Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g00377.F1
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: 4104
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Found at i:1008 original size:43 final size:43
Alignment explanation
Indices: 911--1131 Score: 360
Period size: 43 Copynumber: 5.2 Consensus size: 43
901 TAAAAAAAAC
* *
911 TCATTGCATGCATATTAAAAAATAGGCAACA-C--ACCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
*
951 TCATTGCATACATATTAAAAAATAGTCAACAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
994 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
1037 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
* *
1080 TCATTGCATACATATTAAAAAA-AGTCAATAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
*
1122 TCAGTGCATG
1 TCATTGCATG
1132 TGATCAGCAA
Statistics
Matches: 170, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
40 29 0.17
41 1 0.01
42 27 0.16
43 113 0.66
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.27
Consensus pattern (43 bp):
TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
Found at i:2793 original size:15 final size:15
Alignment explanation
Indices: 2773--2801 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2763 ATGCATCACT
2773 ATCACTACCAGACAC
1 ATCACTACCAGACAC
2788 ATCACTACCAGACA
1 ATCACTACCAGACA
2802 TGTTTTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.38, G:0.07, T:0.14
Consensus pattern (15 bp):
ATCACTACCAGACAC
Found at i:3220 original size:48 final size:48
Alignment explanation
Indices: 3106--3256 Score: 250
Period size: 48 Copynumber: 3.2 Consensus size: 48
3096 AATAAACATC
* * *
3106 ATGGCAGATATACACAATAAACATCAGTTTGATAAT-GTATTCATACA
1 ATGGCAGATATACACAATACACATCAATTTGATAATGGCATTCATACA
*
3153 ATGGCAGATATACACAATACACATCAATTTGATAATGGCATTCATATA
1 ATGGCAGATATACACAATACACATCAATTTGATAATGGCATTCATACA
*
3201 ATGGCAGATATACAAAATACACATCAATTTGATAATGGCATTCATACA
1 ATGGCAGATATACACAATACACATCAATTTGATAATGGCATTCATACA
3249 ATGGCAGA
1 ATGGCAGA
3257 AACAAATAAT
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
47 34 0.35
48 63 0.65
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (48 bp):
ATGGCAGATATACACAATACACATCAATTTGATAATGGCATTCATACA
Found at i:3273 original size:48 final size:47
Alignment explanation
Indices: 3121--3274 Score: 188
Period size: 48 Copynumber: 3.2 Consensus size: 47
3111 AGATATACAC
* * *
3121 AATAAACATCAGTTTGATAAT-GTATTCATACAATGGCAGATATAC-AC
1 AATAAACATCAATTTGATAATGGCATTCATACAATGGCAGA-A-ACAAA
* *
3168 AATACACATCAATTTGATAATGGCATTCATATAATGGCAGATATAC-AA
1 AATAAACATCAATTTGATAATGGCATTCATACAATGGCAGA-A-ACAAA
*
3216 AATACACATCAATTTGATAATGGCATTCATACAATGGCAGAAACAAA
1 AATAAACATCAATTTGATAATGGCATTCATACAATGGCAGAAACAAA
3263 TAATAAACATCA
1 -AATAAACATCA
3275 TGCACATGGC
Statistics
Matches: 97, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
46 2 0.02
47 22 0.23
48 73 0.75
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (47 bp):
AATAAACATCAATTTGATAATGGCATTCATACAATGGCAGAAACAAA
Found at i:3338 original size:6 final size:6
Alignment explanation
Indices: 3329--3389 Score: 50
Period size: 6 Copynumber: 10.2 Consensus size: 6
3319 ATCCAGATCG
* * * * * ** *
3329 AAATCA AAATCA AATTCT AAATCT AAATCG AGATCA AAATTG GAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
3377 AAATCA AAATCA A
1 AAATCA AAATCA A
3390 TGAGTGTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.23
Consensus pattern (6 bp):
AAATCA
Found at i:3451 original size:18 final size:18
Alignment explanation
Indices: 3398--3452 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
3388 AATGAGTGTT
3398 TTAAAATTGAAATCA-AAA
1 TTAAAATTGAAAT-AGAAA
** *
3416 TCGAAATT-AGAATCGAAA
1 TTAAAATTGA-AATAGAAA
3434 TTAAAATTGAAATAGAAA
1 TTAAAATTGAAATAGAAA
3452 T
1 T
3453 AACCCTAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
17 1 0.04
18 26 0.93
19 1 0.04
ACGTcount: A:0.56, C:0.05, G:0.11, T:0.27
Consensus pattern (18 bp):
TTAAAATTGAAATAGAAA
Found at i:3452 original size:12 final size:12
Alignment explanation
Indices: 3398--3446 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
3388 AATGAGTGTT
*
3398 TTAAAATTGAAA
1 TTAAAATCGAAA
*
3410 TCAAAATCGAAA
1 TTAAAATCGAAA
*
3422 TTAGAATCGAAA
1 TTAAAATCGAAA
*
3434 TTAAAATTGAAA
1 TTAAAATCGAAA
3446 T
1 T
3447 AGAAATAACC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (12 bp):
TTAAAATCGAAA
Done.