Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_380 ID=scaffold_380-JGI_221_v2.0
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: 9453
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.27
Warning! 1789 characters in sequence are not A, C, G, or T
Found at i:3446 original size:44 final size:44
Alignment explanation
Indices: 3393--4008 Score: 509
Period size: 44 Copynumber: 13.8 Consensus size: 44
3383 CCTACTATCC
* *
3393 TTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCT
1 TTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTTTCT
* * * *** * * * *
3437 TCGACCTACTCCACCACCAGTATGGGGAGACAATATCTGTTGTAT
1 TTGATCTACTTCA-CACCAGTACATGAAGACAAGATCTGTTTTCT
* * * **
3482 TTGATCTACTTCACGCCAATACATGAAGATAAGATCCATTTTCT
1 TTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTTTCT
* * * *** * *
3526 TCGATCTACTTCGCCACCGGTATGGGAAGACAATATCTGTTATCT
1 TTGATCTACTTC-ACACCAGTACATGAAGACAAGATCTGTTTTCT
** *
3571 TTGATCTACTTCATGCCAGTACATGAAGACAAGATCTGGTTTCT
1 TTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTTTCT
* ** * *** *
3615 TCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCT
1 TTGATCTACTTC-ACACCAGTACATGAAGACAAGATCTGTTTTCT
* * ** * * *
3660 TCGATCTACTTTATGCCAGTACATGAAGATAAAATCTGCTATT-T
1 TTGATCTACTTCACACCAGTACATGAAGACAAGATCTG-TTTTCT
*
3704 TTGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTCT
1 TTGATCTACTTCACACCAGTACATGAAGACAAGATCTG--TT-TTCT
* * *** * *
3751 TTCGATCAACTTCGCCACCAGTATGGGAAGACAAGGTCTGTTATCT
1 TT-GATCTACTTC-ACACCAGTACATGAAGACAAGATCTGTTTTCT
*
3797 TTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCT
1 TTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTTTCT
* *** *
3841 TTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTG-TTTCT
1 TTGATCTACTTCA-CACCAGTACATGAAGACAAGATCTGTTTTCT
** *
3885 TTGATCTACTTCATGCCAGTACATGAAGACAAGATTTGTTTTCT
1 TTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTTTCT
* *** *
3929 TTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTG-TTTCT
1 TTGATCTACTTCA-CACCAGTACATGAAGACAAGATCTGTTTTCT
* *
3973 TTGATCTACTTCACGCCAGTATATGAAGACAAGATC
1 TTGATCTACTTCACACCAGTACATGAAGACAAGATC
4009 NNNNNNNNNN
Statistics
Matches: 433, Mismatches: 127, Indels: 25
0.74 0.22 0.04
Matches are distributed among these distances:
43 37 0.09
44 209 0.48
45 146 0.34
46 7 0.02
47 5 0.01
48 9 0.02
49 20 0.05
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (44 bp):
TTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTTTCT
Found at i:3497 original size:89 final size:89
Alignment explanation
Indices: 3388--3715 Score: 417
Period size: 89 Copynumber: 3.7 Consensus size: 89
3378 CAAGACCTAC
* * * *
3388 TATCCTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGACCTACTCCACCA
1 TATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCA
*
3453 CCAGTATGGGGAGACAATATCTGT
66 CCAGTATGGGAAGACAATATCTGT
* * * **
3477 TGTATTTGATCTACTTCACGCCAATACATGAAGATAAGATCCATTTTCTTCGATCTACTTCGCCA
1 TATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCA
*
3542 CCGGTATGGGAAGACAATATCTGT
66 CCAGTATGGGAAGACAATATCTGT
* * * **
3566 TATCTTTGATCTACTTCATGCCAGTACATGAAGACAAGATCTGGTTTCTTCGATCTGTTTCGCCA
1 TATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCA
*
3631 CCAGTATGGGAAGACAAGATCTGT
66 CCAGTATGGGAAGACAATATCTGT
* * * * * *
3655 TATCTTCGATCTACTTTATGCCAGTACATGAAGATAAAATCTGCTATTT-TT-GATCTACTTC
1 TATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG-T-TTTCTTCGATCTACTTC
3716 ACACCAATAC
Statistics
Matches: 207, Mismatches: 30, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
89 202 0.98
90 2 0.01
91 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.33
Consensus pattern (89 bp):
TATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCA
CCAGTATGGGAAGACAATATCTGT
Found at i:3804 original size:226 final size:221
Alignment explanation
Indices: 3481--3913 Score: 668
Period size: 226 Copynumber: 1.9 Consensus size: 221
3471 ATCTGTTGTA
* * * *
3481 TTTGATCTACTTCACGCCAATACATGAAGATAAGATCCATTTTCTTCGATCTACTTCGCCACCGG
1 TTTGATCTACTTCACACCAATACATGAAGACAAGATCCATTTTCTTCGATCAACTTCGCCACCAG
* *
3546 TATGGGAAGACAATATCTGTTATCTTTGATCTACTTCATGCCAGTACATGAAGACAAGATCTGGT
66 TATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGGT
** * * *
3611 TTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTCGATCTACTTTATGC
131 TTCTTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGTT-TCTTCGATCTACTTCATGC
3676 CAGTACATGAAGATAAAATCTGCTATT
195 CAGTACATGAAGATAAAATCTGCTATT
*
3703 TTTGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTCTTTCGATCAACTTCGCCA
1 TTTGATCTACTTCACACCAATACATGAAGACAAGATC--CATT-TTC-TTCGATCAACTTCGCCA
*
3768 CCAGTATGGGAAGACAAGGTCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATC
62 CCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATC
* * * *
3833 TGTTTTCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTTTCTTTGATCTACTTCA
127 TGGTTTCTTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGTTTCTTCGATCTACTTCA
3898 TGCCAGTACATGAAGA
192 TGCCAGTACATGAAGA
3914 CAAGATTTGT
Statistics
Matches: 190, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
222 35 0.18
224 3 0.02
225 33 0.17
226 119 0.63
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.33
Consensus pattern (221 bp):
TTTGATCTACTTCACACCAATACATGAAGACAAGATCCATTTTCTTCGATCAACTTCGCCACCAG
TATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGGT
TTCTTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGTTTCTTCGATCTACTTCATGCC
AGTACATGAAGATAAAATCTGCTATT
Found at i:3805 original size:137 final size:134
Alignment explanation
Indices: 3551--4008 Score: 435
Period size: 137 Copynumber: 3.4 Consensus size: 134
3541 ACCGGTATGG
* * ** *
3551 GAAGACAATATCTGTTATCTTTGATCTACTTCATGCCAGTACATGAAGACAAGATCTG-GT-TTC
1 GAAGACAAAATCTG-TATTTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTTCTTC
*** * *
3614 TTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTCGATCTACTTTATGCCAG
65 TTCGATCAACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAG
3679 TACAT
130 TACAT
* *
3684 GAAGATAAAATCTGCTATTTTTGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAAATCTG-TATTTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTG-TTTCTT
* *
3749 CTTTCGATCAACTTCGCCACCAGTATGGGAAGACAAGGTCTGTTATCTTTGATCTACTTCACGCC
64 C-TTCGATCAACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCC
3814 AGTACAT
128 AGTACAT
* * * *** *
3821 GAAGACAAGATCTGTTTTCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTTTC-T
1 GAAGACAAAATCTGTATT-TTTGATCTACTTCA-CACCAGTACATGAAGACAAGATCTGTTTCTT
* *** *** * * * * *
3885 -TT-GATCTACTTC-ATGCCAGTACATGAAGACAAGATTTGTTTTCTTTGATCTACTCCACCACC
64 CTTCGATCAACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCA-CGCC
***
3947 AGTATGG
128 AGTACAT
* * * *
3954 GGAGACAAGATCTGT-TTCTTTGATCTACTTCACGCCAGTATATGAAGACAAGATC
1 GAAGACAAAATCTGTATT-TTTGATCTACTTCACACCAGTACATGAAGACAAGATC
4009 NNNNNNNNNN
Statistics
Matches: 273, Mismatches: 45, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
131 19 0.07
132 51 0.19
133 81 0.30
134 2 0.01
135 1 0.00
136 7 0.03
137 92 0.34
138 20 0.07
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (134 bp):
GAAGACAAAATCTGTATTTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGTTTCTTCT
TCGATCAACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAGT
ACAT
Found at i:3962 original size:226 final size:225
Alignment explanation
Indices: 3417--3973 Score: 656
Period size: 226 Copynumber: 2.5 Consensus size: 225
3407 GCCAATACAT
* * * ** *** * * * * *
3417 GAAGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGGAGACAATATCTGTTGTAT
1 GAAGACAAGATCTGTTATCTTCGATCTACTTCA-TGCCAGTACATGAAGACAAAATCTGCTATTT
* * * * ** *
3482 TTGATCTACTTCACGCCAATACATGAAGATAAGATC-CATT-TTC-TTCGATCTACTTCGCCACC
65 TTGATCTACTCCACACCAATACAGGAAGACAAGATCTGTTTCTTCTTTCGATCAACTTCGCCACC
* * *
3544 GGTATGGGAAGACAATATCTGTTATCTTTGATCTACTTCATGCCAGTACATGAAGACAAGATCTG
130 AGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
** * *
3609 GTTTCTTCGATCTGTTTCGCCACCAGTATGG
195 GTTTCTTCGATCTACTCCACCACCAGTATGG
* *
3640 GAAGACAAGATCTGTTATCTTCGATCTACTTTATGCCAGTACATGAAGATAAAATCTGCTATTTT
1 GAAGACAAGATCTGTTATCTTCGATCTACTTCATGCCAGTACATGAAGACAAAATCTGCTATTTT
* *
3705 TGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTCTTTCGATCAACTTCGCCACC
66 TGATCTACTCCACACCAATACAGGAAGACAAGATCTG-TTTCTTCTTTCGATCAACTTCGCCACC
*
3770 AGTATGGGAAGACAAGGTCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
130 AGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
* *
3835 TTTTCTTTGATCTACTCCACCACCAGTATGG
195 GTTTCTTCGATCTACTCCACCACCAGTATGG
* * * * *
3866 GGAGACAAGATCTGTT-TCTTTGATCTACTTCATGCCAGTACATGAAGACAAGATTTG-TTTTCT
1 GAAGACAAGATCTGTTATCTTCGATCTACTTCATGCCAGTACATGAAGACAAAATCTGCTATT-T
* ** *
3929 TTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTTTCTT
65 TTGATCTACTCCA-CACCAATACAGGAAGACAAGATCTGTTTCTT
3974 TGATCTACTT
Statistics
Matches: 285, Mismatches: 43, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
222 54 0.19
223 29 0.10
224 5 0.02
225 58 0.20
226 139 0.49
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (225 bp):
GAAGACAAGATCTGTTATCTTCGATCTACTTCATGCCAGTACATGAAGACAAAATCTGCTATTTT
TGATCTACTCCACACCAATACAGGAAGACAAGATCTGTTTCTTCTTTCGATCAACTTCGCCACCA
GTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGG
TTTCTTCGATCTACTCCACCACCAGTATGG
Done.