Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006824.1 Hibiscus syriacus cultivar Beakdansim tig00017344_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: 67593
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:726 original size:14 final size:14
Alignment explanation
Indices: 707--740 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
697 GGTTAATGTT
*
707 TTATCATTATTGGG
1 TTATCATTAGTGGG
721 TTATCATTAGTGGG
1 TTATCATTAGTGGG
735 TATATC
1 T-TATC
741 CTAATTTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.47
Consensus pattern (14 bp):
TTATCATTAGTGGG
Found at i:2465 original size:3 final size:3
Alignment explanation
Indices: 2457--2486 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2447 TATGGAGTAT
2457 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
2487 AACCCTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:5440 original size:22 final size:22
Alignment explanation
Indices: 5365--5428 Score: 53
Period size: 22 Copynumber: 2.9 Consensus size: 22
5355 TTTAATTTTT
5365 TAAT-TATT-ATTATTTAAAAAA
1 TAATATATTAATTA-TTAAAAAA
*
5386 -AATAAAACTTATATTATTAAAAAA
1 TAAT-ATA-TTA-ATTATTAAAAAA
*
5410 TATTATATTAATTATTAAA
1 TAATATATTAATTATTAAA
5429 CATATAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
20 3 0.09
22 10 0.29
23 5 0.15
24 10 0.29
25 6 0.18
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATATATTAATTATTAAAAAA
Found at i:5506 original size:24 final size:23
Alignment explanation
Indices: 5473--5541 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
5463 TTTATTAGTT
*
5473 TAATTTAATATATAAAATTATTAA
1 TAATTAAATATATAAAATTA-TAA
* *
5497 TAATTAAATATGTAATATTATAA
1 TAATTAAATATATAAAATTATAA
5520 T-ATATAAA-A-ATAATAATTATAA
1 TAAT-TAAATATATAA-AATTATAA
5542 CCAGGATTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 3 0.08
22 10 0.26
23 8 0.21
24 17 0.45
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (23 bp):
TAATTAAATATATAAAATTATAA
Found at i:5923 original size:24 final size:24
Alignment explanation
Indices: 5896--5943 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5886 TAAATCATAC
5896 CTAACGTTTAGTTTTAGTTTCATT
1 CTAACGTTTAGTTTTAGTTTCATT
5920 CTAACGTTTAGTTTTAGTTTCATT
1 CTAACGTTTAGTTTTAGTTTCATT
5944 TCGGTCACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.54
Consensus pattern (24 bp):
CTAACGTTTAGTTTTAGTTTCATT
Found at i:6282 original size:17 final size:16
Alignment explanation
Indices: 6260--6301 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 16
6250 CATGGTTTTT
6260 AGAACCGGACCGGTCA
1 AGAACCGGACCGGTCA
6276 GAGAACCGGACCGGTCA
1 -AGAACCGGACCGGTCA
6293 ACGAACCGG
1 A-GAACCGG
6302 CCGTGCTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.31, C:0.31, G:0.33, T:0.05
Consensus pattern (16 bp):
AGAACCGGACCGGTCA
Found at i:6470 original size:19 final size:20
Alignment explanation
Indices: 6425--6470 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
6415 ACGGTCTGGT
*
6425 CCGGTTTGAACGGTTCAAAG
1 CCGGTTCGAACGGTTCAAAG
6445 CCGGTTCGAACGGTTCAAAG
1 CCGGTTCGAACGGTTCAAAG
6465 -CGGTTC
1 CCGGTTC
6471 ACTAGCACCG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (20 bp):
CCGGTTCGAACGGTTCAAAG
Found at i:14065 original size:29 final size:28
Alignment explanation
Indices: 14023--14125 Score: 131
Period size: 29 Copynumber: 3.7 Consensus size: 28
14013 ACCGTTGACC
14023 GGGTGCTATTTTGGGAATTAATTCGAAA
1 GGGTGCTATTTTGGGAATTAATTCGAAA
14051 TGGGTGCTATTTTGGGAATTAATTC-AAA
1 -GGGTGCTATTTTGGGAATTAATTCGAAA
* *
14079 --ATACTATTTTGGGAATTAATTCGAAAA
1 GGGTGCTATTTTGGGAATTAATTCG-AAA
* *
14106 AGGTGCTATTTTGGTAATTA
1 GGGTGCTATTTTGGGAATTA
14126 TTTAAAAATT
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
25 20 0.31
27 3 0.05
28 3 0.05
29 39 0.60
ACGTcount: A:0.31, C:0.07, G:0.23, T:0.39
Consensus pattern (28 bp):
GGGTGCTATTTTGGGAATTAATTCGAAA
Found at i:14085 original size:25 final size:26
Alignment explanation
Indices: 14028--14105 Score: 104
Period size: 25 Copynumber: 2.9 Consensus size: 26
14018 TGACCGGGTG
* *
14028 CTATTTTGGGAATTAATTCGAAATGGGTG
1 CTATTTTGGGAATTAATTCGAAA---ATA
14057 CTATTTTGGGAATTAATTC-AAAATA
1 CTATTTTGGGAATTAATTCGAAAATA
14082 CTATTTTGGGAATTAATTCGAAAA
1 CTATTTTGGGAATTAATTCGAAAA
14106 AGGTGCTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
25 20 0.43
26 4 0.09
28 3 0.07
29 19 0.41
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (26 bp):
CTATTTTGGGAATTAATTCGAAAATA
Found at i:14111 original size:54 final size:54
Alignment explanation
Indices: 14028--14134 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
14018 TGACCGGGTG
** *
14028 CTATTTTGGGAATTAATTCGAAATGGGTGCTATTTTGGGAATTAATTCAAAATA
1 CTATTTTGGGAATTAATTCGAAAAAGGTGCTATTTTGGGAATTAATTAAAAATA
* *
14082 CTATTTTGGGAATTAATTCGAAAAAGGTGCTATTTTGGTAATTATTTAAAAAT
1 CTATTTTGGGAATTAATTCGAAAAAGGTGCTATTTTGGGAATTAATTAAAAAT
14135 TAGTGTTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.40
Consensus pattern (54 bp):
CTATTTTGGGAATTAATTCGAAAAAGGTGCTATTTTGGGAATTAATTAAAAATA
Found at i:15495 original size:17 final size:19
Alignment explanation
Indices: 15470--15508 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
15460 ATATATGTAT
15470 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
15488 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
15507 TA
1 TA
15509 AGTTGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:17894 original size:18 final size:18
Alignment explanation
Indices: 17867--17933 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 18
17857 CCGGAATGAT
*
17867 CTGACTCGTTGACCCGAC
1 CTGACCCGTTGACCCGAC
*
17885 CTGACCCGTTGA-TCGAC
1 CTGACCCGTTGACCCGAC
* * *
17902 CCGTCCTGTTGACCCGAC
1 CTGACCCGTTGACCCGAC
*
17920 CTGACTCGTTGACC
1 CTGACCCGTTGACC
17934 ACTGACCGGG
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
17 13 0.34
18 25 0.66
ACGTcount: A:0.15, C:0.39, G:0.22, T:0.24
Consensus pattern (18 bp):
CTGACCCGTTGACCCGAC
Found at i:17983 original size:29 final size:29
Alignment explanation
Indices: 17941--18046 Score: 142
Period size: 29 Copynumber: 3.7 Consensus size: 29
17931 ACCACTGACC
* *
17941 GGGTGTTATTTTGGAAATTAATTCGAAAT
1 GGGTGCTATTTTGGGAATTAATTCGAAAT
*
17970 GGGTGCTATTTTGGGAATTAATTCAAAAT
1 GGGTGCTATTTTGGGAATTAATTCGAAAT
*
17999 TGGTGCTATTTTGGGAATTAATTCGAAAT
1 GGGTGCTATTTTGGGAATTAATTCGAAAT
* * *
18028 -GGTGGTAATTTGGTAATTA
1 GGGTGCTATTTTGGGAATTA
18047 TTAAAAAAGG
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
28 16 0.23
29 53 0.77
ACGTcount: A:0.29, C:0.05, G:0.25, T:0.41
Consensus pattern (29 bp):
GGGTGCTATTTTGGGAATTAATTCGAAAT
Found at i:19415 original size:17 final size:19
Alignment explanation
Indices: 19390--19428 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
19380 ATATCTGTAT
19390 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
19408 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
19427 TA
1 TA
19429 AGTTGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:21851 original size:18 final size:18
Alignment explanation
Indices: 21788--21854 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 18
21778 CCGGAATGAT
* *
21788 CCGACTCGTTAACCCGAC
1 CCGACCCGTTGACCCGAC
*
21806 CCGACCCGTTG-TCCGAC
1 CCGACCCGTTGACCCGAC
* *
21823 CCGTCCTGTTGACCCGAC
1 CCGACCCGTTGACCCGAC
*
21841 CTGACCCGTTGACC
1 CCGACCCGTTGACC
21855 ACTGACCGGG
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
17 14 0.36
18 25 0.64
ACGTcount: A:0.15, C:0.45, G:0.21, T:0.19
Consensus pattern (18 bp):
CCGACCCGTTGACCCGAC
Found at i:21932 original size:28 final size:29
Alignment explanation
Indices: 21862--21946 Score: 118
Period size: 28 Copynumber: 3.0 Consensus size: 29
21852 ACCACTGACC
* * **
21862 GGGTGTTATTTTGGGAATTAATTCAAAAT
1 GGGTGCTAATTTGGGAATTAATTTGAAAT
*
21891 GGGTGCTATTTTGGGAATTAATTTGAAAT
1 GGGTGCTAATTTGGGAATTAATTTGAAAT
21920 -GGTGCTAATTTGGGAATTAATTTGAAA
1 GGGTGCTAATTTGGGAATTAATTTGAAA
21947 AAGGTGTTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 26 0.50
29 26 0.50
ACGTcount: A:0.31, C:0.04, G:0.26, T:0.40
Consensus pattern (29 bp):
GGGTGCTAATTTGGGAATTAATTTGAAAT
Found at i:21958 original size:28 final size:28
Alignment explanation
Indices: 21863--21986 Score: 135
Period size: 29 Copynumber: 4.4 Consensus size: 28
21853 CCACTGACCG
* *
21863 GGTGTTATTTTGGGAATTAATTCAAAATG
1 GGTGTTATTTTGGGAATTAATTGAAAA-A
* *
21892 GGTGCTATTTTGGGAATTAATTTG-AAAT
1 GGTGTTATTTTGGGAATTAA-TTGAAAAA
* *
21920 GGTGCTAATTTGGGAATTAATTTGAAAAA
1 GGTGTTATTTTGGGAATTAA-TTGAAAAA
* *
21949 GGTGTTATTTTGGTAATT-ATTAAAAAA
1 GGTGTTATTTTGGGAATTAATTGAAAAA
21976 GGTGTTATTTT
1 GGTGTTATTTT
21987 TGTAAAATGG
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
27 18 0.21
28 24 0.29
29 40 0.48
30 2 0.02
ACGTcount: A:0.31, C:0.02, G:0.23, T:0.43
Consensus pattern (28 bp):
GGTGTTATTTTGGGAATTAATTGAAAAA
Found at i:25714 original size:18 final size:17
Alignment explanation
Indices: 25687--25753 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 17
25677 CCGGAATGAT
*
25687 CCGACTCGTTGACTCGAC
1 CCGACCCGTTGAC-CGAC
*
25705 CCGACCCGTTGACCGAA
1 CCGACCCGTTGACCGAC
* *
25722 CCGTCCTGTTGACCCGAC
1 CCGACCCGTTGA-CCGAC
* *
25740 CTGACCCATTGACC
1 CCGACCCGTTGACC
25754 ACTGACCGGG
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
17 15 0.38
18 24 0.62
ACGTcount: A:0.18, C:0.42, G:0.21, T:0.19
Consensus pattern (17 bp):
CCGACCCGTTGACCGAC
Found at i:25886 original size:57 final size:58
Alignment explanation
Indices: 25762--25895 Score: 175
Period size: 57 Copynumber: 2.3 Consensus size: 58
25752 CCACTGACCG
* *
25762 GGTGTTATTTTGGGAATTAATTCAATATGGGTGCTATTTTGGGAATTAATTCAAAATG
1 GGTGTTATTTTGGGAATTAATTCAATATGGGTGCTAATTTGGGAATTAATTCAAAATA
* * *
25820 GGTGCTATTTTGGGAATTAATTCGAA-AT-GGTGGTAATTTGGGAATTAATTTGAAAA-A
1 GGTGTTATTTTGGGAATTAATTC-AATATGGGTGCTAATTTGGGAATTAA-TTCAAAATA
*
25877 GGTGTTATTTTGGTAATTA
1 GGTGTTATTTTGGGAATTA
25896 TTAAAAAAGG
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
57 35 0.52
58 30 0.45
59 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.25, T:0.41
Consensus pattern (58 bp):
GGTGTTATTTTGGGAATTAATTCAATATGGGTGCTAATTTGGGAATTAATTCAAAATA
Found at i:25908 original size:28 final size:29
Alignment explanation
Indices: 25761--25915 Score: 172
Period size: 29 Copynumber: 5.4 Consensus size: 29
25751 ACCACTGACC
* *
25761 GGGTGTTATTTTGGGAATTAATTCAATAT
1 GGGTGTTATTTTGGGAATTAATTCAAAAA
* *
25790 GGGTGCTATTTTGGGAATTAATTCAAAAT
1 GGGTGTTATTTTGGGAATTAATTCAAAAA
* *
25819 GGGTGCTATTTTGGGAATTAATTC-GAAA
1 GGGTGTTATTTTGGGAATTAATTCAAAAA
* * * *
25847 TGGTGGTAATTTGGGAATTAATTTGAAAAA
1 GGGTGTTATTTTGGGAATTAA-TTCAAAAA
* *
25877 -GGTGTTATTTTGGTAATT-ATTAAAAAA
1 GGGTGTTATTTTGGGAATTAATTCAAAAA
25904 GGGTGTTATTTT
1 GGGTGTTATTTT
25916 TGTAAAATGG
Statistics
Matches: 110, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
27 7 0.06
28 32 0.29
29 68 0.62
30 3 0.03
ACGTcount: A:0.30, C:0.03, G:0.25, T:0.41
Consensus pattern (29 bp):
GGGTGTTATTTTGGGAATTAATTCAAAAA
Found at i:27254 original size:17 final size:19
Alignment explanation
Indices: 27229--27267 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
27219 ATATCTGTAT
27229 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
27247 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
27266 TA
1 TA
27268 AGTTGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:29646 original size:13 final size:13
Alignment explanation
Indices: 29624--29661 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
29614 TTGACCGGAA
29624 TGACCCGACCCGT
1 TGACCCGACCCGT
*
29637 TGACCTGACCCGT
1 TGACCCGACCCGT
29650 TGACCCGACCCG
1 TGACCCGACCCG
29662 ACCGTTGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.16, C:0.45, G:0.24, T:0.16
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:29720 original size:29 final size:29
Alignment explanation
Indices: 29673--29807 Score: 162
Period size: 29 Copynumber: 4.7 Consensus size: 29
29663 CCGTTGACCG
*
29673 GGTGCTATTTTAGGAATTAATTCGAAATA
1 GGTGCTATTTTGGGAATTAATTCGAAATA
* * *
29702 TGTGTTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAATA
* *
29731 GGTGCTATTTTGGGAATTAATTCAAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAATA
* * *
29760 GGTGCTATTGTGGGAATTAATTTGAAAAA
1 GGTGCTATTTTGGGAATTAATTCGAAATA
* * *
29789 TGTGTTATTTTGGTAATTA
1 GGTGCTATTTTGGGAATTA
29808 TTAAAAAAAG
Statistics
Matches: 90, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.30, C:0.04, G:0.24, T:0.41
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAATA
Found at i:29798 original size:58 final size:58
Alignment explanation
Indices: 29673--29824 Score: 164
Period size: 58 Copynumber: 2.7 Consensus size: 58
29663 CCGTTGACCG
* * * * * **
29673 GGTGCTATTTTAGGAATTAATTCGAAATATGTGTTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTCAAAATAGGTGCTATTGTGGGAATTAATTCGAAAAA
* *
29731 GGTGCTATTTTGGGAATTAATTCAAAATGGGTGCTATTGTGGGAATTAATTTGAAAAA
1 GGTGCTATTTTGGGAATTAATTCAAAATAGGTGCTATTGTGGGAATTAATTCGAAAAA
* * * * *
29789 TGTGTTATTTTGGTAATT-ATT-AAAAAAAGTGCTATT
1 GGTGCTATTTTGGGAATTAATTCAAAATAGGTGCTATT
29825 TTTGTAAATT
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
56 12 0.15
57 3 0.04
58 64 0.81
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (58 bp):
GGTGCTATTTTGGGAATTAATTCAAAATAGGTGCTATTGTGGGAATTAATTCGAAAAA
Found at i:29824 original size:27 final size:28
Alignment explanation
Indices: 29674--29826 Score: 110
Period size: 29 Copynumber: 5.4 Consensus size: 28
29664 CGTTGACCGG
* * * *
29674 GTGCTATTTTAGGAATTAATTCGAAATAT
1 GTGCTATTTTGGGAATTAATT-AAAAAAA
* * ***
29703 GTGTTATTTTGGGAATTAATTCGAAATGG
1 GTGCTATTTTGGGAATTAATT-AAAAAAA
***
29732 GTGCTATTTTGGGAATTAATTCAAAATGG
1 GTGCTATTTTGGGAATTAATT-AAAAAAA
* * *
29761 GTGCTATTGTGGGAATTAATTTGAAAAAT
1 GTGCTATTTTGGGAATTAA-TTAAAAAAA
* *
29790 GTGTTATTTTGGTAATT-ATTAAAAAAA
1 GTGCTATTTTGGGAATTAATTAAAAAAA
29817 GTGCTATTTT
1 GTGCTATTTT
29827 TGTAAATTGG
Statistics
Matches: 106, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
27 16 0.15
28 1 0.01
29 87 0.82
30 2 0.02
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.42
Consensus pattern (28 bp):
GTGCTATTTTGGGAATTAATTAAAAAAA
Found at i:31169 original size:17 final size:19
Alignment explanation
Indices: 31144--31182 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
31134 ATATCTGTAT
31144 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
31162 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
31181 TA
1 TA
31183 AGTTGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:40579 original size:23 final size:23
Alignment explanation
Indices: 40520--40596 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
40510 TTCCTGATGT
** *
40520 ACCACATAGGTTTGTCCCAAAGG
1 ACCACATAATTTTGTCCCGAAGG
* * **
40543 ACTACA-AAGGTTTGTCTTGAAGG
1 ACCACATAA-TTTTGTCCCGAAGG
40566 ACCACATAATTTTGTCCCGAAGG
1 ACCACATAATTTTGTCCCGAAGG
*
40589 ATCACATA
1 ACCACATA
40597 GAACCCTCGA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
22 1 0.02
23 39 0.93
24 2 0.05
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (23 bp):
ACCACATAATTTTGTCCCGAAGG
Found at i:45219 original size:2 final size:2
Alignment explanation
Indices: 45212--45247 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
45202 AACAAACCAA
45212 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45248 TAAGTGTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52202 original size:44 final size:44
Alignment explanation
Indices: 52152--52266 Score: 221
Period size: 44 Copynumber: 2.6 Consensus size: 44
52142 GTAAGCATGC
52152 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGTA
*
52196 AAATAAGCTTACGAGATTATGGAATAATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGTA
52240 AAATAAGCTTACGAGCTTATGGAATAA
1 AAATAAGCTTACGAGCTTATGGAATAA
52267 ATAGGTGAGT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 69 1.00
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.29
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGTA
Found at i:60290 original size:21 final size:22
Alignment explanation
Indices: 60266--60317 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
60256 CACCGAAGTG
*
60266 CCACATA-TTTGTCCCGAAAGA
1 CCACATAGTTTATCCCGAAAGA
*
60287 CCACATAGGTTTATGCCGAAAGA
1 CCACATA-GTTTATCCCGAAAGA
60310 CCACATAG
1 CCACATAG
60318 AACCCTCGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 7 0.26
22 1 0.04
23 19 0.70
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (22 bp):
CCACATAGTTTATCCCGAAAGA
Found at i:63408 original size:22 final size:21
Alignment explanation
Indices: 63379--63420 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
63369 CTCTAGGCGA
*
63379 AATTAAATGTCATTGCAAAAG
1 AATTAAATGTCATTACAAAAG
63400 AATTGAAATGTCATTACAAAA
1 AATT-AAATGTCATTACAAAA
63421 TATCTTAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (21 bp):
AATTAAATGTCATTACAAAAG
Done.