Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008236.1 Hibiscus syriacus cultivar Beakdansim tig00110882_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: 1100419
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:15391 original size:2 final size:2
Alignment explanation
Indices: 15384--15424 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
15374 AATAGATAAC
15384 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15425 GGTTAGGATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20995 original size:23 final size:24
Alignment explanation
Indices: 20957--21001 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
20947 TATTTTTTTT
20957 CAAAAAACAAAAAACAA-AAAAGG
1 CAAAAAACAAAAAACAACAAAAGG
20980 CAAAAAA-AAAACAACAACAAAA
1 CAAAAAACAAAA-AACAACAAAA
21002 AAGCCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.80, C:0.16, G:0.04, T:0.00
Consensus pattern (24 bp):
CAAAAAACAAAAAACAACAAAAGG
Found at i:20998 original size:26 final size:27
Alignment explanation
Indices: 20958--21010 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
20948 ATTTTTTTTC
*
20958 AAAAAACAAAAAACAAAAAAGGCAAAA
1 AAAAAACAAAAAACAAAAAAGCCAAAA
*
20985 AAAAAAC-AACAACAAAAAAGCCAAAA
1 AAAAAACAAAAAACAAAAAAGCCAAAA
21011 TTTTAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.79, C:0.15, G:0.06, T:0.00
Consensus pattern (27 bp):
AAAAAACAAAAAACAAAAAAGCCAAAA
Found at i:32665 original size:22 final size:21
Alignment explanation
Indices: 32639--32697 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
32629 TTAGTGCAGA
32639 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCC-TGAAG
* * *
32661 GGGAACCGATTCCCCCTGTAG
1 GGGAATCGATACCCCCTGAAG
32682 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
32698 CTGGGGTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.24, C:0.32, G:0.27, T:0.17
Consensus pattern (21 bp):
GGGAATCGATACCCCCTGAAG
Found at i:34272 original size:18 final size:18
Alignment explanation
Indices: 34246--34299 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
34236 GACGACTCCG
* *
34246 ACGATGAACCAGAACAGC
1 ACGAGGAACAAGAACAGC
*
34264 ACGAGGAACAAGCACGAGC
1 ACGAGGAACAAGAAC-AGC
34283 A-GAGGAACAAGAACAGC
1 ACGAGGAACAAGAACAGC
34300 CAGATGATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 3 0.10
18 24 0.77
19 4 0.13
ACGTcount: A:0.46, C:0.24, G:0.28, T:0.02
Consensus pattern (18 bp):
ACGAGGAACAAGAACAGC
Found at i:36237 original size:20 final size:20
Alignment explanation
Indices: 36209--36267 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
36199 CACTGAATAT
36209 TTGTCCCGAAAGACCACTGA
1 TTGTCCCGAAAGACCACTGA
*
36229 TTGTTCCG-AAGAACCACT-A
1 TTGTCCCGAAAG-ACCACTGA
* *
36248 -TGTCCCGAATGACCATTGA
1 TTGTCCCGAAAGACCACTGA
36267 T
1 T
36268 AATCCCTCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
18 11 0.35
19 7 0.23
20 13 0.42
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (20 bp):
TTGTCCCGAAAGACCACTGA
Found at i:36262 original size:18 final size:19
Alignment explanation
Indices: 36209--36267 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 19
36199 CACTGAATAT
36209 TTGTCCCGAAAGACCACTGA
1 TTGTCCCG-AAGACCACTGA
*
36229 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAG-ACCACTGA
*
36248 -TGTCCCGAATGACCATTGA
1 TTGTCCCGAA-GACCACTGA
36267 T
1 T
36268 AATCCCTCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 13 0.41
19 6 0.19
20 13 0.41
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (19 bp):
TTGTCCCGAAGACCACTGA
Found at i:38237 original size:59 final size:58
Alignment explanation
Indices: 38055--38289 Score: 240
Period size: 60 Copynumber: 3.9 Consensus size: 58
38045 GCATATATCG
* * * * * *
38055 ATAGTTTGAGGATAAAATTTGAACGTTCAAAAGTTTGTAGACATATTTAGAATGAGGGTC
1 ATAGTTTGGGGATGAAATTGGAATGTT-AAAAGTTTGAAGACA-ATTTAGAATGAGGATC
* *
38115 ATAGTTTGGGGATGAAATTGAAATATTTAAAAGTTTGAAGACCAATTTAGAATGA-GAGTC
1 ATAGTTTGGGGATGAAATTGGAAT-GTTAAAAGTTTGAAGA-CAATTTAGAATGAGGA-TC
* * * *
38175 ATAGTTTGGGGATGAAATTGGAATGTTCAAAGTTTGGAGACTAATTTCGAATAAGGATC
1 ATAGTTTGGGGATGAAATTGGAATGTTAAAAGTTTGAAGAC-AATTTAGAATGAGGATC
** *
38234 ATAGTTTGGGGATGAAATCAGAATGTTTAAAAGTTT-ACATATCAATTTAGAATGAG
1 ATAGTTTGGGGATGAAATTGGAATG-TTAAAAGTTTGA-AGA-CAATTTAGAATGAG
38290 TATTATAACT
Statistics
Matches: 146, Mismatches: 21, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
58 1 0.01
59 49 0.34
60 91 0.62
61 5 0.03
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (58 bp):
ATAGTTTGGGGATGAAATTGGAATGTTAAAAGTTTGAAGACAATTTAGAATGAGGATC
Found at i:38267 original size:119 final size:120
Alignment explanation
Indices: 38055--38289 Score: 307
Period size: 119 Copynumber: 2.0 Consensus size: 120
38045 GCATATATCG
* * * *
38055 ATAGTTTGAGGATAAAATTTGAACGTTCAAAAGTTTGTAGACATATTTAGAATGAGGGTCATAGT
1 ATAGTTTGAGGATAAAATTGGAACGTTCAAAAGTTTGGAGACATATTTAGAATAAGGATCATAGT
*
38120 TTGGGGATGAAATTGAAATATTTAAAAGTTTGA-AGACCAATTTAGAATGAGAGTC
66 TTGGGGATGAAATAGAAATATTTAAAAGTTT-ACAGACCAATTTAGAATGAGAGTC
* * * *
38175 ATAGTTTGGGGATGAAATTGGAATGTTC-AAAGTTTGGAGAC-TAATTTCGAATAAGGATCATAG
1 ATAGTTTGAGGATAAAATTGGAACGTTCAAAAGTTTGGAGACAT-ATTTAGAATAAGGATCATAG
* * *
38238 TTTGGGGATGAAATCAG-AATGTTTAAAAGTTTACATATCAATTTAGAATGAG
65 TTTGGGGATGAAAT-AGAAATATTTAAAAGTTTACAGACCAATTTAGAATGAG
38290 TATTATAACT
Statistics
Matches: 100, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
118 2 0.02
119 73 0.73
120 25 0.25
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (120 bp):
ATAGTTTGAGGATAAAATTGGAACGTTCAAAAGTTTGGAGACATATTTAGAATAAGGATCATAGT
TTGGGGATGAAATAGAAATATTTAAAAGTTTACAGACCAATTTAGAATGAGAGTC
Found at i:40440 original size:41 final size:42
Alignment explanation
Indices: 40394--40596 Score: 296
Period size: 41 Copynumber: 5.0 Consensus size: 42
40384 ATTCGCGTTG
40394 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCT
* *
40436 -ATTTCGAGTTGCGATAGTTGAAAATTGCGTTGCGATTTT-T
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCT
40476 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGA--TT-T
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCT
*
40515 CATTTCGAGTTGCGATAGTTGAAAATCGCGTTGCGATTTT-T
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCT
*
40556 CATTTCGCGTTGCGATAGTCT-ACAAT-GTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
40597 CAAATTCGTT
Statistics
Matches: 148, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
39 38 0.26
40 2 0.01
41 107 0.72
42 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (42 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCT
Found at i:40555 original size:80 final size:82
Alignment explanation
Indices: 40394--40596 Score: 342
Period size: 80 Copynumber: 2.5 Consensus size: 82
40384 ATTCGCGTTG
40394 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCTATTTCGAGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCTATTTCGAGTTGCGATAGTTGAAA
*
40459 ATTGCGTTGCGATTTTT
66 ATCGCGTTGCGATTTTT
40476 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGA-TTTC-ATTTCGAGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCTATTTCGAGTTGCGATAGTTGAAA
40539 ATCGCGTTGCGATTTTT
66 ATCGCGTTGCGATTTTT
*
40556 CATTTCGCGTTGCGATAGTCT-ACAAT-GTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
40597 CAAATTCGTT
Statistics
Matches: 116, Mismatches: 2, Indels: 7
0.93 0.02 0.06
Matches are distributed among these distances:
79 1 0.01
80 70 0.60
81 9 0.08
82 36 0.31
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (82 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCTATTTCGAGTTGCGATAGTTGAAA
ATCGCGTTGCGATTTTT
Found at i:40633 original size:121 final size:120
Alignment explanation
Indices: 40394--40614 Score: 324
Period size: 121 Copynumber: 1.8 Consensus size: 120
40384 ATTCGCGTTG
*
40394 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCTATTTCGAGTTGCGATAGTTGAAA
1 CATTTCGAGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCTATTTCGAGTTGCGATAGTTGAAA
* *
40459 ATTGCGTTGCGATTTTTCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTT
66 ATTGCGTTGCGATTTTCCAATTC-CGTTGCGATAGTTGAAAATCGCGTTGCGATTT
*
40515 CATTTCGAGTTGCGATAGTTGAAAATCGCGTTGCGATTTT-TCATTTCGCGTTGCGATAGTCT-A
1 CATTTCGAGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCT-ATTTCGAGTTGCGATAGT-TGA
*
40578 CAA-TGTCGTTGCGATTTTCCAAATT-CGTTGCGATAGT
64 AAATTG-CGTTGCGATTTTCC-AATTCCGTTGCGATAGT
40615 CTACAGTTGT
Statistics
Matches: 91, Mismatches: 5, Indels: 9
0.87 0.05 0.09
Matches are distributed among these distances:
120 15 0.16
121 72 0.79
122 4 0.04
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (120 bp):
CATTTCGAGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCTATTTCGAGTTGCGATAGTTGAAA
ATTGCGTTGCGATTTTCCAATTCCGTTGCGATAGTTGAAAATCGCGTTGCGATTT
Found at i:40787 original size:20 final size:20
Alignment explanation
Indices: 40762--40813 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
40752 ACTGTAGACT
*
40762 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
40782 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
40802 ATCGCAACGCGA
1 ATCGCAACGCGA
40814 TTTTCAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.25, G:0.25, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:40828 original size:21 final size:21
Alignment explanation
Indices: 40802--40855 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
40792 GAAATGGAAA
40802 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
40823 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
40844 ATCGCAACGCGA
1 ATCGCAACGCGA
40856 AATGCAACGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:41440 original size:2 final size:2
Alignment explanation
Indices: 41433--41507 Score: 136
Period size: 2 Copynumber: 38.5 Consensus size: 2
41423 TTTTTAAAAC
41433 TA TA TA 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
41475 TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41508 GAATATCGGG
Statistics
Matches: 71, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 69 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51518 original size:3 final size:3
Alignment explanation
Indices: 51505--51565 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
51495 GTAATATTTA
* * *
51505 AAT AAT AAAT AAT ATT ACT ATT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
51551 TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
51566 TTAAAATGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:51847 original size:76 final size:76
Alignment explanation
Indices: 51721--52481 Score: 1364
Period size: 76 Copynumber: 10.0 Consensus size: 76
51711 GGTCTTATGA
* * *
51721 ATGACCCTAAGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGT
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
51786 AGGGCTTACAG
66 AGGGCTTACAG
*
51797 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
51862 AGGGCTTACAG
66 AGGGCTTACAG
* * *
51873 ATGACCCAAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
51938 A-GGCTTACAG
66 AGGGCTTACAG
51948 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
52012 AGGACTTACAG
66 AGGGCTTACAG
52023 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
52088 AGGACTTACAG
66 AGGGCTTACAG
* *
52099 ATGACCTGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
52164 AGGGCTTACAG
66 AGGGCTTACAG
* *
52175 ATGACCCGAAGGCTTTGACAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
52240 AGGGCTTACAG
66 AGGGCTTACAG
*
52251 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
52316 AGGGCTTACAG
66 AGGGCTTACAG
52327 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
52392 AGGGCTTACAG
66 AGGGCTTACAG
*
52403 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATTATGCACTGA
1 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
52468 AGGACTTACAG
66 AGGGCTTACAG
52479 ATG
1 ATG
52482 TGAGAAATAG
Statistics
Matches: 663, Mismatches: 20, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
74 23 0.03
75 98 0.15
76 542 0.82
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (76 bp):
ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGGCTTACAG
Found at i:53192 original size:21 final size:22
Alignment explanation
Indices: 53157--53210 Score: 101
Period size: 21 Copynumber: 2.5 Consensus size: 22
53147 CATAAAGCTT
53157 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
53179 TCATCTTT-AAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
53200 TCATCTTTGAA
1 TCATCTTTGAA
53211 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:56052 original size:83 final size:83
Alignment explanation
Indices: 55913--56258 Score: 611
Period size: 83 Copynumber: 4.2 Consensus size: 83
55903 CTTATTTCTC
* ** *
55913 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAAATCAGATAACTCAAA
55978 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
55996 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAAATCAGATAACTCAAA
56061 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
56079 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAAATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAAATCAGATAACTCAAA
*
56144 GAACACTTCCAAAAGATG
66 GAACACTTCCAGAAGATG
*
56162 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAAATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAAATCAGATAACTCAAA
56227 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
56245 CTATGGAGCACATT
1 CTAT-GAGCACATT
56259 ACATTTGTTC
Statistics
Matches: 255, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
83 246 0.96
84 9 0.04
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAAATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:58541 original size:21 final size:18
Alignment explanation
Indices: 58515--58564 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
58505 TTGATTTAAA
*
58515 TTTTTTTTCTATTTCTTTCC
1 TTTTTTTT-TCTTT-TTTCC
58535 TTTTTTTTTCTTTTTTCC
1 TTTTTTTTTCTTTTTTCC
*
58553 -TCTTTTTTCTTT
1 TTTTTTTTTCTTT
58565 GCTGGATGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 11 0.39
18 5 0.18
19 4 0.14
20 8 0.29
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTTTTCTTTTTTCC
Found at i:63227 original size:18 final size:17
Alignment explanation
Indices: 63203--63270 Score: 68
Period size: 17 Copynumber: 4.0 Consensus size: 17
63193 ATAAAATGAA
63203 ATATAAATAATATATAT
1 ATATAAATAATATATAT
*
63220 ACTATAAAAAATATATAT
1 A-TATAAATAATATATAT
* *
63238 ATATATATAA-AAATAT
1 ATATAAATAATATATAT
*
63254 AAATAAATTAA-ATATAT
1 ATATAAA-TAATATATAT
63271 GAATTTTTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
16 10 0.24
17 16 0.38
18 16 0.38
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATAAATAATATATAT
Found at i:63237 original size:20 final size:20
Alignment explanation
Indices: 63203--63254 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
63193 ATAAAATGAA
*
63203 ATATAAATAATATATATA-CT
1 ATATAAA-AATATATATATAT
63223 ATA-AAAAATATATATATAT
1 ATATAAAAATATATATATAT
63242 ATATAAAAATATA
1 ATATAAAAATATA
63255 AATAAATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 10 0.34
19 7 0.24
20 12 0.41
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATAAAAATATATATATAT
Found at i:63267 original size:9 final size:10
Alignment explanation
Indices: 63192--63267 Score: 56
Period size: 9 Copynumber: 8.0 Consensus size: 10
63182 AAATACTTGC
63192 AATA-AAATGA
1 AATATAAAT-A
63202 AATATAAAT-
1 AATATAAATA
*
63211 AATATATAT-
1 AATATAAATA
*
63220 ACTATAAA-A
1 AATATAAATA
*
63229 AATATATATA
1 AATATAAATA
*
63239 TATATATAA-A
1 AATATA-AATA
63249 AATATAAATA
1 AATATAAATA
63259 AAT-TAAATA
1 AATATAAATA
63268 TATGAATTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
9 28 0.53
10 20 0.38
11 5 0.09
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (10 bp):
AATATAAATA
Found at i:65494 original size:3 final size:3
Alignment explanation
Indices: 65481--65550 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
65471 GTAATATTTA
* * * *
65481 AAT AAT AAAT AAT ATT ACT ATT ATT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
65527 AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
65551 TTAAAATGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:66189 original size:15 final size:15
Alignment explanation
Indices: 66165--66197 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
66155 TTTTATAAAC
66165 TTTATTTTAATC-CT
1 TTTATTTTAATCGCT
66179 TTTACTTTTAATCGCT
1 TTTA-TTTTAATCGCT
66195 TTT
1 TTT
66198 CAGTTTGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 8 0.47
16 5 0.29
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.64
Consensus pattern (15 bp):
TTTATTTTAATCGCT
Found at i:68411 original size:19 final size:20
Alignment explanation
Indices: 68387--68436 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
68377 GATAAATTTG
*
68387 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
68406 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
68427 TT-ATAATTTT
1 TTAATAATTTT
68437 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:68413 original size:31 final size:31
Alignment explanation
Indices: 68354--68440 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
68344 TTCGATAATA
* * *
68354 TAATAATTATTTTATAGT-ATTTAGATAAATT
1 TAATAAGTATTTTATAATCTTTTA-ATAAATT
**
68385 TGTTAA-TAATTTTATAATCTTTTAATAAATT
1 TAATAAGT-ATTTTATAATCTTTTAATAAATT
*
68416 TAATAAGTATTTTATAATTTTTTAA
1 TAATAAGTATTTTATAATCTTTTAA
68441 ACTTTATTGA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.87
32 5 0.11
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (31 bp):
TAATAAGTATTTTATAATCTTTTAATAAATT
Found at i:69201 original size:31 final size:29
Alignment explanation
Indices: 69165--69251 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 29
69155 TCAATAAAGT
69165 TTAAAAATTTATAAAATACTTATTAAATTTA
1 TTAAAAA-TTATAAAATA-TTATTAAATTTA
*
69196 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAA-ATTATAAAA-TATTATTAAATTTA
* *
69227 TCTAAATACTATAAAATAATTATTA
1 T-TAAAAATTATAAAAT-ATTATTA
69252 TATTATCGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
30 1 0.02
31 40 0.83
32 7 0.15
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (29 bp):
TTAAAAATTATAAAATATTATTAAATTTA
Found at i:69207 original size:20 final size:20
Alignment explanation
Indices: 69169--69218 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
69159 TAAAGTTTAA
*
69169 AAATTTA-TAAAATACTTATT
1 AAATTTATTAAAAGACTTA-T
69189 AAATTTATTAAAAGA-TTAT
1 AAATTTATTAAAAGACTTAT
*
69208 AAAATTATTAA
1 AAATTTATTAA
69219 TAAATTTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
20 10 0.37
21 6 0.22
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
AAATTTATTAAAAGACTTAT
Found at i:69612 original size:21 final size:21
Alignment explanation
Indices: 69586--69628 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
69576 AAAATAAATT
**
69586 ACTGGAATTTGAATGACTGGA
1 ACTGGAAAATGAATGACTGGA
*
69607 ACTGGAAAATGAATTACTGGA
1 ACTGGAAAATGAATGACTGGA
69628 A
1 A
69629 TTTGAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.26
Consensus pattern (21 bp):
ACTGGAAAATGAATGACTGGA
Found at i:69648 original size:14 final size:15
Alignment explanation
Indices: 69607--69652 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
69597 AATGACTGGA
69607 ACTGGAAAATGAATT
1 ACTGGAAAATGAATT
**
69622 ACTGGAATTTGAATT
1 ACTGGAAAATGAATT
69637 A-TGGAAAATGAATT
1 ACTGGAAAATGAATT
69651 AC
1 AC
69653 ATTTTTCTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (15 bp):
ACTGGAAAATGAATT
Found at i:69998 original size:23 final size:23
Alignment explanation
Indices: 69949--70011 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
69939 GTGTTATATT
* **
69949 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
*
69972 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTAATTAAA
69995 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
70012 AAATAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 22 0.65
24 1 0.03
25 11 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:70005 original size:12 final size:12
Alignment explanation
Indices: 69971--70011 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
69961 TATTAATTAG
69971 TATA-TTTTAAA
1 TATATTTTTAAA
69982 TATATTTATTAAA
1 TATATTT-TTAAA
69995 -ATATTATTTAAA
1 TATATT-TTTAAA
70007 TATAT
1 TATAT
70012 AAATAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.15
12 12 0.46
13 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATATTTTTAAA
Found at i:70069 original size:28 final size:28
Alignment explanation
Indices: 69985--70072 Score: 70
Period size: 30 Copynumber: 3.0 Consensus size: 28
69975 TTTTAAATAT
* * * *
69985 ATTTATTAAAATATTATTTAAATATATAA
1 ATTTATT-ATATATTATTAAAATAAAAAA
*
70014 ATAATATTAT-TCATTATTTAATATATAAAAAA
1 AT-TTATTATAT-ATTA-TTAA-A-ATAAAAAA
70046 ATTTATTATATATTATTAAAATAAAAA
1 ATTTATTATATATTATTAAAATAAAAA
70073 TATAATATCT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
28 8 0.17
29 8 0.17
30 11 0.23
31 11 0.23
32 9 0.19
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTTATTATATATTATTAAAATAAAAAA
Found at i:73060 original size:18 final size:18
Alignment explanation
Indices: 73024--73061 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
73014 AATCATCAAA
*
73024 ATCAGAATCACTATAATC
1 ATCAGAATCACCATAATC
*
73042 ATCAGAATCACCATCATC
1 ATCAGAATCACCATAATC
73060 AT
1 AT
73062 ATTTCTTGTT
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:0.42, C:0.26, G:0.05, T:0.26
Consensus pattern (18 bp):
ATCAGAATCACCATAATC
Found at i:73932 original size:29 final size:31
Alignment explanation
Indices: 73897--73957 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
73887 TTATTTCTTC
*
73897 ACTAAAT-ATTT-TTATAACTTT-TTATTGTG
1 ACTAAATAATTTGTTACAA-TTTGTTATTGTG
73926 ACTAAATAATTTGTTACAATTTGTTATTGTG
1 ACTAAATAATTTGTTACAATTTGTTATTGTG
73957 A
1 A
73958 AAGAATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.25
30 7 0.25
31 14 0.50
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.51
Consensus pattern (31 bp):
ACTAAATAATTTGTTACAATTTGTTATTGTG
Found at i:94348 original size:34 final size:34
Alignment explanation
Indices: 94264--94348 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
94254 AACAAAAAGG
*
94264 GGGAGAAGTGTTAAAGCGTTTTTAAATGATAAAT
1 GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
94298 GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
1 GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
94332 GGGAGAAGTGTTAAAGT
1 GGGAGAAGTGTTAAAGT
94349 AAGGGGGAGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.38, C:0.01, G:0.29, T:0.32
Consensus pattern (34 bp):
GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
Found at i:96750 original size:2 final size:2
Alignment explanation
Indices: 96743--96788 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
96733 TTCTCCTTTA
96743 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
96785 AT AT
1 AT AT
96789 TATCATTATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:105822 original size:18 final size:18
Alignment explanation
Indices: 105799--105869 Score: 115
Period size: 18 Copynumber: 3.9 Consensus size: 18
105789 AGGGATTATC
105799 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
105817 AGTGGTTCATCGGGACAT
1 AGTGGTCCTTCGGGACAT
105835 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
105853 AGTGGTCCTACGGGACA
1 AGTGGTCCTTCGGGACA
105870 AATTTCTACG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.20, C:0.21, G:0.34, T:0.25
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:108882 original size:23 final size:24
Alignment explanation
Indices: 108847--108912 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 24
108837 CCACTAGGGG
*
108847 CTATGAATTTGTCCCGAAAGACCA
1 CTATGAATATGTCCCGAAAGACCA
* *
108871 CTATGAA-ATGTCTCGAAGGACCA
1 CTATGAATATGTCCCGAAAGACCA
*
108894 --ATG--TATGTCCCGAATGACC
1 CTATGAATATGTCCCGAAAGACC
108913 TATGAACCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
20 13 0.36
21 3 0.08
23 13 0.36
24 7 0.19
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (24 bp):
CTATGAATATGTCCCGAAAGACCA
Found at i:122804 original size:41 final size:41
Alignment explanation
Indices: 122679--123036 Score: 194
Period size: 41 Copynumber: 8.6 Consensus size: 41
122669 AACTTGTGGT
** * *
122679 GTTTGTATAAAAACGCCACTAAAACACGAGTCTTTAGAGGC
1 GTTTGTATAAAAACGCCACTAAAGTATGAGTCTTTAGCGGC
* * * ** * *
122720 GTTTTTTTTTTTAAAAAAAGCCACTAAAACAAGAGTCTATAGCGGC
1 G----TTTGTAT-AAAAACGCCACTAAAGTATGAGTCTTTAGCGGC
* * *
122766 GTTTATATACAAACGCCGCTAAAGTATGAGTCTTTAGCGGC
1 GTTTGTATAAAAACGCCACTAAAGTATGAGTCTTTAGCGGC
* ** * *
122807 GTTTGTATAAAAACGACACTAAAACA-CATGTCTTTAGCGAC
1 GTTTGTATAAAAACGCCACTAAAGTATGA-GTCTTTAGCGGC
* * * * *
122848 GTTTTTAT-AAAACACCACTACAA-AATGAGTCTTTAACGAC
1 GTTTGTATAAAAACGCCACTA-AAGTATGAGTCTTTAGCGGC
* *
122888 GTTTGTATAAAAACGCCACTAATGTACGAGT-TTATAGCGGC
1 GTTTGTATAAAAACGCCACTAAAGTATGAGTCTT-TAGCGGC
* * * * *
122929 GTTTGT-TGAAACAATGCCACT-ATGTGTGCA-CCTATT-GCGTC
1 GTTTGTAT-AAA-AACGCCACTAAAGTATG-AGTCT-TTAGCGGC
* * * *
122970 GTTTGTATAAAAACGCCGCTAAAGTACT-ATTCTATCGCGGC
1 GTTTGTATAAAAACGCCACTAAAGTA-TGAGTCTTTAGCGGC
* *
123011 ATTTTGTATAAAAACGCCGCTAAAGT
1 -GTTTGTATAAAAACGCCACTAAAGT
123037 TACCATTTTG
Statistics
Matches: 246, Mismatches: 49, Indels: 43
0.73 0.14 0.13
Matches are distributed among these distances:
40 43 0.17
41 125 0.51
42 42 0.17
43 1 0.00
45 5 0.02
46 30 0.12
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (41 bp):
GTTTGTATAAAAACGCCACTAAAGTATGAGTCTTTAGCGGC
Found at i:122932 original size:122 final size:125
Alignment explanation
Indices: 122679--122934 Score: 290
Period size: 122 Copynumber: 2.0 Consensus size: 125
122669 AACTTGTGGT
* * *
122679 GTTTGTATAAAAACGCCACTAAAACACGAGTCTTTAGAGGCGTTTTTTTTTTTAAAAAAAGCCAC
1 GTTTGTATAAAAACGACACTAAAACACGAGTCTTTAGAGACG---TTTTTTATAAAAAAAGCCAC
* * * * *
122744 TAAAACAAGAGTCTATAGCGGCGTTTATATACAAACGCCGCTAAAGTATGAGTCTTTAGCGGC
63 TAAAACAAGAGTCTATAACGACGTTTATATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGC
* *
122807 GTTTGTATAAAAACGACACTAAAACAC-ATGTCTTTAGCGACG-TTTTTAT-AAAACA-CCACTA
1 GTTTGTATAAAAACGACACTAAAACACGA-GTCTTTAGAGACGTTTTTTATAAAAAAAGCCACTA
* * * *
122868 CAAA-ATGAGTCTTTAACGACGTTTGTATAAAAACGCCACTAATGTACGAGT-TTATAGCGGC
65 -AAACAAGAGTCTATAACGACGTTTATATAAAAACGCCACTAAAGTACGAGTCTT-TAGCGGC
122929 GTTTGT
1 GTTTGT
122935 TGAAACAATG
Statistics
Matches: 111, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
121 2 0.02
122 57 0.51
123 8 0.07
124 6 0.05
127 1 0.01
128 37 0.33
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (125 bp):
GTTTGTATAAAAACGACACTAAAACACGAGTCTTTAGAGACGTTTTTTATAAAAAAAGCCACTAA
AACAAGAGTCTATAACGACGTTTATATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGC
Found at i:123583 original size:21 final size:21
Alignment explanation
Indices: 123557--123596 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
123547 CGAATTCGGT
123557 GCCCCCCAATTTTGACTTCTA
1 GCCCCCCAATTTTGACTTCTA
*
123578 GCCCCCCAATTTTGTCTTC
1 GCCCCCCAATTTTGACTTC
123597 CAACAATCTC
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:0.15, C:0.40, G:0.10, T:0.35
Consensus pattern (21 bp):
GCCCCCCAATTTTGACTTCTA
Found at i:126575 original size:16 final size:16
Alignment explanation
Indices: 126554--126593 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
126544 ACCAAATTTT
*
126554 ACTATTCACGAAATTC
1 ACTATTCACAAAATTC
*
126570 ACTATTCACAAAATTT
1 ACTATTCACAAAATTC
126586 ACTATTCA
1 ACTATTCA
126594 TGTAAATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.03, T:0.35
Consensus pattern (16 bp):
ACTATTCACAAAATTC
Found at i:127079 original size:21 final size:21
Alignment explanation
Indices: 127049--127112 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
127039 GAATTCGATG
* *
127049 CCCCCTAATTTTGACTTCCAA
1 CCCCCCAATTTTGTCTTCCAA
127070 CCCCCCAATTTTGTCTTCCAA
1 CCCCCCAATTTTGTCTTCCAA
127091 CCCCCCAATTTTGTCTTCCAA
1 CCCCCCAATTTTGTCTTCCAA
127112 C
1 C
127113 AATAAAAGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.20, C:0.42, G:0.05, T:0.33
Consensus pattern (21 bp):
CCCCCCAATTTTGTCTTCCAA
Found at i:128789 original size:18 final size:19
Alignment explanation
Indices: 128768--128805 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
128758 TATTAAATAA
*
128768 TAATAAATGATTA-ATTAT
1 TAATAAATCATTATATTAT
128786 TAATAAATCATTATATTAT
1 TAATAAATCATTATATTAT
128805 T
1 T
128806 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
TAATAAATCATTATATTAT
Found at i:139734 original size:28 final size:29
Alignment explanation
Indices: 139693--139761 Score: 131
Period size: 28 Copynumber: 2.4 Consensus size: 29
139683 GCAATGCTCT
139693 ATAGTCGGAGGATCATTTTGTAACTTTTA
1 ATAGTCGGAGGATCATTTTGTAACTTTTA
139722 ATAGTC-GAGGATCATTTTGTAACTTTTA
1 ATAGTCGGAGGATCATTTTGTAACTTTTA
139750 ATAGTCGGAGGA
1 ATAGTCGGAGGA
139762 CTCAGTAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 28 0.72
29 11 0.28
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (29 bp):
ATAGTCGGAGGATCATTTTGTAACTTTTA
Found at i:144287 original size:14 final size:15
Alignment explanation
Indices: 144262--144290 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
144252 TGCGAAAGCT
144262 TGGAATGACGAATGA
1 TGGAATGACGAATGA
144277 TGGAA-GACGAATGA
1 TGGAATGACGAATGA
144291 ATATTATTCG
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:0.41, C:0.07, G:0.34, T:0.17
Consensus pattern (15 bp):
TGGAATGACGAATGA
Found at i:146589 original size:19 final size:19
Alignment explanation
Indices: 146565--146617 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
146555 TCGAATGCAT
146565 TAGTGCATCGATGCATAAG
1 TAGTGCATCGATGCATAAG
146584 TAGTGCATCGATGCATAAG
1 TAGTGCATCGATGCATAAG
*
146603 TAGTGCATTGATGCA
1 TAGTGCATCGATGCA
146618 CCCCCTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (19 bp):
TAGTGCATCGATGCATAAG
Found at i:147477 original size:21 final size:21
Alignment explanation
Indices: 147451--147504 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
147441 TTATATGTGT
147451 TCCTTCGGGACATCTAAGTGG
1 TCCTTCGGGACATCTAAGTGG
* *
147472 TCCTTCAGTACATCTAAGTGG
1 TCCTTCGGGACATCTAAGTGG
147493 TCCTTCGGGACA
1 TCCTTCGGGACA
147505 AATTCTATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (21 bp):
TCCTTCGGGACATCTAAGTGG
Found at i:149839 original size:2 final size:2
Alignment explanation
Indices: 149832--149869 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
149822 AGTAAGACAG
149832 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
149870 TGAGTATTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:150722 original size:19 final size:19
Alignment explanation
Indices: 150698--150788 Score: 155
Period size: 19 Copynumber: 4.8 Consensus size: 19
150688 CGAATGCCAT
150698 TAGTGCATCGATGCATAAA
1 TAGTGCATCGATGCATAAA
150717 TAGTGCATCGATGCATAAA
1 TAGTGCATCGATGCATAAA
*
150736 TAGTGCATCAATGCATAAA
1 TAGTGCATCGATGCATAAA
* *
150755 TAGTGCATCTATGCATAAG
1 TAGTGCATCGATGCATAAA
150774 TAGTGCATCGATGCA
1 TAGTGCATCGATGCA
150789 CCCCCTTAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 68 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.27
Consensus pattern (19 bp):
TAGTGCATCGATGCATAAA
Found at i:151738 original size:15 final size:15
Alignment explanation
Indices: 151720--151755 Score: 58
Period size: 13 Copynumber: 2.5 Consensus size: 15
151710 ATTATATGAA
151720 ATGTGATAAAGAACT
1 ATGTGATAAAGAACT
151735 ATGTG--AAAGAACT
1 ATGTGATAAAGAACT
151748 ATGTGATA
1 ATGTGATA
151756 TCAATATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.68
15 6 0.32
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (15 bp):
ATGTGATAAAGAACT
Found at i:158227 original size:23 final size:23
Alignment explanation
Indices: 158191--158250 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
158181 AGTGTTCGCA
* *
158191 AACATGCTCGTTTAACATTCGTG
1 AACATGTTCATTTAACATTCGTG
* * *
158214 AACATGTTCATTTAGCATTTGTT
1 AACATGTTCATTTAACATTCGTG
* *
158237 TATATGTTCATTTA
1 AACATGTTCATTTA
158251 GTTTCCATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (23 bp):
AACATGTTCATTTAACATTCGTG
Found at i:160588 original size:59 final size:59
Alignment explanation
Indices: 160518--160649 Score: 180
Period size: 59 Copynumber: 2.2 Consensus size: 59
160508 ATAGTCAGAT
*
160518 GATCATTTTGTAACTTTTAATAGTC-GAGGCACTCAACAAAGTA-ATTCCCTATAG-TCGGG
1 GATCATTTTGTAACTTTTAATAGTCGGAGG-ACTCAACAAAGTATA-T-CCTATAGTTAGGG
*
160577 GATCATTTTGTAACTTTTAATATTCGGAGGACTCAACAAAGTATATCCTATAGTTAGGG
1 GATCATTTTGTAACTTTTAATAGTCGGAGGACTCAACAAAGTATATCCTATAGTTAGGG
*
160636 GACCATTTGTGTAA
1 GATCATTT-TGTAA
160650 TTTACCCTAT
Statistics
Matches: 66, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
58 7 0.11
59 49 0.74
60 10 0.15
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (59 bp):
GATCATTTTGTAACTTTTAATAGTCGGAGGACTCAACAAAGTATATCCTATAGTTAGGG
Found at i:163892 original size:13 final size:13
Alignment explanation
Indices: 163874--163901 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
163864 GCCTAGTTAC
163874 ATTTTAGGCCAAA
1 ATTTTAGGCCAAA
163887 ATTTTAGGCCAAA
1 ATTTTAGGCCAAA
163900 AT
1 AT
163902 GAAAGAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
ATTTTAGGCCAAA
Found at i:164128 original size:3 final size:3
Alignment explanation
Indices: 164122--164224 Score: 127
Period size: 3 Copynumber: 33.7 Consensus size: 3
164112 TTCATTTAAA
*
164122 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
164167 TAT AAT TAT TAT TAT TAA TAT TAT TATT TAT TAT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
*
164213 TAAA TAT TAT TA
1 T-AT TAT TAT TA
164225 CAAGCCCAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
2 1 0.01
3 79 0.92
4 6 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:164627 original size:14 final size:14
Alignment explanation
Indices: 164605--164639 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
164595 CCCAACCTGC
*
164605 AAAGAAGAAAAAAA
1 AAAGGAGAAAAAAA
164619 AAAGGAGAAAAAAA
1 AAAGGAGAAAAAAA
164633 AGAAGGA
1 A-AAGGA
164640 CCACAACAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAAGGAGAAAAAAA
Found at i:165645 original size:24 final size:23
Alignment explanation
Indices: 165617--165665 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
165607 TAAATATATA
*
165617 TAATAAATAATAATTCATATTTTT
1 TAATAAATAAT-ATTAATATTTTT
* *
165641 TAATAAATTATTTTAATATTTTT
1 TAATAAATAATATTAATATTTTT
165664 TA
1 TA
165666 TCGAAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TAATAAATAATATTAATATTTTT
Found at i:177026 original size:1 final size:1
Alignment explanation
Indices: 177020--177085 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
177010 ATTATATTTG
* * * * * * * * *
177020 AAAAAAAACAAAAAGAAAAAAGAAAGAAAGAAAAAAGAAAGAAAAAAGAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
177085 A
1 A
177086 GGGAGAAATT
Statistics
Matches: 47, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:177039 original size:7 final size:7
Alignment explanation
Indices: 177019--177083 Score: 71
Period size: 7 Copynumber: 9.0 Consensus size: 7
177009 TATTATATTT
177019 GAAAAAA
1 GAAAAAA
*
177026 AACAAAAA
1 GA-AAAAA
177034 GAAAAAA
1 GAAAAAA
177041 GAAAGAAA
1 GAAA-AAA
177049 GAAAAAA
1 GAAAAAA
177056 GAAAGAAA
1 GAAA-AAA
177064 -AAAGAAA
1 GAAA-AAA
177071 -AAAAAA
1 GAAAAAA
177077 GAAAAAA
1 GAAAAAA
177084 AAGGGAGAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
6 3 0.06
7 33 0.63
8 16 0.31
ACGTcount: A:0.85, C:0.02, G:0.14, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:177039 original size:15 final size:14
Alignment explanation
Indices: 177019--177085 Score: 73
Period size: 15 Copynumber: 4.6 Consensus size: 14
177009 TATTATATTT
177019 GAAAAAAAACAAAAA
1 GAAAAAAAA-AAAAA
*
177034 GAAAAAAGAAAGAAA
1 GAAAAAA-AAAAAAA
*
177049 GAAAAAAGAAAGAAA
1 GAAAAAA-AAAAAAA
*
177064 -AAAGAAAAAAAAA
1 GAAAAAAAAAAAAA
177077 GAAAAAAAA
1 GAAAAAAAA
177086 GGGAGAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
13 6 0.13
14 12 0.26
15 26 0.57
16 2 0.04
ACGTcount: A:0.85, C:0.01, G:0.13, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAAAAAA
Found at i:177045 original size:4 final size:4
Alignment explanation
Indices: 177031--177080 Score: 65
Period size: 4 Copynumber: 13.8 Consensus size: 4
177021 AAAAAAACAA
177031 AAAG AAA- AAAG AAAG AAAG AAA- AAAG AAAG AAA- AAAG AAA- AAA-
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
177074 AAAG AAA
1 AAAG AAA
177081 AAAAAGGGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 15 0.36
4 27 0.64
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:177045 original size:11 final size:10
Alignment explanation
Indices: 177020--177085 Score: 89
Period size: 11 Copynumber: 6.4 Consensus size: 10
177010 ATTATATTTG
*
177020 AAAAA-AAAC
1 AAAAAGAAAA
177029 AAAAAGAAAA
1 AAAAAGAAAA
177039 AAGAAAGAAAGA
1 AA-AAAGAAA-A
177051 AAAAAGAAAGA
1 AAAAAGAAA-A
177062 AAAAAGAAAA
1 AAAAAGAAAA
177072 AAAAAGAAAA
1 AAAAAGAAAA
177082 AAAA
1 AAAA
177086 GGGAGAAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
9 5 0.09
10 20 0.38
11 25 0.47
12 3 0.06
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:177053 original size:26 final size:26
Alignment explanation
Indices: 177019--177086 Score: 86
Period size: 26 Copynumber: 2.6 Consensus size: 26
177009 TATTATATTT
177019 GAAAAAAAACAA-AAAGAAAAAAGAAA
1 GAAAAAAAA-AAGAAAGAAAAAAGAAA
*
177045 GAAAGAAAAAAGAAAGAAAAAAGAAA
1 GAAAAAAAAAAGAAAGAAAAAAGAAA
*
177071 -AAAAAAGAAAAAAAAG
1 GAAAAAA-AAAAGAAAG
177087 GGAGAAATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 7 0.19
26 30 0.81
ACGTcount: A:0.84, C:0.01, G:0.15, T:0.00
Consensus pattern (26 bp):
GAAAAAAAAAAGAAAGAAAAAAGAAA
Found at i:179575 original size:114 final size:114
Alignment explanation
Indices: 179360--179579 Score: 336
Period size: 114 Copynumber: 1.9 Consensus size: 114
179350 CACATTCTCG
* * * *
179360 TAGTAGAAATAAGGAGCCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTC
* * *
179425 GGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTGTTCA
66 GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTGTTCA
179474 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTC
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTC
*
179539 GGTAGGAA-TCCAATAACCAATCATT-GAAATTAAAAGATGAA
66 GGTAGGAACCCCAA-AACCAATCATTAG-AATTAAAAGATGAA
179580 CTGCATGATC
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
113 5 0.05
114 91 0.95
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
TAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTC
GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTGTTCA
Found at i:181701 original size:54 final size:53
Alignment explanation
Indices: 181553--181758 Score: 233
Period size: 54 Copynumber: 3.9 Consensus size: 53
181543 AGAAATCTTG
* * * *
181553 GCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAACGCTTTACGAACGTCTAA
1 GCAGAAACCACAGAAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC-TCTGA
*
181607 GCAGAAACCACA-AGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAACCACAGA-AAAAGATGAATGTGTTGTCAAATGTTTTACGAAC-TCTGA
* * * *
181661 GCAGAAGCCACAGAAAAATATGAATGTGTTGTCAAGTGTTTTAC-ATCTC-GA
1 GCAGAAACCACAGAAAAAGATGAATGTGTTGTCAAATGTTTTACGAACTCTGA
* *
181712 -CAGATAA-CACAGGAAAAGATGAATGTATTGTCAAATGTTTTAACGAA
1 GCAGA-AACCACAGAAAAAGATGAATGTGTTGTCAAATGTTTT-ACGAA
181759 TATGTTATTC
Statistics
Matches: 132, Mismatches: 15, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
50 34 0.26
51 5 0.04
52 3 0.02
53 3 0.02
54 86 0.65
55 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (53 bp):
GCAGAAACCACAGAAAAAGATGAATGTGTTGTCAAATGTTTTACGAACTCTGA
Found at i:182132 original size:22 final size:22
Alignment explanation
Indices: 182106--182185 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
182096 TACATCTACA
182106 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
182128 CTCTTCAAAGATGATAAATTCT
1 CTCTTCAAAGATGATAGATTCT
* * *
182150 CTTTTTAAATATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
182172 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
182186 AAGCTTTATG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:182821 original size:113 final size:113
Alignment explanation
Indices: 182618--183538 Score: 1163
Period size: 113 Copynumber: 8.2 Consensus size: 113
182608 CAGCTTTTCC
* *
182618 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCATCACTTGATGGATCA
* *
182683 GCTTTTCCAGAGAAAGTTTATAATGAGAAGAACTCATCTGAAGAAGGA
66 GCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
** * *
182731 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCATCACTTGATGGATCA
* * *
182796 GCATTACCAG-GTCAAGTTCATAATGAGAAGAACTCATCTGAAGAATGA
66 GCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
182844 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT-GAATTCATCA-TTCAATGGAT
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG-TTCAAATCCATCACTT-GATGGAT
* ****
182907 CAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTG-A-AA-GA
64 CAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
182954 A-CA-AA-TTCATAATGAGAAGAATTTGTTCAACTTTTTGTTCAAAACCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCATCACTTGATGGATCA
**
183016 GTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
66 GCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
** * *
183064 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCATCACTTGATGGATCA
* * *
183129 ACATTGCCATGTAG--AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAA
66 GCATTTCCA-G-AGAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGA
* * * * *
183180 AGAAAAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCATCACTTGATGGATCA
*
183245 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
66 GCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * ** * *
183293 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCATCACTTGATGGATCA
* * *
183358 ACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGA
66 GCATTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGA
* * * *
183409 ATAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTCAAATCCATCACTTGATAGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCATCACTTGATGGATCA
*
183474 GCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT---GAA-GA
66 GCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
183518 AGAAGAAGTTCATAATGAGAA
1 AGAAGAAGTTCATAATGAGAA
183539 AATCTGAAGA
Statistics
Matches: 708, Mismatches: 76, Indels: 52
0.85 0.09 0.06
Matches are distributed among these distances:
106 2 0.00
107 79 0.11
108 5 0.01
109 25 0.04
110 9 0.01
111 3 0.00
112 7 0.01
113 371 0.52
114 7 0.01
115 5 0.01
116 194 0.27
117 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCATCACTTGATGGATCA
GCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
Found at i:183282 original size:229 final size:225
Alignment explanation
Indices: 182618--183538 Score: 1299
Period size: 229 Copynumber: 4.1 Consensus size: 225
182608 CAGCTTTTCC
* ** * *
182618 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTTGATGGATCA
* * * * * *
182683 GCTTTTCCAG-AGAAAGTTTATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
66 ACATTGCCAGTAG--AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCATAAT
* * ** * * * * *
182747 GAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCAGCATTACCAG-GTCAA
129 GAGAAGAATTTGTTCAACCTTTTGTTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAA
*
182811 GTTCATAATGAGAAGAACTCATCTGAAGAATGA
193 GTTCATAATGAGAAGAACTCATCTGAAGAAGGA
**
182844 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCAATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTTGATGGATCA
* * *
182909 ACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCT------GAAAGAACAAATTCATAATG
66 ACATTGCCAG-TAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCATAATG
* * *
182968 AGAAGAATTTGTTCAACTTTTTGTTCAAAACCATCACTTGATGGATCAGTTTTTCCAGAGAAAGT
130 AGAAGAATTTGTTCAACCTTTTGTTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGT
183033 TCATAATGAGAAGAACTCATCTGAAGAAGGA
195 TCATAATGAGAAGAACTCATCTGAAGAAGGA
*
183064 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTTGATGGATCA
*
183129 ACATTGCCATGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAAGAAAAAATTCATA
66 ACATTGCCA-GTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGAAAGAAGAAATTCATA
*
183194 ATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
127 ATGAGAAGAATTTGTTCAACCTTTTGTTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
183259 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
192 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
183293 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTTGATGGATCA
* * *
183358 ACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAATAAGAAGTTCATA
66 ACATTGCCA-GTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGAAAGAAGAAATTCATA
*
183423 ATGAGAAGAATTTGTTCAACCTTTTGTTCAAATCCATCACTTGATAGATCAGCTTTTCCAGAGAA
127 ATGAGAAGAATTTGTTCAACCTTTTGTTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
183488 AGTTCATAATGAGAAGAACTCATCT---GAA-GA
192 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
183518 AGAAGAAGTTCATAATGAGAA
1 AGAAGAAGTTCATAATGAGAA
183539 AATCTGAAGA
Statistics
Matches: 638, Mismatches: 44, Indels: 27
0.90 0.06 0.04
Matches are distributed among these distances:
220 190 0.30
221 2 0.00
222 1 0.00
223 6 0.01
225 23 0.04
226 93 0.15
228 1 0.00
229 322 0.50
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (225 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTTGATGGATCA
ACATTGCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCATAATGA
GAAGAATTTGTTCAACCTTTTGTTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTT
CATAATGAGAAGAACTCATCTGAAGAAGGA
Found at i:183534 original size:36 final size:33
Alignment explanation
Indices: 183487--183571 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 33
183477 TTTCCAGAGA
183487 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
1 AAGTTCATAATGAGAAGAA---ATCTGAAGAAGAAG
*
183523 AAGTTCATAATGAG-A-AAATCTGAAGAAGAAT
1 AAGTTCATAATGAGAAGAAATCTGAAGAAGAAG
* *
183554 AAGTTCACAATGAAAAGA
1 AAGTTCATAATGAGAAGA
183572 GCTTGTTCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
31 25 0.57
32 1 0.02
33 1 0.02
34 2 0.05
35 1 0.02
36 14 0.32
ACGTcount: A:0.51, C:0.09, G:0.20, T:0.20
Consensus pattern (33 bp):
AAGTTCATAATGAGAAGAAATCTGAAGAAGAAG
Found at i:183699 original size:124 final size:122
Alignment explanation
Indices: 183544--183800 Score: 288
Period size: 124 Copynumber: 2.1 Consensus size: 122
183534 GAGAAAATCT
* * * *
183544 GAAG-AAGAATAAGTTCACAATGAAAAGAGCTTGTTCAACCTTTTGTATAATTCTATCACAGAAG
1 GAAGAAAGAAGAAGTTCACAATGAAAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAG
* * * * *
183608 CAGATAGATTAGCATCAACCTTTCCAG-AGAAAGTTCATAATGAGAAGAACTTATCTGAA
66 CAAATAGATCAACATCAACC---CCAGCAGAAAATTCATAATGAGAAGAACTCATCTGAA
* * * *
183667 GAAGAAAGAAGAAGTTCATAAT-AAGAATAGCTTATTCAACCTTTTGAATGACTCTATCACATAA
1 GAAGAAAGAAGAAGTTCACAATGAA-AAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAA
* * * *
183731 GGAAATAGGTCAACATCATCCCCAGCGGAAAATTCATAATGAGAAGAACTCATCTGAA
65 GCAAATAGATCAACATCAACCCCAGCAGAAAATTCATAATGAGAAGAACTCATCTGAA
*
183789 GAA-AGAGAAGAA
1 GAAGAAAGAAGAA
183801 TTTATTCAAC
Statistics
Matches: 113, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
121 12 0.11
122 32 0.28
123 6 0.05
124 63 0.56
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.24
Consensus pattern (122 bp):
GAAGAAAGAAGAAGTTCACAATGAAAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAG
CAAATAGATCAACATCAACCCCAGCAGAAAATTCATAATGAGAAGAACTCATCTGAA
Found at i:183942 original size:3 final size:3
Alignment explanation
Indices: 183936--184035 Score: 94
Period size: 3 Copynumber: 32.7 Consensus size: 3
183926 TTCATTTAAA
* * *
183936 TAT TAT T-T ATAT TAT TAT TAT AAT TAT TAT AAT TAT TAT AAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
183981 AAT AAT TAT TAT TAA TAT TAT TATT TAT TAT TAA TAT TAT TAT TAAA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT
184028 TAT TAT TA
1 TAT TAT TA
184036 CAAGCCCAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
2 1 0.01
3 72 0.91
4 6 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:184031 original size:19 final size:19
Alignment explanation
Indices: 183990--184032 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
183980 TAATAATTAT
* *
183990 TATTAATATTATTATTTAT
1 TATTAATATTATTATTAAA
184009 TATTAATATTATTATTAAA
1 TATTAATATTATTATTAAA
184028 TATTA
1 TATTA
184033 TTACAAGCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTAATATTATTATTAAA
Found at i:184437 original size:13 final size:13
Alignment explanation
Indices: 184416--184448 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
184406 CCCAACCTGC
184416 AAAGAAGAAAAAA
1 AAAGAAGAAAAAA
*
184429 AAAGGAGAAAAAA
1 AAAGAAGAAAAAA
184442 AAAGAAG
1 AAAGAAG
184449 GACCACAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGAAGAAAAAA
Found at i:185449 original size:24 final size:23
Alignment explanation
Indices: 185421--185469 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
185411 TAAATATATA
*
185421 TAATAAATAATAATTCATATTTTT
1 TAATAAATAAT-ATTAATATTTTT
* *
185445 TAATAAATTATTTTAATATTTTT
1 TAATAAATAATATTAATATTTTT
185468 TA
1 TA
185470 TCGAAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TAATAAATAATATTAATATTTTT
Found at i:188294 original size:20 final size:20
Alignment explanation
Indices: 188269--188320 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
188259 TAGTTGAAAA
188269 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
188289 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
188309 TTGCGTTGCGAT
1 TCGCGTTGCGAT
188321 AGTCTACTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:188361 original size:22 final size:22
Alignment explanation
Indices: 188333--188375 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
188323 TCTACTTGTC
*
188333 GTCTACAGTTGTTGTTGCGATA
1 GTCTACAGTTGTCGTTGCGATA
188355 GTCTACAGTTGTCGTTGCGAT
1 GTCTACAGTTGTCGTTGCGAT
188376 TTTCCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (22 bp):
GTCTACAGTTGTCGTTGCGATA
Found at i:188496 original size:6 final size:6
Alignment explanation
Indices: 188485--188522 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
188475 GACACGTATT
*
188485 ACCACG ACCACG ACCACG ACCACG ACCATG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
188523 CGAGACGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.32, C:0.50, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:189159 original size:22 final size:22
Alignment explanation
Indices: 189132--189247 Score: 166
Period size: 22 Copynumber: 5.4 Consensus size: 22
189122 AATTTGGAAA
189132 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
189154 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
189176 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * * **
189198 ATCGCAATG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
189217 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
189239 ATCGCAACG
1 ATCGCAACG
189248 TGAAATGGAA
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 12 0.15
20 2 0.02
21 2 0.02
22 65 0.80
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:189264 original size:20 final size:20
Alignment explanation
Indices: 189239--189286 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
189229 ACTGTAGACT
* *
189239 ATCGCAACGTGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
189259 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
189279 ATCGCAAC
1 ATCGCAAC
189287 AGGATTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:192390 original size:32 final size:33
Alignment explanation
Indices: 192354--192434 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 33
192344 ATAGTAAAAA
* *
192354 TTAAATAGAA-ATAAGTCCATAAA-CTAATATTT
1 TTAAATAAAAGATAA-TACATAAAGCTAATATTT
*
192386 TTAAATAAAAGATAATACATAAAGTTAATATTT
1 TTAAATAAAAGATAATACATAAAGCTAATATTT
* *
192419 TAAAATTAAAATATAA
1 TTAAA-TAAAAGATAA
192435 AAATCAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 16 0.39
33 16 0.39
34 9 0.22
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (33 bp):
TTAAATAAAAGATAATACATAAAGCTAATATTT
Found at i:198650 original size:18 final size:19
Alignment explanation
Indices: 198627--198670 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
198617 TTTAAGTAGT
*
198627 AATAAAAACGATT-AAGTA
1 AATAAAAACAATTAAAGTA
*
198645 AATAAAAGCAATTAAAGTA
1 AATAAAAACAATTAAAGTA
198664 AA-AAAAA
1 AATAAAAA
198671 TAAGAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.68, C:0.05, G:0.09, T:0.18
Consensus pattern (19 bp):
AATAAAAACAATTAAAGTA
Found at i:200359 original size:14 final size:14
Alignment explanation
Indices: 200341--200378 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
200331 GTTTTCCATT
*
200341 TTTTTCTTTCATGTC
1 TTTTTCTTTC-TCTC
200356 TTTTT-TTTCTCTC
1 TTTTTCTTTCTCTC
200369 TTTTTCTTTC
1 TTTTTCTTTC
200379 GAACAGCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 8 0.38
14 8 0.38
15 5 0.24
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTTCTTTCTCTC
Found at i:200404 original size:7 final size:7
Alignment explanation
Indices: 200392--200416 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
200382 CAGCTTTTTC
200392 TTTTCTT
1 TTTTCTT
200399 TTTTCTT
1 TTTTCTT
200406 TTTTCTT
1 TTTTCTT
200413 TTTT
1 TTTT
200417 TGAACTGCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:201530 original size:20 final size:20
Alignment explanation
Indices: 201505--201560 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
201495 TTTGTCGTTT
*
201505 AATGAAATTGGCATATTTCA
1 AATGAAATTGGCATAGTTCA
*
201525 AATGAAATTAGCATAGTTCA
1 AATGAAATTGGCATAGTTCA
201545 AATGAAATTGGCATAG
1 AATGAAATTGGCATAG
201561 AAATATTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (20 bp):
AATGAAATTGGCATAGTTCA
Found at i:201793 original size:18 final size:19
Alignment explanation
Indices: 201770--201812 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
201760 TTTAAGTAGT
*
201770 AATAAAAACGATT-AAGTA
1 AATAAAAACAATTAAAGTA
*
201788 AATAAAAGCAATTAAAGTA
1 AATAAAAACAATTAAAGTA
201807 AA-AAAA
1 AATAAAA
201813 TAAGAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.67, C:0.05, G:0.09, T:0.19
Consensus pattern (19 bp):
AATAAAAACAATTAAAGTA
Found at i:212950 original size:11 final size:12
Alignment explanation
Indices: 212934--212979 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
212924 AAAATTTTAT
212934 AAAATTA-AAAA
1 AAAATTATAAAA
*
212945 AAAATTATTAAA
1 AAAATTATAAAA
*
212957 AAAATTATTAAA
1 AAAATTATAAAA
*
212969 AATATT-TAAAA
1 AAAATTATAAAA
212980 TATATGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAATTATAAAA
Found at i:212959 original size:12 final size:12
Alignment explanation
Indices: 212942--212970 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
212932 ATAAAATTAA
212942 AAAAAAATTATT
1 AAAAAAATTATT
212954 AAAAAAATTATT
1 AAAAAAATTATT
212966 AAAAA
1 AAAAA
212971 TATTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAAAAATTATT
Found at i:213873 original size:2 final size:2
Alignment explanation
Indices: 213866--213898 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
213856 ATACCTCGTA
213866 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 A
213899 AGATAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:218544 original size:16 final size:17
Alignment explanation
Indices: 218513--218547 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
218503 TACTATTCAT
*
218513 TTCCCTCCTCTTTTTTC
1 TTCCCTCCTCTCTTTTC
218530 TTCCCT-CTCTCTTTTC
1 TTCCCTCCTCTCTTTTC
218546 TT
1 TT
218548 TCACTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (17 bp):
TTCCCTCCTCTCTTTTC
Found at i:224308 original size:16 final size:16
Alignment explanation
Indices: 224263--224327 Score: 69
Period size: 16 Copynumber: 4.0 Consensus size: 16
224253 CGTTCTCATT
*
224263 TTATTATATATATATA
1 TTATTATATATATTTA
*
224279 TAATTATATATATTTA
1 TTATTATATATATTTA
224295 TTATTAT-TATTATTATA
1 TTATTATATA-TATT-TA
* *
224312 TTATTACAAATATTTA
1 TTATTATATATATTTA
224328 CAAATCAACC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
15 2 0.05
16 26 0.63
17 12 0.29
18 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATTATATATATTTA
Found at i:226170 original size:32 final size:31
Alignment explanation
Indices: 226134--226208 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
226124 GGGGCCACGA
* **
226134 GGCCTACCTAAGAACACATCTTAGGGCCGTGG
1 GGCCTACCTAAGAACA-ATCTCAGGGCCGCAG
* *
226166 GGCCTACCCAA-AATAATCTCAGGGCCGCAG
1 GGCCTACCTAAGAACAATCTCAGGGCCGCAG
*
226196 AGCCTACCTAAGA
1 GGCCTACCTAAGA
226209 GTCACGTTAG
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
30 21 0.60
31 4 0.11
32 10 0.29
ACGTcount: A:0.29, C:0.31, G:0.24, T:0.16
Consensus pattern (31 bp):
GGCCTACCTAAGAACAATCTCAGGGCCGCAG
Found at i:226191 original size:62 final size:62
Alignment explanation
Indices: 226087--226208 Score: 151
Period size: 62 Copynumber: 2.0 Consensus size: 62
226077 ACCTAAGGGA
* * *
226087 ACATCTTAGGGCCTGAGAGCCTACCCAAGAAAGTTTCGGGGCCAC-GAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGAAAATCTCAGGGCCACAGA-GCCTACCTAAGAAC
* *
226149 ACATCTTAGGGCCGTG-GGGCCTACCCAA-AATAATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCC-TGAGAGCCTACCCAAGAA-AATCTCAGGGCCACAGAGCCTACCTAAGA
226209 GTCACGTTAG
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
61 2 0.04
62 46 0.88
63 4 0.08
ACGTcount: A:0.29, C:0.30, G:0.25, T:0.16
Consensus pattern (62 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGAAAATCTCAGGGCCACAGAGCCTACCTAAGAAC
Found at i:231310 original size:30 final size:33
Alignment explanation
Indices: 231252--231336 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 33
231242 CTAAAGGAAC
*
231252 ATCTTAGGGCC-TGAGAGCCTA-CTCAGGAA-AGT
1 ATCTTAGGGCCACGAG-GCCTACCTCAGGAACA-T
*
231284 -T-TTGGGGCCACGAGGCCTACCT-AGGAACAT
1 ATCTTAGGGCCACGAGGCCTACCTCAGGAACAT
*
231314 ATCTTAGGGCCACGGGGCCTACC
1 ATCTTAGGGCCACGAGGCCTACC
231337 CGAAAATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
30 18 0.41
31 8 0.18
32 18 0.41
ACGTcount: A:0.24, C:0.27, G:0.29, T:0.20
Consensus pattern (33 bp):
ATCTTAGGGCCACGAGGCCTACCTCAGGAACAT
Found at i:235447 original size:19 final size:20
Alignment explanation
Indices: 235410--235448 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
235400 CAATAAATAA
*
235410 TCAAAACAATTTCATCATTG
1 TCAAAACAATTTCAGCATTG
*
235430 TCAAATCAA-TTCAGCATTG
1 TCAAAACAATTTCAGCATTG
235449 GTTACGAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (20 bp):
TCAAAACAATTTCAGCATTG
Found at i:236940 original size:19 final size:19
Alignment explanation
Indices: 236912--237016 Score: 102
Period size: 19 Copynumber: 5.2 Consensus size: 19
236902 GCGATTTTGA
*
236912 AAAATATGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
236931 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
236950 AAAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
*
236970 AAAAAATGTGTTGTTGCGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
* * *
236994 AAAAAGTGTTGTGATAGTG
1 AAAATGTGTTGCGATAGTT
237013 AAAA
1 AAAA
237017 ATCCAAAATA
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
19 50 0.68
20 3 0.04
22 8 0.11
24 3 0.04
25 10 0.14
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:237475 original size:21 final size:21
Alignment explanation
Indices: 237451--237599 Score: 108
Period size: 21 Copynumber: 7.2 Consensus size: 21
237441 AAATCACATA
237451 GCGATTTTGTATTATCGCGTT
1 GCGATTTTGTATTATCGCGTT
** * **
237472 GCGA-TAGGCAGAATCGCGTT
1 GCGATTTTGTATTATCGCGTT
* *
237492 GTGATTTTGTATTATCACGTT
1 GCGATTTTGTATTATCGCGTT
** * **
237513 GCGA-TAGGCAGAATCGCGTT
1 GCGATTTTGTATTATCGCGTT
237533 GCGATTTTGTATTATCGCGTT
1 GCGATTTTGTATTATCGCGTT
* ** *
237554 GCGA--TAGTCAGAATCACGTT
1 GCGATTTTGT-ATTATCGCGTT
*
237574 ACGATTTTGTATTATCGCGTT
1 GCGATTTTGTATTATCGCGTT
237595 GCGAT
1 GCGAT
237600 AGTTAGAATT
Statistics
Matches: 89, Mismatches: 34, Indels: 10
0.67 0.26 0.08
Matches are distributed among these distances:
19 3 0.03
20 39 0.44
21 44 0.49
22 3 0.03
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (21 bp):
GCGATTTTGTATTATCGCGTT
Found at i:237489 original size:20 final size:20
Alignment explanation
Indices: 237464--237578 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 20
237454 ATTTTGTATT
237464 ATCGCGTTGCGATAGGCAGA
1 ATCGCGTTGCGATAGGCAGA
* ** * **
237484 ATCGCGTTGTGATTTTGTATT
1 ATCGCGTTGCGA-TAGGCAGA
*
237505 ATCACGTTGCGATAGGCAGA
1 ATCGCGTTGCGATAGGCAGA
** * **
237525 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGA-TAGGCAGA
*
237546 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGGCAGA
* *
237566 ATCACGTTACGAT
1 ATCGCGTTGCGAT
237579 TTTGTATTAT
Statistics
Matches: 66, Mismatches: 27, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
20 38 0.58
21 28 0.42
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGATAGGCAGA
Found at i:237608 original size:41 final size:41
Alignment explanation
Indices: 237451--237601 Score: 257
Period size: 41 Copynumber: 3.7 Consensus size: 41
237441 AAATCACATA
237451 GCGATTTTGTATTATCGCGTTGCGATAGGCAGAATCGCGTT
1 GCGATTTTGTATTATCGCGTTGCGATAGGCAGAATCGCGTT
* *
237492 GTGATTTTGTATTATCACGTTGCGATAGGCAGAATCGCGTT
1 GCGATTTTGTATTATCGCGTTGCGATAGGCAGAATCGCGTT
* *
237533 GCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCACGTT
1 GCGATTTTGTATTATCGCGTTGCGATAGGCAGAATCGCGTT
*
237574 ACGATTTTGTATTATCGCGTTGCGATAG
1 GCGATTTTGTATTATCGCGTTGCGATAG
237602 TTAGAATTGT
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 103 1.00
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.36
Consensus pattern (41 bp):
GCGATTTTGTATTATCGCGTTGCGATAGGCAGAATCGCGTT
Found at i:237653 original size:21 final size:20
Alignment explanation
Indices: 237628--237700 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
237618 CTTTACATAT
237628 TCGCATTGCGATTTTCAAAAA
1 TCGCATTGCGATTTTC-AAAA
* **
237649 TCGCAACT-CGAATTTGGAAAA
1 TCGC-ATTGCG-ATTTTCAAAA
* **
237670 TCGCAATGCGATAGTCAAAA
1 TCGCATTGCGATTTTCAAAA
237690 TCGCATTGCGA
1 TCGCATTGCGA
237701 ATCTGGAAAC
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
20 18 0.45
21 16 0.40
22 6 0.15
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCATTGCGATTTTCAAAA
Found at i:239584 original size:196 final size:199
Alignment explanation
Indices: 239247--239641 Score: 760
Period size: 196 Copynumber: 2.0 Consensus size: 199
239237 ATGTGCTTAC
239247 TCAATTCGGTGATTTCCAAGTTGAATGCCTTCTCAGATGTTAGTAACCAATTATCAGAAATTTTC
1 TCAATTCGGTGATTTCCAAGTTGAATGCCTTCTCAGATGTTAGTAACCAATTATCAGAAATTTTC
239312 CATACAAAAATAGGATCTCAACAATTAAATCCGTACTTAATCGAGTTAAGTACGAATCCTCAAAG
66 CATACAAAAATAGGATCTCAACAATTAAATCCGTACTTAATCGAGTTAAGTACGAATCCTCAAAG
*
239377 TATTTTCTCATTCAAGGTCAACTCGGACTATTTTATCTCTCAAGGGTATTTTCATAATTTCTTAA
131 TATTTTCTCATTCAAGGTCAACTCGGACTATTTTATCTCTCAAGAGTATTTTCATAATTTCTTAA
239442 CCAG
196 CCAG
239446 TCAATTCGGTGATTTCCAAGTTGAATGCCTTCTCAGATGTTAGT-ACCAATTATCA-AAATTTTC
1 TCAATTCGGTGATTTCCAAGTTGAATGCCTTCTCAGATGTTAGTAACCAATTATCAGAAATTTTC
239509 CATAC-AAAATAGGATCTCAACAATTAAATCCGTACTTAATCGAGTTAAGTACGAATCCTCAAAG
66 CATACAAAAATAGGATCTCAACAATTAAATCCGTACTTAATCGAGTTAAGTACGAATCCTCAAAG
239573 TATTTTCTCATTCAAGGTCAACTCGGACTATTTTATCTCTCAAGAGTATTTTCATAATTTCTTAA
131 TATTTTCTCATTCAAGGTCAACTCGGACTATTTTATCTCTCAAGAGTATTTTCATAATTTCTTAA
239638 CCAG
196 CCAG
239642 ATAATTTCTG
Statistics
Matches: 195, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
196 127 0.65
197 13 0.07
198 11 0.06
199 44 0.23
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (199 bp):
TCAATTCGGTGATTTCCAAGTTGAATGCCTTCTCAGATGTTAGTAACCAATTATCAGAAATTTTC
CATACAAAAATAGGATCTCAACAATTAAATCCGTACTTAATCGAGTTAAGTACGAATCCTCAAAG
TATTTTCTCATTCAAGGTCAACTCGGACTATTTTATCTCTCAAGAGTATTTTCATAATTTCTTAA
CCAG
Found at i:244039 original size:42 final size:42
Alignment explanation
Indices: 243988--244166 Score: 304
Period size: 42 Copynumber: 4.3 Consensus size: 42
243978 CATTTTTGCA
* *
243988 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
244030 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * * *
244072 TTGCGATAGTCGAAGTTCGCGCTCCGCTTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
244114 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
244156 TTGCGATAGTC
1 TTGCGATAGTC
244167 CAAAATCGCA
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 127 1.00
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:244926 original size:42 final size:42
Alignment explanation
Indices: 244874--245013 Score: 239
Period size: 42 Copynumber: 3.4 Consensus size: 42
244864 CGTTGCGATT
*
244874 TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
244916 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
244958 TTTGACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
244998 TTCGACTATCGCAACG
1 TTGGACTATCGCAACG
245014 CGAACTTGGA
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
40 31 0.33
41 1 0.01
42 63 0.66
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:245008 original size:21 final size:21
Alignment explanation
Indices: 244874--245038 Score: 153
Period size: 21 Copynumber: 8.0 Consensus size: 21
244864 CGTTGCGATT
*
244874 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
244893 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
244916 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
244935 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
244958 TTTGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
**
244977 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
244998 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
245019 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
245039 TATGTAAATC
Statistics
Matches: 118, Mismatches: 18, Indels: 18
0.77 0.12 0.12
Matches are distributed among these distances:
19 31 0.26
21 68 0.58
23 19 0.16
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:245098 original size:21 final size:21
Alignment explanation
Indices: 245047--245099 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
245037 AATATGTAAA
* *
245047 TCGCATTGCAATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
* *
245068 TCGTGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
245089 TCGCGTTGCGA
1 TCGCGTTGCGA
245100 ATCTGGAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:245940 original size:11 final size:11
Alignment explanation
Indices: 245924--245948 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
245914 AGGAGAGCAA
245924 GAACTGAGGTG
1 GAACTGAGGTG
245935 GAACTGAGGTG
1 GAACTGAGGTG
245946 GAA
1 GAA
245949 ATACTCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.44, T:0.16
Consensus pattern (11 bp):
GAACTGAGGTG
Found at i:248172 original size:21 final size:21
Alignment explanation
Indices: 248132--248172 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
248122 TAAAGTACCT
*
248132 AATAATAATAAAATTGATAAA
1 AATAATAATAAAATTAATAAA
**
248153 AATAATAATAATTTTAATAA
1 AATAATAATAAAATTAATAA
248173 TTTTTTATTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
AATAATAATAAAATTAATAAA
Found at i:249999 original size:2 final size:2
Alignment explanation
Indices: 249988--250047 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
249978 ATTTACTCTT
249988 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
250029 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
250048 GTGGGGATAT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:251336 original size:30 final size:30
Alignment explanation
Indices: 251302--251362 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
251292 TTCGATATAA
*
251302 CAAATTAAGTTAAA-TGGATTTTAAGATTTT
1 CAAATTAAGTTAAAGT-AATTTTAAGATTTT
251332 CAAATTAAGTTAAAGTAATTTTAAGATTTT
1 CAAATTAAGTTAAAGTAATTTTAAGATTTT
251362 C
1 C
251363 CAAACGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
CAAATTAAGTTAAAGTAATTTTAAGATTTT
Found at i:255407 original size:23 final size:20
Alignment explanation
Indices: 255354--255438 Score: 80
Period size: 20 Copynumber: 4.0 Consensus size: 20
255344 TTTTGGTGCA
*
255354 GAGGGAATCGATTCCCCCCT
1 GAGGGAACCGATTCCCCCCT
*
255374 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-CT
*
255395 GAAGAGGAACCGATTCCCCCCA
1 G-AG-GGAACCGATTCCCCCCT
* * *
255417 CAGGGGAATCGATACCCCCCT
1 GA-GGGAACCGATTCCCCCCT
255438 G
1 G
255439 GGGTTCTGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
20 17 0.33
21 17 0.33
22 3 0.06
23 15 0.29
ACGTcount: A:0.24, C:0.35, G:0.25, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCCT
Found at i:257709 original size:30 final size:30
Alignment explanation
Indices: 257675--257739 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
257665 TTTACATAAT
257675 AAATTGAAGTGGTGTTAAAGTAAGGGGGAG
1 AAATTGAAGTGGTGTTAAAGTAAGGGGGAG
257705 AAATTGAAGTGGTGTTAAAGTAAGGGGGAG
1 AAATTGAAGTGGTGTTAAAGTAAGGGGGAG
*
257735 TAATT
1 AAATT
257740 TCAAAACTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.26
Consensus pattern (30 bp):
AAATTGAAGTGGTGTTAAAGTAAGGGGGAG
Found at i:257868 original size:30 final size:30
Alignment explanation
Indices: 257834--257894 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
257824 TTCGATATAA
*
257834 CAAATTAAGTTAAA-TGGATTTTAAGATTTT
1 CAAATTAAGTTAAAGT-AATTTTAAGATTTT
257864 CAAATTAAGTTAAAGTAATTTTAAGATTTT
1 CAAATTAAGTTAAAGTAATTTTAAGATTTT
257894 C
1 C
257895 CAAACGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
CAAATTAAGTTAAAGTAATTTTAAGATTTT
Found at i:259882 original size:41 final size:40
Alignment explanation
Indices: 259837--260020 Score: 155
Period size: 41 Copynumber: 4.5 Consensus size: 40
259827 AATGTATAGT
259837 GGCGTTTTT-TGACAAACGCCGCTAAAGAGTAGTATTGTAGC
1 GGCGTTTTTAT-ACAAACGCCGCTAAAGAGTAGTATT-TAGC
* * *
259878 GGCGTTTTTATAAAAATGCCG-TAATAGGGTCATGTA--TAGC
1 GGCGTTTTTATACAAACGCCGCTAA-AGAGT-A-GTATTTAGC
* **
259918 GGCATTGTTT-TGACAAACGAAGCTAAAGAGTAGTACTTTAGC
1 GGCGTT-TTTAT-ACAAACGCCGCTAAAGAGTAGTA-TTTAGC
* * *
259960 GGCGTTTTTATACAAACGCCGCTATAA-ACTTGTATTTTAGT
1 GGCGTTTTTATACAAACGCCGCTA-AAGAGTAGTA-TTTAGC
260001 GGCGTTTTTATACAAACGCC
1 GGCGTTTTTATACAAACGCC
260021 ATTATAAACT
Statistics
Matches: 115, Mismatches: 16, Indels: 24
0.74 0.10 0.15
Matches are distributed among these distances:
39 3 0.03
40 14 0.12
41 78 0.68
42 17 0.15
43 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (40 bp):
GGCGTTTTTATACAAACGCCGCTAAAGAGTAGTATTTAGC
Found at i:259889 original size:81 final size:82
Alignment explanation
Indices: 259788--259981 Score: 257
Period size: 82 Copynumber: 2.4 Consensus size: 82
259778 AACAGAGTTA
* * * * * *
259788 TACTTTAGCAGTGTTTTTATAAAAACGTCGCAATATGGTAATGTATAGTGGCGTT-TTTTGACAA
1 TACTTTAGCGGCGTTTTTATAAAAACGCCGCAATAGGGTAATGTATAGCGGCATTGTTTTGACAA
**
259852 ACGCCGCTAAAGAGTAG
66 ACGAAGCTAAAGAGTAG
* * *
259869 TA-TTGTAGCGGCGTTTTTATAAAAATGCCGTAATAGGGTCATGTATAGCGGCATTGTTTTGACA
1 TACTT-TAGCGGCGTTTTTATAAAAACGCCGCAATAGGGTAATGTATAGCGGCATTGTTTTGACA
259933 AACGAAGCTAAAGAGTAG
65 AACGAAGCTAAAGAGTAG
*
259951 TACTTTAGCGGCGTTTTTATACAAACGCCGC
1 TACTTTAGCGGCGTTTTTATAAAAACGCCGC
259982 TATAAACTTG
Statistics
Matches: 96, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
80 2 0.02
81 43 0.45
82 49 0.51
83 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (82 bp):
TACTTTAGCGGCGTTTTTATAAAAACGCCGCAATAGGGTAATGTATAGCGGCATTGTTTTGACAA
ACGAAGCTAAAGAGTAG
Found at i:260027 original size:41 final size:41
Alignment explanation
Indices: 259950--260049 Score: 155
Period size: 41 Copynumber: 2.4 Consensus size: 41
259940 CTAAAGAGTA
* * *
259950 GTACTTTAGCGGCGTTTTTATACAAACGCCGCTATAAACTT
1 GTACTTTAGTGGCGTTTTTATACAAACGCCACTATAAACTC
* *
259991 GTATTTTAGTGGCGTTTTTATACAAACGCCATTATAAACTC
1 GTACTTTAGTGGCGTTTTTATACAAACGCCACTATAAACTC
260032 GTACTTTAGTGGCGTTTT
1 GTACTTTAGTGGCGTTTT
260050 CATTTACAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (41 bp):
GTACTTTAGTGGCGTTTTTATACAAACGCCACTATAAACTC
Found at i:263668 original size:85 final size:85
Alignment explanation
Indices: 263494--263913 Score: 462
Period size: 85 Copynumber: 5.0 Consensus size: 85
263484 TTTGTTCCAA
* * * * * *
263494 AAACGCCACTATAGACCTAGATCTTTTACGGCGTTTGTATCAAAAAA-GCCGTTATAGATC-TGA
1 AAACGCCGCTATAGATCTA-ACCTTTTGCGGCGTTTGT-TCAAAAAACGCCGCTATATATCTTGA
**
263557 CCT-TTAGCGGCGTTTGTTCCAA-
64 CCTATT-GCGGCGTTT-TTTGAAC
* * *
263579 AAACGCCGCTATAGATCTAACCTTTTGCTGCGTTTGTTCAAAAAACGCAGCTATATATCTTGACA
1 AAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATATATCTTGACC
*
263644 TATTGCGGTGTTTTTTGAAC
66 TATTGCGGCGTTTTTTGAAC
* * *
263664 AAACGCCGCTAAATG-TCTAACCTTTTGCGGCGTTTGTTCTAAAAATGCCGCTATATATCTTGAC
1 AAACGCCGCTATA-GATCTAACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATATATCTTGAC
*
263728 CTATTGCAGCGTTTTTTGAAC
65 CTATTGCGGCGTTTTTTGAAC
* * *
263749 AAACGCCGCTATATATCTGACCTTTTGCGGTGTTTGTT-ACAAAAAC-CCGCTATATATCTTGAC
1 AAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCA-AAAAACGCCGCTATATATCTTGAC
* * *
263812 CTATTG-TGCCTTTTTTTAAC
65 CTATTGCGGCGTTTTTTGAAC
* * * * *
263832 AAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTATTC-AAAAACGCCGCAATAGATATTGAC
1 AAACGCCGCTATAGATCT-AACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATATATCTTGAC
*
263896 CTATTGCGACGTTTTTTG
65 CTATTGCGGCGTTTTTTG
263914 TTCTCAAACT
Statistics
Matches: 285, Mismatches: 39, Indels: 22
0.82 0.11 0.06
Matches are distributed among these distances:
83 42 0.15
84 90 0.32
85 150 0.53
86 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (85 bp):
AAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATATATCTTGACC
TATTGCGGCGTTTTTTGAAC
Found at i:263897 original size:42 final size:42
Alignment explanation
Indices: 263478--263909 Score: 374
Period size: 42 Copynumber: 10.2 Consensus size: 42
263468 AAGGTAATTA
* * * *
263478 GCGGCGTTTGTTCCAAAAACGCCACTATAGACCTAGATCTTTT
1 GCGGCGTTTGTT-CAAAAACGCCGCTATAGATCTTGACCTTTT
* * * *
263521 ACGGCGTTTGTATCAAAAAAGCCGTTATAGATC-TGACCTTTA
1 GCGGCGTTTGT-TCAAAAACGCCGCTATAGATCTTGACCTTTT
*
263563 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATC-TAACCTTTT
1 GCGGCGTTTGTT-CAAAAACGCCGCTATAGATCTTGACCTTTT
* * * * *
263605 GCTGCGTTTGTTCAAAAAACGCAGCTATATATCTTGACATATT
1 GCGGCGTTTGTTC-AAAAACGCCGCTATAGATCTTGACCTTTT
* * * * *
263648 GCGGTGTTTTTTGAACAAACGCCGCTA-A-ATGTCTAACCTTTT
1 GCGGCGTTTGTTCAA-AAACGCCGCTATAGATCT-TGACCTTTT
* * *
263690 GCGGCGTTTGTTCTAAAAATGCCGCTATATATCTTGACCTATT
1 GCGGCGTTTGTTC-AAAAACGCCGCTATAGATCTTGACCTTTT
* * * *
263733 GCAGCGTTTTTTGAACAAACGCCGCTATATATC-TGACCTTTT
1 GCGGCGTTTGTTCAA-AAACGCCGCTATAGATCTTGACCTTTT
* * *
263775 GCGGTGTTTGTTACAAAAAC-CCGCTATATATCTTGACCTATT
1 GCGGCGTTTGTT-CAAAAACGCCGCTATAGATCTTGACCTTTT
* * * * *
263817 G-TGCCTTTTTTTAACAAACGCCGCTATAGATCTCGACCTTTT
1 GCGGCGTTTGTTCAA-AAACGCCGCTATAGATCTTGACCTTTT
* * * *
263859 GCGGCGTTTATTCAAAAACGCCGCAATAGATATTGACCTATT
1 GCGGCGTTTGTTCAAAAACGCCGCTATAGATCTTGACCTTTT
*
263901 GCGACGTTT
1 GCGGCGTTT
263910 TTTGTTCTCA
Statistics
Matches: 312, Mismatches: 62, Indels: 31
0.77 0.15 0.08
Matches are distributed among these distances:
40 2 0.01
41 27 0.09
42 181 0.58
43 98 0.31
44 4 0.01
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (42 bp):
GCGGCGTTTGTTCAAAAACGCCGCTATAGATCTTGACCTTTT
Found at i:267003 original size:2 final size:2
Alignment explanation
Indices: 266996--267020 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
266986 TTTCTTCCCG
266996 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
267021 TAGGTGATAC
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:277882 original size:3 final size:3
Alignment explanation
Indices: 277874--277922 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
277864 TATATCCTTC
277874 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
277921 AT
1 AT
277923 TTAATATTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Done.