Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003122.1 Hibiscus syriacus cultivar Beakdansim tig00006537_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: 105194
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:997 original size:251 final size:248
Alignment explanation
Indices: 549--1086 Score: 672
Period size: 251 Copynumber: 2.2 Consensus size: 248
539 AACTAATTCA
549 TATTGAATAAAAAT-TTTTTTTTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCG
1 TATTGAATAAAAATATTTTTTTTATTTCGGGTCGGGTTTCTAATTCA-ATATTCGGGTCGGGTCG
*
613 GGTGAAACTTTATTTTGGTCGGGTCGAGTCAGTTTTTTTAAATGTGATATTCGGGTCGGGTCGAG
65 GGTGAAACTTTATTTTGGTCGGGTCGAGTCAGATTTTTTAAATGTGATATTCGGG-CGGGTCGAG
* * * *
678 TTCGGGTTTAGGGTGAAAAATACTCAACCTGAAAATATATATAATTTTACCTTATATATTTTGGA
129 TTCGGGTGTAGGGTGAAAAATACCCAACCAGAAAAAATATATAATTTTACCTTATATATTTTGGA
* * *
743 ATAATTACAATAATACCCCTCTATATATAATTTTTTGCAATTAAGTCACTGA-TTT
194 ATAATTACAATAAAACCACTCTATATATAATTTTTTCCAATTAAGTCACT-ATTTT
*
798 TATTGAATAAAAATAATTTTTTTATTTCGGGTCGGGTCGGATTTCTAATTC-ATATTCGGGTCGG
1 TATTGAATAAAAATATTTTTTTTATTTCGGGTC--G--GG-TTTCTAATTCAATATTCGGGTCGG
* *
862 GTCGGGTGAAACTTTA-TTTGGTTGGGTC-AGGTCA-ATTTTTTAAGTGTGAT-TTC-GG-GGGT
61 GTCGGGTGAAACTTTATTTTGGTCGGGTCGA-GTCAGATTTTTTAAATGTGATATTCGGGCGGGT
*
921 CG-GTTCGGGTGTAGGGTGAAAAATACCCGACCAGACCGACCCAAAATATAT-ATTTTACCTTAT
125 CGAGTTCGGGTGTAGGGTGAAAAATACCCAACCAGA---A---AAAATATATAATTTTACCTTAT
* **
984 AT-TTTTAGGAATAATTACAATAAAACTACTCTATATATTTTTTTTTCCAATTAAGTCACTATTT
184 ATATTTT-GGAATAATTACAATAAAACCACTCTATATATAATTTTTTCCAATTAAGTCACTATTT
1048 T
248 T
*
1049 TATTGAA-AAAACA-ATTTTTTATTATTTCGGGTCAGGTT
1 TATTGAATAAAA-ATATTTTTT-TTATTTCGGGTCGGGTT
1087 GGGTGAAACT
Statistics
Matches: 255, Mismatches: 17, Indels: 37
0.83 0.06 0.12
Matches are distributed among these distances:
246 31 0.12
247 8 0.03
249 17 0.07
250 35 0.14
251 99 0.39
252 24 0.09
253 29 0.11
254 2 0.01
255 10 0.04
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40
Consensus pattern (248 bp):
TATTGAATAAAAATATTTTTTTTATTTCGGGTCGGGTTTCTAATTCAATATTCGGGTCGGGTCGG
GTGAAACTTTATTTTGGTCGGGTCGAGTCAGATTTTTTAAATGTGATATTCGGGCGGGTCGAGTT
CGGGTGTAGGGTGAAAAATACCCAACCAGAAAAAATATATAATTTTACCTTATATATTTTGGAAT
AATTACAATAAAACCACTCTATATATAATTTTTTCCAATTAAGTCACTATTTT
Found at i:1513 original size:18 final size:17
Alignment explanation
Indices: 1471--1514 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1461 TGAAATTGGA
*
1471 TTCAATTCCTGACAGAT
1 TTCAATTCCTCACAGAT
* *
1488 TCCAATTCCTTCACATAT
1 TTCAATTCC-TCACAGAT
1506 TTCAATTCC
1 TTCAATTCC
1515 CTCAAACGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.39
Consensus pattern (17 bp):
TTCAATTCCTCACAGAT
Found at i:3310 original size:25 final size:25
Alignment explanation
Indices: 3281--3328 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
3271 GGTCCACAAC
3281 TTCAATCTAATCGAAAGCCAAAATA
1 TTCAATCTAATCGAAAGCCAAAATA
* *
3306 TTCAATTTAATCGAAAGTCAAAA
1 TTCAATCTAATCGAAAGCCAAAA
3329 GATATTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.48, C:0.17, G:0.08, T:0.27
Consensus pattern (25 bp):
TTCAATCTAATCGAAAGCCAAAATA
Found at i:3399 original size:32 final size:33
Alignment explanation
Indices: 3326--3404 Score: 115
Period size: 32 Copynumber: 2.4 Consensus size: 33
3316 TCGAAAGTCA
* *
3326 AAAGATATTAAACCGGTTTTACAAATTCTTGGC
1 AAAGATATTAAACCGGTTTTACAAATTCTAGAC
*
3359 AAAGATATTAAACCGG-TTTATAAATTCTAGAC
1 AAAGATATTAAACCGGTTTTACAAATTCTAGAC
*
3391 AAATATATTAAACC
1 AAAGATATTAAACC
3405 AGTTAACTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 26 0.62
33 16 0.38
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (33 bp):
AAAGATATTAAACCGGTTTTACAAATTCTAGAC
Found at i:5279 original size:79 final size:79
Alignment explanation
Indices: 5142--5294 Score: 225
Period size: 79 Copynumber: 1.9 Consensus size: 79
5132 AATCAACAAT
* * * *
5142 GATCAAGAGAAAAGCTTTTCATTCTTCGTTCTTTCTTTTCTCTTATACATATAGTGTTTTTGTAA
1 GATCAAGAGAAAAACTTTTAATTCTTCGTTATTTCTTTTCTCTTATACATAGAGTGTTTTTGTAA
*
5207 GCTTTATTTAATAG
66 GCTTAATTTAATAG
* * * *
5221 GATCACGAGAAAAACTTTTAATTCTTTGTTATTTCTTTTCTCTTGTACATAGATTGTTTTTGTAA
1 GATCAAGAGAAAAACTTTTAATTCTTCGTTATTTCTTTTCTCTTATACATAGAGTGTTTTTGTAA
5286 GCTTAATTT
66 GCTTAATTT
5295 GTAAACACCT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 65 1.00
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.49
Consensus pattern (79 bp):
GATCAAGAGAAAAACTTTTAATTCTTCGTTATTTCTTTTCTCTTATACATAGAGTGTTTTTGTAA
GCTTAATTTAATAG
Found at i:15521 original size:26 final size:26
Alignment explanation
Indices: 15479--15531 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
15469 AATGTATTTC
15479 CATTCATTTCAAAGCTTGAG-GATATT
1 CATTCATTTCAAAGCTTG-GTGATATT
*
15505 CATTCA-TTCATAGGCTTGGTGATATT
1 CATTCATTTCA-AAGCTTGGTGATATT
15531 C
1 C
15532 TTAAGTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (26 bp):
CATTCATTTCAAAGCTTGGTGATATT
Found at i:34658 original size:38 final size:38
Alignment explanation
Indices: 34538--34658 Score: 135
Period size: 38 Copynumber: 3.3 Consensus size: 38
34528 AGTTGAAAAA
* * * *
34538 TTCATCTTTAGTAGGTGACCAACTTTGCACAAGGGAAT
1 TTCATCTTTGGTAGGTGGCCAACTTTGCACATGGAAAT
* * *
34576 TTCATC-TTGGTTGGTGGCCAAC-TT--A-TTGGAAAA
1 TTCATCTTTGGTAGGTGGCCAACTTTGCACATGGAAAT
*
34609 TTCATCTTTGGTAGGTGGCCAACTTTGCACATGGTAAT
1 TTCATCTTTGGTAGGTGGCCAACTTTGCACATGGAAAT
34647 TTCATCTTTGGT
1 TTCATCTTTGGT
34659 TCCTAAAATA
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
33 10 0.15
34 16 0.24
35 2 0.03
36 2 0.03
37 14 0.21
38 23 0.34
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.37
Consensus pattern (38 bp):
TTCATCTTTGGTAGGTGGCCAACTTTGCACATGGAAAT
Found at i:37461 original size:31 final size:31
Alignment explanation
Indices: 37420--37481 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
37410 CACGAAACCT
37420 ATTGAAGTAATTCTTTATGAGCTAGCTTCAA
1 ATTGAAGTAATTCTTTATGAGCTAGCTTCAA
* *
37451 ATTGATGTAATTCTTTATGTGCTAGCTTCAA
1 ATTGAAGTAATTCTTTATGAGCTAGCTTCAA
37482 TCATATGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (31 bp):
ATTGAAGTAATTCTTTATGAGCTAGCTTCAA
Found at i:39978 original size:15 final size:15
Alignment explanation
Indices: 39955--39984 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39945 TATCACAATC
*
39955 GCGCGGGATTTCGGG
1 GCGCAGGATTTCGGG
39970 GCGCAGGATTTCGGG
1 GCGCAGGATTTCGGG
39985 AGCACCGTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.20, G:0.50, T:0.20
Consensus pattern (15 bp):
GCGCAGGATTTCGGG
Found at i:54147 original size:20 final size:20
Alignment explanation
Indices: 54122--54172 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
54112 AATTGCCTCA
*
54122 GTATCGATACTGGACCTTGG
1 GTATCGATACTAGACCTTGG
*
54142 GTATCGATACTAGACCTTGT
1 GTATCGATACTAGACCTTGG
54162 GTATCGATACT
1 GTATCGATACT
54173 CCTTGAAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (20 bp):
GTATCGATACTAGACCTTGG
Found at i:55641 original size:18 final size:18
Alignment explanation
Indices: 55614--55652 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
55604 CCTCACCGCC
*
55614 GAGCCGAGCCACCGAGCT
1 GAGCCAAGCCACCGAGCT
*
55632 GAGCCAAGCCGCCGAGCT
1 GAGCCAAGCCACCGAGCT
55650 GAG
1 GAG
55653 TCATCGAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.36, G:0.36, T:0.05
Consensus pattern (18 bp):
GAGCCAAGCCACCGAGCT
Found at i:55646 original size:31 final size:31
Alignment explanation
Indices: 55609--55667 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
55599 CTGAACCTCA
55609 CCGCCGAGCCGAGCCACCGAGCTGAGCCAAG
1 CCGCCGAGCCGAGCCACCGAGCTGAGCCAAG
* * *
55640 CCGCCGAGCTGAGTCATCGAGCTGAGCC
1 CCGCCGAGCCGAGCCACCGAGCTGAGCC
55668 GCTAAGCCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.20, C:0.39, G:0.32, T:0.08
Consensus pattern (31 bp):
CCGCCGAGCCGAGCCACCGAGCTGAGCCAAG
Found at i:61474 original size:21 final size:21
Alignment explanation
Indices: 61449--61539 Score: 80
Period size: 21 Copynumber: 4.2 Consensus size: 21
61439 CACTAAAGTG
61449 CCACATAATTGTCCAGAATGA
1 CCACATAATTGTCCAGAATGA
* *
61470 CCACATAGGTTTGCACCA-AAGTG-
1 CCACATA--ATTG-TCCAGAA-TGA
*
61493 CCACATATTTGT-CACGAATGA
1 CCACATAATTGTCCA-GAATGA
*
61514 CCACATAATTGTCCCGAATGA
1 CCACATAATTGTCCAGAATGA
61535 CCACA
1 CCACA
61540 AAGACCCTCG
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
19 2 0.04
20 2 0.04
21 35 0.61
22 1 0.02
23 12 0.21
24 5 0.09
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.23
Consensus pattern (21 bp):
CCACATAATTGTCCAGAATGA
Found at i:61491 original size:44 final size:44
Alignment explanation
Indices: 61435--61520 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
61425 CAGCTTGTAA
*
61435 TTTGCACTAAAGTGCCACATAATTGTC-CAGAATGACCACATAGG
1 TTTGCACCAAAGTGCCACATAATTGTCAC-GAATGACCACATAGG
*
61479 TTTGCACCAAAGTGCCACATATTTGTCACGAATGACCACATA
1 TTTGCACCAAAGTGCCACATAATTGTCACGAATGACCACATA
61521 ATTGTCCCGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 38 0.97
45 1 0.03
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (44 bp):
TTTGCACCAAAGTGCCACATAATTGTCACGAATGACCACATAGG
Found at i:62409 original size:55 final size:55
Alignment explanation
Indices: 62325--62468 Score: 234
Period size: 55 Copynumber: 2.6 Consensus size: 55
62315 CGAAATGACA
* **
62325 AGGGTATCGATACACTCCTCAGTGTACCGATACACTAATGGCACTCGATGTTTTG
1 AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACACTCGATGTTTTG
*
62380 AGGGTATCGATACACTCCTCAGTGTACCGATACCCAAATAACACTCGATGTTTTG
1 AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACACTCGATGTTTTG
* *
62435 AGGGTATCGATACACTCCTCAGGGTACCAATACA
1 AGGGTATCGATACACTCCTCAGTGTACCGATACA
62469 GACTCATTCA
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 82 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.26
Consensus pattern (55 bp):
AGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACACTCGATGTTTTG
Found at i:63870 original size:32 final size:32
Alignment explanation
Indices: 63807--63880 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
63797 CTAAGGCACC
* *
63807 CTTGGGTAGG-CTTTGCAACCCTGAGATTTTT
1 CTTGGGTAGGCCTTTGCAACCCCGAGAATTTT
***
63838 CTTGGGTAGGCCTTTGTGGCCCCGAGAATTTT
1 CTTGGGTAGGCCTTTGCAACCCCGAGAATTTT
63870 CTTGGGTAGGC
1 CTTGGGTAGGC
63881 TCTTAGGCCC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 10 0.27
32 27 0.73
ACGTcount: A:0.14, C:0.20, G:0.31, T:0.35
Consensus pattern (32 bp):
CTTGGGTAGGCCTTTGCAACCCCGAGAATTTT
Found at i:71634 original size:23 final size:24
Alignment explanation
Indices: 71601--71672 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 24
71591 AAATATACTT
71601 ATTATAT-AAAATTATTTAATAAA
1 ATTATATAAAAATTATTTAATAAA
*
71624 ATTA-ATAAAAA-TATTTAAATGTAA
1 ATTATATAAAAATTATTT-AAT-AAA
*
71648 ATTATATAAAACATGA-TTAATAAA
1 ATTATATAAAA-ATTATTTAATAAA
71672 A
1 A
71673 ATATTGGCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
22 7 0.17
23 11 0.28
24 9 0.22
25 9 0.22
26 3 0.08
27 1 0.03
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (24 bp):
ATTATATAAAAATTATTTAATAAA
Found at i:71737 original size:23 final size:24
Alignment explanation
Indices: 71697--71750 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
71687 CAATGATTAA
71697 ATGTAAATTAATATAGTTTAATTT
1 ATGTAAATTAATATAGTTTAATTT
71721 ATGTAAATT-ATATAGTTTAATTT
1 ATGTAAATTAATATAGTTTAATTT
71744 ATGTAAA
1 ATGTAAA
71751 GAAAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 21 0.70
24 9 0.30
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (24 bp):
ATGTAAATTAATATAGTTTAATTT
Found at i:72819 original size:15 final size:15
Alignment explanation
Indices: 72799--72856 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
72789 GTTTATAAAC
72799 TATAAACTATATTAA
1 TATAAACTATATTAA
*
72814 TATAAATTATAGTTAA
1 TATAAACTATA-TTAA
* * *
72830 GAT-AATTAACATTAA
1 TATAAACT-ATATTAA
72845 TATAAACTATAT
1 TATAAACTATAT
72857 AGTACATTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 23 0.68
16 11 0.32
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (15 bp):
TATAAACTATATTAA
Found at i:72879 original size:20 final size:21
Alignment explanation
Indices: 72838--72879 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
72828 AAGATAATTA
72838 ACATTAATATAAACTATATAGT
1 ACATTAATATAAAC-ATATAGT
72860 ACATTAATATAAAC-TATAGT
1 ACATTAATATAAACATATAGT
72880 TTATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATTAATATAAACATATAGT
Found at i:72896 original size:21 final size:21
Alignment explanation
Indices: 72867--72914 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
72857 AGTACATTAA
* * *
72867 TATAAACTATAGTTTATAAAT
1 TATATACTATAGGTTATAAAC
72888 TATATACTATAGGTTATAAAC
1 TATATACTATAGGTTATAAAC
72909 TATATA
1 TATATA
72915 ATACACTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (21 bp):
TATATACTATAGGTTATAAAC
Found at i:73016 original size:2 final size:2
Alignment explanation
Indices: 73009--73048 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
72999 TACTATAGGT
*
73009 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTT 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
73049 CATACATAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 34 0.97
3 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:73059 original size:20 final size:19
Alignment explanation
Indices: 73021--73061 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
73011 TATATATATA
*
73021 TATATATATATATATAGTT
1 TATATATATATACATAGTT
73040 TATATATATCATACATAGTT
1 TATATATAT-ATACATAGTT
73060 TA
1 TA
73062 CACATACATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (19 bp):
TATATATATATACATAGTT
Found at i:73320 original size:2 final size:2
Alignment explanation
Indices: 73313--73506 Score: 54
Period size: 2 Copynumber: 98.0 Consensus size: 2
73303 TTCTATAAAC
* *
73313 TA TA TA TA TA TA TA TA TA TA TA TA -A TC TA TA GA T- TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
73353 TA T- TA GT- TA TA CA TA CA TA TA TA TA TA CTA TA T- TA -A TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * * *
73393 AA T- TA TA -A TT TA CA AA CTA TA TA CTT TA TA TA GTT TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA -TA TA TA TA
* * *
73434 TA TA TA CTA TA T- TA -A TA TA AA T- TA TA GTT TA TA AA CTA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA
* * *
73474 TA CTT TT TA TA T- TA TA TA TA TA GTT TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
73507 AACTTATATT
Statistics
Matches: 139, Mismatches: 29, Indels: 48
0.64 0.13 0.22
Matches are distributed among these distances:
1 13 0.09
2 113 0.81
3 13 0.09
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:73437 original size:60 final size:58
Alignment explanation
Indices: 73369--73495 Score: 209
Period size: 60 Copynumber: 2.2 Consensus size: 58
73359 TTATACATAC
73369 ATATATATATACTATATTAATATAAATTATAATTTACAAACTATATACTTTATATAGTTT
1 ATATATATATACTATATTAATATAAATTATAATTTACAAACTATATACTTTATATA--TT
* * *
73429 ATATATATATACTATATTAATATAAATTATAGTTTATAAACTATATACTTTTTATATT
1 ATATATATATACTATATTAATATAAATTATAATTTACAAACTATATACTTTATATATT
73487 ATATATATA
1 ATATATATA
73496 GTTTATATAT
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
58 11 0.17
60 53 0.83
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.48
Consensus pattern (58 bp):
ATATATATATACTATATTAATATAAATTATAATTTACAAACTATATACTTTATATATT
Found at i:73505 original size:60 final size:58
Alignment explanation
Indices: 73381--73564 Score: 196
Period size: 60 Copynumber: 3.1 Consensus size: 58
73371 ATATATATAC
* * *
73381 TATATTAATATAAATTATAATTTACAAACTATATACTTTATATAGTTTATATATA-TATA
1 TATATTAATATAAATTAT-ATTTATAAACTATATACTTTTTATA-TTTATATATAGTTTA
73440 CTATATTAATATAAATTATAGTTTATAAACTATATACTTTTTATATTATATATATAGTTTA
1 -TATATTAATATAAATTATA-TTTATAAACTATATACTTTTTATATT-TATATATAGTTTA
* * * * *
73501 TATATAAACT-TATATTATATTAATATAAATTATATAC-TTTAATACTT-TATATAGTTTA
1 TATATTAA-TATAAATTATATT--TATAAACTATATACTTTTTATATTTATATATAGTTTA
73559 TATATT
1 TATATT
73565 GTTTACACAT
Statistics
Matches: 109, Mismatches: 9, Indels: 14
0.83 0.07 0.11
Matches are distributed among these distances:
58 16 0.15
59 6 0.06
60 70 0.64
61 17 0.16
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (58 bp):
TATATTAATATAAATTATATTTATAAACTATATACTTTTTATATTTATATATAGTTTA
Found at i:73560 original size:9 final size:9
Alignment explanation
Indices: 73530--73562 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
73520 TTAATATAAA
73530 TTATATACT
1 TTATATACT
73539 TTA-ATACT
1 TTATATACT
*
73547 TTATATAGT
1 TTATATACT
73556 TTATATA
1 TTATATA
73563 TTGTTTACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (9 bp):
TTATATACT
Found at i:73561 original size:69 final size:68
Alignment explanation
Indices: 73369--73569 Score: 193
Period size: 69 Copynumber: 3.0 Consensus size: 68
73359 TTATACATAC
* * *
73369 ATATATA-TATACTATATTAATATAAATTATAA-TTTACAAAC--TATATACTT-TATATAGTTT
1 ATATATACTATATTATATTAATATAAATTATAACTTTA-ATACTTTATATATTTATATATAGTTT
73429 ATAT
65 ATAT
* ** * *
73433 ATATATACTATATTAATATAAATTATAGTTTATAAACTAT-ATACTTTTTATATTATATATATAG
1 ATATATACTATATT-ATATTAA-TATAAATTAT-AACTTTAATACTTTATATATT-TATATATAG
73497 TTTATAT
62 TTTATAT
*
73504 ATA-A-ACTTATATTATATTAATATAAATTATATACTTTAATACTTTATATAGTTTATATATTGT
1 ATATATAC-TATATTATATTAATATAAATTATA-ACTTTAATACTTTATATA-TTTATATATAGT
73567 TTA
63 TTA
73570 CACATAGTTC
Statistics
Matches: 110, Mismatches: 14, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
64 7 0.06
65 5 0.05
66 6 0.05
67 12 0.11
68 14 0.13
69 39 0.35
70 10 0.09
71 17 0.15
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (68 bp):
ATATATACTATATTATATTAATATAAATTATAACTTTAATACTTTATATATTTATATATAGTTTA
TAT
Found at i:73681 original size:13 final size:13
Alignment explanation
Indices: 73665--73722 Score: 62
Period size: 13 Copynumber: 4.2 Consensus size: 13
73655 CTTAATATAC
73665 TATATATATAAAT
1 TATATATATAAAT
*
73678 TATATACATAAATCT
1 TATATATATAAA--T
*
73693 TATATATTATATATT
1 TATATA-TATA-AAT
73708 TATATATATAAAT
1 TATATATATAAAT
73721 TA
1 TA
73723 CATAGTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 15 0.41
14 4 0.11
15 14 0.38
16 3 0.08
17 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATATAAAT
Found at i:73752 original size:11 final size:11
Alignment explanation
Indices: 73735--73770 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
73725 TAGTTTATTA
73735 ATAAACTACAT
1 ATAAACTACAT
*
73746 GTAAACTACAT
1 ATAAACTACAT
*
73757 ATAAACTATAT
1 ATAAACTACAT
73768 ATA
1 ATA
73771 TATATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.31
Consensus pattern (11 bp):
ATAAACTACAT
Found at i:77483 original size:17 final size:17
Alignment explanation
Indices: 77461--77493 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
77451 GGGAAGGATG
*
77461 GTTCACTTGGTCGAGTA
1 GTTCACTCGGTCGAGTA
77478 GTTCACTCGGTCGAGT
1 GTTCACTCGGTCGAGT
77494 GGAACTAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.21, G:0.30, T:0.33
Consensus pattern (17 bp):
GTTCACTCGGTCGAGTA
Found at i:88348 original size:3 final size:3
Alignment explanation
Indices: 88340--88471 Score: 194
Period size: 3 Copynumber: 43.7 Consensus size: 3
88330 TTTATCCATT
*
88340 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** *
88388 GCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
*
88434 TTA TTA TTA ATA TTA TATA TTA -TA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT
88472 TAATAAATAA
Statistics
Matches: 116, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
2 2 0.02
3 109 0.94
4 5 0.04
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:89758 original size:13 final size:13
Alignment explanation
Indices: 89717--89758 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
89707 TCATTTATTT
89717 TATA-TGTTTTAA
1 TATATTGTTTTAA
*
89729 TTTATTGTTTTTAAA
1 TATATTG-TTTT-AA
89744 TATATTGTTTTAA
1 TATATTGTTTTAA
89757 TA
1 TA
89759 GAATTATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 3 0.12
13 6 0.24
14 8 0.32
15 8 0.32
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (13 bp):
TATATTGTTTTAA
Found at i:90513 original size:11 final size:12
Alignment explanation
Indices: 90489--90536 Score: 61
Period size: 11 Copynumber: 4.4 Consensus size: 12
90479 TTTCAAATTT
90489 TTATTA-TT-TA
1 TTATTATTTATA
90499 TTATT-TTTATA
1 TTATTATTTATA
90510 TTATTATTTATA
1 TTATTATTTATA
90522 TT-TTATTTAT-
1 TTATTATTTATA
90532 TTATT
1 TTATT
90537 TTATTCAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.26
11 17 0.50
12 8 0.24
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTATTATTTATA
Found at i:90513 original size:18 final size:19
Alignment explanation
Indices: 90485--90541 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
90475 TTTCTTTCAA
90485 ATTTT-TATTATTTATTAT
1 ATTTTATATTATTTATTAT
90503 -TTTTATATTA-TTATTTAT
1 ATTTTATATTATTTA-TTAT
*
90521 ATTTTAT-TTATTTATTTT
1 ATTTTATATTATTTATTAT
90539 ATT
1 ATT
90542 CAAGAATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
17 7 0.21
18 18 0.53
19 9 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
ATTTTATATTATTTATTAT
Found at i:90515 original size:14 final size:14
Alignment explanation
Indices: 90485--90533 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
90475 TTTCTTTCAA
90485 ATTTTTATTATTTATT
1 ATTTTTA-TA-TTATT
90501 ATTTTTATATTATT
1 ATTTTTATATTATT
* *
90515 ATTTATATTTTATTT
1 ATTTTTATATTA-TT
90530 ATTT
1 ATTT
90534 ATTTTATTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 15 0.50
15 8 0.27
16 7 0.23
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTTTTATATTATT
Found at i:90515 original size:21 final size:18
Alignment explanation
Indices: 90488--90541 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 18
90478 CTTTCAAATT
90488 TTTATTATTTATTATTTTTA
1 TTTATTATTTA-TA-TTTTA
90508 TATTATTATTTATATTTTA
1 T-TTATTATTTATATTTTA
90527 TTTATTTATTT-TATT
1 TTTA-TTATTTATATT
90542 CAAGAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 7 0.22
19 12 0.38
20 3 0.09
21 10 0.31
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTATTTATATTTTA
Found at i:92033 original size:13 final size:14
Alignment explanation
Indices: 92014--92050 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
92004 ATTTTAAATA
92014 ATTTACATTTACAT
1 ATTTACATTTACAT
*
92028 -TTTACATTTGCAT
1 ATTTACATTTACAT
92041 ATTTACATTT
1 ATTTACATTT
92051 GGCATTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.30, C:0.14, G:0.03, T:0.54
Consensus pattern (14 bp):
ATTTACATTTACAT
Found at i:94650 original size:1 final size:1
Alignment explanation
Indices: 94644--94674 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
94634 AAGAAAGAAG
*
94644 AAAAAAAAAAGAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
94675 GGAAAATCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:94656 original size:14 final size:13
Alignment explanation
Indices: 94637--94674 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
94627 TCCAGCAAAG
94637 AAAGAAGAAAAAAA
1 AAAGAA-AAAAAAA
94651 AAAGAAAAAAAAA
1 AAAGAAAAAAAAA
94664 AAA-AAAAAAAA
1 AAAGAAAAAAAA
94675 GGAAAATCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 8 0.33
13 10 0.42
14 6 0.25
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAA
Found at i:94657 original size:11 final size:11
Alignment explanation
Indices: 94641--94680 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
94631 GCAAAGAAAG
94641 AAGAAAAAAAA
1 AAGAAAAAAAA
94652 AAGAAAAAAAA
1 AAGAAAAAAAA
94663 AA-AAAAAAAA
1 AAGAAAAAAAA
94673 AAGGAAAA
1 AA-GAAAA
94681 TCGAATAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.37
11 13 0.48
12 4 0.15
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:96947 original size:84 final size:84
Alignment explanation
Indices: 96806--97028 Score: 430
Period size: 84 Copynumber: 2.7 Consensus size: 84
96796 TGGAACAAAT
96806 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC-AGAAC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAAG-AC
96870 CAATCATTGAATTTGGAAGA
65 CAATCATTGAATTTGGAAGA
96890 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAAGACC
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAAGACC
96955 AATCATTGAATTTGGAAGA
66 AATCATTGAATTTGGAAGA
96974 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
97029 TGGTATGAAC
Statistics
Matches: 138, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
84 136 0.99
85 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.36
Consensus pattern (84 bp):
ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAAGACC
AATCATTGAATTTGGAAGA
Found at i:97182 original size:114 final size:114
Alignment explanation
Indices: 96982--97300 Score: 541
Period size: 114 Copynumber: 2.8 Consensus size: 114
96972 GAATAATGTG
96982 CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACTCCAAAAT
1 CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACTCCAAAAT
97047 CAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGA
66 CAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGA
97096 CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACTCCAAAAT
1 CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACTCCAAAAT
* *
97161 CAATCATTAGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGA
66 CAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGA
* * * *
97210 CCCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGGTCTGGTTTGGTATGAA-TCCCAGAA
1 CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACT-CCAAAA
* * *
97274 CCAATCATTGGAATTGAAAGGTGAATT
65 TCAATCATTGGATTTGAAAGATGAATT
97301 ACATGATTGT
Statistics
Matches: 194, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
113 1 0.01
114 193 0.99
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (114 bp):
CTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACTCCAAAAT
CAATCATTGGATTTGAAAGATGAATTTGCTCATAGTAGAAATAAGGAGA
Found at i:99350 original size:54 final size:54
Alignment explanation
Indices: 99261--99565 Score: 308
Period size: 54 Copynumber: 5.8 Consensus size: 54
99251 AGAAATCTTG
* *** ** *
99261 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAACGCTTTATGAACGTCTGA
1 GCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATATTTTACAAACATCTGA
* *
99315 GCAAAAACCACA-AGAAAGAATGAATGTGTTGTCAAATATTTTACAAACATCTGA
1 GCAGAAACCACAGA-AAAGGATGAATGTGTTGTCAAATATTTTACAAACATCTGA
* * * * *
99369 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC-ATC--CCGA
1 GCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATATTTTACAAACATCTGA
*
99420 -CAGAAACCACA-AGAAAGAATGAATGTGTTGTCAAATATTTTACAAACATCTGA
1 GCAGAAACCACAGA-AAAGGATGAATGTGTTGTCAAATATTTTACAAACATCTGA
* * * * *
99473 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTAC-ATC--CCGA
1 GCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATATTTTACAAACATCTGA
* *
99524 -CAGAAACCACAGGAAAA-GATGAATGTATTGTCAAATGTTTTA
1 GCAGAAACCACA-GAAAAGGATGAATGTGTTGTCAAATATTTTA
99566 TGAACCAGTG
Statistics
Matches: 211, Mismatches: 31, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
49 1 0.00
50 70 0.33
51 13 0.06
53 8 0.04
54 117 0.55
55 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (54 bp):
GCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATATTTTACAAACATCTGA
Found at i:99467 original size:104 final size:104
Alignment explanation
Indices: 99261--99565 Score: 470
Period size: 104 Copynumber: 2.9 Consensus size: 104
99251 AGAAATCTTG
** * * *
99261 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAACGCTTTATGAACGT-CTGAGCAAAAACCA
1 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTG-TTT-T--ACATCCCGA-CAGAAACCA
99325 CAAGAAAGAATGAATGTGTTGTCAAATATTTTACAAACATCTGA
61 CAAGAAAGAATGAATGTGTTGTCAAATATTTTACAAACATCTGA
99369 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATCCCGACAGAAACCACAAGA
1 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATCCCGACAGAAACCACAAGA
99434 AAGAATGAATGTGTTGTCAAATATTTTACAAACATCTGA
66 AAGAATGAATGTGTTGTCAAATATTTTACAAACATCTGA
*
99473 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATCCCGACAGAAACCACAGGA
1 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATCCCGACAGAAACCACAAGA
* *
99538 AA-AGATGAATGTATTGTCAAATGTTTTA
66 AAGA-ATGAATGTGTTGTCAAATATTTTA
99566 TGAACCAGTG
Statistics
Matches: 187, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
103 1 0.01
104 143 0.76
105 3 0.02
106 1 0.01
107 3 0.02
108 36 0.19
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (104 bp):
GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATCCCGACAGAAACCACAAGA
AAGAATGAATGTGTTGTCAAATATTTTACAAACATCTGA
Found at i:99966 original size:22 final size:22
Alignment explanation
Indices: 99937--99991 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
99927 ATCTACACTC
*
99937 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
99959 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
99981 TTCAAAGATGA
1 TTCAAAGATGA
99992 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:100774 original size:166 final size:164
Alignment explanation
Indices: 100493--100814 Score: 513
Period size: 166 Copynumber: 1.9 Consensus size: 164
100483 AGAATGAGCA
* * *
100493 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAACATAATGAGAAAACGA
1 TTATCTGGAGATTGGGACATGTTACCCAATCAACAGGTTATTT-AAAAACATAATGAGAAAACGA
* **
100558 TTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGA-TTTT
65 TTTCCAAAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTT
100622 CTTAGTTTTTTTACTTATTAAACTATTTCCAACAACC
130 CTTAG-TTTTTTACTTATTAAAC-ATTTCCAACAACC
*
100659 TTATCTGGAGATTGGGACATGTTACCCAATCAACAGGTTATCTT-GAAACATAATGAGAAAACGA
1 TTATCTGGAGATTGGGACATGTTACCCAATCAACAGGTTAT-TTAAAAACATAATGAGAAAACGA
*
100723 TTTCCAAAGTTTCTCATTCAATCTTTTCTGAAAATGAAATTGTTGAAAAGTAAGAAAACTATTTT
65 TTTCCAAAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACGATTTT
100788 TCTTAGTTTTTTACTTATTAAACATTT
129 TCTTAGTTTTTTACTTATTAAACATTT
100815 TCCTTCAAAA
Statistics
Matches: 145, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
165 49 0.34
166 85 0.59
167 11 0.08
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (164 bp):
TTATCTGGAGATTGGGACATGTTACCCAATCAACAGGTTATTTAAAAACATAATGAGAAAACGAT
TTCCAAAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTTC
TTAGTTTTTTACTTATTAAACATTTCCAACAACC
Found at i:100875 original size:36 final size:36
Alignment explanation
Indices: 100812--101093 Score: 230
Period size: 36 Copynumber: 7.7 Consensus size: 36
100802 TTATTAAACA
*
100812 TTTTCCTTCAAAACAACAATTTATCTCACTTGAGATTG
1 TTTTTCTT-AAAACAA-AATTTATCTCACTTGAGATTG
* * **
100850 TTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAG
1 TTTTTCTTAAAACAAAATTTATCTCACTTGAGATTG
** **
100886 TTTCACTCGAAACAACAATTTATCTCACTTGAGATTG
1 TTTTTCTTAAAACAA-AATTTATCTCACTTGAGATTG
* * **
100923 TTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAG
1 TTTTTCTTAAAACAAAATTTATCTCACTTGAGATTG
* *
100959 --TTTCATTCGAAACAGCAATTTATCTCACTTGAGATTG
1 TTTTTC-TT-AAAACA-AAATTTATCTCACTTGAGATTG
* * * **
100996 TTTTTCTTAAAACAAAATTTGTCTCGCTCGAGACAG
1 TTTTTCTTAAAACAAAATTTATCTCACTTGAGATTG
* * *
101032 --TTTCATTCGAAACAGCAATTTATCTCACTTGAAATTG
1 TTTTTC-TT-AAAACA-AAATTTATCTCACTTGAGATTG
* *
101069 TTTTCCTTAAAACAAAATTTGTCTC
1 TTTTTCTTAAAACAAAATTTATCTC
101094 GCTCGAGACA
Statistics
Matches: 187, Mismatches: 46, Indels: 24
0.73 0.18 0.09
Matches are distributed among these distances:
34 8 0.04
35 4 0.02
36 80 0.43
37 77 0.41
38 11 0.06
39 7 0.04
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (36 bp):
TTTTTCTTAAAACAAAATTTATCTCACTTGAGATTG
Found at i:100941 original size:73 final size:73
Alignment explanation
Indices: 100822--101118 Score: 522
Period size: 73 Copynumber: 4.1 Consensus size: 73
100812 TTTTCCTTCA
100822 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAGT
1 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAGT
100887 TTCACTCG
66 TTCACTCG
100895 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAGT
1 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAGT
*
100960 TTCATTCG
66 TTCACTCG
* *
100968 AAACAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGACAGT
1 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAGT
*
101033 TTCATTCG
66 TTCACTCG
* * * *
101041 AAACAGCAATTTATCTCACTTGAAATTGTTTTCCTTAAAACAAAATTTGTCTCGCTCGAGACAGT
1 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAGT
101106 TTCACTCG
66 TTCACTCG
101114 AAACA
1 AAACA
101119 TAAATTTCCA
Statistics
Matches: 218, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 218 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (73 bp):
AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAGT
TTCACTCG
Found at i:101325 original size:113 final size:113
Alignment explanation
Indices: 101137--101682 Score: 894
Period size: 113 Copynumber: 4.8 Consensus size: 113
101127 CATCACTCGA
*
101137 TGGATCAACTTTTCCAGAGAAAGTTCATAATGAAAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
1 TGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* * *
101202 CATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGG
66 CATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATCCATCATTTGG
*
101250 TGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
1 TGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
*
101315 CATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATCCATCATTTGG
66 CATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATCCATCATTTGG
*
101363 TGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
1 TGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* * *
101428 CATAATGAGAAGAATTTGTTCAACCTTTTACCTAAATCCATCATTTGG
66 CATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATCCATCATTTGG
* *
101476 TGGATCATCTTTTCCAGAGAAAGCTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
1 TGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* * * *
101541 CATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGA
66 CATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATCCATCATTTGG
* ** *
101589 TGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 TGGATCAACTTTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
101654 TCATAATGAGAAGAGCTTGTTCAACCTTT
65 TCATAATGAGAAGAACTTGTTCAACCTTT
101683 GTTTGATATC
Statistics
Matches: 406, Mismatches: 26, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
113 343 0.84
114 63 0.16
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
TGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
CATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATCCATCATTTGG
Found at i:101991 original size:3 final size:3
Alignment explanation
Indices: 101978--102100 Score: 160
Period size: 3 Copynumber: 40.7 Consensus size: 3
101968 TTTATCCATT
*
101978 TTA TTA TTTA TTA TTA TTA -TA TTA TTA GTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** *
102023 GCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
102069 TTA TTA ATA -TA TATA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TT
102101 TAATAAATAA
Statistics
Matches: 106, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
2 4 0.04
3 94 0.89
4 8 0.08
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:103388 original size:13 final size:13
Alignment explanation
Indices: 103347--103388 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
103337 TCATTTATTT
103347 TATA-TGTTTTAA
1 TATATTGTTTTAA
*
103359 TTTATTGTTTTTAAA
1 TATATTG-TTTT-AA
103374 TATATTGTTTTAA
1 TATATTGTTTTAA
103387 TA
1 TA
103389 GAATTATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 3 0.12
13 6 0.24
14 8 0.32
15 8 0.32
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (13 bp):
TATATTGTTTTAA
Done.