Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004406.1 Hibiscus syriacus cultivar Beakdansim tig00009658_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: 68437
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:471 original size:22 final size:22
Alignment explanation
Indices: 443--505 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 22
433 TCGCAATGAT
443 TTTGAAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGAGAG
*
465 TTTGAAAAACGTGTTGTTGCGATAG
1 TTTGAAAAA--TG-TGTTGCGAGAG
490 --TGAAAAA-GTGTTGCGA
1 TTTGAAAAATGTGTTGCGA
506 TATTGAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 8 0.22
20 1 0.03
22 9 0.24
23 7 0.19
24 2 0.05
25 10 0.27
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGCGAGAG
Found at i:503 original size:19 final size:19
Alignment explanation
Indices: 479--515 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
469 AAAAACGTGT
479 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAGTGAAAAAG
*
498 TGTTGCGATATTGAAAAA
1 TGTTGCGATAGTGAAAAA
516 TCCAAATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.27, T:0.30
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAAAG
Found at i:1290 original size:12 final size:13
Alignment explanation
Indices: 1265--1295 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1255 TCGTCACGAA
1265 TAAAATATATTTT
1 TAAAATATATTTT
*
1278 TAAATTATATTTT
1 TAAAATATATTTT
1291 TAAAA
1 TAAAA
1296 AATTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAAATATATTTT
Found at i:4538 original size:23 final size:23
Alignment explanation
Indices: 4512--4603 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 23
4502 CACCACAGCT
* *
4512 CGTATAAATACACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
4535 CGTAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
4558 CGTAGAATTGCACCGAAGTACCG
1 CGTAGAAATGCACCGAAGTGCCA
*
4581 CGTA-AAATTGTACCGAAGTGCCA
1 CGTAGAAA-TGCACCGAAGTGCCA
4604 TATAAAATGT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
22 2 0.03
23 57 0.97
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:4611 original size:23 final size:23
Alignment explanation
Indices: 4522--4603 Score: 119
Period size: 23 Copynumber: 3.6 Consensus size: 23
4512 CGTATAAATA
*
4522 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAAAATTG
*
4545 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAAAATTG
* *
4568 CACCGAAGTACCGCGTAAAATTG
1 CACCGAAGTGCCACGTAAAATTG
*
4591 TACCGAAGTGCCA
1 CACCGAAGTGCCA
4604 TATAAAATGT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.17
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAAAATTG
Found at i:9383 original size:14 final size:14
Alignment explanation
Indices: 9364--9432 Score: 67
Period size: 14 Copynumber: 5.1 Consensus size: 14
9354 ACAATTAATA
9364 TTTAAGTATAATTG
1 TTTAAGTATAATTG
9378 TTTAAGTATAA-TG
1 TTTAAGTATAATTG
9391 TTTAAGT-TAATTGAG
1 TTTAAGTATAATT--G
* *
9406 CTTGAG--TAA-TG
1 TTTAAGTATAATTG
9417 TTTAAGTATAATTG
1 TTTAAGTATAATTG
9431 TT
1 TT
9433 AGGAAATATA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
11 5 0.11
12 3 0.07
13 14 0.31
14 18 0.40
15 5 0.11
ACGTcount: A:0.33, C:0.01, G:0.17, T:0.48
Consensus pattern (14 bp):
TTTAAGTATAATTG
Found at i:9392 original size:13 final size:13
Alignment explanation
Indices: 9359--9401 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
9349 TACTAACAAT
*
9359 TAATATTTAAGTA
1 TAATGTTTAAGTA
9372 TAATTGTTTAAGTA
1 TAA-TGTTTAAGTA
9386 TAATGTTTAAGT-
1 TAATGTTTAAGTA
9398 TAAT
1 TAAT
9402 TGAGCTTGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 12 0.43
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.49
Consensus pattern (13 bp):
TAATGTTTAAGTA
Found at i:9822 original size:12 final size:12
Alignment explanation
Indices: 9782--9869 Score: 58
Period size: 13 Copynumber: 7.3 Consensus size: 12
9772 ATGCATTAAG
* *
9782 GCATGAAAGGAT
1 GCATAAAAGAAT
*
9794 GCCATAAATAAAAT
1 G-CATAAA-AGAAT
9808 GCATAAAAGAAT
1 GCATAAAAGAAT
*
9820 GCAT-TAAG---
1 GCATAAAAGAAT
*
9828 GCATGAAAGAAT
1 GCATAAAAGAAT
*
9840 GCCATAAATAAAAT
1 G-CATAAA-AGAAT
9854 GCATAAAAGAAT
1 GCATAAAAGAAT
9866 GCAT
1 GCAT
9870 TAAGGCATGA
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
8 4 0.07
9 3 0.05
11 3 0.05
12 18 0.31
13 22 0.37
14 9 0.15
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.19
Consensus pattern (12 bp):
GCATAAAAGAAT
Found at i:9822 original size:46 final size:45
Alignment explanation
Indices: 9750--10484 Score: 586
Period size: 46 Copynumber: 16.3 Consensus size: 45
9740 AAACCGAATA
*
9750 CATAAATAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGC
1 CATAAATAAAATGCAT-AAAAGATGCATTAAGGCATGAAAGGATGC
*
9796 CATAAATAAAATGCATAAAAGAATGCATTAAGGCATGAAAGAATGC
1 CATAAATAAAATGCATAAAAG-ATGCATTAAGGCATGAAAGGATGC
*
9842 CATAAATAAAATGCATAAAAGAATGCATTAAGGCATGAAAGGATTC
1 CATAAATAAAATGCATAAAAG-ATGCATTAAGGCATGAAAGGATGC
*
9888 CATAAATAAAATGCATCAAAAGATGCATTAAGACATGAAA-GATGC
1 CATAAATAAAATGCAT-AAAAGATGCATTAAGGCATGAAAGGATGC
* *
9933 CATAAATAAAATGCAT--GA-ATGCATTAAGGCATGAAATGATG-
1 CATAAATAAAATGCATAAAAGATGCATTAAGGCATGAAAGGATGC
* * * * * *
9974 CAT---T--AAGGCATGAAAGGATGTCGTAAATAAAATGCATGAAATGATGA
1 CATAAATAAAATGCAT-AAAAGATG-C----AT-TAAGGCATGAAAGGATGC
* * * *
10021 CATAAATTAAATGCATGAAAGGATGCATTAAGGCATGAAAGTATGT
1 CATAAATAAAATGCAT-AAAAGATGCATTAAGGCATGAAAGGATGC
* * *
10067 CGTAAATAAAA-GCATGAAAGGATGCATTAAGGCATGAATGGATGC
1 CATAAATAAAATGCAT-AAAAGATGCATTAAGGCATGAAAGGATGC
* * *
10112 CGTAAATAAAATGCATGAAATGATACATTAAGGCAT-AAAGGATG-
1 CATAAATAAAATGCAT-AAAAGATGCATTAAGGCATGAAAGGATGC
* * *
10156 CAT---T--AAGGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATG-
1 CATAAATAAAATGCAT-AAAAGATG-CAT---T--AAGGCATGAAAGGATGC
* *** * *
10202 CATTAA-GGCATG-A-AGGATGCAT----TAAGGCATGAAAGGATGC
1 CATAAATAAAATGCATA-AAAG-ATGCATTAAGGCATGAAAGGATGC
* *
10242 CATAAATAAAATGCATGAAATGATGCATTAAGGAATGAAAGGATGC
1 CATAAATAAAATGCAT-AAAAGATGCATTAAGGCATGAAAGGATGC
* * *
10288 CATAAATAAAATACATGAAAGGATGTATTAAGGCATGAAAGGATGC
1 CATAAATAAAATGCAT-AAAAGATGCATTAAGGCATGAAAGGATGC
* * * * *
10334 CATAAATAAAATGCATGAAATGATGTATTAAGGCGTGAAAAGATAC
1 CATAAATAAAATGCAT-AAAAGATGCATTAAGGCATGAAAGGATGC
* ** *
10380 CATAAATAAAATGCATGAAATGATTTATTAAGGCATGAAAGGATGT
1 CATAAATAAAATGCAT-AAAAGATGCATTAAGGCATGAAAGGATGC
* * * * *
10426 CATAAATAAAATGCATGAAATGATGCATTATGGCATAAAATGATGT
1 CATAAATAAAATGCAT-AAAAGATGCATTAAGGCATGAAAGGATGC
10472 CATAAATAAAATG
1 CATAAATAAAATG
10485 AAATTTAACG
Statistics
Matches: 584, Mismatches: 62, Indels: 86
0.80 0.08 0.12
Matches are distributed among these distances:
36 6 0.01
38 1 0.00
39 28 0.05
40 11 0.02
41 26 0.04
42 8 0.01
43 4 0.01
44 3 0.01
45 81 0.14
46 381 0.65
47 11 0.02
48 2 0.00
49 3 0.01
50 3 0.01
51 1 0.00
52 15 0.03
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.23
Consensus pattern (45 bp):
CATAAATAAAATGCATAAAAGATGCATTAAGGCATGAAAGGATGC
Found at i:10010 original size:26 final size:25
Alignment explanation
Indices: 9981--10131 Score: 108
Period size: 26 Copynumber: 6.3 Consensus size: 25
9971 ATGCATTAAG
9981 GCATGAAAGGATGTCGTAAATAAAAT
1 GCATGAAAGGATG-CGTAAATAAAAT
* * *
10007 GCATGAAATGATGACATAAATTAAAT
1 GCATGAAAGGATG-CGTAAATAAAAT
* *
10033 GCATGAAAGGATGC----AT-TAAG
1 GCATGAAAGGATGCGTAAATAAAAT
*
10053 GCATGAAAGTATGTCGTAAATAAAA-
1 GCATGAAAGGATG-CGTAAATAAAAT
* *
10078 GCATGAAAGGATGC----AT-TAAG
1 GCATGAAAGGATGCGTAAATAAAAT
*
10098 GCATGAATGGATGCCGTAAATAAAAT
1 GCATGAAAGGATG-CGTAAATAAAAT
10124 GCATGAAA
1 GCATGAAA
10132 TGATACATTA
Statistics
Matches: 97, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
19 2 0.02
20 28 0.29
21 4 0.04
24 1 0.01
25 17 0.18
26 45 0.46
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (25 bp):
GCATGAAAGGATGCGTAAATAAAAT
Found at i:10152 original size:65 final size:66
Alignment explanation
Indices: 10078--10424 Score: 368
Period size: 65 Copynumber: 5.2 Consensus size: 66
10068 GTAAATAAAA
* * *
10078 GCATGAAAGGATGCATTAAGGCATGAATGGATGCCGTAAATAAAATGCATGAAATGATACATTAA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGATGCATTAA
10143 G
66 G
*
10144 GCAT-AAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGATGCATTAA
10208 G
66 G
10209 GCATG-AAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGATGCATTAA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGATGCATTAA
10273 G
66 G
* ** * * *
10274 GAATGAAAGGATGCCATAAATAAAATACATGAAAGGATG---T--AT-TAAGGCATGAAAGGATG
1 GCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGATG
*
10333 CCATAAATAAAAT
60 -CAT---T--AAG
* * * * * **
10346 GCATGAAATGATGTATTAAGGCGTGAAAAGATACCATAAATAAAATGCATGAAATGATTTATTAA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGATGCATTAA
10411 G
66 G
10412 GCATGAAAGGATG
1 GCATGAAAGGATG
10425 TCATAAATAA
Statistics
Matches: 234, Mismatches: 27, Indels: 40
0.78 0.09 0.13
Matches are distributed among these distances:
65 124 0.53
66 50 0.21
67 8 0.03
68 2 0.01
69 2 0.01
70 2 0.01
71 6 0.03
72 40 0.17
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.22
Consensus pattern (66 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATGATGCATTAA
G
Found at i:10161 original size:19 final size:20
Alignment explanation
Indices: 9762--10333 Score: 214
Period size: 20 Copynumber: 25.7 Consensus size: 20
9752 TAAATAAAAT
*
9762 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
9782 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
* *
9808 GCATAAAAGAATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
9828 GCATGAAAGAATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
* *
9854 GCATAAAAGAATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
9874 GCATGAAAGGATTCCATAAATAAAAT
1 GCATGAAAGGA-TGCAT---T--AAG
* *
9900 GCATCAAAAGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * *
9920 ACATGAAA-GATGCCATAAATA
1 GCATGAAAGGATG-CATTAA-G
** * * *
9941 AAATGCATGAATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
9961 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
9981 GCATGAAAGGATGTCGTAAATAAAAT
1 GCATGAAAGGATG-C----AT-TAAG
* *
10007 GCATGAAATGATGACATAAATTAAAT
1 GCATGAAAGGATG-C----ATT-AAG
10033 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * *
10053 GCATGAAAGTATGTCGTAAATAAAA
1 GCATGAAAGGATG-C----ATTAAG
10078 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * *
10098 GCATGAATGGATGCCGTAAATAAAAT
1 GCATGAAAGGATG-C----AT-TAAG
* *
10124 GCATGAAATGATACATTAAG
1 GCATGAAAGGATGCATTAAG
10144 GCAT-AAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
10163 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
10189 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
10209 GCATG-AAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
10228 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
10254 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
10274 GAATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
* *
10300 ACATGAAAGGATGTATTAAG
1 GCATGAAAGGATGCATTAAG
10320 GCATGAAAGGATGC
1 GCATGAAAGGATGC
10334 CATAAATAAA
Statistics
Matches: 421, Mismatches: 72, Indels: 118
0.69 0.12 0.19
Matches are distributed among these distances:
19 40 0.10
20 161 0.38
21 37 0.09
22 9 0.02
24 7 0.02
25 40 0.10
26 127 0.30
ACGTcount: A:0.46, C:0.10, G:0.22, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:20228 original size:23 final size:22
Alignment explanation
Indices: 20174--20234 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
20164 TTTGGTGCAG
*
20174 AGGGAATTGA-TCCCCCCTTGA
1 AGGGAACTGATTCCCCCCTTGA
* *
20195 A-GGAACCGATTCCCCCTTTGA
1 AGGGAACTGATTCCCCCCTTGA
20216 AGGGGAACTGATTCCCCCC
1 A-GGGAACTGATTCCCCCC
20235 ACAGGGGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 6 0.19
21 12 0.38
23 14 0.44
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21
Consensus pattern (22 bp):
AGGGAACTGATTCCCCCCTTGA
Found at i:20253 original size:21 final size:21
Alignment explanation
Indices: 20216--20255 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20206 CCCCCTTTGA
*
20216 AGGGGAACTGATTCCCCCCAC
1 AGGGGAACTGATACCCCCCAC
20237 AGGGGAA-TCGATACCCCCC
1 AGGGGAACT-GATACCCCCC
20256 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (21 bp):
AGGGGAACTGATACCCCCCAC
Found at i:24589 original size:46 final size:46
Alignment explanation
Indices: 24522--25294 Score: 1183
Period size: 46 Copynumber: 16.8 Consensus size: 46
24512 AACCAAATAC
* *
24522 ATGCATTAAGGCATGAAAGGATGACATAAATAAAATGCTTGAAATG
1 ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
*
24568 ATGCATTAAGGCATGAAAGGATGCCACAAATAAAATGCATGAAATG
1 ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
* *
24614 ATGCATTAAGGCATGAAAGGATGTCATAAATAAAATACATGAAATG
1 ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
* * *
24660 ATGCATTATGGAATGAAAGGATGCCATAAATAAAATGCATGAAAGG
1 ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
*
24706 ATGCATTAAGGCATGAAAGCATGCCATAAATAAAATGCATGAAATG
1 ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
* * *
24752 ATGCATTAAGGAATGAAAGGATGTCATAAATAAAATACATGAAATG
1 ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
* *
24798 ATGCATTAAGGCATGAAATGATGCCATAAATAAAATGAATGAAA-G
1 ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
* * *
24843 AATGAATTAAGGCATGAAAGGATGTCGTAAATAAAATGCATGAAATG
1 -ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
24890 ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
1 ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
* * * * *
24936 ATACATTAAGGTATGAAAGGGTGTCATAAATAAAATGCATGAAAGG
1 ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
* *
24982 ATGCATTAAGGTATGAAAGGATGACATAAATAAAATGCATGAAA-G
1 ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
* *
25027 TATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATAAAAGG
1 -ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
* * *
25074 ATGCATTAAGGCATGAAAGGATGCAATAAATAAAATGAATGAAAGG
1 ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
*
25120 ATGCATTAAGGCATGAAAGGATTCCATAAATAAAA-GCATGAAATG
1 ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
* *
25165 ATGCATTAAGGTATGAAAGGATGCCATAAATAAAAATTCATGAAATG
1 ATGCATTAAGGCATGAAAGGATGCCATAAAT-AAAATGCATGAAATG
25212 ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
1 ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
* **
25258 ATGCATTAAGGCATGAAATGATATCATAAATAAAATG
1 ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATG
25295 AAATTTAAAT
Statistics
Matches: 663, Mismatches: 58, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
45 39 0.06
46 583 0.88
47 41 0.06
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.23
Consensus pattern (46 bp):
ATGCATTAAGGCATGAAAGGATGCCATAAATAAAATGCATGAAATG
Found at i:25798 original size:2 final size:2
Alignment explanation
Indices: 25791--25854 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
25781 GAAATGATGT
25791 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25833 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
25855 CTTAAAATGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28393 original size:20 final size:20
Alignment explanation
Indices: 28368--28420 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
28358 ATTTTGAAGA
28368 AACCCCAATGGCTCCAAAAT
1 AACCCCAATGGCTCCAAAAT
28388 AACCCCAATGGCTCCAAAAT
1 AACCCCAATGGCTCCAAAAT
* *
28408 ATCCCCAACGGCT
1 AACCCCAATGGCT
28421 AGAAACGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.36, C:0.38, G:0.11, T:0.15
Consensus pattern (20 bp):
AACCCCAATGGCTCCAAAAT
Found at i:33012 original size:17 final size:18
Alignment explanation
Indices: 32990--33041 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
32980 AATTGGAGTG
32990 CAAAAAGAAAGAAAAGA-
1 CAAAAAGAAAGAAAAGAT
33007 CAAAAAGAAGAGAAAA-AT
1 CAAAAAGAA-AGAAAAGAT
33025 CAGAAAAG-AAGAAAAGA
1 CA-AAAAGAAAGAAAAGA
33042 AGAAGAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 16 0.52
18 10 0.32
19 5 0.16
ACGTcount: A:0.73, C:0.06, G:0.19, T:0.02
Consensus pattern (18 bp):
CAAAAAGAAAGAAAAGAT
Found at i:33022 original size:11 final size:11
Alignment explanation
Indices: 32997--33068 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
32987 GTGCAAAAAG
32997 AAAGAAAAGACAA
1 AAAGAAAAG--AA
*
33010 AAAGAAGAGAA
1 AAAGAAAAGAA
* *
33021 AAATCAGAA-AA
1 AAA-GAAAAGAA
*
33032 GAAGAAAAGAA
1 AAAGAAAAGAA
*
33043 GAAGAAAAG-A
1 AAAGAAAAGAA
33053 AAAGAAAAGAA
1 AAAGAAAAGAA
33064 AAAGA
1 AAAGA
33069 GAAGTTCAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
10 12 0.25
11 26 0.54
12 2 0.04
13 8 0.17
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:33034 original size:5 final size:5
Alignment explanation
Indices: 32992--33065 Score: 61
Period size: 5 Copynumber: 15.8 Consensus size: 5
32982 TTGGAGTGCA
* * **
32992 AAAAG -AAAG AAAAG -ACA- AAAAG AAGAG AAAA- ATCAG AAAAG --AAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
33036 AAAAG AAGAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AA-AAG AAAAG AAAAG AAAAG AAAA
33066 AGAGAAGTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
3 3 0.06
4 10 0.19
5 36 0.67
6 5 0.09
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:33037 original size:8 final size:8
Alignment explanation
Indices: 32992--33058 Score: 57
Period size: 8 Copynumber: 7.9 Consensus size: 8
32982 TTGGAGTGCA
32992 AAAAGAAAG
1 AAAAG-AAG
33001 AAAAGACA-
1 AAAAGA-AG
33009 AAAAGAAG
1 AAAAGAAG
*
33017 AGAAAAATCAG
1 A-AAAGA--AG
33028 AAAAGAAG
1 AAAAGAAG
33036 AAAAGAAG
1 AAAAGAAG
33044 AAGAA-AAG
1 AA-AAGAAG
33052 AAAAGAA
1 AAAAGAA
33059 AAGAAAAAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
7 3 0.06
8 27 0.55
9 12 0.24
10 4 0.08
11 3 0.06
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (8 bp):
AAAAGAAG
Found at i:33045 original size:16 final size:17
Alignment explanation
Indices: 32992--33057 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 17
32982 TTGGAGTGCA
32992 AAAAGAAAGAAAAGACA-
1 AAAAG-AAGAAAAGACAG
*
33009 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGA-AAAGA-CAG
33028 AAAAGAAGAAAAGA-AG
1 AAAAGAAGAAAAGACAG
33044 AAGAA-AAGAAAAGA
1 AA-AAGAAGAAAAGA
33058 AAAGAAAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
16 17 0.40
17 11 0.26
18 6 0.14
19 9 0.21
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.02
Consensus pattern (17 bp):
AAAAGAAGAAAAGACAG
Found at i:33058 original size:16 final size:15
Alignment explanation
Indices: 32992--33065 Score: 61
Period size: 13 Copynumber: 5.3 Consensus size: 15
32982 TTGGAGTGCA
32992 AAAAG-AAAGAAAAG
1 AAAAGAAAAGAAAAG
* *
33006 -ACA-AAAAGAAGAG
1 AAAAGAAAAGAAAAG
**
33019 AAAA-ATCAGAAAAG
1 AAAAGAAAAGAAAAG
33033 --AAGAAAAGAAGAAG
1 AAAAGAAAAGAA-AAG
33047 AAAAGAAAAGAAAAG
1 AAAAGAAAAGAAAAG
33062 AAAA
1 AAAA
33066 AGAGAAGTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
12 2 0.04
13 15 0.33
14 12 0.26
15 7 0.15
16 10 0.22
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (15 bp):
AAAAGAAAAGAAAAG
Found at i:33068 original size:16 final size:16
Alignment explanation
Indices: 33033--33065 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
33023 ATCAGAAAAG
33033 AAGAAAAGAAGAAGAA
1 AAGAAAAGAAGAAGAA
33049 AAGAAAAGAA-AAGAA
1 AAGAAAAGAAGAAGAA
33064 AA
1 AA
33066 AGAGAAGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAGAAAAGAAGAAGAA
Found at i:39437 original size:74 final size:74
Alignment explanation
Indices: 39316--39461 Score: 292
Period size: 74 Copynumber: 2.0 Consensus size: 74
39306 GAAGCTGATT
39316 CCTTGCAAACATCCCTGACATGGCTTCACGGTGTTCTACAAGGTAAAATAGGTCATGGATTGGAT
1 CCTTGCAAACATCCCTGACATGGCTTCACGGTGTTCTACAAGGTAAAATAGGTCATGGATTGGAT
39381 ACCAGGGCA
66 ACCAGGGCA
39390 CCTTGCAAACATCCCTGACATGGCTTCACGGTGTTCTACAAGGTAAAATAGGTCATGGATTGGAT
1 CCTTGCAAACATCCCTGACATGGCTTCACGGTGTTCTACAAGGTAAAATAGGTCATGGATTGGAT
39455 ACCAGGG
66 ACCAGGG
39462 TCCTTGAAGG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (74 bp):
CCTTGCAAACATCCCTGACATGGCTTCACGGTGTTCTACAAGGTAAAATAGGTCATGGATTGGAT
ACCAGGGCA
Found at i:44215 original size:17 final size:17
Alignment explanation
Indices: 44177--44222 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
44167 AAGATCAGAA
*
44177 TTAAATTATTAATATAT
1 TTAAATTATAAATATAT
*
44194 CTAAATATATAAATA-AT
1 TTAAAT-TATAAATATAT
44211 TTAAATT-TAAAT
1 TTAAATTATAAAT
44223 TTTAAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 5 0.20
16 1 0.04
17 12 0.48
18 7 0.28
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAATTATAAATATAT
Found at i:44222 original size:23 final size:22
Alignment explanation
Indices: 44178--44238 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 22
44168 AGATCAGAAT
44178 TAAATT-ATTAATATATCTAAATATA
1 TAAATTAATTAA-AT-T-TAAAT-TA
*
44203 TAAA-TAATTTAAATTTAAATTT
1 TAAATTAA-TTAAATTTAAATTA
44225 TAAATTAATTAAAT
1 TAAATTAATTAAAT
44239 CCACACAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
22 11 0.34
23 8 0.25
24 2 0.06
25 7 0.22
26 4 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAATTAATTAAATTTAAATTA
Found at i:47372 original size:14 final size:14
Alignment explanation
Indices: 47353--47384 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
47343 AGTGCATACC
47353 AAGAAATAAAGAAT
1 AAGAAATAAAGAAT
47367 AAGAAATAAAGAAT
1 AAGAAATAAAGAAT
47381 AAGA
1 AAGA
47385 TAGATGATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (14 bp):
AAGAAATAAAGAAT
Found at i:48171 original size:23 final size:23
Alignment explanation
Indices: 48141--48201 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
48131 CATTATTATA
48141 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
48164 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
48187 CGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
48202 TTTATACGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.25
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:48315 original size:2 final size:2
Alignment explanation
Indices: 48308--48350 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
48298 TAACAAATAC
48308 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48350 T
1 T
48351 GATGGATATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51890 original size:13 final size:13
Alignment explanation
Indices: 51874--51902 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
51864 TTACTTCTAA
51874 TTTTATTATTAGT
1 TTTTATTATTAGT
51887 TTTTATTATTAGT
1 TTTTATTATTAGT
51900 TTT
1 TTT
51903 CTCTAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (13 bp):
TTTTATTATTAGT
Found at i:56188 original size:36 final size:36
Alignment explanation
Indices: 56141--56452 Score: 229
Period size: 36 Copynumber: 8.9 Consensus size: 36
56131 AAAAACGTTT
**
56141 ATATATGTTTTCAAAAATTGTTTTCGAAATTATATA
1 ATATATGTTTTCAAAAATTGTTTTTAAAATTATATA
* *
56177 ATATATGTTTTCAAAAGTTGTTTTTCAAA--A-AT-
1 ATATATGTTTTCAAAAATTGTTTTTAAAATTATATA
* * * * *
56209 ATGTA---TTTCCAAATTTTTTTTTGAAATTATATA
1 ATATATGTTTTCAAAAATTGTTTTTAAAATTATATA
* * *
56242 ATAAATGTTTTCAAAATTTTGTTTTTAAAAATATATA
1 ATATATGTTTTCAAAA-ATTGTTTTTAAAATTATATA
* * *
56279 TTATACGTTTTCAAAAATTGTTTTTGAAAA--CTAT-
1 ATATATGTTTTCAAAAATTGTTTTT-AAAATTATATA
* * *
56313 ATATATGTTTTCAAAAACTATTTTTAAAACTATATA
1 ATATATGTTTTCAAAAATTGTTTTTAAAATTATATA
* * *
56349 ATATACG-TTTCAAAATATTATTTTTAAAAATATATA
1 ATATATGTTTTCAAAA-ATTGTTTTTAAAATTATATA
* * * *
56385 ATATATGTTTTTAAAACA-TATTTTCAAAATCATAT-
1 ATATATGTTTTCAAAA-ATTGTTTTTAAAATTATATA
* *
56420 -TATATATTTTCAAAAAAATGATTTTTAAAATTA
1 ATATATGTTTTC-AAAAATTG-TTTTTAAAATTA
56453 AAAACGTTTA
Statistics
Matches: 221, Mismatches: 38, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
29 17 0.08
31 1 0.00
32 6 0.03
33 9 0.04
34 32 0.14
35 19 0.09
36 95 0.43
37 42 0.19
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.47
Consensus pattern (36 bp):
ATATATGTTTTCAAAAATTGTTTTTAAAATTATATA
Found at i:56250 original size:65 final size:65
Alignment explanation
Indices: 56143--56280 Score: 190
Period size: 65 Copynumber: 2.1 Consensus size: 65
56133 AAACGTTTAT
*
56143 ATATGT-TTTCAAAAATTGTTTTCGAAATTATATAATATATGTTTTCAAAA-GTTGTTTTTCAAA
1 ATATGTATTTCAAAAATTGTTTTCGAAATTATATAATAAATGTTTTCAAAATGTTGTTTTT-AAA
56206 A
65 A
* * * * *
56207 ATATGTATTTCCAAATTTTTTTTTGAAATTATATAATAAATGTTTTCAAAATTTTGTTTTTAAAA
1 ATATGTATTTCAAAAATTGTTTTCGAAATTATATAATAAATGTTTTCAAAATGTTGTTTTTAAAA
*
56272 ATATATATT
1 ATATGTATT
56281 ATACGTTTTC
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
64 6 0.09
65 51 0.78
66 8 0.12
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (65 bp):
ATATGTATTTCAAAAATTGTTTTCGAAATTATATAATAAATGTTTTCAAAATGTTGTTTTTAAAA
Found at i:56395 original size:22 final size:22
Alignment explanation
Indices: 56362--56405 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
56352 TACGTTTCAA
*
56362 AATATTATTTTTAAAAATATAT
1 AATATTATTTTTAAAAACATAT
*
56384 AATA-TATGTTTTTAAAACATAT
1 AATATTAT-TTTTAAAAACATAT
56406 TTTCAAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
AATATTATTTTTAAAAACATAT
Found at i:56424 original size:106 final size:109
Alignment explanation
Indices: 56226--56449 Score: 262
Period size: 106 Copynumber: 2.1 Consensus size: 109
56216 TCCAAATTTT
* * * * * *
56226 TTTTTGAAATTATATAATAAATGTTTTCAAAATTTTGTTTTTAAAAATATATATTATACGTTTTC
1 TTTTTAAAACTATATAATAAACGTTTTCAAAATATTATTTTTAAAAATATATAATATACGTTTTC
* * * *
56291 AAAAATTGTTTTTGAAAACTATATATATGTTTTC-AAAAACT-A
66 AAAAATTGATTTTCAAAACTATATATATATTTTCAAAAAAATGA
* * *
56333 TTTTTAAAACTATATAATATACG-TTTCAAAATATTATTTTTAAAAATATATAATATATGTTTTT
1 TTTTTAAAACTATATAATAAACGTTTTCAAAATATTATTTTTAAAAATATATAATATACGTTTTC
56397 AAAACA-T-ATTTTCAAAA-TCATATTATATATTTTCAAAAAAATGA
66 AAAA-ATTGATTTTCAAAACT-ATA-TATATATTTTCAAAAAAATGA
56441 TTTTTAAAA
1 TTTTTAAAA
56450 TTAAAAACGT
Statistics
Matches: 99, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
104 1 0.01
105 11 0.11
106 51 0.52
107 26 0.26
108 10 0.10
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (109 bp):
TTTTTAAAACTATATAATAAACGTTTTCAAAATATTATTTTTAAAAATATATAATATACGTTTTC
AAAAATTGATTTTCAAAACTATATATATATTTTCAAAAAAATGA
Found at i:60693 original size:15 final size:13
Alignment explanation
Indices: 60662--60699 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
60652 ACTTATCAAC
60662 GAGAGAAAACTAG
1 GAGAGAAAACTAG
60675 GAGAGAAAACTAG
1 GAGAGAAAACTAG
60688 GAGAGAAAACTA
1 GAGAGAAAACTA
60700 ACTTTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.55, C:0.08, G:0.29, T:0.08
Consensus pattern (13 bp):
GAGAGAAAACTAG
Found at i:63678 original size:17 final size:18
Alignment explanation
Indices: 63647--63686 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
63637 CCTTTAAAAA
63647 ATTTTAAATTCTTTTTAT
1 ATTTTAAATTCTTTTTAT
* *
63665 ATTTT-AATTTTTTTTGT
1 ATTTTAAATTCTTTTTAT
63682 ATTTT
1 ATTTT
63687 CTATTAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (18 bp):
ATTTTAAATTCTTTTTAT
Found at i:63825 original size:12 final size:13
Alignment explanation
Indices: 63792--63831 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
63782 TAGTGAGATA
63792 AATATATATA-T-
1 AATATATATATTC
63803 ATATATATATATTC
1 A-ATATATATATTC
63817 AATAT-TATATTC
1 AATATATATATTC
63829 AAT
1 AAT
63832 GAGATTACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 1 0.04
12 19 0.73
13 5 0.19
14 1 0.04
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATATATTC
Done.