Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012253.1 Kokia drynarioides strain JFW-HI SEQ_127254, 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: 4802
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.27
Warning! 82 characters in sequence are not A, C, G, or T
Found at i:1382 original size:218 final size:218
Alignment explanation
Indices: 1114--1893 Score: 1265
Period size: 218 Copynumber: 3.6 Consensus size: 218
1104 NNNNNNNNNN
1114 GAAGTGAATTGAAACAAACGACGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCGAATCA
1 GAAGTGAATTGAAACAAACGACGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCGAATCA
*
1179 AACCCATGCTCGATGTGAGCAAATCTTCAAACCACAGCTTCCTGATGAGATACTGAGAAGCGTGC
66 AACCCATGCTCGATGTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCGTGC
* * *
1244 CGAAGTAATAAAACGATTAGCTTCCGGATCATATTCCTGATGAGGTACGGAGAAGTGGACCAAAT
131 CGAAGTAATAAAACGGTTAGCTTCCGGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAAT
1309 TCATCTTCTTGATGAGATACAGA
196 TCATCTTCTTGATGAGATACAGA
* *
1332 GAAGTGAATTGAAACAAACAACGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCGAATTA
1 GAAGTGAATTGAAACAAACGACGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCGAATCA
1397 AACCCATGCTCGATGTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCGTGC
66 AACCCATGCTCGATGTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCGTGC
* *
1462 CGAAGTAATAAAACGGTTAGCTTCTGGACCATCTTCTTGATGAGGTACGGAGAAGTGGACCAAAT
131 CGAAGTAATAAAACGGTTAGCTTCCGGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAAT
1527 TCATCTTCTTGATGAGATACAGA
196 TCATCTTCTTGATGAGATACAGA
1550 GAAGTGAATTGAAACAAACGACGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCGAATCA
1 GAAGTGAATTGAAACAAACGACGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCGAATCA
* * * * * *
1615 AACCCATGCTCGATGTGAGAAAATATTCGAACCACAACTTCCTGATGAGATACTGAGAAACATGT
66 AACCCATGCTCGATGTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCGTGC
* * * * *
1680 TGAAGTAATAAAACGGTTAGCTTCCTGACCATCTTCCTGATGAGGTACGAAAAAGTGGGCCAAAT
131 CGAAGTAATAAAACGGTTAGCTTCCGGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAAT
* *
1745 TCGTCTTCCTGATGAGATACAGA
196 TCATCTTCTTGATGAGATACAGA
* *
1768 GAAGTGAATTGAAACAAACGACGCCGTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAATCA
1 GAAGTGAATTGAAACAAACGACGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCGAATCA
* * * * * * * *
1833 AACTCACGC-CTGATGTAACCAAATCTTCGAACCCCAGCTTCCTGGTGATACACTGAGAAGC
66 AACCCATGCTC-GATGTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGC
1894 AAGTAATGAA
Statistics
Matches: 522, Mismatches: 39, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
217 1 0.00
218 521 1.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (218 bp):
GAAGTGAATTGAAACAAACGACGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCGAATCA
AACCCATGCTCGATGTGAGCAAATCTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCGTGC
CGAAGTAATAAAACGGTTAGCTTCCGGACCATCTTCCTGATGAGGTACGGAGAAGTGGACCAAAT
TCATCTTCTTGATGAGATACAGA
Found at i:2379 original size:17 final size:17
Alignment explanation
Indices: 2356--2429 Score: 87
Period size: 17 Copynumber: 4.2 Consensus size: 17
2346 CAAACTCCCC
2356 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
* *
2374 -TTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
2391 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
2408 TTTAAATTTAAGTTTAAA
1 TTTAAATTT-ATTTTAAA
2426 TTTA
1 TTTA
2430 TTATCAAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
17 24 0.50
18 24 0.50
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:2397 original size:35 final size:36
Alignment explanation
Indices: 2356--2425 Score: 108
Period size: 35 Copynumber: 1.9 Consensus size: 36
2346 CAAACTCCCC
2356 TTTAAATTTATTTTAAGA-TTAAATTT-GTTTAAAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTAGTTTAAAAA
2391 TTTAAATTTATTTTAAATTTAAATTTAAGTTTAAA
1 TTTAAATTTATTTTAAATTTAAATTT-AGTTTAAA
2426 TTTATTATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
34 1 0.03
35 24 0.75
37 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (36 bp):
TTTAAATTTATTTTAAATTTAAATTTAGTTTAAAAA
Found at i:2399 original size:6 final size:6
Alignment explanation
Indices: 2388--2429 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
2378 ATTTGTTTAA
* *
2388 AAATTT AAATTT -ATTTT AAATTT AAATTT AAGTTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT A
2430 TTATCAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:2427 original size:47 final size:47
Alignment explanation
Indices: 2356--2460 Score: 124
Period size: 47 Copynumber: 2.3 Consensus size: 47
2346 CAAACTCCCC
* * *
2356 TTTAAATTT-ATTTTAAGATTAAATTTGTT-TAAAAATTTAAATTTAT
1 TTTAAATTTAAATTTAAGATTAAATTTATTAT-AAAATTTAAAATTAT
* *
2402 TTTAAATTTAAATTTAAGTTTAAATTTATTATCAAATTTAAAATTAT
1 TTTAAATTTAAATTTAAGATTAAATTTATTATAAAATTTAAAATTAT
* *
2449 TATGAATTTAAA
1 TTTAAATTTAAA
2461 ATAAATAAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
46 9 0.18
47 40 0.80
48 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (47 bp):
TTTAAATTTAAATTTAAGATTAAATTTATTATAAAATTTAAAATTAT
Found at i:2458 original size:17 final size:18
Alignment explanation
Indices: 2420--2462 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2410 TAAATTTAAG
*
2420 TTTAAATTTATTATCAAA
1 TTTAAAATTATTATCAAA
*
2438 TTTAAAATTATTAT-GAA
1 TTTAAAATTATTATCAAA
2455 TTTAAAAT
1 TTTAAAAT
2463 AAATAAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TTTAAAATTATTATCAAA
Found at i:3188 original size:3 final size:3
Alignment explanation
Indices: 3182--3242 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
3172 ATTATATTAT
* * *
3182 TAA TAA TAT TTA T-A TAA TAA TAA TTAA CAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
* * *
3227 TGA CAC TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
3243 TTTTAATAGT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:4371 original size:29 final size:30
Alignment explanation
Indices: 4311--4392 Score: 121
Period size: 29 Copynumber: 2.7 Consensus size: 30
4301 CCCTAGATTG
*
4311 TCCAAAAATCTCATTTTTTAACCTCGAAACT
1 TCCAAAAATCTCA-TTTTTAACCCCGAAACT
*
4342 TCCAAAAATCTCATTTTTACCCCCG-AACT
1 TCCAAAAATCTCATTTTTAACCCCGAAACT
*
4371 TCCAAAAATCCCATTTTTAACC
1 TCCAAAAATCTCATTTTTAACC
4393 TTAAAAATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
29 24 0.51
30 10 0.21
31 13 0.28
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.33
Consensus pattern (30 bp):
TCCAAAAATCTCATTTTTAACCCCGAAACT
Found at i:4528 original size:29 final size:29
Alignment explanation
Indices: 4405--4556 Score: 139
Period size: 29 Copynumber: 5.2 Consensus size: 29
4395 AAAAATTCTA
* * *
4405 TACCCCTAAACTTTCAAAAATCTCATTTT
1 TACCCCGAAACTTCCAAAAATCCCATTTT
* * * * *
4434 TACCTCAAAACTTTCAAAAATTCTATTTT
1 TACCCCGAAACTTCCAAAAATCCCATTTT
4463 TACCCCCG-AACTTCCAAAAA-CACCATTTT
1 TA-CCCCGAAACTTCCAAAAATC-CCATTTT
4492 TAACCCCGAAACTTCCAAAAATCCCATTTT
1 T-ACCCCGAAACTTCCAAAAATCCCATTTT
** * *
4522 TACCCCGAATTTTCCCAAAATTACCA-TTT
1 TACCCCGAAACTT-CCAAAAATCCCATTTT
4551 TACCCC
1 TACCCC
4557 CGGAGATCCG
Statistics
Matches: 103, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
29 68 0.66
30 34 0.33
31 1 0.01
ACGTcount: A:0.34, C:0.32, G:0.02, T:0.32
Consensus pattern (29 bp):
TACCCCGAAACTTCCAAAAATCCCATTTT
Done.