Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008819.1 Hibiscus syriacus cultivar Beakdansim tig00111986_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: 42741
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:6643 original size:20 final size:21
Alignment explanation
Indices: 6620--6663 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
6610 TATTATATGT
**
6620 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
6640 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
6661 ATA
1 ATA
6664 AAAATATCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:7585 original size:20 final size:19
Alignment explanation
Indices: 7539--7586 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
7529 GGTATTAGTT
* *
7539 TGTTTTTTTTTCCTTTCTC
1 TGTTTTTTTCTCCGTTCTC
7558 TGTCTTTTTCTTCTCCGTTCTC
1 TG--TTTTT-TTCTCCGTTCTC
7580 TGTTTTT
1 TGTTTTT
7587 AGTTTCTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 2 0.08
20 5 0.21
21 5 0.21
22 12 0.50
ACGTcount: A:0.00, C:0.23, G:0.08, T:0.69
Consensus pattern (19 bp):
TGTTTTTTTCTCCGTTCTC
Found at i:8072 original size:3 final size:3
Alignment explanation
Indices: 8066--8166 Score: 148
Period size: 3 Copynumber: 33.7 Consensus size: 3
8056 TTAATATATT
* *
8066 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* ** *
8114 TAA TAA TAA TAT TAA TAA TAA TAA GGA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
8162 TAA TA
1 TAA TA
8167 TGGATAAAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:8104 original size:27 final size:27
Alignment explanation
Indices: 8066--8165 Score: 173
Period size: 27 Copynumber: 3.7 Consensus size: 27
8056 TTAATATATT
8066 TAATAATAATAATAATAATGATAATAA
1 TAATAATAATAATAATAATGATAATAA
8093 TAATAATAATAATAATAATGATAATAA
1 TAATAATAATAATAATAATGATAATAA
* *
8120 TAATATTAATAATAATAAGGATAATAA
1 TAATAATAATAATAATAATGATAATAA
*
8147 TAATATTAATAATAATAAT
1 TAATAATAATAATAATAAT
8166 ATGGATAAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (27 bp):
TAATAATAATAATAATAATGATAATAA
Found at i:9663 original size:18 final size:19
Alignment explanation
Indices: 9638--9685 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
9628 TATGAGGACC
*
9638 CTTTATTTCTTTTCATTTT
1 CTTTATTTCTCTTCATTTT
9657 C-TTATTT-TCTTCATTTT
1 CTTTATTTCTCTTCATTTT
9674 CTTTATTTCTCT
1 CTTTATTTCTCT
9686 CATGCTCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 10 0.38
18 12 0.46
19 4 0.15
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (19 bp):
CTTTATTTCTCTTCATTTT
Found at i:9674 original size:9 final size:9
Alignment explanation
Indices: 9649--9681 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
9639 TTTATTTCTT
9649 TTCATTTTC
1 TTCATTTTC
9658 TT-ATTTTC
1 TTCATTTTC
9666 TTCATTTTC
1 TTCATTTTC
*
9675 TTTATTT
1 TTCATTT
9682 CTCTCATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (9 bp):
TTCATTTTC
Found at i:9682 original size:17 final size:17
Alignment explanation
Indices: 9638--9688 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 17
9628 TATGAGGACC
9638 CTTTATTTCTTTTCATTTT
1 CTTTATTTC--TTCATTTT
9657 C-TTATTTTCTTCATTTT
1 CTTTA-TTTCTTCATTTT
9674 CTTTATTTCTCTCAT
1 CTTTATTTCT-TCAT
9689 GCTCTTATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 14 0.48
18 10 0.34
19 5 0.17
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.69
Consensus pattern (17 bp):
CTTTATTTCTTCATTTT
Found at i:10174 original size:20 final size:20
Alignment explanation
Indices: 10149--10186 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
10139 TCTGGGTTTG
*
10149 AGTATCGATATTGGATGAAC
1 AGTATCAATATTGGATGAAC
10169 AGTATCAATATTGGATGA
1 AGTATCAATATTGGATGA
10187 TTTGGGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.32
Consensus pattern (20 bp):
AGTATCAATATTGGATGAAC
Found at i:10243 original size:21 final size:21
Alignment explanation
Indices: 10219--10274 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
10209 TCCAGCCGGA
*
10219 AGTATCGAAATTGCTGGGGAT
1 AGTATCGATATTGCTGGGGAT
10240 AGTATCGATATTGCTGGGGAT
1 AGTATCGATATTGCTGGGGAT
10261 AGTATCGATATTGC
1 AGTATCGATATTGC
10275 CCCTACAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.11, G:0.30, T:0.32
Consensus pattern (21 bp):
AGTATCGATATTGCTGGGGAT
Found at i:16329 original size:16 final size:16
Alignment explanation
Indices: 16305--16337 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
16295 TATTGCCGAC
*
16305 CAAATTTCACTATTCA
1 CAAAATTCACTATTCA
16321 CAAAATTCACTATTCA
1 CAAAATTCACTATTCA
16337 C
1 C
16338 TTGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.33
Consensus pattern (16 bp):
CAAAATTCACTATTCA
Found at i:18956 original size:16 final size:16
Alignment explanation
Indices: 18932--18964 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
18922 TATTGCCGAC
*
18932 CAAATTTCACTATTCA
1 CAAAATTCACTATTCA
18948 CAAAATTCACTATTCA
1 CAAAATTCACTATTCA
18964 C
1 C
18965 TTAAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.33
Consensus pattern (16 bp):
CAAAATTCACTATTCA
Found at i:19849 original size:20 final size:20
Alignment explanation
Indices: 19824--19916 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
19814 TTTTCCCAAT
19824 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
19844 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
*
19864 TTCGCAATGCGAATAAGTATA
1 -TCGCAATGCGAATAAGTAAA
* * *
19885 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAA-TAAGTAAA
19906 TCGCAATGCGA
1 TCGCAATGCGA
19917 TACTGACTAT
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 27 0.47
21 30 0.53
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:19866 original size:41 final size:41
Alignment explanation
Indices: 19821--19916 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
19811 CGATTTTCCC
*
19821 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
*
19862 AATTCGCAATGCGAATAAGTATATCGCAACGCGAATTGAGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
*
19903 AAATCGCAATGCGA
1 AATTCGCAATGCGA
19917 TACTGACTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
Found at i:19928 original size:41 final size:41
Alignment explanation
Indices: 19843--19977 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
19833 GAATAAGTAA
* * *
19843 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-T
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCG-ATACTG-ACT
19884 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
* * * * * *
19925 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
*
19966 TTCGCAACGCGA
1 ATCGCAACGCGA
19978 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
Found at i:19930 original size:20 final size:20
Alignment explanation
Indices: 19905--19999 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
19895 AATTGAGAAA
*
19905 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
19925 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
19946 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
19966 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
19986 TTCGCAACGCGATA
1 ATCGCAACGCGATA
20000 ATATATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:20215 original size:22 final size:22
Alignment explanation
Indices: 20187--20230 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20177 CACTCTCTCA
20187 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
20209 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
20231 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:20519 original size:20 final size:20
Alignment explanation
Indices: 20494--20531 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20484 CGATTCTCTC
20494 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
20514 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
20532 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:21866 original size:18 final size:18
Alignment explanation
Indices: 21845--21889 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
21835 TCCACTTCGG
* *
21845 GAGCCATCACCTCGCCCA
1 GAGCTATCACCTCACCCA
*
21863 GAGCTATCACCTCACCTA
1 GAGCTATCACCTCACCCA
21881 GAGCTATCA
1 GAGCTATCA
21890 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.40, G:0.16, T:0.18
Consensus pattern (18 bp):
GAGCTATCACCTCACCCA
Found at i:22416 original size:19 final size:20
Alignment explanation
Indices: 22362--22428 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
22352 TAGTTTACTT
* *
22362 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
22382 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
22402 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
22421 TCGCAACG
1 TCGCAACG
22429 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:22436 original size:14 final size:14
Alignment explanation
Indices: 22417--22474 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
22407 ATGCGAAATG
22417 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
22431 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
22447 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
22463 AAAATCGCAACG
1 AAAATCGCAACG
22475 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:22459 original size:32 final size:33
Alignment explanation
Indices: 22401--22491 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
22391 GGAAATGGCT
*
22401 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
22434 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
22466 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
22492 TGTGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:22539 original size:32 final size:32
Alignment explanation
Indices: 22503--22613 Score: 204
Period size: 32 Copynumber: 3.4 Consensus size: 32
22493 GTGATTTGTG
22503 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
22535 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
22567 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
*
22600 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
22614 AGCCATTTCC
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 59 0.77
33 18 0.23
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
Found at i:22612 original size:19 final size:18
Alignment explanation
Indices: 22503--22654 Score: 112
Period size: 14 Copynumber: 8.9 Consensus size: 18
22493 GTGATTTGTG
22503 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
22519 TGT--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
22535 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
22551 TGT--CGTTGCGATTTCA
1 TTTCGCGTTGCGATTTCA
22567 TTTCGCGTTGCGATTT--
1 TTTCGCGTTGCGATTTCA
*
22583 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
* **
22600 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGAT-TTCA
*
22619 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGAT-TTCA
*
22639 TTTCGCATTGCGATTT
1 TTTCGCGTTGCGATTT
22655 TAAGTTTCGT
Statistics
Matches: 108, Mismatches: 13, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
14 30 0.28
15 3 0.03
16 10 0.09
17 2 0.02
18 24 0.22
19 22 0.20
20 17 0.16
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.44
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:22632 original size:20 final size:19
Alignment explanation
Indices: 22598--22652 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
22588 TTGCGATTTT
22598 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
* *
22617 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCATTGCGATAGC
22637 CATTTCGCATTGCGAT
1 CATTTCGCATTGCGAT
22653 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:24535 original size:14 final size:14
Alignment explanation
Indices: 24516--24551 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
24506 ATTGTTTAAT
24516 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
24530 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
24544 TGATTTGT
1 TGATTTGT
24552 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:24690 original size:19 final size:19
Alignment explanation
Indices: 24668--24735 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
24658 ATCGCAACGA
24668 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
24687 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
24706 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
24720 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
24736 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:24779 original size:20 final size:20
Alignment explanation
Indices: 24754--24810 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
24744 TCGCATTGCG
*
24754 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
24774 ATTTTCGCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAACC
*
24794 ATTTTCGCATTGCGATA
1 ATTTTCGCGTTGCGATA
24811 GTCAAATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAACC
Found at i:25194 original size:14 final size:14
Alignment explanation
Indices: 25175--25210 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
25165 ATTGTTTAAT
25175 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
25189 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
25203 TGATTTGT
1 TGATTTGT
25211 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:28888 original size:19 final size:19
Alignment explanation
Indices: 28866--28963 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
28856 GGAAATTACT
28866 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
28885 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
28899 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
28918 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
28932 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
28951 ATCGCAACGCGAA
1 ATCGCAATGCGAA
28964 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:28908 original size:33 final size:33
Alignment explanation
Indices: 28866--28959 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
28856 GGAAATTACT
28866 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
28899 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
28932 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
28960 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:28981 original size:19 final size:20
Alignment explanation
Indices: 28959--29001 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
28949 AAATCGCAAC
28959 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
28978 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
28998 GCGA
1 GCGA
29002 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:28986 original size:14 final size:14
Alignment explanation
Indices: 28987--29020 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28977 TGCGATTTTC
28987 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
29001 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
29015 ATTTTC
1 ATTTTC
29021 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:29161 original size:14 final size:14
Alignment explanation
Indices: 29142--29177 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
29132 CATCAATTAA
*
29142 ACAAATCAACTTTT
1 ACAAATCAACCTTT
29156 ACAAATC-ACCTTT
1 ACAAATCAACCTTT
29169 ACAAATCAA
1 ACAAATCAA
29178 TTAAACAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (14 bp):
ACAAATCAACCTTT
Found at i:30593 original size:21 final size:21
Alignment explanation
Indices: 30527--30593 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
30517 TGTGAATCGG
*
30527 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
30547 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
30569 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
30590 CTCT
1 CTCT
30594 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:30612 original size:42 final size:41
Alignment explanation
Indices: 30527--30649 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
30517 TGTGAATCGG
* * * * *
30527 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
30569 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
30611 CTCTTCAACGATAGGAGTGGACTCTTGATGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
30650 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:32334 original size:20 final size:19
Alignment explanation
Indices: 32289--32349 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 19
32279 TCTTTTGGTT
32289 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* * *
32308 GATAATGAGAATTGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
32329 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
32348 GA
1 GA
32350 GAATCGCAAC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 4 0.12
20 26 0.81
21 2 0.06
ACGTcount: A:0.44, C:0.15, G:0.25, T:0.16
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:32371 original size:33 final size:33
Alignment explanation
Indices: 32314--32401 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
32304 ACGAGATAAT
* *
32314 GAGAATTGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
32348 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
32381 GAGAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
32402 AAATCACAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 38 0.75
34 13 0.25
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:32433 original size:19 final size:19
Alignment explanation
Indices: 32411--32477 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
32401 AAAATCACAA
*
32411 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
32430 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
32449 TGCGATAGTT-ATTTCCGCTT
1 TGCGAT-TTTGATTT-CGCGT
32469 TGCGATTTT
1 TGCGATTTT
32478 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:33093 original size:20 final size:20
Alignment explanation
Indices: 33000--33093 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
32990 CGCTAAGTAA
*
33000 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
33020 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
33040 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
33061 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
33081 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
33094 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:33112 original size:41 final size:41
Alignment explanation
Indices: 33021--33155 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
33011 AAAGTCAGTA
* * * ** *
33021 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
33061 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
33103 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
33144 TCGCGTTGCGAT
1 TCGCGTTGCGAT
33156 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:33126 original size:20 final size:20
Alignment explanation
Indices: 33082--33174 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
33072 ATAGTCAGTA
* **
33082 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
33103 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
33123 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
33144 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
33164 TCGCATTGCGA
1 TCGCATTGCGA
33175 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:33156 original size:41 final size:41
Alignment explanation
Indices: 33082--33177 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
33072 ATAGTCAGTA
*
33082 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
33123 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
33164 TCGCATTGCGAATT
1 TCGCATTGCGAATT
33178 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:35179 original size:19 final size:20
Alignment explanation
Indices: 35142--35182 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
35132 TGTATAAAAA
35142 ATTATTTTTATTAAATATTTTT
1 ATTATTTTTATT--ATATTTTT
35164 ATTATTTTTATT-TATTTTT
1 ATTATTTTTATTATATTTTT
35183 TAAATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
22 12 0.63
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
ATTATTTTTATTATATTTTT
Found at i:42506 original size:25 final size:25
Alignment explanation
Indices: 42477--42549 Score: 146
Period size: 25 Copynumber: 2.9 Consensus size: 25
42467 ACCTAAAGTT
42477 AAATATACCCACTAGTGGAACTTTA
1 AAATATACCCACTAGTGGAACTTTA
42502 AAATATACCCACTAGTGGAACTTTA
1 AAATATACCCACTAGTGGAACTTTA
42527 AAATATACCCACTAGTGGAACTT
1 AAATATACCCACTAGTGGAACTT
42550 ACTTCATCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (25 bp):
AAATATACCCACTAGTGGAACTTTA
Done.