Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011044.1 Kokia drynarioides strain JFW-HI SEQ_126015, 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: 63598
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:127 original size:22 final size:22
Alignment explanation
Indices: 102--144 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
92 AAAATATTTC
*
102 ATTA-ATAATTTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
124 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
145 TTATTCTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:4909 original size:12 final size:12
Alignment explanation
Indices: 4892--4931 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
4882 TTCATAACAA
4892 AAAAATATTTTT
1 AAAAATATTTTT
4904 AAAAATATTTTTT
1 AAAAATA-TTTTT
*
4917 AGAAAGTATTTTT
1 A-AAAATATTTTT
4930 AA
1 AA
4932 TTTTTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (12 bp):
AAAAATATTTTT
Found at i:4974 original size:11 final size:10
Alignment explanation
Indices: 4956--5003 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
4946 GTAAAATTTA
4956 TAAAAAAAAT
1 TAAAAAAAAT
4966 TAAAGAAAAAT
1 TAAA-AAAAAT
*
4977 AAAAAAATAAT
1 TAAAAAA-AAT
4988 TAAAAATAAAT
1 TAAAAA-AAAT
*
4999 GAAAA
1 TAAAA
5004 CATTTAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 7 0.22
11 24 0.75
12 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (10 bp):
TAAAAAAAAT
Found at i:4982 original size:18 final size:18
Alignment explanation
Indices: 4958--4997 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4948 AAAATTTATA
4958 AAAAAAATTAAAGAAAAAT
1 AAAAAAA-TAAAGAAAAAT
**
4977 AAAAAAATAATTAAAAAT
1 AAAAAAATAAAGAAAAAT
4995 AAA
1 AAA
4998 TGAAAACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAAAAATAAAGAAAAAT
Found at i:6399 original size:77 final size:76
Alignment explanation
Indices: 6272--6424 Score: 288
Period size: 77 Copynumber: 2.0 Consensus size: 76
6262 TGGAAGATGT
6272 GCTTTGAGTTTTCATCGGCCCCGTGGCATCTTGGACAAGCAGCATCGTTCATAATCTACTTAGCC
1 GCTTTGAGTTTTCATCGGCCCCGTGGCATCTTGGACAAGCAGCATCGTTCATAATCTACTTAGCC
6337 TGCAGATTAAC
66 TGCAGATTAAC
6348 NGCTTTGAGTTTTCATCGGCCCCGTGGCATCTTGGACAAGCAGCATCGTTCATAATCTACTTAGC
1 -GCTTTGAGTTTTCATCGGCCCCGTGGCATCTTGGACAAGCAGCATCGTTCATAATCTACTTAGC
*
6413 CTTCAGATTAAC
65 CTGCAGATTAAC
6425 TAGGTGTGAG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.31
Consensus pattern (76 bp):
GCTTTGAGTTTTCATCGGCCCCGTGGCATCTTGGACAAGCAGCATCGTTCATAATCTACTTAGCC
TGCAGATTAAC
Found at i:12418 original size:15 final size:15
Alignment explanation
Indices: 12391--12427 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
12381 ATAATGTATT
12391 AAAATTT-TTTTAAA
1 AAAATTTCTTTTAAA
*
12405 AATATTTCTTTTAAA
1 AAAATTTCTTTTAAA
12420 AAAATTTC
1 AAAATTTC
12428 ACATCAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
AAAATTTCTTTTAAA
Found at i:12585 original size:32 final size:33
Alignment explanation
Indices: 12513--12586 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 33
12503 CCTAATTGAT
*
12513 TTTTTTAGTGATTGAGAGTTTAATAAGATAGAAA
1 TTTTTTAATGATTGAGAGTTTAATAAGATA-AAA
* *
12547 TTTTTTAATGATTGAGGGTTTGATAAGAT-AAA
1 TTTTTTAATGATTGAGAGTTTAATAAGATAAAA
12579 TTTTTTAA
1 TTTTTTAA
12587 GAACTTAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 11 0.30
34 26 0.70
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (33 bp):
TTTTTTAATGATTGAGAGTTTAATAAGATAAAA
Found at i:17147 original size:52 final size:52
Alignment explanation
Indices: 17055--17300 Score: 377
Period size: 52 Copynumber: 4.7 Consensus size: 52
17045 ATGATGAACA
* *
17055 GATTTTGAGGTTCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACG
1 GATTATGAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACG
* * *
17107 GATTATGAGGTTCAATGACTATGTCTCATCGTGAGCATATGAATCCTTTACG
1 GATTATGAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACG
* * *
17159 TATTATGAGGTCCGATGACTATGTGTCATCATGAGTATATGAATCCTTTACG
1 GATTATGAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACG
* *
17211 GATTATGAGG-TCTGATAACTACGTGTCATCGTGAGTATATGAATCCTTTACG
1 GATTATGAGGTTC-GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACG
*
17263 GATTATGAGGTCCGATGACTATGTGTCATCGTGAGTAT
1 GATTATGAGGTTCGATGACTATGTGTCATCGTGAGTAT
17301 TAAAAAAGAA
Statistics
Matches: 173, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
51 1 0.01
52 171 0.99
53 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (52 bp):
GATTATGAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACG
Found at i:28083 original size:32 final size:32
Alignment explanation
Indices: 28042--28103 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
28032 TGTATATGTC
*
28042 CGATTGGTCCCTTCGCTAGCTCAACAAAAGCT
1 CGATTGGTCCCTTCCCTAGCTCAACAAAAGCT
28074 CGATTGGTCCCTTCCCTAGCTCAACAAAAG
1 CGATTGGTCCCTTCCCTAGCTCAACAAAAG
28104 TTCAATTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (32 bp):
CGATTGGTCCCTTCCCTAGCTCAACAAAAGCT
Found at i:28276 original size:19 final size:21
Alignment explanation
Indices: 28242--28283 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
28232 TGATTTTTGG
*
28242 AAAATTAATTTTAATC-AATT
1 AAAATTAATATTAATCAAATT
28262 AAAATTAA-ATTAATCAAATT
1 AAAATTAATATTAATCAAATT
28282 AA
1 AA
28284 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATTAATATTAATCAAATT
Found at i:28438 original size:11 final size:11
Alignment explanation
Indices: 28376--28441 Score: 59
Period size: 11 Copynumber: 6.2 Consensus size: 11
28366 ATTTCAAAAA
28376 TAATATTATTT
1 TAATATTATTT
*
28387 TAATA-GA--T
1 TAATATTATTT
*
28395 TAATATTATAT
1 TAATATTATTT
*
28406 T-ATATTTAATT
1 TAATA-TTATTT
28417 TAATACTTATTT
1 TAATA-TTATTT
28429 TAATATTATTT
1 TAATATTATTT
28440 TA
1 TA
28442 TTAATTTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
8 6 0.14
9 1 0.02
10 4 0.09
11 20 0.45
12 13 0.30
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (11 bp):
TAATATTATTT
Found at i:28454 original size:11 final size:11
Alignment explanation
Indices: 28394--28456 Score: 55
Period size: 12 Copynumber: 5.9 Consensus size: 11
28384 TTTTAATAGA
28394 TTAATATT-AT
1 TTAATATTAAT
28404 ATT-ATATTTAAT
1 -TTAATA-TTAAT
*
28416 TTAATACTTATT
1 TTAATA-TTAAT
28428 TTAATATT-AT
1 TTAATATTAAT
28438 TT--TATTAAT
1 TTAATATTAAT
28447 TTAATATTAA
1 TTAATATTAA
28457 AATGATTACC
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
8 4 0.09
9 4 0.09
10 6 0.14
11 14 0.33
12 15 0.35
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTAATATTAAT
Found at i:28464 original size:20 final size:18
Alignment explanation
Indices: 28394--28488 Score: 65
Period size: 17 Copynumber: 5.3 Consensus size: 18
28384 TTTTAATAGA
28394 TTAATATT--ATATTATAT
1 TTAATATTAAATATTA-AT
*
28411 TTAAT-TT-AATACTTATT
1 TTAATATTAAATA-TTAAT
**
28428 TTAATATTATTTTATTAAT
1 TTAATATTA-AATATTAAT
**
28447 TTAATATTAAAATGATTACC
1 TTAATATT-AAAT-ATTAAT
28467 TTAATATTAAAT-TTAAT
1 TTAATATTAAATATTAAT
28484 TTAAT
1 TTAAT
28489 GTTTATCTCG
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
16 2 0.03
17 22 0.36
18 5 0.08
19 17 0.28
20 15 0.25
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (18 bp):
TTAATATTAAATATTAAT
Found at i:29488 original size:26 final size:24
Alignment explanation
Indices: 29445--29496 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 24
29435 CTATCTCCTT
*
29445 ATATATATATTTTATAATTGTTTATA
1 ATATATATATTATATAA-TG-TTATA
* *
29471 ATATTTATATTATGTAATGTTATA
1 ATATATATATTATATAATGTTATA
29495 AT
1 AT
29497 TGTGATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 7 0.30
25 2 0.09
26 14 0.61
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (24 bp):
ATATATATATTATATAATGTTATA
Done.