Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008171.1 Hibiscus syriacus cultivar Beakdansim tig00110762_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: 104764
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:20933 original size:28 final size:28
Alignment explanation
Indices: 20876--20941 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
20866 GCTTATTTAT
* *
20876 TTATATCACTGAATTTTTAGTTTTATCAA
1 TTATAACATTGAATTTTTA-TTTTATCAA
* *
20905 TTGTAACATTGAATTTTT-TTTTTTCCAA
1 TTATAACATTGAATTTTTATTTTAT-CAA
20933 TTATAACAT
1 TTATAACAT
20942 CGAACTATAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 5 0.16
28 11 0.35
29 15 0.48
ACGTcount: A:0.30, C:0.11, G:0.06, T:0.53
Consensus pattern (28 bp):
TTATAACATTGAATTTTTATTTTATCAA
Found at i:25096 original size:21 final size:20
Alignment explanation
Indices: 25068--25107 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
25058 TAACACCAAA
25068 CAAAAAATAACA-AAAATAAT
1 CAAAAAATAA-AGAAAATAAT
25088 CAAAGAAATAAAGAAAATAA
1 CAAA-AAATAAAGAAAATAA
25108 AAGAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (20 bp):
CAAAAAATAAAGAAAATAAT
Found at i:27127 original size:2 final size:2
Alignment explanation
Indices: 27120--27154 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
27110 TGTGTTCTCA
*
27120 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27155 CTACAATAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:27462 original size:73 final size:73
Alignment explanation
Indices: 27338--27492 Score: 258
Period size: 73 Copynumber: 2.1 Consensus size: 73
27328 GGATTCAAGA
*
27338 TTTTCAGTAGGAACAACATCTTATATCGTTTGCTATGACAATGGAGAATTTGCATGTCATATTTG
1 TTTTCAGTAGGAACAAAATCTTATATCGTTTGCTATGACAATGGAGAATTTGCATGTCATATTTG
27403 ACTTTTCT
66 ACTTTTCT
* * *
27411 TTTTCAGTATGAATAAAATCTTATATCTTTTGCTATGACAATGGATG-ATTTGCATGTCATATTT
1 TTTTCAGTAGGAACAAAATCTTATATCGTTTGCTATGACAATGGA-GAATTTGCATGTCATATTT
27475 GACTTTTCT
65 GACTTTTCT
27484 TTTTCAGTA
1 TTTTCAGTA
27493 ACAATTCCTT
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
73 76 0.99
74 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.45
Consensus pattern (73 bp):
TTTTCAGTAGGAACAAAATCTTATATCGTTTGCTATGACAATGGAGAATTTGCATGTCATATTTG
ACTTTTCT
Found at i:42294 original size:17 final size:17
Alignment explanation
Indices: 42274--42306 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42264 ATTGTTCTGT
42274 ATTTAA-TATTCTTTTTG
1 ATTTAATTATT-TTTTTG
42291 ATTTAATTATTTTTTT
1 ATTTAATTATTTTTTT
42307 ATATAATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (17 bp):
ATTTAATTATTTTTTTG
Found at i:46017 original size:22 final size:21
Alignment explanation
Indices: 45992--46032 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
45982 ATAAAAAAAT
45992 TATTTTTATTAAATATTTTTTG
1 TATTTTTATTAAAT-TTTTTTG
*
46014 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
46033 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTTG
Found at i:50316 original size:30 final size:30
Alignment explanation
Indices: 50274--50334 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
50264 AATGTATATG
* *
50274 ATTTATGAGTTAAATTGA-TATTTTATCTAA
1 ATTTATGAGTTAAAAT-ACTATATTATCTAA
50304 ATTT-TGAGGTTAAAATACTATATTATCTAA
1 ATTTATGA-GTTAAAATACTATATTATCTAA
50334 A
1 A
50335 GTTCATACGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (30 bp):
ATTTATGAGTTAAAATACTATATTATCTAA
Found at i:51811 original size:21 final size:20
Alignment explanation
Indices: 51797--51835 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
51787 AATTTAAGGG
51797 TTTAGA-TTTAAAATTTTAAC
1 TTTAGAGTTTAAAA-TTTAAC
51817 TTTAGAGTTTAAAATTTAA
1 TTTAGAGTTTAAAATTTAA
51836 AATTTACTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (20 bp):
TTTAGAGTTTAAAATTTAAC
Found at i:51841 original size:21 final size:20
Alignment explanation
Indices: 51797--51841 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
51787 AATTTAAGGG
* *
51797 TTTAGATTTAAAATTTTAAC
1 TTTAGATTTAAAATTTAAAA
51817 TTTAGAGTTTAAAATTTAAAA
1 TTTAGA-TTTAAAATTTAAAA
51838 TTTA
1 TTTA
51842 CTGTTAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (20 bp):
TTTAGATTTAAAATTTAAAA
Found at i:51841 original size:27 final size:27
Alignment explanation
Indices: 51802--51866 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
51792 AAGGGTTTAG
*
51802 ATTTAAAATTTTAACT-TTAGAGTTTAAA
1 ATTTAAAA-TTT-ACTGTTAAAGTTTAAA
*
51830 ATTTAAAATTTACTGTTAAAGTTTAGA
1 ATTTAAAATTTACTGTTAAAGTTTAAA
*
51857 GTTTAAAATT
1 ATTTAAAATT
51867 ATATATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.09
27 22 0.67
28 8 0.24
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (27 bp):
ATTTAAAATTTACTGTTAAAGTTTAAA
Found at i:53409 original size:14 final size:15
Alignment explanation
Indices: 53374--53411 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
53364 AATAAGAGGG
*
53374 ATTAAAATTAAGAAT
1 ATTAAAAATAAGAAT
53389 ATTAAAAATAA-AAT
1 ATTAAAAATAAGAAT
*
53403 TTTAAAAAT
1 ATTAAAAAT
53412 TCTAAATGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
ATTAAAAATAAGAAT
Found at i:54043 original size:30 final size:32
Alignment explanation
Indices: 54008--54083 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 32
53998 ACAGTAATTA
54008 TATTTTATATT-AAT-ATAATTATATAAATAT
1 TATTTTATATTAAATAATAATTATATAAATAT
* * *
54038 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTATATT-AAATAATAATTATATAAATAT
54071 TA-TTTAT-TTAAAT
1 TATTTTATATTAAAT
54084 TTATTAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 14 0.36
31 2 0.05
32 7 0.18
33 16 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TATTTTATATTAAATAATAATTATATAAATAT
Found at i:54046 original size:32 final size:32
Alignment explanation
Indices: 54004--54093 Score: 85
Period size: 32 Copynumber: 2.8 Consensus size: 32
53994 TTAAACAGTA
*
54004 ATTATATTTTATATTAATATAATTATATAAAT
1 ATTATTTTTTATATTAATATAATTATATAAAT
* * *
54036 ATTATTTTTTAT-TAAAATAATATTTATATAATT
1 ATTATTTTTTATAT-TAAT-ATAATTATATAAAT
* *
54069 ATTATTTATTTAAATTTAT-TAATTA
1 ATTATTT-TTTATATTAATATAATTA
54094 ATTATTTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
31 1 0.02
32 19 0.41
33 19 0.41
34 6 0.13
35 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
ATTATTTTTTATATTAATATAATTATATAAAT
Found at i:54254 original size:17 final size:16
Alignment explanation
Indices: 54234--54279 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
54224 ATATTTATTG
54234 TTATGTTTAATTTAAAT
1 TTAT-TTTAATTTAAAT
*
54251 TTATTTTGAATTTATAT
1 TTATTTT-AATTTAAAT
*
54268 TAATTTTAATTT
1 TTATTTTAATTT
54280 TTTATAATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (16 bp):
TTATTTTAATTTAAAT
Found at i:55903 original size:21 final size:22
Alignment explanation
Indices: 55877--55938 Score: 85
Period size: 21 Copynumber: 2.9 Consensus size: 22
55867 GTCATCTCCG
55877 CATGGTTACATTGCTAGCCCA-
1 CATGGTTACATTGCTAGCCCAC
*
55898 CATGGTTACATTCCTAGCCCAC
1 CATGGTTACATTGCTAGCCCAC
55920 CA-GGTTACA-TGCATAGCCC
1 CATGGTTACATTGC-TAGCCC
55939 GCAGGGTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.05
21 33 0.89
22 2 0.05
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (22 bp):
CATGGTTACATTGCTAGCCCAC
Found at i:55946 original size:21 final size:20
Alignment explanation
Indices: 55874--55946 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
55864 TATGTCATCT
55874 CCGCATGGTTACATTGCTAGC
1 CCGCATGGTTACA-TGCTAGC
* *
55895 CCACATGGTTACATTCCTAGC
1 CCGCATGGTTACA-TGCTAGC
*
55916 CCACCA-GGTTACATGCATAGC
1 CC-GCATGGTTACATGC-TAGC
*
55937 CCGCAGGGTT
1 CCGCATGGTT
55947 TTATACCATA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 4 0.09
21 38 0.86
22 2 0.05
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.25
Consensus pattern (20 bp):
CCGCATGGTTACATGCTAGC
Found at i:56511 original size:34 final size:34
Alignment explanation
Indices: 56468--56573 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
56458 ATAAATGTTT
56468 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* * *
56502 TTAAAATACAAATAATATTATTCAAAATTT-AAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* * *
56535 TTTAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
56569 TTAAA
1 TTAAA
56574 TTCAAGTTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
33 28 0.46
34 33 0.54
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.38
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCGAAATTTAAAA
Found at i:56542 original size:33 final size:33
Alignment explanation
Indices: 56471--56574 Score: 138
Period size: 33 Copynumber: 3.1 Consensus size: 33
56461 AATGTTTTTA
*
56471 AAATACAAATTATAGTATTCGAAATTTAAAATTA
1 AAATACAAATTATAGTATTCGAAATTT-AAATTT
* * *
56505 AAATACAAATAATATTATTCAAAATTTAAATTT
1 AAATACAAATTATAGTATTCGAAATTTAAATTT
*
56538 AAATATAAATTATAGTATTCGAAATTTAACA-TT
1 AAATACAAATTATAGTATTCGAAATTTAA-ATTT
56571 AAAT
1 AAAT
56575 TCAAGTTAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
33 36 0.59
34 25 0.41
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.38
Consensus pattern (33 bp):
AAATACAAATTATAGTATTCGAAATTTAAATTT
Found at i:57310 original size:127 final size:126
Alignment explanation
Indices: 56996--57628 Score: 937
Period size: 127 Copynumber: 5.0 Consensus size: 126
56986 GCTCTTTAAA
* ** *
56996 GTCCCCTAAGGAATAATAGGTATTGTTATGAATAGTTCTCGGGTGGAAATAAGTGACATAATAGG
1 GTCCCTTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGG-GGACATAAGTGACATAATAGG
** *
57061 ATAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGCGTCTTCACG
65 GCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGCGCCTTCACG
* * *
57123 GTCCCTTAAGAAATAATAGGTATTGATAT-AATAGTTCCCGGGGGACATAAGTGACATAATAGGG
1 GTCCCTTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
* * * *
57187 CAATGATAACATATTCTCTGATAAAATAATGGAAGGCGCGCCCCCGGGAACACACCTTCACA
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGC-CCCCCGGGAACGCGCCTTCACG
* *
57249 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTATCGGGGGACATAAGTGACATAATAGGG
1 GTCCCTTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
* * * *
57314 CAATGATAACATATTCTCTGACAAAATATTGGAATGTGCACCCCCGGGAATGCGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGC-CCCCCGGGAACGCGCCTTCACG
* * *
57376 GTCTCTTAAGGAATAATAAGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
1 GTCCCTTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
* * *
57441 TAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAATGGGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGCGCCTTCACG
*
57502 GTCCCTTAAGGAATAATAGGTATTGACATGAATAGTTCAT-GGGGGATATAAGTGACATAATAGG
1 GTCCCTTAAGGAATAATAGGTATTGACATGAATAGTTC-TCGGGGGACATAAGTGACATAATAGG
* * *
57566 GCAATGATAACATATTCTCTGACAAAATAATGGAATGCGCGCCCCCGGGAACGCACATTCACG
65 GCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGC-CCCCCGGGAACGCGCCTTCACG
57629 TTAATAGTAC
Statistics
Matches: 456, Mismatches: 46, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
125 57 0.12
126 174 0.38
127 225 0.49
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (126 bp):
GTCCCTTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGCGCCTTCACG
Found at i:57486 original size:253 final size:252
Alignment explanation
Indices: 56995--57628 Score: 975
Period size: 253 Copynumber: 2.5 Consensus size: 252
56985 CGCTCTTTAA
** *
56995 AGTCCCCTAAGGAATAATAGGTATTGTTATGAATAGTTCTCGGGTGGAAATAAGTGACATAATAG
1 AGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTATCGGG-GGAAATAAGTGACATAATAG
** * *
57060 GATAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAACGCGTCTTCACGGT
65 GGCAATGATAACATATTCTCTGACAAAATAATGGAATGCGCCCCCCGGGAACGCGCCTTCACGGT
* *
57125 CCCTTAAGAAATAATAGGTATTGATATAATAGTTCCCGGGGGACATAAGTGACATAATAGGGCAA
130 CCCTTAAGAAATAATAAGTATTGACATAATAGTTCCCGGGGGACATAAGTGACATAATAGGGCAA
*
57190 TGATAACATATTCTCTGATAAAATAATGGAAGGCGCGCCCCCGGGAACACACCTTCAC
195 TGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACACACCTTCAC
*
57248 AGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTATCGGGGGACATAAGTGACATAATAGG
1 AGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTATCGGGGGAAATAAGTGACATAATAGG
* * *
57313 GCAATGATAACATATTCTCTGACAAAATATTGGAATGTGCACCCCCGGGAATGCGCCTTCACGGT
66 GCAATGATAACATATTCTCTGACAAAATAATGGAATGCGC-CCCCCGGGAACGCGCCTTCACGGT
* * *
57378 CTCTTAAGGAATAATAAGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGGTA
130 CCCTTAAGAAATAATAAGTATTGACAT-AATAGTTCCCGGGGGACATAAGTGACATAATAGGGCA
****
57443 ATGATAACATATTCTCTGACAAAATAATGGAAGGCGC-CCCCCGGGAATGGGCCTTCAC
194 ATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACACACCTTCAC
* * *
57501 GGTCCCTTAAGGAATAATAGGTATTGACATGAATAGTTCAT-GGGGGATATAAGTGACATAATAG
1 AGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTT-ATCGGGGGAAATAAGTGACATAATAG
* *
57565 GGCAATGATAACATATTCTCTGACAAAATAATGGAATGCGCGCCCCCGGGAACGCACATTCACG
65 GGCAATGATAACATATTCTCTGACAAAATAATGGAATGCGC-CCCCCGGGAACGCGCCTTCACG
57629 TTAATAGTAC
Statistics
Matches: 348, Mismatches: 30, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
252 55 0.16
253 219 0.63
254 74 0.21
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (252 bp):
AGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTATCGGGGGAAATAAGTGACATAATAGG
GCAATGATAACATATTCTCTGACAAAATAATGGAATGCGCCCCCCGGGAACGCGCCTTCACGGTC
CCTTAAGAAATAATAAGTATTGACATAATAGTTCCCGGGGGACATAAGTGACATAATAGGGCAAT
GATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACACACCTTCAC
Found at i:71247 original size:13 final size:13
Alignment explanation
Indices: 71221--71255 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
71211 CAATCCTGGC
71221 GACATACG-GGGT
1 GACATACGAGGGT
71233 GACATACGAGGGT
1 GACATACGAGGGT
71246 GACATACGAG
1 GACATACGAG
71256 CCATATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.31, C:0.17, G:0.37, T:0.14
Consensus pattern (13 bp):
GACATACGAGGGT
Found at i:71265 original size:11 final size:11
Alignment explanation
Indices: 71249--71282 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
71239 CGAGGGTGAC
71249 ATACGAGCCAT
1 ATACGAGCCAT
71260 ATACGAGCCAT
1 ATACGAGCCAT
*
71271 ATACGAGTCAT
1 ATACGAGCCAT
71282 A
1 A
71283 CGAGCCAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (11 bp):
ATACGAGCCAT
Found at i:71313 original size:22 final size:22
Alignment explanation
Indices: 71282--71361 Score: 79
Period size: 22 Copynumber: 3.4 Consensus size: 22
71272 TACGAGTCAT
*
71282 ACGAGCCAATGGGGAGGATGCA
1 ACGAGCCAATGGGGAGCATGCA
*
71304 ACGAGGCAATGGGGAGCATGCAGGAA
1 ACGAGCCAATGGGGAGCATGC----A
*
71330 TAGAGAGCCAATGGGGAGCATGCA
1 -A-CGAGCCAATGGGGAGCATGCA
71354 ACGAGCCA
1 ACGAGCCA
71362 TATACGAGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
22 25 0.53
23 1 0.02
24 1 0.02
26 1 0.02
27 1 0.02
28 18 0.38
ACGTcount: A:0.34, C:0.19, G:0.39, T:0.09
Consensus pattern (22 bp):
ACGAGCCAATGGGGAGCATGCA
Found at i:71342 original size:28 final size:28
Alignment explanation
Indices: 71310--71475 Score: 188
Period size: 28 Copynumber: 5.6 Consensus size: 28
71300 TGCAACGAGG
71310 CAATGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
* *
71338 CAATGGGGAGCATGCAACGAGCCATATACGAGC
1 CAATGGGGAGCATGC-A-G-G-AATAGA-GAGC
* *
71371 CCACGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
* *
71399 CAATGGGGAGCATGCAACGAGCCATATACGAGC
1 CAATGGGGAGCATGC-A-G-G-AATAGA-GAGC
71432 CAATGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
71460 CAATGGGGAGCATGCA
1 CAATGGGGAGCATGCA
71476 ACGAGCCATA
Statistics
Matches: 116, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
28 52 0.45
29 10 0.09
30 4 0.03
31 4 0.03
32 10 0.09
33 36 0.31
ACGTcount: A:0.34, C:0.20, G:0.36, T:0.11
Consensus pattern (28 bp):
CAATGGGGAGCATGCAGGAATAGAGAGC
Found at i:71343 original size:50 final size:50
Alignment explanation
Indices: 71284--71480 Score: 178
Period size: 61 Copynumber: 3.5 Consensus size: 50
71274 CGAGTCATAC
*
71284 GAGCCAATGGGGAGGATGCAACGAGGCAATGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAGGCAATGGGGAGCATGCAGGAATAGA
*
71334 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCCACGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAGGCA-AT----------GGGGAGCATGCAGGAATAGA
71395 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCAATGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAAC--G------A-G-G-CAATGGGGAGCATGCAGGAATAGA
71456 GAGCCAATGGGGAGCATGCAACGAG
1 GAGCCAATGGGGAGCATGCAACGAG
71481 CCATATACAA
Statistics
Matches: 122, Mismatches: 3, Indels: 42
0.73 0.02 0.25
Matches are distributed among these distances:
50 26 0.21
51 2 0.02
52 1 0.01
53 1 0.01
59 1 0.01
61 84 0.69
63 1 0.01
69 1 0.01
70 1 0.01
71 2 0.02
72 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.37, T:0.10
Consensus pattern (50 bp):
GAGCCAATGGGGAGCATGCAACGAGGCAATGGGGAGCATGCAGGAATAGA
Found at i:71399 original size:61 final size:61
Alignment explanation
Indices: 71304--71494 Score: 337
Period size: 61 Copynumber: 3.1 Consensus size: 61
71294 GGAGGATGCA
* *
71304 ACGAGGCAATGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
*
71365 ACGAGCCCACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
*
71426 ACGAGCCAATGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
*
71487 ACAAGCCA
1 ACGAGCCA
71495 TGCAGGAATA
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 124 1.00
ACGTcount: A:0.35, C:0.21, G:0.34, T:0.10
Consensus pattern (61 bp):
ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
Found at i:71558 original size:29 final size:29
Alignment explanation
Indices: 71508--71616 Score: 184
Period size: 29 Copynumber: 3.8 Consensus size: 29
71498 AGGAATAGAG
* *
71508 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
71537 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
71566 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
71595 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
71617 CCATTCCATC
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
29 75 0.97
30 2 0.03
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:71734 original size:36 final size:37
Alignment explanation
Indices: 71666--71739 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
71656 CATAGATTCC
71666 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
71703 TTCACGTGCTCCCCGCTGCA-TGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
71739 T
1 T
71740 GCATGCATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 17 0.46
37 20 0.54
ACGTcount: A:0.16, C:0.46, G:0.14, T:0.24
Consensus pattern (37 bp):
TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
Found at i:71767 original size:18 final size:18
Alignment explanation
Indices: 71744--71778 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
71734 CCCAATGCAT
71744 GCATGTGAACCATTTGAG
1 GCATGTGAACCATTTGAG
71762 GCATGTGAACCATTTGA
1 GCATGTGAACCATTTGA
71779 TTATTGGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (18 bp):
GCATGTGAACCATTTGAG
Found at i:71896 original size:23 final size:23
Alignment explanation
Indices: 71868--71913 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
71858 AAAAGAAAGA
71868 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
71891 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
71914 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:71928 original size:25 final size:23
Alignment explanation
Indices: 71868--71928 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
71858 AAAAGAAAGA
**
71868 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
71891 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
71914 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
71929 AGAAAGGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:71952 original size:21 final size:21
Alignment explanation
Indices: 71916--71974 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
71906 GATTGCAGCC
71916 GAGAAA-GAAAGAAAGAAAGG
1 GAGAAAGGAAAGAAAGAAAGG
*
71936 GAGAAAGGAAAGGAAGAAAGG
1 GAGAAAGGAAAGAAAGAAAGG
*
71957 GAGAAAGGAAAGTAAGAA
1 GAGAAAGGAAAGAAAGAA
71975 GAAGAAAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 6 0.17
21 30 0.83
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (21 bp):
GAGAAAGGAAAGAAAGAAAGG
Found at i:72153 original size:41 final size:41
Alignment explanation
Indices: 72108--72196 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
72098 TATATGATTG
* *
72108 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
72149 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
72190 TTAGTTT
1 TTAGTTT
72197 GTATTGTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:72240 original size:46 final size:48
Alignment explanation
Indices: 72177--72268 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 48
72167 TTATATAGTT
72177 AAAAAATAATTAATTAGTTTGTATT-GTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
* *
72222 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATAT
72269 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 6 0.15
46 17 0.41
47 3 0.07
48 7 0.17
49 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
Found at i:74586 original size:26 final size:24
Alignment explanation
Indices: 74528--74586 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
74518 CTAATAAACC
*
74528 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
74552 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
74580 TAATAAT
1 TAATAAT
74587 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:75423 original size:25 final size:25
Alignment explanation
Indices: 75395--75469 Score: 104
Period size: 25 Copynumber: 3.2 Consensus size: 25
75385 TTTTATATAA
*
75395 TAATATATAACTTAAACTAATAAAC
1 TAATATATAACTTAAACTAACAAAC
75420 TAATATATAACTTAAACTAACAAAC
1 TAATATATAACTTAAACTAACAAAC
*
75445 TAATA-AT---TTATACTAACAAAC
1 TAATATATAACTTAAACTAACAAAC
75466 TAAT
1 TAAT
75470 TAACTAGATT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
21 17 0.35
24 2 0.04
25 29 0.60
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (25 bp):
TAATATATAACTTAAACTAACAAAC
Found at i:75450 original size:21 final size:21
Alignment explanation
Indices: 75401--75474 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 21
75391 ATAATAATAT
*
75401 ATAACTTAAACTAATAAACTAATA
1 ATAACTTAAACTAACAAAC---TA
75425 TATAACTTAAACTAACAAACTA
1 -ATAACTTAAACTAACAAACTA
* *
75447 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
75468 ATTAACT
1 A-TAACT
75475 AGATTTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
21 20 0.45
22 6 0.14
25 18 0.41
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:76110 original size:29 final size:29
Alignment explanation
Indices: 76078--76157 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
76068 TATACCTTGG
*
76078 AGGTCGCCCGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
76107 AGGTCGCCTGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
76136 AGGTCGCCTGGATTGCATGGCG
1 AGGTCGCCTGGATTGCATGGCG
76158 TCCTATGGCG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.16, C:0.30, G:0.34, T:0.20
Consensus pattern (29 bp):
AGGTCGCCTGGATTGCATGGCGACCTCCA
Found at i:88082 original size:35 final size:35
Alignment explanation
Indices: 88024--88123 Score: 182
Period size: 35 Copynumber: 2.8 Consensus size: 35
88014 CGCGTTGATA
88024 ACTTTTATCAAGGTGTTTTAGTTTAGAGACAAGAAG
1 ACTTTTATCAA-GTGTTTTAGTTTAGAGACAAGAAG
88060 ACTTTTATCAAGTGTTTTAGTTTAGAGACAAGAAG
1 ACTTTTATCAAGTGTTTTAGTTTAGAGACAAGAAG
88095 ACTTTTATCAAGTGGTTTTAGTTTAGAGA
1 ACTTTTATCAAGT-GTTTTAGTTTAGAGA
88124 GGAGAAGAAG
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
35 37 0.59
36 26 0.41
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (35 bp):
ACTTTTATCAAGTGTTTTAGTTTAGAGACAAGAAG
Found at i:90486 original size:2 final size:2
Alignment explanation
Indices: 90479--90507 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
90469 TTTTTAAAAC
90479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
90508 CCCCTATCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:90748 original size:24 final size:24
Alignment explanation
Indices: 90721--90854 Score: 162
Period size: 24 Copynumber: 5.6 Consensus size: 24
90711 CATAATTCAT
* *
90721 GTCAAATATCATATCAAAATCCAG
1 GTCAAATATCATATCAGAATCCAA
* *
90745 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAATATCATATCAGAATCCAA
* *
90769 GTCAAGTATCATATCAGAATCCAT
1 GTCAAATATCATATCAGAATCCAA
* *
90793 GTCATATATCATATCAGAATCCAT
1 GTCAAATATCATATCAGAATCCAA
* *
90817 GTCAAGTATCATATCAGAATTCAA
1 GTCAAATATCATATCAGAATCCAA
90841 GTCGAAA-ATCATAT
1 GTC-AAATATCATAT
90855 AAAATATTCA
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
24 94 0.98
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (24 bp):
GTCAAATATCATATCAGAATCCAA
Found at i:90852 original size:72 final size:72
Alignment explanation
Indices: 90718--90854 Score: 204
Period size: 72 Copynumber: 1.9 Consensus size: 72
90708 AAGCATAATT
*
90718 CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATCATAT
1 CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGAATCATAT
90783 CAGAATC
66 CAGAATC
* * * * *
90790 CATGTCATATATCATATCAGAATCCATGTCAAGTATCATATCAGAATTCAAGTCGAA-AATCATA
1 CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTC-AAGAATCATA
90854 T
65 T
90855 AAAATATTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 56 0.97
73 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.28
Consensus pattern (72 bp):
CATGTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGAATCATAT
CAGAATC
Found at i:98779 original size:24 final size:24
Alignment explanation
Indices: 98752--98799 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
98742 GCTTTACGTT
98752 GATTATTAATTCAATTACCACGGC
1 GATTATTAATTCAATTACCACGGC
*
98776 GATTATTAATTCAATTACCTCGGC
1 GATTATTAATTCAATTACCACGGC
98800 AATGATGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.35
Consensus pattern (24 bp):
GATTATTAATTCAATTACCACGGC
Done.