Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003966.1 Hibiscus syriacus cultivar Beakdansim tig00008593_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: 59058
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:588 original size:55 final size:57
Alignment explanation
Indices: 483--594 Score: 156
Period size: 56 Copynumber: 2.0 Consensus size: 57
473 TTGTAACCAA
* *
483 GTCTCCCATTTCGCTGCCACGTTTACACCGGAGTTGGTGGAGTCAAGAGAGA-AAGG
1 GTCTCCCATTTCGCCGCCACGTTTACACCGGAGTCGGTGGAGTCAAGAGAGAGAAGG
* * * *
539 GTCTCTCATTTCGCCGTCACGTTTATA-CGGAGTCGGTGGAGTCTAGAGAGAGAAGG
1 GTCTCCCATTTCGCCGCCACGTTTACACCGGAGTCGGTGGAGTCAAGAGAGAGAAGG
595 AATCACTCTC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
55 22 0.45
56 27 0.55
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.25
Consensus pattern (57 bp):
GTCTCCCATTTCGCCGCCACGTTTACACCGGAGTCGGTGGAGTCAAGAGAGAGAAGG
Found at i:4465 original size:3 final size:3
Alignment explanation
Indices: 4459--4502 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
4449 CGAGGACGAC
** *
4459 GAT GAT GAT GAT GAT GAT GGC GAT GAT GAT GAT GAT GGT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
4503 CAGTGAGGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.02, G:0.39, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:4706 original size:35 final size:36
Alignment explanation
Indices: 4639--4706 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 36
4629 GTTAGACAAA
* *
4639 TAATTGTATTTTTTTAATTATTTACCATTTAATACT
1 TAATTGTATTTTGTTAATTATTTACCACTTAATACT
* **
4675 TAATT-TATTTTGTTAATTTTTTATTACTTAAT
1 TAATTGTATTTTGTTAATTATTTACCACTTAAT
4707 TCAAGCGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 22 0.81
36 5 0.19
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (36 bp):
TAATTGTATTTTGTTAATTATTTACCACTTAATACT
Found at i:7233 original size:16 final size:16
Alignment explanation
Indices: 7212--7244 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
7202 TAACTCACCA
7212 TTAATTATTGATGAGT
1 TTAATTATTGATGAGT
*
7228 TTAATTATTGATTAGT
1 TTAATTATTGATGAGT
7244 T
1 T
7245 AAATCCATAG
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:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (16 bp):
TTAATTATTGATGAGT
Found at i:8523 original size:16 final size:16
Alignment explanation
Indices: 8502--8534 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
8492 TCAAATAATC
8502 ATATA-TAAAAAATATT
1 ATATATTAAAAAA-ATT
8518 ATATATTAAAAAAATT
1 ATATATTAAAAAAATT
8534 A
1 A
8535 CCTTACAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATATTAAAAAAATT
Found at i:8612 original size:30 final size:30
Alignment explanation
Indices: 8576--8669 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 30
8566 ATCAAAGATA
* *
8576 AGAGGATTGATGGGTGATGTTTATGGGTTG
1 AGAGGATTGATGTGTGATGTTTACGGGTTG
* *
8606 AGAGGATTGTTGTGTGATGTTTACGAGTTG
1 AGAGGATTGATGTGTGATGTTTACGGGTTG
* *
8636 AGAGGATTGCTGTGTGATGTTTACAGGTTG
1 AGAGGATTGATGTGTGATGTTTACGGGTTG
8666 AGAG
1 AGAG
8670 CGTATTATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.21, C:0.03, G:0.39, T:0.36
Consensus pattern (30 bp):
AGAGGATTGATGTGTGATGTTTACGGGTTG
Found at i:13045 original size:17 final size:17
Alignment explanation
Indices: 13023--13056 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13013 TTCATATATT
13023 ATACTAAATATATCTAA
1 ATACTAAATATATCTAA
* *
13040 ATACTAAGTATTTCTAA
1 ATACTAAATATATCTAA
13057 GCGAGTCTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (17 bp):
ATACTAAATATATCTAA
Found at i:13594 original size:41 final size:40
Alignment explanation
Indices: 13552--13748 Score: 279
Period size: 41 Copynumber: 4.8 Consensus size: 40
13542 CTGCATTTCG
* *
13552 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG-
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTT-ACAGT-GT
* * * *
13593 CGTTGCGGTTTTTCATTTCCCGTTGCGATAGCCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAG-TTACAGTGT
13634 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TACAGTGT
*
13675 CGTTGCGGTTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TACAGTGT
13716 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTT
13749 TTAAAAATGG
Statistics
Matches: 141, Mismatches: 12, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
40 2 0.01
41 138 0.98
42 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.39
Consensus pattern (40 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTACAGTGT
Found at i:13680 original size:21 final size:21
Alignment explanation
Indices: 13613--13724 Score: 74
Period size: 21 Copynumber: 5.4 Consensus size: 21
13603 TTTCATTTCC
*
13613 CGTTGCGATAGCCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
13634 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
13652 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
* * * *
13675 CGTTGCGGT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
13693 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
13716 CGTTGCGAT
1 CGTTGCGAT
13725 TTTCCATTTC
Statistics
Matches: 66, Mismatches: 15, Indels: 20
0.65 0.15 0.20
Matches are distributed among these distances:
18 4 0.06
19 7 0.11
20 17 0.26
21 26 0.39
22 8 0.12
23 4 0.06
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.37
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:13692 original size:82 final size:82
Alignment explanation
Indices: 13552--13748 Score: 317
Period size: 82 Copynumber: 2.4 Consensus size: 82
13542 CTGCATTTCG
*
13552 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGGTTTTTCATTTCCCGTT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGGTTTTCCATTTCCCGTT
13617 GCGATAGCCTACAGTGT
66 GCGATAGCCTACAGTGT
* * *
13634 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAGT-GTCGTTGCGGTTTTCCATTTCGCG
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGGTTTTCCATTTCCCG
*
13697 TTGCGATAGTCTACAGTGT
64 TTGCGATAGCCTACAGTGT
13716 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTT
13749 TTAAAAATGG
Statistics
Matches: 108, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
81 2 0.02
82 105 0.97
83 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.39
Consensus pattern (82 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGGTTTTCCATTTCCCGTT
GCGATAGCCTACAGTGT
Found at i:14750 original size:41 final size:41
Alignment explanation
Indices: 14693--14847 Score: 274
Period size: 41 Copynumber: 3.8 Consensus size: 41
14683 CATTTTTAAA
* *
14693 ACTATCGCAGCGCGAAATGGAAAATCACAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
14734 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
14775 ACTATCGCAACGCGAAATGGAAAATCGCAATGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
14816 ACTATCGCAACGCGAAATGGAAAACCGCAACG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACG
14848 CAAAATGGAA
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 109 1.00
ACGTcount: A:0.39, C:0.25, G:0.22, T:0.14
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
Found at i:14762 original size:20 final size:20
Alignment explanation
Indices: 14737--14870 Score: 105
Period size: 20 Copynumber: 6.6 Consensus size: 20
14727 ACTGTAGACT
14737 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
14757 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
14778 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * **
14798 ATCGCAA--TGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
14819 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* *
14839 ACCGCAACGCAAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
14859 ATCGCAACGCGA
1 ATCGCAACGCGA
14871 TTTTCAACTA
Statistics
Matches: 86, Mismatches: 18, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
18 5 0.06
19 6 0.07
20 46 0.53
21 18 0.21
22 6 0.07
23 5 0.06
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:14783 original size:21 final size:21
Alignment explanation
Indices: 14720--14827 Score: 75
Period size: 21 Copynumber: 5.2 Consensus size: 21
14710 TGGAAAATCA
14720 CAACGACACTGTAGACTATCG
1 CAACGACACTGTAGACTATCG
* **
14741 CAACG-CGAAATG--GAAAATCG
1 CAACGAC--ACTGTAGACTATCG
14761 CAACGACACTGTAGACTATCG
1 CAACGACACTGTAGACTATCG
* **
14782 CAACG-CGAAATG--GAAAATCG
1 CAACGAC--ACTGTAGACTATCG
*
14802 CAATGACACTGTAGACTATCG
1 CAACGACACTGTAGACTATCG
14823 CAACG
1 CAACG
14828 CGAAATGGAA
Statistics
Matches: 63, Mismatches: 14, Indels: 20
0.65 0.14 0.21
Matches are distributed among these distances:
19 6 0.10
20 23 0.37
21 28 0.44
22 6 0.10
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (21 bp):
CAACGACACTGTAGACTATCG
Found at i:14886 original size:61 final size:61
Alignment explanation
Indices: 14780--14895 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 61
14770 TGTAGACTAT
* * *
14780 CGCAACGCGAAATGGAAAATCGCAATGACACTGTAGACTATCGCAACGCGAAATGGAAAAC
1 CGCAACGCAAAATGGAAAATCGCAACGACACTGTAGACTACCGCAACGCGAAATGGAAAAC
* *
14841 CGCAACGCAAAATGGAAAATCGCAACG-CGATTTTCA-ACTACCGCAACGCGAAATG
1 CGCAACGCAAAATGGAAAATCGCAACGAC-ACTGT-AGACTACCGCAACGCGAAATG
14896 CAGCGCGAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 1 0.02
61 46 0.96
62 1 0.02
ACGTcount: A:0.40, C:0.25, G:0.22, T:0.14
Consensus pattern (61 bp):
CGCAACGCAAAATGGAAAATCGCAACGACACTGTAGACTACCGCAACGCGAAATGGAAAAC
Found at i:14886 original size:82 final size:81
Alignment explanation
Indices: 14696--14870 Score: 217
Period size: 82 Copynumber: 2.1 Consensus size: 81
14686 TTTTAAAACT
* * * * * *
14696 ATCGCAGCGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGGAAAATCG
1 ATCGCAACGCGAAATGCAAAACCGCAATGACACTGTAGACTATCGCAACGCGAAATGGAAAACCG
* * **
14761 CAACGACACTGTAGACT
66 CAACGAAAATG-AGAAA
* *
14778 ATCGCAACGCGAAATGGAAAATCGCAATGACACTGTAGACTATCGCAACGCGAAATGGAAAACCG
1 ATCGCAACGCGAAATGCAAAACCGCAATGACACTGTAGACTATCGCAACGCGAAATGGAAAACCG
14843 CAACGCAAAATG-GAAA
66 CAACG-AAAATGAGAAA
14859 ATCGCAACGCGA
1 ATCGCAACGCGA
14871 TTTTCAACTA
Statistics
Matches: 84, Mismatches: 8, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
81 14 0.17
82 66 0.79
83 4 0.05
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.13
Consensus pattern (81 bp):
ATCGCAACGCGAAATGCAAAACCGCAATGACACTGTAGACTATCGCAACGCGAAATGGAAAACCG
CAACGAAAATGAGAAA
Found at i:21268 original size:3 final size:3
Alignment explanation
Indices: 21250--21305 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
21240 TCTACAAAAA
* *
21250 TAT TAT AAT ATAT TAT TAT TAT TAT TAT TAT TAT TAA T-T TAT ATAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
*
21296 TAT AAT TAT T
1 TAT TAT TAT T
21306 TTTCGGGCCC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 1 0.02
3 38 0.86
4 5 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:22809 original size:3 final size:3
Alignment explanation
Indices: 22803--22838 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
22793 GTTAAAAAAA
*
22803 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
22839 CTTAATTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:25987 original size:10 final size:9
Alignment explanation
Indices: 25972--26015 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 9
25962 CAATTAGAAC
25972 AAAAAGAGGA
1 AAAAAGA-GA
25982 AAAAAGAAGA
1 AAAAAG-AGA
25992 AAAAAGAGA
1 AAAAAGAGA
*
26001 AAAACAAAGA
1 AAAA-AGAGA
26011 AAAAA
1 AAAAA
26016 CAAAGAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
9 8 0.26
10 22 0.71
11 1 0.03
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAAGAGA
Found at i:25989 original size:19 final size:19
Alignment explanation
Indices: 25967--26004 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
25957 AGATCCAATT
25967 AGAAC-AAAAAGAGGAAAAA
1 AGAACAAAAAAGA-GAAAAA
*
25986 AGAAGAAAAAAGAGAAAAA
1 AGAACAAAAAAGAGAAAAA
26005 CAAAGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (19 bp):
AGAACAAAAAAGAGAAAAA
Found at i:26010 original size:19 final size:20
Alignment explanation
Indices: 25972--26015 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
25962 CAATTAGAAC
25972 AAAAAGAGGAAAAAAGAAGA
1 AAAAAGAGGAAAAAAGAAGA
25992 AAAAAGA-GAAAAACA-AAGA
1 AAAAAGAGGAAAAA-AGAAGA
26011 AAAAA
1 AAAAA
26016 CAAAGAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAGAGGAAAAAAGAAGA
Found at i:26024 original size:23 final size:23
Alignment explanation
Indices: 25983--26043 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
25973 AAAAGAGGAA
*
25983 AAAAGAAGAAA-AAAGAGAAAA-
1 AAAAGAAAAAACAAAGAGAAAAT
26004 ACAAAGAAAAAACAAAGAGAAAAT
1 A-AAAGAAAAAACAAAGAGAAAAT
*
26028 AAAAAAAAGAAACAAA
1 AAAAGAAA-AAACAAA
26044 AACAAAGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 1 0.03
22 9 0.26
23 16 0.47
24 8 0.24
ACGTcount: A:0.80, C:0.05, G:0.13, T:0.02
Consensus pattern (23 bp):
AAAAGAAAAAACAAAGAGAAAAT
Found at i:26055 original size:11 final size:10
Alignment explanation
Indices: 25988--26056 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 10
25978 AGGAAAAAAG
25988 AAGAAAAA-A
1 AAGAAAAACA
*
25997 GAGAAAAACA
1 AAGAAAAACA
26007 AAGAAAAAACA
1 AAG-AAAAACA
*
26018 AAGAGAAAATA
1 AAGA-AAAACA
*
26029 AA-AAAAAGA
1 AAGAAAAACA
*
26038 AACAAAAACA
1 AAGAAAAACA
26048 AAGGAAAAA
1 AA-GAAAAA
26057 GTGAAGAGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
9 14 0.29
10 13 0.27
11 22 0.45
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (10 bp):
AAGAAAAACA
Found at i:32826 original size:51 final size:49
Alignment explanation
Indices: 32759--32873 Score: 126
Period size: 51 Copynumber: 2.3 Consensus size: 49
32749 AGGATTCAAT
* * *
32759 TTATTATTTTAATAGGAATTAAGA-AATAGT-TAAAACATTATTTTTAGTTTA
1 TTATTATTTTATTAGGAACTAAGATAA-A-TCT-AAACATTATCTTT-GTTTA
*
32810 TTATTATTTTATTAGGAACTAGGATAAATCTAAACATTATCTTTGTTTA
1 TTATTATTTTATTAGGAACTAAGATAAATCTAAACATTATCTTTGTTTA
32859 TTATATATTTCTATT
1 TTAT-TATTT-TATT
32874 CACTTGTTAC
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
49 9 0.16
50 18 0.32
51 27 0.48
52 2 0.04
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.50
Consensus pattern (49 bp):
TTATTATTTTATTAGGAACTAAGATAAATCTAAACATTATCTTTGTTTA
Found at i:34560 original size:21 final size:21
Alignment explanation
Indices: 34534--34575 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
34524 TAGGAACCCA
34534 TACTTGTTTGATTCTAAAAAG
1 TACTTGTTTGATTCTAAAAAG
34555 TACTTGTTTGATTCTAAAAAG
1 TACTTGTTTGATTCTAAAAAG
34576 GTTTCTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (21 bp):
TACTTGTTTGATTCTAAAAAG
Found at i:35269 original size:3 final size:3
Alignment explanation
Indices: 35261--35294 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
35251 TCATACCTCT
*
35261 TTC TTC TTC TTG TTC TT- TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
35295 GTTTCCTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:35282 original size:17 final size:17
Alignment explanation
Indices: 35260--35294 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
35250 TTCATACCTC
*
35260 TTTCTTCTTCTTGTTCT
1 TTTCTTCTTCTTCTTCT
35277 TTTCTTCTTCTTCTTCT
1 TTTCTTCTTCTTCTTCT
35294 T
1 T
35295 GTTTCCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTCTTCTTCTTCTTCT
Found at i:37888 original size:13 final size:13
Alignment explanation
Indices: 37870--37894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37860 TCAATACCCT
37870 AAACCCAAATCCG
1 AAACCCAAATCCG
37883 AAACCCAAATCC
1 AAACCCAAATCC
37895 TCTAAAATCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.40, G:0.04, T:0.08
Consensus pattern (13 bp):
AAACCCAAATCCG
Found at i:38586 original size:21 final size:22
Alignment explanation
Indices: 38560--38611 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
38550 AATAAATAAA
* *
38560 ATAATATAAATA-ACTAACTAT
1 ATAATATAAAAATACAAACTAT
38581 ATAATACTAAAAATACAAACTAT
1 ATAATA-TAAAAATACAAACTAT
*
38604 ATATTATA
1 ATAATATA
38612 TGTTTTCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 6 0.23
22 7 0.27
23 13 0.50
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAATATAAAAATACAAACTAT
Found at i:38667 original size:11 final size:11
Alignment explanation
Indices: 38651--38701 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
38641 TATTATACAT
38651 TTTTAAAATTA
1 TTTTAAAATTA
*
38662 TTTTAAAAACTA
1 TTTT-AAAATTA
* *
38674 TTAT-ACATT-
1 TTTTAAAATTA
38683 TTTTAAAATTA
1 TTTTAAAATTA
38694 TTTTAAAA
1 TTTTAAAA
38702 AACTACATAC
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
9 3 0.10
10 7 0.23
11 12 0.39
12 9 0.29
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTTAAAATTA
Found at i:38722 original size:104 final size:104
Alignment explanation
Indices: 38597--38819 Score: 299
Period size: 104 Copynumber: 2.1 Consensus size: 104
38587 CTAAAAATAC
* * *
38597 AAACTATATATTATATGTTTTCAATACCATTTTTAAAAAATATATATTATACATTTTTAAAATTA
1 AAACTATATATTATATATTTTCAAAACCATTTTT-AAAAA-ATATATTATACATTTTCAAAATTA
* *
38662 TTTTAAAAACTATTATAC-AT-T-TTTTAAAATTATTTTAAA
64 TTTTAAAAACTA-TATACTATATGTTTAAAAATCATTTTAAA
* * * **
38701 AAACTACATACTATATATTTTCAAAACCATTTTTAAAAACTATATTATATGTTTTCAAAATTATT
1 AAACTATATATTATATATTTTCAAAACCATTTTTAAAAAATATATTATACATTTTCAAAATTATT
*
38766 TTAAAAACTATATACTATATGTTTAAAAATCGTTTTAAA
66 TTAAAAACTATATACTATATGTTTAAAAATCATTTTAAA
38805 AAACTATATATTATA
1 AAACTATATATTATA
38820 CGTTTTTAAC
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
101 5 0.05
102 34 0.33
103 6 0.06
104 58 0.56
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.45
Consensus pattern (104 bp):
AAACTATATATTATATATTTTCAAAACCATTTTTAAAAAATATATTATACATTTTCAAAATTATT
TTAAAAACTATATACTATATGTTTAAAAATCATTTTAAA
Found at i:38772 original size:69 final size:69
Alignment explanation
Indices: 38603--38813 Score: 223
Period size: 68 Copynumber: 3.1 Consensus size: 69
38593 ATACAAACTA
* ** * * * * *
38603 TATATTATATGTTTTCAATACCATTTTTAAAAAATATATATTATACATTTTTAAAATTA-TTTTA
1 TATATTATATGTTTTCAAAATTA-TTTTAAAAACTATATACTATATATTTTAAAAATCATTTTTA
38667 AAAAC
65 AAAAC
* * * * *
38672 TAT-TATACAT-TTTTTAAAATTATTTTAAAAAACTACATACTATATATTTTCAAAACCATTTTT
1 TATAT-TATATGTTTTCAAAATTATTTT-AAAAACTATATACTATATATTTTAAAAATCATTTTT
38735 AAAAAC
64 AAAAAC
* * *
38741 TATATTATATGTTTTCAAAATTATTTTAAAAACTATATACTATAT-GTTTAAAAATCGTTTTAAA
1 TATATTATATGTTTTCAAAATTATTTTAAAAACTATATACTATATATTTTAAAAATCATTTTTAA
38805 AAAC
66 AAAC
38809 TATAT
1 TATAT
38814 ATTATACGTT
Statistics
Matches: 117, Mismatches: 20, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
67 4 0.03
68 56 0.48
69 41 0.35
70 16 0.14
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (69 bp):
TATATTATATGTTTTCAAAATTATTTTAAAAACTATATACTATATATTTTAAAAATCATTTTTAA
AAAC
Found at i:38807 original size:35 final size:35
Alignment explanation
Indices: 38597--38824 Score: 177
Period size: 36 Copynumber: 6.6 Consensus size: 35
38587 CTAAAAATAC
* * **
38597 AAACTATATATTATATGTTTTCAATACCATTTTTAAA
1 AAACTATATACTATATG-TTTCAAAATTA-TTTTAAA
* *
38634 AAA-TATATATTATACAT-TTTTAAAATTATTTT-AA
1 AAACTATATACTAT--ATGTTTCAAAATTATTTTAAA
*
38668 AAACTATTATAC-AT-T-TTTTAAAATTATTTTAAA
1 AAACTA-TATACTATATGTTTCAAAATTATTTTAAA
* * ** *
38701 AAACTACATACTATATATTTTCAAAACCATTTTTAA
1 AAACTATATACTATAT-GTTTCAAAATTATTTTAAA
38737 AAACTATAT--TATATGTTTTCAAAATTATTTT-AA
1 AAACTATATACTATATG-TTTCAAAATTATTTTAAA
* **
38770 AAACTATATACTATATGTTTAAAAATCGTTTTAAA
1 AAACTATATACTATATGTTTCAAAATTATTTTAAA
* *
38805 AAACTATATATTATACGTTT
1 AAACTATATACTATATGTTT
38825 TTAACACTAT
Statistics
Matches: 159, Mismatches: 19, Indels: 28
0.77 0.09 0.14
Matches are distributed among these distances:
32 20 0.13
33 21 0.13
34 36 0.23
35 34 0.21
36 43 0.27
37 3 0.02
38 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (35 bp):
AAACTATATACTATATGTTTCAAAATTATTTTAAA
Found at i:39937 original size:22 final size:22
Alignment explanation
Indices: 39903--39947 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
39893 TAGTCGTTCA
*
39903 CCGTTGAATTTGGCTTTCGAAC
1 CCGTTGAATTTGGCTCTCGAAC
39925 CCGTCTGAA-TTGGCTCTCGAAC
1 CCGT-TGAATTTGGCTCTCGAAC
39947 C
1 C
39948 TGATTTGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.31
Consensus pattern (22 bp):
CCGTTGAATTTGGCTCTCGAAC
Found at i:39956 original size:23 final size:23
Alignment explanation
Indices: 39906--39956 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
39896 TCGTTCACCG
*
39906 TTGAATTTGGCTTTCGAACCCGT
1 TTGAATTTGGCTCTCGAACCCGT
* *
39929 CTGAA-TTGGCTCTCGAACCTGAT
1 TTGAATTTGGCTCTCGAACCCG-T
39952 TTGAA
1 TTGAA
39957 GTTGATTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (23 bp):
TTGAATTTGGCTCTCGAACCCGT
Found at i:44106 original size:258 final size:258
Alignment explanation
Indices: 43637--44112 Score: 544
Period size: 258 Copynumber: 1.8 Consensus size: 258
43627 AGATCGATTC
* * * * * *
43637 AGTTGGTTGTACCACCGTATGGCTGAACCAGACGGACTCTCCTGGAAATAATTAATCAGGAGTTG
1 AGTTGGTTGTACCACCGGATAGCTGAACCAGACGGACTCTCCTAGAAACAATGAATCAGAAGTTG
* * * * * ** * * * *
43702 GTCGTTTCCTACGTATCCTGTCATCTTTCGATTGAACATGGTAATGTGGGTTGAAGGGCAGCTGT
66 GTCATTTCCCACATATCCTATCATCTTCCGACAGAACATAGTAATATGAGCTGAAGGGCAGCTGT
* * *
43767 TCCCATCGAATTTCTCAAACTCGTGGGATTTGAATTTCAGAGGAAGAAACAAATCTGGGACTAAA
131 TCCCATCGAACTTCTCAAACTCGCGGGATTTGAATTTCAGAGGAAGAAACAAATCTGGGACCAAA
* * **
43832 CTTAGTTCTGTTGCATCAACTCCATAGAAATCATTGTCTCCCTAAACCATCTACATTTGGATG
196 CTCAGCTCCATTGCATCAACTCCATAGAAATCATTGTCTCCCTAAACCATCTACATTTGGATG
* * * * *
43895 AGTTGGTTGTACCACCGGATAGCTGAACCGGACATG-CTCTCCTAGAAGCAATGGATGAGAAGTT
1 AGTTGGTTGTACCACCGGATAGCTGAACCAGAC-GGACTCTCCTAGAAACAATGAATCAGAAGTT
* *
43959 GGTCATTTCCCCCATATCCTATCATCTTCCGACAGAACATAGTGATATGAGCTGAAGGGCAGCTG
65 GGTCATTTCCCACATATCCTATCATCTTCCGACAGAACATAGTAATATGAGCTGAAGGGCAGCTG
* * ** * * *
44024 TTCCCGTCGAACTTCTCGAACTC-CGGGACTTTGAATTTTGGTGGAAGCACCAAATC-GGGAACC
130 TTCCCATCGAACTTCTCAAACTCGCGGGA-TTTGAATTTCAGAGGAAGAAACAAATCTGGG-ACC
* *
44087 AGACTCAGCTCCATTGCATCCACTCC
193 AAACTCAGCTCCATTGCATCAACTCC
44113 GTAGTAGTCG
Statistics
Matches: 175, Mismatches: 40, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
257 7 0.04
258 167 0.95
259 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.28
Consensus pattern (258 bp):
AGTTGGTTGTACCACCGGATAGCTGAACCAGACGGACTCTCCTAGAAACAATGAATCAGAAGTTG
GTCATTTCCCACATATCCTATCATCTTCCGACAGAACATAGTAATATGAGCTGAAGGGCAGCTGT
TCCCATCGAACTTCTCAAACTCGCGGGATTTGAATTTCAGAGGAAGAAACAAATCTGGGACCAAA
CTCAGCTCCATTGCATCAACTCCATAGAAATCATTGTCTCCCTAAACCATCTACATTTGGATG
Found at i:48009 original size:17 final size:18
Alignment explanation
Indices: 47989--48036 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
47979 AGGTAAAGAA
*
47989 AAAAAAATAACAAAA-AT
1 AAAAAAATAAAAAAACAT
* *
48006 AAAAATAGAAAAAAACAT
1 AAAAAAATAAAAAAACAT
48024 AAAATAAATAAAA
1 AAAA-AAATAAAA
48037 GAATAATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 12 0.50
18 6 0.25
19 6 0.25
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.12
Consensus pattern (18 bp):
AAAAAAATAAAAAAACAT
Found at i:48016 original size:27 final size:27
Alignment explanation
Indices: 47985--48036 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
47975 AAAAAGGTAA
47985 AGAAAAAAAAATAACAA-AAATAAAAAT
1 AGAAAAAAAAATAA-AATAAATAAAAAT
*
48012 AGAAAAAAACATAAAATAAATAAAA
1 AGAAAAAAAAATAAAATAAATAAAA
48037 GAATAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.12
Consensus pattern (27 bp):
AGAAAAAAAAATAAAATAAATAAAAAT
Found at i:50224 original size:12 final size:13
Alignment explanation
Indices: 50207--50235 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
50197 TTTCTTTTAT
50207 TTTTTAAA-ATAA
1 TTTTTAAATATAA
50219 TTTTTAAATATAA
1 TTTTTAAATATAA
50232 TTTT
1 TTTT
50236 AAAGGATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTTAAATATAA
Found at i:50377 original size:15 final size:15
Alignment explanation
Indices: 50346--50375 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
50336 TTCAGTAATC
50346 TAAATTTCTACAATT
1 TAAATTTCTACAATT
50361 TAAATTT-TACAATT
1 TAAATTTCTACAATT
50375 T
1 T
50376 TATTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATTTCTACAATT
Found at i:52334 original size:34 final size:34
Alignment explanation
Indices: 52294--52374 Score: 153
Period size: 34 Copynumber: 2.4 Consensus size: 34
52284 TAAGCTCAAC
*
52294 TCAACTCAAACTCATAAGCTAAAAATTATCAAGT
1 TCAACTCAAACTCACAAGCTAAAAATTATCAAGT
52328 TCAACTCAAACTCACAAGCTAAAAATTATCAAGT
1 TCAACTCAAACTCACAAGCTAAAAATTATCAAGT
52362 TCAACTCAAACTC
1 TCAACTCAAACTC
52375 GAAATATAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.46, C:0.25, G:0.05, T:0.25
Consensus pattern (34 bp):
TCAACTCAAACTCACAAGCTAAAAATTATCAAGT
Found at i:53480 original size:2 final size:2
Alignment explanation
Indices: 53473--53507 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
53463 ACATTTAATA
*
53473 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53508 CATAAAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Done.