Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007885.1 Kokia drynarioides strain JFW-HI SEQ_122526, 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: 2704
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Found at i:148 original size:30 final size:30
Alignment explanation
Indices: 114--235 Score: 154
Period size: 30 Copynumber: 4.1 Consensus size: 30
104 TTTTGATATT
* * *
114 TTTCGTTTATTTTTTTAATTTAATTTGTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
144 TTTCGTTTATATTTTAAATTTAATTTCTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
* * * * *
174 TTTCCTATATATTTTAATTTTAACTTGTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
* *
204 TTTCATTTATATTTTAAATTTCATTTCTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
234 TT
1 TT
236 ATTAGTTTTT
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 78 1.00
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.61
Consensus pattern (30 bp):
TTTCGTTTATATTTTAAATTTAATTTCTAA
Found at i:1278 original size:121 final size:118
Alignment explanation
Indices: 1093--1360 Score: 319
Period size: 121 Copynumber: 2.3 Consensus size: 118
1083 ATCGACCAAA
* *
1093 CAATGACCAACACCAAAAAATTTGATTTTTCAAATAAAAAGGTGGTGTCGATCAATGCATGGCCA
1 CAATGACCAACACCAAAAAATTTAATTTTTCAAATAAAAAGGTGGTGTCGACCAATGCATGGCCA
*
1158 ACACAAAAAAAATTTG-AATTTTTTTATCAGATAGAAAGGTGGTGCTGGCCATG
66 ACACAAAAAAAA-TTGAAATTTTTTTATAAGATAGAAAGGTGGTGCTGGCCATG
** *
1211 CAATGACCAACACC-AAAAATTTAATTTTTTTAATCAGATAATAGGTGGTGTCGACCAATGCTTG
1 CAATGACCAACACCAAAAAATTTAATTTTTCAAAT-A-A-AA-AGGTGGTGTCGACCAATGCATG
* * * * *
1275 GCCAACACCAAAAAAATTGAAATTTTTTTATAAGATA-AAACGTGATG-TCGACCATA
62 GCCAACACAAAAAAAATTGAAATTTTTTTATAAGATAGAAAGGTGGTGCT-GGCCATG
* * * *
1331 TAATGACCAACACAAAAAAAATTAGTTTTT
1 CAATGACCAACACCAAAAAATTTAATTTTT
1361 TATCAAATAA
Statistics
Matches: 128, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
117 17 0.13
118 15 0.12
119 2 0.02
120 30 0.23
121 64 0.50
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (118 bp):
CAATGACCAACACCAAAAAATTTAATTTTTCAAATAAAAAGGTGGTGTCGACCAATGCATGGCCA
ACACAAAAAAAATTGAAATTTTTTTATAAGATAGAAAGGTGGTGCTGGCCATG
Found at i:1324 original size:61 final size:60
Alignment explanation
Indices: 1129--1372 Score: 241
Period size: 61 Copynumber: 4.1 Consensus size: 60
1119 TTTTCAAATA
* *
1129 AAAAGGTGGTGTCGATCAATGCATGGCCAACACAAAAAAAATTTGAATTTTTTTATCAGAT
1 AAAAGGTGGTGTCGACCAATGCATGGCCAACACCAAAAAAA-TTGAATTTTTTTATCAGAT
* * *
1190 AGAAAGGTGGTG-CTGGCC-ATGCAATGACCAACACC--AAAAATTTAATTTTTTTAATCAGAT
1 A-AAAGGTGGTGTC-GACCAATGC-ATGGCCAACACCAAAAAAATTGAATTTTTTT-ATCAGAT
* * *
1250 AATAGGTGGTGTCGACCAATGCTTGGCCAACACCAAAAAAATTGAAATTTTTTTATAAGAT
1 AAAAGGTGGTGTCGACCAATGCATGGCCAACACCAAAAAAATTG-AATTTTTTTATCAGAT
* * * * * * *
1311 AAAACGTGATGTCGACCATAT-AATGACCAACACAAAAAAAATT--AGTTTTTTATCAAAT
1 AAAAGGTGGTGTCGACCA-ATGCATGGCCAACACCAAAAAAATTGAATTTTTTTATCAGAT
1369 AAAA
1 AAAA
1373 AAAGGGATAT
Statistics
Matches: 152, Mismatches: 21, Indels: 23
0.78 0.11 0.12
Matches are distributed among these distances:
58 16 0.11
59 33 0.22
60 18 0.12
61 52 0.34
62 33 0.22
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (60 bp):
AAAAGGTGGTGTCGACCAATGCATGGCCAACACCAAAAAAATTGAATTTTTTTATCAGAT
Found at i:1451 original size:60 final size:60
Alignment explanation
Indices: 1206--1463 Score: 174
Period size: 60 Copynumber: 4.3 Consensus size: 60
1196 GTGGTGCTGG
* * * * * *
1206 CCATGCAATGACCAACAC-CAAAAATTTAATTTTTTTAATCAG-ATAATA-GGTGGTGTCGA
1 CCATGCAATGACCAACACAAAAAAATTTAAATTTTTT-ATCTGAAAAAAAGGGT-ATGTCGA
* * * ** * * *
1265 CCAATGC-TTGGCCAACACCAAAAAAATTGAAATTTTTTTATAAGATAAAACGTG-ATGTCGA
1 CC-ATGCAATGACCAACA-CAAAAAAATTTAAA-TTTTTTATCTGAAAAAAAGGGTATGTCGA
** * * *
1326 CCATATAATGACCAACACAAAAAAAATT-AGTTTTTTATCAAAT-AAAAAAAGGGATATAT-G-
1 CCATGCAATGACCAACACAAAAAAATTTAAATTTTTTATC---TGAAAAAAAGGG-TATGTCGA
* * *
1386 TCATGCAATGGCCAATACAAAAAAATTTAAATTTTTTATCTGAAAAAAAGGGTATGTCGA
1 CCATGCAATGACCAACACAAAAAAATTTAAATTTTTTATCTGAAAAAAAGGGTATGTCGA
1446 CCATGCAATGACCAACAC
1 CCATGCAATGACCAACAC
1464 CAAATTTTTT
Statistics
Matches: 147, Mismatches: 36, Indels: 31
0.69 0.17 0.14
Matches are distributed among these distances:
58 13 0.09
59 22 0.15
60 60 0.41
61 40 0.27
62 11 0.07
63 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.28
Consensus pattern (60 bp):
CCATGCAATGACCAACACAAAAAAATTTAAATTTTTTATCTGAAAAAAAGGGTATGTCGA
Found at i:2524 original size:31 final size:31
Alignment explanation
Indices: 2489--2550 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
2479 TTAACTCTTT
2489 CTTAGGACTAATTTGGTAGTTCTCTAAACTG
1 CTTAGGACTAATTTGGTAGTTCTCTAAACTG
2520 CTTAGGACTAATTTGGTAGTTCTCTAAACTG
1 CTTAGGACTAATTTGGTAGTTCTCTAAACTG
2551 GGTAATAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (31 bp):
CTTAGGACTAATTTGGTAGTTCTCTAAACTG
Done.