Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012026.1 Kokia drynarioides strain JFW-HI SEQ_127024, 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: 63998
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:6571 original size:17 final size:15
Alignment explanation
Indices: 6547--6584 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 15
6537 TTCATTTTTA
6547 TTTTCCCTTCTTTCTT
1 TTTTCCCTT-TTTCTT
6563 TTCTTCCCTTTTTCTT
1 TT-TTCCCTTTTTCTT
6579 TTTTCC
1 TTTTCC
6585 ATCCCGGCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 10 0.48
17 7 0.33
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTCCCTTTTTCTT
Found at i:28282 original size:16 final size:17
Alignment explanation
Indices: 28255--28286 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28245 TTCCCATTTT
28255 GTGTTCTTTTAGTGACA
1 GTGTTCTTTTAGTGACA
28272 GTGTT-TTTTAGTGAC
1 GTGTTCTTTTAGTGAC
28287 GGTACACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.16, C:0.09, G:0.25, T:0.50
Consensus pattern (17 bp):
GTGTTCTTTTAGTGACA
Found at i:33788 original size:20 final size:20
Alignment explanation
Indices: 33763--33802 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
33753 CGAGATGTAT
*
33763 GATATTTAGGTTTTACTTGA
1 GATATTTAGATTTTACTTGA
*
33783 GATATTTAGATTTTGCTTGA
1 GATATTTAGATTTTACTTGA
33803 TAGAGTAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (20 bp):
GATATTTAGATTTTACTTGA
Found at i:33790 original size:73 final size:74
Alignment explanation
Indices: 33711--33857 Score: 192
Period size: 73 Copynumber: 2.0 Consensus size: 74
33701 GATGTATACA
* * *
33711 ATATTTAGGTTTTACTTGATAGAGCAAGTGTTGGCGG-TGA-AGCGAG-ATGTATGATATTTAGG
1 ATATTTAGATTTTACTTGATAGAGCAAGTGTTAGCGGAT-ATAGAG-GTATGTATGATATTTAGG
33773 TTTTACTTGAG
64 TTTTACTTGAG
* * *
33784 ATATTTAGATTTTGCTTGATAGAGTAGGTGTTAGCGGCATATAGAGGTATGTATGATATTTAGGT
1 ATATTTAGATTTTACTTGATAGAGCAAGTGTTAGCGG-ATATAGAGGTATGTATGATATTTAGGT
33849 TTTACTTGA
65 TTTACTTGA
33858 TAGAGTAAGT
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
73 32 0.50
74 2 0.03
75 30 0.47
ACGTcount: A:0.27, C:0.06, G:0.27, T:0.40
Consensus pattern (74 bp):
ATATTTAGATTTTACTTGATAGAGCAAGTGTTAGCGGATATAGAGGTATGTATGATATTTAGGTT
TTACTTGAG
Found at i:33870 original size:55 final size:55
Alignment explanation
Indices: 33783--34132 Score: 457
Period size: 55 Copynumber: 6.4 Consensus size: 55
33773 TTTTACTTGA
* * * * * ** ** *
33783 GATATTTAGATTTTGCTTGATAGAGTAGGTGTTAGCGGCATATAGAGGTATGTAT
1 GATATTTAGGTTTTACTTGATAGAATAAGTGTTGGCGGCGGAGGGAGGTGTGTAT
* *
33838 GATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGCGGCGGAGGGAGATGTGTAT
1 GATATTTAGGTTTTACTTGATAGAATAAGTGTTGGCGGCGGAGGGAGGTGTGTAT
* *
33893 GATATTTAAGTTTTACTTGATAGAATAAGTGTTGGCGGCGGAGGGAGATGTGTAT
1 GATATTTAGGTTTTACTTGATAGAATAAGTGTTGGCGGCGGAGGGAGGTGTGTAT
* * * * *
33948 GATATTTAGGTTTTACTTGATAGAGTAAGTTTTGGCGGCAGAGCGATGTGTGTAT
1 GATATTTAGGTTTTACTTGATAGAATAAGTGTTGGCGGCGGAGGGAGGTGTGTAT
* *
34003 GATATTTAGGTTTTTCTTGATAGAATAAATGTTGGCGGCGGAGGGAGGTGTGTAT
1 GATATTTAGGTTTTACTTGATAGAATAAGTGTTGGCGGCGGAGGGAGGTGTGTAT
* * * *
34058 CATATTTAGGTTTTTCTTGATAGAATAAGTGTTGGTGACGGAGGGAGGTGTGTAT
1 GATATTTAGGTTTTACTTGATAGAATAAGTGTTGGCGGCGGAGGGAGGTGTGTAT
* *
34113 CATATTTAGGTTTTTCTTGA
1 GATATTTAGGTTTTACTTGA
34133 GATATTTAGG
Statistics
Matches: 265, Mismatches: 30, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 265 1.00
ACGTcount: A:0.25, C:0.06, G:0.32, T:0.38
Consensus pattern (55 bp):
GATATTTAGGTTTTACTTGATAGAATAAGTGTTGGCGGCGGAGGGAGGTGTGTAT
Found at i:34139 original size:20 final size:20
Alignment explanation
Indices: 34114--34152 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
34104 GGTGTGTATC
*
34114 ATATTTAGGTTTTTCTTGAG
1 ATATTTAGGTTTTACTTGAG
34134 ATATTTAGGTTTTACTTGA
1 ATATTTAGGTTTTACTTGA
34153 TAGAGTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.18, T:0.54
Consensus pattern (20 bp):
ATATTTAGGTTTTACTTGAG
Found at i:34166 original size:240 final size:238
Alignment explanation
Indices: 33893--34612 Score: 786
Period size: 240 Copynumber: 3.0 Consensus size: 238
33883 AGATGTGTAT
* * * *
33893 GATATTTAAGTTTTACTTGATAGAATAAGTGTTGGCGGCGGAGGGAGATGTGTATGATATTTAGG
1 GATATTTAGGTTTTACTTGATAGAATAAGTGTTGGTGGCGGAGAGAGGTGTGTATGATATTTAGG
* ** * * *
33958 TTTTACTTGATAGAGTAAGTTTTGGCGGCAGAGCGATGTGTGTATGATATTTAGGTTTTTCTTGA
66 TTTTACTTGATAGAGTAAGTGTTGGCGGCAGATAGAGGTGTGTATCATATTTAGGTTTTACTTGA
* *
34023 TAGAATAAATGTTGGCGGCGGAGGGAGGTGTGTATCATATTTAGGTTTTTCTTGATAGAATAAGT
131 TAGAATAAGTGTTGGCGGCGGAGGGAGGTGTGTATCATATTTAGGTTTTACTTGATA-AATAAGT
* * * * *
34088 GTTGGTGACGGAGGGAGGTGTGTATCATATTTAGGTTTTTCTTGA
195 GTTGATGACAGA-GAAAGTGTGTATCATATTTAGGTTTTACTTGA
* * * *
34133 GATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGTGGCGGATAAAGGTGTGTATAATATTTAGG
1 GATATTTAGGTTTTACTTGATAGAATAAGTGTTGGTGGCGGAGAGAGGTGTGTATGATATTTAGG
* ** * * * *
34198 TTTTACTTGATGGAGTAAGTGTTGGCGATAAATAAAGGTGTATATTATATTTAGGTTTTACTTGA
66 TTTTACTTGATAGAGTAAGTGTTGGCGGCAGATAGAGGTGTGTATCATATTTAGGTTTTACTTGA
* * * * *
34263 TAGAATAAGTGTTGGCGGCGGAGAGAGGTGTGTATGATATTTAGGTTTTACTTGAGATATTTAG-
131 TAGAATAAGTGTTGGCGGCGGAGGGAGGTGTGTATCATATTTAGGTTTTACTTGATA-AATAAGT
* * * ** ** ** *
34327 GTTTTACTTGATAGAGTAAGTGTTGGTGGCGA-ATAGAGG-GGTGCATT--
195 G-TTGA--TGACAGAGAAAGTG-T-GTATC-ATATTTAGGTTTTAC-TTGA
* * * *
34374 -ATATTTAGGTTTTACTTGATAGACTAAGTGTTGATGACGGAGAGAGGTGTATATGATATTTAGG
1 GATATTTAGGTTTTACTTGATAGAATAAGTGTTGGTGGCGGAGAGAGGTGTGTATGATATTTAGG
* * * *
34438 TTTTACTTGATACAGTAAGTGTTGGCGGCGGATAGAGGTTTGTATCATATTTAGGTTTTACTTAA
66 TTTTACTTGATAGAGTAAGTGTTGGCGGCAGATAGAGGTGTGTATCATATTTAGGTTTTACTTGA
* * *
34503 TTGAATAAGTATTGGCGGCGGAGGGAGGTGTGTATCATATTTAGGTTTTACTTAATAAAGTAAGT
131 TAGAATAAGTGTTGGCGGCGGAGGGAGGTGTGTATCATATTTAGGTTTTACTTGATAAA-TAAGT
* *
34568 GTTGACGACAGATAAATGTGTGTATCATATTTAGGTTTTACTTGA
195 GTTGATGACAGAGAAA-GTGTGTATCATATTTAGGTTTTACTTGA
34613 TAGAGTAAGT
Statistics
Matches: 387, Mismatches: 79, Indels: 29
0.78 0.16 0.06
Matches are distributed among these distances:
236 1 0.00
237 10 0.03
238 10 0.03
239 5 0.01
240 336 0.87
241 6 0.02
242 8 0.02
243 10 0.03
244 1 0.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.38
Consensus pattern (238 bp):
GATATTTAGGTTTTACTTGATAGAATAAGTGTTGGTGGCGGAGAGAGGTGTGTATGATATTTAGG
TTTTACTTGATAGAGTAAGTGTTGGCGGCAGATAGAGGTGTGTATCATATTTAGGTTTTACTTGA
TAGAATAAGTGTTGGCGGCGGAGGGAGGTGTGTATCATATTTAGGTTTTACTTGATAAATAAGTG
TTGATGACAGAGAAAGTGTGTATCATATTTAGGTTTTACTTGA
Found at i:34182 original size:75 final size:75
Alignment explanation
Indices: 34059--34207 Score: 226
Period size: 75 Copynumber: 2.0 Consensus size: 75
34049 GGTGTGTATC
* ** *
34059 ATATTTAGGTTTTTCTTGATAGAATAAGTGTTGGTGACGGAGGGAGGTGTGTATCATATTTAGGT
1 ATATTTAGGTTTTACTTGATAGAATAAGTGTTGGTGACGGAGAAAGGTGTGTATAATATTTAGGT
*
34124 TTTTCTTGAG
66 TTTACTTGAG
* * *
34134 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGTGGCGGATAAAGGTGTGTATAATATTTAGGT
1 ATATTTAGGTTTTACTTGATAGAATAAGTGTTGGTGACGGAGAAAGGTGTGTATAATATTTAGGT
34199 TTTACTTGA
66 TTTACTTGA
34208 TGGAGTAAGT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 66 1.00
ACGTcount: A:0.25, C:0.05, G:0.28, T:0.42
Consensus pattern (75 bp):
ATATTTAGGTTTTACTTGATAGAATAAGTGTTGGTGACGGAGAAAGGTGTGTATAATATTTAGGT
TTTACTTGAG
Found at i:34218 original size:55 final size:55
Alignment explanation
Indices: 34134--34317 Score: 260
Period size: 55 Copynumber: 3.3 Consensus size: 55
34124 TTTTCTTGAG
*
34134 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGTGGCGGATAAAGGTGTGTATA
1 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGCGGCGGATAAAGGTGTGTATA
* **** * *
34189 ATATTTAGGTTTTACTTGATGGAGTAAGTGTTGGCGATAAATAAAGGTGTATATT
1 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGCGGCGGATAAAGGTGTGTATA
* * * *
34244 ATATTTAGGTTTTACTTGATAGAATAAGTGTTGGCGGCGGAGAGAGGTGTGTATG
1 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGCGGCGGATAAAGGTGTGTATA
34299 ATATTTAGGTTTTACTTGA
1 ATATTTAGGTTTTACTTGA
34318 GATATTTAGG
Statistics
Matches: 111, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 111 1.00
ACGTcount: A:0.28, C:0.04, G:0.29, T:0.39
Consensus pattern (55 bp):
ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGCGGCGGATAAAGGTGTGTATA
Found at i:34237 original size:130 final size:130
Alignment explanation
Indices: 34003--34262 Score: 331
Period size: 130 Copynumber: 2.0 Consensus size: 130
33993 ATGTGTGTAT
* ** *
34003 GATATTTAGGTTTTTCTTGATAGAATAAATGTTGGCGGCGGAGGGAGGTGTGTATCATATTTAGG
1 GATATTTAGGTTTTACTTGATAGAATAAATGTTGGCGGCGGAGAAAGGTGTGTATAATATTTAGG
* * ** ** * *
34068 TTTTTCTTGATAGAATAAGTGTTGGTGACGGAGGGAGGTGTGTATCATATTTAGGTTTTTCTTGA
66 TTTTACTTGATAGAATAAGTGTTGGCGACAAAGAAAGGTGTATATCATATTTAGGTTTTACTTGA
* * * *
34133 GATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGTGGCGGATAAAGGTGTGTATAATATTTAGG
1 GATATTTAGGTTTTACTTGATAGAATAAATGTTGGCGGCGGAGAAAGGTGTGTATAATATTTAGG
* * * * *
34198 TTTTACTTGATGGAGTAAGTGTTGGCGATAAATAAAGGTGTATATTATATTTAGGTTTTACTTGA
66 TTTTACTTGATAGAATAAGTGTTGGCGACAAAGAAAGGTGTATATCATATTTAGGTTTTACTTGA
34263 TAGAATAAGT
Statistics
Matches: 109, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.26, C:0.05, G:0.29, T:0.40
Consensus pattern (130 bp):
GATATTTAGGTTTTACTTGATAGAATAAATGTTGGCGGCGGAGAAAGGTGTGTATAATATTTAGG
TTTTACTTGATAGAATAAGTGTTGGCGACAAAGAAAGGTGTATATCATATTTAGGTTTTACTTGA
Found at i:34264 original size:185 final size:185
Alignment explanation
Indices: 33948--34500 Score: 755
Period size: 185 Copynumber: 3.0 Consensus size: 185
33938 AGATGTGTAT
* * * ** * *
33948 GATATTTAGGTTTTACTTGATAGAGTAAGTTTTGGCGGCAGAGCGATGTGTGTATGATATTTAGG
1 GATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGTGGCGGATAGAGGTGTGTATAATATTTAGG
* * * * * *
34013 TTTTTCTTGATAGAATAAATGTTGGCGGCGGAGGGAGGTGTGTATCATATTTAGGTTTTTCTTGA
66 TTTTACTTGATAGAATAAGTGTTGGCGACGGAGAGAGGTGTATATCATATTTAGGTTTTACTTGA
* * * *
34078 TAGAATAAGTGTTGGTGACGGAGGGAGGTGTGTATCATATTTAGGTTTTTCTTGA
131 TAGAATAAGTGTTGGCGGCGGAGAGAGGTGTGTATCATATTTAGGTTTTACTTGA
*
34133 GATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGTGGCGGATAAAGGTGTGTATAATATTTAGG
1 GATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGTGGCGGATAGAGGTGTGTATAATATTTAGG
* * *** * * *
34198 TTTTACTTGATGGAGTAAGTGTTGGCGATAAATAAAGGTGTATATTATATTTAGGTTTTACTTGA
66 TTTTACTTGATAGAATAAGTGTTGGCGACGGAGAGAGGTGTATATCATATTTAGGTTTTACTTGA
*
34263 TAGAATAAGTGTTGGCGGCGGAGAGAGGTGTGTATGATATTTAGGTTTTACTTGA
131 TAGAATAAGTGTTGGCGGCGGAGAGAGGTGTGTATCATATTTAGGTTTTACTTGA
* * * *
34318 GATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGTGGCGAATAGAGGGGTGCATTATATTTAGG
1 GATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGTGGCGGATAGAGGTGTGTATAATATTTAGG
* ** *
34383 TTTTACTTGATAGACTAAGTGTTGATGACGGAGAGAGGTGTATATGATATTTAGGTTTTACTTGA
66 TTTTACTTGATAGAATAAGTGTTGGCGACGGAGAGAGGTGTATATCATATTTAGGTTTTACTTGA
* * * *
34448 TACAGTAAGTGTTGGCGGCGGATAGAGGTTTGTATCATATTTAGGTTTTACTT
131 TAGAATAAGTGTTGGCGGCGGAGAGAGGTGTGTATCATATTTAGGTTTTACTT
34501 AATTGAATAA
Statistics
Matches: 321, Mismatches: 47, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
185 321 1.00
ACGTcount: A:0.25, C:0.06, G:0.30, T:0.39
Consensus pattern (185 bp):
GATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGTGGCGGATAGAGGTGTGTATAATATTTAGG
TTTTACTTGATAGAATAAGTGTTGGCGACGGAGAGAGGTGTATATCATATTTAGGTTTTACTTGA
TAGAATAAGTGTTGGCGGCGGAGAGAGGTGTGTATCATATTTAGGTTTTACTTGA
Found at i:34323 original size:20 final size:20
Alignment explanation
Indices: 34298--34337 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
34288 AGGTGTGTAT
34298 GATATTTAGGTTTTACTTGA
1 GATATTTAGGTTTTACTTGA
34318 GATATTTAGGTTTTACTTGA
1 GATATTTAGGTTTTACTTGA
34338 TAGAGTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (20 bp):
GATATTTAGGTTTTACTTGA
Found at i:34323 original size:130 final size:130
Alignment explanation
Indices: 34189--34447 Score: 392
Period size: 130 Copynumber: 2.0 Consensus size: 130
34179 GGTGTGTATA
* * * *
34189 ATATTTAGGTTTTACTTGATGGAGTAAGTGTTGGCGATAAATAAAGGTGTATATTATATTTAGGT
1 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGCGACAAATAAAGGGGTACATTATATTTAGGT
* * *
34254 TTTACTTGATAGAATAAGTGTTGGCGGCGGAGAGAGGTGTGTATGATATTTAGGTTTTACTTGAG
66 TTTACTTGATAGAATAAGTGTTGACGACGGAGAGAGGTGTATATGATATTTAGGTTTTACTTGAG
* * * * *
34319 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGTGGCGAATAGAGGGGTGCATTATATTTAGGT
1 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGCGACAAATAAAGGGGTACATTATATTTAGGT
* *
34384 TTTACTTGATAGACTAAGTGTTGATGACGGAGAGAGGTGTATATGATATTTAGGTTTTACTTGA
66 TTTACTTGATAGAATAAGTGTTGACGACGGAGAGAGGTGTATATGATATTTAGGTTTTACTTGA
34448 TACAGTAAGT
Statistics
Matches: 115, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
130 115 1.00
ACGTcount: A:0.27, C:0.05, G:0.29, T:0.39
Consensus pattern (130 bp):
ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGCGACAAATAAAGGGGTACATTATATTTAGGT
TTTACTTGATAGAATAAGTGTTGACGACGGAGAGAGGTGTATATGATATTTAGGTTTTACTTGAG
Found at i:34378 original size:75 final size:75
Alignment explanation
Indices: 34244--34392 Score: 235
Period size: 75 Copynumber: 2.0 Consensus size: 75
34234 GGTGTATATT
* * *
34244 ATATTTAGGTTTTACTTGATAGAATAAGTGTTGGCGGCGGAGAGAGGTGTGTATGATATTTAGGT
1 ATATTTAGGTTTTACTTGATAGAATAAGTGTTGGCGGCGAAGAGAGGGGTGCATGATATTTAGGT
34309 TTTACTTGAG
66 TTTACTTGAG
* * * *
34319 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGTGGCGAATAGAGGGGTGCATTATATTTAGGT
1 ATATTTAGGTTTTACTTGATAGAATAAGTGTTGGCGGCGAAGAGAGGGGTGCATGATATTTAGGT
34384 TTTACTTGA
66 TTTACTTGA
34393 TAGACTAAGT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.26, C:0.05, G:0.30, T:0.40
Consensus pattern (75 bp):
ATATTTAGGTTTTACTTGATAGAATAAGTGTTGGCGGCGAAGAGAGGGGTGCATGATATTTAGGT
TTTACTTGAG
Found at i:34403 original size:55 final size:55
Alignment explanation
Indices: 34319--34634 Score: 371
Period size: 55 Copynumber: 5.7 Consensus size: 55
34309 TTTACTTGAG
* * * * *
34319 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGTGGCGAATAGAGGGGTGCATT
1 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGCGGCGGATAGAGGTGTGTATC
* ** * * * *
34374 ATATTTAGGTTTTACTTGATAGACTAAGTGTTGATGACGGAGAGAGGTGTATATG
1 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGCGGCGGATAGAGGTGTGTATC
* *
34429 ATATTTAGGTTTTACTTGATACAGTAAGTGTTGGCGGCGGATAGAGGTTTGTATC
1 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGCGGCGGATAGAGGTGTGTATC
* * * * **
34484 ATATTTAGGTTTTACTTAATTGAATAAGTATTGGCGGCGGAGGGAGGTGTGTATC
1 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGCGGCGGATAGAGGTGTGTATC
* * * * * * *
34539 ATATTTAGGTTTTACTTAATAAAGTAAGTGTTGACGACAGATAAATGTGTGTATC
1 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGCGGCGGATAGAGGTGTGTATC
* *
34594 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTAGCGACGGA
1 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGCGGCGGA
34635 GAGTAAAGGT
Statistics
Matches: 219, Mismatches: 42, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 219 1.00
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.37
Consensus pattern (55 bp):
ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGCGGCGGATAGAGGTGTGTATC
Found at i:34600 original size:165 final size:165
Alignment explanation
Indices: 34319--34634 Score: 416
Period size: 165 Copynumber: 1.9 Consensus size: 165
34309 TTTACTTGAG
* * * * * *
34319 ATATTTAGGTTTTACTTGATAGAGTAAGTGTTGGTGGCGAATAGAGGGGTGCATTATATTTAGGT
1 ATATTTAGGTTTTACTTAATAGAATAAGTATTGGCGGCGAAGAGAGGGGTGCATCATATTTAGGT
* * * * * *
34384 TTTACTTGATAGACTAAGTGTTGATGACGGAGAGAGGTGTATATGATATTTAGGTTTTACTTGAT
66 TTTACTTAATAAACTAAGTGTTGACGACAGAGAAAGGTGTATATCATATTTAGGTTTTACTTGAT
* *
34449 ACAGTAAGTGTTGGCGGCGGATAGAGGTTTGTATC
131 ACAGTAAGTGTTAGCGACGGATAGAGGTTTGTATC
* * * * *
34484 ATATTTAGGTTTTACTTAATTGAATAAGTATTGGCGGCGGAGGGAGGTGTGTATCATATTTAGGT
1 ATATTTAGGTTTTACTTAATAGAATAAGTATTGGCGGCGAAGAGAGGGGTGCATCATATTTAGGT
* * * *
34549 TTTACTTAATAAAGTAAGTGTTGACGACAGATAAATGTGTGTATCATATTTAGGTTTTACTTGAT
66 TTTACTTAATAAACTAAGTGTTGACGACAGAGAAAGGTGTATATCATATTTAGGTTTTACTTGAT
*
34614 AGAGTAAGTGTTAGCGACGGA
131 ACAGTAAGTGTTAGCGACGGA
34635 GAGTAAAGGT
Statistics
Matches: 127, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
165 127 1.00
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.37
Consensus pattern (165 bp):
ATATTTAGGTTTTACTTAATAGAATAAGTATTGGCGGCGAAGAGAGGGGTGCATCATATTTAGGT
TTTACTTAATAAACTAAGTGTTGACGACAGAGAAAGGTGTATATCATATTTAGGTTTTACTTGAT
ACAGTAAGTGTTAGCGACGGATAGAGGTTTGTATC
Found at i:35258 original size:56 final size:55
Alignment explanation
Indices: 35191--35320 Score: 163
Period size: 56 Copynumber: 2.3 Consensus size: 55
35181 GTGTATATGT
* **
35191 TATTTAGGTTTTACTTTATAGAGTAAGTGTTGGTTG-CAGAGGGAAGTGTGAATGA
1 TATTTAGGTTTTACTTAATAGAGTAAGT-TTGGACGACAGAGGGAAGTGTGAATGA
* * * *
35246 TATTTTAGGTTTTACTTAATAGAGTAAGTTTTGACGACGGAGGGAGGTGTGTATGA
1 TA-TTTAGGTTTTACTTAATAGAGTAAGTTTGGACGACAGAGGGAAGTGTGAATGA
*
35302 TATTTAGGTCTTACTTAAT
1 TATTTAGGTTTTACTTAAT
35321 GTATTTAAGT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
55 22 0.34
56 43 0.66
ACGTcount: A:0.27, C:0.05, G:0.28, T:0.40
Consensus pattern (55 bp):
TATTTAGGTTTTACTTAATAGAGTAAGTTTGGACGACAGAGGGAAGTGTGAATGA
Found at i:35327 original size:20 final size:20
Alignment explanation
Indices: 35302--35340 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35292 GTGTGTATGA
*
35302 TATTTAGGTCTTACTTAATG
1 TATTTAAGTCTTACTTAATG
*
35322 TATTTAAGTTTTACTTAAT
1 TATTTAAGTCTTACTTAAT
35341 ATAGTAAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54
Consensus pattern (20 bp):
TATTTAAGTCTTACTTAATG
Found at i:35347 original size:75 final size:75
Alignment explanation
Indices: 35249--35456 Score: 326
Period size: 75 Copynumber: 2.8 Consensus size: 75
35239 TGAATGATAT
* * * ** * * *
35249 TTTAGGTTTTACTTAATAGAGTAAGTTTTGACGACGGAGGGAGGTGTGTATGATATTTAGGTCTT
1 TTTAAGTTTTACTTAATATAGTAAGTGTTGGTGGCGGAGGAATGTGTGTATGATATTTAGGTCTT
35314 ACTTAATGTA
66 ACTTAATGTA
35324 TTTAAGTTTTACTTAATATAGTAAGTGTTGGTGGCGGAGGAATGTGTGTATGATATTTAGGTCTT
1 TTTAAGTTTTACTTAATATAGTAAGTGTTGGTGGCGGAGGAATGTGTGTATGATATTTAGGTCTT
35389 ACTTAATGTA
66 ACTTAATGTA
* *
35399 TTTAAGTTTTACTTAATATATTAAGTGTTGGTGGCAGAGGAATGTGTGTATGATATTT
1 TTTAAGTTTTACTTAATATAGTAAGTGTTGGTGGCGGAGGAATGTGTGTATGATATTT
35457 TAGTTTTACT
Statistics
Matches: 123, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 123 1.00
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.42
Consensus pattern (75 bp):
TTTAAGTTTTACTTAATATAGTAAGTGTTGGTGGCGGAGGAATGTGTGTATGATATTTAGGTCTT
ACTTAATGTA
Found at i:35424 original size:19 final size:20
Alignment explanation
Indices: 35376--35424 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
35366 TGTGTGTATG
* *
35376 ATATTTAGGTCTTACTTAAT
1 ATATTTAAGTTTTACTTAAT
*
35396 GTATTTAAGTTTTACTTAAT
1 ATATTTAAGTTTTACTTAAT
35416 ATA-TTAAGT
1 ATATTTAAGT
35425 GTTGGTGGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (20 bp):
ATATTTAAGTTTTACTTAAT
Found at i:35479 original size:55 final size:55
Alignment explanation
Indices: 35397--35586 Score: 238
Period size: 55 Copynumber: 3.5 Consensus size: 55
35387 TTACTTAATG
* * * * *
35397 TATTTAAGTTTTACTTAATATATTAAGTGTTGGTGGCAGAGGAATGTGTGTATGA
1 TATTTAAGTTTTACTTGATAGAGTAAGTGTTAGTGGCAGAGGAAGGTGTGTATGA
* * *
35452 TATTTTAGTTTTACTTGATAGAGTAAGTGTCAGTGGCGGAGGAAGGTGTGTATGA
1 TATTTAAGTTTTACTTGATAGAGTAAGTGTTAGTGGCAGAGGAAGGTGTGTATGA
* ** * **
35507 TATTTAAGTTTTACTTGATAGAGCAAGTGTTAGCAGTAGATAAAGGTGTGTATGA
1 TATTTAAGTTTTACTTGATAGAGTAAGTGTTAGTGGCAGAGGAAGGTGTGTATGA
35562 TATTTAAGTTTTACTTTG-TAGAGTA
1 TATTTAAGTTTTAC-TTGATAGAGTA
35587 GAAATTTTTT
Statistics
Matches: 116, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
55 113 0.97
56 3 0.03
ACGTcount: A:0.29, C:0.05, G:0.26, T:0.40
Consensus pattern (55 bp):
TATTTAAGTTTTACTTGATAGAGTAAGTGTTAGTGGCAGAGGAAGGTGTGTATGA
Found at i:38512 original size:18 final size:17
Alignment explanation
Indices: 38470--38512 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
38460 TTTTTAAGTT
*
38470 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
38487 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
38505 TATAATTT
1 TATAATTT
38513 AGAACACATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:39836 original size:38 final size:38
Alignment explanation
Indices: 39748--39836 Score: 101
Period size: 38 Copynumber: 2.4 Consensus size: 38
39738 TTTTATGAAA
* *
39748 CAGTCCTTGAAAT-TCAAATTTTACAATTTTTACAATT
1 CAGTCCCTGAAATCTCAAATTTTACAAGTTTTACAATT
* * * *
39785 TAATCTCTAAAATCTCAAA-TTTACACAGTTTTACAATT
1 CAGTCCCTGAAATCTCAAATTTTACA-AGTTTTACAATT
39823 CAGTCCCTGAAATC
1 CAGTCCCTGAAATC
39837 AGATTTTATT
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
37 14 0.35
38 26 0.65
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (38 bp):
CAGTCCCTGAAATCTCAAATTTTACAAGTTTTACAATT
Found at i:41886 original size:24 final size:23
Alignment explanation
Indices: 41853--41904 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
41843 TATTTGAATA
*
41853 AAAATTGAAATATTAAAAAATTT
1 AAAATTGAAAAATTAAAAAATTT
*
41876 AAAATTCGAAAAATTTAAAAATTT
1 AAAATT-GAAAAATTAAAAAATTT
41900 AAAAT
1 AAAAT
41905 GACCAAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAATTGAAAAATTAAAAAATTT
Found at i:41895 original size:8 final size:8
Alignment explanation
Indices: 41851--41903 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
41841 ATTATTTGAA
41851 TAAAAATT
1 TAAAAATT
* *
41859 GAAATATT
1 TAAAAATT
*
41867 AAAAAATT
1 TAAAAATT
41875 T-AAAATT
1 TAAAAATT
*
41882 CGAAAAATT
1 -TAAAAATT
41891 TAAAAATT
1 TAAAAATT
41899 TAAAA
1 TAAAA
41904 TGACCAAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
7 6 0.17
8 24 0.67
9 6 0.17
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (8 bp):
TAAAAATT
Found at i:45024 original size:16 final size:18
Alignment explanation
Indices: 44992--45024 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
44982 ATCAAAGAGT
44992 AAAATTGTTATTCTATTA
1 AAAATTGTTATTCTATTA
45010 AAAATT-TTA-TCTATT
1 AAAATTGTTATTCTATT
45025 TTTATAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (18 bp):
AAAATTGTTATTCTATTA
Found at i:47681 original size:26 final size:26
Alignment explanation
Indices: 47652--47705 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
47642 TGCGAGCAAG
47652 TTTAAACAAATTCTCAATTAGTTTTA
1 TTTAAACAAATTCTCAATTAGTTTTA
*** *
47678 TTTATGTAAATTCTTAATTAGTTTTA
1 TTTAAACAAATTCTCAATTAGTTTTA
47704 TT
1 TT
47706 GATGTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.54
Consensus pattern (26 bp):
TTTAAACAAATTCTCAATTAGTTTTA
Found at i:47710 original size:26 final size:26
Alignment explanation
Indices: 47659--47714 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
47649 AAGTTTAAAC
*
47659 AAATTCTCAATTAGTTTTATTTATGT
1 AAATTCTCAATTAGTTTTATTGATGT
*
47685 AAATTCTTAATTAGTTTTATTGATGT
1 AAATTCTCAATTAGTTTTATTGATGT
47711 AAAT
1 AAAT
47715 ATTCAATATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (26 bp):
AAATTCTCAATTAGTTTTATTGATGT
Found at i:56546 original size:18 final size:17
Alignment explanation
Indices: 56523--56571 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 17
56513 TATATTTTCC
56523 ATAAAATATTAAAAAATT
1 ATAAAATATTAAAAAA-T
*
56541 ATAAAAAAATTAAAAAAT
1 AT-AAAATATTAAAAAAT
56559 ATATAAATATTAA
1 ATA-AAATATTAA
56572 TTTTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 13 0.48
19 13 0.48
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAAAATATTAAAAAAT
Found at i:56565 original size:11 final size:10
Alignment explanation
Indices: 56525--56565 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
56515 TATTTTCCAT
56525 AAAATATTAA
1 AAAATATTAA
56535 AAAAT-TATAA
1 AAAATAT-TAA
56545 AAAA-ATTAA
1 AAAATATTAA
56554 AAAATATATAA
1 AAAATAT-TAA
56565 A
1 A
56566 TATTAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 8 0.30
10 15 0.56
11 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAATATTAA
Found at i:61360 original size:22 final size:20
Alignment explanation
Indices: 61317--61356 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
61307 TATAAAAGTT
*
61317 AATGTAAAAAGTCAAATTTG
1 AATGTAAAAAATCAAATTTG
*
61337 AATGATAAAAAATTAAATTT
1 AATG-TAAAAAATCAAATTT
61357 TGAAATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (20 bp):
AATGTAAAAAATCAAATTTG
Done.