Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001760.1 Hibiscus syriacus cultivar Beakdansim tig00003556_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: 79473
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:4584 original size:3 final size:3
Alignment explanation
Indices: 4576--4634 Score: 59
Period size: 3 Copynumber: 19.3 Consensus size: 3
4566 TGGGTTTTAA
* *
4576 ATT ATT ATT ATT ACTT ATT ATT CTT ATT CATT ATT ATT ACT -TT A-T
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
4621 ATT ATAT ATT ATT A
1 ATT AT-T ATT ATT A
4635 CATTTTGCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
2 3 0.06
3 35 0.74
4 9 0.19
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:4595 original size:13 final size:12
Alignment explanation
Indices: 4576--4634 Score: 59
Period size: 13 Copynumber: 4.8 Consensus size: 12
4566 TGGGTTTTAA
4576 ATTATTATTATT
1 ATTATTATTATT
*
4588 ACTTATTATTCTT
1 A-TTATTATTATT
4601 ATTCATTATTATT
1 ATT-ATTATTATT
*
4614 ACT-TTA-TATT
1 ATTATTATTATT
4624 ATATATTATTA
1 AT-TATTATTA
4635 CATTTTGCAG
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
10 5 0.13
11 4 0.11
12 6 0.16
13 23 0.61
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTATTATTATT
Found at i:4595 original size:16 final size:16
Alignment explanation
Indices: 4576--4635 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
4566 TGGGTTTTAA
4576 ATTATTATTATTACTT
1 ATTATTATTATTACTT
*
4592 ATTATTCTTATT-CATT
1 ATTATTATTATTAC-TT
*
4608 ATTATTACT-TTA--T
1 ATTATTATTATTACTT
4621 ATTATATATTATTAC
1 ATTAT-TATTATTAC
4636 ATTTTGCAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
13 6 0.17
14 3 0.09
15 6 0.17
16 20 0.57
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTATTATTATTACTT
Found at i:4633 original size:10 final size:9
Alignment explanation
Indices: 4576--4634 Score: 59
Period size: 10 Copynumber: 6.4 Consensus size: 9
4566 TGGGTTTTAA
4576 ATTATTATT
1 ATTATTATT
4585 ATTACTTATT
1 ATTA-TTATT
*
4595 ATTCTTATT
1 ATTATTATT
4604 CATTATTATT
1 -ATTATTATT
*
4614 ACT-TTA-T
1 ATTATTATT
4621 ATTATATATT
1 ATTAT-TATT
4631 ATTA
1 ATTA
4635 CATTTTGCAG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
7 3 0.07
8 4 0.10
9 13 0.32
10 21 0.51
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (9 bp):
ATTATTATT
Found at i:12003 original size:36 final size:36
Alignment explanation
Indices: 11963--12144 Score: 89
Period size: 36 Copynumber: 5.2 Consensus size: 36
11953 TCTTTTTCCT
11963 TTGAGATTTTTTTCTTAAGAACAAATTTTGTCTCAC
1 TTGAGATTTTTTTCTTAAGAACAAATTTTGTCTCAC
* * * *
11999 TTGAGATAGTCTTCCTTAAGACACGAA--------CA-
1 TTGAGAT-TTTTTTCTTAAGA-ACAAATTTTGTCTCAC
* * **
12028 TCTGAGATTGTTTTTCTTAAAAACAAAGTTTCGTCTCGT
1 T-TGAGATT-TTTTTCTTAAGAACAAA-TTTTGTCTCAC
** *
12067 TTGAGACAGTTTTTCTTGA-AACAAA-TTTGATCTCAC
1 TTGAGA-TTTTTTTCTTAAGAACAAATTTTG-TCTCAC
* * * *
12103 ATGAGATTATTTTCCTAACAACAAATTTTGTCTCAC
1 TTGAGATTTTTTTCTTAAGAACAAATTTTGTCTCAC
12139 TTGAGA
1 TTGAGA
12145 CAATTTTCCC
Statistics
Matches: 105, Mismatches: 23, Indels: 36
0.64 0.14 0.22
Matches are distributed among these distances:
29 5 0.05
30 17 0.16
35 10 0.10
36 33 0.31
37 20 0.19
38 19 0.18
39 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (36 bp):
TTGAGATTTTTTTCTTAAGAACAAATTTTGTCTCAC
Found at i:12382 original size:66 final size:66
Alignment explanation
Indices: 12299--12464 Score: 278
Period size: 66 Copynumber: 2.5 Consensus size: 66
12289 AAACAAAATT
* * *
12299 CATAAACCTTTGTGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAA
1 CATAAACCTTTGAGATTGTTTCACTTGAAACAAATTTTGTCTCGCTTAAGACAGTTTCTCTTGAA
12364 A
66 A
* *
12365 CATAAACTTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTAAGACAGTTTCTCTTGAA
1 CATAAACCTTTGAGATTGTTTCACTTGAAACAAATTTTGTCTCGCTTAAGACAGTTTCTCTTGAA
12430 A
66 A
*
12431 CTTAAACCTTTGAGATTGTTTCACTTGAAACAAA
1 CATAAACCTTTGAGATTGTTTCACTTGAAACAAA
12465 ATTCATAAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 93 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (66 bp):
CATAAACCTTTGAGATTGTTTCACTTGAAACAAATTTTGTCTCGCTTAAGACAGTTTCTCTTGAA
A
Found at i:12398 original size:169 final size:168
Alignment explanation
Indices: 12208--12632 Score: 534
Period size: 169 Copynumber: 2.5 Consensus size: 168
12198 ATCTCACTTA
* * *
12208 AGATTGTTTCT-TTCAAAACAAATTCGTCTCGCTGGAGACAATTTTCCCTCAAAACACAAA-ATT
1 AGATTGTTTCTCTT-GAAACAAATTCGTCTCGCTGAAGAC-AGTTTCCCTCAAAACACAAACATT
* *
12271 GGGAAATTGTTTCACTTGAAACAAAATTCATAAACCTTTGTGATTGTTTCCCTTGAAACAAATTT
64 -GGAAATTGTTTCACTTGAAACAAAATTCATAAACCTTTGAGATTATTTCCCTTGAAACAAATTT
*
12336 TGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACTTTTG
128 TGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTG
* * * ** ** * *
12377 AGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTAAGACAGTTTCTCTTGAAACTTAAACCTTT
1 AGATTGTTTCTCTTGAAACAAA-TTCGTCTCGCTGAAGACAGTTTCCCTCAAAACACAAACATTG
*
12442 GAGATTGTTTCACTTGAAACAAAATTCATAAACCTTTGAGATTATTTCCCTTGAAACAAATTTTG
65 GAAATTGTTTCACTTGAAACAAAATTCATAAACCTTTGAGATTATTTCCCTTGAAACAAATTTTG
*
12507 TCTTGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTG
130 TCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTG
** * ** *
12546 AGATTGTTTCTCTTGAAACAAATTTTATCTCGCTTG-AGACAGTTTCTCTTGAAACATAAACATT
1 AGATTGTTTCTCTTGAAACAAA-TTCGTCTCGC-TGAAGACAGTTTCCCTCAAAACACAAACATT
** *
12610 TTAGATTGTTTC-CTTGAAACAAA
64 GGAAATTGTTTCACTTGAAACAAA
12633 TTTTATCTCG
Statistics
Matches: 230, Mismatches: 22, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
168 11 0.05
169 200 0.87
170 19 0.08
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (168 bp):
AGATTGTTTCTCTTGAAACAAATTCGTCTCGCTGAAGACAGTTTCCCTCAAAACACAAACATTGG
AAATTGTTTCACTTGAAACAAAATTCATAAACCTTTGAGATTATTTCCCTTGAAACAAATTTTGT
CTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTG
Found at i:12472 original size:103 final size:103
Alignment explanation
Indices: 12365--12567 Score: 343
Period size: 103 Copynumber: 2.0 Consensus size: 103
12355 TCTCTTGAAA
* * *
12365 CATAAACTTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTAAGACAGTTTCTCTTGAA
1 CATAAACCTTTGAGATTATTTCCCTTGAAACAAATTTTGTCTCGCTTAAGACAGTTTCTCTTGAA
*
12430 ACTTAAACCTTTGAGATTGTTTCACTTGAAACAAAATT
66 ACATAAACCTTTGAGATTGTTTCACTTGAAACAAAATT
* *
12468 CATAAACCTTTGAGATTATTTCCCTTGAAACAAATTTTGTCTTGCTTGAGACAGTTTCTCTTGAA
1 CATAAACCTTTGAGATTATTTCCCTTGAAACAAATTTTGTCTCGCTTAAGACAGTTTCTCTTGAA
*
12533 ACATAAACCTTTGAGATTGTTTCTCTTGAAACAAA
66 ACATAAACCTTTGAGATTGTTTCACTTGAAACAAA
12568 TTTTATCTCG
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 93 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (103 bp):
CATAAACCTTTGAGATTATTTCCCTTGAAACAAATTTTGTCTCGCTTAAGACAGTTTCTCTTGAA
ACATAAACCTTTGAGATTGTTTCACTTGAAACAAAATT
Found at i:12547 original size:66 final size:66
Alignment explanation
Indices: 12468--12798 Score: 502
Period size: 66 Copynumber: 5.0 Consensus size: 66
12458 AAACAAAATT
* * * *
12468 CATAAACCTTTGAGATTATTTCCCTTGAAACAAATTTTGTCTTGCTTGAGACAGTTTCTCTTGAA
1 CATAAACATTTGAGATTGTTTCCCTTGAAACAAATTTTATCTCGCTTGAGACAGTTTCTCTTGAA
12533 A
66 A
* *
12534 CATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTATCTCGCTTGAGACAGTTTCTCTTGAA
1 CATAAACATTTGAGATTGTTTCCCTTGAAACAAATTTTATCTCGCTTGAGACAGTTTCTCTTGAA
12599 A
66 A
* * *
12600 CATAAACATTTTAGATTGTTT-CCTTGAAACAAATTTTATCTCGCTTGAGACAGTTCCTATTGAA
1 CATAAACATTTGAGATTGTTTCCCTTGAAACAAATTTTATCTCGCTTGAGACAGTTTCTCTTGAA
12664 A
66 A
* *
12665 CATAAACATTTGAGATTGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCTTTTGAA
1 CATAAACATTTGAGATTGTTTCCCTTGAAACAAATTTTATCTCGCTTGAGACAGTTTCTCTTGAA
*
12730 T
66 A
* * * * *
12731 CATAAACATTTGAGATTGTTTCCGTCGAAACAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTAAA
1 CATAAACATTTGAGATTGTTTCCCTTGAAACAAATTTTATCTCGCTTGAGACAGTTTCTCTTGAA
12796 A
66 A
12797 CA
1 CA
12799 AAATTAATCT
Statistics
Matches: 242, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
65 61 0.25
66 181 0.75
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (66 bp):
CATAAACATTTGAGATTGTTTCCCTTGAAACAAATTTTATCTCGCTTGAGACAGTTTCTCTTGAA
A
Found at i:12664 original size:131 final size:131
Alignment explanation
Indices: 12468--12786 Score: 494
Period size: 131 Copynumber: 2.4 Consensus size: 131
12458 AAACAAAATT
* * * * *
12468 CATAAACCTTTGAGATTATTTCCCTTGAAACAAATTTTGTCTTGCTTGAGACAGTTTCTCTTGAA
1 CATAAACATTTGAGATTGTTT-CCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTCCTATTGAA
* *
12533 ACATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTATCTCGCTTGAGACAGTTTCTCTTGA
65 ACATAAACATTTGAGATTGTTTCCCTTGAAACAAATTTTATCTCGCTTGAGACAGTTTCTCTTGA
12598 AA
130 AA
* *
12600 CATAAACATTTTAGATTGTTTCCTTGAAACAAATTTTATCTCGCTTGAGACAGTTCCTATTGAAA
1 CATAAACATTTGAGATTGTTTCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTCCTATTGAAA
* *
12665 CATAAACATTTGAGATTGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCTTTTGAA
66 CATAAACATTTGAGATTGTTTCCCTTGAAACAAATTTTATCTCGCTTGAGACAGTTTCTCTTGAA
*
12730 T
131 A
* *
12731 CATAAACATTTGAGATTGTTTCCGTCGAAACAAGTTTTGTCTCGCTTGAGACAGTT
1 CATAAACATTTGAGATTGTTTCC-TTGAAACAAATTTTGTCTCGCTTGAGACAGTT
12787 TCTCTTAAAA
Statistics
Matches: 170, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
131 123 0.72
132 47 0.28
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (131 bp):
CATAAACATTTGAGATTGTTTCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTCCTATTGAAA
CATAAACATTTGAGATTGTTTCCCTTGAAACAAATTTTATCTCGCTTGAGACAGTTTCTCTTGAA
A
Found at i:12729 original size:36 final size:36
Alignment explanation
Indices: 12316--12601 Score: 152
Period size: 36 Copynumber: 8.4 Consensus size: 36
12306 CTTTGTGATT
* * *
12316 GTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTATCTCTCTTGAGACA
**
12352 GTTTCTCTTGAAACATAA----A-CT-T-TTGAGATT
1 GTTTCTCTTGAAACA-AATTTTATCTCTCTTGAGACA
* * *
12382 GTTTCTCTTGAAACAAATTTTGTCTCGCTTAAGACA
1 GTTTCTCTTGAAACAAATTTTATCTCTCTTGAGACA
* * **
12418 GTTTCTCTTGAAAC----TTAAAC-CT-TTGAGATT
1 GTTTCTCTTGAAACAAATTTTATCTCTCTTGAGACA
* * * *
12448 GTTTCACTTGAAACAAAATTCATAAAC-CT-TTGAGATTA
1 GTTTCTCTTGAAAC-AAATT--TTATCTCTCTTGAGA-CA
* *
12486 -TTTCCCTTGAAACAAATTTTGTCT-TGCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTATCTCT-CTTGAGACA
**
12521 GTTTCTCTTGAAACATAA----A-C-CT-TTGAGATT
1 GTTTCTCTTGAAACA-AATTTTATCTCTCTTGAGACA
*
12551 GTTTCTCTTGAAACAAATTTTATCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTATCTCTCTTGAGACA
12587 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
12602 TAAACATTTT
Statistics
Matches: 190, Mismatches: 31, Indels: 58
0.68 0.11 0.21
Matches are distributed among these distances:
29 4 0.02
30 60 0.32
31 1 0.01
32 7 0.04
33 1 0.01
34 6 0.03
35 3 0.02
36 78 0.41
37 29 0.15
38 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTATCTCTCTTGAGACA
Found at i:12836 original size:131 final size:124
Alignment explanation
Indices: 12467--12838 Score: 370
Period size: 131 Copynumber: 2.8 Consensus size: 124
12457 GAAACAAAAT
* * *
12467 TCATAAACCTTTGAGATTATTTCCCTTGAAACAAATTTTGTCTTGCTTGAGACAGTTTCTCTTGA
1 TCATAAACATTTGAGATTGTTT-CCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGA
12532 AACATAAACC-TTTGAGATTGTTTCTCTTGAAACAAATTTTATCTCGCTTGAGACAGTTTCTCTT
65 AACAT-AACCATTTGAGATTGTTTCTC------CAAA-TTTATCTCGCTTGAGACAGTTTCTCTT
12596 GAA
122 GAA
* * * * *
12599 ACATAAACATTTTAGATTGTTTCCTTGAAACAAATTTTATCTCGCTTGAGACAGTTCCTATTGAA
1 TCATAAACATTTGAGATTGTTTCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAA
* * * *
12664 ACATAAACATTTGAGATTGTTTCCCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCTTTTGA
66 ACATAACCATTTGAGATTGTTT--C-T---CCAAA-TTTATCTCGCTTGAGACAGTTTCTCTTGA
12729 A
124 A
* * *
12730 TCATAAACATTTGAGATTGTTTCCGTCGAAACAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTAA
1 TCATAAACATTTGAGATTGTTTCC-TTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGA
*
12795 AACAAAATTAATCTCACTTGAGATTGTTGTCTCCAAA-TTATCTC
65 AAC---A-TAA-C-CATTTGAGATTGTT-TCTCCAAATTTATCTC
12839 CAAATTGACC
Statistics
Matches: 202, Mismatches: 23, Indels: 31
0.79 0.09 0.12
Matches are distributed among these distances:
130 3 0.01
131 118 0.58
132 55 0.27
133 5 0.02
134 1 0.00
135 1 0.00
136 4 0.02
137 1 0.00
138 13 0.06
139 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (124 bp):
TCATAAACATTTGAGATTGTTTCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAA
ACATAACCATTTGAGATTGTTTCTCCAAATTTATCTCGCTTGAGACAGTTTCTCTTGAA
Found at i:13114 original size:23 final size:23
Alignment explanation
Indices: 13080--13124 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
13070 ATTTTAAATT
* *
13080 ATTATTATTATTATTACTTTTTA
1 ATTATTAATATTATTACATTTTA
13103 ATTATTAATATTATTACATTTT
1 ATTATTAATATTATTACATTTT
13125 GCAGGCCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTATTAATATTATTACATTTTA
Found at i:13861 original size:24 final size:24
Alignment explanation
Indices: 13829--13877 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
13819 GAAACACATA
*
13829 CCTCGATTTAAAGTGCTGGAAGCT
1 CCTCAATTTAAAGTGCTGGAAGCT
13853 CCTCAATTTAAAGTGCTGGAAGCT
1 CCTCAATTTAAAGTGCTGGAAGCT
13877 C
1 C
13878 GAAGGTCGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
CCTCAATTTAAAGTGCTGGAAGCT
Found at i:18579 original size:27 final size:27
Alignment explanation
Indices: 18548--18600 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
18538 TGAAAGAAAC
18548 CTTCCAAAACCAATGCCATTAAAGGAG
1 CTTCCAAAACCAATGCCATTAAAGGAG
18575 CTTCCAAAACCAATGCCATTAAAGGA
1 CTTCCAAAACCAATGCCATTAAAGGA
18601 CAGCAATACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.26, G:0.13, T:0.19
Consensus pattern (27 bp):
CTTCCAAAACCAATGCCATTAAAGGAG
Found at i:20258 original size:8 final size:8
Alignment explanation
Indices: 20245--20630 Score: 610
Period size: 8 Copynumber: 48.2 Consensus size: 8
20235 ATGGCAATTA
20245 ATACATAC
1 ATACATAC
20253 ATACATAC
1 ATACATAC
*
20261 GTACATAC
1 ATACATAC
*
20269 GTACATAC
1 ATACATAC
*
20277 GTACATAC
1 ATACATAC
* *
20285 GTACGTAC
1 ATACATAC
* *
20293 GTACGTAC
1 ATACATAC
*
20301 ATACGTAC
1 ATACATAC
20309 ATACATAC
1 ATACATAC
*
20317 GTACATAC
1 ATACATAC
*
20325 ATACGTAC
1 ATACATAC
20333 ATACATAC
1 ATACATAC
*
20341 ATACGTAC
1 ATACATAC
*
20349 ATACGTAC
1 ATACATAC
*
20357 ATACGTAC
1 ATACATAC
*
20365 ATACGTAC
1 ATACATAC
20373 ATACATAC
1 ATACATAC
20381 ATACATAC
1 ATACATAC
*
20389 GTACATAC
1 ATACATAC
*
20397 GTACATAC
1 ATACATAC
*
20405 GTACATAC
1 ATACATAC
*
20413 GTACATAC
1 ATACATAC
20421 ATACATAC
1 ATACATAC
20429 ATACATAC
1 ATACATAC
20437 ATACATAC
1 ATACATAC
20445 ATACATAC
1 ATACATAC
20453 ATACATAC
1 ATACATAC
20461 ATACATAC
1 ATACATAC
20469 ATACATAC
1 ATACATAC
20477 ATACATAC
1 ATACATAC
20485 ATACATAC
1 ATACATAC
20493 ATACATAC
1 ATACATAC
20501 ATACATAC
1 ATACATAC
20509 ATACATAC
1 ATACATAC
20517 ATACATAC
1 ATACATAC
20525 ATACATAC
1 ATACATAC
20533 ATACATAC
1 ATACATAC
20541 ATACATAC
1 ATACATAC
20549 ATACATAC
1 ATACATAC
20557 ATACATAC
1 ATACATAC
20565 ATACATAC
1 ATACATAC
20573 ATACATAC
1 ATACATAC
20581 ATACATAC
1 ATACATAC
20589 ATACATAC
1 ATACATAC
20597 ATACATAC
1 ATACATAC
20605 ATACATAC
1 ATACATAC
20613 ATACATAC
1 ATACATAC
20621 ATACATAC
1 ATACATAC
20629 AT
1 AT
20631 CCTCTGCAAG
Statistics
Matches: 366, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 366 1.00
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (8 bp):
ATACATAC
Found at i:29873 original size:74 final size:74
Alignment explanation
Indices: 29779--30015 Score: 271
Period size: 74 Copynumber: 3.1 Consensus size: 74
29769 GAAGCAAAGA
* * * * *
29779 TTCATCTAGTTTGAGATAGTTTCACTCGAAGCAAAAATTTTATCTCACTTGATATTGTTTTTCTT
1 TTCATCTCGCTTGAGATAGTTTCACTCGAAACAAAAATTTTATCTCACTTGAGATAGTTTTTCTT
29844 AAAACAAAC
66 AAAACAAAC
** * *
29853 TTTTTCTCTCTTGAGATAGTTTCACTCGAAACAGAAA-TTTATCTCACTCGAAGTGAGATAGTTT
1 TTCATCTCGCTTGAGATAGTTTCACTCGAAACAAAAATTTTATCTCACT-----TGAGATAGTTT
29917 TTCTTAAAACAAAC
61 TTCTTAAAACAAAC
* * * *
29931 TTCATCTCGCCTGAGACAGTTTTCACTTGAAAC-AAAATTTTATCTCACTTGAGATAGGTTTTCT
1 TTCATCTCGCTTGAGATAG-TTTCACTCGAAACAAAAATTTTATCTCACTTGAGATAGTTTTTCT
*
29995 TAAAACAAAT
65 TAAAACAAAC
*
30005 TTCATTTCGCT
1 TTCATCTCGCT
30016 CAAATCCATC
Statistics
Matches: 136, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
73 11 0.08
74 62 0.46
78 40 0.29
79 23 0.17
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (74 bp):
TTCATCTCGCTTGAGATAGTTTCACTCGAAACAAAAATTTTATCTCACTTGAGATAGTTTTTCTT
AAAACAAAC
Found at i:29885 original size:36 final size:37
Alignment explanation
Indices: 29789--29987 Score: 134
Period size: 38 Copynumber: 5.2 Consensus size: 37
29779 TTCATCTAGT
*
29789 TTGAGATAGTTTCACTCGAAGCAAAAATTTTATCTCAC
1 TTGAGATAGTTTCACTCGAAAC-AAAATTTTATCTCAC
* * ** ** * *
29827 TTGATATTGTTTTTCTTAAAACAAACTTTT-TCTCTC
1 TTGAGATAGTTTCACTCGAAACAAAATTTTATCTCAC
29863 TTGAGATAGTTTCACTCGAAACAGAAA-TTTATCTCAC
1 TTGAGATAGTTTCACTCGAAACA-AAATTTTATCTCAC
** ** * * *
29900 TCGAAGTGAGATAGTTTTTCTTAAAAC-AAACTTCATCTCGC
1 T-----TGAGATAGTTTCACTCGAAACAAAATTTTATCTCAC
* * *
29941 CTGAGACAGTTTTCACTTGAAACAAAATTTTATCTCAC
1 TTGAGATAG-TTTCACTCGAAACAAAATTTTATCTCAC
29979 TTGAGATAG
1 TTGAGATAG
29988 GTTTTCTTAA
Statistics
Matches: 118, Mismatches: 33, Indels: 20
0.69 0.19 0.12
Matches are distributed among these distances:
36 32 0.27
37 25 0.21
38 33 0.28
40 3 0.03
41 8 0.07
42 17 0.14
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (37 bp):
TTGAGATAGTTTCACTCGAAACAAAATTTTATCTCAC
Found at i:29984 original size:38 final size:38
Alignment explanation
Indices: 29789--29993 Score: 145
Period size: 36 Copynumber: 5.4 Consensus size: 38
29779 TTCATCTAGT
* *
29789 TTGAGATAG-TTTCACTCGAAGCAAAAATTTTATCTCAC
1 TTGAGATAGTTTTCACTTGAAAC-AAAATTTTATCTCAC
* * * * * *
29827 TTGATATTGTTTT-TCTTAAAACAAACTTTT-TCTCTC
1 TTGAGATAGTTTTCACTTGAAACAAAATTTTATCTCAC
*
29863 TTGAGATAG-TTTCACTCGAAACAGAAA-TTTATCTCAC
1 TTGAGATAGTTTTCACTTGAAACA-AAATTTTATCTCAC
* * * * *
29900 TCGAAGTGAGATAGTTTT-TCTTAAAAC-AAACTTCATCTCGC
1 T-----TGAGATAGTTTTCACTTGAAACAAAATTTTATCTCAC
* *
29941 CTGAGACAGTTTTCACTTGAAACAAAATTTTATCTCAC
1 TTGAGATAGTTTTCACTTGAAACAAAATTTTATCTCAC
29979 TTGAGATAGGTTTTC
1 TTGAGATA-GTTTTC
29994 TTAAAACAAA
Statistics
Matches: 124, Mismatches: 29, Indels: 27
0.69 0.16 0.15
Matches are distributed among these distances:
35 3 0.02
36 33 0.27
37 22 0.18
38 29 0.23
39 9 0.07
40 3 0.02
41 8 0.06
42 14 0.11
43 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (38 bp):
TTGAGATAGTTTTCACTTGAAACAAAATTTTATCTCAC
Found at i:30254 original size:139 final size:140
Alignment explanation
Indices: 30022--30703 Score: 643
Period size: 139 Copynumber: 5.0 Consensus size: 140
30012 CGCTCAAATC
* *
30022 CATCACATATGGAGTTGAATCAGCGACACCTCACTCGAGGGATTAACATTTCCAGTGAAGAGTTC
1 CATCACATATAGAGTTGAATCAGCGACACCTCACTCGAGGGATCAACATTTCCAGTGAAGAGTTC
* * * * *
30087 ATAATGAGAAGAACTCATCTGCTGAGGGAGAAGATG-ATCATAATAAGAAAAACTTTTTCAACCT
66 ATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTATCATAATAAGAAAAACTTGTTCAACCT
30151 TAGCTCGATT
131 TAGCTCGATT
* * *
30161 CATCGCATATAGAGTTGAATCAGTGACACCTCACTTGAGGGATCAACATTTCCAGTGAAGAGTTC
1 CATCACATATAGAGTTGAATCAGCGACACCTCACTCGAGGGATCAACATTTCCAGTGAAGAGTTC
* * * * * *
30226 ATAATGTGAAGAACTCGTCCGATAAGGGAGAATAAGTTTTATAATAAGAAGAACTTGTTCAACCT
66 ATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTATCATAATAAGAAAAACTTGTTCAACC-
* * *
30291 TTTGCTTGACT
130 TTAGCTCGATT
* * * * *
30302 C-T-ATCGTAGA-AG--GAGAT-A--G--A--TCA----A--CATCAACATTTCCAGCGGAGAGT
1 CATCA-CATATAGAGTTGA-ATCAGCGACACCTCACTCGAGGGATCAACATTTCCAGTGAAGAGT
* * * * * *
30349 TCATAATGAGAAGAACTCATCCGATGAGGGAGAAAAAATTTCATAATGAGAATAACTTGTTCAAC
64 TCATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTATCATAATAAGAAAAACTTGTTCAAC
30414 CTTAGCTCGATT
129 CTTAGCTCGATT
* * * * * * * * * * *
30426 TATCGCATATGGAGTTGAATCAGCGACCCCTTACTCGATGGATCAATATTTCAAATGGATAGTTC
1 CATCACATATAGAGTTGAATCAGCGACACCTCACTCGAGGGATCAACATTTCCAGTGAAGAGTTC
* * * * *
30491 ATAATGAGAAAAACTCATCCAATAAGGGAGAAGAAAT-TCATAATAAGAATAACTTGTTTAACCT
66 ATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTATCATAATAAGAAAAACTTGTTCAACCT
* *
30555 TAGATCAATT
131 TAGCTCGATT
* * * * * * * *
30565 CATCATATATAAAGTTGAATCAACGATACCTTACTCGAGGGATCAACAATACCAGTGGAGAGTTC
1 CATCACATATAGAGTTGAATCAGCGACACCTCACTCGAGGGATCAACATTTCCAGTGAAGAGTTC
* * *
30630 ATAATGAGAAGAACTCATCCGATGAGGGAGAAGAA-TTTCATAATGAGAAGAAA-TTGTTCAACC
66 ATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTATCATAATAAGAA-AAACTTGTTCAACC
30693 TTAGCTCGATT
130 TTAGCTCGATT
30704 TCTGTAACAC
Statistics
Matches: 439, Mismatches: 80, Indels: 48
0.77 0.14 0.08
Matches are distributed among these distances:
124 8 0.02
125 82 0.19
126 2 0.00
127 3 0.01
128 3 0.01
130 1 0.00
131 3 0.01
133 1 0.00
134 2 0.00
135 1 0.00
137 3 0.01
138 4 0.01
139 235 0.54
140 82 0.19
141 9 0.02
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (140 bp):
CATCACATATAGAGTTGAATCAGCGACACCTCACTCGAGGGATCAACATTTCCAGTGAAGAGTTC
ATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTATCATAATAAGAAAAACTTGTTCAACCT
TAGCTCGATT
Found at i:31328 original size:22 final size:22
Alignment explanation
Indices: 31287--31354 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
31277 CTCGTATAAA
31287 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
31310 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
31332 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
31354 T
1 T
31355 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:31632 original size:30 final size:30
Alignment explanation
Indices: 31564--31632 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
31554 TCATATCGCG
*
31564 TAGTCATATTATTTCCATACCTTTATCACA
1 TAGTCATATCATTTCCATACCTTTATCACA
*
31594 TAGACATATCATTT-CATACCTTTATCACA
1 TAGTCATATCATTTCCATACCTTTATCACA
31623 TAGCTCATAT
1 TAG-TCATAT
31633 AACTTTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 18 0.51
30 17 0.49
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (30 bp):
TAGTCATATCATTTCCATACCTTTATCACA
Found at i:32115 original size:66 final size:67
Alignment explanation
Indices: 31991--32140 Score: 198
Period size: 65 Copynumber: 2.2 Consensus size: 67
31981 TTTTTCTCAT
* * *
31991 GGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGTATCGGTT-CCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCAT-TAC-A
32056 -TGAG
63 TTGAG
* * *
32060 GGGGTATCGGTTCCCCCCCT-GGGGTACCGATT-CCCTCTAGCATTCTGGAAATTCATTTCATTG
1 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACATTG
32123 AG
66 AG
32125 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
32141 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
64 1 0.01
65 22 0.30
66 21 0.28
67 11 0.15
68 8 0.11
69 11 0.15
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACATTG
AG
Found at i:32160 original size:66 final size:65
Alignment explanation
Indices: 31991--32140 Score: 178
Period size: 66 Copynumber: 2.2 Consensus size: 65
31981 TTTTTCTCAT
* * *
31991 GGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGTATCGGTT--CCCCCCT-GGGGTACCGATT-CCCTCAAGCAATCTGGAAATTCATATACGA
32056 TGAG
62 TGAG
* * *
32060 GGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCTCTAGCATTCTGGAAATTCAT-TTC-ATTG
1 GGGGTATCGGTT-CCCCCCTGGGGTACCGATTCCCTCAAGCAATCTGGAAATTCATATACGA-TG
32123 AG
64 AG
32125 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
32141 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
64 5 0.07
65 18 0.24
66 21 0.28
67 11 0.15
68 8 0.11
69 11 0.15
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (65 bp):
GGGGTATCGGTTCCCCCCTGGGGTACCGATTCCCTCAAGCAATCTGGAAATTCATATACGATGAG
Found at i:38235 original size:22 final size:22
Alignment explanation
Indices: 38194--38261 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
38184 CTCGTATAAA
38194 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
38217 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
38239 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
38261 T
1 T
38262 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:38520 original size:30 final size:30
Alignment explanation
Indices: 38475--38533 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
38465 ATCGCGTAGT
*
38475 CATATTATTTCCATACCTTTATCACATAGA
1 CATATCATTTCCATACCTTTATCACATAGA
*
38505 CATATCATTTTCATACCTTTATCACATAG
1 CATATCATTTCCATACCTTTATCACATAG
38534 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
CATATCATTTCCATACCTTTATCACATAGA
Found at i:39045 original size:67 final size:68
Alignment explanation
Indices: 38897--39048 Score: 227
Period size: 68 Copynumber: 2.2 Consensus size: 68
38887 TCTTTTTCAT
* * *
38897 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
38962 TGA
66 TGA
* * *
38965 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTC-A
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
39028 TTGA
66 -TGA
39032 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
39049 TTGAATGGGT
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
66 1 0.01
67 22 0.29
68 54 0.70
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.27
Consensus pattern (68 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
TGA
Found at i:39060 original size:67 final size:67
Alignment explanation
Indices: 38897--39070 Score: 210
Period size: 68 Copynumber: 2.6 Consensus size: 67
38887 TCTTTTTCAT
* * *
38897 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
38962 TGA
65 TGA
* * *
38965 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTC-A
1 GGGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
39028 TTGA
65 -TGA
* *
39032 GGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
39071 AACCCAGAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
65 6 0.06
66 1 0.01
67 34 0.36
68 54 0.57
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:40035 original size:139 final size:138
Alignment explanation
Indices: 39784--40800 Score: 685
Period size: 124 Copynumber: 7.7 Consensus size: 138
39774 GTTACAATTT
* * * * * *
39784 CCCTCACTCTAAGGATCAACATTTCAAATAGAGAGTTCATAATAAGAAAAACTCATCTGATAAGG
1 CCCTCACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGATAAGG
* * *
39849 GAGAAGAAGTTCATAATGAGAATAACTTGTTTAACCTTAGCTCAATTCATCATATATAGAGTTAA
66 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCGTATATAGAGTTAA
**
39914 ATCAATGA
131 ATCAGCGA
* * * * *
39922 CACCTCACTCGAGTGATCAACAATTCCAGTGGAGAGTTCATAATAAGAAGAACTCATCTGATGAG
1 C-CCTCACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGATAAG
* * *
39987 GGAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTAGCTCAATTCATCGCATGTAGAGTTA
65 GGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCGTATATAGAGTTA
*
40052 AATCAGCAA
130 AATCAGCGA
* * * *
40061 CCCCCTCACTCGAGGGATCAACATTTCCAATGGATAGTTCATAATGAGATGAAATCATCCGATAA
1 --CCCTCACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGATAA
* * *
40126 GGGAGGAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCGTCGTATAT-GAAGT
64 GGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCGTATATAG-AGT
*
40190 TGAATCAGCGA
128 TAAATCAGCGA
* * * * *
40201 CCTCTCACTCGAGGGATCAATATTTTCAATAGAGAGTTCATAATGAGAAGAACTCATCCGATGAG
1 CC-CTCACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGATAAG
* *
40266 GGAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCT-AGA--C-TC-TAT-T-GCAG
65 GGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTAGCTCA-ATTCATCGTATATAG-AG
*
40324 ---AAT-A-AGA
127 TTAAATCAGCGA
* * * * *
40331 ---T-AGATC-A-GCATCAACATTTCCAATTGAAAGTTCATAATGAGAAGAACTCATCCGATAAG
1 CCCTCA-CTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGATAAG
* * * * * *
40390 GGAGAAAAAGTTTATAATGAGAACAACTTGTTCAACCTTTTA-CTCGA--C-TC-TAT-CACAG-
65 GGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC--TTAGCTCAATTCATCGTATATAGAGT
*
40448 --AAT--GAGA
128 TAAATCAGCGA
* * * * *
40455 ---T-AGATC-A-GCATCAAGATTTCTAATGGAGAGTTCATAATAAGAAGAACTCATCCGATGAG
1 CCCTCA-CTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGATAAG
* * * * * *
40514 GGAGAATAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGTAGA-AG-G-
65 GGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTAGCTCAATTC-ATCGTATATAGAGT
*
40576 -AGAT-----A
128 TAAATCAGCGA
* * * * * * *
40581 ---T-A-TC-A-GCATCAACATTGCTAATAGAGAGTTCATAATGAGAAGAACTCGTCCGACAAGG
1 CCCTCACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGATAAGG
* * * * * * *
40639 GAGATGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGACTCTATCGCAGA-AG-G--
66 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC-CTTAGCTCAATTC-ATCGTATATAGAGTT
*
40700 AGAT-A--GA
129 AAATCAGCGA
* * *
40707 ---TCA-TC----G-TCAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGATGAGG
1 CCCTCACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGATAAGG
* * *
40763 GAGAAAAAGTTCATAATGAAAAGAACTTATTCAACCTT
66 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
40801 TTGCTCGACT
Statistics
Matches: 753, Mismatches: 102, Indels: 63
0.82 0.11 0.07
Matches are distributed among these distances:
123 5 0.01
124 369 0.49
125 5 0.01
126 9 0.01
127 3 0.00
128 3 0.00
129 5 0.01
130 2 0.00
131 1 0.00
132 3 0.00
135 4 0.01
136 3 0.00
137 2 0.00
138 4 0.01
139 210 0.28
140 124 0.16
141 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.26
Consensus pattern (138 bp):
CCCTCACTCGAGGGATCAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGATAAGG
GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCGTATATAGAGTTAA
ATCAGCGA
Found at i:40143 original size:140 final size:139
Alignment explanation
Indices: 39784--40304 Score: 677
Period size: 139 Copynumber: 3.7 Consensus size: 139
39774 GTTACAATTT
* * * *
39784 CCCTCACTCTAAGGATCAACATTTCAAATAGAGAGTTCATAATAAGAA-AAACTCATCTGATAAG
1 CCCTCACTCGAGGGATCAACATTTCCAATAGAGAGTTCATAATAAGAAGAAA-TCATCCGATAAG
* * *
39848 GGAGAAGAAGTTCATAATGAGAATAACTTGTTTAACCTTAGCTCAATTCATCATATATAGAGTTA
65 GGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCGTATATAGAGTTA
**
39913 AATCAATGAC
130 AATCAGCGAC
* * * * * * * *
39923 ACCTCACTCGAGTGATCAACAATTCCAGTGGAGAGTTCATAATAAGAAGAACTCATCTGATGAGG
1 CCCTCACTCGAGGGATCAACATTTCCAATAGAGAGTTCATAATAAGAAGAAATCATCCGATAAGG
* * *
39988 GAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTAGCTCAATTCATCGCATGTAGAGTTAA
66 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCGTATATAGAGTTAA
*
40053 ATCAGCAACC
131 ATCAGCGA-C
* * * *
40063 CCCTCACTCGAGGGATCAACATTTCCAATGGATAGTTCATAATGAGATGAAATCATCCGATAAGG
1 CCCTCACTCGAGGGATCAACATTTCCAATAGAGAGTTCATAATAAGAAGAAATCATCCGATAAGG
* * * *
40128 GAGGAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCGTCGTATAT-GAAGTTG
66 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCGTATATAG-AGTTA
40192 AATCAGCGAC
130 AATCAGCGAC
* * * * * *
40202 CTCTCACTCGAGGGATCAATATTTTCAATAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGG
1 CCCTCACTCGAGGGATCAACATTTCCAATAGAGAGTTCATAATAAGAAGAAATCATCCGATAAGG
*
40267 GAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTT
66 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
40305 TTGCTAGACT
Statistics
Matches: 332, Mismatches: 47, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
139 211 0.64
140 121 0.36
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (139 bp):
CCCTCACTCGAGGGATCAACATTTCCAATAGAGAGTTCATAATAAGAAGAAATCATCCGATAAGG
GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCGTATATAGAGTTAA
ATCAGCGAC
Found at i:40291 original size:279 final size:279
Alignment explanation
Indices: 39784--40304 Score: 751
Period size: 279 Copynumber: 1.9 Consensus size: 279
39774 GTTACAATTT
* *
39784 CCCTCACTCTAAGGATCAACATTTCAAATAGAGAGTTCATAATAAGAAAAACTCATCTGATAAGG
1 CCCTCACTCGAAGGATCAACATTTCAAATAGAGAGTTCATAATAAGAAAAACTCATCCGATAAGG
* *
39849 GAGAAGAAGTTCATAATGAGAATAACTTGTTTAACCTTAGCTCAATTCATCATATATAGAGTTAA
66 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCATATATAGAGTTAA
* * * *
39914 ATCAATGACACCTCACTCGAGTGATCAACAATTCCAGTGGAGAGTTCATAATAAGAAGAACTCAT
131 ATCAACGACACCTCACTCGAGGGATCAACAATTCCAATAGAGAGTTCATAATAAGAAGAACTCAT
* *
39979 CTGATGAGGGAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTAGCTCAATTCATCGCATG
196 CCGATGAGGGAGAAGAAGTTCATAATAAGAAGAACTTATTCAACCTTAGCTCAATTCATCGCATG
40044 TAGAGTTAAATCAGCAACC
261 TAGAGTTAAATCAGCAACC
* * * * * *
40063 CCCTCACTCGAGGGATCAACATTTCCAATGGATAGTTCATAATGAGATGAAA-TCATCCGATAAG
1 CCCTCACTCGAAGGATCAACATTTCAAATAGAGAGTTCATAATAAGA-AAAACTCATCCGATAAG
* * * *
40127 GGAGGAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCGTCGTATAT-GAAGTT
65 GGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCATATATAG-AGTT
* * * * * *
40191 GAATCAGCGAC-CTCTCACTCGAGGGATCAATATTTTCAATAGAGAGTTCATAATGAGAAGAACT
129 AAATCAACGACAC-CTCACTCGAGGGATCAACAATTCCAATAGAGAGTTCATAATAAGAAGAACT
*
40255 CATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTT
193 CATCCGATGAGGGAGAAGAAGTTCATAATAAGAAGAACTTATTCAACCTT
40305 TTGCTAGACT
Statistics
Matches: 212, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
278 2 0.01
279 207 0.98
280 3 0.01
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (279 bp):
CCCTCACTCGAAGGATCAACATTTCAAATAGAGAGTTCATAATAAGAAAAACTCATCCGATAAGG
GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCATATATAGAGTTAA
ATCAACGACACCTCACTCGAGGGATCAACAATTCCAATAGAGAGTTCATAATAAGAAGAACTCAT
CCGATGAGGGAGAAGAAGTTCATAATAAGAAGAACTTATTCAACCTTAGCTCAATTCATCGCATG
TAGAGTTAAATCAGCAACC
Found at i:40376 original size:124 final size:124
Alignment explanation
Indices: 40216--40968 Score: 995
Period size: 124 Copynumber: 6.1 Consensus size: 124
40206 CACTCGAGGG
* * *
40216 ATCAATATTTTCAATAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
* * * **
40281 AATGAGAAGAACTTATTCAACCTTTTGCTAGACTCTATTGCAGAATAAGATAGATCAGC
66 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAGC
* * * * *
40340 ATCAACATTTCCAATTGAAAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAAAAGTTTAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
* * * *
40405 AATGAGAACAACTTGTTCAACCTTTTACTCGACTCTATCACAGAATGAGATAGATCAGC
66 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAGC
* * * *
40464 ATCAAGATTTCTAATGGAGAGTTCATAATAAGAAGAACTCATCCGATGAGGGAGAATAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
* * *
40529 AATAAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGTAGAAGGAGATATATCAGC
66 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAGC
* * * * ** *
40588 ATCAACATTGCTAATAGAGAGTTCATAATGAGAAGAACTCGTCCGACAAGGGAGATGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
* *
40653 AATGAGAAGAACTTGTTCAACTTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCATC
66 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAGC
* * *
40712 GTCAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAAAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
* * * *
40777 AATGAAAAGAACTTATTCAACCTTTTGCTCGACTCTATCACAGAA-GAGATAGATCAGT
66 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAGC
* * * ** * ** *
40835 ATTAACATTTTCAATGGAGAGTTCATAACGAGAAGAACTTTTCCGAAGAGAAAAAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
* * * * * *
40900 AATGAAAAGTATTTATTCAACCTTTTGCTCGACTCTATCTCAGAAGGAGATAGATCAAC
66 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAGC
*
40959 ATAAACATTT
1 ATCAACATTT
40969 TGTTTGATTC
Statistics
Matches: 551, Mismatches: 77, Indels: 2
0.87 0.12 0.00
Matches are distributed among these distances:
123 106 0.19
124 445 0.81
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (124 bp):
ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAGC
Found at i:41018 original size:162 final size:162
Alignment explanation
Indices: 40835--41168 Score: 420
Period size: 162 Copynumber: 2.1 Consensus size: 162
40825 ATAGATCAGT
* * * *
40835 ATTAACATTTTCAATGGAGAGTTCATAACGAGAAGAACTTTTCCGAA-GAGAAAAAAGAAGTTCA
1 ATTAACATTTCCAATGGAGAGTTCATAACAAGAAGAACGTGTCC-AAGGAGAAAAAAGAAGTTCA
* * * * *
40899 TAATGAAAAGTATTTATTCAACC-TTTTGCTCGACTCTATCTCAGAAGGAGATAGATCAACATAA
65 TAATGAAAAGAACTTATTCAACCATGTTGCTCGACTCTATCACAGAAAGAGATAGATCAACATAA
*
40963 ACATTTTGTTTGATTCCATCACAGAAGGAGATGG
130 ACATTTTGTTTGATT-CATCACAGAAGAAGATGG
* * * *
40997 ATTAACATTTCCAATGGAGAGTTCATAATAAGAAGAACGTGTCCAAGGAGGAAGAAGAAGTTCTT
1 ATTAACATTTCCAATGGAGAGTTCATAACAAGAAGAACGTGTCCAAGGAGAAAAAAGAAGTTCAT
* * * * * *
41062 AATGAGAAGAACTTGTTCAACCATGTTGCTTGATTTTATCACAGAAAGAGATAGATCAACATCAA
66 AATGAAAAGAACTTATTCAACCATGTTGCTCGACTCTATCACAGAAAGAGATAGATCAACATAAA
* * *
41127 TATTTTGTTTGATTCTTCACAGAAGAAGTTGG
131 CATTTTGTTTGATTCATCACAGAAGAAGATGG
*
41159 ATCAACATTT
1 ATTAACATTT
41169 GTCATGTTAC
Statistics
Matches: 146, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
161 2 0.01
162 96 0.66
163 48 0.33
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (162 bp):
ATTAACATTTCCAATGGAGAGTTCATAACAAGAAGAACGTGTCCAAGGAGAAAAAAGAAGTTCAT
AATGAAAAGAACTTATTCAACCATGTTGCTCGACTCTATCACAGAAAGAGATAGATCAACATAAA
CATTTTGTTTGATTCATCACAGAAGAAGATGG
Found at i:49771 original size:34 final size:34
Alignment explanation
Indices: 49733--49801 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
49723 TTAGGATAGA
* * **
49733 TAATTTGTTTCAGTTCCTCTATTTATTAATATAC
1 TAATTTCTTTCAATTCCTCTATTTAAGAATATAC
*
49767 TAATTTCTTTCAATTCCTTTATTTAAGAATATAC
1 TAATTTCTTTCAATTCCTCTATTTAAGAATATAC
49801 T
1 T
49802 CAATGACTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.52
Consensus pattern (34 bp):
TAATTTCTTTCAATTCCTCTATTTAAGAATATAC
Found at i:50567 original size:46 final size:46
Alignment explanation
Indices: 50501--50592 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
50491 TCACAATCAC
*
50501 GATACCTATAATCACCGTAATTACATTCACTATTGCCGCAATCATG
1 GATACCTATAATCACCGTAATAACATTCACTATTGCCGCAATCATG
50547 GATACCTATAATC-CCTGTAATAACATTCACTATTGCCGCAATCATG
1 GATACCTATAATCACC-GTAATAACATTCACTATTGCCGCAATCATG
50593 ATAAATATGC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 2 0.05
46 42 0.95
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (46 bp):
GATACCTATAATCACCGTAATAACATTCACTATTGCCGCAATCATG
Found at i:57387 original size:93 final size:93
Alignment explanation
Indices: 57214--57388 Score: 251
Period size: 93 Copynumber: 1.9 Consensus size: 93
57204 GTGTTTGCCA
* * * * *
57214 CACCTTGCTCCCAATGTGGATCATGCGCATTAAAGTCTTCAATTGGTGGAGCACTTTCAATACTC
1 CACCATGCTCCCAAAGTGGACCATGCACATTAAAGTCTTCAATAGGTGGAGCACTTTCAATACTC
**
57279 AAATCTTGTGCATTATTGTTTAACGTCG
66 AAATCTTGCACATTATTGTTTAACGTCG
* * *
57307 CACCATGCTCCCAAAGTGGACCATGCACATTAAAGTCTTCAATAGTTGGAGCACTTTTAATATTC
1 CACCATGCTCCCAAAGTGGACCATGCACATTAAAGTCTTCAATAGGTGGAGCACTTTCAATACTC
*
57372 AAATCTTGCATATTATT
66 AAATCTTGCACATTATT
57389 ATTGTATCCA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (93 bp):
CACCATGCTCCCAAAGTGGACCATGCACATTAAAGTCTTCAATAGGTGGAGCACTTTCAATACTC
AAATCTTGCACATTATTGTTTAACGTCG
Found at i:57609 original size:45 final size:45
Alignment explanation
Indices: 57534--57634 Score: 105
Period size: 45 Copynumber: 2.3 Consensus size: 45
57524 TAATTCAAAT
* * * * *
57534 GGCATGG-CCCATGTTCATGCGTAATCTCTCGCGTGGCTCCAAGC
1 GGCATGGTCCCATGGTCATGAGCAATCTCTCGCATAGCTCCAAGC
* * *
57578 GGCATGGTCCCATGGTCATGAGCATTGTCTCGTATAGCTCCAAGC
1 GGCATGGTCCCATGGTCATGAGCAATCTCTCGCATAGCTCCAAGC
**
57623 GGTGTGGTCCCA
1 GGCATGGTCCCA
57635 ATGTTGGCAC
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
44 7 0.15
45 39 0.85
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.26
Consensus pattern (45 bp):
GGCATGGTCCCATGGTCATGAGCAATCTCTCGCATAGCTCCAAGC
Found at i:66506 original size:23 final size:23
Alignment explanation
Indices: 66440--66498 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
66430 GTCTTATATA
*
66440 GCACTACGGTGCAATTCTACGCG
1 GCACTTCGGTGCAATTCTACGCG
* *
66463 GCACTTTGGTGCAATTCTACGTG
1 GCACTTCGGTGCAATTCTACGCG
66486 GCACTTCGGTGCA
1 GCACTTCGGTGCA
66499 TTTATACGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCG
Done.