Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011237.1 Kokia drynarioides strain JFW-HI SEQ_126215, 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: 67488
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Warning! 59 characters in sequence are not A, C, G, or T
Found at i:1818 original size:29 final size:30
Alignment explanation
Indices: 1786--1844 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
1776 TCACTTGTAT
*
1786 AATTG-CATCAAATTAAAATTCATGTATAC
1 AATTGACATCAAATCAAAATTCATGTATAC
* *
1815 AATTGCACATTAAATCAAAGTTCATGTATA
1 AATTG-ACATCAAATCAAAATTCATGTATA
1845 ATTTTGAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.20
31 20 0.80
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (30 bp):
AATTGACATCAAATCAAAATTCATGTATAC
Found at i:1847 original size:29 final size:27
Alignment explanation
Indices: 1781--1847 Score: 71
Period size: 31 Copynumber: 2.3 Consensus size: 27
1771 GAATTTCACT
*
1781 TGTATAATTGCATCAAATTAAAATTCA
1 TGTATAATTGCATCAAATCAAAATTCA
* *
1808 TGTATACAATTGCACATTAAATCAAAGTTCA
1 TGTAT--AATTG--CATCAAATCAAAATTCA
1839 TGTATAATT
1 TGTATAATT
1848 TTGAGATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 5 0.15
29 9 0.27
31 19 0.58
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (27 bp):
TGTATAATTGCATCAAATCAAAATTCA
Found at i:3137 original size:16 final size:17
Alignment explanation
Indices: 3116--3147 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3106 TTTAATGAAT
3116 AAAATA-TTTTAATTTA
1 AAAATATTTTTAATTTA
3132 AAAATATTTTTAATTT
1 AAAATATTTTTAATTT
3148 TATTAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAAATATTTTTAATTTA
Found at i:12963 original size:24 final size:24
Alignment explanation
Indices: 12918--12965 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
12908 TTACTCTTGA
*
12918 TATATATATATATATATTTTTATT
1 TATATATATATATATATATTTATT
* * *
12942 TATATATGTATGTATGTATTTATT
1 TATATATATATATATATATTTATT
12966 CAATCCCACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (24 bp):
TATATATATATATATATATTTATT
Found at i:13778 original size:5 final size:5
Alignment explanation
Indices: 13762--13808 Score: 64
Period size: 5 Copynumber: 10.0 Consensus size: 5
13752 ATTAAACCCA
*
13762 AAAAG GAAA- AAAA- AAAAG -AAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
13809 GTTGTATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 11 0.29
5 27 0.71
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:13792 original size:15 final size:15
Alignment explanation
Indices: 13761--13807 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
13751 CATTAAACCC
*
13761 AAAAAGGAA-AAAA-
1 AAAAAGAAAGAAAAG
13774 AAAAAGAAAGAAAAG
1 AAAAAGAAAGAAAAG
13789 -AAAAGAAAAGAAAAG
1 AAAAAG-AAAGAAAAG
13804 AAAA
1 AAAA
13808 GGTTGTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 8 0.28
14 9 0.31
15 9 0.31
16 3 0.10
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAGAAAAG
Found at i:15407 original size:18 final size:18
Alignment explanation
Indices: 15358--15409 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
15348 TTTAAGAACT
*
15358 AATTTAGA-AT-ATTTTA
1 AATTTAGAGATAATTTAA
* *
15374 AGTTTAGAGACCAATTTAA
1 AATTTAGAGA-TAATTTAA
15393 AATTTAGAGATAATTTA
1 AATTTAGAGATAATTTA
15410 TTCACCAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 7 0.25
17 1 0.04
18 6 0.21
19 14 0.50
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (18 bp):
AATTTAGAGATAATTTAA
Found at i:19572 original size:31 final size:30
Alignment explanation
Indices: 19536--19606 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
19526 TCCTTATTTA
19536 AAATAAATTATATTTTTAATCACTCAATTAT
1 AAATAAATTATA-TTTTAATCACTCAATTAT
* * * * *
19567 CAATAATTTTTATTTTAATTATTCAATTAT
1 AAATAAATTATATTTTAATCACTCAATTAT
*
19597 AAAAAAATTA
1 AAATAAATTA
19607 CAAATAATCC
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (30 bp):
AAATAAATTATATTTTAATCACTCAATTAT
Found at i:21757 original size:28 final size:31
Alignment explanation
Indices: 21699--21756 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
21689 ATATTAAGTT
* *
21699 AAAAATTAAAAATAATATAAATTTGATTTTA
1 AAAAATAAAAAATAATATAAATTGGATTTTA
*
21730 AAAAATAAAAAAT-ATATGAA-TGGATTT
1 AAAAATAAAAAATAATATAAATTGGATTT
21757 ACAATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.25
30 6 0.25
31 12 0.50
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (31 bp):
AAAAATAAAAAATAATATAAATTGGATTTTA
Found at i:25351 original size:2 final size:2
Alignment explanation
Indices: 25338--25373 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
25328 TGTATGTATG
*
25338 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25374 GCTATTTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35198 original size:24 final size:24
Alignment explanation
Indices: 35162--35213 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
35152 CTTTCGCCTG
*
35162 AAAAGGACCAAACCGATAAACAAC
1 AAAAGGACCAAACCGATAAAAAAC
** *
35186 AAAAGGATTAAACCGGTAAAAAAC
1 AAAAGGACCAAACCGATAAAAAAC
35210 AAAA
1 AAAA
35214 ATGTGAAGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.17, G:0.13, T:0.08
Consensus pattern (24 bp):
AAAAGGACCAAACCGATAAAAAAC
Found at i:38754 original size:26 final size:25
Alignment explanation
Indices: 38723--38783 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
38713 GGATAAAACC
38723 AATAAATAATTTAAAATTA-TTATAAA
1 AATAAATAA-TTAAAA-TAGTTATAAA
*
38749 AATAAAATAATTAAAATAGTTATACA
1 AAT-AAATAATTAAAATAGTTATAAA
*
38775 AATACATAA
1 AATAAATAA
38784 CATAATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 7 0.23
26 18 0.58
27 6 0.19
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (25 bp):
AATAAATAATTAAAATAGTTATAAA
Found at i:38758 original size:27 final size:26
Alignment explanation
Indices: 38726--38778 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
38716 TAAAACCAAT
38726 AAATAATTTAAAATTA-TTATAAAAATA
1 AAATAA-TTAAAA-TAGTTATAAAAATA
*
38753 AAATAATTAAAATAGTTATACAAATA
1 AAATAATTAAAATAGTTATAAAAATA
38779 CATAACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 2 0.08
26 16 0.67
27 6 0.25
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
AAATAATTAAAATAGTTATAAAAATA
Found at i:40518 original size:3 final size:3
Alignment explanation
Indices: 40510--40555 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
40500 TTATTTTTTA
40510 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40556 CTAGAAGTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:42902 original size:2 final size:2
Alignment explanation
Indices: 42897--42923 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42887 CATATATAGG
42897 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
42924 TGAAAGATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:47570 original size:65 final size:65
Alignment explanation
Indices: 47466--47592 Score: 254
Period size: 65 Copynumber: 2.0 Consensus size: 65
47456 ATTTACTACA
47466 TAGCCTTTATTGGGATTCTTGTATTTGACTTCAATTTTTTTTACATTTAGTATAATATTTTTCCT
1 TAGCCTTTATTGGGATTCTTGTATTTGACTTCAATTTTTTTTACATTTAGTATAATATTTTTCCT
47531 TAGCCTTTATTGGGATTCTTGTATTTGACTTCAATTTTTTTTACATTTAGTATAATATTTTT
1 TAGCCTTTATTGGGATTCTTGTATTTGACTTCAATTTTTTTTACATTTAGTATAATATTTTT
47593 ACTTGTTTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (65 bp):
TAGCCTTTATTGGGATTCTTGTATTTGACTTCAATTTTTTTTACATTTAGTATAATATTTTTCCT
Found at i:49305 original size:24 final size:24
Alignment explanation
Indices: 49201--49293 Score: 150
Period size: 24 Copynumber: 3.9 Consensus size: 24
49191 AATCTTTTAG
*
49201 TTAAACTCTGTTTAATTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
*
49225 TTAAACTATGTTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
*
49249 TTAAACTATGTTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
*
49273 TTGAACTCTGTTTATTTGTTT
1 TTAAACTCTGTTTATTTGTTT
49294 GAGTCAAACT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.55
Consensus pattern (24 bp):
TTAAACTCTGTTTATTTGTTTCAA
Found at i:51260 original size:24 final size:24
Alignment explanation
Indices: 51227--51277 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
51217 AGAAATAATC
* *
51227 TTTCAGTTAAACTTTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
*
51251 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAATTG
51275 TTT
1 TTT
51278 GAGTCAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAATTG
Found at i:51286 original size:24 final size:24
Alignment explanation
Indices: 51235--51289 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
51225 TCTTTCAGTT
* *
51235 AAACTTTGTTTAATTGTTTCAATT
1 AAACTCTGTTTAATTGTTTCAATC
* * *
51259 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTAATTGTTTCAATC
51283 AAACTCT
1 AAACTCT
51290 TATTAGTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTAATTGTTTCAATC
Found at i:52103 original size:33 final size:32
Alignment explanation
Indices: 52062--52126 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
52052 CATATCATAA
*
52062 TTATTTATCA-ACATATTAAATCGAACCGTACC
1 TTATTTATCATA-AAATTAAATCGAACCGTACC
52094 TTATATTATCATAAAATTAAATCGAACCGTACC
1 TTAT-TTATCATAAAATTAAATCGAACCGTACC
52127 CAATAAAGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 4 0.13
33 25 0.83
34 1 0.03
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (32 bp):
TTATTTATCATAAAATTAAATCGAACCGTACC
Found at i:57670 original size:31 final size:32
Alignment explanation
Indices: 57611--57670 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
57601 AACAGGTCTC
* *
57611 TGACTTAAATAAAAACCTTATGAATAGTTTAG
1 TGACTTAAATAAAAACATTACGAATAGTTTAG
*
57643 TGACTTAAATTAAAACATT-CGAATAGTT
1 TGACTTAAATAAAAACATTACGAATAGTT
57671 CAATAACCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 8 0.32
32 17 0.68
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (32 bp):
TGACTTAAATAAAAACATTACGAATAGTTTAG
Found at i:59325 original size:303 final size:302
Alignment explanation
Indices: 58774--59412 Score: 956
Period size: 303 Copynumber: 2.1 Consensus size: 302
58764 TCATAATCTA
* * **
58774 ATTTCAGAAGAATTTGAAAATATGTTGGGTTAATTTGCAATGTATTGATATGCTACTGCCCTAAT
1 ATTT-AGAAGAATTTGAAAATAAGTTGGGTTTATTTGCAATACATTGATATGCTACTGCCCTAAT
* *
58839 GCTATCCCTATAAATATGGAATATCTTAGAAGCATTATCTGTAGTTAATTTAGTGCTTAACTTGC
65 GCTATCCCTATAAATATGGAATATCTTAGAAGAATTATCAGTAGTTAATTTAGTGCTTAACTTGC
** *
58904 TGGTCCTTTTGGTAGGTTCTATTTTCAGTTGATAAATGTGTTGTTCAAAGGGTTTGTAGTTGTTG
130 TGGTCCTTTCAGTAGGTTCTATTTTCAGTTGATAAATGTGTTGTTCAAAGGGTCTGTAGTTGTTG
58969 AAATTTCATGGGTTATTTTAATTGGATTTATGCTTTCAATGACGATAATGAAGTCATTAGCTTGT
195 AAATTTCATGGGTTATTTTAATTGGATTTATGCTTTCAATGACGATAATGAAGTCATTAGCTTGT
** * * *
59034 TTCTGTTCATAATCTAATATTTATTTATCAAGTTTCGATGGAT
260 TTCTGTTCATAATCTAATATTTACGTATCAACTTTCAATGAAT
*
59077 ATTTAGAAGAATTTGAAAATAAGTTGGGTTTATTTGCAATACATTGATATGCTAGTGCCCTAATG
1 ATTTAGAAGAATTTGAAAATAAGTTGGGTTTATTTGCAATACATTGATATGCTACTGCCCTAATG
* * * *
59142 CTATCCCTATAAATATTGAATATCTTTGAAGAATTGTGCAGTAGTTAGTTTAGTGCTTAACTTGC
66 CTATCCCTATAAATATGGAATATCTTAGAAGAATTAT-CAGTAGTTAATTTAGTGCTTAACTTGC
*
59207 TGGTCCTTTCAGTAGGTTCTATTTTCTGTTGATAAATGTGTTGTTCAAAGGGTCTGTAGTTGTTG
130 TGGTCCTTTCAGTAGGTTCTATTTTCAGTTGATAAATGTGTTGTTCAAAGGGTCTGTAGTTGTTG
* ** * * *
59272 AAATTTTATGTTTTTTTTTAATTGGATTTATGCTTTCGATGACGATGATGAAGTCATTAGCTTGT
195 AAATTTCATGGGTTATTTTAATTGGATTTATGCTTTCAATGACGATAATGAAGTCATTAGCTTGT
* *
59337 TTCTGTTCATAATGTAATATTTACGTATCGACTTTCAATGAAT
260 TTCTGTTCATAATCTAATATTTACGTATCAACTTTCAATGAAT
* * ** *
59380 GTTCAGAAGAATTTG-GGATAAATTGGGTTTATT
1 ATTTAGAAGAATTTGAAAATAAGTTGGGTTTATT
59413 GATATGCTTA
Statistics
Matches: 302, Mismatches: 33, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
302 104 0.34
303 198 0.66
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.43
Consensus pattern (302 bp):
ATTTAGAAGAATTTGAAAATAAGTTGGGTTTATTTGCAATACATTGATATGCTACTGCCCTAATG
CTATCCCTATAAATATGGAATATCTTAGAAGAATTATCAGTAGTTAATTTAGTGCTTAACTTGCT
GGTCCTTTCAGTAGGTTCTATTTTCAGTTGATAAATGTGTTGTTCAAAGGGTCTGTAGTTGTTGA
AATTTCATGGGTTATTTTAATTGGATTTATGCTTTCAATGACGATAATGAAGTCATTAGCTTGTT
TCTGTTCATAATCTAATATTTACGTATCAACTTTCAATGAAT
Found at i:63473 original size:66 final size:66
Alignment explanation
Indices: 63367--63497 Score: 253
Period size: 66 Copynumber: 2.0 Consensus size: 66
63357 CGGGGGTTTT
*
63367 GTCTTTTTCGAGGGGTTTGTGGAGTGAGAGCACTTAACCAATCAAGGAAGTGTGAGGATTTGCTT
1 GTCTTTTTCGAGGGGTTTATGGAGTGAGAGCACTTAACCAATCAAGGAAGTGTGAGGATTTGCTT
63432 C
66 C
63433 GTCTTTTTCGAGGGGTTTATGGAGTGAGAGCACTTAACCAATCAAGGAAGTGTGAGGATTTGCTT
1 GTCTTTTTCGAGGGGTTTATGGAGTGAGAGCACTTAACCAATCAAGGAAGTGTGAGGATTTGCTT
63498 TTGTTGGGGG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.24, C:0.13, G:0.31, T:0.32
Consensus pattern (66 bp):
GTCTTTTTCGAGGGGTTTATGGAGTGAGAGCACTTAACCAATCAAGGAAGTGTGAGGATTTGCTT
C
Found at i:65765 original size:2 final size:2
Alignment explanation
Indices: 65758--65790 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
65748 TTAAGAGTTA
65758 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65791 TAAATAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.