Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2280
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: 34203
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Found at i:9521 original size:55 final size:52
Alignment explanation
Indices: 9397--9550 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
9387 TAAATTGTAC
* *
9397 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAACATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAACATG
* * *
9450 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAAC-ATG
* * *
9505 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
9551 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 37 0.43
55 45 0.52
56 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAACATG
Found at i:9538 original size:82 final size:80
Alignment explanation
Indices: 9398--9553 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 80
9388 AAATTGTACA
* * *
9398 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAACATGATGCACTAAGTGT
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAACATGA-GCACTAAGTGT
9463 GCGAATTGACCATGCG
65 GCGAATTGACCATGCG
** *
9479 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTG-GCACTAAGT
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGA--ACATGAGCACTAAGT
*
9543 GTGCGAGTTGA
63 GTGCGAATTGA
9554 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
81 17 0.26
82 44 0.68
84 4 0.06
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (80 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAACATGAGCACTAAGTGTG
CGAATTGACCATGCG
Found at i:9555 original size:27 final size:27
Alignment explanation
Indices: 9398--9553 Score: 156
Period size: 27 Copynumber: 5.7 Consensus size: 27
9388 AAATTGTACA
*
9398 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
*
9425 GCACTAAGTGTGCGAAATGAAC-ATGAT-
1 GCACTAAGTGTGCGAATTG-ACTATG-TG
* *
9452 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
9479 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
9507 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
9534 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
9554 TTGTATAGCA
Statistics
Matches: 109, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
26 2 0.02
27 80 0.73
28 27 0.25
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:9564 original size:27 final size:27
Alignment explanation
Indices: 9397--9574 Score: 144
Period size: 27 Copynumber: 6.6 Consensus size: 27
9387 TAAATTGTAC
*
9397 AGCACTAAGTGTGCGA-TTCGACTATGT
1 AGCACTAAGTGTGCGAGTT-GATTATGT
* ** **
9424 TGCACTAAGTGTGCGAAATGAACATG-
1 AGCACTAAGTGTGCGAGTTGATTATGT
* ** *
9450 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
9478 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
* *
9506 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * *
9533 GGCACTAAGTGTGCGAGTTGATTGTAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
9560 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
9575 GGCTCAATAT
Statistics
Matches: 123, Mismatches: 24, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:9565 original size:82 final size:80
Alignment explanation
Indices: 9390--9574 Score: 201
Period size: 82 Copynumber: 2.3 Consensus size: 80
9380 GCGGGATTAA
* * *
9390 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAACATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAACATGA-GCA
9455 CTAAGTGTGCGAATTG
65 CTAAGTGTGCGAATTG
*** * * ** *
9471 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTG-G
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGA--ACATGAG
*
9535 CACTAAGTGTGCGAGTTG
63 CACTAAGTGTGCGAATTG
* *
9553 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
9575 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
81 20 0.24
82 58 0.71
84 4 0.05
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (80 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAACATGAGCAC
TAAGTGTGCGAATTG
Found at i:12199 original size:28 final size:28
Alignment explanation
Indices: 12166--12252 Score: 104
Period size: 28 Copynumber: 3.1 Consensus size: 28
12156 CACATACCTA
* *
12166 TATATGGCCCACAAGGCCCAATCTC-TT
1 TATATGGCCCACTAGGCCCAATCACATT
*
12193 TCATATGGCCTACTAGGCCCAATCACATT
1 T-ATATGGCCCACTAGGCCCAATCACATT
* *
12222 TATGTGGCCCATTAGGCCCAAATCACATT
1 TATATGGCCCACTAGGCCC-AATCACATT
12251 TA
1 TA
12253 CAGTCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
27 1 0.02
28 36 0.71
29 14 0.27
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (28 bp):
TATATGGCCCACTAGGCCCAATCACATT
Found at i:21633 original size:14 final size:15
Alignment explanation
Indices: 21616--21644 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21606 TCACGAAAAT
21616 TTCACACAT-ATAAA
1 TTCACACATAATAAA
21630 TTCACACATAATAAA
1 TTCACACATAATAAA
21645 CATAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:23755 original size:40 final size:40
Alignment explanation
Indices: 23517--23748 Score: 349
Period size: 40 Copynumber: 5.8 Consensus size: 40
23507 TGGATGATAA
* *
23517 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
* *
23557 TCGGGCTAAGTCCCGAAGGCATTTGTGAGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
23597 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
23637 CCGGGCTAAGTCCTGAAGGCATTTGTACGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
23677 CCGGGCTATGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
23717 CCGGGCTATGTCCCGAAGGCATTCGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
23749 AGCTATACCC
Statistics
Matches: 177, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
39 1 0.01
40 176 0.99
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:31776 original size:40 final size:40
Alignment explanation
Indices: 31716--31866 Score: 198
Period size: 40 Copynumber: 3.8 Consensus size: 40
31706 TGGATGATAA
* * * *
31716 CCGGGCTAAGT-CCGAAGGCATTTGCGCTAGTGACCAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
31755 CCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
31795 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
31835 CCGGGCTATGTCCCGAAGGCATTCGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
31867 AGCTATACCG
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 11 0.11
40 89 0.89
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:31842 original size:80 final size:79
Alignment explanation
Indices: 31716--31890 Score: 196
Period size: 80 Copynumber: 2.2 Consensus size: 79
31706 TGGATGATAA
* * * *
31716 CCGGGCTAAGTCCGAAGGCATTTGCGCTAGTGACCAGTTCCAGGCTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGTCCGAAGGCATTGGCGCGAGTGACCAGTTCCAGGCTAAGTCCCGAAGGCATTCGA
31781 GCGAGTTACTATAT
66 GCGAGTTACTATAT
* * * * *
31795 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTA-TATCCGGGCTATGTCCCGAAGGCATTC
1 CCGGGCTAAGT-CCGAAGGCATTGGCGCGAGTGACCAGT-TCCAGGCTAAGTCCCGAAGGCATTC
31859 GAGCGAG-TAGCTATA-
64 GAGCGAGTTA-CTATAT
* *
31874 CC-GGTTAAATCCGAAGG
1 CCGGGCTAAGTCCGAAGG
31891 TACTTGGCTT
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
77 7 0.09
78 6 0.07
79 16 0.20
80 53 0.65
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.23
Consensus pattern (79 bp):
CCGGGCTAAGTCCGAAGGCATTGGCGCGAGTGACCAGTTCCAGGCTAAGTCCCGAAGGCATTCGA
GCGAGTTACTATAT
Done.