Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010306.1 Kokia drynarioides strain JFW-HI SEQ_125165, 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: 4092
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Found at i:972 original size:30 final size:30
Alignment explanation
Indices: 931--1416 Score: 287
Period size: 29 Copynumber: 16.5 Consensus size: 30
921 CAAATTTTTG
931 AAAATCCCATTTTTGACCCCGAAACTTCTA
1 AAAATCCCATTTTTGACCCCGAAACTTCTA
* ** *
961 CAAATTTCATTTTT-ACCCCTAAACTT-TCA
1 AAAATCCCATTTTTGACCCCGAAACTTCT-A
*
990 AAAATCCCATTTTTGACCCCGAAACTTCCA
1 AAAATCCCATTTTTGACCCCGAAACTTCTA
* * * *
1020 AAAATTCCATTTTT-ACCCCTAAATTTCCA
1 AAAATCCCATTTTTGACCCCGAAACTTCTA
* *
1049 AAAATCACATTTTTGACCCTGAAACTTCTA
1 AAAATCCCATTTTTGACCCCGAAACTTCTA
*
1079 AAAATTCCATTTTT-ACCCTCG-AACTT-TA
1 AAAATCCCATTTTTGACCC-CGAAACTTCTA
* * ** *
1107 GAAAATCACATTTTTGACTCTAAAACTTCCA
1 -AAAATCCCATTTTTGACCCCGAAACTTCTA
** * *
1138 AAAATTTCATTTTT-ACCCCTAAACTT-TCG
1 AAAATCCCATTTTTGACCCCGAAACTTCT-A
* *
1167 AAAATCCCATTTTTGACCTCGAAACTTCCA
1 AAAATCCCATTTTTGACCCCGAAACTTCTA
* *
1197 AAAAT--TATGTTTTTACCCTCG-AACTTCCT-
1 AAAATCCCAT-TTTTGACCC-CGAAACTT-CTA
* ** *
1226 TAAATCCCATTTTTGACCTTGAAACTTCCA
1 AAAATCCCATTTTTGACCCCGAAACTTCTA
*
1256 AAAAT--TATGCTTTT-ACCCTCG-AACTTCCT-
1 AAAATCCCAT--TTTTGACCC-CGAAACTT-CTA
* * * ** *
1285 TAAATCTCATTTTTAACCCTAAAACTTCAA
1 AAAATCCCATTTTTGACCCCGAAACTTCTA
* *
1315 AAAATTCC-TTTTTTACCCTCG-AACTTCTA
1 AAAATCCCATTTTTGACCC-CGAAACTTCTA
* * *
1344 AAAATCCCAATTTTGACCCCGAAGCTTCCA
1 AAAATCCCATTTTTGACCCCGAAACTTCTA
* * * *
1374 TAAAT--TATGTTTTTACCCTCG-AACTTCCA
1 AAAATCCCAT-TTTTGACCC-CGAAACTTCTA
1403 AAAATCCCATTTTT
1 AAAATCCCATTTTT
1417 AACCTCAAAA
Statistics
Matches: 342, Mismatches: 79, Indels: 70
0.70 0.16 0.14
Matches are distributed among these distances:
28 8 0.02
29 169 0.49
30 158 0.46
31 7 0.02
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.36
Consensus pattern (30 bp):
AAAATCCCATTTTTGACCCCGAAACTTCTA
Found at i:995 original size:59 final size:59
Alignment explanation
Indices: 892--1416 Score: 510
Period size: 59 Copynumber: 8.9 Consensus size: 59
882 AGAGGTCCCT
* * * **
892 AAACTGTCCAAAAATTTCGTTTTTACCCTCAAATTTTTGAAAATCCCATTTTTGACCCCG
1 AAACT-TCCAAAAATTTCATTTTTACCCTCGAACTTTCAAAAATCCCATTTTTGACCCCG
* * *
952 AAACTTCTACAAATTTCATTTTTACCC-CTAAACTTTCAAAAATCCCATTTTTGACCCCG
1 AAACTTCCAAAAATTTCATTTTTACCCTC-GAACTTTCAAAAATCCCATTTTTGACCCCG
* * * * *
1011 AAACTTCCAAAAATTCCATTTTTACCC-CTAAATTTCCAAAAATCACATTTTTGACCCTG
1 AAACTTCCAAAAATTTCATTTTTACCCTCGAACTTT-CAAAAATCCCATTTTTGACCCCG
* * * * **
1070 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTT-AGAAAATCACATTTTTGACTCTA
1 AAACTTCCAAAAATTTCATTTTTACCCTCGAACTTTCA-AAAATCCCATTTTTGACCCCG
* * *
1129 AAACTTCCAAAAATTTCATTTTTACCC-CTAAACTTTCGAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTTCATTTTTACCCTC-GAACTTTCAAAAATCCCATTTTTGACCCCG
* * ** **
1188 AAACTTCCAAAAATTAT-GTTTTTACCCTCGAACTTCCTTAAATCCCATTTTTGACCTTG
1 AAACTTCCAAAAATT-TCATTTTTACCCTCGAACTTTCAAAAATCCCATTTTTGACCCCG
* ** * * **
1247 AAACTTCCAAAAA-TT-ATGCTTTTACCCTCGAACTTCCTTAAATCTCATTTTTAACCCTA
1 AAACTTCCAAAAATTTCAT--TTTTACCCTCGAACTTTCAAAAATCCCATTTTTGACCCCG
* * * *
1306 AAACTTCAAAAAATTCCTTTTTTACCCTCGAAC-TTCTAAAAATCCCAATTTTGACCCCG
1 AAACTTCCAAAAATTTCATTTTTACCCTCGAACTTTC-AAAAATCCCATTTTTGACCCCG
* * * *
1365 AAGCTTCCATAAATTAT-GTTTTTACCCTCGAACTTCCAAAAATCCCATTTTT
1 AAACTTCCAAAAATT-TCATTTTTACCCTCGAACTTTCAAAAATCCCATTTTT
1417 AACCTCAAAA
Statistics
Matches: 394, Mismatches: 56, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
57 2 0.01
58 11 0.03
59 364 0.92
60 16 0.04
61 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.36
Consensus pattern (59 bp):
AAACTTCCAAAAATTTCATTTTTACCCTCGAACTTTCAAAAATCCCATTTTTGACCCCG
Found at i:1135 original size:177 final size:176
Alignment explanation
Indices: 888--1416 Score: 636
Period size: 177 Copynumber: 3.0 Consensus size: 176
878 CCCCAGAGGT
* * * * * **
888 CCCT-AAACTGTCCAAAAATTTCGTTTTTACCCTCAAATTTTTGAAAATCCCATTTTTGACCCCG
1 CCCTGAAACT-TCCAAAAA-TTCATTTTTACCCTCGAACTTTAGAAAATCACATTTTTGACCCTA
* *
952 AAACTTCTACAAATTTCATTTTTACCCCTAAACTTTCAAAAATCCCATTTTTGACCCCGAAACTT
64 AAACTTCAAAAAATTTCATTTTTACCCCTAAACTTTCAAAAATCCCATTTTTGACCCCGAAACTT
*** * * *
1017 CCAAAAATTCCATTTTTACCC-CTAAATTTCCAAAAATCACATTTTTGA
129 CCAAAAATTATGTTTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGA
* *
1065 CCCTGAAACTTCTAAAAATTCCATTTTTACCCTCGAACTTTAGAAAATCACATTTTTGACTCTAA
1 CCCTGAAACTTCCAAAAATT-CATTTTTACCCTCGAACTTTAGAAAATCACATTTTTGACCCTAA
* * *
1130 AACTTCCAAAAATTTCATTTTTACCCCTAAACTTTCGAAAATCCCATTTTTGACCTCGAAACTTC
65 AACTTCAAAAAATTTCATTTTTACCCCTAAACTTTCAAAAATCCCATTTTTGACCCCGAAACTTC
**
1195 CAAAAATTATGTTTTTACCCTCGAACTTCCTTAAATCCCATTTTTGA
130 CAAAAATTATGTTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
* **** * *
1242 CCTTGAAACTTCCAAAAATT-ATGCTTTTACCCTCGAACTTCCTTAAATCTCATTTTTAACCCTA
1 CCCTGAAACTTCCAAAAATTCAT--TTTTACCCTCGAACTTTAGAAAATCACATTTTTGACCCTA
* * * * *
1306 AAACTTCAAAAAATTCCTTTTTTA-CCCTCGAAC-TTCTAAAAATCCCAATTTTGACCCCGAAGC
64 AAACTTCAAAAAATTTCATTTTTACCCCT-AAACTTTC-AAAAATCCCATTTTTGACCCCGAAAC
*
1369 TTCCATAAATTATGTTTTTACCCTCGAACTTCCAAAAATCCCATTTTT
127 TTCCAAAAATTATGTTTTTACCCTCGAACTTCCAAAAATCCCATTTTT
1417 AACCTCAAAA
Statistics
Matches: 304, Mismatches: 41, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
175 2 0.01
176 9 0.03
177 287 0.94
178 6 0.02
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (176 bp):
CCCTGAAACTTCCAAAAATTCATTTTTACCCTCGAACTTTAGAAAATCACATTTTTGACCCTAAA
ACTTCAAAAAATTTCATTTTTACCCCTAAACTTTCAAAAATCCCATTTTTGACCCCGAAACTTCC
AAAAATTATGTTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
Done.