Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001763.1 Kokia drynarioides strain JFW-HI SEQ_113484, 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: 48934
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:756 original size:17 final size:19
Alignment explanation
Indices: 734--770 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
724 ATATTAGTTG
734 ATGCAT-TAAAATTT-TCA
1 ATGCATATAAAATTTGTCA
*
751 ATGCATATATAATTTGTCA
1 ATGCATATAAAATTTGTCA
770 A
1 A
771 CATATACACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (19 bp):
ATGCATATAAAATTTGTCA
Found at i:1945 original size:60 final size:60
Alignment explanation
Indices: 1791--1961 Score: 202
Period size: 59 Copynumber: 2.9 Consensus size: 60
1781 TTAATATAAC
* * ** * * *
1791 ATTTGGTACTTGAATTTGACATTTTTTCCCTAATTTGATA-CTTAACTTTTTTTGACCCA
1 ATTTGGTACCTGAAATTGACATTTTTTTTCTAATTTGGTACCTAAACTTTTTTTAACCCA
* * * * *
1850 GTTTGGTTCCTGAACTTGGCACTTTTTTT-TAATTTGGTACCTAAACTTTTTTTAACCCA
1 ATTTGGTACCTGAAATTGACATTTTTTTTCTAATTTGGTACCTAAACTTTTTTTAACCCA
* *
1909 ATTTGGTACCTAAAATTGACATTTTTTTTCTAATTTGGTACCTAAGCTTTTTT
1 ATTTGGTACCTGAAATTGACATTTTTTTTCTAATTTGGTACCTAAACTTTTTT
1962 AAGATTCAAT
Statistics
Matches: 92, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
58 9 0.10
59 61 0.66
60 22 0.24
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.49
Consensus pattern (60 bp):
ATTTGGTACCTGAAATTGACATTTTTTTTCTAATTTGGTACCTAAACTTTTTTTAACCCA
Found at i:2700 original size:20 final size:19
Alignment explanation
Indices: 2665--2702 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2655 GACCATTTAC
*
2665 TTGACCATTGATTTTTTTG
1 TTGACCATTGACTTTTTTG
2684 TTGACCAATTGACTTTTTT
1 TTGACC-ATTGACTTTTTT
2703 CGGAAAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.55
Consensus pattern (19 bp):
TTGACCATTGACTTTTTTG
Found at i:4571 original size:36 final size:36
Alignment explanation
Indices: 4524--4601 Score: 147
Period size: 36 Copynumber: 2.2 Consensus size: 36
4514 AAATTAAGCT
4524 AACATTGTTGTAAACAAGAACAAAGAACAAATAGCA
1 AACATTGTTGTAAACAAGAACAAAGAACAAATAGCA
*
4560 AACATTGTTGTAAACAAGAACAAAGAACAAATAGCG
1 AACATTGTTGTAAACAAGAACAAAGAACAAATAGCA
4596 AACATT
1 AACATT
4602 TTAAGATTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.18
Consensus pattern (36 bp):
AACATTGTTGTAAACAAGAACAAAGAACAAATAGCA
Found at i:8935 original size:28 final size:29
Alignment explanation
Indices: 8900--8954 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
8890 GTTTATTAAC
*
8900 ATAAAAATTAAAATT-AAAATTTTAAACA
1 ATAAAAATGAAAATTAAAAATTTTAAACA
*
8928 ATAAAAATGAAACTTAAAAATTTTAAA
1 ATAAAAATGAAAATTAAAAATTTTAAA
8955 ACTTAATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (29 bp):
ATAAAAATGAAAATTAAAAATTTTAAACA
Found at i:16141 original size:2 final size:2
Alignment explanation
Indices: 16136--16166 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16126 ATAATTTCTT
16136 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
16167 GTATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:21051 original size:35 final size:35
Alignment explanation
Indices: 21005--21191 Score: 252
Period size: 35 Copynumber: 5.3 Consensus size: 35
20995 GAGCTTTGCT
* * *
21005 TTGCTTACGTCTCGCTTAGAGTGTAAGGTTATGCA
1 TTGCTTACGTCTCGATTAGAGCGTAAGGTTATGGA
21040 TTGCTTACGTCTCGATTAGAGCGTAAGGTTATGGA
1 TTGCTTACGTCTCGATTAGAGCGTAAGGTTATGGA
*
21075 TTGCTTACGTCTC-AGTTAGAGCGTAAGGTTATGAA
1 TTGCTTACGTCTCGA-TTAGAGCGTAAGGTTATGGA
* * * * *
21110 TTACTTACATCTCGGTTAGAGCGCAATGTTAT-GA
1 TTGCTTACGTCTCGATTAGAGCGTAAGGTTATGGA
*
21144 GTTGCTTATGTCTCGATTAGAGCGTAAGGTTATGGA
1 -TTGCTTACGTCTCGATTAGAGCGTAAGGTTATGGA
21180 TTGCTTACGTCT
1 TTGCTTACGTCT
21192 TAGAGCATAA
Statistics
Matches: 131, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
34 2 0.02
35 127 0.97
36 2 0.02
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (35 bp):
TTGCTTACGTCTCGATTAGAGCGTAAGGTTATGGA
Found at i:26153 original size:17 final size:17
Alignment explanation
Indices: 26127--26163 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
26117 TATTATCTAT
*
26127 TTAATCAATTAAATTAA
1 TTAATCAATTAAATAAA
*
26144 TTAATTAATTAAATAAA
1 TTAATCAATTAAATAAA
26161 TTA
1 TTA
26164 TTTCTCAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATCAATTAAATAAA
Found at i:26178 original size:16 final size:17
Alignment explanation
Indices: 26157--26188 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
26147 ATTAATTAAA
26157 TAAATTA-TTTCTCAAT
1 TAAATTATTTTCTCAAT
26173 TAAATTATTTTCTCAA
1 TAAATTATTTTCTCAA
26189 CCCAATCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATTATTTTCTCAAT
Found at i:33291 original size:16 final size:15
Alignment explanation
Indices: 33266--33300 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
33256 TCTTAGATAT
33266 AAAA-TAAATAAATA
1 AAAATTAAATAAATA
33280 GAAAATTAAATAAATA
1 -AAAATTAAATAAATA
33296 AAAAT
1 AAAAT
33301 AAAAATTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
AAAATTAAATAAATA
Found at i:33304 original size:20 final size:20
Alignment explanation
Indices: 33267--33304 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33257 CTTAGATATA
*
33267 AAATAAATAAATAGAAAATT
1 AAATAAATAAAAAGAAAATT
*
33287 AAATAAATAAAAATAAAA
1 AAATAAATAAAAAGAAAA
33305 ATTGGGTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (20 bp):
AAATAAATAAAAAGAAAATT
Found at i:33306 original size:16 final size:16
Alignment explanation
Indices: 33266--33304 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
33256 TCTTAGATAT
33266 AAAAT-AAATAAATAG
1 AAAATAAAATAAATAG
*
33281 AAAATTAAATAAATA-
1 AAAATAAAATAAATAG
33296 AAAATAAAA
1 AAAATAAAA
33305 ATTGGGTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAATAAAATAAATAG
Found at i:41520 original size:24 final size:24
Alignment explanation
Indices: 41467--41521 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
41457 TCACGAGAAG
*
41467 ATGCTGTCCGAAAATGATAATTATT
1 ATGCTGTCCGAAAATGA-AATTATA
41492 ATGCTGTCC-AAAATTG-AATTATA
1 ATGCTGTCCGAAAA-TGAAATTATA
41515 ATTGCTG
1 A-TGCTG
41522 CCTTAATGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 7 0.26
24 9 0.33
25 11 0.41
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (24 bp):
ATGCTGTCCGAAAATGAAATTATA
Found at i:45027 original size:26 final size:26
Alignment explanation
Indices: 44998--45047 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
44988 AAAACTTTTC
44998 TAAA-AGAAAACTCAAAGATAAATTCT
1 TAAATAGAAAACTCAAAGA-AAATTCT
45024 TAAATAGAAAACTCAAAGAAAATT
1 TAAATAGAAAACTCAAAGAAAATT
45048 TTATTAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.60, C:0.10, G:0.08, T:0.22
Consensus pattern (26 bp):
TAAATAGAAAACTCAAAGAAAATTCT
Found at i:47585 original size:5 final size:6
Alignment explanation
Indices: 47570--47601 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
47560 ACTTATATAA
*
47570 AAAAAT AAAAAT AAAAAT AAAAAC AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
47602 GAAAATAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:48525 original size:12 final size:12
Alignment explanation
Indices: 48499--48531 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
48489 AAACAATTCA
*
48499 TTCTCTCT-TTT
1 TTCTCTCTAGTT
48510 TTCTCTCTAGTT
1 TTCTCTCTAGTT
48522 TTCTCTCTAG
1 TTCTCTCTAG
48532 CCTTCCATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.06, C:0.27, G:0.06, T:0.61
Consensus pattern (12 bp):
TTCTCTCTAGTT
Found at i:48766 original size:12 final size:12
Alignment explanation
Indices: 48749--48773 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48739 TGCTATCATG
48749 ATGAATGCTATT
1 ATGAATGCTATT
48761 ATGAATGCTATT
1 ATGAATGCTATT
48773 A
1 A
48774 ATTATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Done.