Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007952.1 Hibiscus syriacus cultivar Beakdansim tig00110377_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: 3169409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 16
Found at i:388160 original size:40 final size:41
Alignment explanation
Indices: 388079--388168 Score: 128
Period size: 40 Copynumber: 2.2 Consensus size: 41
388069 TGATATATTA
*
388079 AAAAATAAATCATATCAAATTAAATTATATGACAAAATTAAT
1 AAAAATAAA-CATATCAAATCAAATTATATGACAAAATTAAT
* *
388121 AAAAATAAA-ATATCATATCAAATTATATGATAAAATTAAT
1 AAAAATAAACATATCAAATCAAATTATATGACAAAATTAAT
388161 AGAAAATA
1 A-AAAATA
388169 TTAAAAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
40 29 0.66
41 6 0.14
42 9 0.20
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (41 bp):
AAAAATAAACATATCAAATCAAATTATATGACAAAATTAAT
Found at i:388279 original size:22 final size:20
Alignment explanation
Indices: 388253--388293 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
388243 TTAAAATTAA
*
388253 AATCAAACATATACATAAAAAT
1 AATCAAA-ATA-AAATAAAAAT
388275 AATCAAAATAAAATAAAAA
1 AATCAAAATAAAATAAAAA
388294 ATTGATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 3 0.17
22 7 0.39
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.20
Consensus pattern (20 bp):
AATCAAAATAAAATAAAAAT
Found at i:388918 original size:22 final size:22
Alignment explanation
Indices: 388887--388946 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
388877 TAATAAATTT
* *
388887 TATACGCAAATAATTTATTATA
1 TATACACAAATAATTTAATATA
388909 TATACACAAATAATTTAATATA
1 TATACACAAATAATTTAATATA
388931 TA-ATCACAAATAATTT
1 TATA-CACAAATAATTT
388947 TTAATAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (22 bp):
TATACACAAATAATTTAATATA
Found at i:389184 original size:17 final size:17
Alignment explanation
Indices: 389164--389222 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 17
389154 ATATGGGTAT
*
389164 CTAAAAAAAGTTCCAAC
1 CTAAAAATAGTTCCAAC
* *
389181 CTAAAATATGGTTGCAAC
1 CTAAAA-ATAGTTCCAAC
389199 CTAAAAATAGTTCTCAAC
1 CTAAAAATAGTTC-CAAC
*
389217 ATAAAA
1 CTAAAA
389223 TATGGGTATC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
17 11 0.32
18 23 0.68
ACGTcount: A:0.49, C:0.19, G:0.08, T:0.24
Consensus pattern (17 bp):
CTAAAAATAGTTCCAAC
Found at i:389326 original size:104 final size:101
Alignment explanation
Indices: 389095--389397 Score: 342
Period size: 104 Copynumber: 3.0 Consensus size: 101
389085 TCGATATTTA
* * * *
389095 CAACCTAAAAACAAGTTCTAACTTAAAATATGGGTATCTAAAAAAAGTTCCAACTTAAAATATGG
1 CAACCTAAAAACAA-TTCCAACTTAAAATATGGGTATCTAAAACAAGTTTCAACCTAAAATATGG
* * * * *
389160 GT--ATCTAAAAAAAGTTCCAACCTAAAATATGGTTG
65 TTCAACCTAAAACAAGTTCCAACTTAAAATATAGTTG
* * * * *
389195 CAACCTAAAAATAGTTCTCAACATAAAATATGGGTATCTAAAACAAGTTTCAGCCTAAAATATGA
1 CAACCTAAAAACAATTC-CAACTTAAAATATGGGTATCTAAAACAAGTTTCAACCTAAAATATGG
389260 TTACAACCTAAACACAAGTTCCAACTTAAAATATAGTTG
65 TT-CAACCTAAA-ACAAGTTCCAACTTAAAATATAGTTG
* * * *
389299 CATCCTAAAAACACATTCCAACTTAAAATATGGGTACCTAAAACAAG-TTCTAAACTAAAAGATG
1 CAACCTAAAAACA-ATTCCAACTTAAAATATGGGTATCTAAAACAAGTTTC-AACCTAAAATATG
*
389363 GTTGCAACCTAAAACCAAGTTCCACCTTAAAATAT
64 GTT-CAACCTAAAA-CAAGTTCCAACTTAAAATAT
389398 GAGTAACTTA
Statistics
Matches: 170, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
99 3 0.02
100 53 0.31
103 10 0.06
104 101 0.59
105 3 0.02
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.26
Consensus pattern (101 bp):
CAACCTAAAAACAATTCCAACTTAAAATATGGGTATCTAAAACAAGTTTCAACCTAAAATATGGT
TCAACCTAAAACAAGTTCCAACTTAAAATATAGTTG
Found at i:389347 original size:68 final size:67
Alignment explanation
Indices: 389098--389398 Score: 251
Period size: 68 Copynumber: 4.4 Consensus size: 67
389088 ATATTTACAA
* * * *
389098 CCTAAAAACAAGTTCTAACTTAAAATATGGGTATCTAAAAAAAGTTC-CAACTTAAAATATGGGT
1 CCTAAAAACAAGTTCCAACTTAAAATATGGGTACCTAAAACAAGTTCTCAACTTAAAATATGGGC
389162 AT
66 AT
* * *
389164 -CTAAAAA-AAGTTCCAACCTAAAATATGGTTGCAACCTAAAA-ATAGTTCTCAACATAAAATAT
1 CCTAAAAACAAGTTCCAACTTAAAATATGG--G-TACCTAAAACA-AGTTCTCAACTTAAAATAT
*
389226 GGGTAT
62 GGGCAT
* * * **
389232 -CT-AAAACAAGTTTCAGCCTAAAATATGATTACAACCTAAACACAAGTTC-CAACTTAAAATAT
1 CCTAAAAACAAGTTCCAACTTAAAATATGGGT---ACCTAAA-ACAAGTTCTCAACTTAAAATAT
*
389294 AGTTGCAT
62 -G-GGCAT
* *
389302 CCTAAAAACACA-TTCCAACTTAAAATATGGGTACCTAAAACAAGTTCTAAAC-TAAAAGATGGT
1 CCTAAAAACA-AGTTCCAACTTAAAATATGGGTACCTAAAACAAGTTCTCAACTTAAAATATGG-
*
389365 TGCAA
64 -GCAT
* *
389370 CCTAAAACCAAGTTCCACCTTAAAATATG
1 CCTAAAAACAAGTTCCAACTTAAAATATG
389399 AGTAACTTAA
Statistics
Matches: 191, Mismatches: 24, Indels: 38
0.75 0.09 0.15
Matches are distributed among these distances:
64 19 0.10
65 7 0.04
66 2 0.01
67 18 0.09
68 100 0.52
69 17 0.09
70 4 0.02
71 2 0.01
72 21 0.11
73 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (67 bp):
CCTAAAAACAAGTTCCAACTTAAAATATGGGTACCTAAAACAAGTTCTCAACTTAAAATATGGGC
AT
Found at i:389358 original size:32 final size:33
Alignment explanation
Indices: 389097--389398 Score: 210
Period size: 32 Copynumber: 8.9 Consensus size: 33
389087 GATATTTACA
389097 ACCTAAAAACAAGTTCT-AACTTAAAATATGGGT
1 ACCT-AAAACAAGTTCTCAACTTAAAATATGGGT
* *
389130 ATCTAAAAAAAGTTC-CAACTTAAAATATGGGT
1 ACCTAAAACAAGTTCTCAACTTAAAATATGGGT
* * * *
389162 ATCTAAAAAAAGTTC-CAACCTAAAATATGGTTGCA
1 ACCTAAAACAAGTTCTCAACTTAAAATATGG--G-T
*
389197 ACCTAAAA-ATAGTTCTCAACATAAAATATGGGT
1 ACCTAAAACA-AGTTCTCAACTTAAAATATGGGT
* * * **
389230 ATCTAAAACAAGTT-TCAGCCTAAAATATGATT
1 ACCTAAAACAAGTTCTCAACTTAAAATATGGGT
* *
389262 ACAACCTAAACACAAGTTC-CAACTTAAAATATAGTTGC
1 ---ACCTAAA-ACAAGTTCTCAACTTAAAATAT-G-GGT
389300 ATCCTAAAAACACA-TTC-CAACTTAAAATATGGGT
1 A-CCT-AAAACA-AGTTCTCAACTTAAAATATGGGT
* * *
389334 ACCTAAAACAAGTTCTAAAC-TAAAAGATGGTTGCA
1 ACCTAAAACAAGTTCTCAACTTAAAATATGG--G-T
*
389369 ACCTAAAACCAAGTTC-CACCTTAAAATATG
1 ACCTAAAA-CAAGTTCTCAACTTAAAATATG
389399 AGTAACTTAA
Statistics
Matches: 219, Mismatches: 26, Indels: 45
0.76 0.09 0.16
Matches are distributed among these distances:
31 1 0.00
32 87 0.40
33 20 0.09
34 7 0.03
35 30 0.14
36 69 0.32
37 5 0.02
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (33 bp):
ACCTAAAACAAGTTCTCAACTTAAAATATGGGT
Found at i:389417 original size:84 final size:84
Alignment explanation
Indices: 389318--389482 Score: 242
Period size: 84 Copynumber: 2.0 Consensus size: 84
389308 AACACATTCC
* * *
389318 AACTTAAAATATGGGTACCTAAAACAAGTTCTAAACTAAAA-GATGGTTGCAACCTAAAACCAAG
1 AACTTAAAATATGGGTACCTAAAACAAGTTCCAAACTAAAATG-TGATTGCAACCTAAAAACAAG
*
389382 TTCCACCTTAAAATATGAGT
65 TTCCAACTTAAAATATGAGT
* * *
389402 AACTTAAACTATGGGTATCTAAAACAAGTTCCAACCTAAAATGTGATTGCAACCTAAAAACAAGT
1 AACTTAAAATATGGGTACCTAAAACAAGTTCCAAACTAAAATGTGATTGCAACCTAAAAACAAGT
*
389467 TCGAACTTAAAATATG
66 TCCAACTTAAAATATG
389483 GATATCCAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
84 71 0.99
85 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (84 bp):
AACTTAAAATATGGGTACCTAAAACAAGTTCCAAACTAAAATGTGATTGCAACCTAAAAACAAGT
TCCAACTTAAAATATGAGT
Found at i:389507 original size:50 final size:50
Alignment explanation
Indices: 389448--389559 Score: 174
Period size: 50 Copynumber: 2.2 Consensus size: 50
389438 TAAAATGTGA
389448 TTGCAACCTAAAAACAAGTT-CGAACTTAAAATAT-GGATATCCAAAACAAG
1 TTGCAACCTAAAAACAAGTTACG-ACTTAAAATATAGG-TATCCAAAACAAG
*
389498 TTGCAACCTAAAAACAAGTTACGACTTAAAATATAGGTATCTAAAACAAG
1 TTGCAACCTAAAAACAAGTTACGACTTAAAATATAGGTATCCAAAACAAG
*
389548 TTCCAACCTAAA
1 TTGCAACCTAAA
389560 TATGATTGCA
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
50 54 0.93
51 4 0.07
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.23
Consensus pattern (50 bp):
TTGCAACCTAAAAACAAGTTACGACTTAAAATATAGGTATCCAAAACAAG
Found at i:389528 original size:68 final size:68
Alignment explanation
Indices: 389402--389528 Score: 148
Period size: 68 Copynumber: 1.9 Consensus size: 68
389392 AAATATGAGT
* * * *** *
389402 AACTTAAACTATGGGTATCTAAAACAAGTTCCAACCTAAAATGTGATTGCAACCTAAAAACAAGT
1 AACTTAAAATATGGATATCCAAAACAAGTTCCAACCTAAAACAAGATTACAACCTAAAAACAAGT
389467 TCG
66 TCG
* * *
389470 AACTTAAAATATGGATATCCAAAACAAGTTGCAACCTAAAAACAAG-TTACGACTTAAAA
1 AACTTAAAATATGGATATCCAAAACAAGTTCCAACCT-AAAACAAGATTACAACCTAAAA
389529 TATAGGTATC
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
68 43 0.90
69 5 0.10
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (68 bp):
AACTTAAAATATGGATATCCAAAACAAGTTCCAACCTAAAACAAGATTACAACCTAAAAACAAGT
TCG
Found at i:391048 original size:3 final size:3
Alignment explanation
Indices: 391040--391074 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
391030 GCAAACATTG
*
391040 TAA TAA TAA TAT TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
391075 GTATAAGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:391060 original size:15 final size:14
Alignment explanation
Indices: 391040--391074 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
391030 GCAAACATTG
391040 TAATAATAATATTAA
1 TAATAATAATA-TAA
391055 TAATAATAATATAA
1 TAATAATAATATAA
391069 TAATAA
1 TAATAA
391075 GTATAAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATAATAATATAA
Found at i:392042 original size:85 final size:84
Alignment explanation
Indices: 391758--392389 Score: 744
Period size: 85 Copynumber: 7.4 Consensus size: 84
391748 CTCGATAATT
* * * *
391758 TTTGTTTACAGATAACCCTTCTCGCGTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTAAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATG-CCTTGAGCTGAA
* * *
391823 TGAAATCGAATTCGAAGGTTG
65 TGTAATCGAACTCGAAGG-TC
* * * * * * *
391844 TTTGCTAACAGATAGCCCTTCTCGCATTGAGCTAAGTTGTAAATTTGACATTCCCTTGAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATA-TGCCTTGAGCTGAA
* * * *
391909 TGAAATCAAACTTGAA-GTA
65 TGTAATCGAACTCGAAGGTC
* * * ** * * *
391928 TTTGTTGATAGATAACCCTTATCGCCTTGAGTTATACTGTAAATTTGACATGTCCTTAATCTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATG-CCTTGAGCTGAA
*
391993 TGTAATCGAACTCGAAGGTT
65 TGTAATCGAACTCGAAGGTC
* * *
392013 TTTGTTGATAGATAACTCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATGCTTTTGAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATGC-CTTGAGCTGAA
*
392078 TATAATCGAACTCGAAGGTC
65 TGTAATCGAACTCGAAGGTC
* *
392098 TTTGCTGACAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTTGATATGCCTTTGAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATGCC-TTGAGCTGAA
* *
392163 TATAATCGAACTTGAAGGTC
65 TGTAATCGAACTCGAAGGTC
* * * * *
392183 TTGGTTGACAAATAGCCCTTATCGCCTTGAACTATGTTGTAAATTTGATATGCCTTTGAGCTGAA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATGCC-TTGAGCTGAA
*
392248 TGTAATCGAAGTCGAAGGTC
65 TGTAATCGAACTCGAAGGTC
* * * * *
392268 TTTGCTGAAAGATAACCCTTCTTGCCTTGAGTTATGCTGTAAATTTGATAATGCCTTTGAGCTGA
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGAT-ATGCC-TTGAGCTGA
392333 ATGTAATCGAACTCGAAGGTC
64 ATGTAATCGAACTCGAAGGTC
* *
392354 TTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
1 TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
392390 CTGCAAATAG
Statistics
Matches: 466, Mismatches: 74, Indels: 12
0.84 0.13 0.02
Matches are distributed among these distances:
83 1 0.00
84 65 0.14
85 267 0.57
86 132 0.28
87 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (84 bp):
TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATGCCTTGAGCTGAAT
GTAATCGAACTCGAAGGTC
Found at i:392113 original size:170 final size:170
Alignment explanation
Indices: 391765--392389 Score: 824
Period size: 170 Copynumber: 3.7 Consensus size: 170
391755 ATTTTTGTTT
* * * * *
391765 ACAGATAACCCTTCTCGCGTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTAAATGAAATC
1 ACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATC
* * * * * * * *
391830 GAATTCGAAGGTTGTTTGCTAACAGATAGCCCTTCTCGCATTGAGCTAAGTTGTAAATTTGACAT
66 GAACTCGAAGG-TCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATAT
* * * * * *
391895 TCCCTTGAGCTGAATGA-AATCAAACTTGAA-GTATTTGTTG
130 GCCTTTGAGCTGAAT-ATAATCGAACTCGAAGGTCTTTGCTG
* * * * * *
391935 ATAGATAACCCTTATCGCCTTGAGTTATACTGTAAATTTGACATGTCC-TTAATCTGAATGTAAT
1 ACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATG-CCTTTGAGCTGAATGTAAT
* * * * *
391999 CGAACTCGAAGGTTTTTGTTGATAGATAACTCTTCTCGCCTTGAGCTATGTTGTAAATTTGATAT
65 CGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATAT
*
392064 GCTTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGCTG
130 GCCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGCTG
* *
392105 ACAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTTGATATGCCTTTGAGCTGAATATAATC
1 ACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATC
* * * *
392170 GAACTTGAAGGTCTTGGTTGACAAATAGCCCTTATCGCCTTGAACTATGTTGTAAATTTGATATG
66 GAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATG
* *
392235 CCTTTGAGCTGAATGTAATCGAAGTCGAAGGTCTTTGCTG
131 CCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGCTG
* *
392275 AAAGATAACCCTTCTTGCCTTGAGTTATGCTGTAAATTTGATAATGCCTTTGAGCTGAATGTAAT
1 ACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGAT-ATGCCTTTGAGCTGAATGTAAT
392340 CGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
65 CGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
392390 CTGCAAATAG
Statistics
Matches: 395, Mismatches: 55, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
168 1 0.00
169 69 0.17
170 256 0.65
171 69 0.17
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (170 bp):
ACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATC
GAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATG
CCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGCTG
Found at i:392204 original size:255 final size:254
Alignment explanation
Indices: 391730--392389 Score: 835
Period size: 255 Copynumber: 2.6 Consensus size: 254
391720 ATGTATCATC
* * * * *
391730 AAGCTGAATAG-AACCGAACTCGATA-ATTTTTGTTTACAGATAACCCTTCTCGCGTTGAGCTAT
1 AAGCTGAAT-GTAATCGAACTCGA-AGGTTTTTGTTGAAAGATAACCCTTCTCGCCTTGAGCTAT
* * * * *
391793 GCTGTAAATTTGATATGCCCTTGAGCTAAATGA-AATCGAATTCGAAGGTTGTTTGCTAACAGAT
64 GCTGTAAATTTGATATGCCTTTGAGCTGAAT-ATAATCGAACTCGAAGG-TCTTTGCTGACAGAT
* * *
391857 AGCCCTTCTCGCATTGAGCTAAGTTGTAAATTTGACATTCCCTTGAGCTGAATGAAATCAAACTT
127 AGCCCTTCTCGCCTTGAGCTATGTTGTAAATTTGACATGCCCTTGAGCTGAATGAAATCAAACTT
* * * **
391922 GAAGTATTTGTTGATAGATAACCCTTATCGCCTTGAGTTATACTGTAAATTTGACATGTCC-TT
192 GAAGTATTGGTTGACAAATAACCCTTATCGCCTTGAACTATACTGTAAATTTGACATG-CCTTT
* * * *
391985 AATCTGAATGTAATCGAACTCGAAGGTTTTTGTTGATAGATAACTCTTCTCGCCTTGAGCTATGT
1 AAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGAAAGATAACCCTTCTCGCCTTGAGCTATGC
* *
392050 TGTAAATTTGATATGCTTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGCTGACAGATAACC
66 TGTAAATTTGATATGCCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGCTGACAGATAGCC
* * * *
392115 CTTCTCGCCTTGAGTTATGTTGTAAATTTGATATGCCTTTGAGCTGAAT-ATAATCGAACTTGAA
131 CTTCTCGCCTTGAGCTATGTTGTAAATTTGACATGCCCTTGAGCTGAATGA-AATCAAACTTGAA
* * ** *
392179 GGTCTTGGTTGACAAATAGCCCTTATCGCCTTGAACTATGTTGTAAATTTGATATGCCTTT
195 -GTATTGGTTGACAAATAACCCTTATCGCCTTGAACTATACTGTAAATTTGACATGCCTTT
* * * * * *
392240 GAGCTGAATGTAATCGAAGTCGAAGGTCTTTGCTGAAAGATAACCCTTCTTGCCTTGAGTTATGC
1 AAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGAAAGATAACCCTTCTCGCCTTGAGCTATGC
* * *
392305 TGTAAATTTGATAATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGC
66 TGTAAATTTGAT-ATGCCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGCTGACAGATAGC
392370 CCTTCTCGCCTTGAGCTATG
130 CCTTCTCGCCTTGAGCTATG
392390 CTGCAAATAG
Statistics
Matches: 350, Mismatches: 48, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
253 1 0.00
254 76 0.22
255 207 0.59
256 66 0.19
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (254 bp):
AAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGAAAGATAACCCTTCTCGCCTTGAGCTATGC
TGTAAATTTGATATGCCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGCTGACAGATAGCC
CTTCTCGCCTTGAGCTATGTTGTAAATTTGACATGCCCTTGAGCTGAATGAAATCAAACTTGAAG
TATTGGTTGACAAATAACCCTTATCGCCTTGAACTATACTGTAAATTTGACATGCCTTT
Found at i:392610 original size:86 final size:86
Alignment explanation
Indices: 392458--392844 Score: 499
Period size: 86 Copynumber: 4.5 Consensus size: 86
392448 AATTCTTTAA
* ** * * ** * *
392458 ATGACTCCCCTTCATGGGAAA-TCCAAATGGTATATTCTTTAGGTGGTTCTTCTTCGCAGGCCTG
1 ATGACTCCCCTTCACGGGAAAGT-CATGTGGTATATTCTTCAAGTGGTTCCCCTTCGCGGGTCTG
392522 AACCAGGTGAGACGATATTTGG
65 AACCAGGTGAGACGATATTTGG
* * *
392544 ATGACTCCCCTTCGCGGGAAAGTCATGTGGTATATTCTTCAAGTGGTTCCCCTTTGCGGGTTTGA
1 ATGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAAGTGGTTCCCCTTCGCGGGTCTGA
*
392609 ACCAGGTGAGACGATCTTTGG
66 ACCAGGTGAGACGATATTTGG
* *
392630 ATGACTCCCCTTCACAGAAAAGTCATGTGGTATATTCTTCAAGTGGTTCCCCTTCGCGGGTCTGA
1 ATGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAAGTGGTTCCCCTTCGCGGGTCTGA
* *
392695 ACCAGGTGAGATGATCTTTGG
66 ACCAGGTGAGACGATATTTGG
*** * * *
392716 ATGACTTTTCTTAACGGGAAAGTCATGTGGCATATTCTTCACGTGGTTCCCCTTCGCGGGTCTGA
1 ATGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAAGTGGTTCCCCTTCGCGGGTCTGA
*
392781 ACCAGGTGAGATGATATTTGG
66 ACCAGGTGAGACGATATTTGG
* ** *
392802 ATAACTTTCCTTCAC-TGAAAGTCATGTGGTATATTCTTCAAGT
1 ATGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAAGT
392845 TACTCCTCTT
Statistics
Matches: 266, Mismatches: 34, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
85 25 0.09
86 240 0.90
87 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (86 bp):
ATGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAAGTGGTTCCCCTTCGCGGGTCTGA
ACCAGGTGAGACGATATTTGG
Found at i:394958 original size:93 final size:93
Alignment explanation
Indices: 394836--395030 Score: 327
Period size: 93 Copynumber: 2.1 Consensus size: 93
394826 GACAGCTCAA
* * * **
394836 TATTATAATCACTTTTATCAGGCTAGCTGAATCTTATCCATAAAGCTGGGGCATTTAACCAATTG
1 TATTATATTCACCTTTATCAGGCTAGCTGAATCTTATCCAAAAAGCCAGGGCATTTAACCAATTG
*
394901 CTTTAGAGGGACAACTCAAGCTTTATTG
66 CTCTAGAGGGACAACTCAAGCTTTATTG
394929 TATTATATTCACCTTTATCAGGCTAGCTGAATCTTATCCAAAAAGCCAGGGCATTTAACCAATTG
1 TATTATATTCACCTTTATCAGGCTAGCTGAATCTTATCCAAAAAGCCAGGGCATTTAACCAATTG
394994 CTCTAGAGGGACAACTCAAGCTTTATTG
66 CTCTAGAGGGACAACTCAAGCTTTATTG
395022 TATATATAT
1 TAT-TATAT
395031 AATATTATAA
Statistics
Matches: 95, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
93 90 0.95
94 5 0.05
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (93 bp):
TATTATATTCACCTTTATCAGGCTAGCTGAATCTTATCCAAAAAGCCAGGGCATTTAACCAATTG
CTCTAGAGGGACAACTCAAGCTTTATTG
Found at i:399041 original size:16 final size:16
Alignment explanation
Indices: 399020--399050 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
399010 TATGGCTGAT
399020 TTTTTCTTCGTTCGAA
1 TTTTTCTTCGTTCGAA
*
399036 TTTTTCTTTGTTCGA
1 TTTTTCTTCGTTCGA
399051 TCCCCTCGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.16, G:0.13, T:0.61
Consensus pattern (16 bp):
TTTTTCTTCGTTCGAA
Found at i:399572 original size:3 final size:3
Alignment explanation
Indices: 399564--399634 Score: 101
Period size: 3 Copynumber: 23.7 Consensus size: 3
399554 GCAAACATTG
*
399564 TAA TAA TAA TAT TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
399611 TAA TAA TAA GT-A TAA TATA TAA TA
1 TAA TAA TAA -TAA TAA TA-A TAA TA
399635 TATATATATT
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 3 0.05
3 55 0.89
4 4 0.06
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:408669 original size:15 final size:15
Alignment explanation
Indices: 408649--408698 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
408639 ATTTAAAGAT
408649 AAATTTGAATTTATA
1 AAATTTGAATTTATA
* ***
408664 AAATTTTAAGAGAT-
1 AAATTTGAATTTATA
408678 AAATTTGAATTTATA
1 AAATTTGAATTTATA
408693 AAATTT
1 AAATTT
408699 TAAGAGATAA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (15 bp):
AAATTTGAATTTATA
Found at i:408681 original size:29 final size:29
Alignment explanation
Indices: 408640--408712 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
408630 CGATTTTATA
408640 TTTAA-AGATAAATTTGAATTTATAAAAT
1 TTTAAGAGATAAATTTGAATTTATAAAAT
408668 TTTAAGAGATAAATTTGAATTTATAAAAT
1 TTTAAGAGATAAATTTGAATTTATAAAAT
408697 TTTAAGAGATAAATTT
1 TTTAAGAGATAAATTT
408713 TAAATAAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 5 0.11
29 39 0.89
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (29 bp):
TTTAAGAGATAAATTTGAATTTATAAAAT
Found at i:408708 original size:15 final size:14
Alignment explanation
Indices: 408664--408715 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
408654 TGAATTTATA
408664 AAATTTTAAGAGAT
1 AAATTTTAAGAGAT
* ***
408678 AAATTTGAATTTAT
1 AAATTTTAAGAGAT
408692 AAAATTTTAAGAGAT
1 -AAATTTTAAGAGAT
408707 AAATTTTAA
1 AAATTTTAA
408716 ATAAAATAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (14 bp):
AAATTTTAAGAGAT
Found at i:408750 original size:22 final size:20
Alignment explanation
Indices: 408705--408751 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
408695 ATTTTAAGAG
*
408705 ATAAATTTTAAATAAAATAA
1 ATAAATTTTAAAAAAAATAA
*
408725 ATAAATTTTTAATAAAAAATAC
1 ATAAA-TTTTAA-AAAAAATAA
408747 ATAAA
1 ATAAA
408752 ATAAATCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 6 0.26
22 12 0.52
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
ATAAATTTTAAAAAAAATAA
Found at i:409018 original size:3 final size:3
Alignment explanation
Indices: 409004--409070 Score: 116
Period size: 3 Copynumber: 22.0 Consensus size: 3
408994 GTCGAACAAA
409004 TAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
409050 TAT TAT TAT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
409071 CATGCATGCC
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 58 0.95
4 3 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:410720 original size:30 final size:30
Alignment explanation
Indices: 410582--410723 Score: 94
Period size: 30 Copynumber: 4.8 Consensus size: 30
410572 TAAAACTTAA
* *
410582 AATTTTCTGTTTTTTCCATTTTAGTCTTTT
1 AATTTTCTATTTTTTCTATTTTAGTCTTTT
* * * * **
410612 AAATTTC-ATTTTGT-GATATTTGGTCTTCA
1 AATTTTCTATTTTTTCTAT-TTTAGTCTTTT
* * * *
410641 AAATTTCTATTTTTACTAGTCTAG-CTTTTT
1 AATTTTCTATTTTTTCTATTTTAGTC-TTTT
* * *
410671 AAATTTT-TGTTTGTGCTATTTTAGTCTTTT
1 -AATTTTCTATTTTTTCTATTTTAGTCTTTT
410701 AATTTTCTATTTTTTCTATTTTA
1 AATTTTCTATTTTTTCTATTTTA
410724 ATACTTAAAG
Statistics
Matches: 81, Mismatches: 24, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
28 2 0.02
29 27 0.33
30 45 0.56
31 7 0.09
ACGTcount: A:0.20, C:0.11, G:0.08, T:0.61
Consensus pattern (30 bp):
AATTTTCTATTTTTTCTATTTTAGTCTTTT
Found at i:414305 original size:15 final size:17
Alignment explanation
Indices: 414282--414313 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
414272 CCATCTATAA
414282 TAAATAATTAAT-TAAT
1 TAAATAATTAATGTAAT
414298 TAAA-AATTAATGTAAT
1 TAAATAATTAATGTAAT
414314 GCCATTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAATAATTAATGTAAT
Found at i:415313 original size:50 final size:50
Alignment explanation
Indices: 415214--415350 Score: 175
Period size: 50 Copynumber: 2.7 Consensus size: 50
415204 TGTATCAATT
* * * * * *
415214 AACACATACTTATATCGGTGTAAGTATGTACATTTCACAACTTAGAAATA
1 AACACATACTTACACCGGTGTAAGTATGTACATCTCCCAACATAAAAATA
** * * *
415264 AACTTATATTTACACCGGTGCAAGTATGTATATCTCCCAACATAAAAATA
1 AACACATACTTACACCGGTGTAAGTATGTACATCTCCCAACATAAAAATA
415314 AACACATACTTACACCGGTGTAAGTATGTACATCTCC
1 AACACATACTTACACCGGTGTAAGTATGTACATCTCC
415351 TAATATTTTA
Statistics
Matches: 71, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (50 bp):
AACACATACTTACACCGGTGTAAGTATGTACATCTCCCAACATAAAAATA
Found at i:417113 original size:5 final size:5
Alignment explanation
Indices: 417103--417229 Score: 240
Period size: 5 Copynumber: 25.8 Consensus size: 5
417093 CAAGACCATT
417103 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
417153 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
417203 ATATC ATATC --ATC ATATC ATATC ATAT
1 ATATC ATATC ATATC ATATC ATATC ATAT
417230 TATAAATAAA
Statistics
Matches: 120, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
3 3 0.03
5 117 0.98
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATC
Found at i:418498 original size:35 final size:35
Alignment explanation
Indices: 418452--418520 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
418442 TAAACAAAAA
*
418452 AATAATTCTATTCACCAAGGGACATAACTTATTAC
1 AATAAATCTATTCACCAAGGGACATAACTTATTAC
*
418487 AATAAATCTATTCACCAAGTGACATAACTTATTA
1 AATAAATCTATTCACCAAGGGACATAACTTATTA
418521 TAAATATCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (35 bp):
AATAAATCTATTCACCAAGGGACATAACTTATTAC
Found at i:420007 original size:22 final size:20
Alignment explanation
Indices: 419956--420013 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 20
419946 GGAAAATGAG
419956 TTGGTATCGATAC-TCTAGT
1 TTGGTATCGATACTTCTAGT
419975 TTGAGTATCGATACTTCTAGT
1 TTG-GTATCGATACTTCTAGT
419996 ATGTGGTATCGATACTTC
1 -T-TGGTATCGATACTTC
420014 CTTGAGTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.09
20 10 0.29
21 6 0.17
22 14 0.40
23 2 0.06
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGGTATCGATACTTCTAGT
Found at i:421328 original size:26 final size:26
Alignment explanation
Indices: 421292--421350 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
421282 GAGGGTACTG
* * *
421292 AAGTTGCATATATTCCTTGACTTCCC
1 AAGTCGCATATACTCATTGACTTCCC
*
421318 AAGTCGCATATCCTCATTGACTTCCC
1 AAGTCGCATATACTCATTGACTTCCC
421344 AAGTCGC
1 AAGTCGC
421351 CTCTTTAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.32
Consensus pattern (26 bp):
AAGTCGCATATACTCATTGACTTCCC
Found at i:425342 original size:50 final size:51
Alignment explanation
Indices: 425224--425347 Score: 153
Period size: 50 Copynumber: 2.5 Consensus size: 51
425214 AAACAAAGGA
** *
425224 AATTTAA-AAATTAAATCCCAAAACATAAACAACTTTTGTTGAACAATGAG
1 AATTTAATAAATTAAATCTTAAAACATAAACAACTTCTGTTGAACAATGAG
** * * * *
425274 TTTTTAATAAGTTAAATCTTGAAACAT-AATAACTTCTGTTGAACGATGAG
1 AATTTAATAAATTAAATCTTAAAACATAAACAACTTCTGTTGAACAATGAG
425324 AATTTAATAAATTAAATCTTAAAA
1 AATTTAATAAATTAAATCTTAAAA
425348 TAGAAGTACA
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
50 45 0.75
51 15 0.25
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (51 bp):
AATTTAATAAATTAAATCTTAAAACATAAACAACTTCTGTTGAACAATGAG
Found at i:436126 original size:157 final size:156
Alignment explanation
Indices: 435747--436422 Score: 858
Period size: 156 Copynumber: 4.3 Consensus size: 156
435737 AATGTGGTTT
*
435747 AAATTTGGTAAAAAAACAGACTTAAAATAAATGAC-AAATTGAAGGAATAAGGAGATTATGAAAA
1 AAATTTGGT--AAAAACAGACTTAAAATAAATGACGAAA-TGAAGAAATAAGGAGATTATGAAAA
* * * * *
435811 ATTGAAGGGCTAAATTGAAAAATAAAAAGTTTGTTATCAAAAAGAGGAATTAAAAATACACATGT
63 ATTAAAGGACTAAATTGAAAAATAAAAAG-TTGTTATCAAAAAGAGGAATTGAAAGTACACATGC
* *
435876 ATTCTACTATGGTTTACGAGCATGTGGCTC
127 ATTCTACTATGGTTTAGGAGCATGTGACTC
* * * *
435906 AAATTTGGTAAAAGACAGACTTAAAATAAATGACTAATTGAAGAGATAAGGAGATTATGAAAACT
1 AAATTTGGTAAAA-ACAGACTTAAAATAAATGACGAAATGAAGAAATAAGGAGATTATGAAAAAT
* * *
435971 TAAAGGACTAAATTGAAAAGTAAAAAGTTGCTT-TCAAAAAGAGAAATTGAAAGTACACATGTAT
65 TAAAGGACTAAATTGAAAAATAAAAAGTTG-TTATCAAAAAGAGGAATTGAAAGTACACATGCAT
436035 TCTACTATGGTTTAGGAGCATGTGACTC
129 TCTACTATGGTTTAGGAGCATGTGACTC
* * * *
436063 AAATTTGGTAGAAAA-TGACTTAAAATAAATGACGAAATGAAGATATAAGGAGATTATCAAAAAC
1 AAATTTGGTA-AAAACAGACTTAAAATAAATGACGAAATGAAGAAATAAGGAGATTATGAAAAAT
* * *
436127 TAAAGGACTAAATTGAAAAGTAAAAACTTTGTTATCAAAAAGAGGAATTGAAAGTACGCATGCAT
65 TAAAGGACTAAATTGAAAAATAAAAA-GTTGTTATCAAAAAGAGGAATTGAAAGTACACATGCAT
*
436192 TCTACTTTGGTTTAGGAGCATGTGACTC
129 TCTACTATGGTTTAGGAGCATGTGACTC
* ** * * * *
436220 AAATTT-GTGAAAAGGGACTTAAAATAAATTACGAATTGAAGAAAAAAGGAAATTATGAAAAATT
1 AAATTTGGTAAAAACAGACTTAAAATAAATGACGAAATGAAGAAATAAGGAGATTATGAAAAATT
* * * * *
436284 GAAGGAGTAAATTGAAAAATAAAAATTTGTTATCAAAAAGAGGAATTGAAAGTAAATATGCATTC
66 AAAGGACTAAATTGAAAAATAAAAAGTTGTTATCAAAAAGAGGAATTGAAAGTACACATGCATTC
* * **
436349 TAATATGGTTTAGGAGCATGGGGTTC
131 TACTATGGTTTAGGAGCATGTGACTC
* * *
436375 AAATTTGGTAAAAATAGACTTAAAATGAAGGA-GAAATTGAAGAAATAA
1 AAATTTGGTAAAAACAGACTTAAAATAAATGACGAAA-TGAAGAAATAA
436423 TGAAATAAGG
Statistics
Matches: 456, Mismatches: 52, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
155 71 0.16
156 165 0.36
157 136 0.30
158 73 0.16
159 11 0.02
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.26
Consensus pattern (156 bp):
AAATTTGGTAAAAACAGACTTAAAATAAATGACGAAATGAAGAAATAAGGAGATTATGAAAAATT
AAAGGACTAAATTGAAAAATAAAAAGTTGTTATCAAAAAGAGGAATTGAAAGTACACATGCATTC
TACTATGGTTTAGGAGCATGTGACTC
Found at i:438312 original size:33 final size:33
Alignment explanation
Indices: 438265--438377 Score: 136
Period size: 33 Copynumber: 3.4 Consensus size: 33
438255 AGCTCGACTT
* *
438265 CCCTCGGATTCCCTCGCATAGCTCGTTCGGTTG
1 CCCTCGGATGCCCTCGCATAGCTCGTTCGGATG
438298 CCCTCGGATGCCCTCGCATAGCTCGTTCGGATG
1 CCCTCGGATGCCCTCGCATAGCTCGTTCGGATG
* * * * * *
438331 GCCTCGTATGCTCTCGGATGACCTCGGTCGGATG
1 CCCTCGGATGCCCTCGCAT-AGCTCGTTCGGATG
*
438365 GCCTCGGATGCCC
1 CCCTCGGATGCCC
438378 AGCGTGTTGG
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
33 46 0.67
34 23 0.33
ACGTcount: A:0.11, C:0.35, G:0.28, T:0.26
Consensus pattern (33 bp):
CCCTCGGATGCCCTCGCATAGCTCGTTCGGATG
Found at i:438327 original size:23 final size:20
Alignment explanation
Indices: 438300--438356 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 20
438290 TTCGGTTGCC
*
438300 CTCGGATGCCCTCGCATAGCT
1 CTCGGATGACCTCGCAT-GCT
* *
438321 CGTTCGGATGGCCTCGTATGCT
1 C--TCGGATGACCTCGCATGCT
438343 CTCGGATGACCTCG
1 CTCGGATGACCTCG
438357 GTCGGATGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 12 0.39
21 1 0.03
22 4 0.13
23 14 0.45
ACGTcount: A:0.12, C:0.33, G:0.28, T:0.26
Consensus pattern (20 bp):
CTCGGATGACCTCGCATGCT
Found at i:443460 original size:61 final size:61
Alignment explanation
Indices: 443385--443514 Score: 251
Period size: 61 Copynumber: 2.1 Consensus size: 61
443375 ATTTGTCTTG
443385 TAAGATTTTGAAATTAGCATAATTTAGCTTAGTAAATTTCATTGTATTAAGACTGAATTTC
1 TAAGATTTTGAAATTAGCATAATTTAGCTTAGTAAATTTCATTGTATTAAGACTGAATTTC
443446 TAAGATTTTGAAATTAGCATAATTTAGCTTAGTAAATTTCATTGTATTAAGACTGAATTTC
1 TAAGATTTTGAAATTAGCATAATTTAGCTTAGTAAATTTCATTGTATTAAGACTGAATTTC
*
443507 TAAAATTT
1 TAAGATTT
443515 AAAAATTACA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (61 bp):
TAAGATTTTGAAATTAGCATAATTTAGCTTAGTAAATTTCATTGTATTAAGACTGAATTTC
Found at i:444664 original size:28 final size:28
Alignment explanation
Indices: 444624--444692 Score: 120
Period size: 28 Copynumber: 2.5 Consensus size: 28
444614 TCGCAATGCG
444624 ATCGCTAATTCGCAACGCGATCTCCATT
1 ATCGCTAATTCGCAACGCGATCTCCATT
*
444652 ATCGCTAATTCGCAACGCGATCTCTATT
1 ATCGCTAATTCGCAACGCGATCTCCATT
*
444680 ATCGCAAATTCGC
1 ATCGCTAATTCGC
444693 GTTGCATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.29
Consensus pattern (28 bp):
ATCGCTAATTCGCAACGCGATCTCCATT
Found at i:444790 original size:20 final size:21
Alignment explanation
Indices: 444765--444857 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
444755 TTTTCCCAAT
*
444765 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
444785 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
444806 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
444826 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
444847 TCGCAATGCGA
1 TCGCAATGCGA
444858 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:444810 original size:41 final size:41
Alignment explanation
Indices: 444765--444857 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
444755 TTTTCCCAAT
444765 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
444806 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
444847 TCGCAATGCGA
1 TCGCAATGCGA
444858 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:444870 original size:41 final size:41
Alignment explanation
Indices: 444784--444918 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
444774 GAATAAGTAA
** *
444784 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
444825 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
444866 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
444907 TTCGCAACGCGA
1 ATCGCAACGCGA
444919 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:444871 original size:20 final size:20
Alignment explanation
Indices: 444846--444939 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
444836 AATTGGGAAA
*
444846 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * * **
444866 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-TACT
*
444887 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
444907 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
* *
444927 TTAGCAACGCGAT
1 ATCGCAACGCGAT
444940 TTACATAGCG
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:445518 original size:19 final size:19
Alignment explanation
Indices: 445458--445538 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
445448 TTCGAGAATG
445458 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
445478 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
445494 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
445511 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
445530 AAAATCGCA
1 AAAATCGCA
445539 TTGTGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:445567 original size:19 final size:19
Alignment explanation
Indices: 445543--445646 Score: 83
Period size: 19 Copynumber: 5.6 Consensus size: 19
445533 ATCGCATTGT
*
445543 GATTTTCATTTTGCGTTGC
1 GATTTTCATTTCGCGTTGC
445562 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
* **
445581 GATTGTC---T-G-GTCAC
1 GATTTTCATTTCGCGTTGC
**
445595 GATAGTCATTTCCGCGTTGC
1 GATTTTCATTT-CGCGTTGC
* *
445615 GATTCTCATTATCTCGTTGC
1 GATTTTCATT-TCGCGTTGC
445635 GATTTTCATTTC
1 GATTTTCATTTC
445647 AACCAAAAGA
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 1 0.01
17 1 0.01
19 27 0.40
20 27 0.40
21 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.45
Consensus pattern (19 bp):
GATTTTCATTTCGCGTTGC
Found at i:445623 original size:20 final size:20
Alignment explanation
Indices: 445600--445646 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
445590 GTCACGATAG
445600 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
445620 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
445640 TCATTTC
1 TCATTTC
445647 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:446824 original size:21 final size:21
Alignment explanation
Indices: 446791--446859 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
446781 ATCATCCCTC
*
446791 AAGAGTCCACTCCTATCGTTG
1 AAGAGGCCACTCCTATCGTTG
* * * *
446812 AAGAGGCCCCTCCCACCGTTC
1 AAGAGGCCACTCCTATCGTTG
*
446833 AAGAGGCCACT-ATCATCGTTG
1 AAGAGGCCACTCCT-ATCGTTG
446854 AAGAGG
1 AAGAGG
446860 TCCCTCCCAC
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.20
Consensus pattern (21 bp):
AAGAGGCCACTCCTATCGTTG
Found at i:446878 original size:21 final size:20
Alignment explanation
Indices: 446807--446879 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
446797 CCACTCCTAT
*
446807 CGTTGAAGAGGCCCCTCCCAC
1 CGTTCAAGAGG-CCCTCCCAC
** *
446828 CGTTCAAGAGGCCACTATCAT
1 CGTTCAAGAGGCC-CTCCCAC
*
446849 CGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGG-CCCTCCCAC
*
446870 CATTCAAGAG
1 CGTTCAAGAG
446880 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.05
21 36 0.90
22 2 0.05
ACGTcount: A:0.25, C:0.34, G:0.22, T:0.19
Consensus pattern (20 bp):
CGTTCAAGAGGCCCTCCCAC
Found at i:448236 original size:14 final size:14
Alignment explanation
Indices: 448217--448252 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
448207 TTTATTGTTT
448217 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
448231 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
448245 TGATTTGT
1 TGATTTGT
448253 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:448381 original size:19 final size:19
Alignment explanation
Indices: 448357--448423 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
448347 AAAAAGTACT
*
448357 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
448376 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
448390 ATCGCAACGCGAAAATG-AA
1 ATCGCAACGCG-AAATGAAA
448409 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
448424 TAATTCGTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
18 4 0.10
19 20 0.50
20 1 0.03
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:450772 original size:12 final size:12
Alignment explanation
Indices: 450755--450779 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
450745 TCTTCGGGGA
450755 CTTTTTCTTCTT
1 CTTTTTCTTCTT
450767 CTTTTTCTTCTT
1 CTTTTTCTTCTT
450779 C
1 C
450780 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:450988 original size:24 final size:24
Alignment explanation
Indices: 450954--451007 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
450944 CTGAAACATC
* *
450954 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
450978 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
451002 ATCAAA
1 ATCAAA
451008 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:451445 original size:20 final size:20
Alignment explanation
Indices: 451420--451477 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
451410 ATTCATTTGA
*
451420 CTATCGTAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
451440 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
451460 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
451478 CACAATGCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:451520 original size:14 final size:14
Alignment explanation
Indices: 451501--451554 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
451491 GAAAATCGCA
451501 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
451515 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
451532 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
451548 TTGCGAT
1 TTGCGAT
451555 AGCCATTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:451520 original size:33 final size:33
Alignment explanation
Indices: 451483--451553 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
451473 AAAATCACAA
451483 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
451516 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
451549 TGCGA
1 TGCGA
451554 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:451562 original size:33 final size:33
Alignment explanation
Indices: 451496--451573 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
451486 GAAATGAAAA
***
451496 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
451529 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
* *
451562 TCACGTTGCGAT
1 TCGCATTGCGAT
451574 AGTCTGTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:453552 original size:20 final size:19
Alignment explanation
Indices: 453517--453572 Score: 94
Period size: 20 Copynumber: 2.9 Consensus size: 19
453507 GAAACTTAAA
453517 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
453536 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
*
453556 ATCGCAATGCGAAATGA
1 ATCGCAACGCGAAATGA
453573 AAATCACAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:453591 original size:14 final size:14
Alignment explanation
Indices: 453572--453629 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
453562 ATGCGAAATG
*
453572 AAAATCACAACGAC
1 AAAATCGCAACGAC
*
453586 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
453602 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
453618 AAAATCGCAACG
1 AAAATCGCAACG
453630 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:453615 original size:32 final size:33
Alignment explanation
Indices: 453556--453634 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
453546 GGAAATGACT
*
453556 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAACGCGAAATGAAAATCACAACGACAAA
*
453589 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCACAACGACAAA
453621 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
453635 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCACAACGACAAA
Found at i:453667 original size:18 final size:18
Alignment explanation
Indices: 453641--453754 Score: 82
Period size: 18 Copynumber: 6.7 Consensus size: 18
453631 GAAACACAAA
*
453641 TCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
*
453659 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
453675 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
* *
453691 TCGCATTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
*
453707 T--CGTTACGATTTCATT
1 TCGCGTTGCGATTTCATT
* **
453723 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGAT-TTCATT
453742 TCCGCGTTGCGAT
1 T-CGCGTTGCGAT
453755 AGTCATTTTC
Statistics
Matches: 73, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
14 20 0.27
16 8 0.11
18 30 0.41
19 5 0.07
20 10 0.14
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.42
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:453681 original size:14 final size:14
Alignment explanation
Indices: 453662--453718 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 14
453652 TTTCATTTCG
453662 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
453676 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
453692 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
453708 CGTTACGATTT
1 CGTTGCGATTT
453719 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 19 0.53
16 8 0.22
18 9 0.25
ACGTcount: A:0.12, C:0.18, G:0.23, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:453687 original size:32 final size:32
Alignment explanation
Indices: 453646--453734 Score: 160
Period size: 32 Copynumber: 2.8 Consensus size: 32
453636 ACAAATCGCA
*
453646 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
453678 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
*
453710 TTACGATTTCATTTCGCATTGCGAT
1 TTGCGATTTCATTTCGCATTGCGAT
453735 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.46
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCATTGCGATTTTGTCG
Found at i:453741 original size:19 final size:20
Alignment explanation
Indices: 453719--453762 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
453709 GTTACGATTT
453719 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
453738 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
453758 CATTT
1 CATTT
453763 TCGTTGCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:454256 original size:18 final size:18
Alignment explanation
Indices: 454230--454274 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
454220 GTCGATCAGA
*
454230 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
454248 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
454266 TGATGGCTC
1 TGATGGCTC
454275 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:455651 original size:19 final size:19
Alignment explanation
Indices: 455629--455679 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
455619 GAAACTAAAA
455629 TCGCGTTGCGATTTGCATT
1 TCGCGTTGCGATTTGCATT
455648 TCGCGTTGCGATTTGCATT
1 TCGCGTTGCGATTTGCATT
455667 TCGCGTTGCGATT
1 TCGCGTTGCGATT
455680 CTTGGTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.10, C:0.22, G:0.27, T:0.41
Consensus pattern (19 bp):
TCGCGTTGCGATTTGCATT
Found at i:455917 original size:22 final size:22
Alignment explanation
Indices: 455878--455921 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
455868 AGATTAGATA
*
455878 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
455900 GACGGATTTCGTCTGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
455922 TGAGAGAGTG
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:0.18, C:0.14, G:0.43, T:0.25
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:455942 original size:47 final size:47
Alignment explanation
Indices: 455891--455993 Score: 188
Period size: 47 Copynumber: 2.2 Consensus size: 47
455881 GGATTTTGCC
*
455891 GGAGATGGGGACGGATTTCGTCTGAGATGGGTGAGAGAGTGAGAGAT
1 GGAGATGGGGACGGATTTCGTCGGAGATGGGTGAGAGAGTGAGAGAT
*
455938 GGAGATGGGGATGGATTTCGTCGGAGATGGGTGAGAGAGTGAGAGAT
1 GGAGATGGGGACGGATTTCGTCGGAGATGGGTGAGAGAGTGAGAGAT
455985 GGAGATGGG
1 GGAGATGGG
455994 ACTGAGTTGT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.25, C:0.05, G:0.50, T:0.20
Consensus pattern (47 bp):
GGAGATGGGGACGGATTTCGTCGGAGATGGGTGAGAGAGTGAGAGAT
Found at i:456181 original size:20 final size:20
Alignment explanation
Indices: 456156--456249 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
456146 GATTATGTAT
*
456156 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
456176 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
* *** * *
456196 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTAAG
* *
456217 TATCGCATTGCGATAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
456237 TATCGCATTGCGA
1 TATCGCGTTGCGA
456250 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:456250 original size:20 final size:20
Alignment explanation
Indices: 456136--456250 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
456126 CGCTTTGAAA
*
456136 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTAAGT
* * *
456157 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
456177 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * ** * *
456197 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTAAGT
456218 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
456238 ATCGCATTGCGAT
1 ATCGCATTGCGAT
456251 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:456268 original size:21 final size:21
Alignment explanation
Indices: 456239--456331 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
456229 ATAGTAAGTA
456239 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
456260 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
456280 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
456301 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
456321 TCGCATTGCGA
1 TCGCATTGCGA
456332 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:456269 original size:41 final size:41
Alignment explanation
Indices: 456178--456312 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
456168 AAAGTCAGTA
* * * ** *
456178 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
456218 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
456260 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
456301 TCGCGTTGCGAT
1 TCGCGTTGCGAT
456313 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:456313 original size:41 final size:41
Alignment explanation
Indices: 456239--456331 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
456229 ATAGTAAGTA
456239 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
456280 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
456321 TCGCATTGCGA
1 TCGCATTGCGA
456332 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:459202 original size:10 final size:10
Alignment explanation
Indices: 459189--459214 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
459179 GTTAGAGTTC
459189 CACCATCTTT
1 CACCATCTTT
459199 CACCATCTTT
1 CACCATCTTT
459209 CACCAT
1 CACCAT
459215 TAACAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (10 bp):
CACCATCTTT
Found at i:459851 original size:14 final size:14
Alignment explanation
Indices: 459832--459861 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
459822 TCAATGATGG
459832 TTGGATCTCAAGAT
1 TTGGATCTCAAGAT
459846 TTGGATCTCAAGAT
1 TTGGATCTCAAGAT
459860 TT
1 TT
459862 CTAATTCACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (14 bp):
TTGGATCTCAAGAT
Found at i:464062 original size:16 final size:17
Alignment explanation
Indices: 464038--464081 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
464028 TAAACCCTCT
*
464038 TTCACTTTTCTT-ATCA
1 TTCATTTTTCTTCATCA
464054 TTCATTTTT-TTCATCA
1 TTCATTTTTCTTCATCA
464070 TTCATCTTTTCT
1 TTCAT-TTTTCT
464082 AAGCTTCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 17 0.71
17 4 0.17
18 1 0.04
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (17 bp):
TTCATTTTTCTTCATCA
Found at i:465241 original size:18 final size:18
Alignment explanation
Indices: 465215--465249 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
465205 TTGTAGTATT
*
465215 GATATTGTTCTTATAGTC
1 GATAGTGTTCTTATAGTC
*
465233 GATAGTGTTCTTGTAGT
1 GATAGTGTTCTTATAGT
465250 ACAAATATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.09, G:0.23, T:0.49
Consensus pattern (18 bp):
GATAGTGTTCTTATAGTC
Found at i:469937 original size:24 final size:24
Alignment explanation
Indices: 469907--469962 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
469897 TAAAAGTTCG
469907 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
469931 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
469955 ATTGAAGC
1 ATTGAAGC
469963 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:470497 original size:8 final size:8
Alignment explanation
Indices: 470484--470508 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
470474 TGAACCCGGT
470484 TGAACCAG
1 TGAACCAG
470492 TGAACCAG
1 TGAACCAG
470500 TGAACCAG
1 TGAACCAG
470508 T
1 T
470509 ACCTTCACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (8 bp):
TGAACCAG
Found at i:477566 original size:15 final size:15
Alignment explanation
Indices: 477546--477575 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
477536 AGTAAGTTGG
477546 TTGGGTGTACGTTTC
1 TTGGGTGTACGTTTC
477561 TTGGGTGTACGTTTC
1 TTGGGTGTACGTTTC
477576 CAATGCAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.13, G:0.33, T:0.47
Consensus pattern (15 bp):
TTGGGTGTACGTTTC
Found at i:480758 original size:18 final size:17
Alignment explanation
Indices: 480735--480768 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
480725 AGTAAAATAT
480735 TTTAAAGTTTGACATTAA
1 TTTAAAGTTTGA-ATTAA
*
480753 TTTAAATTTTGAATTA
1 TTTAAAGTTTGAATTA
480769 TAAAGCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (17 bp):
TTTAAAGTTTGAATTAA
Found at i:482866 original size:24 final size:24
Alignment explanation
Indices: 482834--482881 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
482824 TGATATTATG
482834 GGTTGTGCTGCTTCCACCAAGCCT
1 GGTTGTGCTGCTTCCACCAAGCCT
482858 GGTTGTGCTGCTTCCACCAAGCCT
1 GGTTGTGCTGCTTCCACCAAGCCT
482882 AGTTCCACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.33, G:0.25, T:0.29
Consensus pattern (24 bp):
GGTTGTGCTGCTTCCACCAAGCCT
Found at i:492876 original size:20 final size:20
Alignment explanation
Indices: 492851--492917 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
492841 AATTCACAAT
492851 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
** * *
492871 GCGAATTGGGAAAATCGCAAT
1 GCGAA-TAAGTAAATCGCAAC
492892 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
492912 GCGAAT
1 GCGAAT
492918 TGGGAAAATC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (20 bp):
GCGAATAAGTAAATCGCAAC
Found at i:492887 original size:21 final size:21
Alignment explanation
Indices: 492861--492936 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
492851 GCGAATAAGT
492861 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
492882 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
492902 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
492923 AAATCGCAATGCGA
1 AAATCGCAACGCGA
492937 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:492950 original size:20 final size:20
Alignment explanation
Indices: 492925--493059 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
492915 AATTGGGAAA
492925 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
492945 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * **
492965 ATCGCAATGCGATAATAAAAA
1 ATCGCAATGCGATACT-GACT
* * *
492986 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
493006 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
493026 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
493046 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
493060 TTTCAAAGCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
19 2 0.02
20 69 0.72
21 25 0.26
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:492951 original size:41 final size:41
Alignment explanation
Indices: 492847--492936 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
492837 TCCCAATTCA
492847 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
1 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
492888 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
1 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
492929 CAATGCGA
1 CAATGCGA
492937 TACTGACTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
Found at i:492969 original size:61 final size:61
Alignment explanation
Indices: 492922--493053 Score: 183
Period size: 61 Copynumber: 2.2 Consensus size: 61
492912 GCGAATTGGG
* * * *
492922 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAA
* * * *
492983 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAA
*
493044 ATAATCGCAA
1 AAAATCGCAA
493054 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAA
Found at i:493252 original size:22 final size:22
Alignment explanation
Indices: 493224--493267 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
493214 CACTCTCTCA
493224 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
493246 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
493268 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:494891 original size:18 final size:18
Alignment explanation
Indices: 494868--494906 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
494858 GGGAGCCATC
* *
494868 TCACCTCGCCCAGAGCTA
1 TCACCTCACCCAGAGCCA
494886 TCACCTCACCCAGAGCCA
1 TCACCTCACCCAGAGCCA
494904 TCA
1 TCA
494907 TCTGATCGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.46, G:0.13, T:0.15
Consensus pattern (18 bp):
TCACCTCACCCAGAGCCA
Found at i:495424 original size:18 final size:20
Alignment explanation
Indices: 495371--495516 Score: 81
Period size: 20 Copynumber: 7.4 Consensus size: 20
495361 TAGTTTACTT
* *
495371 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
495391 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* *
495411 TCGC-ATGC-GAAATGA-AA
1 TCGCAACGCGGAAATGACTA
*** *
495428 TCGCAACGAAAAAATCGCAATGCTT
1 TCGCAACGCGGAAAT-G--A--CTA
*
495453 TCGCAACAC-GAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
495472 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* *
495492 TCGC-ATGC-GAAATGA-AA
1 TCGCAACGCGGAAATGACTA
495509 TCGCAACG
1 TCGCAACG
495517 AAAAAATCGC
Statistics
Matches: 95, Mismatches: 21, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
17 10 0.11
18 16 0.17
19 20 0.21
20 35 0.37
21 1 0.01
22 1 0.01
23 1 0.01
24 4 0.04
25 7 0.07
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:495432 original size:37 final size:37
Alignment explanation
Indices: 495390--495516 Score: 128
Period size: 37 Copynumber: 3.2 Consensus size: 37
495380 GAAAATGACT
495390 ATCGCAACGCGGAAATGGCTATCGCATGCGAAATGAA
1 ATCGCAACGCGGAAATGGCTATCGCATGCGAAATGAA
*** * ** *
495427 ATCGCAACGAAAAAATCGCAATGCTTTCGCAACACGAAATGACT
1 ATCGCAACGCGGAAAT-G----GCTATCGC-ATGCGAAATGA-A
495471 ATCGCAACGCGGAAATGGCTATCGCATGCGAAATGAA
1 ATCGCAACGCGGAAATGGCTATCGCATGCGAAATGAA
495508 ATCGCAACG
1 ATCGCAACG
495517 AAAAAATCGC
Statistics
Matches: 69, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
37 22 0.32
38 10 0.14
39 7 0.10
42 7 0.10
43 10 0.14
44 13 0.19
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.17
Consensus pattern (37 bp):
ATCGCAACGCGGAAATGGCTATCGCATGCGAAATGAA
Found at i:495504 original size:81 final size:82
Alignment explanation
Indices: 495368--495531 Score: 321
Period size: 81 Copynumber: 2.0 Consensus size: 82
495358 GAATAGTTTA
495368 CTTTCGCAACACGAAAATGACTATCGCAACGCGGAAATGGCTATCGCATGCGAAATGAAATCGCA
1 CTTTCGCAACACGAAAATGACTATCGCAACGCGGAAATGGCTATCGCATGCGAAATGAAATCGCA
495433 ACGAAAAAATCGCAATG
66 ACGAAAAAATCGCAATG
495450 CTTTCGCAACACG-AAATGACTATCGCAACGCGGAAATGGCTATCGCATGCGAAATGAAATCGCA
1 CTTTCGCAACACGAAAATGACTATCGCAACGCGGAAATGGCTATCGCATGCGAAATGAAATCGCA
495514 ACGAAAAAATCGCAATG
66 ACGAAAAAATCGCAATG
495531 C
1 C
495532 GAAATGAAAT
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 69 0.84
82 13 0.16
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (82 bp):
CTTTCGCAACACGAAAATGACTATCGCAACGCGGAAATGGCTATCGCATGCGAAATGAAATCGCA
ACGAAAAAATCGCAATG
Found at i:495525 original size:14 final size:14
Alignment explanation
Indices: 495506--495562 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
495496 ATGCGAAATG
495506 AAATCGCAACGAAA
1 AAATCGCAACGAAA
495520 AAATCGCAATGCGAAA
1 AAATCGCAA--CGAAA
*
495536 TGAAATCGCAACGACA
1 --AAATCGCAACGAAA
495552 AAATCGCAACG
1 AAATCGCAACG
495563 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 20 0.53
16 9 0.24
18 9 0.24
ACGTcount: A:0.49, C:0.23, G:0.18, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGAAA
Found at i:495533 original size:32 final size:32
Alignment explanation
Indices: 495491--495579 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
495481 GGAAATGGCT
495491 ATCGC-ATGCGAAATGAAATCGCAACGAAAAA
1 ATCGCAATGCGAAATGAAATCGCAACGAAAAA
*
495522 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGAAAAA
*
495554 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATG-AAATCGCAA
495580 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
31 5 0.09
32 40 0.74
33 9 0.17
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGAAAAA
Found at i:495573 original size:19 final size:19
Alignment explanation
Indices: 495453--495584 Score: 74
Period size: 19 Copynumber: 7.6 Consensus size: 19
495443 CGCAATGCTT
* **
495453 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
495472 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
495492 TCGC-ATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
495509 TCGCAA--CG-AA--AAAA
1 TCGCAACGCGAAATGAAAA
*
495523 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
495541 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
495555 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
495574 TCGCAATGCGA
1 TCGCAACGCGA
495585 TTTGTGTTTC
Statistics
Matches: 91, Mismatches: 8, Indels: 28
0.72 0.06 0.22
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 8 0.09
17 7 0.08
18 17 0.19
19 25 0.27
20 13 0.14
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:495615 original size:14 final size:14
Alignment explanation
Indices: 495596--495653 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
495586 TTGTGTTTCG
495596 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
495610 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
495626 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
495642 CGTTGCGATTTT
1 CGTTGCGATTTT
495654 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:495630 original size:32 final size:33
Alignment explanation
Indices: 495591--495669 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
495581 GCGATTTGTG
495591 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
495623 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
495656 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
495670 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:495668 original size:19 final size:19
Alignment explanation
Indices: 495610--495727 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
495600 GCGATTTTGT
495610 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
495628 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
495642 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
495661 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
495681 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
495700 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
495720 TGTTGCGA
1 CGTTGCGA
495728 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:497643 original size:14 final size:14
Alignment explanation
Indices: 497624--497676 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
497614 CGAAATGGCT
497624 ATCGCAACGATAAA
1 ATCGCAACGATAAA
*
497638 ATCGCAATGCGAAATGAA
1 ATCGCAA--CG--ATAAA
*
497656 ATCGCAACGAGAAA
1 ATCGCAACGATAAA
497670 ATCGCAA
1 ATCGCAA
497677 TGCGATTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 17 0.53
16 4 0.12
18 11 0.34
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (14 bp):
ATCGCAACGATAAA
Found at i:497659 original size:18 final size:16
Alignment explanation
Indices: 497635--497681 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 16
497625 TCGCAACGAT
497635 AAAATCGCAATGCGAA
1 AAAATCGCAATGCGAA
*
497651 ATGAAATCGCAA--CGAG
1 A--AAATCGCAATGCGAA
497667 AAAATCGCAATGCGA
1 AAAATCGCAATGCGA
497682 TTTTCATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 9 0.35
16 8 0.31
18 9 0.35
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (16 bp):
AAAATCGCAATGCGAA
Found at i:497665 original size:32 final size:33
Alignment explanation
Indices: 497605--497681 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 33
497595 AAAACAGACT
* ** *
497605 ATCGCAACGCGAAATGGCTATCGCAACGATAAA
1 ATCGCAATGCGAAATGGAAATCGCAACGAGAAA
497638 ATCGCAATGCGAAAT-GAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGGAAATCGCAACGAGAAA
497670 ATCGCAATGCGA
1 ATCGCAATGCGA
497682 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 26 0.65
33 14 0.35
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGGAAATCGCAACGAGAAA
Found at i:497756 original size:20 final size:20
Alignment explanation
Indices: 497700--497756 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
497690 TCGCATTGCG
*
497700 ATTTTC-CGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
497719 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
497739 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
497757 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 6 0.17
20 30 0.83
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.37
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:501310 original size:33 final size:33
Alignment explanation
Indices: 501268--501391 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
501258 GGAAATTACT
501268 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
501301 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
501333 TTTCGCAATGCGAAATG-AAATCGCAACGAG-G-
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
501364 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
501392 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
30 15 0.18
31 11 0.13
32 12 0.15
33 44 0.54
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:501381 original size:63 final size:66
Alignment explanation
Indices: 501269--501398 Score: 230
Period size: 63 Copynumber: 2.0 Consensus size: 66
501259 GAAATTACTA
*
501269 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
501334 T
66 T
501335 TCGCAATGCGAAATG-AAATCGCAACGAG-G-ATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
501397 T
66 T
501398 T
1 T
501399 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
63 34 0.54
64 1 0.02
65 13 0.21
66 15 0.24
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:501413 original size:19 final size:20
Alignment explanation
Indices: 501391--501433 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
501381 AAATCGCAAC
501391 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
501410 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
501430 GCGA
1 GCGA
501434 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:501588 original size:13 final size:13
Alignment explanation
Indices: 501572--501606 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
501562 CATCAATTAA
501572 ACAAATCAACTTT
1 ACAAATCAACTTT
*
501585 ACAAATCACCTTT
1 ACAAATCAACTTT
501598 ACAAATCAA
1 ACAAATCAA
501607 TTAACAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (13 bp):
ACAAATCAACTTT
Found at i:503009 original size:21 final size:21
Alignment explanation
Indices: 502944--503009 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
502934 TGTGAATCGG
*
502944 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * * * *
502964 CCTCTTCAACGAT-GCAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
502985 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
503006 CTCT
1 CTCT
503010 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
20 12 0.38
21 20 0.62
ACGTcount: A:0.18, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:503029 original size:42 final size:42
Alignment explanation
Indices: 502982--503065 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
502972 ACGATGCAGT
* * *
502982 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
503024 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
503066 CAATCGGGCT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:505147 original size:214 final size:213
Alignment explanation
Indices: 504777--505205 Score: 808
Period size: 214 Copynumber: 2.0 Consensus size: 213
504767 ATTTCTACAA
504777 AAAAACAATAAACATACCCAAGTTAGATATACCAAAAATTACACTGTCAAGATATCCAAAAACAA
1 AAAAACAATAAACATACCCAAGTTAGATATACCAAAAATTACACTGTCAAGATATCCAAAAACAA
504842 AACAATAAACAAAATAGTAGTTTATTTTGAAACTAAAATTGCAACACTATTTTTGTCTTTTGGTT
66 AACAATAAACAAAATAGTAGTTTA-TTTGAAACTAAAATTGCAACACTATTTTTGTCTTTTGGTT
504907 GAAATGAAAATCGCAACGAGATATGAGAATCGCAACGCGGAAATGACTATCGTACGAGAGAACGC
130 GAAATGAAAATCGCAACGAGATATGAGAATCGCAACGCGGAAATGACTATCGTACGAGAGAACGC
504972 AACGCGAAATGACTATCGCG
195 AACGCG-AATGACTATCGCG
504992 AAAAACAATAAACAT-CCCAAGTTAGATATACCAAAAATTACACTGTCAAGATATACCAAAAACA
1 AAAAACAATAAACATACCCAAGTTAGATATACCAAAAATTACACTGTCAAGATAT-CCAAAAACA
505056 AAACAATAAACAAAATAGTAGTTTA-TTGAAACTAAAATTTGCAACACTATTTTTGTCTTTTGGT
65 AAACAATAAACAAAATAGTAGTTTATTTGAAACTAAAA-TTGCAACACTATTTTTGTCTTTTGGT
505120 TGAAATGAAAATCGCAACGAGATATGAGAATCGCAACGCGGAAATGACTATCGTACGAGAGAACG
129 TGAAATGAAAATCGCAACGAGATATGAGAATCGCAACGCGGAAATGACTATCGTACGAGAGAACG
505185 CAACGCGAATGACTATCGCG
194 CAACGCGAATGACTATCGCG
505205 A
1 A
505206 CCAGACAATC
Statistics
Matches: 212, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
213 26 0.12
214 137 0.65
215 49 0.23
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.23
Consensus pattern (213 bp):
AAAAACAATAAACATACCCAAGTTAGATATACCAAAAATTACACTGTCAAGATATCCAAAAACAA
AACAATAAACAAAATAGTAGTTTATTTGAAACTAAAATTGCAACACTATTTTTGTCTTTTGGTTG
AAATGAAAATCGCAACGAGATATGAGAATCGCAACGCGGAAATGACTATCGTACGAGAGAACGCA
ACGCGAATGACTATCGCG
Found at i:505860 original size:41 final size:41
Alignment explanation
Indices: 505801--505878 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
505791 GCGAAGTCAG
* * * *
505801 TATCGCGTTGTGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
*
505842 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
505879 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:505875 original size:20 final size:20
Alignment explanation
Indices: 505783--505875 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
505773 CGCTATGTAA
*
505783 ATCGCGTTGCGA-AGTCAGT
1 ATCGCGTTGCGATAGTAAGT
* *
505802 ATCGCGTTGTGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* ** * *
505822 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTAAGT
*
505843 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
505863 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
505876 TTTCCCAATT
Statistics
Matches: 57, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
19 11 0.19
20 33 0.58
21 13 0.23
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:505893 original size:21 final size:21
Alignment explanation
Indices: 505864--505956 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
505854 ATAGTAAGTA
505864 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
505885 TCGCTTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
505905 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
505926 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
505946 TCGCATTGCGA
1 TCGCATTGCGA
505957 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:505894 original size:41 final size:41
Alignment explanation
Indices: 505844--505956 Score: 138
Period size: 41 Copynumber: 2.8 Consensus size: 41
505834 TTTTTTATTA
505844 TCGCATTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGAT-GTAAGTATTCGCATTGCGATTTTCCCAAT
* * **
505885 TCGCTTTGCGATTTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATGTAAGTATTCGCATTGCGATTTTCCCAAT
* * **
505926 TCGCGTTGCGATTTACTTATTCGCATTGCGA
1 TCGCATTGCGATGTAAGTATTCGCATTGCGA
505957 ATTGGGAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 4 0.06
41 62 0.94
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (41 bp):
TCGCATTGCGATGTAAGTATTCGCATTGCGATTTTCCCAAT
Found at i:506655 original size:112 final size:112
Alignment explanation
Indices: 506452--507023 Score: 905
Period size: 112 Copynumber: 5.1 Consensus size: 112
506442 CGGTTTGTGC
* * * *
506452 CGATAC-TTATAAAAATATATTAATCTATAACAATATAACAGGTAAAAAAATGACAAAACTGGTC
1 CGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTC
* * **
506516 TATAAATGACAAAACAGGTAAAACGCTACCATATATATTGAAAGTGT
66 TATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAAGTGT
* ** *
506563 CGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCAGTC
1 CGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTC
506628 TATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAAGTGT
66 TATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAAGTGT
*
506675 CGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGATAAAAAAATGACAAAACCGGTC
1 CGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTC
* * *
506740 TATAAATGACAAAACAGGTAAAGCGCCACCAGATATATTGAAAGTGT
66 TATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAAGTGT
506787 CGATACTTTATAAAAAAATGTATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGG
1 CGATACTTTAT--AAAAATGTATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGG
*
506852 TCTATAAATGACAAAACATGTAAAGCGCTATCGGATATATTGAAAGTGT
64 TCTATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAAGTGT
* *
506901 CGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCAGTC
1 CGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTC
* * *
506966 TATAAATGACAAAATAGGTAAAACGCTATCGGATATGTT-AATAGTGT
66 TATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAA-AGTGT
507013 CGATACTTTAT
1 CGATACTTTAT
507024 TATAAGTATC
Statistics
Matches: 430, Mismatches: 27, Indels: 7
0.93 0.06 0.02
Matches are distributed among these distances:
111 8 0.02
112 315 0.73
114 107 0.25
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.25
Consensus pattern (112 bp):
CGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTC
TATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAAGTGT
Found at i:506912 original size:226 final size:224
Alignment explanation
Indices: 506452--507023 Score: 932
Period size: 226 Copynumber: 2.5 Consensus size: 224
506442 CGGTTTGTGC
* * * *
506452 CGATAC-TTATAAAAATATATTAATCTATAACAATATAACAGGTAAAAAAATGACAAAACTGGTC
1 CGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTC
*
506516 TATAAATGACAAAACAGGTAAAACGCTACCATATATATTGAAAGTGTCGATACTTTATAAAAATA
66 TATAAATGACAAAACAGGTAAAACGCTACCAGATATATTGAAAGTGTCGATACTTTATAAAAATA
**
506581 TATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCAGTCTATAAATGACAAAACAGG
131 TATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCAGTCTATAAATGACAAAACAGG
506646 TAAAGCGCTATCGGATATATTGAAAGTGT
196 TAAAGCGCTATCGGATATATTGAAAGTGT
*
506675 CGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGATAAAAAAATGACAAAACCGGTC
1 CGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTC
* *
506740 TATAAATGACAAAACAGGTAAAGCGCCACCAGATATATTGAAAGTGTCGATACTTTATAAAAAAA
66 TATAAATGACAAAACAGGTAAAACGCTACCAGATATATTGAAAGTGTCGATACTTTAT--AAAAA
* *
506805 TGTATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAACA
129 TATATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCAGTCTATAAATGACAAAACA
*
506870 TGTAAAGCGCTATCGGATATATTGAAAGTGT
194 GGTAAAGCGCTATCGGATATATTGAAAGTGT
* *
506901 CGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCAGTC
1 CGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTC
* * * *
506966 TATAAATGACAAAATAGGTAAAACGCTATCGGATATGTT-AATAGTGTCGATACTTTAT
66 TATAAATGACAAAACAGGTAAAACGCTACCAGATATATTGAA-AGTGTCGATACTTTAT
507024 TATAAGTATC
Statistics
Matches: 323, Mismatches: 22, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
223 6 0.02
224 108 0.33
225 2 0.01
226 207 0.64
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.25
Consensus pattern (224 bp):
CGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTC
TATAAATGACAAAACAGGTAAAACGCTACCAGATATATTGAAAGTGTCGATACTTTATAAAAATA
TATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACCAGTCTATAAATGACAAAACAGG
TAAAGCGCTATCGGATATATTGAAAGTGT
Found at i:507207 original size:182 final size:182
Alignment explanation
Indices: 506894--507349 Score: 702
Period size: 182 Copynumber: 2.5 Consensus size: 182
506884 GGATATATTG
*
506894 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * *
506959 ACCAGTCT-ATAAATGACAAAATAGGTAAAACGCTATCGGATATGTTAATAGTGTCGATACTTTA
66 ACCAGTCTCA-AAATGACAAAACAGGTAAAACGCTACCAGATATGTTAATAGTGTCGATACTTTA
* * * *
507023 TTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
130 TTATAAGTATCAACACTTTTGGAATTTAAAAGAAAAGAAGTTATAACGCCAAT
* *
507076 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATAACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * *
507141 ACCGGTCTCAAAATGACAAAACCGGTAAAGA-GCTACCAGATATGTTGAA-AGTGTCGATATTTT
66 ACCAGTCTCAAAATGACAAAACAGGTAAA-ACGCTACCAGATATGTT-AATAGTGTCGATACTTT
507204 ATTATAAGTATCAACACTTTTGGAATTTAAAAGAAAAGAAGTTATAACGCCAAT
129 ATTATAAGTATCAACACTTTTGGAATTTAAAAGAAAAGAAGTTATAACGCCAAT
* *
507258 AAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAATAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * *
507323 ATCAGTCTCGAAATGACAAAACTGGTA
66 ACCAGTCTCAAAATGACAAAACAGGTA
507350 GTAAAAAAGT
Statistics
Matches: 250, Mismatches: 21, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
182 246 0.98
183 4 0.02
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.28
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCAGTCTCAAAATGACAAAACAGGTAAAACGCTACCAGATATGTTAATAGTGTCGATACTTTAT
TATAAGTATCAACACTTTTGGAATTTAAAAGAAAAGAAGTTATAACGCCAAT
Found at i:508017 original size:23 final size:23
Alignment explanation
Indices: 507991--508038 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
507981 AAACATGTCA
* *
507991 ATATAATCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
* *
508014 ATATAAGCGTTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
508037 AT
1 AT
508039 TGTACTTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.40
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:509429 original size:24 final size:24
Alignment explanation
Indices: 509393--509501 Score: 128
Period size: 24 Copynumber: 4.5 Consensus size: 24
509383 TTAAAAAGAG
* *
509393 ATATCAGAAATCAAAATAGAATTC
1 ATATCAGAAATCATAACAGAATTC
* *
509417 ATATCAGATATCATAACAGAATCC
1 ATATCAGAAATCATAACAGAATTC
*
509441 ATACCAGAAATCATAACAGAATTC
1 ATATCAGAAATCATAACAGAATTC
* * *
509465 ATATCAGAAATCAGAACATAGTTC
1 ATATCAGAAATCATAACAGAATTC
* *
509489 AAATCGGAAATCA
1 ATATCAGAAATCA
509502 GATAAAATAT
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.23
Consensus pattern (24 bp):
ATATCAGAAATCATAACAGAATTC
Found at i:509430 original size:12 final size:11
Alignment explanation
Indices: 509410--509473 Score: 56
Period size: 12 Copynumber: 5.4 Consensus size: 11
509400 AAATCAAAAT
*
509410 AGAATTCATATC
1 AGAA-TCATAAC
509422 AGATATCATAAC
1 AGA-ATCATAAC
*
509434 AGAATCCATACC
1 AGAAT-CATAAC
509446 AGAAATCATAAC
1 AG-AATCATAAC
*
509458 AGAATTCATATC
1 AGAA-TCATAAC
509470 AGAA
1 AGAA
509474 ATCAGAACAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
11 4 0.09
12 36 0.82
13 4 0.09
ACGTcount: A:0.48, C:0.19, G:0.09, T:0.23
Consensus pattern (11 bp):
AGAATCATAAC
Found at i:511881 original size:14 final size:14
Alignment explanation
Indices: 511864--511890 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
511854 ATCCAGTCGG
511864 CTCGGCTCAAACGA
1 CTCGGCTCAAACGA
511878 CTCGGCTCAAACG
1 CTCGGCTCAAACG
511891 GCTCCCCAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.37, G:0.22, T:0.15
Consensus pattern (14 bp):
CTCGGCTCAAACGA
Found at i:513607 original size:17 final size:17
Alignment explanation
Indices: 513585--513636 Score: 104
Period size: 17 Copynumber: 3.1 Consensus size: 17
513575 ACAGAGCCTT
513585 TGAATCATTCAGACCAC
1 TGAATCATTCAGACCAC
513602 TGAATCATTCAGACCAC
1 TGAATCATTCAGACCAC
513619 TGAATCATTCAGACCAC
1 TGAATCATTCAGACCAC
513636 T
1 T
513637 CATTTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.25
Consensus pattern (17 bp):
TGAATCATTCAGACCAC
Found at i:514873 original size:29 final size:29
Alignment explanation
Indices: 514831--514897 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
514821 CAATGAACTT
* * *
514831 AATAAAGTAGTACCCTATTTATGTATTAA
1 AATAAAGCACTACCCTATTCATGTATTAA
514860 AATAAAGCACTACCCTATTCATGTATTAA
1 AATAAAGCACTACCCTATTCATGTATTAA
514889 AATAAAGCA
1 AATAAAGCA
514898 GTATCATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (29 bp):
AATAAAGCACTACCCTATTCATGTATTAA
Found at i:517746 original size:2 final size:2
Alignment explanation
Indices: 517739--517784 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
517729 AGCAAGCAAC
517739 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
517781 TA TA
1 TA TA
517785 AAAAGAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.