Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008154.1 Hibiscus syriacus cultivar Beakdansim tig00110720_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: 185899
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
File 2 of 2
Found at i:158414 original size:15 final size:15
Alignment explanation
Indices: 158390--158426 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
158380 ACATTTATTT
158390 TACCGCTTTTTA-GG
1 TACCGCTTTTTAGGG
158404 TACCGCTTTTTAGGG
1 TACCGCTTTTTAGGG
158419 TA-CGCTTT
1 TACCGCTTT
158427 ACTGAAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.43
Consensus pattern (15 bp):
TACCGCTTTTTAGGG
Found at i:160626 original size:21 final size:21
Alignment explanation
Indices: 160601--160659 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
160591 TGCTACAGGG
160601 GTATCGATACCCTGCTATGGT
1 GTATCGATACCCTGCTATGGT
160622 GTATCGATACCCTGCTATGGT
1 GTATCGATACCCTGCTATGGT
*
160643 GTATCGATACTCTGCTA
1 GTATCGATACCCTGCTA
160660 CAGTAATTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (21 bp):
GTATCGATACCCTGCTATGGT
Found at i:161471 original size:31 final size:31
Alignment explanation
Indices: 161428--161587 Score: 214
Period size: 31 Copynumber: 5.1 Consensus size: 31
161418 ACTCGTTTAA
*
161428 TAAATTGTCCATATGTCCCAAAGAACATAGG
1 TAAACTGTCCATATGTCCCAAAGAACATAGG
*
161459 TAAACTGTCCATATGTCCCAAATAACATAGG
1 TAAACTGTCCATATGTCCCAAAGAACATAGG
* *
161490 TAAATTGTCCATATGTCCCGAAGAACATAGG
1 TAAACTGTCCATATGTCCCAAAGAACATAGG
* * *
161521 TAATCCTGTCTATATGTCCCGAAGAACATAGG
1 TAA-ACTGTCCATATGTCCCAAAGAACATAGG
*
161553 TAATCATGTCCATATGTCCCGAAAG-ACATAGG
1 TAAAC-TGTCCATATGTCCC-AAAGAACATAGG
161585 TAA
1 TAA
161588 CCCTCGACTA
Statistics
Matches: 115, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
31 61 0.53
32 51 0.44
33 3 0.03
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (31 bp):
TAAACTGTCCATATGTCCCAAAGAACATAGG
Found at i:161541 original size:32 final size:32
Alignment explanation
Indices: 161433--161587 Score: 210
Period size: 32 Copynumber: 4.9 Consensus size: 32
161423 TTTAATAAAT
* *
161433 TGTCCATATGTCCCAAAGAACATAGGTAA-AC
1 TGTCCATATGTCCCGAAGAACATAGGTAATCC
* *
161464 TGTCCATATGTCCCAAATAACATAGGTAAAT--
1 TGTCCATATGTCCCGAAGAACATAGGT-AATCC
161495 TGTCCATATGTCCCGAAGAACATAGGTAATCC
1 TGTCCATATGTCCCGAAGAACATAGGTAATCC
* *
161527 TGTCTATATGTCCCGAAGAACATAGGTAATCA
1 TGTCCATATGTCCCGAAGAACATAGGTAATCC
161559 TGTCCATATGTCCCGAA-AGACATAGGTAA
1 TGTCCATATGTCCCGAAGA-ACATAGGTAA
161588 CCCTCGACTA
Statistics
Matches: 113, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
30 3 0.03
31 52 0.46
32 58 0.51
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (32 bp):
TGTCCATATGTCCCGAAGAACATAGGTAATCC
Found at i:177367 original size:32 final size:31
Alignment explanation
Indices: 177261--177412 Score: 229
Period size: 31 Copynumber: 4.9 Consensus size: 31
177251 TTTAATAAAC
* *
177261 GTCCATATGTCTCGAAGAACATAGGTAA-AT
1 GTCCATATGTCCCGAAGAACATAGGTAATCT
177291 GTCCATATGTCCCGAAGAACATAGGTAAAT-T
1 GTCCATATGTCCCGAAGAACATAGGT-AATCT
177322 GTCCATATGTCCCGAAGAACATAGGTAATCCT
1 GTCCATATGTCCCGAAGAACATAGGTAAT-CT
*
177354 GTCTATATGTCCCGAAGAACATAGGTAATCT
1 GTCCATATGTCCCGAAGAACATAGGTAATCT
177385 GTCCATATGTCCCGAA-AGACATAGGTAA
1 GTCCATATGTCCCGAAGA-ACATAGGTAA
177413 CCCTCGACTA
Statistics
Matches: 114, Mismatches: 3, Indels: 9
0.90 0.02 0.07
Matches are distributed among these distances:
30 29 0.25
31 56 0.49
32 29 0.25
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (31 bp):
GTCCATATGTCCCGAAGAACATAGGTAATCT
Found at i:177388 original size:63 final size:61
Alignment explanation
Indices: 177261--177412 Score: 227
Period size: 63 Copynumber: 2.5 Consensus size: 61
177251 TTTAATAAAC
*
177261 GTCCATATGTCTCGAAGAACATAGGTAAATGTCCATATGTCCCGAAGAACATAGGTAAATT
1 GTCCATATGTCCCGAAGAACATAGGTAAATGTCCATATGTCCCGAAGAACATAGGTAAATT
* *
177322 GTCCATATGTCCCGAAGAACATAGGTAATCCTGTCTATATGTCCCGAAGAACATAGGT-AATCT
1 GTCCATATGTCCCGAAGAACATAGGTAA--ATGTCCATATGTCCCGAAGAACATAGGTAAAT-T
177385 GTCCATATGTCCCGAA-AGACATAGGTAA
1 GTCCATATGTCCCGAAGA-ACATAGGTAA
177413 CCCTCGACTA
Statistics
Matches: 84, Mismatches: 3, Indels: 6
0.90 0.03 0.06
Matches are distributed among these distances:
61 27 0.32
62 4 0.05
63 53 0.63
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (61 bp):
GTCCATATGTCCCGAAGAACATAGGTAAATGTCCATATGTCCCGAAGAACATAGGTAAATT
Done.