Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2712
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: 26275
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Found at i:2199 original size:40 final size:40
Alignment explanation
Indices: 2094--2310 Score: 307
Period size: 40 Copynumber: 5.5 Consensus size: 40
2084 CGGATGATAA
* *
2094 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
2134 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
2173 CCGGGCTACGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
2213 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
2253 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
2293 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
2311 TACTTGGTTT
Statistics
Matches: 162, Mismatches: 12, Indels: 7
0.90 0.07 0.04
Matches are distributed among these distances:
39 50 0.31
40 112 0.69
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:7279 original size:28 final size:27
Alignment explanation
Indices: 7215--7366 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
7205 TTATTAAGTC
* *
7215 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
7242 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
7270 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
7297 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
7325 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
7352 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
7367 GCACAATTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:7299 original size:55 final size:55
Alignment explanation
Indices: 7215--7391 Score: 246
Period size: 55 Copynumber: 3.2 Consensus size: 55
7205 TTATTAAGTC
* * *
7215 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
7270 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * *
7325 CGCACACTTAGTGCTACATATTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
7381 CGCACACTTAG
1 CGCACACTTAG
7392 CGCCAATCTC
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 93 0.85
56 16 0.15
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:15163 original size:55 final size:55
Alignment explanation
Indices: 15102--15253 Score: 241
Period size: 55 Copynumber: 2.8 Consensus size: 55
15092 ATATTAAGTC
* * * * *
15102 CGCACACTCAGTGCTATATAATCAGCTCGCACACCTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
15157 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
15212 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
15254 GCACAATTTA
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 90 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:15168 original size:28 final size:27
Alignment explanation
Indices: 15102--15253 Score: 223
Period size: 27 Copynumber: 5.6 Consensus size: 27
15092 ATATTAAGTC
* * * *
15102 CGCACACTCAGTGCTATATAATCAGCT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
15129 CGCACACCTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
15157 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
15184 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
15212 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
15239 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
15254 GCACAATTTA
Statistics
Matches: 116, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
27 65 0.56
28 51 0.44
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:18525 original size:27 final size:27
Alignment explanation
Indices: 18495--18645 Score: 230
Period size: 27 Copynumber: 5.6 Consensus size: 27
18485 TTATTAAGTC
* *
18495 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
18522 CGCACACTTAGTGCTACATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
18549 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
18576 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* * *
18604 CGCACACTTAGTGCTACATATTTAATT
1 CGCACACTTAGTGCTACATAATCAACT
18631 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
18646 GCACAATTTA
Statistics
Matches: 117, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
27 92 0.79
28 25 0.21
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:18577 original size:54 final size:55
Alignment explanation
Indices: 18495--18670 Score: 237
Period size: 54 Copynumber: 3.2 Consensus size: 55
18485 TTATTAAGTC
* *
18495 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
18549 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * * *
18604 CGCACACTTAGTGCTACATATTTAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
18660 CGCACACTTAG
1 CGCACACTTAG
18671 CGCCAATCTC
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
54 46 0.43
55 46 0.43
56 16 0.15
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:18614 original size:82 final size:81
Alignment explanation
Indices: 18495--18645 Score: 239
Period size: 82 Copynumber: 1.9 Consensus size: 81
18485 TTATTAAGTC
*
18495 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAACTCGCACACTTAG
1 CGCACACTCAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAACTCGCACACTTAG
18560 TGCTACATAGTCAACT
66 TGCTACATAGTCAACT
* * * * *
18576 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATATTTAATTCGCACACTTA
1 CGCACACTCAGTGCTACATAATC-AACTCGCACACTTAGTGCTACATAATCAACTCGCACACTTA
18641 GTGCT
65 GTGCT
18646 GCACAATTTA
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
81 20 0.32
82 43 0.68
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (81 bp):
CGCACACTCAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAACTCGCACACTTAG
TGCTACATAGTCAACT
Found at i:24693 original size:39 final size:40
Alignment explanation
Indices: 24630--24815 Score: 299
Period size: 40 Copynumber: 4.7 Consensus size: 40
24620 TATTCGGATG
* *
24630 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
24670 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
24709 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
24749 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
24789 ATAA-CGGGCTAAGT-CCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
24816 AGCAAGTAGC
Statistics
Matches: 139, Mismatches: 4, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
38 13 0.09
39 46 0.33
40 80 0.58
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:24739 original size:40 final size:40
Alignment explanation
Indices: 24634--24838 Score: 296
Period size: 40 Copynumber: 5.2 Consensus size: 40
24624 CGGATGATAA
* *
24634 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
24674 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
24713 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
24753 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
24792 ACGGGCTAAGT-CCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
24831 CC-GGCTAA
1 CCGGGCTAA
24839 ATTCGAAGGT
Statistics
Matches: 154, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
37 2 0.01
38 28 0.18
39 46 0.30
40 78 0.51
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:24797 original size:79 final size:78
Alignment explanation
Indices: 24630--24815 Score: 286
Period size: 79 Copynumber: 2.4 Consensus size: 78
24620 TATTCGGATG
* *
24630 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
1 ATAA-CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT
24695 TTGTGCGAGTTACT
65 TTGTGCGAGTTACT
* *
24709 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGC
1 ATA-ACGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGC
24773 ATTTGTGCGAGTTACT
63 ATTTGTGCGAGTTACT
24789 ATAACGGGCTAAGT-CCGAAGGCATTTG
1 ATAACGGGCTAAGTCCCGAAGGCATTTG
24816 AGCAAGTAGC
Statistics
Matches: 99, Mismatches: 5, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
78 15 0.15
79 56 0.57
80 28 0.28
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (78 bp):
ATAACGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCATT
TGTGCGAGTTACT
Done.