Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000256.1 Kokia drynarioides strain JFW-HI SEQ_110993, 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: 4224
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:1855 original size:290 final size:290
Alignment explanation
Indices: 1315--2460 Score: 1615
Period size: 290 Copynumber: 4.0 Consensus size: 290
1305 TAAAACATTC
* * * * *
1315 TATACATTTTTTTGTTTTTAGGAGAAGTGAAGCACAAAAATGCAATAGCAGATGGAAGGAAGCAA
1 TATAC-TTTCTTTGTTTTCAGGAGAAGTGAAGCAGAAAAATGCAATAGCAGATGGAAGGAACCGA
* * *
1380 AGAGTTCTTCAAGACATTGGCAACTTGGTCAATGAACGAGCAGCAACACAAGGGAAGGCAGTTCC
65 AGAGTTCTTCAAGACATTGGCAACTTTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTAGTTCC
1445 AGTAAACACAAAAATGTTTCTTTTTCATTATAGTAGCAAATATTAGGTAATCACTGA-TTGCTCT
130 AGTAAACACAAAAATGTTTCTTTTTCATTATAGTAGCAAATATTAGGTAATCACT-ATTTGCTCT
* * *
1509 TGGTGTTTTTTGCTTGTAGAAACCAATCACCGAAGGGGCTGCTGTGGTTTCACAAGCTGTGAAAG
194 TGGTGTTTTTTGCTTGTAGAAACCAATCACCGAAGGGGCT-TTTTGGTTGCACAAGCTGTGAAAG
*
1574 GAGCTCAAAGGAAGCAAGTTGACAAACCATTTT
258 GAGCCCAAAGGAAGCAAGTTGACAAACCATTTT
* *
1607 TATACTTTCTTTGTTTTCAGGAGAAGTGAAGCAGAAAAATGCAATAGCATATGGAA-GAACTGAA
1 TATACTTTCTTTGTTTTCAGGAGAAGTGAAGCAGAAAAATGCAATAGCAGATGGAAGGAACCGAA
1671 GAGTTCTTCAAGACATTGGCAACTTTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTAGTTCCA
66 GAGTTCTTCAAGACATTGGCAACTTTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTAGTTCCA
*
1736 GTAAACACAGAAATGTTTCTTTTTCATTATAGTAGCAAATATTAGGTAATCACTATTTGCTCTTG
131 GTAAACACAAAAATGTTTCTTTTTCATTATAGTAGCAAATATTAGGTAATCACTATTTGCTCTTG
* *
1801 GTGTTTTTTGCTTGTAGAAACCAATCACCGAATGGGCTTTTCTGGTTGCACAAGCTGTTAAAGGA
196 GTGTTTTTTGCTTGTAGAAACCAATCACCGAAGGGGCTTTT-TGGTTGCACAAGCTGTGAAAGGA
* *
1866 GCTCAAAGGAAGCAAGTTGACAAATCATTTT
260 GCCCAAAGGAAGCAAGTTGACAAACCATTTT
* * *
1897 TATACTTTCTTTGTTTTCAGGAGAATTGTAGCAGAAAAATGCAATAGCAGATAGAAGGAACCGAA
1 TATACTTTCTTTGTTTTCAGGAGAAGTGAAGCAGAAAAATGCAATAGCAGATGGAAGGAACCGAA
* * * * * *
1962 GAGTTCTTAAAGACATTTGCAACTTTGTAAATGAACGAGAAGCAGGAAAAGGGAAGGTAGTTCCA
66 GAGTTCTTCAAGACATTGGCAACTTTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTAGTTCCA
* * *
2027 GTAAACACAAAAATGTTTCTTTTTCATTATAGTAGCAAATATTAGGCAAGCACTAATTGCTCTTG
131 GTAAACACAAAAATGTTTCTTTTTCATTATAGTAGCAAATATTAGGTAATCACTATTTGCTCTTG
** *
2092 GTGTTTTTTGCTTGTAGAAACCAATCATTGAAGGGGCTGTTTTGGTTGCACAAACTGTGAAAGGA
196 GTGTTTTTTGCTTGTAGAAACCAATCACCGAAGGGGCT-TTTTGGTTGCACAAGCTGTGAAAGGA
* * *
2157 TCCCAATGGAAGCAAGTTGACAAACTATTTT
260 GCCCAAAGGAAGCAAGTTGACAAACCATTTT
* * * *
2188 TATACTTTATTTGTTTTCTGGAGAAGTGGAGCAG-AAAATGCAATAGGAGATGGAAGGAACCGAA
1 TATACTTTCTTTGTTTTCAGGAGAAGTGAAGCAGAAAAATGCAATAGCAGATGGAAGGAACCGAA
* * * * * * * *
2252 GAGTTGTTTAAGACATTGGAAACGTTGTCAATGAACAAGCAGGAGCACAAGTGAAGGTAGTTCTA
66 GAGTTCTTCAAGACATTGGCAACTTTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTAGTTCCA
* * * *
2317 GTAAGCACAAGAATGTTTCTTTTTCATTATTGTAGCAAATATTAGG------CT-TTTG---GT-
131 GTAAACACAAAAATGTTTCTTTTTCATTATAGTAGCAAATATTAGGTAATCACTATTTGCTCTTG
* *
2371 G-GTTTTTT-CTTGTAGAAGCCAATCACCGAAGGGG-TTATTATGGTTGTACAAGCTGTGAAAGG
196 GTGTTTTTTGCTTGTAGAAACCAATCACCGAAGGGGCTT-TT-TGGTTGCACAAGCTGTGAAAGG
2433 AGCCCAAAGGAAGCAAGTTGACAAACCA
259 AGCCCAAAGGAAGCAAGTTGACAAACCA
2461 AAACCAGAGA
Statistics
Matches: 774, Mismatches: 74, Indels: 27
0.88 0.08 0.03
Matches are distributed among these distances:
275 1 0.00
276 3 0.00
277 68 0.09
278 7 0.01
279 1 0.00
280 1 0.00
283 3 0.00
284 2 0.00
289 2 0.00
290 392 0.51
291 286 0.37
292 8 0.01
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (290 bp):
TATACTTTCTTTGTTTTCAGGAGAAGTGAAGCAGAAAAATGCAATAGCAGATGGAAGGAACCGAA
GAGTTCTTCAAGACATTGGCAACTTTGTCAATGAACGAGCAGCAGCACAAGGGAAGGTAGTTCCA
GTAAACACAAAAATGTTTCTTTTTCATTATAGTAGCAAATATTAGGTAATCACTATTTGCTCTTG
GTGTTTTTTGCTTGTAGAAACCAATCACCGAAGGGGCTTTTTGGTTGCACAAGCTGTGAAAGGAG
CCCAAAGGAAGCAAGTTGACAAACCATTTT
Found at i:3342 original size:3 final size:3
Alignment explanation
Indices: 3329--3442 Score: 76
Period size: 3 Copynumber: 37.7 Consensus size: 3
3319 GACATGTCGT
* *
3329 TTA TTA TTTA TTA TTA TT- TTGC TTA TTA TTT TTA TTTA TTA TTA TTTA
1 TTA TTA -TTA TTA TTA TTA TT-A TTA TTA TTA TTA -TTA TTA TTA -TTA
* * * * *
3377 CTG TTG TTA TTA TT- TTC TT- TT- TTA TTA TTA TT- TTCG TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA -TTA
3420 TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
3443 GTCTAACATC
Statistics
Matches: 93, Mismatches: 8, Indels: 20
0.77 0.07 0.17
Matches are distributed among these distances:
2 10 0.11
3 67 0.72
4 16 0.17
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3357 original size:22 final size:21
Alignment explanation
Indices: 3329--3442 Score: 87
Period size: 22 Copynumber: 5.4 Consensus size: 21
3319 GACATGTCGT
3329 TTATTATTTATTATTATTTTGC
1 TTATTATTTATTATTATTTT-C
* *
3351 TTATTATTT-TTATT-TATTA
1 TTATTATTTATTATTATTTTC
*
3370 TTATTTACTGTTGTTATTATTTTC
1 TTA-TTA-T-TTATTATTATTTTC
3394 -T-TT-TTTATTATTATTTTC
1 TTATTATTTATTATTATTTTC
*
3412 GTTATT-TATTATTATTATTATTA
1 -TTATTAT-TTATTATTATT-TTC
3435 TTATTATT
1 TTATTATT
3443 GTCTAACATC
Statistics
Matches: 75, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
18 13 0.17
19 4 0.05
20 7 0.09
21 11 0.15
22 28 0.37
23 9 0.12
24 3 0.04
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.70
Consensus pattern (21 bp):
TTATTATTTATTATTATTTTC
Found at i:3366 original size:28 final size:28
Alignment explanation
Indices: 3332--3436 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 28
3322 ATGTCGTTTA
3332 TTATTTATTATTATTTTGCTTATTATTT
1 TTATTTATTATTATTTTGCTTATTATTT
*
3360 TTATTTATTATTATTTACTGTTGTTATTATTTT
1 TTATTTATTATTATTT--TG--CTTATTA-TTT
* *
3393 CTTTTTTATTATTATTTT-CGTTATTTATTA
1 -TTATTTATTATTATTTTGC-TTA-TTATTT
3423 TTA-TTATTATTATT
1 TTATTTATTATTATT
3437 ATTATTGTCT
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
28 27 0.42
29 2 0.03
30 7 0.11
31 3 0.05
32 7 0.11
33 3 0.05
34 15 0.23
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (28 bp):
TTATTTATTATTATTTTGCTTATTATTT
Found at i:3371 original size:31 final size:30
Alignment explanation
Indices: 3328--3439 Score: 113
Period size: 31 Copynumber: 3.6 Consensus size: 30
3318 TGACATGTCG
3328 TTTATTATTTATTATTATTTTGCTTATTATT
1 TTTATTA-TTATTATTATTTTGCTTATTATT
*
3359 TTTATTTATTATTATTTACTGTTG-TTATTATT
1 TTTA-TTATTATTA-TTA-TTTTGCTTATTATT
*
3391 TTCT-TTTTTATTATTATTTT-CGTTATTTATT
1 TT-TATTATTATTATTATTTTGC-TTA-TTATT
*
3422 ATTATTATTATTATTATT
1 TTTATTATTATTATTATT
3440 ATTGTCTAAC
Statistics
Matches: 68, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
29 3 0.04
30 7 0.10
31 37 0.54
32 16 0.24
33 5 0.07
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.71
Consensus pattern (30 bp):
TTTATTATTATTATTATTTTGCTTATTATT
Found at i:3406 original size:18 final size:19
Alignment explanation
Indices: 3383--3427 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
3373 TTTACTGTTG
*
3383 TTATTATTTTC-TTTTTTA
1 TTATTATTTTCGTTATTTA
3401 TTATTATTTTCGTTATTTA
1 TTATTATTTTCGTTATTTA
3420 TTATTATT
1 TTATTATT
3428 ATTATTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (19 bp):
TTATTATTTTCGTTATTTA
Found at i:3421 original size:34 final size:33
Alignment explanation
Indices: 3351--3442 Score: 98
Period size: 34 Copynumber: 2.8 Consensus size: 33
3341 ATTATTTTGC
*
3351 TTATTA-TTTTTATTTATTATTATTTACTGTTG
1 TTATTATTTTTTTTTTATTATTATTTACTGTTG
* *
3383 TTATTATTTTCTTTTTTATTATTATTTTC-GTTAT
1 TTATTATTTT-TTTTTTATTATTATTTACTGTT-G
* *
3417 TTATTATTATTATTATTATTATTATT
1 TTATTATT-TTTTTTTTATTATTATT
3443 GTCTAACATC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
32 6 0.12
33 6 0.12
34 37 0.73
35 2 0.04
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (33 bp):
TTATTATTTTTTTTTTATTATTATTTACTGTTG
Done.