Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005018.1 Hibiscus syriacus cultivar Beakdansim tig00011264_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: 97989
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1844 original size:19 final size:20
Alignment explanation
Indices: 1804--1841 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1794 GAAGACATTG
1804 AGGAACAAATTTTCTTGCCA
1 AGGAACAAATTTTCTTGCCA
1824 AGGAA-AAATTTATCTTGC
1 AGGAACAAATTT-TCTTGC
1842 AAGTCTGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (20 bp):
AGGAACAAATTTTCTTGCCA
Found at i:4854 original size:20 final size:20
Alignment explanation
Indices: 4829--4868 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
4819 TCGCAAAGCC
*
4829 ATAATTTATCCTTGAGAGCA
1 ATAATTCATCCTTGAGAGCA
4849 ATAATTCATCCTTGAGAGCA
1 ATAATTCATCCTTGAGAGCA
4869 TTAGAGAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
ATAATTCATCCTTGAGAGCA
Found at i:5811 original size:20 final size:21
Alignment explanation
Indices: 5786--5832 Score: 87
Period size: 20 Copynumber: 2.3 Consensus size: 21
5776 ATTGCGAGAA
5786 GGGAGAATTCACGATGA-GGT
1 GGGAGAATTCACGATGAGGGT
5806 GGGAGAATTCACGATGAGGGT
1 GGGAGAATTCACGATGAGGGT
5827 GGGAGA
1 GGGAGA
5833 TCAAAACATC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.30, C:0.09, G:0.45, T:0.17
Consensus pattern (21 bp):
GGGAGAATTCACGATGAGGGT
Found at i:29767 original size:21 final size:21
Alignment explanation
Indices: 29724--29767 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
29714 TGATAAAATA
* ***
29724 TGGCTTTGTAATAGAGTTTCT
1 TGGCTTTGTAATAAAGCACCT
29745 TGGCTTTGTAATAAAGCACCT
1 TGGCTTTGTAATAAAGCACCT
29766 TG
1 TG
29768 ATTCTTGATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.41
Consensus pattern (21 bp):
TGGCTTTGTAATAAAGCACCT
Found at i:33495 original size:50 final size:50
Alignment explanation
Indices: 33420--33520 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 50
33410 ATGAGTAAGA
33420 TCATTTTTTACCGGATTGACATCTTTCAGAAGAAAGAACAAATCAAGCAC
1 TCATTTTTTACCGGATTGACATCTTTCAGAAGAAAGAACAAATCAAGCAC
** *
33470 TCATTTTTTATTGGATTGACATCTTTCAGAATAAAGAACAAATCAAGCAC
1 TCATTTTTTACCGGATTGACATCTTTCAGAAGAAAGAACAAATCAAGCAC
33520 T
1 T
33521 AATAAAGATT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.32
Consensus pattern (50 bp):
TCATTTTTTACCGGATTGACATCTTTCAGAAGAAAGAACAAATCAAGCAC
Found at i:40331 original size:2 final size:2
Alignment explanation
Indices: 40318--40348 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
40308 AATACTTTAT
*
40318 TA TA TA TG 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 T
40349 TTTTAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47959 original size:42 final size:42
Alignment explanation
Indices: 47907--47988 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
47897 AAAAATAAGC
* *
47907 AAATCATTCGAGCCATCAGTAAATCTTTCAAGCATGATGATT
1 AAATCATTCGAGCCATCAGTAAATCTCTCAAGCAAGATGATT
* * * *
47949 AAATCCTTCGAGTCATCAGTCATTCTCTCAAGCAAGATGA
1 AAATCATTCGAGCCATCAGTAAATCTCTCAAGCAAGATGA
47989 CAAGTCCTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (42 bp):
AAATCATTCGAGCCATCAGTAAATCTCTCAAGCAAGATGATT
Found at i:48132 original size:251 final size:250
Alignment explanation
Indices: 47418--48205 Score: 798
Period size: 251 Copynumber: 3.1 Consensus size: 250
47408 CATTGGGGCA
* * * *
47418 ATCAGTAAGTCTTTCGAGCATGATTATTAAATCCTTTGGGTCATTTGTTAATCTTTAGAGCAAGA
1 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATCTGTCAATCTTCA-AGCAAGA
* * * * *
47483 TGATAAGTCTTTTGAGCCATCTATAAGATCTTCAGGCATGAAGTTTTCATATGGTATTTGAGGAA
65 TGATAAGTCATTTGAGCCATCTATAAGACCTTCAGGCATGATGTTTTCATATGATATTTGAGAAA
* * * * * * **
47548 GCGGTTTTTAAAGTTTCTCATTTAAAAATTTCAGAAAATGAATTTTTTTGAAAAGTAAGAAAGCG
130 GCGATTTTCAAAGTTTCTCATTTAAGATTTTTAGAAAATGAA-ATTTTCAAAAAGTAAGAAAGCG
* * ** ** * * * ** *
47613 ATTTTCAAA-TTTATTAAATGGTAGAGTACTTCCAAAATTATTAAATCCTTCAGGCC
194 ATTTCCAAAGTTTCTTACCTAATAGACTACTTCAAAAATAAGCAAATCATTCAGGCC
* * * * *
47669 ATC-GATAAGTCTTTCGAGCATGATGATCAAATCTTTTGGGTCATCTTTCAGTCTTTCGAGCAAG
1 ATCAG-TAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATCTGTCAATC-TTCAAGCAAG
* * ** * * *
47733 ACGATAAATCATTCAAGCTATCTATAAGACCTTTAGGCATGATGTTTTCATATGATATTTAAGAA
64 ATGATAAGTCATTTGAGCCATCTATAAGACCTTCAGGCATGATGTTTTCATATGATATTTGAGAA
* * *
47798 AGCGATTTTCATAGTTTCTCATTTTAAGATTTTTAGAAAATAAAATTTTCAAAAAGTAAGAAAGT
129 AGCGATTTTCAAAGTTTCTCA-TTTAAGATTTTTAGAAAATGAAATTTTCAAAAAGTAAGAAAGC
* **
47863 GGTTTCCAAAGTTTCTTACCTAATAGACTTTTTCAAAAATAAGCAAATCATTC-GAGCC
193 GATTTCCAAAGTTTCTTACCTAATAGACTACTTCAAAAATAAGCAAATCATTCAG-GCC
* * * * * *
47921 ATCAGTAAATCTTTCAAGCATGATGATTAAATCCTTCGAGTCATCAGTCATTCTCTCAAGCAAGA
1 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATCTGTCAATCT-TCAAGCAAGA
* * * * * *
47986 TGACAAGTCCTTTGGGCCATCTATAAGACCTTCGGGCATGGTGTTTTCGTATGATATTTGAGAAA
65 TGATAAGTCATTTGAGCCATCTATAAGACCTTCAGGCATGATGTTTTCATATGATATTTGAGAAA
* *
48051 GTGATTTTCAAAGGTTT-TCATTTAAGATTTTTAGAAAATGAAATTTTCAAAAAGTAAGAAAACG
130 GCGATTTTCAAA-GTTTCTCATTTAAGATTTTTAGAAAATGAAATTTTCAAAAAGTAAGAAAGCG
* * * * * * * * * *
48115 ATTTCCAAAGTTTCTTACCCAGTATA--ATTTCCAAATTTAGTAAGTCTTTCAGGCC
194 ATTTCCAAAGTTTCTTACCTAATAGACTACTTCAAAAATAAGCAAATCATTCAGGCC
*
48170 ATC-GATATGTCTTTCGAGCATGATGATTAAATCCTT
1 ATCAG-TAAGTCTTTCGAGCATGATGATTAAATCCTT
48206 CAGGTCACTA
Statistics
Matches: 438, Mismatches: 89, Indels: 22
0.80 0.16 0.04
Matches are distributed among these distances:
248 1 0.00
249 51 0.12
250 2 0.00
251 211 0.48
252 168 0.38
253 5 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (250 bp):
ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATCTGTCAATCTTCAAGCAAGAT
GATAAGTCATTTGAGCCATCTATAAGACCTTCAGGCATGATGTTTTCATATGATATTTGAGAAAG
CGATTTTCAAAGTTTCTCATTTAAGATTTTTAGAAAATGAAATTTTCAAAAAGTAAGAAAGCGAT
TTCCAAAGTTTCTTACCTAATAGACTACTTCAAAAATAAGCAAATCATTCAGGCC
Found at i:48664 original size:44 final size:45
Alignment explanation
Indices: 48624--48765 Score: 191
Period size: 44 Copynumber: 3.2 Consensus size: 45
48614 TTTTTTGTTT
* * * *
48624 GATTCCATCATACAAGGAGTTGGATCAGCATCACTC-TTTTGGTC
1 GATTCCATCACATAAGGAGTTGGATCAACATCACTCATTTTGCTC
* *
48668 GATTCCATCACATTAGGAGTTGGATCAACATCAC-CATTTCGCTC
1 GATTCCATCACATAAGGAGTTGGATCAACATCACTCATTTTGCTC
* *
48712 GATTCCATCACATAAGGAGTTGGATTAACATCA-TCATTTTGCTT
1 GATTCCATCACATAAGGAGTTGGATCAACATCACTCATTTTGCTC
48756 GATTCCATCA
1 GATTCCATCA
48766 AAAAGGAAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
43 1 0.01
44 85 0.99
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (45 bp):
GATTCCATCACATAAGGAGTTGGATCAACATCACTCATTTTGCTC
Found at i:52421 original size:20 final size:20
Alignment explanation
Indices: 52396--52468 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
52386 AAAAAAAAAT
*
52396 TGGTCTTCATACCGAGGGAC
1 TGGTCTCCATACCGAGGGAC
***
52416 TGGTCTCCATACCGAAAAAC
1 TGGTCTCCATACCGAGGGAC
52436 TGGTCTCCATACC-AGAGGAC
1 TGGTCTCCATACCGAG-GGAC
*
52456 TGGTATCCATACC
1 TGGTCTCCATACC
52469 AAAGATTGAG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.02
20 43 0.98
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (20 bp):
TGGTCTCCATACCGAGGGAC
Found at i:52434 original size:40 final size:39
Alignment explanation
Indices: 52390--52476 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 39
52380 GTACCAAAAA
* *
52390 AAAAATTGGTCTTCATACC-GAGGGACTGGTCTCCATACC
1 AAAAATTGGTCTCCATACCAGA-GGACTGGTATCCATACC
*
52429 GAAAAACTGGTCTCCATACCAGAGGACTGGTATCCATACC
1 -AAAAATTGGTCTCCATACCAGAGGACTGGTATCCATACC
*
52469 AAAGATTG
1 AAAAATTG
52477 AGTATACATA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 6 0.15
40 33 0.80
41 2 0.05
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (39 bp):
AAAAATTGGTCTCCATACCAGAGGACTGGTATCCATACC
Found at i:52487 original size:40 final size:41
Alignment explanation
Indices: 52403--52489 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 41
52393 AATTGGTCTT
* * *
52403 CATACC-GAGGGACTGGTCTCCATACCGAAAAACTGGTCTC
1 CATACCAGAGGGACTGGTATCCATACCGAAAAACTGGTATA
* *
52443 CATACCAGA-GGACTGGTATCCATACC-AAAGATTGAGTATA
1 CATACCAGAGGGACTGGTATCCATACCGAAAAACTG-GTATA
52483 CATACCA
1 CATACCA
52490 AAGGCTTGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 6 0.15
40 32 0.80
41 2 0.05
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (41 bp):
CATACCAGAGGGACTGGTATCCATACCGAAAAACTGGTATA
Found at i:53221 original size:18 final size:20
Alignment explanation
Indices: 53198--53243 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
53188 TTTTTGGTGC
53198 CGATACTCAA-GG-GAGTAT
1 CGATACTCAAGGGAGAGTAT
53216 CGATAC-CAAGGGTAGAGTAT
1 CGATACTCAAGGG-AGAGTAT
53236 CGATACTC
1 CGATACTC
53244 CCCATAGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 8 0.33
20 12 0.50
21 1 0.04
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.22
Consensus pattern (20 bp):
CGATACTCAAGGGAGAGTAT
Found at i:53324 original size:19 final size:20
Alignment explanation
Indices: 53297--53341 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
53287 GCTAGTTTTT
* * *
53297 GTATTGATACTCAA-GGTGA
1 GTATCGATACCCAAGGGTCA
53316 GTATCGATACCCAAGGGTCA
1 GTATCGATACCCAAGGGTCA
53336 GTATCG
1 GTATCG
53342 TCACTGTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (20 bp):
GTATCGATACCCAAGGGTCA
Found at i:54624 original size:30 final size:30
Alignment explanation
Indices: 54588--54687 Score: 182
Period size: 30 Copynumber: 3.3 Consensus size: 30
54578 GTAAGCCACT
* *
54588 AAACTTTCTAGGTTTACGGAAAATGTCTCC
1 AAACTTTCTAGGTTTATGGAAAATGGCTCC
54618 AAACTTTCTAGGTTTATGGAAAATGGCTCC
1 AAACTTTCTAGGTTTATGGAAAATGGCTCC
54648 AAACTTTCTAGGTTTATGGAAAATGGCTCC
1 AAACTTTCTAGGTTTATGGAAAATGGCTCC
54678 AAACTTTCTA
1 AAACTTTCTA
54688 AATTTGTAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (30 bp):
AAACTTTCTAGGTTTATGGAAAATGGCTCC
Found at i:55043 original size:5 final size:5
Alignment explanation
Indices: 55033--55060 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
55023 ATTGAATTAT
55033 TATGA TATGA TATGA TATGA TATGA TAT
1 TATGA TATGA TATGA TATGA TATGA TAT
55061 TAGATGTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (5 bp):
TATGA
Found at i:56568 original size:47 final size:45
Alignment explanation
Indices: 56493--56617 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
56483 TATAAAATCT
*
56493 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
56538 CTTACCATTTAAATTCCATAAGCTCATAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
56585 CTTTCCA-TTATT-CATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
56618 GCATACTTAC
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
43 20 0.28
44 3 0.04
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:56820 original size:57 final size:57
Alignment explanation
Indices: 56728--56888 Score: 277
Period size: 57 Copynumber: 2.8 Consensus size: 57
56718 TAGTGCTAAT
** *
56728 CCGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAGTC
1 CCGTATGACACATAAGGTCGTACCCACCATATGTACTAGGTATCCTTAAGTACAGTC
56785 CCGTATGACACATAAGGTCGTACCCACCATATGTACTAGGTATCCTTAAGTACAGTC
1 CCGTATGACACATAAGGTCGTACCCACCATATGTACTAGGTATCCTTAAGTACAGTC
**
56842 CCGTATGACACATAAGGTCGTACCCACCATATACACTAGGTATCCTT
1 CCGTATGACACATAAGGTCGTACCCACCATATGTACTAGGTATCCTT
56889 TAGTGTATCC
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 99 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (57 bp):
CCGTATGACACATAAGGTCGTACCCACCATATGTACTAGGTATCCTTAAGTACAGTC
Found at i:58219 original size:21 final size:21
Alignment explanation
Indices: 58193--58497 Score: 134
Period size: 21 Copynumber: 14.6 Consensus size: 21
58183 GATTTACATA
*
58193 TTCGCATTGCGATAGTCTAAG
1 TTCGCATTGCGATAGTCGAAG
58214 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
* *
58235 TTCGCGTTTCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
* * * *
58256 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCATTGCGA--TAGTCGAAG
* * *
58279 TTCG--TTGCGATTTATTCCAAA
1 TTCGCATTGCGA--TAGTCGAAG
* *
58300 TTCG--TTGCGATTTATTCCAAG
1 TTCGCATTGCGA--TAGTCGAAG
58321 TTCG--TTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
* * * * *
58340 TCCGCGTTGCGATTTATTCCAAA
1 TTCGCATTGCGA--TAGTCGAAG
*
58363 TTCG--TTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAG
* * * * *
58382 TTCGCGTTGCAATTTATTCCAAA
1 TTCGCATTGCGA--TAGTCGAAG
58405 TTCG--TTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
* * * *
58424 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCATTGCGA--TAGTCGAAG
*
58447 TTCG--TTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAG
58466 TTCG--TTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
* *
58485 TTCACGTTGCGAT
1 TTCGCATTGCGAT
58498 TTATTCCAAA
Statistics
Matches: 237, Mismatches: 31, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
19 59 0.25
21 138 0.58
23 40 0.17
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:58306 original size:42 final size:40
Alignment explanation
Indices: 58239--58476 Score: 305
Period size: 42 Copynumber: 5.7 Consensus size: 40
58229 TCGAAGTTCG
* *
58239 CGTTTCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTT--CGTTGCGATTTATTCCAAATT
* * *
58281 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTT
1 CGTTGCGA--TAGTCCAAGTTCGTTGCGATTTATTCCAAATT
* *
58323 CGTTGCGATAGTCGAAGTCCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGT--TCGTTGCGATTTATTCCAAATT
*
58365 CGTTGCGATAGTCCAAGTTCGCGTTGCAATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTT--CGTTGCGATTTATTCCAAATT
*
58407 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTT--CGTTGCGATTTATTCCAAATT
58449 CGTTGCGATAGTCCAAGTTCGTTGCGAT
1 CGTTGCGATAGTCCAAGTTCGTTGCGAT
58477 AGTCGAAGTT
Statistics
Matches: 174, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
40 16 0.09
42 150 0.86
44 8 0.05
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (40 bp):
CGTTGCGATAGTCCAAGTTCGTTGCGATTTATTCCAAATT
Found at i:58332 original size:84 final size:82
Alignment explanation
Indices: 58239--58476 Score: 386
Period size: 84 Copynumber: 2.9 Consensus size: 82
58229 TCGAAGTTCG
* * *
58239 CGTTTCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGA--TAGTCCAAGTTCG
*
58304 TTGCGATTTATTCCAAGTT
64 TTGCGATTTATTCCAAATT
*
58323 CGTTGCGATAGTCGAAGTCCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT--CG
*
58388 TTGCAATTTATTCCAAATT
64 TTGCGATTTATTCCAAATT
58407 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTT
58472 GCGAT
66 GCGAT
58477 AGTCGAAGTT
Statistics
Matches: 144, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
82 17 0.12
84 127 0.88
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (82 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTT
GCGATTTATTCCAAATT
Found at i:58513 original size:21 final size:21
Alignment explanation
Indices: 58260--58518 Score: 232
Period size: 21 Copynumber: 12.4 Consensus size: 21
58250 TCGAAGTTCG
58260 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
58281 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
*
58302 CGTTGCGATTTATTCCAAGTT
1 CGTTGCGATTTATTCCAAATT
* * * *
58323 CGTTGCGA--TAGTCGAAGTCCG
1 CGTTGCGATTTATTCCAAAT--T
58344 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
* *
58365 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATT
*
58384 CGCGTTGCAATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
* * *
58407 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
58426 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
* *
58449 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATT
* * *
58468 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
58487 CACGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
58510 CGTTGCGAT
1 CGTTGCGAT
58519 AGTCCAAAAT
Statistics
Matches: 196, Mismatches: 26, Indels: 32
0.77 0.10 0.13
Matches are distributed among these distances:
19 52 0.27
21 112 0.57
23 32 0.16
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:58626 original size:6 final size:6
Alignment explanation
Indices: 58615--58655 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
58605 CGTATATTAT
58615 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGA
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGA
58656 GACGAGACGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:59145 original size:5 final size:5
Alignment explanation
Indices: 59135--59270 Score: 92
Period size: 5 Copynumber: 26.6 Consensus size: 5
59125 CCGCCGCCGC
* *
59135 CGTCT CGTCT CGTCT CGTCT CGTGT CGTGT CCGTCT CGTCT CGTCT CGTCT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT -CGTCT CGTCT CGTCT CGTCT
* * * * * * * * *
59186 CGTGT CGTGT CGTGTCC CGTCC CGTCC CGTCC CGTCC CGTCC CGTCC CGTCT
1 CGTCT CGTCT C--GTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT
* * * * * *
59238 CGTGT CGTGT CGTGT CGTGT CGTGT CGTGT CGT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGT
59271 GGTCGTGGTC
Statistics
Matches: 121, Mismatches: 7, Indels: 6
0.90 0.05 0.04
Matches are distributed among these distances:
5 114 0.94
6 4 0.03
7 3 0.02
ACGTcount: A:0.00, C:0.38, G:0.28, T:0.35
Consensus pattern (5 bp):
CGTCT
Found at i:59303 original size:6 final size:5
Alignment explanation
Indices: 59237--59301 Score: 85
Period size: 5 Copynumber: 12.0 Consensus size: 5
59227 CCGTCCCGTC
59237 TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTGG TCGTGG TCGTGG
1 TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGT-G TCGT-G TCGT-G
59285 TCGTGG TCGTGG TCGTG
1 TCGT-G TCGT-G TCGTG
59302 GTAATACGTG
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
5 30 0.51
6 29 0.49
ACGTcount: A:0.00, C:0.18, G:0.45, T:0.37
Consensus pattern (5 bp):
TCGTG
Found at i:59500 original size:21 final size:21
Alignment explanation
Indices: 59474--59520 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
59464 ATTGCGATAT
*
59474 TGCGAACTTCAATTATCGCAA
1 TGCGAACTTCAACTATCGCAA
* *
59495 TGCGAACTTCGACTATCGCAT
1 TGCGAACTTCAACTATCGCAA
59516 TGCGA
1 TGCGA
59521 TTTACATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (21 bp):
TGCGAACTTCAACTATCGCAA
Found at i:59555 original size:21 final size:21
Alignment explanation
Indices: 59529--59583 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
59519 GATTTACATA
59529 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
59550 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
59571 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
59584 TCTGGAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:65582 original size:21 final size:23
Alignment explanation
Indices: 65539--65589 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
65529 CATTTTCATC
65539 AAAATATTATTTATTAAAATATTT
1 AAAATATTATTTATT-AAATATTT
65563 AAAATA-TATTTATT-AATATTT
1 AAAATATTATTTATTAAATATTT
*
65584 ATAATA
1 AAAATA
65590 ATATAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
23 8 0.31
24 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAATATTATTTATTAAATATTT
Found at i:65603 original size:22 final size:23
Alignment explanation
Indices: 65556--65650 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 23
65546 TATTTATTAA
* *
65556 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
65577 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
65600 -ATATTTTTAATATTATATAAAATAATC
1 AATATTTATAATA--ATAT--AAT-ATT
65627 AATTATATTATAATAATATAATAT
1 AA-TAT-TTATAATAATATAATAT
65651 AAGATATTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
21 11 0.19
22 15 0.25
23 4 0.07
24 4 0.07
25 2 0.03
26 6 0.10
27 2 0.03
28 5 0.08
29 3 0.05
30 7 0.12
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:65613 original size:31 final size:31
Alignment explanation
Indices: 65567--65732 Score: 111
Period size: 29 Copynumber: 5.4 Consensus size: 31
65557 ATATTTAAAA
65567 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTT-TTAATATTTATAATAATATAATAT
*
65599 TATATTTTTAATA-TTAT-ATAAAATAATCAAT
1 TATATTTTTAATATTTATAATAATATAAT--AT
* *
65630 TATA-TTATAATA-ATATAAT-ATA-AGATAT
1 TATATTTTTAATATTTATAATAATATA-ATAT
65658 TATATTTTT-AT-TTTAATAAT-ATATAATAAT
1 TATATTTTTAATATTT-ATAATAATATAAT-AT
*
65688 T-T-TTTTTATATATTTAATAATGAATTATATTATT
1 TATATTTTTA-ATATTT-ATAAT-AA-TATAATA-T
*
65722 TATATATTTAA
1 TATATTTTTAA
65733 ATAATATTTA
Statistics
Matches: 108, Mismatches: 8, Indels: 33
0.72 0.05 0.22
Matches are distributed among these distances:
28 14 0.13
29 24 0.22
30 24 0.22
31 23 0.21
32 7 0.06
33 2 0.02
34 7 0.06
35 2 0.02
36 5 0.05
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (31 bp):
TATATTTTTAATATTTATAATAATATAATAT
Found at i:65681 original size:24 final size:23
Alignment explanation
Indices: 65649--65695 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
65639 ATAATATAAT
* *
65649 ATAAGATATTATATTTTTATTTTA
1 ATAAGATATAATAATTTT-TTTTA
*
65673 ATAATATATAATAATTTTTTTTA
1 ATAAGATATAATAATTTTTTTTA
65696 TATATTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATAAGATATAATAATTTTTTTTA
Found at i:65705 original size:28 final size:28
Alignment explanation
Indices: 65674--65737 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
65664 TTTATTTTAA
* *
65674 TAATATAT-AATAATTTTTTTTATATATT
1 TAATA-ATGAATAATATTATTTATATATT
*
65702 TAATAATGAATTATATTATTTATATATT
1 TAATAATGAATAATATTATTTATATATT
65730 TAAATAAT
1 T-AATAAT
65738 ATTTAGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 23 0.74
29 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
TAATAATGAATAATATTATTTATATATT
Found at i:65902 original size:90 final size:86
Alignment explanation
Indices: 65754--65923 Score: 191
Period size: 90 Copynumber: 1.9 Consensus size: 86
65744 TAAAGATATT
* * * * * *
65754 TAAAATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAATTAATA
1 TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAA-A
65819 CAATTTATAATATTTTATTTCAC
65 CAATTT-TAATATTTTATTTCAC
*
65842 TAAAATATACCAATATTAATATTTTTATTAATAAAATTATAAAAATAATA-TTTAAT-AATAAAT
1 TAAAATATA-CAA-ATTAATATTTTTA-AAATAAAA-TATAAAAATAATACTTTAATAAATAAAT
**
65905 AAATTATTTTAATATTTTA
62 AAACAATTTTAATATTTTA
65924 AAATAATAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
88 19 0.28
89 7 0.10
90 21 0.30
91 12 0.17
92 10 0.14
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (86 bp):
TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAAAC
AATTTTAATATTTTATTTCAC
Found at i:65965 original size:21 final size:21
Alignment explanation
Indices: 65941--65980 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
65931 AATATTAAGT
65941 TTTATGATAAATAATATTTTA
1 TTTATGATAAATAATATTTTA
* **
65962 TTTATTATATTTAATATTT
1 TTTATGATAAATAATATTT
65981 ATAATAAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTATGATAAATAATATTTTA
Found at i:66135 original size:15 final size:15
Alignment explanation
Indices: 66115--66154 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
66105 TATTTTCCAG
66115 AATTCAAATTCTAAT
1 AATTCAAATTCTAAT
* *
66130 AATTCAAATTTTAGT
1 AATTCAAATTCTAAT
66145 AATTCAAATT
1 AATTCAAATT
66155 GCAGTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (15 bp):
AATTCAAATTCTAAT
Found at i:66160 original size:15 final size:14
Alignment explanation
Indices: 66115--66163 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
66105 TATTTTCCAG
*
66115 AATTCAAATTCTAAT
1 AATTCAAATTC-AGT
*
66130 AATTCAAATTTTAGT
1 AATTCAAA-TTCAGT
66145 AATTCAAATTGCAGT
1 AATTCAAATT-CAGT
66160 AATT
1 AATT
66164 TATTTTTCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 2 0.07
15 25 0.86
16 2 0.07
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (14 bp):
AATTCAAATTCAGT
Found at i:71563 original size:22 final size:22
Alignment explanation
Indices: 71535--71576 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
71525 AAATCGAATC
71535 GAATAGAAATTTTGAAAAAATT
1 GAATAGAAATTTTGAAAAAATT
*
71557 GAATAGAAATTTTGAGAAAA
1 GAATAGAAATTTTGAAAAAA
71577 GCGAACGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.29
Consensus pattern (22 bp):
GAATAGAAATTTTGAAAAAATT
Found at i:79022 original size:19 final size:20
Alignment explanation
Indices: 78979--79023 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
78969 TACTATGCTG
78979 GAAATTAATGTTAGAATGTT
1 GAAATTAATGTTAGAATGTT
* *
78999 GAAATTGATGTTAGGATG-T
1 GAAATTAATGTTAGAATGTT
79018 GAAATT
1 GAAATT
79024 TGGCCACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (20 bp):
GAAATTAATGTTAGAATGTT
Found at i:82027 original size:24 final size:24
Alignment explanation
Indices: 82000--82061 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
81990 TCCTATTTGA
*
82000 ATTTTGTTCTGATACCTGACCTGG
1 ATTTTGTTCTGATACCTGACATGG
* *
82024 ATTTTGTTCTAATACCTGATATGG
1 ATTTTGTTCTGATACCTGACATGG
* *
82048 ATTCTGTTATGATA
1 ATTTTGTTCTGATA
82062 TATGATCTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.45
Consensus pattern (24 bp):
ATTTTGTTCTGATACCTGACATGG
Found at i:82067 original size:24 final size:24
Alignment explanation
Indices: 82040--82093 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
82030 TTCTAATACC
*
82040 TGATATGGATTCTGTTATGATATA
1 TGATATGAATTCTGTTATGATATA
* * * *
82064 TGATCTGAATTCTGTTTTGATTTT
1 TGATATGAATTCTGTTATGATATA
82088 TGATAT
1 TGATAT
82094 CTCCGTTTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.06, G:0.19, T:0.52
Consensus pattern (24 bp):
TGATATGAATTCTGTTATGATATA
Found at i:85594 original size:51 final size:47
Alignment explanation
Indices: 85490--85610 Score: 120
Period size: 51 Copynumber: 2.5 Consensus size: 47
85480 GTAACCATGC
*
85490 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAAAATA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTG---AAAATA
* * **
85540 ATAATAAGCTTATGAGCTTATGGAATTTAAATGGTAAGTATTTTG-GTA-A
1 A-AATAAGCTTATGAGCTTATGGAA--T-AATGGCAAGTATATTGAAAATA
85589 AAATAAGCTTATGAGCTTATGG
1 AAATAAGCTTATGAGCTTATGG
85611 GATGAAAGGT
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
48 21 0.34
49 2 0.03
50 2 0.03
51 22 0.35
53 1 0.02
54 14 0.23
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (47 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAATA
Found at i:88520 original size:17 final size:17
Alignment explanation
Indices: 88487--88560 Score: 82
Period size: 17 Copynumber: 4.3 Consensus size: 17
88477 ATAGAAAAAG
*
88487 AAAATGAAAACGAAGAAA
1 AAAATGAAAATG-AGAAA
88505 AAAATGAAAATGAGAAA
1 AAAATGAAAATGAGAAA
88522 GAAAA-G-AAATAGAGAAA
1 -AAAATGAAAAT-GAGAAA
88539 AAAATGAGAAATGA-AAA
1 AAAATGA-AAATGAGAAA
88556 AAAAT
1 AAAAT
88561 ATGCGAGACT
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
16 8 0.16
17 21 0.42
18 17 0.34
19 4 0.08
ACGTcount: A:0.72, C:0.01, G:0.18, T:0.09
Consensus pattern (17 bp):
AAAATGAAAATGAGAAA
Found at i:88551 original size:35 final size:35
Alignment explanation
Indices: 88482--88560 Score: 103
Period size: 34 Copynumber: 2.3 Consensus size: 35
88472 AAAAAATAGA
88482 AAAAGAAAATGAAAACGAAGAAAAAAATGAAAATG
1 AAAAGAAAATGAAAACGAAGAAAAAAATGAAAATG
88517 AGAAAGAAAA-GAAATA-G-AGAAAAAAATGAGAAATG
1 A-AAAGAAAATGAAA-ACGAAGAAAAAAATGA-AAATG
88552 AAAA-AAAAT
1 AAAAGAAAAT
88561 ATGCGAGACT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
33 4 0.10
34 15 0.38
35 12 0.30
36 9 0.22
ACGTcount: A:0.72, C:0.01, G:0.18, T:0.09
Consensus pattern (35 bp):
AAAAGAAAATGAAAACGAAGAAAAAAATGAAAATG
Found at i:92519 original size:51 final size:47
Alignment explanation
Indices: 92415--92535 Score: 120
Period size: 51 Copynumber: 2.5 Consensus size: 47
92405 GTAACCATGC
*
92415 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAAAATA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTG---AAAATA
* * **
92465 ATAATAAGCTTATGAGCTTATGGAATTTAAATGGTAAGTATTTTG-GTA-A
1 A-AATAAGCTTATGAGCTTATGGAA--T-AATGGCAAGTATATTGAAAATA
92514 AAATAAGCTTATGAGCTTATGG
1 AAATAAGCTTATGAGCTTATGG
92536 GATGAAAGGT
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
48 21 0.34
49 2 0.03
50 2 0.03
51 22 0.35
53 1 0.02
54 14 0.23
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (47 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAATA
Found at i:93735 original size:2 final size:2
Alignment explanation
Indices: 93723--93792 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
93713 CACTGGTTAT
93723 TA TA T- 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
93764 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 T
93793 GATGTTATTT
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 66 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:97396 original size:35 final size:33
Alignment explanation
Indices: 97372--97469 Score: 146
Period size: 33 Copynumber: 2.9 Consensus size: 33
97362 ATAATTTTTG
97372 AAAATATTTTGAAA-ATATAGTATATAGTTTTCAA
1 AAAATATTTTGAAATATATA-TATATAG-TTTCAA
97406 AAAATATTTTGAAATATATAT-TATAGTTTCAA
1 AAAATATTTTGAAATATATATATATAGTTTCAA
97438 AAAATATTTTTGAAATATATATTATATAGTTT
1 AAAATA-TTTTGAAATATATA-TATATAGTTT
97470 TTTAAAACGT
Statistics
Matches: 60, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
32 12 0.20
33 19 0.32
34 16 0.27
35 13 0.22
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (33 bp):
AAAATATTTTGAAATATATATATATAGTTTCAA
Found at i:97565 original size:34 final size:33
Alignment explanation
Indices: 97354--97708 Score: 134
Period size: 37 Copynumber: 10.3 Consensus size: 33
97344 TTTTATATAG
* *
97354 TAATATATATA-ATTTTTGAAAATATTTTGAAAA
1 TAATATATATATAGTTTT-AAAACATTTTGAAAA
* *
97387 T-ATA-GTATATAGTTTTCAAAAAATATTTTG-AAA
1 TAATATATATATAGTTTT---AAAACATTTTGAAAA
* *
97420 T-ATATAT-TATAGTTTCAAAAAATATTTTTG-AAA
1 TAATATATATATAGTTT--TAAAACA-TTTTGAAAA
*
97453 T-ATATATTATATAGTTTTTTAAAACGTTTTGAAAA
1 TAATATA-TATATAG--TTTTAAAACATTTTGAAAA
*
97488 CTTAA-ATACAATAATAAGTTTTAAAACATTTTGAAAA
1 --TAATATA-TAT-AT-AGTTTTAAAACATTTTGAAAA
* * *
97525 TTATATAGTATATAGTTTTGAAATCATTTT-CAAA
1 TAATATA-TATATAGTTTT-AAAACATTTTGAAAA
*
97559 T-A-ATATATATAGTTTTTAAAAAACATTTTTGGAAA
1 TAATATATATATAG-TTTT--AAAACA-TTTTGAAAA
*
97594 T-TTATATA-ATAGTTTTTTAAAAAAACATTTTGGAAAA
1 TAATATATATATAG--TTTT---AAAACATTTT-GAAAA
*
97631 CT--TATATA-ATATTTTTAAAATCATTTTTGAAAA
1 -TAATATATATATAGTTTTAAAA-CA-TTTTGAAAA
* *
97664 CT-ATATAATATATAGTTTTGAAAACGTTTTTAAATA
1 -TAATAT-ATATATAGTTTT-AAAACATTTTGAAA-A
97700 TAATATATA
1 TAATATATA
97709 GTTTAAAAAA
Statistics
Matches: 261, Mismatches: 25, Indels: 70
0.73 0.07 0.20
Matches are distributed among these distances:
31 11 0.04
32 25 0.10
33 45 0.17
34 39 0.15
35 51 0.20
36 32 0.12
37 52 0.20
38 4 0.02
39 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (33 bp):
TAATATATATATAGTTTTAAAACATTTTGAAAA
Found at i:97609 original size:35 final size:35
Alignment explanation
Indices: 97556--97673 Score: 136
Period size: 36 Copynumber: 3.4 Consensus size: 35
97546 AATCATTTTC
*
97556 AAATAATATATATAGTTTTTAAAAAACATTTTTGGA
1 AAATTATATA-ATAGTTTTTAAAAAACATTTTTGGA
*
97592 AATTTATATAATAGTTTTTTAAAAAAACA-TTTTGGA
1 AAATTATATAATAG-TTTTT-AAAAAACATTTTTGGA
*
97628 AAACTTATATAATA-TTTTT-AAAATCATTTTT-GA
1 AAA-TTATATAATAGTTTTTAAAAAACATTTTTGGA
*
97661 AAACTATATAATA
1 AAATTATATAATA
97674 TATAGTTTTG
Statistics
Matches: 73, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
32 9 0.12
33 11 0.15
34 4 0.05
35 9 0.12
36 22 0.30
37 18 0.25
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (35 bp):
AAATTATATAATAGTTTTTAAAAAACATTTTTGGA
Found at i:97636 original size:37 final size:35
Alignment explanation
Indices: 97561--97673 Score: 135
Period size: 37 Copynumber: 3.2 Consensus size: 35
97551 TTTTCAAATA
*
97561 ATATATATAGTTTTTAAAAAACATTTTTGG-AAATTT
1 ATATA-ATAGTTTTTAAAAAACA-TTTTGGAAAACTT
97597 ATATAATAGTTTTTTAAAAAAACATTTTGGAAAACTT
1 ATATAATAG-TTTTT-AAAAAACATTTTGGAAAACTT
* *
97634 ATATAATA-TTTTT-AAAATCATTTTTGAAAAC-T
1 ATATAATAGTTTTTAAAAAACATTTTGGAAAACTT
97666 ATATAATA
1 ATATAATA
97674 TATAGTTTTG
Statistics
Matches: 71, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
32 9 0.13
33 16 0.23
35 9 0.13
36 16 0.23
37 21 0.30
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (35 bp):
ATATAATAGTTTTTAAAAAACATTTTGGAAAACTT
Found at i:97700 original size:24 final size:23
Alignment explanation
Indices: 97642--97701 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
97632 TTATATAATA
*
97642 TTTTTAAA-ATCATTTTTGAAAAC
1 TTTTTAAATAT-AGTTTTGAAAAC
* *
97665 TATATAATATATAGTTTTGAAAAC
1 TTTTTAA-ATATAGTTTTGAAAAC
97689 GTTTTTAAATATA
1 -TTTTTAAATATA
97702 ATATATAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
23 5 0.17
24 17 0.59
25 7 0.24
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (23 bp):
TTTTTAAATATAGTTTTGAAAAC
Found at i:97725 original size:31 final size:31
Alignment explanation
Indices: 97666--97725 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
97656 TTTGAAAACT
** *
97666 ATATAATATATAGTTTTGAAAACGTTTTTAA
1 ATATAATATATAGTTTAAAAAACATTTTTAA
*
97697 ATATAATATATAGTTTAAAAAATATTTTT
1 ATATAATATATAGTTTAAAAAACATTTTT
97726 TTGAAACATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (31 bp):
ATATAATATATAGTTTAAAAAACATTTTTAA
Found at i:97728 original size:139 final size:133
Alignment explanation
Indices: 97359--97725 Score: 385
Period size: 139 Copynumber: 2.7 Consensus size: 133
97349 TATAGTAATA
* * *
97359 TATATAAT-TTTTGAAAAT-ATTTTG-AAA-ATATAGTATATAGTTTTCAAAAAATATTTTGAAA
1 TATATAATATTTTTAAAATCATTTTGAAAATATATAGTATATAGTTTTGAAAACAT-TTTT-AAA
*
97420 TAT-ATATTATAGTTTCAAAAAATATTTTT-GAAATATATATTATATAGTTTTTTAAAACGTTTT
64 TATAATA-TATAGTTT-AAAAAATATTTTTGGAAATATATATTATATAGTTTTTTAAAACATTTT
97483 GAAAACT
127 GAAAACT
* *
97490 TAAATACAATAATAAGTTTTAAAA-CATTTTGAAAATTATATAGTATATAGTTTTGAAATCATTT
1 T--AT---ATAAT-ATTTTTAAAATCATTTTGAAAA-TATATAGTATATAGTTTTGAAAACATTT
* * *
97554 TCAAATA-ATATATATAGTTTTTAAAAAACATTTTTGGAAATTTATA-TA-ATAGTTTTTTAAAA
59 TTAAATATA-ATATATAG--TTTAAAAAATATTTTTGGAAATATATATTATATAGTTTTTT---A
97616 AAACATTTTGGAAAACT
118 AAACATTTT-GAAAACT
* *
97633 TATATAATATTTTTAAAATCATTTTTGAAAACTATATAATATATAGTTTTGAAAACGTTTTTAAA
1 TATATAATATTTTTAAAATCA-TTTTGAAAA-TATATAGTATATAGTTTTGAAAACATTTTTAAA
97698 TATAATATATAGTTTAAAAAATATTTTT
64 TATAATATATAGTTTAAAAAATATTTTT
97726 TTGAAACATA
Statistics
Matches: 197, Mismatches: 16, Indels: 40
0.78 0.06 0.16
Matches are distributed among these distances:
131 1 0.01
133 2 0.01
136 5 0.03
137 24 0.12
138 20 0.10
139 71 0.36
140 21 0.11
141 36 0.18
142 9 0.05
143 8 0.04
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (133 bp):
TATATAATATTTTTAAAATCATTTTGAAAATATATAGTATATAGTTTTGAAAACATTTTTAAATA
TAATATATAGTTTAAAAAATATTTTTGGAAATATATATTATATAGTTTTTTAAAACATTTTGAAA
ACT
Found at i:97789 original size:8 final size:8
Alignment explanation
Indices: 97767--97798 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
97757 TTATTAATAT
97767 TTATTTTA
1 TTATTTTA
97775 TTTATTTTA
1 -TTATTTTA
97784 TTATTTTA
1 TTATTTTA
97792 TTATTTT
1 TTATTTT
97799 GTTTTGTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTATTTTA
Found at i:97789 original size:17 final size:16
Alignment explanation
Indices: 97767--97798 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
97757 TTATTAATAT
97767 TTATTTTATTTATTTTA
1 TTATTTTA-TTATTTTA
97784 TTATTTTATTATTTT
1 TTATTTTATTATTTT
97799 GTTTTGTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
TTATTTTATTATTTTA
Done.