Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015358.1 Kokia drynarioides strain JFW-HI SEQ_130405, 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: 211375
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 408 characters in sequence are not A, C, G, or T
Found at i:3036 original size:13 final size:11
Alignment explanation
Indices: 3004--3046 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
2994 CCATTTTCTA
*
3004 AATAAAATAAT
1 AATAAAATATT
3015 AAT-AAATATTT
1 AATAAAATA-TT
3026 AAGTAAAATATT
1 AA-TAAAATATT
3038 AATAAAATA
1 AATAAAATA
3047 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 5 0.18
13 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AATAAAATATT
Found at i:3425 original size:3 final size:3
Alignment explanation
Indices: 3417--3447 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
3407 ATGTACTTCT
3417 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
3448 CACTCCTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4201 original size:20 final size:20
Alignment explanation
Indices: 4123--4211 Score: 51
Period size: 20 Copynumber: 4.3 Consensus size: 20
4113 TAAAATTCTG
4123 TAAAAAAATATTGAAAAAC-TA
1 TAAAAAAATATT--AAAACTTA
*
4144 TAAAAAAAAGTATTTAAA-TTA
1 T-AAAAAAA-TATTAAAACTTA
* *
4165 T-TAAAATTGA-TATAAACTTA
1 TAAAAAAAT-ATTA-AAACTTA
* *
4185 TAAAAAAATATTAAAACATC
1 TAAAAAAATATTAAAACTTA
4205 TAAAAAA
1 TAAAAAA
4212 CTTAAAATGG
Statistics
Matches: 52, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
18 2 0.04
19 8 0.15
20 17 0.33
21 14 0.27
22 7 0.13
23 4 0.08
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.29
Consensus pattern (20 bp):
TAAAAAAATATTAAAACTTA
Found at i:4487 original size:108 final size:109
Alignment explanation
Indices: 4295--4493 Score: 339
Period size: 108 Copynumber: 1.8 Consensus size: 109
4285 ATTAAACCGA
* *
4295 TTGACCTAAGAACCAAATGACTGAACCAATTTTTTTCAATATATATATTTTTTTGTTTTTAATGT
1 TTGACCTAAGAACCAAACGACTCAACCAATTTTTTTCAATATATATATTTTTTTGTTTTTAATGT
4360 TTTATTTAATTGATCTGGATGGATCAGTCGAATTTGCAAACTAG
66 TTTATTTAATTGATCTGGATGGATCAGTCGAATTTGCAAACTAG
* *
4404 TTGACCTAAGAACCAAACGATTCAACCGATTTTTTTCAATATATAT-TTTTTTTGTTTTTAATGT
1 TTGACCTAAGAACCAAACGACTCAACCAATTTTTTTCAATATATATATTTTTTTGTTTTTAATGT
4468 TTTATTTAATTGA-CATGGATGGATCA
66 TTTATTTAATTGATC-TGGATGGATCA
4494 TTGGAACTGG
Statistics
Matches: 85, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
107 1 0.01
108 42 0.49
109 42 0.49
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (109 bp):
TTGACCTAAGAACCAAACGACTCAACCAATTTTTTTCAATATATATATTTTTTTGTTTTTAATGT
TTTATTTAATTGATCTGGATGGATCAGTCGAATTTGCAAACTAG
Found at i:4507 original size:108 final size:108
Alignment explanation
Indices: 4295--4517 Score: 333
Period size: 108 Copynumber: 2.1 Consensus size: 108
4285 ATTAAACCGA
* *
4295 TTGACCTAAGAACCAAATGACTGAACCAATTTTTTTCAATATATATATTTTTTTGTTTTTAATGT
1 TTGACCTAAGAACCAAACGACTCAACCAATTTTTTTCAATATATATATTTTTTTGTTTTTAATGT
* *
4360 TTTATTTAATTGATCTGGATGGATCAGTCGAATTTGCAAACTAG
66 TTTATTTAATTGATCTGGATGGATCAGTCGAACTGGCAAAC-AG
* *
4404 TTGACCTAAGAACCAAACGATTCAACCGATTTTTTTCAATATATAT-TTTTTTTGTTTTTAATGT
1 TTGACCTAAGAACCAAACGACTCAACCAATTTTTTTCAATATATATATTTTTTTGTTTTTAATGT
* *
4468 TTTATTTAATTGA-CATGGATGGATCATTGGAACTGGCAAACAG
66 TTTATTTAATTGATC-TGGATGGATCAGTCGAACTGGCAAACAG
*
4511 ATGACCT
1 TTGACCT
4518 GATCAATTTG
Statistics
Matches: 104, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
107 9 0.09
108 53 0.51
109 42 0.40
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (108 bp):
TTGACCTAAGAACCAAACGACTCAACCAATTTTTTTCAATATATATATTTTTTTGTTTTTAATGT
TTTATTTAATTGATCTGGATGGATCAGTCGAACTGGCAAACAG
Found at i:4872 original size:27 final size:26
Alignment explanation
Indices: 4833--4887 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
4823 AGTTTTAATA
4833 ATTTTATAATTTAT-TAGATTTTTTAT
1 ATTTTATAATTTATCT-GATTTTTTAT
*
4859 ATTTTATAAGTTTATCTGCTTTTTTAT
1 ATTTTATAA-TTTATCTGATTTTTTAT
4886 AT
1 AT
4888 ATTTTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 9 0.35
27 16 0.62
28 1 0.04
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64
Consensus pattern (26 bp):
ATTTTATAATTTATCTGATTTTTTAT
Found at i:17725 original size:17 final size:18
Alignment explanation
Indices: 17703--17737 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
17693 TGACTCTTTC
17703 TAAAAATAAT-AAATTAT
1 TAAAAATAATAAAATTAT
17720 TAAAAATAATAAAATTAT
1 TAAAAATAATAAAATTAT
17738 ATTTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAAATAATAAAATTAT
Found at i:30208 original size:6 final size:6
Alignment explanation
Indices: 30197--30263 Score: 50
Period size: 6 Copynumber: 11.7 Consensus size: 6
30187 GGGCCCAACA
* * * *
30197 AAATTT AAATTT -ATTTT AAGTTT AAATTT -ACTTA AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * *
30243 -ACTAT AAATTT AAGTTT AAAT
1 AAATTT AAATTT AAATTT AAAT
30264 CTATTTAAAT
Statistics
Matches: 45, Mismatches: 13, Indels: 6
0.70 0.20 0.09
Matches are distributed among these distances:
5 10 0.22
6 35 0.78
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:30222 original size:17 final size:17
Alignment explanation
Indices: 30196--30260 Score: 78
Period size: 17 Copynumber: 3.8 Consensus size: 17
30186 CGGGCCCAAC
*
30196 AAAATTTAAATTTATTT
1 AAAATTTAAATTTACTT
* *
30213 TAAGTTTAAATTTACTT
1 AAAATTTAAATTTACTT
30230 AAAATTTAAATTTAC-T
1 AAAATTTAAATTTACTT
*
30246 ATAAATTTAAGTTTA
1 A-AAATTTAAATTTA
30261 AATCTATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
16 2 0.05
17 39 0.95
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
AAAATTTAAATTTACTT
Found at i:30255 original size:34 final size:34
Alignment explanation
Indices: 30196--30260 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
30186 CGGGCCCAAC
* * *
30196 AAAATTTAAATTTATTTTAAGTTTAAATTTACTT
1 AAAATTTAAATTTACTATAAATTTAAATTTACTT
*
30230 AAAATTTAAATTTACTATAAATTTAAGTTTA
1 AAAATTTAAATTTACTATAAATTTAAATTTA
30261 AATCTATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (34 bp):
AAAATTTAAATTTACTATAAATTTAAATTTACTT
Found at i:32087 original size:29 final size:29
Alignment explanation
Indices: 32043--32166 Score: 144
Period size: 29 Copynumber: 4.2 Consensus size: 29
32033 CCCTAGATGT
32043 CTCGAAACTTCCAAAAATTCCATTTTTACC
1 CTCG-AACTTCCAAAAATTCCATTTTTACC
*
32073 CTCGAACTTCTAAAAA-TCACATTTTTGA-C
1 CTCGAACTTCCAAAAATTC-CATTTTT-ACC
* *
32102 ATCAAAACTTCCAAAAATTCCATTTTTACC
1 CTC-GAACTTCCAAAAATTCCATTTTTACC
* * *
32132 CCCGAACTTCCAAAAATTCCATTTTCAAC
1 CTCGAACTTCCAAAAATTCCATTTTTACC
32161 CTCGAA
1 CTCGAA
32167 ACTTTTAAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
28 2 0.03
29 50 0.63
30 25 0.32
31 2 0.03
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.31
Consensus pattern (29 bp):
CTCGAACTTCCAAAAATTCCATTTTTACC
Found at i:32169 original size:59 final size:59
Alignment explanation
Indices: 32043--32170 Score: 186
Period size: 59 Copynumber: 2.2 Consensus size: 59
32033 CCCTAGATGT
* * **
32043 CTCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCTAAAAATCACATTTTTGAC
1 CTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCACATTTTCAAC
* *
32102 ATCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTC-CATTTTCAAC
1 CTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAA-TCACATTTTCAAC
32161 CTCGAAACTT
1 CTCGAAACTT
32171 TTAAAATTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 58 0.97
60 2 0.03
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (59 bp):
CTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCACATTTTCAAC
Found at i:32196 original size:59 final size:57
Alignment explanation
Indices: 32043--32282 Score: 170
Period size: 59 Copynumber: 4.1 Consensus size: 57
32033 CCCTAGATGT
**
32043 CTCGAAACT-TCCAAAAATT-CCATTTTTACCCTCGAACT-TCTAAAAA-TCACATTTTTGAC
1 CTCGAAACTCT-C-AAAATTACCA-TTTTACCC-CGAA-TGTCTAAAAATTC-CATTTTCAAC
* * *
32102 ATCAAAACT-TCCAAAAATT-CCATTTTTACCCCCGAACT-TCCAAAAATTCCATTTTCAAC
1 CTCGAAACTCT-C-AAAATTACCA-TTTTA-CCCCGAA-TGTCTAAAAATTCCATTTTCAAC
* * * * ** *
32161 CTCGAAACTTTTAAAATTTACCATTTTGCCTCCGAATGTCTAGAAACCCCATTTTCGAC
1 CTCGAAACTCTCAAAA-TTACCATTTTACC-CCGAATGTCTAAAAATTCCATTTTCAAC
* * * *
32220 CTCAAAACTCTCAAAATTACCCTTTTACCCCTAATGTCTAAAAATTCCATTTTTAAC
1 CTCGAAACTCTCAAAATTACCATTTTACCCCGAATGTCTAAAAATTCCATTTTCAAC
32277 CTCGAA
1 CTCGAA
32283 TTTTCCCAAA
Statistics
Matches: 148, Mismatches: 26, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
57 27 0.18
58 18 0.12
59 94 0.64
60 9 0.06
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (57 bp):
CTCGAAACTCTCAAAATTACCATTTTACCCCGAATGTCTAAAAATTCCATTTTCAAC
Found at i:32320 original size:27 final size:27
Alignment explanation
Indices: 32288--32347 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
32278 TCGAATTTTC
**
32288 CCAAAATTATGATTTTGCCCCGGGAAT
1 CCAAAATTACCATTTTGCCCCGGGAAT
* *
32315 CCAAAATTACCATTTTGCCCTGGGTAT
1 CCAAAATTACCATTTTGCCCCGGGAAT
32342 CCAAAA
1 CCAAAA
32348 AGTCTCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (27 bp):
CCAAAATTACCATTTTGCCCCGGGAAT
Found at i:45818 original size:123 final size:122
Alignment explanation
Indices: 45591--45821 Score: 390
Period size: 123 Copynumber: 1.9 Consensus size: 122
45581 TGAGCTCCGT
* *
45591 TTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGTCTGACGCAC
1 TTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAAATGACCGCTTCATTGTCTGACCCAC
* * *
45656 TTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTTACATTTAGCTCTGC
66 TTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTTTCACTTACATTTAGCTCTGC
* *
45713 TTCATTGATTTTGGTCTACTTCTCTGTATCTCATTAGGAAAATGACCGCTTCATTGTTTGACCCA
1 TTCATTGA-TTTGGTCTACTTCTCTGTATCTCATCAGGAAAATGACCGCTTCATTGTCTGACCCA
45778 CTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTTTCACTT
65 CTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTTTCACTT
45822 CACTTCATTG
Statistics
Matches: 101, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
122 8 0.08
123 93 0.92
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (122 bp):
TTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAAATGACCGCTTCATTGTCTGACCCAC
TTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTTTCACTTACATTTAGCTCTGC
Found at i:45973 original size:114 final size:114
Alignment explanation
Indices: 45770--46080 Score: 462
Period size: 114 Copynumber: 2.7 Consensus size: 114
45760 GCTTCATTGT
* *
45770 TTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTTTCACTTCACTTCATTGTAT
1 TTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTTTCACTCCACTTCACTGTAT
* * ** * *
45835 CCTCAAGGACGTTGAGCTTGGCTTCGTTGTTCTGATTCAATATACTGTA
66 CCTCAGGGATGTTGAGCTAAGCTTCGTTATTCTGATTCAAGATACTGTA
* *
45884 TTGACCCACTTCTTTGTACCTCACCAAGAAGATGGGATTTGAAGTTTCACTCCACTTCACTGTAT
1 TTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTTTCACTCCACTTCACTGTAT
* *
45949 CCTCAGGGATGTTGAGCTAAGCTTCGTTATTTTGATTCAAGATACTGTT
66 CCTCAGGGATGTTGAGCTAAGCTTCGTTATTCTGATTCAAGATACTGTA
* * *
45998 TTGACCCACTTCTCTGTACCTCACTAGGAAGATGGGATTTGAAGTCTCAC-CCTACTCCACTGTA
1 TTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTTTCACTCC-ACTTCACTGTA
*
46062 TCCTCAGGGGTGTTGAGCT
65 TCCTCAGGGATGTTGAGCT
46081 CTGCTTCATT
Statistics
Matches: 178, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
113 2 0.01
114 176 0.99
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (114 bp):
TTGACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTTTCACTCCACTTCACTGTAT
CCTCAGGGATGTTGAGCTAAGCTTCGTTATTCTGATTCAAGATACTGTA
Found at i:46174 original size:95 final size:95
Alignment explanation
Indices: 46003--46182 Score: 254
Period size: 95 Copynumber: 1.9 Consensus size: 95
45993 CTGTTTTGAC
* *
46003 CCACTTCTCTGTACCTCACTAGGAAGATGGGATTTGAAGTCTCACCCTACTCCACTGTATCCTCA
1 CCACTTCTCTGTACCTCACCAGGAAGATAGGATTTGAAGTCTCACCCTACTCCACTGTATCCTCA
** * *
46068 GGGGTGTTGAGCTCTGCTTCATTATTTTAA
66 GGGACGATGAGCTCTACTTCATTATTTTAA
* * * *
46098 CCACTTTTCTGTACCTCACCAGGAAGATAGGATTTGAAGTCTCACTCTAGTCCACTGTAAT-CTT
1 CCACTTCTCTGTACCTCACCAGGAAGATAGGATTTGAAGTCTCACCCTACTCCACTGT-ATCCTC
46162 AGGGACGATGAGCTCTACTTC
65 AGGGACGATGAGCTCTACTTC
46183 GTTGTTTTGA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 72 0.97
96 2 0.03
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (95 bp):
CCACTTCTCTGTACCTCACCAGGAAGATAGGATTTGAAGTCTCACCCTACTCCACTGTATCCTCA
GGGACGATGAGCTCTACTTCATTATTTTAA
Found at i:46668 original size:99 final size:99
Alignment explanation
Indices: 46541--47170 Score: 534
Period size: 99 Copynumber: 6.4 Consensus size: 99
46531 TGTTTTTAGC
* * * **
46541 GTACAAGGTTCTCCATTGCGGCCTCAACCTTTCCCTTTTATATTTTCATAATACTAGATTCGCCG
1 GTACAAGGTTCGCCGTTGCGGACTCAACCTTTCCC-TTTATATTTTCATGGTACTAGATTCGCCG
* * *
46606 TTGCGGCCTCGATCTTTCCCATCACGTC-TCTAAG
65 TTGCGGCCTCAATCCTTCCCATCACATCTTCTAAG
* * *
46640 GTACAAGGTTCGCTGTTGCGGACTCAACCTTTCCCTTCATATTTTCATGGTA-TCAGATTCGTCG
1 GTACAAGGTTCGCCGTTGCGGACTCAACCTTTCCCTTTATATTTTCATGGTACT-AGATTCGCCG
* * * *
46704 TT-CTGGTCTCAATCATTCCTATCACATCTTCAAAG
65 TTGC-GGCCTCAATCCTTCCCATCACATCTTCTAAG
* * * * * *
46739 GTAC-AGAGTTTGTCGTTGCGGTCAT-AATCTTTCCCTTAATATCTTT-ATGGTACTAGATTCGT
1 GTACAAG-GTTCGCCGTTGCGGAC-TCAACCTTTCCCTTTATAT-TTTCATGGTACTAGATTCGC
** * * *
46801 TATTGCGGCCTCAATCCTTTCCATCACATTTTGTAAG
63 CGTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAG
* ** * * * *
46838 GTACAGGGTTCATCGTTGC-GACCTCAACCTTT-TCTTT-TATTTCCATGGTA-TCGGATTCACC
1 GTACAAGGTTCGCCGTTGCGGA-CTCAACCTTTCCCTTTATATTTTCATGGTACT-AGATTCGCC
* * *
46899 GTTACAGCCTCAATCCTTCCCATCACATCTTTTAAG
64 GTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAG
* * * * *
46935 GTAC-AGTGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTT-ATGGTACCAGATTTGTC
1 GTACAAG-GTTCGCCGTTGCGGACTCAACCTTTCCCTTTATAT-TTTCATGGTACTAGATTCGCC
* **
46998 GTTGTGGTTTCAATCCTTCCCATCACATCTTCTAAG
64 GTTGCGGCCTCAATCCTTCCCATCACATCTTCTAAG
* * * * * * *
47034 GTATAGGGTTCGCCGTTAC-GACCTCAACCTTTCTC-TT-TATTTTCATGATACCAGATTCACCG
1 GTACAAGGTTCGCCGTTGCGGA-CTCAACCTTTCCCTTTATATTTTCATGGTACTAGATTCGCCG
* * * *
47096 TTGTGGCTTCAATCCTTCCCATTACATATTCTAAG
65 TTGCGGCCTCAATCCTTCCCATCACATCTTCTAAG
** *
47131 GTACAAGGTTTACCGTTGCGGCCTCAACCTTTCCCTTTAT
1 GTACAAGGTTCGCCGTTGCGGACTCAACCTTTCCCTTTAT
47171 TTCTGTAGTA
Statistics
Matches: 421, Mismatches: 85, Indels: 50
0.76 0.15 0.09
Matches are distributed among these distances:
96 7 0.02
97 145 0.34
98 60 0.14
99 199 0.47
100 10 0.02
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.37
Consensus pattern (99 bp):
GTACAAGGTTCGCCGTTGCGGACTCAACCTTTCCCTTTATATTTTCATGGTACTAGATTCGCCGT
TGCGGCCTCAATCCTTCCCATCACATCTTCTAAG
Found at i:46857 original size:50 final size:48
Alignment explanation
Indices: 46803--47211 Score: 161
Period size: 50 Copynumber: 8.4 Consensus size: 48
46793 AGATTCGTTA
*
46803 TTGCGGCCTCAATCCTTTCCATCACATTTTGTAAGGTACAGGGTTCATCG
1 TTGCGGCCTCAA-CCTTTCCATCACATTTT-TAAGGTACAGGGTTCACCG
* * *** ** * *
46853 TTGCGACCTCAACCTTTTC-TTTTATTTCCATGGTATC-GGATTCACCG
1 TTGCGGCCTCAACCTTTCCATCACATTTTTAAGGTA-CAGGGTTCACCG
* * * * *
46900 TTACAGCCTCAATCCTTCCCATCACATCTTTTAAGGTACAGTGTTCGCCG
1 TTGCGGCCTCAA-CCTTTCCATCACAT-TTTTAAGGTACAGGGTTCACCG
* * * * * ***
46950 TTGCGGCCTCAACCTTTCCCTTCATATCTTTATGGTACCA-GATTTGTCG
1 TTGCGGCCTCAACCTTT-CCATCACATTTTTAAGGTA-CAGGGTTCACCG
* ** * * * *
46999 TTGTGGTTTCAATCCTTCCCATCACATCTTCTAAGGTATAGGGTTCGCCG
1 TTGCGGCCTCAA-CCTTTCCATCACAT-TTTTAAGGTACAGGGTTCACCG
* * ** * * * *
47049 TTACGACCTCAACCTTT-C-TCTTTATTTTCATGATACCA-GATTCACCG
1 TTGCGGCCTCAACCTTTCCATC-ACATTTTTAAGGTA-CAGGGTTCACCG
* * * * * * *
47096 TTGTGGCTTCAATCCTTCCCATTACATATTCTAAGGTACAAGGTTTACCG
1 TTGCGGCCTCAA-CCTTTCCATCACAT-TTTTAAGGTACAGGGTTCACCG
* ** * *
47146 TTGCGGCCTCAACCTTTCCCT-TTATTTCTGT-A-GTACAAGGTTTACCG
1 TTGCGGCCTCAACCTTTCCATCACATTT-T-TAAGGTACAGGGTTCACCG
*
47193 TTGCAGCCTCAACCTTTCC
1 TTGCGGCCTCAACCTTTCC
47212 CTTTATTTCT
Statistics
Matches: 255, Mismatches: 85, Indels: 41
0.67 0.22 0.11
Matches are distributed among these distances:
47 80 0.31
48 22 0.09
49 61 0.24
50 92 0.36
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (48 bp):
TTGCGGCCTCAACCTTTCCATCACATTTTTAAGGTACAGGGTTCACCG
Found at i:46938 original size:196 final size:196
Alignment explanation
Indices: 46556--47167 Score: 563
Period size: 196 Copynumber: 3.1 Consensus size: 196
46546 AGGTTCTCCA
* * ** * * * *
46556 TTGCGGCCTCAACCTTTCCCTTTTATAT-TTTCATAATACTAGATTCGCCGTTGCGGCCTCGATC
1 TTGCGGCATCAACCTTTCCC-TTAATATCTTT-ATGGTACCAGATTCGTCATTGCGGCCTCAATC
* * * * * * *
46620 TTTCCCATCACGTC-TCTAAGGTACAAGGTTCGCTGTTGCGGA-CTCAACCTTTCCCTTCATATT
64 CTTCCCATCACATCTTCTAAGGTACAGGGTTCACCGTTAC-GACCTCAACCTTTCTCTT--TATT
* * * ** * * * * *
46683 TTCATGGTATCAGATTCGTCGTT-CTGGTCTCAATCATTCCTATCACATCTTCAAAGGTACAGAG
126 TCCATGATACCAGATTCACCGTTAC-AGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGAG
* *
46747 TTTGTCG
190 TTCGCCG
* * *
46754 TTGCGGTCAT-AATCTTTCCCTTAATATCTTTATGGTACTAGATTCGTTATTGCGGCCTCAATCC
1 TTGCGG-CATCAACCTTTCCCTTAATATCTTTATGGTACCAGATTCGTCATTGCGGCCTCAATCC
* * * * *
46818 TTTCCATCACATTTTGTAAGGTACAGGGTTCATCGTTGCGACCTCAACCTTT-TCTTTTATTTCC
65 TTCCCATCACATCTTCTAAGGTACAGGGTTCACCGTTACGACCTCAACCTTTCTC-TTTATTTCC
* * * * *
46882 ATGGTATCGGATTCACCGTTACAGCCTCAATCCTTCCCATCACATCTTTTAAGGTACAGTGTTCG
129 ATGATACCAGATTCACCGTTACAGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGAGTTCG
46947 CCG
194 CCG
* * * * * **
46950 TTGCGGCCTCAACCTTTCCCTTCATATCTTTATGGTACCAGATTTGTCGTTGTGGTTTCAATCCT
1 TTGCGGCATCAACCTTTCCCTTAATATCTTTATGGTACCAGATTCGTCATTGCGGCCTCAATCCT
* * *
47015 TCCCATCACATCTTCTAAGGTATAGGGTTCGCCGTTACGACCTCAACCTTTCTCTTTATTTTCAT
66 TCCCATCACATCTTCTAAGGTACAGGGTTCACCGTTACGACCTCAACCTTTCTCTTTATTTCCAT
*** * * * **
47080 GATACCAGATTCACCGTTGTGGCTTCAATCCTTCCCATTACATATTCTAAGGTACA-AGGTTTAC
131 GATACCAGATTCACCGTTACAGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGA-GTTCGC
47144 CG
195 CG
*
47146 TTGCGGCCTCAACCTTTCCCTT
1 TTGCGGCATCAACCTTTCCCTT
47168 TATTTCTGTA
Statistics
Matches: 342, Mismatches: 63, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
195 2 0.01
196 240 0.70
197 48 0.14
198 50 0.15
199 2 0.01
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.37
Consensus pattern (196 bp):
TTGCGGCATCAACCTTTCCCTTAATATCTTTATGGTACCAGATTCGTCATTGCGGCCTCAATCCT
TCCCATCACATCTTCTAAGGTACAGGGTTCACCGTTACGACCTCAACCTTTCTCTTTATTTCCAT
GATACCAGATTCACCGTTACAGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAGAGTTCGCC
G
Found at i:47202 original size:47 final size:47
Alignment explanation
Indices: 47131--47225 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
47121 ATATTCTAAG
*
47131 GTACAAGGTTTACCGTTGCGGCCTCAACCTTTCCCTTTATTTCTGTA
1 GTACAAGGTTTACCGTTGCAGCCTCAACCTTTCCCTTTATTTCTGTA
47178 GTACAAGGTTTACCGTTGCAGCCTCAACCTTTCCCTTTATTTCTGTA
1 GTACAAGGTTTACCGTTGCAGCCTCAACCTTTCCCTTTATTTCTGTA
47225 G
1 G
47226 AATATGCTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (47 bp):
GTACAAGGTTTACCGTTGCAGCCTCAACCTTTCCCTTTATTTCTGTA
Found at i:47762 original size:42 final size:42
Alignment explanation
Indices: 47684--47798 Score: 117
Period size: 42 Copynumber: 2.7 Consensus size: 42
47674 TAGGGATATA
** * *
47684 AGATTCACCTTTGTAACTTCAATCTAGC-CCTTTACAG-CTTTG
1 AGATTCACCTTTGTGGCTTCAATCT-GCTTCTCTACAGTC-TTG
*
47726 AGATTCACTTTTGTGGCTTCAATCTGCTTCTCTACAGTCTTG
1 AGATTCACCTTTGTGGCTTCAATCTGCTTCTCTACAGTCTTG
* ** *
47768 AGATTTACCTTTACGGCTTCATTCTGCTTCT
1 AGATTCACCTTTGTGGCTTCAATCTGCTTCT
47799 TCTTATTTCG
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
41 2 0.03
42 58 0.95
43 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.42
Consensus pattern (42 bp):
AGATTCACCTTTGTGGCTTCAATCTGCTTCTCTACAGTCTTG
Found at i:47990 original size:99 final size:99
Alignment explanation
Indices: 47859--48484 Score: 493
Period size: 99 Copynumber: 6.4 Consensus size: 99
47849 ATGTTTTTAG
* ** * * * *
47859 GGTACAAGGTTCGCCGTTGCGGTCTCAACCTTTCCCTTCATATTTTTATGGTATCGGATTCA-TC
1 GGTACAAGGTTCACCGTTGTAGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGATTCACT-
* * *
47923 ATTGTGGCCTCAATCCTTCCCATAACATGTTCTAA
65 GTTGTGGCCTCAATCCTTCCCATCACATCTTCTAA
* * * *
47958 GGTACAAAGTTTACCGTTGTAGCCTCAACCTTTCCCTTCATACCTTCACGGTACCGGATTCACTG
1 GGTACAAGGTTCACCGTTGTAGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGATTCACTG
* *
48023 TTGTGGCCGT-AATCCTTTCCATCACAACTTCTAA
66 TTGTGGCC-TCAATCCTTCCCATCACATCTTCTAA
* * * * *
48057 GGTA-AAGGGTTCGCCATTGTGGCCTCAACCTTTCCCTT--TATTTTCATGGTACCGGATTTACT
1 GGTACAA-GGTTCACCGTTGTAGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGATTCACT
*** * *
48119 GTTACAGCCTCAAATCCTTCTCATTACATCTTCTAA
65 GTTGTGGCCTC-AATCCTTCCCATCACATCTTCTAA
* * * * * *
48155 GGTAC-AGGATTCACCGTTGTAACCTTAACCTTTCCATTCATATCTTCATAGTACCAGATTCGCC
1 GGTACAAGG-TTCACCGTTGTAGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGATTC-AC
*
48219 T-TTGTGGCTTCAATCCTTCCCATCACATCTTCTAA
64 TGTTGTGGCCTCAATCCTTCCCATCACATCTTCTAA
* ** * * * * *
48254 GGTACAGGGTTCACCGTTGCGGCCTCAACCTATCCCTTTATATCTTCATGGTACCAGATTCGCCG
1 GGTACAAGGTTCACCGTTGTAGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGATTCACTG
* * * ** * * *
48319 TTGTGACTTCAATCTTTCTTATCACATTTTTTAG
66 TTGTGGCCTCAATCCTTCCCATCACATCTTCTAA
* * ** * ** *
48353 GGTA-TAGAGTTCGCCGTTGCGGCCTCAACCATT--CTTTTTAT-TTCCATGGTACTGGATTCAC
1 GGTACAAG-GTTCACCGTTGTAGCCTCAACCTTTCCCTTCATATCTT-CATGGTACCGGATTCAC
** * * *
48414 CATTGTGGCTTCAATCCTTCCCATCACATTTTCTAT
64 TGTTGTGGCCTCAATCCTTCCCATCACATCTTCTAA
** **
48450 GGTAC-AGGATTCGTCGTTGCGGCCTCAACCTTTCC
1 GGTACAAGG-TTCACCGTTGTAGCCTCAACCTTTCC
48485 TTTTATTTTT
Statistics
Matches: 424, Mismatches: 85, Indels: 36
0.78 0.16 0.07
Matches are distributed among these distances:
96 4 0.01
97 106 0.25
98 52 0.12
99 233 0.55
100 27 0.06
101 2 0.00
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (99 bp):
GGTACAAGGTTCACCGTTGTAGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGATTCACTG
TTGTGGCCTCAATCCTTCCCATCACATCTTCTAA
Found at i:48160 original size:197 final size:196
Alignment explanation
Indices: 47866--48314 Score: 519
Period size: 197 Copynumber: 2.3 Consensus size: 196
47856 TAGGGTACAA
* * * ***
47866 GGTTCGCCGTTGCGGTCTCAACCTTTCCCTTCATATTTTTATGGTATCGGATTCATCATTGTGGC
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTT--TATTTTCATGGTACCGGATTCATCATTACAGC
* * * *
47931 CTCAATCCTTCCCATAACATGTTCTAAGGTACAA-AGTTTACCGTTGTAGCCTCAACCTTTCCCT
64 CTCAATCCTTCCCATAACATCTTCTAAGGTACAAGA-TTCACCGTTGTAACCTCAACCTTTCCAT
* * *
47995 TCATACCTTCACGGTACCGGATTC-ACTGTTGTGGCCGT-AATCCTTTCCATCACAACTTCTAAG
128 TCATACCTTCACAGTACCAGATTCGACT-TTGTGG-CGTCAATCCTTCCCATCACAACTTCTAAG
48058 GTAAAG
191 GTAAAG
* * * *
48064 GGTTCGCCATTGTGGCCTCAACCTTTCCCTTTATTTTCATGGTACCGGATTTA-CTGTTACAGCC
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTATTTTCATGGTACCGGATTCATC-ATTACAGCC
* * * *
48128 TCAAATCCTTCTCATTACATCTTCTAAGGTACAGGATTCACCGTTGTAACCTTAACCTTTCCATT
65 TC-AATCCTTCCCATAACATCTTCTAAGGTACAAGATTCACCGTTGTAACCTCAACCTTTCCATT
* * * * *
48193 CATATCTTCATAGTACCAGATTCGCCTTTGTGGCTTCAATCCTTCCCATCACATCTTCTAAGGTA
129 CATACCTTCACAGTACCAGATTCGACTTTGTGGCGTCAATCCTTCCCATCACAACTTCTAAGGTA
*
48258 CAG
194 AAG
* * *
48261 GGTTCACCGTTGCGGCCTCAACCTATCCCTTTATATCTTCATGGTACCAGATTC
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTAT-T-TTCATGGTACCGGATTC
48315 GCCGTTGTGA
Statistics
Matches: 211, Mismatches: 33, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
195 1 0.00
196 28 0.13
197 135 0.64
198 32 0.15
199 15 0.07
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (196 bp):
GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTATTTTCATGGTACCGGATTCATCATTACAGCCT
CAATCCTTCCCATAACATCTTCTAAGGTACAAGATTCACCGTTGTAACCTCAACCTTTCCATTCA
TACCTTCACAGTACCAGATTCGACTTTGTGGCGTCAATCCTTCCCATCACAACTTCTAAGGTAAA
G
Found at i:48249 original size:49 final size:50
Alignment explanation
Indices: 48196--48332 Score: 129
Period size: 50 Copynumber: 2.8 Consensus size: 50
48186 TTCCATTCAT
*
48196 ATCTTCATAGTACCAGATTCGCCTTTGTGGCTTCAATCCT-TCCCATCAC
1 ATCTTCATAGTACCAGATTCGCCGTTGTGGCTTCAATCCTATCCCATCAC
* * * * * * *
48245 ATCTTC-TAAGGTA-CAGGGTTCACCGTTGCGGCCTCAA-CCTATCCCTTTAT
1 ATCTTCAT-A-GTACCA-GATTCGCCGTTGTGGCTTCAATCCTATCCCATCAC
* *
48295 ATCTTCATGGTACCAGATTCGCCGTTGTGACTTCAATC
1 ATCTTCATAGTACCAGATTCGCCGTTGTGGCTTCAATC
48333 TTTCTTATCA
Statistics
Matches: 67, Mismatches: 14, Indels: 13
0.71 0.15 0.14
Matches are distributed among these distances:
48 1 0.01
49 31 0.46
50 34 0.51
51 1 0.01
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (50 bp):
ATCTTCATAGTACCAGATTCGCCGTTGTGGCTTCAATCCTATCCCATCAC
Found at i:49411 original size:6 final size:6
Alignment explanation
Indices: 49402--49452 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
49392 GACCTCTCTA
* *
49402 TTTTCT TTTTCTT TTTTTT TGTTTCCT TTATC- TTTTCT TTTTCT TTTTCT
1 TTTTCT TTTTC-T TTTTCT T-TTT-CT TTTTCT TTTTCT TTTTCT TTTTCT
49452 T
1 T
49453 CTTTTTGGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 4 0.11
6 21 0.57
7 10 0.27
8 2 0.05
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:54426 original size:37 final size:33
Alignment explanation
Indices: 54360--54427 Score: 100
Period size: 37 Copynumber: 1.9 Consensus size: 33
54350 TTAAAAGATA
54360 AAACGAATTTAAAAAAAAGTTTAAAGGTAAACT
1 AAACGAATTTAAAAAAAAGTTTAAAGGTAAACT
54393 AAACGAATTTAAATTTAAAAGAGTTTAAAGGTAAA
1 AAACGAATTTAAA---AAAA-AGTTTAAAGGTAAA
54428 TTAGTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 13 0.42
36 4 0.13
37 14 0.45
ACGTcount: A:0.56, C:0.04, G:0.13, T:0.26
Consensus pattern (33 bp):
AAACGAATTTAAAAAAAAGTTTAAAGGTAAACT
Found at i:54439 original size:37 final size:38
Alignment explanation
Indices: 54372--54453 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 38
54362 ACGAATTTAA
* *
54372 AAAAAAGTTTAAAGGTAAACTAAACGAA-TTTAAA-TTT
1 AAAAGAGTTTAAAGGTAAACTAAAC-AATTTTAAAGATT
*
54409 AAAAGAGTTTAAAGGTAAATTAGTAA-AATTTTAAAGATT
1 AAAAGAGTTTAAAGGTAAACTA--AACAATTTTAAAGATT
54448 AAAAGA
1 AAAAGA
54454 TAAAGAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
37 22 0.58
38 6 0.16
39 10 0.26
ACGTcount: A:0.55, C:0.02, G:0.13, T:0.29
Consensus pattern (38 bp):
AAAAGAGTTTAAAGGTAAACTAAACAATTTTAAAGATT
Found at i:55572 original size:2 final size:2
Alignment explanation
Indices: 55565--55595 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
55555 ATTTTGTCTG
55565 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 A
55596 AATAGATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71279 original size:32 final size:32
Alignment explanation
Indices: 71243--71307 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
71233 TGAGGGTCAT
* * * *
71243 GGTTTGTTCTAATTTGGTAAATTTTTAATTTA
1 GGTTTGTTATAATTTGATAAAATTTTAAATTA
* *
71275 GGTTTTTTATAATTTTATAAAATTTTAAATTA
1 GGTTTGTTATAATTTGATAAAATTTTAAATTA
71307 G
1 G
71308 TGATAGTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (32 bp):
GGTTTGTTATAATTTGATAAAATTTTAAATTA
Found at i:78266 original size:32 final size:32
Alignment explanation
Indices: 78230--78290 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
78220 TTTTAAGTTA
* *
78230 AATTTGATCTTTAATTTTTTAAAAAGAGTCAG
1 AATTTGATCATAAATTTTTTAAAAAGAGTCAG
*
78262 AATTTGATCATAAATTTTTTTAAAAGAGT
1 AATTTGATCATAAATTTTTTAAAAAGAGT
78291 TAAATAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.44
Consensus pattern (32 bp):
AATTTGATCATAAATTTTTTAAAAAGAGTCAG
Found at i:85934 original size:2 final size:2
Alignment explanation
Indices: 85927--85954 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
85917 TATAAATTTA
85927 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
85955 GATTGTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88507 original size:2 final size:2
Alignment explanation
Indices: 88500--88524 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
88490 TATAAAAATT
88500 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
88525 TAAGTTTAAA
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:101093 original size:21 final size:21
Alignment explanation
Indices: 101067--101106 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
101057 GGGTTTCTCA
101067 AAAAAAGTCAACGGTCAACCT
1 AAAAAAGTCAACGGTCAACCT
*
101088 AAAAAAGTTAACGGTCAAC
1 AAAAAAGTCAACGGTCAAC
101107 GATCAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.20, G:0.15, T:0.15
Consensus pattern (21 bp):
AAAAAAGTCAACGGTCAACCT
Found at i:101133 original size:21 final size:21
Alignment explanation
Indices: 101109--101154 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
101099 CGGTCAACGA
*
101109 TCAAATATCAACGATCAATGG
1 TCAAAGATCAACGATCAATGG
* * *
101130 TCAACGATCAATGGTCAATGG
1 TCAAAGATCAACGATCAATGG
101151 TCAA
1 TCAA
101155 CGGGTTAATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (21 bp):
TCAAAGATCAACGATCAATGG
Found at i:101141 original size:14 final size:14
Alignment explanation
Indices: 101100--101147 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
101090 AAAAGTTAAC
101100 GGTCAACGATCAAAT
1 GGTCAACGATC-AAT
*
101115 -ATCAACGATCAAT
1 GGTCAACGATCAAT
101128 GGTCAACGATCAAT
1 GGTCAACGATCAAT
101142 GGTCAA
1 GGTCAA
101148 TGGTCAACGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 3 0.10
14 27 0.90
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (14 bp):
GGTCAACGATCAAT
Found at i:105856 original size:17 final size:17
Alignment explanation
Indices: 105834--105867 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
105824 CGTCCCATCA
105834 ATGCCCACCTAGAAGGC
1 ATGCCCACCTAGAAGGC
*
105851 ATGCCCACTTAGAAGGC
1 ATGCCCACCTAGAAGGC
105868 TACTGTGCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.15
Consensus pattern (17 bp):
ATGCCCACCTAGAAGGC
Found at i:107166 original size:22 final size:21
Alignment explanation
Indices: 107125--107166 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
107115 TTCGAATTGG
*
107125 ACTTATATATAACATTAATAT
1 ACTTATATATAACATCAATAT
107146 ACTT-TATATGAACATACAATA
1 ACTTATATAT-AACAT-CAATA
107167 CTATGTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (21 bp):
ACTTATATATAACATCAATAT
Found at i:108291 original size:3 final size:3
Alignment explanation
Indices: 108285--108317 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
108275 TAAAATAATA
108285 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
108318 AAGGATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:109666 original size:18 final size:19
Alignment explanation
Indices: 109630--109674 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
109620 AAATATCAGA
*
109630 CAATAATATTTTAATAATT
1 CAATAATTTTTTAATAATT
109649 CAATAATTTTTTAA-AATT
1 CAATAATTTTTTAATAATT
*
109667 AAATAATT
1 CAATAATT
109675 AAAATGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (19 bp):
CAATAATTTTTTAATAATT
Found at i:110036 original size:15 final size:13
Alignment explanation
Indices: 110011--110049 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
110001 TTCAAGTATA
110011 TAAAAAAATATTAT
1 TAAAAAAATATT-T
110025 TAAAATAAATATTT
1 TAAAA-AAATATTT
110039 TATAAAAAATA
1 TA-AAAAAATA
110050 GATATGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAAAAATATTT
Found at i:115087 original size:8 final size:8
Alignment explanation
Indices: 115076--115100 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
115066 TAAAAAGGTG
115076 TGAATTAA
1 TGAATTAA
115084 TGAATTAA
1 TGAATTAA
115092 TGAATTAA
1 TGAATTAA
115100 T
1 T
115101 TAATAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (8 bp):
TGAATTAA
Found at i:117050 original size:19 final size:20
Alignment explanation
Indices: 117001--117050 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
116991 AATTGCGTAC
117001 TTATTGTTT-TTTATTTGATT
1 TTATT-TTTATTTATTTGATT
* *
117021 CTATATTTATTTATTT-ATT
1 TTATTTTTATTTATTTGATT
117040 TTATTTTTATT
1 TTATTTTTATT
117051 ACACCCTACT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (20 bp):
TTATTTTTATTTATTTGATT
Found at i:122445 original size:15 final size:14
Alignment explanation
Indices: 122414--122452 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
122404 TATACGAATG
122414 AATAAATATACAAA
1 AATAAATATACAAA
*
122428 AATAAATATAAGAAA
1 AATAAATAT-ACAAA
122443 AATAAA-ATAC
1 AATAAATATAC
122453 GAATCATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 1 0.05
14 11 0.50
15 10 0.45
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.21
Consensus pattern (14 bp):
AATAAATATACAAA
Found at i:122616 original size:29 final size:29
Alignment explanation
Indices: 122579--122963 Score: 188
Period size: 30 Copynumber: 13.2 Consensus size: 29
122569 AGTTCCGGAG
*
122579 AGTTT-GGGGTTAAAATATAATTTTGGAA
1 AGTTTAGGGGTTAAAATGTAATTTTGGAA
* *
122607 AGTTTAGGGGTAAAAAAATGCAATTTTGGGAA
1 AGTTTAGGGGT--TAAAATGTAATTTT-GGAA
* ** * *
122639 AGTTT-GGGGTAAAAATGTGGTTTTTGAG
1 AGTTTAGGGGTTAAAATGTAATTTTGGAA
* *
122667 AGTTTAGAGG-TAAAATTTAATTTTGGGAA
1 AGTTTAGGGGTTAAAATGTAATTTT-GGAA
* * * *
122696 AGTTCA-AGG-TAAAATGTGATTTT-TAGA
1 AGTTTAGGGGTTAAAATGTAATTTTGGA-A
*
122723 AGTTTAAGGG-T-AAATGTAATTTTAGGAA
1 AGTTTAGGGGTTAAAATGTAATTTT-GGAA
*
122751 AGTTTA-GGG-TAGAAATGTGATTTTTGG-A
1 AGTTTAGGGGTTA-AAATGT-AATTTTGGAA
*** *
122779 AGTTTGAGGGCAAAAATATGT--TTTT-AAGA
1 AGTTT-AGGGGTTAAA-ATGTAATTTTGGA-A
* ** * *
122808 AGTTCAAAGGTAAAAATGTGATTTTTGG-A
1 AGTTTAGGGGTTAAAATGT-AATTTTGGAA
* * * *
122837 AGTTTATGAGTGAAAATGTAATTTTTGAAA
1 AGTTTAGGGGTTAAAATGTAA-TTTTGGAA
* *
122867 AGTTTAGGGGTGAAAATGTAATTTTAGTAA
1 AGTTTAGGGGTTAAAATGTAATTTT-GGAA
* *
122897 AGTTTATGGGTTAAAATTTAATTTTGGAAA
1 AGTTTAGGGGTTAAAATGTAATTTTGG-AA
* * * *
122927 AGTTTAAGGATCAAAATTTAATTTTGGAAA
1 AGTTTAGGGGTTAAAATGTAATTTTGG-AA
122957 AGTTTAG
1 AGTTTAG
122964 AGGTCTTTTG
Statistics
Matches: 279, Mismatches: 51, Indels: 52
0.73 0.13 0.14
Matches are distributed among these distances:
26 1 0.00
27 25 0.09
28 64 0.23
29 66 0.24
30 93 0.33
31 21 0.08
32 9 0.03
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.37
Consensus pattern (29 bp):
AGTTTAGGGGTTAAAATGTAATTTTGGAA
Found at i:122705 original size:28 final size:28
Alignment explanation
Indices: 122674--122956 Score: 105
Period size: 29 Copynumber: 9.8 Consensus size: 28
122664 GAGAGTTTAG
* *
122674 AGGTAAAATTTAATTTTGGGAAAGTTCA
1 AGGTAAAATGTAATTTTAGGAAAGTTCA
* *
122702 AGGTAAAATGTGATTTTTA-G-AAGTTTA
1 AGGTAAAATGT-AATTTTAGGAAAGTTCA
*
122729 AGGGT-AAATGTAATTTTAGGAAAGTTTA
1 A-GGTAAAATGTAATTTTAGGAAAGTTCA
* * * *
122757 GGGTAGAAATGTGATTTTTGG-AAGTTTGA
1 AGGTA-AAATGTAATTTTAGGAAAG-TTCA
* * * ** *
122786 GGGCAAAAATATGTTTTTAAG-AAGTTCAA
1 AGG-TAAAATGTAATTTTAGGAAAGTTC-A
* * *
122815 AGGTAAAAATGTGATTTTTGG-AAGTTTA
1 AGGT-AAAATGTAATTTTAGGAAAGTTCA
* * * *
122843 TGAGTGAAAATGTAATTTTTGAAAAGTTTA
1 AG-GT-AAAATGTAATTTTAGGAAAGTTCA
* * *
122873 GGGGTGAAAATGTAATTTTAGTAAAGTTTA
1 -AGGT-AAAATGTAATTTTAGGAAAGTTCA
* * *
122903 TGGGTTAAAATTTAATTTT-GGAAAAGTTTA
1 -AGG-TAAAATGTAATTTTAGG-AAAGTTCA
*
122933 AGGATCAAAATTTAATTTT-GGAAA
1 AGG-T-AAAATGTAATTTTAGGAAA
122957 AGTTTAGAGG
Statistics
Matches: 205, Mismatches: 34, Indels: 31
0.76 0.13 0.11
Matches are distributed among these distances:
26 6 0.03
27 17 0.08
28 28 0.14
29 81 0.40
30 71 0.35
31 2 0.01
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.37
Consensus pattern (28 bp):
AGGTAAAATGTAATTTTAGGAAAGTTCA
Found at i:122831 original size:58 final size:56
Alignment explanation
Indices: 122646--122861 Score: 195
Period size: 58 Copynumber: 3.8 Consensus size: 56
122636 GAAAGTTTGG
* * * **
122646 GGTAAAAATGTGGTTTTT-GAGAGTTTAGAGGTAAAATTTAATTTTGGGAAAGTTCAA
1 GGTAAAAATGTGATTTTTGGA-AGTTTA-AGGGAAAATATAATTTTAAGAAAGTTCAA
* * * * * *
122703 GGT-AAAATGTGATTTTTAGAAGTTTAAGGGTAAATGTAATTTTAGGAAAGTTTAG
1 GGTAAAAATGTGATTTTTGGAAGTTTAAGGGAAAATATAATTTTAAGAAAGTTCAA
* * **
122758 GGTAGAAATGTGATTTTTGGAAGTTTGAGGGCAAAAATATGTTTTTAAG-AAGTTCAAA
1 GGTAAAAATGTGATTTTTGGAAGTTTAAGGG--AAAATATAATTTTAAGAAAGTTC-AA
* *
122816 GGTAAAAATGTGATTTTTGGAAGTTTATGAGTGAAAATGTAATTTT
1 GGTAAAAATGTGATTTTTGGAAGTTTA--AGGGAAAATATAATTTT
122862 TGAAAAGTTT
Statistics
Matches: 129, Mismatches: 23, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
55 26 0.20
56 43 0.33
57 10 0.08
58 47 0.36
60 3 0.02
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.38
Consensus pattern (56 bp):
GGTAAAAATGTGATTTTTGGAAGTTTAAGGGAAAATATAATTTTAAGAAAGTTCAA
Found at i:124331 original size:20 final size:20
Alignment explanation
Indices: 124284--124331 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
124274 TTCAACTAAA
*
124284 TGCAAGTCTCTTTTCTTCTT
1 TGCAAGTTTCTTTTCTTCTT
124304 TGCAAGTTTCTTTTCTTCTT
1 TGCAAGTTTCTTTTCTTCTT
124324 TGCAAGTT
1 TGCAAGTT
124332 CGGCTTGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.21, G:0.12, T:0.54
Consensus pattern (20 bp):
TGCAAGTTTCTTTTCTTCTT
Found at i:124607 original size:17 final size:17
Alignment explanation
Indices: 124585--124626 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
124575 GAATATTAAT
*
124585 AATTTAAATTTAAAATA
1 AATTTAAACTTAAAATA
124602 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
124619 AATTTAAA
1 AATTTAAA
124627 AATGAGTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTTAAACTTAAAATA
Found at i:125950 original size:19 final size:19
Alignment explanation
Indices: 125926--125962 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
125916 TGTGCCTTGA
125926 ATGTTCAAGCTCGAACTTC
1 ATGTTCAAGCTCGAACTTC
125945 ATGTTCAAGCTCGAACTT
1 ATGTTCAAGCTCGAACTT
125963 GATCCATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (19 bp):
ATGTTCAAGCTCGAACTTC
Found at i:127958 original size:15 final size:14
Alignment explanation
Indices: 127938--127981 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
127928 AAATACACAA
127938 ATATTTTCAAAAAAT
1 ATATTTT-AAAAAAT
*
127953 ATATTTTAAAATAT
1 ATATTTTAAAAAAT
**
127967 ATAAATTAAAAAAT
1 ATATTTTAAAAAAT
127981 A
1 A
127982 ATTATTGACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATTTTAAAAAAT
Found at i:132179 original size:7 final size:7
Alignment explanation
Indices: 132157--132201 Score: 54
Period size: 7 Copynumber: 6.0 Consensus size: 7
132147 TTTTCTTTTC
132157 TTTTCATT
1 TTTTC-TT
132165 TCTTTCTT
1 T-TTTCTT
132173 TTTTCTT
1 TTTTCTT
132180 TTTTCTT
1 TTTTCTT
*
132187 TTTCCTT
1 TTTTCTT
132194 TTCTTCTT
1 TT-TTCTT
132202 CTGTAGAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 21 0.64
8 8 0.24
9 4 0.12
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTCTT
Found at i:132978 original size:24 final size:24
Alignment explanation
Indices: 132942--132990 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
132932 CCAGCAAAGA
* *
132942 CTTCCAACTGATTCGCCTGAGAGG
1 CTTCCAACAGATTCGCCTAAGAGG
*
132966 CTTCCAACAGATTCTCCTAAGAGG
1 CTTCCAACAGATTCGCCTAAGAGG
132990 C
1 C
132991 CTAGGGAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (24 bp):
CTTCCAACAGATTCGCCTAAGAGG
Found at i:133645 original size:6 final size:6
Alignment explanation
Indices: 133634--133686 Score: 106
Period size: 6 Copynumber: 8.8 Consensus size: 6
133624 GCTTCTACGT
133634 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
133682 ATATA
1 ATATA
133687 TAATTGGTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:136222 original size:19 final size:18
Alignment explanation
Indices: 136161--136222 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 18
136151 AGACAAACAT
*
136161 AAAATATATAAATTTATTAA
1 AAAATTTATAAATTTA-T-A
*
136181 AAAATATTA-AAATTGATA
1 AAAAT-TTATAAATTTATA
*
136199 TAAATTTATAAATATTATA
1 AAAATTTATAAAT-TTATA
136218 AAAAT
1 AAAAT
136223 ATAAAAATCT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 3 0.09
18 9 0.26
19 9 0.26
20 11 0.32
21 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AAAATTTATAAATTTATA
Found at i:136230 original size:19 final size:19
Alignment explanation
Indices: 136159--136230 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 19
136149 TAAGACAAAC
**
136159 ATAAAATATATAAATTTATT
1 ATAAAA-ATATAAAAATATT
* *
136179 A-AAAAATATTAAAAT-TG
1 ATAAAAATATAAAAATATT
* * *
136196 ATATAAATTTATAAATATT
1 ATAAAAATATAAAAATATT
136215 ATAAAAATATAAAAAT
1 ATAAAAATATAAAAAT
136231 CTAATAAATT
Statistics
Matches: 38, Mismatches: 12, Indels: 5
0.69 0.22 0.09
Matches are distributed among these distances:
17 2 0.05
18 17 0.45
19 18 0.47
20 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (19 bp):
ATAAAAATATAAAAATATT
Found at i:136237 original size:19 final size:18
Alignment explanation
Indices: 136161--136238 Score: 50
Period size: 20 Copynumber: 4.1 Consensus size: 18
136151 AGACAAACAT
* *
136161 AAAATATATAAATTTATTAA
1 AAAATATA-AAAATTAAT-A
*
136181 AAAATATTAAAATTGATATA
1 AAAATATAAAAATT-A-ATA
** *
136201 AATTTATAAATATT-ATA
1 AAAATATAAAAATTAATA
136218 AAAATATAAAAATCTAATA
1 AAAATATAAAAAT-TAATA
136237 AA
1 AA
136239 TTATATTTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
17 13 0.30
18 1 0.02
19 10 0.23
20 19 0.43
21 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (18 bp):
AAAATATAAAAATTAATA
Found at i:136313 original size:20 final size:20
Alignment explanation
Indices: 136290--136357 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
136280 TATAAAAACG
136290 TATAAAAATTCTTAACAACT
1 TATAAAAATTCTTAACAACT
* *
136310 TATAAAAA-TCATTAAAAATT
1 TATAAAAATTC-TTAACAACT
* *
136330 TAAAAAAATTATTATAC-ACT
1 TATAAAAATTCTTA-ACAACT
136350 TATAAAAA
1 TATAAAAA
136358 AATTTTATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
19 2 0.05
20 34 0.89
21 2 0.05
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (20 bp):
TATAAAAATTCTTAACAACT
Found at i:136326 original size:40 final size:40
Alignment explanation
Indices: 136282--136357 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
136272 TAAAATTTTA
* *
136282 TAAAAACGTATAAAAATTCTTA-ACAACTTATAAAAATCAT
1 TAAAAACGTAAAAAAATTATTATAC-ACTTATAAAAATCAT
**
136322 TAAAAATTTAAAAAAATTATTATACACTTATAAAAA
1 TAAAAACGTAAAAAAATTATTATACACTTATAAAAA
136358 AATTTTATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 29 0.94
41 2 0.06
ACGTcount: A:0.58, C:0.09, G:0.01, T:0.32
Consensus pattern (40 bp):
TAAAAACGTAAAAAAATTATTATACACTTATAAAAATCAT
Found at i:136380 original size:20 final size:20
Alignment explanation
Indices: 136273--136390 Score: 55
Period size: 20 Copynumber: 5.8 Consensus size: 20
136263 AAACATATTT
*
136273 AAAATTTTATAAAAACGTATA
1 AAAATTTTATAAATAC-TATA
*
136294 AAAATTCTTA-ACA-ACTTATA
1 AAAATT-TTATAAATAC-TATA
* * * *
136314 AAAATCATTAAAAAT-TTAAA
1 AAAAT-TTTATAAATACTATA
* *
136334 AAAATTATTATACACTTA-TAAA
1 AAAATT-TTATA-A-ATACTATA
136356 AAAATTTTATAAATACTATA
1 AAAATTTTATAAATACTATA
* *
136376 AAAATATAATAAATA
1 AAAATTTTATAAATA
136391 ATAATATGTA
Statistics
Matches: 75, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
19 2 0.03
20 43 0.57
21 16 0.21
22 14 0.19
ACGTcount: A:0.58, C:0.07, G:0.01, T:0.34
Consensus pattern (20 bp):
AAAATTTTATAAATACTATA
Found at i:136418 original size:26 final size:27
Alignment explanation
Indices: 136375--136426 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
136365 TAAATACTAT
136375 AAAAATATAATAAATAAT-AATATGTAA
1 AAAAATATAATAAATAATGAA-ATGTAA
*
136402 AAAAATATAA-AATTAATGAAATGTA
1 AAAAATATAATAAATAATGAAATGTA
136427 TTTAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (27 bp):
AAAAATATAATAAATAATGAAATGTAA
Found at i:137193 original size:20 final size:20
Alignment explanation
Indices: 137170--137214 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
137160 TTTATATTAA
137170 TTTTAAAGTATTTTATGA-GT
1 TTTTAAAGTATTTTAT-ATGT
* *
137190 TTTTAAATTTTTTTATATGT
1 TTTTAAAGTATTTTATATGT
137210 TTTTA
1 TTTTA
137215 TGAATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (20 bp):
TTTTAAAGTATTTTATATGT
Found at i:137204 original size:30 final size:29
Alignment explanation
Indices: 137140--137235 Score: 72
Period size: 30 Copynumber: 3.3 Consensus size: 29
137130 GTTTTTATGG
* * *
137140 TTTTTTATAA-TTTTT-TTAAATTTATAT
1 TTTTTTATAAGTTTTTATGAATTTTAAAT
* *
137167 TAATTTTA-AAGTATTTTATGAGTTTTTAAAT
1 T-TTTTTATAAGT-TTTTATGA-ATTTTAAAT
*
137198 TTTTTTATATGTTTTTATGAATTTTAAAT
1 TTTTTTATAAGTTTTTATGAATTTTAAAT
*
137227 ATGTTTTAT
1 -TTTTTTAT
137236 TAATTTTGTA
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
27 3 0.06
28 6 0.11
29 12 0.23
30 22 0.42
31 10 0.19
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (29 bp):
TTTTTTATAAGTTTTTATGAATTTTAAAT
Found at i:137221 original size:49 final size:47
Alignment explanation
Indices: 137128--137225 Score: 119
Period size: 49 Copynumber: 2.0 Consensus size: 47
137118 AGTCCAGTAC
*
137128 AAGTTTTTATGGTTTTTTATAATTTTTTTAAATTTATATTAATTTTA
1 AAGTTTTTATGGTTTTTTATAATTTTTTTAAATTTATATGAATTTTA
* *
137175 AAGTATTTTATGAG-TTTTTA-AATTTTTTTATATGTTTTTATGAATTTTA
1 AAGT-TTTTATG-GTTTTTTATAATTTTTTTA-A-ATTTATATGAATTTTA
137224 AA
1 AA
137226 TATGTTTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
47 14 0.32
48 14 0.32
49 16 0.36
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (47 bp):
AAGTTTTTATGGTTTTTTATAATTTTTTTAAATTTATATGAATTTTA
Found at i:137222 original size:21 final size:20
Alignment explanation
Indices: 137204--137242 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
137194 AAATTTTTTT
137204 ATATGTTTTTATGAATTTTAA
1 ATATG-TTTTATGAATTTTAA
*
137225 ATATGTTTTATTAATTTT
1 ATATGTTTTATGAATTTT
137243 GTAATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
ATATGTTTTATGAATTTTAA
Found at i:137307 original size:29 final size:29
Alignment explanation
Indices: 137264--137325 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 29
137254 AAATTTTATA
137264 TTTTTATAATATTTATAAGTTCT-TATCAT
1 TTTTTATAATATTTATAAGTT-TATATCAT
137293 TTTTTATAACT-TTTATAAGTTTATATCAT
1 TTTTTATAA-TATTTATAAGTTTATATCAT
137322 TTTT
1 TTTT
137326 AATATTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
28 1 0.03
29 29 0.94
30 1 0.03
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.61
Consensus pattern (29 bp):
TTTTTATAATATTTATAAGTTTATATCAT
Found at i:144935 original size:37 final size:36
Alignment explanation
Indices: 144883--144955 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 36
144873 TGCTTCTAAA
*
144883 CAAATGCTATCTATATATATATATGTTTTTTTTTTT
1 CAAATGCTATATATATATATATATGTTTTTTTTTTT
144919 NCAAATGCTATATATATATATATATGTTTTTTTTTTT
1 -CAAATGCTATATATATATATATATGTTTTTTTTTTT
144956 TTCAAATTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.58
Consensus pattern (36 bp):
CAAATGCTATATATATATATATATGTTTTTTTTTTT
Found at i:155479 original size:2 final size:2
Alignment explanation
Indices: 155472--155498 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
155462 CAATGCATTC
155472 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 A
155499 GTAAGAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:157637 original size:6 final size:6
Alignment explanation
Indices: 157623--157657 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
157613 CAACATCTTA
*
157623 TAACTC TAACCC TAACCC TAACCC TAACCC TAACC
1 TAACCC TAACCC TAACCC TAACCC TAACCC TAACC
157658 TTAGATGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.46, G:0.00, T:0.20
Consensus pattern (6 bp):
TAACCC
Found at i:157758 original size:6 final size:6
Alignment explanation
Indices: 157738--157781 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
157728 AAATGATATC
* *
157738 ATAGGA ACAGGA ATAGAA ATAGGA ATAGGA ATAGGA ATAGGA AT
1 ATAGGA ATAGGA ATAGGA ATAGGA ATAGGA ATAGGA ATAGGA AT
157782 GAGAAAAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.52, C:0.02, G:0.30, T:0.16
Consensus pattern (6 bp):
ATAGGA
Found at i:162289 original size:16 final size:18
Alignment explanation
Indices: 162263--162300 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
162253 AAAATATAAT
162263 TTTATTATTTTT-TAAAA
1 TTTATTATTTTTATAAAA
*
162280 TTTA-TATTTTTATAAAT
1 TTTATTATTTTTATAAAA
162297 TTTA
1 TTTA
162301 AAATATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTATTATTTTTATAAAA
Found at i:162299 original size:25 final size:24
Alignment explanation
Indices: 162257--162312 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
162247 TTAGTAAAAA
**
162257 TATAATTTTATTATTTTTTAAAATT
1 TATAATTTTA-TAAATTTTAAAATT
*
162282 TATATTTTTATAAATTTTAAAATAT
1 TATAATTTTATAAATTTTAAAAT-T
162307 TA-AATT
1 TATAATT
162313 AAATTTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TATAATTTTATAAATTTTAAAATT
Found at i:162341 original size:31 final size:32
Alignment explanation
Indices: 162285--162369 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 32
162275 TAAAATTTAT
* * *
162285 ATTTTTATAAATTTTAAAATATTAAA-T-TAA
1 ATTTTTATTATTTTTAAAAAATTAAAGTGTAA
162315 ATTTTTATTATTTTTAAAAAAGTTAAAGTGTAA
1 ATTTTTATTATTTTTAAAAAA-TTAAAGTGTAA
*
162348 TTTTATTATTATTAATTTAAAA
1 ATTT-TTATTATT--TTTAAAA
162370 TTTTATAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
30 18 0.40
31 5 0.11
32 1 0.02
33 6 0.13
34 8 0.18
36 7 0.16
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (32 bp):
ATTTTTATTATTTTTAAAAAATTAAAGTGTAA
Found at i:165223 original size:22 final size:22
Alignment explanation
Indices: 165195--165239 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
165185 AAGTTTAAGG
165195 GCTTATTTAAATACAGTGAAAT
1 GCTTATTTAAATACAGTGAAAT
165217 GCTTATTTAAATACAGTGAAAT
1 GCTTATTTAAATACAGTGAAAT
165239 G
1 G
165240 TTGAAGGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
GCTTATTTAAATACAGTGAAAT
Found at i:165537 original size:3 final size:3
Alignment explanation
Indices: 165529--165557 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
165519 TTGGAGACAC
165529 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
165558 AACATGGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:171288 original size:16 final size:17
Alignment explanation
Indices: 171253--171287 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
171243 AAACTATATA
*
171253 TTAAAAATATATTAATT
1 TTAAAAATATAATAATT
*
171270 TTAAAACTATAATAATT
1 TTAAAAATATAATAATT
171287 T
1 T
171288 ATTCAAGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAAAATATAATAATT
Found at i:171667 original size:7 final size:7
Alignment explanation
Indices: 171657--171699 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
171647 AATAAATAAA
171657 AAATATT
1 AAATATT
171664 AAATATT
1 AAATATT
171671 AAATATT
1 AAATATT
*
171678 AAAATAAT
1 -AAATATT
171686 ATAATA-T
1 A-AATATT
171693 AAATATT
1 AAATATT
171700 TGTCTTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
6 4 0.12
7 18 0.56
8 10 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATATT
Found at i:171696 original size:14 final size:14
Alignment explanation
Indices: 171649--171697 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
171639 AGAATTTTAA
*
171649 TAAATAAAAAATAT
1 TAAATAATAAATAT
*
171663 TAAATATTAAATAT
1 TAAATAATAAATAT
171677 TAAAATAATATAATA-
1 T-AAATAATA-AATAT
171692 TAAATA
1 TAAATA
171698 TTTGTCTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 18 0.60
15 8 0.27
16 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAATAATAAATAT
Found at i:174463 original size:369 final size:368
Alignment explanation
Indices: 171901--174536 Score: 4844
Period size: 368 Copynumber: 7.2 Consensus size: 368
171891 GTCCATTAAG
* *
171901 AGAAAAAAAAAAGCCCAATCCATTTATTAACGTTCATTTGCAACAAAGAAAGAGAAGAGAAAGGA
1 AGAAAAAAAAAAGCCCAATCCATTTATTACCGTTCATTTGCAACCAAGAAAGAGAAGAGAAAGGA
171966 ATCGAACGGTTTACCATCAGACATACGAAGTAACCTAGGGAAGTTGAACAGCAACTAACCCCAGG
66 ATCGAACGGTTTACCATCAGACATACGAAGTAACCTAGGGAAGTTGAACAGCAACTAACCCCAGG
172031 GTGAATCATTGAATTTCAGCATGTGGAAATGGAAAAATATTATAATATATTTTGGTAACCATTTT
131 GTGAATCATTGAATTTCAGCATGTGGAAATGGAAAAATATTATAATATATTTTGGTAACCATTTT
* *
172096 TCGTATCTTCCCATGTTTAGCTGCATGGTCCCAACTTAAAAAAAAAACTATTGTAGAGAGCAACG
196 CCGTATCTTCCCATGTTTAGCTGCATGGTCCCAACTTAAAAAAAAAACTATTGTAGAGAGCAATG
*
172161 CATCACACCATAGTCAAAGGTTTTAAACTATGCCTGCTTCACCTGCATGTTATCAACAACCCAGT
261 CATCACACCATAGTCAAAGGTTTTAAACTATGCCTGCTTCACCTGCATGTTATCAGCAACCCAGT
* * *
172226 AATTAGTCTAAGAAAAAACATCGTTAAGCAGCTAGCGCCATTA
326 AATTAGTCTAAGAAAAAACACCGTTAAGCAGCCAGCACCATTA
*
172269 AGAAAAAAAAAAGCCCAATCCATTTATTACCGTTCATTTGCAAACAAGAAAGAGAAGAGAAAGGA
1 AGAAAAAAAAAAGCCCAATCCATTTATTACCGTTCATTTGCAACCAAGAAAGAGAAGAGAAAGGA
172334 ATCGAACGGTTTACCATCAGACATACGAAGTAACCTAGGGAAGTTGAACAGCAACTAACCCCAGG
66 ATCGAACGGTTTACCATCAGACATACGAAGTAACCTAGGGAAGTTGAACAGCAACTAACCCCAGG
* *
172399 GTGAATCATTGAATTTTAGCAAGTGGAAATGGAAAAATATTATAATATATTTTGGTAACCATTTT
131 GTGAATCATTGAATTTCAGCATGTGGAAATGGAAAAATATTATAATATATTTTGGTAACCATTTT
* * *
172464 TCGTATCTTCCCATGTTTAGCTGCATGGTCCCAACTTCAAAAAAAAACTATTGTAGAGAGCAACG
196 CCGTATCTTCCCATGTTTAGCTGCATGGTCCCAACTTAAAAAAAAAACTATTGTAGAGAGCAATG
*
172529 CATCACATCATAGTCAAAGGTTTTAAACTATGCCTGCTTCACCTGCATGTTATCAGCAACCCAGT
261 CATCACACCATAGTCAAAGGTTTTAAACTATGCCTGCTTCACCTGCATGTTATCAGCAACCCAGT
*
172594 AATTAGTCTAAGAAAAAACACCGTTAAGCAACCAGCACCATTA
326 AATTAGTCTAAGAAAAAACACCGTTAAGCAGCCAGCACCATTA
* *
172637 AGAAAAAAAAAAGCCCAATCCATTTATTACCGTTCATTTGCAACCAAGAAAGAGAAGAAAAAGAA
1 AGAAAAAAAAAAGCCCAATCCATTTATTACCGTTCATTTGCAACCAAGAAAGAGAAGAGAAAGGA
*
172702 ATCGAACGGTTTACCATCAGACATATGAAGTAACCTAGGGAAGTTGAACAGCAACTAACCCCAGG
66 ATCGAACGGTTTACCATCAGACATACGAAGTAACCTAGGGAAGTTGAACAGCAACTAACCCCAGG
172767 GTGAATCATTGAATTTCAGCATGTGGAAATGGAAAAATATTATAATATATTTTGGTAACCATTTT
131 GTGAATCATTGAATTTCAGCATGTGGAAATGGAAAAATATTATAATATATTTTGGTAACCATTTT
* * *
172832 CCGTATCTTCCCATGTTTAGCTGCATGGTCCAAACTTAAAAAAAAAACTATTTTAAAGAGCAATG
196 CCGTATCTTCCCATGTTTAGCTGCATGGTCCCAACTTAAAAAAAAAACTATTGTAGAGAGCAATG
*
172897 CATCACACCATAGTCAAAGATTTTAAACTATGCCTGCTTCACCTGCATGTTATCAGCAACCCAGT
261 CATCACACCATAGTCAAAGGTTTTAAACTATGCCTGCTTCACCTGCATGTTATCAGCAACCCAGT
172962 AATTAGTCTAAGAAAAAACACCGTTAAGCAGCCAGCACCATTA
326 AATTAGTCTAAGAAAAAACACCGTTAAGCAGCCAGCACCATTA
173005 AGAAAAAAAAAAGCCCAATCCATTTATTACCGTTCATTTGCAACCAAGAAAGAGAAGAGAAAGGA
1 AGAAAAAAAAAAGCCCAATCCATTTATTACCGTTCATTTGCAACCAAGAAAGAGAAGAGAAAGGA
* * *
173070 ATCAAACGGTTTACCATCAAACATACGAAGTAACCTAGGGAAGTTGAACAGCAACTAACCCCAAG
66 ATCGAACGGTTTACCATCAGACATACGAAGTAACCTAGGGAAGTTGAACAGCAACTAACCCCAGG
173135 GTGAATCATTGAATTTCAGCATGTGGAAATGGAAAAATATTATAATATATTTTGGTAACCATTTT
131 GTGAATCATTGAATTTCAGCATGTGGAAATGGAAAAATATTATAATATATTTTGGTAACCATTTT
173200 CCGTATCTTCCCATGTTTAGCTGCATGGTCCCAACTTAAAAAAAAAACTATTGTAGAGAGCAATG
196 CCGTATCTTCCCATGTTTAGCTGCATGGTCCCAACTTAAAAAAAAAACTATTGTAGAGAGCAATG
173265 CATCACACCATAGTCAAAGGTTTTAAACTATGCCTGCTTCACCTGCATGTTATCAGCAACCCAGT
261 CATCACACCATAGTCAAAGGTTTTAAACTATGCCTGCTTCACCTGCATGTTATCAGCAACCCAGT
173330 AATTAGTCTAAGAAAAAACACCGTTAAGCAGCCAGCACCATTA
326 AATTAGTCTAAGAAAAAACACCGTTAAGCAGCCAGCACCATTA
* * * *
173373 AGAAAAAAAAAAGCCCAATCCATTTATTACCATTTAGTTGCAATCAAGAAAGAGAAGAGAAAGGA
1 AGAAAAAAAAAAGCCCAATCCATTTATTACCGTTCATTTGCAACCAAGAAAGAGAAGAGAAAGGA
*
173438 ATCGAACGGTTTACCATTAGACATACGAAGTAACCTAGGGAAGTTGAACAGCAACTAACCCCAGG
66 ATCGAACGGTTTACCATCAGACATACGAAGTAACCTAGGGAAGTTGAACAGCAACTAACCCCAGG
*
173503 GTGAATCATTGAATTTCAGCATGTGGAAATGGGAAAATATTATAATATATTTTGGTAACCATTTT
131 GTGAATCATTGAATTTCAGCATGTGGAAATGGAAAAATATTATAATATATTTTGGTAACCATTTT
*
173568 CCGTATCTTCCCATGTTTAGCTGCATGGTCCCAACTTAAAAAAAAAACTATTGTAGAGAGCACTG
196 CCGTATCTTCCCATGTTTAGCTGCATGGTCCCAACTTAAAAAAAAAACTATTGTAGAGAGCAATG
* *
173633 CATCACACCATAGTCAAAGGTTTTAAACTATGCCTGCTTCACCTGCATGTTATCAGCTACCCAAT
261 CATCACACCATAGTCAAAGGTTTTAAACTATGCCTGCTTCACCTGCATGTTATCAGCAACCCAGT
173698 AATTAGTCTAAGAAAAAACACCGTTAAGCAGCCAGCACCATTA
326 AATTAGTCTAAGAAAAAACACCGTTAAGCAGCCAGCACCATTA
* * *
173741 AGAAAAAAAAAAGCCCAATCCATTTATTACTGTTTATTTGCAACCAATAAAGAGAAGAGAAAGGA
1 AGAAAAAAAAAAGCCCAATCCATTTATTACCGTTCATTTGCAACCAAGAAAGAGAAGAGAAAGGA
173806 ATCGAACGGTTTACCATCAGACATACGAAGTAACCTAGGGAAGTTGAACAGCAACTAACCCCAGG
66 ATCGAACGGTTTACCATCAGACATACGAAGTAACCTAGGGAAGTTGAACAGCAACTAACCCCAGG
* *
173871 GTGAATCATTGAATTTCAGCATGTGGAAGTGGGAAAATATTATAATATATTTTGGTAACCATTTT
131 GTGAATCATTGAATTTCAGCATGTGGAAATGGAAAAATATTATAATATATTTTGGTAACCATTTT
173936 CCGTATCTTCCCATGTTTAGCTGCATGGTCCCAACTTAAAAAAAAATA-TATTGTAGAGAGCAAT
196 CCGTATCTTCCCATGTTTAGCTGCATGGTCCCAACTTAAAAAAAAA-ACTATTGTAGAGAGCAAT
174000 GCATCACACCATAGTCAAAGGTTTTAAACTATGCCTGCTTCACCTGCATGTTATCAGCAACCCAG
260 GCATCACACCATAGTCAAAGGTTTTAAACTATGCCTGCTTCACCTGCATGTTATCAGCAACCCAG
* * *
174065 TAATTAATCTAAGAAAAAACACTGTTAAGCAACCAGCACCATTA
325 TAATTAGTCTAAGAAAAAACACCGTTAAGCAGCCAGCACCATTA
174109 AGAAAAAAAAAAGCCCAATCCATTTATTACCGTTCATTTGCAACCAAGAAAGAGAAGAGAAAGGA
1 AGAAAAAAAAAAGCCCAATCCATTTATTACCGTTCATTTGCAACCAAGAAAGAGAAGAGAAAGGA
174174 ATCGAACGGTTTACCATCAGACATACGAAGTAACCTAGGGAAGTTGAACAGCAACTAACCCCAGG
66 ATCGAACGGTTTACCATCAGACATACGAAGTAACCTAGGGAAGTTGAACAGCAACTAACCCCAGG
*
174239 GTGAATCATTGAATTTCAGCATGTGGAAGTGGAAAAATATTATAATATATTTTGGTAACCATTTT
131 GTGAATCATTGAATTTCAGCATGTGGAAATGGAAAAATATTATAATATATTTTGGTAACCATTTT
174304 CCGTATCTTCCCATGTTTAGCTGCATGGTCCCAACTTAAAAAAAAAAACTATTGTAGAGAGCAAT
196 CCGTATCTTCCCATGTTTAGCTGCATGGTCCCAACTT-AAAAAAAAAACTATTGTAGAGAGCAAT
174369 GCATCACACCATAGTCAAAGGTTTTAAACTATGCCTGCTTCACCTGCATGTTATCAGCAACCCAG
260 GCATCACACCATAGTCAAAGGTTTTAAACTATGCCTGCTTCACCTGCATGTTATCAGCAACCCAG
174434 TAATTAGTCTAAGAAAAAACACCGTTAAGCAGCCAGCACCATTA
325 TAATTAGTCTAAGAAAAAACACCGTTAAGCAGCCAGCACCATTA
174478 AG-AAAAAAAAAGCCCAATCCATTTATTACCGTTCATTTGCAACCAAGAAAGAGAAGAGA
1 AGAAAAAAAAAAGCCCAATCCATTTATTACCGTTCATTTGCAACCAAGAAAGAGAAGAGA
174537 TAACAGAACA
Statistics
Matches: 2196, Mismatches: 69, Indels: 6
0.97 0.03 0.00
Matches are distributed among these distances:
368 2062 0.94
369 134 0.06
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (368 bp):
AGAAAAAAAAAAGCCCAATCCATTTATTACCGTTCATTTGCAACCAAGAAAGAGAAGAGAAAGGA
ATCGAACGGTTTACCATCAGACATACGAAGTAACCTAGGGAAGTTGAACAGCAACTAACCCCAGG
GTGAATCATTGAATTTCAGCATGTGGAAATGGAAAAATATTATAATATATTTTGGTAACCATTTT
CCGTATCTTCCCATGTTTAGCTGCATGGTCCCAACTTAAAAAAAAAACTATTGTAGAGAGCAATG
CATCACACCATAGTCAAAGGTTTTAAACTATGCCTGCTTCACCTGCATGTTATCAGCAACCCAGT
AATTAGTCTAAGAAAAAACACCGTTAAGCAGCCAGCACCATTA
Found at i:174744 original size:22 final size:22
Alignment explanation
Indices: 174716--174771 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
174706 GTGAGCTTAT
*
174716 TTATAATATATTTCTTTATTTA
1 TTATAATATATTTATTTATTTA
174738 TTATAATATATTTATTTATTTA
1 TTATAATATATTTATTTATTTA
*
174760 TAAT-ATATATTT
1 TTATAATATATTT
174772 TGATAAACAC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATAATATATTTATTTATTTA
Found at i:175614 original size:30 final size:30
Alignment explanation
Indices: 175545--175696 Score: 155
Period size: 30 Copynumber: 5.1 Consensus size: 30
175535 ATATTGTCAT
* * * **
175545 TTTAGCCCCCAAACTTTCC-AAATTTCCTA
1 TTTAACCCCTAAACTTTCCAAAAATTCAAA
* *
175574 TTTGACCCCTAAACTTTTCAAAAATTCAAA
1 TTTAACCCCTAAACTTTCCAAAAATTCAAA
* * *
175604 TTTAACCCCTAAA-TTTCCCCAAGATTCCAA
1 TTTAACCCCTAAACTTT-CCAAAAATTCAAA
* *
175634 TTTAACCCTTAAACTTTCTAAAAATTCAAA
1 TTTAACCCCTAAACTTTCCAAAAATTCAAA
* *
175664 TTTAACCTCTAAAATTTCCAAAAATTCAAA
1 TTTAACCCCTAAACTTTCCAAAAATTCAAA
175694 TTT
1 TTT
175697 GATCCAGATT
Statistics
Matches: 99, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
29 18 0.18
30 78 0.79
31 3 0.03
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.35
Consensus pattern (30 bp):
TTTAACCCCTAAACTTTCCAAAAATTCAAA
Found at i:175648 original size:60 final size:61
Alignment explanation
Indices: 175568--175682 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 61
175558 CTTTCCAAAT
* *
175568 TTCCTATTTGACCCCTAAACTTT-TCAAAAATTCAAATTTAACCCCT-AAATTTCCCCAAGA
1 TTCCAATTTAACCCCTAAACTTTCT-AAAAATTCAAATTTAACCCCTAAAATTTCCCCAAGA
* *
175628 TTCCAATTTAACCCTTAAACTTTCTAAAAATTCAAATTTAACCTCTAAAATTTCC
1 TTCCAATTTAACCCCTAAACTTTCTAAAAATTCAAATTTAACCCCTAAAATTTCC
175683 AAAAATTCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
60 40 0.82
61 9 0.18
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.36
Consensus pattern (61 bp):
TTCCAATTTAACCCCTAAACTTTCTAAAAATTCAAATTTAACCCCTAAAATTTCCCCAAGA
Found at i:180932 original size:8 final size:8
Alignment explanation
Indices: 180931--180968 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
180921 TTTTATATTT
180931 TTTTTATA
1 TTTTTATA
180939 TTTTTATA
1 TTTTTATA
180947 TTTTTA-A
1 TTTTTATA
* *
180954 ATTTAATA
1 TTTTTATA
180962 TTTTTAT
1 TTTTTAT
180969 TTATTGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
7 5 0.20
8 20 0.80
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTTATA
Found at i:184351 original size:33 final size:34
Alignment explanation
Indices: 184273--184340 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
184263 TAAAATTATA
*
184273 ACAAAAAATTATATTATTTAAACCTTAAAAAAAT
1 ACAAAAATTTATATTATTTAAACCTTAAAAAAAT
184307 ACAAAAATTTATATTATTTAAACCTTAAAAAAAT
1 ACAAAAATTTATATTATTTAAACCTTAAAAAAAT
184341 TTTAAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (34 bp):
ACAAAAATTTATATTATTTAAACCTTAAAAAAAT
Found at i:186717 original size:18 final size:17
Alignment explanation
Indices: 186675--186718 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
186665 GCGCTTTTCC
186675 ATTTTTTTGTTATTATT
1 ATTTTTTTGTTATTATT
* *
186692 ATTATTTTTTTTCTTATT
1 ATT-TTTTTGTTATTATT
186710 AGTTTTTTT
1 A-TTTTTTT
186719 AGTATATTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 18 0.78
19 2 0.09
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (17 bp):
ATTTTTTTGTTATTATT
Found at i:202644 original size:15 final size:16
Alignment explanation
Indices: 202624--202657 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
202614 TAACCTTTTA
202624 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
202639 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
202655 AAA
1 AAA
202658 ATTAGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:203536 original size:34 final size:34
Alignment explanation
Indices: 203493--203561 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
203483 TAGTCACTTA
203493 ATTAATTTCCAATAATTAGTTGGTTCTTTCATTC
1 ATTAATTTCCAATAATTAGTTGGTTCTTTCATTC
203527 ATTAATTTCCAATAATTAGTTGGTTCTTTCATTC
1 ATTAATTTCCAATAATTAGTTGGTTCTTTCATTC
203561 A
1 A
203562 ACAAACTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (34 bp):
ATTAATTTCCAATAATTAGTTGGTTCTTTCATTC
Found at i:207292 original size:260 final size:265
Alignment explanation
Indices: 206900--207411 Score: 698
Period size: 260 Copynumber: 1.9 Consensus size: 265
206890 AAAAAAACCA
206900 AATCCACAAAATAATATAAAATCAAACAAAAAATAAAATTTATTTATAATTAACAATAAATAAAA
1 AATCCACAAAATAATATAAAATCAAACAAAAAATAAAATTTATTTATAATTAACAATAAATAAAA
* * * *
206965 GCAAATAGGCAAAAAATAGTTAACTAAAAATTCAAACAAATTAAATATAATAATTTCACATCAAT
66 G-AAATA-GCAAAAAATAGTTAAATAAAAATTCAAACAAATTAAACATAATAATTACACAACAAT
* **
207030 TTAAATATAACTAATAACTTAAACATAAAAATTTCAAATAAATTAGAA-GTTTCATAACAA-T-C
129 TTAAATATAACTAATAACTTAAACATAAAAATTTCAAAAAAATTA-AATGTACCATAACAATTGC
* * * *
207092 -TAAAAAAAAA-TTCCGAACTTAATATTTTCAATCATATATCAAGTATTTGAATCCACAATAATC
193 AAAAAAAAAAATTTCCAAACTTAATATTTTCAATCATATACCAAATATTTGAATCCACAATAATC
207155 TGAATCTG
258 TGAATCTG
*
207163 AATCCATAAAATAATATAAAATCAAACAAAAAAATAAAATTTATTTATAATTAA-AAGTAAATAA
1 AATCCACAAAATAATATAAAATCAAAC-AAAAAATAAAATTTATTTATAATTAACAA-TAAATAA
* ** * * * * *
207227 AAG-TATA-TTAAAAATATTTAAATAACAATTTAAATAAATTAAACATAATAATTACGCAACAAT
64 AAGAAATAGCAAAAAATAGTTAAATAAAAATTCAAACAAATTAAACATAATAATTACACAACAAT
** *
207290 TTAAATATATTTAATAACTTAAACATAAGAATTTCAAAAAAATTAAATGTACCATAACAATTGCA
129 TTAAATATAACTAATAACTTAAACATAAAAATTTCAAAAAAATTAAATGTACCATAACAATTGCA
* *
207355 AAAAAAAAAATTTCTAAACTTAATATTTTCAATCATATGCCAAATATTTGAATCCAC
194 AAAAAAAAAATTTCCAAACTTAATATTTTCAATCATATACCAAATATTTGAATCCAC
207412 CGTGAAATAA
Statistics
Matches: 217, Mismatches: 25, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
259 2 0.01
260 96 0.44
261 1 0.00
262 4 0.02
263 37 0.17
264 77 0.35
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (265 bp):
AATCCACAAAATAATATAAAATCAAACAAAAAATAAAATTTATTTATAATTAACAATAAATAAAA
GAAATAGCAAAAAATAGTTAAATAAAAATTCAAACAAATTAAACATAATAATTACACAACAATTT
AAATATAACTAATAACTTAAACATAAAAATTTCAAAAAAATTAAATGTACCATAACAATTGCAAA
AAAAAAAATTTCCAAACTTAATATTTTCAATCATATACCAAATATTTGAATCCACAATAATCTGA
ATCTG
Found at i:208224 original size:23 final size:23
Alignment explanation
Indices: 208198--208261 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 23
208188 ATTTTATGGC
*
208198 TTTATTTCATGTTTTTTTTAGTA
1 TTTATTTCATGTTTTTTTTAGAA
** *
208221 TTTATTAGAT-TTTATTTTAGAA
1 TTTATTTCATGTTTTTTTTAGAA
* *
208243 TTTAGTTTTATGTGTTTTT
1 TTTA-TTTCATGTTTTTTT
208262 AGTGTGTTTC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
22 14 0.45
23 12 0.39
24 5 0.16
ACGTcount: A:0.20, C:0.02, G:0.11, T:0.67
Consensus pattern (23 bp):
TTTATTTCATGTTTTTTTTAGAA
Done.