Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1300
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: 31251
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Found at i:1681 original size:40 final size:39
Alignment explanation
Indices: 1514--1734 Score: 220
Period size: 39 Copynumber: 5.7 Consensus size: 39
1504 TTGAATGCTG
* * * *
1514 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGT-TATAAA
* * * *
1554 TCC-GGATAAGAT-CCGAAGGCATTTGTGCGAGATACAAGT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATAA-A
*
1593 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAG-TATAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATAAA
*
1630 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-TAAA
*
1670 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-TAAA
* * *
1709 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
1735 AACGAGGAGC
Statistics
Matches: 153, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
37 11 0.07
38 24 0.16
39 72 0.47
40 46 0.30
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATAAA
Found at i:1752 original size:79 final size:78
Alignment explanation
Indices: 1593--1767 Score: 187
Period size: 79 Copynumber: 2.3 Consensus size: 78
1583 AGATACAAGT
* * * *
1593 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGTATAAATCCGGGTTAAGTCCCGAAGGCATTCGT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGTATAAAACCGGGCTAAGTCCCGAAGGCATTCGA
* * *
1657 GCGAGTTATTAAA
66 ACGAGTGACTAAA
* * *
1670 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAG-TA-TAAAACCGGGCTAAGTCCCGAAGGCATTC
*
1734 GAACGAG-GAGCTATA
64 GAACGAGTGA-CTAAA
*
1749 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
1768 TACGTGATTT
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
77 20 0.24
78 26 0.32
79 36 0.44
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.25
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGTATAAAACCGGGCTAAGTCCCGAAGGCATTCGA
ACGAGTGACTAAA
Found at i:9187 original size:39 final size:40
Alignment explanation
Indices: 9052--9275 Score: 242
Period size: 40 Copynumber: 5.7 Consensus size: 40
9042 TTGAATGCTG
* * * *
9052 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
9092 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
* *
9132 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAG-TACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
9171 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
9211 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
9250 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
9276 AACGAGGAGC
Statistics
Matches: 156, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
39 66 0.42
40 82 0.53
41 8 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:9192 original size:79 final size:78
Alignment explanation
Indices: 9052--9275 Score: 254
Period size: 79 Copynumber: 2.8 Consensus size: 78
9042 TTGAATGCTG
* * * *
9052 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGC-GAGT-ACTAAATCCGGGCTAAG-TCCCGAAGGCATT
*
9116 TGTGCGAGATA-CAAGT
63 TGTGCGAGATATCAA-A
* * *
9132 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGTACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
1 TCCGGGTTAAGTCCCGAAGG-CTTTGTGCGAGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
* *
9197 TGCGAGTTATTAAA
65 TGCGAGATATCAAA
* * * *
9211 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAG-TACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
9276 AACGAGGAGC
Statistics
Matches: 123, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
78 10 0.08
79 82 0.67
80 23 0.19
81 8 0.07
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGATATCAAA
Found at i:9293 original size:79 final size:79
Alignment explanation
Indices: 9132--9308 Score: 198
Period size: 79 Copynumber: 2.3 Consensus size: 79
9122 AGATACAAGT
* * * *
9132 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGTACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
** * *
9197 TGCGAGTTATTAAA
66 AACGAGTGACTAAA
* * *
9211 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAG-TACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
9275 GAACGAG-GAGCTATA
65 GAACGAGTGA-CTAAA
*
9290 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
9309 TACGTGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 25 0.30
79 58 0.70
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
AACGAGTGACTAAA
Found at i:17272 original size:27 final size:27
Alignment explanation
Indices: 17233--17284 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
17223 ATGTTTAAAA
*
17233 ACTTTTTTATTTA-TTACTCTTATTTTC
1 ACTTTTATATTTATTTA-TCTTATTTTC
*
17260 ACTTTTATCTTTATTTATCTTATTT
1 ACTTTTATATTTATTTATCTTATTT
17285 AAGCACTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.67
Consensus pattern (27 bp):
ACTTTTATATTTATTTATCTTATTTTC
Found at i:23321 original size:40 final size:40
Alignment explanation
Indices: 23266--23483 Score: 316
Period size: 40 Copynumber: 5.5 Consensus size: 40
23256 CGGATGATAA
* *
23266 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
23306 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
23346 CCGGGCTAAGTCTCGAAGGCATTTGTGCAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
23386 CCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
23426 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
23466 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
23484 TACTTGGTTT
Statistics
Matches: 162, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
39 17 0.10
40 144 0.89
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Done.