Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008748.1 Kokia drynarioides strain JFW-HI SEQ_123430, 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: 46265
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:16729 original size:24 final size:24
Alignment explanation
Indices: 16700--16756 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
16690 TGAATGTTCA
* *
16700 ACCTTTCATCTTCGTTAACTTTTC
1 ACCTTTCATCTTCCTTAACTCTTC
*
16724 ACCTTTCAACTTCCTTAACTCTTC
1 ACCTTTCATCTTCCTTAACTCTTC
16748 ACCTTTCAT
1 ACCTTTCAT
16757 ATTCTTGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.19, C:0.33, G:0.02, T:0.46
Consensus pattern (24 bp):
ACCTTTCATCTTCCTTAACTCTTC
Found at i:16945 original size:135 final size:135
Alignment explanation
Indices: 16703--16954 Score: 418
Period size: 135 Copynumber: 1.9 Consensus size: 135
16693 ATGTTCAACC
* * * * *
16703 TTTCATCTTCGTTAACTTTTCACCTTTCAACTTCCTTAACTCTTCACCTTTCATATTCTTGTAAC
1 TTTCATCTTCATTAACTTTTCACCTTTCAACTTCCTCAACTCTTCAACTTTCACATTCTTATAAC
16768 CCCTTTCCTATTTATGTATTAAAAAATAAGGAGTCTAATCTCCCTATATATATATTTATTTATTT
66 CCCTTTCCTATTTATGTATTAAAAAATAAGGAGTCTAATCTCCCTATATATATATTTATTTATTT
16833 ATTTA
131 ATTTA
16838 TTTCATCTTCATTAACCTTTT-ACCTTTCATA-TTCCTCAACTCTTCAACTTTCACATTCTTATA
1 TTTCATCTTCATTAA-CTTTTCACCTTTCA-ACTTCCTCAACTCTTCAACTTTCACATTCTTATA
*
16901 ACCCCTTTCCTATTTATGTGTTAAAAAATAAGGAGTCTAATCTCCCTATATATA
64 ACCCCTTTCCTATTTATGTATTAAAAAATAAGGAGTCTAATCTCCCTATATATA
16955 GAGAAAGAGA
Statistics
Matches: 109, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
135 103 0.94
136 6 0.06
ACGTcount: A:0.27, C:0.23, G:0.04, T:0.45
Consensus pattern (135 bp):
TTTCATCTTCATTAACTTTTCACCTTTCAACTTCCTCAACTCTTCAACTTTCACATTCTTATAAC
CCCTTTCCTATTTATGTATTAAAAAATAAGGAGTCTAATCTCCCTATATATATATTTATTTATTT
ATTTA
Found at i:21580 original size:19 final size:19
Alignment explanation
Indices: 21556--21603 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
21546 GTCATACATC
21556 TCACGAAAGATCAAATGCA
1 TCACGAAAGATCAAATGCA
*
21575 TCACGAAAGATCAAGTGCA
1 TCACGAAAGATCAAATGCA
21594 TCACGAAAGA
1 TCACGAAAGA
21604 ATAAAACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.15
Consensus pattern (19 bp):
TCACGAAAGATCAAATGCA
Found at i:22597 original size:18 final size:18
Alignment explanation
Indices: 22563--22595 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
22553 TAGTCTTTGG
22563 TCTTTCTTTCTTTTTTTC
1 TCTTTCTTTCTTTTTTTC
22581 TCTTT-TTT-TTTTTTT
1 TCTTTCTTTCTTTTTTT
22596 TTTGAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (18 bp):
TCTTTCTTTCTTTTTTTC
Found at i:23121 original size:19 final size:20
Alignment explanation
Indices: 23088--23126 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
23078 AAAAAAGTTC
*
23088 AAAATAATTTTTAAAAATTT
1 AAAATAATTTATAAAAATTT
23108 AAAAT-ATTTATAAAAATTT
1 AAAATAATTTATAAAAATTT
23127 CAATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAATAATTTATAAAAATTT
Found at i:23134 original size:20 final size:20
Alignment explanation
Indices: 23079--23139 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
23069 TATCTCTCTA
* *
23079 AAAAAGTTCAAAATAATTTTT
1 AAAAATTTCAAAAT-ATTTAT
23100 AAAAATTT-AAAATATTTAT
1 AAAAATTTCAAAATATTTAT
* *
23119 AAAAATTTCAATATATATAT
1 AAAAATTTCAAAATATTTAT
23139 A
1 A
23140 TATATAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 13 0.37
20 15 0.43
21 7 0.20
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAAATTTCAAAATATTTAT
Found at i:24026 original size:17 final size:17
Alignment explanation
Indices: 24006--24091 Score: 55
Period size: 17 Copynumber: 5.3 Consensus size: 17
23996 TAAAATGTTC
24006 ATATTTTATACAATAAA
1 ATATTTTATACAATAAA
24023 ATATTTCT-TAC--T-AA
1 ATATTT-TATACAATAAA
24037 ATA-TTTATA-AATTGTAAA
1 ATATTTTATACAA---TAAA
*
24055 ATATATTTAT-CTATAAA
1 ATAT-TTTATACAATAAA
24072 ATATTTT-T-CAATAAA
1 ATATTTTATACAATAAA
24087 ATATT
1 ATATT
24092 AAGAATATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 24
0.68 0.02 0.29
Matches are distributed among these distances:
12 1 0.02
13 4 0.07
14 5 0.09
15 13 0.23
16 3 0.05
17 18 0.32
18 6 0.11
20 6 0.11
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.47
Consensus pattern (17 bp):
ATATTTTATACAATAAA
Found at i:24077 original size:15 final size:15
Alignment explanation
Indices: 24057--24091 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
24047 ATTGTAAAAT
*
24057 ATATTTATCTATAAA
1 ATATTTATCAATAAA
*
24072 ATATTTTTCAATAAA
1 ATATTTATCAATAAA
24087 ATATT
1 ATATT
24092 AAGAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATTTATCAATAAA
Found at i:26797 original size:37 final size:34
Alignment explanation
Indices: 26757--26963 Score: 106
Period size: 37 Copynumber: 5.8 Consensus size: 34
26747 ATAATACTAT
26757 TTTAATAGTTTAATATTAAATTTAATTTAATAATTA
1 TTTAATAGTTT-ATATT-AATTTAATTTAATAATTA
* *
26793 TTTTAATAGTATTTTATTAATTTAATATTAA-AATGA
1 -TTTAATAGT-TTATATTAATTTAAT-TTAATAATTA
* * **
26829 -TT-AT-CTTAATATTAAATTTAATTTAATGTTTA
1 TTTAATAGTTTATATT-AATTTAATTTAATAATTA
* **
26861 TCTAAT-GTTTATATTGTAAATAAAGATTT--T-ATTA
1 TTTAATAGTTTATA-T-T-AATTTA-ATTTAATAATTA
*
26895 TTTAATAAGATTTAATATTAATTTAATCTAATAATTA
1 TTTAAT-AG-TTT-ATATTAATTTAATTTAATAATTA
*
26932 TCTTGATAAGTATTATATTAATTTAATATTAA
1 T-TTAAT-AGT-TTATATTAATTTAAT-TTAA
26964 AGTGATTAAG
Statistics
Matches: 131, Mismatches: 20, Indels: 37
0.70 0.11 0.20
Matches are distributed among these distances:
31 9 0.07
32 11 0.08
33 3 0.02
34 20 0.15
35 6 0.05
36 21 0.16
37 44 0.34
38 17 0.13
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (34 bp):
TTTAATAGTTTATATTAATTTAATTTAATAATTA
Found at i:26831 original size:20 final size:18
Alignment explanation
Indices: 26757--26855 Score: 62
Period size: 19 Copynumber: 5.3 Consensus size: 18
26747 ATAATACTAT
*
26757 TTTAATAGTTTAATATTAAA
1 TTTAATA-TTAAATATT-AA
*
26777 TTTAAT-TT-AATAATTAT
1 TTTAATATTAAAT-ATTAA
* **
26794 TTTAATAGTATTTTATTAA
1 TTTAATATTA-AATATTAA
26813 TTTAATATTAAAATGATT-A
1 TTTAATATT-AAAT-ATTAA
26832 TCTTAATATTAAAT-TTAA
1 T-TTAATATTAAATATTAA
26850 TTTAAT
1 TTTAAT
26856 GTTTATCTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
17 17 0.27
18 8 0.13
19 19 0.30
20 19 0.30
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTAATATTAAATATTAA
Found at i:26904 original size:18 final size:20
Alignment explanation
Indices: 26883--26921 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
26873 ATTGTAAATA
26883 AAGATTT-TATT-ATTTAAT
1 AAGATTTATATTAATTTAAT
26901 AAGATTTAATATTAATTTAAT
1 AAGATTT-ATATTAATTTAAT
26922 CTAATAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
AAGATTTATATTAATTTAAT
Found at i:41179 original size:39 final size:39
Alignment explanation
Indices: 41136--41346 Score: 141
Period size: 39 Copynumber: 5.4 Consensus size: 39
41126 AGTCTGGTAG
*
41136 TGTTTATAGTGACACTACCTA-TTCAGTATAGCACTTCGA
1 TGTTTATAGTGTCACTACCTAGTTCAGTATAGCA-TTCGA
* * * *
41175 TGTTTATAGTGTCAC--CGTTAGTTTAGTATTGCTTTTCGA
1 TGTTTATAGTGTCACTAC-CTAGTTCAGTATAGC-ATTCGA
* * * * *
41214 TGTTTACAGTGTCACCACC-AATTCAGTTTAGCATTGCAA
1 TGTTTATAGTGTCACTACCTAGTTCAGTATAGCATT-CGA
* * *
41253 TGTTTATAGTGTCACTGCC-AGTTCAGTATCA-CGTTGCAA
1 TGTTTATAGTGTCACTACCTAGTTCAGTAT-AGCATT-CGA
* * * *
41292 TGTTTACAGTGTCATTACC-AGTTCAGTCTAGCGTT-GCA
1 TGTTTATAGTGTCACTACCTAGTTCAGTATAGCATTCG-A
41330 GTGTTTATAGTGTCACT
1 -TGTTTATAGTGTCACT
41347 GCCAATTCCA
Statistics
Matches: 136, Mismatches: 26, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
37 1 0.01
38 6 0.04
39 127 0.93
40 1 0.01
41 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (39 bp):
TGTTTATAGTGTCACTACCTAGTTCAGTATAGCATTCGA
Found at i:41281 original size:78 final size:78
Alignment explanation
Indices: 41136--41350 Score: 234
Period size: 78 Copynumber: 2.8 Consensus size: 78
41126 AGTCTGGTAG
* * * * * ** *
41136 TGTTTATAGTGACACTACCTATTCAGTATAGCACTT-CGATGTTTATAGTGTCACCGTTAGTTTA
1 TGTTTACAGTGTCACTACCAATTCAGTATAGCA-TTGCAATGTTTATAGTGTCACTGCCAGTTCA
** * * *
41200 GTATTGCTTTTCGA
65 GTATCACGTTGCAA
* *
41214 TGTTTACAGTGTCACCACCAATTCAGTTTAGCATTGCAATGTTTATAGTGTCACTGCCAGTTCAG
1 TGTTTACAGTGTCACTACCAATTCAGTATAGCATTGCAATGTTTATAGTGTCACTGCCAGTTCAG
41279 TATCACGTTGCAA
66 TATCACGTTGCAA
* * * * *
41292 TGTTTACAGTGTCATTACCAGTTCAGTCTAGCGTTGCAGTGTTTATAGTGTCACTGCCA
1 TGTTTACAGTGTCACTACCAATTCAGTATAGCATTGCAATGTTTATAGTGTCACTGCCA
41351 ATTCCATAGA
Statistics
Matches: 115, Mismatches: 21, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
77 2 0.02
78 113 0.98
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (78 bp):
TGTTTACAGTGTCACTACCAATTCAGTATAGCATTGCAATGTTTATAGTGTCACTGCCAGTTCAG
TATCACGTTGCAA
Done.