Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold601
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: 46391
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.18
Warning! 19711 characters in sequence are not A, C, G, or T
Found at i:2078 original size:20 final size:19
Alignment explanation
Indices: 2047--2084 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2037 GGCTAGTAAC
*
2047 GAGCTCAATGAGTTGAATT
1 GAGCTCAATGAGCTGAATT
2066 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAGCTGAAT
2085 CGAAAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:4144 original size:30 final size:30
Alignment explanation
Indices: 4089--4149 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
4079 CTCACTCTCT
* * *
4089 TTTTCAGTTTTCTTTTCTTTTTCACAATCA
1 TTTTCAATTTTCTTTTCTATCTCACAATCA
*
4119 TTTTCAATTTTCTTTTCTATCTCACACTCA
1 TTTTCAATTTTCTTTTCTATCTCACAATCA
4149 T
1 T
4150 CTGCTTTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.18, C:0.23, G:0.02, T:0.57
Consensus pattern (30 bp):
TTTTCAATTTTCTTTTCTATCTCACAATCA
Found at i:5241 original size:11 final size:11
Alignment explanation
Indices: 5201--5241 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
5191 AATTTTTTTT
5201 ATTTTTTTCAA
1 ATTTTTTTCAA
* *
5212 AATTTTTTCGA
1 ATTTTTTTCAA
5223 ATTTTTTTCAA
1 ATTTTTTTCAA
5234 ATTTTTTT
1 ATTTTTTT
5242 ACAATCTCGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.66
Consensus pattern (11 bp):
ATTTTTTTCAA
Found at i:31086 original size:33 final size:34
Alignment explanation
Indices: 31039--31194 Score: 105
Period size: 33 Copynumber: 4.6 Consensus size: 34
31029 AGATGCGGTT
31039 GAATCAGCACTTAGCAACCATCAAT-GAATAGGG
1 GAATCAGCACTTAGCAACCATCAATAGAATAGGG
* * *
31072 GAATTAGCACTTAGCAACC--C-CTCG----GGG
1 GAATCAGCACTTAGCAACCATCAATAGAATAGGG
* *
31099 GAATCAGCACTTAGCAACCCCCCTTTCACATTTAAAATACGGTG
1 GAATCAGCACTTAGCAA----CC-ATCA-A--TAGAATA-GG-G
31143 GAATCAGCACTTAGCAACCATCAAT-GAATAGGG
1 GAATCAGCACTTAGCAACCATCAATAGAATAGGG
*
31176 GAATTAGCACTTAGCAACC
1 GAATCAGCACTTAGCAACC
31195 CCTCGGGGGA
Statistics
Matches: 96, Mismatches: 9, Indels: 36
0.68 0.06 0.26
Matches are distributed among these distances:
27 19 0.20
30 1 0.01
31 4 0.04
33 37 0.39
34 3 0.03
35 4 0.04
36 1 0.01
38 2 0.02
39 3 0.03
40 2 0.02
43 2 0.02
44 18 0.19
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (34 bp):
GAATCAGCACTTAGCAACCATCAATAGAATAGGG
Found at i:31181 original size:104 final size:104
Alignment explanation
Indices: 30932--31301 Score: 577
Period size: 104 Copynumber: 3.6 Consensus size: 104
30922 TAACCGTTAT
* * * * * *
30932 CGGTGGATTCCGCACTTAGCAACCACCAATGAATCGGGGAATTAGCACACT-GCAACCCCTTGGG
1 CGGTGGAATCAGCACTTAGCAACCATCAATGAATAGGGGAATTAGCAC-TTAGCAACCCCTCGGG
* * *
30996 GGAATCAGCACTTAGCAA-CCCCC-TTCACATTTCAGATG
65 GGAATCAGCACTTAGCAACCCCCCTTTCACATTTAAAATA
*
31034 CGGTTGAATCAGCACTTAGCAACCATCAATGAATAGGGGAATTAGCACTTAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCATCAATGAATAGGGGAATTAGCACTTAGCAACCCCTCGGGG
31099 GAATCAGCACTTAGCAACCCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCCTTTCACATTTAAAATA
31138 CGGTGGAATCAGCACTTAGCAACCATCAATGAATAGGGGAATTAGCACTTAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCATCAATGAATAGGGGAATTAGCACTTAGCAACCCCTCGGGG
31203 GAATCAGCACTTAGCAACCCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCCTTTCACATTTAAAATA
* **
31242 CGGTGGAATCAGCACTTAGCAACCA-CTAATGAATAGGGGAATCAGCACACAGCAACCCCT
1 CGGTGGAATCAGCACTTAGCAACCATC-AATGAATAGGGGAATTAGCACTTAGCAACCCCT
31302 TTATATGCAA
Statistics
Matches: 250, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
101 1 0.00
102 73 0.29
103 6 0.02
104 170 0.68
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (104 bp):
CGGTGGAATCAGCACTTAGCAACCATCAATGAATAGGGGAATTAGCACTTAGCAACCCCTCGGGG
GAATCAGCACTTAGCAACCCCCCTTTCACATTTAAAATA
Found at i:38074 original size:258 final size:249
Alignment explanation
Indices: 37741--38252 Score: 877
Period size: 258 Copynumber: 2.0 Consensus size: 249
37731 TGGGAAGGGG
* *
37741 TTTTTGGCGGAGAAAAGAATCGCTGAGAGATAGATTCTACTTTTTAGTCAGGACAAATGAGTGGT
1 TTTTTGGCGGAGAAAAGAATCGCTGAGAGATAGATTCTACTATTTAGTCAGGACAAATGAGTGGC
37806 TGTGCAGCATGCTCCGGAGGAGATTGACCCTTCCCCGAGTCAGTCTAGTC-A-GAAAGGGGAGGG
66 TGTGCAGCATGCTCCGGAGGAGATTGACCCTTCCCCGAGTC-GTC-AGTCTAGGAAAGGGGAGGG
37869 CCCACTGTCTAGACTGCATTTCGGGAGTTTGAACACCATCCCATTTCAACCAAAAATACAACCCT
129 CCCACTGTCTAGACTGCATTTCGGGAGTTTGAACACCATCCCATTTCAACCAAAAATACAACCCT
37934 GTCAAAGGTATCTAACCTTCCTTCCTTATGAGTGGAAATCCAATCCCGTTTT-TTT
194 GTCAAAGGTATCTAACCTTCCTTCCTTATGAGTGGAAATCCAATCCCGTTTTGTTT
37989 TNNNNNNNNNNTTTTGGCGGAGAAAAGAATCGCTGAGAGATAGATTCTACTATTTAGTCAGGACA
1 T----------TTTTGGCGGAGAAAAGAATCGCTGAGAGATAGATTCTACTATTTAGTCAGGACA
38054 AATGAGTGGCTGTGCAGCATGCTCCGGAGGAGATTGACCCTTCCCCGAGTCGTCAGTCTAGGAAA
56 AATGAGTGGCTGTGCAGCATGCTCCGGAGGAGATTGACCCTTCCCCGAGTCGTCAGTCTAGGAAA
38119 GGGGAGGGCCCACTGTCTAGACTGCATTTCGGGAGTTTGAACACCATCCCATTTCAACCAAAAAT
121 GGGGAGGGCCCACTGTCTAGACTGCATTTCGGGAGTTTGAACACCATCCCATTTCAACCAAAAAT
38184 ACAACCCTGTCAAAGGTATCTAACCTTCCTTCCTTATGAGTGGAAATCCAATCCCGTTTTGTTT
186 ACAACCCTGTCAAAGGTATCTAACCTTCCTTCCTTATGAGTGGAAATCCAATCCCGTTTTGTTT
38248 TTTTT
1 TTTTT
38253 TTTGCATAAA
Statistics
Matches: 249, Mismatches: 2, Indels: 25
0.90 0.01 0.09
Matches are distributed among these distances:
248 1 0.00
249 4 0.02
256 4 0.02
257 4 0.02
258 232 0.93
259 4 0.02
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.28
Consensus pattern (249 bp):
TTTTTGGCGGAGAAAAGAATCGCTGAGAGATAGATTCTACTATTTAGTCAGGACAAATGAGTGGC
TGTGCAGCATGCTCCGGAGGAGATTGACCCTTCCCCGAGTCGTCAGTCTAGGAAAGGGGAGGGCC
CACTGTCTAGACTGCATTTCGGGAGTTTGAACACCATCCCATTTCAACCAAAAATACAACCCTGT
CAAAGGTATCTAACCTTCCTTCCTTATGAGTGGAAATCCAATCCCGTTTTGTTT
Found at i:43244 original size:72 final size:73
Alignment explanation
Indices: 43100--43247 Score: 185
Period size: 72 Copynumber: 2.0 Consensus size: 73
43090 GCAGGTACAT
43100 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAAGCTGCCGAATTTAATGAGTGCAT
1 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAAGCTGCCGAATTTAATGAGTGCAT
*
43165 GGGACTTG
66 GGAACTTG
* * * * * * *
43173 GGACGGCATTTAAAGATAAA-GTTGCTGTTGTA-TTTTCCCAA-CTAGCCGAGTTTAGTGTGTGC
1 GGACGGCATTTAAAGA-AAAGGTGGCTGCTGCATTTTTCCAAAGCT-GCCGAATTTAATGAGTGC
43235 ATGGAACTTG
64 ATGGAACTTG
43245 GGA
1 GGA
43248 TAGCATTAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
71 2 0.03
72 35 0.54
73 25 0.38
74 3 0.05
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (73 bp):
GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAAGCTGCCGAATTTAATGAGTGCAT
GGAACTTG
Found at i:43254 original size:72 final size:73
Alignment explanation
Indices: 43100--43270 Score: 172
Period size: 72 Copynumber: 2.4 Consensus size: 73
43090 GCAGGTACAT
*
43100 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAAGCTGCCGAATTTAATGAGTGCAT
1 GGACAGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAAGCTGCCGAATTTAATGAGTGCAT
*
43165 GGGACTTG
66 GGAACTTG
* * * * * * * *
43173 GGACGGCATTTAAAGATAAA-GTTGCTGTTGTA-TTTTCCCAA-CTAGCCGAGTTTAGTGTGTGC
1 GGACAGCATTTAAAGA-AAAGGTGGCTGCTGCATTTTTCCAAAGCT-GCCGAATTTAATGAGTGC
43235 ATGGAACTTG
64 ATGGAACTTG
* * *
43245 GGATAGCA-TTAAA-AAGAGGAGGCTGC
1 GGACAGCATTTAAAGAAAAGGTGGCTGC
43271 CGTTGCAATC
Statistics
Matches: 81, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
69 2 0.02
70 6 0.07
71 7 0.09
72 38 0.47
73 25 0.31
74 3 0.04
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (73 bp):
GGACAGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAAGCTGCCGAATTTAATGAGTGCAT
GGAACTTG
Found at i:45483 original size:18 final size:18
Alignment explanation
Indices: 45427--45486 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
45417 AGTGCGAGCG
45427 AGAAAAAGAAATCGAAAGAAA
1 AGAAAAAGAAATC--AA-AAA
* **
45448 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATCAAAAA
45466 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
45484 AGA
1 AGA
45487 GAGTGAGGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 21 0.64
19 1 0.03
21 11 0.33
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Done.