Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000195.1 Hibiscus syriacus cultivar Beakdansim tig00000348_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: 78088
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:5574 original size:13 final size:13
Alignment explanation
Indices: 5556--5604 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
5546 CTTAGCATGT
5556 TTAAAAATAAAAC
1 TTAAAAATAAAAC
5569 TT-AAAATAAAA-
1 TTAAAAATAAAAC
5580 -TAAAAATGAAAAC
1 TTAAAAAT-AAAAC
* *
5593 TTGAAAAGAAAA
1 TTAAAAATAAAA
5605 GAAAAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 1 0.03
11 5 0.17
12 13 0.43
13 6 0.20
14 5 0.17
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.20
Consensus pattern (13 bp):
TTAAAAATAAAAC
Found at i:5591 original size:24 final size:24
Alignment explanation
Indices: 5557--5609 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
5547 TTAGCATGTT
*
5557 TAAAAATAAAACTT-AAAATAAAA
1 TAAAAATAAAACTTGAAAAGAAAA
5580 TAAAAATGAAAACTTGAAAAGAAAA
1 TAAAAAT-AAAACTTGAAAAGAAAA
*
5605 GAAAA
1 TAAAA
5610 GAAAAGAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 7 0.27
24 7 0.27
25 12 0.46
ACGTcount: A:0.72, C:0.04, G:0.08, T:0.17
Consensus pattern (24 bp):
TAAAAATAAAACTTGAAAAGAAAA
Found at i:9681 original size:2 final size:2
Alignment explanation
Indices: 9674--9704 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9664 AATGAAGTAA
9674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9705 AATGAGATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9842 original size:33 final size:33
Alignment explanation
Indices: 9800--9870 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
9790 AAATAAACAT
* *
9800 TATTATTTAATCAAATATGAAATTATTATATTG
1 TATTTTTTAATAAAATATGAAATTATTATATTG
*
9833 TATTTTTTAATAAAATGTGAAATTATTATATTG
1 TATTTTTTAATAAAATATGAAATTATTATATTG
9866 TATTT
1 TATTT
9871 CATGTAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.52
Consensus pattern (33 bp):
TATTTTTTAATAAAATATGAAATTATTATATTG
Found at i:11188 original size:122 final size:123
Alignment explanation
Indices: 10925--11377 Score: 678
Period size: 123 Copynumber: 3.7 Consensus size: 123
10915 TTAAGGAAAT
* *
10925 GTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAT
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
10990 C-TCTTTCTGGAAATGTTGATGTTGATCTATCTCTTTCTGTGATAGAATC-ATTCAAAAG
66 CTTC-CTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGA-TCAAAAG
*
11048 GTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * *
11113 C-ACTTCTGGAAATTTTGATGCTGATCTATCTCCTTCTGTGATAGCGTCGAGCAAAAG
66 CTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGATCAAAAG
* * * *
11170 GTTGAACAAGTTCATCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTATTCTCATTATAAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
11235 CTTCCTCTAGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGAGTTGATCAAAAG
66 CTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGATCAAAAG
*
11293 GTTGAACAAGTTCTTCTCATTATGAACTTCATCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
*
11358 CTTCCTCTGGAAATATTGAT
66 CTTCCTCTGGAAATGTTGAT
11378 CCATCGAGTG
Statistics
Matches: 297, Mismatches: 31, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
122 107 0.36
123 190 0.64
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.41
Consensus pattern (123 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
CTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGATCAAAAG
Found at i:11355 original size:245 final size:246
Alignment explanation
Indices: 10925--11377 Score: 705
Period size: 245 Copynumber: 1.8 Consensus size: 246
10915 TTAAGGAAAT
* * * *
10925 GTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAT
1 GTTGAACAAGTTCATCTCATTATGAACTTCCTCTTCCTCTTCAGATGAGTTATTCTCATTATAAA
* * * *
10990 CTCTTTCTGGAAATGTTGATGTTGATCTATCTCTTTCTGTGATAGAATCATTCAAAAGGTTGAAC
66 CTCTCTCTAGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCATTCAAAAGGTTGAAC
* * *
11055 AAGTTCTTCTCATTATGAACTTCTTTTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC-ACTTC
131 AAGTTCTTCTCATTATGAACTTCATCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTACCTC
*
11119 TGGAAATTTTGATGCTGATCTATCTCCTTCTGTGATAGCGTCGAGCAAAAG
196 TGGAAATATTGATGCTGATCTATCTCCTTCTGTGATAGCGTCGAGCAAAAG
* *
11170 GTTGAACAAGTTCATCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTATTCTCATTATAAA
1 GTTGAACAAGTTCATCTCATTATGAACTTCCTCTTCCTCTTCAGATGAGTTATTCTCATTATAAA
* * *
11235 CT-TCCTCTAGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGAGTTGA-TCAAAAGGTTGA
66 CTCT-CTCTAGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGA-ATCATTCAAAAGGTTGA
*
11298 ACAAGTTCTTCTCATTATGAACTTCATCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTCC
129 ACAAGTTCTTCTCATTATGAACTTCATCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTACC
11363 TCTGGAAATATTGAT
194 TCTGGAAATATTGAT
11378 CCATCGAGTG
Statistics
Matches: 187, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
244 1 0.01
245 169 0.90
246 17 0.09
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.41
Consensus pattern (246 bp):
GTTGAACAAGTTCATCTCATTATGAACTTCCTCTTCCTCTTCAGATGAGTTATTCTCATTATAAA
CTCTCTCTAGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCATTCAAAAGGTTGAAC
AAGTTCTTCTCATTATGAACTTCATCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTACCTC
TGGAAATATTGATGCTGATCTATCTCCTTCTGTGATAGCGTCGAGCAAAAG
Found at i:11477 original size:37 final size:36
Alignment explanation
Indices: 11416--11617 Score: 217
Period size: 36 Copynumber: 5.6 Consensus size: 36
11406 AGTGAAACTG
* ** *
11416 TCTCAAGCGAGACGAATCTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGATAAATTTTGTTTTAAGAAAAACAA
* * **
11452 TCTCAAGTGAGATAAATTGTTGTTTTGAGTAAAACTG
1 TCTCAAGTGAGATAAATT-TTGTTTTAAGAAAAACAA
* *
11489 TCTCAAGCGAGATAAATTTTGTTTTAAGAAAAATAA
1 TCTCAAGTGAGATAAATTTTGTTTTAAGAAAAACAA
** ** **
11525 TCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTG
1 TCTCAAGTGAGATAAATT-TTGTTTTAAGAAAAACAA
*
11562 TCTCAAGTGAGATGCAA-TTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGAT-AAATTTTGTTTTAAGAAAAACAA
11598 TCTCAAGTGAGATAAATTTT
1 TCTCAAGTGAGATAAATTTT
11618 TATTTGAAAA
Statistics
Matches: 132, Mismatches: 30, Indels: 8
0.78 0.18 0.05
Matches are distributed among these distances:
35 2 0.02
36 72 0.55
37 56 0.42
38 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (36 bp):
TCTCAAGTGAGATAAATTTTGTTTTAAGAAAAACAA
Found at i:11511 original size:73 final size:73
Alignment explanation
Indices: 11399--11615 Score: 328
Period size: 73 Copynumber: 3.0 Consensus size: 73
11389 TGGAAATTTC
* * ** *
11399 TGTTTCCAGTGAAACTGTCTCAAGCGAGACGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTAAAACTGTCTCAAGCGAGATAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
11464 TAAATTGT
66 TAAATTGT
* *
11472 TGTTTTGAGTAAAACTGTCTCAAGCGAGATAAATTTTGTTTTAAGAAAAATAATCTCAAGTGAGA
1 TGTTTCGAGTAAAACTGTCTCAAGCGAGATAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
11537 TAAATTGT
66 TAAATTGT
* * *
11545 TGTTTCGAGTGAAACTGTCTCAAGTGAGATGCAA-TTTGTTTTAAGAAAAACAATCTCAAGTGAG
1 TGTTTCGAGTAAAACTGTCTCAAGCGAGAT-AAATTTTGTTTTAAGAAAAACAATCTCAAGTGAG
11609 ATAAATT
65 ATAAATT
11616 TTTATTTGAA
Statistics
Matches: 131, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
73 129 0.98
74 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (73 bp):
TGTTTCGAGTAAAACTGTCTCAAGCGAGATAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
TAAATTGT
Found at i:12367 original size:22 final size:22
Alignment explanation
Indices: 12342--12420 Score: 140
Period size: 22 Copynumber: 3.6 Consensus size: 22
12332 AATAAAGTTT
*
12342 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
12364 TCATCTTTGAAGAGAGAATTTA
1 TCATCTTTGAAGAGAGAATCTA
12386 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
12408 TCATCTTTGAAGA
1 TCATCTTTGAAGA
12421 ATGTAGATGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:20046 original size:36 final size:36
Alignment explanation
Indices: 19982--20053 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
19972 TCTTACCGTA
* * *
19982 GAATGCTTTTGGTATCAATCTAATAGGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
*
20018 GAATACTTTTGGTATTAATATAACAGGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
20054 TGCATAGCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.42
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
Found at i:21532 original size:23 final size:23
Alignment explanation
Indices: 21479--21533 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
21469 ATTCCAAGAA
21479 AATATATTA-ATTTTTATAAATAT
1 AATAT-TTATATTTTTATAAATAT
* *
21502 ATTTTTTATATTTTTATAAATA-
1 AATATTTATATTTTTATAAATAT
21524 AGATATTTAT
1 A-ATATTTAT
21534 TTACTTAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
AATATTTATATTTTTATAAATAT
Found at i:21802 original size:2 final size:2
Alignment explanation
Indices: 21795--21826 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
21785 AAAAATGAAG
*
21795 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21827 AATAAGATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:21994 original size:4 final size:4
Alignment explanation
Indices: 21985--22013 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
21975 TGAATAAAAC
21985 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
22014 GACTATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:27786 original size:41 final size:41
Alignment explanation
Indices: 27730--27812 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
27720 TAATTTATGG
** *
27730 TTTTTATAAGGCTATAAATTCCCTCTTAGGGTAAGCCTAAT
1 TTTTTATAAGGCTATAAACACCCCCTTAGGGTAAGCCTAAT
27771 TTTTTATAAGGCTATAAACACCCCCTTAGGGTAAGCCTAAT
1 TTTTTATAAGGCTATAAACACCCCCTTAGGGTAAGCCTAAT
27812 T
1 T
27813 CATTATTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.36
Consensus pattern (41 bp):
TTTTTATAAGGCTATAAACACCCCCTTAGGGTAAGCCTAAT
Found at i:38065 original size:33 final size:33
Alignment explanation
Indices: 38027--38089 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
38017 GTTCTAGATT
38027 CAGGAGAGCAATAAAAAAGCACAAAAATCTACC
1 CAGGAGAGCAATAAAAAAGCACAAAAATCTACC
*
38060 CAGGAGAGTAATAAAAAAGCACAAAAATCT
1 CAGGAGAGCAATAAAAAAGCACAAAAATCT
38090 TTCTTCGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.56, C:0.17, G:0.16, T:0.11
Consensus pattern (33 bp):
CAGGAGAGCAATAAAAAAGCACAAAAATCTACC
Found at i:41882 original size:6 final size:6
Alignment explanation
Indices: 41867--41911 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
41857 TTTGCAAAGA
* * * *
41867 ATGTAC ATGTAT ATGTTT ATGTAT ATGTTT ATATAT ATGTAT ATG
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATG
41912 ATAATGTCAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (6 bp):
ATGTAT
Found at i:41888 original size:12 final size:12
Alignment explanation
Indices: 41873--41911 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
41863 AAGAATGTAC
41873 ATGTATATGTTT
1 ATGTATATGTTT
41885 ATGTATATGTTT
1 ATGTATATGTTT
* *
41897 ATATATATGTAT
1 ATGTATATGTTT
41909 ATG
1 ATG
41912 ATAATGTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (12 bp):
ATGTATATGTTT
Found at i:48754 original size:16 final size:15
Alignment explanation
Indices: 48733--48775 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
48723 TTTAAATTTA
* *
48733 AAATATAAATATATT
1 AAATATAAAAAAATT
48748 CAAATATTAAAAAAATT
1 -AAATA-TAAAAAAATT
48765 AAATATAAAAA
1 AAATATAAAAA
48776 TACGAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 10 0.42
17 8 0.33
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATATAAAAAAATT
Found at i:48767 original size:26 final size:26
Alignment explanation
Indices: 48706--48771 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
48696 TTATTTTTTT
*
48706 AAATTAAATAT-TTGAAATTTAAATTTA
1 AAATTAAATATATTCAAATTTAAA--TA
48733 AAATATAAATATATTCAAATATTAAA-A
1 AAAT-TAAATATATTCAAAT-TTAAATA
48760 AAATTAAATATA
1 AAATTAAATATA
48772 AAAATACGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
26 8 0.23
27 9 0.26
28 7 0.20
29 6 0.17
30 5 0.14
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (26 bp):
AAATTAAATATATTCAAATTTAAATA
Found at i:62725 original size:18 final size:18
Alignment explanation
Indices: 62680--62716 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
62670 ATCATACCCC
62680 TAAACTTAAGTTATTACT
1 TAAACTTAAGTTATTACT
62698 TAAACTTAAGTTATTACT
1 TAAACTTAAGTTATTACT
62716 T
1 T
62717 GTCCTTAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
TAAACTTAAGTTATTACT
Found at i:67725 original size:31 final size:31
Alignment explanation
Indices: 67689--67751 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
67679 GGACCTATGT
67689 AACTGTCCATATGTTCCGAAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
* *
67720 AACTGTCTATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
67751 A
1 A
67752 CCCTCGACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:74525 original size:62 final size:62
Alignment explanation
Indices: 74449--74573 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 62
74439 TGTCAACCTA
*
74449 TTTTGGGAATCACCAGTAGTCACCCCTTGAGCAAACTTGCGGGAGATAGACTATCGACTCCC
1 TTTTGGGAATCACCAGTAGTCACCCCTTGAGCAAACTTGCGGGAGAAAGACTATCGACTCCC
* *
74511 TTTTGGGAATCACCAGTAGTCACCCCTTGAGCATACTTGTGGGAGAAAGACTATCGACTCCC
1 TTTTGGGAATCACCAGTAGTCACCCCTTGAGCAAACTTGCGGGAGAAAGACTATCGACTCCC
74573 T
1 T
74574 AATAAGTGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (62 bp):
TTTTGGGAATCACCAGTAGTCACCCCTTGAGCAAACTTGCGGGAGAAAGACTATCGACTCCC
Found at i:76911 original size:17 final size:17
Alignment explanation
Indices: 76889--76922 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
76879 GTGGATCTAT
76889 TCTATCGAGTTATTTGA
1 TCTATCGAGTTATTTGA
*
76906 TCTATCGGGTTATTTGA
1 TCTATCGAGTTATTTGA
76923 AGATGCAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (17 bp):
TCTATCGAGTTATTTGA
Found at i:77014 original size:13 final size:13
Alignment explanation
Indices: 76996--77024 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
76986 AATGATATTC
76996 TTTTTTTTTTACT
1 TTTTTTTTTTACT
77009 TTTTTTTTTTACT
1 TTTTTTTTTTACT
77022 TTT
1 TTT
77025 ATTATATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTTTACT
Found at i:77222 original size:2 final size:2
Alignment explanation
Indices: 77215--77252 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
77205 ATTTTTAGAA
*
77215 AT AT AT AT -T AT AC AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
77253 CTAATGTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:77757 original size:21 final size:22
Alignment explanation
Indices: 77731--77777 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
77721 TAAAATAAAT
77731 ATTTTTTAGTAATTTA-ATTTA
1 ATTTTTTAGTAATTTATATTTA
* *
77752 ATTTTTTAGTATTTTATATTTG
1 ATTTTTTAGTAATTTATATTTA
77774 ATTT
1 ATTT
77778 AAATATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (22 bp):
ATTTTTTAGTAATTTATATTTA
Found at i:77801 original size:6 final size:6
Alignment explanation
Indices: 77790--77820 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
77780 ATATTAAAAA
77790 AAATTT AAATTT AAAATTT AAATTT AAATTT
1 AAATTT AAATTT -AAATTT AAATTT AAATTT
77821 TTTTATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:77807 original size:13 final size:13
Alignment explanation
Indices: 77789--77817 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
77779 AATATTAAAA
77789 AAAATTTAAATTT
1 AAAATTTAAATTT
77802 AAAATTTAAATTT
1 AAAATTTAAATTT
77815 AAA
1 AAA
77818 TTTTTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAAATTTAAATTT
Done.