Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014366.1 Kokia drynarioides strain JFW-HI SEQ_129403, 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: 3091
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.38
Warning! 18 characters in sequence are not A, C, G, or T
Found at i:258 original size:16 final size:13
Alignment explanation
Indices: 209--255 Score: 87
Period size: 13 Copynumber: 3.7 Consensus size: 13
199 TTATTAACCA
209 TTAATAATATT-T
1 TTAATAATATTCT
221 TTAATAATATTCT
1 TTAATAATATTCT
234 TTAATAATATTCT
1 TTAATAATATTCT
247 TTAATAATA
1 TTAATAATA
256 ATAAAATCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 11 0.32
13 23 0.68
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAATAATATTCT
Found at i:1007 original size:11 final size:11
Alignment explanation
Indices: 993--1072 Score: 76
Period size: 11 Copynumber: 7.5 Consensus size: 11
983 ACTTTTTTTT
993 AATTTAAATTA
1 AATTTAAATTA
* *
1004 AATTCAATTTA
1 AATTTAAATTA
*
1015 AATTT-AATATC
1 AATTTAAAT-TA
1026 AATTTAAATTA
1 AATTTAAATTA
*
1037 AAATT--ATTA
1 AATTTAAATTA
*
1046 AATTTAAATCA
1 AATTTAAATTA
*
1057 AATTTAAAATA
1 AATTTAAATTA
1068 AATTT
1 AATTT
1073 TAAAAAAGGC
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
9 8 0.15
10 2 0.04
11 41 0.76
12 3 0.06
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:1018 original size:6 final size:6
Alignment explanation
Indices: 993--1064 Score: 53
Period size: 6 Copynumber: 12.3 Consensus size: 6
983 ACTTTTTTTT
* * * *
993 AATTTA AA-TTA AA-TTC AATTTA AATTT- AATATC AATTTA AATTAA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
1038 AATTATTA AATTTA AA-TCA AATTTA AA
1 AA-T-TTA AATTTA AATTTA AATTTA AA
1065 ATAAATTTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
5 17 0.33
6 29 0.56
7 2 0.04
8 4 0.08
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:1782 original size:200 final size:202
Alignment explanation
Indices: 1310--2165 Score: 988
Period size: 202 Copynumber: 4.2 Consensus size: 202
1300 TTACTGATTT
* * * * * *
1310 GGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGTATCGTTTGTTTCGATTCGCTCCTCTATA
1 GGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATTTGCTTCTCTGTA
* * * * * * * * * * *
1375 TCTCATCAAGAAGACGAGTTTGGTTCGCTTCTCAATATTTCATTAGGAGGCTGACC-TTTTGTTG
66 TCTCATCAGGAAGGCGAATTTGGTTCACTTCTTAATATCTCATCAGGAAGCTAACCACTTTATTG
* * * ** * * * * * * *
1439 TTTCTACCTGCTTCTAGGTGTCTCGTCCGGAAGTTAGGGTCCGAAGATTTTGCTCGCTTTGAGCG
131 CTTCGACCCGCTTCTCTGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCC
*
1504 TGGGTTTG
196 T-CGTTTG
* * * * *
1512 ATTTGGTCTTCTTCTCAGTATCTCATTAGGAAGATGACTGAATCGTTTGTTTCAATTCGTTTCTC
1 ----GGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATTTGCTTCTC
* * * *
1577 TGTATCTCA-CTAGGAAGACGAATTTGG-TCTACTTCTTAATACCTCATCAAGAAGCTAACCATT
62 TGTATCTCATC-AGGAAGGCGAATTTGGTTC-ACTTCTTAATATCTCATCAGGAAGCTAACCACT
* * * * * * *
1640 TTATTGCTTCGATCTGATTCTCAGTGTCTCATCAAGAAGCTGGGGTTCCAAGATTTTGCTCACAT
125 TTATTGCTTCGACCCGCTTCTCTGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTT
* *
1705 TGAGCCT-TTTTA
190 TGAGCCTCGTTTG
* * * *
1717 AGTCTTCTTTTCAGTGTCTCATCAGGAAGATGACCGCGTCGTTT-TTTCAATTTGCTTCTCTGTA
1 GGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATTTGCTTCTCTGTA
* * *
1781 TCTCATCAGGAAGGCGAATTTGGTTCACTTCTCAGTATCTCATCAGGTAGCTAACCACTTTATTG
66 TCTCATCAGGAAGGCGAATTTGGTTCACTTCTTAATATCTCATCAGGAAGCTAACCACTTTATTG
*
1846 CTTCGACCCGCTTCTCTGTGTCTCATCAGGAAGTTGGGGTTCGAAGATTTTGCTCACTTTGAGCC
131 CTTCGACCCGCTTCTCTGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCC
1911 TCGTTTG
196 TCGTTTG
* * * *
1918 GGTCTTCTTTTCAGTGTCTTATCAGGAAGATGACCGCGTCGTTTGTTTCAATTTGCTT-TGCTGT
1 GGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATTTGCTTCT-CTGT
* * *
1982 ATCTCATCAGGAAGGCGAATTTGATTCACTT-ATAAGTATCTCATCAGGGAGCTAACCACTTTAT
65 ATCTCATCAGGAAGGCGAATTTGGTTCACTTCTTAA-TATCTCATCAGGAAGCTAACCACTTTAT
*
2046 TGCTTCGACCCGCTTCTCTGTGTCTCATCAGGAAGCTNGGGTTCGAAGATTTTGCTCACTTTGAG
129 TGCTTCGACCCGCTTCTCTGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAG
2111 CCTCGTTTG
194 CCTCGTTTG
* *
2120 GGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCTCATCGTTTGT
1 GGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGT
2166 GGATAATCGT
Statistics
Matches: 565, Mismatches: 76, Indels: 22
0.85 0.11 0.03
Matches are distributed among these distances:
200 129 0.23
201 87 0.15
202 186 0.33
205 6 0.01
206 100 0.18
207 57 0.10
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.38
Consensus pattern (202 bp):
GGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATTTGCTTCTCTGTA
TCTCATCAGGAAGGCGAATTTGGTTCACTTCTTAATATCTCATCAGGAAGCTAACCACTTTATTG
CTTCGACCCGCTTCTCTGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTTGCTCACTTTGAGCC
TCGTTTG
Found at i:2071 original size:402 final size:405
Alignment explanation
Indices: 1311--2165 Score: 1026
Period size: 402 Copynumber: 2.1 Consensus size: 405
1301 TACTGATTTG
* * *
1311 GTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGTATCGTTTGTTTCGATTCGCTCCTCTATAT
1 GTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATTCGCTCCTCTATAT
* * * * * * * *
1376 CTCATCAAGAAGACGAGTTTGGTTCGCTTCTCAATATTTCATTAGGAGGCTGACCTTTTGTTGTT
66 CTCATCAAGAAGACGAATTTGGTTCACTTCTCAATATCTCATCAGGAGGCTAACCCTTTATTGCT
* * * * * *
1441 TCTACCTGCTTCTAGGTGTCTCGTCCGGAAGTTAGGGTCCGAAGATTTTGCTCGCTTTGAGCGTG
131 TCGACCCGCTTCTAGGTGTCTCATCAGGAAGTTAGGGTCCGAAGATTTTGCTCACTTTGAGCCTG
* * *
1506 GGTTTGATTTGGTCTTCTTCTCAGTATCTCATTAGGAAGATGACTGAATCGTTTGTTTCAATTCG
196 CGTTTG---TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGAATCGTTTGTTTCAATTCG
* *
1571 TTTCTCTGTATCTCACTAGGAAGACGAATTTGGTCTACTTCTTAATACCTCATCAAGAAGCTAAC
258 TTTCGCTGTATCTCACTAGGAAGACGAATTTGGTCTACTTCATAATACCTCATCAAGAAGCTAAC
* * *
1636 CATTTTATTGCTTCGATCTGATTCTCAGTGTCTCATCAAGAAGCTGGGGTTCCAAGATTTTGCTC
323 CACTTTATTGCTTCGACCCGATTCTCAGTGTCTCATCAAGAAGCTGGGGTTCCAAGATTTTGCTC
*
1701 ACATTGAGCCT-TTTTAA
388 ACATTGAGCCTCGTTTAA
* * * * * *
1718 GTCTTCTTTTCAGTGTCTCATCAGGAAGATGACCGCGTCGTTT-TTTCAATTTGCTTCTCTGTAT
1 GTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATTCGCTCCTCTATAT
* * *
1782 CTCATCAGGAAGGCGAATTTGGTTCACTTCTCAGTATCTCATCAGGTA-GCTAACCACTTTATTG
66 CTCATCAAGAAGACGAATTTGGTTCACTTCTCAATATCTCATCAGG-AGGCTAACC-CTTTATTG
** * *
1846 CTTCGACCCGCTTCTCTGTGTCTCATCAGGAAGTTGGGGTTCGAAGATTTTGCTCACTTTGAGCC
129 CTTCGACCCGCTTCTAGGTGTCTCATCAGGAAGTTAGGGTCCGAAGATTTTGCTCACTTTGAGCC
* * * ** *
1911 T-CGTTTG-GGTCTTCTTTTCAGTGTCTTATCAGGAAGATGACCGCGTCGTTTGTTTCAATTTGC
194 TGCGTTTGTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGAATCGTTTGTTTCAATTCG-
* * * * *
1974 TTT-GCTGTATCTCA-TCAGGAAGGCGAATTTGAT-TCACTT-ATAAGTATCTCATCAGGGAGCT
258 TTTCGCTGTATCTCACT-AGGAAGACGAATTTGGTCT-ACTTCATAA-TACCTCATCAAGAAGCT
* * * * *
2035 AACCACTTTATTGCTTCGACCCGCTTCTCTGTGTCTCATCAGGAAGCTNGGGTTCGAAGATTTTG
320 AACCACTTTATTGCTTCGACCCGATTCTCAGTGTCTCATCAAGAAGCTGGGGTTCCAAGATTTTG
* **
2100 CTCACTTTGAGCCTCGTTTGG
385 CTCACATTGAGCCTCGTTTAA
* *
2121 GTCTTCTTCTCAGTATCTCATCAAGAAGATGACCTCATCGTTTGT
1 GTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGT
2166 GGATAATCGT
Statistics
Matches: 377, Mismatches: 63, Indels: 19
0.82 0.14 0.04
Matches are distributed among these distances:
401 5 0.01
402 160 0.42
403 44 0.12
404 1 0.00
406 67 0.18
407 100 0.27
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.38
Consensus pattern (405 bp):
GTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATTCGCTCCTCTATAT
CTCATCAAGAAGACGAATTTGGTTCACTTCTCAATATCTCATCAGGAGGCTAACCCTTTATTGCT
TCGACCCGCTTCTAGGTGTCTCATCAGGAAGTTAGGGTCCGAAGATTTTGCTCACTTTGAGCCTG
CGTTTGTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGAATCGTTTGTTTCAATTCGTTT
CGCTGTATCTCACTAGGAAGACGAATTTGGTCTACTTCATAATACCTCATCAAGAAGCTAACCAC
TTTATTGCTTCGACCCGATTCTCAGTGTCTCATCAAGAAGCTGGGGTTCCAAGATTTTGCTCACA
TTGAGCCTCGTTTAA
Done.