Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014174.1 Kokia drynarioides strain JFW-HI SEQ_129207, 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: 39646
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:3876 original size:97 final size:96
Alignment explanation
Indices: 3698--3883 Score: 218
Period size: 97 Copynumber: 1.9 Consensus size: 96
3688 GAAAAGGATA
*** *
3698 TTCGATTATCTCGATTCGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCAGAATCGA
1 TTCGATTATCTCGATTCGAAGAAAAAATGCACCTAGTAAGTTAAGGCACAATATTTCAGAATCGA
*
3763 AGATAAGGAAACATTGCCTCGATTAAGGGTG
66 AAATAAGGAAACATTGCCTCGATTAAGGGTG
* * *
3794 TTCGATTATTTCGATTTGAAGAAAAAAATGCACCTAGTGAGTTAAGGCACAA-ATTTTC-GAAGC
1 TTCGATTATCTCGATTCGAAG-AAAAAATGCACCTAGTAAGTTAAGGCACAATA-TTTCAGAA--
*
3857 TC-AAAATAAAGG-AATATTGCCTCGATT
62 TCGAAAAT-AAGGAAACATTGCCTCGATT
3884 TTTTTTGAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
96 23 0.30
97 47 0.62
98 6 0.08
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.28
Consensus pattern (96 bp):
TTCGATTATCTCGATTCGAAGAAAAAATGCACCTAGTAAGTTAAGGCACAATATTTCAGAATCGA
AAATAAGGAAACATTGCCTCGATTAAGGGTG
Found at i:4747 original size:352 final size:351
Alignment explanation
Indices: 4096--4924 Score: 1182
Period size: 352 Copynumber: 2.3 Consensus size: 351
4086 ACAAGGGGAA
* * *
4096 AAAATGGTAGTTTTGGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGG
1 AAAATGGTAATTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGG
* *
4161 TAATTTTTGAAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTT
66 TAATTTTAG-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCG-GGGTAAAATGGTAATTT
* * *
4226 TGGAAAGGTTTTGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGATAATTTTTGAAA
129 TAGAAAGGTTTAGGGTCAAAAATGGAATTTTTAGAAGTTTAGGGGTAAAATGATAATTTTTGAAA
* * * * *
4291 GGTTCGGTGTCAAAAATGGGATTTTTGGTAGTTAAAGGGTAAAACGGTAATTTTCGGAAGGTTTC
194 GGTTCGGGGTCAAAAATAGGATTTTTGGAAATTAAAGGGTAAAACGGTAATTTTCAGAAGGTTTC
* *
4356 GGGTCAAAAATGGGATTTTTGGAAGTTAGGGGGTAAAATGATAATTTTT-GAAAGGTTCT-TGCT
259 GGGTCAAAAATGGGATTTTTGGAAGTTAGGGGATAAAATGATAATTTTTAG-AAGGTT-TGGGCT
* *
4419 CAAAAAGGGGATTTTTGGAAGTTCGGTGGT
322 CAAAAAGGAGATTTTTGGAAGTTCGGGGGT
* *
4449 AAAATGGTAATTTTGGAAGGTTCGGGGTCAAAAAGGGGATTTTTGGAAGTTCGGGGGTAAAATGG
1 AAAATGGTAATTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGG
4514 TAATTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGATAAAATGGTAATTTT
66 TAATTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG-TAAAATGGTAA-TTT
** * * *
4579 TAG-AAGGTTTAGGGTCAAAAATGGGGTTTTTAGAAGTTTGGGGGTAAAATGGTAATTTTTGGAA
129 TAGAAAGGTTTAGGGTCAAAAATGGAATTTTTAGAAGTTTAGGGGTAAAATGATAATTTTTGAAA
** * * *
4643 GGTTCGGGGTCAAAAATAGGATTTTTGGAAATTCGAGGGTAAAATGGTAATTTTTAGACGG-TTC
194 GGTTCGGGGTCAAAAATAGGATTTTTGGAAATTAAAGGGTAAAACGGTAATTTTCAGAAGGTTTC
* * *
4707 GAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGATAAAATGGTAATTTTTAGAAGGTTTGGGGTC
259 G-GGTCAAAAATGGGATTTTTGGAAGTTAGGGGATAAAATGATAATTTTTAGAAGGTTTGGGCTC
*
4772 AAAAATGAGATTTTTGGAAGTTCGGGGGT
323 AAAAAGGAGATTTTTGGAAGTTCGGGGGT
* * * *
4801 AAAATGATAATTTTAGAAGATTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAATGG
1 AAAATGGTAATTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGG
* *
4866 TAATTTTCGGAAGGTTCGGTGTCAAAAATGGGATTTTTGGAAGTT-GGGGTCGAAAATGG
66 TAATTTT-AGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGT--AAAATGG
4925 GATTTTTGGA
Statistics
Matches: 427, Mismatches: 41, Indels: 16
0.88 0.08 0.03
Matches are distributed among these distances:
351 9 0.02
352 302 0.71
353 116 0.27
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (351 bp):
AAAATGGTAATTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGG
TAATTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGTAAAATGGTAATTTTA
GAAAGGTTTAGGGTCAAAAATGGAATTTTTAGAAGTTTAGGGGTAAAATGATAATTTTTGAAAGG
TTCGGGGTCAAAAATAGGATTTTTGGAAATTAAAGGGTAAAACGGTAATTTTCAGAAGGTTTCGG
GTCAAAAATGGGATTTTTGGAAGTTAGGGGATAAAATGATAATTTTTAGAAGGTTTGGGCTCAAA
AAGGAGATTTTTGGAAGTTCGGGGGT
Found at i:4922 original size:59 final size:58
Alignment explanation
Indices: 4096--4934 Score: 1046
Period size: 59 Copynumber: 14.3 Consensus size: 58
4086 ACAAGGGGAA
* * *
4096 AAAATGGT-AGTTTTGGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCG-GGGT
* *
4154 AAAATGGTAATTTTTGAAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCG-GGGT
** * *
4213 AAAATGGTAA-TTTTGGAAAGGTTTTGGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGT
1 AAAATGGTAATTTTTGG-AAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGT
* * * * **
4272 AAAATGATAATTTTTGAAAGGTTCGGTGTCAAAAATGGGATTTTTGGTAGTTAAAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT-CGGGGT
* * *
4331 AAAACGGTAATTTTCGGAAGGTTTC-GGGTCAAAAATGGGATTTTTGGAAGTTAGGGGGT
1 AAAATGGTAATTTTTGGAAGG-TTCGGGGTCAAAAATGGGATTTTTGGAAGTT-CGGGGT
* * ** * *
4390 AAAATGATAATTTTTGAAAGGTTCTTGCTCAAAAAGGGGATTTTTGGAAGTTCGGTGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGG-GGT
*
4449 AAAATGGTAA-TTTTGGAAGGTTCGGGGTCAAAAAGGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC-GGGGT
*
4507 AAAATGGTAA-TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGAT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG-T
* ** * * *
4565 AAAATGGTAATTTTTAGAAGGTTTAGGGTCAAAAATGGGGTTTTTAGAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGT
* *
4624 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATAGGATTTTTGGAAATTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCG-GGGT
* * *
4683 AAAATGGTAATTTTTAGACGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGAT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG-T
* * *
4742 AAAATGGTAATTTTTAGAAGGTTTGGGGTCAAAAATGAGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC-GGGGT
* * * *
4801 AAAATGATAA-TTTTAGAAGATTCGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCG-GGGT
* *
4859 AAAATGGTAATTTTCGGAAGGTTCGGTGTCAAAAATGGGATTTTTGGAAGTT-GGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGT
*
4916 CGAAAATGG-GATTTTTGGA
1 --AAAATGGTAATTTTTGGA
4935 CAATTTAGGG
Statistics
Matches: 687, Mismatches: 75, Indels: 38
0.86 0.09 0.05
Matches are distributed among these distances:
57 9 0.01
58 190 0.28
59 467 0.68
60 21 0.03
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGT
Found at i:6856 original size:11 final size:11
Alignment explanation
Indices: 6842--6897 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
6832 TGGAAATAAT
*
6842 TTTAAACTTAA
1 TTTAAATTTAA
6853 TTTAAATTTAA
1 TTTAAATTTAA
**
6864 AATAAATTTAAA
1 TTTAAATTT-AA
6876 TTTAAATTTAA
1 TTTAAATTTAA
**
6887 AATAAATTTAA
1 TTTAAATTTAA
6898 AGAGAGTATG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:6860 original size:6 final size:6
Alignment explanation
Indices: 6842--6898 Score: 66
Period size: 6 Copynumber: 10.0 Consensus size: 6
6832 TGGAAATAAT
* *
6842 TTTAAA CTT-AA TTTAAA TTTAAA -ATAAA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
6888 -ATAAA TTTAAA
1 TTTAAA TTTAAA
6899 GAGAGTATGA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
5 12 0.29
6 30 0.71
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:6864 original size:17 final size:17
Alignment explanation
Indices: 6842--6898 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
6832 TGGAAATAAT
*
6842 TTTAAACTTAATTTAAA
1 TTTAAAATTAATTTAAA
*
6859 TTTAAAATAAATTTAAA
1 TTTAAAATTAATTTAAA
* **
6876 TTTAAATTTAAAATAAA
1 TTTAAAATTAATTTAAA
6893 TTTAAA
1 TTTAAA
6899 GAGAGTATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAAATTAATTTAAA
Found at i:6877 original size:23 final size:23
Alignment explanation
Indices: 6851--6898 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
6841 TTTTAAACTT
6851 AATTTAAATTTAAAATAAATTTA
1 AATTTAAATTTAAAATAAATTTA
6874 AATTTAAATTTAAAATAAATTTA
1 AATTTAAATTTAAAATAAATTTA
6897 AA
1 AA
6899 GAGAGTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AATTTAAATTTAAAATAAATTTA
Found at i:6898 original size:11 final size:11
Alignment explanation
Indices: 6855--6898 Score: 70
Period size: 11 Copynumber: 3.9 Consensus size: 11
6845 AAACTTAATT
6855 TAAATTTAAAA
1 TAAATTTAAAA
*
6866 TAAATTTAAATT
1 TAAATTTAAA-A
6878 TAAATTTAAAA
1 TAAATTTAAAA
6889 TAAATTTAAA
1 TAAATTTAAA
6899 GAGAGTATGA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:7506 original size:310 final size:310
Alignment explanation
Indices: 6935--7757 Score: 1342
Period size: 310 Copynumber: 2.6 Consensus size: 310
6925 GGCTTCAACA
*
6935 AACCTAATGGCAATGCTTCCACCAACCAAAATGCCTAGCAAAATATACTAAAATTTCACAGTTTC
1 AACCTAATGGCAATGCTTCCACTAACCAAAATGCCTAGCAAAATATACTAAAATTTCACAGTTTC
* * * *
7000 ATCATGAAAAATATAGCTAGTGCGTGAAAGAACCTTGCATTTCATCAGAAATGAAAAATCCAGAA
66 ATCATGAAAAAGATAGCTAGTGCATGGAAGAACCTTGCA-TTCATCAGAAATG-AAAAT--ACAA
* *
7065 TGAA-ATTTCATCAGTAATCACCATATTAAAATCCCATCACTCTAATTCCTTCCATGAGCAACTT
127 T-AAGTTTTCATCAGTAATTACCATATTAAAATCCCATCACTCTAATTCCTTCCATGAGCAACTT
*
7129 GAGCTTTGGATTCTAAATCAGCTGAAAGCAACACATTACCAAAACATTGCATAGTTCATATAATC
191 GAGCTTTGGATTCTAAATCAGCTGAAAGCAACACATTACCAAAACATTGCATAGTTCATACAATC
* * *
7194 TTTCGCTAAATGCATTCATAATACATTGTTTCTGAATTATCTACTTCAAAGTATG
256 TTTAGCTAAATCCATTCATAATACATTGTTTCTGAATAATCTACTTCAAAGTATG
* * *
7249 AACTTAATGGCAATGCTTCGACTAACCAAAATGCCTAGCAACATATACTAAAATTTCACAGTTTC
1 AACCTAATGGCAATGCTTCCACTAACCAAAATGCCTAGCAAAATATACTAAAATTTCACAGTTTC
7314 ATCATGAAAAAGATAGCTAGTGCATGGAAGAACCTTGCATTCATCAGAAATGAAAATACAATAAG
66 ATCATGAAAAAGATAGCTAGTGCATGGAAGAACCTTGCATTCATCAGAAATGAAAATACAATAAG
7379 TTTTCATCAGTAATTACCATATTAAAATCCCATCACTCTAATTCCTTCCATGAGCAACTTGAGCT
131 TTTTCATCAGTAATTACCATATTAAAATCCCATCACTCTAATTCCTTCCATGAGCAACTTGAGCT
*
7444 TTGGATTCTAAATCAGCTGAAAGCAACACATTACCAAAACATTGCATAGTTGATACAATCTTTAG
196 TTGGATTCTAAATCAGCTGAAAGCAACACATTACCAAAACATTGCATAGTTCATACAATCTTTAG
7509 CTAAATCCATTCATAATACATTGTTTCTGAATAATCTACTTCAAAGTATG
261 CTAAATCCATTCATAATACATTGTTTCTGAATAATCTACTTCAAAGTATG
* *
7559 AACCTAATGGCAATGCTTCCACTAACCAAAATGCCTAGGAAAATATACTAAAATTTCACAGATTC
1 AACCTAATGGCAATGCTTCCACTAACCAAAATGCCTAGCAAAATATACTAAAATTTCACAGTTTC
7624 ATCATGAAAAAGATAGCTAGTGCATGGAAGAACCTTGCATTCATCAGAAATGAAAATACAATAAG
66 ATCATGAAAAAGATAGCTAGTGCATGGAAGAACCTTGCATTCATCAGAAATGAAAATACAATAAG
* * * * * * ** * *
7689 TTTTCATCGGTAATTACTAGATTAAAACTCCCATCAATGTAAATCCTTAGAAGAGCAACTCGAGC
131 TTTTCATCAGTAATTACCATATTAAAA-TCCCATCACTCTAATTCCTTCCATGAGCAACTTGAGC
7754 TTTG
195 TTTG
7758 AATTGCACTG
Statistics
Matches: 477, Mismatches: 30, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
309 2 0.00
310 326 0.68
311 34 0.07
312 5 0.01
313 13 0.03
314 97 0.20
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (310 bp):
AACCTAATGGCAATGCTTCCACTAACCAAAATGCCTAGCAAAATATACTAAAATTTCACAGTTTC
ATCATGAAAAAGATAGCTAGTGCATGGAAGAACCTTGCATTCATCAGAAATGAAAATACAATAAG
TTTTCATCAGTAATTACCATATTAAAATCCCATCACTCTAATTCCTTCCATGAGCAACTTGAGCT
TTGGATTCTAAATCAGCTGAAAGCAACACATTACCAAAACATTGCATAGTTCATACAATCTTTAG
CTAAATCCATTCATAATACATTGTTTCTGAATAATCTACTTCAAAGTATG
Found at i:8855 original size:13 final size:12
Alignment explanation
Indices: 8815--8851 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
8805 AAAGTAATAT
8815 ATTTATTTTTAA
1 ATTTATTTTTAA
8827 ATTTATTTTTAA
1 ATTTATTTTTAA
8839 ATTTATTTTTAA
1 ATTTATTTTTAA
8851 A
1 A
8852 ATTTTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTATTTTTAA
Found at i:10926 original size:43 final size:43
Alignment explanation
Indices: 10844--10928 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
10834 ATTAACATGT
* *
10844 TAAATTATATTACTTAACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTAACTCGTATTAATATGCTTGCATGTTAC
* *
10887 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTAACTCGTATTAATATGCTTG-CATGTTA
10929 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTAACTCGTATTAATATGCTTGCATGTTAC
Found at i:11542 original size:45 final size:45
Alignment explanation
Indices: 11478--11569 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
11468 GCCTAGCTCA
* * *
11478 TCAAGCTAAAGATATCAGCCTTAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAAGATATCAGCCTCAGTTTGACCAGCCACCGCAATAC
* *
11523 TCAAGCCAATGATATCAGCCTCAGTTTGACCAGCCACCGTAATAC
1 TCAAGCCAAAGATATCAGCCTCAGTTTGACCAGCCACCGCAATAC
11568 TC
1 TC
11570 TACTCCTCCC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (45 bp):
TCAAGCCAAAGATATCAGCCTCAGTTTGACCAGCCACCGCAATAC
Found at i:14379 original size:24 final size:24
Alignment explanation
Indices: 14352--14398 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
14342 CACCATACAC
14352 GGAGTTGGATCTTCATTTTCTACT
1 GGAGTTGGATCTTCATTTTCTACT
14376 GGAGTTGGATCTTCATTTTCTAC
1 GGAGTTGGATCTTCATTTTCTAC
14399 AAGTTTCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.45
Consensus pattern (24 bp):
GGAGTTGGATCTTCATTTTCTACT
Found at i:15266 original size:35 final size:36
Alignment explanation
Indices: 15195--15267 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
15185 TCTTTTTATT
* *
15195 AAATTAATAATTTTTTAATATTACTTTAGTCGAATA
1 AAATAAATAATTTTTTAATATTACTTTAGTCAAATA
*
15231 AAATAAATAATTTTTGT-ATATTATTTTAGT-AAATA
1 AAATAAATAATTTTT-TAATATTACTTTAGTCAAATA
15266 AA
1 AA
15268 TATTTTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 6 0.18
36 26 0.79
37 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (36 bp):
AAATAAATAATTTTTTAATATTACTTTAGTCAAATA
Found at i:15297 original size:29 final size:30
Alignment explanation
Indices: 15231--15297 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
15221 TAGTCGAATA
*
15231 AAATAAATAATTTTTGTATATTATTTTAGT
1 AAATAAATAATTTTTATATATTATTTTAGT
* * *
15261 AAATAAATATTTTTTATATTTTATTTTGGT
1 AAATAAATAATTTTTATATATTATTTTAGT
15291 AAA-AAAT
1 AAATAAAT
15298 CAAAACCCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 4 0.12
30 29 0.88
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (30 bp):
AAATAAATAATTTTTATATATTATTTTAGT
Found at i:16471 original size:23 final size:23
Alignment explanation
Indices: 16443--16496 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
16433 CTTTATTTTA
16443 GTTTTT-ATCTGCTTTTGTGACAC
1 GTTTTTCATCTG-TTTTGTGACAC
* *
16466 GTTTTTCTTCTGTTTTGTGTCAC
1 GTTTTTCATCTGTTTTGTGACAC
16489 GCTTTTTC
1 G-TTTTTC
16497 TCTATCTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.07, C:0.19, G:0.17, T:0.57
Consensus pattern (23 bp):
GTTTTTCATCTGTTTTGTGACAC
Found at i:16477 original size:24 final size:24
Alignment explanation
Indices: 16450--16522 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 24
16440 TTAGTTTTTA
16450 TCTGCTTTTGTGACACG-TTTTTCT
1 TCTG-TTTTGTGACACGCTTTTTCT
*
16474 TCTGTTTTGTGTCACGCTTTTTC-
1 TCTGTTTTGTGACACGCTTTTTCT
* *
16497 TCTATCTTGTGGA-ACGCTTTTGTCT
1 TCTGTTTTGT-GACACGCTTTT-TCT
16522 T
1 T
16523 ATGGCACATT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
23 27 0.66
24 13 0.32
25 1 0.02
ACGTcount: A:0.08, C:0.21, G:0.18, T:0.53
Consensus pattern (24 bp):
TCTGTTTTGTGACACGCTTTTTCT
Found at i:20724 original size:17 final size:16
Alignment explanation
Indices: 20702--20764 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 16
20692 TCATGGCAAC
*
20702 AAATATTTAACAATTAA
1 AAATA-TTAAAAATTAA
20719 AAATATTAAAAATTAA
1 AAATATTAAAAATTAA
*
20735 ATGATTATTTAAAAATATAAA
1 A--AATA-TTAAAAAT-T-AA
20756 AAATATTAA
1 AAATATTAA
20765 GAATCTAACT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 11 0.29
17 5 0.13
18 7 0.18
19 11 0.29
20 1 0.03
21 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
AAATATTAAAAATTAA
Found at i:22470 original size:23 final size:23
Alignment explanation
Indices: 22414--22537 Score: 96
Period size: 23 Copynumber: 5.4 Consensus size: 23
22404 ACTAGCGCGA
* *
22414 TCTCTGTTTAACACGTTT-CGTGC
1 TCTCTGTTTAGCAC-TTTGTGTGC
* *
22437 CCTCTGATTAGCACTTTGTGTGC
1 TCTCTGTTTAGCACTTTGTGTGC
*
22460 TCTCTGTTTAGTA-TTGTGTGTGC
1 TCTCTGTTTAGCACTT-TGTGTGC
*
22483 TCTCTGTTGCTCAGCAC-TTATGTGC
1 TCTCTGTT--T-AGCACTTTGTGTGC
* *
22508 TCTCTG-TTAGTACTTTG-GTAC
1 TCTCTGTTTAGCACTTTGTGTGC
22529 TCTCTGTTT
1 TCTCTGTTT
22538 GTTCCGTATA
Statistics
Matches: 81, Mismatches: 12, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
21 13 0.16
22 10 0.12
23 40 0.49
24 1 0.01
25 13 0.16
26 4 0.05
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (23 bp):
TCTCTGTTTAGCACTTTGTGTGC
Found at i:22515 original size:48 final size:47
Alignment explanation
Indices: 22446--22536 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 47
22436 CCCTCTGATT
* *
22446 AGCACTTTGTGTGCTCTCTGTTTAGTA-TTGTGTGTGCTCTCTGTTGCTC
1 AGCACTTTATGTGCTCTCTG-TTAGTACTT-TG-GTACTCTCTGTTGCTC
22495 AGCAC-TTATGTGCTCTCTGTTAGTACTTTGGTACTCTCTGTT
1 AGCACTTTATGTGCTCTCTGTTAGTACTTTGGTACTCTCTGTT
22537 TGTTCCGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
46 11 0.28
47 8 0.21
48 15 0.38
49 5 0.13
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (47 bp):
AGCACTTTATGTGCTCTCTGTTAGTACTTTGGTACTCTCTGTTGCTC
Found at i:26479 original size:30 final size:31
Alignment explanation
Indices: 26433--26625 Score: 221
Period size: 30 Copynumber: 6.5 Consensus size: 31
26423 ATTTGGGAGT
26433 AAAAATGGTAATTTTTGGAAGTTTCGGGGTC
1 AAAAATGGTAATTTTTGGAAGTTTCGGGGTC
*
26464 AAAAATGG-GATTTTTGGAAG-TTCGGGGGT-
1 AAAAATGGTAATTTTTGGAAGTTTC-GGGGTC
26493 -AAAATGGTAATTTTTGGAAGTTTCGGGGTC
1 AAAAATGGTAATTTTTGGAAGTTTCGGGGTC
* *
26523 AAAAATGG-GATTTTTAGAAG-TTCGGGGGT-
1 AAAAATGGTAATTTTTGGAAGTTTC-GGGGTC
26552 -AAAATGGTAATTTTTGGAAGTTTCGGGGTC
1 AAAAATGGTAATTTTTGGAAGTTTCGGGGTC
* * *
26582 AAAAATGG-GATTTTTAGAA-ATTCGAGGGT-
1 AAAAATGGTAATTTTTGGAAGTTTCG-GGGTC
26611 -AAAATGGTAATTTTT
1 AAAAATGGTAATTTTT
26626 TATGTGCAAT
Statistics
Matches: 140, Mismatches: 10, Indels: 26
0.80 0.06 0.15
Matches are distributed among these distances:
28 21 0.15
29 47 0.34
30 50 0.36
31 22 0.16
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.35
Consensus pattern (31 bp):
AAAAATGGTAATTTTTGGAAGTTTCGGGGTC
Found at i:26512 original size:59 final size:59
Alignment explanation
Indices: 26434--26625 Score: 357
Period size: 59 Copynumber: 3.3 Consensus size: 59
26424 TTTGGGAGTA
*
26434 AAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGT
26493 AAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGT
* *
26552 AAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTAGAAATTCGAGGGT
1 AAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGT
26611 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
26626 TATGTGCAAT
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 130 1.00
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGT
Found at i:26705 original size:29 final size:29
Alignment explanation
Indices: 26624--26717 Score: 109
Period size: 31 Copynumber: 3.1 Consensus size: 29
26614 ATGGTAATTT
*
26624 TTTATGTGCAATTGTATACATGAATTATAA
1 TTTATGTGCAATTGTATACATGAATT-TGA
26654 TTTAATGTGCAATTGTATACATGAACTTTGA
1 TTT-ATGTGCAATTGTATACATGAA-TTTGA
* *
26685 TTT-TGTGCAATTTTATGCATGAAATTTTGA
1 TTTATGTGCAATTGTATACATG-AA-TTTGA
26715 TTT
1 TTT
26718 GATCTAATTC
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
29 16 0.28
30 13 0.23
31 26 0.46
32 2 0.04
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (29 bp):
TTTATGTGCAATTGTATACATGAATTTGA
Found at i:27026 original size:24 final size:24
Alignment explanation
Indices: 26994--27041 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
26984 TAAAAAAAAA
26994 GATACAATAAAACATTAGGTATAT
1 GATACAATAAAACATTAGGTATAT
27018 GATACAATAAAACATTAGGTATAT
1 GATACAATAAAACATTAGGTATAT
27042 AATCATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.29
Consensus pattern (24 bp):
GATACAATAAAACATTAGGTATAT
Found at i:31492 original size:42 final size:42
Alignment explanation
Indices: 31433--31515 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
31423 TTTACATGAA
*
31433 TTGCTAGGTATGATCAATTTAATGTCTGGGCCATGTTGTTTG
1 TTGCTAGGTATGATCAATTTAATGTCAGGGCCATGTTGTTTG
31475 TTGCTAGGTATGATCAATTTAATGTCAGGGCCATGTTGTTT
1 TTGCTAGGTATGATCAATTTAATGTCAGGGCCATGTTGTTT
31516 CTAGGACAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.42
Consensus pattern (42 bp):
TTGCTAGGTATGATCAATTTAATGTCAGGGCCATGTTGTTTG
Found at i:34639 original size:29 final size:29
Alignment explanation
Indices: 34584--34641 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
34574 TTGATTTCTG
* * *
34584 TATTTTATAATGTTATTAATTAGTTTAAA
1 TATTTAATAATATTATTAATTAATTTAAA
**
34613 TATTTAATAATATTATTTTTTAATTTAAA
1 TATTTAATAATATTATTAATTAATTTAAA
34642 AATTAACTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (29 bp):
TATTTAATAATATTATTAATTAATTTAAA
Done.