Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012214.1 Kokia drynarioides strain JFW-HI SEQ_127215, 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: 7882
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.34
Warning! 250 characters in sequence are not A, C, G, or T
Found at i:311 original size:110 final size:110
Alignment explanation
Indices: 110--343 Score: 281
Period size: 110 Copynumber: 2.1 Consensus size: 110
100 TCATCAGTTA
* * * * *
110 ATCTGACAAGTACTGGGCACATAAATCGTCAGTTTATCCGACTAGCGCTGGGCGCAAAAATCATT
1 ATCTGACTAGTGCTGGGCACACAAATCGTCAGTTTATCCGACTAACACTGGGCGCAAAAATCATT
* * *
175 GGTTTATCCAATTAGAGCTGGACTCACTTTTTATATCGTCAATTT
66 GGTATATCCAACTAGAGCTGGACTCACCTTTTATATCGTCAATTT
* * * * * *
220 ATCTGACTAGTGCTGGGCACACAATTTGTC-GATTTATCCGACTAACACTGGGCGTAATATTTAT
1 ATCTGACTAGTGCTGGGCACACAAATCGTCAG-TTTATCCGACTAACACTGGGCGCAAAAATCAT
* * **
284 TGGTATATCCAACTAGAGTTGGGCTCACCTTTTATATCGTCGGTTT
65 TGGTATATCCAACTAGAGCTGGACTCACCTTTTATATCGTCAATTT
*
330 ATCCGACTAGTGCT
1 ATCTGACTAGTGCT
344 AAGCGCAAAT
Statistics
Matches: 104, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
109 1 0.01
110 103 0.99
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (110 bp):
ATCTGACTAGTGCTGGGCACACAAATCGTCAGTTTATCCGACTAACACTGGGCGCAAAAATCATT
GGTATATCCAACTAGAGCTGGACTCACCTTTTATATCGTCAATTT
Found at i:837 original size:18 final size:19
Alignment explanation
Indices: 814--854 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
804 TATGTAAATC
*
814 TTCTTTTT-CTTTTTCTTT
1 TTCTTTTTCCTTTTCCTTT
832 TTCTTTTTCCTTTTCCTTT
1 TTCTTTTTCCTTTTCCTTT
851 TTCT
1 TTCT
855 CTCTTCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (19 bp):
TTCTTTTTCCTTTTCCTTT
Found at i:839 original size:13 final size:13
Alignment explanation
Indices: 814--866 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
804 TATGTAAATC
814 TTCTTTTTC-TTT
1 TTCTTTTTCTTTT
826 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
* *
839 TCCTTTTCCTTTT
1 TTCTTTTTCTTTT
852 TCTCTCTTCTTCTTT
1 T-TCT-TT-TTCTTT
867 AAACTTNNNN
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 9 0.27
13 15 0.45
14 2 0.06
15 2 0.06
16 5 0.15
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (13 bp):
TTCTTTTTCTTTT
Found at i:865 original size:6 final size:6
Alignment explanation
Indices: 814--854 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
804 TATGTAAATC
*
814 TTCTTT TTCTTT TTCTTT TTCTTT TTCCTTT TCCTTT TTCT
1 TTCTTT TTCTTT TTCTTT TTCTTT TT-CTTT TTCTTT TTCT
855 CTCTTCTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TTCTTT
Found at i:1563 original size:18 final size:19
Alignment explanation
Indices: 1540--1580 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1530 TATGTAAATC
*
1540 TTCTTTTT-CTTTTTCTTT
1 TTCTTTTTCCTTTTCCTTT
1558 TTCTTTTTCCTTTTCCTTT
1 TTCTTTTTCCTTTTCCTTT
1577 TTCT
1 TTCT
1581 CTCTTCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (19 bp):
TTCTTTTTCCTTTTCCTTT
Found at i:1565 original size:13 final size:13
Alignment explanation
Indices: 1540--1592 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
1530 TATGTAAATC
1540 TTCTTTTTC-TTT
1 TTCTTTTTCTTTT
1552 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
* *
1565 TCCTTTTCCTTTT
1 TTCTTTTTCTTTT
1578 TCTCTCTTCTTCTTT
1 T-TCT-TT-TTCTTT
1593 AAACTTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 9 0.27
13 15 0.45
14 2 0.06
15 2 0.06
16 5 0.15
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (13 bp):
TTCTTTTTCTTTT
Found at i:1591 original size:6 final size:6
Alignment explanation
Indices: 1540--1580 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
1530 TATGTAAATC
*
1540 TTCTTT TTCTTT TTCTTT TTCTTT TTCCTTT TCCTTT TTCT
1 TTCTTT TTCTTT TTCTTT TTCTTT TT-CTTT TTCTTT TTCT
1581 CTCTTCTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TTCTTT
Found at i:4885 original size:641 final size:591
Alignment explanation
Indices: 3663--4888 Score: 1660
Period size: 641 Copynumber: 2.0 Consensus size: 591
3653 TCAGGTATTC
3663 ATTTAGATCCACAAAAGGCTCGTCTCATCGCTTCTGGAGACATCGAAAGGCCACATGAAGGTCCG
1 ATTTAGATCCACAAAAGGCTCGTCTCATCGCTTCTGGAGACATCGAAAGGCCACATGAAGGTCCG
3728 CCACATCGAAGAAGCTTCAGTAAACGAGGTATATTAATATGTAACCATTATGGATTTATGTCAAT
66 CCACATCGAAGAAGCTTCAGTAAACGAGGTATATTAATATGTAACCATTATGGATTTATGTCAAT
3793 TTAAGAGATGGTTGAAAAACTAGTTTCATTTTTGCAGTACTTCACCGACTATCAGAAGCATTCTG
131 TTAAGAGATGGTTGAAAAACTAGTTTCATTTTTGCAGTACTTCACCGACTATCAGAAGCATTCTG
3858 GAAAGGCTTAAAACTTTGTGGTAAGAAGCAATCAACTTTGTTTGTATCAACACATTGGTATTGGA
196 GAAAGGCTTAAAACTTTGTGGTAAGAAGCAATCAACTTTGTTTGTATCAACACATTGGTATTGGA
3923 TTCAGACAAATAAATCTACTTCTTGCCTTCAGTCCCAGGCTTTACAAGCATATATGAGTTAAAGC
261 TTCAGACAAATAAATCTACTTCTTGCCTTCAGTCCCAGGCTTTACAAGCATATATGAGTTAAAGC
3988 TGACACATCTTCAAGCCAGGGAGCTTCTAACTTGCATTTGCCGAGAGGTACCAAATTTAGAAGAC
326 TGACACATCTTCAAGCCAGGGAGCTTCTAACTTGCATTTGCCGAGAGGTACCAAATTTAGAAGAC
*
4053 GAGATAAAACTAGAAACTATCGTGAAAAAAGCACTATTCGTAGCTGTTAAGCAAGGGATCATAGA
391 GAGATAAAACTAGAAACTATCGTGAAAAAAGCACTATTCGAAGCTGTTAAGCAAGGGATCATAGA
*
4118 GTTTGTCACAGAGATTATGAAGCATTATCCTGAAGTGGTATGGTTCTATGATAATAAAGACCGGA
456 GTTTGTCACAGAGATTATGAAGCATTATCCTGAAGTGGTATGGTTCCATGATAATAAAGACCGGA
* *
4183 ACATATTTTTTGTTGCAACAGCTGAACGACAAGAAAAGATTTTCAGCCTTATATATAAAATGGGT
521 ACATATTTTTTGTTGCAACAGCTCAACGACAAGAAAAGATTTTCAACCTTATATATAAAATGGGT
4248 GCTAAG
586 GCTAAG
********************* * * *
4254 ANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTAGATCCACAAA
1 A-----------------------------TTTAGATCCACAAAAGGCTCGTCT-CAT-CGC---
****
4319 AGGCTCGTCTCATCGCTTCTGGAGACATCGAAAGGCCACATGAAGGTCCGCCACATCGAAGAAGC
32 TTCT----------------GGAGACATCGAAAGGCCACATGAAGGTCCGCCACATCGAAGAAGC
4384 TTCAGTAAACGAGGTATATTAATATGTAACCATTATGGATTTATGTCAATTTAAGAGATGGTTGA
81 TTCAGTAAACGAGGTATATTAATATGTAACCATTATGGATTTATGTCAATTTAAGAGATGGTTGA
4449 AAAACTAGTTTCATTTTTGCAGTACTTCACCGACTATCAGAAGCATTCTGGAAAGGCTTAAAACT
146 AAAACTAGTTTCATTTTTGCAGTACTTCACCGACTATCAGAAGCATTCTGGAAAGGCTTAAAACT
4514 TTGTGGTAAGAAGCAATCAACTTTGTTTGTATCAACACATTGGTATTGGATTCAGACAAATAAAT
211 TTGTGGTAAGAAGCAATCAACTTTGTTTGTATCAACACATTGGTATTGGATTCAGACAAATAAAT
4579 CTACTTCTTGCCTTCAGTCCCAGGCTTTACAAGCATATATGAGTTAAAGCTGACACATCTTCAAG
276 CTACTTCTTGCCTTCAGTCCCAGGCTTTACAAGCATATATGAGTTAAAGCTGACACATCTTCAAG
* * *
4644 CCAGGGAGCTTCTAACTTGCATTTGCCGAGAGGTACCAAATTTAGAAGATGAGATACAACTAGAC
341 CCAGGGAGCTTCTAACTTGCATTTGCCGAGAGGTACCAAATTTAGAAGACGAGATAAAACTAGAA
*
4709 ACTATCGTGAAAAAAGCACTATTCGAAGCTGTTAAGCAAGGGATCATGGAGTTTGTCACAGAGAT
406 ACTATCGTGAAAAAAGCACTATTCGAAGCTGTTAAGCAAGGGATCATAGAGTTTGTCACAGAGAT
*
4774 TATGAAGCATTATCCTGAAGTGGTATGGTTCCATGATGATAAAGACCGGAACATATTTTTTGTTG
471 TATGAAGCATTATCCTGAAGTGGTATGGTTCCATGATAATAAAGACCGGAACATATTTTTTGTTG
*
4839 CAACAGCTCAACGACAAGAAAAGATTTTCAACCTTATATGTAAAATGGGT
536 CAACAGCTCAACGACAAGAAAAGATTTTCAACCTTATATATAAAATGGGT
4889 TATAAGAAAA
Statistics
Matches: 547, Mismatches: 38, Indels: 50
0.86 0.06 0.08
Matches are distributed among these distances:
591 1 0.00
620 2 0.00
621 2 0.00
622 2 0.00
641 540 0.99
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.27
Consensus pattern (591 bp):
ATTTAGATCCACAAAAGGCTCGTCTCATCGCTTCTGGAGACATCGAAAGGCCACATGAAGGTCCG
CCACATCGAAGAAGCTTCAGTAAACGAGGTATATTAATATGTAACCATTATGGATTTATGTCAAT
TTAAGAGATGGTTGAAAAACTAGTTTCATTTTTGCAGTACTTCACCGACTATCAGAAGCATTCTG
GAAAGGCTTAAAACTTTGTGGTAAGAAGCAATCAACTTTGTTTGTATCAACACATTGGTATTGGA
TTCAGACAAATAAATCTACTTCTTGCCTTCAGTCCCAGGCTTTACAAGCATATATGAGTTAAAGC
TGACACATCTTCAAGCCAGGGAGCTTCTAACTTGCATTTGCCGAGAGGTACCAAATTTAGAAGAC
GAGATAAAACTAGAAACTATCGTGAAAAAAGCACTATTCGAAGCTGTTAAGCAAGGGATCATAGA
GTTTGTCACAGAGATTATGAAGCATTATCCTGAAGTGGTATGGTTCCATGATAATAAAGACCGGA
ACATATTTTTTGTTGCAACAGCTCAACGACAAGAAAAGATTTTCAACCTTATATATAAAATGGGT
GCTAAG
Done.