Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003542.1 Kokia drynarioides strain JFW-HI SEQ_116389, 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: 5579
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:642 original size:23 final size:23
Alignment explanation
Indices: 612--658 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
602 TTCGATTTGA
612 AGAAAAATTGCACCTAGTAAGTT
1 AGAAAAATTGCACCTAGTAAGTT
635 AGAAAAATTGCACCTAGTAAGTT
1 AGAAAAATTGCACCTAGTAAGTT
658 A
1 A
659 AGGCGCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.26
Consensus pattern (23 bp):
AGAAAAATTGCACCTAGTAAGTT
Found at i:1092 original size:29 final size:28
Alignment explanation
Indices: 1012--1111 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 28
1002 TTCGGGGTTT
1012 AAAATGGAATTTTTAGACATTCGACGGT-
1 AAAATGGAATTTTTAGACATTCGA-GGTG
* **
1040 AAAAGGGTAATTTTTAGAGTTTCGAGGTCG
1 AAAATGG-AATTTTTAGACATTCGAGGT-G
* *
1070 AAAATGGAGTTTTTGGACATTCG-GGTG
1 AAAATGGAATTTTTAGACATTCGAGGTG
1097 CAAAATGGTAATTTT
1 -AAAATGG-AATTTT
1112 GGAAGTTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
27 1 0.02
28 19 0.33
29 32 0.55
30 6 0.10
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTTAGACATTCGAGGTG
Found at i:1754 original size:58 final size:58
Alignment explanation
Indices: 1098--1759 Score: 715
Period size: 59 Copynumber: 11.3 Consensus size: 58
1088 ATTCGGGTGC
**
1098 AAAATGGTAA-TTTTGGAAGTTTTTGGGTCAAAAATG-GCATTTTTGGAAGTTCGGGGGTA
1 AAAATGG-AATTTTTGGAAG-TTTTGGGTCAAAAATGAG-ATTTTTGGAAGTTTAGGGGTA
* *
1157 AAAATGGAATTTTTGGAAGTTTCGGAGTCAAAAAT-AGAATTTTTGGAAG-TTCGGGGATA
1 AAAATGGAATTTTTGGAAGTTTTGG-GTCAAAAATGAG-ATTTTTGGAAGTTTAGGGG-TA
* * *
1216 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGTGATTTTTGGAAGTTCGAGGGGT-
1 AAAATGGAATTTTTGGAAGTTTTG-GGTCAAAAATGAGATTTTTGGAAGTT-TAGGGGTA
* * * *
1275 AAAATGGAATTTTTGGAAGTTTTAGGGTCAAAATTGGGTTTTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTT-GGGTCAAAAATGAG-ATTTTTGGAAGTTTAGGGGTA
*
1335 AAAATGGGATTTTTGGAAGTTTTGGGGTCAAAAATG-GAATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTT-GGGTCAAAAATGAG-ATTTTTGGAAGTTTAGGGGTA
* * * * * *
1394 AAAATTGATTTTTTGGAAGTTTCGAGGT-AAAAATGTGATTTTTGAAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTTG-GGTCAAAAATGAGATTTTTGGAAGTTTAG-GGGTA
* * * *
1452 AAAATTGAATTTTTGGAAGTTTTAGGGTC-AAAATGGGATTTTTTGGAAG-TTCGGGGTT
1 AAAATGGAATTTTTGGAAGTTTT-GGGTCAAAAATGAGA-TTTTTGGAAGTTTAGGGGTA
* *
1510 AAAATAGAAATTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTT-GGGTCAAAAATGAGATTTTTGGAAGTTTAGGGGTA
* * *
1569 AAATTTGAATTTTTGGAGGTTTTGAGGTCAAAAATGAGATTTTTGGAAGTTTA-GGGTA
1 AAAATGGAATTTTTGGAAGTTTTG-GGTCAAAAATGAGATTTTTGGAAGTTTAGGGGTA
* * * *
1627 AAAATGGAATTTTTAGAAGTTTCGGGGT-TAAAATGAGATTTTTAGAA-TTTCAGGGGTA
1 AAAATGGAATTTTTGGAAGTTT-TGGGTCAAAAATGAGATTTTTGGAAGTTT-AGGGGTA
*
1685 AAAATGGAATTTTTGGAAGTTTCT-GGTGAAAAATGAGAGTTTTT-GAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTT-TGGGTCAAAAATGAGA-TTTTTGGAAGTTTAGGGGTA
* *
1743 AAAACGAAATTTTTGGA
1 AAAATGGAATTTTTGGA
1760 CAGTGTAAGG
Statistics
Matches: 525, Mismatches: 52, Indels: 53
0.83 0.08 0.08
Matches are distributed among these distances:
56 3 0.01
57 24 0.05
58 195 0.37
59 249 0.47
60 50 0.10
61 4 0.01
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTTTGGGTCAAAAATGAGATTTTTGGAAGTTTAGGGGTA
Found at i:1756 original size:29 final size:29
Alignment explanation
Indices: 1098--1759 Score: 591
Period size: 29 Copynumber: 22.6 Consensus size: 29
1088 ATTCGGGTGC
**
1098 AAAATGGTAA-TTTTGGAAGTTTTTGGGTCA
1 AAAATGG-AATTTTTGGAAGTTTAGGGGT-A
* **
1128 AAAATGGCATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTA
* *
1157 AAAATGGAATTTTTGGAAGTTTCGGAGTCA
1 AAAATGGAATTTTTGGAAGTTTAGGGGT-A
* *
1187 AAAATAGAATTTTTGGAAG-TTCGGGGATA
1 AAAATGGAATTTTTGGAAGTTTAGGGG-TA
* *
1216 AAAATGGAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTAGGGGT-A
*
1246 AAAATGTG-ATTTTTGGAAGTTCGAGGGGT-
1 AAAATG-GAATTTTTGGAAGTT-TAGGGGTA
1275 AAAATGGAATTTTTGGAAGTTTTA-GGGTCA
1 AAAATGGAATTTTTGGAAG-TTTAGGGGT-A
* ** *
1305 AAATTGGGTTTTTTTGGAAGTTTGGGGGTA
1 AAAAT-GGAATTTTTGGAAGTTTAGGGGTA
* *
1335 AAAATGGGATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTAGGGGT-A
1365 AAAATGGAATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTA
* * * *
1394 AAAATTGATTTTTTGGAAGTTTCGAGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTA
* *
1423 AAAATGTG-ATTTTTGAAAG-TTCGAGGGTA
1 AAAATG-GAATTTTTGGAAGTTTAG-GGGTA
* *
1452 AAAATTGAATTTTTGGAAGTTTTA-GGGTC
1 AAAATGGAATTTTTGGAAG-TTTAGGGGTA
* * *
1481 AAAATGGGATTTTTTGGAAG-TTCGGGGTT
1 AAAAT-GGAATTTTTGGAAGTTTAGGGGTA
* * *
1510 AAAATAGAAATTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTAGGGGT-A
1540 AAAAT-GAGATTTTTGGAAGTTTAGGGGTA
1 AAAATGGA-ATTTTTGGAAGTTTAGGGGTA
* * * * *
1569 AAATTTGAATTTTTGGAGGTTTTGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTAGGGGT-A
1599 AAAAT-GAGATTTTTGGAAGTTTA-GGGTA
1 AAAATGGA-ATTTTTGGAAGTTTAGGGGTA
* * *
1627 AAAATGGAATTTTTAGAAGTTTCGGGGTT
1 AAAATGGAATTTTTGGAAGTTTAGGGGTA
*
1656 AAAAT-GAGATTTTTAGAA-TTTCAGGGGTA
1 AAAATGGA-ATTTTTGGAAGTTT-AGGGGTA
**
1685 AAAATGGAATTTTTGGAAGTTT-CTGGTGA
1 AAAATGGAATTTTTGGAAGTTTAGGGGT-A
*
1714 AAAATGAGAGTTTTT-GAAGTTTAGGGGTA
1 AAAATG-GAATTTTTGGAAGTTTAGGGGTA
* *
1743 AAAACGAAATTTTTGGA
1 AAAATGGAATTTTTGGA
1760 CAGTGTAAGG
Statistics
Matches: 524, Mismatches: 71, Indels: 75
0.78 0.11 0.11
Matches are distributed among these distances:
28 56 0.11
29 265 0.51
30 180 0.34
31 23 0.04
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTAGGGGTA
Done.