Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1885
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: 11060
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Found at i:1250 original size:19 final size:18
Alignment explanation
Indices: 1226--1288 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1216 AAACCATAAA
1226 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
1245 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
1258 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
1277 TGTATCGATACA
1 TGTATCGATACA
1289 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:1263 original size:13 final size:13
Alignment explanation
Indices: 1245--1269 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1235 ACATAAGTGT
1245 TGTATCGATACAA
1 TGTATCGATACAA
1258 TGTATCGATACA
1 TGTATCGATACA
1270 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1265 original size:32 final size:32
Alignment explanation
Indices: 1224--1296 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
1214 ACAAACCATA
1224 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
1256 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
1288 AATGTATCG
1 AATGTATCG
1297 CTACGAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:1339 original size:21 final size:21
Alignment explanation
Indices: 1313--1353 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1303 AGCTACTGCC
1313 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
1334 AAGGAAATGTATCGATACAT
1 AAGGAAATGTATCGATACAT
1354 CGATCTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.27
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:3829 original size:52 final size:51
Alignment explanation
Indices: 3703--4098 Score: 203
Period size: 51 Copynumber: 7.6 Consensus size: 51
3693 TTAAGTTTCT
* * * *
3703 CAATTGTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTT-CAAAACAC
1 CAATTTTTCACAATCGAGGATACTCCAACCCCGATTTT-TTTTCCAAAACAC
* ** * *
3754 CAATTTTCCTTTAATC-ACCGATACTCCAACTCCGATTTTTTTTCCAAAAACAC
1 CAATTTTTC-ACAATCGA-GGATACTCCAACCCCGATTTTTTTTCC-AAAACAC
* ** ** * *
3807 CAATTTTTCACAATCGAGGATACTCCAACCTCG-TTATTTCATCGGGGATACTC
1 CAATTTTTCACAATCGAGGATACTCCAACCCCGATT-TTTTTTC--CAAAACAC
**** * * * * *
3860 CAGCCCCGTT-AC-CTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAATAT
1 CA--ATTTTTCACAAT-CGA--GGATACTCCAACCCCGATTTTTTTTCCAAAACAC
** * * * * *
3914 TTATTTCTCATAATCGGGGATACTCCAACCCC-AGTTTTATTTCTAAAACAC
1 CAATTTTTCACAATCGAGGATACTCCAACCCCGA-TTTTTTTTCCAAAACAC
* * * * *
3965 TAATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTT-TAAAACAC
1 CAATTTTTCACAATCGAGGATACTCCAACCCCGATTTT-TTTTCCAAAACAC
* ** * * * *
4016 CAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAAACAC
1 CAATTTTTC-ACAATCGAGGATACTCCAACCCCGATTTTTTTTC-CAAAACAC
4069 CAATTTTTCACAATCGAGGATACTCCAACC
1 CAATTTTTCACAATCGAGGATACTCCAACC
4099 TCGTTATTTC
Statistics
Matches: 256, Mismatches: 67, Indels: 43
0.70 0.18 0.12
Matches are distributed among these distances:
50 1 0.00
51 92 0.36
52 92 0.36
53 41 0.16
54 8 0.03
55 2 0.01
56 19 0.07
57 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (51 bp):
CAATTTTTCACAATCGAGGATACTCCAACCCCGATTTTTTTTCCAAAACAC
Found at i:3941 original size:51 final size:51
Alignment explanation
Indices: 3878--4098 Score: 257
Period size: 51 Copynumber: 4.3 Consensus size: 51
3868 TTACCTCCGA
* * * * *
3878 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTTA-TTTCTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTC-CATAATC
*
3929 GGGGATACTCCAACCCC-AGTTTTATTTCTAAAACACTAATTTTCCACAATC
1 GGGGATACTCCAACCCCGA-TTTTATTTCTAAAACACTAATTTTCCATAATC
* * * *
3980 GGGGATACTCCAACCCCGGTTTTATTTTTAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTCC-ATAATC
* * * *
4032 GGGGATACTCCAACTCCGATTTTATTTCTAAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAACACTAATTTTCCATAATC
*
4084 GAGGATACTCCAACC
1 GGGGATACTCCAACC
4099 TCGTTATTTC
Statistics
Matches: 146, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
50 1 0.01
51 79 0.54
52 51 0.35
53 15 0.10
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTCCATAATC
Found at i:4184 original size:262 final size:262
Alignment explanation
Indices: 3714--4205 Score: 894
Period size: 262 Copynumber: 1.9 Consensus size: 262
3704 AATTGTTCAT
3714 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCACCGATACT
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCACCGATACT
*
3779 CCAACTCCGATTTTTTTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
66 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
*
3844 TTCATCGGGGATACTCCAGCCCCGTTACCTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAA
131 TTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAA
*
3909 AATATTTATTTCTCATAATCGGGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATTTTCC
196 AATATTGATTTCTCATAATCGGGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATTTTCC
3974 AC
261 AC
* ***
3976 AATCGGGGATACTCCAACCCCGGTTTTATTTTTAAAACACCAATTTTCCTTTAATCGGGGATACT
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCACCGATACT
*
4041 CCAACTCCGATTTTATTTCTAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
66 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
*
4106 TTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGACTTTATTTCTAA
131 TTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAA
*
4171 AATATTGATTTCTCATAATTGGGGATACTCCAACC
196 AATATTGATTTCTCATAATCGGGGATACTCCAACC
4206 TCGTTATTTC
Statistics
Matches: 220, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
262 220 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (262 bp):
AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCACCGATACT
CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
TTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGACTTTATTTCCAA
AATATTGATTTCTCATAATCGGGGATACTCCAACCCCAGTTTTATTTCTAAAACACTAATTTTCC
AC
Found at i:4223 original size:107 final size:108
Alignment explanation
Indices: 4032--4236 Score: 277
Period size: 107 Copynumber: 1.9 Consensus size: 108
4022 TCCTTTAATC
* * *
4032 GGGGATACTCCAACTCCGATTTTATTTCTAAAAACACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCTAAAAACACCAATTTCTCACAATCGAGGATACTCCAA
**
4097 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGA
66 CCTCGTTATTTCAGAGGGGATACTCCAACCCCGTTACCTCCGA
* *** * * *
4140 GGGGATACTCCAACCCCGACTTTATTTCT-AAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCTAAAAACACCAATTTCTCACAATCGAGGATACTCCAA
* *
4204 CCTCGTTATTTCCGAGGGGATACTCCAATCCCG
66 CCTCGTTATTTCAGAGGGGATACTCCAACCCCG
4237 ATTTTATTTC
Statistics
Matches: 83, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
107 56 0.67
108 27 0.33
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (108 bp):
GGGGATACTCCAACCCCGACTTTATTTCTAAAAACACCAATTTCTCACAATCGAGGATACTCCAA
CCTCGTTATTTCAGAGGGGATACTCCAACCCCGTTACCTCCGA
Found at i:4243 original size:79 final size:79
Alignment explanation
Indices: 4111--4345 Score: 269
Period size: 79 Copynumber: 3.0 Consensus size: 79
4101 GTTATTTCAT
** *
4111 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGACTTTATTTCTAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAATAT
* *
4176 TGATTTCTCATAAT
66 TAATTTCTCATAAC
* * *
4190 TGGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAATCCCGATTTTATTTCCT--AATC
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTT-CTAAAAT-
* * *
4253 ATCAATTTTTCACAAC
64 ATTAATTTCTCATAAC
* * * * *
4269 CGGGGATACTCCAACCCCATTATTTTCAAGGGGATACTCCAACCCCG-TTATTATCTCCAAAATA
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATT-TTATTTCTAAAATA
4333 TTAAATTTCTCAT
65 TT-AATTTCTCAT
4346 CGGGACATAT
Statistics
Matches: 128, Mismatches: 22, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
78 6 0.05
79 109 0.85
80 13 0.10
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAATAT
TAATTTCTCATAAC
Done.