Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014359.1 Kokia drynarioides strain JFW-HI SEQ_129396, 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: 32186
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:5221 original size:23 final size:23
Alignment explanation
Indices: 5195--5243 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5185 TTATTTGGTA
*
5195 TTTAAGTTTAATATATATATATT
1 TTTAAATTTAATATATATATATT
* * *
5218 TTTAAATTTAGTATTTATGTATT
1 TTTAAATTTAATATATATATATT
5241 TTT
1 TTT
5244 TTAATATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (23 bp):
TTTAAATTTAATATATATATATT
Found at i:5903 original size:36 final size:34
Alignment explanation
Indices: 5863--5945 Score: 85
Period size: 36 Copynumber: 2.4 Consensus size: 34
5853 TTGTTCTAAA
*
5863 ATGACATTTTGATATGATATATGTGCTTTTGAAAAC
1 ATGACATTTTGATATAATATATGT--TTTTGAAAAC
* * * *
5899 ATGACATTCTGGTTTAATATATGTTTTTGAAAAT
1 ATGACATTTTGATATAATATATGTTTTTGAAAAC
* *
5933 ATGATACTTTGAT
1 ATGACATTTTGAT
5946 CTGAATTATG
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
34 18 0.47
36 20 0.53
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.45
Consensus pattern (34 bp):
ATGACATTTTGATATAATATATGTTTTTGAAAAC
Found at i:7213 original size:21 final size:21
Alignment explanation
Indices: 7188--7240 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
7178 ATTCTACCGA
*
7188 TAGAAGTCTGAGTTGTATCGG
1 TAGAACTCTGAGTTGTATCGG
*
7209 TAGAACCCAT-AGTTGTATCGG
1 TAGAACTC-TGAGTTGTATCGG
*
7230 TAGAATTCTGA
1 TAGAACTCTGA
7241 AGCTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.32
Consensus pattern (21 bp):
TAGAACTCTGAGTTGTATCGG
Found at i:10157 original size:17 final size:17
Alignment explanation
Indices: 10137--10170 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
10127 GGTAACTCTT
10137 TAAGCTATCGAA-CTTAC
1 TAAGCTAT-GAAGCTTAC
10154 TAAGCTATGAAGCTTAC
1 TAAGCTATGAAGCTTAC
10171 CAAAAATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (17 bp):
TAAGCTATGAAGCTTAC
Found at i:15387 original size:497 final size:497
Alignment explanation
Indices: 14453--15446 Score: 1961
Period size: 497 Copynumber: 2.0 Consensus size: 497
14443 TTCTAAGGTC
*
14453 CTACTTTTCCTCTCAACAACTCCATTTTGTTGAGGGTTTTAGGTGCCAAAAATTTATGACTATCA
1 CTACTTTTCCTCTCAACAACTCCATTTTGTTGAGGGTTTTAGGTGCCAAAAATTTATGACTAACA
14518 CCATGTTCATTATAAAAATATCAAAGCCAAGGTTTTCAAATTCTTTTCCATGATCACTTCTTACA
66 CCATGTTCATTATAAAAATATCAAAGCCAAGGTTTTCAAATTCTTTTCCATGATCACTTCTTACA
14583 CTTGAAATTGAATATCCCACTTGGTTTTGAATCATTTTACAGAAAGTAATAAATTTTTCTAAAGC
131 CTTGAAATTGAATATCCCACTTGGTTTTGAATCATTTTACAGAAAGTAATAAATTTTTCTAAAGC
14648 TTCATTTTTTGAAAACAAAAAGAAAACCCATGTATATCTAGAATAGTCATCAACAATAACAAATA
196 TTCATTTTTTGAAAACAAAAAGAAAACCCATGTATATCTAGAATAGTCATCAACAATAACAAATA
14713 TATATTGTTTGCCTCCTAAACTCATAGTTCTAATGGATCCAAAAAGATCAATATGAATAAGTTGG
261 TATATTGTTTGCCTCCTAAACTCATAGTTCTAATGGATCCAAAAAGATCAATATGAATAAGTTGG
14778 ACTACTCTAGATGTAGAAACTATATCTTTAGATTTAAAAGATGCTCTACTATGTTTACCTTTAAC
326 ACTACTCTAGATGTAGAAACTATATCTTTAGATTTAAAAGATGCTCTACTATGTTTACCTTTAAC
14843 ACATGCATCACATATTTTATCAAAGTCAATAGAAAAGTTAGGCATGCCAACAATAAGTTCGTTTT
391 ACATGCATCACATATTTTATCAAAGTCAATAGAAAAGTTAGGCATGCCAACAATAAGTTCGTTTT
14908 TAATAAGCTTTGAAATAACACTCATGCTTGTATGTCCTAATA
456 TAATAAGCTTTGAAATAACACTCATGCTTGTATGTCCTAATA
14950 CTACTTTTCCTCTCAACAACTCCATTTTGTTGAGGGTTTTAGGTGCCAAAAATTTATGACTAACA
1 CTACTTTTCCTCTCAACAACTCCATTTTGTTGAGGGTTTTAGGTGCCAAAAATTTATGACTAACA
15015 CCATGTTCATTATAAAAATATCAAAGCCAAGGTTTTCAAATTCTTTTCCATGATCACTTCTTACA
66 CCATGTTCATTATAAAAATATCAAAGCCAAGGTTTTCAAATTCTTTTCCATGATCACTTCTTACA
15080 CTTGAAATTGAATATCCCACTTGGTTTTGAATCATTTTACAGAAAGTAATAAATTTTTCTAAAGC
131 CTTGAAATTGAATATCCCACTTGGTTTTGAATCATTTTACAGAAAGTAATAAATTTTTCTAAAGC
15145 TTCATTTTTTGAAAACAAAAAGAAAACCCATGTATATCTAGAATAGTCATCAACAATAACAAATA
196 TTCATTTTTTGAAAACAAAAAGAAAACCCATGTATATCTAGAATAGTCATCAACAATAACAAATA
*
15210 TATATTGTTTGCCTCCTAAACTCATAGTTCTAATGGATCCAAAAAGGTCAATATGAATAAGTTGG
261 TATATTGTTTGCCTCCTAAACTCATAGTTCTAATGGATCCAAAAAGATCAATATGAATAAGTTGG
15275 ACTACTCTAGATGTAGAAACTATATCTTTAGATTTAAAAGATGCTCTACTATGTTTACCTTTAAC
326 ACTACTCTAGATGTAGAAACTATATCTTTAGATTTAAAAGATGCTCTACTATGTTTACCTTTAAC
*
15340 ACATGCATCACATATTTTATCAAAGTCAATAGAAAATTTAGGCATGCCAACAATAAGTTCGTTTT
391 ACATGCATCACATATTTTATCAAAGTCAATAGAAAAGTTAGGCATGCCAACAATAAGTTCGTTTT
15405 TAATAAGCTTTGAAATAACACTCATGCTTGTATGTCCTAATA
456 TAATAAGCTTTGAAATAACACTCATGCTTGTATGTCCTAATA
15447 TTTACAACAT
Statistics
Matches: 494, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
497 494 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (497 bp):
CTACTTTTCCTCTCAACAACTCCATTTTGTTGAGGGTTTTAGGTGCCAAAAATTTATGACTAACA
CCATGTTCATTATAAAAATATCAAAGCCAAGGTTTTCAAATTCTTTTCCATGATCACTTCTTACA
CTTGAAATTGAATATCCCACTTGGTTTTGAATCATTTTACAGAAAGTAATAAATTTTTCTAAAGC
TTCATTTTTTGAAAACAAAAAGAAAACCCATGTATATCTAGAATAGTCATCAACAATAACAAATA
TATATTGTTTGCCTCCTAAACTCATAGTTCTAATGGATCCAAAAAGATCAATATGAATAAGTTGG
ACTACTCTAGATGTAGAAACTATATCTTTAGATTTAAAAGATGCTCTACTATGTTTACCTTTAAC
ACATGCATCACATATTTTATCAAAGTCAATAGAAAAGTTAGGCATGCCAACAATAAGTTCGTTTT
TAATAAGCTTTGAAATAACACTCATGCTTGTATGTCCTAATA
Found at i:21673 original size:17 final size:18
Alignment explanation
Indices: 21648--21712 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 18
21638 TACATATAAG
21648 AATGAAAATGCAACT-AC-
1 AATG-AAATGCAACTAACA
21665 AATGCAAATGC-ACTAACA
1 AATG-AAATGCAACTAACA
*
21683 AATGAAATGCAA-TGACA
1 AATGAAATGCAACTAACA
*
21700 AATAAAAATGCAA
1 AAT-GAAATGCAA
21713 TGACAGCTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 3 0.07
17 25 0.61
18 13 0.32
ACGTcount: A:0.55, C:0.15, G:0.12, T:0.17
Consensus pattern (18 bp):
AATGAAATGCAACTAACA
Found at i:27756 original size:43 final size:43
Alignment explanation
Indices: 27646--27995 Score: 373
Period size: 43 Copynumber: 8.2 Consensus size: 43
27636 TTATAACGAA
* * * *
27646 AAACGCTGCTATAGAACATGGTCTTTAGTGGCGC--TTCCCAAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCC-AC
* *** **
27688 AAACGCCGCTAAAGAACATGTTCTTTAGCGGTAATTTTTGCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * * *
27731 AAACGCCGCTAAATACCATGGTCTTTAGTGGCGCTTATCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * * ** *
27774 ATACGCCGCTGAAGAACATGGTCTTCAGCGGCACTTTTTGCAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* *
27817 AAACGCCGCTAAAGAACATGGTCTTCAGAGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * * *
27860 AAATGCCGCTAAAGAACATGGTCTTCAGCGACGCTTTTCCCAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
* * *
27903 AAATGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTTCCCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
*
27946 AAACGCCGCTAAA-AACCATGGTCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTAAAGAA-CATGGTCTTTAGCGGCGCTTTTCCCAC
27989 AAACGCC
1 AAACGCC
27996 ACTGACATTA
Statistics
Matches: 255, Mismatches: 50, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
42 29 0.11
43 223 0.87
44 3 0.01
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCAC
Done.