Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002313.1 Kokia drynarioides strain JFW-HI SEQ_114356, 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: 17929
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:372 original size:58 final size:59
Alignment explanation
Indices: 280--416 Score: 188
Period size: 59 Copynumber: 2.3 Consensus size: 59
270 TTACAAAGGC
* **
280 AATTTTAGGAAAGTTTAGGGTCAAAATGTGATTTTGGG-AAGTTTAGGGGTTAAAATGT
1 AATTTTAGGAAAGTTTAGGGTCAAAATGTAATTTTGGGAAAGTTTAGGGGCCAAAATGT
* *
338 AATTTT-GGGAAGTTTAGGGGTCAAACTGTAATTTTGGGAAAGTTTAGGGGCCAAAATGT
1 AATTTTAGGAAAGTTTA-GGGTCAAAATGTAATTTTGGGAAAGTTTAGGGGCCAAAATGT
* *
397 AATTTTAGAAAATTTTAGGG
1 AATTTTAGGAAAGTTTAGGG
417 GCTAAAATAT
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
57 9 0.13
58 25 0.37
59 27 0.40
60 7 0.10
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (59 bp):
AATTTTAGGAAAGTTTAGGGTCAAAATGTAATTTTGGGAAAGTTTAGGGGCCAAAATGT
Found at i:383 original size:30 final size:30
Alignment explanation
Indices: 280--417 Score: 183
Period size: 29 Copynumber: 4.7 Consensus size: 30
270 TTACAAAGGC
*
280 AATTTTAGGAAAGTTTA-GGGTCAAAATGT
1 AATTTTGGGAAAGTTTAGGGGTCAAAATGT
* *
309 GATTTTGGG-AAGTTTAGGGGTTAAAATGT
1 AATTTTGGGAAAGTTTAGGGGTCAAAATGT
*
338 AATTTTGGG-AAGTTTAGGGGTCAAACTGT
1 AATTTTGGGAAAGTTTAGGGGTCAAAATGT
*
367 AATTTTGGGAAAGTTTAGGGGCCAAAATGT
1 AATTTTGGGAAAGTTTAGGGGTCAAAATGT
* * *
397 AATTTTAGAAAATTTTAGGGG
1 AATTTTGGGAAAGTTTAGGGG
418 CTAAAATATA
Statistics
Matches: 96, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
28 7 0.07
29 53 0.55
30 36 0.38
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.35
Consensus pattern (30 bp):
AATTTTGGGAAAGTTTAGGGGTCAAAATGT
Found at i:418 original size:30 final size:30
Alignment explanation
Indices: 280--441 Score: 181
Period size: 29 Copynumber: 5.5 Consensus size: 30
270 TTACAAAGGC
280 AATTTTAGGAAAGTTTA-GGGTCAAAATGT
1 AATTTTAGGAAAGTTTAGGGGTCAAAATGT
* * *
309 GATTTT-GGGAAGTTTAGGGGTTAAAATGT
1 AATTTTAGGAAAGTTTAGGGGTCAAAATGT
* *
338 AATTTT-GGGAAGTTTAGGGGTCAAACTGT
1 AATTTTAGGAAAGTTTAGGGGTCAAAATGT
* *
367 AATTTTGGGAAAGTTTAGGGGCCAAAATGT
1 AATTTTAGGAAAGTTTAGGGGTCAAAATGT
* * *
397 AATTTTAGAAAATTTTAGGGG-CTAAAATAT
1 AATTTTAGGAAAGTTTAGGGGTC-AAAATGT
*
427 ATTTTTA-GAAAGTTT
1 AATTTTAGGAAAGTTT
442 GAGGATTGCT
Statistics
Matches: 114, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
28 9 0.08
29 55 0.48
30 50 0.44
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (30 bp):
AATTTTAGGAAAGTTTAGGGGTCAAAATGT
Found at i:431 original size:59 final size:60
Alignment explanation
Indices: 280--441 Score: 181
Period size: 59 Copynumber: 2.8 Consensus size: 60
270 TTACAAAGGC
* * **
280 AATTTTAGGAAAGTTTAGGGTC-AAAATGTGATTTTGGG-AAGTTTAGGGGTTAAAATGT
1 AATTTTAGGAAAGTTTAGGGGCTAAAATGTAATTTTGGGAAAGTTTAGGGGCCAAAATGT
* *
338 AATTTT-GGGAAGTTTAGGGG-TCAAACTGTAATTTTGGGAAAGTTTAGGGGCCAAAATGT
1 AATTTTAGGAAAGTTTAGGGGCT-AAAATGTAATTTTGGGAAAGTTTAGGGGCCAAAATGT
* * * **
397 AATTTTAGAAAATTTTAGGGGCTAAAATAT-ATTTTTAGAAAGTTT
1 AATTTTAGGAAAGTTTAGGGGCTAAAATGTAATTTTGGGAAAGTTT
442 GAGGATTGCT
Statistics
Matches: 86, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
57 12 0.14
58 20 0.23
59 37 0.43
60 16 0.19
61 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (60 bp):
AATTTTAGGAAAGTTTAGGGGCTAAAATGTAATTTTGGGAAAGTTTAGGGGCCAAAATGT
Found at i:1606 original size:13 final size:13
Alignment explanation
Indices: 1588--1614 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1578 TTCATGTATT
1588 AATGATAATAATA
1 AATGATAATAATA
1601 AATGATAATAATA
1 AATGATAATAATA
1614 A
1 A
1615 TATATGACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (13 bp):
AATGATAATAATA
Found at i:2721 original size:19 final size:19
Alignment explanation
Indices: 2697--2736 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2687 TCCCCATAAG
2697 TCTATTCCAAAGCCTTCAC
1 TCTATTCCAAAGCCTTCAC
2716 TCTATTCCAAAGCCTTCAC
1 TCTATTCCAAAGCCTTCAC
2735 TC
1 TC
2737 GGGCCACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.38, G:0.05, T:0.33
Consensus pattern (19 bp):
TCTATTCCAAAGCCTTCAC
Found at i:5956 original size:19 final size:17
Alignment explanation
Indices: 5934--5980 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
5924 ATCATTATTT
*
5934 ATATTATAATTTTAAAATA
1 ATATTAT-ATATTAAAA-A
5953 ATA-TATATATTAAAAA
1 ATATTATATATTAAAAA
*
5969 ATATTTTATATT
1 ATATTATATATT
5981 TTTTTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 4 0.16
17 15 0.60
18 3 0.12
19 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATTATATATTAAAAA
Found at i:7987 original size:30 final size:30
Alignment explanation
Indices: 7913--8059 Score: 154
Period size: 29 Copynumber: 5.0 Consensus size: 30
7903 TAAAAATCCT
* * * *
7913 ATTTTGACACTCAAACTTTTCTAAAATTGC
1 ATTTTGACCCTTAAACTTTTCCAAAATTAC
* *
7943 A-TTTAACCCTTAAACTTTTCCAAAATTAT
1 ATTTTGACCCTTAAACTTTTCCAAAATTAC
* *
7972 ATTTTGACTCTTAAACTTTTCTAAAATTAC
1 ATTTTGACCCTTAAACTTTTCCAAAATTAC
* *
8002 ATTTTGACCC-TAAACTTTTACAAAAATAC
1 ATTTTGACCCTTAAACTTTTCCAAAATTAC
* ** *
8031 ATTTTAACCCCAAAACTTCTCCAAAATTA
1 ATTTTGACCCTTAAACTTTTCCAAAATTA
8060 TGATTTTGCC
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
29 48 0.50
30 48 0.50
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39
Consensus pattern (30 bp):
ATTTTGACCCTTAAACTTTTCCAAAATTAC
Found at i:7997 original size:59 final size:59
Alignment explanation
Indices: 7912--8035 Score: 169
Period size: 59 Copynumber: 2.1 Consensus size: 59
7902 TTAAAAATCC
* * *
7912 TATTTTGACACTCAAACTTTTCTAAAATTGCA-TTTAACCCTTAAACTTTTCCAAAATTA
1 TATTTTGACACTCAAACTTTTCTAAAATTACATTTTAACCC-TAAACTTTTACAAAAATA
* * *
7971 TATTTTGACTCTTAAACTTTTCTAAAATTACATTTTGACCCTAAACTTTTACAAAAATA
1 TATTTTGACACTCAAACTTTTCTAAAATTACATTTTAACCCTAAACTTTTACAAAAATA
*
8030 CATTTT
1 TATTTT
8036 AACCCCAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 50 0.88
60 7 0.12
ACGTcount: A:0.35, C:0.19, G:0.03, T:0.43
Consensus pattern (59 bp):
TATTTTGACACTCAAACTTTTCTAAAATTACATTTTAACCCTAAACTTTTACAAAAATA
Found at i:8047 original size:59 final size:59
Alignment explanation
Indices: 7925--8059 Score: 155
Period size: 59 Copynumber: 2.3 Consensus size: 59
7915 TTTGACACTC
* * * * * * **
7925 AAACTTTTCTAAAATTGCATTTAACCCTTAAACTTTTCCAAAATTATATTTTGACTCTT
1 AAACTTTTCTAAAATTACATTTAACCCTTAAACTTTTACAAAAATACATTTTAACCCCA
*
7984 AAACTTTTCTAAAATTACATTTTGACCC-TAAACTTTTACAAAAATACATTTTAACCCCA
1 AAACTTTTCTAAAATTACA-TTTAACCCTTAAACTTTTACAAAAATACATTTTAACCCCA
* *
8043 AAACTTCTCCAAAATTA
1 AAACTTTTCTAAAATTA
8060 TGATTTTGCC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 57 0.89
60 7 0.11
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.39
Consensus pattern (59 bp):
AAACTTTTCTAAAATTACATTTAACCCTTAAACTTTTACAAAAATACATTTTAACCCCA
Found at i:8085 original size:29 final size:29
Alignment explanation
Indices: 8053--8128 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
8043 AAACTTCTCC
* *
8053 AAAATTATGATTTTGCCTTCGAACATCCA
1 AAAATTATCATTTTGCCCTCGAACATCCA
8082 AAAATTATCATTTTGCCCTCGAACATCCA
1 AAAATTATCATTTTGCCCTCGAACATCCA
*
8111 AAAATTACCATTTTGCCC
1 AAAATTATCATTTTGCCC
8129 CTAAATTTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.33
Consensus pattern (29 bp):
AAAATTATCATTTTGCCCTCGAACATCCA
Found at i:9632 original size:45 final size:45
Alignment explanation
Indices: 9583--9676 Score: 179
Period size: 45 Copynumber: 2.1 Consensus size: 45
9573 TTTTTTAAAA
9583 AAAAAAAATTAAAACACATGTCGATGTTCTATTAGCTACTAGCAT
1 AAAAAAAATTAAAACACATGTCGATGTTCTATTAGCTACTAGCAT
*
9628 AAAAAAATTTAAAACACATGTCGATGTTCTATTAGCTACTAGCAT
1 AAAAAAAATTAAAACACATGTCGATGTTCTATTAGCTACTAGCAT
9673 AAAA
1 AAAA
9677 TTTAATGACG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.29
Consensus pattern (45 bp):
AAAAAAAATTAAAACACATGTCGATGTTCTATTAGCTACTAGCAT
Found at i:11219 original size:30 final size:30
Alignment explanation
Indices: 11162--11230 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
11152 ATGTGAGTTG
*
11162 TGAAAAA-TAATAATAAAATAATAAAAATA
1 TGAAAAAGTAATAAAAAAATAATAAAAATA
*
11191 TGAAAAAGTAA-AAAAAAATTATTAAAAATA
1 TGAAAAAGTAATAAAAAAA-TAATAAAAATA
*
11221 AGAAACAAGT
1 TGAAA-AAGT
11231 TATTTGGGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.38
30 17 0.50
31 4 0.12
ACGTcount: A:0.70, C:0.01, G:0.07, T:0.22
Consensus pattern (30 bp):
TGAAAAAGTAATAAAAAAATAATAAAAATA
Found at i:13557 original size:15 final size:15
Alignment explanation
Indices: 13533--13566 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
13523 TAAAGCGTAG
*
13533 TGGTAATGTTTTGAT
1 TGGTAATGTTTTGAA
*
13548 TGGTAGTGTTTTGAA
1 TGGTAATGTTTTGAA
13563 TGGT
1 TGGT
13567 TGAATCTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (15 bp):
TGGTAATGTTTTGAA
Found at i:15477 original size:2 final size:2
Alignment explanation
Indices: 15470--15499 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15460 GAAAACAATC
15470 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15500 TAAAAATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.