Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002922.1 Kokia drynarioides strain JFW-HI SEQ_115363, 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: 31119
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:2218 original size:30 final size:30
Alignment explanation
Indices: 2178--2239 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
2168 CTTAACAAAT
*
2178 AAATGCCTCTAAAATAGTAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
*
2208 AAATGTCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
2238 AA
1 AA
2240 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.24
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAC
Found at i:4787 original size:16 final size:17
Alignment explanation
Indices: 4759--4790 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4749 AGATTTTATA
4759 ATTTTTAATAATTTTTC
1 ATTTTTAATAATTTTTC
4776 ATTTTTAA-AATTTTT
1 ATTTTTAATAATTTTT
4791 AATAATTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTTAATAATTTTTC
Found at i:5234 original size:17 final size:17
Alignment explanation
Indices: 5214--5289 Score: 84
Period size: 16 Copynumber: 4.6 Consensus size: 17
5204 CCAATTTTAA
5214 ATTTTAAATTTTAATTT
1 ATTTTAAATTTTAATTT
* *
5231 A-TTTAAGTTTGAATTT
1 ATTTTAAATTTTAATTT
*
5247 ATTTTAAATTTAAATTT
1 ATTTTAAATTTTAATTT
* * *
5264 ATTTT-GAGTTTAAATT
1 ATTTTAAATTTTAATTT
5280 ATTTTAAATT
1 ATTTTAAATT
5290 AAATTTAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
16 26 0.55
17 21 0.45
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
ATTTTAAATTTTAATTT
Found at i:5256 original size:33 final size:33
Alignment explanation
Indices: 5214--5296 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
5204 CCAATTTTAA
* *
5214 ATTTTAAATTTTAATTTA-TTTAAGTTTGAATTT
1 ATTTTAAATTTAAATTTATTTTAAGTTT-AAATT
*
5247 ATTTTAAATTTAAATTTATTTTGAGTTTAAATT
1 ATTTTAAATTTAAATTTATTTTAAGTTTAAATT
5280 ATTTTAAA-TTAAATTTA
1 ATTTTAAATTTAAATTTA
5297 AATTTAATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 9 0.20
33 29 0.63
34 8 0.17
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (33 bp):
ATTTTAAATTTAAATTTATTTTAAGTTTAAATT
Found at i:5260 original size:6 final size:6
Alignment explanation
Indices: 5209--5303 Score: 60
Period size: 6 Copynumber: 16.8 Consensus size: 6
5199 ATAACCCAAT
* * * *
5209 TTTAAA TTTTAAA TTTTAA TTT--A TTTAAG TTTGAA TTT-AT TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
5255 TTTAAA TTT-AT TTTGAG TTTAAA -TT-AT TTTAAA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
5299 TTTAA
1 TTTAA
5304 TTAAAAATTG
Statistics
Matches: 69, Mismatches: 12, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
4 5 0.07
5 17 0.25
6 41 0.59
7 6 0.09
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:5312 original size:33 final size:33
Alignment explanation
Indices: 5214--5309 Score: 83
Period size: 33 Copynumber: 2.9 Consensus size: 33
5204 CCAATTTTAA
* * *
5214 ATTTTAAATTTTAATTT-ATTT-AAGTTTGAATTT
1 ATTTTAAATTTAAATTTAATTTGAA--TTAAAATT
* * *
5247 ATTTTAAATTTAAATTTATTTTGAGTTTAAATT
1 ATTTTAAATTTAAATTTAATTTGAATTAAAATT
5280 ATTTTAAA-TTAAATTTAAATTT-AATTAAAA
1 ATTTTAAATTTAAATTT-AATTTGAATTAAAA
5310 ATTGTCCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
32 14 0.27
33 34 0.65
34 3 0.06
35 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (33 bp):
ATTTTAAATTTAAATTTAATTTGAATTAAAATT
Found at i:6095 original size:18 final size:18
Alignment explanation
Indices: 6069--6114 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
6059 TCACTAACTC
6069 AAAAAAT-A-ATATTATTA
1 AAAAAATAACATATT-TTA
6086 AAAAAGATAACATATTTTA
1 AAAAA-ATAACATATTTTA
6105 AAAAAA-AACA
1 AAAAAATAACA
6115 CAACAATCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 9 0.35
18 3 0.12
19 9 0.35
20 5 0.19
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAAAATAACATATTTTA
Found at i:6980 original size:29 final size:29
Alignment explanation
Indices: 6947--7168 Score: 222
Period size: 30 Copynumber: 7.5 Consensus size: 29
6937 CTATTTTATT
6947 TAAAAATTACATTTTGA-CCCT-AACTTC
1 TAAAAATTACATTTTGACCCCTAAACTTC
* * * *
6974 ATAAAAAATATATTTTAACCCCTAAACTTT
1 -TAAAAATTACATTTTGACCCCTAAACTTC
* *
7004 TCAAAAATTACATTTTAACCTC-AAACTTTC
1 T-AAAAATTACATTTTGACCCCTAAAC-TTC
*
7034 TAAAAAGTAC-TTTTGACCCC-AAACTT-
1 TAAAAATTACATTTTGACCCCTAAACTTC
*
7060 TACAAAAATTACATTTTGACCCTTAAACTTTC
1 T--AAAAATTACATTTTGACCCCTAAAC-TTC
7092 TAAAAATTACATTTTGACCCCTAAACTTC
1 TAAAAATTACATTTTGACCCCTAAACTTC
*
7121 ATAAAAATTATATTTTTGACCCCTAAACTTTC
1 -TAAAAATTACA-TTTTGACCCCTAAAC-TTC
*
7153 AAAAAATTAACATTTT
1 TAAAAATT-ACATTTT
7169 TCCCGCAAAT
Statistics
Matches: 163, Mismatches: 17, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
26 1 0.01
27 2 0.01
28 34 0.21
29 29 0.18
30 63 0.39
31 28 0.17
32 6 0.04
ACGTcount: A:0.41, C:0.20, G:0.03, T:0.36
Consensus pattern (29 bp):
TAAAAATTACATTTTGACCCCTAAACTTC
Found at i:7039 original size:58 final size:58
Alignment explanation
Indices: 6948--7136 Score: 206
Period size: 58 Copynumber: 3.2 Consensus size: 58
6938 TATTTTATTT
* * * *
6948 AAAAATTACATTTTGACC-CTAAC-TTCATAAAAAATATATTTTAACCCCTAAACTTTTC
1 AAAAATTACATTTTAACCTCAAACTTTC-TAAAAAGTA-ATTTTGACCCCTAAACTTTTC
* *
7006 AAAAATTACATTTTAACCTCAAACTTTCTAAAAAGTACTTTTGACCCC-AAACTTTAC
1 AAAAATTACATTTTAACCTCAAACTTTCTAAAAAGTAATTTTGACCCCTAAACTTTTC
* * * *
7063 AAAAATTACATTTTGACCCTTAAACTTTCTAAAAATTACATTTTGACCCCTAAACTTCAT-
1 AAAAATTACATTTT-AACCTCAAACTTTCTAAAAAGTA-ATTTTGACCCCTAAACTT-TTC
*
7123 AAAAATTATATTTT
1 AAAAATTACATTTT
7137 TGACCCCTAA
Statistics
Matches: 112, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
57 22 0.20
58 46 0.41
59 22 0.20
60 22 0.20
ACGTcount: A:0.41, C:0.20, G:0.03, T:0.37
Consensus pattern (58 bp):
AAAAATTACATTTTAACCTCAAACTTTCTAAAAAGTAATTTTGACCCCTAAACTTTTC
Found at i:7226 original size:90 final size:90
Alignment explanation
Indices: 6947--7201 Score: 208
Period size: 87 Copynumber: 2.9 Consensus size: 90
6937 CTATTTTATT
* * * * * * *
6947 TAAAAATTACA-TTTTGA-CCCTAACTTCATAAAAAATATATTTTAACCC-CTAAACTTT-TCAA
1 TAAAAATTAGATTTTTGACCCCAAACTTTACAAAAATTACATTTTGACCCGC-AAACTTTCT-AA
* * *
7008 AAATTACATTTTAACCTC-AAACTTTC-
64 AAATCACATTTTGACCCCTAAAC-TTCA
* * **
7034 TAAAAAGT--ACTTTTGACCCCAAACTTTACAAAAATTACATTTTGACCCTTAAACTTTCTAAAA
1 TAAAAATTAGATTTTTGACCCCAAACTTTACAAAAATTACATTTTGACCCGCAAACTTTCTAAAA
*
7097 ATTACATTTTGACCCCTAAACTTCA
66 ATCACATTTTGACCCCTAAACTTCA
* *
7122 TAAAAATTATATTTTTGACCCCTAAACTTT-CAAAAAATTAACATTTT-TCCCGCAAA-TTTCTA
1 TAAAAATTAGATTTTTGACCCC-AAACTTTAC-AAAAATT-ACATTTTGACCCGCAAACTTTCTA
*
7184 AAAGTCACATTTTCGACC
63 AAAATCACATTTT-GACC
7202 TCAAATTTTT
Statistics
Matches: 139, Mismatches: 17, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
85 1 0.01
86 6 0.04
87 60 0.43
88 12 0.09
90 29 0.21
91 24 0.17
92 7 0.05
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.36
Consensus pattern (90 bp):
TAAAAATTAGATTTTTGACCCCAAACTTTACAAAAATTACATTTTGACCCGCAAACTTTCTAAAA
ATCACATTTTGACCCCTAAACTTCA
Found at i:7235 original size:29 final size:30
Alignment explanation
Indices: 7203--7267 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
7193 TTTTCGACCT
*
7203 CAAATTTTTC-AAAAGTT-AGATTTTAATCC
1 CAAATTTTTCAAAAAGTTCA-ATTTTAACCC
* *
7232 CAAAATTTTCAAAAATTTCAATTTTAACCC
1 CAAATTTTTCAAAAAGTTCAATTTTAACCC
7262 CAAATT
1 CAAATT
7268 CCTCGTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.30
30 20 0.67
31 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (30 bp):
CAAATTTTTCAAAAAGTTCAATTTTAACCC
Found at i:12922 original size:55 final size:56
Alignment explanation
Indices: 12824--12934 Score: 136
Period size: 55 Copynumber: 2.0 Consensus size: 56
12814 GATACATACT
* * *
12824 AAGGGAAAACTCAAAAACCTCAGTTCTTGATTACATCAAACATTTGCTGACATAGA
1 AAGGAAAAACTCAAAAACCTCAGTTCTTGACTACATCAAACATTTACTGACATAGA
* * * *
12880 AAGGAAAAACTC-AAAATCTCGGTTCTTGACTACATTC-GACATTTACTTACATAGA
1 AAGGAAAAACTCAAAAACCTCAGTTCTTGACTACA-TCAAACATTTACTGACATAGA
12935 GATGAAGGCT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
55 34 0.72
56 13 0.28
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.27
Consensus pattern (56 bp):
AAGGAAAAACTCAAAAACCTCAGTTCTTGACTACATCAAACATTTACTGACATAGA
Found at i:14579 original size:2 final size:2
Alignment explanation
Indices: 14574--14606 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
14564 CATATATATA
14574 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
14607 ACATATATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:20379 original size:20 final size:20
Alignment explanation
Indices: 20354--20421 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
20344 TTAAAAATAA
20354 AAAATTATTAAAATTAATTT
1 AAAATTATTAAAATTAATTT
20374 AAAATTATTTTTTAAAA-TAA---
1 AAAATTA----TTAAAATTAATTT
*
20394 AAAATTATTAAAATTATTTT
1 AAAATTATTAAAATTAATTT
20414 AAAATTAT
1 AAAATTAT
20422 AATCATCATC
Statistics
Matches: 39, Mismatches: 1, Indels: 16
0.70 0.02 0.29
Matches are distributed among these distances:
16 6 0.15
17 2 0.05
20 22 0.56
23 3 0.08
24 6 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATTATTAAAATTAATTT
Found at i:20396 original size:40 final size:41
Alignment explanation
Indices: 20330--20421 Score: 159
Period size: 40 Copynumber: 2.3 Consensus size: 41
20320 AGCAAATGAT
*
20330 TTTAATATTATTTTTTAAAAATAAAAAATTATTAAAATTAA
1 TTTAAAATTATTTTTTAAAAATAAAAAATTATTAAAATTAA
*
20371 TTTAAAATTATTTTTT-AAAATAAAAAATTATTAAAATTAT
1 TTTAAAATTATTTTTTAAAAATAAAAAATTATTAAAATTAA
20411 TTTAAAATTAT
1 TTTAAAATTAT
20422 AATCATCATC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
40 34 0.69
41 15 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (41 bp):
TTTAAAATTATTTTTTAAAAATAAAAAATTATTAAAATTAA
Found at i:25028 original size:17 final size:18
Alignment explanation
Indices: 25002--25039 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
24992 AGTATGAAAT
25002 ATTTGATTGA-GA-TGTA
1 ATTTGATTGATGATTGTA
25018 ATTTAGATTGATGATTGTA
1 ATTT-GATTGATGATTGTA
25037 ATT
1 ATT
25040 GTGTGAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.21
17 6 0.32
18 2 0.11
19 7 0.37
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (18 bp):
ATTTGATTGATGATTGTA
Done.