Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004611.1 Kokia drynarioides strain JFW-HI SEQ_118119, 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: 2877
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Found at i:979 original size:30 final size:29
Alignment explanation
Indices: 942--1281 Score: 152
Period size: 29 Copynumber: 11.6 Consensus size: 29
932 GACATCCGGT
942 GTAAAAATGTAATTTTTTGAAAGTTTGGG
1 GTAAAAATGTAATTTTTTGAAAGTTTGGG
* * *
971 GTTAAAAATGTAA-TTTTTGGAATTTTAGG
1 G-TAAAAATGTAATTTTTTGAAAGTTTGGG
*
1000 GT-AAAATGGTAATTTTTGGAAAGTTTGGG
1 GTAAAAAT-GTAATTTTTTGAAAGTTTGGG
* *
1029 GTCAAAAAAAATGGAA-TTTTTGAAAATTTGGG
1 GT----AAAAATGTAATTTTTTGAAAGTTTGGG
* * **
1061 GT-AAAATGGCAA-TTTTTGGAAGTGAGGGG
1 GTAAAAAT-GTAATTTTTTGAAAGT-TTGGG
* ** * ***
1090 GCAAAAATG-GGTTTTTGGAAAGTTCAAG
1 GTAAAAATGTAATTTTTTGAAAGTTTGGG
* *
1118 GTAAAAAATG--ATATTTTTGGAAGTTCGGGG
1 GT-AAAAATGTAAT-TTTTTGAAAGTT-TGGG
* *
1148 GT-AAAATGGTAATTTTTGGAAAGTTTAGG
1 GTAAAAAT-GTAATTTTTTGAAAGTTTGGG
*
1177 GTCAAAAA--TAATATTTTTG-AAGTTCGAGG
1 GT-AAAAATGTAAT-TTTTTGAAAGTTTG-GG
* * *
1206 GTGAAAATGCAA-TTTTTGAAAAGGTTGAGG
1 GTAAAAATGTAATTTTTTG-AAAGTTTG-GG
*
1236 GT-AAAATGTAATTTTTGTG-AAGTTCGAGG
1 GTAAAAATGTAATTTTT-TGAAAGTTTG-GG
* *
1265 GTCAAAATATAATTTTT
1 GTAAAAATGTAATTTTT
1282 GGGAAGTTCG
Statistics
Matches: 236, Mismatches: 46, Indels: 57
0.70 0.14 0.17
Matches are distributed among these distances:
27 10 0.04
28 44 0.19
29 92 0.39
30 58 0.25
31 8 0.03
32 16 0.07
33 3 0.01
34 5 0.02
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (29 bp):
GTAAAAATGTAATTTTTTGAAAGTTTGGG
Found at i:1069 original size:61 final size:58
Alignment explanation
Indices: 945--1252 Score: 190
Period size: 58 Copynumber: 5.3 Consensus size: 58
935 ATCCGGTGTA
* * * * *
945 AAAAT-GTAATTTTTTGAAAGTTTGGGGTTAAAAATGTAATTTTTGGAATTTTAGGGT
1 AAAATGGTAATTTTTGGAAAGTTTGGGGTAAAAAATGGAATTTTTGAAAATTTAGGGT
*
1002 AAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAAAAATGGAATTTTTGAAAATTTGGGGT
1 AAAATGGTAATTTTTGGAAAGTTTGGGGT---AAAAAATGGAATTTTTGAAAATTTAGGGT
* ** ** * * * *
1063 AAAATGGCAATTTTTGG-AAGTGAGGGGGCAAAAATGG-GTTTTTGGAAAGTTCAAGGT
1 AAAATGGTAATTTTTGGAAAGTTTGGGGTAAAAAATGGAATTTTT-GAAAATTTAGGGT
* * *
1120 AAAAAATGAT-ATTTTTGG-AAGTTCGGGGGT--AAAATGGTAATTTTTGGAAAGTTTAGGGT
1 --AAAATGGTAATTTTTGGAAAGTT-TGGGGTAAAAAATGG-AATTTTT-GAAAATTTAGGGT
* * * * * *
1179 CAAAA--ATAATATTTTTG-AAGTTCGAGGGT-GAAAATGCAATTTTTGAAAAGGTTGAGGGT
1 -AAAATGGTAAT-TTTTGGAAAGTTTG-GGGTAAAAAATGGAATTTTTGAAAA--TTTAGGGT
1238 AAAAT-GTAATTTTTG
1 AAAATGGTAATTTTTG
1253 TGAAGTTCGA
Statistics
Matches: 202, Mismatches: 32, Indels: 33
0.76 0.12 0.12
Matches are distributed among these distances:
56 7 0.03
57 36 0.18
58 67 0.33
59 44 0.22
60 8 0.04
61 40 0.20
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAAGTTTGGGGTAAAAAATGGAATTTTTGAAAATTTAGGGT
Found at i:1167 original size:59 final size:59
Alignment explanation
Indices: 1101--1311 Score: 209
Period size: 59 Copynumber: 3.6 Consensus size: 59
1091 CAAAAATGGG
*
1101 TTTTTGGAAAGTTCAAGGTAAAAAATGATATTTTTGGAAGTTCGGGGGT-AAAATGGTAA
1 TTTTTGGAAAGTTCAAGGTAAAAAATGATATTTTTGGAAGTTCGAGGGTCAAAAT-GTAA
* * * * * *
1160 TTTTTGGAAAGTTTAGGGTCAAAAATAATATTTTT-GAAGTTCGAGGGTGAAAATGCAA
1 TTTTTGGAAAGTTCAAGGTAAAAAATGATATTTTTGGAAGTTCGAGGGTCAAAATGTAA
* * * *
1218 TTTTTGAAAAGGTTGAGGGT--AAAATG-TAATTTTTGTGAAGTTCGAGGGTCAAAATATAA
1 TTTTTGGAAA-GTTCAAGGTAAAAAATGAT-ATTTTTG-GAAGTTCGAGGGTCAAAATGTAA
* *
1277 TTTTTGGGAAGTTCGAAGGTTAAAAAGTGAT-TTTT
1 TTTTTGGAAAGTTC-AAGG-TAAAAAATGATATTTT
1312 GAACAGTTCA
Statistics
Matches: 125, Mismatches: 17, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
56 1 0.01
57 11 0.09
58 27 0.22
59 75 0.60
60 1 0.01
61 4 0.03
62 5 0.04
63 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.36
Consensus pattern (59 bp):
TTTTTGGAAAGTTCAAGGTAAAAAATGATATTTTTGGAAGTTCGAGGGTCAAAATGTAA
Found at i:1282 original size:30 final size:28
Alignment explanation
Indices: 1101--1301 Score: 149
Period size: 30 Copynumber: 6.8 Consensus size: 28
1091 CAAAAATGGG
* *
1101 TTTTTGGAAAGTTC-AAGGTAAAAAATGATA
1 TTTTTGG-AAGTTCGAGGGTAAAATAT-A-A
* *
1131 TTTTTGGAAGTTCGGGGGTAAAATGGTAA
1 TTTTTGGAAGTTCGAGGGTAAAAT-ATAA
*
1160 TTTTTGGAAAGTT-TAGGGTCAAAA-ATAA
1 TTTTTGG-AAGTTCGAGGGT-AAAATATAA
* **
1188 TATTTTTGAAGTTCGAGGGTGAAAATGCAA
1 T-TTTTGGAAGTTCGAGGGT-AAAATATAA
* *
1218 TTTTTGAAAAGGTT-GAGGGTAAAATGTAA
1 TTTTTG-GAA-GTTCGAGGGTAAAATATAA
1247 TTTTTGTGAAGTTCGAGGGTCAAAATATAA
1 TTTTTG-GAAGTTCGAGGGT-AAAATATAA
*
1277 TTTTTGGGAAGTTCGAAGGTTAAAA
1 TTTTT-GGAAGTTCG-AGGGTAAAA
1302 AGTGATTTTT
Statistics
Matches: 139, Mismatches: 19, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
28 12 0.09
29 58 0.42
30 60 0.43
31 9 0.06
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (28 bp):
TTTTTGGAAGTTCGAGGGTAAAATATAA
Done.