Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006080.1 Hibiscus syriacus cultivar Beakdansim tig00014406_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: 64429
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:1756 original size:23 final size:23
Alignment explanation
Indices: 1730--1779 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1720 AATAACTAAC
*
1730 ATAAA-CATAAATATACCATTAAA
1 ATAAAGCATAAACA-ACCATTAAA
**
1753 ATAAAGTTTAAACAACCATTAAA
1 ATAAAGCATAAACAACCATTAAA
1776 ATAA
1 ATAA
1780 CCACCACCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (23 bp):
ATAAAGCATAAACAACCATTAAA
Found at i:5053 original size:20 final size:21
Alignment explanation
Indices: 5028--5069 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
5018 GAGAAAAAAA
*
5028 ATAAAAGTTTAA-AATGAAAG
1 ATAAAAATTTAATAATGAAAG
5048 ATAAAAATTTAATAATGAAAG
1 ATAAAAATTTAATAATGAAAG
5069 A
1 A
5070 GAGAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (21 bp):
ATAAAAATTTAATAATGAAAG
Found at i:8962 original size:21 final size:21
Alignment explanation
Indices: 8921--8962 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8911 TGAGTTATGG
* *
8921 CTTTGAAGTAAGGCACCTTGA
1 CTTTGAAGTAAAGCACATTGA
*
8942 CTTTGAAGTAAAGCTCATTGA
1 CTTTGAAGTAAAGCACATTGA
8963 TTCTTAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (21 bp):
CTTTGAAGTAAAGCACATTGA
Found at i:13529 original size:20 final size:20
Alignment explanation
Indices: 13504--13564 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
13494 CGTTGGGCTT
*
13504 GATATTATTGTAGCAGTATC
1 GATATTACTGTAGCAGTATC
*
13524 GATATTACTGTAACAGTATC
1 GATATTACTGTAGCAGTATC
* *
13544 GATACTACTGTAGTAGTATC
1 GATATTACTGTAGCAGTATC
13564 G
1 G
13565 GTACCCATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (20 bp):
GATATTACTGTAGCAGTATC
Found at i:13652 original size:20 final size:19
Alignment explanation
Indices: 13615--13679 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
13605 TTCATTAATG
* *
13615 TTCACACAATATCGGTACTA
1 TTCATACAATA-CAGTACTA
* *
13635 TTCATATAGTACCAGTACTA
1 TTCATACAATA-CAGTACTA
*
13655 TTCATACAATACAATACTA
1 TTCATACAATACAGTACTA
13674 TTCATA
1 TTCATA
13680 AAAAAATTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
19 13 0.35
20 24 0.65
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (19 bp):
TTCATACAATACAGTACTA
Found at i:15159 original size:23 final size:23
Alignment explanation
Indices: 15133--15191 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
15123 CGTATAAATG
15133 CACCGAAGTGCCACGTAGAATTA
1 CACCGAAGTGCCACGTAGAATTA
* *
15156 CACCGAAGTGCCGCGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTA
15179 CACCGAAGTGCCA
1 CACCGAAGTGCCA
15192 TACAAAATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.15
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTA
Found at i:17957 original size:16 final size:16
Alignment explanation
Indices: 17932--17969 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
17922 ATTCAAAATC
* *
17932 CAAATATCCTTTTACA
1 CAAATCTCCTTATACA
17948 CAAATCTCCTTATACA
1 CAAATCTCCTTATACA
17964 CAAATC
1 CAAATC
17970 ATATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (16 bp):
CAAATCTCCTTATACA
Found at i:21589 original size:13 final size:14
Alignment explanation
Indices: 21571--21600 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
21561 GTAAAAGAAA
21571 GTCAACGGTC-ACG
1 GTCAACGGTCAACG
21584 GTCAACGGTCAACG
1 GTCAACGGTCAACG
21598 GTC
1 GTC
21601 GGGTCGGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:21612 original size:17 final size:17
Alignment explanation
Indices: 21590--21647 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
21580 CACGGTCAAC
21590 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
21607 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
* *
21624 GGCCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
21641 GGTCAAC
1 GGTCAAC
21648 CCGGTTCAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.16, C:0.26, G:0.43, T:0.16
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:21617 original size:7 final size:7
Alignment explanation
Indices: 21571--21600 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
21561 GTAAAAGAAA
21571 GTCAACG
1 GTCAACG
21578 GTC-ACG
1 GTCAACG
21584 GTCAACG
1 GTCAACG
21591 GTCAACG
1 GTCAACG
21598 GTC
1 GTC
21601 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:21665 original size:19 final size:19
Alignment explanation
Indices: 21641--21730 Score: 128
Period size: 19 Copynumber: 4.7 Consensus size: 19
21631 AGTCGGGTCG
*
21641 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
21660 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
21679 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
21698 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
21718 GGTCAAACCGGTT
1 GGTCAAACCGGTT
21731 TTCCAGCAGC
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
18 1 0.02
19 49 0.75
20 15 0.23
ACGTcount: A:0.27, C:0.30, G:0.26, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:21713 original size:10 final size:10
Alignment explanation
Indices: 21643--21730 Score: 94
Period size: 9 Copynumber: 9.1 Consensus size: 10
21633 TCGGGTCGGG
*
21643 TCAACCCGGT
1 TCAAACCGGT
*
21653 TCAGACCGG-
1 TCAAACCGGT
21662 TCAAACCGGT
1 TCAAACCGGT
*
21672 TCAGACCGG-
1 TCAAACCGGT
21681 TCAAACCGGT
1 TCAAACCGGT
*
21691 TCGAACCGG-
1 TCAAACCGGT
21700 TCAAACCGGT
1 TCAAACCGGT
*
21710 TCAAAACTGG-
1 TC-AAACCGGT
21720 TCAAACCGGT
1 TCAAACCGGT
21730 T
1 T
21731 TTCCAGCAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
9 30 0.47
10 28 0.44
11 6 0.09
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:28943 original size:17 final size:17
Alignment explanation
Indices: 28921--28977 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
28911 ACGGTCAACA
28921 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
28938 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
* *
28955 GCCAACAGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
28972 GTCAAC
1 GTCAAC
28978 CCGGTTCAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.16, C:0.26, G:0.42, T:0.16
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGG
Found at i:28995 original size:19 final size:19
Alignment explanation
Indices: 28971--29079 Score: 166
Period size: 19 Copynumber: 5.7 Consensus size: 19
28961 AGTCGGGTCG
*
28971 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
28990 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
29009 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
29028 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
29047 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
29067 GGTCAAACCGGTT
1 GGTCAAACCGGTT
29080 TTCCAGCAGC
Statistics
Matches: 84, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
18 1 0.01
19 68 0.81
20 15 0.18
ACGTcount: A:0.27, C:0.30, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:29062 original size:10 final size:10
Alignment explanation
Indices: 28973--29079 Score: 116
Period size: 9 Copynumber: 11.1 Consensus size: 10
28963 TCGGGTCGGG
*
28973 TCAACCCGGT
1 TCAAACCGGT
*
28983 TCAGACCGG-
1 TCAAACCGGT
28992 TCAAACCGGT
1 TCAAACCGGT
*
29002 TCAGACCGG-
1 TCAAACCGGT
29011 TCAAACCGGT
1 TCAAACCGGT
*
29021 TCAGACCGG-
1 TCAAACCGGT
29030 TCAAACCGGT
1 TCAAACCGGT
*
29040 TCGAACCGG-
1 TCAAACCGGT
29049 TCAAACCGGT
1 TCAAACCGGT
*
29059 TCAAAACTGG-
1 TC-AAACCGGT
29069 TCAAACCGGT
1 TCAAACCGGT
29079 T
1 T
29080 TTCCAGCAGC
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
9 38 0.47
10 36 0.45
11 6 0.08
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:30322 original size:23 final size:23
Alignment explanation
Indices: 30265--30325 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
30255 CTCGTATAAA
*
30265 TGCACCGAAGTACCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
30288 TACACTGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
30311 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
30326 TATAAAATGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.26, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:32886 original size:2 final size:2
Alignment explanation
Indices: 32879--32906 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32869 AATTAAAAAT
32879 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
32907 ACATATACAA
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):
TA
Found at i:33216 original size:53 final size:53
Alignment explanation
Indices: 33138--33352 Score: 177
Period size: 53 Copynumber: 4.1 Consensus size: 53
33128 TAAGGGTTAA
* * * * * *
33138 GGTTAAAGAAGATGAACACATATAGAAGATGAAAATGCTCGTTTTGGGTTTGG
1 GGTTAGAGAAGATGAACAGAGACAGAAGATGAAAATGCTCGGTTTGGGTTTAG
* * * * *
33191 GGTTAGAGAAGATGAACAGAGATAGAAGATGAAGAGGCTCGGTTTGAGTTTAA
1 GGTTAGAGAAGATGAACAGAGACAGAAGATGAAAATGCTCGGTTTGGGTTTAG
* * * * * * * *
33244 GGTTAGAGAATATAAACAAAGGCAGAAAATG-AAGTGGCTAGGTTAGGGTTTAG
1 GGTTAGAGAAGATGAACAGAGACAGAAGATGAAAAT-GCTCGGTTTGGGTTTAG
* * *
33297 GATTAGACAGGATGAACAGAGACAGAA-AGTGAATAA-GCTCGGTTTGGGTTT-G
1 GGTTAGAGAAGATGAACAGAGACAGAAGA-TGAA-AATGCTCGGTTTGGGTTTAG
33349 GGTT
1 GGTT
33353 CAGGTTTGAG
Statistics
Matches: 125, Mismatches: 33, Indels: 9
0.75 0.20 0.05
Matches are distributed among these distances:
52 6 0.05
53 117 0.94
54 1 0.01
55 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.32, T:0.25
Consensus pattern (53 bp):
GGTTAGAGAAGATGAACAGAGACAGAAGATGAAAATGCTCGGTTTGGGTTTAG
Found at i:34115 original size:61 final size:61
Alignment explanation
Indices: 34012--34209 Score: 342
Period size: 61 Copynumber: 3.2 Consensus size: 61
34002 CCTTAGTTTT
* * * * * *
34012 AAATTTGTTCAATTTAATCCAAAGTTAATGATGCAATGTATTAATTTAAGCTTTATATTTA
1 AAATTTGTTCAATTTAGTCCAAATTTAATGTTGTAATTTATTAATTTAAGCTTCATATTTA
34073 AAATTTGTTCAATTTAGTCCAAATTTAATGTTGTAATTTATTAATTTAAGCTTCATATTTA
1 AAATTTGTTCAATTTAGTCCAAATTTAATGTTGTAATTTATTAATTTAAGCTTCATATTTA
34134 AAATTTGTTCAATTTAGTCCAAATTTAATGTTGTAATTTATTAATTTAAGCTTCATATTTA
1 AAATTTGTTCAATTTAGTCCAAATTTAATGTTGTAATTTATTAATTTAAGCTTCATATTTA
34195 AAATTTGTTCAATTT
1 AAATTTGTTCAATTT
34210 GATCCTTATA
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 131 1.00
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.48
Consensus pattern (61 bp):
AAATTTGTTCAATTTAGTCCAAATTTAATGTTGTAATTTATTAATTTAAGCTTCATATTTA
Found at i:34132 original size:21 final size:20
Alignment explanation
Indices: 34054--34200 Score: 55
Period size: 20 Copynumber: 7.2 Consensus size: 20
34044 GCAATGTATT
*
34054 AATTTAAGCTTTATATTTA-A
1 AATTTAAG-TTCATATTTATA
34074 AATTT--GTTCA-ATTTAGTCCA
1 AATTTAAGTTCATATTTA-T--A
* *
34094 AATTTAATGTT-GTAATTTATT
1 AATTTAA-GTTCAT-ATTTATA
34115 AATTTAAGCTTCATATTTA-A
1 AATTTAAG-TTCATATTTATA
34135 AATTT--GTTCA-ATTTAGTCCA
1 AATTTAAGTTCATATTTA-T--A
* *
34155 AATTTAATGTT-GTAATTTATT
1 AATTTAA-GTTCAT-ATTTATA
34176 AATTTAAGCTTCATATTTA-A
1 AATTTAAG-TTCATATTTATA
34196 AATTT
1 AATTT
34201 GTTCAATTTG
Statistics
Matches: 96, Mismatches: 9, Indels: 44
0.64 0.06 0.30
Matches are distributed among these distances:
16 10 0.10
17 7 0.07
18 2 0.02
20 29 0.30
21 28 0.29
22 2 0.02
23 8 0.08
24 10 0.10
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (20 bp):
AATTTAAGTTCATATTTATA
Found at i:34318 original size:18 final size:18
Alignment explanation
Indices: 34297--34335 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
34287 TAACGAACTA
34297 TATAATATATAGTTTATG
1 TATAATATATAGTTTATG
*
34315 TATACTATATAGTTTATG
1 TATAATATATAGTTTATG
34333 TAT
1 TAT
34336 TCTAATGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (18 bp):
TATAATATATAGTTTATG
Found at i:34327 original size:51 final size:50
Alignment explanation
Indices: 34271--34375 Score: 158
Period size: 51 Copynumber: 2.1 Consensus size: 50
34261 TAAATTAATG
*
34271 TATAGTTTATATATAT-TAACGAACTATATAATATATAGTTTATGTATACTA
1 TATAGTTTATATAT-TCTAACGAACTATATAATATATAGTTTATATATA-TA
* *
34322 TATAGTTTATGTATTCTAATGAACTATATAATATATAGTTTATATATATA
1 TATAGTTTATATATTCTAACGAACTATATAATATATAGTTTATATATATA
34372 TATA
1 TATA
34376 TATAGTTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
50 7 0.14
51 43 0.86
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.47
Consensus pattern (50 bp):
TATAGTTTATATATTCTAACGAACTATATAATATATAGTTTATATATATA
Found at i:34369 original size:18 final size:18
Alignment explanation
Indices: 34295--34377 Score: 66
Period size: 18 Copynumber: 4.7 Consensus size: 18
34285 ATTAACGAAC
34295 TATATAATATATAGTTTA
1 TATATAATATATAGTTTA
* *
34313 TGTATACTATATAGTTTA
1 TATATAATATATAGTTTA
* * **
34331 TGTAT--TCTA-A-TGAA
1 TATATAATATATAGTTTA
34345 CTATATAATATATAGTTTA
1 -TATATAATATATAGTTTA
34364 TATATATATATATA
1 TATATA-ATATATA
34378 TAGTTTTTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
14 2 0.04
15 5 0.10
16 3 0.06
17 3 0.06
18 28 0.56
19 9 0.18
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (18 bp):
TATATAATATATAGTTTA
Found at i:34378 original size:21 final size:20
Alignment explanation
Indices: 34346--34392 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 20
34336 TCTAATGAAC
34346 TATATAATATATAGTTTATA
1 TATATAATATATAGTTTATA
*
34366 TATATATATATATAGTTTTTA
1 TATATA-ATATATAGTTTATA
34387 TATATA
1 TATATA
34393 GTTCATATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
TATATAATATATAGTTTATA
Found at i:34466 original size:13 final size:15
Alignment explanation
Indices: 34434--34469 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
34424 AAATATCAAC
34434 TATAGTATATAGTTTA
1 TATA-TATATAGTTTA
*
34450 TATATATATATTTTA
1 TATATATATAGTTTA
34465 TATAT
1 TATAT
34470 GTAGCATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (15 bp):
TATATATATAGTTTA
Found at i:34622 original size:62 final size:60
Alignment explanation
Indices: 34540--34659 Score: 163
Period size: 62 Copynumber: 2.0 Consensus size: 60
34530 GTAAACTACC
*
34540 AAACTATATATATTATATAGTTTACATAATA-TATATATAGTTTATACATATAGTTCATATGT
1 AAACTATATATATTACATAGTTTACAT-ATAGTATATATAGTTTAT--ATATAGTTCATATGT
* *
34602 AAACTATATA-ATATACATAGTTTACATATAGTATATATGGTTTATATATAGTTTATAT
1 AAACTATATATAT-TACATAGTTTACATATAGTATATATAGTTTATATATAGTTCATAT
34660 ACTACTATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
60 12 0.23
61 5 0.09
62 36 0.68
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (60 bp):
AAACTATATATATTACATAGTTTACATATAGTATATATAGTTTATATATAGTTCATATGT
Found at i:34647 original size:11 final size:11
Alignment explanation
Indices: 34613--34660 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
34603 AACTATATAA
*
34613 TATACATAGTT
1 TATATATAGTT
*
34624 TACATATAG--
1 TATATATAGTT
*
34633 TATATATGGTT
1 TATATATAGTT
34644 TATATATAGTT
1 TATATATAGTT
34655 TATATA
1 TATATA
34661 CTACTATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
9 7 0.23
11 23 0.77
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (11 bp):
TATATATAGTT
Found at i:34652 original size:20 final size:20
Alignment explanation
Indices: 34544--34702 Score: 96
Period size: 20 Copynumber: 7.8 Consensus size: 20
34534 ACTACCAAAC
34544 TATATATA-T-TATATAGTT
1 TATATATAGTATATATAGTT
*
34562 TACATAATA-TATATATAGTT
1 TATAT-ATAGTATATATAGTT
*
34582 TATACATATAGT-TCATAT-GTA
1 TAT--ATATAGTAT-ATATAGTT
* * *
34603 AACTATATAATATACATAGTT
1 TA-TATATAGTATATATAGTT
* *
34624 TACATATAGTATATATGGTT
1 TATATATAGTATATATAGTT
* * *
34644 TATATATAGTTTATATACTAC
1 TATATATAGTATATATAGT-T
*
34665 TATATATA-AACTATATAGTT
1 TATATATAGTA-TATATAGTT
*
34685 TATAGATAGTAGTATATA
1 TATATATAGTA-TATATA
34703 TATATTTGGT
Statistics
Matches: 105, Mismatches: 24, Indels: 21
0.70 0.16 0.14
Matches are distributed among these distances:
18 4 0.04
19 4 0.04
20 56 0.53
21 33 0.31
22 8 0.08
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.45
Consensus pattern (20 bp):
TATATATAGTATATATAGTT
Found at i:35236 original size:2 final size:2
Alignment explanation
Indices: 35231--35321 Score: 78
Period size: 2 Copynumber: 44.5 Consensus size: 2
35221 GTATATAAAC
* * *
35231 TA TA TA TA AA CA TA TA TA CTA TA TA TA TA TA TA TA TA TA CTT TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
35275 AA TA TA CA CTA TA TA GTT TA TA T- TA -A 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
35317 TA TA T
1 TA TA T
35322 TAGTTGTTTC
Statistics
Matches: 72, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
1 2 0.03
2 65 0.90
3 5 0.07
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:35247 original size:10 final size:11
Alignment explanation
Indices: 35222--35267 Score: 55
Period size: 10 Copynumber: 4.5 Consensus size: 11
35212 AGTCCCGATG
35222 TATATAAACTA
1 TATATAAACTA
35233 TATATAAAC-A
1 TATATAAACTA
35243 TATAT--ACTA
1 TATATAAACTA
*
35252 TATATATA-TA
1 TATATAAACTA
35262 TATATA
1 TATATA
35268 TACTTTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 2 0.06
9 6 0.19
10 14 0.44
11 10 0.31
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (11 bp):
TATATAAACTA
Found at i:35247 original size:21 final size:20
Alignment explanation
Indices: 35222--35267 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
35212 AGTCCCGATG
35222 TATATAAACTATATATAAACA
1 TATAT-AACTATATATAAACA
* *
35243 TATAT-ACTATATATATATA
1 TATATAACTATATATAAACA
35262 TATATA
1 TATATA
35268 TACTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 17 0.77
21 5 0.23
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATAACTATATATAAACA
Found at i:37877 original size:37 final size:37
Alignment explanation
Indices: 37803--37877 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
37793 TACTATAATT
**
37803 AATTTATATATTTTCTTTAAAAAATTTAAATTCATAA
1 AATTTATATATTTTCTTTAAAAAATTTAAAAACATAA
* * *
37840 AATTTATATAATTTTTTTTACAAAA-TTAAAAAGATAA
1 AATTTATAT-ATTTTCTTTAAAAAATTTAAAAACATAA
37877 A
1 A
37878 TAGGTTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 19 0.59
38 13 0.41
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
AATTTATATATTTTCTTTAAAAAATTTAAAAACATAA
Found at i:50407 original size:18 final size:19
Alignment explanation
Indices: 50372--50407 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
50362 CTTCTCTAAG
50372 TAAAAAAAAATCACTCCAT
1 TAAAAAAAAATCACTCCAT
*
50391 TAAAACAAAATCA-TCCA
1 TAAAAAAAAATCACTCCA
50408 ATTCATACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.22, G:0.00, T:0.19
Consensus pattern (19 bp):
TAAAAAAAAATCACTCCAT
Found at i:51939 original size:25 final size:25
Alignment explanation
Indices: 51911--51959 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
51901 TTAATGATCC
*
51911 AATTTTACACTTCTTCAAATTTTAT
1 AATTTCACACTTCTTCAAATTTTAT
* *
51936 AATTTCACATTTCTTCAATTTTTA
1 AATTTCACACTTCTTCAAATTTTA
51960 ATATAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (25 bp):
AATTTCACACTTCTTCAAATTTTAT
Done.