Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012947.1 Kokia drynarioides strain JFW-HI SEQ_127965, 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: 28417
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 108 characters in sequence are not A, C, G, or T
Found at i:1384 original size:30 final size:29
Alignment explanation
Indices: 1350--1409 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
1340 CCTGCCAGAA
*
1350 GCAAATAA-AAGAGAAAAAAATTAAAAAAAT
1 GCAAATAATAA-A-AAAAAAATAAAAAAAAT
*
1380 GCAAATAATAAAACAAAAATAAAAAAAAT
1 GCAAATAATAAAAAAAAAATAAAAAAAAT
1409 G
1 G
1410 GCTAAAGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 16 0.59
30 9 0.33
31 2 0.07
ACGTcount: A:0.73, C:0.05, G:0.08, T:0.13
Consensus pattern (29 bp):
GCAAATAATAAAAAAAAAATAAAAAAAAT
Found at i:2455 original size:17 final size:17
Alignment explanation
Indices: 2435--2470 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2425 AATACATGAA
2435 AATCTCTAATTGGATCC
1 AATCTCTAATTGGATCC
*
2452 AATCTCTAGTTGGATCC
1 AATCTCTAATTGGATCC
2469 AA
1 AA
2471 ATTAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (17 bp):
AATCTCTAATTGGATCC
Found at i:6677 original size:17 final size:18
Alignment explanation
Indices: 6655--6701 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
6645 AAATACGCTC
6655 TCTCTTTGTTAT-CTCAT
1 TCTCTTTGTTATACTCAT
*
6672 TCTCTTTGTTCTTTACTCAT
1 TCTCTTTG-T-TATACTCAT
6692 TCTCTTTGTT
1 TCTCTTTGTT
6702 CTTTACTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 8 0.31
18 2 0.08
19 3 0.12
20 13 0.50
ACGTcount: A:0.09, C:0.23, G:0.06, T:0.62
Consensus pattern (18 bp):
TCTCTTTGTTATACTCAT
Found at i:6692 original size:20 final size:20
Alignment explanation
Indices: 6667--6709 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
6657 TCTTTGTTAT
6667 CTCATTCTCTTTGTTCTTTA
1 CTCATTCTCTTTGTTCTTTA
6687 CTCATTCTCTTTGTTCTTTA
1 CTCATTCTCTTTGTTCTTTA
6707 CTC
1 CTC
6710 TTTGTCCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.09, C:0.28, G:0.05, T:0.58
Consensus pattern (20 bp):
CTCATTCTCTTTGTTCTTTA
Found at i:7924 original size:72 final size:72
Alignment explanation
Indices: 7802--7946 Score: 272
Period size: 72 Copynumber: 2.0 Consensus size: 72
7792 AAGAGGAGAA
* *
7802 TTACATCACCAAGTTTATATTGAGGTCGGGATCGATCTGGATTCTGAACTAGGACCTTAATTTCT
1 TTACATCACCAAGTTTATATTGAGGTCGGGATCGATCTGGATGCTAAACTAGGACCTTAATTTCT
7867 ACTAACC
66 ACTAACC
7874 TTACATCACCAAGTTTATATTGAGGTCGGGATCGATCTGGATGCTAAACTAGGACCTTAATTTCT
1 TTACATCACCAAGTTTATATTGAGGTCGGGATCGATCTGGATGCTAAACTAGGACCTTAATTTCT
7939 ACTAACC
66 ACTAACC
7946 T
1 T
7947 GCGCACGGAA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (72 bp):
TTACATCACCAAGTTTATATTGAGGTCGGGATCGATCTGGATGCTAAACTAGGACCTTAATTTCT
ACTAACC
Found at i:8500 original size:24 final size:23
Alignment explanation
Indices: 8473--8518 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
8463 TCAGCCCGAC
*
8473 TAATTAATAGGGACTTTCAATTTA
1 TAATTAATA-GCACTTTCAATTTA
* *
8497 TAATTCATATCACTTTCAATTT
1 TAATTAATAGCACTTTCAATTT
8519 CAATTTCACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.46
Consensus pattern (23 bp):
TAATTAATAGCACTTTCAATTTA
Found at i:18122 original size:21 final size:21
Alignment explanation
Indices: 18098--18170 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
18088 TAGACCAGTT
18098 TATAGTGGTTTTTATCGATGA
1 TATAGTGGTTTTTATCGATGA
* * * *
18119 TATACTGGTTTATTCAAAGTCAAAGTT
1 TATAGTGGTTT-TT---A-TCGATG-A
18146 TATAGTGGTTTTTATCGATGA
1 TATAGTGGTTTTTATCGATGA
18167 TATA
1 TATA
18171 CTAGTTTATT
Statistics
Matches: 38, Mismatches: 8, Indels: 12
0.66 0.14 0.21
Matches are distributed among these distances:
21 14 0.37
22 6 0.16
23 1 0.03
25 1 0.03
26 6 0.16
27 10 0.26
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.45
Consensus pattern (21 bp):
TATAGTGGTTTTTATCGATGA
Found at i:18165 original size:48 final size:48
Alignment explanation
Indices: 18094--18192 Score: 189
Period size: 48 Copynumber: 2.1 Consensus size: 48
18084 TATTTAGACC
*
18094 AGTTTATAGTGGTTTTTATCGATGATATACTGGTTTATTCAAAGTCAA
1 AGTTTATAGTGGTTTTTATCGATGATATACTAGTTTATTCAAAGTCAA
18142 AGTTTATAGTGGTTTTTATCGATGATATACTAGTTTATTCAAAGTCAA
1 AGTTTATAGTGGTTTTTATCGATGATATACTAGTTTATTCAAAGTCAA
18190 AGT
1 AGT
18193 CAGAACATGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.43
Consensus pattern (48 bp):
AGTTTATAGTGGTTTTTATCGATGATATACTAGTTTATTCAAAGTCAA
Found at i:19098 original size:10 final size:10
Alignment explanation
Indices: 19083--19111 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
19073 GAAAAGAGAG
19083 ATGGTACAGA
1 ATGGTACAGA
19093 ATGGTACAGA
1 ATGGTACAGA
19103 ATGGTACAG
1 ATGGTACAG
19112 CAGAGAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.31, T:0.21
Consensus pattern (10 bp):
ATGGTACAGA
Found at i:25255 original size:23 final size:24
Alignment explanation
Indices: 25228--25272 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
25218 CTAATTAGGG
25228 AATTA-CTGTTTA-AATTTAATTCT
1 AATTATCT-TTTAGAATTTAATTCT
25251 AATTATCTTTTAGAATTTAATT
1 AATTATCTTTTAGAATTTAATT
25273 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (24 bp):
AATTATCTTTTAGAATTTAATTCT
Found at i:26143 original size:74 final size:74
Alignment explanation
Indices: 26022--26169 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
26012 GGAGTCTTTC
26022 CTGGGTATTATTTGTTTCTTGGTATTGAAACACTTGTTATTTCTTGCTTTAAACTTTGTTGCACT
1 CTGGGTATTATTTGTTTCTTGGTATTGAAACACTTGTTATTTCTTGCTTTAAACTTTGTTGCACT
26087 TTTAGTTTA
66 TTTAGTTTA
26096 CTGGGTATTATTTGTTTCTTGGTATTGAAACACTTGTTATTTCTTGCTTTAAACTTTGTTGCACT
1 CTGGGTATTATTTGTTTCTTGGTATTGAAACACTTGTTATTTCTTGCTTTAAACTTTGTTGCACT
26161 TTTAGTTTA
66 TTTAGTTTA
26170 TTAATTTAGT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.19, C:0.12, G:0.16, T:0.53
Consensus pattern (74 bp):
CTGGGTATTATTTGTTTCTTGGTATTGAAACACTTGTTATTTCTTGCTTTAAACTTTGTTGCACT
TTTAGTTTA
Found at i:26467 original size:29 final size:28
Alignment explanation
Indices: 26413--26467 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
26403 TACTTTAGCA
* *
26413 ATTTTTTTATTTTTGTTTTATTATTTGC
1 ATTTTTTTATTTTTCTTTTATAATTTGC
26441 ATTTTTTTAATTTTTCTATTT-TAATTT
1 ATTTTTTT-ATTTTTCT-TTTATAATTT
26468 TTTTCTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 8 0.35
29 12 0.52
30 3 0.13
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (28 bp):
ATTTTTTTATTTTTCTTTTATAATTTGC
Done.