Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold569
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: 40478
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.32
Warning! 1826 characters in sequence are not A, C, G, or T
Found at i:4605 original size:28 final size:29
Alignment explanation
Indices: 4572--4626 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
4562 ACTATACTAG
4572 TTTTATCA-AATTGGTACATAAACTTTTT
1 TTTTATCAGAATTGGTACATAAACTTTTT
*
4600 TTTTATCAGAATTGGTACCTAAACTTT
1 TTTTATCAGAATTGGTACATAAACTTT
4627 AAACTGTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (29 bp):
TTTTATCAGAATTGGTACATAAACTTTTT
Found at i:6524 original size:14 final size:15
Alignment explanation
Indices: 6505--6539 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
6495 ATATTTATTG
6505 TATAAA-TACTTAAA
1 TATAAAGTACTTAAA
6519 TATAAAGTACTTAAA
1 TATAAAGTACTTAAA
6534 TATAAA
1 TATAAA
6540 AATATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (15 bp):
TATAAAGTACTTAAA
Found at i:7874 original size:44 final size:44
Alignment explanation
Indices: 7776--7929 Score: 131
Period size: 44 Copynumber: 3.6 Consensus size: 44
7766 TATTTAGTCT
* * * * * *
7776 GCTCCACTGCAACTTCAGGGAGATAAGACTAGATGC-GT--TCT
1 GCTCCACTGCAACTTCAGAGAGATAAGATTATAGGCTTTAATCC
* *
7817 GCT-CTCTGCAACTTCAGAGAGATAAGATTCA-AGGTTTTAATCC
1 GCTCCACTGCAACTTCAGAGAGATAAGATT-ATAGGCTTTAATCC
* * * *
7860 GCTTCACTGCAACTTCA-AGGAGATAGGATTATCGGCTTTAATCT
1 GCTCCACTGCAACTTCAGA-GAGATAAGATTATAGGCTTTAATCC
*
7904 GCTCCACTGCAACTTCAGGGAGATAA
1 GCTCCACTGCAACTTCAGAGAGATAA
7930 AATTTGCCAT
Statistics
Matches: 90, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
40 25 0.28
41 5 0.06
43 7 0.08
44 53 0.59
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGAGAGATAAGATTATAGGCTTTAATCC
Found at i:7882 original size:128 final size:129
Alignment explanation
Indices: 7678--7929 Score: 305
Period size: 128 Copynumber: 2.0 Consensus size: 129
7668 AGATGAATTT
* * * *
7678 GATGCGATCTGCTCTACTGTAATTTCAGAGAGATAAGATCCATCATTCTAATCCACTCCGCTACA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
* * *
7743 ACCTTAGGGAGATAGGATT-T-GTTTATTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
66 ACCTTAAGGAGATAGGATTATCG--GATTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACT
7806 A
129 A
* * ** * * * *
7807 GATGCGTTCTGCTCT-CTGCAACTTCAGAGAGATAAGATTCAAGGTTTTAATCCGCTTCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
*
7871 A-CTTCAAGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
66 ACCTT-AAGGAGATAGGATTATCGGATTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
7930 AATTTGCCAT
Statistics
Matches: 104, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
127 3 0.03
128 85 0.82
129 15 0.14
130 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (129 bp):
GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
ACCTTAAGGAGATAGGATTATCGGATTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
Found at i:8290 original size:44 final size:43
Alignment explanation
Indices: 8236--8614 Score: 398
Period size: 44 Copynumber: 8.7 Consensus size: 43
8226 GTTATTTTCC
* *
8236 ACCTACTCCACTGCTGCTCAGGGAGATAGGGTTCACAATCTTCA
1 ACCTATTCCACTGCTGC-CAGGGAGATAGGGTTCACAATCTTTA
*
8280 ACCTATTCCACTGCTGACCAGGGAGATA-GGATCTACAATCTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGGTTC-ACAATCTTTA
* ** * *
8324 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGGTTCACAATCTTTA
*
8368 ACCTATTCCACTGCTGTCCAGGGAGATA-GG-----ATTCTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGGTTCACAATCTTTA
* ** * *
8406 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGGTTCACAATCTTTA
*
8450 ACCTATTCCACTGCTGACCAGGGAGATA-GGATCTACAATCTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGGTTC-ACAATCTTTA
* ** ** *
8494 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTTAATTTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGGTTCACAATCTTTA
8538 ACCTATTCCACTGCTGACCAGGGAGAT-GGGATTCACAATCTTTA
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGG-TTCACAATCTTTA
8582 ACCTATTCCACTGCTGACCAGGGAGATAGGGTT
1 ACCTATTCCACTGCTG-CCAGGGAGATAGGGTT
8615 GGGATCATCA
Statistics
Matches: 278, Mismatches: 44, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
38 32 0.12
43 7 0.03
44 231 0.83
45 8 0.03
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (43 bp):
ACCTATTCCACTGCTGCCAGGGAGATAGGGTTCACAATCTTTA
Found at i:8346 original size:88 final size:87
Alignment explanation
Indices: 8242--8610 Score: 577
Period size: 88 Copynumber: 4.3 Consensus size: 87
8232 TTCCACCTAC
* ** *
8242 TCCACTGCTGCTCAGGGAGATAGGGTTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGAT
1 TCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAGGGAGAT
8307 AGGATCTACAATCTTTAATCTAT
66 AGGAT-TACAATCTTTAATCTAT
*
8330 TCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGTCCAGGGAGAT
1 TCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAGGGAGAT
8395 AGGA-T----TCTTTAATCTAT
66 AGGATTACAATCTTTAATCTAT
8412 TCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAGGGAGAT
1 TCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAGGGAGAT
8477 AGGATCTACAATCTTTAATCTAT
66 AGGAT-TACAATCTTTAATCTAT
* * *
8500 TCCACTGCTGCCCAGGGAGATAGAATTCTTAATTTTTAACCTATTCCACTGCTGACCAGGGAGAT
1 TCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAGGGAGAT
* *
8565 GGGATTCACAATCTTTAACCTAT
66 AGGATT-ACAATCTTTAATCTAT
*
8588 TCCACTGCTGACCAGGGAGATAG
1 TCCACTGCTGCCCAGGGAGATAG
8611 GGTTGGGATC
Statistics
Matches: 262, Mismatches: 12, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
82 80 0.31
84 1 0.00
86 1 0.00
87 1 0.00
88 179 0.68
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (87 bp):
TCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAGGGAGAT
AGGATTACAATCTTTAATCTAT
Found at i:8456 original size:170 final size:172
Alignment explanation
Indices: 8236--8610 Score: 592
Period size: 170 Copynumber: 2.2 Consensus size: 172
8226 GTTATTTTCC
* * **
8236 ACCTACTCCACTGCTGCTCAGGGAGATAGGGTTCACAATCTTCAACCTATTCCACTGCTGACCAG
1 ACCTATTCCACTGCTGCCCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTGCTGACCAG
8301 GGAGATAGGATCTACAATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTT
66 GGAGATAGGATCTACAATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTT
*
8366 CAACCTATTCCACTGCTGTCCAGGGAGATAGGA-T-TCTTTA
131 CAACCTATTCCACTGCTGACCAGGGAGATAGGATTATCTTTA
* *
8406 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAG
1 ACCTATTCCACTGCTGCCCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTGCTGACCAG
* *
8471 GGAGATAGGATCTACAATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTTAATTTT
66 GGAGATAGGATCTACAATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTT
* *
8536 TAACCTATTCCACTGCTGACCAGGGAGATGGGATTCACAATCTTTA
131 CAACCTATTCCACTGCTGACCAGGGAGATAGGATT----ATCTTTA
*
8582 ACCTATTCCACTGCTGACCAGGGAGATAG
1 ACCTATTCCACTGCTGCCCAGGGAGATAG
8611 GGTTGGGATC
Statistics
Matches: 186, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
170 152 0.82
171 1 0.01
176 33 0.18
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (172 bp):
ACCTATTCCACTGCTGCCCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTGCTGACCAG
GGAGATAGGATCTACAATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTT
CAACCTATTCCACTGCTGACCAGGGAGATAGGATTATCTTTA
Found at i:8673 original size:132 final size:132
Alignment explanation
Indices: 8279--8611 Score: 403
Period size: 126 Copynumber: 2.6 Consensus size: 132
8269 CACAATCTTC
* * * *
8279 AACCTATTCCACTGCTGACCAGGGAGATAGGA-TCTACAATCTTTAATCTATTCCACTGCTGCCC
1 AACCTATTCCACTGCTGACCAGGGAGATAGAATTC-ACAATCTTCAACCTATTCCACTGCTGACC
* * * * * * *
8343 AGGGAGATAGAATTCT-CAATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGATTC-----
65 AGGGAGATAGGA-TCTACAATCATCAATCTATTCCACTGCGGCCCAGGAAGATAGAATTCTTAAT
8402 -TTT
129 TTTT
* * *
8405 AATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCA
1 AACCTATTCCACTGCTGACCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTGCTGACCA
* * * *
8470 GGGAGATAGGATCTACAATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTTAATTT
66 GGGAGATAGGATCTACAATCATCAATCTATTCCACTGCGGCCCAGGAAGATAGAATTCTTAATTT
8535 TT
131 TT
* * *
8537 AACCTATTCCACTGCTGACCAGGGAGATGGGATTCACAATCTTTAACCTATTCCACTGCTGACCA
1 AACCTATTCCACTGCTGACCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTGCTGACCA
8602 GGGAGATAGG
66 GGGAGATAGG
8612 GTTGGGATCA
Statistics
Matches: 181, Mismatches: 18, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
125 3 0.02
126 104 0.57
127 2 0.01
132 72 0.40
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (132 bp):
AACCTATTCCACTGCTGACCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTGCTGACCA
GGGAGATAGGATCTACAATCATCAATCTATTCCACTGCGGCCCAGGAAGATAGAATTCTTAATTT
TT
Found at i:9277 original size:88 final size:88
Alignment explanation
Indices: 8625--9276 Score: 1061
Period size: 88 Copynumber: 7.4 Consensus size: 88
8615 GGGATCATCA
* *
8625 ATCTGCTTCGCTGCCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCTA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
* * *
8690 GGAAGGCAAGGCTGGTGTCTTCA
66 GGGAGGCAAGGCTGGTATCTTCG
* * * *
8713 ATCTGCTTCGCTGCCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCACTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
* *
8778 GGGAGGCAAAGCAGGGTATCTTCG
66 GGGAGGCAAGGC-TGGTATCTTCG
*
8802 ATCTGCTTCGCTGTTGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
* *
8867 GTGAGGCAAGGTTGGTATCTTCG
66 GGGAGGCAAGGCTGGTATCTTCG
*
8890 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCGCTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
* * *
8955 GGGAGGCAAGGCTAGTGTCTTTG
66 GGGAGGCAAGGCTGGTATCTTCG
* * * *
8978 ATCTGCTTCGCTGTCAGTACAGAAAGGCAAGATCTGCTATTTTTAACCTGTTCCGCTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
9043 GGGAGGCAAGGCTGGTATCTTCG
66 GGGAGGCAAGGCTGGTATCTTCG
* *
9066 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAACCTGTTCCGCTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
9131 GGGAGGCAAGGCTGGTATCTTCG
66 GGGAGGCAAGGCTGGTATCTTCG
* *
9154 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAACCTGTTCCGCTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
9219 GGGAGGCAAGGCTGGTATCTTCG
66 GGGAGGCAAGGCTGGTATCTTCG
9242 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCT
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCT
9277 ATTGAGAATG
Statistics
Matches: 526, Mismatches: 37, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
88 449 0.85
89 77 0.15
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (88 bp):
ATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA
GGGAGGCAAGGCTGGTATCTTCG
Found at i:14914 original size:15 final size:16
Alignment explanation
Indices: 14885--14915 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
14875 CAACGACATG
14885 TAAAATATCAAATGAA
1 TAAAATATCAAATGAA
14901 TAAAATAT-AAATGAA
1 TAAAATATCAAATGAA
14916 AACACAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (16 bp):
TAAAATATCAAATGAA
Found at i:16021 original size:17 final size:16
Alignment explanation
Indices: 15999--16030 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
15989 AGAACAGATC
15999 AAAAAATAAATAAAAAT
1 AAAAAATAAA-AAAAAT
16016 AAAAAATAAAAAAAA
1 AAAAAATAAAAAAAA
16031 CTTTGAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAAATAAAAAAAAT
Found at i:18745 original size:5 final size:5
Alignment explanation
Indices: 18737--18767 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
18727 GAGATGGAAT
18737 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
18768 ATATTTGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:31433 original size:13 final size:13
Alignment explanation
Indices: 31415--31441 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31405 GCCAAAATAC
31415 ACCATGTGATCAA
1 ACCATGTGATCAA
31428 ACCATGTGATCAA
1 ACCATGTGATCAA
31441 A
1 A
31442 ACACATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (13 bp):
ACCATGTGATCAA
Found at i:31951 original size:67 final size:67
Alignment explanation
Indices: 31805--31936 Score: 201
Period size: 67 Copynumber: 2.0 Consensus size: 67
31795 ATTTGAACCA
* * * * *
31805 TTCAAACATGAATTCGTTTATATGCCAATTTCACATCTTTCATTTCTATACATACATGTTTCAAA
1 TTCAAACATGAATTCATTTATATGCCAATTGCACAGCTTTCATTTCTATACACACACGTTTCAAA
31870 GG
66 GG
* *
31872 TTCAAACATGAATTCATTTATATGCTAATTGCACAGCTTTCGTTTCTATACACACACGTTTCAAA
1 TTCAAACATGAATTCATTTATATGCCAATTGCACAGCTTTCATTTCTATACACACACGTTTCAAA
31937 TGTTAGCAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (67 bp):
TTCAAACATGAATTCATTTATATGCCAATTGCACAGCTTTCATTTCTATACACACACGTTTCAAA
GG
Found at i:34767 original size:11 final size:11
Alignment explanation
Indices: 34751--34777 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
34741 CTATATAATG
34751 CCATAGCTTTT
1 CCATAGCTTTT
34762 CCATAGCTTTT
1 CCATAGCTTTT
34773 CCATA
1 CCATA
34778 CCATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.30, G:0.07, T:0.41
Consensus pattern (11 bp):
CCATAGCTTTT
Found at i:36267 original size:26 final size:26
Alignment explanation
Indices: 36238--36287 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
36228 TTATTTAAAC
36238 CTATGAATTTTAA-ATTGTATTAATTA
1 CTAT-AATTTTAATATTGTATTAATTA
* *
36264 CTATACTTTTAATTTTGTATTAAT
1 CTATAATTTTAATATTGTATTAAT
36288 CATGAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (26 bp):
CTATAATTTTAATATTGTATTAATTA
Found at i:36847 original size:20 final size:21
Alignment explanation
Indices: 36822--36862 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
36812 TTAATCATTC
*
36822 TTTTAAAATTAT-TTATATTT
1 TTTTAAAAATATATTATATTT
36842 TTTTAAAAATATATTATATTT
1 TTTTAAAAATATATTATATTT
36863 AAAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTAAAAATATATTATATTT
Found at i:37444 original size:18 final size:18
Alignment explanation
Indices: 37421--37497 Score: 55
Period size: 18 Copynumber: 3.9 Consensus size: 18
37411 TGTTAGTTAA
37421 TTTTTCTTTCTTTCTTTC
1 TTTTTCTTTCTTTCTTTC
37439 TTTTTCCTATTCTTTTCTTTTTAC
1 TTTTT-CT-TTC-TTTC--TTT-C
* * *
37463 GTTTTCTATCCTTCTTTC
1 TTTTTCTTTCTTTCTTTC
* *
37481 TTTTTCTCTGTTTCTTT
1 TTTTTCTTTCTTTCTTT
37498 TTATTATTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
18 19 0.41
19 5 0.11
20 3 0.07
21 7 0.15
22 2 0.04
23 5 0.11
24 5 0.11
ACGTcount: A:0.04, C:0.22, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTTCTTTCTTTCTTTC
Found at i:38191 original size:63 final size:63
Alignment explanation
Indices: 38054--38200 Score: 177
Period size: 63 Copynumber: 2.3 Consensus size: 63
38044 CCGTGTGATT
* * ** * * *
38054 GGCCGTGTAACCCACTATTTGTGAATTAAGGTCACATGGGCTAGGGACACGAGCGTGTGTCTA
1 GGCCGTGTAACTCACTGTTTGTGAATTAAGGTCACACAGGCCAAGGACACGAGCGTGTGTCCA
* * *
38117 GGCCGTGTAACTCACTGTTTGTGAATTAGGGTCACACAGGCCAAGGACACGGGTGTGTGTCCA
1 GGCCGTGTAACTCACTGTTTGTGAATTAAGGTCACACAGGCCAAGGACACGAGCGTGTGTCCA
* * *
38180 GGCCATGTAACTTATTGTTTG
1 GGCCGTGTAACTCACTGTTTG
38201 CTAATGTCAC
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.27
Consensus pattern (63 bp):
GGCCGTGTAACTCACTGTTTGTGAATTAAGGTCACACAGGCCAAGGACACGAGCGTGTGTCCA
Found at i:39711 original size:17 final size:17
Alignment explanation
Indices: 39689--39730 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
39679 GGCCCGAAGT
*
39689 GGCCCAAACCTAACTA-A
1 GGCCCAAACCAAAC-AGA
39706 GGCCCAAACCAAACAGA
1 GGCCCAAACCAAACAGA
39723 GGCCCAAA
1 GGCCCAAA
39731 GCAGATTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.04
17 22 0.96
ACGTcount: A:0.43, C:0.36, G:0.17, T:0.05
Consensus pattern (17 bp):
GGCCCAAACCAAACAGA
Done.