Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold698
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: 25247
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:1454 original size:6 final size:6
Alignment explanation
Indices: 1436--1517 Score: 62
Period size: 6 Copynumber: 13.3 Consensus size: 6
1426 AAGAAACATT
*
1436 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAG- GTGACAGA ATCAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA
* * *
1485 ATTAGT ATCAG- GTGACAGA ATCAGA ATCAGA AT
1 ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA AT
1518 GTGAATGCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
5 3 0.05
6 49 0.80
7 7 0.11
8 2 0.03
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:1480 original size:31 final size:31
Alignment explanation
Indices: 1445--1517 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
1435 TATCAGAACT
1445 AGAATCAGAATCAGAATCAGGTGACAGAATC
1 AGAATCAGAATCAGAATCAGGTGACAGAATC
* *
1476 AGAATCAGAATTAGTATCAGGTGACAGAATC
1 AGAATCAGAATCAGAATCAGGTGACAGAATC
1507 AGAATCAGAAT
1 AGAATCAGAAT
1518 GTGAATGCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.19
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGGTGACAGAATC
Found at i:1684 original size:27 final size:27
Alignment explanation
Indices: 1636--1688 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1626 GCGAGGCTGC
* *
1636 CAGATATTGTGATGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGATA
* *
1663 CAGATATTGTGGCGAGGCCACCAGAT
1 CAGATATTGTGACGAAGCCACCAGAT
1689 TGCAGCGAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (27 bp):
CAGATATTGTGACGAAGCCACCAGATA
Found at i:1954 original size:27 final size:27
Alignment explanation
Indices: 1924--2280 Score: 410
Period size: 27 Copynumber: 13.2 Consensus size: 27
1914 AACACCCTAG
* *
1924 GGGTAAAATGGTAATTTTATAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* *
1951 GGGTAAAATGGTAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
1978 GGGTAAAATAGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
*
2005 GGGTAAAATAGTAATTTTATAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* * * *
2032 GGGTAAAACAGTAATTCTGTCAATCAA
1 GGGTAAAATAGTAATTTTGTAAATCGA
**
2059 GGGTAAAACGGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* *
2086 GGGTAAAGTAGTAATTTTGTAAATTGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
** * *
2113 GGGTAAAACGGTAATTCTGTAAATTGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* * * *
2140 GGGTAAAACAATAATTATATAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
*
2167 GGGTAAAATGGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
** * *
2194 GGGTAAAAT-GATTGTTTTATAAATTGA
1 GGGTAAAATAG-TAATTTTGTAAATCGA
* * *
2221 GGGTAAAACAGTAATTCTATAAATCGA
1 GGGTAAAATAGTAATTTTGTAAATCGA
* *
2248 GGGTAAAACAGTAATTTTTGTAATTCGA
1 GGGTAAAATAGTAA-TTTTGTAAATCGA
2276 GGGTA
1 GGGTA
2281 CTTTGATAAT
Statistics
Matches: 283, Mismatches: 44, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
26 1 0.00
27 266 0.94
28 16 0.06
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.32
Consensus pattern (27 bp):
GGGTAAAATAGTAATTTTGTAAATCGA
Found at i:2062 original size:81 final size:81
Alignment explanation
Indices: 1924--2280 Score: 462
Period size: 81 Copynumber: 4.4 Consensus size: 81
1914 AACACCCTAG
* * * *
1924 GGGTAAAATGGTAATTTTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATAG
1 GGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAG
*
1989 TAATTTTGTAAATCGA
66 TAATTTTATAAATCGA
* * * * *
2005 GGGTAAAATAGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTGTCAATCAAGGGTAAAACGG
1 GGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAG
*
2070 TAATTTTGTAAATCGA
66 TAATTTTATAAATCGA
* * * *
2086 GGGTAAAGTAGTAATTTTGTAAATTGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAACAA
1 GGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAG
*
2151 TAATTATATAAATCGA
66 TAATTTTATAAATCGA
* * * ** * * *
2167 GGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAATGATTGTTTTATAAATTGAGGGTAAAACAG
1 GGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAG
*
2232 TAATTCTATAAATCGA
66 TAATTTTATAAATCGA
* *
2248 GGGTAAAACAGTAATTTTTGTAATTCGAGGGTA
1 GGGTAAAATAGTAA-TTTTGTAAATCGAGGGTA
2281 CTTTGATAAT
Statistics
Matches: 243, Mismatches: 32, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
81 226 0.93
82 17 0.07
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.32
Consensus pattern (81 bp):
GGGTAAAATAGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAG
TAATTTTATAAATCGA
Found at i:2302 original size:27 final size:26
Alignment explanation
Indices: 2272--2405 Score: 117
Period size: 27 Copynumber: 5.0 Consensus size: 26
2262 TTTTTGTAAT
**
2272 TCGAGGGTACTTTGATAATTTTACATG
1 TCGAGGGTA-TTTGATAATTTTACAAA
* *
2299 TCGAGGGTATTTCAGTAATTTTGCAAA
1 TCGAGGGTATTTGA-TAATTTTACAAA
2326 -CTGAGGGTATTTCGATAATTTTACAAA
1 TC-GAGGGTATTT-GATAATTTTACAAA
* * *
2353 TCGAGGATATTTGGGTAATTTTATAAA
1 TCGAGGGTATTT-GATAATTTTACAAA
* * *
2380 CCGGGGGTACTTTGGTAATTTTACAA
1 TCGAGGGTA-TTTGATAATTTTACAA
2406 CTGGGGGTAT
Statistics
Matches: 88, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
26 5 0.06
27 78 0.89
28 5 0.06
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.38
Consensus pattern (26 bp):
TCGAGGGTATTTGATAATTTTACAAA
Found at i:2303 original size:55 final size:54
Alignment explanation
Indices: 2244--2350 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
2234 ATTCTATAAA
* *
2244 TCGAGGGTAAAACAGTAATTTTTG-TAATTCGAGGGTACTTT-GATAATTTTACATG
1 TCGAGGGTAAAACAGTAA-TTTTGCAAACT-GAGGGTA-TTTCGATAATTTTACATG
***
2299 TCGAGGGTATTTCAGTAATTTTGCAAACTGAGGGTATTTCGATAATTTTACA
1 TCGAGGGTAAAACAGTAATTTTGCAAACTGAGGGTATTTCGATAATTTTACA
2351 AATCGAGGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
53 3 0.07
54 24 0.53
55 18 0.40
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.38
Consensus pattern (54 bp):
TCGAGGGTAAAACAGTAATTTTGCAAACTGAGGGTATTTCGATAATTTTACATG
Found at i:2345 original size:54 final size:54
Alignment explanation
Indices: 2273--2426 Score: 177
Period size: 54 Copynumber: 2.9 Consensus size: 54
2263 TTTTGTAATT
** *
2273 CGAGGGTACTTTGATAATTTTACATGTCGAGGGTATTTCAGTAATTTTGCAAAC
1 CGAGGGTACTTTGATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAAC
* * ** *
2327 TGAGGGTA-TTTCGATAATTTTACAAATCGAGGATATTTGGGTAATTTTATAAAC
1 CGAGGGTACTTT-GATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAAC
* * * *
2381 CGGGGGTACTTTGGTAATTTTACAACT-GGGGGTATTTCAGTAATTT
1 CGAGGGTACTTTGATAATTTTACAAATCGAGGGTATTTCAGTAATTT
2427 GGTAAACTAA
Statistics
Matches: 82, Mismatches: 16, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
53 18 0.22
54 61 0.74
55 3 0.04
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.38
Consensus pattern (54 bp):
CGAGGGTACTTTGATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAAC
Found at i:2423 original size:26 final size:26
Alignment explanation
Indices: 2274--2426 Score: 105
Period size: 27 Copynumber: 5.7 Consensus size: 26
2264 TTTGTAATTC
* **
2274 GAGGGTACTTTGA-TAATTTTACATGT
1 GAGGGTA-TTTCAGTAATTTTACAACT
*
2300 CGAGGGTATTTCAGTAATTTTGCAAACT
1 -GAGGGTATTTCAGTAATTTTAC-AACT
*
2328 GAGGGTATTTC-GATAATTTTACAAAT
1 GAGGGTATTTCAG-TAATTTTACAACT
* ** * *
2354 CGAGGATATTTGGGTAATTTTATAAACC
1 -GAGGGTATTTCAGTAATTTTA-CAACT
* *
2382 GGGGGTACTTT-GGTAATTTTACAACT
1 GAGGGTA-TTTCAGTAATTTTACAACT
*
2408 GGGGGTATTTCAGTAATTT
1 GAGGGTATTTCAGTAATTT
2427 GGTAAACTAA
Statistics
Matches: 102, Mismatches: 16, Indels: 17
0.76 0.12 0.13
Matches are distributed among these distances:
25 3 0.03
26 25 0.25
27 66 0.65
28 8 0.08
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.39
Consensus pattern (26 bp):
GAGGGTATTTCAGTAATTTTACAACT
Found at i:5116 original size:44 final size:43
Alignment explanation
Indices: 5020--5142 Score: 124
Period size: 44 Copynumber: 2.8 Consensus size: 43
5010 GTACAACACT
* * * * **
5020 AACGTCTCAGACGTGGTCTTACATGTAATTA-AATAACGATGCC
1 AACGTCCCAGACGTGGTCTTACACGAAATCACAA-ATTGATGCC
**
5063 ATTGTCCCAGACAG-GGTCTTACACGTAAATCACAAATTGATGCC
1 AACGTCCCAGAC-GTGGTCTTACACG-AAATCACAAATTGATGCC
*
5107 AACGTCCCAGGCGTGGTCTTACACGAAATCACAAAT
1 AACGTCCCAGACGTGGTCTTACACGAAATCACAAAT
5143 CAGAATCTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
43 31 0.48
44 32 0.49
45 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (43 bp):
AACGTCCCAGACGTGGTCTTACACGAAATCACAAATTGATGCC
Done.