Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013260.1 Kokia drynarioides strain JFW-HI SEQ_128281, 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: 8709
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Warning! 65 characters in sequence are not A, C, G, or T
Found at i:1140 original size:59 final size:59
Alignment explanation
Indices: 1048--1391 Score: 439
Period size: 59 Copynumber: 5.8 Consensus size: 59
1038 GTCCCTGAAC
*
1048 CTTCCAAAAATTACCGTTTTACCC-CTGAATTCCCAAAAATCCCATTTTTGACCCCAAAG
1 CTTCCAAAAATTACCGTTTTACCCTC-GAATTCCCAAAAATCCCATTTTTGACCCCGAAG
*
1107 CTTCCAAAAATTACCGTTTTACCCTCAAATTCCCAAAAAATCCCATTTTTGACCCCGAAG
1 CTTCCAAAAATTACCGTTTTACCCTCGAATTCCC-AAAAATCCCATTTTTGACCCCGAAG
* * *
1167 CTTCC-AAAATTATCGTTTTACCCCCGAATTCCCAAAAATCCCATTTTTGACCCCTAAG
1 CTTCCAAAAATTACCGTTTTACCCTCGAATTCCCAAAAATCCCATTTTTGACCCCGAAG
* * * *
1225 CTTCCAAAAATTACCGTTTTACCCTTGAATTCCCAAAAATCTCATTTTTTTTACCTCGAAG
1 CTTCCAAAAATTACCGTTTTACCCTCGAATTCCCAAAAATCCCA--TTTTTGACCCCGAAG
* * * * *
1286 CTTCC-AAAATTACCATATTACCCGCGAACTT-CCAAAAATCCCATTTTTAACCCCGAAT
1 CTTCCAAAAATTACCGTTTTACCCTCGAA-TTCCCAAAAATCCCATTTTTGACCCCGAAG
* *
1344 CTTCCAAAAATTACCGTTTTATCCC-CGAACTT-CCAAAATTACCATTTT
1 CTTCCAAAAATTACCGTTTTA-CCCTCGAA-TTCCCAAAAATCCCATTTT
1392 ACCCTCGAGT
Statistics
Matches: 252, Mismatches: 25, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
58 46 0.18
59 124 0.49
60 63 0.25
61 19 0.08
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.31
Consensus pattern (59 bp):
CTTCCAAAAATTACCGTTTTACCCTCGAATTCCCAAAAATCCCATTTTTGACCCCGAAG
Found at i:1202 original size:118 final size:118
Alignment explanation
Indices: 1048--1364 Score: 458
Period size: 119 Copynumber: 2.7 Consensus size: 118
1038 GTCCCTGAAC
*
1048 CTTCCAAAAATTACCGTTTTACCCCTGAATTCCCAAAAATCCCATTTTTGACCCCAAAGCTTCCA
1 CTTCC-AAAATTACCGTTTTACCCCCGAATTCCCAAAAATCCCATTTTTGACCCCAAAGCTTCCA
1113 AAAATTACCGTTTTACCCTCAAATTCCCAAAAAATCCCA-TTTTTGACCCCGAAG
65 AAAATTACCGTTTTACCCTCAAATTCCC-AAAAATCCCATTTTTTGACCCCGAAG
* *
1167 CTTCCAAAATTATCGTTTTACCCCCGAATTCCCAAAAATCCCATTTTTGACCCCTAAGCTTCCAA
1 CTTCCAAAATTACCGTTTTACCCCCGAATTCCCAAAAATCCCATTTTTGACCCCAAAGCTTCCAA
** * * *
1232 AAATTACCGTTTTACCCTTGAATTCCCAAAAATCTCATTTTTTTTACCTCGAAG
66 AAATTACCGTTTTACCCTCAAATTCCCAAAAATCCCA-TTTTTTGACCCCGAAG
* * * * * *
1286 CTTCCAAAATTACCATATTACCCGCGAACTT-CCAAAAATCCCATTTTTAACCCCGAATCTTCCA
1 CTTCCAAAATTACCGTTTTACCCCCGAA-TTCCCAAAAATCCCATTTTTGACCCCAAAGCTTCCA
1350 AAAATTACCGTTTTA
65 AAAATTACCGTTTTA
1365 TCCCCGAACT
Statistics
Matches: 180, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
117 9 0.05
118 82 0.46
119 87 0.48
120 2 0.01
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.31
Consensus pattern (118 bp):
CTTCCAAAATTACCGTTTTACCCCCGAATTCCCAAAAATCCCATTTTTGACCCCAAAGCTTCCAA
AAATTACCGTTTTACCCTCAAATTCCCAAAAATCCCATTTTTTGACCCCGAAG
Found at i:1273 original size:29 final size:29
Alignment explanation
Indices: 1064--1273 Score: 96
Period size: 30 Copynumber: 7.1 Consensus size: 29
1054 AAAATTACCG
* *
1064 TTTTACCCCTGAATTCCCAAAAATCCCAT
1 TTTTACCCCCGAATTCCCAAAAATCTCAT
* **
1093 TTTTGA-CCCCAAAGCTT-CCAAAAAT-TACCG
1 TTTT-ACCCCCGAA--TTCCCAAAAATCT-CAT
* * *
1123 TTTTACCCTCAAATTCCCAAAAAATCCCAT
1 TTTTACCCCCGAATTCCC-AAAAATCTCAT
* * *
1153 TTTTGA-CCCCGAAGCTT-CCAAAATTATC-G
1 TTTT-ACCCCCGAA--TTCCCAAAAATCTCAT
*
1182 TTTTACCCCCGAATTCCCAAAAATCCCAT
1 TTTTACCCCCGAATTCCCAAAAATCTCAT
* **
1211 TTTTGA-CCCCTAAGCTT-CCAAAAAT-TACCG
1 TTTT-ACCCCCGAA--TTCCCAAAAATCT-CAT
**
1241 TTTTACCCTTGAATTCCCAAAAATCTCAT
1 TTTTACCCCCGAATTCCCAAAAATCTCAT
1270 TTTT
1 TTTT
1274 TTTACCTCGA
Statistics
Matches: 132, Mismatches: 28, Indels: 42
0.65 0.14 0.21
Matches are distributed among these distances:
27 2 0.02
28 13 0.10
29 47 0.36
30 61 0.46
31 7 0.05
32 2 0.02
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.32
Consensus pattern (29 bp):
TTTTACCCCCGAATTCCCAAAAATCTCAT
Found at i:1307 original size:28 final size:28
Alignment explanation
Indices: 1273--1395 Score: 131
Period size: 28 Copynumber: 4.3 Consensus size: 28
1263 ATCTCATTTT
*
1273 TTTTA-CCTCGAAGCTTCCAAAATTACCA
1 TTTTACCCCCGAA-CTTCCAAAATTACCA
* * * *
1301 TATTACCCGCGAACTTCCAAAAATCCCA
1 TTTTACCCCCGAACTTCCAAAATTACCA
* *
1329 TTTTTAACCCCGAATCTTCCAAAAATTACCG
1 -TTTTACCCCCGAA-CTTCC-AAAATTACCA
*
1360 TTTTATCCCCGAACTTCCAAAATTACCA
1 TTTTACCCCCGAACTTCCAAAATTACCA
1388 TTTTACCC
1 TTTTACCC
1396 TCGAGTTGCT
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
28 33 0.42
29 21 0.27
30 17 0.22
31 7 0.09
ACGTcount: A:0.32, C:0.32, G:0.06, T:0.31
Consensus pattern (28 bp):
TTTTACCCCCGAACTTCCAAAATTACCA
Found at i:1324 original size:29 final size:28
Alignment explanation
Indices: 1048--1395 Score: 169
Period size: 29 Copynumber: 11.8 Consensus size: 28
1038 GTCCCTGAAC
*
1048 CTTCCAAAAATTACCGTTTTACCCCTGAA-
1 CTTCC-AAAATTACCATTTTACCCC-GAAG
* * *
1077 -TTCCCAAAAATCCCATTTTTGACCCCAAAG
1 CTT-CCAAAATTACCA-TTTT-ACCCCGAAG
*
1107 CTTCCAAAAATTACCGTTTTACCCTC-AA-
1 CTTCC-AAAATTACCATTTTACCC-CGAAG
* * *
1135 ATTCCCAAAAAATCCCATTTTTGACCCCGAAG
1 CTT-CC-AAAATTACCA-TTTT-ACCCCGAAG
* *
1167 CTTCCAAAATTATCGTTTTACCCCCGAA-
1 CTTCCAAAATTACCATTTTA-CCCCGAAG
* * *
1195 -TTCCCAAAAATCCCATTTTTGACCCCTAAG
1 CTT-CCAAAATTACCA-TTTT-ACCCCGAAG
* *
1225 CTTCCAAAAATTACCGTTTTACCCTTGAA-
1 CTTCC-AAAATTACCATTTTACCC-CGAAG
* *
1254 -TTCCCAAAAAT-CTCATTTTTTTTACCTCGAAG
1 CTT-CCAAAATTAC-CA----TTTTACCCCGAAG
*
1286 CTTCCAAAATTACCATATTACCCGCGAA-
1 CTTCCAAAATTACCATTTTACCC-CGAAG
* * *
1314 CTTCCAAAAATCCCATTTTTAACCCCGAAT
1 CTTCCAAAATTACCA-TTTT-ACCCCGAAG
*
1344 CTTCCAAAAATTACCGTTTTATCCCCGAA-
1 CTTCC-AAAATTACCATTTTA-CCCCGAAG
1373 CTTCCAAAATTACCATTTTACCC
1 CTTCCAAAATTACCATTTTACCC
1396 TCGAGTTGCT
Statistics
Matches: 244, Mismatches: 40, Indels: 72
0.69 0.11 0.20
Matches are distributed among these distances:
27 6 0.02
28 61 0.25
29 68 0.28
30 52 0.21
31 36 0.15
32 18 0.07
33 3 0.01
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.31
Consensus pattern (28 bp):
CTTCCAAAATTACCATTTTACCCCGAAG
Found at i:3622 original size:21 final size:21
Alignment explanation
Indices: 3577--3623 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3567 ATGCCTCAAT
* *
3577 TTGCTTTTGAAAATCTGCAGT
1 TTGCTTTTGAAAATCTACAGA
*
3598 TTGCTTTTGAAAATCTATAGA
1 TTGCTTTTGAAAATCTACAGA
3619 TTGCT
1 TTGCT
3624 GCTGAAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45
Consensus pattern (21 bp):
TTGCTTTTGAAAATCTACAGA
Found at i:6690 original size:21 final size:21
Alignment explanation
Indices: 6664--6737 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
6654 AATGCAGACC
6664 TCTACCGATACAAGTAATAGT
1 TCTACCGATACAAGTAATAGT
* * *
6685 TCTACCAATACAAGTGACAGT
1 TCTACCGATACAAGTAATAGT
** *
6706 TCTACCGATACAAGTCTTACT
1 TCTACCGATACAAGTAATAGT
6727 TCTACCGATAC
1 TCTACCGATAC
6738 CAAAAACTCC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (21 bp):
TCTACCGATACAAGTAATAGT
Found at i:7580 original size:52 final size:52
Alignment explanation
Indices: 7462--7647 Score: 250
Period size: 52 Copynumber: 3.6 Consensus size: 52
7452 ATTTCATTTA
* * *
7462 ATACTCACGATGACACATAGTCATCGGACCT-TTAAATCCAT-TAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCAT-AATCCGTAAAGGATTCAT
* * * **
7513 ATACTCACGATGACACATAGTCATTGGATCTCATATTTTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
7565 ATACTCATGATGACACATAATCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
7617 ATACTCACGATGACACATAGTCATCGAACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
7648 TTTTGCATTT
Statistics
Matches: 115, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
51 32 0.28
52 83 0.72
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Done.