Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01137.N3
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: 5167
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.35
Found at i:2152 original size:33 final size:33
Alignment explanation
Indices: 2094--2156 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
2084 AGTCCATAGC
* *
2094 TGGGTTATGGCATTCTGATGATAAGACCATAAT
1 TGGGTTATGGCATTCGGAAGATAAGACCATAAT
2127 TGGGTTATGGCATTACGGAAG-TAAGACCAT
1 TGGGTTATGGCATT-CGGAAGATAAGACCAT
2157 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:2192 original size:101 final size:101
Alignment explanation
Indices: 2048--2359 Score: 446
Period size: 101 Copynumber: 3.1 Consensus size: 101
2038 ATTCAAAAGG
** * * *
2048 AAGACCATGGTTGGATTATGGCAGCGTTTATATGTAAGTCCATAGCTGGGTTATGGCATTCTGAT
1 AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
*
2113 GATAAGACCATAATTGGGTTATGGCATTACGGAA-GT
66 GATAAGACCATAACTGGGTTATGGCATTAC-GAACGT
* * *
2149 AAGACCATGGTTGGACCATGGCGGTGTTTATATGTAAGACCATAGCTGAGCTATAGCATTCTGAT
1 AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
* *
2214 GATAAGATCATAACTGGATTATGGCATTACGAACGT
66 GATAAGACCATAACTGGGTTATGGCATTACGAACGT
* * *
2250 AATATCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGACATTCTGAT
1 AAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
* * **
2315 GATAAGACCATAACTGGGTTATGGCACTATGAATAT
66 GATAAGACCATAACTGGGTTATGGCATTACGAACGT
2351 AAGACCATG
1 AAGACCATG
2360 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:2353 original size:33 final size:33
Alignment explanation
Indices: 2284--2373 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 33
2274 TGTTTATATG
* * * * *
2284 TAAGACCATAGCTGGGCTATGACATTCTGATGA
1 TAAGACCATAACTGGGTTATGGCACTATGATGA
2317 TAAGACCATAACTGGGTTATGGCACTATGAAT-A
1 TAAGACCATAACTGGGTTATGGCACTATG-ATGA
* * *
2350 TAAGACCATGACAGGGTCATGGCA
1 TAAGACCATAACTGGGTTATGGCA
2374 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:3417 original size:27 final size:27
Alignment explanation
Indices: 3387--3634 Score: 345
Period size: 27 Copynumber: 9.2 Consensus size: 27
3377 AAAGTACTCC
*
3387 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
3414 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
3441 CGATTTTTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
3468 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
3495 C-AGTTTACAGAATTACCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
3522 CGATTTATAGAGTTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** * * *
3549 CGATTTGTAAAATTACTGTTTTACCTT
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
3576 TGATTTACAAAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
3603 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
3630 TGATT
1 CGATT
3635 GTGAAATTAC
Statistics
Matches: 195, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
26 1 0.01
27 193 0.99
28 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:3669 original size:27 final size:27
Alignment explanation
Indices: 3639--3815 Score: 219
Period size: 27 Copynumber: 6.6 Consensus size: 27
3629 TTGATTGTGA
*
3639 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
*
3666 AATTTCCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
** * *
3693 AATTATTGAAATACCCTTATAGGATAG
1 AATTACCGAAATACCCCTATAGGGTAG
* * *
3720 AATTACCAAAATACTCCTGTAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
* * *
3747 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
* *
3774 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
*
3801 AATTACCGAGATACC
1 AATTACCGAAATACC
3816 TTTGTGGGGT
Statistics
Matches: 127, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 127 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTATAGGGTAG
Found at i:3707 original size:54 final size:54
Alignment explanation
Indices: 3639--3805 Score: 244
Period size: 54 Copynumber: 3.1 Consensus size: 54
3629 TTGATTGTGA
* * * *
3639 AATTACTGAAATACCCCTATAGGGTAGAATTTCCGAAATACCCCTATAGGGTAG
1 AATTATTGAAATACCCTTATAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* * *
3693 AATTATTGAAATACCCTTATAGGATAGAATTACCAAAATACTCCTGTAGGGTAG
1 AATTATTGAAATACCCTTATAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* * *
3747 AATTATCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
1 AATTATTGAAATACCCTTATAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
3801 AATTA
1 AATTA
3806 CCGAGATACC
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 100 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (54 bp):
AATTATTGAAATACCCTTATAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
Found at i:4071 original size:27 final size:26
Alignment explanation
Indices: 4033--4115 Score: 121
Period size: 27 Copynumber: 3.1 Consensus size: 26
4023 CGGAGGAAGC
*
4033 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
4060 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* *
4086 GTATCTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
4113 GTT
1 GTT
4116 GACCGATTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
26 10 0.19
27 42 0.81
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:4235 original size:22 final size:22
Alignment explanation
Indices: 4203--4261 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
4193 CCCGTTATTA
*
4203 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
4225 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
4247 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
4262 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:4433 original size:25 final size:27
Alignment explanation
Indices: 4401--4465 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
4391 TATGGCTTTG
*
4401 TGCCACA-TATTCTG-TT-AGGTGGCTT
1 TGCCACATTA-TCTGATTCAGGTGGCTC
*
4426 TGCCACATTATCTGATTCTGGTGGCTC
1 TGCCACATTATCTGATTCAGGTGGCTC
*
4453 TGCCACAATATCT
1 TGCCACATTATCT
4466 ATATCTGGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.32
26 4 0.12
27 19 0.56
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (27 bp):
TGCCACATTATCTGATTCAGGTGGCTC
Found at i:4489 original size:26 final size:27
Alignment explanation
Indices: 4418--4496 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
4408 TATTCTGTTA
* *
4418 GGTGGCTTTGCCACATTATCTGATTCT
1 GGTGGCTCTGCCACAATATCTGATTCT
4445 GGTGGCTCTGCCACAATATCT-ATATCT
1 GGTGGCTCTGCCACAATATCTGAT-TCT
* *
4472 GGT-GCTCTGTCACGATATCTG-TTCT
1 GGTGGCTCTGCCACAATATCTGATTCT
4497 AGCAGCCATG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
25 3 0.07
26 18 0.39
27 25 0.54
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (27 bp):
GGTGGCTCTGCCACAATATCTGATTCT
Found at i:4625 original size:6 final size:6
Alignment explanation
Indices: 4616--4784 Score: 161
Period size: 6 Copynumber: 27.8 Consensus size: 6
4606 TTGCATTCAC
* *
4616 ATTCTG ATTCTG ATTCTG -TCATCTA ATTCTG ATTTTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
4665 -TTACTA ATACTG ATTCTG ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTG
1 ATT-CTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG
*
4714 ATTCTG ATTCTG ATTCTG -TTACTA ATAT-TG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG ATTCTG ATTCTG ATTCTG
4762 -TTACTG ATTCTG ATTCTG ATTCT
1 ATT-CTG ATTCTG ATTCTG ATTCT
4785 CATTTTGGTT
Statistics
Matches: 135, Mismatches: 14, Indels: 28
0.76 0.08 0.16
Matches are distributed among these distances:
5 9 0.07
6 114 0.84
7 9 0.07
8 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:4724 original size:67 final size:67
Alignment explanation
Indices: 4616--4761 Score: 265
Period size: 67 Copynumber: 2.2 Consensus size: 67
4606 TTGCATTCAC
* *
4616 ATTCTGATTCTGATTCTGTCATCTAATTCTGATTTTGATTCTGATTCTGTTACTAATACTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
4681 TG
66 TG
*
4683 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATATTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
4748 TG
66 TG
4750 ATTCTGATTCTG
1 ATTCTGATTCTG
4762 TTACTGATTC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 76 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.49
Consensus pattern (67 bp):
ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
TG
Found at i:4802 original size:30 final size:30
Alignment explanation
Indices: 4616--4805 Score: 186
Period size: 30 Copynumber: 6.1 Consensus size: 30
4606 TTGCATTCAC
* *
4616 ATTCTGATTCTGATTCTGTCATCTAATTCTG
1 ATTCTGATTCTGATTCTGTTA-CCAATTCTG
* *
4647 ATTTTGATTCTGATTCTGTTACTAATACTGATTCTG
1 ATTCTGATTCTGATTCTGTTAC-----C-AATTCTG
*
4683 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTACC-AATTCTG
*
4714 ATTCTGATTCTGATTCTGTTACTAATAT-TG
1 ATTCTGATTCTGATTCTGTTACCAAT-TCTG
**
4744 ATTCTGATTCTGATTCTGTTACTGATTCTG
1 ATTCTGATTCTGATTCTGTTACCAATTCTG
* *
4774 ATTCTGATTCTCATTTTGGTT-CCAATTCTG
1 ATTCTGATTCTGATTCT-GTTACCAATTCTG
4804 AT
1 AT
4806 AATGTTTCTT
Statistics
Matches: 136, Mismatches: 14, Indels: 19
0.80 0.08 0.11
Matches are distributed among these distances:
29 1 0.01
30 57 0.42
31 52 0.38
36 26 0.19
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (30 bp):
ATTCTGATTCTGATTCTGTTACCAATTCTG
Done.