Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000876.1 Hibiscus syriacus cultivar Beakdansim tig00001695_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: 362593
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:7412 original size:19 final size:19
Alignment explanation
Indices: 7388--7459 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 19
7378 AAAGTGACCT
7388 AAAATAATATATTTATTAA
1 AAAATAATATATTTATTAA
* *
7407 AAAATATTATTTTTATTTAA
1 AAAATAATATATTTA-TTAA
* *
7427 TAGAAATAAGGAT-TTAATTAA
1 -A-AAATAA-TATATTTATTAA
7448 AAAATAATATAT
1 AAAATAATATAT
7460 GAAAGACTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
18 2 0.05
19 20 0.48
20 5 0.12
21 5 0.12
22 8 0.19
23 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (19 bp):
AAAATAATATATTTATTAA
Found at i:7712 original size:22 final size:22
Alignment explanation
Indices: 7681--7722 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
7671 TTTCTATCCC
7681 TAGATAAAAACGTATCAAAAAA
1 TAGATAAAAACGTATCAAAAAA
* *
7703 TAGATGAAAACTTATCAAAA
1 TAGATAAAAACGTATCAAAA
7723 CGTGTCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.21
Consensus pattern (22 bp):
TAGATAAAAACGTATCAAAAAA
Found at i:10256 original size:14 final size:14
Alignment explanation
Indices: 10237--10266 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10227 TACAAGTCTC
10237 TGTGTGTACATATA
1 TGTGTGTACATATA
*
10251 TGTGTGTAGATATA
1 TGTGTGTACATATA
10265 TG
1 TG
10267 ATAAACTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.27, T:0.43
Consensus pattern (14 bp):
TGTGTGTACATATA
Found at i:10790 original size:173 final size:173
Alignment explanation
Indices: 10501--10845 Score: 636
Period size: 173 Copynumber: 2.0 Consensus size: 173
10491 TGACCTCACA
* *
10501 AAAAAGCAGGCGTCTTATGAAATAGGGCTCGCCTGAAAGGGCGCTTTTGTTTTATATTGCTAAGG
1 AAAAAGCAGGCGTCTTATGAAACAGGGCTCGCCTGAAAGCGCGCTTTTGTTTTATATTGCTAAGG
*
10566 CACAGTCGAGCCTAGGTGCACGCCTCAGTCCATTCAAGTTTACAATTAAATTTGCAGATGCCATA
66 CACAGTCGAGCCTAGGTGCACGCCTCAATCCATTCAAGTTTACAATTAAATTTGCAGATGCCATA
*
10631 TGCAGACTATATCATTTCAATTGCTTCACACATATTTTTCTAT
131 TGCAGACTATATCATTTCAATTGCTTCAAACATATTTTTCTAT
10674 AAAAAGCAGGCGTCTTATGAAACAGGGCTCGCCTGAAAGCGCGCTTTTGTTTTATATTGCTAAGG
1 AAAAAGCAGGCGTCTTATGAAACAGGGCTCGCCTGAAAGCGCGCTTTTGTTTTATATTGCTAAGG
*
10739 CACAGTCGAGCCTAGGTGCACGCCTCAATTCATTCAAGTTTACAATTAAATTTGCAGATGCCATA
66 CACAGTCGAGCCTAGGTGCACGCCTCAATCCATTCAAGTTTACAATTAAATTTGCAGATGCCATA
*
10804 TGCAGACTATATCATTTCAATTGCTTCAAATATATTTTTCTA
131 TGCAGACTATATCATTTCAATTGCTTCAAACATATTTTTCTA
10846 CAGCTTCCAG
Statistics
Matches: 166, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
173 166 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (173 bp):
AAAAAGCAGGCGTCTTATGAAACAGGGCTCGCCTGAAAGCGCGCTTTTGTTTTATATTGCTAAGG
CACAGTCGAGCCTAGGTGCACGCCTCAATCCATTCAAGTTTACAATTAAATTTGCAGATGCCATA
TGCAGACTATATCATTTCAATTGCTTCAAACATATTTTTCTAT
Found at i:13058 original size:12 final size:12
Alignment explanation
Indices: 13041--13067 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
13031 TGCAAAATTC
13041 TTTATATTGATG
1 TTTATATTGATG
13053 TTTATATTGATG
1 TTTATATTGATG
13065 TTT
1 TTT
13068 GGAAAAGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (12 bp):
TTTATATTGATG
Found at i:16398 original size:3 final size:3
Alignment explanation
Indices: 16392--16431 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
16382 AGAAGAAGAG
16392 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
16432 ATAATAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:16772 original size:3 final size:3
Alignment explanation
Indices: 16764--16801 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
16754 CAAGATCAAT
16764 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
16802 ACAAACTCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16772 original size:389 final size:388
Alignment explanation
Indices: 16044--16779 Score: 1427
Period size: 389 Copynumber: 1.9 Consensus size: 388
16034 TTAATTAAAA
16044 ATAATAATATATAGAGAGGTATTATTGTCATTATCCCTAAATATATAAGGTAATTTTTTTTGTCG
1 ATAATAATATATAGAGAGGTATTATTGTCATTATCCCTAAATATATAAGGTAATTTTTTTTGTCG
16109 GATTGGGTCGAATATTTTTCACCCTAAACCCGAACCCAACTCGATCCGAACATAACCTCTAAAAA
66 GATTGGGTCGAATATTTTTCACCCTAAACCCGAACCCAACTCGATCCGAACATAACCTCTAAAAA
16174 ACCCGATCCAACTCGACCTAAACCAGAATTTTTTTTAAAAACTCGATCCAATCGGATTGGGTCGG
131 ACCCGATCCAACTCGACCTAAACCAGAATTTTTTTTAAAAACTCGATCCAATCGGATTGGGTCGG
16239 AACTCGTCGAGATCGGTTCTCGTGTCCATCCCTAGTCATAACACCCAACTTATATAATCTCGAGT
196 AACTCGTCGAGATCGGTTCTCGTGTCCATCCCTAGTCATAACACCCAACTTATATAATCTCGAGT
16304 TTTCAATTTTGAGAGTTTTTCTTTAAATTTGAACTAGAGGGTTTTCATCGATTGTATTGATCAAG
261 TTTCAATTTTGAGAGTTTTTCTTTAAATTTGAACTAGAGGGTTTTCATCGATTGTATTGATCAAG
*
16369 ATCAATATGAAGAAGAAGAAGAGTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT
326 ATCAATAAGAAGAAGAAGAAGAGTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT
*
16432 ATAATAATAATATAGAGATGTATTATTGTCATTATCCCTAAATATATAAGGTAATTTTTTTTGTC
1 ATAATAAT-ATATAGAGAGGTATTATTGTCATTATCCCTAAATATATAAGGTAATTTTTTTTGTC
16497 GGATTGGGTCGAATATTTTTCACCCTAAACCCGAACCCAACTCGATCCGAACATAACCTCTAAAA
65 GGATTGGGTCGAATATTTTTCACCCTAAACCCGAACCCAACTCGATCCGAACATAACCTCTAAAA
*
16562 AACCCGATCCAACTCGACCTAAACCAGATTTTTTTTTAAAAACTCGATCCAATCGGATTGGGTCG
130 AACCCGATCCAACTCGACCTAAACCAGAATTTTTTTTAAAAACTCGATCCAATCGGATTGGGTCG
16627 GAACTCGTCGAGATCGGTTCTCGTGTCCATCCCTAGTCATAACACCCAACTTATATAATCTCGAG
195 GAACTCGTCGAGATCGGTTCTCGTGTCCATCCCTAGTCATAACACCCAACTTATATAATCTCGAG
*
16692 TTTTCAATTTTGAGAGTTTTTCTTTAAATTTGAATTAGAGGGTTTTCATCGATTGTATTGATCAA
260 TTTTCAATTTTGAGAGTTTTTCTTTAAATTTGAACTAGAGGGTTTTCATCGATTGTATTGATCAA
16757 GATCAATAAGAAGAAGAAGAAGA
325 GATCAATAAGAAGAAGAAGAAGA
16780 AGAAGAAGAA
Statistics
Matches: 343, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
388 8 0.02
389 335 0.98
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (388 bp):
ATAATAATATATAGAGAGGTATTATTGTCATTATCCCTAAATATATAAGGTAATTTTTTTTGTCG
GATTGGGTCGAATATTTTTCACCCTAAACCCGAACCCAACTCGATCCGAACATAACCTCTAAAAA
ACCCGATCCAACTCGACCTAAACCAGAATTTTTTTTAAAAACTCGATCCAATCGGATTGGGTCGG
AACTCGTCGAGATCGGTTCTCGTGTCCATCCCTAGTCATAACACCCAACTTATATAATCTCGAGT
TTTCAATTTTGAGAGTTTTTCTTTAAATTTGAACTAGAGGGTTTTCATCGATTGTATTGATCAAG
ATCAATAAGAAGAAGAAGAAGAGTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT
Found at i:21490 original size:58 final size:58
Alignment explanation
Indices: 21400--21517 Score: 218
Period size: 58 Copynumber: 2.0 Consensus size: 58
21390 GGTACAATCC
21400 CATCGAATTTCTTCTTTATGTTCTTTCCGGTTTAGATTATCTCTTGTCGAAGTTCAGG
1 CATCGAATTTCTTCTTTATGTTCTTTCCGGTTTAGATTATCTCTTGTCGAAGTTCAGG
* *
21458 CATCGAATTTCTTCTTTATGTTCTTTCCGGTTTCGTTTATCTCTTGTCGAAGTTCAGG
1 CATCGAATTTCTTCTTTATGTTCTTTCCGGTTTAGATTATCTCTTGTCGAAGTTCAGG
21516 CA
1 CA
21518 GTAGTATTTG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.16, C:0.20, G:0.17, T:0.47
Consensus pattern (58 bp):
CATCGAATTTCTTCTTTATGTTCTTTCCGGTTTAGATTATCTCTTGTCGAAGTTCAGG
Found at i:26166 original size:12 final size:12
Alignment explanation
Indices: 26149--26177 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
26139 GTGGATTTAG
26149 GGGTTGAAATGA
1 GGGTTGAAATGA
26161 GGGTTGAAATGA
1 GGGTTGAAATGA
26173 GGGTT
1 GGGTT
26178 TCAAAGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.45, T:0.28
Consensus pattern (12 bp):
GGGTTGAAATGA
Found at i:28241 original size:43 final size:44
Alignment explanation
Indices: 28191--28325 Score: 157
Period size: 43 Copynumber: 3.1 Consensus size: 44
28181 GTTATAAATG
* * *
28191 CGCTATATACTA-ACCTTTAACGGCGTTTGTATACTAAAAACGC
1 CGCTATATACCAGATCTTTAACGGCGTTTGTATCCTAAAAACGC
* * * *
28234 CGCTATATACCAGATCATCAGCGACGTTTGTATCCT-AAAACGC
1 CGCTATATACCAGATCTTTAACGGCGTTTGTATCCTAAAAACGC
* * * *
28277 CGCTATATACCAGATCTTTATCTGCGTTTTTATCCTAAAAACAC
1 CGCTATATACCAGATCTTTAACGGCGTTTGTATCCTAAAAACGC
28321 CGCTA
1 CGCTA
28326 AATGTCAAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
43 48 0.63
44 28 0.37
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.30
Consensus pattern (44 bp):
CGCTATATACCAGATCTTTAACGGCGTTTGTATCCTAAAAACGC
Found at i:28371 original size:43 final size:43
Alignment explanation
Indices: 28315--28410 Score: 138
Period size: 43 Copynumber: 2.2 Consensus size: 43
28305 TTTATCCTAA
* * * * *
28315 AAACACCGCTAAATGTCAAAACCTATTGCGGCGTTTTTAATAC
1 AAACGCCGCTAAATGTCAAAACCTATTGCGACATTTGTAAGAC
28358 AAACGCCGCTAAATGTCAAAACCTATTGCGACATTTGTAAGAC
1 AAACGCCGCTAAATGTCAAAACCTATTGCGACATTTGTAAGAC
*
28401 AAACGTCGCT
1 AAACGCCGCT
28411 TACAACCGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAATGTCAAAACCTATTGCGACATTTGTAAGAC
Found at i:30872 original size:162 final size:163
Alignment explanation
Indices: 30460--31251 Score: 703
Period size: 162 Copynumber: 4.8 Consensus size: 163
30450 GTTTCGTTGC
* * * * * * ** *
30460 AGCAGCCGCTCTCAGGTGACGGTCTAAGTAACTGGTCACATTTGTCATCGATGCAGCAGCCGCTT
1 AGCAGCCGCTTTCAGATGTCGGTCCAAGTAATTGGTCACACTTACCATCGATGGAGCAGCCGCTT
* ** * * *
30525 TCAGATG-CTGGTTTAAGTAAT-TGGTCACACTCGCTATCGATGGAGCAGCCTCTTTCAGATGTC
66 TCAGGTGTC-GGTCCAAGTAATCT-GTCACACTCGCCATCGATGGAGCAGCCGCTTTCAGGTGTC
** * * *
30588 GGTCCAAGTAATTGGTCATACT-TGGCATTGATGCA
129 GGTCCAAGTAATCCGTCACACTACGCCATTGATG-A
* * ** * *
30623 GCAGCAGCAGCTTTCA-ACTGTCGATCCAAGTAATCCGTCACAC-TATGCATTGATGGAGCAGCC
1 --AGCAGCCGCTTTCAGA-TGTCGGTCCAAGTAATTGGTCACACTTA-CCATCGATGGAGCAGCC
* * * *
30686 GCTTTCAGGTGTCGATCAAAGTAATCTATCACACTAC-CCATCGATGGAGCAGCCACTTTCAGGT
62 GCTTTCAGGTGTCGGTCCAAGTAATCTGTCACACT-CGCCATCGATGGAGCAGCCGCTTTCAGGT
* *
30750 GTCGGTCCAAGTAATCCGTTACACTAC-CCATCGATGA
126 GTCGGTCCAAGTAATCCGTCACACTACGCCATTGATGA
*
30787 AGCAGCCGCTTTCAGATGTCGGTCCAAGTAATTGGTCACACTTAACATCGATGGAGCAGCCGCTT
1 AGCAGCCGCTTTCAGATGTCGGTCCAAGTAATTGGTCACACTTACCATCGATGGAGCAGCCGCTT
* * * * *
30852 TCAGCTGTCGGTCCAAGTAAT-TGGTCACGCTTGCCATCGATGGAGCAGCCGCTTTCAAGTGTCA
66 TCAGGTGTCGGTCCAAGTAATCT-GTCACACTCGCCATCGATGGAGCAGCCGCTTTCAGGTGTCG
* * * * *
30916 ATCCAAGTAATCCGACGCACT-CGCCATTAATGG
130 GTCCAAGTAATCCGTCACACTACGCCATTGATGA
* * *
30949 AGCAGCCGCTTTCAGGT-TCCGGTCCAAGTAATTGGTCACACTTACCATTGATGCAGCAGCCGCT
1 AGCAGCCGCTTTCAGATGT-CGGTCCAAGTAATTGGTCACACTTACCATCGATGGAGCAGCCGCT
* * * * ** *
31013 TTCTGGTGTTGATCCAAGTATTCCATCACACTCACTGCCGAT-GCA-GGAGCAACCGCTTTCAGG
65 TTCAGGTGTCGGTCCAAGTAATCTGTCACACT--C-GCC-ATCG-ATGGAGCAGCCGCTTTCAGG
* * * *
31076 TGTCGATCCAAGTATTCCATCACACTCACTGCCGA-TGCA-GG
125 TGTCGGTCCAAGTAATCCGTCACACT-AC-GCC-ATTG-ATGA
* ** ** *
31117 AGCAACCGCTTTCAGATGTCGGTCCAAGTAATCCGTCACACTCGCCATCAATGGAGCAGCCGCTT
1 AGCAGCCGCTTTCAGATGTCGGTCCAAGTAATTGGTCACACTTACCATCGATGGAGCAGCCGCTT
* * * * *
31182 TCAGGTGTCGGTCCAAGTAATCCGTCACCCTCGCCATCGAAGAAGCGGCCGCTTTCAGGTGTCGG
66 TCAGGTGTCGGTCCAAGTAATCTGTCACACTCGCCATCGATGGAGCAGCCGCTTTCAGGTGTCGG
31247 TCCAA
131 TCCAA
31252 ACAATGGGCA
Statistics
Matches: 510, Mismatches: 91, Indels: 52
0.78 0.14 0.08
Matches are distributed among these distances:
161 3 0.01
162 211 0.41
163 3 0.01
164 5 0.01
165 192 0.38
166 7 0.01
167 1 0.00
168 85 0.17
169 3 0.01
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (163 bp):
AGCAGCCGCTTTCAGATGTCGGTCCAAGTAATTGGTCACACTTACCATCGATGGAGCAGCCGCTT
TCAGGTGTCGGTCCAAGTAATCTGTCACACTCGCCATCGATGGAGCAGCCGCTTTCAGGTGTCGG
TCCAAGTAATCCGTCACACTACGCCATTGATGA
Found at i:31029 original size:54 final size:54
Alignment explanation
Indices: 30460--31251 Score: 601
Period size: 54 Copynumber: 14.5 Consensus size: 54
30450 GTTTCGTTGC
* * * * * ** *
30460 AGCAGCCGCTCTCAGGTGACGGTCTAAGTAACTGGTCACATTTGTCATCGATGC
1 AGCAGCCGCTTTCAGGTGTCGGTCCAAGTAATTGGTCACACTTACCATCGATGG
* ** ** *
30514 AGCAGCCGCTTTCAGATG-CTGGTTTAAGTAATTGGTCACACTCGCTATCGATGG
1 AGCAGCCGCTTTCAGGTGTC-GGTCCAAGTAATTGGTCACACTTACCATCGATGG
* * * ** *
30568 AGCAGCCTCTTTCAGATGTCGGTCCAAGTAATTGGTCATACTTGGCATTGATGCAG
1 AGCAGCCGCTTTCAGGTGTCGGTCCAAGTAATTGGTCACACTTACCATCGATG--G
* ** * ** * *
30624 CAGCAGCAGCTTTCAACTGTCGATCCAAGTAATCCGTCACAC-TATGCATTGATGG
1 -AGCAGCCGCTTTCAGGTGTCGGTCCAAGTAATTGGTCACACTTA-CCATCGATGG
* * *
30679 AGCAGCCGCTTTCAGGTGTCGATCAAAGTAATCT-ATCACAC-TACCCATCGATGG
1 AGCAGCCGCTTTCAGGTGTCGGTCCAAGTAAT-TGGTCACACTTA-CCATCGATGG
* ** * *
30733 AGCAGCCACTTTCAGGTGTCGGTCCAAGTAATCCGTTACAC-TACCCATCGATGA
1 AGCAGCCGCTTTCAGGTGTCGGTCCAAGTAATTGGTCACACTTA-CCATCGATGG
* *
30787 AGCAGCCGCTTTCAGATGTCGGTCCAAGTAATTGGTCACACTTAACATCGATGG
1 AGCAGCCGCTTTCAGGTGTCGGTCCAAGTAATTGGTCACACTTACCATCGATGG
* * *
30841 AGCAGCCGCTTTCAGCTGTCGGTCCAAGTAATTGGTCACGCTTGCCATCGATGG
1 AGCAGCCGCTTTCAGGTGTCGGTCCAAGTAATTGGTCACACTTACCATCGATGG
* ** ** * * ** **
30895 AGCAGCCGCTTTCAAGTGTCAATCCAAGTAATCCGACGCACTCGCCATTAATGG
1 AGCAGCCGCTTTCAGGTGTCGGTCCAAGTAATTGGTCACACTTACCATCGATGG
* *
30949 AGCAGCCGCTTTCAGGT-TCCGGTCCAAGTAATTGGTCACACTTACCATTGATGC
1 AGCAGCCGCTTTCAGGTGT-CGGTCCAAGTAATTGGTCACACTTACCATCGATGG
* * * ** * ***
31003 AGCAGCCGCTTTCTGGTGTTGATCCAAGT-ATTCCATCACACTCACTGCCGATGCAGG
1 AGCAGCCGCTTTCAGGTGTCGGTCCAAGTAATT-GGTCACACTTACCATCGAT---GG
* * ** * ***
31060 AGCAACCGCTTTCAGGTGTCGATCCAAGT-ATTCCATCACACTCACTGCCGATGCAGG
1 AGCAGCCGCTTTCAGGTGTCGGTCCAAGTAATT-GGTCACACTTACCATCGAT---GG
* * ** ** *
31117 AGCAACCGCTTTCAGATGTCGGTCCAAGTAATCCGTCACACTCGCCATCAATGG
1 AGCAGCCGCTTTCAGGTGTCGGTCCAAGTAATTGGTCACACTTACCATCGATGG
** * ** * *
31171 AGCAGCCGCTTTCAGGTGTCGGTCCAAGTAATCCGTCACCCTCGCCATCGAAGA
1 AGCAGCCGCTTTCAGGTGTCGGTCCAAGTAATTGGTCACACTTACCATCGATGG
*
31225 AGCGGCCGCTTTCAGGTGTCGGTCCAA
1 AGCAGCCGCTTTCAGGTGTCGGTCCAA
31252 ACAATGGGCA
Statistics
Matches: 616, Mismatches: 106, Indels: 32
0.82 0.14 0.04
Matches are distributed among these distances:
53 5 0.01
54 465 0.75
55 5 0.01
56 2 0.00
57 137 0.22
58 2 0.00
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (54 bp):
AGCAGCCGCTTTCAGGTGTCGGTCCAAGTAATTGGTCACACTTACCATCGATGG
Found at i:32584 original size:38 final size:36
Alignment explanation
Indices: 32508--32584 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
32498 TTTTTATATT
*
32508 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
32544 TTTAATTTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAA-TTTTGTAAA-AAAATTATATAAATATTAT-CAA
32582 TTT
1 TTT
32585 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 5 0.14
37 21 0.60
38 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:36316 original size:21 final size:21
Alignment explanation
Indices: 36290--36329 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
36280 CAGAACCCTA
*
36290 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
36311 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
36330 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:36338 original size:23 final size:21
Alignment explanation
Indices: 36312--36369 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 21
36302 TTCCCCTGTG
36312 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
36335 GGGGGAATCGGTT-CCCTCAA
1 GGGGGAATCGGTTCCCCTCAA
*
36355 GGGGG-ATCGATTCCC
1 GGGGGAATCGGTTCCC
36370 TCTGCACCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 6 0.18
20 9 0.27
21 2 0.06
22 3 0.09
23 13 0.39
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:40716 original size:19 final size:20
Alignment explanation
Indices: 40673--40720 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
40663 TCTAAATCCT
*
40673 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
40693 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
40712 TTTTCAAAA
1 TTTTCAAAA
40721 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:41925 original size:21 final size:21
Alignment explanation
Indices: 41899--41940 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
41889 CCCAGAATGG
*
41899 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
41920 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
41941 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:42189 original size:29 final size:31
Alignment explanation
Indices: 42146--42216 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
42136 ATTATTTTTG
42146 TACATTTTGAATAAATTCAATT-AAGTCCAAA
1 TACATTTTG-ATAAATTCAATTCAAGTCCAAA
42177 TACATTTTG-TAAATTCAATTCAAGTCCAAA
1 TACATTTTGATAAATTCAATTCAAGTCCAAA
*
42207 AACCATTTTG
1 TA-CATTTTG
42217 CCTTAAATTG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 11 0.30
30 10 0.27
31 16 0.43
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (31 bp):
TACATTTTGATAAATTCAATTCAAGTCCAAA
Found at i:42536 original size:13 final size:13
Alignment explanation
Indices: 42518--42542 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42508 TTAAAAGATA
42518 AAAGGGTTTAATG
1 AAAGGGTTTAATG
42531 AAAGGGTTTAAT
1 AAAGGGTTTAAT
42543 TTTATTTTAA
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:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (13 bp):
AAAGGGTTTAATG
Found at i:42994 original size:25 final size:25
Alignment explanation
Indices: 42965--43033 Score: 102
Period size: 25 Copynumber: 2.8 Consensus size: 25
42955 ATTAATCATT
*
42965 AATTACGATGTGATTGATTATCTTG
1 AATTACGATGTAATTGATTATCTTG
*
42990 AATTACGTTGTAATTGATTATCTTG
1 AATTACGATGTAATTGATTATCTTG
**
43015 AATTACTTTGTAATTGATT
1 AATTACGATGTAATTGATT
43034 GTCTGATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (25 bp):
AATTACGATGTAATTGATTATCTTG
Found at i:43577 original size:4 final size:4
Alignment explanation
Indices: 43570--43741 Score: 344
Period size: 4 Copynumber: 43.0 Consensus size: 4
43560 TGCATGCATG
43570 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43618 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43666 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43714 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
43742 TATATATTAA
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 168 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:59645 original size:31 final size:30
Alignment explanation
Indices: 59603--59689 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
59593 TCAATTAAGT
59603 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
59634 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
59665 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
59690 TATTATCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:62265 original size:7 final size:7
Alignment explanation
Indices: 62255--62286 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
62245 ATTAAACCCT
62255 AAACTCG
1 AAACTCG
62262 AAACTCG
1 AAACTCG
62269 AAACTCG
1 AAACTCG
62276 AAACTCG
1 AAACTCG
62283 AAAC
1 AAAC
62287 GTTCATTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.47, C:0.28, G:0.12, T:0.12
Consensus pattern (7 bp):
AAACTCG
Found at i:62669 original size:17 final size:17
Alignment explanation
Indices: 62644--62677 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
62634 TTTTAAAATT
* *
62644 TTAGGAGATGAATTTGA
1 TTAGAAGATGAACTTGA
62661 TTAGAAGATGAACTTGA
1 TTAGAAGATGAACTTGA
62678 ACTTATGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.32
Consensus pattern (17 bp):
TTAGAAGATGAACTTGA
Found at i:67759 original size:38 final size:38
Alignment explanation
Indices: 67708--67788 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
67698 AACCTTAATA
67708 ATAAATATTTATTATTAAGGTTTATATTAAATTAACTT
1 ATAAATATTTATTATTAAGGTTTATATTAAATTAACTT
67746 ATAAATATTTATTATTAAGGTTTATATTAAATTAACTT
1 ATAAATATTTATTATTAAGGTTTATATTAAATTAACTT
*
67784 TTAAA
1 ATAAA
67789 GTTGATATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (38 bp):
ATAAATATTTATTATTAAGGTTTATATTAAATTAACTT
Found at i:70012 original size:26 final size:27
Alignment explanation
Indices: 69983--70117 Score: 148
Period size: 26 Copynumber: 4.7 Consensus size: 27
69973 AGATTATTGT
69983 ATATTTATTAGATTATAACCAAAA-AC
1 ATATTTATTAGATTATAACCAAAATAC
**
70009 ATATTTATTAGATTATAACCCATAATTATTGT
1 ATATTTATTAGATTATAA-CCA-AA--A-TAC
*
70041 ATATTTATTAGATTATAACCAAAATTATTGT
1 ATATTTATTAGATTATAACCAAAA-TA---C
70072 ATATTTATTAGATTATAACCAAAA-AC
1 ATATTTATTAGATTATAACCAAAATAC
70098 ATATTTATTAGATTATAACC
1 ATATTTATTAGATTATAACC
70118 CATAATTATT
Statistics
Matches: 96, Mismatches: 4, Indels: 18
0.81 0.03 0.15
Matches are distributed among these distances:
26 38 0.40
27 3 0.03
28 5 0.05
29 1 0.01
30 3 0.03
31 28 0.29
32 18 0.19
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (27 bp):
ATATTTATTAGATTATAACCAAAATAC
Found at i:70052 original size:58 final size:60
Alignment explanation
Indices: 69975--70091 Score: 184
Period size: 58 Copynumber: 1.9 Consensus size: 60
69965 GGTATATCAG
69975 ATTATTGTATATTTATTAGATTATAACCAAAA-A-CATATTTATTAGATTATAACCCATA
1 ATTATTGTATATTTATTAGATTATAACCAAAATATCATATTTATTAGATTATAACCCATA
*
70033 ATTATTGTATATTTATTAGATTATAACCAAAATTATTGTATATTTATTAGATTATAACC
1 ATTATTGTATATTTATTAGATTATAACCAAAA-TA-T-CATATTTATTAGATTATAACC
70092 AAAAACATAT
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
58 32 0.60
60 1 0.02
63 20 0.38
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (60 bp):
ATTATTGTATATTTATTAGATTATAACCAAAATATCATATTTATTAGATTATAACCCATA
Found at i:70121 original size:21 final size:22
Alignment explanation
Indices: 70072--70127 Score: 60
Period size: 26 Copynumber: 2.4 Consensus size: 22
70062 AAATTATTGT
70072 ATATTTATTAGATTATAACCAAAAAC
1 ATATTTATTAGATTATAACC----AC
70098 ATATTTATTAGATTATAACC-C
1 ATATTTATTAGATTATAACCAC
*
70119 ATAATTATT
1 ATATTTATT
70128 GTATATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 9 0.31
26 20 0.69
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.41
Consensus pattern (22 bp):
ATATTTATTAGATTATAACCAC
Found at i:70428 original size:2 final size:2
Alignment explanation
Indices: 70421--70476 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
70411 TCTTCTAACA
70421 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
70463 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
70477 TCTTTATCTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72021 original size:18 final size:19
Alignment explanation
Indices: 71986--72022 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
71976 CACGGAATGT
71986 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
72006 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
72023 TGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:74819 original size:29 final size:28
Alignment explanation
Indices: 74787--74841 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
74777 TTAGGGGGCG
*
74787 AACTTGAACTTTTAAAATTTCTAGGGGAA
1 AACTTGAACTTATAAAATTT-TAGGGGAA
74816 AACTTGAACTTATAAAATTTTAGGGG
1 AACTTGAACTTATAAAATTTTAGGGG
74842 GCGAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (28 bp):
AACTTGAACTTATAAAATTTTAGGGGAA
Found at i:74842 original size:29 final size:29
Alignment explanation
Indices: 74777--74842 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
74767 TGATTTAATG
** *
74777 TTAGGGGGCGAACTTGAACTTTTAAAATT
1 TTAGGGGGAAAACTTGAACTTATAAAATT
74806 TCTA-GGGGAAAACTTGAACTTATAAAATT
1 T-TAGGGGGAAAACTTGAACTTATAAAATT
74835 TTAGGGGG
1 TTAGGGGG
74843 CGAAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 2 0.06
29 28 0.88
30 2 0.06
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.32
Consensus pattern (29 bp):
TTAGGGGGAAAACTTGAACTTATAAAATT
Found at i:82255 original size:31 final size:29
Alignment explanation
Indices: 82190--82262 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 29
82180 GAGTATATAT
82190 ATAATAAAAAATATTAAAAAAATGGACCTC
1 ATAATAAAAAATATTAAAAAAATGGA-CTC
*
82220 -TAATAAAAAGTATTGAAAAAAATTAGG-CTC
1 ATAATAAAAAATATT-AAAAAAA-T-GGACTC
*
82250 ATAATAACAAATA
1 ATAATAAAAAATA
82263 AATATTAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
29 13 0.36
30 10 0.28
31 11 0.31
32 2 0.06
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.25
Consensus pattern (29 bp):
ATAATAAAAAATATTAAAAAAATGGACTC
Found at i:83090 original size:27 final size:27
Alignment explanation
Indices: 83026--83109 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
83016 ATTAACCGAT
* *
83026 AAAA-TAATTTTACTATTTTAAATATATA
1 AAAATTAATTATACT-TTATAAATA-ATA
* *
83054 ATACTT-ATTATACTTTATAAATAATA
1 AAAATTAATTATACTTTATAAATAATA
* *
83080 AAAATTAATTATAATTAAATAAA-AATA
1 AAAATTAATTATACTT-TATAAATAATA
83107 AAA
1 AAA
83110 TTTGATTGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
26 7 0.16
27 23 0.51
28 14 0.31
29 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (27 bp):
AAAATTAATTATACTTTATAAATAATA
Found at i:86667 original size:7 final size:7
Alignment explanation
Indices: 86651--86691 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
86641 AGTAGGCCTC
86651 AATA-AA
1 AATATAA
86657 AATATAA
1 AATATAA
86664 AATATAA
1 AATATAA
86671 AATATAA
1 AATATAA
86678 AATATAAA
1 AATAT-AA
86686 AATATA
1 AATATA
86692 TACACTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 4 0.12
7 22 0.67
8 7 0.21
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AATATAA
Found at i:90161 original size:17 final size:18
Alignment explanation
Indices: 90139--90172 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
90129 TCAGCCGGTC
90139 CGGTTC-GAACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
90156 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
90173 TTAATAGCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Found at i:99984 original size:67 final size:67
Alignment explanation
Indices: 99876--100010 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
99866 GATGGCGGAT
99876 ACATACTTTGGGGTGGGTCGGAATCACCAAATACTCGACCCATTGCCATCCCTATCTGCAGTAGG
1 ACATACTTTGGGGTGGGTCGGAATCACCAAATACTCGACCCATTGCCATCCCTATCTGCAGTAGG
99941 CC
66 CC
*
99943 ACATACTTTGGGGTGGGTCGGAATCACCAAATACTCGACCCATTGCCATCCCTATCTGTAGTAGG
1 ACATACTTTGGGGTGGGTCGGAATCACCAAATACTCGACCCATTGCCATCCCTATCTGCAGTAGG
100008 CC
66 CC
100010 A
1 A
100011 GTTTATCATT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (67 bp):
ACATACTTTGGGGTGGGTCGGAATCACCAAATACTCGACCCATTGCCATCCCTATCTGCAGTAGG
CC
Found at i:102638 original size:21 final size:21
Alignment explanation
Indices: 102614--102654 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
102604 GATAAAAAAT
*
102614 TACCTAAAACATTATTATTTC
1 TACCTAAAACATTAATATTTC
102635 TACCTAAAACATTAATATTT
1 TACCTAAAACATTAATATTT
102655 TTTTAACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTC
Found at i:102966 original size:13 final size:13
Alignment explanation
Indices: 102948--102977 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
102938 TCTTAAAAAT
*
102948 AAAATATTATTTA
1 AAAATAGTATTTA
102961 AAAATAGTATTTA
1 AAAATAGTATTTA
102974 AAAA
1 AAAA
102978 AAATCTGGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
AAAATAGTATTTA
Found at i:106643 original size:25 final size:25
Alignment explanation
Indices: 106537--106631 Score: 127
Period size: 25 Copynumber: 3.8 Consensus size: 25
106527 TTTTTCCAAT
*
106537 GTTGGATTTGGTATTCATTTCCGGC
1 GTTGGATTTGGTATCCATTTCCGGC
* *
106562 GTTAGATTTGGTATCCATTTTCGGC
1 GTTGGATTTGGTATCCATTTCCGGC
* * * *
106587 GCTAGATTTGGTAACCATTTCCGAC
1 GTTGGATTTGGTATCCATTTCCGGC
106612 GTTGGATTTGGTATCCATTT
1 GTTGGATTTGGTATCCATTT
106632 ATGGTGTTGG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.42
Consensus pattern (25 bp):
GTTGGATTTGGTATCCATTTCCGGC
Found at i:107571 original size:30 final size:29
Alignment explanation
Indices: 107529--107585 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
107519 ACTTTAAGGG
107529 TATATCGATTTT-GTCACTAAACTTTTAAA
1 TATATCGATTTTGGT-ACTAAACTTTTAAA
* *
107558 TATATCTATTTTTGGTACTATACTTTTA
1 TATATCGA-TTTTGGTACTAAACTTTTA
107586 TGTTTGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 15 0.62
31 2 0.08
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (29 bp):
TATATCGATTTTGGTACTAAACTTTTAAA
Found at i:109562 original size:5 final size:5
Alignment explanation
Indices: 109552--109589 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
109542 AAAATAACAC
109552 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AAT
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AAT
109590 CCATTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATTA
Found at i:118618 original size:11 final size:11
Alignment explanation
Indices: 118596--118632 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
118586 TTTAATTAAA
118596 AAATTA-TATT
1 AAATTATTATT
118606 AAATTATTATT
1 AAATTATTATT
*
118617 AAATAATTATT
1 AAATTATTATT
118628 AAATT
1 AAATT
118633 TATCAATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
AAATTATTATT
Found at i:122640 original size:328 final size:329
Alignment explanation
Indices: 122115--122777 Score: 1274
Period size: 328 Copynumber: 2.0 Consensus size: 329
122105 AACAATATTT
122115 AATTCAAAATTTTCATCATTAAAAATCTTATTATAAATCTCTTATGGAAAGATAAAAATAGTCAT
1 AATTCAAAATTTTCATCATTAAAAATCTTATTATAAATCTCTTATGGAAAGATAAAAATAGTCAT
122180 TAAATTTTATCAAATTATTATAGAGTGGTCATTAAATATTATCGAACTGTTATAAAATTATTATT
66 TAAATTTTATCAAATTATTATAGAGTGGTCATTAAATATTATCGAACTGTTATAAAATTATTATT
* *
122245 AAATTTATTGAAATTTTACGACTATTATAAAATTACAGACTTTAAGGATGAACTGAAGGGGAGGC
131 AAATTTATTGAAATTGTACGACTATTATAAAATTACAGACTTTAAGGATGAACCGAAGGGGAGGC
*
122310 AAGTGGGGCAGTGGTCAGCCGTCCTCCTAAAAAATTTAAATTCACATATATTTTAAATATTTTAT
196 AAGTGGGGCAGTGGTCAACCGTCCTCCTAAAAAATTTAAATTCACATATATTTTAAATATTTTAT
122375 TTTTATTTTTTATTGATAATCTATTTTCATCCATCCTAAAAATTTAATAAGTTTATCACGCTTAA
261 TTTTATTTTTTATTGATAATCTATTTTCATCCATCCTAAAAATTTAATAAGTTTATCACGCTTAA
122440 AT-A
326 ATAA
122443 AATTCAAAATTTTCATCATTAAAAATCTTATTATAAATCTCTTATGGAAAGATAAAAATAGTCAT
1 AATTCAAAATTTTCATCATTAAAAATCTTATTATAAATCTCTTATGGAAAGATAAAAATAGTCAT
122508 TAAATTTTATCAAATTATTATAGAGTGGTCATTAAATATTATCGAACTGTTATAAAATTATTATT
66 TAAATTTTATCAAATTATTATAGAGTGGTCATTAAATATTATCGAACTGTTATAAAATTATTATT
122573 AAATTTATTGAAATTGTACGACTATTATAAAATTACAGACTTTAAGGATGAACCGAAGGGGAGGC
131 AAATTTATTGAAATTGTACGACTATTATAAAATTACAGACTTTAAGGATGAACCGAAGGGGAGGC
122638 AAGTGGGGCAGTGGTCAACCGTCCTCCTAAAAAATTTAAATTCACATATATTTTAAATATTTTAT
196 AAGTGGGGCAGTGGTCAACCGTCCTCCTAAAAAATTTAAATTCACATATATTTTAAATATTTTAT
* *
122703 TTTTATTTTTTATTGATAATCTATTTTCATCCATCCTAAAAATTTTATAAGTTTATCACGTTTAA
261 TTTTATTTTTTATTGATAATCTATTTTCATCCATCCTAAAAATTTAATAAGTTTATCACGCTTAA
122768 ATAA
326 ATAA
122772 AATTCA
1 AATTCA
122778 TCACACCTAA
Statistics
Matches: 329, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
328 322 0.98
329 7 0.02
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (329 bp):
AATTCAAAATTTTCATCATTAAAAATCTTATTATAAATCTCTTATGGAAAGATAAAAATAGTCAT
TAAATTTTATCAAATTATTATAGAGTGGTCATTAAATATTATCGAACTGTTATAAAATTATTATT
AAATTTATTGAAATTGTACGACTATTATAAAATTACAGACTTTAAGGATGAACCGAAGGGGAGGC
AAGTGGGGCAGTGGTCAACCGTCCTCCTAAAAAATTTAAATTCACATATATTTTAAATATTTTAT
TTTTATTTTTTATTGATAATCTATTTTCATCCATCCTAAAAATTTAATAAGTTTATCACGCTTAA
ATAA
Found at i:123114 original size:59 final size:60
Alignment explanation
Indices: 123048--123214 Score: 148
Period size: 59 Copynumber: 2.8 Consensus size: 60
123038 TTTATATAAC
* * *
123048 AAATAAGTACTTAAAATATATCATCTTTTACATTTAAGTACCTAAAGTA-TTTTTTGTCA
1 AAATAAGTACTTAAAATATATCATCTTTTTCATATAAGTACCTAAAGTATTTTTTTGTAA
* * *
123107 AAATAAGTA-TCTAAAGT-TATC-T-TTTTGGTCAAAATAGGTACCTAAAGTATTTTTTTGTAA
1 AAATAAGTACT-TAAAATATATCATCTTTT--TC-ATATAAGTACCTAAAGTATTTTTTTGTAA
* * * * * *
123167 AAATAGGTACTTACATTAT-TCAACTTTTTCATCTAAGTACATAAAGTA
1 AAATAAGTACTTAAAATATATCATCTTTTTCATATAAGTACCTAAAGTA
123215 CTCTTTAATT
Statistics
Matches: 85, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
56 4 0.05
57 1 0.01
58 6 0.07
59 43 0.51
60 25 0.29
61 2 0.02
62 4 0.05
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (60 bp):
AAATAAGTACTTAAAATATATCATCTTTTTCATATAAGTACCTAAAGTATTTTTTTGTAA
Found at i:123170 original size:29 final size:29
Alignment explanation
Indices: 123085--123176 Score: 123
Period size: 31 Copynumber: 3.1 Consensus size: 29
123075 TTACATTTAA
*
123085 GTACCTAAAGTA-TTTTTTGTCAAAATAA
1 GTACCTAAAGTATTTTTTTGTCAAAATAG
* *
123113 GTATCTAAAGTTATCTTTTTGGTCAAAATAG
1 GTACCTAAAG-TAT-TTTTTTGTCAAAATAG
*
123144 GTACCTAAAGTATTTTTTTGTAAAAATAG
1 GTACCTAAAGTATTTTTTTGTCAAAATAG
123173 GTAC
1 GTAC
123177 TTACATTATT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
28 9 0.16
29 20 0.36
30 3 0.05
31 23 0.42
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (29 bp):
GTACCTAAAGTATTTTTTTGTCAAAATAG
Found at i:123186 original size:29 final size:29
Alignment explanation
Indices: 123097--123186 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 29
123087 ACCTAAAGTA
*
123097 TTTTTTGTCAAAATAAGTA-TCTAAAGTTAT
1 TTTTTTGTCAAAATAGGTACT-TAAA-TTAT
* * *
123127 CTTTTTGGTCAAAATAGGTACCTAAAGTAT
1 -TTTTTTGTCAAAATAGGTACTTAAATTAT
* *
123157 TTTTTTGTAAAAATAGGTACTTACATTAT
1 TTTTTTGTCAAAATAGGTACTTAAATTAT
123186 T
1 T
123187 CAACTTTTTC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 25 0.51
30 3 0.06
31 21 0.43
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.44
Consensus pattern (29 bp):
TTTTTTGTCAAAATAGGTACTTAAATTAT
Found at i:123309 original size:30 final size:30
Alignment explanation
Indices: 123271--123345 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
123261 AAAAGTTTGA
*
123271 ATAA-TTTAGGTAACTA-TTTGACCAATAAG
1 ATAACTTTAGGTAACTACTTTGA-CAAAAAG
**
123300 ATAACTTTAGGTATTTACTTTGACAAAAAG
1 ATAACTTTAGGTAACTACTTTGACAAAAAG
123330 AT-ACTTTAGGTAACTA
1 ATAACTTTAGGTAACTA
123346 AATGTAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 16 0.41
30 18 0.46
31 5 0.13
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (30 bp):
ATAACTTTAGGTAACTACTTTGACAAAAAG
Found at i:126994 original size:20 final size:22
Alignment explanation
Indices: 126960--126999 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
126950 ATTTAAATAT
126960 AATTTAAATATTTAT-TTTTAA
1 AATTTAAATATTTATATTTTAA
126981 AATTTAAA-ATTTATATTTT
1 AATTTAAATATTTATATTTT
127000 TTAGAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTTAAATATTTATATTTTAA
Found at i:127314 original size:16 final size:16
Alignment explanation
Indices: 127295--127336 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
127285 ACCCGATATA
127295 AAATAAAA-ATTTATTT
1 AAATAAAATATTT-TTT
127311 AAATAATAATATTTTTT
1 AAATAA-AATATTTTTT
*
127328 AAAGAAAAT
1 AAATAAAAT
127337 TATATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 10 0.43
18 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AAATAAAATATTTTTT
Found at i:132565 original size:94 final size:97
Alignment explanation
Indices: 132445--132658 Score: 310
Period size: 97 Copynumber: 2.2 Consensus size: 97
132435 TAGTGTATTG
*
132445 GAACAAAGGGTGTGATTGAATTTCTAGGTT-T-TTGGGGGACTGAAAGTAA-TTTGTTTTGTAAA
1 GAACAAAGGGTGTGATTGAATTTCTAGGTTGTGTTGGGGGACTGAAAGTAATTTTGTTTTCTAAA
* * *
132507 CTAAATTATGAATGTGTTCTGTGAAAGTACTC-
66 CAAAATTATGAACGTATTCTGTGAAAGTAC-CA
* * *
132539 GAACAAAGGGTGTGATTGAATTTCTAGGTTGTGTTGGGGGACTTAAATTAATTTTTTTTTCTAAA
1 GAACAAAGGGTGTGATTGAATTTCTAGGTTGTGTTGGGGGACTGAAAGTAATTTTGTTTTCTAAA
*
132604 CAAAATTATGAACGTATTCTGTTAAAGTACCA
66 CAAAATTATGAACGTATTCTGTGAAAGTACCA
*
132636 GAACAAAGGGTGTCATTGAATTT
1 GAACAAAGGGTGTGATTGAATTT
132659 TGAACTGGTG
Statistics
Matches: 107, Mismatches: 9, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
94 30 0.28
95 1 0.01
96 17 0.16
97 59 0.55
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.37
Consensus pattern (97 bp):
GAACAAAGGGTGTGATTGAATTTCTAGGTTGTGTTGGGGGACTGAAAGTAATTTTGTTTTCTAAA
CAAAATTATGAACGTATTCTGTGAAAGTACCA
Found at i:133896 original size:26 final size:28
Alignment explanation
Indices: 133859--133914 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
133849 AAAGCATGCA
* *
133859 TGTACATAAATGG-CCTTGATTATAGGG
1 TGTACATAAATGGCCCTTGAGTATAAGG
133886 TGTA-ATAAATGGCCCTTGAGTATAAGG
1 TGTACATAAATGGCCCTTGAGTATAAGG
133913 TG
1 TG
133915 ATGTTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (28 bp):
TGTACATAAATGGCCCTTGAGTATAAGG
Found at i:133981 original size:28 final size:29
Alignment explanation
Indices: 133939--133997 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
133929 CCTTATGCTT
*
133939 TTAAAAGTTACAAAATGGTC-TTTGACTA
1 TTAAAAGTTACAAAATGGTCATTTCACTA
* *
133967 TTAAAAGTTATAAAATTGTCATTTCACTA
1 TTAAAAGTTACAAAATGGTCATTTCACTA
133996 TT
1 TT
133998 CATATATTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (29 bp):
TTAAAAGTTACAAAATGGTCATTTCACTA
Found at i:134144 original size:28 final size:28
Alignment explanation
Indices: 134111--134167 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
134101 CTATCGTTGT
*
134111 TTTTAAACATT-GGATTGATGACATAATG
1 TTTTAAACATTAGG-TTGATAACATAATG
* *
134139 TTTTAAGCATTAGGTTGATAATATAATG
1 TTTTAAACATTAGGTTGATAACATAATG
134167 T
1 T
134168 AAACAAAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (28 bp):
TTTTAAACATTAGGTTGATAACATAATG
Found at i:134387 original size:60 final size:61
Alignment explanation
Indices: 134288--134425 Score: 158
Period size: 60 Copynumber: 2.3 Consensus size: 61
134278 GTAATTAAGT
* * * *
134288 GATTGTTTTGTAATTTTTAATAGTTGGAAGAATTAACAAAA-TAATGTCTTAT-AGTTGAAG
1 GATTATTTTGTAATTTTTAATAGTTGGAAGAATCAACAAAATTAATATCTTATAAATTG-AG
* * *
134348 GATTATTTTGTAATTTTTAATAGTT-GAGAGACTCGACAAAATTAATATTTTATAAATTGAG
1 GATTATTTTGTAATTTTTAATAGTTGGA-AGAATCAACAAAATTAATATCTTATAAATTGAG
134409 GATTATTTGTGT-ATTTT
1 GATTATTT-TGTAATTTT
134426 ACCCTAAATT
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
59 2 0.03
60 34 0.51
61 24 0.36
62 7 0.10
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.45
Consensus pattern (61 bp):
GATTATTTTGTAATTTTTAATAGTTGGAAGAATCAACAAAATTAATATCTTATAAATTGAG
Found at i:142833 original size:16 final size:15
Alignment explanation
Indices: 142814--142843 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
142804 TTTATTCTAT
142814 ATATAATTTAATAATC
1 ATATAATTT-ATAATC
142830 ATATAATTTATAAT
1 ATATAATTTATAAT
142844 TTGATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATAATTTATAATC
Found at i:146012 original size:6 final size:6
Alignment explanation
Indices: 146001--146033 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
145991 AAAATTAAGA
146001 ACACTG ACACTG ACACTG ACACTG ACACTG ACA
1 ACACTG ACACTG ACACTG ACACTG ACACTG ACA
146034 AATCAGCATA
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:0.36, C:0.33, G:0.15, T:0.15
Consensus pattern (6 bp):
ACACTG
Found at i:155368 original size:19 final size:19
Alignment explanation
Indices: 155294--155369 Score: 71
Period size: 19 Copynumber: 3.9 Consensus size: 19
155284 AATTTCTGAG
155294 TACAAAGTTTCGAAACTTT
1 TACAAAGTTTCGAAACTTT
**
155313 TGTAAAGTTTCGAAACTTT
1 TACAAAGTTTCGAAACTTT
* * * *
155332 TAATAAAATTTTCAAAACTCT
1 T-A-CAAAGTTTCGAAACTTT
*
155353 TACAAAGTTTCTAAACT
1 TACAAAGTTTCGAAACT
155370 ATGAACAATA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 30 0.67
20 1 0.02
21 14 0.31
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.38
Consensus pattern (19 bp):
TACAAAGTTTCGAAACTTT
Found at i:157950 original size:85 final size:86
Alignment explanation
Indices: 157838--158123 Score: 319
Period size: 85 Copynumber: 3.3 Consensus size: 86
157828 GTAAAAATCA
* * *
157838 AGATCTATAGCGGCATTTTTTGAACAAACACCGCAAAAGGTCGAGATCTATAGCGGCGTTTTAG-
1 AGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGA
*
157902 AACAAACACCGAAAAAGGTTG
66 AACAAACGCCGAAAAAGGTTG
* ** * * * *
157923 AGATATATAGCGGTGTTTTTGGTACAAACGCCGCAAAAGATCGAGATCTATAGTGGCATTTTTGA
1 AGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGA
*
157988 AACAAACGCC-ACAAAAGG-TC
66 AACAAACGCCGA-AAAAGGTTG
* * * * *
158008 AGACCTATAGCGGCATTTTTGGATATAAACGCCGCAAAAGGT-TAAATCTATAGCGACGTTTTTG
1 AGATCTATAGCGGCATTTTTGGA-ACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTG
* * *
158072 AAACAAACGCCGCAGAAGGTCG
65 AAACAAACGCCGAAAAAGGTTG
* * *
158094 AGATCTATAGTGACGTTTTTGGAACAAACG
1 AGATCTATAGCGGCATTTTTGGAACAAACG
158124 ACGCTAATTA
Statistics
Matches: 163, Mismatches: 33, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
85 113 0.69
86 50 0.31
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (86 bp):
AGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGA
AACAAACGCCGAAAAAGGTTG
Found at i:157969 original size:43 final size:43
Alignment explanation
Indices: 157821--158123 Score: 317
Period size: 43 Copynumber: 7.1 Consensus size: 43
157811 TGTGAAATAA
* * * * *
157821 AAACGCCGTAAAA-ATCAAGATCTATAGCGGCATTTTTTGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* *
157863 AAACACCGCAAAAGGTCGAGATCTATAGCGGCG-TTTTAGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * * * * *
157905 AAACACCGAAAAAGGTTGAGATATATAGCGGTGTTTTTGGTAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * * *
157948 AAACGCCGCAAAAGATCGAGATCTATAGTGGCATTTTTGAAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * * *
157991 AAACGCCACAAAAGGTC-AGACCTATAGCGGCATTTTTGGATAT
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGA-AC
* * * *
158034 AAACGCCGCAAAAGGT-TAAATCTATAGCGACGTTTTTGAAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * *
158076 AAACGCCGCAGAAGGTCGAGATCTATAGTGACGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
158119 AAACG
1 AAACG
158124 ACGCTAATTA
Statistics
Matches: 216, Mismatches: 40, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
42 84 0.39
43 132 0.61
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.23
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
Found at i:158060 original size:128 final size:127
Alignment explanation
Indices: 157821--158123 Score: 351
Period size: 128 Copynumber: 2.4 Consensus size: 127
157811 TGTGAAATAA
* * * * * *
157821 AAACGCCGTAAAA-ATCAAGATCTATAGCGGCATTTTTTGAACAAACACCGCAAAAGGTCGAGAT
1 AAACGCCGCAAAAGATCGAGATCTATAGTGGCA-TTTTTGAACAAACGCCACAAAAGGTCGAGAC
* ** **
157885 CTATAGCGGCGTTTTAGAACAAACACCGAAAAAGGTTGAGATATATAGCGGTGTTTTTGGTAC
65 CTATAGCGGCGTTTTAGAACAAACACCGAAAAAGGTTGAAATATATAGCGACGTTTTTGAAAC
157948 AAACGCCGCAAAAGATCGAGATCTATAGTGGCATTTTTGAAACAAACGCCACAAAAGGTC-AGAC
1 AAACGCCGCAAAAGATCGAGATCTATAGTGGCATTTTTG-AACAAACGCCACAAAAGGTCGAGAC
* * * * * *
158012 CTATAGCGGCATTTTTGGATATAAACGCCGCAAAAGGTT-AAATCTATAGCGACGTTTTTGAAAC
65 CTATAGCGGC-GTTTTAGA-ACAAACACCGAAAAAGGTTGAAATATATAGCGACGTTTTTGAAAC
* * * *
158076 AAACGCCGCAGAAGGTCGAGATCTATAGTGACGTTTTTGGAACAAACG
1 AAACGCCGCAAAAGATCGAGATCTATAGTGGCATTTTT-GAACAAACG
158124 ACGCTAATTA
Statistics
Matches: 150, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
127 31 0.21
128 102 0.68
129 17 0.11
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.23
Consensus pattern (127 bp):
AAACGCCGCAAAAGATCGAGATCTATAGTGGCATTTTTGAACAAACGCCACAAAAGGTCGAGACC
TATAGCGGCGTTTTAGAACAAACACCGAAAAAGGTTGAAATATATAGCGACGTTTTTGAAAC
Found at i:160931 original size:83 final size:82
Alignment explanation
Indices: 160806--161155 Score: 307
Period size: 83 Copynumber: 4.3 Consensus size: 82
160796 TTTGGTAGCG
* * * * *
160806 TTTTAAAAAAACGCCACTAAAGT-ATGCAT-TTTTGCGGCGTTTGTTGAAAAAATGCCACTATAG
1 TTTTATAAAAACGCCGCTAAAGTAATAC-TCTGTTGCGGCGTTTGTTG-AAAAACGCCACTATAG
* *
160869 ATGAACCCTATTACGACGT
64 ATGAACCCTATTGCGGCGT
* * * * * *
160888 TTTTATACAAACACCGCTAAAGTACTACTCTTTTGCGGTGTTTGTTGAAAAAAAGCCACTATAG-
1 TTTTATAAAAACGCCGCTAAAGTAATACTCTGTTGCGGCGTTTGTTG-AAAAACGCCACTATAGA
* *
160952 TCGAAACCTATTGCGGCAT
65 T-GAACCCTATTGCGGCGT
* * ** ** *
160971 TTTTATAAAAACGCCGCAAAATTAATACTCTGTCACGATGTTTGTTGAGAAACGCCACTATA-AT
1 TTTTATAAAAACGCCGCTAAAGTAATACTCTGTTGCGGCGTTTGTTGAAAAACGCCACTATAGA-
* * *
161035 TGAATCC-ATTGTGGTGT
65 TGAACCCTATTGCGGCGT
* * * * *
161052 TTGTATAAAAATGCCGCTAAAGTATTACTCTGTTGCGGCATTTGTTG-AAAACGCCACTATGGAT
1 TTTTATAAAAACGCCGCTAAAGTAATACTCTGTTGCGGCGTTTGTTGAAAAACGCCACTATAGAT
* *
161116 GAACCATATTGCGTCGT
66 GAACCCTATTGCGGCGT
* *
161133 TTTTATACAAACGCCACTAAAGT
1 TTTTATAAAAACGCCGCTAAAGT
161156 TACCATTTTG
Statistics
Matches: 213, Mismatches: 48, Indels: 15
0.77 0.17 0.05
Matches are distributed among these distances:
80 17 0.08
81 71 0.33
82 39 0.18
83 86 0.40
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (82 bp):
TTTTATAAAAACGCCGCTAAAGTAATACTCTGTTGCGGCGTTTGTTGAAAAACGCCACTATAGAT
GAACCCTATTGCGGCGT
Found at i:165549 original size:11 final size:11
Alignment explanation
Indices: 165533--165558 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
165523 GGACATAGAG
165533 ATTTGTGGGTA
1 ATTTGTGGGTA
165544 ATTTGTGGGTA
1 ATTTGTGGGTA
165555 ATTT
1 ATTT
165559 TACTATACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (11 bp):
ATTTGTGGGTA
Found at i:166155 original size:27 final size:27
Alignment explanation
Indices: 166125--166185 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
166115 TTGATCCTCA
*
166125 AAATATTAATATGATCTTAACATCTTG
1 AAATATCAATATGATCTTAACATCTTG
166152 AAATATCAATATGATCTTAACATCTTG
1 AAATATCAATATGATCTTAACATCTTG
166179 AAATATC
1 AAATATC
166186 TGAAAAAGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.38
Consensus pattern (27 bp):
AAATATCAATATGATCTTAACATCTTG
Found at i:171559 original size:23 final size:23
Alignment explanation
Indices: 171468--171551 Score: 141
Period size: 23 Copynumber: 3.7 Consensus size: 23
171458 CATTATTATA
*
171468 TGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
171491 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
171514 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
171537 CGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
171552 TTTATACGAG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:171670 original size:2 final size:2
Alignment explanation
Indices: 171663--171742 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
171653 AATACAATAC
171663 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
171705 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
171743 GGATATGTTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:173485 original size:2 final size:2
Alignment explanation
Indices: 173480--173508 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
173470 TTTTCTTTTA
173480 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 A
173509 ATTTTGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:173541 original size:35 final size:36
Alignment explanation
Indices: 173494--173562 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
173484 ATATATATAT
173494 ATATATATATATATAATTTTGAAAATAAATAATACC
1 ATATATATATATATAATTTTGAAAATAAATAATACC
*
173530 ATATAT-TATATATAGTTTTGAAAATAAATAATA
1 ATATATATATATATAATTTTGAAAATAAATAATA
173563 GTTTTGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 26 0.81
36 6 0.19
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (36 bp):
ATATATATATATATAATTTTGAAAATAAATAATACC
Found at i:173596 original size:47 final size:47
Alignment explanation
Indices: 173530--173660 Score: 190
Period size: 47 Copynumber: 2.7 Consensus size: 47
173520 AAATAATACC
* *
173530 ATATATTATATATAGTTTTGAAAATAAATAATAGTTTTGAAAATAGT
1 ATATGTTATATATAGTTTTGAAAATAAATAATAGTTTTGAAAACAGT
* *
173577 ATATGTTATTTATAGTTTTGAAAATAAATAATAATTTTGAAAACAGT
1 ATATGTTATATATAGTTTTGAAAATAAATAATAGTTTTGAAAACAGT
* *
173624 ATATAGTACATATATAGTTTTGAAATTAAATAATAGT
1 ATAT-GT-TATATATAGTTTTGAAAATAAATAATAGT
173661 ATACAGTAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
47 47 0.64
48 2 0.03
49 25 0.34
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.42
Consensus pattern (47 bp):
ATATGTTATATATAGTTTTGAAAATAAATAATAGTTTTGAAAACAGT
Found at i:173703 original size:3 final size:3
Alignment explanation
Indices: 173684--173728 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
173674 AAGTATAAAA
*
173684 TAT TAT ATAT T-T TAT TAT TAT TAT TAA T-T TAT T-T TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
173727 TA
1 TA
173729 ATTTAGGTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
2 5 0.14
3 28 0.78
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:173722 original size:16 final size:17
Alignment explanation
Indices: 173684--173733 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
173674 AAGTATAAAA
*
173684 TATTATATATTTTATTAT
1 TATTAT-TAATTTATTAT
173702 TATTATTAATTTATTTTAT
1 TATTATTAATTTA--TTAT
173721 TATTATTAATTTA
1 TATTATTAATTTA
173734 GGTCCACTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.21
18 6 0.21
19 17 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTATTAATTTATTAT
Found at i:178017 original size:13 final size:13
Alignment explanation
Indices: 178001--178025 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
177991 ATTCACCTTG
178001 AAAAAATATTATA
1 AAAAAATATTATA
178014 AAAAAATATTAT
1 AAAAAATATTAT
178026 TAGTTGGGAC
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAAATATTATA
Found at i:182501 original size:19 final size:19
Alignment explanation
Indices: 182464--182504 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
182454 GCTTTGTATA
**
182464 TTAAACTCAGTATTTTATT
1 TTAAACTCAGTATAATATT
*
182483 TTAAACTCAGTGTAATATT
1 TTAAACTCAGTATAATATT
182502 TTA
1 TTA
182505 GGAGCTCCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (19 bp):
TTAAACTCAGTATAATATT
Found at i:183195 original size:20 final size:20
Alignment explanation
Indices: 183166--183216 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
183156 ACATATCAGA
*
183166 AGTATTGATACCCAAACAAG
1 AGTATCGATACCCAAACAAG
183186 AGTATCGATACCCAAACAAG
1 AGTATCGATACCCAAACAAG
183206 AGTATCGATAC
1 AGTATCGATAC
183217 TACTCATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.20
Consensus pattern (20 bp):
AGTATCGATACCCAAACAAG
Found at i:185301 original size:3 final size:3
Alignment explanation
Indices: 185289--185349 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
185279 CTATTCAAAA
185289 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
185336 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
185350 ATAAAGAGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:185399 original size:3 final size:3
Alignment explanation
Indices: 185391--185578 Score: 226
Period size: 3 Copynumber: 64.7 Consensus size: 3
185381 TTTCTCAAAA
* *
185391 ATT ATT ATT A-T ATT ATT ATT ATT AGT ATT ATT ACT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
185437 ATT ATT ACT ATT ATT ACT ATT ATT ACT ATT ATT ATT A-T ATT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
185484 ATT ACT ATT ATT ATT ATT A-T ATT ATT ATT ATT ACT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
185530 AAT ATT ATT ATT ACT ATT ATT ACT ATT ATT ATT ATT A-T AAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
185577 AT
1 AT
185579 ATGAGGAGAA
Statistics
Matches: 157, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
2 12 0.08
3 145 0.92
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:185428 original size:29 final size:29
Alignment explanation
Indices: 185391--185578 Score: 239
Period size: 29 Copynumber: 6.7 Consensus size: 29
185381 TTTCTCAAAA
185391 ATTATTATTA-TATTATTATTATTAGTATT
1 ATTATTATTACTATTATTATTATTA-TATT
*
185420 ATTACTATTA-TATTATTATTATTACTATT
1 ATTATTATTACTATTATTATTATTA-TATT
* * *
185449 ATTACTATTATTACTATTATTATTATATT
1 ATTATTATTACTATTATTATTATTATATT
*
185478 ACTATTATTACTATTATTATTATTATATT
1 ATTATTATTACTATTATTATTATTATATT
185507 ATTATTATTACTATTATTATTA-TA-A-T
1 ATTATTATTACTATTATTATTATTATATT
*
185533 ATTATTATTACTATTATTACTA-T-TATT
1 ATTATTATTACTATTATTATTATTATATT
*
185560 ATTATTA-TAATATTATTAT
1 ATTATTATTACTATTATTAT
185579 ATGAGGAGAA
Statistics
Matches: 145, Mismatches: 11, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
26 34 0.23
27 9 0.06
28 2 0.01
29 87 0.60
30 13 0.09
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.59
Consensus pattern (29 bp):
ATTATTATTACTATTATTATTATTATATT
Found at i:185433 original size:26 final size:27
Alignment explanation
Indices: 185391--185577 Score: 207
Period size: 26 Copynumber: 7.3 Consensus size: 27
185381 TTTCTCAAAA
* *
185391 ATTATTATTA-TATTATTATTATTAGT
1 ATTATTACTATTATTATTATTATTACT
185417 ATTATTACTATTATATTATTATTATTACT
1 ATTATTACTA-T-TATTATTATTATTACT
* *
185446 ATTATTACTATTATTACTATTATTATT
1 ATTATTACTATTATTATTATTATTACT
*
185473 A-TATTACTATTATTACTATTA-T--T
1 ATTATTACTATTATTATTATTATTACT
185496 ATTA-T--TA-TATTATTATTATTACT
1 ATTATTACTATTATTATTATTATTACT
* *
185519 ATTATTATTA-TAATATTATTATTACT
1 ATTATTACTATTATTATTATTATTACT
*
185545 ATTATTACTATTATTATTATTA-TAAT
1 ATTATTACTATTATTATTATTATTACT
185571 ATTATTA
1 ATTATTA
185578 TATGAGGAGA
Statistics
Matches: 141, Mismatches: 9, Indels: 22
0.82 0.05 0.13
Matches are distributed among these distances:
20 10 0.07
21 3 0.02
23 8 0.06
24 3 0.02
25 1 0.01
26 65 0.46
27 25 0.18
28 1 0.01
29 25 0.18
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.59
Consensus pattern (27 bp):
ATTATTACTATTATTATTATTATTACT
Found at i:187005 original size:21 final size:22
Alignment explanation
Indices: 186975--187017 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
186965 TGCTGACGTG
*
186975 GTGGCGGTCCACAGT-GTTGAT
1 GTGGCAGTCCACAGTAGTTGAT
*
186996 GTGGCAGTCCACGGTAGTTGAT
1 GTGGCAGTCCACAGTAGTTGAT
187018 AAGGTGGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.16, C:0.19, G:0.37, T:0.28
Consensus pattern (22 bp):
GTGGCAGTCCACAGTAGTTGAT
Found at i:187027 original size:28 final size:28
Alignment explanation
Indices: 186996--187052 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
186986 CAGTGTTGAT
186996 GTGGCAGTCCACGGTAGTTGATAAGGTG
1 GTGGCAGTCCACGGTAGTTGATAAGGTG
* *
187024 GTGGCGGTCCACGGTAGTTTATAAGGTG
1 GTGGCAGTCCACGGTAGTTGATAAGGTG
187052 G
1 G
187053 CGGATAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.19, C:0.14, G:0.40, T:0.26
Consensus pattern (28 bp):
GTGGCAGTCCACGGTAGTTGATAAGGTG
Found at i:188722 original size:12 final size:12
Alignment explanation
Indices: 188707--188737 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
188697 GTTATTTAAA
*
188707 CGGGTATCGGGT
1 CGGGTATCGGGC
188719 CGGGTATCGGGC
1 CGGGTATCGGGC
188731 CGGGTAT
1 CGGGTAT
188738 ATATATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.19, G:0.48, T:0.23
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:188852 original size:12 final size:12
Alignment explanation
Indices: 188835--188860 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
188825 TTTTAATATT
188835 TATCGGGTCGGG
1 TATCGGGTCGGG
188847 TATCGGGTCGGG
1 TATCGGGTCGGG
188859 TA
1 TA
188861 ATCGAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.12, C:0.15, G:0.46, T:0.27
Consensus pattern (12 bp):
TATCGGGTCGGG
Found at i:188963 original size:29 final size:30
Alignment explanation
Indices: 188894--188969 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
188884 ATCAAATCCG
* * ***
188894 TCCCCGTCCCCGTTTAGCATAAATGGTTTT
1 TCCCCATCCCCGTTTAACATAAATCAATTT
188924 TCCCCATCCCCGTTTAACATAAA-CAATTT
1 TCCCCATCCCCGTTTAACATAAATCAATTT
188953 TCCCCATCCCCGTTTAA
1 TCCCCATCCCCGTTTAA
188970 TTCGGTTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 20 0.49
30 21 0.51
ACGTcount: A:0.22, C:0.36, G:0.09, T:0.33
Consensus pattern (30 bp):
TCCCCATCCCCGTTTAACATAAATCAATTT
Found at i:190825 original size:16 final size:16
Alignment explanation
Indices: 190772--190826 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
190762 CGGGTCATAT
190772 TTTGATTTAT-TCG-AA
1 TTTGATTTATAT-GAAA
*
190787 TTTGATTTGAATAT-AAC
1 TTTGATTT--ATATGAAA
190804 TTTGATTTATATGAAA
1 TTTGATTTATATGAAA
190820 TTTGATT
1 TTTGATT
190827 CGACTTGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
15 12 0.36
16 9 0.27
17 11 0.33
18 1 0.03
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.53
Consensus pattern (16 bp):
TTTGATTTATATGAAA
Found at i:198325 original size:23 final size:23
Alignment explanation
Indices: 198280--198326 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
198270 AGTATATCTG
* *
198280 TATGACATGTTTTCATATGCCTT
1 TATGACACGTTTTCATATACCTT
* *
198303 TATGACACGTTTTCTTCTACCTT
1 TATGACACGTTTTCATATACCTT
198326 T
1 T
198327 TGGAACATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.11, T:0.49
Consensus pattern (23 bp):
TATGACACGTTTTCATATACCTT
Found at i:198801 original size:2 final size:2
Alignment explanation
Indices: 198790--198833 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
198780 TAGCGGGTTC
198790 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
198831 TA T
1 TA T
198834 CATTTTAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:200340 original size:38 final size:38
Alignment explanation
Indices: 200298--200397 Score: 96
Period size: 39 Copynumber: 2.6 Consensus size: 38
200288 TTTTCCTAAT
*
200298 ATTTTCAGTTCAACCGAAAATGTTACT-TTCTTCGTGAC
1 ATTTTCAGTTCAACCGAAAATGTTA-TATTCTTCGTAAC
* * * *
200336 ATTTTC-GATCGCAACCGGAAATATTATATTCTTCGTAAT
1 ATTTTCAG-T-TCAACCGAAAATGTTATATTCTTCGTAAC
* *
200375 ATTTTTAGTTCAACAGAAAATGT
1 ATTTTCAGTTCAACCGAAAATGT
200398 AGAAAAAGAG
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
37 1 0.02
38 18 0.38
39 28 0.58
40 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (38 bp):
ATTTTCAGTTCAACCGAAAATGTTATATTCTTCGTAAC
Found at i:201025 original size:3 final size:3
Alignment explanation
Indices: 201019--201074 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
201009 AAAAACCATG
201019 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
201067 TCT TCT TC
1 TCT TCT TC
201075 AGCCATGTCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:201131 original size:65 final size:65
Alignment explanation
Indices: 201059--201188 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
201049 TCTTCTTCTT
201059 CTTCTTCTTCTTCTTCAGCCATGTCTGTTACTTTGGTTTCAAAAACCATGATTTTCCCAGACCAA
1 CTTCTTCTTCTTCTTCAGCCATGTCTGTTACTTTGGTTTCAAAAACCATGATTTTCCCAGACCAA
201124 CTTCTTCTTCTTCTTCAGCCATGTCTGTTACTTTGGTTTCAAAAACCATGATTTTCCCAGACCAA
1 CTTCTTCTTCTTCTTCAGCCATGTCTGTTACTTTGGTTTCAAAAACCATGATTTTCCCAGACCAA
201189 AAATCAAGCC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.22, C:0.28, G:0.11, T:0.40
Consensus pattern (65 bp):
CTTCTTCTTCTTCTTCAGCCATGTCTGTTACTTTGGTTTCAAAAACCATGATTTTCCCAGACCAA
Found at i:203744 original size:31 final size:31
Alignment explanation
Indices: 203709--203779 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
203699 CGTTGGTCAA
203709 AGGGCCACATTGGATTTATTTTCTGAGTTGG
1 AGGGCCACATTGGATTTATTTTCTGAGTTGG
*
203740 AGGGCCACATTGTATTTATTTTCTGAGTTGG
1 AGGGCCACATTGGATTTATTTTCTGAGTTGG
203771 AGGGCCACA
1 AGGGCCACA
203780 ATGAGAGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.35
Consensus pattern (31 bp):
AGGGCCACATTGGATTTATTTTCTGAGTTGG
Found at i:208948 original size:13 final size:12
Alignment explanation
Indices: 208912--208944 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
208902 CTAAACAAAC
208912 AAAAATACTTTT
1 AAAAATACTTTT
208924 AAAAACTACTTTT
1 AAAAA-TACTTTT
208937 AAAAATAC
1 AAAAATAC
208945 CTTTCACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAAATACTTTT
Found at i:215644 original size:2 final size:2
Alignment explanation
Indices: 215478--215627 Score: 157
Period size: 2 Copynumber: 74.5 Consensus size: 2
215468 TTGAAACAAC
*
215478 TA TA -A TA TA TA TA TA TA TA TA TA TA TA T- TA TA AA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
215519 GTT TA TA TA TA AA GTA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
215562 TA TA TA TA TA TA TA TA AA CTA TA TA GTT TA TA TT TA TA T- TA T-
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
215604 TA TA TA CTA TA TA TA TA TA TA TA T
1 TA TA TA -TA TA TA TA TA TA TA TA T
215628 TATGTATAAA
Statistics
Matches: 125, Mismatches: 12, Indels: 22
0.79 0.08 0.14
Matches are distributed among these distances:
1 5 0.04
2 113 0.90
3 7 0.06
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:215731 original size:61 final size:62
Alignment explanation
Indices: 215653--215859 Score: 158
Period size: 64 Copynumber: 3.4 Consensus size: 62
215643 TAGACCATGG
* *
215653 ATAAATTATATAATTTATATATGAACTAT-TGAACTATATATAAACTACATAATTTATTAAT
1 ATAAATTATATAATTTATATATAAACTATATGAACTATATATAAACTACACAATTTATTAAT
** * * * *
215714 ATAAATTATATTGTTTATATATAAATTATAAATGAATTATATATAAACTATACAATTTA-TATTT
1 ATAAATTATATAATTTATATATAAACTAT--ATGAACTATATATAAACTACACAATTTATTA-AT
* * * * *** * *
215778 ATATATTACATATAA-TTATAAAT-AA-TATAT--ACTATGTATAAATTATGTAGTTTATTAAC
1 ATAAATT--ATATAATTTATATATAAACTATATGAACTATATATAAACTACACAATTTATTAAT
*
215837 ATAAATTATATAGTTTATATATA
1 ATAAATTATATAATTTATATATA
215860 TAGTATAAAT
Statistics
Matches: 114, Mismatches: 23, Indels: 20
0.73 0.15 0.13
Matches are distributed among these distances:
57 5 0.04
58 7 0.06
59 24 0.21
60 2 0.02
61 27 0.24
63 5 0.04
64 33 0.29
65 7 0.06
66 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (62 bp):
ATAAATTATATAATTTATATATAAACTATATGAACTATATATAAACTACACAATTTATTAAT
Found at i:215742 original size:11 final size:11
Alignment explanation
Indices: 215708--215765 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
215698 TACATAATTT
215708 ATTA-ATATAA
1 ATTATATATAA
*
215718 ATTATAT-T-G
1 ATTATATATAA
*
215727 TTTATATATAA
1 ATTATATATAA
* *
215738 ATTATAAATGA
1 ATTATATATAA
215749 ATTATATATAA
1 ATTATATATAA
*
215760 ACTATA
1 ATTATA
215766 CAATTTATAT
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
9 6 0.17
10 6 0.17
11 24 0.67
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (11 bp):
ATTATATATAA
Found at i:215756 original size:22 final size:21
Alignment explanation
Indices: 215708--215765 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
215698 TACATAATTT
*
215708 ATTA-ATATAAATTAT-ATTG
1 ATTATATATAAATTATAAATG
*
215727 TTTATATATAAATTATAAATG
1 ATTATATATAAATTATAAATG
*
215748 AATTATATATAAACTATA
1 -ATTATATATAAATTATA
215766 CAATTTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.09
20 11 0.34
21 3 0.09
22 15 0.47
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (21 bp):
ATTATATATAAATTATAAATG
Found at i:215773 original size:20 final size:20
Alignment explanation
Indices: 215478--215775 Score: 132
Period size: 20 Copynumber: 14.6 Consensus size: 20
215468 TTGAAACAAC
* *
215478 TATAATATATATATATA-TA
1 TATAATTTATATATAAACTA
*
215497 TAT-ATATAT-TATAAACTA
1 TATAATTTATATATAAACTA
* *
215515 TATAGTTTATATATAAAGTA
1 TATAATTTATATATAAACTA
*
215535 TATATATATATATATATATATATTA
1 TATA-AT-T-TATATATA-A-ACTA
215560 TATATATATATATATATAAACTA
1 TATA-AT-T-TATATATAAACTA
* * *
215583 TATAGTTTATATTTATA-T-
1 TATAATTTATATATAAACTA
* * *
215601 TATTATATACTATATATA-TA
1 TATAATTTA-TATATAAACTA
*
215621 TAT-ATATTATGTATAAACTA
1 TATAAT-TTATATATAAACTA
** ** *
215641 TATAGA-CCATGGATAAATTA
1 TATA-ATTTATATATAAACTA
*
215661 TATAATTTATATATGAACTA
1 TATAATTTATATATAAACTA
*
215681 T-TGAA-CTATATATAAACTA
1 TAT-AATTTATATATAAACTA
* *
215700 CATAATTTATTAATATAAATTA
1 TATAATTTA-T-ATATAAACTA
** *
215722 TATTGTTTATATATAAATTA
1 TATAATTTATATATAAACTA
215742 TA-AATGAATTATATATAAACTA
1 TATAAT---TTATATATAAACTA
*
215764 TACAATTTATAT
1 TATAATTTATAT
215776 TTATATATTA
Statistics
Matches: 217, Mismatches: 38, Indels: 47
0.72 0.13 0.16
Matches are distributed among these distances:
17 5 0.02
18 17 0.08
19 41 0.19
20 76 0.35
21 4 0.02
22 33 0.15
23 18 0.08
24 2 0.01
25 21 0.10
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (20 bp):
TATAATTTATATATAAACTA
Found at i:215883 original size:7 final size:7
Alignment explanation
Indices: 215870--215903 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
215860 TAGTATAAAT
215870 GGTTTAG
1 GGTTTAG
*
215877 GGGTTAG
1 GGTTTAG
*
215884 GGTTTAA
1 GGTTTAG
215891 GGTTTAG
1 GGTTTAG
215898 GGTTTA
1 GGTTTA
215904 TGATTTAGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.41
Consensus pattern (7 bp):
GGTTTAG
Found at i:215910 original size:21 final size:21
Alignment explanation
Indices: 215870--215910 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
215860 TAGTATAAAT
*
215870 GGTTTAGGGGTTAGGGTTTAA
1 GGTTTAGGGGTTAGGATTTAA
* *
215891 GGTTTAGGGTTTATGATTTA
1 GGTTTAGGGGTTAGGATTTA
215911 GGATTAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.44
Consensus pattern (21 bp):
GGTTTAGGGGTTAGGATTTAA
Found at i:216057 original size:33 final size:33
Alignment explanation
Indices: 216010--216157 Score: 118
Period size: 33 Copynumber: 4.2 Consensus size: 33
216000 ATATGTAAAT
* *
216010 TATATATATTATATAGTTTACATATGAACTATA
1 TATATAAACTATATAGTTTACATATGAACTATA
* * *
216043 TGTATAAACTATATAAACTCTATATATAAACT-AACTATA
1 TATATAAACTATAT--AGT-T-TACAT--A-TGAACTATA
* *
216082 TAATATATATAGTTTAGTAGTTTACATATGAACTATA
1 T-ATATA-A-ACTATA-TAGTTTACATATGAACTATA
*
216119 TATATAAACTATATAGTTTACGTATGAACTATA
1 TATATAAACTATATAGTTTACATATGAACTATA
216152 TATATA
1 TATATA
216158 GTTTATTAAC
Statistics
Matches: 90, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
33 36 0.40
34 4 0.04
35 3 0.03
36 7 0.08
37 13 0.14
39 13 0.14
40 6 0.07
41 3 0.03
42 4 0.04
43 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (33 bp):
TATATAAACTATATAGTTTACATATGAACTATA
Found at i:216061 original size:22 final size:22
Alignment explanation
Indices: 216031--216092 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
216021 TATAGTTTAC
* *
216031 ATATGAACTATATGTATAAACT
1 ATATAAACTATATATATAAACT
*
216053 ATATAAACTCTATATATAAACT
1 ATATAAACTATATATATAAACT
216075 AACTATATAA-TATATATA
1 -A-TATA-AACTATATATA
216093 GTTTAGTAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 19 0.58
23 1 0.03
24 11 0.33
25 2 0.06
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37
Consensus pattern (22 bp):
ATATAAACTATATATATAAACT
Found at i:216207 original size:2 final size:2
Alignment explanation
Indices: 216187--216522 Score: 56
Period size: 2 Copynumber: 161.0 Consensus size: 2
216177 AAATTATTTT
* * *
216187 TA TA GTA TA TA GTA CA TA TA TA AA CTA TA TA TA CTA TA TA GTT TA
1 TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA
* * * * *
216232 CA TA TGA -A CTA TA TA TA AA AA CTA TA TA TA TA TA AA AA T- TA
1 TA TA T-A TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * *
216273 TA TA AA T- TA TA -A TT TA TA TA TA AA CTA TA TA CTA TA GT- TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA -TA T-A
* * *
216314 TA TT TA TA TA CTA TA TA -A TA TA TA TA GTC TA CA T- TA T- TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * *
216355 TA TA AA CTA TA TA GTT TA CA TA TGA -A T- TA TA TA TA TA GTT TA
1 TA TA TA -TA TA TA -TA TA TA TA T-A TA TA TA TA TA TA TA -TA TA
* * *
216397 T- TA GTGA -A CTA TA TA AA CTA TT TA TA TA GTA TA TA CTA TA TC
1 TA TA -T-A TA -TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA
* * * *
216439 TA TA AA CTA TA GTT TA TA TT TA TA TA CTA T- TGA TA TT TA TA TA
1 TA TA TA -TA TA -TA TA TA TA TA TA TA -TA TA T-A TA TA TA TA TA
*
216482 T- TA TA TA T- TA TA TA TA TA AA T- TA TA TA TA CTA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
216523 GTTTACATAT
Statistics
Matches: 240, Mismatches: 48, Indels: 92
0.63 0.13 0.24
Matches are distributed among these distances:
1 16 0.07
2 184 0.77
3 39 0.16
4 1 0.00
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:216219 original size:29 final size:29
Alignment explanation
Indices: 216187--216248 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
216177 AAATTATTTT
* *
216187 TATAGTATATAGTACATATATAAACTATA
1 TATACTATATAGTACACATATAAACTATA
** *
216216 TATACTATATAGTTTACATATGAACTATA
1 TATACTATATAGTACACATATAAACTATA
216245 TATA
1 TATA
216249 AAAACTATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.40
Consensus pattern (29 bp):
TATACTATATAGTACACATATAAACTATA
Found at i:216263 original size:17 final size:17
Alignment explanation
Indices: 216241--216276 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
216231 ACATATGAAC
216241 TATATATAAAAACTATA
1 TATATATAAAAACTATA
*
216258 TATATATAAAAATTATA
1 TATATATAAAAACTATA
216275 TA
1 TA
216277 AATTATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
TATATATAAAAACTATA
Found at i:216274 original size:15 final size:15
Alignment explanation
Indices: 216241--216296 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
216231 ACATATGAAC
216241 TATATATAAAAACTATA
1 TATATATAAAAA-T-TA
216258 TATATATAAAAATTA
1 TATATATAAAAATTA
* * *
216273 TATAAATTATAATT-
1 TATATATAAAAATTA
216287 TATATATAAA
1 TATATATAAA
216297 CTATATACTA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 7 0.21
15 13 0.39
16 1 0.03
17 12 0.36
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
TATATATAAAAATTA
Found at i:216359 original size:28 final size:30
Alignment explanation
Indices: 216325--216389 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 30
216315 ATTTATATAC
216325 TATATAATA-TATATAGTCTACAT-T-ATTA
1 TATATAA-ACTATATAGTCTACATATAATTA
*
216353 TATATAAACTATATAGTTTACATATGAATTA
1 TATATAAACTATATAGTCTACATAT-AATTA
216384 TATATA
1 TATATA
216390 TAGTTTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 1 0.03
28 20 0.62
29 1 0.03
31 10 0.31
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.45
Consensus pattern (30 bp):
TATATAAACTATATAGTCTACATATAATTA
Found at i:216404 original size:24 final size:24
Alignment explanation
Indices: 216362--216411 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
216352 ATATATAAAC
*
216362 TATATAGTTTACATATGAATTATA
1 TATATAGTTTACATATGAACTATA
*
216386 TATATAGTTTA-TTAGTGAACTATA
1 TATATAGTTTACATA-TGAACTATA
216410 TA
1 TA
216412 AACTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (24 bp):
TATATAGTTTACATATGAACTATA
Found at i:216498 original size:24 final size:22
Alignment explanation
Indices: 216446--216514 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
216436 ATCTATAAAC
216446 TATAGTTTATATTTATATACTAT
1 TATA-TTTATATTTATATACTAT
*
216469 TGATATTTATATATTATATATTA-
1 T-ATATTTATAT-TTATATACTAT
* *
216492 TATATATAAATTATATATACTAT
1 TATATTTATATT-TATATACTAT
216515 ATAGTATAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 1 0.03
22 16 0.42
23 9 0.24
24 12 0.32
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (22 bp):
TATATTTATATTTATATACTAT
Found at i:216499 original size:11 final size:11
Alignment explanation
Indices: 216453--216510 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
216443 AACTATAGTT
216453 TATATT-TATA
1 TATATTATATA
216463 TACTATTGATATTTA
1 TA-TATT-ATA--TA
216478 TATATTATATA
1 TATATTATATA
216489 T-TA-TATATA
1 TATATTATATA
*
216498 TAAATTATATA
1 TATATTATATA
216509 TA
1 TA
216511 CTATATAGTA
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
9 7 0.17
10 5 0.12
11 15 0.38
13 5 0.12
14 4 0.10
15 4 0.10
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (11 bp):
TATATTATATA
Found at i:216587 original size:18 final size:18
Alignment explanation
Indices: 216550--216587 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
216540 ATATAAAAAC
**
216550 TATATAAACTATATTTTA
1 TATATAAACTATATACTA
216568 TATATAAACTATATACTA
1 TATATAAACTATATACTA
216586 TA
1 TA
216588 GTTGATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (18 bp):
TATATAAACTATATACTA
Found at i:216606 original size:7 final size:7
Alignment explanation
Indices: 216592--216656 Score: 50
Period size: 7 Copynumber: 9.7 Consensus size: 7
216582 ACTATAGTTG
216592 ATAT-TT
1 ATATATT
216598 ATATATT
1 ATATATT
*
216605 ATATACT
1 ATATATT
*
216612 ATAGT-TG
1 ATA-TATT
216619 ATAT-TT
1 ATATATT
216625 ATATATT
1 ATATATT
*
216632 ATATAAT
1 ATATATT
216639 ATA-ATT
1 ATATATT
216645 -TATACTT
1 ATATA-TT
216652 ATATA
1 ATATA
216657 ATTTATACTA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
5 2 0.04
6 13 0.28
7 27 0.57
8 5 0.11
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (7 bp):
ATATATT
Found at i:216657 original size:15 final size:15
Alignment explanation
Indices: 216637--216665 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
216627 ATATTATATA
216637 ATATAATTTATACTT
1 ATATAATTTATACTT
216652 ATATAATTTATACT
1 ATATAATTTATACT
216666 ATAAAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATAATTTATACTT
Found at i:216669 original size:27 final size:27
Alignment explanation
Indices: 216577--216669 Score: 125
Period size: 27 Copynumber: 3.4 Consensus size: 27
216567 ATATATAAAC
*
216577 TATATACTATAGTTGATATTTATATAT
1 TATATACTATAATTGATATTTATATAT
*
216604 TATATACTATAGTTGATATTTATATAT
1 TATATACTATAATTGATATTTATATAT
* * *
216631 TATATAATATAATTTATACTTATATAAT
1 TATATACTATAATTGATATTTATAT-AT
216659 T-TATACTATAA
1 TATATACTATAA
216670 AAATTCAAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 57 0.95
28 3 0.05
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (27 bp):
TATATACTATAATTGATATTTATATAT
Found at i:216779 original size:18 final size:19
Alignment explanation
Indices: 216735--216779 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
216725 ATAAAATATT
216735 TATATAG-TATATACTACC
1 TATATAGTTATATACTACC
216753 TATATAGTTATTATA-TA-C
1 TATATAGTTA-TATACTACC
216771 TATATAGTT
1 TATATAGTT
216780 TACATATGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 17 0.68
19 4 0.16
20 4 0.16
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.47
Consensus pattern (19 bp):
TATATAGTTATATACTACC
Found at i:216786 original size:18 final size:20
Alignment explanation
Indices: 216752--216796 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
216742 TATATACTAC
*
216752 CTATATAGTTATTATAT-A-
1 CTATATAGTTATCATATGAG
216770 CTATATAGTT-TACATATGAG
1 CTATATAGTTAT-CATATGAG
216790 CTATATA
1 CTATATA
216797 TAAAAACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 14 0.61
19 1 0.04
20 7 0.30
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (20 bp):
CTATATAGTTATCATATGAG
Found at i:216829 original size:18 final size:18
Alignment explanation
Indices: 216806--216937 Score: 128
Period size: 18 Copynumber: 7.3 Consensus size: 18
216796 ATAAAAACTA
* *
216806 TATATATAAAGTATATGG
1 TATATATAAACTATATAG
216824 TATATATAAACTATATA-
1 TATATATAAACTATATAG
**
216841 T-TATAT-AGTTCAT-TAG
1 TATATATAAACT-ATATAG
*
216857 TATATATAAACTATCTAG
1 TATATATAAACTATATAG
*
216875 TATATATAAACTATATGGTGG
1 TATATATAAACTATA---TAG
*
216896 TATATATAAATTATATAG
1 TATATATAAACTATATAG
*
216914 TATATATAAACTATATAT
1 TATATATAAACTATATAG
216932 TATATA
1 TATATA
216938 GTTCATTAGT
Statistics
Matches: 94, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.04
16 8 0.09
17 8 0.09
18 58 0.62
21 16 0.17
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (18 bp):
TATATATAAACTATATAG
Found at i:216835 original size:31 final size:33
Alignment explanation
Indices: 216793--216870 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
216783 ATATGAGCTA
* *
216793 TATATAAAAACTATATA-TATAAAG-T-ATATGG
1 TATATATAAACTATATATTATAAAGTTCAT-TAG
*
216824 TATATATAAACTATATATTATATAGTTCATTAG
1 TATATATAAACTATATATTATAAAGTTCATTAG
216857 TATATATAAACTAT
1 TATATATAAACTAT
216871 CTAGTATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 16 0.39
32 6 0.15
33 17 0.41
34 2 0.05
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.41
Consensus pattern (33 bp):
TATATATAAACTATATATTATAAAGTTCATTAG
Found at i:216990 original size:90 final size:89
Alignment explanation
Indices: 216794--216990 Score: 236
Period size: 90 Copynumber: 2.2 Consensus size: 89
216784 TATGAGCTAT
*
216794 ATATAAAAACTATATATATAAAGTATATGGTATATATAAACTATATATTATATAGTTCATTAGTA
1 ATATAAAAA-TATATATATAAAGTATATAGTATATATAAACTATATATTATATAGTTCATTAGTA
*
216859 TATATAAACTATCTAGTATATATAA
65 TATATAAACTATATAGTATATATAA
*** * *
216884 ACTAT-ATGGTGGTATATATAAATTATATAGTATATATAAACTATATATTATATAGTTCATTAGT
1 A-TATAAAAAT-ATATATATAAAGTATATAGTATATATAAACTATATATTATATAGTTCATTAGT
* * *
216948 ATATAT-AACTTGTATATTAATTTATAA
64 ATATATAAAC-TATATAGT-ATATATAA
*
216975 ATATAAACATATATAT
1 ATATAAAAATATATAT
216991 TAATTGAAAG
Statistics
Matches: 88, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
89 4 0.05
90 71 0.81
91 13 0.15
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (89 bp):
ATATAAAAATATATATATAAAGTATATAGTATATATAAACTATATATTATATAGTTCATTAGTAT
ATATAAACTATATAGTATATATAA
Found at i:217090 original size:61 final size:61
Alignment explanation
Indices: 217023--217163 Score: 237
Period size: 61 Copynumber: 2.3 Consensus size: 61
217013 TATAAGGATC
*
217023 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGTAACATTAAATTTGGACT
1 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTGGACT
* *
217084 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATATATTGCATCATTAAATTTGGACT
1 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTGGACT
* *
217145 AAATTGAAAAAAATTTAAA
1 AAATTGAACAAATTTTAAA
217164 ACTAGGAGAC
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 75 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.35
Consensus pattern (61 bp):
AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTGGACT
Done.