Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011299.1 Kokia drynarioides strain JFW-HI SEQ_126279, 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: 41167
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:733 original size:16 final size:17
Alignment explanation
Indices: 702--735 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
692 TCCAACATTT
*
702 TTATTTTATGTTTTTTA
1 TTATTTTATATTTTTTA
719 TTATTTT-TATTTTTTA
1 TTATTTTATATTTTTTA
735 T
1 T
736 CCTTGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (17 bp):
TTATTTTATATTTTTTA
Found at i:10481 original size:24 final size:23
Alignment explanation
Indices: 10447--10499 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
10437 TTTAAATCTT
10447 TTAT-TTA-TGTTACTAATTATA
1 TTATATTAGTGTTACTAATTATA
* * *
10468 TTATTATTAGTGTTATTGATTTTA
1 TTA-TATTAGTGTTACTAATTATA
10492 TTATATTA
1 TTATATTA
10500 TTCATGTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.12
22 1 0.04
23 8 0.31
24 14 0.54
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (23 bp):
TTATATTAGTGTTACTAATTATA
Found at i:14745 original size:24 final size:24
Alignment explanation
Indices: 14688--14750 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
14678 GATTAAGAAG
* *
14688 AAACAACTT-TTGTTATCTCTCAA
1 AAACTACTTCTTGTTTTCTCTCAA
**
14711 AAACTTGTTCTTGTTTTCTCTCAA
1 AAACTACTTCTTGTTTTCTCTCAA
*
14735 ATACTACTTC-TGTTTT
1 AAACTACTTCTTGTTTT
14751 TTGGTGATAG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
23 12 0.38
24 20 0.62
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.48
Consensus pattern (24 bp):
AAACTACTTCTTGTTTTCTCTCAA
Found at i:18668 original size:32 final size:31
Alignment explanation
Indices: 18607--18669 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
18597 TACATAATAA
* *
18607 AAAATAATATATACATAAAATACAATAAAAT
1 AAAATAATAAATAAATAAAATACAATAAAAT
* *
18638 AAAATAAATAAATAAATAAATTACATTAAAAT
1 AAAAT-AATAAATAAATAAAATACAATAAAAT
18670 CGGGTCAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (31 bp):
AAAATAATAAATAAATAAAATACAATAAAAT
Found at i:18737 original size:30 final size:30
Alignment explanation
Indices: 18703--18797 Score: 147
Period size: 30 Copynumber: 3.2 Consensus size: 30
18693 AGCTTCAAGA
18703 GTCAAATCAAAATTTTTGGAAAATTTGGGG
1 GTCAAATCAAAATTTTTGGAAAATTTGGGG
* *
18733 GTCAAATCAAAATTTTTGGAAAGTTTAGGG
1 GTCAAATCAAAATTTTTGGAAAATTTGGGG
*
18763 GTCAAATTC-AAATTTTAGGAAAATTTGGGG
1 GTCAAA-TCAAAATTTTTGGAAAATTTGGGG
18793 GTCAA
1 GTCAA
18798 GTTATAATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
30 57 0.97
31 2 0.03
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (30 bp):
GTCAAATCAAAATTTTTGGAAAATTTGGGG
Found at i:18747 original size:60 final size:60
Alignment explanation
Indices: 18683--18797 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
18673 GTCAAATTTG
*
18683 AATTTTTGG-AAGCTTCAAGAGTCAAA-TCAAAATTTTTGGAAAATTTGGGGGTCAAATCAA
1 AATTTTTGGAAAG-TTCAAGAGTCAAATTC-AAATTTTAGGAAAATTTGGGGGTCAAATCAA
* * *
18743 AATTTTTGGAAAGTTTAGGGGTCAAATTCAAATTTTAGGAAAATTTGGGGGTCAA
1 AATTTTTGGAAAGTTCAAGAGTCAAATTCAAATTTTAGGAAAATTTGGGGGTCAA
18798 GTTATAATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 44 0.90
61 5 0.10
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.33
Consensus pattern (60 bp):
AATTTTTGGAAAGTTCAAGAGTCAAATTCAAATTTTAGGAAAATTTGGGGGTCAAATCAA
Found at i:18807 original size:30 final size:29
Alignment explanation
Indices: 18703--18809 Score: 115
Period size: 30 Copynumber: 3.6 Consensus size: 29
18693 AGCTTCAAGA
* *
18703 GTCAAATCAAAATTTTTGGAAAATTTGGGG
1 GTCAAAT-TAAATTTTAGGAAAATTTGGGG
* * * *
18733 GTCAAATCAAAATTTTTGGAAAGTTTAGGG
1 GTCAAAT-TAAATTTTAGGAAAATTTGGGG
18763 GTCAAATTCAAATTTTAGGAAAATTTGGGG
1 GTCAAATT-AAATTTTAGGAAAATTTGGGG
*
18793 GTCAAGTTATAATTTTA
1 GTCAAATTA-AATTTTA
18810 AAATAAAGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
29 1 0.01
30 67 0.99
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (29 bp):
GTCAAATTAAATTTTAGGAAAATTTGGGG
Found at i:26695 original size:17 final size:18
Alignment explanation
Indices: 26674--26721 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
26664 TGTTCATATA
26674 ATTTTATTCATTA--TTT
1 ATTTTATTCATTACTTTT
*
26690 ATTTTTATTTATTACTTTT
1 A-TTTTATTCATTACTTTT
*
26709 ATTTCATTCATTA
1 ATTTTATTCATTA
26722 AATTTGCTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.04
17 11 0.42
18 10 0.38
19 4 0.15
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTATTCATTACTTTT
Found at i:26829 original size:21 final size:22
Alignment explanation
Indices: 26805--26849 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
26795 TATCTTATGA
* *
26805 TATTTAATTGTATTG-ATATTT
1 TATTTAATTGCATGGCATATTT
*
26826 TATTTATTTGCATGGCATATTT
1 TATTTAATTGCATGGCATATTT
26848 TA
1 TA
26850 CCTTGAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.27, C:0.04, G:0.11, T:0.58
Consensus pattern (22 bp):
TATTTAATTGCATGGCATATTT
Found at i:26947 original size:15 final size:16
Alignment explanation
Indices: 26915--26951 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
26905 TCCCTAATCA
*
26915 ATTAATATCTATTGCT
1 ATTATTATCTATTGCT
26931 ATTATTATCTA-TGCT
1 ATTATTATCTATTGCT
26946 ATTATT
1 ATTATT
26952 TTATTATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.54
Consensus pattern (16 bp):
ATTATTATCTATTGCT
Found at i:33466 original size:17 final size:18
Alignment explanation
Indices: 33444--33490 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
33434 GCAAATTATG
33444 ATGTAGTGACAATAA-AA
1 ATGTAGTGACAATAAGAA
*
33461 ATGTAGGGACAA-AAGAA
1 ATGTAGTGACAATAAGAA
33478 ATGT-GATGACAAT
1 ATGTAG-TGACAAT
33491 GATATTACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.49, C:0.06, G:0.23, T:0.21
Consensus pattern (18 bp):
ATGTAGTGACAATAAGAA
Found at i:35815 original size:15 final size:15
Alignment explanation
Indices: 35795--35828 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35785 ACCATTAAGC
35795 CCAAACCAAAGTGAA
1 CCAAACCAAAGTGAA
* *
35810 CCAAACCCATGTGAA
1 CCAAACCAAAGTGAA
35825 CCAA
1 CCAA
35829 GTCCAAACCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.32, G:0.12, T:0.09
Consensus pattern (15 bp):
CCAAACCAAAGTGAA
Found at i:35834 original size:21 final size:21
Alignment explanation
Indices: 35809--35860 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
35799 ACCAAAGTGA
35809 ACCAAACCCATGTGAACCAAG
1 ACCAAACCCATGTGAACCAAG
* *
35830 TCCAAACCCATTTGAACCAAG
1 ACCAAACCCATGTGAACCAAG
35851 ACCAAACCCA
1 ACCAAACCCA
35861 AACCAAGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.42, C:0.37, G:0.10, T:0.12
Consensus pattern (21 bp):
ACCAAACCCATGTGAACCAAG
Found at i:36983 original size:3 final size:3
Alignment explanation
Indices: 36975--37014 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
36965 TTACATCATT
*
36975 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTG TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
37015 TTGGTTTTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:37690 original size:90 final size:90
Alignment explanation
Indices: 37537--37719 Score: 330
Period size: 90 Copynumber: 2.0 Consensus size: 90
37527 AAGAAAAGAG
37537 AGAATAGAAGAAATAAGTTTGAATAGCAAAAGAATTAAGTTTATTTGGGTGGGACAAGAGAATAT
1 AGAATAGAAGAAATAAGTTTGAATAGCAAAAGAATTAAGTTTATTTGGGTGGGACAAGAGAATAT
37602 ATAAAGGTTCATATTGACATTAAAA
66 ATAAAGGTTCATATTGACATTAAAA
* * *
37627 AGAATAGAAGAAATAAGTTTGAATGGCAGAAGAATTAAGTTTATTTGGGTGGGACGAGAGAATAT
1 AGAATAGAAGAAATAAGTTTGAATAGCAAAAGAATTAAGTTTATTTGGGTGGGACAAGAGAATAT
*
37692 ATAGAGGTTCATATTGACATTAAAA
66 ATAAAGGTTCATATTGACATTAAAA
37717 AGA
1 AGA
37720 TTAACACTAC
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.45, C:0.04, G:0.23, T:0.27
Consensus pattern (90 bp):
AGAATAGAAGAAATAAGTTTGAATAGCAAAAGAATTAAGTTTATTTGGGTGGGACAAGAGAATAT
ATAAAGGTTCATATTGACATTAAAA
Found at i:38119 original size:28 final size:27
Alignment explanation
Indices: 38071--38125 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
38061 CACTTTCATT
* *
38071 TTTCCTTCTCGTCCCTTCCCCTATTTTC
1 TTTCCTTCTCGT-CCATCCCCCATTTTC
38099 TTTCCTTCTTC-TCCATCCCCCATTTTC
1 TTTCCTTC-TCGTCCATCCCCCATTTTC
38126 ACTTTTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.54
28 9 0.38
29 2 0.08
ACGTcount: A:0.05, C:0.44, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTCCTTCTCGTCCATCCCCCATTTTC
Done.