Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006180.1 Hibiscus syriacus cultivar Beakdansim tig00014695_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: 72302
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:8823 original size:2 final size:2
Alignment explanation
Indices: 8818--8895 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
8808 ATTTTTTAAT
8818 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
8860 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
8896 ATGAATGATA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10430 original size:16 final size:16
Alignment explanation
Indices: 10409--10453 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
10399 GGTAATAATA
*
10409 TTTTACTATTAAACTC
1 TTTTACTATTAAACCC
10425 TTTTACTAAATTAAACCC
1 TTTTACT--ATTAAACCC
*
10443 TTTTAATATTA
1 TTTTACTATTA
10454 TTATTATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 11 0.44
18 14 0.56
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTTACTATTAAACCC
Found at i:12145 original size:42 final size:42
Alignment explanation
Indices: 12042--12172 Score: 194
Period size: 42 Copynumber: 3.2 Consensus size: 42
12032 TGATGTTGAT
* * *
12042 TTTA-TTTAGACTTATTAAGACTTATTAGTGTTATGATGTTA
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
* *
12083 TTT-TTTTAAACTTATTGAGACTTAATGGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
*
12124 TTTATTTTAGATTTATTGAGACTTAATAGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
12166 TTTATTT
1 TTTATTT
12173 ACTTATTTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
41 38 0.47
42 42 0.52
ACGTcount: A:0.26, C:0.04, G:0.17, T:0.53
Consensus pattern (42 bp):
TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
Found at i:14299 original size:21 final size:21
Alignment explanation
Indices: 14275--14318 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
14265 AAGACAATCA
14275 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* * *
14296 AGAGTTGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
14317 AG
1 AG
14319 GCATAAGGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.32, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:14394 original size:33 final size:33
Alignment explanation
Indices: 14352--14417 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
14342 AAATAGATGG
*
14352 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
14385 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
14418 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:16232 original size:19 final size:19
Alignment explanation
Indices: 16208--16256 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
16198 AATGTAGGGT
16208 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
16227 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
16246 TAATTTTGTAT
1 TAATTTTGTAT
16257 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:17228 original size:399 final size:400
Alignment explanation
Indices: 16490--17452 Score: 1741
Period size: 399 Copynumber: 2.4 Consensus size: 400
16480 AATTTACAAT
*
16490 ATGGCAAACAAGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
16555 CGAAACCCAAAAATATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACATGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCTGTTTT
16620 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
*
16685 AATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATA
196 AATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
16750 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
261 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
*
16815 GTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATA-TTTTGG
326 GTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTAG
16879 TCCAGAATGA
391 TCCAGAATGA
*
16889 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
16954 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCAGTACAAGTATACCTGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCTGTTTT
* *
17019 ATAAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
17084 AATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
196 AATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
17149 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
261 AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
*
17214 GTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTAG
326 GTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTAG
17279 TCCAGAATGA
391 TCCAGAATGA
17289 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
17354 CGAAACCCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCTGTTTT
* * *
17419 ATGGGAGAATTGGTATATAAT-ATGTATCGACACT
131 ATGAGAGAATAGGTCTA-AATAATGTATCGACACT
17453 GTTTAATGTT
Statistics
Matches: 539, Mismatches: 23, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
399 372 0.69
400 164 0.30
401 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (400 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCTGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
AACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCG
GTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTAG
TCCAGAATGA
Found at i:17471 original size:200 final size:200
Alignment explanation
Indices: 16490--17452 Score: 1714
Period size: 200 Copynumber: 4.8 Consensus size: 200
16480 AATTTACAAT
* *
16490 ATGGCAAACAAGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * * **
16555 CGAAACCCAAAAATATAATGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACATGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
16620 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
16685 AATGA
196 AATGA
*
16690 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
16755 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
16820 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATA-TTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
16884 AATGA
196 AATGA
16889 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
16954 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCAGTACAAGTATACCTGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
17019 ATAAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
17084 AATGA
196 AATGA
17089 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
17154 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
17219 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTAGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
17284 AATGA
196 AATGA
*
17289 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
17354 CGAAACCCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
17419 ATGGGAGAATTGGTATATAAT-ATGTATCGACACT
131 ATGAGAGAATAGGTCTA-AATAATGTATCGACACT
17453 GTTTAATGTT
Statistics
Matches: 736, Mismatches: 25, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
199 194 0.26
200 539 0.73
201 3 0.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:18987 original size:3 final size:3
Alignment explanation
Indices: 18949--19001 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
18939 CAAGCGGTCA
* * * * * *
18949 ATG AAG ATG AAG ATG ACG ATG AAG ATG ACG ACG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
18997 ATG AT
1 ATG AT
19002 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.40, C:0.06, G:0.32, T:0.23
Consensus pattern (3 bp):
ATG
Found at i:19001 original size:12 final size:12
Alignment explanation
Indices: 18949--19000 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
18939 CAAGCGGTCA
*
18949 ATGAAGATGAAG
1 ATGACGATGAAG
18961 ATGACGATGAAG
1 ATGACGATGAAG
* *
18973 ATGACGACGATG
1 ATGACGATGAAG
* *
18985 ATGATGATGATG
1 ATGACGATGAAG
18997 ATGA
1 ATGA
19001 TCCAAACAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.40, C:0.06, G:0.33, T:0.21
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:20546 original size:183 final size:183
Alignment explanation
Indices: 20209--20778 Score: 982
Period size: 183 Copynumber: 3.1 Consensus size: 183
20199 CAAAGTTTTC
* *
20209 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTTGATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* * *
20274 CAAAAAGTGTCG--ATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAA
66 CAAAAAGTGTCGACATT---TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
* *
20337 TATAATCGGTATAAATATACCGGTTTTATGAGCGAATAAGTCTACAACCTATATCG
128 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
20393 ACACTTTTTAATATTATGTCGGTACTTTATGTCGAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
20458 CAAAAAATGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
20523 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
20576 ACACTTTTTAATATTGTGTCGGTACTTTATGTCTAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
20641 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* *
20706 AACCGATATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
20759 ACACTTTTTAATATTGTGTC
1 ACACTTTTTAATATTGTGTC
20779 ACTAATTTTA
Statistics
Matches: 369, Mismatches: 15, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
183 294 0.80
184 72 0.20
186 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:24427 original size:21 final size:21
Alignment explanation
Indices: 24401--24440 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
24391 TCGTTGAACA
24401 GGGGGAATCGGTACCCTCTAT
1 GGGGGAATCGGTACCCTCTAT
*
24422 GGGGGAATCGGTTCCCTCT
1 GGGGGAATCGGTACCCTCT
24441 GAGCATTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.25, G:0.35, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTACCCTCTAT
Found at i:27133 original size:21 final size:21
Alignment explanation
Indices: 27107--27146 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27097 CAGAACCCCA
*
27107 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
27128 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
27147 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:27181 original size:20 final size:21
Alignment explanation
Indices: 27129--27189 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
27119 TTCCCCTGTG
27129 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
27152 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
27172 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
27190 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:31042 original size:22 final size:21
Alignment explanation
Indices: 31000--31039 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
30990 GAGTTTGTTT
*
31000 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
31021 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
31040 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:33733 original size:87 final size:87
Alignment explanation
Indices: 33637--33799 Score: 292
Period size: 87 Copynumber: 1.9 Consensus size: 87
33627 AAATAGGTCA
33637 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
33702 CTC-GTTAAATACCTATTTTATT
66 C-CGGTTAAATACCTATTTTATT
* *
33724 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
33789 CCGGTTAAATA
66 CCGGTTAAATA
33800 ATATAACATA
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
86 1 0.01
87 72 0.99
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATACCTATTTTATT
Found at i:33771 original size:23 final size:23
Alignment explanation
Indices: 33721--33765 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
33711 TACCTATTTT
* *
33721 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
33744 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
33766 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:34600 original size:21 final size:21
Alignment explanation
Indices: 34574--34618 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
34564 GATTTCTGGG
* *
34574 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
34595 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
34616 CAA
1 CAA
34619 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:35486 original size:31 final size:31
Alignment explanation
Indices: 35448--35570 Score: 194
Period size: 31 Copynumber: 4.0 Consensus size: 31
35438 GGGTCGAGGG
35448 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
35479 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
35510 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
35541 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
35571 GTCCTTCGGG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
31 84 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:38558 original size:21 final size:21
Alignment explanation
Indices: 38532--38576 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38522 GATTTCTGGG
* *
38532 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
38553 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
38574 CAA
1 CAA
38577 ACGATAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:39565 original size:31 final size:31
Alignment explanation
Indices: 39443--39565 Score: 178
Period size: 31 Copynumber: 4.0 Consensus size: 31
39433 GGGTCGAGGG
39443 TTACCTATGTTCTTCGGAACATATGGACT-A
1 TTACCTATGTTCTTCGGAACATATGGACTGA
*
39473 TTTACCTATGTTCTTCGGAACATATGGACTGT
1 -TTACCTATGTTCTTCGGAACATATGGACTGA
* *
39505 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGA
*
39536 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
39566 GTCCTTCGGG
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
31 82 0.99
32 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGA
Found at i:41097 original size:23 final size:24
Alignment explanation
Indices: 41071--41121 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
41061 TTAATTGTTG
* * *
41071 TTAAATTTTTTTAAA-AGTTTATT
1 TTAAATATTTTTAAACAATTAATT
41094 TT-AATATTTTTAAACAATTAATT
1 TTAAATATTTTTAAACAATTAATT
41117 TTAAA
1 TTAAA
41122 ATACTAGCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 11 0.48
23 10 0.43
24 2 0.09
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TTAAATATTTTTAAACAATTAATT
Found at i:44128 original size:23 final size:23
Alignment explanation
Indices: 44098--44153 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
44088 TGTACTTCTG
44098 TGCTGAATCATTTAGCATTGTTT
1 TGCTGAATCATTTAGCATTGTTT
44121 TGCTGAATCATTTAGCATTGTTT
1 TGCTGAATCATTTAGCATTGTTT
44144 TGCTGAATCA
1 TGCTGAATCA
44154 GTCATCACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (23 bp):
TGCTGAATCATTTAGCATTGTTT
Found at i:44262 original size:48 final size:47
Alignment explanation
Indices: 44200--44299 Score: 155
Period size: 48 Copynumber: 2.1 Consensus size: 47
44190 CGCTGAATGC
* * * *
44200 TGAATGGTTCCATTAAGAGTCAAACAAACAACCCCTAAGTTTTTTTTA
1 TGAATAGTTACATTAAGAGACAAACAAACAA-CCCTAAGCTTTTTTTA
44248 TGAATAGTTACATTAAGAGACAAACAAACAACCCTAAGCTTTTTTTA
1 TGAATAGTTACATTAAGAGACAAACAAACAACCCTAAGCTTTTTTTA
44295 TGAAT
1 TGAAT
44300 GTTTTACTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
47 20 0.42
48 28 0.58
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (47 bp):
TGAATAGTTACATTAAGAGACAAACAAACAACCCTAAGCTTTTTTTA
Found at i:46820 original size:36 final size:36
Alignment explanation
Indices: 46768--46840 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
46758 AATATAAAAT
46768 TTTGCATCTTTTCTTGTTTATAATGACAAGTCAACA
1 TTTGCATCTTTTCTTGTTTATAATGACAAGTCAACA
*
46804 TTTGTATCTTTTCTTGTTTATAATGACAAGTCAACA
1 TTTGCATCTTTTCTTGTTTATAATGACAAGTCAACA
46840 T
1 T
46841 GAAAATATCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (36 bp):
TTTGCATCTTTTCTTGTTTATAATGACAAGTCAACA
Found at i:47798 original size:27 final size:27
Alignment explanation
Indices: 47764--47815 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
47754 ATATATTTTT
*
47764 TTAAATTATAG-TAGTAATAAAATATTC
1 TTAAATTA-AGTTAATAATAAAATATTC
*
47791 TTAAATTAAGTTAATGATAAAATAT
1 TTAAATTAAGTTAATAATAAAATAT
47816 ATTTTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (27 bp):
TTAAATTAAGTTAATAATAAAATATTC
Found at i:47859 original size:31 final size:31
Alignment explanation
Indices: 47815--47883 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
47805 TGATAAAATA
* *
47815 TATTTTATTTTTTAAGTT-TAAACATATATTT
1 TATTTTATATTTTAACTTATAAA-ATATATTT
* *
47846 TATTTTGTATTTTAACTTATTAAATATATTT
1 TATTTTATATTTTAACTTATAAAATATATTT
*
47877 TAATTTA
1 TATTTTA
47884 AAATTAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (31 bp):
TATTTTATATTTTAACTTATAAAATATATTT
Found at i:47971 original size:30 final size:27
Alignment explanation
Indices: 47867--48020 Score: 106
Period size: 27 Copynumber: 5.7 Consensus size: 27
47857 TTAACTTATT
*
47867 AAATATATTTTAATTTAAAATTAAAATA
1 AAATATATTTTAAATTAAAA-TAAAATA
* *
47895 ATATATATTTTTAAATTAAAATAATAATG
1 AAATATA-TTTTAAATTAAAATAA-AATA
* *
47924 AAGTAT-TTTTAAATTAAGATAATAATA
1 AAATATATTTTAAATTAAAATAA-AATA
* *
47951 AAATATATTTAATAAGTTAAGATAAAAT-
1 AAATATATTT--TAAATTAAAATAAAATA
*
47979 --ATATATTTTAAATGT-ATAT-AAA-A
1 AAATATATTTTAAAT-TAAAATAAAATA
*
48002 AAATATTAATTTAAATTAA
1 AAATA-TATTTTAAATTAA
48021 CTATTTTACA
Statistics
Matches: 103, Mismatches: 12, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
23 3 0.03
24 7 0.07
25 5 0.05
26 18 0.17
27 24 0.23
28 12 0.12
29 22 0.21
30 12 0.12
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (27 bp):
AAATATATTTTAAATTAAAATAAAATA
Found at i:48611 original size:226 final size:215
Alignment explanation
Indices: 48009--48615 Score: 934
Period size: 226 Copynumber: 2.8 Consensus size: 215
47999 AAAAAATATT
48009 AATTTAAATTAACTATTTTACACTAAGATACAAAATATATACATATTGTTGTCTACTTTAAAAAC
1 AATTTAAATTAACTATTTTACACTAAGATACAAAATATATACATATTGTTGTCTACTTT-AAAAC
* *
48074 AATAAGTGGTATTGATTCAGTGGTTAGGTTTATGCTTGATTTCTTAAGCCCCTTGAATTGAATCC
65 AAT-AGTGGTCTTGGTTCAGTGGTTAGGTTTATGCTTGATTTCTTAAGCCCCTTGAATTGAATCC
*
48139 TCTTGTCCCCAATTTTGATTGATTTGTTTTCTTTCAACTAGAGGATGACACATGTCACAATCTAA
129 TCTTGTCCCCAATTTTGATTGATTTGTTTTCCTTCAACTAGAGGATGACACATGTCACAATCTAA
**
48204 TTGGTAGAAAATAATGAAAATA
194 TCAGTAGAAAATAATGAAAATA
*
48226 AATTTAAATTAAC---TTTACATTAAGATACAAAATATATACATATTGTTGTCTA-TTGTAAAAC
1 AATTTAAATTAACTATTTTACACTAAGATACAAAATATATACATATTGTTGTCTACTT-TAAAAC
48287 AATATGTGGTCTTGGTTCAGTGGTTAGGTTTATGCTTGATTTCTTAAGCCCCTTGAATTGAATCC
65 AATA-GTGGTCTTGGTTCAGTGGTTAGGTTTATGCTTGATTTCTTAAGCCCCTTGAATTGAATCC
*
48352 TCTTGTCCCCAATTTTGATTGATTTGTTTTCCTTCAACTAGAGGATGACACATGTCACACTCTAA
129 TCTTGTCCCCAATTTTGATTGATTTGTTTTCCTTCAACTAGAGGATGACACATGTCACAATCTAA
48417 TCAGTAGAAAATAAATATATTAAATGAAAATA
194 TCAGTAG------AA-A-A-T-AATGAAAATA
*
48449 AATTTAAATTAACTATTTTACAGTAAGATACAAAATATATACATATTGTTGTCTACTTTAAAACA
1 AATTTAAATTAACTATTTTACACTAAGATACAAAATATATACATATTGTTGTCTACTTTAAAACA
* * *
48514 ATGAGTGGTCTTGGTTCGGTGGTTAGGTTTATGCTTGATTTCTTAAACCCCTTGAATTGAATTCT
66 AT-AGTGGTCTTGGTTCAGTGGTTAGGTTTATGCTTGATTTCTTAAGCCCCTTGAATTGAATCCT
* *
48579 CTTGTCCCCAATTTTGATTGGTTTGCTTTCCTTCAAC
130 CTTGTCCCCAATTTTGATTGATTTGTTTTCCTTCAAC
48616 CACACTCTAA
Statistics
Matches: 360, Mismatches: 13, Indels: 25
0.90 0.03 0.06
Matches are distributed among these distances:
212 1 0.00
213 136 0.38
214 39 0.11
217 13 0.04
219 2 0.01
220 1 0.00
221 1 0.00
222 1 0.00
223 23 0.06
226 140 0.39
227 3 0.01
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (215 bp):
AATTTAAATTAACTATTTTACACTAAGATACAAAATATATACATATTGTTGTCTACTTTAAAACA
ATAGTGGTCTTGGTTCAGTGGTTAGGTTTATGCTTGATTTCTTAAGCCCCTTGAATTGAATCCTC
TTGTCCCCAATTTTGATTGATTTGTTTTCCTTCAACTAGAGGATGACACATGTCACAATCTAATC
AGTAGAAAATAATGAAAATA
Found at i:49586 original size:46 final size:46
Alignment explanation
Indices: 49519--49609 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
49509 ATCATGTAAC
49519 AATATCCAATAACAACACCTTAAAATTTAATTACGACTCGAATTAT
1 AATATCCAATAACAACACCTTAAAATTTAATTACGACTCGAATTAT
49565 AATATCCAATAACAACACCTTAAAATTTAATTACGACTCGAATTA
1 AATATCCAATAACAACACCTTAAAATTTAATTACGACTCGAATTA
49610 AGTAAAAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (46 bp):
AATATCCAATAACAACACCTTAAAATTTAATTACGACTCGAATTAT
Found at i:50358 original size:23 final size:23
Alignment explanation
Indices: 50330--50381 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
50320 TTTACCATGC
* *
50330 AAAATTTTGAACTGCATCAGAGT
1 AAAATTTTGAACTACATCAAAGT
*
50353 AAAATTTTGAACTACATGAAAGT
1 AAAATTTTGAACTACATCAAAGT
50376 AAAATT
1 AAAATT
50382 ATTGCTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (23 bp):
AAAATTTTGAACTACATCAAAGT
Found at i:51903 original size:41 final size:40
Alignment explanation
Indices: 51858--51969 Score: 152
Period size: 40 Copynumber: 2.8 Consensus size: 40
51848 ATGTACCCAA
*
51858 TTGCGGCGTTTGTTTAAAAATGCTACTAAAAAACGATTCTT
1 TTGCGGCGTTTGTTTAAAAATGCCACTAAAAAA-GATTCTT
* **
51899 TTGCGGCGTTTGTTTAGAAATGCCACTAAAGTAGATTCTT
1 TTGCGGCGTTTGTTTAAAAATGCCACTAAAAAAGATTCTT
* * *
51939 TGGTGGCGTTTGTTTAAAAACGCCACTAAAA
1 TTGCGGCGTTTGTTTAAAAATGCCACTAAAA
51970 TTCTTATATG
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
40 33 0.53
41 29 0.47
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (40 bp):
TTGCGGCGTTTGTTTAAAAATGCCACTAAAAAAGATTCTT
Found at i:53160 original size:15 final size:15
Alignment explanation
Indices: 53140--53176 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
53130 CCCTAAAATG
*
53140 AAATGTTAAAATTCA
1 AAATGTTAAAACTCA
*
53155 AAATGTTGAAACTCA
1 AAATGTTAAAACTCA
53170 AAATGTT
1 AAATGTT
53177 TTAAAAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (15 bp):
AAATGTTAAAACTCA
Found at i:56061 original size:21 final size:21
Alignment explanation
Indices: 56036--56077 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
56026 CCAGAATGAG
*
56036 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
56057 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
56078 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:56201 original size:15 final size:15
Alignment explanation
Indices: 56181--56237 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
56171 ACCATGCAGG
56181 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
56196 GGGGAATC-GATACCCC
1 GGGGAATCTG-TA-CCC
*
56212 TGGGGGGAATCTGTTCCC
1 ---GGGGAATCTGTACCC
56230 GGGGAATC
1 GGGGAATC
56238 GATACCCCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 18 0.51
16 3 0.09
18 3 0.09
19 9 0.26
20 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.37, T:0.19
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:56219 original size:34 final size:35
Alignment explanation
Indices: 56179--56258 Score: 144
Period size: 34 Copynumber: 2.3 Consensus size: 35
56169 AAACCATGCA
56179 GGGGGGAATCTGTACCCGGGGAATCGATA-CCCCT
1 GGGGGGAATCTGTACCCGGGGAATCGATACCCCCT
*
56213 GGGGGGAATCTGTTCCCGGGGAATCGATACCCCCT
1 GGGGGGAATCTGTACCCGGGGAATCGATACCCCCT
56248 GGGGGGAATCT
1 GGGGGGAATCT
56259 ATTCTCCCTG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 28 0.64
35 16 0.36
ACGTcount: A:0.19, C:0.25, G:0.38, T:0.19
Consensus pattern (35 bp):
GGGGGGAATCTGTACCCGGGGAATCGATACCCCCT
Found at i:56255 original size:20 final size:20
Alignment explanation
Indices: 56196--56289 Score: 78
Period size: 20 Copynumber: 5.0 Consensus size: 20
56186 ATCTGTACCC
56196 GGGGAATCGATA-CCCCTGG
1 GGGGAATCGATACCCCCTGG
*
56215 GGGGAATCTG-T--TCCC---
1 GGGGAATC-GATACCCCCTGG
56230 GGGGAATCGATACCCCCTGG
1 GGGGAATCGATACCCCCTGG
* * *
56250 GGGGAATCTATTCTCCCTGG
1 GGGGAATCGATACCCCCTGG
56270 GGGGAATCTG-TACCCCCTGG
1 GGGGAATC-GATACCCCCTGG
56290 ACAATCTGAT
Statistics
Matches: 59, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
14 1 0.02
15 9 0.15
17 3 0.05
18 3 0.05
19 9 0.15
20 34 0.58
ACGTcount: A:0.17, C:0.28, G:0.34, T:0.21
Consensus pattern (20 bp):
GGGGAATCGATACCCCCTGG
Found at i:58247 original size:3 final size:3
Alignment explanation
Indices: 58239--58282 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
58229 TACGTCCTCA
* *
58239 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTG TTT TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
58283 CCTTTCTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:59309 original size:32 final size:34
Alignment explanation
Indices: 59273--59342 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
59263 CCTTACAAAC
* *
59273 TCCCTAG-TTTTTC-CGGGCTAAACTAGAACTTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
*
59305 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
59339 TCCC
1 TCCC
59343 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
Found at i:59651 original size:21 final size:21
Alignment explanation
Indices: 59625--59666 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
59615 CCAGAATGGG
**
59625 GGGAATCGGTACCCCTTCATA
1 GGGAATCAATACCCCTTCATA
59646 GGGAATCAATACCCCTTCATA
1 GGGAATCAATACCCCTTCATA
59667 ATATTCAAAT
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:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (21 bp):
GGGAATCAATACCCCTTCATA
Found at i:59800 original size:15 final size:15
Alignment explanation
Indices: 59780--59836 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
59770 AACCATGCAG
59780 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
59795 GGGGAATC-GATACCTC
1 GGGGAATCTG-TACC-C
*
59811 TGGGGGGAATCTGTTCCC
1 ---GGGGAATCTGTACCC
59829 GGGGAATC
1 GGGGAATC
59837 GATACCCCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 20 0.57
16 1 0.03
18 1 0.03
19 11 0.31
20 1 0.03
ACGTcount: A:0.19, C:0.23, G:0.37, T:0.21
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:59819 original size:34 final size:36
Alignment explanation
Indices: 59779--59864 Score: 131
Period size: 34 Copynumber: 2.4 Consensus size: 36
59769 AAACCATGCA
*
59779 GGGGGAATCTGTACCCGGGGAATCGATACCTC-T-G
1 GGGGGAATCTGTACCCGGGGAATCGATACCCCATGG
*
59813 GGGGGAATCTGTTCCCGGGGAATCGATACCCCATGG
1 GGGGGAATCTGTACCCGGGGAATCGATACCCCATGG
*
59849 GGGGGAATCTATACCC
1 GGGGGAATCTGTACCC
59865 CCTGGACAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 30 0.65
35 1 0.02
36 15 0.33
ACGTcount: A:0.21, C:0.24, G:0.35, T:0.20
Consensus pattern (36 bp):
GGGGGAATCTGTACCCGGGGAATCGATACCCCATGG
Found at i:64921 original size:2 final size:2
Alignment explanation
Indices: 64914--64953 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
64904 ACGTGGAACC
64914 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
64954 CCTCTTACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69866 original size:18 final size:17
Alignment explanation
Indices: 69843--69876 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
69833 GCTGTTTGCA
*
69843 GGGGAGGAGGACAAGGGT
1 GGGGAGAAGGA-AAGGGT
69861 GGGGAGAAGGAAAGGG
1 GGGGAGAAGGAAAGGG
69877 GAGGCTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.03, G:0.62, T:0.03
Consensus pattern (17 bp):
GGGGAGAAGGAAAGGGT
Done.