Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005939.1 Hibiscus syriacus cultivar Beakdansim tig00013949_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: 103326
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:6144 original size:7 final size:8
Alignment explanation
Indices: 6132--6160 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
6122 ATGTCATGAA
6132 AAAAAAT-
1 AAAAAATG
6139 AAAAAATG
1 AAAAAATG
6147 AAAAAATG
1 AAAAAATG
6155 AAAAAA
1 AAAAAA
6161 AGAGAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (8 bp):
AAAAAATG
Found at i:6180 original size:19 final size:20
Alignment explanation
Indices: 6135--6181 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
6125 TCATGAAAAA
*
6135 AAATAAAAAATGAAAAAATG
1 AAATAAAAGATGAAAAAATG
6155 AAA-AAAAGA-GAAAAAA-G
1 AAATAAAAGATGAAAAAATG
6172 AGAATAAAAG
1 A-AATAAAAG
6182 GGGATTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 2 0.08
18 9 0.38
19 10 0.42
20 3 0.12
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.09
Consensus pattern (20 bp):
AAATAAAAGATGAAAAAATG
Found at i:6239 original size:46 final size:46
Alignment explanation
Indices: 6183--6292 Score: 166
Period size: 46 Copynumber: 2.4 Consensus size: 46
6173 GAATAAAAGG
* ** *
6183 GGATTTAAGATGAAAATCTGAAAATGGGCGTCTTGAAACCAAATGA
1 GGATTCAAGATGAAAATCTGAAAACCGGCGTCTTGAAACCAAATAA
6229 GGATTCAAGATGAAAATCTGAAAACCGGCGTCTTGAAACCAAATAA
1 GGATTCAAGATGAAAATCTGAAAACCGGCGTCTTGAAACCAAATAA
* *
6275 TGATTCAAGTTGAAAATC
1 GGATTCAAGATGAAAATC
6293 CAAAAAGGAC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.24
Consensus pattern (46 bp):
GGATTCAAGATGAAAATCTGAAAACCGGCGTCTTGAAACCAAATAA
Found at i:9787 original size:18 final size:19
Alignment explanation
Indices: 9766--9801 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
9756 TATGTTGTTG
*
9766 TTTTGTTTTTT-ATTATTA
1 TTTTCTTTTTTAATTATTA
9784 TTTTCTTTTTTAATTATT
1 TTTTCTTTTTTAATTATT
9802 TACTAATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (19 bp):
TTTTCTTTTTTAATTATTA
Found at i:10837 original size:11 final size:11
Alignment explanation
Indices: 10809--10837 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
10799 ATTGAAAGAC
10809 TAAATTTATTT
1 TAAATTTATTT
10820 T-AATTTATTT
1 TAAATTTATTT
10830 TAAATTTA
1 TAAATTTA
10838 ATATACTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TAAATTTATTT
Found at i:11138 original size:29 final size:28
Alignment explanation
Indices: 11090--11149 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 28
11080 AAATTATCTC
11090 TTTATTTTTTTTTAACTTATTAAATATA
1 TTTATTTTTTTTTAACTTATTAAATATA
*
11118 TTTATTTTTTTCTTAATTTATTAAATATA
1 TTTATTTTTTT-TTAACTTATTAAATATA
11147 TTT
1 TTT
11150 TGGTTTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 11 0.37
29 19 0.63
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTATTTTTTTTTAACTTATTAAATATA
Found at i:14424 original size:2 final size:2
Alignment explanation
Indices: 14417--14452 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
14407 ATACAAGTTC
14417 AT AT AT AT AT 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 AT AT AT AT AT
14453 GGATGGGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19921 original size:26 final size:26
Alignment explanation
Indices: 19892--19945 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
19882 ACTTAGTGCA
* *
19892 TATGGTGGGCACAACCTTATGTGTAT
1 TATGATGGGAACAACCTTATGTGTAT
**
19918 TATGATGGGAATGACCTTATGTGTAT
1 TATGATGGGAACAACCTTATGTGTAT
19944 TA
1 TA
19946 ACACTTTGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (26 bp):
TATGATGGGAACAACCTTATGTGTAT
Found at i:22557 original size:23 final size:23
Alignment explanation
Indices: 22487--22583 Score: 86
Period size: 23 Copynumber: 4.1 Consensus size: 23
22477 CATTTAAATG
*
22487 ATAAACGAACACAAATGAATGAAC
1 ATAAACGAACAC-AATAAATGAAC
*** * *
22511 ATAAACGAATGGATGTAAACGAAC
1 ATAAACGAACACA-ATAAATGAAC
* *
22535 ATAAGCGAACATAATAAATGAAC
1 ATAAACGAACACAATAAATGAAC
* *
22558 GTAAACGAACACAATAAATAAAC
1 ATAAACGAACACAATAAATGAAC
22581 ATA
1 ATA
22584 GTGAACGTAA
Statistics
Matches: 55, Mismatches: 17, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
23 30 0.55
24 25 0.45
ACGTcount: A:0.57, C:0.14, G:0.13, T:0.15
Consensus pattern (23 bp):
ATAAACGAACACAATAAATGAAC
Found at i:22791 original size:14 final size:14
Alignment explanation
Indices: 22771--22820 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
22761 TATTGGGCTA
*
22771 AACATAAATGAATG
1 AACATAAATGAACG
* *
22785 TACATAAACGAACG
1 AACATAAATGAACG
22799 AACATAAATGAACG
1 AACATAAATGAACG
22813 AACATAAA
1 AACATAAA
22821 CAAACATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.58, C:0.14, G:0.12, T:0.16
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:23637 original size:3 final size:3
Alignment explanation
Indices: 23629--23655 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
23619 TAATCACCAT
23629 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
23656 CAAATAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:25295 original size:29 final size:30
Alignment explanation
Indices: 25227--25295 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 30
25217 GTGTCAAGCC
* **
25227 TATA-TTTATTTATTTTAATAATATATTTA
1 TATATTTTATTTATTTTAATAAAATATGAA
* *
25256 TATATTGTATTT-TTTTTATAAAATATGAA
1 TATATTTTATTTATTTTAATAAAATATGAA
25285 TATATTTTATT
1 TATATTTTATT
25296 AAATATTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 27 0.82
30 6 0.18
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (30 bp):
TATATTTTATTTATTTTAATAAAATATGAA
Found at i:26149 original size:2 final size:2
Alignment explanation
Indices: 26142--26174 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
26132 TGTTTCGTAA
26142 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
26175 TGAAACACTG
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:27036 original size:19 final size:20
Alignment explanation
Indices: 27012--27062 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
27002 AATGACCAAT
27012 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
27031 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
27051 AAAATCGCAACG
1 AAAATCGCAACG
27063 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:27072 original size:20 final size:20
Alignment explanation
Indices: 27049--27102 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
27039 AACGCGATTT
*
27049 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
27069 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
27089 AGAAAATCGCAACG
1 AGAAAATCGCAACG
27103 CGAGCTTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:27261 original size:123 final size:123
Alignment explanation
Indices: 27116--27369 Score: 409
Period size: 123 Copynumber: 2.1 Consensus size: 123
27106 GCTTCCAAGT
* * * *
27116 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
* * * * *
27181 GCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
66 GCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAATCGCAAAGCGATTGAGAAAA
27239 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
* *
27304 GCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAATCGCAAAGCGATTTAGAAAA
66 GCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAATCGCAAAGCGATTGAGAAAA
27362 TCGCAACG
1 TCGCAACG
27370 TTAAAAAGAA
Statistics
Matches: 120, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
123 120 1.00
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (123 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAATCGCAAAGCGATTGAGAAAA
Found at i:27268 original size:103 final size:103
Alignment explanation
Indices: 27157--27359 Score: 352
Period size: 103 Copynumber: 2.0 Consensus size: 103
27147 CGATTGATAG
* * * *
27157 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATCG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCG
* *
27222 CAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAA
66 CAATGCGATTGAGAGAATCGCAAAGCGATTTAGAAGAA
27260 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCG
27325 CAATGCGATTGAGAGAATCGCAAAGCGATTTAGAA
66 CAATGCGATTGAGAGAATCGCAAAGCGATTTAGAA
27360 AATCGCAACG
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 94 1.00
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (103 bp):
AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCG
CAATGCGATTGAGAGAATCGCAAAGCGATTTAGAAGAA
Found at i:27363 original size:20 final size:20
Alignment explanation
Indices: 27137--27367 Score: 300
Period size: 20 Copynumber: 11.4 Consensus size: 20
27127 TTTAGAAGAA
*
27137 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
*
27157 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
*
27177 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
* *
27197 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
27217 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
27237 AGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGA-TT-G-AGAG
*
27260 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
27280 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
27300 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
27320 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
27340 AATCGCAAAGCGATTTAGAA
1 AATCGCAATGCGATTGAGAG
27360 AATCGCAA
1 AATCGCAA
27368 CGTTAAAAAG
Statistics
Matches: 190, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
20 171 0.90
21 3 0.02
22 2 0.01
23 14 0.07
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:27379 original size:20 final size:20
Alignment explanation
Indices: 27356--27399 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
27346 AAAGCGATTT
*
27356 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
* *
27376 AGAAAATCTCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
27396 AGAA
1 AGAA
27400 TAGTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.14
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:27531 original size:20 final size:20
Alignment explanation
Indices: 27506--27549 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
27496 TTTTTAACTA
*
27506 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
27526 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
27546 TTCT
1 TTCT
27550 AAATCGCGTT
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:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:27576 original size:19 final size:20
Alignment explanation
Indices: 27536--27586 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
27526 TTCTTTTTAA
*
27536 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
27556 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
27575 CGTTGCGATTTT
1 CGTTGCGATTTT
27587 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:28300 original size:28 final size:28
Alignment explanation
Indices: 28268--28367 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
28258 TTTTGATCTT
28268 TAATTTTAAAATTTTAAGTTATTGTCTA
1 TAATTTTAAAATTTTAAGTTATTGTCTA
* *
28296 TAATTTTAAATTTTTTCATCA-TTA-TGATCTT
1 TAATTTTAAA-ATTTT-A--AGTTATTG-TCTA
*
28327 TAATTTTAAAATTTTAAGTTATTATCTA
1 TAATTTTAAAATTTTAAGTTATTGTCTA
28355 TAATTTTAAAATT
1 TAATTTTAAAATT
28368 AACGTTTAAC
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
27 1 0.02
28 29 0.48
29 6 0.10
30 7 0.12
31 16 0.27
32 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (28 bp):
TAATTTTAAAATTTTAAGTTATTGTCTA
Found at i:28333 original size:31 final size:29
Alignment explanation
Indices: 28253--28364 Score: 90
Period size: 28 Copynumber: 3.9 Consensus size: 29
28243 TCATGAAAAA
* *
28253 TATCATTTTGATCTTTAATTTTAAAATTT
1 TATCATTATGATCTTTAATTTTAAATTTT
*
28282 TA--AGTTATTG-TCTATAATTTTAAATTTTT
1 TATCA-TTA-TGATCTTTAATTTTAAA-TTTT
*
28311 TCATCATTATGATCTTTAATTTTAAAATTT
1 T-ATCATTATGATCTTTAATTTTAAATTTT
* *
28341 TA--AGTTATTATCTATAATTTTAAA
1 TATCA-TTATGATCTTTAATTTTAAA
28365 ATTAACGTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
27 2 0.03
28 33 0.49
29 9 0.13
30 7 0.10
31 16 0.24
32 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.55
Consensus pattern (29 bp):
TATCATTATGATCTTTAATTTTAAATTTT
Found at i:28692 original size:15 final size:16
Alignment explanation
Indices: 28672--28705 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28662 ATTGCTAAAA
*
28672 TTTTATA-TTTTAGTT
1 TTTTATACTTTTACTT
28687 TTTTATACTTTTACTT
1 TTTTATACTTTTACTT
28703 TTT
1 TTT
28706 ATAATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTATACTTTTACTT
Found at i:28706 original size:15 final size:15
Alignment explanation
Indices: 28672--28713 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
28662 ATTGCTAAAA
*
28672 TTTTATATTTTAGTT
1 TTTTATATTTTAGCT
28687 TTTTATACTTTTA-CT
1 TTTTATA-TTTTAGCT
*
28702 TTTTATAATTTA
1 TTTTATATTTTA
28714 ATCTCAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.17
15 15 0.62
16 5 0.21
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTTATATTTTAGCT
Found at i:29218 original size:21 final size:21
Alignment explanation
Indices: 29193--29237 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
29183 GAAAATATTA
* *
29193 AAAAATATTAATGTTTTAGAT
1 AAAAATAATAATATTTTAGAT
29214 AAAAATAATAATATTTTAGAT
1 AAAAATAATAATATTTTAGAT
29235 AAA
1 AAA
29238 CTTTTACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
AAAAATAATAATATTTTAGAT
Found at i:30865 original size:37 final size:37
Alignment explanation
Indices: 30820--30897 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 37
30810 TATAGGATAA
*
30820 ATAT-AAAAAGAAAATAG-ATAAATAAATGAGTAAAAT
1 ATATAAAAAAGAAAA-AGCATAAATAAATAAGTAAAAT
* * *
30856 ATATAAAAAAGTAAAAGCATATATATATAAGTAAAAT
1 ATATAAAAAAGAAAAAGCATAAATAAATAAGTAAAAT
30893 A-ATAA
1 ATATAA
30898 TAATAATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 10 0.28
37 26 0.72
ACGTcount: A:0.65, C:0.01, G:0.09, T:0.24
Consensus pattern (37 bp):
ATATAAAAAAGAAAAAGCATAAATAAATAAGTAAAAT
Found at i:30879 original size:20 final size:20
Alignment explanation
Indices: 30854--30891 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30844 AATGAGTAAA
30854 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
30874 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
30892 TAATAATAAT
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:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:30898 original size:3 final size:3
Alignment explanation
Indices: 30890--30916 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
30880 ATATAAGTAA
30890 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
30917 CAAAAGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:31463 original size:35 final size:36
Alignment explanation
Indices: 31393--31492 Score: 130
Period size: 35 Copynumber: 2.8 Consensus size: 36
31383 GTGCTTGTTG
* * *
31393 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGCAAAATTCT
*
31430 ATCCTATTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
*
31465 ATCCTATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTAG-GAGTTTGAATCCTAG
31493 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 27 0.48
36 11 0.20
37 18 0.32
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:32343 original size:109 final size:107
Alignment explanation
Indices: 32002--32886 Score: 525
Period size: 98 Copynumber: 8.6 Consensus size: 107
31992 TGGAACCGGG
*** * * * *
32002 AAATTGTTTGTTGACTGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGT-CT
1 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGC-
* * * * *
32066 A--ATATCCTTCG-CTGTGAAGTTGAAATTGACTCT-AAA-CG-
65 ACGATATCCTCCGTC-GTGGAGTTGAAATCGGCTCTGAAATTGA
* * * *
32104 AAA-T-CTTGTTGACAATCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT-C-
1 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * *
32165 CAATATCCTTCG-C-TGCGAAGTTGAAATTGGCTCTGAAATTTGA
66 CGATATCCTCCGTCGTG-G-AGTTGAAATCGGCTCTGAAA-TTGA
* *
32208 AAAATGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGC
1 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GC
** *
32273 ACGATATCCTCCGTCGTGGAGTTGAAATC-GCGGATGAAACTGA
65 ACGATATCCTCCGTCGTGGAGTTGAAATCGGC-TCTGAAATTGA
*
32316 AAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC-AGGTA
1 AAA-TTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGA-GT-
* *
32380 GCACGATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGGAATTGGG
63 GCACGATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGAAATT-GA
* * *
32426 AAATTGTTTGTTGAAAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAAT-C-
1 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * * * * *
32489 CAATATCCTTCG-CTGTGAAGTTGAGATTGGCTCCGAAA-T--
66 CGATATCCTCCGTC-GTGGAGTTGAAATCGGCTCTGAAATTGA
* * ** * * * * * *
32528 ---TT-CTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGT-C-
1 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * * * * *
32587 CAATATCCTTCG-CTGTGAAGTTGAGATTGGCTC------CG-
66 CGATATCCTCCGTC-GTGGAGTTGAAATCGGCTCTGAAATTGA
* ** * * * * * *
32622 AAATTGTTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGT-C-
1 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * * * * * *
32685 CAATATCCTTCG-CTGTGAAGTTGAGATTGGATC------CG-
66 CGATATCCTCCGTC-GTGGAGTTGAAATCGGCTCTGAAATTGA
* ** * * * * * *
32720 AAATTGTTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGT-C-
1 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* * * * * * * *
32783 CAATATCCTTCGCCGTGAAGTTGAAATTGGCCCTGAAACTGGG
66 CGATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGAAA-TTGA
*
32826 AAATT-ATTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
1 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
32887 CCAATATCCT
Statistics
Matches: 676, Mismatches: 71, Indels: 69
0.83 0.09 0.08
Matches are distributed among these distances:
97 2 0.00
98 262 0.39
99 3 0.00
100 74 0.11
101 4 0.01
102 3 0.00
103 1 0.00
104 3 0.00
105 50 0.07
106 85 0.13
107 1 0.00
108 10 0.01
109 167 0.25
110 9 0.01
111 2 0.00
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (107 bp):
AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
CGATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGAAATTGA
Found at i:32456 original size:218 final size:205
Alignment explanation
Indices: 31954--32914 Score: 800
Period size: 196 Copynumber: 4.7 Consensus size: 205
31944 ATATTGTTCC
* * ** **
31954 GAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACCGGGAAATTGTTTGTTGACTG
1 GAGTCCAATATCCTCCGC-GTGGAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAA
* * * * *
32019 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCTTCGCTGTGAA
65 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTGTGAA
* ** * *
32084 GTTGAAATTGACTCTAAACGAAATCTTGTTGACAATCAGCGGTCCCTTCGTTGTGAAGTTGAACT
130 GTTGAAATCGACGATAAACGAAATCTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACT
*
32149 TGTGTTGTCTT
195 TGTGTTGTCTG
* * * * *
32160 GAGTCCAATATCCTTCGC-TGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACA
1 GAGTCCAATATCCTCCGCGTG-G-AGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACA
* *
32224 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGC-ACGATATCCTCCG-T
64 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGT--CTA--ATATCCTCCGCT
* *
32287 CGTGGAGTTGAAATCG-CGGATGAAACTGAAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTT
125 -GTGAAGTTGAAATCGAC-GAT-AAAC-G-AAA--TCTT-GTTGACAACCAGCCGTCCCTTCGTT
32351 GTGAAGTTGAACTTGTGTTGTCTCAG
182 GTGAAGTTGAACTTGTGTTGTCT--G
* * *
32377 GTAG-CACGATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGTTGAA
1 G-AGTC-CAATATCCTCCG-CGTGGAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGAC
* * *
32441 AACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAATCCAATATCCTTCGCTGTG
63 AACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTGTG
* * * * * ** * *
32506 AAGTTGAGATTG--GCT--CCGAAATTTCTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTG
128 AAGTTGAAATCGACGATAAACGAAA--TCTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTG
* *
32567 AGCTTGTGCTGTCTTG
191 AACTTGTGTTGTC-TG
* * * * * *
32583 G-GTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTC--------CGAAATTGTTTGTCGACAG
1 GAGTCCAATATCCTCCGC-GTGGAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAA
* * * * * * * *
32639 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGCTGTGAA
65 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTGTGAA
* * * * * ** * * *
32704 GTTGAGATTG--GAT--CCGAAATTGTTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAG
130 GTTGAAATCGACGATAAACGAAA-T-CTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAA
*
32765 CTTGTGCTGTCTTG
193 CTTGTGTTGTC-TG
* * * * * *
32779 G-GTCCAATATCCTTCGCCGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATT-ATTGTTGACAA
1 GAGTCCAATATCCTCCG-CGTGGAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAA
* * *
32842 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAA
65 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTGTGAA
*
32907 GTCGAAAT
130 GTTGAAAT
32915 TGACTCTAGC
Statistics
Matches: 635, Mismatches: 85, Indels: 73
0.80 0.11 0.09
Matches are distributed among these distances:
195 2 0.00
196 176 0.28
197 1 0.00
203 73 0.11
204 35 0.06
205 1 0.00
206 91 0.14
207 41 0.06
208 11 0.02
209 24 0.04
210 5 0.01
211 1 0.00
212 3 0.00
213 2 0.00
214 3 0.00
215 67 0.11
216 2 0.00
217 3 0.00
218 90 0.14
219 2 0.00
220 2 0.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (205 bp):
GAGTCCAATATCCTCCGCGTGGAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAAC
CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTGTGAAG
TTGAAATCGACGATAAACGAAATCTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTT
GTGTTGTCTG
Found at i:32559 original size:55 final size:55
Alignment explanation
Indices: 32495--32764 Score: 181
Period size: 55 Copynumber: 5.3 Consensus size: 55
32485 AATCCAATAT
32495 CCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATTTCTTGTCGACAGTCAGCCGCC
1 CCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATTTCTTGTCGACAGTCAGCCGCC
* * *
32550 CCTTCGCTGTGAAGTTGAGCTTGTGCT--G-----TCTTGGGTC--CAAT-A-----T
1 CCTTCGCTGTGAAGTTGAGATTG-GCTCCGAAATTTCTT--GTCGACAGTCAGCCGCC
32593 CCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATTGT-TTGTCGACAGTCAGCCGCC
1 CCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATT-TCTTGTCGACAGTCAGCCGCC
* * *
32648 CCTTCGCTGTGAAGTTGAGCTTGTGCT--G-----TCTTGGGTC--CAAT-A-----T
1 CCTTCGCTGTGAAGTTGAGATTG-GCTCCGAAATTTCTT--GTCGACAGTCAGCCGCC
*
32691 CCTTCGCTGTGAAGTTGAGATTGGATCCGAAATTGT-TTGTCGACAGTCAGCCGCC
1 CCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATT-TCTTGTCGACAGTCAGCCGCC
32746 CCTTCGCTGTGAAGTTGAG
1 CCTTCGCTGTGAAGTTGAG
32765 CTTGTGCTGT
Statistics
Matches: 163, Mismatches: 13, Indels: 78
0.64 0.05 0.31
Matches are distributed among these distances:
42 5 0.03
43 44 0.27
44 2 0.01
47 6 0.04
48 3 0.02
49 22 0.13
50 4 0.02
51 6 0.04
54 2 0.01
55 63 0.39
56 6 0.04
ACGTcount: A:0.17, C:0.24, G:0.27, T:0.32
Consensus pattern (55 bp):
CCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATTTCTTGTCGACAGTCAGCCGCC
Found at i:32594 original size:98 final size:98
Alignment explanation
Indices: 32425--32908 Score: 666
Period size: 98 Copynumber: 4.9 Consensus size: 98
32415 CTGGAATTGG
* * ** * * * * **
32425 GAAATTGTTTGTTGAAAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAATCC
1 GAAATTGTTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCC
32490 AATATCCTTCGCTGTGAAGTTGAGATTGGCTCC
66 AATATCCTTCGCTGTGAAGTTGAGATTGGCTCC
32523 GAAATT-TCTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTC
1 GAAATTGT-TTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTC
32587 CAATATCCTTCGCTGTGAAGTTGAGATTGGCTCC
65 CAATATCCTTCGCTGTGAAGTTGAGATTGGCTCC
32621 GAAATTGTTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCC
1 GAAATTGTTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCC
*
32686 AATATCCTTCGCTGTGAAGTTGAGATTGGATCC
66 AATATCCTTCGCTGTGAAGTTGAGATTGGCTCC
32719 GAAATTGTTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCC
1 GAAATTGTTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCC
* *
32784 AATATCCTTCGCCGTGAAGTTGAAATTGGC-CC
66 AATATCCTTCGCTGTGAAGTTGAGATTGGCTCC
* * ** * * * *
32816 TGAAACTGGGAAATTATTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
1 -GAAA-T-TG----T-TTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTC
* *
32881 TCGAGTCCAATATCCTTCGCTGTGAAGT
58 TTGGGTCCAATATCCTTCGCTGTGAAGT
32909 CGAAATTGAC
Statistics
Matches: 351, Mismatches: 25, Indels: 13
0.90 0.06 0.03
Matches are distributed among these distances:
97 3 0.01
98 277 0.79
99 2 0.01
100 1 0.00
104 1 0.00
105 67 0.19
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.33
Consensus pattern (98 bp):
GAAATTGTTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCC
AATATCCTTCGCTGTGAAGTTGAGATTGGCTCC
Found at i:32598 original size:43 final size:43
Alignment explanation
Indices: 32550--32709 Score: 142
Period size: 43 Copynumber: 3.4 Consensus size: 43
32540 GTCAGCCGCC
32550 CCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATAT
1 CCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATAT
* ** * * *
32593 CCTTCGCTGTGAAGTTGAGATTG-GCTCCGAAATTGTTTGTCGACAGTCAGCCGCC
1 CCTTCGCTGTGAAGTTGAGCTTGTGCT--G-TCTTG--GGTC--CAAT-A-----T
32648 CCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATAT
1 CCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATAT
32691 CCTTCGCTGTGAAGTTGAG
1 CCTTCGCTGTGAAGTTGAG
32710 ATTGGATCCG
Statistics
Matches: 91, Mismatches: 12, Indels: 28
0.69 0.09 0.21
Matches are distributed among these distances:
42 3 0.03
43 41 0.45
44 1 0.01
45 3 0.03
47 3 0.03
48 1 0.01
49 6 0.07
50 1 0.01
51 3 0.03
53 3 0.03
54 1 0.01
55 22 0.24
56 3 0.03
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.34
Consensus pattern (43 bp):
CCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATAT
Found at i:33562 original size:102 final size:103
Alignment explanation
Indices: 33411--33597 Score: 297
Period size: 102 Copynumber: 1.8 Consensus size: 103
33401 AAGATGATGC
* *
33411 TTCAAGAGAAAAATGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 TTCAAGAGAAAAATGTCTCAAGGGAGAAAAAATTTTGTTTAAAGAGAAACTGTCTCAAGAGAGAC
33476 GAAA-TTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
66 -AAAGTTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
* *
33514 TTCAAGAG-AAATTGTCTCAAGGGAGAAAAAATTTTGTTTAAAGGGAAACTGTCTCAAGAGAGAC
1 TTCAAGAGAAAAATGTCTCAAGGGAGAAAAAATTTTGTTTAAAGAGAAACTGTCTCAAGAGAGAC
**
33578 AAAGTTTGTTTCAAGGGAAA
66 AAAGTTCATTTCAAGGGAAA
33598 CTGTCTCAAG
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
101 3 0.04
102 66 0.86
103 8 0.10
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (103 bp):
TTCAAGAGAAAAATGTCTCAAGGGAGAAAAAATTTTGTTTAAAGAGAAACTGTCTCAAGAGAGAC
AAAGTTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
Found at i:33594 original size:36 final size:36
Alignment explanation
Indices: 33511--33615 Score: 147
Period size: 36 Copynumber: 2.9 Consensus size: 36
33501 TCAATGTTTA
* * * * *
33511 TGTTTCAAGAGAAATTGTCTCAAGGGAGAAAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAG-ACAAAGTT
*
33548 TGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
33584 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
33616 TGGTGAGCAC
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
36 37 0.61
37 24 0.39
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
Found at i:34498 original size:22 final size:22
Alignment explanation
Indices: 34473--34523 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
34463 TTGTGTTTGG
34473 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
34495 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
34517 TCAAAGG
1 TCAAAGG
34524 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:35158 original size:20 final size:21
Alignment explanation
Indices: 35135--35193 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
35125 TTGTCCCCTT
*
35135 TTTTTTATTTTTGTTCTTT-C
1 TTTTTTATTCTTGTTCTTTCC
* *
35155 TTTTTTGTTCTTGTTTTTTCC
1 TTTTTTATTCTTGTTCTTTCC
**
35176 TTTTTGCTTCTT-TTCTTT
1 TTTTTTATTCTTGTTCTTT
35194 TTTCTTTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.02, C:0.14, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTTATTCTTGTTCTTTCC
Found at i:35211 original size:22 final size:23
Alignment explanation
Indices: 35168--35210 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
35158 TTTGTTCTTG
*
35168 TTTTTTCCTTTTTGCTTCTTTTC
1 TTTTTTCCTTTTTGCCTCTTTTC
35191 TTTTTT-CTTTTTGCC-CTTTT
1 TTTTTTCCTTTTTGCCTCTTTT
35211 TGTTCTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (23 bp):
TTTTTTCCTTTTTGCCTCTTTTC
Found at i:39491 original size:20 final size:20
Alignment explanation
Indices: 39466--39503 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39456 AATGAGTAAA
39466 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
39486 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
39504 TAATAAAAAA
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:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:39529 original size:39 final size:37
Alignment explanation
Indices: 39460--39535 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
39450 TAAATAAATG
* *
39460 AGTAAAATATATAAAAAAGTAAAAGCATATATATATA
1 AGTAAAATATATAAAAAAATAAAAGAATATATATATA
*
39497 AGTAAAATA-ATAAAAAAAATCAAAAGTAATATATGTATA
1 AGTAAAATATAT-AAAAAAAT-AAAAG-AATATATATATA
39536 TATACATGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 2 0.06
37 16 0.48
38 5 0.15
39 10 0.30
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (37 bp):
AGTAAAATATATAAAAAAATAAAAGAATATATATATA
Found at i:45384 original size:2 final size:2
Alignment explanation
Indices: 45377--45406 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
45367 CGTCCAATCA
45377 AT AT 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 AT AT
45407 GTATTCATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46972 original size:246 final size:243
Alignment explanation
Indices: 46485--46971 Score: 713
Period size: 246 Copynumber: 2.0 Consensus size: 243
46475 GTCGGATCGG
* *
46485 GTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTATGGTGGAAAAAACCGGACCGACCCGAA
1 GTTTTTTAAGTGTGATATTCGGGTCGGGTTAGGGTTTA-----GAAAAAACCGGACAGACCCGAA
46550 AATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTATA
61 AATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTATA
* * *
46615 TTATTTCGGGTCGGGTCGGGTTGGATTTCTAATTTATATATTCGGGTCGGGTCGGATGAAACATT
126 TTATTTCGGGTCGAGTC--G--AGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACATT
*
46680 ATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTT-GGGTCA
187 ATATTGTTC-GGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTTCGGGTCA
46737 GTTTTTTAAGTGTGATATTCGGGTCGGGTTTAGGG-TTA-AAAAAACCGGACAGACCCGAAAATA
1 GTTTTTTAAGTGTGATATTCGGGTCGGG-TTAGGGTTTAGAAAAAACCGGACAGACCCGAAAATA
* *
46800 TATATAATTCGGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATTAT
65 TATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTATATTAT
46865 TTCGGGTCGAGTC-AGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAAC-TT-TATT-TT
130 TTCGGGTCGAGTCGAGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACATTATATTGTT
* * *
46926 -GGTCGGGTTGGGTTTTTTAAGTGTGATATCCGGGTC-AGGTCGGGTC
195 CGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTTCGGGTC
46972 GGGTTCGGGT
Statistics
Matches: 222, Mismatches: 11, Indels: 20
0.88 0.04 0.08
Matches are distributed among these distances:
235 3 0.01
236 39 0.18
238 2 0.01
239 3 0.01
240 2 0.01
241 38 0.17
246 99 0.45
252 31 0.14
253 5 0.02
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (243 bp):
GTTTTTTAAGTGTGATATTCGGGTCGGGTTAGGGTTTAGAAAAAACCGGACAGACCCGAAAATAT
ATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTATATTATT
TCGGGTCGAGTCGAGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACATTATATTGTTC
GGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTTCGGGTCA
Found at i:47835 original size:31 final size:30
Alignment explanation
Indices: 47798--47855 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
47788 AAATAACATA
* *
47798 TTTGATCCTTCAATTATTATTTTATTTCTGT
1 TTTGATCATTCAAATATTATTTT-TTTCTGT
*
47829 TTTGATCATTTAAATATTATTTTTTTC
1 TTTGATCATTCAAATATTATTTTTTTC
47856 AGTCATATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.22, C:0.10, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTGATCATTCAAATATTATTTTTTTCTGT
Found at i:50197 original size:2 final size:2
Alignment explanation
Indices: 50159--50184 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50149 GGAAATTTTA
50159 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
50185 TACAGAATAT
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:59189 original size:20 final size:19
Alignment explanation
Indices: 59148--59189 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
59138 CTCGATGTCG
*
59148 TTTTATTTCTTTAATTTGA
1 TTTTATTTCTTTAAATTGA
59167 TTTTGATTT-TTTAAATTGTA
1 TTTT-ATTTCTTTAAATTG-A
59187 TTT
1 TTT
59190 CACTTTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.69
Consensus pattern (19 bp):
TTTTATTTCTTTAAATTGA
Found at i:66646 original size:35 final size:36
Alignment explanation
Indices: 66595--66680 Score: 129
Period size: 35 Copynumber: 2.4 Consensus size: 36
66585 CTTGCAACAC
* *
66595 ATACATCAATTGCATTCTAAACCCCAAATTCC-AAA
1 ATACTTCAATTACATTCTAAACCCCAAATTCCAAAA
* *
66630 ATATTTCAATTACATTCTAAACCTCAAATTCCAAAA
1 ATACTTCAATTACATTCTAAACCCCAAATTCCAAAA
66666 ATACTTCAATTACAT
1 ATACTTCAATTACAT
66681 GACTAACCAC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 28 0.62
36 17 0.38
ACGTcount: A:0.43, C:0.24, G:0.01, T:0.31
Consensus pattern (36 bp):
ATACTTCAATTACATTCTAAACCCCAAATTCCAAAA
Found at i:66694 original size:36 final size:35
Alignment explanation
Indices: 66595--66695 Score: 114
Period size: 35 Copynumber: 2.9 Consensus size: 35
66585 CTTGCAACAC
* * * *
66595 ATACATCAATTGCATTCTAAACCCCAAATTCCAAA
1 ATACTTCAATTACATACTAAACCACAAATTCCAAA
* * *
66630 ATATTTCAATTACATTCTAAACCTCAAATTCCAAAA
1 ATACTTCAATTACATACTAAACCACAAATTCC-AAA
66666 ATACTTCAATTACATGACT-AACCACAAATT
1 ATACTTCAATTACAT-ACTAAACCACAAATT
66696 AATAATGTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
35 28 0.49
36 27 0.47
37 2 0.04
ACGTcount: A:0.44, C:0.25, G:0.02, T:0.30
Consensus pattern (35 bp):
ATACTTCAATTACATACTAAACCACAAATTCCAAA
Found at i:67687 original size:35 final size:35
Alignment explanation
Indices: 67641--67718 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
67631 TTGTGATAAC
* *
67641 ATGTAAATGAAGTATTTTGAAATTTGAGGTTTAAA
1 ATGTAATTGAAGTATTTTGAAATTTGAGGCTTAAA
* * *
67676 ATGTAATTGAAGTATTTTGAATTTTGGGGCTTAGA
1 ATGTAATTGAAGTATTTTGAAATTTGAGGCTTAAA
67711 ATGTAATT
1 ATGTAATT
67719 TATGACTGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGAAATTTGAGGCTTAAA
Found at i:78317 original size:26 final size:26
Alignment explanation
Indices: 78254--78317 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
78244 TGAAGTACAC
* *
78254 AAATAGTCTTCGACTATGGGATGTAT
1 AAATAGTCCTCGACTATGGGACGTAT
*
78280 AAATAGTGCTCGACTATGGGACGTAT
1 AAATAGTCCTCGACTATGGGACGTAT
*
78306 AAATACTCCTCG
1 AAATAGTCCTCG
78318 GACGTTTGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (26 bp):
AAATAGTCCTCGACTATGGGACGTAT
Found at i:79523 original size:20 final size:20
Alignment explanation
Indices: 79498--79545 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
79488 GTGACGGAAA
79498 GCTTACTTGCCCAGTTAACT
1 GCTTACTTGCCCAGTTAACT
79518 GCTTACTTGCCCAGTTAACT
1 GCTTACTTGCCCAGTTAACT
79538 GCTTACTT
1 GCTTACTT
79546 AGACCGCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.19, C:0.29, G:0.15, T:0.38
Consensus pattern (20 bp):
GCTTACTTGCCCAGTTAACT
Found at i:84210 original size:16 final size:17
Alignment explanation
Indices: 84174--84215 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
84164 ATGAAGGCTT
*
84174 TTATATCTCTTCATCTTC
1 TTAT-TCTCTTAATCTTC
84192 TTATTCTCTTAAT-TTC
1 TTATTCTCTTAATCTTC
84208 TTACTTCT
1 TTA-TTCT
84216 TTCTCATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 12 0.55
18 4 0.18
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATTCTCTTAATCTTC
Found at i:85284 original size:36 final size:35
Alignment explanation
Indices: 85217--85332 Score: 119
Period size: 37 Copynumber: 3.2 Consensus size: 35
85207 GGAAATGTAG
* *
85217 TAAAAACGTATTTTCAAAACCATAT-TATATAT-TTT
1 TAAAAACGT-TTTTAAAAACTATATAT-TATATGTTT
85252 TAAAAACCGATTTTTAAAAACTATATATTATATGCTTT
1 TAAAAA-CG-TTTTTAAAAACTATATATTATATG-TTT
* *
85290 CAAAAATGTTTTCTAAAAACTATATATTATATGTTT
1 TAAAAACGTTTT-TAAAAACTATATATTATATGTTT
85326 TCAAAAA
1 T-AAAAA
85333 ATATTTTCAA
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
35 6 0.09
36 27 0.39
37 28 0.41
38 8 0.12
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.41
Consensus pattern (35 bp):
TAAAAACGTTTTTAAAAACTATATATTATATGTTT
Found at i:85295 original size:38 final size:37
Alignment explanation
Indices: 85238--85332 Score: 129
Period size: 37 Copynumber: 2.5 Consensus size: 37
85228 TTTCAAAACC
* *
85238 ATATTATATATTTTTAAAAACCGATTTT-TAAAAACTAT
1 ATATTATATGTTTTCAAAAA-CG-TTTTCTAAAAACTAT
* *
85276 ATATTATATGCTTTCAAAAATGTTTTCTAAAAACTAT
1 ATATTATATGTTTTCAAAAACGTTTTCTAAAAACTAT
85313 ATATTATATGTTTTCAAAAA
1 ATATTATATGTTTTCAAAAA
85333 ATATTTTCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
36 4 0.08
37 30 0.59
38 17 0.33
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (37 bp):
ATATTATATGTTTTCAAAAACGTTTTCTAAAAACTAT
Found at i:85316 original size:37 final size:38
Alignment explanation
Indices: 85261--85348 Score: 137
Period size: 37 Copynumber: 2.4 Consensus size: 38
85251 TTAAAAACCG
85261 ATTTT-TAAAAACTATATATTATATGCTTTC-AAAAAT
1 ATTTTCTAAAAACTATATATTATATGCTTTCAAAAAAT
* *
85297 GTTTTCTAAAAACTATATATTATATGTTTTCAAAAAAT
1 ATTTTCTAAAAACTATATATTATATGCTTTCAAAAAAT
85335 ATTTTC-AAAAACTA
1 ATTTTCTAAAAACTA
85349 CATTATATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
36 4 0.09
37 32 0.68
38 11 0.23
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.43
Consensus pattern (38 bp):
ATTTTCTAAAAACTATATATTATATGCTTTCAAAAAAT
Found at i:93178 original size:20 final size:19
Alignment explanation
Indices: 93137--93178 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
93127 CTCGATGTCG
*
93137 TTTTATTTCTTTAATTTGA
1 TTTTATTTCTTTAAATTGA
93156 TTTTGATTT-TTTAAATTGTA
1 TTTT-ATTTCTTTAAATTG-A
93176 TTT
1 TTT
93179 CACTTTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.69
Consensus pattern (19 bp):
TTTTATTTCTTTAAATTGA
Found at i:100595 original size:35 final size:36
Alignment explanation
Indices: 100544--100629 Score: 129
Period size: 35 Copynumber: 2.4 Consensus size: 36
100534 CTTGCAACAC
* *
100544 ATACATCAATTGCATTCTAAACCCCAAATTCC-AAA
1 ATACTTCAATTACATTCTAAACCCCAAATTCCAAAA
* *
100579 ATATTTCAATTACATTCTAAACCTCAAATTCCAAAA
1 ATACTTCAATTACATTCTAAACCCCAAATTCCAAAA
100615 ATACTTCAATTACAT
1 ATACTTCAATTACAT
100630 GACTAACCAC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 28 0.62
36 17 0.38
ACGTcount: A:0.43, C:0.24, G:0.01, T:0.31
Consensus pattern (36 bp):
ATACTTCAATTACATTCTAAACCCCAAATTCCAAAA
Found at i:100643 original size:36 final size:35
Alignment explanation
Indices: 100544--100644 Score: 114
Period size: 35 Copynumber: 2.9 Consensus size: 35
100534 CTTGCAACAC
* * * *
100544 ATACATCAATTGCATTCTAAACCCCAAATTCCAAA
1 ATACTTCAATTACATACTAAACCACAAATTCCAAA
* * *
100579 ATATTTCAATTACATTCTAAACCTCAAATTCCAAAA
1 ATACTTCAATTACATACTAAACCACAAATTCC-AAA
100615 ATACTTCAATTACATGACT-AACCACAAATT
1 ATACTTCAATTACAT-ACTAAACCACAAATT
100645 AATAATGTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
35 28 0.49
36 27 0.47
37 2 0.04
ACGTcount: A:0.44, C:0.25, G:0.02, T:0.30
Consensus pattern (35 bp):
ATACTTCAATTACATACTAAACCACAAATTCCAAA
Found at i:101630 original size:35 final size:35
Alignment explanation
Indices: 101584--101661 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
101574 TTGTGATAAC
* *
101584 ATGTAAATGAAGTATTTTGAAATTTGAGGTTTAAA
1 ATGTAATTGAAGTATTTTGAAATTTGAGGCTTAAA
* * *
101619 ATGTAATTGAAGTATTTTGAATTTTGGGGCTTAGA
1 ATGTAATTGAAGTATTTTGAAATTTGAGGCTTAAA
101654 ATGTAATT
1 ATGTAATT
101662 TATGACTGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGAAATTTGAGGCTTAAA
Done.