Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001305.1 Hibiscus syriacus cultivar Beakdansim tig00002545_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: 60672
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:6046 original size:13 final size:13
Alignment explanation
Indices: 6030--6060 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
6020 AATAAAAATT
6030 ATAAATTTATTTA
1 ATAAATTTATTTA
6043 ATAAATTTATTTA
1 ATAAATTTATTTA
6056 ATAAA
1 ATAAA
6061 AAATTAATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATAAATTTATTTA
Found at i:8280 original size:23 final size:23
Alignment explanation
Indices: 8253--8296 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
8243 TTAATACAAA
8253 TAATTTGACAATAAAATAATAAT
1 TAATTTGACAATAAAATAATAAT
* *
8276 TAATTTGATAATAAATTAATA
1 TAATTTGACAATAAAATAATA
8297 TTTCATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (23 bp):
TAATTTGACAATAAAATAATAAT
Found at i:10898 original size:15 final size:15
Alignment explanation
Indices: 10878--10906 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10868 TGCTACCGAT
10878 ATTTGACCTGGACTG
1 ATTTGACCTGGACTG
10893 ATTTGACCTGGACT
1 ATTTGACCTGGACT
10907 TGACCTGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (15 bp):
ATTTGACCTGGACTG
Found at i:14260 original size:38 final size:39
Alignment explanation
Indices: 14175--14270 Score: 122
Period size: 39 Copynumber: 2.5 Consensus size: 39
14165 TTCAATCCAC
* * * *
14175 CGATTTATTTTCTTTTGCAAAATAGGAAAATAAATCTAA
1 CGATTTATTTCCTTTTACAAAATAGAAAAATAAATCGAA
* *
14214 CAAGTTATTTCCTTTTACAAAATAGAAAAAT-AATCGAA
1 CGATTTATTTCCTTTTACAAAATAGAAAAATAAATCGAA
*
14252 TGATTTATTTCCTTTTACA
1 CGATTTATTTCCTTTTACA
14271 TATCAGAATC
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
38 22 0.46
39 26 0.54
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (39 bp):
CGATTTATTTCCTTTTACAAAATAGAAAAATAAATCGAA
Found at i:14409 original size:94 final size:96
Alignment explanation
Indices: 14218--14437 Score: 259
Period size: 94 Copynumber: 2.3 Consensus size: 96
14208 ATCTAACAAG
*
14218 TTATTTCCTTTTACAAAATA-GAAAAATAATCGAATGATTTATTTCCTTTTACATATCAGAATCA
1 TTATTTCCTTTTACAAAATAGGAAAAA-AATCGAATGATTTATTTCCTTTTACAAATCAGAATCA
** * ** ****
14282 TATAAGATTCTTATGAAAATTGATTTTCCGAT
65 TATAAGATTCACAGGAAAATAAATTCAAAGAT
* * * *
14314 TTATTTCATTTTTCAAAATAGGAAAAAAA-C-TATGATTTATTTCTTTTTACAAA-CTAGAATCA
1 TTATTTCCTTTTACAAAATAGGAAAAAAATCGAATGATTTATTTCCTTTTACAAATC-AGAATCA
*
14376 TATAAGATTCACAGGAAAGTAAATTCAAAGAT
65 TATAAGATTCACAGGAAAATAAATTCAAAGAT
14408 TTATTTCCTTTTACAAAATAGGAAAAAAAT
1 TTATTTCCTTTTACAAAATAGGAAAAAAAT
14438 ATACCGATTT
Statistics
Matches: 104, Mismatches: 17, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
93 1 0.01
94 76 0.73
95 1 0.01
96 20 0.19
97 6 0.06
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (96 bp):
TTATTTCCTTTTACAAAATAGGAAAAAAATCGAATGATTTATTTCCTTTTACAAATCAGAATCAT
ATAAGATTCACAGGAAAATAAATTCAAAGAT
Found at i:14448 original size:38 final size:37
Alignment explanation
Indices: 14405--14540 Score: 123
Period size: 39 Copynumber: 3.5 Consensus size: 37
14395 TAAATTCAAA
14405 GATTTATTTCCTTTTACAAAATAGGAAAA-AAATATACC
1 GATTTATTTCCTTTTACAAAATAGGAAAACAAATA-A-C
* * * * * *
14443 GATTTATTTGCTTTCATAAAACAGGAAAACAAACCCAAT
1 GATTTATTTCCTTTTACAAAATAGGAAAACAAA--TAAC
*
14482 GATTTATTTCCTTTTACAAAAT-GTGAAAATGAAATCAAC
1 GATTTATTTCCTTTTACAAAATAG-GAAAA-CAAAT-AAC
*
14521 AATTTATTTCCTTTTACAAA
1 GATTTATTTCCTTTTACAAA
14541 TTAGAATCAT
Statistics
Matches: 78, Mismatches: 14, Indels: 11
0.76 0.14 0.11
Matches are distributed among these distances:
38 26 0.33
39 47 0.60
40 4 0.05
41 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (37 bp):
GATTTATTTCCTTTTACAAAATAGGAAAACAAATAAC
Found at i:14609 original size:40 final size:40
Alignment explanation
Indices: 14565--14652 Score: 115
Period size: 39 Copynumber: 2.2 Consensus size: 40
14555 GATTCTTACA
* * * * * *
14565 AAAATAAATTTTAACAATTTATTTTCTTTTGCAAGATATG
1 AAAATAAATTTCAACAACTTATTTCCTTTTACAAAATAGG
14605 AAAATAAA-TTCAACAACTTATTTCCTTTTACAAAATAGG
1 AAAATAAATTTCAACAACTTATTTCCTTTTACAAAATAGG
14644 AAAATAAAT
1 AAAATAAAT
14653 ACTATGATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 33 0.80
40 8 0.20
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.38
Consensus pattern (40 bp):
AAAATAAATTTCAACAACTTATTTCCTTTTACAAAATAGG
Found at i:14942 original size:57 final size:58
Alignment explanation
Indices: 14866--15053 Score: 238
Period size: 58 Copynumber: 3.2 Consensus size: 58
14856 TAAATGATAA
* * * * * * *
14866 AATCATCCACGATTCTCAAGAAAATAAATTCGATAATTTATTTT-CTTACAAAGTTAG
1 AATCATTCAAGATTTTCAAGGAAATAAATTCAACAATCTATTTTACTTACAAAGTTAG
14923 AATCATTCAAGATTTTCAAGGAAATAAATTCAACAATCTATTTTACTTACAAAGTTAG
1 AATCATTCAAGATTTTCAAGGAAATAAATTCAACAATCTATTTTACTTACAAAGTTAG
* *
14981 AATCA-TCTAAGATTCTT-AAGGAAATAAATTTAACAATCTATTTTCCTTACAAAGTTAG
1 AATCATTC-AAGATT-TTCAAGGAAATAAATTCAACAATCTATTTTACTTACAAAGTTAG
*
15039 AATCAGTGCAAGATT
1 AATCA-TTCAAGATT
15054 CTAAAAATAA
Statistics
Matches: 116, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
57 39 0.34
58 68 0.59
59 8 0.07
60 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (58 bp):
AATCATTCAAGATTTTCAAGGAAATAAATTCAACAATCTATTTTACTTACAAAGTTAG
Found at i:15361 original size:45 final size:45
Alignment explanation
Indices: 15221--15353 Score: 142
Period size: 45 Copynumber: 3.0 Consensus size: 45
15211 TTAGCAACCA
* * * * * * **
15221 AATAATTAAAGGGAATTAATCATTTGATTTTAATCTACACAATC-C
1 AATAATCAAAAGGAACTAATAATTTGATTTTACTTTTGACAA-CAC
* * *
15266 AATAATCGAAAGGAACTAATCATTTGATTTTACTTTTGGCAACAC
1 AATAATCAAAAGGAACTAATAATTTGATTTTACTTTTGACAACAC
*
15311 AATAATCAAAATGAACTAATAATTTGATTTTACTTTTGACAAC
1 AATAATCAAAAGGAACTAATAATTTGATTTTACTTTTGACAAC
15354 CCGATAATTA
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 1 0.01
45 73 0.99
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (45 bp):
AATAATCAAAAGGAACTAATAATTTGATTTTACTTTTGACAACAC
Found at i:15509 original size:22 final size:19
Alignment explanation
Indices: 15466--15517 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
15456 AAACACAATC
15466 AATAATTATTATAATATTT
1 AATAATTATTATAATATTT
15485 AATAATTATTATAATATTT
1 AATAATTATTATAATATTT
*
15504 AATAATAATTATAA
1 AATAATTATTATAA
15518 ACACCAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAATTATTATAATATTT
Found at i:17226 original size:38 final size:38
Alignment explanation
Indices: 17182--17304 Score: 99
Period size: 38 Copynumber: 3.2 Consensus size: 38
17172 AACTAAAATA
17182 AAAAATATTTATTTAAATTTACAATACTTCCAACTTAT
1 AAAAATATTTATTTAAATTTACAATACTTCCAACTTAT
* *** * * * *
17220 AAAAATA-TAAAAAAAATTTGAGATAAACGT-GAA-TTAAAAT
1 AAAAATATTTATTTAAATTT-ACA-ATACTTCCAACTT---AT
*
17260 AAAGATATTTATTTAAATTTACAATACTTCCAACTTAT
1 AAAAATATTTATTTAAATTTACAATACTTCCAACTTAT
17298 AAAAATA
1 AAAAATA
17305 ATGTAAATAG
Statistics
Matches: 59, Mismatches: 18, Indels: 16
0.63 0.19 0.17
Matches are distributed among these distances:
37 10 0.17
38 19 0.32
39 8 0.14
40 12 0.20
41 10 0.17
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.35
Consensus pattern (38 bp):
AAAAATATTTATTTAAATTTACAATACTTCCAACTTAT
Found at i:17249 original size:79 final size:78
Alignment explanation
Indices: 17150--17304 Score: 274
Period size: 78 Copynumber: 2.0 Consensus size: 78
17140 TTCATTGTAC
*
17150 AAAAAAATTTGAGATGAACGTGAACTAAAATAAAAAATATTTATTTAAATTTACAATACTTCCAA
1 AAAAAAATTTGAGATAAACGTGAACTAAAAT-AAAAATATTTATTTAAATTTACAATACTTCCAA
17215 CTTATAAAAATATA
65 CTTATAAAAATATA
* *
17229 AAAAAAATTTGAGATAAACGTGAATTAAAATAAAGATATTTATTTAAATTTACAATACTTCCAAC
1 AAAAAAATTTGAGATAAACGTGAACTAAAATAAAAATATTTATTTAAATTTACAATACTTCCAAC
17294 TTATAAAAATA
66 TTATAAAAATA
17305 ATGTAAATAG
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 44 0.60
79 29 0.40
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.32
Consensus pattern (78 bp):
AAAAAAATTTGAGATAAACGTGAACTAAAATAAAAATATTTATTTAAATTTACAATACTTCCAAC
TTATAAAAATATA
Found at i:30205 original size:82 final size:82
Alignment explanation
Indices: 29875--30189 Score: 416
Period size: 82 Copynumber: 3.8 Consensus size: 82
29865 ATTTAGATCT
* * * * * * *
29875 TGGCAGCATGCAACAGTTCATCATTCAACTTGATTCGATCATGGTAGCATACAACAATTCACCAT
1 TGGCAGCATACAATAATTCATCATTCAACTTGATTTGATCATGGTAGCATGCAATAATTCATCAT
*
29940 TCGA-TCTAATTCAATCA
66 TCAATTC-AATTCAATCA
* * * *
29957 TGGCAGCATACCATATTTCATCATTCAACTTGATTTGATTATGGTAGCATGCAATAATTCACCAT
1 TGGCAGCATACAATAATTCATCATTCAACTTGATTTGATCATGGTAGCATGCAATAATTCATCAT
30022 TCAATTCAATTCAATCA
66 TCAATTCAATTCAATCA
*
30039 TGGCAGCATACAATAATCCATCATTCAACTTGATTTGATCATGGTAGCATGCAATAATTCATCAT
1 TGGCAGCATACAATAATTCATCATTCAACTTGATTTGATCATGGTAGCATGCAATAATTCATCAT
30104 TCAATTCAATTCAATCA
66 TCAATTCAATTCAATCA
* * * ** * * * *
30121 TGGCAGCATACAATACTTCACCATTCAACCTGATTCAACCACGGTAGCATACCATAATTCATCAT
1 TGGCAGCATACAATAATTCATCATTCAACTTGATTTGATCATGGTAGCATGCAATAATTCATCAT
30186 TCAA
66 TCAA
30190 CTTGACTTTA
Statistics
Matches: 208, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
82 206 0.99
83 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.31
Consensus pattern (82 bp):
TGGCAGCATACAATAATTCATCATTCAACTTGATTTGATCATGGTAGCATGCAATAATTCATCAT
TCAATTCAATTCAATCA
Found at i:30222 original size:41 final size:41
Alignment explanation
Indices: 29891--30214 Score: 323
Period size: 41 Copynumber: 7.9 Consensus size: 41
29881 CATGCAACAG
* *
29891 TTCATCATTCAACTTGATTCGATCATGGTAGCATACAACAA
1 TTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAA
* * * * * *
29932 TTCACCATTCGA-TCTAATTCAATCATGGCAGCATACCATAT
1 TTCATCATTCAACT-TGATTCAATCATGGTAGCATACAATAA
** * *
29973 TTCATCATTCAACTTGATTTGATTATGGTAGCATGCAATAA
1 TTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAA
* * *
30014 TTCACCATTCAA-TTCAATTCAATCATGGCAGCATACAATAA
1 TTCATCATTCAACTT-GATTCAATCATGGTAGCATACAATAA
* ** *
30055 TCCATCATTCAACTTGATTTGATCATGGTAGCATGCAATAA
1 TTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAA
* * *
30096 TTCATCATTCAA-TTCAATTCAATCATGGCAGCATACAATAC
1 TTCATCATTCAACTT-GATTCAATCATGGTAGCATACAATAA
* * * * *
30137 TTCACCATTCAACCTGATTCAACCACGGTAGCATACCATAA
1 TTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAA
* *
30178 TTCATCATTCAACTTGACTT-TATCATGGTAACATACA
1 TTCATCATTCAACTTGA-TTCAATCATGGTAGCATACA
30215 TTTATTCACA
Statistics
Matches: 222, Mismatches: 54, Indels: 14
0.77 0.19 0.05
Matches are distributed among these distances:
40 5 0.02
41 211 0.95
42 6 0.03
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.32
Consensus pattern (41 bp):
TTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAA
Found at i:31585 original size:21 final size:21
Alignment explanation
Indices: 31561--31600 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
31551 GCGTAGAATT
31561 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
31582 TGTCCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
31601 AAACACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.15
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:31631 original size:18 final size:18
Alignment explanation
Indices: 31608--31643 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
31598 ATAAAACACA
31608 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
31626 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
31644 ATATAACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:31642 original size:46 final size:46
Alignment explanation
Indices: 31561--31687 Score: 182
Period size: 46 Copynumber: 2.7 Consensus size: 46
31551 GCGTAGAATT
31561 TGTCCCGAAGGACCACATAGATGTCCCGAAGGACCACATAAAACACATA
1 TGTCCCGAAGGACCAC-T--ATGTCCCGAAGGACCACATAAAACACATA
*
31610 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACATATAACACATA
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACATAAAACACATA
* * * *
31656 TATCCCGAAAGACCACTATGTTCCGAATGACC
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACC
31688 GCGTAGACCC
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
46 56 0.77
48 1 0.01
49 16 0.22
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.17
Consensus pattern (46 bp):
TGTCCCGAAGGACCACTATGTCCCGAAGGACCACATAAAACACATA
Found at i:32554 original size:24 final size:20
Alignment explanation
Indices: 32501--32558 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
32491 TTCCCATTGA
*
32501 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
32521 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
32544 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
32559 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
23 2 0.06
24 13 0.39
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:38807 original size:29 final size:29
Alignment explanation
Indices: 38775--38832 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
38765 ATTTTAAAAT
*
38775 TATAATTATGAAAAATATATATTAATTTA
1 TATAATTATAAAAAATATATATTAATTTA
* * *
38804 TATATTTATAAAAAATATTTATTTATTTA
1 TATAATTATAAAAAATATATATTAATTTA
38833 GAAATATCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
TATAATTATAAAAAATATATATTAATTTA
Found at i:38904 original size:17 final size:18
Alignment explanation
Indices: 38882--38919 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
38872 TTTCCTCGAT
38882 ATTAAAAAAAATAA-ATA
1 ATTAAAAAAAATAATATA
* *
38899 ATTAAAACAATTAATATA
1 ATTAAAAAAAATAATATA
38917 ATT
1 ATT
38920 TATAAAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTAAAAAAAATAATATA
Found at i:40541 original size:3 final size:3
Alignment explanation
Indices: 40533--40669 Score: 149
Period size: 3 Copynumber: 45.7 Consensus size: 3
40523 GGCCTGTTTG
**
40533 TAA TAA TAA TAA TTT TAA TAA TAA TAAA TAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
40578 TAAA TAA -AA TAA TAA TAA TAA TAA TAA T-A TAA -AA -AA TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
40620 TAA TAA TAA TAA TAAA TAA TAA TAA TAGA AAA TAGA TAA AAA AAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TA-A TAA TA-A TAA TAA TAA TAA
40668 TA
1 TA
40670 TCTTCAGCTG
Statistics
Matches: 117, Mismatches: 8, Indels: 18
0.82 0.06 0.13
Matches are distributed among these distances:
2 10 0.09
3 93 0.79
4 14 0.12
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:41221 original size:113 final size:113
Alignment explanation
Indices: 41095--41998 Score: 1336
Period size: 113 Copynumber: 8.0 Consensus size: 113
41085 GAATTCAAGT
41095 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
41160 TATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAAC
66 TATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAAC
* * * *
41208 AAAAGGTTAAACAAGTTCTTCTCATTATGAAATTCCTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
41273 TATGAACTCTACCTGGAAATGCTGATCCATCAAATGAT-GAATTCAAGC
66 TATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAA-C
41321 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
41386 TATGAACTCTACCTGAAAATGTTGATCCATCAAGTGATGGATTTGAAC
66 TATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAAC
* * *
41434 AAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
41499 TATGAACTCTACCTGGAAATGTTGATCCAACGAA-TGAT-GAATTCAAGT
66 TATGAACTCTACCTGGAAATGTTGATCCATC-AAGTGATGGATTTGAA-C
* *
41547 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
41612 TATGAACT-TTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGC
66 TATGAACTCTAC-CTGGAAATGTTGATCCATCAAGTGATGGATTTGAAC
* * *
41660 AAAATGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGTTGAGTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
41725 TATGAACT-TTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTGAGC
66 TATGAACTCTAC-CTGGAAATGTTGATCCATCAAGTGATGGATTTGAAC
*
41773 AAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
41838 TATAAACT-TTCTCTGGAAAAGTTGATCTATCAAGTGATGGATTTGAGC
66 TATGAACTCTAC-CTGGAAATGTTGATCCATCAAGTGATGGATTTGAAC
* **
41886 AAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
41951 TATGAACTCGACCTGGTAATGCTGATCCATCGAA-TGATGGATTTGAAC
66 TATGAACTCTACCTGGAAATGTTGATCCATC-AAGTGATGGATTTGAAC
41999 CTTTGCTAAA
Statistics
Matches: 724, Mismatches: 58, Indels: 18
0.90 0.07 0.02
Matches are distributed among these distances:
112 16 0.02
113 692 0.96
114 16 0.02
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAAC
Found at i:41353 original size:226 final size:226
Alignment explanation
Indices: 41053--41989 Score: 1488
Period size: 226 Copynumber: 4.1 Consensus size: 226
41043 ATGAGTTCTT
* * *
41053 CTCTATCTGGCAATGCTGATCCATCGAATGATGAATTCAAGTAAAAAGTTGAACAAGTTCTTCTC
1 CTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTC
*
41118 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAATGT
66 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TACTCTGGAAAAGT
* *
41182 TGATCCATCAAGTGATGGATTTGAACAAAAGGTTAAACAAGTTCTTCTCATTATGAAATTCCTCT
130 TGATCCATCAAGTGATGGATTTGAACAAAAGGTTAAACAAGCTCTTCTCATTATGAACTTCCTCT
41247 TCCTTCTTCAGATGAGTTCTTCTCATTATGAA
195 TCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
41279 CTCTACCTGGAAATGCTGATCCATCAAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTC
1 CTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTC
41344 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CT-GAAAATG
66 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TACTCTGGAAAA-G
*
41407 TTGATCCATCAAGTGATGGATTTGAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTC
129 TTGATCCATCAAGTGATGGATTTGAACAAAAGGTTAAACAAGCTCTTCTCATTATGAACTTCCTC
41472 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
194 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
41505 CTCTACCTGGAAATGTTGATCCAACGAATGATGAATTCAAGTAAAAAGTTGAACAAGTTCTTCTC
1 CTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTC
* * *
41570 ATTATGAACTTCTTATTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTT
66 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGAAAAGTT
* * * *
41635 GATCCATCAAGTGATGGATTTGAGCAAAATGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT
131 GATCCATCAAGTGATGGATTTGAACAAAAGGTTAAACAAGCTCTTCTCATTATGAACTTCCTCTT
*
41700 CCTTCTTCAGTTGAGTTCTTCTCATTATGAA
196 CCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * ** *
41731 CT-TTCTCTGGAAAAGTTGATCCATC-AAGTGATGAATTTGAGCAAAAAGTTGAACAAGCTCTTC
1 CTCTAC-CTGGAAATGCTGATCCATCGAA-TGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTC
* *
41794 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTTTCTCTGGAAAAG
64 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGAAAAG
* * * * *
41859 TTGATCTATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTC
129 TTGATCCATCAAGTGATGGATTTGAACAAAAGGTTAAACAAGCTCTTCTCATTATGAACTTCCTC
41924 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
194 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
41957 CTCGACCTGGTAATGCTGATCCATCGAATGATG
1 CTCTACCTGGAAATGCTGATCCATCGAATGATG
41990 GATTTGAACC
Statistics
Matches: 666, Mismatches: 38, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
225 10 0.02
226 648 0.97
227 8 0.01
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (226 bp):
CTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTC
ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGAAAAGTT
GATCCATCAAGTGATGGATTTGAACAAAAGGTTAAACAAGCTCTTCTCATTATGAACTTCCTCTT
CCTTCTTCAGATGAGTTCTTCTCATTATGAA
Found at i:41991 original size:339 final size:338
Alignment explanation
Indices: 40872--41996 Score: 1448
Period size: 339 Copynumber: 3.3 Consensus size: 338
40862 TGTAATTTGG
*
40872 AAAAGGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAA-GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * ** *
40937 TTATGAACTCTACCTGGAAATGTTGATGATGATCTATCTATTTCTGTGA-TAGAGTCATGCAAAA
65 TTATGAACTCTACCTGG-AA-----ATGCTGATCCATC-AATGATG-GATTTGAG-CA---AAAA
41001 GGTTGAACAAGCTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTC----T-
118 -GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATG
** * ** *
41057 -A---T--CTGGCAATGCTGATCCATCGAA-TGATGAATTCAAGTAAAAAGTTGAACAAGTTCTT
182 AACTCTACCTGAAAATGTTGATCCATC-AAGTGATGAATTTGAGCAAAAAGTTGAACAAGTTCTT
41115 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAAT
246 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAAT
*
41180 GTTGATCCATCAAGTGATGGATTTGAAC
311 GTTGATCCATCAAGTGATGGATTTGAGC
* * *
41208 AAAAGGTTAAACAAGTTCTTCTCATTATGAAATTCCTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** *
41273 TATGAACTCTACCTGGAAATGCTGATCCATCAAATGATGAATTCAAGCAAAAAGTTGAACAAGTT
66 TATGAACTCTACCTGGAAATGCTGATCCATC-AATGATGGATTTGAGCAAAAAGTTGAACAAGCT
41338 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGAA
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGAA
* * * *
41403 AATGTTGATCCATCAAGTGATGGATTTGAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTT
195 AATGTTGATCCATCAAGTGATGAATTTGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
* *
41468 CCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCAACGAA
260 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATC-AA
* ** *
41533 -TGATGAATTCAAGT
324 GTGATGGATTTGAGC
* * *
41547 AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
41612 TATGAACT-TTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAATGTTGAACAAGC
66 TATGAACTCTAC-CTGGAAATGCTGATCCATCAA-TGATGGATTTGAGCAAAAAGTTGAACAAGC
* *
41676 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGTTGAGTTCTTCTCATTATGAACT-TTCTCTG
129 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CT-
*
41740 GAAAA-GTTGATCCATCAAGTGATGAATTTGAGCAAAAAGTTGAACAAGCTCTTCTCATTATGAA
192 GAAAATGTTGATCCATCAAGTGATGAATTTGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAA
* * * *
41804 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACT-TTCTCTGGAAAAGTTGATCTAT
257 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAATGTTGATCCAT
41868 CAAGTGATGGATTTGAGC
321 CAAGTGATGGATTTGAGC
**
41886 AAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
41951 TATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGGATTTGA
66 TATGAACTCTACCTGGAAATGCTGATCCATC-AATGATGGATTTGA
41997 ACCTTTGCTA
Statistics
Matches: 691, Mismatches: 72, Indels: 49
0.85 0.09 0.06
Matches are distributed among these distances:
324 25 0.04
325 4 0.01
327 6 0.01
328 25 0.04
329 18 0.03
332 1 0.00
334 3 0.00
335 73 0.11
336 4 0.01
337 1 0.00
338 12 0.02
339 509 0.74
340 10 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (338 bp):
AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTACCTGGAAATGCTGATCCATCAATGATGGATTTGAGCAAAAAGTTGAACAAGCTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGAAA
ATGTTGATCCATCAAGTGATGAATTTGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCAAGT
GATGGATTTGAGC
Found at i:42423 original size:22 final size:22
Alignment explanation
Indices: 42398--42452 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
42388 GATAAAGCTT
*
42398 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
42420 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
42442 TCATCTTTGAA
1 TCATCTTTGAA
42453 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:45248 original size:114 final size:114
Alignment explanation
Indices: 45046--45267 Score: 354
Period size: 114 Copynumber: 1.9 Consensus size: 114
45036 ACGATCATGC
* * * *
45046 AATTCATCTTCCTAATCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAA
1 AATTCATCTTCCAAATCCAATGATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
45111 GAACACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCAACTATGAGCA
66 GAACACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCAACTATGAGCA
* * *
45160 AATTCATCTTTCAAATCCAATGATTAGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
1 AATTCATCTTCCAAATCCAATGATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
* * *
45225 GAACACTTCCAGAAGATGTTATTGGGTCTCCTTATTTCTACTA
66 GAACACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCAACTA
45268 CGAGAACGTG
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 98 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (114 bp):
AATTCATCTTCCAAATCCAATGATTAGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCAACTATGAGCA
Found at i:46911 original size:17 final size:17
Alignment explanation
Indices: 46872--46911 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
46862 CAATTTTCTT
*
46872 TTTTTTCCTCATTTTTC
1 TTTTTTCATCATTTTTC
* *
46889 CTTTTTCATCTTTTTTC
1 TTTTTTCATCATTTTTC
46906 TTTTTT
1 TTTTTT
46912 TGCTTTCTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTTCATCATTTTTC
Found at i:54053 original size:163 final size:163
Alignment explanation
Indices: 53783--54284 Score: 602
Period size: 163 Copynumber: 3.1 Consensus size: 163
53773 ATAATGAAAT
* * *
53783 CGGTTTTATCATATTTTTATCTGTTATATTGTTATGTATTGATATATTTTTATAAAGTATCAATA
1 CGGTTTTGTCATATTTTTATCTGTTATATTGTTATGTATCGATATATTTTTATAAAGTATCGATA
* * * **
53848 CTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTTCAAAAGTGTCGATACTTATTTGAATAAAA
66 CTTTATAGGCGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAA
*
53913 TCGATACTTTCAACATATCCGGCAGCTCTTTAC
131 TCGATACTTTCAACATATCCGGTAGCTCTTTAC
* *
53946 CGGTTTTGTCATATTTTTATCTGCTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATA
1 CGGTTTTGTCATATTTTTATCTGTTATATTGTTATGTATCGATATATTTTTATAAAGTATCGATA
54011 CTTTATAGGCGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAA
66 CTTTATAGGCGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAA
*
54076 TCGATACTTTCAACATATCCGGTAGGGT-TTTAC
131 TCGATACTTTCAACATATCCGGTA-GCTCTTTAC
* * ** * * ** * * * * *
54109 CAGTTTTGTCAT-TATGAAACTGGTTTTATCATAATTTTACCTGTTATATTGTTAT---GTATCG
1 CGGTTTTGTCATATTTTTATCT-GTTATATTGTTA-TGTATC-GATATATTTTTATAAAGTATCG
* * * * ** *
54170 ATACTTTATAGACGCTATTAC-GCTTTTCTCTTAAATTCTAAAAATGTTAATACTTATTTCAATG
63 ATACTTTATAGGCGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATG
* *
54234 GAATCAATACTTTCAACATATCCGGTAGCGCTTTAC
128 GAATCGATACTTTCAACATATCCGGTAGCTCTTTAC
* *
54270 CGATTTTTTCATATT
1 CGGTTTTGTCATATT
54285 GAACCGGTTT
Statistics
Matches: 292, Mismatches: 41, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
160 1 0.00
161 77 0.26
162 32 0.11
163 166 0.57
164 6 0.02
165 10 0.03
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.45
Consensus pattern (163 bp):
CGGTTTTGTCATATTTTTATCTGTTATATTGTTATGTATCGATATATTTTTATAAAGTATCGATA
CTTTATAGGCGCTATTACTGCTTTTCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGGAA
TCGATACTTTCAACATATCCGGTAGCTCTTTAC
Found at i:56098 original size:34 final size:34
Alignment explanation
Indices: 56044--56115 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
56034 GGGGGTTTAA
* *
56044 AAATAAAATAAAAGATAAAATTAATAAATAA-TT
1 AAATAAAAGAAAAGATAAAATAAATAAATAATTT
*
56077 AAATAAAAGATAAGGATAAAATAAATAAATAATTT
1 AAATAAAAGA-AAAGATAAAATAAATAAATAATTT
56112 AAAT
1 AAAT
56116 TTAAAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 9 0.26
34 19 0.56
35 6 0.18
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (34 bp):
AAATAAAAGAAAAGATAAAATAAATAAATAATTT
Done.