Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003409.1 Hibiscus syriacus cultivar Beakdansim tig00007181_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: 462136
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:424629 original size:5 final size:5
Alignment explanation
Indices: 424610--424654 Score: 72
Period size: 5 Copynumber: 8.6 Consensus size: 5
424600 TTAGTGAGGT
424610 AAATCA AAATAA AAATA AAATA AAATA AAATA AAATA AAATA AAA
1 AAAT-A AAAT-A AAATA AAATA AAATA AAATA AAATA AAATA AAA
424655 AATCCTACCC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 29 0.76
6 9 0.24
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:427148 original size:36 final size:35
Alignment explanation
Indices: 427107--427361 Score: 113
Period size: 35 Copynumber: 7.3 Consensus size: 35
427097 CGTTTTCAAA
427107 ATTATATAGTTTTCAAAAATGTTTTTAAAACTATAT
1 ATTATATA-TTTTCAAAAATGTTTTTAAAACTATAT
* * *
427143 ATTATA-AGTTTT-TAAAATGATTTCAAAACTATAT
1 ATTATATA-TTTTCAAAAATGTTTTTAAAACTATAT
* **
427177 AATATATATATGTTTTC-AAACTGTTTCTTTTTAA--A-A-
1 -AT-TATATA--TTTTCAAAAATG-TT-TTTAAAACTATAT
* **
427213 ATTAT-T-TTAT-AAAAATGTTTTTTAAAACCGTAT
1 ATTATATATTTTCAAAAATG-TTTTTAAAACTATAT
* * * *
427246 A-TATATATTTTTAAAAACGATTTAAAAACTATAT
1 ATTATATATTTTCAAAAATGTTTTTAAAACTATAT
* ** *
427280 ATTATAT-TTATTCCAAAGCGTTTTAAAAACTATAT
1 ATTATATATT-TTCAAAAATGTTTTTAAAACTATAT
* * *
427315 AATATA-ATTGTTTCAAATATGTTTTCAAAACTATATT
1 ATTATATA-T-TTTCAAAAATGTTTTTAAAACTATA-T
427352 ATATATATAT
1 AT-TATATAT
427362 ATATATATAT
Statistics
Matches: 166, Mismatches: 30, Indels: 44
0.69 0.12 0.18
Matches are distributed among these distances:
29 5 0.03
30 11 0.07
32 4 0.02
33 3 0.02
34 39 0.23
35 47 0.28
36 30 0.18
37 5 0.03
38 16 0.10
39 2 0.01
40 4 0.02
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (35 bp):
ATTATATATTTTCAAAAATGTTTTTAAAACTATAT
Found at i:427161 original size:34 final size:36
Alignment explanation
Indices: 427107--427196 Score: 112
Period size: 34 Copynumber: 2.5 Consensus size: 36
427097 CGTTTTCAAA
* *
427107 ATTATATAGTTTTCAAAAATGTTTTTAAAACTATAT
1 ATTATATAGTTTTCAAAAATGATTTCAAAACTATAT
*
427143 ATTATA-AGTTTT-TAAAATGATTTCAAAACTATAT
1 ATTATATAGTTTTCAAAAATGATTTCAAAACTATAT
427177 AATATATATATGTTTTCAAA
1 -AT-TATATA-GTTTTCAAA
427197 CTGTTTCTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 19 0.42
35 8 0.18
36 10 0.22
37 1 0.02
38 5 0.11
39 2 0.04
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (36 bp):
ATTATATAGTTTTCAAAAATGATTTCAAAACTATAT
Found at i:427358 original size:2 final size:2
Alignment explanation
Indices: 427346--427390 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
427336 TTTTCAAAAC
427346 TA TA T- 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
427387 TA TA
1 TA TA
427391 AATGAGACGA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:427839 original size:20 final size:20
Alignment explanation
Indices: 427779--427831 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
427769 GGTCGGGTCA
*
427779 GGTCAGGTTGACTCAGTTCG
1 GGTCAGGTTGACTCAGTTTG
427799 GGTCAGGTTGACTCAGTTTG
1 GGTCAGGTTGACTCAGTTTG
*
427819 GGTCTGGTTGACT
1 GGTCAGGTTGACT
427832 TGGTTTGGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.13, C:0.17, G:0.36, T:0.34
Consensus pattern (20 bp):
GGTCAGGTTGACTCAGTTTG
Found at i:433969 original size:18 final size:20
Alignment explanation
Indices: 433948--433987 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
433938 TATGTTTCTA
433948 TTTTTTC-AAAGCT-TCTTT
1 TTTTTTCTAAAGCTCTCTTT
*
433966 TTTTTTCTAATGCTCTCTTT
1 TTTTTTCTAAAGCTCTCTTT
433986 TT
1 TT
433988 CTCTGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 5 0.26
20 7 0.37
ACGTcount: A:0.12, C:0.17, G:0.05, T:0.65
Consensus pattern (20 bp):
TTTTTTCTAAAGCTCTCTTT
Found at i:434592 original size:3 final size:3
Alignment explanation
Indices: 434571--434613 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
434561 TGCAAAAATG
* * * *
434571 TAA TAA TAT TAA TAG TAA TAA TAA TAG TAA TAA TAT TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
434614 TTAAAATTAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:434613 original size:12 final size:12
Alignment explanation
Indices: 434571--434635 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
434561 TGCAAAAATG
434571 TAATAATATTAA
1 TAATAATATTAA
* *
434583 TAGTAATAATAA
1 TAATAATATTAA
* * *
434595 TAGTAATAATAT
1 TAATAATATTAA
434607 TAATAAT-TTAA
1 TAATAATATTAA
*
434618 -AATTAAAATTAA
1 TAA-TAATATTAA
434630 TAATAA
1 TAATAA
434636 ACAATTAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
10 2 0.05
11 5 0.12
12 34 0.79
13 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:434641 original size:20 final size:20
Alignment explanation
Indices: 434605--434645 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
434595 TAGTAATAAT
*
434605 ATTAATAATTTAAAATTAAA
1 ATTAATAATTAAAAATTAAA
434625 ATTAATAA-TAAACAATTAAA
1 ATTAATAATTAAA-AATTAAA
434645 A
1 A
434646 CCCGGATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
ATTAATAATTAAAAATTAAA
Found at i:435989 original size:33 final size:33
Alignment explanation
Indices: 435942--436009 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
435932 ACTACACATG
435942 GGAAGGGTAAGAACTCCCAAAGCACCCAAAATT
1 GGAAGGGTAAGAACTCCCAAAGCACCCAAAATT
* **
435975 GGAAGGGTATGAACTCCCAAAGCGTCCAAAATT
1 GGAAGGGTAAGAACTCCCAAAGCACCCAAAATT
436008 GG
1 GG
436010 TACCTCTCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (33 bp):
GGAAGGGTAAGAACTCCCAAAGCACCCAAAATT
Found at i:440739 original size:16 final size:18
Alignment explanation
Indices: 440718--440755 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
440708 GGGAAGTGTC
440718 TTTTTC-AAAGCT-TCTT
1 TTTTTCGAAAGCTCTCTT
*
440734 TTTTTCGAATGCTCTCTT
1 TTTTTCGAAAGCTCTCTT
440752 TTTT
1 TTTT
440756 CTCTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 5 0.26
18 8 0.42
ACGTcount: A:0.13, C:0.18, G:0.08, T:0.61
Consensus pattern (18 bp):
TTTTTCGAAAGCTCTCTT
Found at i:441361 original size:3 final size:3
Alignment explanation
Indices: 441340--441382 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
441330 TGCAAAAATG
* * * *
441340 TAA TAA TAT TAA TAT TAA TAA TAA TAG TAA TAA TAT TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
441383 TTTAAATTAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:441361 original size:9 final size:9
Alignment explanation
Indices: 441340--441403 Score: 65
Period size: 9 Copynumber: 6.9 Consensus size: 9
441330 TGCAAAAATG
441340 TAATAATAT
1 TAATAATAT
* *
441349 TAATATTAA
1 TAATAATAT
*
441358 TAATAATAG
1 TAATAATAT
441367 TAATAATAT
1 TAATAATAT
*
441376 TAATAATTT
1 TAATAATAT
*
441385 TAAATTAAAAT
1 T-AA-TAATAT
441396 TAATAATA
1 TAATAATA
441404 AACAATTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
9 35 0.80
10 4 0.09
11 5 0.11
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (9 bp):
TAATAATAT
Found at i:442771 original size:33 final size:33
Alignment explanation
Indices: 442729--442795 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
442719 CTACACATGA
442729 GAAGGGTAAGAACTCCCAAAGCACCCAAAATTG
1 GAAGGGTAAGAACTCCCAAAGCACCCAAAATTG
* **
442762 GAAGGGTAAGAACTCCCAAATCGTCCAAAATTG
1 GAAGGGTAAGAACTCCCAAAGCACCCAAAATTG
442795 G
1 G
442796 TACCTCTCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.15
Consensus pattern (33 bp):
GAAGGGTAAGAACTCCCAAAGCACCCAAAATTG
Found at i:443351 original size:20 final size:20
Alignment explanation
Indices: 443326--443372 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
443316 GTCATGTCAT
443326 GTTGACTCAGTTCGGGTCTG
1 GTTGACTCAGTTCGGGTCTG
*
443346 GTTGACTCAGTTTGGGTCTG
1 GTTGACTCAGTTCGGGTCTG
443366 GTTGACT
1 GTTGACT
443373 TGGTTCGGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.11, C:0.17, G:0.34, T:0.38
Consensus pattern (20 bp):
GTTGACTCAGTTCGGGTCTG
Found at i:446678 original size:3 final size:3
Alignment explanation
Indices: 446657--446699 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
446647 TGCAAAAATG
* * * *
446657 TAA TAA TAT TAA TAG TAA TAA TAA TAG TAA TAA TAT TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
446700 TTAAAATTAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:446699 original size:12 final size:12
Alignment explanation
Indices: 446657--446721 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
446647 TGCAAAAATG
446657 TAATAATATTAA
1 TAATAATATTAA
* *
446669 TAGTAATAATAA
1 TAATAATATTAA
* * *
446681 TAGTAATAATAT
1 TAATAATATTAA
446693 TAATAAT-TTAA
1 TAATAATATTAA
*
446704 -AATTAAAATTAA
1 TAA-TAATATTAA
446716 TAATAA
1 TAATAA
446722 ACAATTAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
10 2 0.05
11 5 0.12
12 34 0.79
13 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:446727 original size:20 final size:20
Alignment explanation
Indices: 446691--446731 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
446681 TAGTAATAAT
*
446691 ATTAATAATTTAAAATTAAA
1 ATTAATAATTAAAAATTAAA
446711 ATTAATAA-TAAACAATTAAA
1 ATTAATAATTAAA-AATTAAA
446731 A
1 A
446732 CCCGGATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
ATTAATAATTAAAAATTAAA
Found at i:448091 original size:33 final size:33
Alignment explanation
Indices: 448044--448111 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
448034 ACTACACATG
448044 GGAAGGGTAAGAACTCCCAAAGCACCCAAAATT
1 GGAAGGGTAAGAACTCCCAAAGCACCCAAAATT
* **
448077 GGAAGGGTATGAACTCCCAAAGCGTCCAAAATT
1 GGAAGGGTAAGAACTCCCAAAGCACCCAAAATT
448110 GG
1 GG
448112 TACCTCTCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (33 bp):
GGAAGGGTAAGAACTCCCAAAGCACCCAAAATT
Found at i:448668 original size:20 final size:20
Alignment explanation
Indices: 448643--448689 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
448633 GTCATGTCAT
*
448643 GTTGACTCAGTTCGGTTCTG
1 GTTGACTCAGTTCGGGTCTG
*
448663 GTTGACTCAGTTTGGGTCTG
1 GTTGACTCAGTTCGGGTCTG
448683 GTTGACT
1 GTTGACT
448690 TGGTTCAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.11, C:0.17, G:0.32, T:0.40
Consensus pattern (20 bp):
GTTGACTCAGTTCGGGTCTG
Found at i:452633 original size:16 final size:17
Alignment explanation
Indices: 452609--452650 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
452599 TCGAATATGT
*
452609 TTCTATTTTTT-AAAGC
1 TTCTTTTTTTTGAAAGC
*
452625 TTCTTTTTTTTGAATGC
1 TTCTTTTTTTTGAAAGC
452642 TCTCTTTTT
1 T-TCTTTTT
452651 CTCTCTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 10 0.45
17 5 0.23
18 7 0.32
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (17 bp):
TTCTTTTTTTTGAAAGC
Found at i:452634 original size:17 final size:18
Alignment explanation
Indices: 452614--452650 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
452604 TATGTTTCTA
452614 TTTTTT-AAAGCT-TCTT
1 TTTTTTGAAAGCTCTCTT
*
452630 TTTTTTGAATGCTCTCTT
1 TTTTTTGAAAGCTCTCTT
452648 TTT
1 TTT
452651 CTCTCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.14, C:0.14, G:0.08, T:0.65
Consensus pattern (18 bp):
TTTTTTGAAAGCTCTCTT
Found at i:453245 original size:24 final size:24
Alignment explanation
Indices: 453213--453277 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
453203 TAGGACTGCA
453213 AAAATGTAATAATATTAATAGTAAT
1 AAAA-GTAATAATATTAATAGTAAT
* * *
453238 AAAAGTAATAATAGTAGTAGTATT
1 AAAAGTAATAATATTAATAGTAAT
* *
453262 AATATTAATAAT-TTAA
1 AAAAGTAATAATATTAA
453278 AATTAAAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 2 0.06
24 27 0.82
25 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (24 bp):
AAAAGTAATAATATTAATAGTAAT
Found at i:453301 original size:20 final size:20
Alignment explanation
Indices: 453259--453305 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
453249 TAGTAGTAGT
* *
453259 ATTAATATTAATAATTTAAA
1 ATTAAAATTAATAATTAAAA
453279 ATTAAAATTAATAA-TAAACA
1 ATTAAAATTAATAATTAAA-A
453299 ATTAAAA
1 ATTAAAA
453306 CCCGGATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTAAAATTAATAATTAAAA
Found at i:454602 original size:42 final size:41
Alignment explanation
Indices: 454497--454632 Score: 143
Period size: 42 Copynumber: 3.3 Consensus size: 41
454487 CTTATTGTAA
* *
454497 AAACGCCGCAATACAGAATA--AATTTTGTGGCATTT-TAGCCC
1 AAACGCCGCAAT--AGAATAGTAATTTAGCGGCATTTATA-CCC
* *
454538 AAACGCCGCAATATAGTAGTAATTTAGCGGCATTTATACCAC
1 AAACGCCGCAATAGAATAGTAATTTAGCGGCATTTATACC-C
* * *
454580 AAACGCCGTAATAGAATGGTAATTTAGCGACATTTATACCTC
1 AAACGCCGCAATAGAATAGTAATTTAGCGGCATTTATACC-C
454622 AAACGCCGCAA
1 AAACGCCGCAA
454633 GGGTATAATA
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
39 4 0.05
41 27 0.34
42 49 0.61
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (41 bp):
AAACGCCGCAATAGAATAGTAATTTAGCGGCATTTATACCC
Found at i:454625 original size:208 final size:208
Alignment explanation
Indices: 454222--454793 Score: 806
Period size: 208 Copynumber: 2.7 Consensus size: 208
454212 AGCAATGAAG
* * * *
454222 AATACCTTTGCGTCGTT-TTTAGACAAACTCCACAAAAGTGTTAATCAATAGCGGCGTTTATTGT
1 AATACTTTTGCGTC-TTGTTTAGACAAACACCACAGAAGGGTTAATCAATAGCGGCGTTTATTGT
*
454286 AAAAACGCCGCAATAGAGAAAAATATTTTGTGGCATTTTAGCCTAAACGCCGCAATATAGTGGTA
65 AAAAACGCCGCAATAGAGAAAAA-ATTTTGTGGCATTTTAGCCCAAACGCCGCAATATAGTGGTA
* ** * * * *
454351 ATTTAGCGACGTTTATAGAACAAATGCCTCAATAGTATGGTAAATTAGCGGCGTTTATAACTCAA
129 ATTTAGCGGCGTTTATACCACAAACGCCTCAATAGAATGGTAAATTAGCGACATTTATAACTCAA
* *
454416 ACACTGTAAGGGGAT
194 ACACCGCAAGGGGAT
* *
454431 AATACTTTTGCGTCTTGTTTAGACAAACGCCACAGAAGGGTTAATCAATAGCGGCGCTTATTGTA
1 AATACTTTTGCGTCTTGTTTAGACAAACACCACAGAAGGGTTAATCAATAGCGGCGTTTATTGTA
* * *
454496 AAAACGCCGCAATACAGAATAAATTTTGTGGCATTTTAGCCCAAACGCCGCAATATAGTAGTAAT
66 AAAACGCCGCAATAGAGAAAAAATTTTGTGGCATTTTAGCCCAAACGCCGCAATATAGTGGTAAT
* * *
454561 TTAGCGGCATTTATACCACAAACGCCGT-AATAGAATGGTAATTTAGCGACATTTATACCTCAAA
131 TTAGCGGCGTTTATACCACAAACGCC-TCAATAGAATGGTAAATTAGCGACATTTATAACTCAAA
* *
454625 CGCCGCAAGGGTAT
195 CACCGCAAGGGGAT
* * *
454639 AATACTTTTGTGTCATGTTTAGACAAACACCACAGAAGGGTTAATCAATAGTGGCGTTTATTGTA
1 AATACTTTTGCGTCTTGTTTAGACAAACACCACAGAAGGGTTAATCAATAGCGGCGTTTATTGTA
* ** * * *
454704 AAAACGCCGCAATAGAGAAGAAATTTTACGACGTTTTAGCCCAAACACCGCAATATAGTGGTAAT
66 AAAACGCCGCAATAGAGAAAAAATTTTGTGGCATTTTAGCCCAAACGCCGCAATATAGTGGTAAT
454769 TTAGCGGCGTTTATACCACAAACGC
131 TTAGCGGCGTTTATACCACAAACGC
454794 TGCAATAAAT
Statistics
Matches: 324, Mismatches: 37, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
208 246 0.76
209 78 0.24
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (208 bp):
AATACTTTTGCGTCTTGTTTAGACAAACACCACAGAAGGGTTAATCAATAGCGGCGTTTATTGTA
AAAACGCCGCAATAGAGAAAAAATTTTGTGGCATTTTAGCCCAAACGCCGCAATATAGTGGTAAT
TTAGCGGCGTTTATACCACAAACGCCTCAATAGAATGGTAAATTAGCGACATTTATAACTCAAAC
ACCGCAAGGGGAT
Found at i:455193 original size:5 final size:6
Alignment explanation
Indices: 455169--455202 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
455159 TTTATCCGGG
455169 ATTTTT ATTGTTTT ATTTTT ATTTTT ATTTTT AT
1 ATTTTT A-T-TTTT ATTTTT ATTTTT ATTTTT AT
455203 AATTATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.73
7 2 0.08
8 5 0.19
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:455580 original size:33 final size:33
Alignment explanation
Indices: 455508--455588 Score: 126
Period size: 34 Copynumber: 2.4 Consensus size: 33
455498 TTTTTCATCC
*
455508 GAAAAAAAGAGAGACCAAAAGCAAAAGATAAGA
1 GAAAAAAACAGAGACCAAAAGCAAAAGATAAGA
* *
455541 GAAAAAAAACAGAGACCAAAAGCAGAAGATCAGA
1 G-AAAAAAACAGAGACCAAAAGCAAAAGATAAGA
455575 GAAAAAAACAGAGA
1 GAAAAAAACAGAGA
455589 TGTTAACCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 14 0.32
34 30 0.68
ACGTcount: A:0.65, C:0.11, G:0.21, T:0.02
Consensus pattern (33 bp):
GAAAAAAACAGAGACCAAAAGCAAAAGATAAGA
Done.