Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001185.1 Kokia drynarioides strain JFW-HI SEQ_112520, 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: 2967
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Found at i:2559 original size:30 final size:28
Alignment explanation
Indices: 2453--2737 Score: 122
Period size: 29 Copynumber: 9.8 Consensus size: 28
2443 AATAAAACAA
* * *
2453 TCGGAGTCAAAAATGAGATTTTTGGATACT
1 TCGGGGTCAAAAATG-GAATTTTGGA-AAT
* ** *
2483 T-GGGGGC-AAAATGGTAATTTTGGTCAC
1 TCGGGGTCAAAAATGG-AATTTTGGAAAT
* * *
2510 TCAGGG-CAAAATTGTAATTTTGGGAAAGT
1 TCGGGGTCAAAAATGGAATTTT-GGAAA-T
* * *
2539 TTGGGGTCAAAAATGGAATTTTTAGATAT
1 TCGGGGTCAAAAATGGAA-TTTTGGAAAT
*
2568 TCGAGGGT--AAAATGATAATTTTTGGAAAGT
1 TCG-GGGTCAAAAATG-GAA-TTTTGGAAA-T
* * *
2598 TCAGGGTCAAAAATGGAATTTTATGACAT
1 TCGGGGTCAAAAATGGAATTTT-GGAAAT
* *
2627 CCGGGAGT--AAAAT-GATTATTTTGGAAAAA
1 TCGGG-GTCAAAAATGGA--ATTTTGG-AAAT
*
2656 TCGAGGTCAAAAATGGAATTTTTGGAAAT
1 TCGGGGTCAAAAATGGAA-TTTTGGAAAT
*
2685 TCGGGGGT-AAAAATGGTAATTTTAGAAAAAT
1 TC-GGGGTCAAAAATGG-AATTTT-G-GAAAT
*
2716 T-GAGGTCAAAAATGGAATTTTG
1 TCGGGGTCAAAAATGGAATTTTG
2738 AAAAGTTTGG
Statistics
Matches: 191, Mismatches: 38, Indels: 54
0.67 0.13 0.19
Matches are distributed among these distances:
27 11 0.06
28 39 0.20
29 71 0.37
30 53 0.28
31 17 0.09
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.32
Consensus pattern (28 bp):
TCGGGGTCAAAAATGGAATTTTGGAAAT
Found at i:2603 original size:29 final size:29
Alignment explanation
Indices: 2510--2619 Score: 91
Period size: 30 Copynumber: 3.7 Consensus size: 29
2500 TTTTGGTCAC
*
2510 TCAGGG-CAAAATTGTAATTTTGGGAAAGT
1 TCAGGGTCAAAA-TGTAATTTTTGGAAAGT
** * * *
2539 TTGGGGTCAAAAATGGAATTTTTAGATA-T
1 TCAGGGTC-AAAATGTAATTTTTGGAAAGT
2568 TCGAGGGT-AAAATGATAATTTTTGGAAAGT
1 TC-AGGGTCAAAATG-TAATTTTTGGAAAGT
*
2598 TCAGGGTCAAAAATGGAATTTT
1 TCAGGGTC-AAAATGTAATTTT
2620 ATGACATCCG
Statistics
Matches: 62, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
28 6 0.10
29 21 0.34
30 25 0.40
31 10 0.16
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.34
Consensus pattern (29 bp):
TCAGGGTCAAAATGTAATTTTTGGAAAGT
Found at i:2664 original size:58 final size:57
Alignment explanation
Indices: 2543--2824 Score: 227
Period size: 59 Copynumber: 4.8 Consensus size: 57
2533 GAAAGTTTGG
* **
2543 GGTCAAAAATGGAATTTTTAGATATTCGAGGGTAAAATGATAATTTTTGGAAAGTTC-A
1 GGTCAAAAATGGAATTTTTAGAAATTCG-GGGTAAAATGATAA-TTTTGGAAAAATCGA
* * *
2601 GGGTCAAAAATGGAA-TTTTATGACATCCGGGAGTAAAATGATTATTTTGGAAAAATCGA
1 -GGTCAAAAATGGAATTTTTA-GAAATTCGGG-GTAAAATGATAATTTTGGAAAAATCGA
* * * *
2660 GGTCAAAAATGGAATTTTTGGAAATTCGGGGGTAAAAATGGTAATTTTAGAAAAATTGA
1 GGTCAAAAATGGAATTTTTAGAAATTC-GGGGT-AAAATGATAATTTTGGAAAAATCGA
* * *
2719 GGTCAAAAATGGAATTTTGA-AAAGTTTGGAGGTAAAAAT-ATATTTTTTTGG-AAAATCGA
1 GGTCAAAAATGGAATTTTTAGAAA-TTCGG-GGT-AAAATGATA--ATTTTGGAAAAATCGA
* * * *
2778 GGTTAAAAAT-AAAATTTTAGAAAGTTTAGGGGTAAAAAT-ATAATTTT
1 GGTCAAAAATGGAATTTTTAGAAA--TTCGGGGT-AAAATGATAATTTT
2825 TTTTAATAAA
Statistics
Matches: 185, Mismatches: 26, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
57 4 0.02
58 52 0.28
59 120 0.65
60 9 0.05
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (57 bp):
GGTCAAAAATGGAATTTTTAGAAATTCGGGGTAAAATGATAATTTTGGAAAAATCGA
Found at i:2755 original size:29 final size:29
Alignment explanation
Indices: 2658--2757 Score: 107
Period size: 29 Copynumber: 3.4 Consensus size: 29
2648 TGGAAAAATC
* *
2658 GAGGTCAAAAATGGAATTTTTGGAAATTCG
1 GAGGTCAAAAATGGAA-TTTTGAAAATTTG
* *
2688 GGGGT-AAAAATGGTAATTTTAGAAAAATT-
1 GAGGTCAAAAATGG-AATTTT-GAAAATTTG
2717 GAGGTCAAAAATGGAATTTTGAAAAGTTTG
1 GAGGTCAAAAATGGAATTTTGAAAA-TTTG
2747 GAGGT-AAAAAT
1 GAGGTCAAAAAT
2758 ATATTTTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
28 5 0.08
29 30 0.51
30 24 0.41
ACGTcount: A:0.42, C:0.03, G:0.26, T:0.29
Consensus pattern (29 bp):
GAGGTCAAAAATGGAATTTTGAAAATTTG
Found at i:2795 original size:29 final size:29
Alignment explanation
Indices: 2645--2795 Score: 85
Period size: 30 Copynumber: 5.1 Consensus size: 29
2635 AAAATGATTA
* *
2645 TTTTGGAAAAATCGAGGTCAAAAATGGAAT
1 TTTTGG-AAAATCGAGGTTAAAAATGAAAT
* * * *
2675 TTTTGGAAATTCGGGGGTAAAAATGGTAAT
1 TTTTGGAAAATCGAGGTTAAAAAT-GAAAT
* * * * *
2705 TTTAGAAAAATTGAGGTCAAAAATGGAA-
1 TTTTGGAAAATCGAGGTTAAAAATGAAAT
* *
2733 TTTT-GAAAAGTTTGGAGG-TAAAAAT-ATATTT
1 TTTTGGAAAA---TCGAGGTTAAAAATGA-A-AT
*
2764 TTTTGGAAAATCGAGGTTAAAAATAAAAT
1 TTTTGGAAAATCGAGGTTAAAAATGAAAT
2793 TTT
1 TTT
2796 AGAAAGTTTA
Statistics
Matches: 90, Mismatches: 21, Indels: 21
0.68 0.16 0.16
Matches are distributed among these distances:
27 4 0.04
28 3 0.03
29 33 0.37
30 40 0.44
31 5 0.06
32 5 0.06
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (29 bp):
TTTTGGAAAATCGAGGTTAAAAATGAAAT
Done.