Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007837.1 Hibiscus syriacus cultivar Beakdansim tig00110186_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: 1003650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:172394 original size:325 final size:322
Alignment explanation
Indices: 171797--172812 Score: 1388
Period size: 325 Copynumber: 3.2 Consensus size: 322
171787 ACCAATCATA
* *
171797 AAGAGAACATCTCTATACTTATTGCTTATAGAAAATAAAGTTTCAAATAGATTATTACAAAG-AA
1 AAGAGAACATCTCTATACTTATTACTTATAGAAAAGAAAGTTTCAAATAGA-TATTACAAAGAAA
* * * *
171861 AAAATATTATTTTGGTGCTCGGAACATCGACTCCCTATATACTGAAAATTATTTGGCCACTATCA
65 AAAATATTATTTTGGTGCTCAGAACATCGATTCCCTATATGCTGAAAATCATTTGGCCACTATCA
171926 TTTGTGGAGAGATGTGAAATTGGAGTTAT--A--AT-A-ATAGAGAATGAATCAGAAAGTAGGAA
130 TTTGTGGAGAGATGTGAAATTGGAGTTATAAATTATAAGATAGAGAATGAATCAGAAAGTAGGAA
* * * * * * *
171985 GTCGTATATTCATTCAGTCAAACAACCTCCAGATGTCCGGCACAACACAAATAGGCTGCACCAGG
195 GTTGTATATTCATTCAGCCAAACAACCCCCAGATGTTCGGCACAGCACAAATAGGTTGCACCAGA
* *
172050 AAAACATCGAGGATGAAACCAATCATAATTACCTCCTATACTTCATCACCTTCATCTCTATTC
260 AAAACATCGAGGCTGAAACCAGTCATAATTACCTCCTATACTTCATCACCTTCATCTCTATTC
* * * *
172113 AATAAAAAAACTCTATACTTATTACTTATAGAAAAGAAAGTTTCAAATAGGATATTACAAAGAAA
1 AAGAGAACATCTCTATACTTATTACTTATAGAAAAGAAAGTTTCAAATA-GATATTACAAAG-AA
* * * * *
172178 AAAAATATTATTTTGGTGCTCAGAACACCGATTTCCTATATGCTGAAAATCATTTGACCATTGTC
64 AAAAATATTATTTTGGTGCTCAGAACATCGATTCCCTATATGCTGAAAATCATTTGGCCACTATC
* * *
172243 ATTAGTGAAGAGATGTGAAATTGGAGTTATAAATTATAAGGATAGAGAATGAATTAGAAAGTAGG
129 ATTTGTGGAGAGATGTGAAATTGGAGTTATAAATTATAA-GATAGAGAATGAATCAGAAAGTAGG
*
172308 AAGTTGTATATTCATTCAGCCAAAAAACCCCCAGATGTTCGGCACAGCACAAATAGGTTGCACCA
193 AAGTTGTATATTCATTCAGCCAAACAACCCCCAGATGTTCGGCACAGCACAAATAGGTTGCACCA
* * * * *
172373 GAAAAACATCGAGGCTGAAACCAGTTATAATTACCTCTTATACTTCATCCCCTTCCTTTCTATTC
258 GAAAAACATCGAGGCTGAAACCAGTCATAATTACCTCCTATACTTCATCACCTTCATCTCTATTC
* * *
172438 AAGAGAACATCTCTATACTTATTGCTTATAGAAAAGAAAGTTCCAAATAAAATATTACAAAGAAA
1 AAGAGAACATCTCTATACTTATTACTTATAGAAAAGAAAGTTTCAAAT-AGATATTACAAAGAAA
* * * * *
172503 AAATTATTATTTTGGTGCTTAGGACATAGATTCCCTATATGCTGAAAATCATTTGGCCACCATCA
65 AAAATATTATTTTGGTGCTCAGAACATCGATTCCCTATATGCTGAAAATCATTTGGCCACTATCA
* * * *
172568 TTTGTGGAGAGATGTAAAATTGGAGTTATAACTTATAAGAATAGAG--TGAATCAGGATGTAGGA
130 TTTGTGGAGAGATGTGAAATTGGAGTTATAAATTATAAG-ATAGAGAATGAATCAGAAAGTAGGA
* * * * *
172631 AGTTGTAAATTCATTCAGCCAAACAACCCTCAGATGATCGGCACAGCAGAAATAGGCTAGCTACA
194 AGTTGTATATTCATTCAGCCAAACAACCCCCAGATGTTCGGCACAGCACAAATAGG-T---TGCA
*
172696 CCA-AGAAAACATCGAGGCTGAAACCAGTCATAATTACCTCCTATACTTCATCATCTTCATCTCT
255 CCAGA-AAAACATCGAGGCTGAAACCAGTCATAATTACCTCCTATACTTCATCACCTTCATCTCT
172760 ATTC
319 ATTC
172764 AAGAGAACATCTCTATACTTATTGA-TTATAGAAAAGAAAGTTTCAAATA
1 AAGAGAACATCTCTATACTTATT-ACTTATAGAAAAGAAAGTTTCAAATA
172813 TATTTCTCTG
Statistics
Matches: 611, Mismatches: 71, Indels: 27
0.86 0.10 0.04
Matches are distributed among these distances:
316 53 0.09
317 2 0.00
318 85 0.14
320 1 0.00
322 67 0.11
323 3 0.00
324 98 0.16
325 193 0.32
326 109 0.18
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.29
Consensus pattern (322 bp):
AAGAGAACATCTCTATACTTATTACTTATAGAAAAGAAAGTTTCAAATAGATATTACAAAGAAAA
AAATATTATTTTGGTGCTCAGAACATCGATTCCCTATATGCTGAAAATCATTTGGCCACTATCAT
TTGTGGAGAGATGTGAAATTGGAGTTATAAATTATAAGATAGAGAATGAATCAGAAAGTAGGAAG
TTGTATATTCATTCAGCCAAACAACCCCCAGATGTTCGGCACAGCACAAATAGGTTGCACCAGAA
AAACATCGAGGCTGAAACCAGTCATAATTACCTCCTATACTTCATCACCTTCATCTCTATTC
Found at i:174645 original size:317 final size:316
Alignment explanation
Indices: 174108--174958 Score: 1299
Period size: 317 Copynumber: 2.7 Consensus size: 316
174098 AACTTAAAAT
* * *
174108 AAAAAATATTATTTTGGTGCTCGGAACACCGACTCCCTATCTACTGAAAATCATTTGGGCACCAT
1 AAAAAATATTATTTTGGTGCTCGGAACACCGATTCCCTATCTACTGAAAATCATTTGGACACTAT
* *
174173 CATTTGTGGAGATATGTGAAATTGGAGTTATAAGAATAGAGAATGAATAAGAAAGTAGGAAGTTG
66 CATTTGT-GAGAGATGTGAAATTGGAGTTATAATAATAGAGAATGAATAAGAAAGTAGGAAGTTG
* * * * *
174238 TATATTCACTCAGCCAAACAACCTCCAGATGTCCGGCACAACACACATAGACTGTACCAGGAAAA
130 TATATTCATTCAGCCAAACAACCTCCAGATGTCCGGCACAGCACAAATAGGCTGCACCAGGAAAA
* * *
174303 CATCGAGGATGAAACCAGTCATAATTACCTCCTATACTTCATTACCTTCCTCTCTATTCAAGAAA
195 CATCGAGGATGAAACCAATCATAATTACCTCCTATACTTCATCACCTTCATCTCTATTCAAGAAA
*
174368 AAATCTCTATACTTATTACTTTTAGAAAAGAAAGTTTCAAATAGGATATTACAAAGA
260 AAATCTCTATACTTATTACTTATAGAAAAGAAAGTTTCAAATAGGATATTACAAAGA
* * * *
174425 AAAAAATATTATTTTGGTGCTTGGAACATCGATTCCCTATATACTGAAAATTATTTGGACACTAT
1 AAAAAATATTATTTTGGTGCTCGGAACACCGATTCCCTATCTACTGAAAATCATTTGGACACTAT
* *
174490 CATTTGTAGAGAGATGTGAAATTGGAGTTATAATAATAGAGAATGAATCAGAAAGTAGGAAGTCG
66 CATTTGT-GAGAGATGTGAAATTGGAGTTATAATAATAGAGAATGAATAAGAAAGTAGGAAGTTG
*
174555 TATATTCATTCAGTCAAACAACCTCCAGATGTCCGGCACAGCACAAATAGGCTGCACCAGGAAAA
130 TATATTCATTCAGCCAAACAACCTCCAGATGTCCGGCACAGCACAAATAGGCTGCACCAGGAAAA
*
174620 CATCGAGGATGAACCCAATCATAATTACCTCCTATACTTCATCACCTTCATCTCTATTCAAGAAA
195 CATCGAGGATGAAACCAATCATAATTACCTCCTATACTTCATCACCTTCATCTCTATTCAAGAAA
174685 AAATCTCTATACTTATTACTTATAGAAAAGAAAGTTTCAAATAGGATATTACAAAGA
260 AAATCTCTATACTTATTACTTATAGAAAAGAAAGTTTCAAATAGGATATTACAAAGA
* * *
174742 AAAAAATATTATTTTGGTGCTCGGAACACCGATTTCCTATCTACTGAAAATCATTT-GACCATTG
1 AAAAAATATTATTTTGGTGCTCGGAACACCGATTCCCTATCTACTGAAAATCATTTGGA-CACTA
*
174806 TCATTTGTGAAGAGATGTGAAATTGGAGTTATAAATTATAATAATAGAGAATGAATTAGAAAGTA
65 TCATTTGTG-AGAGATGTGAAATTGGAG-------TTATAATAATAGAGAATGAATAAGAAAGTA
* * * * *
174871 GGAAGTTGTAAATTCATTCAGCCAAACAACCCCCAGATGTTCGGTATAGCACAAATAGGCTGCAC
122 GGAAGTTGTATATTCATTCAGCCAAACAACCTCCAGATGTCCGGCACAGCACAAATAGGCTGCAC
* *
174936 CAGAAAAACATCGAGGCTGAAAC
187 CAGGAAAACATCGAGGATGAAAC
174959 TAGTAAAACA
Statistics
Matches: 484, Mismatches: 41, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
316 3 0.01
317 374 0.77
324 107 0.22
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (316 bp):
AAAAAATATTATTTTGGTGCTCGGAACACCGATTCCCTATCTACTGAAAATCATTTGGACACTAT
CATTTGTGAGAGATGTGAAATTGGAGTTATAATAATAGAGAATGAATAAGAAAGTAGGAAGTTGT
ATATTCATTCAGCCAAACAACCTCCAGATGTCCGGCACAGCACAAATAGGCTGCACCAGGAAAAC
ATCGAGGATGAAACCAATCATAATTACCTCCTATACTTCATCACCTTCATCTCTATTCAAGAAAA
AATCTCTATACTTATTACTTATAGAAAAGAAAGTTTCAAATAGGATATTACAAAGA
Found at i:174968 original size:23 final size:23
Alignment explanation
Indices: 174934--175008 Score: 132
Period size: 23 Copynumber: 3.3 Consensus size: 23
174924 AATAGGCTGC
*
174934 ACCAGAAAAACATCGAGGCTGAA
1 ACCAGTAAAACATCGAGGCTGAA
*
174957 ACTAGTAAAACATCGAGGCTGAA
1 ACCAGTAAAACATCGAGGCTGAA
174980 ACCAGTAAAACATCGAGGCTGAA
1 ACCAGTAAAACATCGAGGCTGAA
175003 ACCAGT
1 ACCAGT
175009 CATAATTACC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.13
Consensus pattern (23 bp):
ACCAGTAAAACATCGAGGCTGAA
Found at i:175328 original size:370 final size:370
Alignment explanation
Indices: 174610--175328 Score: 1022
Period size: 370 Copynumber: 1.9 Consensus size: 370
174600 AATAGGCTGC
*
174610 ACCAGGAAAACATCGAGGATGAACCCAATCATAATTACCTCCTATACTTCATCACCTTCATCTCT
1 ACCAGGAAAACATCGAGGATGAAACCAATCATAATTACCTCCTATACTTCATCACCTTCATCTCT
* * * *
174675 ATTCAAGAAAAAATCTCTATACTTATTACTTATAGAAAAGAAAGTTTCAAATAGGATATTACAAA
66 ATTCAAGAAAAAATCTCTATACTTATTACTTATAGAAAAGAAAATTCCAAATAGAAAATTACAAA
* * *
174740 GAAAAAAATATTATTTTGGTGCTCGGAACACCGATTTCCTATCTACTGAAAATCATTTGACCATT
131 GAAAAAAATATTATTTTGGTGCTCGGAACACAGATTCCCTATATACTGAAAATCATTTGACCATT
* * * * *
174805 GTCATTTGTGAAGAGATGTGAAATTGGAGTTATAAATTATAATAATAGAGAATGAATTAGAAAGT
196 ATCATTTGTGAAGAGATATGAAATTGGAGTTATAAATTATAAGAATAGAGAATGAATCAGAAAGC
* * *
174870 AGGAAGTTGTAAATTCATTCAGCCAAACAACCCCCAGATGTTCGGTATAGCACAAATAGGCTGCA
261 AGGAAGTTGTAAATTCATTCAGCCAAACAACCCCCAGATGTTCGGCACAGCACAAACAGGCTGCA
174935 CCAGAAAAACATCGAGGCTGAAACTAGTAAAACATCGAGGCTGAA
326 CCAGAAAAACATCGAGGCTGAAACTAGTAAAACATCGAGGCTGAA
* * * * * *
174980 ACCAGTAAAACATCGAGGCTGAAACCAGTCATAATTACCTCCTATACTTCATCCCCTTCTTTTCT
1 ACCAGGAAAACATCGAGGATGAAACCAATCATAATTACCTCCTATACTTCATCACCTTCATCTCT
* * *
175045 ATTCAAGAGAAGATCTCTATACTTGTTGA-TTATAGAAAAGAAAATTCCAAATAGAAAATTAC-A
66 ATTCAAGAAAAAATCTCTATACTTATT-ACTTATAGAAAAGAAAATTCCAAATAGAAAATTACAA
* * *
175108 A-AAAAAAA-ATTATTTTGGTGCTCAGG-ACATAGATTCCCTATATGCTGAAAATCATTTGGCCA
130 AGAAAAAAATATTATTTTGGTGCTC-GGAACACAGATTCCCTATATACTGAAAATCATTTGACCA
* *
175170 TTATCATTTGTGGAGAGATATGAAATTGGAGTTATAACTTATAAGAATAGAGAATGAATCA-AAA
194 TTATCATTTGTGAAGAGATATGAAATTGGAGTTATAAATTATAAGAATAGAGAATGAATCAGAAA
* *
175234 TGCAGGAAGTTGTAAATTCATTCAGCCAAACAA-CCTCAGATGTTCGGCACAGCAGAAACAGGCT
259 -GCAGGAAGTTGTAAATTCATTCAGCCAAACAACCCCCAGATGTTCGGCACAGCACAAACAGGCT
175298 AGCTACACCA-AGAAAACATCGAGGCTGAAAC
323 -G---CACCAGA-AAAACATCGAGGCTGAAAC
175329 CAGTCATAAT
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
366 29 0.09
367 132 0.43
368 9 0.03
369 3 0.01
370 135 0.44
371 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (370 bp):
ACCAGGAAAACATCGAGGATGAAACCAATCATAATTACCTCCTATACTTCATCACCTTCATCTCT
ATTCAAGAAAAAATCTCTATACTTATTACTTATAGAAAAGAAAATTCCAAATAGAAAATTACAAA
GAAAAAAATATTATTTTGGTGCTCGGAACACAGATTCCCTATATACTGAAAATCATTTGACCATT
ATCATTTGTGAAGAGATATGAAATTGGAGTTATAAATTATAAGAATAGAGAATGAATCAGAAAGC
AGGAAGTTGTAAATTCATTCAGCCAAACAACCCCCAGATGTTCGGCACAGCACAAACAGGCTGCA
CCAGAAAAACATCGAGGCTGAAACTAGTAAAACATCGAGGCTGAA
Found at i:180533 original size:19 final size:19
Alignment explanation
Indices: 180511--180550 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
180501 TCGGGTCGGG
180511 TCAGACCGGTCAAACCAGT
1 TCAGACCGGTCAAACCAGT
*
180530 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCAGT
180549 TC
1 TC
180551 GAACCAGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.23, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCAGT
Found at i:180548 original size:9 final size:9
Alignment explanation
Indices: 180509--180598 Score: 54
Period size: 9 Copynumber: 9.3 Consensus size: 9
180499 GGTCGGGTCG
*
180509 GGTCAGACC
1 GGTCAAACC
180518 GGTCAAACC
1 GGTCAAACC
* *
180527 AGTTCAGACC
1 -GGTCAAACC
180537 GGTCAAACC
1 GGTCAAACC
*
180546 GGTTCGAACC
1 GG-TCAAACC
* *
180556 AGTTGAAACC
1 -GGTCAAACC
180566 GGTCAGAACC
1 GGTCA-AACC
*
180576 GGTTGAAAACC
1 GG-T-CAAACC
*
180587 GGTTAAACC
1 GGTCAAACC
180596 GGT
1 GGT
180599 TTCCAGCAGC
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
9 28 0.45
10 25 0.40
11 8 0.13
12 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:180599 original size:9 final size:10
Alignment explanation
Indices: 180515--180599 Score: 70
Period size: 10 Copynumber: 8.7 Consensus size: 10
180505 GTCGGGTCAG
180515 ACCGG-TCAA
1 ACCGGTTCAA
* *
180524 ACCAGTTCAG
1 ACCGGTTCAA
180534 ACCGG-TCAA
1 ACCGGTTCAA
*
180543 ACCGGTTCGA
1 ACCGGTTCAA
* *
180553 ACCAGTTGAA
1 ACCGGTTCAA
180563 ACCGG-TCAGA
1 ACCGGTTCA-A
*
180573 ACCGGTTGAAA
1 ACCGGTT-CAA
180584 ACCGGTT-AA
1 ACCGGTTCAA
180593 ACCGGTT
1 ACCGGTT
180600 TCCAGCAGCC
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
9 23 0.38
10 27 0.45
11 9 0.15
12 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.18
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:183070 original size:40 final size:38
Alignment explanation
Indices: 183026--183104 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 38
183016 TAAAATATTT
*
183026 ATTATGATAATTAAATTA-ATAAATAGACATATTATATAAA
1 ATTAT-ATAATAAAATTATATAAATAGA-A-ATTATATAAA
* *
183066 ATTATTTAATAAAATTATTTAAATAGAAATTATATAAA
1 ATTATATAATAAAATTATATAAATAGAAATTATATAAA
183104 A
1 A
183105 CATAATTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 11 0.31
39 11 0.31
40 13 0.37
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (38 bp):
ATTATATAATAAAATTATATAAATAGAAATTATATAAA
Found at i:183081 original size:39 final size:39
Alignment explanation
Indices: 183033--183118 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 39
183023 TTTATTATGA
* * *
183033 TAATTAAATTA-ATAAATAGACATATTATATAAAA-TTATT
1 TAATAAAATTATATAAATAGA-A-ATTATATAAAACATAAT
*
183072 TAATAAAATTATTTAAATAGAAATTATATAAAACATAAT
1 TAATAAAATTATATAAATAGAAATTATATAAAACATAAT
183111 TAATAAAA
1 TAATAAAA
183119 ATATTGGCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 11 0.27
39 22 0.54
40 8 0.20
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (39 bp):
TAATAAAATTATATAAATAGAAATTATATAAAACATAAT
Found at i:183097 original size:15 final size:14
Alignment explanation
Indices: 183061--183103 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
183051 GACATATTAT
183061 ATAAAATTATTT-A
1 ATAAAATTATTTAA
183074 ATAAAATTATTTAA
1 ATAAAATTATTTAA
*
183088 ATAGAAATTATATAA
1 ATA-AAATTATTTAA
183103 A
1 A
183104 ACATAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 12 0.44
14 4 0.15
15 11 0.41
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:183120 original size:40 final size:40
Alignment explanation
Indices: 183045--183123 Score: 108
Period size: 39 Copynumber: 2.0 Consensus size: 40
183035 ATTAAATTAA
* *
183045 TAAATAGACATATTATATAAAATTATTTAATAAAATTATT
1 TAAATAGACATATTATATAAAAATAATTAATAAAATTATT
*
183085 TAAATAGA-A-ATTATATAAAACATAATTAATAAAAATATT
1 TAAATAGACATATTATATAAAA-ATAATTAATAAAATTATT
183124 GGCATTGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
38 11 0.31
39 16 0.46
40 8 0.23
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (40 bp):
TAAATAGACATATTATATAAAAATAATTAATAAAATTATT
Found at i:183183 original size:23 final size:24
Alignment explanation
Indices: 183143--183196 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
183133 TAATGATTAA
*
183143 ATGTAAATTAATATAGTTTAGTTT
1 ATGTAAATTAATATAGTTTAATTT
183167 ATGTAAATT-ATATAGTTTAATTT
1 ATGTAAATTAATATAGTTTAATTT
183190 ATGTAAA
1 ATGTAAA
183197 GAAAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (24 bp):
ATGTAAATTAATATAGTTTAATTT
Found at i:183467 original size:25 final size:28
Alignment explanation
Indices: 183419--183487 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 28
183409 CCTTAATATA
183419 AATTATATATTATAATTAATATTAATAC
1 AATTATATATTATAATTAATATTAATAC
* *
183447 AATTA-ATATTA-ACTT-ATATTAATAT
1 AATTATATATTATAATTAATATTAATAC
183472 AA-TATAGT-TTATAATT
1 AATTATA-TATTATAATT
183488 TGTAATTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
24 2 0.06
25 15 0.43
26 7 0.20
27 6 0.17
28 5 0.14
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (28 bp):
AATTATATATTATAATTAATATTAATAC
Found at i:183529 original size:31 final size:30
Alignment explanation
Indices: 183491--183677 Score: 108
Period size: 31 Copynumber: 5.8 Consensus size: 30
183481 TATAATTTGT
183491 AATTAATATTAATATAAAATATAGTCTATAA
1 AATTAATATTAATATAAAATATAGT-TATAA
* *
183522 AATTAATATTAATATAAACTATA-TTTTATA
1 AATTAATATTAATATAAAATATAGTTATA-A
* * *
183552 AATTATATAGTATAGTTTATAAATTATAGTTAATAT
1 AATTA-ATA-T-TA--ATATAAAATATAGTT-ATAA
* **
183588 AATTTATATTAATATAGTATATAGTTTATAA
1 AATTAATATTAATATAAAATATAG-TTATAA
* *
183619 ACTATATACTATATTAATATAAATTACAGTTA-AGA
1 A--AT-TA--ATATTAATATAAAATATAGTTATA-A
* *
183654 TAATTAACATTAATATAAACTATA
1 -AATTAATATTAATATAAAATATA
183678 TAGTACATTA
Statistics
Matches: 120, Mismatches: 20, Indels: 32
0.70 0.12 0.19
Matches are distributed among these distances:
29 3 0.03
30 7 0.06
31 53 0.44
32 3 0.03
33 8 0.07
34 5 0.04
35 17 0.14
36 22 0.18
37 2 0.02
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (30 bp):
AATTAATATTAATATAAAATATAGTTATAA
Found at i:183543 original size:24 final size:25
Alignment explanation
Indices: 183498--183544 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
183488 TGTAATTAAT
**
183498 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
183523 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
183545 TTTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:183565 original size:21 final size:21
Alignment explanation
Indices: 183541--183644 Score: 86
Period size: 21 Copynumber: 4.8 Consensus size: 21
183531 TAATATAAAC
183541 TATATTTTATAAATTATATAG
1 TATATTTTATAAATTATATAG
* *
183562 TATAGTTTATAAATTATAGTTAA
1 TATATTTTATAAATTATA--TAG
*
183585 TATAATTTAT--ATTAATATAG
1 TATATTTTATAAATT-ATATAG
* *
183605 TATATAGTTTATAAACTATATAC
1 TATAT--TTTATAAATTATATAG
*
183628 TATATTAATATAAATTA
1 TATATT-TTATAAATTA
183645 CAGTTAAGAT
Statistics
Matches: 66, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
20 6 0.09
21 21 0.32
22 16 0.24
23 21 0.32
24 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (21 bp):
TATATTTTATAAATTATATAG
Found at i:183581 original size:66 final size:64
Alignment explanation
Indices: 183503--183713 Score: 185
Period size: 66 Copynumber: 3.2 Consensus size: 64
183493 TTAATATTAA
* *
183503 TATAAAATATAGTCTATAAAATTAATATTAATATAAACTATATTTTATAAATTATATAGTATAGT
1 TATAAATTATAGT-TATAAAATTAATATTAATATAAACTATATTTTATAAA-TATATACTATAGT
183568 T
64 T
* * * *
183569 TATAAATTATAGTTAATATAATTTATATTAATATAGTA-TATAGTTTATAAACTATATACTATA-
1 TATAAATTATAGTT-ATAAAATTAATATTAATATA-AACTATATTTTATAAA-TATATACTATAG
183632 TT
63 TT
* * ** * * *
183634 AATATAAATTACAGTTA-AGATAATTAACATTAATATAAACTATATAGTACATTAATATAAATTA
1 --TATAAATTATAGTTATA-A-AATTAATATTAATATAAACTATAT--TTTATAAATATATACTA
183698 TAGTT
60 TAGTT
183703 TATAAATTATA
1 TATAAATTATA
183714 TACTATAAGT
Statistics
Matches: 116, Mismatches: 19, Indels: 19
0.75 0.12 0.12
Matches are distributed among these distances:
65 4 0.03
66 54 0.47
67 42 0.36
68 9 0.08
69 7 0.06
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (64 bp):
TATAAATTATAGTTATAAAATTAATATTAATATAAACTATATTTTATAAATATATACTATAGTT
Found at i:183610 original size:15 final size:16
Alignment explanation
Indices: 183562--183626 Score: 57
Period size: 15 Copynumber: 4.2 Consensus size: 16
183552 AATTATATAG
*
183562 TATAGTTTATA-AAT-
1 TATAGTTAATATAATA
*
183576 TATAGTTAATATAATT
1 TATAGTTAATATAATA
*
183592 TATA-TTAATATAGTA
1 TATAGTTAATATAATA
*
183607 TATAGTTTATA-AACTA
1 TATAGTTAATATAA-TA
183623 TATA
1 TATA
183627 CTATATTAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
14 10 0.24
15 17 0.40
16 15 0.36
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.48
Consensus pattern (16 bp):
TATAGTTAATATAATA
Found at i:183617 original size:133 final size:132
Alignment explanation
Indices: 183449--183713 Score: 315
Period size: 133 Copynumber: 2.0 Consensus size: 132
183439 ATTAATACAA
** * * *
183449 TTAATATTAACTTATATTAATATAATATAGTTTATAATTTGTA-ATTAATATTAATATAAAATAT
1 TTAATATTAACTTATATTAATATAATATAGTTTATAAACTATATACT-ATATTAATATAAAATAC
* ** *
183513 AGTCTATA-A-AATTAATATTAATATAAACTATAT-TTTATAAATTATATAGTATAGTTTATAAA
65 AGT-TA-AGATAATTAACATTAATATAAACTATATATACATAAA-TATAAAGTATAGTTTATAAA
183575 TTATAG
127 TTATAG
* *
183581 TTAATA-TAATTTATATTAATATAGTATATAGTTTATAAACTATATACTATATTAATATAAATTA
1 TTAATATTAACTTATATTAATATA--ATATAGTTTATAAACTATATACTATATTAATATAAAATA
* *
183645 CAGTTAAGATAATTAACATTAATATAAACTATATAGTACATTAATATAAATTATAGTTTATAAAT
64 CAGTTAAGATAATTAACATTAATATAAACTATATA-TACATAAATATAAAGTATAGTTTATAAAT
183710 TATA
128 TATA
183714 TACTATAAGT
Statistics
Matches: 113, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
131 17 0.15
132 9 0.08
133 57 0.50
134 25 0.22
135 5 0.04
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.45
Consensus pattern (132 bp):
TTAATATTAACTTATATTAATATAATATAGTTTATAAACTATATACTATATTAATATAAAATACA
GTTAAGATAATTAACATTAATATAAACTATATATACATAAATATAAAGTATAGTTTATAAATTAT
AG
Found at i:183701 original size:20 final size:22
Alignment explanation
Indices: 183660--183762 Score: 97
Period size: 22 Copynumber: 4.8 Consensus size: 22
183650 AAGATAATTA
183660 ACATTAATATAAACTATATAGT
1 ACATTAATATAAACTATATAGT
183682 ACATTAATATAAA-T-TATAGT
1 ACATTAATATAAACTATATAGT
** * *
183702 TTATAAATTATATACTATA-AGT
1 ACATTAA-TATAAACTATATAGT
* *
183724 -TATAAAGTATAAACTATATAGT
1 ACATTAA-TATAAACTATATAGT
*
183746 ACACTAATATAAACTAT
1 ACATTAATATAAACTAT
183763 TGTTTATAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
20 10 0.15
21 22 0.33
22 30 0.45
23 5 0.07
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.38
Consensus pattern (22 bp):
ACATTAATATAAACTATATAGT
Found at i:183720 original size:21 final size:20
Alignment explanation
Indices: 183689--183741 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
183679 AGTACATTAA
* *
183689 TATAAATTATAGTTTATAAAT
1 TATAAACTATAG-TTATAAAG
*
183710 TATATACTATAAGTTATAAAG
1 TATAAACTAT-AGTTATAAAG
183731 TATAAACTATA
1 TATAAACTATA
183742 TAGTACACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.89
22 2 0.07
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (20 bp):
TATAAACTATAGTTATAAAG
Found at i:183742 original size:133 final size:131
Alignment explanation
Indices: 183496--183745 Score: 285
Period size: 133 Copynumber: 1.9 Consensus size: 131
183486 TTTGTAATTA
* * ** *
183496 ATATTAATATAAAATATAGTCTATAAAATTAATATTAATATAAACTATATTTTATAAATTATATA
1 ATATTAATATAAAATACAGTCTATAAAATTAACATTAATATAAACTATATTACATAAATTATAAA
* *
183561 GTATAGTTTATAAATTATAGTTAATATAATTTATATTAATATAGTATATAGTTTATAAACTATAT
66 GTATAGTTTATAAATTATAG-TAATATAAGTTATA-TAATATACTATATAGTTTATAAACTATAT
183626 ACT
129 ACT
* *
183629 ATATTAATATAAATTACAGT-TA-AGATAATTAACATTAATATAAACTATATAGTACATTAA-TA
1 ATATTAATATAAAATACAGTCTATA-A-AATTAACATTAATATAAACTATAT--TACATAAATTA
* *
183691 TAAATTATAGTTTATAAATTATA-TACTATAAGTTATA-AAGTATAAACTATATAGT
62 TAAAGTATAGTTTATAAATTATAGTAATATAAGTTATATAA-TAT--ACTATATAGT
183746 ACACTAATAT
Statistics
Matches: 99, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
130 2 0.02
131 4 0.04
132 15 0.15
133 50 0.51
134 23 0.23
135 5 0.05
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (131 bp):
ATATTAATATAAAATACAGTCTATAAAATTAACATTAATATAAACTATATTACATAAATTATAAA
GTATAGTTTATAAATTATAGTAATATAAGTTATATAATATACTATATAGTTTATAAACTATATAC
T
Found at i:183746 original size:14 final size:14
Alignment explanation
Indices: 183689--183746 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
183679 AGTACATTAA
*
183689 TATAAATTATAGT-T
1 TATAAATTATA-TAG
*
183703 TATAAATTATATAC
1 TATAAATTATATAG
* *
183717 TATAAGTTATAAAG
1 TATAAATTATATAG
*
183731 TATAAACTATATAG
1 TATAAATTATATAG
183745 TA
1 TA
183747 CACTAATATA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
13 1 0.03
14 35 0.97
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.41
Consensus pattern (14 bp):
TATAAATTATATAG
Found at i:183811 original size:20 final size:21
Alignment explanation
Indices: 183781--183887 Score: 109
Period size: 20 Copynumber: 5.2 Consensus size: 21
183771 AACTATAGGT
183781 TACATAT--ATAGTTTATATA
1 TACATATAAATAGTTTATATA
183800 -ACATATAAATAGATTGTATATA
1 TACATATAAATAG-TT-TATATA
*
183822 TACATATAATATAGGTTATATA
1 TACATATAA-ATAGTTTATATA
*
183844 T--ATATATATAGTTTATATA
1 TACATATAAATAGTTTATATA
* *
183863 TAC-TATATATAGTTTATACA
1 TACATATAAATAGTTTATATA
183883 TACAT
1 TACAT
183888 GTACTATAAG
Statistics
Matches: 75, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
18 6 0.08
19 12 0.16
20 28 0.37
21 3 0.04
22 13 0.17
23 9 0.12
24 4 0.05
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (21 bp):
TACATATAAATAGTTTATATA
Found at i:183819 original size:22 final size:24
Alignment explanation
Indices: 183786--183853 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
183776 TAGGTTACAT
183786 ATATAG-TT-TATATA-ACATATA
1 ATATAGATTATATATATACATATA
*
183807 A-ATAGATTGTATATATACATATA
1 ATATAGATTATATATATACATATA
* *
183830 ATATAGGTTATATATATATATATA
1 ATATAGATTATATATATACATATA
183854 GTTTATATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
20 4 0.10
21 3 0.08
22 6 0.15
23 8 0.20
24 19 0.47
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (24 bp):
ATATAGATTATATATATACATATA
Found at i:183845 original size:39 final size:39
Alignment explanation
Indices: 183784--183880 Score: 97
Period size: 41 Copynumber: 2.4 Consensus size: 39
183774 TATAGGTTAC
* *
183784 ATATATAGTTTATATAACATATAAATAGA-TTGTATATATACAT
1 ATATATAGGTTATAT---ATATATATAGAGTT-TATATATAC-T
*
183827 ATAATATAGGTTATATATATATATATAGTTTATATATACT
1 AT-ATATAGGTTATATATATATATAGAGTTTATATATACT
*
183867 ATATATAGTTTATA
1 ATATATAGGTTATA
183881 CATACATGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
39 11 0.23
40 3 0.06
41 18 0.38
42 2 0.04
43 2 0.04
44 12 0.25
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (39 bp):
ATATATAGGTTATATATATATATAGAGTTTATATATACT
Found at i:183907 original size:63 final size:64
Alignment explanation
Indices: 183784--183933 Score: 166
Period size: 63 Copynumber: 2.4 Consensus size: 64
183774 TATAGGTTAC
* * *
183784 ATATATAGTTTATATA-ACATATAAATAGATTGTATATATACATATAATATAGGTTATATATA-T
1 ATATATAGTTTATATATAC-TATATATAGATTGTATACATACATATAATATAAGTTATATATAGT
* *
183847 ATATATAGTTTATATATACTATATATAG-TT-TATACATACATGTACTATAAGTTACGTATATAG
1 ATATATAGTTTATATATACTATATATAGATTGTATACATACATATAATATAAGTTA--TATATAG
183910 T
64 T
* * *
183911 TTATAT-GTATACATATACTATAT
1 ATATATAGTTTATATATACTATAT
183934 GTTACATATA
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
61 20 0.27
62 2 0.03
63 45 0.60
64 8 0.11
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (64 bp):
ATATATAGTTTATATATACTATATATAGATTGTATACATACATATAATATAAGTTATATATAGT
Found at i:183913 original size:35 final size:36
Alignment explanation
Indices: 183867--183943 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
183857 TATATATACT
*
183867 ATATATAGTTTATA-CATACATGTACTATAAGTTAC
1 ATATATAGTTTATAGCATACATATACTATAAGTTAC
* * *
183902 GTATATAGTTTATATGTATACATATACTATATGTTAC
1 ATATATAGTTTATA-GCATACATATACTATAAGTTAC
183939 ATATA
1 ATATA
183944 CTAACTATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 13 0.37
37 22 0.63
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (36 bp):
ATATATAGTTTATAGCATACATATACTATAAGTTAC
Found at i:183941 original size:16 final size:17
Alignment explanation
Indices: 183912--183946 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
183902 GTATATAGTT
183912 TATATGTATACATATAC
1 TATATGTATACATATAC
183929 TATATGT-TACATATAC
1 TATATGTATACATATAC
183945 TA
1 TA
183947 ACTATTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (17 bp):
TATATGTATACATATAC
Found at i:184062 original size:7 final size:7
Alignment explanation
Indices: 184050--184109 Score: 84
Period size: 7 Copynumber: 8.6 Consensus size: 7
184040 TACATATATA
184050 GTTTAGG
1 GTTTAGG
184057 GTTTAGG
1 GTTTAGG
* *
184064 ATATAGG
1 GTTTAGG
184071 GTTTAGG
1 GTTTAGG
184078 GTTTAGG
1 GTTTAGG
* *
184085 ATTTATG
1 GTTTAGG
184092 GTTTAGG
1 GTTTAGG
184099 GTTTAGG
1 GTTTAGG
184106 GTTT
1 GTTT
184110 CTATAAACTA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:184074 original size:21 final size:21
Alignment explanation
Indices: 184050--184105 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
184040 TACATATATA
184050 GTTTAGGGTTTAGGATATAGG
1 GTTTAGGGTTTAGGATATAGG
* *
184071 GTTTAGGGTTTAGGATTTATG
1 GTTTAGGGTTTAGGATATAGG
184092 GTTTAGGGTTTAGG
1 GTTTAGGGTTTAGG
184106 GTTTCTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.43
Consensus pattern (21 bp):
GTTTAGGGTTTAGGATATAGG
Found at i:186460 original size:17 final size:17
Alignment explanation
Indices: 186436--186499 Score: 65
Period size: 19 Copynumber: 3.5 Consensus size: 17
186426 TGTTTAATGA
186436 TATATATATATATATGTGT
1 TATATATATATATA-GT-T
*
186455 TATATATATACATAGTT
1 TATATATATATATAGTT
*
186472 TATATATACTATACATATTT
1 TATATATA-TAT--ATAGTT
186492 TATATATA
1 TATATATA
186500 CATGTATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
17 9 0.23
18 4 0.10
19 13 0.33
20 13 0.33
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (17 bp):
TATATATATATATAGTT
Found at i:186486 original size:20 final size:20
Alignment explanation
Indices: 186455--186500 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
186445 ATATATGTGT
186455 TATATA-TATACATAGTTTA
1 TATATACTATACATAGTTTA
*
186474 TATATACTATACATATTTTA
1 TATATACTATACATAGTTTA
186494 TATATAC
1 TATATAC
186501 ATGTATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (20 bp):
TATATACTATACATAGTTTA
Found at i:186536 original size:7 final size:7
Alignment explanation
Indices: 186524--186549 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
186514 TACATATATA
186524 GTTTAGG
1 GTTTAGG
186531 GTTTAGG
1 GTTTAGG
186538 GTTTAGG
1 GTTTAGG
186545 GTTTA
1 GTTTA
186550 CAGTTTACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:186555 original size:14 final size:14
Alignment explanation
Indices: 186523--186576 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
186513 CTACATATAT
*
186523 AGTTTAGGGTTTAG
1 AGTTTAGGGTTTAA
* *
186537 GGTTTAGGGTTTAC
1 AGTTTAGGGTTTAA
* *
186551 AGTTTACGATTTAA
1 AGTTTAGGGTTTAA
186565 AGTTTAGAGGTT
1 AGTTTAG-GGTT
186577 AGGACTTAGG
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
14 28 0.90
15 3 0.10
ACGTcount: A:0.24, C:0.04, G:0.30, T:0.43
Consensus pattern (14 bp):
AGTTTAGGGTTTAA
Found at i:186603 original size:33 final size:33
Alignment explanation
Indices: 186566--186636 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
186556 ACGATTTAAA
186566 GTTTAGAGGTTAGGACTTAGGGATTGATTTAGG
1 GTTTAGAGGTTAGGACTTAGGGATTGATTTAGG
186599 GTTTAGAGGTTAGGACTTAGGGATTGATTTAGG
1 GTTTAGAGGTTAGGACTTAGGGATTGATTTAGG
186632 GTTTA
1 GTTTA
186637 AAGTTTCTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.24, C:0.03, G:0.35, T:0.38
Consensus pattern (33 bp):
GTTTAGAGGTTAGGACTTAGGGATTGATTTAGG
Found at i:186710 original size:2 final size:2
Alignment explanation
Indices: 186699--186754 Score: 55
Period size: 2 Copynumber: 28.5 Consensus size: 2
186689 TTCTATAAAC
*
186699 TA TA -A TA TA TA TA TA TA TA TA TA TA TA T- TA GT- TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
*
186739 CA TA TA TA TA CTA TA T
1 TA TA TA TA TA -TA TA T
186755 TAATATAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
1 3 0.07
2 39 0.87
3 3 0.07
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:186824 original size:13 final size:13
Alignment explanation
Indices: 186806--186862 Score: 69
Period size: 13 Copynumber: 4.2 Consensus size: 13
186796 TTATACATGT
186806 ATAGTTTATATAC
1 ATAGTTTATATAC
*
186819 ATAGTTTATATAT
1 ATAGTTTATATAC
*
186832 ATAGTTCATATAAAC
1 ATAGTT--TATATAC
*
186847 ATAATTTATATAC
1 ATAGTTTATATAC
186860 ATA
1 ATA
186863 TAACTTATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 27 0.73
15 10 0.27
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (13 bp):
ATAGTTTATATAC
Found at i:186830 original size:15 final size:15
Alignment explanation
Indices: 186812--186858 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
186802 ATGTATAGTT
186812 TATATACATAGTTTA
1 TATATACATAGTTTA
*
186827 TATAT--ATAGTTCA
1 TATATACATAGTTTA
* *
186840 TATAAACATAATTTA
1 TATATACATAGTTTA
186855 TATA
1 TATA
186859 CATATAACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 11 0.42
15 15 0.58
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (15 bp):
TATATACATAGTTTA
Found at i:186842 original size:26 final size:27
Alignment explanation
Indices: 186805--186858 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
186795 CTTATACATG
* *
186805 TATAGTTTATAT-ACATAGTTTATATA
1 TATAGTTCATATAACATAATTTATATA
186831 TATAGTTCATATAAACATAATTTATATA
1 TATAGTTCATAT-AACATAATTTATATA
186859 CATATAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 11 0.46
28 13 0.54
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (27 bp):
TATAGTTCATATAACATAATTTATATA
Found at i:194356 original size:24 final size:24
Alignment explanation
Indices: 194329--194375 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
194319 TTTTGACAAA
*
194329 TTTTAAAATATAACATATAATTTT
1 TTTTAAAACATAACATATAATTTT
*
194353 TTTTGAAACATAACATATAATTT
1 TTTTAAAACATAACATATAATTT
194376 GTTGATTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTTAAAACATAACATATAATTTT
Found at i:206874 original size:2 final size:2
Alignment explanation
Indices: 206867--206907 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
206857 TTCCAGTTCT
206867 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
206908 ATATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:210014 original size:20 final size:19
Alignment explanation
Indices: 209991--210033 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
209981 TAATAAAAAA
209991 TTATTAAAATTATTATTATT
1 TTATTAAAATTATTATT-TT
* **
210011 TTATTGATTTTATTATTTT
1 TTATTAAAATTATTATTTT
210030 TTAT
1 TTAT
210034 CGATTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATTAAAATTATTATTTT
Found at i:210033 original size:19 final size:20
Alignment explanation
Indices: 210000--210046 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
209990 ATTATTAAAA
*
210000 TTATTATTATTTTATTGATT
1 TTATTATTATTTTATCGATT
210020 TTATTATT-TTTTATCGATT
1 TTATTATTATTTTATCGATT
210039 TTATTATT
1 TTATTATT
210047 GTTAGACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.70
Consensus pattern (20 bp):
TTATTATTATTTTATCGATT
Found at i:215893 original size:4 final size:4
Alignment explanation
Indices: 215884--216417 Score: 1052
Period size: 4 Copynumber: 133.5 Consensus size: 4
215874 TCTTTTTTAC
215884 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
215932 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
215980 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
216028 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
216076 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
216124 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
216172 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATAGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT-GT
216221 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
216269 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
216317 ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
216364 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
216412 ATGT AT
1 ATGT AT
216418 ACATTTGCAG
Statistics
Matches: 528, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
3 3 0.01
4 521 0.99
5 4 0.01
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:221294 original size:24 final size:25
Alignment explanation
Indices: 221236--221297 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 25
221226 TTTTTCGGAT
221236 AAAAAACCGGATTTTTATCCGGTTTGA
1 AAAAAACCGG-TTTTTATCCGG-TTGA
221263 AAAAAACCGGTTTTTAATCCGG-T-A
1 AAAAAACCGGTTTTT-ATCCGGTTGA
221287 AAAAAACCGGT
1 AAAAAACCGGT
221298 CGTTCAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
24 12 0.35
25 1 0.03
26 5 0.15
27 16 0.47
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (25 bp):
AAAAAACCGGTTTTTATCCGGTTGA
Found at i:225627 original size:14 final size:14
Alignment explanation
Indices: 225608--225638 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
225598 CGTCGTAGAA
225608 GTCTCGACATCCAT
1 GTCTCGACATCCAT
225622 GTCTCGACATCCAT
1 GTCTCGACATCCAT
225636 GTC
1 GTC
225639 AGCCTTGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.35, G:0.16, T:0.29
Consensus pattern (14 bp):
GTCTCGACATCCAT
Found at i:228640 original size:2 final size:2
Alignment explanation
Indices: 228635--228673 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
228625 AAATCTTTTG
228635 TA TA TA TA 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 TA TA TA TA T
228674 GTATTTAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:229042 original size:23 final size:24
Alignment explanation
Indices: 228994--229054 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 24
228984 CGTTCGTGAA
*
228994 CGTTCGGTTATGTTCGTTTATATG
1 CGTTCAGTTATGTTCGTTTATATG
* *
229018 CGTTTAGTTATGTTCG-TTATGTG
1 CGTTCAGTTATGTTCGTTTATATG
*
229041 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
229055 AACCTAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.13, C:0.11, G:0.23, T:0.52
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATATG
Found at i:232329 original size:64 final size:63
Alignment explanation
Indices: 232244--232404 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
232234 TTGTTTAAGG
* * * *
232244 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAGGATTTA
* * * *
232308 TGCATCGATGCATAAGGAGTGCATTGATGCATCCCCATTAAATACAAACATCGAATATGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAGGATTTA
*
232372 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
232405 ACCTTCATTA
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
63 1 0.01
64 60 0.72
65 21 0.25
66 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATAGGATTTA
Found at i:232719 original size:18 final size:19
Alignment explanation
Indices: 232682--232720 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
232672 GTGTAGTTAA
*
232682 ATTATATGTGATTATCTGT
1 ATTATATGTGATTATATGT
*
232701 ATTATAT-TGATTGTATGT
1 ATTATATGTGATTATATGT
232719 AT
1 AT
232721 GCATGACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (19 bp):
ATTATATGTGATTATATGT
Found at i:234060 original size:145 final size:147
Alignment explanation
Indices: 233772--234082 Score: 547
Period size: 145 Copynumber: 2.1 Consensus size: 147
233762 GAGTCGAGGG
* *
233772 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGA-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
233837 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTGTTA
65 ACTTGATCCCTAGTATATG-ATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
233902 TATGGCACTACGGTGCAAT
129 TATGGCACTACGGTGCAAT
233921 TCTACGCGGTCCTTCGGG-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATA
1 TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATA
233985 CTTGATCCCTAGTATATG-TATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATA
66 CTTGATCCCTAGTATATGATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATA
234049 TGGCACTACGGTGCAAT
131 TGGCACTACGGTGCAAT
234066 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
234083 TGCAATTATA
Statistics
Matches: 158, Mismatches: 3, Indels: 6
0.95 0.02 0.04
Matches are distributed among these distances:
144 1 0.01
145 77 0.49
147 62 0.39
149 18 0.11
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (147 bp):
TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATA
CTTGATCCCTAGTATATGATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATA
TGGCACTACGGTGCAAT
Found at i:234083 original size:23 final size:23
Alignment explanation
Indices: 234050--234094 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
234040 ATTATTATAT
*
234050 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
234073 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
234095 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:237137 original size:10 final size:10
Alignment explanation
Indices: 237122--237173 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
237112 GGGTCTCCAA
237122 CGTTTATGTT
1 CGTTTATGTT
237132 CGTTTATGTT
1 CGTTTATGTT
237142 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* *
237153 ATGTTTGTGTT
1 -CGTTTATGTT
237164 CGTTTATGTT
1 CGTTTATGTT
237174 TGTGTACGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 22 0.65
11 8 0.24
12 4 0.12
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.60
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:237153 original size:16 final size:16
Alignment explanation
Indices: 237128--237192 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
237118 CCAACGTTTA
237128 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
237144 TGTTCATTTATGTTTG
1 TGTTCGTTTATGTTCG
*
237160 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
*
237176 TGTACGTTTATGTTCG
1 TGTTCGTTTATGTTCG
237192 T
1 T
237193 TTATTTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.09, C:0.09, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:237173 original size:26 final size:26
Alignment explanation
Indices: 237144--237196 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
237134 TTTATGTTCG
* * *
237144 TGTTCATTTATGTTTGTGTTCGTTTA
1 TGTTCATGTACGTTTATGTTCGTTTA
**
237170 TGTTTGTGTACGTTTATGTTCGTTTA
1 TGTTCATGTACGTTTATGTTCGTTTA
237196 T
1 T
237197 TTATTAAATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.11, C:0.08, G:0.21, T:0.60
Consensus pattern (26 bp):
TGTTCATGTACGTTTATGTTCGTTTA
Found at i:245231 original size:15 final size:16
Alignment explanation
Indices: 245192--245233 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
245182 ATTCACTCTA
*
245192 ATTTATAATTAAAGAAT
1 ATTTA-AATCAAAGAAT
245209 ATTT-AATCAAA-AAT
1 ATTTAAATCAAAGAAT
245223 ATTTAAATCAA
1 ATTTAAATCAA
245234 CTAACAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 7 0.30
15 12 0.52
17 4 0.17
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (16 bp):
ATTTAAATCAAAGAAT
Found at i:245844 original size:60 final size:58
Alignment explanation
Indices: 245733--245859 Score: 134
Period size: 60 Copynumber: 2.1 Consensus size: 58
245723 ATAATCGAAT
* * *
245733 GATCATTTTGTAACTTTTAATAGTCATAGGACTCAACAAAACGACGTCCTATAGTCGGAG
1 GATCATTTTATAACTTTTAATAGTCAGAGGACTCAACAAAACGACG-CCTATACTCGG-G
*
245793 GATCATTTTATAACTTTTAATAGT-AGAGAGACTTAACAAAGTA-GCAC-CCTATACTCGGG
1 GATCATTTTATAACTTTTAATAGTCAGAG-GACTCAACAAA--ACG-ACGCCTATACTCGGG
*
245852 GACCATTT
1 GATCATTT
245860 GTGTACTTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
59 11 0.19
60 43 0.74
61 1 0.02
62 3 0.05
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (58 bp):
GATCATTTTATAACTTTTAATAGTCAGAGGACTCAACAAAACGACGCCTATACTCGGG
Found at i:255427 original size:117 final size:117
Alignment explanation
Indices: 255276--255499 Score: 376
Period size: 117 Copynumber: 1.9 Consensus size: 117
255266 ACAAAGCAAA
* *
255276 GCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCAAGAGCCATTGAAGT
1 GCTCAGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCAAGAGCCATTGAAGT
* * *
255341 GTTTCCGATGTGATGGAGAACACAAGGTGCGAGATTGCACCAATGAAGCAGG
66 GTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAATGAAGCAGG
* *
255393 GCTCAGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGGTAAAGAAGCGAGAGCCATTGAAGT
1 GCTCAGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCAAGAGCCATTGAAGT
*
255458 GTTTCCAATGCGGTGGACAACACAAGGTGCGAGATTGCACCA
66 GTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCA
255500 CCGAAGTAAA
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 99 1.00
ACGTcount: A:0.32, C:0.20, G:0.32, T:0.16
Consensus pattern (117 bp):
GCTCAGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCAAGAGCCATTGAAGT
GTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAATGAAGCAGG
Found at i:255546 original size:117 final size:116
Alignment explanation
Indices: 255269--255580 Score: 315
Period size: 117 Copynumber: 2.7 Consensus size: 116
255259 TGCCCAAACA
* * * * * * *
255269 AAGCAAAGCTCGGTGCCAATGCGAGTGGCGAAGCAACTAAGCCGAGGATAAAGAAGCAAGAGCCA
1 AAGCAAAGCTCAGTGACAAAGCAAGTGGCCAAGCAAC-AAGCCGAGGGTAAAGAAGCGAGAGCCA
* * * *
255334 TTGAAGTGTTTCCGATGTGATGGAGAACACAAGGTGCGAGATTGCACCAATG
65 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
** * * *
255386 AAGCAGGGCTCAGTGACAATGCGAGTGGCGAAGCAACTAAGCCGAGGGTAAAGAAGCGAGAGCCA
1 AAGCAAAGCTCAGTGACAAAGCAAGTGGCCAAGCAAC-AAGCCGAGGGTAAAGAAGCGAGAGCCA
* *
255451 TTGAAGTGTTTCCAATGCGGTGGACAACACAAGGTGCGAGATTGCACCACCG
65 TTGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
* * * * *
255503 AAGTAAAGCTCGGTG-CGAAAGCCAAG-GGCCAAGCTGAA-GAGCCGAGGGTAAATAAGCGAAAG
1 AAGCAAAGCTCAGTGAC-AAAG-CAAGTGGCCAAGC--AACAAGCCGAGGGTAAAGAAGCGAGAG
* * *
255565 CAACTGGAGTGTTTCC
62 CCATTGAAGTGTTTCC
255581 GGTGCAAAGG
Statistics
Matches: 166, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
116 1 0.01
117 160 0.96
118 3 0.02
119 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.32, T:0.15
Consensus pattern (116 bp):
AAGCAAAGCTCAGTGACAAAGCAAGTGGCCAAGCAACAAGCCGAGGGTAAAGAAGCGAGAGCCAT
TGAAGTGTTTCCAATGCGATGGACAACACAAGGTGCGAGATTGCACCAACG
Found at i:256208 original size:15 final size:15
Alignment explanation
Indices: 256188--256222 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
256178 AGCAAGGCTC
256188 TTCGAGTGAAGCT-TG
1 TTCGAGTGAAG-TGTG
256203 TTCGAGTGAAGTGTG
1 TTCGAGTGAAGTGTG
256218 TTCGA
1 TTCGA
256223 ATGGTGAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.05
15 18 0.95
ACGTcount: A:0.20, C:0.11, G:0.34, T:0.34
Consensus pattern (15 bp):
TTCGAGTGAAGTGTG
Found at i:267039 original size:17 final size:18
Alignment explanation
Indices: 267014--267047 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
267004 AGGTTTATGC
267014 ATGAAAAAG-TAAAAAAT
1 ATGAAAAAGATAAAAAAT
*
267031 ATGACAAAGATAAAAAA
1 ATGAAAAAGATAAAAAA
267048 AGGAAGGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.71, C:0.03, G:0.12, T:0.15
Consensus pattern (18 bp):
ATGAAAAAGATAAAAAAT
Found at i:275735 original size:44 final size:43
Alignment explanation
Indices: 275643--275801 Score: 169
Period size: 43 Copynumber: 3.7 Consensus size: 43
275633 AAAGTCCTTT
* * *
275643 ATTTTTTTCAATCCCACTTTTTA-CTTTCATAATTAAGGCCCCTG
1 ATTTTTTT-AATCTCATTTTTTACCTTT-ATAATTAAGGCCCCTA
* * *
275687 TTTTTTTTAATCTTATTTTTTACCTTTATAATTTAGGCCCCTA
1 ATTTTTTTAATCTCATTTTTTACCTTTATAATTAAGGCCCCTA
* * *
275730 ATTTTTTCAATCTCACTTTATTACCTTTATAATTGAA-GTCCCTA
1 ATTTTTTTAATCTCA-TTTTTTACCTTTATAATT-AAGGCCCCTA
* *
275774 ATTTTTTTAAGCTCACTTTTTACCTTTA
1 ATTTTTTTAATCTCATTTTTTACCTTTA
275802 GGCCCCGTTT
Statistics
Matches: 96, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
43 48 0.50
44 47 0.49
45 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.52
Consensus pattern (43 bp):
ATTTTTTTAATCTCATTTTTTACCTTTATAATTAAGGCCCCTA
Found at i:279269 original size:99 final size:99
Alignment explanation
Indices: 279148--279462 Score: 576
Period size: 99 Copynumber: 3.2 Consensus size: 99
279138 TTTAGGTTAA
279148 ACAGCCAACTGATTTCTCATATAGGAATGAACACAACAGGAAGGATTGTCAATGACTAGAAAAAA
1 ACAGCCAACTGATTTCTCATATAGGAATGAACACAACAGGAAGGATTGTCAATGACTAGAAAAAA
*
279213 AATGGACAAATACGTAGATTCTAAGCTCTAAACC
66 AATGGACAAATAAGTAGATTCTAAGCTCTAAACC
279247 ACAGCCAACTGATTTCTCATATAGGAATGAACACAACAGGAAGGATTGTCAATGACTAGAAAAAA
1 ACAGCCAACTGATTTCTCATATAGGAATGAACACAACAGGAAGGATTGTCAATGACTAGAAAAAA
279312 AATGGACAAATAAGTAGATTCTAAGCTCTAAACC
66 AATGGACAAATAAGTAGATTCTAAGCTCTAAACC
* **
279346 ACAGCCAACTGTTTTCTCATATAGGAATGAACACAACAGGAAGGATTGTCAATGGGTAGAAAAAA
1 ACAGCCAACTGATTTCTCATATAGGAATGAACACAACAGGAAGGATTGTCAATGACTAGAAAAAA
279411 AATGGACAAATAAGTAGATTCTAAGCTCTAAACC
66 AATGGACAAATAAGTAGATTCTAAGCTCTAAACC
* *
279445 ACAGCCAACAGATATCTC
1 ACAGCCAACTGATTTCTC
279463 GTGACTGCCT
Statistics
Matches: 209, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 209 1.00
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.21
Consensus pattern (99 bp):
ACAGCCAACTGATTTCTCATATAGGAATGAACACAACAGGAAGGATTGTCAATGACTAGAAAAAA
AATGGACAAATAAGTAGATTCTAAGCTCTAAACC
Found at i:285026 original size:67 final size:68
Alignment explanation
Indices: 284910--285041 Score: 203
Period size: 67 Copynumber: 2.0 Consensus size: 68
284900 GAAGGTTACC
* * *
284910 AGAAAAATGTAAGGACCTATTAACTTCTAAAAGCTGTTGGTTTTTCCTCTCAGCAATCCCATTCT
1 AGAAAAATGTAAGGACCTAGTAACTTCTAAAAGATGTTAGTTTTTCCTCTCAGCAATCCCATTCT
284975 GTT
66 GTT
* * *
284978 AGAAAAA-GTAAGGACCTAGTAACTTTTAAAATATGTTAGTTTTTCCTCTCAGCAATCTCATTCT
1 AGAAAAATGTAAGGACCTAGTAACTTCTAAAAGATGTTAGTTTTTCCTCTCAGCAATCCCATTCT
285042 ATTGTTTTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
67 51 0.88
68 7 0.12
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (68 bp):
AGAAAAATGTAAGGACCTAGTAACTTCTAAAAGATGTTAGTTTTTCCTCTCAGCAATCCCATTCT
GTT
Found at i:310669 original size:210 final size:210
Alignment explanation
Indices: 310162--310657 Score: 568
Period size: 210 Copynumber: 2.4 Consensus size: 210
310152 TTTTCCTTGC
* ** * * *
310162 TTGATTAAATAATTGAAAGCCACAACATCAGGATGAACCCCTTCATTCATCATTCTATTGAGCAA
1 TTGATTAAAGAATTGAAAATCACAACTTCAGGATGAACACCTTCGTTCATCATTCTATTGAGCAA
* * *
310227 GCTTGCCGCTTCAGTCCATTTGCCAGAATCGCAAAACCCATGTATTAAACAATTGTAGGTGAAAA
66 GCTTGTCGCTTCAGTCCATTTACCAGAATCGCAAAACCCATGTATTAAACAAGTGTAGGTGAAAA
* * * * * ** *
310292 TGTTCGGTTTTATACCTCTTTGAATCATGCGTTCAAACAAGGAAATGGCTTCTTCAATCTTCTTT
131 TGTTAGGTTTTACACCTCTCTGAATCATGAGCTCAAACAAGGAAATAACTTCATCAATCTTCTTT
310357 TACTTGCATAAAACA
196 TACTTGCATAAAACA
** * * *
310372 TCAATTAAAGAACTGAAAATCACGACATT-AGGATGAACACCTTCGTTCATCACTCTATTGAGCA
1 TTGATTAAAGAATTGAAAATCACAAC-TTCAGGATGAACACCTTCGTTCATCATTCTATTGAGCA
* *
310436 AGCTTGTAGCTTCAGTCCATTTACCTA-AATTGCAAAACCCATGTATTAAACAAGTGTAGGTGAC
65 AGCTTGTCGCTTCAGTCCATTTACC-AGAATCGCAAAACCCATGTATTAAACAAGTGTAGGTGA-
* * * * * * * * *
310500 AACT-TTAGGTTTTCCATCTCTCTGACTCATTAGCTCTAACATGGTAATAACTTCATCGATCTTC
128 AAATGTTAGGTTTTACACCTCTCTGAATCATGAGCTCAAACAAGGAAATAACTTCATCAATCTTC
* **
310564 TTTTCCTTGCATAAAGGA
193 TTTTACTTGCATAAAACA
** * *
310582 TTGATTAAAGAATTGAAAATCACAACTTCAGGAT-AGATTCCTTCGTTCATCATTCTGTCGAGCA
1 TTGATTAAAGAATTGAAAATCACAACTTCAGGATGA-ACACCTTCGTTCATCATTCTATTGAGCA
310646 AGCTTGTCGCTT
65 AGCTTGTCGCTT
310658 TTGCCCATTT
Statistics
Matches: 235, Mismatches: 46, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
209 3 0.01
210 227 0.97
211 5 0.02
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (210 bp):
TTGATTAAAGAATTGAAAATCACAACTTCAGGATGAACACCTTCGTTCATCATTCTATTGAGCAA
GCTTGTCGCTTCAGTCCATTTACCAGAATCGCAAAACCCATGTATTAAACAAGTGTAGGTGAAAA
TGTTAGGTTTTACACCTCTCTGAATCATGAGCTCAAACAAGGAAATAACTTCATCAATCTTCTTT
TACTTGCATAAAACA
Found at i:310925 original size:194 final size:194
Alignment explanation
Indices: 310596--310977 Score: 737
Period size: 194 Copynumber: 2.0 Consensus size: 194
310586 TTAAAGAATT
310596 GAAAATCACAACTTCAGGATAGATTCCTTCGTTCATCATTCTGTCGAGCAAGCTTGTCGCTTTTG
1 GAAAATCACAACTTCAGGATAGATTCCTTCGTTCATCATTCTGTCGAGCAAGCTTGTCGCTTTTG
310661 CCCATTTACTCTTTGACTCGTTAGCTCAAACAAGGAAACTGCTTCTTCGGTCTTCTTTTCCTTGC
66 CCCATTTACTCTTTGACTCGTTAGCTCAAACAAGGAAACTGCTTCTTCGGTCTTCTTTTCCTTGC
310726 ATAAAACCTTGATTAAAGAACTGAAAGTCACAACATTAGGATGAAACCCTTCGATCATTCTATC
131 ATAAAACCTTGATTAAAGAACTGAAAGTCACAACATTAGGATGAAACCCTTCGATCATTCTATC
*
310790 GAAAATCACAACTTCAGGATAGATTCCTTCGTTCATCATTCTGTCTAGCAAGCTTGTCGCTTTTG
1 GAAAATCACAACTTCAGGATAGATTCCTTCGTTCATCATTCTGTCGAGCAAGCTTGTCGCTTTTG
*
310855 CCCATTTACTCTTTGACTCGTTAGTTCAAACAAGGAAACTGCTTCTTCGGTCTTCTTTTCCTTGC
66 CCCATTTACTCTTTGACTCGTTAGCTCAAACAAGGAAACTGCTTCTTCGGTCTTCTTTTCCTTGC
*
310920 ATAAAACCTTGATTAAAGAACTGAAAGTCACAACATTAGGATGAAACCCTTCGTTCAT
131 ATAAAACCTTGATTAAAGAACTGAAAGTCACAACATTAGGATGAAACCCTTCGATCAT
310978 CATTCTATTG
Statistics
Matches: 185, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
194 185 1.00
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.34
Consensus pattern (194 bp):
GAAAATCACAACTTCAGGATAGATTCCTTCGTTCATCATTCTGTCGAGCAAGCTTGTCGCTTTTG
CCCATTTACTCTTTGACTCGTTAGCTCAAACAAGGAAACTGCTTCTTCGGTCTTCTTTTCCTTGC
ATAAAACCTTGATTAAAGAACTGAAAGTCACAACATTAGGATGAAACCCTTCGATCATTCTATC
Found at i:312005 original size:21 final size:21
Alignment explanation
Indices: 311979--312025 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
311969 AAATAAAATA
311979 GAAGAGAATTAGCAGGGAGAC
1 GAAGAGAATTAGCAGGGAGAC
312000 GAAGAGAATTAGCAGGGAGAC
1 GAAGAGAATTAGCAGGGAGAC
312021 GAAGA
1 GAAGA
312026 ATGAAACCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.45, C:0.09, G:0.38, T:0.09
Consensus pattern (21 bp):
GAAGAGAATTAGCAGGGAGAC
Found at i:317302 original size:19 final size:19
Alignment explanation
Indices: 317278--317318 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
317268 ATGTGATATT
*
317278 TTTAAAATTATTTTATTAA
1 TTTAAAATTATTTAATTAA
317297 TTTAAAATTATTTAATTAA
1 TTTAAAATTATTTAATTAA
317316 TTT
1 TTT
317319 TATTCAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTAAAATTATTTAATTAA
Found at i:317562 original size:35 final size:35
Alignment explanation
Indices: 317504--317603 Score: 101
Period size: 35 Copynumber: 2.7 Consensus size: 35
317494 TTTCGTCCTA
*
317504 CTAGAATTCAAACTCTCAAAAATATGATAGAATTCTG
1 CTAGAATTC-AACTC-CTAAAATATGATAGAATTCTG
* * *
317541 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGAATTCAACTCCTAAAATATGATAGAATTCTG
** *
317576 CTATGTTTTAAACTCCTAAAGATATGAT
1 CTA-GAATTCAACTCCTAAA-ATATGAT
317604 CCACAAGCAC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 21 0.40
36 18 0.34
37 14 0.26
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (35 bp):
CTAGAATTCAACTCCTAAAATATGATAGAATTCTG
Found at i:318030 original size:2 final size:2
Alignment explanation
Indices: 318025--318051 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
318015 TTAGTGTTAT
318025 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 T
318052 TTCCTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:318183 original size:16 final size:18
Alignment explanation
Indices: 318162--318196 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
318152 TTTACTCATT
318162 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
318178 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
318196 T
1 T
318197 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:321387 original size:24 final size:22
Alignment explanation
Indices: 321360--321437 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 22
321350 AATCAGAATA
321360 AAAAAGGCAAAAAAAAAAAGAAGC
1 AAAAA-GCAAAAAAAAAAAGAA-C
* *
321384 AAAAAACAAAAGCAAAAAAGAAC
1 AAAAAGCAAAA-AAAAAAAGAAC
*
321407 AAAAAG-AAAAAAGAAAAAGGGAC
1 AAAAAGCAAAAAA-AAAAA-GAAC
321430 AAAAAGCA
1 AAAAAGCA
321438 CATGCAAAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
21 1 0.02
22 9 0.20
23 20 0.44
24 15 0.33
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGCAAAAAAAAAAAGAAC
Found at i:321407 original size:16 final size:16
Alignment explanation
Indices: 321374--321421 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
321364 AGGCAAAAAA
321374 AAAAAGAAGCAAAA-AAC
1 AAAAAGAA--AAAAGAAC
321391 -AAAAGCAAAAAAGAAC
1 AAAAAG-AAAAAAGAAC
321407 AAAAAGAAAAAAGAA
1 AAAAAGAAAAAAGAA
321422 AAAGGGACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 4 0.14
16 17 0.61
17 7 0.25
ACGTcount: A:0.79, C:0.08, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAGAAC
Found at i:322050 original size:22 final size:22
Alignment explanation
Indices: 322022--322065 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
322012 AGCTACCCCA
322022 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
322044 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
322066 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:323174 original size:36 final size:36
Alignment explanation
Indices: 323076--323233 Score: 253
Period size: 36 Copynumber: 4.3 Consensus size: 36
323066 ATTGAAAACA
* *
323076 TTTCCCTTGAAATAAATTTTCGTCTCTCTTGAGATAA
1 TTTCCCTTGAAATAAATTTT-GTCTCTCTTGAGACAG
*
323113 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAA-TAAATTTTGTCTCTCTTGAGACAG
* *
323150 TTTCACTTGAAATAAATTTTGTCTCTCTTGAGACAT
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
323186 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
323222 TTTCCCTTGAAA
1 TTTCCCTTGAAA
323234 CAAAATATTT
Statistics
Matches: 112, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
36 68 0.61
37 37 0.33
38 7 0.06
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
Found at i:323182 original size:175 final size:171
Alignment explanation
Indices: 322949--323359 Score: 475
Period size: 175 Copynumber: 2.4 Consensus size: 171
322939 GTTTTTCTTA
* * * * * * *
322949 AAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTAG-AAGAGTTTTGTCCCTCTTGAGACAGTT
1 AAACAAAATTTGTCTCTCTTGAGACAG-TTTCACTTGAAAAAATTTTGTCTCTCTTGAGACAGTT
*
323013 TCCCTTAAAACAAATTTTATCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAA-ACAT
65 TCCCTTAAAACAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA-AAACATTGAAATACAT
* * *
323077 TTCCCTTGAAATAAATTTTCGTCTCTCTTGAGATAATTTCCCTTG
129 TTCCCTTGAAACAAA-TTTCGTC-CCCTTGAGACAATTTCCCTTG
*
323122 AAACAAAATTTTGTCTCTCTTGAGACAGTTTCACTTGAAATAAATTTTGTCTCTCTTGAGACATT
1 AAACAAAA-TTTGTCTCTCTTGAGACAGTTTCACTTGAAA-AAATTTTGTCTCTCTTGAGACAGT
* * * * * * **
323187 TTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTAAATATGT
64 TTCCCTTAAAACAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAAACATTGAAATACAT
* * * **
323252 TTTCTTTGAAACAAATTTCGTCCCCTTGAGACAGTTTCTTTTG
129 TTCCCTTGAAACAAATTTCGTCCCCTTGAGACAATTTCCCTTG
* * * * *
323295 GAACTAAGTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTT
1 AAACAAAATTTGTCTCTCTTGAGACAGTTTCACTTGAAA-AAATTTTGTCTCTCTTGAGACAGTT
323360 ACTCTTGAAA
Statistics
Matches: 202, Mismatches: 32, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
172 53 0.26
173 36 0.18
174 35 0.17
175 78 0.39
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (171 bp):
AAACAAAATTTGTCTCTCTTGAGACAGTTTCACTTGAAAAAATTTTGTCTCTCTTGAGACAGTTT
CCCTTAAAACAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAAACATTGAAATACATTT
CCCTTGAAACAAATTTCGTCCCCTTGAGACAATTTCCCTTG
Found at i:323308 original size:136 final size:138
Alignment explanation
Indices: 323119--323371 Score: 368
Period size: 136 Copynumber: 1.8 Consensus size: 138
323109 ATAATTTCCC
* * *
323119 TTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCACTTGAAATAAATTTTGTCTCTCTTGAGAC
1 TTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCACTTGAAATAAAGTTTGTCTCTCTTGAGAC
* * * *
323184 ATTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTAAATA
66 AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACAAAATATTTAAATA
323249 TGTTTTCT
131 TGTTTTCT
** *
323257 TTGAAAC-AAATTTCGTC-CCCTTGAGACAGTTTCTTTTGGAACT-AAGTTTGTCTCTCTTGAGA
1 TTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCACTT-GAAATAAAGTTTGTCTCTCTTGAGA
* *
323319 CAGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
65 CAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACA
323372 CAAAATCTTC
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
136 82 0.80
137 13 0.13
138 7 0.07
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (138 bp):
TTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCACTTGAAATAAAGTTTGTCTCTCTTGAGAC
AGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACAAAATATTTAAATA
TGTTTTCT
Found at i:323318 original size:36 final size:36
Alignment explanation
Indices: 323252--323371 Score: 156
Period size: 36 Copynumber: 3.4 Consensus size: 36
323242 TTAAATATGT
323252 TTTCT-TTGAAACAAA-TTTCGTC-CCCTTGAGACAG
1 TTTCTCTTGAAACAAAGTTT-GTCTCCCTTGAGACAG
* * * *
323286 TTTCTTTTGGAACTAAGTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAAGTTTGTCTCCCTTGAGACAG
*
323322 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAAGTTTGTCTCCCTTGAGACAG
*
323358 TTACTCTTGAAACA
1 TTTCTCTTGAAACA
323372 CAAAATCTTC
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
34 5 0.07
35 11 0.15
36 58 0.78
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (36 bp):
TTTCTCTTGAAACAAAGTTTGTCTCCCTTGAGACAG
Found at i:324203 original size:106 final size:105
Alignment explanation
Indices: 324044--325331 Score: 1253
Period size: 105 Copynumber: 12.3 Consensus size: 105
324034 GCCATCCGTG
* * * *
324044 ATTTCAACTCCAC-GACGGAGGATATTGTGGCACTCGAGACAACGCAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATA-T-TGG-ACTCCAGACAACACAAGTTCAACTTCACAACGA
*
324108 AGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
62 AGGGACGGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* * * *
324153 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAATGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * *
324218 ACCGCTGCTTGTCAACAATAACTTCTCAATTTCAGAGCCA
66 ACGGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * * * *
324258 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTTAACTTCACTACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
* * *
324323 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACGGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *** *
324363 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGTAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
* * *
324428 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACGGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
324468 ATTTCAACTTCACAGCGAAGGATATTGGAC-CCAAGACAGCACAAGCTCAACTTCACAGCGAAGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACACAAGTTCAACTTCACAACGAAGG
* * ** * * *
324532 GGCGCCTGACTGT---CGACAA----GCAATTTCGGAGCCA
65 GACGGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * * *
324566 ATCTCAACTTCACAGCGAAGGATATTGGACTCGAGATAACACAAGTTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
* * *
324631 ACGGCTGGTTGTCAACAAACAATTTCCCAGTTTCAGGGCCA
66 ACGGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* * *
324672 ATTTCAACTTCACAGCGAAGGATATTGGAC-CCAAGACATCACAAGCTCAACTTCACAGCGAAGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACACAAGTTCAACTTCACAACGAAGG
* ** * * *
324736 GGCGGCTGACTGT---CGACAA----GCAATTTCGGAGCCA
65 GACGGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * *
324770 ATCTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
* * *
324835 ACGGCTGGTTGTCAACAAACAATTTCCCAATTCCAGAGCCG
66 ACGGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* * *
324876 ATTTCAACTCCAC-GACGGAGGATATCGTG-CTACCCGAGACAACACAAGTTCAACTTCACAACG
1 ATTTCAACTTCACAG-CGAAGGATATTG-GACT--CC-AGACAACACAAGTTCAACTTCACAACG
** * ** *
324939 AAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCA-TCCGCG
61 AAGGGACGGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGC-CA
* * * *
324985 ATTTCAACTCCAC-GACGGAGGATATCGTGTTACTCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCCAGACAACACAAGTTCAACTTCACAACGA
** * *
325049 AGGGACGGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
62 AGGGACGGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
** *
325094 ATTTCAACTTCGTAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * *
325159 ACGGCTGATTGTCAACAA-GA-TT-TC--GTTCAGAGTCA
66 ACGGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * * * * * *
325194 ATTTCATA-TTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTTACAGCAAAGG
1 ATTTCA-ACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGG
* * ** * * * *
325258 GGCGACTGACTGTCAACAAACAATTTCCCAGTTCCAGAACCA
65 GACGGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* *
325300 ATTTCAACTTCATAGCGGAGGATATTGGACTC
1 ATTTCAACTTCACAGCGAAGGATATTGGACTC
325332 GGAACAATAT
Statistics
Matches: 1004, Mismatches: 135, Indels: 83
0.82 0.11 0.07
Matches are distributed among these distances:
98 157 0.16
99 2 0.00
100 77 0.08
101 5 0.00
102 18 0.02
103 5 0.00
104 3 0.00
105 287 0.29
106 246 0.25
107 6 0.01
108 3 0.00
109 188 0.19
110 3 0.00
111 2 0.00
112 2 0.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:324609 original size:98 final size:98
Alignment explanation
Indices: 324462--325284 Score: 524
Period size: 98 Copynumber: 8.0 Consensus size: 98
324452 CCCAATCTCA
* *
324462 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGC
1 GAGCCAATCTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACAGC
*
324527 GAAGGGGCGCCTGACTGTCGACAAGCAATTTCG
66 GAAGGGGCGGCTGACTGTCGACAAGCAATTTCG
* * * *
324560 GAGCCAATCTCAACTTCACAGCGAAGGATATTGGACTCGAGATAACACAAGTTCAACTTCACAGC
1 GAGCCAATCTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACAGC
* ** * *
324625 GAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAG
66 GAAGGGGCGGCTGACTGTCGACAAGCAATTT--C-G
* * *
324661 TTTCAGGGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACATCACAAGCTCAACTTC
1 -----GAGCCAATCTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTC
324726 ACAGCGAAGGGGCGGCTGACTGTCGACAAGCAATTTCG
61 ACAGCGAAGGGGCGGCTGACTGTCGACAAGCAATTTCG
* * *
324764 GAGCCAATCTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGC
1 GAGCCAATCTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACAGC
* ** * * *
324829 GAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTCCA
66 GAAGGGGCGGCTGACTGTCGACAAGCAA--T-----TT-CG
* * * * * * *
324870 GAGCCGATTTCAACTCCAC-GACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCA
1 GAGCCAATCTCAACTTCACAG-CGAAGGATAT--TG-GACCCAAGACAACACAAGCTCAACTTCA
* * ** *
324934 CAACGAAGGGACGGCTGGTTGTCAACGAA-CAACTTTTCAG
62 CAGCGAAGGGGCGGCTGACTGTCGAC-AAGCAA--TTTC-G
* * * * * * * * * *
324974 TTTCATCCGCGATTTCAACTCCAC-GACGGAGGATATCGTGTTACTCGAGACAACACAAGTTCAA
1 ---GA-GC-CAATCTCAACTTCACAG-CGAAGGATAT--TG-GACCCAAGACAACACAAGCTCAA
* * ** * * *
325038 CTTCACAACGAAGGGACGGCTGGTTGTCAACAAACATTTTTCAAATTTCA
57 CTTCACAGCGAAGGGGCGGCTGACTGTCGAC--A-A----GC-AATTTCG
* ** * * * *
325088 GAGCCAATTTCAACTTCGTAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAAC
1 GAGCCAATCTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACAGC
* * *
325153 GAAGGGACGGCTGATTGTCAACAAG--ATTTCG
66 GAAGGGGCGGCTGACTGTCGACAAGCAATTTCG
* * * * * * *
325184 TTCAGAGTCAATTTCATA-TTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTT
1 ----GAGCCAATCTCA-ACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTC
* * * *
325248 ACAGCAAAGGGGCGACTGACTGTCAACAAACAATTTC
61 ACAGCGAAGGGGCGGCTGACTGTCGACAAGCAATTTC
325285 CCAGTTCCAG
Statistics
Matches: 607, Mismatches: 75, Indels: 82
0.79 0.10 0.11
Matches are distributed among these distances:
96 5 0.01
98 166 0.27
100 77 0.13
101 2 0.00
102 5 0.01
103 3 0.00
104 4 0.01
105 3 0.00
106 162 0.27
107 3 0.00
108 3 0.00
109 160 0.26
110 5 0.01
111 2 0.00
115 4 0.01
116 1 0.00
117 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (98 bp):
GAGCCAATCTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACAGC
GAAGGGGCGGCTGACTGTCGACAAGCAATTTCG
Found at i:324737 original size:204 final size:204
Alignment explanation
Indices: 324080--325329 Score: 1275
Period size: 204 Copynumber: 6.0 Consensus size: 204
324070 GTGGCACTCG
* ** *
324080 AGACAACGCAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGACTGT---C-AACAA----GCAATTT
* * * *
324145 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC-
58 CGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACA
* * * * * * *
324209 GACGAATGGACCGCTGCTTGTCAAC-AATAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAA
123 G-CGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAG
*
324273 CGAAGGATATTGGACTTC-
187 CGAAGGATATTGGAC-CCA
* * * *
324291 AGACAACGCAAGTTTAACTTCACTACGAAGGGACCGCTG-CTTGTCAACAA-CAACTTCCCAATC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGAC-TGTCAACAAGCAA--T-----T-
* * * ***
324354 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGTAAGTTCAACTTCAC
57 TCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCAC
* * * *
324419 -GACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACA
122 AG-CGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
324482 GCGAAGGATATTGGACCCA
186 GCGAAGGATATTGGACCCA
* * * * * *
324501 AGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGCCTGACTGTCGACAAGCAATTTCGGAGCCA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAGCAATTTCGGAGCCA
* *
324566 ATCTCAACTTCACAGCGAAGGATATTGGACTCGAGATAACACAAGTTCAACTTCACAGCGAAGGG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG
* *
324631 ACGGCTGGTTGTCAACAAACAATTTCCCAGTTTCAGGGCCAATTTCAACTTCACAGCGAAGGATA
131 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATA
324696 TTGGACCCA
196 TTGGACCCA
* * * * *
324705 AGACATCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCGACAAGCAATTTCGGAGCCA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAGCAATTTCGGAGCCA
*
324770 ATCTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG
* * * *
324835 ACGGCTGGTTGTCAACAAACAATTTCCCAATTCCAGAGCCGATTTCAACTCCAC-GACGGAGGAT
131 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGAT
* *
324899 ATCGTGCTACCCG
195 AT--TG-GACCCA
**
324912 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAA-CAACTTTTCAGTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGACTGTCAAC-AAGCAA--TTTC-G--
* * * * * *
324976 TCATCCGCGATTTCAACTCCAC-GACGGAGGATATCGTGTTACTCGAGACAACACAAGTTCAACT
60 -GA-GC-CAATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACT
* * * *
325040 TCACAACGAAGGGACGGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCAATTTCAACTTC
118 TCACAGCGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
** * *
325105 GTAGCGAAGGATATTGGACTCG
183 ACAGCGAAGGATATTGGACCCA
*
325127 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAG--ATTTCGTTCAGA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAGCAATTTCG----GA
* * * * * *
325190 GTCAATTTCATA-TTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTTACAGCA
62 GCCAATTTCA-ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCG
* * ** * * * * *
325254 AAGGGGCGACTGACTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTCAACTTCATAGCGGA
126 AAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
325319 GGATATTGGAC
191 GGATATTGGAC
325330 TCGGAACAAT
Statistics
Matches: 902, Mismatches: 101, Indels: 77
0.84 0.09 0.07
Matches are distributed among these distances:
202 3 0.00
203 79 0.09
204 241 0.27
206 93 0.10
207 54 0.06
208 3 0.00
209 27 0.03
210 179 0.20
211 49 0.05
213 2 0.00
214 4 0.00
215 72 0.08
216 2 0.00
217 2 0.00
218 91 0.10
219 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (204 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAGCAATTTCGGAGCCA
ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG
ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATA
TTGGACCCA
Found at i:325856 original size:35 final size:37
Alignment explanation
Indices: 325793--325867 Score: 118
Period size: 35 Copynumber: 2.1 Consensus size: 37
325783 TTTCGTCCTA
325793 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
* *
325830 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTTTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
325865 CTA
1 CTA
325868 TGTTTTAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 22 0.61
36 5 0.14
37 9 0.25
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
Found at i:326468 original size:17 final size:16
Alignment explanation
Indices: 326436--326469 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
326426 TTTACTCATT
*
326436 TATTTATCTATTTTTA
1 TATTTATCTATATTTA
326452 TATTTATCCTATATTTA
1 TATTTAT-CTATATTTA
326469 T
1 T
326470 GTTTTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTATCTATATTTA
Found at i:327053 original size:31 final size:32
Alignment explanation
Indices: 327015--327074 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
327005 TGATTTTCAA
*
327015 AAAATTAAAAATTTAAATACTAAA-ACATGCT
1 AAAATTAAAAACTTAAATACTAAACACATGCT
*
327046 AAAATTAATAACTTAAATACTAAACACAT
1 AAAATTAAAAACTTAAATACTAAACACAT
327075 AGTTTACCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (32 bp):
AAAATTAAAAACTTAAATACTAAACACATGCT
Found at i:334224 original size:19 final size:18
Alignment explanation
Indices: 334197--334248 Score: 86
Period size: 18 Copynumber: 2.8 Consensus size: 18
334187 TTTTAATTTT
334197 TAATTTTTTTAATTTAAA
1 TAATTTTTTTAATTTAAA
*
334215 TACTTTTTTTAATTTAAA
1 TAATTTTTTTAATTTAAA
334233 TAATTTTTTTTAATTT
1 TAA-TTTTTTTAATTT
334249 TATAAAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 19 0.61
19 12 0.39
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TAATTTTTTTAATTTAAA
Found at i:334253 original size:18 final size:18
Alignment explanation
Indices: 334187--334253 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 18
334177 CTTAAAGAAA
334187 TTTTAATTTT-TAA-TTT
1 TTTTAATTTTATAATTTT
334203 TTTTAA-TTTA-AATACTTT
1 TTTTAATTTTATAAT--TTT
*
334221 TTTTAATTTAAATAATTTT
1 TTTTAATTT-TATAATTTT
334240 TTTTAATTTTATAA
1 TTTTAATTTTATAA
334254 AAACGACATG
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
15 5 0.12
16 6 0.14
18 13 0.31
19 14 0.33
20 1 0.02
21 3 0.07
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTAATTTTATAATTTT
Found at i:349106 original size:165 final size:165
Alignment explanation
Indices: 348834--349341 Score: 854
Period size: 165 Copynumber: 3.0 Consensus size: 165
348824 ATGTGAAATA
*
348834 ACATTACGCTATTTTCACAGTCAAAGGTTTTTCCCTTATCAGTTCCTCAGCTGAAGCATGGTGAA
1 ACATTACGCTATTTTCACAGTCAAAGGTTTTTCCCTTATCAGTTCCTCAGCTCAAGCATGGTGAA
348899 AGTGATAATGTAGTGTCCGGTGAATAGTAGAGAAAGATTGCGCCATTTTCTGAAGAACCACTCGT
66 AGTGATAATGTAGTGTCCGGTGAATAGTAGAGAAAGATTGCGCCATTTTCTGAAGAACCACTCGT
*
348964 GCCTTACAATGATTATGAAAGGAGGGCAGTGGATC
131 GCCTTACAATGATAATGAAAGGAGGGCAGTGGATC
*
348999 ACATTACGCTATTTTCACAGTCAAAGATTTTTCCCTTATCAGTTCCTCAGCTCAAGCATGGTGAA
1 ACATTACGCTATTTTCACAGTCAAAGGTTTTTCCCTTATCAGTTCCTCAGCTCAAGCATGGTGAA
* * *
349064 AGTGATAATGTAATGTCCAGTGAATAGTAGAGAAAGATTGCGCCATTTTCCGAAGAACCACTCGT
66 AGTGATAATGTAGTGTCCGGTGAATAGTAGAGAAAGATTGCGCCATTTTCTGAAGAACCACTCGT
*
349129 GCCTTACAATGATAATGAAAGGAGGACAGTGGATCACATCATC
131 GCCTTACAATGATAATGAAAGGAGGGCAGTGG--------ATC
349172 ACATTACGCTATTTTCACAGTCAAAGGTTTTTCCCTTATCAGTTCCTCAGCTCAAGCATGGTGAA
1 ACATTACGCTATTTTCACAGTCAAAGGTTTTTCCCTTATCAGTTCCTCAGCTCAAGCATGGTGAA
349237 AGTGATAATGTAGTGTCCGGTGAATAGTAGAGAAAGATTGCGCCATTTTCTGAAGAACCACTCGT
66 AGTGATAATGTAGTGTCCGGTGAATAGTAGAGAAAGATTGCGCCATTTTCTGAAGAACCACTCGT
* * *
349302 GCCTTGCAACGATGATGAAAGGAGGGCAGTGGATC
131 GCCTTACAATGATAATGAAAGGAGGGCAGTGGATC
349337 ACATT
1 ACATT
349342 GGTGGGAGGG
Statistics
Matches: 320, Mismatches: 15, Indels: 16
0.91 0.04 0.05
Matches are distributed among these distances:
165 163 0.51
173 157 0.49
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (165 bp):
ACATTACGCTATTTTCACAGTCAAAGGTTTTTCCCTTATCAGTTCCTCAGCTCAAGCATGGTGAA
AGTGATAATGTAGTGTCCGGTGAATAGTAGAGAAAGATTGCGCCATTTTCTGAAGAACCACTCGT
GCCTTACAATGATAATGAAAGGAGGGCAGTGGATC
Found at i:349262 original size:173 final size:172
Alignment explanation
Indices: 348834--349340 Score: 866
Period size: 173 Copynumber: 3.0 Consensus size: 172
348824 ATGTGAAATA
*
348834 ACATTACGCTATTTTCACAGTCAAAGGTTTTTCCCTTATCAGTTCCTCAGCTGAAGCATGGTGAA
1 ACATTACGCTATTTTCACAGTCAAAGGTTTTTCCCTTATCAGTTCCTCAGCTCAAGCATGGTGAA
348899 AGTGATAATGTAGTGTCCGGTGAATAGTAGAGAAAGATTGCGCCATTTTCTGAAGAACCACTCGT
66 AGTGATAATGTAGTGTCCGGTGAATAGTAGAGAAAGATTGCGCCATTTTCTGAAGAACCACTCGT
*
348964 GCCTTACAATGATTATGAAAGGAGGGCAGTGG-------ATC
131 GCCTTACAATGATAATGAAAGGAGGGCAGTGGATCACATATC
*
348999 ACATTACGCTATTTTCACAGTCAAAGATTTTTCCCTTATCAGTTCCTCAGCTCAAGCATGGTGAA
1 ACATTACGCTATTTTCACAGTCAAAGGTTTTTCCCTTATCAGTTCCTCAGCTCAAGCATGGTGAA
* * *
349064 AGTGATAATGTAATGTCCAGTGAATAGTAGAGAAAGATTGCGCCATTTTCCGAAGAACCACTCGT
66 AGTGATAATGTAGTGTCCGGTGAATAGTAGAGAAAGATTGCGCCATTTTCTGAAGAACCACTCGT
*
349129 GCCTTACAATGATAATGAAAGGAGGACAGTGGATCACATCATC
131 GCCTTACAATGATAATGAAAGGAGGGCAGTGGATCACAT-ATC
349172 ACATTACGCTATTTTCACAGTCAAAGGTTTTTCCCTTATCAGTTCCTCAGCTCAAGCATGGTGAA
1 ACATTACGCTATTTTCACAGTCAAAGGTTTTTCCCTTATCAGTTCCTCAGCTCAAGCATGGTGAA
349237 AGTGATAATGTAGTGTCCGGTGAATAGTAGAGAAAGATTGCGCCATTTTCTGAAGAACCACTCGT
66 AGTGATAATGTAGTGTCCGGTGAATAGTAGAGAAAGATTGCGCCATTTTCTGAAGAACCACTCGT
* * *
349302 GCCTTGCAACGATGATGAAAGGAGGGCAGTGGATCACAT
131 GCCTTACAATGATAATGAAAGGAGGGCAGTGGATCACAT
349341 TGGTGGGAGG
Statistics
Matches: 319, Mismatches: 15, Indels: 8
0.93 0.04 0.02
Matches are distributed among these distances:
165 155 0.49
173 164 0.51
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (172 bp):
ACATTACGCTATTTTCACAGTCAAAGGTTTTTCCCTTATCAGTTCCTCAGCTCAAGCATGGTGAA
AGTGATAATGTAGTGTCCGGTGAATAGTAGAGAAAGATTGCGCCATTTTCTGAAGAACCACTCGT
GCCTTACAATGATAATGAAAGGAGGGCAGTGGATCACATATC
Found at i:353131 original size:41 final size:41
Alignment explanation
Indices: 353085--353162 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
353075 TGTCATAAGG
*
353085 ATCCTTTCATGTCCGAATATGTGTCGGAAATGGAGCAAGAA
1 ATCCTTTCATGTCCAAATATGTGTCGGAAATGGAGCAAGAA
*
353126 ATCCTTTCGTGTCCAAATATGTGTCGGAAATGGAGCA
1 ATCCTTTCATGTCCAAATATGTGTCGGAAATGGAGCA
353163 GGAAGCACCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (41 bp):
ATCCTTTCATGTCCAAATATGTGTCGGAAATGGAGCAAGAA
Found at i:357328 original size:20 final size:20
Alignment explanation
Indices: 357250--357320 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
357240 TCCTAATTTG
357250 CGCAATGCGAATACGTAAAT
1 CGCAATGCGAATACGTAAAT
* ** *
357270 CGCAACGCGAATTGGAAAAT
1 CGCAATGCGAATACGTAAAT
357290 CGCAATGCG-ATACGTAAAT
1 CGCAATGCGAATACGTAAAT
357309 CGCAATGCGAAT
1 CGCAATGCGAAT
357321 CTGTAAATTC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 16 0.38
20 26 0.62
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (20 bp):
CGCAATGCGAATACGTAAAT
Found at i:357363 original size:21 final size:21
Alignment explanation
Indices: 357337--357389 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
357327 ATTCTAACTA
357337 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* *
357358 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
* *
357379 TTGCAATGCGA
1 TCGCATTGCGA
357390 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:357437 original size:15 final size:15
Alignment explanation
Indices: 357417--357472 Score: 87
Period size: 15 Copynumber: 3.8 Consensus size: 15
357407 CGAATTTGGA
357417 AAATCGCAATGCCGT
1 AAATCGCAATGCCGT
*
357432 AAATCGCAAT-ACGT
1 AAATCGCAATGCCGT
*
357446 AAATCGCAATGCTGT
1 AAATCGCAATGCCGT
357461 AAATCGCAATGC
1 AAATCGCAATGC
357473 GACGTAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 13 0.35
15 24 0.65
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (15 bp):
AAATCGCAATGCCGT
Found at i:357526 original size:19 final size:20
Alignment explanation
Indices: 357502--357547 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
357492 ATCGATTCTG
357502 TCGCAACT-GAATTTC-AAAT
1 TCGCAACTCG-ATTTCTAAAT
*
357521 TCGCAACTCGATTTCTGAAT
1 TCGCAACTCGATTTCTAAAT
357541 TCGCAAC
1 TCGCAAC
357548 AGGTTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.30
Consensus pattern (20 bp):
TCGCAACTCGATTTCTAAAT
Found at i:358277 original size:24 final size:24
Alignment explanation
Indices: 358250--358303 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
358240 GTATTCGAAA
358250 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
358274 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
358298 TTTGAT
1 TTTGAT
358304 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:360686 original size:20 final size:21
Alignment explanation
Indices: 360661--360752 Score: 120
Period size: 20 Copynumber: 4.6 Consensus size: 21
360651 GACATTCATT
360661 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAATA
* *
360681 TGACTATTGCAACACGGAA-A
1 TGACTATCGCAACGCGGAATA
*
360701 TGACTATCGCAATGCGGAAT-
1 TGACTATCGCAACGCGGAATA
*
360721 TGACTATCGCAACGC-GAAAA
1 TGACTATCGCAACGCGGAATA
360741 TGACTATCGCAA
1 TGACTATCGCAA
360753 TGAGAGAATC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
19 3 0.05
20 56 0.90
21 3 0.05
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
TGACTATCGCAACGCGGAATA
Found at i:360725 original size:40 final size:40
Alignment explanation
Indices: 360661--360754 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
360651 GACATTCATT
* * *
360661 TGACTATCGCAACGCGAATATGACTATTGCAACACGGAAA
1 TGACTATCGCAATGCGAATATGACTATCGCAACACGAAAA
*
360701 TGACTATCGCAATGCGGAAT-TGACTATCGCAACGCGAAAA
1 TGACTATCGCAATGC-GAATATGACTATCGCAACACGAAAA
360741 TGACTATCGCAATG
1 TGACTATCGCAATG
360755 AGAGAATCGC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 45 0.92
41 4 0.08
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.21
Consensus pattern (40 bp):
TGACTATCGCAATGCGAATATGACTATCGCAACACGAAAA
Found at i:360791 original size:53 final size:53
Alignment explanation
Indices: 360706--360846 Score: 192
Period size: 53 Copynumber: 2.6 Consensus size: 53
360696 GGAAATGACT
* ** ** *
360706 ATCGCAATGCGGAATTGACTATCGCAACGCGAAAATGACTATCGCAATGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGCGAAAATGAAAATCGCAACGAGAGA
* *
360760 ATCGCAATGCGAAATGAAAATCGCAATGCGAAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGAAAATGAAAATCGCAACGAGAGA
360813 ATCGCAATGCGAAAATGAAAATCGCAACGCGAAA
1 ATCGCAATGCG-AAATGAAAATCGCAACGCGAAA
360847 TCGTTGCGAT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
53 46 0.60
54 31 0.40
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAACGCGAAAATGAAAATCGCAACGAGAGA
Found at i:360796 original size:20 final size:20
Alignment explanation
Indices: 360759--360846 Score: 109
Period size: 20 Copynumber: 4.8 Consensus size: 20
360749 GCAATGAGAG
360759 AATCGCAATGCG-AAATGAA
1 AATCGCAATGCGAAAATGAA
360778 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
*
360798 AATCGCAA--CG--AGTG--
1 AATCGCAATGCGAAAATGAA
360812 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
*
360832 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
360847 TCGTTGCGAT
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
14 8 0.14
16 5 0.08
18 5 0.08
19 12 0.20
20 29 0.49
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (20 bp):
AATCGCAATGCGAAAATGAA
Found at i:362979 original size:20 final size:20
Alignment explanation
Indices: 362956--363004 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
362946 GAAACTTAAA
362956 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
362976 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
362996 ATCGCAACG
1 ATCGCAACG
363005 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:363074 original size:20 final size:20
Alignment explanation
Indices: 363049--363136 Score: 158
Period size: 20 Copynumber: 4.4 Consensus size: 20
363039 GATTCTTTCG
*
363049 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
363069 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
363089 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
363109 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
363129 TTGCGATA
1 TTGCGATA
363137 ATAAAACTAT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:363093 original size:40 final size:40
Alignment explanation
Indices: 363011--363136 Score: 158
Period size: 40 Copynumber: 3.3 Consensus size: 40
363001 AACGAGAGAA
* **
363011 TCGCAATGCGATTTTCA-TTTCGCATTGCGAT--TC--TT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
363046 TCG--TTGCGATAGTCATTTTTGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
363084 TCGCATTGCGATAGTCATTTTCGCGTTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
363124 TCGCATTGCGATA
1 TCGCATTGCGATA
363137 ATAAAACTAT
Statistics
Matches: 78, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
33 9 0.12
34 13 0.17
35 3 0.04
36 2 0.03
38 5 0.06
40 46 0.59
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
Found at i:365011 original size:20 final size:20
Alignment explanation
Indices: 364988--365027 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
364978 CTGAAACTTT
364988 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
365008 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
365028 CTACCGCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.20, G:0.15, T:0.10
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:365035 original size:20 final size:20
Alignment explanation
Indices: 364992--365037 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
364982 AACTTTAAAT
*
364992 CGCAACACGAAAATGAAAAT
1 CGCAACACGAAAATGAAAAC
**
365012 CGCAACACGAAAATGACTAC
1 CGCAACACGAAAATGAAAAC
365032 CGCAAC
1 CGCAAC
365038 GCAAGAATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.28, G:0.15, T:0.09
Consensus pattern (20 bp):
CGCAACACGAAAATGAAAAC
Found at i:365108 original size:20 final size:20
Alignment explanation
Indices: 365083--365129 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
365073 GATTCTCTCG
365083 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
365103 TTGCGATAGTCATTTTCGCT
1 TTGCGATAGTCAAATTCGCA
365123 TTGCGAT
1 TTGCGAT
365130 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:365771 original size:21 final size:21
Alignment explanation
Indices: 365747--365792 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
365737 TATTCGCATT
365747 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
365768 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
365789 GCGA
1 GCGA
365793 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:374347 original size:2 final size:2
Alignment explanation
Indices: 374340--374392 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
374330 ACATATCAAC
374340 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
374382 TA TA TA TA TA T
1 TA TA TA TA TA T
374393 GTTCTAAAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:381731 original size:8 final size:8
Alignment explanation
Indices: 381718--381747 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
381708 ACCCTATGTT
381718 ACAAGTTG
1 ACAAGTTG
381726 ACAAGTTG
1 ACAAGTTG
*
381734 ACAAATTG
1 ACAAGTTG
381742 ACAAGT
1 ACAAGT
381748 GGCCAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.23
Consensus pattern (8 bp):
ACAAGTTG
Found at i:386947 original size:35 final size:35
Alignment explanation
Indices: 386901--387012 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 35
386891 AAAACATTCC
*
386901 TCAATTTCATTCTAAATCCTAAATTCCAAAGA-AAT
1 TCAATTTCATTCTAAAACCTAAATTCCAAA-ATAAT
*
386936 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAAACCTAAATTCCAAAATAAT
* * * *
386971 TCAATTACATTCTAAAACCCAAATTCTAAAATATT
1 TCAATTTCATTCTAAAACCTAAATTCCAAAATAAT
387006 TCAATTT
1 TCAATTT
387013 AAGGAGGAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
34 1 0.01
35 68 0.99
ACGTcount: A:0.43, C:0.21, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAAACCTAAATTCCAAAATAAT
Found at i:388111 original size:35 final size:34
Alignment explanation
Indices: 388062--388174 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
388052 AAAAAAGACA
* *
388062 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGGG-TTTAGAAT
*
388097 GTAATTGAATTATTTTGGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTT-GGGTTTAGAAT
*
388132 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTG-GGTTTAGAAT
388167 GAAATTGA
1 GAAATTGA
388175 GGATTGTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 67 0.94
36 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
Found at i:392105 original size:19 final size:18
Alignment explanation
Indices: 392077--392116 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
392067 ATATTAAAAT
392077 AAATACATTTTTATAATAA
1 AAATACA-TTTTATAATAA
*
392096 AAATATATTTTATAATAA
1 AAATACATTTTATAATAA
392114 AAA
1 AAA
392117 AGTATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATACATTTTATAATAA
Found at i:393159 original size:12 final size:12
Alignment explanation
Indices: 393142--393168 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
393132 TTTTCATGTG
393142 TTATAATCGTGT
1 TTATAATCGTGT
393154 TTATAATCGTGT
1 TTATAATCGTGT
393166 TTA
1 TTA
393169 AGGTATCACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (12 bp):
TTATAATCGTGT
Found at i:405783 original size:18 final size:18
Alignment explanation
Indices: 405757--405795 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
405747 ATGGCTATGG
405757 ATTTGTTACCTAAATAAT
1 ATTTGTTACCTAAATAAT
* * *
405775 ATTTTTTACCTGATTAAT
1 ATTTGTTACCTAAATAAT
405793 ATT
1 ATT
405796 AAAAACGACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTTGTTACCTAAATAAT
Found at i:407046 original size:17 final size:17
Alignment explanation
Indices: 407024--407073 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
407014 TTAATATTTT
*
407024 GTATTTATTTTATTTAA
1 GTATTTAATTTATTTAA
407041 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
407058 -TATTTTACTTATTTAA
1 GTATTTAATTTATTTAA
407074 TTTTTTTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 14 0.47
17 16 0.53
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:407069 original size:16 final size:16
Alignment explanation
Indices: 407033--407078 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
407023 TGTATTTATT
* *
407033 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTTAC
407050 TTATTTAATATTTTAC
1 TTATTTAATATTTTAC
407066 TTATTTAAT-TTTT
1 TTATTTAATATTTT
407079 TTGCAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTAATATTTTAC
Found at i:409392 original size:2 final size:2
Alignment explanation
Indices: 409385--409416 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
409375 ACTTTGCATA
409385 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
409417 GTTTATGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:410342 original size:20 final size:22
Alignment explanation
Indices: 410312--410374 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 22
410302 TCAATTTCCC
410312 CTTAA-AGTGCATCGATGCATT
1 CTTAACAGTGCATCGATGCATT
410333 C-T-ACAGTGCATCGATGCATT
1 CTTAACAGTGCATCGATGCATT
410353 CTTTAACATGTGCATCGATGCA
1 C-TTAACA-GTGCATCGATGCA
410375 CTACCCATGC
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
19 1 0.03
20 18 0.49
21 1 0.03
22 1 0.03
23 3 0.08
24 13 0.35
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (22 bp):
CTTAACAGTGCATCGATGCATT
Found at i:410468 original size:17 final size:19
Alignment explanation
Indices: 410426--410472 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
410416 TTTTAAGGGG
* *
410426 ATGCATCGATGCACTACTT
1 ATGCATCGATGCACCACAT
410445 ATGCATCGATGCACCA-AT
1 ATGCATCGATGCACCACAT
410463 -TGCATCGATG
1 ATGCATCGATG
410473 TTTCTTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 10 0.38
18 1 0.04
19 15 0.58
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (19 bp):
ATGCATCGATGCACCACAT
Found at i:410989 original size:10 final size:10
Alignment explanation
Indices: 410974--411013 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
410964 GAGATACGGG
410974 AGAAGGAAGA
1 AGAAGGAAGA
410984 AGAAGGAAGA
1 AGAAGGAAGA
*
410994 AGAAGAAAGA
1 AGAAGGAAGA
*
411004 AGAAAGAAGA
1 AGAAGGAAGA
411014 CTCTGGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (10 bp):
AGAAGGAAGA
Found at i:410992 original size:7 final size:7
Alignment explanation
Indices: 410974--411013 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
410964 GAGATACGGG
*
410974 AGAAGGA
1 AGAAGAA
410981 AGAAGAA
1 AGAAGAA
*
410988 GGAAG-A
1 AGAAGAA
410994 AGAAGAA
1 AGAAGAA
411001 AGAAGAA
1 AGAAGAA
411008 AGAAGA
1 AGAAGA
411014 CTCTGGATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (7 bp):
AGAAGAA
Done.