Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga09g01840.M1
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: 8715
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Found at i:2943 original size:20 final size:20
Alignment explanation
Indices: 2918--3106 Score: 150
Period size: 20 Copynumber: 9.3 Consensus size: 20
2908 CCATATAAAA
*
2918 ATTGGTAAATTGATAGAAAT
1 ATTGGTAAATTCATAGAAAT
**
2938 ATTGGTAAATTCACT-TTAAT
1 ATTGGTAAATTCA-TAGAAAT
*
2958 TTTGGTAAAGTT-ATTAGAAAT
1 ATTGGTAAA-TTCA-TAGAAAT
* *
2979 ATTGGTAAACTCATAGAAGT
1 ATTGGTAAATTCATAGAAAT
* *
2999 TTTGGTAAATTGATAGAAAT
1 ATTGGTAAATTCATAGAAAT
* *
3019 ATTGGTAAATTCACATAAAT
1 ATTGGTAAATTCATAGAAAT
*
3039 TTTGGTAAAGTT-ATTAGAAAT
1 ATTGGTAAA-TTCA-TAGAAAT
* * *
3060 ATTGGTAAACTCAGAGAAGT
1 ATTGGTAAATTCATAGAAAT
* **
3080 TTTGGTAAATTGTTAGAAAT
1 ATTGGTAAATTCATAGAAAT
*
3100 TTTGGTA
1 ATTGGTA
3107 CAGTCAGAAA
Statistics
Matches: 131, Mismatches: 31, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
20 100 0.76
21 31 0.24
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (20 bp):
ATTGGTAAATTCATAGAAAT
Found at i:3023 original size:81 final size:81
Alignment explanation
Indices: 2919--3106 Score: 331
Period size: 81 Copynumber: 2.3 Consensus size: 81
2909 CATATAAAAA
* *
2919 TTGGTAAATTGATAGAAATATTGGTAAATTCACTTTAATTTTGGTAAAGTTATTAGAAATATTGG
1 TTGGTAAATTGATAGAAATATTGGTAAATTCACATAAATTTTGGTAAAGTTATTAGAAATATTGG
*
2984 TAAACTCATAGAAGTT
66 TAAACTCAGAGAAGTT
3000 TTGGTAAATTGATAGAAATATTGGTAAATTCACATAAATTTTGGTAAAGTTATTAGAAATATTGG
1 TTGGTAAATTGATAGAAATATTGGTAAATTCACATAAATTTTGGTAAAGTTATTAGAAATATTGG
3065 TAAACTCAGAGAAGTT
66 TAAACTCAGAGAAGTT
* *
3081 TTGGTAAATTGTTAGAAATTTTGGTA
1 TTGGTAAATTGATAGAAATATTGGTA
3107 CAGTCAGAAA
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 102 1.00
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (81 bp):
TTGGTAAATTGATAGAAATATTGGTAAATTCACATAAATTTTGGTAAAGTTATTAGAAATATTGG
TAAACTCAGAGAAGTT
Found at i:3100 original size:61 final size:58
Alignment explanation
Indices: 2919--3106 Score: 171
Period size: 61 Copynumber: 3.1 Consensus size: 58
2909 CATATAAAAA
** *
2919 TTGGTAAATTGATAGAAATATTGGTAAATTCACTTTAATTTTGGTAAAGTTATTAGAAATA
1 TTGGTAAATT-ATAGAAATATTGGTAAATTCA-TAGAATTTTGGTAAA-TTATTAGAAATT
* * * * * * *
2980 TTGGTAAACTCATAGAAGTTTTGGTAAATTGATAGAAATATTGGTAAATTCA-CATAAATT
1 TTGGTAAA-TTATAGAAATATTGGTAAATTCATAG-AATTTTGGTAAATT-ATTAGAAATT
* * *
3040 TTGGTAAAGTTATTAGAAATATTGGTAAACTCAGAGAAGTTTTGGTAAATTGTTAGAAATT
1 TTGGTAAA-TTA-TAGAAATATTGGTAAATTCATAGAA-TTTTGGTAAATTATTAGAAATT
3101 TTGGTA
1 TTGGTA
3107 CAGTCAGAAA
Statistics
Matches: 100, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
60 20 0.20
61 79 0.79
62 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (58 bp):
TTGGTAAATTATAGAAATATTGGTAAATTCATAGAATTTTGGTAAATTATTAGAAATT
Found at i:3114 original size:40 final size:41
Alignment explanation
Indices: 2919--3106 Score: 208
Period size: 41 Copynumber: 4.7 Consensus size: 41
2909 CATATAAAAA
* ***
2919 TTGGTAAA-TTGA-TAGAAATATTGGTAAATTCACTTTAA-TT
1 TTGGTAAAGTT-ATTAGAAATATTGGTAAACTCA-GAGAAGTT
*
2959 TTGGTAAAGTTATTAGAAATATTGGTAAACTCATAGAAGTT
1 TTGGTAAAGTTATTAGAAATATTGGTAAACTCAGAGAAGTT
* * * *
3000 TTGGTAAA-TTGA-TAGAAATATTGGTAAATTCACATAAATT
1 TTGGTAAAGTT-ATTAGAAATATTGGTAAACTCAGAGAAGTT
3040 TTGGTAAAGTTATTAGAAATATTGGTAAACTCAGAGAAGTT
1 TTGGTAAAGTTATTAGAAATATTGGTAAACTCAGAGAAGTT
* *
3081 TTGGTAAA-TTGTTAGAAATTTTGGTA
1 TTGGTAAAGTTATTAGAAATATTGGTA
3107 CAGTCAGAAA
Statistics
Matches: 129, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
40 63 0.49
41 66 0.51
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (41 bp):
TTGGTAAAGTTATTAGAAATATTGGTAAACTCAGAGAAGTT
Found at i:3264 original size:20 final size:20
Alignment explanation
Indices: 3239--3328 Score: 58
Period size: 20 Copynumber: 4.5 Consensus size: 20
3229 GTCGCTATAT
3239 ATATTGGTAAATCTTTAGAA
1 ATATTGGTAAATCTTTAGAA
* ** * *
3259 ATATTGGGAAATAGTTCGAT
1 ATATTGGTAAATCTTTAGAA
** *
3279 ATATT-GTAAAATCCATAGAT
1 ATATTGGT-AAATCTTTAGAA
*
3299 ATTTTGGTAAAT-TTATAGAA
1 ATATTGGTAAATCTT-TAGAA
*
3319 ATTTTGGTAA
1 ATATTGGTAA
3329 TGATTAAAAC
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
19 1 0.02
20 50 0.94
21 2 0.04
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.40
Consensus pattern (20 bp):
ATATTGGTAAATCTTTAGAA
Found at i:3429 original size:19 final size:19
Alignment explanation
Indices: 3405--3450 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
3395 CTCATAAATA
*
3405 TTGGTAAA-TGTTAGATATT
1 TTGGTAAATTGTTAGAT-GT
3424 TTGGTAAATTGTTAGATGT
1 TTGGTAAATTGTTAGATGT
3443 TTGGTAAA
1 TTGGTAAA
3451 ACTTTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (19 bp):
TTGGTAAATTGTTAGATGT
Found at i:3574 original size:20 final size:20
Alignment explanation
Indices: 3549--3610 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
3539 AATATTAATA
*
3549 AAATTGATAGAAAATTTGGT
1 AAATTGATAGAAATTTTGGT
* *
3569 AAATTGTTAGATATTTTGGT
1 AAATTGATAGAAATTTTGGT
* * *
3589 AAACTCATAGGAATTTTGGT
1 AAATTGATAGAAATTTTGGT
3609 AA
1 AA
3611 TTGTTAGGAC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (20 bp):
AAATTGATAGAAATTTTGGT
Found at i:3758 original size:20 final size:20
Alignment explanation
Indices: 3730--3767 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3720 TCTTAGAATC
3730 GTTAAATATATTGGTAAATT
1 GTTAAATATATTGGTAAATT
* *
3750 GTTAGATATTTTGGTAAA
1 GTTAAATATATTGGTAAA
3768 ATTATAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (20 bp):
GTTAAATATATTGGTAAATT
Found at i:3873 original size:20 final size:20
Alignment explanation
Indices: 3850--3965 Score: 94
Period size: 20 Copynumber: 5.8 Consensus size: 20
3840 GGCAAAAGGA
3850 TAGAAATTTTGGTAAATCTT
1 TAGAAATTTTGGTAAATCTT
* *
3870 TAGAAAATTTGATAAA-CTAT
1 TAGAAATTTTGGTAAATCT-T
* * * **
3890 TAGATATATTGGTAAAACAA
1 TAGAAATTTTGGTAAATCTT
3910 TAGAAATTTTGGTAAAT-TCT
1 TAGAAATTTTGGTAAATCT-T
* * *
3930 TAGATATTTTGATAAATCCT
1 TAGAAATTTTGGTAAATCTT
3950 TA-AAAGTTTTGGTAAA
1 TAGAAA-TTTTGGTAAA
3966 CTGTTATATA
Statistics
Matches: 73, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
19 4 0.05
20 68 0.93
21 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.40
Consensus pattern (20 bp):
TAGAAATTTTGGTAAATCTT
Found at i:3902 original size:40 final size:40
Alignment explanation
Indices: 3858--3979 Score: 120
Period size: 40 Copynumber: 3.0 Consensus size: 40
3848 GATAGAAATT
* * *
3858 TTGGTAAATCTTTAGAAAATTTGATAAACTATTAGATATA
1 TTGGTAAATCATTAGAAATTTTGGTAAACTATTAGATATA
* * * * *
3898 TTGGTAAAACAATAGAAATTTTGGTAAATTCTTAGATATT
1 TTGGTAAATCATTAGAAATTTTGGTAAACTATTAGATATA
* * * *
3938 TTGATAAATCCTTA-AAAGTTTTGGTAAACTGTTATATATA
1 TTGGTAAATCATTAGAAA-TTTTGGTAAACTATTAGATATA
3978 TT
1 TT
3980 AGACCTCGAG
Statistics
Matches: 65, Mismatches: 16, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
39 3 0.05
40 62 0.95
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (40 bp):
TTGGTAAATCATTAGAAATTTTGGTAAACTATTAGATATA
Found at i:3962 original size:60 final size:60
Alignment explanation
Indices: 3808--3965 Score: 162
Period size: 60 Copynumber: 2.6 Consensus size: 60
3798 TGGTATAAGG
* * * **
3808 TTTAGAAATTTTGGTAAAGT-CTCAAAAGTATTGGCAAAAGGATAGAAATTTTGGTAAATC
1 TTTAGAAATTTTGATAAA-TCCTTAAAAGTATTGGTAAAACAATAGAAATTTTGGTAAATC
* * *
3868 TTTAGAAAATTTGATAAA-CTATTAGATA-TATTGGTAAAACAATAGAAATTTTGGTAAAT-
1 TTTAGAAATTTTGATAAATC-CTTA-AAAGTATTGGTAAAACAATAGAAATTTTGGTAAATC
* *
3927 TCTTAGATATTTTGATAAATCCTTAAAAGTTTTGGTAAA
1 T-TTAGAAATTTTGATAAATCCTTAAAAGTATTGGTAAA
3966 CTGTTATATA
Statistics
Matches: 79, Mismatches: 13, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
59 3 0.04
60 73 0.92
61 3 0.04
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (60 bp):
TTTAGAAATTTTGATAAATCCTTAAAAGTATTGGTAAAACAATAGAAATTTTGGTAAATC
Found at i:4229 original size:7 final size:7
Alignment explanation
Indices: 4217--4250 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
4207 AATGTTCCCT
4217 ATAAGGG
1 ATAAGGG
4224 ATAAGGG
1 ATAAGGG
4231 ATAAGGG
1 ATAAGGG
4238 ATAAGGG
1 ATAAGGG
4245 ATAAGG
1 ATAAGG
4251 TGATGATGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.41, T:0.15
Consensus pattern (7 bp):
ATAAGGG
Found at i:6023 original size:15 final size:16
Alignment explanation
Indices: 6003--6032 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5993 TTATAAGAAA
6003 AGAATAAAA-TCAAAG
1 AGAATAAAATTCAAAG
6018 AGAATAAAATTCAAA
1 AGAATAAAATTCAAA
6033 AAAAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.07, G:0.10, T:0.17
Consensus pattern (16 bp):
AGAATAAAATTCAAAG
Found at i:6118 original size:21 final size:21
Alignment explanation
Indices: 6070--6118 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
6060 TTGAAAGTTT
*
6070 GAAATTGAAAATTAAAATTTG
1 GAAATTGAAAATTAAAATTTA
*
6091 GATATTGAAAATATAAAA-TTA
1 GAAATTGAAAAT-TAAAATTTA
6112 GAAATTG
1 GAAATTG
6119 GGGATTGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (21 bp):
GAAATTGAAAATTAAAATTTA
Found at i:6139 original size:28 final size:28
Alignment explanation
Indices: 6071--6146 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
6061 TGAAAGTTTG
*
6071 AAATTGAAAATTAAAATTTGGATATTGA
1 AAATTGAAAATTAAAATTTGGAGATTGA
*
6099 AAATAT-AAAATTAGAAA-TTGGGGATTGA
1 AAAT-TGAAAATTA-AAATTTGGAGATTGA
*
6127 AAATTGAAGATTAAGAATTT
1 AAATTGAAAATTAA-AATTT
6147 AGGAAGAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
27 2 0.05
28 32 0.80
29 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (28 bp):
AAATTGAAAATTAAAATTTGGAGATTGA
Done.