Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001390.1 Hibiscus syriacus cultivar Beakdansim tig00002714_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: 54014
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:8141 original size:7 final size:7
Alignment explanation
Indices: 8129--8178 Score: 100
Period size: 7 Copynumber: 7.1 Consensus size: 7
8119 AAGTGTATTT
8129 TTTCGCA
1 TTTCGCA
8136 TTTCGCA
1 TTTCGCA
8143 TTTCGCA
1 TTTCGCA
8150 TTTCGCA
1 TTTCGCA
8157 TTTCGCA
1 TTTCGCA
8164 TTTCGCA
1 TTTCGCA
8171 TTTCGCA
1 TTTCGCA
8178 T
1 T
8179 CTTAATGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.44
Consensus pattern (7 bp):
TTTCGCA
Found at i:10865 original size:20 final size:20
Alignment explanation
Indices: 10840--11031 Score: 323
Period size: 20 Copynumber: 9.7 Consensus size: 20
10830 TTTTCCTAAT
10840 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
10860 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
10880 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
10900 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
10920 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
10940 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
10960 TCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
10980 TCACAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
*
11000 T-GCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
11019 TCGCAACGCGAAT
1 TCGCAATGCGAAT
11032 CTGACTATCG
Statistics
Matches: 161, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
19 16 0.10
20 145 0.90
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:11164 original size:64 final size:64
Alignment explanation
Indices: 11063--11190 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
11053 ACATAGCGTC
*
11063 ATTCGTATCCAACGCGTATTTTTTTTTCAAATTCCAAACACGAATATATTAATATATCGGAACA
1 ATTCGTATCCAACGCGTATTTTTTTTTCAAATTCCAAACACGAATATATTAATATATCAGAACA
11127 ATTCGTATCCAACGCGTATTTTTTTTTCAAATTCCAAACACGAATATATTAATATATCAGAACA
1 ATTCGTATCCAACGCGTATTTTTTTTTCAAATTCCAAACACGAATATATTAATATATCAGAACA
11191 CTGAACCGTC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.36
Consensus pattern (64 bp):
ATTCGTATCCAACGCGTATTTTTTTTTCAAATTCCAAACACGAATATATTAATATATCAGAACA
Found at i:11317 original size:22 final size:22
Alignment explanation
Indices: 11292--11357 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
11282 GGCGACATCC
11292 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
11314 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
11336 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
11358 TTCACGATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:11729 original size:33 final size:34
Alignment explanation
Indices: 11681--11753 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
11671 ACTATCGCAA
** *
11681 TGCGATTCTGTCGTTGCGATTTTC-ATTTCGCGT
1 TGCGATTCTGTCGTTGCGATAGTCAAATTCGCGT
11714 TGCGATTCT-TGCGTTGCGATAGTCAAATTCGCGT
1 TGCGATTCTGT-CGTTGCGATAGTCAAATTCGCGT
11748 TGCGAT
1 TGCGAT
11754 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.57
34 14 0.40
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.40
Consensus pattern (34 bp):
TGCGATTCTGTCGTTGCGATAGTCAAATTCGCGT
Found at i:11764 original size:20 final size:20
Alignment explanation
Indices: 11724--11793 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
11714 TGCGATTCTT
**
11724 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCATTTTC
11744 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCATTTTC
* * **
11764 GTGTTACGATTTTCATTTTC
1 GCGTTGCGATAGTCATTTTC
*
11784 GTGTTGCGAT
1 GCGTTGCGAT
11794 TTAAAGTTTC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.41
Consensus pattern (20 bp):
GCGTTGCGATAGTCATTTTC
Found at i:11803 original size:20 final size:20
Alignment explanation
Indices: 11760--11803 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
11750 CGATAGTCAT
** *
11760 TTTCGTGTTACGATTTTCAT
1 TTTCGTGTTACGATTTAAAG
*
11780 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTACGATTTAAAG
11800 TTTC
1 TTTC
11804 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTACGATTTAAAG
Found at i:13704 original size:20 final size:20
Alignment explanation
Indices: 13679--13862 Score: 135
Period size: 20 Copynumber: 9.8 Consensus size: 20
13669 AGAATAGTTT
13679 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
13699 ACTATCGCAACGCAAAAATG
1 ACTATCGCAATGCGAAAATG
*
13719 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
13739 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
13755 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
13772 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
* **
13788 A--ATTGCAACACGAAAATG
1 ACTATCGCAATGCGAAAATG
*
13806 ACTATCGTAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
** **
13826 ACTATCGCAATATGAATTTG
1 ACTATCGCAATGCGAAAATG
13846 ACTATCGCAATGCGAAA
1 ACTATCGCAATGCGAAA
13863 TGAAAATCGC
Statistics
Matches: 132, Mismatches: 18, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
14 13 0.10
16 10 0.08
17 8 0.06
18 5 0.04
19 7 0.05
20 89 0.67
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:13913 original size:20 final size:20
Alignment explanation
Indices: 13888--13974 Score: 111
Period size: 20 Copynumber: 4.3 Consensus size: 20
13878 GATTCTCTCG
*
13888 TTGCGATAATCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
13908 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
13928 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
** *
13948 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
13968 TTGCGAT
1 TTGCGAT
13975 TTTAAGTTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:13984 original size:20 final size:20
Alignment explanation
Indices: 13902--13984 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 20
13892 GATAATCAAA
* *
13902 TTCGCATTGCGATAGTCAA-A
1 TTCGCGTTGCGATAGT-AAGT
* * *
13922 TTCGCATTGCGATAGTCATT
1 TTCGCGTTGCGATAGTAAGT
* *
13942 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTAAGT
**
13962 TTCGCGTTGCGATTTTAAGT
1 TTCGCGTTGCGATAGTAAGT
13982 TTC
1 TTC
13985 AGATTCTATT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
19 1 0.02
20 54 0.98
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTAAGT
Found at i:15962 original size:14 final size:14
Alignment explanation
Indices: 15943--15978 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
15933 ATTGTTTAAT
15943 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
15957 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
15971 TGATTTGT
1 TGATTTGT
15979 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:16221 original size:20 final size:20
Alignment explanation
Indices: 16194--16287 Score: 145
Period size: 20 Copynumber: 4.7 Consensus size: 20
16184 GCGATTCTCT
16194 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
16214 CATTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
16234 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
16254 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
16274 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
16288 AATGAATGTC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 65 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:18767 original size:24 final size:24
Alignment explanation
Indices: 18716--18767 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
18706 ATCCTAGTAT
** *
18716 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
18740 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
18764 TGAC
1 TGAC
18768 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:19620 original size:20 final size:20
Alignment explanation
Indices: 19595--19681 Score: 156
Period size: 20 Copynumber: 4.3 Consensus size: 20
19585 AAATTCAGTA
19595 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
19615 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
19635 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
19655 TTGCGATAGTCAGATTCACG
1 TTGCGATAGTCAGAATCTCG
19675 TTGCGAT
1 TTGCGAT
19682 TTACATATTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:19691 original size:20 final size:20
Alignment explanation
Indices: 19675--19824 Score: 230
Period size: 20 Copynumber: 7.5 Consensus size: 20
19665 CAGATTCACG
*
19675 TTGCGATTTACATATTCGCA
1 TTGCGATTTACGTATTCGCA
*
19695 TTGCGATTTACGTATCCGCA
1 TTGCGATTTACGTATTCGCA
19715 TTGCGATTTACGTA-TCTGCA
1 TTGCGATTTACGTATTC-GCA
* * *
19735 TTGTGATTTACATATCCGCA
1 TTGCGATTTACGTATTCGCA
*
19755 TTGCGATTTACGTATCCGCA
1 TTGCGATTTACGTATTCGCA
19775 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
19795 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
19815 TTGCGATTTA
1 TTGCGATTTA
19825 GGAAAATCGC
Statistics
Matches: 119, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
19 1 0.01
20 117 0.98
21 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:19841 original size:21 final size:20
Alignment explanation
Indices: 19817--19863 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
19807 TATTCGCATT
19817 GCGATTTAGGAAAATCGCAAC
1 GCGATTT-GGAAAATCGCAAC
*
19838 GCGAATTTGGAAAATCGCAAT
1 GCG-ATTTGGAAAATCGCAAC
19859 GCGAT
1 GCGAT
19864 AGTCAGAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 2 0.08
21 18 0.75
22 4 0.17
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (20 bp):
GCGATTTGGAAAATCGCAAC
Found at i:25538 original size:11 final size:11
Alignment explanation
Indices: 25522--25546 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25512 AATATCATCC
25522 TTTTTTTCTTT
1 TTTTTTTCTTT
25533 TTTTTTTCTTT
1 TTTTTTTCTTT
25544 TTT
1 TTT
25547 CCATTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:26685 original size:3 final size:3
Alignment explanation
Indices: 26664--26713 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
26654 GTATCCTGCA
* *
26664 AAT AATT AAT AAC AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT AAA
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
26709 AAT AA
1 AAT AA
26714 AGATGGGTCC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:26696 original size:14 final size:15
Alignment explanation
Indices: 26664--26704 Score: 66
Period size: 14 Copynumber: 2.7 Consensus size: 15
26654 GTATCCTGCA
26664 AATAATTAATAACAAT
1 AATAA-TAATAACAAT
26680 AATAATAATAA-AAT
1 AATAATAATAACAAT
26694 AATAATAATAA
1 AATAATAATAA
26705 TAAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.56
15 6 0.24
16 5 0.20
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAATAATAACAAT
Found at i:26697 original size:23 final size:23
Alignment explanation
Indices: 26670--26714 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
26660 TGCAAATAAT
*
26670 TAATAACAATAATAATAATAAAA
1 TAATAACAATAATAAAAATAAAA
*
26693 TAATAATAATAATAAAAATAAA
1 TAATAACAATAATAAAAATAAA
26715 GATGGGTCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (23 bp):
TAATAACAATAATAAAAATAAAA
Found at i:26699 original size:17 final size:17
Alignment explanation
Indices: 26677--26709 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
26667 AATTAATAAC
26677 AATAATAATAATAAAAT
1 AATAATAATAATAAAAT
26694 AATAATAATAATAAAA
1 AATAATAATAATAAAA
26710 ATAAAGATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAATAATAATAAAAT
Found at i:28284 original size:33 final size:33
Alignment explanation
Indices: 28224--28287 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
28214 TCACATATAA
* ** *
28224 CAGATTTGTCTTCCCTTGTTTCGTCACCTATTT
1 CAGATTTGTCTTCCCCTACTTCATCACCTATTT
28257 CAGATTTGTCTTCCCCTACTTCATCACCTAT
1 CAGATTTGTCTTCCCCTACTTCATCACCTAT
28288 GACATATTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.16, C:0.31, G:0.09, T:0.44
Consensus pattern (33 bp):
CAGATTTGTCTTCCCCTACTTCATCACCTATTT
Found at i:28297 original size:33 final size:33
Alignment explanation
Indices: 28214--28297 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
28204 TTATGTTAAG
* * * ** *
28214 TCACATATAACAGATTTGTCTTCCCTTGTTTCG
1 TCACCTATGACAGATTTGTCTTCCCCTACTTCA
**
28247 TCACCTATTTCAGATTTGTCTTCCCCTACTTCA
1 TCACCTATGACAGATTTGTCTTCCCCTACTTCA
*
28280 TCACCTATGACATATTTG
1 TCACCTATGACAGATTTG
28298 CTTTCACCAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.21, C:0.27, G:0.10, T:0.42
Consensus pattern (33 bp):
TCACCTATGACAGATTTGTCTTCCCCTACTTCA
Found at i:28569 original size:28 final size:28
Alignment explanation
Indices: 28529--28592 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
28519 TTCTTATTTA
*
28529 CCACCTCACACTCAATGTTTTGTTTCTT
1 CCACCTCACACTCAATGTTTTATTTCTT
28557 CCACCTCACACTCAATGTTTTATTTCTT
1 CCACCTCACACTCAATGTTTTATTTCTT
28585 CCACCTCA
1 CCACCTCA
28593 AAGTTTGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.20, C:0.36, G:0.05, T:0.39
Consensus pattern (28 bp):
CCACCTCACACTCAATGTTTTATTTCTT
Found at i:29847 original size:10 final size:10
Alignment explanation
Indices: 29818--29886 Score: 63
Period size: 10 Copynumber: 7.1 Consensus size: 10
29808 GCTGCTGGAA
29818 AACCGGTTTG
1 AACCGGTTTG
*
29828 -ACCAGTTTTG
1 AACC-GGTTTG
29838 AACCGGTTTG
1 AACCGGTTTG
* *
29848 -ATCGGTCTG
1 AACCGGTTTG
29857 AACCGGTTTG
1 AACCGGTTTG
*
29867 -ACCGGTCTG
1 AACCGGTTTG
*
29876 AACCGGGTTG
1 AACCGGTTTG
29886 A
1 A
29887 CCCGACCCGA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 18 0.39
10 25 0.54
11 3 0.07
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:29860 original size:19 final size:19
Alignment explanation
Indices: 29818--29888 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
29808 GCTGCTGGAA
* *
29818 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
*
29838 AACCGGTTTGATCGGTCTG
1 AACCGGTTTGACCGGTCTG
29857 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
29876 AACCGGGTTGACC
1 AACCGGTTTGACC
29889 CGACCCGACT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 34 0.74
20 12 0.26
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:29904 original size:17 final size:17
Alignment explanation
Indices: 29882--29956 Score: 123
Period size: 17 Copynumber: 4.4 Consensus size: 17
29872 TCTGAACCGG
29882 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
29899 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
* *
29916 GTTGACCTGACCCGAAT
1 GTTGACCCGACCCGACT
*
29933 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
29950 GTTGACC
1 GTTGACC
29957 GTTAACTGTG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 53 1.00
ACGTcount: A:0.19, C:0.39, G:0.24, T:0.19
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:29958 original size:7 final size:7
Alignment explanation
Indices: 29946--30005 Score: 61
Period size: 7 Copynumber: 8.9 Consensus size: 7
29936 GACCCGACCC
29946 GACCGTT
1 GACCGTT
29953 GACCGTT
1 GACCGTT
* *
29960 AACTG-T
1 GACCGTT
29966 GACCGTT
1 GACCGTT
*
29973 GGCCGTT
1 GACCGTT
*
29980 AACCGTT
1 GACCGTT
*
29987 GACTG-T
1 GACCGTT
29993 GACCGTT
1 GACCGTT
30000 GACCGT
1 GACCGT
30006 GGACTTTCTT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
6 9 0.22
7 32 0.78
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (7 bp):
GACCGTT
Found at i:29979 original size:27 final size:27
Alignment explanation
Indices: 29946--30005 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
29936 GACCCGACCC
*
29946 GACCGTTGACCGTTAACTGTGACCGTT
1 GACCGTTAACCGTTAACTGTGACCGTT
* *
29973 GGCCGTTAACCGTTGACTGTGACCGTT
1 GACCGTTAACCGTTAACTGTGACCGTT
30000 GACCGT
1 GACCGT
30006 GGACTTTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (27 bp):
GACCGTTAACCGTTAACTGTGACCGTT
Found at i:29998 original size:20 final size:21
Alignment explanation
Indices: 29950--30010 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
29940 CGACCCGACC
* *
29950 GTTGACCGTTAACTG-TGACC
1 GTTGACCGTTAACCGTTGACT
*
29970 GTTGGCCGTTAACCGTTGACT
1 GTTGACCGTTAACCGTTGACT
* *
29991 G-TGACCGTTGACCGTGGACT
1 GTTGACCGTTAACCGTTGACT
30011 TTCTTTGACC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 29 0.85
21 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.30
Consensus pattern (21 bp):
GTTGACCGTTAACCGTTGACT
Found at i:29999 original size:13 final size:13
Alignment explanation
Indices: 29952--30002 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
29942 ACCCGACCGT
*
29952 TGACCGTTAACTG
1 TGACCGTTGACTG
* *
29965 TGACCGTTGGCCG
1 TGACCGTTGACTG
*
29978 TTAACCGTTGACTG
1 -TGACCGTTGACTG
29992 TGACCGTTGAC
1 TGACCGTTGAC
30003 CGTGGACTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
13 20 0.67
14 10 0.33
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.29
Consensus pattern (13 bp):
TGACCGTTGACTG
Found at i:37239 original size:20 final size:19
Alignment explanation
Indices: 37214--37265 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
37204 GCTGCTGGAA
* *
37214 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
37234 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
37253 AACCGGGTTGACC
1 AACCGGTTTGACC
37266 CGACCCGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:37243 original size:10 final size:10
Alignment explanation
Indices: 37214--37263 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
37204 GCTGCTGGAA
37214 AACCGGTTTG
1 AACCGGTTTG
*
37224 -ACCAGTTTTG
1 AACC-GGTTTG
37234 AACCGGTTTG
1 AACCGGTTTG
*
37244 -ACCGGTCTG
1 AACCGGTTTG
*
37253 AACCGGGTTG
1 AACCGGTTTG
37263 A
1 A
37264 CCCGACCCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 11 0.34
10 18 0.56
11 3 0.09
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:37282 original size:17 final size:17
Alignment explanation
Indices: 37259--37333 Score: 105
Period size: 17 Copynumber: 4.4 Consensus size: 17
37249 TCTGAACCGG
37259 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
37276 ATTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
*
37293 GTTGACCCGACCCGAAT
1 GTTGACCCGACCCGACT
* * *
37310 GTTGGCCCGACCCAACC
1 GTTGACCCGACCCGACT
37327 GTTGACC
1 GTTGACC
37334 ATTGACCGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 50 1.00
ACGTcount: A:0.20, C:0.40, G:0.23, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:37358 original size:20 final size:20
Alignment explanation
Indices: 37329--37383 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
37319 ACCCAACCGT
*
37329 TGACCATTGACCGTTAACTG
1 TGACCGTTGACCGTTAACTG
*
37349 TGACCGTTGACCGTTGACTG
1 TGACCGTTGACCGTTAACTG
*
37369 TGACCGTTAACCGTT
1 TGACCGTTGACCGTT
37384 GACTTTCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (20 bp):
TGACCGTTGACCGTTAACTG
Found at i:37359 original size:7 final size:7
Alignment explanation
Indices: 37324--37386 Score: 67
Period size: 7 Copynumber: 9.3 Consensus size: 7
37314 GCCCGACCCA
37324 ACCGTTG
1 ACCGTTG
*
37331 ACCATTG
1 ACCGTTG
*
37338 ACCGTTA
1 ACCGTTG
*
37345 ACTG-TG
1 ACCGTTG
37351 ACCGTTG
1 ACCGTTG
37358 ACCGTTG
1 ACCGTTG
*
37365 ACTG-TG
1 ACCGTTG
*
37371 ACCGTTA
1 ACCGTTG
37378 ACCGTTG
1 ACCGTTG
37385 AC
1 AC
37387 TTTCTTTGAC
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
6 9 0.20
7 35 0.80
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.29
Consensus pattern (7 bp):
ACCGTTG
Found at i:39683 original size:20 final size:20
Alignment explanation
Indices: 39658--39709 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
39648 AGTTGAAGAA
*
39658 GTATCGATACTGATG-TGAAG
1 GTATCGATACTGAGGAT-AAG
**
39678 GTATCGATACCAAGGATAAG
1 GTATCGATACTGAGGATAAG
39698 GTATCGATACTG
1 GTATCGATACTG
39710 TAAGTAAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (20 bp):
GTATCGATACTGAGGATAAG
Found at i:40373 original size:15 final size:15
Alignment explanation
Indices: 40353--40399 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
40343 ATTTTGCACT
40353 AATATATGATATGTG
1 AATATATGATATGTG
40368 AATATATGATATGTG
1 AATATATGATATGTG
* *
40383 AATAAATGCTATGTG
1 AATATATGATATGTG
40398 AA
1 AA
40400 ATGAAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.36
Consensus pattern (15 bp):
AATATATGATATGTG
Found at i:40628 original size:23 final size:23
Alignment explanation
Indices: 40597--40666 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
40587 AGTCGAGGGT
*
40597 TCTATGTGGTCATTCGAGACAAA
1 TCTAAGTGGTCATTCGAGACAAA
* * *
40620 TCTAAGTGGTCCTTCGGGATAAA
1 TCTAAGTGGTCATTCGAGACAAA
40643 TCTATA-TGGTCATTCGAGACAAA
1 TCTA-AGTGGTCATTCGAGACAAA
40666 T
1 T
40667 ATGTGGTACT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 38 0.97
24 1 0.03
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (23 bp):
TCTAAGTGGTCATTCGAGACAAA
Found at i:43292 original size:22 final size:22
Alignment explanation
Indices: 43262--43311 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
43252 ATTTAGTGTT
43262 TAAACAAACGATATTCATAGTTA
1 TAAA-AAACGATATTCATAGTTA
*
43285 TAAAAAACGATATTTATAGTTA
1 TAAAAAACGATATTCATAGTTA
43307 TAAAA
1 TAAAA
43312 TATTTTTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (22 bp):
TAAAAAACGATATTCATAGTTA
Found at i:46902 original size:2 final size:2
Alignment explanation
Indices: 46897--46951 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
46887 TAAATAACAT
46897 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46939 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
46952 GATTAAAGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:47695 original size:21 final size:21
Alignment explanation
Indices: 47670--47710 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
47660 TATATAAATC
* *
47670 AATATTATACACTAATTACAT
1 AATATCATACACTAAATACAT
*
47691 AATATCATACATTAAATACA
1 AATATCATACACTAAATACA
47711 ATATATAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (21 bp):
AATATCATACACTAAATACAT
Found at i:47716 original size:21 final size:20
Alignment explanation
Indices: 47664--47717 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 20
47654 TTATAATATA
47664 TAAAT-CAATAT-TATACAC
1 TAAATACAATATATATACAC
* *
47682 TAATTAC-ATAATATCATACAT
1 TAAATACAAT-ATAT-ATACAC
47703 TAAATACAATATATA
1 TAAATACAATATATA
47718 AGAGTCATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
18 6 0.21
19 3 0.11
20 2 0.07
21 15 0.54
22 2 0.07
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATACAATATATATACAC
Found at i:47855 original size:6 final size:6
Alignment explanation
Indices: 47844--47877 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
47834 CTATTAAAAA
*
47844 TTTGTT TTTGTT TTTGTT TTT-TT TTTTTT TTTGT
1 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGT
47878 GAATACCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTGTT
Done.