Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005512.1 Hibiscus syriacus cultivar Beakdansim tig00012724_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: 77360
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:3797 original size:21 final size:22
Alignment explanation
Indices: 3752--3798 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
3742 TTGTGCTTCA
* * *
3752 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACATCCATGAAGG
3774 TGCATCGATACA-CCATGAAGG
1 TGCATCGATACATCCATGAAGG
3795 TGCA
1 TGCA
3799 CTGATGCACG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (22 bp):
TGCATCGATACATCCATGAAGG
Found at i:3827 original size:23 final size:23
Alignment explanation
Indices: 3752--3831 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 23
3742 TTGTGCTTCA
*
3752 TGCATCGATGCA-TCCTTGAATG
1 TGCATCGATGCACACCTTGAATG
* *
3774 TGCATCGAT--ACACCATGAAGG
1 TGCATCGATGCACACCTTGAATG
*
3795 TGCA-CTGATGCACGCCTTGAATG
1 TGCATC-GATGCACACCTTGAATG
*
3818 TGAATCGATGCACA
1 TGCATCGATGCACA
3832 AGGCCATGCA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
20 2 0.04
21 14 0.31
22 9 0.20
23 19 0.42
24 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (23 bp):
TGCATCGATGCACACCTTGAATG
Found at i:3848 original size:43 final size:41
Alignment explanation
Indices: 3750--3849 Score: 94
Period size: 44 Copynumber: 2.3 Consensus size: 41
3740 TTTTGTGCTT
* * * *
3750 CATGCATCGATGCATCCTTGAATGTGCATCGATACACCATG
1 CATGCATCGATGCAGCCTTGAATGTGAATCGATACACAAGG
* *
3791 AAGGTGCA-CTGATGCACGCCTTGAATGTGAATCGATGCACAAGG
1 CA--TGCATC-GATGCA-GCCTTGAATGTGAATCGATACACAAGG
3835 CCATGCATCGATGCA
1 -CATGCATCGATGCA
3850 TCAGTCGGGT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
41 1 0.02
42 1 0.02
43 20 0.43
44 23 0.50
45 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (41 bp):
CATGCATCGATGCAGCCTTGAATGTGAATCGATACACAAGG
Found at i:5425 original size:21 final size:21
Alignment explanation
Indices: 5383--5426 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5373 ACTCTGGGAG
*
5383 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
*
5404 CTAGCTCTTCTCGTA-CTCCTC
1 CTAGCTCTTCACG-AGCTCCTC
5425 CT
1 CT
5427 CCTCCTCCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.11, C:0.41, G:0.14, T:0.34
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:6580 original size:17 final size:19
Alignment explanation
Indices: 6552--6600 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
6542 TATTTTGAAA
6552 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
6570 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
6589 CACCGATGCACT
1 CATCGATGCACT
6601 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:8763 original size:21 final size:21
Alignment explanation
Indices: 8737--8800 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
8727 TGAAACAACA
8737 AACATAAAAAAACAAATAAAT
1 AACATAAAAAAACAAATAAAT
* * *
8758 AACATAAAATAATAAATACAT
1 AACATAAAAAAACAAATAAAT
8779 AACATAACATAAAACAAATAAA
1 AACATAA-A-AAAACAAATAAA
8801 AAAAGAAACA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 25 0.71
22 1 0.03
23 9 0.26
ACGTcount: A:0.72, C:0.11, G:0.00, T:0.17
Consensus pattern (21 bp):
AACATAAAAAAACAAATAAAT
Found at i:8778 original size:16 final size:17
Alignment explanation
Indices: 8751--8785 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
8741 TAAAAAAACA
8751 AATAAATAACATAAAAT
1 AATAAATAACATAAAAT
*
8768 AATAAAT-ACATAACAT
1 AATAAATAACATAAAAT
8784 AA
1 AA
8786 CATAAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.23
Consensus pattern (17 bp):
AATAAATAACATAAAAT
Found at i:9001 original size:31 final size:31
Alignment explanation
Indices: 8966--9028 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
8956 ATAAAACAAT
* *
8966 ATAAGAATCAATTAATATCATTCACATTAAC
1 ATAAGAATCAACTAATATCATTCACATCAAC
*
8997 ATAAGAATCAACTAATATCCTTCACATCAAC
1 ATAAGAATCAACTAATATCATTCACATCAAC
9028 A
1 A
9029 AATAAAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.29
Consensus pattern (31 bp):
ATAAGAATCAACTAATATCATTCACATCAAC
Found at i:9038 original size:82 final size:83
Alignment explanation
Indices: 8883--9063 Score: 292
Period size: 82 Copynumber: 2.2 Consensus size: 83
8873 CACATTTAAC
* * * *
8883 ATAAGAATCAACTAATATCATTCATATTAACATTAATAATCATCTATTATCCTTCACATCAACAA
1 ATAAGAATCAACTAATATCATTCACATTAACATTAAGAATCAACTAATATCCTTCACATCAACAA
*
8948 CTAAAAACATAAAACAAT
66 ATAAAAACATAAAACAAT
*
8966 ATAAGAATCAATTAATATCATTCACATTAACA-TAAGAATCAACTAATATCCTTCACATCAACAA
1 ATAAGAATCAACTAATATCATTCACATTAACATTAAGAATCAACTAATATCCTTCACATCAACAA
9030 ATAAAAACATAAAACAAT
66 ATAAAAACATAAAACAAT
*
9048 ATAAGAATCAGCTAAT
1 ATAAGAATCAACTAAT
9064 TCAAAGTCCT
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
82 60 0.67
83 30 0.33
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (83 bp):
ATAAGAATCAACTAATATCATTCACATTAACATTAAGAATCAACTAATATCCTTCACATCAACAA
ATAAAAACATAAAACAAT
Found at i:9198 original size:13 final size:14
Alignment explanation
Indices: 9137--9203 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
9127 TATTTAACTT
9137 ATAAAAAACATAAA
1 ATAAAAAACATAAA
* *
9151 ACAAATAAAAAT-AA
1 ATAAA-AAACATAAA
** *
9165 ATGGAAAACAAAAA
1 ATAAAAAACATAAA
9179 ATAAAAAACATAAA
1 ATAAAAAACATAAA
9193 AT-AAAAACATA
1 ATAAAAAACATA
9204 TAATGAATAT
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
13 13 0.32
14 23 0.56
15 5 0.12
ACGTcount: A:0.76, C:0.07, G:0.03, T:0.13
Consensus pattern (14 bp):
ATAAAAAACATAAA
Found at i:9221 original size:75 final size:74
Alignment explanation
Indices: 9136--9313 Score: 186
Period size: 74 Copynumber: 2.4 Consensus size: 74
9126 TTATTTAACT
* **
9136 TATAAAAAACATAAAACAAATA-AAAATAAATGGAAAACA-AAAAATAAAAA-ACATAAAA-TAA
1 TATAGAAAACATAAAA-AAATAGAAAATAAAAAGAAAACATAAAAATAAAAACACATAAAATTAA
9197 AAACATATAATGAA
65 AAA-A-AT-A-GAA
* * * *
9211 TATAGAAAACA-AATAAAAACAGAAAACAAAAAGAAAACATAAAATTAAAAACATATAAAATTAA
1 TATAGAAAACATAA-AAAAATAGAAAATAAAAAGAAAACATAAAAATAAAAACACATAAAATTAA
9275 AAAAATAGAA
65 AAAAATAGAA
* *
9285 AATAGAAAACATATAAAAATAGAAAATAA
1 TATAGAAAACATAAAAAAATAGAAAATAA
9314 TTAGCAAATA
Statistics
Matches: 86, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
74 32 0.37
75 28 0.33
76 12 0.14
77 8 0.09
78 6 0.07
ACGTcount: A:0.73, C:0.06, G:0.05, T:0.16
Consensus pattern (74 bp):
TATAGAAAACATAAAAAAATAGAAAATAAAAAGAAAACATAAAAATAAAAACACATAAAATTAAA
AAAATAGAA
Found at i:9249 original size:18 final size:17
Alignment explanation
Indices: 9214--9254 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
9204 TAATGAATAT
*
9214 AGAAAACAAATAAAAAC
1 AGAAAACAAAAAAAAAC
9231 AGAAAACAAAAAGAAAAC
1 AGAAAACAAAAA-AAAAC
*
9249 ATAAAA
1 AGAAAA
9255 TTAAAAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.78, C:0.10, G:0.07, T:0.05
Consensus pattern (17 bp):
AGAAAACAAAAAAAAAC
Found at i:9327 original size:24 final size:24
Alignment explanation
Indices: 9212--9312 Score: 78
Period size: 24 Copynumber: 4.1 Consensus size: 24
9202 TATAATGAAT
*
9212 ATAGAAAACAAATAAAAACAGAAA
1 ATAGAAAACAAATAAAAATAGAAA
* * * * *
9236 ACAAAAAGAAAACATAAAATTAAAAA
1 ATAGAAA-ACAA-ATAAAAATAGAAA
* **
9262 CATATAAAATTAA-AAAAATAGAAA
1 -ATAGAAAACAAATAAAAATAGAAA
*
9286 ATAGAAAACATATAAAAATAGAAA
1 ATAGAAAACAAATAAAAATAGAAA
9310 ATA
1 ATA
9313 ATTAGCAAAT
Statistics
Matches: 57, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
23 8 0.14
24 28 0.49
25 4 0.07
26 12 0.21
27 5 0.09
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.15
Consensus pattern (24 bp):
ATAGAAAACAAATAAAAATAGAAA
Found at i:10135 original size:7 final size:7
Alignment explanation
Indices: 10125--10216 Score: 55
Period size: 7 Copynumber: 12.9 Consensus size: 7
10115 AAACGAAAAG
10125 AAATAAA
1 AAATAAA
*
10132 AAATACA
1 AAATAAA
10139 AAAT-AA
1 AAATAAA
*
10145 AAATACA
1 AAATAAA
*
10152 AAATACA
1 AAATAAA
10159 AAATAAA
1 AAATAAA
*
10166 TAATAAA
1 AAATAAA
10173 TCATACA-AAA
1 --A-A-ATAAA
*
10183 CAAATACA
1 -AAATAAA
10191 AAATAAA
1 AAATAAA
*
10198 ATATAAA
1 AAATAAA
10205 AAA-AAA
1 AAATAAA
*
10211 ATATAA
1 AAATAA
10217 TTTTTTTGAC
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
6 10 0.15
7 47 0.70
8 3 0.04
9 2 0.03
10 4 0.06
11 1 0.01
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (7 bp):
AAATAAA
Found at i:10142 original size:14 final size:14
Alignment explanation
Indices: 10125--10211 Score: 71
Period size: 14 Copynumber: 6.6 Consensus size: 14
10115 AAACGAAAAG
10125 AAATAAAAAATACA
1 AAATAAAAAATACA
10139 AAAT-AAAAATACA
1 AAATAAAAAATACA
*
10152 AAATACAAAATA-A
1 AAATAAAAAATACA
**
10165 ATAATAAATCATAC-
1 A-AATAAAAAATACA
*
10179 -AA-AACAAATACA
1 AAATAAAAAATACA
*
10191 AAATAAAATATA-A
1 AAATAAAAAATACA
10204 AAA-AAAAA
1 AAATAAAAA
10212 TATAATTTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
11 6 0.11
12 6 0.11
13 21 0.37
14 24 0.42
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (14 bp):
AAATAAAAAATACA
Found at i:10146 original size:38 final size:40
Alignment explanation
Indices: 10104--10195 Score: 97
Period size: 39 Copynumber: 2.4 Consensus size: 40
10094 AACATACTAC
10104 TAAAAA-ACAGAAA-ACGAAAAGAAATAA-AAA-ATACAAAA
1 TAAAAATACA-AAATAC-AAAAGAAATAATAAACATACAAAA
*
10142 TAAAAATACAAAATACAAAATAAATAATAAATCATAC-AAA
1 TAAAAATACAAAATACAAAAGAAATAATAAA-CATACAAAA
*
10182 -ACAAATACAAAATA
1 TAAAAATACAAAATA
10196 AAATATAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
38 19 0.40
39 21 0.45
40 3 0.06
41 4 0.09
ACGTcount: A:0.73, C:0.10, G:0.03, T:0.14
Consensus pattern (40 bp):
TAAAAATACAAAATACAAAAGAAATAATAAACATACAAAA
Found at i:10148 original size:13 final size:13
Alignment explanation
Indices: 10125--10213 Score: 80
Period size: 13 Copynumber: 6.8 Consensus size: 13
10115 AAACGAAAAG
10125 AAATAAAAAATACA
1 AAAT-AAAAATACA
10139 AAATAAAAATACA
1 AAATAAAAATACA
10152 AAATACAAAATA-A
1 AAATA-AAAATACA
*
10165 ATAATAAATCATAC-
1 A-AATAAA-AATACA
*
10179 AAA-ACAAATACA
1 AAATAAAAATACA
10191 AAATAAAATATA-A
1 AAATAAAA-ATACA
10204 AAA-AAAAATA
1 AAATAAAAATA
10214 TAATTTTTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
11 7 0.11
12 9 0.14
13 27 0.42
14 21 0.33
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (13 bp):
AAATAAAAATACA
Found at i:11271 original size:2 final size:2
Alignment explanation
Indices: 11222--11259 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11212 ACTTTATACT
11222 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
11260 CACTTTATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11332 original size:2 final size:2
Alignment explanation
Indices: 11321--11602 Score: 95
Period size: 2 Copynumber: 136.5 Consensus size: 2
11311 ACTTCAGACT
11321 TA TA -A TA TA TA TA TA TA TA TA TA TA TA T- TA TA TCA TA TCA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T-A TA
* * *
11363 TCA TA TCA TA TCA TA TCA TA TA CA CT- TA TA T- TA TA TA TG TG TA
1 T-A TA T-A TA T-A TA T-A TA TA TA -TA TA TA TA TA TA TA TA TA TA
*
11406 TA TA TA TA TA TA AA CTA TA GTA TA TA GTA TA TA TA -A CT- TA TA
1 TA TA TA TA TA TA TA -TA TA -TA TA TA -TA TA TA TA TA -TA TA TA
* * * * * *
11448 TA TA TA GTT TA CA CA TA GTA TA TA TGG TT TA TA TA TA GTT TA TA
1 TA TA TA -TA TA TA TA TA -TA TA TA T-A TA TA TA TA TA -TA TA TA
* * * *
11492 T- TA -A TA AA CTA TA TA -A TT TA TA CA TA GTA TA TA TA -A TT TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
11532 TGA T- TA TA TA TA GTA TA TA AA TA TA AA CTA TA CA -A TT TA TA
1 T-A TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
11573 TA TA GTT TA TA TA TA -A TT TA TA TA GTA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA T
11603 TAGTTTATAA
Statistics
Matches: 211, Mismatches: 34, Indels: 70
0.67 0.11 0.22
Matches are distributed among these distances:
1 13 0.06
2 165 0.78
3 33 0.16
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:11358 original size:5 final size:5
Alignment explanation
Indices: 11325--11383 Score: 74
Period size: 5 Copynumber: 12.8 Consensus size: 5
11315 CAGACTTATA
*
11325 ATAT- ATAT- ATAT- ATAT- ATAT- ATATT ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
11370 ATATC ATATC ATAT
1 ATATC ATATC ATAT
11384 ACACTTATAT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
4 20 0.38
5 33 0.62
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (5 bp):
ATATC
Found at i:11471 original size:33 final size:31
Alignment explanation
Indices: 11429--11489 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
11419 ACTATAGTAT
11429 ATAGTATATATAACTTATATATATAGTTTACAC
1 ATAGTATATAT-ACTT-TATATATAGTTTACAC
**
11462 ATAGTATATATGGTTTATATATAGTTTA
1 ATAGTATATATACTTTATATATAGTTTA
11490 TATTAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 13 0.50
32 2 0.08
33 11 0.42
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (31 bp):
ATAGTATATATACTTTATATATAGTTTACAC
Found at i:11505 original size:33 final size:32
Alignment explanation
Indices: 11475--11585 Score: 108
Period size: 33 Copynumber: 3.6 Consensus size: 32
11465 GTATATATGG
11475 TTTATATATAGTTTATATTAATAAACTATATAA
1 TTTATATATAGTTTATA-TAATAAACTATATAA
* * *
11508 TTTATACATAG--TATAT-AT-AA-TTTATGA
1 TTTATATATAGTTTATATAATAAACTATATAA
* * *
11535 -TTATATATAGTATATAAATATAAACTATACAA
1 TTTATATATAGTTTATATA-ATAAACTATATAA
11567 TTTATATATAGTTTATATA
1 TTTATATATAGTTTATATA
11586 TAATTTATAT
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
26 9 0.15
27 5 0.08
28 6 0.10
29 2 0.03
30 3 0.05
31 6 0.10
32 4 0.07
33 26 0.43
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.47
Consensus pattern (32 bp):
TTTATATATAGTTTATATAATAAACTATATAA
Found at i:11559 original size:59 final size:59
Alignment explanation
Indices: 11476--11617 Score: 182
Period size: 59 Copynumber: 2.4 Consensus size: 59
11466 TATATATGGT
* *
11476 TTATATATAGTTTAT-ATTAATAAACTATATAATTTATACATAG-TATATATAATTTATGA
1 TTATATATAGTTTATAAAT-ATAAACTATACAATTTATACATAGTTATATATAATTTAT-A
* *
11535 TTATATATAGTATATAAATATAAACTATACAATTTATATATAGTTTATATATAATTTATA
1 TTATATATAGTTTATAAATATAAACTATACAATTTATACATAG-TTATATATAATTTATA
11595 -TAGTATATTAGTTTATAAATATA
1 TTA-TATA-TAGTTTATAAATATA
11618 GTTTATATAT
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
59 38 0.52
60 7 0.10
61 28 0.38
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (59 bp):
TTATATATAGTTTATAAATATAAACTATACAATTTATACATAGTTATATATAATTTATA
Found at i:11621 original size:41 final size:42
Alignment explanation
Indices: 11572--11668 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 42
11562 TACAATTTAT
* * *
11572 ATATAGTTTATATA-TAATTTATATAGTATA-TTAGTTTATAA
1 ATATAGTTTATATATTAA-CTATATAATATATTTAGTTAATAA
* *
11613 ATATAGTTTATATATTAACTATATAATTTATTTAGTTAATAT
1 ATATAGTTTATATATTAACTATATAATATATTTAGTTAATAA
11655 ATATAGTTTATATA
1 ATATAGTTTATATA
11669 AGTATAGTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
41 23 0.47
42 26 0.53
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (42 bp):
ATATAGTTTATATATTAACTATATAATATATTTAGTTAATAA
Found at i:11636 original size:61 final size:60
Alignment explanation
Indices: 11519--11680 Score: 149
Period size: 61 Copynumber: 2.7 Consensus size: 60
11509 TTATACATAG
* *** * *
11519 TATATATAATTTATGAT-TATATATAGTATATAAATATAAACTATACAATTTATATATAGTT
1 TATATATAATTTAT-ATATATAT-TAGTTTATAAATATAGTTTATACAATTAATATATAATT
*
11580 TATATATAATTTATATAGTATATTAGTTTATAAATATAGTTTATA-TATTAACTATATAATT
1 TATATATAATTTATATA-TATATTAGTTTATAAATATAGTTTATACAATTAA-TATATAATT
*
11641 TAT-T-T-AGTTA-ATATATA-TAGTTTATATAAGTATAGTTTAT
1 TATATATAATTTATATATATATTAGTTTATA-AA-TATAGTTTAT
11681 CGGACAGAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
55 9 0.10
56 6 0.07
57 13 0.15
58 4 0.05
59 1 0.01
60 7 0.08
61 43 0.49
62 5 0.06
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (60 bp):
TATATATAATTTATATATATATTAGTTTATAAATATAGTTTATACAATTAATATATAATT
Found at i:11641 original size:72 final size:77
Alignment explanation
Indices: 11501--11674 Score: 191
Period size: 72 Copynumber: 2.3 Consensus size: 77
11491 ATTAATAAAC
11501 TATATAATTTATACATAGTATATATAATTTATGATTATATATAGTATATAAATATAAACTATACA
1 TATATAATTTAT--ATAGTATATATAATTTATGA-TATATATAGTATATAAATATAAACTATACA
11566 ATTTATATATAGTT-TA
63 ATTTAT-T-TAGTTATA
* * * *
11582 TATATAATTTATATAGTATAT-TAGTTTAT-A-A-ATATAGT-T-TATATATTAACTATATAATT
1 TATATAATTTATATAGTATATATAATTTATGATATATATAGTATATAAATATAAACTATACAATT
11641 TATTTAGTTAATA
66 TATTTAGTT-ATA
*
11654 TATATAGTTTATATAAGTATA
1 TATATAATTTATAT-AGTATA
11675 GTTTATCGGA
Statistics
Matches: 85, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
70 5 0.06
71 1 0.01
72 35 0.41
73 7 0.08
74 7 0.08
75 1 0.01
77 1 0.01
78 7 0.08
79 9 0.11
81 12 0.14
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (77 bp):
TATATAATTTATATAGTATATATAATTTATGATATATATAGTATATAAATATAAACTATACAATT
TATTTAGTTATA
Found at i:11668 original size:11 final size:11
Alignment explanation
Indices: 11426--11668 Score: 84
Period size: 11 Copynumber: 22.4 Consensus size: 11
11416 TAAACTATAG
*
11426 TATATAGTATA
1 TATATAGTTTA
*
11437 TATA-ACTTATA
1 TATATAGTT-TA
11448 TATATAGTTTA
1 TATATAGTTTA
* *
11459 CACATAG--TA
1 TATATAGTTTA
*
11468 TATATGGTTTA
1 TATATAGTTTA
11479 TATATAGTTTA
1 TATATAGTTTA
* **
11490 TAT-TAATAAA
1 TATATAGTTTA
*
11500 CTATATAATTTA
1 -TATATAGTTTA
*
11512 TACATAGTATATA
1 TATATAGT-T-TA
* *
11525 TAATTTATGATTA
1 T-ATATA-GTTTA
*
11538 TATATAGTATA
1 TATATAGTTTA
* **
11549 TAAATA-TAAA
1 TATATAGTTTA
* *
11559 CTATACAATTTA
1 -TATATAGTTTA
11571 TATATAGTTTA
1 TATATAGTTTA
*
11582 TATATA-ATT-
1 TATATAGTTTA
11591 TATATAG--TA
1 TATATAGTTTA
11600 TAT-TAGTTTA
1 TATATAGTTTA
11610 TAAATATAG-TT-
1 T--ATATAGTTTA
*
11621 TATATA-TTAA
1 TATATAGTTTA
*
11631 CTATATAATTTA
1 -TATATAGTTTA
11643 T-T-TAGTTAATA
1 TATATAGTT--TA
11654 TATATAGTTTA
1 TATATAGTTTA
11665 TATA
1 TATA
11669 AGTATAGTTT
Statistics
Matches: 171, Mismatches: 34, Indels: 54
0.66 0.13 0.21
Matches are distributed among these distances:
8 4 0.02
9 25 0.15
10 15 0.09
11 85 0.50
12 23 0.13
13 14 0.08
14 4 0.02
15 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:25153 original size:26 final size:26
Alignment explanation
Indices: 25117--25168 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
25107 ACTCGGATAG
*
25117 GATATGAACCAGGATCGACAAACAAA
1 GATATGAACCAGAATCGACAAACAAA
25143 GATATGAACCAGAATCGACAAACAAA
1 GATATGAACCAGAATCGACAAACAAA
25169 CTTTGGCAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.52, C:0.19, G:0.17, T:0.12
Consensus pattern (26 bp):
GATATGAACCAGAATCGACAAACAAA
Found at i:26608 original size:20 final size:19
Alignment explanation
Indices: 26562--26608 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
26552 ATGATTGTAA
*
26562 TAATATATTTTTATATTTT
1 TAATAAATTTTTATATTTT
*
26581 TAATTAAATTTTTATTTTATT
1 TAA-TAAATTTTTATATT-TT
26602 TAATAAA
1 TAATAAA
26609 AATAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 16 0.67
21 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TAATAAATTTTTATATTTT
Found at i:36469 original size:21 final size:21
Alignment explanation
Indices: 36440--36486 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
36430 ATTCTGACTA
36440 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
36461 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
36482 TCGCA
1 TCGCA
36487 ACGCGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:36507 original size:20 final size:20
Alignment explanation
Indices: 36482--36668 Score: 254
Period size: 20 Copynumber: 9.4 Consensus size: 20
36472 TTTTCCTAAT
36482 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
36502 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
36522 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
*
36542 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
36562 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
36582 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
*
36602 TCGCAACGCGAATACGT-AT
1 TCGCAACGCGAATACGTAAA
** *
36621 TCGCATTGCGATTTACGT-AA
1 TCGCAACGCGA-ATACGTAAA
**
36641 TCGCATTGCGAAT-CTGTAAA
1 TCGCAACGCGAATAC-GTAAA
36661 TCGCAACG
1 TCGCAACG
36669 AGATTCTGAC
Statistics
Matches: 152, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
18 1 0.01
19 13 0.09
20 138 0.91
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:40154 original size:20 final size:19
Alignment explanation
Indices: 40111--40268 Score: 102
Period size: 19 Copynumber: 8.7 Consensus size: 19
40101 GCAACGAGAG
*
40111 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
40130 AATCGCAACGTGAATATGAA
1 AATCGCAACGCGAA-ATGAA
* * *
40150 TATCGCAACACGGAAATGAC
1 AATCGCAACGC-GAAATGAA
* * *
40170 TATCGCAATGCAAAATGAA
1 AATCGCAACGCGAAATGAA
*
40189 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
40203 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* **
40222 AATCGTAA--CG--A-GGG
1 AATCGCAACGCGAAATGAA
*
40236 AATCGCAAAGCGAAATGAA
1 AATCGCAACGCGAAATGAA
40255 AATCGCAACGCGAA
1 AATCGCAACGCGAA
40269 TTTAGTTTCG
Statistics
Matches: 106, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
14 18 0.17
15 2 0.02
16 4 0.04
17 3 0.03
18 2 0.02
19 48 0.45
20 26 0.25
21 3 0.03
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:40213 original size:33 final size:33
Alignment explanation
Indices: 40171--40264 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
40161 GGAAATGACT
*
40171 ATCGCAATGCAAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
40204 ATCGCAATGCGAAATGAAAATCGTAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
40237 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
40265 CGAATTTAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:40341 original size:33 final size:33
Alignment explanation
Indices: 40274--40342 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
40264 GCGAATTTAG
* * * **
40274 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
40307 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
40340 TTT
1 TTT
40343 TTGCCTTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
Found at i:41875 original size:21 final size:21
Alignment explanation
Indices: 41812--41878 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
41802 GTGAATCGGG
*
41812 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** *
41832 CCTCTTCAACGATGACAGTGGA
1 -CTCTTGAACGGTGGGAGGGGA
41854 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
41875 CTCT
1 CTCT
41879 CGAGGAATGA
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
21 31 0.91
22 3 0.09
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:42401 original size:33 final size:33
Alignment explanation
Indices: 42359--42448 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
42349 ATGACTATCG
42359 CAACGCGAAATGAAAATCGCAACGAGAGAATCA
1 CAACGCGAAATGAAAATCGCAACGAGAGAATCA
*
42392 CAACGCGAAATGAAAATCGCAACGAGAGAATCG
1 CAACGCGAAATGAAAATCGCAACGAGAGAATCA
* *
42425 CAATGCGTAATGAAAATCGCAACG
1 CAACGCGAAATGAAAATCGCAACG
42449 CGATTATAGT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (33 bp):
CAACGCGAAATGAAAATCGCAACGAGAGAATCA
Found at i:42414 original size:19 final size:19
Alignment explanation
Indices: 42331--42451 Score: 82
Period size: 19 Copynumber: 6.8 Consensus size: 19
42321 TCTGGAACTT
*
42331 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
42352 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
42371 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* *
42385 AGAATCACAACGCGAAATG
1 AAAATCGCAACGCGAAATG
42404 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* * *
42418 AGAATCGCAATGCGTAATG
1 AAAATCGCAACGCGAAATG
42437 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
42452 TTATAGTTTC
Statistics
Matches: 77, Mismatches: 13, Indels: 22
0.69 0.12 0.20
Matches are distributed among these distances:
14 19 0.25
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 35 0.45
21 11 0.14
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:42470 original size:19 final size:19
Alignment explanation
Indices: 42448--42488 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
42438 AAATCGCAAC
42448 GCGATTATAGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
* *
42467 GCGATTTTGGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
42486 GCG
1 GCG
42489 CTTTTGTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.17, G:0.32, T:0.41
Consensus pattern (19 bp):
GCGATTATAGTTTCGCGTT
Found at i:42493 original size:19 final size:19
Alignment explanation
Indices: 42457--42494 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
42447 CGCGATTATA
42457 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
*
42476 GTTTCGCGTTGCGCTTTTG
1 GTTTCGCGTTGCGATTTTG
42495 TCGTTGCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.03, C:0.18, G:0.32, T:0.47
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:42519 original size:19 final size:20
Alignment explanation
Indices: 42490--42547 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
42480 CGCGTTGCGC
*
42490 TTTTGTCGTTGCGATTTTCA
1 TTTTCTCGTTGCGATTTTCA
**
42510 -TTTCTCGTTGCGATAGTCA
1 TTTTCTCGTTGCGATTTTCA
*
42529 TTTTTCACGTTGCGATTTT
1 -TTTTCTCGTTGCGATTTT
42548 AAGTTTCGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 16 0.53
21 14 0.47
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.52
Consensus pattern (20 bp):
TTTTCTCGTTGCGATTTTCA
Found at i:42757 original size:94 final size:92
Alignment explanation
Indices: 42611--42896 Score: 421
Period size: 94 Copynumber: 3.1 Consensus size: 92
42601 ATAGATTGAA
* *
42611 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
*
42676 AAGCAGAATTGGCATCAACCGAACAAAT
66 -AGCAGAATTGGCATCAACCGAATAAAT
*
42704 TTACTTTCAACCAAAAGTCAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG-
* * *
42769 TTAGCAGAATTGACAGCAACCAAATAAAT
64 TTAGCAGAATTGGCATCAACCGAATAAAT
* *
42798 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACATTGTTAAAGAATAAACAGC
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG-
*
42863 TTAGCAGTATTGGCAGT-AACCGAATAAAT
64 TTAGCAGAATTGGCA-TCAACCGAATAAAT
42892 TTACT
1 TTACT
42897 AAGCAATCTA
Statistics
Matches: 174, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
93 22 0.13
94 150 0.86
95 2 0.01
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.22
Consensus pattern (92 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
AGCAGAATTGGCATCAACCGAATAAAT
Found at i:44600 original size:20 final size:20
Alignment explanation
Indices: 44570--44631 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
44560 TTTTGGTTGA
44570 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
** *
44590 AATGACTATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
44609 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
44629 AAT
1 AAT
44632 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:44619 original size:19 final size:19
Alignment explanation
Indices: 44568--44679 Score: 119
Period size: 19 Copynumber: 6.1 Consensus size: 19
44558 TCTTTTGGTT
*
44568 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
44587 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
44607 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
44624 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
44640 GAAACT-AAAATCGCAACGC
1 GAAA-TGAAAATCGCAACGC
*
44659 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
44678 GA
1 GA
44680 TTTTCATTTC
Statistics
Matches: 77, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 44 0.57
20 16 0.21
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:44639 original size:33 final size:36
Alignment explanation
Indices: 44568--44657 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 36
44558 TCTTTTGGTT
44568 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGC
1 GAAATGAAAATCGCAAC--GAGAATGAC-ATCGCAACGC
44607 GAAATGAAAATCGCAACGAG-A-GA-ATCGCAACGC
1 GAAATGAAAATCGCAACGAGAATGACATCGCAACGC
44640 GAAACT-AAAATCGCAACG
1 GAAA-TGAAAATCGCAACG
44658 CGAAATGAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
33 26 0.52
34 1 0.02
35 2 0.04
36 1 0.02
37 3 0.06
39 17 0.34
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (36 bp):
GAAATGAAAATCGCAACGAGAATGACATCGCAACGC
Found at i:44725 original size:21 final size:20
Alignment explanation
Indices: 44706--44777 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
44696 CGATTCTCTC
44706 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
44726 CGTTGCGATAATCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
44747 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
44767 GTTGCGATTTT
1 GTTGCGATTTT
44778 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.14, C:0.17, G:0.18, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:45360 original size:20 final size:20
Alignment explanation
Indices: 45335--45548 Score: 234
Period size: 20 Copynumber: 10.6 Consensus size: 20
45325 CTTTAAAAAT
45335 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
45355 CGCGTTGCGATTTTATGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
45375 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
45396 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
45416 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
45436 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
45456 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
45476 CGCATTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
45496 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
45517 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
45538 CTCGTTGCGAT
1 CGCGTTGCGAT
45549 AGTCAGAATC
Statistics
Matches: 158, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
20 107 0.68
21 51 0.32
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:45532 original size:41 final size:41
Alignment explanation
Indices: 45337--45548 Score: 338
Period size: 41 Copynumber: 5.2 Consensus size: 41
45327 TTAAAAATCG
* *
45337 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
45378 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
45418 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
45458 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
45499 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
45540 CGTTGCGAT
1 CGTTGCGAT
45549 AGTCAGAATC
Statistics
Matches: 158, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 74 0.47
41 84 0.53
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:45955 original size:30 final size:30
Alignment explanation
Indices: 45921--45994 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
45911 TTTGACAACA
* *
45921 AATTTTATATTTTTTTCAATTTAATCATTT
1 AATTTTATATTTTATTCAATTTAATCATTC
* * *
45951 AATTTTGTGTTTTATTCAATTTAGTCATTC
1 AATTTTATATTTTATTCAATTTAATCATTC
*
45981 AATATTTACATTTT
1 AAT-TTTATATTTT
45995 CTATCCTTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
30 28 0.80
31 7 0.20
ACGTcount: A:0.28, C:0.08, G:0.04, T:0.59
Consensus pattern (30 bp):
AATTTTATATTTTATTCAATTTAATCATTC
Found at i:70342 original size:35 final size:33
Alignment explanation
Indices: 70293--70371 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 33
70283 AACTATAAAA
70293 TAATATTATTTTTAATAATT-ATTTATCGATT-TT
1 TAATATTATTTTTAAT-ATTGATTT-TCGATTATT
*
70326 TAATATGTATTTTTTAATATTGATTTTCTATTATT
1 TAATAT-TA-TTTTTAATATTGATTTTCGATTATT
70361 TAATACTTATT
1 TAATA-TTATT
70372 ACTGATAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
33 6 0.15
34 12 0.30
35 21 0.52
36 1 0.03
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (33 bp):
TAATATTATTTTTAATATTGATTTTCGATTATT
Found at i:73308 original size:16 final size:16
Alignment explanation
Indices: 73284--73324 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
73274 CCACACCCAC
*
73284 TATCGAACTGGAGACA
1 TATCCAACTGGAGACA
73300 TATCCAACTGGAGACA
1 TATCCAACTGGAGACA
*
73316 TACCCAACT
1 TATCCAACT
73325 AGACATGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.20
Consensus pattern (16 bp):
TATCCAACTGGAGACA
Found at i:73330 original size:14 final size:15
Alignment explanation
Indices: 73289--73330 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
73279 CCCACTATCG
*
73289 AACTGGAGACATATCC
1 AACT-GAGACATACCC
73305 AACTGGAGACATACCC
1 AACT-GAGACATACCC
73321 AACT-AGACAT
1 AACTGAGACAT
73331 GCCTTACAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
16 19 0.76
ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17
Consensus pattern (15 bp):
AACTGAGACATACCC
Found at i:73642 original size:42 final size:42
Alignment explanation
Indices: 73572--73671 Score: 155
Period size: 42 Copynumber: 2.4 Consensus size: 42
73562 TCAAACCCAT
* *
73572 CACCCGCCCACTACCTGCGACGGATACCAGTTTCTAAATCCA
1 CACCCGCCCACTACCCGCAACGGATACCAGTTTCTAAATCCA
* * *
73614 CACCCGCCCACTACCCGTAACGGGTACCATTTTCTAAATCCA
1 CACCCGCCCACTACCCGCAACGGATACCAGTTTCTAAATCCA
73656 CACCCGCCCACTACCC
1 CACCCGCCCACTACCC
73672 ACTAAAGTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.25, C:0.45, G:0.12, T:0.18
Consensus pattern (42 bp):
CACCCGCCCACTACCCGCAACGGATACCAGTTTCTAAATCCA
Found at i:74504 original size:19 final size:19
Alignment explanation
Indices: 74480--74531 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
74470 AATGCATTTT
* *
74480 ATGCATCGATGCATATACC
1 ATGCATCGATGCACAAACC
74499 ATGCATCGATGCACAAACC
1 ATGCATCGATGCACAAACC
74518 ATGCATCGATGCAC
1 ATGCATCGATGCAC
74532 TCTGGCTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (19 bp):
ATGCATCGATGCACAAACC
Done.