Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008366.1 Hibiscus syriacus cultivar Beakdansim tig00111107_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: 85163
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:5821 original size:2 final size:2
Alignment explanation
Indices: 5809--5838 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5799 AGATCCTCCC
*
5809 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5839 CTTCTCTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9356 original size:17 final size:16
Alignment explanation
Indices: 9336--9468 Score: 76
Period size: 16 Copynumber: 7.9 Consensus size: 16
9326 GGAAAAAACG
9336 AAAAATGAAAAAATAAT
1 AAAAATGAAAAAA-AAT
9353 AAAAATGAGAAAAAGAA-
1 AAAAATGA-AAAAA-AAT
*
9370 AAAGAA-GAAAAGAAGAAAAGG
1 AAA-AATG--AA-AA-AAAA-T
*
9391 AAAAATGAGAAAAAAT
1 AAAAATGAAAAAAAAT
*
9407 AAAAATGAGAAAAAAT
1 AAAAATGAAAAAAAAT
* *
9423 AAAAATTTAAAAAAAAAG
1 AAAAA--TGAAAAAAAAT
* *
9441 AAAAAT--AAAAAGAG
1 AAAAATGAAAAAAAAT
9455 AAAAATGAAAAAAA
1 AAAAATGAAAAAAA
9469 GAAATAAAAG
Statistics
Matches: 95, Mismatches: 8, Indels: 27
0.73 0.06 0.21
Matches are distributed among these distances:
14 13 0.14
16 27 0.28
17 16 0.17
18 25 0.26
19 6 0.06
20 4 0.04
21 4 0.04
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.10
Consensus pattern (16 bp):
AAAAATGAAAAAAAAT
Found at i:9372 original size:16 final size:15
Alignment explanation
Indices: 9322--9472 Score: 64
Period size: 16 Copynumber: 9.6 Consensus size: 15
9312 AAGAAGAAAT
* *
9322 AAAAGGAAAAAACGA
1 AAAAAGAAAAAATGA
* *
9337 AAAATGAAAAAATAA
1 AAAAAGAAAAAATGA
9352 TAAAAATGAGAAAAA-G-
1 -AAAAA-GA-AAAAATGA
9368 AAAAAGAAGAAAA-GA
1 AAAAAGAA-AAAATGA
*
9383 AGAAAAGGAAAAATGA
1 A-AAAAGAAAAAATGA
9399 GAAAAA-ATAAAAATGA
1 -AAAAAGA-AAAAATGA
*
9415 GAAAAA-ATAAAAATTTA
1 -AAAAAGA-AAAAA-TGA
*
9432 AAAAA-AAAGAAA-AA
1 AAAAAGAAA-AAATGA
9446 TAAAAAGAGAAAAATGAA
1 -AAAAAGA-AAAAATG-A
9464 AAAAAGAAA
1 AAAAAGAAA
9473 TAAAAGGAGG
Statistics
Matches: 110, Mismatches: 10, Indels: 31
0.73 0.07 0.21
Matches are distributed among these distances:
13 1 0.01
14 8 0.07
15 29 0.26
16 52 0.47
17 14 0.13
18 6 0.05
ACGTcount: A:0.76, C:0.01, G:0.15, T:0.09
Consensus pattern (15 bp):
AAAAAGAAAAAATGA
Found at i:9380 original size:23 final size:23
Alignment explanation
Indices: 9360--9411 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
9350 AATAAAAATG
9360 AGAAAAAGAAAAA-GAAGAAAAGA
1 AGAAAAAGAAAAATG-AGAAAAGA
*
9383 AGAAAAGGAAAAATGAGAAAA-A
1 AGAAAAAGAAAAATGAGAAAAGA
*
9405 ATAAAAA
1 AGAAAAA
9412 TGAGAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 6 0.24
23 18 0.72
24 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (23 bp):
AGAAAAAGAAAAATGAGAAAAGA
Found at i:9460 original size:54 final size:54
Alignment explanation
Indices: 9311--9459 Score: 158
Period size: 55 Copynumber: 2.6 Consensus size: 54
9301 TATTTCGCTT
*
9311 AAAGAAGAAATAAAAGGAAAAAACGAAAAATGAAAAAATAATAAAAATGAGAAAAAGAA
1 AAAGAAGAAA-AAAA-G-AAAAA-GAAAAATGAGAAAA-AATAAAAATGAGAAAAAGAA
* * *
9370 AAAGAAGAAAAGAAGAAAAGGAAAAATGAGAAAAAATAAAAATGAGAAAAAATAA
1 AAAGAAGAAAAAAAGAAAAAGAAAAATGAGAAAAAATAAAAATGAG-AAAAAGAA
* *
9425 AAATTTAA-AAAAAAAGAAAAATAAAAA-GAGAAAAA
1 AAA--GAAGAAAAAAAGAAAAAGAAAAATGAGAAAAA
9460 TGAAAAAAAG
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
54 12 0.15
55 31 0.39
56 20 0.25
57 3 0.04
58 3 0.04
59 10 0.13
ACGTcount: A:0.76, C:0.01, G:0.15, T:0.09
Consensus pattern (54 bp):
AAAGAAGAAAAAAAGAAAAAGAAAAATGAGAAAAAATAAAAATGAGAAAAAGAA
Found at i:10850 original size:51 final size:51
Alignment explanation
Indices: 10789--11193 Score: 650
Period size: 51 Copynumber: 7.9 Consensus size: 51
10779 AAATTCGTTT
10789 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
10840 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
10891 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
10942 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
*
10993 GTTGAAGATTGAGTCCTATACTCTCTGAATG-ATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* *
11043 GTTGAAGATTGAGTCCTATATTCTCTGAAGGAATAGGGAGCGGACTAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * ** *
11094 GTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * *
11145 ATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGAC
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
11194 CCATTTTATT
Statistics
Matches: 334, Mismatches: 15, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
50 48 0.14
51 253 0.76
54 2 0.01
55 31 0.09
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:10915 original size:102 final size:102
Alignment explanation
Indices: 10789--11300 Score: 661
Period size: 102 Copynumber: 4.9 Consensus size: 102
10779 AAATTCGTTT
*
10789 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
10854 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
66 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
10891 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
*
10956 CCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
66 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
10993 GTTGAAGATTGAGTCCTATACTCTCTGAATG-ATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
* *
11057 CCTATATTCTCTGAAGGAATAGGGAGCGGACTAGTTC
66 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
* * ** **
11094 GTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
* * * * *
11159 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTT
62 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGA-CAAGTTC
* * * * * * *
11201 ATTAAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTT-TTATGAAGAT
1 GTTGAAGATTG----AGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGT-TGAAGA-
*
11265 TGTTCGAGTCTTATACT-TCCTGAAGGAATAGGGAGC
60 --TT-GAGTCCTATACTCT-CTGAAGGAATAGGGAGC
11301 AGGCTCGTCA
Statistics
Matches: 367, Mismatches: 31, Indels: 15
0.89 0.08 0.04
Matches are distributed among these distances:
101 96 0.26
102 154 0.42
105 2 0.01
106 31 0.08
107 13 0.04
110 2 0.01
111 69 0.19
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (102 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
Found at i:11152 original size:203 final size:206
Alignment explanation
Indices: 10789--11193 Score: 663
Period size: 203 Copynumber: 2.0 Consensus size: 206
10779 AAATTCGTTT
10789 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
*
10854 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGA
66 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCCCTGA
* * * *
10919 ATGAATAGGGAGCGGACAAGTTCGTTGAAGA-TT-GAGTCCTATACTCTCTGAATGAATAGGGAG
131 AAGAATAGGGAGCGGACAAGTTCATTGAAGATTTCGAGTCCTATACTCTCTGAAGGAATAGAGAG
10982 CGGACAAGTTC
196 CGGACAAGTTC
*
10993 GTTGAAGATTGAGTCCTATACTCTCTGAATG-ATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
1 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
* *
11057 CCTATATTCTCTGAAGGAATAGGGAGCGGACTAGTTCGTTGAAGATTGAGTCCTATACTCCCTGA
66 CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCCCTGA
** * *
11122 AAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAG
131 AAGAATAGGGAGCGGACAAGTTCATTGAAGA--TTTCGAGTCCTATACTCTCTGAAGGAATAGAG
11187 AGCGGAC
194 AGCGGAC
11194 CCATTTTATT
Statistics
Matches: 185, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
203 121 0.65
204 30 0.16
206 2 0.01
207 32 0.17
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (206 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGT
CCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCCCTGA
AAGAATAGGGAGCGGACAAGTTCATTGAAGATTTCGAGTCCTATACTCTCTGAAGGAATAGAGAG
CGGACAAGTTC
Found at i:11228 original size:56 final size:55
Alignment explanation
Indices: 10799--11300 Score: 243
Period size: 51 Copynumber: 9.6 Consensus size: 55
10789 GTTGAAGATT
* * *** **
10799 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCTTTTATTGAAGATTGTTC
* * *** **
10850 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCTTTTATTGAAGATTGTTC
* * * *** **
10901 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCTTTTATTGAAGATTGTTC
* * * *** **
10952 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCTTTTATTGAAGATTGTTC
* * * *** **
11003 GAGTCCTATACTCTCTGAATG-ATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCTTTTATTGAAGATTGTTC
* * * *** **
11053 GAGTCCTATATTCTCTGAAGGAATAGGGAGCGGACTAGTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCTTTTATTGAAGATTGTTC
* * * * *
11104 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGA-CCTGTTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCT-TTTATTGAAGATTGTTC
*
11159 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACCC-TTTTATTGAAGATTGTTC
* * * *
11215 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGAC-CCTTTTATTGAAGATTGTTC
*
11270 GAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGC
11301 AGGCTCGTCA
Statistics
Matches: 413, Mismatches: 26, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
50 48 0.12
51 241 0.58
54 3 0.01
55 66 0.16
56 52 0.13
57 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (55 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCTTTTATTGAAGATTGTTC
Found at i:11301 original size:55 final size:54
Alignment explanation
Indices: 11104--11302 Score: 215
Period size: 55 Copynumber: 3.6 Consensus size: 54
11094 GTTGAAGATT
* * * * * *
11104 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCT-TTTATTGAAGATTGTTC
* *
11159 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGA-CC-TTTTATTGAAGATTGTTC
* *
11215 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-C-TTTTATTGAAGATTGTTC
*
11270 GAGTCTTATACT-TCCTGAAGGAATAGGGAGCAG
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGCAG
11303 GCTCGTCATT
Statistics
Matches: 124, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
54 1 0.01
55 69 0.56
56 52 0.42
57 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (54 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCTTTTATTGAAGATTGTTC
Found at i:11317 original size:55 final size:55
Alignment explanation
Indices: 11105--11328 Score: 188
Period size: 55 Copynumber: 4.1 Consensus size: 55
11095 TTGAAGATTG
* * * * * * *
11105 AGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC-CTGT-TTATTGAAGATTTTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACAC-GTATTA-TGAAGATTGTTCA
* * * * *
11160 AGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATTAAAGATTGTTCA
1 AGTCT-TATACTCTCTGAAGGAATAGAGAGCAGACACGTATTA-TGAAGATTGTTCA
* * *
11216 AGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTATGAAGATTGTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTATTATGAAGATTGTTCA
* * * *
11271 AGTCTTATACT-TCCTGAAGGAATAGGGAGCAGGCTCGTCATT-TGAAGATTTTTCA
1 AGTCTTATACTCT-CTGAAGGAATAGAGAGCAGACACGT-ATTATGAAGATTGTTCA
11326 AGT
1 AGT
11329 ATTTATCCTG
Statistics
Matches: 142, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
54 1 0.01
55 87 0.61
56 53 0.37
57 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (55 bp):
AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTATTATGAAGATTGTTCA
Found at i:13681 original size:8 final size:8
Alignment explanation
Indices: 13668--13714 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
13658 AACCCGACCC
13668 GACCCGTT
1 GACCCGTT
13676 GACCC---
1 GACCCGTT
13681 GACCCGTT
1 GACCCGTT
13689 GA-CCGTT
1 GACCCGTT
13696 GACCCGTT
1 GACCCGTT
13704 GA-CCGTT
1 GACCCGTT
13711 GACC
1 GACC
13715 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:13681 original size:13 final size:13
Alignment explanation
Indices: 13663--13707 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
13653 GTCACAACCC
13663 GACCCGACCCGTT
1 GACCCGACCCGTT
13676 GACCCGACCCGTT
1 GACCCGACCCGTT
*
13689 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
13704 GACC
1 GACC
13708 GTTGACCGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.16, C:0.42, G:0.24, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:13696 original size:7 final size:7
Alignment explanation
Indices: 13684--13715 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
13674 TTGACCCGAC
13684 CCGTTGA
1 CCGTTGA
13691 CCGTTGA
1 CCGTTGA
13698 CCCGTTGA
1 -CCGTTGA
13706 CCGTTGA
1 CCGTTGA
13713 CCG
1 CCG
13716 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:13701 original size:15 final size:15
Alignment explanation
Indices: 13668--13714 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
13658 AACCCGACCC
*
13668 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
13681 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
13696 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
13711 GACC
1 GACC
13715 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:16271 original size:24 final size:24
Alignment explanation
Indices: 16175--16283 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
16165 GAATATTTTA
* *
16175 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
16199 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
16223 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTCTGT
*
16247 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
* *
16271 TTTGATTTCTGAT
1 TCTGATATCTGAT
16284 ATCTCCGTTT
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
23 1 0.02
24 64 0.97
25 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:19804 original size:14 final size:14
Alignment explanation
Indices: 19785--19821 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
19775 TCTTGTGGCA
19785 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
19799 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
19813 TTCTTCTTC
1 TT-TTCTTC
19822 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:20050 original size:24 final size:24
Alignment explanation
Indices: 20023--20069 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
20013 CAAAATCTGA
20023 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
20047 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
20070 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:20078 original size:24 final size:24
Alignment explanation
Indices: 20027--20078 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
20017 ATCTGAGTAT
** *
20027 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
20051 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
20075 TGAC
1 TGAC
20079 TAGTACTCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:20936 original size:20 final size:20
Alignment explanation
Indices: 20907--20974 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
20897 GAAATTCAGT
* * *
20907 GTTGCAATAGTCAGTATTGC
1 GTTGCGATAGTCAGAATCGC
20927 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
20947 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
20967 GTTGCGAT
1 GTTGCGAT
20975 TTACATATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:20986 original size:20 final size:20
Alignment explanation
Indices: 20963--21013 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
20953 ATAGTCAGAA
*
20963 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
20983 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* *
21003 CCACATTGCGA
1 TCGCATTGCGA
21014 ATTCGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:21036 original size:21 final size:21
Alignment explanation
Indices: 21010--21055 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
21000 TATCCACATT
21010 GCGAATTCGGAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
* * *
21031 GCGAATTTGGAAAATTGCAAT
1 GCGAATTCGGAAAATCGCAAC
21052 GCGA
1 GCGA
21056 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:21748 original size:2 final size:2
Alignment explanation
Indices: 21741--21775 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
21731 AAAAGAGGAC
21741 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21776 ATCGAACCCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25979 original size:44 final size:44
Alignment explanation
Indices: 25918--26001 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
25908 AAAAATCTGC
25918 CCCCCCAAAAGAAAACAAACAAACAAATAGTGACAGAAGATTTG
1 CCCCCCAAAAGAAAACAAACAAACAAATAGTGACAGAAGATTTG
*
25962 CCCCCCAAAAGAAAACAAACAAACAAATCGTGACAGAAGA
1 CCCCCCAAAAGAAAACAAACAAACAAATAGTGACAGAAGA
26002 AAGCCTAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.54, C:0.25, G:0.13, T:0.08
Consensus pattern (44 bp):
CCCCCCAAAAGAAAACAAACAAACAAATAGTGACAGAAGATTTG
Found at i:26729 original size:5 final size:5
Alignment explanation
Indices: 26719--26743 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
26709 TGCCATGAAA
26719 CATTT CATTT CATTT CATTT CATTT
1 CATTT CATTT CATTT CATTT CATTT
26744 AGCTTTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (5 bp):
CATTT
Found at i:39843 original size:28 final size:26
Alignment explanation
Indices: 39789--39844 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 26
39779 TCGTCCACCA
39789 ATATTATATTATATAATATATTTTTT
1 ATATTATATTATATAATATATTTTTT
39815 ATATTATAATGTATATAAT-TATTTATTT
1 ATATTAT-AT-TATATAATATATTT-TTT
39843 AT
1 AT
39845 TTGGGTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 7 0.26
27 7 0.26
28 13 0.48
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (26 bp):
ATATTATATTATATAATATATTTTTT
Found at i:39845 original size:26 final size:26
Alignment explanation
Indices: 39789--39845 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
39779 TCGTCCACCA
*
39789 ATATTATATTATATAATATATTTTTT
1 ATATTATATTATATAATATATTTATT
39815 ATATTATAATGTATATAAT-TATTTATT
1 ATATTAT-AT-TATATAATATATTTATT
39842 -TATT
1 ATATT
39846 TGGGTTACAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 11 0.39
27 9 0.32
28 8 0.29
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (26 bp):
ATATTATATTATATAATATATTTATT
Found at i:41118 original size:30 final size:30
Alignment explanation
Indices: 41072--41130 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
41062 AATTCTTTTA
41072 TTATTATTATTATTATTTTATTTGTTTATT
1 TTATTATTATTATTATTTTATTTGTTTATT
*
41102 TTATT-TTATTACTTATTTTTTTTGTTTAT
1 TTATTATTATTA-TTATTTTATTTGTTTAT
41131 ACACTATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (30 bp):
TTATTATTATTATTATTTTATTTGTTTATT
Found at i:41580 original size:21 final size:23
Alignment explanation
Indices: 41531--41594 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
41521 ATTATATATA
*
41531 TATATATATATATATTTATTCAT
1 TATATATATATATATTTACTCAT
* *
41554 TATATATATATGTTTTTACTCAT
1 TATATATATATATATTTACTCAT
*
41577 TATATATATCTATTATTT
1 TATATATATATA-TATTT
41595 TTATTTTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 30 0.88
24 4 0.12
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (23 bp):
TATATATATATATATTTACTCAT
Found at i:41584 original size:2 final size:2
Alignment explanation
Indices: 41519--41564 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
41509 ATTATTATTA
*
41519 AT AT -T AT AT AT AT AT AT AT AT AT AT AT TT AT -T CAT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
41559 AT AT AT
1 AT AT AT
41565 GTTTTTACTC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 3 0.08
2 34 0.89
3 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:41605 original size:11 final size:11
Alignment explanation
Indices: 41593--41621 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
41583 TATCTATTAT
41593 TTTTA-TTTTA
1 TTTTATTTTTA
41603 TTTTATTTTTA
1 TTTTATTTTTA
41614 TTTTATTT
1 TTTTATTT
41622 GTTGTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:41610 original size:16 final size:16
Alignment explanation
Indices: 41589--41621 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41579 TATATATCTA
41589 TTATTTTTATTTTATT
1 TTATTTTTATTTTATT
41605 TTATTTTTATTTTATT
1 TTATTTTTATTTTATT
41621 T
1 T
41622 GTTGTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTATTTTTATTTTATT
Found at i:41688 original size:18 final size:17
Alignment explanation
Indices: 41655--41707 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
41645 TTGGGTTGCT
41655 TTTTTCATTACTTTTTTTC
1 TTTTTC-TT-CTTTTTTTC
41674 TTTGTTCTTCTTTTTGTTC
1 TTT-TTCTTCTTTTT-TTC
*
41693 TTTTTGTTCTTTTTT
1 TTTTTCTTCTTTTTT
41708 ATTTTTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 1 0.03
18 16 0.52
19 11 0.35
20 3 0.10
ACGTcount: A:0.04, C:0.13, G:0.06, T:0.77
Consensus pattern (17 bp):
TTTTTCTTCTTTTTTTC
Found at i:41705 original size:8 final size:9
Alignment explanation
Indices: 41665--41706 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
41655 TTTTTCATTA
41665 CTTTTT-TT
1 CTTTTTGTT
*
41673 CTTTGTTCTT
1 CTTT-TTGTT
41683 CTTTTTGTT
1 CTTTTTGTT
41692 CTTTTTGTT
1 CTTTTTGTT
41701 CTTTTT
1 CTTTTT
41707 TATTTTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
8 4 0.13
9 21 0.68
10 6 0.19
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (9 bp):
CTTTTTGTT
Found at i:41713 original size:26 final size:27
Alignment explanation
Indices: 41684--41739 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
41674 TTTGTTCTTC
* *
41684 TTTTTGTTCTTTTTGTTCTT-TTT-TAT
1 TTTTTATTCATTTTGTT-TTATTTCTAT
41710 TTTTTATTCATTTTGTTTTATTTCTAT
1 TTTTTATTCATTTTGTTTTATTTCTAT
41737 TTT
1 TTT
41740 ACCATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 2 0.08
26 18 0.69
27 6 0.23
ACGTcount: A:0.09, C:0.07, G:0.05, T:0.79
Consensus pattern (27 bp):
TTTTTATTCATTTTGTTTTATTTCTAT
Found at i:41714 original size:18 final size:20
Alignment explanation
Indices: 41669--41714 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
41659 TCATTACTTT
*
41669 TTTTCTTTGTTCTTCTTTTTG
1 TTTT-TTTGTTCTTCTTTTTA
41690 TTCTTTTTGTTC-T-TTTTTA
1 TT-TTTTTGTTCTTCTTTTTA
41709 TTTTTT
1 TTTTTT
41715 ATTCATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 4 0.17
19 7 0.30
20 1 0.04
21 9 0.39
22 2 0.09
ACGTcount: A:0.02, C:0.11, G:0.07, T:0.80
Consensus pattern (20 bp):
TTTTTTTGTTCTTCTTTTTA
Found at i:44769 original size:2 final size:2
Alignment explanation
Indices: 44762--44787 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44752 TAAAACATTA
44762 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
44788 TAGCCATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46165 original size:57 final size:57
Alignment explanation
Indices: 46096--46211 Score: 205
Period size: 57 Copynumber: 2.0 Consensus size: 57
46086 TCCACTTATA
*
46096 CTTGTATTGTTGGTGGATATAGTGATTGTAGTGGAGCATGGTGGAAAAACGAGGTGT
1 CTTGTATTGTTGGTGGAGATAGTGATTGTAGTGGAGCATGGTGGAAAAACGAGGTGT
* *
46153 CTTGTATTGTTGGTGGAGATAGTGCTTGTAGTGGAGCATGGTGGAAAAATGAGGTGT
1 CTTGTATTGTTGGTGGAGATAGTGATTGTAGTGGAGCATGGTGGAAAAACGAGGTGT
46210 CT
1 CT
46212 ACATCTGCCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.23, C:0.06, G:0.37, T:0.34
Consensus pattern (57 bp):
CTTGTATTGTTGGTGGAGATAGTGATTGTAGTGGAGCATGGTGGAAAAACGAGGTGT
Found at i:46588 original size:134 final size:134
Alignment explanation
Indices: 46417--47013 Score: 901
Period size: 134 Copynumber: 4.5 Consensus size: 134
46407 ATCTGTTCTG
* * *
46417 CTTCTTCTGAAGGGAGTATCAGATCTGGATGAGTTGATCAATTCCGCTGTCACTCAGGGAAGATT
1 CTTCTTCTGAAGGGAATATCAGATCTGAATGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATT
* *
46482 GAATCGTGGTAGACTTGTTCCGCTGTCACTTAGGGAATATCAAATCTTGAAAGAGAATGATCTAT
66 GAATCGTGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAATGATATAT
*
46547 TCCT
131 TCCA
* *
46551 CCTCTTCTGAAGGAAATATCAGATCTGAATGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATT
1 CTTCTTCTGAAGGGAATATCAGATCTGAATGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATT
* * * * * *
46616 GAATCGTGGTAGACTTGCTCTGTTGTTACTCAGGGAATATCAAATCTTGAAAGAGAATAATATGT
66 GAATCGTGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAATGATATAT
46681 TCCA
131 TCCA
* *
46685 CTTCTTCTAAAGGGAATATCAAATCT-AGATGAGTTGATCCATTCCGCTGTCACTCAGGGAAGAT
1 CTTCTTCTGAAGGGAATATCAGATCTGA-ATGAGTTGATCCATTCCGCTGTCACTCAGGGAAGAT
* * * * *
46749 TGAATCGTGGTAGACTTATTCCGCTGTCACTCAGGGAATATTAAATCTTGAAAGAGAGTGATCTG
65 TGAATCGTGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAATGATATA
46814 TTCCA
130 TTCCA
*
46819 CTTCTTCTGAAGGGAATATCAGAT-TTAGATGAGTTGATCCATTCCGCTGTCACTCAGGGAAGAT
1 CTTCTTCTGAAGGGAATATCAGATCTGA-ATGAGTTGATCCATTCCGCTGTCACTCAGGGAAGAT
* *
46883 TGAATCGTGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCCAATCTTGAAAGAGAGTGATATA
65 TGAATCGTGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAATGATATA
*
46948 TTTCA
130 TTCCA
* * * *
46953 CTTCTTCTGAAGGGAATATCAGATCTGGATGAGATGATCCATTCTGTTGTCACTCAGGGAA
1 CTTCTTCTGAAGGGAATATCAGATCTGAATGAGTTGATCCATTCCGCTGTCACTCAGGGAA
47014 TATCAAATCT
Statistics
Matches: 420, Mismatches: 40, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
133 2 0.00
134 417 0.99
135 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (134 bp):
CTTCTTCTGAAGGGAATATCAGATCTGAATGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATT
GAATCGTGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAATGATATAT
TCCA
Found at i:46971 original size:48 final size:47
Alignment explanation
Indices: 46915--47065 Score: 125
Period size: 48 Copynumber: 3.2 Consensus size: 47
46905 GCTGTCACTC
46915 AGGGAATATCCAATCTTGAAAGAGAGTGATATATTTCACTTCTTCTGA
1 AGGGAATATCCAATCTTGAAAGAGAGTGAT-TATTTCACTTCTTCTGA
* * * ** * * *
46963 AGGGAATAT-CAGATC-TGGATGAGA-TGATCCA-TTCTGTTGTCACT-C
1 AGGGAATATCCA-ATCTTGAAAGAGAGTGAT-TATTTCACTTCT-TCTGA
*
47008 AGGGAATATCAAATCTTGAAAGAGAGTGATT-TGTTCTACTTCTTCTGA
1 AGGGAATATCCAATCTTGAAAGAGAGTGATTAT-TTC-ACTTCTTCTGA
47056 AGGGAATATC
1 AGGGAATATC
47066 ATATAGATGG
Statistics
Matches: 76, Mismatches: 18, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
45 18 0.24
46 15 0.20
47 18 0.24
48 25 0.33
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (47 bp):
AGGGAATATCCAATCTTGAAAGAGAGTGATTATTTCACTTCTTCTGA
Found at i:47164 original size:19 final size:19
Alignment explanation
Indices: 47140--47205 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 19
47130 TCAGTGAAGG
47140 CTTAATATGGCCCGGAGGA
1 CTTAATATGGCCCGGAGGA
*
47159 CTTAATCGTCAT-GCTCGGAAGG-
1 CTTAA---T-ATGGCCCGG-AGGA
*
47181 CTTAAGATGGCCCGGAGGA
1 CTTAATATGGCCCGGAGGA
47200 CTTAAT
1 CTTAAT
47206 CGTCATGCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
18 5 0.14
19 15 0.42
22 11 0.31
23 5 0.14
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (19 bp):
CTTAATATGGCCCGGAGGA
Found at i:47184 original size:22 final size:22
Alignment explanation
Indices: 47159--47225 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
47149 GCCCGGAGGA
47159 CTTAATCGTCATGCTCGGAAGG
1 CTTAATCGTCATGCTCGGAAGG
*
47181 CTTAA--G--ATGGCCCGG-AGG
1 CTTAATCGTCAT-GCTCGGAAGG
47199 ACTTAATCGTCATGCTCGGAAGG
1 -CTTAATCGTCATGCTCGGAAGG
47222 CTTA
1 CTTA
47226 CTGATGAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
18 5 0.14
19 10 0.28
20 1 0.03
21 1 0.03
22 14 0.39
23 5 0.14
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (22 bp):
CTTAATCGTCATGCTCGGAAGG
Found at i:47192 original size:41 final size:41
Alignment explanation
Indices: 47135--47225 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
47125 ACTCTTCAGT
*
47135 GAAGGCTTAATATGGCCCGGAGGACTTAATCGTCATGCTCG
1 GAAGGCTTAAGATGGCCCGGAGGACTTAATCGTCATGCTCG
47176 GAAGGCTTAAGATGGCCCGGAGGACTTAATCGTCATGCTCG
1 GAAGGCTTAAGATGGCCCGGAGGACTTAATCGTCATGCTCG
47217 GAAGGCTTA
1 GAAGGCTTA
47226 CTGATGAATT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (41 bp):
GAAGGCTTAAGATGGCCCGGAGGACTTAATCGTCATGCTCG
Found at i:47273 original size:79 final size:79
Alignment explanation
Indices: 47176--47346 Score: 297
Period size: 79 Copynumber: 2.2 Consensus size: 79
47166 GTCATGCTCG
* *
47176 GAAGGCTTAAGATGGCCCGGAGGACTTAATCGTCATGCTCGGAAGGCTTACTGATGAATTTGCTT
1 GAAGGCTTAAGATGGCCCGGAGAACTTAATCGTCATGCTCGGAAGGCCTACTGATGAATTTGCTT
47241 CACTACTCTTCGGT
66 CACTACTCTTCGGT
* * *
47255 GAAGGCTTAAGATGGCCCGGAGAACTTAATCGTCATGCTTGGAAGGCCTACTGATGGATTTGTTT
1 GAAGGCTTAAGATGGCCCGGAGAACTTAATCGTCATGCTCGGAAGGCCTACTGATGAATTTGCTT
47320 CACTACTCTTCGGT
66 CACTACTCTTCGGT
47334 GAAGGCTTAAGAT
1 GAAGGCTTAAGAT
47347 AGATTTGCTT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 87 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (79 bp):
GAAGGCTTAAGATGGCCCGGAGAACTTAATCGTCATGCTCGGAAGGCCTACTGATGAATTTGCTT
CACTACTCTTCGGT
Found at i:47339 original size:38 final size:37
Alignment explanation
Indices: 47296--47383 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
47286 GTCATGCTTG
* * *
47296 GAAGGCCTACTGATGGATTTGTTTCACTACTCTTCGGT
1 GAAGGCCTA-AGATAGATTTGCTTCACTACTCTTCGGT
*
47334 GAAGGCTTAAGATAGATTTGCTTCACTACTCTTCGGT
1 GAAGGCCTAAGATAGATTTGCTTCACTACTCTTCGGT
*
47371 GAAGGCTTAAGAT
1 GAAGGCCTAAGAT
47384 GGCCCGAAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
37 38 0.83
38 8 0.17
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (37 bp):
GAAGGCCTAAGATAGATTTGCTTCACTACTCTTCGGT
Found at i:47353 original size:37 final size:37
Alignment explanation
Indices: 47311--47383 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
47301 CCTACTGATG
*
47311 GATTTGTTTCACTACTCTTCGGTGAAGGCTTAAGATA
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATA
47348 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
47384 GGCCCGAAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (37 bp):
GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATA
Found at i:47384 original size:116 final size:116
Alignment explanation
Indices: 47071--47464 Score: 443
Period size: 116 Copynumber: 3.4 Consensus size: 116
47061 ATATCATATA
* * * * *
47071 GATGGATTTGCTTCACTATTCTTCCGTGAAGGCTTATGATTGATTTGCTTCACTACTCTTCAGTG
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGATTTGCTTCACTACTCTTCGGTG
* * * * * *
47136 AAGGCTTAATATGGCCCGGAGGACTTAATCGTCATGCTCGGAAGGCTTA-A
66 AAGGCTTAAGATGGCCCGAAGAACTTAATCGTCATGCTCAGAAGGCCTACT
*** **** * * * *
47186 GATGG-CCCGGAGGACTTAATCGTCATGCTCGGAAGGCTTACTGAT-GAATTTGCTTCACTACTC
1 GATGGATTTGCTTCAC-TACTCTTC--GGT--GAAGGCTTA-AGATAG-ATTTGCTTCACTACTC
* **
47249 TTCGGTGAAGGCTTAAGATGGCCCGGAGAACTTAATCGTCATGCTTGGAAGGCCTACT
59 TTCGGTGAAGGCTTAAGATGGCCCGAAGAACTTAATCGTCATGCTCAGAAGGCCTACT
*
47307 GATGGATTTGTTTCACTACTCTTCGGTGAAGGCTTAAGATAGATTTGCTTCACTACTCTTCGGTG
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGATTTGCTTCACTACTCTTCGGTG
* * *
47372 AAGGCTTAAGATGGCCCGAAGGACTTAATCGTCATGCTCATAAGGCTTACT
66 AAGGCTTAAGATGGCCCGAAGAACTTAATCGTCATGCTCAGAAGGCCTACT
47423 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAG
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAG
47465 CCCGGATGAC
Statistics
Matches: 234, Mismatches: 35, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
114 3 0.01
115 11 0.05
116 112 0.48
117 11 0.05
119 12 0.05
120 71 0.30
121 11 0.05
122 3 0.01
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.31
Consensus pattern (116 bp):
GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGATTTGCTTCACTACTCTTCGGTG
AAGGCTTAAGATGGCCCGAAGAACTTAATCGTCATGCTCAGAAGGCCTACT
Found at i:47435 original size:79 final size:79
Alignment explanation
Indices: 47334--47510 Score: 275
Period size: 79 Copynumber: 2.3 Consensus size: 79
47324 ACTCTTCGGT
* * *
47334 GAAGGCTTA-AGATAGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGCCCGAAGGACTT
1 GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGCCCGAAGGACTT
*
47398 AATCGTCATGCTCA
66 AATCATCATGCTCA
* * *
47412 TAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGCCCGGATGACTT
1 GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGCCCGAAGGACTT
47477 AATCATCATGCTCA
66 AATCATCATGCTCA
*
47491 GAAGGCTTACTAATGGATTT
1 GAAGGCTTACTGATGGATTT
47511 AATCATCATG
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
78 8 0.09
79 81 0.91
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Consensus pattern (79 bp):
GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGCCCGAAGGACTT
AATCATCATGCTCA
Found at i:54416 original size:2 final size:2
Alignment explanation
Indices: 54411--54450 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
54401 ACATACACAC
*
54411 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54451 TAGCCATGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:54552 original size:17 final size:18
Alignment explanation
Indices: 54508--54552 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
54498 TTAAACATTC
54508 ATACATAAAAATAATATA
1 ATACATAAAAATAATATA
54526 AT-CAT-AAAAT-ATA-A
1 ATACATAAAAATAATATA
54540 ATACATAAGAAAT
1 ATACATAA-AAAT
54553 TTTACTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 3 0.12
15 6 0.25
16 6 0.25
17 7 0.29
18 2 0.08
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (18 bp):
ATACATAAAAATAATATA
Found at i:54735 original size:2 final size:2
Alignment explanation
Indices: 54683--54716 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
54673 TTTTATTTAT
54683 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
54717 CCCACATACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55137 original size:2 final size:2
Alignment explanation
Indices: 55130--55159 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
55120 TTTTGTGGAT
55130 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
55160 CTATTATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55802 original size:24 final size:24
Alignment explanation
Indices: 55775--55861 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
55765 TCCACTTATA
55775 CTTGTATTGTTGGTGGAGATAGTG
1 CTTGTATTGTTGGTGGAGATAGTG
* * *
55799 CTTGTAGTGGAGCATGGTGGAAAAATGAGGTG
1 CTTGTA-T--TG-TTGGTGG--AGAT-A-GTG
55831 TCTTGTATTGTTGGTGGAGATAGTG
1 -CTTGTATTGTTGGTGGAGATAGTG
55856 CTTGTA
1 CTTGTA
55862 GTGGAGCATG
Statistics
Matches: 48, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
24 12 0.25
25 4 0.08
26 1 0.02
27 4 0.08
28 6 0.12
29 6 0.12
30 4 0.08
31 1 0.02
32 4 0.08
33 6 0.12
ACGTcount: A:0.21, C:0.06, G:0.37, T:0.37
Consensus pattern (24 bp):
CTTGTATTGTTGGTGGAGATAGTG
Found at i:55817 original size:28 final size:28
Alignment explanation
Indices: 55785--55876 Score: 84
Period size: 28 Copynumber: 3.2 Consensus size: 28
55775 CTTGTATTGT
55785 TGGTGGAGATAGTGCTTGTAGTGGAGCA
1 TGGTGGAGATAGTGCTTGTAGTGGAGCA
* * *
55813 TGGTGGAAAAATGAGGTGTCTTGTA-T--TG-T
1 TGGTGG--AGAT-A-GTG-CTTGTAGTGGAGCA
55842 TGGTGGAGATAGTGCTTGTAGTGGAGCA
1 TGGTGGAGATAGTGCTTGTAGTGGAGCA
55870 TGGTGGA
1 TGGTGGA
55877 AAAATGAGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
24 6 0.12
25 4 0.08
26 1 0.02
27 4 0.08
28 13 0.27
29 6 0.12
30 4 0.08
31 1 0.02
32 4 0.08
33 6 0.12
ACGTcount: A:0.22, C:0.05, G:0.41, T:0.32
Consensus pattern (28 bp):
TGGTGGAGATAGTGCTTGTAGTGGAGCA
Found at i:55839 original size:57 final size:57
Alignment explanation
Indices: 55775--55886 Score: 224
Period size: 57 Copynumber: 2.0 Consensus size: 57
55765 TCCACTTATA
55775 CTTGTATTGTTGGTGGAGATAGTGCTTGTAGTGGAGCATGGTGGAAAAATGAGGTGT
1 CTTGTATTGTTGGTGGAGATAGTGCTTGTAGTGGAGCATGGTGGAAAAATGAGGTGT
55832 CTTGTATTGTTGGTGGAGATAGTGCTTGTAGTGGAGCATGGTGGAAAAATGAGGT
1 CTTGTATTGTTGGTGGAGATAGTGCTTGTAGTGGAGCATGGTGGAAAAATGAGGT
55887 ATCTACAAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.23, C:0.05, G:0.38, T:0.33
Consensus pattern (57 bp):
CTTGTATTGTTGGTGGAGATAGTGCTTGTAGTGGAGCATGGTGGAAAAATGAGGTGT
Found at i:57908 original size:21 final size:21
Alignment explanation
Indices: 57882--57923 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
57872 CAATTATGTA
57882 TCGATGCACCGCTAAAGTGCT
1 TCGATGCACCGCTAAAGTGCT
* *
57903 TCGATGCACTGCTACAGTGCT
1 TCGATGCACCGCTAAAGTGCT
57924 GCTACAGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (21 bp):
TCGATGCACCGCTAAAGTGCT
Found at i:58657 original size:31 final size:32
Alignment explanation
Indices: 58591--58715 Score: 96
Period size: 31 Copynumber: 4.0 Consensus size: 32
58581 AACCTCAGCA
* * * *
58591 ACTGTCCATA-GGTCCCGATGAACCTAGGTAA-
1 ACTGTCCATATGTTCCCTA-GAACATATGTAAT
*
58622 ACTGTCCATATGTTCCTTAGAACATATGT-AT
1 ACTGTCCATATGTTCCCTAGAACATATGTAAT
* *
58653 ACTGTCCATATG-TCCCGAAAGACATATGTAAT
1 ACTGTCCATATGTTCCCTAGA-ACATATGTAAT
* * * * *
58685 TCTGCCCATATGTTCCGTAGAATATAAGTAA
1 ACTGTCCATATGTTCCCTAGAACATATGTAA
58716 ACCCTCGACT
Statistics
Matches: 74, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
30 6 0.08
31 38 0.51
32 25 0.34
33 5 0.07
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (32 bp):
ACTGTCCATATGTTCCCTAGAACATATGTAAT
Found at i:67983 original size:3 final size:3
Alignment explanation
Indices: 67975--68015 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
67965 CATCTCGTTC
*
67975 TTA TTA TTA TTA -TA TGTA TTA TTA TTA TTA TTA ATA TTA TT
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT
68016 TTACATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:68023 original size:12 final size:12
Alignment explanation
Indices: 67975--68024 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
67965 CATCTCGTTC
*
67975 TTATTATTATTA
1 TTATTATTAATA
*
67987 -TATGTATTATTA
1 TTAT-TATTAATA
67999 TTATTATTAATA
1 TTATTATTAATA
68011 TTATT-TTACATA
1 TTATTATTA-ATA
68023 TT
1 TT
68025 TGGCAGGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
11 6 0.18
12 25 0.74
13 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:80945 original size:27 final size:27
Alignment explanation
Indices: 80903--80965 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
80893 GTATTTCGCT
80903 TGAAAAAAAAATGAAAAAGACAA-AAAA
1 TGAAAAAAAAATGAAAAAGA-AAGAAAA
*
80930 TGAAAAATAAAA-GAAAGAGAAAGAAAA
1 TGAAAAA-AAAATGAAAAAGAAAGAAAA
80957 -GAAAAAAAA
1 TGAAAAAAAA
80966 TAAAAGGAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 3 0.09
26 8 0.24
27 18 0.55
28 4 0.12
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06
Consensus pattern (27 bp):
TGAAAAAAAAATGAAAAAGAAAGAAAA
Found at i:82077 original size:48 final size:48
Alignment explanation
Indices: 82001--82480 Score: 544
Period size: 48 Copynumber: 10.3 Consensus size: 48
81991 TAACTCCCCC
*
82001 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* * *
82049 AGATTTGATATTCCCTTTAGAGTAAGTGGAACAAG----TC-T-GCC-
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* * *
82090 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
** *
82138 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* * * *
82186 AGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
** *
82234 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* * *
82282 AGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* *
82330 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAG----TC-T-ACC-
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* * *
82371 AGATCTGACATTCCCTTCAGAGTAAGTGGAACAGGTCTCT-TTTTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
* * ** *
82418 TGATTTGATATTCCCTTCAGAAG-AAGCGGAACATATCTCT-TTTTCCA
1 AGATTTGATATTCCCTTCAG-AGTAAGTGGAACAGGTCTCTCTTCTCCA
* *
82465 AGGTTTGGTATTCCCT
1 AGATTTGATATTCCCT
82481 GTGACAGCGG
Statistics
Matches: 363, Mismatches: 54, Indels: 31
0.81 0.12 0.07
Matches are distributed among these distances:
41 63 0.17
42 4 0.01
43 2 0.01
44 4 0.01
45 4 0.01
46 3 0.01
47 52 0.14
48 231 0.64
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (48 bp):
AGATTTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
Found at i:82224 original size:96 final size:93
Alignment explanation
Indices: 81999--82455 Score: 646
Period size: 96 Copynumber: 4.9 Consensus size: 93
81989 CTTAACTCCC
*
81999 CCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
* * *
82064 TTTAGAGTAAGTGGAAC-AA---GTCTG
66 TTCAGAGTAAGTGGAACAAATCTATCTT
*
82088 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
82153 TTCAGAGTAAGTGGAACAAATCTATCTTCT
66 TTCAGAGTAAGTGGAACAAATCTATC-T-T
* *
82183 CCAAGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCC
1 CC-AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCC
82248 CTTCAGAGTAAGTGGAACAAATCTATCTTCT
65 CTTCAGAGTAAGTGGAACAAATCTATC-T-T
*
82279 CCAAGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCC
1 CC-AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCC
*
82344 CTTCAGAGTAAGTGGAACAAGTCTA----
65 CTTCAGAGTAAGTGGAACAAATCTATCTT
* * * *
82369 CCAGATCTGACATTCCCTTCAGAGTAAGTGGAACAGGTCTCT-TTTTCCATGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
* *
82433 TTCAGAAG-AAGCGGAACATATCT
66 TTCAG-AGTAAGTGGAACAAATCT
82456 CTTTTTCCAA
Statistics
Matches: 344, Mismatches: 16, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
88 37 0.11
89 118 0.34
90 4 0.01
93 2 0.01
94 1 0.00
95 2 0.01
96 180 0.52
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (93 bp):
CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
TTCAGAGTAAGTGGAACAAATCTATCTT
Found at i:82723 original size:3 final size:3
Alignment explanation
Indices: 82715--82754 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
82705 CATCTCGTTC
82715 TTA TTA TTA TTA -TA TGTA TTA TTA TTA TTA TTA -TA TTA TT
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT
82755 TTACATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 27 0.79
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:82741 original size:21 final size:20
Alignment explanation
Indices: 82715--82754 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
82705 CATCTCGTTC
82715 TTATTATTATTATATGTATTA
1 TTATTATTATTATAT-TATTA
82736 TTATTATTATTATATTATT
1 TTATTATTATTATATTATT
82755 TTACATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (20 bp):
TTATTATTATTATATTATTA
Done.