Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014756.1 Kokia drynarioides strain JFW-HI SEQ_129795, 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: 5264
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.32
Warning! 243 characters in sequence are not A, C, G, or T
Found at i:270 original size:17 final size:18
Alignment explanation
Indices: 245--286 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
235 GATCGGGCCC
* *
245 TTTTAGGTTTAGGG-TTA
1 TTTTGGGTTTAGGGATAA
*
262 TTTTGGGTTTGGGGATAA
1 TTTTGGGTTTAGGGATAA
280 TTTTGGG
1 TTTTGGG
287 CCACTTTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (18 bp):
TTTTGGGTTTAGGGATAA
Found at i:402 original size:7 final size:6
Alignment explanation
Indices: 349--418 Score: 53
Period size: 6 Copynumber: 12.2 Consensus size: 6
339 TTTTGGACTT
*
349 TTTAAA TTTAAT TTTATAA --TAAA TTTAAA TTTCAAA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
*
395 TTTCAAA --TAAA CTTAAA TTTAAA T
1 TTT-AAA TTTAAA TTTAAA TTTAAA T
419 AAATTCAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
4 8 0.15
5 4 0.08
6 33 0.63
7 7 0.13
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:435 original size:16 final size:17
Alignment explanation
Indices: 351--436 Score: 106
Period size: 17 Copynumber: 5.2 Consensus size: 17
341 TTGGACTTTT
*
351 TAAATTT-AATTTTATAA
1 TAAATTTAAATTTCA-AA
368 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
385 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
*
402 TAAACTTAAATTT-AAA
1 TAAATTTAAATTTCAAA
* *
418 TAAA-TTCAATTTCCAA
1 TAAATTTAAATTTCAAA
434 TAA
1 TAA
437 GTCCAGACAA
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
15 7 0.11
16 12 0.19
17 38 0.60
18 6 0.10
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:1046 original size:37 final size:37
Alignment explanation
Indices: 993--1082 Score: 146
Period size: 37 Copynumber: 2.4 Consensus size: 37
983 CCGCTTTTAT
* *
993 GTATCTCATCAAGAAGACGAATTTGGTTTACTTCTCC-
1 GTATCTCATCAGGAAGACGAATTTGGTTCACTTC-CCA
1030 GTATCTCATCAGGAAGACGAATTTGGTTCACTTCCCA
1 GTATCTCATCAGGAAGACGAATTTGGTTCACTTCCCA
1067 GTATCTCATCAGGAAG
1 GTATCTCATCAGGAAG
1083 CTAACCATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
36 2 0.04
37 48 0.96
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (37 bp):
GTATCTCATCAGGAAGACGAATTTGGTTCACTTCCCA
Found at i:1208 original size:237 final size:237
Alignment explanation
Indices: 788--1520 Score: 1184
Period size: 237 Copynumber: 3.1 Consensus size: 237
778 TTTCAATCCG
* *
788 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCCCAGTATCTCATAAGGAAGCTAAC
1 CTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCACTTCCCAGTATCTCATCAGGAAGCTAAC
* * *
853 CATTTA--GCTTCCACCTGCTTCTTAGTGTCTCATCAGGAAGCTGAGGTTCAAAGATTTTGCTCA
66 CATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGATTTTGCTCG
* * *
916 CTTTGAGCCTCGTTTTGTTCTTCTCCTCAGTGTCTCATCAGGAAGATGGTCCCATCATCGTTTCA
131 CTTTGAGCCTTGTTTGGGTCTTCTCCTCAGTGTCTCATCAGGAAGATGGTCCCATCATCGTTTCA
* * *
981 ATCCGCTTTTATGTATCTCATCAAGAAGACGAATTTGGTTTA
196 ATCCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCA
1023 CTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCACTTCCCAGTATCTCATCAGGAAGCTAAC
1 CTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCACTTCCCAGTATCTCATCAGGAAGCTAAC
1088 CATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGATTTTGCTCG
66 CATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGATTTTGCTCG
* * *
1153 CTTTGAGCCTTGTTTGGGTCTTCTCCTCAGTGTCTTATTAGGAAGATGGTCCCATCATCGTTTTA
131 CTTTGAGCCTTGTTTGGGTCTTCTCCTCAGTGTCTCATCAGGAAGATGGTCCCATCATCGTTTCA
1218 ATCCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCA
196 ATCCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCA
1260 CTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCACTTCCCAGTATCTCATCAGGAAGCTAAC
1 CTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCACTTCCCAGTATCTCATCAGGAAGCTAAC
*
1325 CATTTATTGCTTTCACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGATTTTGCTCG
66 CATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGATTTTGCTCG
* * * * ** ** *
1390 CTTTGAGCCTTGTTTGGGTATTCTCCTCAGTGTCTCATCAGGGAGATGACTGCGTTGTTTGTTTC
131 CTTTGAGCCTTGTTTGGGTCTTCTCCTCAGTGTCTCATCAGGAAGATG-GTCCCATCATCGTTTC
*
1455 AA-CTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCA
195 AATC-CGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCA
* *
1498 CTTCTCAGTATCTCATTAGGAAG
1 CTTCTCCGTATCTCATCAGGAAG
1521 CTAATCTTTT
Statistics
Matches: 464, Mismatches: 30, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
235 69 0.15
237 326 0.70
238 69 0.15
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (237 bp):
CTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCACTTCCCAGTATCTCATCAGGAAGCTAAC
CATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGATTTTGCTCG
CTTTGAGCCTTGTTTGGGTCTTCTCCTCAGTGTCTCATCAGGAAGATGGTCCCATCATCGTTTCA
ATCCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCA
Found at i:1273 original size:37 final size:37
Alignment explanation
Indices: 1223--1319 Score: 160
Period size: 37 Copynumber: 2.6 Consensus size: 37
1213 TTTTAATCCG
* *
1223 CTTCTCTGTATCTCATCAAGAAGACGAATTTGGTTCA
1 CTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCA
1260 CTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCA
1 CTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCA
1297 CTTC-CCAGTATCTCATCAGGAAG
1 CTTCTCC-GTATCTCATCAGGAAG
1320 CTAACCATTT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
36 2 0.04
37 55 0.96
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (37 bp):
CTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCA
Found at i:2152 original size:27 final size:27
Alignment explanation
Indices: 2122--2182 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
2112 CCAAGAATTC
*
2122 TATTAAAAAGAGGATCGAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
** * *
2149 TATTAAAGGGAGGGTTAAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
2176 TCATTAA
1 T-ATTAA
2183 TTGAAAATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.51, C:0.07, G:0.23, T:0.20
Consensus pattern (27 bp):
TATTAAAAAGAGGATCAAAGGAAACAA
Done.