Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009000.1 Hibiscus syriacus cultivar Beakdansim tig00112382_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: 1742898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:5490 original size:14 final size:14
Alignment explanation
Indices: 5471--5499 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5461 TGTGGGCATA
5471 TGTATAATATATAG
1 TGTATAATATATAG
5485 TGTATAATATATAG
1 TGTATAATATATAG
5499 T
1 T
5500 TTAGATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (14 bp):
TGTATAATATATAG
Found at i:5649 original size:15 final size:15
Alignment explanation
Indices: 5611--5640 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5601 TAGTAATTGT
5611 ATTGTATATCATATA
1 ATTGTATATCATATA
5626 ATTGTATATCATATA
1 ATTGTATATCATATA
5641 GTTTCATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
ATTGTATATCATATA
Found at i:15467 original size:43 final size:47
Alignment explanation
Indices: 15406--15512 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 47
15396 ATAACTAATG
*
15406 AATAAAATAATAACAAACT-AAA-CATATTTTAACT-C-TAATTCCT
1 AATAAAATAATAACAAACTAAAATAATATTTTAACTACTTAATTCCT
*
15449 AATAAAATAATAATAAACTAAAAATAATATTTTAACTCAACCTTAATTCCT
1 AATAAAATAATAACAAACT-AAAATAATATTTTAACT--A-CTTAATTCCT
15500 AATAAAATAATAA
1 AATAAAATAATAA
15513 ATCTAATCCT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
43 18 0.33
45 3 0.06
46 11 0.20
50 1 0.02
51 21 0.39
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (47 bp):
AATAAAATAATAACAAACTAAAATAATATTTTAACTACTTAATTCCT
Found at i:19090 original size:59 final size:59
Alignment explanation
Indices: 19027--19138 Score: 161
Period size: 59 Copynumber: 1.9 Consensus size: 59
19017 TATATGGATT
* * *
19027 AGTGTCATATCGAACCCTCCTAGTCGGAATGAAAAGGAAAACTTAATAATATGGTTCTA
1 AGTGTCATATCAAACCCTCCTAGTCGCAATGAAAAGGAAAACTCAATAATATGGTTCTA
* * * *
19086 AGTGTCCTATCAAACTCTCCTAGTCGCAATGAAAAGGTAAACTCGATAATATG
1 AGTGTCATATCAAACCCTCCTAGTCGCAATGAAAAGGAAAACTCAATAATATG
19139 ACTCTAACCG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (59 bp):
AGTGTCATATCAAACCCTCCTAGTCGCAATGAAAAGGAAAACTCAATAATATGGTTCTA
Found at i:21557 original size:20 final size:20
Alignment explanation
Indices: 21513--21564 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
21503 AAAATACCTC
21513 AGTATCGATACTGACCCTTTG
1 AGTATCGATACTGACCC-TTG
*
21534 AGTACCGATACTAGACCC-TG
1 AGTATCGATACT-GACCCTTG
21554 AGTATCGATAC
1 AGTATCGATAC
21565 CCCTATGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 12 0.43
21 11 0.39
22 5 0.18
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (20 bp):
AGTATCGATACTGACCCTTG
Found at i:27258 original size:13 final size:13
Alignment explanation
Indices: 27235--27285 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
27225 TCTATATAAA
27235 CAGTTAATCAAAT
1 CAGTTAATCAAAT
**
27248 CAGTTTTTCAAAT
1 CAGTTAATCAAAT
27261 CAGTTAATCAAAT
1 CAGTTAATCAAAT
*
27274 CAGTTAGTCAAA
1 CAGTTAATCAAA
27286 CCAACTACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (13 bp):
CAGTTAATCAAAT
Found at i:27284 original size:26 final size:26
Alignment explanation
Indices: 27235--27285 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
27225 TCTATATAAA
**
27235 CAGTTAATCAAATCAGTTTTTCAAAT
1 CAGTTAATCAAATCAGTTAGTCAAAT
27261 CAGTTAATCAAATCAGTTAGTCAAA
1 CAGTTAATCAAATCAGTTAGTCAAA
27286 CCAACTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (26 bp):
CAGTTAATCAAATCAGTTAGTCAAAT
Found at i:28414 original size:72 final size:72
Alignment explanation
Indices: 28338--28471 Score: 196
Period size: 72 Copynumber: 1.9 Consensus size: 72
28328 CCTTGAAAGT
* * * * *
28338 TTTAGGCTTGCTAGTTTTCGAGTAGAGTCGAGCTCCATTTCACAATTTTCGAGTCGAGTCGAACT
1 TTTAGGCTCGCGAGTTTTCAAGTAGAGTCAAGATCCATTTCACAATTTTCGAGTCGAGTCGAACT
28403 TAAAAAC
66 TAAAAAC
* * *
28410 TTTAGGCTCGCGAGTTTTCAAGTTGAGTCAAGATCCATTTCAGAGTTTTCGAGTCGAGTCGA
1 TTTAGGCTCGCGAGTTTTCAAGTAGAGTCAAGATCCATTTCACAATTTTCGAGTCGAGTCGA
28472 GGTCAGCAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 54 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (72 bp):
TTTAGGCTCGCGAGTTTTCAAGTAGAGTCAAGATCCATTTCACAATTTTCGAGTCGAGTCGAACT
TAAAAAC
Found at i:35767 original size:24 final size:23
Alignment explanation
Indices: 35740--35793 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 23
35730 AACACTTAAT
35740 TCCTAATTAAT-AGTAAACTAAAAA
1 TCCTAATTAATAAGT-AA-TAAAAA
*
35764 TCCTAA-TAATAAGTAATTAAAA
1 TCCTAATTAATAAGTAATAAAAA
35786 TCCTAATT
1 TCCTAATT
35794 CAAATTCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 11 0.41
23 7 0.26
24 9 0.33
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (23 bp):
TCCTAATTAATAAGTAATAAAAA
Found at i:45387 original size:28 final size:29
Alignment explanation
Indices: 45351--45406 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
45341 TTTAAGCCCC
* *
45351 AATTCTATTT-TT-TTTATTATAGTTTTAT
1 AATTATATTTATTATTTAATAT-GTTTTAT
45379 AATTATATTTATTATTTAATATGTTTTA
1 AATTATATTTATTATTTAATATGTTTTA
45407 CCTTAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.38
29 8 0.33
30 7 0.29
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (29 bp):
AATTATATTTATTATTTAATATGTTTTAT
Found at i:46219 original size:20 final size:20
Alignment explanation
Indices: 46194--46245 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
46184 TTTATCTTAT
46194 AGTATCGATACCCAAGGGAG
1 AGTATCGATACCCAAGGGAG
* * **
46214 AGTATCGATACTCATGGGTT
1 AGTATCGATACCCAAGGGAG
46234 AGTATCGATACC
1 AGTATCGATACC
46246 AAGAGGCTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (20 bp):
AGTATCGATACCCAAGGGAG
Found at i:53031 original size:13 final size:13
Alignment explanation
Indices: 53013--53038 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53003 ATTGCACTCG
53013 ATAGCATGAGCAT
1 ATAGCATGAGCAT
53026 ATAGCATGAGCAT
1 ATAGCATGAGCAT
53039 TCATTGAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
ATAGCATGAGCAT
Found at i:67444 original size:45 final size:47
Alignment explanation
Indices: 67388--67540 Score: 194
Period size: 45 Copynumber: 3.4 Consensus size: 47
67378 TGCACCAATC
**
67388 CATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATTT
1 CATGCATCGATGCACTCATGGAATATTTTGAAACATCGAATGCATTT
*
67433 CATGCATCGATGCACTCA--GAGT-TTTATGAAAACATCGAATGCATTT
1 CATGCATCGATGCACTCATGGAATATTT-TG-AAACATCGAATGCATTT
* *
67479 GATGCATCGATGCACTC-TGG-CTATTTTGAAACATCGAATGCATTT
1 CATGCATCGATGCACTCATGGAATATTTTGAAACATCGAATGCATTT
67524 CATGCATCGATGCACTC
1 CATGCATCGATGCACTC
67541 TTAGTGCATC
Statistics
Matches: 95, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
43 1 0.01
44 5 0.05
45 48 0.51
46 37 0.39
47 4 0.04
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (47 bp):
CATGCATCGATGCACTCATGGAATATTTTGAAACATCGAATGCATTT
Found at i:67541 original size:45 final size:46
Alignment explanation
Indices: 67417--67541 Score: 193
Period size: 46 Copynumber: 2.7 Consensus size: 46
67407 GAATAAATTG
*
67417 AACATCGAATGCATTTCATGCATCGATGCACTCAGAGTTTTATGAA
1 AACATCGAATGCATTTCATGCATCGATGCACTCTGAGTTTTATGAA
*
67463 AACATCGAATGCATTTGATGCATCGATGCACTCTG-GCTATTT-TG-A
1 AACATCGAATGCATTTCATGCATCGATGCACTCTGAG-T-TTTATGAA
67508 AACATCGAATGCATTTCATGCATCGATGCACTCT
1 AACATCGAATGCATTTCATGCATCGATGCACTCT
67542 TAGTGCATCG
Statistics
Matches: 74, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
45 35 0.47
46 36 0.49
47 3 0.04
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (46 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTGAGTTTTATGAA
Found at i:68993 original size:18 final size:20
Alignment explanation
Indices: 68957--68993 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
68947 TTTCTTTAAA
*
68957 TTAATATAAGTATTTTCATT
1 TTAATATAAGTATTGTCATT
68977 TTAATAT-A-TATTGTCAT
1 TTAATATAAGTATTGTCAT
68994 ATTATGGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 1 0.06
20 7 0.44
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
TTAATATAAGTATTGTCATT
Found at i:91460 original size:24 final size:24
Alignment explanation
Indices: 91433--91478 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
91423 TTTATTAGTT
* *
91433 TAATTTAATTTATAAAATTATTAA
1 TAATTAAATATATAAAATTATTAA
*
91457 TAATTAAATATATAATATTATT
1 TAATTAAATATATAAAATTATT
91479 GTATATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAATTAAATATATAAAATTATTAA
Found at i:92135 original size:23 final size:23
Alignment explanation
Indices: 92085--92128 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
92075 TTTTTTTCTA
*
92085 TTTATCTT-TATTTTTATGATACT
1 TTTAT-TTCTATTTTTATAATACT
92108 TTTATTTCTATTTTTATAATA
1 TTTATTTCTATTTTTATAATA
92129 TGTTTATCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTATTTCTATTTTTATAATACT
Found at i:93804 original size:24 final size:25
Alignment explanation
Indices: 93777--93823 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
93767 ACAACTAAAT
* *
93777 ATGTTGTATATTATT-TACATTATA
1 ATGTTATATATCATTATACATTATA
93801 ATGTTATATATCATTATACATTA
1 ATGTTATATATCATTATACATTA
93824 AATTTACGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.51
Consensus pattern (25 bp):
ATGTTATATATCATTATACATTATA
Found at i:99082 original size:23 final size:22
Alignment explanation
Indices: 99047--99089 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
99037 ATAATTATTT
99047 AAAAAATTAAATAAAAAATACC
1 AAAAAATTAAATAAAAAATACC
*
99069 AAAAACATTTAATAAAAAATA
1 AAAAA-ATTAAATAAAAAATA
99090 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (22 bp):
AAAAAATTAAATAAAAAATACC
Found at i:99819 original size:17 final size:18
Alignment explanation
Indices: 99797--99830 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
99787 TCAGCCAGTC
99797 CGGTTCGAA-CGGTTCAG
1 CGGTTCGAACCGGTTCAG
*
99814 CGGTTCTAACCGGTTCA
1 CGGTTCGAACCGGTTCA
99831 CTAATAACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCGAACCGGTTCAG
Found at i:102402 original size:25 final size:26
Alignment explanation
Indices: 102374--102422 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
102364 CAAAATCAAA
*
102374 TCCAATG-TCCAAAATAAGTATAATG
1 TCCAATGTTACAAAATAAGTATAATG
*
102399 TCCAATGTTACAAAATAATTATAA
1 TCCAATGTTACAAAATAAGTATAA
102423 GTAATAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (26 bp):
TCCAATGTTACAAAATAAGTATAATG
Found at i:105147 original size:103 final size:103
Alignment explanation
Indices: 104922--105139 Score: 436
Period size: 103 Copynumber: 2.1 Consensus size: 103
104912 GTAGAGGGTC
104922 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
104987 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
105025 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
105090 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
105128 TATGTGGTCCTT
1 TATGTGGTCCTT
105140 ATGGACATTA
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:105190 original size:23 final size:23
Alignment explanation
Indices: 105164--105218 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
105154 ATGGCACTAC
105164 GGTGCAATTCTACATGACACTCT-
1 GGTGCAATTCTACATGACACT-TA
* *
105187 GGTGCAATTCTACGTGGCACTTA
1 GGTGCAATTCTACATGACACTTA
105210 GGTGCAATT
1 GGTGCAATT
105219 ATATGAGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (23 bp):
GGTGCAATTCTACATGACACTTA
Found at i:112108 original size:103 final size:103
Alignment explanation
Indices: 111883--112100 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
111873 GTAGAGGGTC
*
111883 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAAGTGTGAGGTCTGTTGAGACACATAC
111948 TTGATCTTTGGCATATATATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATATATATGATTCTTAAGGAATGA
111986 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAAGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAAGTGTGAGGTCTGTTGAGACACATAC
*
112051 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATATATATGATTCTTAAGGAATGA
112089 TATGTGGTCCTT
1 TATGTGGTCCTT
112101 ATGGACATTA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAAGTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATATATATGATTCTTAAGGAATGA
Found at i:112143 original size:23 final size:23
Alignment explanation
Indices: 112117--112184 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
112107 ATTATTATAT
112117 GGCACTACGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTCTATGC
* * *
112140 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTATGC
*
112163 GGCACTTA-GGTGCAATTATATG
1 GGCAC-TACGGTGCAATTCTATG
112185 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 37 0.97
24 1 0.03
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTATGC
Found at i:114692 original size:21 final size:21
Alignment explanation
Indices: 114668--114737 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
114658 AAGCCTTCGT
*
114668 TATGGATACTATTTCATCCTG
1 TATGGATACTATTTCATCCAG
* *
114689 TATGGATACCA--ACACTCCAG
1 TATGGATACTATTTCA-TCCAG
*
114709 TATGGATACTAGTTT-ATCCGG
1 TATGGATACTA-TTTCATCCAG
114730 TATGGATA
1 TATGGATA
114738 TCAACACTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 2 0.05
20 14 0.36
21 22 0.56
22 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (21 bp):
TATGGATACTATTTCATCCAG
Found at i:114733 original size:41 final size:41
Alignment explanation
Indices: 114668--114747 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
114658 AAGCCTTCGT
*
114668 TATGGATACTATTTCATCCTGTATGGATACCAACACTCCAG
1 TATGGATACTATTTCATCCGGTATGGATACCAACACTCCAG
*
114709 TATGGATACTAGTTT-ATCCGGTATGGATATCAACACTCC
1 TATGGATACTA-TTTCATCCGGTATGGATACCAACACTCC
114748 GGTGTCGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 33 0.92
42 3 0.08
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (41 bp):
TATGGATACTATTTCATCCGGTATGGATACCAACACTCCAG
Found at i:114758 original size:41 final size:41
Alignment explanation
Indices: 114672--114758 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
114662 CTTCGTTATG
* *
114672 GATACTATTTCATCCTGTATGGATACCAACACTCCAGTATG
1 GATACTATTTCATCCGGTATGGATACCAACACTCCAGTATC
* * *
114713 GATACTAGTTT-ATCCGGTATGGATATCAACACTCCGGTGTC
1 GATACTA-TTTCATCCGGTATGGATACCAACACTCCAGTATC
114754 GATAC
1 GATAC
114759 CAAAGGGTCG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 37 0.93
42 3 0.08
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (41 bp):
GATACTATTTCATCCGGTATGGATACCAACACTCCAGTATC
Found at i:121246 original size:114 final size:114
Alignment explanation
Indices: 121041--121276 Score: 445
Period size: 114 Copynumber: 2.1 Consensus size: 114
121031 AAATTACCTA
*
121041 ATGGAATACATATTTCATCTGGCCTGAATGAAGTTGCAGCCTGCAGGCAGCATAGGAAGCACCTG
1 ATGGCATACATATTTCATCTGGCCTGAATGAAGTTGCAGCCTGCAGGCAGCATAGGAAGCACCTG
121106 GTTAAACTAATAATGTCTTCAAAATGTTAGATGCAACAATCAAATATTT
66 GTTAAACTAATAATGTCTTCAAAATGTTAGATGCAACAATCAAATATTT
*
121155 ATGGCATACATATTTCATCTGGCCTGAATGAAGTTGCAGCTTGCAGGCAGCATAGGAAGCACCTG
1 ATGGCATACATATTTCATCTGGCCTGAATGAAGTTGCAGCCTGCAGGCAGCATAGGAAGCACCTG
*
121220 GTTAAACTAATAATGTCTTCAAAATGTTAGATGCAACAATGAAATATTT
66 GTTAAACTAATAATGTCTTCAAAATGTTAGATGCAACAATCAAATATTT
121269 ATGGCATA
1 ATGGCATA
121277 AATCTTCATA
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 119 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (114 bp):
ATGGCATACATATTTCATCTGGCCTGAATGAAGTTGCAGCCTGCAGGCAGCATAGGAAGCACCTG
GTTAAACTAATAATGTCTTCAAAATGTTAGATGCAACAATCAAATATTT
Found at i:125536 original size:114 final size:114
Alignment explanation
Indices: 125342--125547 Score: 294
Period size: 114 Copynumber: 1.8 Consensus size: 114
125332 TCCTGAATTT
** *
125342 CCTGCACAAGCTGCGGCAAATTAGGATCGATCTCCTTCCTCACAGCCACATGATTCTCACTCCTT
1 CCTGCACAAGCTGCCACAAATTAGGATCGATCTCCTTCCTCACAGCCACAAGATTCTCACTCCTT
*
125407 TCCTTTCTCCTATCTCTCCTATGGTTGATGGGCTGCTTAACGAGAACTC
66 TCCTTTCTCCCATCTCTCCTATGGTTGATGGGCTGCTTAACGAGAACTC
* *
125456 CCTGCACAAGCTGCCACAAATTAGGATCGATCTCCTTCCTTACCTG-CACAAGATTCT-AGGC-C
1 CCTGCACAAGCTGCCACAAATTAGGATCGATCTCCTTCCTCA-CAGCCACAAGATTCTCA--CTC
125518 CTTTCCTTT-TCCCCATCTCTCCTATGGTTG
63 CTTTCCTTTCT-CCCATCTCTCCTATGGTTG
125548 GTGGTCCGAC
Statistics
Matches: 82, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
113 2 0.02
114 77 0.94
115 3 0.04
ACGTcount: A:0.20, C:0.33, G:0.16, T:0.31
Consensus pattern (114 bp):
CCTGCACAAGCTGCCACAAATTAGGATCGATCTCCTTCCTCACAGCCACAAGATTCTCACTCCTT
TCCTTTCTCCCATCTCTCCTATGGTTGATGGGCTGCTTAACGAGAACTC
Found at i:138801 original size:43 final size:43
Alignment explanation
Indices: 138704--139029 Score: 383
Period size: 44 Copynumber: 7.5 Consensus size: 43
138694 TGCAAAACAG
* * * * *
138704 GTAAGGTCTTACCCTTACACATAGA-AAAAGAGCCTGGGGAAACG
1 GTAAGG-CTTACCCTTGCACACA-ACAAAGGAACCTGGGGAAACT
* * *
138748 GTAAGGTCTTACCCTTGCACATATCAAAGGAGCCT-GGGAAACT
1 GTAAGG-CTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
* *
138791 ATAAGGTCTTACCCTTGCACACAACAAAGGAACCTGGGGAAATT
1 GTAAGG-CTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
* *
138835 GTAAGGCTTACCCTTG--CAC-ACAAATGAATCTGGGGGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCT-GGGGAAACT
*
138876 GTAAGGCTTACCCTTACACACAACAAAGGAACCTGGGGAGAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGA-AACT
* *
138920 GTAAGGCTTACTCTTGCACACAACAAAGGAACTTGGGGGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCT-GGGGAAACT
* *
138964 GTAAGGCTTACCCTTGCACACATCAAATGAACCTGGGAGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG-GAAACT
*
139008 GTAAGGCTTACCCTTACACACA
1 GTAAGGCTTACCCTTGCACACA
139030 GTAAATGAGT
Statistics
Matches: 249, Mismatches: 24, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
40 10 0.04
41 26 0.10
43 59 0.24
44 149 0.60
45 5 0.02
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.20
Consensus pattern (43 bp):
GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
Found at i:143424 original size:44 final size:44
Alignment explanation
Indices: 143375--143837 Score: 533
Period size: 44 Copynumber: 10.6 Consensus size: 44
143365 AAGTATGCAA
* * * * * *
143375 AAACGGTAAGGTCTTACCCTTTCACATAGCAAAAGAGCCT-GGGA
1 AAACTGTAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGGGGG
* * * *
143419 AAACGGTAAGGTCTTACCCTTTCACATAGCAAAGGAGCCT--GGG
1 AAACTGTAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGGGGG
* *
143462 AAACTATAAGGTTTTACCCTTGCACACAGCAAAGGAACCT-GGGG
1 AAACTGTAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGGGGG
** * *
143506 AAACTGTAAGGCTTACCCTTGCACACAATAAATGTACCTGGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGG
* * * *
143550 AAACTGTTAGACTTACCCTTACACACAGCAAAGGAACCTGGGGA
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGG
* * *
143594 AAACTTTAAGGCTTACCCTTGCATACAACAAAGGAACCTGGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGG
* * *
143638 AAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGAGGA
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGG
* **
143682 AAATTGTAAGGCTTACCCTTGCACACAAAAAAGGAACCTGGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGG
* *
143726 AAACTGTAAGGCTTACCCTTACACACAACAAAGGAACCTGGGGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGG
* * *
143770 AAACTGTAAGGCTTACCCTTGTACACAACAAAGGAGCCT--GGG
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGG
*
143812 AAACAGTAAGGACTTACCCTTGCACA
1 AAACTGTAAGG-CTTACCCTTGCACA
143838 TAGTAGAGGA
Statistics
Matches: 371, Mismatches: 45, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
42 13 0.04
43 72 0.19
44 286 0.77
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (44 bp):
AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGG
Found at i:146275 original size:20 final size:19
Alignment explanation
Indices: 146245--146285 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
146235 TTACTTTTTG
146245 GTCAAAGTCAACGGTCAAT
1 GTCAAAGTCAACGGTCAAT
146264 GTCAACAGTCAACGGTCAAT
1 GTCAA-AGTCAACGGTCAAT
146284 GT
1 GT
146286 TAGTTAACCG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (19 bp):
GTCAAAGTCAACGGTCAAT
Found at i:158770 original size:30 final size:30
Alignment explanation
Indices: 158726--158830 Score: 99
Period size: 30 Copynumber: 3.6 Consensus size: 30
158716 AAAGAATATT
* *
158726 TTAAATTTTATAAAAAAATTAATTAAGTAC
1 TTAAACTTTCTAAAAAAATTAATTAAGTAC
* * * *
158756 TTAAACTTTCTAAAAGAATCAATTAGGTCC
1 TTAAACTTTCTAAAAAAATTAATTAAGTAC
* *
158786 TCAAAC--T-TAGAAAAAATTAATTAAGTTC
1 TTAAACTTTCTA-AAAAAATTAATTAAGTAC
*
158814 TTAAATTTTCTAAAAAA
1 TTAAACTTTCTAAAAAA
158831 TCAATTAGGC
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
27 2 0.03
28 19 0.33
30 35 0.60
31 2 0.03
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.36
Consensus pattern (30 bp):
TTAAACTTTCTAAAAAAATTAATTAAGTAC
Found at i:158828 original size:28 final size:28
Alignment explanation
Indices: 158739--158829 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
158729 AATTTTATAA
158739 AAAAATTAATTAAGTACTTAAACTTTCT
1 AAAAATTAATTAAGTACTTAAACTTTCT
* * * * ***
158767 AAAAGAATCAATTAGGTCCTCAAACTTAGA
1 -AAA-AATTAATTAAGTACTTAAACTTTCT
* *
158797 AAAAATTAATTAAGTTCTTAAATTTTCT
1 AAAAATTAATTAAGTACTTAAACTTTCT
158825 AAAAA
1 AAAAA
158830 ATCAATTAGG
Statistics
Matches: 46, Mismatches: 15, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
28 22 0.48
29 6 0.13
30 18 0.39
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (28 bp):
AAAAATTAATTAAGTACTTAAACTTTCT
Found at i:158850 original size:57 final size:58
Alignment explanation
Indices: 158738--158857 Score: 188
Period size: 58 Copynumber: 2.1 Consensus size: 58
158728 AAATTTTATA
*
158738 AAAAAATTAATTAAGTACTTAAACTTTCTAAAAGAATCAATTAGGTCCTCAAACTTAG
1 AAAAAATTAATTAAGTACTTAAACTTTCTAAAAGAATCAATTAGGCCCTCAAACTTAG
* * *
158796 AAAAAATTAATTAAGTTCTTAAATTTTCTAAAA-AATCAATTAGGCCCTCGAACTTAG
1 AAAAAATTAATTAAGTACTTAAACTTTCTAAAAGAATCAATTAGGCCCTCAAACTTAG
*
158853 TAAAA
1 AAAAA
158858 TAAAAATCAA
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 26 0.46
58 31 0.54
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (58 bp):
AAAAAATTAATTAAGTACTTAAACTTTCTAAAAGAATCAATTAGGCCCTCAAACTTAG
Found at i:158856 original size:29 final size:29
Alignment explanation
Indices: 158738--158857 Score: 89
Period size: 29 Copynumber: 4.1 Consensus size: 29
158728 AAATTTTATA
* * * * **
158738 AAAAAATTAATTAAGTACTTAAACTTTCT
1 AAAAAATCAATTAGGTCCTCAAACTTAGT
158767 AAAAGAATCAATTAGGTCCTCAAACTTAG-
1 AAAA-AATCAATTAGGTCCTCAAACTTAGT
* * * * * **
158796 AAAAAATTAATTAAGTTCTTAAATTTTCT
1 AAAAAATCAATTAGGTCCTCAAACTTAGT
* *
158825 AAAAAATCAATTAGGCCCTCGAACTTAGT
1 AAAAAATCAATTAGGTCCTCAAACTTAGT
158854 AAAA
1 AAAA
158858 TAAAAATCAA
Statistics
Matches: 67, Mismatches: 22, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
28 17 0.25
29 32 0.48
30 18 0.27
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (29 bp):
AAAAAATCAATTAGGTCCTCAAACTTAGT
Found at i:160035 original size:21 final size:21
Alignment explanation
Indices: 160009--160049 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
159999 TGATAAAAAA
*
160009 TACCTAAAACATTATTATTTC
1 TACCTAAAACATTAATATTTC
160030 TACCTAAAACATTAATATTT
1 TACCTAAAACATTAATATTT
160050 TTTAAAATTT
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:160169 original size:27 final size:27
Alignment explanation
Indices: 160131--160198 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
160121 TCGTATATGT
*
160131 TAACAAAACCGGTAAAACGTCCAATAA
1 TAACAAAACCGGTAAAACGGCCAATAA
*
160158 TAACAAAACCGGTAAAATGGCCAATAA
1 TAACAAAACCGGTAAAACGGCCAATAA
*
160185 TAACAAAATCGGTA
1 TAACAAAACCGGTA
160199 GAAATAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.51, C:0.19, G:0.13, T:0.16
Consensus pattern (27 bp):
TAACAAAACCGGTAAAACGGCCAATAA
Found at i:163833 original size:14 final size:15
Alignment explanation
Indices: 163808--163836 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
163798 TTATAAATAT
163808 AATAATATTTTAAAA
1 AATAATATTTTAAAA
163823 AATAA-ATTTTAAAA
1 AATAATATTTTAAAA
163837 TCGTCGGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAATATTTTAAAA
Found at i:164166 original size:30 final size:30
Alignment explanation
Indices: 164098--164166 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
164088 CATGGATCAA
* *
164098 TAAAATTTAAAAAAATATAATTTAGACTCC
1 TAAAATTTTAAAAAATATAATTTAGACACC
*
164128 TAAAATTTTAAAAAAT-TAATTTAGCCACC
1 TAAAATTTTAAAAAATATAATTTAGACACC
164157 TCAAAATTTT
1 T-AAAATTTT
164167 TAGAAATGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 12 0.34
30 23 0.66
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.36
Consensus pattern (30 bp):
TAAAATTTTAAAAAATATAATTTAGACACC
Found at i:165385 original size:7 final size:7
Alignment explanation
Indices: 165352--165383 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
165342 AGTAGACTGG
165352 GGGAAAA
1 GGGAAAA
165359 GGGAAAA
1 GGGAAAA
165366 GGGAAAA
1 GGGAAAA
*
165373 GGGAGAA
1 GGGAAAA
165380 GGGA
1 GGGA
165384 GAGGGGAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (7 bp):
GGGAAAA
Found at i:166656 original size:41 final size:41
Alignment explanation
Indices: 166552--166690 Score: 120
Period size: 41 Copynumber: 3.4 Consensus size: 41
166542 ATAACTCATC
* * *
166552 TATAGTGGTGTTTTTTCAACAAAAGCCGCAATAGAG-TAGTA
1 TATAGTGGTGTTTTTAC-ACAAAAGCCGCAATAGGGTTCGTA
* * * * *
166593 TTTTAG-CGTCGTTGTTATACAAACGCCGCAATAGGGTTCGTA
1 -TATAGTGGT-GTTTTTACACAAAAGCCGCAATAGGGTTCGTA
* ** * *
166635 TATAGTGGTGTTTTTACACAAATGTAGCAATAGGGTTCATC
1 TATAGTGGTGTTTTTACACAAAAGCCGCAATAGGGTTCGTA
166676 TATAGTGGTGTTTTT
1 TATAGTGGTGTTTTT
166691 TTTCCAAAAA
Statistics
Matches: 77, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
41 62 0.81
42 15 0.19
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (41 bp):
TATAGTGGTGTTTTTACACAAAAGCCGCAATAGGGTTCGTA
Found at i:166713 original size:44 final size:41
Alignment explanation
Indices: 166617--166714 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
166607 TTATACAAAC
* *
166617 GCCGCAATAGGGTTCGTATATAGTGGTGTTTTTACACAAAT
1 GCCGCAATAGGGTTCATATATAGTGGTGTTTTTACAAAAAT
** * *
166658 GTAGCAATAGGGTTCATCTATAGTGGTGTTTTTTTTCCAAAAAT
1 GCCGCAATAGGGTTCATATATAGTGGTG---TTTTTACAAAAAT
*
166702 GCCGCAGTAGGGT
1 GCCGCAATAGGGT
166715 AGTATTTTAG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 24 0.53
44 21 0.47
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.35
Consensus pattern (41 bp):
GCCGCAATAGGGTTCATATATAGTGGTGTTTTTACAAAAAT
Found at i:166963 original size:41 final size:41
Alignment explanation
Indices: 166876--167003 Score: 132
Period size: 41 Copynumber: 3.1 Consensus size: 41
166866 AAAAGACTCA
* * * *
166876 TACTTTAGCGGCGTTTGTATACAAACGCCACTAAAGGCTTA
1 TACTTTAGCGGCGTTTGTATACAAACGCCGCTATAGACTTT
* * * *
166917 GACTTTTGTGGCGTTTGTATACAAACACCGCTATAGACTTT
1 TACTTTAGCGGCGTTTGTATACAAACGCCGCTATAGACTTT
* * * *
166958 TACTTTAGGGGCATTTTTATACAAACGTCGCTATAGA-TTT
1 TACTTTAGCGGCGTTTGTATACAAACGCCGCTATAGACTTT
166998 GTACTT
1 -TACTT
167004 GATTTGTACT
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 3 0.04
41 68 0.96
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (41 bp):
TACTTTAGCGGCGTTTGTATACAAACGCCGCTATAGACTTT
Found at i:169670 original size:54 final size:54
Alignment explanation
Indices: 169602--169803 Score: 332
Period size: 54 Copynumber: 3.7 Consensus size: 54
169592 CACCTAAGTG
* *
169602 CACATAGTGCCGATACGGTAATTCATAAACTCATTATGAATTCCATGGGTTGTA
1 CACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTCCATGGGTTGCA
* * *
169656 CACATAGTGTCGATACGATAATTCACAAACTCATTATGAATTTCATGGGTTGCA
1 CACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTCCATGGGTTGCA
* **
169710 CACATAGTGTCGATACGGTAATTCACAAACTCATTATGAATTCGGTGGGTTGCA
1 CACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTCCATGGGTTGCA
169764 CACATAGTGCCGATACGGTAATTCACAAACTCATTATGAA
1 CACATAGTGCCGATACGGTAATTCACAAACTCATTATGAA
169804 AATATGTCAA
Statistics
Matches: 138, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 138 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (54 bp):
CACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTCCATGGGTTGCA
Found at i:172413 original size:40 final size:41
Alignment explanation
Indices: 172369--172466 Score: 117
Period size: 45 Copynumber: 2.3 Consensus size: 41
172359 CTAGAAGGTT
*
172369 TATAAACAAATTATAGATAATATCTATACCAATATACAACTA
1 TATAAATAAATTATAGATAATATCTATACCAATATACAAC-A
* *
172411 TAATGATAATAAATTATAGATCATATCTATACCATTATACAAC-
1 T-AT-A-AATAAATTATAGATAATATCTATACCAATATACAACA
*
172454 TGTAAATAAATTA
1 TATAAATAAATTA
172467 GATGGTATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
40 9 0.18
41 1 0.02
42 2 0.04
43 3 0.06
44 1 0.02
45 33 0.67
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (41 bp):
TATAAATAAATTATAGATAATATCTATACCAATATACAACA
Found at i:175518 original size:21 final size:20
Alignment explanation
Indices: 175494--175553 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 20
175484 TATTATGGAT
*
175494 TTCAAGTTGGTTGTTATGTAC
1 TTCAAGTTTGTTGTTATG-AC
*
175515 TTCAAGTTTGTTGTTATAGAT
1 TTCAAGTTTGTTGTTAT-GAC
175536 TTCAAGTTTGTTGTTATG
1 TTCAAGTTTGTTGTTATG
175554 GATGTCATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.20, C:0.07, G:0.22, T:0.52
Consensus pattern (20 bp):
TTCAAGTTTGTTGTTATGAC
Found at i:179660 original size:3 final size:3
Alignment explanation
Indices: 179652--179691 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
179642 TATCCAGATT
179652 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
179692 CATCATCATC
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:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:179696 original size:3 final size:3
Alignment explanation
Indices: 179690--179721 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
179680 TATTATTATT
*
179690 ATC ATC ATC ATC ATC ATC ATC ATC ATT ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
179722 TGTCATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:179722 original size:6 final size:6
Alignment explanation
Indices: 179654--179729 Score: 53
Period size: 6 Copynumber: 12.7 Consensus size: 6
179644 TCCAGATTTT
* * * * * * * *
179654 ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATCATC ATCATC
1 ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC
* * *
179702 ATCATC ATCATC ATTATC ATTGTC ATTA
1 ATTATC ATTATC ATTATC ATTATC ATTA
179730 ATATTTTTAT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.33, C:0.13, G:0.01, T:0.53
Consensus pattern (6 bp):
ATTATC
Found at i:181230 original size:17 final size:17
Alignment explanation
Indices: 181210--181244 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
181200 ATATAAGTTC
181210 ACATTA-TATATATATTT
1 ACATTAGTAT-TATATTT
181227 ACATTAGTATTATATTT
1 ACATTAGTATTATATTT
181244 A
1 A
181245 TATGCACGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (17 bp):
ACATTAGTATTATATTT
Found at i:188395 original size:2 final size:2
Alignment explanation
Indices: 188388--188412 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
188378 AAGGTATTAC
188388 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 T
188413 TCTGTTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:196713 original size:10 final size:10
Alignment explanation
Indices: 196681--196723 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
196671 CCCGGATGTA
196681 ATTTTTATTT
1 ATTTTTATTT
* *
196691 A-TTTAATTA
1 ATTTTTATTT
196700 ATTTTTATTT
1 ATTTTTATTT
196710 ATTTTTATTT
1 ATTTTTATTT
196720 ATTT
1 ATTT
196724 ATTTGAAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTTTATTT
Found at i:199015 original size:13 final size:13
Alignment explanation
Indices: 198969--199016 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
198959 TCACTTCATG
198969 TCAGGAATTCC-CA
1 TCAGGAA-TCCACA
198982 TCAGGAATCCACA
1 TCAGGAATCCACA
* * *
198995 TGAAGAATCCACG
1 TCAGGAATCCACA
199008 TCAGGAATC
1 TCAGGAATC
199017 TATCAGGCGG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
12 3 0.10
13 26 0.90
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (13 bp):
TCAGGAATCCACA
Found at i:200550 original size:24 final size:23
Alignment explanation
Indices: 200523--200569 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
200513 TTAATATTAT
200523 TTATG-CTAATAATATTATTAAATA
1 TTATGTCT-ATAATATTA-TAAATA
*
200547 TTATGTCTATAATTTTATAAATA
1 TTATGTCTATAATATTATAAATA
200570 AAATATTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 13 0.62
25 2 0.10
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (23 bp):
TTATGTCTATAATATTATAAATA
Found at i:200594 original size:30 final size:31
Alignment explanation
Indices: 200558--200621 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
200548 TATGTCTATA
*
200558 ATTTTA-TAAATAAAATATTAAGATT-ATTAT
1 ATTTTATTAAAT-AAAGATTAAGATTAATTAT
* *
200588 ATTTTATTAAATTAAGATTATGATTAATTAT
1 ATTTTATTAAATAAAGATTAAGATTAATTAT
200619 ATT
1 ATT
200622 AATTATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 16 0.55
31 13 0.45
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (31 bp):
ATTTTATTAAATAAAGATTAAGATTAATTAT
Found at i:202904 original size:85 final size:85
Alignment explanation
Indices: 202761--202922 Score: 306
Period size: 85 Copynumber: 1.9 Consensus size: 85
202751 GCAAATTAAG
* *
202761 CATGCTGATAAACATCTCAAGTATCAAATCCACTGTTCTTTTCTTGAGGTAGAGTTAATTGAATT
1 CATGCTGATAAACATATCAAGTATCAAATCCACTGTTCTTTTCTTGAGATAGAGTTAATTGAATT
202826 ATTTTGATTCTTAGTTTTGA
66 ATTTTGATTCTTAGTTTTGA
202846 CATGCTGATAAACATATCAAGTATCAAATCCACTGTTCTTTTCTTGAGATAGAGTTAATTGAATT
1 CATGCTGATAAACATATCAAGTATCAAATCCACTGTTCTTTTCTTGAGATAGAGTTAATTGAATT
202911 ATTTTGATTCTT
66 ATTTTGATTCTT
202923 TTTTTGAATT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 75 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (85 bp):
CATGCTGATAAACATATCAAGTATCAAATCCACTGTTCTTTTCTTGAGATAGAGTTAATTGAATT
ATTTTGATTCTTAGTTTTGA
Found at i:204387 original size:18 final size:18
Alignment explanation
Indices: 204364--204401 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
204354 ATTAAACTTT
204364 TTCTAAATTCTAATATGA
1 TTCTAAATTCTAATATGA
* *
204382 TTCTAACTTCTAGTATGA
1 TTCTAAATTCTAATATGA
204400 TT
1 TT
204402 TAGACAACAT
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:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (18 bp):
TTCTAAATTCTAATATGA
Found at i:205155 original size:2 final size:2
Alignment explanation
Indices: 205144--205196 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
205134 TTTGTTAATC
205144 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
205185 TA TA TA TA TA TA
1 TA TA TA TA TA TA
205197 ATTTACGACA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:206852 original size:6 final size:6
Alignment explanation
Indices: 206841--206896 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
206831 AAAAACCTGA
** *
206841 AAAAAT AAAAAT ATTAAT AATAAT AAATAAAT AAATAAT -AAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT -AA-AAAT AAA-AAT AAAAAT AAAAAT
206891 AAAAAT
1 AAAAAT
206897 GTAAAACCCG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
5 3 0.07
6 29 0.69
7 7 0.17
8 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (6 bp):
AAAAAT
Found at i:206862 original size:15 final size:16
Alignment explanation
Indices: 206844--206892 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
206834 AACCTGAAAA
*
206844 AATAAAAAT-ATTAAT
1 AATAAAAATAATAAAT
206859 AATAATAAATAAATAAAT
1 AATAA-AAAT-AATAAAT
206877 AAT-AAAATAA-AAAT
1 AATAAAAATAATAAAT
206891 AA
1 AA
206893 AAATGTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.20
15 7 0.23
16 8 0.27
17 1 0.03
18 8 0.27
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AATAAAAATAATAAAT
Found at i:206867 original size:18 final size:19
Alignment explanation
Indices: 206843--206896 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
206833 AAACCTGAAA
*
206843 AAATAAAAATATTAATAAT
1 AAATAAAAATATAAATAAT
206862 -AATAAATAA-ATAAATAAT
1 AAATAAA-AATATAAATAAT
*
206880 AAAATAAAAATAAAAAT
1 -AAATAAAAATATAAAT
206897 GTAAAACCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 14 0.48
19 4 0.14
20 11 0.38
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATAAAAATATAAATAAT
Found at i:206873 original size:26 final size:26
Alignment explanation
Indices: 206843--206893 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
206833 AAACCTGAAA
* *
206843 AAATAAA-AATATTAATAATAATAAAT
1 AAATAAATAATA-AAATAAAAATAAAT
206869 AAATAAATAATAAAATAAAAATAAA
1 AAATAAATAATAAAATAAAAATAAA
206894 AATGTAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (26 bp):
AAATAAATAATAAAATAAAAATAAAT
Found at i:207525 original size:164 final size:163
Alignment explanation
Indices: 207142--207721 Score: 625
Period size: 164 Copynumber: 3.5 Consensus size: 163
207132 GGTCTTTGGC
* * * * * *
207142 TGGCAGATAGCCCTTCTCA-ACTTAAGCTATACTGCAAATGATGTGCCTCGGAGCTGAGTGTAAT
1 TGGCAGATAACCCTTCT-AGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * * * *
207206 CGAACTCGAGGGTCTTTTGGATGGTAGATAGCTCTTCTTGATTTAAGCTATGCTGCAAAT-ATTG
65 CGAACTCGAAGGTC-TTTGG-T-GCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGA-TG
* *
207270 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAG-GTCTTGGT
126 TGCCCTTGAGCTGAGTGTAATCGAACTCG-GGTGTC-T-GT
* * * * *
207310 TGGTAGATAACCCTTCTAGCCCTAAGTTATGCTGCAAACGATGTGCCTTGGAGCTGAACGTAGTC
1 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* * * * * * *
207375 GAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCC
66 GAACTCGAAGGTCTTTGGTG-CAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCC
*
207440 CTCGAAGCTGAGTGTAATCGAACTCGGGTGTCT-T
130 CTTG-AGCTGAGTGTAATCGAACTCGGGTGTCTGT
* * *
207474 TGGCAGATAGCCCTTCTTGACTTAAGATATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* * *
207539 GAACTCGAAGGTCTTT-G-GCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCG
66 GAACTCGAAGGTCTTTGGTGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCC
* * * * *
207602 TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGT
131 TTGAGCTGAGTGTAATCGAACTC--GGGT-GTCTGT
* *
207638 TGGCAG-TCAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TGGCAGAT-AACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
*
207702 CGGACTCGAAGGTCTTTGGT
65 CGAACTCGAAGGTCTTTGGT
207722 TGGCACGATT
Statistics
Matches: 344, Mismatches: 56, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
160 18 0.05
161 37 0.11
162 4 0.01
163 4 0.01
164 148 0.43
165 2 0.01
166 36 0.10
167 31 0.09
168 64 0.19
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (163 bp):
TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
GAACTCGAAGGTCTTTGGTGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCC
TTGAGCTGAGTGTAATCGAACTCGGGTGTCTGT
Found at i:207553 original size:80 final size:80
Alignment explanation
Indices: 207142--207720 Score: 565
Period size: 80 Copynumber: 7.0 Consensus size: 80
207132 GGTCTTTGGC
* * * *
207142 TGGCAGATAGCCCTTCTCA-ACTTAAGCTATACTGCAAATGATGTGCCTCGGAGCTGAGTGTAAT
1 TGGCAGATAGCCCTTCT-AGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
*
207206 CGAACTCGAGGGTCTTTT
65 CGAACTCGAAGGTC--TT
* * * * * *
207224 GGATGGTAGATAGCTCTTCTTGATTTAAGCTATGCTGCAAAT-ATTGTGCCTTTGAGCTGAGTGT
1 ---TGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGA-TGTGCCTTGGAGCTGAGCGT
*
207288 AATCGAACTCGAAGGTCTTGGT
62 AGTCGAACTCGAAGGTC-T--T
* * * * * * *
207310 TGGTAGATAACCCTTCTAGCCCTAAGTTATGCTGCAAACGATGTGCCTTGGAGCTGAACGTAGTC
1 TGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
207375 GAACTCGAAGGTCTT
66 GAACTCGAAGGTCTT
* * * * * * * * * *
207390 TGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAGTGT
1 T-G-G-CAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGT
* *
207455 AATCGAACTCG-GGTGTCTT
62 AGTCGAACTCGAAG-GTCTT
* *
207474 TGGCAGATAGCCCTTCTTGACTTAAGATATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
207539 GAACTCGAAGGTCTT
66 GAACTCGAAGGTCTT
* *
207554 TGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGT
1 TGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGT
*
207618 CGAACTCAAAGGTCTTTTGT
65 CGAACTCGAAGGTC---T-T
* * * *
207638 TGGCAG-TCAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TGGCAGAT-AGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
*
207702 CGGACTCGAAGGTCTT
65 CGAACTCGAAGGTCTT
207718 TGG
1 TGG
207721 TTGGCACGAT
Statistics
Matches: 418, Mismatches: 58, Indels: 41
0.81 0.11 0.08
Matches are distributed among these distances:
80 105 0.25
81 39 0.09
82 3 0.01
83 105 0.25
84 98 0.23
85 67 0.16
86 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (80 bp):
TGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
GAACTCGAAGGTCTT
Found at i:207737 original size:84 final size:84
Alignment explanation
Indices: 207120--207726 Score: 630
Period size: 83 Copynumber: 7.3 Consensus size: 84
207110 CTGAATAAAA
* * *
207120 TCGAACTCGTCAGGTCTTTGGCTGGCAGATAGCCCTTCTCA-ACTTAAGCTATACTGCAAATGAT
1 TCGAACTCG-AAGGTCTTTGGTTGGCAGATAGCCCTTCT-AGACTTAAGCTATGCTGCAAATGAT
* * *
207184 GTGCCTCGGAGCTGAGTGTAA
64 GTGCCTTGGAGCTGAGCGTAG
* * * * * *
207205 TCGAACTCGAGGGTCTTTTGGATGGTAGATAGCTCTTCTTGATTTAAGCTATGCTGCAAAT-ATT
1 TCGAACTCGAAGGTC-TTTGGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGA-T
* * *
207269 GTGCCTTTGAGCTGAGTGTAA
64 GTGCCTTGGAGCTGAGCGTAG
* * * * * *
207290 TCGAACTCGAAGGTC-TTGGTTGGTAGATAACCCTTCTAGCCCTAAGTTATGCTGCAAACGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
*
207354 GCCTTGGAGCTGAACGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * * * *
207373 TCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
* * * *
207437 GCCCTCGAAGCTGAGTGTAA
66 G-CCTTGGAGCTGAGCGTAG
* * * *
207457 TCGAACTCG--GGTGTCT--TTGGCAGATAGCCCTTCTTGACTTAAGATATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
207518 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* *
207537 TCGAACTCGAAGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
207598 GCCGTT-GAGCTGAGCGTAG
66 GCC-TTGGAGCTGAGCGTAG
* * * * * *
207617 TCGAACTCAAAGGTCTTTTGTTGGCAG-TCAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATA
1 TCGAACTCGAAGGTCTTTGGTTGGCAGAT-AGCCCTTCTAGACTTAAGCTATGCTGCAAATGATG
207681 TGCCTTGGAGCTGAGCGTAG
65 TGCCTTGGAGCTGAGCGTAG
*
207701 TCGGACTCGAAGGTCTTTGGTTGGCA
1 TCGAACTCGAAGGTCTTTGGTTGGCA
207727 CGATTCCCTT
Statistics
Matches: 440, Mismatches: 66, Indels: 33
0.82 0.12 0.06
Matches are distributed among these distances:
80 96 0.22
81 38 0.09
82 9 0.02
83 108 0.25
84 108 0.25
85 81 0.18
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.30
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
GCCTTGGAGCTGAGCGTAG
Found at i:208169 original size:106 final size:106
Alignment explanation
Indices: 207973--208824 Score: 1314
Period size: 106 Copynumber: 8.0 Consensus size: 106
207963 GTTGTGAAGT
* *
207973 TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
* **
208038 CTGGAGTCCAATATCATTCATTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* *
208079 TAAAATTGAGAAGTTTTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
208144 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* * *
208185 TGAAATTGAGAAGTTATTTGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACATGCATTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
* *
208250 CTGGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTA
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* * * *
208291 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
*
208356 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
*
208397 TAAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
208462 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
*
208503 TGAAATTGAGAAGTTGTTTGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
*
208568 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* * * * *
208609 TGAAATT-AGGAAGTTGTTTATTGACAACTAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
1 TGAAATTGA-GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTG
*
208673 TCTGGAGTCCACTATCCTTCGCTGTGAAGTTGAAATTGGCTC
65 TCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* * * * * * *
208715 TTG-TATTG-GAAAATTGTTTATTAAAAACCAGCGGTCCCTTCGTCGTGAAGTTTAACTTGCGTT
1 -TGAAATTGAG-AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTT
* * * * *
208778 GTCTGGAGTCCAATTTTCTTCGCTGCGAAGTTGAAATAGACTC
64 GTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
208821 TGAA
1 TGAA
208825 TGAAATTGGA
Statistics
Matches: 687, Mismatches: 54, Indels: 10
0.91 0.07 0.01
Matches are distributed among these distances:
105 4 0.01
106 681 0.99
107 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
Found at i:208407 original size:318 final size:316
Alignment explanation
Indices: 207842--208824 Score: 1457
Period size: 318 Copynumber: 3.1 Consensus size: 316
207832 TATTGTTCCA
* * * * * * * *
207842 AGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTTTGGAACTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* * * * *
207907 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGAAGTCCAATGTCCTTCGT-T---G-
66 CAGTGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGTGTGAAGT
* *
207967 TG-AA---G-TTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
* * *
208027 ACATGCGTTGTCTGGAGTCCAATATCATTCATTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAG
196 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAG
*
208092 TTTTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
261 TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
*
208148 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
208213 CAGTGGTCCCTTCGTCGTGAAGTTGAACATGCATTGTCTGGAGTCCAATATCCTTCGATGTGAAG
66 CAGTGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCG-TGTGAAG
*
208278 TTGAAATTGGCTATGAAATTGGGAAGTTGTTTATTGACAACCAGCGATCCCTTCGTCGTGAAGTT
130 TTGAAATTGGCT-TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
208343 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGA
194 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGA
208408 AGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
259 AGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
208466 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
208531 CAGTGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
66 CAGTGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCG-TGTGAAG
* * * *
208596 TTGAAATTGACTCTGAAATTAGGAAGTTGTTTATTGACAACTAGCGGTCCCTTCGTTGTGAAGTT
130 TTGAAATTGGCT-TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * * ***
208661 GAACTTGTGTTGTCTGGAGTCCACTATCCTTCGCTGTGAAGTTGAAATTGGCTCTTGTATTG-GA
194 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAG-
* * * * * *
208725 AAATTGTTTATTAAAAACCAGCGGTCCCTTCGTCGTGAAGTTTAACTTGCGTTGTCTGG
258 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
* * * * *
208784 AGTCCAATTTTCTTCGCTGCGAAGTTGAAATAGACTCTGAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
208825 TGAAATTGGA
Statistics
Matches: 616, Mismatches: 48, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
306 107 0.17
307 1 0.00
308 1 0.00
311 1 0.00
312 2 0.00
313 2 0.00
316 1 0.00
317 2 0.00
318 499 0.81
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (316 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
CAGTGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGTGTGAAGT
TGAAATTGGCTTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAG
TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
Found at i:214064 original size:30 final size:29
Alignment explanation
Indices: 214030--214088 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
214020 AAACCTGAAA
*
214030 AAATAAAAAAAAATATTAATAATAATAAAT
1 AAATAAAAAAAAATAATAATAATAA-AAAT
* * *
214060 AAATAAATAATAATAATACTAATAAAAAT
1 AAATAAAAAAAAATAATAATAATAAAAAT
214089 GTAAAACCCG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (29 bp):
AAATAAAAAAAAATAATAATAATAAAAAT
Found at i:214093 original size:27 final size:27
Alignment explanation
Indices: 214030--214085 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
214020 AAACCTGAAA
* *
214030 AAATAAA-AAAAAATATTAATAATAAT
1 AAATAAATAAATAATAATAATAATAAT
*
214056 AAATAAATAAATAATAATAATACTAAT
1 AAATAAATAAATAATAATAATAATAAT
214083 AAA
1 AAA
214086 AATGTAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (27 bp):
AAATAAATAAATAATAATAATAATAAT
Found at i:217157 original size:14 final size:14
Alignment explanation
Indices: 217138--217167 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
217128 GCAAGCACTC
217138 AAAGAAGAAAACAA
1 AAAGAAGAAAACAA
*
217152 AAAGAAGAAAATAA
1 AAAGAAGAAAACAA
217166 AA
1 AA
217168 CAAATTTGCA
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:0.80, C:0.03, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAGAAGAAAACAA
Found at i:226630 original size:19 final size:21
Alignment explanation
Indices: 226603--226645 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
226593 CGCTCACTTC
*
226603 TGTATTACTTGCATCG-ATTG
1 TGTATTACTTGCATAGAATTG
226623 TGTA-TACTTGCATAGAATTG
1 TGTATTACTTGCATAGAATTG
226643 TGT
1 TGT
226646 GTCATAACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (21 bp):
TGTATTACTTGCATAGAATTG
Found at i:229196 original size:23 final size:21
Alignment explanation
Indices: 229175--229214 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
229165 TGTTGACTAT
*
229175 TATAT-GAAGTGCCTTAGCAC
1 TATATAGAAGTACCTTAGCAC
229195 TATATAGAAGTACCTTAGCA
1 TATATAGAAGTACCTTAGCA
229215 TTGCTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (21 bp):
TATATAGAAGTACCTTAGCAC
Found at i:266917 original size:17 final size:17
Alignment explanation
Indices: 266895--266933 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
266885 CACAAAGTGT
266895 CAATCAATTTCAAGCTC
1 CAATCAATTTCAAGCTC
266912 CAATCAATTTCAAGCTC
1 CAATCAATTTCAAGCTC
266929 CAATC
1 CAATC
266934 CTTGCAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.36, C:0.31, G:0.05, T:0.28
Consensus pattern (17 bp):
CAATCAATTTCAAGCTC
Found at i:272431 original size:25 final size:26
Alignment explanation
Indices: 272403--272466 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
272393 TAGCATATTT
**
272403 AAAAACAATGCTTGAAAA-TAAAATA
1 AAAAACAAAACTTGAAAAGTAAAATA
**
272428 AAAATGAAAACTTGAAAAGTAAAATA
1 AAAAACAAAACTTGAAAAGTAAAATA
* *
272454 AAATAGAAAACTT
1 AAAAACAAAACTT
272467 TAATAAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 14 0.44
26 18 0.56
ACGTcount: A:0.64, C:0.06, G:0.09, T:0.20
Consensus pattern (26 bp):
AAAAACAAAACTTGAAAAGTAAAATA
Found at i:272462 original size:26 final size:25
Alignment explanation
Indices: 272413--272466 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 25
272403 AAAAACAATG
272413 CTTGAAAATAAAATAAAAATGAAAA
1 CTTGAAAATAAAATAAAAATGAAAA
272438 CTTGAAAAGTAAAAT-AAAATAGAAAA
1 CTTGAAAA-TAAAATAAAAAT-GAAAA
272464 CTT
1 CTT
272467 TAATAAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.63, C:0.06, G:0.09, T:0.22
Consensus pattern (25 bp):
CTTGAAAATAAAATAAAAATGAAAA
Found at i:278996 original size:19 final size:20
Alignment explanation
Indices: 278960--278998 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
278950 AGGGGGATTC
*
278960 AAAAAAAAAAAAGGAAAATG
1 AAAAAAAAAAAAGCAAAATG
*
278980 AAAAGAAAAAAA-CAAAATG
1 AAAAAAAAAAAAGCAAAATG
278999 GGTTTTTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (20 bp):
AAAAAAAAAAAAGCAAAATG
Found at i:285186 original size:20 final size:21
Alignment explanation
Indices: 285149--285187 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
285139 TATGGTCTTG
*
285149 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
285170 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
285188 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:288197 original size:3 final size:3
Alignment explanation
Indices: 288189--288275 Score: 111
Period size: 3 Copynumber: 29.0 Consensus size: 3
288179 ATTGATTTAT
* * * * *
288189 TTA TTA TTA TTA TAA TTA TAA TAA TTA TTA TTA TTA TTA TAA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
288237 TAA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
288276 AATATATATA
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:288409 original size:16 final size:16
Alignment explanation
Indices: 288390--288430 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
288380 CTCTAACCCT
288390 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
288406 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
288422 AGCCGCCTC
1 AGCCGCCTC
288431 AGCCAACGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.07, C:0.56, G:0.20, T:0.17
Consensus pattern (16 bp):
AGCCGCCTCTGCCTCC
Found at i:290386 original size:21 final size:20
Alignment explanation
Indices: 290348--290390 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
290338 TTTATAATCT
290348 TTTTATATATATACATATTA
1 TTTTATATATATACATATTA
* *
290368 TTTTATAGTATTTATATATTA
1 TTTTATA-TATATACATATTA
290389 TT
1 TT
290391 AATATTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTATATATATACATATTA
Found at i:291845 original size:15 final size:14
Alignment explanation
Indices: 291820--291861 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
291810 TTTTCATGCA
291820 TACAT-TTGCATTT
1 TACATCTTGCATTT
291833 TACATCCTTGCATTT
1 TACAT-CTTGCATTT
* *
291848 TTCATTTTGCATTT
1 TACATCTTGCATTT
291862 ATACTGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 12 0.48
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.55
Consensus pattern (14 bp):
TACATCTTGCATTT
Found at i:297636 original size:114 final size:114
Alignment explanation
Indices: 297352--297692 Score: 574
Period size: 114 Copynumber: 3.0 Consensus size: 114
297342 AAGTGCCATG
297352 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
297417 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTTAAAGATGAATT
66 TGGTTTGGTATGAACCCC-AAAACCAATCATTGGATTTAAAAGATGAATT
*
297467 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
297532 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
* *
297581 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * * *
297646 TGATTCGGTAGGAACCCCAGAACCGATCATTGGAATTGAAAGATGAA
66 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAA
297693 CTGCATGATC
Statistics
Matches: 214, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
114 132 0.62
115 82 0.38
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
Found at i:300247 original size:22 final size:22
Alignment explanation
Indices: 300216--300273 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
300206 TACATCTACA
*
300216 CTTTTCAAAGATGATAGATTCC
1 CTTTTCAAAGATGACAGATTCC
* *
300238 CTTTTTAAAGATGACAGATTCT
1 CTTTTCAAAGATGACAGATTCC
300260 CTTTTCAAAGATGA
1 CTTTTCAAAGATGA
300274 AAGCTTTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (22 bp):
CTTTTCAAAGATGACAGATTCC
Found at i:301013 original size:113 final size:113
Alignment explanation
Indices: 300676--301352 Score: 1022
Period size: 113 Copynumber: 6.0 Consensus size: 113
300666 TAGCAAAGAT
* * *
300676 TCAAATCTATCATTTGATGGATTGA-CATTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTG
1 TCAAATCCATCATTTGATGGA-TCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTG
* * *
300740 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGT
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * * * * *
300789 TTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCAT
1 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAG-AAAGTTCATAATAAGAAGAA--C-TCAT
*
300853 CTAAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
62 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
300905 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
300970 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
301018 TCAAATCCATCATTTGATGGATCATCTTTTCCATAGAAAGTTCATAATAAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
* *
301083 AGAATGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
301131 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
*
301196 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
301244 -CTGAATTCATCAATTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTG
1 TC-AAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTG
* *
301307 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA-CTTTT
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
301353 CGCATAATTC
Statistics
Matches: 522, Mismatches: 35, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
111 5 0.01
112 70 0.13
113 346 0.66
114 1 0.00
115 1 0.00
116 98 0.19
117 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (113 bp):
TCAAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:301695 original size:3 final size:3
Alignment explanation
Indices: 301687--301782 Score: 129
Period size: 3 Copynumber: 32.0 Consensus size: 3
301677 ATTGATTTAT
* * * * *
301687 TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TAA TTA CTA TAA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
301735 TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
301783 AATATATATA
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:301914 original size:16 final size:16
Alignment explanation
Indices: 301895--301935 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
301885 CTCTAACCCT
301895 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
*
301911 AGCCACCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
301927 AGCCGCCTC
1 AGCCGCCTC
301936 AGCCAACGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.10, C:0.56, G:0.17, T:0.17
Consensus pattern (16 bp):
AGCCGCCTCTGCCTCC
Found at i:304107 original size:42 final size:43
Alignment explanation
Indices: 304043--304138 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 43
304033 CGGAGCTAAC
*
304043 TGAT-ATGCTATTCCGCCAGATGCTGTTTCTAG-TTGGCTACG
1 TGATGATGCTATTCCCCCAGATGCTGTTTCTAGTTTGGCTACG
* * *
304084 TGATGATGCTATTCCCCCTGATGCTGTTTTTAGTTTTGCTACG
1 TGATGATGCTATTCCCCCAGATGCTGTTTCTAGTTTGGCTACG
*
304127 AGATGATGCTAT
1 TGATGATGCTAT
304139 AAGAGTGCTA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 4 0.08
42 25 0.52
43 19 0.40
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.40
Consensus pattern (43 bp):
TGATGATGCTATTCCCCCAGATGCTGTTTCTAGTTTGGCTACG
Found at i:305166 original size:20 final size:20
Alignment explanation
Indices: 305143--305181 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
305133 TTTACATGGG
* *
305143 GACTACCTTATTTAAAAAAT
1 GACTACCATATTGAAAAAAT
305163 GACTACCATATTGAAAAAA
1 GACTACCATATTGAAAAAA
305182 ATCATGTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (20 bp):
GACTACCATATTGAAAAAAT
Found at i:309638 original size:17 final size:17
Alignment explanation
Indices: 309597--309638 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
309587 AGATTTTTTT
*
309597 AAAAAA-ATTTGAGTTG
1 AAAAAATATTTGAGGTG
**
309613 AAATCATATTTGAGGTG
1 AAAAAATATTTGAGGTG
309630 AAAAAATAT
1 AAAAAATAT
309639 GATCGATTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.31
Consensus pattern (17 bp):
AAAAAATATTTGAGGTG
Found at i:309737 original size:24 final size:24
Alignment explanation
Indices: 309707--309759 Score: 88
Period size: 24 Copynumber: 2.1 Consensus size: 24
309697 TGATAACTAA
309707 TATATATATATATATAATTATGTTTT
1 TATATA-ATAT-TATAATTATGTTTT
309733 TATATAATATTATAATTATGTTTT
1 TATATAATATTATAATTATGTTTT
309757 TAT
1 TAT
309760 TTTTGTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 17 0.63
25 4 0.15
26 6 0.22
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (24 bp):
TATATAATATTATAATTATGTTTT
Found at i:309842 original size:19 final size:19
Alignment explanation
Indices: 309818--309855 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
309808 CACTGTATAA
309818 AACCCTTTTAGTTTTACAC
1 AACCCTTTTAGTTTTACAC
309837 AACCCTTTTAGTTTTACAC
1 AACCCTTTTAGTTTTACAC
309856 TTTTTTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (19 bp):
AACCCTTTTAGTTTTACAC
Found at i:310036 original size:2 final size:2
Alignment explanation
Indices: 310029--310063 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
310019 AACTTATCTC
310029 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
310064 AGTCTAATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:310190 original size:2 final size:2
Alignment explanation
Indices: 310185--310214 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
310175 TTTTTTCAAT
310185 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
310215 AATCAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:310545 original size:6 final size:6
Alignment explanation
Indices: 310534--310559 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
310524 TGGGGGATGC
310534 CCTTTG CCTTTG CCTTTG CCTTTG CC
1 CCTTTG CCTTTG CCTTTG CCTTTG CC
310560 CTCTTGTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.38, G:0.15, T:0.46
Consensus pattern (6 bp):
CCTTTG
Found at i:313570 original size:29 final size:30
Alignment explanation
Indices: 313506--313568 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
313496 ATATAACTTT
*
313506 ATTTTATATTTTAGTCCCTAAACTTTTACA
1 ATTTTATATTTTAGTCCCTAAACTTTCACA
*
313536 ACTTTATATTTTAGT-CCTAAACTTTCA-A
1 ATTTTATATTTTAGTCCCTAAACTTTCACA
313564 ATTTT
1 ATTTT
313569 TACATTCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 5 0.17
29 11 0.37
30 14 0.47
ACGTcount: A:0.30, C:0.16, G:0.03, T:0.51
Consensus pattern (30 bp):
ATTTTATATTTTAGTCCCTAAACTTTCACA
Found at i:313599 original size:13 final size:13
Alignment explanation
Indices: 313583--313607 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
313573 TTCCAATCAC
313583 TAGTCCCAAAATT
1 TAGTCCCAAAATT
313596 TAGTCCCAAAAT
1 TAGTCCCAAAAT
313608 ATCAAATTTA
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:0.24, G:0.08, T:0.28
Consensus pattern (13 bp):
TAGTCCCAAAATT
Found at i:314732 original size:30 final size:30
Alignment explanation
Indices: 314701--314822 Score: 187
Period size: 30 Copynumber: 4.1 Consensus size: 30
314691 TGTTCAATAT
* * *
314701 ATATTTTAACTTAAATTCATAACATTTTAT
1 ATATCTTAACTTAAATTCATAACATTATAA
314731 ATATCTT--CTTAAATTCATAACATTATAA
1 ATATCTTAACTTAAATTCATAACATTATAA
314759 ATATCTTAACTTAAATTCATAACATTATAA
1 ATATCTTAACTTAAATTCATAACATTATAA
314789 ATATCTTAACTTAAATTCATAAC-TTATTAA
1 ATATCTTAACTTAAATTCATAACATTA-TAA
314819 ATAT
1 ATAT
314823 ATTTTGTGCT
Statistics
Matches: 86, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
28 26 0.30
29 3 0.03
30 57 0.66
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.44
Consensus pattern (30 bp):
ATATCTTAACTTAAATTCATAACATTATAA
Found at i:314776 original size:58 final size:59
Alignment explanation
Indices: 314701--314822 Score: 185
Period size: 58 Copynumber: 2.1 Consensus size: 59
314691 TGTTCAATAT
* * *
314701 ATATTTTAACTTAAATTCATAACATTTTATATATCTT-CTTAAATTCATAACATTA-TAA
1 ATATCTTAACTTAAATTCATAACATTATAAATATCTTACTTAAATTCATAAC-TTATTAA
314759 ATATCTTAACTTAAATTCATAACATTATAAATATCTTAACTTAAATTCATAACTTATTAA
1 ATATCTTAACTTAAATTCATAACATTATAAATATCTT-ACTTAAATTCATAACTTATTAA
314819 ATAT
1 ATAT
314823 ATTTTGTGCT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
58 34 0.59
59 3 0.05
60 21 0.36
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.44
Consensus pattern (59 bp):
ATATCTTAACTTAAATTCATAACATTATAAATATCTTACTTAAATTCATAACTTATTAA
Found at i:314820 original size:16 final size:16
Alignment explanation
Indices: 314739--314820 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
314729 ATATATCTTC
314739 TTAAATTCATAACATTA
1 TTAAATTCATAAC-TTA
*
314756 -TAAATATCTTAAC---
1 TTAAAT-TCATAACTTA
314769 TTAAATTCATAACATTA
1 TTAAATTCATAAC-TTA
*
314786 -TAAATATCTTAAC---
1 TTAAAT-TCATAACTTA
314799 TTAAATTCATAACTTA
1 TTAAATTCATAACTTA
314815 TTAAAT
1 TTAAAT
314821 ATATTTTGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 23
0.65 0.05 0.30
Matches are distributed among these distances:
13 12 0.24
14 10 0.20
16 16 0.32
17 12 0.24
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAATTCATAACTTA
Found at i:314854 original size:29 final size:29
Alignment explanation
Indices: 314808--314893 Score: 102
Period size: 30 Copynumber: 2.9 Consensus size: 29
314798 CTTAAATTCA
314808 TAACTTATTAAATATATTTTGTGCTTA-TTT
1 TAACTTA-TAAATATATTTTGT-CTTATTTT
* *
314838 TAACTTAAAAATATATTTTATTCTTATTTT
1 TAACTTATAAATATATTTT-GTCTTATTTT
*
314868 TAACTTATATATATTATTTTGTCTTA
1 TAACTTATAAATA-TATTTTGTCTTA
314894 AGTTAAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
29 15 0.31
30 27 0.56
31 6 0.12
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (29 bp):
TAACTTATAAATATATTTTGTCTTATTTT
Found at i:315028 original size:32 final size:29
Alignment explanation
Indices: 314945--315049 Score: 120
Period size: 29 Copynumber: 3.5 Consensus size: 29
314935 AAAAAAAAAG
* *
314945 TTAAAAATATATTTTATTCCTATTTTAAC
1 TTAAAAATATATTTTATTCTTATATTAAC
* *
314974 TTAAAAATATATTTTATCCTTATAGTAAC
1 TTAAAAATATATTTTATTCTTATATTAAC
* *
315003 TTAAAAAATATATGTTTTATTCTTATCTTCAC
1 TT-AAAAATATA--TTTTATTCTTATATTAAC
*
315035 TTAAAAATATTTTTT
1 TTAAAAATATATTTT
315050 TATTTTAACT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
29 31 0.48
30 9 0.14
31 8 0.12
32 16 0.25
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (29 bp):
TTAAAAATATATTTTATTCTTATATTAAC
Found at i:315144 original size:30 final size:28
Alignment explanation
Indices: 315109--315180 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 28
315099 TGTGTGTTTA
*
315109 TTTAAGGTAAGATAATAATAAAATATAATT
1 TTTAAGGTAAGATAAAAATAAAATAT-A-T
*
315139 TTTAA-GTAAAAATAAAAATAAAATATAT
1 TTTAAGGT-AAGATAAAAATAAAATATAT
*
315167 TTTAAGTTAAGATA
1 TTTAAGGTAAGATA
315181 TGAATTTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 11 0.31
29 4 0.11
30 21 0.58
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (28 bp):
TTTAAGGTAAGATAAAAATAAAATATAT
Found at i:315646 original size:29 final size:28
Alignment explanation
Indices: 315614--315684 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
315604 TTTTCCCTAA
* **
315614 ATTTAAATACAAAATAA-AATTTATTAAGT
1 ATTTAAATACAAAACAAGAA-GAATTAA-T
*
315643 ATTTAAATACAATACAAGAAGAATTAAT
1 ATTTAAATACAAAACAAGAAGAATTAAT
315671 ATTTAAATACAAAA
1 ATTTAAATACAAAA
315685 AATTTGTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 14 0.39
29 20 0.56
30 2 0.06
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (28 bp):
ATTTAAATACAAAACAAGAAGAATTAAT
Found at i:315698 original size:21 final size:21
Alignment explanation
Indices: 315674--315713 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
315664 AATTAATATT
*
315674 TAAATACAAAAAATTTGTAAA
1 TAAATACAAAAAAATTGTAAA
*
315695 TAAATATAAAAAAATTGTA
1 TAAATACAAAAAAATTGTA
315714 CTTAACGGTA
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:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (21 bp):
TAAATACAAAAAAATTGTAAA
Found at i:316733 original size:19 final size:18
Alignment explanation
Indices: 316707--316761 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
316697 ATTTGCAATT
316707 GTTT-AAAATTATTAAAA
1 GTTTAAAAATTATTAAAA
316724 GTTATAAAAA-TATTTAAAAA
1 GTT-TAAAAATTA-TT-AAAA
316744 GTTTAACAAATT-TTAAAA
1 GTTTAA-AAATTATTAAAA
316762 AAATTATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
17 3 0.09
18 7 0.22
19 11 0.34
20 10 0.31
21 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (18 bp):
GTTTAAAAATTATTAAAA
Found at i:316773 original size:19 final size:20
Alignment explanation
Indices: 316720--316776 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
316710 TAAAATTATT
*
316720 AAAAGTTATAAAAATATTTAA
1 AAAAATTAT-AAAATATTTAA
**
316741 AAAGTTTA-ACAAAT-TTTAA
1 AAAAATTATA-AAATATTTAA
316760 AAAAATTATAAAATATT
1 AAAAATTATAAAATATT
316777 ACAGAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 16 0.55
20 7 0.24
21 6 0.21
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (20 bp):
AAAAATTATAAAATATTTAA
Found at i:319146 original size:22 final size:23
Alignment explanation
Indices: 319087--319135 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
319077 TTTTTTATCC
319087 TTAGAAAGTAAAATCTACTTTAA
1 TTAGAAAGTAAAATCTACTTTAA
319110 TTAGAAAGTAAAATCTACTTTAA
1 TTAGAAAGTAAAATCTACTTTAA
319133 TTA
1 TTA
319136 ATTTTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (23 bp):
TTAGAAAGTAAAATCTACTTTAA
Found at i:324029 original size:17 final size:19
Alignment explanation
Indices: 323985--324032 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
323975 TGACGAACAA
323985 TATCGATACTGATGTAAGTGG
1 TATCGATACTGATG--AGTGG
*
324006 TAACGATACTGATG-G-GG
1 TATCGATACTGATGAGTGG
324023 TATCGATACT
1 TATCGATACT
324033 AACAAGGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 11 0.44
18 1 0.04
21 13 0.52
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.31
Consensus pattern (19 bp):
TATCGATACTGATGAGTGG
Found at i:324657 original size:44 final size:44
Alignment explanation
Indices: 324594--324910 Score: 474
Period size: 44 Copynumber: 7.2 Consensus size: 44
324584 AACCGAATTA
*
324594 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATTCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* * *
324638 ATAACCGAAATTCATAATGGTGCATTAAGGCATGAAAGCATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
*
324682 ATAACTGAAAGGCATAATGGTGCATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* *
324726 ATAACTGAAATGCATAAAGGTGCATTAAGGCATGAAAGAATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* * *
324770 ATAACTGAAACGCATAATGGTGTATTAAGGTATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* *
324814 ATAACTGAAACGCATAATGGTGCATTAAGGCATGAAAGTATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* * * *
324858 ATAAATGAAATGCATAACGGTGCAGTAAGGCATGAAA-AATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
*
324901 ATAAATGAAA
1 ATAACTGAAA
324911 ATAATAAATG
Statistics
Matches: 249, Mismatches: 24, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
43 15 0.06
44 234 0.94
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (44 bp):
ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
Found at i:331435 original size:22 final size:21
Alignment explanation
Indices: 331360--331437 Score: 54
Period size: 22 Copynumber: 3.7 Consensus size: 21
331350 ACCGAAAGGG
* *
331360 AGTATCGATACCATAATATACT
1 AGTATCGATACCATAGTATA-A
* *
331382 AGTATCGATA-CTTAGGGA-AA
1 AGTATCGATACCATA-GTATAA
*
331402 GGTATC-AGTACCATAGTATAGA
1 AGTATCGA-TACCATAGTATA-A
331424 AGTATCGATACCAT
1 AGTATCGATACCAT
331438 GGTAGGGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
19 1 0.02
20 9 0.21
21 8 0.19
22 23 0.55
23 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (21 bp):
AGTATCGATACCATAGTATAA
Found at i:331913 original size:44 final size:44
Alignment explanation
Indices: 331858--332218 Score: 481
Period size: 44 Copynumber: 8.2 Consensus size: 44
331848 AAACGAATTA
*
331858 ATAACTGAAATGCATAATGGTGCATTAAGGGATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* * *
331902 ATAACTAAAATGCATAATGTTTCATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* *
331946 ATAAATGAAATGCATAATGGTGCATTAAGGCATGAAATGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* * * * *
331990 ATAACTTAAATGCATAATTGTGCATTAAGGCATTAAAGGACGTC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* *
332034 ATAACTAAAATGCATAATGGTGCATTAAGGCATGAAAGGTTGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* *
332078 ATAACTGAATTGCATAATAGTGCATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* *
332122 ATAAATGAAATACATAATGGTGCATTAAGGCATGAAAGGATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
* * ** * * **
332166 ATAAATGAAATGCTTAACAGTGCAGTAATG-ATGAAAAAATGCC
1 ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
*
332209 ATAAATGAAA
1 ATAACTGAAA
332219 ATAATAAATA
Statistics
Matches: 279, Mismatches: 38, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
43 21 0.08
44 258 0.92
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (44 bp):
ATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGCC
Found at i:338989 original size:20 final size:21
Alignment explanation
Indices: 338946--338989 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
338936 CAACTAACTT
** *
338946 ACATCCATAAATATCCTTATA
1 ACATCCATAAATATCCAAAGA
338967 ACATCCA-AAATATCCAAAGA
1 ACATCCATAAATATCCAAAGA
338987 ACA
1 ACA
338990 CTTAAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.50, C:0.25, G:0.02, T:0.23
Consensus pattern (21 bp):
ACATCCATAAATATCCAAAGA
Found at i:342861 original size:3 final size:3
Alignment explanation
Indices: 342844--342879 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
342834 AAATTACATG
342844 AAT AAT AA- AAGT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
342880 CTAATAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:342891 original size:23 final size:23
Alignment explanation
Indices: 342858--342904 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
342848 ATAAAAGTAA
* *
342858 TAATAATAATA-ATAATAATAATC
1 TAATAAAAATATA-AATAAAAATC
342881 TAATAAAAATATAAATAAAAATC
1 TAATAAAAATATAAATAAAAATC
342904 T
1 T
342905 GAAATATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (23 bp):
TAATAAAAATATAAATAAAAATC
Found at i:343379 original size:15 final size:15
Alignment explanation
Indices: 343359--343392 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
343349 ATCTGATCCG
*
343359 ATTCAAATAACATAA
1 ATTCAAACAACATAA
*
343374 ATTCAAACAACATAT
1 ATTCAAACAACATAA
343389 ATTC
1 ATTC
343393 GAATTCTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (15 bp):
ATTCAAACAACATAA
Found at i:345494 original size:23 final size:23
Alignment explanation
Indices: 345455--345501 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
345445 ATTACATGAA
* *
345455 TAATAAAAGTAATAATAATAATC
1 TAATAAAAATAATAATAAAAATC
345478 TAATAAAAATACA-AATAAAAATC
1 TAATAAAAATA-ATAATAAAAATC
345501 T
1 T
345502 GAAATATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (23 bp):
TAATAAAAATAATAATAAAAATC
Found at i:346441 original size:13 final size:13
Alignment explanation
Indices: 346423--346464 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
346413 GTCATAAATC
*
346423 TATGACGCGTATT
1 TATGACACGTATT
346436 TATGACACGTATT
1 TATGACACGTATT
*
346449 TATGACACGCATT
1 TATGACACGTATT
346462 TAT
1 TAT
346465 AACGTGCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (13 bp):
TATGACACGTATT
Found at i:346552 original size:98 final size:98
Alignment explanation
Indices: 346433--346624 Score: 233
Period size: 98 Copynumber: 2.0 Consensus size: 98
346423 TATGACGCGT
* * * * * *
346433 ATTTATGACACGTATTTATGACACGCATTTATAACGTGCATTGCGCGTAATTGAAGCTCCCGTCA
1 ATTTATGACACGCATTTATGACACACATTTATAACGTACATTGCGCGTAATTGAAGCACACATCA
* *
346498 -TAAATGAAGATGACACACATTTGTGTGTCATAA
66 TTAAA-AAAGATGACACACATTCGTGTGTCATAA
** * * * * *
346531 ATTTATGACACGCATTTATGACTTACATTTATGACTTACATTGCGTGTCATTGAAGCACACATTA
1 ATTTATGACACGCATTTATGACACACATTTATAACGTACATTGCGCGTAATTGAAGCACACATCA
346596 TTAAAAAAGATGACACACATTCGTGTGTC
66 TTAAAAAAGATGACACACATTCGTGTGTC
346625 GTGATTGTAT
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
98 74 0.95
99 4 0.05
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (98 bp):
ATTTATGACACGCATTTATGACACACATTTATAACGTACATTGCGCGTAATTGAAGCACACATCA
TTAAAAAAGATGACACACATTCGTGTGTCATAA
Done.