Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009120.1 Hibiscus syriacus cultivar Beakdansim tig00112609_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: 584398
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:357013 original size:3 final size:3
Alignment explanation
Indices: 356995--357032 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
356985 TGAAGAAAGG
*
356995 GAA G-A GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
357033 TGAGGACGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:359022 original size:20 final size:20
Alignment explanation
Indices: 358981--359062 Score: 123
Period size: 20 Copynumber: 4.2 Consensus size: 20
358971 AATCATATTG
358981 CCCAGGGGGTACCGATTCCCC
1 CCCAGGGGGTACCGATT-CCC
359002 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACCGATTCCC
* *
359022 CCCAGGGGGAACAGATT-CC
1 CCCAGGGGGTACCGATTCCC
359041 CCCA-GGGGTACCGATTCCC
1 CCCAGGGGGTACCGATTCCC
359060 CCC
1 CCC
359063 TGTCTAACGG
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
18 10 0.18
19 11 0.20
20 18 0.32
21 17 0.30
ACGTcount: A:0.17, C:0.41, G:0.28, T:0.13
Consensus pattern (20 bp):
CCCAGGGGGTACCGATTCCC
Found at i:361396 original size:20 final size:19
Alignment explanation
Indices: 361371--361420 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
361361 ATTACAAATT
*
361371 TAATTATTTTATAATTACGA
1 TAATTAATTTATAATTA-GA
* *
361391 TAATTAGTTTATAATTATA
1 TAATTAATTTATAATTAGA
361410 TAATTAATTTA
1 TAATTAATTTA
361421 ATTTAATTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (19 bp):
TAATTAATTTATAATTAGA
Found at i:365480 original size:16 final size:16
Alignment explanation
Indices: 365459--365507 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
365449 ACAAACAAAC
365459 ATAAAAGAACTTAAAA
1 ATAAAAGAACTTAAAA
*
365475 AT--AA-AAC--AAAC
1 ATAAAAGAACTTAAAA
365486 ATAAAAGAACTTAAAA
1 ATAAAAGAACTTAAAA
365502 ATAAAA
1 ATAAAA
365508 CAAACAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
11 5 0.19
13 5 0.19
14 5 0.19
16 11 0.42
ACGTcount: A:0.71, C:0.08, G:0.04, T:0.16
Consensus pattern (16 bp):
ATAAAAGAACTTAAAA
Found at i:365489 original size:27 final size:27
Alignment explanation
Indices: 365451--365513 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
365441 CCAGACAAAC
365451 AAACAAACATAAAAGAACTTAAAAATA
1 AAACAAACATAAAAGAACTTAAAAATA
365478 AAACAAACATAAAAGAACTTAAAAATA
1 AAACAAACATAAAAGAACTTAAAAATA
365505 AAACAAACA
1 AAACAAACA
365514 AAACAACTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.71, C:0.13, G:0.03, T:0.13
Consensus pattern (27 bp):
AAACAAACATAAAAGAACTTAAAAATA
Found at i:367319 original size:28 final size:27
Alignment explanation
Indices: 367287--367352 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 27
367277 TTATAAGGTA
367287 TATTTTATT-CTATTTAATATTTTGTTAG
1 TATTTTATTACTATTTAAT-TTTT-TTAG
*
367315 TATTTTATTTAATTATTTAATTTTTTTAG
1 TATTTTA-TT-ACTATTTAATTTTTTTAG
367344 TATTTTATT
1 TATTTTATT
367353 TAATTATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 9 0.26
29 13 0.38
30 4 0.12
31 8 0.24
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.68
Consensus pattern (27 bp):
TATTTTATTACTATTTAATTTTTTTAG
Found at i:367343 original size:29 final size:29
Alignment explanation
Indices: 367297--367369 Score: 119
Period size: 29 Copynumber: 2.4 Consensus size: 29
367287 TATTTTATTC
367297 TATTTAATATTTTGTTAGTATTTTATTTAAT
1 TATTTAAT-TTTT-TTAGTATTTTATTTAAT
367328 TATTTAATTTTTTTAGTATTTTATTTAAT
1 TATTTAATTTTTTTAGTATTTTATTTAAT
*
367357 TATTTTATTTTTT
1 TATTTAATTTTTT
367370 GCAGTTATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 29 0.71
30 4 0.10
31 8 0.20
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (29 bp):
TATTTAATTTTTTTAGTATTTTATTTAAT
Found at i:367362 original size:13 final size:13
Alignment explanation
Indices: 367315--367366 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
367305 ATTTTGTTAG
367315 TATTTTATTTAAT
1 TATTTTATTTAAT
* * *
367328 TATTTAATTTTTTTAG
1 TA-TT--TTATTTAAT
367344 TATTTTATTTAAT
1 TATTTTATTTAAT
367357 TATTTTATTT
1 TATTTTATTT
367367 TTTGCAGTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
13 18 0.60
14 2 0.07
15 2 0.07
16 8 0.27
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:371365 original size:79 final size:79
Alignment explanation
Indices: 371234--371391 Score: 316
Period size: 79 Copynumber: 2.0 Consensus size: 79
371224 AATTGGAAGA
371234 ATGTTGCGATTATCATCTTGGACAACTGCCAATAGTAAAACTTTCTTGTATTTTCCATACAAGAA
1 ATGTTGCGATTATCATCTTGGACAACTGCCAATAGTAAAACTTTCTTGTATTTTCCATACAAGAA
371299 AGTCTCGTCGATCT
66 AGTCTCGTCGATCT
371313 ATGTTGCGATTATCATCTTGGACAACTGCCAATAGTAAAACTTTCTTGTATTTTCCATACAAGAA
1 ATGTTGCGATTATCATCTTGGACAACTGCCAATAGTAAAACTTTCTTGTATTTTCCATACAAGAA
371378 AGTCTCGTCGATCT
66 AGTCTCGTCGATCT
371392 GGACCATAGG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (79 bp):
ATGTTGCGATTATCATCTTGGACAACTGCCAATAGTAAAACTTTCTTGTATTTTCCATACAAGAA
AGTCTCGTCGATCT
Found at i:373466 original size:274 final size:277
Alignment explanation
Indices: 373035--373589 Score: 1062
Period size: 276 Copynumber: 2.0 Consensus size: 277
373025 AAAAGGATTG
373035 AAGGGTAAAATGGTCATTTGACTATCAAGATAATTATTTGAAATGGGGTTATATTAAGCACACGT
1 AAGGGTAAAATGGTCATTTGACTATCAAGATAATTATTTGAAATGGGGTTATATTAAGCACACGT
373100 GGAAGTAAAGAATAGGCAAAGTCCAGTTTCCAGAGTTCTCTTCTTTTCCTTTCTTCCTTCATACG
66 GGAAGT-AAGAATAGGCAAAGTCCAGTTTCCAGAGTTCTCTTCTTTTCCTTTCTTCCTTCATACG
373165 TGAGAGCCAAGCAAAGGTGAGTCCTCTTGTTAGTTAATTTCTTTCTAAATTTAAGGTTGGTTTA-
130 TGAGAGCCAAGCAAAGGTGAGTCCTCTTGTTAGTTAATTTCTTTCTAAATTTAAGGTTGGTTTAT
*
373229 GATCATTAGATGATAATTAAGCTTAAGG-AAGCTTAATTTGTCTCAAAACAATAAGAATAAGAGA
195 GATCATTAGATGATAATTAAGCTTAAGGAAAGCTTAATTTGTCTCAAAACAATAAGAAGAAGAGA
373293 ATAGAAGGGATTAAAGAA
260 ATAGAAGGGATTAAAGAA
373311 AAGGGTAAAATGGTCATTTGACTATCAAGATAATTATTTGAAATGGGGTTATATTAAGCACACGT
1 AAGGGTAAAATGGTCATTTGACTATCAAGATAATTATTTGAAATGGGGTTATATTAAGCACACGT
373376 GGAAGT-AGAATAGGCAAAGTCCAGTTTCCAGAGTTCTCTTCTTTTCCTTTCTTCCTTCATACGT
66 GGAAGTAAGAATAGGCAAAGTCCAGTTTCCAGAGTTCTCTTCTTTTCCTTTCTTCCTTCATACGT
373440 GAGAGCCAAGCAAAGGTGAGTCCTCTTGTTAGTTAATTTCTTTCTAAATTTAAGGTTGGTTTATG
131 GAGAGCCAAGCAAAGGTGAGTCCTCTTGTTAGTTAATTTCTTTCTAAATTTAAGGTTGGTTTATG
373505 ATCATTAGATGATAATTAAGCTTAAGGAAAGCTTAATTTGTCTCAAAACAATAAGAAGAAGAGAA
196 ATCATTAGATGATAATTAAGCTTAAGGAAAGCTTAATTTGTCTCAAAACAATAAGAAGAAGAGAA
*
373570 TATAAGGGATTAAAGAA
261 TAGAAGGGATTAAAGAA
373587 AAG
1 AAG
373590 AGGGGGATAA
Statistics
Matches: 275, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
274 121 0.44
275 28 0.10
276 126 0.46
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (277 bp):
AAGGGTAAAATGGTCATTTGACTATCAAGATAATTATTTGAAATGGGGTTATATTAAGCACACGT
GGAAGTAAGAATAGGCAAAGTCCAGTTTCCAGAGTTCTCTTCTTTTCCTTTCTTCCTTCATACGT
GAGAGCCAAGCAAAGGTGAGTCCTCTTGTTAGTTAATTTCTTTCTAAATTTAAGGTTGGTTTATG
ATCATTAGATGATAATTAAGCTTAAGGAAAGCTTAATTTGTCTCAAAACAATAAGAAGAAGAGAA
TAGAAGGGATTAAAGAA
Found at i:374686 original size:22 final size:22
Alignment explanation
Indices: 374658--374710 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
374648 TTAAAATATA
374658 TGAAAATATTATATGTGTTATG
1 TGAAAATATTATATGTGTTATG
374680 TGAAAATATTATATGTGTTATG
1 TGAAAATATTATATGTGTTATG
374702 TGAAAATAT
1 TGAAAATAT
374711 GAAATAAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (22 bp):
TGAAAATATTATATGTGTTATG
Found at i:375858 original size:29 final size:30
Alignment explanation
Indices: 375785--375859 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
375775 ACTTCCAACA
* *
375785 TGAGAGGATTGTCGGGTGATATTTACGGGT
1 TGAGAGGATTGTTGTGTGATATTTACGGGT
* * * *
375815 TGAAAGGTTTATTGTGTGAT-TTTTCGGGT
1 TGAGAGGATTGTTGTGTGATATTTACGGGT
375844 TGAGAGGATTGTTGTG
1 TGAGAGGATTGTTGTG
375860 AATGTTTACA
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.19, C:0.04, G:0.37, T:0.40
Consensus pattern (30 bp):
TGAGAGGATTGTTGTGTGATATTTACGGGT
Found at i:376192 original size:21 final size:22
Alignment explanation
Indices: 376155--376196 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
376145 TTGTCATAGG
*
376155 GGAACCGATTCCCCTGCTACAA
1 GGAACCGATTACCCTGCTACAA
376177 GGAACCGA-TACCCTGCTACA
1 GGAACCGATTACCCTGCTACA
376197 TTACTGCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.29, C:0.36, G:0.19, T:0.17
Consensus pattern (22 bp):
GGAACCGATTACCCTGCTACAA
Found at i:376205 original size:11 final size:11
Alignment explanation
Indices: 376189--376223 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
376179 AACCGATACC
*
376189 CTGCTACATTA
1 CTGCTACAGTA
*
376200 CTGCTAGAGTA
1 CTGCTACAGTA
376211 CTGCTACAGTA
1 CTGCTACAGTA
376222 CT
1 CT
376224 TCCGTAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (11 bp):
CTGCTACAGTA
Found at i:376589 original size:59 final size:59
Alignment explanation
Indices: 376497--376614 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
376487 ACAATTACAC
376497 GCTAAGTCGATGACTTAGTGAGGCATATAAGAATATAATGGAAACCATAAAACATTTCA
1 GCTAAGTCGATGACTTAGTGAGGCATATAAGAATATAATGGAAACCATAAAACATTTCA
376556 GCTAAGTCGATGACTTAGTGAGGCATATAAGAATATAATGGAAACCATAAAACATTTCA
1 GCTAAGTCGATGACTTAGTGAGGCATATAAGAATATAATGGAAACCATAAAACATTTCA
376615 TAAAGAAATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (59 bp):
GCTAAGTCGATGACTTAGTGAGGCATATAAGAATATAATGGAAACCATAAAACATTTCA
Found at i:377064 original size:22 final size:22
Alignment explanation
Indices: 377017--377074 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
377007 ATATGAAATT
* *
377017 TGTCCCGAAGGACCTATATATT
1 TGTCCCGAAAGACCTATATATA
* *
377039 TGTCCCGAATGACC-ACTGTATA
1 TGTCCCGAAAGACCTA-TATATA
*
377061 TGTCTCGAAAGACC
1 TGTCCCGAAAGACC
377075 GCGTAGACCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (22 bp):
TGTCCCGAAAGACCTATATATA
Found at i:382348 original size:22 final size:22
Alignment explanation
Indices: 382322--382374 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
382312 CAGTACCGTA
*
382322 TGAACAGTAAAGAACAATACTG
1 TGAACAGTAAAGAACAATAATG
* *
382344 TGAACAATAATGAACAATAATG
1 TGAACAGTAAAGAACAATAATG
382366 TGAACAGTA
1 TGAACAGTA
382375 CCTGAATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.17, T:0.21
Consensus pattern (22 bp):
TGAACAGTAAAGAACAATAATG
Found at i:382476 original size:11 final size:11
Alignment explanation
Indices: 382444--382498 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
382434 CTGATACCTA
*
382444 GCTACGGTACT
1 GCTACAGTACT
* *
382455 ACTACATTACT
1 GCTACAGTACT
*
382466 GCTAGAGTACT
1 GCTACAGTACT
* *
382477 GTTACAGTATT
1 GCTACAGTACT
382488 GCTACAGTACT
1 GCTACAGTACT
382499 TCCGTAAAAC
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (11 bp):
GCTACAGTACT
Found at i:383254 original size:22 final size:22
Alignment explanation
Indices: 383229--383311 Score: 123
Period size: 22 Copynumber: 3.8 Consensus size: 22
383219 GGCATATGAA
383229 ATTTGTCCCGAAGGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
*
383251 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
383273 ATTTGTCCCGAAGGACC-ACTGT
1 ATTTGTCCCGAAGGACCTA-TGT
* *
383295 ATATGTCCCGAATGACC
1 ATTTGTCCCGAAGGACC
383312 GCGTAAACCC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
21 1 0.02
22 55 0.98
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.30
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATGT
Found at i:384965 original size:41 final size:41
Alignment explanation
Indices: 384871--385031 Score: 118
Period size: 42 Copynumber: 3.9 Consensus size: 41
384861 TATAGATGGA
* * * * *
384871 TCTATTGCGGC-ATTTATATAAAAATGCCGCTAAAGTATTAC
1 TCTATTGCGGCGTTTTTTA-AAAAACGCCACTAAAGTACTAC
* *
384912 TCT-TT-CATGGCGTTTTTTGAAAAAACGCCACTACA-TATGTAC
1 TCTATTGC--GGCGTTTTTT-AAAAAACGCCACTAAAGTA-CTAC
* *
384954 -CTATTGCGGCG-TTTATATAAAAACGCCGCTAAAGTACTAC
1 TCTATTGCGGCGTTTTTTA-AAAAACGCCACTAAAGTACTAC
* *
384994 TCTATTGCGGCGTTTGTTTAAGAAACGCCGCTAAAGTA
1 TCTATTGCGGCGTTT-TTTAAAAAACGCCACTAAAGTA
385032 TCATTTTGTG
Statistics
Matches: 96, Mismatches: 12, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
39 2 0.02
40 22 0.23
41 27 0.28
42 40 0.42
43 5 0.05
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (41 bp):
TCTATTGCGGCGTTTTTTAAAAAACGCCACTAAAGTACTAC
Found at i:385006 original size:82 final size:81
Alignment explanation
Indices: 384801--385022 Score: 222
Period size: 82 Copynumber: 2.7 Consensus size: 81
384791 CCCTATTATA
* * * * * *
384801 GCATTTTTATAAAAACACCGCTAAAGTA-TAAATGTTGT--GGCGTTTG-TCAAAAAATGCCACT
1 GCATTTATATAAAAACGCCGCTAAAGTACT-ACTCTT-TCAGGCGTTTGTTTAAAAAACGCCACT
* *
384862 ATAGATGGATCTATTGCG
64 ACAGATGGACCTATTGCG
* *
384880 GCATTTATATAAAAATGCCGCTAAAGTATTACTCTTTCATGGCGTTT-TTTGAAAAAACGCCACT
1 GCATTTATATAAAAACGCCGCTAAAGTACTACTCTTTCA-GGCGTTTGTTT-AAAAAACGCCACT
* *
384944 ACATATGTACCTATTGCG
64 ACAGATGGACCTATTGCG
* *
384962 GCGTTTATATAAAAACGCCGCTAAAGTACTACTCTATTGC-GGCGTTTGTTTAAGAAACGCC
1 GCATTTATATAAAAACGCCGCTAAAGTACTACTCT-TT-CAGGCGTTTGTTTAAAAAACGCC
385023 GCTAAAGTAT
Statistics
Matches: 119, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
78 1 0.01
79 29 0.24
80 1 0.01
81 8 0.07
82 74 0.62
83 5 0.04
84 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (81 bp):
GCATTTATATAAAAACGCCGCTAAAGTACTACTCTTTCAGGCGTTTGTTTAAAAAACGCCACTAC
AGATGGACCTATTGCG
Found at i:385029 original size:42 final size:41
Alignment explanation
Indices: 384871--385031 Score: 152
Period size: 41 Copynumber: 3.9 Consensus size: 41
384861 TATAGATGGA
* * *
384871 TCTATTGCGGCATTTATATAAAAATGCCGCTAAAGTATTAC
1 TCTATTGCGGCGTTTATATAAAAACGCCGCTAAAGTACTAC
* * * *
384912 TCT-TT-CATGGCGTTT-TTTGAAAAAACGCCACTACA-TATGTAC
1 TCTATTGC--GGCGTTTATAT--AAAAACGCCGCTAAAGTA-CTAC
384954 -CTATTGCGGCGTTTATATAAAAACGCCGCTAAAGTACTAC
1 TCTATTGCGGCGTTTATATAAAAACGCCGCTAAAGTACTAC
* *
384994 TCTATTGCGGCGTTTGTTTAAGAAACGCCGCTAAAGTA
1 TCTATTGCGGCGTTTATATAA-AAACGCCGCTAAAGTA
385032 TCATTTTGTG
Statistics
Matches: 97, Mismatches: 12, Indels: 21
0.75 0.09 0.16
Matches are distributed among these distances:
39 1 0.01
40 20 0.21
41 40 0.41
42 35 0.36
43 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (41 bp):
TCTATTGCGGCGTTTATATAAAAACGCCGCTAAAGTACTAC
Found at i:389449 original size:30 final size:30
Alignment explanation
Indices: 389415--389482 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
389405 ATGTTGGTTG
*
389415 TGATGGTGGTTGTGATGTTGCAG-CTTGTGA
1 TGATGGTGCTTGTGATGTTGCAGCCTT-TGA
389445 TGATGGTGCTTGTGATGTTGCAGCCTTTGA
1 TGATGGTGCTTGTGATGTTGCAGCCTTTGA
389475 TGATGGTG
1 TGATGGTG
389483 TGATCCTTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 33 0.92
31 3 0.08
ACGTcount: A:0.13, C:0.09, G:0.38, T:0.40
Consensus pattern (30 bp):
TGATGGTGCTTGTGATGTTGCAGCCTTTGA
Found at i:389476 original size:15 final size:15
Alignment explanation
Indices: 389424--389468 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
389414 GTGATGGTGG
389424 TTGTGATGTTGCAGC
1 TTGTGATGTTGCAGC
* **
389439 TTGTGATGATGGTGC
1 TTGTGATGTTGCAGC
389454 TTGTGATGTTGCAGC
1 TTGTGATGTTGCAGC
389469 CTTTGATGAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.13, C:0.11, G:0.36, T:0.40
Consensus pattern (15 bp):
TTGTGATGTTGCAGC
Found at i:392597 original size:112 final size:111
Alignment explanation
Indices: 392321--392890 Score: 919
Period size: 111 Copynumber: 5.1 Consensus size: 111
392311 TTGTCGGTTT
*
392321 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAGAACC
1 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGT-AAAAAATGACAAAACC
* *
392386 GGTCTATAAATGACAAAACAGGTAAAGCACTACCAGATATATTGAAA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* **
392433 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAATGATAAAACTA
1 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
*
392498 ATCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
392544 ATGTCGATACTTTATAAAAATATATTGATCCATAATAATATAACAGGTAAAAAATGACAAAACCG
1 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
*
392609 GTCTATAAATGAC--AACAAGTAAAGCGCTACCGGATATATTGAAA
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
392653 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
1 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
*
392718 GTCTATAAATGACAAAACATGTAAAGCGCTACCGGATATATTGAAA
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
392764 GTGTCGATACTTTATAAAAATGTATCGATCTATAACAATATAACAGGTAAAAAAATAACAAAACC
1 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGT-AAAAAATGACAAAACC
* * *
392829 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATGTTGATA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
392876 GTGTCGATGCTTTAT
1 GTGTCGATACTTTAT
392891 TATAAGTATC
Statistics
Matches: 429, Mismatches: 26, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
109 104 0.24
111 205 0.48
112 120 0.28
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.26
Consensus pattern (111 bp):
GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:392707 original size:220 final size:222
Alignment explanation
Indices: 392322--392890 Score: 926
Period size: 220 Copynumber: 2.6 Consensus size: 222
392312 TGTCGGTTTG
*
392322 TGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAGAACCG
1 TGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCG
*
392387 GTCTATAAATGACAAAACAGGTAAAGCACTACCAGATATATTGAAAGTGTCGATACTTTATAAAA
66 GTCTATAAATGAC-AAACAGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTATAAAA
* * *
392452 ATATATTGATCCATAACAATATAACAGGTAAAAAATGATAAAACTAATCTATAAATGACAAAACA
130 ATATATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCAATCTATAAATGACAAAACA
392517 GGTAAAGCGCTACCGGATATATTGAAAA
195 GGTAAAGCGCTACCGGATATATTGAAAA
*
392545 TGTCGATACTTTATAAAAATATATTGATCCATAATAATATAACAGGT-AAAAAATGACAAAACCG
1 TGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCG
* *
392609 GTCTATAAATGAC-AACAAGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAA
66 GTCTATAAATGACAAACAGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTATAAAAA
* ** *
392673 TGTATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCGGTCTATAAATGACAAAACAT
131 TATATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCAATCTATAAATGACAAAACAG
*
392738 GTAAAGCGCTACCGGATATATTGAAAG
196 GTAAAGCGCTACCGGATATATTGAAAA
* * * *
392765 TGTCGATACTTTATAAAAATGTATCGATCTATAACAATATAACAGGTAAAAAAATAACAAAACCG
1 TGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCG
* * *
392830 GTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATGTTGATAGTGTCGATGCTTTAT
66 GTCTATAAATGAC-AAACAGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAT
392891 TATAAGTATC
Statistics
Matches: 320, Mismatches: 23, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
220 175 0.55
221 29 0.09
222 29 0.09
223 87 0.27
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.26
Consensus pattern (222 bp):
TGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCG
GTCTATAAATGACAAACAGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTATAAAAA
TATATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCAATCTATAAATGACAAAACAG
GTAAAGCGCTACCGGATATATTGAAAA
Found at i:393023 original size:20 final size:19
Alignment explanation
Indices: 392998--393072 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 19
392988 ACATGTAAAA
392998 AAATGACAAAACCAGTCTTC
1 AAATGACAAAACC-GTCTTC
*
393018 AAATGACAAAACCGGTTTTC
1 AAATGACAAAACC-GTCTTC
*
393038 AAATGACAAAACCGATCTCC
1 AAATGACAAAACCG-TCTTC
393058 AAATGACAAAACCGT
1 AAATGACAAAACCGT
393073 TAAAGAGCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
19 2 0.04
20 48 0.96
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.19
Consensus pattern (19 bp):
AAATGACAAAACCGTCTTC
Found at i:393116 original size:222 final size:222
Alignment explanation
Indices: 392816--393255 Score: 702
Period size: 222 Copynumber: 2.0 Consensus size: 222
392806 ACAGGTAAAA
* * * *
392816 AAATAACAAAACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATGTTGATAGTGTC
1 AAATAACAAAACCGATCTACAAATGACAAAACAGGTAAAGAGCTACCAGATATGTTGAAAGTGTC
* * * *
392881 GATGCTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGTTAATAAA
66 GATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAAAAGTTATAGCGTCAATAAA
* *
392946 GTGTTGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
131 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
393011 AGTCTTC-AAATGACAAAACCGGTTTTC
196 AGTC-TCGAAATGACAAAACCGGTTTTC
* * * * *
393038 AAATGACAAAACCGATCTCCAAATGACAAAACCGTTAAAGAGCTATCAGATATGTTGAAAGTGTC
1 AAATAACAAAACCGATCTACAAATGACAAAACAGGTAAAGAGCTACCAGATATGTTGAAAGTGTC
393103 GATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAAAAGTTATAGCGTCAATAAA
66 GATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAAAAGTTATAGCGTCAATAAA
* *
393168 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATC
131 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
393233 GGTCTCGAAATGACAAAACCGGT
196 AGTCTCGAAATGACAAAACCGGT
393256 AGTAAAAAAG
Statistics
Matches: 199, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
221 2 0.01
222 197 0.99
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (222 bp):
AAATAACAAAACCGATCTACAAATGACAAAACAGGTAAAGAGCTACCAGATATGTTGAAAGTGTC
GATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAAAAGTTATAGCGTCAATAAA
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
AGTCTCGAAATGACAAAACCGGTTTTC
Found at i:398652 original size:115 final size:115
Alignment explanation
Indices: 398450--398681 Score: 455
Period size: 115 Copynumber: 2.0 Consensus size: 115
398440 ACTGAACAAT
*
398450 TCAAAAGTACAAAGTATCATATTAGATATTTTGTTAAAGTATTTGAATTGAATGTGATATTATCC
1 TCAAAAGTACAAAGTATCATATTAGATATTTTGTTAAAGTATTTGAATTGAATATGATATTATCC
398515 CTGAATTATATCAACTATAAACATGAGCTCAGATGGCATTATATATCATA
66 CTGAATTATATCAACTATAAACATGAGCTCAGATGGCATTATATATCATA
398565 TCAAAAGTACAAAGTATCATATTAGATATTTTGTTAAAGTATTTGAATTGAATATGATATTATCC
1 TCAAAAGTACAAAGTATCATATTAGATATTTTGTTAAAGTATTTGAATTGAATATGATATTATCC
398630 CTGAATTATATCAACTATAAACATGAGCTCAGATGGCATTATATATCATA
66 CTGAATTATATCAACTATAAACATGAGCTCAGATGGCATTATATATCATA
398680 TC
1 TC
398682 CTCATTCTCG
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 116 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (115 bp):
TCAAAAGTACAAAGTATCATATTAGATATTTTGTTAAAGTATTTGAATTGAATATGATATTATCC
CTGAATTATATCAACTATAAACATGAGCTCAGATGGCATTATATATCATA
Found at i:403731 original size:28 final size:28
Alignment explanation
Indices: 403699--403753 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
403689 CTCCATTTAT
403699 ATTATGTCGTCAA-ACTAGTACTTAAAAC
1 ATTATGTCGTCAAGAC-AGTACTTAAAAC
* *
403727 ATTATGTTGTCAAGACAGTGCTTAAAA
1 ATTATGTCGTCAAGACAGTACTTAAAA
403754 AATGGCGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (28 bp):
ATTATGTCGTCAAGACAGTACTTAAAAC
Found at i:405570 original size:39 final size:39
Alignment explanation
Indices: 405498--405573 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
405488 AGCTCATCGG
* *
405498 CTTTGTGCTCAAGGTAAGTCTTTACCGCGGGCTCCTCAA
1 CTTTATGCTCAAGGTAAGTCTTTACCGCAGGCTCCTCAA
* *
405537 CTTTATGCTCAGGGTAAGT-TCTTACTGCAGGCTCCTC
1 CTTTATGCTCAAGGTAAGTCT-TTACCGCAGGCTCCTC
405574 TTCTTTGTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.03
39 31 0.97
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (39 bp):
CTTTATGCTCAAGGTAAGTCTTTACCGCAGGCTCCTCAA
Found at i:405958 original size:2 final size:2
Alignment explanation
Indices: 405951--406735 Score: 1510
Period size: 2 Copynumber: 395.5 Consensus size: 2
405941 TACGATTTTC
*
405951 TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
405993 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
406035 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
406077 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
406119 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
406160 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
406202 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
406244 TG TG TG TG TG TG TG -G TG TG TG TG TG TG TG -G TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
406284 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -G
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
406325 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
406367 TG TG TG TG GG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
406409 TG TG TG TG TG TG TG TG -G TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
406450 TG TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
406491 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
406533 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
406575 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
406617 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
406659 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
406701 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
406736 CTTATGAATC
Statistics
Matches: 773, Mismatches: 4, Indels: 12
0.98 0.01 0.02
Matches are distributed among these distances:
1 6 0.01
2 767 0.99
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:411944 original size:39 final size:39
Alignment explanation
Indices: 411901--412007 Score: 119
Period size: 39 Copynumber: 2.7 Consensus size: 39
411891 CAAGCTCCTT
* *
411901 GGCTTTGTACTCATGGTAAGTCCTTA-TCGCAGGATTC-TC
1 GGCTTTGTGCTCATGGTAAGTCCTTACT-GCA-AATTCATC
* *
411940 GGCTTTGTGCTCAGGGTTAGTCCTTACTGCAAATTCATC
1 GGCTTTGTGCTCATGGTAAGTCCTTACTGCAAATTCATC
* * *
411979 TGCTTTGTGCACATGGTAAGCCCTTACTG
1 GGCTTTGTGCTCATGGTAAGTCCTTACTG
412008 GTTGTACAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 4 0.07
39 52 0.91
40 1 0.02
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (39 bp):
GGCTTTGTGCTCATGGTAAGTCCTTACTGCAAATTCATC
Found at i:412378 original size:2 final size:2
Alignment explanation
Indices: 412371--412398 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
412361 CGGTTTTCTG
412371 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
412399 GTTTATCGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:413033 original size:17 final size:18
Alignment explanation
Indices: 413006--413044 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
412996 TAGTCCTTTA
413006 AATTTGTATTTT-ACT-C
1 AATTTGTATTTTGACTAC
413022 AATTTAGTATTTTGACTAC
1 AATTT-GTATTTTGACTAC
413041 AATT
1 AATT
413045 GTTTACAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 5 0.25
17 7 0.35
18 3 0.15
19 5 0.25
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (18 bp):
AATTTGTATTTTGACTAC
Found at i:413480 original size:30 final size:30
Alignment explanation
Indices: 413446--413513 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
413436 TTTTTATTTT
* * *
413446 TAAATTAAGTAATTTCATTGTAATAATTAA
1 TAAATTAAGTAATTTAATTATAATAATCAA
* *
413476 TAAATTAAGTAATTTAATTATTATAATCGA
1 TAAATTAAGTAATTTAATTATAATAATCAA
413506 TAAATTAA
1 TAAATTAA
413514 ATGAATTGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (30 bp):
TAAATTAAGTAATTTAATTATAATAATCAA
Found at i:413896 original size:51 final size:51
Alignment explanation
Indices: 413817--413921 Score: 147
Period size: 51 Copynumber: 2.1 Consensus size: 51
413807 ACCCTTTGCA
* * *
413817 GTAAGGCGCGCGCCCTGCTGCGCGCTTTACGCTGATATGACGCCACGCGGG
1 GTAAGGCGCGCCCCCTGCAGCGCACTTTACGCTGATATGACGCCACGCGGG
* * * *
413868 GTAAGGCGTGCCCCCTGCAGCGCACTTTACGCTGATCTGGCGCCACGTGGG
1 GTAAGGCGCGCCCCCTGCAGCGCACTTTACGCTGATATGACGCCACGCGGG
413919 GTA
1 GTA
413922 TAGCACGGGG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.14, C:0.32, G:0.34, T:0.19
Consensus pattern (51 bp):
GTAAGGCGCGCCCCCTGCAGCGCACTTTACGCTGATATGACGCCACGCGGG
Found at i:414188 original size:17 final size:17
Alignment explanation
Indices: 414162--414194 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
414152 CTTTGTTTTT
414162 AATTTATTTAAGTATTTA
1 AATTTATTTAA-TATTTA
414180 AATTT-TTTAATATTT
1 AATTTATTTAATATTT
414195 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:414196 original size:17 final size:19
Alignment explanation
Indices: 414157--414196 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
414147 TAATACTTTG
*
414157 TTTTTAATTTATTTAAGTA
1 TTTTAAATTTATTTAAGTA
414176 -TTTAAATTT-TTTAA-TA
1 TTTTAAATTTATTTAAGTA
414192 TTTTA
1 TTTTA
414197 TTTAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 2 0.11
17 9 0.47
18 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTAAATTTATTTAAGTA
Found at i:418066 original size:26 final size:28
Alignment explanation
Indices: 418005--418066 Score: 65
Period size: 31 Copynumber: 2.2 Consensus size: 28
417995 GAGTATTGTG
* *
418005 GAGCTCGACTCGACTCAAAAACTTTGAAAT
1 GAGCTCGACTCGACTCAAAAACTTCG--AC
418035 GAAGCTCGACTCGACTCAAAAAC-TCG-C
1 G-AGCTCGACTCGACTCAAAAACTTCGAC
418062 GAGCT
1 GAGCT
418067 TAAAATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 4 0.14
27 1 0.03
30 3 0.10
31 21 0.72
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (28 bp):
GAGCTCGACTCGACTCAAAAACTTCGAC
Found at i:425042 original size:21 final size:21
Alignment explanation
Indices: 424993--425054 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
424983 CGCAAATCAG
424993 TTTCCAAAATCGCAATGCGAT
1 TTTCCAAAATCGCAATGCGAT
** * * *
425014 AGTACAAATTCGCATTGCGAT
1 TTTCCAAAATCGCAATGCGAT
*
425035 TTTCCAAAATCGCAACGCGA
1 TTTCCAAAATCGCAATGCGA
425055 ATATGAAAAT
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (21 bp):
TTTCCAAAATCGCAATGCGAT
Found at i:425103 original size:20 final size:20
Alignment explanation
Indices: 425041--425234 Score: 230
Period size: 20 Copynumber: 9.7 Consensus size: 20
425031 CGATTTTCCA
* ** *
425041 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
425061 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
425081 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
425101 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
425121 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
425141 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
425161 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
425181 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
425201 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
425222 AAATCGCAACGCG
1 AAATCGCAACGCG
425235 ATATTTAAAG
Statistics
Matches: 148, Mismatches: 21, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.86
21 17 0.11
22 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:425655 original size:33 final size:33
Alignment explanation
Indices: 425616--425686 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
425606 TTCACTTAGA
*
425616 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
425649 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
425682 TTTCA
1 TTTCA
425687 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:425810 original size:20 final size:20
Alignment explanation
Indices: 425766--425861 Score: 122
Period size: 21 Copynumber: 4.8 Consensus size: 20
425756 TGCAGAAGAG
*
425766 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
425787 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
425807 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
*
425828 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
425847 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
425862 CGCAACGCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
19 18 0.28
20 20 0.31
21 26 0.41
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:425823 original size:41 final size:40
Alignment explanation
Indices: 425764--425860 Score: 140
Period size: 41 Copynumber: 2.4 Consensus size: 40
425754 TTTGCAGAAG
* *
425764 AGTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGAC
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGA-AATGAA
* *
425805 TGTCGCAACGAGAGAAATGAAAATCGCAACGCGAAATGAA
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAAATGAA
*
425845 AATCGCAACGAGAGAA
1 AGTCGCAACGAGAGAA
425861 TCGCAACGCG
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
40 19 0.38
41 31 0.62
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (40 bp):
AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAAATGAA
Found at i:425902 original size:19 final size:19
Alignment explanation
Indices: 425880--425977 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
425870 GAAACCAAAA
*
425880 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
425899 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
425913 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
425932 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
425946 TCTAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
425965 TCGCGTTGCGATT
1 TCGCGTTGCGATT
425978 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
16 6 0.10
17 6 0.10
19 31 0.50
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:425921 original size:14 final size:14
Alignment explanation
Indices: 425902--425991 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
425892 TTTCATTTCG
425902 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
425916 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
425935 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
425949 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
425968 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
425982 CGTTGCGATT
1 CGTTGCGATT
425992 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 29 0.48
16 6 0.10
17 6 0.10
19 19 0.32
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:425927 original size:33 final size:33
Alignment explanation
Indices: 425885--425999 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
425875 CAAAATCGCA
425885 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
425918 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
425951 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
425984 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
426000 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:427851 original size:93 final size:93
Alignment explanation
Indices: 427692--427974 Score: 541
Period size: 93 Copynumber: 3.1 Consensus size: 93
427682 TAGATTGCTT
*
427692 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
427757 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
427785 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
427850 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
427878 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
427943 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
427970 AGTAA
1 AGTAA
427975 TGCAATCCAT
Statistics
Matches: 187, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
92 6 0.03
93 181 0.97
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:428062 original size:19 final size:19
Alignment explanation
Indices: 428022--428150 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
428012 TAGTTTACTT
* *
428022 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
428042 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
428061 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
428080 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
428094 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
428113 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
428127 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
428146 TCGCA
1 TCGCA
428151 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:428101 original size:33 final size:32
Alignment explanation
Indices: 428058--428150 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
428048 CGCGAAACCA
**
428058 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
428090 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
428123 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
428151 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:428148 original size:52 final size:52
Alignment explanation
Indices: 428022--428150 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
428012 TAGTTTACTT
**
428022 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
428074 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
428127 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
428151 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:428168 original size:19 final size:19
Alignment explanation
Indices: 428146--428280 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
428136 GAAACCAAAA
*
428146 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
428165 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
428181 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
428198 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
428214 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
428231 TCTCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
428250 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
428270 TCGTGTTGCGA
1 TCGCGTTGCGA
428281 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 11, Indels: 21
0.75 0.09 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 45 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:428187 original size:14 final size:14
Alignment explanation
Indices: 428168--428224 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
428158 TTTCATTTCG
428168 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
428182 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
428199 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
428215 CGTTGCGATT
1 CGTTGCGATT
428225 TTCATTTCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:428193 original size:33 final size:33
Alignment explanation
Indices: 428151--428243 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
428141 CAAAATCGCA
*
428151 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
428184 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
428217 TTGCGATTTTCATTTCTCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
428244 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:430223 original size:14 final size:14
Alignment explanation
Indices: 430204--430240 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
430194 GATTGTTTAA
430204 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
430218 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
430232 TTGATTTGT
1 TTGATTTGT
430241 GTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:430371 original size:19 final size:20
Alignment explanation
Indices: 430347--430392 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
430337 AAAATTGACT
430347 ATCGCAATGC-GAAATGAAA
1 ATCGCAATGCGGAAATGAAA
430366 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGGAAATGAAA
430386 ATCGCAA
1 ATCGCAA
430393 CGGGAGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAATGCGGAAATGAAA
Found at i:430429 original size:19 final size:19
Alignment explanation
Indices: 430401--430641 Score: 261
Period size: 19 Copynumber: 13.7 Consensus size: 19
430391 AACGGGAGAA
* *
430401 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
430420 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
430436 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
430453 TCGCACTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
430472 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
430488 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
430505 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
430524 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
430540 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
430557 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
430576 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
430595 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
430613 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
430629 TCGCATTGCGATT
1 TCGCATTGCGATT
430642 CTCTCGTTGC
Statistics
Matches: 187, Mismatches: 14, Indels: 42
0.77 0.06 0.17
Matches are distributed among these distances:
14 29 0.16
16 23 0.12
17 20 0.11
18 1 0.01
19 98 0.52
20 16 0.09
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:430464 original size:52 final size:52
Alignment explanation
Indices: 430401--430655 Score: 367
Period size: 52 Copynumber: 4.9 Consensus size: 52
430391 AACGGGAGAA
* *
430401 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* *
430453 TCGCACTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
430505 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
430557 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATT
*
430613 T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
430656 GTAATTTCCG
Statistics
Matches: 191, Mismatches: 6, Indels: 17
0.89 0.03 0.08
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.02
52 131 0.69
53 24 0.13
54 3 0.02
55 3 0.02
56 3 0.02
58 12 0.06
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:430663 original size:33 final size:33
Alignment explanation
Indices: 430407--430655 Score: 227
Period size: 33 Copynumber: 7.2 Consensus size: 33
430397 AGAATCGCAA
*
430407 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
* * *
430440 TGCGATTTTCATTTCGCACTGCGATTTTAATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG--T
* * * * *
430478 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
430511 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
430544 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
*
430582 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
430616 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
430649 TGCGATT
1 TGCGATT
430656 GTAATTTCCG
Statistics
Matches: 175, Mismatches: 22, Indels: 38
0.74 0.09 0.16
Matches are distributed among these distances:
31 9 0.05
32 6 0.03
33 80 0.46
34 14 0.08
35 7 0.04
36 10 0.06
37 5 0.03
38 23 0.13
39 13 0.07
40 8 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:433120 original size:24 final size:24
Alignment explanation
Indices: 433086--433132 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
433076 CTGAAACATC
433086 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
433110 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
433133 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:433843 original size:20 final size:20
Alignment explanation
Indices: 433815--434124 Score: 343
Period size: 20 Copynumber: 15.5 Consensus size: 20
433805 AAATTTCAGT
* *
433815 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
433835 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
433855 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
433875 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
433895 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
433915 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
433935 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
433955 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
433975 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * * *
433995 GTTACGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
434015 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
434035 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
434055 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
434075 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
434095 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
434115 GTTGCGATTT
1 GTTGCGATTT
434125 TGAAAAATCG
Statistics
Matches: 254, Mismatches: 34, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
20 253 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:434141 original size:21 final size:21
Alignment explanation
Indices: 434111--434189 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
434101 ATTTTCATAT
*
434111 TCGCGTTGCGATTTTGAAAAA
1 TCGCATTGCGATTTTGAAAAA
* * * **
434132 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGAAAAA
434153 TCGCATTGCGATTTT-AAAGAA
1 TCGCATTGCGATTTTGAAA-AA
*
434174 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
434190 GAAACTGATT
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 1 0.02
21 43 0.98
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGAAAAA
Found at i:434184 original size:42 final size:43
Alignment explanation
Indices: 434091--434189 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 43
434081 ATTTATGTGT
*
434091 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGAAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGAAAAA
**
434132 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-AAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGAAA-AA
*
434174 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
434190 GAAACTGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
41 11 0.23
42 34 0.71
43 3 0.06
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGAAAAA
Found at i:437457 original size:17 final size:18
Alignment explanation
Indices: 437435--437468 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
437425 TAATTAAACC
*
437435 TAAAAATTTAT-ATAAGA
1 TAAAAATATATCATAAGA
437452 TAAAAATATATCATAAG
1 TAAAAATATATCATAAG
437469 TCACTCGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (18 bp):
TAAAAATATATCATAAGA
Found at i:439361 original size:12 final size:13
Alignment explanation
Indices: 439344--439383 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
439334 GAGTAATCTC
439344 ATTGAATATA-AT
1 ATTGAATATATAT
439356 ATTGAATATATAT
1 ATTGAATATATAT
439369 A-T-ATATATATAT
1 ATTGA-ATATATAT
439381 ATT
1 ATT
439384 TATCTCACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.04
12 20 0.80
13 4 0.16
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (13 bp):
ATTGAATATATAT
Found at i:439514 original size:24 final size:24
Alignment explanation
Indices: 439468--439519 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
439458 AAAATTTTAA
* *
439468 AAAATAAAAATAAATTACTAATAG
1 AAAATAAAAAAAAATTACAAATAG
*
439492 AAAATACAAAAAAAATTA-AAATAT
1 AAAATA-AAAAAAAATTACAAATAG
439516 AAAA
1 AAAA
439520 AGAATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (24 bp):
AAAATAAAAAAAAATTACAAATAG
Found at i:439528 original size:18 final size:17
Alignment explanation
Indices: 439492--439530 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
439482 TTACTAATAG
439492 AAAATACAAAAAAAATT
1 AAAATACAAAAAAAATT
* *
439509 AAAATATAAAAAGAATT
1 AAAATACAAAAAAAATT
*
439526 TAAAT
1 AAAAT
439531 TTTTAAAGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (17 bp):
AAAATACAAAAAAAATT
Found at i:442512 original size:13 final size:13
Alignment explanation
Indices: 442494--442518 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
442484 TTATAAAAGT
442494 TAGTTTTCTCTCC
1 TAGTTTTCTCTCC
442507 TAGTTTTCTCTC
1 TAGTTTTCTCTC
442519 GTTGATAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.28, G:0.08, T:0.56
Consensus pattern (13 bp):
TAGTTTTCTCTCC
Found at i:446833 original size:37 final size:36
Alignment explanation
Indices: 446792--447083 Score: 206
Period size: 36 Copynumber: 8.2 Consensus size: 36
446782 TAAAAACATA
*
446792 TATATATTTTTAAAAATAATATTTTGAAAACATATAT
1 TATATATTTTTAAAAACAAT-TTTTGAAAACATATAT
* * *
446829 TATATAGTTTTAAAAATAGTTTTTGAAAACATATA-
1 TATATATTTTTAAAAACAATTTTTGAAAACATATAT
* * * *
446864 TATA-GTTTTCAAAAACAATTTTTGAAAACGTATAA
1 TATATATTTTTAAAAACAATTTTTGAAAACATATAT
* *
446899 TATATATTTTTAAAAACAAAATTTTGAAAACATTTAT
1 TATATATTTTTAAAAAC-AATTTTTGAAAACATATAT
** * *** *
446936 TATATAATTTCAAAAAAAAAAAATTG--GA-A-ATA-
1 TATAT-ATTTTTAAAAACAATTTTTGAAAACATATAT
* * *
446968 CATAT-TTTTGAAAAACAACTTTTGAAAACATATAT
1 TATATATTTTTAAAAACAATTTTTGAAAACATATAT
* **
447003 TATATAATTTCGAAAACAATTTTTGAAAACATATA-
1 TATATATTTTTAAAAACAATTTTTGAAAACATATAT
* ** * *
447038 TAAACGTTTTTGAAAACATATTTTTTTGAAAACATAACAT
1 TATATATTTTTAAAAACA-A--TTTTTGAAAACAT-ATAT
447078 TATATA
1 TATATA
447084 GTTTAATTCA
Statistics
Matches: 197, Mismatches: 43, Indels: 27
0.74 0.16 0.10
Matches are distributed among these distances:
30 13 0.07
32 5 0.03
33 3 0.02
34 28 0.14
35 26 0.13
36 51 0.26
37 44 0.22
38 22 0.11
39 2 0.01
40 3 0.02
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (36 bp):
TATATATTTTTAAAAACAATTTTTGAAAACATATAT
Found at i:454638 original size:15 final size:13
Alignment explanation
Indices: 454618--454655 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
454608 CTTTCTTAGC
454618 ATTATCATATATATT
1 ATTATCAT-TAT-TT
454633 ATTATCATTATTT
1 ATTATCATTATTT
454646 A-TATCATTAT
1 ATTATCATTAT
454656 CATCAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.39
13 3 0.13
14 3 0.13
15 8 0.35
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTATCATTATTT
Found at i:454799 original size:2 final size:2
Alignment explanation
Indices: 454792--454818 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
454782 CATATCCATC
454792 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 A
454819 GTATTTGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:454951 original size:23 final size:23
Alignment explanation
Indices: 454925--454985 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
454915 CTCGTATAAA
* *
454925 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
454948 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
454971 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
454986 TATAATAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:463760 original size:74 final size:74
Alignment explanation
Indices: 463639--463783 Score: 290
Period size: 74 Copynumber: 2.0 Consensus size: 74
463629 CCTTCAAGGA
463639 CCTGGTATCCAATCCATGACCTATTTTACCTTGTAGAACACCGTGAAGCCATGTCAGGGATGTTT
1 CCTGGTATCCAATCCATGACCTATTTTACCTTGTAGAACACCGTGAAGCCATGTCAGGGATGTTT
463704 GCAAGGTGC
66 GCAAGGTGC
463713 CCTGGTATCCAATCCATGACCTATTTTACCTTGTAGAACACCGTGAAGCCATGTCAGGGATGTTT
1 CCTGGTATCCAATCCATGACCTATTTTACCTTGTAGAACACCGTGAAGCCATGTCAGGGATGTTT
463778 GCAAGG
66 GCAAGG
463784 AATCAGCTTC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (74 bp):
CCTGGTATCCAATCCATGACCTATTTTACCTTGTAGAACACCGTGAAGCCATGTCAGGGATGTTT
GCAAGGTGC
Found at i:469749 original size:20 final size:20
Alignment explanation
Indices: 469698--469750 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
469688 TGCCGTTTCT
* *
469698 AGCCGTTGGGGATATTTTGG
1 AGCCATTGGGGTTATTTTGG
469718 AGCCATTGGGGTTATTTTGG
1 AGCCATTGGGGTTATTTTGG
469738 AGCCATTGGGGTT
1 AGCCATTGGGGTT
469751 TCTTCAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.15, C:0.11, G:0.38, T:0.36
Consensus pattern (20 bp):
AGCCATTGGGGTTATTTTGG
Found at i:472279 original size:2 final size:2
Alignment explanation
Indices: 472272--472339 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
472262 ACATTTTAAG
472272 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
472314 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
472340 CATCATTTCA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:472885 original size:46 final size:46
Alignment explanation
Indices: 472835--473607 Score: 1158
Period size: 46 Copynumber: 16.8 Consensus size: 46
472825 ATTTAAATTT
** *
472835 CATTTTATTTATGATATCATTTCATGCCTTAATGCATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
472881 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
* *
472927 AATTTTTATTTATGGCATCCTTTCATACCTTAATGCATCATTTCATG
1 CA-TTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
* * *
472974 C-TTTTATTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATT
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
* * *
473019 CATTTTATTTATTGCATCCTTTCATGCCTTAATGCATCCTTTTATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
*
473065 CATTTTATTTATGGCATCCTTTCACGCCTTAATGCAT-ACTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCA-TTTCATG
* * *
473111 CATTTTATTTATGTCATCCTTTCATACCTTAATGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
* * * *
473157 CATTTTATTTATGACACCCTTTCATACCTTAATGTATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
473203 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
* * * *
473249 CA-TTTATTTACGACATCCTTTCATGCCTTAATTCATTC-TTTCATT
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCA-TCATTTCATG
*
473294 CATTTTATTTATGGCATCATTTCATGCCTTAATGCATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
* * *
473340 TATTTTATTTATGACATCCTTTCATTCCTTAATGCATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
* *
473386 CATTTTATTTATGGCATGCTTTCATGCCTTAATGCATCTTTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATC-ATTTCATG
* *
473433 CATTTTATTTATGGCATCCTTTCATTCCATAATGCATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
* *
473479 TATTTTATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
* *
473525 CATTTTATTTGTGGCATCCTTTCATGCCTTAATGCATCATTTCAAG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
*
473571 CATTTTATTTATGTCATCCTTTCATGCCTTAATGCAT
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCAT
473608 GTATTTGGTT
Statistics
Matches: 657, Mismatches: 62, Indels: 16
0.89 0.08 0.02
Matches are distributed among these distances:
45 81 0.12
46 491 0.75
47 85 0.13
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (46 bp):
CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
Found at i:473271 original size:25 final size:24
Alignment explanation
Indices: 472866--473597 Score: 299
Period size: 20 Copynumber: 31.7 Consensus size: 24
472856 TCATGCCTTA
*
472866 ATGCATCATTTCATGCATTTTATTT
1 ATGCATCCTTTCATGCA-TTTATTT
*
472891 ATGGCATCCTTTCATGC-CTTA---
1 AT-GCATCCTTTCATGCATTTATTT
* *
472912 ATGCATCATTTCATGAATTTTTATTT
1 ATGCATCCTTTCATGCA--TTTATTT
* *
472938 ATGGCATCCTTTCATAC-CTTA---
1 AT-GCATCCTTTCATGCATTTATTT
* *
472959 ATGCATCATTTCATGCTTTTATTT
1 ATGCATCCTTTCATGCATTTATTT
* *
472983 ATGGAATCCTTTCATGC-CTTA---
1 AT-GCATCCTTTCATGCATTTATTT
*
473004 ATGCATCCTTTCATTCATTTTATTT
1 ATGCATCCTTTCATGCA-TTTATTT
*
473029 ATTGCATCCTTTCATGC-CTTA---
1 A-TGCATCCTTTCATGCATTTATTT
*
473050 ATGCATCCTTTTATGCATTTTATTT
1 ATGCATCCTTTCATGCA-TTTATTT
* *
473075 ATGGCATCCTTTCACGC-CTTA---
1 AT-GCATCCTTTCATGCATTTATTT
*
473096 ATGCATACTTTCATGCATTTTATTT
1 ATGCATCCTTTCATGCA-TTTATTT
* *
473121 ATGTCATCCTTTCATAC-CTTA---
1 ATG-CATCCTTTCATGCATTTATTT
473142 ATGCATCCTTTCATGCATTTTATTT
1 ATGCATCCTTTCATGCA-TTTATTT
* * *
473167 ATGACACCCTTTCATAC-CTTA---
1 ATG-CATCCTTTCATGCATTTATTT
* *
473188 ATGTATCATTTCATGCATTTTATTT
1 ATGCATCCTTTCATGCA-TTTATTT
*
473213 ATGGCATCCTTTCATGC-CTTA---
1 AT-GCATCCTTTCATGCATTTATTT
*
473234 ATGCATCATTTCATGCATTTATTT
1 ATGCATCCTTTCATGCATTTATTT
* *
473258 ACGACATCCTTTCATGC-CTTA---
1 ATG-CATCCTTTCATGCATTTATTT
* * *
473279 ATTCATTCTTTCATTCATTTTATTT
1 ATGCATCCTTTCATGCA-TTTATTT
* *
473304 ATGGCATCATTTCATGC-CTTA---
1 AT-GCATCCTTTCATGCATTTATTT
* *
473325 ATGCATCATTTCATGTATTTTATTT
1 ATGCATCCTTTCATGCA-TTTATTT
* *
473350 ATGACATCCTTTCATTC-CTTA---
1 ATG-CATCCTTTCATGCATTTATTT
*
473371 ATGCATCATTTCATGCATTTTATTT
1 ATGCATCCTTTCATGCA-TTTATTT
* *
473396 ATGGCATGCTTTCATGC-CTTA---
1 AT-GCATCCTTTCATGCATTTATTT
*
473417 ATGCATCTTTTTCATGCATTTTATTT
1 ATGCATC-CTTTCATGCA-TTTATTT
*
473443 ATGGCATCCTTTCATTCCA--TA---
1 AT-GCATCCTTTCA-TGCATTTATTT
* *
473464 ATGCATCATTTCATGTATTTTATTT
1 ATGCATCCTTTCATGCA-TTTATTT
*
473489 ATGACATCCTTTCATGC-CTTA---
1 ATG-CATCCTTTCATGCATTTATTT
*
473510 ATGCATCATTTCATGCATTTTATTT
1 ATGCATCCTTTCATGCA-TTTATTT
* *
473535 GTGGCATCCTTTCATGC-CTTA---
1 AT-GCATCCTTTCATGCATTTATTT
* *
473556 ATGCATCATTTCAAGCATTTTATTT
1 ATGCATCCTTTCATGCA-TTTATTT
473581 ATGTCATCCTTTCATGC
1 ATG-CATCCTTTCATGC
473598 CTTAATGCAT
Statistics
Matches: 521, Mismatches: 93, Indels: 185
0.65 0.12 0.23
Matches are distributed among these distances:
19 2 0.00
20 169 0.32
21 45 0.09
22 32 0.06
23 6 0.01
24 48 0.09
25 51 0.10
26 149 0.29
27 19 0.04
ACGTcount: A:0.22, C:0.21, G:0.09, T:0.47
Consensus pattern (24 bp):
ATGCATCCTTTCATGCATTTATTT
Found at i:477909 original size:21 final size:21
Alignment explanation
Indices: 477883--477922 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
477873 CAGAACCCCA
*
477883 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
477904 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
477923 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:477946 original size:21 final size:22
Alignment explanation
Indices: 477905--477954 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
477895 TTCCCCTGTG
477905 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCCTTCAAA
*
477928 GGGGGAATCGGTT-CCTTCAAG
1 GGGGGAATCGGTTCCCTTCAAA
477949 GGGGGA
1 GGGGGA
477955 TCAATTCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 13 0.50
23 13 0.50
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCTTCAAA
Found at i:477962 original size:20 final size:21
Alignment explanation
Indices: 477920--477962 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
477910 AATCGGTTCC
**
477920 CCTTCAAAGGGGGAATCGGTT
1 CCTTCAAAGGGGGAATCAATT
*
477941 CCTTC-AAGGGGGGATCAATT
1 CCTTCAAAGGGGGAATCAATT
477961 CC
1 CC
477963 CTCTACACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (21 bp):
CCTTCAAAGGGGGAATCAATT
Found at i:485124 original size:20 final size:20
Alignment explanation
Indices: 485099--485138 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
485089 TCACATTTGA
485099 ATATTTTGGCAAACAATTTC
1 ATATTTTGGCAAACAATTTC
485119 ATATTTTGGCAAACAATTTC
1 ATATTTTGGCAAACAATTTC
485139 TTCTCTCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (20 bp):
ATATTTTGGCAAACAATTTC
Found at i:487775 original size:46 final size:46
Alignment explanation
Indices: 487723--488417 Score: 682
Period size: 46 Copynumber: 15.3 Consensus size: 46
487713 CGTTAAATTT
* * *
487723 CATTTTATTTATGACATCATTTTATGCCATAATGCATCATTTCATG
1 CATTTTATTTATGGCATCATTTCATGCCTTAATGCATCATTTCATG
* * **
487769 CATTTTATTTATGACATCCTTTCATGCCTTAA-AAATCATTTCATG
1 CATTTTATTTATGGCATCATTTCATGCCTTAATGCATCATTTCATG
* * * *
487814 CATTTTATTTATGGTATCTTTTCACGCCTTAATACATCATTTCATG
1 CATTTTATTTATGGCATCATTTCATGCCTTAATGCATCATTTCATG
* * *
487860 CATTTTATTTATGGCATCCTTTCATGCCTTAATACATCCTTTCATG
1 CATTTTATTTATGGCATCATTTCATGCCTTAATGCATCATTTCATG
* *
487906 TATTTTATTTATGGCATCATTTCATTCCTTAATGCATCATTTCATG
1 CATTTTATTTATGGCATCATTTCATGCCTTAATGCATCATTTCATG
* *
487952 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTATTTATGGCATCATTTCATGCCTTAATGCATCATTTCATG
* * * *
487998 C--CTTA---AT-GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATG
1 CATTTTATTTATGGCATCATTTCATGC--CTTA---AT-GCATCATTTCATG
* * * *
488044 C--CTTA---AT-GCATCCTTTTATGCCTTAATGTATCATTTCATG
1 CATTTTATTTATGGCATCATTTCATGCCTTAATGCATCATTTCATG
* *
488084 CATTTTATTTACGGCATCCA-TTCATGCCTTAATGCATCCTTTCATG
1 CATTTTATTTATGGCAT-CATTTCATGCCTTAATGCATCATTTCATG
* * *
488130 C-TTTTATTTACGACAT-ACTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTATTTATGGCATCA-TTTCATGCCTTAATGCATCATTTCATG
* * * * *
488175 CATTTAATTTATGTCATCATTTCATGCATTTTATTTACGACATCCTTTCATG
1 CATTTTATTTATGGCATCATTTCATGC--CTTA---ATG-CATCATTTCATG
*
488227 C--CTTA---AT-GCATCATTTCATGCCTTAATGCATCATTTCATG
1 CATTTTATTTATGGCATCATTTCATGCCTTAATGCATCATTTCATG
* * * *
488267 CATTTTATTTATGGCATCTTTTCATGTCTTAATGCATCTTTTGATG
1 CATTTTATTTATGGCATCATTTCATGCCTTAATGCATCATTTCATG
* * *
488313 CATTTTATTTATGGAATCCTTTCATGCCTTAATGCATTC-TTTTATG
1 CATTTTATTTATGGCATCATTTCATGCCTTAATGCA-TCATTTCATG
488359 CATTTTATTTATGGCATTC-TTTCATGCCTTAATGCATCATTTCATG
1 CATTTTATTTATGGCA-TCATTTCATGCCTTAATGCATCATTTCATG
488405 CATTTTATTTATG
1 CATTTTATTTATG
488418 TATTCGGTTT
Statistics
Matches: 558, Mismatches: 58, Indels: 66
0.82 0.09 0.10
Matches are distributed among these distances:
40 38 0.07
41 6 0.01
42 9 0.02
43 1 0.00
44 9 0.02
45 87 0.16
46 380 0.68
47 8 0.01
48 3 0.01
50 2 0.00
51 2 0.00
52 13 0.02
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.47
Consensus pattern (46 bp):
CATTTTATTTATGGCATCATTTCATGCCTTAATGCATCATTTCATG
Found at i:487944 original size:20 final size:20
Alignment explanation
Indices: 487919--488405 Score: 209
Period size: 20 Copynumber: 21.7 Consensus size: 20
487909 TTTATTTATG
* *
487919 GCATCATTTCATTCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
487939 GCATCATTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
487964 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
487985 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
488005 GCATCCTTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
488030 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
488051 GCATCCTTTTATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* * * *
488071 GTATCATTTCATGCATTTTATTTACG
1 GCATCCTTTCATGC--CTTA---A-T
*
488097 GCATCCATTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
488117 GCATCCTTTCATGCTTTTATTTAC
1 GCATCCTTTCATGC-CTTA---AT
*
488141 GACATACTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
*
488162 GCATCCTTTCATGCATTTAATTTAT
1 GCATCCTTTCATGC-CTT-A---AT
* * *
488187 GTCATCATTTCATGCATTTTATTTAC
1 G-CATCCTTTCATGC--CTTA---AT
488213 GACATCCTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
*
488234 GCATCATTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
488254 GCATCATTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
* *
488279 GGCATCTTTTCATGTCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* * *
488300 GCATCTTTTGATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
*
488325 GGAATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* * *
488346 GCATTCTTTTATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
*
488371 GGCATTCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
488392 GCATCATTTCATGC
1 GCATCCTTTCATGC
488406 ATTTTATTTA
Statistics
Matches: 367, Mismatches: 52, Indels: 96
0.71 0.10 0.19
Matches are distributed among these distances:
20 169 0.46
21 20 0.05
22 19 0.05
24 26 0.07
25 26 0.07
26 104 0.28
27 3 0.01
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:487989 original size:66 final size:66
Alignment explanation
Indices: 487919--488130 Score: 361
Period size: 66 Copynumber: 3.2 Consensus size: 66
487909 TTTATTTATG
* *
487919 GCATCATTTCATTCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAA
1 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAA
487984 T
66 T
*
487985 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAA
1 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAA
488050 T
66 T
* * * *
488051 GCATCCTTTTATGCCTTAATGTATCATTTCATGCATTTTATTTACGGCATCCATTCATGCCTTAA
1 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAA
488116 T
66 T
488117 GCATCCTTTCATGC
1 GCATCCTTTCATGC
488131 TTTTATTTAC
Statistics
Matches: 137, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 137 1.00
ACGTcount: A:0.21, C:0.25, G:0.10, T:0.44
Consensus pattern (66 bp):
GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAA
T
Found at i:487997 original size:112 final size:110
Alignment explanation
Indices: 487873--488418 Score: 431
Period size: 112 Copynumber: 4.8 Consensus size: 110
487863 TTTATTTATG
* *
487873 GCATCCTTTCATGCCTTAATACATCCTTTCATGTATTTTATTTATGGCATCATTTCATTCCTTAA
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATG-ATTTTATTTATGGCATCATTTCATGCCTTAA
* * * *
487938 TGCATCATTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAAT
65 TGCATCCTTTCATGCATTTTATTTATGTCATCATTTCATG-CTTAAC
*
487985 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAA
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATG-ATTTTATTTATGGCATCATTTCATGCCTTAA
* * * * *
488050 TGCATCCTTTTATGCCTTAATGTA-TCATTTCATGCATTTTAT--TT-AC
65 TGCATCCTTTCATGCATT--T-TATTTATGTCAT-CATTTCATGCTTAAC
* * * *
488096 GGCATCCATTCATGCCTTAATGCATCCTTTCATGCTTTTATTTACGACAT-ACTTTCATGCCTTA
1 -GCATCCTTTCATGCCTTAATGCATCCTTTCATGATTTTATTTATGGCATCA-TTTCATGCCTTA
*
488160 ATGCATCCTTTCATGCATTTAATTTATGTCATCATTTCATGCATTTTATTTAC
64 ATGCATCCTTTCATGCATTTTATTTATGTCATCATTTCATGC---TTA---AC
* ** *
488213 GACATCCTTTCATGCCTTAATGCATCATTTCATG-CCTTA---AT-GCATCATTTCATGCATTTT
1 G-CATCCTTTCATGCCTTAATGCATCCTTTCATGATTTTATTTATGGCATCATTTCATGC--CTT
* * * * **
488273 ATTTATGGCATCTTTTCATGTC-TTAATGCATCTT-T-TGATGCATTTTAT--TTATG
63 A---AT-GCATCCTTTCATG-CATT--T-TAT-TTATGTCAT-CATTTCATGCTTAAC
* * *
488326 GAATCCTTTCATGCCTTAATGCATTCTTTTATGCATTTTATTTATGGCATTC-TTTCATGCCTTA
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATG-ATTTTATTTATGGCA-TCATTTCATGCCTTA
*
488390 ATGCATCATTTCATGCATTTTATTTATGT
64 ATGCATCCTTTCATGCATTTTATTTATGT
488419 ATTCGGTTTA
Statistics
Matches: 348, Mismatches: 46, Indels: 82
0.73 0.10 0.17
Matches are distributed among these distances:
108 10 0.03
109 11 0.03
110 2 0.01
111 44 0.13
112 163 0.47
113 7 0.02
114 13 0.04
115 8 0.02
116 10 0.03
117 36 0.10
118 25 0.07
119 3 0.01
120 4 0.01
121 10 0.03
122 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.10, T:0.47
Consensus pattern (110 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGATTTTATTTATGGCATCATTTCATGCCTTAAT
GCATCCTTTCATGCATTTTATTTATGTCATCATTTCATGCTTAAC
Found at i:488182 original size:66 final size:65
Alignment explanation
Indices: 488097--488313 Score: 265
Period size: 66 Copynumber: 3.2 Consensus size: 65
488087 TTTATTTACG
* *
488097 GCATCCATTCATGCCTTAATGCATCCTTTCATGC-TTTTATTTACGACATACTTTCATGCCTTAA
1 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTACGACAT-CTTTCATGCCTTAA
488161 T
65 T
*
488162 GCATCCTTTCATGCATTTAATTTATGTCATCATTTCATGCATTTTATTTACGACATCCTTTCATG
1 GCATCCTTTCATGC-CTT-A---ATG-CATCATTTCATGCATTTTATTTACGACAT-CTTTCATG
488227 CCTTAAT
59 CCTTAAT
* * * *
488234 GCATCATTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGGCATCTTTTCATGTCTTAA
1 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTACGACATC-TTTCATGCCTTAA
488299 T
65 T
* *
488300 GCATCTTTTGATGC
1 GCATCCTTTCATGC
488314 ATTTTATTTA
Statistics
Matches: 133, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
65 14 0.11
66 54 0.41
67 4 0.03
70 4 0.03
71 14 0.11
72 43 0.32
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (65 bp):
GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTACGACATCTTTCATGCCTTAAT
Found at i:488783 original size:13 final size:13
Alignment explanation
Indices: 488765--488808 Score: 70
Period size: 13 Copynumber: 3.3 Consensus size: 13
488755 CTCAAGCTCA
488765 ATTATACTTAAAC
1 ATTATACTTAAAC
488778 ATTATACTTAAAC
1 ATTATACTTAAAC
*
488791 AATTATACTTAAAT
1 -ATTATACTTAAAC
488805 ATTA
1 ATTA
488809 ATTGTTAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTATACTTAAAC
Found at i:488793 original size:27 final size:27
Alignment explanation
Indices: 488734--488808 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
488724 TATATTTCCT
488734 AACAATTATACTTAAACA-T-TACTCA
1 AACAATTATACTTAAACATTATACTCA
* *
488759 AGCTCAATTATACTTAAACATTATACTTA
1 A--ACAATTATACTTAAACATTATACTCA
*
488788 AACAATTATACTTAAATATTA
1 AACAATTATACTTAAACATTA
488809 ATTGTTAGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
25 1 0.02
27 34 0.81
28 1 0.02
29 6 0.14
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (27 bp):
AACAATTATACTTAAACATTATACTCA
Found at i:488797 original size:14 final size:14
Alignment explanation
Indices: 488734--488803 Score: 76
Period size: 14 Copynumber: 5.1 Consensus size: 14
488724 TATATTTCCT
488734 AACAATTATACTTA
1 AACAATTATACTTA
*
488748 AAC-A-T-TACTCA
1 AACAATTATACTTA
*
488759 AGCTCAATTATACTTA
1 A--ACAATTATACTTA
488775 AAC-ATTATACTTA
1 AACAATTATACTTA
488788 AACAATTATACTTA
1 AACAATTATACTTA
488802 AA
1 AA
488804 TATTAATTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
11 6 0.13
12 1 0.02
13 15 0.33
14 17 0.37
15 1 0.02
16 6 0.13
ACGTcount: A:0.47, C:0.17, G:0.01, T:0.34
Consensus pattern (14 bp):
AACAATTATACTTA
Found at i:492151 original size:20 final size:21
Alignment explanation
Indices: 492094--492151 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
492084 ACATAAGGAG
*
492094 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCAC-TGTT-A-GAA
* *
492118 TGCATCGGTACACTGTT-GAA
1 TGCATCGATGCACTGTTAGAA
492138 TGCATCGATGCACT
1 TGCATCGATGCACT
492152 TCAAGGGGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 14 0.48
23 4 0.14
24 11 0.38
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCACTGTTAGAA
Found at i:493731 original size:23 final size:23
Alignment explanation
Indices: 493640--493721 Score: 128
Period size: 23 Copynumber: 3.6 Consensus size: 23
493630 ACATTTTATA
* *
493640 TGGCACTTCGGTACAATTTTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
493663 CGGTACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
493686 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
493709 TGGCACTTCGGTG
1 TGGCACTTCGGTG
493722 TATTTATACG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.17, C:0.24, G:0.27, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:497819 original size:19 final size:19
Alignment explanation
Indices: 497795--497831 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
497785 TTATTTTGGA
497795 TTTTTCAATATCGCAACAC
1 TTTTTCAATATCGCAACAC
*
497814 TTTTTCACTATCGCAACA
1 TTTTTCAATATCGCAACA
497832 ACACGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.38
Consensus pattern (19 bp):
TTTTTCAATATCGCAACAC
Found at i:497855 original size:22 final size:22
Alignment explanation
Indices: 497830--497872 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
497820 ACTATCGCAA
* *
497830 CAACACGTTTTTCAAACTCTCG
1 CAACACATTTTTCAAAATCTCG
497852 CAACACATTTTTCAAAATCTC
1 CAACACATTTTTCAAAATCTC
497873 ATTGCGAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33
Consensus pattern (22 bp):
CAACACATTTTTCAAAATCTCG
Found at i:500874 original size:16 final size:17
Alignment explanation
Indices: 500842--500875 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
500832 ATGCAAAAAT
*
500842 GGTATCGATACCCAAAG
1 GGTACCGATACCCAAAG
500859 GGTACCGATA-CCAAAG
1 GGTACCGATACCCAAAG
500875 G
1 G
500876 AAATGGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.35, C:0.24, G:0.26, T:0.15
Consensus pattern (17 bp):
GGTACCGATACCCAAAG
Found at i:501039 original size:107 final size:106
Alignment explanation
Indices: 500753--501046 Score: 419
Period size: 106 Copynumber: 2.8 Consensus size: 106
500743 CTATTAATAT
* * *
500753 GGTATCGATACCAAAAGTAATGGAAGTATCAATACTCACAAGGTAGTATCGATACTACCCG-CAT
1 GGTACCGATACCAAAGGTAATGGAAGTATCGATACTCACAAGGTAGTATCGATACTA-CCGACAT
*
500817 TGCTCAAATTCCAGAATGCAAAAATGGTATCGATACCCAAAG
65 TGCTCAAATTCCAGAATGCAAAAATGGTACCGATACCCAAAG
* * * ** * *
500859 GGTACCGATACCAAAGGAAATGGAAATATCGATACTAACAAGGTAGTATCGATACTACAAAAAAT
1 GGTACCGATACCAAAGGTAATGGAAGTATCGATACTCACAAGGTAGTATCGATACTACCGACATT
*
500924 GCTCAAATTCTAGAATGCAAAAATGGTACCGATACCCAAAG
66 GCTCAAATTCCAGAATGCAAAAATGGTACCGATACCCAAAG
* *
500965 GGCTACTGATACCAAAGGTAATGGAAGTATCGATACTCACAAGGTAGTATCGTTACTACCGACAT
1 GG-TACCGATACCAAAGGTAATGGAAGTATCGATACTCACAAGGTAGTATCGATACTACCGACAT
* *
501030 TGCTTAAATTTCAGAAT
65 TGCTCAAATTCCAGAAT
501047 AAAATATTAT
Statistics
Matches: 162, Mismatches: 24, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
105 1 0.01
106 94 0.58
107 67 0.41
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.23
Consensus pattern (106 bp):
GGTACCGATACCAAAGGTAATGGAAGTATCGATACTCACAAGGTAGTATCGATACTACCGACATT
GCTCAAATTCCAGAATGCAAAAATGGTACCGATACCCAAAG
Found at i:503453 original size:14 final size:15
Alignment explanation
Indices: 503436--503466 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
503426 TTAAATACTT
503436 TTTTATTTT-TAAAA
1 TTTTATTTTATAAAA
503450 TTTTATTTTATAAAA
1 TTTTATTTTATAAAA
503465 TT
1 TT
503467 GTTCTAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTATTTTATAAAA
Found at i:514757 original size:23 final size:21
Alignment explanation
Indices: 514722--514764 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
514712 TATAAAAAAT
514722 TATTTTTTATTAAATATTTTTAG
1 TATTTTTTATT-AAT-TTTTTAG
514745 TATTTTTGT-TTAATTTTTTA
1 TATTTTT-TATTAATTTTTTA
514765 AATAATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 9 0.47
24 1 0.05
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (21 bp):
TATTTTTTATTAATTTTTTAG
Found at i:529074 original size:20 final size:20
Alignment explanation
Indices: 529045--529087 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
529035 ATTTCACCAC
*
529045 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
529065 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
529085 ATG
1 ATG
529088 GGCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:529709 original size:7 final size:7
Alignment explanation
Indices: 529697--529731 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
529687 CACAGCTTCA
529697 TTTTTTC
1 TTTTTTC
529704 TTTTTTC
1 TTTTTTC
*
529711 TTTTTTT
1 TTTTTTC
529718 TTCTTTTC
1 TT-TTTTC
529726 TTTTTT
1 TTTTTT
529732 TTACAAAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:529719 original size:17 final size:15
Alignment explanation
Indices: 529697--529733 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
529687 CACAGCTTCA
*
529697 TTTTTTCTT-TTTTC
1 TTTTTTTTTCTTTTC
529711 TTTTTTTTTCTTTTC
1 TTTTTTTTTCTTTTC
529726 TTTTTTTT
1 TTTTTTTT
529734 ACAAAGTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTTTTCTTTTC
Found at i:540623 original size:21 final size:21
Alignment explanation
Indices: 540597--540643 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
540587 ACGATGGCAA
540597 TGTGGTAGCAGATGAATATGT
1 TGTGGTAGCAGATGAATATGT
540618 TGTGGTAGCAGATGAATATGT
1 TGTGGTAGCAGATGAATATGT
540639 TGTGG
1 TGTGG
540644 CAAAATGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.04, G:0.36, T:0.34
Consensus pattern (21 bp):
TGTGGTAGCAGATGAATATGT
Found at i:542029 original size:20 final size:20
Alignment explanation
Indices: 542000--542042 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
541990 ATTTCACCAC
*
542000 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
542020 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
542040 ATG
1 ATG
542043 GGCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:564792 original size:21 final size:20
Alignment explanation
Indices: 564767--564823 Score: 87
Period size: 21 Copynumber: 2.8 Consensus size: 20
564757 AATGCTCAGA
564767 GGGAATCGATTCCCCATGAGG
1 GGGAATCGATTCCCCATGA-G
*
564788 GGGAATCGATTTCCCATGAG
1 GGGAATCGATTCCCCATGAG
564808 GGGATATCGATTCCCC
1 GGGA-ATCGATTCCCC
564824 CTGGTTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.15
21 28 0.85
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (20 bp):
GGGAATCGATTCCCCATGAG
Found at i:567781 original size:9 final size:10
Alignment explanation
Indices: 567762--567821 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
567752 TTTGACTGAT
567762 TTTGAACCGG
1 TTTGAACCGG
567772 TTTG-ACCGG
1 TTTGAACCGG
* *
567781 TTTTAAACCAGT
1 -TTTGAACC-GG
567793 TTTGAACCGG
1 TTTGAACCGG
567803 TTTTG-ACCGG
1 -TTTGAACCGG
*
567813 TCTGAACCG
1 TTTGAACCG
567822 ACCCGACCGA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
9 8 0.20
10 17 0.43
11 14 0.35
12 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (10 bp):
TTTGAACCGG
Found at i:567784 original size:20 final size:20
Alignment explanation
Indices: 567749--567813 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
567739 ACTGGAAAAT
* *
567749 CGGTTTGACTGATTTTGAAC
1 CGGTTTGACCGGTTTTGAAC
*
567769 CGGTTTGACCGGTTTTAAAC
1 CGGTTTGACCGGTTTTGAAC
*
567789 CAGTTTTGAACCGGTTTTG-AC
1 C-GGTTTG-ACCGGTTTTGAAC
567810 CGGT
1 CGGT
567814 CTGAACCGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 20 0.54
21 8 0.22
22 9 0.24
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
CGGTTTGACCGGTTTTGAAC
Found at i:567800 original size:11 final size:11
Alignment explanation
Indices: 567761--567813 Score: 67
Period size: 11 Copynumber: 5.1 Consensus size: 11
567751 GTTTGACTGA
567761 TTTTGAACCGG
1 TTTTGAACCGG
567772 -TTTG-ACCGG
1 TTTTGAACCGG
* *
567781 TTTTAAACCAG
1 TTTTGAACCGG
567792 TTTTGAACCGG
1 TTTTGAACCGG
567803 TTTTG-ACCGG
1 TTTTGAACCGG
567813 T
1 T
567814 CTGAACCGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 5 0.14
10 13 0.36
11 18 0.50
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (11 bp):
TTTTGAACCGG
Found at i:567829 original size:5 final size:5
Alignment explanation
Indices: 567819--567848 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
567809 CCGGTCTGAA
567819 CCGAC CCGA- CCGAC CCGAC CCGAC CCGAC C
1 CCGAC CCGAC CCGAC CCGAC CCGAC CCGAC C
567849 GTTGACTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
CCGAC
Found at i:567832 original size:9 final size:9
Alignment explanation
Indices: 567818--567849 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
567808 ACCGGTCTGA
567818 ACCGACCCG
1 ACCGACCCG
567827 ACCGACCCG
1 ACCGACCCG
567836 ACCCGACCCG
1 A-CCGACCCG
567846 ACCG
1 ACCG
567850 TTGACTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.22, C:0.56, G:0.22, T:0.00
Consensus pattern (9 bp):
ACCGACCCG
Found at i:567836 original size:14 final size:15
Alignment explanation
Indices: 567819--567848 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
567809 CCGGTCTGAA
567819 CCGACCCGA-CCGAC
1 CCGACCCGACCCGAC
567833 CCGACCCGACCCGAC
1 CCGACCCGACCCGAC
567848 C
1 C
567849 GTTGACTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (15 bp):
CCGACCCGACCCGAC
Found at i:575107 original size:12 final size:12
Alignment explanation
Indices: 575090--575125 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
575080 CGACCGACCC
575090 GACCCGACCGTT
1 GACCCGACCGTT
575102 GACCCGACC--T
1 GACCCGACCGTT
575112 GACCCGACCGTT
1 GACCCGACCGTT
575124 GA
1 GA
575126 ACGTTGACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.45
12 12 0.55
ACGTcount: A:0.19, C:0.42, G:0.25, T:0.14
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:575109 original size:22 final size:22
Alignment explanation
Indices: 575083--575125 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
575073 TCTGAACCGA
575083 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
*
575105 CCGACCTGACCCGACCGTTGA
1 CCGACCCGACCCGACCGTTGA
575126 ACGTTGACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.47, G:0.23, T:0.12
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:578413 original size:7 final size:8
Alignment explanation
Indices: 578396--578420 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
578386 ATATATACAT
578396 AAAAATAA
1 AAAAATAA
578404 AAAAATAA
1 AAAAATAA
578412 AAAAATAA
1 AAAAATAA
578420 A
1 A
578421 TATCAATACC
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Done.