Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006235.1 Hibiscus syriacus cultivar Beakdansim tig00014862_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: 996025
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:206741 original size:20 final size:20
Alignment explanation
Indices: 206704--206743 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
206694 ACGGAAAACG
**
206704 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
206724 TTTTCCAGAATTCAAATTCA
1 TTTTCCAGAAATCAAATTCA
206744 AATAATTCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:207760 original size:45 final size:40
Alignment explanation
Indices: 207710--207791 Score: 101
Period size: 41 Copynumber: 1.9 Consensus size: 40
207700 AAAGTCTTAT
*
207710 ATTTTAGTTTTTAAAAACAACATATAAATATTAATATCATTAATA
1 ATTTTA-TTTTGAAAAA-AA-ATA-AAATATTAATAT-ATTAATA
*
207755 ATTTTATTTTGAAAAAAAATAAAATTTTAATATATTA
1 ATTTTATTTTGAAAAAAAATAAAATATTAATATATTA
207792 TTTTTTCGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
40 4 0.11
41 11 0.31
42 3 0.09
43 2 0.06
44 9 0.26
45 6 0.17
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (40 bp):
ATTTTATTTTGAAAAAAAATAAAATATTAATATATTAATA
Found at i:208383 original size:87 final size:87
Alignment explanation
Indices: 208276--208461 Score: 311
Period size: 87 Copynumber: 2.1 Consensus size: 87
208266 ACAAATTAGT
208276 TAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAACACAATAACATATTAGGT
1 TAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAACACAATAACATATTAGGT
*
208341 AAT-ATTTATATAATGTAATAGG
66 -ATCACTTATATAATGTAATAGG
* * **
208363 TAGCGCTTATATAATAAAATAGGTTAATTACTAGAAATATTATTAAGTACAATAACATATTAGGT
1 TAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAACACAATAACATATTAGGT
208428 ATCACTTATATAATGTAATAGG
66 ATCACTTATATAATGTAATAGG
208450 TAGCGCTTATAT
1 TAGCGCTTATAT
208462 TGACCTATTT
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
86 2 0.02
87 91 0.98
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (87 bp):
TAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAACACAATAACATATTAGGT
ATCACTTATATAATGTAATAGG
Found at i:208946 original size:198 final size:197
Alignment explanation
Indices: 208463--209140 Score: 918
Period size: 197 Copynumber: 3.4 Consensus size: 197
208453 CGCTTATATT
* ** * *
208463 GACCTATTTTATCATAAAACTGGTATATTTATATCAGTAACATTGCAAATTTACCTATTACATTA
1 GACCTATTTTCTCATAAAACCAGTATATTTATACCAGT-ACATTGTAAATTTACCTATTACATTA
* *
208528 TAATTAT-GGTTTCGATGTTTTTGGGATCGATACAATTT--TAAATGTATCGACACTTTATGCGT
65 TAATTATCGGTTTCGATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGTGT
*
208590 GCACCTCGTTGGACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAACGTGTCGATACATT
129 GCACCTCGTTGGACATTCATTCTGG-AAAAAGTATCGACACAAACTTAAAATGTGTCGATACATT
208655 ATGTA
193 ATGTA
* * *
208660 GACCTATTTTCTCATAAAACCGGTATATTTCTACCAGGTACATTGTAAATTTACCTATTACATTG
1 GACCTATTTTCTCATAAAACCAGTATATTTATACCA-GTACATTGTAAATTTACCTATTACATTA
*
208725 TAATTATCGGTTTGGAT-TTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGTGTG
65 TAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGTGTG
*
208789 CACCTCGTTGGACATTCATTCTGGAAAAAGTATCGACACAAACTTAAAATGTGTCAATACATTAT
130 CACCTCGTTGGACATTCATTCTGGAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTAT
208854 GTA
195 GTA
* * * *
208857 GACCTATTTTCTCATAAAACCAATATATTTCTACCGAGTACATTGTAAATTTATCTATTACATTG
1 GACCTATTTTCTCATAAAACCAGTATATTTATACC-AGTACATTGTAAATTTACCTATTACATTA
*
208922 TAATTATCGGTTTCGATGTTTTTGGGATCTATACTTTTAATAAATGTATCGACACTTTATGTGTG
65 TAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGTGTG
* * ** * *** *
208987 CACCGCGTTTGG-CATTCATTCTGGACAAAATATATTAATAC-TTTTTAAATTTGTGTCGATACA
130 CACCTCG-TTGGACATTCATTCTGGA-AAAA-GTATCGACACAAACTTAAA-ATGTGTCGATACA
209050 TTATGTA
191 TTATGTA
* * * ** *
209057 GACATATTCTCTCATAAAACCATTATATTTATACTGGTTACATTATAAATTTACCTATTACATTA
1 GACCTATTTTCTCATAAAACCAGTATATTTATACCAG-TACATTGTAAATTTACCTATTACATTA
*
209122 TAATTATCGGTTTTGATGT
65 TAATTATCGGTTTCGATGT
209141 AATATATGTG
Statistics
Matches: 434, Mismatches: 36, Indels: 19
0.89 0.07 0.04
Matches are distributed among these distances:
196 3 0.01
197 197 0.45
198 124 0.29
199 14 0.03
200 96 0.22
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (197 bp):
GACCTATTTTCTCATAAAACCAGTATATTTATACCAGTACATTGTAAATTTACCTATTACATTAT
AATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGTGTGC
ACCTCGTTGGACATTCATTCTGGAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTATG
TA
Found at i:209276 original size:14 final size:16
Alignment explanation
Indices: 209240--209284 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
209230 ATTATGATAA
209240 ATAATAAATATAATTT
1 ATAATAAATATAATTT
*
209256 ATAATAAAT-TTATTT
1 ATAATAAATATAATTT
209271 -TAATAAAATATAAT
1 ATAAT-AAATATAAT
209285 AATCATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 4 0.16
15 9 0.36
16 12 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATAAATATAATTT
Found at i:209334 original size:14 final size:14
Alignment explanation
Indices: 209266--209338 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
209256 ATAATAAATT
209266 TATTTTAATAA-AA
1 TATTTTAATAATAA
** *
209279 TATAATAATCATAA
1 TATTTTAATAATAA
* * *
209293 TTTTTTATTTATAA
1 TATTTTAATAATAA
* *
209307 AATTATAGAT-ATAA
1 TATTTTA-ATAATAA
209321 TATTTTAATAATAA
1 TATTTTAATAATAA
209335 TATT
1 TATT
209339 GACATAAATA
Statistics
Matches: 43, Mismatches: 14, Indels: 5
0.69 0.23 0.08
Matches are distributed among these distances:
13 10 0.23
14 32 0.74
15 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (14 bp):
TATTTTAATAATAA
Found at i:209334 original size:28 final size:28
Alignment explanation
Indices: 209266--209334 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
209256 ATAATAAATT
*
209266 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
209293 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
209321 TATTTTAATAATAA
1 TATTTTAATAATAA
209335 TATTGACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:209421 original size:24 final size:25
Alignment explanation
Indices: 209353--209421 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 25
209343 TAAATAATAT
* *
209353 TAAATAA-ATTATTCTTATATTTTAA
1 TAAATAATATTATTATTAT-TGTTAA
*
209378 -AAATAATAATATTATT-TTGTTAA
1 TAAATAATATTATTATTATTGTTAA
209401 TAAATAATATTATT-TTATTGT
1 TAAATAATATTATTATTATTGT
209422 ATTTGATGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 7 0.19
24 23 0.62
25 7 0.19
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (25 bp):
TAAATAATATTATTATTATTGTTAA
Found at i:210194 original size:24 final size:25
Alignment explanation
Indices: 210142--210194 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
210132 ATTATTCTAA
210142 TATT-TTAAAAAATAATATTATTAT
1 TATTGTTAAAAAATAATATTATTAT
* *
210166 T-TTGTTAATAAATAATATTGTT-T
1 TATTGTTAAAAAATAATATTATTAT
210189 TATTGT
1 TATTGT
210195 ATTTGATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.55
Consensus pattern (25 bp):
TATTGTTAAAAAATAATATTATTAT
Found at i:210475 original size:23 final size:23
Alignment explanation
Indices: 210449--210498 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
210439 ACCTATTTTA
*
210449 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
* *
210472 TTATATAATCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
210495 TTAT
1 TTAT
210499 TGTGCTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:210561 original size:23 final size:23
Alignment explanation
Indices: 210526--210576 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
210516 CTAGTAATTA
** *
210526 ACCTATTTTATTATATAAGCGTT
1 ACCTATTACATTATATAAGCGGT
210549 ACCTATTACATTATATAAGCGGT
1 ACCTATTACATTATATAAGCGGT
210572 ACCTA
1 ACCTA
210577 ATATGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGGT
Found at i:210645 original size:23 final size:23
Alignment explanation
Indices: 210610--210729 Score: 161
Period size: 23 Copynumber: 5.2 Consensus size: 23
210600 TTTTCAATTA
** *
210610 ACCTATTTTATTATATAAGTGCT
1 ACCTATTACATTATATAAGCGCT
*
210633 ACCTATTACATTATATAAGCACT
1 ACCTATTACATTATATAAGCGCT
* *
210656 ACTTATTACATTATATAAACGCT
1 ACCTATTACATTATATAAGCGCT
210679 ACCTATTACATTATAT-AGACGCT
1 ACCTATTACATTATATAAG-CGCT
*
210702 ACCTATTACATTATATAAGCGGT
1 ACCTATTACATTATATAAGCGCT
210725 ACCTA
1 ACCTA
210730 ATATGTTATT
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
22 1 0.01
23 82 0.96
24 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:210646 original size:84 final size:86
Alignment explanation
Indices: 210434--210657 Score: 353
Period size: 87 Copynumber: 2.6 Consensus size: 86
210424 CAAATTAAAT
* *
210434 AATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAATCGCTACCTAATATGTTAT
1 AATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTAT
* *
210499 TGTGCTTGATAATGTTTCTAGT
66 TGTGCTTGACAATGTTTCTA-C
* *
210521 AATTAACCTATTTTATTATATAAGCGTTACCTATTACATTATATAAGCGGTACCTAATATGTTAT
1 AATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTAT
210586 TGTGCTTGACAATGTTT-T-C
66 TGTGCTTGACAATGTTTCTAC
* *
210605 AATTAACCTATTTTATTATATAAGTGCTACCTATTACATTATATAAGCACTAC
1 AATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTAC
210658 TTATTACATT
Statistics
Matches: 127, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
84 49 0.39
86 1 0.01
87 77 0.61
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.42
Consensus pattern (86 bp):
AATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTAT
TGTGCTTGACAATGTTTCTAC
Found at i:210815 original size:64 final size:64
Alignment explanation
Indices: 210711--210866 Score: 258
Period size: 64 Copynumber: 2.4 Consensus size: 64
210701 TACCTATTAC
* * ** *
210711 ATTATATAAGCGGTACCTAATATGTTATTGTGCTTGATAATGTTTCTAGTAATTAACATATTTT
1 ATTATATAAGCGCTACCTATTACATTATTGTGCTTAATAATGTTTCTAGTAATTAACATATTTT
*
210775 ATTATATAAGCGCTACCTATTACATTATTGTGCTTAATAATGTTTCTAGTAATTAACCTATTTT
1 ATTATATAAGCGCTACCTATTACATTATTGTGCTTAATAATGTTTCTAGTAATTAACATATTTT
210839 ATTATATAAGCGCTACCTATTACATTAT
1 ATTATATAAGCGCTACCTATTACATTAT
210867 ATAAACGCTA
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 86 1.00
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (64 bp):
ATTATATAAGCGCTACCTATTACATTATTGTGCTTAATAATGTTTCTAGTAATTAACATATTTT
Found at i:210865 original size:23 final size:23
Alignment explanation
Indices: 210830--210891 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
210820 CTAGTAATTA
** *
210830 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAACGCT
210853 ACCTATTACATTATATAAACGCT
1 ACCTATTACATTATATAAACGCT
*
210876 ACCTATTACATCATAT
1 ACCTATTACATTATAT
210892 TTTTACTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAACGCT
Found at i:212657 original size:20 final size:17
Alignment explanation
Indices: 212632--212670 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 17
212622 TTATAGTTAA
212632 AAATTAAATCAATAATATTT
1 AAATT-AAT-AATAAT-TTT
212652 AAATTAATAATAATTTT
1 AAATTAATAATAATTTT
212669 AA
1 AA
212671 TAATGAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 6 0.32
19 3 0.16
20 5 0.26
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTAATAATAATTTT
Found at i:219171 original size:21 final size:21
Alignment explanation
Indices: 219147--219204 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
219137 ATCCTCACTA
219147 TGTATCGATACACTATG-ATAG
1 TGTATCGATACACTATGAAT-G
* *
219168 TGTATCGATGCATTCTTTGAATG
1 TGTATCGATACA--CTATGAATG
219191 TGTATCGATACACT
1 TGTATCGATACACT
219205 TAAGAGTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 13 0.42
23 16 0.52
24 2 0.06
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (21 bp):
TGTATCGATACACTATGAATG
Found at i:219709 original size:13 final size:13
Alignment explanation
Indices: 219686--219724 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
219676 AAAATTACAT
*
219686 ATTGATTTTCAAAC
1 ATTG-TTTTCAAAA
219700 ATTGTTTTCAAAA
1 ATTGTTTTCAAAA
*
219713 ATAGTTTTCAAA
1 ATTGTTTTCAAA
219725 TTTGCACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTGTTTTCAAAA
Found at i:221139 original size:14 final size:15
Alignment explanation
Indices: 221120--221149 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
221110 TAAAACATTT
221120 TTGATAT-TTTTGGA
1 TTGATATGTTTTGGA
221134 TTGATATGTTTTGGA
1 TTGATATGTTTTGGA
221149 T
1 T
221150 GTAATGGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
TTGATATGTTTTGGA
Found at i:221489 original size:13 final size:13
Alignment explanation
Indices: 221467--221500 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
221457 AGGGGGAATA
*
221467 ATTTTCAAAATTG
1 ATTTTCAAAAATG
221480 A-TTTCAAAAATG
1 ATTTTCAAAAATG
221492 ATTTTCAAA
1 ATTTTCAAA
221501 TCTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:222384 original size:19 final size:19
Alignment explanation
Indices: 222360--222403 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
222350 GAATTTGTAA
222360 TTTTCTCATTGGGAGAGAG
1 TTTTCTCATTGGGAGAGAG
*
222379 TTTTCTCTTTGGGAGAGAG
1 TTTTCTCATTGGGAGAGAG
*
222398 TGTTCT
1 TTTTCT
222404 AAAAAATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.16, C:0.11, G:0.30, T:0.43
Consensus pattern (19 bp):
TTTTCTCATTGGGAGAGAG
Found at i:223076 original size:17 final size:17
Alignment explanation
Indices: 223049--223092 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
223039 TTATGGGGTG
223049 AAAAATGATA-TTATTGTA
1 AAAAAT-ATATTTATT-TA
223067 AAAAATATATTTATTTA
1 AAAAATATATTTATTTA
223084 AAATAATAT
1 AAA-AATAT
223093 CTGACTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
AAAAATATATTTATTTA
Found at i:223182 original size:18 final size:17
Alignment explanation
Indices: 223154--223192 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
223144 TCCATCGAAA
223154 TCATAATATTATT-T-TT
1 TCATAATA-TATTATATT
223170 TCATAATATATTATATT
1 TCATAATATATTATATT
223187 TCATAA
1 TCATAA
223193 AAATAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 9 0.43
17 8 0.38
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TCATAATATATTATATT
Found at i:228760 original size:23 final size:23
Alignment explanation
Indices: 228713--228762 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
228703 AATAACATAT
* **
228713 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCACTTATATAATAAAA
228736 TAGGTAGCACTTATATAATAAAA
1 TAGGTAGCACTTATATAATAAAA
228759 TAGG
1 TAGG
228763 CATTTAACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (23 bp):
TAGGTAGCACTTATATAATAAAA
Found at i:228817 original size:23 final size:23
Alignment explanation
Indices: 228791--228849 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
228781 ATCAAGTACA
*
228791 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
228814 ATAATATAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
228837 ATAATAAAATAGG
1 ATAACATAATAGG
228850 CATTTAACCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:228824 original size:87 final size:87
Alignment explanation
Indices: 228676--228925 Score: 446
Period size: 87 Copynumber: 2.9 Consensus size: 87
228666 TATGTTATAT
**
228676 CATTTAACCGGAAATATTATCAAACACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
*
228741 AGCACTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* *
228763 CATTTAACCGGAAAAATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
228828 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
*
228850 CATTTAACCGTAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
228915 AGCGCTTATAT
66 AGCGCTTATAT
228926 TGACCTATTT
Statistics
Matches: 155, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 155 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAGG
Found at i:232235 original size:200 final size:200
Alignment explanation
Indices: 231886--233626 Score: 2255
Period size: 200 Copynumber: 8.8 Consensus size: 200
231876 AGACATTTGG
* * * *
231886 TTATAATTATGTTTTTCGATGTTTTCGAGATCGATACTTGTTATAAATATATCGACACTTTGTTG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTGTTG
* *
231951 TGCACTTGGTTTTTAAAATACAATATGGACAAGATGTATCGATACTTTTTTTATTTGTGTCGATA
66 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTATTTGTGTCGATA
* *
232016 CTTTTTGTACACTTGTTTTCTCAAAAACTGGTATATTTAGGCCGATTACATTAATAATTTACCTA
131 CTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCGATTACATTAATAATTTACCTA
232081 TTACA
196 TTACA
* *
232086 TTATAATTATGTTTTT-GATGTTTTTGGGATCGACAGTTGTTTTAAATGTATCGACACTTTGTTG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTGTTG
* * * * *
232150 TGCACTTGGTTTTTTAAAATACAATTTGGACAAGATATATCGCCACTTTTTTTATTTCTGTCCAT
66 TGCACTTGG-TTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTATTTGTGTCGAT
* *
232215 ACTTTTTGTACACATGTTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTAATAATTTACCT
130 ACTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCGATTACATTAATAATTTACCT
232280 ATTACA
195 ATTACA
* * *
232286 TTATAATTATGTTTTTCGATGTTTTCGTGATCGACACTTGTTTTAAATGTATTGATACTTTGTTG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTGTTG
232351 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTATTTGTGTCGATA
66 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTATTTGTGTCGATA
* *
232416 CTTTTTGTACACCTGTTTTCTCAAAAACTAGTATATTTAGACCGGTTACATTAATAATTTACCTA
131 CTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCGATTACATTAATAATTTACCTA
*
232481 TTATA
196 TTACA
*
232486 TTATAATTATGTTTTTCGATGTTTTCGAGATCGACACTTGTTTTAAATGTATCGACACTTTGTTG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTGTTG
* *
232551 TGCACTTGGTTTTTAAAATACAATATGGACAAGATGTATTGACACTTTTTTTATTTGTGTCGATA
66 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTATTTGTGTCGATA
* * *
232616 CTTTTTGTACACCCGTTTTCTCAAAAACCGGTATATTTAGACC-AGTTACATTAATCATTTACCT
131 CTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCGA-TTACATTAATAATTTACCT
232680 ATTACA
195 ATTACA
* *
232686 TTATAATTATGTTTTTCGATATTTTCGGGATCAACACTTGTTTTAAATGTATCGACACTTTGTTG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTGTTG
232751 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTATTTGTGTCGATA
66 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTATTTGTGTCGATA
* * * *
232816 CTTTTTGTACACCTATTTTCTCAAAAACCGATATATTTAGACCGGTTACATTAATAATTTACCTA
131 CTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCGATTACATTAATAATTTACCTA
232881 TTACA
196 TTACA
* *
232886 TTATAATTATGTTTTTCGATGTTTTCGGGTTCGACACTTATTTTAAATGTATCGACACTTTGTTG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTGTTG
* *
232951 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATTTATCGACATTTTTTTTATTTGTGTCGATA
66 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTATTTGTGTCGATA
*
233016 CTTTTTCTACACCTGTTTTCTCAAAAA-TCGGTATATTTAGACC-AGTTACATTAATAATTTACC
131 CTTTTTGTACACCTGTTTTCTCAAAAACT-GGTATATTTAGACCGA-TTACATTAATAATTTACC
233079 TATTACA
194 TATTACA
*
233086 TTATAATTATGTTTTT-GATGTTTTCGGGATCGACACTTGTTTTGGTTTTAAAATATAATCTGGA
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACAC-----TT-GTTTT-AAATGT-ATC--GA
*** * * * * * * * * *
233150 CAAGATGTATCG-ACACTT--TTTTT----T--TATTTGTGTCGATACT-TTTTGTACACTTGTT
56 CACTTTGT-T-GTGCACTTGGTTTTTAAAATACAATCTG-GACAAGA-TGTATCG-ACACTTTTT
* ***** * * * * * ** *
233205 TTCTCAAAAATCGGTA--TATT-TAGACC-G-GTT-ACATTAA----TA-ATTT--ACCTATTAC
116 TTAT-TTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCGATTAC
233257 ATT-ATAA-TT----------
180 ATTAATAATTTACCTATTACA
*
233266 -----A-TAT-TTTTT-GATGTTTTCGGAATCGACACTTGTTTTAAATGTATCGACACTTTGTTG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTGTTG
*
233323 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGCCACTTTTTTTTATTTGTGTCGAT
66 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACAC-TTTTTTTATTTGTGTCGAT
* * * *
233388 ACTTTTTGTACACTTATTTTCTCAAAAACTAGTATATTTAGACCGGTTACATTAATAATTTACCT
130 ACTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCGATTACATTAATAATTTACCT
233453 ATTACA
195 ATTACA
*
233459 TTATAATTATGTTTTTCGATGTTTTCGGGATCGGCACTTGTTTTAAATGTATCGACACTTTGTTG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTGTTG
* *
233524 TGCACTTGGTTTTTAAAATACAATCTAGACAAGATGTATCGACATTTTTTTTATTTGTGTCGATA
66 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTATTTGTGTCGATA
* *
233589 CTTTTTGTACACCAGTTTTCTCAAAAACCGGTATATTT
131 CTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTT
233627 GAAAAATATA
Statistics
Matches: 1343, Mismatches: 131, Indels: 134
0.84 0.08 0.08
Matches are distributed among these distances:
161 1 0.00
162 6 0.00
163 7 0.01
164 5 0.00
165 3 0.00
166 5 0.00
167 5 0.00
168 12 0.01
169 14 0.01
170 7 0.01
171 4 0.00
173 26 0.02
174 7 0.01
175 1 0.00
178 2 0.00
179 4 0.00
181 10 0.01
182 4 0.00
183 2 0.00
190 2 0.00
191 4 0.00
192 10 0.01
193 1 0.00
194 4 0.00
195 2 0.00
198 1 0.00
199 77 0.06
200 907 0.68
201 141 0.10
202 9 0.01
203 10 0.01
204 14 0.01
205 9 0.01
206 5 0.00
207 3 0.00
208 5 0.00
209 7 0.01
210 6 0.00
211 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (200 bp):
TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTGTTG
TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTATTTGTGTCGATA
CTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCGATTACATTAATAATTTACCTA
TTACA
Found at i:233241 original size:172 final size:172
Alignment explanation
Indices: 232956--233301 Score: 597
Period size: 172 Copynumber: 2.0 Consensus size: 172
232946 TGTTGTGCAC
*
232956 TTGGTTTTTAAAATACAATCTGGACAAGATTTATCGACATTTTTTTTATTTGTGTCGATACTTTT
1 TTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACATTTTTTTTATTTGTGTCGATACTTTT
233021 TCTACACCTGTTTTCTCAAAAATCGGTATATTTAGACCAGTTACATTAATAATTTACCTATTACA
66 TCTACACCTGTTTTCTCAAAAATCGGTATATTTAGACCAGTTACATTAATAATTTACCTATTACA
*
233086 TTATAATTAT-GTTTTTGATGTTTTCGGGATCGACACTTGTT
131 TTATAATTATAGTTTTTGATGTTTTCGGAATCGACACTTGTT
*
233127 TTGG-TTTTAAAATATAATCTGGACAAGATGTATCGACACTTTTTTTTTATTTGTGTCGATACTT
1 TTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACA--TTTTTTTTATTTGTGTCGATACTT
* * *
233191 TTTGTACACTTGTTTTCTCAAAAATCGGTATATTTAGACCGGTTACATTAATAATTTACCTATTA
64 TTTCTACACCTGTTTTCTCAAAAATCGGTATATTTAGACCAGTTACATTAATAATTTACCTATTA
*
233256 CATTATAATTATATTTTTTGATGTTTTCGGAATCGACACTTGTT
129 CATTATAATTATAGTTTTTGATGTTTTCGGAATCGACACTTGTT
233300 TT
1 TT
233302 AAATGTATCG
Statistics
Matches: 165, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
170 32 0.19
171 4 0.02
172 98 0.59
173 31 0.19
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (172 bp):
TTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACATTTTTTTTATTTGTGTCGATACTTTT
TCTACACCTGTTTTCTCAAAAATCGGTATATTTAGACCAGTTACATTAATAATTTACCTATTACA
TTATAATTATAGTTTTTGATGTTTTCGGAATCGACACTTGTT
Found at i:233482 original size:201 final size:201
Alignment explanation
Indices: 233127--233626 Score: 846
Period size: 201 Copynumber: 2.5 Consensus size: 201
233117 GACACTTGTT
*
233127 TTGG-TTTTAAAATATAATCTGGACAAGATGTATCGACACTTTTTTTTTATTTGTGTCGATACTT
1 TTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACAC-TTTTTTTTATTTGTGTCGATACTT
*
233191 TTTGTACACTTGTTTTCTCAAAAA-TCGGTATATTTAGACCGGTTACATTAATAATTTACCTATT
65 TTTGTACACTTATTTTCTCAAAAACT-GGTATATTTAGACCGGTTACATTAATAATTTACCTATT
*
233255 ACATTATAATTATATTTTTTGATGTTTTCGGAATCGACACTTGTTTTAAATGTATCGACACTTTG
129 ACATTATAATTATATTTTTCGATGTTTTCGGAATCGACACTTGTTTTAAATGTATCGACACTTTG
233320 TTGTGCAC
194 TTGTGCAC
*
233328 TTGGTTTTTAAAATACAATCTGGACAAGATGTATCGCCACTTTTTTTTATTTGTGTCGATACTTT
1 TTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGATACTTT
*
233393 TTGTACACTTATTTTCTCAAAAACTAGTATATTTAGACCGGTTACATTAATAATTTACCTATTAC
66 TTGTACACTTATTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTAATAATTTACCTATTAC
* * *
233458 ATTATAATTATGTTTTTCGATGTTTTCGGGATCGGCACTTGTTTTAAATGTATCGACACTTTGTT
131 ATTATAATTATATTTTTCGATGTTTTCGGAATCGACACTTGTTTTAAATGTATCGACACTTTGTT
233523 GTGCAC
196 GTGCAC
*
233529 TTGGTTTTTAAAATACAATCTAGACAAGATGTATCGACA-TTTTTTTTATTTGTGTCGATACTTT
1 TTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGATACTTT
* *
233593 TTGTACAC-CAGTTTTCTCAAAAACCGGTATATTT
66 TTGTACACTTA-TTTTCTCAAAAACTGGTATATTT
233627 GAAAAATATA
Statistics
Matches: 283, Mismatches: 13, Indels: 7
0.93 0.04 0.02
Matches are distributed among these distances:
199 1 0.00
200 54 0.19
201 194 0.69
202 34 0.12
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (201 bp):
TTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGATACTTT
TTGTACACTTATTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTAATAATTTACCTATTAC
ATTATAATTATATTTTTCGATGTTTTCGGAATCGACACTTGTTTTAAATGTATCGACACTTTGTT
GTGCAC
Found at i:236252 original size:15 final size:15
Alignment explanation
Indices: 236212--236269 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
236202 GGGCGATTGA
236212 TTGAGAAGGAGGTTGTGG
1 TTGAGAA-GA-GTTG-GG
236230 TTGAGAAGAGTTGGG
1 TTGAGAAGAGTTGGG
* *
236245 TTGGGAAGAGGTGGG
1 TTGAGAAGAGTTGGG
236260 TTGAGAAGAG
1 TTGAGAAGAG
236270 ATTTAGAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
15 24 0.65
16 4 0.11
17 2 0.05
18 7 0.19
ACGTcount: A:0.26, C:0.00, G:0.50, T:0.24
Consensus pattern (15 bp):
TTGAGAAGAGTTGGG
Found at i:236898 original size:199 final size:199
Alignment explanation
Indices: 236647--237511 Score: 1471
Period size: 199 Copynumber: 4.3 Consensus size: 199
236637 GTTACATTGC
* *
236647 TACCTATTACATTATAATTATGGGTTTCAATGTTTTTGGGATCGACACTTGTTATAAATGTATCG
1 TACCTATTACATTATCATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCG
*
236712 ACACTTTTTAGTGTACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTGATT
66 ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTGATT
* *
236777 TGTGTCTATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCT
131 TGTGTCGATACTTTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCT
236842 AATT
196 AATT
236846 TACCTATTACATTATCATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCG
1 TACCTATTACATTATCATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCG
* *
236911 ACACTTATTAGTGCACTTGGTTTTGAAATACATTATGGACCAAAAGTATCGACACTTGTTTGATT
66 ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTGATT
* * * * * * *
236976 TGTGTCGATACATTTTGTACACATGTTTTCTAAAAAAACGGTATATTTAGACTGGTTAAATTGCT
131 TGTGTCGATACTTTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCT
237041 AATT
196 AATT
237045 TACCTATTACATTATCATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCG
1 TACCTATTACATTATCATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCG
*
237110 ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTAGACCAAAAGTATCGACACTTGTTTGATT
66 ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTGATT
237175 TGTGTCGATACTTTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCT
131 TGTGTCGATACTTTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCT
237240 AATT
196 AATT
* * * * *
237244 TATCTATTCCATTATCATTATGAGTTTTGATATTTTTGGGATCGACACTTGTTATAAATGTATCG
1 TACCTATTACATTATCATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCG
* *
237309 ACACTTTTTAGTGCA-TATGTTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTAGAT
66 ACACTTTTTAGTGCACT-TGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTGAT
*
237373 TTGTGTCGATACTTTTTGTACACCTATTTTCTCAAAAACCGATATATTTAGACCGGTTATATTGC
130 TTGTGTCGATACTTTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGC
237438 TAATT
195 TAATT
* * * *
237443 TACCTATTACATTATAATTATGGTTTTCAATGTTTTTGGGATCGACACTTGTTATAATTGTATCG
1 TACCTATTACATTATCATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCG
237508 ACAC
66 ACAC
237512 ATAAGTTTAC
Statistics
Matches: 625, Mismatches: 40, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
198 1 0.00
199 624 1.00
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.42
Consensus pattern (199 bp):
TACCTATTACATTATCATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCG
ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTGATT
TGTGTCGATACTTTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCT
AATT
Found at i:237881 original size:19 final size:19
Alignment explanation
Indices: 237857--237906 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
237847 TTACATTCAC
*
237857 ATACAAAATTATAAATCGT
1 ATACAAAATTAAAAATCGT
*
237876 ATACAAAATTAAAAATCTT
1 ATACAAAATTAAAAATCGT
237895 ATACAAAATTAA
1 ATACAAAATTAA
237907 CCCTGTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (19 bp):
ATACAAAATTAAAAATCGT
Found at i:239414 original size:18 final size:18
Alignment explanation
Indices: 239378--239416 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
239368 TTCTCCTCAT
* * *
239378 TTCCTCCATTTTTTTTTC
1 TTCCTCCATCTTCTCTTC
239396 TTCCTCCATCTTCTCTTC
1 TTCCTCCATCTTCTCTTC
239414 TTC
1 TTC
239417 AAATTTTTTC
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:0.05, C:0.36, G:0.00, T:0.59
Consensus pattern (18 bp):
TTCCTCCATCTTCTCTTC
Found at i:241425 original size:20 final size:20
Alignment explanation
Indices: 241377--241426 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
241367 CATTTATACA
241377 ACCTA-AAATATCATTTTCT
1 ACCTATAAATATCATTTTCT
*
241396 ACCTAT-AATATCATTTTTT
1 ACCTATAAATATCATTTTCT
241415 ACCTATAAATAT
1 ACCTATAAATAT
241427 TAAATAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 23 0.82
20 5 0.18
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (20 bp):
ACCTATAAATATCATTTTCT
Found at i:242186 original size:11 final size:11
Alignment explanation
Indices: 242170--242194 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
242160 AAGTGTCAAT
242170 AGTTATATTAA
1 AGTTATATTAA
242181 AGTTATATTAA
1 AGTTATATTAA
242192 AGT
1 AGT
242195 ATCGACACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (11 bp):
AGTTATATTAA
Found at i:242332 original size:194 final size:193
Alignment explanation
Indices: 241812--242379 Score: 668
Period size: 194 Copynumber: 3.0 Consensus size: 193
241802 TACACGTACT
* * *** * *
241812 TATTAAAGTATCGACACTTTCAACATATCCGGTAGTGCTTTACCGATTTTGTC-ATTTTGAGAGC
1 TATTAAAGTATCAACACTTTCAACATATCCAGTAGCATTTTACCGGTTTTGTCAATTTTGAGACC
* * *
241876 GGTTTTATCATATTTTTAC-TGTTATACTGTTATGGATCGATACATTTT-TTAAAAGTATCGACA
66 GGTTTTATCATATTTTTACATGTTATATTGTTATAGATCGATACATTTTCAT-AAAGTATCGACA
* * * *
241939 CTTTATAGGCGCTATAAATTATTCT-ATTTAAATTCATAAAGTGTCGATACTTATATTAAA-T-
130 CTTTATAGGCGCTATAACTTATTCTCTTTTAAATTCATAAAGTCTCAATACTTATATTAAATTA
* * * *
242000 TA-TCAA-TAT------TTTCAACATATCCGGTAGCGTTTTACTGGTTTTGTCAATTTTGAGACC
1 TATTAAAGTATCAACACTTTCAACATATCCAGTAGCATTTTACCGGTTTTGTCAATTTTGAGACC
* * **
242057 TGTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACAC
66 GGTTTTATCATATTTTTACATGTTATATTGTTATAGATCGATACATTTTCATAAAGTATCGACAC
** * * *
242122 TTTATAGGTTCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCAATAGTTATATTAAAGTTA
131 TTTATAGGCGCTATAACTTATTCTCTTTTAAATT-CATAAAGTCTCAATACTTATATTAAA-TTA
* * *
242186 TATTAAAGTATCGACACTTTCAACATATCCAGTATCATTTTACCGGTTTTTTC-ATTGTTGAGAC
1 TATTAAAGTATCAACACTTTCAACATATCCAGTAGCATTTTACCGGTTTTGTCAATT-TTGAGAC
*
242250 CGGTTTTATCATATTTTTAGC-TGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGAC
65 CGGTTTTATCATATTTTTA-CATGTTATATTGTTATAGATCGATACATTTTCATAAAGTATCGAC
*
242314 ACGTTT-TAGGCGCTATAACTTATTCTCTTTTAAATTCATAAAGTCTCGATACTTATATTAAATT
129 AC-TTTATAGGCGCTATAACTTATTCTCTTTTAAATTCATAAAGTCTCAATACTTATATTAAATT
242378 A
193 A
242379 T
1 T
242380 CGACACTTTC
Statistics
Matches: 328, Mismatches: 32, Indels: 35
0.83 0.08 0.09
Matches are distributed among these distances:
180 32 0.10
181 28 0.09
182 61 0.19
183 31 0.09
184 2 0.01
185 1 0.00
186 5 0.02
187 6 0.02
188 5 0.02
193 9 0.03
194 144 0.44
195 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (193 bp):
TATTAAAGTATCAACACTTTCAACATATCCAGTAGCATTTTACCGGTTTTGTCAATTTTGAGACC
GGTTTTATCATATTTTTACATGTTATATTGTTATAGATCGATACATTTTCATAAAGTATCGACAC
TTTATAGGCGCTATAACTTATTCTCTTTTAAATTCATAAAGTCTCAATACTTATATTAAATTA
Found at i:242825 original size:65 final size:64
Alignment explanation
Indices: 242722--242883 Score: 184
Period size: 65 Copynumber: 2.5 Consensus size: 64
242712 AATTAAATTG
* * * * * *
242722 AACATCAAATGCATTTCATGCATCGATGCACTTACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCAATGCACTCACCATGCACAGATGCACTCAGGATATTT-TG-
242786 A
64 A
* * * *
242787 AACATCGAATGCATTTGATGCATCAATGCAC-CAGCCATGCATAGATGCACTCTGGCTATTTTGG
1 AACATCGAATGCATTTGATGCATCAATGCACTCA-CCATGCACAGATGCACTCAGGATATTTTGA
*
242851 AACATCGAATGCACTTGATGCATCAATGCACTC
1 AACATCGAATGCATTTGATGCATCAATGCACTC
242884 TTAGTGCACC
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
64 31 0.37
65 49 0.59
66 3 0.04
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCAATGCACTCACCATGCACAGATGCACTCAGGATATTTTGA
Found at i:250944 original size:2 final size:2
Alignment explanation
Indices: 250937--250983 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
250927 CAGCTTAAGC
250937 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
250979 TA TA T
1 TA TA T
250984 CAATTGGCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:251545 original size:65 final size:64
Alignment explanation
Indices: 251471--251654 Score: 196
Period size: 65 Copynumber: 2.9 Consensus size: 64
251461 AATTAAATTG
* * *
251471 AACATCGAATGTATTTCATGCATCGATGTACTTACCATGCACCGATGCACTAAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACTTACCATGCACCGATGCACTAAGGATATTT-TG-
251535 A
64 A
* * ** *
251536 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTTA-CCATGCACCGATGCACTAAGGATATTTTGA
* * *
251600 AACATCGAATGCACTTGATGAATCGATGCACTCTTA--GTGCACCGATGCACTAAGG
1 AACATCGAATGCATTTGATGCATCGATGCA--CTTACCATGCACCGATGCACTAAGG
251655 GTCCAACGGT
Statistics
Matches: 99, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
64 45 0.45
65 49 0.49
66 4 0.04
67 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACTTACCATGCACCGATGCACTAAGGATATTTTGA
Found at i:251646 original size:64 final size:63
Alignment explanation
Indices: 251508--251654 Score: 165
Period size: 64 Copynumber: 2.3 Consensus size: 63
251498 GTACTTACCA
* *
251508 TGCACCGATGCACTAAGGATTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGCC
1 TGCACCGATGCACTAAGGATTTTATGAAAACATCGAATGCACTTGATGAATCGATGCACCAG-C
* ** *
251572 ATGCATCGATGCACTCTGGCTATTT-TG-AAACATCGAATGCACTTGATGAATCGATGCACTCTT
1 -TGCACCGATGCACTAAGGAT-TTTATGAAAACATCGAATGCACTTGATGAATCGATGCAC-C--
251635 AG-
61 AGC
251637 TGCACCGATGCACTAAGG
1 TGCACCGATGCACTAAGG
251655 GTCCAACGGT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
64 45 0.65
65 19 0.28
66 3 0.04
67 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCACCGATGCACTAAGGATTTTATGAAAACATCGAATGCACTTGATGAATCGATGCACCAGC
Found at i:256560 original size:4 final size:4
Alignment explanation
Indices: 256551--256584 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
256541 TAAATTGAAA
*
256551 AAAT AAAT AAAT AAAT AAAT AAAT -ACT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
256585 AAAGAGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 2 0.07
4 25 0.93
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:257842 original size:21 final size:20
Alignment explanation
Indices: 257817--257872 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 20
257807 TAAAAACATA
257817 ATAATAATAATAATAATATGT
1 ATAATAATAATAAT-ATATGT
257838 ATAATGTAAT-ATAATATATGT
1 ATAA--TAATAATAATATATGT
257859 ATATATAATAATAA
1 ATA-ATAATAATAA
257873 AAAACGTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.13
21 17 0.55
22 6 0.19
23 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
ATAATAATAATAATATATGT
Found at i:260067 original size:21 final size:22
Alignment explanation
Indices: 260038--260078 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
260028 GGTTAAAACC
260038 ATAAACTATT-TCGAATGGAGA
1 ATAAACTATTGTCGAATGGAGA
* *
260059 ATAACCTATTGTGGAATGGA
1 ATAAACTATTGTCGAATGGA
260079 TCGGTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (22 bp):
ATAAACTATTGTCGAATGGAGA
Found at i:269226 original size:6 final size:6
Alignment explanation
Indices: 269215--269242 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
269205 AAGATAAAGG
269215 AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAA
269243 GCTCTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:270300 original size:405 final size:406
Alignment explanation
Indices: 269548--270365 Score: 1584
Period size: 405 Copynumber: 2.0 Consensus size: 406
269538 AGTATCGGTG
269548 CCCCTTTGGGTATCAGTATCATTTTTGCATTCTGGAATTTTAGCAATGTTAGTAGTATCGATACT
1 CCCCTTTGGGTATCAGTATCATTTTTGCATTCTGGAATTTTAGCAATGTTAGTAGTATCGATACT
269613 ACCTTAAGAGTATTGATATTTCTCTTACCTTAGATATCAGTACCATATGAACAGTATCGATACTG
66 ACCTTAAGAGTATTGATATTTCTCTTACCTTAGATATCAGTACCATATGAACAGTATCGATACTG
269678 TAAGAACATTATCGGTACTTCATACGTGAAAATCAGTTTTGTGCTCAAATTCACTTTTAATGGAC
131 TAAGAACATTATCGGTACTTCATACGTGAAAATCAGTTTTGTGCTCAAATTCACTTTTAATGGAC
269743 TTTGAATTATTTTTGAAAACTTTGAATAAATTCAATTCAAGTCCAAAAACATTTTGCCTTAAATT
196 TTTGAATTATTTTTGAAAACTTTGAATAAATTCAATTCAAGTCCAAAAACATTTTGCCTTAAATT
269808 GTTATATCAAAACATTATAAAAGCATGGTTCAACAATCTCCCCCTTTTTGATATAACAAAACATT
261 GTTATATCAAAACATTATAAAAGCATGGTTCAACAATCTCCCCCTTTTTGATATAACAAAACATT
269873 TGAAAAATTATTTTTGGCAAAACTCCCCCTTAATAAAATATTTAATGAAAAAGATACTAAATGTT
326 TGAAAAATTATTTTTGGCAAAACTCCCCCTTAATAAAATATTTAATGAAAAAGATACTAAATGTT
*
269938 GGAAAATGTTTAGCTC
391 GGAAAATGTTCAGCTC
*
269954 CCCCTTTGGGTATCGGTATCATTTTTGCATTCTGGAATTTTAGCAATGTTAGTAGTATCGATACT
1 CCCCTTTGGGTATCAGTATCATTTTTGCATTCTGGAATTTTAGCAATGTTAGTAGTATCGATACT
* *
270019 ACCTTAAGAGTATTGATATTTTTCTTACCTTAGATATCGGTACCATATG-ACAGTATCGATACTG
66 ACCTTAAGAGTATTGATATTTCTCTTACCTTAGATATCAGTACCATATGAACAGTATCGATACTG
270083 TAAGAACATTATCGGTACTTCATACGTGAAAATCAGTTTTGTGCTCAAATTCACTTTTAATGGAC
131 TAAGAACATTATCGGTACTTCATACGTGAAAATCAGTTTTGTGCTCAAATTCACTTTTAATGGAC
*
270148 TTTGAATTATTTTTGAAAACTTTGAATAAATTCAATTCAAGTCCAAAAACATTTTGTCTTAAATT
196 TTTGAATTATTTTTGAAAACTTTGAATAAATTCAATTCAAGTCCAAAAACATTTTGCCTTAAATT
270213 GTTATATCAAAACATTATAAAAGCATGGTTCAACAATCTCCCCCTTTTTGATATAACAAAACATT
261 GTTATATCAAAACATTATAAAAGCATGGTTCAACAATCTCCCCCTTTTTGATATAACAAAACATT
270278 TGAAAAATTATTTTTGGCAAAACTCCCCCTTAATAAAATATTTAATGAAAAAGATACTAAATGTT
326 TGAAAAATTATTTTTGGCAAAACTCCCCCTTAATAAAATATTTAATGAAAAAGATACTAAATGTT
270343 GGAAAATGTTCAGCTC
391 GGAAAATGTTCAGCTC
270359 CCCCTTT
1 CCCCTTT
270366 TTCATTGAAA
Statistics
Matches: 407, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
405 296 0.73
406 111 0.27
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (406 bp):
CCCCTTTGGGTATCAGTATCATTTTTGCATTCTGGAATTTTAGCAATGTTAGTAGTATCGATACT
ACCTTAAGAGTATTGATATTTCTCTTACCTTAGATATCAGTACCATATGAACAGTATCGATACTG
TAAGAACATTATCGGTACTTCATACGTGAAAATCAGTTTTGTGCTCAAATTCACTTTTAATGGAC
TTTGAATTATTTTTGAAAACTTTGAATAAATTCAATTCAAGTCCAAAAACATTTTGCCTTAAATT
GTTATATCAAAACATTATAAAAGCATGGTTCAACAATCTCCCCCTTTTTGATATAACAAAACATT
TGAAAAATTATTTTTGGCAAAACTCCCCCTTAATAAAATATTTAATGAAAAAGATACTAAATGTT
GGAAAATGTTCAGCTC
Found at i:273202 original size:18 final size:18
Alignment explanation
Indices: 273134--273212 Score: 81
Period size: 18 Copynumber: 4.5 Consensus size: 18
273124 CAACACTACG
* *
273134 TCTGATAATTGTAAAACA
1 TCTGATAACTGTAAATCA
* * *
273152 CCTGATAACTAT-AATAA
1 TCTGATAACTGTAAATCA
273169 TCTGATAACTGTAAATCA
1 TCTGATAACTGTAAATCA
*
273187 TCTGATAATTGTAAAT-A
1 TCTGATAACTGTAAATCA
*
273204 TATGATAAC
1 TCTGATAAC
273213 GGTGAAATGT
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
17 21 0.43
18 28 0.57
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (18 bp):
TCTGATAACTGTAAATCA
Found at i:273210 original size:35 final size:35
Alignment explanation
Indices: 273136--273212 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
273126 ACACTACGTC
* *
273136 TGATAATTGTAAAACACCTGATAACTATAATAATC
1 TGATAACTGTAAAACACCTGATAACTATAATAATA
* * * *
273171 TGATAACTGTAAATCATCTGATAATTGTAA-ATATA
1 TGATAACTGTAAAACACCTGATAACTATAATA-ATA
273206 TGATAAC
1 TGATAAC
273213 GGTGAAATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 1 0.03
35 34 0.97
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (35 bp):
TGATAACTGTAAAACACCTGATAACTATAATAATA
Found at i:274082 original size:20 final size:20
Alignment explanation
Indices: 274028--274072 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
274018 CTTAGTCTTT
* *
274028 CATCTATATGGCATAAATGA
1 CATCTATCTTGCATAAATGA
274048 CATCTATCTTGCATAAATGA
1 CATCTATCTTGCATAAATGA
274068 CATCT
1 CATCT
274073 TTCTGTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (20 bp):
CATCTATCTTGCATAAATGA
Found at i:275144 original size:59 final size:59
Alignment explanation
Indices: 274315--275117 Score: 1036
Period size: 59 Copynumber: 13.8 Consensus size: 59
274305 TTTCCCATAC
* *
274315 GGAAATTCATACACTTAGTATGAATTT-C---TCAGTTT-GCAC-CCATAGTGCCCCTA-C-
1 GGAAATTCATACACTTAGTATG-ATTTCCTTATCATTTTAGCACACGA-AGTG-CCCTATCT
* * * * * ** * **
274369 AGAAATTAATACACTTAGTATGATTT-CTTAACGTTTTAGCGCACGAAACGCTCTATAG
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* * ** * ** *
274427 GGAAATTCATACACTTAGTAGGATTT-CTTAACATTTTAGCGTATGAAACGCCCTATAT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* ** * *
274485 GGAAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCGTACGAAATGCCCTATAT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* ** * ** *
274543 GGAAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCGTACAAAACGCCCTATAT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* * *
274601 GGAAATTCATACAATTAATATGATTTCCTTATCATTTTAGCACACAAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* * *
274660 GGAAATTCATAAACTTAGAATGATTTCCTTATCATTTTAGCACACGAACTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* *
274719 AGAAAGTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* * *
274778 GGAAATTCATACACTTAGTATGATTTCCTTATCATTATAGCACAAGAAGTGCCTTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* *
274837 GGAAATTCATACACTTAGTATGATTCCCTTATCATTTTAGGACACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
*
274896 GGAGATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
* * *
274955 GGAAATTTATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCTTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
*
275014 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
*
275073 AGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACAC
1 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACAC
275118 TTAGTGCCAT
Statistics
Matches: 678, Mismatches: 63, Indels: 11
0.90 0.08 0.01
Matches are distributed among these distances:
53 5 0.01
54 20 0.03
56 8 0.01
57 5 0.01
58 187 0.28
59 453 0.67
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
Found at i:275523 original size:19 final size:19
Alignment explanation
Indices: 275486--275532 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
275476 TTTTATATTA
* **
275486 TGGTATTGATACCCCTTTT
1 TGGTATCGATACCAATTTT
275505 TGGTATCGATACCAATTTT
1 TGGTATCGATACCAATTTT
*
275524 AGGT-TCGAT
1 TGGTATCGAT
275533 GTTTCTTGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (19 bp):
TGGTATCGATACCAATTTT
Found at i:278023 original size:23 final size:22
Alignment explanation
Indices: 277986--278049 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 22
277976 CAACTCGTAT
* *
277986 AAATACACCGGAGTGCCACGTAG
1 AAATGCACCGAAGTGCCA-GTAG
* * *
278009 AATTGCATCGAAGTGTCGAGTAG
1 AAATGCACCGAAGTG-CCAGTAG
*
278032 AAATGCACCGTAGTGCCA
1 AAATGCACCGAAGTGCCA
278050 TATAAGATGT
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
22 2 0.06
23 27 0.87
24 2 0.06
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.19
Consensus pattern (22 bp):
AAATGCACCGAAGTGCCAGTAG
Found at i:278796 original size:2 final size:2
Alignment explanation
Indices: 278789--278868 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
278779 ACTTATAAAC
278789 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
278831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
278869 CTACTTCTAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:287373 original size:58 final size:58
Alignment explanation
Indices: 287301--287515 Score: 304
Period size: 58 Copynumber: 3.7 Consensus size: 58
287291 TGCCACTATA
* * *
287301 GAAATTCATACACTTAGTATGATTTCTTAACGTTTTAGCATACGAAACGCTCTATAAG
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCATACGAAACGCCCTATATG
* *
287359 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCTTACGAAACTCCCTATATG
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCATACGAAACGCCCTATATG
* * * ** *
287417 AAAATTCATACACTTAGTATGATTTCTTATCATTTTAGCACACGAAGTGCCCTATCTG
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCATACGAAACGCCCTATATG
* *
287475 GAAATTCATACACTAAGTATGATTTCGTTATCATTTTAGCA
1 GAAATTCATACACTTAGTATGATTTC-TTAACATTTTAGCA
287516 CAGGAAGTGC
Statistics
Matches: 141, Mismatches: 15, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
58 127 0.90
59 14 0.10
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (58 bp):
GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCATACGAAACGCCCTATATG
Found at i:287532 original size:59 final size:58
Alignment explanation
Indices: 287248--287530 Score: 303
Period size: 58 Copynumber: 4.9 Consensus size: 58
287238 TCTCATACGA
* * *
287248 AAATTTATACACTTAGTATGAATTTC-T--CAGTTT-GCAC-CCATAGTGCCACTATA--G
1 AAATTCATACACTTAGTATG-ATTTCTTAACATTTTAGCACACGA-AGTGCC-CTATATGG
* * ** * *
287302 AAATTCATACACTTAGTATGATTTCTTAACGTTTTAGCATACGAAACGCTCTATAAGG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCACACGAAGTGCCCTATATGG
** * *
287360 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCTTACGAAACT-CCCTATATGA
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCACACG-AAGTGCCCTATATGG
* *
287418 AAATTCATACACTTAGTATGATTTCTTATCATTTTAGCACACGAAGTGCCCTATCTGG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCACACGAAGTGCCCTATATGG
* * *
287476 AAATTCATACACTAAGTATGATTTCGTTATCATTTTAGCACAGGAAGTGCCCTAT
1 AAATTCATACACTTAGTATGATTTC-TTAACATTTTAGCACACGAAGTGCCCTAT
287531 CTTTAGCACA
Statistics
Matches: 196, Mismatches: 23, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
53 5 0.03
54 20 0.10
56 9 0.05
57 9 0.05
58 123 0.63
59 30 0.15
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.36
Consensus pattern (58 bp):
AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCACACGAAGTGCCCTATATGG
Found at i:287588 original size:82 final size:82
Alignment explanation
Indices: 287450--287614 Score: 240
Period size: 82 Copynumber: 2.0 Consensus size: 82
287440 TTCTTATCAT
* *
287450 TTTAGCACACGAAGTGCCCTATCTGGAAATTCATACACTAAGTATGATTTCGTTATCATTTTAGC
1 TTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTAAGTATGATTTCCTTATCATTTTAGC
*
287515 ACAGGAAGTGCCCTATC
66 ACACGAAGTGCCCTATC
* * * * * *
287532 TTTAGCACACAAAGTGCCTTATTTGGAAATTCATACATTTAGTATGATTTCCTTATCGTTTTAGT
1 TTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTAAGTATGATTTCCTTATCATTTTAGC
*
287597 ACACGAAGTGCCTTATC
66 ACACGAAGTGCCCTATC
287614 T
1 T
287615 GGAAATTCAT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (82 bp):
TTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTAAGTATGATTTCCTTATCATTTTAGC
ACACGAAGTGCCCTATC
Found at i:287647 original size:141 final size:140
Alignment explanation
Indices: 287418--287671 Score: 418
Period size: 141 Copynumber: 1.8 Consensus size: 140
287408 CCCTATATGA
287418 AAATTCATACACTTAGTATGATTTCTTATCATTTTAGCACACGAAGTGCCCTATCTGGAAATTCA
1 AAATTCATACACTTAGTATGATTTCTTATCATTTTAGCACACGAAGTGCCCTATCTGGAAATTCA
* * * *
287483 TACACTAAGTATGATTTCGTTATCATTTTAGCACAGGAAGTGCCCTATCTTTAGCACACAAAGTG
66 TACACTAAGTATGATTTCCTTATCATTATAGCACACGAAATGCCCTATCTTTAGCACACAAAGTG
287548 CCTTATTTGG
131 CCTTATTTGG
* * * *
287558 AAATTCATACATTTAGTATGATTTCCTTATCGTTTTAGTACACGAAGTGCCTTATCTGGAAATTC
1 AAATTCATACACTTAGTATGATTT-CTTATCATTTTAGCACACGAAGTGCCCTATCTGGAAATTC
*
287623 ATACACTTAGTATGATTTCCTTATCATTATAGCACACGAAATGCCCTAT
65 ATACACTAAGTATGATTTCCTTATCATTATAGCACACGAAATGCCCTAT
287672 ATGGAAATTC
Statistics
Matches: 104, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
140 23 0.22
141 81 0.78
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (140 bp):
AAATTCATACACTTAGTATGATTTCTTATCATTTTAGCACACGAAGTGCCCTATCTGGAAATTCA
TACACTAAGTATGATTTCCTTATCATTATAGCACACGAAATGCCCTATCTTTAGCACACAAAGTG
CCTTATTTGG
Found at i:287679 original size:200 final size:198
Alignment explanation
Indices: 287358--287732 Score: 574
Period size: 200 Copynumber: 1.9 Consensus size: 198
287348 CGCTCTATAA
*
287358 GGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCTTACGAAACTCCCTATATGAAAATT
1 GGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCTCACGAAACTCCCTATATGAAAATT
* * *
287423 CATACACTTAGTATGATTTCTTATCATTTTAGCACACGAAGTGCCCTATCTGGAAATTCATACAC
66 CATACACTTAGTATGATTTCTTATCATTATAGCACACGAAATGCCCTATATGGAAATTCATACAC
* *
287488 TAAGTATGATTTCGTTATCATTTTAGCACAGGAAGTGCCCTATCTTTAGCACACAAAGTGCCTTA
131 TAAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTTTAGCACACAAAGTGCCTTA
287553 TTT
196 TTT
* * * * * * *
287556 GGAAATTCATACATTTAGTATGATTTCCTTATCGTTTTAG-TACACG-AAGTGCCTTATCTGGAA
1 GGAAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCT-CACGAAACT-CCCTATATGAAA
287619 ATTCATACACTTAGTATGATTTCCTTATCATTATAGCACACGAAATGCCCTATATGGAAATTCAT
63 ATTCATACACTTAGTATGATTT-CTTATCATTATAGCACACGAAATGCCCTATATGGAAATTCAT
*
287684 ACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
127 ACACTAAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCT
287733 GGAAATTTAT
Statistics
Matches: 159, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
198 29 0.18
199 45 0.28
200 85 0.53
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (198 bp):
GGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCTCACGAAACTCCCTATATGAAAATT
CATACACTTAGTATGATTTCTTATCATTATAGCACACGAAATGCCCTATATGGAAATTCATACAC
TAAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTTTAGCACACAAAGTGCCTTA
TTT
Found at i:288040 original size:59 final size:59
Alignment explanation
Indices: 287532--288013 Score: 784
Period size: 59 Copynumber: 8.2 Consensus size: 59
287522 GTGCCCTATC
* * * * *
287532 TTTAGCACACAAAGTGCCTTATTTGGAAATTCATACATTTAGTATGATTTCCTTATCGT
1 TTTAGCACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
* *
287591 TTTAGTACACGAAGTGCCTTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
1 TTTAGCACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
* * *
287650 TATAGCACACGAAATGCCCTATATGGAAATTCATACACTTAGTATGATTTCCTTATCAT
1 TTTAGCACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
*
287709 TTTAGCACACGAAGTGCCCTATCTGGAAATTTATACACTTAGTATGATTTCCTTATCAT
1 TTTAGCACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
*
287768 TTTAGCACACGAAGTGCCCTATCTGGAAATTCATACTCTTAGTATGATTTCCTTATCAT
1 TTTAGCACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
* * *
287827 TTTAGCACACTATGTGCCTTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
1 TTTAGCACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
* *
287886 TTTAGCACACTAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCTTTATCAT
1 TTTAGCACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
* * *
287945 TTTAGCACACTAAGTGCCCTATCTAGAAATTCATACACTTAGTATGATTTTCTTATCAT
1 TTTAGCACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
288004 TTTAGCACAC
1 TTTAGCACAC
288014 TTAGTGCCAT
Statistics
Matches: 397, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 397 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.38
Consensus pattern (59 bp):
TTTAGCACACGAAGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCAT
Found at i:290369 original size:27 final size:28
Alignment explanation
Indices: 290333--290387 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
290323 CTTATATATA
290333 AAATTCGATA-AAAA-TAAATACGATACTT
1 AAATTCGATATAAAACTAAAT-CG-TACTT
290361 AAATT-GATATAAAACTAAATCGTACTT
1 AAATTCGATATAAAACTAAATCGTACTT
290388 CCATCATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 9 0.36
28 11 0.44
29 5 0.20
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (28 bp):
AAATTCGATATAAAACTAAATCGTACTT
Found at i:293517 original size:17 final size:17
Alignment explanation
Indices: 293495--293546 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
293485 TTTGGGAATT
293495 ATTTTGAAAAATGTGAC
1 ATTTTGAAAAATGTGAC
*
293512 ATTTTG-AGAAT-T---
1 ATTTTGAAAAATGTGAC
293524 ATTTTGAAAAATGTGAC
1 ATTTTGAAAAATGTGAC
293541 ATTTTG
1 ATTTTG
293547 GGAATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
12 6 0.21
13 4 0.14
14 1 0.04
15 1 0.04
16 4 0.14
17 12 0.43
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.42
Consensus pattern (17 bp):
ATTTTGAAAAATGTGAC
Found at i:293522 original size:29 final size:29
Alignment explanation
Indices: 293478--293662 Score: 189
Period size: 29 Copynumber: 6.3 Consensus size: 29
293468 ACCCGACCCA
*
293478 GTGATATTTTGGGAATTATTTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAT
*
293507 GTGACATTTTGAGAATTATTTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAT
*
293536 GTGACATTTTGGGAA-T-TTTTAAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAT
* * *
293563 AAGTGACATTATGGTAATTATTTT-TAAAAT
1 --GTGACATTTTGGGAATTATTTTGAAAAAT
*
293593 GATGACATTTTGGGAATTA-TTTGTAAAAT
1 G-TGACATTTTGGGAATTATTTTGAAAAAT
* * * *
293622 GGTGATATTTTGGTAATTATTTTTAATAAAG
1 -GTGACATTTTGGGAATTATTTTGAA-AAAT
*
293653 GTGATATTTT
1 GTGACATTTT
293663 TGTAATTTTT
Statistics
Matches: 133, Mismatches: 14, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
27 10 0.08
28 5 0.04
29 90 0.68
30 21 0.16
31 7 0.05
ACGTcount: A:0.35, C:0.02, G:0.18, T:0.44
Consensus pattern (29 bp):
GTGACATTTTGGGAATTATTTTGAAAAAT
Found at i:293632 original size:87 final size:87
Alignment explanation
Indices: 293477--293639 Score: 222
Period size: 87 Copynumber: 1.9 Consensus size: 87
293467 AACCCGACCC
* *
293477 AGTGATATTTTGGGAATTATTTTGAAAAATGTGACATTTTGAGAATTATTTTGAAAAATGTGACA
1 AGTGACATTATGGGAATTATTTTGAAAAATGTGACATTTTGAGAATTATTTTGAAAAATGTGACA
293542 TTTTGGGAATTTTTAAAAAATA
66 TTTTGGGAATTTTTAAAAAATA
* * * *
293564 AGTGACATTATGGTAATTATTTT-TAAAATGATGACATTTTGGGAATTA-TTTGTAAAATGGTGA
1 AGTGACATTATGGGAATTATTTTGAAAAATG-TGACATTTTGAGAATTATTTTGAAAAAT-GTGA
* *
293627 TATTTTGGTAATT
64 CATTTTGGGAATT
293640 ATTTTTAATA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
86 15 0.23
87 51 0.77
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.43
Consensus pattern (87 bp):
AGTGACATTATGGGAATTATTTTGAAAAATGTGACATTTTGAGAATTATTTTGAAAAATGTGACA
TTTTGGGAATTTTTAAAAAATA
Found at i:301129 original size:29 final size:29
Alignment explanation
Indices: 301063--301247 Score: 162
Period size: 29 Copynumber: 6.4 Consensus size: 29
301053 ACCCGACCCA
301063 GTGACATTTTGGGAATTATTTTGAAAAA-
1 GTGACATTTTGGGAATTATTTTGAAAAAG
* * *
301091 ATGGCATTTTAGGAATTATTTTGAAAAAG
1 GTGACATTTTGGGAATTATTTTGAAAAAG
* *
301120 GTGATATTTTGGGAATT-TTTAT-AAAAACA
1 GTGACATTTTGGGAATTATTT-TGAAAAA-G
* * * *
301149 GTGACATTCTGGTAATTATTTTTAAAACG
1 GTGACATTTTGGGAATTATTTTGAAAAAG
* *
301178 ATGACATTTTGGGAATTA-TTTGTAAAACG
1 GTGACATTTTGGGAATTATTTTG-AAAAAG
* * * *
301207 GTGATATTTTGGTAATTATTTTTAATAAAA
1 GTGACATTTTGGGAATTATTTTGAA-AAAG
*
301237 GTGATATTTTG
1 GTGACATTTTG
301248 TAATTTTTGA
Statistics
Matches: 126, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
28 36 0.29
29 67 0.53
30 23 0.18
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (29 bp):
GTGACATTTTGGGAATTATTTTGAAAAAG
Found at i:301187 original size:58 final size:58
Alignment explanation
Indices: 301064--301231 Score: 193
Period size: 58 Copynumber: 2.9 Consensus size: 58
301054 CCCGACCCAG
* * *
301064 TGACATTTTGGGAATTATTTTGAAAAA-A-TGGCATTTTAGG-AATTATTTTGAAAAAGG
1 TGACATTTTGGGAATTATTTT-AAAAACAGTGACATTTT-GGTAATTATTTTTAAAAAGA
* * *
301121 TGATATTTTGGGAATT-TTTATAAAAACAGTGACATTCTGGTAATTATTTTTAAAACGA
1 TGACATTTTGGGAATTATTT-TAAAAACAGTGACATTTTGGTAATTATTTTTAAAAAGA
* *
301179 TGACATTTTGGGAATTATTTGT-AAAACGGTGATATTTTGGTAATTATTTTTAA
1 TGACATTTTGGGAATTATTT-TAAAAACAGTGACATTTTGGTAATTATTTTTAA
301232 TAAAAGTGAT
Statistics
Matches: 95, Mismatches: 11, Indels: 9
0.83 0.10 0.08
Matches are distributed among these distances:
56 8 0.08
57 19 0.20
58 64 0.67
59 4 0.04
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (58 bp):
TGACATTTTGGGAATTATTTTAAAAACAGTGACATTTTGGTAATTATTTTTAAAAAGA
Found at i:301210 original size:87 final size:88
Alignment explanation
Indices: 301061--301240 Score: 233
Period size: 87 Copynumber: 2.1 Consensus size: 88
301051 CGACCCGACC
* *
301061 CAGTGACATTTTGGGAATTATTTTGAAAAAATGGCATTTTAGGAATTATTTTGAAAAAGGTGATA
1 CAGTGACATTCTGGGAATTATTTTGAAAAAATGACATTTTAGGAATTATTTTGAAAAAGGTGATA
301126 TTTTGGGAATT-TTTATAA-AAA
66 TTTTGGGAATTATTTATAATAAA
* * * * *
301147 CAGTGACATTCTGGTAATTATTTTTAAAACGATGACATTTTGGGAATTA-TTTGTAAAACGGTGA
1 CAGTGACATTCTGGGAATTATTTTGAAAA-AATGACATTTTAGGAATTATTTTG-AAAAAGGTGA
* *
301211 TATTTTGGTAATTATTTTTAATAAA
64 TATTTTGGGAATTATTTATAATAAA
301236 -AGTGA
1 CAGTGA
301241 TATTTTGTAA
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
86 30 0.37
87 37 0.46
88 11 0.14
89 3 0.04
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.41
Consensus pattern (88 bp):
CAGTGACATTCTGGGAATTATTTTGAAAAAATGACATTTTAGGAATTATTTTGAAAAAGGTGATA
TTTTGGGAATTATTTATAATAAA
Found at i:303619 original size:22 final size:21
Alignment explanation
Indices: 303567--303626 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
303557 GATTTCTGGG
303567 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
303588 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
303608 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
303627 CTCAAGCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.56
21 3 0.08
22 13 0.36
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:303704 original size:23 final size:22
Alignment explanation
Indices: 303660--303704 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
303650 AATCTCATAG
*
303660 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
303682 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
303705 AAAATGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:304551 original size:31 final size:31
Alignment explanation
Indices: 304513--304668 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
304503 AGGGTCGAGG
* *
304513 GTTTACCTATGTTCTTCGGGAAATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
304544 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
304575 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
304606 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
304637 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
304668 G
1 G
304669 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:308431 original size:22 final size:21
Alignment explanation
Indices: 308379--308438 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
308369 GATTTCTGGG
308379 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
308400 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
308420 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
308439 CTCAAGCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.56
21 3 0.08
22 13 0.36
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:308515 original size:22 final size:22
Alignment explanation
Indices: 308472--308515 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
308462 AATCTCATAG
*
308472 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
* *
308494 GGGAATCGATTCCCCTAAAGGA
1 GGGAACCGATTCCCCCAAAGGA
308516 AAAATGTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.27, T:0.14
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:309461 original size:31 final size:31
Alignment explanation
Indices: 309306--309447 Score: 257
Period size: 31 Copynumber: 4.6 Consensus size: 31
309296 AGGGTCGAGG
*
309306 GTTTACCTATGTTCTTCGGGAAATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
309337 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
309368 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
309399 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
309430 GATTACCTAGGTTCTTCG
1 GTTTACCTATGTTCTTCG
309448 AAATCTATGG
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 108 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:309967 original size:21 final size:21
Alignment explanation
Indices: 309942--309984 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
309932 AAAGAATATA
309942 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
309963 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
309984 T
1 T
309985 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:310677 original size:24 final size:24
Alignment explanation
Indices: 310619--310698 Score: 83
Period size: 23 Copynumber: 3.4 Consensus size: 24
310609 CACCGAAGTT
310619 CCACATAG-ATTTGTCCCAAATGA
1 CCACATAGAATTTGTCCCAAATGA
* * *
310642 CCGCGTAAAATTTGTCCCAAATGA
1 CCACATAGAATTTGTCCCAAATGA
* * *
310666 TCACATAGAA-TTGTCCCGAAGGA
1 CCACATAGAATTTGTCCCAAATGA
*
310689 CCACGTAGAA
1 CCACATAGAA
310699 CCCTCGACTC
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
23 24 0.53
24 21 0.47
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (24 bp):
CCACATAGAATTTGTCCCAAATGA
Found at i:310947 original size:57 final size:55
Alignment explanation
Indices: 310796--310978 Score: 163
Period size: 57 Copynumber: 3.3 Consensus size: 55
310786 AATCAAACTG
* * * *
310796 TCATTTGTTCACATAAAACATATATTCATAGTACTTCACATAACATTACTCAATTTA
1 TCATTTATTCACATAAAACATATACTCATAGTATTTCACATAGCATTACT-AA-TTA
* * * * *
310853 TAATTTATTCACATAAAACA-ATTACTTATTGCATTTCACATAGTATTACTAAACTTA
1 TCATTTATTCACATAAAACATA-TACTCATAGTATTTCACATAGCATTACT-AA-TTA
* * * * * *
310910 TCATTTATTCACATAGATCATATACTCATCGTGTTTCATATAGCATTA-TTATTA
1 TCATTTATTCACATAAAACATATACTCATAGTATTTCACATAGCATTACTAATTA
*
310964 TCATTTATTCCCATA
1 TCATTTATTCACATA
310979 GATCATATTC
Statistics
Matches: 102, Mismatches: 22, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
54 17 0.17
55 1 0.01
56 2 0.02
57 81 0.79
58 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (55 bp):
TCATTTATTCACATAAAACATATACTCATAGTATTTCACATAGCATTACTAATTA
Found at i:314243 original size:131 final size:127
Alignment explanation
Indices: 314074--314318 Score: 319
Period size: 131 Copynumber: 1.9 Consensus size: 127
314064 ATTTCCGAGT
* ** * *
314074 ATATAGTTTAATAGGTAACACATTTCATCAAATGCTGGTGTATATTATAATATTCCATATGAAAA
1 ATATAGTTTAATAGGTAACACATTTCATCAAATACTGGTGTATACGACAATAGTCCATATGAAAA
* * *
314139 TAATTGGAAAGAAATTTGGCTTATGGATGGTGAAATATGTGAGATTTCCTCGATTTCCATGC
66 TAATGGGAAAGAAATTTGACTCATGGATGGTGAAATATGTGAGATTTCCTCGATTTCCATGC
** * * *
314201 ATATAGTTTTAATAGGTAATGCATTCCATCATCAAATACTGGTTTATACGACCATAGTCCATCTG
1 ATATAG-TTTAATAGGTAACACATT---TCATCAAATACTGGTGTATACGACAATAGTCCATATG
* *
314266 AAAATAGTGGGAAAGAAATTTGACTCGTGGATGGTGAAATATGTGAGATTTCC
62 AAAATAATGGGAAAGAAATTTGACTCATGGATGGTGAAATATGTGAGATTTCC
314319 AAGTACAGAG
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
127 6 0.06
128 16 0.16
131 77 0.78
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (127 bp):
ATATAGTTTAATAGGTAACACATTTCATCAAATACTGGTGTATACGACAATAGTCCATATGAAAA
TAATGGGAAAGAAATTTGACTCATGGATGGTGAAATATGTGAGATTTCCTCGATTTCCATGC
Found at i:317094 original size:20 final size:20
Alignment explanation
Indices: 317069--317113 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
317059 TTATTCGGAA
*
317069 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGGTCTGAGGTTT
317089 AAAAATCCGGTCTGAGGTTT
1 AAAAATCCGGTCTGAGGTTT
317109 AAAAA
1 AAAAA
317114 ATTGGATGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTCTGAGGTTT
Found at i:318433 original size:16 final size:16
Alignment explanation
Indices: 318409--318442 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
318399 ACAAAATTTT
318409 AAATGATTTGACAAAA
1 AAATGATTTGACAAAA
* *
318425 AAATTATTTGATAAAA
1 AAATGATTTGACAAAA
318441 AA
1 AA
318443 TTAAAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.29
Consensus pattern (16 bp):
AAATGATTTGACAAAA
Found at i:328730 original size:20 final size:20
Alignment explanation
Indices: 328701--328743 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
328691 GAATACGCTG
328701 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
328721 ATGCATCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
328741 ATG
1 ATG
328744 AATTGAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.35, G:0.16, T:0.19
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:328854 original size:66 final size:64
Alignment explanation
Indices: 328749--328910 Score: 229
Period size: 66 Copynumber: 2.5 Consensus size: 64
328739 CCATGAATTG
* * *
328749 AACATCGAATGCATTTTATGCATCGATGCATATACCATGCATAGATGCACTCAGGGT-TTTATGA
1 AACATCGAATGCATTTTATGCATCGATGCACATAACATGCATAGATGCACTCAGGCTATTT-TG-
328813 A
64 A
*
328814 AACATCGAATGCATTTTGATGCATCGATGCACA-AGACATGCATCGATGCACTCAGGCTATTTTG
1 AACATCGAATGCATTTT-ATGCATCGATGCACATA-ACATGCATAGATGCACTCAGGCTATTTTG
328878 A
64 A
*
328879 AACATCGAATGTATTTTATGCATCGATGCACA
1 AACATCGAATGCATTTTATGCATCGATGCACA
328911 CTTAGTGCAC
Statistics
Matches: 89, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
64 15 0.17
65 35 0.39
66 36 0.40
67 3 0.03
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACATAACATGCATAGATGCACTCAGGCTATTTTGA
Found at i:331037 original size:16 final size:16
Alignment explanation
Indices: 331003--331045 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
330993 TTCAGTCGAA
331003 TCGAGT-AGCTCGAGTC
1 TCGAGTCAG-TCGAGTC
331019 TCGAGTCGAGTCGAG-C
1 TCGAGTC-AGTCGAGTC
331035 TCGAGTCAGTC
1 TCGAGTCAGTC
331046 TCGATCGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.16
16 14 0.56
17 5 0.20
18 2 0.08
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.23
Consensus pattern (16 bp):
TCGAGTCAGTCGAGTC
Found at i:333896 original size:20 final size:20
Alignment explanation
Indices: 333868--333915 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
333858 TCTATAAAAT
* * *
333868 TAAATCCTTCGGGTGATTTA
1 TAAAACCTTCGGGTCATCTA
*
333888 TAAAACCTTCGGGTCATCTG
1 TAAAACCTTCGGGTCATCTA
333908 TAAAACCT
1 TAAAACCT
333916 CAGGGTAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (20 bp):
TAAAACCTTCGGGTCATCTA
Found at i:333901 original size:117 final size:119
Alignment explanation
Indices: 333647--334025 Score: 600
Period size: 119 Copynumber: 3.2 Consensus size: 119
333637 TTTTCCACAT
* * *
333647 ATTTATAAAACCTTCGGGTCCTCTGTAAAACCTCAGGGTATTATGTTTTCGCATGCAAATGAGAA
1 ATTTATAAAACCTTCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATGAGAA
**
333712 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCAAGTG
66 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
* *
333766 ATTTATAAGACCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATG-AAATGAGAA
1 ATTTATAAAACCTTCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATGAGAA
* *
333830 AGCGATTTTCAAAGTTT-TCATTTAATGTTCTATAAAATTAAATCCTTCGGGTG
66 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
* *
333883 ATTTATAAAACCTTCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTTGCATGAAAATGAGAA
1 ATTTATAAAACCTTCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATGAGAA
* *
333948 AGCAATTTTCAAAGTTTCTTATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
66 AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
* *
334002 ATTAATTAAATCCTTCGGGTCATC
1 ATTTA-TAAAACCTTCGGGTCATC
334026 CATAAGACCT
Statistics
Matches: 239, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
117 83 0.35
118 51 0.21
119 88 0.37
120 17 0.07
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (119 bp):
ATTTATAAAACCTTCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATGAGAA
AGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAATCCTCCGGGTG
Found at i:335913 original size:3 final size:3
Alignment explanation
Indices: 335902--335953 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
335892 CTATTAATAA
* *
335902 TAT TA- TAT TAT TAT TA- TAC TAT TAT TAT TAT TA- TAT AAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
335946 TAT TAT TA
1 TAT TAT TA
335954 AAAATAATAC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
2 8 0.19
3 34 0.81
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:335915 original size:8 final size:8
Alignment explanation
Indices: 335901--335951 Score: 59
Period size: 8 Copynumber: 6.2 Consensus size: 8
335891 ACTATTAATA
335901 ATATTA-T
1 ATATTATT
335908 ATTATTATT
1 A-TATTATT
*
335917 ATACTATT
1 ATATTATT
335925 ATTATTATT
1 A-TATTATT
*
335934 ATATAATT
1 ATATTATT
335942 ATATTATT
1 ATATTATT
335950 AT
1 AT
335952 TAAAAATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
7 1 0.03
8 27 0.73
9 9 0.24
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (8 bp):
ATATTATT
Found at i:335918 original size:11 final size:11
Alignment explanation
Indices: 335902--335953 Score: 68
Period size: 11 Copynumber: 4.5 Consensus size: 11
335892 CTATTAATAA
335902 TATTATATTAT
1 TATTATATTAT
*
335913 TATTATACTAT
1 TATTATATTAT
335924 TATTATTATTAT
1 TATTA-TATTAT
335936 ATAATTATATTAT
1 -T-ATTATATTAT
335949 TATTA
1 TATTA
335954 AAAATAATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
11 19 0.53
12 6 0.17
13 7 0.19
14 4 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTATATTAT
Found at i:336637 original size:17 final size:17
Alignment explanation
Indices: 336615--336659 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
336605 GGAATAAATG
336615 AGGGTGGTTTCGGGTTT
1 AGGGTGGTTTCGGGTTT
336632 AGGGTGGTTTCGGGTTT
1 AGGGTGGTTTCGGGTTT
336649 AGGGT-GTTTCG
1 AGGGTGGTTTCG
336660 ATTTAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.07, C:0.07, G:0.47, T:0.40
Consensus pattern (17 bp):
AGGGTGGTTTCGGGTTT
Found at i:336743 original size:22 final size:22
Alignment explanation
Indices: 336700--336743 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
336690 GACCACTGTG
* * * *
336700 AATAGTGACTGACGGTGGCCGA
1 AATAATGACCGACGATGACCGA
336722 AATAATGACCGACGATGACCGA
1 AATAATGACCGACGATGACCGA
336744 TCGGTGACCG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.30, T:0.16
Consensus pattern (22 bp):
AATAATGACCGACGATGACCGA
Found at i:337238 original size:29 final size:30
Alignment explanation
Indices: 337178--337247 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
337168 TTTTGTAATA
337178 TTTATAA-TTAACACTATTAATTTTGATAT
1 TTTATAATTTAACACTATTAATTTTGATAT
337207 TTTATAATTTAACCACTA-TAATTTT-A-ACT
1 TTTATAATTTAA-CACTATTAATTTTGATA-T
*
337236 TTTATATTTTAA
1 TTTATAATTTAA
337248 ATAATTATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 1 0.03
29 20 0.54
30 11 0.30
31 5 0.14
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (30 bp):
TTTATAATTTAACACTATTAATTTTGATAT
Found at i:354130 original size:42 final size:42
Alignment explanation
Indices: 354083--354191 Score: 184
Period size: 42 Copynumber: 2.6 Consensus size: 42
354073 TCGAATTCCT
354083 GTGTTTGTTTCACGTAATTCATTTTTCGAAAAATATTTTCTC-
1 GTGTTTGTTTCACGTAATTCATTTTTCGAAAAATATTTT-TCA
*
354125 GTGTTTGTTTCACGTAATTCGTTTTTCGAAAAATATTTTTCA
1 GTGTTTGTTTCACGTAATTCATTTTTCGAAAAATATTTTTCA
*
354167 GTGTTTGTTTCACGTAATTGATTTT
1 GTGTTTGTTTCACGTAATTCATTTT
354192 CCTGAACGTA
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
41 2 0.03
42 61 0.97
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.51
Consensus pattern (42 bp):
GTGTTTGTTTCACGTAATTCATTTTTCGAAAAATATTTTTCA
Found at i:354414 original size:31 final size:31
Alignment explanation
Indices: 354379--354523 Score: 92
Period size: 31 Copynumber: 4.8 Consensus size: 31
354369 AAATATTATT
354379 TATTA-ATTTATTAATATT-TATAATAATATAA
1 TATTATATTT-TTAATATTATATAA-AATATAA
*
354410 TATTATATTTTTAATATTATATAAAATAATCA
1 TATTATATTTTTAATATTATATAAAAT-ATAA
* * *
354442 -ATTATA-TTATAATA--ATATAAGATATTA
1 TATTATATTTTTAATATTATATAAAATATAA
* * *
354469 TATT-TTTATTTTAATAATATATAATAA-AAAA
1 TATTATAT-TTTTAATATTATATAA-AATATAA
* *
354500 TTTTATATATTTAATAATTA-ATAA
1 TATTATATTTTTAAT-ATTATATAA
354524 TATTATTTAT
Statistics
Matches: 90, Mismatches: 13, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
27 4 0.04
28 11 0.12
29 7 0.08
30 7 0.08
31 43 0.48
32 18 0.20
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (31 bp):
TATTATATTTTTAATATTATATAAAATATAA
Found at i:354417 original size:22 final size:23
Alignment explanation
Indices: 354387--354430 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
354377 TTTATTAATT
354387 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
354410 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
354431 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:354506 original size:54 final size:52
Alignment explanation
Indices: 354395--354506 Score: 129
Period size: 54 Copynumber: 2.1 Consensus size: 52
354385 TTTATTAATA
* **
354395 TTTATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTAT
1 TTTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAAAAAT
* *
354447 ATTATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATAAAAAAT
1 TTTATAATAATAT-A-ATATTATATTTTTAATATTATATAA-A-ATAATAAAAAAT
354501 TTTATA
1 TTTATA
354507 TATTTAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
52 16 0.32
53 7 0.14
54 27 0.54
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (52 bp):
TTTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAAAAAT
Found at i:354514 original size:28 final size:28
Alignment explanation
Indices: 354468--354546 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 28
354458 ATAAGATATT
*
354468 ATATTTTTAT-TTTAATAATATATAATAAAA
1 ATATTTATATATTTAAT-A-AT-TAATAAAA
*
354498 A-ATTTTATATATTTAATAATTAATAATA
1 ATA-TTTATATATTTAATAATTAATAAAA
*
354526 TTATTTATATATTTAAATAAT
1 ATATTTATATATTT-AATAAT
354547 ATTTTAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
28 18 0.43
29 10 0.24
30 8 0.19
31 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATATTTATATATTTAATAATTAATAAAA
Found at i:354526 original size:19 final size:20
Alignment explanation
Indices: 354504--354556 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
354494 AAAAAATTTT
354504 ATATATTTAATAATT-AATA
1 ATATATTTAATAATTAAATA
*
354523 ATATTATTTATATATTTAAATA
1 ATA-TATTTA-ATAATTAAATA
354545 ATAT-TTTAATAA
1 ATATATTTAATAA
354557 AGATATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 6 0.21
20 10 0.34
21 6 0.21
22 7 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATTTAATAATTAAATA
Found at i:354546 original size:22 final size:20
Alignment explanation
Indices: 354507--354549 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
354497 AAATTTTATA
354507 TATTTAATAATTAATAATAT
1 TATTTAATAATTAATAATAT
*
354527 TATTTATATATTTAAATAATAT
1 TATTTA-ATAATT-AATAATAT
354549 T
1 T
354550 TTAATAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTTAATAATTAATAATAT
Found at i:354577 original size:23 final size:23
Alignment explanation
Indices: 354551--354595 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
354541 AATAATATTT
354551 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
354574 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
354596 ATATAAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:354723 original size:19 final size:19
Alignment explanation
Indices: 354701--354763 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 19
354691 ATAAAAATAC
354701 TATTTAATAATAAATAAAT
1 TATTTAATAATAAATAAAT
*
354720 TATTTTTAATAATAAA-AAAG
1 TA--TTTAATAATAAATAAAT
*
354740 T-TTT-ATGATAAATAATAT
1 TATTTAATAATAAATAA-AT
354758 TATTTA
1 TATTTA
354764 TTGTATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
16 7 0.20
17 5 0.14
18 2 0.06
19 5 0.14
20 4 0.11
21 12 0.34
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
TATTTAATAATAAATAAAT
Found at i:354919 original size:14 final size:14
Alignment explanation
Indices: 354886--354918 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
354876 AAATGTAATT
354886 CATTTTACGGAAAA
1 CATTTTACGGAAAA
*
354900 CATTTTCCGGAAAA
1 CATTTTACGGAAAA
354914 C-TTTT
1 CATTTT
354919 TTCAGAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (14 bp):
CATTTTACGGAAAA
Found at i:354964 original size:15 final size:15
Alignment explanation
Indices: 354928--355022 Score: 102
Period size: 15 Copynumber: 6.4 Consensus size: 15
354918 TTTCAGAAAT
**
354928 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
354943 G-AATTCAAGTTCCA
1 GTAATTCAAATTCCA
** *
354957 GTAATTCATTTTTCA
1 GTAATTCAAATTCCA
* *
354972 GTAAATCAAATTTCA
1 GTAATTCAAATTCCA
*
354987 GTAATTCAAATTTCA
1 GTAATTCAAATTCCA
355002 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
355017 GTAATT
1 GTAATT
355023 TATTTTCGAA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
14 12 0.17
15 57 0.83
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:354989 original size:30 final size:30
Alignment explanation
Indices: 354928--355028 Score: 132
Period size: 30 Copynumber: 3.4 Consensus size: 30
354918 TTTCAGAAAT
* *
354928 GTAATTCATTTTCCAG-AATTCAAGTTCCA
1 GTAATTCATTTTTCAGTAATTCAAATTCCA
* *
354957 GTAATTCATTTTTCAGTAAATCAAATTTCA
1 GTAATTCATTTTTCAGTAATTCAAATTCCA
**
354987 GTAATTCAAATTTCAGTAATTCAAATTCCA
1 GTAATTCATTTTTCAGTAATTCAAATTCCA
*
355017 GTAATTTATTTT
1 GTAATTCATTTT
355029 CGAAAATCAA
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
29 15 0.25
30 45 0.75
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.43
Consensus pattern (30 bp):
GTAATTCATTTTTCAGTAATTCAAATTCCA
Found at i:356439 original size:17 final size:17
Alignment explanation
Indices: 356419--356453 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
356409 AAAATAAGAA
356419 AGAAAGAAAAAGAAAAG
1 AGAAAGAAAAAGAAAAG
* *
356436 AGAAAGCAAACGAAAAG
1 AGAAAGAAAAAGAAAAG
356453 A
1 A
356454 CAATCTAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.06, G:0.23, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAAAGAAAAG
Found at i:358106 original size:24 final size:23
Alignment explanation
Indices: 358044--358107 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
358034 AACATATAAA
* *
358044 TGAACGATAAACAAAAATGTTCG
1 TGAACGATAAACGAACATGTTCG
* *
358067 TGAACGCTAAATGAACATGTTCG
1 TGAACGATAAACGAACATGTTCG
*
358090 TGAACATATAAACGAACA
1 TGAAC-GATAAACGAACA
358108 CATTTGCCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 24 0.73
24 9 0.27
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (23 bp):
TGAACGATAAACGAACATGTTCG
Found at i:363042 original size:31 final size:31
Alignment explanation
Indices: 363007--363067 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
362997 TCGCGAGCCT
* *
363007 AAAATTTTCAAGCTCGACTCAAACTCGAAAG
1 AAAATATTCAAACTCGACTCAAACTCGAAAG
* *
363038 AAAATATTGAAACTCGACTCGAACTCGAAA
1 AAAATATTCAAACTCGACTCAAACTCGAAA
363068 AAGCTCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.21, G:0.13, T:0.21
Consensus pattern (31 bp):
AAAATATTCAAACTCGACTCAAACTCGAAAG
Found at i:365924 original size:13 final size:14
Alignment explanation
Indices: 365901--365947 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
365891 AATTAAACCA
365901 TAAACCATGAATCC
1 TAAACCATGAATCC
365915 TAAA-CATGAATCC
1 TAAACCATGAATCC
* * *
365928 TAAATCATAAACCC
1 TAAACCATGAATCC
365942 TAAACC
1 TAAACC
365948 CTAAACTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 13 0.45
14 16 0.55
ACGTcount: A:0.47, C:0.28, G:0.04, T:0.21
Consensus pattern (14 bp):
TAAACCATGAATCC
Found at i:365951 original size:34 final size:34
Alignment explanation
Indices: 365894--365984 Score: 94
Period size: 34 Copynumber: 2.7 Consensus size: 34
365884 GTGTATAAAT
* * * *
365894 TAAACCATAAACCATGAATCCTAAAC-ATGAATCC
1 TAAAACATAAACCATAAACCCTAAACTAT-AACCC
* *
365928 TAAATCATAAACCCTAAACCCTAAACTATAACCC
1 TAAAACATAAACCATAAACCCTAAACTATAACCC
* *
365962 TAAAACCTAAATCATAAACCCTA
1 TAAAACATAAACCATAAACCCTA
365985 TCATATAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 45 0.96
35 2 0.04
ACGTcount: A:0.48, C:0.29, G:0.02, T:0.21
Consensus pattern (34 bp):
TAAAACATAAACCATAAACCCTAAACTATAACCC
Found at i:365952 original size:21 final size:21
Alignment explanation
Indices: 365926--365984 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
365916 AAACATGAAT
*
365926 CCTAAATCATAAACCCTAAAC
1 CCTAAATCATAAACCCTAAAA
365947 CCTAAA-C-TATAACCCTAAAA
1 CCTAAATCATA-AACCCTAAAA
365967 CCTAAATCATAAACCCTA
1 CCTAAATCATAAACCCTA
365985 TCATATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 2 0.06
20 16 0.47
21 14 0.41
22 2 0.06
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.20
Consensus pattern (21 bp):
CCTAAATCATAAACCCTAAAA
Found at i:366079 original size:14 final size:14
Alignment explanation
Indices: 366054--366091 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
366044 TAAAATTTTA
366054 TAATTATTAATAATG
1 TAATT-TTAATAATG
*
366069 TATTTTTAATAATG
1 TAATTTTAATAATG
366083 TAATTTTAA
1 TAATTTTAA
366092 AAATCTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (14 bp):
TAATTTTAATAATG
Found at i:367551 original size:60 final size:60
Alignment explanation
Indices: 367485--367628 Score: 198
Period size: 60 Copynumber: 2.4 Consensus size: 60
367475 ACAATCATGT
* * * *
367485 GACCATTCTGTAACTTTTAATAGTCGAGTAACTCAACAAAATGACTCTCTATAGCCGGGG
1 GACCATTTTGTAACTTTTAATAGTCGAATAACTCAACAAAATAACTCCCTATAGCCGGGG
* * * **
367545 GTCCATTTTGTAACTTTTAATAGTCGAATGACTCAACAAAATAAGTCCCTATAGTTGGGG
1 GACCATTTTGTAACTTTTAATAGTCGAATAACTCAACAAAATAACTCCCTATAGCCGGGG
*
367605 GACCTTTTTGTAACTTTTAATAGT
1 GACCATTTTGTAACTTTTAATAGT
367629 TGGGAGATTC
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTCGAATAACTCAACAAAATAACTCCCTATAGCCGGGG
Found at i:371509 original size:51 final size:51
Alignment explanation
Indices: 371454--371561 Score: 162
Period size: 51 Copynumber: 2.1 Consensus size: 51
371444 GGCTATATCG
* * * *
371454 ATATTTATTTATAAATTTGATATGAATATAAAATAATACCTAATTATATAA
1 ATATTTATTTATAAATCTGATATAAATATAAAATAATAACTAACTATATAA
* *
371505 ATATTTATTTATAAATCTGTTATAAATATAAAATAATAACTAACTATATCA
1 ATATTTATTTATAAATCTGATATAAATATAAAATAATAACTAACTATATAA
371556 ATATTT
1 ATATTT
371562 GAATCGTAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.44
Consensus pattern (51 bp):
ATATTTATTTATAAATCTGATATAAATATAAAATAATAACTAACTATATAA
Found at i:372519 original size:20 final size:19
Alignment explanation
Indices: 372496--372542 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
372486 CGATATACCA
372496 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
372516 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
372536 GGTAAAA
1 GGTAAAA
372543 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:372576 original size:163 final size:163
Alignment explanation
Indices: 372303--372630 Score: 487
Period size: 163 Copynumber: 2.0 Consensus size: 163
372293 ATCCAAATTA
* * ***
372303 AAAATGTGTCGATCCAAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAATGTATCGATCCAAAAACGATATAACAGGTAAAAATATGACAAAACCGGTAACAAAATGATA
* * * *
372368 AAACCGGTAAAGCGCTATCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTC
* *
372433 GTGAATTTAAAATAGAAGCAGTTTTAAATCCTAT
130 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTAT
* *
372467 AAAATGTATCGATCC-AAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAATGTATCGATCCAAAAACGATATAACAGGTAAAAATATGACAAAACCGGTAACAAAATGATA
* * *
372531 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTTG
66 AAACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCG
*
372596 TGAATTTAAAAGAGAAGCAGTTTTAGAGCCTAT
131 TGAATTTAAAAGAGAAGCAGTTTTAAAGCCTAT
372629 AA
1 AA
372631 TGTGTCGATA
Statistics
Matches: 147, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
162 51 0.35
163 82 0.56
164 14 0.10
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (163 bp):
AAAATGTATCGATCCAAAAACGATATAACAGGTAAAAATATGACAAAACCGGTAACAAAATGATA
AAACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCG
TGAATTTAAAAGAGAAGCAGTTTTAAAGCCTAT
Found at i:372699 original size:20 final size:19
Alignment explanation
Indices: 372676--372722 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
372666 CGATATAACA
372676 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
372696 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
372716 GGTAAAA
1 GGTAAAA
372723 TGATACCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:372724 original size:17 final size:19
Alignment explanation
Indices: 372685--372727 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
372675 AGGTAAAAAT
372685 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
372705 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
372722 ATGATA
1 ATGATA
372728 CCAGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:374964 original size:21 final size:21
Alignment explanation
Indices: 374940--375004 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
374930 AAGACAATCA
*
374940 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
374961 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
374982 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
375003 AG
1 AG
375005 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:375077 original size:33 final size:33
Alignment explanation
Indices: 375035--375100 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
375025 AAAAAGATGG
*
375035 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
375068 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
375101 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:376914 original size:19 final size:19
Alignment explanation
Indices: 376890--376938 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
376880 AATGTAGGGT
*
376890 TAATTTTGTATAAGGTTTA
1 TAATTTTGTATAAGATTTA
*
376909 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
376928 TAATTTTGTAT
1 TAATTTTGTAT
376939 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:377398 original size:200 final size:200
Alignment explanation
Indices: 377051--377882 Score: 1458
Period size: 200 Copynumber: 4.2 Consensus size: 200
377041 AATTTACAAT
* * *
377051 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATTCATATATAAAAAGTGTCGATCCC--AAA-AT
1 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAAACAT
*
377113 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
377178 ATGAGAGAATAGGCCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
377243 AATGA
196 AATGA
377248 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAAACAT
1 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAAACAT
377313 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
377378 ATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGTTTGTGTCGATATTTTTGGTCCA
131 ATGAGAGAATAGGTCTAAATAATGTGTCGACAC-TTTTTTAGTTTGTGTCGATATTTTTGGTCCA
377443 GAATGA
195 GAATGA
*
377449 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGAT-CCATAAACAT
1 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAAACAT
* *
377513 CG-AACCCAAAAGTATAATGTAATATATAATTTTTCAATCTAACCGGTACAAATATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
377577 ATGAGAGAATAGGTCTAAATAATGTGTTGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAT
131 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
*
377642 AATAA
196 AATGA
*
377647 ATGGCAAACAGGGTGCAACAGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAAACAT
1 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAAACAT
*
377712 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
377777 ATGAGATAATAGGTCTAAATAATGTGTCGACATTTTTTTTAGTTTGTGTCGATATTTTTGGTCCA
131 ATGAGAGAATAGGTCTAAATAATGTGTCGACA-CTTTTTTAGTTTGTGTCGATATTTTTGGTCCA
377842 GAATGA
195 GAATGA
377848 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCC
1 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCC
377883 CATAAATATC
Statistics
Matches: 602, Mismatches: 26, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
197 54 0.09
198 87 0.14
199 105 0.17
200 197 0.33
201 159 0.26
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAAACAT
CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:377793 original size:399 final size:398
Alignment explanation
Indices: 377051--378366 Score: 2188
Period size: 399 Copynumber: 3.3 Consensus size: 398
377041 AATTTACAAT
* * *
377051 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATTCATATATAAAAAGTGTCGATCCCAAA-ATCG
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGT-TCGATCCTAAACATCG
* *
377115 AAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTAT
65 AAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAATATACCGGTTTTAT
* * *
377180 GAGAGAATAGGCCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAA
130 GAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCATAA
377245 TGAATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAAA
195 TGAATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAAA
377310 CATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGT
260 CATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGT
377375 TTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGTTTGTGTCGATATTTTTGGT
325 TTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGTTTGTGTCGATATTTTTGGT
377440 CCAGAATGA
390 CCAGAATGA
*
377449 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCATAAACATC
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGT-TCGATCC-TAAACATC
*
377514 G-AACCCAAAAGTATAATGTAATATATAATTTTTCAATCTAACCGGTACAAATATACCGGTTTTA
64 GAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAATATACCGGTTTTA
*
377578 TGAGAGAATAGGTCTAAATAATGTGTTGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCATA
129 TGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCATA
* *
377643 ATAAATGGCAAACAGGGTGCAACAGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAA
194 ATGAATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAA
*
377708 ACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGA
259 ACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGG
*
377773 TTTTATGAGATAATAGGTCTAAATAATGTGTCGACATTTTTTTTAGTTTGTGTCGATATTTTTGG
324 TTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGTTTGTGTCGATATTTTTGG
377838 TCCAGAATGA
389 TCCAGAATGA
* *
377848 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCC--------------C-A---TAAATATCGA
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTTCGATCCTAAACATCGA
* *
377895 AACCCAAAAGTATAATGTAATATGTAATTTTT-AATCTAACTGGTACATATATACCGGTTTTATG
66 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAATATACCGGTTTTATG
* * *
377959 AGAGAATATGTCTAAATAATGTGTCGACACTTTTGTAGTTTATGTTGATATTTTTGGTCCATAAT
131 AGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCATAAT
378024 GAATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAAAC
196 GAATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAAAC
378089 ATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTT
261 ATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTT
*
378154 TTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGTTTGTGTCGATATTTTTAGTC
326 TTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGTTTGTGTCGATATTTTTGGTC
378219 CAGAATGA
391 CAGAATGA
*
378227 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTTCGATCCCATAAACATC
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTTCGAT-CC-TAAACATC
* * *
378292 GAAACCCATAAGTATAATTGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
64 GAAACCCAAAAGTATAA-TGTAATATGTAATTTTTCAATCTAACCGGTACAAATATACCGGTTTT
378357 ATGAGAGAAT
128 ATGAGAGAAT
378367 TGATATAATA
Statistics
Matches: 857, Mismatches: 36, Indels: 47
0.91 0.04 0.05
Matches are distributed among these distances:
379 330 0.39
380 31 0.04
383 1 0.00
384 1 0.00
393 1 0.00
394 1 0.00
398 53 0.06
399 383 0.45
400 20 0.02
401 36 0.04
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (398 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTTCGATCCTAAACATCGA
AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAATATACCGGTTTTATG
AGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCATAAT
GAATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAAAC
ATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTT
TTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGTTTGTGTCGATATTTTTGGTC
CAGAATGA
Found at i:378056 original size:178 final size:180
Alignment explanation
Indices: 377690--378060 Score: 613
Period size: 178 Copynumber: 2.1 Consensus size: 180
377680 CCATATATAA
*
377690 AAAGTGTCGATCCCGTAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* * *
377755 CCGGTACAAGTATACCGATTTTATGAGATAATAGGTCTAAATAATGTGTCGACATTTTTTTTAGT
66 CCGGTACAAGTATACCGATTTTATGAGAGAATAGGTCTAAATAATGTGTCGACATCTTTTGTAGT
*
377820 TTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCGT
131 TTATGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCGT
*
377870 AAAGTGTCGATCCCATAAATATCGAAACCCAAAAGTATAATGTAATATGTAATTTTT-AATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* * *
377934 CTGGTACATA-TATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACA-CTTTTGTAG
66 CCGGTACA-AGTATACCGATTTTATGAGAGAATAGGTCTAAATAATGTGTCGACATCTTTTGTAG
* *
377997 TTTATGTTGATATTTTTGGTCCATAATGAATGGCAAACAGGGTGCAACCGT
130 TTTATGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCGT
378048 AAAGTGTCGATCC
1 AAAGTGTCGATCC
378061 ATATATAAAA
Statistics
Matches: 179, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
178 68 0.38
179 55 0.31
180 56 0.31
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (180 bp):
AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
CCGGTACAAGTATACCGATTTTATGAGAGAATAGGTCTAAATAATGTGTCGACATCTTTTGTAGT
TTATGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCGT
Found at i:378281 original size:200 final size:200
Alignment explanation
Indices: 377870--378366 Score: 820
Period size: 201 Copynumber: 2.5 Consensus size: 200
377860 GTGCAACCGT
*
377870 AAAGTGTCGATCCCATAAATATCGAAACCCAAAAGTATAATGTAATATGTAATTTTT-AATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* *
377934 CTGGTACATA-TATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTGTAGT
66 CCGGTACA-AGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGT
* * * **
377998 TTATGTTGATATTTTTGGTCCATAATGAATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCAT
130 TTATGTCGATATTTTTAGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCAT
378063 ATATAA
195 ATATAA
*
378069 AAAGTGTCGATCCCGTAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* *
378134 CCGGTACAAGTATACCGGTTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACAC-TTTTGTAGT
*
378199 TTGTGTCGATATTTTTAGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCAT
130 TTATGTCGATATTTTTAGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCAT
378264 ATATAA
195 ATATAA
* *
378270 AAAGT-TCGATCCCATAAACATCGAAACCCATAAGTATAATTGTAATAGGTAATTTTTCAATCTA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAA-TGTAATATGTAATTTTTCAATCTA
378334 ACCGGTACAAGTATACCGGTTTTATGAGAGAAT
65 ACCGGTACAAGTATACCGGTTTTATGAGAGAAT
378367 TGATATAATA
Statistics
Matches: 278, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
199 56 0.20
200 89 0.32
201 133 0.48
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (200 bp):
AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTT
TATGTCGATATTTTTAGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
TATAA
Done.