Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005569.1 Hibiscus syriacus cultivar Beakdansim tig00012917_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: 79868
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2030 original size:34 final size:34
Alignment explanation
Indices: 1987--2067 Score: 135
Period size: 34 Copynumber: 2.4 Consensus size: 34
1977 ATATGAAGAC
*
1987 TATGGTAGGTTCATTCGATGTTGGTAATTCCTTG
1 TATGGTAGGTTCAGTCGATGTTGGTAATTCCTTG
*
2021 TATGGTAGGTTCAGTCGCTGTTGGTAATTCCTTG
1 TATGGTAGGTTCAGTCGATGTTGGTAATTCCTTG
*
2055 TATAGTAGGTTCA
1 TATGGTAGGTTCA
2068 ACACCGACTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.19, C:0.12, G:0.27, T:0.42
Consensus pattern (34 bp):
TATGGTAGGTTCAGTCGATGTTGGTAATTCCTTG
Found at i:2915 original size:2 final size:2
Alignment explanation
Indices: 2908--2937 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2898 GATTTCAAAA
*
2908 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2938 GAATAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6219 original size:21 final size:21
Alignment explanation
Indices: 6193--6265 Score: 128
Period size: 21 Copynumber: 3.5 Consensus size: 21
6183 CAGAGGAGGA
6193 AGAAGAAGAAATGATGGACGG
1 AGAAGAAGAAATGATGGACGG
*
6214 AGAAGAAGAAATGATGGATGG
1 AGAAGAAGAAATGATGGACGG
*
6235 AGAAGAAGAAATAATGGACGG
1 AGAAGAAGAAATGATGGACGG
6256 AGAAGAAGAA
1 AGAAGAAGAA
6266 GTGAGAGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.52, C:0.03, G:0.36, T:0.10
Consensus pattern (21 bp):
AGAAGAAGAAATGATGGACGG
Found at i:6290 original size:42 final size:42
Alignment explanation
Indices: 6193--6283 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
6183 CAGAGGAGGA
* * *
6193 AGAAGAAGAAATGATGGACGGAGAAGAAGAAATGATGGATGG
1 AGAAGAAGAAATAATGGACGGAGAAGAAGAAATGAAGGAAGG
*
6235 AGAAGAAGAAATAATGGACGGAGAAGAAGAAGTGAGAGGAAGG
1 AGAAGAAGAAATAATGGACGGAGAAGAAGAAATGA-AGGAAGG
6278 -GAAGAA
1 AGAAGAA
6284 AGAATAAGGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 39 0.89
43 5 0.11
ACGTcount: A:0.51, C:0.02, G:0.38, T:0.09
Consensus pattern (42 bp):
AGAAGAAGAAATAATGGACGGAGAAGAAGAAATGAAGGAAGG
Found at i:9578 original size:3 final size:3
Alignment explanation
Indices: 9570--9608 Score: 51
Period size: 3 Copynumber: 12.0 Consensus size: 3
9560 TTTTTCCTTG
9570 TCT TCT TCTT TCAT TCT TCT TCT TCAT TCT TCT TCT TCT
1 TCT TCT TC-T TC-T TCT TCT TCT TC-T TCT TCT TCT TCT
9609 CTTTGGCTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
3 24 0.73
4 9 0.27
ACGTcount: A:0.05, C:0.31, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:9597 original size:13 final size:13
Alignment explanation
Indices: 9570--9607 Score: 67
Period size: 13 Copynumber: 2.8 Consensus size: 13
9560 TTTTTCCTTG
9570 TCTTCTTCTTTCAT
1 TCTTCTTC-TTCAT
9584 TCTTCTTCTTCAT
1 TCTTCTTCTTCAT
9597 TCTTCTTCTTC
1 TCTTCTTCTTC
9608 TCTTTGGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.67
14 8 0.33
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.63
Consensus pattern (13 bp):
TCTTCTTCTTCAT
Found at i:10981 original size:22 final size:22
Alignment explanation
Indices: 10956--11012 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
10946 CACTCTCTAA
* *
10956 GACGACATCTGTCCCCATCTCC
1 GACGAAATCCGTCCCCATCTCC
10978 GACGAAATCCGTCCCCATCTCC
1 GACGAAATCCGTCCCCATCTCC
**
11000 GGTGAAATCCGTC
1 GACGAAATCCGTC
11013 TATCTCCATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.40, G:0.18, T:0.21
Consensus pattern (22 bp):
GACGAAATCCGTCCCCATCTCC
Found at i:11382 original size:20 final size:20
Alignment explanation
Indices: 11359--11409 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
11349 TTAAATTCGC
*
11359 AACACGAAAATGAAAATCGT
1 AACACCAAAATGAAAATCGT
**
11379 AACACCAAAATGAAAATCAC
1 AACACCAAAATGAAAATCGT
11399 AACACCAAAAT
1 AACACCAAAAT
11410 CGCAACGCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.59, C:0.22, G:0.08, T:0.12
Consensus pattern (20 bp):
AACACCAAAATGAAAATCGT
Found at i:13287 original size:21 final size:21
Alignment explanation
Indices: 13263--13304 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13253 CGCTACATGG
* * *
13263 TGAGGTATCTACTTTACGTGA
1 TGAGGTAGCCACTCTACGTGA
13284 TGAGGTAGCCACTCTACGTGA
1 TGAGGTAGCCACTCTACGTGA
13305 GATTATTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (21 bp):
TGAGGTAGCCACTCTACGTGA
Found at i:13638 original size:42 final size:42
Alignment explanation
Indices: 13586--13702 Score: 146
Period size: 42 Copynumber: 2.8 Consensus size: 42
13576 GATTCACCTG
* *
13586 TCATCGTTCAAGAGGCGCCTC-CTATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTCAC-ACCGTTCAAGAGGCCCCTC
* * *
13628 TCATCATTCAAGAGGCCCCTCACACCGTTCAAGAGGCCCGTG
1 TCATCGTTCAAGAGGCCCCTCACACCGTTCAAGAGGCCCCTC
* * *
13670 TCATCGTTCAAGAGGTCCCTCCCACTGTTCAAG
1 TCATCGTTCAAGAGGCCCCTCACACCGTTCAAG
13703 TGCCAGATTC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 64 0.98
43 1 0.02
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCACACCGTTCAAGAGGCCCCTC
Found at i:13699 original size:21 final size:20
Alignment explanation
Indices: 13587--13702 Score: 108
Period size: 21 Copynumber: 5.5 Consensus size: 20
13577 ATTCACCTGT
13587 CATCGTTCAAGAGGCGCCTCC
1 CATCGTTCAAGAGGC-CCTCC
* *
13608 TATCGTTCAAGAGGCCCCTCT
1 CATCGTTCAAGAGG-CCCTCC
* *
13629 CATCATTCAAGAGGCCCCTCA
1 CATCGTTCAAGAGG-CCCTCC
* **
13650 CACCGTTCAAGAGGCCCGTGT
1 CATCGTTCAAGAGGCCC-TCC
13671 CATCGTTCAAGAGGTCCCTCC
1 CATCGTTCAAGAGG-CCCTCC
13692 CA-CTGTTCAAG
1 CATC-GTTCAAG
13703 TGCCAGATTC
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
20 4 0.05
21 71 0.90
22 4 0.05
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.22
Consensus pattern (20 bp):
CATCGTTCAAGAGGCCCTCC
Found at i:15635 original size:19 final size:21
Alignment explanation
Indices: 15611--15654 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
15601 TTACAGACAG
15611 ATATCTCGTCA-CATATC-TT
1 ATATCTCGTCATCATATCATT
*
15630 ATATCTTGTCATCATATCATT
1 ATATCTCGTCATCATATCATT
15651 ATAT
1 ATAT
15655 ATAAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
20 6 0.27
21 6 0.27
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (21 bp):
ATATCTCGTCATCATATCATT
Found at i:17809 original size:64 final size:64
Alignment explanation
Indices: 17694--17851 Score: 271
Period size: 64 Copynumber: 2.5 Consensus size: 64
17684 TTAATTGAAT
17694 TTTACATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
1 TTTA-ATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
* * * *
17759 TTTAATTTATTTATAAAAGTTGATTTGTTTAATTGATGTGTAAATAAGAATTATTTTTTGCTTG
1 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
17823 TTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTAATTGATTTGTAAAAGTTGATTTGTT
17852 GTTAAATTAA
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
64 83 0.95
65 4 0.05
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.51
Consensus pattern (64 bp):
TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
Found at i:17989 original size:34 final size:34
Alignment explanation
Indices: 17914--17990 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 34
17904 CTTTCACAAC
* * *
17914 GCGATTTTCTCGCTGTGATAGTCAAATTCGCATT
1 GCGATTTTCGCGCTGCGAAAGTCAAATTCGCATT
* * **
17948 GCAATTTTCGCGTTGCGAAAGTCAAATTCGTGTT
1 GCGATTTTCGCGCTGCGAAAGTCAAATTCGCATT
17982 GCGATTTTC
1 GCGATTTTC
17991 AGTTTGTGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (34 bp):
GCGATTTTCGCGCTGCGAAAGTCAAATTCGCATT
Found at i:18070 original size:20 final size:20
Alignment explanation
Indices: 18045--18083 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18035 ATCGCGAAAA
18045 TCGCGTGGCGAATATGACTT
1 TCGCGTGGCGAATATGACTT
* *
18065 TCGCGTTGCGAATTTGACT
1 TCGCGTGGCGAATATGACT
18084 ATTGCAACGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.21, G:0.28, T:0.33
Consensus pattern (20 bp):
TCGCGTGGCGAATATGACTT
Found at i:20735 original size:12 final size:12
Alignment explanation
Indices: 20714--20747 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20704 GGTTGTGGGT
*
20714 TTTGAGATTGTG
1 TTTGATATTGTG
20726 TTTGATATTGTG
1 TTTGATATTGTG
*
20738 TTTGGTATTG
1 TTTGATATTG
20748 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:21365 original size:16 final size:16
Alignment explanation
Indices: 21343--21382 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
21333 GAAATCATTG
*
21343 AAAAATTATATAGAAA
1 AAAAATTATATAAAAA
* *
21359 TAAAATTATGTAAAAA
1 AAAAATTATATAAAAA
21375 AAAAATTA
1 AAAAATTA
21383 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAAATTATATAAAAA
Found at i:21561 original size:19 final size:20
Alignment explanation
Indices: 21537--21629 Score: 93
Period size: 19 Copynumber: 4.7 Consensus size: 20
21527 AACTAAAACC
21537 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAAATTGAAATTCG
*
21556 TGTTGCG-AATTCGAAAATCG
1 TGTTGCGAAATT-GAAATTCG
* *
21576 AGTTGCGAATTTGAAATT-G
1 TGTTGCGAAATTGAAATTCG
* *
21595 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAAATTGAAATTC-G
*
21616 TGTTGCGAATTTGA
1 TGTTGCGAAATTGA
21630 CTTATGTATT
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
18 4 0.06
19 26 0.41
20 17 0.27
21 17 0.27
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (20 bp):
TGTTGCGAAATTGAAATTCG
Found at i:21600 original size:39 final size:41
Alignment explanation
Indices: 21538--21629 Score: 118
Period size: 39 Copynumber: 2.3 Consensus size: 41
21528 ACTAAAACCT
* *
21538 GTTGCGAAATT-AAATTCGTGTTGCGAATTCGAAAATC-GA
1 GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCAGA
* * *
21577 GTTGCGAATTTGAAATT-GAGTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCAGA
21617 GTTGCGAATTTGA
1 GTTGCGAATTTGA
21630 CTTATGTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
39 27 0.59
40 19 0.41
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (41 bp):
GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCAGA
Found at i:23651 original size:6 final size:6
Alignment explanation
Indices: 23642--23680 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
23632 CATTACCATT
23642 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
23681 CGAGCCGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:35774 original size:5 final size:5
Alignment explanation
Indices: 35759--35788 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
35749 AATTTAATAC
35759 TATTT TA-TT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT T
35789 TCTCATTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:35796 original size:19 final size:19
Alignment explanation
Indices: 35759--35807 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
35749 AATTTAATAC
*
35759 TATTTTATTTATTTTATTT
1 TATTTTATTTATTTCATTT
35778 TATTTTATTT-TTCTCATTT
1 TATTTTATTTATT-TCATTT
35797 TGAGTTTTATT
1 T-A-TTTTATT
35808 CTTAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 2 0.08
19 16 0.62
20 1 0.04
21 7 0.27
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (19 bp):
TATTTTATTTATTTCATTT
Found at i:36539 original size:14 final size:14
Alignment explanation
Indices: 36487--36542 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
36477 TGAGTTGAAT
*
36487 ATAAACGAACGAAC
1 ATAAATGAACGAAC
36501 ATAAATG-AC---C
1 ATAAATGAACGAAC
**
36511 ATAAATGAATAAAC
1 ATAAATGAACGAAC
36525 ATAAATGAACGAAC
1 ATAAATGAACGAAC
36539 ATAA
1 ATAA
36543 CGAACAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
13 2 0.06
14 23 0.68
ACGTcount: A:0.59, C:0.14, G:0.11, T:0.16
Consensus pattern (14 bp):
ATAAATGAACGAAC
Found at i:37574 original size:3 final size:3
Alignment explanation
Indices: 37566--37613 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
37556 TCACAGGCCA
37566 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
37614 GTATGCAACC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:40382 original size:9 final size:9
Alignment explanation
Indices: 40370--40421 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
40360 TAATATTTTG
40370 TATTTAATT
1 TATTTAATT
*
40379 TATTTAA-G
1 TATTTAATT
40387 TATTTAATT
1 TATTTAATT
40396 TATTTAA--
1 TATTTAATT
* *
40403 TATTTTACT
1 TATTTAATT
40412 TATTTAATT
1 TATTTAATT
40421 T
1 T
40422 TTTTGCACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:40391 original size:17 final size:17
Alignment explanation
Indices: 40369--40418 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
40359 TTAATATTTT
40369 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
40386 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
40403 -TATTTTACTTATTTAA
1 GTATTTAATTTATTTAA
40419 TTTTTTTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:40414 original size:16 final size:16
Alignment explanation
Indices: 40378--40423 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
40368 TGTATTTAAT
* *
40378 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTTAC
40395 TTATTTAATATTTTAC
1 TTATTTAATATTTTAC
40411 TTATTTAAT-TTTT
1 TTATTTAATATTTT
40424 TTGCACATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTAATATTTTAC
Found at i:41553 original size:2 final size:2
Alignment explanation
Indices: 41546--41577 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41536 TGATAAAAAT
41546 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
41578 CATTTGTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43288 original size:13 final size:13
Alignment explanation
Indices: 43267--43313 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
43257 GTCAGCATAA
43267 GGCGCGCTTCAGG
1 GGCGCGCTTCAGG
*
43280 GGCGTGCTTCAGGG
1 GGCGCGCTTCA-GG
*
43294 GGAGCGCTTCAAGG
1 GGCGCGCTTC-AGG
43308 GG-GCGC
1 GGCGCGC
43314 CTTACCCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 14 0.48
14 14 0.48
15 1 0.03
ACGTcount: A:0.11, C:0.26, G:0.49, T:0.15
Consensus pattern (13 bp):
GGCGCGCTTCAGG
Found at i:49677 original size:18 final size:18
Alignment explanation
Indices: 49654--49693 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
49644 GTTAGGAAAT
49654 AAACGAGTAATTTTCCTA
1 AAACGAGTAATTTTCCTA
49672 AAACGAGTAATTTTCCTA
1 AAACGAGTAATTTTCCTA
49690 AAAC
1 AAAC
49694 TAGATTAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.30
Consensus pattern (18 bp):
AAACGAGTAATTTTCCTA
Found at i:54033 original size:45 final size:45
Alignment explanation
Indices: 53934--54037 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 45
53924 ATGCACAGGA
* *
53934 AGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGTAGTT
1 AGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGTAGTT
*
53979 AGTGCATCGATGCACACCCTT-AAAATGAAAACATCGAAGGT-GATT
1 AGTGCATCGATGCAC-CCATTAAAAATGAAAACATCGAAGGTAG-TT
* *
54024 GGTGTATCGATGCA
1 AGTGCATCGATGCA
54038 TGGGTAGTGC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 1 0.02
45 47 0.90
46 4 0.08
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (45 bp):
AGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGTAGTT
Found at i:54090 original size:20 final size:22
Alignment explanation
Indices: 54045--54102 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
54035 GCATGGGTAG
54045 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
54069 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
54089 TGTATCGATGCACT
1 TGCATCGATGCACT
54103 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:55874 original size:16 final size:16
Alignment explanation
Indices: 55853--55923 Score: 115
Period size: 16 Copynumber: 4.4 Consensus size: 16
55843 GGTATTACCC
*
55853 GACCTGTTTTCAACCT
1 GACCTGTTTTTAACCT
*
55869 GACCTGATTTTAACCT
1 GACCTGTTTTTAACCT
*
55885 GACCTGTTTTTAACTT
1 GACCTGTTTTTAACCT
55901 GACCTGTTTTTAACCT
1 GACCTGTTTTTAACCT
55917 GACCTGT
1 GACCTGT
55924 AAATGATCCG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (16 bp):
GACCTGTTTTTAACCT
Found at i:56218 original size:14 final size:14
Alignment explanation
Indices: 56196--56242 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
56186 TGCAAAGGAA
*
56196 AATTAATATAGTTT
1 AATTTATATAGTTT
56210 AATTTATATA----
1 AATTTATATAGTTT
56220 AA-TTATATAGTTT
1 AATTTATATAGTTT
56233 AATTTATATA
1 AATTTATATA
56243 AATAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:56229 original size:23 final size:24
Alignment explanation
Indices: 56195--56245 Score: 95
Period size: 23 Copynumber: 2.2 Consensus size: 24
56185 ATGCAAAGGA
56195 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
56219 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
56242 AAAT
1 AAAT
56246 AAAAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:56526 original size:2 final size:2
Alignment explanation
Indices: 56521--56564 Score: 52
Period size: 2 Copynumber: 21.0 Consensus size: 2
56511 TTATATAGTT
* *
56521 TA TA TA TA TA TA TA TA TA CA TA TA TA TA GTT TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
56565 CATGGTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 33 0.92
3 3 0.08
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:56572 original size:20 final size:21
Alignment explanation
Indices: 56531--56584 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
56521 TATATATATA
*
56531 TATATATACATATATATAGTT
1 TATATATACATATACATAGTT
*
56552 TATATATAC-TATACATGGTT
1 TATATATACATATACATAGTT
*
56572 TATACATACATAT
1 TATATATACATAT
56585 TATATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (21 bp):
TATATATACATATACATAGTT
Found at i:56853 original size:20 final size:20
Alignment explanation
Indices: 56828--56872 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
56818 AAAATAAGTT
56828 CATTTGCAATAGTGATAGTC
1 CATTTGCAATAGTGATAGTC
56848 CATTTGCAATAGTGATAGTC
1 CATTTGCAATAGTGATAGTC
56868 CATTT
1 CATTT
56873 ACATTAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (20 bp):
CATTTGCAATAGTGATAGTC
Found at i:56880 original size:20 final size:20
Alignment explanation
Indices: 56828--56880 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
56818 AAAATAAGTT
*
56828 CATTTGCAATAGTGATAGTC
1 CATTTACAATAGTGATAGTC
*
56848 CATTTGCAATAGTGATAGTC
1 CATTTACAATAGTGATAGTC
*
56868 CATTTACATTAGT
1 CATTTACAATAGT
56881 TTACATAGGC
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:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (20 bp):
CATTTACAATAGTGATAGTC
Found at i:56995 original size:7 final size:7
Alignment explanation
Indices: 56956--57023 Score: 66
Period size: 7 Copynumber: 9.7 Consensus size: 7
56946 TTTATATTAG
56956 GGTTTAT
1 GGTTTAT
*
56963 GGCTTA-
1 GGTTTAT
56969 GTGTTTAT
1 G-GTTTAT
*
56977 GGTTTAA
1 GGTTTAT
*
56984 AGTTTAT
1 GGTTTAT
56991 GGTTTAT
1 GGTTTAT
56998 GGTTTAT
1 GGTTTAT
* *
57005 GATTTAG
1 GGTTTAT
*
57012 GGTTTAG
1 GGTTTAT
57019 GGTTT
1 GGTTT
57024 CTATAAACTA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
6 1 0.02
7 48 0.96
8 1 0.02
ACGTcount: A:0.18, C:0.01, G:0.29, T:0.51
Consensus pattern (7 bp):
GGTTTAT
Found at i:57766 original size:22 final size:22
Alignment explanation
Indices: 57729--57771 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
57719 ACCGAATTTG
*
57729 ACGCCCCCATTCTTGATTTTTA
1 ACGCCCCCATTCTTGACTTTTA
57751 ACGCCCCCAATT-TTGACTTTT
1 ACGCCCCC-ATTCTTGACTTTT
57772 CCAACATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.40
Consensus pattern (22 bp):
ACGCCCCCATTCTTGACTTTTA
Found at i:57931 original size:470 final size:470
Alignment explanation
Indices: 57045--57935 Score: 1489
Period size: 470 Copynumber: 1.9 Consensus size: 470
57035 ATACTCTCTA
*
57045 AACTCACAAGAATAATCTCTAAACTCTTTAGTATTGGGAGAAATAAATGATTTTGAATGATTTTG
1 AACTCACAAGAATAATCTCTAAACTCTTTAGTATTGGGAGAAATAAATAATTTTGAATGATTTTG
*
57110 AAGCTAAATGGGTTAGGATATTTATAGTTGAAGCTTAAGGACTAAATTTGTAAATACCCTAAAGT
66 AAGCTAAATGGGTTAGGATATTTATAGTTGAAGCTTAAGGACTAAACTTGTAAATACCCTAAAGT
* * ** *
57175 ATGTAGGGATTAAAATTTAATTTCTCCATTACCATTTTCAACAAAATTAATTGTACCAAATTCGA
131 ATGCAGGGACTAAAATGCAATTTCTCCATTACCATTTTCAACAAAATTAATTGCACCAAATTCGA
* *
57240 TGCCCAATTCACCGAATTCGCGCCCCCATTCTTGATTTTTAACGCCCCAAATTTTGACTTTTTCT
196 TGCCCAATTCACCGAATTCGCGCCCCCATTCTTGATTTTTAACGCCCCAAATTTTGACTTTTCCA
57305 ACATGTTCATGTTCGTTCGTTTAACTTTAATCGAACAAATAAACGAATACGAACATAAACGAATA
261 ACATGTTCATGTTCGTTCGTTTAACTTTAATCGAACAAATAAACGAATACGAACATAAACGAATA
57370 AAAAAATTATTGTTCCTTAAAGAATGTAGCTTATTCATGTTCGTTCGTGTTTGTTCATTTAAATG
326 AAAAAATTATTGTTCCTTAAAGAATGTAGCTTATTCATGTTCGTTCGTGTTTGTTCATTTAAATG
* *
57435 ATAAACGAACACAAATTAACAAACATAAACTCTTTAAACTCACAAATGAGAAAAATTACAGATGT
391 ATAAACAAACACAAATGAACAAACATAAACTCTTTAAACTCACAAATGAGAAAAATTACAGATGT
57500 TTACAAAATACTTAC
456 TTACAAAATACTTAC
* * *
57515 AACTCGCAAGAATACTCTCTAAACTCTTTAGTATTGGGAGAAATAAATAATTTTGGATGATTTTG
1 AACTCACAAGAATAATCTCTAAACTCTTTAGTATTGGGAGAAATAAATAATTTTGAATGATTTTG
*
57580 AAGCTAAATGGGTT-CGAGTATTTATAGTTGAAGCTTAAGGACTAAACTTGTAAATACCCTAAAG
66 AAGCTAAATGGGTTAGGA-TATTTATAGTTGAAGCTTAAGGACTAAACTTGTAAATACCCTAAAG
* * * * * *
57644 TGTGCATGGACTAATATGCAATTTCTCCATTACCATTTTCAA-TAATTTAATTGCACCGAATTCG
130 TATGCAGGGACTAAAATGCAATTTCTCCATTACCATTTTCAACAAAATTAATTGCACCAAATTCG
* * * *
57708 GTGTCCAATTCACCGAATTTGACGCCCCCATTCTTGATTTTTAACGCCCCCAATTTTGACTTTTC
195 ATGCCCAATTCACCGAATTCG-CGCCCCCATTCTTGATTTTTAACGCCCCAAATTTTGACTTTTC
*
57773 CAACATGTTCATGTTCGTTCGTTTAACTTTAATCGAACAAATAAATGAATACGAACATAAACGAA
259 CAACATGTTCATGTTCGTTCGTTTAACTTTAATCGAACAAATAAACGAATACGAACATAAACGAA
* * *
57838 TAAAAAAATTATTGTTCCTTAAAGAATGTAGCTTGTTCGTGTTCGTTCTTGTTTGTTCATTTAAA
324 TAAAAAAATTATTGTTCCTTAAAGAATGTAGCTTATTCATGTTCGTTCGTGTTTGTTCATTTAAA
57903 TGATAAACAAACACAAATGAACAAACATAAACT
389 TGATAAACAAACACAAATGAACAAACATAAACT
57936 AATTGATGTA
Statistics
Matches: 390, Mismatches: 29, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
469 38 0.10
470 352 0.90
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (470 bp):
AACTCACAAGAATAATCTCTAAACTCTTTAGTATTGGGAGAAATAAATAATTTTGAATGATTTTG
AAGCTAAATGGGTTAGGATATTTATAGTTGAAGCTTAAGGACTAAACTTGTAAATACCCTAAAGT
ATGCAGGGACTAAAATGCAATTTCTCCATTACCATTTTCAACAAAATTAATTGCACCAAATTCGA
TGCCCAATTCACCGAATTCGCGCCCCCATTCTTGATTTTTAACGCCCCAAATTTTGACTTTTCCA
ACATGTTCATGTTCGTTCGTTTAACTTTAATCGAACAAATAAACGAATACGAACATAAACGAATA
AAAAAATTATTGTTCCTTAAAGAATGTAGCTTATTCATGTTCGTTCGTGTTTGTTCATTTAAATG
ATAAACAAACACAAATGAACAAACATAAACTCTTTAAACTCACAAATGAGAAAAATTACAGATGT
TTACAAAATACTTAC
Found at i:57989 original size:23 final size:23
Alignment explanation
Indices: 57944--58023 Score: 58
Period size: 23 Copynumber: 3.6 Consensus size: 23
57934 CTAATTGATG
* *
57944 TAAACGAACATAAACGAATACAA
1 TAAACGAACATAAACAAACACAA
* *
57967 TAAACGGACGTAAACAAACAC-A
1 TAAACGAACATAAACAAACACAA
** *
57989 -AAA-GAACATAAATGAACAAAA
1 TAAACGAACATAAACAAACACAA
* *
58010 CAAACGAACGTAAA
1 TAAACGAACATAAA
58024 TGAACATAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
20 11 0.25
21 4 0.09
22 4 0.09
23 25 0.57
ACGTcount: A:0.61, C:0.17, G:0.11, T:0.10
Consensus pattern (23 bp):
TAAACGAACATAAACAAACACAA
Found at i:58024 original size:23 final size:23
Alignment explanation
Indices: 57979--58034 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
57969 AACGGACGTA
57979 AACAAACACAAAAGAACATAAATG
1 AACAAA-ACAAAAGAACATAAATG
* *
58003 AACAAAACAAACGAACGTAAATG
1 AACAAAACAAAAGAACATAAATG
58026 AACATAAAC
1 AACA-AAAC
58035 TGCAACAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 19 0.66
24 10 0.34
ACGTcount: A:0.64, C:0.18, G:0.09, T:0.09
Consensus pattern (23 bp):
AACAAAACAAAAGAACATAAATG
Found at i:58296 original size:24 final size:24
Alignment explanation
Indices: 58269--58330 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
58259 CATAAACAAG
58269 CATAAACAAACGA-AAACGAACGAA
1 CATAAACAAAC-ATAAACGAACGAA
* * *
58293 CATAAACGAACATAAATGAATGAA
1 CATAAACAAACATAAACGAACGAA
58317 CATAAACAAACATA
1 CATAAACAAACATA
58331 TTATCGTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.61, C:0.18, G:0.10, T:0.11
Consensus pattern (24 bp):
CATAAACAAACATAAACGAACGAA
Found at i:66785 original size:22 final size:21
Alignment explanation
Indices: 66760--66801 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
66750 GAGTTCGAAT
66760 TTCAACATCTACAACTTTTTTC
1 TTCAACA-CTACAACTTTTTTC
* *
66782 TTCAATACTACACCTTTTTT
1 TTCAACACTACAACTTTTTT
66802 TCAATAACGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (21 bp):
TTCAACACTACAACTTTTTTC
Found at i:69211 original size:88 final size:88
Alignment explanation
Indices: 69102--69272 Score: 324
Period size: 88 Copynumber: 1.9 Consensus size: 88
69092 TCTTTTAGAA
* *
69102 TATACTGCCAATCAAACAAGTTTCGTCAAATGATAATATAACAAACTATACACCTTCAGAGATTG
1 TATACTGCCAATCAAACAAGTTTCGTCAAATGATAAAATAACAAACTATAAACCTTCAGAGATTG
69167 GACATGCACTCAGTGTAACAAAC
66 GACATGCACTCAGTGTAACAAAC
69190 TATACTGCCAATCAAACAAGTTTCGTCAAATGATAAAATAACAAACTATAAACCTTCAGAGATTG
1 TATACTGCCAATCAAACAAGTTTCGTCAAATGATAAAATAACAAACTATAAACCTTCAGAGATTG
69255 GACATGCACTCAGTGTAA
66 GACATGCACTCAGTGTAA
69273 GACAAGATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 81 1.00
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (88 bp):
TATACTGCCAATCAAACAAGTTTCGTCAAATGATAAAATAACAAACTATAAACCTTCAGAGATTG
GACATGCACTCAGTGTAACAAAC
Found at i:72689 original size:21 final size:20
Alignment explanation
Indices: 72652--72690 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
72642 TTAAAAATTT
*
72652 TAAAAACAAAAATAATATAA
1 TAAAAACAAAAAAAATATAA
*
72672 TAAAAATAAAATAAAATAT
1 TAAAAACAAAA-AAAATAT
72691 GAAATGCCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (20 bp):
TAAAAACAAAAAAAATATAA
Found at i:72882 original size:28 final size:27
Alignment explanation
Indices: 72817--72882 Score: 62
Period size: 28 Copynumber: 2.3 Consensus size: 27
72807 CGTGAGTTAT
* *
72817 TAAATAATTTGATTTTAAGATTATATAA
1 TAAATAA-TTAATTTTAAAATTATATAA
*
72845 -AAATTAAATTAATTTTAAAATTTTATAA
1 TAAA-T-AATTAATTTTAAAATTATATAA
72873 CTAAATAATT
1 -TAAATAATT
72883 TCTAATATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
27 3 0.10
28 22 0.71
29 3 0.10
30 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (27 bp):
TAAATAATTAATTTTAAAATTATATAA
Done.