Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold642
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: 31295
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:5666 original size:46 final size:46
Alignment explanation
Indices: 5616--5791 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
5606 TGGTTGAGCA
5616 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
5662 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
5707 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
5755 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5792 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:5772 original size:93 final size:93
Alignment explanation
Indices: 5613--5784 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
5603 GGATGGTTGA
* *
5613 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5678 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
5706 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5771 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
5785 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:7157 original size:15 final size:15
Alignment explanation
Indices: 7137--7182 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
7127 AAATAAACCC
7137 AAAACCAACCCAAAT
1 AAAACCAACCCAAAT
*
7152 AAAACCAAACC---T
1 AAAACCAACCCAAAT
*
7164 AAAACCAGCCCAAAT
1 AAAACCAACCCAAAT
7179 AAAA
1 AAAA
7183 AAAATCCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
12 10 0.40
15 15 0.60
ACGTcount: A:0.61, C:0.30, G:0.02, T:0.07
Consensus pattern (15 bp):
AAAACCAACCCAAAT
Found at i:7162 original size:27 final size:27
Alignment explanation
Indices: 7131--7182 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
7121 TCACATAAAT
7131 AAACCCAAAACCAACCCAAATAAAACC
1 AAACCCAAAACCAACCCAAATAAAACC
* *
7158 AAACCTAAAACCAGCCCAAATAAAA
1 AAACCCAAAACCAACCCAAATAAAA
7183 AAAATCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.60, C:0.33, G:0.02, T:0.06
Consensus pattern (27 bp):
AAACCCAAAACCAACCCAAATAAAACC
Found at i:13649 original size:21 final size:21
Alignment explanation
Indices: 13617--13657 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
13607 AGGCTCTAGG
13617 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
13638 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
13658 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:21252 original size:37 final size:37
Alignment explanation
Indices: 21202--21278 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
21192 AAAATAGAAA
21202 AGAAAAAGGAAAAAGAACCAAATGTGATCAAGTAAAC
1 AGAAAAAGGAAAAAGAACCAAATGTGATCAAGTAAAC
21239 AGAAAAAGGAAAAAGAACCAAATGTGATCAAGTAAAC
1 AGAAAAAGGAAAAAGAACCAAATGTGATCAAGTAAAC
21276 AGA
1 AGA
21279 TACTTAGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.60, C:0.10, G:0.19, T:0.10
Consensus pattern (37 bp):
AGAAAAAGGAAAAAGAACCAAATGTGATCAAGTAAAC
Found at i:28210 original size:14 final size:14
Alignment explanation
Indices: 28193--28229 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
28183 GATATACAAA
28193 ACATATAAATACAT
1 ACATATAAATACAT
*
28207 ACATATAAATATAT
1 ACATATAAATACAT
*
28221 ACTTATAAA
1 ACATATAAA
28230 AATAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (14 bp):
ACATATAAATACAT
Found at i:28365 original size:22 final size:23
Alignment explanation
Indices: 28339--28387 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
28329 TACAAGCACT
*
28339 TATA-TGATAATA-ATAAGATATA
1 TATATTGAAAATACATAAG-TATA
28361 TATATTTGAAAATACATAAGTATA
1 TATA-TTGAAAATACATAAGTATA
28385 TAT
1 TAT
28388 GAATAGAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (23 bp):
TATATTGAAAATACATAAGTATA
Found at i:28432 original size:3 final size:3
Alignment explanation
Indices: 28421--28473 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
28411 CAATAATACC
* * *
28421 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
28466 AAT AAT AA
1 AAT AAT AA
28474 AGTTAACAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 1 0.02
3 41 0.98
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:29867 original size:88 final size:88
Alignment explanation
Indices: 29718--29913 Score: 383
Period size: 88 Copynumber: 2.2 Consensus size: 88
29708 GTCTTGTTGC
*
29718 TTCAATCCATTCCACTGCATTTTAGAGAGATGCGTCCTGTAGCCTTTATCTTCTTCGTAGCAACT
1 TTCAATCTATTCCACTGCATTTTAGAGAGATGCGTCCTGTAGCCTTTATCTTCTTCGTAGCAACT
29783 TCAGGGGGACGAGGTTTGTGGTT
66 TCAGGGGGACGAGGTTTGTGGTT
29806 TTCAATCTATTCCACTGCATTTTAGAGAGATGCGTCCTGTAGCCTTTATCTTCTTCGTAGCAACT
1 TTCAATCTATTCCACTGCATTTTAGAGAGATGCGTCCTGTAGCCTTTATCTTCTTCGTAGCAACT
29871 TCAGGGGGACGAGGTTTGTGGTT
66 TCAGGGGGACGAGGTTTGTGGTT
29894 TTCAATCTATTCCACTGCAT
1 TTCAATCTATTCCACTGCAT
29914 CTTCAGGGAA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 107 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (88 bp):
TTCAATCTATTCCACTGCATTTTAGAGAGATGCGTCCTGTAGCCTTTATCTTCTTCGTAGCAACT
TCAGGGGGACGAGGTTTGTGGTT
Found at i:30084 original size:44 final size:43
Alignment explanation
Indices: 29988--30293 Score: 204
Period size: 44 Copynumber: 7.1 Consensus size: 43
29978 TTTTAACCCA
* **
29988 CTCCACTGTAA-CTTCAGGGAGATAGGAT-AGTGTCTTCGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTCTG-CTTCGATCTG
* * *
30031 CTCCGCTGTAATCTCGGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCT-GCTTCGATCTG
* * * *
30075 CTCCACTGTAA-CTTCAGGGGGATAAGATCTGCAATTCTTCGGTCTA
1 CTCCACTGTAATC-TCAGGGAGATAAGATCT-C--TGCTTCGATCTG
* * *
30121 CTCCACTGTAATCTCAGGAAGATAAGA-C-CTGATGT-GATCTT
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCTGCT-TCGATCTG
* * * *
30162 CTCTACTGTAA-CTTCAGAGAGATAAGATC-CT--TT-AATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTCTGCTTCGATCTG
* * * * *
30201 CTCCATTGTAATCTCAAGGAGATAGGAT-TACTATCTTTGATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCT-CT-GCTTCGATCTG
* *
30245 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTCT-GCTTCGATCTG
30289 CTCCA
1 CTCCA
30294 ATGCAACCGA
Statistics
Matches: 203, Mismatches: 41, Indels: 37
0.72 0.15 0.13
Matches are distributed among these distances:
39 25 0.12
40 5 0.02
41 28 0.14
42 4 0.02
43 27 0.13
44 78 0.38
45 4 0.02
46 30 0.15
47 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (43 bp):
CTCCACTGTAATCTCAGGGAGATAAGATCTCTGCTTCGATCTG
Found at i:30367 original size:45 final size:45
Alignment explanation
Indices: 30316--30545 Score: 139
Period size: 44 Copynumber: 5.2 Consensus size: 45
30306 GAGGCAAGGC
* *
30316 TTTGTCTTTGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCT
1 TTTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
* * * ** ** * * * *
30361 TTTGTCTTCAACCAGC-TCTATCACAACCGAAAG-AGGCAAGGT-T
1 TTTGTCTTCGATCTGCTTCGCTGTCAA-TGTAGGAAGGCAAGATCT
*
30404 TGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 TTTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
* * * ** ** * * * *
30449 TTTGTCTTCAACCAGC-TCTATCACAACCGAAAG-AGGCAAGGT-T
1 TTTGTCTTCGATCTGCTTCGCTGTCAA-TGTAGGAAGGCAAGATCT
* * * *
30492 TGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCC
1 TTTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
30537 TTTGTCTTC
1 TTTGTCTTC
30546 ATTGATCTGT
Statistics
Matches: 125, Mismatches: 52, Indels: 16
0.65 0.27 0.08
Matches are distributed among these distances:
43 31 0.25
44 55 0.44
45 39 0.31
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (45 bp):
TTTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
Found at i:30433 original size:88 final size:88
Alignment explanation
Indices: 30297--30546 Score: 421
Period size: 88 Copynumber: 2.9 Consensus size: 88
30287 TGCTCCAATG
** * * *
30297 CAACCGATGGAGGCAAGGCTT-TGTCTTTGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
30361 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCTATCA
30384 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
30449 TTTGTCTTCAACCAGCTCTATCA
66 TTTGTCTTCAACCAGCTCTATCA
* * *
30472 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCC
1 CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
30537 TTTGTCTTCA
66 TTTGTCTTCA
30547 TTGATCTGTC
Statistics
Matches: 154, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
87 18 0.12
88 136 0.88
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (88 bp):
CAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
TTTGTCTTCAACCAGCTCTATCA
Done.