Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01136.N1
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: 4395
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Found at i:370 original size:33 final size:33
Alignment explanation
Indices: 312--374 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
302 AGTCCATAGC
* *
312 TGGGTTATGGCATTCTGATGATAAGACCATAAT
1 TGGGTTATGGCATTCGGAAGATAAGACCATAAT
345 TGGGTTATGGCATTACGGAAG-TAAGACCAT
1 TGGGTTATGGCATT-CGGAAGATAAGACCAT
375 GGTTGGACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 23 0.85
34 4 0.15
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (33 bp):
TGGGTTATGGCATTCGGAAGATAAGACCATAAT
Found at i:410 original size:101 final size:101
Alignment explanation
Indices: 266--577 Score: 446
Period size: 101 Copynumber: 3.1 Consensus size: 101
256 ATTCAAAAGG
** * * *
266 AAGACCATGGTTGGATTATGGCAGCGTTTATATGTAAGTCCATAGCTGGGTTATGGCATTCTGAT
1 AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
*
331 GATAAGACCATAATTGGGTTATGGCATTACGGAA-GT
66 GATAAGACCATAACTGGGTTATGGCATTAC-GAACGT
* * *
367 AAGACCATGGTTGGACCATGGCGGTGTTTATATGTAAGACCATAGCTGAGCTATAGCATTCTGAT
1 AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
* *
432 GATAAGATCATAACTGGATTATGGCATTACGAACGT
66 GATAAGACCATAACTGGGTTATGGCATTACGAACGT
* * *
468 AATATCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGACATTCTGAT
1 AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
* * **
533 GATAAGACCATAACTGGGTTATGGCACTATGAATAT
66 GATAAGACCATAACTGGGTTATGGCATTACGAACGT
569 AAGACCATG
1 AAGACCATG
578 ACAGGGTCAT
Statistics
Matches: 185, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
100 3 0.02
101 182 0.98
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (101 bp):
AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
GATAAGACCATAACTGGGTTATGGCATTACGAACGT
Found at i:571 original size:33 final size:33
Alignment explanation
Indices: 502--591 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 33
492 TGTTTATATG
* * * * *
502 TAAGACCATAGCTGGGCTATGACATTCTGATGA
1 TAAGACCATAACTGGGTTATGGCACTATGATGA
535 TAAGACCATAACTGGGTTATGGCACTATGAAT-A
1 TAAGACCATAACTGGGTTATGGCACTATG-ATGA
* * *
568 TAAGACCATGACAGGGTCATGGCA
1 TAAGACCATAACTGGGTTATGGCA
592 ATGCATATGT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 46 0.96
34 2 0.04
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (33 bp):
TAAGACCATAACTGGGTTATGGCACTATGATGA
Found at i:1635 original size:27 final size:27
Alignment explanation
Indices: 1605--1763 Score: 167
Period size: 27 Copynumber: 5.9 Consensus size: 27
1595 AAAGTACTCC
1605 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
1632 CGATTTTTAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** * **
1659 CGATTTGTAAAATTATTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
1686 TGATTTACAGAATTACTGGTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
1713 C-AGTTTACAAAATTATCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
1740 TGATTTACAGAATTACCATTTTAC
1 CGATTTACAGAATTACCGTTTTAC
1764 ACTTGATTGT
Statistics
Matches: 109, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
26 1 0.01
27 107 0.98
28 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:1754 original size:81 final size:81
Alignment explanation
Indices: 1606--1754 Score: 185
Period size: 81 Copynumber: 1.8 Consensus size: 81
1596 AAGTACTCCC
* ** * **
1606 GATTTACAGAATTACCGTTTTACCCTCGATTTTTAGAATTACTGTTTTACCCTCGATTTGTAAAA
1 GATTTACAGAATTACCGGTTTACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACAAAA
1671 TTATTGTTTTACCCTT
66 TTATTGTTTTACCCTT
* * *
1687 GATTTACAGAATTACTGGTTTACCCTC-AGTTTACAAAATTA-TCGTTTTACCCTTGATTTACAG
1 GATTTACAGAATTACCGGTTTACCCTCGA-TTTACAAAATTACT-GTTTTACCCTCGATTTACAA
1750 AATTA
64 AATTA
1755 CCATTTTACA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
80 2 0.04
81 55 0.96
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.43
Consensus pattern (81 bp):
GATTTACAGAATTACCGGTTTACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTACAAAA
TTATTGTTTTACCCTT
Found at i:1763 original size:54 final size:54
Alignment explanation
Indices: 1605--1755 Score: 205
Period size: 54 Copynumber: 2.8 Consensus size: 54
1595 AAAGTACTCC
* * * **
1605 CGATTTACAGAATTACCGTTTTACCCTCGATTTTTAGAATTACTGTTTTACCCT
1 CGATTTACAAAATTATCGTTTTACCCTTGATTTACAGAATTACTGTTTTACCCT
** * *
1659 CGATTTGTAAAATTATTGTTTTACCCTTGATTTACAGAATTACTGGTTTACCCT
1 CGATTTACAAAATTATCGTTTTACCCTTGATTTACAGAATTACTGTTTTACCCT
1713 C-AGTTTACAAAATTATCGTTTTACCCTTGATTTACAGAATTAC
1 CGA-TTTACAAAATTATCGTTTTACCCTTGATTTACAGAATTAC
1756 CATTTTACAC
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 83 0.99
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.42
Consensus pattern (54 bp):
CGATTTACAAAATTATCGTTTTACCCTTGATTTACAGAATTACTGTTTTACCCT
Found at i:1814 original size:27 final size:27
Alignment explanation
Indices: 1776--1971 Score: 230
Period size: 27 Copynumber: 7.3 Consensus size: 27
1766 TTGATTGTGA
*
1776 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
1803 AATTTCCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
1830 AATTACTGAAATACCCTTATAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
1857 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
1884 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
1911 AAATGCCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* ** * *
1938 AATTACCGAGATACCTTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
1965 AATTACC
1 AATTACC
1972 ATTTTGCCCC
Statistics
Matches: 141, Mismatches: 28, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 141 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:1840 original size:54 final size:54
Alignment explanation
Indices: 1776--1972 Score: 261
Period size: 54 Copynumber: 3.6 Consensus size: 54
1766 TTGATTGTGA
* * * *
1776 AATTACTGAAATACCCCTGTAGGGTAGAATTTCCGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
* *
1830 AATTACTGAAATACCCTTATAGGATAGAATTACCAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
* *
1884 AATTA-TCGAAATACCCTTGTAGGGTAGAAATGCCAAAATACCCCTGTAGGGTAG
1 AATTACT-GAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
* * * * *
1938 AATTACCGAGATACCTTTGTGGGGTAAAATTACCA
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACCA
1973 TTTTGCCCCT
Statistics
Matches: 124, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 123 0.99
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (54 bp):
AATTACTGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
Found at i:2237 original size:27 final size:26
Alignment explanation
Indices: 2170--2252 Score: 105
Period size: 27 Copynumber: 3.1 Consensus size: 26
2160 CGGAGGAAGC
*
2170 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
2197 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* *
2223 GTATCTGGTGACTCT-CTTACAATATCT
1 GT-TCTGGTGGCTCTGC-CACAATATCT
2250 GTT
1 GTT
2253 GACTCTGTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
26 11 0.22
27 40 0.78
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:2248 original size:21 final size:21
Alignment explanation
Indices: 2224--2276 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2214 ACAATATCTG
* *
2224 TATCTGGTGACTCTCTTACAA
1 TATCTGTTGACTCTCTCACAA
*
2245 TATCTGTTGACTCTGTCACAA
1 TATCTGTTGACTCTCTCACAA
2266 TATCTGTTGAC
1 TATCTGTTGAC
2277 CGATCGATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (21 bp):
TATCTGTTGACTCTCTCACAA
Found at i:2393 original size:22 final size:23
Alignment explanation
Indices: 2368--2419 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2358 TTAATTGCTC
2368 TGTGCCAACCTAGA-TATGGCTT
1 TGTGCCAACCTAGACTATGGCTT
* *
2390 TGTGCC-ATCTTGACTATGGCTT
1 TGTGCCAACCTAGACTATGGCTT
*
2412 CGTGCCAA
1 TGTGCCAA
2420 ACGTATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.20
22 19 0.76
23 1 0.04
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (23 bp):
TGTGCCAACCTAGACTATGGCTT
Found at i:2606 original size:27 final size:27
Alignment explanation
Indices: 2576--2652 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
2566 TATTCTGTTA
* *
2576 GGTGGCTTTGCCACATTATCTG-ATTCT
1 GGTGGCTCTGCCACAATATCTGTA-TCT
2603 GGTGGCTCTGCCACAATATCTGTATCT
1 GGTGGCTCTGCCACAATATCTGTATCT
* * *
2630 GGTGACTCTGTCACGATATCTGT
1 GGTGGCTCTGCCACAATATCTGT
2653 TTTGGCAGCC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 43 0.98
28 1 0.02
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (27 bp):
GGTGGCTCTGCCACAATATCTGTATCT
Found at i:2770 original size:6 final size:6
Alignment explanation
Indices: 2759--2932 Score: 126
Period size: 6 Copynumber: 28.7 Consensus size: 6
2749 CTGGATTGGG
* *
2759 TTCTGA TTCTGA TTCTG- TCACCTAA TTCTGA TTCTGA TTCTGA TTCTG-
1 TTCTGA TTCTGA TTCTGA T--TCTGA TTCTGA TTCTGA TTCTGA TTCTGA
* * * * *
2807 TTACTAA TACTGA TTCTGA TTCTGA TTCTGA TTCTAA TTCTG- TCACCTAA
1 TT-CTGA TTCTGA TTCTGA TTCTGA TTCTGA TTCTGA TTCTGA T--TCTGA
* * *
2857 TTTTGA TTCTGA TTCTGA TTCTG- TTACTAA TAT-TGA TTCTAA TTCTGA
1 TTCTGA TTCTGA TTCTGA TTCTGA TT-CTGA T-TCTGA TTCTGA TTCTGA
* *
2905 TTCTG- TTATTGG TTCTGA TTCTGA TTCT
1 TTCTGA TT-CTGA TTCTGA TTCTGA TTCT
2933 CATTTTGGTT
Statistics
Matches: 131, Mismatches: 23, Indels: 28
0.72 0.13 0.15
Matches are distributed among these distances:
5 9 0.07
6 111 0.85
7 8 0.06
8 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.49
Consensus pattern (6 bp):
TTCTGA
Found at i:2921 original size:73 final size:73
Alignment explanation
Indices: 2759--2909 Score: 266
Period size: 73 Copynumber: 2.1 Consensus size: 73
2749 CTGGATTGGG
*
2759 TTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTCT
1 TTCTGATTCTAATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTCT
*
2824 GATTCTGA
66 AATTCTGA
* *
2832 TTCTGATTCTAATTCTGTCACCTAATTTTGATTCTGATTCTGATTCTGTTACTAATATTGATTCT
1 TTCTGATTCTAATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTCT
2897 AATTCTGA
66 AATTCTGA
2905 TTCTG
1 TTCTG
2910 TTATTGGTTC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (73 bp):
TTCTGATTCTAATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTCT
AATTCTGA
Found at i:2940 original size:24 final size:23
Alignment explanation
Indices: 2893--2953 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
2883 CTAATATTGA
*
2893 TTCTAATTCTGATTCTGTTATTGG
1 TTCTAATTCTGATTCTATT-TTGG
*
2917 TTCTGATTCTGATTCTCATTTTGG
1 TTCTAATTCTGATTCT-ATTTTGG
*
2941 TTCCAATTCTGAT
1 TTCTAATTCTGAT
2954 AATGTTTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 30 0.94
25 2 0.06
ACGTcount: A:0.16, C:0.16, G:0.15, T:0.52
Consensus pattern (23 bp):
TTCTAATTCTGATTCTATTTTGG
Done.