTAGGAAACTAAATTTATTATGT
194 GTCACTGTTATTAGCAGTTTAATTAGGCATGGTTCTAACCACGTAGGAAACTAAATTTATTATGT
*
31609 ATGTGTAGCCTGAAAGGACCATCAATATGTATAAAAGCAACTGTAAAACTTGAAAACGTTACTGT
259 ATGTGTAGCCTGAAAGGACCATCAATATGTATAAAAGCAACTGTAAAACTTGAAAAAGTTACTGT
*
31674 GAAGGCCAATAGACTAAAGCTTTTTCCAAAAAGTTAGACTTAGTAATCAATGACGGAGCATAGTG
324 GAAGGCCAATAGACTAAAGCCTTTTCCAAAAAGTTAGACTTAGTAATCAATGACGGAGCATAGTG
31739 GAGATCTGGGAGTCATGATTCATTCTAAAATGGTAAAATTTTAATTTAG
389 GAGATCTGGGAGTCATGATTCATTCTAAAATGGTAAAATTTTAATTTAG
31788 ACTTTTTATAATTTATAAAATTTTAAAATAGTAATAGTAAAATTGCATTTTGATCATTCAAAAAT
1 ACTTTTTATAATTTATAAAATTTTAAAATAGTAATAGTAAAATTGCATTTTGATCATTCAAAAAT
*
31853 AATAAAAATTTGATTTAACCCTTT-AAAATTATAAAGATATAGGCTATTAAAATGATGAAATTAC
66 AATAAAAATTTGATTTAACCCTTTAAAAATTATAAAGATATAAGCTATTAAAATGATGAAATTAC
* *
31917 ATTTTAATTATTATAAAAATATATAATTTAGTTCCAACCTCTCAAAACAAATTTTTTAACCCCGT
131 ATTTTAACTATTATAAAAATATATAATTTAGTTCCGACCTCTCAAAACAAATTTTTTAACCCCGT
31982 CACTGTTATTAGCAGTTTAATTAGGCATGGTTCTAACCACGTAGGAAACTAAATTTATTATGTAT
196 CACTGTTATTAGCAGTTTAATTAGGCATGGTTCTAACCACGTAGGAAACTAAATTTATTATGTAT
32047 GTGTAG-CTCGAAAGGACCATCAATATGTATAAAAGCAACTGTAAAACTTGAAAAAGTTACTGTG
261 GTGTAGCCT-GAAAGGACCATCAATATGTATAAAAGCAACTGTAAAACTTGAAAAAGTTACTGTG
*
32111 AAGGCCAATAGACTAAAGCCTTTTCCAAAAAGTTAGACTTAGTAATCAAAGACGGAGCATAGTGG
325 AAGGCCAATAGACTAAAGCCTTTTCCAAAAAGTTAGACTTAGTAATCAATGACGGAGCATAGTGG
*
32176 AGATCTGGGAGTCATGATTCATTCTAAAATAGTAAAATTTTAATTTAG
390 AGATCTGGGAGTCATGATTCATTCTAAAATGGTAAAATTTTAATTTAG
32224 ACTTTTTATAATTTATAAAATTTTAAAATAGTAATAGTAAAATTGCATTTTGATCATTCAAAAAT
1 ACTTTTTATAATTTATAAAATTTTAAAATAGTAATAGTAAAATTGCATTTTGATCATTCAAAAAT
*
32289 AATAAAAATTTGATTTAACCCTTTAAAAATTATAAAGATAT-AGACTATTGAAATGATGAAATTA
66 AATAAAAATTTGATTTAACCCTTTAAAAATTATAAAGATATAAG-CTATTAAAATGATGAAATTA
32353 CATTTTAACTATTATAAAAATATATAATTTAGTTCCGACCTCTCAAAACAAATTTTTTAACCCCG
130 CATTTTAACTATTATAAAAATATATAATTTAGTTCCGACCTCTCAAAACAAATTTTTTAACCCCG
*
32418 TCACTATTATTAGCAGTTTAATTAGGCATGGTTCTAACCACGTAGGAAACTAAATTTATTATGTA
195 TCACTGTTATTAGCAGTTTAATTAGGCATGGTTCTAACCACGTAGGAAACTAAATTTATTATGTA
* * * ** *
32483 TGTGTAGTCTGAAAGGACCATCATTATGTATAAAAGTAGTTGTGAAACTTGAAAAAGTTACTGTG
260 TGTGTAGCCTGAAAGGACCATCAATATGTATAAAAGCAACTGTAAAACTTGAAAAAGTTACTGTG
*
32548 AAGGCCAATAAACTAAAGCCTTTTCCAAAAAGTTA
325 AAGGCCAATAGACTAAAGCCTTTTCCAAAAAGTTA
32583 TGTTGAAGCC
Statistics
Matches: 1147, Mismatches: 65, Indels: 28
0.93 0.05 0.02
Matches are distributed among these distances:
422 2 0.00
423 45 0.04
424 9 0.01
425 70 0.06
426 42 0.04
427 3 0.00
429 3 0.00
435 3 0.00
436 374 0.33
437 411 0.36
438 183 0.16
439 2 0.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (437 bp):
ACTTTTTATAATTTATAAAATTTTAAAATAGTAATAGTAAAATTGCATTTTGATCATTCAAAAAT
AATAAAAATTTGATTTAACCCTTTAAAAATTATAAAGATATAAGCTATTAAAATGATGAAATTAC
ATTTTAACTATTATAAAAATATATAATTTAGTTCCGACCTCTCAAAACAAATTTTTTAACCCCGT
CACTGTTATTAGCAGTTTAATTAGGCATGGTTCTAACCACGTAGGAAACTAAATTTATTATGTAT
GTGTAGCCTGAAAGGACCATCAATATGTATAAAAGCAACTGTAAAACTTGAAAAAGTTACTGTGA
AGGCCAATAGACTAAAGCCTTTTCCAAAAAGTTAGACTTAGTAATCAATGACGGAGCATAGTGGA
GATCTGGGAGTCATGATTCATTCTAAAATGGTAAAATTTTAATTTAG
Found at i:32565 original size:873 final size:861
Alignment explanation
Indices: 30927--32582 Score: 2663
Period size: 873 Copynumber: 1.9 Consensus size: 861
30917 AAAAAAAAAT
* *
30927 ACTTTTTATAATTTATAAAATTTTAAATTAATAATAATAAAATTGCACTTTGGGCTTCAAAAATA
1 ACTTTTTATAATTTATAAAATTTTAAAATAATAATAATAAAATTGCACTTTGAGCTTCAAAAATA
*
30992 TAAAAATTTGATTTAAACCTTTAAAAATTATAAAGATATAAGCTATTAAAATGATTAAATTAAAT
66 TAAAAATTTGATTTAAACCTTTAAAAATTATAAAGATATAAGCTATTAAAATGATGAAATTAAAT
* * *
31057 TTTTACTATTATAAAAATATATAATTTAGTTTCGACCTCTCAAAACAAATTTTTTAACCCCACCA
131 TTTAACTATTATAAAAATATATAATTTAGTTCCAACCTCTCAAAACAAATTTTTTAACCCCACCA
*
31122 CTGTTAATTAGGCATGGTTCCAACCAAGTAGGAAACTAAATTTATTATGTATGTCTAGCCCGAAA
196 CAGTTAATTAGGCATGGTTCCAACCAAGTAGGAAACTAAATTTATTATGTATGTCTAGCCCGAAA
* * * *
31187 GGACCATTAGTATGTATAAAAGCAACTGTGAAACTTGAAAAAGTTATTGTGAAGGCAATAGACTA
261 GGACCATCAATATGTATAAAAGCAACTGTAAAACTTGAAAAAGTTACTGTGAAGGCAATAGACTA
* * ** *
31252 AAGCCTTTTCCAAAAAGTTAGACTTAGTAGTTAGTGACGGAGCGTAGTGGAGATCCGAGAGTCAT
326 AAGCCTTTTCCAAAAAGTTAGACTTAGTAATCAAAGACGGAGCATAGTGGAGATCCGAGAGTCAT
* *
31317 GGTTCATTCTAAAATGGAAAAATTTTAATTTAGATTCTTTATAATTTATAAAATTTTAAAATAGT
391 GATTCATTCTAAAATAGAAAAATTTTAATTTAGATTCTTTATAATTTATAAAATTTTAAAATAGT
* *
31382 AATAGTAAAATTACATTTTGATCATTCAAAAATGAGAAAAATTTGATTTAACTCTTTAAAAATTA
456 AATAGTAAAATTACATTTTGATCATTCAAAAATAAGAAAAATTTGATTTAACCCTTTAAAAATTA
*
31447 TAAATATATAATCTATTAAAATGATGAAATTACATTTTAACTATTATAAAAAATATATAATTTAG
521 TAAAGATATAATCTATTAAAATGATGAAATTACATTTTAACTATTATAAAAAATATATAATTTAG
* * *
31512 TTCCGACCTCTCAAAATAGATTTTTTAACCCCGTCACTGTTATTAACAGTTTAATTAGGCATGGT
586 TTCCGACCTCTCAAAACAAATTTTTTAACCCCGTCACTATTATTAACAGTTTAATTAGGCATGGT
31577 TCTAACCACGTAGGAAACTAAATTTATTATGTATGTGTAGCCTGAAAGGACCATCAATATGTATA
651 TCTAACCACGTAGGAAACTAAATTTATTATGTATGTGTAGCCTGAAAGGACCATCAATATGTATA
* * *
31642 AAAGCAACTGTAAAACTTGAAAACGTTACTGTGAAGGCCAATAGACTAAAGCTTTTTCCAAAAAG
716 AAAGCAACTGTAAAACTTGAAAAAGTTACTGTGAAGGCCAATAAACTAAAGCCTTTTCCAAAAAG
31707 TTAGACTTAGTAATCAATGACGGAGCATAGTGGAGATCTGGGAGTCATGATTCATTCTAAAATGG
781 TTAGACTTAGTAATCAATGACGGAGCATAGTGGAGATCTGGGAGTCATGATTCATTCTAAAATGG
31772 TAAAATTTTAATTTAG
846 TAAAATTTTAATTTAG
* * * *
31788 ACTTTTTATAATTTATAAAATTTTAAAATAGTAATAGTAAAATTGCATTTTGATCATTCAAAAAT
1 ACTTTTTATAATTTATAAAATTTTAAAATAATAATAATAAAATTGCACTTTGAGC-TTCAAAAAT
* * *
31853 AATAAAAATTTGATTTAACCCTTT-AAAATTATAAAGATATAGGCTATTAAAATGATGAAATTAC
65 -ATAAAAATTTGATTTAAACCTTTAAAAATTATAAAGATATAAGCTATTAAAATGATGAAATTAA
*
31917 ATTTTAATTATTATAAAAATATATAATTTAGTTCCAACCTCTCAAAACAAATTTTTTAACCCCGT
129 ATTTTAACTATTATAAAAATATATAATTTAGTTCCAACCTCTCAAAACAAATTTTTTAA-CCC--
* * *
31982 CACTGTTATTAGCAGTTTAATTAGGCATGGTTCTAACCACGTAGGAAACTAAATTTATTATGTAT
191 CAC------CA-CAG-TTAATTAGGCATGGTTCCAACCAAGTAGGAAACTAAATTTATTATGTAT
* *
32047 GTGTAGCTCGAAAGGACCATCAATATGTATAAAAGCAACTGTAAAACTTGAAAAAGTTACTGTGA
248 GTCTAGCCCGAAAGGACCATCAATATGTATAAAAGCAACTGTAAAACTTGAAAAAGTTACTGTGA
32112 AGGCCAATAGACTAAAGCCTTTTCCAAAAAGTTAGACTTAGTAATCAAAGACGGAGCATAGTGGA
313 AGG-CAATAGACTAAAGCCTTTTCCAAAAAGTTAGACTTAGTAATCAAAGACGGAGCATAGTGGA
* * *
32177 GATCTGGGAGTCATGATTCATTCTAAAATAGTAAAATTTTAATTTAGACTT-TTTATAATTTATA
377 GATCCGAGAGTCATGATTCATTCTAAAATAGAAAAATTTTAATTTAGA-TTCTTTATAATTTATA
* *
32241 AAATTTTAAAATAGTAATAGTAAAATTGCATTTTGATCATTCAAAAATAATAAAAATTTGATTTA
441 AAATTTTAAAATAGTAATAGTAAAATTACATTTTGATCATTCAAAAATAAGAAAAATTTGATTTA
*
32306 ACCCTTTAAAAATTATAAAGATATAGA-CTATTGAAATGATGAAATTACATTTTAACTATTAT-A
506 ACCCTTTAAAAATTATAAAGATATA-ATCTATTAAAATGATGAAATTACATTTTAACTATTATAA
*
32369 AAAATATATAATTTAGTTCCGACCTCTCAAAACAAATTTTTTAACCCCGTCACTATTATTAGCAG
570 AAAATATATAATTTAGTTCCGACCTCTCAAAACAAATTTTTTAACCCCGTCACTATTATTAACAG
*
32434 TTTAATTAGGCATGGTTCTAACCACGTAGGAAACTAAATTTATTATGTATGTGTAGTCTGAAAGG
635 TTTAATTAGGCATGGTTCTAACCACGTAGGAAACTAAATTTATTATGTATGTGTAGCCTGAAAGG
* * ** *
32499 ACCATCATTATGTATAAAAGTAGTTGTGAAACTTGAAAAAGTTACTGTGAAGGCCAATAAACTAA
700 ACCATCAATATGTATAAAAGCAACTGTAAAACTTGAAAAAGTTACTGTGAAGGCCAATAAACTAA
32564 AGCCTTTTCCAAAAAGTTA
765 AGCCTTTTCCAAAAAGTTA
32583 TGTTGAAGCC
Statistics
Matches: 726, Mismatches: 53, Indels: 20
0.91 0.07 0.03
Matches are distributed among these distances:
861 49 0.07
862 101 0.14
863 25 0.03
865 3 0.00
871 1 0.00
872 2 0.00
873 311 0.43
874 231 0.32
875 3 0.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (861 bp):
ACTTTTTATAATTTATAAAATTTTAAAATAATAATAATAAAATTGCACTTTGAGCTTCAAAAATA
TAAAAATTTGATTTAAACCTTTAAAAATTATAAAGATATAAGCTATTAAAATGATGAAATTAAAT
TTTAACTATTATAAAAATATATAATTTAGTTCCAACCTCTCAAAACAAATTTTTTAACCCCACCA
CAGTTAATTAGGCATGGTTCCAACCAAGTAGGAAACTAAATTTATTATGTATGTCTAGCCCGAAA
GGACCATCAATATGTATAAAAGCAACTGTAAAACTTGAAAAAGTTACTGTGAAGGCAATAGACTA
AAGCCTTTTCCAAAAAGTTAGACTTAGTAATCAAAGACGGAGCATAGTGGAGATCCGAGAGTCAT
GATTCATTCTAAAATAGAAAAATTTTAATTTAGATTCTTTATAATTTATAAAATTTTAAAATAGT
AATAGTAAAATTACATTTTGATCATTCAAAAATAAGAAAAATTTGATTTAACCCTTTAAAAATTA
TAAAGATATAATCTATTAAAATGATGAAATTACATTTTAACTATTATAAAAAATATATAATTTAG
TTCCGACCTCTCAAAACAAATTTTTTAACCCCGTCACTATTATTAACAGTTTAATTAGGCATGGT
TCTAACCACGTAGGAAACTAAATTTATTATGTATGTGTAGCCTGAAAGGACCATCAATATGTATA
AAAGCAACTGTAAAACTTGAAAAAGTTACTGTGAAGGCCAATAAACTAAAGCCTTTTCCAAAAAG
TTAGACTTAGTAATCAATGACGGAGCATAGTGGAGATCTGGGAGTCATGATTCATTCTAAAATGG
TAAAATTTTAATTTAG
Found at i:32708 original size:17 final size:17
Alignment explanation
Indices: 32657--32748 Score: 75
Period size: 17 Copynumber: 5.4 Consensus size: 17
32647 TTCATTTTGG
*
32657 GTTTAAATTTAATTTAAA
1 GTTTAAATTTAAATT-AA
**
32675 GTTTAAACTTT-TCTTAA
1 GTTTAAA-TTTAAATTAA
32692 GTTTAAATTTAAATTAA
1 GTTTAAATTTAAATTAA
* *
32709 GTTTAAAATTAATTTGAA
1 GTTTAAATTTAAATT-AA
32727 -TTTAAAATTT-AATTAA
1 GTTT-AAATTTAAATTAA
32743 -TTTAAA
1 GTTTAAA
32749 AAAGTCCAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
15 3 0.05
16 8 0.13
17 32 0.52
18 16 0.26
19 3 0.05
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (17 bp):
GTTTAAATTTAAATTAA
Found at i:32731 original size:34 final size:34
Alignment explanation
Indices: 32657--32749 Score: 95
Period size: 35 Copynumber: 2.7 Consensus size: 34
32647 TTCATTTTGG
* * *
32657 GTTTAAATTTAATTTAAAGTTTAAACTTTTCTTAA
1 GTTTAAATTTAAATT-AAGTTTAAAATTTTCTGAA
32692 GTTTAAATTTAAATTAAGTTTAAAATTAATT-TGAA
1 GTTTAAATTTAAATTAAGTTTAAAATT--TTCTGAA
32727 -TTTAAAATTT-AATTAA-TTTAAAA
1 GTTT-AAATTTAAATTAAGTTTAAAA
32750 AAGTCCAGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
33 7 0.13
34 20 0.38
35 23 0.44
36 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.48
Consensus pattern (34 bp):
GTTTAAATTTAAATTAAGTTTAAAATTTTCTGAA
Done.