Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010959.1 Kokia drynarioides strain JFW-HI SEQ_125927, 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: 4529
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:906 original size:59 final size:59
Alignment explanation
Indices: 807--1419 Score: 657
Period size: 59 Copynumber: 10.4 Consensus size: 59
797 GGAGGTCCCT
* * * * *
807 AAACTATCCAAAAACTCCAATTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCA
1 AAACT-TCCAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCA
* * ** * * *
867 AAACCT-CAAAACTTTCTATTTTTACCCTTGAACTTCCAAAAATCTCATTTTTAGCCCTA
1 AAACTTCCAAAA-ATTCTATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCA
* * *
926 AAATTTCCAAAAATTCTAGTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCTCA
1 AAACTTCCAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCA
* * * ** *
985 AAACTTCC-AAAATTTTCATTTTTACCCCCAAACTTTCAAAAATCCCATTTTTGGCCCCT
1 AAACTTCCAAAAATTCT-ATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCA
* * * * * *
1044 AAATTTCCAAAAATTCTATTTTTACCCTCAAACCTCTAAAAATCTCATTTTTGACCCTA
1 AAACTTCCAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCA
* * * * *
1103 AAACTTCCAAAATTTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCT
1 AAACTTCCAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCA
* *
1162 AAACTTCCAAAAAATCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAA-CCCA
1 AAACTTCCAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCA
* * * * *
1220 AGACTTCCAAAAATTCCATTTTCACCC-CTAAACTTCAAAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCTATTTTTACCCTC-AAACTTCCAAAAATCCCATTTTTAACCCCA
* * * *
1279 AAAC-TCCTAAAAATTCCATTTTTACCC-CTAAACTTTCAAATATCCCATTTTTAACCCGA
1 AAACTTCC-AAAAATTCTATTTTTACCCTC-AAACTTCCAAAAATCCCATTTTTAACCCCA
* * * ** *
1338 AAAC-TCTCAAAAATTCCATTTTTACCCTTAAACATAAAAAAATCCCATTTTTAA-CCCG
1 AAACTTC-CAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCA
*
1396 AAACTCCCAAAAATTCTATTTTTA
1 AAACTTCCAAAAATTCTATTTTTA
1420 AACCCTGGAT
Statistics
Matches: 466, Mismatches: 77, Indels: 22
0.82 0.14 0.04
Matches are distributed among these distances:
57 1 0.00
58 86 0.18
59 362 0.78
60 17 0.04
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCCCA
Found at i:1420 original size:29 final size:29
Alignment explanation
Indices: 807--1420 Score: 431
Period size: 29 Copynumber: 20.9 Consensus size: 29
797 GGAGGTCCCT
* * *
807 AAACTATCCAAAAACTCCAATTTT-ACCCTC
1 AAACT-TCCAAAAATTCCATTTTTAACCC-A
*
837 GAACTTCCAAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTAA-CCCA
* * * *
867 AAACCT-CAAAACTTTCTATTTTT-ACCCTT
1 AAACTTCCAAAA-ATTCCATTTTTAACCC-A
* *
896 GAACTTCCAAAAA-TCTCATTTTTAGCCCTA
1 AAACTTCCAAAAATTC-CATTTTTAACCC-A
* * * *
926 AAATTTCCAAAAATTCTAGTTTT-ACCCTC
1 AAACTTCCAAAAATTCCATTTTTAACCC-A
*
955 AAACTTCCAAAAATCCCATTTTTAACCTCA
1 AAACTTCCAAAAATTCCATTTTTAACC-CA
* * * *
985 AAACTTCCAAAATTTTCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTAACCCA
* * ** *
1014 AAACTTTCAAAAATCCCATTTTTGGCCCCT
1 AAACTTCCAAAAATTCCATTTTT-AACCCA
* * *
1044 AAATTTCCAAAAATTCTATTTTT-ACCCTC
1 AAACTTCCAAAAATTCCATTTTTAACCC-A
* * *
1073 AAACCTCTAAAAA-TCTCATTTTTGACCCTA
1 AAACTTCCAAAAATTC-CATTTTTAACCC-A
* * *
1103 AAACTTCCAAAATTTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTAACCCA
* * *
1132 AAACTTCCAAAAATCCCATTTTTGACCCCT
1 AAACTTCCAAAAATTCCATTTTT-AACCCA
* * *
1162 AAACTTCCAAAAAATCTATTTTT-ACCCTC
1 AAACTTCCAAAAATTCCATTTTTAACCC-A
* *
1191 GAACTTCCAAAAATCCCATTTTTAACCCA
1 AAACTTCCAAAAATTCCATTTTTAACCCA
* * * *
1220 AGACTTCCAAAAATTCCATTTTCACCCCT
1 AAACTTCCAAAAATTCCATTTTTAACCCA
* *
1249 AAACTTCAAAAAATCCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTTAACCC-A
* *
1279 AAAC-TCCTAAAAATTCCATTTTTACCCCT
1 AAACTTCC-AAAAATTCCATTTTTAACCCA
* * *
1308 AAACTTTCAAATATCCCATTTTTAACCCGA
1 AAACTTCCAAAAATTCCATTTTTAACCC-A
*
1338 AAAC-TCTCAAAAATTCCATTTTT-ACCCTT
1 AAACTTC-CAAAAATTCCATTTTTAACCC-A
* ** * *
1367 AAACATAAAAAAATCCCATTTTTAACCCG
1 AAACTTCCAAAAATTCCATTTTTAACCCA
* *
1396 AAACTCCCAAAAATTCTATTTTTAA
1 AAACTTCCAAAAATTCCATTTTTAA
1421 ACCCTGGATC
Statistics
Matches: 456, Mismatches: 103, Indels: 51
0.75 0.17 0.08
Matches are distributed among these distances:
28 13 0.03
29 242 0.53
30 193 0.42
31 8 0.02
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTAACCCA
Found at i:2685 original size:6 final size:6
Alignment explanation
Indices: 2674--2737 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
2664 ATTTGTTTAG
* *
2674 AAATTT AAATTT ATA-TT AAATTT AAATTT --ATTT CGAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT
*
2720 -AATTT AAGTTT AAATTT A
1 AAATTT AAATTT AAATTT A
2738 TTTTCCAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.08
5 9 0.19
6 31 0.65
7 4 0.08
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:2696 original size:17 final size:16
Alignment explanation
Indices: 2642--2769 Score: 98
Period size: 17 Copynumber: 7.4 Consensus size: 16
2632 CCAAACTCCC
2642 TTTAAATTTATTTTAAGA
1 TTTAAATTTA-TTTAA-A
* *
2660 -ATAAATTTGTTTAGAAA
1 TTTAAATTTATTT--AAA
2677 TTTAAATTTATATTAAA
1 TTTAAATTTAT-TTAAA
*
2694 TTTAAATTTATTTCGAA
1 TTTAAATTTATTT-AAA
*
2711 TTTAAATTTAATTTAAG
1 TTTAAATTT-ATTTAAA
2728 TTTAAATTTATTTTCCAAA
1 TTTAAATTTA-TTT--AAA
2747 TTTAAGA-TTATTATAAA
1 TTTAA-ATTTATT-TAAA
2764 TTTAAA
1 TTTAAA
2770 ATAAATAAGG
Statistics
Matches: 91, Mismatches: 8, Indels: 24
0.74 0.07 0.20
Matches are distributed among these distances:
16 7 0.08
17 54 0.59
18 16 0.18
19 13 0.14
20 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:2718 original size:34 final size:35
Alignment explanation
Indices: 2642--2740 Score: 114
Period size: 34 Copynumber: 2.9 Consensus size: 35
2632 CCAAACTCCC
* * *
2642 TTTAAATTTATTTTAAGA-ATAAATTTGTTTAGAAA
1 TTTAAATTTATATTAA-ATTTAAATTTATTTAGAAA
*
2677 TTTAAATTTATATTAAATTTAAATTTATTTCG-AA
1 TTTAAATTTATATTAAATTTAAATTTATTTAGAAA
*
2711 TTTAAATTTA-ATTTAAGTTTAAATTTATTT
1 TTTAAATTTATA-TTAAATTTAAATTTATTT
2741 TCCAAATTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
33 1 0.02
34 30 0.53
35 26 0.46
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (35 bp):
TTTAAATTTATATTAAATTTAAATTTATTTAGAAA
Found at i:3544 original size:3 final size:3
Alignment explanation
Indices: 3538--3571 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
3528 AATATTTTCT
*
3538 TAA TAA TAA TAA TAA TAA TAA TAT TAA TGAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
3572 AAAAAACACG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Done.