Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003857.1 Hibiscus syriacus cultivar Beakdansim tig00008291_pilon, 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: 276966
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:276376 original size:264 final size:262
Alignment explanation
Indices: 276037--276545 Score: 812
Period size: 264 Copynumber: 1.9 Consensus size: 262
276027 GGAGACAAAA
* * *
276037 TTTGTTTCAAGGGAACTATCTCATGAGTGACAAAATTCATTTCAAGGAAAATGTTTTCAATGTTA
1 TTTGTTTCAAGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGAAAATGTTTTCAATGTTA
*
276102 TATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG-TTCAAGGGAACTTATCTCAAGAGAG
66 TATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTA-CTCAAGAGAG
276166 ACAAAATTCATCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGGA
130 AC-AAATTCATCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGA-GA
*
276231 CAAAACTTAGTTCCAAAAG-AAATGTCTCAAGGGAGACGAAATTTG-TTTCAAGGGAACAGATTC
193 -AAAACCTAGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTTCAAGGGAACAGATTC
276294 AAAGAT
257 AAAGAT
276300 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAA-GAGAAATG-TTTCAATGT
1 TTTGTTTCAAG-GAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGA-AAATGTTTTCAATG-
*
276363 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTACTCAAGAG
63 TTATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTACTCAAGAG
* * * *
276428 AGACAAATTCATTTTAAGGGAAATTTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGA
128 AGACAAATTCATCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGA
* *
276493 GAAACCTAGTTCTAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTTCAAG
193 AAAACCTAGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTTCAAG
276546 AGAGACAAGA
Statistics
Matches: 228, Mismatches: 12, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
261 15 0.07
262 28 0.12
263 83 0.36
264 89 0.39
265 13 0.06
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (262 bp):
TTTGTTTCAAGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGAAAATGTTTTCAATGTTA
TATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTACTCAAGAGAGA
CAAATTCATCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAAAA
ACCTAGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTTCAAGGGAACAGATTCAAAG
AT
Found at i:276426 original size:100 final size:102
Alignment explanation
Indices: 276293--276494 Score: 320
Period size: 100 Copynumber: 2.0 Consensus size: 102
276283 GGAACAGATT
276293 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAA-TGTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC-AAATTCATTTCAAGAGAAATTGTTT
*
276357 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
65 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
* * * * *
276395 CAAA-ATTTTGTTTCAAGGGAACCTA-CTCAAGAGAGACAAATTCATTTTAAGGGAAATTTTTTC
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAATTCATTTCAAGAGAAATTGTTTC
276458 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
66 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
276495 AACCTAGTTC
Statistics
Matches: 93, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
99 17 0.18
100 53 0.57
101 19 0.20
102 4 0.04
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (102 bp):
CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAATTCATTTCAAGAGAAATTGTTTC
AATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
Found at i:276472 original size:164 final size:164
Alignment explanation
Indices: 276131--276494 Score: 438
Period size: 164 Copynumber: 2.2 Consensus size: 164
276121 TCAAGGGAGA
* *
276131 CAAA-ATTTTG-TTCAAG-GGAACTTATCTCAAGAGAGACAAAATTCATCTCAAGGGAAATGTTT
1 CAAAGATTTTGTTTCAAGAGAAAC-TATCTCAAGAGAGACAAAATTCATCTCAAGAGAAATGTTT
*
276193 TCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGGACAAAACTTAGTTCCAAAAGAAATGTCT
65 TCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGGACAAAACTTAGTTCCAAAAGAAATGACT
* **
276258 CAAGGGAGACGAAATTTGTTTCAAGGGAACAGATT
130 CAAGAGAGACGAAATTCATTTCAAGGGAACAGATT
*
276293 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAATG-TTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATCTCAAGAGAAATGTTTT
* * * * * ** *
276357 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCT-AC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAG-GACAAAACTTAGTTCCAAAAGAA-ATGAC
* **
276421 TCAAGAGAGAC-AAATTCATTTTAAGGGAA-ATTTTTT
129 TCAAGAGAGACGAAATTCATTTCAAGGGAACA--GATT
* *
276457 CAATG-TTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
1 CAAAGATTT-TGTTTCAAGAGAAACTATCTCAAGAGAGA
276495 AACCTAGTTC
Statistics
Matches: 174, Mismatches: 20, Indels: 14
0.84 0.10 0.07
Matches are distributed among these distances:
162 5 0.03
163 60 0.34
164 104 0.60
165 5 0.03
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (164 bp):
CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATCTCAAGAGAAATGTTTT
CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGGACAAAACTTAGTTCCAAAAGAAATGACTC
AAGAGAGACGAAATTCATTTCAAGGGAACAGATT
Done.