Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008494.1 Kokia drynarioides strain JFW-HI SEQ_123169, 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: 31740
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Found at i:4830 original size:52 final size:50
Alignment explanation
Indices: 4747--4924 Score: 230
Period size: 52 Copynumber: 3.4 Consensus size: 50
4737 ATTTCACTTC
* * *
4747 ATTCATATACTCACGATGACCTATAGCCATCGGACCTTATAATCCGTAAGGG
1 ATTCATATACTCACGATGACC-ATAGTCATCGGA-CTTTTAATCCGTAAAGG
* * *
4799 ATTCGTATACTCACGATGACACAGAGTCATCGGACTTCTTAATCCGCAAAGG
1 ATTCATATACTCACGATGAC-CATAGTCATCGGACTT-TTAATCCGTAAAGG
* *
4851 ATCCATATACTCACGATGACGCTTAGTCATCGGACTGTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGAC-CATAGTCATCGGACT-TTTAATCCGTAAAGG
4903 ATTCATATACTCACGATGACCA
1 ATTCATATACTCACGATGACCA
4925 ATAAGACTTC
Statistics
Matches: 109, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
51 4 0.04
52 103 0.94
53 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (50 bp):
ATTCATATACTCACGATGACCATAGTCATCGGACTTTTAATCCGTAAAGG
Found at i:8383 original size:23 final size:23
Alignment explanation
Indices: 8350--8394 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
8340 GGGTTTAAAG
*
8350 TTAAAAGGGTCTAATTTTTTTTT
1 TTAAAAAGGTCTAATTTTTTTTT
8373 TTAAAAAGGTCTAATTTTTTTT
1 TTAAAAAGGTCTAATTTTTTTT
8395 AAACTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.04, G:0.11, T:0.56
Consensus pattern (23 bp):
TTAAAAAGGTCTAATTTTTTTTT
Found at i:8454 original size:31 final size:30
Alignment explanation
Indices: 8419--8491 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
8409 AAAAAAAAAA
* *
8419 TTATCAATTTTTAAGGGTCCCAAATTTTTTT
1 TTATCAATTTTTAAGAGACCCAAA-TTTTTT
* **
8450 TTATCAATTTTTGAGAGACTTAAATTTTTT
1 TTATCAATTTTTAAGAGACCCAAATTTTTT
8480 TT-TCAATTTTTA
1 TTATCAATTTTTA
8492 TTATTTTGCT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 9 0.25
30 8 0.22
31 19 0.53
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.55
Consensus pattern (30 bp):
TTATCAATTTTTAAGAGACCCAAATTTTTT
Found at i:10189 original size:22 final size:22
Alignment explanation
Indices: 10139--10182 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
10129 GCAGGGATCG
* * *
10139 AGATTTAATTATAATTTTTTAT
1 AGATTAAAATATAATTATTTAT
10161 AGATTAAAATATAATTATTTAT
1 AGATTAAAATATAATTATTTAT
10183 GTATTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
AGATTAAAATATAATTATTTAT
Found at i:10195 original size:22 final size:21
Alignment explanation
Indices: 10143--10191 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
10133 GGATCGAGAT
*
10143 TTAATTATAATTTTTTATAGA
1 TTAATTATAATTATTTATAGA
*
10164 TTAAAATATAATTATTTAT-GTA
1 TT-AATTATAATTATTTATAG-A
10186 TTAATT
1 TTAATT
10192 TATACTTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
TTAATTATAATTATTTATAGA
Found at i:10405 original size:83 final size:85
Alignment explanation
Indices: 10233--10396 Score: 215
Period size: 83 Copynumber: 1.9 Consensus size: 85
10223 AAATAATTTC
* * * ** *
10233 TTTTTCATTTTTAGAGGGGTTAAAGTATAATTTTTCTATATATTAATTTATAATTTCTTTATTGA
1 TTTTTCATTTTTAGAGGAGTCAAAATATAATTTCACTATATATTAATTTATAATTTCTATATTGA
* **
10298 TAAGCGGATTTAATTGAAAA
66 TAAGAGGATCAAATTGAAAA
*
10318 TTTTTCA-TTTTAGA-GAGTCAAAATATAATTTCACTATATATTAATTTATAATTTCTATATTTA
1 TTTTTCATTTTTAGAGGAGTCAAAATATAATTTCACTATATATTAATTTATAATTTCTATATTGA
10381 TAAGAGGACTCAAATT
66 TAAGAGGA-TCAAATT
10397 TTTTTTTTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
83 49 0.72
84 12 0.18
85 7 0.10
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.48
Consensus pattern (85 bp):
TTTTTCATTTTTAGAGGAGTCAAAATATAATTTCACTATATATTAATTTATAATTTCTATATTGA
TAAGAGGATCAAATTGAAAA
Found at i:16033 original size:6 final size:6
Alignment explanation
Indices: 16022--16047 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16012 TATATGCGTG
16022 TGTGCA TGTGCA TGTGCA TGTGCA TG
1 TGTGCA TGTGCA TGTGCA TGTGCA TG
16048 GTAGAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.35, T:0.35
Consensus pattern (6 bp):
TGTGCA
Found at i:23032 original size:30 final size:30
Alignment explanation
Indices: 22998--23054 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
22988 AACTACAACC
*
22998 GTTGTCGCCCTGACGCAACCTCTAGCTATT
1 GTTGTCGCCCTAACGCAACCTCTAGCTATT
* * *
23028 GTTGTCGCCTTAACTCGACCTCTAGCT
1 GTTGTCGCCCTAACGCAACCTCTAGCT
23055 TCTCTCCAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.16, C:0.33, G:0.19, T:0.32
Consensus pattern (30 bp):
GTTGTCGCCCTAACGCAACCTCTAGCTATT
Done.