Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006166.1 Kokia drynarioides strain JFW-HI SEQ_120723, 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: 51091
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3539 original size:101 final size:101
Alignment explanation
Indices: 3411--3596 Score: 257
Period size: 101 Copynumber: 1.8 Consensus size: 101
3401 TTGAAGCTAC
* *
3411 GAAAGAGAATCCTTATCTCTCTAAAGTTGCAA-TAGAGCAAGATGAAGCTACAAAACCAAATCCT
1 GAAAGAAAATCCTTATCTCTCTAAAGTTG-AAGTAGAGCAAGATGAAACTACAAAACCAAATCCT
*
3475 ATAACCCTGAAGTTGTAGTGGGTCAGATTAAAATCAT
65 ATAACCCTGAAGTTGAAGTGGGTCAGATTAAAATCAT
* * * * * *
3512 GAAAGAAAATCTTTATCTCTCTGAAGTTGAAGTAGAGTAAGATGAAACTAGAACATCAAATCCTA
1 GAAAGAAAATCCTTATCTCTCTAAAGTTGAAGTAGAGCAAGATGAAACTACAAAACCAAATCCTA
* *
3577 TATCCTTGAAGTTGAAGTGG
66 TAACCCTGAAGTTGAAGTGG
3597 ATTGGATTGG
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
100 2 0.03
101 71 0.97
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (101 bp):
GAAAGAAAATCCTTATCTCTCTAAAGTTGAAGTAGAGCAAGATGAAACTACAAAACCAAATCCTA
TAACCCTGAAGTTGAAGTGGGTCAGATTAAAATCAT
Found at i:4051 original size:4 final size:4
Alignment explanation
Indices: 4042--4097 Score: 78
Period size: 4 Copynumber: 14.2 Consensus size: 4
4032 TTAAAAGACC
* * *
4042 TATT TATT TATT TATT TATT TATT TATT CATT CATT CATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
4090 TA-T TATT T
1 TATT TATT T
4098 TATAAATAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 3 0.06
4 46 0.94
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:4131 original size:15 final size:14
Alignment explanation
Indices: 4099--4136 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
4089 TTATTATTTT
*
4099 ATAAATAAAAATAC
1 ATAAATAAAAACAC
4113 ATAAATAAAAACAC
1 ATAAATAAAAACAC
4127 A-ATAATAAAA
1 ATA-AATAAAA
4137 TAATCCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 1 0.05
14 21 0.95
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (14 bp):
ATAAATAAAAACAC
Found at i:6370 original size:43 final size:43
Alignment explanation
Indices: 6317--6661 Score: 422
Period size: 43 Copynumber: 8.0 Consensus size: 43
6307 ATCTGTTAAT
* * *
6317 TTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGACTATGTTN
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
* * * * * *
6360 TTTAGCGGCGTTTGTGTGAAAGGCGTCGCTAAAAATCATGTTT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
* * * *
6403 TTTAACGGCGTTTGTGGGAGAAGCGTCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
* * *
6446 TTTAGTGGCGTTTGTGGGAGAAGCACCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
* ** *
6489 TTTAGCGGCATTTGTGGGAAAAGCATCGCTAAAGACCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
* * *
6532 TTTAGCGGGGTTTGTGGGAGAAGCGCCGCTAAAGACCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
** * * *
6575 TTTAATGGCATTTGTGGGAAAAGCG-TGACTAAAGACCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCG-CTAAAGACCATGTTC
6618 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
6661 T
1 T
6662 ATAGTGACAT
Statistics
Matches: 260, Mismatches: 40, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
42 1 0.00
43 258 0.99
44 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
Found at i:8202 original size:2 final size:2
Alignment explanation
Indices: 8189--8249 Score: 63
Period size: 2 Copynumber: 30.5 Consensus size: 2
8179 ATAAAATACG
*
8189 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT -T GCT CT -T GCT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -CT CT CT -CT
* *
8231 CT CT CT CT TT CG CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
8250 ATCCTCTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
1 2 0.04
2 45 0.92
3 2 0.04
ACGTcount: A:0.00, C:0.48, G:0.05, T:0.48
Consensus pattern (2 bp):
CT
Found at i:14856 original size:14 final size:14
Alignment explanation
Indices: 14837--14867 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
14827 TTAAAATATA
14837 AAATACCAAACCCT
1 AAATACCAAACCCT
*
14851 AAATACCAAACTCT
1 AAATACCAAACCCT
14865 AAA
1 AAA
14868 ACCTTAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.29, G:0.00, T:0.16
Consensus pattern (14 bp):
AAATACCAAACCCT
Found at i:15085 original size:23 final size:24
Alignment explanation
Indices: 15047--15095 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
15037 TCGAAGTAAA
15047 AAAAAATATTTGTTT-A-TAATTT
1 AAAAAATATTTGTTTAAGTAATTT
15069 AAAAAATAATTAT-TTTAAGTAATTT
1 AAAAAAT-ATT-TGTTTAAGTAATTT
15094 AA
1 AA
15096 TTAAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 7 0.30
23 6 0.26
24 2 0.09
25 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (24 bp):
AAAAAATATTTGTTTAAGTAATTT
Found at i:15268 original size:15 final size:16
Alignment explanation
Indices: 15218--15273 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 16
15208 TATCTTTTAA
*
15218 TATTATCTTAATCTAATT
1 TATTGTCTT-ATCTAA-T
*
15236 TATTCTCTTATACTAAT
1 TATTGTCTTAT-CTAAT
15253 TATTGT-TTATCTAAT
1 TATTGTCTTATCTAAT
15268 TATTGT
1 TATTGT
15274 AATATAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 11 0.31
16 4 0.11
17 8 0.23
18 12 0.34
ACGTcount: A:0.29, C:0.11, G:0.04, T:0.57
Consensus pattern (16 bp):
TATTGTCTTATCTAAT
Found at i:19090 original size:8 final size:8
Alignment explanation
Indices: 19071--19104 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
19061 ATTATATTGT
19071 TTTAAT-A
1 TTTAATAA
19078 TTTAATAA
1 TTTAATAA
19086 TTTAATAA
1 TTTAATAA
19094 TTTAATAA
1 TTTAATAA
19102 TTT
1 TTT
19105 TTTATTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTAATAA
Found at i:25721 original size:2 final size:2
Alignment explanation
Indices: 25714--25738 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25704 CACTTTATTT
25714 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
25739 TCATTAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44276 original size:17 final size:19
Alignment explanation
Indices: 44254--44293 Score: 66
Period size: 17 Copynumber: 2.2 Consensus size: 19
44244 ATAGTTTGCA
44254 TGCATTTTTA-TT-GTCAT
1 TGCATTTTTATTTAGTCAT
44271 TGCATTTTTATTTAGTCAT
1 TGCATTTTTATTTAGTCAT
44290 TGCA
1 TGCA
44294 ATAGTTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 10 0.48
18 2 0.10
19 9 0.43
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.55
Consensus pattern (19 bp):
TGCATTTTTATTTAGTCAT
Found at i:44932 original size:25 final size:25
Alignment explanation
Indices: 44891--44943 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
44881 GTCACTTGAT
*
44891 AAAGAAAAATGAGAAG-AAGAAAGAA
1 AAAGAAAAATGAAAAGAAAG-AAGAA
44916 AAAG-AAAATAGAAAAGAAAGAAGAA
1 AAAGAAAAAT-GAAAAGAAAGAAGAA
44941 AAA
1 AAA
44944 AAGTTTTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 5 0.20
25 17 0.68
26 3 0.12
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (25 bp):
AAAGAAAAATGAAAAGAAAGAAGAA
Found at i:46805 original size:7 final size:7
Alignment explanation
Indices: 46788--46846 Score: 64
Period size: 7 Copynumber: 8.4 Consensus size: 7
46778 ACCCAAAAAG
*
46788 TCAACTA
1 TCAACGA
*
46795 TCAACGG
1 TCAACGA
46802 TCAACGA
1 TCAACGA
*
46809 TCAACTA
1 TCAACGA
46816 TCAACGA
1 TCAACGA
*
46823 TCAACGG
1 TCAACGA
* *
46830 TCAATGG
1 TCAACGA
46837 TCAACGA
1 TCAACGA
46844 TCA
1 TCA
46847 GGTTCGATCA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.20
Consensus pattern (7 bp):
TCAACGA
Found at i:46813 original size:21 final size:21
Alignment explanation
Indices: 46788--46846 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
46778 ACCCAAAAAG
*
46788 TCAACTATCAACGGTCAACGA
1 TCAACTATCAACGATCAACGA
*
46809 TCAACTATCAACGATCAACGG
1 TCAACTATCAACGATCAACGA
*
46830 TCAA-TGGTCAACGATCA
1 TCAACT-ATCAACGATCA
46847 GGTTCGATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 1 0.03
21 33 0.97
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.20
Consensus pattern (21 bp):
TCAACTATCAACGATCAACGA
Found at i:46920 original size:22 final size:22
Alignment explanation
Indices: 46895--46938 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
46885 GTGGGTCAAC
46895 TCGAATTGGGTTTAGGGTTTGG
1 TCGAATTGGGTTTAGGGTTTGG
* *
46917 TCGATTTGGTTTTAGGGTTTGG
1 TCGAATTGGGTTTAGGGTTTGG
46939 GTATTGAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.11, C:0.05, G:0.39, T:0.45
Consensus pattern (22 bp):
TCGAATTGGGTTTAGGGTTTGG
Found at i:51053 original size:3 final size:3
Alignment explanation
Indices: 51045--51091 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
51035 CCCACAAGTT
51045 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.