Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009602.1 Hibiscus syriacus cultivar Beakdansim tig00116982_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: 1420948
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:218378 original size:25 final size:24
Alignment explanation
Indices: 218350--218420 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
218340 ATTTGAAAAT
218350 AAAATAAAATATAATAAATATTATG
1 AAAATAAAA-ATAATAAATATTATG
* * *
218375 AAAATAATAAGTAATAAAAATTTTG
1 AAAATAA-AAATAATAAATATTATG
*
218400 -AAATAAAAGA-ATTAAATATTA
1 AAAATAAAA-ATAATAAATATTA
218421 AATAAATATG
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
23 10 0.27
24 6 0.16
25 19 0.51
26 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (24 bp):
AAAATAAAAATAATAAATATTATG
Found at i:219373 original size:17 final size:17
Alignment explanation
Indices: 219329--219378 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
219319 TATTAAAAGG
*
219329 ATAATAATACAATCAAAT
1 ATAATATTA-AATCAAAT
* *
219347 -TAAAATTAAATTAAAT
1 ATAATATTAAATCAAAT
219363 ATAATATTAAATCAAA
1 ATAATATTAAATCAAA
219379 CAATGATCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAATATTAAATCAAAT
Found at i:220610 original size:15 final size:14
Alignment explanation
Indices: 220577--220610 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
220567 TATTATTAGG
*
220577 TTTGGGCCAGTCTA
1 TTTGGGCCAGTCAA
220591 TTTGGGCCAGTTCAA
1 TTTGGGCCAG-TCAA
220606 TTTGG
1 TTTGG
220611 ATCACTGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.15, C:0.18, G:0.29, T:0.38
Consensus pattern (14 bp):
TTTGGGCCAGTCAA
Found at i:220645 original size:3 final size:3
Alignment explanation
Indices: 220631--220697 Score: 91
Period size: 3 Copynumber: 22.0 Consensus size: 3
220621 TTTGTATCTG
* *
220631 TAA TAA -AA TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
220676 TAA TAA TAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA
220698 AAAAAACCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 2 0.04
3 50 0.88
4 5 0.09
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:223604 original size:29 final size:29
Alignment explanation
Indices: 223561--223619 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
223551 GGAAGAAAAG
*
223561 TGCTTCTAATGAATCTACAACTCATGACC
1 TGCTTCTAATAAATCTACAACTCATGACC
223590 TGCTTCTAATAAATCTACAACTCATGACC
1 TGCTTCTAATAAATCTACAACTCATGACC
223619 T
1 T
223620 AAAGAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.32
Consensus pattern (29 bp):
TGCTTCTAATAAATCTACAACTCATGACC
Found at i:228239 original size:20 final size:20
Alignment explanation
Indices: 228216--228284 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
228206 ATTAAGTCTA
228216 AAACAATAAAATCCATAAAC
1 AAACAATAAAATCCATAAAC
* * ** **
228236 AAACCATAATATTAAGTCTA-
1 AAACAATAAAATCCA-TAAAC
228256 AAACAATAAAATCCATAAAC
1 AAACAATAAAATCCATAAAC
228276 AAACAATAA
1 AAACAATAA
228285 TATTAAAATG
Statistics
Matches: 35, Mismatches: 12, Indels: 4
0.69 0.24 0.08
Matches are distributed among these distances:
19 2 0.06
20 31 0.89
21 2 0.06
ACGTcount: A:0.62, C:0.17, G:0.01, T:0.19
Consensus pattern (20 bp):
AAACAATAAAATCCATAAAC
Found at i:228243 original size:40 final size:40
Alignment explanation
Indices: 228185--228290 Score: 185
Period size: 40 Copynumber: 2.6 Consensus size: 40
228175 ATCTTTCGAG
* *
228185 AATCCATATACAACCCATAATATTAAGTCTAAAACAATAA
1 AATCCATAAACAAACCATAATATTAAGTCTAAAACAATAA
228225 AATCCATAAACAAACCATAATATTAAGTCTAAAACAATAA
1 AATCCATAAACAAACCATAATATTAAGTCTAAAACAATAA
*
228265 AATCCATAAACAAACAATAATATTAA
1 AATCCATAAACAAACCATAATATTAA
228291 AATGTCAAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.57, C:0.18, G:0.02, T:0.24
Consensus pattern (40 bp):
AATCCATAAACAAACCATAATATTAAGTCTAAAACAATAA
Found at i:229881 original size:21 final size:20
Alignment explanation
Indices: 229857--229903 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
229847 GGAATATATT
229857 CCCCCTGGGGGGGAATCGGTA
1 CCCCCT-GGGGGGAATCGGTA
*
229878 CCCCCTGGGGGGAATCTGTA
1 CCCCCTGGGGGGAATCGGTA
229898 CCCCCT
1 CCCCCT
229904 AGGCAATCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.13, C:0.36, G:0.34, T:0.17
Consensus pattern (20 bp):
CCCCCTGGGGGGAATCGGTA
Found at i:233699 original size:21 final size:21
Alignment explanation
Indices: 233656--233716 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
233646 CCGTTAGACA
* *
233656 GGGGGGAATCGGTACCCTC-T
1 GGGGGGAATCTGTACCCCCTT
*
233676 GGGGGGAATCTGTTCCCCCTT
1 GGGGGGAATCTGTACCCCCTT
233697 GGGGGGAATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
233717 AGGCAATCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.13, C:0.28, G:0.36, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTT
Found at i:240670 original size:21 final size:21
Alignment explanation
Indices: 240644--240683 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
240634 CCCCCTTTGA
*
240644 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
240665 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
240684 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:248166 original size:39 final size:38
Alignment explanation
Indices: 248109--248224 Score: 117
Period size: 39 Copynumber: 3.0 Consensus size: 38
248099 TAAGGGCTCG
* *
248109 CGGTAAAGACTTACCCTGTGCACAAAGCAGAGGAGTCTGT
1 CGGTAAGGACTTA-CCTGTGCACAAAGCAGAGGAGCCT-T
* ** *
248149 -GGTAAGGGCTTATCCTGTATACAAAGCAAAGGAGCCTT
1 CGGTAAGGACTTA-CCTGTGCACAAAGCAGAGGAGCCTT
**
248187 CGGTAAGGACTTACCATGTGCATGAAGCAGAGGAGCCT
1 CGGTAAGGACTTACC-TGTGCACAAAGCAGAGGAGCCT
248225 ACGGCAATTA
Statistics
Matches: 61, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
38 3 0.05
39 58 0.95
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (38 bp):
CGGTAAGGACTTACCTGTGCACAAAGCAGAGGAGCCTT
Found at i:249288 original size:26 final size:26
Alignment explanation
Indices: 249158--249280 Score: 192
Period size: 26 Copynumber: 4.7 Consensus size: 26
249148 GTAATGACGA
* ** *
249158 TATTTAGGTCATTCCAAAACTCGAGAG
1 TATTTCGGTCATTTTAAAGCTCGAG-G
249185 TATTTCGGTCATTTTAAAGCTCGAGG
1 TATTTCGGTCATTTTAAAGCTCGAGG
249211 TATTTCGGTCATTTTAAAGCTCGAGG
1 TATTTCGGTCATTTTAAAGCTCGAGG
*
249237 TATTTCGGTCATTTTAAAGCTCAAGG
1 TATTTCGGTCATTTTAAAGCTCGAGG
249263 TATTTCGGTCATTTTAAA
1 TATTTCGGTCATTTTAAA
249281 ACTCAAGGGG
Statistics
Matches: 91, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
26 70 0.77
27 21 0.23
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (26 bp):
TATTTCGGTCATTTTAAAGCTCGAGG
Found at i:256852 original size:35 final size:35
Alignment explanation
Indices: 256805--256877 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
256795 TCTCCCTATT
*
256805 GGGCTCACGCAGTGACGTGGAATTGATAGAATTTA
1 GGGCTCACGCAGTGACGTGGAACTGATAGAATTTA
* *
256840 GGGCTCATGCAGTGACGTTGAACTGATAGAATTTA
1 GGGCTCACGCAGTGACGTGGAACTGATAGAATTTA
256875 GGG
1 GGG
256878 GTTAACTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.27, C:0.14, G:0.33, T:0.26
Consensus pattern (35 bp):
GGGCTCACGCAGTGACGTGGAACTGATAGAATTTA
Found at i:262078 original size:22 final size:23
Alignment explanation
Indices: 262047--262093 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
262037 ATTATTATCA
* *
262047 TTATTATTCTT-TTTTCTTCATT
1 TTATTATTCTTATTGTATTCATT
*
262069 TTATTTTTCTTATTGTATTCATT
1 TTATTATTCTTATTGTATTCATT
262092 TT
1 TT
262094 TATCTTCACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (23 bp):
TTATTATTCTTATTGTATTCATT
Found at i:262140 original size:8 final size:8
Alignment explanation
Indices: 262129--262177 Score: 66
Period size: 8 Copynumber: 6.2 Consensus size: 8
262119 TATTTCGGTC
262129 ATTTTTTT
1 ATTTTTTT
262137 ATTTTTTT
1 ATTTTTTT
262145 ATTTTTTT
1 ATTTTTTT
*
262153 ATTCTATTT
1 ATT-TTTTT
262162 A--TTTTT
1 ATTTTTTT
262168 ATTTTTTT
1 ATTTTTTT
262176 AT
1 AT
262178 CTAACACGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
6 5 0.14
8 26 0.72
9 5 0.14
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (8 bp):
ATTTTTTT
Found at i:265093 original size:12 final size:13
Alignment explanation
Indices: 265068--265120 Score: 65
Period size: 12 Copynumber: 4.2 Consensus size: 13
265058 CAATCAGAAC
265068 AAAAA-AAAGAGA
1 AAAAACAAAGAGA
265080 AAAAACAAAG-GA
1 AAAAACAAAGAGA
*
265092 AAAAACAAAGATA
1 AAAAACAAAGAGA
*
265105 AAATAAAAAAGAGA
1 AAA-AACAAAGAGA
265119 AA
1 AA
265121 CAAAAACTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 17 0.49
13 8 0.23
14 10 0.29
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.04
Consensus pattern (13 bp):
AAAAACAAAGAGA
Found at i:266280 original size:32 final size:32
Alignment explanation
Indices: 266210--266281 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
266200 GCACCTTTGA
* * *
266210 AGATTCAACATCAAATGTTGGGGCATTTTTGG
1 AGATTCAACATCAAATATTGGGGCATCTTCGG
* *
266242 AAATTCAACATCGAATATTGGGGCATCTTCGG
1 AGATTCAACATCAAATATTGGGGCATCTTCGG
*
266274 GGATTCAA
1 AGATTCAA
266282 AATCCTGATA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (32 bp):
AGATTCAACATCAAATATTGGGGCATCTTCGG
Found at i:266998 original size:110 final size:110
Alignment explanation
Indices: 266805--267194 Score: 665
Period size: 110 Copynumber: 3.5 Consensus size: 110
266795 TCGAGACAAG
*
266805 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
1 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATA
266870 TTGGACTCGAGACAACACAAGCTCAACTTCACAGTGAAGGGGCGA
66 TTGGACTCGAGACAACACAAGCTCAACTTCACAGTGAAGGGGCGA
* * * *
266915 CTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTTAATTTCACAGCGAAGGATA
1 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATA
* *
266980 TTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAATGGGCGA
66 TTGGACTCGAGACAACACAAGCTCAACTTCACAGTGAAGGGGCGA
* * *
267025 ATGACTGTCAACAAACAACGTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAATGATA
1 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATA
*
267090 TTGGACTCGAGACAACACAAGCTCAACTTCACAACT-AAGGGGCGA
66 TTGGACTCGAGACAACACAAGCTCAACTTCAC-AGTGAAGGGGCGA
267135 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAA
1 CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAA
267195 AAATATTGAA
Statistics
Matches: 262, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
110 261 1.00
111 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (110 bp):
CTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATA
TTGGACTCGAGACAACACAAGCTCAACTTCACAGTGAAGGGGCGA
Found at i:268350 original size:37 final size:37
Alignment explanation
Indices: 268307--268415 Score: 200
Period size: 37 Copynumber: 2.9 Consensus size: 37
268297 AACATAACGT
*
268307 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
268344 TCGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
268381 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAG
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAG
268416 AATCCATAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
Found at i:268788 original size:3 final size:3
Alignment explanation
Indices: 268780--268880 Score: 81
Period size: 3 Copynumber: 34.3 Consensus size: 3
268770 TTTTACTTAC
268780 TAT TAT TAT TA- TAT ATACT TCAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT -TA-T T-AT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
268827 TAT TAT TA- TAT T-T TA- TAT GTTT TAT T-T TGT T-T TAT T-T TTT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
268867 TATT TAT TAT TAT T
1 TA-T TAT TAT TAT T
268881 TTTTAAAACA
Statistics
Matches: 83, Mismatches: 3, Indels: 24
0.75 0.03 0.22
Matches are distributed among these distances:
2 14 0.17
3 57 0.69
4 10 0.12
5 2 0.02
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:268985 original size:2 final size:2
Alignment explanation
Indices: 268980--269040 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
268970 ATTATTTATC
268980 TA TA TA T- 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
269021 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
269041 CATTTTTTCA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:269171 original size:3 final size:3
Alignment explanation
Indices: 269163--269200 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
269153 TACTTACTGT
269163 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
269201 CTATTTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:269227 original size:19 final size:19
Alignment explanation
Indices: 269166--269215 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 19
269156 TTACTGTTTA
*
269166 TTATTATTATTATTATTATT
1 TTATTATTATTATT-CTATT
269186 ATTATTATTATTATTCTATT
1 -TTATTATTATTATTCTATT
269206 TTATT-TTATT
1 TTATTATTATT
269216 TATTTATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 5 0.18
19 5 0.18
20 4 0.14
21 14 0.50
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTATTATTATTCTATT
Found at i:269314 original size:19 final size:18
Alignment explanation
Indices: 269242--269324 Score: 58
Period size: 19 Copynumber: 4.3 Consensus size: 18
269232 TTTTTTCCTC
*
269242 TATTTCATTTTTATTTTTAT
1 TATTT-ATTTATATTTTT-T
** *
269262 TCCTTATTTTTATTTTTT
1 TATTTATTTATATTTTTT
* *
269280 TATCTTCTTTACATTTGTTT
1 TAT-TTATTTATATTT-TTT
*
269300 TATTTATTTGTATTTTTTT
1 TATTTATTTATA-TTTTTT
269319 TATTTA
1 TATTTA
269325 CTCGTTTATT
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
18 2 0.04
19 36 0.72
20 12 0.24
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.73
Consensus pattern (18 bp):
TATTTATTTATATTTTTT
Found at i:269336 original size:3 final size:3
Alignment explanation
Indices: 269330--269366 Score: 56
Period size: 3 Copynumber: 11.7 Consensus size: 3
269320 ATTTACTCGT
269330 TTA TTA TGTA TATA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TT
269367 CTTTTTTCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
3 26 0.81
4 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:270529 original size:20 final size:20
Alignment explanation
Indices: 270496--270533 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
270486 GAGGTATGTA
*
270496 TTTAAATATTATTATATACT
1 TTTAAATATCATTATATACT
*
270516 TTTAATTATCATTATATA
1 TTTAAATATCATTATATA
270534 ATTAGAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTAAATATCATTATATACT
Found at i:271156 original size:21 final size:21
Alignment explanation
Indices: 271127--271187 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
271117 TACATTCTAC
271127 AGCCGTTTCAGATGGTACCGA
1 AGCCGTTTCAGATGGTACCGA
* *
271148 TGTCGTTTCAGATGGTACCGA
1 AGCCGTTTCAGATGGTACCGA
271169 AGCCGTTTCAGATGGTACC
1 AGCCGTTTCAGATGGTACC
271188 ACAACCATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (21 bp):
AGCCGTTTCAGATGGTACCGA
Found at i:271198 original size:21 final size:21
Alignment explanation
Indices: 271132--271199 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
271122 TCTACAGCCG
*** *
271132 TTTCAGATGGTACCGATGTCG
1 TTTCAGATGGTACCGAAACCA
* *
271153 TTTCAGATGGTACCGAAGCCG
1 TTTCAGATGGTACCGAAACCA
271174 TTTCAGATGGTACC-ACAACCA
1 TTTCAGATGGTACCGA-AACCA
271195 TTTCA
1 TTTCA
271200 TATGCCACTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (21 bp):
TTTCAGATGGTACCGAAACCA
Found at i:271688 original size:19 final size:18
Alignment explanation
Indices: 271664--271701 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
271654 GTTTACCAGC
271664 AATTATAATTTTTTTATTT
1 AATTATAA-TTTTTTATTT
*
271683 AATTATGATTTTTTATTT
1 AATTATAATTTTTTATTT
271701 A
1 A
271702 TTTTGTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
AATTATAATTTTTTATTT
Found at i:271766 original size:23 final size:24
Alignment explanation
Indices: 271717--271770 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 24
271707 TTTCTTAATG
271717 TTTTTATTATTTAATTGTTTGAATTA
1 TTTTTATTATTTAATTGTTT--ATTA
*
271743 TTTTTATTATTTAGTTGTTT-TTA
1 TTTTTATTATTTAATTGTTTATTA
271766 TTTTT
1 TTTTT
271771 GAGTTTATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 8 0.30
26 19 0.70
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.72
Consensus pattern (24 bp):
TTTTTATTATTTAATTGTTTATTA
Found at i:274169 original size:60 final size:59
Alignment explanation
Indices: 274076--274194 Score: 184
Period size: 60 Copynumber: 2.0 Consensus size: 59
274066 CTCCACGATG
* * * *
274076 TCGACATTTAGGTCGAACAAGCTGGTAGTTGAATGCCTTCCCCTTGAACTTGAAGGCATC
1 TCGACATTGAGGTCGAACAAGCTCGCAGTTGAATGCC-TCCCCTAGAACTTGAAGGCATC
*
274136 TCGACATTGAGGTCGAAGAAGCTCGCAGTTGAATGCCTCCCCTAGAACTTGAAGGCATC
1 TCGACATTGAGGTCGAACAAGCTCGCAGTTGAATGCCTCCCCTAGAACTTGAAGGCATC
274195 GTGTCAAATG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
59 21 0.39
60 33 0.61
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.25
Consensus pattern (59 bp):
TCGACATTGAGGTCGAACAAGCTCGCAGTTGAATGCCTCCCCTAGAACTTGAAGGCATC
Found at i:275628 original size:18 final size:19
Alignment explanation
Indices: 275589--275630 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
275579 TAAAAAATTA
*
275589 AATTTAATAATATACTATT
1 AATTTAATAATATAATATT
275608 AATTTAA-AATATGAATA-T
1 AATTTAATAATAT-AATATT
275626 AATTT
1 AATTT
275631 TATTGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
AATTTAATAATATAATATT
Found at i:277433 original size:16 final size:15
Alignment explanation
Indices: 277395--277454 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 15
277385 AATCCAACAT
* *
277395 TTTTATTTATATGTA
1 TTTTATTTATTTTTA
* *
277410 TATATATTTATTATTTC
1 T-TTTATTTATT-TTTA
277427 TTTTATTTATTTTTA
1 TTTTATTTATTTTTA
*
277442 TTTTATTAATTTT
1 TTTTATTTATTTT
277455 CCATACATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
15 16 0.44
16 17 0.47
17 3 0.08
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (15 bp):
TTTTATTTATTTTTA
Found at i:277892 original size:15 final size:15
Alignment explanation
Indices: 277872--277904 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
277862 TCTCCCTCTT
277872 TTTATCTAATATTTA
1 TTTATCTAATATTTA
*
277887 TTTATCTAATTTTTA
1 TTTATCTAATATTTA
277902 TTT
1 TTT
277905 TCCAATCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATCTAATATTTA
Found at i:280198 original size:95 final size:93
Alignment explanation
Indices: 280087--280285 Score: 292
Period size: 95 Copynumber: 2.1 Consensus size: 93
280077 AGATTATAAT
*
280087 ATTATATATATACAATAAAGCTTGAGATG-CTCCTCTAAAGCAATTGGTTAAATGCCCCGACTTT
1 ATTATA-ATATACAATAAAGCTTGAGATGTC-CCTCTAAAGCAATTGGTTAAATG-CCCAACTTT
**
280151 ATGGATAAGATTCAGGTAGCCTGATAAAGGTA
63 ATGGATAAGATTCAACTAG-CTGATAAAGGTA
* *
280183 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGCCCAACTTTATG
1 ATTATAATATACAATAAAGCTTGAGATGTCCCTCTAAAGCAATTGGTTAAATGCCCAACTTTATG
* *
280248 GATAATATTCAACTAGCTGATAAAGGTG
66 GATAAGATTCAACTAGCTGATAAAGGTA
280276 ATTATAATAT
1 ATTATAATAT
280286 CTATAATGAT
Statistics
Matches: 95, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
93 21 0.22
94 24 0.25
95 43 0.45
96 7 0.07
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (93 bp):
ATTATAATATACAATAAAGCTTGAGATGTCCCTCTAAAGCAATTGGTTAAATGCCCAACTTTATG
GATAAGATTCAACTAGCTGATAAAGGTA
Found at i:280320 original size:94 final size:94
Alignment explanation
Indices: 280087--280332 Score: 250
Period size: 94 Copynumber: 2.6 Consensus size: 94
280077 AGATTATAAT
* * *
280087 ATTATATATATACAATAAAGCTTGAGATGCTCC-TCTA-AAGCAATTGGTTAAATGCCCCGACTT
1 ATTATA-ATATACAATAAAGATTGAGCTG-TCCATCTACAA-CAATTGGTTAAATG-CCCAACTT
**
280150 TATGGATAAGATTCAGGTAGCCTGATAAAGGTA
62 TATGGATAAGATTCAACTAGCCTGATAAAGGTA
* * * * *
280183 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGCCCAACTTTATG
1 ATTATAATATACAATAAAGATTGAGCTGTCCATCTACAACAATTGGTTAAATGCCCAACTTTATG
* *
280248 GATAATATTCAACTAG-CTGATAAAGGTG
66 GATAAGATTCAACTAGCCTGATAAAGGTA
* * * *
280276 ATTATAATAT-CTATAATGATATTGAGCTGT-CATACTACAACAATTAGTTAAACGCCC
1 ATTATAATATACAATAA--AGATTGAGCTGTCCAT-CTACAACAATTGGTTAAATGCCC
280333 CGGCTTTATG
Statistics
Matches: 129, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
92 5 0.04
93 23 0.18
94 55 0.43
95 39 0.30
96 7 0.05
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (94 bp):
ATTATAATATACAATAAAGATTGAGCTGTCCATCTACAACAATTGGTTAAATGCCCAACTTTATG
GATAAGATTCAACTAGCCTGATAAAGGTA
Found at i:281612 original size:85 final size:85
Alignment explanation
Indices: 281497--282637 Score: 1319
Period size: 85 Copynumber: 13.4 Consensus size: 85
281487 GGAAATATTA
* * * * *
281497 ACAGCATAGCTCAAGGCAAGAAAGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAG
* *
281562 CTCAAAGGAACATCAAATTT
66 CTCAAAGGCATATCAAATTT
* * * *
281582 ATAGCATAACACAAGGCGAGAAGGGCTATCTATCAACCAAGACCTTCGAGTTCGATTACACTCAG
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAG
*
281647 CTCAAAGGCATATCAAATTC
66 CTCAAAGGCATATCAAATTT
** * * * * *
281667 GTAGCATAACTCAAGGCGAGAAGGGTTTTCTGCCAACAAAATACCTTCGAGTTCGATTACATTCA
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCA
* *
281732 GCTCAAAGGCATAACAAATTC
65 GCTCAAAGGCATATCAAATTT
* * * ** *
281753 GCAGCATAACTCAAGACAAGAAGGATTATCTGCCAACAAAGACCTTCGAGTTCGATTACACTCAG
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAG
*
281818 CTCAAAGGCATATCAAATTC
66 CTCAAAGGCATATCAAATTT
* * * *
281838 GCAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACATTCA
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCA
* * * *
281903 ACTTAAAGGCATATCAGATTC
65 GCTCAAAGGCATATCAAATTT
* * * *
281924 ATAGCATAACTCAAGGCGAGAA-GGCTTATCTGCCAACAAAAGTCCTTCGAGTTTGATTACACTC
1 ACAGCATAACTCAAGGCGAGAAGGGC-TATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTC
* *
281988 AGCTCAAAGGTACATCAAATTT
64 AGCTCAAAGGCATATCAAATTT
* * * * * * * * *
282010 ATAACATAGCTCAAGGCGAGAAGGGTTATCTGTTAACCAAGATCTTCGAGTTTGATTACATTCA-
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAG
* *
282074 CTCAAAGACATATCAAATTCG
66 CTCAAAGGCATATCAAATT-T
* * * * * * *
282095 A-AGTATAACTCAAGGCGAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCAATTACATTAA
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAA-CAAAGACCTTCGAGTTCGATTACACTCA
*
282159 GCTCAAAGGCACATCAAATTT
65 GCTCAAAGGCATATCAAATTT
* * * * * *
282180 ACAACATAGCTTAAGGCG-G-AGGCCTATCTGTCAACTAAGACCTTCGAGTTTGATTACACTCAG
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAG
* *
282243 CTCAAATGCATATCAAACTT
66 CTCAAAGGCATATCAAATTT
* * * * *
282263 ACAACATAACTCAAGGCGAGAAGGGTTCTCTATCAACCAAGACCTTCGAGTTCGATTACACTCAG
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAG
*
282328 CTCAAAGGCACATCAAATTT
66 CTCAAAGGCATATCAAATTT
* * *
282348 ACAGCATAGCTCAAGGCGTGAAGGGCTATCTATCAACAAAGACCTTCGAGTTCGATTACACTCAG
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAG
282413 CTCAAAGGCATATCAAATTT
66 CTCAAAGGCATATCAAATTT
* * * *
282433 ACAGCATAGCTCAATGCGAGAAGGGCTATTTG-CTAGA-AAAGACCTTCGAGTTCGATTACATTC
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTC-A-ACAAAGACCTTCGAGTTCGATTACACTC
282496 AGCTCAAAGGCATATCAAATTT
64 AGCTCAAAGGCATATCAAATTT
* * * * * *
282518 ACAGCATAGCTCAAGGCGAGAAGGTCTATCTGTTC-ACCAGGACATTCAAGTTCGATTACACTCA
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTG-TCAACAAAGACCTTCGAGTTCGATTACACTCA
282582 GCTCAAAGGCATATCAAATTT
65 GCTCAAAGGCATATCAAATTT
* * *
282603 ATAGCATAGCTCAAGGCGAGATGGGCTAT-TGTCAA
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAA
282638 TAAAAACTTT
Statistics
Matches: 916, Mismatches: 124, Indels: 33
0.85 0.12 0.03
Matches are distributed among these distances:
83 58 0.06
84 63 0.07
85 542 0.59
86 250 0.27
87 3 0.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (85 bp):
ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAG
CTCAAAGGCATATCAAATTT
Found at i:283338 original size:2 final size:2
Alignment explanation
Indices: 283331--283375 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
283321 GTCCATGAAA
283331 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
283372 AT AT
1 AT AT
283376 TACTTAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:284593 original size:24 final size:24
Alignment explanation
Indices: 284560--284605 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
284550 TATATATATT
284560 TATTATTTCTTTTATTTCTTTTTTA
1 TATTATTTCTTTTATTT-TTTTTTA
284585 TATT-TTTCTTTTATTTTTTTT
1 TATTATTTCTTTTATTTTTTTT
284606 ATTTTTCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (24 bp):
TATTATTTCTTTTATTTTTTTTTA
Found at i:284596 original size:13 final size:12
Alignment explanation
Indices: 284558--284603 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
284548 TGTATATATA
*
284558 TTTATTATTTCT
1 TTTATTTTTTCT
*
284570 TTTATTTCTT-T
1 TTTATTTTTTCT
284581 TTTATATTTTTCT
1 TTTAT-TTTTTCT
284594 TTTATTTTTT
1 TTTATTTTTT
284604 TTATTTTTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 6 0.21
12 17 0.59
13 6 0.21
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTATTTTTTCT
Found at i:286998 original size:80 final size:80
Alignment explanation
Indices: 286912--287551 Score: 1027
Period size: 80 Copynumber: 8.1 Consensus size: 80
286902 TCCTTAGAAT
* * * *
286912 CGTAGGGTTACCTTAAGCACACAGCTAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCA
1 CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCCTACCCA
* *
286977 AGATATCATAAGGTC
66 AGATATCCTTAGGTC
* * *
286992 CGTAGGGTTACCTTATGCACACAGCAAAGAAAACCAACCTAAGGATATACCTTGGAGCCTACCCA
1 CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCCTACCCA
287057 AGATATCCTTAGGTC
66 AGATATCCTTAGGTC
* *
287072 CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAAGATATGCCTTGGGGCTTACCCA
1 CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCCTACCCA
287137 AGATATCCTTAGGTC
66 AGATATCCTTAGGTC
* ** * *
287152 CATAGGGTTACCTTATGCGGACAGCAAAGGAAACCAACCTAAGGATGTGCCTT-GGGCCTACACA
1 CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCCTACCCA
287216 AGATATCCTTAGGTC
66 AGATATCCTTAGGTC
*
287231 CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATACCTTGGGGCCTACCCA
1 CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCCTACCCA
287296 AGATATCCTTAGGTC
66 AGATATCCTTAGGTC
*
287311 CGTAGGGTTACCTTATGCACACAACAAAGGAAACCAACCTAAGGATATGCCTTGGGGCCTACCCA
1 CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCCTACCCA
*
287376 AGATATACTTAGGTC
66 AGATATCCTTAGGTC
*
287391 CGTAGGGTTACCTTATGCACACAGCAAA-GAAACCAACCTAAGGATATGCCTTGGGGCCTACCTA
1 CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCCTACCCA
287455 AGATATCCTTAGGT-
66 AGATATCCTTAGGTC
* ** * *
287469 TGTAGGGTTACCTTATGCACACAATAAAGGAAACCAACCTAAGGATGTGCCTT-GGGCCTATCCA
1 CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCCTACCCA
287533 AGATATCCTTAGGTC
66 AGATATCCTTAGGTC
287548 CGTA
1 CGTA
287552 AGGACTTAGC
Statistics
Matches: 519, Mismatches: 38, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
78 48 0.09
79 146 0.28
80 325 0.63
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (80 bp):
CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCCTACCCA
AGATATCCTTAGGTC
Found at i:287278 original size:159 final size:159
Alignment explanation
Indices: 286912--287551 Score: 1032
Period size: 159 Copynumber: 4.0 Consensus size: 159
286902 TCCTTAGAAT
* * *
286912 CGTAGGGTTACCTTAAGCACACAGCTAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCA
1 CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATACCTTGGGGCCTACCCA
* * * * *
286977 AGATATCATAAGGTCCGTAGGGTTACCTTATGCACACAGCAAAGAAAACCAACCTAAGGATATAC
66 AGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAACAAAGGAAACCAACCTAAGGATATGC
287042 CTTGGAGCCTACCCAAGATATCCTTAGGTC
131 CTTGG-GCCTACCCAAGATATCCTTAGGTC
* * *
287072 CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAAGATATGCCTTGGGGCTTACCCA
1 CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATACCTTGGGGCCTACCCA
* ** * *
287137 AGATATCCTTAGGTCCATAGGGTTACCTTATGCGGACAGCAAAGGAAACCAACCTAAGGATGTGC
66 AGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAACAAAGGAAACCAACCTAAGGATATGC
*
287202 CTTGGGCCTACACAAGATATCCTTAGGTC
131 CTTGGGCCTACCCAAGATATCCTTAGGTC
287231 CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATACCTTGGGGCCTACCCA
1 CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATACCTTGGGGCCTACCCA
287296 AGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAACAAAGGAAACCAACCTAAGGATATGC
66 AGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAACAAAGGAAACCAACCTAAGGATATGC
*
287361 CTTGGGGCCTACCCAAGATATACTTAGGTC
131 CTT-GGGCCTACCCAAGATATCCTTAGGTC
* *
287391 CGTAGGGTTACCTTATGCACACAGCAAA-GAAACCAACCTAAGGATATGCCTTGGGGCCTACCTA
1 CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATACCTTGGGGCCTACCCA
* * *
287455 AGATATCCTTAGGT-TGTAGGGTTACCTTATGCACACAATAAAGGAAACCAACCTAAGGATGTGC
66 AGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAACAAAGGAAACCAACCTAAGGATATGC
*
287519 CTTGGGCCTATCCAAGATATCCTTAGGTC
131 CTTGGGCCTACCCAAGATATCCTTAGGTC
287548 CGTA
1 CGTA
287552 AGGACTTAGC
Statistics
Matches: 447, Mismatches: 32, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
157 28 0.06
158 50 0.11
159 196 0.44
160 173 0.39
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (159 bp):
CGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATACCTTGGGGCCTACCCA
AGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAACAAAGGAAACCAACCTAAGGATATGC
CTTGGGCCTACCCAAGATATCCTTAGGTC
Found at i:287293 original size:239 final size:239
Alignment explanation
Indices: 286914--287551 Score: 1023
Period size: 239 Copynumber: 2.7 Consensus size: 239
286904 CTTAGAATCG
* * * *
286914 TAGGGTTACCTTAAGCACACAGCTAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAG
1 TAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCCTA-CCAAG
* * *
286979 ATATCATAAGGTCCGTAGGGTTACCTTATGCACACAGCAAAGAAAACCAACCTAAGGATATACCT
65 ATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATACCT
* *
287044 TGGAGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAA
130 TGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAACAAAGGAAACCAA
* *
287109 CCTAAAGATATGCCTTGGGGCTTACCCAAGATATCCTTAGGTCCA
195 CCTAAAGATATGCCTTGGGGCCTACCCAAGATATACTTAGGTCCA
** *
287154 TAGGGTTACCTTATGCGGACAGCAAAGGAAACCAACCTAAGGATGTGCCTT-GGGCCTACACAAG
1 TAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCCTAC-CAAG
287218 ATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATACCT
65 ATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATACCT
287283 TGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAACAAAGGAAACCAA
130 TGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAACAAAGGAAACCAA
* *
287348 CCTAAGGATATGCCTTGGGGCCTACCCAAGATATACTTAGGTCCG
195 CCTAAAGATATGCCTTGGGGCCTACCCAAGATATACTTAGGTCCA
287393 TAGGGTTACCTTATGCACACAGCAAA-GAAACCAACCTAAGGATATGCCTTGGGGCCTACCTAAG
1 TAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCCTACC-AAG
* ** * *
287457 ATATCCTTAGGT-TGTAGGGTTACCTTATGCACACAATAAAGGAAACCAACCTAAGGATGTGCCT
65 ATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATACCT
*
287521 T-GGGCCTATCCAAGATATCCTTAGGTCCGTA
130 TGGGGCCTACCCAAGATATCCTTAGGTCCGTA
287552 AGGACTTAGC
Statistics
Matches: 370, Mismatches: 25, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
237 29 0.08
238 73 0.20
239 224 0.61
240 44 0.12
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (239 bp):
TAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCCTACCAAGA
TATCCTTAGGTCCGTAGGGTTACCTTATGCACACAGCAAAGGAAACCAACCTAAGGATATACCTT
GGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACACAACAAAGGAAACCAAC
CTAAAGATATGCCTTGGGGCCTACCCAAGATATACTTAGGTCCA
Found at i:292696 original size:80 final size:80
Alignment explanation
Indices: 292555--293007 Score: 671
Period size: 80 Copynumber: 5.7 Consensus size: 80
292545 CAACAAAAAG
* * * * * *
292555 GGAATCCAGCCTAAGGATATACCTTGAGTCC-ACCCAAGGACATCCTTAGAT-CGTAGGGTTACC
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACC
** *
292618 TTAAACACACAGCTAA
65 TTATGCACACAGCAAA
*
292634 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
292699 TATGCACACAGCAAA
66 TATGCACACAGCAAA
* * *
292714 GGAAACCATCCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTTCGTAGAGTTACCT
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
292779 TATGCACACAGCAAA
66 TATGCACACAGCAAA
*
292794 GGAAACCAACCTAAGGATATGCCTTGGGG-CTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
292858 TATGCACACAGCAAA
66 TATGCACACAGCAAA
* * * **
292873 GGAAACTAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCCTAGGTTTGTAGGGTTACCT
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
292938 TATGCACACAGCAAA
66 TATGCACACAGCAAA
* * *
292953 GAAAACCAACCTAAGGATGTGCCTT-GGGCCTACCCAAGATATCCTTAGGTCCGTA
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTA
293008 AGGACTTACA
Statistics
Matches: 343, Mismatches: 28, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
79 140 0.41
80 203 0.59
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (80 bp):
GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
TATGCACACAGCAAA
Found at i:292853 original size:159 final size:159
Alignment explanation
Indices: 292555--293007 Score: 694
Period size: 159 Copynumber: 2.8 Consensus size: 159
292545 CAACAAAAAG
* * * * * *
292555 GGAATCCAGCCTAAGGATATACCTTGAGTCC-ACCCAAGGACATCCTTA-GATCGTAGGGTTACC
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAA-GATATCCTTAGGTTCGTAGGGTTACC
** * * *
292618 TTAAACACACAGCTAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAG
65 TTATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGG-CTACCCAAGATATCCTTAG
292683 GTCCGTAGGGTTACCTTATGCACACAGCAAA
129 GTCCGTAGGGTTACCTTATGCACACAGCAAA
* *
292714 GGAAACCATCCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTTCGTAGAGTTACCT
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTTCGTAGGGTTACCT
292779 TATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCTACCCAAGATATCCTTAGGT
66 TATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCTACCCAAGATATCCTTAGGT
292844 CCGTAGGGTTACCTTATGCACACAGCAAA
131 CCGTAGGGTTACCTTATGCACACAGCAAA
* * * *
292873 GGAAACTAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCCTAGGTTTGTAGGGTTACCT
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTTCGTAGGGTTACCT
* * *
292938 TATGCACACAGCAAAGAAAACCAACCTAAGGATGTGCCTTGGGCCTACCCAAGATATCCTTAGGT
66 TATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCTACCCAAGATATCCTTAGGT
293003 CCGTA
131 CCGTA
293008 AGGACTTACA
Statistics
Matches: 271, Mismatches: 21, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
159 212 0.78
160 59 0.22
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (159 bp):
GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTTCGTAGGGTTACCT
TATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCTACCCAAGATATCCTTAGGT
CCGTAGGGTTACCTTATGCACACAGCAAA
Found at i:295352 original size:28 final size:28
Alignment explanation
Indices: 295321--295374 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
295311 ATATGCAGTT
*
295321 GAAAGTGCCTCATAGATAATTTGCACTC
1 GAAAGTACCTCATAGATAATTTGCACTC
295349 GAAAGTACCTCATAGATAATTTGCAC
1 GAAAGTACCTCATAGATAATTTGCAC
295375 CATAGGTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (28 bp):
GAAAGTACCTCATAGATAATTTGCACTC
Found at i:317895 original size:23 final size:23
Alignment explanation
Indices: 317859--317914 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
317849 CAGAGGGAAT
317859 CGATACCCCC-TTGAAGGGAAAC
1 CGATACCCCCTTTGAAGGGAAAC
* *
317881 CGATTCCCCCTTTGAAGGGGAAC
1 CGATACCCCCTTTGAAGGGAAAC
*
317904 TGATACCCCCT
1 CGATACCCCCT
317915 AGGGTTCTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.25, C:0.34, G:0.21, T:0.20
Consensus pattern (23 bp):
CGATACCCCCTTTGAAGGGAAAC
Found at i:328225 original size:21 final size:22
Alignment explanation
Indices: 328178--328238 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
328168 CCCCCCCTGA
**
328178 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCAT-AAG
328201 GGGAACCGATTCCCCCCAT-AG
1 GGGAACCGATTCCCCCCATAAG
* *
328222 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
328239 TGGGGTTCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 17 0.50
23 17 0.50
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCATAAG
Found at i:331718 original size:2 final size:2
Alignment explanation
Indices: 331711--331772 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
331701 CACTATACTA
331711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
331753 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
331773 TGAAATGATA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:337978 original size:2 final size:2
Alignment explanation
Indices: 337971--338024 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
337961 ATATACATTG
337971 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
338013 AT AC AT AT AT AT
1 AT AT AT AT AT AT
338025 TGTATTTAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:338764 original size:13 final size:13
Alignment explanation
Indices: 338746--338772 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
338736 CATAGTTGAA
338746 CAGTCTTCATATG
1 CAGTCTTCATATG
338759 CAGTCTTCATATG
1 CAGTCTTCATATG
338772 C
1 C
338773 GCGTATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:346406 original size:18 final size:18
Alignment explanation
Indices: 346383--346417 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
346373 TTCCATCCGG
*
346383 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
346401 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
346418 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:347723 original size:8 final size:8
Alignment explanation
Indices: 347710--347768 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
347700 TCCGGTCAAT
347710 GGTCAACG
1 GGTCAACG
347718 GGTCAAC-
1 GGTCAACG
347725 GGTCAACG
1 GGTCAACG
347733 GGT---CG
1 GGTCAACG
347738 GGTCAACG
1 GGTCAACG
**
347746 GGTCGGGTCG
1 GGTC--AACG
347756 GGTCAACG
1 GGTCAACG
347764 GGTCA
1 GGTCA
347769 GGTAAACGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
5 5 0.12
7 7 0.17
8 23 0.56
10 6 0.15
ACGTcount: A:0.19, C:0.24, G:0.42, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:347723 original size:15 final size:15
Alignment explanation
Indices: 347703--347749 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
347693 GGTCAACTCC
*
347703 GGTCAATGGTCAACG
1 GGTCAACGGTCAACG
347718 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
347733 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
347746 GGTC
1 GGTC
347750 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 12 0.40
15 18 0.60
ACGTcount: A:0.21, C:0.23, G:0.38, T:0.17
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:347754 original size:18 final size:18
Alignment explanation
Indices: 347731--347801 Score: 82
Period size: 18 Copynumber: 4.3 Consensus size: 18
347721 CAACGGTCAA
347731 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
347749 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
* *
347762 CGGGTCAGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
347780 CGGGTC-GGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
347797 CGGGT
1 CGGGT
347802 TGTGACCGGT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
13 11 0.24
17 15 0.33
18 19 0.42
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:347763 original size:31 final size:30
Alignment explanation
Indices: 347724--347801 Score: 129
Period size: 31 Copynumber: 2.6 Consensus size: 30
347714 AACGGGTCAA
*
347724 CGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGTCAACGGGTCGGGTAAACGGGTCGGGT
*
347754 CGGGTCAACGGGTCAGGTAAACGGGTCGGGT
1 C-GGTCAACGGGTCGGGTAAACGGGTCGGGT
347785 CGGTCAACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
347802 TGTGACCGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 16 0.36
31 28 0.64
ACGTcount: A:0.15, C:0.22, G:0.46, T:0.17
Consensus pattern (30 bp):
CGGTCAACGGGTCGGGTAAACGGGTCGGGT
Found at i:347767 original size:13 final size:13
Alignment explanation
Indices: 347710--347754 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
347700 TCCGGTCAAT
*
347710 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
347725 GGTCAACGGGTCG
1 GGTCAACGGGTCG
347738 GGTCAACGGGTCG
1 GGTCAACGGGTCG
347751 GGTC
1 GGTC
347755 GGGTCAACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:347820 original size:9 final size:9
Alignment explanation
Indices: 347806--347851 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
347796 TCGGGTTGTG
347806 ACCGGTCAA
1 ACCGGTCAA
347815 ACCGGTCAA
1 ACCGGTCAA
* *
347824 ACAGTTCCAAA
1 ACCGGT-C-AA
347835 ACCGGTCAA
1 ACCGGTCAA
347844 ACCGGTCA
1 ACCGGTCA
347852 CTTTTTCCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 23 0.74
10 2 0.06
11 6 0.19
ACGTcount: A:0.35, C:0.33, G:0.20, T:0.13
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:351599 original size:18 final size:18
Alignment explanation
Indices: 351576--351610 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
351566 TTCCATCCGG
*
351576 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
351594 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
351611 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:352917 original size:8 final size:8
Alignment explanation
Indices: 352904--352962 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
352894 TCCGGTCAAT
352904 GGTCAACG
1 GGTCAACG
352912 GGTCAAC-
1 GGTCAACG
352919 GGTCAACG
1 GGTCAACG
352927 GGT---CG
1 GGTCAACG
352932 GGTCAACG
1 GGTCAACG
**
352940 GGTCGGGTCG
1 GGTC--AACG
352950 GGTCAACG
1 GGTCAACG
352958 GGTCA
1 GGTCA
352963 GGTAAACGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
5 5 0.12
7 7 0.17
8 23 0.56
10 6 0.15
ACGTcount: A:0.19, C:0.24, G:0.42, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:352917 original size:15 final size:15
Alignment explanation
Indices: 352897--352943 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
352887 GGTCAACTCC
*
352897 GGTCAATGGTCAACG
1 GGTCAACGGTCAACG
352912 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
352927 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
352940 GGTC
1 GGTC
352944 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 12 0.40
15 18 0.60
ACGTcount: A:0.21, C:0.23, G:0.38, T:0.17
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:352948 original size:18 final size:18
Alignment explanation
Indices: 352925--352996 Score: 91
Period size: 18 Copynumber: 4.3 Consensus size: 18
352915 CAACGGTCAA
352925 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
352943 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
* *
352956 CGGGTCAGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
352974 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
352992 CGGGT
1 CGGGT
352997 TGTGACCGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
13 11 0.24
18 34 0.76
ACGTcount: A:0.14, C:0.21, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:352957 original size:31 final size:31
Alignment explanation
Indices: 352919--352996 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
352909 ACGGGTCAAC
*
352919 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
*
352950 GGTCAACGGGTCAGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
352981 GGTCAACGGGTCGGGT
1 GGTCAACGGGTCGGGT
352997 TGTGACCGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.17
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
Found at i:352996 original size:13 final size:13
Alignment explanation
Indices: 352904--352948 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
352894 TCCGGTCAAT
*
352904 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
352919 GGTCAACGGGTCG
1 GGTCAACGGGTCG
352932 GGTCAACGGGTCG
1 GGTCAACGGGTCG
352945 GGTC
1 GGTC
352949 GGGTCAACGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:356787 original size:18 final size:18
Alignment explanation
Indices: 356764--356798 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
356754 TTCCATCCGG
*
356764 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
356782 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
356799 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:358105 original size:15 final size:15
Alignment explanation
Indices: 358085--358117 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
358075 GGTCAACTCC
*
358085 GGTCAATGGTCAACG
1 GGTCAACGGTCAACG
358100 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
358115 GGT
1 GGT
358118 TGGGTCAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.36, T:0.18
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:358125 original size:13 final size:13
Alignment explanation
Indices: 358092--358136 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
358082 TCCGGTCAAT
*
358092 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
*
358107 GGTCAACGGGTTG
1 GGTCAACGGGTCG
358120 GGTCAACGGGTCG
1 GGTCAACGGGTCG
358133 GGTC
1 GGTC
358137 GGGTCAACGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 16 0.59
15 11 0.41
ACGTcount: A:0.18, C:0.22, G:0.42, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:358140 original size:18 final size:18
Alignment explanation
Indices: 358113--358184 Score: 82
Period size: 18 Copynumber: 4.3 Consensus size: 18
358103 CAACGGTCAA
*
358113 CGGGTTGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
358131 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
* *
358144 CGGGTCAGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
358162 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
358180 CGGGT
1 CGGGT
358185 TGTGACCGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
13 11 0.25
18 33 0.75
ACGTcount: A:0.14, C:0.19, G:0.49, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:358145 original size:31 final size:31
Alignment explanation
Indices: 358107--358184 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
358097 ACGGGTCAAC
* *
358107 GGTCAACGGGTTGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
*
358138 GGTCAACGGGTCAGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
358169 GGTCAACGGGTCGGGT
1 GGTCAACGGGTCGGGT
358185 TGTGACCGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.15, C:0.19, G:0.47, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
Found at i:358184 original size:13 final size:13
Alignment explanation
Indices: 358131--358167 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
358121 GTCAACGGGT
358131 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
* *
358144 CGGGTCAGGTAAA
1 CGGGTCGGGTCAA
358157 CGGGTCGGGTC
1 CGGGTCGGGTC
358168 GGGTCAACGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.46, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:359613 original size:13 final size:13
Alignment explanation
Indices: 359595--359628 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
359585 AATGGGCAAT
359595 TTTGAAAACTAA-G
1 TTTGAAAAC-AAGG
359608 TTTGAAAACAAGG
1 TTTGAAAACAAGG
359621 TTTGAAAA
1 TTTGAAAA
359629 TCAATATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 18 0.90
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (13 bp):
TTTGAAAACAAGG
Found at i:360131 original size:23 final size:22
Alignment explanation
Indices: 360060--360130 Score: 74
Period size: 23 Copynumber: 3.3 Consensus size: 22
360050 CAGACCCCGT
* *
360060 AGGGGGTATCGATT-CCCTA-A
1 AGGGGGAATCGGTTCCCCTACA
* *
360080 AGGGGGAATCGGTTCCCATTCAA
1 AGGGGGAATCGGTTCCCCTAC-A
*
360103 AGGGGGAATTGGTTCCCCTACA
1 AGGGGGAATCGGTTCCCCTACA
360125 AGGGGG
1 AGGGGG
360131 GTATCGATTC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 12 0.29
21 3 0.07
22 7 0.17
23 19 0.46
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.21
Consensus pattern (22 bp):
AGGGGGAATCGGTTCCCCTACA
Found at i:360141 original size:23 final size:22
Alignment explanation
Indices: 360060--360141 Score: 69
Period size: 23 Copynumber: 3.7 Consensus size: 22
360050 CAGACCCCGT
*
360060 AGGGGGTATCGATT-CCCTA-A
1 AGGGGGAATCGATTCCCCTACA
* * *
360080 AGGGGGAATCGGTTCCCATTCAA
1 AGGGGGAATCGATTCCCCTAC-A
* *
360103 AGGGGGAATTGGTTCCCCTACA
1 AGGGGGAATCGATTCCCCTACA
*
360125 AGGGGGGTATCGATTCC
1 A-GGGGGAATCGATTCC
360142 TCCTGCACTA
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
20 12 0.25
21 3 0.06
22 2 0.04
23 31 0.65
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTACA
Found at i:365581 original size:19 final size:20
Alignment explanation
Indices: 365543--365581 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
365533 TGTTATGAGA
365543 TGGGGGGAATCGGTATCCCT
1 TGGGGGGAATCGGTATCCCT
365563 TGGGGGGAATCGGTA-CCCT
1 TGGGGGGAATCGGTATCCCT
365582 AAGAGTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.15, C:0.21, G:0.41, T:0.23
Consensus pattern (20 bp):
TGGGGGGAATCGGTATCCCT
Found at i:365842 original size:18 final size:19
Alignment explanation
Indices: 365819--365857 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
365809 AATTTAATCG
*
365819 AATATATAA-TTAAAATTC
1 AATATAAAACTTAAAATTC
365837 AATATAAAATCTTAAAATTC
1 AATATAAAA-CTTAAAATTC
365857 A
1 A
365858 TTAACACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (19 bp):
AATATAAAACTTAAAATTC
Found at i:366949 original size:3 final size:3
Alignment explanation
Indices: 366936--367014 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
366926 GAAATCAAAC
366936 ATA AT- 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
366983 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
367015 GATAGTAATG
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 73 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:369503 original size:32 final size:32
Alignment explanation
Indices: 369416--369503 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 32
369406 ACACTAACAA
* *
369416 TTGTGCATTACT-TGAATGCAACATTGACACTG
1 TTGTGCATTA-TATGAATGCAACACTGAAACTG
* * *
369448 TTGTGCATTATCA-AAATGAAACACT-AAAGTTG
1 TTGTGCATTAT-ATGAATGCAACACTGAAA-CTG
369480 TTGTGCATTATATGAATGCAACAC
1 TTGTGCATTATATGAATGCAACAC
369504 ACCACTAGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
31 4 0.09
32 41 0.91
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (32 bp):
TTGTGCATTATATGAATGCAACACTGAAACTG
Found at i:370682 original size:20 final size:20
Alignment explanation
Indices: 370657--370694 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
370647 TTTCATCTCA
*
370657 GTTCATCTAGTATCGATATT
1 GTTCATCCAGTATCGATATT
370677 GTTCATCCAGTATCGATA
1 GTTCATCCAGTATCGATA
370695 CTGAGAGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (20 bp):
GTTCATCCAGTATCGATATT
Found at i:370897 original size:20 final size:20
Alignment explanation
Indices: 370872--370909 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
370862 TTTTGTCCTA
*
370872 GTTCATCTAGTATTGATATT
1 GTTCATCTAGTATCGATATT
370892 GTTCATCTAGTATCGATA
1 GTTCATCTAGTATCGATA
370910 CTTAAACTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (20 bp):
GTTCATCTAGTATCGATATT
Found at i:371550 original size:20 final size:21
Alignment explanation
Indices: 371516--371577 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
371506 ATATTTTTTA
*
371516 ATTTTAAAATATTATTTTTAGT
1 ATTTTAATAT-TTATTTTTAGT
371538 ATTTTAAT-TTTATTTTTTAGT
1 ATTTTAATATTTA-TTTTTAGT
* *
371559 ATTTTTATATATATTTTTA
1 ATTTTAATATTTATTTTTA
371578 AATTTTTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 3 0.09
21 22 0.63
22 10 0.29
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (21 bp):
ATTTTAATATTTATTTTTAGT
Found at i:371575 original size:21 final size:20
Alignment explanation
Indices: 371523--371577 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
371513 TTAATTTTAA
371523 AATATTATTTTTAGTATTTT
1 AATATTATTTTTAGTATTTT
*
371543 AATTTTATTTTTTAGTATTTT
1 AATATTA-TTTTTAGTATTTT
*
371564 TATATATATTTTTA
1 AATAT-TATTTTTA
371578 AATTTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.20
21 22 0.73
22 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (20 bp):
AATATTATTTTTAGTATTTT
Found at i:371611 original size:23 final size:23
Alignment explanation
Indices: 371574--371622 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
371564 TATATATATT
* *
371574 TTTAAATTTTTGAAT-ATTTTATA
1 TTTAAAATTTAGAATAATTTTA-A
371597 TTTAAAATTTAGAATAATTTTAA
1 TTTAAAATTTAGAATAATTTTAA
371620 TTT
1 TTT
371623 TTTAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTAAAATTTAGAATAATTTTAA
Found at i:372172 original size:25 final size:25
Alignment explanation
Indices: 372138--372188 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
372128 TTTTATTAAG
372138 AAAAATATATTATCAATACTTTTTA
1 AAAAATATATTATCAATACTTTTTA
372163 AAAAATATATTATCAATACTTTTTA
1 AAAAATATATTATCAATACTTTTTA
372188 A
1 A
372189 CATGTGGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (25 bp):
AAAAATATATTATCAATACTTTTTA
Found at i:372963 original size:30 final size:29
Alignment explanation
Indices: 372929--372993 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
372919 ATGAAAAGTC
* *
372929 ATAAATCGATCACTCACGTTATCATTTGTT
1 ATAAAT-GATCACTAACATTATCATTTGTT
* *
372959 ATAAAATGGTCACTAACATTATCGTTTGTT
1 AT-AAATGATCACTAACATTATCATTTGTT
372989 ATAAA
1 ATAAA
372994 ATAGTCACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 3 0.10
30 23 0.77
31 4 0.13
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (29 bp):
ATAAATGATCACTAACATTATCATTTGTT
Found at i:372994 original size:30 final size:30
Alignment explanation
Indices: 372938--373002 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
372928 CATAAATCGA
* * *
372938 TCACTCACGTTATCATTTGTTATAAAATGG
1 TCACTAACATTATCATTTGTTATAAAATAG
*
372968 TCACTAACATTATCGTTTGTTATAAAATAG
1 TCACTAACATTATCATTTGTTATAAAATAG
372998 TCACT
1 TCACT
373003 TTACATTAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (30 bp):
TCACTAACATTATCATTTGTTATAAAATAG
Found at i:374493 original size:73 final size:73
Alignment explanation
Indices: 374374--374519 Score: 265
Period size: 73 Copynumber: 2.0 Consensus size: 73
374364 ATTAAATAAT
* *
374374 TAATTTATAATTCAAATTGAATTGGTAAAGTAAAATCATACAACTAGTGTAACTAAATGAACCAT
1 TAATTTATAATTCAAATTGAATTGGTAAAATAAAAGCATACAACTAGTGTAACTAAATGAACCAT
374439 TTCCTTAA
66 TTCCTTAA
*
374447 TAATTTATAATTCAAATTGAATTGGTAAAATAAAAGCATACAACTAGTGTAACTAAATGAATCAT
1 TAATTTATAATTCAAATTGAATTGGTAAAATAAAAGCATACAACTAGTGTAACTAAATGAACCAT
374512 TTCCTTAA
66 TTCCTTAA
374520 ATAAAAATGA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.34
Consensus pattern (73 bp):
TAATTTATAATTCAAATTGAATTGGTAAAATAAAAGCATACAACTAGTGTAACTAAATGAACCAT
TTCCTTAA
Found at i:378724 original size:19 final size:18
Alignment explanation
Indices: 378702--378742 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
378692 CCACCAACAT
*
378702 AAATTAAACATAACAAATA
1 AAATTAAA-ATAAAAAATA
*
378721 AAATTAAAATAAAAAATT
1 AAATTAAAATAAAAAATA
378739 AAAT
1 AAAT
378743 ACGACATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATTAAAATAAAAAATA
Found at i:389539 original size:36 final size:35
Alignment explanation
Indices: 389499--389569 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 35
389489 TTTCTTGCAG
*
389499 GTTTACTCTTCATTTCATTTATTTCTCATTAGTTTT
1 GTTTACTCTTCATTTCATTT-CTTCTCATTAGTTTT
*
389535 GTTTACTCTTCATTTCATTTCTTCTCATTATTTTT
1 GTTTACTCTTCATTTCATTTCTTCTCATTAGTTTT
389570 TAAGAATTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 13 0.39
36 20 0.61
ACGTcount: A:0.15, C:0.18, G:0.04, T:0.62
Consensus pattern (35 bp):
GTTTACTCTTCATTTCATTTCTTCTCATTAGTTTT
Found at i:394098 original size:20 final size:20
Alignment explanation
Indices: 394073--394112 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
394063 CAAAGTAATG
394073 ATTTTCTATGGATTAGGCTC
1 ATTTTCTATGGATTAGGCTC
394093 ATTTTCTATGGATTAGGCTC
1 ATTTTCTATGGATTAGGCTC
394113 CCCAATTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (20 bp):
ATTTTCTATGGATTAGGCTC
Found at i:402645 original size:24 final size:24
Alignment explanation
Indices: 402597--402648 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
402587 ATGGAAGACC
*
402597 AAAATTAACAAAATAAATTATATA
1 AAAATTAAAAAAATAAATTATATA
402621 AAAATTACAAAAACATAAA-TA-ATA
1 AAAATTA-AAAAA-ATAAATTATATA
402645 AAAA
1 AAAA
402649 CCTTAATTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 14 0.56
25 6 0.24
26 5 0.20
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (24 bp):
AAAATTAAAAAAATAAATTATATA
Found at i:402740 original size:27 final size:27
Alignment explanation
Indices: 402696--402749 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
402686 ATTAGAATAC
* *
402696 TAATTAAAACATCTTAATCAAAATAAA
1 TAATTAAAAAATCATAATCAAAATAAA
* * *
402723 TAATTAAAAAATGATAATTAAATTAAA
1 TAATTAAAAAATCATAATCAAAATAAA
402750 AAAGAATAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (27 bp):
TAATTAAAAAATCATAATCAAAATAAA
Found at i:403176 original size:123 final size:123
Alignment explanation
Indices: 403041--403287 Score: 449
Period size: 123 Copynumber: 2.0 Consensus size: 123
403031 GACCAATCTA
* *
403041 CAAAAACAAACAAAGATTAGATGATCTTAAAGAGAATAACCCCAAATGTTAATATGAAAACATTA
1 CAAAAACAAACAAAGATAAGATGATCTTAAAGAGAATAACCCCAAATGTTAATATGAAAACATAA
* *
403106 AAAAGGAAAATAGCTAAATGAGGACACTTAGTTTAAAATGAAATGAAAAGAACAAATC
66 AAAAGGAAAATAGCGAAATGAGGACACTTAATTTAAAATGAAATGAAAAGAACAAATC
403164 CAAAAACAAACAAAGATAAGATGATCTTAAAGAGAATAACCCCAAATGTTAATATGAAAACATAA
1 CAAAAACAAACAAAGATAAGATGATCTTAAAGAGAATAACCCCAAATGTTAATATGAAAACATAA
*
403229 AAAAGGAAAATAGCGAAATGAGGACATTTAATTTAAAATGAAATGAAAAGAACAAATC
66 AAAAGGAAAATAGCGAAATGAGGACACTTAATTTAAAATGAAATGAAAAGAACAAATC
403287 C
1 C
403288 TGGTGACCAA
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 119 1.00
ACGTcount: A:0.55, C:0.11, G:0.14, T:0.19
Consensus pattern (123 bp):
CAAAAACAAACAAAGATAAGATGATCTTAAAGAGAATAACCCCAAATGTTAATATGAAAACATAA
AAAAGGAAAATAGCGAAATGAGGACACTTAATTTAAAATGAAATGAAAAGAACAAATC
Found at i:410266 original size:29 final size:29
Alignment explanation
Indices: 410216--410282 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
410206 CTTTACGTAA
*
410216 TTAAAGTA-TTTTTAGTCAAAATA-GATAC
1 TTAAAATATTTTTTAGTCAAAATATG-TAC
* *
410244 TTAAAATATTTTTTTGTTAAAATATGTAC
1 TTAAAATATTTTTTAGTCAAAATATGTAC
410273 TTAAAATATT
1 TTAAAATATT
410283 CAATTTTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 7 0.21
29 26 0.76
30 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.46
Consensus pattern (29 bp):
TTAAAATATTTTTTAGTCAAAATATGTAC
Found at i:410415 original size:26 final size:25
Alignment explanation
Indices: 410364--410416 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
410354 TAAAAATAAG
410364 TATTTTAAATATGTTTTAACCAAAAA
1 TATTTTAAATATGTTTTAA-CAAAAA
*
410390 TATTTTAAATATTTGTTTTAATAAAAA
1 TATTTTAAATA--TGTTTTAACAAAAA
410417 AATACTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 11 0.46
27 5 0.21
28 8 0.33
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (25 bp):
TATTTTAAATATGTTTTAACAAAAA
Found at i:410416 original size:28 final size:27
Alignment explanation
Indices: 410355--410426 Score: 74
Period size: 29 Copynumber: 2.6 Consensus size: 27
410345 TTTAGATGAT
410355 AAAAATAAGTATTTTAAATATGTTTTAAC
1 AAAAA-AA-TATTTTAAATATGTTTTAAC
* *
410384 -CAAAAATATTTTAAATATTTGTTTTAAT
1 AAAAAAATATTTTAAATA--TGTTTTAAC
*
410412 AAAAAAATACTTTAA
1 AAAAAAATATTTTAA
410427 CTAAAAAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 11 0.31
27 2 0.06
28 11 0.31
29 12 0.33
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (27 bp):
AAAAAAATATTTTAAATATGTTTTAAC
Found at i:410425 original size:16 final size:18
Alignment explanation
Indices: 410406--410438 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
410396 AAATATTTGT
410406 TTTAA-TAAAAA-AATAC
1 TTTAACTAAAAAGAATAC
410422 TTTAACTAAAAAGAATA
1 TTTAACTAAAAAGAATA
410439 TATTTTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (18 bp):
TTTAACTAAAAAGAATAC
Found at i:411373 original size:22 final size:22
Alignment explanation
Indices: 411345--411399 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
411335 ACTGAACCTG
*
411345 CAAAGATCGGTTTTAAAATATA
1 CAAAGATCGGTTCTAAAATATA
411367 CAAAGATCGGTTCTAAAATATA
1 CAAAGATCGGTTCTAAAATATA
411389 CAAAGATCGGT
1 CAAAGATCGGT
411400 GCAGAAGCCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (22 bp):
CAAAGATCGGTTCTAAAATATA
Found at i:416874 original size:19 final size:19
Alignment explanation
Indices: 416852--416899 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
416842 CTTTTAAAGT
416852 TTTTCTTTTATTTAGTAAC
1 TTTTCTTTTATTTAGTAAC
416871 TTTTCTTTTATTTAGTAAC
1 TTTTCTTTTATTTAGTAAC
416890 TTTTCTTTTA
1 TTTTCTTTTA
416900 CTTTTTGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.19, C:0.10, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTTCTTTTATTTAGTAAC
Found at i:433372 original size:16 final size:16
Alignment explanation
Indices: 433351--433399 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
433341 ATCACACCAT
433351 CAGTCCCCATATGCTA
1 CAGTCCCCATATGCTA
* *
433367 CAGTCCCCATATGTTG
1 CAGTCCCCATATGCTA
433383 CAGTCCCCATATGCTA
1 CAGTCCCCATATGCTA
433399 C
1 C
433400 CTTTACTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.22, C:0.37, G:0.14, T:0.27
Consensus pattern (16 bp):
CAGTCCCCATATGCTA
Found at i:436552 original size:15 final size:16
Alignment explanation
Indices: 436525--436554 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
436515 TAATTCTGGG
436525 TTTCTTATCTTTTTTT
1 TTTCTTATCTTTTTTT
436541 TTTCTT-TCTTTTTT
1 TTTCTTATCTTTTTT
436555 GGTTTTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTCTTATCTTTTTTT
Found at i:438553 original size:17 final size:17
Alignment explanation
Indices: 438531--438588 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
438521 AATGTATGAG
438531 GGAATTGGAATATGTGA
1 GGAATTGGAATATGTGA
*
438548 GGAATTGAAATATGTGAA
1 GGAATTGGAATATGTG-A
*
438566 GGAATTGGAATATGTCA
1 GGAATTGGAATATGTGA
438583 GGAATT
1 GGAATT
438589 AGAGTTCAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 22 0.59
18 15 0.41
ACGTcount: A:0.38, C:0.02, G:0.31, T:0.29
Consensus pattern (17 bp):
GGAATTGGAATATGTGA
Found at i:439224 original size:38 final size:37
Alignment explanation
Indices: 439166--439259 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 37
439156 TTTTCACTCT
439166 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGACCCGAATATCACACTT-AAA
*
439205 AAACCCGACCCGACTCGACCCGAATATCACACTTAAA
1 AAACCCGACCCGACCCGACCCGAATATCACACTTAAA
*
439242 AAACCCGACCTGACCCGA
1 AAACCCGACCCGACCCGA
439260 ACAAAATAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
37 19 0.37
38 26 0.50
39 7 0.13
ACGTcount: A:0.38, C:0.39, G:0.12, T:0.11
Consensus pattern (37 bp):
AAACCCGACCCGACCCGACCCGAATATCACACTTAAA
Found at i:444202 original size:13 final size:13
Alignment explanation
Indices: 444184--444209 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
444174 GATGAAGTAT
444184 TTTAGATAAAAAC
1 TTTAGATAAAAAC
444197 TTTAGATAAAAAC
1 TTTAGATAAAAAC
444210 ATTCATCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTAGATAAAAAC
Found at i:445324 original size:35 final size:33
Alignment explanation
Indices: 445259--445354 Score: 102
Period size: 33 Copynumber: 2.7 Consensus size: 33
445249 TGAAAATACG
* *
445259 TATATAATATATAGTTTTTAAAACATTTTTAAC
1 TATATAATATATAGTTTTTAAAAAAGTTTTAAC
*
445292 TATATAATATATAGTTTTTTAAAAAACGTTTTAAAAAA
1 TATATAATATATAG-TTTTTAAAAAA-GTTTT---AAC
445330 TATAGATAATATATAGTTTTTAAAA
1 TAT--ATAATATATAGTTTTTAAAA
445355 TCATTTTTGA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
33 14 0.26
34 10 0.19
35 4 0.08
38 5 0.09
39 9 0.17
40 11 0.21
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (33 bp):
TATATAATATATAGTTTTTAAAAAAGTTTTAAC
Found at i:445377 original size:38 final size:36
Alignment explanation
Indices: 445259--445719 Score: 367
Period size: 37 Copynumber: 12.2 Consensus size: 36
445249 TGAAAATACG
*
445259 TATATAATATATAGTTTTTAAAACATTTTT--AA-C
1 TATATAATATATAGTTTTTAAAACATTTTTGAAATT
* ** *
445292 TATATAATATATAGTTTTTTAAAAAACGTTTTAAAAAATA
1 TATATAATATATAG-TTTTT--AAAACATTTT-TGAAATT
*
445332 TAGATAATATATAGTTTTTAAAATCATTTTTGAAATCT
1 TATATAATATATAGTTTTTAAAA-CATTTTTGAAAT-T
* *
445370 TATATAATATATAATTTTGAAAACATTTTTGAAAATT
1 TATATAATATATAGTTTTTAAAACATTTTTG-AAATT
*
445407 TATATAATATATAGTTTTGAAAACA-TTTTGAAAACATT
1 TATATAATATATAGTTTTTAAAACATTTTTG--AA-ATT
** *
445445 TATATGTTATATAGTTTTTTAAAAAAACATTTTTGGAAATA
1 TATATAATATATAG-TTTTT---AAAACATTTTT-GAAATT
* * *
445486 TATATAATATATAATTTTGAAAACATTTTTAAAAATT
1 TATATAATATATAGTTTTTAAAACATTTTT-GAAATT
*
445523 TATATAATATATAGTTTTGAAAACA-TTTTGAAAACATT
1 TATATAATATATAGTTTTTAAAACATTTTTG--AA-ATT
** *
445561 TATATGTTATATAGTTTTTTAAAAAACATTTTTGAAAATA
1 TATATAATATATAG-TTTTT--AAAACATTTTTG-AAATT
* * *
445601 TATATAATATATAATTTTTAAAACATTTTTAAAAATA
1 TATATAATATATAGTTTTTAAAACATTTTT-GAAATT
* * * * *
445638 CATATATTATATAGTTTTTTGAAACGTTTTTGAAA-A
1 TATATAATATATAG-TTTTTAAAACATTTTTGAAATT
*
445674 TACGTATAATATATAGTTTTTAAAAAATATTTTGAAAATT
1 TA--TATAATATATAGTTTTTAAAACAT-TTTTG-AAATT
445714 TATATA
1 TATATA
445720 TTATGAGCTT
Statistics
Matches: 351, Mismatches: 45, Indels: 59
0.77 0.10 0.13
Matches are distributed among these distances:
33 14 0.04
34 5 0.01
36 20 0.06
37 124 0.35
38 93 0.26
39 23 0.07
40 32 0.09
41 22 0.06
42 13 0.04
43 4 0.01
44 1 0.00
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTTGAAATT
Found at i:445437 original size:11 final size:11
Alignment explanation
Indices: 445421--445445 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
445411 TAATATATAG
445421 TTTTGAAAACA
1 TTTTGAAAACA
445432 TTTTGAAAACA
1 TTTTGAAAACA
445443 TTT
1 TTT
445446 ATATGTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:445553 original size:11 final size:11
Alignment explanation
Indices: 445537--445561 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
445527 TAATATATAG
445537 TTTTGAAAACA
1 TTTTGAAAACA
445548 TTTTGAAAACA
1 TTTTGAAAACA
445559 TTT
1 TTT
445562 ATATGTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:445650 original size:115 final size:115
Alignment explanation
Indices: 445247--445719 Score: 540
Period size: 116 Copynumber: 4.1 Consensus size: 115
445237 GCAAACGATC
* * *
445247 TTTGAAAATACGTATATAATATATAGTTTTTAAAACATTTTT---AA-CTATATAATATATAGTT
1 TTTGAAAATA--TATATAATATATAATTTTGAAAACATTTTTAAAAATTTATATAATATATAG-T
* * * * * * *
445308 TTTTAAAAAACGTTTT-AAAAAATATAGATAATATATAGTTTTT-AAAATCATT
63 TTTT-GAAAACATTTTGAAAACATTTATATGATATATAGTTTTTAAAAAACATT
* *
445360 TTTG-AAATCTTATATAATATATAATTTTGAAAACATTTTTGAAAATTTATATAATATATAG-TT
1 TTTGAAAAT-ATATATAATATATAATTTTGAAAACATTTTTAAAAATTTATATAATATATAGTTT
*
445423 TTGAAAACATTTTGAAAACATTTATATGTTATATAGTTTTTTAAAAAAACATT
65 TTGAAAACATTTTGAAAACATTTATATGATATATAG-TTTTT-AAAAAACATT
*
445476 TTTGGAAATATATATAATATATAATTTTGAAAACATTTTTAAAAATTTATATAATATATAG-TTT
1 TTTGAAAATATATATAATATATAATTTTGAAAACATTTTTAAAAATTTATATAATATATAGTTTT
*
445540 TGAAAACATTTTGAAAACATTTATATGTTATATAGTTTTTTAAAAAACATT
66 TGAAAACATTTTGAAAACATTTATATGATATATAG-TTTTTAAAAAACATT
* ** *
445591 TTTGAAAATATATATAATATATAATTTTTAAAACATTTTTAAAAATACATATATTATATAGTTTT
1 TTTGAAAATATATATAATATATAATTTTGAAAACATTTTTAAAAATTTATATAATATATAG-TTT
* * ** *
445656 TTG-AAACGTTTTTGAAAATACGTATA--ATATATAGTTTTTAAAAAATA-T
65 TTGAAAAC-ATTTTGAAAACATTTATATGATATATAGTTTTTAAAAAACATT
*
445704 TTTGAAAATTTATATA
1 TTTGAAAATATATATA
445720 TTATGAGCTT
Statistics
Matches: 321, Mismatches: 26, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
111 28 0.09
112 13 0.04
113 41 0.13
114 19 0.06
115 87 0.27
116 110 0.34
117 23 0.07
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (115 bp):
TTTGAAAATATATATAATATATAATTTTGAAAACATTTTTAAAAATTTATATAATATATAGTTTT
TGAAAACATTTTGAAAACATTTATATGATATATAGTTTTTAAAAAACATT
Found at i:445744 original size:3 final size:3
Alignment explanation
Indices: 445736--445765 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
445726 GCTTTTGAAC
445736 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
445766 TCTAATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:446981 original size:23 final size:26
Alignment explanation
Indices: 446940--447000 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
446930 TACCTCTTAC
446940 TATTTCTTTATTTCATTTTTATT-TA-A
1 TATTT-TTT-TTTCATTTTTATTATATA
* *
446966 TATTTTTTTTT-ATTTTTCTTATATC
1 TATTTTTTTTTCATTTTTATTATATA
446991 TATTTTTTTT
1 TATTTTTTTT
447001 AAAAAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 8 0.26
24 5 0.16
25 13 0.42
26 5 0.16
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (26 bp):
TATTTTTTTTTCATTTTTATTATATA
Found at i:450401 original size:22 final size:22
Alignment explanation
Indices: 450376--450417 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
450366 ATGTTGCATA
*
450376 CATTTTAGAGCAT-CATATTTAT
1 CATTTTACA-CATACATATTTAT
450398 CATTTTACACATACATATTT
1 CATTTTACACATACATATTT
450418 TTTTGCAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (22 bp):
CATTTTACACATACATATTTAT
Found at i:451334 original size:319 final size:318
Alignment explanation
Indices: 450589--452054 Score: 2453
Period size: 319 Copynumber: 4.6 Consensus size: 318
450579 GAGAGCGGAT
*
450589 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* *
450653 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
66 CAACTTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* * *
450718 CTGGTTGTCAACAAACAATTTCCCAATTTCAGATCCAATTCCAACTTCACAACGAAGGATATTGG
131 CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
450783 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
196 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
450848 AATTTCAGAGCC------AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
261 AATTTCAGAGCCAATTTAAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *
450900 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
*
450965 CAACTTCACAGCGAATGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCG
66 CAACTTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* *
451030 CTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
131 CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
451095 ACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGCCAACAAACAACTTATC
196 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
451160 AATTTCAGAGCCAATTTAAAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATG
261 AATTTCAGAGCCAATTT-AAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
451219 TTCAACTTCACGACGAAGGGACCGCGGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
*
451284 CAACTTCACAGCGAATGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCG
66 CAACTTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* *
451349 CTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
131 CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
451414 ACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
196 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
451479 AATTTCAGAGCCAATTTAAAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATG
261 AATTTCAGAGCCAATTT-AAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
451538 TTCAACTTCACGACGAAGGGACCGCGGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* * * *
451603 CAACTTTACAACGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACCG
66 CAACTTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
*
451668 CTGGTTGTCAACAAACAATTTCCCAATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
131 CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
451733 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCC
196 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* * *
451798 AATTTCAGATCCAATTTCAACTTCACAACGAAGGATATTGTACTCCAGACAACGCAAG
261 AATTTCAGAGCCAATTTAAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * *
451856 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAATAACTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* * * * *
451921 CAACTTCACAGCAAATGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGG
66 CAACTTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* * *
451986 CTGGTTGTCAACAAACAATTTCCCGATTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTG
131 CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTG
452050 GACTC
195 GACTC
452055 GGAACAATGC
Statistics
Matches: 1093, Mismatches: 53, Indels: 11
0.94 0.05 0.01
Matches are distributed among these distances:
311 39 0.04
312 218 0.20
317 1 0.00
318 218 0.20
319 617 0.56
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (318 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
CAACTTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
AATTTCAGAGCCAATTTAAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:452055 original size:106 final size:106
Alignment explanation
Indices: 450589--452054 Score: 2397
Period size: 106 Copynumber: 13.9 Consensus size: 106
450579 GAGAGCGGAT
*
450589 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
450653 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * * *
450694 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGATCCAATTC
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
450759 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
450800 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAG-C-----
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
450859 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *
450900 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* * *
450965 CAACTTCACAGCGAATGATATTGGACTCCAGACAACGCATG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
451006 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* *
451071 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *
451112 TTCAACTTCACGACGAAGGGACCGCTGGTTGCCAACAAACAACTTATCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* *
451177 AAAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATG
66 -CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
451219 TTCAACTTCACGACGAAGGGACCGCGGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* * *
451284 CAACTTCACAGCGAATGATATTGGACTCCAGACAACGCATG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
451325 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* *
451390 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
451431 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* *
451496 AAAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATG
66 -CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
451538 TTCAACTTCACGACGAAGGGACCGCGGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* *
451603 CAACTTTACAACGAAGGATATTGGACTCCAGATAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * *
451644 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGATCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
*
451709 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * * *
451750 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCAGATCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
*
451815 CAACTTCACAACGAAGGATATTGTACTCCAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * *
451856 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAATAACTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* * * * *
451921 CAACTTCACAGCAAATGATATTGGACTCGAGACAACACAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * * * * *
451962 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGATTCCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
* *
452027 CAACTTCACGACGGAGGATATTGGACTC
66 CAACTTCACAACGAAGGATATTGGACTC
452055 GGAACAATGC
Statistics
Matches: 1290, Mismatches: 62, Indels: 17
0.94 0.05 0.01
Matches are distributed among these distances:
100 97 0.08
101 1 0.00
105 41 0.03
106 947 0.73
107 204 0.16
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (106 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:452324 original size:84 final size:84
Alignment explanation
Indices: 452202--452878 Score: 780
Period size: 84 Copynumber: 8.1 Consensus size: 84
452192 TCCAACTCAA
452202 AGAAGTGTTATCTGTCACAAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
1 AGAAGTGTTATCTGTCACAAAAAGA-CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
452267 TTACAGCATAACTCAAGGCT
65 TTACAGCATAACTCAAGGCT
* * *
452287 AGAAGGGTTATCTGTCAC-CAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
1 AGAAGTGTTATCTGTCACAAAAAGACC-CCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
* * ** *
452351 TTGCAGCATAACTTAAATCG
65 TTACAGCATAACTCAAGGCT
* * * ** * * * *
452371 AGAAGGGTTATCT-AC-CAACCAAAGACCTTCGAGTTCGACCACGCTCAGC-TCCAAGGCATATC
1 AGAAGTGTTATCTGTCACAA--AAAGACC-CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
* * * * * *
452433 ATTTGCAGTATAGCTTAAGTCG
63 ATTTACAGCATAACTCAAGGCT
* * * *
452455 AGAAGGGCTATCTG-C-C--AAAGTCCCCCGAGTTCGATTACACTCAGCTTCGAGGGTACATCAT
1 AGAAGTGTTATCTGTCACAAAAAG-ACCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
452516 TTACAGCATAACTCAAGGCT
65 TTACAGCATAACTCAAGGCT
* *
452536 AGAAGTGTTATCTGTCACGAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGTACATCAT
1 AGAAGTGTTATCTGTCACAAAAAGA-CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
452601 TTACAGCATAACTCAAGGCT
65 TTACAGCATAACTCAAGGCT
* * * * *
452621 AGAAGTGTTATCTGTCATAAAAAGACCCCAGAATTCGATTACACTCAACTCCGAGGGTACATCAT
1 AGAAGTGTTATCTGTCACAAAAAGACCCC-GAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
452686 TTACAGCATAACTCAAGGCT
65 TTACAGCATAACTCAAGGCT
* * * *
452706 AGAAGTGTTATCTGTCACAAAAAGACCCCAGAATTCGATTACACTCAAC-TCCAAGGCACATCAT
1 AGAAGTGTTATCTGTCACAAAAAGACCCC-GAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
452770 TTACAGCATAACTCAAGGCT
65 TTACAGCATAACTCAAGGCT
* * * * *
452790 AGAAGTGTTATCTGTCACAAAAAGACCCCATAATTCGATTACACTCAAC-TCCAAGGCACATCAT
1 AGAAGTGTTATCTGTCACAAAAAGACCCC-GAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
* * *
452854 TTACAACATAGCTCAAGGCA
65 TTACAGCATAACTCAAGGCT
452874 AGAAG
1 AGAAG
452879 GGCTATATGT
Statistics
Matches: 527, Mismatches: 52, Indels: 27
0.87 0.09 0.04
Matches are distributed among these distances:
80 21 0.04
81 39 0.07
82 2 0.00
83 4 0.01
84 232 0.44
85 229 0.43
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (84 bp):
AGAAGTGTTATCTGTCACAAAAAGACCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
TACAGCATAACTCAAGGCT
Found at i:452548 original size:165 final size:168
Alignment explanation
Indices: 452202--452878 Score: 664
Period size: 169 Copynumber: 4.0 Consensus size: 168
452192 TCCAACTCAA
** * ** * *
452202 AGAAGTGTTATCTGTCACAAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
1 AGAAGTGTTATCTACCACGAAAAGACCCCCGAGTTCGACCACACTCAGCTTCCAAGGCACATCAT
* * * **
452267 TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGATTACACTC
66 TTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCA-AAAAGACCCCCGAGTTCGATTACACTC
* * * ** *
452332 AGCTTCGAGGGCACATCATTTGCAGCATAACTTAAATCG
130 AGCTTCGAGGGTACATCATTTACAGCATAACTCAAGGCT
* * ** * *
452371 AGAAGGGTTATCTACCAAC-CAAAGACCTTCGAGTTCGACCACGCTCAGC-TCCAAGGCATATCA
1 AGAAGTGTTATCTACC-ACGAAAAGACCCCCGAGTTCGACCACACTCAGCTTCCAAGGCACATCA
* * * * * * *
452434 TTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG-C-CAAAGTCCCCCGAGTTCGATTACACTC
65 TTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAAAAAGACCCCCGAGTTCGATTACACTC
452497 AGCTTCGAGGGTACATCATTTACAGCATAACTCAAGGCT
130 AGCTTCGAGGGTACATCATTTACAGCATAACTCAAGGCT
** ** * * *
452536 AGAAGTGTTATCTGTCACGAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGTACATCAT
1 AGAAGTGTTATCTACCACGAAAAGACCCCCGAGTTCGACCACACTCAGCTTCCAAGGCACATCAT
* * * * *
452601 TTACAGCATAACTCAAGGCTAGAAGTGTTATCTGTCATAAAAAGACCCCAGAATTCGATTACACT
66 TTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTC--AAAAAGACCCCCGAGTTCGATTACACT
* *
452666 CAACTCCGAGGGTACATCATTTACAGCATAACTCAAGGCT
129 CAGCTTCGAGGGTACATCATTTACAGCATAACTCAAGGCT
** * * * ** *
452706 AGAAGTGTTATCTGTCACAAAAAGACCCCAGAATTCGATTACACTCAAC-TCCAAGGCACATCAT
1 AGAAGTGTTATCTACCACGAAAAGACCCCCGAGTTCGACCACACTCAGCTTCCAAGGCACATCAT
* * * ** *
452770 TTACAGCATAACTCAAGGCTAGAAGTGTTATCTGTCACAAAAAGACCCCATAATTCGATTACACT
66 TTACAGCATAACTCAAGGCGAGAAGGGCTATCTGT--CAAAAAGACCCCCGAGTTCGATTACACT
* * * * * * *
452835 CAAC-TCCAAGGCACATCATTTACAACATAGCTCAAGGCA
129 CAGCTTCGAGGGTACATCATTTACAGCATAACTCAAGGCT
452874 AGAAG
1 AGAAG
452879 GGCTATATGT
Statistics
Matches: 429, Mismatches: 70, Indels: 19
0.83 0.14 0.04
Matches are distributed among these distances:
164 2 0.00
165 94 0.22
166 37 0.09
167 2 0.00
168 72 0.17
169 114 0.27
170 107 0.25
171 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (168 bp):
AGAAGTGTTATCTACCACGAAAAGACCCCCGAGTTCGACCACACTCAGCTTCCAAGGCACATCAT
TTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAAAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGGTACATCATTTACAGCATAACTCAAGGCT
Found at i:452578 original size:85 final size:85
Alignment explanation
Indices: 452202--452878 Score: 807
Period size: 85 Copynumber: 8.1 Consensus size: 85
452192 TCCAACTCAA
452202 AGAAGTGTTATCTGTCACAAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
1 AGAAGTGTTATCTGTCACAAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
452267 TTACAGCATAACTCAAGGCT
66 TTACAGCATAACTCAAGGCT
* * **
452287 AGAAGGGTTATCTGTCAC-CAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
1 AGAAGTGTTATCTGTCACAAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
* * ** *
452351 TTGCAGCATAACTTAAATCG
66 TTACAGCATAACTCAAGGCT
* * ** ** * * * *
452371 AGAAGGGTTATCT-AC-CAACCAAAGACCTTCGAGTTCGACCACGCTCAGC-TCCAAGGCATATC
1 AGAAGTGTTATCTGTCACAA--AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
* * * * * *
452433 ATTTGCAGTATAGCTTAAGTCG
64 ATTTACAGCATAACTCAAGGCT
* * * *
452455 AGAAGGGCTATCTG-C-C--AAAGTCCCCCGAGTTCGATTACACTCAGCTTCGAGGGTACATCAT
1 AGAAGTGTTATCTGTCACAAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
452516 TTACAGCATAACTCAAGGCT
66 TTACAGCATAACTCAAGGCT
* *
452536 AGAAGTGTTATCTGTCACGAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGTACATCAT
1 AGAAGTGTTATCTGTCACAAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
452601 TTACAGCATAACTCAAGGCT
66 TTACAGCATAACTCAAGGCT
* * * * * *
452621 AGAAGTGTTATCTGTCATAAAAAGACCCCAGAATTCGATTACACTCAACTCCGAGGGTACATCAT
1 AGAAGTGTTATCTGTCACAAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
452686 TTACAGCATAACTCAAGGCT
66 TTACAGCATAACTCAAGGCT
* * * * *
452706 AGAAGTGTTATCTGTCACAAAAAGACCCCAGAATTCGATTACACTCAAC-TCCAAGGCACATCAT
1 AGAAGTGTTATCTGTCACAAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
452770 TTACAGCATAACTCAAGGCT
66 TTACAGCATAACTCAAGGCT
** * * * *
452790 AGAAGTGTTATCTGTCACAAAAAGACCCCATAATTCGATTACACTCAAC-TCCAAGGCACATCAT
1 AGAAGTGTTATCTGTCACAAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
* * *
452854 TTACAACATAGCTCAAGGCA
66 TTACAGCATAACTCAAGGCT
452874 AGAAG
1 AGAAG
452879 GGCTATATGT
Statistics
Matches: 528, Mismatches: 55, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
80 23 0.04
81 37 0.07
82 2 0.00
83 2 0.00
84 230 0.44
85 234 0.44
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (85 bp):
AGAAGTGTTATCTGTCACAAAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
TTACAGCATAACTCAAGGCT
Found at i:453465 original size:2 final size:2
Alignment explanation
Indices: 453448--453485 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
453438 TTATTTATTT
*
453448 TA TA CA TA TA TA -A TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
453486 GTTTGCAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:453475 original size:19 final size:19
Alignment explanation
Indices: 453448--453485 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
453438 TTATTTATTT
453448 TATACATATATAATATATA
1 TATACATATATAATATATA
* *
453467 TATATATATATATTATATA
1 TATACATATATAATATATA
453486 GTTTGCAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
TATACATATATAATATATA
Found at i:453577 original size:35 final size:33
Alignment explanation
Indices: 453512--453607 Score: 102
Period size: 33 Copynumber: 2.7 Consensus size: 33
453502 TGAAAATACG
* *
453512 TATATAATATATAGTTTTTAAAACATTTTTAAC
1 TATATAATATATAGTTTTTAAAAAAGTTTTAAC
*
453545 TATATAATATATAGTTTTTTAAAAAACGTTTTAAAAAA
1 TATATAATATATAG-TTTTTAAAAAA-GTTTT---AAC
453583 TATAGATAATATATAGTTTTTAAAA
1 TAT--ATAATATATAGTTTTTAAAA
453608 TCATTTTTGA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
33 14 0.26
34 10 0.19
35 4 0.08
38 5 0.09
39 9 0.17
40 11 0.21
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (33 bp):
TATATAATATATAGTTTTTAAAAAAGTTTTAAC
Found at i:453630 original size:38 final size:36
Alignment explanation
Indices: 453512--453972 Score: 376
Period size: 37 Copynumber: 12.2 Consensus size: 36
453502 TGAAAATACG
*
453512 TATATAATATATAGTTTTTAAAACATTTTT--AA-C
1 TATATAATATATAGTTTTTAAAACATTTTTGAAATT
* ** *
453545 TATATAATATATAGTTTTTTAAAAAACGTTTTAAAAAATA
1 TATATAATATATAG-TTTTT--AAAACATTTT-TGAAATT
*
453585 TAGATAATATATAGTTTTTAAAATCATTTTTGAAATCT
1 TATATAATATATAGTTTTTAAAA-CATTTTTGAAAT-T
* *
453623 TATATAATATATAATTTTGAAAACATTTTTGAAAATT
1 TATATAATATATAGTTTTTAAAACATTTTTG-AAATT
*
453660 TATATAATATATAGTTTTGAAAACA-TTTTGAAAACATT
1 TATATAATATATAGTTTTTAAAACATTTTTG--AA-ATT
** *
453698 TATATGTTATATAGTTTTTTAAAAAAACATTTTTGAAAATA
1 TATATAATATATAG-TTTTT---AAAACATTTTTG-AAATT
* *
453739 TATATAATATATAATTTTGAAAACATTTTTGAAAATT
1 TATATAATATATAGTTTTTAAAACATTTTTG-AAATT
*
453776 TATATAATATATAGTTTTGAAAACA-TTTTGAAAACATT
1 TATATAATATATAGTTTTTAAAACATTTTTG--AA-ATT
** *
453814 TATATGTTATATAGATTTTTAAAAAACATTTTTGAAAATA
1 TATATAATATATAG-TTTTT--AAAACATTTTTG-AAATT
* * *
453854 TATATAATATATAATTTTTAAAACATTTTTAAAAATG
1 TATATAATATATAGTTTTTAAAACATTTTT-GAAATT
* * * * *
453891 CATATATTATATAGTTTTTTGAAACGTTTTTGAAA-A
1 TATATAATATATAG-TTTTTAAAACATTTTTGAAATT
*
453927 TACGTATAATATATAGTTTTTAAAAAATATTTTGGAAATT
1 TA--TATAATATATAGTTTTTAAAACAT-TTTT-GAAATT
453967 TATATA
1 TATATA
453973 TTATGAGCTT
Statistics
Matches: 354, Mismatches: 44, Indels: 55
0.78 0.10 0.12
Matches are distributed among these distances:
33 14 0.04
34 5 0.01
36 20 0.06
37 126 0.36
38 92 0.26
39 24 0.07
40 32 0.09
41 22 0.06
42 14 0.04
43 5 0.01
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTTGAAATT
Done.