Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000852.1 Hibiscus syriacus cultivar Beakdansim tig00001645_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: 83121
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1647 original size:19 final size:19
Alignment explanation
Indices: 1623--1660 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1613 CGGTAAGTAG
1623 GGATACTTGTTGCAATTGA
1 GGATACTTGTTGCAATTGA
1642 GGATACTTGTTGCAATTGA
1 GGATACTTGTTGCAATTGA
1661 AGGTGTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (19 bp):
GGATACTTGTTGCAATTGA
Found at i:4017 original size:17 final size:17
Alignment explanation
Indices: 3988--4021 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3978 AAATTAAACC
3988 TAAACAGTGGCAATAATG
1 TAAACAGTGGCAA-AATG
4006 TAAACA-TGGCAAAATG
1 TAAACAGTGGCAAAATG
4022 GGGACCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 6 0.38
18 6 0.38
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.21
Consensus pattern (17 bp):
TAAACAGTGGCAAAATG
Found at i:5605 original size:21 final size:19
Alignment explanation
Indices: 5570--5619 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
5560 GACCCGAAAT
5570 AATAAAAATATTTT-ATTC
1 AATAAAAATATTTTAATTC
*
5588 AATAAAAATAGTGATTTAATTG
1 AATAAAAATA-T--TTTAATTC
5610 AA-AAAAATAT
1 AATAAAAATAT
5620 AAAGTAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 10 0.37
19 1 0.04
20 1 0.04
21 10 0.37
22 5 0.19
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (19 bp):
AATAAAAATATTTTAATTC
Found at i:6566 original size:22 final size:22
Alignment explanation
Indices: 6536--6588 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
6526 TGTATAAACA
*
6536 GTATTGATACCCTATGGTAGA-G
1 GTATCGATACCCTAT-GTAGAGG
*
6558 GTATCGATA-CCTATGTGGAGG
1 GTATCGATACCCTATGTAGAGG
6579 GTATCGATAC
1 GTATCGATAC
6589 ATGGGGAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 4 0.15
21 15 0.56
22 8 0.30
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (22 bp):
GTATCGATACCCTATGTAGAGG
Found at i:7758 original size:19 final size:20
Alignment explanation
Indices: 7734--7784 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
7724 AAATGACCAA
*
7734 CAAATTCGCAACGCGATCT-
1 CAAATTCGCAACGCGAACTC
*
7753 CAAATTCACAACGCGAACTC
1 CAAATTCGCAACGCGAACTC
*
7773 CAATTTCGCAAC
1 CAAATTCGCAAC
7785 CCATTTTCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.35, C:0.33, G:0.12, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGAACTC
Found at i:7864 original size:20 final size:20
Alignment explanation
Indices: 7839--7885 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
7829 TTTTCCAAAT
7839 TCGCAACGCAAATCTGTAAA
1 TCGCAACGCAAATCTGTAAA
* *
7859 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCAAATCTGTAAA
7879 TCGCAAC
1 TCGCAAC
7886 ATAGAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (20 bp):
TCGCAACGCAAATCTGTAAA
Found at i:7902 original size:20 final size:20
Alignment explanation
Indices: 7879--7938 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
7869 AATTTGTAAA
7879 TCGCAACATAGA-AGTCAAAT
1 TCGCAACA-AGATAGTCAAAT
*
7899 TCGCAACACGATAGTCAAAT
1 TCGCAACAAGATAGTCAAAT
* ***
7919 TTGCAATGCGATAGTCAAAT
1 TCGCAACAAGATAGTCAAAT
7939 ATTTTACGCG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.06
20 33 0.94
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (20 bp):
TCGCAACAAGATAGTCAAAT
Found at i:8421 original size:14 final size:14
Alignment explanation
Indices: 8387--8439 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
8377 AAGAAACCCT
*
8387 AAATCGCAACACCA
1 AAATCGCAACACGA
* *
8401 AATTCGCAACGCGA
1 AAATCGCAACACGA
* *
8415 AAATCGCAAAAATGA
1 AAATCGC-AACACGA
8430 AAATCGCAAC
1 AAATCGCAAC
8440 GCGGTTTTAG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.49, C:0.26, G:0.13, T:0.11
Consensus pattern (14 bp):
AAATCGCAACACGA
Found at i:11961 original size:21 final size:21
Alignment explanation
Indices: 11937--11976 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11927 CAATGGGATT
*
11937 AGGATTAGGAATTGGATTTTG
1 AGGATTAGGAAGTGGATTTTG
*
11958 AGGATTTGGAAGTGGATTT
1 AGGATTAGGAAGTGGATTT
11977 GGTTGACGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.38
Consensus pattern (21 bp):
AGGATTAGGAAGTGGATTTTG
Found at i:12689 original size:21 final size:21
Alignment explanation
Indices: 12663--12702 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12653 CAGAACCCCA
*
12663 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
12684 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
12703 TCAAAAGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:20192 original size:21 final size:21
Alignment explanation
Indices: 20145--20243 Score: 76
Period size: 21 Copynumber: 4.7 Consensus size: 21
20135 GATGCACCTA
**
20145 TCATCATTCAAGAGGTGCCTC
1 TCATCATTCAAGAGGCCCCTC
20166 -CTATCATTCAAGAGGCCCCTC
1 TC-ATCATTCAAGAGGCCCCTC
* *
20187 TCATCA-TCGGAGAAGCCCCTC
1 TCATCATTC-AAGAGGCCCCTC
* * * * * *
20208 CCACCGTTCAAAAGGCCTCTG
1 TCATCATTCAAGAGGCCCCTC
20229 TCATCATTCAAGAGG
1 TCATCATTCAAGAGG
20244 TCCCGTCTGC
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
20 3 0.05
21 52 0.90
22 3 0.05
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.23
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCCTC
Found at i:21689 original size:14 final size:14
Alignment explanation
Indices: 21670--21708 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
21660 TTTTGATTAA
21670 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
21684 TTGATTTGT-AAAG
1 TTGATTTGTAAAAG
*
21697 TTGATGTGTAAA
1 TTGATTTGTAAA
21709 TAAAAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:21701 original size:60 final size:63
Alignment explanation
Indices: 21620--21757 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 63
21610 TTTTACATTG
* * *
21620 AAAGTTGATTTGTTTAATTGATGAGGAAAT-CAGA-T-TTATTT-TTTGATTAATTGATTTGTA
1 AAAGTTGATTTG-TAAATTGATGAGGAAATAAAAATTATTATTTGTTTGATTAATTGATTTGTA
* * * *
21680 AAAGTTGATTTGTAAAGTTGATGTGTAAATAAAAATTATTTTTTGTTTGTTTAATTGATTTGTA
1 AAAGTTGATTTGTAAA-TTGATGAGGAAATAAAAATTATTATTTGTTTGATTAATTGATTTGTA
*
21744 AAATTTTGATTTGT
1 AAA-GTTGATTTGT
21758 TGTTTTTAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
59 3 0.05
60 23 0.36
61 2 0.03
62 1 0.02
63 5 0.08
64 21 0.33
65 9 0.14
ACGTcount: A:0.32, C:0.01, G:0.17, T:0.50
Consensus pattern (63 bp):
AAAGTTGATTTGTAAATTGATGAGGAAATAAAAATTATTATTTGTTTGATTAATTGATTTGTA
Found at i:21933 original size:20 final size:20
Alignment explanation
Indices: 21895--21933 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21885 GATTTTTAGT
*
21895 TTGCAAATTTGACTTTCGCG
1 TTGCAAATTTGACTATCGCG
*
21915 TTGCAAATTTGGCTATCGC
1 TTGCAAATTTGACTATCGC
21934 AACGCTTATT
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:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCAAATTTGACTATCGCG
Found at i:22200 original size:39 final size:39
Alignment explanation
Indices: 22146--22232 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
22136 TCAAGTTGTA
22146 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
22185 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
22224 GATTTTGAT
1 GATTTTGAT
22233 GAGCATCGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:22599 original size:24 final size:24
Alignment explanation
Indices: 22544--22589 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
22534 TGAAATTTAT
22544 ATTGAAATTCAAACTCAAATTAAA
1 ATTGAAATTCAAACTCAAATTAAA
* *
22568 ATTTAAATTCAAACTCCAATTA
1 ATTGAAATTCAAACTCAAATTA
22590 CATATGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (24 bp):
ATTGAAATTCAAACTCAAATTAAA
Found at i:23437 original size:18 final size:18
Alignment explanation
Indices: 23414--23449 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
23404 AAGCCGGTTG
*
23414 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
23432 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
23450 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:25741 original size:24 final size:24
Alignment explanation
Indices: 25707--25760 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
25697 CCATCACATC
25707 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
25731 ATCAAAGTCCGGGTATTGATCAAG
1 ATCAAAATCCGAGTATTGACCAAG
25755 ATCAAA
1 ATCAAA
25761 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:26477 original size:16 final size:16
Alignment explanation
Indices: 26456--26489 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
26446 AAATCATTGA
*
26456 AAAATTATATAGAAAT
1 AAAATTATATAAAAAT
*
26472 AAAATTATGTAAAAAT
1 AAAATTATATAAAAAT
26488 AA
1 AA
26490 TTAGAGATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAATTATATAAAAAT
Found at i:26671 original size:19 final size:19
Alignment explanation
Indices: 26624--26674 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
26614 TACCCAAAAG
26624 ATTTGTGTTGCGAAACTAA
1 ATTTGTGTTGCGAAACTAA
*** *
26643 A-ACCTGTTGCGAAATTAA
1 ATTTGTGTTGCGAAACTAA
26661 ATTTGTGTTGCGAA
1 ATTTGTGTTGCGAA
26675 TTCAAAAATC
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (19 bp):
ATTTGTGTTGCGAAACTAA
Found at i:26710 original size:20 final size:20
Alignment explanation
Indices: 26687--26778 Score: 80
Period size: 20 Copynumber: 4.6 Consensus size: 20
26677 CAAAAATCTA
*
26687 GTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
* * * *
26707 GTTGTGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGC
*
26727 GTTGTGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
* *
26747 ATTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGAC-TA-TCGC
26767 GTTGCGAATTTG
1 GTTGCGAATTTG
26779 GAAAATTGCA
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
18 2 0.04
19 5 0.09
20 45 0.80
21 4 0.07
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:26794 original size:21 final size:21
Alignment explanation
Indices: 26770--26836 Score: 116
Period size: 21 Copynumber: 3.2 Consensus size: 21
26760 GATTCGCGTT
26770 GCGAATTTGGAAAATTGCAAC
1 GCGAATTTGGAAAATTGCAAC
26791 GCGAATTTGGAAAATTGCAAC
1 GCGAATTTGGAAAATTGCAAC
* *
26812 GCGAATTTGGAAAATCGCAAT
1 GCGAATTTGGAAAATTGCAAC
26833 GCGA
1 GCGA
26837 TTTACATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.22
Consensus pattern (21 bp):
GCGAATTTGGAAAATTGCAAC
Found at i:27873 original size:21 final size:21
Alignment explanation
Indices: 27847--27901 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
27837 ATGAAATTTG
*
27847 TCCCGAAGGACCACTGTATTA
1 TCCCGAATGACCACTGTATTA
*
27868 TCCCGAATGACCACTGTATTG
1 TCCCGAATGACCACTGTATTA
27889 TCCCGAATGACCA
1 TCCCGAATGACCA
27902 ATGAAACCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (21 bp):
TCCCGAATGACCACTGTATTA
Found at i:35268 original size:22 final size:22
Alignment explanation
Indices: 35242--35294 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
35232 TGTATGAACA
35242 GTATCGATACCCTATGGTAGA-G
1 GTATCGATACCCTAT-GTAGAGG
*
35264 GTATCGATA-CCTATGTGGAGG
1 GTATCGATACCCTATGTAGAGG
35285 GTATCGATAC
1 GTATCGATAC
35295 ATGGGGAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 4 0.14
21 15 0.54
22 9 0.32
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (22 bp):
GTATCGATACCCTATGTAGAGG
Found at i:36425 original size:2 final size:2
Alignment explanation
Indices: 36418--36456 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
36408 GATATGGGTG
36418 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36457 GATGTTTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:37179 original size:15 final size:15
Alignment explanation
Indices: 37155--37193 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
37145 AAAATGTAAA
*
37155 TTAATATTTTTTTAT
1 TTAATATTTTTGTAT
*
37170 TTAATTTTTTTGTAT
1 TTAATATTTTTGTAT
37185 TTAATATTT
1 TTAATATTT
37194 ATATGTGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (15 bp):
TTAATATTTTTGTAT
Found at i:37281 original size:3 final size:3
Alignment explanation
Indices: 37273--37308 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
37263 TGTACTTAAT
* *
37273 TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
37309 AAGTATTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:37359 original size:3 final size:3
Alignment explanation
Indices: 37346--37420 Score: 55
Period size: 3 Copynumber: 24.0 Consensus size: 3
37336 ACGATATTAC
* *
37346 TAA TAAA TAA TAA TAA TAC T-A TAA T-A TAAA TATA TGA TAA GTAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA T-AA TA-A TAA TAA -TAA TAA
* *
37393 GAGA TAG TAA TAA TAA TAA TAA TAA TAA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA
37421 AAGTTAAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
2 3 0.05
3 42 0.74
4 12 0.21
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:44078 original size:31 final size:31
Alignment explanation
Indices: 44024--44083 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
44014 CAACTGATGG
* *
44024 ACTAAAATGGAACGAATCGATAACATTAGTA
1 ACTAAAATCGAACGAATCAATAACATTAGTA
*
44055 ACTAAAATCGAACTG-ATCAATAACGTTAG
1 ACTAAAATCGAAC-GAATCAATAACATTAG
44084 GAATCATTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (31 bp):
ACTAAAATCGAACGAATCAATAACATTAGTA
Found at i:44672 original size:29 final size:29
Alignment explanation
Indices: 44617--44672 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
44607 CTCAACAAAA
*
44617 TAATTTTCTATAGTCGTGAGACTATTTTG
1 TAATTTTCTATAGTCGTGAGACCATTTTG
44646 TAATTTT-TAATAGTCGGTGA-ACCATTT
1 TAATTTTCT-ATAGTC-GTGAGACCATTT
44673 ATATATTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 1 0.04
29 19 0.79
30 4 0.17
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (29 bp):
TAATTTTCTATAGTCGTGAGACCATTTTG
Found at i:45733 original size:20 final size:20
Alignment explanation
Indices: 45710--45760 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
45700 ACTCAGTTTC
45710 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACAGAAGT
*
45730 CAAATTCGCAACACATAAGT
1 CAAATTCGCAACACAGAAGT
45750 CAAATTCGCAA
1 CAAATTCGCAA
45761 AGCGCATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.45, C:0.25, G:0.12, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACACAGAAGT
Found at i:45924 original size:22 final size:22
Alignment explanation
Indices: 45899--45940 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
45889 GGCGACATCC
*
45899 GTCCCCATCTTCGACGAAATAT
1 GTCCCCATCTCCGACGAAATAT
* *
45921 GTCCTCATCTCCGGCGAAAT
1 GTCCCCATCTCCGACGAAAT
45941 CCGTCTATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATAT
Found at i:46053 original size:16 final size:17
Alignment explanation
Indices: 46019--46053 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
46009 GAGGGTTAGT
*
46019 TTTTTAAATTATTTTTA
1 TTTTTAAATTATTTGTA
46036 TTTTTAAATT-TTTGTA
1 TTTTTAAATTATTTGTA
46052 TT
1 TT
46054 ATTATTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTAAATTATTTGTA
Found at i:46055 original size:19 final size:17
Alignment explanation
Indices: 46019--46067 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 17
46009 GAGGGTTAGT
*
46019 TTTTTAAATTATTTTTA
1 TTTTTAAATTTTTTTTA
46036 TTTTTAAATTTTTGTATTA
1 TTTTTAAATTTTT-T-TTA
* *
46055 TTATTAGATTTTT
1 TTTTTAAATTTTT
46068 CATATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 12 0.44
18 1 0.04
19 14 0.52
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (17 bp):
TTTTTAAATTTTTTTTA
Found at i:46336 original size:19 final size:20
Alignment explanation
Indices: 46314--46363 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
46304 TTGCAACGCA
*
46314 ATTTT-AGTTTTGCGTTGCG
1 ATTTTAAGTTTCGCGTTGCG
*
46333 ATTTTCA-TTTCGCGTTGCG
1 ATTTTAAGTTTCGCGTTGCG
46352 ATTTTAAGTTTC
1 ATTTTAAGTTTC
46364 AGAAACTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
ATTTTAAGTTTCGCGTTGCG
Found at i:51330 original size:14 final size:14
Alignment explanation
Indices: 51311--51373 Score: 83
Period size: 14 Copynumber: 4.6 Consensus size: 14
51301 GTTTGTTTAA
51311 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
**
51325 TTGATTTGTTTAA-
1 TTGATTTGTAAAAG
* *
51338 TTAATGTGTAAAAG
1 TTGATTTGTAAAAG
51352 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
51366 TTGATTTG
1 TTGATTTG
51374 CGAATTTGAC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
13 9 0.22
14 31 0.77
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:51347 original size:27 final size:27
Alignment explanation
Indices: 51302--51360 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
51292 TTATTTTTTG
* *
51302 TTTGTTTAATTGATTTGTAAAAGTTGA
1 TTTGTTTAATTAATGTGTAAAAGTTGA
51329 TTTGTTTAATTAATGTGTAAAAGTTGA
1 TTTGTTTAATTAATGTGTAAAAGTTGA
51356 TTTGT
1 TTTGT
51361 AAAAGTTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.53
Consensus pattern (27 bp):
TTTGTTTAATTAATGTGTAAAAGTTGA
Found at i:53887 original size:24 final size:24
Alignment explanation
Indices: 53853--53906 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
53843 CTAAAACATC
53853 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
53877 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
53901 ATCAAA
1 ATCAAA
53907 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:53920 original size:24 final size:24
Alignment explanation
Indices: 53853--53920 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
53843 CTAAAACATC
* * *
53853 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
53877 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
53901 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
53921 TAGTGCTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:54053 original size:12 final size:12
Alignment explanation
Indices: 54032--54065 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54022 TGTTGTGGGT
*
54032 TTTGAGATTGTG
1 TTTGATATTGTG
54044 TTTGATATTGTG
1 TTTGATATTGTG
*
54056 TTTGGTATTG
1 TTTGATATTG
54066 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:54880 original size:20 final size:20
Alignment explanation
Indices: 54855--54964 Score: 68
Period size: 20 Copynumber: 5.5 Consensus size: 20
54845 AACTAAAACC
54855 TGTTGCGAAATTAAAATTCA
1 TGTTGCGAAATTAAAATTCA
*
54875 TGTTGCG-AATTCAAAAATCGA
1 TGTTGCGAAATT-AAAATTC-A
** *
54896 -GTTGCGAAAACAAAATTCG
1 TGTTGCGAAATTAAAATTCA
*
54915 CGTTGCG-AATTCAGAAA-TCGA
1 TGTTGCGAAATT-A-AAATTC-A
* *
54936 -GTTGCGAATTTGAAATTCA
1 TGTTGCGAAATTAAAATTCA
54955 GTGTTGCGAA
1 -TGTTGCGAA
54965 TTTGACTTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
19 10 0.14
20 42 0.61
21 17 0.25
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCA
Found at i:54901 original size:40 final size:40
Alignment explanation
Indices: 54856--54966 Score: 150
Period size: 40 Copynumber: 2.8 Consensus size: 40
54846 ACTAAAACCT
54856 GTTGCGAAATTAAAATTCATGTTGCGAATTCAAAAATCGA
1 GTTGCGAAATTAAAATTCATGTTGCGAATTCAAAAATCGA
** ** *
54896 GTTGCGAAAACAAAATTCGCGTTGCGAATTCAGAAATCGA
1 GTTGCGAAATTAAAATTCATGTTGCGAATTCAAAAATCGA
* *
54936 GTTGCGAATTTGAAATTCAGTGTTGCGAATT
1 GTTGCGAAATTAAAATTCA-TGTTGCGAATT
54967 TGACTTTTGT
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
40 49 0.83
41 10 0.17
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.30
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCATGTTGCGAATTCAAAAATCGA
Found at i:54980 original size:20 final size:20
Alignment explanation
Indices: 54936--54990 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
54926 CAGAAATCGA
54936 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTG-AATTCAGT
* **
54957 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGAATTCAGT
54977 GTTGCGAATTTGAA
1 GTTGCGAATTTGAA
54991 AAATCGCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGAATTCAGT
Found at i:55305 original size:28 final size:28
Alignment explanation
Indices: 55249--55306 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
55239 TTATTATTCA
*
55249 ATAATTTTTTTAAAATTATATGAATTTT
1 ATAATTTTTTTAAAATTATATAAATTTT
*
55277 ATAATTTTTTTTAAATTATA-AAATATTT
1 ATAATTTTTTTAAAATTATATAAAT-TTT
55305 AT
1 AT
55307 TATTATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 3 0.11
28 24 0.89
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
ATAATTTTTTTAAAATTATATAAATTTT
Found at i:59888 original size:16 final size:18
Alignment explanation
Indices: 59856--59888 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
59846 ATACAAATAT
59856 ATATACATATATTTAAAC
1 ATATACATATATTTAAAC
59874 ATATA-ATAT-TTTAAA
1 ATATACATATATTTAAA
59889 ATTTAAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATACATATATTTAAAC
Found at i:60187 original size:13 final size:13
Alignment explanation
Indices: 60169--60194 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60159 ATTATTTAAA
60169 TTTATTTTAAAAT
1 TTTATTTTAAAAT
60182 TTTATTTTAAAAT
1 TTTATTTTAAAAT
60195 ATGAATTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTATTTTAAAAT
Found at i:60210 original size:22 final size:22
Alignment explanation
Indices: 60182--60350 Score: 234
Period size: 22 Copynumber: 7.7 Consensus size: 22
60172 ATTTTAAAAT
60182 TTTATTTTAAAATATGAATTGA
1 TTTATTTTAAAATATGAATTGA
60204 TTTATTTTAAAATAT-AGATTGA
1 TTTATTTTAAAATATGA-ATTGA
**
60226 TTTATTTTAAAATATAGAA-AAA
1 TTTATTTTAAAATAT-GAATTGA
*
60248 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGAATTGA
* ***
60270 TTTATTTTAAAATATGGACAAA
1 TTTATTTTAAAATATGAATTGA
*
60292 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGAATTGA
60314 TTTATTTTAAAATATGAATTGA
1 TTTATTTTAAAATATGAATTGA
60336 TTTATTTTAAAATAT
1 TTTATTTTAAAATAT
60351 TTATTATTGT
Statistics
Matches: 131, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
21 3 0.02
22 126 0.96
23 1 0.01
24 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.49
Consensus pattern (22 bp):
TTTATTTTAAAATATGAATTGA
Found at i:60230 original size:44 final size:44
Alignment explanation
Indices: 60182--60350 Score: 259
Period size: 44 Copynumber: 3.8 Consensus size: 44
60172 ATTTTAAAAT
** *
60182 TTTATTTTAAAATATGAATTGATTTATTTTAAAATATAGATTGA
1 TTTATTTTAAAATATGAATAAATTTATTTTAAAATATGGATTGA
60226 TTTATTTTAAAATATAGAA-AAATTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATAT-GAATAAATTTATTTTAAAATATGGATTGA
* *
60270 TTTATTTTAAAATATGGACAAATTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGAATAAATTTATTTTAAAATATGGATTGA
**
60314 TTTATTTTAAAATATGAATTGATTTATTTTAAAATAT
1 TTTATTTTAAAATATGAATAAATTTATTTTAAAATAT
60351 TTATTATTGT
Statistics
Matches: 115, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
43 2 0.02
44 110 0.96
45 3 0.03
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.49
Consensus pattern (44 bp):
TTTATTTTAAAATATGAATAAATTTATTTTAAAATATGGATTGA
Found at i:60255 original size:66 final size:66
Alignment explanation
Indices: 60177--60350 Score: 258
Period size: 66 Copynumber: 2.6 Consensus size: 66
60167 AATTTATTTT
* ***
60177 AAAATTTTATTTTAAAATATGAATTGATTTATTTTAAAATATAGATTGATTTATTTTAAAATATA
1 AAAAATTTATTTTAAAATATGAATTGATTTATTTTAAAATATAGACAAATTTATTTTAAAATATA
60242 G
66 G
* * *
60243 AAAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGACAAATTTATTTTAAAATATG
1 AAAAATTTATTTTAAAATATGAATTGATTTATTTTAAAATATAGACAAATTTATTTTAAAATATA
60308 G
66 G
***
60309 ATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATAT
1 AAAAATTTATTTTAAAATATGAATTGATTTATTTTAAAATAT
60351 TTATTATTGT
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 97 1.00
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.48
Consensus pattern (66 bp):
AAAAATTTATTTTAAAATATGAATTGATTTATTTTAAAATATAGACAAATTTATTTTAAAATATA
G
Found at i:61270 original size:21 final size:21
Alignment explanation
Indices: 61246--61309 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
61236 GCAAATTCGC
61246 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
61267 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
61287 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
61308 GT
1 GT
61310 CTACAATGTC
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:61295 original size:41 final size:41
Alignment explanation
Indices: 61250--61352 Score: 133
Period size: 41 Copynumber: 2.5 Consensus size: 41
61240 ATTCGCGTTG
61250 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCT-AAAAT-GTCGTTGCGATTTTC
*
61291 CATTTCGCGTTGCGATAGTCTACAATGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTAAAATGTCGTTGCGATTTTC
*
61332 CAAATT--CGTTGCGATAGTCTA
1 C-ATTTCGCGTTGCGATAGTCTA
61353 CAGTTGTTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
40 16 0.28
41 37 0.65
42 4 0.07
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTCTAAAATGTCGTTGCGATTTTC
Found at i:61361 original size:19 final size:20
Alignment explanation
Indices: 61299--61381 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 20
61289 TCCATTTCGC
*
61299 GTTGCGATAGTCTACAATGTC
1 GTTGCGATAGTCTAC-ATGTT
** * * *
61320 GTTGCGATTTTCCAAAT-TC
1 GTTGCGATAGTCTACATGTT
61339 GTTGCGATAGTCTACAGTTGTT
1 GTTGCGATAGTCTACA--TGTT
*
61361 GTTGCGAAAGTCTACA-GTT
1 GTTGCGATAGTCTACATGTT
61380 GT
1 GT
61382 CGTTGCGATT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
19 19 0.39
20 2 0.04
21 12 0.24
22 16 0.33
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCTACATGTT
Found at i:61366 original size:22 final size:22
Alignment explanation
Indices: 61298--61390 Score: 95
Period size: 22 Copynumber: 4.4 Consensus size: 22
61288 TTCCATTTCG
*
61298 CGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
61319 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
61338 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* *
61360 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
61382 CGTTGCGAT
1 CGTTGCGAT
61391 TTTCCAAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
19 14 0.24
20 2 0.03
21 14 0.24
22 28 0.48
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:62031 original size:16 final size:16
Alignment explanation
Indices: 62010--62060 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
62000 GGGTCGTGGT
62010 CGTGGTCGTGGTAATA
1 CGTGGTCGTGGTAATA
62026 CGTGGTCGTGGTAATA
1 CGTGGTCGTGGTAATA
*
62042 CGTGGTTGTGGTAATA
1 CGTGGTCGTGGTAATA
62058 CGT
1 CGT
62061 ATCTTCGACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.18, C:0.12, G:0.37, T:0.33
Consensus pattern (16 bp):
CGTGGTCGTGGTAATA
Found at i:62162 original size:19 final size:19
Alignment explanation
Indices: 62138--62181 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
62128 TTAACTATCA
*
62138 CAACGAATTTGGAAAATCG
1 CAACGAATTTGAAAAATCG
62157 CAACGAATTTGAAAAATCG
1 CAACGAATTTGAAAAATCG
62176 CAACGA
1 CAACGA
62182 CAACTGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (19 bp):
CAACGAATTTGAAAAATCG
Found at i:62804 original size:15 final size:14
Alignment explanation
Indices: 62786--62853 Score: 50
Period size: 14 Copynumber: 4.7 Consensus size: 14
62776 AATATTGTTT
62786 TATATATTTACTTAA
1 TATATATTTA-TTAA
62801 TATATTATTT-TTAA
1 TATA-TATTTATTAA
*
62815 TACTAT-TTTAATAA
1 TA-TATATTTATTAA
* *
62829 AATATTAATTATTAA
1 TATA-TATTTATTAA
*
62844 AATATATTTA
1 TATATATTTA
62854 CTAAAATGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
13 5 0.12
14 17 0.40
15 16 0.37
16 5 0.12
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TATATATTTATTAA
Found at i:62858 original size:29 final size:29
Alignment explanation
Indices: 62787--62860 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
62777 ATATTGTTTT
* *
62787 ATATATTTACTTAATATATTATTTTTAATA
1 ATATATTTAC-TAAAATATTATTATTAATA
* *
62817 CTAT-TTTAATAAAATATTAATTATTAA-A
1 ATATATTTACTAAAATATT-ATTATTAATA
62845 ATATATTTACTAAAAT
1 ATATATTTACTAAAAT
62861 GTTCAGGGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
28 12 0.33
29 21 0.58
30 3 0.08
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (29 bp):
ATATATTTACTAAAATATTATTATTAATA
Found at i:64327 original size:15 final size:16
Alignment explanation
Indices: 64307--64338 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
64297 TAGTTGTTAC
64307 AAATTTCATTAT-TAA
1 AAATTTCATTATATAA
64322 AAATTTCATTATATAA
1 AAATTTCATTATATAA
64338 A
1 A
64339 TTAATCACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATTTCATTATATAA
Found at i:81726 original size:17 final size:18
Alignment explanation
Indices: 81687--81726 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
81677 TAATATTAGC
*
81687 TGTTGACCGTCAATTTTTT
1 TGTTGACCGTCAA-TTATT
81706 TGTTGACCGTCAA-TATT
1 TGTTGACCGTCAATTATT
81723 TGTT
1 TGTT
81727 TATTTTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
19 13 0.65
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.50
Consensus pattern (18 bp):
TGTTGACCGTCAATTATT
Done.