Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014454.1 Kokia drynarioides strain JFW-HI SEQ_129493, 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: 26167
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Warning! 113 characters in sequence are not A, C, G, or T
Found at i:7672 original size:60 final size:58
Alignment explanation
Indices: 7590--7856 Score: 245
Period size: 60 Copynumber: 4.5 Consensus size: 58
7580 TTTACTAATC
**
7590 AAACTTTCCAAAAATTTGATTTTAACCCCTAAA-TTTTCTAAAAATTTA-ATTTTAACCCTT
1 AAACTTTCC-AAAA-TACATTTTAACCCCTAAACTTTTCT-AAAA-TTACATTTTAACCCTT
* * * *
7650 AAACTTTTCCAAAATAACATTTTAACCCTTAAACTTTTCCAAAATTATATTTTGAACCCTC
1 AAAC-TTTCCAAAAT-ACATTTTAACCCCTAAACTTTTCTAAAATTACATTTT-AACCCTT
* * * *
7711 AAACTTTCCAAAACTATATTTTGACCCCTTAAACTCTTCTAAAATTACATTTTAACCC-A
1 AAACTTTCCAAAA-TACATTTTAACCCC-TAAACTTTTCTAAAATTACATTTTAACCCTT
* * * * * *
7770 AAAATTTCCTAAATTTACCTTTTAA-CCCTAAGCTTCTCTAAAATTACATTTTAACCCCT
1 AAACTTTCC-AAA-ATACATTTTAACCCCTAAACTTTTCTAAAATTACATTTTAACCCTT
*
7829 AAACTTCCCAAAATCACATTTTAACCCC
1 AAACTTTCCAAAAT-ACATTTTAACCCC
7857 CAAAATTCTC
Statistics
Matches: 170, Mismatches: 25, Indels: 25
0.77 0.11 0.11
Matches are distributed among these distances:
57 1 0.01
58 37 0.22
59 25 0.15
60 65 0.38
61 42 0.25
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.37
Consensus pattern (58 bp):
AAACTTTCCAAAATACATTTTAACCCCTAAACTTTTCTAAAATTACATTTTAACCCTT
Found at i:7856 original size:29 final size:29
Alignment explanation
Indices: 7590--7870 Score: 181
Period size: 30 Copynumber: 9.4 Consensus size: 29
7580 TTTACTAATC
* **
7590 AAACTTTCCAAAAATTTGATTTTAACCCCT
1 AAAC-TTCCCAAAATTACATTTTAACCCCT
* ** *
7620 AAATTTTCTAAAAATTTA-ATTTTAACCCTT
1 AAA-CTTCCCAAAA-TTACATTTTAACCCCT
* * *
7650 AAACTTTTCCAAAATAACATTTTAACCCTT
1 AAAC-TTCCCAAAATTACATTTTAACCCCT
* *
7680 AAACTTTTCCAAAATTATATTTTGAA-CCCT
1 AAAC-TTCCCAAAATTACATTTT-AACCCCT
* * * *
7710 CAAACTTTCCAAAACTATATTTTGACCCCTT
1 -AAACTTCCCAAAATTACATTTTAACCCC-T
* * **
7741 AAACTCTTCTAAAATTACATTTTAACCCAA
1 AAACT-TCCCAAAATTACATTTTAACCCCT
* * * *
7771 AAATTTCCTAAATTTACCTTTTAA-CCCT
1 AAACTTCCCAAAATTACATTTTAACCCCT
* *
7799 AAGCTTCTCTAAAATTACATTTTAACCCCT
1 AAACTTC-CCAAAATTACATTTTAACCCCT
* *
7829 AAACTTCCCAAAATCACATTTTAACCCCC
1 AAACTTCCCAAAATTACATTTTAACCCCT
* *
7858 AAAATTCTCAAAA
1 AAACTTCCCAAAA
7871 ACTTCACCTT
Statistics
Matches: 204, Mismatches: 36, Indels: 23
0.78 0.14 0.09
Matches are distributed among these distances:
28 7 0.03
29 64 0.31
30 106 0.52
31 27 0.13
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.36
Consensus pattern (29 bp):
AAACTTCCCAAAATTACATTTTAACCCCT
Found at i:13279 original size:28 final size:28
Alignment explanation
Indices: 13231--13364 Score: 128
Period size: 28 Copynumber: 4.8 Consensus size: 28
13221 GAAAGCAAAC
** *
13231 CAAAGCTCTACTTGAGCTATAAACAG-GT
1 CAAAGCTCTACCCGAGTTATAAA-AGAGT
* *
13259 CAAAGCTCTACCCGAGTTATAAATGATT
1 CAAAGCTCTACCCGAGTTATAAAAGAGT
* * *
13287 CAAAGCTCTACCCGAATTGTAATAG-GT
1 CAAAGCTCTACCCGAGTTATAAAAGAGT
* * * * *
13314 CAAAACTCTACCCAAGCTATAAATGAAT
1 CAAAGCTCTACCCGAGTTATAAAAGAGT
13342 CAAAGCTCTACCCGAGTTATAAA
1 CAAAGCTCTACCCGAGTTATAAA
13365 TGAATTAGAG
Statistics
Matches: 83, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
27 20 0.24
28 63 0.76
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (28 bp):
CAAAGCTCTACCCGAGTTATAAAAGAGT
Found at i:13365 original size:28 final size:28
Alignment explanation
Indices: 13258--13385 Score: 143
Period size: 28 Copynumber: 4.6 Consensus size: 28
13248 TATAAACAGG
*
13258 TCAAAGCTCTACCCGAGTTATAAATGAT
1 TCAAAGCTCTACCCGAGTTATAAATGAA
* * *
13286 TCAAAGCTCTACCCGAATTGT-AAT-AGG
1 TCAAAGCTCTACCCGAGTTATAAATGA-A
* * *
13313 TCAAAACTCTACCCAAGCTATAAATGAA
1 TCAAAGCTCTACCCGAGTTATAAATGAA
13341 TCAAAGCTCTACCCGAGTTATAAATGAA
1 TCAAAGCTCTACCCGAGTTATAAATGAA
* * *
13369 TTAGAGCTCTACTCGAG
1 TCAAAGCTCTACCCGAG
13386 CCACCATTCA
Statistics
Matches: 82, Mismatches: 15, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
26 1 0.01
27 19 0.23
28 61 0.74
29 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.26
Consensus pattern (28 bp):
TCAAAGCTCTACCCGAGTTATAAATGAA
Found at i:17425 original size:19 final size:19
Alignment explanation
Indices: 17403--17440 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
17393 GGTTTTTGGT
*
17403 TCTCGGGTTCAATTTTCAA
1 TCTCGGGTCCAATTTTCAA
17422 TCTCGGGTCCAATTTTCAA
1 TCTCGGGTCCAATTTTCAA
17441 GTTTAATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (19 bp):
TCTCGGGTCCAATTTTCAA
Found at i:20648 original size:21 final size:21
Alignment explanation
Indices: 20624--20664 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20614 TTAAAAATTA
*
20624 TGATTTT-TAAATTATTTTTAT
1 TGATTTTCT-AATAATTTTTAT
20645 TGATTTTCTAATAATTTTTA
1 TGATTTTCTAATAATTTTTA
20665 GTTTAAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.63
Consensus pattern (21 bp):
TGATTTTCTAATAATTTTTAT
Found at i:24734 original size:20 final size:21
Alignment explanation
Indices: 24709--24748 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
24699 CATGTGACAG
24709 AAAAATAATAAAAAT-TAAAT
1 AAAAATAATAAAAATATAAAT
* *
24729 AAAAATTATGAAAATATAAA
1 AAAAATAATAAAAATATAAA
24749 AGTATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (21 bp):
AAAAATAATAAAAATATAAAT
Found at i:24742 original size:10 final size:9
Alignment explanation
Indices: 24709--24806 Score: 65
Period size: 9 Copynumber: 10.7 Consensus size: 9
24699 CATGTGACAG
*
24709 AAAAATAAT
1 AAAAATTAT
24718 AAAAATTAAAT
1 AAAAATT--AT
24729 AAAAATTAT
1 AAAAATTAT
*
24738 GAAAA-TAT
1 AAAAATTAT
*
24746 -AAAAGTAT
1 AAAAATTAT
*
24754 AAAAATATTT
1 AAAAAT-TAT
* *
24764 TAAAATCAT
1 AAAAATTAT
24773 AAAAATTAT
1 AAAAATTAT
24782 AGAAAATTAT
1 A-AAAATTAT
**
24792 TTAAATTAT
1 AAAAATTAT
*
24801 ATAAAT
1 AAAAAT
24807 ACATTATAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
7 4 0.06
8 6 0.08
9 37 0.52
10 15 0.21
11 9 0.13
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:24794 original size:29 final size:27
Alignment explanation
Indices: 24710--24817 Score: 87
Period size: 29 Copynumber: 3.7 Consensus size: 27
24700 ATGTGACAGA
*
24710 AAAATAATAAAAATTAAATAAAAATTA-TG
1 AAAAT-ATAAAAATT--ATAAAAATTATTT
*
24739 AAAATAT-AAAAGTATAAAAA-TATTTT
1 AAAATATAAAAATTATAAAAATTA-TTT
24765 AAAATCATAAAAATTATAGAAAATTATTT
1 AAAAT-ATAAAAATTATA-AAAATTATTT
24794 AAATTATATAAATACATTATAAAA
1 AAA--ATATAAA-A-ATTATAAAA
24818 TATAAAAATA
Statistics
Matches: 66, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
24 2 0.03
25 7 0.11
26 6 0.09
27 7 0.11
28 10 0.15
29 15 0.23
30 7 0.11
31 6 0.09
32 6 0.09
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (27 bp):
AAAATATAAAAATTATAAAAATTATTT
Found at i:24797 original size:28 final size:26
Alignment explanation
Indices: 24710--24834 Score: 85
Period size: 29 Copynumber: 4.5 Consensus size: 26
24700 ATGTGACAGA
*
24710 AAAATAATAAAAATTAAATAAAAATTATG
1 AAAAT-ATAAAAATT--ATAAAAATTATT
* *
24739 AAAATAT-AAAAGTATAAAAATATTTT
1 AAAATATAAAAATTATAAAAAT-TATT
24765 AAAATCATAAAAATTATAGAAAATTATTT
1 AAAAT-ATAAAAATTATA-AAAATTA-TT
*
24794 AAATTATATAAATACATTAT-AAAA-TATA
1 AAA--ATATAAA-A-ATTATAAAAATTATT
24822 AAAATATAGAAAA
1 AAAATATA-AAAA
24835 AAAATTAATA
Statistics
Matches: 80, Mismatches: 6, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
25 9 0.11
26 13 0.16
27 9 0.11
28 15 0.19
29 17 0.21
30 9 0.11
31 3 0.04
32 5 0.06
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (26 bp):
AAAATATAAAAATTATAAAAATTATT
Found at i:24838 original size:21 final size:22
Alignment explanation
Indices: 24814--24868 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
24804 AATACATTAT
24814 AAAATATAAAAATATAGA-AAA
1 AAAATATAAAAATATAGATAAA
**
24835 AAAAT-TAATAAATATTTATAAA
1 AAAATATAA-AAATATAGATAAA
24857 AAAATCATAAAA
1 AAAAT-ATAAAA
24869 TTTGTTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 3 0.11
21 12 0.43
22 8 0.29
23 2 0.07
24 3 0.11
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAATATAAAAATATAGATAAA
Found at i:25104 original size:18 final size:17
Alignment explanation
Indices: 25083--25126 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
25073 AAGAAAAATG
25083 ATAAAAAAATTAAAATCA-
1 ATAAAAAAA-TAAAAT-AT
*
25101 ATAAAAACATAAAATAT
1 ATAAAAAAATAAAATAT
25118 ATAAAAAAA
1 ATAAAAAAA
25127 AAAGTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 1 0.04
17 14 0.61
18 8 0.35
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (17 bp):
ATAAAAAAATAAAATAT
Found at i:25158 original size:31 final size:32
Alignment explanation
Indices: 25123--25188 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
25113 AATATATAAA
*
25123 AAAAAAAGTT-G-AAAAGTATAAAACAATTATT
1 AAAAAAAGTTAGAAAAAG-ATAAAAAAATTATT
*
25154 -AAAAAATTTAGAAAAAGATAAAAAAATTATT
1 AAAAAAAGTTAGAAAAAGATAAAAAAATTATT
25185 AAAA
1 AAAA
25189 GTATAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
30 8 0.27
31 14 0.47
32 8 0.27
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.24
Consensus pattern (32 bp):
AAAAAAAGTTAGAAAAAGATAAAAAAATTATT
Found at i:25179 original size:20 final size:20
Alignment explanation
Indices: 25153--25208 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
25143 AAACAATTAT
25153 TAAAAAATTTAGAAAAAG-A
1 TAAAAAATTTAGAAAAAGTA
* **
25172 TAAAAAAATTATTAAAAGTA
1 TAAAAAATTTAGAAAAAGTA
25192 TAAAAAATTATAGAAAA
1 TAAAAAATT-TAGAAAA
25209 TTATAGAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 15 0.52
20 9 0.31
21 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (20 bp):
TAAAAAATTTAGAAAAAGTA
Found at i:25208 original size:29 final size:28
Alignment explanation
Indices: 25176--25265 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 28
25166 AAAAGATAAA
25176 AAAATTATTAAAAGTATAAAAAATTATAG
1 AAAATTATTAAAA-TATAAAAAATTATAG
* * *
25205 AAAATTA-TAGAAAAATAATAAAAATATAT
1 AAAATTATTA-AAATATAA-AAAATTATAG
*
25234 AAAAATATTATAGAATAT-AAAAA-TATAG
1 AAAATTATTA-A-AATATAAAAAATTATAG
25262 AAAA
1 AAAA
25266 AAATTGAACA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
28 14 0.28
29 28 0.56
30 4 0.08
31 4 0.08
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (28 bp):
AAAATTATTAAAATATAAAAAATTATAG
Found at i:25213 original size:20 final size:20
Alignment explanation
Indices: 25147--25248 Score: 93
Period size: 20 Copynumber: 5.0 Consensus size: 20
25137 AGTATAAAAC
25147 AATTATTAAAAAATT-TAGAA
1 AATTA-TAAAAAATTATAGAA
** *
25167 AAAGATAAAAAAATTAT-TAA
1 AATTAT-AAAAAATTATAGAA
*
25187 AAGTATAAAAAATTATAGAA
1 AATTATAAAAAATTATAGAA
*
25207 AATTATAGAAAAATAATA-AA
1 AATTATA-AAAAATTATAGAA
25227 AATATATAAAAATATTATAGAA
1 AAT-TATAAAAA-ATTATAGAA
25249 TATAAAAATA
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
19 11 0.17
20 34 0.52
21 19 0.29
22 2 0.03
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (20 bp):
AATTATAAAAAATTATAGAA
Found at i:25232 original size:19 final size:18
Alignment explanation
Indices: 25174--25256 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 18
25164 GAAAAAGATA
* *
25174 AAAAAATTATTAAAAGTAT
1 AAAAAA-TAATAAAAATAT
*
25193 AAAAAATTATAGAAAATTAT
1 AAAAAATAATA-AAAA-TAT
25213 AGAAAAATAATAAAAATAT
1 A-AAAAATAATAAAAATAT
* *
25232 ATAAAAATATTATAGAATAT
1 A-AAAAATAATA-AAAATAT
25252 AAAAA
1 AAAAA
25257 TATAGAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
18 3 0.06
19 26 0.49
20 15 0.28
21 9 0.17
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAAAATAATAAAAATAT
Found at i:25250 original size:20 final size:19
Alignment explanation
Indices: 25190--25256 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 19
25180 TTATTAAAAG
*
25190 TATAAAAAATTATAGAAAA
1 TATAAAAAATTATAGAATA
* *
25209 TTATAGAAAAATAATAAAAATA
1 -TATA-AAAAATTAT-AGAATA
25231 TATAAAAATATTATAGAATA
1 TATAAAAA-ATTATAGAATA
25251 TA-AAAA
1 TATAAAA
25257 TATAGAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 4 0.10
20 15 0.38
21 16 0.41
22 4 0.10
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (19 bp):
TATAAAAAATTATAGAATA
Found at i:25265 original size:10 final size:10
Alignment explanation
Indices: 25155--25266 Score: 65
Period size: 10 Copynumber: 11.5 Consensus size: 10
25145 ACAATTATTA
*
25155 AAAAATTTAG
1 AAAAATATAG
* *
25165 AAAAAGATAA
1 AAAAATATAG
*
25175 AAAAAT-TATT
1 AAAAATATA-G
*
25185 AAAAGTATA-
1 AAAAATATAG
25194 AAAAATTATAG
1 AAAAA-TATAG
*
25205 AAAATTATAG
1 AAAAATATAG
*
25215 AAAAATA-AT
1 AAAAATATAG
*
25224 AAAAATATAT
1 AAAAATATAG
25234 AAAAATATTA-
1 AAAAATA-TAG
* *
25244 TAGAATAT--
1 AAAAATATAG
25252 AAAAATATAG
1 AAAAATATAG
25262 AAAAA
1 AAAAA
25267 AATTGAACAT
Statistics
Matches: 80, Mismatches: 14, Indels: 16
0.73 0.13 0.15
Matches are distributed among these distances:
8 6 0.08
9 15 0.19
10 51 0.64
11 8 0.10
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (10 bp):
AAAAATATAG
Done.