Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003402.1 Hibiscus syriacus cultivar Beakdansim tig00007167_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: 62190
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:617 original size:90 final size:89
Alignment explanation
Indices: 465--641 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 89
455 AACTAAACAC
* * *
465 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGTTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGATTTTATTATTTCAAATTAATTAAATCTATA
* *
530 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
*
554 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCA-GGATTTTATTATTTCAAATTAATTAAATCTAT
619 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
642 TCCGGATTAT
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 29 0.36
90 52 0.64
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGATTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAAATAAT
Found at i:5622 original size:29 final size:31
Alignment explanation
Indices: 5575--5637 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
5565 TTTGGTCCCT
*
5575 TAAACCTTTCCAAACTTTATACTTTAGTCAC
1 TAAACCTTTCCAAAATTTATACTTTAGTCAC
* *
5606 TAAA-CTTT-CAAAATTTATATTTTGGTCAC
1 TAAACCTTTCCAAAATTTATACTTTAGTCAC
5635 TAA
1 TAA
5638 CTAAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 21 0.72
30 4 0.14
31 4 0.14
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (31 bp):
TAAACCTTTCCAAAATTTATACTTTAGTCAC
Found at i:8603 original size:22 final size:23
Alignment explanation
Indices: 8578--8623 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
8568 TATTTAATTT
* *
8578 TTAAAA-AATATTAAATTGAATG
1 TTAAAATAATAATAAATTAAATG
*
8600 TTAAAATAGTAATAAATTAAATG
1 TTAAAATAATAATAAATTAAATG
8623 T
1 T
8624 ATTCCACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (23 bp):
TTAAAATAATAATAAATTAAATG
Found at i:9394 original size:2 final size:2
Alignment explanation
Indices: 9389--9421 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9379 TATATATATA
9389 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
9422 ATCATTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9709 original size:179 final size:171
Alignment explanation
Indices: 9417--9762 Score: 593
Period size: 179 Copynumber: 2.0 Consensus size: 171
9407 AGAGAGAGAG
* *
9417 AGAGAATCATTATAATGTTTTTAGATGATTACCTAAAACAGATTGGTTGATTGATGTTTGTGAAT
1 AGAGAATCATTATAATGCTTTTAGATGATTACCTAAAACAGATTGGTTGATTGATGTTTGTAAAT
9482 TTGTTTGTTTAAGAATGATTCAATCTAAGCCCTTTTACATATAATCTAGTCTGGCTTTGATTGAG
66 TTGTTTGTTTAAGAATGATTCAATCTAAGCCCTTTTACATATAATCTAGTCTGGCTTTGATTGAG
9547 GTATTAAGCTTTATGGTGCTTGGAATTCTAGGTGAAGATAA
131 GTATTAAGCTTTATGGTGCTTGGAATTCTAGGTGAAGATAA
*
9588 AGAGAATCATTATAATGCTTTTAGATGATTATCTAAAACAGATTGGTTGATTGGTTGATTGATGT
1 AGAGAATCATTATAATGCTTTTAGATGATTACCTAAAAC--A------GATTGGTTGATTGATGT
9653 TTGTAAATTTGTTTGTTTAAGAATGATTCAATCTAAGCCCTTTTACATATAATCTAGTCTGGCTT
58 TTGTAAATTTGTTTGTTTAAGAATGATTCAATCTAAGCCCTTTTACATATAATCTAGTCTGGCTT
9718 TGATTGAGGTATTAAGCTTTATGGTGCTTGGAATTCTAGGTGAAG
123 TGATTGAGGTATTAAGCTTTATGGTGCTTGGAATTCTAGGTGAAG
9763 GATGTTTGCT
Statistics
Matches: 164, Mismatches: 3, Indels: 8
0.94 0.02 0.05
Matches are distributed among these distances:
171 37 0.23
173 1 0.01
179 126 0.77
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (171 bp):
AGAGAATCATTATAATGCTTTTAGATGATTACCTAAAACAGATTGGTTGATTGATGTTTGTAAAT
TTGTTTGTTTAAGAATGATTCAATCTAAGCCCTTTTACATATAATCTAGTCTGGCTTTGATTGAG
GTATTAAGCTTTATGGTGCTTGGAATTCTAGGTGAAGATAA
Found at i:10778 original size:277 final size:277
Alignment explanation
Indices: 10284--10831 Score: 1078
Period size: 277 Copynumber: 2.0 Consensus size: 277
10274 ACATCTGCTG
10284 AAGATGGTATAGGTTTTGGTGATTCTGATTTCCACCATAAGGTACTTGTGCGGTTCCATTTCCCT
1 AAGATGGTATAGGTTTTGGTGATTCTGATTTCCACCATAAGGTACTTGTGCGGTTCCATTTCCCT
10349 CCAGTTTTCCTTTTACCTTGCATTGAACATGTTGGATCACCCCTCAAGTGTCTTACTGTTCTAAC
66 CCAGTTTTCCTTTTACCTTGCATTGAACATGTTGGATCACCCCTCAAGTGTCTTACTGTTCTAAC
10414 AATGGCATTTTCCTTTTAAGACTCGCCAGTTGATTTATCCAATCATGTACTATTCTTAATCCCTG
131 AATGGCATTTTCCTTTTAAGACTCGCCAGTTGATTTATCCAATCATGTACTATTCTTAATCCCTG
*
10479 ATATTGGTTCGATACTGGCCTCTCCGAGTTTTTTAGTATATTTTCCTGCACAAACTAGTGGGATG
196 ATATTGGTTCGATACTGGCCTCTCCCAGTTTTTTAGTATATTTTCCTGCACAAACTAGTGGGATG
10544 TTAATATTTTCATGTTT
261 TTAATATTTTCATGTTT
10561 AAGATGGTATAGGTTTTGGTGATTCTGATTTCCACCATAAGGTACTTGTGCGGTTCCATTTCCCT
1 AAGATGGTATAGGTTTTGGTGATTCTGATTTCCACCATAAGGTACTTGTGCGGTTCCATTTCCCT
*
10626 CCAGTTTTCCTTTTCCCTTGCATTGAACATGTTGGATCACCCCTCAAGTGTCTTACTGTTCTAAC
66 CCAGTTTTCCTTTTACCTTGCATTGAACATGTTGGATCACCCCTCAAGTGTCTTACTGTTCTAAC
10691 AATGGCATTTTCCTTTTAAGACTCGCCAGTTGATTTATCCAATCATGTACTATTCTTAATCCCTG
131 AATGGCATTTTCCTTTTAAGACTCGCCAGTTGATTTATCCAATCATGTACTATTCTTAATCCCTG
10756 ATATTGGTTCGATACTGGCCTCTCCCAGTTTTTTAGTATATTTTCCTGCACAAACTAGTGGGATG
196 ATATTGGTTCGATACTGGCCTCTCCCAGTTTTTTAGTATATTTTCCTGCACAAACTAGTGGGATG
10821 TTAATATTTTC
261 TTAATATTTTC
10832 TTGTCACTTT
Statistics
Matches: 269, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
277 269 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.40
Consensus pattern (277 bp):
AAGATGGTATAGGTTTTGGTGATTCTGATTTCCACCATAAGGTACTTGTGCGGTTCCATTTCCCT
CCAGTTTTCCTTTTACCTTGCATTGAACATGTTGGATCACCCCTCAAGTGTCTTACTGTTCTAAC
AATGGCATTTTCCTTTTAAGACTCGCCAGTTGATTTATCCAATCATGTACTATTCTTAATCCCTG
ATATTGGTTCGATACTGGCCTCTCCCAGTTTTTTAGTATATTTTCCTGCACAAACTAGTGGGATG
TTAATATTTTCATGTTT
Found at i:16770 original size:15 final size:15
Alignment explanation
Indices: 16684--16775 Score: 50
Period size: 15 Copynumber: 6.2 Consensus size: 15
16674 GTATCGGGCC
16684 AAATATATATAT-TT
1 AAATATATATATATT
*
16698 AAAT-TAAATATA-T
1 AAATATATATATATT
16711 AAATATTATATATATT
1 AAATA-TATATATATT
** * * *
16727 -TTTTTAATTTAAATT
1 AAATAT-ATATATATT
*
16742 AAATTTAT-TAATATT
1 AAATATATAT-ATATT
16757 AAATATATATATATAT
1 AAATATATATATAT-T
16773 AAA
1 AAA
16776 AATAATTATT
Statistics
Matches: 58, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
13 11 0.19
14 6 0.10
15 32 0.55
16 9 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATATATATATATT
Found at i:17202 original size:21 final size:20
Alignment explanation
Indices: 17178--17249 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
17168 AAGAATCATA
17178 GTTTAGGGTATAGTGTTTAAG
1 GTTTAGGGTATAGT-TTTAAG
*
17199 GTTTAGGGTTTAAGTTTTAAG
1 GTTTAGGGTAT-AGTTTTAAG
* * * * *
17220 ATTTAAGGTTTAGATAT-AG
1 GTTTAGGGTATAGTTTTAAG
17239 GTTTAGGGTAT
1 GTTTAGGGTAT
17250 GAGATTGTGG
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 10 0.24
20 4 0.10
21 25 0.60
22 3 0.07
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.44
Consensus pattern (20 bp):
GTTTAGGGTATAGTTTTAAG
Found at i:17217 original size:7 final size:7
Alignment explanation
Indices: 17192--17231 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
17182 AGGGTATAGT
17192 GTTTAAG
1 GTTTAAG
*
17199 GTTTAGG
1 GTTTAAG
17206 GTTTAAG
1 GTTTAAG
*
17213 TTTTAAG
1 GTTTAAG
*
17220 ATTTAAG
1 GTTTAAG
17227 GTTTA
1 GTTTA
17232 GATATAGGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (7 bp):
GTTTAAG
Found at i:17217 original size:14 final size:14
Alignment explanation
Indices: 17178--17232 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
17168 AAGAATCATA
* * *
17178 GTTTAGGGTATAGT
1 GTTTAAGGTTTAGG
17192 GTTTAAGGTTTAGG
1 GTTTAAGGTTTAGG
* *
17206 GTTTAAGTTTTAAG
1 GTTTAAGGTTTAGG
*
17220 ATTTAAGGTTTAG
1 GTTTAAGGTTTAG
17233 ATATAGGTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.45
Consensus pattern (14 bp):
GTTTAAGGTTTAGG
Found at i:20562 original size:18 final size:18
Alignment explanation
Indices: 20539--20575 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20529 AGGCATTTGA
* *
20539 TCCTCTGGTTGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
20557 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
20575 T
1 T
20576 TCTCGTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.27, G:0.24, T:0.49
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:22196 original size:22 final size:23
Alignment explanation
Indices: 22170--22230 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
22160 AGAACCCCAG
*
22170 GGGGGTATCGATTCCCCTTTAAA
1 GGGGGTATCGATTCCCCTTCAAA
* *
22193 GGGGGAATCGGTTCCCCTTC-AA
1 GGGGGTATCGATTCCCCTTCAAA
22215 GGGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
22231 TCTGCACTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
22 16 0.48
23 17 0.52
ACGTcount: A:0.18, C:0.25, G:0.31, T:0.26
Consensus pattern (23 bp):
GGGGGTATCGATTCCCCTTCAAA
Found at i:22202 original size:23 final size:22
Alignment explanation
Indices: 22170--22230 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
22160 AGAACCCCAG
22170 GGGGGTATCGATTCCCCTTTAAA
1 GGGGGTATCGATTCCCC-TTAAA
* * *
22193 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGTATCGATTCCCCTTAAA
22215 GGGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
22231 TCTGCACTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
22 18 0.55
23 15 0.45
ACGTcount: A:0.18, C:0.25, G:0.31, T:0.26
Consensus pattern (22 bp):
GGGGGTATCGATTCCCCTTAAA
Found at i:28009 original size:20 final size:20
Alignment explanation
Indices: 27984--28035 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
27974 AACCATTCAG
27984 GGGGGAATCGGTACCCCCTT
1 GGGGGAATCGGTACCCCCTT
28004 GGGGGAATCGGTACCCCCTT
1 GGGGGAATCGGTACCCCCTT
28024 GGGGGAATCGGT
1 GGGGGAATCGGT
28036 TCCCTCTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.15, C:0.25, G:0.40, T:0.19
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTT
Found at i:30804 original size:17 final size:17
Alignment explanation
Indices: 30782--30814 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
30772 ATTTGGTGAC
30782 ATTTTGTAGCAGGTAAT
1 ATTTTGTAGCAGGTAAT
30799 ATTTTGTAGCAGGTAA
1 ATTTTGTAGCAGGTAA
30815 CACTGCTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.39
Consensus pattern (17 bp):
ATTTTGTAGCAGGTAAT
Found at i:40746 original size:22 final size:20
Alignment explanation
Indices: 40720--40762 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
40710 GTTATATTTT
*
40720 TTATTTTTTAATAATAAAAATA
1 TTATTTTTT--TAAAAAAAATA
40742 TTATTTTTTTAAAAAAAATA
1 TTATTTTTTTAAAAAAAATA
40762 T
1 T
40763 ATCAAAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
22 9 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATTTTTTTAAAAAAAATA
Found at i:42362 original size:21 final size:22
Alignment explanation
Indices: 42327--42368 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
42317 GTTGATTTTG
42327 ATCGGTTAGTGAGTGAATGATA
1 ATCGGTTAGTGAGTGAATGATA
*
42349 ATCGGTTA-TGAGTGCATGAT
1 ATCGGTTAGTGAGTGAATGAT
42369 CATTGAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.29, C:0.07, G:0.31, T:0.33
Consensus pattern (22 bp):
ATCGGTTAGTGAGTGAATGATA
Found at i:44490 original size:21 final size:21
Alignment explanation
Indices: 44465--44526 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
44455 TTTTTTTTTA
*
44465 ATTTTTATCTTTATAATTAAT
1 ATTTTTATATTTATAATTAAT
* * **
44486 ATTTTTAATTTTTGTAA-TCCT
1 ATTTTT-ATATTTATAATTAAT
44507 ATTTTTATATTTATAATTAA
1 ATTTTTATATTTATAATTAA
44527 AGTCTTTAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
20 8 0.26
21 15 0.48
22 8 0.26
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTTTATATTTATAATTAAT
Found at i:44520 original size:42 final size:42
Alignment explanation
Indices: 44465--44568 Score: 122
Period size: 42 Copynumber: 2.4 Consensus size: 42
44455 TTTTTTTTTA
* *
44465 ATTTTTATCTTTATAATTAATA-TTTTTAATTTTTGTAATC-C
1 ATTTTTATATTTATAATTAA-AGTCTTTAATTTTTGTAATCTC
*
44506 TATTTTTATATTTATAATTAAAGTCTTTAATTTTTTTAATCTC
1 -ATTTTTATATTTATAATTAAAGTCTTTAATTTTTGTAATCTC
*
44549 ATTTTTCTACATTTATAATT
1 A-TTTT-TATATTTATAATT
44569 GATGACTCTA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
41 1 0.02
42 36 0.67
43 5 0.09
44 12 0.22
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.61
Consensus pattern (42 bp):
ATTTTTATATTTATAATTAAAGTCTTTAATTTTTGTAATCTC
Found at i:44581 original size:44 final size:42
Alignment explanation
Indices: 44491--44584 Score: 100
Period size: 44 Copynumber: 2.2 Consensus size: 42
44481 TTAATATTTT
* * *
44491 TAATTTTTGTAATCCTATTTTTATATTTATAATTAAAGTCTT
1 TAATTTTTGTAATCCTATTTTTACATTTATAATTAAAGACTC
* * *
44533 TAATTTTTTTAAT-CTCATTTTTCTACATTTATAATTGATGACTC
1 TAATTTTTGTAATCCT-A-TTTT-TACATTTATAATTAAAGACTC
44577 TAATTTTT
1 TAATTTTT
44585 CAATTCCACT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
41 2 0.05
42 13 0.30
43 4 0.09
44 24 0.56
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.57
Consensus pattern (42 bp):
TAATTTTTGTAATCCTATTTTTACATTTATAATTAAAGACTC
Found at i:50050 original size:17 final size:15
Alignment explanation
Indices: 50028--50061 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
50018 CAACTGTATA
50028 CTCATATCATATGTCTG
1 CTCATAT-ATATGT-TG
50045 CTCATATATATGTTG
1 CTCATATATATGTTG
50060 CT
1 CT
50062 TGAAAATGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 6 0.35
17 7 0.41
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.44
Consensus pattern (15 bp):
CTCATATATATGTTG
Found at i:50866 original size:179 final size:178
Alignment explanation
Indices: 50530--50872 Score: 652
Period size: 178 Copynumber: 1.9 Consensus size: 178
50520 GGAGAGAGAA
50530 CAACAGGTCGAGCTCCCCAATGATGTTGGAGCCTTTATTCATGCACCCTTCTTTAACCGAGCAAA
1 CAACAGGTCGAGCTCCCCAATGATGTTGGAGCCTTTATTCATGCACCCTTCTTTAACCGAGCAAA
*
50595 CCACAATGGCTTGTGTGTATCATCAACAAATGATTCTTTACCCTCCAAACCACCCCCTCAACCCC
66 CCACAATGGCTTGTGTGTATCATCAACAAATGATTCTTTACCCTCCAAACCACCCCATCAACCCC
50660 ATGGCCAAAGCTTGCTCAATCTACTCCAATACAAGGAGGAGAGAACAG
131 ATGGCCAAAGCTTGCTCAATCTACTCCAATACAAGGAGGAGAGAACAG
50708 CAACAGGTCGAGCTCCCCAATGATGTTGGAGCCTTTAATTCATGCA-CCTTCTTTAACCGAGCAA
1 CAACAGGTCGAGCTCCCCAATGATGTTGGAGCCTTT-ATTCATGCACCCTTCTTTAACCGAGCAA
50772 ACCACAATGGCTTGTGTGTATCATCAACAAATGAATTCTTTACCCTCCAAACCACCCCATCAACC
65 ACCACAATGGCTTGTGTGTATCATCAACAAATG-ATTCTTTACCCTCCAAACCACCCCATCAACC
50837 CCATGGCCAAAGCTTGCTCAATCTACTCCAATACAA
129 CCATGGCCAAAGCTTGCTCAATCTACTCCAATACAA
50873 TTCTCACCCC
Statistics
Matches: 162, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
178 87 0.54
179 75 0.46
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.24
Consensus pattern (178 bp):
CAACAGGTCGAGCTCCCCAATGATGTTGGAGCCTTTATTCATGCACCCTTCTTTAACCGAGCAAA
CCACAATGGCTTGTGTGTATCATCAACAAATGATTCTTTACCCTCCAAACCACCCCATCAACCCC
ATGGCCAAAGCTTGCTCAATCTACTCCAATACAAGGAGGAGAGAACAG
Found at i:51253 original size:2 final size:2
Alignment explanation
Indices: 51246--51272 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
51236 GTTTAGGGTT
51246 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
51273 TTGTATACAA
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:51396 original size:26 final size:28
Alignment explanation
Indices: 51354--51417 Score: 93
Period size: 26 Copynumber: 2.5 Consensus size: 28
51344 TGGGTGATTT
51354 TGGAATGAAAATACAGGAAGACTTTTTA
1 TGGAATGAAAATACAGGAAGACTTTTTA
51382 TGGAATG-AAAT-CAGGAAGAC-TTTTA
1 TGGAATGAAAATACAGGAAGACTTTTTA
51407 T--AATGAAAATA
1 TGGAATGAAAATA
51418 ATAATATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.12
24 4 0.12
25 6 0.18
26 9 0.26
27 4 0.12
28 7 0.21
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.28
Consensus pattern (28 bp):
TGGAATGAAAATACAGGAAGACTTTTTA
Found at i:54372 original size:39 final size:40
Alignment explanation
Indices: 54271--54527 Score: 200
Period size: 39 Copynumber: 6.4 Consensus size: 40
54261 TAGTGGTATT
* * * *
54271 TTTAGTGGCGTTTTTAGAACAAATGCCGCTAAATACTCGTAA
1 TTTAGTGGC-TTTTTA-TACAAACGCCGCTAAAGACTCGTAC
* * *
54313 TTTAGTGG--TTTTATATAAACGCCACTAAAGACT-GTAA
1 TTTAGTGGCTTTTTATACAAACGCCGCTAAAGACTCGTAC
** *
54350 TTTAGTGGCTTTTTATACAAACGCCGCTGGAGACT-ATAC
1 TTTAGTGGCTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * *
54389 TTTAGTGGCGTTTTATTCAAACGCCG-AAAAGAGTCGTAC
1 TTTAGTGGCTTTTTATACAAACGCCGCTAAAGACTCGTAC
** * *
54428 TTTAGTGATATTTTTATATAAACGCCGCTATAGACTCGTAC
1 TTTAGTG-GCTTTTTATACAAACGCCGCTAAAGACTCGTAC
*** * * **
54469 TTTAGTTATATTTTTATACAAACACCGCTATAGACTAATAC
1 TTTAG-TGGCTTTTTATACAAACGCCGCTAAAGACTCGTAC
*
54510 TTTAGTGACGTTTTTATA
1 TTTAGTGGC-TTTTTATA
54528 TAATACGCTA
Statistics
Matches: 174, Mismatches: 34, Indels: 15
0.78 0.15 0.07
Matches are distributed among these distances:
37 12 0.07
38 19 0.11
39 62 0.36
40 15 0.09
41 57 0.33
42 9 0.05
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (40 bp):
TTTAGTGGCTTTTTATACAAACGCCGCTAAAGACTCGTAC
Found at i:54453 original size:40 final size:41
Alignment explanation
Indices: 54321--54565 Score: 148
Period size: 39 Copynumber: 6.1 Consensus size: 41
54311 AATTTAGTGG
* * * **
54321 TTTTATATAAACGCCACTAAAGACT-GTAATTTAGTG-GCT
1 TTTTATATAAACGCCGCAAAAGACTCGTACTTTAGTGATAT
* *** * ***
54360 TTTTATACAAACGCCGCTGGAGACT-ATACTTTAGTG-GCG
1 TTTTATATAAACGCCGCAAAAGACTCGTACTTTAGTGATAT
*
54399 TTTTAT-TCAAACGCCG-AAAAGAGTCGTACTTTAGTGATAT
1 TTTTATAT-AAACGCCGCAAAAGACTCGTACTTTAGTGATAT
* * *
54439 TTTTATATAAACGCCGCTATAGACTCGTACTTTAGTTATAT
1 TTTTATATAAACGCCGCAAAAGACTCGTACTTTAGTGATAT
* * * * ** **
54480 TTTTATACAAACACCGCTATAGACTAATACTTTAGTGACGT
1 TTTTATATAAACGCCGCAAAAGACTCGTACTTTAGTGATAT
* **
54521 TTTTATATAATACG-C-TAAAA-ACTCGTACAATAGTGATAGT
1 TTTTATATAA-ACGCCGCAAAAGACTCGTACTTTAGTGATA-T
54561 TTTTA
1 TTTTA
54566 AATCCCACAC
Statistics
Matches: 161, Mismatches: 38, Indels: 13
0.76 0.18 0.06
Matches are distributed among these distances:
38 4 0.02
39 68 0.42
40 22 0.14
41 65 0.40
42 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (41 bp):
TTTTATATAAACGCCGCAAAAGACTCGTACTTTAGTGATAT
Found at i:54480 original size:41 final size:41
Alignment explanation
Indices: 54321--54535 Score: 172
Period size: 41 Copynumber: 5.3 Consensus size: 41
54311 AATTTAGTGG
* * * **
54321 TTTTATATAAACGCCACTAAAGACT-GTAATTTAGTG-GCT
1 TTTTATATAAACGCCGCTATAGACTCGTACTTTAGTGATAT
* ** * ***
54360 TTTTATACAAACGCCGCTGGAGACT-ATACTTTAGTG-GCG
1 TTTTATATAAACGCCGCTATAGACTCGTACTTTAGTGATAT
* * *
54399 TTTTAT-TCAAACGCCG-AAAAGAGTCGTACTTTAGTGATAT
1 TTTTATAT-AAACGCCGCTATAGACTCGTACTTTAGTGATAT
*
54439 TTTTATATAAACGCCGCTATAGACTCGTACTTTAGTTATAT
1 TTTTATATAAACGCCGCTATAGACTCGTACTTTAGTGATAT
* * ** **
54480 TTTTATACAAACACCGCTATAGACTAATACTTTAGTGACGT
1 TTTTATATAAACGCCGCTATAGACTCGTACTTTAGTGATAT
54521 TTTTATATAATACGC
1 TTTTATATAA-ACGC
54536 TAAAAACTCG
Statistics
Matches: 141, Mismatches: 29, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
38 4 0.03
39 56 0.40
40 14 0.10
41 64 0.45
42 3 0.02
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (41 bp):
TTTTATATAAACGCCGCTATAGACTCGTACTTTAGTGATAT
Found at i:54555 original size:121 final size:119
Alignment explanation
Indices: 54321--54565 Score: 282
Period size: 121 Copynumber: 2.0 Consensus size: 119
54311 AATTTAGTGG
* * * *
54321 TTTTATATAAACGCCACTAAAGACTGTAATTTAGTGGCTTTTTATACAAACGCCGCTGGAGACTA
1 TTTTATATAAACGCCACTAAAGACTGTAATTTAGTAGATTTTTATACAAACACCGCTAGAGACTA
* * **
54386 TACTTTAGTGGCGTTTTATTCAAACGCCGAAAAGAGTCGTACTTTAGTGATA-T
66 TACTTTAGTGACGTTTTATTCAAACGCCGAAAAGACTCGTACAATAGTGATAGT
* * * * *
54439 TTTTATATAAACGCCGCTATAGACTCGTACTTTAGTTATATTTTTATACAAACACCGCTATAGAC
1 TTTTATATAAACGCCACTAAAGACT-GTAATTTAG-TAGATTTTTATACAAACACCGCTAGAGAC
*
54504 TAATACTTTAGTGACGTTTTTATAT-AATACG-CTAAAA-ACTCGTACAATAGTGATAGT
64 T-ATACTTTAGTGACG-TTTTAT-TCAA-ACGCCGAAAAGACTCGTACAATAGTGATAGT
54561 TTTTA
1 TTTTA
54566 AATCCCACAC
Statistics
Matches: 106, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
118 23 0.22
119 8 0.08
120 24 0.23
121 28 0.26
122 19 0.18
123 4 0.04
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (119 bp):
TTTTATATAAACGCCACTAAAGACTGTAATTTAGTAGATTTTTATACAAACACCGCTAGAGACTA
TACTTTAGTGACGTTTTATTCAAACGCCGAAAAGACTCGTACAATAGTGATAGT
Found at i:56424 original size:38 final size:39
Alignment explanation
Indices: 56373--56447 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
56363 TGCACATGTA
*
56373 TAATCTCAATC-TTTGGTCTGTTTTGACCTCATATTTTG
1 TAATCTCAATCTTTTGGTCTGTTTTGACCTCAGATTTTG
56411 TAATCTCAATCTTTTGGTCTGTTTTGACCTCAGATTT
1 TAATCTCAATCTTTTGGTCTGTTTTGACCTCAGATTT
56448 GTTAAAACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 11 0.31
39 24 0.69
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (39 bp):
TAATCTCAATCTTTTGGTCTGTTTTGACCTCAGATTTTG
Found at i:60232 original size:20 final size:20
Alignment explanation
Indices: 60209--60252 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
60199 AACTAATCCT
60209 CTAACAGATTTCTAAGTTCC
1 CTAACAGATTTCTAAGTTCC
* *
60229 CTAACTGATTTCTAATTTCC
1 CTAACAGATTTCTAAGTTCC
60249 CTAA
1 CTAA
60253 TAACTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (20 bp):
CTAACAGATTTCTAAGTTCC
Done.