Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012633.1 Kokia drynarioides strain JFW-HI SEQ_127642, 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: 2980
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.25
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:62 original size:43 final size:43
Alignment explanation
Indices: 1--1107 Score: 1201
Period size: 43 Copynumber: 25.8 Consensus size: 43
* *
1 ATCTATACTAGCACACACAGTGCATCATCGGGTAAATCGAAGC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* * * ** *
44 ATCTACACTGGTACACACAGTGTATCATCGAATAAATCGAAGC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* * * * * *
87 ATTTATACTAGCATACACAGTGTATCATCAGGTAAATCGAGAC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* * * * * *
130 ATCTATATTGGCACACATAATGCATTATCAGATAAATCG-GGAC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGG-C
* * **
173 ATTTATACT-G-ACACACAGTGCATCATCGAGTAAATCGATTC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* * *
214 ATTTATACTGGCACACACAGTGCATTATCGGGTAAATCAAGGC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* * * *
257 ATTTATACTGGTACACAGAGTGCATCATCGGGTAAATCGATGC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* * * * * * *
300 ATCTATACTAGCACACAAAGTGCATCATCTGGTAAACCAATGT
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* * * * ** * *
343 ATTTATACTGACACACACAGTGCATAATCGAGTAACCCGAAGA
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* * * *
386 ATCTATACTGGCACACACAGTACGTCATCGAGTAAACCG-GTGC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAG-GC
* * *
429 ATCTATACTAGCACACACAATGCATCATCGGG-AAAACTGAGGC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATC-GAGGC
* * *
472 ATCTATACTGACACACAGAGTGCATCATCGGGTAAATCGATGC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* * * * *
515 ATTTATATTGGCACATAGAGTGCATCATCAGGTAAA-CTGAGGC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATC-GAGGC
*
558 ATCTATACTGACACACACAGTGCATCATCGGGTAAATCGAGGC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* *
601 ATCTATACTGGCGCACACTCAGTGCATCATCGGGTAAACCGAGGC
1 ATCTATACT-G-GCACACACAGTGCATCATCGGGTAAATCGAGGC
*
646 ATCTATACTGG--CACACAGTGCATCATCGGGTAAA-CTGAGAC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATC-GAGGC
* *
687 ATCTATACTGGCACACACAGTGCATTATCGGGTAAACCGAGGC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* * *
730 ATCTATACTGGTACACACAGTGCATCATCGGGTAAACCGTGGC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* *
773 ATTTATACTGGCACACACAGTGCATCATCGGGCAAATCGAGGC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* *
816 ATTTATACTGGCACACACAGTGCATCATCGAGTAAATCGAGGC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* * * * *
859 ATTTATACTAGCACACACAGTGCATCATCGGGTAAACCAAGAC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* * * * *
902 ATCTATACTAGCACACATAGTGCATCCTTGGGTAAACCGAGGC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* * * *
945 ATCTATATTGGCACACACAGTGCATAATCGAGTAAATCGAGGT
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* * * **
988 ATTTATATTAG--CACACAGTGCATCATCAAGTAAATCGAGGC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* *
1029 ATTTATACTGGCACACACAGTGCATCATCGAGTAAATCGAGGC
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
* *
1072 ATTTATACTAGCACACACAGTGCATCATCGGGTAAA
1 ATCTATACTGGCACACACAGTGCATCATCGGGTAAA
1108 CCNNNNNNNN
Statistics
Matches: 902, Mismatches: 144, Indels: 36
0.83 0.13 0.03
Matches are distributed among these distances:
40 1 0.00
41 104 0.12
42 8 0.01
43 741 0.82
44 9 0.01
45 39 0.04
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (43 bp):
ATCTATACTGGCACACACAGTGCATCATCGGGTAAATCGAGGC
Found at i:281 original size:23 final size:22
Alignment explanation
Indices: 213--281 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
203 TAAATCGATT
*
213 CATTTATACTGGCACACACAGTG
1 CATTTATACTGGTACACA-AGTG
* *
236 CA-TTAT-CGGGTAAATCAAG-G
1 CATTTATACTGGTACA-CAAGTG
256 CATTTATACTGGTACACAGAGTG
1 CATTTATACTGGTACACA-AGTG
279 CAT
1 CAT
282 CATCGGGTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
20 3 0.08
21 13 0.36
22 14 0.39
23 6 0.17
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (22 bp):
CATTTATACTGGTACACAAGTG
Found at i:1227 original size:43 final size:43
Alignment explanation
Indices: 1161--1432 Score: 314
Period size: 43 Copynumber: 6.4 Consensus size: 43
1151 NNNNNNNAGA
* * * * * *
1161 CATCTATACTAGCACACATAGTGCATCCTTGGGTAAACCGAGG
1 CATCTATACTGGCACACACAGTGCATCATCGAGTAAATCGAGG
* *
1204 CATCTATATTGGCACACACAGTGCATCATCGAGTAAACCGAGG
1 CATCTATACTGGCACACACAGTGCATCATCGAGTAAATCGAGG
* * * * *
1247 TATTTATATTAGCACACACAGTGCATCATCAAGTAAATCGAGG
1 CATCTATACTGGCACACACAGTGCATCATCGAGTAAATCGAGG
* * ** *
1290 CATTTATAGTTACACACACAGTGCATCATCAAGTAAATCGAGG
1 CATCTATACTGGCACACACAGTGCATCATCGAGTAAATCGAGG
* * *
1333 CATTTATAGTGGCACACACAGTGCATCATCGGGTAAATCGAGG
1 CATCTATACTGGCACACACAGTGCATCATCGAGTAAATCGAGG
* * *
1376 CATCTATACT-G-ACACACAGTGCATCGTCGGGTAAATCGATG
1 CATCTATACTGGCACACACAGTGCATCATCGAGTAAATCGAGG
1417 CATCTATACTGGCACA
1 CATCTATACTGGCACA
1433 TTCTGGGAAT
Statistics
Matches: 204, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
41 38 0.19
42 2 0.01
43 164 0.80
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (43 bp):
CATCTATACTGGCACACACAGTGCATCATCGAGTAAATCGAGG
Found at i:1248 original size:260 final size:213
Alignment explanation
Indices: 4--1432 Score: 641
Period size: 215 Copynumber: 6.7 Consensus size: 213
1 ATC
** * * * * * *
4 TATACT-AGCACACACAGTGCATCATCGGGTAAATCGAAGCATCTACACTGGTACACACAGTGTA
1 TATACTGA-CACACACAGTGCATCATCAAGTAAATCGAGGCATTTATACTAGCACACACAGTGCA
** * * * * * * ** * *
68 TCATCGAATAAATC-GAAGCATTTATACTAGCATACACAGTGTATCATCAGGTAAATCGAGACAT
65 TCATCGGGTAAACCAG-A-CATCTATACTAGCACACATAGTGCATCCTTGGGTAAACCGAGGCAT
* * * * * *
132 CTATATTGGCACACATAATGCATTATC-AGATAAATCG-GGACATTTATACT-GACACACAGTGC
128 CTATATTGGCACACACAGTGCATAATCGAG-TAAACCGAGG-TATTTATATTAGACACACAGTGC
* **
194 ATCATCGAGTAAATCGATTCATT
191 ATCATCAAGTAAATCGAGGCATT
* * ** * * * *
217 TATACTGGCACACACAGTGCATTATCGGGTAAATCAAGGCATTTATACTGGTACACAGAGTGCAT
1 TATACTGACACACACAGTGCATCATCAAGTAAATCGAGGCATTTATACTAGCACACACAGTGCAT
* * * * * *
282 CATCGGGTAAATC-GATGCATCTATACTAGCACACAAAGTGCATCATCT-GGTAAACCAATGTAT
66 CATCGGGTAAACCAGA--CATCTATACTAGCACACATAGTGCATCCT-TGGGTAAACCGAGGCAT
* * * * * * * * * * *
345 TTATACTGACACACACAGTGCATAATCGAGTAACCCGAAGAATCTATACTGGCACACACAGTACG
128 CTATATTGGCACACACAGTGCATAATCGAGTAAACCGAGGTATTTATATTAG-ACACACAGTGCA
* * *
410 TCATCGAGTAAACCG-GTGCATC
192 TCATCAAGTAAATCGAG-GCATT
* * * * * *
432 TATACT-AGCACACACAATGCATCATC-GGGAAAACTGAGGCATCTATACT-GACACACAGAGTG
1 TATACTGA-CACACACAGTGCATCATCAAGTAAATC-GAGGCATTTATACTAG-CACACACAGTG
* * * * * * * ** *
494 CATCATCGGGTAAATC-GATGCATTTATATTGGCACATAGAGTGCATCATCAGGTAAACTGAGGC
63 CATCATCGGGTAAACCAGA--CATCTATACTAGCACACATAGTGCATCCTTGGGTAAACCGAGGC
* * * * * * * ** *
558 ATCTATACTGACACACACAGTGCATCATCGGGTAAATCGAGGCATCTATACTGGCGCACACTCAG
126 ATCTATATTGGCACACACAGTGCATAATCGAGTAAACCGAGGTATTTATA-T-TAG-ACACACAG
** * *
623 TGCATCATCGGGTAAACCGAGGCATC
188 TGCATCATCAAGTAAATCGAGGCATT
* ** * * *
649 TATACTG--GCACACAGTGCATCATCGGGTAAA-CTGAGACATCTATACTGGCACACACAGTGCA
1 TATACTGACACACACAGTGCATCATCAAGTAAATC-GAGGCATTTATACTAGCACACACAGTGCA
* * * * * * * * *
711 TTATCGGGTAAACCGAGGCATCTATACTGGTACACACAGTGCATCATCGGGTAAACCGTGGCATT
65 TCATCGGGTAAACC-AGACATCTATACTAGCACACATAGTGCATCCTTGGGTAAACCGAGGCATC
* * * * * * * *
776 TATACTGGCACACACAGTGCATCATCGGGCAAATCGAGGCATTTATACTGGCACACACAGTGCAT
129 TATATTGGCACACACAGTGCATAATCGAGTAAACCGAGGTATTTATATTAG-ACACACAGTGCAT
*
841 CATCGAGTAAATCGAGGCATT
193 CATCAAGTAAATCGAGGCATT
** * * * * *
862 TATACT-AGCACACACAGTGCATCATCGGGTAAACCAAGACATCTATACTAGCACACATAGTGCA
1 TATACTGA-CACACACAGTGCATCATCAAGTAAATCGAGGCATTTATACTAGCACACACAGTGCA
* * * * * * ** * * * * *
926 TCCTTGGGTAAACCGAGGCATCTATATTGGCACACACAGTGCATAATCGAGTAAATCGAGGTATT
65 TCATCGGGTAAACC-AGACATCTATACTAGCACACATAGTGCATCCTTGGGTAAACCGAGGCATC
* * * * * * *
991 TATATTAG--CACACAGTGCATCATCAAGTAAATCGAGGCATTTATACTGGCACACACAGTGCAT
129 TATATTGGCACACACAGTGCATAATCGAGTAAACCGAGGTATTTATATTAG-ACACACAGTGCAT
*
1054 CATCGAGTAAATCGAGGCATT
193 CATCAAGTAAATCGAGGCATT
** * ************************
1075 TATACT-AGCACACACAGTGCATCATCGGGTAAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
1 TATACTGA-CACACACAGTGCATCATCAAGTAAATC-----GAGGCATTTATACTAGCACACACA
*******************
1139 NNNNNNNNNNNNNNNNNNNAGACATCTATACTAGCACACATAGTGCATCCTTGGGTAAACCGAGG
60 GTGCATCATCGGGTAAACCAGACATCTATACTAGCACACATAGTGCATCCTTGGGTAAACCGAGG
*
1204 CATCTATATTGGCACACACAGTGCATCATCGAGTAAACCGAGGTATTTATATTAGCACACACAGT
125 CATCTATATTGGCACACACAGTGCATAATCGAGTAAACCGAGGTATTTATATTAG-ACACACAGT
1269 GCATCATCAAGTAAATCGAGGCATT
189 GCATCATCAAGTAAATCGAGGCATT
* * * *
1294 TATAGTTACACACACAGTGCATCATCAAGTAAATCGAGGCATTTATAGTGGCACACACAGTGCAT
1 TATACTGACACACACAGTGCATCATCAAGTAAATCGAGGCATTTATACTAGCACACACAGTGCAT
* * * * * * *
1359 CATCGGGTAAATCGAGGCATCTATACT-G-ACACACAGTGCATCGTCGGGTAAATCGATGCATCT
66 CATCGGGTAAA-CCAGACATCTATACTAGCACACATAGTGCATCCTTGGGTAAACCGAGGCATCT
*
1422 ATACTGGCACA
130 ATATTGGCACA
1433 TTCTGGGAAT
Statistics
Matches: 953, Mismatches: 230, Indels: 66
0.76 0.18 0.05
Matches are distributed among these distances:
212 1 0.00
213 324 0.34
214 12 0.01
215 425 0.45
216 7 0.01
217 83 0.09
218 1 0.00
219 99 0.10
220 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.23
Consensus pattern (213 bp):
TATACTGACACACACAGTGCATCATCAAGTAAATCGAGGCATTTATACTAGCACACACAGTGCAT
CATCGGGTAAACCAGACATCTATACTAGCACACATAGTGCATCCTTGGGTAAACCGAGGCATCTA
TATTGGCACACACAGTGCATAATCGAGTAAACCGAGGTATTTATATTAGACACACAGTGCATCAT
CAAGTAAATCGAGGCATT
Found at i:1272 original size:303 final size:255
Alignment explanation
Indices: 12--1432 Score: 915
Period size: 258 Copynumber: 5.5 Consensus size: 255
2 TCTATACTAG
** * * * * * *
12 CACACACAGTGCATCATCGGGTAAATCGAAGCATCTACACTGGTACACACAGTGTATCATCGAAT
1 CACACACAGTGCATCATCAAGTAAATCGAGGCATTTATACTGGCACACACAGTGCATCATCGAGT
* * * * * * * *
77 AAATCGAAGCATTTATACTAGCATACACAGTGTATCATCAGGTAAATCGAGACATCTATATTGGC
66 AAATCGAGGCATCTATACT-G-ACACACAGTGCATCATCGGGTAAA-CCAGACATCTATACTAGC
* * * * * * ** *
142 ACACATAATGCATTATCAGATAAATCGGGACATTTATACT-G-ACACACAGTGCATCATCGAGTA
128 ACACACAGTGCATCATCGGGTAAACCAAGACATCTATACTAGCACACACAGTGCATCATCGAGTA
* ** * * * * ** * * **
205 AATCGATTCATTTATACTGGCACACACAGTGCATTATCGGGTAAATCAAGGCATTTATACTGG
193 AACCGAGGCATCTATATTAGCACACACAGTGCATAATCAAGTAAATCGAGGCATTTATAGTTA
* * ** * * * *
268 TACACAGAGTGCATCATCGGGTAAATCGATGCATCTATACTAGCACACAAAGTGCATCATCTG-G
1 CACACACAGTGCATCATCAAGTAAATCGAGGCATTTATACTGGCACACACAGTGCATCATC-GAG
* * * * * * * * *
332 TAAACCAATGTATTTATACTGACACACACAGTGCATAATCGAGTAACCCGAAGA-ATCTATACTG
65 TAAATCGAGGCATCTATACTG--ACACACAGTGCATCATCGGGTAAACC--AGACATCTATACTA
* * * * * * *
396 GCACACACAGTACGTCATCGAGTAAACC-GGTGCATCTATACTAGCACACACAATGCATCATCGG
126 GCACACACAGTGCATCATCGGGTAAACCAAG-ACATCTATACTAGCACACACAGTGCATCATCGA
* * * * * ** *
460 GAAAACTGAGGCATCTATACT-GACACACAGAGTGCATCATCGGGTAAATCGATGCATTTATA-T
190 GTAAACCGAGGCATCTATATTAG-CACACACAGTGCATAATCAAGTAAATCGAGGCATTTATAGT
*
523 TGG
254 T-A
* * * * * *
526 CACATAGAGTGCATCATCAGGTAAA-CTGAGGCATCTATACTGACACACACAGTGCATCATCGGG
1 CACACACAGTGCATCATCAAGTAAATC-GAGGCATTTATACTGGCACACACAGTGCATCATCGAG
* *
590 TAAATCGAGGCATCTATACTGGCGCACACTCAGTGCATCATCGGGTAAACCGAGGCATCTATACT
65 TAAATCGAGGCATCTATACT---G-ACACACAGTGCATCATCGGGTAAACC-AGACATCTATACT
* ** * * *
655 -G-GCACACAGTGCATCATCGGGTAAACTGAGACATCTATACTGGCACACACAGTGCATTATCGG
125 AGCACACACAGTGCATCATCGGGTAAACCAAGACATCTATACTAGCACACACAGTGCATCATCGA
* * * * ** * * * *
718 GTAAACCGAGGCATCTATACTGGTACACACAGTGCATCATCGGGTAAACCGTGGCATTTATACTG
190 GTAAACCGAGGCATCTATATTAGCACACACAGTGCATAATCAAGTAAATCGAGGCATTTATAGTT
*
783 G
255 A
** *
784 CACACACAGTGCATCATCGGGCAAATCGAGGCATTTATACTGGCACACACAGTGCATCATCGAGT
1 CACACACAGTGCATCATCAAGTAAATCGAGGCATTTATACTGGCACACACAGTGCATCATCGAGT
*
849 AAATCGAGGCATTTATACTAGCACACACAGTGCATCATCGGGTAAACCAAGACATCTATACTAGC
66 AAATCGAGGCATCTATACT-G-ACACACAGTGCATCATCGGGTAAACC-AGACATCTATACTAGC
* * * * * * * *
914 ACACATAGTGCATCCTTGGGTAAACCGAGGCATCTATATTGGCACACACAGTGCATAATCGAGTA
128 ACACACAGTGCATCATCGGGTAAACCAAGACATCTATACTAGCACACACAGTGCATCATCGAGTA
* * * * * **
979 AATCGAGGTATTTATATTAG--CACACAGTGCATCATCAAGTAAATCGAGGCATTTATACTGG
193 AACCGAGGCATCTATATTAGCACACACAGTGCATAATCAAGTAAATCGAGGCATTTATAGTTA
* * *
1040 CACACACAGTGCATCATCGAGTAAATCGAGGCATTTATACTAGCACACACAGTGCATCATCGGGT
1 CACACACAGTGCATCATCAAGTAAATCGAGGCATTTATACTGGCACACACAGTGCATCATCGAGT
* *****************************************
1105 AAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGACATCTATAC
66 AAATC-------GAGGCATCTATACTGACACACAGTGCATCATCGGGTAAACCAGACATCTATAC
* * * * * * *
1170 TAGCACACATAGTGCATCCTTGGGTAAACCGAGGCATCTATATTGGCACACACAGTGCATCATCG
124 TAGCACACACAGTGCATCATCGGGTAAACCAAGACATCTATACTAGCACACACAGTGCATCATCG
* * *
1235 AGTAAACCGAGGTATTTATATTAGCACACACAGTGCATCATCAAGTAAATCGAGGCATTTATAGT
189 AGTAAACCGAGGCATCTATATTAGCACACACAGTGCATAATCAAGTAAATCGAGGCATTTATAGT
1300 TA
254 TA
* *
1302 CACACACAGTGCATCATCAAGTAAATCGAGGCATTTATAGTGGCACACACAGTGCATCATCGGGT
1 CACACACAGTGCATCATCAAGTAAATCGAGGCATTTATACTGGCACACACAGTGCATCATCGAGT
* * *
1367 AAATCGAGGCATCTATACTGACACACAGTGCATCGTCGGGTAAATC-GATGCATCTATACTGGCA
66 AAATCGAGGCATCTATACTGACACACAGTGCATCATCGGGTAAACCAGA--CATCTATACTAGCA
1431 CA
129 CA
1433 TTCTGGGAAT
Statistics
Matches: 925, Mismatches: 208, Indels: 64
0.77 0.17 0.05
Matches are distributed among these distances:
254 2 0.00
255 4 0.00
256 281 0.30
257 10 0.01
258 385 0.42
259 7 0.01
260 131 0.14
261 1 0.00
262 104 0.11
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.23
Consensus pattern (255 bp):
CACACACAGTGCATCATCAAGTAAATCGAGGCATTTATACTGGCACACACAGTGCATCATCGAGT
AAATCGAGGCATCTATACTGACACACAGTGCATCATCGGGTAAACCAGACATCTATACTAGCACA
CACAGTGCATCATCGGGTAAACCAAGACATCTATACTAGCACACACAGTGCATCATCGAGTAAAC
CGAGGCATCTATATTAGCACACACAGTGCATAATCAAGTAAATCGAGGCATTTATAGTTA
Done.