Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003934.1 Hibiscus syriacus cultivar Beakdansim tig00008504_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: 118641
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:5532 original size:120 final size:120
Alignment explanation
Indices: 5314--5771 Score: 436
Period size: 120 Copynumber: 3.8 Consensus size: 120
5304 GTATGATCCG
* * * ** * *
5314 GATGAAAGTGACGACTTGCCTTCAAACCCCGATGGTGTCACCGGAGGGTGCAGCGAACCGGTTGA
1 GATGAAAGTGCCGACTTGCCTTTAAGCCCCGATGGCATCACCGGAAGGTGCAGCGAACCGGCTGA
* * * * *
5379 GAAGCAGCTCATCGAAACCGATGTAAATGCAGATAAGCCGATTAGCCCCAAAATC
66 GAAGCAGCTCATTGAAACCGATGTAAATTCAGATGAGTCGATTAGCCCCGAAATC
* * * *
5434 GATGGAAGTGCCGCCTTGCCTTTAAGCCCCGATGGCCTCACCGGAGGGTGCAGCGAACCGGCTGA
1 GATGAAAGTGCCGACTTGCCTTTAAGCCCCGATGGCATCACCGGAAGGTGCAGCGAACCGGCTGA
*
5499 GAAGCAGCTCATTGAAACCGATGTAAATTCAGATGAGTCTATTA-CGCCCGAAATC
66 GAAGCAGCTCATTGAAACCGATGTAAATTCAGATGAGTCGATTAGC-CCCGAAATC
* ** * *** * * * *
5554 GATAAAAGTACTGTTGACTTG-CTTTTAGAATTCGCTGACATCATCGGAAGGTGCAGCGAACCTG
1 GATGAAAG---TGCCGACTTGCCTTTAAG-CCCCGATGGCATCACCGGAAGGTGCAGCGAACCGG
* * * * *
5618 CTGAGAAGCGGCTCATTGAAACCGTTGTAAATTCAGATGAGTTGATTGGCGCCGAAATC
62 CTGAGAAGCAGCTCATTGAAACCGATGTAAATTCAGATGAGTCGATTAGCCCCGAAATC
* * * * ** **
5677 GATGGAAGTGCCAAGTTGCCTTTAATCCCCGATGGCATCATTGGAAGGTGCAGCGAACTC-TTTG
1 GATGAAAGTGCCGACTTGCCTTTAAGCCCCGATGGCATCACCGGAAGGTGCAGCGAAC-CGGCTG
* * * *
5741 GGAAGCAGCTAATTGAAACCGACGTGAATTC
65 AGAAGCAGCTCATTGAAACCGATGTAAATTC
5772 GAAGCAATGC
Statistics
Matches: 273, Mismatches: 57, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
119 1 0.00
120 169 0.62
121 6 0.02
122 6 0.02
123 90 0.33
124 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (120 bp):
GATGAAAGTGCCGACTTGCCTTTAAGCCCCGATGGCATCACCGGAAGGTGCAGCGAACCGGCTGA
GAAGCAGCTCATTGAAACCGATGTAAATTCAGATGAGTCGATTAGCCCCGAAATC
Found at i:12500 original size:33 final size:33
Alignment explanation
Indices: 12455--12553 Score: 139
Period size: 33 Copynumber: 3.1 Consensus size: 33
12445 AGTTGGCAAG
* *
12455 TTGAAAATTTCATCTTGGTTGGTGCCCAACTTA
1 TTGAAAAATTCATCTTGGTTGGTGGCCAACTTA
12488 TTGAAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGAAAAATTCATCTTGGTTGGTGGCCAACTTA
* * *
12521 TTGGAAAATTC-T-TTAGTAGGTGGCCAACTTA
1 TTGAAAAATTCATCTTGGTTGGTGGCCAACTTA
12552 TT
1 TT
12554 TTTCATGTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 19 0.31
32 1 0.02
33 41 0.67
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.38
Consensus pattern (33 bp):
TTGAAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:16385 original size:120 final size:120
Alignment explanation
Indices: 16157--16468 Score: 421
Period size: 120 Copynumber: 2.6 Consensus size: 120
16147 AAAATGATGA
* * * *
16157 CTTGCCTTTAAGCCCCGATGGCGTCACCTGGGGTTGCAGCGAACCGGTTGAGAAGCAGCTCGTTG
1 CTTGCCTGTAACCCCCGATGGCGTCACCTGGGGGTGCAGCGAACCGGTTGAGAAGCAGCTCATTG
16222 AAACCGATGTAAATTCAGATAAGCCGATTAGCCCCATAATCGATGGAAGTGCCAC
66 AAACCGATGTAAATTCAGATAAGCCGATTAGCCCCATAATCGATGGAAGTGCCAC
* ** *
16277 CTTTCCTGTAAGTCTCGATGGCGTCACCTGGGGGTGCAGCGAACCGGTTGAGAAGCAGCTCATTG
1 CTTGCCTGTAACCCCCGATGGCGTCACCTGGGGGTGCAGCGAACCGGTTGAGAAGCAGCTCATTG
* * *
16342 AAACCGATGTAAATTCAGATAAGCCGATTAGCCTCGA-GATCGATGGAAGTGCCGC
66 AAACCGATGTAAATTCAGATAAGCCGATTAGCC-CCATAATCGATGGAAGTGCCAC
* * * * * ** *
16397 CTTGCCTTTAACCCCCGATGACATCATC-GGAAGGTGCAGCGAACCCTTTGAGAAGCAGCTCACT
1 CTTGCCTGTAACCCCCGATGGCGTCACCTGG-GGGTGCAGCGAACCGGTTGAGAAGCAGCTCATT
16461 GAAACCGA
65 GAAACCGA
16469 CGTGAATGTG
Statistics
Matches: 169, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
119 2 0.01
120 165 0.98
121 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.21
Consensus pattern (120 bp):
CTTGCCTGTAACCCCCGATGGCGTCACCTGGGGGTGCAGCGAACCGGTTGAGAAGCAGCTCATTG
AAACCGATGTAAATTCAGATAAGCCGATTAGCCCCATAATCGATGGAAGTGCCAC
Found at i:24416 original size:6 final size:6
Alignment explanation
Indices: 24407--24441 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
24397 TGAAGAAGGA
24407 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGA
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGA
24442 AGGTCAACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:26571 original size:2 final size:2
Alignment explanation
Indices: 26564--26601 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
26554 AGAACATTGA
26564 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26602 GAGGCAGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28030 original size:2 final size:2
Alignment explanation
Indices: 28023--28049 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28013 TTGCTCAAGT
28023 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 T
28050 GAATTGCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29885 original size:23 final size:23
Alignment explanation
Indices: 29859--29909 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
29849 TTGTTTCATT
29859 TTAGTATCCCGCCGTTAAAAAAA
1 TTAGTATCCCGCCGTTAAAAAAA
* **
29882 TTAGTTTTTCGCCGTTAAAAAAA
1 TTAGTATCCCGCCGTTAAAAAAA
29905 TTAGT
1 TTAGT
29910 TTTTGTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (23 bp):
TTAGTATCCCGCCGTTAAAAAAA
Found at i:29912 original size:22 final size:23
Alignment explanation
Indices: 29868--29913 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
29858 TTTAGTATCC
29868 CGCCGTTAAAAAAATTAGTTTTT
1 CGCCGTTAAAAAAATTAGTTTTT
29891 CGCCGTTAAAAAAATTAGTTTTT
1 CGCCGTTAAAAAAATTAGTTTTT
29914 GTTTCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (23 bp):
CGCCGTTAAAAAAATTAGTTTTT
Found at i:32323 original size:49 final size:49
Alignment explanation
Indices: 32227--32323 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 49
32217 GTGTATGTGT
* **
32227 ATAATATATGATCTTGACATATAACAATTAAATAAATATAATTTTTGAA
1 ATAATATATGATCTTCACATATAACAATTAAATAAATATAAAATTTGAA
* * *
32276 ATAATATTTGCTCTTCACGTATAACAATTAAATAAATATAAAATTTGA
1 ATAATATATGATCTTCACATATAACAATTAAATAAATATAAAATTTGA
32324 TTCTTGGGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.38
Consensus pattern (49 bp):
ATAATATATGATCTTCACATATAACAATTAAATAAATATAAAATTTGAA
Found at i:32379 original size:4 final size:4
Alignment explanation
Indices: 32370--32416 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
32360 AAAGGCACTG
* * *
32370 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAT ATAG ATAG ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
32417 GATACTGAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:32905 original size:60 final size:60
Alignment explanation
Indices: 32841--32963 Score: 140
Period size: 60 Copynumber: 2.0 Consensus size: 60
32831 AATATAATAA
* * * * * * *
32841 ATAGTCAGGTGACCATTTTATAATTTTTAATAGTCAAGTGATTCAACA-AAGTAATATCCT
1 ATAGTCAGGGGACCATTTAATAACTTATAATAATCAAGGGACTCAACATAA-TAATATCCT
* * *
32901 ATAGTCAGGGGGCCGTTTAATAACTTATAATAATCAAGGGACTCAACATAATAATATCGT
1 ATAGTCAGGGGACCATTTAATAACTTATAATAATCAAGGGACTCAACATAATAATATCCT
32961 ATA
1 ATA
32964 ATCGAGGGAT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 50 0.96
61 2 0.04
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (60 bp):
ATAGTCAGGGGACCATTTAATAACTTATAATAATCAAGGGACTCAACATAATAATATCCT
Found at i:34323 original size:21 final size:20
Alignment explanation
Indices: 34237--34394 Score: 95
Period size: 21 Copynumber: 7.8 Consensus size: 20
34227 AAATGACCAA
**
34237 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* * *
34256 AAAAATCGCAACGCGATCTC
1 CAAAATCGCAACGCGATTTT
* ** *
34276 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
34296 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
34317 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
34338 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
34358 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
34379 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
34395 ACACATAAAT
Statistics
Matches: 105, Mismatches: 28, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:34385 original size:20 final size:20
Alignment explanation
Indices: 34361--34590 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
34351 CGATTTTCCA
** *
34361 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
34381 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
34401 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
34421 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
34441 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
34461 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
34481 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
34501 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
34521 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
* *
34541 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
* *
34561 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
34581 AAATCACAAC
1 AAATCGCAAC
34591 ACTGAAATTT
Statistics
Matches: 186, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 185 0.99
21 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:35312 original size:24 final size:24
Alignment explanation
Indices: 35273--35319 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
35263 AAATTTGGTC
35273 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
35297 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
35320 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:37833 original size:33 final size:34
Alignment explanation
Indices: 37763--37982 Score: 215
Period size: 33 Copynumber: 6.4 Consensus size: 34
37753 GCATTTGACT
* * * *
37763 ATCGCAATACGGAAATTACAATCGCAACGA-GAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGATGAAA
*
37797 ATCGCAATGCGAAATGAAAATCCCAAC-ATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGATGAAA
*
37830 ATCGCAATGCGGAAATGAAAATCGCAACGA-GAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGATGAAA
37864 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAAA
*
37902 ATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAAA
*
37935 ATCGCAATGCGAAATGAAAATCGCAACGA-GAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGATGAAA
37968 ATCGCAATGCGAAAT
1 ATCGCAATGCGAAAT
37983 TATAAACGCA
Statistics
Matches: 162, Mismatches: 11, Indels: 27
0.81 0.05 0.14
Matches are distributed among these distances:
32 1 0.01
33 90 0.56
34 40 0.25
35 5 0.03
36 4 0.02
37 2 0.01
38 20 0.12
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGAAATGAAAATCGCAACGATGAAA
Found at i:37887 original size:19 final size:19
Alignment explanation
Indices: 37796--37960 Score: 189
Period size: 19 Copynumber: 9.4 Consensus size: 19
37786 GCAACGAGAG
37796 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
37815 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
37829 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
37849 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
37863 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37882 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
37901 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
37915 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37934 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
37953 AATCGCAA
1 AATCGCAA
37961 CGAGAGAATC
Statistics
Matches: 124, Mismatches: 6, Indels: 32
0.77 0.04 0.20
Matches are distributed among these distances:
14 32 0.26
15 2 0.02
16 5 0.04
17 4 0.03
18 3 0.02
19 65 0.52
20 13 0.10
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:37998 original size:52 final size:52
Alignment explanation
Indices: 37824--37982 Score: 309
Period size: 52 Copynumber: 3.0 Consensus size: 52
37814 AAATCCCAAC
37824 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
37877 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
37929 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
37981 AT
1 AT
37983 TATAAACGCA
Statistics
Matches: 106, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 90 0.85
53 16 0.15
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:38101 original size:52 final size:53
Alignment explanation
Indices: 37989--38104 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
37979 AAATTATAAA
*
37989 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1 CGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
38042 CGCATTGCGATTATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
1 CGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
38094 CGCATTGCGAT
1 CGCATTGCGAT
38105 AGTCATTTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (53 bp):
CGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
Found at i:38112 original size:19 final size:19
Alignment explanation
Indices: 38007--38104 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
37997 GATTCTCTCG
38007 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
38027 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
38046 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
38060 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
38079 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
38098 TTGCGAT
1 TTGCGAT
38105 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:38230 original size:14 final size:13
Alignment explanation
Indices: 38202--38259 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 13
38192 TTATGTTCGC
*
38202 ATCAATTACACAA
1 ATCAATTATACAA
38215 ATCAACTTATACAA
1 ATCAA-TTATACAA
* *
38229 ATCATCTTTTACAA
1 ATCA-ATTATACAA
*
38243 ATCAATTAAAC-A
1 ATCAATTATACAA
38255 ATCAA
1 ATCAA
38260 AAAATAAGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
12 6 0.16
13 9 0.24
14 22 0.59
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (13 bp):
ATCAATTATACAA
Found at i:40245 original size:14 final size:14
Alignment explanation
Indices: 40226--40282 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
40216 GCGAAATGAA
*
40226 AATCGCAACGACAG
1 AATCGCAACGAAAG
40240 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
40257 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
40273 AATCGCAACG
1 AATCGCAACG
40283 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:40253 original size:33 final size:33
Alignment explanation
Indices: 40207--40299 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
40197 GCGAAACCAA
*
40207 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
40240 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
40273 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
40300 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:40264 original size:19 final size:19
Alignment explanation
Indices: 40170--40304 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
40160 TAGTTTACTT
* *
40170 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
40190 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
40209 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
40228 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
40242 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
40261 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
40275 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
40294 TCGCAATGCGA
1 TCGCAACGCGA
40305 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:40322 original size:19 final size:19
Alignment explanation
Indices: 40300--40428 Score: 107
Period size: 19 Copynumber: 7.3 Consensus size: 19
40290 AAAATCGCAA
40300 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
40319 TGCGA---T-CTTAC-CGT
1 TGCGATTTTGGTTTCGCGT
40333 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
40352 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
40366 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
40385 TGCGATTTTGGTATCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
40404 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
40424 TGCGA
1 TGCGA
40429 AAGTAAACTA
Statistics
Matches: 86, Mismatches: 13, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
14 19 0.22
15 3 0.03
16 2 0.02
17 2 0.02
18 4 0.05
19 44 0.51
20 12 0.14
ACGTcount: A:0.10, C:0.18, G:0.28, T:0.44
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:40391 original size:33 final size:33
Alignment explanation
Indices: 40300--40391 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
40290 AAAATCGCAA
40300 TGCGATTTTGGTTTCGCGTTGCGA-TCTTACCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTTA-CGT
40333 TGCGATTTTGGTTTCGCGTTGCGATTCTGT-CGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCT-TACGT
**
40366 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
40392 TTGGTATCGC
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
33 51 0.93
34 3 0.05
35 1 0.02
ACGTcount: A:0.09, C:0.20, G:0.27, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTTACGT
Found at i:40635 original size:93 final size:93
Alignment explanation
Indices: 40476--41035 Score: 1104
Period size: 93 Copynumber: 6.0 Consensus size: 93
40466 ATGGATTGCA
40476 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
40541 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
40569 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
40634 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
40662 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
40727 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
40755 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
40820 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
40848 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
40913 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
40941 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
41005 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
41033 TTA
1 TTA
41036 TTAAGCAATC
Statistics
Matches: 466, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
92 64 0.14
93 402 0.86
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:42763 original size:14 final size:14
Alignment explanation
Indices: 42744--42833 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
42734 TTGAAATGAA
42744 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
42758 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
42777 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
42791 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
42810 AATCGCAACGAGAG
1 AATCGCAACGAGAG
42824 AATCGCAACG
1 AATCGCAACG
42834 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:42781 original size:33 final size:33
Alignment explanation
Indices: 42736--42850 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
42726 TCTTTTGGTT
42736 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
42769 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
42802 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
42835 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
42851 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:42782 original size:19 final size:19
Alignment explanation
Indices: 42758--42855 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
42748 GCAACGAGAG
*
42758 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
42777 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
42791 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
42810 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
42824 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
42843 AATCGCAATGCGA
1 AATCGCAACGCGA
42856 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 32 0.50
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:42899 original size:33 final size:33
Alignment explanation
Indices: 42851--42931 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
42841 AAAATCGCAA
** *
42851 TGCGATTTTGGTTTCGCGTTGCGATTCTCTTGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
42884 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
42917 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
42932 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.22, T:0.48
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:42964 original size:41 final size:41
Alignment explanation
Indices: 42907--42984 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
42897 TCGCGTTGCG
*
42907 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
42948 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
42985 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:42969 original size:20 final size:21
Alignment explanation
Indices: 42908--42983 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
42898 CGCGTTGCGA
42908 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
42929 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
42949 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
42970 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
42984 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:43105 original size:33 final size:33
Alignment explanation
Indices: 43063--43133 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
43053 AATACTAACT
*
43063 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
43096 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
43129 TGAAA
1 TGAAA
43134 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:43367 original size:22 final size:22
Alignment explanation
Indices: 43315--43369 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
43305 TGGTTGTGAG
**
43315 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
43337 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
43359 GGATTTCTTCG
1 GGATTTCTTCG
43370 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:43541 original size:20 final size:20
Alignment explanation
Indices: 43516--43668 Score: 191
Period size: 20 Copynumber: 7.7 Consensus size: 20
43506 CTTTAAATAT
43516 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
43536 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
43556 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
43576 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
43596 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
43616 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
43636 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
43656 CGCGTTGCGATTT
1 CGCGTTGCGATTT
43669 TGGAAAATCG
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
20 114 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:43685 original size:21 final size:21
Alignment explanation
Indices: 43655--43737 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
43645 ATTTTCATAT
*
43655 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
43676 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
43697 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
43718 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
43738 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:43728 original size:42 final size:43
Alignment explanation
Indices: 43635--43733 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
43625 ATTTATGTGT
* *
43635 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
43676 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
43718 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
43734 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:44674 original size:60 final size:60
Alignment explanation
Indices: 44562--44674 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
44552 ATAGTCGAGT
* * **
44562 GATCATTTTGTAACTTTTAATAGTGGAAGGGCTTAATAAAACAATATTCTATAGTCAAAA
1 GATCATTTTATAACTTTCAATAGTGGAAGGGCTTAATAAAACAATACCCTATAGTCAAAA
* *
44622 GATCATTTTATAACTTTCAATAGTTG-AGGGACTTAATAAAATAATACCCTATA
1 GATCATTTTATAACTTTCAATAGTGGAAGGG-CTTAATAAAACAATACCCTATA
44675 ATCGATGGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 4 0.09
60 42 0.91
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (60 bp):
GATCATTTTATAACTTTCAATAGTGGAAGGGCTTAATAAAACAATACCCTATAGTCAAAA
Found at i:47670 original size:184 final size:180
Alignment explanation
Indices: 47349--47724 Score: 585
Period size: 184 Copynumber: 2.1 Consensus size: 180
47339 ATTTTATAAT
* *
47349 TTATATA-AAAATTAAATATTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TTATATATAATATTAAATATTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
* * *
47413 TATAAAATAAAAATTTTAGATAATTTTTTAATTAATTAATATTAATTTATGTTTAAAAGTTATTG
66 TATAAAATAAAAATTTTAGATAAATTTTTAATTAATTAATATTAATTTAGGCTTAAAAGTTATTG
** *
47478 GATCTTAAATTATTAATTG-GATTTTAAATGGTTTGGGCTGAGCCCATATG
131 GATCTTAAATTATTAATTGAG-TTTTAAATGGTTTGGGCAAAACCCATATG
* *
47528 TTATATATAATATTTAATATTTTTTAATTCAAAAAAACAGTTTGCAATTAATTTAAATAATATAT
1 TTATATATAATATTAAATA-TTTTTAATTC-AAAAAA-AGTTTACAATTAATTTAAATAATATAT
* *
47593 AATTATAAAATAAAAATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGCTTAAAAGTT
63 AATTATAAAATAAAAATTTTAGAT-AAATTTTTAATTAATTAATATTAATTTAGGCTTAAAAGTT
47658 ATTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCAAAACCCATATG
127 ATTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCAAAACCCATATG
47712 TTATATATAATAT
1 TTATATATAATAT
47725 ATTTAAAATT
Statistics
Matches: 179, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
179 7 0.04
180 9 0.05
181 10 0.06
182 6 0.03
183 48 0.27
184 98 0.55
185 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (180 bp):
TTATATATAATATTAAATATTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAATTTTAGATAAATTTTTAATTAATTAATATTAATTTAGGCTTAAAAGTTATTG
GATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCAAAACCCATATG
Found at i:48301 original size:30 final size:30
Alignment explanation
Indices: 48262--48331 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
48252 TATCAGTTCA
* *
48262 AAGAGATAAAGTATAATTAATCATATAAAAT
1 AAGAAATAAAGTACAATTAATCATA-AAAAT
*
48293 AA-AAATAAAGTACAATTAATTATAAAAAT
1 AAGAAATAAAGTACAATTAATCATAAAAAT
48322 AAGAAATAAA
1 AAGAAATAAA
48332 ATCAAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 7 0.20
30 26 0.74
31 2 0.06
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (30 bp):
AAGAAATAAAGTACAATTAATCATAAAAAT
Found at i:65185 original size:6 final size:6
Alignment explanation
Indices: 65174--65209 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
65164 AGAACCGAAC
* *
65174 CGAAGA CGAAGA CGAAGA CGAAGA AGAAGA AGAAGA
1 CGAAGA CGAAGA CGAAGA CGAAGA CGAAGA CGAAGA
65210 AACACCAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.56, C:0.11, G:0.33, T:0.00
Consensus pattern (6 bp):
CGAAGA
Found at i:67144 original size:37 final size:37
Alignment explanation
Indices: 67094--67172 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
67084 ATACGTATAG
*
67094 ATGTTTCCAACACAGTGATTAGATTCAGAGTCCATGT
1 ATGTTTCCAACACACTGATTAGATTCAGAGTCCATGT
* * *
67131 ATGTTTCCAACACACTGGTTATATTCAGAGTTCATGT
1 ATGTTTCCAACACACTGATTAGATTCAGAGTCCATGT
67168 ATGTT
1 ATGTT
67173 CTATATGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (37 bp):
ATGTTTCCAACACACTGATTAGATTCAGAGTCCATGT
Found at i:71124 original size:12 final size:13
Alignment explanation
Indices: 71099--71123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71089 ACGCTGAGAT
71099 TGTTTTTAAAAAA
1 TGTTTTTAAAAAA
71112 TGTTTTTAAAAA
1 TGTTTTTAAAAA
71124 TATTTTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGTTTTTAAAAAA
Found at i:71752 original size:15 final size:15
Alignment explanation
Indices: 71713--71755 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
71703 GACAATAAAA
*
71713 TAGTGATTAAAAGTT
1 TAGTGATTAAAATTT
* **
71728 TAATTTTTAAAATTT
1 TAGTGATTAAAATTT
71743 TAGTGATTAAAAT
1 TAGTGATTAAAAT
71756 AAAAATAAAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (15 bp):
TAGTGATTAAAATTT
Found at i:83641 original size:2 final size:2
Alignment explanation
Indices: 83591--83624 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
83581 TCGGGGTATC
83591 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
83625 CAAGCCATCA
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):
AT
Found at i:86527 original size:45 final size:45
Alignment explanation
Indices: 86455--86623 Score: 205
Period size: 45 Copynumber: 3.8 Consensus size: 45
86445 GAGATAAGGT
* * * * *
86455 TGTTTCGGAAGGAAAGAAGATTAATATTGTATCAGAAAATGATAC
1 TGTTTTGGAAGAAAAGAGGATTGATATTGCATCAGAAAATGATAC
*
86500 TGTTTTGGAAGAAAAGAGGATTGATATTGCATCA-AAAGATGATAT
1 TGTTTTGGAAGAAAAGAGGATTGATATTGCATCAGAAA-ATGATAC
* * * *
86545 TGTTTTGGAAGAAAAGAGAATTGATCTTGCATCCGAAAACGATAC
1 TGTTTTGGAAGAAAAGAGGATTGATATTGCATCAGAAAATGATAC
* * *
86590 AGTTTTGGATGAAAAGAGGATTGATCTTGCATCA
1 TGTTTTGGAAGAAAAGAGGATTGATATTGCATCA
86624 AATGATGGCA
Statistics
Matches: 107, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
44 3 0.03
45 101 0.94
46 3 0.03
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (45 bp):
TGTTTTGGAAGAAAAGAGGATTGATATTGCATCAGAAAATGATAC
Found at i:86560 original size:23 final size:23
Alignment explanation
Indices: 86493--86561 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
86483 GTATCAGAAA
*
86493 ATGATACTGTTTTGGAAGAAAAG
1 ATGATATTGTTTTGGAAGAAAAG
* * * **
86516 A-G-GATTGATATTGCATCAAAAG
1 ATGATATTG-TTTTGGAAGAAAAG
86538 ATGATATTGTTTTGGAAGAAAAG
1 ATGATATTGTTTTGGAAGAAAAG
86561 A
1 A
86562 GAATTGATCT
Statistics
Matches: 32, Mismatches: 11, Indels: 6
0.65 0.22 0.12
Matches are distributed among these distances:
21 3 0.09
22 12 0.38
23 13 0.41
24 4 0.12
ACGTcount: A:0.41, C:0.04, G:0.25, T:0.30
Consensus pattern (23 bp):
ATGATATTGTTTTGGAAGAAAAG
Found at i:86607 original size:90 final size:90
Alignment explanation
Indices: 86454--86630 Score: 239
Period size: 90 Copynumber: 2.0 Consensus size: 90
86444 GGAGATAAGG
* * * *
86454 TTGTTTCGGAAGGAAAGAAGATTAATATTGTATCAGAAAATGATACTGTTTTGGAAGAAAAGAGG
1 TTGTTTCGGAAGAAAAGAAGATTAATATTGCATCAGAAAACGATACAGTTTTGGAAGAAAAGAGG
86519 ATTGATATTGCATCAAAAGATGATA
66 ATTGATATTGCATCAAAAGATGATA
* * * * *
86544 TTGTTTTGGAAGAAAAG-AGAATTGATCTTGCATCCGAAAACGATACAGTTTTGGATGAAAAGAG
1 TTGTTTCGGAAGAAAAGAAG-ATTAATATTGCATCAGAAAACGATACAGTTTTGGAAGAAAAGAG
* *
86608 GATTGATCTTGCATCAAATGATG
65 GATTGATATTGCATCAAAAGATG
86631 GCACTCTTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
89 2 0.03
90 73 0.97
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (90 bp):
TTGTTTCGGAAGAAAAGAAGATTAATATTGCATCAGAAAACGATACAGTTTTGGAAGAAAAGAGG
ATTGATATTGCATCAAAAGATGATA
Found at i:86641 original size:45 final size:43
Alignment explanation
Indices: 86490--86645 Score: 163
Period size: 45 Copynumber: 3.5 Consensus size: 43
86480 ATTGTATCAG
*
86490 AAAATGAT-ACTGTTTTGGAAGAAAAGAGGATTGATATTGCATC
1 AAAA-GATGACTGTTTTGGAAGAAAAGAGGATTGATCTTGCATC
* *
86533 AAAAGATGATATTGTTTTGGAAGAAAAGAGAATTGATCTTGCATCC
1 AAAAGATG--ACTGTTTTGGAAGAAAAGAGGATTGATCTTGCAT-C
* *
86579 GAAAACGAT-ACAGTTTTGGATGAAAAGAGGATTGATCTTGCATC
1 -AAAA-GATGACTGTTTTGGAAGAAAAGAGGATTGATCTTGCATC
* *
86623 AAATGATGGCACTCTTTTGGAAG
1 AAAAGAT-G-ACTGTTTTGGAAG
86646 GATATAGCAC
Statistics
Matches: 93, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
42 6 0.06
43 7 0.08
44 1 0.01
45 71 0.76
46 1 0.01
47 4 0.04
48 3 0.03
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (43 bp):
AAAAGATGACTGTTTTGGAAGAAAAGAGGATTGATCTTGCATC
Found at i:87145 original size:63 final size:63
Alignment explanation
Indices: 87044--87174 Score: 219
Period size: 63 Copynumber: 2.1 Consensus size: 63
87034 TTATGATGTT
* *
87044 ACTCCGGTTACTATCAATGATCAAAACAGCAGAAAATCTTTTC-GAGACGATGATGATCCCATC
1 ACTCCGGTTACTATCAATGATCAAAACAGCAGAAAATC-TTTCGGAGACGACGATGAACCCATC
*
87107 ACTCCGGTTACTATCAATGATCAAAACAGCAGACAATCTTTCGGAGACGACGATGAACCCATC
1 ACTCCGGTTACTATCAATGATCAAAACAGCAGAAAATCTTTCGGAGACGACGATGAACCCATC
87170 ACTCC
1 ACTCC
87175 TATTGGTGCC
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
62 4 0.06
63 60 0.94
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (63 bp):
ACTCCGGTTACTATCAATGATCAAAACAGCAGAAAATCTTTCGGAGACGACGATGAACCCATC
Found at i:88046 original size:2 final size:2
Alignment explanation
Indices: 88041--88074 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
88031 TTATCAAAAA
88041 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
88075 TTTTAAATAA
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):
AT
Found at i:88119 original size:2 final size:2
Alignment explanation
Indices: 88112--88177 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
88102 AATTTTAAGA
88112 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
88154 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
88178 TATTATTAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88602 original size:31 final size:31
Alignment explanation
Indices: 88550--88610 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
88540 TGAGATACAA
88550 TTTTATTGAGTTCTTTAATTATTAAAAGTTG
1 TTTTATTGAGTTCTTTAATTATTAAAAGTTG
* *
88581 TTTTGTTGAG-TCATTTGATTATTAAAAGTT
1 TTTTATTGAGTTC-TTTAATTATTAAAAGTT
88611 ATAAAGTGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (31 bp):
TTTTATTGAGTTCTTTAATTATTAAAAGTTG
Found at i:89304 original size:20 final size:20
Alignment explanation
Indices: 89257--89577 Score: 273
Period size: 20 Copynumber: 15.9 Consensus size: 20
89247 AATGACCAAC
89257 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
*
89276 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* * **
89296 AAAAACGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
*
89316 AAAATCGTAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
89338 AGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTCAG
89358 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
89380 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
89400 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
89420 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
* *
89440 AGAATCGCAACGCGTTTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
89460 AGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTCAG
89480 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* * *
89500 AGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTCAG
* *
89520 AGAATCGCAACGCGTTTCCA-
1 AAAATCGCAACGCGATT-CAG
* * *
89540 AGAATCGCAATGCAATTCAG
1 AAAATCGCAACGCGATTCAG
89560 AAAATCGCAACGCGATTC
1 AAAATCGCAACGCGATTC
89578 CAACAATTGT
Statistics
Matches: 247, Mismatches: 35, Indels: 39
0.77 0.11 0.12
Matches are distributed among these distances:
18 1 0.00
19 29 0.12
20 177 0.72
21 9 0.04
22 28 0.11
23 3 0.01
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:89430 original size:40 final size:40
Alignment explanation
Indices: 89259--89580 Score: 400
Period size: 40 Copynumber: 8.0 Consensus size: 40
89249 TGACCAACAA
* *
89259 AATCGCAACGCGATATC--AAAATCGCAACGCGATT-TAGAA
1 AATCGCAACGCGAT-TCAGAAAATCGCAACGCGATTCCA-AG
* * ** *
89298 AAACGCAACGTTGA-AAAGAAAATCGTAACGCGATCTTCCAAG
1 AATCGCAACG-CGATTCAGAAAATCGCAACGCGA--TTCCAAG
*
89340 AATCGCAATGCGATTCAGAAAATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGA--TTCCAAG
89382 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAG
* *
89422 AATCGCAACGCGATTCAGAGAATCGCAACGCGTTTCCAAG
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAG
*
89462 AATCGCAATGCGATTCAGAAAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAG
* * * *
89502 AATCGCAATGCGATTAAGAGAATCGCAACGCGTTTCCAAG
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAG
* *
89542 AATCGCAATGCAATTCAGAAAATCGCAACGCGATTCCAA
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAA
89581 CAATTGTTCC
Statistics
Matches: 250, Mismatches: 26, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
39 9 0.04
40 170 0.68
41 2 0.01
42 68 0.27
43 1 0.00
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.18
Consensus pattern (40 bp):
AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAG
Found at i:89492 original size:80 final size:80
Alignment explanation
Indices: 89314--89580 Score: 444
Period size: 80 Copynumber: 3.3 Consensus size: 80
89304 AACGTTGAAA
* *
89314 AGAAAATCGTAACGCGATCTTCCAAGAATCGCAATGCGATTCAGAAAATCGCAACGCGATCTTCC
1 AGAAAATCGCAACGCGA--TTCCAAGAATCGCAATGCGATTCAGAGAATCGCAACGCG-T-TTCC
*
89379 AAGAATCGCAACGCGATTC
62 AAGAATCGCAATGCGATTC
*
89398 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAGAGAATCGCAACGCGTTTCCAAGA
1 AGAAAATCGCAACGCGATTCCAAGAATCGCAATGCGATTCAGAGAATCGCAACGCGTTTCCAAGA
89463 ATCGCAATGCGATTC
66 ATCGCAATGCGATTC
*
89478 AGAAAATCGCAACGCGATTCCAAGAATCGCAATGCGATTAAGAGAATCGCAACGCGTTTCCAAGA
1 AGAAAATCGCAACGCGATTCCAAGAATCGCAATGCGATTCAGAGAATCGCAACGCGTTTCCAAGA
*
89543 ATCGCAATGCAATTC
66 ATCGCAATGCGATTC
89558 AGAAAATCGCAACGCGATTCCAA
1 AGAAAATCGCAACGCGATTCCAA
89581 CAATTGTTCC
Statistics
Matches: 176, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
80 122 0.69
81 1 0.01
82 37 0.21
84 16 0.09
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (80 bp):
AGAAAATCGCAACGCGATTCCAAGAATCGCAATGCGATTCAGAGAATCGCAACGCGTTTCCAAGA
ATCGCAATGCGATTC
Found at i:89745 original size:6 final size:6
Alignment explanation
Indices: 89734--89766 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
89724 GACACGTATT
89734 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
89767 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:89949 original size:20 final size:20
Alignment explanation
Indices: 89923--90263 Score: 361
Period size: 20 Copynumber: 16.9 Consensus size: 20
89913 ACAATTGTTG
89923 GAATCGCGTTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
* * *
89943 TAATCGCATTGCGATTCTT-G
1 GAATCGCGTTGCGATT-TTCT
* *
89963 GAAACGCGTTGCGATTCTCT
1 GAATCGCGTTGCGATTTTCT
*
89983 GAATCGCGTTGCGATTCTCT
1 GAATCGCGTTGCGATTTTCT
*
90003 GAATCGCGTTGCGATTCTCT
1 GAATCGCGTTGCGATTTTCT
*
90023 GAATCGCGTTGCGATTCTCT
1 GAATCGCGTTGCGATTTTCT
*
90043 GAATCGCGTTGCGATTCTCT
1 GAATCGCGTTGCGATTTTCT
*
90063 GAATCGCGTTGCGATTCTCT
1 GAATCGCGTTGCGATTTTCT
*
90083 GAATCGCGTTGCGATTCTCT
1 GAATCGCGTTGCGATTTTCT
*
90103 GAATCGCGTTGCGATTCTT-G
1 GAATCGCGTTGCGATT-TTCT
*
90123 GAAAATCGCGTTGCGATTCTCT
1 G--AATCGCGTTGCGATTTTCT
90145 GAATCGCGTTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
* *
90165 GAATCGCATTGCGATTCTT-G
1 GAATCGCGTTGCGATT-TTCT
*
90185 GAAGATCGCGTTGCGATATTCT
1 G-A-ATCGCGTTGCGATTTTCT
** * * *
90207 -TTTCAACGTTGCGTTTTTTT
1 GAATC-GCGTTGCGATTTTCT
*
90227 AAATCGCGTTGCGA-TTT-T
1 GAATCGCGTTGCGATTTTCT
90245 GATATCGCGTTGCGATTTT
1 GA-ATCGCGTTGCGATTTT
90264 GTTGGTCATT
Statistics
Matches: 277, Mismatches: 30, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
18 2 0.01
19 18 0.06
20 218 0.79
21 11 0.04
22 28 0.10
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.37
Consensus pattern (20 bp):
GAATCGCGTTGCGATTTTCT
Found at i:89964 original size:40 final size:39
Alignment explanation
Indices: 89923--90261 Score: 407
Period size: 40 Copynumber: 8.4 Consensus size: 39
89913 ACAATTGTTG
* * *
89923 GAATCGCGTTGCGATTTTCTTAATCGCATTGCGATTCTT
1 GAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTT
*
89962 GGAAACGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTCT
1 -GAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCT-T
90003 GAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTCT
1 GAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCT-T
90043 GAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTCT
1 GAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCT-T
90083 GAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTT
1 GAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTT
*
90122 GGAAAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTTTCT
1 -G--AATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCT-T
*
90165 GAATCGCATTGCGATTCT-TGGAAGATCGCGTTGCGATATTCTT
1 GAATCGCGTTGCGATTCTCT-G-A-ATCGCGTTGCG--ATTCTT
* * * * * *
90208 --TTCAACGTTGCGTTTTTTTAAATCGCGTTGCGATT-TT
1 GAATC-GCGTTGCGATTCTCTGAATCGCGTTGCGATTCTT
90245 GATATCGCGTTGCGATT
1 GA-ATCGCGTTGCGATT
90262 TTGTTGGTCA
Statistics
Matches: 267, Mismatches: 17, Indels: 31
0.85 0.05 0.10
Matches are distributed among these distances:
37 2 0.01
38 3 0.01
39 11 0.04
40 182 0.68
41 5 0.02
42 57 0.21
43 3 0.01
44 4 0.01
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (39 bp):
GAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTT
Found at i:90016 original size:60 final size:59
Alignment explanation
Indices: 89923--90261 Score: 418
Period size: 60 Copynumber: 5.6 Consensus size: 59
89913 ACAATTGTTG
* *
89923 GAATCGCGTTGCGATTTTCTT-AATCGCATTGCGATTCT-TGGAAACGCGTTGCGATTCTCT
1 GAATCGCGTTGCGA--TTCTTGAATCGCGTTGCGATTCTCT-GAATCGCGTTGCGATTCTCT
89983 GAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTCT
1 GAATCGCGTTGCGATTCT-TGAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTCT
90043 GAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTCT
1 GAATCGCGTTGCGATTCT-TGAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTCT
*
90103 GAATCGCGTTGCGATTCTTGGAAAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTTTCT
1 GAATCGCGTTGCGATTCTT-G--AATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTCT
* ** * * * *
90165 GAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATAT-TCT-TTTCAACGTTGCGTTTTTTT
1 GAATCGCGTTGCGATTCTT-G-A-ATCGCGTTGCGAT-TCTCTGAATC-GCGTTGCGATTCTCT
*
90227 AAATCGCGTTGCGATT-TTGATATCGCGTTGCGATT
1 GAATCGCGTTGCGATTCTTGA-ATCGCGTTGCGATT
90262 TTGTTGGTCA
Statistics
Matches: 258, Mismatches: 12, Indels: 20
0.89 0.04 0.07
Matches are distributed among these distances:
58 5 0.02
59 16 0.06
60 129 0.50
61 7 0.03
62 100 0.39
63 1 0.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (59 bp):
GAATCGCGTTGCGATTCTTGAATCGCGTTGCGATTCTCTGAATCGCGTTGCGATTCTCT
Found at i:90953 original size:15 final size:15
Alignment explanation
Indices: 90933--90963 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
90923 TCGTGATGGC
90933 GAGTAGAGATAGAGA
1 GAGTAGAGATAGAGA
*
90948 GAGTAGAGATCGAGA
1 GAGTAGAGATAGAGA
90963 G
1 G
90964 CTTCTAATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.42, T:0.13
Consensus pattern (15 bp):
GAGTAGAGATAGAGA
Found at i:94492 original size:55 final size:55
Alignment explanation
Indices: 94384--94494 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
94374 ATACTTCTTG
* *
94384 CTGTTATATCTGTACTACAAAAGAAGTCGTAACCAGGGATATGAAAATTGATTGT
1 CTGTTATATCTGTACTACAAAAGAAGTCGTAACCAGGGATACGAAAATAGATTGT
**
94439 CTGTTATATCTGTACTACAAAAGAAGTCGTAACCAGGGATACGAAGGTAGATTGT
1 CTGTTATATCTGTACTACAAAAGAAGTCGTAACCAGGGATACGAAAATAGATTGT
94494 C
1 C
94495 GATGATTATA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (55 bp):
CTGTTATATCTGTACTACAAAAGAAGTCGTAACCAGGGATACGAAAATAGATTGT
Found at i:111194 original size:37 final size:36
Alignment explanation
Indices: 111160--111228 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
111150 TACAAATTGT
*
111160 AAAATATTTATGT-ATTTTATTTAAAAAATTAAATTC
1 AAAATATTTATATAATTTT-TTTAAAAAATTAAATTC
* *
111196 ATAATATTTATATAATTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTAAAAAATTAAA
111229 AATATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 24 0.83
37 5 0.17
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTTTAAAAAATTAAATTC
Found at i:116944 original size:35 final size:35
Alignment explanation
Indices: 116903--116978 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
116893 AAAACAGTCC
* * *
116903 TCAATTTCATTTTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
116938 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
116973 TCAATT
1 TCAATT
116979 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:117504 original size:128 final size:129
Alignment explanation
Indices: 117372--117617 Score: 363
Period size: 130 Copynumber: 1.9 Consensus size: 129
117362 TTATTATATA
* *
117372 ATCAATTTGGTTCTAAATT-AATAGAATTTATTATAAATTAATCATTT-A-AGGATCTGACATGT
1 ATCAATTTGGTCCTAAATTAAATAAAATTTA--ATAAATTAATCATTTAACAGGATCTGACATGT
* * *
117434 GTTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGC
64 GTTAACACATGATCATGACACATGTCATTAGTGACACATGTCACCACCTAATTATTTATATATGC
117499 T
129 T
117500 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAA-CAGGATCTGACATGTG
* * * *
117565 TTAACACATGATCATTATATATGTTATTAGTGACACATGTCACCACCTAATTA
65 TTAACACATGATCATGACACATGTCATTAGTGACACATGTCACCACCTAATTA
117618 GAAGAAAATT
Statistics
Matches: 105, Mismatches: 9, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
127 15 0.14
128 19 0.18
129 10 0.10
130 61 0.58
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (129 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACAGGATCTGACATGTGT
TAACACATGATCATGACACATGTCATTAGTGACACATGTCACCACCTAATTATTTATATATGCT
Done.