Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013710.1 Kokia drynarioides strain JFW-HI SEQ_128738, 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: 78468
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 332 characters in sequence are not A, C, G, or T
Found at i:10826 original size:494 final size:484
Alignment explanation
Indices: 9899--10866 Score: 1846
Period size: 494 Copynumber: 2.0 Consensus size: 484
9889 GTCAAAACTT
9899 CTACTGGGGCAACACCATTCTCGTTGGCATACGGTATGGAAGCAGTCTTGCCTATTGAGGTTGAA
1 CTACTGGGGCAACACCATTCTCGTTGGCATACGGTATGGAAGCAGTCTTGCCTATTGAGGTTGAA
9964 ATACCCTCCCTTTGAGTCTTAACAGAGCTTCAACTTGACGAGGCTGAATGAGTCCAAGCTCGATA
66 ATACCCTCCCTTTGAGTCTTAACAGAGCTTCAACTTGACGAGGCTGAATGAGTCCAAGCTCGATA
10029 TGACCAGTTGAATTTAATCGAGGAAAAGAGATTAAAAGCCATCCGCCAAGGCTAGATGTACCAAA
131 TGACCAGTTGAATTTAATCGAGGAAAAGAGATTAAAAGCCATCCGCCAAGGCTAGATGTACCAAA
10094 AAAGAATGATGCGAGCTTACGACAAAAAGGTTCGTCCCAGGGAATTCTATGAGGGAGATCTAGTT
196 AAAGAATGATGCGAGCTTACGACAAAAAGGTTCGTCCCAGGGAATTCTATGAGGGAGATCTAGTT
10159 TTGAAAAAGATACTTCCTATACACAAAGATTTCTGTGGGAAATAGATGCCCAATTGGGAAGGGCC
261 TTGAAAAAGATACTTCCTATACACAAAGATTTCTGTGGGAAATAGATGCCCAATTGGGAAGGGCC
10224 TTATGTGGTAAAAAAGGTTTTTTCAATAGGAGCTCTCATTTTAACAGAGATGGACGAGAAGGAGC
326 TTATGTGGTAAAAAAGGTTTTTTCAATAGGAGCTCTCATTTTAACAGAGATGGACGAGAAGGAGC
10289 TGTACAACTCCGTCAATTCAGACTCGGTGAAAAAATATTTCGCTTAAAACAAAATGGGAAACCGC
391 TGTACAACTCCGTCAATTCAGACTCGGTGAAAAAATATTTCGCTTAAAACAAAATGGGAAACCGC
10354 AAAGGGCGTCTATTAAAAAAAAAAAAAGG
456 AAAGGGCGTCTATTAAAAAAAAAAAAAGG
10383 NNNNNNNNNNCTACTGGGGCAACACCATTCTCGTTGGCATACGGTATGGAAGCAGTCTTGCCTAT
1 ----------CTACTGGGGCAACACCATTCTCGTTGGCATACGGTATGGAAGCAGTCTTGCCTAT
10448 TGAGGTTGAAATACCCTCCCTTTGAGTCTTAACAGAGCTTCAACTTGACGAGGCTGAATGAGTCC
56 TGAGGTTGAAATACCCTCCCTTTGAGTCTTAACAGAGCTTCAACTTGACGAGGCTGAATGAGTCC
10513 AAGCTCGATATGACCAGTTGAATTTAATCGAGGAAAAGAGATTAAAAGCCATCCGCCAAGGCTAG
121 AAGCTCGATATGACCAGTTGAATTTAATCGAGGAAAAGAGATTAAAAGCCATCCGCCAAGGCTAG
10578 ATGTACCAAAAAAGAATGATGCGAGCTTACGACAAAAAGGTTCGTCCCAGGGAATTCTATGAGGG
186 ATGTACCAAAAAAGAATGATGCGAGCTTACGACAAAAAGGTTCGTCCCAGGGAATTCTATGAGGG
10643 AGATCTAGTTTTGAAAAAGATACTTCCTATACACAAAGATTTCTGTGGGAAATAGATGCCCAATT
251 AGATCTAGTTTTGAAAAAGATACTTCCTATACACAAAGATTTCTGTGGGAAATAGATGCCCAATT
10708 GGGAAGGGCCTTATGTGGTAAAAAAGGTTTTTTCAATAGGAGCTCTCATTTTAACAGAGATGGAC
316 GGGAAGGGCCTTATGTGGTAAAAAAGGTTTTTTCAATAGGAGCTCTCATTTTAACAGAGATGGAC
10773 GAGAAGGAGCTGTACAACTCCGTCAATTCAGACTCGGTGAAAAAATATTTCGCTTAAAACAAAAT
381 GAGAAGGAGCTGTACAACTCCGTCAATTCAGACTCGGTGAAAAAATATTTCGCTTAAAACAAAAT
10838 GGGAAACCGCAAAGGGCGTCTATTAAAAA
446 GGGAAACCGCAAAGGGCGTCTATTAAAAA
10867 NNNNNNNNNN
Statistics
Matches: 474, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
494 474 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (484 bp):
CTACTGGGGCAACACCATTCTCGTTGGCATACGGTATGGAAGCAGTCTTGCCTATTGAGGTTGAA
ATACCCTCCCTTTGAGTCTTAACAGAGCTTCAACTTGACGAGGCTGAATGAGTCCAAGCTCGATA
TGACCAGTTGAATTTAATCGAGGAAAAGAGATTAAAAGCCATCCGCCAAGGCTAGATGTACCAAA
AAAGAATGATGCGAGCTTACGACAAAAAGGTTCGTCCCAGGGAATTCTATGAGGGAGATCTAGTT
TTGAAAAAGATACTTCCTATACACAAAGATTTCTGTGGGAAATAGATGCCCAATTGGGAAGGGCC
TTATGTGGTAAAAAAGGTTTTTTCAATAGGAGCTCTCATTTTAACAGAGATGGACGAGAAGGAGC
TGTACAACTCCGTCAATTCAGACTCGGTGAAAAAATATTTCGCTTAAAACAAAATGGGAAACCGC
AAAGGGCGTCTATTAAAAAAAAAAAAAGG
Found at i:11153 original size:28 final size:27
Alignment explanation
Indices: 11121--11181 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
11111 CAATTTTCAA
*
11121 TTAATGATTGCTTT-CTTTGACCCTCTTT
1 TTAAT-ATTG-TTTCCTTCGACCCTCTTT
*
11149 TTAATATTGTTTCCTTCGATCCTCTTT
1 TTAATATTGTTTCCTTCGACCCTCTTT
11176 TTAATA
1 TTAATA
11182 GAATTCTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 3 0.10
27 22 0.73
28 5 0.17
ACGTcount: A:0.18, C:0.20, G:0.08, T:0.54
Consensus pattern (27 bp):
TTAATATTGTTTCCTTCGACCCTCTTT
Found at i:12034 original size:31 final size:31
Alignment explanation
Indices: 11992--12051 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
11982 TTAGCTTCCT
* *
11992 GACCATCTTCCTGATGAGGTACAGAGAAGTG
1 GACCATATTCCTGATGAGATACAGAGAAGTG
12023 GACCATATTCCTGATGAGATACAGAGAAG
1 GACCATATTCCTGATGAGATACAGAGAAG
12052 CGAATTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (31 bp):
GACCATATTCCTGATGAGATACAGAGAAGTG
Found at i:12180 original size:212 final size:214
Alignment explanation
Indices: 11852--12755 Score: 1192
Period size: 212 Copynumber: 4.2 Consensus size: 214
11842 ATTATCCACA
*
11852 AAACGACGCGGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACTCACG-CCGATG
1 AAACGACGCGGTCATCTTCCAGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCCCGATG
* *
11916 TGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGAAAGTCGAAGTAATAAAACG
66 TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAAACG
* * * *
11981 GTTAGCTTCCTGACCATCTTCCTGATGAGGTACAGAGAAGTGGACC-A-TATTCCTGATGAGATA
131 GTTAGCTTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAATTCTTCCTGAGGAGACA
*
12044 CAGAGAAGCGAATTGAAAC
196 CAGAGAAGCAAATTGAAAC
* * *
12063 AAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAAAAGACCAAATCAAACTCACGCCCGATG
1 AAACGACGCGGTCATCTTCCAGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCCCGATG
12128 TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAAACG
66 TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAAACG
12193 GTTAGCTTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAATTCGTCTTCCTGAGGA
131 GTTAGCTTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACC-AA-T--TCTTCCTGAGGA
* *
12258 GACACAGAAAAGTAAATTGAAAC
192 GACACAGAGAAGCAAATTGAAAC
* * * * * * *
12281 AAGCGATGCGGTCATTTTTCAGATGAGATACTGAGAA-AAGGACCAAATCAAA-TCCATGCTCAA
1 AAACGACGCGGTCATCTTCCAGATGAGATACTGAGAAGAA-GACCAAATCAAACT-CACGCCCGA
* *
12344 TGTGAGCAAAATCTT-G-------GCTTCCTGATGAGTTACTAAGAAGCAAGTCGAAGTAATAAA
64 TGTGAGC-AAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAA
* * *
12401 ACGGTTAGCTTCTTGACCATCTTCTTGATGAGGTAC-GAGGAAGTGGACC-A-TCTTCCTGATGA
128 ACGGTTAGCTTCCTGACCATCTTCCTGATGAGGTACGGA-GAAGTGGACCAATTCTTCCTGAGGA
* * * * *
12463 GATATAAAGAAGCGAATTAAAAC
192 GACACAGAGAAGCAAATTGAAAC
* *
12486 AAACGACGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCCCGATG
1 AAACGACGCGGTCATCTTCCAGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCCCGATG
*
12551 TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAAGTCGAAGTAATAAAACG
66 TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAAACG
* * * *
12616 GTTTGTTTCCTGACAATCTTCCTGATGAAGTACGGAGAAGTGGACCAAATTCGTCTTCCTGAGGA
131 GTTAGCTTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACC-AA-T--TCTTCCTGAGGA
* *
12681 GACATAGAGAAGTAAATTGAAAC
192 GACACAGAGAAGCAAATTGAAAC
** * * *
12704 AGGCGATGCGGTCATTTTCCAGATGAGATACTGAGAAGAGGACCAAATCAAA
1 AAACGACGCGGTCATCTTCCAGATGAGATACTGAGAAGAAGACCAAATCAAA
12756 TCCACGCTTA
Statistics
Matches: 601, Mismatches: 64, Indels: 49
0.84 0.09 0.07
Matches are distributed among these distances:
204 7 0.01
205 84 0.14
206 3 0.00
209 1 0.00
210 2 0.00
211 138 0.23
212 192 0.32
213 2 0.00
214 2 0.00
217 3 0.00
218 160 0.27
219 7 0.01
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (214 bp):
AAACGACGCGGTCATCTTCCAGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCCCGATG
TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAAACG
GTTAGCTTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAATTCTTCCTGAGGAGACA
CAGAGAAGCAAATTGAAAC
Found at i:12462 original size:423 final size:423
Alignment explanation
Indices: 11859--12805 Score: 1479
Period size: 423 Copynumber: 2.2 Consensus size: 423
11849 ACAAAACGAC
* * *
11859 GCGGTCATCTTCCCGATGAGATACTGAGAAGAA-GACCAAATCAAA-CTCACGC-CGATGTGAGC
1 GCGGTCATTTTCCAGATGAGATACTGAGAA-AAGGACCAAATCAAATC-CACGCTCAATGTGAGC
* * *
11921 AAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGAAAGTCGAAGTAATAAAACGGTTAG
64 -AA------AATCCCAGCTTCCTGATGAGATACTAAGAAGAAAGTCGAAGTAATAAAACGGTTAG
*
11986 CTTCCTGACCATCTTCCTGATGAGGTACAGAGAAGTGGACCATATTCCTGATGAGATACAGAGAA
122 CTTCCTGACCATCTTCCTGATGAGGTACAGAGAAGTGGACCATATTCCTGATGAGATACAAAGAA
* *
12051 GCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAAAAGACCAAATCAAAC
187 GCGAATTAAAACAAACGACGCAGTCATCTTCCCGATGAGATACTGAGAAAAAGACCAAATCAAAC
12116 TCACGCCCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGA
252 TCACGCCCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGA
* *
12181 AGTAATAAAACGGTTAGCTTCCTGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAATTCG
317 AGTAATAAAACGGTTAGCTTCCTGACAATCTTCCTGATGAAGTACGGAGAAGTGGACCAAATTCG
12246 TCTTCCTGAGGAGACACAGAAAAGTAAATTGAAACAAGCGAT
382 TCTTCCTGAGGAGACACAGAAAAGTAAATTGAAACAAGCGAT
* *
12288 GCGGTCATTTTTCAGATGAGATACTGAGAAAAGGACCAAATCAAATCCATGCTCAATGTGAGCAA
1 GCGGTCATTTTCCAGATGAGATACTGAGAAAAGGACCAAATCAAATCCACGCTCAATGTGAGCAA
*** * * *
12353 AATCTTGGCTTCCTGATGAGTTACTAAGAAGCAAGTCGAAGTAATAAAACGGTTAGCTTCTTGAC
66 AATCCCAGCTTCCTGATGAGATACTAAGAAGAAAGTCGAAGTAATAAAACGGTTAGCTTCCTGAC
* * *
12418 CATCTTCTTGATGAGGTAC-GAGGAAGTGGACCATCTTCCTGATGAGATATAAAGAAGCGAATTA
131 CATCTTCCTGATGAGGTACAGA-GAAGTGGACCATATTCCTGATGAGATACAAAGAAGCGAATTA
*
12482 AAACAAACGACGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCCC
195 AAACAAACGACGCAGTCATCTTCCCGATGAGATACTGAGAAAAAGACCAAATCAAACTCACGCCC
*
12547 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAAGTCGAAGTAATAA
260 GATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAA
* *
12612 AACGGTTTGTTTCCTGACAATCTTCCTGATGAAGTACGGAGAAGTGGACCAAATTCGTCTTCCTG
325 AACGGTTAGCTTCCTGACAATCTTCCTGATGAAGTACGGAGAAGTGGACCAAATTCGTCTTCCTG
* * *
12677 AGGAGACATAGAGAAGTAAATTGAAACAGGCGAT
390 AGGAGACACAGAAAAGTAAATTGAAACAAGCGAT
* *
12711 GCGGTCATTTTCCAGATGAGATACTGAGAAGAGGACCAAATCAAATCCACGCTTAATGTGAGCAA
1 GCGGTCATTTTCCAGATGAGATACTGAGAAAAGGACCAAATCAAATCCACGCTCAATGTGAGCAA
* *
12776 AATCCCAGCTTCCTGATGAGACACAAAGAA
66 AATCCCAGCTTCCTGATGAGATACTAAGAA
12806 ATTGATCAAA
Statistics
Matches: 475, Mismatches: 39, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
422 2 0.00
423 416 0.88
428 2 0.00
429 45 0.09
430 10 0.02
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (423 bp):
GCGGTCATTTTCCAGATGAGATACTGAGAAAAGGACCAAATCAAATCCACGCTCAATGTGAGCAA
AATCCCAGCTTCCTGATGAGATACTAAGAAGAAAGTCGAAGTAATAAAACGGTTAGCTTCCTGAC
CATCTTCCTGATGAGGTACAGAGAAGTGGACCATATTCCTGATGAGATACAAAGAAGCGAATTAA
AACAAACGACGCAGTCATCTTCCCGATGAGATACTGAGAAAAAGACCAAATCAAACTCACGCCCG
ATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAA
ACGGTTAGCTTCCTGACAATCTTCCTGATGAAGTACGGAGAAGTGGACCAAATTCGTCTTCCTGA
GGAGACACAGAAAAGTAAATTGAAACAAGCGAT
Found at i:13212 original size:17 final size:17
Alignment explanation
Indices: 13188--13261 Score: 103
Period size: 17 Copynumber: 4.4 Consensus size: 17
13178 TTGGAAATTG
13188 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
13205 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
13222 AGTTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
13239 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
13256 AATTTA
1 AATTTA
13262 GAAAAGTCCA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:15052 original size:29 final size:29
Alignment explanation
Indices: 15013--15248 Score: 238
Period size: 29 Copynumber: 8.0 Consensus size: 29
15003 GAAGGTCCCT
* *
15013 AAACTGTCCAAAAATTACGTTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCCC
* * *
15043 AAACTTCCAAAAATTCCATTTTGACCGCG
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *
15072 AAACTTCCAAAAATTCCGTTATTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
15101 GAAACTTCCAAAAATTCCATTTTTACCCCC
1 -AAACTTCCAAAAATTCCATTTTTACCCCC
* * * * *
15131 GAACTTCCAAAAATCCCAATTTTGACCTCA
1 AAACTTCCAAAAATTCC-ATTTTTACCCCC
*
15161 AAACTTCCAAAAATTCTATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
** * **
15190 AAACTTCCAAAAACGCCATTTTTTATCCTG
1 AAACTTCCAAAAATTCCA-TTTTTACCCCC
* ** *
15220 AAATTTCTTAAAATTCTATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
15249 GAATGTCTAA
Statistics
Matches: 165, Mismatches: 38, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
29 90 0.55
30 75 0.45
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:15114 original size:59 final size:57
Alignment explanation
Indices: 15013--15202 Score: 229
Period size: 59 Copynumber: 3.2 Consensus size: 57
15003 GAAGGTCCCT
* * *
15013 AAACTGTCCAAAAATTACGTTTTTACCCCCAAACTTCCAAAAATTCCATTTTGACCGCG
1 AAACT-TCCAAAAATTCCG-TTTTACCCCCAAACTTCCAAAAATTCCATTTTTACCCCG
15072 AAACTTCCAAAAATTCCGTTATTACCCCCGAAACTTCCAAAAATTCCATTTTTACCCCCG
1 AAACTTCCAAAAATTCCGTT-TTACCCCC-AAACTTCCAAAAATTCCATTTTTA-CCCCG
* * * * * *
15132 -AACTTCCAAAAATCCCAATTTTGACCTCAAAACTTCCAAAAATTCTATTTTTACCCCC
1 AAACTTCCAAAAATTCC-GTTTT-ACCCCCAAACTTCCAAAAATTCCATTTTTACCCCG
15190 AAACTTCCAAAAA
1 AAACTTCCAAAAA
15203 CGCCATTTTT
Statistics
Matches: 116, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
57 2 0.02
58 24 0.21
59 80 0.69
60 10 0.09
ACGTcount: A:0.36, C:0.31, G:0.05, T:0.28
Consensus pattern (57 bp):
AAACTTCCAAAAATTCCGTTTTACCCCCAAACTTCCAAAAATTCCATTTTTACCCCG
Found at i:15233 original size:59 final size:59
Alignment explanation
Indices: 15043--15248 Score: 204
Period size: 59 Copynumber: 3.5 Consensus size: 59
15033 TTTTACCCCC
* * * * * * * *
15043 AAACTTCCAAAAATTCCATTTTGACCGCGAAACTTCCAAAAATTCC-GTTATT-ACCCCCG
1 AAACTTCCAAAAATTCTATTTTTACCCCCAAACTTCCAAAAATCCCAATT-TTGA-CCTCA
* *
15102 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCAATTTTGACCTCA
1 AAACTTCCAAAAATTCTATTTTTACCCCCAAACTTCCAAAAATCCCAATTTTGACCTCA
* * *
15161 AAACTTCCAAAAATTCTATTTTTACCCCCAAACTTCCAAAAA-CGCCATTTTTTATCCT-G
1 AAACTTCCAAAAATTCTATTTTTACCCCCAAACTTCCAAAAATC-CCAATTTTGA-CCTCA
* **
15220 AAATTTCTTAAAATTCTATTTTTACCCCC
1 AAACTTCCAAAAATTCTATTTTTACCCCC
15249 GAATGTCTAA
Statistics
Matches: 127, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
58 1 0.01
59 120 0.94
60 6 0.05
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATTCTATTTTTACCCCCAAACTTCCAAAAATCCCAATTTTGACCTCA
Found at i:17659 original size:66 final size:66
Alignment explanation
Indices: 17553--17685 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
17543 CAACCTTCAA
17553 ACAGTCACTAGATTAGATGAACCATACATATATATTCATAAAATATGTTCATATTTAAAGACCCT
1 ACAGTCACTAGATTAGATGAACCATACATATATATTCATAAAATATGTTCATATTTAAAGACCCT
17618 T
66 T
17619 ACAGTCACTAGATTAGATGAACCATACATATATATTCATAAAATATGTTCATATTTAAAGACCCT
1 ACAGTCACTAGATTAGATGAACCATACATATATATTCATAAAATATGTTCATATTTAAAGACCCT
17684 T
66 T
17685 A
1 A
17686 ATAAAAATAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (66 bp):
ACAGTCACTAGATTAGATGAACCATACATATATATTCATAAAATATGTTCATATTTAAAGACCCT
T
Found at i:25970 original size:16 final size:17
Alignment explanation
Indices: 25941--25972 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25931 TATATTTATG
25941 ATATTTTTTAAATATAA
1 ATATTTTTTAAATATAA
25958 ATATTTTTT-AATATA
1 ATATTTTTTAAATATA
25973 TTTTTAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATTTTTTAAATATAA
Found at i:33607 original size:88 final size:89
Alignment explanation
Indices: 33457--33623 Score: 257
Period size: 88 Copynumber: 1.9 Consensus size: 89
33447 GACAGTACAC
* * * *
33457 TAGAGGTGATCAAATTCAGTTAAAAACTGGCAAATTTGCACTAATGACATTCCTCTGGAGTGAGG
1 TAGAGGCGATCAAATGCAGTTAAAAAATAGCAAATTTGCACTAATGACATTCCTCTGGAGTGAGG
*
33522 TTGAGTAAGTCAACTTCAAAGACT
66 TTGAGCAAGTCAACTTCAAAGACT
*
33546 TAGAGGCGAT-AAATGCATTTAAAAAATAGCAAATTTG-ACTAATGACATTCCTCTTGGAGTGAG
1 TAGAGGCGATCAAATGCAGTTAAAAAATAGCAAATTTGCACTAATGACATTCCTC-TGGAGTGAG
33609 GTTGAGCAAGTCAAC
65 GTTGAGCAAGTCAAC
33624 CATTCATTAC
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
87 16 0.23
88 46 0.65
89 9 0.13
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.28
Consensus pattern (89 bp):
TAGAGGCGATCAAATGCAGTTAAAAAATAGCAAATTTGCACTAATGACATTCCTCTGGAGTGAGG
TTGAGCAAGTCAACTTCAAAGACT
Found at i:42190 original size:22 final size:22
Alignment explanation
Indices: 42156--42202 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
42146 TGGGATAAAG
42156 AAAAACTCCAAGTATCAAATTGA
1 AAAAACTCCAAGTATCAAATT-A
* *
42179 AAAAACT-TAAGTATCACATTA
1 AAAAACTCCAAGTATCAAATTA
42200 AAA
1 AAA
42203 CATAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 11 0.50
23 7 0.32
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.23
Consensus pattern (22 bp):
AAAAACTCCAAGTATCAAATTA
Found at i:49262 original size:22 final size:22
Alignment explanation
Indices: 49234--49283 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
49224 GAAGAGCTGT
49234 GTTTTT-GTTATGG-GGTGTCTTG
1 GTTTTTGGTT-TGGTGG-GTCTTG
*
49256 GTTTTTGGTTTGGTGGGTGTTG
1 GTTTTTGGTTTGGTGGGTCTTG
49278 GTTTTT
1 GTTTTT
49284 TCTGAGGTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.02, C:0.02, G:0.38, T:0.58
Consensus pattern (22 bp):
GTTTTTGGTTTGGTGGGTCTTG
Found at i:53922 original size:21 final size:20
Alignment explanation
Indices: 53898--53946 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
53888 ATATTAAAAA
*
53898 ATATTTTTTTTCATAAGTTTT
1 ATATTTTTTTTAAT-AGTTTT
* *
53919 ATATCTTTTTTAATATTTTT
1 ATATTTTTTTTAATAGTTTT
53939 A-ATTTTTT
1 ATATTTTTT
53947 AAAAATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 6 0.25
20 6 0.25
21 12 0.50
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (20 bp):
ATATTTTTTTTAATAGTTTT
Found at i:53971 original size:20 final size:20
Alignment explanation
Indices: 53930--53973 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
53920 TATCTTTTTT
* *
53930 AATATTTTTAATTTTTTAAA
1 AATATTTTTAAATTTGTAAA
53950 AATATTTTTTAAATTTGTAAA
1 AATA-TTTTTAAATTTGTAAA
53971 AAT
1 AAT
53974 TAAAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
AATATTTTTAAATTTGTAAA
Found at i:54985 original size:19 final size:20
Alignment explanation
Indices: 54937--54989 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
54927 TATCAAATCC
54937 ACATAAATAA-TACA-AAATT
1 ACATAAATAATTACATAAA-T
*
54956 ATATAAA-AATTACATAAA-
1 ACATAAATAATTACATAAAT
54974 ACATAAATAATTACAT
1 ACATAAATAATTACAT
54990 TAACTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 8 0.28
19 18 0.62
20 3 0.10
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (20 bp):
ACATAAATAATTACATAAAT
Found at i:55381 original size:11 final size:9
Alignment explanation
Indices: 55356--55406 Score: 66
Period size: 9 Copynumber: 5.2 Consensus size: 9
55346 ATGTCAAGGG
55356 ATTATTTTA
1 ATTATTTTA
55365 ATTATTTTA
1 ATTATTTTA
55374 TTATTATTTTA
1 --ATTATTTTA
55385 ATTATTTTA
1 ATTATTTTA
55394 TTATTATTTTA
1 --ATTATTTTA
55405 AT
1 AT
55407 ACACCTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
9 20 0.53
11 18 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
ATTATTTTA
Found at i:55381 original size:20 final size:20
Alignment explanation
Indices: 55356--55406 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
55346 ATGTCAAGGG
55356 ATTATTTTAATTATTTTATT
1 ATTATTTTAATTATTTTATT
55376 ATTATTTTAATTATTTTATT
1 ATTATTTTAATTATTTTATT
55396 ATTATTTTAAT
1 ATTATTTTAAT
55407 ACACCTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTATTTTAATTATTTTATT
Found at i:55772 original size:26 final size:28
Alignment explanation
Indices: 55702--55773 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 28
55692 ATAGGACAAT
*
55702 AAAGTGTTATAACTCAAATTTATTAAAAA
1 AAAGTATTATAACTCAAA-TTATTAAAAA
* ** *
55731 AAAATATTATTTCTCAAA-TATT-TAAA
1 AAAGTATTATAACTCAAATTATTAAAAA
55757 AAAGTATTATAACTCAA
1 AAAGTATTATAACTCAA
55774 CCTTTCATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
26 17 0.49
27 4 0.11
29 14 0.40
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.36
Consensus pattern (28 bp):
AAAGTATTATAACTCAAATTATTAAAAA
Found at i:59585 original size:3 final size:3
Alignment explanation
Indices: 59577--59606 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
59567 TTAATATTTC
59577 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
59607 CAATTTTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:64586 original size:16 final size:17
Alignment explanation
Indices: 64565--64600 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
64555 ATTCAAATTC
64565 TTTGTGCTTTTTCT-TT
1 TTTGTGCTTTTTCTATT
*
64581 TTTGTGGTTTTTCTATT
1 TTTGTGCTTTTTCTATT
64598 TTT
1 TTT
64601 TCGAACTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.03, C:0.08, G:0.14, T:0.75
Consensus pattern (17 bp):
TTTGTGCTTTTTCTATT
Found at i:65947 original size:19 final size:20
Alignment explanation
Indices: 65923--65960 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
65913 TAATTTTAAT
65923 TATTTTATA-ATAAAATAAA
1 TATTTTATATATAAAATAAA
*
65942 TATTTTATATTTAAAATAA
1 TATTTTATATATAAAATAA
65961 GAAAAATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTTTATATATAAAATAAA
Found at i:65960 original size:25 final size:24
Alignment explanation
Indices: 65922--65977 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
65912 TTAATTTTAA
*
65922 TTATTTTATAATAA-AATAAATATT
1 TTATTTTAAAATAAGAA-AAATATT
*
65946 TTATATTTAAAATAAGAAAAATAACT
1 TTAT-TTTAAAATAAGAAAAAT-ATT
65972 TTATTT
1 TTATTT
65978 CTTTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 15 0.56
26 8 0.30
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
TTATTTTAAAATAAGAAAAATATT
Found at i:69936 original size:28 final size:31
Alignment explanation
Indices: 69905--69961 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
69895 GTTTTAATTT
69905 TTCA-GACAAAGAC-ATTTTTTTT-TTCTTA
1 TTCACGACAAAGACAATTTTTTTTATTCTTA
*
69933 TTCACGACATAGACAATTTTTTTTATTCT
1 TTCACGACAAAGACAATTTTTTTTATTCT
69962 GAAGTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 8 0.32
30 9 0.36
31 4 0.16
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (31 bp):
TTCACGACAAAGACAATTTTTTTTATTCTTA
Found at i:71919 original size:34 final size:35
Alignment explanation
Indices: 71871--71943 Score: 139
Period size: 34 Copynumber: 2.1 Consensus size: 35
71861 GTTCTAAAAA
71871 TTTTACATAACTTTATCTATAACTATACAACTCAC
1 TTTTACATAACTTTATCTATAACTATACAACTCAC
71906 TTTT-CATAACTTTATCTATAACTATACAACTCAC
1 TTTTACATAACTTTATCTATAACTATACAACTCAC
71940 TTTT
1 TTTT
71944 TATCCATTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 34 0.89
35 4 0.11
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.44
Consensus pattern (35 bp):
TTTTACATAACTTTATCTATAACTATACAACTCAC
Done.