Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1322
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: 32519
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Found at i:519 original size:11 final size:11
Alignment explanation
Indices: 459--527 Score: 52
Period size: 11 Copynumber: 6.1 Consensus size: 11
449 AGATTGTTCC
459 TAAACATAATAA
1 TAAA-ATAATAA
*
471 TAAATTAAATTAA
1 TAAAAT-AA-TAA
*
484 -AAAATAAAAA
1 TAAAATAATAA
* *
494 GAAACA-AATAG
1 TAAA-ATAATAA
505 TAAAATAATAA
1 TAAAATAATAA
516 TAAAATAATAA
1 TAAAATAATAA
527 T
1 T
528 TTATTTTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
10 3 0.07
11 28 0.62
12 11 0.24
13 3 0.07
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:682 original size:54 final size:53
Alignment explanation
Indices: 577--685 Score: 121
Period size: 55 Copynumber: 2.0 Consensus size: 53
567 TAAATTATAA
* * *
577 CCTAAATTACCTAACGAACAAATTAATAAATCTTGTACTCAAAAACCAAAAAT
1 CCTAAATTACCTAACGAAAAAATCAATAAATCTTGTACTCAAAAACAAAAAAT
* * * *
630 CCTAAATTTGCCTAACGAATAAAATCAATAAATTTTG-ACCTTAAAAAAAAAAAAT
1 CCTAAA-TTACCTAACGAA-AAAATCAATAAATCTTGTA-CTCAAAAACAAAAAAT
685 C
1 C
686 TTAACATGCA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
53 6 0.13
54 12 0.26
55 28 0.61
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (53 bp):
CCTAAATTACCTAACGAAAAAATCAATAAATCTTGTACTCAAAAACAAAAAAT
Found at i:1220 original size:15 final size:16
Alignment explanation
Indices: 1202--1239 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
1192 AAGATATTTT
1202 AACAAATGAAATTAA-
1 AACAAATGAAATTAAC
1217 AACAAATGAAATTAAC
1 AACAAATGAAATTAAC
1233 AACAAAT
1 AACAAAT
1240 ATGGTGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18
Consensus pattern (16 bp):
AACAAATGAAATTAAC
Found at i:19603 original size:11 final size:11
Alignment explanation
Indices: 19543--19611 Score: 52
Period size: 11 Copynumber: 6.1 Consensus size: 11
19533 AGATTGTTCC
19543 TAAACATAATAA
1 TAAA-ATAATAA
*
19555 TAAATTAAATTAA
1 TAAAAT-AA-TAA
*
19568 -AAAATAAAAA
1 TAAAATAATAA
* *
19578 GAAACA-AATAG
1 TAAA-ATAATAA
19589 TAAAATAATAA
1 TAAAATAATAA
19600 TAAAATAATAA
1 TAAAATAATAA
19611 T
1 T
19612 TTATTTTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
10 3 0.07
11 28 0.62
12 11 0.24
13 3 0.07
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:19772 original size:56 final size:56
Alignment explanation
Indices: 19662--19774 Score: 138
Period size: 56 Copynumber: 2.0 Consensus size: 56
19652 AATATTATAA
* **
19662 CCTAAATTAACCTAACGAACAAAATTAATAAATCTTGTACCTCAAAAACCAAAAAT
1 CCTAAATTAACCTAACGAACAAAATCAATAAATCTTGTACCTCAAAAAAAAAAAAT
** * * *
19718 CCTAAATTTGCCTAACGAATAAAATCAATAAATTTTG-ACCTTAAAAGAAAAAAAAT
1 CCTAAATTAACCTAACGAACAAAATCAATAAATCTTGTACCTCAAAA-AAAAAAAAT
19774 C
1 C
19775 TTAAGAACAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
55 8 0.17
56 40 0.83
ACGTcount: A:0.51, C:0.19, G:0.05, T:0.25
Consensus pattern (56 bp):
CCTAAATTAACCTAACGAACAAAATCAATAAATCTTGTACCTCAAAAAAAAAAAAT
Found at i:29100 original size:22 final size:22
Alignment explanation
Indices: 29060--29101 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
29050 ATTAAATTAA
*
29060 AAAATAAAAAGAAACGAATAGT
1 AAAATAAAAAGAAAAGAATAGT
* *
29082 AAAATAATAATAAAAGAATA
1 AAAATAAAAAGAAAAGAATA
29102 ATTTATTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAATAAAAAGAAAAGAATAGT
Found at i:29805 original size:15 final size:16
Alignment explanation
Indices: 29787--29824 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
29777 AAGATATTTT
29787 AACAAATGAAATTAA-
1 AACAAATGAAATTAAC
*
29802 AACAAATGAATTTAAC
1 AACAAATGAAATTAAC
29818 AACAAAT
1 AACAAAT
29825 ACAGTGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.63, C:0.11, G:0.05, T:0.21
Consensus pattern (16 bp):
AACAAATGAAATTAAC
Done.