Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000935.1 Hibiscus syriacus cultivar Beakdansim tig00001869_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: 730910
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:265095 original size:4 final size:4
Alignment explanation
Indices: 265088--265124 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
265078 CACACATATA
*
265088 TATG TATG TATG TATG TATG TATG TATG CATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
265125 GTGCATGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:265129 original size:12 final size:12
Alignment explanation
Indices: 265088--265131 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
265078 CACACATATA
*
265088 TATGTATGTATG
1 TATGCATGTATG
*
265100 TATGTATGTATG
1 TATGCATGTATG
265112 TATGCATGTATG
1 TATGCATGTATG
*
265124 TGTGCATG
1 TATGCATG
265132 CATACTGACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.23, C:0.05, G:0.27, T:0.45
Consensus pattern (12 bp):
TATGCATGTATG
Found at i:265853 original size:33 final size:33
Alignment explanation
Indices: 265787--265853 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
265777 GTTTACGTTG
* * *
265787 TTAATTATCGTTGTTAATATTGTTAACATTGTC
1 TTAATTAACGTTGTTAATAGTGTTAACACTGTC
*
265820 TTAATTAACGTTGTTAATAGTGTTAATACTGTC
1 TTAATTAACGTTGTTAATAGTGTTAACACTGTC
265853 T
1 T
265854 AATATGATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.49
Consensus pattern (33 bp):
TTAATTAACGTTGTTAATAGTGTTAACACTGTC
Found at i:274178 original size:25 final size:23
Alignment explanation
Indices: 274149--274204 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
274139 TTTTGTATGC
*
274149 TTTTATGTCACGATTATTCATTTAT
1 TTTTATGACACGATT-TTC-TTTAT
*
274174 TTTTATGACATGATTTTCTTTAT
1 TTTTATGACACGATTTTCTTTAT
*
274197 TATTATGA
1 TTTTATGA
274205 TAGTTTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 12 0.43
24 3 0.11
25 13 0.46
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.57
Consensus pattern (23 bp):
TTTTATGACACGATTTTCTTTAT
Found at i:274202 original size:23 final size:25
Alignment explanation
Indices: 274151--274204 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
274141 TTGTATGCTT
* *
274151 TTATGTCACGATTATTCATTTATTT
1 TTATGACACGATTATTCATTTATTA
*
274176 TTATGACATGATT-TTC-TTTATTA
1 TTATGACACGATTATTCATTTATTA
274199 TTATGA
1 TTATGA
274205 TAGTTTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 12 0.46
24 3 0.12
25 11 0.42
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (25 bp):
TTATGACACGATTATTCATTTATTA
Found at i:285484 original size:2 final size:2
Alignment explanation
Indices: 285479--285508 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
285469 AAAATAAAAT
285479 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
285509 TTATTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:288677 original size:11 final size:12
Alignment explanation
Indices: 288654--288685 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
288644 TATATACTTA
288654 TAAAAATATATT
1 TAAAAATATATT
288666 TAAAAATA-ATT
1 TAAAAATATATT
288677 TAAAAATAT
1 TAAAAATAT
288686 TTTTTGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAAAATATATT
Found at i:291274 original size:15 final size:15
Alignment explanation
Indices: 291254--291288 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
291244 CCGTAGGACC
291254 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
291269 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
291284 ACTAC
1 ACTAC
291289 AATACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:291994 original size:19 final size:20
Alignment explanation
Indices: 291958--291995 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
291948 TTTCCTTTAG
291958 GGGGGAATCAATACCCCCCA
1 GGGGGAATCAATACCCCCCA
*
291978 GGGGGAATCGATACCCCC
1 GGGGGAATCAATACCCCC
291996 TGGACATATT
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:0.34, G:0.29, T:0.11
Consensus pattern (20 bp):
GGGGGAATCAATACCCCCCA
Found at i:298216 original size:15 final size:15
Alignment explanation
Indices: 298193--298227 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
298183 CCGTAGGACC
298193 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
*
298208 ACTATGTCCCGAAGG
1 ACTACGTCCCGAAGG
298223 ACTAC
1 ACTAC
298228 AATACCCTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:300477 original size:25 final size:25
Alignment explanation
Indices: 300429--300477 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
300419 GGTTTTTTTG
300429 TTTTTTAAAATTAAAATATTAAATCT
1 TTTTTTAAAA-TAAAATATTAAATCT
*
300455 TTTTTTAAAA-AAATTATTGAAAT
1 TTTTTTAAAATAAAATATT-AAAT
300478 TTTATATGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 4 0.19
26 10 0.48
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTTTTAAAATAAAATATTAAATCT
Found at i:301171 original size:23 final size:23
Alignment explanation
Indices: 301126--301200 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
301116 AAAACTACCA
* *
301126 AAAGGCAGAGA-AAACGTGTCAC
1 AAAGACAGAGATAAACGTGCCAC
* *
301148 AAAGATAGAGATAAATGTGCCAC
1 AAAGACAGAGATAAACGTGCCAC
* * * *
301171 AAAGGCAGAGATAAACATGTCAA
1 AAAGACAGAGATAAACGTGCCAC
301194 AAAGACA
1 AAAGACA
301201 AAATTATTCT
Statistics
Matches: 41, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
22 9 0.22
23 32 0.78
ACGTcount: A:0.51, C:0.15, G:0.23, T:0.12
Consensus pattern (23 bp):
AAAGACAGAGATAAACGTGCCAC
Found at i:301610 original size:87 final size:87
Alignment explanation
Indices: 301464--301626 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
301454 TATGTTATAT
* *
301464 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGTTAACACTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATGTAATAGGT
301529 AGCACTTATATAATAAAATAGG
66 AGCACTTATATAATAAAATAGG
* *
301551 CATTTAACCGAAAATATTATCAAGTACAATAACATATTGGGTAGCACTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATGTAATAGGT
*
301616 AGCGCTTATAT
66 AGCACTTATAT
301627 TGACCTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATGTAATAGGT
AGCACTTATATAATAAAATAGG
Found at i:302200 original size:200 final size:199
Alignment explanation
Indices: 301848--302325 Score: 588
Period size: 200 Copynumber: 2.4 Consensus size: 199
301838 TTCTATCGGC
* * *
301848 TACATTGTAAATTTACTTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCAATACTTTT
1 TACATTGTAAATTTACCTATTACATTATAATTAT-GGTTTCGATGTTTTTGGGATCGATACTTTT
* * * *
301913 AATAAATATATC-AACACTTTATGTGTGTACCCCATTTGGCATTCATTCTGGACAAAATATATCG
65 TATAAATGTATCGAACACTTTATGCGTGCACCCCATTTGGCATTCATTCTGGACAAAATATATCG
* * *
301977 ACACAAATTTAAAAAGCGTCGATACATTATGTTGACCTATTCTCTAATAAAATCGGTATATTTAT
130 ACACAAATTCAAAAAGCGTCGATACATTATGTTGACCTATTCTCTAAT-AAACCAGTATATTTAT
302042 ACCGAT
194 ACCGAT
* * *
302048 TACATTG-AAAATTACCTATTACATTATAATTATGTGTTTCGATATTTTTGAGATCGATACTTTT
1 TACATTGTAAATTTACCTATTACATTATAATTATG-GTTTCGATGTTTTTGGGATCGATACTTTT
* * * * *
302112 TATAAATGTATCGAA-ATTTTATGCGTGCACCTCGTTTGGGTATTCATTCTGGACAATAA-GTAT
65 TATAAATGTATCGAACACTTTATGCGTGCACCCCATTT-GGCATTCATTCTGGACAA-AATATAT
* * * * * *
302175 CGACACAAATTCCACAAGTGTCGATACATTATGTTGACCTCTTTTCTAATTAACCAGTATATTTA
128 CGACACAAATTCAAAAAGCGTCGATACATTATGTTGACCTATTCTCTAATAAACCAGTATATTTA
* *
302240 TATCGGT
193 TACCGAT
* * *
302247 TACATTGTTAATTTACCTATTACATTATAATTAATGGTTTCAATGTTTTTGGGGTCGATAC-TTT
1 TACATTGTAAATTTACCTATTACATTATAATT-ATGGTTTCGATGTTTTTGGGATCGATACTTTT
*
302311 TAGAAAATGTATCGA
65 TA-TAAATGTATCGA
302326 CACATATTTA
Statistics
Matches: 238, Mismatches: 33, Indels: 14
0.84 0.12 0.05
Matches are distributed among these distances:
198 1 0.00
199 105 0.44
200 127 0.53
201 5 0.02
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (199 bp):
TACATTGTAAATTTACCTATTACATTATAATTATGGTTTCGATGTTTTTGGGATCGATACTTTTT
ATAAATGTATCGAACACTTTATGCGTGCACCCCATTTGGCATTCATTCTGGACAAAATATATCGA
CACAAATTCAAAAAGCGTCGATACATTATGTTGACCTATTCTCTAATAAACCAGTATATTTATAC
CGAT
Found at i:304815 original size:19 final size:19
Alignment explanation
Indices: 304791--304838 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
304781 TTACATTCAC
304791 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
304810 ATACAAAATTATGAATCGT
1 ATACAAAATTATAAATCGT
304829 ATACAAAATT
1 ATACAAAATT
304839 TCCCCTACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:306811 original size:198 final size:198
Alignment explanation
Indices: 306466--307058 Score: 934
Period size: 199 Copynumber: 3.0 Consensus size: 198
306456 CGCGTAATTT
* * *
306466 AAAGTATCGACATAACTTTAAAAAGTGTCGATACTTGATGTAGACTTATTTTCTAATTAACCGGT
1 AAAGTATCGACATAACTTTAAAAAGTATCGATACTTTATGTAGACCTATTTTCTAATTAACCGGT
* * *
306531 ATATGTCTACCAGTTACATTGGAAATTGACCTATTATATTATAATTATCGTATTCGATGTTTTTG
66 ATATTTCTACTAGTTACATTGGAAATTGACCTATTACATTATAATTATCGTATTCGATGTTTTTG
* *
306596 GGATCGATACGTTTTATAAATGTATTGACACTTTATAGTGCACCTCGTTGGGCATTCATTCTGGT
131 GGATCGATACTTTTTATAAATGTATCGACACTTTATAGTGCACCTCGTTGGGCATTCATTCTGGT
306661 CAA
196 CAA
* * * * **
306664 AAAGTATCAACACAACTTTAAAAAGTTTCGATACTTTATATAGACCTATTTTCTAATTAACCTCT
1 AAAGTATCGACATAACTTTAAAAAGTATCGATACTTTATGTAGACCTATTTTCTAATTAACCGGT
* *
306729 ATATTTCTACTGGTTACATTGGAAATTGACCTATTACATTCTAATTATCGTATTCGATGTTTTTG
66 ATATTTCTACTAGTTACATTGGAAATTGACCTATTACATTATAATTATCGTATTCGATGTTTTTG
*
306794 GGATCGATACTTTTTATAAATGTATCGACACTTTATAGTACACCTCGATTGGGCATTCATTCTGG
131 GGATCGATACTTTTTATAAATGTATCGACACTTTATAGTGCACCTCG-TTGGGCATTCATTCTGG
*
306859 TTAA
195 TCAA
*
306863 AAAGTATCGACATAACTTTAAAAAGTATCGATACATTATGTAGACCTATTTTCTAATTAACCGGT
1 AAAGTATCGACATAACTTTAAAAAGTATCGATACTTTATGTAGACCTATTTTCTAATTAACCGGT
* *
306928 ATATTTCTACTAGTTACATTGGAAATTGACCTACTACATTATAATTATCTTATTCGATGTTTTTG
66 ATATTTCTACTAGTTACATTGGAAATTGACCTATTACATTATAATTATCGTATTCGATGTTTTTG
* * * *
306993 GGATCGATACTTTTTATAAATGTATCGACATTTTATTCGTGCACCTCGGTTGGTCATTTATTCTG
131 GGATCGATACTTTTTATAAATGTATCGACACTTTA-TAGTGCACCTC-GTTGGGCATTCATTCTG
307058 G
194 G
307059 AGATGACTGA
Statistics
Matches: 359, Mismatches: 33, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
198 161 0.45
199 173 0.48
200 24 0.07
201 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.40
Consensus pattern (198 bp):
AAAGTATCGACATAACTTTAAAAAGTATCGATACTTTATGTAGACCTATTTTCTAATTAACCGGT
ATATTTCTACTAGTTACATTGGAAATTGACCTATTACATTATAATTATCGTATTCGATGTTTTTG
GGATCGATACTTTTTATAAATGTATCGACACTTTATAGTGCACCTCGTTGGGCATTCATTCTGGT
CAA
Found at i:308637 original size:11 final size:11
Alignment explanation
Indices: 308621--308645 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
308611 TATACATAAC
308621 AATGTTCAAAT
1 AATGTTCAAAT
308632 AATGTTCAAAT
1 AATGTTCAAAT
308643 AAT
1 AAT
308646 CAAACGCACA
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:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (11 bp):
AATGTTCAAAT
Found at i:310884 original size:17 final size:15
Alignment explanation
Indices: 310857--310899 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
310847 CAATTGGTTC
310857 AGAAGGAGCTTGTCCTTG
1 AGAA-GAGCTTG--CTTG
*
310875 AGAAGAGCTTGGTTG
1 AGAAGAGCTTGCTTG
310890 AGAAGAGCTT
1 AGAAGAGCTT
310900 TGAGAAAGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 13 0.54
17 7 0.29
18 4 0.17
ACGTcount: A:0.28, C:0.12, G:0.35, T:0.26
Consensus pattern (15 bp):
AGAAGAGCTTGCTTG
Found at i:311543 original size:200 final size:200
Alignment explanation
Indices: 311190--312224 Score: 1511
Period size: 200 Copynumber: 5.2 Consensus size: 200
311180 GCAAAATTTT
* * * * *
311190 AAAAGGTATTGACACAAGTTCAACCAGTGTCGATACATTATGTAGACCTATTTTCTCATGAAACC
1 AAAAAGTATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
*
311255 GGTAAATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
66 GGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
* * *
311320 TTGGGATCAATACTTTTTATAAATGTATCGACACTTTATGCGTGTACCCTTTTGGGCATTTATTC
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATTC
*
311385 TTGAC
196 TGGAC
* *
311390 AAAAAGTATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACCTATTTTTTTC-TTAAAC
1 AAAAAGTATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACCTA-TTTTCTCATAAAAC
* *
311454 CGGTAAATTTCTACCGATTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTT
65 CGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTT
* *
311519 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTGCACTCTTTTGGGCATTCATT
130 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATT
311584 CTGGAC
195 CTGGAC
* * * * * * *
311590 AAAACGTATCGACACAAGTTCCAAAATTGTCGATACATTATATAAACCTATTTTTTC-TTAAACC
1 AAAAAGTATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
* * * *
311654 GGTAAATTTCTATCGGTTACATTGTAAATTTACATATTACATTATAATTATGAGTTTCGATGTTT
66 GGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
*
311719 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTTATTC
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATTC
311784 TGGAC
196 TGGAC
* * * * * **
311789 AACAAGTATCGACACAAGTTCTACAAGTGTCAATACATTATGTAGACCAATTCTCTCATAAAATT
1 AAAAAGTATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
* * * *
311854 GGTATATTTATACCGGTTACAATGAAAAATTACCTATTACATTATAATTATGGGTTTCGAT-TTT
66 GGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
* * *
311918 TTTGGATCGATACTTTTTATAAATGTATCGACATTTTAAGCGTGCACCCCTTTTGGGCATTCATT
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCA-CCCTTTTGGGCATTCATT
*
311983 ATGGAC
195 CTGGAC
* *
311989 AAAAAGTATCGACACAAGTTCCATAAGTGTCG-TAACATTATGTAGACCTATTATCTCATAAAAC
1 AAAAAGTATCGACACAAGTTCCACAAGTGTCGAT-ACATTATGTAGACCTATTTTCTCATAAAAC
* * * * * * * *
312053 TGATATATTTATACCGATTACATTGAAAAATTACCTATTACATTATAATTATAGGTTTCAATGTT
65 CGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTT
* *
312118 TTTTGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCTTTGGGCATTCATT
130 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATT
312183 CTGGAC
195 CTGGAC
*
312189 AAAAAGTATCGACACAAGTTCCACAAGTGTCAATAC
1 AAAAAGTATCGACACAAGTTCCACAAGTGTCGATAC
312225 GTTTGGGAAC
Statistics
Matches: 757, Mismatches: 72, Indels: 12
0.90 0.09 0.01
Matches are distributed among these distances:
199 235 0.31
200 468 0.62
201 54 0.07
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (200 bp):
AAAAAGTATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
GGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTT
TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATTC
TGGAC
Found at i:311990 original size:399 final size:400
Alignment explanation
Indices: 311190--312224 Score: 1533
Period size: 399 Copynumber: 2.6 Consensus size: 400
311180 GCAAAATTTT
* * * *
311190 AAAAGGTATTGACACAAGTT-CAACCAGTGTCGATACATTATGTAGACCTATTTTCTCATGAAAC
1 AAAAAGTATCGACACAAGTTCCAA-AAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAAC
*
311254 CGGTAAATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTT
65 CGGTAAATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATGAGTTTCGATGTT
* *
311319 TTTGGGATCAATACTTTTTATAAATGTATCGACACTTTATGCGTGTACCCTTTTGGGCATTTATT
130 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTTATT
* * * * *
311384 CTTGACAAAAAGTATCGACACAAGTTCCACAAGTGTCGATACATTATGTAGACCTATTTTTTTCT
195 CTGGACAAAAAGTATCGACACAAGTTCCACAAGTGTCAATACATTATGTAGACCTAATTCTCTCT
* * * * *
311449 TAAACCGGTAAATTTCTACCGATTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCG
260 AAAACCGGTAAATTTATACCGATTACAATGAAAAATTACCTATTACATTATAATTATGGGTTTCG
* * *
311514 ATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTGCACTCTTTTGGGCAT
325 ATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTAAGCGTGCACCCTTTTGGGCAT
*
311579 TCATTCTGGAC
390 TCATTATGGAC
* * * * * *
311590 AAAACGTATCGACACAAGTTCCAAAATTGTCGATACATTATATAAACCTATTTTTTC-TTAAACC
1 AAAAAGTATCGACACAAGTTCCAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
* *
311654 GGTAAATTTCTATCGGTTACATTGTAAATTTACATATTACATTATAATTATGAGTTTCGATGTTT
66 GGTAAATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATGAGTTTCGATGTTT
311719 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTTATTC
131 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTTATTC
* *
311784 TGGACAACAAGTATCGACACAAGTTCTACAAGTGTCAATACATTATGTAGACC-AATTCTCTCAT
196 TGGACAAAAAGTATCGACACAAGTTCCACAAGTGTCAATACATTATGTAGACCTAATTCTCTC-T
** * *
311848 AAAATTGGTATATTTATACCGGTTACAATGAAAAATTACCTATTACATTATAATTATGGGTTTCG
260 AAAACCGGTAAATTTATACCGATTACAATGAAAAATTACCTATTACATTATAATTATGGGTTTCG
* *
311913 AT-TTTTTTGGATCGATACTTTTTATAAATGTATCGACATTTTAAGCGTGCACCCCTTTTGGGCA
325 ATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTAAGCGTGCA-CCCTTTTGGGCA
311977 TTCATTATGGAC
389 TTCATTATGGAC
* *
311989 AAAAAGTATCGACACAAGTTCCATAAGTGTCG-TAACATTATGTAGACCTATTATCTCATAAAAC
1 AAAAAGTATCGACACAAGTTCCAAAAGTGTCGAT-ACATTATGTAGACCTATTTTCTCATAAAAC
* * * * * * * *
312053 TGATATATTTATACCGATTACATTGAAAAATTACCTATTACATTATAATTAT-AGGTTTCAATGT
65 CGGTAAATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATGA-GTTTCGATGT
* * *
312117 TTTTTGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCCTTTGGGCATTCAT
129 TTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTTAT
312182 TCTGGACAAAAAGTATCGACACAAGTTCCACAAGTGTCAATAC
194 TCTGGACAAAAAGTATCGACACAAGTTCCACAAGTGTCAATAC
312225 GTTTGGGAAC
Statistics
Matches: 571, Mismatches: 58, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
398 52 0.09
399 310 0.54
400 206 0.36
401 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (400 bp):
AAAAAGTATCGACACAAGTTCCAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
GGTAAATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATGAGTTTCGATGTTT
TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTTATTC
TGGACAAAAAGTATCGACACAAGTTCCACAAGTGTCAATACATTATGTAGACCTAATTCTCTCTA
AAACCGGTAAATTTATACCGATTACAATGAAAAATTACCTATTACATTATAATTATGGGTTTCGA
TGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTAAGCGTGCACCCTTTTGGGCATT
CATTATGGAC
Found at i:312572 original size:19 final size:19
Alignment explanation
Indices: 312548--312596 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
312538 TTACATTTAC
312548 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
312567 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
312586 ATACAAAATTA
1 ATACAAAATTA
312597 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:314894 original size:23 final size:24
Alignment explanation
Indices: 314864--314919 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
314854 AACATGCATT
*
314864 TATAATAAAAAT-TTATCATTTTA
1 TATAATAAAAATACTATCATTTTA
**
314887 TATAATAACTATACTATCATTTTA
1 TATAATAAAAATACTATCATTTTA
314911 TATAA-AAAA
1 TATAATAAAA
314920 CAAAAATGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (24 bp):
TATAATAAAAATACTATCATTTTA
Found at i:315410 original size:60 final size:60
Alignment explanation
Indices: 315316--315549 Score: 299
Period size: 60 Copynumber: 3.9 Consensus size: 60
315306 CAGAACAGGT
* * * * *
315316 ATCCATAAGGACTTACCTTACATCTCTAGGATCTAGGAGTCCAATATCGAAGATATATGC
1 ATCCATAAGGACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATCGAAGATACATGC
* *
315376 ATCCATAAGGACTTACCCTAGACCACTAGAATCTAAGAGTCCAATA-CGGAAGATACATGC
1 ATCCATAAGGACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATC-GAAGATACATGC
* * * * *
315436 ATTCATAAGGACTTACCCTAGACCTCTAGGATCTAGGAGTCAAATATGGAAGATACATAC
1 ATCCATAAGGACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATCGAAGATACATGC
* * * * *
315496 GTCCATAGGGACTTACCTTATACCACTAGGATCTAGGAGTCCAATATGGAAGAT
1 ATCCATAAGGACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATCGAAGAT
315550 TAGAACAGGC
Statistics
Matches: 151, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
59 1 0.01
60 150 0.99
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (60 bp):
ATCCATAAGGACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATCGAAGATACATGC
Found at i:315536 original size:120 final size:120
Alignment explanation
Indices: 315319--315549 Score: 336
Period size: 120 Copynumber: 1.9 Consensus size: 120
315309 AACAGGTATC
* * * * *
315319 CATAAGGACTTACCTTACATCTCTAGGATCTAGGAGTCCAATATCGAAGATATATGCATCCATAA
1 CATAAGGACTTACCCTACACCTCTAGGATCTAGGAGTCAAATATCGAAGATACATACATCCATAA
315384 GGACTTACCCTAGACCACTAGAATCTAAGAGTCCAATACGGAAGATACATGCATT
66 GGACTTACCCTAGACCACTAGAATCTAAGAGTCCAATACGGAAGATACATGCATT
* * * *
315439 CATAAGGACTTACCCTAGACCTCTAGGATCTAGGAGTCAAATATGGAAGATACATACGTCCATAG
1 CATAAGGACTTACCCTACACCTCTAGGATCTAGGAGTCAAATATCGAAGATACATACATCCATAA
* * * * *
315504 GGACTTACCTTATACCACTAGGATCTAGGAGTCCAATATGGAAGAT
66 GGACTTACCCTAGACCACTAGAATCTAAGAGTCCAATACGGAAGAT
315550 TAGAACAGGC
Statistics
Matches: 97, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
120 97 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (120 bp):
CATAAGGACTTACCCTACACCTCTAGGATCTAGGAGTCAAATATCGAAGATACATACATCCATAA
GGACTTACCCTAGACCACTAGAATCTAAGAGTCCAATACGGAAGATACATGCATT
Found at i:320565 original size:22 final size:22
Alignment explanation
Indices: 320522--320629 Score: 126
Period size: 22 Copynumber: 4.9 Consensus size: 22
320512 TATATGCCAG
* *
320522 CAGTGCTAAGGAACTTTAGTAT
1 CAGTGCTAAGGCACTTTCGTAT
* * *
320544 CAATGCGAATGCACTTTCGTAT
1 CAGTGCTAAGGCACTTTCGTAT
* *
320566 CAGTTCTAAGGCACTTTCATAT
1 CAGTGCTAAGGCACTTTCGTAT
* *
320588 CAGTGCTAAGGCACTTTAGTAC
1 CAGTGCTAAGGCACTTTCGTAT
*
320610 CAGTTCTAAGGCACTTTCGT
1 CAGTGCTAAGGCACTTTCGT
320630 GTATTGTTGG
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 70 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (22 bp):
CAGTGCTAAGGCACTTTCGTAT
Found at i:323631 original size:59 final size:59
Alignment explanation
Indices: 323539--323658 Score: 177
Period size: 59 Copynumber: 2.0 Consensus size: 59
323529 ACAATTGTTA
* * * * * *
323539 ATAGCATTAATGTCTTCTTTTTCCAATCTGCTATTTAATATATTATCTTTTCCTAAATT
1 ATAGCATTAATGCCATCTTTTCCCAATATGCTATTTAATACATTATCTTTTCCCAAATT
*
323598 ATAGCATTAATGCCATCTTTTCCCAATATGCTATTTATTACATTATCTTTTCCCAAATT
1 ATAGCATTAATGCCATCTTTTCCCAATATGCTATTTAATACATTATCTTTTCCCAAATT
323657 AT
1 AT
323659 GCAGTACAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.47
Consensus pattern (59 bp):
ATAGCATTAATGCCATCTTTTCCCAATATGCTATTTAATACATTATCTTTTCCCAAATT
Found at i:323815 original size:44 final size:45
Alignment explanation
Indices: 323726--323820 Score: 147
Period size: 44 Copynumber: 2.1 Consensus size: 45
323716 AATTTAATTT
* *
323726 ATATTACTTTAAACATCTATAATGTTATTAATATTGAATACTTTA
1 ATATTACTTTAAACATCAATAATGTGATTAATATTGAATACTTTA
* *
323771 ATATTATTTTAAACATCAATAAT-TGATTAATATTGAATATTTTA
1 ATATTACTTTAAACATCAATAATGTGATTAATATTGAATACTTTA
323815 ATATTA
1 ATATTA
323821 ATCATAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 25 0.54
45 21 0.46
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (45 bp):
ATATTACTTTAAACATCAATAATGTGATTAATATTGAATACTTTA
Found at i:337044 original size:19 final size:17
Alignment explanation
Indices: 337021--337068 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
337011 GATTTAATAA
337021 AATAAAATAGATAATAAT
1 AATAAAATAGATAA-AAT
337039 ATATAAAA-AGA-AAAAT
1 A-ATAAAATAGATAAAAT
337055 AATAAAATA-ATAAA
1 AATAAAATAGATAAA
337069 TACTAATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
15 7 0.26
16 8 0.30
17 2 0.07
18 4 0.15
19 6 0.22
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (17 bp):
AATAAAATAGATAAAAT
Found at i:337823 original size:76 final size:76
Alignment explanation
Indices: 337738--337921 Score: 263
Period size: 70 Copynumber: 2.5 Consensus size: 76
337728 ACTTAAAATT
*
337738 ATTTCAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATCCTAAAACTTAATTAAAA
1 ATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATCCTAAAACTTAATTAAAA
*
337803 TAATAAAACCA
66 CAATAAAACCA
337814 ATTTAAACTAAAATACCTAAAACAAAG-----ATA-AAAAATAATATCCTAAAACTTAATTAAAA
1 ATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATCCTAAAACTTAATTAAAA
* * *
337873 CACTAAAATCT
66 CAATAAAACCA
* *
337884 ATTTAAACTAAACTACCTAAAACAAATATAAAATATAA
1 ATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
337922 TATTTTAAAT
Statistics
Matches: 95, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
70 61 0.64
71 3 0.03
75 3 0.03
76 28 0.29
ACGTcount: A:0.60, C:0.14, G:0.01, T:0.26
Consensus pattern (76 bp):
ATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATCCTAAAACTTAATTAAAA
CAATAAAACCA
Found at i:337872 original size:25 final size:25
Alignment explanation
Indices: 337773--337872 Score: 70
Period size: 25 Copynumber: 4.2 Consensus size: 25
337763 AGATAAAATA
337773 TAAAAATAATATCCTAAAACTTAAT
1 TAAAAATAATATCCTAAAACTTAAT
*
337798 T-AAAAT-A-A---TAAAAC-CAAT
1 TAAAAATAATATCCTAAAACTTAAT
* * * **
337816 TTAAACTAAAATACCTAAAACAAAGAT
1 TAAAAATAATAT-CCTAAAACTTA-AT
*
337843 AAAAAATAATATCCTAAAACTTAAT
1 TAAAAATAATATCCTAAAACTTAAT
337868 TAAAA
1 TAAAA
337873 CACTAAAATC
Statistics
Matches: 56, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
18 4 0.07
19 10 0.18
20 1 0.02
21 1 0.02
22 1 0.02
23 1 0.02
24 5 0.09
25 13 0.23
26 10 0.18
27 10 0.18
ACGTcount: A:0.61, C:0.12, G:0.01, T:0.26
Consensus pattern (25 bp):
TAAAAATAATATCCTAAAACTTAAT
Found at i:337880 original size:70 final size:69
Alignment explanation
Indices: 337718--337924 Score: 261
Period size: 70 Copynumber: 2.9 Consensus size: 69
337708 TCTTAAATCC
* *
337718 TAATTAAAACACTTAAAATTATTTCAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
1 TAATTAAAACAC-TAAAACTATTTAAACTAAAATACCTAAAACAAAG-----ATA-AAAAATAAT
337783 ATCCTAAAACT
59 ATCCTAAAACT
* * *
337794 TAATTAAAATAATAAAACCAATTTAAACTAAAATACCTAAAACAAAGATAAAAAATAATATCCTA
1 TAATTAAAACACTAAAA-CTATTTAAACTAAAATACCTAAAACAAAGATAAAAAATAATATCCTA
337859 AAACT
65 AAACT
* * *
337864 TAATTAAAACACTAAAATCTATTTAAACTAAACTACCTAAAACAAATATAAAATATAATAT
1 TAATTAAAACACTAAAA-CTATTTAAACTAAAATACCTAAAACAAAGATAAAAAATAATAT
337925 TTTAAATATT
Statistics
Matches: 118, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
70 74 0.63
71 3 0.03
75 5 0.04
76 36 0.31
ACGTcount: A:0.59, C:0.13, G:0.01, T:0.27
Consensus pattern (69 bp):
TAATTAAAACACTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAAAATAATATCCTAA
AACT
Found at i:345257 original size:19 final size:18
Alignment explanation
Indices: 345230--345289 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
345220 CAGGTAAAGT
*
345230 TAAAAAGAT-TTAATAAAA
1 TAAAAAGATAATAA-AAAA
345248 TAAAATAGATAATAAAAAA
1 TAAAA-AGATAATAAAAAA
*
345267 TAAAAAGAGAAATAATAAAA
1 TAAAAAGA-TAATAA-AAAA
345287 TAA
1 TAA
345290 TAAATAGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
18 8 0.22
19 18 0.50
20 10 0.28
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.22
Consensus pattern (18 bp):
TAAAAAGATAATAAAAAA
Found at i:346129 original size:70 final size:70
Alignment explanation
Indices: 345950--346176 Score: 276
Period size: 70 Copynumber: 3.2 Consensus size: 70
345940 AACAAGCTAA
* * * *
345950 AATATCTTAAATCCTAATTAAAACACTTAAAA-CTATTTCAACTAAAATAACTAAAACAAAGATA
1 AATATCTTAAAACTTAATTAAAACAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAG---
346014 AAATATAAAAAT
62 --ATA-AAAAAT
* * *
346026 AATATCCTAAAGCTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAA
1 AATATCTTAAAACTTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAA
346091 AAAAT
66 AAAAT
* * *
346096 AATATCTTAAAACTTAATTAAAACACTAAAACCTATTGAAACTAAAATACATAAAACAAATATAA
1 AATATCTTAAAACTTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAA
*
346161 TAAAT
66 AAAAT
*
346166 AATATTTTAAA
1 AATATCTTAAA
346177 TATTATCTTA
Statistics
Matches: 136, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
70 79 0.58
71 3 0.02
75 5 0.04
76 49 0.36
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.28
Consensus pattern (70 bp):
AATATCTTAAAACTTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAA
AAAAT
Found at i:346605 original size:20 final size:20
Alignment explanation
Indices: 346569--346606 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
346559 TCAAAATCAT
* *
346569 TTTTCAAAATTTCATTTTTA
1 TTTTCAAAATCTAATTTTTA
346589 TTTTCAAAATCTAATTTT
1 TTTTCAAAATCTAATTTT
346607 GCTTTGGAAA
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:0.32, C:0.11, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTCAAAATCTAATTTTTA
Found at i:349800 original size:20 final size:20
Alignment explanation
Indices: 349763--349801 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
349753 CTCAAAATCA
* * *
349763 TTTTTTAAAATTTCATTTTG
1 TTTTTAAAAATCTAATTTTG
349783 TTTTTAAAAATCTAATTTT
1 TTTTTAAAAATCTAATTTT
349802 TCTTTCGTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTTAAAAATCTAATTTTG
Found at i:357179 original size:22 final size:21
Alignment explanation
Indices: 357129--357180 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
357119 AATTCCTTAT
*
357129 AGTATCGATACCTTTATATTG
1 AGTATCGATACCTTTATATTA
*
357150 AGTATCGATA-CTTCTCTATTA
1 AGTATCGATACCTT-TATATTA
357171 AGGTATCGAT
1 A-GTATCGAT
357181 TCCATCCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 3 0.11
21 16 0.59
22 8 0.30
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (21 bp):
AGTATCGATACCTTTATATTA
Found at i:372636 original size:20 final size:20
Alignment explanation
Indices: 372613--372676 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
372603 CGATATAACA
*
372613 GGTA-AAAATATGATAAAATC
1 GGTATAAAA-ATGATAAAACC
*
372633 GGTATCAAAATGATAAAACC
1 GGTATAAAAATGATAAAACC
*
372653 GGTATCAAAATGATAAAACC
1 GGTATAAAAATGATAAAACC
372673 GGTA
1 GGTA
372677 AAGCACTATC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
20 38 0.93
21 3 0.07
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.22
Consensus pattern (20 bp):
GGTATAAAAATGATAAAACC
Found at i:374882 original size:21 final size:21
Alignment explanation
Indices: 374823--374887 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
374813 AAGACAATCA
*
374823 AGAGTCGAAGAGAAACTTAAG
1 AGAGTCGAAGAGAAACTTGAG
374844 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* * *
374865 AGCGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
374886 AG
1 AG
374888 GCATAAGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.42, C:0.12, G:0.31, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:374958 original size:33 final size:33
Alignment explanation
Indices: 374921--374986 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
374911 AAATAGATGG
374921 AGTGGTGAAAGAAGTAAAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAAAGGTGTTAAGGGGTGA
**
374954 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAAAGGTGTTAAGGGGTGA
374987 TCTTAAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.44, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAAAGGTGTTAAGGGGTGA
Found at i:377302 original size:201 final size:201
Alignment explanation
Indices: 377067--378006 Score: 1623
Period size: 201 Copynumber: 4.7 Consensus size: 201
377057 GGTAAAATTT
*
377067 TCGATCCCATAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
* * *
377132 TAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTGTTTAATTTTGTAT
66 TAAATATACCGGTTTTATGAGAGAATAGGTATACAACATGTATCGACACTTGTTTAATTTTGTGT
* * *
377197 CGATACTTTTAGTCCATAATGGATGCCAAAAAGGGTGAACACATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
377262 AAAGTG
196 AAAGTG
* *
377268 TCGATCTCAAAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
* * *
377333 TAAATATACCGGTTTTATGATAGAATATGTATACAACGTGTATCGACACTTGTTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTATACAACATGTATCGACACTTGTTTAATTTTGTGT
377398 CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
377463 AAAGTG
196 AAAGTG
*
377469 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGATA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
* *
377534 TAAATATACCAGTTTTATGAGGGAATAGGTATACAACATGTATCGACACTT-TTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTATACAACATGTATCGACACTTGTTTAATTTTGTGT
* *
377598 CGATACTTTTGGTCCAGAATTGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATGCATTTTCAA
131 CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
377663 AAAGTG
196 AAAGTG
377669 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
*
377734 TAAATATACCGATTTTATGAGAGAATAGGTATACAACATGTATCGACACTTGTTTAATTTTGTGT
66 TAAATATACCGGTTTTATGAGAGAATAGGTATACAACATGTATCGACACTTGTTTAATTTTGTGT
*
377799 CGATACTTTTGGTCCAGAATGGATGCTAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
377864 AAAGTG
196 AAAGTG
* * * *
377870 TCGATCCTAGAAACATATGCATCCATAAGTATAATGTAATATGCAAATTTACAATGTAACCGATA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
* * *
377935 TAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGTATCGAAACTTGTTTAATTTTGTGG
66 TAAATATACCGGTTTTATGAGAGAATAGGTATACAACATGTATCGACACTTGTTTAATTTTGT-G
378000 T-GATACT
130 TCGATACT
378007 AATTTAAATA
Statistics
Matches: 703, Mismatches: 34, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
200 194 0.28
201 507 0.72
202 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (201 bp):
TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
TAAATATACCGGTTTTATGAGAGAATAGGTATACAACATGTATCGACACTTGTTTAATTTTGTGT
CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
AAAGTG
Found at i:377811 original size:401 final size:402
Alignment explanation
Indices: 377067--378006 Score: 1650
Period size: 401 Copynumber: 2.3 Consensus size: 402
377057 GGTAAAATTT
* *
377067 TCGATCCCATAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGATA
* * *
377132 TAAATATACCGGTTTTATGAGAGAATATGTCTACAACATGTATCGACACTTGTTTAATTTTGTAT
66 TAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
*
377197 CGATACTTTTAGTCCATAATGGATGCCAAAAAGGGTGAACACATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTAGTCCAGAATGGATGCCAAAAAGGGTGAACACATAAAGTGTCGATACATTTTCAA
*
377262 AAAGTGTCGATCTCAAAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAA
196 AAAGTGTCGATCCCAAAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAA
* * * *
377327 CCGGTATAAATATACCGGTTTTATGATAGAATATGTATACAACGTGTATCGACACTTGTTTAATT
261 CCGGTATAAATATACCGATTTTATGAGAGAATAGGTATACAACATGTATCGACACTTGTTTAATT
377392 TTGTGTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACAT
326 TTGTGTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACAT
377457 TTTCAAAAAGTG
391 TTTCAAAAAGTG
377469 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGATA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGATA
* *
377534 TAAATATACCAGTTTTATGAGGGAATAGGTATACAACATGTATCGACACTT-TTTAATTTTGTGT
66 TAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
* * * *
377598 CGATACTTTTGGTCCAGAATTGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATGCATTTTCAA
131 CGATACTTTTAGTCCAGAATGGATGCCAAAAAGGGTGAACACATAAAGTGTCGATACATTTTCAA
*
377663 AAAGTGTCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAA
196 AAAGTGTCGATCCCAAAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAA
377728 CCGGTATAAATATACCGATTTTATGAGAGAATAGGTATACAACATGTATCGACACTTGTTTAATT
261 CCGGTATAAATATACCGATTTTATGAGAGAATAGGTATACAACATGTATCGACACTTGTTTAATT
*
377793 TTGTGTCGATACTTTTGGTCCAGAATGGATGCTAAAAAGGGTGAACGCATAAAGTGTCGATACAT
326 TTGTGTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACAT
377858 TTTCAAAAAGTG
391 TTTCAAAAAGTG
* * *
377870 TCGATCCTAGAAACATATGCATCCATAAGTATAATGTAATATGCAAATTTACAATGTAACCGATA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGATA
*
377935 TAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGTATCGAAACTTGTTTAATTTTGTGG
66 TAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGT-G
378000 T-GATACT
130 TCGATACT
378007 AATTTAAATA
Statistics
Matches: 511, Mismatches: 25, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
401 382 0.75
402 127 0.25
403 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (402 bp):
TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGATA
TAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTGTTTAATTTTGTGT
CGATACTTTTAGTCCAGAATGGATGCCAAAAAGGGTGAACACATAAAGTGTCGATACATTTTCAA
AAAGTGTCGATCCCAAAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAA
CCGGTATAAATATACCGATTTTATGAGAGAATAGGTATACAACATGTATCGACACTTGTTTAATT
TTGTGTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACAT
TTTCAAAAAGTG
Found at i:379440 original size:18 final size:18
Alignment explanation
Indices: 379417--379468 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
379407 CAAGCGGTCA
379417 ATGAAGATGAAGATGACG
1 ATGAAGATGAAGATGACG
379435 ATGAAGATGACA-ATGACG
1 ATGAAGATGA-AGATGACG
* *
379453 ATGATGATGATGATGA
1 ATGAAGATGAAGATGA
379469 TCCAAACAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 29 0.97
19 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.31, T:0.21
Consensus pattern (18 bp):
ATGAAGATGAAGATGACG
Found at i:379469 original size:6 final size:6
Alignment explanation
Indices: 379417--379468 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
379407 CAAGCGGTCA
* * * *
379417 ATGAAG ATGAAG ATGACG ATGAAG ATGACA- ATGACG ATGATG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGA-AG ATGAAG ATGAAG ATGAAG
379465 ATGA
1 ATGA
379469 TCCAAACAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
6 39 0.98
7 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.31, T:0.21
Consensus pattern (6 bp):
ATGAAG
Found at i:379469 original size:12 final size:12
Alignment explanation
Indices: 379417--379468 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
379407 CAAGCGGTCA
*
379417 ATGAAGATGAAG
1 ATGACGATGAAG
379429 ATGACGATGAAG
1 ATGACGATGAAG
* *
379441 ATGACAATGACG
1 ATGACGATGAAG
* *
379453 ATGATGATGATG
1 ATGACGATGAAG
379465 ATGA
1 ATGA
379469 TCCAAACAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.42, C:0.06, G:0.31, T:0.21
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:381283 original size:20 final size:20
Alignment explanation
Indices: 381235--381283 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
381225 ATCGAAACCC
381235 ATAATTATAATGTAACAGGT
1 ATAATTATAATGTAACAGGT
*
381255 A-AATTTATAATGTAACCGGT
1 ATAA-TTATAATGTAACAGGT
*
381275 ATAAATATA
1 ATAATTATA
381284 CCGGTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.08
20 21 0.84
21 2 0.08
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
ATAATTATAATGTAACAGGT
Found at i:384116 original size:73 final size:73
Alignment explanation
Indices: 383947--384104 Score: 191
Period size: 73 Copynumber: 2.2 Consensus size: 73
383937 AACAGGTCAA
* * * * * *
383947 CATAATGTATCGACACTTG-TGTAATTTGTGTCGATACTTATTGTCCAGGATGAATGCACAAACG
1 CATAAAGTGTCGACACTTGAT-AAATTTGTGTCGATACTTATTGTCCAGAATGAATCCACAAAAG
384011 AGGTGCACG
65 AGGTGCACG
384020 CATAAAGTGTCGACACTTGATAAATTTGTGTCGATACTT-TTGGTCCAGAATGAATACCA-AAAA
1 CATAAAGTGTCGACACTTGATAAATTTGTGTCGATACTTATT-GTCCAGAATGAAT-CCACAAAA
384083 G-GGTGCAAC-
64 GAGGTGC-ACG
384092 CATAAAGTGTCGA
1 CATAAAGTGTCGA
384105 TACATTTATA
Statistics
Matches: 75, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
72 20 0.27
73 52 0.69
74 3 0.04
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28
Consensus pattern (73 bp):
CATAAAGTGTCGACACTTGATAAATTTGTGTCGATACTTATTGTCCAGAATGAATCCACAAAAGA
GGTGCACG
Found at i:384509 original size:64 final size:64
Alignment explanation
Indices: 384436--384563 Score: 186
Period size: 64 Copynumber: 2.0 Consensus size: 64
384426 ATAAGCGTTA
384436 CCTATTACATTATATAAGAACTAACTAATATGTTATTATACTTGATAATA-TTTCTGGTTAAATG
1 CCTATTACATTATATAAGAACTAACTAATATGTTATTATACTTGATAATATTTTC-GGTTAAATG
*** * * *
384500 CCTATTACATTATATAAGCGTTACCTAATATGTTTTTGTACTTGATAATATTTTCGGTTAAATG
1 CCTATTACATTATATAAGAACTAACTAATATGTTATTATACTTGATAATATTTTCGGTTAAATG
384564 ATATAACATT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
64 53 0.93
65 4 0.07
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (64 bp):
CCTATTACATTATATAAGAACTAACTAATATGTTATTATACTTGATAATATTTTCGGTTAAATG
Found at i:384661 original size:13 final size:13
Alignment explanation
Indices: 384643--384669 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
384633 TTTAACCGCC
384643 ATACAACAGAACT
1 ATACAACAGAACT
384656 ATACAACAGAACT
1 ATACAACAGAACT
384669 A
1 A
384670 CCCTAATAGC
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:0.56, C:0.22, G:0.07, T:0.15
Consensus pattern (13 bp):
ATACAACAGAACT
Found at i:386344 original size:2 final size:2
Alignment explanation
Indices: 386333--386432 Score: 71
Period size: 2 Copynumber: 56.0 Consensus size: 2
386323 GAACCCGAAA
* * *
386333 AT AT -T AT AT AT AT A- AT -T A- AT AT AA AA AT AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
386370 -T AT AT AT AT A- AT -T A- AT AT A- AA AT AT AT A- AA AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
386405 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
386433 CGGGTCGGGT
Statistics
Matches: 81, Mismatches: 5, Indels: 24
0.74 0.05 0.22
Matches are distributed among these distances:
1 12 0.15
2 69 0.85
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:386354 original size:9 final size:8
Alignment explanation
Indices: 386332--386423 Score: 53
Period size: 9 Copynumber: 10.8 Consensus size: 8
386322 CGAACCCGAA
*
386332 AATATTAT
1 AATATAAT
386340 ATATATAATT
1 A-ATATAA-T
*
386350 AATATAAA
1 AATATAAT
386358 AATATAA-
1 AATATAAT
*
386365 AATATTAT
1 AATATAAT
386373 ATATATAATT
1 A-ATATAA-T
386383 AATATAA-
1 AATATAAT
*
386390 AATATATAA
1 AATATA-AT
*
386399 AATATTAT
1 AATATAAT
386407 ATATATATAT
1 A-ATATA-AT
386417 ATATATA
1 A-ATATA
386424 TATATATATC
Statistics
Matches: 68, Mismatches: 7, Indels: 16
0.75 0.08 0.18
Matches are distributed among these distances:
7 12 0.18
8 12 0.18
9 31 0.46
10 13 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
AATATAAT
Found at i:386412 original size:18 final size:17
Alignment explanation
Indices: 386330--386431 Score: 90
Period size: 18 Copynumber: 6.1 Consensus size: 17
386320 CCCGAACCCG
386330 AAAATAT-TATATATAT
1 AAAATATATATATATAT
*
386346 AATTAATATA-A-AAATAT
1 AA--AATATATATATATAT
386363 AAAATAT-TATATATAT
1 AAAATATATATATATAT
*
386379 AATTAATATA-AAATATAT
1 AA--AATATATATATATAT
386397 AAAATAT-TATATATAT
1 AAAATATATATATATAT
*
386413 ATATATATATATATATAT
1 A-AAATATATATATATAT
386431 A
1 A
386432 TCGGGTCGGG
Statistics
Matches: 70, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
15 6 0.09
16 22 0.31
17 12 0.17
18 30 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATATATATATATAT
Found at i:386421 original size:33 final size:34
Alignment explanation
Indices: 386330--386413 Score: 161
Period size: 33 Copynumber: 2.5 Consensus size: 34
386320 CCCGAACCCG
386330 AAAATATTATATATATAATTAATATAAAA-ATAT
1 AAAATATTATATATATAATTAATATAAAATATAT
386363 AAAATATTATATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAATATAT
386397 AAAATATTATATATATA
1 AAAATATTATATATATA
386414 TATATATATA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 29 0.58
34 21 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAATATAT
Found at i:388365 original size:56 final size:56
Alignment explanation
Indices: 388312--388430 Score: 143
Period size: 57 Copynumber: 2.1 Consensus size: 56
388302 TTCATGCATC
* *
388312 GATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTT
1 GATGCACCA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCACTT
* * * *
388369 GATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTT
1 GATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCACTT
388425 GATGCA
1 GATGCA
388431 TCGATGCACT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
56 22 0.41
57 27 0.50
58 5 0.09
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (56 bp):
GATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCACTT
Found at i:388384 original size:57 final size:56
Alignment explanation
Indices: 388322--388430 Score: 148
Period size: 56 Copynumber: 1.9 Consensus size: 56
388312 GATGCACATA
* *
388322 CCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGCACCAG
1 CCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCACTTGATGCACCAG
* * *
388379 CCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCA
1 CCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATGCA
388431 TCGATGCACT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
56 22 0.48
57 21 0.46
58 3 0.07
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (56 bp):
CCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATGCACCAG
Found at i:394131 original size:24 final size:24
Alignment explanation
Indices: 394104--394188 Score: 161
Period size: 24 Copynumber: 3.5 Consensus size: 24
394094 ACACTTAACA
*
394104 GTGCACCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
394128 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
394152 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
394176 GTGCATCGATGCA
1 GTGCATCGATGCA
394189 CATGGTCATG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:396261 original size:57 final size:56
Alignment explanation
Indices: 396190--396308 Score: 152
Period size: 57 Copynumber: 2.1 Consensus size: 56
396180 TTCATGCATC
*
396190 GATGCACATACCATGCACCGATGCACTGAGAAT-TTTATGAAAACATCGAATGCATTT
1 GATGCACATACCATGCACCGATGCACTCAGAATATTT-TG-AAACATCGAATGCATTT
* * **
396247 GATGCACCA-ACCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTT
1 GATGCA-CATACCATGCACCGATGCACTCAGAATATTTTGAAACATCGAATGCATTT
396303 GATGCA
1 GATGCA
396309 TCGATGCACT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
56 23 0.42
57 27 0.49
58 5 0.09
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (56 bp):
GATGCACATACCATGCACCGATGCACTCAGAATATTTTGAAACATCGAATGCATTT
Found at i:396888 original size:12 final size:12
Alignment explanation
Indices: 396866--396915 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
396856 GGTCCGACCC
*
396866 GACCCGGCCGTT
1 GACCCGACCGTT
*
396878 GACCCAACCGTT
1 GACCCGACCGTT
*
396890 GACCCGACC--C
1 GACCCGACCGTT
396900 GACCCGACCGTT
1 GACCCGACCGTT
396912 GACC
1 GACC
396916 GGTGATATTC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 9 0.29
12 22 0.71
ACGTcount: A:0.18, C:0.46, G:0.24, T:0.12
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:396977 original size:29 final size:29
Alignment explanation
Indices: 396916--396982 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
396906 ACCGTTGACC
* ** *
396916 GGTGATATTCTGGGAATTAATTCGATTTT
1 GGTGATATTCTGAGAATTAATTCGAAATG
*
396945 GGTGTTATTCTGAGAATTAATTCGAAATG
1 GGTGATATTCTGAGAATTAATTCGAAATG
*
396974 GGTGCTATT
1 GGTGATATT
396983 TTGGTAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.42
Consensus pattern (29 bp):
GGTGATATTCTGAGAATTAATTCGAAATG
Found at i:397040 original size:28 final size:28
Alignment explanation
Indices: 396999--397097 Score: 101
Period size: 29 Copynumber: 3.5 Consensus size: 28
396989 AATTTTTTGG
*
396999 GAAAAG-TGATATTTTGGGAATTAATTT
1 GAAAAGATGCTATTTTGGGAATTAATTT
* *
397026 GAAATGATGCTATTTTGGGAATTAATTCA
1 GAAAAGATGCTATTTTGGGAATTAATT-T
* * * *
397055 AAAAAGGTGCTATTTTGGTAATTAGTTT
1 GAAAAGATGCTATTTTGGGAATTAATTT
*
397083 GAAAAGGGTGCTATT
1 GAAAA-GATGCTATT
397098 ATTGTTATTA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
27 5 0.08
28 23 0.39
29 31 0.53
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.38
Consensus pattern (28 bp):
GAAAAGATGCTATTTTGGGAATTAATTT
Found at i:397069 original size:86 final size:87
Alignment explanation
Indices: 396917--397075 Score: 212
Period size: 86 Copynumber: 1.8 Consensus size: 87
396907 CCGTTGACCG
** * * * **
396917 GTGATATTCTGGGAATTAATTCGATTTTGGTGTTATTCTGAGAATTAATTCGAAATGGGTGCTAT
1 GTGATATTCTGGGAATTAATTCGATAATGATGCTATTCTGAGAATTAATTCAAAAAAGGTGCTAT
396982 TTTGGTAAATTTTTTGGGAAAA
66 TTTGGTAAATTTTTTGGGAAAA
* * * *
397004 GTGATATTTTGGGAATTAATTTGA-AATGATGCTATTTTGGGAATTAATTCAAAAAAGGTGCTAT
1 GTGATATTCTGGGAATTAATTCGATAATGATGCTATTCTGAGAATTAATTCAAAAAAGGTGCTAT
397068 TTTGGTAA
66 TTTGGTAA
397076 TTAGTTTGAA
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
86 39 0.64
87 22 0.36
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (87 bp):
GTGATATTCTGGGAATTAATTCGATAATGATGCTATTCTGAGAATTAATTCAAAAAAGGTGCTAT
TTTGGTAAATTTTTTGGGAAAA
Found at i:397107 original size:29 final size:29
Alignment explanation
Indices: 397033--397127 Score: 102
Period size: 29 Copynumber: 3.3 Consensus size: 29
397023 TTTGAAATGA
* * * *
397033 TGCTATTTTGGGAATTAATTCAAAAAAGG
1 TGCTATTTTGGTAATTAGTTTAAAAAGGG
*
397062 TGCTATTTTGGTAATTAGTTTGAAAAGGG
1 TGCTATTTTGGTAATTAGTTTAAAAAGGG
* *
397091 TGCTATTATT-GTTATTATTTTAAAAAGGG
1 TGCTATT-TTGGTAATTAGTTTAAAAAGGG
*
397120 TACTATTT
1 TGCTATTT
397128 ATGTAAAATG
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
28 1 0.02
29 53 0.95
30 2 0.04
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (29 bp):
TGCTATTTTGGTAATTAGTTTAAAAAGGG
Found at i:398608 original size:14 final size:14
Alignment explanation
Indices: 398574--398612 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
398564 TTGATTGTTT
398574 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
398588 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
398602 TGTTGATTTGT
1 AATTGATTTGT
398613 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:398832 original size:20 final size:20
Alignment explanation
Indices: 398778--398864 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 20
398768 GAAAATCGCA
*
398778 GCGATAACCATTTTCGCGTT
1 GCGATAGCCATTTTCGCGTT
*** **
398798 GCGATTTTTCA-TTTCGAATT
1 GCGA-TAGCCATTTTCGCGTT
*
398818 GCGATAGCCATTTTCGCGTG
1 GCGATAGCCATTTTCGCGTT
398838 GCGATAGCCATTTTCGCGTT
1 GCGATAGCCATTTTCGCGTT
398858 GCGATAG
1 GCGATAG
398865 TCAAATGAAT
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 3 0.06
20 47 0.89
21 3 0.06
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (20 bp):
GCGATAGCCATTTTCGCGTT
Found at i:399182 original size:20 final size:21
Alignment explanation
Indices: 399138--399189 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
399128 ATAGTCAGTA
*
399138 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
399159 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
399179 TCGCATTGCGA
1 TCGCATTGCGA
399190 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:399994 original size:24 final size:24
Alignment explanation
Indices: 399967--400020 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
399957 GTATTCGAAA
*
399967 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
399991 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
400015 TTTGAT
1 TTTGAT
400021 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:402572 original size:91 final size:90
Alignment explanation
Indices: 402397--402581 Score: 300
Period size: 91 Copynumber: 2.0 Consensus size: 90
402387 ATTTCAAACT
*
402397 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
402462 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
402490 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
402554 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
402581 T
1 T
402582 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 42 0.48
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:404299 original size:20 final size:19
Alignment explanation
Indices: 404269--404322 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 19
404259 CTTTTGATTA
404269 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGAG
* *
404288 ATAATGAGAATCGCAACGCG
1 A-AATGAAAATCGCAACGAG
404308 AAATGAAAATCGCAA
1 AAATGAAAATCGCAA
404323 TGCGATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (19 bp):
AAATGAAAATCGCAACGAG
Found at i:404318 original size:19 final size:19
Alignment explanation
Indices: 404269--404327 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
404259 CTTTTGATTA
*
404269 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
*
404288 ATAATGAGAATCGCAACGCG
1 A-AATGAAAATCGCAACGCG
*
404308 AAATGAAAATCGCAATGCG
1 AAATGAAAATCGCAACGCG
404327 A
1 A
404328 TTTTGGTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:404356 original size:19 final size:19
Alignment explanation
Indices: 404323--404367 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
404313 AAAATCGCAA
*
404323 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
404342 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
404361 TGCGATT
1 TGCGATT
404368 CTCTCGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:404951 original size:20 final size:20
Alignment explanation
Indices: 404910--404980 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
404900 GCTATGTAAA
* *
404910 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
404930 TCGCATTGCGATTTAC-TAAT
1 TCGCATTGCGATTTACGT-AT
*
404950 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
404970 TCGCATTGCGA
1 TCGCATTGCGA
404981 ATTATGAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
19 2 0.05
20 41 0.93
21 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:405013 original size:20 final size:20
Alignment explanation
Indices: 404988--405043 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
404978 CGAATTATGA
404988 AAATCGCAACGCGAATACGT
1 AAATCGCAACGCGAATACGT
405008 AAATCGCAACGCGAATACGT
1 AAATCGCAACGCGAATACGT
*
405028 AAATCGCAATGCGAAT
1 AAATCGCAACGCGAAT
405044 TAGGAAAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
AAATCGCAACGCGAATACGT
Found at i:405061 original size:21 final size:20
Alignment explanation
Indices: 404970--405062 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
404960 ATTTACGTAT
* *
404970 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAA-TACGAAAA
* *
404991 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGAAAA
* *
405011 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGAAAA
*
405031 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGAAAA
*
405052 TCGCATTGCGA
1 TCGCAATGCGA
405063 TAGTCAGTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 37 0.59
21 26 0.41
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGAAAA
Found at i:405080 original size:20 final size:20
Alignment explanation
Indices: 405051--405124 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
405041 AATTAGGAAA
405051 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* ** *
405071 ATCCCATTGCGATTTTCCA-A
1 ATCGCATTGCGATAGT-CAGT
405091 ATTCGCATTGCGATAGTCAGT
1 A-TCGCATTGCGATAGTCAGT
405112 ATCGCATTGCGAT
1 ATCGCATTGCGAT
405125 TTTCCAAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:405082 original size:41 final size:41
Alignment explanation
Indices: 405037--405145 Score: 137
Period size: 41 Copynumber: 2.7 Consensus size: 41
405027 TAAATCGCAA
**
405037 TGCGAATTAGGAAAATCGCATTGCGATAGTCAGTATCCCAT
1 TGCGAATTACCAAAATCGCATTGCGATAGTCAGTATCCCAT
* * * *
405078 TGCGATTTTCCAAATTCGCATTGCGATAGTCAGTATCGCAT
1 TGCGAATTACCAAAATCGCATTGCGATAGTCAGTATCCCAT
* * *
405119 TGCGATTTTCCAAATTCGCATTGCGAT
1 TGCGAATTACCAAAATCGCATTGCGAT
405146 TTACTTATTC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (41 bp):
TGCGAATTACCAAAATCGCATTGCGATAGTCAGTATCCCAT
Found at i:405101 original size:21 final size:21
Alignment explanation
Indices: 405075--405147 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
405065 GTCAGTATCC
405075 CATTGCGATTTTCCAAATTCG
1 CATTGCGATTTTCCAAATTCG
** *
405096 CATTGCGATAGT-C-AGTATCG
1 CATTGCGATTTTCCAAAT-TCG
405116 CATTGCGATTTTCCAAATTCG
1 CATTGCGATTTTCCAAATTCG
405137 CATTGCGATTT
1 CATTGCGATTT
405148 ACTTATTCGT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.05
20 14 0.33
21 25 0.58
22 2 0.05
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
CATTGCGATTTTCCAAATTCG
Found at i:405699 original size:117 final size:117
Alignment explanation
Indices: 405487--405773 Score: 434
Period size: 117 Copynumber: 2.5 Consensus size: 117
405477 TATTTCAGGA
* * *
405487 TCCTTTGTTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAAC
1 TCCTTTGCTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGAGGAAC
* * * *
405552 CTACACATTGTAGTGAGTGGAGTGATTGGATGGGGAAGTTATTACTGCAGAC
66 CTACACATTGTAGTGAGTGAAGCGACTGGATGGAGAAGTTATTACTGCAGAC
*
405604 TCCTTTGCTGTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGAGGAAC
1 TCCTTTGCTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGAGGAAC
* *
405669 CTACACATTGTAGTGA-TGAAAGCGACTGGATGGAGACGTTATTACTGCAGGC
66 CTACACATTGTAGTGAGTG-AAGCGACTGGATGGAGAAGTTATTACTGCAGAC
**
405721 TCCTCAGCT-TCGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
1 TCCTTTGCTGT-GTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
405774 TTTCGGAAAA
Statistics
Matches: 155, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
116 3 0.02
117 152 0.98
ACGTcount: A:0.18, C:0.15, G:0.34, T:0.32
Consensus pattern (117 bp):
TCCTTTGCTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGAGGAAC
CTACACATTGTAGTGAGTGAAGCGACTGGATGGAGAAGTTATTACTGCAGAC
Found at i:407683 original size:36 final size:37
Alignment explanation
Indices: 407612--407683 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 37
407602 TATATTTTTT
*
407612 ATTTTGTAAAAAAAATTATATAAATATTATGAATTTA
1 ATTTTGTAAAAAAAATTATATAAATATTATCAATTTA
* *
407649 ATTTT-TAAAGAAAA-TATATAAATATTTTACAATTT
1 ATTTTGTAAAAAAAATTATATAAATATTAT-CAATTT
407684 GTAATATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 13 0.42
36 13 0.42
37 5 0.16
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.44
Consensus pattern (37 bp):
ATTTTGTAAAAAAAATTATATAAATATTATCAATTTA
Found at i:407865 original size:20 final size:20
Alignment explanation
Indices: 407829--407866 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
407819 ATCCTATTCC
**
407829 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
407849 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
407867 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:407928 original size:2 final size:2
Alignment explanation
Indices: 407907--408055 Score: 99
Period size: 2 Copynumber: 78.0 Consensus size: 2
407897 TATAACGTAG
* *
407907 TA TA -A TA TT TA TA T- TA TA TA TA CA -A TA GTA TA T- TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
*
407945 TA TA TA TA TA TA TA TA TA T- TA TA GTA TC TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* *
407986 AA CTA T- TA TA T- TA TA TA GTA TA TA TA T- TA TA TA TA GTG T-
1 TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA
*
408025 TA TA T- TA TG TA -A TA TA TA TA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
408056 GTAAATAGAA
Statistics
Matches: 118, Mismatches: 10, Indels: 38
0.71 0.06 0.23
Matches are distributed among these distances:
1 13 0.11
2 95 0.81
3 10 0.08
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:407985 original size:35 final size:34
Alignment explanation
Indices: 407907--408055 Score: 112
Period size: 33 Copynumber: 4.4 Consensus size: 34
407897 TATAACGTAG
* * **
407907 TATAATATTTATATTATATATACAATAGT-ATAT-
1 TATAATATATATACTAT-TATATTATAGTAATATA
* *
407940 TATAATATATATATATATATATATTATAGTATCTATA
1 TATAATATATATA-CTAT-TATATTATAGTA-ATATA
*
407977 TATAATATA-A-ACTATTATATTATA-TAGTATA
1 TATAATATATATACTATTATATTATAGTAATATA
* * *
408008 TATATTATATATAGTGTTATATTAT-GTAATATA
1 TATAATATATATACTATTATATTATAGTAATATA
408041 TATATATAGTATATA
1 TATA-ATA-TATATA
408056 GTAAATAGAA
Statistics
Matches: 95, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
31 12 0.13
32 3 0.03
33 42 0.44
34 18 0.19
35 7 0.07
36 4 0.04
37 9 0.09
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (34 bp):
TATAATATATATACTATTATATTATAGTAATATA
Found at i:408056 original size:35 final size:34
Alignment explanation
Indices: 407936--408196 Score: 75
Period size: 35 Copynumber: 7.5 Consensus size: 34
407926 ATACAATAGT
407936 ATATTATAATATATATATATATATATATTATAGTATCT
1 ATATTAT-ATA-ATATATATATATATA-TATAGTAT-T
407974 ATATATAATATAA-ACTAT-TATAT-TATATAGTATAT
1 ATAT-T-ATATAATA-TATATATATATATATAGTAT-T
* *
408009 ATATTATAT-ATAGTGTTATATTATGTAATATA-TATAT
1 ATATTATATAATA-T-ATATA-TATAT-ATATAGTAT-T
* * * * * *
408046 ATAGTATATAGTAAATAGA-ATCTACATAGTATAGT
1 ATATTATATAATATATATATATATATATAGTAT--T
** *
408081 ATATTATATGGTATAT-TATATATGGTAT--TATT
1 ATATTATATAATATATATATATAT-ATATAGTATT
* * *
408113 AT-TATAGTATAATATTTGGTCTATAT-TATAGTATAT
1 ATAT-TA-TATAATATAT-ATATATATATATAGTAT-T
* *
408149 ATAATATATAA-AAATA-AGTATTATATATAGTA-T
1 ATATTATATAATATATATA-TA-TATATATAGTATT
408182 ATATTAT-TAATATAT
1 ATATTATATAATATAT
408197 TTATTATGTT
Statistics
Matches: 168, Mismatches: 29, Indels: 57
0.66 0.11 0.22
Matches are distributed among these distances:
31 1 0.01
32 9 0.05
33 32 0.19
34 17 0.10
35 53 0.32
36 15 0.09
37 20 0.12
38 15 0.09
39 4 0.02
40 2 0.01
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (34 bp):
ATATTATATAATATATATATATATATATAGTATT
Found at i:408104 original size:14 final size:14
Alignment explanation
Indices: 408085--408123 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
408075 TATAGTATAT
408085 TATATGGTATATTA
1 TATATGGTATATTA
408099 TATATGGTATTATTA
1 TATATGGTA-TATTA
*
408114 T-TATAGTATA
1 TATATGGTATA
408124 ATATTTGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 2 0.09
14 15 0.65
15 6 0.26
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (14 bp):
TATATGGTATATTA
Found at i:408203 original size:3 final size:3
Alignment explanation
Indices: 408183--408260 Score: 63
Period size: 3 Copynumber: 26.3 Consensus size: 3
408173 ATATAGTATA
* * *
408183 TAT TAT TAA TA- TATT TAT TA- TGT TAT TAT TAT CAT TAT TAT TA-
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
408226 TAT TAC TAT TAT TGCT TAT TGT TAT TAT TAT TAT T
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT T
408261 TTTAGTTTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
2 5 0.08
3 50 0.85
4 4 0.07
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:408208 original size:20 final size:20
Alignment explanation
Indices: 408185--408223 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
408175 ATAGTATATA
408185 TTATTAATAT-ATTTATTATG
1 TTATTAATATCA-TTATTATG
*
408205 TTATTATTATCATTATTAT
1 TTATTAATATCATTATTAT
408224 TATATTACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
TTATTAATATCATTATTATG
Found at i:408235 original size:11 final size:11
Alignment explanation
Indices: 408167--408259 Score: 68
Period size: 11 Copynumber: 8.5 Consensus size: 11
408157 TAAAAATAAG
*
408167 TATTATATATAG
1 TATTATAT-TAT
408179 TA-TATATTAT
1 TATTATATTAT
*
408189 TAATATA-T-T
1 TATTATATTAT
*
408198 TATTATGTTAT
1 TATTATATTAT
408209 TATTATCATTAT
1 TATTAT-ATTAT
*
408221 TATTATATTAC
1 TATTATATTAT
**
408232 TATTAT-TGCT
1 TATTATATTAT
*
408242 TATTGTTATTAT
1 TATT-ATATTAT
408254 TATTAT
1 TATTAT
408260 TTTTAGTTTT
Statistics
Matches: 63, Mismatches: 12, Indels: 13
0.72 0.14 0.15
Matches are distributed among these distances:
9 6 0.10
10 11 0.17
11 28 0.44
12 18 0.29
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.59
Consensus pattern (11 bp):
TATTATATTAT
Found at i:413162 original size:9 final size:9
Alignment explanation
Indices: 413150--413183 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
413140 TAATATTTTG
413150 TATTTAATT
1 TATTTAATT
*
413159 TATTTAA-G
1 TATTTAATT
413167 TATTTAATT
1 TATTTAATT
413176 TATTTAAT
1 TATTTAAT
413184 ATTTTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:413189 original size:17 final size:17
Alignment explanation
Indices: 413149--413187 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
413139 TTAATATTTT
413149 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
413166 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
413183 -TATTT
1 GTATTT
413188 TACTTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:420578 original size:32 final size:32
Alignment explanation
Indices: 420542--420606 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
420532 CCGGTGGTAG
* * *
420542 CAACATCATTAGTCTTTTACTATCGGTGACAA
1 CAACATCATCAGTCTTTCACTACCGGTGACAA
* *
420574 CAACATCATCATTCTTTCACTGCCGGTGACAA
1 CAACATCATCAGTCTTTCACTACCGGTGACAA
420606 C
1 C
420607 GATTGGTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (32 bp):
CAACATCATCAGTCTTTCACTACCGGTGACAA
Found at i:422211 original size:48 final size:48
Alignment explanation
Indices: 422154--422248 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
422144 TCCTTCAAAG
422154 CTAATGTAAGGTACATAAATGCATGACAATGCTTACAATTGACATAAT
1 CTAATGTAAGGTACATAAATGCATGACAATGCTTACAATTGACATAAT
**
422202 CTAATGTAAGGTACATAAATGCATGTTAATGCTTACAATTGACATAA
1 CTAATGTAAGGTACATAAATGCATGACAATGCTTACAATTGACATAA
422249 AAAGGTTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (48 bp):
CTAATGTAAGGTACATAAATGCATGACAATGCTTACAATTGACATAAT
Found at i:429643 original size:2 final size:2
Alignment explanation
Indices: 429632--429666 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
429622 GACCTTTGGG
429632 TA TA -A 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
429667 ACTAAACGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:432430 original size:13 final size:14
Alignment explanation
Indices: 432412--432441 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
432402 ATCGTATAAA
432412 AATTATGTTAC-AG
1 AATTATGTTACAAG
432425 AATTATGTTACAAG
1 AATTATGTTACAAG
432439 AAT
1 AAT
432442 AAGACGTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (14 bp):
AATTATGTTACAAG
Found at i:439937 original size:88 final size:88
Alignment explanation
Indices: 439824--440094 Score: 445
Period size: 88 Copynumber: 3.1 Consensus size: 88
439814 CAAAATCACC
* *
439824 TGACTAGATCTCCTCATTATATAGGAGATGTGTCAACTTAGATAACCAGCCATCCCCATCAGAGT
1 TGACCAGATCTCCTCATTATGTAGGAGATGTGTCAACTTAGATAACCAGCCATCCCCATCAGAGT
*
439889 GGAACCGTGCTATCACCTTTAGA
66 GGAACCGTGTTATCACCTTTAGA
439912 TGACCAGATCTCCTCATTATGTAGGAGATGTGTCAACTTAGATAACCAGCCATCCCCATCAGAGT
1 TGACCAGATCTCCTCATTATGTAGGAGATGTGTCAACTTAGATAACCAGCCATCCCCATCAGAGT
439977 GGAACCGTGTTATCACCTTTAGA
66 GGAACCGTGTTATCACCTTTAGA
* * * * *
440000 TGACCAGATTTCCTCATTATGTAGGAGCTGTGTCAAATTAGATAACTAGCTATCCCCATCAGAGT
1 TGACCAGATCTCCTCATTATGTAGGAGATGTGTCAACTTAGATAACCAGCCATCCCCATCAGAGT
*
440065 GGAATCGTGTTATCACC-TTAGA
66 GGAACCGTGTTATCACCTTTAGA
*
440087 TGGCCAGA
1 TGACCAGA
440095 ACTTTTCATC
Statistics
Matches: 173, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
87 12 0.07
88 161 0.93
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (88 bp):
TGACCAGATCTCCTCATTATGTAGGAGATGTGTCAACTTAGATAACCAGCCATCCCCATCAGAGT
GGAACCGTGTTATCACCTTTAGA
Found at i:439960 original size:42 final size:42
Alignment explanation
Indices: 439829--439960 Score: 110
Period size: 42 Copynumber: 3.0 Consensus size: 42
439819 TCACCTGACT
*
439829 AGATCTCCTCATTATATAGGAGATGTGTCAACTTAGATAACC
1 AGATCTCCTCATTATGTAGGAGATGTGTCAACTTAGATAACC
* * * * *
439871 AGCCATC-CC-CATCAGAGT-GGA-ACCGTGCTATCACCTTTAGATGACC
1 AG--ATCTCCTCATTA-TGTAGGAGA---TG-TGTCAAC-TTAGATAACC
439917 AGATCTCCTCATTATGTAGGAGATGTGTCAACTTAGATAACC
1 AGATCTCCTCATTATGTAGGAGATGTGTCAACTTAGATAACC
439959 AG
1 AG
439961 CCATCCCCAT
Statistics
Matches: 67, Mismatches: 11, Indels: 24
0.66 0.11 0.24
Matches are distributed among these distances:
41 1 0.01
42 20 0.30
43 8 0.12
44 10 0.15
45 9 0.13
46 18 0.27
47 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (42 bp):
AGATCTCCTCATTATGTAGGAGATGTGTCAACTTAGATAACC
Found at i:440240 original size:127 final size:128
Alignment explanation
Indices: 440000--440417 Score: 362
Period size: 127 Copynumber: 3.3 Consensus size: 128
439990 CACCTTTAGA
* * * * ** * * *
440000 TGACCAGATTTCCTCATTATGTAGGAGCTGTGTCAA-ATTAGATAA-CTAGCTATCCCCATCAGA
1 TGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCCTAGATAACCAATC-ATCCCCAACAGA
* * * **
440063 GTGGAATCGTGTTATCA-CCTTAGATGGCCAGAACTTTTCATCAC-GTATGAGCCGTGTCATCAC
65 GTAGAACCATGTTATCACCCTTAGATGGCCAGAACTCATCA-CACAG-ATGAGCCGTGTCATCAC
440126 C
128 C
* * * **
440127 TGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAATCATCCCTATTAGAG
1 TGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCCTAGATAACCAATCATCCCCAACAGAG
* * *
440192 TAGAACCATGTTATCACCCTTAGATGGCCTAG-ACTCATGA-ACAGATGAGCAGTGTCATCACA
66 TAGAACCATGTTATCACCCTTAGATGGCC-AGAACTCATCACACAGATGAGCCGTGTCATCACC
* * * * * * * * * * *
440254 TGATCATATTTCCTCATTATGTAGGAGCTGTGTCAACCTTTGATAACCAGTCGTCCCCAACATAG
1 TGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCCTAGATAACCAATCATCCCCAACAGAG
* * * * *
440319 TGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACATATGAGCCGTGTCATCACC
66 TAGAACCATGTTATCACCCTTAGATGGCCAGAACTCATCA-CACAGATGAGCCGTGTCATCACC
* ** * *
440383 CGACTTGATCTCCTTATCACGTAGGAGTCGTGTCA
1 TGACCAGATCTCCTCATCACGTAGGAGCCGTGTCA
440418 GCTTTGGATA
Statistics
Matches: 228, Mismatches: 55, Indels: 14
0.77 0.19 0.05
Matches are distributed among these distances:
126 2 0.01
127 129 0.57
128 32 0.14
129 63 0.28
130 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (128 bp):
TGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCCTAGATAACCAATCATCCCCAACAGAG
TAGAACCATGTTATCACCCTTAGATGGCCAGAACTCATCACACAGATGAGCCGTGTCATCACC
Found at i:440428 original size:129 final size:126
Alignment explanation
Indices: 440051--440534 Score: 401
Period size: 127 Copynumber: 3.7 Consensus size: 126
440041 ATAACTAGCT
* * *
440051 ATCCCCATCAGAGTGGAATCGTGTTATCACCTTAGATGGCCAGAACTTTTCATCACGTATGAGCC
1 ATCCCCATCAGAGTGGAACCGTGTTATCACCTTAGATGGCCAGAACTCTTCATCACATATGAGCC
* * *
440116 GTGTCATCACCTGACCA-GACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAATC
66 GTGTCATCACCTGA-CATGATCTCCTCATCACGTAGGAG-CGTGTCA-CCTTTGATAACCAATC
* * * * * * *
440179 ATCCCTATTAGAGTAGAACCATGTTATCACCCTTAGATGGCCTAG-ACTCATGA--ACAGATGAG
1 ATCCCCATCAGAGTGGAACCGTGTTATCA-CCTTAGATGGCC-AGAACTCTTCATCACATATGAG
* * * * * *
440241 CAGTGTCATCACATGATCAT-ATTTCCTCATTATGTAGGAGCTGTGTCAACCTTTGATAACCAGT
64 CCGTGTCATCACCTGA-CATGATCTCCTCATCACGTAGGAGC-GTGTC-ACCTTTGATAACCAAT
440305 C
126 C
* * *
440306 GTCCCCAACATAGTGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACATATGAGC
1 ATCCCCATCAGAGTGGAACCGTGTTATCACC-TTAGATGGCCAGAACTCTTCATCACATATGAGC
* * * * *
440371 CGTGTCATCACCCGACTTGATCTCCTTATCACGTAGGAGTCGTGTCAGCTTTGGATAACCAA-A
65 CGTGTCATCACCTGACATGATCTCCTCATCACGTAGGAG-CGTGTCACCTTT-GATAACCAATC
** *
440434 ACTCTTCATCACGTA-T-GAGCCGTGTTATCACCCTTCCTAAAGATGGCCAAGAACTCTTCATCA
1 A-TCCCCATCA-G-AGTGGAACCGTGTTATCA-CC-T--T--AGATGGCC-AGAACTCTTCATCA
* * * *
440497 CATAGGAGCAGTGTCATCCCCTGAC-TAGATTTCCTCAT
56 CATATGAGCCGTGTCATCACCTGACAT-GATCTCCTCAT
440535 TATATAGGAA
Statistics
Matches: 281, Mismatches: 53, Indels: 37
0.76 0.14 0.10
Matches are distributed among these distances:
126 5 0.02
127 95 0.34
128 32 0.11
129 86 0.31
130 8 0.03
131 1 0.00
132 1 0.00
134 9 0.03
135 44 0.16
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (126 bp):
ATCCCCATCAGAGTGGAACCGTGTTATCACCTTAGATGGCCAGAACTCTTCATCACATATGAGCC
GTGTCATCACCTGACATGATCTCCTCATCACGTAGGAGCGTGTCACCTTTGATAACCAATC
Found at i:440572 original size:135 final size:134
Alignment explanation
Indices: 440340--440594 Score: 296
Period size: 135 Copynumber: 1.9 Consensus size: 134
440330 TATCACCTTT
* * * * *
440340 AGATGGCCAGAACTCTTCATCACATATGAGCCGTGTCATCACCCGACTTGATCTCCTTATCACGT
1 AGATGGCCAGAACTCTTCATCACATAGGAGCAGTGTCATCACCCGACTAGATCTCCTCATCACAT
* * * * * * * *
440405 AGGAGTCGTGTCAGCTTTGGATAACCAAAACTCTTCATCACGTATGAGCCGTGTTATCACCCTTC
66 AGGAATCGTGTCACCCTTAGACAACCAAAACTCTACATCAAGTATGAGCAGTGTTATCACCCTTC
440470 CTAA
131 CTAA
* * *
440474 AGATGGCCAAGAACTCTTCATCACATAGGAGCAGTGTCATC-CCCTGACTAGATTTCCTCATTAT
1 AGATGGCC-AGAACTCTTCATCACATAGGAGCAGTGTCATCACCC-GACTAGATCTCCTCATCAC
* * * **
440538 ATAGGAATTGTGTTACCCTTAGACGACCCGAACTCTACATCAAGTATGAGCAGTGTT
64 ATAGGAATCGTGTCACCCTTAGACAACCAAAACTCTACATCAAGTATGAGCAGTGTT
440595 GTCTTCCAAT
Statistics
Matches: 98, Mismatches: 21, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
134 11 0.11
135 87 0.89
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (134 bp):
AGATGGCCAGAACTCTTCATCACATAGGAGCAGTGTCATCACCCGACTAGATCTCCTCATCACAT
AGGAATCGTGTCACCCTTAGACAACCAAAACTCTACATCAAGTATGAGCAGTGTTATCACCCTTC
CTAA
Found at i:441501 original size:2 final size:2
Alignment explanation
Indices: 441490--441524 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
441480 GACCTTTGGG
441490 TA TA -A 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
441525 GCTAAATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:445785 original size:49 final size:49
Alignment explanation
Indices: 445732--445827 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 49
445722 TGAGAACATG
* *
445732 TAGAGACATTGGTAGAGGTACATAATGATTAAAATACCCATAAGTAGCA
1 TAGAGACATTGCTAGAGGTACAGAATGATTAAAATACCCATAAGTAGCA
* ** *
445781 TAGAGACCTTGCTAGAGGTAGGGAATGATTAAAATACCCTTAAGTAG
1 TAGAGACATTGCTAGAGGTACAGAATGATTAAAATACCCATAAGTAG
445828 AGAGTGACCA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (49 bp):
TAGAGACATTGCTAGAGGTACAGAATGATTAAAATACCCATAAGTAGCA
Found at i:449010 original size:3 final size:3
Alignment explanation
Indices: 449002--449059 Score: 91
Period size: 3 Copynumber: 19.3 Consensus size: 3
448992 ATGAGTATGA
449002 AAG AAG AAG -AG AAAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
449047 AAG AAG AAA AAG A
1 AAG AAG AAG AAG A
449060 GACAAAAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.92
4 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:454706 original size:20 final size:20
Alignment explanation
Indices: 454681--454718 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
454671 TAACGAATAA
*
454681 TATCGATACTGTTGCTATAG
1 TATCGATACTGTCGCTATAG
*
454701 TATCGATATTGTCGCTAT
1 TATCGATACTGTCGCTAT
454719 GGGGTGCACT
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:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (20 bp):
TATCGATACTGTCGCTATAG
Found at i:465364 original size:44 final size:45
Alignment explanation
Indices: 465243--465366 Score: 214
Period size: 45 Copynumber: 2.8 Consensus size: 45
465233 TTTAAAATTT
*
465243 CTTACTATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
465288 CTTACCATTTATCCCATAATCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
465333 CTTACCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
465367 GCATGCTTAC
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
44 25 0.33
45 50 0.67
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:465583 original size:61 final size:61
Alignment explanation
Indices: 465476--465590 Score: 178
Period size: 61 Copynumber: 1.9 Consensus size: 61
465466 GTAGTGCTAA
* *
465476 ACCTGCACTAAGCTTACGCCATAGTGCTAATCCGGACAATACACATAAGGTCGTGCCCACC
1 ACCTGCACTAAGCTCACGCCATAGTGCTAATCCAGACAATACACATAAGGTCGTGCCCACC
* *
465537 ACCTGCACTAAGCTCACGCTATAGTGCTAATCCAGAC-ATGATACATAAGGTCGT
1 ACCTGCACTAAGCTCACGCCATAGTGCTAATCCAGACAAT-ACACATAAGGTCGT
465591 ATCCACCTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
60 2 0.04
61 47 0.96
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (61 bp):
ACCTGCACTAAGCTCACGCCATAGTGCTAATCCAGACAATACACATAAGGTCGTGCCCACC
Found at i:469285 original size:20 final size:20
Alignment explanation
Indices: 469262--469314 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
469252 TTTCCATTAT
469262 TTTTCTTCTTTTTCTTTTTC
1 TTTTCTTCTTTTTCTTTTTC
469282 TTTTCTTC-TTTTCTTTTTC
1 TTTTCTTCTTTTTCTTTTTC
*
469301 TATTTATT-TTTTTC
1 T-TTTCTTCTTTTTC
469315 CTATTTTTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTCTTCTTTTTCTTTTTC
Found at i:469312 original size:19 final size:18
Alignment explanation
Indices: 469270--469312 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
469260 ATTTTTCTTC
*
469270 TTTTTCTTTTTCTTTTCT
1 TTTTTCTTTTTCTTTTAT
469288 TCTTTTCTTTTTCTATTTAT
1 T-TTTTCTTTTTCT-TTTAT
469308 TTTTT
1 TTTTT
469313 TCCTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 16 0.73
20 5 0.23
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTCTTTTTCTTTTAT
Found at i:472106 original size:44 final size:45
Alignment explanation
Indices: 471985--472108 Score: 214
Period size: 45 Copynumber: 2.8 Consensus size: 45
471975 TTTAAAATTT
*
471985 CTTACTATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
472030 CTTACCATTTATCCCATAATCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
472075 CTTACCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
472109 GCATGCTTAC
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
44 25 0.33
45 50 0.67
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:472339 original size:61 final size:61
Alignment explanation
Indices: 472221--472339 Score: 177
Period size: 61 Copynumber: 2.0 Consensus size: 61
472211 GTGCTAAACT
* *
472221 TGCACTAAGCTTACGCCATAGTGCTAATCCGGACAATACACATAAGGTCGTGCCCACCACC
1 TGCACTAAGCTCACGCCATAGTGCTAATCCGGACAATACACATAAGGTCGTACCCACCACC
* * *
472282 TGCACTAAGCTCACGCTATAGTGCTAATCCGGAC-ATGATACATAAGGTCGTATCCACC
1 TGCACTAAGCTCACGCCATAGTGCTAATCCGGACAAT-ACACATAAGGTCGTACCCACC
472340 TTTCCCGCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
60 2 0.04
61 50 0.96
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.22
Consensus pattern (61 bp):
TGCACTAAGCTCACGCCATAGTGCTAATCCGGACAATACACATAAGGTCGTACCCACCACC
Found at i:473368 original size:30 final size:31
Alignment explanation
Indices: 473327--473388 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
473317 TACAATCATT
* *
473327 CCCAACTTTTTCCAAAATTATAAATTGGTCC
1 CCCAACTTTTTCAAAAATTATAAAATGGTCC
473358 CCCAAC-TTTTCAAAAATTATAAAATGGTCC
1 CCCAACTTTTTCAAAAATTATAAAATGGTCC
473388 C
1 C
473389 TGAATTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (31 bp):
CCCAACTTTTTCAAAAATTATAAAATGGTCC
Found at i:480789 original size:20 final size:20
Alignment explanation
Indices: 480749--480790 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
480739 AATGCAAAAA
**
480749 AGAAAAAACACTATTTGAAT
1 AGAAAAAACACTATTCCAAT
*
480769 AGAAAAAATACTATTCCAAT
1 AGAAAAAACACTATTCCAAT
480789 AG
1 AG
480791 TGTAGAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.24
Consensus pattern (20 bp):
AGAAAAAACACTATTCCAAT
Found at i:482429 original size:15 final size:16
Alignment explanation
Indices: 482409--482441 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
482399 GTTTTCTTTA
482409 TTAAATTTAT-TTTCT
1 TTAAATTTATATTTCT
*
482424 TTAAATTTTTATTTCT
1 TTAAATTTATATTTCT
482440 TT
1 TT
482442 TTAATTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (16 bp):
TTAAATTTATATTTCT
Found at i:482444 original size:18 final size:18
Alignment explanation
Indices: 482401--482450 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
482391 AAAGGCTGGT
482401 TTTCTTTATTAAA--TTTA
1 TTTCTTT-TTAAATTTTTA
*
482418 TTT-TCTTTAAATTTTTA
1 TTTCTTTTTAAATTTTTA
482435 TTTCTTTTT-AATTTTT
1 TTTCTTTTTAAATTTTT
482451 GAAACAACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 5 0.18
16 2 0.07
17 17 0.61
18 4 0.14
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTCTTTTTAAATTTTTA
Found at i:485368 original size:15 final size:15
Alignment explanation
Indices: 485348--485396 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
485338 TTAAGGATTA
485348 AATCTTTGGATTTTT
1 AATCTTTGGATTTTT
* * *
485363 AATC-TTGTA-ATTA
1 AATCTTTGGATTTTT
485376 AATCTTTGGATTTTT
1 AATCTTTGGATTTTT
485391 AATCTT
1 AATCTT
485397 GTAAGAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
13 6 0.23
14 8 0.31
15 12 0.46
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (15 bp):
AATCTTTGGATTTTT
Found at i:485384 original size:28 final size:28
Alignment explanation
Indices: 485344--485400 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
485334 TGTTTTAAGG
485344 ATTAAATCTTTGGATTTTTAATCTTGTA
1 ATTAAATCTTTGGATTTTTAATCTTGTA
485372 ATTAAATCTTTGGATTTTTAATCTTGTA
1 ATTAAATCTTTGGATTTTTAATCTTGTA
485400 A
1 A
485401 GAAAATTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.53
Consensus pattern (28 bp):
ATTAAATCTTTGGATTTTTAATCTTGTA
Found at i:488115 original size:3 final size:3
Alignment explanation
Indices: 488107--488142 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
488097 CTACTTGGTC
488107 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
488143 CAACAACAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:498157 original size:18 final size:18
Alignment explanation
Indices: 498106--498158 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
498096 TGAATTAAAA
498106 CAATTAAAATTAAAGAAT
1 CAATTAAAATTAAAGAAT
* **
498124 CAA-TAAGCATGCAAGAAT
1 CAATTAA-AATTAAAGAAT
*
498142 GAATTAAAATTAAAGAA
1 CAATTAAAATTAAAGAA
498159 ATAGTAGGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.23
Consensus pattern (18 bp):
CAATTAAAATTAAAGAAT
Found at i:499706 original size:40 final size:40
Alignment explanation
Indices: 499634--499860 Score: 170
Period size: 42 Copynumber: 5.6 Consensus size: 40
499624 CTCTGAAATA
* * * * *
499634 TTGACCCAACTCCTT-TGCGATGGTTGACCCAAGGTGATG
1 TTGATCCAACTCCTTATGTGATGGATGAGCCAAGATGATG
* * * * *
499673 CTAATCCAACTCCTTATGTGATGGACGAGCCAAGGTGATA
1 TTGATCCAACTCCTTATGTGATGGATGAGCCAAGATGATG
* * * **
499713 ATGATCCAAATCCTTATGTGATGAATGAGTGAAATGATGATG
1 TTGATCCAACTCCTTATGTGATGGATGAG-CCAA-GATGATG
* * * * * *
499755 TTGATCCATCTTCTTATGTGATGGACGAGCAAAATTATAATG
1 TTGATCCAACTCCTTATGTGATGGATGAGC-CAA-GATGATG
* **
499797 TTGATCCAACTCCTTATGCGATGGATGAGCCAAGACCAGTG
1 TTGATCCAACTCCTTATGTGATGGATGAGCCAAGATGA-TG
499838 TT-ATTCCAACTCCTTATGTGATG
1 TTGA-TCCAACTCCTTATGTGATG
499861 AAATCAAGCT
Statistics
Matches: 147, Mismatches: 35, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
39 12 0.08
40 46 0.31
41 26 0.18
42 63 0.43
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (40 bp):
TTGATCCAACTCCTTATGTGATGGATGAGCCAAGATGATG
Found at i:500053 original size:117 final size:114
Alignment explanation
Indices: 499848--500100 Score: 364
Period size: 117 Copynumber: 2.2 Consensus size: 114
499838 TTATTCCAAC
* * *
499848 TCCTTATGTGATGAAATC-AAGCTAAGGTTGAACAAGTTCTCATTATGAACATCTTCTCCCTCAT
1 TCCTTCTGTGATGGAATCGAA-CCAAGGTTGAACAAGTTCTCATTATGAACATCTTCTCCCTCAT
*
499912 CGGATGGGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACA
65 CGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACA
* *
499962 TCCTTCTGTGATGGAATCGAACCAAGGTTGAACAAGTTTTTCTCGTTATGAACTTCTTCTCCCTC
1 TCCTTCTGTGATGGAATCGAACCAAGGTTGAACAAG---TTCTCATTATGAACATCTTCTCCCTC
* * * *
500027 ATCGGATGAGTTCTTCTCATTGTGAACTCTTCACTGGAAATGTTGATCCACC
63 ATCGGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACA
*
500079 TTCTTCTGTGATGGAATCGAAC
1 TCCTTCTGTGATGGAATCGAAC
500101 AAAGTGATAA
Statistics
Matches: 124, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
114 30 0.24
115 2 0.02
117 92 0.74
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.35
Consensus pattern (114 bp):
TCCTTCTGTGATGGAATCGAACCAAGGTTGAACAAGTTCTCATTATGAACATCTTCTCCCTCATC
GGATGAGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGATCCACA
Found at i:500371 original size:204 final size:203
Alignment explanation
Indices: 499962--500501 Score: 701
Period size: 204 Copynumber: 2.7 Consensus size: 203
499952 TTGATCCACA
* * * * * * * *
499962 TCCTTCTGTGATGGAATCGAACCAAGGTTGAACAAGTTTTTCTCGTTATGAACTTCTTCTCCCTC
1 TCCTTATGTGATGGAATCGAGCTAAGATTGAACAAGTTCTTCTCATTATGAATTTCTTCTCCCTT
* * *
500027 ATCGGATGAGTTCTTCTCATTGTGAACTCTTCACTGGAAATGTTGATCCACCTTC-TTCTGTGAT
66 ATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCCACC-TCATTCTGTGAT
* *
500091 GGAATCGAACAAAGTGATAATGCTAATCCAACTCCATATACGATAGATGAGACAAGTATTAGTGT
130 GGAATCAAACAAAGTGATAATGATAATCCAACTCCATATACGATAGATGAGACAAGTATTAGTGT
500156 TGTTCCAAC
195 TGTTCCAAC
*
500165 TCCTTATGTGATGGAATCGAGCTAAGTTTGAACAAGTTCTTCTCATTATGAATTTCTTCTCCCTT
1 TCCTTATGTGATGGAATCGAGCTAAGATTGAACAAGTTCTTCTCATTATGAATTTCTTCTCCCTT
* * * *
500230 ATCGGATTAGTTCTTCTCATTATGTACTCTCCCATTTGAAATGTTGATCCACCTCATTCTGTGGT
66 ATCGGATGAGTTCTTCTCATTATGAACTCT-CCATTGGAAATGTTGATCCACCTCATTCTGTGAT
* * * * * ** * *
500295 GGAATTAAAGAAAGTGATGATGATGATCCAAGTTTATATGCGATAGATGA-ACCAAGTATTGGTG
130 GGAATCAAACAAAGTGATAATGATAATCCAACTCCATATACGATAGATGAGA-CAAGTATTAGTG
*
500359 TTGTTTCAAC
194 TTGTTCCAAC
*
500369 TCCTTATGTGAAT-GAATCGAGCTAAGATTGAACAAGTTCTTCTCATTATGAATTTATTC-CCCT
1 TCCTTATGTG-ATGGAATCGAGCTAAGATTGAACAAGTTCTTCTCATTATGAATTTCTTCTCCC-
* * * *
500432 TTATCAGACGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGTTGATCCACCTTATTCTGTG
64 TTATCGGATGAGTTCTTCTCATTATGAACTC-TCCATTGGAAATGTTGATCCACCTCATTCTGTG
500497 ATGGA
128 ATGGA
500502 TTCGAACAGA
Statistics
Matches: 294, Mismatches: 37, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
203 90 0.31
204 201 0.68
205 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (203 bp):
TCCTTATGTGATGGAATCGAGCTAAGATTGAACAAGTTCTTCTCATTATGAATTTCTTCTCCCTT
ATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTGATCCACCTCATTCTGTGATG
GAATCAAACAAAGTGATAATGATAATCCAACTCCATATACGATAGATGAGACAAGTATTAGTGTT
GTTCCAAC
Found at i:503375 original size:18 final size:18
Alignment explanation
Indices: 503352--503390 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
503342 TGAAATGGTT
503352 GTTGCGCTATGTTTACTA
1 GTTGCGCTATGTTTACTA
503370 GTTGCGCTATGTTTACTA
1 GTTGCGCTATGTTTACTA
503388 GTT
1 GTT
503391 CCCAACCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (18 bp):
GTTGCGCTATGTTTACTA
Found at i:504085 original size:29 final size:27
Alignment explanation
Indices: 504030--504094 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
504020 TCTTGAAGTA
*
504030 TTTTTC-TTTCTTCTTTTTTACTTTTT
1 TTTTTCTTTTCTTCTTTTTTACTGTTT
504056 TGTTTTCTTTTCTCTCTTTTTTA-TGGTTT
1 T-TTTTCTTTTCT-TCTTTTTTACT-GTTT
*
504085 TTCTTCTTTT
1 TTTTTCTTTT
504095 TGTTATATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 1 0.03
27 5 0.15
28 14 0.42
29 13 0.39
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.77
Consensus pattern (27 bp):
TTTTTCTTTTCTTCTTTTTTACTGTTT
Found at i:507835 original size:18 final size:18
Alignment explanation
Indices: 507784--507836 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
507774 TGAATTAAAA
507784 CAATTAAAATTAAAGAAT
1 CAATTAAAATTAAAGAAT
* **
507802 CAA-TAAGCATGCAAGAAT
1 CAATTAA-AATTAAAGAAT
*
507820 GAATTAAAATTAAAGAA
1 CAATTAAAATTAAAGAA
507837 ATAAAATTAA
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.23
Consensus pattern (18 bp):
CAATTAAAATTAAAGAAT
Done.