Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004861.1 Hibiscus syriacus cultivar Beakdansim tig00010967_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: 131178
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1029 original size:15 final size:15
Alignment explanation
Indices: 1011--1039 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1001 GGTTGTATGG
1011 GGGATGACGATGAGA
1 GGGATGACGATGAGA
1026 GGGATGACGATGAG
1 GGGATGACGATGAG
1040 GAAAACAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.48, T:0.14
Consensus pattern (15 bp):
GGGATGACGATGAGA
Found at i:1214 original size:33 final size:33
Alignment explanation
Indices: 1177--1243 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1167 AAATAGATGG
*
1177 AGTGGTGAAAGAAGTTGATGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1210 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1243 A
1 A
1244 CTTAAGAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.46, T:0.25
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
Found at i:3011 original size:19 final size:19
Alignment explanation
Indices: 2987--3035 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
2977 AATGTAGAGT
2987 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
3006 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
3025 TAATTTTGTAT
1 TAATTTTGTAT
3036 TTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:4344 original size:393 final size:388
Alignment explanation
Indices: 3324--4435 Score: 1173
Period size: 393 Copynumber: 2.9 Consensus size: 388
3314 GTAAGCAGAT
* *
3324 GTGTCGATACATTTAAAAAGTATCGATCCCAAAAACATCGAAACCTATAATTATAATGTAATAGG
1 GTGTCGATACATTTAAAAAGTATCGAT-CCAGAAACATCGAAACCCATAATTATAATGTAATAGG
* * *
3389 TAATTTTGTAATATAACCGGTATAAATATACCTGTTTTATGTGAGAATAGGTCTACATAATGTAT
65 TAATTTTGTAATGTAACC-ATATAAATATACCTGTTTTATGTGAGAATAGGTCTA-A-AATATAT
* *
3454 CGACACTTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGCC--------C-CTCA-TA
127 CGACAC-TTTGGAATTGGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAGGTGCACCCATTA
* * *
3509 AGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAATATCGAAACCCATAATTATAATGTAAT
191 AGTGTCGATACATTTTTAAAAAGTATCG-TCCCAAAAACATCGAAACCCATAATTATAATGTAAT
* * *
3574 AGGTAAATTTACAATGTAACC-G-A-AACTATACCGATTTTATGAGAGAATA-G-T-C-TAATGT
255 AGGTAAATTTATAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGCTACATAATGT
** * * * *
3632 ATCG-C-C-TTGGAATTTGTGTCGATACTGTTTGTCCAGAAGGAATGCCCAAAAGGGTGTACCCA
320 ATCGACACTTTTTAATTTGTGTCGATACTGTTTGTCCAGAAGGAATACCAAAAAGGGTGCAACCA
3694 TAAA
385 TAAA
* * *
3698 GTGTCGATACATTTTTTAAAAGTGTCGATCCAGAGACATCGAAACCCATAATTATAATGTAATAG
1 GTGTCGATACA--TTTAAAAAGTATCGATCCAGAAACATCGAAACCCATAATTATAATGTAATAG
* * * *
3763 GTAATTTTGTAATGTAACCAGTATAAATATATCAGTTTTATATGAGAATAGGTC-----TACATC
64 GTAATTTTGTAATGTAACCA-TATAAATATACCTGTTTTATGTGAGAATAGGTCTAAAATATATC
* * * * *
3823 GTACA-TTT-GAAATGGTGTCGATACTTTTCGTCCAGAATGAATGCCCAAAATGGTGAACGCATA
128 G-ACACTTTGGAATTGGTGTCGATACTTTTTGTCCAGAATGAATG-CCAAAA-GGTGCACCCATT
* *
3886 AAGTGTCGATACATTTTTAAAAAGTGTCGGTCCCAAAGACATCGAAACCCATAATTATAATGTAA
190 AAGTGTCGATACATTTTTAAAAAGTATC-GTCCCAAAAACATCGAAACCCATAATTATAATGTAA
* * * * *
3951 TAGGTAATTTTTTAATGTAACCGGTATAAATATACTGGTTTTATGTGAGCATAGGCCTACATAAT
254 TAGGTAAATTTATAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGG-CTACATAAT
* * * *
4016 GTATCGACACTTTTTAATTTTGTGTCGATACAT-TTTTTCCATAATGAATTACCAAAAAAATGGT
318 GTATCGACACTTTTTAA-TTTGTGTCGATAC-TGTTTGTCCAGAAGGAA-TACC--AAAAAGGGT
*
4080 GCAAGCATAAA
378 GCAACCATAAA
*
4091 GTGTCGATACATTATAAAAAGTATCGATCCAGAAACATCGAAACCCATGATTATAATGTAATA-G
1 GTGTCGATACATT-TAAAAAGTATCGATCCAGAAACATCGAAACCCATAATTATAATGTAATAGG
* * *
4155 TAATTTT-CAATGTAACCATAT-AA-ATA-CTGGTTTATGCGAGAATAGGTCTAGAAAATATATC
65 TAATTTTGTAATGTAACCATATAAATATACCTGTTTTATGTGAGAATAGGTCT--AAAATATATC
** * *
4216 GACACTTCTGGAATTTATGTCAATACTTTTTGTCCAGAAGGAATGCCAAAAGGGTGCACCCATTA
128 GACACTT-TGGAATTGGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAA-GGTGCACCCATTA
*
4281 AGTGTCGATACATTTTT-AAAAG-ATTCAGTCCCAAAAACATCGAAACCGATAATTATAATGTAA
191 AGTGTCGATACATTTTTAAAAAGTA-TC-GTCCCAAAAACATCGAAACCCATAATTATAATGTAA
* * * * *
4344 TAGGTAAATTTCTAATGTAACTGGTATAAATATTCCAGTTTTATGAGAAAATAGG-TCAGCATAA
254 TAGGTAAATTTATAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGCT-A-CATAA
* *
4408 -GTATCGACAATTGTTAAATTTGTGTCGA
317 TGTATCGACACTT-TTTAATTTGTGTCGA
4436 CACCATTTAA
Statistics
Matches: 613, Mismatches: 77, Indels: 78
0.80 0.10 0.10
Matches are distributed among these distances:
366 32 0.05
367 5 0.01
368 5 0.01
369 3 0.00
374 11 0.02
375 81 0.13
376 14 0.02
377 3 0.00
378 77 0.13
379 2 0.00
380 1 0.00
381 21 0.03
382 1 0.00
384 1 0.00
385 1 0.00
386 28 0.05
387 4 0.01
388 3 0.00
389 7 0.01
390 35 0.06
391 15 0.02
392 70 0.11
393 130 0.21
394 34 0.06
395 29 0.05
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (388 bp):
GTGTCGATACATTTAAAAAGTATCGATCCAGAAACATCGAAACCCATAATTATAATGTAATAGGT
AATTTTGTAATGTAACCATATAAATATACCTGTTTTATGTGAGAATAGGTCTAAAATATATCGAC
ACTTTGGAATTGGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAGGTGCACCCATTAAGTGT
CGATACATTTTTAAAAAGTATCGTCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAA
ATTTATAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGCTACATAATGTATCGAC
ACTTTTTAATTTGTGTCGATACTGTTTGTCCAGAAGGAATACCAAAAAGGGTGCAACCATAAA
Found at i:7272 original size:18 final size:18
Alignment explanation
Indices: 7251--7287 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7241 GTAATTGGAG
7251 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
7269 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
7287 T
1 T
7288 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:7294 original size:24 final size:24
Alignment explanation
Indices: 7243--7295 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
7233 TTTCATATGT
* * *
7243 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
7267 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
7291 AATTT
1 AATTT
7296 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:7893 original size:199 final size:195
Alignment explanation
Indices: 7522--8280 Score: 983
Period size: 199 Copynumber: 3.8 Consensus size: 195
7512 TAAAGTTTCC
* *
7522 CATAAAGTGTGGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCTAAAAAACATCGAAACCGAAAATTATAAT
* * * * *
7587 GTAATAGGTAAATTTACAATGTGACCGATATAAATATACCTATTTTATGAGCAAATAGGTCAGCA
66 GTAATAGGTAAATTTACAATGTAACCAATATAAATATACCGATTTTATGAGAAAATAGGTCAACA
* * ** * * * *
7652 TAAAGTATCGACACCTTTTAAATTTGTGTCGATACTTTTTGTCTGAGCCTTTGCTCAATGAGCTT
131 TAATGTATCGACA-CTTTTAAATTTGTGTCGATACATTTTGTCT-AGAATTTGC-AAACG-GGTA
7717 CACG
192 CACG
*
7721 CATAAAAGTGTCGATACATTTA-AAATTA-TATCGATCTAAAAAACATCGAAACCGAAAATTATA
1 CAT-AAAGTGTCGATACATTTATAAA-AAGTATCGATCTAAAAAACATCGAAACCGAAAATTATA
* *
7784 ATGTAATAGGTAAATATACAATGTAACCAATATAAATATACCGGTTTTATGAGAAAATAGGT-AT
64 ATGTAATAGGTAAATTTACAATGTAACCAATATAAATATACCGATTTTATGAGAAAATAGGTCA-
7848 ACATAATGTATCGACACTGTTTAAATTTGTGTCGATACATTTTGTCCATAATGAATTT-CAAACG
128 ACATAATGTATCGACACT-TTTAAATTTGTGTCGATACATTTTGT-C-T-A-GAATTTGCAAAC-
*
7912 GGGTGCACG
187 GGGTACACG
* * *
7921 CATAAAGTGTCGAT--ATTTTTAAAAAGTATCGATCTCAAAAACATCGAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCTAAAAAACATCGAAACCGAAAATTATAAT
* * *
7984 GTAATAGGTAAATTTACAATGTAACCAATATAAGTATACCGATTTTATGAGAAAATAAGTGAACA
66 GTAATAGGTAAATTTACAATGTAACCAATATAAATATACCGATTTTATGAGAAAATAGGTCAACA
* *
8049 TAATGTATCGACACTTTTTCATATTTGTGTCGATACATTTTGTCTATAATTAATGCAAAACGGGT
131 TAATGTATCGACAC-TTTT-AAATTTGTGTCGATACATTTTGTCTAGAATT--TGC-AAACGGGT
8114 ACACG
191 ACACG
*
8119 CATAAAGTGTCGATACATTTATAAAAAGTATCGATC-CAAAAACATCGAAACCGAAAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCTAAAAAACATCGAAACCGAAAATTATAAT
* ** * *
8183 GTAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTTAACA
66 GTAATAGGTAAATTTACAATGTAACCAATATAAATATACCGATTTTATGAGAAAATAGGTCAACA
* * *
8248 TATTATATCGATACTTTTAAATTTGTGTCGATA
131 TAATGTATCGACACTTTTAAATTTGTGTCGATA
8281 TGTTTTTAAA
Statistics
Matches: 498, Mismatches: 43, Indels: 40
0.86 0.07 0.07
Matches are distributed among these distances:
195 4 0.01
196 1 0.00
197 21 0.04
198 145 0.29
199 270 0.54
200 49 0.10
201 4 0.01
202 4 0.01
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (195 bp):
CATAAAGTGTCGATACATTTATAAAAAGTATCGATCTAAAAAACATCGAAACCGAAAATTATAAT
GTAATAGGTAAATTTACAATGTAACCAATATAAATATACCGATTTTATGAGAAAATAGGTCAACA
TAATGTATCGACACTTTTAAATTTGTGTCGATACATTTTGTCTAGAATTTGCAAACGGGTACACG
Found at i:12405 original size:198 final size:198
Alignment explanation
Indices: 11906--12435 Score: 656
Period size: 200 Copynumber: 2.7 Consensus size: 198
11896 TGTCCAGAAT
* * *
11906 ATAAAGTGTCGATACATTTATTAAAAGTATCGACCCCAATAACATCAAAACCGATAATTATAATG
1 ATAAAGTGTCGATACATTTA-TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATG
* * *
11971 TAATAGGTAAATTTACAATGCAACTGGTATAAATATATCAGTTTTATAAGAAAATAGGTCAACAT
65 TAATAGGTAAATTTACAATGTAAC-AGTATAAATATATCGGTTTTATAAGAAAATAGGTCAACAT
* * * * * *
12036 AAAGTATCGACACTATTTAAATTTGTGTCGATACTTTTTGTCCATAATGAATGTCAAATGGGGTG
129 AAAGTATCGACACTATTTAAATTTATGTCGATACTCTTTATCCAGAATGAATGCCAAATGAGGTG
12101 CACGA
194 CACGA
* *
12106 ATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCACAAACATCGAAACCGATAATTACAATG
1 ATAAAGTGTCGATACATTTA-TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATG
* * * * * *
12171 TGATAGGTAAATTTACAATGTACCCAATAGAAATATACCGGTTTTATGAGAAAATAGGTCTAA-A
65 TAATAGGTAAATTTACAATGTA-ACAGTATAAATATATCGGTTTTATAAGAAAATAGGTC-AACA
* * * * *
12235 TAATGTATCGACACTTTTTAAGTTTATGTCGATAC-CTTTATCCAGAATGAATGCCCAGTGAGGT
128 TAAAGTATCGACACTATTTAAATTTATGTCGATACTCTTTATCCAGAATGAATGCCAAATGAGGT
*
12299 GCA-TA
193 GCACGA
* *
12304 CATAAAGTGTCGATACATTTA-AAATTGTATCGATCCAAAAAACATCGAAACCGATAATTATAAT
1 -ATAAAGTGTCGATACATTTATAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * * *
12368 GTAATAGGTAAATTTGCAATGTTATCAGTATAAATATATCGG-TTTACTTAGAAAATAGGTCAAT
64 GTAATAGGTAAATTTACAATG-TAACAGTATAAATATATCGGTTTTA-TAAGAAAATAGGTCAAC
12432 ATAA
127 ATAA
12436 GCGCTACCTA
Statistics
Matches: 286, Mismatches: 37, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
197 9 0.03
198 86 0.30
199 47 0.16
200 141 0.49
201 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (198 bp):
ATAAAGTGTCGATACATTTATAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGT
AATAGGTAAATTTACAATGTAACAGTATAAATATATCGGTTTTATAAGAAAATAGGTCAACATAA
AGTATCGACACTATTTAAATTTATGTCGATACTCTTTATCCAGAATGAATGCCAAATGAGGTGCA
CGA
Found at i:12525 original size:87 final size:87
Alignment explanation
Indices: 12430--12592 Score: 283
Period size: 87 Copynumber: 1.9 Consensus size: 87
12420 AAATAGGTCA
* *
12430 ATATAAGCGCTACCTATTACATTATATAAGTGCTACCTAATA-TGTTATTGTACTTGATAATATT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAA-AGTGTTATTGCACTTGATAATATT
12494 TCCGGTTAAATGCCTATTTTATT
65 TCCGGTTAAATGCCTATTTTATT
12517 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAAAGTGTTATTGCACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAAAGTGTTATTGCACTTGATAATATTT
*
12582 TCGGTTAAATG
66 CCGGTTAAATG
12593 ATATAACATA
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
86 1 0.01
87 71 0.99
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAAAGTGTTATTGCACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:16791 original size:20 final size:20
Alignment explanation
Indices: 16766--16807 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
16756 AAATTTGACA
16766 CCAAAATAAATATTATAACT
1 CCAAAATAAATATTATAACT
* *
16786 CCAAAATAAATTTTCTAACT
1 CCAAAATAAATATTATAACT
16806 CC
1 CC
16808 GCACTATGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (20 bp):
CCAAAATAAATATTATAACT
Found at i:18732 original size:2 final size:2
Alignment explanation
Indices: 18727--18759 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
18717 ATATTTCTGT
*
18727 TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18760 GCAGTTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19421 original size:32 final size:31
Alignment explanation
Indices: 19354--19427 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
19344 ATTAGGCTAC
19354 AAAT-AAA-ATATATTTTTAAGTAAAGACAA
1 AAATAAAATATATATTTTTAAGTAAAGACAA
* * *
19383 AGATAAAAATATATATTTTTATATTAAA-ATAA
1 AAAT-AAAATATATATTTTTA-AGTAAAGACAA
19415 AAATAAAATATAT
1 AAATAAAATATAT
19428 TAAAAATTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 3 0.08
31 12 0.32
32 17 0.46
33 5 0.14
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.35
Consensus pattern (31 bp):
AAATAAAATATATATTTTTAAGTAAAGACAA
Found at i:19751 original size:2 final size:2
Alignment explanation
Indices: 19746--19782 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
19736 GTGTGAAATA
19746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19783 AGAGTTTGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21261 original size:20 final size:20
Alignment explanation
Indices: 21236--21365 Score: 120
Period size: 20 Copynumber: 6.5 Consensus size: 20
21226 AATTTGGAAA
*
21236 TTTCGCAATACGAATTTCTT
1 TTTCGCAACACGAATTTCTT
21256 TTTCGCAACACGAATTTCTT
1 TTTCGCAACACGAATTTCTT
* *
21276 TTTTGCAACTCG-ATTT-TT
1 TTTCGCAACACGAATTTCTT
* * *
21294 AAATTCGCAACACGAGTTTCCT
1 --TTTCGCAACACGAATTTCTT
* * *
21316 TTTCGCAACTCGATTTTCTA
1 TTTCGCAACACGAATTTCTT
* * *
21336 ATTCGCAACACGAGTTTCCT
1 TTTCGCAACACGAATTTCTT
21356 TTTCGCAACA
1 TTTCGCAACA
21366 AGATTTTCTA
Statistics
Matches: 87, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
18 2 0.02
19 4 0.05
20 77 0.89
21 3 0.03
22 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.39
Consensus pattern (20 bp):
TTTCGCAACACGAATTTCTT
Found at i:21264 original size:62 final size:60
Alignment explanation
Indices: 21195--21324 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 60
21185 AAATTTGGAA
* *
21195 TTCGCAACATAGAA-GTCTAATTTGCAACTCGAATTTGGAAATTTCGCAATACGAATTTCTTT
1 TTCGCAACA-AGAATGTCTAATTTGCAACTCG-ATTTGGAAA-TTCGCAACACGAATTTCCTT
* * ** ** *
21257 TTCGCAACACGAATTTCTTTTTTGCAACTCGATTTTTAAATTCGCAACACGAGTTTCCTT
1 TTCGCAACAAGAATGTCTAATTTGCAACTCGATTTGGAAATTCGCAACACGAATTTCCTT
21317 TTCGCAAC
1 TTCGCAAC
21325 TCGATTTTCT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
60 25 0.43
61 10 0.17
62 23 0.40
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (60 bp):
TTCGCAACAAGAATGTCTAATTTGCAACTCGATTTGGAAATTCGCAACACGAATTTCCTT
Found at i:21306 original size:40 final size:40
Alignment explanation
Indices: 21257--21430 Score: 197
Period size: 40 Copynumber: 4.2 Consensus size: 40
21247 GAATTTCTTT
* * *
21257 TTCGCAACACGAATTTCTTTTTTGCAACTCGATTTT-TAAA
1 TTCGCAACACGAGTTTCCTTTTCGCAACTCGATTTTCT-AA
21297 TTCGCAACACGAGTTTCCTTTTCGCAACTCGATTTTCTAA
1 TTCGCAACACGAGTTTCCTTTTCGCAACTCGATTTTCTAA
**
21337 TTCGCAACACGAGTTTCCTTTTCGCAACAAGATTTTCTAA
1 TTCGCAACACGAGTTTCCTTTTCGCAACTCGATTTTCTAA
* ** *
21377 TTTGCAATGCGAGTTTCAATTTCGTTTTCGCAACTCGATTTTCGAA
1 TTCGCAACACGAGTTTC-----C-TTTTCGCAACTCGATTTTCTAA
21423 TTCGCAAC
1 TTCGCAAC
21431 GCGAATTAAA
Statistics
Matches: 114, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
40 87 0.76
41 1 0.01
45 1 0.01
46 25 0.22
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.39
Consensus pattern (40 bp):
TTCGCAACACGAGTTTCCTTTTCGCAACTCGATTTTCTAA
Found at i:21344 original size:60 final size:62
Alignment explanation
Indices: 21210--21344 Score: 166
Period size: 60 Copynumber: 2.2 Consensus size: 62
21200 AACATAGAAG
* *
21210 TCTAATTTGCAACTCGAATTTGGAAATTTCGCAATACGAATTTCTTTTTCGCAACACGAATT
1 TCTAATTTGCAACTCGAATTTGGAAATTTCGCAACACGAATTTCCTTTTCGCAACACGAATT
** ** * * *
21272 TCTTTTTTGCAACTCG-ATTTTTAAA-TTCGCAACACGAGTTTCCTTTTCGCAACTCGATTT
1 TCTAATTTGCAACTCGAATTTGGAAATTTCGCAACACGAATTTCCTTTTCGCAACACGAATT
*
21332 TCTAATTCGCAAC
1 TCTAATTTGCAAC
21345 ACGAGTTTCC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 40 0.66
61 7 0.11
62 14 0.23
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (62 bp):
TCTAATTTGCAACTCGAATTTGGAAATTTCGCAACACGAATTTCCTTTTCGCAACACGAATT
Found at i:21383 original size:20 final size:20
Alignment explanation
Indices: 21327--21383 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
21317 TTCGCAACTC
* *
21327 GATTTTCTAATTCGCAACAC
1 GATTTTCTAATTTGCAACAA
*
21347 GAGTTTCCT--TTTCGCAACAA
1 GA-TTTTCTAATTT-GCAACAA
21367 GATTTTCTAATTTGCAA
1 GATTTTCTAATTTGCAA
21384 TGCGAGTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
19 7 0.24
20 14 0.48
21 8 0.28
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (20 bp):
GATTTTCTAATTTGCAACAA
Found at i:21587 original size:22 final size:22
Alignment explanation
Indices: 21562--21609 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
21552 TCTCTCACTC
*
21562 TCTCCGGCGACATCAGTCCCAA
1 TCTCCGACGACATCAGTCCCAA
* *
21584 TCTCCGACGACATCCGTCCCCA
1 TCTCCGACGACATCAGTCCCAA
21606 TCTC
1 TCTC
21610 TAATCTTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.46, G:0.15, T:0.21
Consensus pattern (22 bp):
TCTCCGACGACATCAGTCCCAA
Found at i:29878 original size:20 final size:20
Alignment explanation
Indices: 29853--29916 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
29843 ACAACTCGAA
29853 TTTCATTTTCGAGTTGCGAT
1 TTTCATTTTCGAGTTGCGAT
* * * *
29873 TTTCATTTTCGTGTTACAAA
1 TTTCATTTTCGAGTTGCGAT
29893 TTTCATTTTCGAGTTGCGAT
1 TTTCATTTTCGAGTTGCGAT
29913 TTTC
1 TTTC
29917 GTGTTGCGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.16, G:0.16, T:0.52
Consensus pattern (20 bp):
TTTCATTTTCGAGTTGCGAT
Found at i:29937 original size:34 final size:34
Alignment explanation
Indices: 29877--29945 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
29867 TGCGATTTTC
*
29877 ATTTTCGTGTTACAAATTTCATTTTCGAGTTGCG
1 ATTTTCGTGTTACAAATTTCATTTTCGAATTGCG
* * *
29911 ATTTTCGTGTTGCGAATTT-GTGTTTCGAATTGCG
1 ATTTTCGTGTTACAAATTTCAT-TTTCGAATTGCG
29945 A
1 A
29946 ATTCGATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 1 0.03
34 29 0.97
ACGTcount: A:0.19, C:0.13, G:0.22, T:0.46
Consensus pattern (34 bp):
ATTTTCGTGTTACAAATTTCATTTTCGAATTGCG
Found at i:29937 original size:54 final size:54
Alignment explanation
Indices: 29857--29979 Score: 135
Period size: 54 Copynumber: 2.3 Consensus size: 54
29847 CTCGAATTTC
* **
29857 ATTTTCGAGTTGCGATTTTCATTTTCGTGTTACAAATTTC-ATTTTCGAGTTGCG
1 ATTTTCGAGTTGCGAATTTCATTTTCGAATTACAAA-TTCGATTTTCGAGTTGCG
* * * *
29911 ATTTTCGTGTTGCGAATTT-GTGTTTCGAATTGCGAATTCGATTTTCGAGTTGCG
1 ATTTTCGAGTTGCGAATTTCAT-TTTCGAATTACAAATTCGATTTTCGAGTTGCG
*
29965 AATTT-GAGTTGCGAA
1 ATTTTCGAGTTGCGAA
29980 AAAGTTTAGA
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
53 13 0.22
54 45 0.78
ACGTcount: A:0.20, C:0.13, G:0.23, T:0.45
Consensus pattern (54 bp):
ATTTTCGAGTTGCGAATTTCATTTTCGAATTACAAATTCGATTTTCGAGTTGCG
Found at i:29943 original size:20 final size:20
Alignment explanation
Indices: 29910--29971 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
29900 TTCGAGTTGC
**
29910 GATTTTCGTGTTGCGAATTT
1 GATTTTCGAATTGCGAATTT
*
29930 G-TGTTTCGAATTGCGAATTC
1 GAT-TTTCGAATTGCGAATTT
*
29950 GATTTTCGAGTTGCGAATTT
1 GATTTTCGAATTGCGAATTT
29970 GA
1 GA
29972 GTTGCGAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.19, C:0.11, G:0.26, T:0.44
Consensus pattern (20 bp):
GATTTTCGAATTGCGAATTT
Found at i:29975 original size:13 final size:13
Alignment explanation
Indices: 29903--29979 Score: 57
Period size: 13 Copynumber: 5.8 Consensus size: 13
29893 TTTCATTTTC
*
29903 GAGTTGCGATTTT
1 GAGTTGCGAATTT
*
29916 CGTGTTGCGAATTT
1 -GAGTTGCGAATTT
* * *
29930 GTGTTTCGAATTGC
1 GAGTTGCGAATT-T
* *
29944 GAATT-CGATTTT
1 GAGTTGCGAATTT
29956 CGAGTTGCGAATTT
1 -GAGTTGCGAATTT
29970 GAGTTGCGAA
1 GAGTTGCGAA
29980 AAAGTTTAGA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
13 30 0.60
14 20 0.40
ACGTcount: A:0.19, C:0.12, G:0.29, T:0.40
Consensus pattern (13 bp):
GAGTTGCGAATTT
Found at i:30400 original size:2 final size:2
Alignment explanation
Indices: 30393--30435 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
30383 CTAATATAGA
30393 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
30435 A
1 A
30436 AATGACAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34266 original size:21 final size:21
Alignment explanation
Indices: 34248--34372 Score: 103
Period size: 21 Copynumber: 6.0 Consensus size: 21
34238 ATGTGGATTT
* *
34248 TGAACGATGTGGGGTGGATCC
1 TGAACGATGAGAGGTGGATCC
*
34269 TGAATGATGAGAGGTGGATCC
1 TGAACGATGAGAGGTGGATCC
* * *
34290 TGAACGATGGGAGG-GGCCTCT
1 TGAACGATGAGAGGTGG-ATCC
* *
34311 TGAACGATGAGAGATGAATCC
1 TGAACGATGAGAGGTGGATCC
* *
34332 TGAA-GAATGGGAGGTGGACCC
1 TGAACG-ATGAGAGGTGGATCC
*
34353 TGAACAATG-GTAGGTGGATC
1 TGAACGATGAG-AGGTGGATC
34373 AGGCTTTTTC
Statistics
Matches: 81, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
20 4 0.05
21 76 0.94
22 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.38, T:0.21
Consensus pattern (21 bp):
TGAACGATGAGAGGTGGATCC
Found at i:34357 original size:42 final size:42
Alignment explanation
Indices: 34248--34357 Score: 120
Period size: 42 Copynumber: 2.6 Consensus size: 42
34238 ATGTGGATTT
* * * *
34248 TGAACGATGTGG-GGTGGATCCTGAATGATGAGAGGTGGATCC
1 TGAACGATG-GGAGGTGGACCCTGAACGATGAGAGATGAATCC
34290 TGAACGATGGGAGG-GG-CCTCTTGAACGATGAGAGATGAATCC
1 TGAACGATGGGAGGTGGACC-C-TGAACGATGAGAGATGAATCC
34332 TGAA-GAATGGGAGGTGGACCCTGAAC
1 TGAACG-ATGGGAGGTGGACCCTGAAC
34358 AATGGTAGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
40 1 0.02
41 6 0.10
42 46 0.79
43 3 0.05
44 2 0.03
ACGTcount: A:0.27, C:0.15, G:0.38, T:0.20
Consensus pattern (42 bp):
TGAACGATGGGAGGTGGACCCTGAACGATGAGAGATGAATCC
Found at i:34728 original size:21 final size:21
Alignment explanation
Indices: 34704--34915 Score: 248
Period size: 21 Copynumber: 10.1 Consensus size: 21
34694 TGAAACAATC
*
34704 TCACGTAGAGCACCTACCTCA
1 TCACGTAAAGCACCTACCTCA
**
34725 TCACGTAAAGCA-CTATTGTCA
1 TCACGTAAAGCACCTA-CCTCA
*
34746 TCACGTAAAGCACCTACATCA
1 TCACGTAAAGCACCTACCTCA
*
34767 TCACGTAAAGCACCTACATCA
1 TCACGTAAAGCACCTACCTCA
* **
34788 TCACGTAAAGAACC-ATTGTCA
1 TCACGTAAAGCACCTA-CCTCA
**
34809 TCACGTAAAGCAGTTACCTCA
1 TCACGTAAAGCACCTACCTCA
* *
34830 CCACGTAAAGCACATACCTCA
1 TCACGTAAAGCACCTACCTCA
*
34851 TCACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCTACCTCA
*
34872 TCACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCTACCTCA
* *
34893 TCACGTAAAGCACTTAACTCA
1 TCACGTAAAGCACCTACCTCA
34914 TC
1 TC
34916 CCGTGGAGGT
Statistics
Matches: 165, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
20 4 0.02
21 157 0.95
22 4 0.02
ACGTcount: A:0.35, C:0.33, G:0.12, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACCTACCTCA
Found at i:34782 original size:63 final size:63
Alignment explanation
Indices: 34704--34915 Score: 282
Period size: 63 Copynumber: 3.4 Consensus size: 63
34694 TGAAACAATC
* * *
34704 TCACGTAGAGCACCTACCTCATCACGTAAAGCACTATTGTCATCACGTAAAGCACCTACATCA
1 TCACGTAAAGCACCTACCTCATCACGTAAAGCACCATTGTCATCACGTAAAGCACCTACCTCA
* * **
34767 TCACGTAAAGCACCTACATCATCACGTAAAGAACCATTGTCATCACGTAAAGCAGTTACCTCA
1 TCACGTAAAGCACCTACCTCATCACGTAAAGCACCATTGTCATCACGTAAAGCACCTACCTCA
* * ** *
34830 CCACGTAAAGCACATACCTCATCACGTAAAGCACCGA-CCTCATCACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCTACCTCATCACGTAAAGCACC-ATTGTCATCACGTAAAGCACCTACCTCA
* *
34893 TCACGTAAAGCACTTAACTCATC
1 TCACGTAAAGCACCTACCTCATC
34916 CCGTGGAGGT
Statistics
Matches: 129, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
63 128 0.99
64 1 0.01
ACGTcount: A:0.35, C:0.33, G:0.12, T:0.20
Consensus pattern (63 bp):
TCACGTAAAGCACCTACCTCATCACGTAAAGCACCATTGTCATCACGTAAAGCACCTACCTCA
Found at i:35112 original size:42 final size:41
Alignment explanation
Indices: 35017--35179 Score: 199
Period size: 42 Copynumber: 4.0 Consensus size: 41
35007 GATGGAATAA
* *
35017 GTGATGGATTTCGGTGTCGAGGTGTAGAGTCGGCT--A-GAG
1 GTGATGGATCTCGGTGTCGAGGTGTAGAATC-GCTCGATGAG
35056 GTGATGGATCTCGGTGTCGAGGTGTAGAATCAGCTCGATGAG
1 GTGATGGATCTCGGTGTCGAGGTGTAGAATC-GCTCGATGAG
* * *
35098 GTGATGGATCTCGGTGCCGAAGTGGAGAATCGACTCGATGAG
1 GTGATGGATCTCGGTGTCGAGGTGTAGAATCG-CTCGATGAG
* *
35140 GTGATGGATCTCGGTGTCGAAGTGGAG-ATCGACTCGATGA
1 GTGATGGATCTCGGTGTCGAGGTGTAGAATCG-CTCGATGA
35180 AAAAGTAGGG
Statistics
Matches: 113, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
39 32 0.28
41 15 0.13
42 66 0.58
ACGTcount: A:0.21, C:0.14, G:0.39, T:0.25
Consensus pattern (41 bp):
GTGATGGATCTCGGTGTCGAGGTGTAGAATCGCTCGATGAG
Found at i:35351 original size:2 final size:2
Alignment explanation
Indices: 35344--35374 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35334 AGTAATAAAT
35344 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35375 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37513 original size:60 final size:60
Alignment explanation
Indices: 37415--37544 Score: 156
Period size: 60 Copynumber: 2.2 Consensus size: 60
37405 GTTTATATAT
* * * *
37415 GTGTTGCGAAATTTAAATTAACGTTGCGAATACGAAAATCGAGTTGCGAAAATAAAATTC
1 GTGTTGCGAAATTGAAATTAACGTTGCGAATACAAAAATCGAGTTGCGAAAACAAAACTC
* * *
37475 GTGTTGCGAAATTGAAACTT-GCGTTGCGAATTA-AAAAATCGAGTTTCGAAAACGAAACTC
1 GTGTTGCGAAATTGAAA-TTAACGTTGCGAA-TACAAAAATCGAGTTGCGAAAACAAAACTC
*
37535 GTGCTGCGAA
1 GTGTTGCGAA
37545 TTTAAAAATC
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
60 56 0.93
61 4 0.07
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (60 bp):
GTGTTGCGAAATTGAAATTAACGTTGCGAATACAAAAATCGAGTTGCGAAAACAAAACTC
Found at i:37525 original size:40 final size:40
Alignment explanation
Indices: 37488--37566 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
37478 TTGCGAAATT
* * * *
37488 GAAACTTGCGTTGCGAATTAAAAAATCGAGTTTCGAAAAC
1 GAAACTCGCGCTGCGAATTAAAAAATCGACTTACGAAAAC
* *
37528 GAAACTCGTGCTGCGAATTTAAAAATCGACTTACGAAAA
1 GAAACTCGCGCTGCGAATTAAAAAATCGACTTACGAAAA
37567 AGACATTCGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (40 bp):
GAAACTCGCGCTGCGAATTAAAAAATCGACTTACGAAAAC
Found at i:51423 original size:12 final size:12
Alignment explanation
Indices: 51408--51433 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
51398 GTATTTGATA
51408 TTTATAAAAAAT
1 TTTATAAAAAAT
51420 TTTATAAAAAAT
1 TTTATAAAAAAT
51432 TT
1 TT
51434 ACTAATCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TTTATAAAAAAT
Found at i:53918 original size:17 final size:17
Alignment explanation
Indices: 53896--53943 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
53886 ATTACAATAC
53896 TAACTTCAAGTCTTTAA
1 TAACTTCAAGTCTTTAA
53913 TAACTTCAAGTCTTTAA
1 TAACTTCAAGTCTTTAA
*
53930 TAACTTCAATTCTT
1 TAACTTCAAGTCTT
53944 ATGTAACATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (17 bp):
TAACTTCAAGTCTTTAA
Found at i:55931 original size:23 final size:22
Alignment explanation
Indices: 55882--55941 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 22
55872 ATAAATTGCA
55882 CCGAAGTG-CCACATA-TTTGTC
1 CCGAAG-GACCACATAGTTTGTC
55903 CCGAAGGACCACATAGTTTTGTC
1 CCGAAGGACCACATAG-TTTGTC
*
55926 CTGAAGGACCACATAG
1 CCGAAGGACCACATAG
55942 AACCCTCAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
20 1 0.03
21 13 0.37
23 21 0.60
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (22 bp):
CCGAAGGACCACATAGTTTGTC
Found at i:62960 original size:23 final size:23
Alignment explanation
Indices: 62934--62995 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
62924 CATAGTTGTT
* *
62934 CCGAATGACCATATAGGATTATC
1 CCGAAGGACCACATAGGATTATC
**
62957 CCGAAGGACCACATAGTTTTATC
1 CCGAAGGACCACATAGGATTATC
*
62980 CCGAAGAACCACATAG
1 CCGAAGGACCACATAG
62996 AACCCTCGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (23 bp):
CCGAAGGACCACATAGGATTATC
Found at i:68433 original size:24 final size:23
Alignment explanation
Indices: 68380--68437 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
68370 TTATCATGTT
*
68380 TAAAAATAAAACTTAAAATAAAA
1 TAAAAAGAAAACTTAAAATAAAA
68403 TAAAAAGGAAAACTTGAAAATAAAA
1 TAAAAA-GAAAACTT-AAAATAAAA
68428 T-AAAAGAAAA
1 TAAAAAGAAAA
68438 GAAATAACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 11 0.34
24 11 0.34
25 10 0.31
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.17
Consensus pattern (23 bp):
TAAAAAGAAAACTTAAAATAAAA
Found at i:68731 original size:13 final size:13
Alignment explanation
Indices: 68713--68738 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
68703 TGCCATGTCA
68713 GACCATGTCATGC
1 GACCATGTCATGC
68726 GACCATGTCATGC
1 GACCATGTCATGC
68739 CTAGAGTCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (13 bp):
GACCATGTCATGC
Found at i:71787 original size:22 final size:22
Alignment explanation
Indices: 71700--71797 Score: 115
Period size: 22 Copynumber: 4.5 Consensus size: 22
71690 ATGTGAAATT
* * *
71700 TGTCCCGAATGACCTATGTATT
1 TGTCCCGAAGGACCTCTGTATA
71722 TGTCCCGAAGGACCTCTGTATA
1 TGTCCCGAAGGACCTCTGTATA
*
71744 TGTCCCGAAGCACCTCTGTATA
1 TGTCCCGAAGGACCTCTGTATA
* * *
71766 TGTTCAGAAGGACCTTTGTATA
1 TGTCCCGAAGGACCTCTGTATA
* *
71788 TATCCTGAAG
1 TGTCCCGAAG
71798 CACCGTGTAG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (22 bp):
TGTCCCGAAGGACCTCTGTATA
Found at i:72012 original size:15 final size:16
Alignment explanation
Indices: 71982--72016 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
71972 TATGTTCATG
*
71982 TATACATCACATAACA
1 TATACAACACATAACA
71998 TATACAACA-ATAACA
1 TATACAACACATAACA
72013 TATA
1 TATA
72017 AACTTATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.26
Consensus pattern (16 bp):
TATACAACACATAACA
Found at i:82546 original size:29 final size:30
Alignment explanation
Indices: 82514--82580 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 30
82504 TTGCTTCAAC
*
82514 ATTAAAAGTAACA-TTTTTAT-TTTA-TATTT
1 ATTAAAA--AACATTTTTTATATTTATTATCT
*
82543 ATTATAAAAATATTTTTTATATTTATTATCT
1 ATTA-AAAAACATTTTTTATATTTATTATCT
82574 ATTAAAA
1 ATTAAAA
82581 TAATGAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
28 3 0.09
29 11 0.34
30 10 0.31
31 8 0.25
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (30 bp):
ATTAAAAAACATTTTTTATATTTATTATCT
Found at i:82569 original size:28 final size:29
Alignment explanation
Indices: 82527--82582 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
82517 AAAAGTAACA
*
82527 TTTTTATTTTATATTTAT-TATAAAAATAT
1 TTTTTATATTATA-TTATCTATAAAAATAT
*
82556 TTTTTATATT-TATTATCTATTAAAATA
1 TTTTTATATTATATTATCTATAAAAATA
82583 ATGAAATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.17
28 11 0.46
29 9 0.38
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTTTATATTATATTATCTATAAAAATAT
Found at i:82934 original size:6 final size:6
Alignment explanation
Indices: 82923--82974 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
82913 TTGACCCAAG
82923 GATGGA GATGGA GATGGA GATGGA GATGGA GATGGA GATGGA GATGGA
1 GATGGA GATGGA GATGGA GATGGA GATGGA GATGGA GATGGA GATGGA
82971 GATG
1 GATG
82975 TTGAGAGTAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.50, T:0.17
Consensus pattern (6 bp):
GATGGA
Found at i:87302 original size:13 final size:13
Alignment explanation
Indices: 87279--87313 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
87269 ATTATCACAA
87279 AACAC-CAAAAAT
1 AACACACAAAAAT
*
87291 AACATACAAAAAT
1 AACACACAAAAAT
87304 AACACACAAA
1 AACACACAAA
87314 GAAGCAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.69, C:0.23, G:0.00, T:0.09
Consensus pattern (13 bp):
AACACACAAAAAT
Found at i:88376 original size:3 final size:3
Alignment explanation
Indices: 88370--88419 Score: 64
Period size: 3 Copynumber: 15.3 Consensus size: 3
88360 CACCCCCGGG
88370 TCT TCT TCT TCT TCCT TCTT TCT TCCT TCT TCCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT T-CT TC-T TCT T-CT TCT T-CT TCT TCT TCT TCT TCT
88419 T
1 T
88420 TCGTTAGCTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
3 31 0.72
4 12 0.28
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:89281 original size:3 final size:3
Alignment explanation
Indices: 89273--89316 Score: 52
Period size: 3 Copynumber: 13.3 Consensus size: 3
89263 CTTAAAACTT
89273 AGA AGA AGA AGA AGAA AGA AGAA AGAA AGA AGGA AGA AGA AGA A
1 AGA AGA AGA AGA AG-A AGA AG-A AG-A AGA A-GA AGA AGA AGA A
89317 AACCTGGGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 25 0.66
4 13 0.34
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:89291 original size:7 final size:7
Alignment explanation
Indices: 89275--89317 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
89265 TAAAACTTAG
89275 AAGAAG-
1 AAGAAGA
89281 AAGAAGA
1 AAGAAGA
89288 AAGAAGA
1 AAGAAGA
89295 AAGAAAGA
1 AAG-AAGA
*
89303 AGGAAG-
1 AAGAAGA
89309 AAGAAGA
1 AAGAAGA
89316 AA
1 AA
89318 ACCTGGGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 11 0.34
7 15 0.47
8 6 0.19
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:89303 original size:21 final size:21
Alignment explanation
Indices: 89278--89317 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
89268 AACTTAGAAG
89278 AAGAA-GAAGAAAGAAGAAAGA
1 AAGAAGGAAG-AAGAAGAAAGA
89299 AAGAAGGAAGAAGAAGAAA
1 AAGAAGGAAGAAGAAGAAA
89318 ACCTGGGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (21 bp):
AAGAAGGAAGAAGAAGAAAGA
Found at i:95104 original size:16 final size:16
Alignment explanation
Indices: 95058--95107 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
95048 AAATAATGCA
*
95058 TTTAGTACCTAAAC-T
1 TTTAGTACTTAAACTT
* * *
95073 GTTAGT-TTTAACCTT
1 TTTAGTACTTAAACTT
95088 TTTAGTACTTAAACTT
1 TTTAGTACTTAAACTT
95104 TTTA
1 TTTA
95108 ATTTTTTAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
14 4 0.15
15 11 0.42
16 11 0.42
ACGTcount: A:0.28, C:0.14, G:0.08, T:0.50
Consensus pattern (16 bp):
TTTAGTACTTAAACTT
Found at i:99884 original size:2 final size:2
Alignment explanation
Indices: 99877--99914 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
99867 ACTTTGTATG
99877 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
99915 TGTATAAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:100162 original size:6 final size:6
Alignment explanation
Indices: 100151--100179 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
100141 TCTCCCTCTA
100151 ATTAAG ATTAAG ATTAAG ATTAAG ATTAA
1 ATTAAG ATTAAG ATTAAG ATTAAG ATTAA
100180 ATTTAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
ATTAAG
Found at i:100941 original size:22 final size:20
Alignment explanation
Indices: 100881--100942 Score: 52
Period size: 22 Copynumber: 2.9 Consensus size: 20
100871 AGGGAAAAAT
* *
100881 ATAAAAAATGTTAAAAGAGA
1 ATAAAAAAGGTTAAAAAAGA
* *
100901 ATAAAAAATGCTTTTAAAAAGA
1 ATAAAAAA-G-GTTAAAAAAGA
100923 ATTTAAAAAAGGTTAAAAAA
1 A--TAAAAAAGGTTAAAAAA
100943 TAAAATAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
20 8 0.25
22 16 0.50
23 1 0.03
24 7 0.22
ACGTcount: A:0.63, C:0.02, G:0.11, T:0.24
Consensus pattern (20 bp):
ATAAAAAAGGTTAAAAAAGA
Found at i:102021 original size:13 final size:14
Alignment explanation
Indices: 102005--102058 Score: 62
Period size: 13 Copynumber: 4.1 Consensus size: 14
101995 TTGGACCTAA
102005 AAATGAAAATAAA-
1 AAATGAAAATAAAT
102018 AAAT-AAAATAAAT
1 AAATGAAAATAAAT
*
102031 AAGTG-AAATAAAT
1 AAATGAAAATAAAT
*
102044 AAAT-AATATAAAT
1 AAATGAAAATAAAT
102057 AA
1 AA
102059 CTAACTATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
12 8 0.23
13 27 0.77
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (14 bp):
AAATGAAAATAAAT
Found at i:102032 original size:4 final size:4
Alignment explanation
Indices: 102011--102058 Score: 53
Period size: 4 Copynumber: 11.5 Consensus size: 4
102001 CTAAAAATGA
*
102011 AAAT AAA- AAAT AAAAT AAAT AAGT GAAAT AAAT AAAT AATAT AAAT AA
1 AAAT AAAT AAAT -AAAT AAAT AAAT -AAAT AAAT AAAT AA-AT AAAT AA
102059 CTAACTATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
3 3 0.08
4 24 0.63
5 11 0.29
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:102157 original size:2 final size:2
Alignment explanation
Indices: 102146--102197 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
102136 TTTTCGAAAC
102146 TA TA -A 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
102187 TA TA TA TA TA T
1 TA TA TA TA TA T
102198 GTTTTCACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:102227 original size:36 final size:37
Alignment explanation
Indices: 102185--102331 Score: 173
Period size: 36 Copynumber: 4.1 Consensus size: 37
102175 TATATATATA
* *
102185 TATATATATATATGTTTTCACAAATTATTTTTCAAAAC
1 TATATA-ATATATATTTTCACAAATTAGTTTTCAAAAC
* *
102223 TATAT-A-ATATATTTTCA-AAAATCGTTTTCAAAAC
1 TATATAATATATATTTTCACAAATTAGTTTTCAAAAC
*
102257 TATATAATATATATTTT--CAAATATCGTTTTCAAAAC
1 TATATAATATATATTTTCACAAAT-TAGTTTTCAAAAC
*
102293 TATATAATATAT-TTTTCAAAAATT-GTTTTCAAAAC
1 TATATAATATATATTTTCACAAATTAGTTTTCAAAAC
102328 TATA
1 TATA
102332 CATGCTTTCA
Statistics
Matches: 97, Mismatches: 6, Indels: 15
0.82 0.05 0.13
Matches are distributed among these distances:
34 19 0.20
35 33 0.34
36 36 0.37
37 4 0.04
38 5 0.05
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (37 bp):
TATATAATATATATTTTCACAAATTAGTTTTCAAAAC
Found at i:102404 original size:38 final size:36
Alignment explanation
Indices: 102218--102416 Score: 112
Period size: 36 Copynumber: 5.6 Consensus size: 36
102208 ATTATTTTTC
* * *
102218 AAAACTATATAATATATTTTCAAAAATCG-TTTTC-A
1 AAAATTATATTATAT-TTTTCAAAAACCGATTTTCTA
* * * *
102253 AAACTATATAATATATATTTTCAAATATCG-TTTTC-A
1 AAAAT-TATATTATAT-TTTTCAAAAACCGATTTTCTA
* * **
102289 AAACTATATAATATATTTTTCAAAAATTG-TTTTC--
1 AAAAT-TATATTATATTTTTCAAAAACCGATTTTCTA
* * ** * *
102323 AAAACTATA-CAT-GCTTTCAAAAACTGATTTTTTA
1 AAAATTATATTATATTTTTCAAAAACCGATTTTCTA
102357 AAAAGTATATATTATATGTTTTCAAAAACCG-TTTTCTA
1 AAAA-T-TATATTATAT-TTTTCAAAAACCGATTTTCTA
102395 AAAATTATATTATATTTTTCAA
1 AAAATTATATTATATTTTTCAA
102417 GAACTATACT
Statistics
Matches: 135, Mismatches: 20, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
31 11 0.08
32 6 0.04
33 4 0.03
34 7 0.05
35 26 0.19
36 57 0.42
37 3 0.02
38 10 0.07
39 11 0.08
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.43
Consensus pattern (36 bp):
AAAATTATATTATATTTTTCAAAAACCGATTTTCTA
Found at i:103315 original size:201 final size:200
Alignment explanation
Indices: 102741--103317 Score: 719
Period size: 201 Copynumber: 2.9 Consensus size: 200
102731 AAGGTGGCTT
* * * * * ** *
102741 CTTGTTGCCAAATCGTAGTCAACCTTGGTCTTCTTCTCGGTTTAAAGACCTCAGTTTGAAAATTC
1 CTTGTTGCTAAATCGCAGCCAACCTAGGTCTTCTTCTTGACTTAAAGACCTCAGTTT-AAACTTC
** *
102806 AACCGGAAAGTAGTTCCTCGATGCTACCATGTGGTTGATATGCCCTCAAGCTGAATGGAATCGAA
65 AACCGGAAAGTAGTTCCTCGATGCTACCATGTGGTTGATA-GTTCTCGAGCTGAATGGAATCGAA
* * ** * * **
102871 CTCG-AAGATTTTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGTTGTGACTTAGGTTAGGA
129 CTCGAAAG-TTTTCGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCCGTAAATTAGACTAGGA
102935 GATAGTTC
193 GATAGTTC
* *
102943 CTTGTTGTTAAATCGCAACCAACCTAGGTCTTCTTCTTGACTTAAAGACCTCAGTTTAAACTTCA
1 CTTGTTGCTAAATCGCAGCCAACCTAGGTCTTCTTCTTGACTTAAAGACCTCAGTTTAAACTTCA
* * * * * * *
103008 ACTGGAAAATAGTTCCTC-ATTACTACCATGCGGTTGAT-GTTCCCTTGAGCTGAATTGAATCAA
66 ACCGGAAAGTAGTTCCTCGA-TGCTACCATGTGGTTGATAGTT--CTCGAGCTGAATGGAATCGA
* *
103071 ACTCGAAAGTTTTCGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCCGTAAATTTGACTGGGA
128 ACTCGAAAGTTTTCGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCCGTAAATTAGACTAGGA
103136 GATAGTTC
193 GATAGTTC
*
103144 CTTGTTGCTAAATCGCAGCCAACCTAGGTCTTCTTCTTGACTTAAAGACCTTAGTTTAAACTTCA
1 CTTGTTGCTAAATCGCAGCCAACCTAGGTCTTCTTCTTGACTTAAAGACCTCAGTTTAAACTTCA
* * * *
103209 ACCAGAAAGTAATTCCTCGCTGCTACCATGTGGCTGATAAGTTCTCGAGCTGAATGGAATCGAAC
66 ACCGGAAAGTAGTTCCTCGATGCTACCATGTGGTTGAT-AGTTCTCGAGCTGAATGGAATCGAAC
* * * *
103274 TCGAAAGTTTTCATTGACATATAACCCTTCTTGCATTGAGCTAT
130 TCGAAAGTTTTCGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
103318 TCTGTGAATG
Statistics
Matches: 320, Mismatches: 48, Indels: 15
0.84 0.13 0.04
Matches are distributed among these distances:
199 1 0.00
200 1 0.00
201 264 0.82
202 51 0.16
203 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (200 bp):
CTTGTTGCTAAATCGCAGCCAACCTAGGTCTTCTTCTTGACTTAAAGACCTCAGTTTAAACTTCA
ACCGGAAAGTAGTTCCTCGATGCTACCATGTGGTTGATAGTTCTCGAGCTGAATGGAATCGAACT
CGAAAGTTTTCGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCCGTAAATTAGACTAGGAGAT
AGTTC
Found at i:120595 original size:15 final size:15
Alignment explanation
Indices: 120575--120605 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
120565 CAAATTCTTT
120575 CCTTGCTATCTCTAG
1 CCTTGCTATCTCTAG
120590 CCTTGCTATCTCTAG
1 CCTTGCTATCTCTAG
120605 C
1 C
120606 TCAGAGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.35, G:0.13, T:0.39
Consensus pattern (15 bp):
CCTTGCTATCTCTAG
Found at i:124208 original size:12 final size:12
Alignment explanation
Indices: 124193--124220 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
124183 CCTAAAAACA
124193 AAAATAAATAAT
1 AAAATAAATAAT
124205 AAAATAAATAAT
1 AAAATAAATAAT
124217 AAAA
1 AAAA
124221 ATAACTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:124292 original size:36 final size:37
Alignment explanation
Indices: 124247--124469 Score: 110
Period size: 36 Copynumber: 5.9 Consensus size: 37
124237 AAAAATTATC
*
124247 ATTTTCAAAATCGCTTTTAAAAACTAT-ATAT-TATAT
1 ATTTTCAAAAT-GATTTTAAAAACTATAATATATATAT
* *
124283 ATTTTCAAAATTATTTTCAAAACTATAATATATATAT
1 ATTTTCAAAATGATTTTAAAAACTATAATATATATAT
* * * *
124320 A-TAT-ATATATG-TTTTCACAAATTATTTTTCAAAATTATATAATAT
1 ATTTTCA-AAATGATTTT-A-AAA--A---CT-ATAA-TATAT-ATAT
* *
124365 ATTTTCAAAAATCATTTTCAAAACTAT-ATA-ATATAT
1 ATTTTC-AAAATGATTTTAAAAACTATAATATATATAT
*
124401 ATTTTCAAAAATTG-TTTTCAAAACTAT-ATA-ATATAT
1 ATTTTC-AAAA-TGATTTTAAAAACTATAATATATATAT
* *
124437 A-TTTCAAAAATTATTTTCAAAACTAT-ATATATA
1 ATTTTC-AAAATGATTTTAAAAACTATAATATATA
124470 CTTTCAAAAA
Statistics
Matches: 150, Mismatches: 17, Indels: 40
0.72 0.08 0.19
Matches are distributed among these distances:
34 1 0.01
35 42 0.28
36 61 0.41
37 12 0.08
38 2 0.01
39 2 0.01
40 1 0.01
41 1 0.01
42 1 0.01
43 3 0.02
44 6 0.04
45 5 0.03
46 5 0.03
47 3 0.02
48 5 0.03
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTTCAAAATGATTTTAAAAACTATAATATATATAT
Found at i:124323 original size:48 final size:47
Alignment explanation
Indices: 124271--124366 Score: 135
Period size: 47 Copynumber: 2.1 Consensus size: 47
124261 TTTTAAAAAC
124271 TATATAT-TATATATTTTCA-AAATTA-TTTTCAAAACTATAATATATA
1 TATATATATATATATTTTCACAAATTATTTTTCAAAACTAT-ATA-ATA
* *
124317 TATATATATATATGTTTTCACAAATTATTTTTCAAAATTATATAATA
1 TATATATATATATATTTTCACAAATTATTTTTCAAAACTATATAATA
124364 TAT
1 TAT
124367 TTTCAAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
46 7 0.16
47 17 0.38
48 9 0.20
49 12 0.27
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (47 bp):
TATATATATATATATTTTCACAAATTATTTTTCAAAACTATATAATA
Found at i:124360 original size:34 final size:33
Alignment explanation
Indices: 124321--124509 Score: 207
Period size: 35 Copynumber: 5.4 Consensus size: 33
124311 TATATATATA
* * *
124321 TATATATATGTTTTCACAAATTATTTTTCAAAAT
1 TATATATATATTTTCAAAAATTA-TTTTCAAAAC
*
124355 TATATAATATATTTTCAAAAATCATTTTCAAAAC
1 TATAT-ATATATTTTCAAAAATTATTTTCAAAAC
*
124389 TATATAATATATATTTTCAAAAATTGTTTTCAAAAC
1 --TAT-ATATATATTTTCAAAAATTATTTTCAAAAC
124425 TATATAATATATATTTCAAAAATTATTTTCAAAAC
1 TATAT-ATATAT-TTTCAAAAATTATTTTCAAAAC
* ***
124460 TATATATATACTTTCAAAAACCGTTTTCTAAAAAC
1 TATATATATATTTTCAAAAATTATTTTC--AAAAC
124495 TATATATTATATTTT
1 TATATA-TATATTTT
124510 TTTTCAATAA
Statistics
Matches: 134, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
33 16 0.12
34 28 0.21
35 52 0.39
36 36 0.27
37 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (33 bp):
TATATATATATTTTCAAAAATTATTTTCAAAAC
Found at i:127394 original size:23 final size:22
Alignment explanation
Indices: 127360--127412 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 22
127350 TATTCATATG
127360 AAAGAACCGGATGAAATGATCTA
1 AAAG-ACCGGATGAAATGATCTA
*
127383 AAAGACCTGGATGAAATGATCTG
1 AAAGACC-GGATGAAATGATCTA
127406 AAAGACC
1 AAAGACC
127413 ATTGAGATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 3 0.11
23 25 0.89
ACGTcount: A:0.45, C:0.15, G:0.23, T:0.17
Consensus pattern (22 bp):
AAAGACCGGATGAAATGATCTA
Found at i:128736 original size:32 final size:31
Alignment explanation
Indices: 128676--128782 Score: 119
Period size: 32 Copynumber: 3.4 Consensus size: 31
128666 TCCTTACAGA
128676 CCTAAGGTGA-TCA-TTGGGTAGGCTCTTAGGC
1 CCTAAGGT-ACTCACTT-GGTAGGCTCTTAGGC
* *
128707 CCTAAGTTACTCACTTGGATAGGTTCTTAGGC
1 CCTAAGGTACTCACTTGG-TAGGCTCTTAGGC
* * *
128739 CCCAAGGTACTCCCTTAGGTAGGCTCTAAGGC
1 CCTAAGGTACTCACTT-GGTAGGCTCTTAGGC
128771 CCTAAGGTACTC
1 CCTAAGGTACTC
128783 CATTGTGTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
30 1 0.02
31 12 0.19
32 49 0.77
33 2 0.03
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.28
Consensus pattern (31 bp):
CCTAAGGTACTCACTTGGTAGGCTCTTAGGC
Found at i:128783 original size:32 final size:31
Alignment explanation
Indices: 128692--128783 Score: 121
Period size: 32 Copynumber: 2.9 Consensus size: 31
128682 GTGATCATTG
* *
128692 GGTAGGCTCTTAGGCCCTAAGTTACTCACTT
1 GGTAGGCTCTTAGGCCCTAAGGTACTCCCTT
* *
128723 GGATAGGTTCTTAGGCCCCAAGGTACTCCCTT
1 GG-TAGGCTCTTAGGCCCTAAGGTACTCCCTT
*
128755 AGGTAGGCTCTAAGGCCCTAAGGTACTCC
1 -GGTAGGCTCTTAGGCCCTAAGGTACTCC
128784 ATTGTGTATG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 2 0.04
32 48 0.92
33 2 0.04
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (31 bp):
GGTAGGCTCTTAGGCCCTAAGGTACTCCCTT
Found at i:128801 original size:32 final size:32
Alignment explanation
Indices: 128687--128803 Score: 96
Period size: 32 Copynumber: 3.7 Consensus size: 32
128677 CTAAGGTGAT
* * * *
128687 CATTGGGTAGGCTCTTAGGCCCTAAGTTACT-
1 CATTAGGTAGGCTCTAAGGCCCCAAGGTACTC
* *
128718 CACTT-GGATAGGTTCTTAGGCCCCAAGGTACTC
1 CA-TTAGG-TAGGCTCTAAGGCCCCAAGGTACTC
* *
128751 CCTTAGGTAGGCTCTAAGGCCCTAAGGTACTC
1 CATTAGGTAGGCTCTAAGGCCCCAAGGTACTC
* *
128783 CATT-GTGTATGCTTTAAGGCC
1 CATTAG-GTAGGCTCTAAGGCC
128804 TCAATGCACT
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
31 5 0.07
32 63 0.89
33 3 0.04
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (32 bp):
CATTAGGTAGGCTCTAAGGCCCCAAGGTACTC
Found at i:128803 original size:64 final size:64
Alignment explanation
Indices: 128692--128822 Score: 142
Period size: 64 Copynumber: 2.0 Consensus size: 64
128682 GTGATCATTG
* * * * *
128692 GGTAGGCTCTTAGGCCCTAAGTTACTCACTTGGATAGGTTCTTAGGCCCCAAGGTACTCCCTTA
1 GGTAGGCTCTAAGGCCCTAAGGTACTCACTTGGATAGCTTCTAAGGCCCCAAGGCACTCCCTTA
* * *
128756 GGTAGGCTCTAAGGCCCTAAGGTACTC-CATTGTG-TATGCTT-TAAGGCCTCAATGCACTCTCT
1 GGTAGGCTCTAAGGCCCTAAGGTACTCAC-TTG-GATA-GCTTCTAAGGCCCCAAGGCACTCCCT
128818 TA
63 TA
128820 GGT
1 GGT
128823 TGACTCCTAC
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
63 1 0.02
64 51 0.91
65 4 0.07
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (64 bp):
GGTAGGCTCTAAGGCCCTAAGGTACTCACTTGGATAGCTTCTAAGGCCCCAAGGCACTCCCTTA
Done.