Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_909 ID=scaffold_909-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: 3816
ACGTcount: A:0.20, C:0.16, G:0.13, T:0.16
Warning! 1324 characters in sequence are not A, C, G, or T
Found at i:902 original size:302 final size:303
Alignment explanation
Indices: 1--1563 Score: 2446
Period size: 304 Copynumber: 5.1 Consensus size: 303
*
1 GTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTGTCGCAGTTGCGCCTCGAATTTAA
1 GTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAGTTGCGCCTCGAATTTAA
*
66 ATGCAAATTCGACCAAATATCGTTTCAAGTTATTTGTTTCACAAAACGCAAATAACGAATGAGTT
66 ATGCAAATTCGACCAAATATCGTTTCAAGTTATTTATTTCACAAAACGCAAATAACGAATGAGTT
* ***
131 ACACCACGTCGAGAAAATGCAAATAAAAAAAACACCCCTATGAAATAAAATGGGAGGGGTGCAAC
131 ACACCACGTCGAGAAAATGCAACTAAAAAAAACA-TTATATGAAATAAAATGGGAGGGGTGCAAC
*
196 ACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAAATGCGGA
195 ACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGA
261 GTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCC
260 GTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCC
* * * *
305 GTCAACTCTTGCACAATCTATTCATATATAGGCTGCCCCTTATCGCATTTGCACCTCGAATTTAA
1 GTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAGTTGCGCCTCGAATTTAA
* * * *
370 ATGCAAATTCGAGCAAATATCGTTTCAAATTATTTATTTCACACAACGAAAATAACGAATGAGTT
66 ATGCAAATTCGACCAAATATCGTTTCAAGTTATTTATTTCACAAAACGCAAATAACGAATGAGTT
* * * *
435 ACACCACGTCAAGAAAATCCAACTAAAAAAAAACATTATATGAAATAAAATGGGTGGGGTGCAGC
131 ACACCACGTCGAGAAAATGCAACT-AAAAAAAACATTATATGAAATAAAATGGGAGGGGTGCAAC
* *
500 ACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAGGCACGCTTAGCTGCGGA
195 ACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGA
*
565 GTTCTGATGGGATCCGGTGCATTAGTGCCGGTATGATCGCACCC
260 GTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCC
* * * **
609 GCCAACTCTTGCGTAATCTATTAATATAAAGGCTGCCCCTTATCTTAGTTGCGCCTCGAATTTAA
1 GTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAGTTGCGCCTCGAATTTAA
* * *
674 ATGCAACTTCGACCAAATATCGTTTCAAGTTATTTATTTCAGAAAACGCAGATAACGAATGAGTT
66 ATGCAAATTCGACCAAATATCGTTTCAAGTTATTTATTTCACAAAACGCAAATAACGAATGAGTT
* * * *
739 ATACCACGTCTAGAAAACGCAACT-AAAAAAACATTATATGAAATAAAATAGGAGGGGTGCAACA
131 ACACCACGTCGAGAAAATGCAACTAAAAAAAACATTATATGAAATAAAATGGGAGGGGTGCAACA
* *
803 CGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCACGAGCACGCTTAACTGCGGAG
196 CGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAG
*
868 TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGTACCC
261 TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCC
* * *
911 GTCAACTCTTGCGCAATCTATTCACATAAAGGCTGCCCCTAATCGTAGTTGCGCCTCGAATTTAA
1 GTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAGTTGCGCCTCGAATTTAA
* * *
976 ATGCAACTTCGACCAAATATCGTTTCAAGTTATTTATTTCAGAAAACGCAGATAACGAATGAGTT
66 ATGCAAATTCGACCAAATATCGTTTCAAGTTATTTATTTCACAAAACGCAAATAACGAATGAGTT
* * ** **** * *** *
1041 ATACCACGTCTAGAAAATGCAACCCCTATTTATCCCCATTATATGAAATAAAACGCCCCGCGGTG
131 ACACCACGTCGAGAAAATGCAA---CTA-AAAAAAACATTATATGAAATAAAATG-GGAGGGGTG
*
1106 CAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCGAGCACGCTTAACTG
191 CAACACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTG
1171 CGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCC
256 CGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCC
* * *
1219 GTCAACTCTTGCGCAATCTATTCACATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATATAA
1 GTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAGTTGCGCCTCGAATTTAA
* *
1284 ATGCAAATTCGACCAAATATCGTTTCAAGTTGTTTATTTCACAAAACGCAAATAACGAATGACTT
66 ATGCAAATTCGACCAAATATCGTTTCAAGTTATTTATTTCACAAAACGCAAATAACGAATGAGTT
1349 ACACCACGTCGAGAAAATGCAACTAAAAAAAACATTATATGAAATAAAATGGGAGGGGTGCAACA
131 ACACCACGTCGAGAAAATGCAACTAAAAAAAACATTATATGAAATAAAATGGGAGGGGTGCAACA
* * * *
1414 TGAGGACTTCCCAGGAGATCACCCATCCTAGTACTACTCTCGCCCAAGCACGTTTAACTGC-GAT
196 CGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAG
1478 TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCC
261 TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCC
*
1521 GACAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTAT
1 GTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTAT
1564 NNNNNNNNNN
Statistics
Matches: 1151, Mismatches: 101, Indels: 16
0.91 0.08 0.01
Matches are distributed among these distances:
302 370 0.32
303 67 0.06
304 424 0.37
305 15 0.01
307 18 0.02
308 257 0.22
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (303 bp):
GTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAGTTGCGCCTCGAATTTAA
ATGCAAATTCGACCAAATATCGTTTCAAGTTATTTATTTCACAAAACGCAAATAACGAATGAGTT
ACACCACGTCGAGAAAATGCAACTAAAAAAAACATTATATGAAATAAAATGGGAGGGGTGCAACA
CGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAG
TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCC
Found at i:1378 original size:610 final size:607
Alignment explanation
Indices: 1--1560 Score: 2469
Period size: 610 Copynumber: 2.6 Consensus size: 607
*
1 GTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTGTCGCAGTTGCGCCTCGAATTTAA
1 GTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAGTTGCGCCTCGAATTTAA
*
66 ATGCAAATTCGACCAAATATCGTTTCAAGTTATTTGTTTCACAAAACGCAAATAACGAATGAGTT
66 ATGCAAATTCGACCAAATATCGTTTCAAGTTATTTATTTCACAAAACGCAAATAACGAATGAGTT
* ***
131 ACACCACGTCGAGAAAATGCAAATAAAAAAAACACCCCTATGAAATAAAATGGGAGGGGTGCAAC
131 ACACCACGTCGAGAAAATGCAACTAAAAAAAACA-TTATATGAAATAAAATGGGAGGGGTGCAAC
*
196 ACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAAATGCGGA
195 ACGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGA
*
261 GTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCACAATCTAT
260 GTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTAT
* * * *
326 TCATATATAGGCTGCCCCTTATCGCATTTGCACCTCGAATTTAAATGCAAATTCGAGCAAATATC
325 TCATATAAAGGCTGCCCCTAATCGCAGTTGCACCTCGAATTTAAATGCAAATTCGACCAAATATC
*
391 GTTTCAAATTATTTATTTCACACAACGAAAATAACGAATGAGTTACACCACGTCAAGAAAATCCA
390 GTTTCAAATTATTTATTTCACAAAACGAAAATAACGAATGAGTTACACCACGTCAAGAAAATCCA
* *** * *
456 ACTAAAAAAAAACATTATATGAAATAAAATGGGTGGGGTGCAGCACGAGGACTTCCCAGGAGGTC
455 ACTAAAAAAAAACATTATATGAAATAAAACGCCCGCGGTGCAACACGAGGACTTCCCAGGAGGTC
*
521 ACCCATCCTAGTACTACTCTCGCCCAGGCACGCTTAGCTGCGGAGTTCTGATGGGATCCGGTGCA
520 ACCCATCCTAGTACTACTCTCGCCCAGGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCA
586 TTAGTGCCGGTATGATCGCACCC
585 TTAGTGCCGGTATGATCGCACCC
* * * **
609 GCCAACTCTTGCGTAATCTATTAATATAAAGGCTGCCCCTTATCTTAGTTGCGCCTCGAATTTAA
1 GTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAGTTGCGCCTCGAATTTAA
* * *
674 ATGCAACTTCGACCAAATATCGTTTCAAGTTATTTATTTCAGAAAACGCAGATAACGAATGAGTT
66 ATGCAAATTCGACCAAATATCGTTTCAAGTTATTTATTTCACAAAACGCAAATAACGAATGAGTT
* * * *
739 ATACCACGTCTAGAAAACGCAACT-AAAAAAACATTATATGAAATAAAATAGGAGGGGTGCAACA
131 ACACCACGTCGAGAAAATGCAACTAAAAAAAACATTATATGAAATAAAATGGGAGGGGTGCAACA
* *
803 CGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCACGAGCACGCTTAACTGCGGAG
196 CGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAG
*
868 TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGTACCCGTCAACTCTTGCGCAATCTATT
261 TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTATT
* * * *
933 CACATAAAGGCTGCCCCTAATCGTAGTTGCGCCTCGAATTTAAATGCAACTTCGACCAAATATCG
326 CATATAAAGGCTGCCCCTAATCGCAGTTGCACCTCGAATTTAAATGCAAATTCGACCAAATATCG
* * * * * * *
998 TTTCAAGTTATTTATTTCAGAAAACGCAGATAACGAATGAGTTATACCACGTCTAGAAAATGCAA
391 TTTCAAATTATTTATTTCACAAAACGAAAATAACGAATGAGTTACACCACGTCAAGAAAATCCAA
*** ****
1063 CCCCTATTTATCCCCATTATATGAAATAAAACGCCCCGCGGTGCAACACGAGGACTTCCCAGGAG
456 ---CTAAAAAAAAACATTATATGAAATAAAACG-CCCGCGGTGCAACACGAGGACTTCCCAGGAG
1128 GTCACCCATCCTAGTACTACTCTCGCCC-GAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGG
517 GTCACCCATCCTAGTACTACTCTCGCCCAG-GCACGCTTAACTGCGGAGTTCTGATGGGATCCGG
*
1192 TGCATTAGTGCTGGTATGATCGCACCC
581 TGCATTAGTGCCGGTATGATCGCACCC
* * *
1219 GTCAACTCTTGCGCAATCTATTCACATAAAGGCTGCCCCTTATCGCACTTGCGCCTCGAATATAA
1 GTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAGTTGCGCCTCGAATTTAA
* *
1284 ATGCAAATTCGACCAAATATCGTTTCAAGTTGTTTATTTCACAAAACGCAAATAACGAATGACTT
66 ATGCAAATTCGACCAAATATCGTTTCAAGTTATTTATTTCACAAAACGCAAATAACGAATGAGTT
1349 ACACCACGTCGAGAAAATGCAACTAAAAAAAACATTATATGAAATAAAATGGGAGGGGTGCAACA
131 ACACCACGTCGAGAAAATGCAACTAAAAAAAACATTATATGAAATAAAATGGGAGGGGTGCAACA
* * * *
1414 TGAGGACTTCCCAGGAGATCACCCATCCTAGTACTACTCTCGCCCAAGCACGTTTAACTGC-GAT
196 CGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAG
*
1478 TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGACAACTCTTGCGCAATCTATT
261 TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTATT
1543 CATATAAAGGCTGCCCCT
326 CATATAAAGGCTGCCCCT
1561 TATNNNNNNN
Statistics
Matches: 866, Mismatches: 80, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
606 266 0.31
607 9 0.01
608 140 0.16
609 23 0.03
610 333 0.38
611 95 0.11
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (607 bp):
GTCAACTCTTGCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAGTTGCGCCTCGAATTTAA
ATGCAAATTCGACCAAATATCGTTTCAAGTTATTTATTTCACAAAACGCAAATAACGAATGAGTT
ACACCACGTCGAGAAAATGCAACTAAAAAAAACATTATATGAAATAAAATGGGAGGGGTGCAACA
CGAGGACTTCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAG
TTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCCGTCAACTCTTGCGCAATCTATT
CATATAAAGGCTGCCCCTAATCGCAGTTGCACCTCGAATTTAAATGCAAATTCGACCAAATATCG
TTTCAAATTATTTATTTCACAAAACGAAAATAACGAATGAGTTACACCACGTCAAGAAAATCCAA
CTAAAAAAAAACATTATATGAAATAAAACGCCCGCGGTGCAACACGAGGACTTCCCAGGAGGTCA
CCCATCCTAGTACTACTCTCGCCCAGGCACGCTTAACTGCGGAGTTCTGATGGGATCCGGTGCAT
TAGTGCCGGTATGATCGCACCC
Found at i:3452 original size:301 final size:303
Alignment explanation
Indices: 2888--3576 Score: 1116
Period size: 301 Copynumber: 2.3 Consensus size: 303
2878 NNNNNNNNNN
*
2888 ACATTATATGAAATAAAATGGG-GGGGTGCAACACCAGGACTTCCCAGGAGGTCACCCATCCTAG
1 ACATTATATGAAATAAAATGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAG
* * * *
2952 TACTAGTCTCGCCCAAGCACGCTTCACTGCGGAGTTCAGATGGGATCCGGTGCATTAGTGCGGGT
66 TACTACTCTCGCCCAAGCACGCTTAACAGCGGAGTTCAGATGCGATCCGGTGCATTAGTGCGGGT
* *
3017 ATGATCGCACCCGTCAACTCTTCCGCAATCTATTCATATAAAGGCTGCCCCTTATCGCAGTTGCG
131 ATGATCGCACCCGCCAACTCTTCCGCAATCTATTCATATAAAGGATGCCCCTTATCGCAGTTGCG
* * * *
3082 CCTCAAATTTAAATGCAAATTCGACCAAATATCGTTTCAAATTGTTTATTTCACAAAACGCAAAT
196 CCTCAAATTTAAATGAAAATTCGACCAAATATCGCTTCAAATTATTTATTTCACAAAACGAAAAT
3147 AACGAATGAGTTACACCACGTCGAGAAAATGCAAC-TAAAAAA
261 AACGAATGAGTTACACCACGTCGAGAAAATGCAACATAAAAAA
*
3189 A-ATTTTATGAAATAAAATGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAG
1 ACATTATATGAAATAAAATGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAG
* * * *
3253 TACTACTCTCGCCCAAGCACGCTTAACAGTGGTGTTCCGATGCGATCCGGTGCATTAGTGCTGGT
66 TACTACTCTCGCCCAAGCACGCTTAACAGCGGAGTTCAGATGCGATCCGGTGCATTAGTGCGGGT
*
3318 ATGATCGCACCCGCCAACTCTTGCGCAATCTATTCATATAAAGGATGCCCCTTATCGCAGTTGCG
131 ATGATCGCACCCGCCAACTCTTCCGCAATCTATTCATATAAAGGATGCCCCTTATCGCAGTTGCG
* * *
3383 CCTCGAATTTAAATGAAAATTCGAGCAAATATCGCTTCAAATTATTTATTTCACACAACGAAAAT
196 CCTCAAATTTAAATGAAAATTCGACCAAATATCGCTTCAAATTATTTATTTCACAAAACGAAAAT
*
3448 AACGAATGAGTTACACCACGTCGAGAAGATGCAACTATAAAAAA
261 AACGAATGAGTTACACCACGTCGAGAAAATGCAAC-ATAAAAAA
*
3492 ACATTATAT-AAATAAAATGGGGAGGGGTGCAACACGAGGACTTCCCCGGAGGTCACCCATCCTA
1 ACATTATATGAAATAAAAT-GGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTA
*
3556 TTACTACTCCTCGCCCAAGCA
65 GTACTACT-CTCGCCCAAGCA
3577 ACGCATAAAT
Statistics
Matches: 358, Mismatches: 24, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
300 19 0.05
301 253 0.71
303 17 0.05
304 57 0.16
305 12 0.03
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (303 bp):
ACATTATATGAAATAAAATGGGAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCATCCTAG
TACTACTCTCGCCCAAGCACGCTTAACAGCGGAGTTCAGATGCGATCCGGTGCATTAGTGCGGGT
ATGATCGCACCCGCCAACTCTTCCGCAATCTATTCATATAAAGGATGCCCCTTATCGCAGTTGCG
CCTCAAATTTAAATGAAAATTCGACCAAATATCGCTTCAAATTATTTATTTCACAAAACGAAAAT
AACGAATGAGTTACACCACGTCGAGAAAATGCAACATAAAAAA
Done.