Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008228.1 Hibiscus syriacus cultivar Beakdansim tig00110864_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3739947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 20
Found at i:304955 original size:85 final size:87
Alignment explanation
Indices: 304809--305026 Score: 214
Period size: 85 Copynumber: 2.5 Consensus size: 87
304799 AAAAATGATT
* * * * *
304809 AAATTAGGGGCTTAAATTATAAAAGTAAAAAGT-ATGATTGAAAAAATTAGGGACCCCAATTATA
1 AAATTAAGGGCATCAATTATAAAAGTAAAAAGTGATGATTGAAAAAAATAGGGACCCAAATTATA
* *
304873 -AAGGTAAAAAGTAATATT-AAAA
66 GAA--TAAAAAATAAGATTAAAAA
* * ** *
304895 AAA-TAAGGGCATCAATTTTAAACGTAAAAAGTGATGA-TGAAAAAAATAGGGGTCTAAATTATA
1 AAATTAAGGGCATCAATTATAAAAGTAAAAAGTGATGATTGAAAAAAATAGGGACCCAAATTATA
**
304958 TGAATAAAAAATGGGATTAAAAA
66 -GAATAAAAAATAAGATTAAAAA
* * *
304981 AAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGAT-ATTGAAAAAA
1 AAATTAAGGGCATCAATTATAAAAGTAAAAAGTGATGATTGAAAAAA
305027 GCATGAGCTT
Statistics
Matches: 108, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
85 55 0.51
86 15 0.14
87 38 0.35
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.25
Consensus pattern (87 bp):
AAATTAAGGGCATCAATTATAAAAGTAAAAAGTGATGATTGAAAAAAATAGGGACCCAAATTATA
GAATAAAAAATAAGATTAAAAA
Found at i:305067 original size:129 final size:130
Alignment explanation
Indices: 304849--305145 Score: 300
Period size: 129 Copynumber: 2.3 Consensus size: 130
304839 AGTATGATTG
* * * *
304849 AAAAAATTAGGGACCCCAATTATAAAGGTAAAAAGTAATATTAAAAAAATAAGGGCATCAATTTT
1 AAAAAATTAGGGACCTCAATTATAAAGGTAAAAAGTAATATTAAAAAAACAAGAGCATCAATTAT
* * * *
304914 AAACGTAAAAAGTGATGATGAAAAAAATAGGGGTC-TAAATTAT-ATGAATAAAAAATGGGATT-
66 AAACGTAAAAAGTGAGGATAAAAAAAATA-AGATCATAAATTATAATGAA-AAAAAATGGGATTG
304976 AA
129 AA
* * * * *
304978 AAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGTGATATTGAAAAAAGCATGAGC-TTAATTA
1 AAAAAATTAGGGACCTCAATTATAAAGGTAAAAAGTAATATT-AAAAAAACAAGAGCATCAATTA
* * * ** * *
305042 TAAAGGTACAAGGTG-GGATTAAAAAACTTAAGATCATCAATTATAAATGTAAAAAAATGGGATT
65 TAAACGTAAAAAGTGAGGA-TAAAAAAAATAAGATCATAAATTAT-AATGAAAAAAAATGGGATT
305106 GAA
128 GAA
* *
305109 AAAAAATTAAGGACCTTC-ATTATAAAGATAAAAAGTA
1 AAAAAATTAGGGACC-TCAATTATAAAGGTAAAAAGTA
305146 GGATTACAAA
Statistics
Matches: 137, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
128 5 0.04
129 71 0.52
130 23 0.17
131 36 0.26
132 2 0.01
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.25
Consensus pattern (130 bp):
AAAAAATTAGGGACCTCAATTATAAAGGTAAAAAGTAATATTAAAAAAACAAGAGCATCAATTAT
AAACGTAAAAAGTGAGGATAAAAAAAATAAGATCATAAATTATAATGAAAAAAAATGGGATTGAA
Found at i:305315 original size:2 final size:2
Alignment explanation
Indices: 305308--305334 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
305298 TAATAGCAAA
305308 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
305335 ATTTTAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:313620 original size:14 final size:14
Alignment explanation
Indices: 313601--313633 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
313591 AAATCAATAT
313601 TTAAATACATTCAA
1 TTAAATACATTCAA
313615 TTAAATACATTCAA
1 TTAAATACATTCAA
313629 TTAAA
1 TTAAA
313634 CCATTTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (14 bp):
TTAAATACATTCAA
Found at i:314044 original size:22 final size:22
Alignment explanation
Indices: 314016--314067 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
314006 ATCATTAGTG
*
314016 TCAAATAAATTTAACTCTCATA
1 TCAAATAAATTTAACTCCCATA
*
314038 TCAAATAAATTTAACTCCCGTA
1 TCAAATAAATTTAACTCCCATA
314060 TCAAATAA
1 TCAAATAA
314068 TAACCTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (22 bp):
TCAAATAAATTTAACTCCCATA
Found at i:314263 original size:39 final size:39
Alignment explanation
Indices: 314194--314362 Score: 187
Period size: 39 Copynumber: 4.3 Consensus size: 39
314184 ATTTATCTTT
*
314194 TATTTTAAATATTTTTAACTTTGAATTTTTAAGTAATTTA
1 TATTTTAAATA-TTTTAACTTTAAATTTTTAAGTAATTTA
* * * *
314234 TATTTTGAATATTTTAACTTTAAAATTTTAAGTTATCTTT
1 TATTTTAAATATTTTAACTTTAAATTTTTAAGTAAT-TTA
** * *
314274 TATTTTAAATATTTTATTTTTAATTTTTTAAATAATTTA
1 TATTTTAAATATTTTAACTTTAAATTTTTAAGTAATTTA
* *
314313 TATTATAAATATTTT-CCTTTTAAATTTTTAAGTAATTTA
1 TATTTTAAATATTTTAAC-TTTAAATTTTTAAGTAATTTA
*
314352 TAATTATAAAT
1 T-ATTTTAAAT
314363 TAAACCCTTC
Statistics
Matches: 108, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
39 58 0.54
40 50 0.46
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (39 bp):
TATTTTAAATATTTTAACTTTAAATTTTTAAGTAATTTA
Found at i:314324 original size:79 final size:80
Alignment explanation
Indices: 314186--314345 Score: 218
Period size: 79 Copynumber: 2.0 Consensus size: 80
314176 CTAGTATAAT
* * *
314186 TTATCTTTTATTTTAAATATTTTTAACTTTGAATTTTTAAGTAATTTATATTTTGAATATTTTAA
1 TTATCTTTTATTTTAAATATTTTTAACTTTGAATTTTTAAATAATTTATATTATAAATATTTT-A
314251 C-TTTAAAATTTTAAG
65 CTTTTAAAATTTTAAG
* * *
314266 TTATCTTTTATTTTAAATA-TTTT-ATTTTTAATTTTTTAAATAATTTATATTATAAATATTTTC
1 TTATCTTTTATTTTAAATATTTTTAACTTTGAA-TTTTTAAATAATTTATATTATAAATATTTTA
*
314329 CTTTTAAATTTTTAAG
65 CTTTTAAAATTTTAAG
314345 T
1 T
314346 AATTTATAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
78 7 0.10
79 45 0.63
80 19 0.27
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (80 bp):
TTATCTTTTATTTTAAATATTTTTAACTTTGAATTTTTAAATAATTTATATTATAAATATTTTAC
TTTTAAAATTTTAAG
Found at i:314423 original size:22 final size:22
Alignment explanation
Indices: 314398--314439 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
314388 ATTTTTTTGA
*
314398 AATTTTAAATTTAAATAAATCG
1 AATTTAAAATTTAAATAAATCG
*
314420 AATTTAAAATTTATATAAAT
1 AATTTAAAATTTAAATAAAT
314440 TATTTGAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTTAAAATTTAAATAAATCG
Found at i:319326 original size:21 final size:20
Alignment explanation
Indices: 319240--319397 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
319230 AAATGACCAA
**
319240 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
319259 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
319279 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
319299 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
319320 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
319341 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
319361 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
319382 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
319398 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:319388 original size:20 final size:20
Alignment explanation
Indices: 319364--319514 Score: 187
Period size: 20 Copynumber: 7.5 Consensus size: 20
319354 CGATTTTCCA
* ** *
319364 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
319384 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
319404 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
319424 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
319444 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
319464 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
319484 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
319504 AAATCGCAACG
1 AAATCGCAACG
319515 ATAATATATA
Statistics
Matches: 112, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
19 1 0.01
20 109 0.97
21 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:319448 original size:60 final size:60
Alignment explanation
Indices: 319364--319537 Score: 204
Period size: 60 Copynumber: 2.9 Consensus size: 60
319354 CGATTTTCCA
* ** * *
319364 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
319424 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* ** *
319484 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATATATAAAATCGCAACGCG
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCG
319538 ATATTTAAAG
Statistics
Matches: 93, Mismatches: 20, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
60 81 0.87
61 12 0.13
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:319958 original size:33 final size:33
Alignment explanation
Indices: 319919--319989 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
319909 TTCACTTAGA
* *
319919 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
319952 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
319985 TTTCA
1 TTTCA
319990 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:320115 original size:20 final size:19
Alignment explanation
Indices: 320069--320174 Score: 78
Period size: 19 Copynumber: 5.7 Consensus size: 19
320059 TGCAGAAGAG
* *
320069 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAG--AGATGACAA
**
320090 TCGCAACGAGAGATTGACTG
1 TCGCAACGAGAGA-TGACAA
*
320110 TCGCAACGCGAGATGACAA
1 TCGCAACGAGAGATGACAA
320129 TCGCAACGA-A-A-G--AA
1 TCGCAACGAGAGATGACAA
* * *
320143 TCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGATGACAA
320162 TCGCAACGAGAGA
1 TCGCAACGAGAGA
320175 ATCGCAACGC
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
14 10 0.15
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 27 0.40
20 15 0.22
21 10 0.15
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (19 bp):
TCGCAACGAGAGATGACAA
Found at i:320146 original size:14 final size:14
Alignment explanation
Indices: 320127--320183 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
320117 GCGAGATGAC
320127 AATCGCAACGAAAG
1 AATCGCAACGAAAG
320141 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
*
320158 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
320174 AATCGCAACG
1 AATCGCAACG
320184 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 6 0.16
17 5 0.14
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:320152 original size:33 final size:33
Alignment explanation
Indices: 320110--320199 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
320100 AGATTGACTG
* *
320110 TCGCAACGCGAGATGACAATCGCAACGAAAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
*
320143 TCGCAACGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
**
320176 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAATGAAAATCGCA
320200 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.43, C:0.26, G:0.22, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
Found at i:320217 original size:19 final size:19
Alignment explanation
Indices: 320195--320292 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
320185 GAAACCAAAA
*
320195 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
320214 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
320228 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
320247 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
320261 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
320280 TCGCGTTGCGATT
1 TCGCGTTGCGATT
320293 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:320236 original size:14 final size:14
Alignment explanation
Indices: 320217--320306 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
320207 TTTCATTTCG
320217 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
320231 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
320250 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
320264 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
320281 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
320297 CGTTGCGATT
1 CGTTGCGATT
320307 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:320242 original size:33 final size:33
Alignment explanation
Indices: 320200--320314 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
320190 CAAAATCGCA
320200 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
320233 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
320266 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
320299 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
320315 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:322172 original size:93 final size:93
Alignment explanation
Indices: 322013--322579 Score: 1107
Period size: 93 Copynumber: 6.1 Consensus size: 93
322003 TAGATTGCTT
*
322013 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
322078 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
322106 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
322171 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
322199 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
322264 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
322292 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
322357 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
322385 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
322450 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
322478 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
322543 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
322571 AGTAAATTT
1 AGTAAATTT
322580 ATCCATTCAA
Statistics
Matches: 471, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 471 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:322663 original size:19 final size:19
Alignment explanation
Indices: 322623--322751 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
322613 TAGTTTACTT
* *
322623 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
322643 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
322662 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
322681 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
322695 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
322714 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
322728 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
322747 TCGCA
1 TCGCA
322752 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:322702 original size:33 final size:32
Alignment explanation
Indices: 322659--322751 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
322649 CGCGAAACCA
**
322659 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
322691 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
322724 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
322752 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:322749 original size:52 final size:52
Alignment explanation
Indices: 322623--322751 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
322613 TAGTTTACTT
**
322623 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
322675 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
322728 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
322752 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:322769 original size:19 final size:19
Alignment explanation
Indices: 322747--322881 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
322737 GAAACCAAAA
*
322747 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
322766 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
322782 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
322799 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
322815 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
322832 TCGCGTAGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
322851 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
322871 TCGTGTTGCGA
1 TCGCGTTGCGA
322882 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 44 0.47
20 12 0.13
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:322788 original size:14 final size:14
Alignment explanation
Indices: 322769--322825 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
322759 TTTCATTTCG
322769 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
322783 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
322800 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
322816 CGTTGCGATT
1 CGTTGCGATT
322826 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:322794 original size:33 final size:33
Alignment explanation
Indices: 322752--322844 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
322742 CAAAATCGCA
*
322752 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
322785 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
322818 TTGCGATTTTCATTTCGCGTAGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
322845 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:324825 original size:14 final size:14
Alignment explanation
Indices: 324806--324841 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
324796 ATTGTTTAAT
324806 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
324820 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
324834 TGATTTGT
1 TGATTTGT
324842 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:324972 original size:19 final size:19
Alignment explanation
Indices: 324948--325047 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
324938 AAAATTGACT
324948 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
324967 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
324986 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
325000 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
325019 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
325039 ATCGCAATG
1 ATCGCAATG
325048 GGAGAATCGC
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.53
20 18 0.25
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:325077 original size:53 final size:53
Alignment explanation
Indices: 324948--325064 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
324938 AAAATTGACT
324948 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
325000 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
325053 ATCGCAATGCGA
1 ATCGCAATGCGA
325065 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:325082 original size:19 final size:19
Alignment explanation
Indices: 325054--325202 Score: 139
Period size: 19 Copynumber: 8.6 Consensus size: 19
325044 AATGGGAGAA
* *
325054 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
325073 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
325089 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
325106 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
325125 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
325141 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
325158 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
325174 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
325191 TCCGCATTGCGA
1 T-CGCATTGCGA
325203 AATGTAATGG
Statistics
Matches: 107, Mismatches: 7, Indels: 31
0.74 0.05 0.21
Matches are distributed among these distances:
14 18 0.17
16 21 0.20
17 19 0.18
18 2 0.02
19 41 0.38
20 6 0.06
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:325117 original size:52 final size:52
Alignment explanation
Indices: 325054--325170 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
325044 AATGGGAGAA
*
325054 TCGCAATGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
* *
325106 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
325158 TCGCATTGCGATT
1 TCGCATTGCGATT
325171 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
Found at i:325148 original size:33 final size:33
Alignment explanation
Indices: 325111--325202 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
325101 TCATTTCGCA
325111 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
325144 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
325177 TTGCGATTTTCATTTCCGCATTGCGA
1 TTGCGATTTTCATTT-CGCATTGCGA
325203 AATGTAATGG
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 48 0.83
34 10 0.17
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:325149 original size:14 final size:14
Alignment explanation
Indices: 325130--325184 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
325120 TCATTTCGCA
325130 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
325144 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
325161 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
325177 TTGCGATT
1 TTGCGATT
325185 TTCATTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:325289 original size:19 final size:19
Alignment explanation
Indices: 325265--325358 Score: 135
Period size: 19 Copynumber: 5.2 Consensus size: 19
325255 TTGACTATCA
325265 CAATGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
325284 CAATGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
*
325303 CAA--CG--AT-AGAATCG
1 CAATGCGAAATGAAAATCG
325317 CAATGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
325336 CAATGCGGAAATGAAAATCG
1 CAATGC-GAAATGAAAATCG
325356 CAA
1 CAA
325359 CGAGAGAATC
Statistics
Matches: 67, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
14 9 0.13
15 2 0.03
16 2 0.03
17 2 0.03
18 2 0.03
19 34 0.51
20 16 0.24
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
CAATGCGAAATGAAAATCG
Found at i:325369 original size:53 final size:52
Alignment explanation
Indices: 325265--325377 Score: 208
Period size: 53 Copynumber: 2.2 Consensus size: 52
325255 TTGACTATCA
*
325265 CAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGATAGAATCG
1 CAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG
325317 CAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG
1 CAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCG
325370 CAATGCGA
1 CAATGCGA
325378 TTTTCATTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 25 0.42
53 34 0.58
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (52 bp):
CAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG
Found at i:325900 original size:20 final size:20
Alignment explanation
Indices: 325872--326120 Score: 266
Period size: 20 Copynumber: 12.4 Consensus size: 20
325862 AAATTTCAGT
* * *
325872 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
325892 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
**
325912 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
325932 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
325952 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
325972 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
325992 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
326012 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
326032 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
326052 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
326072 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
326092 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
326112 GTTGCGATT
1 GTTGCGATT
326121 CTGTAAAATC
Statistics
Matches: 204, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 203 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:329967 original size:32 final size:33
Alignment explanation
Indices: 329931--330005 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
329921 CATAAATAGA
* *
329931 TAAAATAATATATAG-AAAAACCAAACATTCAT
1 TAAAAAAATAAATAGAAAAAACCAAACATTCAT
* *
329963 TAAAAAAATAAATAGAAAAAACTAATCATTCAT
1 TAAAAAAATAAATAGAAAAAACCAAACATTCAT
329996 TCAAAAAAAT
1 T-AAAAAAAT
330006 CGAACCACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 13 0.35
33 16 0.43
34 8 0.22
ACGTcount: A:0.63, C:0.11, G:0.03, T:0.24
Consensus pattern (33 bp):
TAAAAAAATAAATAGAAAAAACCAAACATTCAT
Found at i:331831 original size:30 final size:30
Alignment explanation
Indices: 331797--331856 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
331787 ATCCTGGGCC
331797 ATATTTAACACACTTTGCATATGTAGTTTT
1 ATATTTAACACACTTTGCATATGTAGTTTT
331827 ATATTTAACACACTTTGCATATGTAGTTTT
1 ATATTTAACACACTTTGCATATGTAGTTTT
331857 TTTTGTTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (30 bp):
ATATTTAACACACTTTGCATATGTAGTTTT
Found at i:335715 original size:21 final size:22
Alignment explanation
Indices: 335674--335715 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
335664 ATCACATATT
335674 TATTTACTATGACTAAATTTGG
1 TATTTACTATGACTAAATTTGG
335696 TATTTCACTAT-ACT-AATTTG
1 TATTT-ACTATGACTAAATTTG
335716 ATATCTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (22 bp):
TATTTACTATGACTAAATTTGG
Found at i:339172 original size:2 final size:2
Alignment explanation
Indices: 339167--339198 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
339157 AGTTCATACG
339167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
339199 CAGAAAACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:341577 original size:21 final size:21
Alignment explanation
Indices: 341553--341595 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
341543 TATTTGGCAA
* *
341553 ATTAGGCTCATTTTGAACATC
1 ATTAGACTCATTTGGAACATC
*
341574 ATTAGACTCATTTGGAAGATC
1 ATTAGACTCATTTGGAACATC
341595 A
1 A
341596 ATTTCAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (21 bp):
ATTAGACTCATTTGGAACATC
Found at i:345254 original size:177 final size:177
Alignment explanation
Indices: 344958--345306 Score: 610
Period size: 177 Copynumber: 2.0 Consensus size: 177
344948 GTTTTATTTG
* *
344958 CATTATTTGGAATGTTAACATCAATGGACTTACAAGCCAATTTCAAAGTAGGAGAAGTTGGATGC
1 CATTATTTGGAATGTTAACATCAATGGACTTACAAGCCAATTTCAAAGTAGAAAAAGTTGGATGC
* *
345023 TCTAATCTCCTATGCCAGAGTTCAAATGAATTACAAGAAACATTCATTGAAAAATCCTCTGCATT
66 TCTAATCTCCTATGCCAGAGTTCAAACGAATTACAAGAAACATTCATTGAAAAATCCTCTACATT
*
345088 ATTACAAGTAGTTGGTTTACTATCCAAAGTAAATTTATAAAGACTCC
131 AGTACAAGTAGTTGGTTTACTATCCAAAGTAAATTTATAAAGACTCC
345135 CATTATTTGGAATGTTAACATCAATGGACTTACAAGCCAATTTCAAAGTAGAAAAAGTTGGATG-
1 CATTATTTGGAATGTTAACATCAATGGACTTACAAGCCAATTTCAAAGTAGAAAAAGTTGGATGC
* * *
345199 TCCTAATCTCCTATGCTAGAGTTCAAACGAATTAGAAGAACCATTCATTGAAAAATCCTCTACAT
66 T-CTAATCTCCTATGCCAGAGTTCAAACGAATTACAAGAAACATTCATTGAAAAATCCTCTACAT
345264 TAGTACAAGTAGTTGGTTTACTATCCAAAGTAAATTTATAAAG
130 TAGTACAAGTAGTTGGTTTACTATCCAAAGTAAATTTATAAAG
345307 GCCCCCTTGA
Statistics
Matches: 163, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
176 1 0.01
177 162 0.99
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (177 bp):
CATTATTTGGAATGTTAACATCAATGGACTTACAAGCCAATTTCAAAGTAGAAAAAGTTGGATGC
TCTAATCTCCTATGCCAGAGTTCAAACGAATTACAAGAAACATTCATTGAAAAATCCTCTACATT
AGTACAAGTAGTTGGTTTACTATCCAAAGTAAATTTATAAAGACTCC
Found at i:352544 original size:23 final size:21
Alignment explanation
Indices: 352436--352603 Score: 183
Period size: 21 Copynumber: 7.9 Consensus size: 21
352426 TTGAGGGTTT
*
352436 TATGTGGTCCTTCGGGACATG
1 TATGTGGTCCTTCGGGACATA
* * *
352457 TATGTGATCCTTTGGAACATA
1 TATGTGGTCCTTCGGGACATA
* *
352478 TATGAGGTCCTTCAGGACATA
1 TATGTGGTCCTTCGGGACATA
* ** ** *
352499 TATTTGGTTATTTAGAACATA
1 TATGTGGTCCTTCGGGACATA
*
352520 TATGTGGTCCTTAGGGACAATTA
1 TATGTGGTCCTTCGGGAC-A-TA
352543 TATGTGGTCCTTCGGGACATA
1 TATGTGGTCCTTCGGGACATA
*
352564 TATGTGGTCTTTCGGGACATA
1 TATGTGGTCCTTCGGGACATA
*
352585 TATGAGGTCCTTCGGGACA
1 TATGTGGTCCTTCGGGACA
352604 ATTTTATATT
Statistics
Matches: 120, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
21 99 0.82
22 2 0.02
23 19 0.16
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACATA
Found at i:352561 original size:65 final size:65
Alignment explanation
Indices: 352476--352606 Score: 174
Period size: 65 Copynumber: 2.0 Consensus size: 65
352466 CTTTGGAACA
* * *
352476 TATATGAGGTCCTTCAGGACATATATTTGGT-TATTTAGAACATATATGTGGTCCTTAGGGACAA
1 TATATGAGGTCCTTCAGGACATATATGTGGTCT-TTCAGAACATATATGAGGTCCTTAGGGACAA
352540 T
65 T
* * * * *
352541 TATATGTGGTCCTTCGGGACATATATGTGGTCTTTCGGGACATATATGAGGTCCTTCGGGACAAT
1 TATATGAGGTCCTTCAGGACATATATGTGGTCTTTCAGAACATATATGAGGTCCTTAGGGACAAT
352606 T
1 T
352607 TTATATTGCA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 56 0.98
66 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (65 bp):
TATATGAGGTCCTTCAGGACATATATGTGGTCTTTCAGAACATATATGAGGTCCTTAGGGACAAT
Found at i:353748 original size:21 final size:20
Alignment explanation
Indices: 353702--353749 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
353692 GAGTGCTACT
**
353702 TAAAATGTTATTTTTATATC
1 TAAAATGTTATTTCAATATC
**
353722 GGAAATGTTAATTTCAATATC
1 TAAAATGTT-ATTTCAATATC
353743 TAAAATG
1 TAAAATG
353750 AATATTTAAG
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (20 bp):
TAAAATGTTATTTCAATATC
Found at i:355464 original size:21 final size:21
Alignment explanation
Indices: 355440--355486 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
355430 ATTCTGACTA
*
355440 TCGCATTGTGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
355461 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
355482 TCGCA
1 TCGCA
355487 ATGCAAATAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:355507 original size:20 final size:20
Alignment explanation
Indices: 355482--355593 Score: 125
Period size: 20 Copynumber: 5.5 Consensus size: 20
355472 TTTTCCTAAT
* *
355482 TCGCAATGCAAATACGTAAA
1 TCGCAATGCGATTACGTAAA
* ** *
355502 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCG-ATTACGTAAA
*
355523 TCGCAATGTGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
* *
355543 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
355563 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
*
355583 TCACAATGCGA
1 TCGCAATGCGA
355594 ATCTATAAAT
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 62 0.82
21 14 0.18
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:355576 original size:40 final size:39
Alignment explanation
Indices: 355482--355608 Score: 137
Period size: 40 Copynumber: 3.2 Consensus size: 39
355472 TTTTCCTAAT
* * * * *
355482 TCGCAATGCAAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGATTACGTAAATCGCAATGCGAA--TCGTAAA
* *
355523 TCGCAATGTGATTACGTAAATCGCAATGTGAATACGTAAA
1 TCGCAATGCGATTACGTAAATCGCAATGCGAAT-CGTAAA
* *
355563 TCGCAATGCGATTACGTAAATCACAATGCGAATCTATAAA
1 TCGCAATGCGATTACGTAAATCGCAATGCGAATC-GTAAA
355603 TCGCAA
1 TCGCAA
355609 CGAGATTCTG
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.03
40 44 0.60
41 27 0.37
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (39 bp):
TCGCAATGCGATTACGTAAATCGCAATGCGAATCGTAAA
Found at i:356516 original size:24 final size:24
Alignment explanation
Indices: 356470--356523 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
356460 GTATTCGAAA
*
356470 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATAACCGGAC
* *
356494 TTTGATCTTGGTCAATAATCGGAT
1 TTTGATCTTGGTCAATAACCGGAC
356518 TTTGAT
1 TTTGAT
356524 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATAACCGGAC
Found at i:359010 original size:20 final size:20
Alignment explanation
Indices: 358979--359038 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
358969 AATATTAACA
358979 CGGAAATGACTATCGCAACG
1 CGGAAATGACTATCGCAACG
358999 C-GAAATTGACTATCGCAACG
1 CGGAAA-TGACTATCGCAACG
359019 CGGAAATGACTATCGCAACG
1 CGGAAATGACTATCGCAACG
359039 AGAGAATCGC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.11
20 30 0.79
21 4 0.11
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (20 bp):
CGGAAATGACTATCGCAACG
Found at i:359067 original size:19 final size:19
Alignment explanation
Indices: 359043--359088 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
359033 GCAACGAGAG
*
359043 AATCGCAATGTAAAATGAA
1 AATCGCAATGCAAAATGAA
*
359062 AATCGCAATGCGAAATGAA
1 AATCGCAATGCAAAATGAA
*
359081 AAGCGCAA
1 AATCGCAA
359089 CGAGTGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.50, C:0.15, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCAAAATGAA
Found at i:359079 original size:52 final size:53
Alignment explanation
Indices: 359010--359130 Score: 172
Period size: 53 Copynumber: 2.3 Consensus size: 53
359000 GAAATTGACT
** * *
359010 ATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAATG-TAAAATGAAA
1 ATCGCAACGC-GAAATGAAAAGCGCAACGAGAGAATCGCAATGAGAAAATGAAA
* *
359063 ATCGCAATGCGAAATGAAAAGCGCAACGAGTGAATCGCAATGAGAAAATGAAA
1 ATCGCAACGCGAAATGAAAAGCGCAACGAGAGAATCGCAATGAGAAAATGAAA
359116 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
359131 TAGTTTCACG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
52 28 0.47
53 32 0.53
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (53 bp):
ATCGCAACGCGAAATGAAAAGCGCAACGAGAGAATCGCAATGAGAAAATGAAA
Found at i:359129 original size:20 final size:20
Alignment explanation
Indices: 358948--359129 Score: 59
Period size: 20 Copynumber: 9.8 Consensus size: 20
358938 CGCAACGCGG
*
358948 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAAAATGA
* *** * *
358968 CAATATTAACACGGAAATGA
1 AAATCGCAACGCGAAAATGA
** *
358988 CTATCGCAACGCGAAATTGA
1 AAATCGCAACGCGAAAATGA
** *
359008 CTATCGCAACGCGGAAATGA
1 AAATCGCAACGCGAAAATGA
**
359028 CTATCGCAA--CG---A-GA
1 AAATCGCAACGCGAAAATGA
* * *
359042 GAATCGCAATG-TAAAATGA
1 AAATCGCAACGCGAAAATGA
*
359061 AAATCGCAATGCG-AAATGA
1 AAATCGCAACGCGAAAATGA
* *
359080 AAAGCGCAA--CG--AGTG-
1 AAATCGCAACGCGAAAATGA
* *
359095 -AATCGCAATGAGAAAATGA
1 AAATCGCAACGCGAAAATGA
359114 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
359130 TTAGTTTCAC
Statistics
Matches: 121, Mismatches: 28, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
14 16 0.13
15 1 0.01
16 4 0.03
17 2 0.02
18 6 0.05
19 26 0.21
20 66 0.55
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.15
Consensus pattern (20 bp):
AAATCGCAACGCGAAAATGA
Found at i:359221 original size:33 final size:33
Alignment explanation
Indices: 359139--359223 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
359129 ATTAGTTTCA
359139 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
* * *
359173 CATTGCGCTTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
359206 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
359224 CGCGTTGCAG
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:359352 original size:14 final size:14
Alignment explanation
Indices: 359333--359369 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
359323 CATCAATTAA
359333 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
359347 ACAAATCATCTTTT
1 ACAAATCAACATTT
359361 ACAAATCAA
1 ACAAATCAA
359370 TCAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:360824 original size:42 final size:42
Alignment explanation
Indices: 360717--360828 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
360707 TCTAGAATGT
* *
360717 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACAG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACAG
* * ** *
360759 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAAC-G
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACAG
360800 ATAGGG-GAGGCCTCTTGAACGATGACAGG
1 -T-GGGAGAGGCCTCTTGAACGATGACAGG
360829 TGAGTCGGGC
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
41 1 0.02
42 50 0.89
43 5 0.09
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACAG
Found at i:361351 original size:20 final size:21
Alignment explanation
Indices: 361308--361355 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
361298 GAAACTTAAA
* *
361308 ATCGCAACGCGAAAATTTACT
1 ATCGCAACACGAAAATTGACT
361329 ATCGCAACACGAAAA-TGACT
1 ATCGCAACACGAAAATTGACT
361349 ATCGCAA
1 ATCGCAA
361356 TGAGAGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.19
Consensus pattern (21 bp):
ATCGCAACACGAAAATTGACT
Found at i:361421 original size:20 final size:20
Alignment explanation
Indices: 361396--361464 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
361386 CAACAAAAAA
361396 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
361416 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
361436 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
361456 ATCGCAACG
1 ATCGCAACG
361465 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:361536 original size:20 final size:20
Alignment explanation
Indices: 361507--361652 Score: 196
Period size: 20 Copynumber: 7.6 Consensus size: 20
361497 GCGATTTTTT
* **
361507 CATTGTGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
361527 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
361547 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
361567 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
* *
361587 TATTGCGAT--TC--TCTCG
1 CATTGCGATAGTCATTTTCG
361603 --TTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
361621 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
361641 CATTGCGATAGT
1 CATTGCGATAGT
361653 AAACTATTCT
Statistics
Matches: 113, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
14 7 0.06
16 6 0.05
18 6 0.05
20 94 0.83
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:363577 original size:20 final size:20
Alignment explanation
Indices: 363552--363620 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
363542 GCAAAACTTT
363552 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
363572 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
363592 CTATCGCAACGCG-AAATGA
1 AAATCGCAACACGAAAATGA
363611 AAATCGCAAC
1 AAATCGCAAC
363621 GACAGAATCA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 14 0.32
20 30 0.68
ACGTcount: A:0.49, C:0.23, G:0.16, T:0.12
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:364018 original size:22 final size:22
Alignment explanation
Indices: 363957--364018 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 22
363947 TGACCGTTAA
* *
363957 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
363979 TGATATCGTC---G-TGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
363997 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
364019 GGATGTCGCC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 15 0.47
19 1 0.03
21 1 0.03
22 15 0.47
ACGTcount: A:0.19, C:0.16, G:0.39, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:364218 original size:20 final size:20
Alignment explanation
Indices: 364193--364284 Score: 112
Period size: 20 Copynumber: 4.5 Consensus size: 20
364183 GCTATGTAAA
364193 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
*
364213 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAT
* * **
364233 TCGCATTACGATTTTTCAAAT
1 TCGCATTGCGA-TTTACGTAT
**
364254 TCGTGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
364274 TCGCATTGCGA
1 TCGCATTGCGA
364285 ATAAGGAAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 44 0.77
21 13 0.23
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:364305 original size:21 final size:21
Alignment explanation
Indices: 364281--364326 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
364271 TATTCGCATT
364281 GCGAATAAGGAAAATCGCAAC
1 GCGAATAAGGAAAATCGCAAC
** * *
364302 GCGAATTTGGGAAATCGCAAT
1 GCGAATAAGGAAAATCGCAAC
364323 GCGA
1 GCGA
364327 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.28, T:0.15
Consensus pattern (21 bp):
GCGAATAAGGAAAATCGCAAC
Found at i:368532 original size:15 final size:15
Alignment explanation
Indices: 368491--368542 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
368481 ATAGTACAAT
368491 ATTATTATTTTAATA
1 ATTATTATTTTAATA
* *
368506 ATTAATAATTTAATA
1 ATTATTATTTTAATA
* *
368521 TTTTTTATTTTAATA
1 ATTATTATTTTAATA
*
368536 ATAATTA
1 ATTATTA
368543 ATATAATTTA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATTATTTTAATA
Found at i:368560 original size:30 final size:30
Alignment explanation
Indices: 368478--368567 Score: 78
Period size: 30 Copynumber: 3.0 Consensus size: 30
368468 GATATAATTT
* * *
368478 TTAATAGTACAATA-TTATTATTTTAATAA
1 TTAATAATATAATATTTAGTATTTTAATAA
* **
368507 TTAATAATTTAATATTTTTTATTTTAATAA
1 TTAATAATATAATATTTAGTATTTTAATAA
368537 -TAATTAATATAAT-TTATAGTATTTTTAATAA
1 TTAA-TAATATAATATT-TAGTA-TTTTAATAA
368568 AATACAATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
29 16 0.32
30 25 0.50
31 9 0.18
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (30 bp):
TTAATAATATAATATTTAGTATTTTAATAA
Found at i:369579 original size:31 final size:31
Alignment explanation
Indices: 369544--369684 Score: 174
Period size: 31 Copynumber: 4.5 Consensus size: 31
369534 TAAAAGTTAA
* * * *
369544 ATAAAATATTAAATAAATCTTTAAATTTTAG
1 ATAAAATATTAATTTAATCTTTGAACTTTAG
* *
369575 ATAAAATATTAATTTGATCTATGAACTTTAG
1 ATAAAATATTAATTTAATCTTTGAACTTTAG
*
369606 ATAAAATATTCATTTAATCTTTGAACTTTAG
1 ATAAAATATTAATTTAATCTTTGAACTTTAG
* * *
369637 ATAAAATATTAATTTTATCTTTGAATTTTAA
1 ATAAAATATTAATTTAATCTTTGAACTTTAG
* *
369668 ATAAAACATCAATTTAA
1 ATAAAATATTAATTTAA
369685 AATTAACAGT
Statistics
Matches: 94, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 94 1.00
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.43
Consensus pattern (31 bp):
ATAAAATATTAATTTAATCTTTGAACTTTAG
Found at i:381448 original size:14 final size:14
Alignment explanation
Indices: 381431--381466 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
381421 ATGTCATATA
381431 AAAAAAATTAAAAG
1 AAAAAAATTAAAAG
* *
381445 AAAAAAAGTAAATG
1 AAAAAAATTAAAAG
381459 AAAAAAAT
1 AAAAAAAT
381467 ATTAAATTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (14 bp):
AAAAAAATTAAAAG
Found at i:381564 original size:24 final size:25
Alignment explanation
Indices: 381533--381579 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
381523 AAAATTAAAC
381533 AAAATAAAAT-AAAAAAGAAGTGAA
1 AAAATAAAATAAAAAAAGAAGTGAA
381557 AAAATAAAATAAAAAAAGAAGTG
1 AAAATAAAATAAAAAAAGAAGTG
381580 TCAAATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (25 bp):
AAAATAAAATAAAAAAAGAAGTGAA
Found at i:383109 original size:86 final size:86
Alignment explanation
Indices: 382995--383373 Score: 553
Period size: 86 Copynumber: 4.4 Consensus size: 86
382985 CGGTCATAAT
* * * * *
382995 TCTTTAGATGACTCCCCTTCACGAGAAAGTAAAGTGGTATATTCTTCAGGTGGTTCCCCTTCACG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCG
383060 GGTCTGAACCAGGTGAGATGA
66 GGTCTGAACCAGGTGAGATGA
** * * *
383081 TCTTTGGATGACTCCCCTTCATTGGAAAGTCATGTGGTTTATTCTTCAGGTGATTCCCCTTTGCG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCG
* *
383146 GGTCTAAACCAGGTGAGATTA
66 GGTCTGAACCAGGTGAGATGA
* * * * *
383167 TCTTTGGATGACTCCTCTTCACGGGAAAGTCATGTGGTATATTCTTTAGGTGGTTTCTCTTTGCG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCG
*
383232 GGTTTGAACCAGGTGAGATGA
66 GGTCTGAACCAGGTGAGATGA
383253 TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCG
* *
383318 GGTCTTAACCAGGTGAGATTA
66 GGTCTGAACCAGGTGAGATGA
* *
383339 TCTTTGGATGAC-CCCATTCATGGGAAAGTCATGTG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTG
383374 AGATGTTCTT
Statistics
Matches: 260, Mismatches: 33, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
85 21 0.08
86 239 0.92
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.34
Consensus pattern (86 bp):
TCTTTGGATGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCG
GGTCTGAACCAGGTGAGATGA
Found at i:389590 original size:61 final size:59
Alignment explanation
Indices: 389481--389599 Score: 136
Period size: 61 Copynumber: 2.0 Consensus size: 59
389471 ATTAAATTTA
* ** *
389481 AAAAAATAAATCAAAGAAGGAAATATTAAATTTAAAAATGTTATATAAAAATATTAAAAG
1 AAAAAATAAATCAAAGAAGAAAATATTAAATTTAAAAATAATATAT-AAAATATAAAAAG
389541 AAAAAATAAAAT-AAATGAAGAAAATATTAAATTTCAGAAAA-AATA-ATAAAATATAAAAA
1 AAAAAAT-AAATCAAA-GAAGAAAATATTAAATTT-A-AAAATAATATATAAAATATAAAAA
389600 ATGTTAAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
60 21 0.41
61 23 0.45
62 3 0.06
63 4 0.08
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (59 bp):
AAAAAATAAATCAAAGAAGAAAATATTAAATTTAAAAATAATATATAAAATATAAAAAG
Found at i:389598 original size:17 final size:17
Alignment explanation
Indices: 389578--389645 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
389568 TAAATTTCAG
*
389578 AAAAAATAATAAAATAT
1 AAAAAATAATAAAAGAT
**
389595 AAAAAATGTTAAAAGAT
1 AAAAAATAATAAAAGAT
* * *
389612 AAAATAAAAATAAAACAA
1 AAAA-AATAATAAAAGAT
*
389630 AACAAAATAAAAAAAG
1 AA-AAAATAATAAAAG
389646 TGGTAAAATA
Statistics
Matches: 38, Mismatches: 11, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
17 18 0.47
18 18 0.47
19 2 0.05
ACGTcount: A:0.76, C:0.03, G:0.04, T:0.16
Consensus pattern (17 bp):
AAAAAATAATAAAAGAT
Found at i:389718 original size:21 final size:20
Alignment explanation
Indices: 389693--389745 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
389683 AATTTTAAAG
389693 AAAATACAAAATAATTA-TAAT
1 AAAATA-AAAATAA-TAGTAAT
389714 AAAATAATAAATAATAGTAAT
1 AAAATAA-AAATAATAGTAAT
389735 AAAGATAAAAA
1 AAA-ATAAAAA
389746 GAAGGTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.10
21 22 0.76
22 4 0.14
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (20 bp):
AAAATAAAAATAATAGTAAT
Found at i:389791 original size:18 final size:18
Alignment explanation
Indices: 389770--389812 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
389760 GTTGTTTTTA
*
389770 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
389788 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
389806 AAATAAA
1 AAATAAA
389813 TAATATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:390442 original size:2 final size:2
Alignment explanation
Indices: 390424--390470 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
390414 CAAAGATAAA
390424 AT AT A- AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
390463 AT AT AT AT
1 AT AT AT AT
390471 TAAATAAGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:391369 original size:16 final size:17
Alignment explanation
Indices: 391345--391382 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
391335 TAACATATAA
*
391345 TTTATATTAATAAT-TT
1 TTTAAATTAATAATATT
*
391361 TTTAAATTAATTATATT
1 TTTAAATTAATAATATT
391378 TTTAA
1 TTTAA
391383 TAAAGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAAATTAATAATATT
Found at i:391783 original size:17 final size:17
Alignment explanation
Indices: 391763--391814 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
391753 TTTAATTGTC
391763 TTTATAAATAAATTTAT
1 TTTATAAATAAATTTAT
*
391780 TTTATAGTAATAAAATTAAT
1 TTTATA--AAT-AAATTTAT
*
391800 ATT-TAAATAAATTTA
1 TTTATAAATAAATTTA
391815 AAATGTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 6 0.21
17 9 0.31
19 5 0.17
20 9 0.31
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
TTTATAAATAAATTTAT
Found at i:391815 original size:17 final size:18
Alignment explanation
Indices: 391788--391826 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
391778 ATTTTATAGT
*
391788 AATAAAATTAATAT-TTA
1 AATAAAATTAAAATGTTA
*
391805 AATAAATTTAAAATGTTA
1 AATAAAATTAAAATGTTA
391823 AATA
1 AATA
391827 TCTATAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
AATAAAATTAAAATGTTA
Found at i:392497 original size:24 final size:22
Alignment explanation
Indices: 392440--392499 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 22
392430 CCGACTATAT
392440 ATATATATATATTTAATATTTTAA
1 ATATAT-TAT-TTTAATATTTTAA
* *
392464 ATATTTTTATTTTTATATTGTTAAA
1 ATA-TATTATTTTAATATT-TT-AA
392489 ATATATTATTT
1 ATATATTATTT
392500 AATTATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 8 0.27
24 15 0.50
25 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATATATTATTTTAATATTTTAA
Found at i:392506 original size:24 final size:23
Alignment explanation
Indices: 392442--392541 Score: 70
Period size: 21 Copynumber: 4.5 Consensus size: 23
392432 GACTATATAT
392442 ATATATATATTTAA-TATTTT-AA
1 ATATAT-TATTTAATTATTTTAAA
* *
392464 ATATTTTTATTT-TTATATTGTTAAA
1 ATA-TATTATTTAAT-TATT-TTAAA
392489 ATATATTATTTAATTA--TTAAA
1 ATATATTATTTAATTATTTTAAA
* * *
392510 A-ATA-TAATAAATTATTATAAA
1 ATATATTATTTAATTATTTTAAA
392531 ATATATTATTT
1 ATATATTATTT
392542 TAACAATTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 19
0.68 0.10 0.22
Matches are distributed among these distances:
19 8 0.14
20 3 0.05
21 11 0.19
22 11 0.19
23 9 0.15
24 11 0.19
25 6 0.10
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (23 bp):
ATATATTATTTAATTATTTTAAA
Found at i:392537 original size:42 final size:41
Alignment explanation
Indices: 392485--392581 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 41
392475 TTTATATTGT
** *
392485 TAAAATATATTATTTAATTA-TTAAAAATATAATAAATTATTA
1 TAAAATATATTATTTAACAATTTAAAAATA-AA-AAATGATTA
392527 TAAAATATATTATTTTAACAATTTAAAAATAAAAAATGATTA
1 TAAAATATATTA-TTTAACAATTTAAAAATAAAAAATGATTA
392569 T-AAATATATTATT
1 TAAAATATATTATT
392582 ATAAAATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
40 2 0.04
41 10 0.20
42 21 0.42
43 8 0.16
44 9 0.18
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (41 bp):
TAAAATATATTATTTAACAATTTAAAAATAAAAAATGATTA
Found at i:392590 original size:15 final size:15
Alignment explanation
Indices: 392515--392596 Score: 66
Period size: 15 Copynumber: 5.7 Consensus size: 15
392505 TTAAAAATAT
*
392515 AATAAATTATTATAA
1 AATATATTATTATAA
*
392530 AATATATTATTTTAA
1 AATATATTATTATAA
* **
392545 CAAT-T-TAAAAATAA
1 -AATATATTATTATAA
*
392559 AA-A-ATGATTAT-A
1 AATATATTATTATAA
392571 AATATATTATTATAA
1 AATATATTATTATAA
392586 AATATATTATT
1 AATATATTATT
392597 TTAATTATTT
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
12 3 0.06
13 7 0.14
14 12 0.24
15 26 0.51
16 3 0.06
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (15 bp):
AATATATTATTATAA
Found at i:392780 original size:73 final size:73
Alignment explanation
Indices: 392643--392780 Score: 215
Period size: 73 Copynumber: 1.9 Consensus size: 73
392633 TCGGGTCAGA
* * * *
392643 GTTTTAATTTAAAAATCAAAACGGATTCTAGACGGAAGAAAAACTAAAAATTATCGGGATGGATC
1 GTTTTAATTTAAAAATCAAAACGGATTCGAGACGAAAGAAAAACTAAAAATTATCGGAACGGATC
392708 GGATCGTG
66 GGATCGTG
*
392716 GTTTTAATTTAAAAATTAAAA-GGAATTCGAGACGAAAGAAAAACTAAAAATTATCGGAACGGAT
1 GTTTTAATTTAAAAATCAAAACGG-ATTCGAGACGAAAGAAAAACTAAAAATTATCGGAACGGAT
392780 C
65 C
392781 AAGACCGGGT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
72 2 0.03
73 57 0.97
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (73 bp):
GTTTTAATTTAAAAATCAAAACGGATTCGAGACGAAAGAAAAACTAAAAATTATCGGAACGGATC
GGATCGTG
Found at i:393986 original size:24 final size:22
Alignment explanation
Indices: 393959--394010 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
393949 TTTTTAAAGA
393959 TTTTTTCGAAATACTTATAGGG
1 TTTTTTCGAAATACTTATAGGG
*
393981 ATTTTTTCGAAATACTTTTAGGG
1 -TTTTTTCGAAATACTTATAGGG
394004 TTCTTTT
1 TT-TTTT
394011 TATGAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 2 0.07
23 25 0.93
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.52
Consensus pattern (22 bp):
TTTTTTCGAAATACTTATAGGG
Found at i:394017 original size:25 final size:23
Alignment explanation
Indices: 393957--394003 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
393947 GTTTTTTAAA
393957 GATTTTTTCGAAATACTTATAGG
1 GATTTTTTCGAAATACTTATAGG
*
393980 GATTTTTTCGAAATACTTTTAGG
1 GATTTTTTCGAAATACTTATAGG
394003 G
1 G
394004 TTCTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.45
Consensus pattern (23 bp):
GATTTTTTCGAAATACTTATAGG
Found at i:397538 original size:15 final size:15
Alignment explanation
Indices: 397499--397554 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
397489 ACAATGATTA
397499 CACCATCATCA-AAG
1 CACCATCATCACAAG
*
397513 -ACTGCAACATCACAAG
1 CAC--CATCATCACAAG
*
397529 CACCATCATCACAAC
1 CACCATCATCACAAG
*
397544 CACTATCATCA
1 CACCATCATCA
397555 TCACAAGCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
15 27 0.79
16 3 0.09
17 2 0.06
ACGTcount: A:0.41, C:0.38, G:0.05, T:0.16
Consensus pattern (15 bp):
CACCATCATCACAAG
Found at i:403255 original size:3 final size:3
Alignment explanation
Indices: 403247--403272 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
403237 TCCGAGATAC
403247 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
403273 ATATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:403744 original size:21 final size:21
Alignment explanation
Indices: 403720--403772 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
403710 GTTAAGACTT
*
403720 TTTCGATGAAATGACTTAAT-C
1 TTTCGATGAAAGGACTT-ATCC
* *
403741 TTTCAATTAAAGGACTTATCC
1 TTTCGATGAAAGGACTTATCC
*
403762 TTTTGATGAAA
1 TTTCGATGAAA
403773 AGTGCTTAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (21 bp):
TTTCGATGAAAGGACTTATCC
Found at i:403802 original size:21 final size:21
Alignment explanation
Indices: 403749--403814 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
403739 TCTTTCAATT
* * *
403749 AAAGGACTTATCCTTTTGATG
1 AAAGGGCTTAACCTTTTCATG
*
403770 AAAAGTGCTTAACCTTTTCATG
1 -AAAGGGCTTAACCTTTTCATG
* * *
403792 AAAGGGTTTAATCGTTTCATG
1 AAAGGGCTTAACCTTTTCATG
403813 AA
1 AA
403815 GAGAATTGTT
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 19 0.53
22 17 0.47
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (21 bp):
AAAGGGCTTAACCTTTTCATG
Found at i:406170 original size:2 final size:2
Alignment explanation
Indices: 406163--406228 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
406153 TATCTCAGAT
406163 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
406205 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
406229 GAATTTGTCT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:406395 original size:3 final size:3
Alignment explanation
Indices: 406389--406421 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
406379 AAAATAATAT
406389 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
406422 CTCGGATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:406958 original size:3 final size:3
Alignment explanation
Indices: 406952--406976 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
406942 TTTTTTCTTC
406952 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
406977 TATGTACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:407108 original size:14 final size:15
Alignment explanation
Indices: 407089--407122 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
407079 ATATATTATT
*
407089 ATTTATTTT-ATTTC
1 ATTTATTTTAATTTA
407103 ATTTATTTTAATTTA
1 ATTTATTTTAATTTA
407118 ATTTA
1 ATTTA
407123 AAATATCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTATTTTAATTTA
Found at i:409101 original size:15 final size:16
Alignment explanation
Indices: 409061--409102 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
409051 GTAGACCTTG
409061 AAAAGAAGGACGAGACA
1 AAAAGAA-GACGAGACA
*
409078 AATAAGAAGAC-AGAGA
1 AA-AAGAAGACGAGACA
409094 AAAAGAAGA
1 AAAAGAAGA
409103 ACATTAGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 7 0.30
16 6 0.26
17 5 0.22
18 5 0.22
ACGTcount: A:0.64, C:0.07, G:0.26, T:0.02
Consensus pattern (16 bp):
AAAAGAAGACGAGACA
Found at i:413379 original size:21 final size:21
Alignment explanation
Indices: 413353--413406 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
413343 TTGTGCACGG
*
413353 TGTATCGATACATCCTCGCTA
1 TGTATCGATACATCCTCCCTA
413374 TGTATCGATACATCCTCCCTA
1 TGTATCGATACATCCTCCCTA
413395 TGTATCGATACA
1 TGTATCGATACA
413407 CTATGAATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATCCTCCCTA
Found at i:418877 original size:13 final size:12
Alignment explanation
Indices: 418859--418910 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 12
418849 GTCATAAATC
418859 TATGACGTGCATT
1 TATGACGT-CATT
**
418872 TATGACACACATT
1 TATGAC-GTCATT
418885 TATGACGCTCATT
1 TATGACG-TCATT
418898 TATGACGTTCATT
1 TATGACG-TCATT
418911 AAACGTCATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (12 bp):
TATGACGTCATT
Found at i:423797 original size:21 final size:21
Alignment explanation
Indices: 423768--423808 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
423758 GACTATCACA
*
423768 TTGCGATTTCCCAAATTCGCG
1 TTGCAATTTCCCAAATTCGCG
* *
423789 TTGCAATTTTCCTAATTCGC
1 TTGCAATTTCCCAAATTCGC
423809 AATGCGAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.39
Consensus pattern (21 bp):
TTGCAATTTCCCAAATTCGCG
Found at i:423830 original size:20 final size:20
Alignment explanation
Indices: 423805--423911 Score: 128
Period size: 20 Copynumber: 5.3 Consensus size: 20
423795 TTTTCCTAAT
423805 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
423825 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
423846 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
423866 TCGCAATGCG-ATAACGTAAA
1 TCGCAATGCGAAT-ACGTAAA
423886 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
423906 TCGCAA
1 TCGCAA
423912 CGAGATTCTG
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.03
20 54 0.74
21 17 0.23
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:424799 original size:24 final size:24
Alignment explanation
Indices: 424772--424849 Score: 111
Period size: 24 Copynumber: 3.2 Consensus size: 24
424762 GTATTCGAAA
424772 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
**
424796 TTTGATCTTGGTCAATACCCATAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
424820 TTTGATCTTGGTCTATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
424844 TTTGAT
1 TTTGAT
424850 GATTTTTCAG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:427287 original size:20 final size:20
Alignment explanation
Indices: 427262--427335 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
427252 GACATTCATT
*
427262 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
*
427282 TGACTATCGCAACGCGGAAT
1 TGACTATCGCAACGCGGAAA
* *
427302 TGACTATCGCAATGCGAAAA
1 TGACTATCGCAACGCGGAAA
*
427322 TAACTATCGCAACG
1 TGACTATCGCAACG
427336 AGAGAATCGC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:427370 original size:14 final size:14
Alignment explanation
Indices: 427327--427375 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
427317 GAAAATAACT
*
427327 ATCGCAACGAGAGA
1 ATCGCAACGGGAGA
427341 ATCGCAACGGGAGA
1 ATCGCAACGGGAGA
*
427355 ATCGTAACAGGG-GA
1 ATCGCAAC-GGGAGA
427369 ATCGCAA
1 ATCGCAA
427376 TGCGAAATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 28 0.90
15 3 0.10
ACGTcount: A:0.39, C:0.20, G:0.31, T:0.10
Consensus pattern (14 bp):
ATCGCAACGGGAGA
Found at i:427392 original size:19 final size:19
Alignment explanation
Indices: 427368--427455 Score: 96
Period size: 19 Copynumber: 4.8 Consensus size: 19
427358 GTAACAGGGG
427368 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
427387 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
427406 AAGCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
427420 AATCGCAATGCGAAAATGAAA
1 AATCGCAATGCG-AAATG-AA
*
427441 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
427456 CTAATTTCAC
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
14 7 0.12
16 5 0.09
17 2 0.04
18 3 0.05
19 26 0.46
20 3 0.05
21 11 0.19
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:427522 original size:33 final size:34
Alignment explanation
Indices: 427465--427540 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
427455 ACTAATTTCA
427465 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
* *
427499 CGTTGCGCTTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
427532 CGTTGCGAT
1 CGTTGCGAT
427541 AGTCATTTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 26 0.67
34 13 0.33
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:427547 original size:33 final size:33
Alignment explanation
Indices: 427465--427549 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
427455 ACTAATTTCA
427465 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
* *
427499 CGTTGCGCTTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
427532 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
427550 CGCGTTATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 33 0.72
34 13 0.28
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:427681 original size:14 final size:14
Alignment explanation
Indices: 427662--427698 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
427652 CATCAATTAA
427662 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
427676 ACAAATCATCTTTT
1 ACAAATCAACATTT
427690 ACAAATCAA
1 ACAAATCAA
427699 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:429662 original size:20 final size:20
Alignment explanation
Indices: 429634--429682 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
429624 GAAACTTAAA
429634 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCAAAAATGACT
* *
429654 ATCGTAACGCGAAAATGACT
1 ATCGCAACGCAAAAATGACT
429674 ATCGCAACG
1 ATCGCAACG
429683 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCAAAAATGACT
Found at i:429717 original size:2 final size:2
Alignment explanation
Indices: 429710--429741 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
429700 AATGAAAACT
429710 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
429742 AAGGTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:431445 original size:29 final size:28
Alignment explanation
Indices: 431408--431553 Score: 109
Period size: 29 Copynumber: 4.9 Consensus size: 28
431398 AAAGGCAATG
*
431408 AAGATAAATAAACTAAAGAAAAATAAAATA
1 AAGA-AAATAAAATAAA-AAAAATAAAATA
* *
431438 AAGGAAATAAAAATAAATAAAATAAAGATA
1 AAGAAAAT-AAAATAAAAAAAATAAA-ATA
431468 ACGAGCAAAATAAAATAAAAATAAGAATAAAATA
1 A--AG-AAAATAAAAT-AAAA-AA-AATAAAATA
*
431502 AAGAAAAT-ACAT-AAAAAAATAAAATA
1 AAGAAAATAAAATAAAAAAAATAAAATA
* *
431528 AATATAAA-AAACTAAATAAAAATAAA
1 AAGA-AAATAAAATAAA-AAAAATAAA
431554 GAACATAAAA
Statistics
Matches: 95, Mismatches: 9, Indels: 25
0.74 0.07 0.19
Matches are distributed among these distances:
26 12 0.13
27 7 0.07
28 5 0.05
29 21 0.22
30 17 0.18
31 5 0.05
32 9 0.09
33 7 0.07
34 6 0.06
35 6 0.06
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.16
Consensus pattern (28 bp):
AAGAAAATAAAATAAAAAAAATAAAATA
Found at i:431459 original size:9 final size:9
Alignment explanation
Indices: 431411--431553 Score: 65
Period size: 9 Copynumber: 15.0 Consensus size: 9
431401 GGCAATGAAG
431411 ATAAATAAA
1 ATAAATAAA
* *
431420 CTAAAGAAAA
1 ATAAA-TAAA
431430 ATAAAATAAA
1 AT-AAATAAA
**
431440 GGAAATAAAA
1 ATAAAT-AAA
431450 ATAAATAAA
1 ATAAATAAA
* *
431459 ATAAAGATA
1 ATAAATAAA
** **
431468 ACGAGCAAA
1 ATAAATAAA
431477 ATAAAATAAAA
1 AT-AAAT-AAA
431488 ATAAGAATAAA
1 AT-A-AATAAA
*
431499 ATAAAGAAA
1 ATAAATAAA
*
431508 ATACATAAA
1 ATAAATAAA
431517 A-AAATAAA
1 ATAAATAAA
431525 ATAAATATAA
1 ATAAATA-AA
431535 A-AAACTAAA
1 ATAAA-TAAA
*
431544 TAAAAATAAA
1 -ATAAATAAA
431554 GAACATAAAA
Statistics
Matches: 100, Mismatches: 23, Indels: 21
0.69 0.16 0.15
Matches are distributed among these distances:
8 7 0.07
9 46 0.46
10 26 0.26
11 18 0.18
12 3 0.03
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (9 bp):
ATAAATAAA
Found at i:431534 original size:6 final size:5
Alignment explanation
Indices: 431413--431536 Score: 67
Period size: 5 Copynumber: 23.6 Consensus size: 5
431403 CAATGAAGAT
* **
431413 AAATA AACTA AAGA-A AAATA AAAT- AAAGG AAATA AAA-A TAAATA AAATA
1 AAATA AAATA AA-ATA AAATA AAATA AAATA AAATA AAATA -AAATA AAATA
** *
431462 AAGATA ACGAGCA AAATA AAATAA AAATA AGAATA AAAT- AAAGA AAATA
1 AA-ATA A--AATA AAATA AAAT-A AAATA A-AATA AAATA AAATA AAATA
*
431511 CATAAAA AAATA AAATA AATATA AAA
1 -A-AATA AAATA AAATA AA-ATA AAA
431537 AACTAAATAA
Statistics
Matches: 92, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
4 8 0.09
5 56 0.61
6 22 0.24
7 5 0.05
8 1 0.01
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.16
Consensus pattern (5 bp):
AAATA
Found at i:431567 original size:9 final size:9
Alignment explanation
Indices: 431505--431581 Score: 54
Period size: 9 Copynumber: 8.7 Consensus size: 9
431495 TAAAATAAAG
*
431505 AAAATACAT
1 AAAAAACAT
431514 AAAAAA-AT
1 AAAAAACAT
*
431522 AAAATAAATAT
1 -AAA-AAACAT
431533 AAAAAAC-T
1 AAAAAACAT
*
431541 AAATAAAAAT
1 AAA-AAACAT
*
431551 AAAGAACAT
1 AAAAAACAT
431560 AAAAAACA-
1 AAAAAACAT
*
431568 AAAGAA-AT
1 AAAAAACAT
431576 AAAAAA
1 AAAAAA
431582 TGAAGAAATG
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
7 1 0.02
8 16 0.30
9 25 0.46
10 10 0.19
11 2 0.04
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (9 bp):
AAAAAACAT
Found at i:431587 original size:15 final size:15
Alignment explanation
Indices: 431541--431608 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
431531 ATAAAAAACT
431541 AAAT-AAAAATAAAG
1 AAATAAAAAATAAAG
*
431555 AACATAAAAAACAAAAG
1 AA-ATAAAAAA-TAAAG
*
431572 AAATAAAAAATGAAG
1 AAATAAAAAATAAAG
* * *
431587 AAATGAAGAA-AAAT
1 AAATAAAAAATAAAG
431601 AAATAAAA
1 AAATAAAA
431609 TAAAGATAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
14 10 0.24
15 13 0.31
16 13 0.31
17 6 0.14
ACGTcount: A:0.76, C:0.03, G:0.09, T:0.12
Consensus pattern (15 bp):
AAATAAAAAATAAAG
Found at i:431632 original size:50 final size:46
Alignment explanation
Indices: 431427--431655 Score: 153
Period size: 50 Copynumber: 4.8 Consensus size: 46
431417 AAACTAAAGA
* * * *
431427 AAAATAAAATAAAGGA-AATAAAAATAAATAAAATAAAGATAACGAGC
1 AAAATAAAATAAA-AATAAGAAAAATAAAGAAAATAAAGA-AACAAGC
* * * **
431474 AAAATAAAATAAAAATAAGAATAAAATAAAGAAAATACATAAAAAAAT
1 AAAATAAAATAAAAATAAG-A-AAAATAAAGAAAATAAAGAAACAAGC
* *
431522 AAAATAAATATAAAAAACTAAATAAAAATAAAGAACATAAA-AAACAAAAG-
1 AAAATAAA-AT-AAAAA-T-AAGAAAAATAAAGAAAATAAAGAAAC--AAGC
* * *
431572 AAATAAAAAATGAAGAAATGAAGAAAAATAAATAAAATAAAGATAACGAGC
1 AAA-ATAAAAT-AA-AAAT-AAGAAAAATAAAGAAAATAAAGA-AACAAGC
*
431623 AAAATAAAATAAAAATAAG-AATA-AAAGAAAATA
1 AAAATAAAATAAAAATAAGAAAAATAAAGAAAATA
431656 CTAATAATTG
Statistics
Matches: 144, Mismatches: 24, Indels: 30
0.73 0.12 0.15
Matches are distributed among these distances:
45 9 0.06
46 4 0.03
47 18 0.12
48 16 0.11
49 23 0.16
50 54 0.38
51 15 0.10
52 5 0.03
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (46 bp):
AAAATAAAATAAAAATAAGAAAAATAAAGAAAATAAAGAAACAAGC
Found at i:431764 original size:36 final size:34
Alignment explanation
Indices: 431707--431773 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 34
431697 AATACAAATG
* *
431707 AAAATAAATATATAAATAAAACTAATATAAAATAAT
1 AAAATAAATATAGAAAAAAAAC-AA-ATAAAATAAT
431743 AAAATAAA-ATAGAAGAAAAAACAAATAAAAT
1 AAAATAAATATAGAA-AAAAAACAAATAAAAT
431774 GAGCAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 7 0.25
35 7 0.25
36 14 0.50
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (34 bp):
AAAATAAATATAGAAAAAAAACAAATAAAATAAT
Found at i:431786 original size:5 final size:5
Alignment explanation
Indices: 431695--431773 Score: 54
Period size: 5 Copynumber: 15.0 Consensus size: 5
431685 TAACAAGAGA
*
431695 AAAAT ACAAAT GAAAAT AAATAT ATAAAT AAAACT AATAT AAAAT --AAT
1 AAAAT A-AAAT -AAAAT AAA-AT A-AAAT AAAA-T AAAAT AAAAT AAAAT
* * *
431743 AAAAT AAAAT AGAAG AAAAA ACAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT
431774 GAGCAAAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
3 3 0.05
5 31 0.53
6 22 0.37
7 3 0.05
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:432613 original size:2 final size:2
Alignment explanation
Indices: 432606--432653 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
432596 TAGATTGAGA
432606 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
432648 AT AT AT
1 AT AT AT
432654 TGAGTACGAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:435559 original size:20 final size:20
Alignment explanation
Indices: 435536--435575 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
435526 TTAATCTCAT
435536 AATATCGATACTCAC-TGAAC
1 AATATCGATAC-CACATGAAC
435556 AATATCGATACCACATGAAC
1 AATATCGATACCACATGAAC
435576 GGGTATCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (20 bp):
AATATCGATACCACATGAAC
Found at i:439841 original size:35 final size:35
Alignment explanation
Indices: 439775--439842 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 35
439765 CATAATTATA
439775 TTCTTTTTTCATTTATTTATTTATATTTTTTTTCT
1 TTCTTTTTTCATTTATTTATTTATATTTTTTTTCT
439810 TTCTGTTTTT-ATTTA-TTA-TTATTATTATTTTTT
1 TTCT-TTTTTCATTTATTTATTTA-TATT-TTTTTT
439843 AAAATATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
33 3 0.10
34 7 0.23
35 15 0.50
36 5 0.17
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.76
Consensus pattern (35 bp):
TTCTTTTTTCATTTATTTATTTATATTTTTTTTCT
Found at i:440079 original size:19 final size:20
Alignment explanation
Indices: 440036--440080 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
440026 TTCCTTTTAT
* *
440036 ATTTATTTAATTTCTCTATTT
1 ATTT-TTTAATTTCACTATTG
440057 ATTTTTTAATTT-ACTATTG
1 ATTTTTTAATTTCACTATTG
440076 ATTTT
1 ATTTT
440081 ATTTATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 10 0.45
20 8 0.36
21 4 0.18
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTTTTTAATTTCACTATTG
Found at i:440111 original size:21 final size:21
Alignment explanation
Indices: 440087--440126 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
440077 TTTTATTTAT
440087 TTATTT-ATTTTATTTTCTTCC
1 TTATTTCA-TTTATTTTCTTCC
440108 TTATTTCATTTATTTTCTT
1 TTATTTCATTTATTTTCTT
440127 TATTTTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.72
Consensus pattern (21 bp):
TTATTTCATTTATTTTCTTCC
Found at i:440230 original size:13 final size:11
Alignment explanation
Indices: 440186--440234 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
440176 ATTTTGTTTA
440186 TTTT-ATCTTT
1 TTTTCATCTTT
440196 TTTTCATTCTTT
1 TTTTCA-TCTTT
*
440208 TTTTCCTCTTT
1 TTTTCATCTTT
440219 TTATCTCATCTTT
1 TT-T-TCATCTTT
440232 TTT
1 TTT
440235 ATTTTTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 4 0.12
11 8 0.24
12 12 0.36
13 9 0.27
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTCATCTTT
Found at i:440245 original size:23 final size:24
Alignment explanation
Indices: 440219--440264 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
440209 TTTCCTCTTT
440219 TTATCTCATCT-TTTTTATTTTTA
1 TTATCTCATCTATTTTTATTTTTA
* *
440242 TTATTTCATTTATTTTTATTTTT
1 TTATCTCATCTATTTTTATTTTT
440265 TATCTAACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (24 bp):
TTATCTCATCTATTTTTATTTTTA
Done.