Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002188.1 Kokia drynarioides strain JFW-HI SEQ_114160, 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: 3967
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Found at i:175 original size:29 final size:30
Alignment explanation
Indices: 99--176 Score: 115
Period size: 29 Copynumber: 2.7 Consensus size: 30
89 GGATACCCGA
* *
99 GGGTAAAACGGTAA-TTTTGGACACTTCAG
1 GGGTAACATGGTAATTTTTGGACACTTCAG
*
128 GGGCAACATGGTAATTTTTGGACAC-TCAG
1 GGGTAACATGGTAATTTTTGGACACTTCAG
157 GGGTAACATGGTAATTTTTG
1 GGGTAACATGGTAATTTTTG
177 AAAAGTTTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 34 0.77
30 10 0.23
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (30 bp):
GGGTAACATGGTAATTTTTGGACACTTCAG
Found at i:232 original size:29 final size:29
Alignment explanation
Indices: 164--393 Score: 98
Period size: 29 Copynumber: 7.8 Consensus size: 29
154 CAGGGGTAAC
* * * *
164 ATGGTAATTTTTGAAAAGTTTGGGGTTAAAT
1 ATGG-AATTTTTG-GAAGTTCGAGGTTAAAA
195 ATGTG-ATTTTTGGAAGTTCGAGGTTAAAA
1 ATG-GAATTTTTGGAAGTTCGAGGTTAAAA
* * *
224 ATGGAATTTTTAGACATTTAG-GGTT-AAA
1 ATGGAATTTTTGGA-AGTTCGAGGTTAAAA
**
252 ATGGTAA-TTTTGGAAAAATCGAGGTTAAAA
1 ATGG-AATTTTTGG-AAGTTCGAGGTTAAAA
* ** * *
282 ATAGAATTTTTGTGAAGTTTAAGGGTCAAA
1 ATGGAATTTTTG-GAAGTTCGAGGTTAAAA
* * *
312 ATGTAATTGTTGGAAAACTT-G-GGATT-AAA
1 ATGGAATTTTTGG--AAGTTCGAGG-TTAAAA
* * *
341 ATGTAAATTTTGGAAGTTC-AGGGGTAAAA
1 ATGGAATTTTTGGAAGTTCGA-GGTTAAAA
* *
370 ATGTAATTTTTGGAAAGTTTGAGG
1 ATGGAATTTTTGG-AAGTTCGAGG
394 GTCCAAATAT
Statistics
Matches: 151, Mismatches: 30, Indels: 37
0.69 0.14 0.17
Matches are distributed among these distances:
27 4 0.03
28 17 0.11
29 71 0.47
30 49 0.32
31 9 0.06
32 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.37
Consensus pattern (29 bp):
ATGGAATTTTTGGAAGTTCGAGGTTAAAA
Found at i:274 original size:58 final size:60
Alignment explanation
Indices: 169--431 Score: 186
Period size: 58 Copynumber: 4.5 Consensus size: 60
159 GTAACATGGT
* * * * * ** *
169 AATTTTTGAAAAGTTT-GGGGTTAAATATGTGATTTTTGG-AAGTTCGAGGTTAAAAATGG
1 AATTTTTGAGAAGTTTAAGGGTCAAA-ATGTAATTGTTGGAAAAATCGAGGTTAAAAATAG
*
228 AATTTTT-AGACA-TTT-AGGGTTAAAATGGTAATT-TTGGAAAAATCGAGGTTAAAAATAG
1 AATTTTTGAGA-AGTTTAAGGGTCAAAAT-GTAATTGTTGGAAAAATCGAGGTTAAAAATAG
* * *
286 AATTTTTGTGAAGTTTAAGGGTCAAAATGTAATTGTTGGAAAACTTG-GGATT-AAAAT-G
1 AATTTTTGAGAAGTTTAAGGGTCAAAATGTAATTGTTGGAAAAATCGAGG-TTAAAAATAG
* * * * * ** * * ** *
344 TAAATTTTG-GAAGTTCAGGGGTAAAAATGTAATTTTTGGAAAGTTTGAGGGTCCAAATAT
1 -AATTTTTGAGAAGTTTAAGGGTCAAAATGTAATTGTTGGAAAAATCGAGGTTAAAAATAG
*
404 AATTTTTGAAAAGTTTAAGGGTCAAAAT
1 AATTTTTGAGAAGTTTAAGGGTCAAAAT
432 ATGTTTTTAG
Statistics
Matches: 166, Mismatches: 25, Indels: 25
0.77 0.12 0.12
Matches are distributed among these distances:
57 6 0.04
58 77 0.46
59 46 0.28
60 37 0.22
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (60 bp):
AATTTTTGAGAAGTTTAAGGGTCAAAATGTAATTGTTGGAAAAATCGAGGTTAAAAATAG
Found at i:313 original size:30 final size:29
Alignment explanation
Indices: 286--431 Score: 125
Period size: 30 Copynumber: 4.9 Consensus size: 29
276 TTAAAAATAG
286 AATTTTTGTGAAGTTTAAGGGTCAAAATGT
1 AATTTTTG-GAAGTTTAAGGGTCAAAATGT
* ** *
316 AATTGTTGGAAAACTT--GGGATTAAAATGT
1 AATTTTTGG-AAGTTTAAGGG-TCAAAATGT
* * * *
345 AAATTTTGGAAGTTCAGGGGTAAAAATGT
1 AATTTTTGGAAGTTTAAGGGTCAAAATGT
* * *
374 AATTTTTGGAAAGTTTGAGGGTCCAAATAT
1 AATTTTTGG-AAGTTTAAGGGTCAAAATGT
*
404 AATTTTTGAAAAGTTTAAGGGTCAAAAT
1 AATTTTTG-GAAGTTTAAGGGTCAAAAT
432 ATGTTTTTAG
Statistics
Matches: 90, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
28 6 0.07
29 32 0.36
30 52 0.58
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (29 bp):
AATTTTTGGAAGTTTAAGGGTCAAAATGT
Found at i:981 original size:27 final size:26
Alignment explanation
Indices: 942--992 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
932 TTTGCCTTTT
942 AAAAATAAATTTTGCCATTCCCTTAAA
1 AAAAATAAATTTT-CCATTCCCTTAAA
**
969 AAAAATAGTTTTTCCATTCCCTTA
1 AAAAATAAATTTTCCATTCCCTTA
993 TTCTTTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (26 bp):
AAAAATAAATTTTCCATTCCCTTAAA
Found at i:1477 original size:9 final size:9
Alignment explanation
Indices: 1461--1511 Score: 54
Period size: 9 Copynumber: 6.0 Consensus size: 9
1451 GACTTTTTTT
1461 TTAATATTA
1 TTAATATTA
*
1470 TTATTATTA
1 TTAATATTA
1479 TTAATATTA
1 TTAATATTA
* *
1488 TTAGTGTTA
1 TTAATATTA
1497 -TAATA--A
1 TTAATATTA
1503 TTAATATTA
1 TTAATATTA
1512 ATATTAATGG
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
6 1 0.03
7 5 0.15
8 3 0.09
9 24 0.73
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (9 bp):
TTAATATTA
Found at i:2263 original size:6 final size:6
Alignment explanation
Indices: 2242--2363 Score: 63
Period size: 6 Copynumber: 21.0 Consensus size: 6
2232 TTAAAACCAT
* * ** **
2242 TTTAAA TTT-AA -CTAAA TTTAAA TATAAA TTTAAA AATAAA AATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** * * **
2288 TATAAA TTTAAA TTTAAA AATAAA TTTAAG TTCAAA AATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
2336 -ATCAA TTTAAA CTT-AA TATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
2364 ATCAAAAGTT
Statistics
Matches: 84, Mismatches: 28, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
4 1 0.01
5 10 0.12
6 73 0.87
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (6 bp):
TTTAAA
Found at i:2271 original size:12 final size:12
Alignment explanation
Indices: 2254--2346 Score: 80
Period size: 12 Copynumber: 7.8 Consensus size: 12
2244 TAAATTTAAC
2254 TAAATTTAAATA
1 TAAATTTAAATA
*
2266 TAAATTTAAAAA
1 TAAATTTAAATA
**
2278 TAAAAATAAATA
1 TAAATTTAAATA
*
2290 TAAATTTAAATT
1 TAAATTTAAATA
** *
2302 TAAAAATAAATT
1 TAAATTTAAATA
* * *
2314 TAAGTTCAAAAA
1 TAAATTTAAATA
2326 TAAATTTAAA-A
1 TAAATTTAAATA
*
2337 TCAATTTAAA
1 TAAATTTAAA
2347 CTTAATATAA
Statistics
Matches: 63, Mismatches: 18, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
11 10 0.16
12 53 0.84
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.35
Consensus pattern (12 bp):
TAAATTTAAATA
Found at i:2287 original size:24 final size:24
Alignment explanation
Indices: 2260--2346 Score: 95
Period size: 24 Copynumber: 3.7 Consensus size: 24
2250 TAACTAAATT
2260 TAAATATAAATTTAAAAATAAAAA
1 TAAATATAAATTTAAAAATAAAAA
**
2284 TAAATATAAATTTAAATTTAAAAA
1 TAAATATAAATTTAAAAATAAAAA
* * * **
2308 TAAATTTAAGTTCAAAAATAAATT
1 TAAATATAAATTTAAAAATAAAAA
*
2332 TAAA-ATCAATTTAAA
1 TAAATATAAATTTAAA
2347 CTTAATATAA
Statistics
Matches: 50, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 7 0.14
24 43 0.86
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.34
Consensus pattern (24 bp):
TAAATATAAATTTAAAAATAAAAA
Found at i:2324 original size:18 final size:18
Alignment explanation
Indices: 2289--2340 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
2279 AAAAATAAAT
*
2289 ATAAATTTAAATTTAAAA
1 ATAAATTTAAATTCAAAA
*
2307 ATAAATTTAAGTTCAAAA
1 ATAAATTTAAATTCAAAA
*
2325 ATAAATTTAAAATCAA
1 ATAAATTTAAATTCAA
2341 TTTAAACTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (18 bp):
ATAAATTTAAATTCAAAA
Found at i:2351 original size:17 final size:17
Alignment explanation
Indices: 2284--2363 Score: 53
Period size: 17 Copynumber: 4.9 Consensus size: 17
2274 AAAATAAAAA
*
2284 TAAATATAAATTTAAATT
1 TAAA-ATAAATTTAAACT
*
2302 TAAAAATAAATTT-AAGT
1 T-AAAATAAATTTAAACT
* *
2319 T-CAA-AAA--TAAATT
1 TAAAATAAATTTAAACT
*
2332 TAAAATCAATTTAAACT
1 TAAAATAAATTTAAACT
*
2349 TAATATAAATTTAAA
1 TAAAATAAATTTAAA
2364 ATCAAAAGTT
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
12 1 0.02
13 4 0.08
14 5 0.10
15 4 0.08
17 22 0.46
18 9 0.19
19 3 0.06
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (17 bp):
TAAAATAAATTTAAACT
Found at i:3036 original size:209 final size:208
Alignment explanation
Indices: 2676--3474 Score: 1024
Period size: 209 Copynumber: 3.8 Consensus size: 208
2666 TTTGGTGTCG
* * *
2676 TTGATTTGGTCTACTTCTCAGTATCTTATCAAGAAGATGACCGTATCACTTGTTTCAATCCACTT
1 TTGATTTGGTATACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCAC-T
* * * *
2741 TTCTGTATCTCATCAGGAAGGCGAATTTTGTCCATTTCTCAGTATCTCATCAGGTAGCTAACCAT
65 TTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * * *
2806 TTTATTGCTTCGACTTGCTTCTTAGTATCTCATCAGGAAGCTGAGGTTCAAAGTTTCGCTCATAT
130 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCATAT
2871 TGAGCTTTGTTTCA
195 TGAGCTTTGTTTCA
* * * * * **
2885 TTGATTTGGTATGCTTCTCTGTATCTTATCAAGAAGATGATCGCATCACTTATTTTGATCCAC-T
1 TTGATTTGGTATACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCACTT
* * * * * * * * *
2949 TCATTGTGTCTCATCCGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATTAGGAAGGTAACCG
66 TC--TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * * * *
3014 CTTTATTGCTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTGGGGTTTGAAGTTTCACTCACA
129 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCATA
*
3079 TTGAGCTTTATTTCA
194 TTGAGCTTTGTTTCA
* * * * * * * *
3094 TTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACTGCCTCACTTGTTTTAATTCGCTT
1 TTGATTTGGTATACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCAC-T
* * *
3159 TTCCGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTGACCAT
65 TTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * *
3224 TTTATTGTTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCCGGGGTTCGAAGTTTCGCTCATAT
130 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCATAT
3289 TGAGCTTTGTTTCA
195 TGAGCTTTGTTTCA
* * * *
3303 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCTTCACTTGTTTCAATCCGCTT
1 TTGATTTGGTATACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCACTT
** * *
3368 CTCTGTATCTCATCAGGAAGAAAAATTTGGTCCACTTCTCAGTATCTAATTAGGAAGCTAACCAT
66 -TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * *
3433 TTTATTGCTTTGACCTGCTTCTTAGTATCTCATCACGAAGCT
130 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT
3475 AACCATTTTA
Statistics
Matches: 503, Mismatches: 82, Indels: 10
0.85 0.14 0.02
Matches are distributed among these distances:
207 3 0.01
208 2 0.00
209 495 0.98
211 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.38
Consensus pattern (208 bp):
TTGATTTGGTATACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCACTT
TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCATATT
GAGCTTTGTTTCA
Found at i:3473 original size:48 final size:48
Alignment explanation
Indices: 3402--3522 Score: 188
Period size: 48 Copynumber: 2.5 Consensus size: 48
3392 ATTTGGTCCA
* * *
3402 CTTCTCAGTATCTAATTAGGAAGCTAACCATTTTATTGCTTTGACCTG
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTAGACCTG
* * *
3450 CTTCTTAGTATCTCATCACGAAGCTAACCATTTTATTGCTTAGACTTG
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTAGACCTG
3498 CTTCTCAGTATCTCATCAGGAAGCT
1 CTTCTCAGTATCTCATCAGGAAGCT
3523 GGGGTTCGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (48 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTAGACCTG
Found at i:3660 original size:257 final size:256
Alignment explanation
Indices: 3193--3730 Score: 797
Period size: 257 Copynumber: 2.1 Consensus size: 256
3183 ATTTGGTCCA
* * *
3193 CTTCTCAGTATCTCATCAAGAAGCTGACCATTTTATTGTTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTAGACCTGCTTCTCAGTATCTCATC
* * * * **
3258 AAGAAGCCGGGGTTCGAAGTTTCGCTCATATTGAGCTTTGTTTCATTGATTTGGTCTACTTCTCA
66 AAGAAGCCGGGGTTCGAAGTTTCGCTCACATGGAGCTTTGTTCCATTGAGTTGGGATACTTCTCA
* *
3323 GTATCTCATCAGGAAGATGACCGCTTCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAG
131 GTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAAGAAG
** * *
3388 AAAAATTTGGTCCACTTCTCAGTATCTAATTAGGAAGCTAACCATTTTATTGCTTTGACCTG
196 AAAAATTCAGTCCACTTCTCAGTATCTAATCAGGAAGCTAACCA-TTTATTGCTTCGACCTG
* * *
3450 CTTCTTAGTATCTCATCACGAAGCTAACCATTTTATTGCTTAGACTTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTAGACCTGCTTCTCAGTATCTCATC
* * * *
3515 AGGAAGCTGGGGTTCGAAGTTTCGCTCGCATGGAGCTTTGTTCCATTGAGTTGGGATACTTCTCT
66 AAGAAGCCGGGGTTCGAAGTTTCGCTCACATGGAGCTTTGTTCCATTGAGTTGGGATACTTCTCA
* *
3580 GTATCTCATCAGGAAGATGACTGCCTCACTTGTTTCAATTCGCTTCTCTGTATCTCATCAAGAAG
131 GTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAAGAAG
** * * *
3645 ACTAATTCAGTCCACTTCTCATTATCTCATCAGGAAGCTAACCATTTATTTCTTCGACCTG
196 AAAAATTCAGTCCACTTCTCAGTATCTAATCAGGAAGCTAACCATTTATTGCTTCGACCTG
*
3706 CTTCTCAGTATCTCATCAGGAAGCT
1 CTTCTCAGTATCTCATCAAGAAGCT
3731 GGGGCTCGAA
Statistics
Matches: 250, Mismatches: 31, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
256 38 0.15
257 212 0.85
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (256 bp):
CTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTAGACCTGCTTCTCAGTATCTCATC
AAGAAGCCGGGGTTCGAAGTTTCGCTCACATGGAGCTTTGTTCCATTGAGTTGGGATACTTCTCA
GTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAAGAAG
AAAAATTCAGTCCACTTCTCAGTATCTAATCAGGAAGCTAACCATTTATTGCTTCGACCTG
Done.