Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008111.1 Hibiscus syriacus cultivar Beakdansim tig00110647_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: 1666726
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 64 characters in sequence are not A, C, G, or T
File 2 of 9
Found at i:233404 original size:23 final size:22
Alignment explanation
Indices: 233358--233432 Score: 82
Period size: 23 Copynumber: 3.4 Consensus size: 22
233348 CACCGAAGTG
233358 CCACATA--TTTGTCCCGAATGA
1 CCACATAGTTTTGTCCCGAA-GA
* *
233379 CCACATATTTTTTTCCCGAAGAA
1 CCACATAGTTTTGTCCCGAAG-A
*
233402 CCACATAGTTTTGCCCCGAAGGA
1 CCACATAGTTTTGTCCCGAA-GA
233425 CCACATAG
1 CCACATAG
233433 AACCCTCGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.15
22 1 0.02
23 37 0.80
24 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (22 bp):
CCACATAGTTTTGTCCCGAAGA
Found at i:237100 original size:147 final size:147
Alignment explanation
Indices: 236833--237121 Score: 497
Period size: 147 Copynumber: 2.0 Consensus size: 147
236823 TATGGTTTGG
* * *
236833 GTATAGTTCTGAGAGTATAAAGTTACATTGATCCATTAGTGATAGAGTTTTTTGAGAACCTAGGG
1 GTATAGTTCTGAGAGTATAAAGTTACATTGATCAAGTAGTGATAGAGTTTTATGAGAACCTAGGG
* *
236898 AAAGGCACGAATCCTGCACCAGCAATTTTGGAAGAGACATATCGTTCCTTGAGTTATTATCAATA
66 AAAGGCACGAATCCTGCACCAGCAATTTTGGAAGAGACATATAGTTCCTTGAGTTATTATCAACA
236963 ATCAATGGGAGTTTAGT
131 ATCAATGGGAGTTTAGT
* *
236980 GTATATTTCTGAGAGTATAAGGTTACATTGATCAAGTAGTGATAGAGTTTTATGAGAACCTAGGG
1 GTATAGTTCTGAGAGTATAAAGTTACATTGATCAAGTAGTGATAGAGTTTTATGAGAACCTAGGG
* *
237045 AAAGGCACGAATCTTGCACCAGCAATTTTGGCAGAGACATATAGTTCCTTGAGTTATTATCAACA
66 AAAGGCACGAATCCTGCACCAGCAATTTTGGAAGAGACATATAGTTCCTTGAGTTATTATCAACA
237110 ATCAATGGGAGT
131 ATCAATGGGAGT
237122 CGATTTTCGG
Statistics
Matches: 133, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
147 133 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (147 bp):
GTATAGTTCTGAGAGTATAAAGTTACATTGATCAAGTAGTGATAGAGTTTTATGAGAACCTAGGG
AAAGGCACGAATCCTGCACCAGCAATTTTGGAAGAGACATATAGTTCCTTGAGTTATTATCAACA
ATCAATGGGAGTTTAGT
Found at i:238578 original size:5 final size:5
Alignment explanation
Indices: 238568--238617 Score: 93
Period size: 5 Copynumber: 10.2 Consensus size: 5
238558 ATTGTATACA
238568 TGCAT TGCAT TGCAT TGCAT TGCAT TGCAT TGCAT TGCAT TGCAT T-CAT
1 TGCAT TGCAT TGCAT TGCAT TGCAT TGCAT TGCAT TGCAT TGCAT TGCAT
238617 T
1 T
238618 TTATCTTCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.09
5 41 0.91
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (5 bp):
TGCAT
Found at i:241516 original size:86 final size:88
Alignment explanation
Indices: 241383--241545 Score: 206
Period size: 86 Copynumber: 1.9 Consensus size: 88
241373 GCTAAAGTTC
*
241383 GCGGCGTTTGGTAACAAAAAACGCCGCAATAGGTAACGATATATAGCGGCATTTGTTGG-ACAAA
1 GCGGCGTTTGGTAACAAAAAACACCGCAATAGGTAACGATATATAGCGGCATTT-TTGGAACAAA
*
241447 CGCCGCAATAGGTGTTGATATTTA
65 CGCCGCAACAGGTGTTGATATTTA
* * *** * **
241471 GCGGCGTTT-G-ACCAACAAACACCGCAATAGGTGTTGATATTTAGCGGTGTTTTTGGAACAAAC
1 GCGGCGTTTGGTAACAAAAAACACCGCAATAGGTAACGATATATAGCGGCATTTTTGGAACAAAC
241534 GCCGCAACAGGT
66 GCCGCAACAGGT
241546 CAGATCTATA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
85 4 0.06
86 50 0.78
87 1 0.02
88 9 0.14
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (88 bp):
GCGGCGTTTGGTAACAAAAAACACCGCAATAGGTAACGATATATAGCGGCATTTTTGGAACAAAC
GCCGCAACAGGTGTTGATATTTA
Found at i:241623 original size:84 final size:85
Alignment explanation
Indices: 241512--241711 Score: 287
Period size: 84 Copynumber: 2.4 Consensus size: 85
241502 TGTTGATATT
* * *
241512 TAGCGGTGTTTTTGGAACAAACGCCGCAACA-GGTCAGATCTATAGTGGCGTTTTTGGA-ACAAA
1 TAGCGGCGTTTTTGGAACAAACACCGCAA-ATGGTCAGATCTATAGCGGCGTTTTTGGATACAAA
*
241575 CGCCGCAAAAGGTCAGATCTA
65 CGCCGCAAAAGCTCAGATCTA
* *
241596 TAGCGGCGTTTTTGGAATAAACACCGCAAATGGTCATATCTATAGCGGCGTTTTTGGATACAAAC
1 TAGCGGCGTTTTTGGAACAAACACCGCAAATGGTCAGATCTATAGCGGCGTTTTTGGATACAAAC
*
241661 GCCGCAAAAGCTCATATCTA
66 GCCGCAAAAGCTCAGATCTA
* *
241681 TAGCGGCGTTTTTTGATACAAACGCCGCAAA
1 TAGCGGCGTTTTTGGA-ACAAACACCGCAAA
241712 AAAGCTCATT
Statistics
Matches: 103, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
83 1 0.01
84 51 0.50
85 39 0.38
86 12 0.12
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (85 bp):
TAGCGGCGTTTTTGGAACAAACACCGCAAATGGTCAGATCTATAGCGGCGTTTTTGGATACAAAC
GCCGCAAAAGCTCAGATCTA
Found at i:241711 original size:43 final size:42
Alignment explanation
Indices: 241401--241712 Score: 302
Period size: 43 Copynumber: 7.3 Consensus size: 42
241391 TGGTAACAAA
* * * *
241401 AAACGCCGCAATAGGTAACGATATATAGCGGCATTTGTTGG-AC
1 AAACGCCGCAAAAGGTCA-GATCTATAGCGGCGTTT-TTGGAAC
* ** * * ****
241444 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGACCAAC
1 AAACGCCGCAAAAGGT-CAGATCTATAGCGGCGTTTTTGGAAC
* * ** * * *
241487 AAACACCGCAATAGGTGTTGATATTTAGCGGTGTTTTTGGAAC
1 AAACGCCGCAAAAGGT-CAGATCTATAGCGGCGTTTTTGGAAC
* *
241530 AAACGCCGCAACAGGTCAGATCTATAGTGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
*
241572 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAT
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
* * *
241614 AAACACCGCAAATGGTCATATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
* * *
241657 AAACGCCGCAAAAGCTCATATCTATAGCGGCGTTTTTTGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
241700 AAACGCCGCAAAA
1 AAACGCCGCAAAA
241713 AAGCTCATTA
Statistics
Matches: 233, Mismatches: 33, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
42 96 0.41
43 137 0.59
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
Found at i:244789 original size:17 final size:17
Alignment explanation
Indices: 244769--244815 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
244759 TTAATTAATT
*
244769 TTATGAAGCAATTGGGA
1 TTATGAAGCAAATGGGA
244786 TTATGAAGCAAATGGGA
1 TTATGAAGCAAATGGGA
244803 TTATGAAGCAAAT
1 TTATGAAGCAAAT
244816 TGATTGTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.40, C:0.06, G:0.26, T:0.28
Consensus pattern (17 bp):
TTATGAAGCAAATGGGA
Found at i:245308 original size:43 final size:44
Alignment explanation
Indices: 245241--245326 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 44
245231 CGAGTCTATT
245241 ACAAACGCCACTAAAATACAAGTCTTTAGCGGCGTT-TATAAAC
1 ACAAACGCCACTAAAATACAAGTCTTTAGCGGCGTTGTATAAAC
* * *
245284 ACAAACGCCATTAAAGTACGAGTCTTTAGCGGCGTTGTATAAA
1 ACAAACGCCACTAAAATACAAGTCTTTAGCGGCGTTGTATAAA
245327 AGCCACTAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 33 0.85
44 6 0.15
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.24
Consensus pattern (44 bp):
ACAAACGCCACTAAAATACAAGTCTTTAGCGGCGTTGTATAAAC
Found at i:245396 original size:41 final size:38
Alignment explanation
Indices: 245296--245396 Score: 109
Period size: 37 Copynumber: 2.6 Consensus size: 38
245286 AAACGCCATT
*
245296 AAAGTACGAGTCTTTAGCGGCG-TTGTATAAAAGCCAC
1 AAAGTACGAGTCTATAGCGGCGTTTGTATAAAAGCCAC
* * *
245333 TAAGTACGAGTCTGTAGC-GCGTTTGTATAAAAAACGTCAC
1 AAAGTACGAGTCTATAGCGGCGTTTGTAT--AAAA-GCCAC
245373 AAAAGTACGAGTCTAT-GCGGCGTT
1 -AAAGTACGAGTCTATAGCGGCGTT
245397 GTGTCTAGCG
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
36 3 0.06
37 22 0.42
39 4 0.08
40 6 0.11
41 18 0.34
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (38 bp):
AAAGTACGAGTCTATAGCGGCGTTTGTATAAAAGCCAC
Found at i:245486 original size:40 final size:40
Alignment explanation
Indices: 245437--245571 Score: 135
Period size: 41 Copynumber: 3.3 Consensus size: 40
245427 GTTTGTCTAA
* *
245437 AAACGCCACTAAAGTATAGTCTTTAGCGGCGTTTTTATAC
1 AAACGCCACTAAAGTACAATCTTTAGCGGCGTTTTTATAC
* * * * * *
245477 AAACTCCACTAAAGTACATTCTTTGGTGGCATTTTTTTTAC
1 AAACGCCACTAAAGTACAATCTTTAGCGGC-GTTTTTATAC
* * * * *
245518 AAATGCCGCTAATGTACAATCTTTAGCGGCGTTTATTCTAA
1 AAACGCCACTAAAGTACAATCTTTAGCGGCGTTT-TTATAC
245559 AAACGCCACTAAA
1 AAACGCCACTAAA
245572 AATGCCGTTA
Statistics
Matches: 73, Mismatches: 20, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
40 28 0.38
41 45 0.62
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (40 bp):
AAACGCCACTAAAGTACAATCTTTAGCGGCGTTTTTATAC
Found at i:246003 original size:118 final size:116
Alignment explanation
Indices: 245692--246294 Score: 617
Period size: 117 Copynumber: 5.1 Consensus size: 116
245682 TTTCAGCAAG
* * * * *
245692 GAGTTCACAATGAGAAGAACTCATTCA-ATAGGGGCGAAAAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCCACA-AAGGGAGAAGAAGTTCATAATGAGAAGAACTTG-T
* * *
245756 TCAA-CTTATGCTCAAATCCATCATAAAATGAGGCGGATTAACATTTCAATAAA
64 TCAACCTTATGCTCAAATCCATCATAAAAGGAGGTGGATTAACATTTCAAT-GA
* * * *
245809 CAGTTTATAATGAGAAAAACTCATTCA-ATAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCCACA-AAGGGAGAAGAAGTTCATAATGAGAAGAACTTG-T
*
245873 TC-ACCTTATGCTCAAATCCATCATAAAAGGATGTGGATTAACATTTCCAATGGA
64 TCAACCTTATGCTCAAATCCATCATAAAAGGAGGTGGATTAACATTT-CAAT-GA
* *
245927 GAGTTCATAATGAGAAGAACTCATCCACAGAGGGAGAATAAGTTCATAATGAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCCACAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * *
245992 AACATTTTGCTCAAATCCATCATAGAAGGAGATAGATTAACATTTCAATGA
66 AACCTTATGCTCAAATCCATCATAAAAGGAGGTGGATTAACATTTCAATGA
* * * * * * *
246043 GGAGTTCATAATGAGAATAACTCGTCCACAAAGAGAAAAGAAGTTCACAATGAGAAGCACTTGAT
1 -GAGTTCATAATGAGAAGAACTCATCCACAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * *
246108 CGACCTT-TCGCTCAAATCCATTATAGAAGGAGGTGGACTAACATTTCAATTGA
65 CAACCTTAT-GCTCAAATCCATCATAAAAGGAGGTGGATTAACATTTCAA-TGA
* * * * * * ** **
246161 GGAGTTCATACTAAGAGGGATTCATCTACGGAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 -GAGTTCATAATGAGAAGAACTCATCCACAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
** * * *
246226 CAACCTTATATTTAAATCCATCACAGAAA-GAGGTGGA-TCACATTCTCAATGA
65 CAACCTTATGCTCAAATCCATCATA-AAAGGAGGTGGATTAACATT-TCAATGA
246278 GAAGTTCATAATGAGAA
1 G-AGTTCATAATGAGAA
246295 AAACGTTTTC
Statistics
Matches: 410, Mismatches: 65, Indels: 22
0.82 0.13 0.04
Matches are distributed among these distances:
116 5 0.01
117 222 0.54
118 179 0.44
119 4 0.01
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (116 bp):
GAGTTCATAATGAGAAGAACTCATCCACAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTATGCTCAAATCCATCATAAAAGGAGGTGGATTAACATTTCAATGA
Found at i:246123 original size:235 final size:234
Alignment explanation
Indices: 245690--246298 Score: 694
Period size: 235 Copynumber: 2.6 Consensus size: 234
245680 CATTTCAGCA
* * * *
245690 AGGAGTTCACAATGAGAAGAACTCATTCA-ATAGGGGCGAAAAAGTTCATAATGAGAAGAACTTG
1 AGGAGTTCATAATGAGAAGAACTCATCCACAGA-GGGAGAAAAAGTTCATAATGAGAAGAACTTG
* * *
245754 TTTCAACTTATGCTCAAATCCATCATA-AAATGAGGCGGATTAACATTTCAAT-AAACAGTTTAT
65 -TTCAACTTATGCTCAAATCCATCATAGAAA-GAGGTGGATTAACATTTCAATGAGA-AGTTCAT
* * * * *
245817 AATGAGAAAAACTCATTCAATAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTTCACCTTAT
127 AATGAGAAAAACTCATCCAATAAGAGAAAAGAAGTTCACAATGAGAAGAACTTGTATCACCTTAT
* *
245882 GCTCAAATCCATCATAAAAGGATGTGGATTAACATTTCCAATGG
192 GCTCAAATCCATCATAAAAGGAGGTGGACTAACATTT-CAATGG
*
245926 A-GAGTTCATAATGAGAAGAACTCATCCACAGAGGGAGAATAAGTTCATAATGAGAAGAACTTGT
1 AGGAGTTCATAATGAGAAGAACTCATCCACAGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGT
* * * * *
245990 TCAACATTTTGCTCAAATCCATCATAGAAGGAGATAGATTAACATTTCAATGAGGAGTTCATAAT
66 TCAAC-TTATGCTCAAATCCATCATAGAAAGAGGTGGATTAACATTTCAATGAGAAGTTCATAAT
* * *
246055 GAGAATAACTCGTCCACA-AAGAGAAAAGAAGTTCACAATGAGAAGCACTTG-ATCGACCTT-TC
130 GAGAAAAACTCATCCA-ATAAGAGAAAAGAAGTTCACAATGAGAAGAACTTGTATC-ACCTTAT-
* * *
246117 GCTCAAATCCATTATAGAAGGAGGTGGACTAACATTTCAATTG
192 GCTCAAATCCATCATAAAAGGAGGTGGACTAACATTTCAATGG
* * * * * * * ** *
246160 AGGAGTTCATACTAAGAGGGATTCATCTACGGAGAAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGGAGTTCATAATGAGAAGAACTCATCCACAGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGT
** * * *
246225 TCAACCTTATATTTAAATCCATCACAGAAAGAGGTGGA-TCACATTCTCAATGAGAAGTTCATAA
66 TCAA-CTTATGCTCAAATCCATCATAGAAAGAGGTGGATTAACATT-TCAATGAGAAGTTCATAA
246289 TGAGAAAAAC
129 TGAGAAAAAC
246299 GTTTTCATTC
Statistics
Matches: 316, Mismatches: 47, Indels: 21
0.82 0.12 0.05
Matches are distributed among these distances:
234 21 0.07
235 287 0.91
236 8 0.03
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.25
Consensus pattern (234 bp):
AGGAGTTCATAATGAGAAGAACTCATCCACAGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGT
TCAACTTATGCTCAAATCCATCATAGAAAGAGGTGGATTAACATTTCAATGAGAAGTTCATAATG
AGAAAAACTCATCCAATAAGAGAAAAGAAGTTCACAATGAGAAGAACTTGTATCACCTTATGCTC
AAATCCATCATAAAAGGAGGTGGACTAACATTTCAATGG
Found at i:251701 original size:31 final size:31
Alignment explanation
Indices: 251663--251725 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
251653 TTTAATAGTT
*
251663 GAGAGACTCAACAAAACAACATAGTATAATC
1 GAGAGACTCAACAAAACAACACAGTATAATC
*
251694 GAGAGACTCAACAAAACAACACATTATAATC
1 GAGAGACTCAACAAAACAACACAGTATAATC
251725 G
1 G
251726 GACTATTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.16
Consensus pattern (31 bp):
GAGAGACTCAACAAAACAACACAGTATAATC
Found at i:252191 original size:205 final size:207
Alignment explanation
Indices: 251837--252249 Score: 812
Period size: 205 Copynumber: 2.0 Consensus size: 207
251827 ATGTTTTTCT
251837 ATTAAATGATTTTATTTCTATTTAAAACAAAGACAAAATGATAATTTATGTTCTTGGAAGGATAA
1 ATTAAATGATTTTATTTCTATTTAAAACAAAGACAAAATGATAATTTATGTTCTTGGAAGGATAA
251902 TTAAACTTATAAAGTTACATGATTACATAAAAGATTAATAGTGATAAGAATGTGTGGATAATGGA
66 TTAAACTTATAAAGTTACATGATTACATAAAAGATTAATAGTGATAAGAATGTGTGGATAATGGA
251967 AGTCTGGACCCTAAACCTAAGGCAAGTGTTGCCCGAGTTGGTGGGAGGCAGAATGATTTTTACAC
131 AGTCTGGACCCTAAACCTAAGGCAAGTGTTGCCCGAGTTGGTGGGAGGCAGAATGATTTTTACAC
252032 ATACGCAAAGGA
196 ATACGCAAAGGA
252044 ATTAAATGATTTTATTTCTATTTAAAACAAAGAC-AAATGATAATTTATGTTCTTGGAAGGATAA
1 ATTAAATGATTTTATTTCTATTTAAAACAAAGACAAAATGATAATTTATGTTCTTGGAAGGATAA
252108 TTAAAC-TATAAAGTTACATGATTACATAAAAGATTAATAGTGATAAGAATGTGTGGATAATGGA
66 TTAAACTTATAAAGTTACATGATTACATAAAAGATTAATAGTGATAAGAATGTGTGGATAATGGA
252172 AGTCTGGACCCTAAACCTAAGGCAAGTGTTGCCCGAGTTGGTGGGAGGCAGAATGATTTTTACAC
131 AGTCTGGACCCTAAACCTAAGGCAAGTGTTGCCCGAGTTGGTGGGAGGCAGAATGATTTTTACAC
252237 ATACGCAAAGGA
196 ATACGCAAAGGA
252249 A
1 A
252250 AGGGGCGTTG
Statistics
Matches: 206, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
205 136 0.66
206 36 0.17
207 34 0.17
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (207 bp):
ATTAAATGATTTTATTTCTATTTAAAACAAAGACAAAATGATAATTTATGTTCTTGGAAGGATAA
TTAAACTTATAAAGTTACATGATTACATAAAAGATTAATAGTGATAAGAATGTGTGGATAATGGA
AGTCTGGACCCTAAACCTAAGGCAAGTGTTGCCCGAGTTGGTGGGAGGCAGAATGATTTTTACAC
ATACGCAAAGGA
Found at i:252692 original size:3 final size:3
Alignment explanation
Indices: 252684--252714 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
252674 TTGATGCTTT
252684 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
252715 AAACACATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:253820 original size:14 final size:13
Alignment explanation
Indices: 253797--253850 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 13
253787 TTCGGTAATA
253797 TGTTCGTTTATGT
1 TGTTCGTTTATGT
*
253810 CTGTTCATTTATGT
1 -TGTTCGTTTATGT
253824 TCGTTCGTTTATGT
1 T-GTTCGTTTATGT
*
253838 TCATTCGTTTATG
1 T-GTTCGTTTATG
253851 CTCGTTTATG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
13 1 0.03
14 35 0.97
ACGTcount: A:0.11, C:0.13, G:0.19, T:0.57
Consensus pattern (13 bp):
TGTTCGTTTATGT
Found at i:253848 original size:28 final size:28
Alignment explanation
Indices: 253798--253856 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
253788 TCGGTAATAT
* *
253798 GTTCGTTTATGTCTGTTCATTTATGTTC
1 GTTCGTTTATGTCTATTCATTTATGCTC
*
253826 GTTCGTTTATGT-TCATTCGTTTATGCTC
1 GTTCGTTTATGTCT-ATTCATTTATGCTC
253854 GTT
1 GTT
253857 TATGTGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.10, C:0.15, G:0.19, T:0.56
Consensus pattern (28 bp):
GTTCGTTTATGTCTATTCATTTATGCTC
Found at i:253872 original size:24 final size:24
Alignment explanation
Indices: 253795--253874 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
253785 CGTTCGGTAA
* *
253795 TATGTTCGTTTATGTCTGTTCATT
1 TATGCTCGTTTATGTCAGTTCATT
*
253819 TATGTTCGTTCGTTTATGTTCA-TTCGTT
1 TATG--C--TCGTTTATG-TCAGTTCATT
*
253847 TATGCTCGTTTATGTGAGTTCATT
1 TATGCTCGTTTATGTCAGTTCATT
253871 TATG
1 TATG
253875 TTTATCCCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
23 2 0.04
24 22 0.49
26 1 0.02
28 18 0.40
29 2 0.04
ACGTcount: A:0.14, C:0.12, G:0.19, T:0.55
Consensus pattern (24 bp):
TATGCTCGTTTATGTCAGTTCATT
Found at i:254129 original size:33 final size:33
Alignment explanation
Indices: 254067--254130 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
254057 TTCGTTTATG
* *
254067 TTCATTTATTGTGTTCGTTTACGTTCGTTCGTT
1 TTCATTTATTGTGTTCGTTTACATCCGTTCGTT
*
254100 TTCATTTATTGTGTTCGTTTATATCCGTTCG
1 TTCATTTATTGTGTTCGTTTACATCCGTTCG
254131 ATTATGTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.11, C:0.16, G:0.17, T:0.56
Consensus pattern (33 bp):
TTCATTTATTGTGTTCGTTTACATCCGTTCGTT
Found at i:254212 original size:35 final size:35
Alignment explanation
Indices: 254166--254287 Score: 210
Period size: 35 Copynumber: 3.5 Consensus size: 35
254156 CTATCATTTA
*
254166 AATGAACGAACATGAACAAGCTACTTTTCTTAACG
1 AATGAACGAACACGAACAAGCTACTTTTCTTAACG
254201 AATGAACGAACACGAACAAGCTACTTTTCTTAACG
1 AATGAACGAACACGAACAAGCTACTTTTCTTAACG
*
254236 AATGAACGAACACGAATAAGCTAC-TTTCATTAACG
1 AATGAACGAACACGAACAAGCTACTTTTC-TTAACG
254271 AATGAACGAACACGAAC
1 AATGAACGAACACGAAC
254288 GAGAAATTTT
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
34 4 0.05
35 79 0.95
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (35 bp):
AATGAACGAACACGAACAAGCTACTTTTCTTAACG
Found at i:258871 original size:38 final size:38
Alignment explanation
Indices: 258820--258896 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
258810 TCTTTCTCTA
258820 ATCTCTAATGGCGGATAAAACGAGAGCCTCGGCTTACT
1 ATCTCTAATGGCGGATAAAACGAGAGCCTCGGCTTACT
258858 ATCTCTAATGGCGGATAAAACGAGAGCCTCGGCTTACT
1 ATCTCTAATGGCGGATAAAACGAGAGCCTCGGCTTACT
258896 A
1 A
258897 CTAACATTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (38 bp):
ATCTCTAATGGCGGATAAAACGAGAGCCTCGGCTTACT
Found at i:260330 original size:18 final size:18
Alignment explanation
Indices: 260303--260341 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
260293 CTTCAGGTAA
*
260303 CTTCTTAATCCCTAATCT
1 CTTCTCAATCCCTAATCT
*
260321 CTTCTCAATCCCTAATTT
1 CTTCTCAATCCCTAATCT
260339 CTT
1 CTT
260342 TCGATGCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.46
Consensus pattern (18 bp):
CTTCTCAATCCCTAATCT
Found at i:265495 original size:18 final size:18
Alignment explanation
Indices: 265472--265506 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
265462 AGGTAACTTT
265472 TCAATCCCTAATCTCTTC
1 TCAATCCCTAATCTCTTC
*
265490 TCAATCCCTAATTTCTT
1 TCAATCCCTAATCTCTT
265507 TCGATGCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.43
Consensus pattern (18 bp):
TCAATCCCTAATCTCTTC
Found at i:267854 original size:46 final size:46
Alignment explanation
Indices: 267774--267866 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 46
267764 ACTCGGGTTT
* *
267774 TTTTTTTGTTTTTGATGGATTGTTTAATGATTGGTAATGGCTACTGG
1 TTTTTTTGTTCTTGATGGA-TGTTTAATGATTGGTAATGGCCACTGG
*
267821 TTTTTTTGTTCTTGATGGA-GTATTAATGGTTGGTAATGGCCACTGG
1 TTTTTTTGTTCTTGATGGATGT-TTAATGATTGGTAATGGCCACTGG
267867 ATTCTCCTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
45 2 0.05
46 22 0.52
47 18 0.43
ACGTcount: A:0.17, C:0.06, G:0.27, T:0.49
Consensus pattern (46 bp):
TTTTTTTGTTCTTGATGGATGTTTAATGATTGGTAATGGCCACTGG
Found at i:268341 original size:55 final size:55
Alignment explanation
Indices: 268274--268600 Score: 416
Period size: 55 Copynumber: 6.0 Consensus size: 55
268264 TTCGAATGAT
*
268274 GGGTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAAC
1 GGGTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAAC
* * * * *
268329 GTGTCTGTTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAATAAAC
1 GGGTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAAC
*
268384 GGGTCCGCTCCCTATTCGTTCAGGGAGTAT-AGAACTCGAACAATCTTCATA-AAAC
1 GGGTCCGCTCCCTATTCCTTCAGGGAGTATAAG-ACTCGAACAATCTTCA-ACAAAC
* * *
268439 GGGTCCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAATAAAC
1 GGGTCCGCTCCCTATTCCTTCAGGGAGTATAAG-ACTCGAACAATCTTCAACAAAC
* * * *
268494 GGGTCCGCTCCCTATTCGTTCAGGGAGTATAAAACTCGAGCAATCTTCAACGAAC
1 GGGTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAAC
** * *
268549 TTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAAC
1 GGGTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAAC
268600 G
1 G
268601 AGTTTGCTTC
Statistics
Matches: 240, Mismatches: 28, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
51 14 0.06
54 3 0.01
55 221 0.92
56 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (55 bp):
GGGTCCGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAAC
Found at i:270049 original size:24 final size:24
Alignment explanation
Indices: 269989--270035 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
269979 TTTTCATCAT
269989 TTTTTTCTCTTTTTCCCTTTTTTA
1 TTTTTTCTCTTTTTCCCTTTTTTA
270013 TTTTTTCTCTTTTTCCCTTTTTT
1 TTTTTTCTCTTTTTCCCTTTTTT
270036 TTAATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTTTCTCTTTTTCCCTTTTTTA
Found at i:270060 original size:12 final size:12
Alignment explanation
Indices: 270045--270078 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
270035 TTTAATTATT
270045 TTTTTATTTCTC
1 TTTTTATTTCTC
*
270057 TTTTT-TTTCTT
1 TTTTTATTTCTC
270068 TTTTTATTTCT
1 TTTTTATTTCT
270079 TTTCAGGCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTATTTCTC
Found at i:270060 original size:23 final size:23
Alignment explanation
Indices: 270034--270078 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
270024 TTTCCCTTTT
270034 TTTTAATTATTTTTTTATTTCTC
1 TTTTAATTATTTTTTTATTTCTC
** *
270057 TTTTTTTTCTTTTTTTATTTCT
1 TTTTAATTATTTTTTTATTTCT
270079 TTTCAGGCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTAATTATTTTTTTATTTCTC
Found at i:270079 original size:12 final size:12
Alignment explanation
Indices: 270031--270081 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
270021 CTTTTTCCCT
* *
270031 TTTTTTTAATTA
1 TTTTTTTATTTC
270043 TTTTTTTATTTC
1 TTTTTTTATTTC
*
270055 TCTTTTT-TTTC
1 TTTTTTTATTTC
270066 TTTTTTTATTTC
1 TTTTTTTATTTC
270078 TTTT
1 TTTT
270082 CAGGCGAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 10 0.29
12 24 0.71
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTATTTC
Found at i:270081 original size:11 final size:11
Alignment explanation
Indices: 270044--270081 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
270034 TTTTAATTAT
270044 TTTTTTATTTC
1 TTTTTTATTTC
270055 TCTTTTT-TTTC
1 T-TTTTTATTTC
270066 TTTTTTTATTTC
1 -TTTTTTATTTC
270078 TTTT
1 TTTT
270082 CAGGCGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTATTTC
Found at i:279788 original size:45 final size:47
Alignment explanation
Indices: 279723--279820 Score: 146
Period size: 45 Copynumber: 2.1 Consensus size: 47
279713 CGTTATTCAT
*
279723 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC-TTGTTCG
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
* *
279769 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATTCG
279816 AAAAA
1 AAAAA
279821 ATGAAAATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
45 28 0.60
46 8 0.17
47 11 0.23
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (47 bp):
AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
Found at i:282644 original size:46 final size:47
Alignment explanation
Indices: 282564--282659 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 47
282554 CGACTCGGGT
* * * *
282564 TTTTTTTGTTTTTGATGGATTGTTTAATGATTGGTAATGGCTACTGG
1 TTTTTTTGTTCTTGATGGAGTGTTTAATGATTGGTAATGACCACTGG
*
282611 TTTTTTTGTTCTTGATGGAGTG-TTAATGGTTGGTAATGACCACTGG
1 TTTTTTTGTTCTTGATGGAGTGTTTAATGATTGGTAATGACCACTGG
282657 TTT
1 TTT
282660 CTCCTCTGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
46 24 0.55
47 20 0.45
ACGTcount: A:0.17, C:0.06, G:0.26, T:0.51
Consensus pattern (47 bp):
TTTTTTTGTTCTTGATGGAGTGTTTAATGATTGGTAATGACCACTGG
Found at i:284984 original size:31 final size:31
Alignment explanation
Indices: 284943--285003 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
284933 GAACCAATCT
284943 CGTTGATAAGTGATTAATTATTTAAATAACC
1 CGTTGATAAGTGATTAATTATTTAAATAACC
* *
284974 CGTTGGTAAGTTATTAATTATTTAAATAAC
1 CGTTGATAAGTGATTAATTATTTAAATAAC
285004 ATGCATTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (31 bp):
CGTTGATAAGTGATTAATTATTTAAATAACC
Found at i:285401 original size:15 final size:15
Alignment explanation
Indices: 285381--285416 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
285371 TTTTTAGTAT
285381 ATTACCGGGAATGTC
1 ATTACCGGGAATGTC
285396 ATTACCGGGAATGTC
1 ATTACCGGGAATGTC
285411 ATTACC
1 ATTACC
285417 TCTTTTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (15 bp):
ATTACCGGGAATGTC
Found at i:285890 original size:18 final size:16
Alignment explanation
Indices: 285844--285893 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
285834 AAAATACAAC
285844 ATTCCC-AGTAATCTT
1 ATTCCCTAGTAATCTT
*
285859 ATTCCCTGGTAATCTT
1 ATTCCCTAGTAATCTT
285875 ATTCTCACTAGTAATCTT
1 ATTC-C-CTAGTAATCTT
285893 A
1 A
285894 CATTCCGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 6 0.20
16 12 0.40
17 1 0.03
18 11 0.37
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (16 bp):
ATTCCCTAGTAATCTT
Found at i:290779 original size:22 final size:22
Alignment explanation
Indices: 290754--290817 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
290744 ATATTGTATG
290754 CATGTAGTGCATATGAGGTTAA
1 CATGTAGTGCATATGAGGTTAA
290776 CA--T-GTGCATA--A--TAT-A
1 CATGTAGTGCATATGAGGT-TAA
290791 CATGTAGTGCATATGAGGTTAA
1 CATGTAGTGCATATGAGGTTAA
290813 CATGT
1 CATGT
290818 GCATAGTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 18
0.65 0.00 0.35
Matches are distributed among these distances:
15 4 0.12
16 1 0.03
17 2 0.06
18 7 0.21
19 7 0.21
20 2 0.06
21 1 0.03
22 9 0.27
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (22 bp):
CATGTAGTGCATATGAGGTTAA
Found at i:290784 original size:19 final size:19
Alignment explanation
Indices: 290760--290822 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
290750 TATGCATGTA
290760 GTGCATATGAGGTTAACAT
1 GTGCATATGAGGTTAACAT
290779 GTGCATA--A---TATACATGT
1 GTGCATATGAGGTTA-ACA--T
290796 AGTGCATATGAGGTTAACAT
1 -GTGCATATGAGGTTAACAT
290816 GTGCATA
1 GTGCATA
290823 GTATGGCATG
Statistics
Matches: 35, Mismatches: 0, Indels: 18
0.66 0.00 0.34
Matches are distributed among these distances:
14 2 0.06
15 3 0.09
17 2 0.06
18 7 0.20
19 14 0.40
20 2 0.06
22 3 0.09
23 2 0.06
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (19 bp):
GTGCATATGAGGTTAACAT
Found at i:292080 original size:19 final size:20
Alignment explanation
Indices: 292011--292085 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
292001 AATTTTGAAC
* *
292011 ATCAGTACTGTTCATACAGT
1 ATCAGTACTATTCATACAAT
** *
292031 ATTGGTACTATTTATACAAT
1 ATCAGTACTATTCATACAAT
* *
292051 ATTAATACTATTCATACAAT
1 ATCAGTACTATTCATACAAT
292071 A-CAGTACTATTCATA
1 ATCAGTACTATTCATA
292086 AAACCATTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 12 0.27
20 33 0.73
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (20 bp):
ATCAGTACTATTCATACAAT
Found at i:294810 original size:23 final size:23
Alignment explanation
Indices: 294750--294815 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 23
294740 AAACCAATCC
*
294750 ATATTTATATAAATTAATTTTATAT
1 ATATTTATATAAA-T-ATTTGATAT
*
294775 ATAGTTTCTATAAATATTTGA-AT
1 ATA-TTTATATAAATATTTGATAT
294798 ATATTTATAATAAA-ATTT
1 ATATTTAT-ATAAATATTT
294816 TATAAAACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
22 8 0.22
23 10 0.28
24 5 0.14
25 4 0.11
26 9 0.25
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (23 bp):
ATATTTATATAAATATTTGATAT
Found at i:294901 original size:20 final size:21
Alignment explanation
Indices: 294878--294919 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
294868 TTTAAACTAA
294878 TTAA-AAATAATTTTAATATT
1 TTAATAAATAATTTTAATATT
* *
294898 TTAATAAATTATTTTATTATT
1 TTAATAAATAATTTTAATATT
294919 T
1 T
294920 AGTCTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAATAAATAATTTTAATATT
Found at i:295650 original size:25 final size:25
Alignment explanation
Indices: 295614--295662 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
295604 ATCTTCAATC
* *
295614 TCTTACATAACACACTCCTTTCATA
1 TCTTACACAACAAACTCCTTTCATA
*
295639 TCTTACACAACAAACTCTTTTCAT
1 TCTTACACAACAAACTCCTTTCAT
295663 CTAACCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.37
Consensus pattern (25 bp):
TCTTACACAACAAACTCCTTTCATA
Found at i:297457 original size:18 final size:18
Alignment explanation
Indices: 297434--297468 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
297424 TTAGCATTTG
297434 TCATTAAT-TATTTTTTCT
1 TCATTAATGT-TTTTTTCT
297452 TCATTAATGTTTTTTTC
1 TCATTAATGTTTTTTTC
297469 AATAACATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.20, C:0.11, G:0.03, T:0.66
Consensus pattern (18 bp):
TCATTAATGTTTTTTTCT
Found at i:311591 original size:33 final size:33
Alignment explanation
Indices: 311545--311633 Score: 160
Period size: 33 Copynumber: 2.7 Consensus size: 33
311535 GACATAAAAC
*
311545 AATAGTGACTAAATTATAATAAATCAGAATAAT
1 AATAGTGATTAAATTATAATAAATCAGAATAAT
311578 AATAGTGATTAAATTATAATAAATCAGAATAAT
1 AATAGTGATTAAATTATAATAAATCAGAATAAT
*
311611 AATAGTGATTAAATTAAAATAAA
1 AATAGTGATTAAATTATAATAAA
311634 ATAAAACATA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.31
Consensus pattern (33 bp):
AATAGTGATTAAATTATAATAAATCAGAATAAT
Found at i:316195 original size:3 final size:3
Alignment explanation
Indices: 316187--316218 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
316177 AACTGAAGGC
*
316187 GAT GAT GAT GAT GAT GAT GAT GAT GAA GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
316219 AGAGAGGGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:320318 original size:54 final size:54
Alignment explanation
Indices: 320236--320345 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
320226 CACCAGAGGC
320236 TAGGGGTAGTAGACTAAGTTTGACAGATTTCTAATGCCTAAACTCAAACATGAT
1 TAGGGGTAGTAGACTAAGTTTGACAGATTTCTAATGCCTAAACTCAAACATGAT
320290 TAGGGGTAGTAGACTAAGTTTGACAGATTTCTAATGCCTAAACTCAAACATGAT
1 TAGGGGTAGTAGACTAAGTTTGACAGATTTCTAATGCCTAAACTCAAACATGAT
320344 TA
1 TA
320346 CTAGCACGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (54 bp):
TAGGGGTAGTAGACTAAGTTTGACAGATTTCTAATGCCTAAACTCAAACATGAT
Found at i:323541 original size:50 final size:50
Alignment explanation
Indices: 323466--323565 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
323456 GTTGGTTGGG
323466 CTTGAATGCTCCATACGGAAGATTTTGGATGGAGAAGTGGGAGTCTGGAA
1 CTTGAATGCTCCATACGGAAGATTTTGGATGGAGAAGTGGGAGTCTGGAA
323516 CTTGAATGCTCCATACGGAAGATTTTGGATGGAGAAGTGGGAGTCTGGAA
1 CTTGAATGCTCCATACGGAAGATTTTGGATGGAGAAGTGGGAGTCTGGAA
323566 GGACTTGGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.28, C:0.12, G:0.34, T:0.26
Consensus pattern (50 bp):
CTTGAATGCTCCATACGGAAGATTTTGGATGGAGAAGTGGGAGTCTGGAA
Found at i:324031 original size:55 final size:56
Alignment explanation
Indices: 323945--324127 Score: 198
Period size: 55 Copynumber: 3.3 Consensus size: 56
323935 AACAATTATT
* *
323945 TTTTTAAAATTATTTTTGATACTATCATTAATAGTTAATAATATATTATAGATAATA
1 TTTTTAATATTATTTTT-ATACTATCATTAATAGTTAATAATATATAATAGATAATA
* * * *
324002 TTTTTAATATTATATTATT-T-TTAT-ATTAATAGTTAAT-ATGATA-AACA-ATTATT
1 TTTTTAATATTAT-TT-TTATACTATCATTAATAGTTAATAAT-ATATAATAGATAATA
* *
324055 TTTTTAATATTATTTTTGATACTATCATTAATAGTTAATAATATATCATAGACAATA
1 TTTTTAATATTATTTTT-ATACTATCATTAATAGTTAATAATATATAATAGATAATA
324112 TTTTTAATATTGATTT
1 TTTTTAATATT-ATTT
324128 AATAATATAA
Statistics
Matches: 103, Mismatches: 12, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
51 2 0.02
52 2 0.02
53 18 0.17
54 7 0.07
55 32 0.31
56 7 0.07
57 27 0.26
58 6 0.06
59 2 0.02
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (56 bp):
TTTTTAATATTATTTTTATACTATCATTAATAGTTAATAATATATAATAGATAATA
Found at i:324051 original size:110 final size:110
Alignment explanation
Indices: 323924--324122 Score: 371
Period size: 110 Copynumber: 1.8 Consensus size: 110
323914 ATGGATCATT
323924 TTAATATGATAAACAATTATTTTTTTAAAATTATTTTTGATACTATCATTAATAGTTAATAATAT
1 TTAATATGATAAACAATTATTTTTTTAAAATTATTTTTGATACTATCATTAATAGTTAATAATAT
* *
323989 ATTATAGATAATATTTTTAATATTATATTATTTTTATATTAATAG
66 ATCATAGACAATATTTTTAATATTATATTATTTTTATATTAATAG
*
324034 TTAATATGATAAACAATTATTTTTTTAATATTATTTTTGATACTATCATTAATAGTTAATAATAT
1 TTAATATGATAAACAATTATTTTTTTAAAATTATTTTTGATACTATCATTAATAGTTAATAATAT
324099 ATCATAGACAATATTTTTAATATT
66 ATCATAGACAATATTTTTAATATT
324123 GATTTAATAA
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 86 1.00
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.51
Consensus pattern (110 bp):
TTAATATGATAAACAATTATTTTTTTAAAATTATTTTTGATACTATCATTAATAGTTAATAATAT
ATCATAGACAATATTTTTAATATTATATTATTTTTATATTAATAG
Found at i:326312 original size:30 final size:30
Alignment explanation
Indices: 326268--326324 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
326258 CTACGAGTCC
* *
326268 AATTTTTTTGTATTTTTTATTA-GAGATCT
1 AATTTTTTTATATTTGTTATTATGAGATCT
326297 AATTTTTTTAATATTTGTTATTATGAGA
1 AATTTTTTT-ATATTTGTTATTATGAGA
326325 ATACTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.38
30 11 0.46
31 4 0.17
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.60
Consensus pattern (30 bp):
AATTTTTTTATATTTGTTATTATGAGATCT
Found at i:326524 original size:15 final size:15
Alignment explanation
Indices: 326506--326534 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
326496 GTCCAAAATT
326506 GTTATATCCACAATC
1 GTTATATCCACAATC
326521 GTTATATCCACAAT
1 GTTATATCCACAAT
326535 AGTATATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (15 bp):
GTTATATCCACAATC
Found at i:327341 original size:17 final size:16
Alignment explanation
Indices: 327299--327341 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
327289 ATAAAATATA
*
327299 AATAAATATATTTACT
1 AATAAATATATTTAAT
*
327315 ATATACATATA-TTAAT
1 A-ATAAATATATTTAAT
327331 AATAAATATAT
1 AATAAATATAT
327342 GCAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
15 8 0.36
16 6 0.27
17 8 0.36
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAAATATATTTAAT
Found at i:328699 original size:3 final size:3
Alignment explanation
Indices: 328693--328751 Score: 93
Period size: 3 Copynumber: 19.7 Consensus size: 3
328683 TAATATTTAT
*
328693 TAA TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
328741 T-A TAAA TAA TA
1 TAA T-AA TAA TA
328752 TTCAAATAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 2 0.04
3 48 0.92
4 2 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:329225 original size:113 final size:113
Alignment explanation
Indices: 329090--329389 Score: 447
Period size: 113 Copynumber: 2.7 Consensus size: 113
329080 ATAGAGTCAT
* *
329090 GCAAAAGGTCGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* ** * * *
329155 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAA
66 ATTATGAACTCTAACTGGAAAAGCTGATCCACCAAGTGATGAATTCAA
* *
329203 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* ** * *
329268 ATTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTCGA
66 ATTATGAACTCTAACTGGAAAAGCTGATCCACCAAGTGATGAATTCAA
* *
329316 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
329381 ATTATGAAC
66 ATTATGAAC
329390 CCTTCTGGAA
Statistics
Matches: 168, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
113 168 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTAACTGGAAAAGCTGATCCACCAAGTGATGAATTCAA
Found at i:330224 original size:22 final size:22
Alignment explanation
Indices: 330199--330316 Score: 200
Period size: 22 Copynumber: 5.4 Consensus size: 22
330189 GATAAAGCTT
*
330199 TCATATTTAAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
330221 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
* *
330243 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
*
330265 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
330287 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
330309 TCATCTTT
1 TCATCTTT
330317 GAAGAATGTA
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 91 1.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.34
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:331829 original size:76 final size:75
Alignment explanation
Indices: 331613--331936 Score: 337
Period size: 76 Copynumber: 4.3 Consensus size: 75
331603 ACAGGATGAT
* ** * * *
331613 ATGGGCCTTCAGCATGCCCCAACAATTGCTGATACGAACGTTCAAAATACATCAACATTCTTGAT
1 ATGGGCTTTCAGCATGCCCCAACAATTGCTGATATAAACATTCAAAATACATCAACATTCCTCAT
*
331678 TCTGATTGAA
66 TCTGATTAAA
** * * * *
331688 ATATGCTTTCAGCATGCCCCATCAATTGCTGATACGAAA-GTTCAAAATACATCAACATTCTTCA
1 ATGGGCTTTCAGCATGCCCCAACAATTGCTGATA-TAAACATTCAAAATACATCAACATTCCTCA
*
331752 TTCTAATTAAA
65 TTCTGATTAAA
* * * **
331763 AGGGGCTTTCAGCATGCCCTAACATTTTGCTGATATAAACATTCATGATACATCAACATTCCTCA
1 ATGGGCTTTCAGCATGCCCCAACA-ATTGCTGATATAAACATTCAAAATACATCAACATTCCTCA
*
331828 TTCTGATTGAA
65 TTCTGATTAAA
* * * * * ** *
331839 ATGGGTTTTCAGCATGTCCCAGCATTTTACTGATATAAACATTCATGATACATCAACATTCCTGA
1 ATGGGCTTTCAGCATGCCCCAACA-ATTGCTGATATAAACATTCAAAATACATCAACATTCCTCA
331904 TTCTGATTGAAA
65 TTCTGATT-AAA
*
331916 A-GGGTTTTCAGCATGCCCCAA
1 ATGGGCTTTCAGCATGCCCCAA
331937 TATTTGCTTC
Statistics
Matches: 213, Mismatches: 32, Indels: 7
0.85 0.13 0.03
Matches are distributed among these distances:
75 85 0.40
76 125 0.59
77 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (75 bp):
ATGGGCTTTCAGCATGCCCCAACAATTGCTGATATAAACATTCAAAATACATCAACATTCCTCAT
TCTGATTAAA
Found at i:331943 original size:151 final size:150
Alignment explanation
Indices: 331615--331944 Score: 376
Period size: 151 Copynumber: 2.2 Consensus size: 150
331605 AGGATGATAT
* * * * * *
331615 GGGCCTTCAGCATGCCCCAACAATTGCTGATACGAACGTTCAAAATACATCAACATTCTTGATTC
1 GGGCTTTCAGCATGCCCCAACATTTGCTGATACAAACATTCAAAATACATCAACATTCCTCATTC
* * * *
331680 TGATTGAAATATGCTTTCAGCATGCCCCATCAATTGCTGATACGAAAGTTCAAAATACATCAACA
66 TGATTGAAATAGGCTTTCAGCATGCCCCAGCAATTACTGATACGAAAATTCAAAATACATCAACA
*
331745 TTCTTCATTCTAATTAAAAG
131 TTCCTCATTCTAATTAAAAG
* * **
331765 GGGCTTTCAGCATGCCCTAACATTTTGCTGATATAAACATTCATGATACATCAACATTCCTCATT
1 GGGCTTTCAGCATGCCCCAACA-TTTGCTGATACAAACATTCAAAATACATCAACATTCCTCATT
* * * * * **
331830 CTGATTGAAATGGGTTTTCAGCATGTCCCAGCATTTTACTGATA-TAAACATTCATGATACATCA
65 CTGATTGAAATAGGCTTTCAGCATGCCCCAGCA-ATTACTGATACGAAA-ATTCAAAATACATCA
* *
331894 ACATTCCTGATTCTGATTGAAAA-
128 ACATTCCTCATTCTAATT-AAAAG
* *
331917 GGGTTTTCAGCATGCCCCAATATTTGCT
1 GGGCTTTCAGCATGCCCCAACATTTGCT
331945 TCTTGTTAAT
Statistics
Matches: 149, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
150 20 0.13
151 71 0.48
152 54 0.36
153 4 0.03
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.32
Consensus pattern (150 bp):
GGGCTTTCAGCATGCCCCAACATTTGCTGATACAAACATTCAAAATACATCAACATTCCTCATTC
TGATTGAAATAGGCTTTCAGCATGCCCCAGCAATTACTGATACGAAAATTCAAAATACATCAACA
TTCCTCATTCTAATTAAAAG
Found at i:337102 original size:27 final size:27
Alignment explanation
Indices: 337072--337127 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
337062 GTAATTATGT
337072 AAAAATGAAAATGTAAATACAAACGTA
1 AAAAATGAAAATGTAAATACAAACGTA
* * *
337099 AAAAATGTAAATGTAAATGCAAATGTA
1 AAAAATGAAAATGTAAATACAAACGTA
337126 AA
1 AA
337128 TATGTGAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.61, C:0.05, G:0.12, T:0.21
Consensus pattern (27 bp):
AAAAATGAAAATGTAAATACAAACGTA
Found at i:337216 original size:8 final size:7
Alignment explanation
Indices: 337187--337228 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
337177 ATAAAAGTAT
337187 AAATGCA
1 AAATGCA
* *
337194 CAATGAA
1 AAATGCA
337201 AAATGCA
1 AAATGCA
337208 AATATGCA
1 AA-ATGCA
337216 AAATG-A
1 AAATGCA
337222 AAATGCA
1 AAATGCA
337229 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.57, C:0.12, G:0.14, T:0.17
Consensus pattern (7 bp):
AAATGCA
Found at i:338736 original size:26 final size:28
Alignment explanation
Indices: 338705--338762 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
338695 ACTTGAAAAT
*
338705 AAAATAAT-A-TACATATAAATATTATG
1 AAAATAATAAGTACATATAAAAATTATG
* *
338731 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAATAAGTACATATAAAAATTATG
338759 AAAA
1 AAAA
338763 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAATAATAAGTACATATAAAAATTATG
Found at i:339770 original size:13 final size:13
Alignment explanation
Indices: 339752--339776 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
339742 AAAATTAAAA
339752 TTATATCAAATTC
1 TTATATCAAATTC
339765 TTATATCAAATT
1 TTATATCAAATT
339777 AAAAGAAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
TTATATCAAATTC
Found at i:340899 original size:3 final size:3
Alignment explanation
Indices: 340893--340947 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
340883 TAATATTTAT
* * *
340893 TAA TAA TAA -AA TAA AAA TAA TAA TTA TTA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
340939 TAAA TAA TA
1 T-AA TAA TA
340948 TTCAAATGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 4 0.09
3 39 0.87
4 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:340919 original size:27 final size:27
Alignment explanation
Indices: 340881--340938 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
340871 TTGGGCCTGT
*
340881 AATAATATTTATTAATAATAA-AATAAA
1 AATAATAATTATT-ATAATAATAATAAA
*
340908 AATAATAATTATTATAATAATAATAAT
1 AATAATAATTATTATAATAATAATAAA
340935 AATA
1 AATA
340939 TAAATAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
AATAATAATTATTATAATAATAATAAA
Found at i:346258 original size:20 final size:20
Alignment explanation
Indices: 346209--346282 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
346199 AAATTGTTTG
* *
346209 TGGGTACTGATACTAAGCCCC
1 TGGGTATTGATACTAA-CCTC
** * *
346230 TTAGTATTGATATTGACCTC
1 TGGGTATTGATACTAACCTC
346250 TGGGTATTGATACTAACCTC
1 TGGGTATTGATACTAACCTC
* *
346270 TTGGTATAGATAC
1 TGGGTATTGATAC
346283 CACTGACTTA
Statistics
Matches: 41, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
20 30 0.73
21 11 0.27
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (20 bp):
TGGGTATTGATACTAACCTC
Found at i:346419 original size:44 final size:44
Alignment explanation
Indices: 346370--346475 Score: 160
Period size: 44 Copynumber: 2.4 Consensus size: 44
346360 GTATCAATAT
*
346370 TTTTCTAAGTATCAATATTGAATTTGGCTTCGATG-TTTGTAAAA
1 TTTTCTAAGTATCAATACTGAATTTGGCTTCGATGTTTTG-AAAA
* *
346414 TTTTCTGAGTATCGATACTGAATTTGGCTTCGATGTTTTGAAAA
1 TTTTCTAAGTATCAATACTGAATTTGGCTTCGATGTTTTGAAAA
*
346458 TTGTCTAAGTATCAATAC
1 TTTTCTAAGTATCAATAC
346476 CCCTATTTGA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 51 0.93
45 4 0.07
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (44 bp):
TTTTCTAAGTATCAATACTGAATTTGGCTTCGATGTTTTGAAAA
Found at i:354151 original size:22 final size:22
Alignment explanation
Indices: 354126--354173 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
354116 GGCTTAAGGA
*
354126 AAGTTCAAGGATGTTTAAAACT
1 AAGTTCAAGGATGTTCAAAACT
354148 AAGTTCAAGGATGTTCAAAACT
1 AAGTTCAAGGATGTTCAAAACT
354170 AAGT
1 AAGT
354174 AATTAGTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (22 bp):
AAGTTCAAGGATGTTCAAAACT
Found at i:355452 original size:54 final size:55
Alignment explanation
Indices: 355056--355439 Score: 451
Period size: 54 Copynumber: 7.1 Consensus size: 55
355046 CTATGTGTAC
* * * * *
355056 TATCGACACTAGGTATGCAGCCCACA-AAATTCATCATATGTTGATGAACAATCG
1 TATCGGCACTAAGTGTGCAACCCACAGAAATTCATCATATGTTGATGAACAACCG
* * **
355110 TATCGGCACTAAGTATGCAACCCAC-GAAATTCATTATATGTTGATGAACAACTA
1 TATCGGCACTAAGTGTGCAACCCACAGAAATTCATCATATGTTGATGAACAACCG
* * *
355164 TATCGACACTAAGTGTGCAACCCACAG-AATTCATCATAAGTT-ATTGAACAACCA
1 TATCGGCACTAAGTGTGCAACCCACAGAAATTCATCATATGTTGA-TGAACAACCG
* *
355218 TATCGGCACTAAGTGTGGAACCCACAG-AATTCATCATATGTTGATGAACAACTG
1 TATCGGCACTAAGTGTGCAACCCACAGAAATTCATCATATGTTGATGAACAACCG
* * * *
355272 TATCGACACTAAGTGTGCAACCCACA-TAATTTATCATATGTTGATGAACAACTG
1 TATCGGCACTAAGTGTGCAACCCACAGAAATTCATCATATGTTGATGAACAACCG
* * * *
355326 TATCGACACTAAGTGTGCAACCCACA-AAATTCATCATATATTGATGAACGATCG
1 TATCGGCACTAAGTGTGCAACCCACAGAAATTCATCATATGTTGATGAACAACCG
* * * * * *
355380 TATTGGCACCAAGTGTGCAACCCA-AGAAATTCATAATGTGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAGAAATTCATCATATGTTGATGAACAACCG
355434 TATCGG
1 TATCGG
355440 TATTACGTGT
Statistics
Matches: 289, Mismatches: 35, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
53 2 0.01
54 285 0.99
55 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (55 bp):
TATCGGCACTAAGTGTGCAACCCACAGAAATTCATCATATGTTGATGAACAACCG
Found at i:355452 original size:162 final size:163
Alignment explanation
Indices: 355071--355439 Score: 498
Period size: 162 Copynumber: 2.3 Consensus size: 163
355061 ACACTAGGTA
* * *
355071 TGCAGCCCACA-AAATTCATCATATGTTGATGAACAATCGTATCGGCACTAAGTATGCAACCCAC
1 TGCAACCCACAGAAATTCATCATATGTTGATGAACAACCGTATCGGCACTAAGTGTGCAACCCAC
* *
355135 GAAATTCATTATATGTTGATGAACAACTATATCGACACTAAGTGTGCAACCCACAGAATTCATCA
66 GAAATTCATCATATGTTGATGAACAACTATATCGACACTAAGTGTGCAACCCACAAAATTCATCA
*
355200 TAAGTTATTGAACAACCATATCGGCACTAAGTG
131 TAAGTTATTGAACAACCATATCGGCACCAAGTG
* * *
355233 TGGAACCCACAG-AATTCATCATATGTTGATGAACAACTGTATCGACACTAAGTGTGCAACCCAC
1 TGCAACCCACAGAAATTCATCATATGTTGATGAACAACCGTATCGGCACTAAGTGTGCAACCCAC
* *
355297 -ATAATTTATCATATGTTGATGAACAACTGTATCGACACTAAGTGTGCAACCCACAAAATTCATC
66 GA-AATTCATCATATGTTGATGAACAACTATATCGACACTAAGTGTGCAACCCACAAAATTCATC
* * * *
355361 ATATA-TTGA-TGAACGATCGTATTGGCACCAAGTG
130 ATA-AGTT-ATTGAACAACCATATCGGCACCAAGTG
* * * *
355395 TGCAACCCA-AGAAATTCATAATGTGTTTATGAACGACCGTATCGG
1 TGCAACCCACAGAAATTCATCATATGTTGATGAACAACCGTATCGG
355440 TATTACGTGT
Statistics
Matches: 180, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
161 3 0.02
162 175 0.97
163 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.27
Consensus pattern (163 bp):
TGCAACCCACAGAAATTCATCATATGTTGATGAACAACCGTATCGGCACTAAGTGTGCAACCCAC
GAAATTCATCATATGTTGATGAACAACTATATCGACACTAAGTGTGCAACCCACAAAATTCATCA
TAAGTTATTGAACAACCATATCGGCACCAAGTG
Found at i:361548 original size:54 final size:54
Alignment explanation
Indices: 361479--361814 Score: 377
Period size: 54 Copynumber: 6.2 Consensus size: 54
361469 CATTATCGAT
* * * * *
361479 ACTAAGTATGCAACCCACGAAATTCATTATATGTTGATGAACAATCGTATTGGC
1 ACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACAACCGTATCGGC
* * * *
361533 AATAAGTGTGCAACCCACAGAATTCATCACAAGTTGATGAACAACCGTATCGGC
1 ACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACAACCGTATCGGC
* *
361587 ACTAAGTGTGGAACCCACAAAATTCATCATATGTTGATGAACAACAGTATCGGC
1 ACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACAACCGTATCGGC
* * *
361641 ACTAAGTGTGCAACCCA-AAGAATTTATTATATGTTGATGAACAACCGTATCGAC
1 ACTAAGTGTGCAACCCACAA-AATTCATCATATGTTGATGAACAACCGTATCGGC
* * * * * ** *
361695 ACTAAGTTTACAACACACAAAATTCATCATATGCTGATGAACGACCAAATTGGC
1 ACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACAACCGTATCGGC
* * * * * * *
361749 ACCAAGTGTGCAACCCACGAAATTCATAATGTGTTTATGAACGACCTTATCGGC
1 ACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACAACCGTATCGGC
* *
361803 ATTACGTGTGCA
1 ACTAAGTGTGCA
361815 TTTCAAAGAA
Statistics
Matches: 234, Mismatches: 46, Indels: 4
0.82 0.16 0.01
Matches are distributed among these distances:
53 2 0.01
54 230 0.98
55 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (54 bp):
ACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACAACCGTATCGGC
Found at i:362515 original size:22 final size:22
Alignment explanation
Indices: 362476--362518 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
362466 ATATCGTTCG
**
362476 ATGAGCTTTATTTAAAGAGTAT
1 ATGAGCTTTATGGAAAGAGTAT
*
362498 ATGAGCTTTATGGCAAGAGTA
1 ATGAGCTTTATGGAAAGAGTA
362519 ATAATCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (22 bp):
ATGAGCTTTATGGAAAGAGTAT
Found at i:362772 original size:22 final size:22
Alignment explanation
Indices: 362719--362775 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
362709 CGATCCAAAG
* * * *
362719 AAAACTCACAGACAGTAGCAGC
1 AAAACTCACCGAGAGCAGCAAC
362741 AAAACTCACCGAGAGCAGCAAC
1 AAAACTCACCGAGAGCAGCAAC
362763 AAAACTCACCGAG
1 AAAACTCACCGAG
362776 GATAAAGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.46, C:0.30, G:0.18, T:0.07
Consensus pattern (22 bp):
AAAACTCACCGAGAGCAGCAAC
Found at i:363274 original size:4 final size:4
Alignment explanation
Indices: 363267--363329 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
363257 TATATATATA
363267 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
363315 TATG TATG TATG TAT
1 TATG TATG TATG TAT
363330 TATACATTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:364253 original size:33 final size:27
Alignment explanation
Indices: 364192--364249 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
364182 TTGAATATTC
364192 TTTATCTTTCTAAAAAGGCTTGGTAAT
1 TTTATCTTTCTAAAAAGGCTTGGTAAT
364219 TTTATCTTTCTAAAAAGGCTTGGTAAT
1 TTTATCTTTCTAAAAAGGCTTGGTAAT
364246 TTTA
1 TTTA
364250 ATTTAATCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (27 bp):
TTTATCTTTCTAAAAAGGCTTGGTAAT
Found at i:364499 original size:22 final size:24
Alignment explanation
Indices: 364467--364510 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
364457 ACATACCTCA
*
364467 AATTTGTTATTT-TAATTAAAAGT
1 AATTTGTTATTTCTAATGAAAAGT
364490 AATTT-TTATTTCTAATGAAAA
1 AATTTGTTATTTCTAATGAAAA
364511 AACATTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (24 bp):
AATTTGTTATTTCTAATGAAAAGT
Found at i:366159 original size:94 final size:94
Alignment explanation
Indices: 366032--366235 Score: 248
Period size: 94 Copynumber: 2.2 Consensus size: 94
366022 TTTCTGGCTC
* * * * * * *
366032 CCTAGTATCGATACTACTACCCTGGTACCGATACTTCTATACTATGGTACCGATA-TCCCTTCCG
1 CCTAGTATCGATAC-CCTACCATGGTACCGATACTACCATACTATGGTACCGATACCCCCTTACA
*
366096 GTATCGATACCAATTTTAGGTTCGATGTTG
65 GTATCGATACCAATTTTAGATTCGATGTTG
* * *
366126 CCTAGTATCGATACCCTTACCATGGTATCGATACTACCATACTATGTTACCGATACCCCCTTATA
1 CCTAGTATCGATACCC-TACCATGGTACCGATACTACCATACTATGGTACCGATACCCCCTTACA
* *
366191 GTATTGATACCCATTTTAGATTCGATGTTG
65 GTATCGATACCAATTTTAGATTCGATGTTG
* *
366221 CTTGGTATCGATACC
1 CCTAGTATCGATACC
366236 TATCGATACC
Statistics
Matches: 93, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
93 1 0.01
94 47 0.51
95 45 0.48
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (94 bp):
CCTAGTATCGATACCCTACCATGGTACCGATACTACCATACTATGGTACCGATACCCCCTTACAG
TATCGATACCAATTTTAGATTCGATGTTG
Found at i:378239 original size:43 final size:41
Alignment explanation
Indices: 378171--378288 Score: 134
Period size: 43 Copynumber: 2.9 Consensus size: 41
378161 ACTTAGTAAG
*
378171 TCCTTTGGGCCATCAGTAAGACTTTCGAGCATGATGATTAAAA
1 TCCTTTGGGCCATCAGTAAGACTTTCGAGCAAGATGA-T-AAA
* * *
378214 TCCTTTGGGTCATCCA-TAAGTCTTTCGAGCAAGATGATAAG
1 TCCTTTGGGCCAT-CAGTAAGACTTTCGAGCAAGATGATAAA
* *
378255 TCCTTTGGGCCAT-A-TAAGACCTTCGGGCAAGATG
1 TCCTTTGGGCCATCAGTAAGACTTTCGAGCAAGATG
378289 TTTCCACGTG
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 18 0.27
41 14 0.21
42 1 0.02
43 31 0.47
44 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (41 bp):
TCCTTTGGGCCATCAGTAAGACTTTCGAGCAAGATGATAAA
Found at i:378716 original size:228 final size:228
Alignment explanation
Indices: 378402--379037 Score: 866
Period size: 228 Copynumber: 2.8 Consensus size: 228
378392 TCGAAGATGA
* * * *
378402 TAAGTCATTC-GAGCCATCATTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGGTCATAC-GT
1 TAAGTCCTTCGGA-CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCAT-CTGC
* * *
378465 AAGTCTTTCAAGCAATATGATAAGTCATTCGAGCCATCAATAAGACCTTCGGGCAGGATGTTTTC
64 AAGTCTTTCAAGCAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTC
*
378530 ATATGAATTTGAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTAAGAAAATGAA
129 ATATGAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTAAGAAAATGAA
* *
378595 AAGTAAGAAAGAGATTTCCCAAGTTTCTGACTTAG
194 AAGTAAGAAAGAGATTTCCAAAGTTTCTGACATAG
* * * *
378630 TAAGTCCTTCGGACCATTAGTAAGCCTTTCGAGCATGATGATTGAATCTTTCGGGTCATCTGCAA
1 TAAGTCCTTCGGACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGCAA
* * * * *
378695 GTCTTTCAAGCAAGATGATAAGTCCTTTGGGCCATTTATAAGACCTTCAGGCAGGATGTTTTCAC
66 GTCTTTCAAGCAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCAT
* * * *
378760 AGGAATTTCAAAAATGAGAAAGCGATTTTAAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAAA
131 ATGAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTAAGAAAATGAAAA
* * * * *
378825 TTAAGAAAGCGTTTTCCAAATTTTCTTACATAG
196 GTAAGAAAGAGATTTCCAAAGTTTCTGACATAG
* *
378858 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCTGGTCATCTGTC-
1 TAAGTCCTTCGGACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTG-CA
* *
378922 AGTCTTTCAAGCAAGATGATAAGACATTCGGGCCATCTATAAGACCTTCGGGCAAGATGCTTTT-
65 AGTCTTTCAAGCAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGCAGGATG-TTTTC
* *
378986 ATATGGTATTTGTAAGAAAATGATAAAGCGATTTTCAAAGTTTCTCATTTAA
129 ATAT-GAATTTG--A-AAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAA
379038 AATAAAAAAA
Statistics
Matches: 354, Mismatches: 46, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
227 1 0.00
228 306 0.86
229 12 0.03
231 1 0.00
232 34 0.10
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (228 bp):
TAAGTCCTTCGGACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGCAA
GTCTTTCAAGCAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCAT
ATGAATTTGAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTAAGAAAATGAAAA
GTAAGAAAGAGATTTCCAAAGTTTCTGACATAG
Found at i:378926 original size:42 final size:42
Alignment explanation
Indices: 378862--378958 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
378852 ACATAGTAAG
* *
378862 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATGATTAAA
* * * *
378904 TCCTTCTGGTCATCTGTCAGTCTTTCAAGCAAGATGA-TAAGA
1 TCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATGATTAA-A
*
378946 -CATTCGGGCCATC
1 TCCTTCGGGCCATC
378959 TATAAGACCT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 13 0.29
42 32 0.71
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.31
Consensus pattern (42 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCAAGCAAGATGATTAAA
Found at i:379063 original size:24 final size:24
Alignment explanation
Indices: 379036--379081 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
379026 TTTCTCATTT
379036 AAAATAAAAAAATAATAAAAAGAA
1 AAAATAAAAAAATAATAAAAAGAA
* *
379060 AAAATGAAATAATAATAAAAAG
1 AAAATAAAAAAATAATAAAAAG
379082 TGAAAGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (24 bp):
AAAATAAAAAAATAATAAAAAGAA
Found at i:380498 original size:2 final size:2
Alignment explanation
Indices: 380491--380521 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
380481 ATTTGTGACT
380491 TA TA TA TA TA 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
380522 GTATTATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:390639 original size:436 final size:435
Alignment explanation
Indices: 389869--390655 Score: 928
Period size: 436 Copynumber: 1.8 Consensus size: 435
389859 AATTGACTTT
* * *
389869 AATTTGTCTTAACTCAACGGTAAGGAGCCATCTTTTAGTTAAATTTTTCAAAGTCAACTTCAACT
1 AATTTGGCTTAACTCAACGGTAAGAAGCCATCTTCTAGTTAAATTTTTCAAAGTCAACTTCAACT
* * * * * *
389934 CTACGACGGAGGATATTGGATTCGAAAGCAAATTCAAGATCGACTGCAATTTAGCTTAACTCAAC
66 CAAAGACGGAGGATATTGGATTAGAAAGCAAATTCAAGATCAACTACAATCTAGCTTAACTCAAC
* * * *
389999 GACGAGGAGCTAGTTTCTAATTAAAGTTTTCATGCCAAGTTTCAACTTCACAGTGAAGGATACTT
131 GACGAGGAGCTAGTTTCCAATTAAAGTTTTCAGGCAAAGTTTCAACTTCACAGAGAAGGATACTT
* * * * * *
390064 AACCCGGAAATACATTCAAAACTGACTATAATTTGGTTTAACTCAACGACGATAAGCTATCTTTT
196 AACCCGGAAACACATTCAAAACTGACTACAATTTGGCTTAACTCAACGACAATAAGCCATCTTCT
* * * *
390129 AATTAAATCTTTCCGAAGTCAACTTAAACTCCACGATGGAGGATTTTGTGCTCAAAATCCAATTT
261 AATCAAATCTTTCCAAAGTCAACTTAAACTCCACGATGGAGGATTTAGTGCTCAAAATCCAATTC
390194 AAAATTGACTACAATCTAGATTAACTCAAAGGCAATGAGCTAGTTTCATGCCAGATTTTAACTTC
326 AAAATTGACTACAATCTAGATTAACTCAAAGGCAATGAGCTAGTTTCATGCCAGATTTTAACTTC
390259 ATGATGAATGATACTTGACCCTGAAACACATTCAGAACTAACTAC
391 ATGATGAATGATACTTGACCCTGAAACACATTCAGAACTAACTAC
* * *
390304 AATTTGGCTTAATTCAATGGTGAGAAGCCATCTTCTAGTTAAATCCTTTT-AAAGTCAACTTCAA
1 AATTTGGCTTAACTCAACGGTAAGAAGCCATCTTCTAGTTAAAT--TTTTCAAAGTCAACTTCAA
** * **
390368 CTCAAAGGTGGAGGATATTGGATTAGAAAGCTAATCTTTA-ATCAACTACAATCTAGCTTAACTC
64 CTCAAAGACGGAGGATATTGGATTAGAAAGCAAAT-TCAAGATCAACTACAATCTAGCTTAACTC
* * *
390432 -A-GTAGCGAGGAGCTAGTTTCCAGTTGAAA-TTTTTAGGCAAAGTTTTAACTTCAC-GAAGAAG
128 AACG-A-CGAGGAGCTAGTTTCCAATT-AAAGTTTTCAGGCAAAGTTTCAACTTCACAG-AGAAG
* * * * * * * *
390493 GATATTTGA-CCTGAAAGCACATTCAGAACTGATTGCAATTTTGCTTAACTCAAC-AGCAATGAG
189 GATACTTAACCCGGAAA-CACATTCAAAACTGACTACAATTTGGCTTAACTCAACGA-CAATAAG
* * * * * *
390556 CCATCTTCTAGTCAAATTTTTTCAAAGTCAATTTCAACTCCACGATGGAGGATATTAG-GTTCAA
252 CCATCTTCTAATCAAATCTTTCCAAAGTCAACTTAAACTCCACGATGGAGGAT-TTAGTGCTCAA
* * * * *
390620 AA-GCAGATTCAAGATTGACTACGATTTAGCTTAACT
316 AATCCA-ATTCAAAATTGACTACAATCTAGATTAACT
390656 TAACGATGAG
Statistics
Matches: 288, Mismatches: 53, Indels: 21
0.80 0.15 0.06
Matches are distributed among these distances:
434 1 0.00
435 50 0.17
436 225 0.78
437 12 0.04
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (435 bp):
AATTTGGCTTAACTCAACGGTAAGAAGCCATCTTCTAGTTAAATTTTTCAAAGTCAACTTCAACT
CAAAGACGGAGGATATTGGATTAGAAAGCAAATTCAAGATCAACTACAATCTAGCTTAACTCAAC
GACGAGGAGCTAGTTTCCAATTAAAGTTTTCAGGCAAAGTTTCAACTTCACAGAGAAGGATACTT
AACCCGGAAACACATTCAAAACTGACTACAATTTGGCTTAACTCAACGACAATAAGCCATCTTCT
AATCAAATCTTTCCAAAGTCAACTTAAACTCCACGATGGAGGATTTAGTGCTCAAAATCCAATTC
AAAATTGACTACAATCTAGATTAACTCAAAGGCAATGAGCTAGTTTCATGCCAGATTTTAACTTC
ATGATGAATGATACTTGACCCTGAAACACATTCAGAACTAACTAC
Found at i:391290 original size:11 final size:12
Alignment explanation
Indices: 391274--391320 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
391264 TAAATATCAC
391274 TTTATT-TTTAT
1 TTTATTATTTAT
391285 TTTATTATTTAT
1 TTTATTATTTAT
*
391297 TATTACTATTTAT
1 T-TTATTATTTAT
391310 TATTAATTATT
1 T-TT-ATTATT
391321 ATATATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
11 6 0.19
12 6 0.19
13 14 0.45
14 5 0.16
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTATTATTTAT
Found at i:391297 original size:7 final size:7
Alignment explanation
Indices: 391275--391320 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
391265 AAATATCACT
391275 TTATTT-
1 TTATTTA
391281 TTATTTTA
1 TTA-TTTA
391289 TTATTTA
1 TTATTTA
391296 TTA-TTA
1 TTATTTA
*
391302 CTATTTA
1 TTATTTA
*
391309 TTATTAA
1 TTATTTA
391316 TTATT
1 TTATT
391321 ATATATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
6 8 0.24
7 23 0.68
8 3 0.09
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (7 bp):
TTATTTA
Found at i:391308 original size:13 final size:13
Alignment explanation
Indices: 391280--391314 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
391270 TCACTTTATT
*
391280 TTTATT-TTATTA
1 TTTATTATTACTA
391292 TTTATTATTACTA
1 TTTATTATTACTA
391305 TTTATTATTA
1 TTTATTATTA
391315 ATTATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATTATTACTA
Found at i:391363 original size:3 final size:3
Alignment explanation
Indices: 391275--391350 Score: 57
Period size: 3 Copynumber: 24.7 Consensus size: 3
391265 AAATATCACT
* *
391275 TTA TTT TTA TT- TTA TTA TTTA TTA TTA CTA TTTA TTA TTAA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TT-A TTA TTA
* * *
391322 -TA TATA ATA TTA TTA TCA TTA TTA GTA TT
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT
391351 GTACAAATTA
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
2 4 0.07
3 43 0.75
4 10 0.18
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:407513 original size:226 final size:225
Alignment explanation
Indices: 406877--407572 Score: 1169
Period size: 226 Copynumber: 3.1 Consensus size: 225
406867 GTTATATTGT
* * *
406877 AAAGTATCTATCCTTTTATAAAAGTGTCCATACTTATTTCACTGT-GAAAATATATTT-TTATTA
1 AAAGTATATATCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTA-T-
*
406940 TCTTTGG-TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAA
64 TCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC-AAATAATCAAA
*
407004 TAATTTTGTGTGTAAATG-AATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
128 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
407068 AAAAATTGAAACATAAATTACATAACTTT-AAA
193 AAAAATTGAAACATAAATTACATAACTTTAAAA
**
407100 AAAGTATATATCATTTTTATAAAAGTGTTTATACTTATTTCACTGTGGAAAACATATTTATTA-T
1 AAAGTATATATC-TTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
407164 CTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATA-TTT-TAAAATATC-AATAATCAAATA
65 CTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATA
407226 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
130 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
*
407291 AATTTGAAACATAAATTACATAACTTTAAAA
195 AAATTGAAACATAAATTACATAACTTTAAAA
407322 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATC-TTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
407387 CTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATA
65 CTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATA
407452 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
130 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAA
407517 AAAATTGAAACATAAATTACATAACTTTAAAA
194 AAAATTGAAACATAAATTACATAACTTTAAAA
*
407549 AAAATAT-TGATTCTTTTTATAAAA
1 AAAGTATAT-A-TCTTTTTATAAAA
407573 AGTATGGACA
Statistics
Matches: 448, Mismatches: 12, Indels: 22
0.93 0.02 0.05
Matches are distributed among these distances:
220 26 0.06
221 74 0.17
222 73 0.16
223 60 0.13
224 64 0.14
225 20 0.04
226 77 0.17
227 52 0.12
228 2 0.00
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.40
Consensus pattern (225 bp):
AAAGTATATATCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATTC
TTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAA
TTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAA
AATTGAAACATAAATTACATAACTTTAAAA
Found at i:407638 original size:23 final size:23
Alignment explanation
Indices: 407612--407667 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
407602 AAATATGATA
407612 TAATAGGTAGCGCTTATATAATG
1 TAATAGGTAGCGCTTATATAATG
* *
407635 TAATAGGTATCGTTTATATAATG
1 TAATAGGTAGCGCTTATATAATG
407658 TAATAGGTAG
1 TAATAGGTAG
407668 TTGTAAAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (23 bp):
TAATAGGTAGCGCTTATATAATG
Found at i:408109 original size:23 final size:23
Alignment explanation
Indices: 408083--408146 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
408073 AATAGGTAAA
*
408083 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
408106 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
408129 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
408147 TTGTAAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:408270 original size:479 final size:483
Alignment explanation
Indices: 407373--410919 Score: 6378
Period size: 479 Copynumber: 7.5 Consensus size: 483
407363 ACTGTGGAAA
*
407373 ACATATTTATTA-T-TCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAAT
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
*
407436 ATC-AAATAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
66 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
* * * *
407500 ATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAA-TATTGATTCTT
131 ATAAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTGTCGATCCTT
*
407564 TTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATATAATAGGTAGCGCTTAT
196 TTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
407629 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
261 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
*
407694 AAGTGTCCATACTTTTTCCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
326 AAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
407759 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTAT
391 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTAT
** *
407824 TATCTTAAAAACAATAAATATATATATT
456 TAAATTAAAAACAATAAACATATATATT
407852 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATA-TA-TTTATAAAAT
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
*
407915 ATCAAAACAATTAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
66 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
* *
407980 AAAAAATACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTGTCGATCCTT
131 ATAAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTGTCGATCCTT
408045 TTTA-AAAAAGTATGGACACTTTCAATATAATAGGT-AAAATATGATGTAATAGGTAGCGCTTAT
196 TTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
408108 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
261 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
*
408173 AAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
326 AAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
408238 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTAT
391 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTAT
408303 TAAATTAAAAACAATAAACATATATATT
456 TAAATTAAAAACAATAAACATATATATT
408331 ACATATTTATTATTATC-TTGGTTAATATTGTTAAATTTAAATTCTAAAATATTATTTTATAAAA
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCT-AAATATTATTTTATAAAA
408395 TATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATT-ATATTGTAGGTGGAAAA
65 TATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAA
*
408459 CATAAAACACTATTAAAAAAAAATGAAACATAAATTACATAACTTT--AAAAAAGTGTCGATCCT
130 CATAAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTGTCGATCCT
408522 TTTTATAAAAAGTATGGACACTTTC-A-ATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
195 TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTA
408585 TATAATGTAATAGGTATCG-TTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATA
260 TATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATA
*
408649 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
325 AAAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
*
408714 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACATTACGATATATATTATTA
390 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
408779 TTAAATTAAAAACAATAAACATATATATT
455 TTAAATTAAAAACAATAAACATATATATT
408808 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
408873 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
66 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
408938 ATAAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTGTCGATCCTT
131 ATAAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTGTCGATCCTT
409003 TTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
196 TTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
409068 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
261 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
*
409133 AAGTGTCCATAC-TTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
326 AAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
*
409197 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACATTACGATATATATTATTAT
391 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTAT
409262 TAAATTAAAAACAATAAAC--ATATATT
456 TAAATTAAAAACAATAAACATATATATT
409288 ACATATTTATTA-TATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
**
409352 ATCAAATTAATCAAATAATTTTTTGTGTAAATG-AATTATTAAATTAATA-T-TAGGTGGAAAAC
66 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
409414 ATAAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAA-TGTCGATCCTT
131 ATAAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTGTCGATCCTT
409478 TTTATAAAAAGTATGGACACTTTCAATATAATAGGT-AAAA-AT-ATGTAATAGGTAGCGCTTAT
196 TTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
*
409540 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTGTCTATCCTTTTTATAA
261 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
409605 AAGTGTCCATACTTTTTTCATTGTGG-AAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
326 AAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
409669 GATATTAA-TTAGTAATTATAGGCGTCTAATGATTTA-TTTTTACGTTACG--ATATATTATTAT
391 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTAT
409730 TAAATTAAAAACAATAAAC--ATATATT
456 TAAATTAAAAACAATAAACATATATATT
409756 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTA-TTTATAAAAT
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
409820 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
66 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
*
409885 ATAAAACACAATTAAAAAAAATTGAAACATAAATTACATAACTTT-AAAAAAAGTGTCGATCCTT
131 ATAAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTGTCGATCCTT
409949 TTTAT-AAAAGTATGGACAC-TTCAATATAATAGGT-AAAATATGATGTAATAGGTAGCGCTTAT
196 TTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
410011 ATAATGTAATAGGTATCGTTTATAT--TGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
261 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
*
410074 AAGTGTCTATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
326 AAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
*
410139 GATATTAATTTAGTAATTATAGGCATCTAATGATTTATTTTTTACGTTACGATATATA-TATTAT
391 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTAT
410203 TAAATTAAAAACAATAAACATATATA-T
456 TAAATTAAAAACAATAAACATATATATT
410230 ACATA--T-TTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
410292 ATCAAAACAATCAAATAATTTTTTGTGT-AATGAAATTATTAAATTAATATTGTAGGTGG-AAAC
66 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
410355 ATAAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTGTCGATCCTT
131 ATAAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTGTCGATCCTT
410420 TTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
196 TTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
410485 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
261 ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
*
410550 AAGTGTCCATACTTTTTTCATTGTGAAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
326 AAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
*
410615 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTAGGATATATATTATTAT
391 GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTAT
* *
410680 TAAATTAAAAATAATAAAAATATATATT
456 TAAATTAAAAACAATAAACATATATATT
410708 ACATA-TTA-TATTATCTTTGGTTAATA-TGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
1 ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
* *
410770 ATCAAAACAATCAAATAATTTTTTGTG-CAATGAAATTATTAAATTAATATTGTAGGTGAAAAAC
66 ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
* * *
410834 ATGAAACACTATT--AAAAAATTGAAACAT-AATTACATAACTTTAAAAAAAATTATCGATCC-T
131 ATAAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTGTCGATCCTT
410895 TTTA-AAAAAGTATGGACACTTTCAA
196 TTTATAAAAAGTATGGACACTTTCAA
410920 CATATTATAA
Statistics
Matches: 2982, Mismatches: 42, Indels: 93
0.96 0.01 0.03
Matches are distributed among these distances:
468 91 0.03
469 138 0.05
470 130 0.04
471 272 0.09
472 208 0.07
473 54 0.02
474 89 0.03
475 57 0.02
476 252 0.08
477 340 0.11
478 302 0.10
479 429 0.14
480 266 0.09
481 104 0.03
482 192 0.06
483 58 0.02
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.40
Consensus pattern (483 bp):
ACATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAAT
ATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAAC
ATAAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTGTCGATCCTT
TTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTAT
ATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTTGTAAAGTATCTATCCTTTTTATAA
AAGTGTCCATACTTTTTTCATTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
GATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTAT
TAAATTAAAAACAATAAACATATATATT
Found at i:408610 original size:22 final size:23
Alignment explanation
Indices: 408561--408623 Score: 101
Period size: 22 Copynumber: 2.8 Consensus size: 23
408551 ATAGGTAAAA
*
408561 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
408584 ATATAATGTAATAGGTATCG-TT
1 ATATAATGTAATAGGTAGCGCTT
408606 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
408624 TTGTAAAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
22 19 0.51
23 18 0.49
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:409074 original size:23 final size:23
Alignment explanation
Indices: 409043--409106 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
409033 ATAGGTAAAA
*
409043 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
409066 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
409089 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
409107 TTGTAAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:409546 original size:23 final size:23
Alignment explanation
Indices: 409520--409578 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
409510 AGGTAAAAAT
409520 ATGTAATAGGTAGCGCTTATATA
1 ATGTAATAGGTAGCGCTTATATA
* *
409543 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTAGCGCTTATATA
409566 ATGTAATAGGTAG
1 ATGTAATAGGTAG
409579 TTGTAAAGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.37
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTATATA
Found at i:410039 original size:21 final size:23
Alignment explanation
Indices: 409986--410047 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
409976 AATAGGTAAA
*
409986 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
410009 ATATAATGTAATAGGTATCG-TT
1 ATATAATGTAATAGGTAGCGCTT
*
410031 -TATATTGTAATAGGTAG
1 ATATAATGTAATAGGTAG
410048 TTGTAAAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 15 0.43
22 2 0.06
23 18 0.51
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:410491 original size:23 final size:23
Alignment explanation
Indices: 410460--410523 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
410450 ATAGGTAAAA
*
410460 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
410483 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
410506 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
410524 TTGTAAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:414343 original size:32 final size:32
Alignment explanation
Indices: 414302--414388 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
414292 AGTCGAGGGT
*
414302 TTACCTATGTTCTACGGAACATATAGACAGAA
1 TTACCTATGTTCTAAGGAACATATAGACAGAA
** * * *
414334 TTACCTATG-TCTTTTGGGACATATGGACAGTA
1 TTACCTATGTTC-TAAGGAACATATAGACAGAA
414366 -TACCTATGTTCTAAGGAACATAT
1 TTACCTATGTTCTAAGGAACATAT
414389 GAACAGTTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
31 19 0.42
32 26 0.58
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (32 bp):
TTACCTATGTTCTAAGGAACATATAGACAGAA
Found at i:414387 original size:31 final size:32
Alignment explanation
Indices: 414303--414426 Score: 112
Period size: 31 Copynumber: 4.0 Consensus size: 32
414293 GTCGAGGGTT
* * *
414303 TACCTATGTTC-TACGGAACATATAGACAGAA
1 TACCTATGTTCTTAAGGAACATATGGACAGTA
** *
414334 TTACCTATG-TCTTTTGGGACATATGGACAGTA
1 -TACCTATGTTCTTAAGGAACATATGGACAGTA
* *
414366 TACCTATGTTC-TAAGGAACATATGAACAGTT
1 TACCTATGTTCTTAAGGAACATATGGACAGTA
* * *
414397 TACCTAGGTTCTTCAGG-ACCTATGGACAGT
1 TACCTATGTTCTTAAGGAACATATGGACAGT
414427 TGTCGAGGTT
Statistics
Matches: 75, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
31 46 0.61
32 29 0.39
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (32 bp):
TACCTATGTTCTTAAGGAACATATGGACAGTA
Found at i:415296 original size:22 final size:21
Alignment explanation
Indices: 415255--415297 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
415245 GTAGCAGTAT
*
415255 TGTAGCAGGGTATCGATTCCC
1 TGTAGCAGGGAATCGATTCCC
*
415276 TGTAGCAGGGGAATCGGTTCCC
1 TGTAGCA-GGGAATCGATTCCC
415298 CTATTACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.19, C:0.23, G:0.33, T:0.26
Consensus pattern (21 bp):
TGTAGCAGGGAATCGATTCCC
Found at i:415618 original size:20 final size:20
Alignment explanation
Indices: 415593--415642 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
415583 AAACCCCAAA
415593 TTCTTTTTCGATCTCGAATT
1 TTCTTTTTCGATCTCGAATT
*
415613 TTCTTTTTCAATCTCGAATT
1 TTCTTTTTCGATCTCGAATT
*
415633 TCCTTTTTCG
1 TTCTTTTTCG
415643 CTTATCTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.14, C:0.22, G:0.08, T:0.56
Consensus pattern (20 bp):
TTCTTTTTCGATCTCGAATT
Found at i:418841 original size:41 final size:39
Alignment explanation
Indices: 418776--418852 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 39
418766 TCACTTCACC
* *
418776 GAAAGTGGGGGGCTTTAGTCAGAAATAAGACAAAAAGAG
1 GAAAGTGGGGGACTTTAGTCAGAAATAAAACAAAAAGAG
*
418815 GAAAGTGGGAGAGACTTTAGTTAGAAATAAAACAAAAA
1 GAAAGTGGG-G-GACTTTAGTCAGAAATAAAACAAAAA
418853 AATGAGTCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 9 0.27
40 1 0.03
41 23 0.70
ACGTcount: A:0.48, C:0.06, G:0.29, T:0.17
Consensus pattern (39 bp):
GAAAGTGGGGGACTTTAGTCAGAAATAAAACAAAAAGAG
Found at i:419198 original size:38 final size:38
Alignment explanation
Indices: 419156--419228 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
419146 ACTTATAAGT
* * *
419156 AAAATATTAAAGAAAT-ATATATATATATATATATAATA
1 AAAATAGTAAA-AAATCAAATAAATATATATATATAATA
419194 AAAATAGTAAAAAATCAAATAAATATATATATATA
1 AAAATAGTAAAAAATCAAATAAATATATATATATA
419229 TATTATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 4 0.13
38 27 0.87
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (38 bp):
AAAATAGTAAAAAATCAAATAAATATATATATATAATA
Found at i:419220 original size:46 final size:45
Alignment explanation
Indices: 419153--419251 Score: 144
Period size: 46 Copynumber: 2.2 Consensus size: 45
419143 TAGACTTATA
* *
419153 AGTAAAATATTAAAGAAATATATATATATATATATATAATAAAAAT
1 AGTAAAAAATCAAAGAAATATATATATATATAT-TATAATAAAAAT
* *
419199 AGTAAAAAATCAAATAAATATATATATATATATTATAATATAAAT
1 AGTAAAAAATCAAAGAAATATATATATATATATTATAATAAAAAT
*
419244 AATAAAAA
1 AGTAAAAA
419252 TAAATGAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 18 0.38
46 30 0.62
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (45 bp):
AGTAAAAAATCAAAGAAATATATATATATATATTATAATAAAAAT
Found at i:419681 original size:35 final size:35
Alignment explanation
Indices: 419642--419712 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
419632 TAAAAAACCT
*
419642 TATTTTATACTAATATTTGAGTCCTAATTCAACTC
1 TATTTTAAACTAATATTTGAGTCCTAATTCAACTC
* *
419677 TATTTTAAACTAATATTTGATTTCTAATTCAACTC
1 TATTTTAAACTAATATTTGAGTCCTAATTCAACTC
419712 T
1 T
419713 TCTTTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.48
Consensus pattern (35 bp):
TATTTTAAACTAATATTTGAGTCCTAATTCAACTC
Found at i:420786 original size:76 final size:74
Alignment explanation
Indices: 420697--420835 Score: 206
Period size: 74 Copynumber: 1.9 Consensus size: 74
420687 TATTTTGTTC
* * * * *
420697 TTTTTGTTCTTTTTTTTTTTTTCATTTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAA
1 TTTTTGTTCTTTTTTGTTTTTTC--TTTCTCCAACTTAGGACGCCCTTTCGGGTTTTCACCCTAA
420762 ACGTTTTTCAG
64 ACGTTTTTCAG
*
420773 TTTTTGTTCTTTTTTGTTTTTTCTTTCTCCAACTTAGGACGCCCTTTCGGGTTTTCATCCTAA
1 TTTTTGTTCTTTTTTGTTTTTTCTTTCTCCAACTTAGGACGCCCTTTCGGGTTTTCACCCTAA
420836 GCGAAGTATT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 35 0.61
76 22 0.39
ACGTcount: A:0.12, C:0.20, G:0.13, T:0.55
Consensus pattern (74 bp):
TTTTTGTTCTTTTTTGTTTTTTCTTTCTCCAACTTAGGACGCCCTTTCGGGTTTTCACCCTAAAC
GTTTTTCAG
Found at i:428849 original size:14 final size:14
Alignment explanation
Indices: 428795--428865 Score: 58
Period size: 14 Copynumber: 5.1 Consensus size: 14
428785 CAAGGTAAAG
* *
428795 AAAACAAATAAGAT
1 AAAATAAATAAAAT
428809 AAAGAT-AATAAAAT
1 AAA-ATAAATAAAAT
**
428823 AAAAGGGAA-AAAAT
1 AAAA-TAAATAAAAT
428837 AAAATAAATAAAAT
1 AAAATAAATAAAAT
*
428851 -AAATAAATAAGAT
1 AAAATAAATAAAAT
428864 AA
1 AA
428866 GGAAAAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
13 15 0.33
14 28 0.61
15 3 0.07
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.17
Consensus pattern (14 bp):
AAAATAAATAAAAT
Found at i:428865 original size:9 final size:9
Alignment explanation
Indices: 428833--428857 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
428823 AAAAGGGAAA
428833 AAATAAAAT
1 AAATAAAAT
428842 AAATAAAAT
1 AAATAAAAT
428851 AAATAAA
1 AAATAAA
428858 TAAGATAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:429256 original size:2 final size:2
Alignment explanation
Indices: 429217--429242 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
429207 AAAAAATAAT
429217 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
429243 ATTATAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:429535 original size:17 final size:18
Alignment explanation
Indices: 429502--429537 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
429492 ATATATACGT
*
429502 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
429520 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
429537 A
1 A
429538 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:434102 original size:2 final size:2
Alignment explanation
Indices: 434062--434086 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
434052 AAAGCGAAAA
434062 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
434087 AAATTATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:434185 original size:2 final size:2
Alignment explanation
Indices: 434142--434169 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
434132 ATAATTAAGA
434142 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
434170 TAATAATAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:434389 original size:17 final size:18
Alignment explanation
Indices: 434356--434391 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
434346 ATATATACGT
*
434356 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
434374 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
434391 A
1 A
434392 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:438549 original size:2 final size:2
Alignment explanation
Indices: 438542--438644 Score: 206
Period size: 2 Copynumber: 51.5 Consensus size: 2
438532 GCAGCATGAT
438542 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
438584 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
438626 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
438645 TTGTTATATC
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 101 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:438872 original size:28 final size:28
Alignment explanation
Indices: 438845--438898 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
438835 AATTTAATAT
*
438845 TAATTAAA-ATTAAAATAATACATTATA
1 TAATTAAATAATAAAATAATACATTATA
* *
438872 TATTTAAATAATAAAATAATATATTAT
1 TAATTAAATAATAAAATAATACATTAT
438899 CGATGAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
TAATTAAATAATAAAATAATACATTATA
Found at i:438914 original size:21 final size:21
Alignment explanation
Indices: 438890--438957 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
438880 TAATAAAATA
438890 ATATATTATCGATGAATTTTT
1 ATATATTATCGATGAATTTTT
* * **
438911 ATATA-AAT-AAT-TTTTATTT
1 ATATATTATCGATGAATT-TTT
438930 AAATATATTATCGATGAATTTTT
1 -A-TATATTATCGATGAATTTTT
438953 ATATA
1 ATATA
438958 AATAATTTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
18 2 0.06
19 5 0.15
20 3 0.09
21 13 0.39
22 3 0.09
23 5 0.15
24 2 0.06
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (21 bp):
ATATATTATCGATGAATTTTT
Found at i:438914 original size:42 final size:42
Alignment explanation
Indices: 438878--438963 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 42
438868 TATATATTTA
438878 AATAATAAAAT-AATATATTATCGATGAATTTTTATATAAAT
1 AATAATAAAATAAATATATTATCGATGAATTTTTATATAAAT
** * **
438919 AATTTTTATTTAAATATATTATCGATGAATTTTTATATAAAT
1 AATAATAAAATAAATATATTATCGATGAATTTTTATATAAAT
438961 AAT
1 AAT
438964 TTTTATTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 6 0.15
42 33 0.85
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (42 bp):
AATAATAAAATAAATATATTATCGATGAATTTTTATATAAAT
Found at i:438924 original size:15 final size:15
Alignment explanation
Indices: 438904--438976 Score: 64
Period size: 15 Copynumber: 5.1 Consensus size: 15
438894 ATTATCGATG
438904 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
438919 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
* **
438934 -A--TAT-TATCGAT
1 AATTTTTATATAAAT
438945 GAATTTTTATATAAAT
1 -AATTTTTATATAAAT
*
438961 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
438976 A
1 A
438977 TTTAGAATTT
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
11 4 0.09
12 2 0.05
13 1 0.02
14 1 0.02
15 31 0.70
16 5 0.11
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:438964 original size:42 final size:42
Alignment explanation
Indices: 438889--438977 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
438879 ATAATAAAAT
438889 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
438931 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
438973 AATAT
1 AATAT
438978 TTAGAATTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (42 bp):
AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
Found at i:439153 original size:18 final size:19
Alignment explanation
Indices: 439130--439173 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
439120 CCAGTAATCC
*
439130 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTA
439148 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
439168 TATTCC
1 TATTCC
439174 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:439161 original size:20 final size:20
Alignment explanation
Indices: 439136--439173 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
439126 ATCCTATTCC
*
439136 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
439156 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
439174 GTGAACCAAA
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:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:446405 original size:65 final size:64
Alignment explanation
Indices: 446314--446469 Score: 197
Period size: 65 Copynumber: 2.4 Consensus size: 64
446304 TAAACTTGGG
* * * * * *
446314 GTGCATCGGTACACTAATTACGTTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGTC
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAATAA-AGCCAAGAGTGCATCGATGCATGG-A
446378 T
64 T
* **
446379 GTGTATCGGTACACAAAATGCATTCGATGTTTCAATAAATTCAAGAGTGCATCGATGCATGGAT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAAGCCAAGAGTGCATCGATGCATGGAT
*
446443 GTGCATCAGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
446470 AATAGGGTGT
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 26 0.33
65 51 0.65
66 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAAGCCAAGAGTGCATCGATGCATGGAT
Found at i:446950 original size:38 final size:37
Alignment explanation
Indices: 446908--447131 Score: 215
Period size: 38 Copynumber: 6.3 Consensus size: 37
446898 ATTTTCGAAA
*
446908 ATATAGTTTTGAAAACGATTTTCGAAAATATATAT-AT
1 ATATAGTTTTGAAAAC-ATTTTTGAAAATATATATAAT
446945 CATATAGTTTTGAAAAC----------ATATATATAAT
1 -ATATAGTTTTGAAAACATTTTTGAAAATATATATAAT
* *
446973 ATATAGTTTTTGAAAATA-TGTTGAAAATATATATAAT
1 ATATAG-TTTTGAAAACATTTTTGAAAATATATATAAT
*
447010 ATATAGTTTTGAAAACATTTTTGAGAATATATATAAT
1 ATATAGTTTTGAAAACATTTTTGAAAATATATATAAT
*
447047 ATATAG-TTTGAAAATCATTTTTTGAATATATATATAAT
1 ATATAGTTTTGAAAA-CA-TTTTTGAAAATATATATAAT
* * * *
447085 GTATAGTTTTGAAAGCCTTTTTTGAAAATATAAATAAT
1 ATATAGTTTTGAAA-ACATTTTTGAAAATATATATAAT
447123 AT-TAGTTTT
1 ATATAGTTTT
447132 TTATACTATA
Statistics
Matches: 158, Mismatches: 12, Indels: 33
0.78 0.06 0.16
Matches are distributed among these distances:
27 14 0.09
28 11 0.07
36 18 0.11
37 49 0.31
38 58 0.37
39 8 0.05
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (37 bp):
ATATAGTTTTGAAAACATTTTTGAAAATATATATAAT
Found at i:446965 original size:25 final size:26
Alignment explanation
Indices: 446926--446975 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
446916 TTGAAAACGA
* *
446926 TTTTCGAAAATATATATATCATATAG
1 TTTTCGAAAACATATATATAATATAG
446952 TTTT-GAAAACATATATATAATATA
1 TTTTCGAAAACATATATATAATATA
446976 TAGTTTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (26 bp):
TTTTCGAAAACATATATATAATATAG
Done.