Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011723.1 Kokia drynarioides strain JFW-HI SEQ_126717, 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: 71287
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:6024 original size:200 final size:202
Alignment explanation
Indices: 5648--6588 Score: 1082
Period size: 200 Copynumber: 4.7 Consensus size: 202
5638 CAAAGCAAGC
* * * * *
5648 AAAACCTTCGAACCCCAGC-TCTTTGATGAGACATTGAGAAGTAGGTCGAAGCAAT-AAAGGTTA
1 AAAATCTTCGAACCCCAACTTC-CTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTA
*
5711 GCTTCCTGATGAGATACTGA-AGAGTCAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGA
65 GCTTCCTGATGAGATACTGAGA-AGTCAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGA
* * * *
5775 GTTGAAACAAACAACG-CG-G-TTATCTTCCTGATGAGACATTGAGAAGAAGACCCAAACAAGGC
129 ATTGAAACAAACAGCGACGTGATCATCTTCCTGATGAGACACT--GAAGAAGACCCAAACAAGGC
5837 TCAAAGTGCGT
192 TCAAAGTGCGT
*
5848 AAAATCTTCGAA-CCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAAAAGGTTAG
1 AAAATCTTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
* **
5912 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTTTTGATGAGATACAGAGAAGCGAAT
66 CTTCCTGATGAGATACTGAGAAGTCAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
* * *
5977 TGAAACAAACAGCGATGTGATCATCTTCCTGATGAGGCACTAAGAAGAAGACCCAAACGAGGCTC
131 TGAAACAAACAGCGACGTGATCATCTTCCTGATGAGACACT--GAAGAAGACCCAAACAAGGCTC
*
6042 AAAGTGAGT
194 AAAGTGCGT
* *
6051 AAAATCTTCGAACCCCAGC-TCCTTGATGAGATA-TCGAGAAGCAGGTCGAAGCAAT-AAAGGTT
1 AAAATCTTCGAACCCCAACTTCC-TGATGAGACACT-GAGAAGCAGGTCGAAGCAATAAAAGGTT
* *
6113 AGCTTCCTGATGAGATACTGA-AGAGTCAACCAAATTCGCCTTCCTGATGAGATACAGAGAACCG
64 AGCTTCCTGATGAGATACTGAGA-AGTCAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
* * *
6177 AGTTAAAACAAACA---ACGCGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACAAGG
128 AATTGAAACAAACAGCGACGTGATCATCTTCCTGATGAGACACT--GAAGAAGACCCAAACAAGG
* * *
6239 CTTAAAGTGTGC
191 CTCAAAGTGCGT
* * * *
6251 AAAATCTTCAAACCCCAACTTCTTGATGAGACACTGAGAAGTAGGTCGAAGCGATAAAAGGTTAG
1 AAAATCTTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
* * * *
6316 CTTCCTGATGAGATACTGAGAAGTAAACCAAATTCGTCTTCCTGATGAAATACTGAGGAGCGAAT
66 CTTCCTGATGAGATACTGAGAAGTCAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
* * * * *
6381 TGAAACAAACAGTGATGTGATCATCTTCCTGATGAGGCACTGAGAAGAAGTCCCAAACGAGGCTC
131 TGAAACAAACAGCGACGTGATCATCTTCCTGATGAGACACT--GAAGAAGACCCAAACAAGGCTC
*
6446 GAAATGAGCG-
194 -AAA-GTGCGT
* * * ** *
6456 -AAATCTTCGAACCCCAGCTT-CT--T--G--ATTGAGAGGCAGGTTAAAGCAATAAAATGATTA
1 AAAATCTTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA-GGTTA
* * * ** * *
6513 GCTTCTTGATGAAATACTAAGAAGTGGACCAAATTCGTCTTTCTGATGAGATACAGAGAAGCGTA
65 GCTTCCTGATGAGATACTGAGAAGTCAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
6578 TTGAAACAAAC
130 TTGAAACAAAC
6589 GATGTAGTCG
Statistics
Matches: 642, Mismatches: 79, Indels: 42
0.84 0.10 0.06
Matches are distributed among these distances:
197 21 0.03
198 70 0.11
199 35 0.05
200 189 0.29
201 81 0.13
202 3 0.00
203 141 0.22
204 96 0.15
205 3 0.00
206 3 0.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (202 bp):
AAAATCTTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
CTTCCTGATGAGATACTGAGAAGTCAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
TGAAACAAACAGCGACGTGATCATCTTCCTGATGAGACACTGAAGAAGACCCAAACAAGGCTCAA
AGTGCGT
Found at i:6467 original size:404 final size:402
Alignment explanation
Indices: 5645--6572 Score: 1404
Period size: 403 Copynumber: 2.3 Consensus size: 402
5635 CCACAAAGCA
* * * *
5645 AGCAAAACCTTCGAACCCCAGCTCTTTGATGAGACATTGAGAAGTAGGTCGAAGCAATAAAGGTT
1 AGCAAAATCTTCGAACCCCAGCTCCTTGATGAGATA-TGAGAAGCAGGTCGAAGCAATAAAGGTT
*
5710 AGCTTCCTGATGAGATACTGAAGAGTCAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGA
65 AGCTTCCTGATGAGATACTGAAGAGTCAACCAAATTCGCCTTCCTGATGAGATACAGAGAACCGA
* * * *
5775 GTTGAAACAAACAACGCGGTTATCTTCCTGATGAGACATTGAGAAGAAGACCCAAACAAGGCTCA
130 GTTAAAACAAACAACGCGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACAAGGCTCA
* *
5840 AAGTGCGTAAAATCTTCGAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAAA
195 AAGTGCGCAAAATCTTCAAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAAA
* ** *
5905 AGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTTTTGATGAGATACAGAGA
260 AGGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAATTCGTCTTCCTGATGAAATACAGAGA
5970 AGCGAATTGAAACAAACAGCGATGTGATCATCTTCCTGATGAGGCACTAAGAAGAAGACCCAAAC
325 AGCGAATTGAAACAAACAGCGATGTGATCATCTTCCTGATGAGGCACTAAGAAGAAGACCCAAAC
6035 GAGGCTCAAAGTG
390 GAGGCTCAAAGTG
*
6048 AGTAAAATCTTCGAACCCCAGCTCCTTGATGAGATATCGAGAAGCAGGTCGAAGCAATAAAGGTT
1 AGCAAAATCTTCGAACCCCAGCTCCTTGATGAGATAT-GAGAAGCAGGTCGAAGCAATAAAGGTT
6113 AGCTTCCTGATGAGATACTGAAGAGTCAACCAAATTCGCCTTCCTGATGAGATACAGAGAACCGA
65 AGCTTCCTGATGAGATACTGAAGAGTCAACCAAATTCGCCTTCCTGATGAGATACAGAGAACCGA
*
6178 GTTAAAACAAACAACGCGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACAAGGCTTA
130 GTTAAAACAAACAACGCGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACAAGGCTCA
* * *
6243 AAGTGTGCAAAATCTTCAAACCCCAACTTCTTGATGAGACACTGAGAAGTAGGTCGAAGCGATAA
195 AAGTGCGCAAAATCTTCAAA-CCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAA
*
6308 AAGGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAATTCGTCTTCCTGATGAAATACTGAG
259 AAGGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAATTCGTCTTCCTGATGAAATACAGAG
* * * *
6373 GAGCGAATTGAAACAAACAGTGATGTGATCATCTTCCTGATGAGGCACTGAGAAGAAGTCCCAAA
324 AAGCGAATTGAAACAAACAGCGATGTGATCATCTTCCTGATGAGGCACTAAGAAGAAGACCCAAA
6438 CGAGGCTCGAAA-TG
389 CGAGGCTC-AAAGTG
* * * ** *
6452 AGCGAAATCTTCGAACCCCAGCTTC-T--T--GAT-TGAGAGGCAGGTTAAAGCAATAAAATGAT
1 AGCAAAATCTTCGAACCCCAGCTCCTTGATGAGATATGAGAAGCAGGTCGAAGCAAT-AAA-GGT
* * ** * *
6511 TAGCTTCTTGATGAAATACT-AAGAAGTGGACCAAATTCGTCTTTCTGATGAGATACAGAGAA
64 TAGCTTCCTGATGAGATACTGAAG-AGTCAACCAAATTCGCCTTCCTGATGAGATACAGAGAA
6573 GCGTATTGAA
Statistics
Matches: 481, Mismatches: 38, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
397 17 0.04
398 7 0.01
399 57 0.12
401 1 0.00
402 1 0.00
403 200 0.42
404 195 0.41
405 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (402 bp):
AGCAAAATCTTCGAACCCCAGCTCCTTGATGAGATATGAGAAGCAGGTCGAAGCAATAAAGGTTA
GCTTCCTGATGAGATACTGAAGAGTCAACCAAATTCGCCTTCCTGATGAGATACAGAGAACCGAG
TTAAAACAAACAACGCGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACAAGGCTCAA
AGTGCGCAAAATCTTCAAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAAAA
GGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAATTCGTCTTCCTGATGAAATACAGAGAA
GCGAATTGAAACAAACAGCGATGTGATCATCTTCCTGATGAGGCACTAAGAAGAAGACCCAAACG
AGGCTCAAAGTG
Found at i:6720 original size:404 final size:402
Alignment explanation
Indices: 5645--6750 Score: 1312
Period size: 403 Copynumber: 2.7 Consensus size: 402
5635 CCACAAAGCA
* * * * * * *
5645 AGCAAAACCTTCGAACCCCAGCTCTTTGATGAGACATTGAGAAGTAGGTCGAAGCAATAAAGGTT
1 AGCAAAATCTTCGAACCCCAGCTCCTT-AT-AGATATCGAGAAGCAGGTCAAAGCAATAAAGATT
* *
5710 AGCTTCCTGATGAGATACTGAAGAGTCAACCAAATTCGCCTTCCTGATGAGATACAGAGAAGCGA
64 AGCTTCCTGATGAAATACTGAAGAGTCAACCAAATTCGCCTTCCTGATGAGATACAGAGAACCGA
* * * * * * *
5775 GTTGAAACAAACAACGCGGTTATCTTCCTGATGAGACATTGAGAAGAAGACCCAAACAAGGCTCA
129 GTTAAAACAAACAACGAGATCATCTTCCTGATGAGACACTGAGAAGAAGACACAAACAAGGCTGA
* * * * *
5840 AAGTGCGTAAAATCTTCGAA-CCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCGATAA
194 AAGTGAGCAAAATCTTCAAACCCCAACTTCTTGATAAGACACTGAGAAGCAGGTCGAAGCGATAA
* ** *
5904 AAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTTTTGATGAGATACAGAG
259 AAGGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAATTCGTCTTCCTGATGAAATACAGAG
5969 AAGCGAATTGAAACAAACAGCGATGTGATCATCTTCCTGATGAGGCACTAAGAAGAAGACCCAAA
324 AAGCGAATTGAAACAAACAGCGATGTGATCATCTTCCTGATGAGGCACTAAGAAGAAGACCCAAA
6034 CGAGGCTCAAAGTG
389 CGAGGCTCAAAGTG
* * *
6048 AGTAAAATCTTCGAACCCCAGCTCCTTGATGAGATATCGAGAAGCAGGTCGAAGCAATAAAGGTT
1 AGCAAAATCTTCGAACCCCAGCTCCTT-AT-AGATATCGAGAAGCAGGTCAAAGCAATAAAGATT
*
6113 AGCTTCCTGATGAGATACTGAAGAGTCAACCAAATTCGCCTTCCTGATGAGATACAGAGAACCGA
64 AGCTTCCTGATGAAATACTGAAGAGTCAACCAAATTCGCCTTCCTGATGAGATACAGAGAACCGA
* * *
6178 GTTAAAACAAACAACGCGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACAAGGCTTA
129 GTTAAAACAAACAACGAGATCATCTTCCTGATGAGACACTGAGAAGAAGACACAAACAAGGCTGA
* * *
6243 AAGTGTGCAAAATCTTCAAACCCCAACTTCTTGATGAGACACTGAGAAGTAGGTCGAAGCGATAA
194 AAGTGAGCAAAATCTTCAAACCCCAACTTCTTGATAAGACACTGAGAAGCAGGTCGAAGCGATAA
*
6308 AAGGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAATTCGTCTTCCTGATGAAATACTGAG
259 AAGGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAATTCGTCTTCCTGATGAAATACAGAG
* * * *
6373 GAGCGAATTGAAACAAACAGTGATGTGATCATCTTCCTGATGAGGCACTGAGAAGAAGTCCCAAA
324 AAGCGAATTGAAACAAACAGCGATGTGATCATCTTCCTGATGAGGCACTAAGAAGAAGACCCAAA
6438 CGAGGCTCGAAA-TG
389 CGAGGCTC-AAAGTG
* * * *
6452 AGCGAAATCTTCGAACCCCAGCTTC-T-T-GAT-T-GAGAGGCAGGTTAAAGCAATAAAATGATT
1 AGCAAAATCTTCGAACCCCAGCTCCTTATAGATATCGAGAAGCAGGTCAAAGCAAT-AAA-GATT
* ** * * *
6512 AGCTTCTTGATGAAATACT-AAGAAGTGGACCAAATTCGTCTTTCTGATGAGATACAGAGAAGCG
64 AGCTTCCTGATGAAATACTGAAG-AGTCAACCAAATTCGCCTTCCTGATGAGATACAGAGAACCG
* * * * *
6576 TA-TTGAAACAAACGATGTAG-TCGTCTT-CTAGATGAGATACTGAGAAGAAGATCAAAACAAAC
128 -AGTTAAAACAAACAACG-AGATCATCTTCCT-GATGAGACACTGAGAAGAAGA-C---ACAAA-
* * * * *
6638 CCAA-GCTCGATA-TGAGC-AAATCTTCGAACCCC-ACTATCTT-AGTAATATACTGGGAAGCAG
185 -CAAGGCT-GAAAGTGAGCAAAATCTTCAAACCCCAACT-TCTTGA-TAAGACACTGAGAAGCAG
** *
6698 GTCGAAGTAATAAAACGGTTAGC-TCCTAGATGAGATATTGAGAAG-AAAGCCAA
246 GTCGAAGCGATAAAA-GGTTAGCTTCCT-GATGAGATACTGAGAAGTAAA-CCAA
6751 GTCAATGAAA
Statistics
Matches: 624, Mismatches: 59, Indels: 39
0.86 0.08 0.05
Matches are distributed among these distances:
397 17 0.03
398 9 0.01
399 97 0.16
400 3 0.00
401 1 0.00
402 4 0.01
403 256 0.41
404 229 0.37
405 8 0.01
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (402 bp):
AGCAAAATCTTCGAACCCCAGCTCCTTATAGATATCGAGAAGCAGGTCAAAGCAATAAAGATTAG
CTTCCTGATGAAATACTGAAGAGTCAACCAAATTCGCCTTCCTGATGAGATACAGAGAACCGAGT
TAAAACAAACAACGAGATCATCTTCCTGATGAGACACTGAGAAGAAGACACAAACAAGGCTGAAA
GTGAGCAAAATCTTCAAACCCCAACTTCTTGATAAGACACTGAGAAGCAGGTCGAAGCGATAAAA
GGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAATTCGTCTTCCTGATGAAATACAGAGAA
GCGAATTGAAACAAACAGCGATGTGATCATCTTCCTGATGAGGCACTAAGAAGAAGACCCAAACG
AGGCTCAAAGTG
Found at i:7104 original size:17 final size:17
Alignment explanation
Indices: 7073--7148 Score: 109
Period size: 17 Copynumber: 4.5 Consensus size: 17
7063 CTATTGGAAA
7073 TTAAATTTA-TTTAAAT
1 TTAAATTTATTTTAAAT
*
7089 TTAAGTTTATTTTAAAT
1 TTAAATTTATTTTAAAT
*
7106 TTAAATTTATTTGAAAT
1 TTAAATTTATTTTAAAT
* *
7123 TTAAATTTATTATAAAA
1 TTAAATTTATTTTAAAT
7140 TTAAATTTA
1 TTAAATTTA
7149 GAAAGTCCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
16 8 0.15
17 45 0.85
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:7124 original size:7 final size:6
Alignment explanation
Indices: 7073--7148 Score: 58
Period size: 6 Copynumber: 13.5 Consensus size: 6
7063 CTATTGGAAA
* *
7073 TTAAAT TT--AT TTAAAT TTAAGT TT-ATT TTAAAT TTAAAT TT--AT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
7116 TTGAAAT TTAAAT TT--AT TATAAAA TTAAAT TTA
1 TT-AAAT TTAAAT TTAAAT T-TAAAT TTAAAT TTA
7149 GAAAGTCCAA
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
4 11 0.20
5 5 0.09
6 34 0.61
7 6 0.11
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:7132 original size:34 final size:33
Alignment explanation
Indices: 7070--7148 Score: 122
Period size: 34 Copynumber: 2.4 Consensus size: 33
7060 GACCTATTGG
* *
7070 AAATTAAATTTATTTAAATTTAAGTTTATTTTA
1 AAATTAAATTTATTTAAATTTAAATTTATTATA
*
7103 AATTTAAATTTATTTGAAATTTAAATTTATTATA
1 AAATTAAATTTATTT-AAATTTAAATTTATTATA
7137 AAATTAAATTTA
1 AAATTAAATTTA
7149 GAAAGTCCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 14 0.34
34 27 0.66
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.52
Consensus pattern (33 bp):
AAATTAAATTTATTTAAATTTAAATTTATTATA
Found at i:7259 original size:15 final size:15
Alignment explanation
Indices: 7180--7249 Score: 113
Period size: 15 Copynumber: 4.7 Consensus size: 15
7170 AAAACAAAGT
7180 CCAATTACAAATGGC
1 CCAATTACAAATGGC
*
7195 CCAATTACAAACGGC
1 CCAATTACAAATGGC
7210 CCAATTACAAATGGC
1 CCAATTACAAATGGC
* *
7225 TCAAATACAAATGGC
1 CCAATTACAAATGGC
7240 CCAATTACAA
1 CCAATTACAA
7250 GCGACCCAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 49 1.00
ACGTcount: A:0.43, C:0.27, G:0.11, T:0.19
Consensus pattern (15 bp):
CCAATTACAAATGGC
Found at i:7892 original size:16 final size:16
Alignment explanation
Indices: 7871--7924 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
7861 TTAATGACTA
7871 TTAATAATAAATA-TT
1 TTAATAATAAATATTT
*
7886 TT--TAAT-AATATTA
1 TTAATAATAAATATTT
*
7899 ATAATAATAAATATTT
1 TTAATAATAAATATTT
7915 TTAATAATAA
1 TTAATAATAA
7925 TAAATAACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
12 4 0.13
13 6 0.19
15 6 0.19
16 15 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAATAATAAATATTT
Found at i:7911 original size:19 final size:19
Alignment explanation
Indices: 7889--7946 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
7879 AAATATTTTT
7889 AATAATATTAATAATAATA
1 AATAATATTAATAATAATA
* *
7908 AATATTTTTAATAATAATA
1 AATAATATTAATAATAATA
* *
7927 AATAACATT-TTAATAATA
1 AATAATATTAATAATAATA
7945 AA
1 AA
7947 AAGGGAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 10 0.30
19 23 0.70
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AATAATATTAATAATAATA
Found at i:7922 original size:22 final size:21
Alignment explanation
Indices: 7896--7945 Score: 77
Period size: 19 Copynumber: 2.5 Consensus size: 21
7886 TTTAATAATA
*
7896 TTAATAATAATAAAT-A-TTT
1 TTAATAATAATAAATAACATT
7915 TTAATAATAATAAATAACATT
1 TTAATAATAATAAATAACATT
7936 TTAATAATAA
1 TTAATAATAA
7946 AAAGGGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 15 0.54
20 1 0.04
21 12 0.43
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAATAATAATAAATAACATT
Found at i:14016 original size:14 final size:14
Alignment explanation
Indices: 13997--14024 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13987 CCGACTTAAG
13997 AAAACCCACTCAAC
1 AAAACCCACTCAAC
14011 AAAACCCACTCAAC
1 AAAACCCACTCAAC
14025 TTGGTCGTAA
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:0.50, C:0.43, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAACCCACTCAAC
Found at i:17261 original size:37 final size:37
Alignment explanation
Indices: 17211--17367 Score: 136
Period size: 40 Copynumber: 4.1 Consensus size: 37
17201 TACATCTAAA
*
17211 TATTCGAGCTTTGTGCCTATTAGGCTTCGTGTCGGTG
1 TATTCGAGCTTTGTGCCTAGTAGGCTTCGTGTCGGTG
* *
17248 TATTCGTGCTTTGTGCCTAGTAGGCTTCGTGTTGGTG
1 TATTCGAGCTTTGTGCCTAGTAGGCTTCGTGTCGGTG
** * * *
17285 TATTTATC-AGGCTTAATGCCTAGAAGGCTTCATGTCGATG
1 TA--T-TCGA-GCTTTGTGCCTAGTAGGCTTCGTGTCGGTG
* * * *
17325 TATTTATCGGGCTTAGTGCATAGCAGGCTTCGTGTCGGTG
1 TA--T-TCGAGCTTTGTGCCTAGTAGGCTTCGTGTCGGTG
17365 TAT
1 TAT
17368 ACCATCAGGC
Statistics
Matches: 99, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
37 36 0.36
38 1 0.01
39 1 0.01
40 61 0.62
ACGTcount: A:0.15, C:0.17, G:0.29, T:0.39
Consensus pattern (37 bp):
TATTCGAGCTTTGTGCCTAGTAGGCTTCGTGTCGGTG
Found at i:17327 original size:40 final size:40
Alignment explanation
Indices: 17232--17367 Score: 145
Period size: 40 Copynumber: 3.5 Consensus size: 40
17222 TGTGCCTATT
** *
17232 AGGCTTCGTGTCGGTGTA--T-TC-GTGCTTTGTGCCTAGT
1 AGGCTTCGTGTCGGTGTATTTATCAG-GCTTAATGCCTAGA
*
17269 AGGCTTCGTGTTGGTGTATTTATCAGGCTTAATGCCTAGA
1 AGGCTTCGTGTCGGTGTATTTATCAGGCTTAATGCCTAGA
* * * * * *
17309 AGGCTTCATGTCGATGTATTTATCGGGCTTAGTGCATAGC
1 AGGCTTCGTGTCGGTGTATTTATCAGGCTTAATGCCTAGA
17349 AGGCTTCGTGTCGGTGTAT
1 AGGCTTCGTGTCGGTGTAT
17368 ACCATCAGGC
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
37 17 0.21
39 1 0.01
40 63 0.77
41 1 0.01
ACGTcount: A:0.15, C:0.17, G:0.30, T:0.38
Consensus pattern (40 bp):
AGGCTTCGTGTCGGTGTATTTATCAGGCTTAATGCCTAGA
Found at i:24423 original size:92 final size:87
Alignment explanation
Indices: 24282--24537 Score: 332
Period size: 89 Copynumber: 2.8 Consensus size: 87
24272 TCTCACAAAC
** * *
24282 TGTCCAATGTGGTATTTATACTTTGAAAATGTCTAATGTAGTACATAAACTATCAATATGCGTTT
1 TGTCCAATGTGGTACATGTACTTTGAAAATGTCTAATGTGGTA-ATAAACTAT-AATATGCGTTT
24347 TATTATGGTATTTGTATTTTTATAAAA
64 TATTATGGTATTTG---TTTTATAAAA
* *
24374 TGTCTAATGTGGTACATGTACTTTGAAAATGTCTAATGTGGTAATTAAACTATAGATATGCATTT
1 TGTCCAATGTGGTACATGTACTTTGAAAATGTCTAATGTGGTAA-TAAACTATA-ATATGCGTTT
* *
24439 TATTACGATATTTGTTTTATAAAA
64 TATTATGGTATTTGTTTTATAAAA
* * *
24463 TGTCCAATGTGGTACATGTACTTTGAAAATGTCCAATGTGATAACTAAACTATTAATATGTGTTT
1 TGTCCAATGTGGTACATGTACTTTGAAAATGTCTAATGTGGTAA-TAAACTA-TAATATGCGTTT
24528 TATTATGGTA
64 TATTATGGTA
24538 CATGATGTTA
Statistics
Matches: 145, Mismatches: 16, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
89 74 0.51
90 2 0.01
91 2 0.01
92 67 0.46
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.43
Consensus pattern (87 bp):
TGTCCAATGTGGTACATGTACTTTGAAAATGTCTAATGTGGTAATAAACTATAATATGCGTTTTA
TTATGGTATTTGTTTTATAAAA
Found at i:26580 original size:54 final size:55
Alignment explanation
Indices: 26493--26605 Score: 201
Period size: 54 Copynumber: 2.1 Consensus size: 55
26483 AACTTTAGGA
*
26493 ATTGCTATGACTTTAGTATTGGTATTTGTGCTTATATTATTACCTATGTGTTTGG
1 ATTGCTATGACTTTAGAATTGGTATTTGTGCTTATATTATTACCTATGTGTTTGG
*
26548 ATTG-TATGAGTTTAGAATTGGTATTTGTGCTTATATTATTACCTATGTGTTTGG
1 ATTGCTATGACTTTAGAATTGGTATTTGTGCTTATATTATTACCTATGTGTTTGG
26602 ATTG
1 ATTG
26606 AATGGTTGTT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
54 52 0.93
55 4 0.07
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.50
Consensus pattern (55 bp):
ATTGCTATGACTTTAGAATTGGTATTTGTGCTTATATTATTACCTATGTGTTTGG
Found at i:29628 original size:32 final size:32
Alignment explanation
Indices: 29586--29648 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
29576 TAAACACTAG
* *
29586 GTACTGTAATAAAACGCATATTGATAGTTCAA
1 GTACTATAATAAAACACATATTGATAGTTCAA
*
29618 GTACTATAATAAAATACATATTGATAGTTCA
1 GTACTATAATAAAACACATATTGATAGTTCA
29649 TATATTACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (32 bp):
GTACTATAATAAAACACATATTGATAGTTCAA
Found at i:29689 original size:30 final size:31
Alignment explanation
Indices: 29655--29716 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
29645 TTCATATATT
*
29655 ACATTGGACATTTT-TCAAAGTATAAGTACC
1 ACATTGAACATTTTATCAAAGTATAAGTACC
* * *
29685 ACATTGAATATTTTATGAAAGTATAGGTACC
1 ACATTGAACATTTTATCAAAGTATAAGTACC
29716 A
1 A
29717 AGTGTGACAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (31 bp):
ACATTGAACATTTTATCAAAGTATAAGTACC
Found at i:43759 original size:36 final size:36
Alignment explanation
Indices: 43712--43786 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
43702 TGTGGCATCA
43712 TGTAGCTCGGACTTGGCAATCGGATTGGGTATGGGG
1 TGTAGCTCGGACTTGGCAATCGGATTGGGTATGGGG
43748 TGTAGCTCGGACTTGGCAATCGGATTGGGTATGGGG
1 TGTAGCTCGGACTTGGCAATCGGATTGGGTATGGGG
43784 TGT
1 TGT
43787 GGCATAATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.16, C:0.13, G:0.41, T:0.29
Consensus pattern (36 bp):
TGTAGCTCGGACTTGGCAATCGGATTGGGTATGGGG
Found at i:46434 original size:2 final size:2
Alignment explanation
Indices: 46429--46482 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
46419 TATATGGTTA
46429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46471 AT AT AT AT AT AT
1 AT AT AT AT AT AT
46483 CAGTTAAAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57431 original size:18 final size:18
Alignment explanation
Indices: 57408--57445 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
57398 TAATACAATT
*
57408 TTATTCG-GTTTATTTGAA
1 TTATTCGAG-TTATTCGAA
57426 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
57444 TT
1 TT
57446 CGAAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.53
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:58898 original size:204 final size:204
Alignment explanation
Indices: 58548--58955 Score: 771
Period size: 204 Copynumber: 2.0 Consensus size: 204
58538 AGAAAAGCAA
* *
58548 CAGCTGAAATGGAATCTATTCTGTAGAATATATATTATATATACACATTCTTGAAGTTTCAGATC
1 CAGCTGAAATGGAATCTATTCCGTAGAATATATATTATATATACACATTCTTGAAGCTTCAGATC
* * *
58613 CCATGTTCGGCTCTCTGTCTTGCACTAAACCCTCAAAAGAATGCAATTTTTATGTGAATGTTTGC
66 CCATGTTCGGCTCTCTGTCTTCCACTAAACCCTCAAAAGAATGCAATTTCTATGCGAATGTTTGC
58678 CAACACATCCATGATATATGAAGATGATGCTGCATCTGCAAAGCAACAAGGAAACTTACCAGCTC
131 CAACACATCCATGATATATGAAGATGATGCTGCATCTGCAAAGCAACAAGGAAACTTACCAGCTC
58743 CTCTATTAT
196 CTCTATTAT
58752 CAGCTGAAATGGAATCTATTCCGTAGAATATATATTATATATACACATTCTTGAAGCTTCAGATC
1 CAGCTGAAATGGAATCTATTCCGTAGAATATATATTATATATACACATTCTTGAAGCTTCAGATC
58817 CCATGTTCGGCTCTCTGTCTTCCACTAAACCCTCAAAAGAATGCAATTTCTATGCGAATGTTTGC
66 CCATGTTCGGCTCTCTGTCTTCCACTAAACCCTCAAAAGAATGCAATTTCTATGCGAATGTTTGC
58882 CAACACATCCATGATATATGAAGATGATGCTGCATCTGCAAAGCAACAAGGAAACTTACCAGCTC
131 CAACACATCCATGATATATGAAGATGATGCTGCATCTGCAAAGCAACAAGGAAACTTACCAGCTC
58947 CTCTATTAT
196 CTCTATTAT
58956 TGACTGATAA
Statistics
Matches: 199, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
204 199 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (204 bp):
CAGCTGAAATGGAATCTATTCCGTAGAATATATATTATATATACACATTCTTGAAGCTTCAGATC
CCATGTTCGGCTCTCTGTCTTCCACTAAACCCTCAAAAGAATGCAATTTCTATGCGAATGTTTGC
CAACACATCCATGATATATGAAGATGATGCTGCATCTGCAAAGCAACAAGGAAACTTACCAGCTC
CTCTATTAT
Found at i:61203 original size:108 final size:108
Alignment explanation
Indices: 61014--61224 Score: 422
Period size: 108 Copynumber: 2.0 Consensus size: 108
61004 GAAAGTATGA
61014 ACAGATACTACCATGTAATCACATTAGTATATTAAAAAAATGTGAATGGAATTGCTAATATATAA
1 ACAGATACTACCATGTAATCACATTAGTATATTAAAAAAATGTGAATGGAATTGCTAATATATAA
61079 AAGAAATTTAAATGAATAGTTGATATTAAGTGAATAATATTGG
66 AAGAAATTTAAATGAATAGTTGATATTAAGTGAATAATATTGG
61122 ACAGATACTACCATGTAATCACATTAGTATATTAAAAAAATGTGAATGGAATTGCTAATATATAA
1 ACAGATACTACCATGTAATCACATTAGTATATTAAAAAAATGTGAATGGAATTGCTAATATATAA
61187 AAGAAATTTAAATGAATAGTTGATATTAAGTGAATAAT
66 AAGAAATTTAAATGAATAGTTGATATTAAGTGAATAAT
61225 TGTTACATGA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 103 1.00
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.32
Consensus pattern (108 bp):
ACAGATACTACCATGTAATCACATTAGTATATTAAAAAAATGTGAATGGAATTGCTAATATATAA
AAGAAATTTAAATGAATAGTTGATATTAAGTGAATAATATTGG
Found at i:69266 original size:31 final size:31
Alignment explanation
Indices: 69231--69326 Score: 76
Period size: 31 Copynumber: 3.1 Consensus size: 31
69221 TTGGTATTTG
69231 AACTTGAAATTTTTTCCTAATTTGGTACCTA
1 AACTTGAAATTTTTTCCTAATTTGGTACCTA
** *
69262 AACTT--TTTTTTTGGTCC-AATTTGATA-CTCA
1 AACTTGAAATTTTT--TCCTAATTTGGTACCT-A
* *
69292 AACTTGACACTTTTTT-CTAATTTGGTACCCA
1 AACTTGA-AATTTTTTCCTAATTTGGTACCTA
69323 AACT
1 AACT
69327 AAACACTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
29 7 0.14
30 15 0.30
31 22 0.44
32 1 0.02
33 5 0.10
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.45
Consensus pattern (31 bp):
AACTTGAAATTTTTTCCTAATTTGGTACCTA
Found at i:69333 original size:31 final size:31
Alignment explanation
Indices: 69279--69338 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
69269 TTTTTGGTCC
* **
69279 AATTTGATACTCAAACTTGACACTTTTTTCT
1 AATTTGATACCCAAACTAAACACTTTTTTCT
*
69310 AATTTGGTACCCAAACTAAACACTTTTTT
1 AATTTGATACCCAAACTAAACACTTTTTT
69339 TTTAAGTTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.42
Consensus pattern (31 bp):
AATTTGATACCCAAACTAAACACTTTTTTCT
Done.