Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1407
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: 1832
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Found at i:109 original size:42 final size:41
Alignment explanation
Indices: 63--393 Score: 288
Period size: 42 Copynumber: 7.9 Consensus size: 41
53 GCGTTTTTGT
* * *
63 AAAAAAGCGCAGCTAAAGAACATGTTCTTTAGCGGTGCTTAG
1 AAAAAA-CGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* * *
105 AAAAAAATGCCGCTAAATACCATGTTCTTTAGCGGTGCTTAG
1 -AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
*
147 AAAAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
1 -AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* *
189 AAAGGAACGCCGCTAAAGACCATGGTCTTTAGCGGCGTTCCTT--
1 AAA-AAACGCCGCTAAAGACCATGTTCTTTAGCGGCG---CTTAG
*** * * * * **
232 TCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTT
1 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG-CTTAG
*** * * * *
274 TCTAAACGCCTCTAAAGACCATGGTCTTTAGAGGCGTTTAG
1 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
315 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAG
1 -AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT-AG
* * * * *
358 AAAAAACGTCGTTAAAGAACATGATCTTGAGCGGCG
1 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
394 TTTTTATCTA
Statistics
Matches: 245, Mismatches: 35, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
40 2 0.01
41 6 0.02
42 226 0.92
43 8 0.03
45 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (41 bp):
AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
Found at i:302 original size:126 final size:126
Alignment explanation
Indices: 63--435 Score: 354
Period size: 126 Copynumber: 3.0 Consensus size: 126
53 GCGTTTTTGT
* * * * * * * *
63 AAAAAAGCGCAGCTAAAGAACATGTTCTTTAGCGGTGCTT-AGAAAAAAATGCCGCTAAATACCA
1 AAAAAAACGCCGCTAAAGACCATGGTCTTTAGCGGCGCTTAAG-AAAAAACGCCGCTAAAGAACA
* * * * ** *** * * *
127 TGTTCTTTAGCGGTGCTTAGAAAAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
65 TGATCTTGAGCGGCGTTTTTATCTAAACGCCTCTAAAGACCATGGTCTTTAGCGGCGCTTAG
** ****** *
189 AAAGGAACGCCGCTAAAGACCATGGTCTTTAGCGGCG-TTCCTTTCTAAGCGCCGCTAAAGAACA
1 AAAAAAACGCCGCTAAAGACCATGGTCTTTAGCGGCGCTT-AAGAAAAAACGCCGCTAAAGAACA
* * * * *
253 TGGTCTTTAGCGGCGTTTTTTTCTAAACGCCTCTAAAGACCATGGTCTTTAGAGGCGTTTAG
65 TGATCTTGAGCGGCGTTTTTATCTAAACGCCTCTAAAGACCATGGTCTTTAGCGGCGCTTAG
* * *
315 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAGAAAAAACGTCGTTAAAGAACAT
1 AAAAAAACGCCGCTAAAGACCATGGTCTTTAGCGGCGCTTAAGAAAAAACGCCGCTAAAGAACAT
* * *
380 GATCTTGAGCGGCGTTTTTATCTAAGCGCCTCTAAAGAACATGGTATTTAGCGGCG
66 GATCTTGAGCGGCGTTTTTATCTAAACGCCTCTAAAGACCATGGTCTTTAGCGGCG
436 TTTTTTTCTA
Statistics
Matches: 195, Mismatches: 49, Indels: 6
0.78 0.20 0.02
Matches are distributed among these distances:
125 2 0.01
126 191 0.98
127 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (126 bp):
AAAAAAACGCCGCTAAAGACCATGGTCTTTAGCGGCGCTTAAGAAAAAACGCCGCTAAAGAACAT
GATCTTGAGCGGCGTTTTTATCTAAACGCCTCTAAAGACCATGGTCTTTAGCGGCGCTTAG
Found at i:396 original size:84 final size:83
Alignment explanation
Indices: 63--396 Score: 326
Period size: 84 Copynumber: 4.0 Consensus size: 83
53 GCGTTTTTGT
* * * * *
63 AAAAAAGCGCAGCTAAAGAACATGTTCTTTAGCGGTGCTTAGAAAAAAATGCCGCTAAATACCAT
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG-AAAAAACGCCGCTAAAGACCAT
* * *
128 GTTCTTTAGCGGTGCTTAG
65 GGTCTTTAGCGGCGTTTAG
* * *
147 AAAAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAGGAACGCCGCTAAAGACCAT
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAA-AAACGCCGCTAAAGACCAT
***
212 GGTCTTTAGCGGCGTTCCT
65 GGTCTTTAGCGGCGTTTAG
**** * * * ***** *
231 TTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAACGCCTCTAAAGACCAT
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-CTTAGAAAAAACGCCGCTAAAGACCAT
*
296 GGTCTTTAGAGGCGTTTAG
65 GGTCTTTAGCGGCGTTTAG
* * * *
315 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAGAAAAAACGTCGTTAAAGAACAT
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTT-AGAAAAAACGCCGCTAAAGACCAT
* *
380 GATCTTGAGCGGCGTTT
65 GGTCTTTAGCGGCGTTT
397 TTATCTAAGC
Statistics
Matches: 193, Mismatches: 54, Indels: 6
0.76 0.21 0.02
Matches are distributed among these distances:
83 5 0.03
84 186 0.96
85 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (83 bp):
AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAACGCCGCTAAAGACCATG
GTCTTTAGCGGCGTTTAG
Found at i:415 original size:84 final size:82
Alignment explanation
Indices: 67--435 Score: 272
Period size: 84 Copynumber: 4.4 Consensus size: 82
57 TTTTGTAAAA
* * * * * * *
67 AAGCGCAGCTAAAGAACATGTTCTTTAGCGGTGCTTAGAAAAAAATGCCGCTAAATACCATGTTC
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTAG-AAAAAACG-CGTTAAAGACCATGGTC
* * ** ***
132 TTTAGCGGTGCTTAGAAAA
64 TTTAGCGGCGTTTTTATCT
** * * * *
151 AAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAGGAACGCCGCTAAAGACCATGGTC
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTAGAAA-AAACG-CGTTAAAGACCATGGTC
*
216 TTTAGCGGCGTTCCTT-TCT
64 TTTAGCGGCGTT-TTTATCT
* ***** *
235 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAACGCCTCTAAAGACCATGGTC
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCG-CTTAGAAAAAACGCGT-TAAAGACCATGGTC
* ** ***
300 TTTAGAGGCGTTTAGAAAA
64 TTTAGCGGCGTTTTTATCT
* * * * *
319 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAGAAAAAACGTCGTTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGCTT-AGAAAAAACG-CGTTAAAGACCATGGTC
*
384 TTGAGCGGCGTTTTTATCT
64 TTTAGCGGCGTTTTTATCT
* *
403 AAGCGCCTCTAAAGAACATGGTATTTAGCGGCG
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCG
436 TTTTTTTCTA
Statistics
Matches: 217, Mismatches: 61, Indels: 14
0.74 0.21 0.05
Matches are distributed among these distances:
83 6 0.03
84 207 0.95
85 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (82 bp):
AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTAGAAAAAACGCGTTAAAGACCATGGTCTT
TAGCGGCGTTTTTATCT
Found at i:416 original size:42 final size:42
Alignment explanation
Indices: 194--482 Score: 285
Period size: 42 Copynumber: 6.9 Consensus size: 42
184 CTTAGAAAGG
* *
194 AACGCCGCTAAAGACCATGGTCTTTAGCGGCGTTCCTT-TCTA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGTT-TTTATCTA
* *
236 AGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTATCTA
* * * ** ***
278 AACGCCTCTAAAGACCATGGTCTTTAGAGGCGTTTAGAAAAA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTATCTA
* * * * ***
320 AACGCCGCTAAAGACCATGTTCTTTAGCGGCG-CTTAAGAAAA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTA-TCTA
* * * *
362 AACGTCGTTAAAGAACATGATCTTGAGCGGCGTTTTTATCTA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTATCTA
* * * *
404 AGCGCCTCTAAAGAACATGGTATTTAGCGGCGTTTTTTTCTA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTATCTA
* *
446 AGCACCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
483 GTTTGTAAAC
Statistics
Matches: 204, Mismatches: 40, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
41 4 0.02
42 197 0.97
43 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29
Consensus pattern (42 bp):
AACGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTATCTA
Found at i:436 original size:126 final size:126
Alignment explanation
Indices: 159--479 Score: 356
Period size: 126 Copynumber: 2.5 Consensus size: 126
149 AAAAATGCCG
* * **
159 CTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAGGAACGCCGCTAAAGACCATGGTCTTTAGCGG
1 CTAAAGACCATGGTCTTTAGCGGCGTTTAGAAAAAAACGCCGCTAAAGACCATGGTCTTTAGCGG
****** * * * *
224 CGTTCCTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAACGCCT
66 CGTTCAAGAAAAAACGCCGCTAAAGAACATGATCTTGAGCGGCGTTTTTATCTAAACGCCT
* *
285 CTAAAGACCATGGTCTTTAGAGGCGTTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGG
1 CTAAAGACCATGGTCTTTAGCGGCGTTTAGAAAAAAACGCCGCTAAAGACCATGGTCTTTAGCGG
* * *
350 CGCTT-AAGAAAAAACGTCGTTAAAGAACATGATCTTGAGCGGCGTTTTTATCTAAGCGCCT
66 CG-TTCAAGAAAAAACGCCGCTAAAGAACATGATCTTGAGCGGCGTTTTTATCTAAACGCCT
* * ****** * * *
411 CTAAAGAACATGGTATTTAGCGGCGTTTTTTTCTAAGCACCGCTAAAGAACATGGTCTTTAGCGG
1 CTAAAGACCATGGTCTTTAGCGGCGTTTAGAAAAAAACGCCGCTAAAGACCATGGTCTTTAGCGG
476 CGTT
66 CGTT
480 TTTGTTTGTA
Statistics
Matches: 162, Mismatches: 32, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
125 2 0.01
126 158 0.98
127 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (126 bp):
CTAAAGACCATGGTCTTTAGCGGCGTTTAGAAAAAAACGCCGCTAAAGACCATGGTCTTTAGCGG
CGTTCAAGAAAAAACGCCGCTAAAGAACATGATCTTGAGCGGCGTTTTTATCTAAACGCCT
Done.