Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2414
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: 2790
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Found at i:890 original size:466 final size:469
Alignment explanation
Indices: 174--2787 Score: 3042
Period size: 466 Copynumber: 5.5 Consensus size: 469
164 ATTAGGATAC
* * * * * *
174 ATGACATTGATGATTTGGTGTCGCAAGAAAAGCTTTTCTTTACACCGTTTTAGATCGAATCAAAG
1 ATGACATTGATGATATGGTGTCGCAAGAAAAACTTTTCTTTCCATCATTTT-GATAGAATCAAAG
* * * * * * **
239 TTCCTCCCTCAAAAGAGGCAAACGTGAATAGTCATACTAATCCTCATTCTTTTTAGGATTAGGTG
65 TTCATCCCTCAAAAGAGACAAACATGAATAGTCATACTAATCCGCATTATTTTCAGGATTAGGCA
* ** *
304 CCATAAACAAAGTCTTCCCGTTATTATAGATGACAATGATGCTTTGGCTTCTCAAAAAGGCTTTC
130 CCATAAACAAAGTCTTCCCATTAGGATAGATGATAATGATGCTTTGGCTTCTCAAAAAGGCTTTC
* * * *
369 TTCCCACCAGTGTTAT--AAAGCCTAACTTTGTGCCTCAAATGAGACAAACATAGATTCTAGTAA
195 TTCTCTCCAAT-TTTTGCAAAGCCTAACTTTGTGCCTCAAATGAGACAAACATAGATTCTAGTAA
432 TGATCTTCATTCA-TTTGTGATTAGACACTATAAAAACAATCTCCTCATTAGGATAAATGATACC
259 TGATCTTCATTCATTTTGTGATTAGACACTATAAAAACAATCTCCTCATTAGGATAAATGATACC
496 GATCATTTTCTTTTGCATGTAAATCTTTTCCTTGCCTTATTTTCGTTAAAATCAAAGTTCATCCC
324 GATCATTTTCTTTTGCATGTAAATCTTTTCCTTGCCTTATTTTCGTTAAAATCAAAGTTCATCCC
561 AAAAATAAGACTAGCAAGGA-TCTTGTAAAGTCTCCATTCTTTTAAGATTGGGAAAAAAAGACAT
389 AAAAATAAGACTAGCAAGGACTCTTGTAAAGTCTCCATTCTTTTAAGATTGGGAAAAAAAGACAT
*
625 TGCGTTCGTTAGAGGT
454 TGCGTTCATTAGAGGT
641 ATGACATTGATGATATGGTGTCGCAAGAAAAACTTTTCTTTCCATCATTTTGATAGAATCAAAGT
1 ATGACATTGATGATATGGTGTCGCAAGAAAAACTTTTCTTTCCATCATTTTGATAGAATCAAAGT
* * *
706 TCATCCCTCAAAGGAGACAAACATGAATAGTCATACTAAT-CGCATTATTTTCAAGATTTGGCAC
66 TCATCCCTCAAAAGAGACAAACATGAATAGTCATACTAATCCGCATTATTTTCAGGATTAGGCAC
** *
770 CATAAACAAAGT-TGTGTCATTAGGATAGATGATATTGATGC-TTGGCTTCTCAAGAAAGGCTTT
131 CATAAACAAAGTCT-TCCCATTAGGATAGATGATAATGATGCTTTGGCTTCTCAA-AAAGGCTTT
* * * *
833 CTTCTCTCCAATTTTTGCAAAGTCTAACTTTGTGCCTCAAATGAGTCAAATATAGATTCTAGCAA
194 CTTCTCTCCAATTTTTGCAAAGCCTAACTTTGTGCCTCAAATGAGACAAACATAGATTCTAGTAA
* * * * * * * **
898 TGATCATCATTCATTTTCTGATTTGACACTATAAAAACATTCTCCTTATTCGGATAAACGATATT
259 TGATCTTCATTCATTTTGTGATTAGACACTATAAAAACAATCTCCTCATTAGGATAAATGATACC
* * * * *
963 GATAATTTTCTTTTGCATCG-AAATC-TTTCCTTACCCTATTTTCCTTAAAATCAATGTTCATCC
324 GATCATTTTCTTTTGCAT-GTAAATCTTTTCCTTGCCTTATTTTCGTTAAAATCAAAGTTCATCC
** ** ** * * * * *
1026 CGTAAATAAGACTAGCATCGACTCTCATAACAGTCTCCTTTCTTTCCCAA-AATCGAAACCAAAA
388 CAAAAATAAGACTAGCAAGGACTCTTGTAA-AGTCTCCATTCTTT--TAAGATTGGGAA--AAAA
* * ** *
1090 ACACATTCCCATCATTAG-GAT
448 AGACATTGCGTTCATTAGAGGT
* * * * * *
1111 ACATGACATTGATGATTTGGTGTCGCAAGAAAAGC-TTTCTTTTCACACCGTTTAGATCGAATCA
1 --ATGACATTGATGATATGGTGTCGCAAGAAAAACTTTTC-TTTC-CATCATTTTGATAGAATCA
* * * * * *
1175 AAGTTCCTCCCTCAAAAGAGGCAAACGTGAATAGTCATACTAATCCTCATTCTTTTTAGGATTAG
62 AAGTTCATCCCTCAAAAGAGACAAACATGAATAGTCATACTAATCCGCATTATTTTCAGGATTAG
** * **
1240 GTGCCATAAACAAAGTCTTCCCGTTATTATAGATGATAATGATGCTTTGGCTTCTCAAAAAGGCT
127 GCACCATAAACAAAGTCTTCCCATTAGGATAGATGATAATGATGCTTTGGCTTCTCAAAAAGGCT
* ** ** *
1305 TTCTT-TCCCCAATTGCTATAAA-CCTAACTTCGTGCCTCAAATGAGACAAACATAGATTCTAGT
192 TTCTTCTCTCCAATTTTTGCAAAGCCTAACTTTGTGCCTCAAATGAGACAAACATAGATTCTAGT
1368 AATGATCTTCATTCATTTTGTGATTAGACACTATAAAAACAATCTCCTCATTAGGATAAATGATA
257 AATGATCTTCATTCATTTTGTGATTAGACACTATAAAAACAATCTCCTCATTAGGATAAATGATA
1433 CCGATCATTTTCTTTTGCATG-AAATCTTTTCCTTGCCTTATTTTCGTT-AAATCAAAGTTCATC
322 CCGATCATTTTCTTTTGCATGTAAATCTTTTCCTTGCCTTATTTTCGTTAAAATCAAAGTTCATC
*
1496 CCAAAAATAAGACTAGCAAGGATTC-TGTAAAGTCTCCATTCTTTTAAAGATTGGGAAAAAAAGA
387 CCAAAAATAAGACTAGCAAGGACTCTTGTAAAGTCTCCATTCTTTT-AAGATTGGGAAAAAAAGA
* *
1560 CATTGCGTTCGTTAGGATGT
451 CATTGCGTTCATTA-GAGGT
1580 A-GACATTGATGATATGGTGTCGCAAGAAAAACTTTTCTTTCCATCATTTTTGATAGAATCAAAG
1 ATGACATTGATGATATGGTGTCGCAAGAAAAACTTTTCTTTCCATCA-TTTTGATAGAATCAAAG
* *
1644 TTCATCCCTCAAAGGAGACAAACATGAATAGTCATACTAAT-CGCATTATTTTCAGGATTTGGCA
65 TTCATCCCTCAAAAGAGACAAACATGAATAGTCATACTAATCCGCATTATTTTCAGGATTAGGCA
** *
1708 CCATAAACAAAGT-TGTGTCATTAGGATAGAT-ATATTGATGCTTTGGCTTCTCAAGAAAGGCTT
130 CCATAAACAAAGTCT-TCCCATTAGGATAGATGATAATGATGCTTTGGCTTCTCAA-AAAGGCTT
* * *
1771 TCTTCTCTCTCCAATTTTTGCAAAGTCTAAC-TTGTGCCTCAAATGAGTCAAATATAGATTCTAG
193 TC-T-TCTCTCCAATTTTTGCAAAGCCTAACTTTGTGCCTCAAATGAGACAAACATAGATTCTAG
* * * * * * * *
1835 CAATGATCATCATTCA-TTTCTGATTTGACACTATAAAAACATTCTCCTTATT-CGATAAACGAT
256 TAATGATCTTCATTCATTTTGTGATTAGACACTATAAAAACAATCTCCTCATTAGGATAAATGAT
** * * * * *
1898 ATTGAT-ATTTTCTTTTGCATCGAAATCGAAATATTTTCCTTACCCTATTTTCCTTAAAATCAAT
321 ACCGATCATTTTCTTTTGCAT-G---T--AAATCTTTTCCTTGCCTTATTTTCGTTAAAATCAAA
** ** * ** * * *
1962 GTTCATCCCGTAAATAAGACTAGCATA-GACTCTCATAACAGTCTCCTTTCTTCCCAA-AATCGA
380 GTTCATCCCAAAAATAAGACTAGCA-AGGACTCTTGTAA-AGTCTCCATTCTT-TTAAGATTGGG
* * ** *
2025 AACCAAAAACAACATTCCCATCATTAG-GAT
442 AA--AAAAA-GACATTGCGTTCATTAGAGGT
* * * *
2055 ACATGACATTGAT--T-TGGTGGT-GCAAGAAAAGCTTTTCTTTACA-CGTTTTAGATCGAATCA
1 --ATGACATTGATGATATGGT-GTCGCAAGAAAAACTTTTCTTTCCATCATTTT-GATAGAATCA
* * * * *
2115 AAGTTCCTCCCCCTCAAAAGAGGCAAACTGTGAATAGTCATACTATATCCTCATCT-TTTTTAGG
62 AAGTTCAT--CCCTCAAAAGAGACAAAC-ATGAATAGTCATACTA-ATCCGCAT-TATTTTCAGG
** * **
2179 ATTAGGTGCCATAAACAAAGTCTTCCCGTTATTATAGATGATAATGATGCTTTGGCTTCTCAAAA
122 ATTAGGCACCATAAACAAAGTCTTCCCATTAGGATAGATGATAATGATGCTTTGGCTTCTCAAAA
* * * *
2244 AGGCTTTCTT-TCCACCAATTGTAT--AAAGCCTAACTTCGTGCCTCAAATGAGACAAACAGAGA
187 AGGCTTTCTTCT-CTCCAATT-TTTGCAAAGCCTAACTTTGTGCCTCAAATGAGACAAACATAGA
2306 TTCTAGTAATGATCTTCATTCATTTTGTGATTAGACACTATAAAAACAATCTCCTCATTAGGATA
250 TTCTAGTAATGATCTTCATTCATTTTGTGATTAGACACTATAAAAACAATCTCCTCATTAGGATA
2371 AATGATACCGATCATTTTCTTTTTGCATGTAAATCTTTTCCTTGCCTTATTTTCGTTAAAATCAA
315 AATGATACCGATCATTTTC-TTTTGCATGTAAATCTTTTCCTTGCCTTATTTTCGTTAAAATCAA
*
2436 AGTTCATCCCAAAAATAAGACTAGCAAGGATTCTTGTAAAGTCTCCATTCTTTTAAAGATTGGGA
379 AGTTCATCCCAAAAATAAGACTAGCAAGGACTCTTGTAAAGTCTCCATTCTTTT-AAGATTGGGA
*
2501 AAAAAAGACATTGCGTTCATTAGGATGT
443 AAAAAAGACATTGCGTTCATTA-GAGGT
2529 ATGACATTGATGATATGGTGTCGCAAGAAAAACTTTTCTTTCCATCATTTTGATAGAATCAAAGT
1 ATGACATTGATGATATGGTGTCGCAAGAAAAACTTTTCTTTCCATCATTTTGATAGAATCAAAGT
* * *
2594 TCATCCCTCAAAGGAGACAAACATGAATCA-TCCTACTAAT-CGCATTATTTTCAGGATTTGGCA
66 TCATCCCTCAAAAGAGACAAACATGAAT-AGTCATACTAATCCGCATTATTTTCAGGATTAGGC-
* *
2657 ACCATAAACAAAGT-TT-GCATTAGGATAGGATAGACAATATTGATGCTTTGGCTTCTCAAGAAA
129 ACCATAAACAAAGTCTTCCCATTAGGATA-GAT-G---ATAATGATGCTTTGGCTTCTCAA-AAA
* * *
2720 GGCTTTCTTCTCTCCAATTTTTGCAAAGTCTAACTTTGTGCCTCAAATGAAGTCAAATATAGATT
188 GGCTTTCTTCTCTCCAATTTTTGCAAAGCCTAACTTTGTGCCTCAAATG-AGACAAACATAGATT
2785 CTA
252 CTA
2788 AGC
Statistics
Matches: 1780, Mismatches: 277, Indels: 170
0.80 0.12 0.08
Matches are distributed among these distances:
464 39 0.02
465 135 0.08
466 255 0.14
467 171 0.10
468 73 0.04
469 37 0.02
470 28 0.02
471 77 0.04
472 222 0.12
473 128 0.07
474 131 0.07
475 178 0.10
476 64 0.04
477 94 0.05
478 46 0.03
479 63 0.04
480 31 0.02
481 8 0.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.34
Consensus pattern (469 bp):
ATGACATTGATGATATGGTGTCGCAAGAAAAACTTTTCTTTCCATCATTTTGATAGAATCAAAGT
TCATCCCTCAAAAGAGACAAACATGAATAGTCATACTAATCCGCATTATTTTCAGGATTAGGCAC
CATAAACAAAGTCTTCCCATTAGGATAGATGATAATGATGCTTTGGCTTCTCAAAAAGGCTTTCT
TCTCTCCAATTTTTGCAAAGCCTAACTTTGTGCCTCAAATGAGACAAACATAGATTCTAGTAATG
ATCTTCATTCATTTTGTGATTAGACACTATAAAAACAATCTCCTCATTAGGATAAATGATACCGA
TCATTTTCTTTTGCATGTAAATCTTTTCCTTGCCTTATTTTCGTTAAAATCAAAGTTCATCCCAA
AAATAAGACTAGCAAGGACTCTTGTAAAGTCTCCATTCTTTTAAGATTGGGAAAAAAAGACATTG
CGTTCATTAGAGGT
Done.