Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013979.1 Kokia drynarioides strain JFW-HI SEQ_129010, 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: 2819
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Found at i:1069 original size:29 final size:29
Alignment explanation
Indices: 1027--1409 Score: 183
Period size: 29 Copynumber: 12.9 Consensus size: 29
1017 CCCCGAAGGT
1027 CCCTAAACTTCCAAAAATCACATTTTTAA
1 CCCTAAACTTCCAAAAATCACATTTTTAA
*
1056 CCCTAAACTTCCAAAAATTACCA-TTTT-A
1 CCCTAAACTTCCAAAAATCA-CATTTTTAA
* *
1084 CCCTCAAACTTCC-AAAACCCCATTTTTAA
1 CCCT-AAACTTCCAAAAATCACATTTTTAA
* *
1113 CCCCAAACCTTCCAAAAATC-CTATTTTTTTAT
1 CCCTAAA-CTTCCAAAAATCAC-A--TTTTTAA
**
1145 CCCCGAACTTCCAAAAAT-ATCATTTTTAA
1 CCCTAAACTTCCAAAAATCA-CATTTTTAA
* * * *
1174 CCTCGAACCTTCCAAAAATTAC-TATTTTAGC
1 CC-CTAAACTTCCAAAAATCACAT-TTTTA-A
* * * *
1205 CCCGAACCTTCCAAAAATCCCATTTTAAA
1 CCCTAAACTTCCAAAAATCACATTTTTAA
* * *
1234 CCCTGAACCTTCCAAAAATTACCA-TTTTAC
1 CCCT-AAACTTCCAAAAATCA-CATTTTTAA
** * * *
1264 CCCCGAACCTCCAAAAAGTCCCATTTTTTAT
1 CCCTAAACTTCCAAAAA-TCACA-TTTTTAA
* * * * *
1295 CCCGAACCTTCCAAATATTACCA-TTTTAC
1 CCCTAAACTTCCAAAAATCA-CATTTTTAA
** * *
1324 CCCCGAACTTCCAAAAATCCCATTTTTTTAT
1 CCCTAAACTTCCAAAAATCACA--TTTTTAA
* * * * *
1355 CCCGAACCTTCC-AAAATTACCA-TTCTAC
1 CCCTAAACTTCCAAAAATCA-CATTTTTAA
* *
1383 CCCTGAACTTCCAAAAATCCCATTTTT
1 CCCTAAACTTCCAAAAATCACATTTTT
1410 GACTCCGAAC
Statistics
Matches: 269, Mismatches: 57, Indels: 56
0.70 0.15 0.15
Matches are distributed among these distances:
27 2 0.01
28 33 0.12
29 92 0.34
30 76 0.28
31 53 0.20
32 13 0.05
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.31
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATCACATTTTTAA
Found at i:1186 original size:30 final size:30
Alignment explanation
Indices: 1034--1440 Score: 306
Period size: 30 Copynumber: 13.6 Consensus size: 30
1024 GGTCCCTAAA
* *
1034 CTTCCAAAAAT-CACATTTTTAA-CCCTAAA
1 CTTCCAAAAATAC-CATTTTTAACCCCGAAC
*
1063 CTTCCAAAAATTACCA-TTTT-ACCCTC-AAA
1 CTTCCAAAAA-TACCATTTTTAACCC-CGAAC
** *
1092 CTTCC-AAAACCCCATTTTTAACCCCAAAC
1 CTTCCAAAAATACCATTTTTAACCCCGAAC
*
1121 CTTCCAAAAAT-CCTATTTTTTTATCCCCGAA-
1 CTTCCAAAAATACC-A--TTTTTAACCCCGAAC
* *
1152 CTTCCAAAAATATCATTTTTAACCTCGAAC
1 CTTCCAAAAATACCATTTTTAACCCCGAAC
* *
1182 CTTCCAAAAATTACTA-TTTTAGCCCCGAAC
1 CTTCCAAAAA-TACCATTTTTAACCCCGAAC
* * *
1212 CTTCCAAAAATCCCATTTTAAACCCTGAAC
1 CTTCCAAAAATACCATTTTTAACCCCGAAC
*
1242 CTTCCAAAAATTACCA-TTTTACCCCCGAAC
1 CTTCCAAAAA-TACCATTTTTAACCCCGAAC
* * *
1272 C-TCCAAAAAGTCCCATTTTTTATCCCGAAC
1 CTTCCAAAAA-TACCATTTTTAACCCCGAAC
* *
1302 CTTCCAAATATTACCA-TTTTACCCCCGAA-
1 CTTCCAAA-AATACCATTTTTAACCCCGAAC
* * *
1331 CTTCCAAAAATCCCATTTTTTTATCCCGAAC
1 CTTCCAAAAATACCA-TTTTTAACCCCGAAC
* *
1362 CTTCCAAAATTACCA-TTCT-ACCCCTGAA-
1 CTTCCAAAAATACCATTTTTAACCCC-GAAC
* * *
1390 CTTCCAAAAATCCCATTTTTGACTCCGAAC
1 CTTCCAAAAATACCATTTTTAACCCCGAAC
* *
1420 GTTCCCCAAAACTACCATTTT
1 CTT--CCAAAAATACCATTTT
1441 GCCCCCGTGC
Statistics
Matches: 302, Mismatches: 48, Indels: 53
0.75 0.12 0.13
Matches are distributed among these distances:
27 3 0.01
28 32 0.11
29 84 0.28
30 112 0.37
31 43 0.14
32 28 0.09
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.31
Consensus pattern (30 bp):
CTTCCAAAAATACCATTTTTAACCCCGAAC
Found at i:1219 original size:60 final size:57
Alignment explanation
Indices: 1032--1445 Score: 445
Period size: 60 Copynumber: 7.0 Consensus size: 57
1022 AAGGTCCCTA
* * * *
1032 AACTTCCAAAAATCACATTTTTAACCCTAAACTTCCAAAAATTACCATTTTACCCTCA
1 AACTTCCAAAAATCCCATTTTTAACCCGAACCTTCCAAAAATTACCATTTTACCC-CG
* * ***
1090 AACTTCC-AAAACCCCATTTTTAACCCCAAACCTTCCAAAAATCCTATTTTTTTATCCCCG
1 AACTTCCAAAAATCCCATTTTTAA-CCCGAACCTTCCAAAAAT--TACCATTTTA-CCCCG
** *
1150 AACTTCCAAAAATATCATTTTTAACCTCGAACCTTCCAAAAATTACTATTTTAGCCCCG
1 AACTTCCAAAAATCCCATTTTTAACC-CGAACCTTCCAAAAATTACCATTTTA-CCCCG
*
1209 AACCTTCCAAAAATCCCATTTTAAACCCTGAACCTTCCAAAAATTACCATTTTACCCCCG
1 AA-CTTCCAAAAATCCCATTTTTAACCC-GAACCTTCCAAAAATTACCATTTTA-CCCCG
* * *
1269 AACCTCCAAAAAGTCCCATTTTTTATCCCGAACCTTCCAAATATTACCATTTTACCCCCG
1 AACTTCCAAAAA-TCCCA-TTTTTAACCCGAACCTTCCAAAAATTACCATTTTA-CCCCG
* *
1329 AACTTCCAAAAATCCCATTTTTTTATCCCGAACCTTCC-AAAATTACCATTCTACCCCTG
1 AACTTCCAAAAATCCCA--TTTTTAACCCGAACCTTCCAAAAATTACCATTTTACCCC-G
* * * * *
1388 AACTTCCAAAAATCCCATTTTTGACTCCGAACGTTCCCCAAAACTACCATTTTGCCCC
1 AACTTCCAAAAATCCCATTTTTAAC-CCGAACCTT-CCAAAAATTACCATTTTACCCC
1446 CGTGCATCCG
Statistics
Matches: 308, Mismatches: 33, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
57 20 0.06
58 35 0.11
59 63 0.20
60 151 0.49
61 39 0.13
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.30
Consensus pattern (57 bp):
AACTTCCAAAAATCCCATTTTTAACCCGAACCTTCCAAAAATTACCATTTTACCCCG
Found at i:1436 original size:119 final size:116
Alignment explanation
Indices: 1027--1447 Score: 454
Period size: 119 Copynumber: 3.5 Consensus size: 116
1017 CCCCGAAGGT
* * * * * *
1027 CCCTAAACTTCCAAAAATCACATTTTTAACCCTAAACTTCCAAAAATTACCATTTTACCCTCAAA
1 CCCTGAACTTCCAAAAATCCCATTTTTAACCCGAACCTTCCAAAAATTACCATTTTACCCCCGAA
* * * *
1092 CTTCC-AAAACCCCATTTTTAACCCCAAACCTTCCAAAAAT-CCTATTTTTTTATC
66 CTTCCAAAAATCCCATTTTTAAACCCGAACCTTCCAAAATTACC-A---TTTTA-C
** * *
1146 CCC-GAACTTCCAAAAATATCATTTTTAACCTCGAACCTTCCAAAAATTACTATTTTAGCCCCGA
1 CCCTGAACTTCCAAAAATCCCATTTTTAACC-CGAACCTTCCAAAAATTACCATTTTACCCCCGA
1210 ACCTTCCAAAAATCCCA-TTTTAAACCCTGAACCTTCCAAAAATTACCATTTTAC
65 A-CTTCCAAAAATCCCATTTTTAAACCC-GAACCTTCC-AAAATTACCATTTTAC
* * * *
1264 CCCCGAACCTCCAAAAAGTCCCATTTTTTATCCCGAACCTTCCAAATATTACCATTTTACCCCCG
1 CCCTGAACTTCCAAAAA-TCCCA-TTTTTAACCCGAACCTTCCAAAAATTACCATTTTACCCCCG
* * *
1329 AACTTCCAAAAATCCCATTTTTTTATCCCGAACCTTCCAAAATTACCATTCTAC
64 AACTTCCAAAAATCCCA-TTTTTAAACCCGAACCTTCCAAAATTACCATTTTAC
* * * * *
1383 CCCTGAACTTCCAAAAATCCCATTTTTGACTCCGAACGTTCCCCAAAACTACCATTTTGCCCCCG
1 CCCTGAACTTCCAAAAATCCCATTTTTAAC-CCGAACCTT-CCAAAAATTACCATTTTACCCCCG
1448 TGCATCCGTA
Statistics
Matches: 257, Mismatches: 32, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
117 6 0.02
118 41 0.16
119 113 0.44
120 57 0.22
121 32 0.12
122 6 0.02
123 2 0.01
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.30
Consensus pattern (116 bp):
CCCTGAACTTCCAAAAATCCCATTTTTAACCCGAACCTTCCAAAAATTACCATTTTACCCCCGAA
CTTCCAAAAATCCCATTTTTAAACCCGAACCTTCCAAAATTACCATTTTAC
Done.