Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3187
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: 23379
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Found at i:1202 original size:151 final size:151
Alignment explanation
Indices: 516--1312 Score: 1204
Period size: 153 Copynumber: 5.2 Consensus size: 151
506 ATTTTGACCT
**
516 TTTGTTCGTATTTTTTTTTAGATTTTATTACTTTAAAAAAATATATTATTTTCTAATTTTATTA-
1 TTTGTTCGTATTTTTTTTCGGATTTTATTACTTTAAAAAAATATATTATTTTCTAATTTTATTAT
* * * *
580 TTTACATTATTTTAGTACATTATTTTTGAAATGTATTCATTTAGTTTGATTTTTAAATAAATTTA
66 TTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTA
*
645 AAAAAACCCTTATTTCGGCCC
131 AAAAAACCCTTATTTCGGCCA
* * * *
666 TTTGTTCGTATTTTTTTTCGAATTTTATTACTTTCAATAAAATATATTCTTTTCTTATTTTATTA
1 TTTGTTCGTATTTTTTTTCGGATTTTATTACTTT-AAAAAAATATATTATTTTCTAATTTTATTA
*
731 TTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAAATAAATT
65 TTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTT-AAATAAATT
* *
796 TAAAAAAAACTCTTATTTCGGCCT
129 T-AAAAAAACCCTTATTTCGGCCA
** *
820 TTTGTTCGTATTTTTTCCCGGATTTTATTACTTTAAAACAATATATTATTTTCTAATTTTATTAT
1 TTTGTTCGTATTTTTTTTCGGATTTTATTACTTTAAAAAAATATATTATTTTCTAATTTTATTAT
* * *
885 TTTACATTATTTTAGTACATTATTTTTGAAATGTATTCATTTAGTGTGTGTTTTAAATAAATTTA
66 TTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTT-
*
950 AAAAAAAACCCTTATTTCGGCCC
130 -AAAAAAACCCTTATTTCGGCCA
* * * * *
973 TTTGTTCGTATTTTTTTCCGAATTTTATTTCTTTCAATAAAAATATATTATTTTTTCATTTTATT
1 TTTGTTCGTATTTTTTTTCGGATTTTATTACTTT-AA-AAAAATATATTATTTTCTAATTTTATT
*
1038 ATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAATGTGTTTTTTAAATAAA-T
64 ATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATT
*
1102 TAAAAAAA-CCTTATTTCTGCCA
129 TAAAAAAACCCTTATTTCGGCCA
*
1124 TTTGTTCGTATTTTTTTCTCCGGATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATT
1 TTTGTTCGTATTTTTTT-T-CGGATTTTATTACTTTAAAAAAATATATTATTTTCTAATTTTATT
*
1189 ATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTTATTTAGTGTGTTTTTTAAATAAATT
64 ATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAA-T
1254 TTAAAAAAACCCTTATTTCGGCCA
128 TTAAAAAAACCCTTATTTCGGCCA
1278 TTTGTTCGTATTTTTTTCTCGGATTTTATTACTTT
1 TTTGTTCGTATTTTTTT-TCGGATTTTATTACTTT
1313 TAATTTATTT
Statistics
Matches: 588, Mismatches: 47, Indels: 21
0.90 0.07 0.03
Matches are distributed among these distances:
150 31 0.05
151 141 0.24
152 68 0.12
153 178 0.30
154 87 0.15
155 83 0.14
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.53
Consensus pattern (151 bp):
TTTGTTCGTATTTTTTTTCGGATTTTATTACTTTAAAAAAATATATTATTTTCTAATTTTATTAT
TTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTA
AAAAAACCCTTATTTCGGCCA
Found at i:1619 original size:155 final size:153
Alignment explanation
Indices: 1314--1696 Score: 579
Period size: 155 Copynumber: 2.5 Consensus size: 153
1304 TATTACTTTT
* *
1314 AATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATGATGTACTAAAATAGTGTAAAAT
1 AATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT
* * *
1379 AATAAAATACAAAAATAATATATTTTTTAAAAGTAATAAAATCTGAGAAAAAAATACGAACAAAT
66 AATAAAATACAAAAATAATATATTTTTTAAAAGAAATAAAATCGGAGAAAAAAATACGAACAAAG
*
1444 GGCCGAAATAAGGGTTTTTTTAAA
131 GGCCAAAATAAGGG-TTTTTTAAA
1468 AATTTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
1 AA-TTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
* *
1533 TAATAAAATGCAAAAATAATATATTTTTATTGAAAGAAATAAAATCCGGA-AAAAAAATACGAAC
65 TAATAAAATACAAAAATAATATA-TTTT-TTAAAAGAAATAAAAT-CGGAGAAAAAAATACGAAC
**
1597 AAAGGGCCAAAATAAGGGTTTTTTTTA
127 AAAGGGCCAAAATAAGGGTTTTTTAAA
* * * * *
1624 AATTTATTTAAAAATCAAACTAAATGAATACATTTCAAAAATAATGTACTAAAATAATGTAAAAT
1 AATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT
1689 AATAAAAT
66 AATAAAAT
1697 CCGGGAAAAA
Statistics
Matches: 210, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
154 2 0.01
155 148 0.70
156 13 0.06
157 44 0.21
158 3 0.01
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.30
Consensus pattern (153 bp):
AATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT
AATAAAATACAAAAATAATATATTTTTTAAAAGAAATAAAATCGGAGAAAAAAATACGAACAAAG
GGCCAAAATAAGGGTTTTTTAAA
Found at i:1770 original size:118 final size:119
Alignment explanation
Indices: 1570--1814 Score: 458
Period size: 118 Copynumber: 2.1 Consensus size: 119
1560 TATTGAAAGA
1570 AATAAAATCCGGAAAAAAAATACGAACAAAGGGCCAAAATAAGGGTTTTTTTTAAATTTATTTAA
1 AATAAAATCCGGAAAAAAAATACGAACAAAGGGCCAAAATAAGGGTTTTTTTTAAATTTATTTAA
1635 AAATCAAACTAAATGAATACATTTCAAAAATAATGTACTAAAATAATGTAAAAT
66 AAATCAAACTAAATGAATACATTTCAAAAATAATGTACTAAAATAATGTAAAAT
*
1689 AATAAAATCCGGGAAAAAAGATACGAACAAAGGGCCAAAATAAGGG-TTTTTTT-AATTTATTTA
1 AATAAAATCC-GGAAAAAAAATACGAACAAAGGGCCAAAATAAGGGTTTTTTTTAAATTTATTTA
1752 AAAATCAAACTAAATGAATACATTTCAAAAATAATGTACTAAAATAATGTAAAAT
65 AAAATCAAACTAAATGAATACATTTCAAAAATAATGTACTAAAATAATGTAAAAT
1807 AATAAAAT
1 AATAAAAT
1815 ACGAAAATAG
Statistics
Matches: 124, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
118 73 0.59
119 17 0.14
120 34 0.27
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.27
Consensus pattern (119 bp):
AATAAAATCCGGAAAAAAAATACGAACAAAGGGCCAAAATAAGGGTTTTTTTTAAATTTATTTAA
AAATCAAACTAAATGAATACATTTCAAAAATAATGTACTAAAATAATGTAAAAT
Found at i:7921 original size:2 final size:2
Alignment explanation
Indices: 7914--7938 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7904 TTAGATCCCT
7914 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
7939 TCAAACTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17734 original size:94 final size:94
Alignment explanation
Indices: 17573--17760 Score: 342
Period size: 94 Copynumber: 2.0 Consensus size: 94
17563 TCCCAACCTG
*
17573 AAACAGACATAAAACAGTAAATTTTAAATATGTATATTATGAAAAAAGAAAGCCATGTAGACATT
1 AAACAGACATAAAACAGTAAAATTTAAATATGTATATTATGAAAAAAGAAAGCCATGTAGACATT
17638 TACAATCACTGTCCGATAGTTAGCAAAGA
66 TACAATCACTGTCCGATAGTTAGCAAAGA
*
17667 AAACAGACATAGAACAG-AAAATTTAAATATGTATATTATGACAAAAAGAAAGCCATGTAGACAT
1 AAACAGACATAAAACAGTAAAATTTAAATATGTATATTATGA-AAAAAGAAAGCCATGTAGACAT
17731 TTACAATCACTGTCCGATAGTTAGCAAAGA
65 TTACAATCACTGTCCGATAGTTAGCAAAGA
17761 TAATAAAAGT
Statistics
Matches: 91, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
93 23 0.25
94 68 0.75
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.24
Consensus pattern (94 bp):
AAACAGACATAAAACAGTAAAATTTAAATATGTATATTATGAAAAAAGAAAGCCATGTAGACATT
TACAATCACTGTCCGATAGTTAGCAAAGA
Found at i:18522 original size:55 final size:55
Alignment explanation
Indices: 18438--18547 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
18428 AATAAAAGAA
18438 AACCAAAAGCAATGCTCATACCAGCAAAAGGTCCAATCCACTAATATTTTATCCC
1 AACCAAAAGCAATGCTCATACCAGCAAAAGGTCCAATCCACTAATATTTTATCCC
18493 AACCAAAAGCAATGCTCATACCAGCAAAAGGTCCAATCCACTAATATTTTATCCC
1 AACCAAAAGCAATGCTCATACCAGCAAAAGGTCCAATCCACTAATATTTTATCCC
18548 CTTACCTTGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.40, C:0.29, G:0.09, T:0.22
Consensus pattern (55 bp):
AACCAAAAGCAATGCTCATACCAGCAAAAGGTCCAATCCACTAATATTTTATCCC
Done.