Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold765
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: 44580
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Found at i:6352 original size:40 final size:40
Alignment explanation
Indices: 6322--6542 Score: 263
Period size: 40 Copynumber: 5.5 Consensus size: 40
6312 GCTACTCGTT
* *
6322 CAAATGCCTTCGGGACATAGCCCGGTTATAGTGACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
6362 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
6402 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* * * *
6442 CCAATGCCTTCGGG-CTTAGCCCAG-AATCAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT-AGTAACTCGCA
* * * * *
6481 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
6522 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
6543 AGGACATCAT
Statistics
Matches: 157, Mismatches: 16, Indels: 16
0.83 0.08 0.08
Matches are distributed among these distances:
38 3 0.02
39 28 0.18
40 111 0.71
41 15 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:6500 original size:119 final size:120
Alignment explanation
Indices: 6324--6539 Score: 287
Period size: 119 Copynumber: 1.8 Consensus size: 120
6314 TACTCGTTCA
* * * *
6324 AATGCCTTCGGGACATAGCCCGGTTATAGTGACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT
1 AATGCCTTCGGGACATAGCCCAGTAATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
*
6389 ATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * *
6444 AATGCCTTCGGG-CTTAGCCCAG-AATCAGTAACTTGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCAGTAAT-AGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGG
* *
6506 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTA
6540 GCCAGGACAT
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 5 0.06
119 58 0.70
120 20 0.24
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCAGTAATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:8888 original size:12 final size:12
Alignment explanation
Indices: 8871--8896 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8861 TGGAGGTGGG
8871 ACTAGCAGTAAA
1 ACTAGCAGTAAA
8883 ACTAGCAGTAAA
1 ACTAGCAGTAAA
8895 AC
1 AC
8897 ATTTTGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.15
Consensus pattern (12 bp):
ACTAGCAGTAAA
Found at i:9633 original size:27 final size:26
Alignment explanation
Indices: 9589--10036 Score: 186
Period size: 27 Copynumber: 16.7 Consensus size: 26
9579 TTAGTTTACC
*
9589 AAATTACTGAAATA-CCCCCAGTTGTA
1 AAATTAC-GAAATACCCCCCACTTGTA
* * *
9615 AAATTACCAAAGTACCCCCGACTTATA
1 AAATTACGAAA-TACCCCCCACTTGTA
** * *
9642 AAATTATCGAAATA-CCGTCAATTGTC
1 AAATTA-CGAAATACCCCCCACTTGTA
* * *
9668 AAATTACTGAAATACCCTCAATTTGTA
1 AAATTAC-GAAATACCCCCCACTTGTA
* * *
9695 AAATTACCGAAATA-CCCTCAGTTTGCA
1 AAATTA-CGAAATACCCCCCA-CTTGTA
* * *
9722 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTAC-GAAATACCCCCCACTTGTA
* *
9749 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTAC-GAAATACCCCCCACTTGTA
* ** * *
9776 AAATTACCAAAGTACCCCTGATTTATA
1 AAATTACGAAA-TACCCCCCACTTGTA
* * * * *
9803 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTA-CGAAATACCCCCCACTTGTA
** ** *
9830 AAACCACGGAAATACCATCGA-TTGTA
1 AAATTAC-GAAATACCCCCCACTTGTA
* ** *
9856 AAATTACTGACATACCTTCGACTTGTA
1 AAATTAC-GAAATACCCCCCACTTGTA
* *
9883 AAATTACCGAAATA-CCCTCAGTTTGTA
1 AAATTA-CGAAATACCCCCCA-CTTGTA
* * * *
9910 AAATTACTGAAATACCCTCAATTTGTG
1 AAATTAC-GAAATACCCCCCACTTGTA
* * * *
9937 AAATTACTGAAATACCCTCGACCTATA
1 AAATTAC-GAAATACCCCCCACTTGTA
* * * *
9964 AATTTACTGAAATACCCTCGACCTGTA
1 AAATTAC-GAAATACCCCCCACTTGTA
* * *
9991 AATTTACTGAAATACCCTCGACTTGTA
1 AAATTAC-GAAATACCCCCCACTTGTA
*
10018 AAATTACCAAAGTACCCCC
1 AAATTACGAAA-TACCCCC
10037 GATTTACAGA
Statistics
Matches: 339, Mismatches: 65, Indels: 35
0.77 0.15 0.08
Matches are distributed among these distances:
25 4 0.01
26 62 0.18
27 256 0.76
28 17 0.05
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (26 bp):
AAATTACGAAATACCCCCCACTTGTA
Found at i:9857 original size:161 final size:161
Alignment explanation
Indices: 9589--9979 Score: 443
Period size: 161 Copynumber: 2.4 Consensus size: 161
9579 TTAGTTTACC
* * * *
9589 AAATTACTGAAATACCC-CCAGTTGTAAAATTACCAAAGTACCCCCGACTTATAAAATTATCGAA
1 AAATTACTGAAATACCCTCAACTTGTAAAATTACCAAAGTACCCCCGACTTATAAAATTACCCAA
* ** * * *
9653 ATACCGTCAATTGTCAAATTACTGAAATACCCTCAATTTGTAAAATTACCGAAATACCCTC-AGT
66 ATACCGTCAATTGTAAAACCACGGAAATACCATCAATTTGTAAAATTACCGAAATACCCTCGA-C
*
9717 TTGCAAAATTACTGAAATACCCTC-GATTTGTA
130 TTGCAAAATTACCGAAATACCCTCAG-TTTGTA
* * *
9749 AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCTGATTTATAAAATTACCCAA
1 AAATTACTGAAATACCCTCAACTTGTAAAATTACCAAAGTACCCCCGACTTATAAAATTACCCAA
* * * * *
9814 ATATCC-TCGATTTGTAAAACCACGGAAATACCATCGA-TTGTAAAATTACTGACATACCTTCGA
66 ATA-CCGTC-AATTGTAAAACCACGGAAATACCATCAATTTGTAAAATTACCGAAATACCCTCGA
*
9877 CTTGTAAAATTACCGAAATACCCTCAGTTTGTA
129 CTTGCAAAATTACCGAAATACCCTCAGTTTGTA
* * * * * * **
9910 AAATTACTGAAATACCCTCAATTTGTGAAATTACTGAAA-TACCCTCGACCTATAAATTTACTGA
1 AAATTACTGAAATACCCTCAACTTGTAAAATTAC-CAAAGTACCCCCGACTTATAAAATTACCCA
9974 AATACC
65 AATACC
9980 CTCGACCTGT
Statistics
Matches: 195, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
160 19 0.10
161 148 0.76
162 28 0.14
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (161 bp):
AAATTACTGAAATACCCTCAACTTGTAAAATTACCAAAGTACCCCCGACTTATAAAATTACCCAA
ATACCGTCAATTGTAAAACCACGGAAATACCATCAATTTGTAAAATTACCGAAATACCCTCGACT
TGCAAAATTACCGAAATACCCTCAGTTTGTA
Found at i:10034 original size:54 final size:54
Alignment explanation
Indices: 9589--10024 Score: 431
Period size: 54 Copynumber: 8.1 Consensus size: 54
9579 TTAGTTTACC
* * * * * *
9589 AAATTACTGAAATACCC-CCAGTTGTAAAATTAC-CAAAGTACCCCCGACTTATA
1 AAATTACTGAAATACCCTCGACTTGTAAAATTACTGAAA-TACCCTCGATTTGTA
* * * *
9642 AAATTA-TCGAAATACCGTC-AATTGTCAAATTACTGAAATACCCTCAATTTGTA
1 AAATTACT-GAAATACCCTCGACTTGTAAAATTACTGAAATACCCTCGATTTGTA
* * *
9695 AAATTACCGAAATACCCTC-AGTTTGCAAAATTACTGAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGA-CTTGTAAAATTACTGAAATACCCTCGATTTGTA
* *
9749 AAATTACTGAAATACCCTCGACTTGTAAAATTAC-CAAAGTACCC-CTGATTTATA
1 AAATTACTGAAATACCCTCGACTTGTAAAATTACTGAAA-TACCCTC-GATTTGTA
** * * ** * *
9803 AAATTACCCAAATATCCTCGATTTGTAAAACCACGGAAATACCATCGA-TTGTA
1 AAATTACTGAAATACCCTCGACTTGTAAAATTACTGAAATACCCTCGATTTGTA
* * *
9856 AAATTACTGACATACCTTCGACTTGTAAAATTACCGAAATACCCTC-AGTTTGTA
1 AAATTACTGAAATACCCTCGACTTGTAAAATTACTGAAATACCCTCGA-TTTGTA
* * * ** *
9910 AAATTACTGAAATACCCTCAATTTGTGAAATTACTGAAATACCCTCGACCTATA
1 AAATTACTGAAATACCCTCGACTTGTAAAATTACTGAAATACCCTCGATTTGTA
* * * *
9964 AATTTACTGAAATACCCTCGACCTGTAAATTTACTGAAATACCCTCGACTTGTA
1 AAATTACTGAAATACCCTCGACTTGTAAAATTACTGAAATACCCTCGATTTGTA
10018 AAATTAC
1 AAATTAC
10025 CAAAGTACCC
Statistics
Matches: 314, Mismatches: 56, Indels: 25
0.79 0.14 0.06
Matches are distributed among these distances:
52 2 0.01
53 98 0.31
54 208 0.66
55 6 0.02
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.29
Consensus pattern (54 bp):
AAATTACTGAAATACCCTCGACTTGTAAAATTACTGAAATACCCTCGATTTGTA
Found at i:10049 original size:27 final size:27
Alignment explanation
Indices: 10017--10088 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 27
10007 CTCGACTTGT
*
10017 AAAATTACCAAAGTACCCCCGATTTAC
1 AAAATTACCAAAATACCCCCGATTTAC
* **** *
10044 AGAATTACCGTTTTACCCTCGATTTAC
1 AAAATTACCAAAATACCCCCGATTTAC
*
10071 AAAATTACAAAAATACCC
1 AAAATTACCAAAATACCC
10089 TTGTAACGTA
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.26
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCCGATTTAC
Found at i:10061 original size:81 final size:80
Alignment explanation
Indices: 9589--10089 Score: 472
Period size: 81 Copynumber: 6.2 Consensus size: 80
9579 TTAGTTTACC
* * * *
9589 AAATTACTGAAATACCC-CCAGTTGTAAAATTACCAAAGTACCCCCGACTTATAAAATTATCGAA
1 AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAA-TACCCCCGATTTATAAAATTACCGAA
* * *
9653 ATACCGTC-AATTGTC
65 ATACCCTCGATTTGTA
* * * ** *
9668 AAATTACTGAAATACCCTCAATTTGTAAAATTACCGAAATACCCTC-AGTTTGCAAAATTACTGA
1 AAATTACTGAAATACCCTCGACTTGTAAAATTACC-AAATACCCCCGA-TTTATAAAATTACCGA
9732 AATACCCTCGATTTGTA
64 AATACCCTCGATTTGTA
* *
9749 AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCTGATTTATAAAATTACCCAA
1 AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAA-TACCCCCGATTTATAAAATTACCGAA
*
9814 ATATCCTCGATTTGTA
65 ATACCCTCGATTTGTA
** * * * * ** * *
9830 AAACCACGGAAATACCATCGA-TTGTAAAATTACTGACATACCTTCGACTTGTAAAATTACCGAA
1 AAATTACTGAAATACCCTCGACTTGTAAAATTAC-CAAATACCCCCGATTTATAAAATTACCGAA
9894 ATACCCTC-AGTTTGTA
65 ATACCCTCGA-TTTGTA
* * * * * ** * *
9910 AAATTACTGAAATACCCTCAATTTGTGAAATTACTGAAATACCCTCGACCTATAAATTTACTGAA
1 AAATTACTGAAATACCCTCGACTTGTAAAATTAC-CAAATACCCCCGATTTATAAAATTACCGAA
**
9975 ATACCCTCGACCTGTA
65 ATACCCTCGATTTGTA
* * * **
9991 AATTTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCCGATTTACAGAATTACCGTT
1 AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAA-TACCCCCGATTTATAAAATTACCGAA
* **
10056 TTACCCTCGATTTACA
65 ATACCCTCGATTTGTA
**
10072 AAATTACAAAAATACCCT
1 AAATTACTGAAATACCCT
10090 TGTAACGTAG
Statistics
Matches: 342, Mismatches: 69, Indels: 20
0.79 0.16 0.05
Matches are distributed among these distances:
79 19 0.06
80 107 0.31
81 214 0.63
82 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (80 bp):
AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAATACCCCCGATTTATAAAATTACCGAAA
TACCCTCGATTTGTA
Found at i:10126 original size:27 final size:27
Alignment explanation
Indices: 10096--10214 Score: 121
Period size: 27 Copynumber: 4.4 Consensus size: 27
10086 CCCTTGTAAC
10096 GTAGAATTACCGAAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCCTATAGG
* ** * *
10123 GTAGAATTACTGAAATACCATTGTGGG
1 GTAGAATTACCGAAATACCCCTATAGG
* * *
10150 GTAAAAATACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTATAGG
* * * *
10177 ATAGAATTACCGAGATACCCTTATGGG
1 GTAGAATTACCGAAATACCCCTATAGG
*
10204 GTAAAATTACC
1 GTAGAATTACC
10215 ATTTTGCCCT
Statistics
Matches: 72, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 72 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.24
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTATAGG
Found at i:10131 original size:54 final size:54
Alignment explanation
Indices: 10073--10186 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
10063 CGATTTACAA
* * * *
10073 AATTACAAAAATACCCTTGTAACGTAGAATTACCGAAATACCCCTATAGGGTAG
1 AATTACAAAAATACCATTGTAACGTAAAAATACCGAAATACCCCTATAGGATAG
** *** *
10127 AATTACTGAAATACCATTGTGGGGTAAAAATACCGAAATACCCCTGTAGGATAG
1 AATTACAAAAATACCATTGTAACGTAAAAATACCGAAATACCCCTATAGGATAG
10181 AATTAC
1 AATTAC
10187 CGAGATACCC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (54 bp):
AATTACAAAAATACCATTGTAACGTAAAAATACCGAAATACCCCTATAGGATAG
Found at i:10195 original size:54 final size:54
Alignment explanation
Indices: 10103--10214 Score: 161
Period size: 54 Copynumber: 2.1 Consensus size: 54
10093 AACGTAGAAT
* * *
10103 TACCGAAATACCCCTATAGGGTAGAATTACTGAAATACCATTGTGGGGTAAAAA
1 TACCGAAATACCCCTATAGGATAGAATTACCGAAATACCATTATGGGGTAAAAA
* * * *
10157 TACCGAAATACCCCTGTAGGATAGAATTACCGAGATACCCTTATGGGGTAAAAT
1 TACCGAAATACCCCTATAGGATAGAATTACCGAAATACCATTATGGGGTAAAAA
10211 TACC
1 TACC
10215 ATTTTGCCCT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (54 bp):
TACCGAAATACCCCTATAGGATAGAATTACCGAAATACCATTATGGGGTAAAAA
Found at i:10694 original size:22 final size:22
Alignment explanation
Indices: 10642--10706 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
10632 TTAAAGTCTT
* *
10642 CTGATTATGGCTTTGCGCCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
10664 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
*
10686 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
10707 ACGCATTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:10895 original size:27 final size:26
Alignment explanation
Indices: 10865--10971 Score: 108
Period size: 27 Copynumber: 4.0 Consensus size: 26
10855 ATTCTGTTAA
* *
10865 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTATGCCACAATATCTG-TTCTG
10892 GTGGCTATGCCACAAATATCTG-TCTG
1 GTGGCTATGCCAC-AATATCTGTTCTG
* *
10918 GTGGCTCTGCCACAATATCTATATCTG
1 GTGGCTATGCCACAATATCTGT-TCTG
* * * *
10945 GTGACTCTGTCACAATATCTATTCTG
1 GTGGCTATGCCACAATATCTGTTCTG
10971 G
1 G
10972 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
25 7 0.10
26 21 0.30
27 36 0.51
28 7 0.10
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (26 bp):
GTGGCTATGCCACAATATCTGTTCTG
Found at i:10971 original size:53 final size:53
Alignment explanation
Indices: 10865--10964 Score: 130
Period size: 53 Copynumber: 1.9 Consensus size: 53
10855 ATTCTGTTAA
* * * * *
10865 GTGGCTTTGCCACATTATCTGTTTCTGGTGGCTATGCCACAAATATCTGTCTG
1 GTGGCTCTGCCACAATATCTATATCTGGTGACTATGCCACAAATATCTGTCTG
* *
10918 GTGGCTCTGCCACAATATCTATATCTGGTGACTCTGTCAC-AATATCT
1 GTGGCTCTGCCACAATATCTATATCTGGTGACTATGCCACAAATATCT
10965 ATTCTGGCAG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
52 7 0.17
53 33 0.82
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (53 bp):
GTGGCTCTGCCACAATATCTATATCTGGTGACTATGCCACAAATATCTGTCTG
Found at i:11098 original size:6 final size:6
Alignment explanation
Indices: 11089--11181 Score: 68
Period size: 6 Copynumber: 15.3 Consensus size: 6
11079 TTGCATTCCC
* *
11089 ATTCTG ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG GTTCTG ATTCT-
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG
* * *
11137 ATCACCTG ATTCTG ATTCTA ATTCTC ATT-TG ATTCT- AGTTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
11182 AATGTTTCTT
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
5 9 0.13
6 51 0.74
7 6 0.09
8 3 0.04
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.47
Consensus pattern (6 bp):
ATTCTG
Found at i:11120 original size:25 final size:25
Alignment explanation
Indices: 11092--11161 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
11082 CATTCCCATT
* *
11092 CTGATTCTGATTCTGATTCTGTTAC
1 CTGATTCTGATTCTGATTCTATCAC
* *
11117 CTGATACTGGTTCTGATTCTATCAC
1 CTGATTCTGATTCTGATTCTATCAC
*
11142 CTGATTCTGATTCTAATTCT
1 CTGATTCTGATTCTGATTCT
11162 CATTTGATTC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.46
Consensus pattern (25 bp):
CTGATTCTGATTCTGATTCTATCAC
Found at i:14784 original size:30 final size:30
Alignment explanation
Indices: 14750--14810 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
14740 TCCTTAACTC
14750 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
14780 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
14810 A
1 A
14811 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:25101 original size:85 final size:85
Alignment explanation
Indices: 24958--25192 Score: 296
Period size: 84 Copynumber: 2.8 Consensus size: 85
24948 ATCTGAGACA
* *
24958 TCGTGTAAGACCGTGTCTGGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGTCTGGGA
1 TCGTGTAAGACCGTGTCTGGGACACAGGCCTCTATTGAGATTTACATATAAGACCATGTCTGGGA
*
25023 CATCGGTATCGTATCTAATT
66 CATCGGCATCGTATCTAATT
* * * *
25043 TCGTGTAAGACTGTGTTTGGGATACAGGCCTCTATTGAGATTTACATATAAGACCATGT-TTGGA
1 TCGTGTAAGACCGTGTCTGGGACACAGGCCTCTATTGAGATTTACATATAAGACCATGTCTGGGA
* *
25107 CATCTGCATCGTATCTGATT
66 CATCGGCATCGTATCTAATT
* * * * * *
25127 TCATGTAAGACCCTGTCTGGGACAGAGGCATCGATATTGA-A-TTACATGTAAGACCATGTCCGG
1 TCGTGTAAGACCGTGTCTGGGACACAGGCCTC--TATTGAGATTTACATATAAGACCATGTCTGG
25190 GAC
64 GAC
25193 GTTGATATTG
Statistics
Matches: 128, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
84 63 0.49
85 59 0.46
86 6 0.05
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (85 bp):
TCGTGTAAGACCGTGTCTGGGACACAGGCCTCTATTGAGATTTACATATAAGACCATGTCTGGGA
CATCGGCATCGTATCTAATT
Found at i:25181 original size:43 final size:42
Alignment explanation
Indices: 24961--25192 Score: 163
Period size: 43 Copynumber: 5.5 Consensus size: 42
24951 TGAGACATCG
* * *
24961 TGTAAGACCGTGTCTGGGACACAGGCCTCG-ATTGAGATTTACG
1 TGTAAGACCATGTCTGGGACACAGGCATCGTATTGA-A-TTACA
* * * *
25004 TATAAGACCATGTCTGGGACATC-GGTATCGTATCT-AATTTCG
1 TGTAAGACCATGTCTGGGACA-CAGGCATCGTAT-TGAATTACA
** * * *
25046 TGTAAGACTGTGTTTGGGATACAGGCCTC-TATTGAGATTTACA
1 TGTAAGACCATGTCTGGGACACAGGCATCGTATTGA-A-TTACA
* * * *
25089 TATAAGACCATGT-TTGGACATC-TGCATCGTATCTG-ATTTCA
1 TGTAAGACCATGTCTGGGACA-CAGGCATCGTAT-TGAATTACA
* *
25130 TGTAAGACCCTGTCTGGGACAGAGGCATCGATATTGAATTACA
1 TGTAAGACCATGTCTGGGACACAGGCATCG-TATTGAATTACA
*
25173 TGTAAGACCATGTCCGGGAC
1 TGTAAGACCATGTCTGGGAC
25193 GTTGATATTG
Statistics
Matches: 145, Mismatches: 30, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
40 1 0.01
41 20 0.14
42 49 0.34
43 68 0.47
44 6 0.04
45 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACACAGGCATCGTATTGAATTACA
Found at i:38843 original size:59 final size:59
Alignment explanation
Indices: 38780--38897 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
38770 AGGGAAGATG
* *
38780 AGTTTGTGCCAAAATAGGATTATTGCTTCTCAATTTCAGATTTGGTGGATATCCTCATT
1 AGTTTGTGCCAAAATAGGATTATTGCTTCTCAAGTTCAAATTTGGTGGATATCCTCATT
38839 AGTTTGTGCCAAAATAGGATTATTGCTTCTCAAGTTCAAATTTGGTGGATATCCTCATT
1 AGTTTGTGCCAAAATAGGATTATTGCTTCTCAAGTTCAAATTTGGTGGATATCCTCATT
38898 CCCTTTTCAG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (59 bp):
AGTTTGTGCCAAAATAGGATTATTGCTTCTCAAGTTCAAATTTGGTGGATATCCTCATT
Found at i:40151 original size:26 final size:26
Alignment explanation
Indices: 40121--40178 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
40111 GTATACCTAG
* *
40121 ACCCTAAATTGATAAATGACTATTTT
1 ACCCTAAATGGAAAAATGACTATTTT
* *
40147 TCCCTTATATGGAAAAATGACTATTTT
1 ACCC-TAAATGGAAAAATGACTATTTT
40174 ACCCT
1 ACCCT
40179 TATACGGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (26 bp):
ACCCTAAATGGAAAAATGACTATTTT
Found at i:40164 original size:27 final size:27
Alignment explanation
Indices: 40134--40205 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
40124 CTAAATTGAT
* *
40134 AAATGACTATTTTTCCCTTATATGGAA
1 AAATGACTATTTTACCCTTATACGGAA
*
40161 AAATGACTATTTTACCCTTATACGGTA
1 AAATGACTATTTTACCCTTATACGGAA
* * *
40188 AGATGACTGTTTTGCCCT
1 AAATGACTATTTTACCCT
40206 ATGTGATGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (27 bp):
AAATGACTATTTTACCCTTATACGGAA
Found at i:40596 original size:18 final size:18
Alignment explanation
Indices: 40569--40618 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
40559 GTTTAAACTG
*
40569 TTACTACACTGATTACTA
1 TTACTGCACTGATTACTA
* *
40587 TTACTGCACTGTTTACTG
1 TTACTGCACTGATTACTA
*
40605 TTACTGCATTGATT
1 TTACTGCACTGATT
40619 GTTTGTAACA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (18 bp):
TTACTGCACTGATTACTA
Found at i:41589 original size:28 final size:27
Alignment explanation
Indices: 41542--41646 Score: 106
Period size: 27 Copynumber: 3.8 Consensus size: 27
41532 TGCTAGAAAG
* * *
41542 GATAATGTGACAGAGTCACCCGATACA
1 GATAATGTGGCAGAGCCACCAGATACA
41569 GATAATCGTGGCAGAGCCACCAGA-ACA
1 GATAAT-GTGGCAGAGCCACCAGATACA
*
41596 GATATATGTGGTAGAGCCACCAGAT-CA
1 GATA-ATGTGGCAGAGCCACCAGATACA
* *
41623 AATAATTTGTGGCATAGCCACCAG
1 GATAA--TGTGGCAGAGCCACCAG
41647 GACGCTTCCT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.02
27 34 0.52
28 31 0.47
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (27 bp):
GATAATGTGGCAGAGCCACCAGATACA
Done.