Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold770
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: 22524
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Found at i:5606 original size:50 final size:50
Alignment explanation
Indices: 5530--5693 Score: 274
Period size: 50 Copynumber: 3.3 Consensus size: 50
5520 AATAGAAAAT
*
5530 GCATGCATGGGAAAGCATAAAGATTGCAATTGGAGACAAAACATGCAGAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
* * *
5580 GCATGCATGGGAAAACACAAAAATTGCAATTGGAGACAAAACATGCGGAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
*
5630 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGTAGAG
1 GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
*
5680 ACATGCATGGGAAA
1 GCATGCATGGGAAA
5694 TGAAAAAAGC
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 105 1.00
ACGTcount: A:0.43, C:0.14, G:0.27, T:0.16
Consensus pattern (50 bp):
GCATGCATGGGAAAGCATAAAAATTGCAATTGGAGACAAAACATGCAGAG
Found at i:7350 original size:53 final size:50
Alignment explanation
Indices: 7246--7367 Score: 140
Period size: 53 Copynumber: 2.4 Consensus size: 50
7236 GCTCGTAATT
*
7246 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTT-CTTCAATC
* **
7297 GAGGGGATACTCCAACCCCGGTTTTA-TTTCTAAAATATTAATTT-TTCACAATC
1 --GGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTCTT--CAATC
7350 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
7368 TTATTTTCGA
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
51 20 0.32
52 4 0.06
53 38 0.61
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (50 bp):
GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTTCAATC
Found at i:7522 original size:79 final size:79
Alignment explanation
Indices: 7296--7603 Score: 501
Period size: 79 Copynumber: 3.9 Consensus size: 79
7286 TTCCTTTAAT
* *
7296 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTCC
1 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCC
*
7361 AACCCCGTTATTTT
66 AACCCCGTTATTTC
* * *
7375 CGAGGGGATACTCCAA-CCCGGTTTTATCTCTAAAATATTAATTTTTCACAATCGGGGATACTCC
1 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCC
7439 AACCCCGTTATTTC
66 AACCCCGTTATTTC
* *
7453 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCC
1 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCC
7518 AACCCCGTTATTTC
66 AACCCCGTTATTTC
* * **
7532 CGAGGGGATACTCCAACCTCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTTT
1 CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCC
7597 AACCCCG
66 AACCCCG
7604 ATTTTATCTT
Statistics
Matches: 217, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
78 76 0.35
79 141 0.65
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (79 bp):
CGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCC
AACCCCGTTATTTC
Found at i:21279 original size:121 final size:122
Alignment explanation
Indices: 21084--21623 Score: 706
Period size: 121 Copynumber: 4.4 Consensus size: 122
21074 AAAGAGCAGA
* * * * *
21084 CGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTAC
1 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAAGACGCCTTT-T
*
21149 CTTTTAAAGCCCACACAAGCTGGTGGCACCTTT-AGTCTTC-AAGAGCAGGACGCTTT
65 CTTTTAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCTTT
*
21205 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCGGTCCTCAAAGAGCAAGACGCCTTTTC
1 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAAGACGCCTTTTC
* * *
21270 TTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTCAGTCCTCAAAAAGCAGGACACCTT
66 TTTT-AAAGCCCACACAAGCTGGTGGCACC-TTTCAGTCCTCAAAGAGCAGGACGCTTT
* * *
21329 CGCCTTT-AAAGCCCACACAAGCTGCTGGCACCTTT--AGTCCTCAAAGAGCAAGACGCCTTTTC
1 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAAGACGCCTTTT-
*
21391 CTTTTAAAGCCCACACAAGCTGGTGTGCACCTTT-AGTCTTCAAAGAGCAGGACGCTTT
65 CTTTTAAAGCCCACACAAGCTGGTG-GCACCTTTCAGTCCTCAAAGAGCAGGACGCTTT
*
21449 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCC-TTTC
1 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAAGACGCCTTTTC
* * *
21512 TTTTCAAAGCCCACGCAAGTTGGTGGCACTTTTCCAGTCCTC-AAGAGCAGGACGCCTTT
66 TTTT-AAAGCCCACACAAGCTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACG-CTTT
* * * * *
21571 -TCTTTTCAAAAAGCCCACACGAGTTGGTGGCAC-CTTCCAGCCCTCAAAGAGCA
1 CGCCTTTC--AAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCA
21624 GGATACACTT
Statistics
Matches: 373, Mismatches: 31, Indels: 28
0.86 0.07 0.06
Matches are distributed among these distances:
120 44 0.12
121 194 0.52
122 46 0.12
123 69 0.18
124 20 0.05
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (122 bp):
CGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAAGACGCCTTTTC
TTTTAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCTTT
Found at i:21358 original size:61 final size:61
Alignment explanation
Indices: 21084--21626 Score: 623
Period size: 61 Copynumber: 8.9 Consensus size: 61
21074 AAAGAGCAGA
* * *
21084 CGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCTAGTCCTCAAAGAGCAGGACGCCTT
1 CGCCTTTCAAAGCCCACACAAGCTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTT
** * * * *
21146 TACCTTTTAAAGCCCACACAAGCTGGTGGCACCTTT-AGTCTTC-AAGAGCAGGACGCTTT
1 CGCCTTTCAAAGCCCACACAAGCTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTT
* * *
21205 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCGGTCCTCAAAGAGCAAGACGCCTT
1 CGCCTTTCAAAGCCCACACAAGCTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTT
** * * *
21267 TTCTTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTCAGTCCTCAAAAAGCAGGACACCTT
1 CGCCTTTCAAAGCCCACACAAGCTGGTGGCA-CTTTTCAGTCCTCAAAGAGCAGGACGCCTT
* * *
21329 CGCCTTT-AAAGCCCACACAAGCTGCTGGCACCTTT-AGTCCTCAAAGAGCAAGACGCCTT
1 CGCCTTTCAAAGCCCACACAAGCTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTT
** * * * *
21388 TTCCTTTTAAAGCCCACACAAGCTGGTGTGCACCTTT-AGTCTTCAAAGAGCAGGACGCTTT
1 CGCCTTTCAAAGCCCACACAAGCTGGTG-GCACTTTTCAGTCCTCAAAGAGCAGGACGCCTT
*
21449 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTT
1 CGCCTTTCAAAGCCCACACAAGCTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTT
* * * *
21510 -TCTTTTCAAAGCCCACGCAAGTTGGTGGCACTTTTCCAGTCCTC-AAGAGCAGGACGCCTT
1 CGCCTTTCAAAGCCCACACAAGCTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTT
** * * * * * *
21570 TTCTTTTCAAAAAGCCCACACGAGTTGGTGGCACCTTCCAGCCCTCAAAGAGCAGGA
1 CGCCTTTC--AAAGCCCACACAAGCTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
21627 TACACTTTAT
Statistics
Matches: 416, Mismatches: 53, Indels: 23
0.85 0.11 0.05
Matches are distributed among these distances:
59 72 0.17
60 84 0.20
61 117 0.28
62 104 0.25
63 39 0.09
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (61 bp):
CGCCTTTCAAAGCCCACACAAGCTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTT
Found at i:21459 original size:182 final size:179
Alignment explanation
Indices: 21084--21626 Score: 671
Period size: 182 Copynumber: 3.0 Consensus size: 179
21074 AAAGAGCAGA
* *
21084 CGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTAC
1 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGCC-TTAC
* * *
21149 CTTTTAAAGCCCACACAAGCTGGTGGCACCTTTAGTCTTCAAGAGCAGGACG-CTTTCGCCTTTC
64 C-TTTAAAGCCCACACAAGCTGGTGGCACCTTTAGTCCTCAAGAGCAGGACGCCTTT-TCCTTTT
* * *
21213 AAAGCCCACACAAGTTGGTGGCACTTTTCCGGTCCTCAAAGAGCAAGACGCCTTT
127 AAAGCCCACACAAGTTGGTGGCACCTTT--AGTCCTCAAAGAGCAGGACGCCTTT
* * * * * *
21268 -TCTTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTCAGTCCTCAAAAAGCAGGACACCTTCGC
1 CGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAGCAGGACGCCTT-AC
* *
21332 CTTTAAAGCCCACACAAGCTGCTGGCACCTTTAGTCCTCAAAGAGCAAGACGCCTTTTCCTTTTA
64 CTTTAAAGCCCACACAAGCTGGTGGCACCTTTAGTCCTC-AAGAGCAGGACGCCTTTTCCTTTTA
* *
21397 AAGCCCACACAAGCTGGTGTGCACCTTTAGTCTTCAAAGAGCAGGACG-CTTT
128 AAGCCCACACAAGTTGGTG-GCACCTTTAGTCCTCAAAGAGCAGGACGCCTTT
* *
21449 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCTT
1 CGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTACCT
* * *
21514 TTCAAAGCCCACGCAAGTTGGTGGCACTTTTCCAGTCCTCAAGAGCAGGACGCCTTTT-CTTTTC
66 TT-AAAGCCCACACAAGCTGGTGGCACCTTT--AGTCCTCAAGAGCAGGACGCCTTTTCCTTTT-
* * *
21578 AAAAAGCCCACACGAGTTGGTGGCACCTTCCAGCCCTCAAAGAGCAGGA
127 --AAAGCCCACACAAGTTGGTGGCACCTT-TAGTCCTCAAAGAGCAGGA
21627 TACACTTTAT
Statistics
Matches: 311, Mismatches: 35, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
180 4 0.01
181 61 0.20
182 99 0.32
183 97 0.31
184 50 0.16
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (179 bp):
CGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTACCT
TTAAAGCCCACACAAGCTGGTGGCACCTTTAGTCCTCAAGAGCAGGACGCCTTTTCCTTTTAAAG
CCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTT
Done.