Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2044
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: 42600
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Found at i:1560 original size:85 final size:85
Alignment explanation
Indices: 1454--1609 Score: 237
Period size: 85 Copynumber: 1.8 Consensus size: 85
1444 CAACTCGCAC
* *
1454 AAATGCCCTTCGGGTCTTAGCCCGGATTATAGGTCA-ATAGCACAAA-TGCCTTCGGACTTGGCC
1 AAATGCCCTTCGGGACTTAGCCCGGATTATA-GTCACATAGCACAAATTGCCTTCGGACTTAGCC
1517 CGGGATATAGTCACTAGCACCA
65 C-GGATATAGTCACTAGCACCA
*
1539 AAATG-CCTTCGGGACTTTAGCCCGGATTATAGTCACTTAGCACAAATTGCCTTCGGACTTAGCC
1 AAATGCCCTTCGGGAC-TTAGCCCGGATTATAGTCACATAGCACAAATTGCCTTCGGACTTAGCC
1603 CGGATAT
65 CGGATAT
1610 CATTCGAATA
Statistics
Matches: 65, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
84 13 0.20
85 35 0.54
86 17 0.26
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (85 bp):
AAATGCCCTTCGGGACTTAGCCCGGATTATAGTCACATAGCACAAATTGCCTTCGGACTTAGCCC
GGATATAGTCACTAGCACCA
Found at i:1571 original size:44 final size:41
Alignment explanation
Indices: 1437--1607 Score: 188
Period size: 42 Copynumber: 4.0 Consensus size: 41
1427 TAGCCGGGGT
* *
1437 ATTATAG-CAACTCGCAC-AAATGCCCTTCGGGTCTTAGCCCGG
1 ATTATAGTC-ACTAGCACAAAATG-CCTTC-GGACTTAGCCCGG
* *
1479 ATTATAGGTCAATAGCAC-AAATGCCTTCGGACTTGGCCCGGG
1 ATTATA-GTCACTAGCACAAAATGCCTTCGGACTTAGCCC-GG
1521 A-TATAGTCACTAGCACCAAAATGCCTTCGGGACTTTAGCCCGG
1 ATTATAGTCACTAGCA-CAAAATGCCTTC-GGAC-TTAGCCCGG
*
1564 ATTATAGTCACTTAGCACAAATTGCCTTCGGACTTAGCCCGG
1 ATTATAGTCAC-TAGCACAAAATGCCTTCGGACTTAGCCCGG
1606 AT
1 AT
1608 ATCATTCGAA
Statistics
Matches: 113, Mismatches: 7, Indels: 18
0.82 0.05 0.13
Matches are distributed among these distances:
40 9 0.08
41 14 0.12
42 35 0.31
43 23 0.20
44 27 0.24
45 5 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (41 bp):
ATTATAGTCACTAGCACAAAATGCCTTCGGACTTAGCCCGG
Found at i:1632 original size:23 final size:23
Alignment explanation
Indices: 1606--1655 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 23
1596 CTTAGCCCGG
*
1606 ATATCATTCGAATAATCATG-CAC
1 ATATCATTC-AAAAATCATGACAC
1629 ATAT-A-TCAAAAATCATGACAC
1 ATATCATTCAAAAATCATGACAC
1650 AT-TCAT
1 ATATCAT
1656 ATTCATTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
20 10 0.43
21 8 0.35
22 1 0.04
23 4 0.17
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (23 bp):
ATATCATTCAAAAATCATGACAC
Found at i:4416 original size:14 final size:14
Alignment explanation
Indices: 4397--4423 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4387 CTAAAACTGC
4397 TTTAGAACGGGTAA
1 TTTAGAACGGGTAA
4411 TTTAGAACGGGTA
1 TTTAGAACGGGTA
4424 GGCCACTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (14 bp):
TTTAGAACGGGTAA
Found at i:16140 original size:31 final size:32
Alignment explanation
Indices: 16104--16167 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
16094 GAGAATGTTT
* *
16104 AAAACCCAGACATGAT-AATAAAATTTCCGAA
1 AAAACCCAAACATGATAAAAAAAATTTCCGAA
*
16135 AAAACCGAAACATGATAAAAAAAATTTCCGAA
1 AAAACCCAAACATGATAAAAAAAATTTCCGAA
16167 A
1 A
16168 TCTAATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 14 0.48
32 15 0.52
ACGTcount: A:0.56, C:0.17, G:0.09, T:0.17
Consensus pattern (32 bp):
AAAACCCAAACATGATAAAAAAAATTTCCGAA
Found at i:17860 original size:2 final size:2
Alignment explanation
Indices: 17853--17889 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17843 TGGTACCACT
17853 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
17890 CCCACAATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21928 original size:24 final size:24
Alignment explanation
Indices: 21901--21949 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
21891 GAAAATAGCC
21901 TTTGAATTGAAACAAAAGTGAATG
1 TTTGAATTGAAACAAAAGTGAATG
* *
21925 TTTGAATTTACACAAAAGTGAATG
1 TTTGAATTGAAACAAAAGTGAATG
21949 T
1 T
21950 CGTGACATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (24 bp):
TTTGAATTGAAACAAAAGTGAATG
Found at i:35223 original size:78 final size:81
Alignment explanation
Indices: 35088--35271 Score: 227
Period size: 78 Copynumber: 2.3 Consensus size: 81
35078 TTGAATGATG
*
35088 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
35152 TGT-CGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
35166 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
35228 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
35246 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
35272 AACGAGGAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
77 1 0.01
78 39 0.43
79 36 0.40
80 15 0.16
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:35230 original size:40 final size:40
Alignment explanation
Indices: 35088--35271 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
35078 TTGAATGATG
* * * *
35088 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
35128 TCCGGACTAAGAT-CCGAAGGCATTTGT-CGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
35167 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
35206 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
35247 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
35272 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 14 0.11
39 35 0.28
40 68 0.54
41 8 0.06
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:35289 original size:80 final size:77
Alignment explanation
Indices: 35089--35304 Score: 188
Period size: 79 Copynumber: 2.7 Consensus size: 77
35079 TGAATGATGT
** * * * *
35089 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGG-TTAA-ATCCCGAAGGCATT
*
35152 TGTCGAGATACTAATT
62 TGTCGAGATACTAATA
** * *
35168 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCC-GGTTAAATCCCGAAGGCATTTGT
*
35233 GCGAGTTACT-ATAA
65 -CGAGATACTAAT-A
* * *
35247 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCCGGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGTTAAATCCCGAAGG
35305 TACGTGATTT
Statistics
Matches: 115, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
77 1 0.01
78 38 0.33
79 51 0.44
80 25 0.22
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (77 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGTTAAATCCCGAAGGCATTTGTC
GAGATACTAATA
Found at i:35302 original size:79 final size:78
Alignment explanation
Indices: 35140--35304 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 78
35130 CGGACTAAGA
* ** *
35140 TCCGAAGGCATTTGTCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 TCCGAAGGCATTTGTCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
35205 ATCCGGGTTAAGT
66 ATCCGGGTTAAAT
* * *
35218 CCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 TCCGAAGGCATTTGT-CGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
*
35281 CTATATCC-GGTTAAAT
62 CTAAATCCGGGTTAAAT
35297 TCCGAAGG
1 TCCGAAGG
35305 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
78 16 0.22
79 32 0.44
80 25 0.34
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (78 bp):
TCCGAAGGCATTTGTCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAAT
Done.