Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1437
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: 37757
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3014 original size:40 final size:40
Alignment explanation
Indices: 2954--3137 Score: 230
Period size: 40 Copynumber: 4.6 Consensus size: 40
2944 TATTCGAATG
*
2954 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
2994 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * * *
3034 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
*
3074 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
*
3114 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
3138 CTTGTGCGAG
Statistics
Matches: 124, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
39 1 0.01
40 120 0.97
41 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:3087 original size:80 final size:80
Alignment explanation
Indices: 2954--3173 Score: 279
Period size: 80 Copynumber: 2.8 Consensus size: 80
2944 TATTCGAATG
* * * *
2954 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGCTAAGATCCCGAAGGC
* *
3018 ATTTGTGCGAGTTG-CT
65 ATTTATGCGAG-TGACC
*
3034 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAG-TCCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGCTAAGATCCCGAAGGC
*
3098 ATTTATGCTAGTGACC
65 ATTTATGCGAGTGACC
* * *
3114 ATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGCTAAGATCCCGAAG
3174 ATACTTGGGT
Statistics
Matches: 124, Mismatches: 13, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
78 14 0.11
79 20 0.16
80 90 0.73
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGCTAAGATCCCGAAGGCA
TTTATGCGAGTGACC
Found at i:11130 original size:40 final size:40
Alignment explanation
Indices: 11070--11253 Score: 244
Period size: 40 Copynumber: 4.6 Consensus size: 40
11060 CATTCGAATG
* *
11070 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
* * * * *
11110 ATATCCGGACTGAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGACT
* * *
11150 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
* *
11190 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
11230 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
11254 CTTGTGCGAG
Statistics
Matches: 123, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 120 0.98
41 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
Found at i:11210 original size:80 final size:79
Alignment explanation
Indices: 11070--11289 Score: 266
Period size: 80 Copynumber: 2.8 Consensus size: 79
11060 CATTCGAATG
* * * *
11070 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTGAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGACTAAG-TCCCGAAGGC
* *
11134 ATTTGTGCGAGTTG-CT
64 ATTTATGCGAG-TGACC
* *
11150 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGACTAAGTCCCGAAGGCA
*
11215 TTTATGCTAGTGACC
65 TTTATGCGAGTGACC
* * * *
11230 ATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCC-GACTAAATCCCGAAG
1 ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGACTAAGTCCCGAAG
11290 ATACTTGGGT
Statistics
Matches: 122, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
78 13 0.11
79 20 0.16
80 89 0.73
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGACTAAGTCCCGAAGGCAT
TTATGCGAGTGACC
Found at i:17356 original size:32 final size:32
Alignment explanation
Indices: 17315--17376 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
17305 ATCGTAGACT
17315 ATAAAAATACAATAAAAATAAATTTTCTTACC
1 ATAAAAATACAATAAAAATAAATTTTCTTACC
17347 ATAAAAATACAATAAAAATAAATTTTCTTA
1 ATAAAAATACAATAAAAATAAATTTTCTTA
17377 TGTCAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (32 bp):
ATAAAAATACAATAAAAATAAATTTTCTTACC
Found at i:20727 original size:12 final size:14
Alignment explanation
Indices: 20712--20743 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20702 GTGAGAACAC
20712 ATGTGTA-G-TACT
1 ATGTGTAGGCTACT
20724 ATGTGTAGGCTACT
1 ATGTGTAGGCTACT
20738 ATGTGT
1 ATGTGT
20744 TTAAGACAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 1 0.06
14 10 0.56
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (14 bp):
ATGTGTAGGCTACT
Found at i:20830 original size:50 final size:50
Alignment explanation
Indices: 20766--21002 Score: 237
Period size: 50 Copynumber: 4.7 Consensus size: 50
20756 TAGGTCACGT
*
20766 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTGATAGGTCGCAC
1 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCAC
* * ** * **
20816 GTGTAGTACAAAGTGCAGGCTACTATGCATACCCG-TT-A-ACTTCGATCAC
1 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCG--CAC
* * * * * *
20865 GTGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATGGATAAGTCACAT
1 --GTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCAC
* * * *
20917 GTGTGGTACTAAGTGCAAGCTACTACGTGTATCAGATTGATAGGTCGCAT
1 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCAC
* *
20967 GTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
1 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA
21003 GAGCTTCGGT
Statistics
Matches: 152, Mismatches: 28, Indels: 14
0.78 0.14 0.07
Matches are distributed among these distances:
47 4 0.03
48 1 0.01
49 5 0.03
50 105 0.69
51 30 0.20
52 3 0.02
53 1 0.01
54 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (50 bp):
GTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCAC
Found at i:20890 original size:101 final size:101
Alignment explanation
Indices: 20760--20941 Score: 274
Period size: 101 Copynumber: 1.8 Consensus size: 101
20750 CAGTTTTAGG
* * * *
20760 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTGATAGGTCGCACGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGATAAGTCACACGTGTAGTAC
*
20825 AAAGTGCAGGCTACTATGCATACCCGTTAACTTCGA
66 AAAGTGCAAGCTACTATGCATACCCGTTAACTTCGA
* * * *
20861 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATGGATAAGTCACATGTGTGGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGATAAGTCACACGTGTAGTAC
*
20926 TAAGTGCAAGCTACTA
66 AAAGTGCAAGCTACTA
20942 CGTGTATCAG
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 71 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (101 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGGATAAGTCACACGTGTAGTAC
AAAGTGCAAGCTACTATGCATACCCGTTAACTTCGA
Found at i:20989 original size:151 final size:153
Alignment explanation
Indices: 20713--20999 Score: 416
Period size: 151 Copynumber: 1.9 Consensus size: 153
20703 TGAGAACACA
* * * ** * *
20713 TGTGTAGTACTATGTGTAGGCTACTATGTGTTTAAGACAGTTTTAGGTCACGTGTGTAGTACTAA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTATAAGACAGTGATAAGTCACATGTGTAGTACTAA
* *
20778 GTGCAGGCTACTACGTGTACCGGATTGATAGGTCGCACGTGTAGTACAAAGTGCAGGCTACTATG
66 GTGCAAGCTACTACGTGTACCAGATTGATAGGTCGCACGTGTAGTACAAAGTGCAGGCTACTATG
20843 CATACCCGTTAACTTCGATCACG
131 CATACCCGTTAACTTCGATCACG
* * *
20866 TGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGA-TG-GATAAGTCACATGTGTGGTACTAA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTATAAGACAGTGATAAGTCACATGTGTAGTACTAA
* * *
20929 GTGCAAGCTACTACGTGTATCAGATTGATAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATG
66 GTGCAAGCTACTACGTGTACCAGATTGATAGGTCGCACGTGTAGTACAAAGTGCAGGCTACTATG
*
20994 CGTACC
131 CATACC
21000 AGAGAGCTTC
Statistics
Matches: 118, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
151 84 0.71
152 1 0.01
153 33 0.28
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (153 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGTGTATAAGACAGTGATAAGTCACATGTGTAGTACTAA
GTGCAAGCTACTACGTGTACCAGATTGATAGGTCGCACGTGTAGTACAAAGTGCAGGCTACTATG
CATACCCGTTAACTTCGATCACG
Found at i:21818 original size:180 final size:180
Alignment explanation
Indices: 21561--21897 Score: 469
Period size: 180 Copynumber: 1.9 Consensus size: 180
21551 CTGAGATCTA
* * *
21561 TACCATGAGATAAATAATTTTTAGTGAAGAAAAATCGGAACTGTCGAACAGTGAAACAGGGGTAT
1 TACCATGAGATAAATAATTTTTAGTAAAGAAAAATCAGAACTATCGAACAGTGAAACAGGGGTAT
* *
21626 CTTTAATGAATAAACTGTACTAATTTGCTAAACCAAAAATTAAT-AAAATTTTATGCTAATAATA
66 CTTTAATGAATAAACTGTACTAATTGGCTAAACCAAAAATT-ATGAAAATTTTATGCTAAGAATA
* * * * *
21690 TATGTTAGTCTATTTTCTTGGAGAATTAGTAGTTCTTAATTTGGAGTCCCG
130 TATATGAGTCTAGTTTCTGGGAAAATTAGTAGTTCTTAATTTGGAGTCCCG
* ** * * * * *
21741 TACCATGAGATAAATAATTTTTAGTAAAGAGAGTTCAGAACTATTGGACAGTGAAATAGTGGTGT
1 TACCATGAGATAAATAATTTTTAGTAAAGAAAAATCAGAACTATCGAACAGTGAAACAGGGGTAT
* * *
21806 CTTTAATGAATAAATTGTACTAATTGGCTAAACCAAAAATTATGAAAATTTTATGGTAAGAGTAT
66 CTTTAATGAATAAACTGTACTAATTGGCTAAACCAAAAATTATGAAAATTTTATGCTAAGAATAT
21871 ATATGAGTCTAGTTTCTGGGAAAATTA
131 ATATGAGTCTAGTTTCTGGGAAAATTA
21898 TTGGATATTA
Statistics
Matches: 135, Mismatches: 21, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
179 2 0.01
180 133 0.99
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (180 bp):
TACCATGAGATAAATAATTTTTAGTAAAGAAAAATCAGAACTATCGAACAGTGAAACAGGGGTAT
CTTTAATGAATAAACTGTACTAATTGGCTAAACCAAAAATTATGAAAATTTTATGCTAAGAATAT
ATATGAGTCTAGTTTCTGGGAAAATTAGTAGTTCTTAATTTGGAGTCCCG
Found at i:24779 original size:29 final size:29
Alignment explanation
Indices: 24740--24818 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
24730 CTTAATAATC
*
24740 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
24770 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
24799 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
24819 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Done.