Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1800
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: 12125
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Found at i:899 original size:37 final size:39
Alignment explanation
Indices: 776--994 Score: 214
Period size: 40 Copynumber: 5.6 Consensus size: 39
766 TTGAATGCTG
* * * * * *
776 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
816 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGGTAC-AAG
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAAA
*
855 TCC-GGTTAAGCCCCGAAGGCATTGTGCGAG-TA-TAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
*
891 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
931 TCCGGGTTAAGTCCCGAAGGCATTGTGGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGT-GCGAGTTACTAAA
* * *
971 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
995 TGAACGAGGG
Statistics
Matches: 152, Mismatches: 18, Indels: 18
0.81 0.10 0.10
Matches are distributed among these distances:
36 7 0.05
37 28 0.18
38 21 0.14
39 8 0.05
40 81 0.53
41 7 0.05
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:8452 original size:40 final size:40
Alignment explanation
Indices: 8317--8539 Score: 233
Period size: 39 Copynumber: 5.7 Consensus size: 40
8307 TTGAATGCTG
* * *
8317 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAA
* *
8357 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
8396 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
8436 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* * *
8475 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
* *
8514 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
8540 AACGAGGAGC
Statistics
Matches: 156, Mismatches: 20, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
38 7 0.04
39 85 0.54
40 53 0.34
41 10 0.06
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:8561 original size:78 final size:79
Alignment explanation
Indices: 8396--8572 Score: 205
Period size: 78 Copynumber: 2.3 Consensus size: 79
8386 GAGATACAAT
* * * *
8396 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
8461 GTGCGAGTATTAAA
66 GAACGAGGACTAAA
* * * *
8475 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
8539 GAACGAGGAGCTATA
66 GAACGAGGA-CTAAA
*
8554 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
8573 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
78 58 0.70
79 25 0.30
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGGACTAAA
Found at i:10721 original size:40 final size:40
Alignment explanation
Indices: 10607--10834 Score: 327
Period size: 40 Copynumber: 5.7 Consensus size: 40
10597 TATTCGGATG
* *
10607 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
** *
10647 A-ATTTCGGGCTAAG-CCCGAAGGAATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
10686 ATAACCGGGCTAAGTCCCGAAGGTATTTGTACGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
10726 ATAACCGGGCTAATTCCCGAAGGCATTTGTGTGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
10766 ATAA-CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
10805 ATAAACTGGGCTAAGTCCCGAAGGCATTTG
1 AT-AACCGGGCTAAGTCCCGAAGGCATTTG
10835 AGCAAGTAGC
Statistics
Matches: 167, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 68 0.41
40 76 0.46
41 23 0.14
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:10738 original size:79 final size:79
Alignment explanation
Indices: 10607--10834 Score: 316
Period size: 79 Copynumber: 2.9 Consensus size: 79
10597 TATTCGGATG
* * ** *
10607 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTTCGGGCTAAGCCCGAAGGAA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-ACCGGGCTAAGCCCGAAGGCA
10671 TTTGTGCGAGTTACT
65 TTTGTGCGAGTTACT
* * *
10686 ATAACCGGGCTAAGTCCCGAAGGTATTTGTACGAGTTACTATAACCGGGCTAATTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAA-GCCCGAAGGCA
*
10751 TTTGTGTGAGTTACT
65 TTTGTGCGAGTTACT
*
10766 ATAA-CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAACTGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AACCGGGCTAAG-CCCGAAGGC
10830 ATTTG
64 ATTTG
10835 AGCAAGTAGC
Statistics
Matches: 132, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
79 80 0.61
80 52 0.39
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGCCCGAAGGCAT
TTGTGCGAGTTACT
Done.