Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002261.1 Hibiscus syriacus cultivar Beakdansim tig00004601_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: 113586
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1405 original size:18 final size:18
Alignment explanation
Indices: 1360--1406 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1350 TCTATCACAT
* *
1360 ATATATCATATCAAATTC
1 ATATATCACATCAAATAC
*
1378 ATATCA-CACATCATATAC
1 ATAT-ATCACATCAAATAC
1396 ATATATCACAT
1 ATATATCACAT
1407 ACATTGTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATATCACATCAAATAC
Found at i:1734 original size:23 final size:22
Alignment explanation
Indices: 1708--1798 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 22
1698 CACCACAGCT
*
1708 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCG-AGTGCCA
1731 CGTAGAATTGCACCGAGTGCCA
1 CGTAGAATTGCACCGAGTGCCA
* *
1753 CGTAGAATTACACCGGAGTGCCG
1 CGTAGAATTGCACC-GAGTGCCA
1776 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCG-AGTGCCA
1799 TAATAATGTC
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
22 21 0.34
23 40 0.66
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.20
Consensus pattern (22 bp):
CGTAGAATTGCACCGAGTGCCA
Found at i:1782 original size:45 final size:46
Alignment explanation
Indices: 1708--1798 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
1698 CACCACAGCT
* *
1708 CGTATAATTGCACCGAAGTGCCACGTAGAATTGCACCG-AGTGCCA
1 CGTAGAATTACACCGAAGTGCCACGTAGAATTGCACCGTAGTGCCA
* *
1753 CGTAGAATTACACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTACACCGAAGTGCCACGTAGAATTGCACCGTAGTGCCA
1799 TAATAATGTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 34 0.83
46 7 0.17
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.20
Consensus pattern (46 bp):
CGTAGAATTACACCGAAGTGCCACGTAGAATTGCACCGTAGTGCCA
Found at i:1978 original size:99 final size:97
Alignment explanation
Indices: 1804--2014 Score: 266
Period size: 99 Copynumber: 2.1 Consensus size: 97
1794 TGCCATAATA
* * * *
1804 ATGTCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATTAGGGATCAAGTATGTATCT
1 ATGTCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATCAGAGATCAAGTATCTATCT
* *
1869 TATCAGACTTCACACATATTCCAAAGAATACATAT
66 CACCAGACTTCACACATATT-CAAAGAATAC--AT
* *
1904 ATGTCCGAAGGACCACATATCATT-CTTGAGAATCATATACATATGCCA-AGATC-AGTATCTGT
1 ATGTCCGAAGGACCACATATCATTCCTTAAGAATCATATACATAT--CAGAGATCAAGTATCTAT
*
1966 CTCACCAGACTTCACACATGTTCAAAGAATACAT
64 CTCACCAGACTTCACACATATTCAAAGAATACAT
2000 ATGTCCCGAAGGACC
1 ATGT-CCGAAGGACC
2015 GCGTAGACCC
Statistics
Matches: 99, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
96 6 0.06
97 10 0.10
98 10 0.10
99 45 0.45
100 27 0.27
101 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.27
Consensus pattern (97 bp):
ATGTCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATCAGAGATCAAGTATCTATCT
CACCAGACTTCACACATATTCAAAGAATACAT
Found at i:3389 original size:22 final size:21
Alignment explanation
Indices: 3364--3422 Score: 84
Period size: 20 Copynumber: 2.8 Consensus size: 21
3354 TTCGCTTGAG
*
3364 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
3386 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
*
3406 GGGTACCGGTTCCCCTT
1 GGGTACCGATTCCCCTT
3423 ACCCATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 16 0.47
21 8 0.24
22 10 0.29
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.31
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:4323 original size:16 final size:17
Alignment explanation
Indices: 4285--4326 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
4275 GCATCAGTTC
*
4285 TTATCACTCAAAATCAT
1 TTATCAATCAAAATCAT
* *
4302 TAATCAATCAAATTC-T
1 TTATCAATCAAAATCAT
4318 TTATCAATC
1 TTATCAATC
4327 TTTAATTACC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (17 bp):
TTATCAATCAAAATCAT
Found at i:6698 original size:18 final size:18
Alignment explanation
Indices: 6650--6699 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
6640 CCCCTATCAC
6650 ACATATATCATCATGCAAT
1 ACATATATCA-CATGCAAT
*
6669 TCATATCA-CACAT-CATAT
1 ACATAT-ATCACATGCA-AT
6687 ACATATATCACAT
1 ACATATATCACAT
6700 ACATTGTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
17 3 0.12
18 15 0.58
19 7 0.27
20 1 0.04
ACGTcount: A:0.42, C:0.24, G:0.02, T:0.32
Consensus pattern (18 bp):
ACATATATCACATGCAAT
Found at i:7044 original size:23 final size:23
Alignment explanation
Indices: 7018--7127 Score: 157
Period size: 23 Copynumber: 4.8 Consensus size: 23
7008 CAGCTTGTAA
* * *
7018 AATTGCACCGAAGTGGCACATAG
1 AATTGCACCGGAGTGCCACGTAG
7041 AATTGCACCGGAGTGCCACGTAG
1 AATTGCACCGGAGTGCCACGTAG
* *
7064 AATTGCACCGGAGTGCCGCGTAA
1 AATTGCACCGGAGTGCCACGTAG
*
7087 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGGAGTGCCACGTAG
*
7110 AATTGCACCGTAGTGCCA
1 AATTGCACCGGAGTGCCA
7128 TATAATAATG
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 79 1.00
ACGTcount: A:0.27, C:0.25, G:0.29, T:0.18
Consensus pattern (23 bp):
AATTGCACCGGAGTGCCACGTAG
Found at i:7326 original size:99 final size:102
Alignment explanation
Indices: 7129--7351 Score: 355
Period size: 101 Copynumber: 2.2 Consensus size: 102
7119 GTAGTGCCAT
** *
7129 ATAATA-ATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAA
1 ATAATATATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAA
7193 GTATGTGTCTCACCAGACTTCACACATGTTCCAAAGA
66 GTATGTGTCTCACCAGACTTCACACATGTTCCAAAGA
* * *
7230 AT-ATATATGTTCCGAAGGACTACATATCATTCCTTAAGAATCATATACATATGC-AAGGAT-AA
1 ATAATATATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAA
7292 GTATGTGTCTCACCAGACTTCACACATGTTCCAAAGA
66 GTATGTGTCTCACCAGACTTCACACATGTTCCAAAGA
7329 ATACATATATGTCCCGAAGGACC
1 ATA-ATATATGTCCCGAAGGACC
7352 GCGTAGACCC
Statistics
Matches: 111, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
99 41 0.37
100 8 0.07
101 62 0.56
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (102 bp):
ATAATATATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAA
GTATGTGTCTCACCAGACTTCACACATGTTCCAAAGA
Found at i:8647 original size:22 final size:22
Alignment explanation
Indices: 8622--8680 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
8612 TTTCCTTTAA
8622 GGGGAATCGATTCCCTCCTGTG
1 GGGGAATCGATTCCCTCCTGTG
8644 GGGGAATCGATTCCCTCCTGTG
1 GGGGAATCGATTCCCTCCTGTG
*
8666 GGGGAATCGGTTCCC
1 GGGGAATCGATTCCC
8681 CTATGAGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.14, C:0.27, G:0.34, T:0.25
Consensus pattern (22 bp):
GGGGAATCGATTCCCTCCTGTG
Found at i:8740 original size:22 final size:21
Alignment explanation
Indices: 8715--8772 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
8705 TCGCTTGAGG
*
8715 GGTATCGATTCCCCATTGAATA
1 GGTACCGATTCCCC-TTGAATA
*
8737 GGTACCGATT-CCCTTGAATG
1 GGTACCGATTCCCCTTGAATA
8757 GGTACCGATTCCCCTT
1 GGTACCGATTCCCCTT
8773 ACCAAAATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 16 0.48
21 8 0.24
22 9 0.27
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.31
Consensus pattern (21 bp):
GGTACCGATTCCCCTTGAATA
Found at i:9866 original size:57 final size:58
Alignment explanation
Indices: 9791--9902 Score: 147
Period size: 58 Copynumber: 1.9 Consensus size: 58
9781 ATAATAGGGT
*
9791 GACCGTTTTATAACTTTTAATAG-TCGAGACTAAACAAAGCAACT-TCTTATAGTCCGA
1 GACCATTTTATAACTTTTAATAGTTCGAGACTAAACAAAGC-ACTATCTTATAGTCCGA
* * * * *
9848 GACCATTTTGTAACTTTTAATAGTTGGTGACTCAACAAAGCAGTATCTTATAGTC
1 GACCATTTTATAACTTTTAATAGTTCGAGACTAAACAAAGCACTATCTTATAGTC
9903 AGGGAACCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 23 0.49
58 24 0.51
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (58 bp):
GACCATTTTATAACTTTTAATAGTTCGAGACTAAACAAAGCACTATCTTATAGTCCGA
Found at i:9916 original size:58 final size:57
Alignment explanation
Indices: 9791--9919 Score: 143
Period size: 58 Copynumber: 2.2 Consensus size: 57
9781 ATAATAGGGT
* * *
9791 GACCGTTTTATAACTTTTAATAGTCGAGACTAAACAAAGCAACTTCTTATAGTCCGA
1 GACCATTTTGTAACTTTTAATAGTCGAGACTAAACAAAGCAACTTCTTATAGTCAGA
* * * * *
9848 GACCATTTTGTAACTTTTAATAGTTGGTGACTCAACAAAGC-AGTATCTTATAGTCAGG
1 GACCATTTTGTAACTTTTAATAG-TCGAGACTAAACAAAGCAACT-TCTTATAGTCAGA
9906 GAACCATTTGTGTA
1 G-ACCATTT-TGTA
9920 GTTTACCCTA
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
57 23 0.38
58 26 0.43
59 7 0.12
60 4 0.07
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (57 bp):
GACCATTTTGTAACTTTTAATAGTCGAGACTAAACAAAGCAACTTCTTATAGTCAGA
Found at i:10951 original size:21 final size:21
Alignment explanation
Indices: 10927--11014 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 21
10917 AAATGTTAAG
*
10927 ACATTTTGATGAAAGGATTTA
1 ACATTTTGATAAAAGGATTTA
*
10948 ACATTTTGATTAAAA-GATTTC
1 ACATTTTGA-TAAAAGGATTTA
* * * *
10969 TCCTTTTGCTAAAAGGGTTTA
1 ACATTTTGATAAAAGGATTTA
* * *
10990 ACCTTTTCATAAAATGATTTA
1 ACATTTTGATAAAAGGATTTA
11011 ACAT
1 ACAT
11015 GAAGAGAATT
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 5 0.10
21 43 0.83
22 4 0.08
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.41
Consensus pattern (21 bp):
ACATTTTGATAAAAGGATTTA
Found at i:14126 original size:65 final size:65
Alignment explanation
Indices: 14056--14212 Score: 217
Period size: 65 Copynumber: 2.4 Consensus size: 65
14046 CACACCCATT
* *
14056 TCGAATGCATTTTGTGTACCGATGCACA-AGCCATGCATCGATGCACTCTTGAATATTTTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAGA-CCATACATCGATGCACTCCTGAATATTTTGAAAC
14120 A
65 A
* ** *
14121 TCGAATGCATTTTGTGTACCGATGCACAGATCATACATCGATGCACTCCTGGCTCTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATACATCGATGCACTCCTGAATATTTTGAAACA
* * *
14186 TCGAATGTAATTTGTGTACCAATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
14213 CCATAGTGTA
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
65 81 0.99
66 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAGACCATACATCGATGCACTCCTGAATATTTTGAAACA
Found at i:19941 original size:23 final size:22
Alignment explanation
Indices: 19910--19983 Score: 96
Period size: 23 Copynumber: 3.3 Consensus size: 22
19900 AAGAGTGTAC
19910 CGATGCATCCCTTGAATGTGCAT
1 CGATGCAT-CCTTGAATGTGCAT
* * *
19933 CGATACAT-CATGAAGGTGCAT
1 CGATGCATCCTTGAATGTGCAT
19954 CGATGCATTCCTTGAATGTGCAT
1 CGATGCA-TCCTTGAATGTGCAT
19977 CGATGCA
1 CGATGCA
19984 CTATGTTATG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
21 17 0.40
22 1 0.02
23 25 0.58
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (22 bp):
CGATGCATCCTTGAATGTGCAT
Found at i:19951 original size:21 final size:23
Alignment explanation
Indices: 19922--19980 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 23
19912 ATGCATCCCT
19922 TGAATGTGCATCGATACA-T-CA
1 TGAATGTGCATCGATACATTCCA
* * *
19943 TGAAGGTGCATCGATGCATTCCT
1 TGAATGTGCATCGATACATTCCA
19966 TGAATGTGCATCGAT
1 TGAATGTGCATCGAT
19981 GCACTATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 16 0.50
22 1 0.03
23 15 0.47
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (23 bp):
TGAATGTGCATCGATACATTCCA
Found at i:22340 original size:13 final size:13
Alignment explanation
Indices: 22322--22351 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
22312 GTGGGAGTAA
*
22322 TTTCAAAAATTAT
1 TTTCAAAAATGAT
22335 TTTCAAAAATGAT
1 TTTCAAAAATGAT
22348 TTTC
1 TTTC
22352 CAAGAAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (13 bp):
TTTCAAAAATGAT
Found at i:30436 original size:21 final size:20
Alignment explanation
Indices: 30351--30507 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
30341 AATGACCAAT
** *
30351 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
30370 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
30390 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
30410 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
30431 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
30452 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
30473 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
30493 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
30508 ACACATAAAT
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:30536 original size:20 final size:20
Alignment explanation
Indices: 30474--30666 Score: 228
Period size: 20 Copynumber: 9.7 Consensus size: 20
30464 CGATTTTCCA
* ** *
30474 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
30494 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
30514 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
30534 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
30554 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
30574 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
30594 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
30614 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* *
30634 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
30654 AAATCGCAACGCG
1 AAATCGCAACGCG
30667 ATATTTAAAG
Statistics
Matches: 148, Mismatches: 21, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 144 0.97
21 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:30838 original size:22 final size:22
Alignment explanation
Indices: 30813--30867 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
30803 CTCTCTACGG
*
30813 CGAAGAAATCTGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
30835 CGAAGATTTCCGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
30857 CGGCGAAATCC
1 CGAAGAAATCC
30868 CTCACAACCA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.38, G:0.16, T:0.22
Consensus pattern (22 bp):
CGAAGAAATCCGTCCCCATCTC
Found at i:31188 original size:20 final size:20
Alignment explanation
Indices: 31164--31238 Score: 98
Period size: 19 Copynumber: 3.8 Consensus size: 20
31154 TGCAGAAGAG
***
31164 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
31184 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
*
31205 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
31224 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
31239 CGCAACGCGA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 18 0.38
20 15 0.31
21 15 0.31
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:31279 original size:19 final size:19
Alignment explanation
Indices: 31257--31354 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
31247 GAAACCAAAA
*
31257 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
31276 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
31290 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
31309 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
31323 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
*
31342 TCGTGTTGCGATT
1 TCGCGTTGCGATT
31355 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 31 0.50
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:31298 original size:14 final size:14
Alignment explanation
Indices: 31279--31368 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
31269 TTTCATTTCG
31279 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
31293 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
31312 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
31326 CGTTGCGATTGTCATTT
1 CGTTGCGA-T-TC-TCT
31343 CGTGTTGCGATTCTCT
1 C--GTTGCGATTCTCT
31359 CGTTGCGATT
1 CGTTGCGATT
31369 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 27 0.44
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 17 0.27
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:31304 original size:33 final size:33
Alignment explanation
Indices: 31262--31376 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
31252 CAAAATCGCA
31262 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
31295 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
31328 TTGCGATTGTCATTTCGTGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
31361 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
31377 AACCCAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:32478 original size:221 final size:220
Alignment explanation
Indices: 32080--32525 Score: 858
Period size: 221 Copynumber: 2.0 Consensus size: 220
32070 ATGGAATCTG
32080 TTTCCGTGGGGTTCATATATATGGAAAGCTACTTGGACTAAGTTGTCGTCTGCCTTTGATGACCG
1 TTTCCGTGGGGTTCATATATATGGAAAGCTACTTGGACTAAGTTGTCGTCTGCCTTTGATGACCG
32145 CAAAAGTTTGCGGGGCGATGGGTCCAAATACACTTTGTCAGGCTTTGTTTGGGCCTTTAAGGTAA
66 CAAAAGTTTGCGGGGCGATGGGTCCAAATACACTTTGTCAGGCTTTGTTTGGGCCTTTAAGGTAA
32210 GAATTTCTATATAATGTTTCTAAAATTATAATTAATTATTTAACAATTACTAATTTGTTATTATA
131 GAATTTCTATATAATGTTTCTAAAATTATAATTAATTATTTAACAATTACTAA-TT-TTATTATA
32275 TTGTTTGTAGATTTGGATATTCGAGGC
194 TTGTTTGTAGATTTGGATATTCGAGGC
32302 TTTCCGTGGGGTTC-TATATATGGAAAGCTACTTGGACTAAGTTGTCGTCTGCCTTTGATGACCG
1 TTTCCGTGGGGTTCATATATATGGAAAGCTACTTGGACTAAGTTGTCGTCTGCCTTTGATGACCG
32366 CAAAAGTTTGCGGGGCGATGGGTCCAAATACACTTTGTCAGGCTTTGTTTGGGCCTTTAAGGTAA
66 CAAAAGTTTGCGGGGCGATGGGTCCAAATACACTTTGTCAGGCTTTGTTTGGGCCTTTAAGGTAA
*
32431 GAATTTCTATATAATGTTTCTAAAATTATAATTAATTATTTAACAATTACTAATTTTGTTATATT
131 GAATTTCTATATAATGTTTCTAAAATTATAATTAATTATTTAACAATTACTAATTTTATTATATT
32496 GTTTGTAGATTTGGATATTCGAGGC
196 GTTTGTAGATTTGGATATTCGAGGC
32521 TTTCC
1 TTTCC
32526 CCAGCATGCG
Statistics
Matches: 223, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
219 39 0.17
220 2 0.01
221 168 0.75
222 14 0.06
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.39
Consensus pattern (220 bp):
TTTCCGTGGGGTTCATATATATGGAAAGCTACTTGGACTAAGTTGTCGTCTGCCTTTGATGACCG
CAAAAGTTTGCGGGGCGATGGGTCCAAATACACTTTGTCAGGCTTTGTTTGGGCCTTTAAGGTAA
GAATTTCTATATAATGTTTCTAAAATTATAATTAATTATTTAACAATTACTAATTTTATTATATT
GTTTGTAGATTTGGATATTCGAGGC
Found at i:33393 original size:93 final size:93
Alignment explanation
Indices: 33234--33608 Score: 718
Period size: 93 Copynumber: 4.1 Consensus size: 93
33224 TAGATTGCTT
*
33234 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
33299 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
33327 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
33392 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
33420 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
33485 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
33513 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTA-TCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
33577 TTTGTCTTTGTTTTGTCTATTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
33604 AGTAA
1 AGTAA
33609 TGCAATCCAT
Statistics
Matches: 280, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
91 6 0.02
92 47 0.17
93 227 0.81
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:33693 original size:19 final size:19
Alignment explanation
Indices: 33671--33783 Score: 120
Period size: 19 Copynumber: 6.5 Consensus size: 19
33661 CACGAAACTT
33671 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
**
33690 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACC
33709 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
33723 AGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
33742 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
33756 AAGATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
33775 AAAATCGCA
1 AAAATCGCA
33784 TTGCGATTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
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 46 0.60
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:33734 original size:33 final size:32
Alignment explanation
Indices: 33691--33783 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
33681 CGCGAAACCA
**
33691 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
33723 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
33756 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
33784 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:33781 original size:52 final size:51
Alignment explanation
Indices: 33671--33783 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 51
33661 CACGAAACTT
* *
33671 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAAGCGAAAC-AC
* * *
33723 AGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGATCGCAACGCGAAAC-C
1 AAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-AT-GAAAAGCGAAACAC
33775 AAAATCGCA
1 AAAATCGCA
33784 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
52 41 0.79
53 3 0.06
54 8 0.15
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (51 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAAGCGAAACAC
Found at i:33801 original size:19 final size:18
Alignment explanation
Indices: 33779--33897 Score: 92
Period size: 19 Copynumber: 6.8 Consensus size: 18
33769 GAAACCAAAA
*
33779 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
33798 TCGCGTTGCGA--TTCTT
1 TCGCGTTGCGATTTTCTT
* *
33814 T--CGTTGTGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
*
33831 TCGCGTTGCGA--TTCTG
1 TCGCGTTGCGATTTTCTT
*
33847 T--CGTTGCGATTTTAATT
1 TCGCGTTGCGATTTT-CTT
*
33864 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
33883 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
33898 AAGTTTCGTG
Statistics
Matches: 80, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.19
16 9 0.11
17 10 0.12
19 46 0.57
ACGTcount: A:0.09, C:0.18, G:0.25, T:0.48
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCTT
Found at i:33833 original size:33 final size:33
Alignment explanation
Indices: 33784--33913 Score: 143
Period size: 33 Copynumber: 3.8 Consensus size: 33
33774 CAAAATCGCA
* *
33784 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTAATTTCGCGTTGCGATTCTGTCG
* **
33817 TTGTGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTAATTTCGCGTTGCGATTCTGTCG
*
33850 TTGCGATTTTAATTTCGCGTTGCGATTTTGGTTTCGCG
1 TTGCGATTTTAATTTCGCGTTGCGATTCT-G--T--CG
*
33888 TTGCGATTTTAAGTTTCGTGTTGCGA
1 TTGCGATTTTAA-TTTCGCGTTGCGA
33914 AAGTAAACTA
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
33 54 0.66
34 1 0.01
36 1 0.01
38 14 0.17
39 12 0.15
ACGTcount: A:0.10, C:0.16, G:0.26, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTAATTTCGCGTTGCGATTCTGTCG
Found at i:33905 original size:20 final size:20
Alignment explanation
Indices: 33848--33913 Score: 100
Period size: 19 Copynumber: 3.4 Consensus size: 20
33838 GCGATTCTGT
33848 CGTTGCGATTTTAA-TTTCG
1 CGTTGCGATTTTAAGTTTCG
*
33867 CGTTGCGATTTT-GGTTTCG
1 CGTTGCGATTTTAAGTTTCG
33886 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTAAGTTTCG
*
33906 TGTTGCGA
1 CGTTGCGA
33914 AAGTAAACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.12, C:0.15, G:0.27, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTAAGTTTCG
Found at i:35827 original size:14 final size:14
Alignment explanation
Indices: 35808--35843 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
35798 ATTGTTTAAT
35808 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
35822 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
35836 TGATTTGT
1 TGATTTGT
35844 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:35962 original size:19 final size:19
Alignment explanation
Indices: 35946--36043 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
35936 AAAAATGACT
35946 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
35965 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
35984 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
35998 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
36017 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
36037 ATCGCAA
1 ATCGCAA
36044 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:36075 original size:53 final size:53
Alignment explanation
Indices: 35946--36062 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
35936 AAAAATGACT
35946 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
35998 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
36051 ATCGCAATGCGA
1 ATCGCAATGCGA
36063 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:36080 original size:19 final size:19
Alignment explanation
Indices: 36052--36220 Score: 172
Period size: 19 Copynumber: 9.7 Consensus size: 19
36042 AACGAGAGAA
*
36052 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
36071 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
36090 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
36106 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
36123 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
36141 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
*
36157 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
36174 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
36192 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
36208 TCGCATTGCGATT
1 TCGCATTGCGATT
36221 CTCTCGTTGC
Statistics
Matches: 125, Mismatches: 9, Indels: 32
0.75 0.05 0.19
Matches are distributed among these distances:
14 23 0.18
16 15 0.12
17 13 0.10
18 21 0.17
19 42 0.34
20 11 0.09
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:36115 original size:52 final size:52
Alignment explanation
Indices: 36058--36192 Score: 245
Period size: 51 Copynumber: 2.6 Consensus size: 52
36048 AGAATCGCAA
36058 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
36110 TGCGATTTTCATTTCGCATTGCGA-TTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
36161 TGCGATTTTTATTTCCGCATTGCGATTTTCAT
1 TGCGATTTTCATTT-CGCATTGCGATTTTCAT
36193 GTTGGGATTT
Statistics
Matches: 80, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 40 0.50
52 34 0.43
53 6 0.08
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:36218 original size:33 final size:34
Alignment explanation
Indices: 36058--36234 Score: 165
Period size: 33 Copynumber: 5.2 Consensus size: 34
36048 AGAATCGCAA
36058 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCA--TCG--T
*
36096 TGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCA--TCG--T
*
36129 TGCGA-TTTCATTTCGCATTGCGATTCTC-TCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATCGT
*
36161 TGCGATTTTTATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTTTCATCGT
* *
36195 TGGGATTTTCATTTCGCATTGCGATTCTC-TCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATCGT
36228 TGCGATT
1 TGCGATT
36235 GTAATTTCCG
Statistics
Matches: 122, Mismatches: 9, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
32 7 0.06
33 54 0.44
34 34 0.28
35 9 0.07
36 3 0.02
37 10 0.08
38 5 0.04
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (34 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATCGT
Found at i:38555 original size:12 final size:12
Alignment explanation
Indices: 38538--38562 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38528 TCTTCGAGGA
38538 CTTTTTCTTCTT
1 CTTTTTCTTCTT
38550 CTTTTTCTTCTT
1 CTTTTTCTTCTT
38562 C
1 C
38563 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:38771 original size:24 final size:24
Alignment explanation
Indices: 38737--38783 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
38727 CTGAAACATC
38737 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
38761 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
38784 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:39519 original size:20 final size:20
Alignment explanation
Indices: 39494--39738 Score: 258
Period size: 20 Copynumber: 12.2 Consensus size: 20
39484 TGCCCTACCG
* *
39494 GATTTACAGATTCTCGTTGC
1 GATTTACGGATTCGCGTTGC
**
39514 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCGCGTTGC
**
39534 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCGCGTTGC
*
39554 GATTTACGGATTCTCGTTGC
1 GATTTACGGATTCGCGTTGC
** *
39574 GATTTACGGATTATCATTGC
1 GATTTACGGATTCGCGTTGC
*
39594 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCGCGTTGC
* * *
39614 GATATACGGATACGCATTGC
1 GATTTACGGATTCGCGTTGC
** *
39634 GATTTACCCATACGCGTTGC
1 GATTTACGGATTCGCGTTGC
* *
39654 GATTTACGGATACACGTTGC
1 GATTTACGGATTCGCGTTGC
*
39674 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCGCGTTGC
*
39694 GATTTATGTG-TTCGCGTTGC
1 GATTTACG-GATTCGCGTTGC
* **
39714 GATTTTCATATTCGCGTTGC
1 GATTTACGGATTCGCGTTGC
39734 GATTT
1 GATTT
39739 TGGAAAATCG
Statistics
Matches: 198, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
GATTTACGGATTCGCGTTGC
Found at i:39755 original size:21 final size:21
Alignment explanation
Indices: 39725--39807 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
39715 ATTTTCATAT
*
39725 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
39746 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
39767 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
39788 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
39808 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:39798 original size:42 final size:43
Alignment explanation
Indices: 39705--39803 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
39695 ATTTATGTGT
* *
39705 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
39746 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
39788 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
39804 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:40004 original size:2 final size:2
Alignment explanation
Indices: 39997--40033 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
39987 ACTATTTTCC
39997 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40034 GTTTTAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41239 original size:2 final size:2
Alignment explanation
Indices: 41232--41261 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41222 AATCTAATTA
41232 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41262 CATGATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41800 original size:22 final size:24
Alignment explanation
Indices: 41766--41812 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
41756 AAATGTGCTA
*
41766 AAAGATAGAAG-AAAACGTGTCAT
1 AAAGACAGAAGAAAAACGTGTCAT
*
41789 AAAGACAG-AGAAAAATGTGTCAT
1 AAAGACAGAAGAAAAACGTGTCAT
41812 A
1 A
41813 TATGTAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.17
Consensus pattern (24 bp):
AAAGACAGAAGAAAAACGTGTCAT
Found at i:45168 original size:67 final size:67
Alignment explanation
Indices: 45060--45194 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
45050 CACCGTCTCC
45060 ACCCAGTTGTCAAGCACAAGAGAAAAGGCAGAGAAGAAGAAGTTAGACTCGAAGAAAGGAATTTG
1 ACCCAGTTGTCAAGCACAAGAGAAAAGGCAGAGAAGAAGAAGTTAGACTCGAAGAAAGGAATTTG
45125 GG
66 GG
*
45127 ACCCAGTTGTCATGCACAAGAGAAAAGGCAGAGAAGAAGAAGTTAGACTCGAAGAAAGGAATTTG
1 ACCCAGTTGTCAAGCACAAGAGAAAAGGCAGAGAAGAAGAAGTTAGACTCGAAGAAAGGAATTTG
45192 GG
66 GG
45194 A
1 A
45195 ATTACTAAGG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.43, C:0.13, G:0.30, T:0.14
Consensus pattern (67 bp):
ACCCAGTTGTCAAGCACAAGAGAAAAGGCAGAGAAGAAGAAGTTAGACTCGAAGAAAGGAATTTG
GG
Found at i:50490 original size:21 final size:21
Alignment explanation
Indices: 50464--50503 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
50454 CAGAACCCCA
*
50464 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
50485 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
50504 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:50532 original size:19 final size:20
Alignment explanation
Indices: 50486--50545 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
50476 TTCCCCTGTG
50486 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TC-AA
50509 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
50528 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
50546 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:59508 original size:22 final size:22
Alignment explanation
Indices: 59476--59534 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
59466 TAAAAGGGTT
59476 GGTCAAAGGAAAATATTTTCCC
1 GGTCAAAGGAAAATATTTTCCC
*
59498 GGTTAAAGGAAAATATTTTCCC
1 GGTCAAAGGAAAATATTTTCCC
59520 GGTCAAAGGAAAATA
1 GGTCAAAGGAAAATA
59535 ACCCCCTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (22 bp):
GGTCAAAGGAAAATATTTTCCC
Found at i:60491 original size:226 final size:225
Alignment explanation
Indices: 60033--60781 Score: 972
Period size: 228 Copynumber: 3.3 Consensus size: 225
60023 AAAGTTTCAC
* * *
60033 CCGACCCGACCCGAATATATGAATTAGAAATCGACCCGACCCGAAATAATAAAAAATTATTTTTA
1 CCGACCCGACCCAAATATATGAATTAGAAACCGACCCGACCCGAAATAATAAAAAAATATTTTTA
*
60098 TTCAATAAAAAACAATGACTTAATTG--GAAAAAAATATAGAGAGTGA-TATTATTATAATTATT
66 TTCAAT-AAAAACAATGACTTAATTGAAAAAAAAAATATAGAGAG-GAGTATTATTATAATTATT
* *
60160 CATAAATATATAAGGTAAAATTATATAT-TTTTTGGGTCGGGTTTGGTA-TTTTCACCTTAAACC
129 CATAAATATATAAGGTAAAATTATATATATTTTTGGGAC-GGTCTGGTATTTTTCACCTTAAACC
*
60223 CGAACCCGACCCGAATATCACACTTAAAAAAAT
193 CGAACCCGACCCGAATATCACACTTAAAAAAAA
*
60256 CCGACCCGACCCAAATATATGAATTAGAAACCGACACGACCCGAAATAATAAAAAAATATTTTTA
1 CCGACCCGACCCAAATATATGAATTAGAAACCGACCCGACCCGAAATAATAAAAAAATATTTTTA
**
60321 TTCAATAAAAACAGCGACTTAATTGAAAAAAAAAATATAGAGAGGAGTATTATTATAATTATTCA
66 TTCAATAAAAACAATGACTTAATTGAAAAAAAAAATATAGAGAGGAGTATTATTATAATTATTCA
60386 TAAATATATAAGGTAAAATTATATATATTTTTGGGACGAGTCTGGTATTTTTCACCTTAAACCCG
131 TAAATATATAAGGTAAAATTATATATATTTTTGGGACG-GTCTGGTATTTTTCACCTTAAACCCG
*
60451 AACCCGATCCGAATATCACACTTAAAAAAAA
195 AACCCGACCCGAATATCACACTTAAAAAAAA
** * *
60482 CCGACCCGACCTGAATATATGAATTAGAAATCCGACCTGACCTGAAATAATAAAAAAATTATTTT
1 CCGACCCGACCCAAATATATGAATTAGAAA-CCGACCCGACCCGAAATAATAAAAAAA-TATTTT
* *
60547 TATTCAATAAAAACAATGACTTAATTGAAAAAAATTATATATAGAGA-G-GTATTATTGTAATTA
64 TATTCAATAAAAACAATGACTTAATTGAAAAAAA--AAATATAGAGAGGAGTATTATTATAATTA
* *
60610 TTCCTAAATATATAAGGTAAAATTATATATATTTTT---A-GGTCGGGTATTTTTCACCCTAAAC
127 TTCATAAATATATAAGGTAAAATTATATATATTTTTGGGACGGTCTGGTATTTTTCA-CCT----
* *
60671 CTAAACTCG-ACCCGACCCGAATATCACACTTTAAAAAATTGAC
187 -TAAACCCGAACCCGACCCGAATATCACAC-TTAAAAAA---AA
* ** * * *
60714 CCGACCCGA-CCAAA-ATA-AAATT-TCACCCGACCCGACTCGAAATAATAAAAAAATATTTCTA
1 CCGACCCGACCCAAATATATGAATTAGAAACCGACCCGACCCGAAATAATAAAAAAATATTTTTA
*
60775 TTTAATA
66 TTCAATA
60782 TATAAATAAA
Statistics
Matches: 470, Mismatches: 36, Indels: 37
0.87 0.07 0.07
Matches are distributed among these distances:
222 17 0.04
223 83 0.18
224 65 0.14
225 17 0.04
226 87 0.19
227 48 0.10
228 107 0.23
229 20 0.04
230 13 0.03
231 3 0.01
232 10 0.02
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (225 bp):
CCGACCCGACCCAAATATATGAATTAGAAACCGACCCGACCCGAAATAATAAAAAAATATTTTTA
TTCAATAAAAACAATGACTTAATTGAAAAAAAAAATATAGAGAGGAGTATTATTATAATTATTCA
TAAATATATAAGGTAAAATTATATATATTTTTGGGACGGTCTGGTATTTTTCACCTTAAACCCGA
ACCCGACCCGAATATCACACTTAAAAAAAA
Found at i:62559 original size:41 final size:41
Alignment explanation
Indices: 62544--62816 Score: 314
Period size: 41 Copynumber: 6.6 Consensus size: 41
62534 AGAGTAGTAT
** * *
62544 TTTAGTGGCGTTTTTATACAAACGTTGCTAAAGATTTGTAC
1 TTTAGTGGCGTTTTTATACAAACGCAGCTATAGACTTGTAC
* * *
62585 TTTAGTGGTGTTTTTATACAAATGCAGTTATAGACTTGTAC
1 TTTAGTGGCGTTTTTATACAAACGCAGCTATAGACTTGTAC
* *
62626 TTTAGTGGCGTTTTTATACAAATGCAGCTATACACTTGTAC
1 TTTAGTGGCGTTTTTATACAAACGCAGCTATAGACTTGTAC
* * *
62667 TTTAGTGGCGTTTATATACAAACGCTGCTATACACTTGTAC
1 TTTAGTGGCGTTTTTATACAAACGCAGCTATAGACTTGTAC
*
62708 TTTAGTGGCGTTTTTATACAAACGCCGCTATACG-CTTGTAC
1 TTTAGTGGCGTTTTTATACAAACGCAGCTATA-GACTTGTAC
** * ** * *
62749 TTTAGTATCGTTTATATACTTACGCCGCTATAGACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCAGCTATAGACTTGTAC
* *
62790 TTTAGTGGTGTTTGTTTTTACAAACGC
1 TTTAGTGGCG-TT-TTTATACAAACGC
62817 CGTAAGTTTA
Statistics
Matches: 199, Mismatches: 29, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
40 1 0.01
41 187 0.94
42 2 0.01
43 9 0.05
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.40
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAACGCAGCTATAGACTTGTAC
Found at i:62600 original size:82 final size:82
Alignment explanation
Indices: 62504--62816 Score: 313
Period size: 82 Copynumber: 3.8 Consensus size: 82
62494 GGTTCATCCA
* * * * * * * *
62504 TAGTGGTGTCTTTTAAACAAACGCCGCAACAGAGTAGTATTTTAGTGGCGTTTTTATACAAACGT
1 TAGTGGTGT-TTTTATACAAACGCAGCTATAGACTTGTACTTTAGTGGCGTTTTTATACAAACGC
* * *
62569 TGCTAAAGATTTGTACTT
65 AGCTAAACACTTGTACTT
* * *
62587 TAGTGGTGTTTTTATACAAATGCAGTTATAGACTTGTACTTTAGTGGCGTTTTTATACAAATGCA
1 TAGTGGTGTTTTTATACAAACGCAGCTATAGACTTGTACTTTAGTGGCGTTTTTATACAAACGCA
*
62652 GCTATACACTTGTACTT
66 GCTAAACACTTGTACTT
* * * * *
62669 TAGTGGCGTTTATATACAAACGCTGCTATACACTTGTACTTTAGTGGCGTTTTTATACAAACGCC
1 TAGTGGTGTTTTTATACAAACGCAGCTATAGACTTGTACTTTAGTGGCGTTTTTATACAAACGCA
* *
62734 GCTATACGCTTGTACTT
66 GCTAAACACTTGTACTT
* * ** * * * *
62751 TAGT-ATCGTTTATATACTTACGCCGCTATAGACTCGTACTTTAGTGGTGTTTGTTTTTACAAAC
1 TAGTGGT-GTTTTTATACAAACGCAGCTATAGACTTGTACTTTAGTGGCG-TT-TTTATACAAAC
62815 GC
63 GC
62817 CGTAAGTTTA
Statistics
Matches: 194, Mismatches: 33, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
82 171 0.88
83 11 0.06
84 12 0.06
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (82 bp):
TAGTGGTGTTTTTATACAAACGCAGCTATAGACTTGTACTTTAGTGGCGTTTTTATACAAACGCA
GCTAAACACTTGTACTT
Found at i:63997 original size:138 final size:139
Alignment explanation
Indices: 63749--64023 Score: 462
Period size: 138 Copynumber: 2.0 Consensus size: 139
63739 TTCTTTGAGA
*
63749 ACTTATCTGCATTTTTACTAGAATGTTTATTGGATAAAGGTTTAAATTTTGAATTTATCACCTTA
1 ACTTATCTGCATTTTTACTAGAATGTTTATTGGACAAAGGTTTAAATTTTGAATTTATCACCTTA
* * * * *
63814 CTTAAATATTTCACCATGAAGTTGTTTTTCTTCTGTAGAGACAAGCTCT-TATGCTTATATCATG
66 CTAAAATATTTCACAATGAAGCTGCTTTTCTTCTGCAGAGACAAGCTCTGTATGCTTATATCATG
63878 TTTTTCAGG
131 TTTTTCAGG
*
63887 ACTTATCTGCATTTTTACTAGAATGTTTATTGGACAAAGGTTTAAATTTTGAATTTATCATCTTA
1 ACTTATCTGCATTTTTACTAGAATGTTTATTGGACAAAGGTTTAAATTTTGAATTTATCACCTTA
*
63952 CTAAAATATTTCACAATGAAGCTGCTTTTCTTCTGCAGGGACAAGCTCTGGTATGCTTATATCAT
66 CTAAAATATTTCACAATGAAGCTGCTTTTCTTCTGCAGAGACAAGCTCT-GTATGCTTATATCAT
64017 GTTTTTC
130 GTTTTTC
64024 TGGTTGGTTT
Statistics
Matches: 127, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
138 106 0.83
140 21 0.17
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (139 bp):
ACTTATCTGCATTTTTACTAGAATGTTTATTGGACAAAGGTTTAAATTTTGAATTTATCACCTTA
CTAAAATATTTCACAATGAAGCTGCTTTTCTTCTGCAGAGACAAGCTCTGTATGCTTATATCATG
TTTTTCAGG
Found at i:65697 original size:43 final size:43
Alignment explanation
Indices: 65636--65770 Score: 191
Period size: 43 Copynumber: 3.2 Consensus size: 43
65626 TATCATTAGC
* * *
65636 CTTTTTGCGGTGTTTGTATCTAAAAACGTCGCTATAGATCTAA
1 CTTTTTGCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGA
* *
65679 CTTTTTGCGGCGTTTGTATCCAAAAACGTCGTTATATATCTGA
1 CTTTTTGCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGA
* * *
65722 CATTTTGCGGCGTTTAT-TCCGAAAACGTCGCTATAGATCTGA
1 CTTTTTGCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGA
65764 CTTTTTG
1 CTTTTTG
65771 TAGAGTTTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 28 0.35
43 53 0.65
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (43 bp):
CTTTTTGCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGA
Found at i:70308 original size:24 final size:24
Alignment explanation
Indices: 70281--70338 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
70271 TTGACACTAT
*
70281 TATTATTATTACAATGTTATGTAC
1 TATTATTATTACAATGTGATGTAC
** *
70305 TATTATTATTTTAATGTGGTGTAC
1 TATTATTATTACAATGTGATGTAC
70329 TATTAATTAT
1 TATT-ATTAT
70339 AAACTTTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.53
Consensus pattern (24 bp):
TATTATTATTACAATGTGATGTAC
Found at i:70608 original size:20 final size:21
Alignment explanation
Indices: 70569--70619 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
70559 CAAAGTTTTA
*
70569 TAAAATATAATTATATAAAAG
1 TAAAATATAATTATATAAAAC
70590 TAAAAT-TAACTTA-ATAAAAC
1 TAAAATATAA-TTATATAAAAC
*
70610 TAAAAGATAA
1 TAAAATATAA
70620 AGAATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (21 bp):
TAAAATATAATTATATAAAAC
Found at i:70748 original size:14 final size:14
Alignment explanation
Indices: 70729--70755 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
70719 CCAAACAATG
70729 GAAAAATATTTTTT
1 GAAAAATATTTTTT
70743 GAAAAATATTTTT
1 GAAAAATATTTTT
70756 CGTAAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
GAAAAATATTTTTT
Found at i:72678 original size:2 final size:2
Alignment explanation
Indices: 72673--72714 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
72663 TCAGAAATTA
72673 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
72713 AG
1 AG
72715 CGTTGTTGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:77104 original size:28 final size:29
Alignment explanation
Indices: 77047--77103 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
77037 GTGGGTAGAG
*
77047 GTGCACAAAAAATCCGAATATCCGATTTT
1 GTGCAAAAAAAATCCGAATATCCGATTTT
* *
77076 GTGCAAAAAAATATCTGAA-ATCGGATTT
1 GTGCAAAAAAA-ATCCGAATATCCGATTT
77104 GAGGAAAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (29 bp):
GTGCAAAAAAAATCCGAATATCCGATTTT
Found at i:77158 original size:13 final size:13
Alignment explanation
Indices: 77140--77164 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
77130 ATCGGATTTT
77140 TTTTAACCGGTTA
1 TTTTAACCGGTTA
77153 TTTTAACCGGTT
1 TTTTAACCGGTT
77165 TGGAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTTAACCGGTTA
Found at i:79554 original size:21 final size:21
Alignment explanation
Indices: 79530--79571 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
79520 AGTTTATTTT
79530 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
79551 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
79572 AACTTGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:79608 original size:33 final size:33
Alignment explanation
Indices: 79566--79669 Score: 174
Period size: 33 Copynumber: 3.2 Consensus size: 33
79556 TTTGTTTCAA
*
79566 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
79599 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
79632 TTATCGAACTTGGAAGTATTTAAGTATTTCAA-
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
79664 TTATCG
1 TTATCG
79670 TAAACTTTGT
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 6 0.09
33 62 0.91
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:79730 original size:14 final size:14
Alignment explanation
Indices: 79711--79755 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
79701 TTTAATAATA
*
79711 TTATAATCGGTTTT
1 TTATAACCGGTTTT
79725 TTATAACCGGTTTT
1 TTATAACCGGTTTT
79739 TTATAACCGGTTTT
1 TTATAACCGGTTTT
79753 TTA
1 TTA
79756 AAAAAACCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.53
Consensus pattern (14 bp):
TTATAACCGGTTTT
Found at i:79765 original size:17 final size:17
Alignment explanation
Indices: 79743--79776 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
79733 GGTTTTTTAT
79743 AACCGGTTTTTTAAAAA
1 AACCGGTTTTTTAAAAA
79760 AACCGGTTTTTTAAAAA
1 AACCGGTTTTTTAAAAA
79777 CCGAAACCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
AACCGGTTTTTTAAAAA
Found at i:82100 original size:22 final size:22
Alignment explanation
Indices: 82075--82132 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 22
82065 GAAATATAAT
*
82075 TTTTATTTTTAGTATTTTTATA
1 TTTTATTTTTAATATTTTTATA
82097 TTTTATTTTTTGAATATTTTTATA
1 TTTTA-TTTTT-AATATTTTTATA
*
82121 TTTTAGTTTTAA
1 TTTTATTTTTAA
82133 AACAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 7 0.22
23 9 0.28
24 16 0.50
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (22 bp):
TTTTATTTTTAATATTTTTATA
Found at i:82141 original size:24 final size:24
Alignment explanation
Indices: 82090--82146 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
82080 TTTTTAGTAT
* ** * *
82090 TTTTATATTTTATTTTTTGAATAT
1 TTTTATATTTTAGTTTTAAAACAA
82114 TTTTATATTTTAGTTTTAAAACAA
1 TTTTATATTTTAGTTTTAAAACAA
*
82138 TTTTTTATT
1 TTTTATATT
82147 AAAAAATAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTTATATTTTAGTTTTAAAACAA
Found at i:82918 original size:60 final size:60
Alignment explanation
Indices: 82842--82954 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
82832 AATGATCCAT
* * * * *
82842 CAACTATATGGTGTTGCTTTGTTGAATCATTCAACTATTAAAAGTTATAAAATAGTCCTC
1 CAACTATAAGGCGTTGCTTTGTTGAATCACTCAACTATTAAAAATTACAAAATAGTCCTC
* *
82902 CAACTATAAGGCGTTGCTTTGTTGAGTCCCTCAACTATTAAAAATTACAAAAT
1 CAACTATAAGGCGTTGCTTTGTTGAATCACTCAACTATTAAAAATTACAAAAT
82955 GATCACTCGA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (60 bp):
CAACTATAAGGCGTTGCTTTGTTGAATCACTCAACTATTAAAAATTACAAAATAGTCCTC
Found at i:82968 original size:60 final size:59
Alignment explanation
Indices: 82831--82968 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 59
82821 AAAAGTAAAT
* * * * *
82831 AAATGATCCATCAACTATATGGTGTTGCTTTGTTGAATCATTCAACTATTAAAAGTTATA
1 AAATGATCC-TCAACTATAAGGCGTTGCTTTGTTGAATCACTCAACTATTAAAAATTACA
* *
82891 AAAT-AGTCCTCCAACTATAAGGCGTTGCTTTGTTGAGTCCCTCAACTATTAAAAATTACA
1 AAATGA-TCCT-CAACTATAAGGCGTTGCTTTGTTGAATCACTCAACTATTAAAAATTACA
*
82951 AAATGATCACTCGACTAT
1 AAATGATC-CTCAACTAT
82969 TCATATGTTC
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
59 2 0.03
60 61 0.92
61 3 0.05
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (59 bp):
AAATGATCCTCAACTATAAGGCGTTGCTTTGTTGAATCACTCAACTATTAAAAATTACA
Found at i:83900 original size:60 final size:60
Alignment explanation
Indices: 83834--83983 Score: 210
Period size: 60 Copynumber: 2.5 Consensus size: 60
83824 AGAGTGTTGC
* * * *
83834 TTTGTTGAATTTCCCGACTATTAAAAGTTACAAAACGATATTCTAATTATATAATATTAT
1 TTTGTTGAGTTTCCTGACTATTAAAAATTACAAAACGATATTCTAATTATATAACATTAT
* * * *
83894 TTTGTTGAGTTTTCTGACTATTAAAAATTACAAAATGATTTTCTAATTATATAGCATTAT
1 TTTGTTGAGTTTCCTGACTATTAAAAATTACAAAACGATATTCTAATTATATAACATTAT
* *
83954 TTTATTGAGTCTCCTGACTATTAAAAATTA
1 TTTGTTGAGTTTCCTGACTATTAAAAATTA
83984 TAAATTAGTC
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 79 1.00
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (60 bp):
TTTGTTGAGTTTCCTGACTATTAAAAATTACAAAACGATATTCTAATTATATAACATTAT
Found at i:85325 original size:33 final size:33
Alignment explanation
Indices: 85288--85354 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
85278 TTTGTCTCCC
** *
85288 TCATTCTCTATGGTTAATTATATTTTACCCCCT
1 TCATTCTCTATACTTAATTATAATTTACCCCCT
* * *
85321 TCATTTTTTATACTTAATTATAATTTGCCCCCT
1 TCATTCTCTATACTTAATTATAATTTACCCCCT
85354 T
1 T
85355 GAGTTGGAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.51
Consensus pattern (33 bp):
TCATTCTCTATACTTAATTATAATTTACCCCCT
Found at i:85810 original size:61 final size:60
Alignment explanation
Indices: 85694--85879 Score: 225
Period size: 61 Copynumber: 3.1 Consensus size: 60
85684 TGGCTGCCCA
* * * *
85694 TGGGGATGAAATT-GAAAGATTCAAAAGTATGAGGACTAATTTAGAATGAGGGTCATAGTT
1 TGGGGATGAAATTGGAATG-TTCAAAAGTTTAAGGACTAATTTAGAATGAAGGTCATAGTT
* *
85754 TGGGGATGAAATTGGAATGTTCAAAAGTTTCAAGGACTAATTTAGAATGAAAGTCATAATT
1 TGGGGATGAAATTGGAATGTTCAAAAGTTT-AAGGACTAATTTAGAATGAAGGTCATAGTT
* * * * *
85815 TGGGGATTAAATTGG-ATATTCAAAAGTTTAAGGACCAATTTAAAATG-AGGATCATAGCT
1 TGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAAGG-TCATAGTT
85874 TGGGGA
1 TGGGGA
85880 CATATGATGC
Statistics
Matches: 110, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
58 2 0.02
59 28 0.25
60 36 0.33
61 44 0.40
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.30
Consensus pattern (60 bp):
TGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAAGGTCATAGTT
Found at i:86329 original size:47 final size:47
Alignment explanation
Indices: 86245--86367 Score: 160
Period size: 47 Copynumber: 2.7 Consensus size: 47
86235 TATACATAAC
* **
86245 TTTA-TAAAGGCACAAGGCCA-ATTTTATTTCACCCAGGTTACTTCA
1 TTTACTAAAGGCACAAGGCCAGAGTTTATTTCACCCAGGTTACACCA
* * *
86290 TTTACTAAAGGCACAAGGCTAGGGTTTATTTCACTCAGGTTACACCA
1 TTTACTAAAGGCACAAGGCCAGAGTTTATTTCACCCAGGTTACACCA
* *
86337 TTGACTAAAGGCACAAGGCCAGTGTTTATTT
1 TTTACTAAAGGCACAAGGCCAGAGTTTATTT
86368 ACGTCAATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
45 4 0.06
46 15 0.22
47 48 0.72
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (47 bp):
TTTACTAAAGGCACAAGGCCAGAGTTTATTTCACCCAGGTTACACCA
Found at i:107281 original size:16 final size:17
Alignment explanation
Indices: 107260--107292 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
107250 AAGAAGTTGT
*
107260 CACCAAC-CTTCAATTC
1 CACCAACGCATCAATTC
107276 CACCAACGCATCAATTC
1 CACCAACGCATCAATTC
107293 TCGAATCAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.42, G:0.03, T:0.21
Consensus pattern (17 bp):
CACCAACGCATCAATTC
Done.