Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004065.1 Hibiscus syriacus cultivar Beakdansim tig00008888_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: 82658
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:13398 original size:17 final size:17
Alignment explanation
Indices: 13378--13498 Score: 72
Period size: 17 Copynumber: 6.9 Consensus size: 17
13368 AAAATTTTAT
13378 AAGAAGAAAAAAAATAG
1 AAGAAGAAAAAAAATAG
13395 AAGAAGAAAAACAAATAG
1 AAGAAGAAAAA-AAATAG
* * *
13413 AAAAATAAAATGAAAA-CG
1 AAGAAGAAAA--AAAATAG
13431 AAGAAGAAGAAAAAAT-G
1 AAGAAGAA-AAAAAATAG
*
13448 AA-AATGAGAAAGAAA-AG
1 AAGAA-GA-AAAAAAATAG
* *
13465 AAAAAGAGAAAAAGAT-G
1 AAGAAGA-AAAAAAATAG
*
13482 AGAGATGAAAAAAAATA
1 A-AGAAGAAAAAAAATA
13499 TTTCACTTGT
Statistics
Matches: 81, Mismatches: 11, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
16 2 0.02
17 45 0.56
18 28 0.35
19 5 0.06
20 1 0.01
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.07
Consensus pattern (17 bp):
AAGAAGAAAAAAAATAG
Found at i:13405 original size:18 final size:18
Alignment explanation
Indices: 13378--13446 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
13368 AAAATTTTAT
13378 AAGAAG-AAAAAAAATAG
1 AAGAAGAAAAAAAAATAG
*
13395 AAGAAGAAAAACAAATAG
1 AAGAAGAAAAAAAAATAG
* * * *
13413 AAAAATAAAATGAAAA-CG
1 AAGAAGAAAA-AAAAATAG
*
13431 AAGAAGAAGAAAAAAT
1 AAGAAGAAAAAAAAAT
13447 GAAAATGAGA
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
17 10 0.26
18 26 0.67
19 3 0.08
ACGTcount: A:0.74, C:0.03, G:0.16, T:0.07
Consensus pattern (18 bp):
AAGAAGAAAAAAAAATAG
Found at i:13468 original size:23 final size:22
Alignment explanation
Indices: 13414--13468 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
13404 AACAAATAGA
13414 AAAATAAAATGAAAACGAAGAAG
1 AAAA-AAAATGAAAACGAAGAAG
*
13437 AAGAAAAAATGAAAATG-AGAAAG
1 AA-AAAAAATGAAAACGAAG-AAG
13460 AAAAGAAAA
1 AAAA-AAAA
13469 AGAGAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 4 0.14
23 22 0.79
24 2 0.07
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (22 bp):
AAAAAAAATGAAAACGAAGAAG
Found at i:13469 original size:6 final size:6
Alignment explanation
Indices: 13381--13476 Score: 54
Period size: 6 Copynumber: 16.3 Consensus size: 6
13371 ATTTTATAAG
* * * * * *
13381 AAGAAA AA-AAA TAGAAG AAGAAA AACAAA TAGAAA AATAAA ATGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* * * * * *
13428 ACGAAG AAGAAG AA-AAA ATGAAA ATGAGA AAG-AA AAGAAA AAGAGAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGA-AA
13475 AA
1 AA
13477 AGATGAGAGA
Statistics
Matches: 67, Mismatches: 19, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
5 11 0.16
6 52 0.78
7 4 0.06
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06
Consensus pattern (6 bp):
AAGAAA
Found at i:17456 original size:43 final size:44
Alignment explanation
Indices: 17408--17525 Score: 139
Period size: 48 Copynumber: 2.6 Consensus size: 44
17398 GTAAGTATGC
*
17408 AAATAAGCTTACGAGCTTATGAATAATGGCAAGT-GTATTGATA
1 AAATAAGCTTACGAGCTTATGAATAATGGCAAATAGTATTGATA
* * * *
17451 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAATATTTTTGGTA
1 AAATAAGCTTACGAGCTTAT-GAA--T-AATGGCAAATAGTATTGATA
17499 AAATAAGCTTACGAGCTTATGAGATAA
1 AAATAAGCTTACGAGCTTATGA-ATAA
17526 ATAATAAGAG
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
43 20 0.31
44 3 0.05
45 2 0.03
46 2 0.03
47 10 0.16
48 27 0.42
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.32
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGAATAATGGCAAATAGTATTGATA
Found at i:18388 original size:16 final size:15
Alignment explanation
Indices: 18354--18384 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18344 ATTTTTCAAA
18354 TCAAAAATTTATTTT
1 TCAAAAATTTATTTT
*
18369 TCAAAAATTTCTTTT
1 TCAAAAATTTATTTT
18384 T
1 T
18385 TCAATTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (15 bp):
TCAAAAATTTATTTT
Found at i:20386 original size:21 final size:21
Alignment explanation
Indices: 20360--20412 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
20350 TCAAACCTTT
*
20360 AGTATCGATACTATTTTAATC
1 AGTATCGATACTATTTGAATC
20381 AGTATCGATACTATTTGAATC
1 AGTATCGATACTATTTGAATC
20402 AGTATCGATAC
1 AGTATCGATAC
20413 CAACCCACCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
AGTATCGATACTATTTGAATC
Found at i:23248 original size:37 final size:37
Alignment explanation
Indices: 23158--23262 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
23148 CCTTTTCGTC
*
23158 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
23195 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
23232 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
23263 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:23803 original size:2 final size:2
Alignment explanation
Indices: 23796--23827 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
23786 ATTTTCCTAT
23796 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23828 TATTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:24039 original size:2 final size:2
Alignment explanation
Indices: 24027--24064 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
24017 CATACATTTT
24027 TA TA T- TA TA TA 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 TA TA TA TA TA TA T
24065 TATTATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:28829 original size:8 final size:8
Alignment explanation
Indices: 28795--28836 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
28785 AGATCCAATC
28795 AAGAACAAA
1 AAGAA-AAA
*
28804 AAGAAAAG
1 AAGAAAAA
*
28812 AAGCAAAA
1 AAGAAAAA
28820 AAGAAAAA
1 AAGAAAAA
28828 AAGAAAAA
1 AAGAAAAA
28836 A
1 A
28837 TCAAAAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
8 24 0.83
9 5 0.17
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:29703 original size:24 final size:24
Alignment explanation
Indices: 29675--29735 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
29665 GGGACAATAT
*
29675 TTTCAAAACTTTTAATTAAACATC
1 TTTCAAAACTCTTAATTAAACATC
*
29699 TTTCAAAACTCTTGATTAAACATC
1 TTTCAAAACTCTTAATTAAACATC
*
29723 TTTTAAAACTCTT
1 TTTCAAAACTCTT
29736 TTTTGATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.43
Consensus pattern (24 bp):
TTTCAAAACTCTTAATTAAACATC
Found at i:30448 original size:36 final size:37
Alignment explanation
Indices: 30400--30475 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 37
30390 GTGTCCACCA
*
30400 TTGTCTCTCTTGAGACAGTTTCCCTT-GAAACAAA-CT
1 TTGTCTCCCTTGAGACAGTTTCCCTTAGAAA-AAACCT
30436 TTGTCTCCCTTGAGACAGTTTCCCTTAGAAAAAACCT
1 TTGTCTCCCTTGAGACAGTTTCCCTTAGAAAAAACCT
30473 TTG
1 TTG
30476 AAATCATTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
36 28 0.76
37 9 0.24
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (37 bp):
TTGTCTCCCTTGAGACAGTTTCCCTTAGAAAAAACCT
Found at i:30707 original size:37 final size:37
Alignment explanation
Indices: 30637--30708 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
30627 TGGAGCTAAG
* * * *
30637 TTTTGTCTCTCTTGAGATAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
* *
30674 TTTTGTCTCCCTTGAGACCGTTTCTCATGAAACAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAA
30709 CAAATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.42
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
Found at i:31289 original size:43 final size:43
Alignment explanation
Indices: 31241--31361 Score: 206
Period size: 43 Copynumber: 2.8 Consensus size: 43
31231 ATGAAGGGGT
* *
31241 CATCCACGATTTCAACTCCATGACGGAGGATATTGTTCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTTCCCACA
31284 CATCCACGATTTCAACTCCACGACGGAGGATATCGTTCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTTCCCACA
* *
31327 CATCCACGATTTCAACTCCACAATGGAGGATATCG
1 CATCCACGATTTCAACTCCACGACGGAGGATATCG
31362 CGCCATCTGA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 74 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTTCCCACA
Found at i:31523 original size:106 final size:105
Alignment explanation
Indices: 31370--31989 Score: 752
Period size: 106 Copynumber: 6.0 Consensus size: 105
31360 CGCGCCATCT
31370 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCA-TT
*
31435 TCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTC
65 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* * * * * * * * ** *
31476 AATATAGCACAAGCTCAACTTCACAGCGAAGGGGCGGTTGACTGTCAACAAACAACTTCCCAATT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC-ATT
* * *
31541 TCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGGACCC
65 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* * * * * *
31582 AAGATAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTCAAC-AA-AATTT--CA-TT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCATTT
* *
31642 CAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
*
31682 GAGACAACACAAGTTCAACTTCACAAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAT
1 GAGACAACACAAGTTCAACTTCAC-AACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC-AT
* *
31747 TTCAGAGCCAATTTCAACTTCATAGCAAAGGATATTGGACTC
64 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* * *
31789 GATACAACACAAGTTCAACTTCACAATGAAGGGACGGTTGGTTGTCAACAAA-AA------ATTT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCATTT
*
31847 C----CCAATTTCAACTTCATAGCGAAGGATATTGGACTC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* **
31883 GAGACAACACAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCTCGGTT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTC-CCATT
* *
31948 CCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
65 TCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
31989 G
1 G
31990 GAACAATGCT
Statistics
Matches: 443, Mismatches: 50, Indels: 42
0.83 0.09 0.08
Matches are distributed among these distances:
94 82 0.19
95 2 0.00
98 5 0.01
100 58 0.13
101 23 0.05
102 6 0.01
103 4 0.01
104 4 0.01
105 6 0.01
106 191 0.43
107 62 0.14
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (105 bp):
GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCATTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
Found at i:31756 original size:207 final size:206
Alignment explanation
Indices: 31371--31968 Score: 769
Period size: 207 Copynumber: 2.9 Consensus size: 206
31361 GCGCCATCTG
31371 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AA-AATTT--CA--TT
* * * * * *
31436 CAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCAATATAGCACAAGCTCAACTTCACA
60 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACA
* * * **
31501 GCGAAGGGGCGGTTGACTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC-TCAG
125 ACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCAT-AG
* *
31565 CGAAGGATCTTGGACCCA
189 CAAAGGATATTGGACCCA
* * * * * *
31583 AGATAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTCAACAAAATTTCATTCAGAGT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAATTTCATTCAGAGC
*
31648 CAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGTTCAACTTCACAAACGAA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCAC-AACGAA
31713 GGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCATAGCAAAGG
130 GGGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCATAGCAAAGG
* *
31778 ATATTGGACTCG
195 ATATTGGACCCA
* * * **
31790 ATACAACACAAGTTCAACTTCACAATGAAGGGACGGTTGGTTGTCAACAAAAAAT--TTC----C
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAATTTCATTCAGAGC
*
31849 CAATTTCAACTTCATAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* * * ** *
31914 GGATGGCTGGTTGTCAACAAACAATTTCTCGGTTCCAGAGCCAATTTCAACTTCA
131 GGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCA
31969 CGACGGAGGA
Statistics
Matches: 343, Mismatches: 41, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
200 56 0.16
201 56 0.16
205 3 0.01
206 58 0.17
207 117 0.34
208 3 0.01
210 5 0.01
211 2 0.01
212 43 0.13
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (206 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAATTTCATTCAGAGC
CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
GGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCATAGCAAAGGA
TATTGGACCCA
Found at i:33306 original size:2 final size:2
Alignment explanation
Indices: 33293--33493 Score: 220
Period size: 2 Copynumber: 103.5 Consensus size: 2
33283 CCTTATTATT
*
33293 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33335 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * * *
33377 TA -A TT TA TT TA T- TA TA GT- TC TC TT TT TT TG TG T- TA TA T-
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* *
33415 TA TA T- TA T- TT TCC TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33455 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
33494 TATTTTTTTA
Statistics
Matches: 179, Mismatches: 10, Indels: 20
0.86 0.05 0.10
Matches are distributed among these distances:
1 8 0.04
2 169 0.94
3 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:33757 original size:28 final size:27
Alignment explanation
Indices: 33700--33757 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
33690 TTTATATTTT
*
33700 TTTATATATATATATATTATTATTTTA
1 TTTATATATATATATATTATTATTATA
* *
33727 TTTATACTATTTATTTATT-TTCATTATA
1 TTTATA-TATATATATATTATT-ATTATA
33755 TTT
1 TTT
33758 TTAGTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTATATATATATATATTATTATTATA
Found at i:49956 original size:54 final size:55
Alignment explanation
Indices: 49806--49968 Score: 204
Period size: 55 Copynumber: 3.0 Consensus size: 55
49796 ATACAGTTAA
*
49806 CAACCCCACAAAATTCATAATGAGTTTATGAATTTCCGTATTAGCACTATGTGTG
1 CAACCCCACAAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTG
* * *
49861 TAACCCCACAAAATTGATAATGAGTTTATGAATTTCTGTATTGGCACTATGTGTG
1 CAACCCCACAAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTG
* * * * * * *
49916 CAA-CCTA-AGTAATTTATACTGAGTTTGTGAATTACCGTATTGTCACTATGTGT
1 CAACCCCACA-AAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTGT
49969 AATGAGTTTG
Statistics
Matches: 94, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 40 0.43
55 53 0.56
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (55 bp):
CAACCCCACAAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTATGTGTG
Found at i:49982 original size:36 final size:36
Alignment explanation
Indices: 49935--50003 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
49925 TAATTTATAC
* *
49935 TGAGTTTGTGAATTACCGTATTGTCACTATGTGTAA
1 TGAGTTTGTGAATTACCGTATCGGCACTATGTGTAA
49971 TGAGTTTGTGAATTACCGTATCGGCACTATGTG
1 TGAGTTTGTGAATTACCGTATCGGCACTATGTG
50004 CGTAAAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.39
Consensus pattern (36 bp):
TGAGTTTGTGAATTACCGTATCGGCACTATGTGTAA
Found at i:57067 original size:20 final size:19
Alignment explanation
Indices: 57034--57072 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 19
57024 CATCCATATT
57034 CTAAAAAAGCCCA-TAAAA
1 CTAAAAAAGCCCATTAAAA
57052 CTAAAAAGATGCCCATTAAAA
1 CTAAAAA-A-GCCCATTAAAA
57073 AAGAGTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 1 0.06
20 5 0.28
21 5 0.28
ACGTcount: A:0.56, C:0.21, G:0.08, T:0.15
Consensus pattern (19 bp):
CTAAAAAAGCCCATTAAAA
Found at i:58514 original size:12 final size:12
Alignment explanation
Indices: 58497--58526 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
58487 GTGGATTTAC
*
58497 TGTTAGTATATA
1 TGTTAGTATAGA
58509 TGTTAGTATAGA
1 TGTTAGTATAGA
58521 TGTTAG
1 TGTTAG
58527 GGAGTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (12 bp):
TGTTAGTATAGA
Found at i:59646 original size:30 final size:31
Alignment explanation
Indices: 59583--59649 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
59573 TAATGAAACT
* *
59583 GAAATT-GATGAAGCAGAACCAGTTGAACTA
1 GAAATTAGATGAACCAGAACCAGTTGAACCA
**
59613 GAAATTAG-TGAACCAGAACCAGTTGTGCCA
1 GAAATTAGATGAACCAGAACCAGTTGAACCA
59643 GAAATTA
1 GAAATTA
59650 ATAAACCTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (31 bp):
GAAATTAGATGAACCAGAACCAGTTGAACCA
Found at i:61557 original size:13 final size:13
Alignment explanation
Indices: 61550--61636 Score: 117
Period size: 13 Copynumber: 6.7 Consensus size: 13
61540 ATATTCTTCA
61550 TGCATATTGTTAT
1 TGCATATTGTTAT
61563 TGCATGA-TGTTAT
1 TGCAT-ATTGTTAT
61576 TGCATATTGTTCA-
1 TGCATATTGTT-AT
61589 TGCATATTGTTAT
1 TGCATATTGTTAT
*
61602 TACATATTGTTCA-
1 TGCATATTGTT-AT
61615 TGCATATTGTTAT
1 TGCATATTGTTAT
61628 TGCATATTG
1 TGCATATTG
61637 GAATAATTGA
Statistics
Matches: 66, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
12 3 0.05
13 60 0.91
14 3 0.05
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.49
Consensus pattern (13 bp):
TGCATATTGTTAT
Found at i:61583 original size:39 final size:39
Alignment explanation
Indices: 61539--61636 Score: 130
Period size: 39 Copynumber: 2.5 Consensus size: 39
61529 CTTGCTAATA
* *
61539 CATATTCTTCATGCATATTGTTATTGCATGA-TGTT-ATTG
1 CATATTGTTCATGCATATTGTTATTACAT-ATTGTTCA-TG
61578 CATATTGTTCATGCATATTGTTATTACATATTGTTCATG
1 CATATTGTTCATGCATATTGTTATTACATATTGTTCATG
61617 CATATTGTT-ATTGCATATTG
1 CATATTGTTCA-TGCATATTG
61637 GAATAATTGA
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
38 2 0.04
39 51 0.94
40 1 0.02
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.49
Consensus pattern (39 bp):
CATATTGTTCATGCATATTGTTATTACATATTGTTCATG
Found at i:61586 original size:26 final size:26
Alignment explanation
Indices: 61550--61636 Score: 133
Period size: 26 Copynumber: 3.3 Consensus size: 26
61540 ATATTCTTCA
61550 TGCATATTGTT-ATTGCATGA-TGTTAT
1 TGCATATTGTTCA-TGCAT-ATTGTTAT
61576 TGCATATTGTTCATGCATATTGTTAT
1 TGCATATTGTTCATGCATATTGTTAT
*
61602 TACATATTGTTCATGCATATTGTTAT
1 TGCATATTGTTCATGCATATTGTTAT
61628 TGCATATTG
1 TGCATATTG
61637 GAATAATTGA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
25 1 0.02
26 55 0.96
27 1 0.02
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.49
Consensus pattern (26 bp):
TGCATATTGTTCATGCATATTGTTAT
Found at i:62331 original size:16 final size:17
Alignment explanation
Indices: 62305--62358 Score: 69
Period size: 16 Copynumber: 3.3 Consensus size: 17
62295 TCAAAACTTC
62305 CATTATGTTTTAGATTGA
1 CATT-TGTTTTAGATTGA
*
62323 C-TTTGTTTTAGCTTG-
1 CATTTGTTTTAGATTGA
62338 CATTTGTTTTAGATTGA
1 CATTTGTTTTAGATTGA
62355 -ATTT
1 CATTT
62359 TTTATTGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 1 0.03
16 28 0.88
17 2 0.06
18 1 0.03
ACGTcount: A:0.20, C:0.07, G:0.17, T:0.56
Consensus pattern (17 bp):
CATTTGTTTTAGATTGA
Found at i:63108 original size:26 final size:26
Alignment explanation
Indices: 63072--63123 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
63062 TACATACATT
63072 GCATCTTCAATTCTAACACAAGTCTA
1 GCATCTTCAATTCTAACACAAGTCTA
63098 GCATCTTCAATTCTAACACAAGTCTA
1 GCATCTTCAATTCTAACACAAGTCTA
63124 TTAACCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.31
Consensus pattern (26 bp):
GCATCTTCAATTCTAACACAAGTCTA
Found at i:63696 original size:23 final size:23
Alignment explanation
Indices: 63652--63697 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
63642 ATGTTTTAAT
*
63652 TGACGTGGCGTGCTGTAAGTCCA
1 TGACGTGGCGTGCTGCAAGTCCA
*
63675 TGACGTGGCGTGCTGCATGTCCA
1 TGACGTGGCGTGCTGCAAGTCCA
63698 ACCTGAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.24, G:0.35, T:0.26
Consensus pattern (23 bp):
TGACGTGGCGTGCTGCAAGTCCA
Found at i:63795 original size:30 final size:29
Alignment explanation
Indices: 63761--63832 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
63751 TTAACGGATA
*
63761 GTGGTCTGATTGA-ATCAATTAAAA-AGTTTG
1 GTGGTCTGATTGAGAT-AA--AAAATAGTTCG
*
63791 GTGGTCTAATTGAGATAAAAAATAGTTCG
1 GTGGTCTGATTGAGATAAAAAATAGTTCG
*
63820 GTGGTCAGATTGA
1 GTGGTCTGATTGA
63833 TTAAAGATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 4 0.11
29 16 0.44
30 14 0.39
31 2 0.06
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33
Consensus pattern (29 bp):
GTGGTCTGATTGAGATAAAAAATAGTTCG
Found at i:69010 original size:21 final size:21
Alignment explanation
Indices: 68984--69033 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
68974 CAATTAACAT
*
68984 TTATAAAAG-TAAAATAATTAA
1 TTATAAAAGTTAAAAT-AGTAA
*
69005 TTATAAAAGTTTAAATAGTAA
1 TTATAAAAGTTAAAATAGTAA
69026 TTATAAAA
1 TTATAAAA
69034 TAAGAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (21 bp):
TTATAAAAGTTAAAATAGTAA
Found at i:69751 original size:2 final size:2
Alignment explanation
Indices: 69744--69832 Score: 169
Period size: 2 Copynumber: 44.5 Consensus size: 2
69734 TTCCAGTGAA
*
69744 AT AT AT AT AT GT 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 AT AT AT
69786 AT AT AT 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 AT AT AT
69828 AT AT A
1 AT AT A
69833 GACCATATAA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:72615 original size:2 final size:2
Alignment explanation
Indices: 72608--72653 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
72598 GGTTTGATAA
72608 AT AT AT 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 AT AT AT
72650 AT AT
1 AT AT
72654 CACTGGAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.