Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010023.1 Kokia drynarioides strain JFW-HI SEQ_124788, whole genome shotgun sequence
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: 11750
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.26
Warning! 180 characters in sequence are not A, C, G, or T
Found at i:750 original size:29 final size:29
Alignment explanation
Indices: 712--1221 Score: 349
Period size: 30 Copynumber: 17.3 Consensus size: 29
702 TAGAGGTCCC
712 CGAACCTTCCAAAAATTACTATTTTACCCT
1 CGAA-CTTCCAAAAATTACTATTTTACCCT
* *
742 CGAACTTCCAAAAA-TCCCATTTTTGA-CCT
1 CGAACTTCCAAAAATTACTA-TTTT-ACCCT
*
771 CGAACCTTCCAAAAATTACTATTTTACCCC
1 CGAA-CTTCCAAAAATTACTATTTTACCCT
* *
801 CGAACTTCCAAAAA-TCCCATTTTTGACCC-
1 CGAACTTCCAAAAATTACTA-TTTT-ACCCT
830 CGAACCTTCCAAAAATTACTATTTTACCC-
1 CGAA-CTTCCAAAAATTACTATTTTACCCT
* * * *
859 CAAAACTTCCAAAAA-TCCCATTTTAACCT
1 C-GAACTTCCAAAAATTACTATTTTACCCT
*
888 CGAACCTT-CAAAAACTTACTATTTTACCCC
1 CGAA-CTTCCAAAAA-TTACTATTTTACCCT
* * *
918 CAAACTTCCAAAAA-TCCCATTTTTGA-CCT
1 CGAACTTCCAAAAATTACTA-TTTT-ACCCT
*
947 CGAACCTTCCAAAAATTACTATTTTACCCCC
1 CGAA-CTTCCAAAAATTACTATTTTA-CCCT
* *
978 CGAACTTCCAAAAATCA-AATATTTAGCCC-
1 CGAACTTCCAAAAATTACTAT-TTTA-CCCT
* *
1007 CGAACTTTCTAAAAATTACAATTTTACCCT
1 CGAAC-TTCCAAAAATTACTATTTTACCCT
* * *
1037 CGAACTTCTAAAAA-TCCCATTTTTAACCC-
1 CGAACTTCCAAAAATTACTA-TTTT-ACCCT
*
1066 CGAATCTTCCAAGAATTACTATTTTACCC-
1 CGAA-CTTCCAAAAATTACTATTTTACCCT
* *
1095 CTAAACTCCCAAAAA-T-CTCATTTTTAGCCC-
1 C-GAACTTCCAAAAATTACT-A-TTTTA-CCCT
*
1125 CGAACCTTTCAAAAATTACTATTTTACCCT
1 CGAA-CTTCCAAAAATTACTATTTTACCCT
* * *
1155 CGAACTCCCAAAAA-TCCCATTTTTGA-CCT
1 CGAACTTCCAAAAATTACTA-TTTT-ACCCT
* * *
1184 CGGATCTT-CTAAAATTACAATTTTACCCT
1 C-GAACTTCCAAAAATTACTATTTTACCCT
1213 CGAACTTCC
1 CGAACTTCC
1222 CAAGATCCTA
Statistics
Matches: 384, Mismatches: 53, Indels: 87
0.73 0.10 0.17
Matches are distributed among these distances:
27 2 0.01
28 41 0.11
29 152 0.40
30 164 0.43
31 23 0.06
32 2 0.01
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.31
Consensus pattern (29 bp):
CGAACTTCCAAAAATTACTATTTTACCCT
Found at i:805 original size:59 final size:59
Alignment explanation
Indices: 709--1238 Score: 674
Period size: 59 Copynumber: 9.0 Consensus size: 59
699 CCCTAGAGGT
*
709 CCCCGAACCTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
*
768 CCTCGAACCTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
** *
827 CCCCGAACCTTCCAAAAATTACTATTTTACCCCAAAACTTCCAAAAATCCCA-TTTTAA
1 CCCCGAACCTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* *
885 CCTCGAACCTT-CAAAAACTTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAA-TTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* ** *
944 CCTCGAACCTTCCAAAAATTACTATTTTACCCCCCGAACTTCCAAAAATCAAATATTT-A
1 CCCCGAACCTTCCAAAAATTACTATTTTA-CCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * * * *
1003 GCCCCGAACTTTCTAAAAATTACAATTTTACCCTCGAACTTCTAAAAATCCCATTTTTAA
1 -CCCCGAACCTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * ** * *
1063 CCCCGAATCTTCCAAGAATTACTATTTTACCCCTAAACTCCCAAAAATCTCATTTTT-A
1 CCCCGAACCTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * *
1121 GCCCCGAACCTTTCAAAAATTACTATTTTACCCTCGAACTCCCAAAAATCCCATTTTTGA
1 -CCCCGAACCTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * * * * * * *
1181 CCTCGGATCTT-CTAAAATTACAATTTTACCCTCGAACTTCCCAAGATCCTATTTTTGA
1 CCCCGAACCTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
1239 TTCCGGACAT
Statistics
Matches: 414, Mismatches: 49, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
57 6 0.01
58 90 0.22
59 261 0.63
60 57 0.14
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (59 bp):
CCCCGAACCTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
Found at i:1254 original size:295 final size:295
Alignment explanation
Indices: 709--1255 Score: 778
Period size: 295 Copynumber: 1.9 Consensus size: 295
699 CCCTAGAGGT
* * *
709 CCCCGAACCTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGA
1 CCCCGAACCTTCCAAAAATTACAATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCGA
* *
774 ACCTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTC
66 ACCTTCCAAAAATTACTATTTTACCCCCAAACTCCCAAAAATCCCATTTTTGACCCCGAACCTTC
*
839 CAAAAATTACTATTTTACCCCAAAACTTCCAAAAATCCCATTTTAACCTCGAACCTTCAAAAACT
131 CAAAAATTACTATTTTACCCCAAAACTCCCAAAAATCCCATTTTAACCTCGAACCTTCAAAAACT
* *
904 TACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCCAAAAATTACTAT
196 TACAATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAACATTCCAAAAATTACTAT
969 TTTACCCCCCGAACTTCCAAAAATCAAATATTTAG
261 TTTACCCCCCGAACTTCCAAAAATCAAATATTTAG
* * *
1004 CCCCGAACTTTCTAAAAATTACAATTTTACCCTCGAACTTCTAAAAATCCCATTTTTAACCCCGA
1 CCCCGAACCTTCCAAAAATTACAATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCGA
* * * *
1069 ATCTTCCAAGAATTACTATTTTACCCCTAAACTCCCAAAAATCTCATTTTT-AGCCCCGAACCTT
66 ACCTTCCAAAAATTACTATTTTACCCCCAAACTCCCAAAAATCCCATTTTTGA-CCCCGAACCTT
* * * * * *
1133 TCAAAAATTACTATTTTACCCTC-GAACTCCCAAAAATCCCATTTTTGACCTCGGATCTTCTAAA
130 CCAAAAATTACTATTTTACCC-CAAAACTCCCAAAAATCCCA-TTTTAACCTCGAACCTTCAAAA
* * * * * * *
1197 A-TTACAATTTTACCCTCGAACTTCCCAAGATCCTATTTTTGA-TTCCGGACATTCCAAAA
193 ACTTACAATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCT-CGAACATTCCAAAA
1256 CTACCATTTT
Statistics
Matches: 220, Mismatches: 28, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
294 2 0.01
295 198 0.90
296 20 0.09
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (295 bp):
CCCCGAACCTTCCAAAAATTACAATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCGA
ACCTTCCAAAAATTACTATTTTACCCCCAAACTCCCAAAAATCCCATTTTTGACCCCGAACCTTC
CAAAAATTACTATTTTACCCCAAAACTCCCAAAAATCCCATTTTAACCTCGAACCTTCAAAAACT
TACAATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAACATTCCAAAAATTACTAT
TTTACCCCCCGAACTTCCAAAAATCAAATATTTAG
Found at i:1596 original size:83 final size:82
Alignment explanation
Indices: 1509--1662 Score: 188
Period size: 83 Copynumber: 1.9 Consensus size: 82
1499 TCTAATATCA
* * **
1509 AGGCAATATTCTT-TTAT-TTTGAGTTCCGAAAAT-TTGCGTCTTAACTCACTAGGTGCAATTTT
1 AGGCAATATT-TTCTTATCTTCGA-TTCC-AAAATATTGCGCCTTAACTCACTAGGTGCAA-CCT
1571 TTCTTCAAATACCTTTAATCG
62 TTCTTCAAATACCTTTAATCG
* * *
1592 AGGCAATGTTTTCTTATCTTCGATTTCAAAATATTGCGCCTTAACTTACTAGGTGCAACCTTTCT
1 AGGCAATATTTTCTTATCTTCGATTCCAAAATATTGCGCCTTAACTCACTAGGTGCAACCTTTCT
1657 TCAAAT
66 TCAAAT
1663 CGAGATAATC
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
82 18 0.30
83 39 0.64
84 4 0.07
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (82 bp):
AGGCAATATTTTCTTATCTTCGATTCCAAAATATTGCGCCTTAACTCACTAGGTGCAACCTTTCT
TCAAATACCTTTAATCG
Done.