Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1923
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: 99926
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Found at i:280 original size:118 final size:120
Alignment explanation
Indices: 60--321 Score: 465
Period size: 118 Copynumber: 2.2 Consensus size: 120
50 ATAGTAACTC
60 GCACAAATGCCTTCGGGACTTAACTAACCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAG
1 GCACAAA-GCCTTCGGGACTTAAC--ACCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAG
* *
125 CCCGGAATTAGTAACTCGTACAAATGCCTTCGGATCTTAGTCCGGATATGGTCATTTA
63 CCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCAGATATGGTCATTTA
183 GCACAAAGCCTTCGGGACTTAAC-CCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAG-CC
1 GCACAAAGCCTTCGGGACTTAACACCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCC
246 GGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCAGATATGGTCATTTA
66 GGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCAGATATGGTCATTTA
301 GCACAAAGCCTTCGGGACTTA
1 GCACAAAGCCTTCGGGACTTA
322 GCCTGGACAT
Statistics
Matches: 137, Mismatches: 2, Indels: 5
0.95 0.01 0.03
Matches are distributed among these distances:
118 76 0.55
119 38 0.28
122 16 0.12
123 7 0.05
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (120 bp):
GCACAAAGCCTTCGGGACTTAACACCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCC
GGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCAGATATGGTCATTTA
Found at i:322 original size:40 final size:39
Alignment explanation
Indices: 23--322 Score: 184
Period size: 40 Copynumber: 7.5 Consensus size: 39
13 GCTACTCATT
** * *
23 CAAATGCCTTCGGGACGAAG-CACGGTTATAGTAACTCGCA
1 CAAA-GCCTTCGGGACTTAGTC-CGGATATAGTAACTAGCA
* * *
63 CAAATGCCTTCGGGACTTAACTAACCGGATTTAGTAACTCGCA
1 CAAA-GCCTTCGGGACTT-AGT--CCGGATATAGTAACTAGCA
* * * *
106 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGTA
1 -CAAAGCCTTCGGGACTTAGTCCGGATA-TAGTAACTAGCA
* **
145 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCATTTAGCA
1 CAAA-GCCTTCGGGA-CTTAGTCCGGATATAGT-AACTAGCA
** * *
186 CAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAAGCCTTCGGGACTTAGTCCGGATATAGTAACTAGCA
* *
225 CCAATGCCTTCGGG-CTTAG-CCGGA-ATTAGTAACTCGCA
1 -CAAAGCCTTCGGGACTTAGTCCGGATA-TAGTAACTAGCA
* * **
263 CAAATGCCTTC-GGATCTTAGTCCAGATATGGTCATTTAGCA
1 CAAA-GCCTTCGGGA-CTTAGTCCGGATATAGT-AACTAGCA
304 CAAAGCCTTCGGGACTTAG
1 CAAAGCCTTCGGGACTTAG
323 CCTGGACATC
Statistics
Matches: 206, Mismatches: 33, Indels: 42
0.73 0.12 0.15
Matches are distributed among these distances:
37 5 0.02
38 28 0.14
39 36 0.17
40 78 0.38
41 27 0.13
42 3 0.01
43 25 0.12
44 4 0.02
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAAGCCTTCGGGACTTAGTCCGGATATAGTAACTAGCA
Found at i:6030 original size:46 final size:45
Alignment explanation
Indices: 5973--6147 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 45
5963 TGGTTGAGCA
5973 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATG
* * * * *
6019 TTCAAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAA-T--G
*
6064 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATG
* * *
6112 CCCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGG
6148 GGCGGGTTAC
Statistics
Matches: 106, Mismatches: 14, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 58 0.55
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAATG
Found at i:6129 original size:93 final size:93
Alignment explanation
Indices: 5970--6140 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
5960 GGATGGTTGA
* **
5970 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTTCAAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACGCCCAAACTCGTTGAGT
6035 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
6063 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACGCCCAAACTCGTTGAGT
*
6128 TGAGTTCGAGTTC
66 TGAGTCCGAGTTC
6141 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACGCCCAAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:13603 original size:46 final size:45
Alignment explanation
Indices: 13537--13713 Score: 168
Period size: 46 Copynumber: 3.9 Consensus size: 45
13527 TGGTTGAACA
*
13537 TCCGAACTCGTTGA--TGAGTCCGAGTTCACTTACGGATGCGAATG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATG
* * * *
13581 TTCGAACTCATTGAGTTGAGTCCGAGTTC-GTGA-GATG-TAACTAGG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTAGGATGCGAA-T--G
* *
13626 AATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATG
* *
13674 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTAGG-TGCG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTAGGATGCG
13714 GGTCACATGA
Statistics
Matches: 108, Mismatches: 14, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 16 0.15
45 5 0.05
46 44 0.41
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (45 bp):
TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTAGGATGCGAATG
Found at i:17233 original size:30 final size:30
Alignment explanation
Indices: 17199--17255 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
17189 ATGAATCGGA
*
17199 AGCTTTGGCACTAAGTGTGGGATTTAAAGT
1 AGCTTTGGCACTAAGTGTGCGATTTAAAGT
17229 AGCTTTGGCACTAAGTGTGCGATTTAA
1 AGCTTTGGCACTAAGTGTGCGATTTAA
17256 CTAGCTTCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (30 bp):
AGCTTTGGCACTAAGTGTGCGATTTAAAGT
Found at i:20683 original size:30 final size:30
Alignment explanation
Indices: 20647--20703 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
20637 ATGAATCGGA
**
20647 AGCTTTGGCACTAAGTGTGGGATTTAAAGT
1 AGCTTTGGCACTAAGTGTCCGATTTAAAGT
20677 AGCTTTGGCACTAAGTGTCCGATTTAA
1 AGCTTTGGCACTAAGTGTCCGATTTAA
20704 CTAGCTTCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (30 bp):
AGCTTTGGCACTAAGTGTCCGATTTAAAGT
Found at i:22175 original size:27 final size:27
Alignment explanation
Indices: 22111--22163 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
22101 GACCCTAGTT
* *
22111 TGTAAAATCACCGAAATACCCTTGTAA
1 TGTAAAATGACCGAAATACCCCTGTAA
*
22138 TGTAAAATGACCGTAATACCCCTGTA
1 TGTAAAATGACCGAAATACCCCTGTA
22164 TGGTAGAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (27 bp):
TGTAAAATGACCGAAATACCCCTGTAA
Found at i:22653 original size:27 final size:28
Alignment explanation
Indices: 22589--22653 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
22579 GCATTTGATA
*
22589 CTGATTCTG-TATTGGGCTTAGGCCCAC
1 CTGATTCTGTTATTGGGCTAAGGCCCAC
*
22616 TTGATTCTGTTATT-GGCTAAGGCCCAC
1 CTGATTCTGTTATTGGGCTAAGGCCCAC
*
22643 CTGATACTGTT
1 CTGATTCTGTT
22654 TCGTGATGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 29 0.88
28 4 0.12
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (28 bp):
CTGATTCTGTTATTGGGCTAAGGCCCAC
Found at i:31283 original size:40 final size:40
Alignment explanation
Indices: 31228--31499 Score: 454
Period size: 40 Copynumber: 6.8 Consensus size: 40
31218 ATTTGAATAC
*
31228 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
31268 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
31308 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGACATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG--ATAT
31350 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
* *
31390 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
* *
31430 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
* * *
31470 ACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
31500 TTGTGGTTAT
Statistics
Matches: 219, Mismatches: 11, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
40 179 0.82
42 40 0.18
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
Found at i:31445 original size:122 final size:122
Alignment explanation
Indices: 31220--31499 Score: 467
Period size: 122 Copynumber: 2.3 Consensus size: 122
31210 GCATGAGCAT
*
31220 TTGA-ATACATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCC
1 TTGACATATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCC
* * *
31284 GAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
66 GAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
*
31341 TTGACATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCC
1 TTGACATATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCC
31406 GAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
66 GAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
* * *
31463 TTG-C-TATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 TTGACATATATCCGGGCTAAGACCCGAAGGCATTTGTGC
31500 TTGTGGTTAT
Statistics
Matches: 150, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
120 30 0.20
121 5 0.03
122 115 0.77
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (122 bp):
TTGACATATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCC
GAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
Found at i:39736 original size:40 final size:40
Alignment explanation
Indices: 39681--39952 Score: 454
Period size: 40 Copynumber: 6.8 Consensus size: 40
39671 ATTTGAATAC
*
39681 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
39721 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
39761 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGACATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG--ATAT
39803 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
* *
39843 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
* *
39883 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
* * *
39923 ACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
39953 TTGTGGTTAT
Statistics
Matches: 219, Mismatches: 11, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
40 179 0.82
42 40 0.18
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
Found at i:39898 original size:122 final size:122
Alignment explanation
Indices: 39673--39952 Score: 467
Period size: 122 Copynumber: 2.3 Consensus size: 122
39663 GCATGAGCAT
*
39673 TTGA-ATACATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCC
1 TTGACATATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCC
* * *
39737 GAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG
66 GAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
*
39794 TTGACATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCC
1 TTGACATATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCC
39859 GAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
66 GAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
* * *
39916 TTG-C-TATACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 TTGACATATATCCGGGCTAAGACCCGAAGGCATTTGTGC
39953 TTGTGGTTAT
Statistics
Matches: 150, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
120 30 0.20
121 5 0.03
122 115 0.77
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (122 bp):
TTGACATATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCC
GAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
Found at i:50792 original size:40 final size:40
Alignment explanation
Indices: 50730--50840 Score: 111
Period size: 40 Copynumber: 2.8 Consensus size: 40
50720 CATTTAAACT
** *
50730 GAAGCTATCTCCGTATCGCACACTTAGTGCCTCA-TATAGCC
1 GAAGCTATCT-CAAATCGCACACTAAGTGCCT-ATTATAGCC
* *
50771 GAAGCTAT-TCCAATTCGCACACTAAATG-CTATTTATAGCC
1 GAAGCTATCT-CAAATCGCACACTAAGTGCCTA-TTATAGCC
*
50811 GAAGCTATCTCAAAACGCACACTAAGTGCC
1 GAAGCTATCTCAAATCGCACACTAAGTGCC
50841 AAACACAGTA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
38 1 0.02
39 2 0.03
40 45 0.78
41 10 0.17
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (40 bp):
GAAGCTATCTCAAATCGCACACTAAGTGCCTATTATAGCC
Found at i:51078 original size:218 final size:219
Alignment explanation
Indices: 50700--51118 Score: 653
Period size: 218 Copynumber: 1.9 Consensus size: 219
50690 CTCCAAGAAC
* * **
50700 TCACACACTTAGTGTCATTACATTTAAACTGAAGCTATCTCCGTATCGCACACTTAGTGCCTCAT
1 TCACACACTTAGTGCCATCACATTTAAACCAAAGCTATCTCCGTATCGCACACTTAGTGCCTCAT
*
50765 ATAGCCGAAGCTATTCCAATTCGCACACTAAATGCTATTTATAGCCGAAGCTATCTCAAAACGCA
66 ATAGCCGAAGCTATTCCAATTCACACACTAAATGCTATTTATAGCCGAAGCTATCTCAAAACGCA
* * * * *
50830 CACTAAGTGCCAAACACAGTAGACTTGTCGTTGTACACAGTCGTAATTGCAAATA-ACAATTTAT
131 CACTAAGTGACAAACACAGTAGACTTGTCGTCGTACACAGTCATAATCGCAAATATACAATTGAT
50894 GCATTAGCCGAAGCTATAACAATT
196 GCATTAGCCGAAGCTATAACAATT
* * *
50918 TCACACACTTCGTGCCATCACATTTAAACCAAAGCTATCTCGGTATTGCACACTTAGTGCCTCAT
1 TCACACACTTAGTGCCATCACATTTAAACCAAAGCTATCTCCGTATCGCACACTTAGTGCCTCAT
* * *
50983 ATAGCCGAAGCTATTCCAATTCACACACTAAGTGC-ATTTTATAGCTGAAGCTATCTCAAAATGC
66 ATAGCCGAAGCTATTCCAATTCACACACTAAATGCTA-TTTATAGCCGAAGCTATCTCAAAACGC
* *
51047 ACACTAAGTGACAAACATAGTAGACTTGTCGTCGTACACAGTCATAGTCGCAAATATACAATTGA
130 ACACTAAGTGACAAACACAGTAGACTTGTCGTCGTACACAGTCATAATCGCAAATATACAATTGA
51112 TGCATTA
195 TGCATTA
51119 TCAAAGCATT
Statistics
Matches: 181, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
217 1 0.01
218 166 0.92
219 14 0.08
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.28
Consensus pattern (219 bp):
TCACACACTTAGTGCCATCACATTTAAACCAAAGCTATCTCCGTATCGCACACTTAGTGCCTCAT
ATAGCCGAAGCTATTCCAATTCACACACTAAATGCTATTTATAGCCGAAGCTATCTCAAAACGCA
CACTAAGTGACAAACACAGTAGACTTGTCGTCGTACACAGTCATAATCGCAAATATACAATTGAT
GCATTAGCCGAAGCTATAACAATT
Found at i:54339 original size:40 final size:40
Alignment explanation
Indices: 54255--54439 Score: 227
Period size: 40 Copynumber: 4.7 Consensus size: 40
54245 TCGAATGATG
* *
54255 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
54294 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
54335 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
54374 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
54413 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
54440 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
39 36 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:54391 original size:79 final size:81
Alignment explanation
Indices: 54255--54437 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 81
54245 TCGAATGATG
* *
54255 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
54319 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * **
54334 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCA
54396 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
54414 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
54438 TGAACGAGTA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 1 0.01
79 60 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:54461 original size:79 final size:78
Alignment explanation
Indices: 54256--54472 Score: 237
Period size: 79 Copynumber: 2.7 Consensus size: 78
54246 CGAATGATGT
* *
54256 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTAG-CTATATCCGG-TTAAG-TCCGAAGGCATT
*
54319 TGTGCGAGTTACTAATT
62 TGTGCGAGTTACTAATA
* *
54336 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTA-CTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTATATCC-GGTTAAGT-CCGAAGGCATTT
54399 GTGCGAGTTACT-ATAA
63 GTGCGAGTTACTAAT-A
* ** *
54415 CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTT-AAGTCCGAAGG
54473 TACGTGATTC
Statistics
Matches: 117, Mismatches: 11, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
78 3 0.03
79 68 0.58
80 46 0.39
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (78 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGTCCGAAGGCATTTGTG
CGAGTTACTAATA
Found at i:62460 original size:79 final size:81
Alignment explanation
Indices: 62327--62506 Score: 235
Period size: 79 Copynumber: 2.3 Consensus size: 81
62317 AATGATGTCT
* *
62327 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTTGT
1 GGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTTGT
*
62391 GCGAGTTACTA-ATTCC
66 GCGAGTTACTATA-ACC
* * **
62407 GGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCATTTG
62469 TGCGAGTTACTATAACC
65 TGCGAGTTACTATAACC
*
62486 GGGCTATGTCCCGAAGGCATT
1 GGGCTAAGTCCCGAAGGCATT
62507 TGAACGAGTA
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
78 1 0.01
79 60 0.68
80 27 0.31
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
GGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTTGT
GCGAGTTACTATAACC
Found at i:62522 original size:40 final size:40
Alignment explanation
Indices: 62327--62508 Score: 221
Period size: 40 Copynumber: 4.6 Consensus size: 40
62317 AATGATGTCT
* * *
62327 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACC
* *
62367 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-ACC
*
62407 GGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CC
*
62446 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
*
62486 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
62509 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 80 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
Found at i:62530 original size:79 final size:78
Alignment explanation
Indices: 62358--62540 Score: 212
Period size: 79 Copynumber: 2.3 Consensus size: 78
62348 GTGCTAAGTG
* *
62358 ACTATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGG
1 ACTATATCCGG-TTAAGATCCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGG
**
62423 CATTGGTGCGAGTT
65 CATTGGAACGAGTT
* *
62437 ACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGA
1 ACTATATCC-GGTTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGA
*
62500 AGGCATTTGAACGAG-T
62 AGGCATTGGAACGAGTT
*
62516 AGCTATATCCGGTTAA-ATTCGAAGG
1 A-CTATATCCGGTTAAGATCCGAAGG
62541 TACGTGATTC
Statistics
Matches: 89, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
78 9 0.10
79 54 0.61
80 26 0.29
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (78 bp):
ACTATATCCGGTTAAGATCCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGC
ATTGGAACGAGTT
Found at i:74114 original size:46 final size:45
Alignment explanation
Indices: 73964--74129 Score: 169
Period size: 46 Copynumber: 3.6 Consensus size: 45
73954 AGCTCATATT
* *
73964 TCATGTTGATGCCATGTCCCAGACATGGTCTTACAGTGACTATCATC
1 TCATGTCGATGCCATGTCCCAGACAT-GTCTTACACTGACT-TCATC
* *
74011 TCATAGTCGATG-CATGTCCCAGACATGTCTTACACTGGCTTACGTC
1 TCAT-GTCGATGCCATGTCCCAGACATGTCTTACACTGACTT-CATC
* *
74057 TCAAGGCCGATG-CATGTCCCAGACATGTCTTACACTAGAAC-TCATC
1 TC-ATGTCGATGCCATGTCCCAGACATGTCTTACACT-G-ACTTCATC
*
74103 TCGATGTCGATGCCAT-TCCCAAACATG
1 TC-ATGTCGATGCCATGTCCCAGACATG
74130 GTCATACATT
Statistics
Matches: 101, Mismatches: 12, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
45 1 0.01
46 69 0.68
47 24 0.24
48 7 0.07
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (45 bp):
TCATGTCGATGCCATGTCCCAGACATGTCTTACACTGACTTCATC
Found at i:81643 original size:47 final size:46
Alignment explanation
Indices: 81592--81756 Score: 140
Period size: 47 Copynumber: 3.5 Consensus size: 46
81582 ATGTCGATGC
*
81592 CATGTCCCAGACATGGTCTTACACTGACTATCATCTCGTAGCCTATG
1 CATGTCCCAGACAT-GTCTTACACTGACTATCATATCGTAGCCTATG
* * * * * *
81639 CATGTCCCAGGCATGTCTTATACTAAC-ACTCGTTTCG-ATGCCGATG
1 CATGTCCCAGACATGTCTTACACTGACTA-TCATATCGTA-GCCTATG
* * *
81685 CCGTGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTAG-CTGATG
1 -CATGTCCCAGACAT-GTCTTACACTGACTATCAT-ATCGTAGCCT-ATG
*
81733 CATGTCCCGGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
81757 AGCCCATAAT
Statistics
Matches: 93, Mismatches: 17, Indels: 17
0.73 0.13 0.13
Matches are distributed among these distances:
45 2 0.02
46 33 0.35
47 38 0.41
48 18 0.19
49 2 0.02
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGACTATCATATCGTAGCCTATG
Found at i:81706 original size:94 final size:93
Alignment explanation
Indices: 81578--81757 Score: 249
Period size: 94 Copynumber: 1.9 Consensus size: 93
81568 CTAGCTCATA
* *
81578 TTTCATGTCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCAT-CTCGTAGCCT-ATGCA
1 TTTCATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATAAT-GTAG-CTGATGCA
*
81641 TGTCCCAGG-CATGTCTTATACTAACACTCG
64 TGTCCC-GGACATGTCTTACACTAACACTCG
* * *
81671 TTTCGATGCCGATGCCGTGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTAGCTGATGCAT
1 TTTC-ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATAATGTAGCTGATGCAT
81736 GTCCCGGACATGTCTTACACTA
65 GTCCCGGACATGTCTTACACTA
81758 GCCCATAATA
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
93 8 0.10
94 68 0.88
95 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (93 bp):
TTTCATGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATAATGTAGCTGATGCATG
TCCCGGACATGTCTTACACTAACACTCG
Found at i:86609 original size:29 final size:29
Alignment explanation
Indices: 86567--86640 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
86557 TAATCAACCG
*
86567 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
86596 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
86625 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
86641 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:93732 original size:42 final size:42
Alignment explanation
Indices: 93578--93720 Score: 196
Period size: 42 Copynumber: 3.4 Consensus size: 42
93568 CTCAATTTGA
* *
93578 GATTTACGTGTAAGACCATGTCTGGGACATCAGCATCATATCT
1 GATTT-CGTGTAAGACCATGTCTGGGACATCGGCATCGTATCT
* * * *
93621 GATTTCATGTAAGACCATGTCTGCGACATTGGCATCGTATCC
1 GATTTCGTGTAAGACCATGTCTGGGACATCGGCATCGTATCT
*
93663 GATGTCGTGTAAGACCATGTCTGGGACATCGGCATCGTATCT
1 GATTTCGTGTAAGACCATGTCTGGGACATCGGCATCGTATCT
* *
93705 TATTTCGTGGAAGACC
1 GATTTCGTGTAAGACC
93721 CCGTTTGGGA
Statistics
Matches: 86, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 81 0.94
43 5 0.06
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (42 bp):
GATTTCGTGTAAGACCATGTCTGGGACATCGGCATCGTATCT
Found at i:93739 original size:42 final size:42
Alignment explanation
Indices: 93584--93741 Score: 111
Period size: 42 Copynumber: 3.8 Consensus size: 42
93574 TTGAGATTTA
* * * * * *
93584 CGTGTAAGACCATGTCTGGGACATCA-GCATCATATCTGATTT
1 CGTGGAAGACCACGTCTGGGACA-GAGGCATCGTATCCGATGT
* * * * **
93626 CATGTAAGACCATGTCTGCGACATTGGCATCGTATCCGATGT
1 CGTGGAAGACCACGTCTGGGACAGAGGCATCGTATCCGATGT
* * ** ** *
93668 CGTGTAAGACCATGTCTGGGACATCGGCATCGTATCTTATTT
1 CGTGGAAGACCACGTCTGGGACAGAGGCATCGTATCCGATGT
* *
93710 CGTGGAAGACCCCGTTTGGGACAGAGGCATCG
1 CGTGGAAGACCACGTCTGGGACAGAGGCATCG
93742 ATACTAAATT
Statistics
Matches: 96, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 96 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (42 bp):
CGTGGAAGACCACGTCTGGGACAGAGGCATCGTATCCGATGT
Found at i:93739 original size:84 final size:84
Alignment explanation
Indices: 93584--93741 Score: 217
Period size: 84 Copynumber: 1.9 Consensus size: 84
93574 TTGAGATTTA
* *
93584 CGTGTAAGACCATGTCTGGGACATCAGCATCATATCTGATTTCATGTAAGACCATGTCTGCGACA
1 CGTGTAAGACCATGTCTGGGACATCAGCATCATATCTGATTTCATGGAAGACCACGTCTGCGACA
**
93649 TTGGCATCGTATCCGATGT
66 GAGGCATCGTATCCGATGT
* * * * * * *
93668 CGTGTAAGACCATGTCTGGGACATCGGCATCGTATCTTATTTCGTGGAAGACCCCGTTTGGGACA
1 CGTGTAAGACCATGTCTGGGACATCAGCATCATATCTGATTTCATGGAAGACCACGTCTGCGACA
93733 GAGGCATCG
66 GAGGCATCG
93742 ATACTAAATT
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (84 bp):
CGTGTAAGACCATGTCTGGGACATCAGCATCATATCTGATTTCATGGAAGACCACGTCTGCGACA
GAGGCATCGTATCCGATGT
Found at i:97926 original size:39 final size:40
Alignment explanation
Indices: 97823--97999 Score: 227
Period size: 40 Copynumber: 4.5 Consensus size: 40
97813 AAGCCAAGTA
* * * * *
97823 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATA
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
97862 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
97902 CCTTC-GGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
97941 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
97981 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
98000 TTATCATCCA
Statistics
Matches: 124, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
39 51 0.41
40 73 0.59
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:97956 original size:79 final size:80
Alignment explanation
Indices: 97823--97999 Score: 227
Period size: 79 Copynumber: 2.2 Consensus size: 80
97813 AAGCCAAGTA
* * * *
97823 CCTTCGGGATTTA-ACCGGATATAGCTACTCGCTCGAATACCTTCGGGACATAGCCCGGATA-TA
1 CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATACCTTCGGGACATAGCCCGGA-ACTA
*
97886 GTAACTCGCACAAATG
65 GTAACTAGCACAAATG
* *
97902 CCTTC-GGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAACTA
1 CCTTCGGGACTTAGCCCGGATATAGCT-ACTCGCACAAATACCTTCGGGACATAGCCCGGAACTA
* *
97965 GTCACTAGCGCAAATG
65 GTAACTAGCACAAATG
97981 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
98000 TTATCATCCA
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
78 8 0.09
79 64 0.75
80 13 0.15
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATACCTTCGGGACATAGCCCGGAACTAG
TAACTAGCACAAATG
Done.