Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014376.1 Kokia drynarioides strain JFW-HI SEQ_129414, 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: 44332
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4384 original size:6 final size:6
Alignment explanation
Indices: 4373--4407 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
4363 ATATTGAATT
4373 AAATAA AAAT-- AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A
4408 TTTTTGTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
6 23 0.85
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:4387 original size:10 final size:10
Alignment explanation
Indices: 4372--4408 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
4362 GATATTGAAT
4372 TAAATAAAAA
1 TAAATAAAAA
4382 TAAATAAAAA
1 TAAATAAAAA
4392 TAAAAATAAAAA
1 T--AAATAAAAA
4404 TAAAT
1 TAAAT
4409 TTTTGTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 15 0.60
12 10 0.40
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
TAAATAAAAA
Found at i:8577 original size:75 final size:75
Alignment explanation
Indices: 8454--8605 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
8444 TCTACCTCAC
8454 AAGCTCATCATTCTTATGTTCTTGAAATTTTACTCACAATTGTTTACTTCAGGTCATCCCTGGAT
1 AAGCTCATCATTCTTATGTTCTTGAAATTTTACTCACAATTGTTTACTTCAGGTCATCCCTGGAT
8519 AAAAAATTAT
66 AAAAAATTAT
8529 AAGCTCATCATTCTTATGTTCTTGAAATTTTACTCACAATTGTTTACTTCAGGTCATCCCTGGAT
1 AAGCTCATCATTCTTATGTTCTTGAAATTTTACTCACAATTGTTTACTTCAGGTCATCCCTGGAT
8594 AAAAAATTAT
66 AAAAAATTAT
8604 AA
1 AA
8606 CGATGTGAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (75 bp):
AAGCTCATCATTCTTATGTTCTTGAAATTTTACTCACAATTGTTTACTTCAGGTCATCCCTGGAT
AAAAAATTAT
Found at i:8734 original size:30 final size:30
Alignment explanation
Indices: 8698--8763 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
8688 TTAAGGGTGC
8698 GTATATGGTGATATGTCTCAGCACTATTCT
1 GTATATGGTGATATGTCTCAGCACTATTCT
8728 GTATATGGTGATATGTCTCAGCACTATTCT
1 GTATATGGTGATATGTCTCAGCACTATTCT
8758 GTATAT
1 GTATAT
8764 CTTATTCTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (30 bp):
GTATATGGTGATATGTCTCAGCACTATTCT
Found at i:25052 original size:17 final size:17
Alignment explanation
Indices: 25030--25064 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
25020 GTATGCAAAT
25030 AATAAATGAGAAATATG
1 AATAAATGAGAAATATG
25047 AATAAATGAGAAATATG
1 AATAAATGAGAAATATG
25064 A
1 A
25065 GGTTCGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (17 bp):
AATAAATGAGAAATATG
Found at i:28994 original size:22 final size:22
Alignment explanation
Indices: 28945--28990 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
28935 TACAATATTC
* *
28945 AAATAATATTAAAAAAACAGTG
1 AAATAATAGTAAAAAAACAGTA
*
28967 AAATAATAGTAAAAACACA-TA
1 AAATAATAGTAAAAAAACAGTA
28988 AAA
1 AAA
28991 ATAACAGCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (22 bp):
AAATAATAGTAAAAAAACAGTA
Found at i:29023 original size:12 final size:11
Alignment explanation
Indices: 29001--29117 Score: 80
Period size: 12 Copynumber: 10.2 Consensus size: 11
28991 ATAACAGCCA
*
29001 AACAACAAAAAT
1 AACAAC-AAAAC
29013 AACAATCAAAAC
1 AACAA-CAAAAC
*
29025 AACAACAAAAAT
1 AACAAC-AAAAC
29037 AACAACAAAAC
1 AACAACAAAAC
29048 AACAA-AAATAGC
1 AACAACAAA-A-C
29060 AAC-A-AAAAC
1 AACAACAAAAC
*
29069 AACAACAAAAAT
1 AACAAC-AAAAC
*
29081 AACAGCAAAAAC
1 AACAAC-AAAAC
*
29093 AAC-ACGAAAAT
1 AACAAC-AAAAC
29104 AACAACTAAAAC
1 AACAAC-AAAAC
29116 AA
1 AA
29118 TAAAAAAGCA
Statistics
Matches: 86, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
9 4 0.05
10 5 0.06
11 23 0.27
12 53 0.62
13 1 0.01
ACGTcount: A:0.71, C:0.21, G:0.03, T:0.06
Consensus pattern (11 bp):
AACAACAAAAC
Found at i:29028 original size:24 final size:24
Alignment explanation
Indices: 29001--29117 Score: 147
Period size: 24 Copynumber: 5.1 Consensus size: 24
28991 ATAACAGCCA
29001 AACAACAAAAATAACAATC-AAAAC
1 AACAACAAAAATAACAA-CAAAAAC
29025 AACAACAAAAATAACAAC---AA-
1 AACAACAAAAATAACAACAAAAAC
*
29045 AACAACAAAAATAGCAACAAAAAC
1 AACAACAAAAATAACAACAAAAAC
*
29069 AACAACAAAAATAACAGCAAAAAC
1 AACAACAAAAATAACAACAAAAAC
* *
29093 AAC-ACGAAAATAACAACTAAAAC
1 AACAACAAAAATAACAACAAAAAC
29116 AA
1 AA
29118 TAAAAAAGCA
Statistics
Matches: 83, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
20 17 0.20
21 2 0.02
23 22 0.27
24 42 0.51
ACGTcount: A:0.71, C:0.21, G:0.03, T:0.06
Consensus pattern (24 bp):
AACAACAAAAATAACAACAAAAAC
Found at i:29036 original size:44 final size:44
Alignment explanation
Indices: 28987--29117 Score: 183
Period size: 44 Copynumber: 2.9 Consensus size: 44
28977 AAAAACACAT
*
28987 AAAAATAACAGCCAAACAACAAAAATAACAATC-AAAACAACAAC
1 AAAAATAACAGCAAAACAACAAAAATAACAA-CAAAAACAACAAC
* *
29031 AAAAATAACAACAAAACAACAAAAATAGCAACAAAAACAACAAC
1 AAAAATAACAGCAAAACAACAAAAATAACAACAAAAACAACAAC
*
29075 AAAAATAACAGCAAAAACAACACGAAAATAACAACTAAAACAA
1 AAAAATAACAGC-AAAACAACA--AAAATAACAACAAAAACAA
29118 TAAAAAAGCA
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
43 1 0.01
44 50 0.65
45 9 0.12
47 17 0.22
ACGTcount: A:0.70, C:0.21, G:0.03, T:0.06
Consensus pattern (44 bp):
AAAAATAACAGCAAAACAACAAAAATAACAACAAAAACAACAAC
Found at i:30397 original size:5 final size:5
Alignment explanation
Indices: 30364--30432 Score: 57
Period size: 5 Copynumber: 12.6 Consensus size: 5
30354 TTGGGCCCTT
* * *
30364 TTTAA TTTAT TTTAAA TTTGA TTTAAA TTTAA TTTTAA ATTAA TCTTAAA
1 TTTAA TTTAA TTT-AA TTTAA TTT-AA TTTAA -TTTAA TTTAA T-TT-AA
30414 TTTAAA TTTAA TTTAA TTT
1 TTT-AA TTTAA TTTAA TTT
30433 CAAAATTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
5 27 0.51
6 23 0.43
7 3 0.06
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (5 bp):
TTTAA
Found at i:30400 original size:23 final size:23
Alignment explanation
Indices: 30367--30441 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
30357 GGCCCTTTTT
*
30367 AATTT-ATTTTAAATTTGATTTA
1 AATTTAATTTTAAATTTAATTTA
30389 AATTTAATTTTAAA-TTAATCTTA
1 AATTTAATTTTAAATTTAAT-TTA
*
30412 AATTTAAATTT-AATTTAATTTCA
1 AATTTAATTTTAAATTTAATTT-A
*
30435 AAATTAA
1 AATTTAA
30442 AAAGTCCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
22 13 0.28
23 33 0.72
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (23 bp):
AATTTAATTTTAAATTTAATTTA
Found at i:30406 original size:17 final size:17
Alignment explanation
Indices: 30386--30442 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
30376 TAAATTTGAT
30386 TTAAATTTAATTTTAAA
1 TTAAATTTAATTTTAAA
*
30403 TT-AATCTTAAATTTAAA
1 TTAAAT-TTAATTTTAAA
* *
30420 TTTAATTTAATTTCAAAA
1 TTAAATTTAATTT-TAAA
30438 TTAAA
1 TTAAA
30443 AAGTCCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
16 3 0.09
17 20 0.61
18 10 0.30
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAAATTTAATTTTAAA
Found at i:30426 original size:11 final size:11
Alignment explanation
Indices: 30367--30432 Score: 73
Period size: 11 Copynumber: 5.9 Consensus size: 11
30357 GGCCCTTTTT
*
30367 AATTTATTTTA
1 AATTTAATTTA
*
30378 AATTTGATTTA
1 AATTTAATTTA
30389 AATTTAATTTTA
1 AATTTAA-TTTA
30401 AA-TTAATCTTA
1 AATTTAAT-TTA
30412 AATTTAAATTT-
1 AATTT-AATTTA
30423 AATTTAATTT
1 AATTTAATTT
30433 CAAAATTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
10 6 0.12
11 29 0.60
12 10 0.21
13 3 0.06
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:31112 original size:24 final size:24
Alignment explanation
Indices: 31062--31113 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
31052 AAATATCATT
* **
31062 AATAATATTATTAATTATATTGGC
1 AATAATATTACTAATTATATTAAC
31086 AATAATATTACTAA-TATTATTAAC
1 AATAATATTACTAATTA-TATTAAC
31110 AATA
1 AATA
31114 TTAATGACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (24 bp):
AATAATATTACTAATTATATTAAC
Found at i:31127 original size:15 final size:15
Alignment explanation
Indices: 31107--31148 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
31097 TAATATTATT
*
31107 AACAATATTAATGAC
1 AACAATAATAATGAC
31122 AACAATAATAATGAC
1 AACAATAATAATGAC
*
31137 ATCAATAATAAT
1 AACAATAATAAT
31149 ATTTAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.57, C:0.12, G:0.05, T:0.26
Consensus pattern (15 bp):
AACAATAATAATGAC
Found at i:32242 original size:29 final size:29
Alignment explanation
Indices: 32195--32524 Score: 250
Period size: 29 Copynumber: 11.2 Consensus size: 29
32185 TACCTAAACT
*
32195 TTCCAAAAATTACCA-TTTTACCCTCGAAC
1 TTCCAAAAA-TCCCATTTTTACCCTCGAAC
* *
32224 TT-TAGAAAATCCCATTTTTTTCCC-CGAACC
1 TTCCA-AAAATCCCA-TTTTTACCCTCGAA-C
* * *
32254 ATCCAAAAATTACCA-TTTTACCCTTGAAC
1 TTCCAAAAA-TCCCATTTTTACCCTCGAAC
*
32283 TTCCAAAAATCTCATTTTTGA--CTCGAACC
1 TTCCAAAAATCCCATTTTT-ACCCTCGAA-C
* *
32312 ATCCAAAAATTACCA-TTTTACCCTCGAAC
1 TTCCAAAAA-TCCCATTTTTACCCTCGAAC
*
32341 TTCCAAAAATCCCATTTTTGACCCCCGAAC
1 TTCCAAAAATCCCATTTTT-ACCCTCGAAC
* * *
32371 TCCCAAAAATCCCATTTTGACCCTTGAAAC
1 TTCCAAAAATCCCATTTTTACCCTCG-AAC
* *
32401 TTCTAAAAATTACCA-TTTTACCCTCGAAC
1 TTCCAAAAA-TCCCATTTTTACCCTCGAAC
* * *
32430 TCCCAAAAATCCCATTTTGACCC-CAAAAC
1 TTCCAAAAATCCCATTTTTACCCTC-GAAC
* * *
32459 TTCTAAAAATTACCA-TTTTACCCTCAAAC
1 TTCCAAAAA-TCCCATTTTTACCCTCGAAC
32488 TTCCAAAAATCCCATTTTTGACCC-CGAAAC
1 TTCCAAAAATCCCATTTTT-ACCCTCG-AAC
*
32518 ATCCAAA
1 TTCCAAA
32525 GATTACTATT
Statistics
Matches: 237, Mismatches: 40, Indels: 47
0.73 0.12 0.15
Matches are distributed among these distances:
28 27 0.11
29 112 0.47
30 89 0.38
31 9 0.04
ACGTcount: A:0.35, C:0.31, G:0.05, T:0.30
Consensus pattern (29 bp):
TTCCAAAAATCCCATTTTTACCCTCGAAC
Done.