Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold214
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: 1307275
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 88184 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:251608 original size:50 final size:50
Alignment explanation
Indices: 251568--251681 Score: 228
Period size: 50 Copynumber: 2.3 Consensus size: 50
251558 AACCCCTAAC
251568 CCCTAAACCTTAAATCCCAACCCTTAAACCATAATCCCTAAATTCATACT
1 CCCTAAACCTTAAATCCCAACCCTTAAACCATAATCCCTAAATTCATACT
251618 CCCTAAACCTTAAATCCCAACCCTTAAACCATAATCCCTAAATTCATACT
1 CCCTAAACCTTAAATCCCAACCCTTAAACCATAATCCCTAAATTCATACT
251668 CCCTAAACCTTAAA
1 CCCTAAACCTTAAA
251682 ATATGAACTC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (50 bp):
CCCTAAACCTTAAATCCCAACCCTTAAACCATAATCCCTAAATTCATACT
Found at i:252168 original size:41 final size:40
Alignment explanation
Indices: 251972--252281 Score: 200
Period size: 41 Copynumber: 7.8 Consensus size: 40
251962 TAAAAAGTTT
* * * * *
251972 TTAGCGGCGCTTATCCAAAAACACCACTAAAACAATGAGCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGC-CTGAGCA
* * * *
252013 TTAGCGACGCTTTCTCAAAAAAGGCCGCTAAAACACTGAGCA
1 TTAGCGGCGCTTT-TCCAAAAACGCCGCTAAAGC-CTGAGCA
* * * * *
252055 TTAGCAGC-ATTTTCTCAAAAATGCAGCTAAAACACTGAGCA
1 TTAGCGGCGCTTTTC-CAAAAACGCCGCTAAAGC-CTGAGCA
*
252096 TTAGCGGCGAATTTT-CAAAAACGCCGCTAAAGCCTGGAGCA
1 TTAGCGGCG-CTTTTCCAAAAACGCCGCTAAAGCCT-GAGCA
252137 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCT-AG--
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCTGAGCA
* * *
252174 --A-----G-TTCAT-GAAAAATGCCGCTAAAGCCCTGAGCA
1 TTAGCGGCGCTT-TTCCAAAAACGCCGCTAAAG-CCTGAGCA
* *
252207 TTAGCGGCGCTTTAT-AAAAAACGCCGCTAAAGCCCAGAGCA
1 TTAGCGGCGCTTT-TCCAAAAACGCCGCTAAAG-CCTGAGCA
* ** *
252248 TTAGCGACGCTTTTTAAAAAATGCCGCTAAAGCC
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCC
252282 CCGAAAGATA
Statistics
Matches: 221, Mismatches: 27, Indels: 43
0.76 0.09 0.15
Matches are distributed among these distances:
29 17 0.08
30 5 0.02
31 2 0.01
35 2 0.01
39 2 0.01
40 12 0.05
41 147 0.67
42 29 0.13
43 5 0.02
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (40 bp):
TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCTGAGCA
Found at i:252195 original size:70 final size:70
Alignment explanation
Indices: 252112--252245 Score: 209
Period size: 70 Copynumber: 1.9 Consensus size: 70
252102 GCGAATTTTC
* *
252112 AAAAACGCCGCTAAAG-CCTGGAGCATTAGCGGCGCTTT-TCCAAAAACGCCGCTAAAGCCTAGA
1 AAAAACGCCGCTAAAGCCCT-GAGCATTAGCGGCGCTTTAT-AAAAAACGCCGCTAAAGCCCAGA
252175 GTTCATG
64 GTTCATG
*
252182 AAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATAAAAAACGCCGCTAAAGCCCAGAG
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATAAAAAACGCCGCTAAAGCCCAGAG
252246 CATTAGCGAC
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
70 55 0.93
71 4 0.07
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (70 bp):
AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTATAAAAAACGCCGCTAAAGCCCAGAGT
TCATG
Found at i:252268 original size:111 final size:111
Alignment explanation
Indices: 252071--252281 Score: 307
Period size: 111 Copynumber: 1.9 Consensus size: 111
252061 GCATTTTCTC
* **
252071 AAAAATGCAGCTAAAACACTGAGCATTAGCGGCGAATTTTCAAAAACGCCGCTAAAGCCTGGAGC
1 AAAAATGCAGCTAAAACACTGAGCATTAGCGGCGAATTTTAAAAAACGCCGCTAAAGCCCAGAGC
* *
252136 ATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCTAGAGTTCATG
66 ATTAGCGACGCTTTTCAAAAAACGCCGCTAAAGCCTAGAGTTCATG
* * * *
252182 AAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCG-CTTTATAAAAAACGCCGCTAAAGCCCAGAG
1 AAAAATGCAGCTAAAACACTGAGCATTAGCGGCGAATTT-TAAAAAACGCCGCTAAAGCCCAGAG
* *
252246 CATTAGCGACGCTTTTTAAAAAATGCCGCTAAAGCC
65 CATTAGCGACGCTTTTCAAAAAACGCCGCTAAAGCC
252282 CCGAAAGATA
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
110 3 0.03
111 85 0.97
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (111 bp):
AAAAATGCAGCTAAAACACTGAGCATTAGCGGCGAATTTTAAAAAACGCCGCTAAAGCCCAGAGC
ATTAGCGACGCTTTTCAAAAAACGCCGCTAAAGCCTAGAGTTCATG
Found at i:256234 original size:26 final size:26
Alignment explanation
Indices: 256176--256227 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
256166 GGAAAAGGGT
* **
256176 TTCTTTAGTCAAAACATGCAAGGGTA
1 TTCTTTAGTCAAAACACGCAAGACTA
*
256202 TTCTTTAGTCAAAACACGCTAGACTA
1 TTCTTTAGTCAAAACACGCAAGACTA
256228 ATTTTTAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (26 bp):
TTCTTTAGTCAAAACACGCAAGACTA
Found at i:259521 original size:106 final size:107
Alignment explanation
Indices: 259336--259548 Score: 419
Period size: 106 Copynumber: 2.0 Consensus size: 107
259326 AATGTTTATG
259336 AGTTGTAGTTTATATTTCTAGATTCCTTATTGAGTCTATTTTCTTTAAAAACAAGTGAAAACACC
1 AGTTGTAGTTTATATTTCTAGATTCCTTATTGAGTCTATTTTCTTTAAAAACAAGTGAAAACACC
259401 ATATGAACATTCTACAATGAGAAAGCTTA-TTTTAGTGACAA
66 ATATGAACATTCTACAATGAGAAAGCTTATTTTTAGTGACAA
259442 AGTTGTAGTTTATATTTCTAGATTCCTTATTGAGTCTATTTTCTTTAAAAACAAGTGAAAACACC
1 AGTTGTAGTTTATATTTCTAGATTCCTTATTGAGTCTATTTTCTTTAAAAACAAGTGAAAACACC
259507 ATATGAACATTCTACAATGAGAAAGCTTATTTTTAGTGACAA
66 ATATGAACATTCTACAATGAGAAAGCTTATTTTTAGTGACAA
259549 GAGGTCAGGA
Statistics
Matches: 106, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
106 94 0.89
107 12 0.11
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (107 bp):
AGTTGTAGTTTATATTTCTAGATTCCTTATTGAGTCTATTTTCTTTAAAAACAAGTGAAAACACC
ATATGAACATTCTACAATGAGAAAGCTTATTTTTAGTGACAA
Found at i:269569 original size:20 final size:20
Alignment explanation
Indices: 269534--269582 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
269524 ATCATGGTCT
*
269534 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTGTTTACTTAC
269553 TCT-CTTACTTGTTTACTTAC
1 T-TGCTTACTTGTTTACTTAC
269573 TTGCTTACTT
1 TTGCTTACTT
269583 AAATAACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTGTTTACTTAC
Found at i:278189 original size:6 final size:6
Alignment explanation
Indices: 278174--278213 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
278164 TTCTTGTTTC
278174 TTTTTA -TTTTA TTTTTA TTTTTA TTTTTA TTTATTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA TTTT
278214 CGTATTCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.16
6 21 0.66
7 6 0.19
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:278678 original size:298 final size:305
Alignment explanation
Indices: 278130--278740 Score: 932
Period size: 298 Copynumber: 2.0 Consensus size: 305
278120 TTTGGGAATG
*
278130 TAACTGAAAGATACTATGATTATTTTGGATTTGGTTCTTGTTTCTTTTTATTTTATTTTTATTTT
1 TAACTGAAAGATACTATGATTATTTTGGATTTGGTTCTTCTTTCTTTTTATTTTATTTTTA-TTT
* * *
278195 TATTTTTATTTATTATTTTCGTATTCTTTTATTTTTGTGTGTTTGTTTTCTTGTCTATGTAGGTC
65 TA--TTTATTTATCATTATCG--TTCTTTTATTTTTGTGTGTTTGTTTTCTTGTCTATGTAGGCC
* ** * **
278260 ACCCACTCAAGGATTGTACTATACTTTCGAGCTTTAACGGAGAGGAGGACTACTTCAATCTACCT
126 ACCCACTCAAGGATTGTACTACACTTTCGAGCTTTAACAAAGAGGAGCACTACTAAAATCTACCT
* *
278325 CATGTTGCTTCAAGAAAAATGGGGGAGTTTGAAACTCTTAGCTTTACATTGGGAGCACATTAGGG
191 CATGTTGCTGCAAGAAAAATGGGGGAGTTTGAAACTCTTAGCTTTACATTGGGAGCACACTAGGG
* * * * *
278390 ACAATTGATTTGTCGTATTTCTATACGTCAAATTAAGTTCTTTTGATACT
256 AAAATTGATCTGTCGTAATTATATACGTCAAAATAAGTTCTTTTGATACT
*
278440 TAACTGAAAGATACTATGATTATTTTGGATTTGGTTCTTCTTTCTTTTTCTTTTATTTTTA-TTT
1 TAACTGAAAGATACTATGATTATTTTGGATTTGGTTCTTCTTTCTTTTTATTTTATTTTTATTTT
*
278504 A-TTATTT-TCA-TAT-G-T-TTTTATTTTTGTGTGTTTGTTTTCTTTTCTATGTAGGCCACCCA
66 ATTTATTTATCATTATCGTTCTTTTATTTTTGTGTGTTTGTTTTCTTGTCTATGTAGGCCACCCA
278563 CTCAAGGATTGTACTACACTTTCGAGCTTTAACAAAGAGGAGCACTACTAAAATCTACCTCATGT
131 CTCAAGGATTGTACTACACTTTCGAGCTTTAACAAAGAGGAGCACTACTAAAATCTACCTCATGT
*
278628 TGCTGCAAGAAAAATGGGGGAGTTCT-AAACTCTTAGCTTTACATTGGGAGCACACTGGGGAAAA
196 TGCTGCAAGAAAAATGGGGGAGTT-TGAAACTCTTAGCTTTACATTGGGAGCACACTAGGGAAAA
278692 TTGATCTGTCGTAATTATATACGTCAAAATAAGTTCTTTTGATACT
260 TTGATCTGTCGTAATTATATACGTCAAAATAAGTTCTTTTGATACT
278738 TAA
1 TAA
278741 AGAGCTTTGT
Statistics
Matches: 280, Mismatches: 20, Indels: 14
0.89 0.06 0.04
Matches are distributed among these distances:
298 204 0.73
299 2 0.01
302 1 0.00
303 2 0.01
304 2 0.01
305 6 0.02
308 4 0.01
310 59 0.21
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (305 bp):
TAACTGAAAGATACTATGATTATTTTGGATTTGGTTCTTCTTTCTTTTTATTTTATTTTTATTTT
ATTTATTTATCATTATCGTTCTTTTATTTTTGTGTGTTTGTTTTCTTGTCTATGTAGGCCACCCA
CTCAAGGATTGTACTACACTTTCGAGCTTTAACAAAGAGGAGCACTACTAAAATCTACCTCATGT
TGCTGCAAGAAAAATGGGGGAGTTTGAAACTCTTAGCTTTACATTGGGAGCACACTAGGGAAAAT
TGATCTGTCGTAATTATATACGTCAAAATAAGTTCTTTTGATACT
Found at i:280429 original size:12 final size:12
Alignment explanation
Indices: 280414--280439 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
280404 TTAAACCTTT
280414 CTTTAAGTTTTA
1 CTTTAAGTTTTA
280426 CTTTAAGTTTTA
1 CTTTAAGTTTTA
280438 CT
1 CT
280440 ACATAGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.58
Consensus pattern (12 bp):
CTTTAAGTTTTA
Found at i:294603 original size:18 final size:19
Alignment explanation
Indices: 294580--294616 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
294570 TTTCTTAAGC
*
294580 AATAAAAATAATA-ATTAA
1 AATAAAAAGAATATATTAA
294598 AATAAAAAGAATATATTAA
1 AATAAAAAGAATATATTAA
294617 GTAAAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (19 bp):
AATAAAAAGAATATATTAA
Found at i:300936 original size:35 final size:35
Alignment explanation
Indices: 300852--301002 Score: 142
Period size: 35 Copynumber: 4.3 Consensus size: 35
300842 AATCCAACCA
* * * * *
300852 AAACACACTAGATGCTCATAAGATCCAATCCATCC-
1 AAACACACCA-ATGCTCGTAAGAGCTAATCCCTCCG
**
300887 AAACACACCAATGCTCGTAAGAGCTAATCCCTCTT
1 AAACACACCAATGCTCGTAAGAGCTAATCCCTCCG
* * *
300922 AAGCACACCAATGCTCATAAGAGCTAATCCTTCCG
1 AAACACACCAATGCTCGTAAGAGCTAATCCCTCCG
* * * ** *
300957 AAACACATCAGTGCTCGTAAGAGCTAGTCCAACTG
1 AAACACACCAATGCTCGTAAGAGCTAATCCCTCCG
300992 AAACACACCAA
1 AAACACACCAA
301003 AACATAGAGT
Statistics
Matches: 94, Mismatches: 21, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
34 19 0.20
35 75 0.80
ACGTcount: A:0.38, C:0.30, G:0.13, T:0.19
Consensus pattern (35 bp):
AAACACACCAATGCTCGTAAGAGCTAATCCCTCCG
Found at i:300999 original size:70 final size:69
Alignment explanation
Indices: 300842--301002 Score: 187
Period size: 70 Copynumber: 2.3 Consensus size: 69
300832 GTACATCGAC
** * *
300842 AATCCAACCAAAACACACTAGATGCTCATAAGATCCAATCCATCCAAACACACCAATGCTCGTAA
1 AATCCAACTGAAACACACCA-ATGCTCATAAGAGCCAATCCATCCAAACACACCAATGCTCGTAA
300907 GAGCT
65 GAGCT
** * * * * * *
300912 AATCCCTCTTAAGCACACCAATGCTCATAAGAGCTAATCCTTCCGAAACACATCAGTGCTCGTAA
1 AATCCAACTGAAACACACCAATGCTCATAAGAGCCAATCCATCC-AAACACACCAATGCTCGTAA
300977 GAGCT
65 GAGCT
*
300982 AGTCCAACTGAAACACACCAA
1 AATCCAACTGAAACACACCAA
301003 AACATAGAGT
Statistics
Matches: 74, Mismatches: 16, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
69 21 0.28
70 53 0.72
ACGTcount: A:0.39, C:0.31, G:0.12, T:0.19
Consensus pattern (69 bp):
AATCCAACTGAAACACACCAATGCTCATAAGAGCCAATCCATCCAAACACACCAATGCTCGTAAG
AGCT
Found at i:317457 original size:12 final size:12
Alignment explanation
Indices: 317440--317469 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
317430 CATTACATGC
317440 CTGTGTGCTAGG
1 CTGTGTGCTAGG
317452 CTGTGTGCTAGG
1 CTGTGTGCTAGG
*
317464 CCGTGT
1 CTGTGT
317470 AACAGTCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.20, G:0.40, T:0.33
Consensus pattern (12 bp):
CTGTGTGCTAGG
Found at i:318532 original size:31 final size:30
Alignment explanation
Indices: 318476--318534 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
318466 TCAAGTTCCG
*
318476 ATATACATGTAACATCTATATCATGTATCT
1 ATATACATGTAAAATCTATATCATGTATCT
*
318506 ATATATCATGTAAAAT-TATTTCCATGTAT
1 ATATA-CATGTAAAATCTATAT-CATGTAT
318535 TTCATGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (30 bp):
ATATACATGTAAAATCTATATCATGTATCT
Found at i:337593 original size:3 final size:3
Alignment explanation
Indices: 337585--337634 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
337575 AGGTCGGATA
*
337585 ATG ATG ATG GTG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
337633 AT
1 AT
337635 AAAGAGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:338488 original size:87 final size:86
Alignment explanation
Indices: 338384--338549 Score: 253
Period size: 87 Copynumber: 1.9 Consensus size: 86
338374 AGTTTAAATT
* * *
338384 CGGTGAATTATTCAAGTCCGTCTCAATAGGACTACCCAAATTCTAGGATATGAACTCATTAAGAT
1 CGGTGAATTATTCAAGTCCATCTCAATAGGACCACCCAAATTCTAGGATATGAACTCATTAAGAG
*
338449 TAAGAAACTCAACCTAACATGC
66 TAAG-AACCCAACCTAACATGC
* *
338471 CGGTGAATTCA-TCAAGTCCATCTCAATAGGACCACCCAAATTCTGGGATATGAATTCATTAAGA
1 CGGTGAATT-ATTCAAGTCCATCTCAATAGGACCACCCAAATTCTAGGATATGAACTCATTAAGA
338535 GTAAGAACCCAACCT
65 GTAAGAACCCAACCT
338550 TATTCGTGTA
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
86 9 0.12
87 62 0.86
88 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (86 bp):
CGGTGAATTATTCAAGTCCATCTCAATAGGACCACCCAAATTCTAGGATATGAACTCATTAAGAG
TAAGAACCCAACCTAACATGC
Found at i:345211 original size:24 final size:24
Alignment explanation
Indices: 345179--345231 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
345169 ATGTTTTCCG
345179 TAATGGAGTTTTGTATGCTATCCC
1 TAATGGAGTTTTGTATGCTATCCC
*
345203 TAATGGAGTTTTGTATGCTATCCG
1 TAATGGAGTTTTGTATGCTATCCC
345227 TAATG
1 TAATG
345232 CCCATAAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.42
Consensus pattern (24 bp):
TAATGGAGTTTTGTATGCTATCCC
Found at i:350318 original size:16 final size:17
Alignment explanation
Indices: 350299--350332 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
350289 AAATACTATG
350299 AAATAAAAAT-AAACAA
1 AAATAAAAATCAAACAA
*
350315 AAATAAACATCAAACAA
1 AAATAAAAATCAAACAA
350332 A
1 A
350333 CGCCATCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (17 bp):
AAATAAAAATCAAACAA
Found at i:355815 original size:20 final size:20
Alignment explanation
Indices: 355767--355816 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
355757 TATGGAATGA
* *
355767 TTATGCAAAAACATGAATCT
1 TTATGCAACAACATGAACCT
* *
355787 ATATGCAACGACATGAACCT
1 TTATGCAACAACATGAACCT
355807 TTATGCAACA
1 TTATGCAACA
355817 CTATTTAGAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (20 bp):
TTATGCAACAACATGAACCT
Found at i:373617 original size:3 final size:3
Alignment explanation
Indices: 373609--373645 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
373599 AAGAGACCAA
*
373609 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
373646 CCTTTCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:385914 original size:22 final size:22
Alignment explanation
Indices: 385889--385948 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
385879 TTTGAACCAT
385889 TACCAATTCGTACCAAATTCC-A
1 TACCAATTCGTACC-AATTCCAA
*
385911 TACCATTTCGTACCAATTCCTAAA
1 TACCAATTCGTACCAATTCC--AA
*
385935 TACCAAATCGTACC
1 TACCAATTCGTACC
385949 TAAACCAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 6 0.19
22 13 0.41
24 13 0.41
ACGTcount: A:0.35, C:0.32, G:0.05, T:0.28
Consensus pattern (22 bp):
TACCAATTCGTACCAATTCCAA
Found at i:393102 original size:71 final size:71
Alignment explanation
Indices: 392986--393128 Score: 234
Period size: 71 Copynumber: 2.0 Consensus size: 71
392976 TTTTACAGCT
*
392986 TCGCTAATTTTTCAGTTAGAAAATTTTAAATAATATACATTTTATATTTATATTATGCTATTTTG
1 TCGCTAATTTTCCAGTTAGAAAATTTTAAATAATATACATTTTATATTTATATTATGCTATTTTG
393051 ATTTCA
66 ATTTCA
** *
393057 TCGCTAATTATTCCA-TTAGAATTTTTTAAATTATATACATTTTATATTTATATTATGCTATTTT
1 TCGCTAATT-TTCCAGTTAGAAAATTTTAAATAATATACATTTTATATTTATATTATGCTATTTT
393121 GATTTCA
65 GATTTCA
393128 T
1 T
393129 ATTACAATTA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 63 0.94
72 4 0.06
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.52
Consensus pattern (71 bp):
TCGCTAATTTTCCAGTTAGAAAATTTTAAATAATATACATTTTATATTTATATTATGCTATTTTG
ATTTCA
Found at i:393681 original size:20 final size:20
Alignment explanation
Indices: 393631--393682 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
393621 AGTAGCCACG
* *
393631 TGACTAAAAACATGTTGTAA
1 TGACTAAAAACATGCTATAA
393651 TGAACCTAAAAACATGCTATAA
1 TG-A-CTAAAAACATGCTATAA
393673 TGACTAAAAA
1 TGACTAAAAA
393683 TATGAAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 9 0.32
21 2 0.07
22 17 0.61
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (20 bp):
TGACTAAAAACATGCTATAA
Found at i:393979 original size:14 final size:14
Alignment explanation
Indices: 393960--393987 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
393950 AAAAACTTAA
393960 CTTGATTGAGCTTG
1 CTTGATTGAGCTTG
393974 CTTGATTGAGCTTG
1 CTTGATTGAGCTTG
393988 TTTACTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (14 bp):
CTTGATTGAGCTTG
Found at i:394681 original size:11 final size:12
Alignment explanation
Indices: 394658--394687 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
394648 AAGTAAATAG
394658 ATATTATATAAA
1 ATATTATATAAA
394670 ATATTA-ATAAA
1 ATATTATATAAA
394681 ATATTAT
1 ATATTAT
394688 TTTTATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATTATATAAA
Found at i:395930 original size:20 final size:20
Alignment explanation
Indices: 395905--395942 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
395895 TTATAAATCA
395905 TAAAAATAGAAATCCAAAAT
1 TAAAAATAGAAATCCAAAAT
*
395925 TAAAAATATAAATCCAAA
1 TAAAAATAGAAATCCAAA
395943 GAGGCCATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.21
Consensus pattern (20 bp):
TAAAAATAGAAATCCAAAAT
Found at i:413909 original size:8 final size:8
Alignment explanation
Indices: 413896--413924 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
413886 GTATAGTAAA
413896 AAAAATAT
1 AAAAATAT
413904 AAAAATAT
1 AAAAATAT
413912 AAAAATAT
1 AAAAATAT
413920 AAAAA
1 AAAAA
413925 GAATGGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATAT
Found at i:414308 original size:9 final size:9
Alignment explanation
Indices: 414294--414323 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
414284 TGTTTAAAAC
414294 AATAAAGAA
1 AATAAAGAA
414303 AATAAAGAA
1 AATAAAGAA
414312 AATAAAGGAA
1 AATAAA-GAA
414322 AA
1 AA
414324 AATATTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 15 0.75
10 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (9 bp):
AATAAAGAA
Found at i:420894 original size:22 final size:24
Alignment explanation
Indices: 420869--420913 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
420859 AAAGCAGGAA
*
420869 GCTTGAATCAACA-AT-CTTATTT
1 GCTTCAATCAACACATACTTATTT
*
420891 GCTTCCATCAACACATACTTATT
1 GCTTCAATCAACACATACTTATT
420914 AACTTATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (24 bp):
GCTTCAATCAACACATACTTATTT
Found at i:423388 original size:16 final size:18
Alignment explanation
Indices: 423362--423395 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
423352 TTAAAATCGG
423362 GTTGAGAAAATT-ATTTA
1 GTTGAGAAAATTAATTTA
423379 GTTG-GAAAATTAATTTA
1 GTTGAGAAAATTAATTTA
423396 TTTAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (18 bp):
GTTGAGAAAATTAATTTA
Found at i:433545 original size:25 final size:24
Alignment explanation
Indices: 433506--433597 Score: 103
Period size: 25 Copynumber: 3.7 Consensus size: 24
433496 TCATGTATAT
* *
433506 GTATGCTCATACGAGCTATGAATTG
1 GTATGCTCACACGAGCTAT-AATCG
* *
433531 GTATGCTCACTCGAGCTGTAGATCG
1 GTATGCTCACACGAGCTATA-ATCG
* *
433556 GTATGCTCTCACGAGCTATAAATCA
1 GTATGCTCACACGAGCTAT-AATCG
433581 GTATGCTCACACGAGCT
1 GTATGCTCACACGAGCT
433598 GTGGGTCGGA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
24 1 0.02
25 54 0.96
26 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (24 bp):
GTATGCTCACACGAGCTATAATCG
Found at i:436345 original size:15 final size:16
Alignment explanation
Indices: 436325--436354 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
436315 TAATAACTAA
436325 TATATAAT-TATATTT
1 TATATAATATATATTT
436340 TATATAATATATATT
1 TATATAATATATATT
436355 AATTGTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:443320 original size:23 final size:23
Alignment explanation
Indices: 443273--443341 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 23
443263 TCTAATGTTC
443273 TTTTCAC-TTTCTTTTTCTGATT-T
1 TTTTCACTTTTCTTTTTCT--TTCT
443296 TTTTCACTTTTCTTTTT-TTTCT
1 TTTTCACTTTTCTTTTTCTTTCT
443318 TTTTCATTCTTTTCTTTTTCTTTC
1 TTTTCA--CTTTTCTTTTTCTTTC
443342 ATTTGAGTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
21 2 0.05
22 7 0.17
23 8 0.20
24 20 0.49
25 4 0.10
ACGTcount: A:0.06, C:0.19, G:0.01, T:0.74
Consensus pattern (23 bp):
TTTTCACTTTTCTTTTTCTTTCT
Found at i:443327 original size:19 final size:19
Alignment explanation
Indices: 443305--443344 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
443295 TTTTTCACTT
*
443305 TTCTTTT-TTTTCTTTTTCA
1 TTCTTTTCTTTT-TCTTTCA
443324 TTCTTTTCTTTTTCTTTCA
1 TTCTTTTCTTTTTCTTTCA
443343 TT
1 TT
443345 TGAGTGATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (19 bp):
TTCTTTTCTTTTTCTTTCA
Found at i:459861 original size:25 final size:25
Alignment explanation
Indices: 459797--459863 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
459787 TTACGGATAC
* * * *
459797 TCAGCTCGTATGAGCGTACCGTTAT
1 TCAGCTCGAAAGAGCTTACCATTAT
*
459822 TCAGCTCAAAAGAGCTTACCATTAT
1 TCAGCTCGAAAGAGCTTACCATTAT
* *
459847 TCAGCTCGGAGGAGCTT
1 TCAGCTCGAAAGAGCTT
459864 GCAGTTTACA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (25 bp):
TCAGCTCGAAAGAGCTTACCATTAT
Found at i:466983 original size:8 final size:8
Alignment explanation
Indices: 466969--466999 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
466959 AATTAGGGAT
466969 TAAATTGA
1 TAAATTGA
*
466977 AAAATTGA
1 TAAATTGA
466985 TAAATTGA
1 TAAATTGA
466993 TAAATTG
1 TAAATTG
467000 TGTGGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (8 bp):
TAAATTGA
Found at i:467527 original size:25 final size:25
Alignment explanation
Indices: 467469--467560 Score: 89
Period size: 25 Copynumber: 3.7 Consensus size: 25
467459 GTTATTAGGG
* * * *
467469 TTACCGAT-TTCAGCTCTTATAAGC
1 TTACCGATACTCAGCTCATATGAGA
* *
467493 TTACCGATACTCATCTCGTATGAGA
1 TTACCGATACTCAGCTCATATGAGA
*
467518 TTACCGATACTCAGCTCATATGAGC
1 TTACCGATACTCAGCTCATATGAGA
*
467543 TTACC-ATTATTCAGCTCA
1 TTACCGA-TACTCAGCTCA
467561 GAGGAGCTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.16
25 48 0.84
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (25 bp):
TTACCGATACTCAGCTCATATGAGA
Found at i:467567 original size:25 final size:25
Alignment explanation
Indices: 467528--467595 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
467518 TTACCGATAC
* *
467528 TCAGCTCATATGAGCTTACCATTAT
1 TCAGCTCAGAGGAGCTTACCATTAT
467553 TCAGCTCAGAGGAGCTTACCATTAT
1 TCAGCTCAGAGGAGCTTACCATTAT
* * *
467578 GCATCTCGGAGGAGCTTA
1 TCAGCTCAGAGGAGCTTA
467596 TCGTTTACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (25 bp):
TCAGCTCAGAGGAGCTTACCATTAT
Found at i:472301 original size:50 final size:50
Alignment explanation
Indices: 472209--472343 Score: 171
Period size: 50 Copynumber: 2.7 Consensus size: 50
472199 TCCTGTACTA
* * * * ***
472209 CCAATGTCATATCCCTGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCACTCATATCGGTG
* * * *
472259 CCCATGCTATGTCCCAGACATGGTCTTACAGGGGACCACTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCACTCATATCGGTG
472309 CCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGA
472344 TCTCATCCCC
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.27
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCACTCATATCGGTG
Found at i:476444 original size:13 final size:13
Alignment explanation
Indices: 476428--476453 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
476418 GAAATAATTT
476428 TTTGAAAATTTAG
1 TTTGAAAATTTAG
476441 TTTGAAAATTTAG
1 TTTGAAAATTTAG
476454 ACGTTTGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TTTGAAAATTTAG
Found at i:477521 original size:45 final size:45
Alignment explanation
Indices: 477448--477629 Score: 215
Period size: 45 Copynumber: 4.1 Consensus size: 45
477438 TACTACGTGT
*
477448 ACCGAGTATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAATATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
* ** * * *
477493 ATCGGGTACCATTGATTATAAAGGTGGTTGCTATGTGCTCACTCC
1 ACCGAATATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
* ** * *
477538 ACCGAAAATCATTGAAAATAAAGGTGGTTGCTATATACTGATTCC
1 ACCGAATATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
* * *
477583 ACCGAATATAATTGATTATAAGGGTGG-TGCTATGTGATGA-TCC
1 ACCGAATATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
477626 ACCG
1 ACCG
477630 TGTAACGGTT
Statistics
Matches: 113, Mismatches: 24, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
43 7 0.06
44 10 0.09
45 96 0.85
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (45 bp):
ACCGAATATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCC
Found at i:481167 original size:88 final size:88
Alignment explanation
Indices: 481018--481193 Score: 343
Period size: 88 Copynumber: 2.0 Consensus size: 88
481008 CGATCGTCGG
481018 GTCTAGATCTTAAGTATTACTTCACAAACTTAGAAAATTTTTAAAACAATCAACAGTTATTATTT
1 GTCTAGATCTTAAGTATTACTTCACAAACTTAGAAAATTTTTAAAACAATCAACAGTTATTATTT
481083 ACTTAAAACATTTTTCTTATTAA
66 ACTTAAAACATTTTTCTTATTAA
*
481106 GTCTAGATCTTAAGTATTACTTCACAAACTTAGAAAATTTTTAAAACAATCAACATTTATTATTT
1 GTCTAGATCTTAAGTATTACTTCACAAACTTAGAAAATTTTTAAAACAATCAACAGTTATTATTT
481171 ACTTAAAACATTTTTCTTATTAA
66 ACTTAAAACATTTTTCTTATTAA
481194 TTTATTTAAA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.41
Consensus pattern (88 bp):
GTCTAGATCTTAAGTATTACTTCACAAACTTAGAAAATTTTTAAAACAATCAACAGTTATTATTT
ACTTAAAACATTTTTCTTATTAA
Found at i:483671 original size:26 final size:26
Alignment explanation
Indices: 483635--483734 Score: 101
Period size: 27 Copynumber: 3.8 Consensus size: 26
483625 TGGTGTGACA
* *
483635 TTTACTGTCCCAGCGGACTACCCTTG
1 TTTAATGTCCCATCGGACTACCCTTG
* * *
483661 TTTAACGTCCCATCAGACTATCCCTAG
1 TTTAATGTCCCATCGGACTA-CCCTTG
* *
483688 TTTAATGTCTCATCGGACTATCCTGTG
1 TTTAATGTCCCATCGGACTACCCT-TG
* *
483715 TTTAATGTCCTATTGGACTA
1 TTTAATGTCCCATCGGACTA
483735 ACTATGATGC
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
26 19 0.32
27 40 0.68
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (26 bp):
TTTAATGTCCCATCGGACTACCCTTG
Found at i:485443 original size:35 final size:35
Alignment explanation
Indices: 485397--485467 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
485387 TTAGGGATCA
*
485397 CTTTGCATTTATTTTATTTAATTTAATTTAGCAAT
1 CTTTACATTTATTTTATTTAATTTAATTTAGCAAT
* *
485432 CTTTACATTTATTTTATTTTATTTTATTTAGCAAT
1 CTTTACATTTATTTTATTTAATTTAATTTAGCAAT
485467 C
1 C
485468 AGTCACTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.27, C:0.10, G:0.04, T:0.59
Consensus pattern (35 bp):
CTTTACATTTATTTTATTTAATTTAATTTAGCAAT
Found at i:485804 original size:45 final size:43
Alignment explanation
Indices: 485694--485825 Score: 147
Period size: 45 Copynumber: 2.9 Consensus size: 43
485684 GCTATCAAAG
* * *
485694 GATGTCATAGCATCTTTCAGCGATAGTCTTAGTCATGTTTCTATCAT
1 GATGTCATA-CATCTTTCAGCTATGGTCTTACTCA--TTT-TATCAT
*
485741 GATGCCATAACATCTTTCAGCTATGGTCTTACTCATCTTTATCAT
1 GATGTCAT-ACATCTTTCAGCTATGGTCTTACTCAT-TTTATCAT
* *
485786 GATGTCATGACATTTTTCAACTATGGTCTTACTCATTTTA
1 GATGTCAT-ACATCTTTCAGCTATGGTCTTACTCATTTTA
485826 AGCGATAGCC
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
44 4 0.05
45 39 0.52
46 2 0.03
47 29 0.39
48 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (43 bp):
GATGTCATACATCTTTCAGCTATGGTCTTACTCATTTTATCAT
Found at i:489239 original size:18 final size:17
Alignment explanation
Indices: 489214--489261 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
489204 CTTTTCTTTC
489214 ATAA-ATTATTTTTAATA
1 ATAATATTATTTTTAA-A
489231 ATAATATTA-TTTTAAA
1 ATAATATTATTTTTAAA
489247 A-AATATTAATTTTTA
1 ATAATATT-ATTTTTA
489262 GAGTGGTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 6 0.21
16 3 0.11
17 15 0.54
18 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATAATATTATTTTTAAA
Found at i:494564 original size:19 final size:19
Alignment explanation
Indices: 494540--494578 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
494530 TATCATCTCC
*
494540 ATAATGACTGTATAGGCAA
1 ATAATGACTATATAGGCAA
494559 ATAATGACTATATAGGCAA
1 ATAATGACTATATAGGCAA
494578 A
1 A
494579 ATATGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (19 bp):
ATAATGACTATATAGGCAA
Found at i:498484 original size:3 final size:3
Alignment explanation
Indices: 498478--498563 Score: 52
Period size: 3 Copynumber: 28.7 Consensus size: 3
498468 TATTCAATAA
* * **
498478 TAT TAT TAT TAAT CTAT TAT TAT TAA T-T TAT TAT TAT TAT CAT CGT
1 TAT TAT TAT T-AT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
498524 TAT TAC TACT GA- TAT TAT TAT TAA TAT TGT TAT TA- TAT TA
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
498564 ATTTATATAT
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
2 4 0.06
3 53 0.84
4 5 0.08
5 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:498497 original size:14 final size:14
Alignment explanation
Indices: 498478--498516 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
498468 TATTCAATAA
498478 TATTATTATTAATC
1 TATTATTATTAATC
*
498492 TATTATTATTAATT
1 TATTATTATTAATC
498506 TATTATTATTA
1 TATTATTATTA
498517 TCATCGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTATTATTAATC
Found at i:498500 original size:17 final size:17
Alignment explanation
Indices: 498478--498517 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
498468 TATTCAATAA
498478 TATTATT-ATTAATCTAT
1 TATTATTAATTAAT-TAT
*
498495 TATTATTAATTTATTAT
1 TATTATTAATTAATTAT
498512 TATTAT
1 TATTAT
498518 CATCGTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATTAATTAATTAT
Found at i:498508 original size:11 final size:12
Alignment explanation
Indices: 498475--498563 Score: 54
Period size: 14 Copynumber: 6.7 Consensus size: 12
498465 TACTATTCAA
498475 TAATATTATTAT
1 TAATATTATTAT
498487 TAATCTATTATTAT
1 TAA--TATTATTAT
498501 TAATTTATTATTAT
1 TAA--TATTATTAT
*
498515 TATCATCGTTATTACT
1 TA--AT-ATTATTA-T
*
498531 ACTGATATTATTAT
1 --TAATATTATTAT
*
498545 TAATATTGTTAT
1 TAATATTATTAT
498557 T-ATATTA
1 TAATATTA
498564 ATTTATATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
11 5 0.08
12 14 0.23
14 26 0.42
15 12 0.19
16 4 0.06
18 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (12 bp):
TAATATTATTAT
Found at i:498578 original size:30 final size:31
Alignment explanation
Indices: 498492--498579 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 31
498482 ATTATTAATC
* *
498492 TATTATTATTAATTTATTATTATTATCATCGT
1 TATTACTATTAATTTATTATT-TAATCATCGT
* * *
498524 TATTACTACTGATATTATTA-TTAAT-ATTGT
1 TATTACTATTAAT-TTATTATTTAATCATCGT
498554 TATTA-TATTAATTTATATATTTAATC
1 TATTACTATTAATTTAT-TATTTAATC
498580 GCCATTATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.09
29 7 0.16
30 14 0.31
31 3 0.07
32 11 0.24
33 6 0.13
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (31 bp):
TATTACTATTAATTTATTATTTAATCATCGT
Found at i:516082 original size:7 final size:6
Alignment explanation
Indices: 516044--516104 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
516034 AGTCAGATTC
* * * *
516044 AAACAA AAA-AA AATCAA AATCAA AAACAA AAACAA AAA-AA GAAGAA
1 AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA
*
516090 AAAGAA AAATCAA AA
1 AAACAA AAA-CAA AA
516105 TCAAGGTCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
5 8 0.17
6 35 0.74
7 4 0.09
ACGTcount: A:0.80, C:0.10, G:0.05, T:0.05
Consensus pattern (6 bp):
AAACAA
Found at i:517708 original size:30 final size:30
Alignment explanation
Indices: 517674--517730 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
517664 AGGTTGGAAA
517674 TTTGAGAAAGAAGAGTCTAAATTTGGATTT
1 TTTGAGAAAGAAGAGTCTAAATTTGGATTT
517704 TTTGAGAAAGAAGAGTCTAAATTTGGA
1 TTTGAGAAAGAAGAGTCTAAATTTGGA
517731 CTTTCTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.33
Consensus pattern (30 bp):
TTTGAGAAAGAAGAGTCTAAATTTGGATTT
Found at i:518569 original size:131 final size:131
Alignment explanation
Indices: 518335--519095 Score: 1188
Period size: 131 Copynumber: 5.8 Consensus size: 131
518325 TCGGTGAAAT
*
518335 CACAAGTCCTATGTCCCTGGTCAA-CAGTGGAGTAGGTTGGAAGTTACAGATCTTGTCTCCCTAA
1 CACAAGTCCTATGTCCCTGGT-AAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAA
* *
518399 GTAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGTAGATTTAA
65 GCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGCAGATTTAA
518464 GC
130 GC
*
518466 CACAAGTCCTATGTCCCTGGTAAGCAGTGGAGTAGGTTGGAAATTACAGATATTGTCTCCCTAAG
1 CACAAGTCCTATGTCCCTGGTAAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * *
518531 CAGTAGTGGAGTAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGCAGATTTAAG
518596 C
131 C
* *
518597 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTGAG
1 CACAAGTCCTATGTCCCTGGTAAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* * * *
518662 CAGTAGCGGAGCAAATCGAAGACGGCGAATCCTATCTTCCCCAGGAGTAGGGAAACAGATTTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGCAGATTTAAG
518727 C
131 C
* *
518728 CACAAGTCCTATGTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTGAG
1 CACAAGTCCTATGTCCCTGGTAAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
* *
518793 CAGTAGCGGAGCAGATTGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGCAGATGTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGCAGATTTAAG
518858 C
131 C
* * * *
518859 CACAAGTCCTATCTCCCTGGTCAGCAGTGAAGTAGGTTGGAAATTACAGATCTTGTCTACCTAAG
1 CACAAGTCCTATGTCCCTGGTAAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
*
518924 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCTCTAGGAGTAGGGAAGCAGATTTAAG
66 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGCAGATTTAAG
518989 C
131 C
* * *
518990 CACAAGTCCTATCTCCCTGGTCAA-CAGTGGAGTAGGTTTGAAATTACAGATCTCGTCTCCCTAA
1 CACAAGTCCTATGTCCCTGGT-AAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAA
* * * * *
519054 GCAATAGTGGAGCTA-ATCGAAAATGGTGAATCTTATC-TCCCT
65 GCAGTAGCGGAGC-AGATCGAAGACGGCGAATCTTATCTTCCCT
519096 GAGATTACAG
Statistics
Matches: 588, Mismatches: 39, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
130 6 0.01
131 580 0.99
132 2 0.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (131 bp):
CACAAGTCCTATGTCCCTGGTAAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAG
CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGCAGATTTAAG
C
Found at i:519328 original size:44 final size:42
Alignment explanation
Indices: 519081--519328 Score: 148
Period size: 44 Copynumber: 5.9 Consensus size: 42
519071 CGAAAATGGT
* *
519081 GAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCA
1 GAATCTTATCTCCCTGAGATTACAGTGGAACAGATTGAA-CCA
* * * * * **
519124 GTAATCCTATTTCCCTGAAATTACAGTGGAACGGATTAAAATAAA
1 G-AATCTTATCTCCCTGAGATTACAGTGGAACAGATT-GAA-CCA
* * * ** * * * *
519169 GGATCTTATCTCTCTGAAGA-TACAGTAGAGTACATCGTATCA
1 GAATCTTATCTCCCTG-AGATTACAGTGGAACAGATTGAACCA
* * **
519211 G-GTCTTATCTCCCTGAGATTACAGTGGAATAGACCG-A--A
1 GAATCTTATCTCCCTGAGATTACAGTGGAACAGATTGAACCA
* * *
519249 GAATCTTATCTCCCTGAAGGTTACAG-AGAGCAGATTGAAGCCA
1 GAATCTTATCTCCCTG-AGATTACAGTGGAACAGATTGAA-CCA
*
519292 GAAATCTTATCTCCCTGAGATTACAGTGGAATAGATT
1 G-AATCTTATCTCCCTGAGATTACAGTGGAACAGATT
519329 AAAACCACAT
Statistics
Matches: 151, Mismatches: 42, Indels: 23
0.70 0.19 0.11
Matches are distributed among these distances:
38 2 0.01
39 19 0.13
40 13 0.09
41 25 0.17
42 2 0.01
43 12 0.08
44 72 0.48
45 6 0.04
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (42 bp):
GAATCTTATCTCCCTGAGATTACAGTGGAACAGATTGAACCA
Found at i:519397 original size:50 final size:50
Alignment explanation
Indices: 519343--519506 Score: 163
Period size: 50 Copynumber: 3.3 Consensus size: 50
519333 CCACATTGGT
* *
519343 GAATCTCGCTTCCCCAATATTGCAGTTAAAAAGATTAAAGCTACAACAGC
1 GAATCTTGCTTCCCCAACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
* * * * * * *
519393 GAATCTTAC-TCCCCAAGCGA-TGCAGTGAAGCAA-ATTAAAGCCACATCGGT
1 GAATCTTGCTTCCCCAA-C-ATTGCAGTTAA-AAAGATTAAAGCTACAACAGC
* * *
519443 GAATCTTGCTTCCCCGACATTACAGTTAAAAAGATTAAAGCTACAATAGC
1 GAATCTTGCTTCCCCAACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
*
519493 GAATCTTACTTCCC
1 GAATCTTGCTTCCC
519507 AAGCGGTGTA
Statistics
Matches: 88, Mismatches: 20, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
49 10 0.11
50 69 0.78
51 9 0.10
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (50 bp):
GAATCTTGCTTCCCCAACATTGCAGTTAAAAAGATTAAAGCTACAACAGC
Found at i:519528 original size:50 final size:50
Alignment explanation
Indices: 519374--519536 Score: 136
Period size: 50 Copynumber: 3.3 Consensus size: 50
519364 GCAGTTAAAA
* * * * *
519374 AGATTAAAGCTACAACAGCGAATCTTACTCCCCAAGCGATGCAGTGAAGC
1 AGATTAAAGCTACAATAGCGAATCTTACTTCCCAAGCGATGTAATGAAAC
* * * * * * * *
519424 AAATTAAAGCCAC-ATCGGTGAATCTTGCTTCCC-CGAC-AT-TACAGTTAAAA
1 AGATTAAAGCTACAAT-AGCGAATCTTACTTCCCAAG-CGATGTA-A-TGAAAC
*
519474 AGATTAAAGCTACAATAGCGAATCTTACTTCCCAAGCGGTGTAATGAAAC
1 AGATTAAAGCTACAATAGCGAATCTTACTTCCCAAGCGATGTAATGAAAC
519524 AGATTAAAGCTAC
1 AGATTAAAGCTAC
519537 GACGACAAAT
Statistics
Matches: 83, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
48 1 0.01
49 4 0.05
50 71 0.86
51 5 0.06
52 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCTACAATAGCGAATCTTACTTCCCAAGCGATGTAATGAAAC
Found at i:519530 original size:100 final size:100
Alignment explanation
Indices: 519324--519533 Score: 303
Period size: 100 Copynumber: 2.1 Consensus size: 100
519314 ACAGTGGAAT
* * * *
519324 AGATTAAAACCACATTGGTGAATCTCGCTTCCCCAATATTGCAGTTAAAAAGATTAAAGCTACAA
1 AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCAACATTACAGTTAAAAAGATTAAAGCTACAA
* *
519389 CAGCGAATCTTACTCCCCAAGCGATGCAGTGAAGC
66 CAGCGAATCTTACTCCCCAAGCGATGCAATGAAAC
* * *
519424 AAATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTACAGTTAAAAAGATTAAAGCTACAA
1 AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCAACATTACAGTTAAAAAGATTAAAGCTACAA
* * * *
519489 TAGCGAATCTTACTTCCCAAGCGGTGTAATGAAAC
66 CAGCGAATCTTACTCCCCAAGCGATGCAATGAAAC
519524 AGATTAAAGC
1 AGATTAAAGC
519534 TACGACGACA
Statistics
Matches: 96, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (100 bp):
AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCAACATTACAGTTAAAAAGATTAAAGCTACAA
CAGCGAATCTTACTCCCCAAGCGATGCAATGAAAC
Found at i:519548 original size:100 final size:100
Alignment explanation
Indices: 519344--519568 Score: 281
Period size: 100 Copynumber: 2.2 Consensus size: 100
519334 CACATTGGTG
* * *
519344 AATCTCGCTTCCCCAATATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAA
1 AATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAA
* * ***
519409 GCGATGCAGTGAAGCAAATTAAAGCCACATCGGTG
66 GCGATGCAATGAAACAAATTAAAGCCACATCGACA
* * *
519444 AATCTTGCTTCCCCGACATTACAGTTAAAAAGATTAAAGCTACAATAGCGAATCTTACTTCCCAA
1 AATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAA
* * * *
519509 GCGGTGTAATGAAACAGATTAAAGCTACGA-CGACA
66 GCGATGCAATGAAACAAATTAAAGCCAC-ATCGACA
* *
519544 AATCTTGTTTCCCAGACATTGCAGT
1 AATCTTGCTTCCCCGACATTGCAGT
519569 CAGACAGAAG
Statistics
Matches: 106, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
100 105 0.99
101 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (100 bp):
AATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAA
GCGATGCAATGAAACAAATTAAAGCCACATCGACA
Found at i:521210 original size:3 final size:3
Alignment explanation
Indices: 521204--521289 Score: 52
Period size: 3 Copynumber: 28.7 Consensus size: 3
521194 TATTCAATAA
* * **
521204 TAT TAT TAT TAAT CTAT TAT TAT TAA T-T TAT TAT TAT TAT CAT CGT
1 TAT TAT TAT T-AT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
521250 TAT TAC TACT GA- TAT TAT TAT TAA TAT TGT TAT TA- TAT TA
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
521290 ATTTATATAT
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
2 4 0.06
3 53 0.84
4 5 0.08
5 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:521223 original size:14 final size:14
Alignment explanation
Indices: 521204--521242 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
521194 TATTCAATAA
521204 TATTATTATTAATC
1 TATTATTATTAATC
*
521218 TATTATTATTAATT
1 TATTATTATTAATC
521232 TATTATTATTA
1 TATTATTATTA
521243 TCATCGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTATTATTAATC
Found at i:521226 original size:17 final size:17
Alignment explanation
Indices: 521204--521243 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
521194 TATTCAATAA
521204 TATTATT-ATTAATCTAT
1 TATTATTAATTAAT-TAT
*
521221 TATTATTAATTTATTAT
1 TATTATTAATTAATTAT
521238 TATTAT
1 TATTAT
521244 CATCGTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATTAATTAATTAT
Found at i:521234 original size:11 final size:12
Alignment explanation
Indices: 521201--521289 Score: 54
Period size: 14 Copynumber: 6.7 Consensus size: 12
521191 TACTATTCAA
521201 TAATATTATTAT
1 TAATATTATTAT
521213 TAATCTATTATTAT
1 TAA--TATTATTAT
521227 TAATTTATTATTAT
1 TAA--TATTATTAT
*
521241 TATCATCGTTATTACT
1 TA--AT-ATTATTA-T
*
521257 ACTGATATTATTAT
1 --TAATATTATTAT
*
521271 TAATATTGTTAT
1 TAATATTATTAT
521283 T-ATATTA
1 TAATATTA
521290 ATTTATATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
11 5 0.08
12 14 0.23
14 26 0.42
15 12 0.19
16 4 0.06
18 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (12 bp):
TAATATTATTAT
Found at i:521304 original size:30 final size:31
Alignment explanation
Indices: 521218--521305 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 31
521208 ATTATTAATC
* *
521218 TATTATTATTAATTTATTATTATTATCATCGT
1 TATTACTATTAATTTATTATT-TAATCATCGT
* * *
521250 TATTACTACTGATATTATTA-TTAAT-ATTGT
1 TATTACTATTAAT-TTATTATTTAATCATCGT
521280 TATTA-TATTAATTTATATATTTAATC
1 TATTACTATTAATTTAT-TATTTAATC
521306 GCCATTATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.09
29 7 0.16
30 14 0.31
31 3 0.07
32 11 0.24
33 6 0.13
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (31 bp):
TATTACTATTAATTTATTATTTAATCATCGT
Found at i:522989 original size:4 final size:4
Alignment explanation
Indices: 522976--523006 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
522966 GGTTTTTTCA
522976 AATT -ATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT
523007 GAAGTTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
AATT
Found at i:523229 original size:110 final size:111
Alignment explanation
Indices: 523092--523313 Score: 437
Period size: 110 Copynumber: 2.0 Consensus size: 111
523082 AGATTCTTTT
523092 ATGGTAAAGTTGCCATGATTTTAAAAGAATTAGAATTGGGTTGAGAAATTTATTTAAATGGAAAA
1 ATGGTAAAGTTGCCATGATTTTAAAAGAATTAGAATTGGGTTGAGAAATTTATTTAAATGGAAAA
523157 TTTTAATTTATTTAAATTAATTTGATAACTAATATTTATTTTGGGA
66 TTTTAATTTATTTAAATTAATTTGATAACTAATATTTATTTTGGGA
523203 ATGGTAAAGTT-CCATGATTTTAAAAGAATTAGAATTGGGTTGAGAAATTTATTTAAATGGAAAA
1 ATGGTAAAGTTGCCATGATTTTAAAAGAATTAGAATTGGGTTGAGAAATTTATTTAAATGGAAAA
523267 TTTTAATTTATTTAAATTAATTTGATAACTAATATTTATTTTGGGA
66 TTTTAATTTATTTAAATTAATTTGATAACTAATATTTATTTTGGGA
523313 A
1 A
523314 ATAGAAAAAT
Statistics
Matches: 111, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
110 100 0.90
111 11 0.10
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (111 bp):
ATGGTAAAGTTGCCATGATTTTAAAAGAATTAGAATTGGGTTGAGAAATTTATTTAAATGGAAAA
TTTTAATTTATTTAAATTAATTTGATAACTAATATTTATTTTGGGA
Found at i:525374 original size:17 final size:18
Alignment explanation
Indices: 525354--525387 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
525344 TTTTTGGGGG
525354 GGATTGT-TTTTGGTTTC
1 GGATTGTATTTTGGTTTC
*
525371 GGATTTTATTTTGGTTT
1 GGATTGTATTTTGGTTT
525388 TCTAGCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.03, G:0.26, T:0.62
Consensus pattern (18 bp):
GGATTGTATTTTGGTTTC
Found at i:527414 original size:20 final size:20
Alignment explanation
Indices: 527385--527423 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
527375 CGACATGTAT
*
527385 TATCTATTAAGGCTTATCTA
1 TATCTATTAAGCCTTATCTA
*
527405 TATCTTTTAAGCCTTATCT
1 TATCTATTAAGCCTTATCT
527424 TATGGATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.49
Consensus pattern (20 bp):
TATCTATTAAGCCTTATCTA
Found at i:531229 original size:22 final size:24
Alignment explanation
Indices: 531196--531240 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
531186 GTATAAATTT
*
531196 AAAATTTTTATT-ATTTATTTATC
1 AAAATTTTTATTGATTTAATTATC
531219 AAAA-TTTTATTGATTTAATTAT
1 AAAATTTTTATTGATTTAATTAT
531241 ATAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
AAAATTTTTATTGATTTAATTATC
Found at i:531983 original size:13 final size:13
Alignment explanation
Indices: 531965--531991 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
531955 GAGCTAGGTC
531965 AGGCAAGAGTTTA
1 AGGCAAGAGTTTA
531978 AGGCAAGAGTTTA
1 AGGCAAGAGTTTA
531991 A
1 A
531992 CATTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.30, T:0.22
Consensus pattern (13 bp):
AGGCAAGAGTTTA
Found at i:532692 original size:3 final size:3
Alignment explanation
Indices: 532684--532710 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
532674 AATTACACAA
532684 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
532711 TAGAGATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:533328 original size:101 final size:102
Alignment explanation
Indices: 533206--533408 Score: 399
Period size: 101 Copynumber: 2.0 Consensus size: 102
533196 AATTGAATTC
533206 CAATTATTAAATTAAAATAATATAAAATTAAATTTATATTTAATTATAATGATAATAATATAATA
1 CAATTATTAAATTAAAATAATATAAAATTAAATTTATATTTAATTATAATGATAATAATATAATA
533271 TCAAACTCAACTAAAACTTAATATATTTTTCTAACAT
66 TCAAACTCAACTAAAACTTAATATATTTTTCTAACAT
533308 CAATTATT-AATTAAAATAATATAAAATTAAATTTATATTTAATTATAATGATAATAATATAATA
1 CAATTATTAAATTAAAATAATATAAAATTAAATTTATATTTAATTATAATGATAATAATATAATA
533372 TCAAACTCAACTAAAACTTAATATATTTTTCTAACAT
66 TCAAACTCAACTAAAACTTAATATATTTTTCTAACAT
533409 AAATACGCGG
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
101 93 0.92
102 8 0.08
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.40
Consensus pattern (102 bp):
CAATTATTAAATTAAAATAATATAAAATTAAATTTATATTTAATTATAATGATAATAATATAATA
TCAAACTCAACTAAAACTTAATATATTTTTCTAACAT
Found at i:541364 original size:27 final size:25
Alignment explanation
Indices: 541333--541400 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
541323 CATCTTGACC
541333 CACAACTTGTGTGAGCAAACCCATATT
1 CACAACTTGTGTGAGC-AA-CCATATT
* * **
541360 CACAACTCGTGCGAGC-ATTATATT
1 CACAACTTGTGTGAGCAACCATATT
*
541384 CACAACTTATGTGAGCA
1 CACAACTTGTGTGAGCA
541401 TTTCTATCCT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
24 18 0.55
25 1 0.03
27 14 0.42
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (25 bp):
CACAACTTGTGTGAGCAACCATATT
Found at i:541399 original size:24 final size:24
Alignment explanation
Indices: 541355--541402 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
541345 GAGCAAACCC
*
541355 ATATTCACAACTCGTGCGAGCATT
1 ATATTCACAACTCATGCGAGCATT
* *
541379 ATATTCACAACTTATGTGAGCATT
1 ATATTCACAACTCATGCGAGCATT
541403 TCTATCCTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (24 bp):
ATATTCACAACTCATGCGAGCATT
Found at i:545418 original size:21 final size:21
Alignment explanation
Indices: 545393--545433 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
545383 TACTGCATTT
*
545393 ATCCATGACAT-AGATAAATTC
1 ATCCATAACATAAG-TAAATTC
545414 ATCCATAACATAAGTAAATT
1 ATCCATAACATAAGTAAATT
545434 TCTCACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.29
Consensus pattern (21 bp):
ATCCATAACATAAGTAAATTC
Found at i:547056 original size:44 final size:45
Alignment explanation
Indices: 547007--547096 Score: 164
Period size: 44 Copynumber: 2.0 Consensus size: 45
546997 TCGGTTGTGT
*
547007 TAGAGAAGAAACCAAAAAGATGATAATATTTAAGCCTTTT-TTTC
1 TAGAGAAGAAACAAAAAAGATGATAATATTTAAGCCTTTTGTTTC
547051 TAGAGAAGAAACAAAAAAGATGATAATATTTAAGCCTTTTGTTTC
1 TAGAGAAGAAACAAAAAAGATGATAATATTTAAGCCTTTTGTTTC
547096 T
1 T
547097 TTTAATTTCA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 39 0.89
45 5 0.11
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32
Consensus pattern (45 bp):
TAGAGAAGAAACAAAAAAGATGATAATATTTAAGCCTTTTGTTTC
Found at i:548440 original size:97 final size:97
Alignment explanation
Indices: 548274--548466 Score: 341
Period size: 97 Copynumber: 2.0 Consensus size: 97
548264 TAGCTTTGAT
* *
548274 TGTTCATGAATTTGCTGATATTTTCCCAAAAGAATTGCCAGGGTTACTACCAATCAGGGAGGTTG
1 TGTTCATGAATTTGCTGATATTTTCCCAAAAGAATTGCCAAGGTTACCACCAATCAGGGAGGTTG
*
548339 AATTTGCTATTGAATTGGCATCGGGAACTTCC
66 AATTTGCTATTGAATTGGCATCGAGAACTTCC
*
548371 TGTTCATGAATTTGCTGATGTTTTCCCAAAAGAATTGCCAAGGTTACCACCAATCAGGGAGGTTG
1 TGTTCATGAATTTGCTGATATTTTCCCAAAAGAATTGCCAAGGTTACCACCAATCAGGGAGGTTG
*
548436 AATTTGCTATTGAATTGGCATCTAGAACTTC
66 AATTTGCTATTGAATTGGCATCGAGAACTTC
548467 TCCAATATTG
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
97 91 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (97 bp):
TGTTCATGAATTTGCTGATATTTTCCCAAAAGAATTGCCAAGGTTACCACCAATCAGGGAGGTTG
AATTTGCTATTGAATTGGCATCGAGAACTTCC
Found at i:553831 original size:28 final size:28
Alignment explanation
Indices: 553780--553840 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
553770 TATGAATGCT
*
553780 ATGAAATATGTTTGAATAAGGTGTTTAA
1 ATGAAATATGTTTGAATAAGGTGTATAA
** *
553808 ATGAAATATTGTTTGTTTAA-GTGTATAT
1 ATGAAATA-TGTTTGAATAAGGTGTATAA
553836 ATGAA
1 ATGAA
553841 TGCTAGATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.43
Consensus pattern (28 bp):
ATGAAATATGTTTGAATAAGGTGTATAA
Found at i:554858 original size:22 final size:24
Alignment explanation
Indices: 554828--554872 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
554818 AGCACCCGCT
*
554828 AAAACCCAATATT-TT-TTTTATA
1 AAAAACCAATATTGTTGTTTTATA
554850 AAAAACCAATATTGTTGTTTTAT
1 AAAAACCAATATTGTTGTTTTAT
554873 GATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 2 0.10
24 6 0.30
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.44
Consensus pattern (24 bp):
AAAAACCAATATTGTTGTTTTATA
Found at i:555284 original size:5 final size:5
Alignment explanation
Indices: 555276--555310 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
555266 TAAATAATTA
555276 AAAAT AAAATT AAAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAAT AAA
555311 CCCAATTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 22 0.79
6 2 0.07
7 4 0.14
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:555286 original size:12 final size:12
Alignment explanation
Indices: 555271--555307 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
555261 TAAATTAAAT
555271 AATTAAAAATAA
1 AATTAAAAATAA
555283 AATTAAAAATAA
1 AATTAAAAATAA
555295 AA-T-AAAATAA
1 AATTAAAAATAA
555305 AAT
1 AAT
555308 AAACCCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
12 14 0.58
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATTAAAAATAA
Found at i:556158 original size:58 final size:60
Alignment explanation
Indices: 556086--556265 Score: 196
Period size: 60 Copynumber: 3.3 Consensus size: 60
556076 ATAAAATTAA
556086 ATATTTATCTAAATAAAATATAATAGATAAAACTTAATCTTAATTAAAATATTAATAAAT
1 ATATTTATCTAAATAAAATATAATAGATAAAACTTAATCTTAATTAAAATATTAATAAAT
* * * *
556146 ATATTTA-C-AAAT--AATAT--TA-A-AAAA--TAA---AAATAAAAAGA-TAA-AATAA
1 ATATTTATCTAAATAAAATATAATAGATAAAACTTAATCTTAATTAAAATATTAATAA-AT
556192 ATATTTATCTAAATAAAATATAATAGATAAAACTTAATCTTAATTAAAATATTAATAAAT
1 ATATTTATCTAAATAAAATATAATAGATAAAACTTAATCTTAATTAAAATATTAATAAAT
556252 ATATTTA-C-AAATAA
1 ATATTTATCTAAATAA
556266 TATTAAAAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 34
0.70 0.06 0.25
Matches are distributed among these distances:
45 2 0.02
46 11 0.11
47 9 0.09
48 4 0.04
50 8 0.08
52 6 0.06
53 2 0.02
54 6 0.06
56 8 0.08
58 10 0.10
59 10 0.10
60 18 0.19
61 2 0.02
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (60 bp):
ATATTTATCTAAATAAAATATAATAGATAAAACTTAATCTTAATTAAAATATTAATAAAT
Found at i:556178 original size:35 final size:34
Alignment explanation
Indices: 556139--556285 Score: 97
Period size: 35 Copynumber: 4.2 Consensus size: 34
556129 TTAAAATATT
556139 AATAAATATATTTACAAATAATATTAAAAAATAAA
1 AATAAATATATTTA-AAATAATATTAAAAAATAAA
** **
556174 AATAAA-A-AGATAAAATAAATATTTATCTAAAT-AA
1 AATAAATATATTTAAAAT-AATA-TTA-AAAAATAAA
* * **
556208 AATATAATAGA--TAAAACTTAATCTTAATTAAAATATT
1 AATA-AATATATTTAAAA--TAATATTAA--AAAATAAA
556245 AATAAATATATTTACAAATAATATTAAAAAATAAA
1 AATAAATATATTTA-AAATAATATTAAAAAATAAA
556280 AATAAA
1 AATAAA
556286 ATAATCGTAA
Statistics
Matches: 85, Mismatches: 13, Indels: 28
0.67 0.10 0.22
Matches are distributed among these distances:
32 4 0.05
33 7 0.08
34 10 0.12
35 32 0.38
36 13 0.15
37 14 0.16
38 2 0.02
39 3 0.04
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (34 bp):
AATAAATATATTTAAAATAATATTAAAAAATAAA
Found at i:556268 original size:106 final size:107
Alignment explanation
Indices: 556072--556286 Score: 423
Period size: 106 Copynumber: 2.0 Consensus size: 107
556062 TCAAATTCTT
556072 AAAGATAAAATTAAATATTTATCTAAATAAAATATAATAGATAAAACTTAATCTTAATTAAAATA
1 AAAGATAAAATTAAATATTTATCTAAATAAAATATAATAGATAAAACTTAATCTTAATTAAAATA
556137 TTAATAAATATATTTACAAATAATATTAAAAAATAAAAATAA
66 TTAATAAATATATTTACAAATAATATTAAAAAATAAAAATAA
556179 AAAGATAAAA-TAAATATTTATCTAAATAAAATATAATAGATAAAACTTAATCTTAATTAAAATA
1 AAAGATAAAATTAAATATTTATCTAAATAAAATATAATAGATAAAACTTAATCTTAATTAAAATA
556243 TTAATAAATATATTTACAAATAATATTAAAAAATAAAAATAA
66 TTAATAAATATATTTACAAATAATATTAAAAAATAAAAATAA
556285 AA
1 AA
556287 TAATCGTAAT
Statistics
Matches: 108, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
106 98 0.91
107 10 0.09
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (107 bp):
AAAGATAAAATTAAATATTTATCTAAATAAAATATAATAGATAAAACTTAATCTTAATTAAAATA
TTAATAAATATATTTACAAATAATATTAAAAAATAAAAATAA
Found at i:560226 original size:19 final size:19
Alignment explanation
Indices: 560202--560239 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
560192 CTAAAAAATT
560202 TGAGAGAATGATGA-ATGAG
1 TGAGAG-ATGATGAGATGAG
560221 TGAGAGATGATGAGATGAG
1 TGAGAGATGATGAGATGAG
560240 GGATGATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.21
Consensus pattern (19 bp):
TGAGAGATGATGAGATGAG
Found at i:563336 original size:28 final size:28
Alignment explanation
Indices: 563291--563379 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 28
563281 AACACGATAG
* *
563291 AAAATAATAGCCTTTGTGGCGAATCGTA
1 AAAAGAATAACCTTTGTGGCGAATCGTA
* * *
563319 AAAAGAATAACCTCTGTGGAGAATTGTA
1 AAAAGAATAACCTTTGTGGCGAATCGTA
* * *
563347 AAAAGAA-AAGCCTTTATGGCGGATCATA
1 AAAAGAATAA-CCTTTGTGGCGAATCGTA
563375 AAAAG
1 AAAAG
563380 GAAAGCTTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
27 2 0.04
28 47 0.96
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (28 bp):
AAAAGAATAACCTTTGTGGCGAATCGTA
Found at i:564788 original size:31 final size:31
Alignment explanation
Indices: 564750--564815 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
564740 TTTTTTTTGT
564750 TTAATTTGATACCTAAACTTGATACATTTTC
1 TTAATTTGATACCTAAACTTGATACATTTTC
* * **
564781 TTAATTTGGTATCTAAACTTGATATTTTTTC
1 TTAATTTGATACCTAAACTTGATACATTTTC
564812 TTAA
1 TTAA
564816 GTTGGTACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (31 bp):
TTAATTTGATACCTAAACTTGATACATTTTC
Found at i:564821 original size:31 final size:31
Alignment explanation
Indices: 564762--564822 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
564752 AATTTGATAC
*
564762 CTAAACTTGATACATTTTCTTAATTTGGTAT
1 CTAAACTTGATACATTTTCTTAAGTTGGTAT
**
564793 CTAAACTTGATATTTTTTCTTAAGTTGGTA
1 CTAAACTTGATACATTTTCTTAAGTTGGTA
564823 CTTAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.49
Consensus pattern (31 bp):
CTAAACTTGATACATTTTCTTAAGTTGGTAT
Found at i:565389 original size:59 final size:59
Alignment explanation
Indices: 565285--565428 Score: 175
Period size: 59 Copynumber: 2.4 Consensus size: 59
565275 ATTTAATAAA
* * * * *
565285 TTTAGGTACTAAATTAGGAAAACATGTCAAGTTCAACTATCAAATTGGGCCCAAAAAAGT
1 TTTA-GTACCAAATTAAGAAAAAATGTCAAGTTCAACTATCAAATTGGGCCAAAAAAAAT
* *
565345 TTTAGTACCAAATTAAGAAAAAATGTCAAGTTCAAGTA-CTAAATTGGGCTAAAAAAAAT
1 TTTAGTACCAAATTAAGAAAAAATGTCAAGTTCAACTATC-AAATTGGGCCAAAAAAAAT
* *
565404 TTAAATACCAAATTAA-AAAAAATGT
1 TTTAGTACCAAATTAAGAAAAAATGT
565429 TAAGATCAGT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
58 10 0.14
59 60 0.81
60 4 0.05
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (59 bp):
TTTAGTACCAAATTAAGAAAAAATGTCAAGTTCAACTATCAAATTGGGCCAAAAAAAAT
Found at i:570793 original size:6 final size:6
Alignment explanation
Indices: 570784--570811 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
570774 ATCAAAATCA
570784 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
570812 GGAGAGGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:571723 original size:47 final size:46
Alignment explanation
Indices: 571654--571742 Score: 142
Period size: 47 Copynumber: 1.9 Consensus size: 46
571644 AGGAGAAGGG
* * *
571654 ACCAAGGTGAAAACCTGCAAAGGGCGCTTTGAGTTTCAAAAAAAAAT
1 ACCAAGGTGAAAACCCGCAAAGGGCACTTTGAG-TCCAAAAAAAAAT
571701 ACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCAAAAAA
1 ACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCAAAAAA
571743 TAAAAATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 8 0.21
47 31 0.79
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (46 bp):
ACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCAAAAAAAAAT
Found at i:573168 original size:45 final size:45
Alignment explanation
Indices: 572989--573170 Score: 283
Period size: 45 Copynumber: 4.0 Consensus size: 45
572979 CAGATCAGTA
*
572989 AAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCA
1 AAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCG
* * *
573034 AAAATAGCAGATCTTGTCTTCCTATATTGGTAGCAAAGTAGATCG
1 AAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCG
* * *
573079 AAGATAACGGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCG
1 AAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCG
* *
573124 AAAACAGCAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCG
1 AAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCG
573169 AA
1 AA
573171 GACAGAAGTA
Statistics
Matches: 122, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 122 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (45 bp):
AAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCG
Found at i:573325 original size:44 final size:44
Alignment explanation
Indices: 573275--573384 Score: 175
Period size: 44 Copynumber: 2.5 Consensus size: 44
573265 ATCCAGTCTC
* * * *
573275 ATCTCCCCGAGGTTGCAGTGGAACAGATTGAATAAGCCAATCTT
1 ATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGAAACCAATCCT
573319 ATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGAAACCAATCCT
1 ATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGAAACCAATCCT
*
573363 ATCTCCCTGAAGTTGCAGTGGA
1 ATCTCCCTGAGGTTGCAGTGGA
573385 GTGGATCAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 61 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (44 bp):
ATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGAAACCAATCCT
Found at i:573986 original size:22 final size:22
Alignment explanation
Indices: 573926--573983 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
573916 AATCTTCAAG
573926 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
573945 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
573967 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
573984 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:580688 original size:58 final size:58
Alignment explanation
Indices: 580559--580691 Score: 196
Period size: 58 Copynumber: 2.3 Consensus size: 58
580549 ATTTATAAGA
* * * *
580559 TAGTCCTTAACGGACTTCCCAACGCTAGATAGTCCTAACGAACATCCTCTTCATTCGT
1 TAGTCCTTAGCGGACTTCCCAACCCTAGATAATCATAACGAACATCCTCTTCATTCGT
* *
580617 TAGTCCTTGGCGGACTTCCCAACCCTAGATAATCATAACGGACATCCTCTTCATTCGT
1 TAGTCCTTAGCGGACTTCCCAACCCTAGATAATCATAACGAACATCCTCTTCATTCGT
580675 TAGT-CTCTAGCGGACTT
1 TAGTCCT-TAGCGGACTT
580692 TATAGAACAA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 2 0.03
58 65 0.97
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (58 bp):
TAGTCCTTAGCGGACTTCCCAACCCTAGATAATCATAACGAACATCCTCTTCATTCGT
Found at i:585316 original size:21 final size:21
Alignment explanation
Indices: 585291--585343 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
585281 AGCGGTGGCG
*
585291 GTGAGATTAGTTACTGTAGTA
1 GTGAGATTAGATACTGTAGTA
* *
585312 GTGAGATTGGATACTGTAG-C
1 GTGAGATTAGATACTGTAGTA
585332 GATGAGATTAGA
1 G-TGAGATTAGA
585344 AACAATGGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.32
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGTA
Found at i:589215 original size:30 final size:30
Alignment explanation
Indices: 589179--589240 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
589169 NNNNNNNNNN
589179 TACATATATTTTTTTATTTTTAAAATACAC
1 TACATATATTTTTTTATTTTTAAAATACAC
589209 TACATATATTTTTTTATTTTTAAAATACAC
1 TACATATATTTTTTTATTTTTAAAATACAC
589239 TA
1 TA
589241 ATACAGTGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (30 bp):
TACATATATTTTTTTATTTTTAAAATACAC
Found at i:589327 original size:13 final size:13
Alignment explanation
Indices: 589309--589333 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
589299 CCGTGCCCTC
589309 CTCCCATTTCCCA
1 CTCCCATTTCCCA
589322 CTCCCATTTCCC
1 CTCCCATTTCCC
589334 CTCTTCCACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.56, G:0.00, T:0.32
Consensus pattern (13 bp):
CTCCCATTTCCCA
Found at i:591794 original size:22 final size:22
Alignment explanation
Indices: 591775--591860 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 22
591765 ACCAAGAACA
591775 AAGCAAAAAAGAGGGGAGAAAC
1 AAGCAAAAAAGAGGGGAGAAAC
* * *
591797 CAGCAAAAACGAGGGG-CAAAC
1 AAGCAAAAAAGAGGGGAGAAAC
* *
591818 CAGCAAGAACA-A-GGGAGAAAC
1 AAGCAA-AAAAGAGGGGAGAAAC
* * *
591839 CAGCAAGAACGAGGGGAGAAAC
1 AAGCAAAAAAGAGGGGAGAAAC
591861 TGCTGTTTTG
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
20 4 0.08
21 22 0.43
22 25 0.49
ACGTcount: A:0.51, C:0.17, G:0.31, T:0.00
Consensus pattern (22 bp):
AAGCAAAAAAGAGGGGAGAAAC
Found at i:591817 original size:21 final size:20
Alignment explanation
Indices: 591776--591855 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 20
591766 CCAAGAACAA
*
591776 AGCAAAAAAGAGGGGAGAAACC
1 AGCAAAAACGA-GGG-GAAACC
591798 AGCAAAAACGAGGGGCAAACC
1 AGCAAAAACGAGGGG-AAACC
* *
591819 AGCAAGAACAAGGGAGAAACC
1 AGCAAAAACGAGGG-GAAACC
*
591840 AGCAAGAACGAGGGGA
1 AGCAAAAACGAGGGGA
591856 GAAACTGCTG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
20 3 0.06
21 38 0.73
22 11 0.21
ACGTcount: A:0.50, C:0.17, G:0.33, T:0.00
Consensus pattern (20 bp):
AGCAAAAACGAGGGGAAACC
Found at i:596357 original size:16 final size:16
Alignment explanation
Indices: 596338--596369 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
596328 AAAAAAAAGA
596338 AAGTACCTGAAGAAGG
1 AAGTACCTGAAGAAGG
596354 AAGTACCTGAAGAAGG
1 AAGTACCTGAAGAAGG
596370 TAAACTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.31, T:0.12
Consensus pattern (16 bp):
AAGTACCTGAAGAAGG
Found at i:598245 original size:51 final size:52
Alignment explanation
Indices: 598142--598245 Score: 165
Period size: 51 Copynumber: 2.0 Consensus size: 52
598132 CGCTATCTTG
*
598142 GAATTGAGTGAAATTGCATTTTGTGTTTTTTTATTGAAAAATGATAAATTAAT
1 GAATTGAGTGAAATTGCATTTTGTG-TTTTTTATTGAAAAATAATAAATTAAT
**
598195 GAATTGAGTGAAATTTTATTTTGTG-TTTTTATTGAAAAATAATAAATTAAT
1 GAATTGAGTGAAATTGCATTTTGTGTTTTTTATTGAAAAATAATAAATTAAT
598246 CTTATAAGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
51 25 0.52
53 23 0.48
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.46
Consensus pattern (52 bp):
GAATTGAGTGAAATTGCATTTTGTGTTTTTTATTGAAAAATAATAAATTAAT
Found at i:598265 original size:24 final size:23
Alignment explanation
Indices: 598238--598284 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
598228 GAAAAATAAT
598238 AAATTAATCTTATAAGTTAGAAAA
1 AAATTAATCTTATAAGTTA-AAAA
* * *
598262 AAATTATTTTTTTAAGTTAAAAA
1 AAATTAATCTTATAAGTTAAAAA
598285 TGTTATCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.40
Consensus pattern (23 bp):
AAATTAATCTTATAAGTTAAAAA
Found at i:599212 original size:18 final size:18
Alignment explanation
Indices: 599185--599220 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
599175 AAGTTACATC
599185 GAGTACTTTGTTAGTAAT
1 GAGTACTTTGTTAGTAAT
*
599203 GAGTATTTTGTTAGTAAT
1 GAGTACTTTGTTAGTAAT
599221 ATGTTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.22, T:0.47
Consensus pattern (18 bp):
GAGTACTTTGTTAGTAAT
Found at i:599476 original size:22 final size:21
Alignment explanation
Indices: 599451--599498 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
599441 CTCTTAAAAG
599451 CAAAGAAGAACGGCTATCGTTT
1 CAAA-AAGAACGGCTATCGTTT
***
599473 CAAAATTTACGGCTATCGTTT
1 CAAAAAGAACGGCTATCGTTT
599494 CAAAA
1 CAAAA
599499 TTTTTTTCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (21 bp):
CAAAAAGAACGGCTATCGTTT
Found at i:599484 original size:21 final size:21
Alignment explanation
Indices: 599460--599501 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
599450 GCAAAGAAGA
599460 ACGGCTATCGTTTCAAAATTT
1 ACGGCTATCGTTTCAAAATTT
599481 ACGGCTATCGTTTCAAAATTT
1 ACGGCTATCGTTTCAAAATTT
599502 TTTTCACCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (21 bp):
ACGGCTATCGTTTCAAAATTT
Found at i:604332 original size:41 final size:41
Alignment explanation
Indices: 604216--604371 Score: 136
Period size: 41 Copynumber: 3.8 Consensus size: 41
604206 ACAACGGTTA
* * *
604216 TCTGATTCACA-ACACTGGCACGAAGCCTACTAGGCCCAAGG
1 TCTGATTC-CATACACTGACACGAAGCCTGCTAGGCTCAAGG
* * * * * * * *
604257 TCTAATTTCATACACCGGCACAAATCCTGATAGGCTTAAGG
1 TCTGATTCCATACACTGACACGAAGCCTGCTAGGCTCAAGG
* *
604298 TCTGATTCCATACACTGACACGAAGCTTGCTAGGCTGAAGG
1 TCTGATTCCATACACTGACACGAAGCCTGCTAGGCTCAAGG
* * *
604339 CCTGATTTCATACACT-AGCTCGAAGCCTGCTAG
1 TCTGATTCCATACACTGA-CACGAAGCCTGCTAG
604372 ATTCAAAACC
Statistics
Matches: 91, Mismatches: 22, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
40 3 0.03
41 88 0.97
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
TCTGATTCCATACACTGACACGAAGCCTGCTAGGCTCAAGG
Found at i:619163 original size:21 final size:22
Alignment explanation
Indices: 619131--619186 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
619121 ACTGTTGTTG
*
619131 AGAAGAAAGTTGCTT-CTGTAGA
1 AGAAG-AAGTTGCTTGCTGAAGA
*
619153 AGAGGAAGTTG-TTGCTGAAGA
1 AGAAGAAGTTGCTTGCTGAAGA
619174 AGAAGAAGTTGCT
1 AGAAGAAGTTGCT
619187 GAAAATGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 22 0.76
22 5 0.17
ACGTcount: A:0.36, C:0.07, G:0.32, T:0.25
Consensus pattern (22 bp):
AGAAGAAGTTGCTTGCTGAAGA
Found at i:619503 original size:15 final size:14
Alignment explanation
Indices: 619483--619513 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
619473 CTTAAAAGAT
*
619483 AAAAAAGGGAGGAG
1 AAAAAAAGGAGGAG
619497 AAAAAAAGGAGGAG
1 AAAAAAAGGAGGAG
619511 AAA
1 AAA
619514 GAAACATCAT
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (14 bp):
AAAAAAAGGAGGAG
Found at i:619650 original size:17 final size:17
Alignment explanation
Indices: 619628--619661 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
619618 GATAAATATA
* *
619628 TATTGTGATTGCATTTT
1 TATTGTCATTACATTTT
619645 TATTGTCATTACATTTT
1 TATTGTCATTACATTTT
619662 CATGTTAGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.59
Consensus pattern (17 bp):
TATTGTCATTACATTTT
Found at i:624208 original size:62 final size:59
Alignment explanation
Indices: 624096--624294 Score: 145
Period size: 68 Copynumber: 3.2 Consensus size: 59
624086 ATCACTTTAG
* * ** * *
624096 TATTAAATTAATATAATATTTATTAAGATAAATGTTAGATTTAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATCT
*
624155 TATTAAAATAATAGAATGTTTATCTACAAGATAAACATTAAATTAAATTTAATATTAAGATAATC
1 TATTAAAATAATAGAATATTTAT-T--AAGATAAACATTAAATTAAATTTAATATT---A-AAT-
624220 ACTT
58 -C-T
* * * * *
624224 TAATTTTAAATTAATAAAATA-CTATTAAGATAAATATTAAATTTAATTTAATATTAAA-C-
1 T-A--TTAAAATAATAGAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATCT
624283 -ATTAAAATAATA
1 TATTAAAATAATA
624295 TTATCTTTGG
Statistics
Matches: 113, Mismatches: 14, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
55 10 0.09
57 1 0.01
59 20 0.18
60 1 0.01
61 1 0.01
62 25 0.22
64 2 0.02
65 2 0.02
66 3 0.03
68 28 0.25
69 2 0.02
70 2 0.02
71 3 0.03
72 13 0.12
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (59 bp):
TATTAAAATAATAGAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:624251 original size:25 final size:27
Alignment explanation
Indices: 624196--624251 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
624186 TAAACATTAA
*
624196 ATTAAATTTAATATTAAGATAATCACT
1 ATTAAATTTAATATTAAGAAAATCACT
* *
624223 -TTAATTTTAA-ATTAATAAAAT-ACT
1 ATTAAATTTAATATTAAGAAAATCACT
624247 ATTAA
1 ATTAA
624252 GATAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 3 0.12
25 13 0.52
26 9 0.36
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (27 bp):
ATTAAATTTAATATTAAGAAAATCACT
Found at i:627015 original size:13 final size:13
Alignment explanation
Indices: 626997--627029 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
626987 CGAGATAATC
626997 GGAATTGAAGCTT
1 GGAATTGAAGCTT
*
627010 GGAATTAAAGCTT
1 GGAATTGAAGCTT
627023 GGAATTG
1 GGAATTG
627030 CCTAGTTGAT
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:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (13 bp):
GGAATTGAAGCTT
Found at i:632977 original size:33 final size:33
Alignment explanation
Indices: 632939--633004 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
632929 GAGTAAGTTC
632939 GTAAATATTATTATTTAATATTTACGAGTAGAA
1 GTAAATATTATTATTTAATATTTACGAGTAGAA
632972 GTAAATATTATTATTTAATATTTACGAGTAGAA
1 GTAAATATTATTATTTAATATTTACGAGTAGAA
633005 TATGGTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (33 bp):
GTAAATATTATTATTTAATATTTACGAGTAGAA
Found at i:639339 original size:30 final size:30
Alignment explanation
Indices: 639303--639363 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
639293 TGACTTGGGT
639303 CACATGCCCATGTGTGTTACCT-GTGTGTGA
1 CACATGCCCATGTGTGTT-CCTCGTGTGTGA
*
639333 CACATGCCCATGTGTGTTGCTCGTGTGTGA
1 CACATGCCCATGTGTGTTCCTCGTGTGTGA
639363 C
1 C
639364 TATCTTTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.15, C:0.25, G:0.28, T:0.33
Consensus pattern (30 bp):
CACATGCCCATGTGTGTTCCTCGTGTGTGA
Found at i:639384 original size:8 final size:8
Alignment explanation
Indices: 639371--639403 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
639361 GACTATCTTT
639371 TTCTTTTC
1 TTCTTTTC
*
639379 TTCTTTAC
1 TTCTTTTC
639387 TT-TTTTC
1 TTCTTTTC
639394 TTCTTTTC
1 TTCTTTTC
639402 TT
1 TT
639404 TGTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:639394 original size:15 final size:15
Alignment explanation
Indices: 639374--639404 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
639364 TATCTTTTTC
639374 TTTTCTTCTTTACTT
1 TTTTCTTCTTTACTT
*
639389 TTTTCTTCTTTTCTT
1 TTTTCTTCTTTACTT
639404 T
1 T
639405 GTTAAATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCTTCTTTACTT
Found at i:643137 original size:42 final size:42
Alignment explanation
Indices: 643088--643279 Score: 196
Period size: 42 Copynumber: 4.6 Consensus size: 42
643078 CGGCTTTATA
* * *
643088 CTTCAGTTTAGCCGATGATGCACTTATGTACCAATATATTCG
1 CTTCAGTTTAGCTGATGATGCACTTATGTGCCAGTATATTCG
*
643130 CTTCAGTTTAGCTGATGATGAACTTATGTGCCAGTATATTCG
1 CTTCAGTTTAGCTGATGATGCACTTATGTGCCAGTATATTCG
* *
643172 CTT-TGTTTTAGCTAATGATGCACTTATGTGCCAGTATAATT-G
1 CTTCAG-TTTAGCTGATGATGCACTTATGTGCCAGTAT-ATTCG
* *
643214 CCTC-GACTT-GTCTGATGATGCACTTATGTGCCAGTATATTTC-
1 CTTCAG-TTTAG-CTGATGATGCACTTATGTGCCAGTATA-TTCG
* * **
643256 CTTCGGTTTATCCAATGATGCACT
1 CTTCAGTTTAGCTGATGATGCACT
643280 GTGGTGCTAG
Statistics
Matches: 126, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
41 3 0.02
42 119 0.94
43 4 0.03
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.39
Consensus pattern (42 bp):
CTTCAGTTTAGCTGATGATGCACTTATGTGCCAGTATATTCG
Done.