Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold7473.1
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: 6835
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1678 original size:311 final size:311
Alignment explanation
Indices: 1115--1737 Score: 1192
Period size: 311 Copynumber: 2.0 Consensus size: 311
1105 GTTTTCTTAT
*
1115 GACAAACTGTTCTATTTAGCAATCAAATATGAATCAACACCTCCTTCCTAGGATGATGTAATGTA
1 GACAAACTGTTCTATTTAACAATCAAATATGAATCAACACCTCCTTCCTAGGATGATGTAATGTA
1180 ATGCAATTATAAACAAAACAAAAATAAAACACGTTAGTGTAGGATAAATAAATAACAAATAAAGC
66 ATGCAATTATAAACAAAACAAAAATAAAACACGTTAGTGTAGGATAAATAAATAACAAATAAAGC
1245 AATTCGGGTGACCATTAGGGGTTCGGAGTGGCTCTACCTAGGGTGGGCTCCTAGATCTCTCTATA
131 AATTCGGGTGACCATTAGGGGTTCGGAGTGGCTCTACCTAGGGTGGGCTCCTAGATCTCTCTATA
**
1310 TGTGGTTTGGTTCTAGAGTAAGGGTACCTGAACCAGCAGATTCCTCGATCCTCACCCATTATAGG
196 TGTAATTTGGTTCTAGAGTAAGGGTACCTGAACCAGCAGATTCCTCGATCCTCACCCATTATAGG
*
1375 CTCATTTGAGTCGAGTTCAATTCAAGAGAATACATTTCCTTATAGCTACAC
261 CTCATTTGAGTCGAGTTCAATTCAAGAGAATACATTTCCCTATAGCTACAC
1426 GACAAACTGTTCTATTTAACAATCAAATATGAATCAACACCTCCTTCCTAGGATGATGTAATGTA
1 GACAAACTGTTCTATTTAACAATCAAATATGAATCAACACCTCCTTCCTAGGATGATGTAATGTA
1491 ATGCAATTATAAACAAAACAAAAATAAAACACGTTAGTGTAGGATAAATAAATAACAAATAAAGC
66 ATGCAATTATAAACAAAACAAAAATAAAACACGTTAGTGTAGGATAAATAAATAACAAATAAAGC
*
1556 AATTCGGGTGACCATTAGGGGTTCGGAGTGGCTCTACCTAGGGTGGGCTCCTAGGTCTCTCTATA
131 AATTCGGGTGACCATTAGGGGTTCGGAGTGGCTCTACCTAGGGTGGGCTCCTAGATCTCTCTATA
1621 TGTAATTTGGTTCTAGAGTAAGGGTACCTGAACCAGCAGATTCCTCGATCCTCACCCATTATAGG
196 TGTAATTTGGTTCTAGAGTAAGGGTACCTGAACCAGCAGATTCCTCGATCCTCACCCATTATAGG
*
1686 CTCATTTGAGTCGAGTTCAATTCAAGAGAATACATTTCCCTATGGCTACAC
261 CTCATTTGAGTCGAGTTCAATTCAAGAGAATACATTTCCCTATAGCTACAC
1737 G
1 G
1738 GAGATGAAAA
Statistics
Matches: 306, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
311 306 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (311 bp):
GACAAACTGTTCTATTTAACAATCAAATATGAATCAACACCTCCTTCCTAGGATGATGTAATGTA
ATGCAATTATAAACAAAACAAAAATAAAACACGTTAGTGTAGGATAAATAAATAACAAATAAAGC
AATTCGGGTGACCATTAGGGGTTCGGAGTGGCTCTACCTAGGGTGGGCTCCTAGATCTCTCTATA
TGTAATTTGGTTCTAGAGTAAGGGTACCTGAACCAGCAGATTCCTCGATCCTCACCCATTATAGG
CTCATTTGAGTCGAGTTCAATTCAAGAGAATACATTTCCCTATAGCTACAC
Found at i:2254 original size:200 final size:200
Alignment explanation
Indices: 1911--2312 Score: 795
Period size: 200 Copynumber: 2.0 Consensus size: 200
1901 CTTGAAATGA
1911 TTAAAGAAAATAGGAATAAAATGATGAAAACAGTACGAAAAACGGGTGAAACGCAATGAAGAGAT
1 TTAAAGAAAATAGGAATAAAATGATGAAAACAGTACGAAAAACGGGTGAAACGCAATGAAGAGAT
1976 CGTATATCAAAACCAAATTCTCAATTTTCGAAAAAAGACAAAAGTTAATCAACTTGTGGCTTGAC
66 CGTATATCAAAACCAAATTCTCAATTTTCGAAAAAAGACAAAAGTTAATCAACTTGTGGCTTGAC
2041 TCTCTTATAAAACTCCCCAGTGGAGTCGCCAAGCTGTCGTAACCATTCTTTTGAAAAAACGGGTA
131 TCTCTTATAAAACTCCCCAGTGGAGTCGCCAAGCTGTCGTAACCATTCTTTTGAAAAAACGGGTA
2106 TAGAC
196 TAGAC
2111 TTAAAGAAAATAGGAATAAAATGATGAAAACAGTACGAAAAACGGGTGAAACGCAATGAAGAGAT
1 TTAAAGAAAATAGGAATAAAATGATGAAAACAGTACGAAAAACGGGTGAAACGCAATGAAGAGAT
2176 CGTATATCAAAACCAAATTCTCAATTTTCGAAAAAAGACAAAAGTTAATCAACTTGTGGCTTGAC
66 CGTATATCAAAACCAAATTCTCAATTTTCGAAAAAAGACAAAAGTTAATCAACTTGTGGCTTGAC
*
2241 TCTCTTATAAAACTCCCCAGTGGAGTCGCCAAGCTGTCGTAACCATTTTTTTGAAAAAACGGGTA
131 TCTCTTATAAAACTCCCCAGTGGAGTCGCCAAGCTGTCGTAACCATTCTTTTGAAAAAACGGGTA
2306 TAGAC
196 TAGAC
2311 TT
1 TT
2313 GGAGAAAAAA
Statistics
Matches: 201, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 201 1.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (200 bp):
TTAAAGAAAATAGGAATAAAATGATGAAAACAGTACGAAAAACGGGTGAAACGCAATGAAGAGAT
CGTATATCAAAACCAAATTCTCAATTTTCGAAAAAAGACAAAAGTTAATCAACTTGTGGCTTGAC
TCTCTTATAAAACTCCCCAGTGGAGTCGCCAAGCTGTCGTAACCATTCTTTTGAAAAAACGGGTA
TAGAC
Found at i:3101 original size:12 final size:12
Alignment explanation
Indices: 3086--3115 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3076 ACAATAATAC
3086 TATATATAAATG
1 TATATATAAATG
*
3098 TATATATATATG
1 TATATATAAATG
3110 TATATA
1 TATATA
3116 ATAGAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TATATATAAATG
Found at i:3218 original size:19 final size:17
Alignment explanation
Indices: 3194--3240 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
3184 AATTAAAGTA
*
3194 ATAAAAAATAATACTATAT
1 ATAAAAAAT-ATA-TATAC
*
3213 ATAAAATATATATATAC
1 ATAAAAAATATATATAC
3230 AT-AAAAATATA
1 ATAAAAAATATA
3241 CACTAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 3 0.12
19 8 0.32
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAATATATATAC
Found at i:3236 original size:18 final size:19
Alignment explanation
Indices: 3197--3245 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
3187 TAAAGTAATA
*
3197 AAAAATA-ATACTATATAT
1 AAAAATATATACTATACAT
3215 -AAAATATATA-TATACAT
1 AAAAATATATACTATACAT
*
3232 AAAAATATACACTA
1 AAAAATATATACTA
3246 ATATATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 12 0.46
18 12 0.46
19 2 0.08
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATATATACTATACAT
Found at i:3472 original size:3 final size:3
Alignment explanation
Indices: 3459--3544 Score: 60
Period size: 3 Copynumber: 29.3 Consensus size: 3
3449 GAGGGCATAT
3459 ATA AT- ATA ATA ATA AT- ATA A-A A-A ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A -ATA ATA
* *
3503 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3545 AACAAAGCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 13 0.19
3 46 0.68
4 7 0.10
5 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:3485 original size:18 final size:18
Alignment explanation
Indices: 3464--3544 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
3454 CATATATAAT
3464 ATAATAATAATATAAAAA
1 ATAATAATAATATAAAAA
* *
3482 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-ATAAAAA
*
3503 ATAATAATAATATAAATA
1 ATAATAATAATATAAAAA
*
3521 ATAGTAA-AA-ATAATAAA
1 ATAATAATAATATAA-AAA
3538 ATAATAA
1 ATAATAA
3545 AACAAAGCTC
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
16 4 0.08
17 10 0.19
18 18 0.34
19 5 0.09
20 5 0.09
21 11 0.21
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (18 bp):
ATAATAATAATATAAAAA
Found at i:3910 original size:22 final size:23
Alignment explanation
Indices: 3882--3930 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
3872 TTTTTCCAAA
3882 AAAACAAA-AAAAAACCTCCTCC
1 AAAACAAAGAAAAAACCTCCTCC
* * *
3904 AAAACAAAGAACAATCCTTCTCC
1 AAAACAAAGAAAAAACCTCCTCC
3927 AAAA
1 AAAA
3931 AACCAAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.57, C:0.29, G:0.02, T:0.12
Consensus pattern (23 bp):
AAAACAAAGAAAAAACCTCCTCC
Done.