Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga09g01738.F1
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: 3713
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Found at i:2049 original size:438 final size:429
Alignment explanation
Indices: 1054--2995 Score: 1487
Period size: 438 Copynumber: 4.5 Consensus size: 429
1044 TGCTTGCATT
* * * *
1054 CCATGAGTCTAACCAGACGTAGTCAGGTGTCTACCTTTGATATGATGGTGGGGACTGTTACTTGT
1 CCATGAGTCCAACCAGACGTAGTCAGGTGTCTACCTTAGATATGATGGTAGGGACTGTTACATGT
* ** * **
1119 CTGGAAAATAAAAGATAGGGAAGGAATCAATGGTTTGGGTTTCCTCTCTATCTATTAGCCATCCC
66 CTGGAAAATAAAAGATAGGGAAGGAGTTGATAGTTTGGGTTTCCAATCTATCTATTAGCCATCCC
*
1184 TTGAAGGAGTCCATCGTTGCCCAGTACTATTTGTTTGGTTATTACTTGAGCTACATCTGGACACT
131 TTGAAGGAGTCCATCGTTGCCCAGTACTATGTGTTT-GTTATTACTTGAGCTACATCTGGACACT
* * * * * *
1249 ACATCTCTCAACAACTC--TACT-TCA-GTAGTCGATCTATGCATTCTAGTATG-AGGCTGTTCT
195 ACATCTCTCAACACCTCTTTA-TAT-ATG-AGTCAATCTATACATTCAAGTATGAAGGC-ATCCT
** * * *
1309 TATTTTGGATATA-TGGA-CCACTCCTGTGAATC----TG--TTCTAAGAGATGGT-AAAGC-AA
256 TATTTTGGATATAGTGGATCCA-TGTTGTGAATCTGTTTGTTTTTTAAGGGATAGTGAAA-CAAA
***** * * * *
1364 TGATAGTGATGTGGTTTAGGGGAGAAAATAGC--AGCAATATTTAGTTGCTCT-CTATTCTTAAA
319 TGATA---ATAACACTT-----A-AATAT-GCTTTGGAA-A--TACTT-C-CTGC--TTCTT---
* * * * * * * * **
1426 GCAACTTATTTTGAATATTGATGCATTTATAGATGTTTGTCTATGAACTGTTTTTTAATATTTAG
364 --TA--TCTTTTGAATATAGATGCATTT-TA-TTGTTTATCTGTAAACTATTAATTAATATTT-G
* *
1491 TTATTTGCGTT
422 ---TTTGTGTC
* * * * * **
1502 CCATGATTCTAACCAGACATAGTCAGGTGTCTACCTTTGATATGGTTTTAGGGACTGTTACATGT
1 CCATGAGTCCAACCAGACGTAGTCAGGTGTCTACCTTAGATATGATGGTAGGGACTGTTACATGT
* * * * * * **
1567 CTGGAAAATAAAAGATAGGAAAGTAGTTGATGGTTTGGGTTTCCATTATATCTGTTATACATCCC
66 CTGGAAAATAAAAGATAGGGAAGGAGTTGATAGTTTGGGTTTCCAATCTATCTATTAGCCATCCC
* * * * *
1632 TTGAAGGAGTCCATCATTGCCCGGTACTATGTGTTCTGTTATTACTTGAGCTATATCTGGGCATT
131 TTGAAGGAGTCCATCGTTGCCCAGTACTATGTGTT-TGTTATTACTTGAGCTACATCTGGACACT
*
1697 ACATCTCTCAACACCTCTTTATATATGCAGCCAATCTATACATTCAAGTATGAAGGTCATCCTTA
195 ACATCTCTCAACACCTCTTTATATATG-AGTCAATCTATACATTCAAGTATGAAGG-CATCCTTA
* * *
1762 TTTTGGACATAGTGGATCGCATGTTGTGAATCTGTTTGTTTTTTAATGGGATACTGAAACAAATT
258 TTTTGGATATAGTGGATC-CATGTTGTGAATCTGTTTGTTTTTTAA-GGGATAGTGAAACAAATG
**
1827 ATAATAACACTTAATATATGCGTTTGGAAATACTTCCCGTGCTTCTTTATCTTTTGAATGCAGAT
321 ATAATAACACTTAA-ATATGC-TTTGGAAATACTT-CC-TGCTTCTTTATCTTTTGAATATAGAT
1892 GCATTTTATTGTTTATCTGTAAACTATTAATTAATATTTGTTTGTGTC
382 GCATTTTATTGTTTATCTGTAAACTATTAATTAATATTTGTTTGTGTC
*
1940 CCATGAGTCCAACCAGACGTAGTCAGGTGTCTACCTTAGATTTGATGGTAGGGACTGTTACATGT
1 CCATGAGTCCAACCAGACGTAGTCAGGTGTCTACCTTAGATATGATGGTAGGGACTGTTACATGT
* *
2005 CTGGAAAATAGATGATAGGGAAGGAGTTGATAGTTTGGGTTTCCAATCTATCTATTAGCCATCCC
66 CTGGAAAATAAAAGATAGGGAAGGAGTTGATAGTTTGGGTTTCCAATCTATCTATTAGCCATCCC
* *
2070 TTGAAAGAGTCCATCGTTGCCCAGTACTATTTGTTTAGTTATTACTTGAGCTACATCTGGACACT
131 TTGAAGGAGTCCATCGTTGCCCAGTACTATGTGTTT-GTTATTACTTGAGCTACATCTGGACACT
* ** * * *
2135 ACATCTCTCAACTCCTC--TACTCCA-GTAGTCAA-CTTATGCATTCTAGTATG-AGGCCATTCT
195 ACATCTCTCAACACCTCTTTA-TATATG-AGTCAATC-TATACATTCAAGTATGAAGG-CATCCT
* ** * *
2195 TATTTTGGATAT-GTTGA-CCACTCCTCTGAATCTGTTTG----TTAAGAGATAGT-AAAGCAAA
256 TATTTTGGATATAGTGGATCCA-TGTTGTGAATCTGTTTGTTTTTTAAGGGATAGTGAAA-CAAA
* * * * * * * *
2253 TGATAGTAGCACTT-AA-ATGCTCT--CAATTCTT-AT-ATTAAC-TTA--TTTTGAATATTGAT
319 TGATAATAACACTTAAATATGCTTTGGAAATACTTCCTGCTT--CTTTATCTTTTGAATATAGAT
* * * * * *
2309 GCATTTTTAGGTGTTTGTCTATGAACTATTATTTAATATTTAG-TTGT-TT
382 GCA-TTTTA-TTGTTTATCTGTAAACTATTAATTAATATTT-GTTTGTGTC
* * * * * *
2358 ACACG-TTCC-A-C-GA-GTAGTTAGGTGTCTACCTTGGAATATGATTGTAGGGACTGTTACATG
1 CCATGAGTCCAACCAGACGTAGTCAGGTGTCTACCTTAG-ATATGATGGTAGGGACTGTTACATG
** * *
2418 TCTGGAAAATAAAAGATAGGGAAGTTGTTGATGGTTTGGGTTTCCAATCTATCTATTAGTCATCC
65 TCTGGAAAATAAAAGATAGGGAAGGAGTTGATAGTTTGGGTTTCCAATCTATCTATTAGCCAT-C
*** *
2483 CCTTGAAGGAGTCCATCGTTGCCCAGTACTATGTGTTTTGTTATTACACAAGCTACATCTGGGCA
129 CCTTGAAGGAGTCCATCGTTGCCCAGTACTATGTG-TTTGTTATTACTTGAGCTACATCTGGACA
* * * *
2548 CTACATCTCTCGAA-ACCTCTTTCTATCAAT-ATTCAATCTATACATCCAAGCATGAAGG---CC
193 CTACATCTCTC-AACACCTCTTTATAT--ATGAGTCAATCTATACATTCAAGTATGAAGGCATCC
* * * * *
2608 --A-TCTGGATATAGTGGAT-CATTTGTTGCGAATCTGTTTGTTTTCTAAAGGGGTAGTGAAGCA
255 TTATTTTGGATATAGTGGATCCA--TGTTGTGAATCTGTTTGTTTT-TTAAGGGATAGTGAAACA
2669 AATGATAATAACAC--AACATATGCATTTGGAAATACTTTCTCTGCTT-TTGTATCTTTTGAATA
317 AATGATAATAACACTTAA-ATATGC-TTTGGAAATAC-TTC-CTGCTTCTT-TATCTTTTGAATA
* * *
2731 TAGATGCATTTT-TGGTGTTTATCTGGAAAC---T-ATTAATAGTTGTTTGCGTC
377 TAGATGCATTTTAT--TGTTTATCTGTAAACTATTAATTAATATTTGTTTGTGTC
* * *
2781 CCATGAG-CCTAACCAGACGTAGTCAGGTGTCTACCTAAGATTTGATGGTAGTGACTGTTACATG
1 CCATGAGTCC-AACCAGACGTAGTCAGGTGTCTACCTTAGATATGATGGTAGGGACTGTTACATG
* * * *
2845 TCTGGAAAATAGAAGATAAGGAAGGAGTTGATAGTTTGGGTTTCCAATCTGTCTATGAGCCATCC
65 TCTGGAAAATAAAAGATAGGGAAGGAGTTGATAGTTTGGGTTTCCAATCTATCTATTAGCCATCC
* * ** * *
2910 CTTGATGGAGTCCATCGTTGCCCAGTA-TCA-GTCTAAAGTTGTTATTTGAGCTACATCTGGACA
130 CTTGAAGGAGTCCATCGTTGCCCAGTACT-ATGTGT-TTGTTATTACTTGAGCTACATCTGGACA
2973 CTACATCTCTCAACACCTCTTTA
193 CTACATCTCTCAACACCTCTTTA
2996 CTTAAGTGGT
Statistics
Matches: 1205, Mismatches: 207, Indels: 187
0.75 0.13 0.12
Matches are distributed among these distances:
411 8 0.01
412 7 0.01
413 32 0.03
414 83 0.07
415 72 0.06
416 7 0.01
417 36 0.03
418 40 0.03
419 40 0.03
420 4 0.00
421 1 0.00
422 21 0.02
423 9 0.01
424 6 0.00
425 50 0.04
426 48 0.04
427 99 0.08
428 39 0.03
429 4 0.00
432 2 0.00
433 15 0.01
434 4 0.00
435 20 0.02
436 22 0.02
437 3 0.00
438 190 0.16
441 1 0.00
442 24 0.02
443 2 0.00
444 18 0.01
446 1 0.00
448 185 0.15
449 3 0.00
450 24 0.02
451 24 0.02
452 14 0.01
453 15 0.01
454 3 0.00
455 3 0.00
457 2 0.00
458 4 0.00
459 5 0.00
460 6 0.00
461 9 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (429 bp):
CCATGAGTCCAACCAGACGTAGTCAGGTGTCTACCTTAGATATGATGGTAGGGACTGTTACATGT
CTGGAAAATAAAAGATAGGGAAGGAGTTGATAGTTTGGGTTTCCAATCTATCTATTAGCCATCCC
TTGAAGGAGTCCATCGTTGCCCAGTACTATGTGTTTGTTATTACTTGAGCTACATCTGGACACTA
CATCTCTCAACACCTCTTTATATATGAGTCAATCTATACATTCAAGTATGAAGGCATCCTTATTT
TGGATATAGTGGATCCATGTTGTGAATCTGTTTGTTTTTTAAGGGATAGTGAAACAAATGATAAT
AACACTTAAATATGCTTTGGAAATACTTCCTGCTTCTTTATCTTTTGAATATAGATGCATTTTAT
TGTTTATCTGTAAACTATTAATTAATATTTGTTTGTGTC
Done.