Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2242
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: 78431
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:967 original size:3 final size:3
Alignment explanation
Indices: 949--989 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
939 ACCCTTTAAC
*
949 AAG AGG AAG CAAG AAG AAG -AG AAG AAG AAG -AG AAG AAG AAG
1 AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
990 TCATTGAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.61, C:0.02, G:0.37, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:975 original size:11 final size:11
Alignment explanation
Indices: 959--989 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
949 AAGAGGAAGC
959 AAGAAGAAGAG
1 AAGAAGAAGAG
970 AAGAAGAAGAG
1 AAGAAGAAGAG
981 AAGAAGAAG
1 AAGAAGAAG
990 TCATTGAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (11 bp):
AAGAAGAAGAG
Found at i:5101 original size:40 final size:40
Alignment explanation
Indices: 5043--5251 Score: 232
Period size: 39 Copynumber: 5.3 Consensus size: 40
5033 ATTTGAATGA
* *
5043 TATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
* * **
5083 TATCCGGGCCAAGACCCGAAGGCATTTGTGCGAGT--TGC
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
* * *
5121 TATACCCGGATAAGACCCGAAGGCAATTGTGCTAGTGATTT
1 TAT-CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
* *
5162 TATCCGGGCTAAGA-CCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTT
* *
5201 TATCCGGGCTAAGACCCGAGGGCATTTGTGCTTGTG-TTT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
5240 ATATCC-GGCTAA
1 -TATCCGGGCTAA
5252 ATTCCGAAGA
Statistics
Matches: 140, Mismatches: 22, Indels: 15
0.79 0.12 0.08
Matches are distributed among these distances:
38 4 0.03
39 68 0.49
40 64 0.46
41 4 0.03
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
Found at i:5260 original size:79 final size:79
Alignment explanation
Indices: 5042--5251 Score: 309
Period size: 79 Copynumber: 2.7 Consensus size: 79
5032 CATTTGAATG
* *
5042 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCCAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGA-CCGAAGGCA
*
5107 TTTGTGCGAGTTGCT
65 TTTGTGCGAGTTGAT
* *
5122 ATA-CCCGGATAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCGAAGGCAT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCGAAGGCAT
5186 TTGTGCGAGTTGAT
66 TTGTGCGAGTTGAT
* * *
5200 ATATCCGGGCTAAGACCCGAGGGCATTTGTGCTTGTG-TTTATATCC-GGCTAA
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTT-TATCCGGGCTAA
5252 ATTCCGAAGA
Statistics
Matches: 118, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
78 35 0.30
79 80 0.68
80 3 0.03
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCGAAGGCAT
TTGTGCGAGTTGAT
Found at i:13163 original size:40 final size:40
Alignment explanation
Indices: 13104--13315 Score: 268
Period size: 40 Copynumber: 5.3 Consensus size: 40
13094 CATTTGAATG
* *
13104 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
13144 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
13184 ATACCCGGGATAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
13224 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
13264 ATATCCGGGCTAAGACCCGAGGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
13304 ATATCC-GGCTAA
1 ATATCCGGGCTAA
13316 ATTCCGAAGA
Statistics
Matches: 147, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
39 10 0.07
40 132 0.90
41 5 0.03
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:13241 original size:80 final size:80
Alignment explanation
Indices: 13108--13315 Score: 328
Period size: 80 Copynumber: 2.6 Consensus size: 80
13098 TGAATGATAT
*
13108 CCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
*
13173 TGCGAGTTGCTATAC
66 TGCGAGTTGATATAC
*
13188 CCGGGATAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
*
13253 TGCGAGTTGATATAT
66 TGCGAGTTGATATAC
* * * * *
13268 CCGGGCTAAGACCCGAGGGCATTTGTGCTTGTGGTTATATCC-GGCTAA
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAA
13316 ATTCCGAAGA
Statistics
Matches: 118, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 6 0.05
80 112 0.95
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
TGCGAGTTGATATAC
Found at i:25351 original size:45 final size:45
Alignment explanation
Indices: 25200--25497 Score: 243
Period size: 44 Copynumber: 6.7 Consensus size: 45
25190 TCTATTGCAA
* * * * *
25200 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGTATTTTTA-T
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATCTG-CTATCTTCAGT
* * **
25245 CCTGCTCAACTGCAACTTCAGAGAGATAAGGAT-TG-TGGCTTC-GAT
1 -CTGCTCCACTGCAACTTCAGGGAGATAA-GATCTGCTATCTTCAG-T
*
25290 CTGCTCCACTGCAACTTCAGGGAGACAAGATCTGCTATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCTATCTTCAGT
* * * * **
25335 TTGCTCCATTACAACTTCAGGGAGATAAGA-CTTGTTAT-TTCAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATC-TGCTATCTTCAGT
** * * * * * **
25379 CCACTCTACTACAACTTCAGAGAGATAAGGTTTG-TGGCTTC-GAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCTATCTTCAG-T
* *
25423 CTGCTCCACTGCAACTTCAGGTAGACAAGATCTGCTATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCTATCTTCAGT
25468 CTGCTCCACTGCAACTTCAGGGAGATAAGA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGA
25498 CTTGTTACTT
Statistics
Matches: 196, Mismatches: 44, Indels: 25
0.74 0.17 0.09
Matches are distributed among these distances:
43 4 0.02
44 88 0.45
45 72 0.37
46 30 0.15
47 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (45 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGATCTGCTATCTTCAGT
Found at i:25427 original size:133 final size:133
Alignment explanation
Indices: 25200--25545 Score: 521
Period size: 133 Copynumber: 2.6 Consensus size: 133
25190 TCTATTGCAA
** * * * *
25200 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGTATTTTTATCCTGCTCAACTGCAACTTCA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGT-TA-TTTCAACCCGCTCTACTGCAACTTCA
*
25265 GAGAGATAAGGATTGTGGCTTCGATCTGCTCCACTGCAACTTCAGGGAGACAAGATCTGCTATCT
64 GAGAGATAAGGTTTGTGGCTTCGATCTGCTCCACTGCAACTTCAGGGAGACAAGATCTGCTATCT
25330 TCAGT
129 TCAGT
* * * * *
25335 TTGCTCCATTACAACTTCAGGGAGATAAGACTTGTTATTTCAACCCACTCTACTACAACTTCAGA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATTTCAACCCGCTCTACTGCAACTTCAGA
*
25400 GAGATAAGGTTTGTGGCTTCGATCTGCTCCACTGCAACTTCAGGTAGACAAGATCTGCTATCTTC
66 GAGATAAGGTTTGTGGCTTCGATCTGCTCCACTGCAACTTCAGGGAGACAAGATCTGCTATCTTC
25465 AGT
131 AGT
* * *
25468 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTACTTCAACCCGCTTTACTGCAACTTCAAA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATTTCAACCCGCTCTACTGCAACTTCAGA
*
25533 TAGATAAGGTTTG
66 GAGATAAGGTTTG
25546 CATATTTTTA
Statistics
Matches: 189, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
133 157 0.83
134 2 0.01
135 30 0.16
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (133 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATTTCAACCCGCTCTACTGCAACTTCAGA
GAGATAAGGTTTGTGGCTTCGATCTGCTCCACTGCAACTTCAGGGAGACAAGATCTGCTATCTTC
AGT
Found at i:25486 original size:89 final size:86
Alignment explanation
Indices: 25200--25496 Score: 244
Period size: 89 Copynumber: 3.3 Consensus size: 86
25190 TCTATTGCAA
* * *
25200 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGTATTTTTATCCTGCTCAACTGCAACTTCA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTG-A-CTTCAT-CTGCTCCACTGCAACTTCA
**
25265 GAGAGATAAGGAT-TGTGGCTTC-GAT
63 G-GAGATAA-GATCTGTATCTTCAG-T
* * * * * *
25290 CTGCTCCACTGCAACTTCAGGGAGACAAGATCTGCT-ATCTTCAGTTTGCTCCATTACAACTTCA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG-TGA-CTTCA-TCTGCTCCACTGCAACTTCA
**
25354 GGGAGATAAGA-CTTGTTAT-TTCAAC
63 -GGAGATAAGATC-TG-TATCTTCAGT
** * * * *
25379 CCACTCTACTACAACTTCAGAGAGATAAGGTTTGTGGCTTCGATCTGCTCCACTGCAACTTCAGG
1 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGACTTC-ATCTGCTCCACTGCAACTTCAGG
*
25444 TAGACAAGATCTGCTATCTTCAGT
65 -AGATAAGATCTG-TATCTTCAGT
25468 CTGCTCCACTGCAACTTCAGGGAGATAAG
1 CTGCTCCACTGCAACTTCAGGGAGATAAG
25497 ACTTGTTACT
Statistics
Matches: 161, Mismatches: 34, Indels: 25
0.73 0.15 0.11
Matches are distributed among these distances:
87 2 0.01
88 36 0.22
89 88 0.55
90 34 0.21
91 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (86 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGACTTCATCTGCTCCACTGCAACTTCAGGA
GATAAGATCTGTATCTTCAGT
Found at i:25525 original size:44 final size:44
Alignment explanation
Indices: 25202--25530 Score: 205
Period size: 44 Copynumber: 7.4 Consensus size: 44
25192 TATTGCAACT
** * * * *
25202 GCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGTATTTTTATCCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGT-TA-CTTCAACCC
* * ** * * *
25248 GCTCAACTGCAACTTCAGAGAGATAAGGA-TTGTGGCTTCGATCT
1 GCTCCACTGCAACTTCAGGGAGATAA-GACTTGTTACTTCAACCC
* * ****
25292 GCTCCACTGCAACTTCAGGGAGACAAGA-TCTGCTATCTTCAGTTT
1 GCTCCACTGCAACTTCAGGGAGATAAGACT-TGTTA-CTTCAACCC
* * *
25337 GCTCCATTACAACTTCAGGGAGATAAGACTTGTTATTTCAACCC
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTTACTTCAACCC
* * * * ** ** * * *
25381 ACTCTACTACAACTTCAGAGAGATAAGGTTTGTGGCTTCGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTTACTTCAACCC
* * * ** *
25425 GCTCCACTGCAACTTCAGGTAGACAAGA-TCTGCTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACT-TGTTA-CTTCAACCC
25470 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTTACTTCAACCC
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTTACTTCAACCC
**
25514 GCTTTACTGCAACTTCA
1 GCTCCACTGCAACTTCA
25531 AATAGATAAG
Statistics
Matches: 216, Mismatches: 60, Indels: 16
0.74 0.21 0.05
Matches are distributed among these distances:
43 4 0.02
44 109 0.50
45 72 0.33
46 30 0.14
47 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTTGTTACTTCAACCC
Found at i:30424 original size:26 final size:24
Alignment explanation
Indices: 30395--30443 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
30385 GGACCAAGAT
30395 AATTACTCCGACGGAAAGAATAAAAA
1 AATTACT-CG-CGGAAAGAATAAAAA
* *
30421 AATTACTTGTGGAAAGAATAAAA
1 AATTACTCGCGGAAAGAATAAAA
30444 GAATATTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 1 0.05
26 7 0.33
ACGTcount: A:0.53, C:0.10, G:0.16, T:0.20
Consensus pattern (24 bp):
AATTACTCGCGGAAAGAATAAAAA
Found at i:31448 original size:24 final size:24
Alignment explanation
Indices: 31397--31449 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
31387 TGTGCCATCG
*
31397 AATGCAGACAAGGGCAATCTATTT
1 AATGCAGACAAGGGCAATCTATTC
*
31421 AATGTAGACAAGGGCAATAC-ATTC
1 AATGCAGACAAGGGCAAT-CTATTC
31445 AATGC
1 AATGC
31450 TGACCCATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (24 bp):
AATGCAGACAAGGGCAATCTATTC
Found at i:43404 original size:23 final size:23
Alignment explanation
Indices: 43315--43404 Score: 76
Period size: 23 Copynumber: 4.0 Consensus size: 23
43305 GACTCACCAT
* * *
43315 AGCTCATTGGAGCTTACCGATTC
1 AGCTCAATAGAGCTTACCGTTTC
*
43338 AGCTCGAA-AGAGCTTACTG-TTC
1 AGCTC-AATAGAGCTTACCGTTTC
* ** *
43360 AACTTGATAGAGCTTACCGTTTT
1 AGCTCAATAGAGCTTACCGTTTC
*
43383 AGCTCAATAGAGCTTACTGTTT
1 AGCTCAATAGAGCTTACCGTTT
43405 ATCAACTCAG
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
21 1 0.02
22 16 0.31
23 34 0.65
24 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (23 bp):
AGCTCAATAGAGCTTACCGTTTC
Found at i:43596 original size:20 final size:20
Alignment explanation
Indices: 43571--43628 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
43561 ATAAGCTATG
*
43571 TTGAAATGGATGAGTTACTA
1 TTGAAATGGATGAATTACTA
*
43591 TTGAAATGAATGAATTACTA
1 TTGAAATGGATGAATTACTA
* *
43611 TTGATACGGATGAATTAC
1 TTGAAATGGATGAATTAC
43629 AATTTATACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (20 bp):
TTGAAATGGATGAATTACTA
Found at i:43637 original size:20 final size:20
Alignment explanation
Indices: 43600--43638 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43590 ATTGAAATGA
*
43600 ATGAATTACTATTGATACGG
1 ATGAATTACAATTGATACGG
*
43620 ATGAATTACAATTTATACG
1 ATGAATTACAATTGATACG
43639 AATAGAGATG
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:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (20 bp):
ATGAATTACAATTGATACGG
Found at i:46830 original size:40 final size:40
Alignment explanation
Indices: 46775--47057 Score: 396
Period size: 40 Copynumber: 7.1 Consensus size: 40
46765 TCGAATGATG
*
46775 TCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
46815 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
*
46855 TCCGGGCTAAGT-CCGAATGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
*
46894 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA
* *
46933 TTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
*
46973 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
* * * * **
47013 ACCGAGCTATGTCCCGAAAGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATA
47053 TCCGG
1 TCCGG
47058 TTAAATTCCG
Statistics
Matches: 219, Mismatches: 18, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
39 73 0.33
40 146 0.67
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
Found at i:46911 original size:79 final size:80
Alignment explanation
Indices: 46775--47057 Score: 396
Period size: 79 Copynumber: 3.6 Consensus size: 80
46765 TCGAATGATG
*
46775 TCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTT
46840 GTGCGAGTTACTATA
66 GTGCGAGTTACTATA
* *
46855 TCCGGGCTAAGT-CCGAATGCATTTGTGCGAGTTACTATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAG-TCCCGAAGGCATT
46918 TGTGCGAGTTACTA-A
65 TGTGCGAGTTACTATA
* * *
46933 TTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATT
46997 TGTGCGAGTTACTATA
65 TGTGCGAGTTACTATA
* * * * **
47013 ACCGAGCTATGTCCCGAAAGCATTTGAACGAG-TAGCTATATCCGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGG
47058 TTAAATTCCG
Statistics
Matches: 180, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
78 2 0.01
79 139 0.77
80 39 0.22
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGTTACTATA
Found at i:47045 original size:119 final size:118
Alignment explanation
Indices: 46779--47057 Score: 386
Period size: 119 Copynumber: 2.3 Consensus size: 118
46769 ATGATGTCCG
* *
46779 GGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGC
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTGGTGC
* * *
46844 GAGTTACTATATCCGGGCTAAGTCCGAATGCATTTGTGCGAGTTACTATATCC
66 GAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAACC
46897 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATTCCGGGCTAAG-CCCGAAGGCATTGG
1 GG-CTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTGG
*
46959 TGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
63 TGCGAGTTACTAAATCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAACC
* * **
47016 GAGCTATGTCCCGAAAGCATTTGAACGAG-TAGCTATATCCGG
1 G-GCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGG
47058 TTAAATTCCG
Statistics
Matches: 143, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
118 43 0.30
119 97 0.68
120 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (118 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTGGTGC
GAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAACC
Found at i:55031 original size:39 final size:40
Alignment explanation
Indices: 54924--55204 Score: 394
Period size: 40 Copynumber: 7.1 Consensus size: 40
54914 TCGAATGATG
54924 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
54964 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
*
55004 TCCGGGCTAAGT-CCGAATGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
*
55043 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA
* *
55082 TTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
*
55122 TCC-GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
* * * * **
55161 ACCGAGCTATGTCCCGAAAGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATA
55201 TCCG
1 TCCG
55205 TTAAATTCCA
Statistics
Matches: 218, Mismatches: 16, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
38 6 0.03
39 94 0.43
40 118 0.54
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
Found at i:55060 original size:79 final size:79
Alignment explanation
Indices: 54924--55204 Score: 392
Period size: 79 Copynumber: 3.6 Consensus size: 79
54914 TCGAATGATG
54924 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC-GGCTAAGTCCCGAAGGCATTT
54989 GTGCGAGTTACTATA
65 GTGCGAGTTACTATA
*
55004 TCCGGGCTAAGT-CCGAATGCATTTGTGCGAGTTACTATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG-CTAAG-TCCCGAAGGCATT
55067 TGTGCGAGTTACTA-A
64 TGTGCGAGTTACTATA
* * *
55082 TTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGTTAAGTCCCGAAGGCATTT
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGCTAAGTCCCGAAGGCATTT
55146 GTGCGAGTTACTATA
65 GTGCGAGTTACTATA
* * * * **
55161 ACCGAGCTATGTCCCGAAAGCATTTGAACGAG-TAGCTATATCCG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCG
55205 TTAAATTCCA
Statistics
Matches: 180, Mismatches: 13, Indels: 17
0.86 0.06 0.08
Matches are distributed among these distances:
77 1 0.01
78 42 0.23
79 124 0.69
80 13 0.07
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTATA
Found at i:63064 original size:40 final size:40
Alignment explanation
Indices: 63009--63269 Score: 354
Period size: 40 Copynumber: 6.6 Consensus size: 40
62999 TCGAATGATG
63009 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
63049 CCGGGCTAAGTCCCGAAAGCA-TTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
63088 CCGGGCTAAGTCCCGAATG-ATTTGTTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTG-TGCGAGTTACTATAT
*
63128 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
63168 CCGGGCTAAG-CCCGAAGGC-TATGGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCAT-TTGTGCGAGTTACTATAT
* *
63207 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
63247 CCGAGCTATGTCCCGAAAGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
63270 GAACGAGTAG
Statistics
Matches: 197, Mismatches: 14, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
38 2 0.01
39 72 0.37
40 116 0.59
41 7 0.04
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:63144 original size:79 final size:79
Alignment explanation
Indices: 63009--63263 Score: 347
Period size: 79 Copynumber: 3.2 Consensus size: 79
62999 TCGAATGATG
*
63009 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAAGCA-TTG
1 CCGGGCTAAGTCCCGAAGG-ATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
63073 TGCGAGTTACTATAT
65 TGCGAGTTACTATAT
* *
63088 CCGGGCTAAGTCCCGAATGATTTGTTGCGAGTTACTATATCCGGACTAAGAT-CCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGATTTG-TGCGAGTTACTATATCCGGGCTAAG-TCCCGAAGGCATTT
63152 GTGCGAGTTACTA-ATT
64 GTGCGAGTTACTATA-T
* * * *
63168 CCGGGCTAAG-CCCGAAGGCTATGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGAT-TTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
*
63232 TGCGAGTTACTATAA
65 TGCGAGTTACTATAT
* *
63247 CCGAGCTATGTCCCGAA
1 CCGGGCTAAGTCCCGAA
63264 AGCATTGAAC
Statistics
Matches: 156, Mismatches: 12, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
78 6 0.04
79 114 0.73
80 36 0.23
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGTTACTATAT
Found at i:63263 original size:119 final size:118
Alignment explanation
Indices: 63012--63269 Score: 362
Period size: 119 Copynumber: 2.2 Consensus size: 118
63002 AATGATGCCG
*
63012 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAAGCATTGTGCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAAGCATGGTGCG
* * *
63077 AGTTACTATATCCGGGCTAAGTCCCGAATGATTTGTTGCGAGTTACTATATCC
66 AGTTACTAAATCCGGGCTAAGTCCCGAAGGATTTGTTGCGAGTTACTATAACC
*
63130 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATTCCGGGCTAAG-CCCGAAGGCTATGG
1 GG-CTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAAGC-ATGG
*
63192 TGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG-TGCGAGTTACTATAACC
62 TGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGG-ATTTGTTGCGAGTTACTATAACC
* *
63249 GAGCTATGTCCCGAAAGCATT
1 G-GCTAAGTCCCGAAGGCATT
63270 GAACGAGTAG
Statistics
Matches: 125, Mismatches: 8, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
118 12 0.10
119 106 0.85
120 7 0.06
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (118 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAAGCATGGTGCG
AGTTACTAAATCCGGGCTAAGTCCCGAAGGATTTGTTGCGAGTTACTATAACC
Found at i:63277 original size:79 final size:79
Alignment explanation
Indices: 63009--63302 Score: 343
Period size: 79 Copynumber: 3.7 Consensus size: 79
62999 TCGAATGATG
*
63009 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAAGCA-TTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGT-CCGAAGGCATTTG
63073 TGCGAGTTACTATAT
65 TGCGAGTTACTATAT
* *
63088 CCGGGCTAAGTCCCGAATG-ATTTGTTGCGAGTTACTATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTG-TGCGAGTTACTATATCCGGGCTAAG-TCCGAAGGCATTT
63152 GTGCGAGTTACTA-ATT
64 GTGCGAGTTACTATA-T
* * *
63168 CCGGGCTAAG-CCCGAAGGC-TATGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCAT-TTGTGCGAGTTACTATATCCGGGCTAAGT-CCGAAGGCATTT
*
63231 GTGCGAGTTACTATAA
64 GTGCGAGTTACTATAT
* * * ** * *
63247 CCGAGCTATGTCCCGAAAGCA-TTGAACGAG-TAGCTATATCC-GGTTAAATCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCCGAAGG
63303 TACGTGATTC
Statistics
Matches: 187, Mismatches: 17, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
77 7 0.04
78 15 0.08
79 127 0.68
80 38 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTGT
GCGAGTTACTATAT
Found at i:69854 original size:39 final size:41
Alignment explanation
Indices: 69711--69905 Score: 196
Period size: 39 Copynumber: 4.9 Consensus size: 41
69701 GAAGTTGAGA
*
69711 AACTCGCAC-CAATAGCCTTCGGG--TTAGCCTCGGA-ATTAGCT
1 AACTCGCACAAAAT-GCCTTCGGGACTTAGCC-CGGATA-TAG-T
* *
69752 AACTCGCACAAAATGCCTTTCCGGATCTTTAGTCC-GATATAGT
1 AACTCGCACAAAATGCC-TTCGGGA-C-TTAGCCCGGATATAGT
* * *
69795 -ACTCGCACAAATTGCATTCGGGAC-TAGGCCGGATATAGT
1 AACTCGCACAAAATGCCTTCGGGACTTAGCCCGGATATAGT
69834 AACTCGCACAAAAT-CCTTC-GGACTTAGCCCGGATATAGT
1 AACTCGCACAAAATGCCTTCGGGACTTAGCCCGGATATAGT
69873 AACTCGCAC-AAATGCCTTC-GGACTTAGCCCGGA
1 AACTCGCACAAAATGCCTTCGGGACTTAGCCCGGA
69906 CATTCATTCG
Statistics
Matches: 133, Mismatches: 10, Indels: 24
0.80 0.06 0.14
Matches are distributed among these distances:
38 13 0.10
39 54 0.41
40 13 0.10
41 18 0.14
42 22 0.17
43 1 0.01
44 5 0.04
45 2 0.02
46 5 0.04
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
AACTCGCACAAAATGCCTTCGGGACTTAGCCCGGATATAGT
Done.