Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013559.1 Kokia drynarioides strain JFW-HI SEQ_128585, 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, 854
Length: 1424
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.36
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:812 original size:56 final size:58
Alignment explanation
Indices: 752--900 Score: 176
Period size: 59 Copynumber: 2.6 Consensus size: 58
742 TGGTATAAAA
*
752 TAATTTATTTTGTA-C-CATTTTGGTAAATAATATGATAGGGATATTATTTTCATAAT
1 TAATTTATTTTATATCACATTTTGGTAAATAATATGATAGGGATATTATTTTCATAAT
* * * * *
808 TAATTATTTTTTATATCATATTTTGGTCAATAATATGATGGGGATATTATTTTGATAAT
1 TAATT-TATTTTATATCACATTTTGGTAAATAATATGATAGGGATATTATTTTCATAAT
* * * *
867 TAATTATTTTTTATATTATATTTTGGTAATTAAT
1 TAATT-TATTTTATATCACATTTTGGTAAATAAT
901 TAGCTAAGNN
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
56 5 0.06
57 7 0.09
58 1 0.01
59 68 0.84
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.52
Consensus pattern (58 bp):
TAATTTATTTTATATCACATTTTGGTAAATAATATGATAGGGATATTATTTTCATAAT
Found at i:841 original size:59 final size:59
Alignment explanation
Indices: 768--900 Score: 221
Period size: 59 Copynumber: 2.3 Consensus size: 59
758 ATTTTGTACC
768 ATTTTGGTAAATAATATGATAGGGATATTATTTTCATAATTAATTATTTTTTATATCAT
1 ATTTTGGTAAATAATATGATAGGGATATTATTTTCATAATTAATTATTTTTTATATCAT
* * * *
827 ATTTTGGTCAATAATATGATGGGGATATTATTTTGATAATTAATTATTTTTTATATTAT
1 ATTTTGGTAAATAATATGATAGGGATATTATTTTCATAATTAATTATTTTTTATATCAT
*
886 ATTTTGGTAATTAAT
1 ATTTTGGTAAATAAT
901 TAGCTAAGNN
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 68 1.00
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (59 bp):
ATTTTGGTAAATAATATGATAGGGATATTATTTTCATAATTAATTATTTTTTATATCAT
Found at i:870 original size:29 final size:29
Alignment explanation
Indices: 768--870 Score: 68
Period size: 29 Copynumber: 3.5 Consensus size: 29
758 ATTTTGTACC
* *
768 ATTTTGGTAAATAATATGATAGGGATATT
1 ATTTTGATAATTAATATGATAGGGATATT
* ****
797 ATTTTCATAATTAAT-T-ATTTTTTATATCAT
1 ATTTTGATAATTAATATGA-TAGGGATAT--T
* *
827 ATTTTGGTCAA-TAATATGATGGGGATATT
1 ATTTTGAT-AATTAATATGATAGGGATATT
856 ATTTTGATAATTAAT
1 ATTTTGATAATTAAT
871 TATTTTTTAT
Statistics
Matches: 53, Mismatches: 14, Indels: 14
0.65 0.17 0.17
Matches are distributed among these distances:
27 1 0.02
28 8 0.15
29 24 0.45
30 11 0.21
31 8 0.15
32 1 0.02
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.49
Consensus pattern (29 bp):
ATTTTGATAATTAATATGATAGGGATATT
Found at i:874 original size:16 final size:16
Alignment explanation
Indices: 853--902 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
843 TGATGGGGAT
853 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
869 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
884 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
899 ATTA
1 ATTA
903 GCTAAGNNNN
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:891 original size:30 final size:30
Alignment explanation
Indices: 796--902 Score: 87
Period size: 30 Copynumber: 3.6 Consensus size: 30
786 ATAGGGATAT
* *
796 TATTTTCATAATTAATTATTTTTTATATCA
1 TATTTTGATAATTAATTATTTTTTATATTA
* ****
826 TATTTTGGTCAA-TAA-TATGATGGGGATA-T-
1 TATTTTGAT-AATTAATTAT--TTTTTATATTA
855 TATTTTGATAATTAATTATTTTTTATATTA
1 TATTTTGATAATTAATTATTTTTTATATTA
*
885 TATTTTGGTAATTAATTA
1 TATTTTGATAATTAATTA
903 GCTAAGNNNN
Statistics
Matches: 57, Mismatches: 13, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
28 6 0.11
29 15 0.26
30 30 0.53
31 6 0.11
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (30 bp):
TATTTTGATAATTAATTATTTTTTATATTA
Found at i:1223 original size:31 final size:31
Alignment explanation
Indices: 1187--1283 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 31
1177 ATTATTTTTT
1187 ATATTATATTTTGGTCAATAATATGATGGGG
1 ATATTATATTTTGGTCAATAATATGATGGGG
* * ***
1218 ATA-T-TATTTTGAT-AATTAATTAT-TTTTTG
1 ATATTATATTTTGGTCAA-TAA-TATGATGGGG
1247 -TATTATATTTTGGTCAATAATATGATGGGG
1 ATATTATATTTTGGTCAATAATATGATGGGG
1277 ATATTAT
1 ATATTAT
1284 TTTGATAATT
Statistics
Matches: 49, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
28 4 0.08
29 17 0.35
30 17 0.35
31 11 0.22
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.49
Consensus pattern (31 bp):
ATATTATATTTTGGTCAATAATATGATGGGG
Found at i:1257 original size:30 final size:30
Alignment explanation
Indices: 1163--1328 Score: 110
Period size: 30 Copynumber: 5.6 Consensus size: 30
1153 ATGGGGATAT
* *
1163 TATTTTCATAATTAATTATTTTTTATATTA
1 TATTTTGATAATTAATTATTTTTTGTATTA
* ** ** *
1193 TATTTTGGTCAA-TAA-TATGATGGGGA-TA
1 TATTTTGAT-AATTAATTATTTTTTGTATTA
1221 TTATTTTGATAATTAATTATTTTTTGTATTA
1 -TATTTTGATAATTAATTATTTTTTGTATTA
* ** ** *
1252 TATTTTGGTCAA-TAA-TATGATGGGGA-TA
1 TATTTTGAT-AATTAATTATTTTTTGTATTA
*
1280 TTATTTTGATAATTAATTATTTTTTATATTA
1 -TATTTTGATAATTAATTATTTTTTGTATTA
*
1311 TATTTTGGTAATTAATTA
1 TATTTTGATAATTAATTA
1329 GCCAAGTATA
Statistics
Matches: 98, Mismatches: 28, Indels: 20
0.67 0.19 0.14
Matches are distributed among these distances:
28 8 0.08
29 33 0.34
30 49 0.50
31 8 0.08
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (30 bp):
TATTTTGATAATTAATTATTTTTTGTATTA
Found at i:1300 original size:16 final size:16
Alignment explanation
Indices: 1279--1328 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1269 TGATGGGGAT
1279 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
1295 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
1310 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
1325 ATTA
1 ATTA
1329 GCCAAGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:1353 original size:59 final size:59
Alignment explanation
Indices: 1135--1319 Score: 352
Period size: 59 Copynumber: 3.1 Consensus size: 59
1125 ATTTTGTACC
*
1135 ATTTTGGTCAATAATATGATGGGGATATTATTTTCATAATTAATTATTTTTTATATTAT
1 ATTTTGGTCAATAATATGATGGGGATATTATTTTGATAATTAATTATTTTTTATATTAT
*
1194 ATTTTGGTCAATAATATGATGGGGATATTATTTTGATAATTAATTATTTTTTGTATTAT
1 ATTTTGGTCAATAATATGATGGGGATATTATTTTGATAATTAATTATTTTTTATATTAT
1253 ATTTTGGTCAATAATATGATGGGGATATTATTTTGATAATTAATTATTTTTTATATTAT
1 ATTTTGGTCAATAATATGATGGGGATATTATTTTGATAATTAATTATTTTTTATATTAT
1312 ATTTTGGT
1 ATTTTGGT
1320 AATTAATTAG
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 123 1.00
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.53
Consensus pattern (59 bp):
ATTTTGGTCAATAATATGATGGGGATATTATTTTGATAATTAATTATTTTTTATATTAT
Done.