Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003442.1 Kokia drynarioides strain JFW-HI SEQ_116227, 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: 40605
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:16783 original size:21 final size:21
Alignment explanation
Indices: 16759--16803 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
16749 AGAAAAGTAT
* *
16759 AAAATTTTATAAAATCGT-AAG
1 AAAATTATAGAAAAT-GTAAAG
16780 AAAATTATAGAAAATGTAAAG
1 AAAATTATAGAAAATGTAAAG
16801 AAA
1 AAA
16804 TATAAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.60, C:0.02, G:0.11, T:0.27
Consensus pattern (21 bp):
AAAATTATAGAAAATGTAAAG
Found at i:16804 original size:20 final size:20
Alignment explanation
Indices: 16741--16804 Score: 55
Period size: 21 Copynumber: 3.3 Consensus size: 20
16731 ATATATATAT
*
16741 AGAAA-TATAGAAAA-GTAT
1 AGAAATTATAGAAAATGTAA
* *
16759 A-AAATTTTATAAAATCGT-A
1 AGAAATTATAGAAAAT-GTAA
16778 AGAAAATTATAGAAAATGTAA
1 AG-AAATTATAGAAAATGTAA
16799 AGAAAT
1 AGAAAT
16805 ATAAAATTCG
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
17 3 0.09
18 8 0.23
19 1 0.03
20 8 0.23
21 15 0.43
ACGTcount: A:0.59, C:0.02, G:0.12, T:0.27
Consensus pattern (20 bp):
AGAAATTATAGAAAATGTAA
Found at i:16817 original size:19 final size:20
Alignment explanation
Indices: 16765--16818 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 20
16755 GTATAAAATT
16765 TTATAAAATCGT-AAGAAAA
1 TTATAAAATCGTAAAGAAAA
16784 TTATAGAAAAT-GTAAAG-AAA
1 TTAT--AAAATCGTAAAGAAAA
16804 -TATAAAATTCGTAAA
1 TTATAAAA-TCGTAAA
16819 AAGTTATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
17 4 0.13
18 1 0.03
19 12 0.40
20 5 0.17
21 8 0.27
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.28
Consensus pattern (20 bp):
TTATAAAATCGTAAAGAAAA
Found at i:16821 original size:21 final size:23
Alignment explanation
Indices: 16797--16851 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
16787 TAGAAAATGT
16797 AAAGAAATATAAAA-TTCGTA-A
1 AAAGAAATATAAAATTTCGTACA
** *
16818 AAAGTTATAAAAAATTTCGTACCA
1 AAAGAAATATAAAATTTCGTA-CA
16842 AAAGAAATAT
1 AAAGAAATAT
16852 TTTATAATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
21 11 0.44
22 6 0.24
24 8 0.32
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.25
Consensus pattern (23 bp):
AAAGAAATATAAAATTTCGTACA
Found at i:16826 original size:19 final size:17
Alignment explanation
Indices: 16765--16829 Score: 51
Period size: 19 Copynumber: 3.5 Consensus size: 17
16755 GTATAAAATT
16765 TTATAAAATCGTAAGAAAA
1 TTATAAAATCGT-A-AAAA
16784 TTATAGAAAAT-GTAAAGAA
1 TTAT--AAAATCGTAAA-AA
*
16803 ATATAAAATTCGTAAAAA
1 TTATAAAA-TCGTAAAAA
16821 GTTATAAAA
1 -TTATAAAA
16830 AATTTCGTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
17 4 0.11
18 5 0.13
19 22 0.58
20 2 0.05
21 5 0.13
ACGTcount: A:0.58, C:0.03, G:0.11, T:0.28
Consensus pattern (17 bp):
TTATAAAATCGTAAAAA
Found at i:17494 original size:15 final size:15
Alignment explanation
Indices: 17476--17517 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
17466 CATATAGAAA
*
17476 TTTATGAAGGAAAAT
1 TTTACGAAGGAAAAT
17491 TTTAACGAAGGAAAAT
1 TTT-ACGAAGGAAAAT
17507 TTTAACGAAGG
1 TTT-ACGAAGG
17518 CATGAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 3 0.12
16 22 0.88
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (15 bp):
TTTACGAAGGAAAAT
Found at i:17502 original size:16 final size:16
Alignment explanation
Indices: 17481--17517 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
17471 AGAAATTTAT
17481 GAAGGAAAATTTTAAC
1 GAAGGAAAATTTTAAC
17497 GAAGGAAAATTTTAAC
1 GAAGGAAAATTTTAAC
17513 GAAGG
1 GAAGG
17518 CATGAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.24, T:0.22
Consensus pattern (16 bp):
GAAGGAAAATTTTAAC
Found at i:30472 original size:17 final size:17
Alignment explanation
Indices: 30452--30488 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
30442 AAGTAGTTAC
*
30452 AAGAATATGAAAGATTA
1 AAGAAGATGAAAGATTA
*
30469 AAGAAGATGAAAGGTTA
1 AAGAAGATGAAAGATTA
30486 AAG
1 AAG
30489 GTCAAGGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.19
Consensus pattern (17 bp):
AAGAAGATGAAAGATTA
Found at i:30488 original size:24 final size:24
Alignment explanation
Indices: 30461--30508 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
30451 CAAGAATATG
*
30461 AAAGATTAAAGAAGATGAAAGGTT
1 AAAGATCAAAGAAGATGAAAGGTT
* * *
30485 AAAGGTCAAGGGAGATGAAAGGTT
1 AAAGATCAAAGAAGATGAAAGGTT
30509 GAATATCTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.31, T:0.19
Consensus pattern (24 bp):
AAAGATCAAAGAAGATGAAAGGTT
Found at i:31304 original size:37 final size:35
Alignment explanation
Indices: 31263--31351 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
31253 ATTTTATATT
* *
31263 TTTTATAATTTGATCCTTGAAATCTAAATTTTTACTA
1 TTTTATAATTTAATCCTTCAAA--TAAATTTTTACTA
* * **
31300 TTTTATAATTTAATTCTTCAAATACATTTTTTTTA
1 TTTTATAATTTAATCCTTCAAATAAATTTTTACTA
*
31335 TTTTATAATTCAATCCT
1 TTTTATAATTTAATCCT
31352 AAATCTTGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 25 0.57
37 19 0.43
ACGTcount: A:0.31, C:0.11, G:0.02, T:0.55
Consensus pattern (35 bp):
TTTTATAATTTAATCCTTCAAATAAATTTTTACTA
Found at i:32647 original size:12 final size:12
Alignment explanation
Indices: 32630--32662 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
32620 CAATGCTACA
32630 TGTACATATAGT
1 TGTACATATAGT
32642 TGTACATATAGT
1 TGTACATATAGT
*
32654 TATACATAT
1 TGTACATAT
32663 TTCTAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (12 bp):
TGTACATATAGT
Done.