Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2484
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: 28699
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Found at i:3391 original size:13 final size:13
Alignment explanation
Indices: 3373--3397 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3363 ATATCACCTT
3373 GCAAAGACAAGGC
1 GCAAAGACAAGGC
3386 GCAAAGACAAGG
1 GCAAAGACAAGG
3398 AGCATACTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.32, T:0.00
Consensus pattern (13 bp):
GCAAAGACAAGGC
Found at i:12924 original size:405 final size:403
Alignment explanation
Indices: 12172--12981 Score: 1386
Period size: 405 Copynumber: 2.0 Consensus size: 403
12162 CAAAAAGAAA
12172 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
1 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
* *
12237 TTGAAAACAATTCAGCAGTTAAGAGTAGGTAACAACACATGCTGCTTGGATGCAAATAAAGACCT
66 TCGAAAACAATTCAACAGTTAAGAGTAGGTAACAACACATGCTGCTTGGATGCAAATAAAGACCT
* * * *
12302 TTGCGTTTATTAGCAACACATTACATTTAAGAGATAAAGCTTGACACGCCTTGCATCAAGCAACT
131 CTGCCTTTATTAGAAACACATTACATTTAAGAGATAAAGCTTGACACGCCTGGCATCAAGCAACT
** *
12367 AACCAGAATTGACAATAAGAATGATAACAGCATGATTTTATCAAAATGCCTTCAGCATGTAATAC
196 AACCAGAATCAACAATAAGAATGATAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAATAC
* *
12432 TTTCCAACTTATAACCAGAATTCATCATACAAAGAAAGAAATACAGGAAATGTACTTTAAATGGA
261 TTTCCAACTTAAAACCAGAATTCATCATACAAAGAAAGAAATACAGGAAATGTACTTTAAAGGGA
* * *
12497 TGGAAAGGATGTACGATAATTTGATTGGATAAGGTAAGAAGAGTAAGGTAAAGATAAGGAAAATT
326 TGGAAAGGATGTACGATAATTTGATTGGACAAGGTAAGAAGAGTAAGGTAAAGAGAAGGAAAATG
12562 ATGCTTTATTGTC
391 ATGCTTTATTGTC
*
12575 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCGGGAATTGGAGAAAGAGT
1 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
12640 TCGAAAACAATTCAACAGTTAAGAGTAGGTAACAACACATATGCTGCTTGGATGCAAATAAAGAC
66 TCGAAAACAATTCAACAGTTAAGAGTAGGTAACAACAC--ATGCTGCTTGGATGCAAATAAAGAC
* * *
12705 CTCTGCCTTTATTAGAAACACATTATATTTAAGAGATAAAGGTTGACACGCCTGGCGTCAAGCAA
129 CTCTGCCTTTATTAGAAACACATTACATTTAAGAGATAAAGCTTGACACGCCTGGCATCAAGCAA
* *
12770 CTAACCAGAATCAACAATAAGAATGTTAACAGCATGATTTCATTAAAATGCCTTCAGCATGTAAT
194 CTAACCAGAATCAACAATAAGAATGATAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAAT
*
12835 ACTTTCCAACTTAAAACCAGAATTCATCATACATAGAAAGAAATACAGGAAATGTACTTTAAAGG
259 ACTTTCCAACTTAAAACCAGAATTCATCATACAAAGAAAGAAATACAGGAAATGTACTTTAAAGG
* * *
12900 GATGGAAAGGATGTACGTTAATTTGATTGGACAAGGTAAGAAGATTAAGGTAAAGGGAAGGAAAA
324 GATGGAAAGGATGTACGATAATTTGATTGGACAAGGTAAGAAGAGTAAGGTAAAGAGAAGGAAAA
12965 TGATGCTTTATTGTC
389 TGATGCTTTATTGTC
12980 TG
1 TG
12982 TTGGAGGAGA
Statistics
Matches: 381, Mismatches: 24, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
403 100 0.26
405 281 0.74
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (403 bp):
TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
TCGAAAACAATTCAACAGTTAAGAGTAGGTAACAACACATGCTGCTTGGATGCAAATAAAGACCT
CTGCCTTTATTAGAAACACATTACATTTAAGAGATAAAGCTTGACACGCCTGGCATCAAGCAACT
AACCAGAATCAACAATAAGAATGATAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAATAC
TTTCCAACTTAAAACCAGAATTCATCATACAAAGAAAGAAATACAGGAAATGTACTTTAAAGGGA
TGGAAAGGATGTACGATAATTTGATTGGACAAGGTAAGAAGAGTAAGGTAAAGAGAAGGAAAATG
ATGCTTTATTGTC
Found at i:13681 original size:31 final size:31
Alignment explanation
Indices: 13643--13704 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
13633 GATAACCATC
13643 ACATAGTACCGAAAATTCAAAAGGTAACACT
1 ACATAGTACCGAAAATTCAAAAGGTAACACT
*
13674 ACATAGTACCGGAAATTCAAAAGGTAACACT
1 ACATAGTACCGAAAATTCAAAAGGTAACACT
13705 CAATTAACCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (31 bp):
ACATAGTACCGAAAATTCAAAAGGTAACACT
Found at i:16229 original size:15 final size:13
Alignment explanation
Indices: 16202--16226 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16192 GCAAGAGCAT
16202 AAAAAAAGGAAAC
1 AAAAAAAGGAAAC
16215 AAAAAAAGGAAA
1 AAAAAAAGGAAA
16227 AACGAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAAAGGAAAC
Found at i:26508 original size:22 final size:19
Alignment explanation
Indices: 26464--26509 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 19
26454 TACAAATAAA
*
26464 AGAAAGCAATTATGAGATG
1 AGAAAGCAATTATGAAATG
26483 AGAAAGCAAATTAATTGAAATG
1 AGAAAGC-AATT-A-TGAAATG
26505 AGAAA
1 AGAAA
26510 ACAACAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 4 0.17
21 1 0.04
22 11 0.48
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.20
Consensus pattern (19 bp):
AGAAAGCAATTATGAAATG
Done.