Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold321
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: 24601
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.31
Found at i:6564 original size:93 final size:93
Alignment explanation
Indices: 6405--6575 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
6395 GGATGGTTGA
6405 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
6470 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
6498 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCC-GAACTCGTTGAG
6562 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
6576 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:6578 original size:46 final size:45
Alignment explanation
Indices: 6409--6580 Score: 206
Period size: 46 Copynumber: 3.7 Consensus size: 45
6399 GGTTGAGCAT
*
6409 CCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
6454 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAGATGTAACTAG-GCAT-
1 -CCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATG-GA-T-GCGAATG
6502 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
6547 CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
6581 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 3 0.03
46 61 0.57
47 31 0.29
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:15266 original size:27 final size:27
Alignment explanation
Indices: 15234--15438 Score: 214
Period size: 27 Copynumber: 7.6 Consensus size: 27
15224 ATATTGAGTC
* *
15234 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
15261 CACACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
15288 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
15316 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
15343 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
15370 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
15397 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
15424 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
15439 GTACAATTTA
Statistics
Matches: 154, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
27 130 0.84
28 24 0.16
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:15394 original size:54 final size:54
Alignment explanation
Indices: 15234--15437 Score: 248
Period size: 54 Copynumber: 3.8 Consensus size: 54
15224 ATATTGAGTC
* * * * * * * *
15234 CGCACACTCAGTGCTATATAATCAACTCACACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAATCGCACACTTAGTGCAACATAGTCAAAT
** * *
15288 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAA-TCGCACACTTAGTGCAACATAGTCAAAT
* **
15343 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAAATCGCACACTTAGTGCAACATAGTCAAAT
15397 CGCACACTTAGTGCTACATAGTCAAATCGCACACTTAGTGC
1 CGCACACTTAGTGCTACATAGTCAAATCGCACACTTAGTGC
15438 TGTACAATTT
Statistics
Matches: 126, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
54 83 0.66
55 43 0.34
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAAATCGCACACTTAGTGCAACATAGTCAAAT
Found at i:23345 original size:27 final size:27
Alignment explanation
Indices: 23314--23518 Score: 259
Period size: 27 Copynumber: 7.6 Consensus size: 27
23304 TATATGAGTC
* * * *
23314 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
23341 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
23368 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
23396 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
23423 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
23450 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
23477 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
23504 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
23519 GTACAATTAC
Statistics
Matches: 157, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
27 133 0.85
28 24 0.15
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:23542 original size:109 final size:109
Alignment explanation
Indices: 23312--23517 Score: 290
Period size: 109 Copynumber: 1.9 Consensus size: 109
23302 GGTATATGAG
* * ** * *
23312 TCCGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACT
1 TCCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAATCAAATCGCACACT
***
23376 TAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAA
65 TAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCACAATCAA
* *
23421 TTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
1 TCCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAATCAAATCGCACACTT
23486 AGTGCTACATAGTCAAA-TCGCACACTTAGTGC
66 AGTGCTACATAGTCAAACTCGCACACTTAGTGC
23518 TGTACAATTA
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
108 17 0.19
109 71 0.81
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (109 bp):
TCCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAATCAAATCGCACACTT
AGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCACAATCAA
Done.