Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007563.1 Hibiscus syriacus cultivar Beakdansim tig00021489_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: 85924
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:5490 original size:21 final size:21
Alignment explanation
Indices: 5465--5505 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5455 GTTACACAGG
5465 GGGGAATCGGTGCCCCCTGAA
1 GGGGAATCGGTGCCCCCTGAA
* *
5486 GGGGAATCGGTTCCCTCTGA
1 GGGGAATCGGTGCCCCCTGA
5506 GCATACTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.27, G:0.37, T:0.20
Consensus pattern (21 bp):
GGGGAATCGGTGCCCCCTGAA
Found at i:13892 original size:25 final size:25
Alignment explanation
Indices: 13864--13912 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
13854 CAATGGTCAA
13864 CGGGTCGGGTCGAGTCAGGTCAAAC
1 CGGGTCGGGTCGAGTCAGGTCAAAC
* *
13889 CGGGTTGGGTCGGGTCAGGTCAAA
1 CGGGTCGGGTCGAGTCAGGTCAAA
13913 GAGTTGGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.18, C:0.20, G:0.43, T:0.18
Consensus pattern (25 bp):
CGGGTCGGGTCGAGTCAGGTCAAAC
Found at i:23345 original size:14 final size:13
Alignment explanation
Indices: 23326--23372 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
23316 TATTACTCCT
23326 AAGAAACAAAAGAA
1 AAGAAA-AAAAGAA
23340 AAGAAAAGAAA-AA
1 AAGAAAA-AAAGAA
*
23353 AAGAAAAAGAAGAG
1 AAGAAAAA-AAGAA
23367 AAGAAA
1 AAGAAA
23373 TGAGAGTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 1 0.03
13 12 0.41
14 16 0.55
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAGAA
Found at i:24644 original size:136 final size:136
Alignment explanation
Indices: 24398--25110 Score: 813
Period size: 136 Copynumber: 5.2 Consensus size: 136
24388 ATCAATCAAA
** * * *
24398 ATTTCCAATTAAGTGTTCATAATGAGAAGTACTCATCTGACAAAGGGAGAAGAAGCTCATAATGA
1 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGCTCATAATGA
* * * * * * *
24463 GAAAAACTTGTTCGACCTATTGCTCGATTCACGTCATTTTGAATCAGTAATGCCTCTCATGAGGG
66 GAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTCGAATCAGCAACGCCTCGCTTGAGGG
24528 ATTAAC
131 ATTAAC
* * * *
24534 ATTTCCAATGGAGAGTTCATAATGAGAAGAGCTCATCCGATAGAGGGAGAAGAAGTTCATAATGA
1 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGCTCATAATGA
* * * * * * *
24599 GAAGAACTTGTTCGACCTATTGCACAATTCATGGCATTTCAAATCAGCAACGGCTCACTTGAGGG
66 GAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTCGAATCAGCAACGCCTCGCTTGAGGG
* *
24664 ATCAAT
131 ATTAAC
* * * * *
24670 ATTTCC--TGTATGAAGATCATGATGAGAAGAACTCATCCAAAAAAGGGAGAAGAAGCTCATAAT
1 ATTTCCAATGGA-G-AGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGCTCATAAT
**
24733 GAGAAGAACTTGTTCGACCTATTGCTTTATTCACGACATTTCGAATCAGCAACGCCTCGCTTGAG
64 GAGAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTCGAATCAGCAACGCCTCGCTTGAG
24798 GGATTAAC
129 GGATTAAC
* * * * *
24806 ATTTCTAATGGAGAGTTCATAATGAGAATAACTCATCCGACATAGTGATAAGAAGCTCATAATGA
1 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGCTCATAATGA
* * * * * **
24871 GAAGAACTTTTTCGACCTATTGCTCGATTCACGATATTTTGAATTAGAAACATCTCGCTTGA-GG
66 GAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTCGAATCAGCAACGCCTCGCTTGAGGG
24935 ATTAAC
131 ATTAAC
* * * * *
24941 ATTTCCAATGGAGAGTTCATAATGAGAAGAACACATCCGACAGAGGGAGAACAAGTTTATAATGA
1 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGCTCATAATGA
* * ** * *
25006 GAAGAACTTGTTCGACCTATTG-TACGATTCATGGCATTTCGAATCAGCAACGGATCACTTGAGA
66 GAAGAACTTGTTCGACCTATTGCT-CGATTCACGACATTTCGAATCAGCAACGCCTCGCTTGAGG
*
25070 GATCAAC
130 GATTAAC
** * * * *
25077 ATTTCCTGTAGAAAGATCATGATGAGAAGAACTC
1 ATTTCCAATGGAGAGTTCATAATGAGAAGAACTC
25111 GTAGCTTTAA
Statistics
Matches: 482, Mismatches: 89, Indels: 12
0.83 0.15 0.02
Matches are distributed among these distances:
134 4 0.01
135 114 0.24
136 360 0.75
137 1 0.00
138 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (136 bp):
ATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGCTCATAATGA
GAAGAACTTGTTCGACCTATTGCTCGATTCACGACATTTCGAATCAGCAACGCCTCGCTTGAGGG
ATTAAC
Found at i:31831 original size:17 final size:18
Alignment explanation
Indices: 31809--31843 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31799 AGGACACTTT
31809 ATATCAAT-AAAAATATA
1 ATATCAATAAAAAATATA
31826 ATATCAATAAAAAATATA
1 ATATCAATAAAAAATATA
31844 TGATAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
ATATCAATAAAAAATATA
Found at i:34474 original size:97 final size:97
Alignment explanation
Indices: 34323--34603 Score: 456
Period size: 97 Copynumber: 2.9 Consensus size: 97
34313 GTAGATTTCG
* ** * * * *
34323 TGATTCATAAATCAATAATGATAATATTTTCCAGTGAAAACAGGAAACCCGATAACATATTTCAG
1 TGATCCATAAATCAGGAACGATCATAATTTCCAGTGAAAACAGGAAACCCGATAACACATTTCAG
* *
34388 GCAACCATAGTTCATAAAACCAGTACGTTCTA
66 GTAACCATAGTTCATAAAACCAGTACGTTCCA
*
34420 TGATCCATAAATCAGGAACGATCATAATTTCCAGTGAAAACAGGAAACCAGATAACACATTTCAG
1 TGATCCATAAATCAGGAACGATCATAATTTCCAGTGAAAACAGGAAACCCGATAACACATTTCAG
34485 GTAACCATAGTTCATAAAACCAGTACGTTCCA
66 GTAACCATAGTTCATAAAACCAGTACGTTCCA
*
34517 TGATCCATAAACCAGGAACGATCATAATTTCCAGTGAAAACAGGAAACCCGATAACACATTTCAG
1 TGATCCATAAATCAGGAACGATCATAATTTCCAGTGAAAACAGGAAACCCGATAACACATTTCAG
34582 GTAACCATAGTTCAT-AAACCAG
66 GTAACCATAGTTCATAAAACCAG
34604 GAAATCAGTG
Statistics
Matches: 172, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
96 7 0.04
97 165 0.96
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (97 bp):
TGATCCATAAATCAGGAACGATCATAATTTCCAGTGAAAACAGGAAACCCGATAACACATTTCAG
GTAACCATAGTTCATAAAACCAGTACGTTCCA
Found at i:36105 original size:24 final size:24
Alignment explanation
Indices: 36054--36213 Score: 149
Period size: 24 Copynumber: 6.8 Consensus size: 24
36044 ACATATGGTG
36054 TAGTTTTTGAAAACATAT--TATA
1 TAGTTTTTGAAAACATATAATATA
* **
36076 TTGTTTTAAAAAACATATAATATA
1 TAGTTTTTGAAAACATATAATATA
*
36100 TAGTTTTTGAAAATATAT-ATAGTA
1 TAGTTTTTGAAAACATATAATA-TA
*
36124 TAGTTTTT-AAAACATATTAT-TA
1 TAGTTTTTGAAAACATATAATATA
*
36146 TATGGTTTTGAAAAC--AT-ATATA
1 TA-GTTTTTGAAAACATATAATATA
36168 TAGTTTTTGAAAAACATATGTAATATA
1 TAGTTTTTG-AAAACATA--TAATATA
36195 TA-TATTTTGAAAACATATA
1 TAGT-TTTTGAAAACATATA
36214 TATGATTTTG
Statistics
Matches: 114, Mismatches: 10, Indels: 26
0.76 0.07 0.17
Matches are distributed among these distances:
21 8 0.07
22 30 0.26
23 16 0.14
24 38 0.33
26 10 0.09
27 12 0.11
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (24 bp):
TAGTTTTTGAAAACATATAATATA
Found at i:36214 original size:19 final size:19
Alignment explanation
Indices: 36190--36240 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
36180 AACATATGTA
36190 ATATATATATTTTGAAAAC
1 ATATATATATTTTGAAAAC
* *
36209 ATATATATGATTTTGATAAT
1 ATATATAT-ATTTTGAAAAC
36229 ATAATATATATT
1 AT-ATATATATT
36241 ATATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 8 0.29
20 14 0.50
21 6 0.21
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (19 bp):
ATATATATATTTTGAAAAC
Found at i:36216 original size:48 final size:46
Alignment explanation
Indices: 36057--36255 Score: 176
Period size: 48 Copynumber: 4.2 Consensus size: 46
36047 TATGGTGTAG
* *
36057 TTTTTGAAAACATAT-TATATTGTTTTAAAAAACATA-TAATATATA
1 TTTTTGAAAACATATATATAGT-TTTTGAAAAACATATTAATATATA
* * *
36102 GTTTTTGAAAATATATATAGTATAGTTTTT--AAAACATATTATTATATG
1 -TTTTTG-AAA-ACATATA-TATAGTTTTTGAAAAACATATTAATATATA
*
36150 GTTTTGAAAACATATATATAGTTTTTGAAAAACATATGTAATATATA
1 TTTTTGAAAACATATATATAGTTTTTGAAAAACATAT-TAATATATA
* *
36197 TATTTTGAAAACATATATAT-GATTTTGATAATATA-ATATATATTATATA
1 T-TTTTGAAAACATATATATAGTTTTTGA-AA-A-ACATAT-TAATATATA
*
36246 TTTTTTAAAA
1 TTTTTGAAAA
36256 GTATATTATT
Statistics
Matches: 128, Mismatches: 13, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
44 10 0.08
45 6 0.05
46 18 0.14
47 30 0.23
48 40 0.31
49 18 0.14
50 6 0.05
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (46 bp):
TTTTTGAAAACATATATATAGTTTTTGAAAAACATATTAATATATA
Found at i:36223 original size:20 final size:21
Alignment explanation
Indices: 36031--36238 Score: 98
Period size: 22 Copynumber: 9.2 Consensus size: 21
36021 AAATATGTAG
* *
36031 TATAG-TTTTAAAAACATATGG
1 TATAGATTTTGAAAACATAT-A
* *
36052 TGTAGTTTTTGAAAACATATTA
1 TATAGATTTTGAAAACATA-TA
* *
36074 TATTG-TTTTAAAAAACATATAATA
1 TATAGATTTT-GAAAAC--AT-ATA
* *
36098 TATAGTTTTTGAAAATATATA
1 TATAGATTTTGAAAACATATA
* *
36119 TAGTATAGTTTTTAAAACATATTA
1 TA-TAGA-TTTTGAAAACATA-TA
*
36143 TTATATGGTTTTGAAAACATATA
1 -TATA-GATTTTGAAAACATATA
*
36166 TATAGTTTTTGAAAAACATATGTAATA
1 TATAGATTTTG-AAAAC--A--T-ATA
*
36193 TATATATTTTGAAAACATATA
1 TATAGATTTTGAAAACATATA
* *
36214 TAT-GATTTTGATAATATAATA
1 TATAGATTTTGAAAACAT-ATA
36235 TATA
1 TATA
36239 TTATATATTT
Statistics
Matches: 145, Mismatches: 22, Indels: 39
0.70 0.11 0.19
Matches are distributed among these distances:
20 11 0.08
21 31 0.21
22 34 0.23
23 14 0.10
24 30 0.21
25 7 0.05
26 6 0.04
27 12 0.08
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (21 bp):
TATAGATTTTGAAAACATATA
Found at i:36246 original size:47 final size:45
Alignment explanation
Indices: 36058--36249 Score: 160
Period size: 47 Copynumber: 4.1 Consensus size: 45
36048 ATGGTGTAGT
* * *
36058 TTTTGAAAACATATTATATTG-TTTTAAAAAACATA-TAATATATA
1 TTTTGAAAACATA-TATATAGATTTTGAAAAACATATTATTATATA
* * * *
36102 GTTTTTGAAAATATATATAGTATAGTTTT-TAAAACATATTATTATATGG
1 --TTTTGAAAACATATATA-TAGA-TTTTGAAAAACATATTATTATAT-A
*
36151 TTTTGAAAACATATATATAGTTTTTGAAAAACATATGTAATATATATA
1 TTTTGAAAACATATATATAGATTTTGAAAAACATAT-T-AT-TATATA
36199 TTTTGAAAACATATATAT-GATTTTGATAATATA-ATATATATTATATA
1 TTTTGAAAACATATATATAGATTTTGA-AA-A-ACATAT-TATTATATA
36246 TTTT
1 TTTT
36250 TTAAAAGTAT
Statistics
Matches: 121, Mismatches: 13, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
45 8 0.07
46 24 0.20
47 42 0.35
48 35 0.29
49 11 0.09
50 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (45 bp):
TTTTGAAAACATATATATAGATTTTGAAAAACATATTATTATATA
Found at i:36267 original size:3 final size:3
Alignment explanation
Indices: 36259--36331 Score: 75
Period size: 3 Copynumber: 25.3 Consensus size: 3
36249 TTTAAAAGTA
*
36259 TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAA T-T TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
*
36303 TAT T-T TAT TA- TAT CAT TATT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT T
36332 TTTGGTTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
2 9 0.15
3 44 0.75
4 6 0.10
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:37648 original size:15 final size:15
Alignment explanation
Indices: 37628--37700 Score: 69
Period size: 15 Copynumber: 4.8 Consensus size: 15
37618 ATTCTTGGCT
*
37628 TTTAATTATTTCCAA
1 TTTAATTATTTTCAA
*
37643 TTTAA-TATTTTTAA
1 TTTAATTATTTTCAA
* *
37657 TTTAATTTTTTTCTA
1 TTTAATTATTTTCAA
37672 TTTAATTATGATTT-AA
1 TTTAATTAT--TTTCAA
37688 TTTAATTTATTTT
1 TTTAA-TTATTTT
37701 TTTACTTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
14 12 0.26
15 22 0.47
16 6 0.13
17 7 0.15
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (15 bp):
TTTAATTATTTTCAA
Found at i:40617 original size:10 final size:10
Alignment explanation
Indices: 40602--40670 Score: 54
Period size: 10 Copynumber: 8.1 Consensus size: 10
40592 CATTTAATAA
40602 ATAAACGAAC
1 ATAAACGAAC
40612 ATAAACGAAC
1 ATAAACGAAC
40622 ----ACGAAC
1 ATAAACGAAC
40628 ATAAACGAAC
1 ATAAACGAAC
40638 ----ACGAAC
1 ATAAACGAAC
40644 ATAAACGAAC
1 ATAAACGAAC
40654 ----ACGAAC
1 ATAAACGAAC
40660 ATAAACGAAC
1 ATAAACGAAC
40670 A
1 A
40671 CGAACATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 24
0.66 0.00 0.34
Matches are distributed among these distances:
6 18 0.38
10 29 0.62
ACGTcount: A:0.58, C:0.23, G:0.12, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:40627 original size:16 final size:16
Alignment explanation
Indices: 40606--40698 Score: 177
Period size: 16 Copynumber: 5.8 Consensus size: 16
40596 TAATAAATAA
40606 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
40622 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
40638 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
40654 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
40670 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
40686 ACGAACATAAACG
1 ACGAACATAAACG
40699 TTGGAGACCC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 75 1.00
ACGTcount: A:0.56, C:0.24, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:40692 original size:6 final size:6
Alignment explanation
Indices: 40616--40676 Score: 53
Period size: 6 Copynumber: 11.2 Consensus size: 6
40606 ACGAACATAA
* *
40616 ACGAAC ACGAAC A-TAA- ACGAAC ACGAAC A-TAA- ACGAAC ACGAAC
1 ACGAAC ACGAAC ACGAAC ACGAAC ACGAAC ACGAAC ACGAAC ACGAAC
*
40660 A-TAA- ACGAAC ACGAAC A
1 ACGAAC ACGAAC ACGAAC A
40677 TAAATGAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
4 3 0.07
5 12 0.28
6 28 0.65
ACGTcount: A:0.56, C:0.26, G:0.13, T:0.05
Consensus pattern (6 bp):
ACGAAC
Found at i:41798 original size:10 final size:10
Alignment explanation
Indices: 41783--41837 Score: 78
Period size: 10 Copynumber: 5.7 Consensus size: 10
41773 AACATAAATG
41783 AACGAACATA
1 AACGAACATA
41793 AACGAACATA
1 AACGAACATA
*
41803 AACGAAC--G
1 AACGAACATA
41811 AACGAACATA
1 AACGAACATA
41821 AACGAACATA
1 AACGAACATA
*
41831 ACCGAAC
1 AACGAAC
41838 GTTCACGAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
8 7 0.17
10 33 0.82
ACGTcount: A:0.56, C:0.24, G:0.13, T:0.07
Consensus pattern (10 bp):
AACGAACATA
Found at i:41814 original size:28 final size:28
Alignment explanation
Indices: 41782--41838 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
41772 AAACATAAAT
41782 GAACGAACATAAACGAACATAAACGAAC
1 GAACGAACATAAACGAACATAAACGAAC
*
41810 GAACGAACATAAACGAACATAACCGAAC
1 GAACGAACATAAACGAACATAAACGAAC
41838 G
1 G
41839 TTCACGAACG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.54, C:0.23, G:0.16, T:0.07
Consensus pattern (28 bp):
GAACGAACATAAACGAACATAAACGAAC
Found at i:41816 original size:18 final size:18
Alignment explanation
Indices: 41793--41827 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
41783 AACGAACATA
41793 AACGAACATAAACGAACG
1 AACGAACATAAACGAACG
41811 AACGAACATAAACGAAC
1 AACGAACATAAACGAAC
41828 ATAACCGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.23, G:0.14, T:0.06
Consensus pattern (18 bp):
AACGAACATAAACGAACG
Found at i:50966 original size:16 final size:16
Alignment explanation
Indices: 50945--50975 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
50935 AAGCAATCAG
50945 GCAAAGTAAAATGTGT
1 GCAAAGTAAAATGTGT
50961 GCAAAGTAAAATGTG
1 GCAAAGTAAAATGTG
50976 GAAGATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.26, T:0.23
Consensus pattern (16 bp):
GCAAAGTAAAATGTGT
Found at i:52515 original size:13 final size:13
Alignment explanation
Indices: 52497--52522 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52487 CAATTTAATA
52497 CAAGGAACCGACG
1 CAAGGAACCGACG
52510 CAAGGAACCGACG
1 CAAGGAACCGACG
52523 GAGTGAATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.31, T:0.00
Consensus pattern (13 bp):
CAAGGAACCGACG
Found at i:52571 original size:43 final size:43
Alignment explanation
Indices: 52505--52684 Score: 261
Period size: 43 Copynumber: 4.1 Consensus size: 43
52495 TACAAGGAAC
*
52505 CGACGCAAGGAACCGACGGAGTGAATGGTGGTGACTGAAGGCG
1 CGACGCAAGGAACCGACGGAGTGAATGGTGGCGACTGAAGGCG
* * *
52548 CGACGCACGGAACCAACGCAGTGAATGGTGGCGACTGAAGGCGCGACG
1 CGACGCAAGGAACCGACGGAGTGAATGGTGGCGACTGAA---G-G-CG
*
52596 CGACGCAAGGAACCGACGGAGTGAATGGTGGTGACTGAAGGCG
1 CGACGCAAGGAACCGACGGAGTGAATGGTGGCGACTGAAGGCG
*
52639 CGACGCAAGGAACCGACAGAGTGAATGGTGGCGACTGAAGGCG
1 CGACGCAAGGAACCGACGGAGTGAATGGTGGCGACTGAAGGCG
52682 CGA
1 CGA
52685 TTTACTGAAG
Statistics
Matches: 122, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
43 81 0.66
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 37 0.30
ACGTcount: A:0.28, C:0.22, G:0.40, T:0.10
Consensus pattern (43 bp):
CGACGCAAGGAACCGACGGAGTGAATGGTGGCGACTGAAGGCG
Found at i:52633 original size:91 final size:91
Alignment explanation
Indices: 52505--52684 Score: 326
Period size: 91 Copynumber: 2.0 Consensus size: 91
52495 TACAAGGAAC
*
52505 CGACGCAAGGAACCGACGGAGTGAATGGTGGTGACTGAAGGCGCGACGCACGGAACCAAC-GCAG
1 CGACGCAAGGAACCGACGGAGTGAATGGTGGTGACTGAAGGCGCGACGCAAGGAACCAACAG-AG
52569 TGAATGGTGGCGACTGAAGGCGCGACG
65 TGAATGGTGGCGACTGAAGGCGCGACG
*
52596 CGACGCAAGGAACCGACGGAGTGAATGGTGGTGACTGAAGGCGCGACGCAAGGAACCGACAGAGT
1 CGACGCAAGGAACCGACGGAGTGAATGGTGGTGACTGAAGGCGCGACGCAAGGAACCAACAGAGT
52661 GAATGGTGGCGACTGAAGGCGCGA
66 GAATGGTGGCGACTGAAGGCGCGA
52685 TTTACTGAAG
Statistics
Matches: 86, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
91 85 0.99
92 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.40, T:0.10
Consensus pattern (91 bp):
CGACGCAAGGAACCGACGGAGTGAATGGTGGTGACTGAAGGCGCGACGCAAGGAACCAACAGAGT
GAATGGTGGCGACTGAAGGCGCGACG
Found at i:54240 original size:22 final size:22
Alignment explanation
Indices: 54210--54258 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
54200 CACGTTTTCA
54210 AAAGCTATTAT-TTTCCTATTCG
1 AAAGCTATTATATTT-CTATTCG
* *
54232 AAAGTTATTATATTTCTATTGG
1 AAAGCTATTATATTTCTATTCG
54254 AAAGC
1 AAAGC
54259 AAAAAAACAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (22 bp):
AAAGCTATTATATTTCTATTCG
Found at i:59193 original size:136 final size:136
Alignment explanation
Indices: 58948--59575 Score: 943
Period size: 136 Copynumber: 4.6 Consensus size: 136
58938 ACCTGCTTAA
* * * *
58948 AATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAACAATGTCTCGCTC
1 AATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGCAACGCCTCGCTT
* * *
59013 GAGGGATAAAAATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAA
66 GAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGGGAGAAGAA
*
59078 GTTCAC
131 GTTCAT
* * *
59084 AATGAGAAGAACTTGTTTGACCTATTTCTCGATTCACGGCATTTCGAATCAGCAATGCCTCGCTT
1 AATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGCAACGCCTCGCTT
* *
59149 GAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGAGAGAAAAA
66 GAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGGGAGAAGAA
59214 GTTCAT
131 GTTCAT
* * *
59220 AATGAGAAGAACTTGTTCAACCTATTGCTCGATTCACGACATTTCGAATCATCAACGCCTCGCTT
1 AATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGCAACGCCTCGCTT
* * *
59285 GAGGGATTAACATTTCCAATTGAGAGTTCATAATAAGAA-AACTCATCCGACAGAGGAAGAAGAA
66 GAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGGGAGAAGAA
**
59349 ACTCAT
131 GTTCAT
* * ** *
59355 AATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGTATTTCGAATCAGAAACATCTAGCTT
1 AATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGCAACGCCTCGCTT
59420 GAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGGGAGAAGAA
66 GAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGGGAGAAGAA
59485 GTTCAT
131 GTTCAT
* * * * *
59491 AATGAGAAGAACTTGTTCGACCTATTGCACGATTCATGGCTTTTCGAATCAGCAACACCTCACTT
1 AATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGCAACGCCTCGCTT
* * *
59556 CAAGGATCAACATTTCCAAT
66 GAGGGATTAACATTTCCAAT
59576 AGGAAGATCA
Statistics
Matches: 443, Mismatches: 48, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
135 120 0.27
136 323 0.73
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (136 bp):
AATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGCAACGCCTCGCTT
GAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGGGAGAAGAA
GTTCAT
Found at i:59432 original size:271 final size:272
Alignment explanation
Indices: 58948--59575 Score: 952
Period size: 271 Copynumber: 2.3 Consensus size: 272
58938 ACCTGCTTAA
* * *
58948 AATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAACAATGTCTCGCTC
1 AATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAACAACGCCTCGCTT
* * *
59013 GAGGGATAAAAATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAA
66 GAGGGATAAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGACAGAGGAAGAAGAA
** * * * **
59078 GTTCACAATGAGAAGAACTTGTTTGACCTATTTCTCGATTCACGGCATTTCGAATCAGCAATGCC
131 ACTCACAATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGAAACACC
*
59143 TCGCTTGAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGAGA
196 TAGCTTGAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGAGA
59208 GAAAAAGTTCAT
261 GAAAAAGTTCAT
* * *
59220 AATGAGAAGAACTTGTTCAACCTATTGCTCGATTCACGACATTTCGAATCATCAACGCCTCGCTT
1 AATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAACAACGCCTCGCTT
* *
59285 GAGGGATTAACATTTCCAATTGAGAGTTCATAATAAGAA-AACTCATCCGACAGAGGAAGAAGAA
66 GAGGGATAAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGACAGAGGAAGAAGAA
* * *
59349 ACTCATAATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGTATTTCGAATCAGAAACATC
131 ACTCACAATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGAAACACC
*
59414 TAGCTTGAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGGGA
196 TAGCTTGAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGAGA
*
59479 GAAGAAGTTCAT
261 GAAAAAGTTCAT
* * * * * *
59491 AATGAGAAGAACTTGTTCGACCTATTGCACGATTCATGGCTTTTCGAATCAGCAACACCTCACTT
1 AATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAACAACGCCTCGCTT
* * *
59556 CAAGGATCAACATTTCCAAT
66 GAGGGATAAACATTTCCAAT
59576 AGGAAGATCA
Statistics
Matches: 321, Mismatches: 35, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
271 227 0.71
272 94 0.29
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (272 bp):
AATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAACAACGCCTCGCTT
GAGGGATAAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGACAGAGGAAGAAGAA
ACTCACAATGAGAAGAACTTGTTCGACCTATTGCTCGATTCACGGCATTTCGAATCAGAAACACC
TAGCTTGAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAATAACTCATCCGACAGAGAGA
GAAAAAGTTCAT
Found at i:60837 original size:44 final size:44
Alignment explanation
Indices: 60778--60874 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
60768 GGCGTTTTTA
* *
60778 ATACAAACGCCGCAAAAAAACTGGTAAATTGAGGCATTTTTCGG
1 ATACAAACGCCGCAAAAAAACTAGTAAATAGAGGCATTTTTCGG
* *** * *
60822 ATACAAACGCTGCAAAAGGTCTAGTATATAGCGGCATTTTTCGG
1 ATACAAACGCCGCAAAAAAACTAGTAAATAGAGGCATTTTTCGG
60866 ATACAAACG
1 ATACAAACG
60875 TCGTAAAAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.24
Consensus pattern (44 bp):
ATACAAACGCCGCAAAAAAACTAGTAAATAGAGGCATTTTTCGG
Found at i:60883 original size:44 final size:43
Alignment explanation
Indices: 60810--60950 Score: 176
Period size: 44 Copynumber: 3.2 Consensus size: 43
60800 GGTAAATTGA
60810 GGCATTTTTCGGATACAAACGCTGCAAAAGGTCTAGTATATAGC
1 GGCATTTTTCGGATACAAACGC-GCAAAAGGTCTAGTATATAGC
*
60854 GGCATTTTTCGGATACAAACGTCGTAAAAGGTCTAGTATATAGC
1 GGCATTTTTCGGATACAAACG-CGCAAAAGGTCTAGTATATAGC
* * * * *
60898 GGTGA-TTTTCGGATACAAATGCCACAAAAGGTCTGGTATATAGT
1 GG-CATTTTTCGGATACAAACG-CGCAAAAGGTCTAGTATATAGC
*
60942 GGCGTTTTT
1 GGCATTTTT
60951 TGTTACAAAC
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
44 82 0.98
45 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (43 bp):
GGCATTTTTCGGATACAAACGCGCAAAAGGTCTAGTATATAGC
Found at i:67161 original size:32 final size:32
Alignment explanation
Indices: 67120--67188 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
67110 TCATGTTTCA
67120 TAGTTAAAGAGAGGAAGGAAGAACTTAAAACC
1 TAGTTAAAGAGAGGAAGGAAGAACTTAAAACC
*
67152 TAGTTAAAGAGAGGGAGGAAGAACTTAAAACC
1 TAGTTAAAGAGAGGAAGGAAGAACTTAAAACC
*
67184 AAGTT
1 TAGTT
67189 CATTACCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.48, C:0.09, G:0.26, T:0.17
Consensus pattern (32 bp):
TAGTTAAAGAGAGGAAGGAAGAACTTAAAACC
Found at i:70333 original size:83 final size:83
Alignment explanation
Indices: 70191--70487 Score: 355
Period size: 83 Copynumber: 3.6 Consensus size: 83
70181 ATAAGTTTGA
** * * *
70191 GGCGTTTGTAAAAAAACGCCTACTATAGTGCTAA-TATATCGCGGCGTCTACTTAAAAAACACCA
1 GGCGTTTGTACGAAAACGCCT-CTATAGTGC-AACTCTATCGCGGCGTTTACTTAAAAAACGCCA
*
70255 CTACTGTCCAACTGTATAGC
64 CTACTGTCCAACTCTATAGC
* * ** *
70275 GACGTTTGTACGAAAATGCCTCTATAGTGCAACTCTATCGCAACGTTTACTTAAAAAACGCCATT
1 GGCGTTTGTACGAAAACGCCTCTATAGTGCAACTCTATCGCGGCGTTTACTTAAAAAACGCCACT
70340 ACTGTCCAACTCTATAGC
66 ACTGTCCAACTCTATAGC
* * * *
70358 GGCGTTTGTACGAAAACGCCTCTATAGTGTAACTCTATCGTGGCGTTTAC-TAAAAAATGCCACA
1 GGCGTTTGTACGAAAACGCCTCTATAGTGCAACTCTATCGCGGCGTTTACTTAAAAAACGCCACT
* *
70422 AATGTTCAACTCTATAGC
66 ACTGTCCAACTCTATAGC
** * * * *
70440 GGCGTTTGTACGAAAACAACTCTATAGTTCAACTATGTTGCGGCGTTT
1 GGCGTTTGTACGAAAACGCCTCTATAGTGCAACTCTATCGCGGCGTTT
70488 GTTGAAGAAA
Statistics
Matches: 182, Mismatches: 30, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
82 69 0.38
83 96 0.53
84 17 0.09
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (83 bp):
GGCGTTTGTACGAAAACGCCTCTATAGTGCAACTCTATCGCGGCGTTTACTTAAAAAACGCCACT
ACTGTCCAACTCTATAGC
Found at i:70403 original size:41 final size:41
Alignment explanation
Indices: 70263--70489 Score: 140
Period size: 41 Copynumber: 5.5 Consensus size: 41
70253 CACTACTGTC
* * * *
70263 CAACTGTATAGCGACGTTTGTACGAAAATGCCTCTATAGTG
1 CAACTCTATCGCGGCGTTTGTACGAAAACGCCTCTATAGTG
** * * *
70304 CAACTCTATCGCAACGTTTACTTA-AAAAACGCCAT-TACT-GTC
1 CAACTCTATCGCGGCGTTT--GTACGAAAACGCC-TCTA-TAGTG
*
70346 CAACTCTATAGCGGCGTTTGTACGAAAACGCCTCTATAGTG
1 CAACTCTATCGCGGCGTTTGTACGAAAACGCCTCTATAGTG
* * * * * * * *
70387 TAACTCTATCGTGGCGTTTACTA-AAAAATGCCAC-AAATGTT
1 CAACTCTATCGCGGCGTTT-GTACGAAAACGCCTCTATA-GTG
* ** *
70428 CAACTCTATAGCGGCGTTTGTACGAAAACAACTCTATAGTT
1 CAACTCTATCGCGGCGTTTGTACGAAAACGCCTCTATAGTG
* * *
70469 CAACTATGTTGCGGCGTTTGT
1 CAACTCTATCGCGGCGTTTGT
70490 TGAAGAAAAA
Statistics
Matches: 140, Mismatches: 35, Indels: 22
0.71 0.18 0.11
Matches are distributed among these distances:
40 8 0.06
41 97 0.69
42 31 0.22
43 4 0.03
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (41 bp):
CAACTCTATCGCGGCGTTTGTACGAAAACGCCTCTATAGTG
Found at i:75094 original size:16 final size:15
Alignment explanation
Indices: 75073--75102 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
75063 ATTTGATTAA
75073 AATTTAAATAATATTC
1 AATTTAAAT-ATATTC
75089 AATTTAAATATATT
1 AATTTAAATATATT
75103 TGATTCTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTAAATATATTC
Found at i:80066 original size:32 final size:31
Alignment explanation
Indices: 80030--80106 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
80020 TGGGGCCACG
*
80030 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
80062 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
80093 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
80107 GTTACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Done.