Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002423.1 Hibiscus syriacus cultivar Beakdansim tig00004958_pilon, 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: 115551
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2322 original size:30 final size:31
Alignment explanation
Indices: 2281--2343 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
2271 TTTCCATTTA
*
2281 TTACAAATGATTTCCATCTATGGA-GGGACT
1 TTACAAATGATTTCCATCTATGAAGGGGACT
*
2311 TTACTAATGATTTCCATCTATGAAGGGGACT
1 TTACAAATGATTTCCATCTATGAAGGGGACT
2342 TT
1 TT
2344 TGTCCCAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.37
Consensus pattern (31 bp):
TTACAAATGATTTCCATCTATGAAGGGGACT
Found at i:3660 original size:19 final size:19
Alignment explanation
Indices: 3636--3673 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3626 CTACTCTTTC
3636 ACATATAAAAGC-ACCACAT
1 ACATAT-AAAGCAACCACAT
3655 ACATATAAAGCAACCACAT
1 ACATATAAAGCAACCACAT
3674 TCAAGCATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.53, C:0.26, G:0.05, T:0.16
Consensus pattern (19 bp):
ACATATAAAGCAACCACAT
Found at i:6707 original size:66 final size:65
Alignment explanation
Indices: 6601--6731 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 65
6591 CACTACCTAA
* *
6601 GCTCCTTACTTAGGATTTTCCAACAAATCTACTAATTTGTTCTTTCTTTTTTCAAGGATCAAGAG
1 GCTCCTCACTTAGGATTTTCCAACAAATCCACTAATTTGTTCTTTC-TTTTTCAAGGATCAAGAG
6666 T
65 T
6667 GCTCCTCACTTAGGATTTTCCAACAAATCCACTAATTTGTTCTTTCTTTTTCAAGGATCAAGAGT
1 GCTCCTCACTTAGGATTTTCCAACAAATCCACTAATTTGTTCTTTCTTTTTCAAGGATCAAGAGT
6732 AACATTTACA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 19 0.30
66 44 0.70
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (65 bp):
GCTCCTCACTTAGGATTTTCCAACAAATCCACTAATTTGTTCTTTCTTTTTCAAGGATCAAGAGT
Found at i:7150 original size:20 final size:20
Alignment explanation
Indices: 7137--7243 Score: 81
Period size: 20 Copynumber: 5.8 Consensus size: 20
7127 AAACTTTAGG
7137 GAAAGTTTCGAAACTCTTGA
1 GAAAGTTTCGAAACTCTTGA
*
7157 GATAGTTTCGAAACTCTT-A
1 GAAAGTTTCGAAACTCTTGA
* * *
7176 AAAAGTATCGAAACATTTTGA
1 GAAAGTTTCGAAAC-TCTTGA
7197 GAAA--TT-G----TCTTG-
1 GAAAGTTTCGAAACTCTTGA
*
7209 TAAAGTTTCGAAACTCTTGTA
1 GAAAGTTTCGAAACTCTTG-A
7230 G-AAGTTTCGAAACT
1 GAAAGTTTCGAAACT
7244 TCTGGTTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 22
0.67 0.10 0.22
Matches are distributed among these distances:
12 3 0.05
13 4 0.06
14 2 0.03
15 1 0.02
18 1 0.02
19 18 0.27
20 33 0.50
21 4 0.06
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.34
Consensus pattern (20 bp):
GAAAGTTTCGAAACTCTTGA
Found at i:8821 original size:12 final size:12
Alignment explanation
Indices: 8804--8839 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
8794 TTGACAATTT
*
8804 CCTCTTCTTTAC
1 CCTCTTCTTCAC
8816 CCTCTTCTTCAC
1 CCTCTTCTTCAC
8828 CCTCTTCTTCAC
1 CCTCTTCTTCAC
8840 TTGAGGTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.08, C:0.47, G:0.00, T:0.44
Consensus pattern (12 bp):
CCTCTTCTTCAC
Found at i:8910 original size:15 final size:16
Alignment explanation
Indices: 8885--8914 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
8875 GAAACACATT
8885 TTTCTTTCTTTTCTTG
1 TTTCTTTCTTTTCTTG
8901 TTTC-TTCTTTTCTT
1 TTTCTTTCTTTTCTT
8915 CTTGTCCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTCTTTCTTTTCTTG
Found at i:13750 original size:60 final size:60
Alignment explanation
Indices: 13673--13851 Score: 175
Period size: 60 Copynumber: 3.0 Consensus size: 60
13663 CATATGTCCC
* *
13673 CAAATTATGACTCTCATT-TCAAATTAGTTCTTAAACTTTTAAACATTTCAATTTCATCCT
1 CAAAATATGACTCTCATTCT-AAATTAGTCCTTAAACTTTTAAACATTTCAATTTCATCCT
** ** ** * *
13733 CAAAATATGACTCTCATTCTTTATTAGTCCTTAAACTTTCGAGTATTCCAATTTTAT-CT
1 CAAAATATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTTCAATTTCATCCT
* * * * *
13792 CTAAACTATGAATCTCATTCTAAATTAATCCCTAAACTTTTATATC-TTTCAATTTCATCC
1 C-AAAATATGACTCTCATTCTAAATTAGTCCTTAAACTTTTA-AACATTTCAATTTCATCC
13852 ATAAATTCAT
Statistics
Matches: 93, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
59 3 0.03
60 87 0.94
61 3 0.03
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (60 bp):
CAAAATATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTTCAATTTCATCCT
Found at i:14101 original size:60 final size:61
Alignment explanation
Indices: 13977--14105 Score: 140
Period size: 60 Copynumber: 2.1 Consensus size: 61
13967 CATGTAATTT
* *
13977 AGGAT-AAAATTGAAATATTCAAAAAGTATGGGACTAATTTAGAATGGAGATCACAGTTTG
1 AGGATGAAAATTGAAATATTCAAAAAGTATAGGACTAATTTAGAATGGAGATCACAGTTTA
* * * * * *
14037 AGGATGAAAA-TGAAATGTTC-AAAAGTTTAAGGACTGATTTAGAAT-GATAGTCATATTTTA
1 AGGATGAAAATTGAAATATTCAAAAAGTAT-AGGACTAATTTAGAATGGAGA-TCACAGTTTA
14097 AGGATGAAA
1 AGGATGAAA
14106 TTAAAAGTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
59 10 0.17
60 44 0.76
61 4 0.07
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.29
Consensus pattern (61 bp):
AGGATGAAAATTGAAATATTCAAAAAGTATAGGACTAATTTAGAATGGAGATCACAGTTTA
Found at i:15553 original size:3 final size:3
Alignment explanation
Indices: 15547--15596 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
15537 AAAAAAAAAT
* *
15547 TAA TAA TAA TAA TTA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
15595 TA
1 TA
15597 TCACTGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:16241 original size:24 final size:23
Alignment explanation
Indices: 16195--16243 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
16185 AATTTAAAAT
*
16195 AATAAAAAATATATTAAATTTTA
1 AATAAAAAATATATCAAATTTTA
16218 AATATAAAAATAT-TCAAATATTTA
1 AATA-AAAAATATATCAAAT-TTTA
16242 AA
1 AA
16244 AAATTAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
AATAAAAAATATATCAAATTTTA
Found at i:16282 original size:23 final size:24
Alignment explanation
Indices: 16233--16283 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
16223 AAAAATATTC
* *
16233 AAATATTTAAAAAATTAATTGTAA
1 AAATATTTAAAAAATAAATTATAA
16257 AAATATTT-AAAAATAAATTAATAA
1 AAATATTTAAAAAATAAATT-ATAA
16281 AAA
1 AAA
16284 ATTATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATATTTAAAAAATAAATTATAA
Found at i:16291 original size:2 final size:2
Alignment explanation
Indices: 16286--16322 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
16276 AATAAAAAAT
16286 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16323 GAACAAGGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17038 original size:2 final size:2
Alignment explanation
Indices: 17033--17059 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17023 AAACCTTAAT
17033 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
17060 TAAAAATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17310 original size:2 final size:2
Alignment explanation
Indices: 17303--17332 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17293 CTATAATTAA
17303 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
17333 TAAAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17341 original size:274 final size:268
Alignment explanation
Indices: 16819--17349 Score: 712
Period size: 274 Copynumber: 2.0 Consensus size: 268
16809 AACGTATTAC
* * * * *
16819 GATGACATGGATTCCTATTTAAAATTGAAAACTCAAGAAAAAAACAATGGCATAGTATGAAAAAG
1 GATGACATAGATTCCTACTTAAAATTGAAAACTCAAAAAAAAAACAATGACATAATATGAAAAAG
* * * *
16884 AATAAGAAAAAATAATAATCACCGACGATTAACAATCAATATTAAAATTAGTACTGTCAGCGACT
66 AACAAGAAAAAATAATAATCACCAACGATCAACAATCAATATTAAAATTAGTACTATCAGCGACT
*
16949 AAACAAAAATCAAGGAAAAAGAGGGAGACAACACAAAAATATTGAGAAAAGGTTTAGGTAAGAGG
131 AAACAAAAATCAAAGAAAAAGAGGGAGACAACACAAAAATATTGAGAAAAGGTTT--GTAAGAGG
** *
17014 AAAAAAGAAAAACCTTAATTATATATATATATATATATATATATATTAAAAATACTAAGATTTTT
194 AAAAAAGAAAAAAATTAATTATATATATATATATATATATATATATTAAAAATAATAAGATTTTT
17079 AATGTGTCAT
259 AATGTGTCAT
*
17089 GATGACATAGATTCCTACTTAAATTTGAAAAAACTCAAAAAAAAAAAACAAATGACATAATATGA
1 GATGACATAGATTCCTACTTAAAATTG--AAAACTC--AAAAAAAAAAC-AATGACATAATATGA
* * * *
17154 AAAAGAACAAG-AAAAATAATAATCACCAATGATCGACAATCAATATTAAAATTGGTACTATCGG
61 AAAAGAACAAGAAAAAATAATAATCACCAACGATCAACAATCAATATTAAAATTAGTACTATCAG
* * *
17218 CGACTAAACAAAAATCAAAGAAAAAGAGGGAGA-TATATAAAAATATTGAGAAAA-G-TT-TAAG
126 CGACTAAACAAAAATCAAAGAAAAAGAGGGAGACAACACAAAAATATTGAGAAAAGGTTTGTAAG
*
17279 AGGAATAAAGAAAACTATAATTAAATATATATATATATATATATATATATATATTAAAAAATAAT
191 AGGAAAAAAGAAAA--A-AATT-AAT-TATATATATATATATATATATATATATT-AAAAATAAT
17344 AAGATT
250 AAGATT
17350 ATTATTAAAA
Statistics
Matches: 228, Mismatches: 22, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
268 17 0.07
270 25 0.11
271 4 0.02
272 11 0.05
273 46 0.20
274 102 0.45
275 23 0.10
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.25
Consensus pattern (268 bp):
GATGACATAGATTCCTACTTAAAATTGAAAACTCAAAAAAAAAACAATGACATAATATGAAAAAG
AACAAGAAAAAATAATAATCACCAACGATCAACAATCAATATTAAAATTAGTACTATCAGCGACT
AAACAAAAATCAAAGAAAAAGAGGGAGACAACACAAAAATATTGAGAAAAGGTTTGTAAGAGGAA
AAAAGAAAAAAATTAATTATATATATATATATATATATATATATTAAAAATAATAAGATTTTTAA
TGTGTCAT
Found at i:17590 original size:24 final size:24
Alignment explanation
Indices: 17563--17610 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
17553 AGAAAACATA
* *
17563 GTAAGTTTCGGCTAATCCAAAATT
1 GTAAGTCTCGACTAATCCAAAATT
*
17587 GTAAGTCTCGACTAATTCAAAATT
1 GTAAGTCTCGACTAATCCAAAATT
17611 TGTTTTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (24 bp):
GTAAGTCTCGACTAATCCAAAATT
Found at i:21340 original size:39 final size:41
Alignment explanation
Indices: 21268--21395 Score: 172
Period size: 42 Copynumber: 3.2 Consensus size: 41
21258 AAAAAGAAAC
* *
21268 GCCGCTAAAGGTTATG-TTTTTAGAGGCATTTTTTACAAA-
1 GCCGCTAAAGGTTATGATATTTAGCGGCATTTTTTACAAAT
*
21307 GCCGCTAAAGGTAATGATATTTAGCGGCATTTTTTTACAAAT
1 GCCGCTAAAGGTTATGATATTTAGCGGCA-TTTTTTACAAAT
* * *
21349 GCTGCTAAAGGTTATGATATTTAGCGGCA-TTTTTCCAACT
1 GCCGCTAAAGGTTATGATATTTAGCGGCATTTTTTACAAAT
21389 GCCGCTA
1 GCCGCTA
21396 TTTATCTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 15 0.19
40 25 0.32
41 11 0.14
42 27 0.35
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (41 bp):
GCCGCTAAAGGTTATGATATTTAGCGGCATTTTTTACAAAT
Found at i:21481 original size:44 final size:44
Alignment explanation
Indices: 21418--21509 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
21408 TTTGTGGTGT
* *
21418 TTTG-TCCCAAAAATGCCGCTAAATGTTCTGACATATAGTGGCA
1 TTTGTTCCCAAAAATGCCGCTAAATATTATGACATATAGTGGCA
* * * *
21461 TTTGTTCCCAAAAATTCCGCTAAATATTATGTCATATGGTGGCG
1 TTTGTTCCCAAAAATGCCGCTAAATATTATGACATATAGTGGCA
21505 TTTGT
1 TTTGT
21510 GAATGTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 4 0.10
44 38 0.90
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (44 bp):
TTTGTTCCCAAAAATGCCGCTAAATATTATGACATATAGTGGCA
Found at i:25070 original size:41 final size:41
Alignment explanation
Indices: 25022--25421 Score: 271
Period size: 41 Copynumber: 9.8 Consensus size: 41
25012 AAAAAATAAA
25022 GCCACTAAAGTACGAGTCTTTAGCGACGTTTGTATAAAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGACGTTTGTATAAAAAC
*
25063 GCCACTAAAGTACGAGTCTATA-CTGACGTTTGTATAAAAAC
1 GCCACTAAAGTACGAGTCTTTAGC-GACGTTTGTATAAAAAC
* * * * * *
25104 GACACTAAATTATGAGTTTTTAGCAACGTTTGTATACAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGACGTTTGTATAAAAAC
* * ** * * *
25145 GCAACTAATGTACTGA-TAAATT-GCGTCGTTTAT-TCAAAAAAT
1 GCCACTAAAGTAC-GAGT-CTTTAGCGACGTTTGTAT--AAAAAC
* * * *** * **
25187 GCCATTACAA-TATGAATCTCTTA-CGGTATTTTTCCAAAAAC
1 GCCACTA-AAGTACGAGTCT-TTAGCGACGTTTGTATAAAAAC
* * * * * *
25228 ACAATTATA-TACGTGTCCTATTA-CGGCGTTTGTATAAAAAC
1 GCCACTAAAGTACGAGT-CT-TTAGCGACGTTTGTATAAAAAC
* ** *
25269 ACCACTAAAGTACGAGTCTTTAGCGGTGTTTGTATATAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGACGTTTGTATAAAAAC
* * *
25310 TCCACTAAAGTACGAGTCTATGGCTG-CGTTTGTATAAAAAC
1 GCCACTAAAGTACGAGTCTTTAGC-GACGTTTGTATAAAAAC
* * * *
25351 ACCACTAAAGTA-TAGTCTTTAGCGGCGTTTATATAAAAAC
1 GCCACTAAAGTACGAGTCTTTAGCGACGTTTGTATAAAAAC
*
25391 GCCACTAAAGTACGAGTATTTAGCGACGTTT
1 GCCACTAAAGTACGAGTCTTTAGCGACGTTT
25422 TTGCGTAAAA
Statistics
Matches: 278, Mismatches: 64, Indels: 34
0.74 0.17 0.09
Matches are distributed among these distances:
39 1 0.00
40 43 0.15
41 201 0.72
42 32 0.12
43 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (41 bp):
GCCACTAAAGTACGAGTCTTTAGCGACGTTTGTATAAAAAC
Found at i:29190 original size:21 final size:21
Alignment explanation
Indices: 29164--29233 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
29154 TTCTGGTGTG
29164 GATACCAGTTCATCCAATATA
1 GATACCAGTTCATCCAATATA
** * ** * *
29185 GATACCAACTCACCCGGTGTG
1 GATACCAGTTCATCCAATATA
29206 GATACCAGTTCATCCAATATA
1 GATACCAGTTCATCCAATATA
29227 GATACCA
1 GATACCA
29234 ACTCACCCGG
Statistics
Matches: 35, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.24
Consensus pattern (21 bp):
GATACCAGTTCATCCAATATA
Found at i:29207 original size:42 final size:42
Alignment explanation
Indices: 29158--29251 Score: 179
Period size: 42 Copynumber: 2.2 Consensus size: 42
29148 CCAAATTTCT
29158 GGTGTGGATACCAGTTCATCCAATATAGATACCAACTCACCC
1 GGTGTGGATACCAGTTCATCCAATATAGATACCAACTCACCC
29200 GGTGTGGATACCAGTTCATCCAATATAGATACCAACTCACCC
1 GGTGTGGATACCAGTTCATCCAATATAGATACCAACTCACCC
*
29242 GGTATGGATA
1 GGTGTGGATA
29252 GCAGCCCACC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (42 bp):
GGTGTGGATACCAGTTCATCCAATATAGATACCAACTCACCC
Found at i:29251 original size:21 final size:21
Alignment explanation
Indices: 29185--29251 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
29175 ATCCAATATA
*
29185 GATACCAACTCACCCGGTGTG
1 GATACCAACTCACCCGGTATG
** * ** *
29206 GATACCAGTTCATCCAATATA
1 GATACCAACTCACCCGGTATG
29227 GATACCAACTCACCCGGTATG
1 GATACCAACTCACCCGGTATG
29248 GATA
1 GATA
29252 GCAGCCCACC
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
GATACCAACTCACCCGGTATG
Found at i:31532 original size:47 final size:44
Alignment explanation
Indices: 31458--31547 Score: 117
Period size: 47 Copynumber: 2.0 Consensus size: 44
31448 CTTAAAAAAT
*
31458 TATTAATTTACTAAAAAATAATTAAAAAATACGATAAATTACTAATC
1 TATTAATTTACTAAAAAACAA-TAAAAAATAC--TAAATTACTAATC
* * *
31505 TATTAATTTTCTAATAAACAATAAAAAATACTAAATTATTAAT
1 TATTAATTTACTAAAAAACAATAAAAAATACTAAATTACTAAT
31548 TAATATTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
44 11 0.28
46 10 0.26
47 18 0.46
ACGTcount: A:0.54, C:0.08, G:0.01, T:0.37
Consensus pattern (44 bp):
TATTAATTTACTAAAAAACAATAAAAAATACTAAATTACTAATC
Found at i:32764 original size:21 final size:21
Alignment explanation
Indices: 32738--32777 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
32728 TAGAAAGTTA
32738 GCATTTTTGGGCCCAAATAAG
1 GCATTTTTGGGCCCAAATAAG
32759 GCATTTTTGGGCCCAAATA
1 GCATTTTTGGGCCCAAATA
32778 TTGGTACTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (21 bp):
GCATTTTTGGGCCCAAATAAG
Found at i:35806 original size:77 final size:79
Alignment explanation
Indices: 35700--35852 Score: 181
Period size: 77 Copynumber: 2.0 Consensus size: 79
35690 CAAATTTTAA
**
35700 AAAAACTTATTTAATTAATTCAAATTAAATAT-ACATT-AAAGACTTATAATCTGAATTAAAATC
1 AAAAACTTATTTAATTAATTCAAATTAAATATCA-ATTAAAAGACTTATAATCAAAATTAAAATC
35763 -TTTAATGTTTATTT
65 TTTTAATGTTTATTT
* * * * *
35777 AAAATCTTATTTAATT-ATTCTGAAA-TAAATATCAATTAAAAGAGTTGTAATCAAAATTACATT
1 AAAAACTTATTTAATTAATTC--AAATTAAATATCAATTAAAAGACTTATAATCAAAATTAAAAT
35840 CTTTTAATGTTTA
64 CTTTTAATGTTTA
35853 CTTACTATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
76 4 0.06
77 25 0.39
78 24 0.38
79 11 0.17
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (79 bp):
AAAAACTTATTTAATTAATTCAAATTAAATATCAATTAAAAGACTTATAATCAAAATTAAAATCT
TTTAATGTTTATTT
Found at i:38581 original size:21 final size:23
Alignment explanation
Indices: 38556--38602 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
38546 TCTATAAAAA
38556 TAAAAATATT-ATAT-TATATTT
1 TAAAAATATTAATATATATATTT
*
38577 TAAAATTATTAATATATATATTT
1 TAAAAATATTAATATATATATTT
38600 TAA
1 TAA
38603 GGAATTTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.39
22 4 0.17
23 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAAAAATATTAATATATATATTT
Found at i:38866 original size:23 final size:23
Alignment explanation
Indices: 38824--38879 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
38814 ATTATTATAT
38824 TATATTATTAAAAATATTAATAAA
1 TATATT-TTAAAAATATTAATAAA
* * *
38848 TATATTTTAAATATGTTAATAAT
1 TATATTTTAAAAATATTAATAAA
38871 TAATATTTT
1 T-ATATTTT
38880 TATTAAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATAAA
Found at i:40666 original size:20 final size:20
Alignment explanation
Indices: 40641--40705 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
40631 GAGTCCTTTC
*
40641 CAAATTCACAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
40661 CAAATTCGCAACAC-ATAAGT
1 CAAATTCGCAACGCGA-AAGT
* *
40681 CAAATTGGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
40701 CAAAT
1 CAAAT
40706 GTTTTTACGC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 36 0.95
21 1 0.03
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:40856 original size:22 final size:22
Alignment explanation
Indices: 40831--40878 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
40821 CTACGGCGAC
40831 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
40853 ATCCGTCCCCATTTCCGATGAA
1 ATCCGTCCCCATCTCCGACGAA
40875 ATCC
1 ATCC
40879 ATCTATCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.42, G:0.12, T:0.23
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:41162 original size:20 final size:21
Alignment explanation
Indices: 41137--41183 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
41127 AACACCAAAT
41137 TCGCAACGCG-AAAATAAAAA
1 TCGCAACGCGAAAAATAAAAA
*
41157 TCGCAACGCGAAAAATGAAAA
1 TCGCAACGCGAAAAATAAAAA
41178 TCGCAA
1 TCGCAA
41184 TTTTAGTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.51, C:0.21, G:0.17, T:0.11
Consensus pattern (21 bp):
TCGCAACGCGAAAAATAAAAA
Found at i:43706 original size:13 final size:13
Alignment explanation
Indices: 43688--43721 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
43678 GGGTTTCTTC
43688 AACAAAAAGACAA
1 AACAAAAAGACAA
*
43701 AACAAAAAGATAA
1 AACAAAAAGACAA
43714 AACAAAAA
1 AACAAAAA
43722 CAAATGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.79, C:0.12, G:0.06, T:0.03
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:43998 original size:22 final size:22
Alignment explanation
Indices: 43936--44000 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
43926 GAGATAGATG
* *
43936 GATTTCGTCGGAAATGGGAACA
1 GATTTCGTCGGAGATGGGGACA
43958 GATTTCGTCGGAGATGGGGACA
1 GATTTCGTCGGAGATGGGGACA
43980 GATTTCGTCGGAGATGGGGAC
1 GATTTCGTCGGAGATGGGGAC
44001 GGATGTCGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.25, C:0.14, G:0.38, T:0.23
Consensus pattern (22 bp):
GATTTCGTCGGAGATGGGGACA
Found at i:47321 original size:22 final size:22
Alignment explanation
Indices: 47296--47340 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
47286 AAATCTATCT
* *
47296 AATATGTATGTAGTGTCAATCA
1 AATATGTATATAATGTCAATCA
*
47318 AATATTTATATAATGTCAATCA
1 AATATGTATATAATGTCAATCA
47340 A
1 A
47341 GAATATTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (22 bp):
AATATGTATATAATGTCAATCA
Found at i:51907 original size:22 final size:22
Alignment explanation
Indices: 51879--52192 Score: 466
Period size: 22 Copynumber: 14.2 Consensus size: 22
51869 ATTTTAAAAT
51879 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
51901 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
51923 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
* ***
51945 TTTATTTTAAAATATGAAAAAA
1 TTTATTTTAAAATATGGATTGA
* ***
51967 TTTATTTTAAAATATGAAAAAA
1 TTTATTTTAAAATATGGATTGA
* ***
51989 TTTATTTTAAAATATTGAAAAA
1 TTTATTTTAAAATATGGATTGA
52011 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
52033 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
52055 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
*
52077 TTTATTTTAAAATATAGATTGA
1 TTTATTTTAAAATATGGATTGA
* ***
52099 TTTATTTTAAAATATGAAAAAA
1 TTTATTTTAAAATATGGATTGA
52121 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
52143 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
52165 TTTATTTTTAAAATATGGATTGA
1 TTTA-TTTTAAAATATGGATTGA
52188 TTTAT
1 TTTAT
52193 GTTTGGATTT
Statistics
Matches: 271, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
22 249 0.92
23 22 0.08
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
TTTATTTTAAAATATGGATTGA
Found at i:53722 original size:22 final size:22
Alignment explanation
Indices: 53697--53766 Score: 140
Period size: 22 Copynumber: 3.2 Consensus size: 22
53687 GAAACGTTTA
53697 AAAATATGGATTGATTTATTTT
1 AAAATATGGATTGATTTATTTT
53719 AAAATATGGATTGATTTATTTT
1 AAAATATGGATTGATTTATTTT
53741 AAAATATGGATTGATTTATTTT
1 AAAATATGGATTGATTTATTTT
53763 AAAA
1 AAAA
53767 AATTTATTAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (22 bp):
AAAATATGGATTGATTTATTTT
Found at i:53847 original size:31 final size:31
Alignment explanation
Indices: 53790--53848 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
53780 AGTTGTATGG
*
53790 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
53821 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
53849 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:58980 original size:17 final size:18
Alignment explanation
Indices: 58948--58984 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
58938 CAAGAATCAA
*
58948 AAGAAACCATGAAAATTG
1 AAGAAACCAAGAAAATTG
58966 AAGAAA-CAAGAAAATTG
1 AAGAAACCAAGAAAATTG
58983 AA
1 AA
58985 TCCAACTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.62, C:0.08, G:0.16, T:0.14
Consensus pattern (18 bp):
AAGAAACCAAGAAAATTG
Found at i:64985 original size:156 final size:157
Alignment explanation
Indices: 64816--65189 Score: 482
Period size: 156 Copynumber: 2.4 Consensus size: 157
64806 ATTGGTTTCA
* * * * * *
64816 TTATTTCTTCAATTCCTCCTTCATTTTAAGTTCATTTTCACTAAATTTGAACCACATGCAACTAA
1 TTATTTCTTCAATTCATCATTTATTTTAAGTCCATTTTTACCAAATTTGAACCACATGCAACTAA
* * *
64881 ACCATAGAAGAATACATGTTTACTTTCAATTCCTCTTTTTGATAACAAATTTTGTATTTTTTTAA
66 ACCATAGAAGAATACATGTGTAATTTCAATTCCTCTTTTTGATAACAAATTTTGTA-TTTTTCAA
*
64946 TTTAGTCCTTC-ATTTTTCATAATCTCC
130 TTGAGTCCTTCAATTTTTCATAATCTCC
* * ** * **
64973 TT-TTTCTTCAATTCGTCATTTATTTTAAGTCCGTTTTTACCAAATTTGAGTCATATGCTCCTAA
1 TTATTTCTTCAATTCATCATTTATTTTAAGTCCATTTTTACCAAATTTGAACCACATGCAACTAA
* * * *
65037 ACCCTAGTAGAATACATGTGTAATTTCAATTCCTCTTTTTGATAACAATTTTTTTATTTTTCAAT
66 ACCATAGAAGAATACATGTGTAATTTCAATTCCTCTTTTTGATAACAAATTTTGTATTTTTCAAT
65102 TGAGTCCTTCAATTTTTCATAATCTCC
131 TGAGTCCTTCAATTTTTCATAATCTCC
* * **
65129 TTATTCCTTCAATTTATGGTTTATTTTAAGTCCATTTTTTTACCAAATTTGAACCACATGC
1 TTATTTCTTCAATTCATCATTTATTTTAAGTCCA--TTTTTACCAAATTTGAACCACATGC
65190 TCATATACCA
Statistics
Matches: 184, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
155 17 0.09
156 118 0.64
157 27 0.15
159 22 0.12
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.47
Consensus pattern (157 bp):
TTATTTCTTCAATTCATCATTTATTTTAAGTCCATTTTTACCAAATTTGAACCACATGCAACTAA
ACCATAGAAGAATACATGTGTAATTTCAATTCCTCTTTTTGATAACAAATTTTGTATTTTTCAAT
TGAGTCCTTCAATTTTTCATAATCTCC
Found at i:67289 original size:18 final size:17
Alignment explanation
Indices: 67252--67333 Score: 92
Period size: 18 Copynumber: 4.7 Consensus size: 17
67242 TATGGAATTG
*
67252 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
67269 GATTCTAATTCCTTCACA
1 GATTCCAATTCC-TCACA
* *
67287 GATTCCAATTCCTGATA
1 GATTCCAATTCCTCACA
* *
67304 GATTCTAATTCTTTCACA
1 GATTCCAATTC-CTCACA
67322 GATTCCAATTCC
1 GATTCCAATTCC
67334 CTCAGAAACA
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
17 24 0.46
18 28 0.54
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.37
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:67295 original size:35 final size:35
Alignment explanation
Indices: 67252--67333 Score: 146
Period size: 35 Copynumber: 2.3 Consensus size: 35
67242 TATGGAATTG
67252 GATTCCAATTCCTGACAGATTCTAATTCCTTCACA
1 GATTCCAATTCCTGACAGATTCTAATTCCTTCACA
* *
67287 GATTCCAATTCCTGATAGATTCTAATTCTTTCACA
1 GATTCCAATTCCTGACAGATTCTAATTCCTTCACA
67322 GATTCCAATTCC
1 GATTCCAATTCC
67334 CTCAGAAACA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.37
Consensus pattern (35 bp):
GATTCCAATTCCTGACAGATTCTAATTCCTTCACA
Found at i:68280 original size:406 final size:405
Alignment explanation
Indices: 67522--68463 Score: 1663
Period size: 406 Copynumber: 2.3 Consensus size: 405
67512 CAAAATATTC
*
67522 AAATTATTGTTATTCCTTGAGGTCCAGGTTCGAGCACTAGAAATACTAGGGGTGTGAGCGTTCAA
1 AAATTATTGTTATTCCTTGAGGTCCAGGTTCGAGCACCAGAAATACTAGGGGTGTGAGCGTTCAA
67587 TGTCAAATGATTGAAAGTTATCTTTAAACAAATAGTCTTGTACTTACCTCATATTATTAAAAAAC
66 TGTCAAATGATTGAAAGTTATCTTTAAACAAATAGTCTTGTACTTACCTCATATTATTAAAAAAC
*
67652 AAAAAAAAAAGTCTTGACGTGGTAGTTAACAAAATTGGTATAATTATATTCGAATGCTCACCCTT
131 AAAAAAAAAAGTCTTGACGTGGTAGTTAACAAAATTGGTATAATTATATTCGAATGCTCACCCCT
67717 ACTTTTAGGGGATTTAAGAATGATTCTCAACTACCTAACCAATTGCACTATGATGCCATTAAAAT
196 ACTTTTAGGGGATTTAAGAATGATTCTCAACTACCTAACCAATTGCACTATGATGCCATTAAAAT
* *
67782 ATAGGGTAAACTATACCATTGATCATTTAACTATTTAGCTTTTTTACTTTTACCACCGATTTTTC
261 ATAGGGTAAACTATACCATTGATCAGTTAACTATTTAGCCTTTTTACTTTTACCACCGATTTTTC
67847 AATTTTGTCAATCATATCTCCAAAATATTCAAATGATGCCAATCAAGCCACTTGTCGAACCAAGC
326 AATTTTGTCAATCATATCTCCAAAATATTCAAATG-TGCCAATCAAGCCACTTGTCGAACCAAGC
67912 GAGTTCAGTGGTAAAG
390 GAGTTCAGTGGTAAAG
* * *
67928 AAATTGTTGTTATTCTTTGAGGTCCCAGGTTCTAGCACCAGAAATACTAGGGGTGTGAGCGTTCA
1 AAATTATTGTTATTCCTTGAGGT-CCAGGTTCGAGCACCAGAAATACTAGGGGTGTGAGCGTTCA
*
67993 ATGTCAAATGATTGAAAGTTATCTTTAAACAAATAGTCTTGTACTTACCTCATATTATTAAAACA
65 ATGTCAAATGATTGAAAGTTATCTTTAAACAAATAGTCTTGTACTTACCTCATATTATTAAAAAA
68058 CAAAAAAAAAA-TCTTGACGTGGTAGTTAACAAAATTGGTATAATTATATTCGAATGCTCACCCC
130 CAAAAAAAAAAGTCTTGACGTGGTAGTTAACAAAATTGGTATAATTATATTCGAATGCTCACCCC
68122 TACTTTTAGGGGATTTAAGAATGATTCTCAACTACCTAACCAATTGCACTATGATGCCATTAAAA
195 TACTTTTAGGGGATTTAAGAATGATTCTCAACTACCTAACCAATTGCACTATGATGCCATTAAAA
* *
68187 TATAGGGTAAACTATATCATTGATCAGTTAACTATTTAGCCTTTTTACTTTTACCGCCGATTTTT
260 TATAGGGTAAACTATACCATTGATCAGTTAACTATTTAGCCTTTTTACTTTTACCACCGATTTTT
* * * *
68252 CAATTTTGTCAATCATATCTCCAAAATATTCAAATGTTCCAATCAAGCTACTTGTTGTACCAAGC
325 CAATTTTGTCAATCATATCTCCAAAATATTCAAATGTGCCAATCAAGCCACTTGTCGAACCAAGC
*
68317 GAGTTCGGTGGTAAAG
390 GAGTTCAGTGGTAAAG
*
68333 AAATTATTGTTATTCCTTGAGGTAC-GAGTTCGAGCACCAGAAATACTAGGGGTGTGAGCGTTCA
1 AAATTATTGTTATTCCTTGAGGTCCAG-GTTCGAGCACCAGAAATACTAGGGGTGTGAGCGTTCA
* *
68397 ATGTCAAATGATTGAAAGTTATCTTTAAACAAATATTGTCTTGTACTTGCATCATATTATTAAAA
65 ATGTCAAATGATTGAAAGTTATCTTTAAACAAATA--GTCTTGTACTTACCTCATATTATTAAAA
68462 AA
128 AA
68464 AGTCTTGACA
Statistics
Matches: 510, Mismatches: 22, Indels: 8
0.94 0.04 0.01
Matches are distributed among these distances:
403 1 0.00
404 72 0.14
405 61 0.12
406 262 0.51
407 114 0.22
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (405 bp):
AAATTATTGTTATTCCTTGAGGTCCAGGTTCGAGCACCAGAAATACTAGGGGTGTGAGCGTTCAA
TGTCAAATGATTGAAAGTTATCTTTAAACAAATAGTCTTGTACTTACCTCATATTATTAAAAAAC
AAAAAAAAAAGTCTTGACGTGGTAGTTAACAAAATTGGTATAATTATATTCGAATGCTCACCCCT
ACTTTTAGGGGATTTAAGAATGATTCTCAACTACCTAACCAATTGCACTATGATGCCATTAAAAT
ATAGGGTAAACTATACCATTGATCAGTTAACTATTTAGCCTTTTTACTTTTACCACCGATTTTTC
AATTTTGTCAATCATATCTCCAAAATATTCAAATGTGCCAATCAAGCCACTTGTCGAACCAAGCG
AGTTCAGTGGTAAAG
Found at i:70999 original size:17 final size:18
Alignment explanation
Indices: 70970--71006 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
70960 TCGTACACCC
*
70970 TCAAAATATATTTTTTAT
1 TCAAAATATATTTTTGAT
70988 TCAAAA-ATATTTTTGAT
1 TCAAAATATATTTTTGAT
71005 TC
1 TC
71007 CATAATTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (18 bp):
TCAAAATATATTTTTGAT
Found at i:74230 original size:19 final size:19
Alignment explanation
Indices: 74206--74245 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
74196 TTTCAAGCAA
74206 AAATTAACCTATCAGAAAT
1 AAATTAACCTATCAGAAAT
74225 AAATTAACCTATCAGAAAT
1 AAATTAACCTATCAGAAAT
74244 AA
1 AA
74246 CTGAATGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.15, G:0.05, T:0.25
Consensus pattern (19 bp):
AAATTAACCTATCAGAAAT
Found at i:85614 original size:19 final size:19
Alignment explanation
Indices: 85590--85633 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
85580 TTTTTTATCG
85590 GAAATCAGGAAATCGACCC
1 GAAATCAGGAAATCGACCC
*
85609 GAAATCTGGAAATCGACCC
1 GAAATCAGGAAATCGACCC
85628 GAAATC
1 GAAATC
85634 GACCCTAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAATCAGGAAATCGACCC
Found at i:87399 original size:13 final size:13
Alignment explanation
Indices: 87380--87424 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
87370 GTCACAACCC
87380 GACCCGACCCGTT
1 GACCCGACCCGTT
*
87393 TACCCGACCCGTT
1 GACCCGACCCGTT
87406 GACCCGACCCGTT
1 GACCCGACCCGTT
87419 GACCCG
1 GACCCG
87425 TTGACCGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:87409 original size:8 final size:8
Alignment explanation
Indices: 87398--87437 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
87388 CCGTTTACCC
87398 GACCCGTT
1 GACCCGTT
87406 GACCC---
1 GACCCGTT
87411 GACCCGTT
1 GACCCGTT
87419 GACCCGTT
1 GACCCGTT
87427 GA-CCGTT
1 GACCCGTT
87434 GACC
1 GACC
87438 GGAGTTGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (8 bp):
GACCCGTT
Found at i:88773 original size:18 final size:18
Alignment explanation
Indices: 88747--88782 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
88737 TCGAAAGGAC
*
88747 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
88765 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
88783 CAGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:90005 original size:24 final size:24
Alignment explanation
Indices: 89909--90017 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
89899 GAATATTTTA
* *
89909 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
89933 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
89957 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
89981 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
90005 TTTGATTTCTGAT
1 TCTGATATCTGAT
90018 ATCTCCGTTT
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 63 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:90185 original size:2 final size:2
Alignment explanation
Indices: 90178--90212 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
90168 CGGATGGGGG
90178 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
90213 GTTTTAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:92186 original size:13 final size:13
Alignment explanation
Indices: 92167--92211 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
92157 GTCACAACCC
92167 GACCCGACCCGTT
1 GACCCGACCCGTT
*
92180 TACCCGACCCGTT
1 GACCCGACCCGTT
92193 GACCCGACCCGTT
1 GACCCGACCCGTT
92206 GACCCG
1 GACCCG
92212 TTGACCGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:92196 original size:8 final size:8
Alignment explanation
Indices: 92185--92224 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
92175 CCGTTTACCC
92185 GACCCGTT
1 GACCCGTT
92193 GACCC---
1 GACCCGTT
92198 GACCCGTT
1 GACCCGTT
92206 GACCCGTT
1 GACCCGTT
92214 GA-CCGTT
1 GACCCGTT
92221 GACC
1 GACC
92225 GGAGTTGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (8 bp):
GACCCGTT
Found at i:93557 original size:18 final size:18
Alignment explanation
Indices: 93531--93566 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
93521 TCGAAAGGAC
*
93531 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
93549 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
93567 CAGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:94788 original size:24 final size:24
Alignment explanation
Indices: 94692--94800 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
94682 GAATATTTTA
* *
94692 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
94716 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
94740 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
94764 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
94788 TTTGATTTCTGAT
1 TCTGATATCTGAT
94801 ATCTCCGTTT
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 63 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:94968 original size:2 final size:2
Alignment explanation
Indices: 94961--95015 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
94951 CGGATGGGGG
94961 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
95003 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
95016 GTTTTAAAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:102500 original size:13 final size:13
Alignment explanation
Indices: 102482--102536 Score: 83
Period size: 13 Copynumber: 4.2 Consensus size: 13
102472 TGCGTCATAA
*
102482 ATTTATGACGTGC
1 ATTTATGACGCGC
*
102495 ATTTATGACACGC
1 ATTTATGACGCGC
102508 ATTTATGACGCGC
1 ATTTATGACGCGC
*
102521 ATTTATGACGCTC
1 ATTTATGACGCGC
102534 ATT
1 ATT
102537 GAGCGTCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:102613 original size:85 final size:85
Alignment explanation
Indices: 102508--102673 Score: 212
Period size: 85 Copynumber: 2.0 Consensus size: 85
102498 TATGACACGC
* * *
102508 ATTTATGACGCGCATTTATGACGCT-CATTGAGCGTCATTGAAGCCCCCGTCA-TA-AATGAAGA
1 ATTTATGACACGCATTTATGAC-CTACATTGAGCGTCATTGAAGCACACGTCATTAGAA--AAGA
*
102570 CGACACACATTTGTGTGTCATAA
63 CGACACACATTCGTGTGTCATAA
* * * *
102593 ATTTATGACACGCATTTATGACTTACATTGCGTGTCATTGAAGCACACGTCATTAGAAAAGATGA
1 ATTTATGACACGCATTTATGACCTACATTGAGCGTCATTGAAGCACACGTCATTAGAAAAGACGA
102658 CACACATTCGTGTGTC
66 CACACATTCGTGTGTC
102674 GTGATTGTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
84 1 0.01
85 65 0.93
86 2 0.03
87 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (85 bp):
ATTTATGACACGCATTTATGACCTACATTGAGCGTCATTGAAGCACACGTCATTAGAAAAGACGA
CACACATTCGTGTGTCATAA
Found at i:102767 original size:2 final size:2
Alignment explanation
Indices: 102760--102797 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
102750 CTCATAATAC
102760 TA TA TA TA TA TA TA TA TA TA TA TA TCA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
102798 AGCAATCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:104999 original size:16 final size:16
Alignment explanation
Indices: 104963--104996 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
104953 CACGTGAGGA
104963 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
104979 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
104996 T
1 T
104997 ATTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:111374 original size:21 final size:21
Alignment explanation
Indices: 111331--111374 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
111321 TTACTTTTTC
* *
111331 TTTTCTCTTTCTTTATTCATT
1 TTTTCTCTTTCATTATTAATT
*
111352 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAATT
111372 TTT
1 TTT
111375 ACTTTTTCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAATT
Found at i:114222 original size:23 final size:23
Alignment explanation
Indices: 114167--114222 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
114157 AGCTGACACT
*
114167 GGACAGCTATCTCTGCACGTGAA
1 GGACAGCTGTCTCTGCACGTGAA
*
114190 GGACAACTGTCTCTGCACGTGAA
1 GGACAGCTGTCTCTGCACGTGAA
*
114213 GGACTGCTGT
1 GGACAGCTGT
114223 AACCGTCTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (23 bp):
GGACAGCTGTCTCTGCACGTGAA
Done.