Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: COLO4_32374
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, 781
Length: 1302
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Found at i:199 original size:15 final size:15
Alignment explanation
Indices: 179--218 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
169 ATACTCAACC
179 AGCCTGAGTTGCCTA
1 AGCCTGAGTTGCCTA
194 AGCCTGAGTTGCCTA
1 AGCCTGAGTTGCCTA
*
209 AGCCGGAGTT
1 AGCCTGAGTT
219 ATCAAAGCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.25
Consensus pattern (15 bp):
AGCCTGAGTTGCCTA
Found at i:290 original size:33 final size:33
Alignment explanation
Indices: 253--332 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 33
243 TGAACAACAA
*
253 AAAGTTTCTGAGCTGTC-AAAACCTGAATTGTCC-
1 AAAGTTTCTGAGCTGTCGAAAA-CTGAAGT-TCCT
* * *
286 AAAGTTTCGGAGTTGTCGAAGACTGAAGTTCCT
1 AAAGTTTCTGAGCTGTCGAAAACTGAAGTTCCT
*
319 AAAATTTCTGAGCT
1 AAAGTTTCTGAGCT
333 ACAAAAGTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
32 3 0.08
33 32 0.84
34 3 0.08
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (33 bp):
AAAGTTTCTGAGCTGTCGAAAACTGAAGTTCCT
Found at i:429 original size:15 final size:15
Alignment explanation
Indices: 409--447 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
399 ACCCAACCGG
409 CCTGAGTTGCCTAAA
1 CCTGAGTTGCCTAAA
* *
424 CCTGAGTTACCTAAG
1 CCTGAGTTGCCTAAA
439 CCTGAGTTG
1 CCTGAGTTG
448 TCAAAACCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (15 bp):
CCTGAGTTGCCTAAA
Found at i:566 original size:213 final size:211
Alignment explanation
Indices: 195--903 Score: 913
Period size: 213 Copynumber: 3.3 Consensus size: 211
185 AGTTGCCTAA
* * *
195 GCCTGAGTTGCCTAAGCCGGAGTTATCAAAGCCCGAGTCGCGAAAACCTGAACAACAAAAAGTTT
1 GCCTGAGTTGCCTAAGCCGGAGTTACCAAAGCCTGAGTTGC-AAAACCTGAACAACAAAAAGTTT
* * * * *
260 CTGAGCTGTCAAAACCTGAATTGTCCAAAGTTTCGGAGTTGTCGAAGACTGAAGTTCCTAAAATT
65 CTGAGATGTCAAAACCTGAATTGTCGAAAGTTCCGGAGTTGTCGAAGCCTGAAGTTCCTAAAGTT
*
325 TCTGAGCTACAAAAGTCTAAAGTTCCGGATGAACTCTCAAAACCAGAGCAACCAAATGTTCCAAA
130 TCTGAGCTACAAAAGTCGAAAGTTCCGGATGAACTCTCAAAACCAGAGC-ACCAAATGTTCCAAA
*
390 GCCGAACATACCCAACCG
194 GCCAAACATACCCAACCG
* * * *
408 GCCTGAGTTGCCTAAACCTGAGTTACCTAAGCCTGAGTTGTCAAAACC-GAAACAACAAAATGTT
1 GCCTGAGTTGCCTAAGCCGGAGTTACCAAAGCCTGAGTTG-CAAAACCTG-AACAACAAAAAGTT
* * *
472 TATGAGTTGACAAAACCTGAATTGTCGAAAGTTCCGGAGTTGTCGAAGCCTGCAA-TTCCTAAAG
64 TCTGAGATGTCAAAACCTGAATTGTCGAAAGTTCCGGAGTTGTCGAAGCCTG-AAGTTCCTAAAG
* * *
536 TTTCTGAGTTGCAAAAGTCGAAAATTCCGGATGAACTCTCAAAACCAGAGC-CCAGAAATGTTCC
128 TTTCTGAGCTACAAAAGTCGAAAGTTCCGGATGAACTCTCAAAACCAGAGCACC--AAATGTTCC
*
600 AAAGCCAAACATACCCAACCA
191 AAAGCCAAACATACCCAACCG
* * * * * * **
621 GCTTGAGTTGCTTAAGCCTGAGTTAGCAAAGCTTGAGTTGCCAAAACCTGAACAAGAAAAAGACT
1 GCCTGAGTTGCCTAAGCCGGAGTTACCAAAGCCTGAGTTG-CAAAACCTGAACAACAAAAAGTTT
* ** *
686 CTGAAATGTCAAAATTTGAATTGTCGAAAGGTCCGGAGTTGTCGAAGCCTGAAGCTT-CTAAAGT
65 CTGAGATGTCAAAACCTGAATTGTCGAAAGTTCCGGAGTTGTCGAAGCCTGAAG-TTCCTAAAGT
* * * *
750 CTCTGAGCTACAAAAGTCGAAAGTTTCGGATGAACTCTCAAAACCAGAGCACCCTAATGTTTCAA
129 TTCTGAGCTACAAAAGTCGAAAGTTCCGGATGAACTCTCAAAACCAGAGCA-CCAAATGTTCCAA
815 AGCCAAACATACCCAACCG
193 AGCCAAACATACCCAACCG
* * * **
834 GCTTGAGTTGTCTAAGCCGGAGTTACCAAAGCCTGAGTTGCCAATATTTGAACAACAAAAAGTTT
1 GCCTGAGTTGCCTAAGCCGGAGTTACCAAAGCCTGAGTTG-CAAAACCTGAACAACAAAAAGTTT
899 CTGAG
65 CTGAG
904 CTACAAAAGT
Statistics
Matches: 428, Mismatches: 58, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
211 2 0.00
212 3 0.01
213 415 0.97
214 6 0.01
215 2 0.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (211 bp):
GCCTGAGTTGCCTAAGCCGGAGTTACCAAAGCCTGAGTTGCAAAACCTGAACAACAAAAAGTTTC
TGAGATGTCAAAACCTGAATTGTCGAAAGTTCCGGAGTTGTCGAAGCCTGAAGTTCCTAAAGTTT
CTGAGCTACAAAAGTCGAAAGTTCCGGATGAACTCTCAAAACCAGAGCACCAAATGTTCCAAAGC
CAAACATACCCAACCG
Found at i:996 original size:147 final size:147
Alignment explanation
Indices: 745--1058 Score: 423
Period size: 147 Copynumber: 2.1 Consensus size: 147
735 TGAAGCTTCT
* * * *
745 AAAGTCTCTGAGCTACAAAAGTCGAAAGTTTCGGATGAACTCTCAAAACCAGAGCACCCTAATGT
1 AAAGTTTCTGAGCTACAAAAGTCGAAAGTTCCAGATGAACTCTCAAAACCAGAGCACCCAAATGT
* * * * * **
810 TTCAAAGCCAAACATACCCAACCGGCTTGAGTTGTCTAAGCCGGAGTTACCAAAGCCTGAGTTGC
66 TCCAAAGCCAAACATACCCAACCAGCTTCAATTGCCTAAGCCAAAGTTACCAAAGCCTGAGTTGC
* *
875 CAATATTTGAACAACAA
131 CAAAATCTGAACAACAA
* * * *
892 AAAGTTTCTGAGCTACAAAAGTTGAAAGTTCCAGATGAACTCTCACAACCCGAGCGCCCAAATGT
1 AAAGTTTCTGAGCTACAAAAGTCGAAAGTTCCAGATGAACTCTCAAAACCAGAGCACCCAAATGT
* * *
957 TCCAAAGCCAAACATACCCAACCA-ATCTCAATTGCCTAAGCCAAAGTTAGCAGAGCCTGAGTTG
66 TCCAAAGCCAAACATACCCAACCAGCT-TCAATTGCCTAAGCCAAAGTTACCAAAGCCTGAGTTG
1021 CCAAAATCTGAACAACAA
130 CCAAAATCTGAACAACAA
1039 AAAGTTTCTGAGCTATCAAA
1 AAAGTTTCTGAGCTA-CAAA
1059 GCCTGAATTG
Statistics
Matches: 145, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
146 1 0.01
147 140 0.97
148 4 0.03
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (147 bp):
AAAGTTTCTGAGCTACAAAAGTCGAAAGTTCCAGATGAACTCTCAAAACCAGAGCACCCAAATGT
TCCAAAGCCAAACATACCCAACCAGCTTCAATTGCCTAAGCCAAAGTTACCAAAGCCTGAGTTGC
CAAAATCTGAACAACAA
Found at i:1076 original size:33 final size:33
Alignment explanation
Indices: 1039--1124 Score: 86
Period size: 33 Copynumber: 2.6 Consensus size: 33
1029 TGAACAACAA
*
1039 AAAGTTTCTGAGCTATCAAAGCCTGAA-TTGTCG
1 AAAGTTTCTGAGCTATCAAAGCCTGAAGTT-CCG
* * * *
1072 AAAGTTT-TAGAGTTGTCGAAGCCTGAAGTTCCT
1 AAAGTTTCT-GAGCTATCAAAGCCTGAAGTTCCG
*
1105 AAAGTTTCTGAGCTACCAAA
1 AAAGTTTCTGAGCTATCAAA
1125 CTCGAAAGTT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
32 1 0.02
33 37 0.90
34 3 0.07
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (33 bp):
AAAGTTTCTGAGCTATCAAAGCCTGAAGTTCCG
Found at i:1203 original size:360 final size:360
Alignment explanation
Indices: 532--1262 Score: 984
Period size: 360 Copynumber: 2.0 Consensus size: 360
522 TGCAATTCCT
* * * *
532 AAAGTTTCTGAGTTGCAAAAGTCGAAAATTCCGGATGAACTCTCAAAACCAGAGCCCAGAAATGT
1 AAAGTTTCTGAGCTACAAAAGTCGAAAATTCCAGATGAACTCTCAAAACCAGAGCCCACAAATGT
* * * ** *
597 TCCAAAGCCAAACATACCCAACCAGCTTGAGTTGCTTAAGCCTGAGTTAGCAAAGCTTGAGTTGC
66 TCCAAAGCCAAACATACCCAACCAGCTTCAATTGCCTAAGCCAAAGTTAGCAAAGCCTGAGTTGC
* * ** *
662 CAAAACCTGAACAAGAAAAAGACTCTGAAATGTCAAAATTTGAATTGTCGAAAGGTCCGGAGTTG
131 CAAAACCTGAACAACAAAAAGACTCTGAAATATCAAAACCTGAATTGTCGAAAGGTCCAGAGTTG
* *
727 TCGAAGCCTGAAGCTTCTAAAGTCTCTGAGCTACAAAAGTCGAAAGTTTCGGATGAACTCTCAAA
196 TCGAAGCCTGAAGCTTCTAAAGTCTCTGAGCTACAAAACTCGAAAGTTCCGGATGAACTCTCAAA
* * * * * * * *
792 ACCAGAGCACCCTAATGTTTCAAAGCCAAACATACCCAACCGGCTTGAGTTGTCTAAGCCGGAGT
261 ACCACAACACCCAAATGTTCCAAAGCAAAACATACCCAACCAGCCTGAGTTGCCTAAGCCGGAGT
* * *
857 TACCAAAGCCTGAGTTGCCAATATTTGAACAACAA
326 TACCAAAGCCAGAGTTGCCAAAACTTGAACAACAA
* * * *
892 AAAGTTTCTGAGCTACAAAAGTTGAAAGTTCCAGATGAACTCTCACAACCCGAGCGCC-CAAATG
1 AAAGTTTCTGAGCTACAAAAGTCGAAAATTCCAGATGAACTCTCAAAACCAGAGC-CCACAAATG
* *
956 TTCCAAAGCCAAACATACCCAACCA-ATCTCAATTGCCTAAGCCAAAGTTAGCAGAGCCTGAGTT
65 TTCCAAAGCCAAACATACCCAACCAGCT-TCAATTGCCTAAGCCAAAGTTAGCAAAGCCTGAGTT
* ** ** * * **
1020 GCCAAAATCTGAACAACAAAAAGTTTCTGAGCTATCAAAGCCTGAATTGTCGAAAGTTTTAGAGT
129 GCCAAAACCTGAACAACAAAAAGACTCTGAAATATCAAAACCTGAATTGTCGAAAGGTCCAGAGT
* *
1085 TGTCGAAGCCTGAAG-TTCCTAAAGTTTCTGAGCTACCAAACTCGAAAGTTCCGGATGAACTCTC
194 TGTCGAAGCCTGAAGCTT-CTAAAGTCTCTGAGCTACAAAACTCGAAAGTTCCGGATGAACTCTC
1149 AAAACCACAACACCCAAATGTTCCAAAGCAAAACATACCCAACCAGCCTGAGTTGCCTAAGCCGG
258 AAAACCACAACACCCAAATGTTCCAAAGCAAAACATACCCAACCAGCCTGAGTTGCCTAAGCCGG
* *
1214 AGTTACCAAAGGCAGAGTTGCCAAAACTTGATCAACAA
323 AGTTACCAAAGCCAGAGTTGCCAAAACTTGAACAACAA
1252 AAA-TTTCTGAG
1 AAAGTTTCTGAG
1263 TTGTCAAAAT
Statistics
Matches: 321, Mismatches: 47, Indels: 7
0.86 0.13 0.02
Matches are distributed among these distances:
359 11 0.03
360 308 0.96
361 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (360 bp):
AAAGTTTCTGAGCTACAAAAGTCGAAAATTCCAGATGAACTCTCAAAACCAGAGCCCACAAATGT
TCCAAAGCCAAACATACCCAACCAGCTTCAATTGCCTAAGCCAAAGTTAGCAAAGCCTGAGTTGC
CAAAACCTGAACAACAAAAAGACTCTGAAATATCAAAACCTGAATTGTCGAAAGGTCCAGAGTTG
TCGAAGCCTGAAGCTTCTAAAGTCTCTGAGCTACAAAACTCGAAAGTTCCGGATGAACTCTCAAA
ACCACAACACCCAAATGTTCCAAAGCAAAACATACCCAACCAGCCTGAGTTGCCTAAGCCGGAGT
TACCAAAGCCAGAGTTGCCAAAACTTGAACAACAA
Done.