Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010168.1 Kokia drynarioides strain JFW-HI SEQ_124973, 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: 2275
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.27
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:127 original size:41 final size:40
Alignment explanation
Indices: 80--632 Score: 201
Period size: 39 Copynumber: 13.9 Consensus size: 40
70 TACAACCTTC
*
80 AATCTTTTACCCTAACCAGAGGGCAAGATTTAA-AACCATAT
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGAA--ATAT
* * * *
121 GATCTTTTA-CCTCGATCATG-GGGC-AGATTGAAGAAATCT
1 AATCTTTTACCCT-AACCA-GAGGGCAAGATTGAAGAAATAT
* * *
160 AATCTTTTACCCTAACCAGAAGGCAAGATTGAAGATCATTT
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGA-AATAT
* * * * **
201 GATATTTTAACCC-GATCATG-GGGC-AGATTGAAGAAATCC
1 AATCTTTT-ACCCTAACCA-GAGGGCAAGATTGAAGAAATAT
* * *
240 AATCTTTTATCCTAACCAGAGGGCAAGA-TGAAAGATCATCT
1 AATCTTTTACCCTAACCAGAGGGCAAGATTG-AAGA-AATAT
* ** * * * *
281 GATCTTTTACCCCGATCATG-GGG-TAGATGGAAGAAATTT
1 AATCTTTTACCCTAACCA-GAGGGCAAGATTGAAGAAATAT
* * * *
320 AAT-TTTTACCCTAACTAGAGGGTAAGATTGAAGACCATCT
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGA-AATAT
* ** * * **
360 GATCTTTTACCCCGATCA-TGGG-ACAGATTGAAGAAATCC
1 AATCTTTTACCCTAACCAGAGGGCA-AGATTGAAGAAATAT
* * * *
399 AATCTTTTACCCTAACCAGAGGGAAATATTGAAGACCATCT
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGA-AATAT
* ** * * **
440 GATCTTTTACCCCGATCATG-GGG-TAGATTGAAGAAATCC
1 AATCTTTTACCCTAACCA-GAGGGCAAGATTGAAGAAATAT
** * * **
479 AATCTTTTACCCCGATCATG-GGGC-AGTTTGAAGAAATCC
1 AATCTTTTACCCTAACCA-GAGGGCAAGATTGAAGAAATAT
* * * * * **
518 AATNTTTTATCATAATCAGAGGGCAAGATTGAAGACCATCC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGA-AATAT
* * ** * *
559 GATCTTTAACCCCGATCATG-GGGC-AGATTAAAGAAAT-T
1 AATCTTTTACCCTAACCA-GAGGGCAAGATTGAAGAAATAT
* *
597 CAATCTTTTACCCTAACTAGAGGGTAAGATTGAAGA
1 -AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGA
633 CCATCCGATC
Statistics
Matches: 384, Mismatches: 95, Indels: 67
0.70 0.17 0.12
Matches are distributed among these distances:
37 1 0.00
38 20 0.05
39 139 0.36
40 113 0.29
41 102 0.27
42 9 0.02
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (40 bp):
AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGAAATAT
Found at i:217 original size:80 final size:80
Alignment explanation
Indices: 79--807 Score: 621
Period size: 80 Copynumber: 9.2 Consensus size: 80
69 TTACAACCTT
* * * *
79 CAATCTTTTACCCTAACCAGAGGGCAAGATTTAAAACCATATGATCTTTTACCTCGATCATGGGG
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGGGG
144 CAGATTGAAGAAATC
66 CAGATTGAAGAAATC
* * * * * *
159 TAATCTTTTACCCTAACCAGAAGGCAAGATTGAAGATCATTTGATATTTTAACCCGATCATGGGG
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGGGG
224 CAGATTGAAGAAATC
66 CAGATTGAAGAAATC
* *
239 CAATCTTTTATCCTAACCAGAGGGCAAGA-TGAAAGATCATCTGATCTTTTACCCCGATCATGGG
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTG-AAGACCATCTGATCTTTTACCCCGATCATGGG
* * *
303 GTAGATGGAAGAAATT
65 GCAGATTGAAGAAATC
* * * *
319 TAAT-TTTTACCCTAACTAGAGGGTAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGGGA
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGGGG
383 CAGATTGAAGAAATC
66 CAGATTGAAGAAATC
* *
398 CAATCTTTTACCCTAACCAGAGGGAAATATTGAAGACCATCTGATCTTTTACCCCGATCATGGGG
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGGGG
*
463 TAGATTGAAGAAATC
66 CAGATTGAAGAAATC
** * * * ** * * ***
478 CAATCTTTTACCCCGATCATG-GGGC-AGTTTGAAGA-AATCCAATNTTTTATCATAATCA-GAG
1 CAATCTTTTACCCTAACCA-GAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATG-G
*
539 GGCAAGATTGAAGACCATC
64 GGC-AGATTGAAGA-AATC
* * ** * * * * * *
558 CGATCTTTAACCCCGATCATG-GGGC-AGATTAAAGA-AAT-TCAATCTTTTA-CCCTAAC-TAG
1 CAATCTTTTACCCTAACCA-GAGGGCAAGATTGAAGACCATCT-GATCTTTTACCCCGATCAT-G
* *
617 AGGGTAAGATTGAAGACCATC
63 -GGG-CAGATTGAAGA-AATC
* * * * * * ** *
638 CGATCTTTCACCCCAATCATG-GGG-TAGATTGAAGA-AATCCAATCTTTTACCCCGA-CTATGA
1 CAATCTTTTACCCTAACCA-GAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATC-ATGG
* * *
699 GGTAGATCGAAGCAATC
64 GGCAGATTGAAGAAATC
* * * * *
716 CAATCTTTTACCCCAACCAGATGGCAA-ATTGAAGACCATCCGATCTCTTACCCCGACCATGGGG
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGGGG
*
780 CAGATTGAA-ATAATT
66 CAGATTGAAGA-AATC
795 CAATCTTTTACCC
1 CAATCTTTTACCC
808 CTAAAACTAT
Statistics
Matches: 545, Mismatches: 83, Indels: 43
0.81 0.12 0.06
Matches are distributed among these distances:
77 2 0.00
78 47 0.09
79 144 0.26
80 345 0.63
81 6 0.01
82 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (80 bp):
CAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGGGG
CAGATTGAAGAAATC
Found at i:433 original size:199 final size:199
Alignment explanation
Indices: 282--807 Score: 738
Period size: 199 Copynumber: 2.7 Consensus size: 199
272 AGATCATCTG
* ** *
282 ATCTTTTACCCCGATCATGGGGTAGATGGAAGAAATTTAAT-TTTTACCCTAACTAGAGGGTAAG
1 ATCTTTTACCCCGATCATGGGGTAGATCGAAGAAATCCAATCTTTTACCCTAACTAGAGGGCAAG
* * *
346 ATTGAAGACCATCTGATCTTTTACCCCGATCATGGGACAGATTGAAGAAATCCAATCTTTTACCC
66 ATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATTCAATCTTTTACCC
* * *
411 TAACCAGAGGGAAATATTGAAGACCATCTGATCTTTTACCCCGATCATGGGGTAGATTGAAGAAA
131 TAACCAGAGGGAAAGATTGAAGACCATCCGATCTTTTACCCCAATCATGGGGTAGATTGAAGAAA
476 TCCA
196 TCCA
* * * * * *
480 ATCTTTTACCCCGATCATGGGGCAGTTTGAAGAAATCCAATNTTTTATCATAA-TCAGAGGGCAA
1 ATCTTTTACCCCGATCATGGGGTAGATCGAAGAAATCCAATCTTTTACCCTAACT-AGAGGGCAA
* *
544 GATTGAAGACCATCCGATCTTTAACCCCGATCATGGGGCAGATTAAAGAAATTCAATCTTTTACC
65 GATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATTCAATCTTTTACC
* * *
609 CTAACTAGAGGGTAAGATTGAAGACCATCCGATCTTTCACCCCAATCATGGGGTAGATTGAAGAA
130 CTAACCAGAGGGAAAGATTGAAGACCATCCGATCTTTTACCCCAATCATGGGGTAGATTGAAGAA
674 ATCCA
195 ATCCA
* * * * *
679 ATCTTTTACCCCGA-CTATGAGGTAGATCGAAGCAATCCAATCTTTTACCCCAACCAGATGGCAA
1 ATCTTTTACCCCGATC-ATGGGGTAGATCGAAGAAATCCAATCTTTTACCCTAACTAGAGGGCAA
* *
743 -ATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCAGATTGAA-ATAATTCAATCTTTTAC
65 GATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGA-AATTCAATCTTTTAC
806 CC
129 CC
808 CTAAAACTAT
Statistics
Matches: 289, Mismatches: 34, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
197 1 0.00
198 97 0.34
199 191 0.66
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.27
Consensus pattern (199 bp):
ATCTTTTACCCCGATCATGGGGTAGATCGAAGAAATCCAATCTTTTACCCTAACTAGAGGGCAAG
ATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATTCAATCTTTTACCC
TAACCAGAGGGAAAGATTGAAGACCATCCGATCTTTTACCCCAATCATGGGGTAGATTGAAGAAA
TCCA
Found at i:510 original size:159 final size:160
Alignment explanation
Indices: 79--808 Score: 636
Period size: 159 Copynumber: 4.6 Consensus size: 160
69 TTACAACCTT
* * * *
79 CAATCTTTTACCCTAACCAGAGGGCAAGATTTAAAACCATATGATCTTTTACCTCGATCATGGGG
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGGGG
* * * * * * *** *
144 CAGATTGAAGAAATCTAATCTTTTACCCTAACCA-GAAGGCAAGATTGAAGATCATTTGATATTT
66 TAGATTGAAGAAATCCAATCTTTTACCCCAATCATGAGGGC-AGATTGAAGA-AATCCAATCTTT
*
208 TAACCCGATCATG-GGGCAGATTGAAGAAATC
129 TACCCCGATCATGAGGGCAGATTGAAGAAATC
* *
239 CAATCTTTTATCCTAACCAGAGGGCAAGA-TGAAAGATCATCTGATCTTTTACCCCGATCATGGG
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTG-AAGACCATCTGATCTTTTACCCCGATCATGGG
* ** * * * **
303 GTAGATGGAAGAAATTTAAT-TTTTACCCTAA-C-TAGAGGGTAAGATTGAAGACCATCTGATCT
65 GTAGATTGAAGAAATCCAATCTTTTACCCCAATCAT-GAGGG-CAGATTGAAGA-AATCCAATCT
*
365 TTTACCCCGATCATG-GGACAGATTGAAGAAATC
127 TTTACCCCGATCATGAGGGCAGATTGAAGAAATC
* *
398 CAATCTTTTACCCTAACCAGAGGGAAATATTGAAGACCATCTGATCTTTTACCCCGATCATGGGG
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGGGG
* * *
463 TAGATTGAAGAAATCCAATCTTTTACCCCGATCATG-GGGCAGTTTGAAGAAATCCAATNTTTTA
66 TAGATTGAAGAAATCCAATCTTTTACCCCAATCATGAGGGCAGATTGAAGAAATCCAATCTTTTA
* *** *
527 TCATAATCA-GAGGGCAAGATTGAAGACCATC
131 CCCCGATCATGAGGGC-AGATTGAAGA-AATC
* * ** * * * * * *
558 CGATCTTTAACCCCGATCATG-GGGC-AGATTAAAGA-AAT-TCAATCTTTTA-CCCTAAC-TAG
1 CAATCTTTTACCCTAACCA-GAGGGCAAGATTGAAGACCATCT-GATCTTTTACCCCGATCAT-G
* * * *
617 AGGGTAAGATTGAAGACCATCCGATCTTTCACCCCAATCATG-GGGTAGATTGAAGAAATCCAAT
63 -GGGT-AGATTGAAGA-AATCCAATCTTTTACCCCAATCATGAGGGCAGATTGAAGAAATCCAAT
* * *
681 CTTTTACCCCGA-CTATGA-GGTAGATCGAAGCAATC
125 CTTTTACCCCGATC-ATGAGGGCAGATTGAAGAAATC
* * * * *
716 CAATCTTTTACCCCAACCAGATGGCAA-ATTGAAGACCATCCGATCTCTTACCCCGACCATGGGG
1 CAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGGGG
* *
780 CAGATTGAA-ATAATTCAATCTTTTACCCC
66 TAGATTGAAGA-AATCCAATCTTTTACCCC
809 TAAAACTATA
Statistics
Matches: 463, Mismatches: 82, Indels: 53
0.77 0.14 0.09
Matches are distributed among these distances:
156 1 0.00
157 24 0.05
158 69 0.15
159 198 0.43
160 164 0.35
161 6 0.01
162 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (160 bp):
CAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGGGG
TAGATTGAAGAAATCCAATCTTTTACCCCAATCATGAGGGCAGATTGAAGAAATCCAATCTTTTA
CCCCGATCATGAGGGCAGATTGAAGAAATC
Found at i:859 original size:50 final size:51
Alignment explanation
Indices: 796--891 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 51
786 GAAATAATTC
* * *
796 AATCTTTTACCCCTAAAACTATAGAGGGGCAAATTGAAACT-ACAGAAGAA
1 AATCTTATACCCCTAAAACTATAGAGGAGCAAATTAAAACTCACAGAAGAA
* *
846 AATCTTATACCCCTAAAATTATAGAGGAGCGAATTAAAACTCACAG
1 AATCTTATACCCCTAAAACTATAGAGGAGCAAATTAAAACTCACAG
892 TAGTAAACCT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 36 0.90
51 4 0.10
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.23
Consensus pattern (51 bp):
AATCTTATACCCCTAAAACTATAGAGGAGCAAATTAAAACTCACAGAAGAA
Found at i:1542 original size:39 final size:39
Alignment explanation
Indices: 1464--1728 Score: 194
Period size: 39 Copynumber: 6.7 Consensus size: 39
1454 NNNNNNNNNN
* * * *
1464 GATTGAAGACCATCCGATCTTTTACCCCGA-TCATGGGGCA
1 GATTGAAGA-AATCCAATCTTTTACCCCAACT-ATAGGGCA
* *
1504 GATTGAAGAAATCCAATCTTTTACCCTAACTAAAGGGCAA
1 GATTGAAGAAATCCAATCTTTTACCCCAACTATAGGGC-A
* * * * * *
1544 GATTAAAGACCATCCGATCTTTCACCCCAA-TCATGGGGTA
1 GATTGAAGA-AATCCAATCTTTTACCCCAACT-ATAGGGCA
* * *
1584 GATTGAAGAAATCCAATCTTTTACCCCGACTATGGGGTA
1 GATTGAAGAAATCCAATCTTTTACCCCAACTATAGGGCA
* * * * *
1623 GATCGAAGCAATCCAATCTTTTACCCCAACCAGATGGCA
1 GATTGAAGAAATCCAATCTTTTACCCCAACTATAGGGCA
* * * * * *
1662 GATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCA
1 GATTGAAGA-AATCCAATCTTTTACCCCAACTATAGGGCA
* *
1702 AATTGAA-ATAATTCAATCTTTTACCCC
1 GATTGAAGA-AATCCAATCTTTTACCCC
1729 TAAAACTATA
Statistics
Matches: 177, Mismatches: 42, Indels: 13
0.76 0.18 0.06
Matches are distributed among these distances:
39 98 0.55
40 59 0.33
41 20 0.11
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (39 bp):
GATTGAAGAAATCCAATCTTTTACCCCAACTATAGGGCA
Found at i:1721 original size:79 final size:78
Alignment explanation
Indices: 1500--1728 Score: 199
Period size: 79 Copynumber: 2.9 Consensus size: 78
1490 CCGATCATGG
* ** * ** ** * *
1500 GGCAGATTGAAGAAATCCAATCTTTTACCCTAACTAAAGGGCAAGATTAAAGACCATCCGATCTT
1 GGCAGATTGAAGAAATCCAATCTCTTACCCCGACCATGGGGCAA-ATCGAA-ACAATCCAATCTT
* * *
1565 TCACCCCAATCATG-G
64 TTACCCCAACCA-GAT
* * * * * *
1580 GGTAGATTGAAGAAATCCAATCTTTTACCCCGACTATGGGGTAGATCGAAGCAATCCAATCTTTT
1 GGCAGATTGAAGAAATCCAATCTCTTACCCCGACCATGGGGCAAATCGAAACAATCCAATCTTTT
1645 ACCCCAACCAGAT
66 ACCCCAACCAGAT
* * * * *
1658 GGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCAAATTGAAATAATTCAATCTTT
1 GGCAGATTGAAGA-AATCCAATCTCTTACCCCGACCATGGGGCAAATCGAAACAATCCAATCTTT
1723 TACCCC
65 TACCCC
1729 TAAAACTATA
Statistics
Matches: 121, Mismatches: 26, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
77 1 0.01
78 32 0.26
79 51 0.42
80 37 0.31
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (78 bp):
GGCAGATTGAAGAAATCCAATCTCTTACCCCGACCATGGGGCAAATCGAAACAATCCAATCTTTT
ACCCCAACCAGAT
Found at i:1806 original size:50 final size:51
Alignment explanation
Indices: 1716--1811 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 51
1706 GAAATAATTC
* * *
1716 AATCTTTTACCCCTAAAACTATAGAGGGGAAAATTGAAACT-ACAGAAGAA
1 AATCTTATACCCCTAAAACTATAGAGGAGAAAATTAAAACTCACAGAAGAA
* ***
1766 AATCTTATACCCCTAAAATTATAGAGGAGCTGATTAAAACTCACAG
1 AATCTTATACCCCTAAAACTATAGAGGAGAAAATTAAAACTCACAG
1812 TAGTAAACCT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 34 0.89
51 4 0.11
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.24
Consensus pattern (51 bp):
AATCTTATACCCCTAAAACTATAGAGGAGAAAATTAAAACTCACAGAAGAA
Done.