Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008429.1 Hibiscus syriacus cultivar Beakdansim tig00111215_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: 508731
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:203175 original size:76 final size:76
Alignment explanation
Indices: 203022--203183 Score: 186
Period size: 76 Copynumber: 2.1 Consensus size: 76
203012 AAAAAATAAT
* * * *
203022 ATTTTCGGTTTTAACAAAAAATGTTATATTTTTTTGTAATATTTTCGATTTCAACTAAACTGTTA
1 ATTTTCGGTTTTAACAAAAAATGATATATTTTTTTGTAATATTTTCGATTGCAACAAAAATGTTA
203087 TATTTTTGTAC
66 TATTTTTGTAC
** * *
203098 ATTTTCGGTTTTAACCTAAAAT-AT-TATTTTTTT-TAATATTTTGGGTTGCTAACAAAAATGTT
1 ATTTTCGGTTTTAACAAAAAATGATATATTTTTTTGTAATATTTTCGATTGC-AACAAAAATGTT
*
203160 ATCTTTTTCGTTAC
65 ATATTTTT-G-TAC
*
203174 ATTTTAGGTT
1 ATTTTCGGTT
203184 ACAATTACTA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
73 13 0.18
74 26 0.36
75 2 0.03
76 32 0.44
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.52
Consensus pattern (76 bp):
ATTTTCGGTTTTAACAAAAAATGATATATTTTTTTGTAATATTTTCGATTGCAACAAAAATGTTA
TATTTTTGTAC
Found at i:206225 original size:21 final size:21
Alignment explanation
Indices: 206182--206225 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
206172 TTTGGAGAAG
* * *
206182 TTTGTTTAGATTAATTGCGAA
1 TTTGTTTACATTAATTACAAA
*
206203 TTTGTTTACATTAATTATAAA
1 TTTGTTTACATTAATTACAAA
206224 TT
1 TT
206226 AAAATTGTGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (21 bp):
TTTGTTTACATTAATTACAAA
Found at i:209409 original size:30 final size:32
Alignment explanation
Indices: 209374--209438 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
209364 ATTATTTTAG
* * *
209374 AAAATA-TATAT-TATTTATAATATTAATTTT
1 AAAATATTATATATATATATAACATTAATTAT
209404 AAAATATTATATATATATATAACATTAATTAT
1 AAAATATTATATATATATATAACATTAATTAT
209436 AAA
1 AAA
209439 GCATAATGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 6 0.20
31 5 0.17
32 19 0.63
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (32 bp):
AAAATATTATATATATATATAACATTAATTAT
Found at i:210203 original size:60 final size:60
Alignment explanation
Indices: 210082--210212 Score: 133
Period size: 60 Copynumber: 2.2 Consensus size: 60
210072 GGGTGATCAA
* * * * *
210082 TTTGTAACTTTTAATAGTCTAGAGACTTAACAAAGTAACATTCCATAGTTGAAGGATCAT
1 TTTGTAACTTTTAATAATCAAGAGACTTAACAAAGCAACATCCCATAGTTGAAGGACCAT
* * * *
210142 TTTGTAACTTTTAATAATCAAGGGACTTAATAAAGCAATA-CCCTATAGTT-AGGGGACCAT
1 TTTGTAACTTTTAATAATCAAGAGACTTAACAAAGCAACATCCC-ATAGTTGA-AGGACCAT
210202 TTGTGT-ACTTT
1 TT-TGTAACTTT
210213 ACCTTTTAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
59 3 0.05
60 53 0.90
61 3 0.05
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (60 bp):
TTTGTAACTTTTAATAATCAAGAGACTTAACAAAGCAACATCCCATAGTTGAAGGACCAT
Found at i:223316 original size:27 final size:27
Alignment explanation
Indices: 223285--223372 Score: 167
Period size: 27 Copynumber: 3.3 Consensus size: 27
223275 TCTATTTACA
*
223285 AAATCATATCTCTATAGGAATGGCAAC
1 AAATCATATCTCTATAGGAATGGTAAC
223312 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
223339 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
223366 AAATCAT
1 AAATCAT
223373 CTCTATGATT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:226681 original size:27 final size:27
Alignment explanation
Indices: 226650--226744 Score: 142
Period size: 27 Copynumber: 3.6 Consensus size: 27
226640 TCTATTTACA
*
226650 AAATCATATCTCTATAGGAATGACAAC
1 AAATCATATCTCTATAGGAATGATAAC
*
226677 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGATAAC
226704 AAATCATATCTCTATAGGAAT-AGTAAC
1 AAATCATATCTCTATAGGAATGA-TAAC
226731 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
226745 ATTCCTACAA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
25 9 0.14
27 55 0.86
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGATAAC
Found at i:229193 original size:15 final size:15
Alignment explanation
Indices: 229135--229195 Score: 59
Period size: 15 Copynumber: 3.7 Consensus size: 15
229125 AGAAAGGAAA
229135 AAAAGCAACAGAATC
1 AAAAGCAACAGAATC
*
229150 AAGAGCAACAAGATATGC
1 AAAAGCAAC-AGA-AT-C
229168 AGCATAAGCAACAGAATC
1 A--A-AAGCAACAGAATC
229186 AAAAGCAACA
1 AAAAGCAACA
229196 AGATATGCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
15 16 0.42
16 4 0.11
17 2 0.05
18 4 0.11
19 2 0.05
20 4 0.11
21 6 0.16
ACGTcount: A:0.56, C:0.20, G:0.16, T:0.08
Consensus pattern (15 bp):
AAAAGCAACAGAATC
Found at i:232785 original size:35 final size:36
Alignment explanation
Indices: 232739--232825 Score: 101
Period size: 35 Copynumber: 2.5 Consensus size: 36
232729 TAGTATTTTT
* *
232739 TAAATATTTATTATATTTTA-TATTAA-AATATTTATG
1 TAAATA-TTATTATATTTTATTA-AAATAATATTTATA
232775 TAAATATTATTAT-TTTTATTAAAATAATATTTATA
1 TAAATATTATTATATTTTATTAAAATAATATTTATA
*
232810 TAATTATTATT-TATTT
1 TAAATATTATTATATTT
232826 AGAATTATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
34 8 0.18
35 31 0.69
36 6 0.13
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (36 bp):
TAAATATTATTATATTTTATTAAAATAATATTTATA
Found at i:232816 original size:32 final size:33
Alignment explanation
Indices: 232747--232821 Score: 93
Period size: 32 Copynumber: 2.3 Consensus size: 33
232737 TTTAAATATT
*
232747 TATTA-TATTTTATATTAAAATATTTATGTAAA
1 TATTATTATTTTATATTAAAATATATATGTAAA
* *
232779 TATTATTATTTT-TATTAAAATA-ATATTTATA
1 TATTATTATTTTATATTAAAATATATATGTAAA
232810 TAATTATTATTT
1 T-ATTATTATTT
232822 ATTTAGAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 7 0.18
32 25 0.66
33 6 0.16
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (33 bp):
TATTATTATTTTATATTAAAATATATATGTAAA
Found at i:232851 original size:20 final size:18
Alignment explanation
Indices: 232810--232853 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
232800 AATATTTATA
232810 TAATTATTATTTATTTAG
1 TAATTATTATTTATTTAG
*
232828 -AATTATTAATTTTTTTTAG
1 TAATTATT-A-TTTATTTAG
232847 TAATTAT
1 TAATTAT
232854 ATTGTTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 1 0.05
19 8 0.36
20 6 0.27
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
TAATTATTATTTATTTAG
Found at i:232988 original size:17 final size:17
Alignment explanation
Indices: 232966--233019 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
232956 AATGTTAATA
232966 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
232983 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
233000 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
233017 TTT
1 TTT
233020 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:234799 original size:36 final size:37
Alignment explanation
Indices: 234738--234812 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 37
234728 CATCAAGCAA
234738 CTAGAATCAAGAGAGAATCAAAGAGAAAGCATCAAAC
1 CTAGAATCAAGAGAGAATCAAAGAGAAAGCATCAAAC
234775 CTAGAATCAAGAG-GAATCAAAGAGAAAGCATCAAAC
1 CTAGAATCAAGAGAGAATCAAAGAGAAAGCATCAAAC
234811 CT
1 CT
234813 CAAGTTTGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 25 0.66
37 13 0.34
ACGTcount: A:0.52, C:0.17, G:0.19, T:0.12
Consensus pattern (37 bp):
CTAGAATCAAGAGAGAATCAAAGAGAAAGCATCAAAC
Found at i:240324 original size:21 final size:21
Alignment explanation
Indices: 240298--240337 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
240288 CCCCCTTTGA
*
240298 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
240319 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
240338 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:244170 original size:21 final size:21
Alignment explanation
Indices: 244140--244187 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
244130 GCAGGAGTAC
* *
244140 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
244161 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
244182 ATGCCA
1 ATGCCA
244188 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:244217 original size:21 final size:21
Alignment explanation
Indices: 244191--244284 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
244181 TATGCCATCT
244191 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
244212 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
244233 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
244254 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
244275 CCGCAGGGTT
1 CCGCAGGGTT
244285 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.28, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:244900 original size:34 final size:34
Alignment explanation
Indices: 244803--244904 Score: 132
Period size: 35 Copynumber: 3.0 Consensus size: 34
244793 GATAAATATT
* *
244803 TTTAAAATACAAATTATATTATTCAAAATTTAAA
1 TTTAAAATAAAAATTATATTATTCGAAATTTAAA
* * *
244837 ATAAAAATAAAAATAAATATTATTCGAAATTTAAA
1 TTTAAAATAAAAAT-TATATTATTCGAAATTTAAA
* *
244872 TTTAAAATATAAATTATAGTATTCGAAATTTAA
1 TTTAAAATAAAAATTATATTATTCGAAATTTAA
244905 CATTAAATTT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
34 28 0.49
35 29 0.51
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (34 bp):
TTTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:244911 original size:34 final size:33
Alignment explanation
Indices: 244804--244911 Score: 126
Period size: 34 Copynumber: 3.2 Consensus size: 33
244794 ATAAATATTT
* *
244804 TTAAAATACAAATTATATTATTCAAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
244838 TAAAAATAAAAATAAATATTATTCGAAATTTAAA
1 TTAAAATAAAAAT-TATATTATTCGAAATTTAAA
* *
244872 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
244907 TTAAA
1 TTAAA
244912 TTTCAACTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
34 36 0.57
35 27 0.43
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.37
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:250527 original size:32 final size:32
Alignment explanation
Indices: 250481--250547 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
250471 GATCGGTGGG
*
250481 TTAACTTAAAATTTTAAAAAACTTTAAAGGGT
1 TTAAATTAAAATTTTAAAAAACTTTAAAGGGT
* * ** *
250513 TTAAATTAAGATTTTTAAAATTTTTGAAGGGT
1 TTAAATTAAAATTTTAAAAAACTTTAAAGGGT
250545 TTA
1 TTA
250548 GTTTATTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.43
Consensus pattern (32 bp):
TTAAATTAAAATTTTAAAAAACTTTAAAGGGT
Found at i:251087 original size:38 final size:38
Alignment explanation
Indices: 251036--251159 Score: 148
Period size: 38 Copynumber: 3.4 Consensus size: 38
251026 GTGTGTTCAG
251036 TTCGTTTATGTTCACGAACAAGCTCGTTTATCGACTCT
1 TTCGTTTATGTTCACGAACAAGCTCGTTTATCGACTCT
** * * **
251074 TTCGTTTATGTTCATTAACAAGTTC-TTT-T--AATGG
1 TTCGTTTATGTTCACGAACAAGCTCGTTTATCGACTCT
* *
251108 TTGGTTTATATTCACGAACAAGCTCGTTTATCGACTCT
1 TTCGTTTATGTTCACGAACAAGCTCGTTTATCGACTCT
251146 TTCGTTTATGTTCA
1 TTCGTTTATGTTCA
251160 TAAATGTGAG
Statistics
Matches: 66, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
34 22 0.33
35 3 0.05
36 2 0.03
37 3 0.05
38 36 0.55
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (38 bp):
TTCGTTTATGTTCACGAACAAGCTCGTTTATCGACTCT
Found at i:251227 original size:32 final size:32
Alignment explanation
Indices: 251181--251247 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
251171 GATCAGTGGG
*
251181 TTAACTTAAAATTTTAAAAAACTTTAAAGGGT
1 TTAAATTAAAATTTTAAAAAACTTTAAAGGGT
* * ** *
251213 TTAAATTAAGATTTTTAAAATTTTTGAAGGGT
1 TTAAATTAAAATTTTAAAAAACTTTAAAGGGT
251245 TTA
1 TTA
251248 GTTTATTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.43
Consensus pattern (32 bp):
TTAAATTAAAATTTTAAAAAACTTTAAAGGGT
Found at i:251803 original size:697 final size:699
Alignment explanation
Indices: 250465--251815 Score: 2607
Period size: 697 Copynumber: 1.9 Consensus size: 699
250455 TCGAGAATTG
*
250465 GTGAGAGATCGGTGGGTTAACTTAAAATTTTAAAAAACTTTAAAGGGTTTAAATTAAGATTTTTA
1 GTGAGAGATCAGTGGGTTAACTTAAAATTTTAAAAAACTTTAAAGGGTTTAAATTAAGATTTTTA
250530 AAATTTTTGAAGGGTTTAGTTTATTTTTTTCCCTAAAAATTAAGGTCTAATCAATTTTTTTTTGA
66 AAATTTTTGAAGGGTTTAGTTTATTTTTTTCCCTAAAAATTAAGGTCTAATCAATTTTTTTTTGA
*
250595 AAAAAATTGAGGTTTAATGATATTTTTTAAAAATTATGGGAGGTATTTAATTAAAAATTCAAAAA
131 AAAAAATTGAGGTTTAATGATATTTTTTAAAAATTATGGGAGGGATTTAATTAAAAATTC-AAAA
*
250660 AAAATTAAAATTTAATTTAAATTTCTAAAAGTTTTAGGAGGTCAAATTAAAATTTTCAAAAAATT
195 AAAATTAAAATTTAATTTAAATTTCTAAAAGTTTTACGAGGTCAAATTAAAATTTTCAAAAAATT
250725 TAAAGGTCTAAATTATAATTTTACTTAATGATCTTATTCTTACTTTAATGTTCTTTATTTCTGTT
260 TAAAGGTCTAAATTATAATTTTACTTAATGATCTTATTCTTACTTTAATGTTCTTTATTTCTGTT
*
250790 TGTTGTCAGCAAGTCTTCACAAGAGTTGGTGAAATGTCTGCAGTTTATAAACAGCCAACTTCCGG
325 TGTTGTCAGCAAGTCTTCACAAGAGTTGCTGAAATGTCTGCAGTTTATAAACAGCCAACTTCCGG
250855 TGAGGACCGGCTCAAGGCTCTCCAGGTATCATTTTACCGGTTCTCATATGCATTCGTGGGATTGT
390 TGAGGACCGGCTCAAGGCTCTCCAGGTATCATTTTACCGGTTCTCATATGCATTCGTGGGATTGT
250920 AAATGAACAAAACATTCGGTGAACTGTTCGTATAACGTTCGTTTAAAAAAACGAGTATGAACAAA
455 AAATGAACAAAACATTCGGTGAACTGTTCGTATAACGTTCGTTTAAAAAAACGAGTATGAACAAA
250985 ACTTTTATGTTCATTCAATAAACGAACAAACACAAATAAATGTGTGTTCAGTTCGTTTATGTTCA
520 ACTTTTATGTTCATTCAATAAACGAACAAACACAAATAAATGTGTGTTCAGTTCGTTTATGTTCA
251050 CGAACAAGCTCGTTTATCGACTCTTTCGTTTATGTTCATTAACAAGTTCTTTTAATGGTTGGTTT
585 CGAACAAGCTCGTTTATCGACTCTTTCGTTTATGTTCATTAACAAGTTCTTTTAATGGTTGGTTT
251115 ATATTCACGAACAAGCTCGTTTATCGACTCTTTCGTTTATGTTCATAAAT
650 ATATTCACGAACAAGCTCGTTTATCGACTCTTTCGTTTATGTTCATAAAT
251165 GTGAGAGATCAGTGGGTTAACTTAAAATTTTAAAAAACTTTAAAGGGTTTAAATTAAGATTTTTA
1 GTGAGAGATCAGTGGGTTAACTTAAAATTTTAAAAAACTTTAAAGGGTTTAAATTAAGATTTTTA
*
251230 AAATTTTTGAAGGGTTTAGTTTATTTTTTTCCCTAAAAATTAAGTTCTAATCAA-TTTTTTTTGA
66 AAATTTTTGAAGGGTTTAGTTTATTTTTTTCCCTAAAAATTAAGGTCTAATCAATTTTTTTTTGA
251294 AAAAAATTGAGGTTTAATGATATTTTTTAAAAATTATGGGAGGGATTTAATTAAAAATTC-AAAA
131 AAAAAATTGAGGTTTAATGATATTTTTTAAAAATTATGGGAGGGATTTAATTAAAAATTCAAAAA
*
251358 AATTTAAAATTTAATTTAAATTTCTAAAAGTTTTACGAGGTCAAATTAAAATTTTCAAAAAATTT
196 AAATTAAAATTTAATTTAAATTTCTAAAAGTTTTACGAGGTCAAATTAAAATTTTCAAAAAATTT
251423 AAAGGTCTAAATTATAATTTTACTTAATGATCTTATTCTTACTTTAATGTTCTTTATTTCTGTTT
261 AAAGGTCTAAATTATAATTTTACTTAATGATCTTATTCTTACTTTAATGTTCTTTATTTCTGTTT
251488 GTTGTCAGCAAGTCTTCACAAGAGTTGCTGAAATGTCTGCAGTTTATAAACAGCCAACTTCCGGT
326 GTTGTCAGCAAGTCTTCACAAGAGTTGCTGAAATGTCTGCAGTTTATAAACAGCCAACTTCCGGT
251553 GAGGACCGGCTCAAGGCTCTCCAGGTATCATTTTACCGGTTCTCATATGCATTCGTGGGATTGTA
391 GAGGACCGGCTCAAGGCTCTCCAGGTATCATTTTACCGGTTCTCATATGCATTCGTGGGATTGTA
* *
251618 AATGAACAAAACGTTCGGTGAATTGTTCGTATAACGTTCGTTTAAAAAAACGAGTATGAACAAAA
456 AATGAACAAAACATTCGGTGAACTGTTCGTATAACGTTCGTTTAAAAAAACGAGTATGAACAAAA
251683 CTTTTATGTTCATTCAATAAACGAACAAACACAAATAAATGTGTGTTCAGTTCGTTTATGTTCAC
521 CTTTTATGTTCATTCAATAAACGAACAAACACAAATAAATGTGTGTTCAGTTCGTTTATGTTCAC
251748 GAACAAGCTCGTTTATCGACTCTTTCGTTTATGTTCATTAACAAGTTCTTTTAATGGTTGGTTTA
586 GAACAAGCTCGTTTATCGACTCTTTCGTTTATGTTCATTAACAAGTTCTTTTAATGGTTGGTTTA
251813 TAT
651 TAT
251816 GCTTTTTACG
Statistics
Matches: 643, Mismatches: 8, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
697 457 0.71
699 69 0.11
700 117 0.18
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (699 bp):
GTGAGAGATCAGTGGGTTAACTTAAAATTTTAAAAAACTTTAAAGGGTTTAAATTAAGATTTTTA
AAATTTTTGAAGGGTTTAGTTTATTTTTTTCCCTAAAAATTAAGGTCTAATCAATTTTTTTTTGA
AAAAAATTGAGGTTTAATGATATTTTTTAAAAATTATGGGAGGGATTTAATTAAAAATTCAAAAA
AAATTAAAATTTAATTTAAATTTCTAAAAGTTTTACGAGGTCAAATTAAAATTTTCAAAAAATTT
AAAGGTCTAAATTATAATTTTACTTAATGATCTTATTCTTACTTTAATGTTCTTTATTTCTGTTT
GTTGTCAGCAAGTCTTCACAAGAGTTGCTGAAATGTCTGCAGTTTATAAACAGCCAACTTCCGGT
GAGGACCGGCTCAAGGCTCTCCAGGTATCATTTTACCGGTTCTCATATGCATTCGTGGGATTGTA
AATGAACAAAACATTCGGTGAACTGTTCGTATAACGTTCGTTTAAAAAAACGAGTATGAACAAAA
CTTTTATGTTCATTCAATAAACGAACAAACACAAATAAATGTGTGTTCAGTTCGTTTATGTTCAC
GAACAAGCTCGTTTATCGACTCTTTCGTTTATGTTCATTAACAAGTTCTTTTAATGGTTGGTTTA
TATTCACGAACAAGCTCGTTTATCGACTCTTTCGTTTATGTTCATAAAT
Found at i:253941 original size:104 final size:102
Alignment explanation
Indices: 253746--253950 Score: 302
Period size: 104 Copynumber: 2.0 Consensus size: 102
253736 TACTCGAACT
* * *
253746 CGGGTGTTTGTGTCGGATACGGTTATGAATCCGACGTGGTGTTTTCTAAGCTTTTTCACATATTT
1 CGGGTGTATGTGTCGGATACGGTTACGAATCCGACATGGTGTTTTCTAAGCTTTTTCACATATTT
* *
253811 GGAGGGTCGTATCCTATATCCATAGTCGGATATGTGC
66 GGAGGGTCATATCCCATATCCATAGTCGGATATGTGC
* *
253848 CGGGTGTATGTGTCGGATACGGTTACGAATCTGACATGGTATTTTCTCTAAGCTTTTTCACATAT
1 CGGGTGTATGTGTCGGATACGGTTACGAATCCGACATGGT-GTTT-TCTAAGCTTTTTCACATAT
* * *
253913 TTGGAGGGTCATATCCCATATTCGTAGTCGGGTATGTG
64 TTGGAGGGTCATATCCCATATCCATAGTCGGATATGTG
253951 TTGTAAATGT
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
102 36 0.40
103 3 0.03
104 52 0.57
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (102 bp):
CGGGTGTATGTGTCGGATACGGTTACGAATCCGACATGGTGTTTTCTAAGCTTTTTCACATATTT
GGAGGGTCATATCCCATATCCATAGTCGGATATGTGC
Found at i:261330 original size:21 final size:22
Alignment explanation
Indices: 261306--261444 Score: 112
Period size: 21 Copynumber: 6.5 Consensus size: 22
261296 ACTTCGACTA
*
261306 TCGCATTGCGA-TAGTCCAAGT
1 TCGCGTTGCGATTAGTCCAAGT
*
261327 TCGCGTTGCGA-TAGTCGAAGT
1 TCGCGTTGCGATTAGTCCAAGT
* *
261348 TCGCGTTGCGATTTATTCCAAAT
1 TCGCGTTGCGA-TTAGTCCAAGT
* *
261371 T--CGTTGCGATTTATTCCAAAT
1 TCGCGTTGCGA-TTAGTCCAAGT
*
261392 T--CGTTGCGA-TAGTCGAAGT
1 TCGCGTTGCGATTAGTCCAAGT
* *
261411 TCGTGTTGCGATTTATTCCAAGT
1 TCGCGTTGCGA-TTAGTCCAAGT
*
261434 TCGTGTTGCGA
1 TCGCGTTGCGA
261445 ACTTCGACTA
Statistics
Matches: 101, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
19 8 0.08
21 66 0.65
23 27 0.27
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.36
Consensus pattern (22 bp):
TCGCGTTGCGATTAGTCCAAGT
Found at i:261553 original size:63 final size:63
Alignment explanation
Indices: 261454--261876 Score: 471
Period size: 63 Copynumber: 6.8 Consensus size: 63
261444 AACTTCGACT
*
261454 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTAGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
* *
261517 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAATTTGG-A-AA
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
* * * * *
261578 ATCGCAACGCGAACTTGGACT--ATCGCAA--CGAA-TTTGAAATAAATCGCAACGCGAACTTCG
1 ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTCG-ACT--ATCGCAA--CGAATTTGG
*
261638 ACT--
59 AATAA
* *
261641 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACT--
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA--CGAATTTGGAATAA
* *
261704 ATCGCAACGAATTTGGAATAAATCGCAACGCGAATTTCGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
* * *
261767 ATCGCAACGAATTTGGAATAAATCGTAATGCGAACTTCGACTATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
* * *
261828 ATCGCAACGTGAACTTCGACT--ATCGCAACGCGAACTTGGACTATCGCAA
1 ATCGCAAC--GAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
261877 TGCGAATATG
Statistics
Matches: 314, Mismatches: 28, Indels: 38
0.83 0.07 0.10
Matches are distributed among these distances:
58 3 0.01
59 6 0.02
61 78 0.25
62 2 0.01
63 216 0.69
65 6 0.02
66 3 0.01
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (63 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
Found at i:261881 original size:21 final size:20
Alignment explanation
Indices: 261441--261882 Score: 274
Period size: 21 Copynumber: 21.2 Consensus size: 20
261431 AGTTCGTGTT
*
261441 GCGAACTTCGACTATCGCAA
1 GCGAACTTGGACTATCGCAA
*
261461 -CGAACTTGGAATAAATCGCAA
1 GCGAACTTGGACT--ATCGCAA
*
261482 CGCGAACTTAGACTATCGCAA
1 -GCGAACTTGGACTATCGCAA
* *
261503 -CGAATTTGGAATAAATCGCAA
1 GCGAACTTGGACT--ATCGCAA
* *
261524 -CGAATTTGGAATAAATCGCAA
1 GCGAACTTGGACT--ATCGCAA
* *
261545 CGCGAACTTCGACTATCACAA
1 -GCGAACTTGGACTATCGCAA
* **
261566 -CGAATTTGGAAAATCGCAA
1 GCGAACTTGGACTATCGCAA
261585 CGCGAACTTGGACTATCGCAA
1 -GCGAACTTGGACTATCGCAA
* * *
261606 -CGAATTTGAAATAAATCGCAA
1 GCGAACTTGGACT--ATCGCAA
*
261627 CGCGAACTTCGACTATCGCAA
1 -GCGAACTTGGACTATCGCAA
*
261648 -CGAACTTGGAATAAATCGCAA
1 GCGAACTTGGACT--ATCGCAA
*
261669 CGCGAACTTCGACTATCGCAA
1 -GCGAACTTGGACTATCGCAA
261690 CGCGAACTTGGACTATCGCAA
1 -GCGAACTTGGACTATCGCAA
* *
261711 -CGAATTTGGAATAAATCGCAA
1 GCGAACTTGGACT--ATCGCAA
* *
261732 CGCGAATTTCGACTATCGCAA
1 -GCGAACTTGGACTATCGCAA
* *
261753 -CGAATTTGGAATAAATCGCAA
1 GCGAACTTGGACT--ATCGCAA
* * *
261774 -CGAATTTGGAATAAATCGTAA
1 GCGAACTTGGACT--ATCGCAA
*
261795 TGCGAACTTCGACTATCGCAA
1 -GCGAACTTGGACTATCGCAA
* **
261816 -CGAATTTGGAAAATCGCAA
1 GCGAACTTGGACTATCGCAA
* *
261835 CGTGAACTTCGACTATCGCAA
1 -GCGAACTTGGACTATCGCAA
261856 CGCGAACTTGGACTATCGCAA
1 -GCGAACTTGGACTATCGCAA
261877 TGCGAA
1 -GCGAA
261883 TATGTAAAAT
Statistics
Matches: 340, Mismatches: 54, Indels: 55
0.76 0.12 0.12
Matches are distributed among these distances:
19 87 0.26
21 197 0.58
23 56 0.16
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
GCGAACTTGGACTATCGCAA
Found at i:261926 original size:21 final size:21
Alignment explanation
Indices: 261900--261943 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
261890 AATGCAATGA
*
261900 GATAGTCGAAGTTCGCTTTGC
1 GATAGTCGAAGTTCGCGTTGC
*
261921 GATAGTTGAAGTTCGCGTTGC
1 GATAGTCGAAGTTCGCGTTGC
261942 GA
1 GA
261944 ATCTGGAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (21 bp):
GATAGTCGAAGTTCGCGTTGC
Found at i:262892 original size:3 final size:3
Alignment explanation
Indices: 262884--262938 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
262874 CAATTAATTC
262884 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
262932 ATA ATA A
1 ATA ATA A
262939 CACCTTACCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:264852 original size:32 final size:32
Alignment explanation
Indices: 264815--264875 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
264805 TGATTGGTTA
264815 TTGTTAAATTTCTCCTAATCTGCATTTGATTG
1 TTGTTAAATTTCTCCTAATCTGCATTTGATTG
* * *
264847 TTGTTAAATTTCTCTTCATTTGCATTTGA
1 TTGTTAAATTTCTCCTAATCTGCATTTGA
264876 CTGCATCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.21, C:0.15, G:0.11, T:0.52
Consensus pattern (32 bp):
TTGTTAAATTTCTCCTAATCTGCATTTGATTG
Found at i:271090 original size:49 final size:50
Alignment explanation
Indices: 271018--271116 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 50
271008 AAAGCTATTT
271018 GGAATTCTGCAACACTCATTCTTGTCCTTATAGTT-AGTCTTCTTGGTTA
1 GGAATTCTGCAACACTCATTCTTGTCCTTATAGTTAAGTCTTCTTGGTTA
271067 GGAATTCTGCAACACTCATTCTTGTCCTTATAGTTAAGTCTTCTTGGTTA
1 GGAATTCTGCAACACTCATTCTTGTCCTTATAGTTAAGTCTTCTTGGTTA
271117 TCATTTAGGT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 35 0.71
50 14 0.29
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.42
Consensus pattern (50 bp):
GGAATTCTGCAACACTCATTCTTGTCCTTATAGTTAAGTCTTCTTGGTTA
Found at i:273727 original size:20 final size:21
Alignment explanation
Indices: 273702--273753 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
273692 TTTTCCCAAT
*
273702 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
* **
273722 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGAAAAA
273743 TCGCAATGCGA
1 TCGCAATGCGA
273754 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:273770 original size:20 final size:20
Alignment explanation
Indices: 273742--273855 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
273732 AATTGGAAAA
273742 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
273762 ATCGTAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
273782 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
273803 ATCGCAACGAGATACCGACT
1 ATCGCAATGCGATACTGACT
* * *
273823 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
273843 TTCGCAACGCGAT
1 ATCGCAATGCGAT
273856 TTACATAGTG
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
19 2 0.03
20 61 0.79
21 12 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:273788 original size:61 final size:61
Alignment explanation
Indices: 273739--273855 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 61
273729 GCGAATTGGA
* * * * * * *
273739 AAAATCGCAATGCGATACTGACTATCGTAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACCGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
273800 AAAATCGCAACGAGATACCGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACCGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
273856 TTACATAGTG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 46 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACCGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:274415 original size:19 final size:19
Alignment explanation
Indices: 274377--274443 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
274367 TTCGAGAATG
274377 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
274397 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* *
274416 AAAAACGCAACGCGAAACA
1 AAAATCGCAACGCGAAATA
274435 AAAATCGCA
1 AAAATCGCA
274444 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.51, C:0.24, G:0.16, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:274485 original size:20 final size:19
Alignment explanation
Indices: 274439--274509 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
274429 GAAACAAAAA
*
274439 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
274458 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
274477 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
274497 TCGCGTTGCGATT
1 TCGCGTTGCGATT
274510 GTCTGGTCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 30 0.62
20 18 0.38
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:274520 original size:39 final size:39
Alignment explanation
Indices: 274444--274520 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
274434 AAAAATCGCA
* **
274444 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
274483 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
274521 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:274550 original size:14 final size:14
Alignment explanation
Indices: 274533--274565 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
274523 AGTCATTTCG
*
274533 CGTTGCGATTCTCT
1 CGTTGCGATTCTAT
274547 CGTTGCGATTCTAT
1 CGTTGCGATTCTAT
274561 CGTTG
1 CGTTG
274566 TGATAGTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.24, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTAT
Found at i:274555 original size:33 final size:33
Alignment explanation
Indices: 274482--274555 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
274472 TTATTTCGCG
** * *
274482 GTTGCGATTTTCATTTCGCGTTGCGATTGTCTG
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
*
274515 GTCGCGATAGTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
274548 GTTGCGAT
1 GTTGCGAT
274556 TCTATCGTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.22, G:0.27, T:0.41
Consensus pattern (33 bp):
GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
Found at i:276704 original size:21 final size:21
Alignment explanation
Indices: 276680--276746 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
276670 TCATTCCTCG
276680 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
276701 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
276722 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
276743 AGAG
1 AGAG
276747 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:276704 original size:42 final size:42
Alignment explanation
Indices: 276653--276746 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
276643 CCACTCTTAT
* *
276653 CGTTGAAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCAC
* * *
276695 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
*
276737 CATTCAAGAG
1 CGTTCAAGAG
276747 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 38 0.86
43 2 0.05
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
Found at i:278123 original size:14 final size:14
Alignment explanation
Indices: 278104--278139 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
278094 ATTGTTTAAT
278104 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
278118 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
278132 TGATTTGT
1 TGATTTGT
278140 TTAATTGATG
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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:278363 original size:33 final size:32
Alignment explanation
Indices: 278321--278447 Score: 157
Period size: 33 Copynumber: 3.9 Consensus size: 32
278311 ATTAAATTCG
*
278321 CGTTGCGATTTTTATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
278354 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
**
278387 CGTTGCGATTTTCATTTCGCATTGTTATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
278420 CGTTGCGATTTTCATTTCACATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
278448 AGTAATTTCC
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
31 3 0.04
33 74 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:278380 original size:19 final size:19
Alignment explanation
Indices: 278317--278447 Score: 60
Period size: 19 Copynumber: 7.7 Consensus size: 19
278307 CGAAATTAAA
* *
278317 TTCGCGTTGCGATTTTTAT
1 TTCGCATTGCGATTTTCAT
*
278336 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
278352 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
278369 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
278383 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
278402 TTCGCATT--G-TTATTC-T
1 TTCGCATTGCGATT-TTCAT
*
278418 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
278435 TTCACATTGCGAT
1 TTCGCATTGCGAT
278448 AGTAATTTCC
Statistics
Matches: 80, Mismatches: 15, Indels: 34
0.62 0.12 0.26
Matches are distributed among these distances:
14 19 0.24
16 16 0.20
17 14 0.17
19 31 0.39
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:278410 original size:66 final size:66
Alignment explanation
Indices: 278314--278446 Score: 212
Period size: 66 Copynumber: 2.0 Consensus size: 66
278304 ACGCGAAATT
* * *
278314 AAATTCGCGTTGCGATTTTTATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGC
278379 G
66 G
** *
278380 AAATTAGCGTTGCGATTTTCATTTCGCATTGTTATTCTCTCGTTGCGATTTTCATTTCACATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGC
278445 G
66 G
278446 A
1 A
278447 TAGTAATTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCACATTGC
G
Found at i:280760 original size:12 final size:12
Alignment explanation
Indices: 280743--280767 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
280733 TCTTCGGGGA
280743 CTTTTTCTTCTT
1 CTTTTTCTTCTT
280755 CTTTTTCTTCTT
1 CTTTTTCTTCTT
280767 C
1 C
280768 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:280976 original size:24 final size:24
Alignment explanation
Indices: 280942--280995 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
280932 CTGAAACATC
* * *
280942 ATCAAAATCCGTGTATTGACTAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
280966 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
280990 ATCAAA
1 ATCAAA
280996 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:282081 original size:20 final size:20
Alignment explanation
Indices: 282052--282109 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
282042 ATTCATTTGA
*
282052 CTATCACAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
282072 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
282092 ATATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
282110 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:282152 original size:14 final size:14
Alignment explanation
Indices: 282133--282186 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
282123 GAAAATCGCA
282133 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
282147 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
282164 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
282180 TTGCGAT
1 TTGCGAT
282187 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:282152 original size:33 final size:33
Alignment explanation
Indices: 282115--282185 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
282105 AAAATCGCAA
282115 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
282148 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
282181 TGCGA
1 TGCGA
282186 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:282186 original size:33 final size:33
Alignment explanation
Indices: 282128--282205 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
282118 GAAATGAAAA
***
282128 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
282161 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
282194 TCGCGTTGCGAT
1 TCGCATTGCGAT
282206 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:282311 original size:14 final size:14
Alignment explanation
Indices: 282292--282328 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
282282 CATCAATTAA
282292 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
282306 ACAAATCATCTTTT
1 ACAAATCAACATTT
282320 ACAAATCAA
1 ACAAATCAA
282329 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:284218 original size:19 final size:18
Alignment explanation
Indices: 284176--284280 Score: 74
Period size: 20 Copynumber: 5.7 Consensus size: 18
284166 TAGTTTACTT
*
284176 TCGCAACACGAAACTTAATA
1 TCGCAACGCGAAA--TAATA
284196 TCGCAACGCGAAATAACTA
1 TCGCAACGCGAAATAA-TA
**
284215 TCGCAACGCAGAAATGGCTA
1 TCGCAACGC-GAAAT-AATA
* *
284235 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAAT-AATA
*
284254 TCGCAA--CGACA-AA-A
1 TCGCAACGCGAAATAATA
284268 TCGCAACGCGAAA
1 TCGCAACGCGAAA
284281 CACAAATCGC
Statistics
Matches: 71, Mismatches: 9, Indels: 14
0.76 0.10 0.15
Matches are distributed among these distances:
14 7 0.10
15 2 0.03
16 4 0.06
17 4 0.06
18 3 0.04
19 24 0.34
20 27 0.38
ACGTcount: A:0.43, C:0.25, G:0.18, T:0.14
Consensus pattern (18 bp):
TCGCAACGCGAAATAATA
Found at i:284309 original size:19 final size:16
Alignment explanation
Indices: 284287--284382 Score: 65
Period size: 19 Copynumber: 5.7 Consensus size: 16
284277 GAAACACAAA
284287 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTT-ATT
*
284306 TCGCGTTGCGATTT-TG
1 TCGC-TTGCGATTTATT
284322 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTT-ATT
*
284338 TCGCGTTGCGATTT-TG
1 TCGC-TTGCGATTTATT
284354 TCG-TTGCGATTTTTATT
1 TCGCTTGCGA--TTTATT
284371 TCGCATTGCGAT
1 TCGC-TTGCGAT
284383 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 15 0.24
16 15 0.24
17 5 0.08
18 12 0.19
19 16 0.25
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (16 bp):
TCGCTTGCGATTTATT
Found at i:284328 original size:14 final size:14
Alignment explanation
Indices: 284309--284366 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
284299 TTTCATTTCG
284309 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
284323 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
284339 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
284355 CGTTGCGATTTT
1 CGTTGCGATTTT
284367 TATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:284339 original size:32 final size:33
Alignment explanation
Indices: 284292--284382 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
284282 ACAAATCGCA
284292 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
284325 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
284357 TTGCGATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
284383 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 32 0.58
33 23 0.42
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:284390 original size:19 final size:20
Alignment explanation
Indices: 284368--284410 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
284358 TGCGATTTTT
284368 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
284387 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
284407 ATTT
1 ATTT
284411 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:284401 original size:20 final size:20
Alignment explanation
Indices: 284376--284421 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
284366 TTATTTCGCA
284376 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
284396 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
284416 TTGCGA
1 TTGCGA
284422 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:284929 original size:18 final size:18
Alignment explanation
Indices: 284903--284947 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
284893 GTCGATCAGA
*
284903 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
284921 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
284939 TGATGGCTC
1 TGATGGCTC
284948 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:286315 original size:20 final size:20
Alignment explanation
Indices: 286267--286325 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
286257 AATAGTTTCT
** *
286267 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
286287 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
** *
286307 GAATTTGACTATTGCAACG
1 GAAAATGACTATCGCAACG
286326 AGATAATCGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:286615 original size:22 final size:22
Alignment explanation
Indices: 286588--286631 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
286578 GATGGAGATA
286588 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
286610 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
286632 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:286881 original size:20 final size:20
Alignment explanation
Indices: 286819--286932 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
286809 GATTATGTAT
286819 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
286839 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
286859 TATCGCGTTGCGAAAGT-ATG
1 TATCGCGTTGCGAAAGTCA-G
* ** *
286879 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
286900 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
286920 TATCGCATTGCGA
1 TATCGCGTTGCGA
286933 TTTTCCCAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
19 4 0.05
20 62 0.77
21 11 0.14
22 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:286933 original size:20 final size:19
Alignment explanation
Indices: 286799--286933 Score: 99
Period size: 20 Copynumber: 6.7 Consensus size: 19
286789 CGCTTTGAAA
* *
286799 ATCGCATTGCGATTATGTATT
1 ATCGCGTTGCGA-TA-GTAGT
* *
286820 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGATAGT-AGT
*
286840 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGT-AGT
*
286860 ATCGCGTTGCGAAAGTATGT
1 ATCGCGTTGCGATAGTA-GT
* * *
286880 ATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGA--TAGTAGT
*
286901 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGT-AGT
*
286921 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
286934 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
19 6 0.06
20 65 0.68
21 22 0.23
22 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATAGTAGT
Found at i:286951 original size:21 final size:21
Alignment explanation
Indices: 286922--287014 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
286912 ATAGTCAGTA
286922 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
286943 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
286963 TCACATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
286984 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
287004 TCGCATTGCGA
1 TCGCATTGCGA
287015 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:286952 original size:41 final size:41
Alignment explanation
Indices: 286925--287014 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
286915 GTCAGTATCG
* *
286925 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCA
1 CATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTATTCA
* * *
286966 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 CATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTATTCA
287007 CATTGCGA
1 CATTGCGA
287015 ATTGGGAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (41 bp):
CATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTATTCA
Found at i:291549 original size:23 final size:20
Alignment explanation
Indices: 291518--291564 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
291508 GGAATCTGAG
291518 CCTTCATGGTAGTATCGATACTA
1 CCTTCATGGT--T-TCGATACTA
*
291541 CCTTGATGGTTTCGATACTA
1 CCTTCATGGTTTCGATACTA
291561 CCTT
1 CCTT
291565 TGCCTATGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 13 0.57
21 1 0.04
23 9 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (20 bp):
CCTTCATGGTTTCGATACTA
Found at i:299274 original size:105 final size:106
Alignment explanation
Indices: 299092--299310 Score: 422
Period size: 105 Copynumber: 2.1 Consensus size: 106
299082 ATAAAGAACT
299092 TAAGTGATCATCGATATTTAAAAAATCACCACTTTAATCATATCAGTAGTTAAAGGAATCGTTGT
1 TAAGTGATCATCGATATTTAAAAAATCACCACTTTAATCATATCAGTAGTTAAAGGAATCGTTGT
299157 TGTTCCTAAATATTACGAGTTCGAGCACCAACAACTACGG-
66 TGTTCCTAAATATTACGAGTTCGAGCACCAACAACTACGGC
299197 TAAGTGATCATCGATATTTAAAAAATCACCACTTTAATCATATCAGTAGTTAAAGGAATCGTTGT
1 TAAGTGATCATCGATATTTAAAAAATCACCACTTTAATCATATCAGTAGTTAAAGGAATCGTTGT
299262 TGTTCCTAAATATTACGAGTTCGAGCACCAACAACTACGGC
66 TGTTCCTAAATATTACGAGTTCGAGCACCAACAACTACGGC
*
299303 AAAGTGAT
1 TAAGTGAT
299311 TGAACATTCA
Statistics
Matches: 112, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
105 105 0.94
106 7 0.06
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (106 bp):
TAAGTGATCATCGATATTTAAAAAATCACCACTTTAATCATATCAGTAGTTAAAGGAATCGTTGT
TGTTCCTAAATATTACGAGTTCGAGCACCAACAACTACGGC
Found at i:300565 original size:15 final size:15
Alignment explanation
Indices: 300545--300576 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
300535 TCTATTTCAA
300545 TTTTCAAATATATAT
1 TTTTCAAATATATAT
*
300560 TTTTCAATTATATAT
1 TTTTCAAATATATAT
300575 TT
1 TT
300577 GATTTTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTCAAATATATAT
Found at i:301347 original size:13 final size:13
Alignment explanation
Indices: 301329--301353 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
301319 ATAGACGCGA
301329 ATATGAAGACTGC
1 ATATGAAGACTGC
301342 ATATGAAGACTG
1 ATATGAAGACTG
301354 TTCAACTATG
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:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
ATATGAAGACTGC
Found at i:301536 original size:3 final size:3
Alignment explanation
Indices: 301528--301576 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
301518 GAATATGATT
301528 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
301576 T
1 T
301577 ATAGAGATGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:310954 original size:2 final size:2
Alignment explanation
Indices: 310947--311004 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
310937 TTTTATTTAT
310947 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
310989 TA TA TA TA -A TA T- TA TA
1 TA TA TA TA TA TA TA TA TA
311005 GATTATTAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:317328 original size:403 final size:408
Alignment explanation
Indices: 316372--317596 Score: 1934
Period size: 403 Copynumber: 3.0 Consensus size: 408
316362 TCTGCCACTA
* *
316372 AGTTCGTAG-AAAACTTCAGAGTTTCATATCCTCTGGCTAATTATAGTGTCCTGACTTGACTGTT
1 AGTTCTTAGAAAAACTTCAGAGTTTCATATCCTCTGGCTAATTATAGTGTCCTGACTTGACTGAT
* *
316436 GTTAATCTGATCAACGTTAAATCTACGATATAGCAACAATGTCTACTCATCTATCGACCTGTAAA
66 GTTAATCTCATCAACGTTAAATCTACGATATAGCAACAATGTCTACTCACCTATCGACCTGTAAA
* *
316501 ATAGTAATCATCATCCTAAACTTGACACTAACATTAAGAGCCTATATATAAACCTCATGCTAAGT
131 ATAGTAATCATCATCCTAAACTTGACTCTAACGTTAAGAGCC--TATATAAACCTCATGCTAAGT
* * **
316566 TAA-GGCGTCTCTATCTAATTCTAGATTATTGCTCG-TTTCTTATCCAACATGTTTATCTCCCCT
194 TAAGGGCATTTCTATCTAATTCTAGGCTATTGCTCGTTTTCTTATCCAACATGTTTATCTCCCCT
*
316629 TTTACATCTACAAAACTTTCATATATGGTTATGTGTTCAAATCAGAAAGGGATAAAATTATCAAG
259 TTTACATCTACAAAACTTTCATATATGGTTCTGTGTTCAAATCAG-AAGGGATAAAATTATCAAG
316694 CGCTATTACAATCACATTTCTCCTATATATAAACCTCATGTTGAGCT-AAGGGTCTCTCTAATTC
323 CGCTATTACAATCACATTTCTCCTATATATAAACCTCATGTTGAGCTAAAGGG-CTCTCTAATTC
316758 T-AGGCTAAATTTAGATTTGTT
387 TAAGGCTAAATTTAGATTTGTT
316779 AGTTCTTAGAAAAAACTTCAGAGTTTCATATCCTCTGGCTAATTATAGTGTCCTGACTTGACTGA
1 AGTTCTTAG-AAAAACTTCAGAGTTTCATATCCTCTGGCTAATTATAGTGTCCTGACTTGACTGA
*
316844 TGTTAATCTCATCAACGTTAAATCTACGATATAGCAACAATGTCTACTCACCTATCGACTTGT-A
65 TGTTAATCTCATCAACGTTAAATCTACGATATAGCAACAATGTCTACTCACCTATCGACCTGTAA
316908 AATAGTAATCATCATCCTAAACTTGACTCTAACGTTAAGAGCCTATATAAACCTCATGCTAAGTT
130 AATAGTAATCATCATCCTAAACTTGACTCTAACGTTAAGAGCCTATATAAACCTCATGCTAAGTT
316973 AAAGGGCATTTCT-TCTAATTCTAGGGCTATTGCTCGTTTTCTTATCCAACATGTTTATCTCCCC
195 -AAGGGCATTTCTATCTAATTCTA-GGCTATTGCTCGTTTTCTTATCCAACATGTTTATCTCCCC
317037 TTTTACATCTAC-AAACTTTCA-ATATGGTTCTGTGTTCAAATCAGAA-GGATAAAATTATCAAG
258 TTTTACATCTACAAAACTTTCATATATGGTTCTGTGTTCAAATCAGAAGGGATAAAATTATCAAG
*
317099 CGCTATTACAATCACATTTCTCCTATATATAAACCTCATGTTGAGCTAAATGG-TCTCTAATTCT
323 CGCTATTACAATCACATTTCTCCTATATATAAACCTCATGTTGAGCTAAAGGGCTCTCTAATTCT
317163 AAGGCTAAA-TTAGATTTGTT
388 AAGGCTAAATTTAGATTTGTT
* *
317183 AGTTCTTAGAAAAACTTCATAGTTTCATATCCTCTGGCTAATTATAGTGTTCTGACTTGACTGAT
1 AGTTCTTAGAAAAACTTCAGAGTTTCATATCCTCTGGCTAATTATAGTGTCCTGACTTGACTGAT
317248 G-TAATCTCATCAACGTTAAATCTACGATATAGCAACAATGTCTACTCACCTATCGACCTGTAAA
66 GTTAATCTCATCAACGTTAAATCTACGATATAGCAACAATGTCTACTCACCTATCGACCTGTAAA
**
317312 ATAGTAATCATCATCCTAAAC-TGACTCTAACGTTAAGAGCCTATTATAAACCTCATGCTAAGCC
131 ATAGTAATCATCATCCTAAACTTGACTCTAACGTTAAGAGCCTA-TATAAACCTCATGCTAAGTT
* *
317376 AAGGGCATCTT-TCTCTAATTCTAAGGCTATTGCTCGTTTTC-TATCCAACATG---ATCTCCTC
195 AAGGGCAT-TTCTATCTAATTCT-AGGCTATTGCTCGTTTTCTTATCCAACATGTTTATCTCCCC
* * *
317436 TTTTACATCTACAAAAACTTTCATATATGATTCTGTGTTCAAATCAGAAGGGACAAAATTGTCAA
258 TTTTACATCTAC-AAAACTTTCATATATGGTTCTGTGTTCAAATCAGAAGGGATAAAATTATCAA
* * *
317501 GCGCTATTACAAATTACATTTC-CCTATAT-TAAACCTCATGCTAAGCTAAAGGGTCTCTCTCTA
322 GCGCTATTAC-AATCACATTTCTCCTATATATAAACCTCATGTTGAGCTAAAGGG---CTCTCTA
317564 ATTCTAAGGCTAAATTTAGATTTGTT
383 ATTCTAAGGCTAAATTTAGATTTGTT
*
317590 AATTCTT
1 AGTTCTT
317597 CAAATAAATC
Statistics
Matches: 768, Mismatches: 27, Indels: 46
0.91 0.03 0.05
Matches are distributed among these distances:
399 19 0.02
401 9 0.01
402 146 0.19
403 154 0.20
404 42 0.05
405 71 0.09
406 48 0.06
407 59 0.08
408 68 0.09
409 152 0.20
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (408 bp):
AGTTCTTAGAAAAACTTCAGAGTTTCATATCCTCTGGCTAATTATAGTGTCCTGACTTGACTGAT
GTTAATCTCATCAACGTTAAATCTACGATATAGCAACAATGTCTACTCACCTATCGACCTGTAAA
ATAGTAATCATCATCCTAAACTTGACTCTAACGTTAAGAGCCTATATAAACCTCATGCTAAGTTA
AGGGCATTTCTATCTAATTCTAGGCTATTGCTCGTTTTCTTATCCAACATGTTTATCTCCCCTTT
TACATCTACAAAACTTTCATATATGGTTCTGTGTTCAAATCAGAAGGGATAAAATTATCAAGCGC
TATTACAATCACATTTCTCCTATATATAAACCTCATGTTGAGCTAAAGGGCTCTCTAATTCTAAG
GCTAAATTTAGATTTGTT
Found at i:318438 original size:2 final size:2
Alignment explanation
Indices: 318433--318460 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
318423 AATTTTTTCC
318433 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
318461 TTACCTAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:319541 original size:278 final size:278
Alignment explanation
Indices: 319036--319593 Score: 1011
Period size: 278 Copynumber: 2.0 Consensus size: 278
319026 GAATAAGGAG
319036 ATGATTTTTGTAGGAACTTATGTTGACTTATAGCATCCTAATGCGAGGGGACTTGCTTTAATGTT
1 ATGATTTTTGTAGGAACTTATGTTGACTTATAGCATCCTAATGCGAGGGGACTTGCTTTAATGTT
319101 GGTAAATGATGGAAACATTGGTCAAGGGCCACATTGAATTTTTTTTAATTGAGAACCACATTAAG
66 GGTAAATGATGGAAACATTGGTCAAGGGCCACATTGAATTTTTTTTAATTGAGAACCACATTAAG
319166 AAAAAATAATACGAGTGCCACATTGATTTTTTTAGAAATACAAGGCTTAAGCCTTTTGCCTTAAT
131 AAAAAATAATACGAGTGCCACATTGATTTTTTTAGAAATACAAGGCTTAAGCCTTTTGCCTTAAT
*
319231 ATTTAATGATTAATATAAAATATTTAAAATTTAAGTACTGACTTTAATAGTTTGCGCGAGTAAAA
196 AATTAATGATTAATATAAAATATTTAAAATTTAAGTACTGACTTTAATAGTTTGCGCGAGTAAAA
319296 TTTAGATTACAAAATTAAC
261 TTTAGATTAC-AAATTAAC
319315 ATGATTTTTGTAGGAACTTA-GTTGACTTATAGCATCCTAATAGCGA-GGGACTTGCTTTAATGT
1 ATGATTTTTGTAGGAACTTATGTTGACTTATAGCATCCTAAT-GCGAGGGGACTTGCTTTAATGT
319378 TGGTAAATGATGGAAAACATTGGTCAAAGGGCCACATTGAATTTTTTTTAATTGGAGAACCACAT
65 TGGTAAATGATGG-AAACATTGGTC-AAGGGCCACATTGAATTTTTTTTAATT-GAGAACCACAT
319443 TAAGAAAAAAATAATACGAGTGCCACATTGATTTTTTTAGAAATACAAGGCTTAAG-CTTTTGCC
127 TAAG-AAAAAATAATACGAGTGCCACATTGATTTTTTTAGAAATACAAGGCTTAAGCCTTTTGCC
319507 TTAATAATTAATGATTAATAT-AAATA-TT-AAATTTAAGTACTGACTTTAATAGTTTGCGCGAG
191 TTAATAATTAATGATTAATATAAAATATTTAAAATTTAAGTACTGACTTTAATAGTTTGCGCGAG
319569 TAAAATTTAGATTACAAATTAAC
256 TAAAATTTAGATTACAAATTAAC
319592 AT
1 AT
319594 AAAGTTAGTT
Statistics
Matches: 273, Mismatches: 1, Indels: 12
0.95 0.00 0.04
Matches are distributed among these distances:
277 10 0.04
278 100 0.37
279 37 0.14
280 32 0.12
281 43 0.16
282 51 0.19
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.35
Consensus pattern (278 bp):
ATGATTTTTGTAGGAACTTATGTTGACTTATAGCATCCTAATGCGAGGGGACTTGCTTTAATGTT
GGTAAATGATGGAAACATTGGTCAAGGGCCACATTGAATTTTTTTTAATTGAGAACCACATTAAG
AAAAAATAATACGAGTGCCACATTGATTTTTTTAGAAATACAAGGCTTAAGCCTTTTGCCTTAAT
AATTAATGATTAATATAAAATATTTAAAATTTAAGTACTGACTTTAATAGTTTGCGCGAGTAAAA
TTTAGATTACAAATTAAC
Found at i:322687 original size:5 final size:5
Alignment explanation
Indices: 322677--322702 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
322667 GAAAATTCAA
322677 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
322703 TTAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:323694 original size:44 final size:44
Alignment explanation
Indices: 323631--323714 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
323621 CTGATGGGAT
* *
323631 ATTTTGACCCAATTGATGATATTAATTTCTTTTTGATAATTTCA
1 ATTTTGACCAAATTGATGATATTAATTTCATTTTGATAATTTCA
323675 ATTTTGACCAAATTGATGATATTAATTTCATTTTGATAAT
1 ATTTTGACCAAATTGATGATATTAATTTCATTTTGATAAT
323715 CTCAGTTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.49
Consensus pattern (44 bp):
ATTTTGACCAAATTGATGATATTAATTTCATTTTGATAATTTCA
Found at i:324542 original size:39 final size:39
Alignment explanation
Indices: 324488--324607 Score: 213
Period size: 39 Copynumber: 3.1 Consensus size: 39
324478 TTCATATATA
324488 CGAGAATATGTTACTCGAACCCGGATACACAGGTATGTT
1 CGAGAATATGTTACTCGAACCCGGATACACAGGTATGTT
*
324527 CGAGAATATGTTACTCGAACCCGGATACACGGGTATGTT
1 CGAGAATATGTTACTCGAACCCGGATACACAGGTATGTT
**
324566 CGAGAATATGTTACTCGAACCCGGATATGCAGGTATGTT
1 CGAGAATATGTTACTCGAACCCGGATACACAGGTATGTT
324605 CGA
1 CGA
324608 TTTTTCTAAG
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (39 bp):
CGAGAATATGTTACTCGAACCCGGATACACAGGTATGTT
Found at i:328700 original size:199 final size:199
Alignment explanation
Indices: 328355--328719 Score: 493
Period size: 199 Copynumber: 1.8 Consensus size: 199
328345 TCCCTTTTTA
* * * *
328355 ACAACGCACATTGTCAAAACAAAAGACATTCGTAACCGATTTCAATCGTGGGAAAATCGAATCCG
1 ACAACGCACATTGTCAAAACAAAAGACATTCATAACCAATTTCAATCATGCGAAAATCGAATCCG
* * *
328420 ACACTCACACTCGAGTCTAAATAACATAGCTTCAATGATCAAATTCGTGTGTATCGTACAAAAAC
66 ACACTCACACCCGAGTCTAAATAACATAGCATCAATGATCAAATTCGTGTGTATCATACAAAAAC
* * *
328485 TCAAATTTACCTTGAAACCGAGTGCATGATCTACCAAGTAAACAGAAGCAGAAGCAAGGACTAGC
131 TCAAATTTACCTTGAAACCAAGAGCAGGATCTACCAAGTAAACAGAAGCAGAAGCAAGGACTAGC
328550 AGAC
196 AGAC
* * * *
328554 ACAATGCACATTGT-AAAAGCAAAAGACATTCATAACCAATTTGATTCAT-CGAAAACTCGTATC
1 ACAACGCACATTGTCAAAA-CAAAAGACATTCATAACCAATTTCAATCATGCGAAAA-TCGAATC
* * * * **
328617 TGATACTCACACCCGAGTCTAAATAACATAGCATCGATGATCGAATTCGTGTGTATCATATGAAA
64 CGACACTCACACCCGAGTCTAAATAACATAGCATCAATGATCAAATTCGTGTGTATCATACAAAA
*
328682 ACTCAAAATTT-CCTTGAAAGCAAGAGCAGGATCTACCA
129 ACTC-AAATTTACCTTGAAACCAAGAGCAGGATCTACCA
328720 CACTCCACAC
Statistics
Matches: 142, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
198 9 0.06
199 127 0.89
200 6 0.04
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (199 bp):
ACAACGCACATTGTCAAAACAAAAGACATTCATAACCAATTTCAATCATGCGAAAATCGAATCCG
ACACTCACACCCGAGTCTAAATAACATAGCATCAATGATCAAATTCGTGTGTATCATACAAAAAC
TCAAATTTACCTTGAAACCAAGAGCAGGATCTACCAAGTAAACAGAAGCAGAAGCAAGGACTAGC
AGAC
Found at i:328869 original size:165 final size:166
Alignment explanation
Indices: 328560--328887 Score: 482
Period size: 165 Copynumber: 2.0 Consensus size: 166
328550 AGACACAATG
* * * *
328560 CACATTGTAAAAGCAAAAGACATTCATAACCAATTTGATTCATCGAAAACTCGTATCTGATACTC
1 CACATTGTAAAAGCAAAAGACATTCATAACCAATGTAAATCATCGAAAACTCGTATCTGACACTC
** *
328625 ACACCCGAGTCTAAATAACATAGCATCGATGATCGAATTCGTGTGTATCATATGAAAACTCAAAA
66 ACACCCGAG-CTAAATAACATAGCATAAATGATCAAATTCGTGTGTATCATATGAAAACTCAAAA
328690 TTTCCTTGAAAGCAAGAGCAGGATCTACCACACTCCA
130 TTTCCTTGAAAGCAAGAGCAGGATCTACCACACTCCA
* * * *
328727 CACATTGTCAAAA-CAAAAGACATTCGTAACCGATGTAAATCGTTGAAAACTCGTATCTGACACT
1 CACATTGT-AAAAGCAAAAGACATTCATAACCAATGTAAATCATCGAAAACTCGTATCTGACACT
* * *
328791 CACACCCGAG-TAAATAACATGGCTTAAATGATCAAATTCGTGTGTATCATATGAAAACTC-AAT
65 CACACCCGAGCTAAATAACATAGCATAAATGATCAAATTCGTGTGTATCATATGAAAACTCAAAA
328854 TTTACCTTGAAAGCAAGAGCAGGATCTACCACAC
130 TTT-CCTTGAAAGCAAGAGCAGGATCTACCACAC
328888 ATTGTCAAAA
Statistics
Matches: 145, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
164 5 0.03
165 75 0.52
167 61 0.42
168 4 0.03
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (166 bp):
CACATTGTAAAAGCAAAAGACATTCATAACCAATGTAAATCATCGAAAACTCGTATCTGACACTC
ACACCCGAGCTAAATAACATAGCATAAATGATCAAATTCGTGTGTATCATATGAAAACTCAAAAT
TTCCTTGAAAGCAAGAGCAGGATCTACCACACTCCA
Found at i:331881 original size:22 final size:22
Alignment explanation
Indices: 331853--331911 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
331843 TGTTTACTGT
*
331853 TGAATGCTGAACCGTTCATCGC
1 TGAATGCTGAACCGTTCAACGC
331875 TGAATGCTGAACCGTTCAACGC
1 TGAATGCTGAACCGTTCAACGC
331897 TGAATGCTGAACCGT
1 TGAATGCTGAACCGT
331912 CAGCGTGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (22 bp):
TGAATGCTGAACCGTTCAACGC
Found at i:333954 original size:17 final size:16
Alignment explanation
Indices: 333918--333986 Score: 79
Period size: 15 Copynumber: 4.3 Consensus size: 16
333908 AATCGGGTAT
*
333918 CGGGTACCCGATTA-C
1 CGGGTACCCGAATATC
*
333933 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AATATC
*
333950 CGGGTACCCGATTA-C
1 CGGGTACCCGAATATC
333965 CGGGTACCCGTAATATC
1 CGGGTACCCG-AATATC
333982 CGGGT
1 CGGGT
333987 CGTGACACGG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
15 21 0.47
16 7 0.16
17 17 0.38
ACGTcount: A:0.22, C:0.32, G:0.28, T:0.19
Consensus pattern (16 bp):
CGGGTACCCGAATATC
Found at i:333959 original size:32 final size:32
Alignment explanation
Indices: 333918--333986 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
333908 AATCGGGTAT
333918 CGGGTACCCGATTACCGGGTACCCGCAAAATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
* *
333950 CGGGTACCCGATTACCGGGTACCCGTAATATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
333982 CGGGT
1 CGGGT
333987 CGTGACACGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.22, C:0.32, G:0.28, T:0.19
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGCAAAATC
Found at i:334087 original size:6 final size:6
Alignment explanation
Indices: 334076--334117 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
334066 CTTAAGCCCT
* *
334076 TGATCA TGATCA TGATCA TGATCA TGATCG TCATCA TG-TCA T
1 TGATCA TGATCA TGATCA TGATCA TGATCA TGATCA TGATCA T
334118 AACCAAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (6 bp):
TGATCA
Found at i:334505 original size:16 final size:16
Alignment explanation
Indices: 334484--334514 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
334474 AAGTGTCAAT
334484 TTTTACAAAATCATAC
1 TTTTACAAAATCATAC
334500 TTTTACAAAATCATA
1 TTTTACAAAATCATA
334515 TCTAAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (16 bp):
TTTTACAAAATCATAC
Found at i:335402 original size:19 final size:19
Alignment explanation
Indices: 335378--335414 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
335368 AATAAAATTA
*
335378 ATTAAATAATAATTTAAAC
1 ATTAAAAAATAATTTAAAC
335397 ATTAAAAAATAATTTAAA
1 ATTAAAAAATAATTTAAA
335415 AATGCCACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTAAAAAATAATTTAAAC
Found at i:335552 original size:31 final size:31
Alignment explanation
Indices: 335509--335567 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
335499 AAATCAAAAT
335509 TTTAAGTACTAAAACATATCAAAAGTGAAAC
1 TTTAAGTACTAAAACATATCAAAAGTGAAAC
* *
335540 TTTAGGTACTAAAATATATCAAAAGTGA
1 TTTAAGTACTAAAACATATCAAAAGTGA
335568 TTATATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (31 bp):
TTTAAGTACTAAAACATATCAAAAGTGAAAC
Found at i:339037 original size:34 final size:34
Alignment explanation
Indices: 338990--339054 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
338980 ACGGTCCTCC
338990 GACTATAGAATGATGTTTTATTAAGTCGTTTTCT
1 GACTATAGAATGATGTTTTATTAAGTCGTTTTCT
*
339024 GACTATAGGATGATGTTTTATTAAGTCGTTT
1 GACTATAGAATGATGTTTTATTAAGTCGTTT
339055 GACTAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.46
Consensus pattern (34 bp):
GACTATAGAATGATGTTTTATTAAGTCGTTTTCT
Found at i:341297 original size:31 final size:31
Alignment explanation
Indices: 341262--341332 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
341252 AAGAAGTCAG
341262 ATTTTATCTAAAATTTAAAAGTTAAATT-GT
1 ATTTTATCTAAAATTTAAAAGTTAAATTAGT
* ** *
341292 AATTTTATCTAAATTTTAGGAGTTGAATTAGT
1 -ATTTTATCTAAAATTTAAAAGTTAAATTAGT
341324 ATTTTATCT
1 ATTTTATCT
341333 GAAGTTCAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 33 0.94
32 2 0.06
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (31 bp):
ATTTTATCTAAAATTTAAAAGTTAAATTAGT
Found at i:343979 original size:22 final size:25
Alignment explanation
Indices: 343954--344016 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
343944 ATATATTAAC
343954 TTAAAT-T-TTTTA-GATTAACTTA
1 TTAAATATATTTTATGATTAACTTA
*
343976 TTAAATATATTTTATTATTAACTTAA
1 TTAAATATATTTTATGATTAACTT-A
344002 TTTAAA-ATATTTTAT
1 -TTAAATATATTTTAT
344017 TTTTAATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
22 6 0.17
23 1 0.03
24 5 0.14
25 8 0.23
26 10 0.29
27 5 0.14
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (25 bp):
TTAAATATATTTTATGATTAACTTA
Found at i:344036 original size:28 final size:27
Alignment explanation
Indices: 343967--344039 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 27
343957 AATTTTTTAG
*
343967 ATTAACTT-A-TTAAATATATTTTATT
1 ATTAACTTAATTTAAAAATATTTTATT
343992 ATTAACTTAATTT-AAAATATTTTATT
1 ATTAACTTAATTTAAAAATATTTTATT
* * *
344018 TTTAATTTTCATTTAAAAATAT
1 ATTAA-CTTAATTTAAAAATAT
344040 ATATTTTATG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 8 0.20
26 17 0.43
27 8 0.20
28 7 0.17
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (27 bp):
ATTAACTTAATTTAAAAATATTTTATT
Found at i:344066 original size:31 final size:32
Alignment explanation
Indices: 344008--344070 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
343998 TTAATTTAAA
* * *
344008 ATATTTTATTTTTAATTTTCATTTAAAAATAT
1 ATATTTTATGTTAAAATTTCATTTAAAAATAT
344040 ATATTTTATGTTAAAATTT-ATTTAAAAATAT
1 ATATTTTATGTTAAAATTTCATTTAAAAATAT
344071 GATTAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (32 bp):
ATATTTTATGTTAAAATTTCATTTAAAAATAT
Found at i:349269 original size:131 final size:130
Alignment explanation
Indices: 348972--349333 Score: 442
Period size: 131 Copynumber: 2.8 Consensus size: 130
348962 CGATATTGAA
* * * *
348972 AATAGTAATATCCTTTCATTTCGGTTGGAGTAATAAATGATTGCTCTAAGGTACGAGAGACCATT
1 AATAGTAATAT-CTTTCATTTCGGTTGGAGTAATAAATGACTGCTTTAAGGTATGAGAGATCATT
* * * * * * * **
349037 TATTCTCTATTGGAAATAATTCA-ATGTTA--ATATTCTCTCGAATTAATATTGATTTTTAAGGT
65 TATTCTCGATTGGAAATAATT-AGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGAC
349099 GG
129 GG
* * * *
349101 AATAGTAATATCTTTTCGTTTTGGTTGGGGTAATAAATGACTGCTTTAAGGTATGAGAGGTCATT
1 AATAGTAATATC-TTTCATTTCGGTTGGAGTAATAAATGACTGCTTTAAGGTATGAGAGATCATT
* * *
349166 TATTCTCGATTGGAAATCATTAGATATTATCGTTTTCACTCGTATCGATATTGAATTTTAAGACG
65 TATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGACG
349231 G
130 G
* * * *
349232 AATAGTAATATATGTTCATTTCGATTGGAGTAATAAATGACTGTTTTAAGGTATGAGAGTTCATT
1 AATAGTAATATCT-TTCATTTCGGTTGGAGTAATAAATGACTGCTTTAAGGTATGAGAGATCATT
*
349297 TATTCTCGATTGGAAATAATTAGATATCATCGTTTTC
65 TATTCTCGATTGGAAATAATTAGATATTATCGTTTTC
349334 TCTCTTAAAA
Statistics
Matches: 199, Mismatches: 29, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
128 2 0.01
129 79 0.40
130 1 0.01
131 117 0.59
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (130 bp):
AATAGTAATATCTTTCATTTCGGTTGGAGTAATAAATGACTGCTTTAAGGTATGAGAGATCATTT
ATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGAATTTTAAGACGG
Found at i:351397 original size:2 final size:2
Alignment explanation
Indices: 351387--351431 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
351377 AAAAAAATTG
*
351387 AT AT GT 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
351429 AT A
1 AT A
351432 ATTGTTATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:351508 original size:112 final size:110
Alignment explanation
Indices: 351299--351508 Score: 350
Period size: 110 Copynumber: 1.9 Consensus size: 110
351289 GATTTAATCC
*
351299 ATATATATATATATATATATATTTGTTATTATATTTTAAAAATTAAAAAAAAATACTAGTATATA
1 ATATATATATATATATATATAATTGTTATTATATTTTAAAAATT--AAAAAAATACTAGTATATA
351364 AATTATTTTAGATAAAAAAATTGATATGTATATATATATATATATAT
64 AATTATTTTAGATAAAAAAATTGATATGTATATATATATATATATAT
* *
351411 ATATATATATATATATATATAATTGTTATTATATTTTAAAAAATT-TAAAAATATTAGTATATAA
1 ATATATATATATATATATATAATTGTTATTATATTTT-AAAAATTAAAAAAATACTAGTATATAA
*
351475 ATTATTTTAGATAAAAAAATTGATATGTTTATAT
65 ATTATTTTAGATAAAAAAATTGATATGTATATAT
351509 TGGCCCGGTC
Statistics
Matches: 93, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
110 50 0.54
112 36 0.39
113 7 0.08
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (110 bp):
ATATATATATATATATATATAATTGTTATTATATTTTAAAAATTAAAAAAATACTAGTATATAAA
TTATTTTAGATAAAAAAATTGATATGTATATATATATATATATAT
Found at i:351855 original size:2 final size:2
Alignment explanation
Indices: 351848--351881 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
351838 CCCATATGCC
351848 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
351882 TAATATTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:363051 original size:45 final size:47
Alignment explanation
Indices: 362999--363087 Score: 155
Period size: 45 Copynumber: 1.9 Consensus size: 47
362989 CCGAATAAAT
362999 GCATGCGAACTAGATATCATGCGGTTAGG-TTTATTTTT-TGAACAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
*
363044 GCATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
363088 TAACAAAGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 28 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
Found at i:372755 original size:19 final size:19
Alignment explanation
Indices: 372731--372777 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
372721 ATTTTGCTTG
372731 AAGAAGAAATAAAAGAGAA
1 AAGAAGAAATAAAAGAGAA
*
372750 AAGAAGAAA-AAATGAGAA
1 AAGAAGAAATAAAAGAGAA
*
372768 AAGAAAAAAT
1 AAGAAGAAAT
372778 GATGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (19 bp):
AAGAAGAAATAAAAGAGAA
Found at i:372771 original size:15 final size:16
Alignment explanation
Indices: 372753--372785 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
372743 AAGAGAAAAG
372753 AAGAAAAAATGA-GAA
1 AAGAAAAAATGATGAA
372768 AAGAAAAAATGATGAA
1 AAGAAAAAATGATGAA
372784 AA
1 AA
372786 AAACCGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (16 bp):
AAGAAAAAATGATGAA
Found at i:372776 original size:25 final size:25
Alignment explanation
Indices: 372741--372845 Score: 83
Period size: 26 Copynumber: 4.2 Consensus size: 25
372731 AAGAAGAAAT
*
372741 AAAAGAGAAAAGAAGAAAAAATGAG
1 AAAAGAAAAAAGAAGAAAAAATGAG
* ***
372766 AAAAGAAAAAATGATGAAAAAAACCG
1 AAAAGAAAAAA-GAAGAAAAAATGAG
372792 AAAA-AAAAGAAG-AGAAAAAATG-G
1 AAAAGAAAA-AAGAAGAAAAAATGAG
*
372815 AAAAAGAAAGAAA-AAGAGAAAAATGAA
1 -AAAAGAAA-AAAGAAGA-AAAAATGAG
372842 AAAA
1 AAAA
372846 AAGGAAATAA
Statistics
Matches: 63, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
23 1 0.02
24 11 0.17
25 23 0.37
26 28 0.44
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (25 bp):
AAAAGAAAAAAGAAGAAAAAATGAG
Found at i:372787 original size:18 final size:17
Alignment explanation
Indices: 372734--372787 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 17
372724 TTGCTTGAAG
*
372734 AAGAAATAAAAGAGAAAA
1 AAGAAA-AAATGAGAAAA
372752 GAAGAAAAAATGAG--AA
1 -AAGAAAAAATGAGAAAA
372768 AAGAAAAAATGATGAAAA
1 AAGAAAAAATGA-GAAAA
372786 AA
1 AA
372788 ACCGAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 12 0.39
16 3 0.10
18 10 0.32
19 6 0.19
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (17 bp):
AAGAAAAAATGAGAAAA
Found at i:372837 original size:19 final size:19
Alignment explanation
Indices: 372794--372852 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
372784 AAAAACCGAA
372794 AAAAAAGAAGAGAAAAA-ATG
1 AAAAAAGAA-AGAAAAAGA-G
*
372814 GAAAAAGAAAGAAAAAGAG
1 AAAAAAGAAAGAAAAAGAG
*
372833 AAAAATGAAA-AAAAAG-G
1 AAAAAAGAAAGAAAAAGAG
372850 AAA
1 AAA
372853 TAAAAGGAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 4 0.11
18 6 0.17
19 16 0.46
20 9 0.26
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.03
Consensus pattern (19 bp):
AAAAAAGAAAGAAAAAGAG
Found at i:374053 original size:51 final size:51
Alignment explanation
Indices: 373988--374397 Score: 660
Period size: 51 Copynumber: 8.0 Consensus size: 51
373978 AAGCAAATTC
*
373988 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
374039 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
374090 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
*
374141 GTTCATTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
374192 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
*
374243 GTTCATTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
* * * **
374294 GTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGTGAGCGGACCT
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
** * *
374345 GTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGG-GCGGAC
1 GTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAG-GGAGCGGAC
374398 CCGTTTTATT
Statistics
Matches: 338, Mismatches: 16, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
51 306 0.91
54 2 0.01
55 29 0.09
56 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (51 bp):
GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
Found at i:374435 original size:56 final size:56
Alignment explanation
Indices: 374002--374504 Score: 273
Period size: 51 Copynumber: 9.6 Consensus size: 56
373992 GTTGAAGATT
* * ** **
374002 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
374053 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** *
374104 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCATTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
374155 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** *
374206 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCATTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
374257 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * * * *
374308 GAGTCCTATACTCCCTGAAAGAATAGTGAGCGGACCTG-TTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * *
374363 GAGT-TCTATACTCTCTGAAGGAATAGAGGGCGGACCCGTTTTATTAAATATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * *
374419 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
*
374474 GAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGC
374505 AGGCTCATCA
Statistics
Matches: 413, Mismatches: 31, Indels: 12
0.91 0.07 0.03
Matches are distributed among these distances:
51 292 0.71
54 3 0.01
55 67 0.16
56 50 0.12
57 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (56 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
Found at i:374521 original size:55 final size:55
Alignment explanation
Indices: 374351--374532 Score: 154
Period size: 55 Copynumber: 3.3 Consensus size: 55
374341 ACCTGTTTAT
* * * * * * *
374351 TGAAGATTTTTCGAGT-TCTATACTCTCTGAAGGAATAGAGGGCGGACCCGTTTTA
1 TGAAGATTGTTCAAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGACACATATTA
* * * * *
374406 TTAAATATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA
1 -TGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACATATTA
* * * *
374462 TGAAGATTGTTCGAGTCTTATACT-TCCTGAAGGAATAGGGAGCAGGCTCATCATT-
1 TGAAGATTGTTCAAGTCTTATACTCT-CTGAAGGAATAGAGAGCAGACACAT-ATTA
*
374517 TGAAGATTTTTCAAGT
1 TGAAGATTGTTCAAGT
374533 ATTTATCCTA
Statistics
Matches: 104, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
54 1 0.01
55 55 0.53
56 47 0.45
57 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (55 bp):
TGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACATATTA
Found at i:375640 original size:16 final size:16
Alignment explanation
Indices: 375619--375661 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
375609 GTTAAATTAG
375619 TTTAGGTTTTAGCTTA
1 TTTAGGTTTTAGCTTA
375635 TTTAGGTTTTAGCTTA
1 TTTAGGTTTTAGCTTA
375651 TTTAGGTTTTA
1 TTTAGGTTTTA
375662 TATTAATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.58
Consensus pattern (16 bp):
TTTAGGTTTTAGCTTA
Found at i:380727 original size:39 final size:39
Alignment explanation
Indices: 380671--380828 Score: 181
Period size: 39 Copynumber: 4.0 Consensus size: 39
380661 ACCATACACC
* *
380671 CAGTAAGGACTTACCCTGTGCACAAAGAAGAGGAGTCTG
1 CAGTAAGGACTTACCCTGAGCACAAAGAAGAGGAGCCTG
* ** *
380710 CGGTAAGGACTTACCCTGAGCACAAAGTTGAGGAGCATG
1 CAGTAAGGACTTACCCTGAGCACAAAGAAGAGGAGCCTG
* * * *
380749 CAATAAGGTCTTATCCTGTGCACAAAGAAAGAGGAGCCTG
1 CAGTAAGGACTTACCCTGAGCACAAAG-AAGAGGAGCCTG
* * **
380789 TAGTAAGGACTTACCTTGAGCACAAAGCCGAGGAGCCTG
1 CAGTAAGGACTTACCCTGAGCACAAAGAAGAGGAGCCTG
380828 C
1 C
380829 GGAAAACGGT
Statistics
Matches: 95, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 65 0.68
40 30 0.32
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.18
Consensus pattern (39 bp):
CAGTAAGGACTTACCCTGAGCACAAAGAAGAGGAGCCTG
Found at i:380809 original size:79 final size:78
Alignment explanation
Indices: 380674--380824 Score: 221
Period size: 79 Copynumber: 1.9 Consensus size: 78
380664 ATACACCCAG
* * **
380674 TAAGGACTTACCCTGTGCACAAAGAAGAGGAGTCTGCGGTAAGGACTTACCCTGAGCACAAAGTT
1 TAAGGACTTACCCTGTGCACAAAGAAGAGGAGCCTGCAGTAAGGACTTACCCTGAGCACAAAGCC
380739 GAGGAGCATGCAA
66 GAGGAGCATGCAA
* * * *
380752 TAAGGTCTTATCCTGTGCACAAAGAAAGAGGAGCCTGTAGTAAGGACTTACCTTGAGCACAAAGC
1 TAAGGACTTACCCTGTGCACAAAG-AAGAGGAGCCTGCAGTAAGGACTTACCCTGAGCACAAAGC
380817 CGAGGAGC
65 CGAGGAGC
380825 CTGCGGAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
78 22 0.34
79 42 0.66
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.19
Consensus pattern (78 bp):
TAAGGACTTACCCTGTGCACAAAGAAGAGGAGCCTGCAGTAAGGACTTACCCTGAGCACAAAGCC
GAGGAGCATGCAA
Found at i:386204 original size:26 final size:29
Alignment explanation
Indices: 386151--386205 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
386141 AACATATATG
386151 TATACATATATCAAAAAACTGCATAAAATA
1 TATACATATATCAAAAAACTGCA-AAAATA
*
386181 TATACATAT-T-AAAATACTGCAAAAA
1 TATACATATATCAAAAAACTGCAAAAA
386206 CCGTATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 10 0.42
29 1 0.04
30 9 0.38
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.27
Consensus pattern (29 bp):
TATACATATATCAAAAAACTGCAAAAATA
Found at i:386212 original size:28 final size:30
Alignment explanation
Indices: 386150--386212 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 30
386140 AAACATATAT
*
386150 GTATACATATATCAAAAAACTGCATAAAAT
1 GTATACATATATCAAAAAACTGCATAAAAC
* *
386180 ATATACATAT-T-AAAATACTGCA-AAAACC
1 GTATACATATATCAAAAAACTGCATAAAA-C
386208 GTATA
1 GTATA
386213 AAATATTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 4 0.14
28 14 0.50
29 1 0.04
30 9 0.32
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.27
Consensus pattern (30 bp):
GTATACATATATCAAAAAACTGCATAAAAC
Found at i:386514 original size:39 final size:38
Alignment explanation
Indices: 386470--386626 Score: 154
Period size: 39 Copynumber: 4.0 Consensus size: 38
386460 ACATGTACAC
* * *
386470 CAGTAAGGACTTTCCTTGTGCATAAAGCAGAGGAGCCTG
1 CAGTAAGGACTTACC-TGAGCACAAAGCAGAGGAGCCTG
* *
386509 TAGTAAGGACTTACCCTAAGCACAAAGTC-GAGGAGCCTG
1 CAGTAAGGACTTA-CCTGAGCACAAAG-CAGAGGAGCCTG
* * * * * *
386548 CACTGAGGTCTTATCCTGTGCATAAAGCAGATGAGCCTG
1 CAGTAAGGACTTA-CCTGAGCACAAAGCAGAGGAGCCTG
*
386587 CAGTAAGGACTTACCGTGAGCACAAAGCCGAGGAGCCTG
1 CAGTAAGGACTTACC-TGAGCACAAAGCAGAGGAGCCTG
386626 C
1 C
386627 GGAAAGCGGT
Statistics
Matches: 93, Mismatches: 21, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
38 3 0.03
39 87 0.94
40 3 0.03
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (38 bp):
CAGTAAGGACTTACCTGAGCACAAAGCAGAGGAGCCTG
Found at i:387947 original size:11 final size:12
Alignment explanation
Indices: 387924--387952 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
387914 GTTACTTTCT
387924 AAATTTAAATCA
1 AAATTTAAATCA
387936 AAATTT-AATCA
1 AAATTTAAATCA
387947 AAATTT
1 AAATTT
387953 CACTTAGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATTTAAATCA
Found at i:392884 original size:26 final size:26
Alignment explanation
Indices: 392840--392892 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
392830 ATATTCAATA
*
392840 TTAATTTAAATTATATT-AATATATTC
1 TTAAATTAAATTATATTAAAT-TATTC
392866 TTAAATTAAATTA-ATTTAAATTATTC
1 TTAAATTAAATTATA-TTAAATTATTC
392892 T
1 T
392893 ATTGTTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 1 0.04
26 20 0.83
27 3 0.12
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (26 bp):
TTAAATTAAATTATATTAAATTATTC
Found at i:395285 original size:2 final size:2
Alignment explanation
Indices: 395278--395305 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
395268 AGTATCATTC
395278 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
395306 GACCAGCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:399978 original size:41 final size:41
Alignment explanation
Indices: 399933--400014 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
399923 GAAATCGAGT
399933 TAGAAAATGCTCTTAG-TTGTGATAACAAAGACAATTTGCAA
1 TAGAAAATGCTCTT-GCTTGTGATAACAAAGACAATTTGCAA
*
399974 TAGAAAATGCTCTTGCTTGTGATAATAAAGACAATTTGCAA
1 TAGAAAATGCTCTTGCTTGTGATAACAAAGACAATTTGCAA
400015 ATATTTTATG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 1 0.03
41 38 0.97
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (41 bp):
TAGAAAATGCTCTTGCTTGTGATAACAAAGACAATTTGCAA
Found at i:402917 original size:488 final size:486
Alignment explanation
Indices: 401763--403225 Score: 2421
Period size: 492 Copynumber: 3.0 Consensus size: 486
401753 CCATGCTCTG
**
401763 AATTTGGAAATCAGGTAATATGATTCTTTGATCCTAGTATACTTCAATATATATTTTAGTTAATC
1 AATTTGGAAATCAGGTAATATGATTCTTTGATCCTAGTGGACTTCAATATATATTTTAGTTAATC
* *
401828 CATTACCATCTATATTTAGCATGTTCCAACCTGAAAAAAGAAGTTTGTAAGATGATGGTTATGGT
66 CGTTGCCATCTATATTTAGCATGTTCCAACCTGAAAAAAGAAGTTTGTAAGATGATGGTTATGGT
* *
401893 AGAAAGTCTTGCCAAATAGTTAATCATTTTAATGGGGATATTACTTTTTGGGGAGCTAAACCTTT
131 AGAAAGTCTTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTGGGGAGCTAAACCTTT
401958 TGCTGTTAGTTTCATACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGTGCTTATT
196 TGCTGTTAGTTTCATACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGTGCTTATT
*
402023 TCAGTTTTGAGGAACTTAGATTGGAATCCTGTTGAACCCTGTTGCATTTA-ACCCTATAACTGGA
261 TCAGTTTTGAGGAACTTAGATTGGAATCCTGTTGAACCCTGTTGCATTTATCCCCTATAACTGGA
*
402087 ACTAATCTTTCTATTTCTCATTTATTACAGTTGCTCCAACTACTGCTGTTCCCTCTGCTTCAACC
326 ACTAATCTTTCTATTTCTCA-TCATTACAGTTGCTCCAACTACTGCTGTTCCCTCTGCTTCAACC
402152 AATGCTGAAACAAACTTACTGGATGTTCGGTCTGATTCATTTGCCATTGTCCCAGTTACACCTGA
390 AATGCT------AACTTACTGGATGTTCGGTCTGATTCATTTGCCATTGTCCCAGTTACACCTGA
* *
402217 AAACCTTGCTACTGAATTTGGAAATCACCCGACATTTA
449 AAACCATGCTACTGAATTTGGAAATCACCCGACATGTA
* *
402255 AATTTGGAAATCCGGTAATATGATTCTTTGATCCTAGTGGACTTCAATATGTATTTTAGTTAATC
1 AATTTGGAAATCAGGTAATATGATTCTTTGATCCTAGTGGACTTCAATATATATTTTAGTTAATC
* * *
402320 CGTTGCCATCTATATTTAGCATGTTCAAACCTGAAAAATGAAGTTTGTAAGATGATGGTCATGGT
66 CGTTGCCATCTATATTTAGCATGTTCCAACCTGAAAAAAGAAGTTTGTAAGATGATGGTTATGGT
*
402385 AGAAAGTCTTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTAGGGG-GCCAAACCTT
131 AGAAAGTCTTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTT-GGGGAGCTAAACCTT
*
402449 TTGCTGTTAGTTTCATACTAGTGAAAGTTTTAAATTAAAACATAAAAGGATATTTTGGTGACTTA
195 TTGCTGTTAGTTTCATACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGTG-CTTA
* **
402514 TTTAAGTTTTGACTAACTTAGATTGGAATCCTGTTGAA-CCTGTTGCATTTATCCCCTATAACTG
259 TTTCAGTTTTGAGGAACTTAGATTGGAATCCTGTTGAACCCTGTTGCATTTATCCCCTATAACTG
*
402578 GAACTAATCTTTCTATTTCTCATCAGTTACAGTTGTTCCAACTACTGCTGTTCCCTCTGCTTCAA
324 GAACTAATCTTTCTATTTCTCATCA-TTACAGTTGCTCCAACTACTGCTGTTCCCTCTGCTTCAA
* * **
402643 CCAATGCT-ACTTATTGGATGTTCGGTTTGATTCCGTTGCCATTGTCCCAGTTACACCTGAAAAC
388 CCAATGCTAACTTACTGGATGTTCGGTCTGATTCATTTGCCATTGTCCCAGTTACACCTGAAAAC
* * *
402707 CATACTACTAAATTTGGAAATCAGCCGACATGTA
453 CATGCTACTGAATTTGGAAATCACCCGACATGTA
402741 AATTTGGAAATCAGGTAATATGATTCTTTGATCCTAGTGGACTTCAATATATATATTTTAGTTAA
1 AATTTGGAAATCAGGTAATATGATTCTTTGATCCTAGTGGACTTC-A-ATATATATTTTAGTTAA
402806 TCCGTTGCCATCTATATTTAGCATGTTCCAACCTGAAAAAAGAAGTTTGTAAGATGATGGTTATG
64 TCCGTTGCCATCTATATTTAGCATGTTCCAACCTGAAAAAAGAAGTTTGTAAGATGATGGTTATG
402871 GTAGAAAGTCTTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTGGGGAGCTAAACCT
129 GTAGAAAGTCTTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTGGGGAGCTAAACCT
402936 TTTGCTGTTAGTTTCATACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGTGGCTT
194 TTTGCTGTTAGTTTCATACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGT-GCTT
* *
403001 ATTTCAGTTTTGAGGAACTTAGATTGGAATCCTATTGAACCCTGTTGCATTTATCCACTATAACT
258 ATTTCAGTTTTGAGGAACTTAGATTGGAATCCTGTTGAACCCTGTTGCATTTATCCCCTATAACT
*
403066 GGAACTAATCTTTCTATTTCTCATCAATTACAGTTGCTCCAACTACTGATGTTCCCTCTGCTTCA
323 GGAACTAATCTTTCTATTTCTCATC-ATTACAGTTGCTCCAACTACTGCTGTTCCCTCTGCTTCA
* *
403131 ACCAATGCTGAAACAAACTTACTGGATGTTCGGTCTGATTCATTTGCCATTGTCTCAGTTACATC
387 ACCAATGCT------AACTTACTGGATGTTCGGTCTGATTCATTTGCCATTGTCCCAGTTACACC
403196 TGAAAACCATGCTACTGAATTTGGAAATCA
446 TGAAAACCATGCTACTGAATTTGGAAATCA
403226 AGTAATATGA
Statistics
Matches: 904, Mismatches: 50, Indels: 30
0.92 0.05 0.03
Matches are distributed among these distances:
486 125 0.14
487 5 0.01
488 234 0.26
489 95 0.11
490 1 0.00
492 251 0.28
493 122 0.13
496 71 0.08
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (486 bp):
AATTTGGAAATCAGGTAATATGATTCTTTGATCCTAGTGGACTTCAATATATATTTTAGTTAATC
CGTTGCCATCTATATTTAGCATGTTCCAACCTGAAAAAAGAAGTTTGTAAGATGATGGTTATGGT
AGAAAGTCTTGCCAAATAGTTAGTCATTTAAATGGGGATATTACTTTTTGGGGAGCTAAACCTTT
TGCTGTTAGTTTCATACTAGTGAAAGTTTTAAATTAAAACATAAAAGGCTATTTTGGTGCTTATT
TCAGTTTTGAGGAACTTAGATTGGAATCCTGTTGAACCCTGTTGCATTTATCCCCTATAACTGGA
ACTAATCTTTCTATTTCTCATCATTACAGTTGCTCCAACTACTGCTGTTCCCTCTGCTTCAACCA
ATGCTAACTTACTGGATGTTCGGTCTGATTCATTTGCCATTGTCCCAGTTACACCTGAAAACCAT
GCTACTGAATTTGGAAATCACCCGACATGTA
Found at i:411245 original size:23 final size:24
Alignment explanation
Indices: 411202--411247 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
411192 CACCACAGCT
*
411202 CGTATAATTGCAACCGAAGTGCCG
1 CGTAGAATTGCAACCGAAGTGCCG
*
411226 CGTAGAATTGC-ACCGTAGTGCC
1 CGTAGAATTGCAACCGAAGTGCC
411248 ATATGATGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (24 bp):
CGTAGAATTGCAACCGAAGTGCCG
Found at i:411482 original size:149 final size:148
Alignment explanation
Indices: 411215--411528 Score: 494
Period size: 149 Copynumber: 2.1 Consensus size: 148
411205 ATAATTGCAA
*
411215 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATGATGTCCATAAGGACCACATAGAATTC
1 CCGAAG-GACCGCGTAGAATTGCACCGGAGTGCCATATGATGTCCATAAGGACCACATAGAATTC
*
411279 CTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCA
65 CTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTATCCAGACTTCACACATGTTCCA
*
411344 AAG-A-ATATACATATGTC
130 AAGAATATATACATATATC
411361 CCGAAGGACCGCGTAGAATTGCACCGGAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGGAGTGCC--AT-ATGATGTCCATAAGGACCACATAGAAT
*
411426 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTCAT-CAGACTTCACACATGT
63 TCCTTAAGAATCATATACATATACTAGGGATCA-AGTATGTGTCT-ATCCAGACTTCACACATGT
*
411489 TCCAAAGAATATATATATATATC
126 TCCAAAGAATATATACATATATC
411512 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
411529 CCATCGACTC
Statistics
Matches: 155, Mismatches: 5, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
145 1 0.01
146 30 0.19
148 2 0.01
149 91 0.59
150 3 0.02
151 28 0.18
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (148 bp):
CCGAAGGACCGCGTAGAATTGCACCGGAGTGCCATATGATGTCCATAAGGACCACATAGAATTCC
TTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTATCCAGACTTCACACATGTTCCAA
AGAATATATACATATATC
Found at i:412441 original size:18 final size:18
Alignment explanation
Indices: 412420--412454 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
412410 TCCCATCTAG
412420 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
412438 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
412455 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:413078 original size:21 final size:21
Alignment explanation
Indices: 413036--413080 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
413026 TCTTGTTCGT
* * *
413036 TTGAAGGGGTATCGGTTTCCC
1 TTGAAGGGGTACCGATTCCCC
*
413057 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
413078 TTG
1 TTG
413081 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:415499 original size:25 final size:26
Alignment explanation
Indices: 415453--415507 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
415443 TGTTAAAACG
415453 AAAATAACTAATAGTTTAC-TTTTTT
1 AAAATAACTAATAGTTTACTTTTTTT
415478 AAAATAACCTAACTA-TTT-CTTTTTTT
1 AAAATAA-CTAA-TAGTTTACTTTTTTT
415504 AAAA
1 AAAA
415508 ATCATACTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 8 0.30
26 17 0.63
27 2 0.07
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (26 bp):
AAAATAACTAATAGTTTACTTTTTTT
Found at i:415939 original size:38 final size:38
Alignment explanation
Indices: 415885--415964 Score: 101
Period size: 38 Copynumber: 2.2 Consensus size: 38
415875 TTATTATAGT
* * * *
415885 AATATAGTATAT-TTTTTTA-AAAATGTTTTTTGAAAA
1 AATATAATATATAATTTTTAGAAAATGGTTTTCGAAAA
415921 AATATAATATATAATTTTTAGAAAATGGTTTTCGAAAA
1 AATATAATATATAATTTTTAGAAAATGGTTTTCGAAAA
*
415959 TATATA
1 AATATA
415965 TGTTATATAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 11 0.30
37 6 0.16
38 20 0.54
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.45
Consensus pattern (38 bp):
AATATAATATATAATTTTTAGAAAATGGTTTTCGAAAA
Found at i:416025 original size:37 final size:37
Alignment explanation
Indices: 415912--416385 Score: 381
Period size: 37 Copynumber: 12.8 Consensus size: 37
415902 TAAAAATGTT
* **
415912 TTTTGAAAA-A-ATATAATATATAATTTTTAGAAAATGG
1 TTTTGAAAATATATATAATATATAGTTTTT-GAAAA-CA
** *
415949 TTTTCGAAAATATATATGTTATATAG-TTTTGAATACA
1 TTTT-GAAAATATATATAATATATAGTTTTTGAAAACA
*
415986 TTTTGAAAATATATATAGTATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
* * ** *
416023 TTTTTCAAAA-ATATATAATATATACTCTCCT--CAACA
1 -TTTTGAAAATATATATAATATATAGT-TTTTGAAAACA
*
416059 TTTT-AATATATATATATAATATATAGCTTTTGAAAACA
1 TTTTGAA-A-ATATATATAATATATAGTTTTTGAAAACA
* *
416097 TTTTTGAAAACATATATATTATATAG-TTTTGAAAACA
1 -TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
* * *
416134 TTTTTGAAAACAAATATATTATATAGTTTTT-AAAACA
1 -TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
* *
416171 TTTTTTAAAACATATATATAATATATAGTTTTT-AAAATA
1 --TTTTGAAA-ATATATATAATATATAGTTTTTGAAAACA
* *
416210 TTTTGAATATATATATATAATATATAGTTTTTTAAAATA
1 TTTTGAA-A-ATATATATAATATATAGTTTTTGAAAACA
*
416249 TTTTGAAAACT-TATATAATATATAGTTATTTAAAAAAACA
1 TTTTGAAAA-TATATATAATATATAGTT-TTT--GAAAACA
***
416289 TTTTGAAAATATATAT--TATATA--TTAAAAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
* *
416322 TTTTGAAAA-CTATATAATATATA-ATTTTGAAAAC-
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
* *
416356 TTTTTAAAATTATATATAATATATCGTTTT
1 TTTTGAAAA-TATATATAATATATAGTTTT
416386 AAATCTTTTT
Statistics
Matches: 366, Mismatches: 42, Indels: 58
0.79 0.09 0.12
Matches are distributed among these distances:
32 5 0.01
33 16 0.04
34 16 0.04
35 13 0.04
36 39 0.11
37 114 0.31
38 84 0.23
39 48 0.13
40 31 0.08
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
Done.