Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003222.1 Hibiscus syriacus cultivar Beakdansim tig00006786_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: 100737
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:2605 original size:34 final size:35
Alignment explanation
Indices: 2554--2708 Score: 190
Period size: 35 Copynumber: 4.4 Consensus size: 35
2544 TGGTAACCAA
*
2554 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAATGATTTTCAAAGTTTGGTAAATGTTT
2590 CTTTGAAAA-GATTTTCAAAG-TTGGTAAATGTTT
1 CTTTGAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
2623 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGATTTTCAAAGTTTGGTAAATGTTT
* * *
2658 CTTTGAAAAATAGTTTTTTCAAATTTTGGTAGATGTTT
1 CTTTG-AAAAT-G-ATTTTCAAAGTTTGGTAAATGTTT
*
2696 -GTTGAAAAATGAT
1 CTTTG-AAAATGAT
2709 AATGGGATAA
Statistics
Matches: 107, Mismatches: 7, Indels: 11
0.86 0.06 0.09
Matches are distributed among these distances:
33 22 0.21
34 20 0.19
35 23 0.21
36 11 0.10
37 10 0.09
38 21 0.20
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.45
Consensus pattern (35 bp):
CTTTGAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:2656 original size:35 final size:35
Alignment explanation
Indices: 2554--2703 Score: 198
Period size: 33 Copynumber: 4.3 Consensus size: 35
2544 TGGTAACCAA
2554 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
2590 CTTTGAAAA-GATTTTCAAAG-TTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
2623 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* * *
2658 CTTTGAAAAATAGTTTTTTCAAATTTTGGTAGATGTTT
1 CTTTG-AAAAT-G-GTTTTCAAAGTTTGGTAAATGTTT
*
2696 -GTTGAAAA
1 CTTTGAAAA
2704 ATGATAATGG
Statistics
Matches: 103, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
33 22 0.21
34 20 0.19
35 22 0.21
36 14 0.14
37 4 0.04
38 21 0.20
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:7268 original size:36 final size:36
Alignment explanation
Indices: 7154--7273 Score: 156
Period size: 35 Copynumber: 3.3 Consensus size: 36
7144 TGGTAACCAA
7154 CTTTGAAAAAATGGTTTTT-AAAGTTTGGTAAATGTTT
1 CTTTG-AAAAAT-GTTTTTCAAAGTTTGGTAAATGTTT
*
7191 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
* *
7226 CTTTGAAAAATAGTTTTTCAAATTTTGGTAGATGTTT
1 CTTTGAAAAAT-GTTTTTCAAAGTTTGGTAAATGTTT
*
7263 -GTTGAAAAATG
1 CTTTGAAAAATG
7274 ATAATGGGAT
Statistics
Matches: 75, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
34 5 0.07
35 29 0.39
36 14 0.19
37 27 0.36
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:10534 original size:2 final size:2
Alignment explanation
Indices: 10527--10552 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10517 GGAATATTTG
10527 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
10553 GATAGATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21659 original size:23 final size:25
Alignment explanation
Indices: 21633--21680 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
21623 TAAATATCTT
21633 AAATTTAAATATATTA-TATAAAAA
1 AAATTTAAATATATTATTATAAAAA
21657 AATATTTAAATAT-TTATTATAAAA
1 AA-ATTTAAATATATTATTATAAAA
21681 TAATTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AAATTTAAATATATTATTATAAAAA
Found at i:23593 original size:10 final size:10
Alignment explanation
Indices: 23568--23597 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
23558 TCAACAGTCG
23568 GGTCGGGTCA
1 GGTCGGGTCA
23578 -GTCGGGTCA
1 GGTCGGGTCA
23587 GGTCGGGTCA
1 GGTCGGGTCA
23597 G
1 G
23598 ACCGGTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.10, C:0.20, G:0.50, T:0.20
Consensus pattern (10 bp):
GGTCGGGTCA
Found at i:23604 original size:19 final size:19
Alignment explanation
Indices: 23568--23605 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
23558 TCAACAGTCG
* *
23568 GGTCGGGTCAGTCGGGTCA
1 GGTCGGGTCAGACCGGTCA
23587 GGTCGGGTCAGACCGGTCA
1 GGTCGGGTCAGACCGGTCA
23606 AACCGGTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (19 bp):
GGTCGGGTCAGACCGGTCA
Found at i:23638 original size:20 final size:19
Alignment explanation
Indices: 23592--23662 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 19
23582 GGTCAGGTCG
23592 GGTCAGACCGGTC-AAACC
1 GGTCAGACCGGTCAAAACC
23610 GGTTC-GAACCGGTCAAAACC
1 GG-TCAG-ACCGGTCAAAACC
* *
23630 AGTCAGAACCGGTTAAAAACC
1 GGTCAG-ACCGG-TCAAAACC
23651 GGTCAGACCGGT
1 GGTCAGACCGGT
23663 TTCCAGCCCT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
18 3 0.07
19 12 0.27
20 18 0.40
21 12 0.27
ACGTcount: A:0.31, C:0.28, G:0.27, T:0.14
Consensus pattern (19 bp):
GGTCAGACCGGTCAAAACC
Found at i:30794 original size:7 final size:7
Alignment explanation
Indices: 30782--30818 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
30772 GTCAAAGGAA
30782 GTCAACG
1 GTCAACG
30789 GTCAACG
1 GTCAACG
30796 GTC-ACG
1 GTCAACG
30802 GTCAACG
1 GTCAACG
*
30809 GTCAAAG
1 GTCAACG
30816 GTC
1 GTC
30819 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:30804 original size:13 final size:13
Alignment explanation
Indices: 30786--30812 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30776 AAGGAAGTCA
30786 ACGGTCAACGGTC
1 ACGGTCAACGGTC
30799 ACGGTCAACGGTC
1 ACGGTCAACGGTC
30812 A
1 A
30813 AAGGTCGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:30863 original size:20 final size:20
Alignment explanation
Indices: 30830--30884 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 20
30820 GGTCGGGTCG
* *
30830 GGTCAGACCGGGTTTG-AACT
1 GGTCAAACC-GGTTTGAAACC
30850 GGTCGAAACCGG-TTGAAAACC
1 GGTC-AAACCGGTTTG-AAACC
30871 GGTCAAACCGGTTT
1 GGTCAAACCGGTTT
30885 CCAGCCCTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 3 0.10
20 13 0.45
21 13 0.45
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (20 bp):
GGTCAAACCGGTTTGAAACC
Found at i:31847 original size:42 final size:42
Alignment explanation
Indices: 31795--31924 Score: 208
Period size: 42 Copynumber: 3.1 Consensus size: 42
31785 ATTATCAACC
*
31795 GAAGCATTAGGTGAATCATTGGAATTTCCAATAGGATTATTA
1 GAAGTATTAGGTGAATCATTGGAATTTCCAATAGGATTATTA
* *
31837 GAAGTATTAGGTGAATCATTGAAATTTTCAATAGGATTATTA
1 GAAGTATTAGGTGAATCATTGGAATTTCCAATAGGATTATTA
*
31879 GAAGTATTAGGTGAATCATTGGAATTTCTAATCA-GATTATTA
1 GAAGTATTAGGTGAATCATTGGAATTTCCAAT-AGGATTATTA
31921 GAAG
1 GAAG
31925 GTTTAACCGG
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
42 80 0.99
43 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (42 bp):
GAAGTATTAGGTGAATCATTGGAATTTCCAATAGGATTATTA
Found at i:32157 original size:14 final size:14
Alignment explanation
Indices: 32138--32164 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
32128 TGTTGTTGAC
32138 TTGTTCTTTCTCAT
1 TTGTTCTTTCTCAT
32152 TTGTTCTTTCTCA
1 TTGTTCTTTCTCA
32165 CAATCAACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.07, T:0.63
Consensus pattern (14 bp):
TTGTTCTTTCTCAT
Found at i:33592 original size:18 final size:19
Alignment explanation
Indices: 33571--33606 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
33561 AATTTTAAGA
*
33571 TTAATTTTA-ATTCGATTT
1 TTAAATTTATATTCGATTT
33589 TTAAATTTATATTCGATT
1 TTAAATTTATATTCGATT
33607 CAACCATTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (19 bp):
TTAAATTTATATTCGATTT
Found at i:36797 original size:43 final size:43
Alignment explanation
Indices: 36736--36824 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
36726 CGAGATCCAG
36736 TGTTTGTTTCAATTCACCATCAGGCCAACTGTACACATGCAAA
1 TGTTTGTTTCAATTCACCATCAGGCCAACTGTACACATGCAAA
36779 TGTTTGTTTCAATTCACCATCAGGCCAACTGTACACATGCAAA
1 TGTTTGTTTCAATTCACCATCAGGCCAACTGTACACATGCAAA
36822 TGT
1 TGT
36825 CTACCGTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (43 bp):
TGTTTGTTTCAATTCACCATCAGGCCAACTGTACACATGCAAA
Found at i:39737 original size:22 final size:22
Alignment explanation
Indices: 39710--39770 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
39700 TTATAAGGTT
*
39710 TTTAATTTTTATAATTTAGTCC
1 TTTAATTTTTATAATTTAATCC
* **
39732 TTTAATTTTCTTTAATTTAATTT
1 TTTAATTTT-TATAATTTAATCC
*
39755 TTTTATTTTTATAATT
1 TTTAATTTTTATAATT
39771 GAGGTCCTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTAATTTTTATAATTTAATCC
Found at i:55799 original size:23 final size:21
Alignment explanation
Indices: 55747--55808 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
55737 TTTTGGTGTA
*
55747 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
55767 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
55788 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
55809 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:61296 original size:21 final size:21
Alignment explanation
Indices: 61233--61305 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
61223 AGACCTCTAG
*
61233 TTTTTTAATCTCACTTTTTTAC
1 TTTTATAATCTCAC-TTTTTAC
* * **
61255 TTTTATAATTGTGAC-CCTTAC
1 TTTTATAA-TCTCACTTTTTAC
*
61276 TTTTTTAATCTCACTTTTTAC
1 TTTTATAATCTCACTTTTTAC
*
61297 CTTTATAAT
1 TTTTATAAT
61306 TGAGGCACTA
Statistics
Matches: 37, Mismatches: 12, Indels: 5
0.69 0.22 0.09
Matches are distributed among these distances:
20 4 0.11
21 22 0.59
22 7 0.19
23 4 0.11
ACGTcount: A:0.22, C:0.18, G:0.03, T:0.58
Consensus pattern (21 bp):
TTTTATAATCTCACTTTTTAC
Found at i:61333 original size:41 final size:42
Alignment explanation
Indices: 61210--61337 Score: 134
Period size: 43 Copynumber: 3.0 Consensus size: 42
61200 ATTACTTTCA
* * *
61210 ACCTTTAAAATTTAGAC-CTCTAGTTTTTTAATCTCACTTTTTT
1 ACCTTTATAATTGAGACACT-TAATTTTTTAATCTCAC-TTTTT
* * * *
61253 ACTTTTATAATTGTGACCCTTACTTTTTTAATCTCACTTTTT
1 ACCTTTATAATTGAGACACTTAATTTTTTAATCTCACTTTTT
* * *
61295 ACCTTTATAATTGAGGCAC-TAATTTTTAAATCCCACTTTTT
1 ACCTTTATAATTGAGACACTTAATTTTTTAATCTCACTTTTT
61336 AC
1 AC
61338 TTATCACTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
41 21 0.29
42 20 0.28
43 29 0.40
44 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.05, T:0.49
Consensus pattern (42 bp):
ACCTTTATAATTGAGACACTTAATTTTTTAATCTCACTTTTT
Found at i:64150 original size:25 final size:24
Alignment explanation
Indices: 64122--64192 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
64112 AACTCAAAAA
* *
64122 AAAATTAGAAGTTCGATTGAAGCCT
1 AAAATTAG-AGCTCAATTGAAGCCT
*
64147 AAAATTTGAGCTCAATTGAAGCCT
1 AAAATTAGAGCTCAATTGAAGCCT
*
64171 AAAATTTGAGCTCAATTGAAGC
1 AAAATTAGAGCTCAATTGAAGC
64193 GAAAGAATAG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
24 36 0.84
25 7 0.16
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (24 bp):
AAAATTAGAGCTCAATTGAAGCCT
Found at i:64166 original size:24 final size:24
Alignment explanation
Indices: 64137--64192 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
64127 TAGAAGTTCG
64137 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
64161 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
64185 ATTGAAGC
1 ATTGAAGC
64193 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:64795 original size:2 final size:2
Alignment explanation
Indices: 64788--64818 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
64778 AAAACGAATT
64788 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 T
64819 TTCACCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:65198 original size:17 final size:16
Alignment explanation
Indices: 65176--65209 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
65166 TTAAAGGTTA
*
65176 TTTGTACTATTTCTCTC
1 TTTGTAATATTTC-CTC
65193 TTTGTAATATTTCCTC
1 TTTGTAATATTTCCTC
65209 T
1 T
65210 ATTAGTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.15, C:0.21, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTGTAATATTTCCTC
Found at i:70365 original size:28 final size:30
Alignment explanation
Indices: 70292--70366 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 30
70282 ATCCTAATTG
*
70292 TAGTTCTAATGTTACTTTTCTACTTATTAA
1 TAGTTCTAATCTTACTTTTCTACTTATTAA
* * *
70322 TAATTCTAATCATACTTTT-T-TTTATTAA
1 TAGTTCTAATCTTACTTTTCTACTTATTAA
*
70350 TAGTTCTAATTTTACTT
1 TAGTTCTAATCTTACTT
70367 GGAGGAAAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 21 0.55
29 1 0.03
30 16 0.42
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.56
Consensus pattern (30 bp):
TAGTTCTAATCTTACTTTTCTACTTATTAA
Found at i:84854 original size:12 final size:12
Alignment explanation
Indices: 84826--84874 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
84816 ATTACAATAA
*
84826 TTATTATTATTG
1 TTATTATTATTT
*
84838 CTATTATTATTT
1 TTATTATTATTT
*
84850 TTATTTTTATTT
1 TTATTATTATTT
*
84862 TTATTAATATTT
1 TTATTATTATTT
84874 T
1 T
84875 ACAGGCCCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (12 bp):
TTATTATTATTT
Found at i:84860 original size:18 final size:18
Alignment explanation
Indices: 84825--84874 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
84815 TATTACAATA
**
84825 ATTATTATTATTGCTATT
1 ATTATTATTATTTTTATT
*
84843 ATTATTTTTATTTTTATT
1 ATTATTATTATTTTTATT
* *
84861 TTTATTAATATTTT
1 ATTATTATTATTTT
84875 ACAGGCCCAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (18 bp):
ATTATTATTATTTTTATT
Found at i:85638 original size:15 final size:15
Alignment explanation
Indices: 85601--85632 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
85591 GTGAAAAACG
85601 AAAAA-AAAATAGAA
1 AAAAACAAAATAGAA
85615 AAAAACAAAA-AGAA
1 AAAAACAAAATAGAA
85629 AAAA
1 AAAA
85633 GTCAAAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.88, C:0.03, G:0.06, T:0.03
Consensus pattern (15 bp):
AAAAACAAAATAGAA
Found at i:91755 original size:45 final size:45
Alignment explanation
Indices: 91705--91938 Score: 368
Period size: 45 Copynumber: 5.2 Consensus size: 45
91695 TGATATATGG
91705 TTATGGAATAATGGCAAGTGTATTGGTAAAAATAAGCTTACGAGC
1 TTATGGAATAATGGCAAGTGTATTGGTAAAAATAAGCTTACGAGC
*
91750 TTATGGAATAATGTCAAGTGTATTGGTAAAAATAAGCTTACGAGC
1 TTATGGAATAATGGCAAGTGTATTGGTAAAAATAAGCTTACGAGC
91795 TTATGGAATAATGGCAAGTGTATTGGTAAAAATAAGCTTACGAGC
1 TTATGGAATAATGGCAAGTGTATTGGTAAAAATAAGCTTACGAGC
*
91840 TTATGG-ATAAATGGTAAGTGTATTGGT-AAAATAAGCTTACGAGC
1 TTATGGAAT-AATGGCAAGTGTATTGGTAAAAATAAGCTTACGAGC
* * *
91884 TTATGG-ATAAATGGTAACTATATTGGT-AAAATAAGCTTACGAGC
1 TTATGGAAT-AATGGCAAGTGTATTGGTAAAAATAAGCTTACGAGC
*
91928 TTATGGGATAA
1 TTATGGAATAA
91939 ATGATAAGAA
Statistics
Matches: 182, Mismatches: 5, Indels: 5
0.95 0.03 0.03
Matches are distributed among these distances:
44 69 0.38
45 113 0.62
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.31
Consensus pattern (45 bp):
TTATGGAATAATGGCAAGTGTATTGGTAAAAATAAGCTTACGAGC
Found at i:91851 original size:24 final size:24
Alignment explanation
Indices: 91824--91895 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
91814 GTATTGGTAA
91824 AAATAAGCTTACGAGCTTATGGAT
1 AAATAAGCTTACGAGCTTATGGAT
*
91848 AAAT--G-GTA--AG-TGTATTGG-T
1 AAATAAGCTTACGAGCT-TA-TGGAT
91867 AAAATAAGCTTACGAGCTTATGGAT
1 -AAATAAGCTTACGAGCTTATGGAT
91892 AAAT
1 AAAT
91896 GGTAACTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 20
0.62 0.03 0.34
Matches are distributed among these distances:
18 1 0.03
19 5 0.14
20 7 0.19
21 2 0.06
22 2 0.06
23 2 0.06
24 11 0.31
25 5 0.14
26 1 0.03
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (24 bp):
AAATAAGCTTACGAGCTTATGGAT
Found at i:92454 original size:20 final size:20
Alignment explanation
Indices: 92427--92474 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
92417 GTTCACGGGT
* *
92427 ACTATTCACTGTTAATGTTC
1 ACTATTCACGGGTAATGTTC
* *
92447 ACTTTTCACGGGTACTGTTC
1 ACTATTCACGGGTAATGTTC
92467 ACTATTCA
1 ACTATTCA
92475 TAAAAAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (20 bp):
ACTATTCACGGGTAATGTTC
Found at i:92893 original size:26 final size:28
Alignment explanation
Indices: 92833--92894 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
92823 GAGTATTGCT
*
92833 GAGCTCGACTCGACTCGAAAACTCTGAAATT
1 GAGCTCGACTCGACTCGAAAACTCTG--A-C
92864 GAGCTCGACTCGACTCGAAAACTC-G-C
1 GAGCTCGACTCGACTCGAAAACTCTGAC
92890 GAGCT
1 GAGCT
92895 TAAAATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 1 0.03
31 24 0.80
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Found at i:94331 original size:2 final size:2
Alignment explanation
Indices: 94324--94351 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
94314 GTGTTTGCGG
94324 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
94352 GAATAAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:95208 original size:192 final size:192
Alignment explanation
Indices: 94881--95261 Score: 726
Period size: 192 Copynumber: 2.0 Consensus size: 192
94871 TATGCTTTTG
94881 TGAGATGAATTGTATCATATGATTTGAATGATGATATGTGTATTGCGTGGTTAAATGAGTTATGT
1 TGAGATGAATTGTATCATATGATTTGAATGATGATATGTGTATTGCGTGGTTAAATGAGTTATGT
* *
94946 TGGTTGAAATGTTACGTACGAAAGGATATTATTACAAGATATAAATAATAATCATATTAATAGTA
66 TGGTTAAAATGTTACATACGAAAGGATATTATTACAAGATATAAATAATAATCATATTAATAGTA
95011 AAGTAATGTTAATGATGGAAAGAATGAATGATGTGTATATATGTACATTTGATTACATGTTC
131 AAGTAATGTTAATGATGGAAAGAATGAATGATGTGTATATATGTACATTTGATTACATGTTC
95073 TGAGATGAATTGTATCATATGATTTGAATGATGATATGTGTATTGCGTGGTTAAATGAGTTATGT
1 TGAGATGAATTGTATCATATGATTTGAATGATGATATGTGTATTGCGTGGTTAAATGAGTTATGT
* *
95138 TGGTTAAAATGTTACATACGAAAGGATGTTATTACAAGATATAAATAATAATCATATTGATAGTA
66 TGGTTAAAATGTTACATACGAAAGGATATTATTACAAGATATAAATAATAATCATATTAATAGTA
95203 AAGTAATGTTAATGATGGAAAGAATGAATGATGTGTATATATGTACATTTGATTACATG
131 AAGTAATGTTAATGATGGAAAGAATGAATGATGTGTATATATGTACATTTGATTACATG
95262 AAATGCTATA
Statistics
Matches: 185, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
192 185 1.00
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.37
Consensus pattern (192 bp):
TGAGATGAATTGTATCATATGATTTGAATGATGATATGTGTATTGCGTGGTTAAATGAGTTATGT
TGGTTAAAATGTTACATACGAAAGGATATTATTACAAGATATAAATAATAATCATATTAATAGTA
AAGTAATGTTAATGATGGAAAGAATGAATGATGTGTATATATGTACATTTGATTACATGTTC
Found at i:96094 original size:21 final size:18
Alignment explanation
Indices: 96050--96123 Score: 112
Period size: 18 Copynumber: 3.9 Consensus size: 18
96040 AGGGATTATC
*
96050 AGTGGTCCTTCGCGACAT
1 AGTGGTCCTTCGGGACAT
96068 AGTGGTCCTTCGGGACATAT
1 AGTGGTCCTTCGGGAC--AT
96088 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
96107 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
96124 AATATTCAGT
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
18 32 0.62
19 2 0.04
20 2 0.04
21 16 0.31
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:96100 original size:39 final size:39
Alignment explanation
Indices: 96046--96123 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
96036 GTCGAGGGAT
96046 TATCAGTGGTCCTTCGCGACATAGTGGTCCTTCGGGACA
1 TATCAGTGGTCCTTCGCGACATAGTGGTCCTTCGGGACA
*
96085 TATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACA
1 TATCAGTGGTCCTTCGCGACATAGTGGTCCTTCGGGACA
96124 AATATTCAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.28
Consensus pattern (39 bp):
TATCAGTGGTCCTTCGCGACATAGTGGTCCTTCGGGACA
Done.