Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001600.1 Hibiscus syriacus cultivar Beakdansim tig00003183_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: 61876
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:1477 original size:19 final size:19
Alignment explanation
Indices: 1453--1502 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
1443 ATTAACGGGT
1453 TGGTGCTTGTTAAAAATGA
1 TGGTGCTTGTTAAAAATGA
1472 TGGTGCTTGTTAAAAATGA
1 TGGTGCTTGTTAAAAATGA
1491 TGGTGCTTGTTA
1 TGGTGCTTGTTA
1503 TATGGTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.26, C:0.06, G:0.28, T:0.40
Consensus pattern (19 bp):
TGGTGCTTGTTAAAAATGA
Found at i:2121 original size:15 final size:15
Alignment explanation
Indices: 2074--2143 Score: 52
Period size: 15 Copynumber: 4.7 Consensus size: 15
2064 CAACTTGTGA
2074 TGATGATGGTGC-TT
1 TGATGATGGTGCTTT
* *** *
2088 TGATGTTGCAACTTG
1 TGATGATGGTGCTTT
2103 TGATGATGGTGCTTT
1 TGATGATGGTGCTTT
* ** *
2118 TGATGTTGCAGCCTT
1 TGATGATGGTGCTTT
2133 TGATGATGGTG
1 TGATGATGGTG
2144 TAATCGTTGT
Statistics
Matches: 38, Mismatches: 17, Indels: 1
0.68 0.30 0.02
Matches are distributed among these distances:
14 8 0.21
15 30 0.79
ACGTcount: A:0.16, C:0.10, G:0.33, T:0.41
Consensus pattern (15 bp):
TGATGATGGTGCTTT
Found at i:2122 original size:30 final size:29
Alignment explanation
Indices: 2074--2143 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 29
2064 CAACTTGTGA
2074 TGATGATGGTGCTTTGATGTTGCA-ACTT
1 TGATGATGGTGCTTTGATGTTGCAGACTT
*
2102 GTGATGATGGTGCTTTTGATGTTGCAGCCTT
1 -TGATGATGGTGC-TTTGATGTTGCAGACTT
2133 TGATGATGGTG
1 TGATGATGGTG
2144 TAATCGTTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
29 12 0.32
30 23 0.61
31 3 0.08
ACGTcount: A:0.16, C:0.10, G:0.33, T:0.41
Consensus pattern (29 bp):
TGATGATGGTGCTTTGATGTTGCAGACTT
Found at i:5688 original size:21 final size:21
Alignment explanation
Indices: 5662--5718 Score: 87
Period size: 22 Copynumber: 2.7 Consensus size: 21
5652 TGTTTTTATA
5662 AAAAAAACCTAAAAGTATTTC
1 AAAAAAACCTAAAAGTATTTC
*
5683 AAAAAATCCCTAAAAGTATTTC
1 AAAAAA-ACCTAAAAGTATTTC
*
5705 AAAAAAAACTAAAA
1 AAAAAAACCTAAAA
5719 AAACGTCAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 12 0.38
22 20 0.62
ACGTcount: A:0.61, C:0.14, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAAAAACCTAAAAGTATTTC
Found at i:6814 original size:2 final size:2
Alignment explanation
Indices: 6807--6868 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
6797 AGAAGCATGC
6807 AT AT AT AT AT AT 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 AT AT AT AT AT AT
*
6849 AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
6869 GATTCCGTTC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7233 original size:43 final size:43
Alignment explanation
Indices: 7186--7488 Score: 204
Period size: 43 Copynumber: 7.1 Consensus size: 43
7176 GGCCTTAAAA
* * *
7186 TTTTTAATCTTCCTTTTTATTTTTATAATTGAGGTCCTTAATT
1 TTTTTAATCTTCCTTTTTATATTTATAATTGAGGCCCCTAATT
* ** * * * *
7229 TTTTTAATTTTATTTTTTCTCTTTATAATTAAGGCCCTTAA--
1 TTTTTAATCTTCCTTTTTATATTTATAATTGAGGCCCCTAATT
* ** * * * *
7270 TTTTTAATTTTATTTTTTCTCTTTATAATTGAGACCCCTAAAT
1 TTTTTAATCTTCCTTTTTATATTTATAATTGAGGCCCCTAATT
* ** * * *
7313 TTTGTAATCTTATTTTTTTACATTTATAATGGAGACCCCTAATT
1 TTTTTAATCTT-CCTTTTTATATTTATAATTGAGGCCCCTAATT
* * * *
7357 TTTGTCAATC-CCACTTTTTACATTTATAATTGTGGCCCCTAATT
1 TTT-TTAATCTTC-CTTTTTATATTTATAATTGAGGCCCCTAATT
* * *
7401 TTTTCAATC-TCACTTTTTATATTTATAGTTGAAGCCCCTAA-T
1 TTTTTAATCTTC-CTTTTTATATTTATAATTGAGGCCCCTAATT
* ** * *
7443 TTTTCAATC-TCACTTTTTACCTTTATAATTGAGACCCATAATT
1 TTTTTAATCTTC-CTTTTTATATTTATAATTGAGGCCCCTAATT
7486 TTT
1 TTT
7489 CCAATCCCAC
Statistics
Matches: 217, Mismatches: 37, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
41 38 0.18
42 36 0.17
43 80 0.37
44 59 0.27
45 4 0.02
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.52
Consensus pattern (43 bp):
TTTTTAATCTTCCTTTTTATATTTATAATTGAGGCCCCTAATT
Found at i:7340 original size:44 final size:43
Alignment explanation
Indices: 7291--7505 Score: 240
Period size: 44 Copynumber: 5.0 Consensus size: 43
7281 ATTTTTTCTC
* *
7291 TTTATAATTGAGACCCCTAAATTTTGT-AATCTTATTTTTTTACA
1 TTTATAATTGAGACCCCTAAATTTT-TCAATCTCA-CTTTTTACA
* * *
7335 TTTATAATGGAGACCCCTAATTTTTGTCAATCCCACTTTTTACA
1 TTTATAATTGAGACCCCTAAATTTT-TCAATCTCACTTTTTACA
* * * *
7379 TTTATAATTGTGGCCCCTAATTTTTTCAATCTCACTTTTTATA
1 TTTATAATTGAGACCCCTAAATTTTTCAATCTCACTTTTTACA
* *
7422 TTTATAGTTGA-AGCCCCT-AATTTTTCAATCTCACTTTTTACC
1 TTTATAATTGAGA-CCCCTAAATTTTTCAATCTCACTTTTTACA
* *
7464 TTTATAATTGAGACCCAT-AATTTTTCCAATCCCACTTTTTAC
1 TTTATAATTGAGACCCCTAAATTTTT-CAATCTCACTTTTTAC
7506 TATTAAAATT
Statistics
Matches: 148, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
42 42 0.28
43 46 0.31
44 55 0.37
45 5 0.03
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.46
Consensus pattern (43 bp):
TTTATAATTGAGACCCCTAAATTTTTCAATCTCACTTTTTACA
Found at i:7485 original size:85 final size:83
Alignment explanation
Indices: 7184--7509 Score: 255
Period size: 85 Copynumber: 3.8 Consensus size: 83
7174 AAGGCCTTAA
** ** * * * * * *
7184 AATTTTTAATCTTC-CTTTTTATTTTTATAATTGAGGTCCTTAATTTTTTTAATTTTATTTTTTC
1 AATTTTTAATC-TCACTTTTTACCTTTATAATTGAGACCCCTAATTTTTTCAATCTCACTTTTTA
* *
7248 TCTTTATAATT-AAGGCCCTT
65 TATTTAT-ATTGAA-GCCCCT
* * * * * *
7268 AATTTTTAATTTTA-TTTTTTCTCTTTATAATTGAGACCCCTAAATTTTGT-AATCTTATTTTTT
1 AATTTTTAATCTCACTTTTTAC-CTTTATAATTGAGACCCCT-AATTTTTTCAATCTCA-CTTTT
* * *
7331 TACATTTATAATGGAGACCCCT
63 TATATTTATATTGAAG-CCCCT
* * * *
7353 AATTTTTGTCAATCCCACTTTTTACATTTATAATTGTGGCCCCTAATTTTTTCAATCTCACTTTT
1 AA-TTTT-T-AATCTCACTTTTTACCTTTATAATTGAGACCCCTAATTTTTTCAATCTCACTTTT
7418 TATATTTATAGTTGAAGCCCCT
63 TATATTTATA-TTGAAGCCCCT
* * *
7440 AATTTTTCAATCTCACTTTTTACCTTTATAATTGAGACCCATAATTTTTCCAATCCCACTTTTTA
1 AATTTTT-AATCTCACTTTTTACCTTTATAATTGAGACCCCTAATTTTTTCAATCTCACTTTTTA
7505 CTATT
65 -TATT
7510 AAAATTTAGG
Statistics
Matches: 193, Mismatches: 36, Indels: 24
0.76 0.14 0.09
Matches are distributed among these distances:
83 6 0.03
84 34 0.18
85 77 0.40
86 12 0.06
87 28 0.15
88 30 0.16
89 6 0.03
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.52
Consensus pattern (83 bp):
AATTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCCTAATTTTTTCAATCTCACTTTTTAT
ATTTATATTGAAGCCCCT
Found at i:7505 original size:43 final size:43
Alignment explanation
Indices: 7291--7505 Score: 256
Period size: 43 Copynumber: 5.0 Consensus size: 43
7281 ATTTTTTCTC
* * *
7291 TTTATAATTGAGACCCCTAAATTTTGT-AATCTTATTTTTTTACA
1 TTTATAATTGAGACCCCT-AATTTTTTCAATCTCA-CTTTTTACA
* *
7335 TTTATAATGGAGACCCCTAATTTTTGTCAATCCCACTTTTTACA
1 TTTATAATTGAGACCCCTAATTTTT-TCAATCTCACTTTTTACA
* * *
7379 TTTATAATTGTGGCCCCTAATTTTTTCAATCTCACTTTTTATA
1 TTTATAATTGAGACCCCTAATTTTTTCAATCTCACTTTTTACA
* *
7422 TTTATAGTTGA-AGCCCCTAA-TTTTTCAATCTCACTTTTTACC
1 TTTATAATTGAGA-CCCCTAATTTTTTCAATCTCACTTTTTACA
* * *
7464 TTTATAATTGAGACCCATAATTTTTCCAATCCCACTTTTTAC
1 TTTATAATTGAGACCCCTAATTTTTTCAATCTCACTTTTTAC
7506 TATTAAAATT
Statistics
Matches: 147, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
42 36 0.24
43 58 0.39
44 48 0.33
45 5 0.03
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.46
Consensus pattern (43 bp):
TTTATAATTGAGACCCCTAATTTTTTCAATCTCACTTTTTACA
Found at i:9629 original size:14 final size:14
Alignment explanation
Indices: 9612--9700 Score: 54
Period size: 14 Copynumber: 6.3 Consensus size: 14
9602 GCGCAATAGG
9612 TAAAGGACTAAAAT
1 TAAAGGACTAAAAT
* * *
9626 TAAAGTATTGAAAAA
1 TAAAGGACT-AAAAT
*
9641 TATAAGGA-AAAAAT
1 TA-AAGGACTAAAAT
* * *
9655 AAAAAGACAAAAAT
1 TAAAGGACTAAAAT
* * *
9669 TAAAGTAATGAAAT
1 TAAAGGACTAAAAT
*
9683 TAAATGACTAAAAT
1 TAAAGGACTAAAAT
9697 TAAA
1 TAAA
9701 TAAATAAAAA
Statistics
Matches: 54, Mismatches: 18, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
13 4 0.07
14 40 0.74
15 6 0.11
16 4 0.07
ACGTcount: A:0.63, C:0.03, G:0.11, T:0.22
Consensus pattern (14 bp):
TAAAGGACTAAAAT
Found at i:10384 original size:63 final size:63
Alignment explanation
Indices: 10304--10438 Score: 225
Period size: 63 Copynumber: 2.1 Consensus size: 63
10294 ACCTAAACAC
* * *
10304 GATTAACCCTTTGTTTTGGTGACAAAAACCTGAAGTACACTGGAAATGGAGGACCTAACGCAT
1 GATTTACCCTTTATTTTGGTGACAAAAACATGAAGTACACTGGAAATGGAGGACCTAACGCAT
*
10367 GATTTACCCTTTATTTTGGTGACAAAAGCATGAAGTACACTGGAAATGGAGGACCTAACGCAT
1 GATTTACCCTTTATTTTGGTGACAAAAACATGAAGTACACTGGAAATGGAGGACCTAACGCAT
*
10430 GATATACCC
1 GATTTACCC
10439 AAAAGTTTTG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (63 bp):
GATTTACCCTTTATTTTGGTGACAAAAACATGAAGTACACTGGAAATGGAGGACCTAACGCAT
Found at i:10676 original size:22 final size:22
Alignment explanation
Indices: 10648--10691 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
10638 AATATACGAT
**
10648 ATGAACAATACTGTGAACAGTA
1 ATGAACAATACCCTGAACAGTA
10670 ATGAACAATACCCTGAACAGTA
1 ATGAACAATACCCTGAACAGTA
10692 CCAAATGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.20
Consensus pattern (22 bp):
ATGAACAATACCCTGAACAGTA
Found at i:10746 original size:21 final size:21
Alignment explanation
Indices: 10720--10764 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
10710 CAGATTACTG
10720 ACAGGGAACCGATACCCTGCT
1 ACAGGGAACCGATACCCTGCT
10741 ACAGGGAACCGATACCCTGCT
1 ACAGGGAACCGATACCCTGCT
10762 ACA
1 ACA
10765 ATACTGCTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.33, G:0.22, T:0.13
Consensus pattern (21 bp):
ACAGGGAACCGATACCCTGCT
Found at i:11537 original size:31 final size:31
Alignment explanation
Indices: 11464--11539 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
11454 ATAGGTCCCG
* * *
11464 AAGAACCTAGGTAAACTGTCCATATGTTCCT
1 AAGAACATAGGTAAACTATCCATATGTTCCA
* *
11495 TAGAACATAGGTAAACTATCCATATGTCTCGA
1 AAGAACATAGGTAAACTATCCATATGT-TCCA
*
11527 AAG-ACTTAGGTAA
1 AAGAACATAGGTAA
11540 CCCTCGACTC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
31 33 0.89
32 4 0.11
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (31 bp):
AAGAACATAGGTAAACTATCCATATGTTCCA
Found at i:12619 original size:23 final size:21
Alignment explanation
Indices: 12568--12649 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
12558 AGGGTGTCAA
12568 AGTGCATCCATGCACTCCTAC
1 AGTGCATCCATGCACTCCTAC
*
12589 AGTGCATCCATTCACCTACC-AC
1 AGTGCATCCATGCA-CT-CCTAC
* * * *
12611 TAGTGCATCGATGGAC-CATGC
1 -AGTGCATCCATGCACTCCTAC
12632 AGTGCATCCATGCACTCC
1 AGTGCATCCATGCACTCC
12650 ATTTCGAATG
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
20 14 0.30
21 15 0.32
22 5 0.11
23 13 0.28
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACTCCTAC
Found at i:12692 original size:12 final size:12
Alignment explanation
Indices: 12674--12704 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
12664 TAGTGCATCA
12674 ATGCATCTTGCT
1 ATGCATCTTGCT
*
12686 GTGCATCTTGCT
1 ATGCATCTTGCT
12698 ATGCATC
1 ATGCATC
12705 CATGTACGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (12 bp):
ATGCATCTTGCT
Found at i:16089 original size:21 final size:21
Alignment explanation
Indices: 16065--16182 Score: 141
Period size: 21 Copynumber: 5.4 Consensus size: 21
16055 TAATTCAAAG
16065 TCCATGCACTCCTGCAGTGCA
1 TCCATGCACTCCTGCAGTGCA
16086 TCCATGCACTCCTGCAGTGCA
1 TCCATGCACTCCTGCAGTGCA
*
16107 TCCATGCACTCCTGTAGTGCA
1 TCCATGCACTCCTGCAGTGCA
*
16128 TCCATGCACCTTCC-ACTAGTGCA
1 TCCATGCA-C-TCCTGC-AGTGCA
*
16151 TCCATGCACCTTCC-ACTAGTGCA
1 TCCATGCA-C-TCCTGC-AGTGCA
16174 TCCATGCAC
1 TCCATGCAC
16183 CTTCCACTAG
Statistics
Matches: 91, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
21 49 0.54
22 2 0.02
23 40 0.44
ACGTcount: A:0.20, C:0.38, G:0.16, T:0.25
Consensus pattern (21 bp):
TCCATGCACTCCTGCAGTGCA
Found at i:16126 original size:42 final size:43
Alignment explanation
Indices: 16065--16226 Score: 177
Period size: 46 Copynumber: 3.7 Consensus size: 43
16055 TAATTCAAAG
* *
16065 TCCATGCACTCCTGCAGTGCATCCATGCAC-TCCTGC-AGTGCA
1 TCCATGCACTCCTGTAGTGCATCCATGCACTTCC-ACTAGTGCA
16107 TCCATGCACTCCTGTAGTGCATCCATGCACCTTCCACTAGTGCA
1 TCCATGCACTCCTGTAGTGCATCCATGCA-CTTCCACTAGTGCA
**
16151 TCCATGCACCTTCCACTAGTGCATCCATGCACCTTCCACTAGTGCA
1 TCCATGCA-C-TCCTGTAGTGCATCCATGCA-CTTCCACTAGTGCA
** * * *
16197 TGGATGCAC-CATGTAGTTCATCCGTGCACT
1 TCCATGCACTCCTGTAGTGCATCCATGCACT
16227 CCATTTCGAA
Statistics
Matches: 104, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
42 30 0.29
43 16 0.15
44 17 0.16
45 2 0.02
46 39 0.38
ACGTcount: A:0.20, C:0.36, G:0.17, T:0.27
Consensus pattern (43 bp):
TCCATGCACTCCTGTAGTGCATCCATGCACTTCCACTAGTGCA
Found at i:16151 original size:23 final size:23
Alignment explanation
Indices: 16080--16206 Score: 165
Period size: 23 Copynumber: 5.7 Consensus size: 23
16070 GCACTCCTGC
*
16080 AGTGCATCCATGCA-C-TCCTGC-
1 AGTGCATCCATGCACCTTCC-ACT
**
16101 AGTGCATCCATGCA-C-TCCTGT
1 AGTGCATCCATGCACCTTCCACT
16122 AGTGCATCCATGCACCTTCCACT
1 AGTGCATCCATGCACCTTCCACT
16145 AGTGCATCCATGCACCTTCCACT
1 AGTGCATCCATGCACCTTCCACT
16168 AGTGCATCCATGCACCTTCCACT
1 AGTGCATCCATGCACCTTCCACT
**
16191 AGTGCATGGATGCACC
1 AGTGCATCCATGCACC
16207 ATGTAGTTCA
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
21 32 0.33
22 1 0.01
23 64 0.66
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.25
Consensus pattern (23 bp):
AGTGCATCCATGCACCTTCCACT
Found at i:16275 original size:20 final size:20
Alignment explanation
Indices: 16246--16298 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
16236 ATGCACTTAG
* *
16246 TGCATAGATGCATCCTGCTA
1 TGCATCGATGCATCCTACTA
*
16266 TGCATCGATGCATCCTACTG
1 TGCATCGATGCATCCTACTA
*
16286 TGCATCCATGCAT
1 TGCATCGATGCAT
16299 GAAGGCTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (20 bp):
TGCATCGATGCATCCTACTA
Found at i:16448 original size:20 final size:22
Alignment explanation
Indices: 16410--16449 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
16400 TTTTAGTAGA
16410 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
16432 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
16450 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:16728 original size:32 final size:34
Alignment explanation
Indices: 16671--16733 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
16661 AAGGGGACTG
*
16671 GTTCTAGCTTATCCCGTGTAAAAGCTAGGGAAAT
1 GTTCTAGCTTAGCCCGTGTAAAAGCTAGGGAAAT
*
16705 GTTCTAGTTTAGCCCG-G-AAAAGCTAGGGA
1 GTTCTAGCTTAGCCCGTGTAAAAGCTAGGGA
16734 GTTGTAAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 12 0.44
33 1 0.04
34 14 0.52
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (34 bp):
GTTCTAGCTTAGCCCGTGTAAAAGCTAGGGAAAT
Found at i:19583 original size:102 final size:102
Alignment explanation
Indices: 19390--19633 Score: 280
Period size: 102 Copynumber: 2.4 Consensus size: 102
19380 ATCTCAAGCA
* * *
19390 AAATTGATTTTAAGAAAAACCATCTCAAGT--GATAAATTTTTGTTTCTAGTGAAACAATTTCAA
1 AAATTGATTTTAAGAAAAACCATCTCAAGTGAGATAAATTTTTGTTTCAAGTCAAACAAATTCAA
* *
19453 AATTTGTGTTTTAAGGGAAACCGCCTCAAAAAAGACG
66 AATTTGTATTTCAAGGGAAACCGCCTCAAAAAAGACG
* *
19490 AAATTGATTTTAAGAGAAACCATCTCTAGTGAGATAAATTTTTGTTTCAAGTC-AACAAAATTC-
1 AAATTGATTTTAAGAAAAACCATCTCAAGTGAGATAAATTTTTGTTTCAAGTCAAAC-AAATTCA
* ** * *** *
19553 AAATTTTTATTTCAAGGGAAAATTGTCTCAAGCGAGATG
65 AAATTTGTATTTCAAGGG-AAACCGCCTCAAAAAAGACG
* * *
19592 AAATTTATTTTAAGAAAAATCATCTCAACTGAGATAAATTTT
1 AAATTGATTTTAAGAAAAACCATCTCAAGTGAGATAAATTTT
19634 GATATTTGCT
Statistics
Matches: 120, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
100 28 0.23
101 18 0.15
102 74 0.62
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (102 bp):
AAATTGATTTTAAGAAAAACCATCTCAAGTGAGATAAATTTTTGTTTCAAGTCAAACAAATTCAA
AATTTGTATTTCAAGGGAAACCGCCTCAAAAAAGACG
Found at i:22632 original size:41 final size:41
Alignment explanation
Indices: 22579--22658 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
22569 ATAATACAAG
*
22579 TTAGGTGGGCAAGGCCCAAACTCAGCACTACTGTACAATTA
1 TTAGGTGAGCAAGGCCCAAACTCAGCACTACTGTACAATTA
* * * * *
22620 TTAGGTGAGCAAGGCTCGACCTCAGCACTATTGTGCAAT
1 TTAGGTGAGCAAGGCCCAAACTCAGCACTACTGTACAAT
22659 ATTCGAATCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (41 bp):
TTAGGTGAGCAAGGCCCAAACTCAGCACTACTGTACAATTA
Found at i:26602 original size:55 final size:55
Alignment explanation
Indices: 26517--26658 Score: 162
Period size: 55 Copynumber: 2.6 Consensus size: 55
26507 TGGTTTCTGC
* * *
26517 ACACTTAGTGCCGATAC-AATAATTCATAAACTCATTATAAAGTACATGGGGTTGC
1 ACACATAGTGCCAATACTAA-AATTCATAAACTCATTATAAAGTACATGGGGTTGA
* * * * ***
26572 ACATATAGTTCCAATA-TGAAAATTCATAAACTCATTATGAATTTTGTGGGGTTGA
1 ACACATAGTGCCAATACT-AAAATTCATAAACTCATTATAAAGTACATGGGGTTGA
26627 ACACATAGTGCCAATACTAAAATTCATAAACT
1 ACACATAGTGCCAATACTAAAATTCATAAACT
26659 TGTTATGAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
55 69 0.96
56 3 0.04
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (55 bp):
ACACATAGTGCCAATACTAAAATTCATAAACTCATTATAAAGTACATGGGGTTGA
Found at i:26665 original size:55 final size:55
Alignment explanation
Indices: 26537--26671 Score: 164
Period size: 55 Copynumber: 2.5 Consensus size: 55
26527 CCGATACAAT
* * *** * * *
26537 AATTCATAAACTCATTATAAAGTACATGGGGTTGCACATATAGTTCCAATATGAA
1 AATTCATAAACTCATTATGAATTTTGTGGGGTTGAACACATAGTGCCAATATGAA
26592 AATTCATAAACTCATTATGAATTTTGTGGGGTTGAACACATAGTGCCAATACT-AA
1 AATTCATAAACTCATTATGAATTTTGTGGGGTTGAACACATAGTGCCAATA-TGAA
**
26647 AATTCATAAACTTGTTATGAATTTT
1 AATTCATAAACTCATTATGAATTTT
26672 TTAGGTTGCA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
55 68 0.99
56 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (55 bp):
AATTCATAAACTCATTATGAATTTTGTGGGGTTGAACACATAGTGCCAATATGAA
Found at i:32290 original size:55 final size:55
Alignment explanation
Indices: 32216--32359 Score: 173
Period size: 55 Copynumber: 2.6 Consensus size: 55
32206 ACATGGTTTC
* *
32216 TGCACACTTAGTGTCAATACGATAATTCATAAAATCATTATAAACTACAT-GGGGT
1 TGCACACATAGTGCCAATACGA-AATTCATAAAATCATTATAAACTACATGGGGGT
* * * * * * *
32271 TTCACACATAGTGCCAATACGAAAATGCATAAACTCATTATGAATTTCGTGGGGGT
1 TGCACACATAGTGCCAATACG-AAATTCATAAAATCATTATAAACTACATGGGGGT
32327 TGCACACATAGTGCCAATACGGAAATTCATAAA
1 TGCACACATAGTGCCAATAC-GAAATTCATAAA
32360 CTTGTTATGA
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
55 39 0.52
56 35 0.47
57 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (55 bp):
TGCACACATAGTGCCAATACGAAATTCATAAAATCATTATAAACTACATGGGGGT
Found at i:32360 original size:56 final size:54
Alignment explanation
Indices: 32216--32394 Score: 198
Period size: 56 Copynumber: 3.3 Consensus size: 54
32206 ACATGGTTTC
* * * * * *
32216 TGCACACTTAGTGTCAATAC-GATAATTCATAAAATCATTATAAACTACATGGGGT
1 TGCACACATAGTGCCAATACGGA-AATTCATAAACTCATTATGAATTTC-TGGGGT
* * *
32271 TTCACACATAGTGCCAATACGAAAATGCATAAACTCATTATGAATTTCGTGGGGGT
1 TGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTC-T-GGGGT
** **
32327 TGCACACATAGTGCCAATACGGAAATTCATAAACTTGTTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTGGGGT
32381 TGCACACATAGTGC
1 TGCACACATAGTGC
32395 TCATTCGACA
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
54 17 0.16
55 39 0.37
56 49 0.47
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (54 bp):
TGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTGGGGT
Found at i:35911 original size:17 final size:18
Alignment explanation
Indices: 35878--35919 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
35868 CAGATTCGTG
35878 ATCTAGAAATTGTGTTAAA
1 ATCTAGAAA-TGTGTTAAA
35897 ATCTAGAAA-GTGTTAAA
1 ATCTAGAAATGTGTTAAA
*
35914 GTCTAG
1 ATCTAG
35920 TAAAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.59
19 9 0.41
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (18 bp):
ATCTAGAAATGTGTTAAA
Found at i:39219 original size:95 final size:95
Alignment explanation
Indices: 39093--39282 Score: 263
Period size: 95 Copynumber: 2.0 Consensus size: 95
39083 ATATCGATGA
* * *
39093 GGTAGCATCGATACCATTATAAGGGTATCGATACCAAGCAACATCGAATCTAAAATTGGTATCGA
1 GGTAGCATCGATACCATGATAAGGGTATCGATACCAAGCAACATCGAACCTAAAATTGGTACCGA
* *
39158 TACTAGAAGGGAGTATCGGTACCATAGTAT
66 TACCAGAAGGGAGTATCGATACCATAGTAT
* * * * *
39188 GGTAGTATTGATACCATGGTAAGGGTATCGATACCAGGCAACATCGAACCTAAGATTGGTACCGA
1 GGTAGCATCGATACCATGATAAGGGTATCGATACCAAGCAACATCGAACCTAAAATTGGTACCGA
* * *
39253 TACCGGTAGGGGGTATCGATACCATAGTAT
66 TACCAGAAGGGAGTATCGATACCATAGTAT
39283 AGAAGTATAG
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
95 82 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (95 bp):
GGTAGCATCGATACCATGATAAGGGTATCGATACCAAGCAACATCGAACCTAAAATTGGTACCGA
TACCAGAAGGGAGTATCGATACCATAGTAT
Found at i:39290 original size:95 final size:95
Alignment explanation
Indices: 39102--39316 Score: 261
Period size: 95 Copynumber: 2.3 Consensus size: 95
39092 AGGTAGCATC
** * * *
39102 GATACCATTATAAGGGTATCGATACCAAGCAACATCGAATCTAAAATTGGTATCGATACTAGAAG
1 GATACCATGGTAAGGGTATCGATACCAAGCAACATCGAACCTAAAATTGGTACCGATACCAGAAG
* * * *
39167 GGAGTATCGGTACCATAGTATGGTAGTATT
66 GGAGTATCGATACCATAGTATAGAAGTATA
* * * *
39197 GATACCATGGTAAGGGTATCGATACCAGGCAACATCGAACCTAAGATTGGTACCGATACCGGTAG
1 GATACCATGGTAAGGGTATCGATACCAAGCAACATCGAACCTAAAATTGGTACCGATACCAGAAG
*
39262 GGGGTATCGATACCATAGTATAGAAGTATA
66 GGAGTATCGATACCATAGTATAGAAGTATA
* * *
39292 GGTACCAAGGT-AGTAGTATCGATAC
1 GATACCATGGTAAG-GGTATCGATAC
39317 TATAGAGCCA
Statistics
Matches: 102, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
94 2 0.02
95 100 0.98
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (95 bp):
GATACCATGGTAAGGGTATCGATACCAAGCAACATCGAACCTAAAATTGGTACCGATACCAGAAG
GGAGTATCGATACCATAGTATAGAAGTATA
Found at i:39767 original size:59 final size:59
Alignment explanation
Indices: 39541--39747 Score: 301
Period size: 59 Copynumber: 3.5 Consensus size: 59
39531 TGGGCACTTT
* * * *
39541 TTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTGTGTGCTAAAATG
1 TTAAGAAATTCATACAAAGTGTATGAATTTCCATATTGGGCAATTTGTGTGCTAAAATG
* *
39600 TTTAGAAATTCATA-ATAAGTGTATGAATTTCCATATTGGGCTATTTGTGTGCTAAAATG
1 TTAAGAAATTCATACA-AAGTGTATGAATTTCCATATTGGGCAATTTGTGTGCTAAAATG
* *
39659 TTTAA-AAATTCATACTAAGTGTATGAATTTCCATACTGGGCAATTTGTGTGCTAAAATG
1 -TTAAGAAATTCATACAAAGTGTATGAATTTCCATATTGGGCAATTTGTGTGCTAAAATG
*
39718 TTAAGAAAATCATACAAAGTGTATGAATTT
1 TTAAGAAATTCATACAAAGTGTATGAATTT
39748 TCGTATGGAA
Statistics
Matches: 132, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
58 4 0.03
59 125 0.95
60 3 0.02
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (59 bp):
TTAAGAAATTCATACAAAGTGTATGAATTTCCATATTGGGCAATTTGTGTGCTAAAATG
Found at i:40215 original size:68 final size:68
Alignment explanation
Indices: 40104--40376 Score: 375
Period size: 68 Copynumber: 4.0 Consensus size: 68
40094 AAAGATTAAC
* * *
40104 GGCCTTACTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGAGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
40169 TGA
66 TGA
* * * ** *
40172 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAAGTATGTCAGTTAGATAAAACTCTAAGTGCTTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
*
40237 TCA
66 TGA
* *
40240 GGCCTAATTGTGCATTTGACAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
40305 TGA
66 TGA
* ** * * * *
40308 GGCGTAACTGTGCATTTGACAGAAACATGTCAATCATTCTAGTTAGATGAAATGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
40373 TGA
66 TGA
40376 G
1 G
40377 TAAAAGACAA
Statistics
Matches: 177, Mismatches: 28, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 177 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.29
Consensus pattern (68 bp):
GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
TGA
Found at i:40448 original size:45 final size:44
Alignment explanation
Indices: 40392--40665 Score: 326
Period size: 43 Copynumber: 6.2 Consensus size: 44
40382 GACAAGATGT
* *
40392 ATAAGTGAAATGTAAAATGGTATATAAAAGGCATGAAAGGATGCC
1 ATAAATGAAATGTAAAATGGTGTATAAAAGGCATGAAA-GATGCC
* *
40437 ATAAATGAAATGTAAAATAGTGTATAAAAGGTATGAAAGGATGCC
1 ATAAATGAAATGTAAAATGGTGTATAAAAGGCATGAAA-GATGCC
* *
40482 ATAAATGAAATGTATAATGGTATATAAAAGGCATGAAAGATTG-C
1 ATAAATGAAATGTAAAATGGTGTATAAAAGGCATGAAAGA-TGCC
* * *
40526 TTAAAAGAAATGT-AAATGATGTATAAAAGGCATGAAAGATTG-C
1 ATAAATGAAATGTAAAATGGTGTATAAAAGGCATGAAAGA-TGCC
* *
40569 TTAAAAGAAATGT-AAATGGTGTATAAAAGGCATGAAATGATGCC
1 ATAAATGAAATGTAAAATGGTGTATAAAAGGCATGAAA-GATGCC
* * *
40613 ATAAATG-AA-GTATAATGGTGTATAAAAGGTATGAACAGTTGCC
1 ATAAATGAAATGTAAAATGGTGTATAAAAGGCATGAA-AGATGCC
40656 ATAAATGAAA
1 ATAAATGAAA
40666 AGGCATAATG
Statistics
Matches: 204, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
42 2 0.01
43 100 0.49
44 25 0.12
45 77 0.38
ACGTcount: A:0.47, C:0.05, G:0.22, T:0.25
Consensus pattern (44 bp):
ATAAATGAAATGTAAAATGGTGTATAAAAGGCATGAAAGATGCC
Found at i:40486 original size:22 final size:22
Alignment explanation
Indices: 40415--40486 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
40405 AAAATGGTAT
*
40415 ATAAAAGGCATGAAAGGATGCC
1 ATAAAAGGAATGAAAGGATGCC
* * ** *
40437 ATAAATGAAATGTAAAATAGTG-T
1 ATAAAAGGAATG-AAAGGA-TGCC
*
40460 ATAAAAGGTATGAAAGGATGCC
1 ATAAAAGGAATGAAAGGATGCC
40482 ATAAA
1 ATAAA
40487 TGAAATGTAT
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
21 2 0.06
22 18 0.51
23 13 0.37
24 2 0.06
ACGTcount: A:0.50, C:0.07, G:0.22, T:0.21
Consensus pattern (22 bp):
ATAAAAGGAATGAAAGGATGCC
Found at i:40531 original size:21 final size:21
Alignment explanation
Indices: 40506--40575 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
40496 TAATGGTATA
40506 TAAAAGGCATGAAAGATTGCT
1 TAAAAGGCATGAAAGATTGCT
**
40527 TAAAAGAAATGTAAATGA-TG-T
1 TAAAAGGCATG-AAA-GATTGCT
40548 ATAAAAGGCATGAAAGATTGCT
1 -TAAAAGGCATGAAAGATTGCT
40570 TAAAAG
1 TAAAAG
40576 AAATGTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
20 2 0.05
21 21 0.52
22 15 0.38
23 2 0.05
ACGTcount: A:0.49, C:0.06, G:0.21, T:0.24
Consensus pattern (21 bp):
TAAAAGGCATGAAAGATTGCT
Found at i:40616 original size:22 final size:21
Alignment explanation
Indices: 40505--40617 Score: 86
Period size: 22 Copynumber: 5.2 Consensus size: 21
40495 ATAATGGTAT
40505 ATAAAAGGCATGAAA-GATTGC
1 ATAAAAGGCATGAAATGA-TGC
* ** *
40526 TTAAAAGAAATGTAAATGATGT
1 ATAAAAGGCATG-AAATGATGC
40548 ATAAAAGGCATGAAA-GATTGC
1 ATAAAAGGCATGAAATGA-TGC
* ** * *
40569 TTAAAAGAAATGTAAATGGTGT
1 ATAAAAGGCATG-AAATGATGC
40591 ATAAAAGGCATGAAATGATGCC
1 ATAAAAGGCATGAAATGATG-C
40613 ATAAA
1 ATAAA
40618 TGAAGTATAA
Statistics
Matches: 68, Mismatches: 18, Indels: 11
0.70 0.19 0.11
Matches are distributed among these distances:
20 2 0.03
21 30 0.44
22 33 0.49
23 3 0.04
ACGTcount: A:0.49, C:0.06, G:0.21, T:0.24
Consensus pattern (21 bp):
ATAAAAGGCATGAAATGATGC
Found at i:42079 original size:18 final size:17
Alignment explanation
Indices: 42025--42073 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
42015 TTGGACCCTT
* *
42025 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
42043 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
42061 AGTGCATTCGATG
1 AGTGCA-TCGATG
42074 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:42181 original size:65 final size:65
Alignment explanation
Indices: 42044--42204 Score: 175
Period size: 65 Copynumber: 2.5 Consensus size: 65
42034 GTGCACTAAG
* *
42044 AGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
* * * * * * * *
42108 GGTGCATCGATACATCAAATACATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGTAT-GT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGC
42171 T
65 T
* *
42172 AAGTGCATCGATGCATGAAATGCATTCAATGTT
1 -AGTGCATCGATGCATCAAATGCATTCGATGTT
42205 CAATTTAATT
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
64 28 0.35
65 48 0.61
66 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
Found at i:44377 original size:13 final size:13
Alignment explanation
Indices: 44349--44387 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
44339 TGGACAATGT
*
44349 TTTGAAAA-ACTA
1 TTTGAAAATAATA
44361 TTTGAAAATAATA
1 TTTGAAAATAATA
*
44374 TTTGTAAATAATA
1 TTTGAAAATAATA
44387 T
1 T
44388 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:50759 original size:17 final size:17
Alignment explanation
Indices: 50718--50797 Score: 61
Period size: 19 Copynumber: 4.4 Consensus size: 17
50708 TTGGACCCTT
* *
50718 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
*
50736 GAGTGCATCGATTCATCA
1 -AGTGCATCGATGCATCA
*
50754 AGTGCATTCGATGCATGACT
1 AGTGCA-TCGATGCAT--CA
*
50774 GGTGCATCGATGCATCA
1 AGTGCATCGATGCATCA
*
50791 AATGCAT
1 AGTGCAT
50798 TTGATGTTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
17 12 0.24
18 10 0.20
19 21 0.43
20 6 0.12
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:50909 original size:65 final size:64
Alignment explanation
Indices: 50754--50920 Score: 171
Period size: 65 Copynumber: 2.6 Consensus size: 64
50744 CGATTCATCA
* *
50754 AGTGCATTCGATGCAT-GACTGGTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAAATCC
1 AGTGCA-TCGATGCATGGATTGGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-C
50818 TC
63 TC
* ** * **
50820 AGTGCATCGGTGCATGG-TAAGTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TC
1 AGTGCATCGATGCATGGATTGGTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTC
*
50882 ATGGTGCATCGATGCATGGATTGGTGCATCGGTGCATCA
1 A--GTGCATCGATGCATGGATTGGTGCATCGATGCATCA
50921 CTTTGAAAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 20 0.24
65 50 0.60
66 7 0.08
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (64 bp):
AGTGCATCGATGCATGGATTGGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTC
Found at i:52188 original size:18 final size:18
Alignment explanation
Indices: 52165--52200 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
52155 AAGATAGAGA
52165 GGGTATGGAAATTATAGT
1 GGGTATGGAAATTATAGT
52183 GGGTATGGAAATTATAGT
1 GGGTATGGAAATTATAGT
52201 TTTTAGTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (18 bp):
GGGTATGGAAATTATAGT
Found at i:53591 original size:59 final size:60
Alignment explanation
Indices: 53511--53671 Score: 274
Period size: 59 Copynumber: 2.7 Consensus size: 60
53501 ATGGTACTAA
53511 GTGTGC-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCT-ATATTAGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTCATATTAGGCACTTT
* * *
53569 GTGTGCTAAAATGTTAAAAAATTCATACTAAGTGTATGAATTT-TCGTATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTCATATTAGGCACTTT
53628 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTC
53672 AGTATGGGAA
Statistics
Matches: 96, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
58 7 0.07
59 89 0.93
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (60 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTCATATTAGGCACTTT
Found at i:54140 original size:68 final size:68
Alignment explanation
Indices: 54027--54869 Score: 1265
Period size: 68 Copynumber: 12.4 Consensus size: 68
54017 AAATTATTAA
* * * *
54027 AGGCCTAATTGTGCATTTGACATAAAGGTGTTAATTATGCCAGTTAGATAAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
54092 TTG
66 TTG
* * * * *
54095 AGGCCTAAATGTGCATTTGACAGAAAGGTGTTAATTATGCTAGTTAGATAAAAGGCTAAGTGCAT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
54160 TTG
66 TTG
* *
54163 AGGCCTAAATGTGCATTTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
54228 TTG
66 TTG
* * * *
54231 AGGCCTAACTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCAAAATGCCA
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
54296 TTG
66 TTG
** * * *
54299 AGGCCTAACTGTGTGTTTGACAGAAAGGTGTCAACTATGCCAGTTAGATGGAAGGCTAAGTGTCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
54364 TTG
66 TTG
* *
54367 AGGCCTAACTGTGCATTTGACATAAAGGTGTCAATTATACCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
54432 TTG
66 TTG
* * * * *
54435 ATGCTTAACTGTGCATTTGACAGAAAGGTGTCAATTATTCTAGTTAGATGAAAGGCTAAGTGTCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
54500 TTG
66 TTG
* * *
54503 AGGCCTAACTGTGCATTTGACAGAAAGGTTTCAATTATGCCAGTTACATGAAAGGCTAAGTGCTT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
*
54568 TTC
66 TTG
54571 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
54636 TTG
66 TTG
* * *
54639 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAATTAGATGAAAGGTTATGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
54704 TTG
66 TTG
* * *
54707 AGACCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAACTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
54772 TTG
66 TTG
* * * * *
54775 AGGCCTAACTGTGTATTTGATATAACA-GTGTCAATCATGCTAGTTAGATGAAAGGCTAAGTGCC
1 AGGCCTAACTGTGCATTTGACAGAA-AGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
54839 TTTG
65 TTTG
* * *
54843 AGGCCTAATTTTGCATTTGACACAAAG
1 AGGCCTAACTGTGCATTTGACAGAAAG
54870 TCTTCGACTT
Statistics
Matches: 703, Mismatches: 70, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
67 1 0.00
68 701 1.00
69 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:56076 original size:13 final size:13
Alignment explanation
Indices: 56058--56084 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
56048 CAGAGCCTCT
56058 TATCCTGACATTC
1 TATCCTGACATTC
56071 TATCCTGACATTC
1 TATCCTGACATTC
56084 T
1 T
56085 TGATAGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.30, G:0.07, T:0.41
Consensus pattern (13 bp):
TATCCTGACATTC
Found at i:57439 original size:16 final size:16
Alignment explanation
Indices: 57418--57455 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
57408 GTATCGTTCT
57418 TCATTATGATTTGACA
1 TCATTATGATTTGACA
57434 TCATTATGATTTGACA
1 TCATTATGATTTGACA
57450 TCATTA
1 TCATTA
57456 AAATCCATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (16 bp):
TCATTATGATTTGACA
Found at i:57960 original size:19 final size:19
Alignment explanation
Indices: 57936--57979 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
57926 ATTTTCTATA
*
57936 TAAAGTTTGGTTATAGAAT
1 TAAAGTTTGGTTATAGAAC
57955 TAAAGTTTGGTTATAGAAC
1 TAAAGTTTGGTTATAGAAC
57974 TAAAGT
1 TAAAGT
57980 GTAATACCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (19 bp):
TAAAGTTTGGTTATAGAAC
Found at i:59091 original size:24 final size:24
Alignment explanation
Indices: 59059--59113 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
59049 AAACTCTATC
*
59059 ATTTGGTACCATTATTGCTTGGTA
1 ATTTGGTACCATTATTGCTTGCTA
59083 ATTTGGTACCATTATTGCTTGCTA
1 ATTTGGTACCATTATTGCTTGCTA
59107 ATTTGGT
1 ATTTGGT
59114 TTGTGTTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (24 bp):
ATTTGGTACCATTATTGCTTGCTA
Done.