Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3698
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: 48294
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:429 original size:29 final size:29
Alignment explanation
Indices: 396--451 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
386 CATTTAATAC
396 AACTTTGGAAAAATTACACTTTTGCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCTA
* * *
425 AACTTTTGCATAATTACACTTTTGCCC
1 AACTTTGGAAAAATTACACTTTTGCCC
452 CTAGGCTCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (29 bp):
AACTTTGGAAAAATTACACTTTTGCCCTA
Found at i:4875 original size:46 final size:45
Alignment explanation
Indices: 4819--4985 Score: 179
Period size: 43 Copynumber: 3.7 Consensus size: 45
4809 TGGTTGAGCA
4819 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCA-CTATGGATGCGAATG
* *
4865 TCCGAACTCG-TGAGTTGAGTCCGAGTT---TGTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATG-GATGCGAA-T--G
4909 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAATG
*
4956 -CC-AGCTCGTTGAGTTGAGTCCGAGTTCACT
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
4986 TAGGGCGGGT
Statistics
Matches: 104, Mismatches: 5, Indels: 28
0.76 0.04 0.20
Matches are distributed among these distances:
41 5 0.05
42 6 0.06
43 26 0.25
44 3 0.03
45 17 0.16
46 20 0.19
47 18 0.17
50 4 0.04
51 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAATG
Found at i:4928 original size:92 final size:90
Alignment explanation
Indices: 4816--4981 Score: 280
Period size: 92 Copynumber: 1.8 Consensus size: 90
4806 GGATGGTTGA
4816 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCG-TGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAA-G-CC-AACTCGTTGAGT
4880 TGAGTCCGAGTTTGTGAGATGTAACTAG
63 TGAGTCCGAGTTTGTGAGATGTAACTAG
* *
4908 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGCCAGCTCGTTGAGTTGA
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAAGCCAACTCGTTGAGTTGA
4973 GTCCGAGTT
66 GTCCGAGTT
4982 CACTTAGGGC
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
89 5 0.07
90 19 0.27
91 1 0.01
92 46 0.65
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (90 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAAGCCAACTCGTTGAGTTGA
GTCCGAGTTTGTGAGATGTAACTAG
Found at i:11316 original size:46 final size:46
Alignment explanation
Indices: 11154--11322 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
11144 GGTTGAGCAT
* *
11154 CCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGA--CGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * *
11197 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
11242 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *
11290 CCGAGCTCGTTGAGTTGATTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
11323 GGGGCGGGTT
Statistics
Matches: 104, Mismatches: 10, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
41 2 0.02
42 2 0.02
43 29 0.28
45 1 0.01
46 31 0.30
47 28 0.27
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:19444 original size:43 final size:43
Alignment explanation
Indices: 19396--19482 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 43
19386 AAGTCGTACA
*
19396 ATGCCAAC-GTCCCAAAC-GTGGTCTTACATGTAATCACATATCG
1 ATGCC-ACTGTCCCAAACAG-GGTCTTACATGTAAACACATATCG
* *
19439 ATGCCACTGTCCCAGACAGGGTCTTACTTGTAAACACATATCG
1 ATGCCACTGTCCCAAACAGGGTCTTACATGTAAACACATATCG
19482 A
1 A
19483 AATCACATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
42 2 0.05
43 36 0.92
44 1 0.03
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCCACTGTCCCAAACAGGGTCTTACATGTAAACACATATCG
Found at i:31486 original size:26 final size:26
Alignment explanation
Indices: 31451--31502 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
31441 AATGTGAAAG
*
31451 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
31477 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
31503 TTTCATTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:31532 original size:104 final size:103
Alignment explanation
Indices: 31376--31638 Score: 406
Period size: 104 Copynumber: 2.6 Consensus size: 103
31366 GTATATAAAA
** *
31376 GGGTTGCTGTGTGCTGATTCCCCG-TTCATTGGTGGTGCTATGTGCG-TGATCCACCATATCTTT
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCTTT
*
31439 GAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCGAG
65 GAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCGAG
*
31478 GGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTTT
1 GGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTT
31543 GAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCGAG
65 GAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCGAG
* * *
31582 GGGTTGCTAAGTGCTGATTCCCCAATTCAGTGGTGGTGCTAAGTGCGAGATCCACCA
1 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
31639 ATAACGGTTA
Statistics
Matches: 148, Mismatches: 9, Indels: 7
0.90 0.05 0.04
Matches are distributed among these distances:
102 22 0.15
103 53 0.36
104 72 0.49
105 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.31
Consensus pattern (103 bp):
GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTG
AAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCGAG
Found at i:39091 original size:103 final size:103
Alignment explanation
Indices: 38851--39113 Score: 433
Period size: 102 Copynumber: 2.6 Consensus size: 103
38841 TGTATATAAA
** *
38851 AGGGGTTGCTGTGTGCTGATTCCCCGTT-ATTGGTGGTGCTATGTGCG-TGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCTT
*
38914 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
38953 AGGGGTTGCTAAGTGCTGATTCCCCGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTT
39018 GAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 GAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
39055 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCG-TTCATTGGTGGTGCTAAGTGCGATATCCACCA
39114 ATAACGGTTA
Statistics
Matches: 152, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
102 82 0.54
103 69 0.45
104 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTT
GAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:45243 original size:15 final size:15
Alignment explanation
Indices: 45223--45252 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
45213 TTCACGGAAT
45223 TTTCGAAAAATTTCG
1 TTTCGAAAAATTTCG
45238 TTTCGAAAAATTTCG
1 TTTCGAAAAATTTCG
45253 ACGTTTGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
TTTCGAAAAATTTCG
Done.