Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_869 ID=scaffold_869-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: 4822
ACGTcount: A:0.18, C:0.12, G:0.14, T:0.16
Warning! 1914 characters in sequence are not A, C, G, or T
Found at i:275 original size:132 final size:132
Alignment explanation
Indices: 38--2600 Score: 3781
Period size: 132 Copynumber: 19.4 Consensus size: 132
28 TATATGAGGG
* * * * *
38 CTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATTTTATCTTTCCAACATAGTGGGAAACATAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
* * *
103 TTAAGTCACCAAGCATTGTCTCCCTGAGCAGCAGCGGAGTGGGTTCAAAATTATAGATCTTATCT
66 TTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
168 CC
131 CC
* * * * *
170 CTAAGCAATAGTAGTGCAGGTCGAAGACGGCAAATCTTATCTTTCCAAAATAGTGGGAAGCAGAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
* *
235 TTAAGTCACCAA-CCATTGTCTCCTTTAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATC
66 TTAAGTCACCAAGCC-TTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATC
299 TCC
130 TCC
*
302 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCCAAGATAGTGGGAAGCAGAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
*
367 TTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
66 TTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
432 CC
131 CC
* * * *
434 CTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTCCCAAGATAGTGAGAAGTAGAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
* * * *
499 TTAAGTCACCAAACATTGTCTCCCTGAGCAGCAACGGTGTGGGTTGAAAATTGTAGATCTTATCT
66 TTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
564 CC
131 CC
* * * *
566 CTAAGCAGTAGTGCAGCAGATCGAA-ATGGGAAATCTTATCTTTCCAAGATAATGGGAAGCAGAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
*
630 TTAAGTCACCAAGCATTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
66 TTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
695 CC
131 CC
**
697 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAATAGAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
* * *
762 TTAAGCCACCAAGCCTTGCCTGCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
66 TTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
827 CC
131 CC
* * * * *
829 TTAAGCAGTAGTGTAGCAGATCGAAGACGACAAATCTTATCTTTCTAAGATAGTGAGAAGCAGAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
* * * *
894 TTAAGTCACCAAACATTGTCTCCCTGTGCAGCAGTGGTA-TGGGTTGAAAATTGTAGATCTTATC
66 TTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGG-AGTGGGTTGAAAATTGTAGATCTTATC
958 TCC
130 TCC
* * * * * **
961 CGAAGCAGTAGTGCAGCAGATCGAAGATGGCAAATTTTATCTTTCCAACATAGTGGGAAATAGAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
* * * *
1026 TTAAGTCACCAAACATTGCCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTATAGATCTTATCT
66 TTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
1091 CC
131 CC
* * * * * *
1093 TTAAGCAATAGTAGTGCAGATCGAAGACGGCAAATCTTATCTTTCCAAAATAGTGGGAAGCAGGT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
* * *
1158 TTAAGTCACCAAGTCTTGTCTCCCTGAGCAGCAGTGGAGTGGGTTGAAAACTGTAGATCTTATCT
66 TTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
*
1223 CT
131 CC
* * *
1225 CTAAGCAGTAGTGCAGCAGATCGAAGATGGCAAATCTTATCTTTCCAAGATAATGGGAAGCAGAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
* * *
1290 TTAAGTCACCAAGCCTTTTCTCCCTGAGCAGCAGCGGAGTGGGTTGAGAATAGTAGATCTTATCT
66 TTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
1355 CC
131 CC
* * * *
1357 CTAAGCAGTAGTGGAGCTGATCGATGACGGTAAATCTTATCTTTCCAAAATAGTGGGAAGCAGAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
* * *
1422 TTAAGTCACCAAACATTGTCTCCCTGAGCAGCAGGGGAGTGGGTTGAAAATTGTAGATCTTATCT
66 TTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
1487 CC
131 CC
* * *
1489 CTAAGCAGTAGTGCAGCAGATCGAAGATGGCAAATCTTATCTTTCCAAGATAATGGGAAGCAGAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
* *
1554 TTAAGTCACCAAGCCTTGTTTCCCTGAGCAGCAGCGGAGTGGGTTAAAAATTGTAGATCTTATCT
66 TTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
1619 CC
131 CC
* * *
1621 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATTTTATCTTTCCAACATAGTGGGAAACAGAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
* * * * *
1686 TTAAGTCACCAAACATTGCCTCCCTGAGCAGCAGCAGAGTGGGTTGAAAATTATAGATCTTATCT
66 TTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
1751 CC
131 CC
* * *
1753 CTAAGCAATAGTAGTGCAGATCGAAGACGGCAAATCTTATCTTTCCAA-AGTAGTGGGAAGCAGA
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGA-TAGTGGGAAGCAGA
*
1817 TTTAAGTCACCAAGTCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATC
65 TTTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATC
1882 TCC
130 TCC
* * * * *
1885 CTAAGCAATAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTGCAAAATAGTGGGAAGCAGAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
* *
1950 TTAAGTCAACAAGCCTTGTCTCCCTGAGCAGCAGCGGTGTGGGTTGAAAATTGTAGATCTTATCT
66 TTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
2015 CC
131 CC
* * * *
2017 CTAAGCAGTAGTGCAGCAGATCGAAGATGGAAAATCTTATCTTTCCAAGATAATGGGAAGCAGAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
*
2082 TTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTAAAAATTGTAGATCTTATCT
66 TTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
2147 CC
131 CC
*
2149 CTAAGCAGTTGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
* *
2214 TTAA-TCCACCAAGCCTTGTCTCCGTGAGCAGCAGCGGAGTGGGTTAAAAATTGTAGATCTTATC
66 TTAAGT-CACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATC
2278 TCC
130 TCC
* * * *
2281 CTAAGCAGTAGTGGAGCATATCGAAGACGGCAAATTTTATCTTTCCAACATAGTGGGAAACAGAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
** * * *
2346 TTAAGTCACCAA-CCATTGGGTGCCTGAGCAGCAGCGGAGTGGGTTGAAAATTATATATCTTATC
66 TTAAGTCACCAAGCC-TTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATC
2410 TCC
130 TCC
* * * * *
2413 CTAAGCAATAGTAGTGCAGATCGAAGACGGCAAATCTTATCTTTCCAAAATAGTGGGAAGTAGAT
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
* * * * *
2478 GTTAAGTTACCAATCTCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAATATGTGTATATCATA
66 -TTAAGTCACCAAGC-CTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAAT-TGTAGATCTTA
2543 TCTTCC
128 TC-TCC
* * * * * *
2549 ATAAGCAGTAGTGCAGCAGATCGAACACGAC-AATCGTATCTTCCCAAGATAG
1 CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAG
2601 NNNNNNNNNN
Statistics
Matches: 2187, Mismatches: 229, Indels: 27
0.90 0.09 0.01
Matches are distributed among these distances:
131 126 0.06
132 1955 0.89
133 16 0.01
134 33 0.02
135 30 0.01
136 27 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (132 bp):
CTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGAT
TTAAGTCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAGATCTTATCT
CC
Found at i:339 original size:44 final size:44
Alignment explanation
Indices: 291--475 Score: 133
Period size: 44 Copynumber: 4.2 Consensus size: 44
281 AAAATTGTAG
291 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAA
** * **
335 ATCTTATCTTCCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCGAAGACGGCAA
** * * * * ** * * * ** * *
379 GCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGTTGAAAATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAA
*
423 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAA
467 ATCTTATCT
1 ATCTTATCT
476 TCCCAAGATA
Statistics
Matches: 97, Mismatches: 38, Indels: 12
0.66 0.26 0.08
Matches are distributed among these distances:
42 4 0.04
43 7 0.07
44 77 0.79
45 7 0.07
46 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAA
Found at i:4755 original size:132 final size:132
Alignment explanation
Indices: 4517--4822 Score: 549
Period size: 132 Copynumber: 2.3 Consensus size: 132
4507 NNNNNNNNTA
4517 AAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTT
1 AAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTT
*
4582 CCAAGATAGTGCGAAGCAGATTTAAGTCACCAAGCCATGTCTCCCTGAGCAGCAGAGGAGTGGGT
66 CCAAGATAGTGCGAAGCAGATTTAAGCCACCAAGCCATGTCTCCCTGAGCAGCAGAGGAGTGGGT
4647 TG
131 TG
* *
4649 AAAATTGTAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCGATGACGGCAAATCTTATCTTT
1 AAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTT
* * *
4714 CCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTGGGT
66 CCAAGATAGTGCGAAGCAGATTTAAGCCACCAAGCCATGTCTCCCTGAGCAGCAGAGGAGTGGGT
4779 TG
131 TG
*
4781 AAAATTGTAGATCTTATCTCCCTAAGCAATAGTGGAGCAGAT
1 AAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
Statistics
Matches: 166, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 166 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (132 bp):
AAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTT
CCAAGATAGTGCGAAGCAGATTTAAGCCACCAAGCCATGTCTCCCTGAGCAGCAGAGGAGTGGGT
TG
Done.