Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_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: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 30
Found at i:235210 original size:32 final size:32
Alignment explanation
Indices: 235152--235262 Score: 186
Period size: 32 Copynumber: 3.4 Consensus size: 32
235142 GGAAATGGCT
*
235152 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
* *
235185 AGCGCAACGCGAAATGAAATCGCAACGATAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
235217 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
235249 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
235263 CACAAATCGC
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
32 59 0.81
33 14 0.19
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:235220 original size:14 final size:14
Alignment explanation
Indices: 235168--235257 Score: 63
Period size: 14 Copynumber: 5.9 Consensus size: 14
235158 ATGCGAAATG
*
235168 AAAATCGCAACGAC
1 AAAATCGCAACGAT
*
235182 AAAAGCGCAACGCGAAAT
1 AAAATCGCAA--CG--AT
*
235200 GAAATCGCAACGAT
1 AAAATCGCAACGAT
235214 AAAATCGCAACGCGAAAT
1 AAAATCGCAA--CG--AT
* *
235232 GAAATCGCAACGAC
1 AAAATCGCAACGAT
235246 AAAATCGCAACG
1 AAAATCGCAACG
235258 CGAAACACAA
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
14 32 0.53
16 8 0.13
18 20 0.33
ACGTcount: A:0.48, C:0.24, G:0.19, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAT
Found at i:235291 original size:19 final size:19
Alignment explanation
Indices: 235269--235408 Score: 130
Period size: 19 Copynumber: 7.6 Consensus size: 19
235259 GAAACACAAA
*
235269 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
235288 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
235304 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
235320 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
235339 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
235358 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
235378 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
235398 TCGTGTTGCGA
1 TCGCGTTGCGA
235409 AAGTAAACTA
Statistics
Matches: 101, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
14 11 0.11
16 4 0.04
18 11 0.11
19 46 0.46
20 29 0.29
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:235366 original size:39 final size:38
Alignment explanation
Indices: 235316--235389 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
235306 GTTGCGATTT
**
235316 CATTTCGCGTTGCGATTTTCATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGTCATTTCGCATTGCGATAGC
*
235354 CATTTCCGCGTTGCGATAGTCATTTCGCGTTGCGAT
1 CATTT-CGCGTTGCGATAGTCATTTCGCATTGCGAT
235390 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 5 0.16
39 27 0.84
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (38 bp):
CATTTCGCGTTGCGATAGTCATTTCGCATTGCGATAGC
Found at i:237278 original size:14 final size:14
Alignment explanation
Indices: 237259--237294 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
237249 ATTGTTTAAT
237259 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
237273 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
237287 TGATTTGT
1 TGATTTGT
237295 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:237420 original size:14 final size:15
Alignment explanation
Indices: 237401--237477 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
237391 CGAAATGGCT
237401 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
237415 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
237433 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
237452 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
237466 ATCGCAATGCGA
1 ATCGCAA-GCGA
237478 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:237433 original size:19 final size:19
Alignment explanation
Indices: 237411--237477 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
237401 ATCGCAACGA
237411 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
237430 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
237448 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
237462 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
237478 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:237910 original size:14 final size:14
Alignment explanation
Indices: 237891--237926 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
237881 TTTGTTTAAT
237891 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
237905 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
237919 TGATTTGT
1 TGATTTGT
237927 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:238052 original size:14 final size:15
Alignment explanation
Indices: 238033--238109 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
238023 CGAAATGGCT
238033 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
238047 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
238065 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
238084 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
238098 ATCGCAATGCGA
1 ATCGCAA-GCGA
238110 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:238065 original size:19 final size:19
Alignment explanation
Indices: 238043--238109 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
238033 ATCGCAACGA
238043 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
238062 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
238080 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
238094 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
238110 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:238216 original size:632 final size:633
Alignment explanation
Indices: 237009--238347 Score: 2644
Period size: 632 Copynumber: 2.1 Consensus size: 633
236999 TGGTAAGTCA
237009 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
237074 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
66 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
237139 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
131 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
237204 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTGATTGTTTAATTGATTTGTAA
196 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTT-ATTGTTTAATTGATTTGTAA
237269 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
260 AAGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAG
237334 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
325 TTGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGG
237399 CTATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGA
390 CTATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGA
237464 AAATCGCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGCGTTGC
455 AAATCGCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGCGTTGC
237529 GATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACT
520 GATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACT
237594 AATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
585 AATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
237643 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
237708 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
66 TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
237773 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
131 CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
237838 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTT-TTGTTTAATTGATTTGTAAA
196 TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTATTGTTTAATTGATTTGTAAA
237902 AGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAGT
261 AGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAGT
237967 TGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGC
326 TGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGC
238032 TATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGAA
391 TATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGAA
238097 AATCGCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGCGTTGCG
456 AATCGCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGCGTTGCG
238162 ATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTA
521 ATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTA
238227 ATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
586 ATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
* *
238275 AATGCAAGTTTTGTTAACATATATACTCCTTTTGTTTTGAAAATGTTTGGTTAAGTAACTAGAAT
1 AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
238340 TCAATAAT
66 TCAATAAT
238348 AATTGTTAAA
Statistics
Matches: 703, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
632 464 0.66
634 239 0.34
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (633 bp):
AATGCAAGTTTTGTTAACATATATACTCCTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAAT
TCAATAATTTGCTGTTTGTAGGTTTTAGATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTT
CTGCAGGTTAATCCTTAAGTGAGCTGCGTGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCT
TGATTCAATAATTGATGAAGAAATAAGAATTATTATTATTTTTTATTGTTTAATTGATTTGTAAA
AGATGATTTGTAAATGTTGATTTGTTTAATTGATGTGTACATAATTTGTGTTGAAATGTAATAGT
TGATTTGTTGATTTTCAATCTGCTTTATGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGC
TATCGCAACGAGAAAATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAACGAGAA
AATCGCAATGCGATTTTCATTTCGCGTTGCGATATTCTCGTTGCGATAACCATTTTCGCGTTGCG
ATAGTCAAATGAATTAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTA
ATACATGCCTAACTGAAAATGTTAAAAGTGCACACATAAAATACACAT
Found at i:239270 original size:24 final size:24
Alignment explanation
Indices: 239214--239272 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
239204 AGTCAGTATT
* *
239214 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
239238 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
239262 CGAATTTTGAT
1 CGAAATTTGAT
239273 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:239464 original size:12 final size:12
Alignment explanation
Indices: 239447--239471 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
239437 ATATAATCCT
239447 GAAGAAGAAAAA
1 GAAGAAGAAAAA
239459 GAAGAAGAAAAA
1 GAAGAAGAAAAA
239471 G
1 G
239472 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:241788 original size:19 final size:19
Alignment explanation
Indices: 241766--241852 Score: 77
Period size: 19 Copynumber: 5.1 Consensus size: 19
241756 GGAAATTACT
241766 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
241785 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
241799 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
241818 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
241832 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
241851 AT
1 AT
241853 TACAACGCGA
Statistics
Matches: 52, Mismatches: 6, Indels: 20
0.67 0.08 0.26
Matches are distributed among these distances:
14 19 0.37
15 2 0.04
16 4 0.08
17 4 0.08
18 2 0.04
19 21 0.40
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:241789 original size:39 final size:35
Alignment explanation
Indices: 241766--241863 Score: 123
Period size: 33 Copynumber: 2.9 Consensus size: 35
241756 GGAAATTACT
*
241766 ATCGCAATGCGAAATGAAAATCGCAA--CGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGAAAGA
**
241799 ATCGCAATGCGAAATGAAAATCGCAA--CGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGAAAGA
**
241832 ATCGCAATGCGAAATGAAAATTACAACGCGAA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGAA
241864 TTTAATTTCG
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
33 56 0.95
35 3 0.05
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.13
Consensus pattern (35 bp):
ATCGCAATGCGAAATGAAAATCGCAACGCGAAAGA
Found at i:241859 original size:33 final size:33
Alignment explanation
Indices: 241766--241852 Score: 165
Period size: 33 Copynumber: 2.6 Consensus size: 33
241756 GGAAATTACT
241766 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
241799 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
241832 ATCGCAATGCGAAATGAAAAT
1 ATCGCAATGCGAAATGAAAAT
241853 TACAACGCGA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:241881 original size:19 final size:20
Alignment explanation
Indices: 241859--241901 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
241849 AAATTACAAC
241859 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
241878 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
241898 GCGA
1 GCGA
241902 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:241886 original size:14 final size:14
Alignment explanation
Indices: 241887--241920 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
241877 TGCGATTTTC
241887 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
241901 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
241915 ATTTTC
1 ATTTTC
241921 ATTTCGAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:242061 original size:14 final size:14
Alignment explanation
Indices: 242042--242078 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
242032 CATCAATTAA
242042 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
242056 ACAAATCACCTTTT
1 ACAAATCAACTTTT
242070 ACAAATCAA
1 ACAAATCAA
242079 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:243520 original size:42 final size:42
Alignment explanation
Indices: 243435--243528 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
243425 GTGAATCGGG
* *
243435 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
* * *
243477 CTCTTGAACGGTGGGAGGAGA-CTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGG-GACCTCTTCAACG-ATGACAGGGGC
*
243519 CTCTTCAACG
1 CTCTTGAACG
243529 ATAGGAGTGG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 38 0.86
43 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
Found at i:243542 original size:42 final size:42
Alignment explanation
Indices: 243465--243557 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 42
243455 CCTCTTCAAC
* * * * *
243465 GATGACAGTGGCCTCTTGAACGGTGGGAGGAGACTCTCGA-G
1 GATGATAGGGGCCTCTTCAACGATAGGAGGAGACTCTCGATG
*
243506 GAATGATAGGGGCCTCTTCAACGATAGGAGTG-GACTCTTGATG
1 G-ATGATAGGGGCCTCTTCAACGATAGGAG-GAGACTCTCGATG
243549 GATGATAGG
1 GATGATAGG
243558 CGAGTCGGGC
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.02
42 39 0.91
43 3 0.07
ACGTcount: A:0.25, C:0.16, G:0.37, T:0.23
Consensus pattern (42 bp):
GATGATAGGGGCCTCTTCAACGATAGGAGGAGACTCTCGATG
Found at i:245639 original size:33 final size:33
Alignment explanation
Indices: 245582--245680 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
245572 ACGAGATAAT
* *
245582 GAGAATTGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
245616 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
245649 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
245681 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 46 0.78
34 13 0.22
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:245674 original size:19 final size:19
Alignment explanation
Indices: 245652--245702 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
245642 GCGACGAGAG
245652 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
245671 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
245690 AATCGCAATGCGA
1 AATCGCAACGCGA
245703 TTTTGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:245731 original size:19 final size:19
Alignment explanation
Indices: 245698--245764 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
245688 AAAATCGCAA
**
245698 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
245717 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
** *
245736 TGCGATAGTTATTTCCGCTT
1 TGCGATTTTTATTT-CGCGT
245756 TGCGATTTT
1 TGCGATTTT
245765 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:246358 original size:41 final size:41
Alignment explanation
Indices: 246306--246383 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
246296 CGAAAGTCAG
* ** *
246306 TATCGCGTTGCGAAAGTAAGTATTTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
246347 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
246384 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:246380 original size:20 final size:20
Alignment explanation
Indices: 246287--246380 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
246277 CGCTAAGTAA
*
246287 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
246307 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
** ** * *
246327 ATTTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
246348 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
246368 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
246381 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 46 0.79
21 12 0.21
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:246399 original size:41 final size:41
Alignment explanation
Indices: 246369--246464 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
246359 ATAGTCAGTA
* * *
246369 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
246410 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
246451 TCGCATTGCGAATT
1 TCGCATTGCGAATT
246465 GGGGAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:246413 original size:20 final size:20
Alignment explanation
Indices: 246369--246461 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
246359 ATAGTCAGTA
* **
246369 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
246390 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
246410 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
246431 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
246451 TCGCATTGCGA
1 TCGCATTGCGA
246462 ATTGGGGAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:248753 original size:2 final size:2
Alignment explanation
Indices: 248748--248809 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
248738 ACACACACAC
248748 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
248790 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
248810 CTGTGAACAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:249750 original size:2 final size:2
Alignment explanation
Indices: 249743--249774 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
249733 TAATACTCAC
249743 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
249775 TCAATTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:258844 original size:15 final size:15
Alignment explanation
Indices: 258826--258881 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
258816 TAACCGGTTT
258826 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
* *
258841 CGGTTTTTTTAAAAATC
1 CGG--TTTTAAAAAAAC
*
258858 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
258873 CGATTTTAA
1 CGGTTTTAA
258882 TATTATTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 19 0.59
17 13 0.41
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:258854 original size:17 final size:17
Alignment explanation
Indices: 258829--258879 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
258819 CCGGTTTCGG
258829 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
* *
258846 TTTTTAAAAATCCGG--
1 TTTTAAAAAAACCGGTT
* *
258861 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
258878 TT
1 TT
258880 AATATTATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
15 11 0.42
17 15 0.58
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:258959 original size:32 final size:33
Alignment explanation
Indices: 258923--259031 Score: 161
Period size: 33 Copynumber: 3.4 Consensus size: 33
258913 ACAAAGTTTA
*
258923 CGAT-AATTGAAATACTTAAATACTTTCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTTCAAGTT
* *
258955 CGATAAATTAAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTTCAAGTT
*
258988 CGATAAATTCAAATACTTAAAAAC-TTCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTTCAAGTT
259020 CGAT-AATTGAAA
1 CGATAAATTGAAA
259032 CAAAGTTTAC
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
31 7 0.10
32 15 0.21
33 48 0.69
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (33 bp):
CGATAAATTGAAATACTTAAAAACTTTCAAGTT
Found at i:259044 original size:21 final size:21
Alignment explanation
Indices: 259020--259061 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
259010 ACTTCAAGTT
*
259020 CGATAATTGAAACAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
*
259041 CGATAATTAAAATAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
259062 AAAATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (21 bp):
CGATAATTAAAACAAAGTTTA
Found at i:263698 original size:150 final size:154
Alignment explanation
Indices: 263505--263838 Score: 430
Period size: 150 Copynumber: 2.2 Consensus size: 154
263495 AGGTACATAG
* * * * * * * *
263505 GTATTCTATTGTGGTATATGAGCATATGGTTTAAATTTAGTAAAAACAAACTTAAAATAAATGAC
1 GTATTCTACTATGGTTTAGGAGCATGTGGATCAAATTTAGTAAAAACAAAATTAAAATAAATGAC
* *
263570 AAATTGAA-AGAATAAGGAGATTATGAAAAATT-GAAG-C-ATT-AAATTAA-AAAAA-TTGTTA
66 AAATTGAAGA-AATAAGGAGATTATAAAAAATTAAAAGACAATTGAAA--AATAAAAATTTGTTA
* * *
263628 TCAAAAAGAAGAATTGAAGGTATACGT
128 TCAAAAAGAAGAATTAAAAGTATACAT
*
263655 GTATTCTACTATGGTTTAGGAGCATGTGGATCAAATTTGGTAAAAACAAAATTAAAATAAATGAC
1 GTATTCTACTATGGTTTAGGAGCATGTGGATCAAATTTAGTAAAAACAAAATTAAAATAAATGAC
*
263720 GAATTGAAGAAATAAGGAGATTATAAAAAATTAAAAGACCAAATTGAAAAATAAAAATTTGTTAT
66 AAATTGAAGAAATAAGGAGATTATAAAAAATTAAAAGA-C-AATTGAAAAATAAAAATTTGTTAT
*
263785 CAAAAAGATGAATTAAAAGTATACAT
129 CAAAAAGAAGAATTAAAAGTATACAT
263811 GTATTCTACTATGGTTTAGGAGCATGTG
1 GTATTCTACTATGGTTTAGGAGCATGTG
263839 ACTCAAACTT
Statistics
Matches: 159, Mismatches: 16, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
150 84 0.53
151 4 0.03
153 1 0.01
154 2 0.01
155 8 0.05
156 60 0.38
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (154 bp):
GTATTCTACTATGGTTTAGGAGCATGTGGATCAAATTTAGTAAAAACAAAATTAAAATAAATGAC
AAATTGAAGAAATAAGGAGATTATAAAAAATTAAAAGACAATTGAAAAATAAAAATTTGTTATCA
AAAAGAAGAATTAAAAGTATACAT
Found at i:268188 original size:2 final size:2
Alignment explanation
Indices: 268149--268175 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
268139 TATAGTTTTC
268149 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
268176 AGCCTTATAT
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:271643 original size:20 final size:21
Alignment explanation
Indices: 271618--271710 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
271608 TTTTCCCAAT
*
271618 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
271638 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
271659 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
271679 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
271700 TCGCAATGCGA
1 TCGCAATGCGA
271711 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:271724 original size:20 final size:20
Alignment explanation
Indices: 271699--271813 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
271689 AATTGGGAAA
*
271699 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
271719 ATCGCAATGTGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
271740 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
271760 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
271780 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
271800 TTCGCAACGCGATA
1 ATCGCAACGCGATA
271814 ATACATAATC
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:271725 original size:41 final size:41
Alignment explanation
Indices: 271618--271710 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
271608 TTTTCCCAAT
271618 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
271659 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
271700 TCGCAATGCGA
1 TCGCAATGCGA
271711 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:271741 original size:41 final size:41
Alignment explanation
Indices: 271696--271833 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
271686 GCGAATTGGG
* * * *
271696 AAAATCGCAATGCGATACTGACTATCGCAATGTGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
271737 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
271779 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
271818 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
271834 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.40
41 43 0.55
42 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:272361 original size:20 final size:20
Alignment explanation
Indices: 272309--272365 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
272299 GATTCTCTCA
**
272309 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCATTTTCGCG
*
272329 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCG
**
272349 TTGCGATTTTCATTTTC
1 TTGCGATAGTCATTTTC
272366 AGAAACTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.44
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:273706 original size:18 final size:18
Alignment explanation
Indices: 273685--273729 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
273675 TCCACTTCGG
*
273685 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
273703 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
273721 GAGCCATCA
1 GAGCCATCA
273730 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:274230 original size:20 final size:20
Alignment explanation
Indices: 274205--274250 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
274195 TAGTTTACTT
274205 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
274225 TCGCAACGTGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
274245 TCGCAA
1 TCGCAA
274251 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:274259 original size:19 final size:19
Alignment explanation
Indices: 274216--274270 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
274206 CGCAACACGA
274216 AAATGACTATCGCAACGTGG
1 AAATGACTATCGCAAC-TGG
*
274236 AAATGGCTATCGCAA-TGCG
1 AAATGACTATCGCAACTG-G
**
274255 AAATGAAAATCGCAAC
1 AAATGACTATCGCAAC
274271 GACAAAATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 2 0.07
19 13 0.45
20 14 0.48
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (19 bp):
AAATGACTATCGCAACTGG
Found at i:274279 original size:14 final size:14
Alignment explanation
Indices: 274260--274317 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
274250 ATGCGAAATG
274260 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
274274 AAAATCGCAAAGCGAA
1 AAAATCGC-AA-CGAC
*
274290 ATGAAATCGCAATGAC
1 A--AAATCGCAACGAC
274306 AAAATCGCAACG
1 AAAATCGCAACG
274318 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 18 0.50
15 2 0.06
16 7 0.19
17 2 0.06
18 7 0.19
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:274335 original size:33 final size:33
Alignment explanation
Indices: 274244--274336 Score: 152
Period size: 32 Copynumber: 2.8 Consensus size: 33
274234 GGAAATGGCT
* *
274244 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAAAGCGAAATGAAAATCGCAATGACAAA
274277 ATCGCAAAGCGAAATG-AAATCGCAATGACAAA
1 ATCGCAAAGCGAAATGAAAATCGCAATGACAAA
*
274309 ATCGCAACGCGAAATGAAAATCGCAATG
1 ATCGCAAAGCGAAATGAAAATCGCAATG
274337 CGATTTGTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.54
33 26 0.46
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAAAGCGAAATGAAAATCGCAATGACAAA
Found at i:274370 original size:14 final size:14
Alignment explanation
Indices: 274351--274408 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
274341 TTGTGTTTCG
274351 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
274365 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
274381 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
274397 CGTTGCGATTTT
1 CGTTGCGATTTT
274409 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:274385 original size:32 final size:33
Alignment explanation
Indices: 274346--274424 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
274336 GCGATTTGTG
274346 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
274378 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
274411 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
274425 AGCCATTTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:274436 original size:20 final size:20
Alignment explanation
Indices: 274411--274464 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
274401 GCGATTTTCA
*
274411 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
274431 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
274451 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
274465 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:274474 original size:20 final size:20
Alignment explanation
Indices: 274411--274480 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
274401 GCGATTTTCA
* ** *
274411 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGTAAG
* *
274431 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTAAG
**
274451 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATAGTAAG
*
274471 TTTCGTGTTG
1 TTTCGCGTTG
274481 TGAAAGTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTAAG
Found at i:276506 original size:19 final size:19
Alignment explanation
Indices: 276484--276551 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
276474 ATCGCAACGA
276484 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
276503 GAAAATTGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
276522 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
276536 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
276552 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
19 28 0.64
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:276595 original size:20 final size:20
Alignment explanation
Indices: 276570--276627 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
276560 TCGCATTGCG
*
276570 ATTTTCTCGTTGCGATAGCC
1 ATTTTCACGTTGCGATAGCC
*
276590 ATTTTCGCGTTGCGATAGCC
1 ATTTTCACGTTGCGATAGCC
276610 ATTTTCACGTTGCGATAG
1 ATTTTCACGTTGCGATAG
276628 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCACGTTGCGATAGCC
Found at i:277730 original size:24 final size:24
Alignment explanation
Indices: 277684--277737 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
277674 GTATTCGAAA
* *
277684 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
* *
277708 TTTGATATTGGTCAATATACGGAT
1 TTTGATATTGGTCAATACACGGAC
277732 TTTGAT
1 TTTGAT
277738 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:277929 original size:12 final size:12
Alignment explanation
Indices: 277912--277936 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
277902 ATATAATCCT
277912 GAAGAAGAAAAA
1 GAAGAAGAAAAA
277924 GAAGAAGAAAAA
1 GAAGAAGAAAAA
277936 G
1 G
277937 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:280239 original size:19 final size:19
Alignment explanation
Indices: 280217--280333 Score: 119
Period size: 19 Copynumber: 6.7 Consensus size: 19
280207 GGAAATTACT
280217 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
280236 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
280250 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
280269 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
280288 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
280302 ATCGCATTGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
280321 ATCGCAACGCGAA
1 ATCGCAATGCGAA
280334 TTTAATTTCG
Statistics
Matches: 79, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
14 18 0.23
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 49 0.62
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:280276 original size:52 final size:52
Alignment explanation
Indices: 280217--280333 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
280207 GGAAATTACT
280217 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* *
280269 ATCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCATTGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAA
*
280321 ATCGCAACGCGAA
1 ATCGCAATGCGAA
280334 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:280380 original size:33 final size:33
Alignment explanation
Indices: 280329--280418 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
280319 AAATCGCAAC
* * *
280329 GCGAATTTAATTTCGCGTTGTGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
280362 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
280395 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
280419 AGTACTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:280382 original size:19 final size:19
Alignment explanation
Indices: 280358--280418 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
280348 GTGATTCTCT
280358 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
280377 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
280391 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
280410 CATTGCGAT
1 CGTTGCGAT
280419 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:280396 original size:14 final size:14
Alignment explanation
Indices: 280344--280400 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
280334 TTTAATTTCG
*
280344 CGTTGTGATTCTCT
1 CGTTGCGATTCTCT
*
280358 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
280377 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
280391 CGTTGCGATT
1 CGTTGCGATT
280401 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:280544 original size:14 final size:14
Alignment explanation
Indices: 280525--280561 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
280515 CATCAATTAA
280525 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
280539 ACAAATCACCTTTT
1 ACAAATCAACTTTT
280553 ACAAATCAA
1 ACAAATCAA
280562 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:281984 original size:21 final size:21
Alignment explanation
Indices: 281918--281984 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
281908 GTGAATCGGG
*
281918 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
281938 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
281960 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
281981 CTCT
1 CTCT
281985 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:284154 original size:19 final size:19
Alignment explanation
Indices: 284132--284201 Score: 122
Period size: 19 Copynumber: 3.7 Consensus size: 19
284122 GCGATGAGAG
*
284132 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
284151 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
284170 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
284189 AATCGCAATGCGA
1 AATCGCAACGCGA
284202 TTTTTGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:284156 original size:33 final size:33
Alignment explanation
Indices: 284064--284147 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
284054 GAGATAATGT
284064 GAATCGCAACGCGGAAATGACTATCGCAACGAGA
1 GAATCGCAACGC-GAAATGACTATCGCAACGAGA
* *
284098 GAATCGCAACGCGAAATGACTATCGCGATGAGA
1 GAATCGCAACGCGAAATGACTATCGCAACGAGA
284131 GAATCGCAACGCGAAAT
1 GAATCGCAACGCGAAAT
284148 AAAAATCGCA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 36 0.75
34 12 0.25
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.13
Consensus pattern (33 bp):
GAATCGCAACGCGAAATGACTATCGCAACGAGA
Found at i:284219 original size:19 final size:19
Alignment explanation
Indices: 284197--284263 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
284187 AAAATCGCAA
*
284197 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
* *
284216 TGCGTTTTTTATTTCTCGT
1 TGCGATTTTTATTTCGCGT
**
284235 TGCGATAGTTATTTCTGCGT
1 TGCGATTTTTATTTC-GCGT
284255 TGCGATTTT
1 TGCGATTTT
284264 CATTCTCGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
19 28 0.74
20 10 0.26
ACGTcount: A:0.09, C:0.15, G:0.22, T:0.54
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:285726 original size:31 final size:30
Alignment explanation
Indices: 285666--285743 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 30
285656 TTCAATGTCA
* * *
285666 AAGTGACCAAAGCTTAATAAAAACGATAACAT
1 AAGTGA-CAAAACTTAATAAAAACAATAAC-C
285698 AAGTGACAAAAACTTAAT-AAAACAATAACC
1 AAGTGAC-AAAACTTAATAAAAACAATAACC
285728 AAGTGATCAAAACTTA
1 AAGTGA-CAAAACTTA
285744 TGTTTTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 14 0.34
31 12 0.29
32 15 0.37
ACGTcount: A:0.55, C:0.15, G:0.10, T:0.19
Consensus pattern (30 bp):
AAGTGACAAAACTTAATAAAAACAATAACC
Found at i:286081 original size:18 final size:19
Alignment explanation
Indices: 286060--286097 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
286050 ATTTATAAAC
286060 TTATAAAATTT-GAATAAT
1 TTATAAAATTTAGAATAAT
*
286078 TTATAAATTTTAGAATAAT
1 TTATAAAATTTAGAATAAT
286097 T
1 T
286098 ATTTATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
TTATAAAATTTAGAATAAT
Found at i:291014 original size:29 final size:29
Alignment explanation
Indices: 290981--291050 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
290971 ATTGTTGAAA
* * **
290981 GTTCAAAGTTTGGCACCGATTGGTGTATG
1 GTTCAAAGTTTGGCACCGAATAGTACATG
291010 GTTCAAAGTTTGGCACCGAATAGTACATG
1 GTTCAAAGTTTGGCACCGAATAGTACATG
291039 GTTCAAAGTTTG
1 GTTCAAAGTTTG
291051 ACAGATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.33
Consensus pattern (29 bp):
GTTCAAAGTTTGGCACCGAATAGTACATG
Found at i:291420 original size:22 final size:22
Alignment explanation
Indices: 291392--291435 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
291382 GGGAAATTAC
291392 TCGTTTAATTTACAAACACGAA
1 TCGTTTAATTTACAAACACGAA
*
291414 TCGTTTAATTTCCAAACACGAA
1 TCGTTTAATTTACAAACACGAA
291436 CCCGTAACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (22 bp):
TCGTTTAATTTACAAACACGAA
Found at i:293170 original size:16 final size:17
Alignment explanation
Indices: 293149--293180 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
293139 ATTTGCAAAA
293149 TAAATATTAT-AATAAT
1 TAAATATTATGAATAAT
293165 TAAATATTATGAATAA
1 TAAATATTATGAATAA
293181 AGTAGAGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAATATTATGAATAAT
Found at i:293785 original size:12 final size:12
Alignment explanation
Indices: 293768--293792 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
293758 ATATTTTTAA
293768 TAAAATATTATT
1 TAAAATATTATT
293780 TAAAATATTATT
1 TAAAATATTATT
293792 T
1 T
293793 TTTATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:293850 original size:19 final size:19
Alignment explanation
Indices: 293828--293866 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
293818 ATTATCTTCC
* *
293828 AATATTAATATTTTTAATA
1 AATAATAATATTTTAAATA
293847 AATAATAATATTTTAAATA
1 AATAATAATATTTTAAATA
293866 A
1 A
293867 TACTTTACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAATAATATTTTAAATA
Found at i:301744 original size:32 final size:32
Alignment explanation
Indices: 301708--301771 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
301698 CATTTAACGG
*
301708 TTTTCTTGTGTAAAAGGATTATTTTGGTCAAA
1 TTTTCTTATGTAAAAGGATTATTTTGGTCAAA
*
301740 TTTTCTTATGTAAAATGATTATTTTGGTCAAA
1 TTTTCTTATGTAAAAGGATTATTTTGGTCAAA
301772 ATAAAAACGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48
Consensus pattern (32 bp):
TTTTCTTATGTAAAAGGATTATTTTGGTCAAA
Found at i:309138 original size:20 final size:20
Alignment explanation
Indices: 309115--309166 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
309105 AACGCGATCC
309115 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
309135 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
309155 CCAAAATCGCAA
1 CCAGAATCGCAA
309167 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:309183 original size:21 final size:20
Alignment explanation
Indices: 309156--309254 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
309146 AATCAGTTTC
309156 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
309177 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
309198 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
309218 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
309239 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
309255 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:309283 original size:20 final size:20
Alignment explanation
Indices: 309221--309414 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
309211 CGATTTTCCA
* ** *
309221 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
309241 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
309261 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
309281 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
309301 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
* *
309321 AAATCGCAATGCTTATCCGT
1 AAATCGCAACGCGTATCCGT
*
309341 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
309361 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
309381 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
309402 AAATCGCAACGCG
1 AAATCGCAACGCG
309415 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:309305 original size:60 final size:60
Alignment explanation
Indices: 309221--309414 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
309211 CGATTTTCCA
* ** * *
309221 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** * *
309281 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCTTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
309341 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
309402 AAATCGCAACGCG
1 AAATCGCAACGCG
309415 ATATTTAAAG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 80 0.73
61 30 0.27
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:309835 original size:33 final size:33
Alignment explanation
Indices: 309796--309866 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
309786 TTCACTTAGA
*
309796 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
309829 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
309862 TTTCA
1 TTTCA
309867 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:311115 original size:12 final size:12
Alignment explanation
Indices: 311098--311122 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
311088 TCTTCGGGGA
311098 CTTTTTCTTCTT
1 CTTTTTCTTCTT
311110 CTTTTTCTTCTT
1 CTTTTTCTTCTT
311122 C
1 C
311123 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:311331 original size:24 final size:24
Alignment explanation
Indices: 311297--311343 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
311287 CTGAAACATC
311297 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
311321 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
311344 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:312043 original size:20 final size:20
Alignment explanation
Indices: 312015--312403 Score: 480
Period size: 20 Copynumber: 19.4 Consensus size: 20
312005 AAATTTCAGT
* * * *
312015 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
312035 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
312055 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
312075 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
312095 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
312115 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
312135 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
312155 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
312175 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
312195 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
312215 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
312235 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
312255 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
312275 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
**
312295 GTTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
312315 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
312335 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
312355 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
312375 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
312395 GTTGCGATT
1 GTTGCGATT
312404 ATGGAAAATC
Statistics
Matches: 329, Mismatches: 32, Indels: 16
0.87 0.08 0.04
Matches are distributed among these distances:
19 5 0.02
20 319 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:313385 original size:21 final size:21
Alignment explanation
Indices: 313356--313395 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
313346 ATAAATTATT
*
313356 TAAATATACAAAAAATAAATA
1 TAAAAATACAAAAAATAAATA
*
313377 TAAAAATACTAAAAATAAA
1 TAAAAATACAAAAAATAAA
313396 ACTTAAATGA
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:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAAAATACAAAAAATAAATA
Found at i:314578 original size:25 final size:26
Alignment explanation
Indices: 314550--314598 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
314540 AATCGAGACT
314550 TACAAAATTTAAATTAGTC-AAAACA
1 TACAAAATTTAAATTAGTCGAAAACA
* **
314575 TACAAATTTTGGATTAGTCGAAAA
1 TACAAAATTTAAATTAGTCGAAAA
314599 TTACTATGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (26 bp):
TACAAAATTTAAATTAGTCGAAAACA
Found at i:315142 original size:2 final size:2
Alignment explanation
Indices: 315135--315195 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
315125 CAAAATTTTA
315135 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
315177 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
315196 ATAATATTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:315859 original size:32 final size:32
Alignment explanation
Indices: 315796--315860 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
315786 ACCCAACCAA
* * * * *
315796 ACCCGAAAATTTTACATCTTTCACCCGACCCG
1 ACCCGAAAAATATACATCCTTCAACCAACCCG
*
315828 ACCCGAAAAATATACATCCTTCAACTAACCCG
1 ACCCGAAAAATATACATCCTTCAACCAACCCG
315860 A
1 A
315861 TTTTTTTATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.35, G:0.08, T:0.22
Consensus pattern (32 bp):
ACCCGAAAAATATACATCCTTCAACCAACCCG
Found at i:316616 original size:5 final size:5
Alignment explanation
Indices: 316608--316649 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
316598 ACATATTTTA
*
316608 TTAAT TTAATT TTAAT TTCAAT TTAAT TTAA- TAAAT TTAAT T
1 TTAAT TTAA-T TTAAT TT-AAT TTAAT TTAAT TTAAT TTAAT T
316650 CTCAAATCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.09
5 19 0.59
6 10 0.31
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (5 bp):
TTAAT
Found at i:319275 original size:59 final size:62
Alignment explanation
Indices: 319181--319296 Score: 143
Period size: 59 Copynumber: 1.9 Consensus size: 62
319171 AGAAAAGAAA
*
319181 AGAAATGAAATAGAATAAAATAAAAATAAGAAAAAAATAAA-AAATAA-AA-AATAAATTGC
1 AGAAATAAAATAGAATAAAATAAAAATAAGAAAAAAATAAATAAATAATAATAATAAATTGC
* * *
319240 AGAAATAAAAT-GAGATAAAATACAAAA-AGGGAAAAATTAAATAAATAATAATAATAA
1 AGAAATAAAATAGA-ATAAAATA-AAAATAAGAAAAAAATAAATAAATAATAATAATAA
319297 TAAATAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
58 2 0.04
59 29 0.60
60 10 0.21
61 2 0.04
62 5 0.10
ACGTcount: A:0.71, C:0.02, G:0.09, T:0.18
Consensus pattern (62 bp):
AGAAATAAAATAGAATAAAATAAAAATAAGAAAAAAATAAATAAATAATAATAATAAATTGC
Found at i:320496 original size:37 final size:37
Alignment explanation
Indices: 320454--320748 Score: 260
Period size: 37 Copynumber: 8.1 Consensus size: 37
320444 AATATACTAT
320454 AAAAATATTTTCAAAAAC-ATATAATATATA-AGTTTTC
1 AAAAATATTTT-AAAAACTATATAATATATATA-TTTTC
320491 AAAAATGATTTTAAAAACTATAT-ATATTATATATTTTC
1 AAAAAT-ATTTTAAAAACTATATAATA-TATATATTTTC
* * * *
320529 -TAAA-A-TGT--AAACTATATATTATATA-ATTTTA
1 AAAAATATTTTAAAAACTATATAATATATATATTTTC
*
320560 AAAAATGTTTTAAAAA-T-TAT-ATA-ATATATTTTC
1 AAAAATATTTTAAAAACTATATAATATATATATTTTC
* * *
320593 AAAAATGTTTTCAAAACTATATATTATATA-AGTTTTC
1 AAAAATATTTTAAAAACTATATAATATATATA-TTTTC
* *
320630 -AAAATGATTTCAAAAACTATATATTATATATATTTTC
1 AAAAAT-ATTTTAAAAACTATATAATATATATATTTTC
* *
320667 TAAAATGTTTTAAAAACTATATAATATATATATTTTC
1 AAAAATATTTTAAAAACTATATAATATATATATTTTC
* * **
320704 AAAAATGTCTTTAGAAACTATATGTTATATACGTATTTTC
1 AAAAATAT-TTTAAAAACTATATAATATATA--TATTTTC
320744 AAAAA
1 AAAAA
320749 ACGTTTGCAA
Statistics
Matches: 215, Mismatches: 21, Indels: 41
0.78 0.08 0.15
Matches are distributed among these distances:
31 5 0.02
32 19 0.09
33 24 0.11
34 8 0.04
35 5 0.02
36 11 0.05
37 87 0.40
38 43 0.20
39 1 0.00
40 12 0.06
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (37 bp):
AAAAATATTTTAAAAACTATATAATATATATATTTTC
Found at i:320726 original size:138 final size:136
Alignment explanation
Indices: 320454--320716 Score: 343
Period size: 138 Copynumber: 1.9 Consensus size: 136
320444 AATATACTAT
*
320454 AAAAATATTTTCAAAAACATATAATATATAAGTTTTCAAAAATGATTTTAAAAACTATATATATT
1 AAAAATATTTTCAAAAACATATAATATATAAGTTTTCAAAAATGATTTCAAAAACTATATATATT
* *
320519 ATATATTTTCTAAAATGTAAACTATATATTATATAATTTTAAAAAATGTTTTAAAAATTATATAA
66 ATATATTTTCTAAAATGTAAACTATATAATATATAATTTTAAAAAATGTTTT---AATGATATAA
320584 TATATTTTC
128 TATATTTTC
* *
320593 AAAAATGTTTTC-AAAACTATATATTATATAAGTTTTC-AAAATGATTTCAAAAACTATATAT-T
1 AAAAATATTTTCAAAAAC-ATATAATATATAAGTTTTCAAAAATGATTTCAAAAACTATATATAT
*
320655 ATATATATTTTCTAAAATGTTTTAAAAACTATATAATATATATATTTTCAAAAATGTCTTTA
65 -TATATATTTTCTAAAATG---T--AAACTATATAATATATA-ATTTTAAAAAATGT-TTTA
320717 GAAACTATAT
Statistics
Matches: 110, Mismatches: 5, Indels: 15
0.85 0.04 0.12
Matches are distributed among these distances:
137 1 0.01
138 46 0.42
139 29 0.26
141 1 0.01
142 1 0.01
143 16 0.15
144 13 0.12
145 3 0.03
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (136 bp):
AAAAATATTTTCAAAAACATATAATATATAAGTTTTCAAAAATGATTTCAAAAACTATATATATT
ATATATTTTCTAAAATGTAAACTATATAATATATAATTTTAAAAAATGTTTTAATGATATAATAT
ATTTTC
Found at i:330640 original size:2 final size:2
Alignment explanation
Indices: 330633--330692 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
330623 ATTGAAAAGC
330633 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
330674 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
330693 GACTAAAATT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:333094 original size:2 final size:2
Alignment explanation
Indices: 333089--333120 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
333079 ACACACACAC
333089 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
333121 GGCAACAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:336453 original size:36 final size:36
Alignment explanation
Indices: 336413--336487 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
336403 AAAAAATGTA
336413 ATTGGCATGACTGCAGAGGAAGTAAACATAAAATAT
1 ATTGGCATGACTGCAGAGGAAGTAAACATAAAATAT
336449 ATTGGCATGACTGCAGAGGAAGTAAACATAAAATAT
1 ATTGGCATGACTGCAGAGGAAGTAAACATAAAATAT
336485 ATT
1 ATT
336488 CTAATTTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (36 bp):
ATTGGCATGACTGCAGAGGAAGTAAACATAAAATAT
Found at i:337217 original size:170 final size:167
Alignment explanation
Indices: 336902--337220 Score: 390
Period size: 170 Copynumber: 1.9 Consensus size: 167
336892 AATTTTATCC
*
336902 CCAAATTCACCCAAATATGTAATTAATTTCAATCATAATTTAACCTAAATTTTGTTTTTTCAAAC
1 CCAAATTCACCCAAATATGTAATTAATTTCAATCATAATTTAAACTAAATTTTGTTTTTTCAAAC
* * * * *
336967 ATATATTAGTATAACTTGCCCTAACAATTTTATTAACAAGGGATGTGATTAGTATATACATATAA
66 ATATAATAATATAACTTGCCCTAACAATTTTATTAACAAGAGATATGATCAGTATATACATATAA
*
337032 TTTGGGATAAAATTAAAATGCTTAAAAAGTTTAGGGA
131 TTTAGGATAAAATTAAAATGCTTAAAAAGTTTAGGGA
* * * * *
337069 CCAATTTCATCCAAATATGTGATTAATTTCAA-CTATAGTTTAAATTAAATTTTGTTTTTCTTTC
1 CCAAATTCACCCAAATATGTAATTAATTTCAATC-ATAATTTAAACTAAATTTTG--TTT-TTTC
* ** * * *
337133 AAACATATAATAATATAATTTGGCCC-AATGATTTTATTAACAAGAGATATTATCATTATATACG
62 AAACATATAATAATATAACTT-GCCCTAACAATTTTATTAACAAGAGATATGATCAGTATATACA
* * *
337197 TATAGTTTATGATGAAATTAAAAT
126 TATAATTTAGGATAAAATTAAAAT
337221 ATTCAAAAAA
Statistics
Matches: 126, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
166 1 0.01
167 46 0.37
169 3 0.02
170 72 0.57
171 4 0.03
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (167 bp):
CCAAATTCACCCAAATATGTAATTAATTTCAATCATAATTTAAACTAAATTTTGTTTTTTCAAAC
ATATAATAATATAACTTGCCCTAACAATTTTATTAACAAGAGATATGATCAGTATATACATATAA
TTTAGGATAAAATTAAAATGCTTAAAAAGTTTAGGGA
Found at i:355071 original size:9 final size:9
Alignment explanation
Indices: 355057--355089 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
355047 TTTTGTTTAC
355057 ATTTTTTGA
1 ATTTTTTGA
355066 A-TTTTTGA
1 ATTTTTTGA
*
355074 ATTTTTTGT
1 ATTTTTTGA
355083 ATTTTTT
1 ATTTTTT
355090 ATTGGTCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (9 bp):
ATTTTTTGA
Found at i:380220 original size:68 final size:68
Alignment explanation
Indices: 380140--380276 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
380130 CACCCACCTA
380140 CAAGAAAATACTACATCTCTGCTGATGTCACTTTTGTTGAAAAATAGAGTTATTTTACCGTTCAT
1 CAAGAAAATACTACATCTCTGCTGATGTCACTTTTGTTGAAAAATAGAGTTATTTTACCGTTCAT
380205 TAT
66 TAT
*
380208 CAAGAAAATACTACATCTCTGTTGATGTCACTTTTGTTGAAAAATAGAGTTATTTTACCGTTCAT
1 CAAGAAAATACTACATCTCTGCTGATGTCACTTTTGTTGAAAAATAGAGTTATTTTACCGTTCAT
380273 TAT
66 TAT
380276 C
1 C
380277 TTCAGGGGGA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (68 bp):
CAAGAAAATACTACATCTCTGCTGATGTCACTTTTGTTGAAAAATAGAGTTATTTTACCGTTCAT
TAT
Found at i:384039 original size:28 final size:28
Alignment explanation
Indices: 383962--384045 Score: 96
Period size: 31 Copynumber: 2.9 Consensus size: 28
383952 TTAAGTCCCG
* * *
383962 AAGTATTTTTTGGTCAAAATAAGCACCTA
1 AAGTATTTTTT-GTCAAAATAGGTAACTA
*
383991 AAGTTATCTTTTCGGTCAAAATAGGTAACTA
1 AAG-TAT-TTTT-TGTCAAAATAGGTAACTA
384022 AAGTATTTTTTGTCAAAATAGGTA
1 AAGTATTTTTTGTCAAAATAGGTA
384046 CCTATCTAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
28 13 0.28
29 7 0.15
30 6 0.13
31 21 0.45
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (28 bp):
AAGTATTTTTTGTCAAAATAGGTAACTA
Found at i:387805 original size:25 final size:25
Alignment explanation
Indices: 387762--387833 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
387752 CATTCGAAGT
* *
387762 ATTAAGTCATACATTACATTATAAAC
1 ATTAACTC-TACATTACATTAGAAAC
* *
387788 ATTAACTCTACATTACATTCGAAGC
1 ATTAACTCTACATTACATTAGAAAC
* *
387813 GTTAACTCCTATATTACATTA
1 ATTAACT-CTACATTACATTA
387834 CATTACATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 20 0.53
26 18 0.47
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (25 bp):
ATTAACTCTACATTACATTAGAAAC
Found at i:388657 original size:151 final size:148
Alignment explanation
Indices: 388242--388664 Score: 450
Period size: 151 Copynumber: 2.8 Consensus size: 148
388232 GAGCATGACT
* * * * * *
388242 ATATAACATTGAAAAGTTATGGTGAAATAATTATTATATGGTCTGATCAATTATTAAACATGGCC
1 ATATATCATTGAAAAGTCATGGTGAAATTATTATGATA-GGTCTGATCAATTATTAAATATGGTC
* * **
388307 AATATGTTTAAAAATAAGGTGATATATCATTGAAAAGAAAAATGACATTTTGAATTCAAATATCA
65 AA-AAGTTTAAAAATAAGGTGATATATCAATGAAAAG-AAAATGATGTTTTGAATTCAAATATCA
* **
388372 CTGAAAAGTCGTTTTGAGGCG
128 CTGAAAAATAATTTTGAGGCG
* * * * ***
388393 ATATATTACTGAAAAGTCATGATGAAATTCTTATGATAGGGTCTGATCAATTATTAAATAAACAC
1 ATATATCATTGAAAAGTCATGGTGAAATTATTATGATA-GGTCTGATCAATTATTAAAT--ATGG
* * * * * * * ** *
388458 TGAAAAGTTCAAAAATTAGGTGATATGTTAATGAAAGGAAAATAATGTTTTTCATTCAGATATCA
63 TCAAAAGTTTAAAAATAAGGTGATATATCAATGAAAAGAAAATGATGTTTTGAATTCAAATATCA
*
388523 CTGAAAAATAATTTTGAGGTG
128 CTGAAAAATAATTTTGAGGCG
*
388544 ATATATCATTGAAAAGTCATGGTGAAATTATTATGATAGAATCTGATCAATTATTAAATATGGTC
1 ATATATCATTGAAAAGTCATGGTGAAATTATTATGATAG-GTCTGATCAATTATTAAATATGGTC
* * *
388609 AACAAGTTTAGAAATGAGGTGATATATCACTGAAAAGAAAATTGATGTTTTGAATT
65 AA-AAGTTTAAAAATAAGGTGATATATCAATGAAAAGAAAA-TGATGTTTTGAATT
388665 ATTATGATAA
Statistics
Matches: 216, Mismatches: 51, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
149 4 0.02
150 32 0.15
151 150 0.69
152 27 0.12
153 3 0.01
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.34
Consensus pattern (148 bp):
ATATATCATTGAAAAGTCATGGTGAAATTATTATGATAGGTCTGATCAATTATTAAATATGGTCA
AAAGTTTAAAAATAAGGTGATATATCAATGAAAAGAAAATGATGTTTTGAATTCAAATATCACTG
AAAAATAATTTTGAGGCG
Found at i:388691 original size:23 final size:23
Alignment explanation
Indices: 388661--388705 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
388651 TGATGTTTTG
388661 AATTATTATGATAAAGTCTAATT
1 AATTATTATGATAAAGTCTAATT
*
388684 AATTATTATGATAAGGTCTAAT
1 AATTATTATGATAAAGTCTAAT
388706 ATATCACTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.42
Consensus pattern (23 bp):
AATTATTATGATAAAGTCTAATT
Found at i:391856 original size:2 final size:2
Alignment explanation
Indices: 391849--391889 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
391839 TTTGTTTGTT
391849 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
391890 TAAAATTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:391995 original size:59 final size:58
Alignment explanation
Indices: 391928--392087 Score: 164
Period size: 59 Copynumber: 2.7 Consensus size: 58
391918 AATTATGATC
**
391928 CTTATTCTAAATTAGTCTCTAAACTTTTAAACA-TTCTAATCACATCCTTAAACTATAA-
1 CTTATTCTAAATT-GTCTCTAAACTTTTAAACATTTC-AATCACATCCCCAAACTATAAT
* **
391986 CTATATTCTAAATTGATCT-TAAAACTTTTAAACATTTCATTTTCATCCCCAAACTATAAT
1 CT-TATTCTAAATTG-TCTCT-AAACTTTTAAACATTTCAATCACATCCCCAAACTATAAT
* *
392046 CTTCATTCTAAATTGGTCCCTAAACTTTTTGAACATTTCAAT
1 CTT-ATTCTAAATT-GTCTCTAAAC-TTTTAAACATTTCAAT
392088 TTCATCCCAC
Statistics
Matches: 85, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
58 4 0.05
59 44 0.52
60 21 0.25
61 16 0.19
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (58 bp):
CTTATTCTAAATTGTCTCTAAACTTTTAAACATTTCAATCACATCCCCAAACTATAAT
Found at i:392347 original size:29 final size:29
Alignment explanation
Indices: 392254--392365 Score: 84
Period size: 29 Copynumber: 3.8 Consensus size: 29
392244 AAGATTCAAA
* *
392254 AGTTTAGGGATCAATTTAGAATGAGAGTCAT
1 AGTTTAAGGATGAATTTAGAAT--GAGTCAT
* ** *
392285 AGTTTAAGGATGAAATT-GAAAT-TTTCAA
1 AGTTTAAGGATGAATTTAG-AATGAGTCAT
*
392313 ATGTTTAAGGAGGAATTTAGAATGAGTCAT
1 A-GTTTAAGGATGAATTTAGAATGAGTCAT
** *
392343 AGTTTGGGGATGAATTTGGAATG
1 AGTTTAAGGATGAATTTAGAATG
392366 CTTACAAGTT
Statistics
Matches: 62, Mismatches: 15, Indels: 10
0.71 0.17 0.11
Matches are distributed among these distances:
28 4 0.06
29 35 0.56
30 6 0.10
31 17 0.27
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.34
Consensus pattern (29 bp):
AGTTTAAGGATGAATTTAGAATGAGTCAT
Found at i:392377 original size:58 final size:58
Alignment explanation
Indices: 392266--392412 Score: 138
Period size: 58 Copynumber: 2.5 Consensus size: 58
392256 TTTAGGGATC
** * * *
392266 AATTTAGAATGAGAGTCATAGTTTAAGGATGAAATTGAAATTTTCAAATGTTTAAGGAGG
1 AATTTAGAAT--GAGTCATAGTTTGGGGATGAAATTGAAATTTACAAATGTTTAAGAACG
* * *
392326 AATTTAGAATGAGTCATAGTTTGGGGATGAATTTGGAATGCTTAC-AA-GTTTAAGAACT
1 AATTTAGAATGAGTCATAGTTTGGGGATGAAATTGAAAT--TTACAAATGTTTAAGAACG
392384 AATTT-GAAATGAGGATCATAGTTTGGGGA
1 AATTTAG-AATGA-G-TCATAGTTTGGGGA
392413 CATATAATAC
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
57 1 0.01
58 43 0.58
59 3 0.04
60 27 0.36
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (58 bp):
AATTTAGAATGAGTCATAGTTTGGGGATGAAATTGAAATTTACAAATGTTTAAGAACG
Found at i:393488 original size:57 final size:58
Alignment explanation
Indices: 393392--393500 Score: 193
Period size: 57 Copynumber: 1.9 Consensus size: 58
393382 GATCCTCGAT
*
393392 TATAGGGTGATGCTTTGTTGAGTCTCCCGACTATTAAAAGTTACAAAATGATCCTAAC
1 TATAAGGTGATGCTTTGTTGAGTCTCCCGACTATTAAAAGTTACAAAATGATCCTAAC
*
393450 TATAAGGTGCTGCTTTGTTGAGTC-CCCGACTATTAAAAGTTACAAAATGAT
1 TATAAGGTGATGCTTTGTTGAGTCTCCCGACTATTAAAAGTTACAAAATGAT
393501 TACCTGACAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
57 27 0.55
58 22 0.45
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (58 bp):
TATAAGGTGATGCTTTGTTGAGTCTCCCGACTATTAAAAGTTACAAAATGATCCTAAC
Found at i:394398 original size:18 final size:18
Alignment explanation
Indices: 394360--394398 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
394350 ATGTAATTTC
*
394360 TTTTAAAAAAATTATTGT
1 TTTTAAAAAAATTATTAT
* *
394378 TTTTAATAAAATTCTTAT
1 TTTTAAAAAAATTATTAT
394396 TTT
1 TTT
394399 ATACCGGGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTTAAAAAAATTATTAT
Found at i:395200 original size:22 final size:22
Alignment explanation
Indices: 395145--395194 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
395135 ACTTAATACT
395145 TTAAAAAGTTCAGTGGTATAAA
1 TTAAAAAGTTCAGTGGTATAAA
*
395167 TTAAAAAGTTCAGTGGTTTAAA
1 TTAAAAAGTTCAGTGGTATAAA
395189 TTAAAA
1 TTAAAA
395195 TTTTCAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.46, C:0.04, G:0.16, T:0.34
Consensus pattern (22 bp):
TTAAAAAGTTCAGTGGTATAAA
Found at i:396007 original size:29 final size:30
Alignment explanation
Indices: 395931--396009 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 30
395921 TTGATTTTGT
**
395931 CCCCTCATTTTTTATGATTAATTATACTTTA
1 CCCCTCA-TTTTTATGATTAATTATACTCGA
395962 CCCCTCATTTTTATGATTAATTATAC-CGA
1 CCCCTCATTTTTATGATTAATTATACTCGA
*
395991 -CCCTCATTTTCCATGATTA
1 CCCCTCATTTT-TATGATTA
396010 GTATACTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 10 0.23
29 8 0.18
30 19 0.43
31 7 0.16
ACGTcount: A:0.25, C:0.24, G:0.05, T:0.46
Consensus pattern (30 bp):
CCCCTCATTTTTATGATTAATTATACTCGA
Found at i:396781 original size:32 final size:31
Alignment explanation
Indices: 396701--396786 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 31
396691 GAGTGTGGTG
*
396701 TTTGAAAATTTTAATCCTTTATCTCTTTTAT
1 TTTGAAAATTTTAATCCTTTATCTATTTTAT
* * * *
396732 TTTG-TAACTCTAGTCCTTTATACTA-TTTAT
1 TTTGAAAATTTTAATCCTTTAT-CTATTTTAT
396762 ATTTGAAAATTTTAATCCTTTATCT
1 -TTTGAAAATTTTAATCCTTTATCT
396787 CCCGATTGCA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
30 18 0.42
31 12 0.28
32 13 0.30
ACGTcount: A:0.27, C:0.14, G:0.05, T:0.55
Consensus pattern (31 bp):
TTTGAAAATTTTAATCCTTTATCTATTTTAT
Found at i:400849 original size:17 final size:18
Alignment explanation
Indices: 400810--400857 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
400800 TATTTCTGAG
*
400810 GGAATTGAAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
400828 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
*
400845 GGAATTTGAATCT
1 GGAATTGGAATCT
400858 AATTCCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.31
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:402383 original size:10 final size:10
Alignment explanation
Indices: 402370--402423 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
402360 GTTTGATTTG
402370 ATTTGTTTTT
1 ATTTGTTTTT
*
402380 ATTT-TATTAT
1 ATTTGT-TTTT
402390 ATTTGTTTTT
1 ATTTGTTTTT
*
402400 ATTT-TATTAT
1 ATTTGT-TTTT
402410 ATTTGTTTTT
1 ATTTGTTTTT
402420 ATTT
1 ATTT
402424 TTGACTGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
9 2 0.06
10 32 0.89
11 2 0.06
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.76
Consensus pattern (10 bp):
ATTTGTTTTT
Found at i:402395 original size:20 final size:20
Alignment explanation
Indices: 402370--402424 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
402360 GTTTGATTTG
402370 ATTTGTTTTTATTTTATTAT
1 ATTTGTTTTTATTTTATTAT
402390 ATTTGTTTTTATTTTATTAT
1 ATTTGTTTTTATTTTATTAT
402410 ATTTGTTTTTATTTT
1 ATTTGTTTTTATTTT
402425 TGACTGATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (20 bp):
ATTTGTTTTTATTTTATTAT
Found at i:402685 original size:19 final size:19
Alignment explanation
Indices: 402653--402704 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
402643 CAAAAAATAA
*
402653 ATAA-ATAAAAATAAAAAT
1 ATAATATAAATATAAAAAT
*
402671 ATAAT-TATAATATAAATAT
1 ATAATATA-AATATAAAAAT
*
402690 ATTATATAAATATAA
1 ATAATATAAATATAA
402705 TAGTAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 6 0.21
19 20 0.71
20 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAATATAAATATAAAAAT
Found at i:402702 original size:6 final size:6
Alignment explanation
Indices: 402653--402704 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
402643 CAAAAAATAA
* * * *
402653 ATAAAT AAAAAT AAAAAT ATAATT AT-AAT ATAAAT ATATTAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATA-AAT ATAAAT
402701 ATAA
1 ATAA
402705 TAGTAATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
5 4 0.11
6 29 0.76
7 5 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATAAAT
Found at i:403730 original size:19 final size:20
Alignment explanation
Indices: 403687--403730 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
403677 TCAATAAGGC
** *
403687 TATCGATACTGGCCCTTGGG
1 TATCGATACTCACCCTTGAG
403707 TATCGATACTCACCC-TGAG
1 TATCGATACTCACCCTTGAG
403726 TATCG
1 TATCG
403731 CTACCAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (20 bp):
TATCGATACTCACCCTTGAG
Found at i:403801 original size:21 final size:21
Alignment explanation
Indices: 403769--403844 Score: 125
Period size: 21 Copynumber: 3.6 Consensus size: 21
403759 AAATGCCATG
*
403769 GTATTAATACTCTTATGGGGA
1 GTATCAATACTCTTATGGGGA
*
403790 GTATCAACACTCTTATGGGGA
1 GTATCAATACTCTTATGGGGA
*
403811 GTATCAATACTCTTATGAGGA
1 GTATCAATACTCTTATGGGGA
403832 GTATCAATACTCT
1 GTATCAATACTCT
403845 ACCCTGGGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (21 bp):
GTATCAATACTCTTATGGGGA
Found at i:403868 original size:41 final size:42
Alignment explanation
Indices: 403769--403870 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
403759 AAATGCCATG
* * **
403769 GTATTAATACTCTTATGGGGAGTATCAACACTCTTATGGGGA
1 GTATCAATACTCTTATGAGGAGTATCAACACTCTTACCGGGA
* *
403811 GTATCAATACTCTTATGAGGAGTATCAATACTC-TACCCTGG-
1 GTATCAATACTCTTATGAGGAGTATCAACACTCTTA-CCGGGA
*
403852 GTATCGATACTCTTATGAG
1 GTATCAATACTCTTATGAG
403871 TATCAATACC
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 20 0.38
42 32 0.62
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (42 bp):
GTATCAATACTCTTATGAGGAGTATCAACACTCTTACCGGGA
Found at i:406597 original size:43 final size:43
Alignment explanation
Indices: 406489--406975 Score: 395
Period size: 43 Copynumber: 11.7 Consensus size: 43
406479 CCGCTAATGT
* * * * **
406489 TAGCGGCGTTTGTAAAATAAAAATGCCGCAAAAAATCAAGATCTA
1 TAGCGGCGTTT-TTATATACAAACGCCGCAAAAGGTC-AGATCTA
406534 TAGCGGCGTTTTTGA-A-ACAAACGCCGCAAAAGGGT-AGATCTA
1 TAGCGGCGTTTTT-ATATACAAACGCCGCAAAA-GGTCAGATCTA
* * *
406576 TAGCGACGTTTTTATATACAAACGCCACAAAAGGTTGAGATCTA
1 TAGCGGCGTTTTTATATACAAACGCCGCAAAAGG-TCAGATCTA
* *
406620 TAGCGGCGTTTTTAGA-ACAAACACCGCAAAAGGTCAGATCTA
1 TAGCGGCGTTTTTATATACAAACGCCGCAAAAGGTCAGATCTA
* * * *
406662 TAGCGGCGATTTTGTATATAAACGCCGCAAAAGGTCATATCTA
1 TAGCGGCGTTTTTATATACAAACGCCGCAAAAGGTCAGATCTA
* * * * * *
406705 TAGCGACGATTTTGTATATAAACGCCACAAAAGGTCAGATCTG
1 TAGCGGCGTTTTTATATACAAACGCCGCAAAAGGTCAGATCTA
* *
406748 TA---GC------A-A-A-AAATGCCGCAAAAGGTCATATCTA
1 TAGCGGCGTTTTTATATACAAACGCCGCAAAAGGTCAGATCTA
* * *
406779 TAGCGGCGGTTTTGTATACAAACGCCGCAAAAGGTCAGATCTG
1 TAGCGGCGTTTTTATATACAAACGCCGCAAAAGGTCAGATCTA
** * * * *
406822 TAGCACCATTTTT-TGA-ACAAACACCGCAAAAAGTCATATCTA
1 TAGCGGCGTTTTTAT-ATACAAACGCCGCAAAAGGTCAGATCTA
*
406864 TAGCGGCAG-TTTTA-ATACAAATGCCGCAAAAGGTCAGATCTA
1 TAGCGGC-GTTTTTATATACAAACGCCGCAAAAGGTCAGATCTA
* * * * *
406906 TAGTGGCCTTTTTTTATACAAACGCCGCAAAAGGTCATATCTG
1 TAGCGGCGTTTTTATATACAAACGCCGCAAAAGGTCAGATCTA
* **
406949 TAGCAGCGTTTTTGGA-ACAAACGCCGC
1 TAGCGGCGTTTTTATATACAAACGCCGC
406976 TAATTACCAT
Statistics
Matches: 359, Mismatches: 58, Indels: 53
0.76 0.12 0.11
Matches are distributed among these distances:
31 22 0.06
32 1 0.00
33 1 0.00
34 2 0.01
40 1 0.00
41 3 0.01
42 119 0.33
43 174 0.48
44 24 0.07
45 12 0.03
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTTTATATACAAACGCCGCAAAAGGTCAGATCTA
Found at i:406624 original size:86 final size:85
Alignment explanation
Indices: 406529--406975 Score: 419
Period size: 85 Copynumber: 5.4 Consensus size: 85
406519 AAAAATCAAG
406529 ATCTATAGCGGCGTTTTTGAAACAAACGCCGCAAAAGGGT-AGATCTATAGCGACGTTTTTATAT
1 ATCTATAGCGGCGTTTTTGAAACAAACGCCGCAAAA-GGTCAGATCTATAGCGACGTTTTTATAT
* * *
406593 ACAAACGCCACAAAAGGTTGAG
65 ACAAACGCCGCAAAAGG-TCAT
* * * *
406615 ATCTATAGCGGCGTTTTT-AGAACAAACACCGCAAAAGGTCAGATCTATAGCGGCGATTTTGTAT
1 ATCTATAGCGGCGTTTTTGA-AACAAACGCCGCAAAAGGTCAGATCTATAGCGACGTTTTTATAT
*
406679 ATAAACGCCGCAAAAGGTCAT
65 ACAAACGCCGCAAAAGGTCAT
* * * * * *
406700 ATCTATAGCGACGATTTTGTATATAAACGCCACAAAAGGTCAGATCTGTA--G-C------A-A-
1 ATCTATAGCGGCGTTTTTG-AAACAAACGCCGCAAAAGGTCAGATCTATAGCGACGTTTTTATAT
*
406754 A-AAATGCCGCAAAAGGTCAT
65 ACAAACGCCGCAAAAGGTCAT
* * * *
406774 ATCTATAGCGGCGGTTTTGTATACAAACGCCGCAAAAGGTCAGATCTGTAGC-ACCATTTTT-TG
1 ATCTATAGCGGCGTTTTTG-AAACAAACGCCGCAAAAGGTCAGATCTATAGCGA-CGTTTTTAT-
* *
406837 A-ACAAACACCGCAAAAAGTCAT
63 ATACAAACGCCGCAAAAGGTCAT
* * * * *
406859 ATCTATAGCGGCAG-TTTT-AATACAAATGCCGCAAAAGGTCAGATCTATAGTGGCCTTTTTTTA
1 ATCTATAGCGGC-GTTTTTGAA-ACAAACGCCGCAAAAGGTCAGATCTATAGCGACGTTTTTATA
406922 TACAAACGCCGCAAAAGGTCAT
64 TACAAACGCCGCAAAAGGTCAT
* * *
406944 ATCTGTAGCAGCGTTTTTGGAACAAACGCCGC
1 ATCTATAGCGGCGTTTTTGAAACAAACGCCGC
406976 TAATTACCAT
Statistics
Matches: 301, Mismatches: 36, Indels: 49
0.78 0.09 0.13
Matches are distributed among these distances:
74 64 0.21
75 1 0.00
76 1 0.00
77 1 0.00
83 2 0.01
84 38 0.13
85 98 0.33
86 95 0.32
87 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (85 bp):
ATCTATAGCGGCGTTTTTGAAACAAACGCCGCAAAAGGTCAGATCTATAGCGACGTTTTTATATA
CAAACGCCGCAAAAGGTCAT
Found at i:406810 original size:74 final size:74
Alignment explanation
Indices: 406685--406826 Score: 248
Period size: 74 Copynumber: 1.9 Consensus size: 74
406675 GTATATAAAC
*
406685 GCCGCAAAAGGTCATATCTATAGCGACGATTTTGTATATAAACGCCACAAAAGGTCAGATCTGTA
1 GCCGCAAAAGGTCATATCTATAGCGACGATTTTGTATACAAACGCCACAAAAGGTCAGATCTGTA
406750 GCAAAAAAT
66 GCAAAAAAT
* * *
406759 GCCGCAAAAGGTCATATCTATAGCGGCGGTTTTGTATACAAACGCCGCAAAAGGTCAGATCTGTA
1 GCCGCAAAAGGTCATATCTATAGCGACGATTTTGTATACAAACGCCACAAAAGGTCAGATCTGTA
406824 GCA
66 GCA
406827 CCATTTTTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 64 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (74 bp):
GCCGCAAAAGGTCATATCTATAGCGACGATTTTGTATACAAACGCCACAAAAGGTCAGATCTGTA
GCAAAAAAT
Found at i:410724 original size:41 final size:42
Alignment explanation
Indices: 410626--411007 Score: 355
Period size: 41 Copynumber: 9.4 Consensus size: 42
410616 TTGTAAACAC
* * *
410626 AAACGCCACTAAAGTACGAGTTTTTAGC-GC-GTTTTTA-AA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCAGTTTGTATAA
* *
410665 AAACGCCACTAAAG-ACGAGTTTATAGCGGCAATTT-TATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCAGTTTGTATAA
*
410705 AAACGCCACTAATGTACGAGTCTATAGCGGC-GTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCAGTTTGTATAA
** * *
410746 AAACGCCACTAAAGTACGAGTCTATAGCATCA-TTTTTTTAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCAGTTTGTATAA
* * * *
410787 AAACGCCACTAAAATACCAGTTTTTAGC-G-ATGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCA-GTTTGTATAA
* * *** *
410828 AAACGCCGCTAAAGTATGAGTCTATAGC-ATTGTTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCAGTTTGTATAA
* *
410869 AAATGCCACTAAAGTACGAGTCTATAGTGGC-GTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCAGTTTGTATAA
* * *
410910 AAACGCCACTAAAGT--GTTGCTCTATCGCTGC-GTTTTGTATAA
1 AAACGCCACTAAAGTACG-AG-TCTATAGCGGCAG-TTTGTATAA
* *
410952 AAACGCCACT-AAGTACGAGTATATAGCGG-TGTTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCAG-TTTGTATAA
*
410993 AAACGCCGCTAAAGT
1 AAACGCCACTAAAGT
411008 TACCATTTTG
Statistics
Matches: 283, Mismatches: 43, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
38 12 0.04
39 20 0.07
40 22 0.08
41 204 0.72
42 24 0.08
43 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (42 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCAGTTTGTATAA
Found at i:410790 original size:82 final size:82
Alignment explanation
Indices: 410626--411007 Score: 418
Period size: 82 Copynumber: 4.7 Consensus size: 82
410616 TTGTAAACAC
* * * *
410626 AAACGCCACTAAAGTACGAGTTTTTAGC-GCGTTTTTA-AAAAACGCCACTAAAG-ACGAGTTTA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
** *
410688 TAGCGGCAATTTTATAA
66 TAGCATCATTTTTATAA
*
410705 AAACGCCACTAATGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
*
410770 TAGCATCATTTTTTTAA
66 TAGCATCATTTTTATAA
* * * * ** * *
410787 AAACGCCACTAAAATACCAGTTTTTAGCGATGTTTGTATAAAAACGCCGCTAAAGTATGAGTCTA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
** *
410852 TAGCATTGTTTATATAA
66 TAGCATCATTTTTATAA
* * *
410869 AAATGCCACTAAAGTACGAGTCTATAGTGGCGTTTGTATAAAAACGCCACTAAAGT--GTTGCTC
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACG-AG-TC
* *
410932 TATCGC-TGCGTTTTGTATAA
64 TATAGCAT-CATTTT-TATAA
* * *
410952 AAACGCCACT-AAGTACGAGTATATAGCGGTGTTTTGTATAAAAACGCCGCTAAAGT
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCG-TTTGTATAAAAACGCCACTAAAGT
411008 TACCATTTTG
Statistics
Matches: 255, Mismatches: 40, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
79 25 0.10
80 9 0.04
81 18 0.07
82 166 0.65
83 37 0.15
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (82 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTA
TAGCATCATTTTTATAA
Done.