Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006727.1 Hibiscus syriacus cultivar Beakdansim tig00016852_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: 121893
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1283 original size:22 final size:21
Alignment explanation
Indices: 1218--1283 Score: 55
Period size: 22 Copynumber: 3.1 Consensus size: 21
1208 GTTTGAGATT
*
1218 TGATTTAGGCTTAGG-TTTCAA
1 TGATTTAGGTTTAGGATTT-AA
* * *
1239 -GGTTTAGGTTTATGATTTTA
1 TGATTTAGGTTTAGGATTTAA
*
1259 TGATTTAGGGTTTAGGGTTTAA
1 TGATTTA-GGTTTAGGATTTAA
1281 TGA
1 TGA
1284 AAATAAAATG
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
20 12 0.35
21 8 0.24
22 14 0.41
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.47
Consensus pattern (21 bp):
TGATTTAGGTTTAGGATTTAA
Found at i:2308 original size:14 final size:14
Alignment explanation
Indices: 2291--2328 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 14
2281 TTTATTCATC
2291 AATAATGTATTTTT
1 AATAATGTATTTTT
2305 AAT-A--TATTTTT
1 AATAATGTATTTTT
2316 AATAATGTATTTT
1 AATAATGTATTTT
2329 AAAAAATCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 1 0.05
14 9 0.43
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:8853 original size:17 final size:17
Alignment explanation
Indices: 8831--8863 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
8821 AAAAAATATG
*
8831 AAAATCAAGTTGCAATA
1 AAAATCAAGATGCAATA
8848 AAAATCAAGATGCAAT
1 AAAATCAAGATGCAAT
8864 GAATTCAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (17 bp):
AAAATCAAGATGCAATA
Found at i:10776 original size:81 final size:80
Alignment explanation
Indices: 10684--10840 Score: 287
Period size: 81 Copynumber: 1.9 Consensus size: 80
10674 TTAACCTTCG
*
10684 TAGAATTTTTATTATTCAATGATAGAATAAGGATATTTTTTAAAGAAAAAAAAATTAAGGACGTT
1 TAGAATTTTTATTATTCAATGACAGAATAAGGATATTTTTTAAAG-AAAAAAAATTAAGGACGTT
10749 TTAGTCCAAAACGCCC
65 TTAGTCCAAAACGCCC
*
10765 TAGAATTTTTATTATTCAATGACAGAATAAGGATATTTTTTAAAGAAAAAAAATTAAGGGCGTTT
1 TAGAATTTTTATTATTCAATGACAGAATAAGGATATTTTTTAAAGAAAAAAAATTAAGGACGTTT
10830 TAGTCCAAAAC
66 TAGTCCAAAAC
10841 TCCGGTAATC
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
80 30 0.41
81 44 0.59
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (80 bp):
TAGAATTTTTATTATTCAATGACAGAATAAGGATATTTTTTAAAGAAAAAAAATTAAGGACGTTT
TAGTCCAAAACGCCC
Found at i:11341 original size:13 final size:13
Alignment explanation
Indices: 11323--11349 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11313 CATAGGTGAA
11323 CAGTCTTCATATG
1 CAGTCTTCATATG
11336 CAGTCTTCATATG
1 CAGTCTTCATATG
11349 C
1 C
11350 GTGTATGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:12464 original size:25 final size:25
Alignment explanation
Indices: 12430--12479 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
12420 CGAAAATCAT
*
12430 ACACCATGGAACACCGTCTGGTGTC
1 ACACCATGGAACACCATCTGGTGTC
12455 ACACCATGGAACACCATCTGGTGTC
1 ACACCATGGAACACCATCTGGTGTC
12480 GCACAATAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.32, G:0.22, T:0.20
Consensus pattern (25 bp):
ACACCATGGAACACCATCTGGTGTC
Found at i:13295 original size:2 final size:2
Alignment explanation
Indices: 13288--13316 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13278 GATATACTTT
13288 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 T
13317 TAAAGAAACA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14974 original size:325 final size:323
Alignment explanation
Indices: 14385--15024 Score: 1003
Period size: 325 Copynumber: 2.0 Consensus size: 323
14375 AATTCCAGCA
* *
14385 AGCTACTGTATTGTGTAGGTCAATTGGTTTAGGGGAGAAAATTCATGGTAAGGTTATTTATTTCT
1 AGCTACTGTATTGTGTAGGCCAATTGGTTTAGGGGAGAAAATTCATGGTAAGGTTATTGATTTCT
* *
14450 TGATTTGAATGCAATTCTTATCATGTGAATTTGGTTTATTTGATTTTGGGATTGAGTATTTTGCT
66 TGATTTGAATGCAATTCTTATCATGTGAATTTGGTTTATTTGATTTTGGGATTGAATATGTTGCT
* * *
14515 TGCTTTCCTATATTTTATGGGTATATAGATTTTGTTAACTTACTCGGTAGCAGTTTGTCTTATCA
131 TGCTCTCATATATTTTATGGGTATATAAATTTTGTTAACTTACTCGGTAGCAGTTTGTCTTATCA
* * *
14580 TGTATGGTTGATTTAAATTATTTGGTGTCTGAAGGAGCTTTTAAGAATTGAAGTTTTAATATTGG
196 TGTATGGTTGATTTAAATTATTTGGTGTCTGAAAGAGCTTTCAAGAATTGAAGTTTTAATATAGG
**
14645 GATTGATATATCATCATGTCTAGCCGTTTTAAGGTATATGATGGGTGGTTGGTTAGTGGTGTCT
261 GATTGATATATCATCATGTCTAGCCG-TTTAAGGTATATGATGCATGGTTGGTTAGTGGTGTCT
* *
14709 AGCTACTGTTTTGTGTAGGCCAATTGGTTTAGGGGAGAAAATTCATGGTAAGGTTATTGATTTTT
1 AGCTACTGTATTGTGTAGGCCAATTGGTTTAGGGGAGAAAATTCATGGTAAGGTTATTGA-TTTC
* * *
14774 TTTATTTGAATGCAATTCTTGTCATGTGAATTTGGATTTGTTTGATTTTGGGATTGAATATGTTG
65 TTGATTTGAATGCAATTCTTATCATGTGAATTTGG-TTTATTTGATTTTGGGATTGAATATGTTG
* * * * *
14839 CTTGCTCTCATATGTTTTATGGGTATATAAATTTTGTTAACTTACTCTGTAGCTGTTTTTCTTGT
129 CTTGCTCTCATATATTTTATGGGTATATAAATTTTGTTAACTTACTCGGTAGCAGTTTGTCTTAT
*
14904 CATGTATGGTTG-TTTAGATTATTTGGTGTCTGAAAGAGCTTTCAAGAATTGAAGTTTTAATATA
194 CATGTATGGTTGATTTAAATTATTTGGTGTCTGAAAGAGCTTTCAAGAATTGAAGTTTTAATATA
* * * *
14968 GGGATTGATATGTCATTATGTCTAGCTGTTTAAGGTATATGATTCATGGTTGGTTAG
259 GGGATTGATATATCATCATGTCTAGCCGTTTAAGGTATATGATGCATGGTTGGTTAG
15025 CGATGCCTTG
Statistics
Matches: 287, Mismatches: 27, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
324 83 0.29
325 109 0.38
326 95 0.33
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.45
Consensus pattern (323 bp):
AGCTACTGTATTGTGTAGGCCAATTGGTTTAGGGGAGAAAATTCATGGTAAGGTTATTGATTTCT
TGATTTGAATGCAATTCTTATCATGTGAATTTGGTTTATTTGATTTTGGGATTGAATATGTTGCT
TGCTCTCATATATTTTATGGGTATATAAATTTTGTTAACTTACTCGGTAGCAGTTTGTCTTATCA
TGTATGGTTGATTTAAATTATTTGGTGTCTGAAAGAGCTTTCAAGAATTGAAGTTTTAATATAGG
GATTGATATATCATCATGTCTAGCCGTTTAAGGTATATGATGCATGGTTGGTTAGTGGTGTCT
Found at i:23111 original size:11 final size:12
Alignment explanation
Indices: 23081--23134 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
23071 GTTATTTAAA
23081 CGGGTATTGGGC
1 CGGGTATTGGGC
*
23093 CGGGTATTGGGT
1 CGGGTATTGGGC
23105 C-GGTATTGGGC
1 CGGGTATTGGGC
* *
23116 CGGGAATCGGGC
1 CGGGTATTGGGC
23128 CGGGTAT
1 CGGGTAT
23135 ATATATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
11 10 0.28
12 26 0.72
ACGTcount: A:0.11, C:0.17, G:0.48, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:23139 original size:2 final size:2
Alignment explanation
Indices: 23132--23231 Score: 77
Period size: 2 Copynumber: 53.0 Consensus size: 2
23122 TCGGGCCGGG
* *
23132 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA AA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
23173 TA AA TA TA TA T- TT TT TA TT TA AA T- TA AA TT TA T- 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
23211 T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
23232 AATAATTATT
Statistics
Matches: 77, Mismatches: 15, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
1 6 0.08
2 71 0.92
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:23646 original size:20 final size:20
Alignment explanation
Indices: 23623--23747 Score: 155
Period size: 20 Copynumber: 6.3 Consensus size: 20
23613 AACCCAATTT
*
23623 TCAATTTCGCAACACGATAG
1 TCAAATTCGCAACACGATAG
* *
23643 TCAAATTCACAACGCGATAG
1 TCAAATTCGCAACACGATAG
*
23663 TCAAATTCGCAACAC-AAAG
1 TCAAATTCGCAACACGATAG
23682 TCAAATTCGCAACACAGA-AG
1 TCAAATTCGCAACAC-GATAG
*
23702 TCAAATTCGCAACGCGATAG
1 TCAAATTCGCAACACGATAG
* * *
23722 TCAAATTTGCAACGCGAAAG
1 TCAAATTCGCAACACGATAG
23742 TCAAAT
1 TCAAAT
23748 GTTTTTACGC
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
19 20 0.22
20 72 0.77
21 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (20 bp):
TCAAATTCGCAACACGATAG
Found at i:23656 original size:60 final size:59
Alignment explanation
Indices: 23584--23747 Score: 188
Period size: 59 Copynumber: 2.7 Consensus size: 59
23574 AAATGACCAA
* * ** *
23584 CAAATTCGCAACGCGA-ACTCCAATTTCGCAACCCAATTTTCAATTTCGCAACAC-GATAGT
1 CAAATTCGCAACGCGATACT-CAAATTCGCAACACAA-AGTCAAATTCGCAACACAGA-AGT
* *
23644 CAAATTCACAACGCGATAGTCAAATTCGCAACACAAAGTCAAATTCGCAACACAGAAGT
1 CAAATTCGCAACGCGATACTCAAATTCGCAACACAAAGTCAAATTCGCAACACAGAAGT
* * *
23703 CAAATTCGCAACGCGATAGTCAAATTTGCAACGCGAAAGTCAAAT
1 CAAATTCGCAACGCGATACTCAAATTCGCAACAC-AAAGTCAAAT
23748 GTTTTTACGC
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
59 48 0.53
60 41 0.45
61 2 0.02
ACGTcount: A:0.39, C:0.26, G:0.14, T:0.21
Consensus pattern (59 bp):
CAAATTCGCAACGCGATACTCAAATTCGCAACACAAAGTCAAATTCGCAACACAGAAGT
Found at i:24188 original size:13 final size:13
Alignment explanation
Indices: 24170--24201 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
24160 AGTATTTGTC
24170 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
24183 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
24196 TTTGTT
1 TTTGTT
24202 GAAGAAACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.16, T:0.78
Consensus pattern (13 bp):
TTTGTTTTGTCTT
Found at i:27948 original size:63 final size:65
Alignment explanation
Indices: 27872--28015 Score: 176
Period size: 63 Copynumber: 2.3 Consensus size: 65
27862 TTTTACATTG
27872 AAAGTTGATTTGTTGTTTAATTGATGAGGAAATAAG-A-T-TTATTTT-TTGATTAATTGATTTG
1 AAAGTTGATTTGTTGTTTAATT--TGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTG
27933 TA
64 TA
* * * *
27935 AAAGTTGA--T-TTGTTTAATTTGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTGTTTAATTTGAGGAAATAAGAATTATTATTTT-CTTGATTAATTGATTTGT
27997 A
65 A
27998 AAAGTTGATTTGTTGTTT
1 AAAGTTGATTTGTTGTTT
28016 CTAAAAAATT
Statistics
Matches: 69, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
58 10 0.14
59 1 0.01
60 11 0.16
61 7 0.10
63 33 0.48
65 1 0.01
66 6 0.09
ACGTcount: A:0.29, C:0.01, G:0.18, T:0.52
Consensus pattern (65 bp):
AAAGTTGATTTGTTGTTTAATTTGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGTA
Found at i:28346 original size:39 final size:39
Alignment explanation
Indices: 28291--28376 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 39
28281 CAAGTTGTAG
*
28291 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
1 ATTTTGATTACCTTTTGCTTGGCACCATATGAGATTTGA
* * * *
28330 ATTTTGATTACTTTTTGTTTGGCACCATATGAGCTTTGG
1 ATTTTGATTACCTTTTGCTTGGCACCATATGAGATTTGA
28369 ATTTTGAT
1 ATTTTGAT
28377 GAGCATCATA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTACCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:29661 original size:14 final size:15
Alignment explanation
Indices: 29625--29662 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
29615 GAAATCATTG
29625 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
29640 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
29655 AAAAATTA
1 AAAAATTA
29663 GAGATGAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:29970 original size:115 final size:115
Alignment explanation
Indices: 29762--29998 Score: 402
Period size: 115 Copynumber: 2.1 Consensus size: 115
29752 TAGGTTATGA
29762 GTTGCTGCTGCTGCGTTATTATATACCCAAAACATTTGTGTTGCGAAACTAAAACCTGTTGCGAA
1 GTTGC-GCTGCTGCGTTATTATATACCCAAAACATTTGTGTTGCGAAACTAAAACCTGTTGCGAA
*
29827 ATTAAATTCGCGTTGCGAATTTGACTTTTGTATTACGAATTTGACTGTCGC
65 ATTAAATTCGCGTTGCGAATTTGACTTTTGTATTACGAATTTGACTATCGC
* * *
29878 TTTGCGCTGCTGCGTTTTTATATACCCAAAACATTTGTGTTGTGAAACTAAAACCTGTTGCGAAA
1 GTTGCGCTGCTGCGTTATTATATACCCAAAACATTTGTGTTGCGAAACTAAAACCTGTTGCGAAA
* * *
29943 TTAAATTTGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGC
66 TTAAATTCGCGTTGCGAATTTGACTTTTGTATTACGAATTTGACTATCGC
29993 GTTGCG
1 GTTGCG
29999 ATTTACAGAT
Statistics
Matches: 113, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
115 109 0.96
116 4 0.04
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (115 bp):
GTTGCGCTGCTGCGTTATTATATACCCAAAACATTTGTGTTGCGAAACTAAAACCTGTTGCGAAA
TTAAATTCGCGTTGCGAATTTGACTTTTGTATTACGAATTTGACTATCGC
Found at i:29976 original size:20 final size:20
Alignment explanation
Indices: 29948--29999 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
29938 CGAAATTAAA
29948 TTTGCGTTGCGAATTTGACT
1 TTTGCGTTGCGAATTTGACT
*
29968 TTTGTGTTGCGAATTTGACT
1 TTTGCGTTGCGAATTTGACT
* *
29988 ATCGCGTTGCGA
1 TTTGCGTTGCGA
30000 TTTACAGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.42
Consensus pattern (20 bp):
TTTGCGTTGCGAATTTGACT
Found at i:30012 original size:20 final size:20
Alignment explanation
Indices: 29989--30079 Score: 182
Period size: 20 Copynumber: 4.5 Consensus size: 20
29979 AATTTGACTA
29989 TCGCGTTGCGATTTACAGAT
1 TCGCGTTGCGATTTACAGAT
30009 TCGCGTTGCGATTTACAGAT
1 TCGCGTTGCGATTTACAGAT
30029 TCGCGTTGCGATTTACAGAT
1 TCGCGTTGCGATTTACAGAT
30049 TCGCGTTGCGATTTACAGAT
1 TCGCGTTGCGATTTACAGAT
30069 TCGCGTTGCGA
1 TCGCGTTGCGA
30080 ATTTGGAAAC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (20 bp):
TCGCGTTGCGATTTACAGAT
Found at i:30017 original size:40 final size:41
Alignment explanation
Indices: 29973--30079 Score: 168
Period size: 40 Copynumber: 2.7 Consensus size: 41
29963 TGACTTTTGT
*
29973 GTTGCGAATTTGAC-TA-TCGCGTTGCGATTTACAGATTCGC
1 GTTGCGAATTT-ACAGATTCGCGTTGCGATTTACAGATTCGC
30013 GTTGCG-ATTTACAGATTCGCGTTGCGATTTACAGATTCGC
1 GTTGCGAATTTACAGATTCGCGTTGCGATTTACAGATTCGC
30053 GTTGCG-ATTTACAGATTCGCGTTGCGA
1 GTTGCGAATTTACAGATTCGCGTTGCGA
30080 ATTTGGAAAC
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
38 2 0.03
39 5 0.08
40 57 0.89
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (41 bp):
GTTGCGAATTTACAGATTCGCGTTGCGATTTACAGATTCGC
Found at i:30019 original size:60 final size:61
Alignment explanation
Indices: 29951--30084 Score: 170
Period size: 60 Copynumber: 2.2 Consensus size: 61
29941 AATTAAATTT
* * * *
29951 GCGTTGCGAATTTGAC-TTTTGTGTTGCGAATTTGAC-TA-TCGCGTTGCGATTTACAGATTC
1 GCGTTGCGAATTTGACAATTCGCGTTGCG-ATTT-ACAGATTCGCGTTGCGATTTACAGATTC
30011 GCGTTGCG-ATTT-ACAGATTCGCGTTGCGATTTACAGATTCGCGTTGCGATTTACAGATTC
1 GCGTTGCGAATTTGACA-ATTCGCGTTGCGATTTACAGATTCGCGTTGCGATTTACAGATTC
30071 GCGTTGCGAATTTG
1 GCGTTGCGAATTTG
30085 GAAACTGGGT
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
58 4 0.06
59 9 0.14
60 47 0.73
61 4 0.06
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (61 bp):
GCGTTGCGAATTTGACAATTCGCGTTGCGATTTACAGATTCGCGTTGCGATTTACAGATTC
Found at i:32806 original size:2 final size:2
Alignment explanation
Indices: 32799--32828 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
32789 AAACAAATGG
32799 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
32829 ACACTATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35801 original size:34 final size:34
Alignment explanation
Indices: 35758--35882 Score: 129
Period size: 34 Copynumber: 3.8 Consensus size: 34
35748 TTCGTCCTAC
35758 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
35792 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
35827 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
35856 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
35883 CCACAAGCAC
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 39 0.53
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:36261 original size:15 final size:15
Alignment explanation
Indices: 36239--36277 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
36229 ATTATATGGA
*
36239 TATT-TTATTCATTT
1 TATTATTATTCATGT
*
36253 TTTTATTATTCATGT
1 TATTATTATTCATGT
36268 TATTATTATT
1 TATTATTATT
36278 ATATGTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (15 bp):
TATTATTATTCATGT
Found at i:36352 original size:23 final size:21
Alignment explanation
Indices: 36324--36371 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
36314 TTTTTTTTAC
*
36324 TATATTTTTTTATATATTATAT
1 TATATTTCTTTA-ATATTATAT
*
36346 ATATATTTCTTTAATATTTTAT
1 -TATATTTCTTTAATATTATAT
36368 TATA
1 TATA
36372 AGTCTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 8 0.35
23 11 0.48
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
TATATTTCTTTAATATTATAT
Found at i:36786 original size:2 final size:2
Alignment explanation
Indices: 36779--36804 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36769 TAATACTTTG
36779 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
36805 TTTTTTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41115 original size:183 final size:183
Alignment explanation
Indices: 40807--41156 Score: 637
Period size: 183 Copynumber: 1.9 Consensus size: 183
40797 ATTAAATCCG
40807 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** *
40872 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
40937 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAAGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
40990 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
41055 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGTTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
41120 TTGTCAAGCCAAAGACTTTGTGATGAGATGAACCCTT
131 TTGTCAAGCCAAAGACTTTGTGATGAGACGAACCCTT
41157 TAGTTAAACC
Statistics
Matches: 160, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 160 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAAGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
Found at i:42509 original size:37 final size:37
Alignment explanation
Indices: 42442--42528 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
42432 ATTGAAAACA
** * *
42442 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
42478 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
42515 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
42529 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:42534 original size:102 final size:102
Alignment explanation
Indices: 42353--42657 Score: 486
Period size: 102 Copynumber: 3.0 Consensus size: 102
42343 TTAAAACAAG
* * * *
42353 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACAGTTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAA-TTTTGTCTCCCTTGAGACAGTTTCT
* *
42418 CTTTAAACACAAACATTGAAAACATTTCCCTTGAAATGA
64 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
42457 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
42522 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* * *
42559 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCTTTGAGACAGCTTCTAT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
*
42623 TGAAACATAAACTTTGAAAACAGTTTCCCTTGAAA
66 TGAAACATAAACATTGAAAACA-TTTCCCTTGAAA
42658 CAAAATCTTT
Statistics
Matches: 190, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
101 48 0.25
102 107 0.56
103 3 0.02
104 32 0.17
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (102 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
Found at i:42591 original size:36 final size:36
Alignment explanation
Indices: 42544--42612 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
42534 ATTGAAAACA
**
42544 TTTCCCTTGAAATGAATTTTGTCT-CTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCT-TTGAGATAG
42580 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGA
1 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGA
42613 CAGCTTCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 28 0.93
37 2 0.07
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGATAG
Found at i:42626 original size:36 final size:36
Alignment explanation
Indices: 42558--42629 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
42548 CCTTGAAATG
* * *
42558 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 AATTTTGTCTCTCTTGAGACAGCTTCCATTGAAACA
*
42594 AATTTTGTCTC-CTTTGAGACAGCTTCTATTGAAACA
1 AATTTTGTCTCTC-TTGAGACAGCTTCCATTGAAACA
42630 TAAACTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 1 0.03
36 30 0.97
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (36 bp):
AATTTTGTCTCTCTTGAGACAGCTTCCATTGAAACA
Found at i:42755 original size:67 final size:65
Alignment explanation
Indices: 42642--42828 Score: 180
Period size: 67 Copynumber: 2.8 Consensus size: 65
42632 AACTTTGAAA
* * * * *
42642 ACAGTTTCCCTTG-AA-ACAAAATCTTTGAATATGTTTTACATTAAACAAATTTCGTCTCTCTTG
1 ACAGTTTCTCTTGAAACACAAAATCTTTGAGT-T-TTTTCCCTTAAACAAATTTCGTCTCCCTTG
42705 AG
64 AG
*
42707 ACAGTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCCTTAAAACAAATTTTGTCTCCCTTG
1 ACAGTTTCTCTTGAAACACAAAATCTTTGAGTTT-TTTCCCTT-AAACAAATTTCGTCTCCCTTG
42772 AG
64 AG
* * * * * *
42774 GCCGTTTCTCATGAAACAACATATATCTTTAAGATTGTTTCCCTTGAAACAAATT
1 ACAGTTTCTCTTGAAAC-ACA-AAATCTTTGAG-TTTTTTCCCTT-AAACAAATT
42829 CTGTCTTTTT
Statistics
Matches: 102, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
65 13 0.13
66 9 0.09
67 49 0.48
68 3 0.03
69 26 0.25
70 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (65 bp):
ACAGTTTCTCTTGAAACACAAAATCTTTGAGTTTTTTCCCTTAAACAAATTTCGTCTCCCTTGAG
Found at i:43338 original size:106 final size:107
Alignment explanation
Indices: 43147--43379 Score: 326
Period size: 106 Copynumber: 2.2 Consensus size: 107
43137 GGTTTTAGCT
* *
43147 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAATACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
** *
43212 CGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCCCAATTTC
66 CGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAATTCC
* ** * *
43253 GGAGCCAATTTCAACTTCACATTGAAAGG-CATTGGACTCGAGACAGCACAAGTTCAACTTCACA
1 AGAGCCAATTTCAACTTCACAGCG-AAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACA
*
43317 ACGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAGTTCC
65 ACGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAATTCC
* *
43360 AGAACCAACTTCAACTTCAC
1 AGAGCCAATTTCAACTTCAC
43380 GACAGAAGAT
Statistics
Matches: 111, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
106 74 0.67
107 37 0.33
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (107 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
CGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAATTCC
Found at i:43916 original size:34 final size:34
Alignment explanation
Indices: 43873--43997 Score: 129
Period size: 34 Copynumber: 3.8 Consensus size: 34
43863 TTCGTCCTAC
43873 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
43907 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
43942 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
43971 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
43998 CCACAAGCAC
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 39 0.53
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:44376 original size:15 final size:15
Alignment explanation
Indices: 44354--44392 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
44344 ATTATATGGA
*
44354 TATT-TTATTCATTT
1 TATTATTATTCATGT
*
44368 TTTTATTATTCATGT
1 TATTATTATTCATGT
44383 TATTATTATT
1 TATTATTATT
44393 ATATGTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (15 bp):
TATTATTATTCATGT
Found at i:44492 original size:28 final size:27
Alignment explanation
Indices: 44441--44493 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
44431 TTTTTTTTAC
*
44441 TATATTTTTTATTATTATTATTATATA
1 TATATTTTTTAATATTATTATTATATA
44468 TATATTTCTTTAATATT-TTATT-TATA
1 TATATTT-TTTAATATTATTATTATATA
44494 AGTCTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 12 0.50
28 8 0.33
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (27 bp):
TATATTTTTTAATATTATTATTATATA
Found at i:44904 original size:2 final size:2
Alignment explanation
Indices: 44897--44928 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
44887 TAATACTTTG
44897 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
44929 TTCTTTTTCC
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:45018 original size:26 final size:27
Alignment explanation
Indices: 44967--45018 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
44957 TATATAATTA
*
44967 TTACTTTACTATTTTTTTTTTCTTATC
1 TTACTTTACTATTTTTTTATTCTTATC
*
44994 TTAC-TTATTATTTTATTTATT-TTAT
1 TTACTTTACTATTTT-TTTATTCTTAT
45019 TTTTCTCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (27 bp):
TTACTTTACTATTTTTTTATTCTTATC
Found at i:51418 original size:36 final size:36
Alignment explanation
Indices: 51371--51447 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
51361 GCAGAGTTAT
*
51371 AAAATTTTAGAGACTGTGAAATTACGTAATTAATAG
1 AAAATTTTAGAGACTGTGAAATTAAGTAATTAATAG
51407 AAAATTTTAGAGACTGTGAAATTAAGTAATTAATAG
1 AAAATTTTAGAGACTGTGAAATTAAGTAATTAATAG
*
51443 GAAAT
1 AAAAT
51448 ACAATGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.47, C:0.04, G:0.17, T:0.32
Consensus pattern (36 bp):
AAAATTTTAGAGACTGTGAAATTAAGTAATTAATAG
Found at i:60083 original size:3 final size:3
Alignment explanation
Indices: 60038--60064 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
60028 ATAACTTTTT
60038 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
60065 TATACTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:63180 original size:14 final size:14
Alignment explanation
Indices: 63161--63190 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
63151 TTTAGATATT
*
63161 TTAAAATTACATTA
1 TTAAAAATACATTA
63175 TTAAAAATACATTA
1 TTAAAAATACATTA
63189 TT
1 TT
63191 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:63351 original size:14 final size:14
Alignment explanation
Indices: 63277--63360 Score: 61
Period size: 14 Copynumber: 6.2 Consensus size: 14
63267 AGGGTTTATG
*
63277 GTTTAGTATTTAGA
1 GTTTAGGATTTAGA
*
63291 GTTTATGG-TATA-A
1 GTTTA-GGATTTAGA
* *
63304 GTTAAGG-TTTAGG
1 GTTTAGGATTTAGA
*
63317 GTTTAGTATTTAGA
1 GTTTAGGATTTAGA
63331 GTTTAGGATTT-GA
1 GTTTAGGATTTAGA
*
63344 TGTTTAGGGTTTA-A
1 -GTTTAGGATTTAGA
63358 GTT
1 GTT
63361 ATGTACATGA
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
12 5 0.09
13 15 0.27
14 34 0.62
15 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (14 bp):
GTTTAGGATTTAGA
Found at i:65072 original size:18 final size:18
Alignment explanation
Indices: 65049--65085 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
65039 GCGGGCGGAT
65049 GTGGGGTGGGCGGATGTG
1 GTGGGGTGGGCGGATGTG
65067 GTGGGGTGGGCGGATGTG
1 GTGGGGTGGGCGGATGTG
65085 G
1 G
65086 GGCGGGCGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.05, G:0.68, T:0.22
Consensus pattern (18 bp):
GTGGGGTGGGCGGATGTG
Found at i:65103 original size:15 final size:15
Alignment explanation
Indices: 65037--65105 Score: 84
Period size: 15 Copynumber: 4.4 Consensus size: 15
65027 ATATTTAGCT
65037 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGTG
*
65052 GGGTGGGCGGATGTGGTG
1 GGGCGGGCGGA--T-GTG
*
65070 GGGTGGGCGGATGTG
1 GGGCGGGCGGATGTG
*
65085 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGTG
65100 GGGCGG
1 GGGCGG
65106 ATGTGGGGCG
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
15 32 0.67
16 1 0.02
17 1 0.02
18 14 0.29
ACGTcount: A:0.06, C:0.12, G:0.68, T:0.14
Consensus pattern (15 bp):
GGGCGGGCGGATGTG
Found at i:66322 original size:230 final size:231
Alignment explanation
Indices: 65903--66364 Score: 883
Period size: 231 Copynumber: 2.0 Consensus size: 231
65893 CGAGTTCGAG
65903 TCGAGCTTGAAAATTTTAGGCTTACGTCGAGTACTTTTGAAAGTTTCTAGTTCGAGTCGAGTTCG
1 TCGAGCTTGAAAATTTTAGGCTTACGTCGAGTACTTTTGAAAGTTTCTAGTTCGAGTCGAGTTCG
*
65968 GCAATACTCGAGCTCGACTCGGTCGTTTCACCCCAGGCTTAATGCCCAAATAAGTGCTAAAATTA
66 GCAATACTCGAGCTCGACTCGGTCGTTACACCCCAGGCTTAATGCCCAAATAAGTGCTAAAATTA
66033 TGCTTTTTTCCAAATAAATGTCTTTGGTTTTTCTTTTTACATATCTAGACGTCTAACGTTACAAA
131 TGCTTTTTTCCAAATAAATGTCTTTGGTTTTTCTTTTTACATATCTAGACGTCTAACGTTACAAA
66098 TGTTATCCTTTTAGGTATTCAAGTCGTCAACGTCCT
196 TGTTATCCTTTTAGGTATTCAAGTCGTCAACGTCCT
66134 TCGAGCTTGAAAA-TTTAGGCTTACGTCGAGTACTTTTGAAAGTTTTCTAGTTCGAGTCGAGTTC
1 TCGAGCTTGAAAATTTTAGGCTTACGTCGAGTACTTTTGAAAG-TTTCTAGTTCGAGTCGAGTTC
*
66198 GGCAATACTCGAGCTCGACTCGGTCGTTACACCCTAGGCTTAATGCCCAAATAAGTGCTAAAATT
65 GGCAATACTCGAGCTCGACTCGGTCGTTACACCCCAGGCTTAATGCCCAAATAAGTGCTAAAATT
66263 ATGCTTTTTTCCAAATAAATGTC-TTGGTTTTTCTTTTTACATATCTAGACGTCTAACGTTACAA
130 ATGCTTTTTTCCAAATAAATGTCTTTGGTTTTTCTTTTTACATATCTAGACGTCTAACGTTACAA
66327 ATGTTATCCTTTTAGGTATTCAAGTCGTCAACGTCCT
195 ATGTTATCCTTTTAGGTATTCAAGTCGTCAACGTCCT
66364 T
1 T
66365 TTCCTGTTAA
Statistics
Matches: 228, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
230 108 0.47
231 120 0.53
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (231 bp):
TCGAGCTTGAAAATTTTAGGCTTACGTCGAGTACTTTTGAAAGTTTCTAGTTCGAGTCGAGTTCG
GCAATACTCGAGCTCGACTCGGTCGTTACACCCCAGGCTTAATGCCCAAATAAGTGCTAAAATTA
TGCTTTTTTCCAAATAAATGTCTTTGGTTTTTCTTTTTACATATCTAGACGTCTAACGTTACAAA
TGTTATCCTTTTAGGTATTCAAGTCGTCAACGTCCT
Found at i:66824 original size:22 final size:22
Alignment explanation
Indices: 66799--66850 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
66789 GGGTTATTTC
* *
66799 AAAATTTAT-GTTTTTTCTTTTT
1 AAAATTTATAATTTTAT-TTTTT
*
66821 AAAAGTATATAATTTTATTTTTT
1 AAAA-TTTATAATTTTATTTTTT
66844 AAAATTT
1 AAAATTT
66851 GATATAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 6 0.25
23 13 0.54
24 5 0.21
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (22 bp):
AAAATTTATAATTTTATTTTTT
Found at i:67187 original size:15 final size:15
Alignment explanation
Indices: 67167--67195 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
67157 CAGTTATTGC
67167 TCATTAATATTTGTA
1 TCATTAATATTTGTA
67182 TCATTAATATTTGT
1 TCATTAATATTTGT
67196 TGTTTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (15 bp):
TCATTAATATTTGTA
Found at i:68609 original size:33 final size:33
Alignment explanation
Indices: 68518--68612 Score: 172
Period size: 33 Copynumber: 2.9 Consensus size: 33
68508 TGTTCAAAGT
*
68518 TTGGCCACCAACCAAGATGAAATTTCCAATAAG
1 TTGGCCACCAACCAAGATGAAATTTTCAATAAG
*
68551 TTGACCACCAACCAAGATGAAATTTTCAATAAG
1 TTGGCCACCAACCAAGATGAAATTTTCAATAAG
68584 TTGGCCACCAACCAAGATGAAATTTTCAA
1 TTGGCCACCAACCAAGATGAAATTTTCAA
68613 CTTGTCAACT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (33 bp):
TTGGCCACCAACCAAGATGAAATTTTCAATAAG
Found at i:71618 original size:16 final size:17
Alignment explanation
Indices: 71599--71635 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
71589 ATTTTCAACA
71599 AAAATATA-AAAAAATT
1 AAAATATATAAAAAATT
71615 AAAATATATAAAAAATT
1 AAAATATATAAAAAATT
71632 AAAA
1 AAAA
71636 ATTTTCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATATATAAAAAATT
Found at i:83455 original size:20 final size:21
Alignment explanation
Indices: 83430--83481 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
83420 TTTTCCCAAT
*
83430 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
83450 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
83471 TCGCAATGCGA
1 TCGCAATGCGA
83482 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:83494 original size:41 final size:41
Alignment explanation
Indices: 83467--83544 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
83457 GCGAATTGGG
* * *
83467 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
83508 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
83545 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:83495 original size:20 final size:20
Alignment explanation
Indices: 83470--83564 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
83460 AATTGGGAAA
*
83470 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
83490 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
83511 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
83531 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
83551 TTCGCAACGCGATA
1 ATCGCAACGCGATA
83565 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:83780 original size:22 final size:22
Alignment explanation
Indices: 83752--83795 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
83742 CACTCTCTCA
83752 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
83774 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
83796 TATCTCCATC
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:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:84084 original size:20 final size:20
Alignment explanation
Indices: 84059--84096 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
84049 CGATTCTCTC
84059 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
84079 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
84097 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:85436 original size:18 final size:18
Alignment explanation
Indices: 85415--85459 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
85405 TCCACTTCTG
*
85415 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
85433 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
85451 GAGCCATCA
1 GAGCCATCA
85460 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:85995 original size:19 final size:20
Alignment explanation
Indices: 85941--86007 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
85931 TAGTTTACTT
* *
85941 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
85961 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
85981 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
86000 TCGCAACG
1 TCGCAACG
86008 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:86074 original size:14 final size:14
Alignment explanation
Indices: 86055--86112 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
86045 TTTCATTTCG
86055 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
86069 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
86085 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
86101 CGTTGCGATTTT
1 CGTTGCGATTTT
86113 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:86119 original size:33 final size:33
Alignment explanation
Indices: 86038--86128 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
86028 ACAAATCGCA
*
86038 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
86071 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
86103 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
86129 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:86135 original size:19 final size:19
Alignment explanation
Indices: 86113--86167 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
86103 TTGCGATTTT
86113 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
* *
86132 CATTTC-CACGTTACGATAGT
1 CATTTCGCA--TTGCGATAGC
*
86152 CATTTCGCGTTGCGAT
1 CATTTCGCATTGCGAT
86168 TTTAAGTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 2 0.07
19 12 0.41
20 14 0.48
21 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:88052 original size:14 final size:14
Alignment explanation
Indices: 88033--88068 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
88023 ATTGTTTAAT
88033 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
88047 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
88061 TGATTTGT
1 TGATTTGT
88069 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:88207 original size:19 final size:19
Alignment explanation
Indices: 88185--88252 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
88175 ATCGCAACGA
88185 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
88204 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
88223 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
88237 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
88253 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:88296 original size:20 final size:20
Alignment explanation
Indices: 88271--88348 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
88261 TCGCATTGCG
*
88271 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
88291 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
88311 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
88331 ATTTTCGCATTGCGATAG
1 ATTTTCGCGTTGCGATAG
88349 TCAAATGAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:88304 original size:34 final size:34
Alignment explanation
Indices: 88259--88346 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 34
88249 GCGATTTTCA
*
88259 TTTCGCATTGCGATTTTCTCGTTGCGATAGCCAT
1 TTTCGCATTGCGATTTTCGCGTTGCGATAGCCAT
*
88293 TTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCCAT
1 TTTCGCATTGC----G--ATTTTCGCGTTGCGATAGCCAT
88333 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
88347 AGTCAAATGA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
34 12 0.27
36 1 0.02
38 1 0.02
40 31 0.69
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.39
Consensus pattern (34 bp):
TTTCGCATTGCGATTTTCGCGTTGCGATAGCCAT
Found at i:89438 original size:24 final size:24
Alignment explanation
Indices: 89411--89464 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
89401 GTATTCGAAA
* *
89411 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
89435 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
89459 TTTGAT
1 TTTGAT
89465 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:89656 original size:12 final size:12
Alignment explanation
Indices: 89639--89663 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
89629 ATATAATCCT
89639 GAAGAAGAAAAA
1 GAAGAAGAAAAA
89651 GAAGAAGAAAAA
1 GAAGAAGAAAAA
89663 G
1 G
89664 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:92185 original size:14 final size:14
Alignment explanation
Indices: 92166--92202 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
92156 CATCAATTAA
92166 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
92180 ACAAATCACCTTTT
1 ACAAATCAACTTTT
92194 ACAAATCAA
1 ACAAATCAA
92203 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:93627 original size:21 final size:21
Alignment explanation
Indices: 93561--93627 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
93551 GTGAATCGGG
*
93561 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
93581 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
93603 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
93624 CTCT
1 CTCT
93628 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:95764 original size:33 final size:33
Alignment explanation
Indices: 95707--95805 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
95697 ACGAGATAAT
*
95707 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
95741 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
95774 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
95806 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:95799 original size:19 final size:19
Alignment explanation
Indices: 95682--95865 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
95672 GTCTTTGGTT
*
95682 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
95701 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
95721 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
95739 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
95755 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
95773 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
95788 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
95808 GAAAT-AAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
95826 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
95845 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
95864 GA
1 GA
95866 TTTTGGTTTC
Statistics
Matches: 138, Mismatches: 13, Indels: 28
0.77 0.07 0.16
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 12 0.09
19 64 0.46
20 35 0.25
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:95894 original size:19 final size:19
Alignment explanation
Indices: 95861--95927 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
95851 AAAATCGCAA
**
95861 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
95880 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
95899 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
95919 TGCGATTTT
1 TGCGATTTT
95928 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:96529 original size:20 final size:20
Alignment explanation
Indices: 96444--96537 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
96434 CGCTATGTAA
* *
96444 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGATAGTCAGT
*
96464 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
96484 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCAGT
*
96505 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
96525 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
96538 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:96556 original size:41 final size:41
Alignment explanation
Indices: 96464--96558 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
96454 GAAAGTCAGA
* * * ** *
96464 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
*
96505 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAAT
96547 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
96559 TTACTTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:96648 original size:21 final size:21
Alignment explanation
Indices: 96608--96648 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
96598 ATTGTCTACC
**
96608 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
96629 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
96649 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:97344 original size:22 final size:24
Alignment explanation
Indices: 97283--97391 Score: 89
Period size: 28 Copynumber: 4.2 Consensus size: 24
97273 AAAATAAATT
*
97283 ATATATTTTTAAGTGAA-AATAAAA
1 ATATA-TTTTAAGTTAATAATAAAA
*
97307 ATATATTTTAAATTAAGTTAATAATAAA
1 ATATATTTTAAGTTAA--TAAT-A-AAA
97335 ATATATTTAATAAGTTAAT-ATAAAA
1 ATATATTT--TAAGTTAATAATAAAA
97360 ATAT-TTTTAAGTTAATATATATAAA
1 ATATATTTTAAGTTAATA-ATA-AAA
97385 ATTATAT
1 A-TATAT
97392 AACATATAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 21
0.74 0.03 0.22
Matches are distributed among these distances:
22 9 0.13
23 9 0.13
24 11 0.16
25 11 0.16
26 7 0.10
27 4 0.06
28 12 0.17
30 7 0.10
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (24 bp):
ATATATTTTAAGTTAATAATAAAA
Found at i:97354 original size:25 final size:25
Alignment explanation
Indices: 97263--97376 Score: 96
Period size: 25 Copynumber: 4.6 Consensus size: 25
97253 AGTCATACTA
*
97263 TTAATAAATTAA-AATAAATTATATAT
1 TTAATAAGTTAATAATAAA--ATATAT
* *
97289 TT-TTAAGTGAA-AATAAAAATATATT
1 TTAATAAGTTAATAAT-AAAATATA-T
97314 TTAAATTAAGTTAATAATAAAATATAT
1 TT-AA-TAAGTTAATAATAAAATATAT
97341 TTAATAAGTTAAT-ATAAAA-ATAT
1 TTAATAAGTTAATAATAAAATATAT
*
97364 TT-TTAAGTTAATA
1 TTAATAAGTTAATA
97377 TATATAAAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
22 9 0.12
23 6 0.08
24 11 0.15
25 21 0.28
26 7 0.09
27 3 0.04
28 15 0.20
29 3 0.04
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
TTAATAAGTTAATAATAAAATATAT
Found at i:97385 original size:25 final size:25
Alignment explanation
Indices: 97318--97386 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 25
97308 TATATTTTAA
97318 ATTAAGTTAATA-ATAAAATATATTT
1 ATTAAGTTAATATATAAAA-ATATTT
*
97343 AATAAGTT-A-ATATAAAAATATTT
1 ATTAAGTTAATATATAAAAATATTT
97366 -TTAAGTTAATATATATAAAAT
1 ATTAAGTTAATATATA-AAAAT
97387 TATATAACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 6 0.16
23 8 0.21
24 12 0.32
25 12 0.32
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
ATTAAGTTAATATATAAAAATATTT
Found at i:97392 original size:53 final size:52
Alignment explanation
Indices: 97278--97392 Score: 128
Period size: 53 Copynumber: 2.2 Consensus size: 52
97268 AAATTAAAAT
*
97278 AAATTATATATTTTTAAGTGAAAATAAAAATATATTTTAAATTAAGTTAATA
1 AAATTATATATTTATAAGTGAAAATAAAAATATATTTTAAATTAAGTTAATA
* * * *
97330 ATAA-AATATATTTAATAAGTTAATATAAAAATAT-TTTTAAGTTAA-TATATATA
1 A-AATTATATATTT-ATAAGTGAAAATAAAAATATATTTTAAATTAAGT-TA-ATA
97383 AAATTATATA
1 AAATTATATA
97393 ACATATAATC
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
51 1 0.02
52 23 0.44
53 28 0.54
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (52 bp):
AAATTATATATTTATAAGTGAAAATAAAAATATATTTTAAATTAAGTTAATA
Found at i:97554 original size:14 final size:14
Alignment explanation
Indices: 97526--97586 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
97516 AATCCACACA
97526 TAAAATTTAAA-AAT
1 TAAAA-TTAAATAAT
*
97540 TCAAATTAAATAAT
1 TAAAATTAAATAAT
* *
97554 TAAAATAAAATTAT
1 TAAAATTAAATAAT
*
97568 TAAAAATAAA-AAT
1 TAAAATTAAATAAT
*
97581 AAAAAT
1 TAAAAT
97587 ATAATTAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
13 11 0.30
14 26 0.70
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAAATTAAATAAT
Found at i:98734 original size:2 final size:2
Alignment explanation
Indices: 98727--98759 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
98717 AAGGGAAATA
98727 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
98760 CACTCCAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:99252 original size:16 final size:16
Alignment explanation
Indices: 99226--99263 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
99216 TTTATTTCAA
99226 AATGA-TTAAATATTG
1 AATGATTTAAATATTG
*
99241 AATGATTTAAATGTTG
1 AATGATTTAAATATTG
99257 AATGATT
1 AATGATT
99264 CAGAGGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (16 bp):
AATGATTTAAATATTG
Found at i:99355 original size:27 final size:27
Alignment explanation
Indices: 99317--99380 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
99307 GATAATGGCT
99317 CTGAATCATTAAGAATGTACTTCTGTG
1 CTGAATCATTAAGAATGTACTTCTGTG
99344 CTGAATCATTAAGAATGTACTTCTGTG
1 CTGAATCATTAAGAATGTACTTCTGTG
99371 CTGAATCATT
1 CTGAATCATT
99381 CAACATTGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (27 bp):
CTGAATCATTAAGAATGTACTTCTGTG
Found at i:99406 original size:23 final size:23
Alignment explanation
Indices: 99372--99429 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
99362 ACTTCTGTGC
* *
99372 TGAATCATTCAACATTGTTTTGT
1 TGAATCAGTCAACACTGTTTTGT
99395 TGAATCAGTCAACACTGTTTTGT
1 TGAATCAGTCAACACTGTTTTGT
99418 TGAATCAGTCAA
1 TGAATCAGTCAA
99430 TACTAAATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (23 bp):
TGAATCAGTCAACACTGTTTTGT
Found at i:101829 original size:82 final size:81
Alignment explanation
Indices: 101690--101846 Score: 278
Period size: 82 Copynumber: 1.9 Consensus size: 81
101680 TTTGGGTGTC
* * *
101690 AACTTGATATTTTTAAAAAATAGAGGTTTAAATTAAAATTTTCAAATAATTTGAAGAGTTCAATT
1 AACTTGAAATTTTTAAAAAATAGAGGTTTAAATTAAAATTATCAAATAATTTAAAGAGTTCAATT
101755 TACATCTTTTTTACCA
66 TACATCTTTTTTACCA
101771 AACTTGAAATTTTTTAAAAAATAGAGGTTTAAATTAAAATTATCAAATAATTTAAAGAGTTCAAT
1 AACTTGAAA-TTTTTAAAAAATAGAGGTTTAAATTAAAATTATCAAATAATTTAAAGAGTTCAAT
101836 TTACATCTTTT
65 TTACATCTTTT
101847 CCAAACAAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
81 8 0.11
82 64 0.89
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (81 bp):
AACTTGAAATTTTTAAAAAATAGAGGTTTAAATTAAAATTATCAAATAATTTAAAGAGTTCAATT
TACATCTTTTTTACCA
Found at i:112821 original size:17 final size:17
Alignment explanation
Indices: 112799--112833 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
112789 TATTACTGAA
112799 AATACATATTAGCTCAT
1 AATACATATTAGCTCAT
112816 AATACATATTAGCTCAT
1 AATACATATTAGCTCAT
112833 A
1 A
112834 TATATTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (17 bp):
AATACATATTAGCTCAT
Found at i:113978 original size:28 final size:28
Alignment explanation
Indices: 113911--113979 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
113901 TTTTTTATTA
*
113911 TATTATATTTATTTTATATTTAATTATTTG
1 TATTAT-TTT-TTTTATATCTAATTATTTG
* * *
113941 AATAAATTTTTTTATA-CTAATTATTTTG
1 TATTATTTTTTTTATATCTAATTA-TTTG
113969 TATTATTTTTT
1 TATTATTTTTT
113980 ACGGTTGTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
27 6 0.19
28 19 0.61
29 3 0.10
30 3 0.10
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.65
Consensus pattern (28 bp):
TATTATTTTTTTTATATCTAATTATTTG
Done.