Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2314
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: 519745
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
File 2 of 2
Found at i:497160 original size:38 final size:40
Alignment explanation
Indices: 497086--497165 Score: 103
Period size: 38 Copynumber: 2.0 Consensus size: 40
497076 TTTTATTTCT
**
497086 CCCTTAATCAAAATAAATTTAACAAATTTGTACATTCTCC
1 CCCTTAATCAAAATAAATTTAACAAATTTACACATTCTCC
*
497126 CCCTTAAT-AAAAT-AATTGTAAC-AATTTACGCATTCTCC
1 CCCTTAATCAAAATAAATT-TAACAAATTTACACATTCTCC
497164 CC
1 CC
497166 TTTATCTCCC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 19 0.53
39 9 0.25
40 8 0.22
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.34
Consensus pattern (40 bp):
CCCTTAATCAAAATAAATTTAACAAATTTACACATTCTCC
Found at i:501008 original size:15 final size:15
Alignment explanation
Indices: 500988--501018 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
500978 ATTTCGTTTG
*
500988 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
501003 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
501018 G
1 G
501019 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:502850 original size:21 final size:21
Alignment explanation
Indices: 502821--502865 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
502811 AAGTTTTCAT
*
502821 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
502841 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
502863 TTT
1 TTT
502866 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:505100 original size:13 final size:13
Alignment explanation
Indices: 505082--505107 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
505072 ATATTTTTTG
505082 TGTATCGATACAT
1 TGTATCGATACAT
505095 TGTATCGATACAT
1 TGTATCGATACAT
505108 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:505118 original size:32 final size:33
Alignment explanation
Indices: 505061--505125 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
505051 TATAAGCCAA
505061 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
505095 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
505126 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:505119 original size:19 final size:19
Alignment explanation
Indices: 505061--505125 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
505051 TATAAGCCAA
505061 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
505082 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
505095 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
505114 TGTATCGATACA
1 TGTATCGATACA
505126 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:507636 original size:13 final size:13
Alignment explanation
Indices: 507618--507655 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
507608 ATAATCCCCT
507618 TGTATCGATACAG
1 TGTATCGATACAG
*
507631 TGTATCGATACAT
1 TGTATCGATACAG
507644 TGTATCGATACA
1 TGTATCGATACA
507656 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:513531 original size:32 final size:30
Alignment explanation
Indices: 513495--513553 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
513485 GAAATCAAAT
513495 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
513527 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
513554 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:513852 original size:13 final size:13
Alignment explanation
Indices: 513834--513859 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
513824 ATATTTTTTG
513834 TGTATCGATACAT
1 TGTATCGATACAT
513847 TGTATCGATACAT
1 TGTATCGATACAT
513860 ATTTTGTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:513872 original size:32 final size:33
Alignment explanation
Indices: 513813--513877 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
513803 TACAAGCCAA
*
513813 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTATATCGATACAT
513847 TGTATCGATACATA-TTTTGTATATCGATACA
1 TGTATCGATACATATTTTTGTATATCGATACA
513878 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 16 0.53
34 14 0.47
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTATATCGATACAT
Found at i:516540 original size:473 final size:474
Alignment explanation
Indices: 514840--518369 Score: 4013
Period size: 473 Copynumber: 7.5 Consensus size: 474
514830 TACAATAAAC
* * * * * *
514840 ACAATCATCAATTCTCGTAACTGTCTACATTCTTTTCAAGATTTGGAACCAAGAACGCATTCCCT
1 ACAAGCATCGATTCTCGTAACTGTCTCCATTCTTTTCAAAATTGGGAACCAAGAATGCATTCCCT
** * *
514905 TCATTAGGATACAAGACATTGA-GGATCGGGGTCACAAGAAAAGGTTTTCTTTCCATCGTTTTTG
66 TCATTAGGATACAAGACATTGATGCTTTGGGGTCACAAGAAAAGGTTTTCTTTCCACCGTTTTTG
* *
514969 ATAGAATCAAAGTTTGCCTCTTAAAAAAGACAAACATGAATAGTCATACTAATCCCATTCTTTTT
131 ATAGAATCAAAGTTTGCCTCCTAAATAAGACAAACATGAATAGTCATACTAATCCCATTCTTTTT
* *
515034 AGGATTAGTCACCATAAACATAGTCATCTCATTAAGATAGACGAAATCGAAGCTTTGGTTTCGCA
196 AGGATTAGGCACCATAAACATAGTCATCTCATTAGGATAGACGAAATCGAAGCTTTGGTTTCGCA
* * * *
515099 AAAGAAGCTTTCTTCACTCCAATTTCTACAAAGTCTAAGTTCGTGCTTGAAATGGGGCAAACATG
261 AAA-AAGCTTTCTTCACTCCAATTTCTATAAAGTCTAAGTTCGTGCCTCAAATGAGGCAAACATG
515164 GATTCTAGTAA--ATCTTCATTCATTTTGTGATTTGGCATGATAAACACAATCCCCTTATTAGGA
325 GATTCTAGTAATGATCTTCATTCATTTTGTGATTTGGCATGATAAACACAATCCCCTTATTAGGA
*
515227 TAAATGATGTTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAAAAT-A
390 TAAATGATATTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAAAATAA
* *
515291 AAATTTATCCCTTAAATATA
455 AAATTCATCCCTTAAATATG
* **
515311 ACAAGCATCGATTCTCGTAACTGTCTCCATTGTTTTCAAAATTGGGAGTCAAGAATGCATTCCCT
1 ACAAGCATCGATTCTCGTAACTGTCTCCATTCTTTTCAAAATTGGGAACCAAGAATGCATTCCCT
* * * * **
515376 TCATTAGGATACATGACACTGATGCTTTGGGATCGCAAGAAAAGGTTTTCTTTCTTCCGTTTTTG
66 TCATTAGGATACAAGACATTGATGCTTTGGGGTCACAAGAAAAGGTTTTCTTTCCACCGTTTTTG
* * *
515441 ATAGAATTAAAGTTTACCTCCTAAATAAGACAAACATGAATAGTCATACTAGTCCCAATTCTTTT
131 ATAGAATCAAAGTTTGCCTCCTAAATAAGACAAACATGAATAGTCATACTAATCCC-ATTCTTTT
* * * * * * *
515506 CAAGATTAGGCACCTTAAATATAGTCATCTCATTAGGATAAACGAAATTGAAGCTTTGGTTTCAC
195 TAGGATTAGGCACCATAAACATAGTCATCTCATTAGGATAGACGAAATCGAAGCTTTGGTTTCGC
* * * * * *
515571 GAAAAAA-CTTTTCTTCACTCCGATTTCTGTAAAGTCTAAGTCCATAGCCTTAAATGATGCAAAC
260 -AAAAAAGC-TTTCTTCACTCCAATTTCTATAAAGTCTAAGTTCGT-GCCTCAAATGAGGCAAAC
* *
515635 ATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTTGGCATGATAAAACACATTCCCCTTAGT
322 ATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTTGGCATGAT-AAACACAATCCCCTTATT
*
515700 AGGATAAATGATATTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTACCCTATTTTCCTTAAA
386 AGGATAAATGATATTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAAA
*
515765 ATAAAAACTCATCCCTTAAATATG
451 ATAAAAATTCATCCCTTAAATATG
* * * * *
515789 ACAAGCATTGATTCTCGTAATTATCTCCATTCTTTTC---------AACCAAAAATGCATTCCTT
1 ACAAGCATCGATTCTCGTAACTGTCTCCATTCTTTTCAAAATTGGGAACCAAGAATGCATTCCCT
515845 TCATTAGGATACAAGA-ATTTGATGCTTTGGGGTCACAAGAAAAGGTTTTCTTTCCACCGTTTTT
66 TCATTAGGATACAAGACA-TTGATGCTTTGGGGTCACAAGAAAAGGTTTTCTTTCCACCGTTTTT
* * * *
515909 GATAGAATCAAAATTTACCCTCCTAAATAAAACAAACATGAATAGTCATACCAATCTCCATTCTT
130 GATAGAATCAAAGTTT-GCCTCCTAAATAAGACAAACATGAATAGTCATACTAATC-CCATTCTT
** * * *
515974 TCCAAGATTAGGCACCACAAACATAGTCATTTCATTAGGATAGACGAAATCGAAGCTTTGGTTTC
193 TTTAGGATTAGGCACCATAAACATAGTCATCTCATTAGGATAGACGAAATCGAAGCTTTGGTTTC
* *
516039 GCAAAAGAAG-TTTCTTCACTCCAATTTCTATAAAGTCTAAGTTTGTGCCTCAAATAAGGCAAAC
258 GCAAAA-AAGCTTTCTTCACTCCAATTTCTATAAAGTCTAAGTTCGTGCCTCAAATGAGGCAAAC
* * * * ** * *
516103 ATGGATTCTGGTAATTATCCTCATTCATTTTGTGATTTGGTACAATAAACACAATCCCCGTATTG
322 ATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTTGGCATGATAAACACAATCCCCTTATTA
*
516168 GGATAAA-GATATTGATCAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTT-AAA
387 GGATAAATGATATTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAAAA
* **
516231 TAAAAATTTATCTTTTAAATATG
452 TAAAAATTCATCCCTTAAATATG
*
516254 ACAAGCATCGATTCTCGTAATTGTCTCCATTCTTTTTCAAAATTGGGAACCAAGAATGCATTCCC
1 ACAAGCATCGATTCTCGTAACTGTCTCCATTC-TTTTCAAAATTGGGAACCAAGAATGCATTCCC
* * *
516319 TTTATTAGGATACATGACA-CGATGCTTTGGGGTCACAAGAAAAGGTTTTTCTTTCCACCGTTTT
65 TTCATTAGGATACAAGACATTGATGCTTTGGGGTCACAAGAAAAGG-TTTTCTTTCCACCGTTTT
* *
516383 TGATAGAATCAAAGTTTGCCTCTTAAAAAAGACAAACATGAATAG-CAATACTAATCCCATTCTT
129 TGATAGAATCAAAGTTTGCCTCCTAAATAAGACAAACATGAATAGTC-ATACTAATCCCATTCTT
* * *
516447 TTTAGGATCAGGCACCATAAACATAGTCATCTCATTAAGATAGATGAAATCGAAGCTTTGG-TTC
193 TTTAGGATTAGGCACCATAAACATAGTCATCTCATTAGGATAGACGAAATCGAAGCTTTGGTTTC
* *
516511 GCAAAAGAAGCTTTCATCACTCCAATTTCTATAAAGTCTAAGTTCGTGCCTGAAAT-AGGGCAAA
258 GCAAAA-AAGCTTTCTTCACTCCAATTTCTATAAAGTCTAAGTTCGTGCCTCAAATGA-GGCAAA
* ** *
516575 TATGGATTCTAGTAATGATCTTCACCCATTTTGTGATTTGGCATGATAAACACATTCCCCTTATT
321 CATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTTGGCATGATAAACACAATCCCCTTATT
* *
516640 AGGATAAATGATATTGATGAATTTCCTTTGCGTGGAAATC-TTTCTTTGCCCTATTTTTCTTAAA
386 AGGATAAATGATATTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAAA
516704 ATAAAAATTCATCCCTTAAATATG
451 ATAAAAATTCATCCCTTAAATATG
* * *
516728 ACAACCATCAATTCTCGTAACTGTCTCCATTCTTTTCAAAATTAGGAACCAAGAATGCATTCCCT
1 ACAAGCATCGATTCTCGTAACTGTCTCCATTCTTTTCAAAATTGGGAACCAAGAATGCATTCCCT
* ** *
516793 TCATTAGGATACAAGAC-TTGATGCTTTAGGGTCGTAAGAAAAGGTTTTCATTCCACCGTTTTTG
66 TCATTAGGATACAAGACATTGATGCTTTGGGGTCACAAGAAAAGGTTTTCTTTCCACCGTTTTTG
* * *
516857 ATAGAATCCAAGTTTTGCCTCCTGAATAAGACAAACATGAATAGTCATACCAATCCCAATTCTTT
131 ATAGAATCAAAG-TTTGCCTCCTAAATAAGACAAACATGAATAGTCATACTAATCCC-ATTCTTT
* * * * * * * *
516922 TCAGGATTACGCACCACAAATATAGTCATCTCATTAGGATAGAAGAAATTGATGCTTTGGTTTTG
194 TTAGGATTAGGCACCATAAACATAGTCATCTCATTAGGATAGACGAAATCGAAGCTTTGGTTTCG
* * * * * * * *
516987 CAAGAAAGGCTTGCTTCCCCCCTAATTTTTGTAAAGTCTAAGTTCGTACCTCAAA-GAGACAAAC
259 CAA-AAAAGCTTTCTTCACTCC-AATTTCTATAAAGTCTAAGTTCGTGCCTCAAATGAGGCAAAC
* * * *
517051 ATGGATTCTAGTAATGATCTTCATTCATTTTGTGTTTTGGCATGATAAACACATTTCCCTCATTA
322 ATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTTGGCATGATAAACACAATCCCCTTATTA
* * * *
517116 GGATAAATAATATTGATGATTTTCTTTTGCTTGGAAATCTTTTCTTTGCCCTATTTTCCTTAAAA
387 GGATAAATGATATTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAAAA
* *
517181 TAAAAATTCAAT-CCTTAATTACG
452 TAAAAATTC-ATCCCTTAAATATG
* * * * *
517204 ACAAGCATTGATTCTCGTAACAGTCTCCATTC-TTTCAAGATTGGGAA-CAAGAACGCATTTCCT
1 ACAAGCATCGATTCTCGTAACTGTCTCCATTCTTTTCAAAATTGGGAACCAAGAATGCATTCCCT
* * * *
517267 TCATTAGGATGA-AAGACATTGATGCTTTGGTG-CTGCAAGAAAAGGTTTTCCTTCCACCATTTT
66 TCATTAGGAT-ACAAGACATTGATGCTTTGGGGTC-ACAAGAAAAGGTTTTCTTTCCACC-GTTT
* * * * * *
517330 TTGCTAGAAT-AAAGTTTGTCTCTTAAATAAGACAAGCTTGAATAGTCATACTAATCCC-TGTTT
128 TTGATAGAATCAAAGTTTGCCTCCTAAATAAGACAAACATGAATAGTCATACTAATCCCAT-TCT
* * * ** * * * * *
517393 ATTTTCAGGATTACGCACCACAAATATAACCATCTCAATAGGGGTGGACAAAAT-TAATGCTTTG
192 -TTTT-AGGATTAGGCACCATAAACATAGTCATCTCATTA-GGATAGACGAAATCGAA-GCTTTG
* * * * * * *
517457 ATTTCACAAGAAACGCTTTTTTCTCACCAACTTT-TGTAAAGTCTAAGTTCGTGCCTC-AATGAG
253 GTTTCGCAA-AAAAGCTTTCTTCACTCCAA-TTTCTATAAAGTCTAAGTTCGTGCCTCAAATGAG
* * * * * * *
517520 ACAAACATGGATTTCTAGTAATGATCTTAAATCA-TTTGTGATTTGGCTTGATAAGCAC-ATTCT
316 GCAAACATGGA-TTCTAGTAATGATCTTCATTCATTTTGTGATTTGGCATGATAAACACAATCCC
* *
517583 CTTCATTAGGATAGATGATATTGATGAATTTCCTTTGCATGGAGATCTTTTCTTTGCCCTATTTT
380 CTT-ATTAGGATAAATGATATTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTT
* * *
517648 CCTTGAAATAAAAATTCATCCATTAATTATG
444 CCTTAAAATAAAAATTCATCCCTTAAATATG
* * * * * * * * *
517679 ACAAGCATCGATTCTTGTAAATCTCTGCATTCTTTTCAAGATTGGTAACCAAGAACGTAATCCCT
1 ACAAGCATCGATTCTCGTAACTGTCTCCATTCTTTTCAAAATTGGGAACCAAGAATGCATTCCCT
* * *
517744 TCATTAGGATA-AAGACATTGATGCTTTGGGGTCACAAGAAAAGGTTTTCTTTCTAGCATTTTTG
66 TCATTAGGATACAAGACATTGATGCTTTGGGGTCACAAGAAAAGGTTTTCTTTCCACCGTTTTTG
* * *
517808 GTAGAATCAAAGTTTGCCTCATAAATAAGACAAACATGAGTAGTCATACTAATCCCTATTCTTTT
131 ATAGAATCAAAGTTTGCCTCCTAAATAAGACAAACATGAATAGTCATACTAATCCC-ATTCTTTT
* ** *
517873 TAAGGATTAGGAACCATAAACATAGTCAGGTCATTAGG-TCA-ACGAAATTGAAGCTTTGGGTTT
195 T-AGGATTAGGCACCATAAACATAGTCATCTCATTAGGAT-AGACGAAATCGAAGCTTT-GGTTT
* * *
517936 CGCAAGAAAGCTTTCTTCCACT--AATTTTTGA-AAAGTCTAAGTTCATGCCTCAAATGAGAG-A
257 CGCAAAAAAGCTTTCTT-CACTCCAATTTCT-ATAAAGTCTAAGTTCGTGCCTCAAATGAG-GCA
* * * * * * *
517997 AAAATTGATTCAAGTAATGATCTTTATTCATTTGGTGATTAGGCCACT-AT-AACAC-ATTCCCT
319 AACATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTTGG-CA-TGATAAACACAATCCCCT
* * * * * **
518059 CAGTAGGAGAAATGATAATTGATG-TTTGTCTTTTGCATGG-AATC-TTTCTTTGCGTTATTTTC
382 TATTAGGATAAATGAT-ATTGATGAATT-TCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTC
*
518121 CTTAAAAT--AAATTCATCCC-TAAATTTG
445 CTTAAAATAAAAATTCATCCCTTAAATATG
* * * *
518148 AC-AGAATCGATTCTTGGCAACTGGTCTCCATTCTTTTTTTCAAAATT-GGAACCAAGAA-AC-T
1 ACAAGCATCGATTC-TCGTAACT-GTCTCCATTC---TTTTCAAAATTGGGAACCAAGAATGCAT
** * * * *
518209 T-CC-TCATTAGGATAACGGGACATTGATGCGTTGGGTGTGACTAG-AAATGTATTTC-TTCCAA
61 TCCCTTCATTAGGAT-ACAAGACATTGATGCTTTGGG-GTCACAAGAAAAGGT-TTTCTTTCC-A
* * * * * * *
518270 CTGTTTTTGTTAGTATCAAAG-TTGCACT--TAAA-AAGATAAACATGAAATAGTTATACGAAGC
122 CCGTTTTTGATAGAATCAAAGTTTGC-CTCCTAAATAAGACAAACATG-AATAGTCATACTAATC
* * *
518331 CCATTCTTTTCAAGATTAGGCCCGCAATAAACATAGTCA
185 CCATTCTTTTTAGGATTAGGCAC-C-ATAAACATAGTCA
518370 AACCTCATAT
Statistics
Matches: 2620, Mismatches: 351, Indels: 178
0.83 0.11 0.06
Matches are distributed among these distances:
465 52 0.02
466 56 0.02
467 31 0.01
468 96 0.04
469 167 0.06
470 149 0.06
471 107 0.04
472 167 0.06
473 465 0.18
474 381 0.15
475 459 0.18
476 329 0.13
477 109 0.04
478 52 0.02
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (474 bp):
ACAAGCATCGATTCTCGTAACTGTCTCCATTCTTTTCAAAATTGGGAACCAAGAATGCATTCCCT
TCATTAGGATACAAGACATTGATGCTTTGGGGTCACAAGAAAAGGTTTTCTTTCCACCGTTTTTG
ATAGAATCAAAGTTTGCCTCCTAAATAAGACAAACATGAATAGTCATACTAATCCCATTCTTTTT
AGGATTAGGCACCATAAACATAGTCATCTCATTAGGATAGACGAAATCGAAGCTTTGGTTTCGCA
AAAAAGCTTTCTTCACTCCAATTTCTATAAAGTCTAAGTTCGTGCCTCAAATGAGGCAAACATGG
ATTCTAGTAATGATCTTCATTCATTTTGTGATTTGGCATGATAAACACAATCCCCTTATTAGGAT
AAATGATATTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAAAATAAA
AATTCATCCCTTAAATATG
Found at i:517291 original size:475 final size:475
Alignment explanation
Indices: 514840--518369 Score: 4014
Period size: 475 Copynumber: 7.5 Consensus size: 475
514830 TACAATAAAC
* * * * * *
514840 ACAATCATCAATTCTCGTAACTGTCTACATTCTTTTCAAGATTTGGAACCAAGAACGCATTCCCT
1 ACAAGCATCGATTCTCGTAACTGTCTCCATTCTTTTCAAAATTGGGAACCAAGAATGCATTCCCT
** * *
514905 TCATTAGGATACAAGACATTGA-GGATCGGGGTCACAAGAAAAGGTTTTCTTTCCATCGTTTTTG
66 TCATTAGGATACAAGACATTGATGCTTTGGGGTCACAAGAAAAGGTTTTCTTTCCACCGTTTTTG
* * *
514969 ATAGAATCAAAGTTTGCCTCTTAAAAAAGACAAACATGAATAGTCATACTAATCCCATTCTTTTT
131 ATAGAATCAAAGTTTGCCTCCTAAATAAGACAAACATGAATAGTCATACTAATCCCATTCTTTTC
* * * *
515034 AGGATTAGTCACCATAAACATAGTCATCTCATTAAGATAGACGAAATCGAAGCTTTGGTTTCGCA
196 AGGATTAGGCACCATAAACATAGTCATCTCATTAGGATAGAAGAAATTGAAGCTTTGGTTTCGCA
** * * * *
515099 A-AAGAAGCTTTCTTCACTCCAATTTCTACAAAGTCTAAGTTCGTGCTTGAAATGGGGCAAACAT
261 AGAA-AAGCTTTCTTCACTCCAATTTCTGTAAAGTCTAAGTTCGTGCCTCAAATGAGACAAACAT
* *
515163 GGATTCTAGTAA--ATCTTCATTCATTTTGTGATTTGGCATGATAAACACAATCCCCTTATTAGG
325 GGATTCTAGTAATGATCTTCATTCATTTTGTGATTTGGCATGATAAACACATTCCCCTCATTAGG
*
515226 ATAAATGATGTTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAAAAT-
390 ATAAATGATATTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAAAATA
* *
515290 AAAATTTATCCCTTAAATATA
455 AAAATTCATCCCTTAAATATG
* **
515311 ACAAGCATCGATTCTCGTAACTGTCTCCATTGTTTTCAAAATTGGGAGTCAAGAATGCATTCCCT
1 ACAAGCATCGATTCTCGTAACTGTCTCCATTCTTTTCAAAATTGGGAACCAAGAATGCATTCCCT
* * * * **
515376 TCATTAGGATACATGACACTGATGCTTTGGGATCGCAAGAAAAGGTTTTCTTTCTTCCGTTTTTG
66 TCATTAGGATACAAGACATTGATGCTTTGGGGTCACAAGAAAAGGTTTTCTTTCCACCGTTTTTG
* * *
515441 ATAGAATTAAAGTTTACCTCCTAAATAAGACAAACATGAATAGTCATACTAGTCCCAATTCTTTT
131 ATAGAATCAAAGTTTGCCTCCTAAATAAGACAAACATGAATAGTCATACTAATCCC-ATTCTTTT
* * * *
515506 CAAGATTAGGCACCTTAAATATAGTCATCTCATTAGGATA-AACGAAATTGAAGCTTTGGTTTCA
195 CAGGATTAGGCACCATAAACATAGTCATCTCATTAGGATAGAA-GAAATTGAAGCTTTGGTTTCG
* * * *
515570 CGAA-AAAA-CTTTTCTTCACTCCGATTTCTGTAAAGTCTAAGTCCATAGCCTTAAATGATG-CA
259 C-AAGAAAAGC-TTTCTTCACTCCAATTTCTGTAAAGTCTAAGTTCGT-GCCTCAAATGA-GACA
*
515632 AACATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTTGGCATGATAAAACACATTCCCCTT
320 AACATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTTGGCATGAT-AAACACATTCCCCTC
* *
515697 AGTAGGATAAATGATATTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTACCCTATTTTCCTT
384 ATTAGGATAAATGATATTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTT
*
515762 AAAATAAAAACTCATCCCTTAAATATG
449 AAAATAAAAATTCATCCCTTAAATATG
* * * * *
515789 ACAAGCATTGATTCTCGTAATTATCTCCATTCTTTTC---------AACCAAAAATGCATTCCTT
1 ACAAGCATCGATTCTCGTAACTGTCTCCATTCTTTTCAAAATTGGGAACCAAGAATGCATTCCCT
515845 TCATTAGGATACAAGA-ATTTGATGCTTTGGGGTCACAAGAAAAGGTTTTCTTTCCACCGTTTTT
66 TCATTAGGATACAAGACA-TTGATGCTTTGGGGTCACAAGAAAAGGTTTTCTTTCCACCGTTTTT
* * * *
515909 GATAGAATCAAAATTTACCCTCCTAAATAAAACAAACATGAATAGTCATACCAATCTCCATTCTT
130 GATAGAATCAAAGTTT-GCCTCCTAAATAAGACAAACATGAATAGTCATACTAATC-CCATTCTT
* * * * * *
515974 TCCAAGATTAGGCACCACAAACATAGTCATTTCATTAGGATAGACGAAATCGAAGCTTTGGTTTC
193 TTCAGGATTAGGCACCATAAACATAGTCATCTCATTAGGATAGAAGAAATTGAAGCTTTGGTTTC
* * * *
516039 GCAA-AAGAAG-TTTCTTCACTCCAATTTCTATAAAGTCTAAGTTTGTGCCTCAAATAAGGCAAA
258 GCAAGAA-AAGCTTTCTTCACTCCAATTTCTGTAAAGTCTAAGTTCGTGCCTCAAATGAGACAAA
* * * * ** *
516102 CATGGATTCTGGTAATTATCCTCATTCATTTTGTGATTTGGTACAATAAACACAATCCCCGT-AT
322 CATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTTGGCATGATAAACACATTCCCC-TCAT
* *
516166 TGGGATAAA-GATATTGATCAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTT-A
386 TAGGATAAATGATATTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAA
* **
516229 AATAAAAATTTATCTTTTAAATATG
451 AATAAAAATTCATCCCTTAAATATG
*
516254 ACAAGCATCGATTCTCGTAATTGTCTCCATTCTTTTTCAAAATTGGGAACCAAGAATGCATTCCC
1 ACAAGCATCGATTCTCGTAACTGTCTCCATTC-TTTTCAAAATTGGGAACCAAGAATGCATTCCC
* * *
516319 TTTATTAGGATACATGACA-CGATGCTTTGGGGTCACAAGAAAAGGTTTTTCTTTCCACCGTTTT
65 TTCATTAGGATACAAGACATTGATGCTTTGGGGTCACAAGAAAAGG-TTTTCTTTCCACCGTTTT
* *
516383 TGATAGAATCAAAGTTTGCCTCTTAAAAAAGACAAACATGAATAG-CAATACTAATCCCATTCTT
129 TGATAGAATCAAAGTTTGCCTCCTAAATAAGACAAACATGAATAGTC-ATACTAATCCCATTCTT
* * * * *
516447 TTTAGGATCAGGCACCATAAACATAGTCATCTCATTAAGATAGATGAAATCGAAGCTTTGG-TTC
193 TTCAGGATTAGGCACCATAAACATAGTCATCTCATTAGGATAGAAGAAATTGAAGCTTTGGTTTC
* * * *
516511 GCAA-AAGAAGCTTTCATCACTCCAATTTCTATAAAGTCTAAGTTCGTGCCTGAAAT-AGGGCAA
258 GCAAGAA-AAGCTTTCTTCACTCCAATTTCTGTAAAGTCTAAGTTCGTGCCTCAAATGA-GACAA
* ** *
516574 ATATGGATTCTAGTAATGATCTTCACCCATTTTGTGATTTGGCATGATAAACACATTCCCCTTAT
321 ACATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTTGGCATGATAAACACATTCCCCTCAT
* *
516639 TAGGATAAATGATATTGATGAATTTCCTTTGCGTGGAAATC-TTTCTTTGCCCTATTTTTCTTAA
386 TAGGATAAATGATATTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAA
516703 AATAAAAATTCATCCCTTAAATATG
451 AATAAAAATTCATCCCTTAAATATG
* * *
516728 ACAACCATCAATTCTCGTAACTGTCTCCATTCTTTTCAAAATTAGGAACCAAGAATGCATTCCCT
1 ACAAGCATCGATTCTCGTAACTGTCTCCATTCTTTTCAAAATTGGGAACCAAGAATGCATTCCCT
* ** *
516793 TCATTAGGATACAAGAC-TTGATGCTTTAGGGTCGTAAGAAAAGGTTTTCATTCCACCGTTTTTG
66 TCATTAGGATACAAGACATTGATGCTTTGGGGTCACAAGAAAAGGTTTTCTTTCCACCGTTTTTG
* * *
516857 ATAGAATCCAAGTTTTGCCTCCTGAATAAGACAAACATGAATAGTCATACCAATCCCAATTCTTT
131 ATAGAATCAAAG-TTTGCCTCCTAAATAAGACAAACATGAATAGTCATACTAATCCC-ATTCTTT
* * * * *
516922 TCAGGATTACGCACCACAAATATAGTCATCTCATTAGGATAGAAGAAATTGATGCTTTGGTTTTG
194 TCAGGATTAGGCACCATAAACATAGTCATCTCATTAGGATAGAAGAAATTGAAGCTTTGGTTTCG
* * * * * *
516987 CAAGAAAGGCTTGCTTCCCCCCTAATTTTTGTAAAGTCTAAGTTCGTACCTCAAA-GAGACAAAC
259 CAAGAAAAGCTTTCTTCACTCC-AATTTCTGTAAAGTCTAAGTTCGTGCCTCAAATGAGACAAAC
* *
517051 ATGGATTCTAGTAATGATCTTCATTCATTTTGTGTTTTGGCATGATAAACACATTTCCCTCATTA
323 ATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTTGGCATGATAAACACATTCCCCTCATTA
* * * *
517116 GGATAAATAATATTGATGATTTTCTTTTGCTTGGAAATCTTTTCTTTGCCCTATTTTCCTTAAAA
388 GGATAAATGATATTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAAAA
* *
517181 TAAAAATTCAAT-CCTTAATTACG
453 TAAAAATTC-ATCCCTTAAATATG
* * * * *
517204 ACAAGCATTGATTCTCGTAACAGTCTCCATTC-TTTCAAGATTGGGAA-CAAGAACGCATTTCCT
1 ACAAGCATCGATTCTCGTAACTGTCTCCATTCTTTTCAAAATTGGGAACCAAGAATGCATTCCCT
* * * *
517267 TCATTAGGATGA-AAGACATTGATGCTTTGGTG-CTGCAAGAAAAGGTTTTCCTTCCACCATTTT
66 TCATTAGGAT-ACAAGACATTGATGCTTTGGGGTC-ACAAGAAAAGGTTTTCTTTCCACC-GTTT
* * * * * * *
517330 TTGCTAGAAT-AAAGTTTGTCTCTTAAATAAGACAAGCTTGAATAGTCATACTAATCCCTGTTTA
128 TTGATAGAATCAAAGTTTGCCTCCTAAATAAGACAAACATGAATAGTCATACTAATCCC--ATTC
* * * ** * * *
517394 TTTTCAGGATTACGCACCACAAATATAACCATCTCAATAGGGGTGGACA-AAATT-AATGCTTTG
191 TTTTCAGGATTAGGCACCATAAACATAGTCATCTCATTA-GGATAGA-AGAAATTGAA-GCTTTG
* * * * * *
517457 ATTTCACAAGAAACGCTTTTTTCTCACCAACTTT-TGTAAAGTCTAAGTTCGTGCCTC-AATGAG
253 GTTTCGCAAGAAAAGCTTTCTTCACTCCAA-TTTCTGTAAAGTCTAAGTTCGTGCCTCAAATGAG
* * * * *
517520 ACAAACATGGATTTCTAGTAATGATCTTAAATCA-TTTGTGATTTGGCTTGATAAGCACATTCTC
317 ACAAACATGGA-TTCTAGTAATGATCTTCATTCATTTTGTGATTTGGCATGATAAACACATTCCC
* * *
517584 TTCATTAGGATAGATGATATTGATGAATTTCCTTTGCATGGAGATCTTTTCTTTGCCCTATTTTC
381 CTCATTAGGATAAATGATATTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTC
* * *
517649 CTTGAAATAAAAATTCATCCATTAATTATG
446 CTTAAAATAAAAATTCATCCCTTAAATATG
* * * * * * * * *
517679 ACAAGCATCGATTCTTGTAAATCTCTGCATTCTTTTCAAGATTGGTAACCAAGAACGTAATCCCT
1 ACAAGCATCGATTCTCGTAACTGTCTCCATTCTTTTCAAAATTGGGAACCAAGAATGCATTCCCT
* * *
517744 TCATTAGGATA-AAGACATTGATGCTTTGGGGTCACAAGAAAAGGTTTTCTTTCTAGCATTTTTG
66 TCATTAGGATACAAGACATTGATGCTTTGGGGTCACAAGAAAAGGTTTTCTTTCCACCGTTTTTG
* * *
517808 GTAGAATCAAAGTTTGCCTCATAAATAAGACAAACATGAGTAGTCATACTAATCCCTATTCTTTT
131 ATAGAATCAAAGTTTGCCTCCTAAATAAGACAAACATGAATAGTCATACTAATCCC-ATTC-TTT
* * ** *
517873 TAAGGATTAGGAACCATAAACATAGTCAGGTCATTAGG-TCA-ACGAAATTGAAGCTTTGGGTTT
194 TCAGGATTAGGCACCATAAACATAGTCATCTCATTAGGAT-AGAAGAAATTGAAGCTTT-GGTTT
* * * *
517936 CGCAAG-AAAGCTTTCTTCCACT--AATTTTTGAAAAGTCTAAGTTCATGCCTCAAATGAGAGAA
257 CGCAAGAAAAGCTTTCTT-CACTCCAATTTCTGTAAAGTCTAAGTTCGTGCCTCAAATGAGACAA
* * * * * *
517998 AAATTGATTCAAGTAATGATCTTTATTCATTTGGTGATTAGGCCACT-AT-AACACATT-CCCTC
321 ACATGGATTCTAGTAATGATCTTCATTCATTTTGTGATTTGG-CA-TGATAAACACATTCCCCTC
* * * * **
518060 AGTAGGAGAAATGATAATTGATG-TTTGTCTTTTGCATGG-AATC-TTTCTTTGCGTTATTTTCC
384 ATTAGGATAAATGAT-ATTGATGAATT-TCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCC
*
518122 TTAAAAT--AAATTCATCCC-TAAATTTG
447 TTAAAATAAAAATTCATCCCTTAAATATG
* * * *
518148 AC-AGAATCGATTCTTGGCAACTGGTCTCCATTCTTTTTTTCAAAATT-GGAACCAAGAA-AC-T
1 ACAAGCATCGATTC-TCGTAACT-GTCTCCATTC---TTTTCAAAATTGGGAACCAAGAATGCAT
** * * * *
518209 T-CC-TCATTAGGATAACGGGACATTGATGCGTTGGGTGTGACTAG-AAATGTATTTC-TTCCAA
61 TCCCTTCATTAGGAT-ACAAGACATTGATGCTTTGGG-GTCACAAGAAAAGGT-TTTCTTTCC-A
* * * * * * *
518270 CTGTTTTTGTTAGTATCAAAG-TTGCACT--TAAA-AAGATAAACATGAAATAGTTATACGAAGC
122 CCGTTTTTGATAGAATCAAAGTTTGC-CTCCTAAATAAGACAAACATG-AATAGTCATACTAATC
* *
518331 CCATTCTTTTCAAGATTAGGCCCGCAATAAACATAGTCA
185 CCATTCTTTTCAGGATTAGGCAC-C-ATAAACATAGTCA
518370 AACCTCATAT
Statistics
Matches: 2624, Mismatches: 345, Indels: 182
0.83 0.11 0.06
Matches are distributed among these distances:
465 52 0.02
466 56 0.02
467 35 0.01
468 92 0.04
469 167 0.06
470 147 0.06
471 108 0.04
472 168 0.06
473 464 0.18
474 370 0.14
475 476 0.18
476 330 0.13
477 108 0.04
478 51 0.02
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (475 bp):
ACAAGCATCGATTCTCGTAACTGTCTCCATTCTTTTCAAAATTGGGAACCAAGAATGCATTCCCT
TCATTAGGATACAAGACATTGATGCTTTGGGGTCACAAGAAAAGGTTTTCTTTCCACCGTTTTTG
ATAGAATCAAAGTTTGCCTCCTAAATAAGACAAACATGAATAGTCATACTAATCCCATTCTTTTC
AGGATTAGGCACCATAAACATAGTCATCTCATTAGGATAGAAGAAATTGAAGCTTTGGTTTCGCA
AGAAAAGCTTTCTTCACTCCAATTTCTGTAAAGTCTAAGTTCGTGCCTCAAATGAGACAAACATG
GATTCTAGTAATGATCTTCATTCATTTTGTGATTTGGCATGATAAACACATTCCCCTCATTAGGA
TAAATGATATTGATGAATTTCCTTTGCATGGAAATCTTTTCTTTGCCCTATTTTCCTTAAAATAA
AAATTCATCCCTTAAATATG
Done.