Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2122
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: 15096
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Found at i:4280 original size:40 final size:40
Alignment explanation
Indices: 4225--4413 Score: 333
Period size: 40 Copynumber: 4.7 Consensus size: 40
4215 TGAGCATTGG
4225 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
4265 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGAT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
4305 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
4345 AATATATCCGGGCTAAGACCTGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* *
4385 AATATGTCCGGGCTATGACCCGAAGGCAA
1 AATATATCCGGGCTAAGACCCGAAGGCAA
4414 AGGTGGTTGC
Statistics
Matches: 141, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 141 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (40 bp):
AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
Found at i:5881 original size:41 final size:42
Alignment explanation
Indices: 5794--5922 Score: 183
Period size: 41 Copynumber: 3.1 Consensus size: 42
5784 TACATCGGAG
*
5794 ACCATCGGCACCTCGGTGCTAT-GATGTGCGGGAGCCTCGAGC
1 ACCATCGGCACCTTGGTGCT-TGGATGTGCGGGAGCCTCGAGC
*
5836 ACCATCGGCACCTTGGTACTTGGATGTGC-GGAGCCTCGAGC
1 ACCATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCGAGC
* *
5877 ACCATCGGCACCTTGGTGCATGGATGAGCGGGAGCCTTC-AGC
1 ACCATCGGCACCTTGGTGCTTGGATGTGCGGGAGCC-TCGAGC
5919 ACCA
1 ACCA
5923 AAGCTAAAGT
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
41 39 0.49
42 38 0.48
43 2 0.03
ACGTcount: A:0.19, C:0.30, G:0.32, T:0.19
Consensus pattern (42 bp):
ACCATCGGCACCTTGGTGCTTGGATGTGCGGGAGCCTCGAGC
Found at i:6155 original size:24 final size:24
Alignment explanation
Indices: 6128--6206 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 24
6118 CCGGTTAGGT
*
6128 TCCCGGTGGTGCTCCGGCGATCCG
1 TCCCGGTGGTGCTCCGGCGAACCG
*
6152 TCCCGGCGGTGCTCCGGCGAACCG
1 TCCCGGTGGTGCTCCGGCGAACCG
*
6176 TCCC-GTCGGTGCTCCGGTGAACCG
1 TCCCGGT-GGTGCTCCGGCGAACCG
*
6200 TTCCGGT
1 TCCCGGT
6207 AGCATAGGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
23 1 0.02
24 45 0.94
25 2 0.04
ACGTcount: A:0.06, C:0.38, G:0.35, T:0.20
Consensus pattern (24 bp):
TCCCGGTGGTGCTCCGGCGAACCG
Found at i:6332 original size:43 final size:43
Alignment explanation
Indices: 6211--7358 Score: 1084
Period size: 43 Copynumber: 26.9 Consensus size: 43
6201 TCCGGTAGCA
6211 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
** * * * * *
6254 T-GGTGCTAGGAT-GTGCAGGAGCCCCGGACACCATCGGCAAAC
1 TAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* ** *
6296 TAAGCCCTTGGTATTGCGGGAGCCTCGGGCGCCATCGGC-ACC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* ** *
6338 TCGGTGCTTCGAT-GTGCGGGAGCCTCGGGCACCATCGGCAACC
1 TAGGCCCTT-GGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
6381 TAGGCCCTTGGTCGTGC-GGAGCCTCGGGCACCATCGGC-ACC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* ** * * **
6422 TCGGTGCTATGAT-GTGCGGGAGCCTCGGACACTGTCGGCAACC
1 TAGGCCCT-TGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
*
6465 TAGGCCCTTGGTCGTGCGGGAGCCTCGAGCACCATCGGC-ACC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* ** * * * *
6507 TTGGTGCTTGGAT-GTGCGAGAACCTCGCGTACCATCGGCAACC
1 TAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* * *
6550 TAGGCCCTTGGTCGTGCGAGAGGCTCGGGCACCATCGGCAAAC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* * **
6593 TAAGCCCTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCAAAA
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* * *
6636 TAGGCCCTTGGTCGTTCGGGAGCCTCGGACACCATCGGCAAAC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
*
6679 TAGGCCCTTGGTCGTGCGGGAGCCTCGGCCACCATCGGC-ACC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* ** * * * **
6721 TCGGTGCTATGAT-GGGCGGGAGCCTCGGACACTGTCGGCAACC
1 TAGGCCCT-TGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
*
6764 TAGGCCCTTGGTCGTGCGGGAGCCTCGAGCACCATCGGC-ACC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* ** * * * * *
6806 TTGGTGCTTGGAT-GTCCGAGAACCTCGCGCACCATCGACAACC
1 TAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* * *
6849 TAGGCCCTTGGTCGTGCGAGAGGCTCGGGCACCATCGGCAAAC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* **
6892 TAAGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAAAA
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* *
6935 TAGGCCCTTGGTCGTGCGGGAGCCTCGGCCACCATCGGC-TCC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
** * * * *
6977 TAGGTGCTGGGAT-GTGCGGGAGCCTCGGACACTATCGGCAAAC
1 TAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* *
7020 TAGGCCCTTGGTCGTGCGGGAGCCTCGAGCACCATCGAC-ACC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* ** * *
7062 TTGGTGCTTGGAT-GTGCCGGAACCTCGGGCACCATCGGCAACC
1 TAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* * * **
7105 TAGACCCTTGGTCGTGCGAGAGGCTCGGGCACCATCGGCAAAA
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* *
7148 TAGGCCCTTGGTCGTGCGGGGGCCTCGGCCACCATCGGC-ACC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
*
7190 TGGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* ** *
7232 TTGGTGGCTCGGAT-GTGCGGGAGCCTCGGGC-CGCATCGGC-ACC
1 TAGG-CCCTTGG-TCGTGCGGGAGCCTCGGGCAC-CATCGGCAACC
* ** * ** * *
7275 TCGGTGGCTAGGAGGTGCGGGAGCCTCGGACACCGTCGGCAA-C
1 TAGG-CCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
* **
7318 TTGGTGCTTGGAT-GTGCGGGAGCCTCGGGCACCCATCGGCA
1 TAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCA-CCATCGGCA
7359 CCTTGGTGCC
Statistics
Matches: 902, Mismatches: 170, Indels: 66
0.79 0.15 0.06
Matches are distributed among these distances:
41 12 0.01
42 343 0.38
43 544 0.60
44 3 0.00
ACGTcount: A:0.16, C:0.32, G:0.34, T:0.18
Consensus pattern (43 bp):
TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACC
Found at i:6360 original size:85 final size:84
Alignment explanation
Indices: 6211--7381 Score: 839
Period size: 85 Copynumber: 13.7 Consensus size: 84
6201 TCCGGTAGCA
* *
6211 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAACCT-GGTGCTAGGATGTGCAGGAG
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTCGGTGCT-TGATGTGCGGGAG
* *
6275 CCCCGGACACCATCGGCAAAC
64 CCTCGGACACCATCGGCAACC
* ** *
6296 TAAGCCCTTGGTATTGCGGGAGCCTCGGGCGCCATCGGCACCTCGGTGCTTCGATGTGCGGGAGC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTCGGTGCTT-GATGTGCGGGAGC
*
6361 CTCGGGCACCATCGGCAACC
65 CTCGGACACCATCGGCAACC
6381 TAGGCCCTTGGTCGTGC-GGAGCCTCGGGCACCATCGGCACCTCGGTGCTATGATGTGCGGGAGC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTCGGTGCT-TGATGTGCGGGAGC
**
6445 CTCGGACACTGTCGGCAACC
65 CTCGGACACCATCGGCAACC
* * * *
6465 TAGGCCCTTGGTCGTGCGGGAGCCTCGAGCACCATCGGCACCTTGGTGCTTGGATGTGCGAGAAC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTCGGTGCTT-GATGTGCGGGAGC
*
6530 CTCGCG-TACCATCGGCAACC
65 CTCG-GACACCATCGGCAACC
* * * ** ** *
6550 TAGGCCCTTGGTCGTGCGAGAGGCTCGGGCACCATCGGCAAACTAAGCCCTTGGTCGTGCGGGAG
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTCGGTGCTTGAT-GTGCGGGAG
* **
6615 CCTCGGCCACCATCGGCAAAA
64 CCTCGGACACCATCGGCAACC
* * * * ** *
6636 TAGGCCCTTGGTCGTTCGGGAGCCTCGGACACCATCGGCAAACTAGGCCCTTGGTCGTGCGGGAG
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTCGGTGCTTGAT-GTGCGGGAG
*
6701 CCTCGGCCACCATCGGC-ACC
64 CCTCGGACACCATCGGCAACC
* ** * * * ** * ** *
6721 TCGGTGCTATGAT-GGGCGGGAGCCTCGGACACTGTCGGCAACCTAGGCCCTTGGTCGTGCGGGA
1 TAGGCCCT-TGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTCGGTGCTTGAT-GTGCGGGA
6785 GCCTC-GAGCACCATCGGC-ACC
63 GCCTCGGA-CACCATCGGCAACC
* ** * * * * * * ** * *
6806 TTGGTGCTTGGAT-GTCCGAGAACCTCGCGCACCATCGACAACCTAGGCCCTTGGTCGTGCGAGA
1 TAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTCGGTGCTTGAT-GTGCGGGA
* * *
6870 GGCTCGGGCACCATCGGCAAAC
63 GCCTCGGACACCATCGGCAACC
* ** * ** *
6892 TAAGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCAAAATAGGCCCTTGGTCGTGCGGGAG
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTCGGTGCTTGAT-GTGCGGGAG
* *
6957 CCTCGGCCACCATCGGC-TCC
64 CCTCGGACACCATCGGCAACC
** * * * * * ** *
6977 TAGGTGCTGGGAT-GTGCGGGAGCCTCGGACACTATCGGCAAACTAGGCCCTTGGTCGTGCGGGA
1 TAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTCGGTGCTTGAT-GTGCGGGA
*
7041 GCCTC-GAGCACCATCGAC-ACC
63 GCCTCGGA-CACCATCGGCAACC
* ** * * * *** * *
7062 TTGGTGCTTGGAT-GTGCCGGAACCTCGGGCACCATCGGCAACCTAGACCCTTGGTCGTGCGAGA
1 TAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCACCATCGGC-ACCTCGGTGCTTGAT-GTGCGGGA
* * **
7126 GGCTCGGGCACCATCGGCAAAA
63 GCCTCGGACACCATCGGCAACC
* * * ** *
7148 TAGGCCCTTGGTCGTGCGGGGGCCTCGGCCACCATCGGCACCTGGGCCCTTGGTCGTGCGGGAGC
1 TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTCGGTGCTTGAT-GTGCGGGAGC
*
7213 CTCGGGCACCATCGGC-ACC
65 CTCGGACACCATCGGCAACC
* ** * * *
7232 TTGGTGGCTCGGAT-GTGCGGGAGCCTCGGGC-CGCATCGGCACCTCGGTGGCTAGGAGGTGCGG
1 TAGG-CCCTTGG-TCGTGCGGGAGCCTCGGGCAC-CATCGGCACCTCGGT-GCT-TGATGTGCGG
*
7295 GAGCCTCGGACACCGTCGGCAA-C
61 GAGCCTCGGACACCATCGGCAACC
* ** * *
7318 TTGGTGCTTGGAT-GTGCGGGAGCCTCGGGCACCCATCGGCACCTTGGTGCCTGGGATGTGCGGG
1 TAGGCCCTTGG-TCGTGCGGGAGCCTCGGGCA-CCATCGGCACCTCGGTG-CT-TGATGTGCGGG
7382 CTAAAGAAGA
Statistics
Matches: 916, Mismatches: 141, Indels: 57
0.82 0.13 0.05
Matches are distributed among these distances:
84 92 0.10
85 550 0.60
86 271 0.30
87 3 0.00
ACGTcount: A:0.16, C:0.32, G:0.35, T:0.18
Consensus pattern (84 bp):
TAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTCGGTGCTTGATGTGCGGGAGCC
TCGGACACCATCGGCAACC
Found at i:6842 original size:256 final size:253
Alignment explanation
Indices: 6351--7358 Score: 1154
Period size: 256 Copynumber: 3.9 Consensus size: 253
6341 GTGCTTCGAT
* **
6351 GTGCGGGAGCCTCGGGCACCATCGGCAACCTAGGCCCTTGGTCGTGC-GGAGCCTCGGGCACCAT
1 GTGCGAGAGCCTCGGGCACCATCGGCAAAATAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCAT
* * ** * * ** **
6415 CGGCACCTCGGTGCTATGAT-GTGCGGGAGCCTCGGACACTGTCGGCAACCTAGGCCCTTGG-TC
66 CGGCAACTAGGCCCT-TGGTCGTGCGGGAGCCTCGGCCACCATCGGC-ACCTAGGTGC-TGGAT-
* * ** * * * *
6478 GTGCGGGAGCCTC-GAGCACCATCGGCACCTTGGTGCTTGGAT-GTGCGAGAACCTCGCGTACCA
127 GTGCGGGAGCCTCGGA-CACTATCGGCACCTAGGCCCTTGG-TCGTGCGGGAGCCTCGAGCACCA
* ** * ** *
6541 TCGGCAACCTAGGCCCTTGG-TCGTGCGAGAGGCTCGGGCACCATCGGCAAACTAAGCCCTTGGT
190 TCGGC-ACCTTGGTGCTTGGAT-GTCCGAGAACCTCGGGCACCATCGGCAACCTAAGCCCTTGGT
6605 C
253 C
* * * *
6606 GTGCGGGAGCCTCGGCCACCATCGGCAAAATAGGCCCTTGGTCGTTCGGGAGCCTCGGACACCAT
1 GTGCGAGAGCCTCGGGCACCATCGGCAAAATAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCAT
* * *
6671 CGGCAAACTAGGCCCTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCACCTCGGTGCTATGATGG
66 CGGC-AACTAGGCCCTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCACCTAGGTGCT-GGATGT
*
6736 GCGGGAGCCTCGGACACTGTCGGCAACCTAGGCCCTTGGTCGTGCGGGAGCCTCGAGCACCATCG
129 GCGGGAGCCTCGGACACTATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGAGCACCATCG
* * *
6801 GCACCTTGGTGCTTGGATGTCCGAGAACCTCGCGCACCATCGACAACCTAGGCCCTTGGTC
193 GCACCTTGGTGCTTGGATGTCCGAGAACCTCGGGCACCATCGGCAACCTAAGCCCTTGGTC
* * *
6862 GTGCGAGAGGCTCGGGCACCATCGGCAAACTAAGCCCTTGGTCGTGCGGGAGCCTCGGGCACCAT
1 GTGCGAGAGCCTCGGGCACCATCGGCAAAATAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCAT
* *
6927 CGGCAAAATAGGCCCTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCTCCTAGGTGCTGGGATGT
66 CGGC-AACTAGGCCCTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCACCTAGGTGCT-GGATGT
*
6992 GCGGGAGCCTCGGACACTATCGGCAAACTAGGCCCTTGGTCGTGCGGGAGCCTCGAGCACCATCG
129 GCGGGAGCCTCGGACACTATCGGC-ACCTAGGCCCTTGGTCGTGCGGGAGCCTCGAGCACCATCG
*
7057 ACACCTTGGTGCTTGGATGTGCCG-GAACCTCGGGCACCATCGGCAACCT-AGACCCTTGGTC
193 GCACCTTGGTGCTTGGATGT-CCGAGAACCTCGGGCACCATCGGCAACCTAAG-CCCTTGGTC
* * *
7118 GTGCGAGAGGCTCGGGCACCATCGGCAAAATAGGCCCTTGGTCGTGCGGGGGCCTCGGCCACCAT
1 GTGCGAGAGCCTCGGGCACCATCGGCAAAATAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCAT
* * * *
7183 CGGCACCTGGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCATCGGCACCTTGGTGGCTCGGATGT
66 CGGCAACTAGGCCCTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCACCTAGGT-GCT-GGATGT
* * * ** * ** *
7248 GCGGGAGCCTCGGGC-CGCATCGGCACCTCGGTGGCTAGGAGGTGCGGGAGCCTCG-GACACCGT
129 GCGGGAGCCTCGGACAC-TATCGGCACCTAGG-CCCTTGGTCGTGCGGGAGCCTCGAG-CACCAT
* * * *
7311 CGGCAACTTGGTGCTTGGATGTGCGGGAGCCTCGGGCACCCATCGGCA
191 CGGCACCTTGGTGCTTGGATGTCCGAGAACCTCGGGCA-CCATCGGCA
7359 CCTTGGTGCC
Statistics
Matches: 655, Mismatches: 81, Indels: 32
0.85 0.11 0.04
Matches are distributed among these distances:
255 98 0.15
256 478 0.73
257 79 0.12
ACGTcount: A:0.16, C:0.32, G:0.34, T:0.18
Consensus pattern (253 bp):
GTGCGAGAGCCTCGGGCACCATCGGCAAAATAGGCCCTTGGTCGTGCGGGAGCCTCGGGCACCAT
CGGCAACTAGGCCCTTGGTCGTGCGGGAGCCTCGGCCACCATCGGCACCTAGGTGCTGGATGTGC
GGGAGCCTCGGACACTATCGGCACCTAGGCCCTTGGTCGTGCGGGAGCCTCGAGCACCATCGGCA
CCTTGGTGCTTGGATGTCCGAGAACCTCGGGCACCATCGGCAACCTAAGCCCTTGGTC
Done.