Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010388.1 Kokia drynarioides strain JFW-HI SEQ_125266, 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: 151991
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 102 characters in sequence are not A, C, G, or T
Found at i:316 original size:3 final size:3
Alignment explanation
Indices: 308--352 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
298 ACCTTTCGAT
* *
308 TTA TTA TTA TTA TTA TTT TTA TCTA ATA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT
353 CATTTAATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 35 0.95
4 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6250 original size:151 final size:151
Alignment explanation
Indices: 5976--6282 Score: 569
Period size: 151 Copynumber: 2.0 Consensus size: 151
5966 TTTACCAACT
5976 AAATTCAAATTGGATGGACAAGAATTACAAATGATCTTCTCCTACACTTGGTCCAGCTGACCACA
1 AAATTCAAATTGGATGGACAAGAATTACAAATGATCTTCTCCTACACTTGGTCCAGCTGACCACA
* *
6041 TTAGCAAAGAGGCACACGTTTTAATTATGTTATACAACTTCATTTGCGTAATGTGTGCAAACACA
66 TTAGCAAAGAGGCACACGTTTTAATTATGTTAGAAAACTTCATTTGCGTAATGTGTGCAAACACA
6106 TGGTTATCATAAAAGTTAACC
131 TGGTTATCATAAAAGTTAACC
**
6127 AAATTCAAATTGGATGGACAAGAATTACAAATGATCTTCTCCTACGTTTGGTCCAGCTGACCACA
1 AAATTCAAATTGGATGGACAAGAATTACAAATGATCTTCTCCTACACTTGGTCCAGCTGACCACA
6192 TTAGCAAAGAGGCACACGTTTTAATTATGTTAGAAAACTTCATTTGCGTAATGTGTGCAAACACA
66 TTAGCAAAGAGGCACACGTTTTAATTATGTTAGAAAACTTCATTTGCGTAATGTGTGCAAACACA
*
6257 TGGTTATGATAAAAGTTAACC
131 TGGTTATCATAAAAGTTAACC
6278 AAATT
1 AAATT
6283 AGGGCATACA
Statistics
Matches: 151, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
151 151 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (151 bp):
AAATTCAAATTGGATGGACAAGAATTACAAATGATCTTCTCCTACACTTGGTCCAGCTGACCACA
TTAGCAAAGAGGCACACGTTTTAATTATGTTAGAAAACTTCATTTGCGTAATGTGTGCAAACACA
TGGTTATCATAAAAGTTAACC
Found at i:12251 original size:123 final size:123
Alignment explanation
Indices: 12032--12280 Score: 455
Period size: 123 Copynumber: 2.0 Consensus size: 123
12022 TGCATATGTA
*
12032 AATGAATTCGTATTATATCTGTATTTGGAATTGTATTCATAGTATGTCTGACCTTCTGCTATGTG
1 AATGAATTCGTATTATATCTGTATTTGGAATTGTATTCATAGTATGCCTGACCTTCTGCTATGTG
*
12097 TCTGAAATGAACTTTTGTTGTCACTTATGAAATGTGAGTAATTGAGACCTAAAGTAAT
66 TCTGAAATGAACTTTTGTTGTCACTTATGAAATGTGAGTAACTGAGACCTAAAGTAAT
*
12155 AATGAA-TCTGTATTATTTCTGTATTTGGAATTGTATTCATAGTATGCCTGACCTTCTGCTATGT
1 AATGAATTC-GTATTATATCTGTATTTGGAATTGTATTCATAGTATGCCTGACCTTCTGCTATGT
12219 GTCTGAAATGAACTTTTGTTGTCACTTATGAAATGTGAGTAACTGAGACCTAAAGTAAT
65 GTCTGAAATGAACTTTTGTTGTCACTTATGAAATGTGAGTAACTGAGACCTAAAGTAAT
12278 AAT
1 AAT
12281 AAGTTCGACT
Statistics
Matches: 122, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
122 2 0.02
123 120 0.98
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.40
Consensus pattern (123 bp):
AATGAATTCGTATTATATCTGTATTTGGAATTGTATTCATAGTATGCCTGACCTTCTGCTATGTG
TCTGAAATGAACTTTTGTTGTCACTTATGAAATGTGAGTAACTGAGACCTAAAGTAAT
Found at i:12889 original size:14 final size:14
Alignment explanation
Indices: 12870--12899 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12860 GATGAAAATT
*
12870 TTCAATTTAATCCC
1 TTCAATTGAATCCC
12884 TTCAATTGAATCCC
1 TTCAATTGAATCCC
12898 TT
1 TT
12900 TAAATTCTAA
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:0.27, C:0.27, G:0.03, T:0.43
Consensus pattern (14 bp):
TTCAATTGAATCCC
Found at i:16922 original size:15 final size:15
Alignment explanation
Indices: 16902--16940 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
16892 GTTCCCCTTC
*
16902 TATAGGAGATGTTTT
1 TATAGGAGATGTCTT
16917 TATAGGAGATGTCTT
1 TATAGGAGATGTCTT
*
16932 TAGAGGAGA
1 TATAGGAGA
16941 GAGATAAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.36
Consensus pattern (15 bp):
TATAGGAGATGTCTT
Found at i:17058 original size:13 final size:13
Alignment explanation
Indices: 17040--17069 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17030 ATTGCTAAAA
17040 AATAATATCCCAT
1 AATAATATCCCAT
*
17053 AATAATATCCTAT
1 AATAATATCCCAT
17066 AATA
1 AATA
17070 TCTCATTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAATATCCCAT
Found at i:17114 original size:56 final size:56
Alignment explanation
Indices: 17022--17176 Score: 220
Period size: 56 Copynumber: 2.8 Consensus size: 56
17012 ACAAAAATAG
* * *
17022 GGAATCAAATTGCTAAAAAATAATATCCCATAATAATATCCTATAATATCTCATTA
1 GGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTATAACATCCCATTA
* * * *
17078 TGAATTAAATTGCTAAGAGATAATATCCCGTAATAATATCCTATAACATCCCATTA
1 GGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTATAACATCCCATTA
* * *
17134 GGAATCAAATTGCTAAAAGATGATATCTCATGATAATATCCTA
1 GGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTA
17177 ACACCCCCTC
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 85 1.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (56 bp):
GGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTATAACATCCCATTA
Found at i:19436 original size:6 final size:6
Alignment explanation
Indices: 19425--19507 Score: 59
Period size: 6 Copynumber: 14.5 Consensus size: 6
19415 GGCCCAACAG
** * *
19425 AATTTA AATTTA TTTTTA AA-TTA AATTT- ATTTTA AGTTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * *
19470 ACTTAA AATTTA AATTT- -ATTATA AATTTA AGTTTA AAT
1 AATTTA AATTTA AATTTA AATT-TA AATTTA AATTTA AAT
19508 CTATTTAAAT
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
4 3 0.05
5 13 0.22
6 39 0.67
7 3 0.05
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:19470 original size:34 final size:34
Alignment explanation
Indices: 19425--19504 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
19415 GGCCCAACAG
* * *
19425 AATTTAAATTTATTTTTAAA-TTAAATTTATTTTA
1 AATTTAAATTTA-CTTAAAATTTAAATTTATTATA
*
19459 AGTTTAAATTTACTTAAAATTTAAATTTATTATA
1 AATTTAAATTTACTTAAAATTTAAATTTATTATA
*
19493 AATTTAAGTTTA
1 AATTTAAATTTA
19505 AATCTATTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 5 0.13
34 34 0.87
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (34 bp):
AATTTAAATTTACTTAAAATTTAAATTTATTATA
Found at i:19497 original size:17 final size:18
Alignment explanation
Indices: 19425--19504 Score: 87
Period size: 17 Copynumber: 4.7 Consensus size: 18
19415 GGCCCAACAG
* *
19425 AATTTAAATTTATTTTTA
1 AATTTAAATTTACTTATA
*
19443 AA-TTAAATTTA-TTTTA
1 AATTTAAATTTACTTATA
*
19459 AGTTTAAATTTACTTA-A
1 AATTTAAATTTACTTATA
19476 AATTTAAATTTA-TTATA
1 AATTTAAATTTACTTATA
*
19493 AATTTAAGTTTA
1 AATTTAAATTTA
19505 AATCTATTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
16 9 0.16
17 42 0.76
18 4 0.07
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (18 bp):
AATTTAAATTTACTTATA
Found at i:33341 original size:210 final size:210
Alignment explanation
Indices: 32980--33864 Score: 956
Period size: 210 Copynumber: 4.3 Consensus size: 210
32970 ATCCACAAAT
* * *
32980 AGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATG-AAATAAGGCTCA
1 AGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAAACAACGCTCA
* * *
33044 AAGTGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA
66 AAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAACAGGTCAAAGCAATAAA
33109 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATATAGAG
131 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATATAGAG
33174 AAGCATATTGAAACA
196 AAGCATATTGAAACA
* * *
33189 AGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAAAAAAGGCTCA
1 AGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAAACAACGCTCA
* * * ** *
33254 AAGCGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATAATGAGAAGTAGGTCGAAGCAATAAA
66 AAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAACAGGTCAAAGCAATAAA
* * * * *
33319 ATGGTTAGCTCCCTGATGAGATACTGAGAAGTAGACCAAATTCGTCTTCCTAGT-AGGATACAAA
131 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGA-GATATAGA
*
33383 AAAGCGA-ATTGAAACA
195 GAAGC-ATATTGAAACA
* * * * * *
33399 AGCTATGCTGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATC----AAACCCACGCTCG
1 AGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAAACAACGCTCA
* * * * * * *
33460 ATGTGAGCAAAT-TTCCGTACCTCAGCTT-TTGATGAGATACTGGGAAACAGATCAAAGTAATAA
66 AAGTGAGCAAATCTT-CGAACCCCAGCTTCCTGATGAGATACTGAGAAACAGGTCAAAGCAATAA
* * ** * * * * *
33523 AATGGTTAGCTTCCTAATGAGGTACCAAGAATTGGACCAATTTCGCCTTCCTGATGAGATA-CGA
130 AATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATATAG-
**
33587 AGAAGCGGATTGAAACA
194 AGAAGCATATTGAAACA
* * * * * * *
33604 AGTGATGCAGTCATCTTCCTGATGAGATACCGAGAAGAATACCAAATC----AAACCCACGCTCG
1 AGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAAACAACGCTCA
* * *
33665 ATGTGAGCAGATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAACAGGTCAAAGCAATAAA
66 AAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAACAGGTCAAAGCAATAAA
** * * * * * * * *
33730 ATTATTAGCTTCCTGATGAGATACAGAGAAGTGAATCAAATTCGTCCTCCTGATAAAACATAGAG
131 ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATATAGAG
**
33795 AA--ATGGATCAAAACA
196 AAGCAT--ATTGAAACA
* * * * *
33810 AGTGATGCGGTCATCTTCATGATGAGATACTAAGAAGAAGGCCAAGTCAATGAAA
1 AGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAA
33865 CCAGACTCAA
Statistics
Matches: 570, Mismatches: 90, Indels: 31
0.82 0.13 0.04
Matches are distributed among these distances:
205 167 0.29
206 160 0.28
207 1 0.00
209 53 0.09
210 188 0.33
211 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.23
Consensus pattern (210 bp):
AGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAAACAACGCTCA
AAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAACAGGTCAAAGCAATAAA
ATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATATAGAG
AAGCATATTGAAACA
Found at i:34207 original size:17 final size:17
Alignment explanation
Indices: 34182--34228 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
34172 TGGCCCAACA
*
34182 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTAT
*
34199 AAGTTTAAATTTATTAT
1 AAATTTAAATTTATTAT
*
34216 AAATTTAAGTTTA
1 AAATTTAAATTTA
34229 AATCTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
AAATTTAAATTTATTAT
Found at i:34222 original size:23 final size:22
Alignment explanation
Indices: 34196--34241 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
34186 TTAAATTTAT
*
34196 TTTAAGTTTAAATTTATTATAAA
1 TTTAAGTTTAAATCTATT-TAAA
34219 TTTAAGTTTAAATCTATTTAAA
1 TTTAAGTTTAAATCTATTTAAA
34241 T
1 T
34242 CAAAGTCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (22 bp):
TTTAAGTTTAAATCTATTTAAA
Found at i:35067 original size:3 final size:3
Alignment explanation
Indices: 35061--35100 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
35051 AATAAGGCTT
35061 TAA TAA TAA TAA TAA TAA TAA TAA TAA -ATA TCAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A T-AA TAA TAA
35101 ATGGCATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 30 0.88
4 2 0.06
5 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:36210 original size:29 final size:28
Alignment explanation
Indices: 36157--36389 Score: 209
Period size: 29 Copynumber: 8.0 Consensus size: 28
36147 CCTTGAAGGT
36157 CCCTAAACTTCCCAAAAATTACATTTTTA
1 CCCTAAACTT-CCAAAAATTACATTTTTA
* * *
36186 CCCCTAAACTTTCTAAAATTCCATTTTTGA
1 -CCCTAAACTTCCAAAAATTACATTTTT-A
***
36216 CCCTATTTTTTCCAAAAATTACATTTTTA
1 CCCTA-AACTTCCAAAAATTACATTTTTA
* * * *
36245 CCCTCGAACTTCCCAAAATTATATTTTGA
1 CCCT-AAACTTCCAAAAATTACATTTTTA
*
36274 CCCCAAAACTTCCAAAAATTAACA-TTTTA
1 -CCCTAAACTTCCAAAAATT-ACATTTTTA
*
36303 CCCTCAAACTTCCAAAAATTCCATTTTTGA
1 CCCT-AAACTTCCAAAAATTACATTTTT-A
*
36333 CCTTGAAACTTCCAAAAATTACCA-TTTTA
1 CCCT-AAACTTCCAAAAATTA-CATTTTTA
* *
36362 CCCTTAAACTTCTAAAAATTTCATTTTT
1 CCC-TAAACTTCCAAAAATTACATTTTT
36390 GAGCCAAAAA
Statistics
Matches: 163, Mismatches: 29, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
28 7 0.04
29 98 0.60
30 56 0.34
31 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (28 bp):
CCCTAAACTTCCAAAAATTACATTTTTA
Found at i:36255 original size:59 final size:57
Alignment explanation
Indices: 36157--36391 Score: 244
Period size: 59 Copynumber: 4.0 Consensus size: 57
36147 CCTTGAAGGT
*
36157 CCCTAAACTTCCCAAAAATTACATTTTTACCC-CTAAACTTTCTAAAATTCCATTTTTGA
1 CCCTAAACTT-CCAAAAATTACA-TTTTACCCTC-AAACTTCCTAAAATTCCATTTTTGA
*** * *
36216 CCCTATTTTTTCCAAAAATTACATTTTTACCCTCGAACTTCCCAAAATT--ATATTTTGA
1 CCCTA-AACTTCCAAAAATTACA-TTTTACCCTCAAACTTCCTAAAATTCCAT-TTTTGA
* *
36274 CCCCAAAACTTCCAAAAATTAACATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGA
1 -CCCTAAACTTCCAAAAATT-ACATTTTACCCTCAAACTTCCTAAAATTCCATTTTTGA
* * *
36333 CCTTGAAACTTCCAAAAATTACCATTTTACCCTTAAACTT-CTAAAAATTTCATTTTTGA
1 CCCT-AAACTTCCAAAAATTA-CATTTTACCCTCAAACTTCCT-AAAATTCCATTTTTGA
36392 GCCAAAAAAT
Statistics
Matches: 149, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
57 2 0.01
58 44 0.30
59 98 0.66
60 5 0.03
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.37
Consensus pattern (57 bp):
CCCTAAACTTCCAAAAATTACATTTTACCCTCAAACTTCCTAAAATTCCATTTTTGA
Found at i:36372 original size:117 final size:118
Alignment explanation
Indices: 36161--36373 Score: 283
Period size: 117 Copynumber: 1.8 Consensus size: 118
36151 GAAGGTCCCT
* * ***
36161 AAACTTCCCAAAAATTACATTTTTACCCCTAAACTTTCTAAAATTCCATTTTTGACCCTATTTTT
1 AAACTTCCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCTATAACT
*
36226 TCCAAAAATTACATTTTTACCCTCGAACTTCCCAAAATTATATTTTGACCCCA
66 TCCAAAAATTACATTTTTACCCTCAAACTTCCCAAAATTATATTTTGACCCCA
*
36279 AAACTT-CCAAAAATTAACA-TTTTA-CCCTCAAACTTCCAAAAATTCCATTTTTGACCTTGA-A
1 AAACTTCCCAAAAATT-ACATTTTTACCCCT-AAACTTCCAAAAATTCCATTTTTGACCCT-ATA
*
36340 ACTTCCAAAAATTACCA-TTTTACCCTTAAACTTC
63 ACTTCCAAAAATTA-CATTTTTACCCTCAAACTTC
36374 TAAAAATTTC
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
116 4 0.05
117 67 0.81
118 12 0.14
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.36
Consensus pattern (118 bp):
AAACTTCCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCTATAACT
TCCAAAAATTACATTTTTACCCTCAAACTTCCCAAAATTATATTTTGACCCCA
Found at i:36488 original size:109 final size:108
Alignment explanation
Indices: 36287--36500 Score: 236
Period size: 109 Copynumber: 2.0 Consensus size: 108
36277 CAAAACTTCC
** *
36287 AAAAATTAACATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTTGAAACTTCCAAAAAT
1 AAAAATTAACATTTTACCCTCAAACTTCCAAAAATTCCATTTTAAACCCT-AAACTTCCAAAAAT
* ** * * *
36352 TACCATTTTACCCTTAAACTTCTAAAAATTTCATTTTTGAGCCA
65 CACCATTTTACCCGGAAACTTCCAAAAACTCCATTTTTGAGCCA
* *
36396 AAAAATTACCATTTTACCAC-CAAACTTCCAAAAATTCCATTTTAAACCCT-AATTTCTCAAAAA
1 AAAAATTAACATTTTACC-CTCAAACTTCCAAAAATTCCATTTTAAACCCTAAACTTC-C-AAAA
* * *
36459 ATCACCATTTTATCTCGGGATC-TCCAAAAACTCCATTTTTGA
63 ATCACCATTTTA-CCCGGAAACTTCCAAAAACTCCATTTTTGA
36501 CCCCGATTTT
Statistics
Matches: 87, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
107 5 0.06
108 1 0.01
109 76 0.87
110 5 0.06
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (108 bp):
AAAAATTAACATTTTACCCTCAAACTTCCAAAAATTCCATTTTAAACCCTAAACTTCCAAAAATC
ACCATTTTACCCGGAAACTTCCAAAAACTCCATTTTTGAGCCA
Found at i:39765 original size:13 final size:13
Alignment explanation
Indices: 39747--39782 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
39737 ATTACTAAAA
39747 AATAATATCTCAT
1 AATAATATCTCAT
39760 AATAATAT-TC-T
1 AATAATATCTCAT
39771 -ATAATATCTCAT
1 AATAATATCTCAT
39783 TATGGTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.33
11 3 0.14
12 3 0.14
13 8 0.38
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (13 bp):
AATAATATCTCAT
Found at i:43640 original size:13 final size:13
Alignment explanation
Indices: 43622--43647 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43612 TGACAATTGG
43622 CTTCTTTTTCTTT
1 CTTCTTTTTCTTT
43635 CTTCTTTTTCTTT
1 CTTCTTTTTCTTT
43648 ATTTGGGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
CTTCTTTTTCTTT
Found at i:45826 original size:28 final size:28
Alignment explanation
Indices: 45746--45843 Score: 74
Period size: 28 Copynumber: 3.5 Consensus size: 28
45736 TGAGTAATTT
* * * *
45746 TGATTCTGACTTGGAAAGAGCGATA-TC
1 TGATTCTGGCTCGGATAGAACGATATTC
* * *
45773 TTGATTCTAGCTCAGATA-AAGTGATATTC
1 -TGATTCTGGCTCGGATAGAA-CGATATTC
*
45802 TGATTCTGGCTCGGATAGAACGATATTT
1 TGATTCTGGCTCGGATAGAACGATATTC
*
45830 TGTATTTTGGCTCG
1 TG-ATTCTGGCTCG
45844 TATGAGAAAT
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
27 1 0.02
28 39 0.72
29 14 0.26
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (28 bp):
TGATTCTGGCTCGGATAGAACGATATTC
Found at i:50701 original size:4 final size:4
Alignment explanation
Indices: 50692--50735 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
50682 AATACTTGCC
50692 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
50736 TATATATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:50740 original size:2 final size:2
Alignment explanation
Indices: 50733--50757 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50723 ACATACATAC
50733 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 A
50758 AGAGTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51771 original size:17 final size:17
Alignment explanation
Indices: 51749--51783 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
51739 GCTTGCTGTC
51749 ACCCGTTAATGAAACAA
1 ACCCGTTAATGAAACAA
*
51766 ACCCGTTGATGAAACAA
1 ACCCGTTAATGAAACAA
51783 A
1 A
51784 GGCATGCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.14, T:0.17
Consensus pattern (17 bp):
ACCCGTTAATGAAACAA
Found at i:54937 original size:16 final size:18
Alignment explanation
Indices: 54916--54949 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
54906 ATTATTGTAG
54916 CTTCCAC-T-CCTTCAAC
1 CTTCCACTTGCCTTCAAC
54932 CTTCCACTTGCCTTCAAC
1 CTTCCACTTGCCTTCAAC
54950 AACTACAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.18, C:0.47, G:0.03, T:0.32
Consensus pattern (18 bp):
CTTCCACTTGCCTTCAAC
Found at i:75992 original size:31 final size:31
Alignment explanation
Indices: 75896--76091 Score: 133
Period size: 30 Copynumber: 6.5 Consensus size: 31
75886 GTTCGGGGGA
**
75896 AAAATGGTAA-TTTTGGATGAGTTTG-GGGTC
1 AAAAT-GTAATTTTTGGAAAAGTTTGAGGGTC
* * *
75926 AAAATATAA-ATTTGGGAAAGTTT-AGGAGTC
1 AAAATGTAATTTTTGGAAAAGTTTGAGG-GTC
*
75956 AAAAATGCAATTTTTGGAAAAGTTTGAGGGTC
1 -AAAATGTAATTTTTGGAAAAGTTTGAGGGTC
* * *
75988 AAAATATAATTTTT--ATGAAGTTCGAGGGTC
1 AAAATGTAATTTTTGGA-AAAGTTTGAGGGTC
* * *
76018 AAAATGTAATTTTT--ACGAAGTTTAAGGGGTT
1 AAAATGTAATTTTTGGA-AAAGTTTGA-GGGTC
**
76049 AAAATGTAA-TTTTGG-AAAGTTCAAGGGTC
1 AAAATGTAATTTTTGGAAAAGTTTGAGGGTC
*
76078 AAAATGTGATTTTT
1 AAAATGTAATTTTT
76092 ACGAAGTTCA
Statistics
Matches: 134, Mismatches: 22, Indels: 20
0.76 0.12 0.11
Matches are distributed among these distances:
29 28 0.21
30 56 0.42
31 32 0.24
32 15 0.11
33 3 0.02
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (31 bp):
AAAATGTAATTTTTGGAAAAGTTTGAGGGTC
Found at i:76022 original size:61 final size:61
Alignment explanation
Indices: 75906--76031 Score: 141
Period size: 61 Copynumber: 2.1 Consensus size: 61
75896 AAAATGGTAA
** * *
75906 TTTTGGATGAGTTTGGGGTCAAAATATAAATTTGGGAAAGTTTAGGAGTCAAAAATGCAAT
1 TTTTGGAAAAGTTTGGGGTCAAAATATAAATTTAGGAAAGTTGAGGAGTCAAAAATGCAAT
* * *
75967 TTTTGGAAAAGTTTGAGGGTCAAAATATAATTTTTATG-AAGTTCGAGG-GTC-AAAATGTAAT
1 TTTTGGAAAAGTTTG-GGGTCAAAATATAA-ATTTAGGAAAGTT-GAGGAGTCAAAAATGCAAT
76028 TTTT
1 TTTT
76032 ACGAAGTTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
61 26 0.47
62 22 0.40
63 7 0.13
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (61 bp):
TTTTGGAAAAGTTTGGGGTCAAAATATAAATTTAGGAAAGTTGAGGAGTCAAAAATGCAAT
Found at i:76099 original size:30 final size:30
Alignment explanation
Indices: 75982--76102 Score: 147
Period size: 30 Copynumber: 4.0 Consensus size: 30
75972 GAAAAGTTTG
* * *
75982 AGGGTCAAAATATAATTTTTATGAAGTTCG
1 AGGGTCAAAATGTAATTTTTACGAAGTTCA
*
76012 AGGGTCAAAATGTAATTTTTACGAAGTTTA
1 AGGGTCAAAATGTAATTTTTACGAAGTTCA
* *
76042 AGGGGTTAAAATGTAA-TTTT-GGAAAGTTCA
1 A-GGGTCAAAATGTAATTTTTACG-AAGTTCA
*
76072 AGGGTCAAAATGTGATTTTTACGAAGTTCA
1 AGGGTCAAAATGTAATTTTTACGAAGTTCA
76102 A
1 A
76103 AGGCCTCCAA
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
29 13 0.17
30 50 0.65
31 14 0.18
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.35
Consensus pattern (30 bp):
AGGGTCAAAATGTAATTTTTACGAAGTTCA
Found at i:77289 original size:14 final size:14
Alignment explanation
Indices: 77270--77300 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
77260 CCTTGACTGA
77270 TATGGAGTGTTTGG
1 TATGGAGTGTTTGG
77284 TATGGAGTGTTTGG
1 TATGGAGTGTTTGG
77298 TAT
1 TAT
77301 TCTGCCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (14 bp):
TATGGAGTGTTTGG
Found at i:78141 original size:29 final size:30
Alignment explanation
Indices: 78075--78145 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
78065 AATCTTAAAA
* *
78075 TTATACAAGAATTTTAATTTTATGTGTAAT
1 TTATACATGAATTTTAATTTTAGGTGTAAT
*
78105 TTAATACATGAATTTTAA-TTT-GGTGTGAT
1 TT-ATACATGAATTTTAATTTTAGGTGTAAT
78134 TATATACATGAA
1 T-TATACATGAA
78146 ACTTTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 16 0.44
30 6 0.17
31 14 0.39
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (30 bp):
TTATACATGAATTTTAATTTTAGGTGTAAT
Found at i:78606 original size:56 final size:56
Alignment explanation
Indices: 78531--78645 Score: 212
Period size: 56 Copynumber: 2.1 Consensus size: 56
78521 ATTATATATT
* *
78531 AAACGAAAATTCATGTATAATTTTAAAATTTATACCATTATGTTTTAAATGAAATA
1 AAACCAAAATTCATATATAATTTTAAAATTTATACCATTATGTTTTAAATGAAATA
78587 AAACCAAAATTCATATATAATTTTAAAATTTATACCATTATGTTTTAAATGAAATA
1 AAACCAAAATTCATATATAATTTTAAAATTTATACCATTATGTTTTAAATGAAATA
78643 AAA
1 AAA
78646 GGCAATGGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (56 bp):
AAACCAAAATTCATATATAATTTTAAAATTTATACCATTATGTTTTAAATGAAATA
Found at i:83270 original size:8 final size:8
Alignment explanation
Indices: 83259--83291 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
83249 AATTTTTTCA
83259 TTTAAATT
1 TTTAAATT
83267 TTTAAATT
1 TTTAAATT
83275 TTTAAAATT
1 TTT-AAATT
83284 TTTAAATT
1 TTTAAATT
83292 AATAAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTTAAATT
Found at i:83297 original size:17 final size:17
Alignment explanation
Indices: 83262--83298 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
83252 TTTTTCATTT
**
83262 AAATTTTTAAATTTTTA
1 AAATTTTTAAATTAATA
83279 AAATTTTTAAATTAATA
1 AAATTTTTAAATTAATA
83296 AAA
1 AAA
83299 GTAAAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTTTTAAATTAATA
Found at i:83401 original size:33 final size:33
Alignment explanation
Indices: 83362--83425 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
83352 AAAAATTATA
83362 AAGATATAAGATATTCAAATGGTGCAATTGTTT
1 AAGATATAAGATATTCAAATGGTGCAATTGTTT
83395 AAGATATAAGATATTCAAATGGTGCAATTGT
1 AAGATATAAGATATTCAAATGGTGCAATTGT
83426 ATTTTTACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (33 bp):
AAGATATAAGATATTCAAATGGTGCAATTGTTT
Found at i:91623 original size:7 final size:7
Alignment explanation
Indices: 91607--91693 Score: 51
Period size: 7 Copynumber: 12.7 Consensus size: 7
91597 TTTTTTATTC
*
91607 TAAACTT
1 TAAACCT
91614 TAAACCT
1 TAAACCT
91621 TAAATCC-
1 TAAA-CCT
91628 TAAACCT
1 TAAACCT
91635 TGAAACCT
1 T-AAACCT
*
91643 T-AACCC
1 TAAACCT
91649 TAAA-CT
1 TAAACCT
*
91655 CAAA-CT
1 TAAACCT
**
91661 CCGAA-CT
1 -TAAACCT
91668 TAAACCT
1 TAAACCT
91675 TAAA-CT
1 TAAACCT
91681 GTAAACCT
1 -TAAACCT
91689 TAAAC
1 TAAAC
91694 ATGTAAGGTT
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
6 17 0.26
7 37 0.57
8 11 0.17
ACGTcount: A:0.43, C:0.28, G:0.03, T:0.26
Consensus pattern (7 bp):
TAAACCT
Found at i:91632 original size:21 final size:20
Alignment explanation
Indices: 91606--91654 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
91596 ATTTTTTATT
* *
91606 CTAAACTTTAAACCTTAAATC
1 CTAAACTTGAAACCTT-AACC
91627 CTAAACCTTGAAACCTTAACC
1 CTAAA-CTTGAAACCTTAACC
91648 CTAAACT
1 CTAAACT
91655 CAAACTCCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 13 0.52
22 10 0.40
ACGTcount: A:0.41, C:0.29, G:0.02, T:0.29
Consensus pattern (20 bp):
CTAAACTTGAAACCTTAACC
Found at i:91687 original size:14 final size:14
Alignment explanation
Indices: 91664--91699 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
91654 TCAAACTCCG
91664 AACT-TAAACCTTA
1 AACTGTAAACCTTA
91677 AACTGTAAACCTTA
1 AACTGTAAACCTTA
91691 AACATGTAA
1 AAC-TGTAA
91700 GGTTTAGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.19
14 12 0.57
15 5 0.24
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (14 bp):
AACTGTAAACCTTA
Found at i:92324 original size:21 final size:21
Alignment explanation
Indices: 92296--92348 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
92286 ATATATACGG
92296 TAAC-AATCTAACTACTCTGC
1 TAACTAATCTAACTACTCTGC
*
92316 TAACTAATCTAACTGCTCTGC
1 TAACTAATCTAACTACTCTGC
*
92337 TAATTAATCTAA
1 TAACTAATCTAA
92349 TTGAACGAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.34
Consensus pattern (21 bp):
TAACTAATCTAACTACTCTGC
Found at i:92909 original size:25 final size:27
Alignment explanation
Indices: 92881--92932 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
92871 CGAACATTAT
92881 TTAATTT-TTTTAAA-AATAAATTCTC
1 TTAATTTATTTTAAATAATAAATTCTC
*
92906 TTAATTTAATTTTAAATAATATATTCT
1 TTAATTT-ATTTTAAATAATAAATTCT
92933 TATTCAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
27 7 0.30
28 9 0.39
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (27 bp):
TTAATTTATTTTAAATAATAAATTCTC
Found at i:93077 original size:13 final size:12
Alignment explanation
Indices: 93042--93094 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
93032 AGTGACACGT
*
93042 AATTTT-TTATT
1 AATTTTATTATA
93053 AATTTTATTATA
1 AATTTTATTATA
93065 AATTTTAATTATA
1 AATTTT-ATTATA
*
93078 TATTTT-TTATA
1 AATTTTATTATA
93089 TAATTT
1 -AATTT
93095 CTAGAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 11 0.31
12 14 0.39
13 11 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATTTTATTATA
Found at i:100308 original size:14 final size:14
Alignment explanation
Indices: 100286--100316 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
100276 ATTTAAATTA
*
100286 TAATTATTTTTAAT
1 TAATAATTTTTAAT
100300 TAATAATTTTTAAT
1 TAATAATTTTTAAT
100314 TAA
1 TAA
100317 AATATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TAATAATTTTTAAT
Found at i:101041 original size:14 final size:14
Alignment explanation
Indices: 101011--101049 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
101001 AAAATTATTT
*
101011 TATATTAA-AACAA
1 TATATTAATAAAAA
*
101024 TATATTTATAAAAA
1 TATATTAATAAAAA
101038 TATATTAATAAA
1 TATATTAATAAA
101050 TGATTATTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
TATATTAATAAAAA
Found at i:102979 original size:25 final size:23
Alignment explanation
Indices: 102951--102996 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
102941 GTTGGATCCA
102951 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATT-TAAAAA-ATAATTTG
*
102976 AATTAAATTTAAACAATAATT
1 AATTAAATTTAAAAAATAATT
102997 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (23 bp):
AATTAAATTTAAAAAATAATTTG
Found at i:104069 original size:235 final size:235
Alignment explanation
Indices: 103658--104128 Score: 888
Period size: 235 Copynumber: 2.0 Consensus size: 235
103648 ACAAGAGTTG
* *
103658 ACATCCTCACTAAAGATTCATTCAAAGCACTCAAAGTGTTTAAGGTTTATTAAATAAGCTCTCAA
1 ACATCCTCACTAAAGATTCACTCAAAGCACTCAAAGTGTTTAAGGTTCATTAAATAAGCTCTCAA
103723 TTGTCAAACACAAAATGTTATTACCATAAGCTTGCTTGAAAATCAAATCTCCACCACTGTAAAAT
66 TTGTCAAACACAAAATGTTATTACCATAAGCTTGCTTGAAAATCAAATCTCCACCACTGTAAAAT
103788 GACATGACACACCAATCAGGAGGTCTTTACAAGGTTGTAATGGGGCTAAGGTTATGGGTATGGAA
131 GACATGACACACCAATCAGGAGGTCTTTACAAGGTTGTAATGGGGCTAAGGTTATGGGTATGGAA
*
103853 AAGGCTAGAAAAATTGGTTAAAATCGAGATCGAGTTGATA
196 AAAGCTAGAAAAATTGGTTAAAATCGAGATCGAGTTGATA
*
103893 ACATCCTCATTAAAGATTCACTCAAAGCACTCAAAGTGTTTAAGGTTCATTAAATAAGCTCTCAA
1 ACATCCTCACTAAAGATTCACTCAAAGCACTCAAAGTGTTTAAGGTTCATTAAATAAGCTCTCAA
103958 TTGTCAAACACAAAATGTTATTACCATAAGCTTGCTTGAAAATCAAATCTCCACCACTGTAAAAT
66 TTGTCAAACACAAAATGTTATTACCATAAGCTTGCTTGAAAATCAAATCTCCACCACTGTAAAAT
104023 GACATGACACACCAATCAGGAGGTCTTTACAAGGTTGTAATGGGGCTAAGGTTATGGGTATGGAA
131 GACATGACACACCAATCAGGAGGTCTTTACAAGGTTGTAATGGGGCTAAGGTTATGGGTATGGAA
* *
104088 AAAGCTAGAAGAATTGGTTAAAATCGAGATTGAGTTGATA
196 AAAGCTAGAAAAATTGGTTAAAATCGAGATCGAGTTGATA
104128 A
1 A
104129 GTTACCAAAC
Statistics
Matches: 230, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
235 230 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.28
Consensus pattern (235 bp):
ACATCCTCACTAAAGATTCACTCAAAGCACTCAAAGTGTTTAAGGTTCATTAAATAAGCTCTCAA
TTGTCAAACACAAAATGTTATTACCATAAGCTTGCTTGAAAATCAAATCTCCACCACTGTAAAAT
GACATGACACACCAATCAGGAGGTCTTTACAAGGTTGTAATGGGGCTAAGGTTATGGGTATGGAA
AAAGCTAGAAAAATTGGTTAAAATCGAGATCGAGTTGATA
Found at i:104284 original size:22 final size:22
Alignment explanation
Indices: 104259--104317 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
104249 ATTTTTGTCT
104259 TTTTCTTCTATTTTTTTTTC-AA
1 TTTTCTTCT-TTTTTTTTTCGAA
*
104281 TTTTCTT-TTTTTTTTTTCGAC
1 TTTTCTTCTTTTTTTTTTCGAA
104302 TTTT-TTCTTTTTTTTT
1 TTTTCTTCTTTTTTTTT
104318 CTAAATAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 12 0.35
21 15 0.44
22 7 0.21
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTTCTTCTTTTTTTTTTCGAA
Found at i:104296 original size:19 final size:20
Alignment explanation
Indices: 104264--104318 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
104254 TGTCTTTTTC
*
104264 TTCTATTTTTTTTTC-AATT
1 TTCTTTTTTTTTTTCGAATT
*
104283 TTCTTTTTTTTTTTTCGACTT
1 TTC-TTTTTTTTTTTCGAATT
104304 TT-TTCTTTTTTTTTC
1 TTCTT-TTTTTTTTTC
104319 TAAATAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 5 0.16
20 21 0.68
21 5 0.16
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (20 bp):
TTCTTTTTTTTTTTCGAATT
Found at i:125778 original size:21 final size:21
Alignment explanation
Indices: 125754--125793 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
125744 TTGTTGAGTG
*
125754 GAAAGGTGGAGAA-TGGAAAGA
1 GAAA-GTGGAAAATTGGAAAGA
125775 GAAAGTGGAAAATTGGAAA
1 GAAAGTGGAAAATTGGAAA
125794 AAAAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.38, T:0.12
Consensus pattern (21 bp):
GAAAGTGGAAAATTGGAAAGA
Found at i:132402 original size:24 final size:24
Alignment explanation
Indices: 132372--132433 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
132362 GAATTCAGAT
132372 GAGGATGGCATTGACGGTTCTAAG
1 GAGGATGGCATTGACGGTTCTAAG
132396 GAGGATGGCATTGACGGTTCTAAG
1 GAGGATGGCATTGACGGTTCTAAG
*
132420 GAGGATGCCATTGA
1 GAGGATGGCATTGA
132434 TAGAACTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.26, C:0.13, G:0.37, T:0.24
Consensus pattern (24 bp):
GAGGATGGCATTGACGGTTCTAAG
Done.