Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1075
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: 8185
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Found at i:3746 original size:70 final size:71
Alignment explanation
Indices: 3621--3778 Score: 282
Period size: 70 Copynumber: 2.2 Consensus size: 71
3611 CGATACAAAG
* *
3621 CATAATGTATCGATACATCTGGGTGGAGTATCGATACATTCAAGGTTTTGACCTTTGTTGCCTAA
1 CATAATGTATCGATACATCTGGGTGGAGTATCGATACATTCAAGGGTTTGACCTTTGTAGCCTAA
3686 GTCAAC
66 GTCAAC
*
3692 CATAATGTATCGATACATCTGGGT-GAGTATCGATACATTCAAGGGTTTGACCTTTGTAGCCTCA
1 CATAATGTATCGATACATCTGGGTGGAGTATCGATACATTCAAGGGTTTGACCTTTGTAGCCTAA
3756 GTCAAC
66 GTCAAC
3762 CATAATGTATCGATACA
1 CATAATGTATCGATACA
3779 ATACTTATGT
Statistics
Matches: 84, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
70 60 0.71
71 24 0.29
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (71 bp):
CATAATGTATCGATACATCTGGGTGGAGTATCGATACATTCAAGGGTTTGACCTTTGTAGCCTAA
GTCAAC
Found at i:7671 original size:472 final size:473
Alignment explanation
Indices: 3994--8185 Score: 5054
Period size: 473 Copynumber: 8.9 Consensus size: 473
3984 GATCCTAACA
* * * *
3994 CATCCTAT-AAAAGACAAGCATCGATTCTCATAATAATCTCCATTCGTTTAAAGATTGGGAACCA
1 CATCCTATAAAAAGACAAGCATCGATTCTCGTAATAGTCTCCATTCTTTTCAAGATTGGGAACCA
* * *
4058 AAGCACATTCCCTTCATTAGGATACTTGACATTGATGCTTTGGAGTCGCAAAAGGAAAAGCTGTT
66 AAACACATTCCCTTCATTAGGATACTTGACATTGATGCTTTGGTGTCGC--AA-GAAAAACTGTT
*
4123 CTTTTCACATCACCGTTTTTGATAGAATCAAAGTTTGCCTTTTAATAAGACAAACATGAATACTC
128 CTTTT--C--CACCGTTTTTGATAGAATCAAAGTTTGCCTTTAAATAAGACAAACATGAATACTC
* *
4188 ATAGTAAT-CCA-TCTTTTATGGA-TAGCTACCATAAACATAGGC--CTCATTAGGATACACGAT
189 ATAGTAATCCCATTCTTTTATGGATTAGGTACCATAAACATAGTCTTCTCATTAGGATACACGAT
*
4248 ATTGATGC-TTGGTTTCGCAAGAAA-GCCTTTTTCCCAACCAA--TTGTGAAGTCTAAGTTCGTG
254 ATTGATGCTTTGGTTTCGCAAGAAAGGCCTTTTTCCCAACCAATTTTGTAAAGTCTAAGTTCGTG
* * *
4309 CCTCAAATGAGACAAAC-AGGATTCTAGTAATGATCTTCTTTCA-TTTGTGATTAGGCACGATGA
319 CCTCAAATGAGACAAACTTGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACAAT-A
* ** * *
4372 A--ACATTCTCCTCATTAGGATAAATGATA-TGACGATTTTCTTTCACGTGGAAATCTTTTCTTT
383 AGCACATTCTCCTCATTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAATCTTTTCTTT
* *
4434 GCCCTATTTTCCGT-AAA-CAAAGTA
448 GCCCTATTTTCCTTGAAATCAAAGTT
* * * * *
4458 CATCTTTTTAAAAGACAAGCAGCGATTCTCG-AACAGTC-CCAATTTCTTTTCAAGATTGGGAAC
1 CATCCTATAAAAAGACAAGCATCGATTCTCGTAATAGTCTCC-A-TTCTTTTCAAGATTGGGAAC
* * * * *
4521 CAAAAACACATTCCCGTTCATTAGGATA--TGAACATTAATGCTTGGGAGGGTCGCTAGAAAAGC
64 C-AAAACACATTCCC-TTCATTAGGATACTTG-ACATTGATGCTT-TG-GTGTCGCAAGAAAAAC
* * * *
4584 TTTTC-TTTCACACC-TTTTTGATAGAGTC-AAGTTTGTCTCTTAAATAAGACAAGCATGAATAC
124 TGTTCTTTTC-CACCGTTTTTGATAGAATCAAAGTTTGCCT-TTAAATAAGACAAACATGAATAC
* * * * *
4646 TCATAGTAATCCCCAAT-TTTTATGGATTAGGTACCACAAACATAGTCTTCTCATTTGTATAAAC
187 TCATAGTAAT-CCCATTCTTTTATGGATTAGGTACCATAAACATAGTCTTCTCATTAGGATACAC
* *
4710 GATATTGATGCTTTGGTTTCGCAAGAAAGGGCTTTTTCCCAACCGATTTTTGTAAAGTCTAAGTT
251 GATATTGATGCTTTGGTTTCGCAAGAAAGGCCTTTTTCCCAACC-AATTTTGTAAAGTCTAAGTT
* * * * * *
4775 CGTGTCTCAAATGAGACAAACTTGGATTCTAGTATTAATCTTCATTCATTTTGTAATTATGCACT
315 CGTGCCTCAAATGAGACAAACTTGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACA
* * * * * * *
4840 GTAA-CACATTC-CTCTCAATAGAATAAATGATATTGATGATTTTC-TTTCCGTGGAAATATTTT
380 ATAAGCACATTCTC-CTCATTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAATCTTTT
* * *
4902 CATTACCCTATTTT-C-TGTATAATTAAAGTT
444 CTTTGCCCTATTTTCCTTG-A-AATCAAAGTT
* * * * *
4932 CATCCCT-TAAGTAAGACAAGCAGCGATTCTCATAATAGTCTCCATTCTTTTCGAGATTGGAAAC
1 CAT-CCTATAA-AAAGACAAGCATCGATTCTCGTAATAGTCTCCATTCTTTTCAAGATTGGGAAC
* * * *
4996 CAAAA-ACATTCCCTTCATTTGGATACTTGGCATTGATGCTTTGG-GTGGCAAGAAAAGCT-TTC
64 CAAAACACATTCCCTTCATTAGGATACTTGACATTGATGCTTTGGTGTCGCAAGAAAAACTGTTC
* * *
5058 -TTT-CA-CATTTTT-ATA-AATCCAAGTTTTGTCTCTTAAAT-AGACAAACATGAATACTCATA
129 TTTTCCACCGTTTTTGATAGAATCAAAG-TTTGCCT-TTAAATAAGACAAACATGAATACTCATA
* * * * * *
5117 GTAATCCCCATTTTTTTATGGATTAGGTACCACAAACATAGTCTTCTCATTTGTATAAATGATAT
192 GTAAT-CCCATTCTTTTATGGATTAGGTACCATAAACATAGTCTTCTCATTAGGATACACGATAT
*
5182 TGATGCTTTGGTTTCGCAAGAAAGG-CTTTTTCCCAACCAATTTTTGTAAA-ACTAAGTTCGTGC
256 TGATGCTTTGGTTTCGCAAGAAAGGCCTTTTTCCCAACCAA-TTTTGTAAAGTCTAAGTTCGTGC
**
5245 CTC-AATGAGACAAACTTGGATTCTAGTAATGATCTTCATTCATTTTGTGACGCA-GCACAATAA
320 CTCAAATGAGACAAACTTGGATTCTAGTAATGATCTTCATTCATTTTGTGA-TTAGGCACAATAA
* * *
5308 TCACATTCTCCTCATTAGGATAAATGACATTGATGATTTTCTTTTGCATGAAAATCTTTTCTTTA
384 GCACATTCTCCTCATTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAATCTTTTCTTTG
5373 CCCTATTTTCCTTGAAAATCAAAGTT
449 CCCTATTTTCCTTG-AAATCAAAGTT
* *
5399 CATCCTATAAAAAGGCAAGCATCGATTCTCGTAATAG--TCCATT-ATTTCAAGATTGGGAACCA
1 CATCCTATAAAAAGACAAGCATCGATTCTCGTAATAGTCTCCATTCTTTTCAAGATTGGGAACC-
* * * * *
5461 AAAACAAATTCCCTTCATTAGGATACTTGATATTGATGTTTTAGTGTCGCAAGAAAAACTGTTGT
65 AAAACACATTCCCTTCATTAGGATACTTGACATTGATGCTTTGGTGTCGCAAGAAAAACTGTTCT
5526 TTTCCACCGTTTTTGATAGAATCAAAGTTTGCCTTTTAAATAAGACAAAACATGGAATACTCATA
130 TTTCCACCGTTTTTGATAGAATCAAAGTTTGCC-TTTAAATAAGAC-AAACAT-GAATACTCATA
* * **
5591 ATAATCCCTATTCTTTTATGGAATAGGTACCATAAATGTAGTCTTCTCATTAGGATACACGATAT
192 GTAATCCC-ATTCTTTTATGGATTAGGTACCATAAACATAGTCTTCTCATTAGGATACACGATAT
* * * * * * *
5656 TGATGC-TTAGTTTTGCATGAAA-GCCTTCTT-CCTACCGATTTTTGTAAAGTCTAAGCTCGTGC
256 TGATGCTTTGGTTTCGCAAGAAAGGCCTTTTTCCCAACC-AATTTTGTAAAGTCTAAGTTCGTGC
* * * *
5718 CTCAAATGAGAC-AACTTGGACTCTAGTAATGATCTTCATTCATTTCGTGATTAGGCGCTATAAG
320 CTCAAATGAGACAAACTTGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACAATAAG
* *
5782 CACATTCTCCAT-ATTAGGATAAATGATATTGATGATTTTCTTTTGCATGGAAATCTTTTTTTTG
385 CACATTCTCC-TCATTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAATCTTTTCTTTG
*
5846 CCCTATTTT-CTTAAAATCAAAGTT
449 CCCTATTTTCCTTGAAATCAAAGTT
* *
5870 CATCCTAAAAAAAGAC-AGCATCGATTCTCGTAATAATCTCCATTCTTTTCAA-ATTGGGAACCA
1 CATCCTATAAAAAGACAAGCATCGATTCTCGTAATAGTCTCCATTCTTTTCAAGATTGGGAACCA
* * * *
5933 AAACACATT-CCTTAATTAGGATACTTGACATTGATGCTTTAGTGTCGTAAGAAAAA-TTTTC-T
66 AAACACATTCCCTTCATTAGGATACTTGACATTGATGCTTTGGTGTCGCAAGAAAAACTGTTCTT
* **
5995 TTCCGCCGTTTTTGATAGAATCGTAGTTTGCCTTT-AATAAGACAAACATGAATACTCATAGTAA
131 TTCCACCGTTTTTGATAGAATCAAAGTTTGCCTTTAAATAAGACAAACATGAATACTCATAGTAA
* *
6059 TCCCAATTCTTTTATGGATTAGGCACCATAAACATAGTCTTCTCAATAGGATACACGAT-TTGAT
196 TCCC-ATTCTTTTATGGATTAGGTACCATAAACATAGTCTTCTCATTAGGATACACGATATTGAT
* * * *
6123 GCTTTGGTTTCGCAAGAAA-GCCTTTTTCCCTACCAATTTTGTGAAGTCTTAGTTTGTGCCTCAA
260 GCTTTGGTTTCGCAAGAAAGGCCTTTTTCCCAACCAATTTTGTAAAGTCTAAGTTCGTGCCTCAA
* * * * *
6187 ATGAGACAAACATGGATTCTAGTAATGATCTTCTTTCATTTTGTGATTAAGCAC--TATGAACAT
325 ATGAGACAAACTTGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACAATAAGCACAT
* * *
6250 TCTCCTCATCAGGATAAA-GATATTGATGATTATT-TTTTGCGTGGAAATCTTTTCTTTGCCCTA
390 TCTCCTCATTAGGATAAATGATATTGATGATT-TTCTTTTGCATGAAAATCTTTTCTTTGCCCTA
*
6313 TTTTCCTTAAAATCAAAGTT
454 TTTTCCTTGAAATCAAAGTT
* * *
6333 CATCCTATAAAAAGACAAGCATCGATTCACGTAATAATCTCCATTCTTTTCAGGATTGGGAACCA
1 CATCCTATAAAAAGACAAGCATCGATTCTCGTAATAGTCTCCATTCTTTTCAAGATTGGGAACC-
* * * * * *
6398 AAAACATATTCCCTTCGTTATGATACTTGACATTGATGC-TTGGTGTCACAAGAAAAGCTGTTAT
65 AAAACACATTCCCTTCATTAGGATACTTGACATTGATGCTTTGGTGTCGCAAGAAAAACTGTTCT
*
6462 TTT-CACCGTTTTTGATAGAATCAAAGTTGGCCCTTTAAATAAGACAAACATGAAT-CTCATAGT
130 TTTCCACCGTTTTTGATAGAATCAAAGTTTG-CCTTTAAATAAGACAAACATGAATACTCATAGT
* * * **
6525 AATCCCCATTCTTTTATGGATTAGGTACCGTAAACATAGTCTTCTTATTAGGATACATGATAGAG
194 AAT-CCCATTCTTTTATGGATTAGGTACCATAAACATAGTCTTCTCATTAGGATACACGATATTG
* **
6590 ATGCTTTGGTTTTGCAAGAAA-GCCTTTTTCCCTAA-CAATTTTTGTAAAGTCTAAGTTTATGCC
258 ATGCTTTGGTTTCGCAAGAAAGGCCTTTTTCCC-AACCAA-TTTTGTAAAGTCTAAGTTCGTGCC
* * * * *
6653 TCAAATGAGACAAA-TATGGATTCTAGCAATGATCTTCTTTCA-ATTGATGATTAGGCGCTATAA
321 TCAAATGAGACAAACT-TGGATTCTAGTAATGATCTTCATTCATTTTG-TGATTAGGCACAATAA
* * *
6716 GCACATTCTCCTCATTAGGATAAATGATATTAATGATTTTCTTTTGCGTGAAAATCTTTTCTATG
384 GCACATTCTCCTCATTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAATCTTTTCTTTG
* *
6781 CCCTATTTTACTTAAAATCAAAGTT
449 CCCTATTTTCCTTGAAATCAAAGTT
* * ** * * * *
6806 CATCCTTTAAATAAGACAAGCATTGATTCTTATAGTAGTCTCCCTTCTTTTCAGGATTGGGAGCC
1 CATCCTATAAA-AAGACAAGCATCGATTCTCGTAATAGTCTCCATTCTTTTCAAGATTGGGAACC
* * * * * *
6871 TAAACACATTCCCTTCCTTAAGAT-TTATGACATTGATGCTTTGGTGTCGCAAGAAAAGCTTTTC
65 AAAACACATTCCCTTCATTAGGATACT-TGACATTGATGCTTTGGTGTCGCAAGAAAAACTGTTC
* * **
6935 TTTT-CACCATTTTTGATAGAGTCAAAGTTTATCTCTTAAATAAGACAAACATGAATACTCATAG
129 TTTTCCACCGTTTTTGATAGAATCAAAGTTTGCCT-TTAAATAAGACAAACATGAATACTCATAG
* * * * * * *
6999 TAAT-CCTTTTTTTTATGGATTAGGTACCACAAACATAGTCTTCTCATTTGTATAAATGAT-TTG
193 TAATCCCATTCTTTTATGGATTAGGTACCATAAACATAGTCTTCTCATTAGGATACACGATATTG
** * *
7062 ATGC-TTGGTTTCATAAGAAAGGCTTTTTTTCCCAACCAATTTTTGTAAAATCTAAGTTCGTGCC
258 ATGCTTTGGTTTCGCAAGAAAGGC-CTTTTTCCCAACCAA-TTTTGTAAAGTCTAAGTTCGTGCC
* **
7126 TCAAATTAGACAAACTTGGATTCTAGTAATGATCTTCATTCATTTGTGTGATGCGGCACAATAAG
321 TCAAATGAGACAAACTTGGATTCTAGTAATGATCTTCATTCATTT-TGTGATTAGGCACAATAAG
7191 CACATTCTCCTCATTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAATC-TTTCTTTGC
385 CACATTCTCCTCATTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAATCTTTTCTTTGC
*
7255 CCCATTTTCCTTGAAATCAAAGTT
450 CCTATTTTCCTTGAAATCAAAGTT
* * *
7279 CATCCTACAAAAAGGCAAGCATCGATTCTCGTAATAGTCTCCATTTTTTTCAAGATTGGGAACCA
1 CATCCTATAAAAAGACAAGCATCGATTCTCGTAATAGTCTCCATTCTTTTCAAGATTGGGAACCA
* *
7344 AAACAAATTCCCTTCATTAGGATACTTGACATTGATGCTTTGGGGTCGCAAGAAAAAACTGTTCT
66 AAACACATTCCCTTCATTAGGATACTTGACATTGATGCTTTGGTGTCGCAAG-AAAAACTGTTCT
* * *
7409 TTTCCACCATTTTTGATAGAATCAAAGTTTGCCTTTAAATAAGGCAAACATGAATACTCATAATA
130 TTTCCACCGTTTTTGATAGAATCAAAGTTTGCCTTTAAATAAGACAAACATGAATACTCATAGTA
* **
7474 ATCCGCATTCTTTTATGGAATAGGTACCAT-AATGTAGTCTTCTCATTAGGATACACGATATTGA
195 ATCC-CATTCTTTTATGGATTAGGTACCATAAACATAGTCTTCTCATTAGGATACACGATATTGA
** * * * * * *
7538 TGC-TTAATTT-GCAAGAAAGGCTTTTTTCCCAACCAATTTTGTAAAATATAAGTTCATGTCTCC
259 TGCTTTGGTTTCGCAAGAAAGGCCTTTTTCCCAACCAATTTTGTAAAGTCTAAGTTCGTGCCTCA
* **
7601 AATGAGACAAAACTTGGATTCTAGCAATGATCTTCATTCATTTTGTGATGCGGCACAATAAGCAC
324 AATGAGAC-AAACTTGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACAATAAGCAC
7666 ATTCTCCTCATTAGGATAAATGATATTGATGATTTTC-TTTGCATGAAAATCTTTTCTTTGTCCC
388 ATTCTCCTCATTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAATCTTTTCTTTG-CCC
*
7730 -ATTTTCCTTGAAATCAAATTT
452 TATTTTCCTTGAAATCAAAGTT
* * * *
7751 CATCCTATAAAAAGGCAAGCATCGATTCTCGTAATAGT-T-CAGTATTTTCAAGATTGGGAACTA
1 CATCCTATAAAAAGACAAGCATCGATTCTCGTAATAGTCTCCATTCTTTTCAAGATTGGGAACCA
* *
7814 GAAACAAATTCCCTTCATTAGGATACTTGACATTGATGCTTTGGTGTCGCAA-AAAAACTG-TGT
66 -AAACACATTCCCTTCATTAGGATACTTGACATTGATGCTTTGGTGTCGCAAGAAAAACTGTTCT
* * *
7877 TTTCCACCGTTTTTGATAGAATCAAAGTTTGCCTTTTAAATAAGAAAAACATGAATATTCATGGT
130 TTTCCACCGTTTTTGATAGAATCAAAGTTTGCC-TTTAAATAAGACAAACATGAATACTCATAGT
* * * * * * *
7942 AATCCCCATTTTTTTATGGATTAGGCACCATAAACATAGTCGTCTCATTTGTATAAATGATATTG
194 AAT-CCCATTCTTTTATGGATTAGGTACCATAAACATAGTCTTCTCATTAGGATACACGATATTG
* * *
8007 ATGCTTTGGTTTCGCAAGAAAGGCTTTTTTCCAAACCAATTTTTGTAAAATCTAAGTTCGTGCCT
258 ATGCTTTGGTTTCGCAAGAAAGGCCTTTTTCCCAACCAA-TTTTGTAAAGTCTAAGTTCGTGCCT
* ** *
8072 TAAATGAGACAAACTTGGATTCTAGTAATGATCTTCATTCATTTTGTGACGCA-GCATAATAAGC
322 CAAATGAGACAAACTTGGATTCTAGTAATGATCTTCATTCATTTTGTGA-TTAGGCACAATAAGC
*
8136 ACATTCTCCTCATTAGGATCAATG--ATTGATGATTTTCTTTTGCATGAAAA
386 ACATTCTCCTCATTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAA
Statistics
Matches: 3256, Mismatches: 349, Indels: 239
0.85 0.09 0.06
Matches are distributed among these distances:
459 9 0.00
460 44 0.01
461 4 0.00
462 58 0.02
463 96 0.03
464 229 0.07
465 224 0.07
466 198 0.06
467 196 0.06
468 145 0.04
469 129 0.04
470 253 0.08
471 170 0.05
472 499 0.15
473 572 0.18
474 335 0.10
475 86 0.03
476 7 0.00
477 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (473 bp):
CATCCTATAAAAAGACAAGCATCGATTCTCGTAATAGTCTCCATTCTTTTCAAGATTGGGAACCA
AAACACATTCCCTTCATTAGGATACTTGACATTGATGCTTTGGTGTCGCAAGAAAAACTGTTCTT
TTCCACCGTTTTTGATAGAATCAAAGTTTGCCTTTAAATAAGACAAACATGAATACTCATAGTAA
TCCCATTCTTTTATGGATTAGGTACCATAAACATAGTCTTCTCATTAGGATACACGATATTGATG
CTTTGGTTTCGCAAGAAAGGCCTTTTTCCCAACCAATTTTGTAAAGTCTAAGTTCGTGCCTCAAA
TGAGACAAACTTGGATTCTAGTAATGATCTTCATTCATTTTGTGATTAGGCACAATAAGCACATT
CTCCTCATTAGGATAAATGATATTGATGATTTTCTTTTGCATGAAAATCTTTTCTTTGCCCTATT
TTCCTTGAAATCAAAGTT
Done.