Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006650.1 Hibiscus syriacus cultivar Beakdansim tig00016402_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: 76525
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:1455 original size:18 final size:19
Alignment explanation
Indices: 1428--1463 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1418 CATTAACATC
*
1428 ATCATTTTCACCA-AATAT
1 ATCATCTTCACCACAATAT
1446 ATCATCTTCACCACAATA
1 ATCATCTTCACCACAATA
1464 ACTCATCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (19 bp):
ATCATCTTCACCACAATAT
Found at i:1670 original size:17 final size:18
Alignment explanation
Indices: 1634--1690 Score: 82
Period size: 17 Copynumber: 3.3 Consensus size: 18
1624 TCATCACCAT
* *
1634 CATCACTACCACCTTCAC
1 CATCACCACTACCTTCAC
1652 CATCACCACTACC-TCAC
1 CATCACCACTACCTTCAC
1669 CATCA-CACTACCTTCAC
1 CATCACCACTACCTTCAC
1686 CATCA
1 CATCA
1691 TCATCATCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
16 7 0.19
17 18 0.50
18 11 0.31
ACGTcount: A:0.30, C:0.49, G:0.00, T:0.21
Consensus pattern (18 bp):
CATCACCACTACCTTCAC
Found at i:3499 original size:24 final size:23
Alignment explanation
Indices: 3467--3512 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
3457 GCTGATTAGC
*
3467 TGTAACTGTTTCTGGTTAAGTTGT
1 TGTAACTGTTCCTGGTT-AGTTGT
3491 TGTAACTGTTCCTGGTTAGTTG
1 TGTAACTGTTCCTGGTTAGTTG
3513 GGCCGTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.15, C:0.11, G:0.26, T:0.48
Consensus pattern (23 bp):
TGTAACTGTTCCTGGTTAGTTGT
Found at i:3526 original size:19 final size:19
Alignment explanation
Indices: 3502--3550 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
3492 GTAACTGTTC
3502 CTGGTTAGTTGGGCCGTTT
1 CTGGTTAGTTGGGCCGTTT
3521 CTGGTTAGTTGGGCCGTTT
1 CTGGTTAGTTGGGCCGTTT
3540 CTGGTTAGTTG
1 CTGGTTAGTTG
3551 AGCTAGTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.06, C:0.14, G:0.37, T:0.43
Consensus pattern (19 bp):
CTGGTTAGTTGGGCCGTTT
Found at i:4422 original size:17 final size:19
Alignment explanation
Indices: 4400--4440 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
4390 GTAAATTCTA
*
4400 TTAATTTGA-TCA-TAATT
1 TTAATTTGATTCATTAAAT
4417 TTAATTTGATTCATTAAAT
1 TTAATTTGATTCATTAAAT
4436 TTAAT
1 TTAAT
4441 CATCTATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 3 0.14
19 9 0.43
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (19 bp):
TTAATTTGATTCATTAAAT
Found at i:4953 original size:26 final size:26
Alignment explanation
Indices: 4922--4977 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
4912 CGAAACGATT
4922 TTTTCTTAAAAAGTGAAAAAATGAGA
1 TTTTCTTAAAAAGTGAAAAAATGAGA
*
4948 TTTTCTTAAAGAGTGAAAAAATGAGA
1 TTTTCTTAAAAAGTGAAAAAATGAGA
4974 TTTT
1 TTTT
4978 GAAAACCACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.36
Consensus pattern (26 bp):
TTTTCTTAAAAAGTGAAAAAATGAGA
Found at i:19295 original size:40 final size:41
Alignment explanation
Indices: 19245--19323 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 41
19235 CTCGAACTCC
19245 AATTTCGCAACACAATTTCTAAATTC-CTAACGCGAATTTGG
1 AATTTCGCAACACAATTTCTAAATTCGC-AACGCGAATTTGG
* * *
19286 AATTT-GCAACACAGTTTTTAAATTCGCAACTCGAATTT
1 AATTTCGCAACACAATTTCTAAATTCGCAACGCGAATTT
19324 CCCAAATTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 28 0.82
41 6 0.18
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (41 bp):
AATTTCGCAACACAATTTCTAAATTCGCAACGCGAATTTGG
Found at i:19314 original size:20 final size:20
Alignment explanation
Indices: 19286--19356 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
19276 GCGAATTTGG
* * *
19286 AATTTGCAACACAGTTTTTA
1 AATTCGCAACTCAGTTTTCA
* *
19306 AATTCGCAACTCGAATTTCCCA
1 AATTCGCAACTC-AGTTT-TCA
19328 AATTCGCAACTCAGTTTTCA
1 AATTCGCAACTCAGTTTTCA
*
19348 AATTTGCAA
1 AATTCGCAA
19357 TTTGAATTCG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 20 0.49
21 8 0.20
22 13 0.32
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.34
Consensus pattern (20 bp):
AATTCGCAACTCAGTTTTCA
Found at i:19538 original size:22 final size:22
Alignment explanation
Indices: 19513--19558 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
19503 TTCGCAACTC
*
19513 AAATTGGCGCATTCGAGTTGCG
1 AAATTGGCGAATTCGAGTTGCG
19535 AAATTGGCGAATTCGAGTTGCG
1 AAATTGGCGAATTCGAGTTGCG
19557 AA
1 AA
19559 TTTTTTCTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.26
Consensus pattern (22 bp):
AAATTGGCGAATTCGAGTTGCG
Found at i:19638 original size:20 final size:20
Alignment explanation
Indices: 19615--19674 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
19605 CGAATTCGAA
19615 TTGCGAATTTGAAAACTGAG
1 TTGCGAATTTGAAAACTGAG
** *
19635 TTGCGAATTTTGGAAATTTGTG
1 TTGCGAA-TTT-GAAAACTGAG
*
19657 TTGCGAATTTGGAAACTG
1 TTGCGAATTTGAAAACTG
19675 TGTTTTCGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 12 0.38
21 6 0.19
22 14 0.44
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.37
Consensus pattern (20 bp):
TTGCGAATTTGAAAACTGAG
Found at i:19678 original size:20 final size:20
Alignment explanation
Indices: 19615--19678 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 20
19605 CGAATTCGAA
* *
19615 TTGCGAATTTGAAAACTGAG
1 TTGCGAATTTGGAAACTGTG
*
19635 TTGCGAATTTTGGAAATTTGTG
1 TTGCGAA-TTTGGAAA-CTGTG
19657 TTGCGAATTTGGAAACTGTG
1 TTGCGAATTTGGAAACTGTG
19677 TT
1 TT
19679 TTCGAAATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 13 0.34
21 15 0.39
22 10 0.26
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.39
Consensus pattern (20 bp):
TTGCGAATTTGGAAACTGTG
Found at i:19684 original size:21 final size:21
Alignment explanation
Indices: 19615--19690 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
19605 CGAATTCGAA
* *
19615 TTGCGAATTTGAAAACTGAG-
1 TTGCGAATTTGGAAACTGTGT
*
19635 TTGCGAATTTTGGAAA-TTTGT
1 TTGCGAA-TTTGGAAACTGTGT
19656 GTTGCGAATTTGGAAACTGTGT
1 -TTGCGAATTTGGAAACTGTGT
* *
19678 TTTCGAAATTGGA
1 TTGCGAATTTGGA
19691 GTTCGTCTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 9 0.20
21 26 0.57
22 11 0.24
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (21 bp):
TTGCGAATTTGGAAACTGTGT
Found at i:24067 original size:21 final size:21
Alignment explanation
Indices: 24043--24083 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
24033 ATATGTTTCG
* *
24043 CTCCCCCTAAATTTTAATTCT
1 CTCCACCTAAATTTAAATTCT
24064 CTCCACCTAAATTTAAATTC
1 CTCCACCTAAATTTAAATTC
24084 ACCCTCTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (21 bp):
CTCCACCTAAATTTAAATTCT
Found at i:33749 original size:27 final size:27
Alignment explanation
Indices: 33711--33787 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
33701 ATCAATTCCT
* *
33711 CTTTTCTTTTTTTTTTCTTTTTCTAAC
1 CTTTTCTATTTTTTTTCTTTTTCGAAC
* * *
33738 CTTTTCTATTTTTGTTGTTGTTCGAAC
1 CTTTTCTATTTTTTTTCTTTTTCGAAC
* *
33765 CATTTTTTCTTTTTTTTCTTTTT
1 C-TTTTCTATTTTTTTTCTTTTT
33788 TCTCGAACGT
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.08, C:0.16, G:0.05, T:0.71
Consensus pattern (27 bp):
CTTTTCTATTTTTTTTCTTTTTCGAAC
Found at i:35062 original size:46 final size:47
Alignment explanation
Indices: 34976--35064 Score: 144
Period size: 46 Copynumber: 1.9 Consensus size: 47
34966 AGTAGAGCGT
*
34976 TACCTAAAATGTTATTTTTTTCTACCGGAAATATTAATATCGGGCGC
1 TACCTAAAATGTTATTTTTTTCTACCAGAAATATTAATATCGGGCGC
* *
35023 TACCTAAAATGTTA-TTTTTTCTACCAGAAATGTTTATATCGG
1 TACCTAAAATGTTATTTTTTTCTACCAGAAATATTAATATCGG
35065 AAATATTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 25 0.64
47 14 0.36
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (47 bp):
TACCTAAAATGTTATTTTTTTCTACCAGAAATATTAATATCGGGCGC
Found at i:35822 original size:15 final size:15
Alignment explanation
Indices: 35802--35830 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35792 ATTGAGGAAG
35802 TAAAATGTTAGTTTC
1 TAAAATGTTAGTTTC
35817 TAAAATGTTAGTTT
1 TAAAATGTTAGTTT
35831 TTAGATTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (15 bp):
TAAAATGTTAGTTTC
Found at i:41671 original size:18 final size:20
Alignment explanation
Indices: 41648--41695 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
41638 AAAGAAGAAA
*
41648 CATCGATTGCA-AATG-GTG
1 CATCGATTGCATAAGGAGTG
41666 CATCGA-TGCATAAGGAGTG
1 CATCGATTGCATAAGGAGTG
41685 CATCGA-TGCAT
1 CATCGATTGCAT
41696 CCCTTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 9 0.33
19 14 0.52
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (20 bp):
CATCGATTGCATAAGGAGTG
Found at i:41713 original size:64 final size:63
Alignment explanation
Indices: 41623--41759 Score: 152
Period size: 64 Copynumber: 2.2 Consensus size: 63
41613 GGTAAGGTGT
* **
41623 ATCGATGCACTCTTTAAAGAAGAAACATCGATTGCAAATGGTGCATCGATGCATAAGG-AGTGC
1 ATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAAATGGTGCATCGATGCAT-AGGTAGTGC
* * * * * *
41686 ATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTAGTGC
1 ATCGATGCA-CCCTTTAAAGAAG-AAACATCGAAGGCAAATGGTGCATCGATGCATAGGTAGTGC
41750 ATCGATGCAC
1 ATCGATGCAC
41760 ATGTTAAAGA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
63 14 0.23
64 48 0.77
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (63 bp):
ATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAAATGGTGCATCGATGCATAGGTAGTGC
Found at i:41795 original size:20 final size:23
Alignment explanation
Indices: 41747--41802 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 23
41737 GCATGGGTAG
41747 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATGTT-AAGAA
*
41771 TGCATCGATGCAC-TG-T-AGCA
1 TGCATCGATGCACATGTTAAGAA
41791 TGCATCGATGCA
1 TGCATCGATGCA
41803 GTTCAAGGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 2 0.06
24 13 0.42
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (23 bp):
TGCATCGATGCACATGTTAAGAA
Found at i:42793 original size:31 final size:31
Alignment explanation
Indices: 42755--42850 Score: 158
Period size: 31 Copynumber: 3.1 Consensus size: 31
42745 AGAGTCGAGG
42755 GTTTACCTAGGTTCTTCGGGACCTATGAACA
1 GTTTACCTAGGTTCTTCGGGACCTATGAACA
42786 GTTTACCTAGGTTCTTCGGGACCTAT-AGACA
1 GTTTACCTAGGTTCTTCGGGACCTATGA-ACA
* *
42817 GTTTACCTAGGTTCGTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGGGACCTATGAACA
42848 GTT
1 GTT
42851 GTCGAGGTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
30 1 0.02
31 60 0.98
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.32
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGGGACCTATGAACA
Found at i:45938 original size:24 final size:20
Alignment explanation
Indices: 45923--45960 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
45913 CACATGTTAA
45923 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
45943 AGCATGCATCGATGCACT
1 AGAATGCATCGATGCACT
45961 TCAAGGGGAA
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:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:46948 original size:31 final size:31
Alignment explanation
Indices: 46910--46974 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
46900 AGAGTCGAGG
*
46910 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCGTCGGGACCTATGGACA
46941 GTTTACCTAGGTTCGTCGGGACCTATGGACA
1 GTTTACCTAGGTTCGTCGGGACCTATGGACA
46972 GTT
1 GTT
46975 GCCGAGGTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.32
Consensus pattern (31 bp):
GTTTACCTAGGTTCGTCGGGACCTATGGACA
Found at i:47016 original size:29 final size:30
Alignment explanation
Indices: 46960--47031 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
46950 GGTTCGTCGG
* * * *
46960 GACCTATGGACAGTTGCCGAGGTTCTTTAT
1 GACCTCTGGATAGTTACCGAGGGTCTTTAT
*
46990 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGATAGTTACCGAGGGTCTTTAT
47019 GACCTCTGGATAG
1 GACCTCTGGATAG
47032 GTCCTTCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGGTCTTTAT
Found at i:49005 original size:25 final size:26
Alignment explanation
Indices: 48967--49017 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
48957 TATTTTAAAA
*
48967 AATTATTTCTAAATTTATAATATAAT
1 AATTATTTCAAAATTTATAATATAAT
*
48993 AATT-TTTCAAAATTTATAATTTAAT
1 AATTATTTCAAAATTTATAATATAAT
49018 TTCAAACTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
AATTATTTCAAAATTTATAATATAAT
Found at i:49783 original size:15 final size:16
Alignment explanation
Indices: 49763--49803 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
49753 ATTCCTTTAT
49763 TTTAATTTTAATAA-A
1 TTTAATTTTAATAATA
49778 TTTAATTTT--TAATA
1 TTTAATTTTAATAATA
*
49792 TGTAATTTTAAT
1 TTTAATTTTAAT
49804 TTTTAAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
13 3 0.14
14 9 0.41
15 9 0.41
16 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
TTTAATTTTAATAATA
Found at i:50026 original size:22 final size:22
Alignment explanation
Indices: 49967--50026 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 22
49957 TAATTATATA
*
49967 TATATTAATTTAAAAATACTTT
1 TATATTAACTTAAAAATACTTT
49989 TATATTAACTTATTAAATATA-TTT
1 TATATTAACTTA--AAA-ATACTTT
50013 TATTATTAACTTAA
1 TA-TATTAACTTAA
50027 TTTAAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
22 11 0.33
23 1 0.03
24 8 0.24
25 13 0.39
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
TATATTAACTTAAAAATACTTT
Found at i:50031 original size:27 final size:27
Alignment explanation
Indices: 49971--50064 Score: 113
Period size: 27 Copynumber: 3.6 Consensus size: 27
49961 TATATATATA
49971 TTAATTTAAAAATACTTTTA-TATTAAC
1 TTAATTTAAAAATA-TTTTATTATTAAC
*
49998 TT-A-TTAAATATATTTTATTATTAAC
1 TTAATTTAAAAATATTTTATTATTAAC
* **
50023 TTAATTTAAAAATATTTTATTTTTATT
1 TTAATTTAAAAATATTTTATTATTAAC
*
50050 TTCATTTAAAAATAT
1 TTAATTTAAAAATAT
50065 ATAATTTATT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
24 5 0.09
25 17 0.29
26 2 0.03
27 34 0.59
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (27 bp):
TTAATTTAAAAATATTTTATTATTAAC
Found at i:50077 original size:26 final size:27
Alignment explanation
Indices: 50026--50083 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
50016 TATTAACTTA
* * *
50026 ATTTAAAAATATTTTATTTTTATTTTC
1 ATTTAAAAATATATAATTTATATTTTC
*
50053 ATTTAAAAATATATAATTTAT-TTTTT
1 ATTTAAAAATATATAATTTATATTTTC
50079 ATTTA
1 ATTTA
50084 TTAAAAGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (27 bp):
ATTTAAAAATATATAATTTATATTTTC
Found at i:50858 original size:27 final size:27
Alignment explanation
Indices: 50818--50878 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
50808 AATATCATGA
* *
50818 AAAATGTAATATTTTCGGTTGCAACCT
1 AAAATGTAACATTTTCGGTTGAAACCT
50845 AAAATGTAACATTTTCGGTTGAAACCT
1 AAAATGTAACATTTTCGGTTGAAACCT
50872 AAAATGT
1 AAAATGT
50879 TACAAAGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (27 bp):
AAAATGTAACATTTTCGGTTGAAACCT
Found at i:51365 original size:14 final size:14
Alignment explanation
Indices: 51346--51375 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
51336 CGTTAAAATG
*
51346 ATAAACGGACACAA
1 ATAAACGAACACAA
51360 ATAAACGAACACAA
1 ATAAACGAACACAA
51374 AT
1 AT
51376 GAACACAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.20, G:0.10, T:0.10
Consensus pattern (14 bp):
ATAAACGAACACAA
Found at i:51397 original size:53 final size:53
Alignment explanation
Indices: 51334--51439 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
51324 TTAATGCTAG
51334 TTCGTTAAAATGATAAACGGACACAAATAAACGAACACAAATGAACACAAACA
1 TTCGTTAAAATGATAAACGGACACAAATAAACGAACACAAATGAACACAAACA
51387 TTCGTTAAAATGATAAACGGACACAAATAAACGAACACAAATGAACACAAACA
1 TTCGTTAAAATGATAAACGGACACAAATAAACGAACACAAATGAACACAAACA
51440 AACGAACATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.55, C:0.19, G:0.11, T:0.15
Consensus pattern (53 bp):
TTCGTTAAAATGATAAACGGACACAAATAAACGAACACAAATGAACACAAACA
Found at i:51418 original size:14 final size:14
Alignment explanation
Indices: 51399--51457 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 14
51389 CGTTAAAATG
*
51399 ATAAACGGACACAA
1 ATAAACGAACACAA
51413 ATAAACGAACACAA
1 ATAAACGAACACAA
51427 AT----GAACACAA
1 ATAAACGAACACAA
* *
51437 ACAAACGAACATAA
1 ATAAACGAACACAA
*
51451 ATGAACG
1 ATAAACG
51458 TAAACAAACA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
10 9 0.25
14 27 0.75
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.08
Consensus pattern (14 bp):
ATAAACGAACACAA
Found at i:51434 original size:24 final size:24
Alignment explanation
Indices: 51407--51466 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
51397 TGATAAACGG
*
51407 ACACAAATAAACGAACACAAATGA
1 ACACAAACAAACGAACACAAATGA
*
51431 ACACAAACAAACGAACATAAATGA
1 ACACAAACAAACGAACACAAATGA
**
51455 ACGTAAACAAAC
1 ACACAAACAAAC
51467 ATAAATGAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.62, C:0.22, G:0.08, T:0.08
Consensus pattern (24 bp):
ACACAAACAAACGAACACAAATGA
Found at i:51467 original size:20 final size:20
Alignment explanation
Indices: 51439--51476 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
51429 GAACACAAAC
*
51439 AAACGAACATAAATGAACGT
1 AAACAAACATAAATGAACGT
51459 AAACAAACATAAATGAAC
1 AAACAAACATAAATGAAC
51477 AAACCTAAAA
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:0.61, C:0.16, G:0.11, T:0.13
Consensus pattern (20 bp):
AAACAAACATAAATGAACGT
Found at i:51693 original size:14 final size:14
Alignment explanation
Indices: 51674--51714 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
51664 TGGGTTAAAT
51674 ATAAACGAACAAAC
1 ATAAACGAACAAAC
* *
51688 ATAAACTAATAAAC
1 ATAAACGAACAAAC
51702 ATAAACGAACAAA
1 ATAAACGAACAAA
51715 TAATCTAACG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.05, T:0.12
Consensus pattern (14 bp):
ATAAACGAACAAAC
Found at i:56792 original size:21 final size:21
Alignment explanation
Indices: 56767--56834 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
56757 AACTAACAAT
56767 CTAACTAATTAATAACAGCAA
1 CTAACTAATTAATAACAGCAA
56788 CTAACTAATT-ATCAACAGC-A
1 CTAACTAATTAAT-AACAGCAA
* *
56808 -TAACTAATCAAATAACAGAAAA
1 CTAACTAAT-TAATAACAG-CAA
56830 CTAAC
1 CTAAC
56835 ACTCCCCCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 8 0.21
20 8 0.21
21 18 0.46
22 1 0.03
23 4 0.10
ACGTcount: A:0.53, C:0.21, G:0.04, T:0.22
Consensus pattern (21 bp):
CTAACTAATTAATAACAGCAA
Found at i:58604 original size:12 final size:12
Alignment explanation
Indices: 58587--58619 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
58577 AGAAAGAATG
58587 GGTTGAGGTGAA
1 GGTTGAGGTGAA
58599 GGTTGAGGTGAA
1 GGTTGAGGTGAA
58611 GGTTGAGGT
1 GGTTGAGGT
58620 AAAATGGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.52, T:0.27
Consensus pattern (12 bp):
GGTTGAGGTGAA
Found at i:61361 original size:22 final size:22
Alignment explanation
Indices: 61336--61379 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
61326 AGCCTAACTG
*
61336 ACAATCTAACTAATTAACAACA
1 ACAACCTAACTAATTAACAACA
*
61358 ACAACCTAACTAATTATCAACA
1 ACAACCTAACTAATTAACAACA
61380 GCCTAACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.25, G:0.00, T:0.23
Consensus pattern (22 bp):
ACAACCTAACTAATTAACAACA
Found at i:74006 original size:95 final size:96
Alignment explanation
Indices: 73835--74011 Score: 223
Period size: 95 Copynumber: 1.9 Consensus size: 96
73825 TACCGATGAG
* * *
73835 GTAGTATCGATACCATGATAAGGGGTATCGATACCAATAAACAACTAATCTAATTTTGGTATCGA
1 GTAGTATCGATACCATGATAAGGGGTATCGATACCAAGAAACAACGAACCTAATTTTGGTATCGA
* * *
73900 TATCGGTAGGGGATATCGATACCCTAGTAAA
66 TACCCGAAGGGGATATCGATACCCTAGTAAA
* * * * *
73931 GTAGTATCGATACCAT-AGTGA-GGGTATCGATACCAGGCAACATCGAACCTATTTTTGGTATCG
1 GTAGTATCGATACCATGA-TAAGGGGTATCGATACCAAGAAACAACGAACCTAATTTTGGTATCG
*
73994 ATACCCGAAGGGGGTATC
65 ATACCCGAAGGGGATATC
74012 AGTACCATAG
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
95 50 0.74
96 18 0.26
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (96 bp):
GTAGTATCGATACCATGATAAGGGGTATCGATACCAAGAAACAACGAACCTAATTTTGGTATCGA
TACCCGAAGGGGATATCGATACCCTAGTAAA
Found at i:74023 original size:95 final size:96
Alignment explanation
Indices: 73835--74032 Score: 222
Period size: 95 Copynumber: 2.1 Consensus size: 96
73825 TACCGATGAG
* * *
73835 GTAGTATCGATACCATGATAAGGGGTATCGATACCAATAAACAACTAATCTAATTTTGGTATCGA
1 GTAGTATCGATACCATGATAAGGGGTATCGATACCAAGAAACAACGAACCTAATTTTGGTATCGA
* * * *
73900 TATCGGTAGGGGATATCGATACCCTAGTAAA
66 TACCCGAAGGGGATATCGATACCATAGTAAA
* * * * *
73931 GTAGTATCGATACCAT-AGTGA-GGGTATCGATACCAGGCAACATCGAACCTATTTTTGGTATCG
1 GTAGTATCGATACCATGA-TAAGGGGTATCGATACCAAGAAACAACGAACCTAATTTTGGTATCG
* *
73994 ATACCCGAAGGGGGTATC-AGTACCATAGTATA
65 ATACCCGAAGGGGATATCGA-TACCATAGTAAA
*
74026 GAAGTAT
1 GTAGTAT
74033 TTGTACTAGG
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
94 1 0.01
95 66 0.78
96 18 0.21
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (96 bp):
GTAGTATCGATACCATGATAAGGGGTATCGATACCAAGAAACAACGAACCTAATTTTGGTATCGA
TACCCGAAGGGGATATCGATACCATAGTAAA
Found at i:74425 original size:58 final size:58
Alignment explanation
Indices: 74363--74536 Score: 206
Period size: 58 Copynumber: 3.0 Consensus size: 58
74353 ATTACCAAAT
* ** *
74363 GGCACTTCGTGTGCAAAATTTTAAGAAATTCATACTAAGTGTATGAATTGCCGTATAG
1 GGCACTTCGTGCGCAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAG
* * * * *
74421 GGCACTTCGTGCGCTAACATGATAAGAAATCCATACTAAATGTATGAATTTCTGTATTG
1 GGCACTTCGTGCGC-AAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAG
* * * *
74480 GGCACCTT-GTGGGCTAAAGGATAAGAAATTCATACTAAGTGTATAAATTTCCGTATA
1 GGCA-CTTCGTGCGCAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATA
74537 AGAAATATAT
Statistics
Matches: 96, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
58 48 0.50
59 45 0.47
60 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (58 bp):
GGCACTTCGTGCGCAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAG
Found at i:74459 original size:59 final size:58
Alignment explanation
Indices: 74384--74536 Score: 209
Period size: 59 Copynumber: 2.6 Consensus size: 58
74374 TGCAAAATTT
* *
74384 TAAGAAATTCATACTAAGTGTATGAATTGCCGTATAGGGCA-CTTCGTGCGCTAACATGA
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTT-GTGCGCTAA-AGGA
* * * * *
74443 TAAGAAATCCATACTAAATGTATGAATTTCTGTATTGGGCACCTTGTGGGCTAAAGGA
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTTGTGCGCTAAAGGA
*
74501 TAAGAAATTCATACTAAGTGTATAAATTTCCGTATA
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATA
74537 AGAAATATAT
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
58 34 0.42
59 44 0.54
60 3 0.04
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (58 bp):
TAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTTGTGCGCTAAAGGA
Found at i:75293 original size:202 final size:203
Alignment explanation
Indices: 74908--75295 Score: 573
Period size: 202 Copynumber: 1.9 Consensus size: 203
74898 AGATCAGTAG
* * * *
74908 GCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTATGTGCCTTT
1 GCCTAACTGTGCATATGA-ACAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCTTT
*
74973 GAGGCCTAACTGTGCATATGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTC
65 GAGGCCTAACTGTGCATATGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCC
* *
75038 TTGGAGGACTAACTGTGTATATGATAGAAAGGTGTCATTAATACCAGTTAGATGAAAGGCTTAGT
130 TTGGAGGACAAACTGTGCATATGATAGAAAGGTGTCATTAATACCAGTTAGATGAAAGGCTTAGT
75103 GCCTTTGAA
195 GCCTTTGAA
* * * *
75112 GCCTAATTGTGCATATG-ACAAATGTGTCAATTATGCTAGTTAGATGAAAGACTAAGTGTCTTTG
1 GCCTAACTGTGCATATGAACAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCTTTG
* *
75176 AGGCCTAACTGTGCATATGACATAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
66 AGGCCTAACTGTGCATATGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCT
* * * * * *
75241 TTGAGGCCAAACTGTGCGTATGATAGAAAGTTGTCAATT-ATGCTAGTTAGATGAA
131 TGGAGGACAAACTGTGCATATGATAGAAAGGTGTC-ATTAATACCAGTTAGATGAA
75296 CGGTTAAGTA
Statistics
Matches: 164, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
202 145 0.88
203 3 0.02
204 16 0.10
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.30
Consensus pattern (203 bp):
GCCTAACTGTGCATATGAACAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCTTTG
AGGCCTAACTGTGCATATGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCT
TGGAGGACAAACTGTGCATATGATAGAAAGGTGTCATTAATACCAGTTAGATGAAAGGCTTAGTG
CCTTTGAA
Found at i:75313 original size:68 final size:68
Alignment explanation
Indices: 74906--75304 Score: 525
Period size: 68 Copynumber: 5.9 Consensus size: 68
74896 AAAGATCAGT
* * *
74906 AGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTATGTGCCT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
74971 TTG
66 TTG
* * *
74974 AGGCCTAACTGTGCATATGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTCT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
*
75039 TGG
66 TTG
* * * * *
75042 AGGACTAACTGTGTATATGATAGAAAGGTGTC-ATTAATACCAGTTAGATGAAAGGCTTAGTGCC
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATT-ATGCCAGTTAGATGAAAGGCTAAGTGCC
75106 TTTG
65 TTTG
* * * * * *
75110 AAGCCTAATTGTGCATATGAC--AAATGTGTCAATTATGCTAGTTAGATGAAAGACTAAGTGTCT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
75173 TTG
66 TTG
* *
75176 AGGCCTAACTGTGCATATGACATAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
75241 TTG
66 TTG
* * * * * * *
75244 AGGCCAAACTGTGCGTATGATAGAAAGTTGTCAATTATGCTAGTTAGATGAACGGTTAAGT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
75305 ACGGTTGAGT
Statistics
Matches: 284, Mismatches: 43, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
66 54 0.19
67 6 0.02
68 224 0.79
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (68 bp):
AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:75387 original size:81 final size:81
Alignment explanation
Indices: 75267--75810 Score: 772
Period size: 81 Copynumber: 6.7 Consensus size: 81
75257 CGTATGATAG
* *
75267 AAAGTTGTCAATTATGCTAGTTAGATGAACGGTTAAGTACGGTTGAGTAAAAGAAAAATGGCCTA
1 AAAG-TGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCTA
75332 GCTGTGCAATTGGCAGA
65 GCTGTGCAATTGGCAGA
* *
75349 AAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATTGTCTAG
1 AAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCTAG
75414 CTGTGCAATTGGCAGA
66 CTGTGCAATTGGCAGA
* * * *
75430 AAGGTGTCGATTATGCTAGTTAGATGAACGGTTATGTACCGTTGAGTAAAAGAAAAATGG-CTAA
1 AAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCT-A
*
75494 GCTGTGCAATTGGAAGA
65 GCTGTGCAATTGGCAGA
* * *
75511 AATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAATAAAAATGGTCTAG
1 AAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCTAG
75576 CTGTGCAATTGGCAGA
66 CTGTGCAATTGGCAGA
* * *
75592 AATGTGTCAATTATGCCAGTTAGATGAACGATGAAGTACCGTTGAGTAAAAGAAAAATGGCCTAG
1 AAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCTAG
* * *
75657 TTGTGTAATTGGCATA
66 CTGTGCAATTGGCAGA
75673 AACA-TGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCTA
1 AA-AGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCTA
* *
75737 ACTGTGC-ATTGGCGGA
65 GCTGTGCAATTGGCAGA
* * * * * * * *
75753 GAGGTGTCAATTATACCAGTTAGACGAAC-GTTAAATACTGTTGAATAAGAGAATAAAT
1 AAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAA-AAAT
75811 AAATTTTAAT
Statistics
Matches: 418, Mismatches: 39, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
79 20 0.05
80 37 0.09
81 355 0.85
82 6 0.01
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (81 bp):
AAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCTAG
CTGTGCAATTGGCAGA
Found at i:76080 original size:13 final size:14
Alignment explanation
Indices: 76058--76091 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
76048 ACTAAGAGAT
*
76058 AAATGGAAAGGAA-
1 AAATGTAAAGGAAG
76071 AAATGTAAAGGAAG
1 AAATGTAAAGGAAG
76085 AAATGTA
1 AAATGTA
76092 TGCTAGCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (14 bp):
AAATGTAAAGGAAG
Done.