Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012764.1 Kokia drynarioides strain JFW-HI SEQ_127776, 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: 14544
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:591 original size:6 final size:6
Alignment explanation
Indices: 580--674 Score: 67
Period size: 6 Copynumber: 16.7 Consensus size: 6
570 TTTGAACATT
* * *
580 AATTTA AATTTA AATTT- AACTCA AATTTA TAA--TA AATTTA AATTTT
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA
* * * * *
626 AA-GTA AATTTA AACTTA AA-ATA AATTTA ATTTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
671 AATT
1 AATT
675 CTGTTGGGCC
Statistics
Matches: 67, Mismatches: 15, Indels: 14
0.70 0.16 0.15
Matches are distributed among these distances:
4 2 0.03
5 16 0.24
6 47 0.70
7 2 0.03
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:622 original size:17 final size:17
Alignment explanation
Indices: 580--674 Score: 109
Period size: 17 Copynumber: 5.6 Consensus size: 17
570 TTTGAACATT
* *
580 AATTTAAATTTAAATTT
1 AATTTAAATTTAAAATA
* * *
597 AACTCAAATTTATAATA
1 AATTTAAATTTAAAATA
* *
614 AATTTAAATTTTAAGTA
1 AATTTAAATTTAAAATA
*
631 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
*
648 AATTTAATTTTAAAATA
1 AATTTAAATTTAAAATA
665 AATTTAAATT
1 AATTTAAATT
675 CTGTTGGGCC
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 62 1.00
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:1348 original size:206 final size:206
Alignment explanation
Indices: 975--1511 Score: 749
Period size: 206 Copynumber: 2.6 Consensus size: 206
965 TCTGGTTTCA
* * * * ** ** **
975 TTGACTTGGCCTTCTTCTCAGTATATCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCTGCTT
* * ** *
1040 CTTTAAGTTT-T-ATCGGGAAGAC-AGATTTGGTTTACTTCTCCGTATCTCATCAGGAAGCTAAC
66 CTCT-A-TTTCTCATCAGGAAGACGA-ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
* * *
1102 CACTTTATTGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGAGTTTCGAAGATTTGCTCT
128 CACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCA
1167 CATCAAGCGTGGGT
193 CATCAAGCGTGGGT
*
1181 TTGATTTGGTCTTATTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCTGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCTGCTT
*
1246 CTCTATTTCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAG
66 CTCTATTTCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAC
* * *
1311 TTTATTGCTTTGCCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACAT
*
1376 CGAGCGTGGGT
196 CAAGCGTGGGT
* * *
1387 TTGATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGATCGCGTCGTTTGTTTCAAT-TCGCT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCT-GCT
* *
1451 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTA
65 TCTCTATTTCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTA
1512 GAGTTCGAAG
Statistics
Matches: 297, Mismatches: 30, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
204 3 0.01
205 3 0.01
206 290 0.98
207 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCTGCTT
CTCTATTTCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAC
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACAT
CAAGCGTGGGT
Found at i:12947 original size:96 final size:96
Alignment explanation
Indices: 12763--12954 Score: 264
Period size: 96 Copynumber: 2.0 Consensus size: 96
12753 ATTTTGGGAA
* **
12763 AAGGATATTCGATTATCTCGATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTTA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTTA
*
12828 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* * *
12859 AAGGGTATTCGATTATTTCTATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTT-
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTTA
*
12923 GAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
66 G-AA-TCGAAGATAAAGA-AACATTGCCTCGATT
12955 TTAAAGTTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
95 2 0.02
96 78 0.92
97 5 0.06
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTTA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:13204 original size:28 final size:27
Alignment explanation
Indices: 13171--13229 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
13161 AAATGAAACC
13171 TTTTGGATACCCGAGGGCAAAATGGTAA
1 TTTTGGATACCCG-GGGCAAAATGGTAA
* ** *
13199 TTTTGGATTCTTGGGGCTAAATGGTAA
1 TTTTGGATACCCGGGGCAAAATGGTAA
13226 TTTT
1 TTTT
13230 AGGAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.37
Consensus pattern (27 bp):
TTTTGGATACCCGGGGCAAAATGGTAA
Found at i:13366 original size:57 final size:58
Alignment explanation
Indices: 13217--13436 Score: 202
Period size: 57 Copynumber: 3.8 Consensus size: 58
13207 TCTTGGGGCT
* * * * *
13217 AAATGGTAATTTTAGGAAAATTT-AGGGTTAAAAATGGAATTTTTAGACATTCGAGGGTA
1 AAATGGTAATTTT--GAAAGTTTCGGGGTCAAAAATGGAATTTTTGGACATTCGAGGGGA
* * * * *
13276 AAAGGGTAATTTCGAAAGTTTCGAGGTCGAAAATGGAGTTTTTGGACATTCG-GGGGA
1 AAATGGTAATTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGACATTCGAGGGGA
** *
13333 AAATGGTAATTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGA-AGTTTTAGGGTAA
1 AAATGGTAATTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGACA-TTCGAGGG-GA
*
13392 AAATGG-AATTTTTGGAAG-TTCGTGGGT-AAAAATTGG-ATTTTTGGA
1 AAATGGTAA-TTTTGAAAGTTTCG-GGGTCAAAAA-TGGAATTTTTGGA
13437 AGCTTCGGGG
Statistics
Matches: 135, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
56 1 0.01
57 54 0.40
58 47 0.35
59 33 0.24
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.34
Consensus pattern (58 bp):
AAATGGTAATTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGACATTCGAGGGGA
Found at i:13373 original size:29 final size:29
Alignment explanation
Indices: 13217--13501 Score: 212
Period size: 30 Copynumber: 9.7 Consensus size: 29
13207 TCTTGGGGCT
* * * *
13217 AAATGGTAATTTTAGGAAAATTTAGGGTTAA
1 AAATGG-AATTTTTGG-AAGTTTCGGGGTAA
*
13248 AAATGGAATTTTTAGACA--TTCGAGGGT-A
1 AAATGGAATTTTTGGA-AGTTTCG-GGGTAA
* * * * *
13276 AAAGGGTAA-TTTCGAAAGTTTCGAGGTCGA
1 AAATGG-AATTTTTGGAAGTTTCGGGGT-AA
* *
13306 AAATGGAGTTTTTGGACA--TTCGGGG-GA
1 AAATGGAATTTTTGGA-AGTTTCGGGGTAA
*
13333 AAATGGTAA-TTTTGAAAGTTTCGGGGTCAA
1 AAATGG-AATTTTTGGAAGTTTCGGGGT-AA
**
13363 AAATGGAATTTTTGGAAGTTTTAGGGTAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTAA
13392 AAATGGAATTTTTGGAAG-TTCGTGGGTAA
1 AAATGGAATTTTTGGAAGTTTCG-GGGTAA
*
13421 AAATTGG-ATTTTTGGAAGCTTCGGGGTAAA
1 AAA-TGGAATTTTTGGAAGTTTCGGGGT-AA
*
13451 AAATGGAATTTTTGGAAGTTTAGGGGTAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTAA
**
13480 AAATATAATTTTTTGGAAGTTT
1 AAATGGAA-TTTTTGGAAGTTT
13502 AGGGACCTCC
Statistics
Matches: 207, Mismatches: 26, Indels: 43
0.75 0.09 0.16
Matches are distributed among these distances:
26 1 0.00
27 15 0.07
28 26 0.13
29 74 0.36
30 84 0.41
31 7 0.03
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAGTTTCGGGGTAA
Found at i:13453 original size:59 final size:59
Alignment explanation
Indices: 13332--13483 Score: 195
Period size: 59 Copynumber: 2.6 Consensus size: 59
13322 CATTCGGGGG
* * *
13332 AAAATGGTAA-TTTTGAAAGTTTCGGGGTCAAAAA-TGGAATTTTTGGAAGTTTTAGGGTA
1 AAAATGG-AATTTTTGGAAGTTTCGGGGT-AAAAATTGGAATTTTTGGAAGCTTCAGGGTA
*
13391 AAAATGGAATTTTTGGAAG-TTCGTGGGTAAAAATTGG-ATTTTTGGAAGCTTCGGGGTAA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTAAAAATTGGAATTTTTGGAAGCTTCAGGGT-A
*
13450 AAAATGGAATTTTTGGAAGTTTAGGGGTAAAAAT
1 AAAATGGAATTTTTGGAAGTTTCGGGGTAAAAAT
13484 ATAATTTTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
58 28 0.34
59 52 0.63
60 3 0.04
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTAAAAATTGGAATTTTTGGAAGCTTCAGGGTA
Found at i:14497 original size:3 final size:3
Alignment explanation
Indices: 14489--14544 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
14479 TTACCACCGT
* *
14489 TTA TTA TTA ATG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
14537 TTA TTA TT
1 TTA TTA TT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Done.