Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold967
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: 27043
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Found at i:1277 original size:27 final size:27
Alignment explanation
Indices: 1245--1450 Score: 310
Period size: 28 Copynumber: 7.6 Consensus size: 27
1235 TAATTAAGTC
* *
1245 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
1272 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
1300 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
1328 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATC-AACT
1356 CGCACACTTAGTGCTACATAATCAA-T
1 CGCACACTTAGTGCTACATAATCAACT
1382 CGCACACTTA-TGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAA-CT
1409 CGCACACTTAGTGCTACA-AATCAAGCT
1 CGCACACTTAGTGCTACATAATCAA-CT
1436 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1451 GTACAATTTA
Statistics
Matches: 172, Mismatches: 3, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
25 14 0.08
26 11 0.06
27 59 0.34
28 88 0.51
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:1468 original size:29 final size:27
Alignment explanation
Indices: 1244--1475 Score: 229
Period size: 28 Copynumber: 8.4 Consensus size: 27
1234 ATAATTAAGT
* *
1244 CCGCACACTCAGTGCTATATAATC-AAC
1 CCGCACACTTAGTGCTACA-AATCAAAC
* *
1271 TCGCACACTTAGTGCTATATAATCAAAC
1 CCGCACACTTAGTGCTACA-AATCAAAC
*
1299 TCGCACACTTAGTGCTACATAATCAAAC
1 CCGCACACTTAGTGCTACA-AATCAAAC
* *
1327 TCGCACACTTAGTGCTACATAATCAAAT
1 CCGCACACTTAGTGCTACA-AATCAAAC
*
1355 TCGCACACTTAGTGCTACATAATC-AA-
1 CCGCACACTTAGTGCTACA-AATCAAAC
* *
1381 TCGCACACTTA-TGCTACATAATCAAGC
1 CCGCACACTTAGTGCTACA-AATCAAAC
* *
1408 TCGCACACTTAGTGCTACAAATCAAGC
1 CCGCACACTTAGTGCTACAAATCAAAC
* * *
1435 TCGCACACTTAGTGCTGTACAATTTAAAC
1 CCGCACACTTAGTGC--TACAAATCAAAC
1464 CCGCACACTTAG
1 CCGCACACTTAG
1476 CGCCAATCTC
Statistics
Matches: 190, Mismatches: 9, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
25 12 0.06
26 12 0.06
27 58 0.31
28 88 0.46
29 20 0.11
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (27 bp):
CCGCACACTTAGTGCTACAAATCAAAC
Found at i:9570 original size:28 final size:28
Alignment explanation
Indices: 9507--9716 Score: 332
Period size: 28 Copynumber: 7.5 Consensus size: 28
9497 ATATTAAGTC
* *
9507 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
9534 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
9562 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
9590 CGCACACCTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAACT
*
9618 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
9646 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
9674 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
9702 CGTACACTTAGTGCT
1 CGCACACTTAGTGCT
9717 GTACAATTTA
Statistics
Matches: 174, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 22 0.13
28 152 0.87
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:12961 original size:40 final size:40
Alignment explanation
Indices: 12887--13148 Score: 402
Period size: 40 Copynumber: 6.6 Consensus size: 40
12877 AACCCAAGTA
* *
12887 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
* * *
12926 CCTTCGGGTCTTAGCCCTGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
12966 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
13006 CCTTCGGGACTTAGCTCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
13046 CCTTCAGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* * *
13086 CCTTCGGGACTTAGCCCAGATATAGTCACTAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
13126 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
13149 CATTCGAATA
Statistics
Matches: 203, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
39 12 0.06
40 188 0.93
41 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:17377 original size:43 final size:43
Alignment explanation
Indices: 17267--17380 Score: 149
Period size: 43 Copynumber: 2.7 Consensus size: 43
17257 GTCCCTGGCG
* * * * **
17267 TGGTCTTACATGTAATCTCATATCAATGCCACTGTCCCAGGTA
1 TGGTCTTACACGTAATCACATATCGATGCCACTATCCCAGACA
*
17310 GGGTCTTACACGTAATCACATATCGATGCCAAC-ATCCCAGACA
1 TGGTCTTACACGTAATCACATATCGATGCC-ACTATCCCAGACA
17353 TGGTCTTACACGTAATCACATATCGATG
1 TGGTCTTACACGTAATCACATATCGATG
17381 TCCCATATAA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
43 60 0.97
44 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (43 bp):
TGGTCTTACACGTAATCACATATCGATGCCACTATCCCAGACA
Found at i:17717 original size:67 final size:67
Alignment explanation
Indices: 17646--17780 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
17636 CGTCAAACAT
17646 AAATTATTTTTCATTACTGAATGCCAATTCGTAATTTGCTTCTAATTATTACAATTATTTATAAA
1 AAATTATTTTTCATTACTGAATGCCAATTCGTAATTTGCTTCTAATTATTACAATTATTTATAAA
17711 TC
66 TC
*
17713 AAATTATTTTTCATTACTGAATGCCGATTCGTAATTTGCTTCTAATTATTACAATTATTTATAAA
1 AAATTATTTTTCATTACTGAATGCCAATTCGTAATTTGCTTCTAATTATTACAATTATTTATAAA
17778 TC
66 TC
17780 A
1 A
17781 CATATATTGA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.46
Consensus pattern (67 bp):
AAATTATTTTTCATTACTGAATGCCAATTCGTAATTTGCTTCTAATTATTACAATTATTTATAAA
TC
Found at i:23088 original size:27 final size:27
Alignment explanation
Indices: 23058--23235 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
23048 ATATTGAGTC
* *
23058 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
23085 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
23112 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
23140 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
23167 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
23194 CGCAAACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
23221 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
23236 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:23197 original size:82 final size:81
Alignment explanation
Indices: 23079--23234 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
23069 TGCTATATAA
* * *
23079 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCAAACTTAGTGCAACATAGTCAAA-TCGCA
23144 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
23161 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCAAACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCAAACTTAGTGCAACATAGTCAAATCGCA
23225 CACTTAGTGC
65 CACTTAGTGC
23235 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCAAACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:23218 original size:54 final size:54
Alignment explanation
Indices: 23058--23234 Score: 196
Period size: 54 Copynumber: 3.3 Consensus size: 54
23048 ATATTGAGTC
* * * *
23058 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
23112 CGCACACTTAGTGC-TACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* ** *
23167 CGCACACTTAGTGCATCATATTCATTTCGCAAACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
23221 CGCACACTTAGTGC
1 CGCACACTTAGTGC
23235 TGTACAATTT
Statistics
Matches: 103, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
52 1 0.01
54 56 0.54
55 45 0.44
56 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Done.