Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014367.1 Kokia drynarioides strain JFW-HI SEQ_129404, 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: 9904
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:811 original size:21 final size:21
Alignment explanation
Indices: 738--804 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
728 TTCTTTTTCA
* **
738 CCTCTTCAACATGGACTTCCT
1 CCTCTCCAACATCAACTTCCT
759 CCTCTCCAACATCAACTTCCT
1 CCTCTCCAACATCAACTTCCT
780 CCTCTCCAACATCAACTTCCT
1 CCTCTCCAACATCAACTTCCT
801 CCTC
1 CCTC
805 AACAACAGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.21, C:0.46, G:0.03, T:0.30
Consensus pattern (21 bp):
CCTCTCCAACATCAACTTCCT
Found at i:4452 original size:17 final size:17
Alignment explanation
Indices: 4430--4462 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4420 ACTAACATTT
*
4430 AAATGCAATGACAATGA
1 AAATGCAACGACAATGA
4447 AAATGCAACGACAATG
1 AAATGCAACGACAATG
4463 CTTACTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.18, T:0.15
Consensus pattern (17 bp):
AAATGCAACGACAATGA
Found at i:4774 original size:512 final size:512
Alignment explanation
Indices: 3978--5006 Score: 1932
Period size: 512 Copynumber: 2.0 Consensus size: 512
3968 AATTGCGCTG
*
3978 ACATACACTTTTGCAACGACAACCTTTGGCCAGATTCATTTTTCTAACACTTACATTGGAGTGTT
1 ACATACACTCTTGCAACGACAACCTTTGGCCAGATTCATTTTTCTAACACTTACATTGGAGTGTT
*
4043 TCCTCTTGAACAGTTCACAATACACCCACATTGGAGTGTTTCTTATTTAATACAATATATATATA
66 TCCTCTTGAACAGCTCACAATACACCCACATTGGAGTGTTTCTTATTTAATACAATATATATATA
*
4108 AGCAACTATAAAAGGCAGATTCATTCAAGATTCAGAGAATGCTATTAGTCATCCATTACTAATGC
131 AGCAACTATAAAAGGCAGATTCATTCAAGATTCAAAGAATGCTATTAGTCATCCATTACTAATGC
* *
4173 AATCTAAATCATTCATCAAATAATTGAAGATACAACATTCAGTCAAATTTATCCAATTCATTCAT
196 AATCTAAATCATTCATCAAAGAATTGAAGATACAACATTCAGTCAAATTTATCCAACTCATTCAT
*
4238 TGATAGTTCACATGATTCAAGAATTAAGCATCGAATGTAACAAAAAAATTTCAAACACATTTGCA
261 TGACAGTTCACATGATTCAAGAATTAAGCATCGAATGTAACAAAAAAATTTCAAACACATTTGCA
4303 TTAACCATTCATAATCTTGCATGCTTCATTAAATTCAAAAAAAAAATTGAAATGTGAGTGCATCT
326 TTAACCATTCATAATCTTGCATGCTTCATTAAATTCAAAAAAAAAATTGAAATGTGAGTGCATCT
4368 CCAAACCTCATATGCATTCCCCCAAACTTAAAGTTTGCATTGTCCTGAATGCACTAACATTTAAA
391 CCAAACCTCATATGCATTCCCCCAAACTTAAAGTTTGCATTGTCCTGAATGCACTAACATTTAAA
* *
4433 TGCAATGACAATGAAAATGCAACGACAATGCTTACTAACAAAATAAAAATTACAGCT
456 TCCAATGACAATGAAAATGCAACAACAATGCTTACTAACAAAATAAAAATTACAGCT
* *
4490 ACATACACTCTTGCAACGATAACCTTTGGCCAGATTCATTTTTCTAACACTTGCATTGGAGTGTT
1 ACATACACTCTTGCAACGACAACCTTTGGCCAGATTCATTTTTCTAACACTTACATTGGAGTGTT
4555 TCCTCTTGAACAGCTCACAATACACCCACATTGGAGTGTTTCTTATTTAATACAATATATATATA
66 TCCTCTTGAACAGCTCACAATACACCCACATTGGAGTGTTTCTTATTTAATACAATATATATATA
*
4620 AGCAGCTATAAAAGGCAGATTCATTCAAGATTCAAAGAATGCTATTAGTCATCCATTACTAATGC
131 AGCAACTATAAAAGGCAGATTCATTCAAGATTCAAAGAATGCTATTAGTCATCCATTACTAATGC
4685 AATCTAAATCATTCATCAAAGAATTGAAGATACAACATTCAGTCAAATTTATCCAACTCATTCAT
196 AATCTAAATCATTCATCAAAGAATTGAAGATACAACATTCAGTCAAATTTATCCAACTCATTCAT
*
4750 TGACAGTTCACATGATTCAAGAATTAAGCATTGAATGTAACAAAAAAATTTCAAACACATTTGCA
261 TGACAGTTCACATGATTCAAGAATTAAGCATCGAATGTAACAAAAAAATTTCAAACACATTTGCA
*
4815 TTAACCATTCATAATCTTGCATGCTTCATTAAATTCAAAAAAAAATTTGAAATGTGAGTGCATCT
326 TTAACCATTCATAATCTTGCATGCTTCATTAAATTCAAAAAAAAAATTGAAATGTGAGTGCATCT
*
4880 CCAAACCTCATATGCATTCCCCTAAACTTAAAGTTTGCATTGTCCTGAATGCACTAACATTTAAA
391 CCAAACCTCATATGCATTCCCCCAAACTTAAAGTTTGCATTGTCCTGAATGCACTAACATTTAAA
4945 TCCAATGACAATGAAAATGCAACAACAATGCTTACTAACAAAATAAAAATTACAGCT
456 TCCAATGACAATGAAAATGCAACAACAATGCTTACTAACAAAATAAAAATTACAGCT
5002 ACATA
1 ACATA
5007 AAAAACATGA
Statistics
Matches: 503, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
512 503 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.31
Consensus pattern (512 bp):
ACATACACTCTTGCAACGACAACCTTTGGCCAGATTCATTTTTCTAACACTTACATTGGAGTGTT
TCCTCTTGAACAGCTCACAATACACCCACATTGGAGTGTTTCTTATTTAATACAATATATATATA
AGCAACTATAAAAGGCAGATTCATTCAAGATTCAAAGAATGCTATTAGTCATCCATTACTAATGC
AATCTAAATCATTCATCAAAGAATTGAAGATACAACATTCAGTCAAATTTATCCAACTCATTCAT
TGACAGTTCACATGATTCAAGAATTAAGCATCGAATGTAACAAAAAAATTTCAAACACATTTGCA
TTAACCATTCATAATCTTGCATGCTTCATTAAATTCAAAAAAAAAATTGAAATGTGAGTGCATCT
CCAAACCTCATATGCATTCCCCCAAACTTAAAGTTTGCATTGTCCTGAATGCACTAACATTTAAA
TCCAATGACAATGAAAATGCAACAACAATGCTTACTAACAAAATAAAAATTACAGCT
Found at i:7173 original size:9 final size:9
Alignment explanation
Indices: 7159--7224 Score: 58
Period size: 9 Copynumber: 8.2 Consensus size: 9
7149 TTAAAAAAAA
7159 AATAATTTT
1 AATAATTTT
7168 AATAATTTT
1 AATAATTTT
*
7177 -ATAATTTA
1 AATAATTTT
*
7185 AAAAATTTT
1 AATAATTTT
7194 -AT-ATTTT
1 AATAATTTT
7201 AA-AA----
1 AATAATTTT
7205 AATAATTTT
1 AATAATTTT
7214 AATAATTTT
1 AATAATTTT
7223 AA
1 AA
7225 AATCATTTGT
Statistics
Matches: 45, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
7 5 0.11
8 10 0.22
9 26 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
AATAATTTT
Found at i:7180 original size:17 final size:17
Alignment explanation
Indices: 7160--7223 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 17
7150 TAAAAAAAAA
7160 ATAATTTTAATAATTTT
1 ATAATTTTAATAATTTT
* *
7177 ATAATTTAAAAAATTTT
1 ATAATTTTAATAATTTT
*
7194 AT-ATTTTAA-AA---A
1 ATAATTTTAATAATTTT
7206 ATAATTTTAATAATTTT
1 ATAATTTTAATAATTTT
7223 A
1 A
7224 AAATCATTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
12 2 0.05
13 7 0.19
14 2 0.05
15 2 0.05
16 6 0.16
17 18 0.49
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATAATTTTAATAATTTT
Found at i:7184 original size:16 final size:16
Alignment explanation
Indices: 7131--7205 Score: 60
Period size: 17 Copynumber: 4.6 Consensus size: 16
7121 AATTAAAATT
* *
7131 ATTTAATAATTTTATT
1 ATTTAAAAATTTTATA
****
7147 ATTTAAAAAAAAAATA
1 ATTTAAAAATTTTATA
*
7163 ATTTTAATAATTTTATA
1 A-TTTAAAAATTTTATA
7180 ATTTAAAAAATTTTATA
1 ATTT-AAAAATTTTATA
*
7197 TTTTAAAAA
1 ATTTAAAAA
7206 ATAATTTTAA
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
16 19 0.43
17 25 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTAAAAATTTTATA
Found at i:7585 original size:19 final size:19
Alignment explanation
Indices: 7563--7600 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
7553 ACATGTAATA
7563 TTTGAAA-ATAAATGTAGTT
1 TTTGAAATATAAAT-TAGTT
7582 TTTGAAATATAAATTAGTT
1 TTTGAAATATAAATTAGTT
7601 ACATTAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (19 bp):
TTTGAAATATAAATTAGTT
Done.