Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011208.1 Kokia drynarioides strain JFW-HI SEQ_126185, 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: 2373
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.36
Found at i:556 original size:30 final size:28
Alignment explanation
Indices: 521--1028 Score: 222
Period size: 30 Copynumber: 17.5 Consensus size: 28
511 AAACTGTCCG
521 AAAATTCCATTTTTATCCCATAACTTCTTA
1 AAAATTCCATTTTTA-CCCATAACTTC-TA
* *
551 AAAATTCCATTTTTAACCCCAAAACTTC-C
1 AAAATTCCATTTTT-A-CCCATAACTTCTA
* * *
580 AAAATTCTATTTTTACCCTTAAACTTCCA
1 AAAATTCCATTTTTACCCAT-AACTTCTA
*
609 AAAATTCCATTTTTAACCCCA-AAGCTTCCAA
1 AAAATTCCATTTTT-A-CCCATAA-CTT-CTA
* * *
640 AAAAAT-CA-TTTTACCCCTAAACTTCCA
1 AAAATTCCATTTTTACCCAT-AACTTCTA
*
667 AAAATTCCATTTTCGACCTCGA-AACTTCTA
1 AAAATTCCATTTT-TACC-C-ATAACTTCTA
**
697 AAAATTCCATTTTTACCCCCGAACTTCTA
1 AAAATTCCATTTTTA-CCCATAACTTCTA
*
726 AAAATTCCATTTTTGACCTCGA-AACTTC-C
1 AAAATTCCATTTTT-ACC-C-ATAACTTCTA
* * *
755 AAAATTCCAATTTTGA-CCTTGAAACTTCAA
1 AAAATTCC-ATTTTTACCCAT--AACTTCTA
* ** *
785 AAAATTCTA-TTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTTA-CCCATAACTTCTA
*
813 AAAATTCCATTTTTGACCCCGA-AACTTCCA
1 AAAATTCCATTTTT-A-CCC-ATAACTTCTA
* * * *
843 AAAATCCCATTTTTTCCTC-GAACTTCCA
1 AAAATTCCATTTTTACC-CATAACTTCTA
* * *
871 AAAATTCCATTTTTTCCTC-GAACTTCCA
1 AAAATTCCATTTTTACC-CATAACTTCTA
* * * *
899 AAAATTCCATTTTCGACCCCGTAACTCCCA
1 AAAATTCCATTTT-TA-CCCATAACTTCTA
* ** *
929 AAAATTCCATTTTTGCCCCCGAA-TGTCCA
1 AAAATTCCATTTTT-ACCCATAACT-TCTA
* * * *
958 AAAACTCTATTTTCGACCTCGA-AAC-TCCA
1 AAAATTCCATTTT-TACC-C-ATAACTTCTA
*
987 AAAATTCCA-TTTTACCCAGAA-TGTCTA
1 AAAATTCCATTTTTACCCATAACT-TCTA
1014 AAAATTCCATTTTTA
1 AAAATTCCATTTTTA
1029 ACCCCGATTT
Statistics
Matches: 382, Mismatches: 52, Indels: 90
0.73 0.10 0.17
Matches are distributed among these distances:
25 1 0.00
26 3 0.01
27 29 0.08
28 92 0.24
29 117 0.31
30 118 0.31
31 22 0.06
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCATAACTTCTA
Found at i:584 original size:29 final size:29
Alignment explanation
Indices: 511--1062 Score: 456
Period size: 29 Copynumber: 19.0 Consensus size: 29
501 GAAGGTCCCT
* *
511 AAACTGTCCGAAAATTCCATTTTTATCCC-
1 AAACT-TCCAAAAATTCCATTTTTACCCCG
* *
540 ATAACTTCTTAAAAATTCCATTTTTAACCCCA
1 A-AACTTC-CAAAAATTCCATTTTT-ACCCCG
* **
572 AAACTTCC-AAAATTCTATTTTTACCCTT
1 AAACTTCCAAAAATTCCATTTTTACCCCG
600 AAACTTCCAAAAATTCCATTTTTAACCCC-
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
* *
629 AAAGCTTCCAAAAAAAT-CA-TTTTACCCCT
1 AAA-CTTCC-AAAAATTCCATTTTTACCCCG
* *
658 AAACTTCCAAAAATTCCATTTTCGACCTCG
1 AAACTTCCAAAAATTCCATTTT-TACCCCG
*
688 AAACTTCTAAAAATTCCATTTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTTA-CCCCG
* *
718 -AACTTCTAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
* **
747 AAACTTCC-AAAATTCCAATTTTGACCTTG
1 AAACTTCCAAAAATTCC-ATTTTTACCCCG
* *
776 AAACTTCAAAAAATTCTA-TTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTTA-CCCCG
805 -AACTTCCAAAAATTCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
* * *
834 AAACTTCCAAAAATCCCATTTTTTCCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCG
* *
863 -AACTTCCAAAAATTCCATTTTTTCCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCG
*
891 -AACTTCCAAAAATTCCATTTTCGACCCCG
1 AAACTTCCAAAAATTCCATTTT-TACCCCG
* * *
920 TAACTCCCAAAAATTCCATTTTTGCCCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
* * * *
950 -AA-TGTCCAAAAACTCTATTTTCGACCTCG
1 AAACT-TCCAAAAATTCCATTTT-TACCCCG
*
979 AAAC-TCCAAAAATTCCA-TTTTACCCAG
1 AAACTTCCAAAAATTCCATTTTTACCCCG
*
1006 -AA-TGTCTAAAAATTCCATTTTTAACCCCG
1 AAACT-TCCAAAAATTCCATTTTT-ACCCCG
*** *
1035 ATTTTTCCCAAAATTACCA-TTTTACCCC
1 AAACTTCCAAAAATT-CCATTTTTACCCC
1063 CGAGTATCCA
Statistics
Matches: 433, Mismatches: 55, Indels: 70
0.78 0.10 0.13
Matches are distributed among these distances:
26 2 0.00
27 22 0.05
28 99 0.23
29 151 0.35
30 138 0.32
31 20 0.05
32 1 0.00
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCG
Found at i:1467 original size:96 final size:96
Alignment explanation
Indices: 1287--1478 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 96
1277 AAAACTTTAA
* * ***
1287 AATCGAGGCAATATTCTTTTATTTCGAGTTTCGAAAATTTGTGCCTTAACTTACTAGGTGCAGTT
1 AATCGAGGCAATATTCTCTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
*
1352 TTTCTTCAAATCGAAATAATCGAATACCCTT
66 TTTCTTCAAATAGAAATAATCGAATACCCTT
* *
1383 AATCGAGGCAATGTT-TCCTTATCTTCGA-TTTTG-AAATATTGCGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAATATTCT-CTTAT-TTCGAGTTTCGAAAAT-TTGCGCCTTAACTTACTAGGTGCA
* *
1445 ACCTTTCTTCAAAATAG-GATAATCGAATATCCTT
63 ACCTTTCTTC-AAATAGAAATAATCGAATACCCTT
1479 TTCACAAAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
95 5 0.06
96 67 0.82
97 10 0.12
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (96 bp):
AATCGAGGCAATATTCTCTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
TTTCTTCAAATAGAAATAATCGAATACCCTT
Done.