Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010939.1 Kokia drynarioides strain JFW-HI SEQ_125907, 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: 302541
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 240 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:246319 original size:17 final size:17
Alignment explanation
Indices: 246299--246346 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
246289 TTTTTTAAAA
246299 AATATTTATTTTATTTT
1 AATATTTATTTTATTTT
* *
246316 AATATTTA-ATAATTTT
1 AATATTTATTTTATTTT
*
246332 -ATATATATTTTATTT
1 AATATTTATTTTATTT
246347 ATTGAAAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 6 0.24
16 11 0.44
17 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AATATTTATTTTATTTT
Found at i:269444 original size:16 final size:16
Alignment explanation
Indices: 269422--269493 Score: 110
Period size: 16 Copynumber: 4.5 Consensus size: 16
269412 CGTTTGATTC
269422 ATTGTAATGGAATA-A
1 ATTGTAATGGAATAGA
269437 AGTTGTAATGGAATAGA
1 A-TTGTAATGGAATAGA
*
269454 ATTGTAATAGAATAGA
1 ATTGTAATGGAATAGA
*
269470 ATTGTAATGAAATAGA
1 ATTGTAATGGAATAGA
269486 ATTGTAAT
1 ATTGTAAT
269494 CAGTAATTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
15 1 0.02
16 49 0.94
17 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.33
Consensus pattern (16 bp):
ATTGTAATGGAATAGA
Found at i:272836 original size:60 final size:58
Alignment explanation
Indices: 272695--273069 Score: 238
Period size: 59 Copynumber: 6.4 Consensus size: 58
272685 GAGGTCCCTA
* * *
272695 AACCTTCTAAAAATTAGCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTG
1 AACCTTC-CAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
* ** *
272754 AACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAGGTCCCATTTTTTTTACCCCG
1 AACCTTCC-AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA--TTTTTGACCCCG
* * *
272815 AACCTTCCAAAATTACCATTTTACCCCCGAACTT-AAAAAATTACCA-TTTT-ACCCCC
1 AACCTTCCAAAATTACCATTTTACCCCCGAACTTCCAAAAA-TCCCATTTTTGACCCCG
* * * * *
272871 AAACTTCCAAAAATCCCATTTTTGA-CCTCGAACCTTCCAAAAATTACCA-TTTT-ACCCCCG
1 AACCTTCCAAAATTACCA-TTTT-ACCCCCGAA-CTTCCAAAAA-TCCCATTTTTGA-CCCCG
** * * * * *
272931 AA-CTTCCAAAGGTCCCATTTTTAACCCTGAACCTTCCAAAAATTACCA-TTTT-ATCCTCG
1 AACCTTCCAAAATTACCA-TTTTACCCCCGAA-CTTCCAAAAA-TCCCATTTTTGA-CCCCG
* * *
272990 AA-CTTCCAAAAGTCCCATTTTTGA-CCCCGAACCTTCCAAAAATTACCA-TTTT-ACCCCCG
1 AACCTTCCAAAATTACCA-TTTT-ACCCCCGAA-CTTCCAAAAA-TCCCATTTTTGA-CCCCG
* *
273049 AA-CTTCCAAAAATCCCATTTT
1 AACCTTCCAAAATTACCATTTT
273070 TGATCCTGAA
Statistics
Matches: 275, Mismatches: 30, Indels: 23
0.84 0.09 0.07
Matches are distributed among these distances:
56 20 0.07
57 14 0.05
58 9 0.03
59 178 0.65
60 36 0.13
61 18 0.07
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.30
Consensus pattern (58 bp):
AACCTTCCAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:272893 original size:147 final size:146
Alignment explanation
Indices: 272703--273069 Score: 485
Period size: 147 Copynumber: 2.5 Consensus size: 146
272693 TAAACCTTCT
* *
272703 AAAAATTAGCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTGAACCTTCCAAAAAT
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCTGAACCTTCCAAAAAT
*
272768 TACCATTTTACCCCCAAACTTCCAAAGGTCCCATTTTTTTTACCCCGAACCTTCC-AAAATTACC
66 TACCATTTTACCCCCAAACTTCCAAAGGTCCCA--TTTTTAACCCCGAACCTTCCAAAAATTACC
272832 ATTTTACCCCCGAACTTA
129 ATTTTACCCCCGAACTTA
272850 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA-CCTCGAACCTTCCAAAAA
1 AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCT-GAACCTTCCAAAAA
* *
272914 TTACCATTTTACCCCCGAACTTCCAAAGGTCCCATTTTTAACCCTGAACCTTCCAAAAATTACCA
65 TTACCATTTTACCCCCAAACTTCCAAAGGTCCCATTTTTAACCCCGAACCTTCCAAAAATTACCA
* * *
272979 TTTTATCCTCGAACTTC
130 TTTTACCCCCGAACTTA
* * * * * * *
272996 CAAAAGTCCCATTTTTGACCCCGAACCTTCCAAAAATTACCA-TTTT-ACCCCCGAA-CTTCCAA
1 AAAAATTACCA-TTTT-ACCCCCAAACTTCCAAAAA-TCCCATTTTTGA-CCCTGAACCTTCCAA
*
273058 AAA-TCCCATTTT
62 AAATTACCATTTT
273070 TGATCCTGAA
Statistics
Matches: 197, Mismatches: 16, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
145 18 0.09
146 43 0.22
147 106 0.54
148 24 0.12
149 6 0.03
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.30
Consensus pattern (146 bp):
AAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCTGAACCTTCCAAAAAT
TACCATTTTACCCCCAAACTTCCAAAGGTCCCATTTTTAACCCCGAACCTTCCAAAAATTACCAT
TTTACCCCCGAACTTA
Found at i:273129 original size:59 final size:59
Alignment explanation
Indices: 272805--273109 Score: 397
Period size: 59 Copynumber: 5.2 Consensus size: 59
272795 GTCCCATTTT
* *
272805 TTTTA-CCCCGAACCTTCCAAAATTACCA-TTTT-ACCCCCGAA-CTT-AAAAAATTACCA
1 TTTTACCCCCGAA-CTTCCAAAAATCCCATTTTTGA-CCCCGAACCTTCAAAAAATTACCA
* * *
272861 TTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCAAAAATTACCA
1 TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCAAAAAATTACCA
** * * *
272920 TTTTACCCCCGAACTTCCAAAGGTCCCATTTTTAACCCTGAACCTTCCAAAAATTACCA
1 TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCAAAAAATTACCA
* * * *
272979 TTTTATCCTCGAACTTCCAAAAGTCCCATTTTTGACCCCGAACCTTCCAAAAATTACCA
1 TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCAAAAAATTACCA
* *
273038 TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGATCCTGAACCTTCAAAAAATTA-CA
1 TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCAAAAAATTACCA
273096 TTTTTACCCCCGAA
1 -TTTTACCCCCGAA
273110 TGTTTGAAAT
Statistics
Matches: 221, Mismatches: 22, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
56 18 0.08
57 16 0.07
58 6 0.03
59 181 0.82
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.30
Consensus pattern (59 bp):
TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCAAAAAATTACCA
Found at i:276133 original size:25 final size:23
Alignment explanation
Indices: 276089--276134 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
276079 CCACTTAGGG
276089 AATTATTGTTTAGATTTAATTCT
1 AATTATTGTTTAGATTTAATTCT
*
276112 AATTATCTTTTTAGAGTTTAATT
1 AATTAT-TGTTTAGA-TTTAATT
276135 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCT
Found at i:283958 original size:93 final size:93
Alignment explanation
Indices: 283799--283984 Score: 354
Period size: 93 Copynumber: 2.0 Consensus size: 93
283789 TTCTGTATTT
283799 TTTTATTCTACAAACTTCGATGAACATTCAAATGATTGGAATCCCTCGCAAACATGGACAAGTTT
1 TTTTATTCTACAAACTTCGATGAACATTCAAATGATTGGAATCCCTCGCAAACATGGACAAGTTT
283864 GGAGGGATTCCATTCGCAACCCCTACGA
66 GGAGGGATTCCATTCGCAACCCCTACGA
*
283892 TTTTATTCTACAAACTTCGATGAACATTCAAATGATTGGAATCCCTCGCAAACATGTACAAGTTT
1 TTTTATTCTACAAACTTCGATGAACATTCAAATGATTGGAATCCCTCGCAAACATGGACAAGTTT
*
283957 GGAGGGATTCCGTTCGCAACCCCTACGA
66 GGAGGGATTCCATTCGCAACCCCTACGA
283985 CGATAGTGCA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (93 bp):
TTTTATTCTACAAACTTCGATGAACATTCAAATGATTGGAATCCCTCGCAAACATGGACAAGTTT
GGAGGGATTCCATTCGCAACCCCTACGA
Found at i:284667 original size:17 final size:17
Alignment explanation
Indices: 284642--284695 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
284632 TTTAAATAAG
*
284642 TTTATAATAAATTTAAA
1 TTTAAAATAAATTTAAA
*
284659 TTTCAAATAAATTTAAA
1 TTTAAAATAAATTTAAA
**
284676 CCTAAAATAAATTTAAA
1 TTTAAAATAAATTTAAA
284693 TTT
1 TTT
284696 TGTTGGGCTC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:285675 original size:49 final size:49
Alignment explanation
Indices: 285600--286375 Score: 490
Period size: 49 Copynumber: 15.8 Consensus size: 49
285590 ATGTTTCTAA
* * * *
285600 GGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTTTATATCCTTGT
1 GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCCTTGT
* * * * **
285649 GGTACTAGATTAGCCGTTGC-AGCTTAAATCTTTCCTTTCATGCTCC-TAA
1 GGTACTAGATTCGCCGTTGCGA-CTTAAACCTTTCCCTTCAT-ATCCTTGT
* * * *
285698 GGTACAAGGTTCGCCGTTGCGACTTAAACATTTCCCTTTATAT-CTTGT
1 GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCCTTGT
* * * *
285746 GGTACTAGATTTGCCGTTGTGACTTAAATCTTTCCCTTCATAT--TTCT
1 GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCCTTGT
* * * * * *
285793 AAGGTACAAGGTTTGTCGTTGCGACTTAAACTTTTCCCTTCAAAT-CTTCGT
1 --GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCCTT-GT
* * * * *
285844 GGTACTGGATTCGCCGTTGCGGCTTAAATCC-TTCCCTTCAT-GCTTTTGA
1 GGTACTAGATTCGCCGTTGCGACTTAAA-CCTTTCCCTTCATATC-CTTGT
* * * * **
285893 GGTACAAGGTTCGCCGTTGCGACTTAAACCTTGCCCTCCATATCCTCAT
1 GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCCTTGT
* * * * * * *
285942 GGTACTGGATTCGTCGTTGCGACTTAAATCTCTCCCTTCAT-GCTTCTGA
1 GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCCT-TGT
* * ** *
285991 GGTACAAGGTTTACCGTTGCGACTTAAACCTTTCCCTCCATTAT-CTTCGT
1 GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCA-TATCCTT-GT
* * * * * * * *
286041 GGTACTGGATTCGCCATTGTGGCTTAAATCTTTCCCTTCAT-GCTTCTGA
1 GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCCT-TGT
* * * * **
286090 GGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTCCATATCCTCAT
1 GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCCTTGT
* * * * * *
286139 GGTACTGGATTCGCCGTTAC-AGCTTAAATCTTTCCCTTCAT-GCTTCTGA
1 GGTACTAGATTCGCCGTTGCGA-CTTAAACCTTTCCCTTCATATCCT-TGT
* * * * * * *
286188 GGTGCAAGGTTCGTCGTTGCGACATAAACCTTTCCCTCCATTAT-CTTCAT
1 GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCA-TATCCTT-GT
* * * ** *
286238 GGTACTGGATTCGCCGTTGTGACTTAAATCTTTCCCTTC--ATGGTTGA
1 GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCCTTGT
* * *
286285 GGTACAAGGTTCGCCGTTACGACTTAAACCTTTCCC-TCTATTAT-CTTCGT
1 GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTC-A-TATCCTT-GT
* * *
286335 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
1 GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCAT
286376 GTCTTCATGG
Statistics
Matches: 535, Mismatches: 159, Indels: 66
0.70 0.21 0.09
Matches are distributed among these distances:
46 2 0.00
47 36 0.07
48 48 0.09
49 333 0.62
50 113 0.21
51 3 0.01
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.36
Consensus pattern (49 bp):
GGTACTAGATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCCTTGT
Found at i:285901 original size:98 final size:98
Alignment explanation
Indices: 285588--286381 Score: 1047
Period size: 98 Copynumber: 8.1 Consensus size: 98
285578 ATCTTTTTCG
* * * **
285588 TCATGTTTCTAAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTTTATATCCTT-GTGGT
1 TCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATAT-CTTCGTGGT
* * * *
285652 ACTAGATTAGCCGTTGCAGCTTAAATCTTTCCTT
65 ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
* * * **
285686 TCATGCTCCTAAGGTACAAGGTTCGCCGTTGCGACTTAAACATTTCCCTTTATATCTT-GTGGTA
1 TCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
* * * *
285750 CTAGATTTGCCGTTGTGACTTAAATCTTTCCCT
66 CTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
** * * * * * *
285783 TCATATTTCTAAGGTACAAGGTTTGTCGTTGCGACTTAAACTTTTCCCTTCAAATCTTCGTGGTA
1 TCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
*
285848 CTGGATTCGCCGTTGCGGCTTAAATCCTTCCCT
66 CTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
* * * *
285881 TCATGCTTTTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTGCCCTCCATATCCTCATGGTA
1 TCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
* * *
285946 CTGGATTCGTCGTTGCGACTTAAATCTCTCCCT
66 CTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
**
285979 TCATGCTTCTGAGGTACAAGGTTTACCGTTGCGACTTAAACCTTTCCCTCCATTATCTTCGTGGT
1 TCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCA-TATCTTCGTGGT
* *
286044 ACTGGATTCGCCATTGTGGCTTAAATCTTTCCCT
65 ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
* * *
286078 TCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTCCATATCCTCATGGTA
1 TCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
* *
286143 CTGGATTCGCCGTTACAGCTTAAATCTTTCCCT
66 CTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
* * * *
286176 TCATGCTTCTGAGGTGCAAGGTTCGTCGTTGCGACATAAACCTTTCCCTCCATTATCTTCATGGT
1 TCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCA-TATCTTCGTGGT
* *
286241 ACTGGATTCGCCGTTGTGACTTAAATCTTTCCCT
65 ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
* * *
286275 TCATG-GT-TGAGGTACAAGGTTCGCCGTTACGACTTAAACCTTTCCCTCTATTATCTTCGTGGT
1 TCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCA-TATCTTCGTGGT
286338 ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
65 ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
286372 TCATGTCTTC
1 TCATG-CTTC
286382 ATGGTAATGA
Statistics
Matches: 613, Mismatches: 77, Indels: 10
0.88 0.11 0.01
Matches are distributed among these distances:
97 174 0.28
98 304 0.50
99 135 0.22
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (98 bp):
TCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
CTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
Found at i:286101 original size:197 final size:196
Alignment explanation
Indices: 285588--286381 Score: 1067
Period size: 197 Copynumber: 4.0 Consensus size: 196
285578 ATCTTTTTCG
* **
285588 TCATGTTTCTAAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTTTATATCCTT-GTGGT
1 TCATGCTTCTAAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTCCATAT-CTTCGTGGT
* * * * * *
285652 ACTAGATTAGCCGTTGCAGCTTAAATCTTTCCTTTCATGCTCCTAAGGTACAAGGTTCGCCGTTG
65 ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTG
* ** ** * * *
285717 CGACTTAAACATTTCCCTTTATAT-CTTGTGGTACTAGATTTGCCGTTGTGACTTAAATCTTTCC
130 CGACTTAAACCTTTCCCTCCATATCCTCATGGTACTGGATTCGCCGTTGCGACTTAAATCTTTCC
285781 CT
195 CT
** * * * *
285783 TCATATTTCTAAGGTACAAGGTTTGTCGTTGCGACTTAAACTTTTCCCTTCAAATCTTCGTGGTA
1 TCATGCTTCTAAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
* *
285848 CTGGATTCGCCGTTGCGGCTTAAATCCTTCCCTTCATGCTTTTGAGGTACAAGGTTCGCCGTTGC
66 CTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGC
* * *
285913 GACTTAAACCTTGCCCTCCATATCCTCATGGTACTGGATTCGTCGTTGCGACTTAAATCTCTCCC
131 GACTTAAACCTTTCCCTCCATATCCTCATGGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCC
285978 T
196 T
* ***
285979 TCATGCTTCTGAGGTACAAGGTTTACCGTTGCGACTTAAACCTTTCCCTCCATTATCTTCGTGGT
1 TCATGCTTCTAAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTCCA-TATCTTCGTGGT
* * *
286044 ACTGGATTCGCCATTGTGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTG
65 ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTG
*
286109 CGACTTAAACCTTTCCCTCCATATCCTCATGGTACTGGATTCGCCGTTAC-AGCTTAAATCTTTC
130 CGACTTAAACCTTTCCCTCCATATCCTCATGGTACTGGATTCGCCGTTGCGA-CTTAAATCTTTC
286173 CCT
194 CCT
* * * *
286176 TCATGCTTCTGAGGTGCAAGGTTCGTCGTTGCGACATAAACCTTTCCCTCCATTATCTTCATGGT
1 TCATGCTTCTAAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTCCA-TATCTTCGTGGT
* * * *
286241 ACTGGATTCGCCGTTGTGACTTAAATCTTTCCCTTCATG-GT-TGAGGTACAAGGTTCGCCGTTA
65 ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTG
* * * *
286304 CGACTTAAACCTTTCCCTCTATTATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTC
130 CGACTTAAACCTTTCCCTCCA-TATCCTCATGGTACTGGATTCGCCGTTGCGACTTAAATCTTTC
286369 CCT
194 CCT
286372 TCATGTCTTC
1 TCATG-CTTC
286382 ATGGTAATGA
Statistics
Matches: 535, Mismatches: 57, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
194 3 0.01
195 172 0.32
196 128 0.24
197 232 0.43
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (196 bp):
TCATGCTTCTAAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
CTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGC
GACTTAAACCTTTCCCTCCATATCCTCATGGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCC
T
Found at i:287445 original size:16 final size:15
Alignment explanation
Indices: 287398--287438 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
287388 CCTCGACCTC
287398 TCCTTTTTTCATTTT
1 TCCTTTTTTCATTTT
*
287413 TCTCTATTTTCATTTT
1 TC-CTTTTTTCATTTT
287429 TCCTTTTTTC
1 TCCTTTTTTC
287439 TTCTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (15 bp):
TCCTTTTTTCATTTT
Found at i:288343 original size:15 final size:16
Alignment explanation
Indices: 288311--288343 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
288301 TTGACTTTTC
*
288311 TTCCTTTTCTTTCTTT
1 TTCCTTTTCTTACTTT
288327 TTCCTTTTC-TACTTT
1 TTCCTTTTCTTACTTT
288342 TT
1 TT
288344 TATTGGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (16 bp):
TTCCTTTTCTTACTTT
Found at i:294010 original size:17 final size:17
Alignment explanation
Indices: 293985--294031 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
293975 TAGATAAATT
*
293985 TAAACTTAAATTT-ATAA
1 TAAATTTAAATTTCA-AA
294002 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
294019 TAAATTTAAATTT
1 TAAATTTAAATTT
294032 TGTTGGGCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 27 0.96
18 1 0.04
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:294011 original size:6 final size:6
Alignment explanation
Indices: 293979--294031 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
293969 TTAATTTAGA
*
293979 TAAATT TAAACT TAAATT TATAA-- TAAATT TAAATT TCAAA-- TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT
294025 TAAATT T
1 TAAATT T
294032 TGTTGGGCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
4 5 0.13
5 3 0.08
6 26 0.67
7 5 0.13
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:294022 original size:11 final size:10
Alignment explanation
Indices: 293971--294029 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
293961 TGGACTTTTT
*
293971 AATTTAGATA
1 AATTTAAATA
293981 AATTTAAACTTA
1 AATTTAAA--TA
293993 AATTTATAATA
1 AATTTA-AATA
294004 AATTTAAAT-
1 AATTTAAATA
*
294013 --TTCAAATA
1 AATTTAAATA
294021 AATTTAAAT
1 AATTTAAAT
294030 TTTGTTGGGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
7 6 0.15
10 16 0.40
11 8 0.20
12 8 0.20
13 2 0.05
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (10 bp):
AATTTAAATA
Found at i:294312 original size:19 final size:19
Alignment explanation
Indices: 294270--294312 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
294260 TATTAGAATC
*
294270 AAAAAGTTTAATTAAAATA
1 AAAAAGTATAATTAAAATA
*
294289 GAAAAGTATAA-TAAAAGTA
1 AAAAAGTATAATTAAAA-TA
294308 AAAAA
1 AAAAA
294313 AAAATTGCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.23
Consensus pattern (19 bp):
AAAAAGTATAATTAAAATA
Found at i:297926 original size:17 final size:17
Alignment explanation
Indices: 297880--297926 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
297870 TGGGCCCAAC
*
297880 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTAT
* **
297897 AAAGTTATGTTTATTAT
1 AAATTTAAATTTATTAT
297914 AAATTTAAATTTA
1 AAATTTAAATTTA
297927 AAATTTATTT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
AAATTTAAATTTATTAT
Found at i:298012 original size:15 final size:15
Alignment explanation
Indices: 297994--298027 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
297984 TGGCCCAATT
297994 AAATT-CAGATGACCC
1 AAATTACAGA-GACCC
298009 AAATTACAGAGACCC
1 AAATTACAGAGACCC
298024 AAAT
1 AAAT
298028 AAGCCCAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.18
Consensus pattern (15 bp):
AAATTACAGAGACCC
Found at i:298056 original size:24 final size:24
Alignment explanation
Indices: 298019--298065 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
298009 AAATTACAGA
*
298019 GACCCAAATAAGCCCAAACCAAAT
1 GACCCAAATAAGCCCAAAACAAAT
*
298043 GACCCAAACT-AGCCTAAAACAAA
1 GACCCAAA-TAAGCCCAAAACAAA
298066 GTTAAACCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.51, C:0.32, G:0.09, T:0.09
Consensus pattern (24 bp):
GACCCAAATAAGCCCAAAACAAAT
Found at i:300472 original size:6 final size:6
Alignment explanation
Indices: 300456--300504 Score: 64
Period size: 6 Copynumber: 8.2 Consensus size: 6
300446 ATATTTATAA
* *
300456 TAAATTT TAAATT TAAATA TAAATC TAAATT TAAA-T TAAATT TAAATT
1 TAAA-TT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
300504 T
1 T
300505 TAAAACATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.13
6 29 0.76
7 4 0.11
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:300484 original size:18 final size:17
Alignment explanation
Indices: 300463--300504 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
300453 TAATAAATTT
300463 TAAATTTAAATATAAATC
1 TAAATTTAAAT-TAAATC
*
300481 TAAATTTAAATTAAATT
1 TAAATTTAAATTAAATC
300498 TAAATTT
1 TAAATTT
300505 TAAAACATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATTTAAATTAAATC
Found at i:300506 original size:18 final size:18
Alignment explanation
Indices: 300455--300539 Score: 77
Period size: 18 Copynumber: 4.6 Consensus size: 18
300445 AATATTTATA
300455 ATAAATTTTAAATTTAAAT
1 ATAAA-TTTAAATTTAAAT
*
300474 ATAAATCTAAATTTAAAT
1 ATAAATTTAAATTTAAAT
*
300492 -TAAATTTAAATTTTAAAAC
1 ATAAATTTAAA-TTT-AAAT
*
300511 ATCAATTT-AATCTTAAA-
1 ATAAATTTAAAT-TTAAAT
300528 ATAAATCTTAAA
1 ATAAAT-TTAAA
300540 ATGAGTTTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
17 14 0.25
18 21 0.38
19 14 0.25
20 6 0.11
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAAATTTAAATTTAAAT
Done.