Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga09g00833.P2
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: 11576
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:1951 original size:20 final size:20
Alignment explanation
Indices: 1890--1956 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
1880 CCAAAAAAAG
*
1890 AAAAAAGAAAAACCTAACCC
1 AAAAAAAAAAAACCTAACCC
** *
1910 AAAAAAAAAAAGA-AGAA--G
1 AAAAAAAAAAA-ACCTAACCC
1928 AAAAAAAAAAAACCTAACCC
1 AAAAAAAAAAAACCTAACCC
1948 AAAAAAAAA
1 AAAAAAAAA
1957 TAATAAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
17 1 0.03
18 13 0.36
20 21 0.58
21 1 0.03
ACGTcount: A:0.76, C:0.15, G:0.06, T:0.03
Consensus pattern (20 bp):
AAAAAAAAAAAACCTAACCC
Found at i:2573 original size:23 final size:23
Alignment explanation
Indices: 2536--2667 Score: 63
Period size: 25 Copynumber: 5.5 Consensus size: 23
2526 CCTTTTTTGT
2536 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATATTA
* *
2559 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATATTA
** *
2581 TATTAGGTATATT-TTAAATTTTA
1 TATTATATATATTCTT-AATATTA
* * *
2604 TATTACGTATATATATATTTTATACTA
1 TATTA--TATATAT-T-CTTAATATTA
* *
2631 TTTTATGTATATATCTTTAATATTA
1 TATTATATATAT-TC-TTAATATTA
* *
2656 TATGATTTATAT
1 TATTATATATAT
2668 ATATATATAT
Statistics
Matches: 80, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
21 2 0.03
22 15 0.19
23 19 0.24
24 4 0.05
25 29 0.36
26 1 0.01
27 8 0.10
28 2 0.03
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (23 bp):
TATTATATATATTCTTAATATTA
Found at i:2641 original size:25 final size:25
Alignment explanation
Indices: 2613--2671 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
2603 ATATTACGTA
* * *
2613 TATATATATTTTATACTATTTTATG
1 TATATATATTTAATACTATATGATG
* * *
2638 TATATATCTTTAATATTATATGATT
1 TATATATATTTAATACTATATGATG
2663 TATATATAT
1 TATATATAT
2672 ATATATATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (25 bp):
TATATATATTTAATACTATATGATG
Found at i:2731 original size:22 final size:24
Alignment explanation
Indices: 2703--2761 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
2693 ACATGTTATC
2703 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
2725 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
2750 TTATGTACATAT
1 TTATGTATATAT
2762 TTTTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 2 0.07
25 15 0.50
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATGTATATATCTTAACACTATA
Found at i:2751 original size:25 final size:25
Alignment explanation
Indices: 2719--2767 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2709 ATATATCTTA
**
2719 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
2744 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
2768 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:2946 original size:16 final size:15
Alignment explanation
Indices: 2922--2969 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
2912 TAATTATTAT
*
2922 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
2938 TATTTTAATATTTTA
1 TATTTTAATATTTTA
2953 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
2969 T
1 T
2970 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:2957 original size:7 final size:8
Alignment explanation
Indices: 2922--2973 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
2912 TAATTATTAT
*
2922 TATTCTAA
1 TATTTTAA
*
2930 TATTTTGA
1 TATTTTAA
2938 TATTTTAA
1 TATTTTAA
2946 TATTTT-A
1 TATTTTAA
2953 TATTTTATA
1 TATTTTA-A
*
2962 TATTTTAT
1 TATTTTAA
2970 TATT
1 TATT
2974 CACATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:9855 original size:72 final size:71
Alignment explanation
Indices: 9779--9922 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 71
9769 TTTTTCAGAA
* * *
9779 TCAACTCATATTGCTAGAGGTAAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT
1 TCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGT-T
*
9844 TTTAATT
65 TTCAATT
* *
9851 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTTT
9916 TCAATT
66 TCAATT
9922 T
1 T
9923 ACGTTGTTCA
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
71 8 0.12
72 58 0.88
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (71 bp):
TCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTTT
TCAATT
Found at i:10027 original size:140 final size:140
Alignment explanation
Indices: 9855--10342 Score: 870
Period size: 140 Copynumber: 3.5 Consensus size: 140
9845 TTAATTTCAA
9855 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
9920 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
9985 TCAAAATCAG
131 TCAAAATCAG
* *
9995 CTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
10060 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
10125 TCAAAATCAG
131 TCAAAATCAG
10135 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
* *
10200 TTTATGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
*
10265 TCAAAATTAG
131 TCAAAATCAG
* *
10275 CTAATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAGTTTCTGTCTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCAC--GCTGAGGTATTTTCAATTTCTGT-TT
10339 TCAA
62 TCAA
10343 AAAAAAAAAT
Statistics
Matches: 335, Mismatches: 9, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
139 2 0.01
140 305 0.91
142 22 0.07
143 6 0.02
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (140 bp):
CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
TCAAAATCAG
Found at i:10198 original size:13 final size:13
Alignment explanation
Indices: 10180--10213 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
10170 CGCTGAGGTA
*
10180 TTTTCAATTTCTG
1 TTTTCAATTTATG
10193 TTTTCAATTTATG
1 TTTTCAATTTATG
10206 TTGTTCAA
1 TT-TTCAA
10214 GAATCAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTTCAATTTATG
Found at i:10465 original size:72 final size:72
Alignment explanation
Indices: 10348--10488 Score: 273
Period size: 72 Copynumber: 2.0 Consensus size: 72
10338 TTCAAAAAAA
*
10348 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
10413 TGTTTTC
66 TGTTTTC
10420 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
10485 TGTT
66 TGTT
10489 CAAAATGAGT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (72 bp):
AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTAATTTCAATTTC
TGTTTTC
Found at i:10499 original size:49 final size:50
Alignment explanation
Indices: 10442--10538 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 50
10432 ATATTGCGAG
**
10442 AAATGAGTTGAACCTCAAG-ACACGTTGAGGTAATTTCAATTTCTGTTCA
1 AAATGAGTTGAACCTCAAGCACACGCCGAGGTAATTTCAATTTCTGTTCA
* * *
10491 AAATGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCTGT
1 AAATGAGTTGAACCTCAAG-CACACGCCGAGGTAATTTCAATTTCTGT
10539 CTTTCAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
49 17 0.41
51 24 0.59
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (50 bp):
AAATGAGTTGAACCTCAAGCACACGCCGAGGTAATTTCAATTTCTGTTCA
Found at i:10723 original size:74 final size:74
Alignment explanation
Indices: 10494--10895 Score: 466
Period size: 77 Copynumber: 5.2 Consensus size: 74
10484 CTGTTCAAAA
* *
10494 TGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAAAAACATC
1 TGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATTTCTGT-TGTC-----AAAAAA-ATC
10559 AACTCATATTGCGAGAGG
57 AACTCATATTGCGAGAGG
* * * * * *
10577 TGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACT
1 TGAGTTGAGCCTCAG--GACACGCTGAGGTA--TTTTCAATTTCT-GTTGTCAAAAAAATCAACT
* *
10642 CACATTGCGAGATG
61 CATATTGCGAGAGG
*
10656 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCATAT
10721 TGCGAGAGG
66 TGCGAGAGG
* * * *
10730 TGAGTTGAGCCTCGGGACACACTGAGGTATTGTCAATTTTTCGTATGTTTC-AAAAAATCAACTC
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT-GT-TG--TCAAAAAAATCAACTC
10794 ATATTGCGAGAGG
62 ATATTGCGAGAGG
* *
10807 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATTTCTGTTGT-AAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCATAT
10871 TGCGAGAGG
66 TGCGAGAGG
*
10880 CGAGTTGAGCCTCAGG
1 TGAGTTGAGCCTCAGG
10896 TCACACGTCA
Statistics
Matches: 280, Mismatches: 29, Indels: 30
0.83 0.09 0.09
Matches are distributed among these distances:
73 41 0.15
74 65 0.23
75 15 0.05
76 4 0.01
77 73 0.26
78 2 0.01
79 33 0.12
80 6 0.02
83 25 0.09
85 15 0.05
86 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (74 bp):
TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCATAT
TGCGAGAGG
Found at i:10826 original size:151 final size:150
Alignment explanation
Indices: 10494--10901 Score: 525
Period size: 151 Copynumber: 2.6 Consensus size: 150
10484 CTGTTCAAAA
* *
10494 TGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCTGTCTTTCAAAAAAAAAAACATC
1 TGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATTTCTGT-TGTC-----AAAAAA-ATC
* * ** *
10559 AACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTCAATTTATAT
57 AACTCGTATTGCGAGAGGTGAGTTGAGCCTC-G-GGACACACTGAGGTA-TTTGTCAATTTATAT
* *
10624 TTTTCAAAAAAATCAACTCACATTGCGAGATG
119 GTTTCAAAAAAATCAACTCACATTGCGAGAGG
10656 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
*
10721 TGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTA-TTGTCAATTTTTCGTATGTTTC-AAA
66 TGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTTGTCAA--TTT-ATATGTTTCAAAA
*
10784 AAATCAACTCATATTGCGAGAGG
128 AAATCAACTCACATTGCGAGAGG
*
10807 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATTTCTGTTGT-AAAAAAATCAACTCGTAT
1 TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
* * *
10871 TGCGAGAGGCGAGTTGAGCCTCAGGTCACAC
66 TGCGAGAGGTGAGTTGAGCCTCGGGACACAC
10902 GTCAAGTGAG
Statistics
Matches: 228, Mismatches: 15, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
149 6 0.03
150 46 0.20
151 85 0.37
152 8 0.04
153 32 0.14
154 6 0.03
159 3 0.01
160 26 0.11
162 16 0.07
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (150 bp):
TGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTTGTCAAAAAAATCAACTCGTAT
TGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTTGTCAATTTATATGTTTCAAAAAAA
TCAACTCACATTGCGAGAGG
Done.