Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1719
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: 16157
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Found at i:9882 original size:80 final size:80
Alignment explanation
Indices: 9713--9918 Score: 202
Period size: 80 Copynumber: 2.6 Consensus size: 80
9703 GAGATAATAA
* * * * ** * *
9713 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTAGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAATG
*
9777 ATTAGAAAAAAAAAAT
65 ATTAGAAAAAAAAAAC
*
9793 CGGGATTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAAT-A
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
* ** * *
9857 TTTTGGGAAATAAAGC
66 -TTAGAAAAAAAAAAC
* * *
9873 CGGGGTTGGAGTATCCCCTCGGAAGTAAC-AGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGA-GGTTGGAGTATCCCC
9919 GATGAAATAA
Statistics
Matches: 104, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
79 8 0.08
80 96 0.92
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (80 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
TTAGAAAAAAAAAAC
Found at i:9915 original size:28 final size:27
Alignment explanation
Indices: 9875--9944 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
9865 AATAAAGCCG
** *
9875 GGGTTGGAGTATCCCCTCGGAAGTAAC
1 GGGTTGGAGTATCCCCGAGGAAATAAC
*
9902 AGGGTTGGAGTATCCCCGATGAAATAAC
1 -GGGTTGGAGTATCCCCGAGGAAATAAC
9930 GAGGTTGGAGTATCC
1 G-GGTTGGAGTATCC
9945 TCGATTGTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 1 0.03
28 36 0.97
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.23
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCGAGGAAATAAC
Found at i:9989 original size:108 final size:106
Alignment explanation
Indices: 9798--10212 Score: 337
Period size: 108 Copynumber: 3.9 Consensus size: 106
9788 AAAATCGGGA
* * * * * *
9798 TTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCC--CGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTG
* * *
9863 GAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAACAGGG
64 GAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACAGGG
* *
9906 TTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTG
1 TTGGAGTATCCCCGA--AAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTG
* * *
9971 GAAATAAAATCGGAGTTGGAGTAT-CCC-C-G-ATTAA-AGGAAAA
64 GAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACAGG---G
* ** * *
10012 TTGGCGT-T--TTGAAAATAAAACCAGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT
1 TTGGAGTATCCCCGAAAAT--AACGAGG-TTGGAGTATCCCCGATTGT-GAAAAATTAGTATTTT
* * * * *
10074 AGCG--ATAAAACCAGAGTTGGAGCATCCCCTCGAAAATAACGGGG
62 TG-GAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACAGGG
* * * * *
10118 TTGGAGTATCCCCGATAATTAACGGGGTTGGAGTATCCTCGATTGTGAAGAAATTGGTGTTTTTT
1 TTGGAGTATCCCCGA-AAATAACGAGGTTGGAGTATCCCCGATTGTGAA-AAATT--AGTATTTT
* *
10183 TGGAAATAAAATCGGAGTTAGAGTATCCCC
62 TGGAAATAAAACCGGAGTTGGAGTATCCCC
10213 GATTATAGAA
Statistics
Matches: 241, Mismatches: 42, Indels: 46
0.73 0.13 0.14
Matches are distributed among these distances:
101 4 0.02
103 11 0.05
104 40 0.17
105 20 0.08
106 21 0.09
107 27 0.11
108 83 0.34
109 11 0.05
110 24 0.10
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.28
Consensus pattern (106 bp):
TTGGAGTATCCCCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGGA
AATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACAGGG
Found at i:10002 original size:52 final size:52
Alignment explanation
Indices: 9933--10102 Score: 159
Period size: 52 Copynumber: 3.3 Consensus size: 52
9923 AAATAACGAG
* * * *
9933 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGG-AGTTTTGAAAATAAAACCAGGA
** * *
9985 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGAGTTTTGAAAATAAAACCAGGA
* * **
10038 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCGATAAAACCA-GA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGAGTTTTGA-AAATAAAACCAGGA
*
10089 GTTGGAGCATCCCC
1 GTTGGAGTATCCCC
10103 TCGAAAATAA
Statistics
Matches: 97, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
51 3 0.03
52 82 0.85
53 12 0.12
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.29
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGAGTTTTGAAAATAAAACCAGGA
Found at i:10121 original size:28 final size:28
Alignment explanation
Indices: 10089--10155 Score: 93
Period size: 27 Copynumber: 2.4 Consensus size: 28
10079 TAAAACCAGA
*
10089 GTTGGAGCATCCCCTCGA-AAATAACGGG
1 GTTGGAGTATCCCC-CGATAAATAACGGG
*
10117 GTTGGAGTAT-CCCCGATAATTAACGGG
1 GTTGGAGTATCCCCCGATAAATAACGGG
10144 GTTGGAGTATCC
1 GTTGGAGTATCC
10156 TCGATTGTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 3 0.09
27 22 0.63
28 10 0.29
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (28 bp):
GTTGGAGTATCCCCCGATAAATAACGGG
Found at i:10123 original size:212 final size:213
Alignment explanation
Indices: 9877--10272 Score: 602
Period size: 212 Copynumber: 1.9 Consensus size: 213
9867 TAAAGCCGGG
* * *
9877 GTTGGAGTATCCCCTCGGAAGTAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTA
1 GTTGGAGCATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGAT-AAATAACGAGGTTGGAGTA
*
9942 TCCTCGATTGTGAA-AAATT-G-GTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTA
65 TCCTCGATTGTGAAGAAATTGGTGTATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTA
* * *
10004 AAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTGGAAAAATTAG
130 AA-GAAAATTAGCGTTTTGAAAATAAAACC-GGAGTTAGAATATCCCCGATTGTGGAAAAATTAG
10068 TGTTTTAGCGATAAAACCAGA
193 TGTTTTAGCGATAAAACCAGA
* * *
10089 GTTGGAGCATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATAATTAACGGGGTTGGAGTAT
1 GTTGGAGCATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATAAATAACGAGGTTGGAGTAT
* *
10154 CCTCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAT
66 CCTCGATTGTGAAGAAATTGGTGTATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAA
* * *
10219 AGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTAGAATATCCTCGATTGTGGA
131 AGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTAGAATATCCCCGATTGTGGA
10273 GAATTGATAA
Statistics
Matches: 165, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
211 31 0.19
212 49 0.30
213 44 0.27
214 41 0.25
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (213 bp):
GTTGGAGCATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATAAATAACGAGGTTGGAGTAT
CCTCGATTGTGAAGAAATTGGTGTATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAA
AGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTAGAATATCCCCGATTGTGGAAAAATTAGTGT
TTTAGCGATAAAACCAGA
Found at i:12648 original size:13 final size:13
Alignment explanation
Indices: 12630--12655 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12620 ACAAAGATCC
12630 ATGTATCGATACA
1 ATGTATCGATACA
12643 ATGTATCGATACA
1 ATGTATCGATACA
12656 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:12651 original size:33 final size:33
Alignment explanation
Indices: 12609--12675 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
12599 AAAATTTCCA
***
12609 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
12642 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
12675 A
1 A
12676 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:12719 original size:19 final size:18
Alignment explanation
Indices: 12695--12762 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
12685 CAGTAGCTAA
12695 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
12714 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
12729 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
12746 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
12763 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:12735 original size:13 final size:13
Alignment explanation
Indices: 12717--12741 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12707 ACAATACTTA
12717 TGTATCGATACAT
1 TGTATCGATACAT
12730 TGTATCGATACA
1 TGTATCGATACA
12742 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:12739 original size:32 final size:32
Alignment explanation
Indices: 12698--12760 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
12688 TAGCTAATTA
*
12698 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
12730 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
12761 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Done.