Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009821.1 Kokia drynarioides strain JFW-HI SEQ_124542, 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: 36931
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 142 characters in sequence are not A, C, G, or T
Found at i:2648 original size:18 final size:17
Alignment explanation
Indices: 2612--2649 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2602 GCAAATGTCT
2612 TTAAAATAATAACAAAA
1 TTAAAATAATAACAAAA
2629 TTAACAATAA-AACAAGAA
1 TTAA-AATAATAACAA-AA
2647 TTA
1 TTA
2650 TATAACATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.66, C:0.08, G:0.03, T:0.24
Consensus pattern (17 bp):
TTAAAATAATAACAAAA
Found at i:4169 original size:68 final size:68
Alignment explanation
Indices: 4058--4192 Score: 216
Period size: 68 Copynumber: 2.0 Consensus size: 68
4048 GTTGTTTTTG
* *
4058 CATTAATCACGAATAAACGCACCGCACATCTAAACCAACATTAAATATGTTGAAATTTCTCTTTT
1 CATTAATCACGAATAAACACACCGCACATCTAAACCAACATTAAATATGTTAAAATTTCTCTTTT
4123 AAA
66 AAA
* * * *
4126 CATTAATCACGAATAAACACACTGTATATCTAAACCAATATTAAATATGTTAAAATTTCTCTTTT
1 CATTAATCACGAATAAACACACCGCACATCTAAACCAACATTAAATATGTTAAAATTTCTCTTTT
4191 AA
66 AA
4193 TGAAATTGAC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (68 bp):
CATTAATCACGAATAAACACACCGCACATCTAAACCAACATTAAATATGTTAAAATTTCTCTTTT
AAA
Found at i:14547 original size:23 final size:23
Alignment explanation
Indices: 14495--14548 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
14485 TTGATCTCGA
* *
14495 AACTCGAATTACTCATTCAAGTT
1 AACTCGAATAACTCATTCAAATT
* *
14518 GATTCGAATAACTCGATT-AAATT
1 AACTCGAATAACTC-ATTCAAATT
14541 AACTCGAA
1 AACTCGAA
14549 GTTCAAATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (23 bp):
AACTCGAATAACTCATTCAAATT
Found at i:15455 original size:12 final size:13
Alignment explanation
Indices: 15440--15479 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
15430 TGCTTTATAA
15440 TATTTCTTA-TCC
1 TATTTCTTATTCC
15452 TA-TTCTTATTCC
1 TATTTCTTATTCC
*
15464 TA-TTCCTATTCC
1 TATTTCTTATTCC
15476 TATT
1 TATT
15480 CAATTTTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 6 0.24
12 18 0.72
13 1 0.04
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTTCTTATTCC
Found at i:15467 original size:6 final size:6
Alignment explanation
Indices: 15449--15480 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
15439 ATATTTCTTA
*
15449 TCCTAT TCTTAT TCCTAT TCCTAT TCCTAT TC
1 TCCTAT TCCTAT TCCTAT TCCTAT TCCTAT TC
15481 AATTTTATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.31, G:0.00, T:0.53
Consensus pattern (6 bp):
TCCTAT
Found at i:28924 original size:27 final size:27
Alignment explanation
Indices: 28894--28976 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
28884 GATGAATTAC
28894 TTTCGTAAAAAGTATATGATAAAGAGT
1 TTTCGTAAAAAGTATATGATAAAGAGT
* ** *
28921 TTTC---AAAAGCA-ATTGGATGAATTA-C
1 TTTCGTAAAAAGTATA-T-GAT-AAAGAGT
28946 TTTCGTAAAAAGTATATGATAAAGAGT
1 TTTCGTAAAAAGTATATGATAAAGAGT
28973 TTTC
1 TTTC
28977 AATCATAGTA
Statistics
Matches: 40, Mismatches: 8, Indels: 16
0.62 0.12 0.25
Matches are distributed among these distances:
23 1 0.03
24 7 0.17
25 7 0.17
26 6 0.15
27 11 0.28
28 7 0.17
29 1 0.03
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (27 bp):
TTTCGTAAAAAGTATATGATAAAGAGT
Found at i:28952 original size:52 final size:52
Alignment explanation
Indices: 28874--28978 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
28864 GTCATTGGAC
*
28874 AAAGCAGTTGGATGAATTACTTTCGTAAAAAGTATATGATAAAGAGTTTTCA
1 AAAGCAATTGGATGAATTACTTTCGTAAAAAGTATATGATAAAGAGTTTTCA
28926 AAAGCAATTGGATGAATTACTTTCGTAAAAAGTATATGATAAAGAGTTTTCA
1 AAAGCAATTGGATGAATTACTTTCGTAAAAAGTATATGATAAAGAGTTTTCA
28978 A
1 A
28979 TCATAGTATT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (52 bp):
AAAGCAATTGGATGAATTACTTTCGTAAAAAGTATATGATAAAGAGTTTTCA
Found at i:28956 original size:28 final size:28
Alignment explanation
Indices: 28874--28957 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 28
28864 GTCATTGGAC
*
28874 AAAGCAGTTGGATGAATTACTTTCGTAA
1 AAAGCAATTGGATGAATTACTTTCGTAA
* ** * *
28902 AAAG-TATAT-GAT-AAAGAGTTT--TCA
1 AAAGCAAT-TGGATGAATTACTTTCGTAA
28926 AAAGCAATTGGATGAATTACTTTCGTAA
1 AAAGCAATTGGATGAATTACTTTCGTAA
28954 AAAG
1 AAAG
28958 TATATGATAA
Statistics
Matches: 39, Mismatches: 11, Indels: 12
0.63 0.18 0.19
Matches are distributed among these distances:
24 7 0.18
25 5 0.13
26 12 0.31
27 4 0.10
28 11 0.28
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (28 bp):
AAAGCAATTGGATGAATTACTTTCGTAA
Found at i:29310 original size:16 final size:15
Alignment explanation
Indices: 29250--29307 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
29240 AAAGAATTTT
29250 TTTTGA-AAAATTAA
1 TTTTGAGAAAATTAA
* * *
29264 TTTT-AGAAAGTGAT
1 TTTTGAGAAAATTAA
29278 TTTTGAGAAAATTAA
1 TTTTGAGAAAATTAA
*
29293 TTTTGATAAAATTAA
1 TTTTGAGAAAATTAA
29308 ATTAAATTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
13 1 0.03
14 13 0.37
15 21 0.60
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (15 bp):
TTTTGAGAAAATTAA
Found at i:30944 original size:23 final size:23
Alignment explanation
Indices: 30899--30989 Score: 69
Period size: 22 Copynumber: 3.8 Consensus size: 23
30889 GATATATAAA
**
30899 AAAAGTTTTAAAATA-ATTTTTAT
1 AAAA-TTTTAAAATATATAATTAT
30922 AAAATTTTAAAATATATAATTAT
1 AAAATTTTAAAATATATAATTAT
* *
30945 -AAATTTAAAAAATAAAATAATATAT
1 AAAATTT-TAAAAT-ATATAAT-TAT
* *
30970 AAAACTTGAAAATATTATAA
1 AAAATTTTAAAATA-TATAA
30990 AAATTAAGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
22 16 0.29
23 15 0.27
24 7 0.13
25 12 0.22
26 5 0.09
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAATTTTAAAATATATAATTAT
Found at i:31933 original size:7 final size:6
Alignment explanation
Indices: 31898--31933 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
31888 ACAAAACACA
*
31898 AAAGAC AAGGAC AAAGAC AAAGAC AAAGACC AAAGA
1 AAAGAC AAAGAC AAAGAC AAAGAC AAAGA-C AAAGA
31934 GATGAGATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.64, C:0.17, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAGAC
Found at i:32886 original size:4 final size:4
Alignment explanation
Indices: 32877--32906 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
32867 AAATTTACCC
32877 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
32907 TAAAACTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:36894 original size:18 final size:18
Alignment explanation
Indices: 36857--36907 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
36847 AAAAAAGAAA
36857 AAAAAGAAAAT-ATA-AGT
1 AAAAAGAAAATAATATA-T
* *
36874 AAAAGGGAAATAATATAT
1 AAAAAGAAAATAATATAT
36892 AAAAAGAAAATAATAT
1 AAAAAGAAAATAATAT
36908 TTTTTTTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 9 0.32
18 18 0.64
19 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.20
Consensus pattern (18 bp):
AAAAAGAAAATAATATAT
Done.