Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003636.1 Hibiscus syriacus cultivar Beakdansim tig00007701_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: 75251
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Found at i:2314 original size:36 final size:36
Alignment explanation
Indices: 2274--2353 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 36
2264 TTGAGATAGA
2274 AAGATGAAAATTTTATGATAAGAACTGTATAAGTAG
1 AAGATGAAAATTTTATGATAAGAACTGTATAAGTAG
*
2310 AAGATGAAAATTTTATGATAAGAATTGTATAAGTAG
1 AAGATGAAAATTTTATGATAAGAACTGTATAAGTAG
2346 AAGATGAA
1 AAGATGAA
2354 TAGATTGAGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.49, C:0.01, G:0.20, T:0.30
Consensus pattern (36 bp):
AAGATGAAAATTTTATGATAAGAACTGTATAAGTAG
Found at i:4450 original size:54 final size:54
Alignment explanation
Indices: 4368--4489 Score: 199
Period size: 54 Copynumber: 2.3 Consensus size: 54
4358 ATTTACTGAA
**
4368 TGGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTTGTAT
1 TGGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCAGTAT
* *
4422 TGGCATTGTGTGTGCATCTTAAGAAATTCATAATAAGTTTATGAATTTCAGTAT
1 TGGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCAGTAT
*
4476 TGGCACTATGTGTG
1 TGGCACTGTGTGTG
4490 AAACCTCAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (54 bp):
TGGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCAGTAT
Found at i:8414 original size:53 final size:54
Alignment explanation
Indices: 8305--8419 Score: 151
Period size: 53 Copynumber: 2.1 Consensus size: 54
8295 TGGCATTGTC
* * ** *
8305 TGTGCAACTTAAGAAATTTATAATAAGTTTATGAATTCCCGTATTGGCACTGTG
1 TGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTCCAGTATTAACACTATG
* *
8359 TGTGGAACTTAAGAAATTCATAATAAG-TTATGAATTTCAGTATTAACACTATG
1 TGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTCCAGTATTAACACTATG
*
8412 TGTACAAC
1 TGTGCAAC
8420 CTCAAAGAAC
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
53 27 0.52
54 25 0.48
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (54 bp):
TGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTCCAGTATTAACACTATG
Found at i:13264 original size:54 final size:54
Alignment explanation
Indices: 13182--13927 Score: 910
Period size: 54 Copynumber: 13.9 Consensus size: 54
13172 ATTTACCGAA
* * **
13182 TGGCACTCTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATAT
1 TGGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
* * *
13236 TGGCACTGTGTGCGCAA-CTCAAGAAATTCATAATAAGTTTATGAATTTTTGTAC
1 TGGCACTGTGTGTGCAACCT-AAGAAATTCATAATAAGTTTATGAATTTCTGTAT
* * * **
13290 TGACACTATGTGTGCAACCTAAGAATTTCATAATAAGTTTATGAATTTCCCTAT
1 TGGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
* * *
13344 TGGCACTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTAT
1 TGGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
* * *
13398 TGGCACTGTGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCGGCAT
1 TGGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
* * *
13452 TGGCACTATGTGTGCAACCTAATAAATTCATAATAAGTTTATGAATTTCCGTAT
1 TGGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
* *
13506 TGGCAC--TGTGTACAACCTAAGAAATTCATAATAATTTTATGAATTT-TCGTAT
1 TGGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCT-GTAT
* * *
13558 TGGTACTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCTGTAT
1 TGGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
* ** * * *
13612 TGGCACTGTGTGTACAAGTTAATAAATTCATAATAAGTTTTTGAATTTATGTAT
1 TGGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
* * * *
13666 TGACAATGTGTGTGCAACTTCAGAAATTCATAATAAGTTTATGAATTTCTGTAT
1 TGGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
* ** * *
13720 TGGTACTGTGTGTGCAATTTAATAAATTCATAATTAGTTTATGAAATTT-TGTAT
1 TGGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATG-AATTTCTGTAT
* * * * * *
13774 TGCCACTATGTATGCAACCTAAGAAATTCATAATTAGTTTATAAATTTTTGTAT
1 TGGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
*
13828 TGGCACTGTGTGTACAACCTAAGAAATTCATAATTAA-TTTATGAATTTCTGTAT
1 TGGCACTGTGTGTGCAACCTAAGAAATTCATAA-TAAGTTTATGAATTTCTGTAT
* * * * * * * *
13882 TGGCATTATGTGTGCACCCCACGTAATTCATAATGAGCTTATGAAT
1 TGGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT
13928 GACCATATCG
Statistics
Matches: 599, Mismatches: 83, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
52 46 0.08
53 8 0.01
54 535 0.89
55 10 0.02
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.38
Consensus pattern (54 bp):
TGGCACTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
Found at i:14499 original size:71 final size:71
Alignment explanation
Indices: 14383--14521 Score: 269
Period size: 71 Copynumber: 2.0 Consensus size: 71
14373 TTGTAATATC
*
14383 AGTAAGACATCCTATAATGTAATTTTTGACTTAGTTTAGTTGCATGTACTTATGAATGTCCTATT
1 AGTAAGACATCCTATAATGTAATTTTTGACTTAGTTTAGTGGCATGTACTTATGAATGTCCTATT
14448 AGCACT
66 AGCACT
14454 AGTAAGACATCCTATAATGTAATTTTTGACTTAGTTTAGTGGCATGTACTTATGAATGTCCTATT
1 AGTAAGACATCCTATAATGTAATTTTTGACTTAGTTTAGTGGCATGTACTTATGAATGTCCTATT
14519 AGC
66 AGC
14522 TCTAATTAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (71 bp):
AGTAAGACATCCTATAATGTAATTTTTGACTTAGTTTAGTGGCATGTACTTATGAATGTCCTATT
AGCACT
Found at i:16589 original size:21 final size:21
Alignment explanation
Indices: 16563--16613 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
16553 AAATCTTTAT
16563 GGATGACTTCTCCGTTTCTGG
1 GGATGACTTCTCCGTTTCTGG
*
16584 GGATGACTTCTCTGTTTCTGG
1 GGATGACTTCTCCGTTTCTGG
*
16605 AGATGACTT
1 GGATGACTT
16614 TGAGAAATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.14, C:0.20, G:0.27, T:0.39
Consensus pattern (21 bp):
GGATGACTTCTCCGTTTCTGG
Found at i:30038 original size:21 final size:21
Alignment explanation
Indices: 30012--30086 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
30002 AAAACAACGA
* *
30012 AGGGATTGATCC-TTTCTTTCG
1 AGGGATCGATCCTTTTC-CTCG
*
30033 AGGGATCGATCATTTTCCTCG
1 AGGGATCGATCCTTTTCCTCG
*
30054 AGGGATCGATCCTTTTCCCCG
1 AGGGATCGATCCTTTTCCTCG
* *
30075 AAGGATCAATCC
1 AGGGATCGATCC
30087 ATTGCACAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
21 42 0.91
22 4 0.09
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (21 bp):
AGGGATCGATCCTTTTCCTCG
Found at i:31193 original size:432 final size:429
Alignment explanation
Indices: 30378--31233 Score: 1191
Period size: 432 Copynumber: 2.0 Consensus size: 429
30368 TTTTCCTCAT
* * * *
30378 TATATATTTGGCGTCAAAATCTTCCAGCCAAAGCTTTTGGTGGGAAATCTTTTAATGACATTCAG
1 TATATATTTGGCGCCAAAATCTTCCAGCCAAAACTTTTGGTAGGAAATCTTTTAATAACATTCAG
* * * *
30443 ATAAAATAGTGACGTTGTAAAATTGTCTCCAATGGAAAAAAAAGTATTAGTGGCGTTTTATTATA
66 ATAAAATAGTGACATTGTAAAATCGTCTCCAATAGAAAAAAAAGTATTAGTGACGTTTTATTATA
** * * *
30508 GTGACGATGCGATTTGAATTCGTGATGTTGCACATTTCTCACTAATAAATTTTATTTGACACTTT
131 AAGAAGATGCGATTTAAATTCGTGACGTTGCACATTTCTCACTAATAAATTTTATTTGACACTTT
* *
30573 GATTCGTCATATTTTATAAGACATTAAAAGAGGTTATTTATTATTGTCACAAAAATAGATTTAGC
196 GATTCGTCATATTTTATAAGACATTAAAAGAGATTATTTATTATTGCCACAAAAATAGATTTAGC
*
30638 ATGACAAAATCAATTATTTGTCACTCATTGTTATATTTTTTTATATGATGAATTTTAAAGACATC
261 ATGAAAAAATCAATTATTTGTCACTCATTGTTATATTTTTTTATATGATGAATTTTAAAGACATC
*
30703 GTGAAATTACATCACTTAGTATACTGCACCAAGAATATTTTATACATTATTGTGACAGATTGAAA
326 GTGAAATTACATCACTTAATATACTGCACCAAGAATATTTTATACATTATTGTGACAGATTGAAA
** *
30768 ATATTTTATACCAAGTGTGACGGTGGTAGGATTTGTCAC
391 ATATTTTATACCAAGAATGACAGTGGTAGGATTTGTCAC
* * * * * * *
30807 TATATGTTTGTCGCCAAAATCTTCCCGTCAAAATTTTTGGTAGGAAA-CTTTTTAATAATATTTA
1 TATATATTTGGCGCCAAAATCTTCCAGCCAAAACTTTTGGTAGGAAATC-TTTTAATAACATTCA
*
30871 GATAAAATAGTGACATTGTAAAGTCGTCTCCAATAG-AAAAAAAGTATTAGTGACGTTTTATTAT
65 GATAAAATAGTGACATTGTAAAATCGTCTCCAATAGAAAAAAAAGTATTAGTGACGTTTTATTAT
* * * * *
30935 AAAGAAGATGTGATTTAAATTCGTGGCGTTGCACATTTGTCACTAATAATTTTTATTCGTGATAC
130 AAAGAAGATGCGATTTAAATTCGTGACGTTGCACATTTCTCACTAATAAATTTTATT--TGACAC
* * *
31000 TTTGATTTGTCATATTTTATAA-AGCATTAAAAGTGATGT-TTTATTCTTGCCACAAAAAATAGA
193 TTTGATTCGTCATATTTTATAAGA-CATTAAAAGAGAT-TATTTATTATTGCCAC-AAAAATAGA
* *
31063 TTTAGCATGAAAAAATTAATTATTTGTCACTCATTGTTATATCTTTTTTATATGATGAGTTTTAA
255 TTTAGCATGAAAAAATCAATTATTTGTCACTCATTGTTATAT-TTTTTTATATGATGAATTTTAA
* * ** * * *
31128 ATACGTCGTGAAATTATTTCACTTAATGTATTGCACCAAGAATATTTTATACCTTATCT-TGACA
319 AGACATCGTGAAATTACATCACTTAATATACTGCACCAAGAATATTTTATACATTAT-TGTGACA
*
31192 GATTGAAAATATTTTATACCAAGAATGACAGTGGTGGGATTT
383 GATTGAAAATATTTTATACCAAGAATGACAGTGGTAGGATTT
31234 AAACTTGTGC
Statistics
Matches: 373, Mismatches: 46, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
428 76 0.20
429 84 0.23
430 49 0.13
431 50 0.13
432 113 0.30
433 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (429 bp):
TATATATTTGGCGCCAAAATCTTCCAGCCAAAACTTTTGGTAGGAAATCTTTTAATAACATTCAG
ATAAAATAGTGACATTGTAAAATCGTCTCCAATAGAAAAAAAAGTATTAGTGACGTTTTATTATA
AAGAAGATGCGATTTAAATTCGTGACGTTGCACATTTCTCACTAATAAATTTTATTTGACACTTT
GATTCGTCATATTTTATAAGACATTAAAAGAGATTATTTATTATTGCCACAAAAATAGATTTAGC
ATGAAAAAATCAATTATTTGTCACTCATTGTTATATTTTTTTATATGATGAATTTTAAAGACATC
GTGAAATTACATCACTTAATATACTGCACCAAGAATATTTTATACATTATTGTGACAGATTGAAA
ATATTTTATACCAAGAATGACAGTGGTAGGATTTGTCAC
Found at i:33020 original size:19 final size:19
Alignment explanation
Indices: 32996--33036 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
32986 GAAGTTAATA
32996 TTTTAGCTTG-TTTCTTCTG
1 TTTTAGCTTGTTTTC-TCTG
33015 TTTTAGCTTGTTTTCTCTG
1 TTTTAGCTTGTTTTCTCTG
33034 TTT
1 TTT
33037 CATACATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.05, C:0.15, G:0.15, T:0.66
Consensus pattern (19 bp):
TTTTAGCTTGTTTTCTCTG
Found at i:33126 original size:41 final size:43
Alignment explanation
Indices: 33062--33152 Score: 150
Period size: 41 Copynumber: 2.1 Consensus size: 43
33052 AAAATTTTGT
*
33062 AAAACACTGATATGTATATGGAAGTCC-AA-TAAAAAACAAAAG
1 AAAA-ACTGATATGTATACGGAAGTCCAAATTAAAAAACAAAAG
33104 AAAAACTGATATGTATACGGAAGTCCAAATTAAAAAACAAAAG
1 AAAAACTGATATGTATACGGAAGTCCAAATTAAAAAACAAAAG
33147 AAAAAC
1 AAAAAC
33153 AGTTTGTTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
41 21 0.46
42 6 0.13
43 19 0.41
ACGTcount: A:0.57, C:0.12, G:0.13, T:0.18
Consensus pattern (43 bp):
AAAAACTGATATGTATACGGAAGTCCAAATTAAAAAACAAAAG
Found at i:34939 original size:14 final size:15
Alignment explanation
Indices: 34920--34948 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
34910 TTGGTTTTTC
34920 CATTATAT-TGGTGA
1 CATTATATATGGTGA
34934 CATTATATATGGTGA
1 CATTATATATGGTGA
34949 TTTTATGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (15 bp):
CATTATATATGGTGA
Found at i:35277 original size:192 final size:191
Alignment explanation
Indices: 34951--35337 Score: 460
Period size: 192 Copynumber: 2.0 Consensus size: 191
34941 TATGGTGATT
* * *
34951 TTATGCATAATCATCATTCATAATATTATTAGTTAATGATAAATTATCTCATTAAAAATGTGACT
1 TTATGCATAATCATCATTCATAATATTATTAGGTAATCATAAATTATCTCACTAAAAATGTGACT
* * * * *
35016 ATCTCTTTATTCATATATAAGTTGATTTTAATGTATTATTTGTGACAATATAATTAATCAGTAAT
66 ATCTCTTTATTCACATATAAGTTGATTTTAATGTATTATCTGTGACAACATAAATAATCAATAAT
** * *
35081 GAAATCTTATTTAATTTAGTGA-TGTAACTAATTTTCATAGAATATAAATTATAAAGTGACG
131 GAAATCTTACATAATTTAGTGACAG-AACTAATTGTCATAGAATATAAATTATAAAGTGACG
* ** *
35142 TTATGCATAAAT-GTCATTCATAATATTATTAGGTAA-CATTTA-TATTGTCACTAAAAATGTGA
1 TTATGCAT-AATCATCATTCATAATATTATTAGGTAATCATAAATTA-TCTCACTAAAAATGTGA
* ** *
35204 CAATATCTCTTTCA-TCACATATATGTTGATTTTAATGTATTATCTGTGATGACATAAATCATCA
64 C--TATCTCTTT-ATTCACATATAAGTTGATTTTAATGTATTATCTGTGACAACATAAATAATCA
* * * * *
35268 ATAATGAAATTTTACATAATTTAGTGACAGAATTAATTGTCATTGAATATCAATTATATAGTGAC
126 ATAATGAAATCTTACATAATTTAGTGACAGAACTAATTGTCATAGAATATAAATTATAAAGTGAC
35333 G
191 G
35334 TTAT
1 TTAT
35338 ATAGAAAAGT
Statistics
Matches: 165, Mismatches: 25, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
189 2 0.01
190 19 0.12
191 30 0.18
192 112 0.68
193 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.42
Consensus pattern (191 bp):
TTATGCATAATCATCATTCATAATATTATTAGGTAATCATAAATTATCTCACTAAAAATGTGACT
ATCTCTTTATTCACATATAAGTTGATTTTAATGTATTATCTGTGACAACATAAATAATCAATAAT
GAAATCTTACATAATTTAGTGACAGAACTAATTGTCATAGAATATAAATTATAAAGTGACG
Found at i:38790 original size:9 final size:9
Alignment explanation
Indices: 38776--38804 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
38766 CTAATTTATA
38776 TTTTTTTAG
1 TTTTTTTAG
38785 TTTTTTTAG
1 TTTTTTTAG
38794 TTTTTTT-G
1 TTTTTTTAG
38802 TTT
1 TTT
38805 GAATGTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.83
Consensus pattern (9 bp):
TTTTTTTAG
Found at i:41089 original size:19 final size:18
Alignment explanation
Indices: 41047--41092 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
41037 GTAATTGTTG
41047 GAAAAATGCAATTCCTAT
1 GAAAAATGCAATTCCTAT
*
41065 GAAAAAATGCAATTCCTGT
1 G-AAAAATGCAATTCCTAT
41084 AGAAAAATG
1 -GAAAAATG
41093 AGAACCAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 23 0.92
20 1 0.04
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (18 bp):
GAAAAATGCAATTCCTAT
Found at i:44234 original size:54 final size:54
Alignment explanation
Indices: 44150--44697 Score: 646
Period size: 54 Copynumber: 10.1 Consensus size: 54
44140 AATGGTGCTG
* * * *
44150 TGTGAGCAACTTAAGAAATTCATAAGAAGTTTATGAATTTTTGCATTGGCACTA
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* *
44204 TCTGTGGAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* * *
44258 TGTGTGCAACCTAATAAATTCATAATTAGTTTATGAATTTTCGTATTGGCACTA
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* *
44312 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACTA
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* * * ** *
44366 TGTGTGCAACATAAGATATACATAATAAGTTTATGAATTTTTATATTGGCATTA
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* * *
44420 TGTGTGCAACCTAAGAAATTCATAATAAGCTTATGAATTTTCGTATTGTCACTA
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* * * * * * * *
44474 TGAGTGCAACCTAAGAAATTCAAAATTAGTTAATGAATTTTTGTATTGGCAATG
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* * * * * *
44528 TCTGTACAACTTAAGAAATTCATAATGAGGTTGTGAATTTCCGTATTGGCACTA
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* * * * * *
44582 TATGTGTAACTTAAGAAATTCTTAATAAGTTTATGACTTTTCATATTGGCACTG
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
* * * *** * * * *
44636 TATGTGCAACCTAAGAAATTCATATTTCTTTTATTAATTTCCATATTCGCACTA
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
44690 TGTGTGCA
1 TGTGTGCA
44698 CCCCACGTAA
Statistics
Matches: 418, Mismatches: 76, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 418 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (54 bp):
TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTA
Found at i:47615 original size:36 final size:36
Alignment explanation
Indices: 47575--47654 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 36
47565 TTGAGATAGA
47575 AAGATGAAAATTTTATGATAAGAACTGTATAAGTAG
1 AAGATGAAAATTTTATGATAAGAACTGTATAAGTAG
*
47611 AAGATGAAAATTTTATGATAAGAATTGTATAAGTAG
1 AAGATGAAAATTTTATGATAAGAACTGTATAAGTAG
47647 AAGATGAA
1 AAGATGAA
47655 TAGATTGAGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.49, C:0.01, G:0.20, T:0.30
Consensus pattern (36 bp):
AAGATGAAAATTTTATGATAAGAACTGTATAAGTAG
Found at i:49835 original size:55 final size:55
Alignment explanation
Indices: 49692--49836 Score: 152
Period size: 55 Copynumber: 2.6 Consensus size: 55
49682 ATTTACTGAA
* * **
49692 TGGCACTGTGTGTGCAA-CTTAAGAAATTCATAATAAGTTTATGAATTTTTTGTAT
1 TGGCACTATGTGTG-AACCTAAAGAAATTCATAATAAGTTTATGAATTTTCAGTAT
* * * * *
49747 TGGCATTGTGTGTGCATCTTAAGAAATTCATAATAAGTTTATGAA-TTTCAGTAT
1 TGGCACTATGTGTGAACCTAAAGAAATTCATAATAAGTTTATGAATTTTCAGTAT
*
49801 TGGCACTATGTGTGAAACCTCAAAGAACTT-ATAATA
1 TGGCACTATGTGTG-AACCT-AAAGAAATTCATAATA
49837 TTATGAAAGC
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
54 20 0.26
55 50 0.65
56 7 0.09
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (55 bp):
TGGCACTATGTGTGAACCTAAAGAAATTCATAATAAGTTTATGAATTTTCAGTAT
Found at i:53745 original size:53 final size:54
Alignment explanation
Indices: 53636--53750 Score: 151
Period size: 53 Copynumber: 2.1 Consensus size: 54
53626 TGGCACTGTC
* * ** *
53636 TGTGCAACTTAAGAAATTTATAATAAGTTTATGAATTCCCGTATTGGCACTGTG
1 TGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTCCAGTATTAACACTATG
* *
53690 TGTGGAACTTAAGAAATTCATAATAAG-TTATGAATTTCAGTATTAACACTATG
1 TGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTCCAGTATTAACACTATG
*
53743 TGTACAAC
1 TGTGCAAC
53751 CTCAAAGAAC
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
53 27 0.52
54 25 0.48
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (54 bp):
TGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTCCAGTATTAACACTATG
Found at i:58601 original size:54 final size:54
Alignment explanation
Indices: 58522--59259 Score: 903
Period size: 54 Copynumber: 13.7 Consensus size: 54
58512 AATGGAACTC
* **
58522 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACTG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTG
* * * * *
58576 TGTGCGCAA-CTCAAGAAATTCATAATAAGTTTATGAATTTTTGTACTGACACTA
1 TGTGTGCAACCT-AAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTG
* ** *
58630 TGTGTGCAACCTAAGAATTTCATAATAAGTTTATGAATTTCCCTATTGGCACTA
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTG
* *
58684 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGGCACTG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTG
* * * *
58738 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCGGCATTGGCACTA
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTG
* *
58792 TGTGTGCAACCTAATAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAC--
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTG
* * * *
58844 TGTGTACAACCTAAGAAATTCATAATAATTTTATGAATTT-TCGTATTGGTACTA
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCT-GTATTGGCACTG
*
58898 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCTGTATTGGCACTG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTG
* ** * * * * *
58952 TGTGTACAAGTTAATAAATTCATAATAAGTTTTTGAATTTATGTATTGACAATG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTG
* * *
59006 TGTGTGCAACTTCAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGTACTG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTG
** * * * *
59060 TGTGTGCAATTTAATAAATTCATAATTAGTTTATGAAATTT-TGTATTGCCACTA
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATG-AATTTCTGTATTGGCACTG
* * * *
59114 TGTATGCAACCTAAGAAATTCATAATTAGTTTATAAATTTTTGTATTGGCACTG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTG
* * *
59168 TGTGTACAACCTAAGAAATTCATAATTAA-TTTATGAATTTCTGTATTGGCATTA
1 TGTGTGCAACCTAAGAAATTCATAA-TAAGTTTATGAATTTCTGTATTGGCACTG
* * * * * *
59222 TGTGTGCACCCCACGTAATTCATAATGAGCTTATGAAT
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT
59260 GACCATATCG
Statistics
Matches: 592, Mismatches: 82, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
52 46 0.08
53 8 0.01
54 528 0.89
55 10 0.02
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.39
Consensus pattern (54 bp):
TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTG
Found at i:59829 original size:71 final size:71
Alignment explanation
Indices: 59713--59851 Score: 269
Period size: 71 Copynumber: 2.0 Consensus size: 71
59703 TTGTAATATC
*
59713 AGTAAGACATCCTATAATGTAATTTTTGACTTAGTTTAGTTGCATGTACTTATGAATGTCCTATT
1 AGTAAGACATCCTATAATGTAATTTTTGACTTAGTTTAGTGGCATGTACTTATGAATGTCCTATT
59778 AGCACT
66 AGCACT
59784 AGTAAGACATCCTATAATGTAATTTTTGACTTAGTTTAGTGGCATGTACTTATGAATGTCCTATT
1 AGTAAGACATCCTATAATGTAATTTTTGACTTAGTTTAGTGGCATGTACTTATGAATGTCCTATT
59849 AGC
66 AGC
59852 TCTAATTAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (71 bp):
AGTAAGACATCCTATAATGTAATTTTTGACTTAGTTTAGTGGCATGTACTTATGAATGTCCTATT
AGCACT
Found at i:61919 original size:21 final size:21
Alignment explanation
Indices: 61893--61943 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
61883 AAATCTTTAT
61893 GGATGACTTCTCCGTTTCTGG
1 GGATGACTTCTCCGTTTCTGG
*
61914 GGATGACTTCTCTGTTTCTGG
1 GGATGACTTCTCCGTTTCTGG
*
61935 AGATGACTT
1 GGATGACTT
61944 TGAGAAATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.14, C:0.20, G:0.27, T:0.39
Consensus pattern (21 bp):
GGATGACTTCTCCGTTTCTGG
Done.