Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold970
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: 33961
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Found at i:3299 original size:38 final size:37
Alignment explanation
Indices: 3193--3347 Score: 214
Period size: 38 Copynumber: 4.2 Consensus size: 37
3183 AGCTACTTTC
3193 CAAATGCCTTC-GGAC-TAG-CG-TATAGTAACTCGCA
1 CAAATG-CTTCGGGACTTAGCCGTTATAGTAACTCGCA
3227 CAAATGCTTCGGGACTTAGCCGTTATAGTAACTCG-A
1 CAAATGCTTCGGGACTTAGCCGTTATAGTAACTCGCA
3263 CAAATGCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCTTCGGGACTTAG-CC-GTTATAGTAACTCGCA
*
3302 CAAATGCCTTCGGGACTTAGCCAGATATAGT-ACTCGCA
1 CAAATG-CTTCGGGACTTAGCC-GTTATAGTAACTCGCA
3340 CAAATGCT
1 CAAATGCT
3348 CGGTTAGCCC
Statistics
Matches: 111, Mismatches: 2, Indels: 13
0.88 0.02 0.10
Matches are distributed among these distances:
33 4 0.04
34 10 0.09
35 3 0.03
36 22 0.20
37 16 0.14
38 27 0.24
39 16 0.14
40 13 0.12
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (37 bp):
CAAATGCTTCGGGACTTAGCCGTTATAGTAACTCGCA
Found at i:3308 original size:75 final size:74
Alignment explanation
Indices: 3213--3390 Score: 240
Period size: 74 Copynumber: 2.4 Consensus size: 74
3203 CGGACTAGCG
*
3213 TATAGTAACTCGCACAAATG-CTTCGGGACTTAGCC-GTTATAGTAACTCG-ACAAATGCTTCGG
1 TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCAGATATAGT-ACTCGCACAAATGC-TC-G
3275 GACTTAGCCCGG-T
63 G--TTAGCCCGGAT
3288 TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCAGATATAGTACTCGCACAAATGCTCGGTT
1 TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCAGATATAGTACTCGCACAAATGCTCGGTT
3353 AGCCCGGAAT
66 AGCCCGG-AT
* *
3363 T-TAGTCACTAGCACAAATGCCTTCGGGA
1 TATAGTAACTCGCACAAATGCCTTCGGGA
3391 TTACTACGGT
Statistics
Matches: 95, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
73 9 0.09
74 25 0.26
75 24 0.25
76 22 0.23
77 15 0.16
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (74 bp):
TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCAGATATAGTACTCGCACAAATGCTCGGTT
AGCCCGGAT
Found at i:11205 original size:40 final size:40
Alignment explanation
Indices: 11161--11387 Score: 388
Period size: 40 Copynumber: 5.7 Consensus size: 40
11151 GCTACTTGCT
11161 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
11201 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
11240 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
11280 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
11320 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
11359 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
11388 CATCCGAATA
Statistics
Matches: 178, Mismatches: 5, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
38 1 0.01
39 73 0.41
40 103 0.58
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:11259 original size:79 final size:79
Alignment explanation
Indices: 11161--11384 Score: 389
Period size: 79 Copynumber: 2.8 Consensus size: 79
11151 GCTACTTGCT
11161 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
11226 TATAGTAACTCGCA
66 TATAGTAACTCGCA
11240 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
11305 ATATAGTAACTCGCA
66 -TATAGTAACTCGCA
* * *
11320 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
11383 GT
65 GT
11385 TATCATCCGA
Statistics
Matches: 140, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
78 2 0.01
79 110 0.79
80 28 0.20
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
TATAGTAACTCGCA
Found at i:11360 original size:119 final size:119
Alignment explanation
Indices: 11161--11387 Score: 402
Period size: 119 Copynumber: 1.9 Consensus size: 119
11151 GCTACTTGCT
*
11161 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
* *
11226 TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
66 AATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
11280 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
11344 AATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
66 AA-TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
11388 CATCCGAATA
Statistics
Matches: 103, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
118 11 0.11
119 92 0.89
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (119 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:19327 original size:40 final size:40
Alignment explanation
Indices: 19278--19505 Score: 397
Period size: 40 Copynumber: 5.7 Consensus size: 40
19268 TAGCTACTTT
19278 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
19318 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
19358 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
19398 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
19438 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
19477 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
19506 CATCCGAATA
Statistics
Matches: 180, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
38 1 0.01
39 34 0.19
40 144 0.80
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:24501 original size:45 final size:46
Alignment explanation
Indices: 24443--24530 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 46
24433 CCCTAATAAT
**
24443 AACTCTTCAGAGTTACCTGTTAAGT-TTAATAAGCTTCCTGATTAA
1 AACTCTTCAGAGTTACCTGTTAAGTCCGAATAAGCTTCCTGATTAA
* *
24488 AACTCTT-ATGAGTTTCCTGTTTAGTCCGAATAAGCTTCCTGAT
1 AACTCTTCA-GAGTTACCTGTTAAGTCCGAATAAGCTTCCTGAT
24531 ACATGGTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 1 0.03
45 21 0.57
46 15 0.41
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (46 bp):
AACTCTTCAGAGTTACCTGTTAAGTCCGAATAAGCTTCCTGATTAA
Done.