Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007880.1 Kokia drynarioides strain JFW-HI SEQ_122521, 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: 35465
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:2164 original size:19 final size:19
Alignment explanation
Indices: 2119--2164 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
2109 GTATGATATC
*
2119 TTTTTAAAATCGTATTTTA
1 TTTTTAAAATCGTATTTAA
*
2138 TTTATTAAAATCTTATTTAA
1 TTT-TTAAAATCGTATTTAA
2158 TTTTTAA
1 TTTTTAA
2165 TAGATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTTAAAATCGTATTTAA
Found at i:5410 original size:28 final size:28
Alignment explanation
Indices: 5371--5448 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
5361 CCCTCCTTAA
5371 TCAA-TCTAGTGTTTACGGTTTAGAGTT
1 TCAAGTCTAGTGTTTACGGTTTAGAGTT
* * *
5398 TCAAGTCTAGTGTTTATGATTTAGGGTT
1 TCAAGTCTAGTGTTTACGGTTTAGAGTT
* * *
5426 TGAAGTTTAG-GTTTTAGGGTTTA
1 TCAAGTCTAGTG-TTTACGGTTTA
5449 ATGTTATGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 5 0.12
28 37 0.88
ACGTcount: A:0.22, C:0.06, G:0.26, T:0.46
Consensus pattern (28 bp):
TCAAGTCTAGTGTTTACGGTTTAGAGTT
Found at i:5818 original size:45 final size:45
Alignment explanation
Indices: 5705--5839 Score: 189
Period size: 45 Copynumber: 3.0 Consensus size: 45
5695 GGGAGGAATA
* * ** **
5705 GAGTATTGTGGTGGCTCGTCAAACTCAGAATGATATCCTTCCCTT
1 GAGTATTGTGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTT
*
5750 GAGTATTATGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTT
1 GAGTATTGTGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTT
* *
5795 GAGTATTGCGGTGGCTCGTCAAATTGAGGCTGATATCTTTGGCTT
1 GAGTATTGTGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTT
5840 AATGAGCTAT
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 80 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (45 bp):
GAGTATTGTGGTGGCTCGTCAAATTGAGGCTGATATCCTTGGCTT
Found at i:8105 original size:13 final size:13
Alignment explanation
Indices: 8087--8111 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8077 ATAATCTAAT
8087 ATTTTTTTAATTA
1 ATTTTTTTAATTA
8100 ATTTTTTTAATT
1 ATTTTTTTAATT
8112 TCATATTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTTTAATTA
Found at i:8326 original size:20 final size:21
Alignment explanation
Indices: 8301--8343 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
8291 TACTTACTAC
8301 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
8321 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
8342 TA
1 TA
8344 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:8731 original size:17 final size:17
Alignment explanation
Indices: 8709--8755 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
8699 TCCCCTTATT
8709 TTTCTTTTTCCTTCTTC
1 TTTCTTTTTCCTTCTTC
* *
8726 TTTCTTTCTTTC-TCTTT
1 TTTCTTT-TTCCTTCTTC
8743 TTTC-TTTTCCTTC
1 TTTCTTTTTCCTTC
8756 AATTTTCGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.12
16 4 0.16
17 15 0.60
18 3 0.12
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTCTTTTTCCTTCTTC
Found at i:8747 original size:21 final size:21
Alignment explanation
Indices: 8709--8749 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
8699 TCCCCTTATT
*
8709 TTTCTTTTTCCTTCTTCTTTC
1 TTTCTTTCTCCTTCTTCTTTC
* *
8730 TTTCTTTCTCTTTTTTCTTT
1 TTTCTTTCTCCTTCTTCTTT
8750 TCCTTCAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTCTTTCTCCTTCTTCTTTC
Found at i:15988 original size:25 final size:25
Alignment explanation
Indices: 15954--16008 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
15944 GATGAAACCG
15954 GCCAAAACGGGTATTTCTTTAGTCC
1 GCCAAAACGGGTATTTCTTTAGTCC
15979 GCCAAAACGGGTATTTCTTTAGTCC
1 GCCAAAACGGGTATTTCTTTAGTCC
16004 GCCAA
1 GCCAA
16009 TTATAGCGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (25 bp):
GCCAAAACGGGTATTTCTTTAGTCC
Found at i:19909 original size:24 final size:24
Alignment explanation
Indices: 19851--19909 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
19841 ACATTCCGAT
*
19851 CATCCCGTAATTTCACATTCTAAC
1 CATCCCGTAATCTCACATTCTAAC
* * *
19875 AATCTCATAATCTCACATTAC-AAC
1 CATCCCGTAATCTCACATT-CTAAC
19899 CATCCCGTAAT
1 CATCCCGTAAT
19910 ATAAGGTGTA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (24 bp):
CATCCCGTAATCTCACATTCTAAC
Found at i:22645 original size:2 final size:2
Alignment explanation
Indices: 22638--22665 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22628 TGAAATTTGG
22638 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
22666 AAGTTATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29529 original size:35 final size:35
Alignment explanation
Indices: 29483--29555 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
29473 ACAAAACTAC
*
29483 GTCGTTTTAATAATTGTTTATCCATCAAGCTAAAA
1 GTCGTTCTAATAATTGTTTATCCATCAAGCTAAAA
29518 GTCGTTCTAATAATTGTTTATCCATCAAGCTAAAA
1 GTCGTTCTAATAATTGTTTATCCATCAAGCTAAAA
29553 GTC
1 GTC
29556 AAGACCATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (35 bp):
GTCGTTCTAATAATTGTTTATCCATCAAGCTAAAA
Done.