Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005135.1 Hibiscus syriacus cultivar Beakdansim tig00011559_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: 55282
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3941 original size:19 final size:20
Alignment explanation
Indices: 3917--3959 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3907 AGCATTTATC
*
3917 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
3936 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
3956 TTCA
1 TTCA
3960 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:6148 original size:23 final size:26
Alignment explanation
Indices: 6122--6176 Score: 82
Period size: 23 Copynumber: 2.3 Consensus size: 26
6112 AAATCCAGCA
6122 AAGAAAATT-AAAGCACTCAAA-A-G
1 AAGAAAATTGAAAGCACTCAAAGAGG
6145 AAG-AAATTGAAAGCACTCAAAGAGG
1 AAGAAAATTGAAAGCACTCAAAGAGG
6170 AAGAAAA
1 AAGAAAA
6177 AAAGAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.18
23 15 0.54
24 1 0.04
25 4 0.14
26 3 0.11
ACGTcount: A:0.60, C:0.11, G:0.18, T:0.11
Consensus pattern (26 bp):
AAGAAAATTGAAAGCACTCAAAGAGG
Found at i:6186 original size:5 final size:5
Alignment explanation
Indices: 6176--6204 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
6166 GAGGAAGAAA
6176 AAAAG AAAAG AAAAG AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
6205 TTGAAAGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:8965 original size:11 final size:13
Alignment explanation
Indices: 8933--8962 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
8923 TGGCCAAAGA
8933 TGAAAAGGTATGT
1 TGAAAAGGTATGT
8946 TGAAAAGGTATG-
1 TGAAAAGGTATGT
8958 TGAAA
1 TGAAA
8963 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:10913 original size:65 final size:65
Alignment explanation
Indices: 10809--10939 Score: 208
Period size: 65 Copynumber: 2.0 Consensus size: 65
10799 TATACTAGCC
*
10809 CCATGTGCCTTGCATGAGGAACATTTAGGGGCCAAGATGAAGAGTTCTCTCCCTATTCGGCCAAG
1 CCATGTGCCTTGCATGAGGAACATTTAGGGGCCAAGATGAAGAGCTCTCTCCCTATTCGGCCAAG
* *** *
10874 CCATGTGCCTTGCATGTGGTTTATTTAGGTGCCAAGATGAAGAGCTCTCTCCCTATTCGGCCAAG
1 CCATGTGCCTTGCATGAGGAACATTTAGGGGCCAAGATGAAGAGCTCTCTCCCTATTCGGCCAAG
10939 C
1 C
10940 ACCATTTCCC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (65 bp):
CCATGTGCCTTGCATGAGGAACATTTAGGGGCCAAGATGAAGAGCTCTCTCCCTATTCGGCCAAG
Found at i:12050 original size:13 final size:12
Alignment explanation
Indices: 12030--12068 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12020 TGCTGCAACA
12030 AAAGAGAAAAAG
1 AAAGAGAAAAAG
12042 AAAGAAGAAAAAG
1 AAAG-AGAAAAAG
* *
12055 AAACAGAAACAG
1 AAAGAGAAAAAG
12067 AA
1 AA
12069 GAAAAGACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAGAGAAAAAG
Found at i:13621 original size:33 final size:33
Alignment explanation
Indices: 13579--13647 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
13569 GTTGATGAAT
*
13579 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
13612 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
13645 GAA
1 GAA
13648 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:13652 original size:13 final size:12
Alignment explanation
Indices: 13633--13729 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
13623 TTATTGGCGT
13633 GATATGGTGATG
1 GATATGGTGATG
13645 GAATATGGTGAT-
1 G-ATATGGTGATG
*
13657 GATATAGGCG-T-
1 GATAT-GGTGATG
13668 GATAATGGTGATG
1 GAT-ATGGTGATG
13681 GACTATGGTGAT-
1 GA-TATGGTGATG
*
13693 GATATAGGCG-T-
1 GATAT-GGTGATG
*
13704 GATAATGGAGATG
1 GAT-ATGGTGATG
13717 GATTATGGTGATG
1 GA-TATGGTGATG
13730 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:13688 original size:36 final size:36
Alignment explanation
Indices: 13618--13730 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
13608 AATGGAAGGA
* *
13618 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
13653 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
13689 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
13725 TGATGA
1 TGATGA
13731 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:18131 original size:33 final size:33
Alignment explanation
Indices: 18089--18157 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
18079 GTTGATGAAT
*
18089 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
18122 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
18155 GAA
1 GAA
18158 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:18162 original size:13 final size:12
Alignment explanation
Indices: 18143--18239 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
18133 TTATTGGCGT
18143 GATATGGTGATG
1 GATATGGTGATG
18155 GAATATGGTGAT-
1 G-ATATGGTGATG
*
18167 GATATAGGCG-T-
1 GATAT-GGTGATG
18178 GATAATGGTGATG
1 GAT-ATGGTGATG
18191 GACTATGGTGAT-
1 GA-TATGGTGATG
*
18203 GATATAGGCG-T-
1 GATAT-GGTGATG
*
18214 GATAATGGAGATG
1 GAT-ATGGTGATG
18227 GATTATGGTGATG
1 GA-TATGGTGATG
18240 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:18198 original size:36 final size:36
Alignment explanation
Indices: 18128--18240 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
18118 AATGGAAGGA
* *
18128 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
18163 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
18199 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
18235 TGATGA
1 TGATGA
18241 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:20267 original size:33 final size:33
Alignment explanation
Indices: 20225--20293 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
20215 GTTGATGAAT
*
20225 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
20258 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
20291 GAA
1 GAA
20294 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:20298 original size:13 final size:12
Alignment explanation
Indices: 20279--20375 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
20269 TTATTGGCGT
20279 GATATGGTGATG
1 GATATGGTGATG
20291 GAATATGGTGAT-
1 G-ATATGGTGATG
*
20303 GATATAGGCG-T-
1 GATAT-GGTGATG
20314 GATAATGGTGATG
1 GAT-ATGGTGATG
20327 GACTATGGTGAT-
1 GA-TATGGTGATG
*
20339 GATATAGGCG-T-
1 GATAT-GGTGATG
*
20350 GATAATGGAGATG
1 GAT-ATGGTGATG
20363 GATTATGGTGATG
1 GA-TATGGTGATG
20376 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:20334 original size:36 final size:36
Alignment explanation
Indices: 20264--20376 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
20254 AATGGAAGGA
* *
20264 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
20299 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
20335 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
20371 TGATGA
1 TGATGA
20377 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:29474 original size:14 final size:15
Alignment explanation
Indices: 29446--29489 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
29436 TTGCTTCACT
*
29446 TTTTCTTTGCTTTTTT
1 TTTTCTTT-CTTTTTC
29462 TTATTC-TTCTTTTTC
1 TT-TTCTTTCTTTTTC
29477 TTTTCTTTCTTTT
1 TTTTCTTTCTTTT
29490 GCACTCCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.12
15 15 0.60
16 4 0.16
17 3 0.12
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTCTTTCTTTTTC
Found at i:29938 original size:33 final size:33
Alignment explanation
Indices: 29896--29964 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
29886 GTTGATGAAT
*
29896 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
29929 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
29962 GAA
1 GAA
29965 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:29969 original size:13 final size:12
Alignment explanation
Indices: 29950--30046 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
29940 TTATTGGCGT
29950 GATATGGTGATG
1 GATATGGTGATG
29962 GAATATGGTGAT-
1 G-ATATGGTGATG
*
29974 GATATAGGCG-T-
1 GATAT-GGTGATG
29985 GATAATGGTGATG
1 GAT-ATGGTGATG
29998 GACTATGGTGAT-
1 GA-TATGGTGATG
*
30010 GATATAGGCG-T-
1 GATAT-GGTGATG
*
30021 GATAATGGAGATG
1 GAT-ATGGTGATG
30034 GATTATGGTGATG
1 GA-TATGGTGATG
30047 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:30005 original size:36 final size:36
Alignment explanation
Indices: 29935--30047 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
29925 AATGGAAGGA
* *
29935 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
29970 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
30006 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
30042 TGATGA
1 TGATGA
30048 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:30727 original size:19 final size:21
Alignment explanation
Indices: 30684--30735 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
30674 GAAACCCCTT
*
30684 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTGTAAA
30705 TGAAAATACATGA-TTGT-AA
1 TGAAAATACATGACTTGTAAA
*
30724 TGAAGATACATG
1 TGAAAATACATG
30736 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (21 bp):
TGAAAATACATGACTTGTAAA
Found at i:34756 original size:19 final size:21
Alignment explanation
Indices: 34713--34764 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
34703 GAAACCCCTT
*
34713 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTGTAAA
34734 TGAAAATACATGA-TTGT-AA
1 TGAAAATACATGACTTGTAAA
*
34753 TGAAGATACATG
1 TGAAAATACATG
34765 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (21 bp):
TGAAAATACATGACTTGTAAA
Found at i:42772 original size:36 final size:36
Alignment explanation
Indices: 42720--42822 Score: 163
Period size: 36 Copynumber: 2.9 Consensus size: 36
42710 GATACTATTT
*
42720 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
42756 TCATCACCATAGTCCATCCCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
42792 TCATCACCATATTCCATCACCA-TATCACGCC
1 TCATCACCATAATCCATCACCATTATCACGCC
42823 AATAACATTA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 9 0.14
36 54 0.86
ACGTcount: A:0.29, C:0.39, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:45235 original size:22 final size:21
Alignment explanation
Indices: 45194--45237 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
45184 CACCATCTCC
*
45194 ACTTCATCATCAACATCATCA
1 ACTTCATCATCAACACCATCA
*
45215 ACTTCATCCATCAAGACCATCA
1 ACTTCAT-CATCAACACCATCA
45237 A
1 A
45238 TTCCGTAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.39, C:0.34, G:0.02, T:0.25
Consensus pattern (21 bp):
ACTTCATCATCAACACCATCA
Found at i:45604 original size:13 final size:12
Alignment explanation
Indices: 45556--45610 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 12
45546 GTGCAAAAAG
45556 AAAGAAAAAGACAA
1 AAAG-AAAAGA-AA
*
45570 AAAGAAGAGAAA
1 AAAGAAAAGAAA
45582 AATCAGAAAAGAATA
1 AA--AGAAAAGAA-A
45597 AAAGAAAAGAAA
1 AAAGAAAAGAAA
45609 AA
1 AA
45611 GAATTTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
12 7 0.19
13 14 0.39
14 12 0.33
15 3 0.08
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:45610 original size:19 final size:19
Alignment explanation
Indices: 45588--45627 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
45578 GAAAAATCAG
45588 AAAAGAA-TAAAAGAAAAGA
1 AAAAGAATTAAAA-AAAAGA
*
45607 AAAAGAATTTAAAAAAAGA
1 AAAAGAATTAAAAAAAAGA
45626 AA
1 AA
45628 GCAAGCCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (19 bp):
AAAAGAATTAAAAAAAAGA
Found at i:49614 original size:22 final size:21
Alignment explanation
Indices: 49573--49616 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
49563 CACCATCTCC
*
49573 ACTTCATCATCAACATCATCA
1 ACTTCATCATCAACACCATCA
*
49594 ACTTCATCCATCAAGACCATCA
1 ACTTCAT-CATCAACACCATCA
49616 A
1 A
49617 TTCCGCAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.39, C:0.34, G:0.02, T:0.25
Consensus pattern (21 bp):
ACTTCATCATCAACACCATCA
Found at i:51925 original size:17 final size:17
Alignment explanation
Indices: 51865--51928 Score: 53
Period size: 17 Copynumber: 3.7 Consensus size: 17
51855 AATTCGAGTG
51865 AAAAAAGAAAGAAAAG-A
1 AAAAAAG-AAGAAAAGAA
*
51882 CAAAAAGAA-AAAA-AA
1 AAAAAAGAAGAAAAGAA
*
51897 ATCAGAATAGAAGAAAAGAA
1 A--A-AAAAGAAGAAAAGAA
51917 AAAAAAGAAGAA
1 AAAAAAGAAGAA
51929 TTTCAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
15 5 0.14
16 2 0.05
17 16 0.43
18 7 0.19
19 4 0.11
20 3 0.08
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (17 bp):
AAAAAAGAAGAAAAGAA
Found at i:51928 original size:25 final size:25
Alignment explanation
Indices: 51865--51929 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 25
51855 AATTCGAGTG
*
51865 AAAAAAGAAAGAAAAGACAAAAAGAA
1 AAAAAAG-AAGAATAGACAAAAAGAA
51891 AAAAAA-ATCAGAATAGA-AGAAAAGAA
1 AAAAAAGA--AGAATAGACA-AAAAGAA
51917 AAAAAAGAAGAAT
1 AAAAAAGAAGAAT
51930 TTCAAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
24 1 0.03
25 6 0.18
26 26 0.76
27 1 0.03
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (25 bp):
AAAAAAGAAGAATAGACAAAAAGAA
Found at i:55039 original size:31 final size:32
Alignment explanation
Indices: 54988--55056 Score: 131
Period size: 31 Copynumber: 2.2 Consensus size: 32
54978 CTTCCCATCC
54988 TTAGCCGAATCATTAAGGCTTTTCATGAAGGA
1 TTAGCCGAATCATTAAGGCTTTTCATGAAGGA
55020 TTAGCCGAATCA-TAAGGCTTTTCATGAAGGA
1 TTAGCCGAATCATTAAGGCTTTTCATGAAGGA
55051 TTAGCC
1 TTAGCC
55057 AAACCATCAC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 25 0.68
32 12 0.32
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (32 bp):
TTAGCCGAATCATTAAGGCTTTTCATGAAGGA
Done.