Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007121.1 Hibiscus syriacus cultivar Beakdansim tig00018608_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: 81555
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:4817 original size:26 final size:27
Alignment explanation
Indices: 4781--4833 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
4771 TACCTTTATA
4781 TTGCTTCTTC-TACTAATAATTAAATT
1 TTGCTTCTTCTTACTAATAATTAAATT
4807 TTGCTTCTTCTTATACTAATAATTAAA
1 TTGCTTCTTC-T-TACTAATAATTAAA
4834 ATTAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 10 0.42
29 14 0.58
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.49
Consensus pattern (27 bp):
TTGCTTCTTCTTACTAATAATTAAATT
Found at i:6005 original size:60 final size:60
Alignment explanation
Indices: 5912--6072 Score: 182
Period size: 60 Copynumber: 2.7 Consensus size: 60
5902 ACGATAATGG
* * * * *
5912 ACTATGATTATCATTCTAAATTGATCTCTAAACTTTTGAATATT-CAAATTTCATCCCTAA
1 ACTATGACTCTCATTCTAAATTGGTCTCCAAACTTTTGAATATTCCAAA-TTCATCCCCAA
* * *
5972 ACTATGACTCTCATTCTAAATTGGTCTCCAAACTTTTAAACATTCCAAATTCCTCCCCAA
1 ACTATGACTCTCATTCTAAATTGGTCTCCAAACTTTTGAATATTCCAAATTCATCCCCAA
* * * *
6032 ACTATG-GTCCTCATTTTATATTGGTCCCCAAACTTTTGAAT
1 ACTATGACT-CTCATTCTAAATTGGTCTCCAAACTTTTGAAT
6073 GATTATATGG
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
59 1 0.01
60 80 0.94
61 4 0.05
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.39
Consensus pattern (60 bp):
ACTATGACTCTCATTCTAAATTGGTCTCCAAACTTTTGAATATTCCAAATTCATCCCCAA
Found at i:7031 original size:15 final size:15
Alignment explanation
Indices: 7011--7039 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
7001 TTGTATTTGT
7011 TAAATTAAAATAAAA
1 TAAATTAAAATAAAA
7026 TAAATTAAAATAAA
1 TAAATTAAAATAAA
7040 GTTAGTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATTAAAATAAAA
Found at i:8858 original size:23 final size:22
Alignment explanation
Indices: 8831--8880 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
8821 CTATCATATA
8831 TATTTACTATTATCTTTTTTTAT
1 TATTTACTATTAT-TTTTTTTAT
*
8854 TATTTATTATTATTTTTTTTAT
1 TATTTACTATTATTTTTTTTAT
8876 T-TTTA
1 TATTTA
8881 TTTCATCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 4 0.15
22 10 0.38
23 12 0.46
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (22 bp):
TATTTACTATTATTTTTTTTAT
Found at i:8863 original size:10 final size:9
Alignment explanation
Indices: 8847--8882 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
8837 CTATTATCTT
8847 TTTTTATTA
1 TTTTTATTA
8856 TTTATTATTA
1 TTT-TTATTA
*
8866 TTTTTTTTA
1 TTTTTATTA
8875 TTTTTATT
1 TTTTTATT
8883 TCATCTCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTATTA
Found at i:14206 original size:14 final size:14
Alignment explanation
Indices: 14189--14216 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
14179 GGAGGTTTGT
14189 GCTACTGGAGAATC
1 GCTACTGGAGAATC
14203 GCTACTGGAGAATC
1 GCTACTGGAGAATC
14217 ATCAGACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (14 bp):
GCTACTGGAGAATC
Found at i:19495 original size:16 final size:17
Alignment explanation
Indices: 19469--19500 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
19459 CCCTAAATTG
19469 AAAAAAGGAAAAAGAAC
1 AAAAAAGGAAAAAGAAC
19486 AAAAAA-GAAAAAGAA
1 AAAAAAGGAAAAAGAA
19501 AAATAAGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAAGGAAAAAGAAC
Found at i:20111 original size:14 final size:14
Alignment explanation
Indices: 20092--20118 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20082 GATCGGAACT
20092 TCAAGATTCCAGAA
1 TCAAGATTCCAGAA
20106 TCAAGATTCCAGA
1 TCAAGATTCCAGA
20119 CAGGTAACCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAA
Found at i:22992 original size:2 final size:2
Alignment explanation
Indices: 22985--23027 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
22975 AGTATCCTAT
22985 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23025 TA T
1 TA T
23028 TATCTTCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23028 original size:12 final size:11
Alignment explanation
Indices: 22982--23030 Score: 75
Period size: 10 Copynumber: 4.5 Consensus size: 11
22972 TTTAGTATCC
22982 TATTATATATA
1 TATTATATATA
22993 TA-TATATATA
1 TATTATATATA
23003 TA-TATATATA
1 TATTATATATA
23013 TATTATATATAA
1 TATTATATAT-A
23025 TATTAT
1 TATTAT
23031 CTTCTTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
10 20 0.56
11 9 0.25
12 7 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TATTATATATA
Found at i:23177 original size:4 final size:4
Alignment explanation
Indices: 23170--23194 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
23160 TCTTGTTTGT
23170 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
23195 CCTTTTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:25496 original size:2 final size:2
Alignment explanation
Indices: 25489--25514 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25479 GGGAGCATGC
25489 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
25515 GATTCTAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45272 original size:28 final size:28
Alignment explanation
Indices: 45226--45281 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 28
45216 ACGTGATTGA
45226 TAGATTAAATTGATTTTTTATTAAGTTT
1 TAGATTAAATTGATTTTTTATTAAGTTT
45254 TAGAGTTAAATTGATTTTTT-TTAAGTTT
1 TAGA-TTAAATTGATTTTTTATTAAGTTT
45282 AGGGACTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (28 bp):
TAGATTAAATTGATTTTTTATTAAGTTT
Found at i:45328 original size:15 final size:15
Alignment explanation
Indices: 45305--45363 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
45295 AATTTTTAAA
*
45305 AAATTTAAAAAAATT
1 AAATATAAAAAAATT
45320 AAATATAAAATATAA--
1 AAATATAAAA-A-AATT
* *
45335 AAATTTCAAAAAATT
1 AAATATAAAAAAATT
45350 AAATATAAAAAAAT
1 AAATATAAAAAAAT
45364 AAGAAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
13 2 0.06
14 1 0.03
15 29 0.83
16 1 0.03
17 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATATAAAAAAATT
Found at i:45339 original size:30 final size:30
Alignment explanation
Indices: 45303--45359 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
45293 TAAATTTTTA
45303 AAAAATTTAAAAAAATTAAATATAAAATAT
1 AAAAATTTAAAAAAATTAAATATAAAATAT
*
45333 AAAAATTTCAAAAAATTAAATATAAAA
1 AAAAATTTAAAAAAATTAAATATAAAA
45360 AAATAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (30 bp):
AAAAATTTAAAAAAATTAAATATAAAATAT
Found at i:45370 original size:23 final size:22
Alignment explanation
Indices: 45305--45381 Score: 64
Period size: 23 Copynumber: 3.4 Consensus size: 22
45295 AATTTTTAAA
* * * *
45305 AAATTTAAAAAAATTAAATATA
1 AAATATAAAAAAATAAAAAATT
**
45327 AAATATAAAAATTTCAAAAAATT
1 AAATATAAAAAAAT-AAAAAATT
*
45350 AAATATAAAAAAATAAGAAAAAT
1 AAATATAAAAAAATAA-AAAATT
*
45373 AAAAATAAA
1 AAATATAAA
45382 TTATTAAAAG
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
22 13 0.30
23 30 0.70
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.25
Consensus pattern (22 bp):
AAATATAAAAAAATAAAAAATT
Found at i:45378 original size:30 final size:29
Alignment explanation
Indices: 45312--45377 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
45302 AAAAAATTTA
* **
45312 AAAAAATTAAATATAAAATATAAAAATTT
1 AAAAAATTAAATATAAAAAATAAAAAAAT
45341 CAAAAAATTAAATATAAAAAAATAAGAAAAAT
1 -AAAAAATTAAATAT-AAAAAATAA-AAAAAT
45373 AAAAA
1 AAAAA
45378 TAAATTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 14 0.45
31 13 0.42
32 4 0.13
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (29 bp):
AAAAAATTAAATATAAAAAATAAAAAAAT
Found at i:45747 original size:22 final size:22
Alignment explanation
Indices: 45698--45748 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
45688 ACATACATAT
45698 AATTTTATATTTTTATATTTAA
1 AATTTTATATTTTTATATTTAA
**
45720 TTTTTTATATTTTTATATTTAA
1 AATTTTATATTTTTATATTTAA
45742 AATTTTA
1 AATTTTA
45749 AACTTAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
AATTTTATATTTTTATATTTAA
Found at i:45825 original size:21 final size:19
Alignment explanation
Indices: 45796--45837 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
45786 GATTTTTTTT
45796 AAAAAAAATTTAGTCAAATC
1 AAAAAAAATTTAG-CAAATC
*
45816 AAAAACAAATTTAGCACATC
1 AAAAA-AAATTTAGCAAATC
45836 AA
1 AA
45838 TCACGTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.60, C:0.14, G:0.05, T:0.21
Consensus pattern (19 bp):
AAAAAAAATTTAGCAAATC
Found at i:48293 original size:12 final size:12
Alignment explanation
Indices: 48276--48302 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
48266 TAATTACTCT
48276 CAAATAAGACTA
1 CAAATAAGACTA
48288 CAAATAAGACTA
1 CAAATAAGACTA
48300 CAA
1 CAA
48303 GTGAGAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.19, G:0.07, T:0.15
Consensus pattern (12 bp):
CAAATAAGACTA
Found at i:59803 original size:21 final size:21
Alignment explanation
Indices: 59761--59803 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
59751 TTTCTAGGCT
* *
59761 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
59782 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
59803 A
1 A
59804 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:59856 original size:20 final size:20
Alignment explanation
Indices: 59831--59868 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
59821 GAATGCTAGA
*
59831 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
59851 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
59869 TAATGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:60676 original size:103 final size:103
Alignment explanation
Indices: 60348--60668 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
60338 GTAGAGGGTC
*
60348 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
*
60413 TTGATCCTTGGTATATGTATATGGTTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
60451 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
60516 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
60554 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
* *
60619 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
60657 TATGTGGTCCTT
1 TATGTGGTCCTT
60669 ATGGACATTA
Statistics
Matches: 213, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 213 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:60718 original size:23 final size:23
Alignment explanation
Indices: 60685--60747 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
60675 ATTATTATAT
60685 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
60708 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
60731 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
60748 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:64483 original size:209 final size:206
Alignment explanation
Indices: 64098--64521 Score: 715
Period size: 209 Copynumber: 2.0 Consensus size: 206
64088 TCAAAAGTTT
* * *
64098 TATGCCAAACCATCAATCTGCAGGTGTCATTAAACAAGGAGCAAGCGATTAAATTCCTGACAATG
1 TATG-CAAACCATCAATCTGCAGGTGTCATTAAACAAGAAGCAAGCGATTAAATTCCCGACAAGG
64163 CAAAACAGCTAACTTTGAGCCCGCTTTCCTTAATTTGAGCATTAGAAAATCAAAGTTACAAGCAA
65 CAAAACAGCTAACTTTGAGCCCGCTTTCCTTAATTTGAGCATTAGAAAATCAAAGTTACAAGCAA
* *
64228 GAAACATCAAGTGAGATCAAAACATATTCAATAAGGATTGCTGATGAGAGATGCAAACCATTAGC
130 GAAACAACAAGTGAGATCAAAACATATTCAATAAGGATTGCTGATGAGAGATGCAAACCATCAGC
*
64293 ATATTGTCATCA
195 ATATTGCCATCA
*
64305 TATGCAAACCATCAATCTGCAGGTGTCATTAAACAAGAAGCAAGCGATTAAATTCCCGACAAGGG
1 TATGCAAACCATCAATCTGCAGGTGTCATTAAACAAGAAGCAAGCGATTAAATTCCCGACAAGGC
*
64370 AAAACAGCTAACTAACTATGAGCCCGCTTTCCTTAATTTGAGCA-TAGCAAATCAAAGTTACAAG
66 AAAACAGCTAACT---T-TGAGCCCGCTTTCCTTAATTTGAGCATTAGAAAATCAAAGTTACAAG
*
64434 CAAGAAACAACAAGTGAGATCAAAACATATTGAATAAGGATTGCTGATGAGAGATGCAAACCATC
127 CAAGAAACAACAAGTGAGATCAAAACATATTCAATAAGGATTGCTGATGAGAGATGCAAACCATC
64499 AGCATATTGCCATCA
192 AGCATATTGCCATCA
64514 TATGCAAA
1 TATGCAAA
64522 ACATATGGTA
Statistics
Matches: 204, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
206 70 0.34
207 4 0.02
209 104 0.51
210 26 0.13
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (206 bp):
TATGCAAACCATCAATCTGCAGGTGTCATTAAACAAGAAGCAAGCGATTAAATTCCCGACAAGGC
AAAACAGCTAACTTTGAGCCCGCTTTCCTTAATTTGAGCATTAGAAAATCAAAGTTACAAGCAAG
AAACAACAAGTGAGATCAAAACATATTCAATAAGGATTGCTGATGAGAGATGCAAACCATCAGCA
TATTGCCATCA
Found at i:66222 original size:40 final size:37
Alignment explanation
Indices: 66173--66280 Score: 119
Period size: 40 Copynumber: 2.8 Consensus size: 37
66163 ATTTTTTTAT
66173 TTTTATTTTAATAAATAATTAATAATTAA-TTATATATTA
1 TTTTATTTTAATAAATAATTAAT-A-TAATTTATA-ATTA
* * *
66212 TTCTTGTTTTAATAAATAATTACTATAATTTATAATAA
1 TT-TTATTTTAATAAATAATTAATATAATTTATAATTA
66250 TTTTATTTTAATAAAATATATTAATCATAAT
1 TTTTATTTTAAT-AAATA-ATTAAT-ATAAT
66281 ATTTTTATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
37 9 0.15
38 13 0.22
39 13 0.22
40 24 0.41
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (37 bp):
TTTTATTTTAATAAATAATTAATATAATTTATAATTA
Found at i:66312 original size:29 final size:32
Alignment explanation
Indices: 66242--66314 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 32
66232 TACTATAATT
*
66242 TATAATAATTTTATTTTAATAAAATATATTAA
1 TATAATATTTTTATTTTAATAAAATATATTAA
66274 TCATAATATTTTTA-TTT-ATAAAAT-TA-TAGA
1 T-ATAATATTTTTATTTTAATAAAATATATTA-A
66304 TATAATATTTT
1 TATAATATTTT
66315 AATAATAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 12 0.32
30 4 0.11
31 7 0.18
32 4 0.11
33 11 0.29
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (32 bp):
TATAATATTTTTATTTTAATAAAATATATTAA
Found at i:66322 original size:14 final size:14
Alignment explanation
Indices: 66239--66326 Score: 63
Period size: 14 Copynumber: 6.2 Consensus size: 14
66229 AATTACTATA
**
66239 ATTTATAATAATTTT
1 ATTT-TAATAATAAT
66254 ATTTTAATAA-AAT
1 ATTTTAATAATAAT
* *
66267 ATATTAATCATAAT
1 ATTTTAATAATAAT
* * *
66281 ATTTTTATTTATAAA
1 A-TTTTAATAATAAT
*
66296 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
66310 ATTTTAATAATAAT
1 ATTTTAATAATAAT
66324 ATT
1 ATT
66327 GACATAAATA
Statistics
Matches: 57, Mismatches: 12, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
13 11 0.19
14 31 0.54
15 15 0.26
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:67675 original size:12 final size:12
Alignment explanation
Indices: 67658--67683 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
67648 CTGCTACTAT
67658 TCTAATATTAAG
1 TCTAATATTAAG
67670 TCTAATATTAAG
1 TCTAATATTAAG
67682 TC
1 TC
67684 GAGTGTCTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (12 bp):
TCTAATATTAAG
Found at i:69856 original size:27 final size:28
Alignment explanation
Indices: 69810--69864 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
69800 TTTATTGTTG
69810 ATTTATTTTTGTCTTTAAAATTTTATAA
1 ATTTATTTTTGTCTTTAAAATTTTATAA
69838 ATTTATTATTT-T-TTTAAAATTTTATAA
1 ATTTATT-TTTGTCTTTAAAATTTTATAA
69865 GTTCATTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 15 0.58
28 8 0.31
29 3 0.12
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (28 bp):
ATTTATTTTTGTCTTTAAAATTTTATAA
Found at i:71157 original size:17 final size:16
Alignment explanation
Indices: 71093--71157 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 16
71083 ATTTAAATTC
*
71093 AAATAAATATATTTAT
1 AAATAAATATATTTTT
* *
71109 AGAATATATATATTATT
1 A-AATAAATATATTTTT
* *
71126 -AATAGATAATTTTTTT
1 AAATAAAT-ATATTTTT
71142 AAATAAATATTATTTT
1 AAATAAATA-TATTTT
71158 ATAATTATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
15 6 0.16
16 8 0.22
17 23 0.62
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
AAATAAATATATTTTT
Found at i:71478 original size:13 final size:13
Alignment explanation
Indices: 71460--71499 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
71450 TGTTTCGGAT
71460 TTAATTATTTAAA
1 TTAATTATTTAAA
*
71473 TTAATTAATTTAAT
1 TTAATT-ATTTAAA
71487 TTAA-TATTTAAA
1 TTAATTATTTAAA
71499 T
1 T
71500 ATTATGGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 7 0.29
14 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAATTATTTAAA
Found at i:71530 original size:18 final size:17
Alignment explanation
Indices: 71507--71542 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
71497 AATATTATGG
*
71507 TTTAAATTTAATTTAAAA
1 TTTAAA-TTAAATTAAAA
71525 TTTAAATTAAATTAAAA
1 TTTAAATTAAATTAAAA
71542 T
1 T
71543 CAATCAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAATTAAATTAAAA
Found at i:72103 original size:21 final size:21
Alignment explanation
Indices: 72079--72122 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
72069 TGACATAAAA
*
72079 AACAACAAACTTGAAATTCAT
1 AACAACAAACTTGAAATCCAT
*
72100 AACAAGAAACTTGAAATCCAT
1 AACAACAAACTTGAAATCCAT
72121 AA
1 AA
72123 TAATAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.55, C:0.18, G:0.07, T:0.20
Consensus pattern (21 bp):
AACAACAAACTTGAAATCCAT
Found at i:74073 original size:41 final size:41
Alignment explanation
Indices: 73993--74408 Score: 226
Period size: 41 Copynumber: 10.2 Consensus size: 41
73983 CTATAAACTT
* *
73993 GCGGCGTTTGTAAACACAAACGACACTAAAGTACGAGTCTTTA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGAGTCTTTA
* * *
74036 GCGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * * *
74077 GCGACTTTTGTATAAAAACGTCACTAAAATATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
74118 GCGACTTTTGTATAAAAATGCCATTAAAGTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * * * **
74159 GCGGTGTTTGTATACAAACGCCCCTAATGTATTGA-TAAATT-
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTA-CGAGT-CTTTA
* * * * * * *
74200 GCGGCATTTATTAAAAAAATGCCATTAAAGTATGAATCTCTTA
1 GCGGCGTTT-GTATAAAAACGCCACTAAAGTACGAGTCT-TTA
** * * * * * * *
74243 -CGTTGTTT-TTTAAAAAATGTCATTATA-TATGTGTCCTATTA
1 GCGGCGTTTGTAT-AAAAACGCCACTAAAGTACGAGT-CT-TTA
* *
74284 -CGGCGTTTGTATAAAAACGCCACTAAAGTATGAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
** * *
74324 ATGGCGTTTGTATAAAAA-G-CACTAAAGT-CCACTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * * *
74362 GCGGC-ATTATATAAAAAC-ACACTAAAGTA-AAGTATTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
*
74400 GAGGCGTTT
1 GCGGCGTTT
74409 TTACTTAAAA
Statistics
Matches: 285, Mismatches: 73, Indels: 34
0.73 0.19 0.09
Matches are distributed among these distances:
37 10 0.04
38 28 0.10
39 11 0.04
40 9 0.03
41 178 0.62
42 36 0.13
43 13 0.05
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
Done.