Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013705.1 Kokia drynarioides strain JFW-HI SEQ_128733, 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: 5146
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Warning! 49 characters in sequence are not A, C, G, or T
Found at i:111 original size:3 final size:3
Alignment explanation
Indices: 103--129 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
93 AACGGTTTTT
103 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
130 ATTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:135 original size:32 final size:32
Alignment explanation
Indices: 99--162 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
89 AATGAACGGT
*
99 TTTTTAATAATAATAATAA-TAATAATAATAAA
1 TTTTT-ATAATAAAAATAATTAATAATAATAAA
* **
131 TTTTTTTTTTAAAAATAATTAATAATAATAAA
1 TTTTTATAATAAAAATAATTAATAATAATAAA
163 GGTATTCGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
TTTTTATAATAAAAATAATTAATAATAATAAA
Found at i:1257 original size:59 final size:59
Alignment explanation
Indices: 1165--1654 Score: 686
Period size: 59 Copynumber: 8.3 Consensus size: 59
1155 AAATTGTTCG
*
1165 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
* * *
1224 AAAATTACCATTTTACCCTCGAA-TTCCCAAAAATCCCATTTTTTACCCCGAACCTTCCA
1 AAAATTACCATTTTACCCCCGAACTT-CCAAAAATCCCATTTTTGACCCCGAACCTTCTA
* *
1283 TAAAATTACCA-TTTACCCCCGAACTTCTAAAAATCCCATTTTTGACCCCGAACCTTCTG
1 -AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
* *
1342 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTAT-
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
* * * *
1400 AAAATTACCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTTACCCTGAACCTT-TT
1 AAAATTACCA-TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
* * *
1459 AAAATTACCATTTTACCCTCGAACTTCAAAAAATCCCATTTTTGACCCCGAACCTTCCA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
*
1518 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCCA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
** * * *
1577 AAAATTACCATTTTACCTTCAAACTTCGCAAAAA-CCCATTTTTTGACTCCGAACCTTC-C
1 AAAATTACCATTTTACCCCCGAACTTC-CAAAAATCCCA-TTTTTGACCCCGAACCTTCTA
* *
1636 AAAATTACGATTTTGCCCC
1 AAAATTACCATTTTACCCC
1655 GATGCATCCG
Statistics
Matches: 391, Mismatches: 31, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
58 64 0.16
59 291 0.74
60 36 0.09
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTA
Found at i:1639 original size:30 final size:30
Alignment explanation
Indices: 1175--1639 Score: 375
Period size: 30 Copynumber: 15.8 Consensus size: 30
1165 AAAATTACCA
1175 TTTT-ACCCTCGAA-CTTCCAAAAATCCCAT
1 TTTTGACCC-CGAACCTTCCAAAAATCCCAT
* *
1204 TTTTGACCCCGAACCTTCTAAAAATTACCA-
1 TTTTGACCCCGAACCTTCCAAAAA-TCCCAT
1234 TTTT-ACCCTCGAA--TTCCCAAAAATCCCAT
1 TTTTGACCC-CGAACCTT-CCAAAAATCCCAT
* *
1263 TTTTTACCCCGAACCTTCCATAAAATTACCA-
1 TTTTGACCCCGAACCTTCCA-AAAA-TCCCAT
*
1294 -TTT-ACCCCCGAA-CTTCTAAAAATCCCAT
1 TTTTGA-CCCCGAACCTTCCAAAAATCCCAT
* * *
1322 TTTTGACCCCGAACCTTCTGAAAATTACCA-
1 TTTTGACCCCGAACCTTC-CAAAAATCCCAT
1352 TTTT-ACCCCCGAA-CTTCCAAAAATCCCAT
1 TTTTGA-CCCCGAACCTTCCAAAAATCCCAT
* ** * *
1381 TTTTAACCCCGAACCTTATAAAATTACCAT
1 TTTTGACCCCGAACCTTCCAAAAATCCCAT
* *
1411 TTTT-ACCCCCAAACTTCCAAAAATCCCAT
1 TTTTGACCCCGAACCTTCCAAAAATCCCAT
* * ** * *
1440 TTTTTACCCTGAACCTTTTAAAATTACCA-
1 TTTTGACCCCGAACCTTCCAAAAATCCCAT
*
1469 TTTT-ACCCTCGAA-CTTCAAAAAATCCCAT
1 TTTTGACCC-CGAACCTTCCAAAAATCCCAT
*
1498 TTTTGACCCCGAACCTTCCAAAAATTACCA-
1 TTTTGACCCCGAACCTTCCAAAAA-TCCCAT
1528 TTTT-ACCCCCGAA-CTTCCAAAAATCCCAT
1 TTTTGA-CCCCGAACCTTCCAAAAATCCCAT
*
1557 TTTTGACCCCGAACCTTCCAAAAATTACCA-
1 TTTTGACCCCGAACCTTCCAAAAA-TCCCAT
* *
1587 TTTT-ACCTTC-AAACTTCGCAAAAA-CCCATT
1 TTTTGACC-CCGAACCTTC-CAAAAATCCCA-T
*
1617 TTTTGACTCCGAACCTTCCAAAA
1 TTTTGACCCCGAACCTTCCAAAA
1640 TTACGATTTT
Statistics
Matches: 353, Mismatches: 45, Indels: 75
0.75 0.10 0.16
Matches are distributed among these distances:
27 4 0.01
28 40 0.11
29 127 0.36
30 144 0.41
31 34 0.10
32 4 0.01
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (30 bp):
TTTTGACCCCGAACCTTCCAAAAATCCCAT
Found at i:1649 original size:29 final size:29
Alignment explanation
Indices: 1165--1656 Score: 329
Period size: 29 Copynumber: 16.8 Consensus size: 29
1155 AAATTGTTCG
1165 AAAATTACCATTTT-ACCCTCGAA-CTTCC
1 AAAATTACCATTTTGACCC-CGAACCTTCC
* * *
1193 AAAAATCCCATTTTTGACCCCGAACCTTCTA
1 AAAATTACCA-TTTTGACCCCGAACCTTC-C
1224 AAAATTACCATTTT-ACCCTCGAA--TTCCC
1 AAAATTACCATTTTGACCC-CGAACCTT-CC
* * *
1252 AAAAATCCCATTTTTTACCCCGAACCTTCC
1 AAAATTACCA-TTTTGACCCCGAACCTTCC
*
1282 ATAAAATTACCA-TTT-ACCCCCGAA-CTTCT
1 --AAAATTACCATTTTGA-CCCCGAACCTTCC
* * *
1311 AAAAATCCCATTTTTGACCCCGAACCTTCTG
1 AAAATTACCA-TTTTGACCCCGAACCTTC-C
1342 AAAATTACCATTTT-ACCCCCGAA-CTTCC
1 AAAATTACCATTTTGA-CCCCGAACCTTCC
* * * **
1370 AAAAATCCCATTTTTAACCCCGAACCTTAT
1 AAAATTACCA-TTTTGACCCCGAACCTTCC
* * *
1400 AAAATTACCATTTTTACCCCCAAACTTCC
1 AAAATTACCATTTTGACCCCGAACCTTCC
* * * * **
1429 AAAAATCCCATTTTTTACCCTGAACCTTTT
1 AAAATTACCA-TTTTGACCCCGAACCTTCC
*
1459 AAAATTACCATTTT-ACCCTCGAA-CTTCA
1 AAAATTACCATTTTGACCC-CGAACCTTCC
* *
1487 AAAAATCCCATTTTTGACCCCGAACCTTCC
1 AAAATTACCA-TTTTGACCCCGAACCTTCC
1517 AAAAATTACCATTTT-ACCCCCGAA-CTTCC
1 -AAAATTACCATTTTGA-CCCCGAACCTTCC
* *
1546 AAAAATCCCATTTTTGACCCCGAACCTTCC
1 AAAATTACCA-TTTTGACCCCGAACCTTCC
* *
1576 AAAAATTACCATTTT-ACCTTC-AAACTTCGC
1 -AAAATTACCATTTTGACC-CCGAACCTTC-C
*
1606 AAAA--ACCCATTTTTTGACTCCGAACCTTCC
1 AAAATTA-CCA--TTTTGACCCCGAACCTTCC
*
1636 AAAATTACGATTTTG-CCCCGA
1 AAAATTACCATTTTGACCCCGA
1657 TGCATCCGAA
Statistics
Matches: 366, Mismatches: 56, Indels: 84
0.72 0.11 0.17
Matches are distributed among these distances:
27 9 0.02
28 57 0.16
29 124 0.34
30 123 0.34
31 44 0.12
32 9 0.02
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (29 bp):
AAAATTACCATTTTGACCCCGAACCTTCC
Done.