Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_422 ID=scaffold_422-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: 7833
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.29
Warning! 644 characters in sequence are not A, C, G, or T
Found at i:313 original size:46 final size:46
Alignment explanation
Indices: 261--579 Score: 325
Period size: 46 Copynumber: 6.6 Consensus size: 46
251 TTTGAGTACT
*
261 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCAGCTACACTTA
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
** * *
307 TCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-AGCTACACTTA
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* *
352 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * * *
404 TCTGATCAAGAGACAAAGTGATAAGTGATAGTTTCGGCTACACTTA
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * *
450 TCTAATCAAGTGACAAGTGAAAGTGATAAGTGATAGTTTCGGCTACACTTA
1 TCTGATCAAGTG---A-T-AAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
501 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTA
* *
553 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTG
580 GCTACACTTA
Statistics
Matches: 237, Mismatches: 23, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
45 23 0.10
46 84 0.35
49 3 0.01
51 67 0.28
52 60 0.25
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:404 original size:52 final size:52
Alignment explanation
Indices: 313--568 Score: 339
Period size: 52 Copynumber: 5.1 Consensus size: 52
303 CTTATCTGAT
* * *
313 CAAGTGGCAAAGTGATAAGTGGTAGCCT-AGCTACACTTATCTGATCAAGTGA
1 CAAGTGG-AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
* *
365 CAAGTGGAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGA
1 CAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
* *
417 C------AAAGTGATAAGTGATAGTTTCGGCTACACTTATCTAATCAAGTGA
1 CAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
*
463 CAAGT-GAAAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
* ** *
514 CAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
1 CAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
566 CAA
1 CAA
569 AGTGATAAGT
Statistics
Matches: 182, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
46 42 0.23
51 67 0.37
52 73 0.40
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (52 bp):
CAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
Found at i:421 original size:97 final size:96
Alignment explanation
Indices: 275--579 Score: 403
Period size: 97 Copynumber: 3.1 Consensus size: 96
265 ATCAAGTGAT
* * * * *
275 AAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
340 TAGCTACACTTATCTGATCAAGTGACAAGTGG
66 TAGCTACACTTATCTGATCAAGTGACAAGT-G
* * *
372 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGTT
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
* *
437 TCGGCTACACTTATCTAATCAAGTGACAAGTG
66 T-AGCTACACTTATCTGATCAAGTGACAAGTG
*
469 AAAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC------AAAGTGATAAGTG
*
534 ATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTG
60 ATAGC-TTAGCTACACTTATCTGATCAAGTGAC-AAGTG
573 ATAAGTG
1 A-AAGTG
580 GCTACACTTA
Statistics
Matches: 181, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
97 102 0.56
98 27 0.15
103 39 0.22
104 8 0.04
105 5 0.03
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (96 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
TAGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:535 original size:149 final size:143
Alignment explanation
Indices: 261--579 Score: 449
Period size: 149 Copynumber: 2.2 Consensus size: 143
251 TTTGAGTACT
* * * *
261 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGGCAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTAATCAAGTGGCAAAGT
* *
326 GATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCT
66 GATAAGTGATAGCCTAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCT
* *
391 TCGGCTATACTTA
131 TCAGCTACACTTA
* * *
404 TCTGATCAAGAGACAAAGTGATAAGTGATAGTTTCGGCTACACTTATCTAATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTAATCAAGTG----G-C
** *
469 AAAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
61 AAAGTGATAAGTGATAGCCT-AGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
*
534 ATAGCTTTAGCTACACTTA
125 ATAGCTTCAGCTACACTTA
553 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTG
580 GCTACACTTA
Statistics
Matches: 155, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
143 52 0.34
147 1 0.01
148 17 0.11
149 85 0.55
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (143 bp):
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTAATCAAGTGGCAAAGT
GATAAGTGATAGCCTAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCT
TCAGCTACACTTA
Found at i:587 original size:37 final size:37
Alignment explanation
Indices: 543--651 Score: 195
Period size: 37 Copynumber: 3.0 Consensus size: 37
533 GATAGCTTTA
543 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
580 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
617 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
652 ATCATACGTA
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
35 12 0.17
36 5 0.07
37 54 0.76
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Done.