Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2512
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: 23550
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Found at i:467 original size:15 final size:15
Alignment explanation
Indices: 447--497 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
437 AGACACACAG
447 GTGTGTGTCTCGGCC
1 GTGTGTGTCTCGGCC
*
462 GTGTGTGTCACACGG--
1 GTGTGTGT--CTCGGCC
477 GTGTGTGTCTCGGCC
1 GTGTGTGTCTCGGCC
492 GTGTGT
1 GTGTGT
498 AACACACGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 4 0.13
15 22 0.73
17 4 0.13
ACGTcount: A:0.04, C:0.22, G:0.41, T:0.33
Consensus pattern (15 bp):
GTGTGTGTCTCGGCC
Found at i:480 original size:30 final size:30
Alignment explanation
Indices: 439--506 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
429 ACACGGGTAG
* *
439 ACACACAGGTGTGTGTCTCGGCCGTGTGTG
1 ACACACGGGTGTGTGTCTCGGCCGTGTGTA
*
469 TCACACGGGTGTGTGTCTCGGCCGTGTGTA
1 ACACACGGGTGTGTGTCTCGGCCGTGTGTA
499 ACACACGG
1 ACACACGG
507 TATTCCCATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.15, C:0.25, G:0.35, T:0.25
Consensus pattern (30 bp):
ACACACGGGTGTGTGTCTCGGCCGTGTGTA
Found at i:5072 original size:46 final size:46
Alignment explanation
Indices: 4965--5187 Score: 188
Period size: 46 Copynumber: 4.8 Consensus size: 46
4955 ATTTGAGTGT
* * *
4965 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACAA
1 GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGC-TCGAGACGA
* * *
5013 GAGCTAGTGTAAGA-CATGTCTAGGACATGCACCGGGCTCGAGACGTA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATC-GGCTCGAGACG-A
* *
5060 -AGCCAGTGTAAGA-CATGTTTGGGACATGTC-TCGGCTACGAGATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATG-CATCGGCT-CGAGACGA
* * * * *
5105 TAGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGA-TA
1 GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCTCGAGACGA
* *
5151 TGAGCCAGTGTAA-AACTTGTCTGGGACATGGCATCGG
1 -GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGG
5188 TACCTTACCC
Statistics
Matches: 145, Mismatches: 21, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
45 5 0.03
46 76 0.52
47 45 0.31
48 19 0.13
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.22
Consensus pattern (46 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCTCGAGACGA
Found at i:9552 original size:27 final size:27
Alignment explanation
Indices: 9522--9699 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
9512 ATATTAAGTC
* * *
9522 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
9549 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
9577 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
9604 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
9631 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
9658 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
9685 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9700 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 105 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:9606 original size:55 final size:54
Alignment explanation
Indices: 9522--9699 Score: 232
Period size: 54 Copynumber: 3.3 Consensus size: 54
9512 ATATTAAGTC
* * *
9522 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAA-T
* * * *
9577 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* ** *
9631 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
9685 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9700 GTACAATTTA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:9688 original size:81 final size:82
Alignment explanation
Indices: 9543--9698 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
9533 TGCTATATAA
* *
9543 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
9608 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
9625 TCAATTCGCACACTTAGTG-CATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
9688 ACACTTAGTGC
65 ACACTTAGTGC
9699 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 43 0.64
82 24 0.36
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Found at i:17656 original size:27 final size:27
Alignment explanation
Indices: 17626--17803 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
17616 ATATTAAGTC
* * *
17626 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
17653 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
17681 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
17708 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
17735 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* * *
17762 CGCACACTTAGTGCAATATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
17789 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17804 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 104 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:17710 original size:55 final size:54
Alignment explanation
Indices: 17626--17803 Score: 223
Period size: 54 Copynumber: 3.3 Consensus size: 54
17616 ATATTAAGTC
* * *
17626 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAA-T
* * * *
17681 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* ** * *
17735 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAATATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
17789 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17804 GTACAATTTA
Statistics
Matches: 106, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 59 0.56
55 46 0.43
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:17792 original size:81 final size:82
Alignment explanation
Indices: 17647--17802 Score: 226
Period size: 81 Copynumber: 1.9 Consensus size: 82
17637 TGCTATATAA
* *
17647 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
17712 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * ** *
17729 TCAATTCGCACACTTAGTG-CATCATATTC-ATTTCGCACACTTAGTGCAATATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
17792 ACACTTAGTGC
65 ACACTTAGTGC
17803 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 42 0.64
82 24 0.36
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Done.