Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007437.1 Kokia drynarioides strain JFW-HI SEQ_122058, 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: 36373
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:399 original size:30 final size:30
Alignment explanation
Indices: 365--430 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
355 AAGTTGTGGA
365 TTTAGTTTATATATTTTTAATTTGGAT-AAT
1 TTTAGTTTATATATTTTTAATTTGG-TCAAT
* * *
395 TTTAGTTTTTATTTTTTTTATTTGGTCAAT
1 TTTAGTTTATATATTTTTAATTTGGTCAAT
425 TTTAGT
1 TTTAGT
431 CTTGACTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.23, C:0.02, G:0.11, T:0.65
Consensus pattern (30 bp):
TTTAGTTTATATATTTTTAATTTGGTCAAT
Found at i:3632 original size:24 final size:24
Alignment explanation
Indices: 3591--3644 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
3581 TCAATTTTTT
*
3591 TTTATAT-TGAATAAATATAATTA
1 TTTATATATGAATAAATATAAATA
3614 TTTATATATGAA-AATATATAAATA
1 TTTATATATGAATAA-ATATAAATA
3638 -TTATATA
1 TTTATATA
3645 AATAATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
TTTATATATGAATAAATATAAATA
Found at i:4173 original size:23 final size:23
Alignment explanation
Indices: 4134--4177 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
4124 TTTTTATTTA
*
4134 TGTTGCATTTAGTTTATTTTTCG
1 TGTTGCATTTAGATTATTTTTCG
4157 TGTTGCATTCTA-ATTATTTTT
1 TGTTGCATT-TAGATTATTTTT
4178 TGTTTTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.16, C:0.09, G:0.14, T:0.61
Consensus pattern (23 bp):
TGTTGCATTTAGATTATTTTTCG
Found at i:5253 original size:17 final size:17
Alignment explanation
Indices: 5230--5273 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
5220 AATTCACTTT
5230 TTTAAATTTATGTTAAGA
1 TTTAAATTTATGTTAA-A
*
5248 -TTAAATTTATTTTAAA
1 TTTAAATTTATGTTAAA
5264 TTTAAATTTA
1 TTTAAATTTA
5274 AATTTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATGTTAAA
Found at i:5262 original size:11 final size:11
Alignment explanation
Indices: 5248--5291 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
5238 TATGTTAAGA
*
5248 TTAAATTTATT
1 TTAAATTTAAT
5259 TTAAATTTAAAT
1 TTAAATTT-AAT
5271 TTAAATTTAAT
1 TTAAATTTAAT
*
5282 TTAAGTTTAA
1 TTAAATTTAA
5292 AATTATTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:5267 original size:6 final size:6
Alignment explanation
Indices: 5248--5310 Score: 69
Period size: 6 Copynumber: 11.0 Consensus size: 6
5238 TATGTTAAGA
* * *
5248 TTAAAT TT-ATT TTAAAT TTAAAT TTAAAT TT-AAT TTAAGT TTAAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
5294 TT-ATT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT
5311 AAATAAAAGT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
5 12 0.26
6 34 0.74
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:5268 original size:23 final size:22
Alignment explanation
Indices: 5242--5310 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
5232 TAAATTTATG
*
5242 TTAAGATTAAATTTATTTTAAAT
1 TTAA-ATTAAATTTAATTTAAAT
*
5265 TTAAATTTAAATTTAATTTAAGT
1 TTAAA-TTAAATTTAATTTAAAT
*
5288 TTAAAATT-ATTTTAAATTTAAAT
1 TT-AAATTAAATTT-AATTTAAAT
5311 AAATAAAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 5 0.13
23 31 0.79
24 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (22 bp):
TTAAATTAAATTTAATTTAAAT
Found at i:5276 original size:40 final size:40
Alignment explanation
Indices: 5230--5310 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
5220 AATTCACTTT
*
5230 TTTAAATTT-ATGTTAAGATTAAATTTATTTTAAATTTAAA
1 TTTAAATTTAAT-TTAAGATTAAAATTATTTTAAATTTAAA
*
5270 TTTAAATTTAATTTAAGTTTAAAATTATTTTAAATTTAAA
1 TTTAAATTTAATTTAAGATTAAAATTATTTTAAATTTAAA
5310 T
1 T
5311 AAATAAAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 36 0.95
41 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (40 bp):
TTTAAATTTAATTTAAGATTAAAATTATTTTAAATTTAAA
Found at i:5282 original size:17 final size:17
Alignment explanation
Indices: 5248--5310 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
5238 TATGTTAAGA
*
5248 TTAAATTT-ATTTTAAAT
1 TTAAATTTAAATTT-AAT
5265 TTAAATTTAAATTTAAT
1 TTAAATTTAAATTTAAT
* * *
5282 TTAAGTTTAAAATTATT
1 TTAAATTTAAATTTAAT
5299 TTAAATTTAAAT
1 TTAAATTTAAAT
5311 AAATAAAAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 35 0.90
18 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TTAAATTTAAATTTAAT
Found at i:5327 original size:33 final size:34
Alignment explanation
Indices: 5264--5330 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
5254 TTATTTTAAA
* ** *
5264 TTTAAATTTAAATTTAATTTAAGTTTAAAATTAT
1 TTTAAATTTAAATTAAATAAAAGTTAAAAATTAT
5298 TTTAAATTTAAA-TAAATAAAAGTTAAAAATTAT
1 TTTAAATTTAAATTAAATAAAAGTTAAAAATTAT
5331 AAGCCCAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (34 bp):
TTTAAATTTAAATTAAATAAAAGTTAAAAATTAT
Found at i:5353 original size:27 final size:25
Alignment explanation
Indices: 5311--5370 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
5301 AAATTTAAAT
* * *
5311 AAATAAAAGTTAAAAATTATAAGCCC
1 AAATAAAAGGTAAAAA-TACAAACCC
*
5337 AAATTAAAAGGTCAAAATACAAACCC
1 AAA-TAAAAGGTAAAAATACAAACCC
5363 AAATAAAA
1 AAATAAAA
5371 TGTTTATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 5 0.17
26 13 0.45
27 11 0.38
ACGTcount: A:0.62, C:0.13, G:0.07, T:0.18
Consensus pattern (25 bp):
AAATAAAAGGTAAAAATACAAACCC
Found at i:7206 original size:29 final size:30
Alignment explanation
Indices: 7110--7219 Score: 108
Period size: 29 Copynumber: 3.8 Consensus size: 30
7100 AAAGGTCCCT
7110 GAACTTTCCAAAAATTA-CA--TTTGACCCC
1 GAACTTTCCAAAAATTACCATTTTTGA-CCC
* * *
7138 CAAATTTCCCAAAAATTACCATTTTAG-CCTC
1 GAACTTT-CCAAAAATTACCATTTTTGACC-C
*
7169 GAA-TATCCAAAAATTA-CATTTTTGACCC
1 GAACTTTCCAAAAATTACCATTTTTGACCC
7197 GAACTTTCC-AAAATTACCATTTT
1 GAACTTTCCAAAAATTACCATTTT
7220 ACCCTTTAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
28 23 0.34
29 32 0.48
30 6 0.09
31 3 0.04
32 3 0.04
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.33
Consensus pattern (30 bp):
GAACTTTCCAAAAATTACCATTTTTGACCC
Found at i:7241 original size:57 final size:58
Alignment explanation
Indices: 7116--7224 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 58
7106 CCCTGAACTT
*
7116 TCCAAAAATTACATTTGACCCCCAAATTTCCCAAAAATTACCATTTTAGCCTCGAATA
1 TCCAAAAATTACATTTGACCCCCAAATTTCCCAAAAATTACCATTTTACCCTCGAATA
* *
7174 TCCAAAAATTACATTTTTGA-CCCGAACTTT-CC-AAAATTACCATTTTACCCT
1 TCCAAAAATTACA--TTTGACCCCCAAATTTCCCAAAAATTACCATTTTACCCT
7225 TTAATGTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
57 18 0.39
58 15 0.33
59 8 0.17
60 5 0.11
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.32
Consensus pattern (58 bp):
TCCAAAAATTACATTTGACCCCCAAATTTCCCAAAAATTACCATTTTACCCTCGAATA
Found at i:7386 original size:17 final size:17
Alignment explanation
Indices: 7364--7398 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
7354 TTTTAATTAT
7364 TATTCTTTCATATTTTA
1 TATTCTTTCATATTTTA
* *
7381 TATTCTTTTATTTTTTA
1 TATTCTTTCATATTTTA
7398 T
1 T
7399 TTTTGTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTCTTTCATATTTTA
Found at i:19342 original size:209 final size:208
Alignment explanation
Indices: 18767--19732 Score: 950
Period size: 209 Copynumber: 4.7 Consensus size: 208
18757 TATCTGGAAC
* * *
18767 AGTGATGC-GATCATCTTCTTGATGAGATATTGAGAAGTAAACCAAATCAAT---CCAAGCTCAA
1 AGTGATGCAG-TCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAACAAAGCTCAA
* * * * * * *
18828 AGTGAGCAAATCTTTGAACCCTAGCTTCCAGATGAGATACTGAGAAGCAGTTCGAAACAATAAAA
65 TGCGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
* * * * * * *
18893 TGGTTGGCTTCCTGATGAGATACAGAGAAGTGAATCAGATCCGTCTTCCTGATTAGACACAGAGA
130 TGGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAAAGA
*
18958 AGTGGATTAAAACA
195 AGCGGATTAAAACA
* * * * *
18972 AGTGATGCGGTCGTCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACCAAAGCTCG
1 AGTGATGCAGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATG-AA-CAAAGCTCA
** * *
19037 ATGCGAGTGAAACTTCGGA-CCTCAGCTTCCTGATGAGATACT-ATGAAGCAGGTTGAAGCAATA
64 ATGCGAGCAAAACTTCGAACCCT-AGCTTCCTGATGAGATACTGA-GAAGCAGGTCGAAGCAATA
* * * * * *
19100 AAATAGTCAGCTTCCTGATGAGGTACAGAGAAGTGGACCAAATTCGTCTTCTTTATGAGATACAA
127 AAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAA
*
19165 AGAAGCGGATTGAAACA
192 AGAAGCGGATTAAAACA
* * * *
19182 AGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCGATGAAGTAAAGCTCGA
1 AGTGATGCAGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAA-CAAAGCTCAA
* * *
19247 TGTGAGCAAAACTTCGAACCCAAG-TGTCCTGATGAGATACTGAGAAGCAGGTCGAATCAATAAA
65 TGCGAGCAAAACTTCGAACCCTAGCT-TCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA
* * * ** **
19311 ATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCAAATGAGATACTGAG
129 ATGGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAAAG
*
19376 AAGCGGATTGAAACA
194 AAGCGGATTAAAACA
* * * * *
19391 AGTGAGGCAGTCATCTTATTGATGAGATACAGAGAAGTATA-CAAACTCAATGAAACAAGGCTCA
1 AGTGATGCAGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAA-TCAATG-AACAAAGCTCA
* * * * *
19455 ATGCAAGCGAAACTTCGAACCCTAGCTTCCTAATGAGATACTGAGAAGCAAGTTGAAGCAATAAA
64 ATGCGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA
* * * * *
19520 GTGGTT-GTCTTCCTGATGAGATATAGAGAAGTGGACCAAATCCGTTTTCTTGATGAGTTACAAA
129 ATGGTTAG-CTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAAA
* * *
19584 GAAGCAGATCAAAATA
193 GAAGCGGATTAAAACA
* * *
19600 AGTGATGCGGTCGTCTTC-T--T--G--A-T--G-AGTAGACCAAATCAATGAAACCAAAGCTCG
1 AGTGATGCAGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATG-AA-CAAAGCTCA
* * * ** *
19654 ATGTGAGCGAAACTTTGAA-CCTCAGCTTCCCAATGAGATA-TGGAGAAGCAGGTCGAAGCAAGA
64 ATGCGAGCAAAACTTCGAACCCT-AGCTTCCTGATGAGATACT-GAGAAGCAGGTCGAAGCAATA
* *
19717 AAATGGTCATCTTCCT
127 AAATGGTTAGCTTCCT
19733 AATGGTACGC
Statistics
Matches: 634, Mismatches: 107, Indels: 46
0.81 0.14 0.06
Matches are distributed among these distances:
198 18 0.03
199 74 0.12
202 1 0.00
204 1 0.00
205 44 0.07
206 2 0.00
208 7 0.01
209 313 0.49
210 174 0.27
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.24
Consensus pattern (208 bp):
AGTGATGCAGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAACAAAGCTCAAT
GCGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAT
GGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAAAGAA
GCGGATTAAAACA
Found at i:20167 original size:17 final size:17
Alignment explanation
Indices: 20145--20186 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
20135 ACCACTTTTA
20145 TAAATTTATGTTAAGA-T
1 TAAATTTATGTTAA-ATT
*
20162 TAAATTTATTTTAAATT
1 TAAATTTATGTTAAATT
20179 TAAATTTA
1 TAAATTTA
20187 AATTTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.04
17 22 0.96
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
TAAATTTATGTTAAATT
Found at i:20177 original size:11 final size:11
Alignment explanation
Indices: 20161--20209 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
20151 TATGTTAAGA
*
20161 TTAAATTTATT
1 TTAAATTTAAT
20172 TTAAATTTAAAT
1 TTAAATTT-AAT
*
20184 TTAAATTTAAA
1 TTAAATTTAAT
*
20195 TTAAGTTTAAAT
1 TTAAATTT-AAT
20207 TTA
1 TTA
20210 TTTTTAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 17 0.53
12 15 0.47
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:20180 original size:6 final size:6
Alignment explanation
Indices: 20161--20241 Score: 69
Period size: 6 Copynumber: 14.0 Consensus size: 6
20151 TATGTTAAGA
* *
20161 TTAAAT TT-ATT TTAAAT TTAAAT TTAAAT TTAAA- TTAAGT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
** * * * *
20207 TTATTT TTAAAT TCAAAA TT-ATT TTAAAC TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
20242 AAATAAAAGT
Statistics
Matches: 56, Mismatches: 16, Indels: 6
0.72 0.21 0.08
Matches are distributed among these distances:
5 11 0.20
6 45 0.80
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:20187 original size:23 final size:23
Alignment explanation
Indices: 20161--20245 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 23
20151 TATGTTAAGA
**
20161 TTAAATTTATTTTAAATTTAAAT
1 TTAAATTTAAATTAAATTTAAAT
*
20184 TTAAATTTAAATTAAGTTTAAAT
1 TTAAATTTAAATTAAATTTAAAT
** * *
20207 TTATTTTTAAATTCAAAATT-ATT
1 TTAAATTTAAATT-AAATTTAAAT
*
20230 TTAAACTTAAA-TAAAT
1 TTAAATTTAAATTAAAT
20246 AAAAGTCCAA
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
21 3 0.06
22 1 0.02
23 41 0.84
24 4 0.08
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (23 bp):
TTAAATTTAAATTAAATTTAAAT
Found at i:20193 original size:29 final size:29
Alignment explanation
Indices: 20161--20241 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 29
20151 TATGTTAAGA
20161 TTAAATTTATTTTAAATTTAAATTTAAAT
1 TTAAATTTATTTTAAATTTAAATTTAAAT
* * **
20190 TTAAATTAAGTTTAAATTTATTTTTAAAT
1 TTAAATTTATTTTAAATTTAAATTTAAAT
* * *
20219 TCAAAATTATTTTAAACTTAAAT
1 TTAAATTTATTTTAAATTTAAAT
20242 AAATAAAAGT
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (29 bp):
TTAAATTTATTTTAAATTTAAATTTAAAT
Found at i:20198 original size:17 final size:17
Alignment explanation
Indices: 20155--20209 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
20145 TAAATTTATG
*
20155 TTAAGATTAAATTT-ATT
1 TTAA-ATTAAATTTAAAT
20172 TTAAATTTAAATTTAAAT
1 TTAAA-TTAAATTTAAAT
*
20190 TTAAATTAAGTTTAAAT
1 TTAAATTAAATTTAAAT
20207 TTA
1 TTA
20210 TTTTTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 1 0.03
17 26 0.76
18 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (17 bp):
TTAAATTAAATTTAAAT
Found at i:20288 original size:26 final size:26
Alignment explanation
Indices: 20242--20301 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
20232 AAACTTAAAT
*
20242 AAATAAAAGTCCAAAATTACAAGCCC
1 AAATAAAAGTCCAAAATTACAAACCC
20268 AAATTAAAAGGTCC-AAA-TACAAACCC
1 AAA-TAAAA-GTCCAAAATTACAAACCC
20294 AAATAAAA
1 AAATAAAA
20302 TGTCTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 5 0.16
26 14 0.45
27 8 0.26
28 4 0.13
ACGTcount: A:0.58, C:0.20, G:0.07, T:0.15
Consensus pattern (26 bp):
AAATAAAAGTCCAAAATTACAAACCC
Found at i:22095 original size:29 final size:29
Alignment explanation
Indices: 22052--22508 Score: 206
Period size: 29 Copynumber: 15.8 Consensus size: 29
22042 CCCAAAAGGT
22052 CCCT-GAACTTTCCAAAAATTA-TATTTGA
1 CCCTCGAAC-TTCCAAAAATTACTATTTGA
* *
22080 CCCTCGAACTTCCCAAATATTACCATTT-A
1 CCCTCGAACTT-CCAAAAATTACTATTTGA
*
22109 GCCCT-GAA-TGTCCAAAAATTACATTTTTGA
1 -CCCTCGAACT-TCCAAAAATTAC-TATTTGA
* * *
22139 CCCT-AAACTTTCCAAAAATTACCATTTTA
1 CCCTCGAAC-TTCCAAAAATTACTATTTGA
22168 CCCTCGAA-TGTCCAAAAATTACATATTTGA
1 CCCTCGAACT-TCCAAAAATTAC-TATTTGA
** * *
22198 -CAACGAACTTTCC-AAAATTACCATTTTA
1 CCCTCGAAC-TTCCAAAAATTACTATTTGA
*
22226 CCCTCGAA-TGTCCAAAAATTACTATTTTA
1 CCCTCGAACT-TCCAAAAATTACTATTTGA
* * * *
22255 CCCTTGAACATCCAAAAATTACCATTTTA
1 CCCTCGAACTTCCAAAAATTACTATTTGA
*
22284 CCC-C-AAGTGTCCAAAAAATTATCGT-TTT-A
1 CCCTCGAACT-TCC-AAAAATTA-C-TATTTGA
* ** *
22313 CCCTCG-AGTGTCCAAAAATTACCGTTTTA
1 CCCTCGAACT-TCCAAAAATTACTATTTGA
* *
22342 CCC-CCAAATGTCCAAAAATTA-TATTTTTGA
1 CCCTCGAACT-TCCAAAAATTACTA--TTTGA
* * * *
22372 -CCTCAAACTTTCAAAAAATTACCATTTTA
1 CCCTCGAAC-TTCCAAAAATTACTATTTGA
* * *
22401 -CCTTGGA-TGTCCAAAAATTACATTTTTGA
1 CCCTCGAACT-TCCAAAAATTAC-TATTTGA
* * *
22430 CCCT-AAACTTTCC-AAAATTACCATTTTA
1 CCCTCGAAC-TTCCAAAAATTACTATTTGA
*
22458 CCCT-GAA-TGTCCAAAAATTACTATTTTA
1 CCCTCGAACT-TCCAAAAATTACTATTTGA
* * *
22486 CCCCCGAATTGTCTAAAAATTAC
1 CCCTCGAACT-TCCAAAAATTAC
22509 CGTTTTACCG
Statistics
Matches: 335, Mismatches: 53, Indels: 80
0.72 0.11 0.17
Matches are distributed among these distances:
26 1 0.00
27 7 0.02
28 72 0.21
29 171 0.51
30 79 0.24
31 5 0.01
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (29 bp):
CCCTCGAACTTCCAAAAATTACTATTTGA
Found at i:22148 original size:58 final size:58
Alignment explanation
Indices: 22052--22484 Score: 442
Period size: 58 Copynumber: 7.4 Consensus size: 58
22042 CCCAAAAGGT
* * * * *
22052 CCCTGAACTTTCCAAAAATT--ATATTTGACCCTCGAACTTCCCAAATATTACCA-TTTA
1 CCCTGAA-TGTCCAAAAATTACATTTTTGACCCT-AAACTTTCCAAAAATTACCATTTTA
22109 GCCCTGAATGTCCAAAAATTACATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTA
1 -CCCTGAATGTCCAAAAATTACATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTA
* * *
22168 CCCTCGAATGTCCAAAAATTACATATTTGACAAC-GAACTTTCC-AAAATTACCATTTTA
1 CCCT-GAATGTCCAAAAATTACATTTTTGAC-CCTAAACTTTCCAAAAATTACCATTTTA
* *
22226 CCCTCGAATGTCCAAAAATTAC-TATTTT-ACCCTTGAAC-ATCCAAAAATTACCATTTTA
1 CCCT-GAATGTCCAAAAATTACAT-TTTTGACCC-TAAACTTTCCAAAAATTACCATTTTA
* * ** * * *
22284 CCC-CAAGTGTCCAAAAAATTATC-GTTTT-ACCCTCGAGTGTCCAAAAATTACCGTTTTA
1 CCCTGAA-TGTCC-AAAAATTA-CATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTA
** * *
22342 CCCCCAAATGTCCAAAAATTATATTTTTGA-CCTCAAACTTTCAAAAAATTACCATTTTA
1 -CCCTGAATGTCCAAAAATTACATTTTTGACCCT-AAACTTTCCAAAAATTACCATTTTA
* *
22401 CCTTGGATGTCCAAAAATTACATTTTTGACCCTAAACTTTCC-AAAATTACCATTTTA
1 CCCTGAATGTCCAAAAATTACATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTA
22458 CCCTGAATGTCCAAAAATTACTATTTT
1 CCCTGAATGTCCAAAAATTAC-ATTTT
22485 ACCCCCGAAT
Statistics
Matches: 320, Mismatches: 35, Indels: 40
0.81 0.09 0.10
Matches are distributed among these distances:
56 3 0.01
57 58 0.18
58 176 0.55
59 80 0.25
60 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (58 bp):
CCCTGAATGTCCAAAAATTACATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTA
Found at i:22229 original size:87 final size:84
Alignment explanation
Indices: 22123--22542 Score: 255
Period size: 87 Copynumber: 4.8 Consensus size: 84
22113 TGAATGTCCA
*
22123 AAAATTA-CATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAAT
1 AAAATTACCA-TTTT-ACCCTAAA-TGTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAAT
*
22187 TACATATTTGACAACGAACTTTCC
63 TACAT-TTTGAC-ACAAACTTTCC
* * * **
22211 AAAATTACCATTTTACCCTCGAATGTCCAAAAATTACTATTTTACCCTTGAACATCCAAAAATTA
1 AAAATTACCATTTTACCCT-AAATGTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAATTA
* * * *
22276 CCATTTT-ACCCCAAGTGTCC
65 -CATTTTGACACAAACTTTCC
* * * * * * *
22296 AAAAAATTATCGTTTTACCCTCGAGTGTCCAAAAATTACCGTTTTACCCCCAAATGTCCAAAAAT
1 --AAAATTACCATTTTACCCT-AAATGTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAAT
* * *
22361 TATATTTTTGACCTCAAACTTTCAA
63 TACA-TTTTGA-CACAAACTTTC-C
* ** * *
22386 AAAATTACCATTTTACCTTGGATGTCCAAAAATTA-CATTTTTGACCCT-AAACTTTCC-AAAAT
1 AAAATTACCATTTTACCCTAAATGTCCAAAAATTACCA-TTTT-ACCCTCGAA-TGTCCAAAAAT
* * *
22448 TACCATTTT-ACCCTGAA-TGTCC
63 TA-CATTTTGACAC-AAACTTTCC
* * * * * *
22470 AAAAATTACTATTTTACCCCCGAATTGTCTAAAAATTACCGTTTTACCGCCCGACA--TCCAAAA
1 -AAAATTACCATTTTA--CCCTAAATGTCCAAAAATTACCATTTTACC-CTCGA-ATGTCCAAAA
22533 ATTACATTTT
61 ATTACATTTT
22543 TGACTCCATT
Statistics
Matches: 261, Mismatches: 49, Indels: 46
0.73 0.14 0.13
Matches are distributed among these distances:
85 26 0.10
86 19 0.07
87 162 0.62
88 44 0.17
89 10 0.04
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (84 bp):
AAAATTACCATTTTACCCTAAATGTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAATTAC
ATTTTGACACAAACTTTCC
Found at i:22354 original size:174 final size:173
Alignment explanation
Indices: 22062--22546 Score: 531
Period size: 174 Copynumber: 2.8 Consensus size: 173
22052 CCCTGAACTT
* * *
22062 TCCAAAAATTA-TATTTGACCCTCGAACTTCCCAAATATTACCA-TTTAGCCCTGAATGTCCAAA
1 TCCAAAAATTACTATTTTACCCTTGAACTT-CCAAAAATTACCATTTTA-CCCTGAATGTCCAAA
* ** * * * *
22125 AATTACATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAATTAC
64 AATTACAATTTT-ACCCTCGACTGTCCAAAAATTACCGTTTTACCCCCAAATGTCCAAAAATTAC
* * *
22190 ATATTTGACAACGAACTTTC-CAAAATTACCATTTTACCCTCGAATG
128 ATTTTTGACAACAAACTTTCAAAAAATTACCATTTTA-CCTCGAATG
* *
22236 TCCAAAAATTACTATTTTACCCTTGAACATCCAAAAATTACCATTTTACCC-CAAGTGTCCAAAA
1 TCCAAAAATTACTATTTTACCCTTGAACTTCCAAAAATTACCATTTTACCCTGAA-TGTCC-AAA
* * *
22300 AATTATC-GTTTTACCCTCGAGTGTCCAAAAATTACCGTTTTACCCCCAAATGTCCAAAAATTAT
64 AATTA-CAATTTTACCCTCGACTGTCCAAAAATTACCGTTTTACCCCCAAATGTCCAAAAATTAC
** * *
22364 ATTTTTGACCTCAAACTTTCAAAAAATTACCATTTTACCTTGGATG
128 ATTTTTGACAACAAACTTTCAAAAAATTACCATTTTACCTCGAATG
*
22410 TCCAAAAATTAC-ATTTTTGACCC-TAAACTTTCC-AAAATTACCATTTTACCCTGAATGTCCAA
1 TCCAAAAATTACTA-TTTT-ACCCTTGAAC-TTCCAAAAATTACCATTTTACCCTGAATGTCCAA
* * * * *
22472 AAATTACTATTTTACCCCCGAATTGTCTAAAAATTACCGTTTTACCGCCCGACA--TCCAAAAAT
63 AAATTACAATTTTACCCTCG-ACTGTCCAAAAATTACCGTTTTACC-CCC-AAATGTCCAAAAAT
22535 TACATTTTTGAC
125 TACATTTTTGAC
22547 TCCATTTATT
Statistics
Matches: 267, Mismatches: 30, Indels: 28
0.82 0.09 0.09
Matches are distributed among these distances:
172 1 0.00
173 21 0.08
174 184 0.69
175 58 0.22
176 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (173 bp):
TCCAAAAATTACTATTTTACCCTTGAACTTCCAAAAATTACCATTTTACCCTGAATGTCCAAAAA
TTACAATTTTACCCTCGACTGTCCAAAAATTACCGTTTTACCCCCAAATGTCCAAAAATTACATT
TTTGACAACAAACTTTCAAAAAATTACCATTTTACCTCGAATG
Found at i:25071 original size:7 final size:7
Alignment explanation
Indices: 25059--25084 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
25049 TATAGATATT
25059 AAATTTA
1 AAATTTA
25066 AAATTTA
1 AAATTTA
25073 AAATTTA
1 AAATTTA
25080 AAATT
1 AAATT
25085 AGTAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTTA
Found at i:25265 original size:2 final size:2
Alignment explanation
Indices: 25258--25289 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
25248 ACATCTAATC
25258 AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
25290 ACAAAATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25417 original size:12 final size:12
Alignment explanation
Indices: 25400--25425 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25390 AGAGTAGTAG
25400 AACTAAATCCTT
1 AACTAAATCCTT
25412 AACTAAATCCTT
1 AACTAAATCCTT
25424 AA
1 AA
25426 GGACTAGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (12 bp):
AACTAAATCCTT
Found at i:27098 original size:14 final size:14
Alignment explanation
Indices: 27060--27110 Score: 59
Period size: 13 Copynumber: 3.5 Consensus size: 14
27050 AATATTTACA
27060 TTCTTATTTTTTCTTC
1 TTCTT-TTTTTT-TTC
*
27076 TTTCCTTTTTTTTT-
1 -TTCTTTTTTTTTTC
27090 TTCTTTTTTTTTTC
1 TTCTTTTTTTTTTC
27104 TTCTTTT
1 TTCTTTT
27111 ATTAACAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 12 0.39
14 7 0.23
15 2 0.06
16 6 0.19
17 4 0.13
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (14 bp):
TTCTTTTTTTTTTC
Found at i:28904 original size:52 final size:52
Alignment explanation
Indices: 28829--29067 Score: 370
Period size: 52 Copynumber: 4.6 Consensus size: 52
28819 TAAATGAAAT
* *
28829 AGGTCCGATGACTATGTGCCATCGTGAGTATATGAATCCTTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
28881 AAGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
28933 AGGTCTGATGACTATGTGTCATCGTGAGTATATGGATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * *
28985 AGGTCCGATGACTATTTGTTATCGTGAGTATATGAATCTTTTACGAATTAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
29037 AGGTTCGATGACCATGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
29068 TAAATGAAAT
Statistics
Matches: 170, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 170 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:29115 original size:60 final size:60
Alignment explanation
Indices: 29016--29132 Score: 157
Period size: 60 Copynumber: 1.9 Consensus size: 60
29006 TCGTGAGTAT
* * * *
29016 ATGAATCTTTTACGAATTAAGAGGTTCGATGACCATGTGTCATCGTGAGTATTAAATGAA
1 ATGAATCTATTACGAATTAAGAGGTCCAATGACCATGTGTCATCGTGAGTATCAAATGAA
*
29076 ATGAATCTCATTACGGATTAA-AGGTCCAATGACTC-TGTGTCATCGTGAGTATCAAAT
1 ATGAATCT-ATTACGAATTAAGAGGTCCAATGAC-CATGTGTCATCGTGAGTATCAAAT
29133 ACACATGAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
60 39 0.78
61 11 0.22
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (60 bp):
ATGAATCTATTACGAATTAAGAGGTCCAATGACCATGTGTCATCGTGAGTATCAAATGAA
Found at i:29819 original size:21 final size:22
Alignment explanation
Indices: 29793--29863 Score: 71
Period size: 21 Copynumber: 3.4 Consensus size: 22
29783 GAAGTTTTTA
*
29793 GTATCGGTAGAATTAAG-ATTT
1 GTATCGGTAGAATTAAGCACTT
*
29814 GTATCGGTA-AA-AAAGTCACTT
1 GTATCGGTAGAATTAAG-CACTT
29835 GTATCGGTAGAATT--GTCACTT
1 GTATCGGTAGAATTAAG-CACTT
29856 GTATCGGT
1 GTATCGGT
29864 GGAGGTCTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
19 3 0.07
20 2 0.05
21 36 0.84
22 2 0.05
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (22 bp):
GTATCGGTAGAATTAAGCACTT
Found at i:30895 original size:21 final size:21
Alignment explanation
Indices: 30869--30923 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
30859 TAGTACAGAT
** *
30869 TTCTACCGGTACTTGTATTAG
1 TTCTACCGGTACAAGTATAAG
30890 TTCTACCGGTACAAGTATAAG
1 TTCTACCGGTACAAGTATAAG
*
30911 TTCTACCGATACA
1 TTCTACCGGTACA
30924 TGTCATGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (21 bp):
TTCTACCGGTACAAGTATAAG
Found at i:31699 original size:61 final size:61
Alignment explanation
Indices: 31573--31743 Score: 240
Period size: 61 Copynumber: 2.8 Consensus size: 61
31563 GTTTCACTCG
* * * * * *
31573 CATTTATTACTCACGATGACACAAAGTCATCAGACC-CTTGTT-CGCATTGGAACTCATTT
1 CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTGTTCCGTATAGGAACTCATTT
*
31632 CATTTAATAGTCACGATGACATATAGTCATCGGACCTCTTGTTCCGTATAGGAACTCATTT
1 CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTGTTCCGTATAGGAACTCATTT
*
31693 CATTTAATACTCACGATGACATATAGTCATCGAACCTCTTGTTTCC-TATAG
1 CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTG-TTCCGTATAG
31744 AAATTCATAT
Statistics
Matches: 100, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
59 31 0.31
60 6 0.06
61 59 0.59
62 4 0.04
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (61 bp):
CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTGTTCCGTATAGGAACTCATTT
Done.