Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold244
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: 271570
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 2
Found at i:183637 original size:10 final size:9
Alignment explanation
Indices: 183617--183648 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
183607 ATTTCTTTGA
183617 TTTTTGATT
1 TTTTTGATT
183626 TTTTTGATT
1 TTTTTGATT
183635 TTTTTGAATT
1 TTTTTG-ATT
183645 TTTT
1 TTTT
183649 AAATTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (9 bp):
TTTTTGATT
Found at i:184282 original size:44 final size:44
Alignment explanation
Indices: 184232--185436 Score: 933
Period size: 44 Copynumber: 27.7 Consensus size: 44
184222 AAGTTTATAG
* * * *
184232 GGTCAAAGCTGACAGACAGACTTGAGGATAAAAGAAATCTCTAA
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCCAA
* * * *
184276 GGTCAAAGCTGACAGGCAAACTTAAGGGTAAAGGAAGTCTCCAG
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCCAA
* * * *
184320 GGACAAAGCCGACAGGCAGACTTAAGG-TAAAAGAAGTCTTCAG
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCCAA
* ** * * * *
184363 GGTCAAAGCCGACAACCAGACTTAAGG--GAAGGAAGTCTCTAG
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCCAA
* * * * * *
184405 GGTCAAAGCTGACAAGTAAACTTGAGG-GAAAAGAAAGTCTCCAG
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAG-AAGTCTCCAA
* * * *
184449 GGTCAAAGCTGACAGGTAAACTTGAGG-GAAAAGAAAGTCTCCAA
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAG-AAGTCTCCAA
* * * *
184493 GATCAAAGCTGACACGTAGACTTAAGGATAAAGGAAGTCTCCAA
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCCAA
** * * *
184537 GGTCAAAATTGACAAGCAGACTTGATGGA-AAAAGAAGTCTCCAG
1 GGTCAAAGCTGACAGGCAGACTT-AAGGATAAAAGAAGTCTCCAA
* * *
184581 GGTCAAAGCTGACAGGCAGACTTGAGG--AAAGGAAGTCT-CTA
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCCAA
* * * * *
184622 CGTCAAAGCTTGATAGGCAGATTTGAGG--AAAGGAAGTCTCCAA
1 GGTCAAAGC-TGACAGGCAGACTTAAGGATAAAAGAAGTCTCCAA
** * * *
184665 GGTCAAAGCCAATAGGCAGACTTGAGCG-TAAAAGAAGTCTTCAA
1 GGTCAAAGCTGACAGGCAGACTTAAG-GATAAAAGAAGTCTCCAA
* * * * * * * *
184709 GGACGAAGCCGACAGGCAGACTTAAGGAT--AGGAAATTTCTAG
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCCAA
*
184751 GGTCAAAG-TCGACAGGCAGACTTAAGGATAAAGGAAGTCTCCAA
1 GGTCAAAGCT-GACAGGCAGACTTAAGGATAAAAGAAGTCTCCAA
* * * * *
184795 GGTCAAAGCCGATAGGTAGACTTGAGGGA-AAATGAAGTCTCCAA
1 GGTCAAAGCTGACAGGCAGACTT-AAGGATAAAAGAAGTCTCCAA
* * *
184839 GGTCAAATCCGACAGGCAGACTTAAGGATAAAGGAAGTCTCCAA
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCCAA
* * * *
184883 GGTCAAAACTGATAGGCAGACTTGAGG-GAAAAGAAAGTCTCCAA
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAG-AAGTCTCCAA
* * *
184927 AGTCAAAGCTGACAGGCAGACTTAAGGATAAAGGAAGTCTCTAA
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCCAA
* * * * * *
184971 GGTCAAAGCTAACAAGCAGACTTGAGGGA-AGAAGAAGTCTCTAG
1 GGTCAAAGCTGACAGGCAGACTT-AAGGATAAAAGAAGTCTCCAA
* * * *
185015 GGTCAAA-TTCGACAAGCAGACTTAAGGATAAAAGAA-TCTCTAG
1 GGTCAAAGCT-GACAGGCAGACTTAAGGATAAAAGAAGTCTCCAA
* * * * *
185058 GGTCAAAACTGACAGGTAGACTTGAGGATAAAGGAAGTCTTCAA
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCCAA
* * * * * *
185102 GGACAACGCTGACATGCAGACTTGAGGATAAAGGAAGTCTCAAA
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCCAA
* * * *
185146 GGTCAAAGAC-GATAGGTAGACTTAAGGGA-AAAAGAAGTTTCCAG
1 GGTCAAAG-CTGACAGGCAGACTTAA-GGATAAAAGAAGTCTCCAA
* * * * * *
185190 GGTCAAAGCCGATAGGCAGACTTAAAGAT-AAAGAAAGTCGCTAG
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAG-AAGTCTCCAA
** * *
185234 GGTCAAAGCCAATAAGCAGACTTGAAGG-TAAAAGAAGTCTCCGAA
1 GGTCAAAGCTGACAGGCAGACTT-AAGGATAAAAGAAGTCTCC-AA
* * * * *
185279 -GACAAAGCCGATAGGCAGACTTAAGG--AAAAGAAATC-CCTAG
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCC-AA
* *
185320 GGTCAAAGCTGACAGGCAGACTTAAGGCA-AAAGGAAGTCTCCAG
1 GGTCAAAGCTGACAGGCAGACTTAAGG-ATAAAAGAAGTCTCCAA
* *
185364 GGTCAAAGCTGATAGGCAGACTTAAAGAT-AAAGAAAGTCTCCAA
1 GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAG-AAGTCTCCAA
* *
185408 GGTTAAAGCCT-ACAGGCAGACTTGAGGAT
1 GGTCAAAG-CTGACAGGCAGACTTAAGGAT
185437 GCATGATGCA
Statistics
Matches: 955, Mismatches: 169, Indels: 74
0.80 0.14 0.06
Matches are distributed among these distances:
41 12 0.01
42 148 0.15
43 119 0.12
44 640 0.67
45 36 0.04
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (44 bp):
GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCCAA
Found at i:184327 original size:88 final size:88
Alignment explanation
Indices: 184212--185430 Score: 1036
Period size: 88 Copynumber: 14.0 Consensus size: 88
184202 CAGGTAAACA
* ** * * *
184212 AAGGG-AAAGGAAGTTTATAGGGTCAAAGCTGACAGACAGACTTGAGGATAAAAGAAATCTCTAA
1 AAGGGAAAAGGAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCTAA
*
184276 GGTCAAAGCTGACAGGCAAACTT
66 GGTCAAAGCTGACAGGCAGACTT
* * *
184299 AAGGGTAAAGGAAGTCTCCAGGGACAAAGCCGACAGGCAGACTTAAGG-TAAAAGAAGTCT-TCA
1 AAGGGAAAAGGAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCT-A
* * **
184362 GGGTCAAAGCCGACAACCAGACTT
65 AGGTCAAAGCTGACAGGCAGACTT
* * * * * * *
184386 AAGGG--AAGGAAGTCTCTAGGGTCAAAGCTGACAAGTAAACTTGAGG-GAAAAGAAAGTCTCCA
1 AAGGGAAAAGGAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTAAGGATAAAAG-AAGTCTCTA
* * *
184448 GGGTCAAAGCTGACAGGTAAACTT
65 AGGTCAAAGCTGACAGGCAGACTT
* * * * * * * *
184472 GAGGGAAAAGAAAGTCTCCAAGATCAAAGCTGACACGTAGACTTAAGGATAAAGGAAGTCTCCAA
1 AAGGGAAAAGGAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCTAA
** *
184537 GGTCAAAATTGACAAGCAGACTT
66 GGTCAAAGCTGACAGGCAGACTT
* * * * *
184560 GATGGAAAAAGAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTGAGG--AAAGGAAGTCTCT-A
1 AAGGGAAAAGGAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCTAA
* * *
184622 CGTCAAAGCTTGATAGGCAGATTT
66 GGTCAAAGC-TGACAGGCAGACTT
* * ** * *
184646 GA-GG-AAAGGAAGTCTCCAAGGTCAAAGCCAATAGGCAGACTTGAGCG-TAAAAGAAGTCT-TC
1 AAGGGAAAAGGAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTAAG-GATAAAAGAAGTCTCT-
* * *
184707 AAGGACGAAGCCGACAGGCAGACTT
64 AAGGTCAAAGCTGACAGGCAGACTT
* * * * * *
184732 AA-GG-ATAGGAAATTTCTAGGGTCAAAG-TCGACAGGCAGACTTAAGGATAAAGGAAGTCTCCA
1 AAGGGAAAAGGAAGTCTCCAGGGTCAAAGCT-GACAGGCAGACTTAAGGATAAAAGAAGTCTCTA
* * *
184794 AGGTCAAAGCCGATAGGTAGACTT
65 AGGTCAAAGCTGACAGGCAGACTT
* * * * * * *
184818 GAGGGAAAATGAAGTCTCCAAGGTCAAATCCGACAGGCAGACTTAAGGATAAAGGAAGTCTCCAA
1 AAGGGAAAAGGAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCTAA
* *
184883 GGTCAAAACTGATAGGCAGACTT
66 GGTCAAAGCTGACAGGCAGACTT
* * ** *
184906 GAGGGAAAAGAAAGTCTCCAAAGTCAAAGCTGACAGGCAGACTTAAGGATAAAGGAAGTCTCTAA
1 AAGGGAAAAGGAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCTAA
* *
184971 GGTCAAAGCTAACAAGCAGACTT
66 GGTCAAAGCTGACAGGCAGACTT
* * * *
184994 GAGGGAAGAA-GAAGTCTCTAGGGTCAAA-TTCGACAAGCAGACTTAAGGATAAAAGAA-TCTCT
1 AAGGGAA-AAGGAAGTCTCCAGGGTCAAAGCT-GACAGGCAGACTTAAGGATAAAAGAAGTCTCT
* * *
185056 AGGGTCAAAACTGACAGGTAGACTT
64 AAGGTCAAAGCTGACAGGCAGACTT
* * * * * * * * *
185081 GA-GGATAAAGGAAGTCTTCAAGGACAACGCTGACATGCAGACTTGAGGATAAAGGAAGTCTCAA
1 AAGGGA-AAAGGAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCTA
* *
185145 AGGTCAAAGAC-GATAGGTAGACTT
65 AGGTCAAAG-CTGACAGGCAGACTT
* * * * * *
185169 AAGGGAAAAAGAAGTTTCCAGGGTCAAAGCCGATAGGCAGACTTAAAGAT-AAAGAAAGTCGCTA
1 AAGGGAAAAGGAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTAAGGATAAAAG-AAGTCTCTA
* ** * *
185233 GGGTCAAAGCCAATAAGCAGACTT
65 AGGTCAAAGCTGACAGGCAGACTT
* * * * * * *
185257 GAAGGTAAAA-GAAGTCTCC-GAAGACAAAGCCGATAGGCAGACTTAAGG--AAAAGAAATCCCT
1 -AAGGGAAAAGGAAGTCTCCAG-GGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCT
*
185318 AGGGTCAAAGCTGACAGGCAGACTT
64 AAGGTCAAAGCTGACAGGCAGACTT
* * * *
185343 AAGGCAAAAGGAAGTCTCCAGGGTCAAAGCTGATAGGCAGACTTAAAGAT-AAAGAAAGTCTCCA
1 AAGGGAAAAGGAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTAAGGATAAAAG-AAGTCTCTA
*
185407 AGGTTAAAGCCT-ACAGGCAGACTT
65 AGGTCAAAG-CTGACAGGCAGACTT
185431 GAGGATGCAT
Statistics
Matches: 922, Mismatches: 173, Indels: 73
0.79 0.15 0.06
Matches are distributed among these distances:
84 36 0.04
85 59 0.06
86 208 0.23
87 129 0.14
88 470 0.51
89 20 0.02
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (88 bp):
AAGGGAAAAGGAAGTCTCCAGGGTCAAAGCTGACAGGCAGACTTAAGGATAAAAGAAGTCTCTAA
GGTCAAAGCTGACAGGCAGACTT
Found at i:185494 original size:6 final size:6
Alignment explanation
Indices: 185485--185511 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
185475 ATTTGTATTC
185485 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
185512 TGAAAACCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:199278 original size:52 final size:51
Alignment explanation
Indices: 199210--199308 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 51
199200 GCTTTGTTGG
* *
199210 TTTTTTTTTTTACCCATGTTCCCCATTCTTCTCCATCATTTGCTTTGCTAT
1 TTTTTTTTTTTACCCATGCTCCCCATTCATCTCCATCATTTGCTTTGCTAT
* * * *
199261 TTTTTTCTTTTTGCCCATGCTGCTCATTCATCTTCATCATTTGCTTTG
1 TTTTTT-TTTTTACCCATGCTCCCCATTCATCTCCATCATTTGCTTTG
199309 TTGTCTTTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
51 6 0.15
52 35 0.85
ACGTcount: A:0.11, C:0.26, G:0.08, T:0.55
Consensus pattern (51 bp):
TTTTTTTTTTTACCCATGCTCCCCATTCATCTCCATCATTTGCTTTGCTAT
Found at i:200288 original size:17 final size:17
Alignment explanation
Indices: 200266--200302 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
200256 AGATGAACAT
* *
200266 ATGAAATGCATGTATGC
1 ATGAAATGAATATATGC
200283 ATGAAATGAATATATGC
1 ATGAAATGAATATATGC
200300 ATG
1 ATG
200303 CATGAAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (17 bp):
ATGAAATGAATATATGC
Found at i:200431 original size:24 final size:23
Alignment explanation
Indices: 200400--200456 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 23
200390 AAGTTTTCTC
*
200400 TTTTTTTTTCTTTCTTTGATTTT
1 TTTTTTTTTATTTCTTTGATTTT
*
200423 TTTTGTTTTGATTTCTTTGATTTT
1 TTTT-TTTTTATTTCTTTGATTTT
200447 TTATTTTTTT
1 TT-TTTTTTT
200457 TTGATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.14
24 23 0.79
25 2 0.07
ACGTcount: A:0.07, C:0.05, G:0.07, T:0.81
Consensus pattern (23 bp):
TTTTTTTTTATTTCTTTGATTTT
Found at i:200441 original size:9 final size:8
Alignment explanation
Indices: 200414--200507 Score: 50
Period size: 9 Copynumber: 11.0 Consensus size: 8
200404 TTTTTCTTTC
200414 TTTGATTT
1 TTTGATTT
200422 TTT--TTGT
1 TTTGATT-T
200429 TTTGATTT
1 TTTGATTT
200437 CTTTGATTT
1 -TTTGATTT
200446 TTT-ATTTTTT
1 TTTGA---TTT
200456 TTTGATTTT
1 TTTGA-TTT
200465 TTTGAATTT
1 TTTG-ATTT
*
200474 TTTAAATTAT
1 TTT-GATT-T
*
200484 TTTTATTT
1 TTTGATTT
* *
200492 TTTTAATT
1 TTTGATTT
200500 TTTGATTT
1 TTTGATTT
200508 CTACTTATTA
Statistics
Matches: 70, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
6 2 0.03
7 5 0.07
8 21 0.30
9 30 0.43
10 11 0.16
11 1 0.01
ACGTcount: A:0.16, C:0.01, G:0.07, T:0.76
Consensus pattern (8 bp):
TTTGATTT
Found at i:200453 original size:27 final size:27
Alignment explanation
Indices: 200410--200477 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
200400 TTTTTTTTTC
200410 TTTCTTTGA--TTTT-TTTTGTTTTGA
1 TTTCTTTGATTTTTTATTTTGTTTTGA
*
200434 TTTCTTTGATTTTTTATTTTTTTTTGA
1 TTTCTTTGATTTTTTATTTTGTTTTGA
*
200461 TTTTTTTGAATTTTTTA
1 TTTCTTTG-ATTTTTTA
200478 AATTATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 9 0.24
26 4 0.11
27 17 0.45
28 8 0.21
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.76
Consensus pattern (27 bp):
TTTCTTTGATTTTTTATTTTGTTTTGA
Found at i:200474 original size:18 final size:18
Alignment explanation
Indices: 200428--200507 Score: 60
Period size: 18 Copynumber: 4.5 Consensus size: 18
200418 ATTTTTTTTG
*
200428 TTTTGATTTCTTTG-ATT
1 TTTTGATTTTTTTGAATT
*
200445 TTTT-ATTTTTTTTTGATTT
1 TTTTGA--TTTTTTTGAATT
* *
200464 TTTTGAATTTTTTAAATT
1 TTTTGATTTTTTTGAATT
*
200482 ATTTTTATTTTTTT-AA-T
1 -TTTTGATTTTTTTGAATT
200499 TTTTGATTT
1 TTTTGATTT
200508 CTACTTATTA
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
16 9 0.18
17 5 0.10
18 18 0.36
19 17 0.34
20 1 0.02
ACGTcount: A:0.17, C:0.01, G:0.06, T:0.75
Consensus pattern (18 bp):
TTTTGATTTTTTTGAATT
Found at i:204793 original size:23 final size:23
Alignment explanation
Indices: 204767--204817 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 23
204757 ATGAAAAGTC
*
204767 AATATTATGTAGGAAATACTTTT
1 AATATTATGTAAGAAATACTTTT
204790 -A-A-TATGTAAGAAATACTTTT
1 AATATTATGTAAGAAATACTTTT
204810 AATATTAT
1 AATATTAT
204818 ATATTTACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 17 0.71
21 2 0.08
22 2 0.08
23 3 0.12
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (23 bp):
AATATTATGTAAGAAATACTTTT
Found at i:204795 original size:20 final size:20
Alignment explanation
Indices: 204772--204814 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
204762 AAGTCAATAT
*
204772 TATGTAGGAAATACTTTTAA
1 TATGTAAGAAATACTTTTAA
204792 TATGTAAGAAATACTTTTAA
1 TATGTAAGAAATACTTTTAA
204812 TAT
1 TAT
204815 TATATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (20 bp):
TATGTAAGAAATACTTTTAA
Found at i:205366 original size:23 final size:23
Alignment explanation
Indices: 205340--205384 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
205330 CAAATAGACA
205340 AAATTGAAATGAGTAAACTCATC
1 AAATTGAAATGAGTAAACTCATC
205363 AAATTGAAATGAGTAAACTCAT
1 AAATTGAAATGAGTAAACTCAT
205385 ATACCTCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.27
Consensus pattern (23 bp):
AAATTGAAATGAGTAAACTCATC
Found at i:206733 original size:2 final size:2
Alignment explanation
Indices: 206721--206754 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
206711 GCACTTGCGC
*
206721 AT AT CT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
206755 GAACATCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:207055 original size:24 final size:24
Alignment explanation
Indices: 207028--207075 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
207018 ATTTTAAATA
207028 TAAATATAATATA-TATCATTTATT
1 TAAATATAATATATTAT-ATTTATT
*
207052 TAAATATATTATATTATATTTATT
1 TAAATATAATATATTATATTTATT
207076 ATATTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TAAATATAATATATTATATTTATT
Found at i:207059 original size:19 final size:20
Alignment explanation
Indices: 207035--207082 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
207025 ATATAAATAT
207035 AATATA-TATCATT-TATTTA
1 AATATATTAT-ATTATATTTA
207054 AATATATTATATTATATTT-
1 AATATATTATATTATATTTA
*
207073 ATTATATTAT
1 AATATATTAT
207083 TTTTATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
AATATATTATATTATATTTA
Found at i:207077 original size:14 final size:14
Alignment explanation
Indices: 207058--207088 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
207048 TATTTAAATA
207058 TATTATATTATATT
1 TATTATATTATATT
*
207072 TATTATATTATTTT
1 TATTATATTATATT
207086 TAT
1 TAT
207089 AAAATATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATATTATATT
Found at i:207796 original size:16 final size:16
Alignment explanation
Indices: 207775--207805 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
207765 TTATTGAATA
*
207775 ATTTTTTTTTCTTTTC
1 ATTTTTTTTTATTTTC
207791 ATTTTTTTTTATTTT
1 ATTTTTTTTTATTTT
207806 GTTAGATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (16 bp):
ATTTTTTTTTATTTTC
Found at i:209048 original size:19 final size:20
Alignment explanation
Indices: 209011--209053 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
209001 CAGTGAAATT
*
209011 ATTAAAAAAACCAACATAAA
1 ATTAAAAAAACCAAAATAAA
*
209031 ATTAAAACAA-CAAAATAAA
1 ATTAAAAAAACCAAAATAAA
209050 ATTA
1 ATTA
209054 GAGATGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.19
Consensus pattern (20 bp):
ATTAAAAAAACCAAAATAAA
Found at i:209336 original size:12 final size:12
Alignment explanation
Indices: 209321--209357 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
209311 ATAAATAATA
209321 AATATATAATTT
1 AATATATAATTT
*
209333 AATATAAAATTT
1 AATATATAATTT
209345 AA-ATAT-ATTT
1 AATATATAATTT
209355 AAT
1 AAT
209358 TAATCTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
10 6 0.27
11 3 0.14
12 13 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AATATATAATTT
Found at i:211697 original size:24 final size:23
Alignment explanation
Indices: 211670--211731 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
211660 ATATATTTAT
*
211670 ATAATATGAATATGATATTAAAAA
1 ATAATATGAATATAATA-TAAAAA
* *
211694 ATAAT-TAAAATATAATATGAAAA
1 ATAATAT-GAATATAATATAAAAA
211717 ATAATATGAATATAA
1 ATAATATGAATATAA
211732 CATAGATATG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (23 bp):
ATAATATGAATATAATATAAAAA
Found at i:211722 original size:12 final size:12
Alignment explanation
Indices: 211690--211726 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
211680 TATGATATTA
211690 AAAAATAAT-T-
1 AAAAATAATATG
211700 AAAATATAATATG
1 AAAA-ATAATATG
211713 AAAAATAATATG
1 AAAAATAATATG
211725 AA
1 AA
211727 TATAACATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.17
11 5 0.21
12 11 0.46
13 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (12 bp):
AAAAATAATATG
Found at i:211985 original size:19 final size:19
Alignment explanation
Indices: 211958--212013 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
211948 TATAAGCTTA
211958 AACTAAATACATATTTTAT
1 AACTAAATACATATTTTAT
* *
211977 AACTCAATACATTATATTAT
1 AACTAAATACA-TATTTTAT
211997 AACTAAATACATATTTT
1 AACTAAATACATATTTT
212014 TTTATTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (19 bp):
AACTAAATACATATTTTAT
Found at i:213180 original size:2 final size:2
Alignment explanation
Indices: 213173--213199 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
213163 TTGCTCTTGG
213173 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
213200 TTTTTTCCTG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:213405 original size:3 final size:3
Alignment explanation
Indices: 213397--213437 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
213387 TTAGAAAGGT
213397 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
213438 GTTTTATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:213484 original size:33 final size:32
Alignment explanation
Indices: 213459--213555 Score: 149
Period size: 33 Copynumber: 3.0 Consensus size: 32
213449 GTTCTTGCGG
*
213459 TTGTTTCACTTTGTTGATCTGTTGTTTTTTGCA
1 TTGTTTGACTTTGTTGATCTGTTG-TTTTTGCA
*
213492 TTGTTTGACTTTGTTGATCTGTTGTGTTTTACA
1 TTGTTTGACTTTGTTGATCTGTTGT-TTTTGCA
*
213525 ATGTTTGACTTTGTTGATCTGTTGTTTTTGC
1 TTGTTTGACTTTGTTGATCTGTTGTTTTTGC
213556 GTAGCGAGTA
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 6 0.10
33 53 0.90
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.59
Consensus pattern (32 bp):
TTGTTTGACTTTGTTGATCTGTTGTTTTTGCA
Found at i:219519 original size:32 final size:32
Alignment explanation
Indices: 219424--219524 Score: 105
Period size: 32 Copynumber: 3.1 Consensus size: 32
219414 AAACCGATCG
* *
219424 ACCCAAACCCAAAAATGATCCGAACTCAAAATA
1 ACCCAAACCC-AAAATGATCCGAACCCGAAATA
* * * *
219457 ACCCGAACCCAAAATGA-CTCGGACCTGAAATG
1 ACCCAAACCCAAAATGATC-CGAACCCGAAATA
* *
219489 ACCTAAACCCGAAATGATCCGAACCCGAAATA
1 ACCCAAACCCAAAATGATCCGAACCCGAAATA
219521 ACCC
1 ACCC
219525 GAACAATTAA
Statistics
Matches: 53, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
31 1 0.02
32 42 0.79
33 10 0.19
ACGTcount: A:0.44, C:0.33, G:0.12, T:0.12
Consensus pattern (32 bp):
ACCCAAACCCAAAATGATCCGAACCCGAAATA
Found at i:219526 original size:16 final size:16
Alignment explanation
Indices: 219436--219528 Score: 78
Period size: 16 Copynumber: 5.8 Consensus size: 16
219426 CCAAACCCAA
* * *
219436 AAATGATCCGAACTCA
1 AAATGACCCGAACCCG
* *
219452 AAATAACCCGAACCCA
1 AAATGACCCGAACCCG
* * *
219468 AAATGACTCGGACCTG
1 AAATGACCCGAACCCG
**
219484 AAATGACCTAAACCCG
1 AAATGACCCGAACCCG
*
219500 AAATGATCCGAACCCG
1 AAATGACCCGAACCCG
*
219516 AAATAACCCGAAC
1 AAATGACCCGAAC
219529 AATTAATCCA
Statistics
Matches: 59, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 59 1.00
ACGTcount: A:0.43, C:0.30, G:0.14, T:0.13
Consensus pattern (16 bp):
AAATGACCCGAACCCG
Found at i:226730 original size:27 final size:28
Alignment explanation
Indices: 226670--226731 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
226660 ATAGACATTA
* * * *
226670 TTTTTTGTTTTCTTTTAATTTTTTAGAT
1 TTTTTTATTTTCTTCTAAATTTTTAAAT
*
226698 TATTTTATTTT-TTCTAAATTTTTAAAT
1 TTTTTTATTTTCTTCTAAATTTTTAAAT
226725 TTTTTTA
1 TTTTTTA
226732 AAAAATATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (28 bp):
TTTTTTATTTTCTTCTAAATTTTTAAAT
Found at i:227067 original size:24 final size:23
Alignment explanation
Indices: 227040--227091 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
227030 AAAATTTGAA
227040 TAAAATTT-AATTTAATTAAAAATT
1 TAAAATTTAAATTTAA--AAAAATT
227064 TAAAAATTTAAATTTAAAAAAATT
1 T-AAAATTTAAATTTAAAAAAATT
227088 TAAA
1 TAAA
227092 CTTGAATAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.12
24 9 0.35
25 7 0.27
26 7 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAAATTTAAATTTAAAAAAATT
Found at i:228375 original size:22 final size:23
Alignment explanation
Indices: 228350--228396 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
228340 ACAATAATAT
228350 TTATAAGTATATGTA-ATA-TAAA
1 TTATAA-TATATGTACATATTAAA
*
228372 TTATAATATATTTACATATTAAA
1 TTATAATATATGTACATATTAAA
228395 TT
1 TT
228397 CAAATTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 9 0.41
23 6 0.27
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (23 bp):
TTATAATATATGTACATATTAAA
Found at i:228489 original size:18 final size:18
Alignment explanation
Indices: 228468--228507 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
228458 TTATAATAAA
*
228468 TTATTTAACAAATTGATT
1 TTATGTAACAAATTGATT
*
228486 TTATGTAACAAATTTATT
1 TTATGTAACAAATTGATT
228504 TTAT
1 TTAT
228508 ATATTTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (18 bp):
TTATGTAACAAATTGATT
Found at i:229477 original size:22 final size:21
Alignment explanation
Indices: 229452--229500 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
229442 AATAAATTTT
*
229452 TTTATAAATAATTTAAAGTTAA
1 TTTATAAATAA-TTAAAATTAA
* *
229474 TTTAATAAATTATTAAAATTTA
1 TTT-ATAAATAATTAAAATTAA
229496 TTTAT
1 TTTAT
229501 TATTTAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.09
22 14 0.61
23 7 0.30
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTATAAATAATTAAAATTAA
Found at i:229815 original size:30 final size:31
Alignment explanation
Indices: 229754--229836 Score: 83
Period size: 30 Copynumber: 2.9 Consensus size: 31
229744 ATTTTAAATA
229754 AATAAATATAAATATAAA-AT-TA-AAATTTTT
1 AATAAATATAAAT-TAAATATATATAAA-TTTT
229784 AATAAATATAAATTAAATATATATAAA-TTT
1 AATAAATATAAATTAAATATATATAAATTTT
*
229814 -A-AAA-ATAAA-TAAATATAAATAAA
1 AATAAATATAAATTAAATATATATAAA
229837 AATCAATTCG
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
26 13 0.27
27 5 0.10
28 3 0.06
29 5 0.10
30 18 0.37
31 2 0.04
32 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (31 bp):
AATAAATATAAATTAAATATATATAAATTTT
Found at i:235082 original size:2 final size:2
Alignment explanation
Indices: 235075--235124 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
235065 AATAAATTTC
* * * * *
235075 AT AT AT AT AT AT AT AT GT AT AC AT AC AT AG AT AC 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
235117 AT AT AT AT
1 AT AT AT AT
235125 GGGTTAAATA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (2 bp):
AT
Found at i:236304 original size:6 final size:6
Alignment explanation
Indices: 236293--236327 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
236283 TTGGTGTATA
*
236293 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTA ATTTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
236328 AAATTTGAAT
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:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (6 bp):
ATTTTG
Found at i:236316 original size:18 final size:18
Alignment explanation
Indices: 236291--236335 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
236281 TTTTGGTGTA
236291 TAATTTTGATTTTGATTT
1 TAATTTTGATTTTGATTT
* *
236309 TGATTTTGATTTTAATTT
1 TAATTTTGATTTTGATTT
*
236327 TAAATTTGA
1 TAATTTTGA
236336 ATTTCTGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.62
Consensus pattern (18 bp):
TAATTTTGATTTTGATTT
Found at i:240229 original size:23 final size:23
Alignment explanation
Indices: 240199--240242 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
240189 TTTACCTTAC
*
240199 TGTACAGTTCATGACTATTTAGT
1 TGTACAGTTCATAACTATTTAGT
240222 TGTACAGTTCATAACTATTTA
1 TGTACAGTTCATAACTATTTA
240243 AGATTCACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (23 bp):
TGTACAGTTCATAACTATTTAGT
Found at i:240846 original size:34 final size:34
Alignment explanation
Indices: 240803--240873 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
240793 AGTTGCAACC
240803 TTTGTGAATAGAAAAGATCAGGTTAAGATACAAA
1 TTTGTGAATAGAAAAGATCAGGTTAAGATACAAA
*
240837 TTTGTGAATAGAAAAGATCATGTTAAGATACAAA
1 TTTGTGAATAGAAAAGATCAGGTTAAGATACAAA
240871 TTT
1 TTT
240874 CAAGCATGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (34 bp):
TTTGTGAATAGAAAAGATCAGGTTAAGATACAAA
Found at i:241913 original size:22 final size:21
Alignment explanation
Indices: 241860--241913 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
241850 AAATGACAAG
*
241860 AATTTAATTAATTTTAAATTTA
1 AATTTAATTAATATTAAA-TTA
* * *
241882 ATTTTGATTACTATTAAATTA
1 AATTTAATTAATATTAAATTA
241903 AATTCTAATTA
1 AATT-TAATTA
241914 GGTTAAATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (21 bp):
AATTTAATTAATATTAAATTA
Found at i:242201 original size:22 final size:22
Alignment explanation
Indices: 242176--242218 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
242166 GCCCCAATTA
242176 TTATTTAAAAATAAAAATATTT
1 TTATTTAAAAATAAAAATATTT
*
242198 TTATTTAAAAATATAAATATT
1 TTATTTAAAAATAAAAATATT
242219 AATATAAAGA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTATTTAAAAATAAAAATATTT
Found at i:242445 original size:30 final size:30
Alignment explanation
Indices: 242410--242484 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
242400 AAATTACGAG
242410 CTTATTTGAGTATAAATTAAAAGCTAAGAA
1 CTTATTTGAGTATAAATTAAAAGCTAAGAA
* * * * *
242440 TTTATTTGAATATTAATTAAAGGCTAAGAG
1 CTTATTTGAGTATAAATTAAAAGCTAAGAA
*
242470 CTTATTTGGGTATAA
1 CTTATTTGAGTATAA
242485 TAAAAATATA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (30 bp):
CTTATTTGAGTATAAATTAAAAGCTAAGAA
Found at i:242968 original size:12 final size:12
Alignment explanation
Indices: 242947--242997 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
242937 AAATTTGAGT
*
242947 AAAAGAAAAAATG
1 AAAAG-AAAAATA
*
242960 AAAAGAAAAACA
1 AAAAGAAAAATA
*
242972 AAAACAAAAATA
1 AAAAGAAAAATA
*
242984 AAAAGAGAAATA
1 AAAAGAAAAATA
242996 AA
1 AA
242998 TTATTAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 27 0.84
13 5 0.16
ACGTcount: A:0.80, C:0.04, G:0.10, T:0.06
Consensus pattern (12 bp):
AAAAGAAAAATA
Found at i:250809 original size:51 final size:51
Alignment explanation
Indices: 250752--250870 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
250742 TCATTTCTGA
* * * *
250752 GAGGATACTCCAACCCCGGTTTTTTTTCTAAAACACCAAATTTCCATAATC
1 GAGGATACTCCAACCCCGATTTTATTTCCAAAACACCAAATTTCCACAATC
* * * *
250803 GGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTTCACAATC
1 GAGGATACTCCAACCCCGATTTTATTTCCAAAACACCAAATTTCCACAATC
250854 GAGGATACTCCAACCCC
1 GAGGATACTCCAACCCC
250871 ATTATTTTCA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (51 bp):
GAGGATACTCCAACCCCGATTTTATTTCCAAAACACCAAATTTCCACAATC
Found at i:250933 original size:130 final size:130
Alignment explanation
Indices: 250791--251074 Score: 329
Period size: 130 Copynumber: 2.2 Consensus size: 130
250781 AAAACACCAA
* **
250791 ATTTC-CATAATCGGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTTCACAATCG
1 ATTTCTCATAATCGGGGATACTCCAACCCCGACCTTATTTCCAAAACACCAATTTTTCACAATCG
* **
250855 AGGATACTCCAACCCCATTATTTTCAAGGGGATACTCCAACCCCGACTGTATTTACAAAATATTG
66 AGGATACTCCAACCCCATTATTTTCAAGGGAATACTCCAACCCCGACTGTATTTACAAAATACCG
* * * ** * *
250920 ATTTCTCATAATCGGGGATACTTCAACCCCGGCCTTATTTCTAAATTATCGATTTTTCACAATCG
1 ATTTCTCATAATCGGGGATACTCCAACCCCGACCTTATTTCCAAAACACCAATTTTTCACAATCG
* * * ** * * * *
250985 GGGATACTCTAATCCTGTTATTTTCGAGGGAATACTCCAACCCCGATTTTATTTTCAAAATACCG
66 AGGATACTCCAACCCCATTATTTTCAAGGGAATACTCCAACCCCGACTGTATTTACAAAATACCG
**
251050 ATTT-TCTATAATTAGGGATACTCCA
1 ATTTCTC-ATAATCGGGGATACTCCA
251075 TCCCTGTTAT
Statistics
Matches: 128, Mismatches: 25, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
129 7 0.05
130 121 0.95
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (130 bp):
ATTTCTCATAATCGGGGATACTCCAACCCCGACCTTATTTCCAAAACACCAATTTTTCACAATCG
AGGATACTCCAACCCCATTATTTTCAAGGGAATACTCCAACCCCGACTGTATTTACAAAATACCG
Found at i:250939 original size:79 final size:79
Alignment explanation
Indices: 250803--250949 Score: 186
Period size: 79 Copynumber: 1.9 Consensus size: 79
250793 TTCCATAATC
* * * * *
250803 GGGGATACTCCAACCTCGATTTTATTTCCAAAACACCAATTTTTCACAATCGAGGATACTCCAAC
1 GGGGATACTCCAACCCCGACTGTATTTACAAAACACCAATTTCTCACAATCGAGGATACTCCAAC
250868 CCCATTATTTTCAA
66 CCCATTATTTTCAA
* *** * * *
250882 GGGGATACTCCAACCCCGACTGTATTTACAAAATATTGATTTCTCATAATCGGGGATACTTCAAC
1 GGGGATACTCCAACCCCGACTGTATTTACAAAACACCAATTTCTCACAATCGAGGATACTCCAAC
250947 CCC
66 CCC
250950 GGCCTTATTT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
79 56 1.00
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGACTGTATTTACAAAACACCAATTTCTCACAATCGAGGATACTCCAAC
CCCATTATTTTCAA
Found at i:250959 original size:51 final size:51
Alignment explanation
Indices: 250882--250993 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 51
250872 TTATTTTCAA
* *
250882 GGGGATACTCCAACCCCGACTGTATTTAC-AAAATATTGATTTCTCATAATC
1 GGGGATACTCCAACCCCGACTGTATTT-CTAAAATATCGATTTCTCACAATC
* * * *
250933 GGGGATACTTCAACCCCGGCCT-TATTTCTAAATTATCGATTTTTCACAATC
1 GGGGATACTCCAACCCC-GACTGTATTTCTAAAATATCGATTTCTCACAATC
250984 GGGGATACTC
1 GGGGATACTC
250994 TAATCCTGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
50 1 0.02
51 48 0.92
52 3 0.06
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGACTGTATTTCTAAAATATCGATTTCTCACAATC
Found at i:251164 original size:79 final size:79
Alignment explanation
Indices: 250970--251153 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 79
250960 CTAAATTATC
* * * *
250970 GATTTTTCACAATCGGGGATACTCTAATCCTGTTATTTTCGAGGGAATACTCCAACCCCGATTTT
1 GATTTTCCATAATCGGGGATACTCCAACCCTGTTATTTTCGAGGGAATACTCCAACCCCGATTTT
* *
251035 ATTTTCAAAATACC
66 ATTTTCAAAACACA
* ** * * *
251049 GATTTTCTATAATTAGGGATACTCCATCCCTGTTA-TTTCTGAGGGGATATTCCAACCCC-AGTT
1 GATTTTCCATAATCGGGGATACTCCAACCCTGTTATTTTC-GAGGGAATACTCCAACCCCGA-TT
*
251112 TTATTTTCAGAACACA
64 TTATTTTCAAAACACA
251128 GATTTTCCATAATCGGGGATACTCCA
1 GATTTTCCATAATCGGGGATACTCCA
251154 GCCCCATTAT
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
78 5 0.06
79 82 0.94
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.35
Consensus pattern (79 bp):
GATTTTCCATAATCGGGGATACTCCAACCCTGTTATTTTCGAGGGAATACTCCAACCCCGATTTT
ATTTTCAAAACACA
Found at i:252977 original size:34 final size:35
Alignment explanation
Indices: 252939--253005 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
252929 CCTTACAACA
252939 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
252973 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
253006 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:253528 original size:33 final size:32
Alignment explanation
Indices: 253489--253564 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 32
253479 ATAGATACAC
253489 TGTATCGATACATGAATAGTGATGAACAGTGA
1 TGTATCGATACATGAATAGTGATGAACAGTGA
*
253521 TTTTATCGATACATGAATAGTGATGAACAGTGA
1 -TGTATCGATACATGAATAGTGATGAACAGTGA
253554 TGTATCGATAC
1 TGTATCGATAC
253565 TATTCATAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 10 0.24
33 31 0.76
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATGAATAGTGATGAACAGTGA
Found at i:253556 original size:98 final size:94
Alignment explanation
Indices: 253439--253615 Score: 275
Period size: 98 Copynumber: 1.8 Consensus size: 94
253429 GCTTTTATTA
*
253439 AATAGTGTGAACAGTGATGTATCGATACTATTCATAATATATAGATACACTGTATC-GATACATG
1 AATAGTGTGAACAGTGATGTATCGATACTATTCATAATATATAGATACA-TG-AACAG-TA-ATG
253503 AATAGTGATGAACAGTGATTTTATCGATACATG
62 AATAGTGATGAACAGTGATTTTATCGATACATG
* *
253536 AATAGTGATGAACAGTGATGTATCGATACTATTCATAATATATCGATGCATGAACAGTAATGAAT
1 AATAGTG-TGAACAGTGATGTATCGATACTATTCATAATATATAGATACATGAACAGTAATGAAT
253601 AGTGATGAACAGTGA
65 AGTGATGAACAGTGA
253616 AAAATGAGAT
Statistics
Matches: 75, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
95 21 0.28
96 4 0.05
97 10 0.13
98 40 0.53
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (94 bp):
AATAGTGTGAACAGTGATGTATCGATACTATTCATAATATATAGATACATGAACAGTAATGAATA
GTGATGAACAGTGATTTTATCGATACATG
Found at i:257059 original size:17 final size:17
Alignment explanation
Indices: 257033--257067 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
257023 TTGCTGGAAT
257033 TGATCCGATAGAATAGA
1 TGATCCGATAGAATAGA
*
257050 TGATCTGATAGAATAGA
1 TGATCCGATAGAATAGA
257067 T
1 T
257068 AACCAAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (17 bp):
TGATCCGATAGAATAGA
Found at i:258595 original size:22 final size:22
Alignment explanation
Indices: 258552--258595 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
258542 CTTGTAGTGG
*
258552 TATAATTAAAAATAATATATTA
1 TATAATTAAAAATAATAAATTA
258574 TATAATTAAAAA-AATTAAATTA
1 TATAATTAAAAATAA-TAAATTA
258596 AGTTAAGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TATAATTAAAAATAATAAATTA
Found at i:262857 original size:16 final size:16
Alignment explanation
Indices: 262836--262868 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
262826 CCTTAATAGT
*
262836 AATAGCAGAGTGTGAG
1 AATAGCAAAGTGTGAG
262852 AATAGCAAAGTGTGAG
1 AATAGCAAAGTGTGAG
262868 A
1 A
262869 TATTTCAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.33, T:0.18
Consensus pattern (16 bp):
AATAGCAAAGTGTGAG
Found at i:265944 original size:30 final size:30
Alignment explanation
Indices: 265910--265980 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
265900 GATGTTTCAT
265910 GTATTTTAGA-GCCATTTTAATACATTTTAA
1 GTATTTTAGATG-CATTTTAATACATTTTAA
*
265940 GTATTTTAGATGCATTTTAATACCTTTTAA
1 GTATTTTAGATGCATTTTAATACATTTTAA
* *
265970 GCACTTTAGAT
1 GTATTTTAGAT
265981 TGTTTAGATC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 36 0.97
31 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (30 bp):
GTATTTTAGATGCATTTTAATACATTTTAA
Done.