Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_71 ID=scaffold_71-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: 17333
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.28
Warning! 626 characters in sequence are not A, C, G, or T
Found at i:6341 original size:29 final size:30
Alignment explanation
Indices: 6309--6365 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
6299 CCTCGACTCT
6309 AACTTTT-CAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* * *
6338 AACTTTTACATAATTACATTTTTTCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
6366 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.32, C:0.25, G:0.02, T:0.42
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:14296 original size:104 final size:104
Alignment explanation
Indices: 14109--14302 Score: 273
Period size: 104 Copynumber: 1.9 Consensus size: 104
14099 TTTTTTAATC
* * * *
14109 TTAGCAAAATTTGTTATCCTGATTAATTTATTCATCTCGAGCTTTGCTCTAAATAAAATTTCATT
1 TTAGCAAAATTTGTTATCCTGATTAACTCATTCATCTCGAGCTTTGCTCTAAATAAAATCTCATC
*
14174 TTGTCCATTATAATAATCTTTTTCATCTCATTTCGTATA
66 TTGTCCATTATAACAATCTTTTTCATCTCATTTCGTATA
* * **
14213 TTAGCAAAATTT-TCTATCCTTATTAACTCATTCATCTCGAGCTTTGTTCTCCATAAAATCTCAT
1 TTAGCAAAATTTGT-TATCCTGATTAACTCATTCATCTCGAGCTTTGCTCTAAATAAAATCTCAT
* *
14277 CTTGTCCATTGTGACAATCTTTTTCA
65 CTTGTCCATTATAACAATCTTTTTCA
14303 AAAGTTTTTT
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
103 1 0.01
104 77 0.99
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (104 bp):
TTAGCAAAATTTGTTATCCTGATTAACTCATTCATCTCGAGCTTTGCTCTAAATAAAATCTCATC
TTGTCCATTATAACAATCTTTTTCATCTCATTTCGTATA
Found at i:15245 original size:44 final size:44
Alignment explanation
Indices: 15171--15866 Score: 140
Period size: 44 Copynumber: 15.6 Consensus size: 44
15161 AACATATCTC
* * **
15171 ATCTCTCTAAAGTTGCAGTAGAGCCGGTTGAA-ATAGCAACCCTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAAGTTGAAGATA-CAACCCTT
* **
15215 ATC-CCCATGAAGTTGCAGTAGGGCAAGTTGAAGATACAAGTCTT
1 ATCTCCC-TGAAGTTGCAGTAGAGCAAGTTGAAGATACAACCCTT
* * *
15259 ATCTCCCTGAAGTTGCAGTGGAGC-AGATTGAAGTTACTAATCC-T
1 ATCTCCCTGAAGTTGCAGTAGAGCAAG-TTGAAGATAC-AACCCTT
* * * * * * ** *
15303 ACCTCCTTGAAGTTACAGTGGAGC-GGATT-AAAATGATGGATCC-T
1 ATCTCCCTGAAGTTGCAGTAGAGCAAG-TTGAAGAT-A-CAACCCTT
* * * * **
15347 ATCTCTCTGAAGTTGTAGTGGAGC-AGATTAAAGATAGCAAATCTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAAG-TTGAAGATA-CAACCCTT
* * * * * * * ** * *
15392 ATTTCCTTGAAGTTGCAATGGAACAAATTAAATCTACCATAACAGATCTC
1 ATCTCCCTGAAGTTGCAGTAGAGCAAGTTGAAGATA-C--AAC---CCTT
* * * * *
15442 ATCTCTCTAAAGTTGCAGTAGAGCAGGTTGAA-ATAGTAAACCTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAAGTTGAAGATA-CAACCCTT
* * * **
15486 ATC-CCTATGAAGTTGCAGTGGGGCAAGTTGAAGATACAAGTCTT
1 ATCTCC-CTGAAGTTGCAGTAGAGCAAGTTGAAGATACAACCCTT
* * *
15530 ATCTCCCTGAAGTTGTAGTAGAGC-AGATTGAAGTTACGAATCC-T
1 ATCTCCCTGAAGTTGCAGTAGAGCAAG-TTGAAGATAC-AACCCTT
* * * * * ** *
15574 ACCTCCCTAAAGTTGCAGTGGAGC-GGATT-AAAATGATGGATCC-T
1 ATCTCCCTGAAGTTGCAGTAGAGCAAG-TTGAAGAT-A-CAACCCTT
* * ***
15618 ATCTCCCTGAAGTTGCAGTGGAGC-AGATTAAAGATAGCAAATATT
1 ATCTCCCTGAAGTTGCAGTAGAGCAAG-TTGAAGATA-CAACCCTT
* * * * ** * *
15663 ATTTCCCTGAAGTTGCAGTGGAAC-AGATTAAATCTACCATAACAGATCTC
1 ATCTCCCTGAAGTTGCAGTAGAGCAAG-TTGAAGATA-C--AAC---CCTT
* * * * * * * *
15713 ATATCTCTAAAGTTGCAGTAGAGCAA-AT-CATAT-CAAACTTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAAGTTGAAGATACAACCCTT
* * * *
15754 ATCTCTCTGAAGTTGCAGTACAGCAGGTTGAA-ATAGCAAACCTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAAGTTGAAGATA-CAACCCTT
* * * **
15798 ATC-CCTATGAAGTTGCAGTAGGGGAAGTTGAAGATACAATTCTT
1 ATCTCC-CTGAAGTTGCAGTAGAGCAAGTTGAAGATACAACCCTT
* *
15842 ATCTCCTTGAAGTTGCAGTGGAGCA
1 ATCTCCCTGAAGTTGCAGTAGAGCA
15867 GACTGAAGAT
Statistics
Matches: 481, Mismatches: 134, Indels: 74
0.70 0.19 0.11
Matches are distributed among these distances:
41 23 0.05
42 3 0.01
43 15 0.03
44 288 0.60
45 91 0.19
46 2 0.00
47 6 0.01
48 3 0.01
49 3 0.01
50 46 0.10
51 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (44 bp):
ATCTCCCTGAAGTTGCAGTAGAGCAAGTTGAAGATACAACCCTT
Found at i:15275 original size:88 final size:90
Alignment explanation
Indices: 15166--15900 Score: 310
Period size: 88 Copynumber: 8.2 Consensus size: 90
15156 ACCATAACAT
* * * * *
15166 ATCTCATCTCTCTAAAGTTGCAGTAGAGCCGGTTGAA-ATAGCAACCCTTATCCCCATGAAGTTG
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATAGCAAACCTTATCCCCATGAAGTTG
15230 CAGTAGG-GCAAGTTGAAGATACAAG
66 CAGT-GGAGCAAGTTGAAGATACAAG
* * * * *
15255 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTA-CTAATCC-TA-CCTCCTTGAAGT
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATAGC-AAACCTTATCC-CCATGAAGT
* * * **
15316 TACAGTGGAGC-GGATT-AAAATGA-TGG
64 TGCAGTGGAGCAAG-TTGAAGAT-ACAAG
* * * * * ** *
15342 ATCCTATCTCTCTGAAGTTGTAGTGGAGCAGATTAAAGATAGCAAATCTTATTTCCTTGAAGTTG
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATAGCAAACCTTATCCCCATGAAGTTG
* * * * **
15407 CAATGGAACAAATTAAATCTACCATAACAG
66 CAGTGGAGCAAGTTGAAGATA-C---A-AG
* * * * *
15437 ATCTCATCTCTCTAAAGTTGCAGTAGAGCAGGTTGAA-ATAGTAAACCTTATCCCTATGAAGTTG
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATAGCAAACCTTATCCCCATGAAGTTG
*
15501 CAGTGGGGCAAGTTGAAGATACAAG
66 CAGTGGAGCAAGTTGAAGATACAAG
* * * * * *
15526 -TCTTATCTCCCTGAAGTTGTAGTAGAGCAGATTGAAGTTA-CGAATCC-TA-CCTCCCTAAAGT
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATAGC-AAACCTTATCC-CCATGAAGT
* * **
15587 TGCAGTGGAGC-GGATT-AAAATGA-TGG
64 TGCAGTGGAGCAAG-TTGAAGAT-ACAAG
* * * * ** *
15613 ATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCAAATATTATTTCCC-TGAAGTT
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATAGCAAACCTTA-TCCCCATGAAGTT
* * **
15677 GCAGTGGAAC-AGATTAAATCTACCATAACAG
65 GCAGTGGAGCAAG-TTGAAGATA-C---A-AG
* * * ** * * *
15708 ATCTCATATCTCTAAAGTTGCAGTAGAGCA-A---ATCATATCAAACTTTATCTCTC-TGAAGTT
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATAGCAAACCTTATC-CCCATGAAGTT
** *
15768 GCAGTACAGCAGGTTGAA-ATAGCAA-
65 GCAGTGGAGCAAGTTGAAGATA-CAAG
* * * * * ** * *
15793 ACCTTATCCCTATGAAGTTGCAGTAGGGGA-AGTTGAAGATA-CAATTCTTATCTCCTTGAAGTT
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TTGAAGATAGCAAACCTTATCCCCATGAAGTT
*
15856 GCAGTGGAGC-AGACTGAAGATAGCAA-
65 GCAGTGGAGCAAG-TTGAAGATA-CAAG
*
15882 ATCTTA-C-CTTTGAAGTTGC
1 ATCTTATCTCTCTGAAGTTGC
15901 GTCGCAGCAA
Statistics
Matches: 477, Mismatches: 125, Indels: 90
0.69 0.18 0.13
Matches are distributed among these distances:
85 23 0.05
86 1 0.00
87 32 0.07
88 206 0.43
89 76 0.16
90 13 0.03
91 32 0.07
92 1 0.00
93 1 0.00
94 36 0.08
95 56 0.12
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (90 bp):
ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGATAGCAAACCTTATCCCCATGAAGTTG
CAGTGGAGCAAGTTGAAGATACAAG
Found at i:15556 original size:271 final size:271
Alignment explanation
Indices: 15071--15737 Score: 1136
Period size: 271 Copynumber: 2.5 Consensus size: 271
15061 ATCACCACAA
* *
15071 ATCCTATCTCCCTGAAGTTGTAGTGGAGTAGATTAAAGATCGCAAATCTTATTTCCCTGAAGTTG
1 ATCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGATAGCAAATCTTATTTCCCTGAAGTTG
* * *
15136 TAGTGGAACAGATTAAATCTACCATAACATATCTCATCTCTCTAAAGTTGCAGTAGAGCCGGTTG
66 CAGTGGAACAGATTAAATCTACCATAACAGATCTCATCTCTCTAAAGTTGCAGTAGAGCAGGTTG
*
15201 AAATAGCAACCCTTATCCCCATGAAGTTGCAGTAGGGCAAGTTGAAGATACAAGTCTTATCTCCC
131 AAATAGCAAACCTTATCCCCATGAAGTTGCAGTAGGGCAAGTTGAAGATACAAGTCTTATCTCCC
* * * *
15266 TGAAGTTGCAGTGGAGCAGATTGAAGTTACTAATCCTACCTCCTTGAAGTTACAGTGGAGCGGAT
196 TGAAGTTGCAGTAGAGCAGATTGAAGTTACGAATCCTACCTCCCTAAAGTTACAGTGGAGCGGAT
15331 TAAAATGATGG
261 TAAAATGATGG
* *
15342 ATCCTATCTCTCTGAAGTTGTAGTGGAGCAGATTAAAGATAGCAAATCTTATTTCCTTGAAGTTG
1 ATCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGATAGCAAATCTTATTTCCCTGAAGTTG
* *
15407 CAATGGAACAAATTAAATCTACCATAACAGATCTCATCTCTCTAAAGTTGCAGTAGAGCAGGTTG
66 CAGTGGAACAGATTAAATCTACCATAACAGATCTCATCTCTCTAAAGTTGCAGTAGAGCAGGTTG
* * *
15472 AAATAGTAAACCTTATCCCTATGAAGTTGCAGTGGGGCAAGTTGAAGATACAAGTCTTATCTCCC
131 AAATAGCAAACCTTATCCCCATGAAGTTGCAGTAGGGCAAGTTGAAGATACAAGTCTTATCTCCC
* *
15537 TGAAGTTGTAGTAGAGCAGATTGAAGTTACGAATCCTACCTCCCTAAAGTTGCAGTGGAGCGGAT
196 TGAAGTTGCAGTAGAGCAGATTGAAGTTACGAATCCTACCTCCCTAAAGTTACAGTGGAGCGGAT
15602 TAAAATGATGG
261 TAAAATGATGG
* *
15613 ATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAGCAAATATTATTTCCCTGAAGTTG
1 ATCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGATAGCAAATCTTATTTCCCTGAAGTTG
*
15678 CAGTGGAACAGATTAAATCTACCATAACAGATCTCATATCTCTAAAGTTGCAGTAGAGCA
66 CAGTGGAACAGATTAAATCTACCATAACAGATCTCATCTCTCTAAAGTTGCAGTAGAGCA
15738 AATCATATCA
Statistics
Matches: 370, Mismatches: 26, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
271 370 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (271 bp):
ATCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGATAGCAAATCTTATTTCCCTGAAGTTG
CAGTGGAACAGATTAAATCTACCATAACAGATCTCATCTCTCTAAAGTTGCAGTAGAGCAGGTTG
AAATAGCAAACCTTATCCCCATGAAGTTGCAGTAGGGCAAGTTGAAGATACAAGTCTTATCTCCC
TGAAGTTGCAGTAGAGCAGATTGAAGTTACGAATCCTACCTCCCTAAAGTTACAGTGGAGCGGAT
TAAAATGATGG
Found at i:15874 original size:44 final size:43
Alignment explanation
Indices: 15752--15900 Score: 112
Period size: 44 Copynumber: 3.4 Consensus size: 43
15742 ATATCAAACT
** * *
15752 TTATCT-CTCTGAAGTTGCAGTACAGCAGGTTGAA-ATAGCAAACC
1 TTATCTCCT-TGAAGTTGCAGTGGAGCAGATTGAAGATA-C-AATC
* *
15796 TTATC-CCTATGAAGTTGCAGTAGGGGAAG-TTGAAGATACAATTC
1 TTATCTCCT-TGAAGTTGCAGT-GGAGCAGATTGAAGATACAA-TC
*
15840 TTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATC
1 TTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGATA-C-AATC
*
15885 TTA-C-CTTTGAAGTTGC
1 TTATCTCCTTGAAGTTGC
15901 GTCGCAGCAA
Statistics
Matches: 87, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
43 18 0.21
44 52 0.60
45 15 0.17
46 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (43 bp):
TTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGATACAATC
Done.