Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_970 ID=scaffold_970-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: 3442
ACGTcount: A:0.14, C:0.13, G:0.10, T:0.16
Warning! 1636 characters in sequence are not A, C, G, or T
Found at i:328 original size:132 final size:132
Alignment explanation
Indices: 1--706 Score: 1137
Period size: 132 Copynumber: 5.3 Consensus size: 132
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAA-CCACACCGCTGCTGCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCCACACCGCTGCTGCT
*
65 CAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCATTATCCTTGGAAAGATAAGATTTGCCA
66 CAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCATTAT-CTTGGAAAGATAAGATTTGCCG
130 TCT
130 TCT
*
133 TCGATCTGCTCGCACTACTGCCTTAGGGAGATAAGATCTACAATTTTCAACCCACACCACTGCTG
1 TCGATCTGCTC-CACTACTG-CTTAGGGAGATAAGATCTACAATTTTCAACCCACACCGCTGCTG
* * * * * *
198 CTCAGGGATACAATGTTTGGTGACTTAAATCTGCTTCCCACTATGTTGGAAAGATAAGATTTGAC
64 CTCAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCATTATCTTGGAAAGATAAGATTTGCC
263 GTCT
129 GTCT
* * *
267 TCGATCTGCTCCCCTACTGCTTAGGAAGATAAGATCTACAATTTTCAACCCACCCCGCTGCTGCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCCACACCGCTGCTGCT
*
332 CAGGGAGACAAGGCTTGGTGACTTAAATCTGCTT-CCATTATCTTGGAAAGATAAGATTTACCGT
66 CAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCATTATCTTGGAAAGATAAGATTTGCCGT
396 CT
131 CT
* *
398 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTCCAACCCACTCCGCTGCTGCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCCACACCGCTGCTGCT
* *
463 CAGGGAGACAAGGCTTAGTGGCTTAAATCTGCTTCCCATTATCTTGGAAAGATAAGATTTGCCGT
66 CAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCATTATCTTGGAAAGATAAGATTTGCCGT
*
528 CA
131 CT
*
530 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCCACACCGCTGCTGCT
* * * *
595 CAGGGAGACATGGCTTGGTGACTTAAATCTGCTTCGCACTATTTTGGAAAGATAAGATTTGCCGT
66 CAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCATTATCTTGGAAAGATAAGATTTGCCGT
660 CT
131 CT
* * * *
662 TCGATCTGCACGACTATTGCTTAGGGAGATAAGATCTATAATTTT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTT
707 NNNNNNNNNN
Statistics
Matches: 531, Mismatches: 39, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
131 121 0.23
132 280 0.53
133 15 0.03
134 62 0.12
135 53 0.10
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (132 bp):
TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCCACACCGCTGCTGCT
CAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCATTATCTTGGAAAGATAAGATTTGCCGT
CT
Found at i:430 original size:44 final size:44
Alignment explanation
Indices: 380--564 Score: 108
Period size: 44 Copynumber: 4.2 Consensus size: 44
370 TATCTTGGAA
*
380 AGATAAGATTTACCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * ** * * *
424 AGATAAGATCTACAAT-TTCCAACCCACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTACCGTCTT-CAATCTGCTCCACTACTGCTTAGGG
* ** ** * * * *
468 AGACAAGGCTTAGTGGCTTAAATCTGCTTCCCATTA-T-CTT-GGAA
1 AGATAAGATTTACCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* * *
512 AGATAAGATTTGCCGTCATCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
556 AGATAAGAT
1 AGATAAGAT
565 CTACAATTTT
Statistics
Matches: 94, Mismatches: 39, Indels: 16
0.63 0.26 0.11
Matches are distributed among these distances:
42 5 0.05
43 6 0.06
44 74 0.79
45 6 0.06
46 3 0.03
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (44 bp):
AGATAAGATTTACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:492 original size:263 final size:263
Alignment explanation
Indices: 1--705 Score: 1133
Period size: 263 Copynumber: 2.7 Consensus size: 263
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAA-CCACACCGCTGCTGCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCCACACCGCTGCTGCT
*
65 CAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCATTATCCTTGGAAAGATAAGATTTGCCA
66 CAGGGAGACAAGGCTTGGTGACTTAAATCTGCTT-CCATTAT-CTTGGAAAGATAAGATTTGCCG
*
130 TCTTCGATCTGCTCGCACTACTGCCTTAGGGAGATAAGATCTACAATTTTCAACCCACACCACTG
129 TCTTCGATCTGCTC-CACTACTG-CTTAGGGAGATAAGATCTACAATTTCCAACCCACACCACTG
* * * * *
195 CTGCTCAGGGATACAATGTTTGGTGACTTAAATCTGCTTCCCACTATGTTGGAAAGATAAGATTT
192 CTGCTCAGGGAGACAAGGCTTAGTGACTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTT
*
260 GACGTCT
257 GACGTCA
* * *
267 TCGATCTGCTCCCCTACTGCTTAGGAAGATAAGATCTACAATTTTCAACCCACCCCGCTGCTGCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCCACACCGCTGCTGCT
*
332 CAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCATTATCTTGGAAAGATAAGATTTACCGTC
66 CAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCATTATCTTGGAAAGATAAGATTTGCCGTC
* *
397 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTCCAACCCACTCCGCTGCTGC
131 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTCCAACCCACACCACTGCTGC
* * *
462 TCAGGGAGACAAGGCTTAGTGGCTTAAATCTGCTTCCCATTATCTTGGAAAGATAAGATTTGCCG
196 TCAGGGAGACAAGGCTTAGTGACTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGACG
527 TCA
261 TCA
*
530 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCCACACCGCTGCTGCT
* * *
595 CAGGGAGACATGGCTTGGTGACTTAAATCTGCTTCGCACTATTTTGGAAAGATAAGATTTGCCGT
66 CAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTC-CATTATCTTGGAAAGATAAGATTTGCCGT
* * * *
660 CTTCGATCTGCACGACTATTGCTTAGGGAGATAAGATCTATAATTT
130 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTT
706 TNNNNNNNNN
Statistics
Matches: 409, Mismatches: 28, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
263 197 0.48
264 76 0.19
265 34 0.08
266 53 0.13
267 49 0.12
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (263 bp):
TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCCACACCGCTGCTGCT
CAGGGAGACAAGGCTTGGTGACTTAAATCTGCTTCCATTATCTTGGAAAGATAAGATTTGCCGTC
TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTCCAACCCACACCACTGCTGC
TCAGGGAGACAAGGCTTAGTGACTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGACG
TCA
Found at i:2553 original size:44 final size:44
Alignment explanation
Indices: 2505--3349 Score: 108
Period size: 44 Copynumber: 19.2 Consensus size: 44
2495 TATCTTGGAA
*
2505 AGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * ** * * *
2549 AGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** ** * * * *
2593 AGACAAGGCTTGTTGACTTAAATCTGCTTCCCACTA-T--TTTGGAA
1 AGATAAGATTTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* * *
2637 AGATAAGATTTGTCGTCTTCGATCTGCTCCACTATTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * ** * * *
2681 AGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** ** * * * * *
2725 AGACAAGGCTTGGTGACTTAAATCTGCTTCACATTA-T-ATT-GGAA
1 AGATAAGATTTGCCGTCTTCAATCTGC-TC-CACTACTGCTTAGG-G
* * * * * * *
2769 AGATAAGGTTTTCCATTTTCGATCTGCTGCACTACTGCTTAGGA
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * ** * * * *
2813 AGATAAGATCTACAATTTTCAACCCACACCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
** * * *
2857 AGATAATG-TTTGGTGACTTAAAGCTGCTTCTCACTA-T-CTT-GGG
1 AGATAA-GATTTGCCGTCTTCAATCTGC-TC-CACTACTGCTTAGGG
* * *
2900 AAGATAAGATTTGTCGTCTTCGATCTGCTACACTACTGCTTAGGG
1 -AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * ** * * *
2945 AGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** ** * * * *
2989 AGACAAGGCTTGGTGGCTTAAATCTACTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* * *
3033 AGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTCCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * ** ** * * *
3077 AGATAAGATCTACAATTTTCAGCCCACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* *** ** * * *
3121 AGACAAGGCCTGGTGACTTAAATCTGCTTGCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* *
3165 AGATAAGATTTGCCGTCATCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * ** * * *
3209 AGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** ** * * * *
3253 AGACATGGCTTGGTGACTTAAATCTGCTTCGCACTA-T--TTTGGAA
1 AGATAAGATTTGCCGTCTTCAATCTGC-TC-CACTACTGCTTAGG-G
* * *
3297 AGATAAGATTTGCCGTCTTCAATCTGCACTACTATTGCTTAGGG
1 AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
3341 AGATAAGAT
1 AGATAAGAT
3350 CTATAATTTT
Statistics
Matches: 510, Mismatches: 253, Indels: 76
0.61 0.30 0.09
Matches are distributed among these distances:
42 31 0.06
43 28 0.05
44 399 0.78
45 32 0.06
46 20 0.04
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (44 bp):
AGATAAGATTTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:2622 original size:132 final size:132
Alignment explanation
Indices: 2343--3439 Score: 1753
Period size: 132 Copynumber: 8.3 Consensus size: 132
2333 NNNNNNNNNN
*
2343 AAATCTGCTTCCCACTATCCTTGGAAAGATAAGAATTTGCCCGTCTTTCGATCTGCTCTACTACT
1 AAATCTGCTTCCCACTAT-CTTGGAAAGATAAG-ATTTG-CCGTC-TTCGATCTGCTCCACTACT
2408 GCTTAGGGAGATAAGATCTACAATTTTCAACCCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTG
62 GCTTAGGGAGATAAGATCTACAATTTTCAA-CCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTG
2473 GTGACTT
126 GTGACTT
2480 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTT
1 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTT
*
2545 AGGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTGTTGAC
66 AGGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGAC
2610 TT
131 TT
* * *
2612 AAATCTGCTTCCCACTATTTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTATTGCTT
1 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTT
2677 AGGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGAC
66 AGGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGAC
2742 TT
131 TT
* * * * * * * *
2744 AAATCTGCTTCACATTATATTGGAAAGATAAGGTTTTCCATTTTCGATCTGCTGCACTACTGCTT
1 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTT
* * * * *
2809 AGGAAGATAAGATCTACAATTTTCAACCCACACCGCTGCTGCTCAGGGAGATAATGTTTGGTGAC
66 AGGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGAC
2874 TT
131 TT
* * * * *
2876 AAAGCTGCTTCTCACTATCTTGGGAAGATAAGATTTGTCGTCTTCGATCTGCTACACTACTGCTT
1 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTT
*
2941 AGGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
66 AGGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGAC
3006 TT
131 TT
* * *
3008 AAATCTACTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTTCGATCTGCTCCACTACTCCTT
1 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTT
* *
3073 AGGGAGATAAGATCTACAATTTTCAGCCCACTCCGCTGCTGCTCAGGGAGACAAGGCCTGGTGAC
66 AGGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGAC
3138 TT
131 TT
* *
3140 AAATCTGCTTGCCACTATCTTGGAAAGATAAGATTTGCCGTCATCGATCTGCTCCACTACTGCTT
1 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTT
*
3205 AGGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACATGGCTTGGTGAC
66 AGGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGAC
3270 TT
131 TT
* * * * * *
3272 AAATCTGCTTCGCACTATTTTGGAAAGATAAGATTTGCCGTCTTCAATCTGCACTACTATTGCTT
1 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTT
* * *
3337 AGGGAGATAAGATCTATAATTTTCAACACACTCCGCTGCTGCTCAGGGAGACAATGCTTGGTGAC
66 AGGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGAC
3402 TT
131 TT
* * *
3404 AAATCTGTTTCCCACTATGTTGGAAAGATAAAATTT
1 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTT
3440 TCC
Statistics
Matches: 889, Mismatches: 71, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
132 799 0.90
133 48 0.05
134 5 0.01
135 5 0.01
136 14 0.02
137 18 0.02
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (132 bp):
AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTT
AGGGAGATAAGATCTACAATTTTCAACCCACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGAC
TT
Done.