Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008943.1 Hibiscus syriacus cultivar Beakdansim tig00112264_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: 1742779
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 1 of 5
Found at i:979 original size:23 final size:22
Alignment explanation
Indices: 905--979 Score: 75
Period size: 23 Copynumber: 3.5 Consensus size: 22
895 ACACTAGACA
*
905 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATACAT-CCTTGAAT
* *
928 GTGCATCGATACA-CATT--AG
1 GTGCATCGATACATCCTTGAAT
*
947 GTGCACCGATACACTCCTTGAAT
1 GTGCATCGATACA-TCCTTGAAT
970 GTGCATCGAT
1 GTGCATCGAT
980 GAACAATGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
19 13 0.32
21 6 0.15
23 22 0.54
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (22 bp):
GTGCATCGATACATCCTTGAAT
Found at i:3184 original size:22 final size:22
Alignment explanation
Indices: 3156--3198 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3146 AAGGGGGAGT
3156 ATATAGTAAGGGGGAGTAATTA
1 ATATAGTAAGGGGGAGTAATTA
*
3178 ATATAGTAAGTGGGAGTAATT
1 ATATAGTAAGGGGGAGTAATT
3199 TTTTCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (22 bp):
ATATAGTAAGGGGGAGTAATTA
Found at i:3684 original size:65 final size:65
Alignment explanation
Indices: 3608--3764 Score: 199
Period size: 65 Copynumber: 2.4 Consensus size: 65
3598 CACACCCATT
* * * * *
3608 TCGAATACATTTTTTGTACCGATGCACA-AGCCATGCATCGATGTACTCTTGAATATTTTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAGA-CCATGCATCAATGCACTCCTGAATATTTTGAAAC
3672 A
65 A
** *
3673 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCAATGCACTCCTGGCTCTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCAATGCACTCCTGAATATTTTGAAACA
* * *
3738 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
3765 CCCTAGTGTA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
65 79 0.99
66 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCAATGCACTCCTGAATATTTTGAAACA
Found at i:7617 original size:37 final size:38
Alignment explanation
Indices: 7555--7626 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
7545 TATAATGTAG
*
7555 TTTTTGAAAATATTTTTTGAAAGCATATAACATATAAC
1 TTTTAGAAAATATTTTTTGAAAGCATATAACATATAAC
* *
7593 TTTTAGAAAATGTTTTTT-AAAGCATATAATATAT
1 TTTTAGAAAATATTTTTTGAAAGCATATAACATAT
7627 GGTTTTTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 15 0.48
38 16 0.52
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (38 bp):
TTTTAGAAAATATTTTTTGAAAGCATATAACATATAAC
Found at i:7725 original size:23 final size:23
Alignment explanation
Indices: 7694--7753 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 23
7684 GAAAACATTT
* *
7694 TTTTGAAAACATATAATGTCTAG
1 TTTTGAAAACATATAATATATAG
*
7717 TTTTAAAAACGTATATAATATATAG
1 TTTTGAAAAC--ATATAATATATAG
7742 TTTTGAAAACAT
1 TTTTGAAAACAT
7754 TTTTGAAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 11 0.35
25 20 0.65
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (23 bp):
TTTTGAAAACATATAATATATAG
Found at i:7802 original size:33 final size:33
Alignment explanation
Indices: 7716--7835 Score: 127
Period size: 33 Copynumber: 3.5 Consensus size: 33
7706 ATAATGTCTA
7716 GTTTTAAAAACGTATATAATATATAGTTTTGAAAAC
1 GTTTTAAAAACGTATAT-A-ATATAGTTTTG-AAAC
* * * *
7752 ATTTTTGAAAACG--TATAATATGGTTTTGAAGC
1 -GTTTTAAAAACGTATATAATATAGTTTTGAAAC
*
7784 GTTTTAAAAACGTATATAATATAGTTTTGAAAA
1 GTTTTAAAAACGTATATAATATAGTTTTGAAAC
*
7817 GATTTTGAAAACGTATATA
1 G-TTTTAAAAACGTATATA
7836 GTTTTGAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
31 10 0.14
32 3 0.04
33 27 0.39
34 17 0.24
35 3 0.04
37 10 0.14
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (33 bp):
GTTTTAAAAACGTATATAATATAGTTTTGAAAC
Found at i:7842 original size:18 final size:18
Alignment explanation
Indices: 7819--7853 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
7809 TTTGAAAAGA
*
7819 TTTTGAAAACGTATATAG
1 TTTTGAAAACATATATAG
7837 TTTTGAAAACATATATA
1 TTTTGAAAACATATATA
7854 TATATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (18 bp):
TTTTGAAAACATATATAG
Found at i:7878 original size:50 final size:53
Alignment explanation
Indices: 7784--7886 Score: 142
Period size: 50 Copynumber: 2.0 Consensus size: 53
7774 GTTTTGAAGC
*
7784 GTTTTAAAAACGTATATAATATAGTTTTGAAAAGATTTTGAAAACGT-ATATA
1 GTTTTAAAAACATATATAATATAGTTTTGAAAAGATTTTGAAAACGTAATATA
* *
7836 GTTTTGAAAACATATAT-ATATA-TTTT-AAATGATTTTTGAAAACGTAATATA
1 GTTTTAAAAACATATATAATATAGTTTTGAAAAGA-TTTTGAAAACGTAATATA
7887 CTATATTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
49 5 0.11
50 16 0.35
51 10 0.22
52 15 0.33
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.41
Consensus pattern (53 bp):
GTTTTAAAAACATATATAATATAGTTTTGAAAAGATTTTGAAAACGTAATATA
Found at i:9905 original size:16 final size:16
Alignment explanation
Indices: 9884--9914 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9874 TATTATTTAT
9884 AAACTATATAATATGC
1 AAACTATATAATATGC
9900 AAACTATATAATATG
1 AAACTATATAATATG
9915 TAACACACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (16 bp):
AAACTATATAATATGC
Found at i:9969 original size:13 final size:13
Alignment explanation
Indices: 9951--9975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9941 GCAACATGAC
9951 ATGTAATATGAAA
1 ATGTAATATGAAA
9964 ATGTAATATGAA
1 ATGTAATATGAA
9976 TTAAAATATG
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:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTAATATGAAA
Found at i:10023 original size:20 final size:20
Alignment explanation
Indices: 9977--10014 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
9967 TAATATGAAT
9977 TAAAATATGCCATGCAATAC
1 TAAAATATGCCATGCAATAC
9997 TAAAATATGCCATGCAAT
1 TAAAATATGCCATGCAAT
10015 TATTTAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (20 bp):
TAAAATATGCCATGCAATAC
Found at i:10141 original size:16 final size:16
Alignment explanation
Indices: 10120--10156 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
10110 ATGTATAGAA
10120 ACTATAAATATTATAT
1 ACTATAAATATTATAT
10136 ACTAT--ATATTATAT
1 ACTATAAATATTATAT
*
10150 ATTATAA
1 ACTATAA
10157 TACACCACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
14 13 0.72
16 5 0.28
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (16 bp):
ACTATAAATATTATAT
Found at i:11542 original size:10 final size:9
Alignment explanation
Indices: 11510--11571 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
11500 TCTATTTTCC
11510 CTTTTTTTT
1 CTTTTTTTT
*
11519 GTTTTTTTGT
1 CTTTTTTT-T
11529 -TTTTTTTCT
1 CTTTTTTT-T
11538 CTTTTTCTTT
1 CTTTTT-TTT
*
11548 CTTTTTGTT
1 CTTTTTTTT
*
11557 ATTCTTTTTT
1 CTT-TTTTTT
11567 CTTTT
1 CTTTT
11572 CAAAACTGTG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
9 21 0.49
10 20 0.47
11 2 0.05
ACGTcount: A:0.02, C:0.11, G:0.05, T:0.82
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:12271 original size:6 final size:6
Alignment explanation
Indices: 12256--12325 Score: 54
Period size: 6 Copynumber: 11.3 Consensus size: 6
12246 TCATTTCTCT
* * *
12256 TTTTTA TTTTTC TTTTCTT TTTTGTC TTTTTC TTTTTC -TATTC TTTTCTC
1 TTTTTC TTTTTC TTTT-TC TTTT-TC TTTTTC TTTTTC TTTTTC TTTT-TC
*
12306 GTTTTC TTTTAT- TTTTTC TT
1 TTTTTC TTTT-TC TTTTTC TT
12326 CTTCAAGCAT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
5 5 0.10
6 30 0.59
7 16 0.31
ACGTcount: A:0.04, C:0.14, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:12272 original size:20 final size:20
Alignment explanation
Indices: 12244--12291 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
12234 TTGAACCCTC
*
12244 TTTCATTTCTCTTTTT-TATT
1 TTTCTTTTCT-TTTTTGTATT
*
12264 TTTCTTTTCTTTTTTGTCTT
1 TTTCTTTTCTTTTTTGTATT
12284 TTTCTTTT
1 TTTCTTTT
12292 TCTATTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTCTTTTCTTTTTTGTATT
Found at i:20232 original size:95 final size:95
Alignment explanation
Indices: 20093--20297 Score: 263
Period size: 95 Copynumber: 2.2 Consensus size: 95
20083 ATTCAATTAG
* * * * * *
20093 TATCGATACCA-A-TAAGGTAATATCGATACCATGGTAAGGGTATCGATACTAGGTAACATCGAA
1 TATCGATACCATAGTATGGTAGTACCGATACCATGGAAAGGGTATCGATACCAGGAAACATCGAA
**
20156 TCTAAAATTAGTATCGATACTGGAAGGGAA
66 TCTAAAATTAGTATCGATACCAGAAGGGAA
* *
20186 TATC-AGTACCATAGTATGGTAGTACCGATACCATGGAAAGGGTATCGATACCGGGAAACATTGA
1 TATCGA-TACCATAGTATGGTAGTACCGATACCATGGAAAGGGTATCGATACCAGGAAACATCGA
* **
20250 ATCTAAAATTGGTATCGATACCAGAAGGGGG
65 ATCTAAAATTAGTATCGATACCAGAAGGGAA
20281 TATCGATACCATAGTAT
1 TATCGATACCATAGTAT
20298 AGAAGTATCA
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
92 1 0.01
93 9 0.09
94 1 0.01
95 83 0.87
96 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (95 bp):
TATCGATACCATAGTATGGTAGTACCGATACCATGGAAAGGGTATCGATACCAGGAAACATCGAA
TCTAAAATTAGTATCGATACCAGAAGGGAA
Found at i:20326 original size:20 final size:21
Alignment explanation
Indices: 20280--20331 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
20270 CCAGAAGGGG
20280 GTATCGATACCATAGTATAGAA
1 GTATCGATACCATAG-ATAGAA
* *
20302 GTATCAATACCATAG-TAGTA
1 GTATCGATACCATAGATAGAA
20322 GTATCGATAC
1 GTATCGATAC
20332 TACTGAGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 13 0.48
22 14 0.52
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (21 bp):
GTATCGATACCATAGATAGAA
Found at i:20326 original size:95 final size:95
Alignment explanation
Indices: 20118--20331 Score: 225
Period size: 95 Copynumber: 2.3 Consensus size: 95
20108 GGTAATATCG
* * * * * **
20118 ATACCATGGTAAGGGTATCGATACTAGGTAACATCGAATCTAAAATTAGTATCGATACTGGAAGG
1 ATACCATAGAAAGAGTATCGATACCAGGAAACATCGAATCTAAAATTAGTATCGATACCAGAAGG
* * *
20183 GAATATCAGTACCATAGTATGGTAGTACCG
66 GAATATCAGTACCATAGTATAGAAGTACCA
* * * * *
20213 ATACCATGGAAAGGGTATCGATACCGGGAAACATTGAATCTAAAATTGGTATCGATACCAGAAGG
1 ATACCATAGAAAGAGTATCGATACCAGGAAACATCGAATCTAAAATTAGTATCGATACCAGAAGG
** *
20278 GGGTATC-GATACCATAGTATAGAAGTATCA
66 GAATATCAG-TACCATAGTATAGAAGTACCA
*
20308 ATACCATAG-TAGTAGTATCGATAC
1 ATACCATAGAAAG-AGTATCGATAC
20332 TACTGAGCTT
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
94 3 0.03
95 97 0.97
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (95 bp):
ATACCATAGAAAGAGTATCGATACCAGGAAACATCGAATCTAAAATTAGTATCGATACCAGAAGG
GAATATCAGTACCATAGTATAGAAGTACCA
Found at i:20805 original size:20 final size:20
Alignment explanation
Indices: 20780--20994 Score: 124
Period size: 20 Copynumber: 9.5 Consensus size: 20
20770 ATTAAAATGA
20780 ATGAAAGGATGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
*
20800 ATGAAAGGATGTCGTAATTAAAATGC
1 ATGAAAGGATG-C---ATT--AAGGC
*
20826 ATGAAAGGATGCATTAAGGA
1 ATGAAAGGATGCATTAAGGC
*
20846 ATGAAAGGATGCCATAATTAAAATGC
1 ATGAAAGGATG-C---ATT--AAGGC
*
20872 ATGAAAGGATGCCTTAAGGC
1 ATGAAAGGATGCATTAAGGC
*
20892 ATGAAAGGATGCCATAATTAAAATGC
1 ATGAAAGGATG-C---ATT--AAGGC
20918 ATGAAAGGATGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
** *
20938 ATGAAATAATGTCATAAACTAAAATGC
1 ATGAAAGGATG-CAT----T--AAGGC
*
20965 ATGAAAGGATACATTAAGGC
1 ATGAAAGGATGCATTAAGGC
20985 ATGAAAGGAT
1 ATGAAAGGAT
20995 TCCATAATTT
Statistics
Matches: 153, Mismatches: 17, Indels: 50
0.70 0.08 0.23
Matches are distributed among these distances:
20 67 0.44
21 6 0.04
22 9 0.06
24 8 0.05
25 4 0.03
26 47 0.31
27 12 0.08
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (20 bp):
ATGAAAGGATGCATTAAGGC
Found at i:20828 original size:26 final size:24
Alignment explanation
Indices: 20723--20929 Score: 142
Period size: 20 Copynumber: 9.0 Consensus size: 24
20713 ATTGAATACA
* *
20723 TAATTAAAATGCATGAATGGAGGC
1 TAATTAAAATGCATGAAAGGATGC
*
20747 --ATT--AAGGCATGAAA-GATGTC
1 TAATTAAAATGCATGAAAGGATG-C
*
20767 ATAATTAAAATGAATGAAAGGATGC
1 -TAATTAAAATGCATGAAAGGATGC
*
20792 --ATT--AAGGCATGAAAGGATGTC
1 TAATTAAAATGCATGAAAGGATG-C
20813 GTAATTAAAATGCATGAAAGGATGC
1 -TAATTAAAATGCATGAAAGGATGC
* *
20838 --ATT--AAGGAATGAAAGGATGCC
1 TAATTAAAATGCATGAAAGGATG-C
20859 ATAATTAAAATGCATGAAAGGATGC
1 -TAATTAAAATGCATGAAAGGATGC
* *
20884 --CTT--AAGGCATGAAAGGATGCC
1 TAATTAAAATGCATGAAAGGATG-C
20905 ATAATTAAAATGCATGAAAGGATGC
1 -TAATTAAAATGCATGAAAGGATGC
20930 ATTAAGGCAT
Statistics
Matches: 142, Mismatches: 16, Indels: 49
0.69 0.08 0.24
Matches are distributed among these distances:
19 3 0.02
20 53 0.37
21 3 0.02
22 11 0.08
23 3 0.02
24 8 0.06
25 13 0.09
26 48 0.34
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.23
Consensus pattern (24 bp):
TAATTAAAATGCATGAAAGGATGC
Found at i:20830 original size:46 final size:46
Alignment explanation
Indices: 20721--21012 Score: 435
Period size: 46 Copynumber: 6.3 Consensus size: 46
20711 AAATTGAATA
* *
20721 CATAATTAAAATGCATGAATGGAGGCATTAAGGCATGAAA-GATGT
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
*
20766 CATAATTAAAATGAATGAAAGGATGCATTAAGGCATGAAAGGATGT
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
* * *
20812 CGTAATTAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
* *
20858 CATAATTAAAATGCATGAAAGGATGCCTTAAGGCATGAAAGGATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
**
20904 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAATAATGT
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
* *
20950 CATAAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGAT-T
1 CAT-AATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
*
20996 CCATAATTTAAATGCAT
1 -CATAATTAAAATGCAT
21013 AAATTGATGT
Statistics
Matches: 224, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
45 37 0.17
46 147 0.66
47 40 0.18
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (46 bp):
CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
Found at i:27804 original size:13 final size:13
Alignment explanation
Indices: 27786--27810 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27776 GCAACATGGC
27786 ATGTAATATGAAA
1 ATGTAATATGAAA
27799 ATGTAATATGAA
1 ATGTAATATGAA
27811 TTAAAATATG
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:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTAATATGAAA
Found at i:27948 original size:7 final size:7
Alignment explanation
Indices: 27938--27969 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
27928 ATATAAACTA
27938 TATATAT
1 TATATAT
*
27945 TATATAC
1 TATATAT
27952 TATATAT
1 TATATAT
27959 TATATAT
1 TATATAT
27966 TATA
1 TATA
27970 ATACACCACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (7 bp):
TATATAT
Found at i:38977 original size:10 final size:10
Alignment explanation
Indices: 38954--38982 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
38944 TATGTTTCAC
38954 TTTATTTTTG
1 TTTATTTTTG
38964 -TTATTTTTG
1 TTTATTTTTG
38973 TTTATTTTTG
1 TTTATTTTTG
38983 GCATGTAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (10 bp):
TTTATTTTTG
Found at i:44580 original size:8 final size:8
Alignment explanation
Indices: 44567--44592 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
44557 ATCAAGTAGT
44567 AACATATG
1 AACATATG
44575 AACATATG
1 AACATATG
44583 AACATATG
1 AACATATG
44591 AA
1 AA
44593 ATAGACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.23
Consensus pattern (8 bp):
AACATATG
Found at i:53987 original size:8 final size:8
Alignment explanation
Indices: 53974--54018 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
53964 CTCCTGAATC
53974 TTTTATTT
1 TTTTATTT
53982 TTTTATTT
1 TTTTATTT
53990 ATTTTA---
1 -TTTTATTT
53996 TTTTA-TT
1 TTTTATTT
54003 TTTTATTT
1 TTTTATTT
54011 TTTTATTT
1 TTTTATTT
54019 AGTCAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.15
7 5 0.15
8 18 0.55
9 5 0.15
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTATTT
Found at i:53996 original size:17 final size:17
Alignment explanation
Indices: 53974--54011 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
53964 CTCCTGAATC
53974 TTTTATTTT-TTTATTTA
1 TTTTATTTTATTT-TTTA
53991 TTTTATTTTATTTTTTA
1 TTTTATTTTATTTTTTA
54008 TTTT
1 TTTT
54012 TTTATTTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTATTTTATTTTTTA
Found at i:58895 original size:167 final size:165
Alignment explanation
Indices: 58622--58956 Score: 582
Period size: 167 Copynumber: 2.0 Consensus size: 165
58612 ATTAAAATTC
58622 TTTTAATTTAATTTGTTATATCGAACAACAAAATGTTTTCAACAATCTCCCCCTTTTTGATATAA
1 TTTTAATTTAATTTGTTATATCGAACAACAAAATGTTTTCAACAATCTCCCCCTTTTTGATATAA
*
58687 CAAAACATTTTAAGATTTTCTAATTTCAAAATGAATTTTGATTTTGAAAAATACTA-CCCCCTTA
66 CAAAACATTTTAAGACTTTCTAATTTCAAAATGAATTTTGATTTTGAAAAATACTACCCCCCTTA
58751 CTTTAACACTACTCCTCTTTTAAAAACACAAACAT
131 CTTTAACACTACTCCTCTTTTAAAAACACAAACAT
* *
58786 TTTTAATTTAATTTGTTATATCGAAACAACAAAATGTTTTCAACAATCTCTCCCTTTTTTTTATA
1 TTTTAATTTAATTTGTTATATCG-AACAACAAAATGTTTTCAACAATCTC-CCC-CTTTTTGATA
*
58851 TAACAAAACGTTTTAAGACTTTCTAATTTCAAAATGAATTTTGATTTTGAAAAATACTACTCCCC
63 TAACAAAACATTTTAAGACTTTCTAATTTCAAAATGAATTTTGATTTTGAAAAATACTAC-CCCC
*
58916 CTTACTTTAACACTACTCCTCTTTTAAAAACACAAATAT
127 CTTACTTTAACACTACTCCTCTTTTAAAAACACAAACAT
58955 TT
1 TT
58957 CTCCCCCTTT
Statistics
Matches: 161, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
164 23 0.14
165 26 0.16
166 3 0.02
167 65 0.40
169 44 0.27
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (165 bp):
TTTTAATTTAATTTGTTATATCGAACAACAAAATGTTTTCAACAATCTCCCCCTTTTTGATATAA
CAAAACATTTTAAGACTTTCTAATTTCAAAATGAATTTTGATTTTGAAAAATACTACCCCCCTTA
CTTTAACACTACTCCTCTTTTAAAAACACAAACAT
Found at i:60738 original size:24 final size:23
Alignment explanation
Indices: 60689--60749 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
60679 ATTCCCCTAT
60689 GGGGAATC-AGTT-CCCATTCAAAG
1 GGGGAATCGA-TTCCCCATTC-AAG
*
60712 GGGGAATCGATTCCCCCTTCAAG
1 GGGGAATCGATTCCCCATTCAAG
*
60735 GGGGTATCGATTCCC
1 GGGGAATCGATTCCC
60750 TCTGCCCTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 27 0.79
24 7 0.21
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (23 bp):
GGGGAATCGATTCCCCATTCAAG
Found at i:64702 original size:21 final size:23
Alignment explanation
Indices: 64676--64726 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
64666 AGGGAATTGA
64676 TCCCCCCATG-A-GGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
**
64697 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
64720 TCCCCCC
1 TCCCCCC
64727 CCACAGGGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 8 0.32
22 1 0.04
23 16 0.64
ACGTcount: A:0.20, C:0.41, G:0.22, T:0.18
Consensus pattern (23 bp):
TCCCCCCATGAAGGGGAACCGAT
Found at i:73094 original size:12 final size:12
Alignment explanation
Indices: 73077--73108 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
73067 AAAGCAAAAT
73077 GAATATTGAAAG
1 GAATATTGAAAG
73089 GAATATTGAAAG
1 GAATATTGAAAG
*
73101 GAAAATTG
1 GAATATTG
73109 GCTTGATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (12 bp):
GAATATTGAAAG
Found at i:83065 original size:132 final size:132
Alignment explanation
Indices: 82828--83161 Score: 438
Period size: 132 Copynumber: 2.5 Consensus size: 132
82818 TATAAAACTC
*
82828 GATTCAATCTTCCCTAAAGAATAGTTG-AGTGAATCAAAGTTTCCAGATCTGATCTACCCTGAAG
1 GATTCAATCTTCCCTAAAGAGTAG-TGAAGTGAATCAAAGTTTCCAGATCTGATCTACCCTGAAG
* * ** * * * *
82892 AGAAGTGGAGCATATTTACTTTTTCCAGATTTGATATTCCCTGAGGAGCAGTGGAATAAATCTTC
65 AGAAGCGAAGCATATCCACTTTCTCCAGATTTAATATTCCCTAAGGAGCAGTGGAATAAATCTAC
82957 CTA
130 CTA
* * * * *
82960 GATTCAATTTTCTCTAAAGTGTAGTGAAGTGAATCAATGTTTCCAAATCTGATCTACCCTGAAGA
1 GATTCAATCTTCCCTAAAGAGTAGTGAAGTGAATCAAAGTTTCCAGATCTGATCTACCCTGAAGA
* * * *
83025 GCAGCGAAGCATATCCCCTTTCTCTAGATTTAATCTTCCCTAAGGAGCAGTGGAATAAATCTACC
66 GAAGCGAAGCATATCCACTTTCTCCAGATTTAATATTCCCTAAGGAGCAGTGGAATAAATCTACC
*
83090 TC
131 TA
* * *
83092 GATTCAATCTTCCCTAAAGAGAACTGAAGTGAATCAACA-TTTCTAGATCTGATCTACCCTGAAG
1 GATTCAATCTTCCCTAAAGAGTAGTGAAGTGAATCAA-AGTTTCCAGATCTGATCTACCCTGAAG
83156 AGAAGC
65 AGAAGC
83162 AAAGACAATC
Statistics
Matches: 172, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
131 2 0.01
132 170 0.99
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (132 bp):
GATTCAATCTTCCCTAAAGAGTAGTGAAGTGAATCAAAGTTTCCAGATCTGATCTACCCTGAAGA
GAAGCGAAGCATATCCACTTTCTCCAGATTTAATATTCCCTAAGGAGCAGTGGAATAAATCTACC
TA
Found at i:86738 original size:21 final size:22
Alignment explanation
Indices: 86690--86752 Score: 110
Period size: 21 Copynumber: 2.9 Consensus size: 22
86680 CATCAAGGCC
*
86690 TTTGTTGAAGCCATAAAATCAT
1 TTTGTCGAAGCCATAAAATCAT
86712 TTTGTCGAAGCCATAAAATCA-
1 TTTGTCGAAGCCATAAAATCAT
86733 TTTGTCGAAGCCATAAAATC
1 TTTGTCGAAGCCATAAAATC
86753 TTGCAGTGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
21 20 0.50
22 20 0.50
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (22 bp):
TTTGTCGAAGCCATAAAATCAT
Found at i:92145 original size:54 final size:54
Alignment explanation
Indices: 92081--92423 Score: 373
Period size: 54 Copynumber: 6.4 Consensus size: 54
92071 AGTGTTGATG
* * * ** *
92081 CGGTCGTTCATAAACATATTATGAATTACGTGGGTTGCACACTTAGTGCCTATA
1 CGGTCATTCATCAACATATGATGAATTTTGTGGGTTGCACACTTAGTGCCAATA
** * * * * *
92135 CAATTATTCATCAATATATAATGAAGTTTT-TGGTTTGCACACCTAGTGCCAATA
1 CGGTCATTCATCAACATATGATGAA-TTTTGTGGGTTGCACACTTAGTGCCAATA
*
92189 CGGTCATTCATCAACATATGATGAATTTTGTGGGTTGCACACTTAGTGCCGATA
1 CGGTCATTCATCAACATATGATGAATTTTGTGGGTTGCACACTTAGTGCCAATA
* * * * * *
92243 TGGTCGTTCATTAACATATGATGAATTTTGTGGGTTGCACACTTTGTGTCGATA
1 CGGTCATTCATCAACATATGATGAATTTTGTGGGTTGCACACTTAGTGCCAATA
* * * * * *
92297 CGGTCGTTCGTCAACATATGATGAATTTTGTGGGTTACACACTTTGTGTCGATA
1 CGGTCATTCATCAACATATGATGAATTTTGTGGGTTGCACACTTAGTGCCAATA
* * * * * *
92351 CGGTCGTTCATCAACATATGATGAATTCTATGGGTTACACACTTAGTACCGATA
1 CGGTCATTCATCAACATATGATGAATTTTGTGGGTTGCACACTTAGTGCCAATA
*
92405 CGGTCATTCATCATCATAT
1 CGGTCATTCATCAACATAT
92424 TCCTTTAACA
Statistics
Matches: 250, Mismatches: 37, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
53 4 0.02
54 244 0.98
55 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (54 bp):
CGGTCATTCATCAACATATGATGAATTTTGTGGGTTGCACACTTAGTGCCAATA
Found at i:92269 original size:162 final size:162
Alignment explanation
Indices: 92081--92415 Score: 411
Period size: 162 Copynumber: 2.1 Consensus size: 162
92071 AGTGTTGATG
* * *
92081 CGGTCGTTCATAAACATATTATGAATTACGTGGGTTGCACACTTAGTGCCTATACAATTATTCAT
1 CGGTCGTTCATAAACATATGATGAATTACGTGGGTTGCACACTTAGTGCCGATACAATCATTCAT
* * *
92146 CAATATATAATGAAGTTTT-TGGTTTGCACACCTAGTGCCAATACGGTCATTCATCAACATATGA
66 CAACATATAATGAA-TTTTGTGGGTTACACACCTAGTGCCAATACGGTCATTCATCAACATATGA
* * * *
92210 TGAATTTTGTGGGTTGCACACTTAGTGCCGATA
130 TGAATTCTATGGGTTACACACTTAGTACCGATA
* * ** * * ** * *
92243 TGGTCGTTCATTAACATATGATGAATTTTGTGGGTTGCACACTTTGTGTCGATACGGTCGTTCGT
1 CGGTCGTTCATAAACATATGATGAATTACGTGGGTTGCACACTTAGTGCCGATACAATCATTCAT
* * * * * *
92308 CAACATATGATGAATTTTGTGGGTTACACACTTTGTGTCGATACGGTCGTTCATCAACATATGAT
66 CAACATATAATGAATTTTGTGGGTTACACACCTAGTGCCAATACGGTCATTCATCAACATATGAT
92373 GAATTCTATGGGTTACACACTTAGTACCGATA
131 GAATTCTATGGGTTACACACTTAGTACCGATA
*
92405 CGGTCATTCAT
1 CGGTCGTTCAT
92416 CATCATATTC
Statistics
Matches: 144, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
161 4 0.03
162 140 0.97
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (162 bp):
CGGTCGTTCATAAACATATGATGAATTACGTGGGTTGCACACTTAGTGCCGATACAATCATTCAT
CAACATATAATGAATTTTGTGGGTTACACACCTAGTGCCAATACGGTCATTCATCAACATATGAT
GAATTCTATGGGTTACACACTTAGTACCGATA
Found at i:94627 original size:280 final size:283
Alignment explanation
Indices: 94091--94655 Score: 1048
Period size: 280 Copynumber: 2.0 Consensus size: 283
94081 ACTTGAAATT
94091 CAATTTCTTTTTTTTCCAAATCAGCATAAGATATCTGTCGATCGGAGGCTATCTTTAGATTATCA
1 CAATTTCTTTTTTTTCCAAATCAGCATAAGATA-CTGTCGATCGGAGGCTATCTTTAGATTATCA
94156 TGGATAATATTTACTTTCTCCACCATTTCTTTCATCAAATCTGGGCCAACTAGATCTCGATCTTT
65 TGGATAATATTTACTTTCTCCACCATTTCTTTCATCAAATCTGGGCCAACTAGATCTCGATCTTT
*
94221 GAGTTCAAACTAATTTAATGGCGTTCGACACTTCCTCCTATACAAAGCTTCATACGGGGCCATCT
130 GAGTTCAAACCAATTTAATGGCGTTCGACACTTCCTCCTATACAAAGCTTCATACGGGGCCATCT
*
94286 TAATACTAGATTGGTAACTGTTGTTATAAATAAATTATGCTAAAGAAAAATACATTTCCAATGAT
195 TAATACTAGATTGATAACTGTTGTTATAAATAAATTATGCTAAAGAAAAATACATTTCCAATGAT
94351 CCTTTAAACTCAAT-ACACATGCC
260 CCTTTAAACTCAATAACACATGCC
94374 CAATTTC-TTTTTTTCCAAATCAGCATAAGATA-TGTCGATCGGAGGCTATCTTTAGATTATCAT
1 CAATTTCTTTTTTTTCCAAATCAGCATAAGATACTGTCGATCGGAGGCTATCTTTAGATTATCAT
*
94437 GGATAATATTTACTTTCTCCACCATTTCTTTCATCAAAT-TCGGGCCAACTAGATCTTGATCTTT
66 GGATAATATTTACTTTCTCCACCATTTCTTTCATCAAATCT-GGGCCAACTAGATCTCGATCTTT
94501 GAGTTCAAACCAATTTAATGGCGTTCGACACTTCCTCCTATACAAAGCTTCATACGGGGCCATCT
130 GAGTTCAAACCAATTTAATGGCGTTCGACACTTCCTCCTATACAAAGCTTCATACGGGGCCATCT
*
94566 TAATACTAGATTGATAACTGTTGTTATAAATAAATTATGCTAGAGAAAAATACATTTCCAATGAT
195 TAATACTAGATTGATAACTGTTGTTATAAATAAATTATGCTAAAGAAAAATACATTTCCAATGAT
94631 CCTTTAAACTCAATAACACATGCC
260 CCTTTAAACTCAATAACACATGCC
94655 C
1 C
94656 TTAGCATATC
Statistics
Matches: 276, Mismatches: 4, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
279 1 0.00
280 233 0.84
281 10 0.04
282 25 0.09
283 7 0.03
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (283 bp):
CAATTTCTTTTTTTTCCAAATCAGCATAAGATACTGTCGATCGGAGGCTATCTTTAGATTATCAT
GGATAATATTTACTTTCTCCACCATTTCTTTCATCAAATCTGGGCCAACTAGATCTCGATCTTTG
AGTTCAAACCAATTTAATGGCGTTCGACACTTCCTCCTATACAAAGCTTCATACGGGGCCATCTT
AATACTAGATTGATAACTGTTGTTATAAATAAATTATGCTAAAGAAAAATACATTTCCAATGATC
CTTTAAACTCAATAACACATGCC
Found at i:98817 original size:54 final size:54
Alignment explanation
Indices: 98720--99279 Score: 546
Period size: 54 Copynumber: 10.5 Consensus size: 54
98710 CAAGTAATGC
* * * * * * ** *
98720 CGATACGGTCATTCATAAATATATTATGCATTCA-GTGAGTTGCACAGATAGTGC
1 CGATACGGTCGTTCATCAACATATGATGAATT-ATGTGGGTTGCACACTTAGTGT
* * *
98774 CTATACGGTAGTTCATCAACATATGATGAATTATGTGGTTTGCACACTTAGTGT
1 CGATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACTTAGTGT
** * * ** *
98828 CGATACTATCGTTCATCAAC--AT-ATCAATT-TTTGGGTTATATACTTAGTGT
1 CGATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACTTAGTGT
* * * *
98878 CTATACAGTCGTTCATCAACATATGATGAATT-TCGTGGATTACACACTTAGTG-
1 CGATACGGTCGTTCATCAACATATGATGAATTAT-GTGGGTTGCACACTTAGTGT
* ** * * * *
98931 CTGATACGGTTC-TTCATCAACATTTGATGAATTCCGTGTGTTACATACTTAGTGC
1 C-GATACGG-TCGTTCATCAACATATGATGAATTATGTGGGTTGCACACTTAGTGT
** * *
98986 CGATAAAGTCATTCATCAACATATGATGAATTATGTGGGTTGTACACTTAGTGT
1 CGATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACTTAGTGT
* * *
99040 CGATACGGTCGTTCATCAACATATGATGAATTCTATGGGTTGCACTCTTAGTGT
1 CGATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACTTAGTGT
* * * * **
99094 CGAAATGGTCGTTCATCAACATATGATGAATT-TATGGGTTGTACACTTAGTAC
1 CGATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACTTAGTGT
* *
99147 CGATACGGTCATTCATCAACATATGATGAATTCA-GTGGGTTGTACACTTAGTGT
1 CGATACGGTCGTTCATCAACATATGATGAATT-ATGTGGGTTGCACACTTAGTGT
* * * * * *
99201 CGATGCGGTCGTTCATCAACATATGATGAATTGTGTAGGTTGCTCTCTTAGTGC
1 CGATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACTTAGTGT
99255 CGATACGGTCGTTCATCAACATATG
1 CGATACGGTCGTTCATCAACATATG
99280 TCTTTAAGAG
Statistics
Matches: 418, Mismatches: 75, Indels: 26
0.81 0.14 0.05
Matches are distributed among these distances:
50 33 0.08
51 6 0.01
52 4 0.01
53 57 0.14
54 315 0.75
55 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (54 bp):
CGATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACTTAGTGT
Found at i:99202 original size:161 final size:158
Alignment explanation
Indices: 98776--99279 Score: 588
Period size: 161 Copynumber: 3.1 Consensus size: 158
98766 GATAGTGCCT
* * *
98776 ATACGGTAGTTCATCAACATATGATGAA-TTATGTGGTTTGCACACTTAGTGTCGATACTA-TCG
1 ATACGGTCGTTCATCAACATATGATGAATTTATG-GG-TTGCACACTTAGTGCCGATAC-AGTCA
* ** * * * *
98839 TTCATCAAC--AT-ATCAATTTTTGGGTTATATACTTAGTGTCTATACAGTCGTTCATCAACATA
63 TTCATCAACATATGATGAATTAGTGGGTTGTACACTTAGTGTCGATACGGTCGTTCATCAACATA
* * *
98901 TGATGAATTTCGTGGATTACACACTTAGTGCTG
128 TGATGAATTT-GTGGGTTGCACTCTTAGTGC-G
* ** * * * *
98934 ATACGGTTC-TTCATCAACATTTGATGAATTCCGTGTGTTACATACTTAGTGCCGATAAAGTCAT
1 ATACGG-TCGTTCATCAACATATGATGAATT-TATGGGTTGCACACTTAGTGCCGATACAGTCAT
98998 TCATCAACATATGATGAATTATGTGGGTTGTACACTTAGTGTCGATACGGTCGTTCATCAACATA
64 TCATCAACATATGATGAATTA-GTGGGTTGTACACTTAGTGTCGATACGGTCGTTCATCAACATA
*
99063 TGATGAATTCTATGGGTTGCACTCTTAGTGTCG
128 TGATGAATT-TGTGGGTTGCACTCTTAGTG-CG
* * * * *
99096 AAATGGTCGTTCATCAACATATGATGAATTTATGGGTTGTACACTTAGTACCGATACGGTCATTC
1 ATACGGTCGTTCATCAACATATGATGAATTTATGGGTTGCACACTTAGTGCCGATACAGTCATTC
*
99161 ATCAACATATGATGAATTCAGTGGGTTGTACACTTAGTGTCGATGCGGTCGTTCATCAACATATG
66 ATCAACATATGATGAATT-AGTGGGTTGTACACTTAGTGTCGATACGGTCGTTCATCAACATATG
* *
99226 ATGAATTGTGTAGGTTGCTCTCTTAGTGCCG
130 ATGAATT-TGTGGGTTGCACTCTTAGTG-CG
99257 ATACGGTCGTTCATCAACATATG
1 ATACGGTCGTTCATCAACATATG
99280 TCTTTAAGAG
Statistics
Matches: 293, Mismatches: 41, Indels: 21
0.83 0.12 0.06
Matches are distributed among these distances:
157 1 0.00
158 52 0.18
159 3 0.01
160 4 0.01
161 143 0.49
162 88 0.30
163 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (158 bp):
ATACGGTCGTTCATCAACATATGATGAATTTATGGGTTGCACACTTAGTGCCGATACAGTCATTC
ATCAACATATGATGAATTAGTGGGTTGTACACTTAGTGTCGATACGGTCGTTCATCAACATATGA
TGAATTTGTGGGTTGCACTCTTAGTGCG
Found at i:101705 original size:89 final size:89
Alignment explanation
Indices: 101554--101802 Score: 408
Period size: 89 Copynumber: 2.8 Consensus size: 89
101544 ACACACCCTT
* * *
101554 TTATAGCCAAGTTACCCTAATCATAATAGAGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATATCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
101619 ATTAACTGGAATTTAATAATCCTC
66 ATTAACTGGAATTTAATAATCCTC
* *
101643 TTATATCCAAGTTACCCTAATCACATTAGGGTTTTATTATTTCAAAATAATTAAATCTATATTTA
1 TTATATCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
*
101708 ATTAATTGGAATTTAATAATCCTC
66 ATTAACTGGAATTTAATAATCCTC
* * *
101732 CTGTATCCAAGTTACCCTAATCATATTAGGGATTTTAATATTTCAAATTAATTAAATCTATATTT
1 TTATATCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
101797 AATTAA
65 AATTAA
101803 TTGAAATTAA
Statistics
Matches: 148, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
89 111 0.75
90 37 0.25
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (89 bp):
TTATATCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAACTGGAATTTAATAATCCTC
Found at i:103977 original size:54 final size:54
Alignment explanation
Indices: 103912--104035 Score: 155
Period size: 54 Copynumber: 2.3 Consensus size: 54
103902 ACGTAGCACC
* *
103912 GATACGGTCATTCAT-AAATATATTATGCATTCAGTGGG-T-CACATATATAGTGCT
1 GATACGGTCATTCATCAAA-ATATGATGAATTCAGTGGGTTGCACA-AT-TAGTGCT
* *
103966 TATACGGTCATTCATCAAAATATGATGAATTCAGTGGGTTGCACACTTAGTGCT
1 GATACGGTCATTCATCAAAATATGATGAATTCAGTGGGTTGCACAATTAGTGCT
*
104020 GATACGGTCGTTCATC
1 GATACGGTCATTCATC
104036 TGTTAGAGTA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
54 52 0.85
55 5 0.08
56 4 0.07
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (54 bp):
GATACGGTCATTCATCAAAATATGATGAATTCAGTGGGTTGCACAATTAGTGCT
Found at i:136776 original size:20 final size:20
Alignment explanation
Indices: 136734--136777 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
136724 GATTTTTTTA
* *
136734 TGAATAGGGAACAATACCTG
1 TGAATAGGGAACAATAACAG
* *
136754 TGAATAGTGAATAATAACAG
1 TGAATAGGGAACAATAACAG
136774 TGAA
1 TGAA
136778 AATATCTGTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (20 bp):
TGAATAGGGAACAATAACAG
Found at i:139130 original size:45 final size:45
Alignment explanation
Indices: 139075--139254 Score: 175
Period size: 45 Copynumber: 4.0 Consensus size: 45
139065 TACAACTTTC
* *
139075 TTACCAATATACATATCATTTATCCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTATCATTTATTCCATAAGCTCGTAAGCTTATT
* * * * * * * *
139120 TTATCAATATACTTACCTTTTAATCTAAAAGCTTGTAAGCTTGTT
1 TTACCAATATACTTATCATTTATTCCATAAGCTCGTAAGCTTATT
* * * *
139165 TTACCAACATA-TTATCATTTATTTCCATAAGCACGTGAGCTAATT
1 TTACCAATATACTTATCATTTA-TTCCATAAGCTCGTAAGCTTATT
* ** *
139210 TTACCAATATACTTGT-AAGTATTCCATAATCTCGTAAGCTTATT
1 TTACCAATATACTTATCATTTATTCCATAAGCTCGTAAGCTTATT
139254 T
1 T
139255 GCATACTGAC
Statistics
Matches: 103, Mismatches: 30, Indels: 5
0.75 0.22 0.04
Matches are distributed among these distances:
44 28 0.27
45 72 0.70
46 3 0.03
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (45 bp):
TTACCAATATACTTATCATTTATTCCATAAGCTCGTAAGCTTATT
Found at i:139663 original size:21 final size:20
Alignment explanation
Indices: 139645--139684 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
139635 CGAAATATCA
139645 TTCATGATAAAAATCATATATG
1 TTCATGAT-AAAATCATATA-G
*
139667 TTCATGATAACATCATAT
1 TTCATGATAAAATCATAT
139685 GCAAAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (20 bp):
TTCATGATAAAATCATATAG
Found at i:142049 original size:14 final size:15
Alignment explanation
Indices: 142029--142069 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
142019 GCCTGCCTGA
142029 CTGAGTCAACTCAGG
1 CTGAGTCAACTCAGG
142044 -TGAGTCAACTC-GG
1 CTGAGTCAACTCAGG
*
142057 CTGAATCAACTCA
1 CTGAGTCAACTCA
142070 CTAGGTCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (15 bp):
CTGAGTCAACTCAGG
Found at i:142128 original size:29 final size:28
Alignment explanation
Indices: 142081--142151 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 28
142071 TAGGTCGACT
* *
142081 CGTTAACTTTGACCAAGTCAACCCTTGA
1 CGTTGACTTTAACCAAGTCAACCCTTGA
* *
142109 GCGTTGACTTTAACCTAGTCAACCGTTGA
1 -CGTTGACTTTAACCAAGTCAACCCTTGA
*
142138 CTATTGACTTTAAC
1 C-GTTGACTTTAAC
142152 TTTGACCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
28 1 0.03
29 35 0.97
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.32
Consensus pattern (28 bp):
CGTTGACTTTAACCAAGTCAACCCTTGA
Found at i:144425 original size:47 final size:45
Alignment explanation
Indices: 144357--144481 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
144347 ATAAAATCTA
* *
144357 TTATCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATAT
1 TTATCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* *
144402 TTATCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAC
1 TTATCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
** *
144449 TTGCCA-TTATT-CATAAGCTCGTTAGCTTATTTT
1 TTATCATTTATTCCATAAGCTCGTAAGCTTATTTT
144482 CATACTTACC
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
43 21 0.30
44 3 0.04
45 9 0.13
46 2 0.03
47 36 0.51
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.43
Consensus pattern (45 bp):
TTATCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:144488 original size:38 final size:41
Alignment explanation
Indices: 144370--144494 Score: 112
Period size: 47 Copynumber: 2.9 Consensus size: 41
144360 TCATTTATCC
* * *
144370 CATAAGCTCGTAAGCTTATTTTACCAAAATATTTATCATTTAAATT
1 CATAAGCTCGTAAGCTTATTTTATC--AATACTTACCA-TT--ATT
*
144416 CCATAAGCTCGTAAGCTTATTTTATCAATATACTTGCCATTATT
1 -CATAAGCTCGTAAGCTTATTTTATC-A-ATACTTACCATTATT
*
144460 CATAAGCTCGTTAGCTTA-TTT-TC-ATACTTACCATT
1 CATAAGCTCGTAAGCTTATTTTATCAATACTTACCATT
144495 TATTAACCAA
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
38 11 0.15
41 2 0.03
42 3 0.04
43 17 0.24
44 3 0.04
46 4 0.06
47 31 0.44
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (41 bp):
CATAAGCTCGTAAGCTTATTTTATCAATACTTACCATTATT
Found at i:151282 original size:47 final size:45
Alignment explanation
Indices: 151213--151338 Score: 168
Period size: 47 Copynumber: 2.8 Consensus size: 45
151203 TATAAAATCT
*
151213 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAA-ATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA-CAAATATA
* *
151258 TTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATAAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACAAATATA
*
151305 CTTGCCA-TTATT-CATAAGCTCGTAAGCTTATTTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
151339 CATACTTACC
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
43 22 0.30
44 3 0.04
45 9 0.12
46 5 0.07
47 34 0.47
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACAAATATA
Found at i:160401 original size:16 final size:16
Alignment explanation
Indices: 160380--160412 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
160370 CATAGTTTAA
*
160380 TTAATATTAATTATAT
1 TTAATACTAATTATAT
160396 TTAATACTAATTATAT
1 TTAATACTAATTATAT
160412 T
1 T
160413 AAGAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATACTAATTATAT
Found at i:162594 original size:29 final size:29
Alignment explanation
Indices: 162536--162604 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
162526 ACACAACAAT
*
162536 CCATAACTTTCTAAAATTACTAATTTGATC
1 CCATAACTTTTTAAAATTACTAA-TTGATC
162566 CCATAACTTTTTAAAATTACATAA-TGATC
1 CCATAACTTTTTAAAATTAC-TAATTGATC
*
162595 CC-TAAATTTT
1 CCATAACTTTT
162605 CTAAGGCTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 7 0.19
29 7 0.19
30 19 0.53
31 3 0.08
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.41
Consensus pattern (29 bp):
CCATAACTTTTTAAAATTACTAATTGATC
Found at i:185821 original size:24 final size:24
Alignment explanation
Indices: 185792--185839 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
185782 ACATGATATG
*
185792 GTACATAGATGTTTTATACATCAT
1 GTACATAGATGTATTATACATCAT
185816 GTACATAGATGTATTATACATCAT
1 GTACATAGATGTATTATACATCAT
185840 CTAGAAGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (24 bp):
GTACATAGATGTATTATACATCAT
Found at i:205536 original size:65 final size:64
Alignment explanation
Indices: 205422--205623 Score: 207
Period size: 65 Copynumber: 3.1 Consensus size: 64
205412 AGTGATTCAC
* * *
205422 CGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGCATTTCATG
1 CGATGCACCAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGCATTTGATG
205484 CAT
62 CAT
* *
205487 CGATGCA-TATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGC
1 CGATGCACCA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCATTTGATGC
205550 AT
63 AT
* * * * * *
205552 CGATGCACCAGCCATGCATCGATTCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCAT
1 CGATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTGATGCAT
205616 CGATGCAC
1 CGATGCAC
205624 TAAGGGTCCA
Statistics
Matches: 116, Mismatches: 13, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 47 0.41
65 62 0.53
66 4 0.03
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (64 bp):
CGATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTGATGCAT
Found at i:210547 original size:12 final size:12
Alignment explanation
Indices: 210530--210556 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
210520 ATTATGTTTA
210530 GTGTCTGCTTAT
1 GTGTCTGCTTAT
210542 GTGTCTGCTTAT
1 GTGTCTGCTTAT
210554 GTG
1 GTG
210557 CTAGATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (12 bp):
GTGTCTGCTTAT
Found at i:213074 original size:21 final size:21
Alignment explanation
Indices: 213032--213075 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
213022 ACTCTAGGAG
* *
213032 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
213053 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
213074 CT
1 CT
213076 CCTCCAGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:213635 original size:2 final size:2
Alignment explanation
Indices: 213628--213670 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
213618 TAGCTTAAAC
213628 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
213670 T
1 T
213671 TTAATCAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:214232 original size:65 final size:63
Alignment explanation
Indices: 214144--214268 Score: 144
Period size: 65 Copynumber: 1.9 Consensus size: 63
214134 ATGCACCAAT
* *
214144 CCATGCATCGATGCACCATGATTTAAATTG-AACAGCGAATGCATTTCATGCATCGATGCATATA
1 CCATGCACCGATGCACCAGGATTT-AA-TGAAACAGCGAATGCATTTCATGCATCGATGCATATA
* * * * *
214208 CCATGCACCGATGCACTGAGGATTTTATGAAAACATCGAATGTATTTGATGCATCGATGCA
1 CCATGCACCGATGCAC-CAGGATTTAATG-AAACAGCGAATGCATTTCATGCATCGATGCA
214269 CCAGCCATGC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
63 2 0.04
64 16 0.31
65 33 0.65
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (63 bp):
CCATGCACCGATGCACCAGGATTTAATGAAACAGCGAATGCATTTCATGCATCGATGCATATA
Found at i:214277 original size:65 final size:64
Alignment explanation
Indices: 214174--214330 Score: 183
Period size: 65 Copynumber: 2.4 Consensus size: 64
214164 ATTTAAATTG
* * *
214174 AACAGCGAATGCATTTCATGCATCGATGCATATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACATACCATGCACCGATGCACTGAGGATATTT-TG-
214238 A
64 A
* * * ** *
214239 AACATCGAATGTATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACTTTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CATACCATGCACCGATGCACTGAGGATATTTTGA
*
214303 AACATCGAATGCACTTGATGCATCGATG
1 AACATCGAATGCATTTGATGCATCGATG
214331 AACTCTTACT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 27 0.34
65 48 0.61
66 4 0.05
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACATACCATGCACCGATGCACTGAGGATATTTTGA
Found at i:214349 original size:64 final size:65
Alignment explanation
Indices: 214174--214353 Score: 161
Period size: 65 Copynumber: 2.8 Consensus size: 65
214164 ATTTAAATTG
* * * * * *
214174 AACAGCGAATGCATTTCATGCATCGATGCA-TATACCATGCACCGATGCACTGAGGATTTTATGA
1 AACATCGAATGCACTTGATGCATCGATGAACCAGA-CATGCACCGATGCACTGAGGATTTTATGA
214238 A
65 A
* * * * * ** *
214239 AACATCGAATGTATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTTTGGCTATTT-TG-
1 AACATCGAATGCACTTGATGCATCGATGAACCAGACATGCACCGATGCACTGAGGAT-TTTATGA
214302 A
65 A
**
214303 AACATCGAATGCACTTGATGCATCGATGAACTCTTAC-TGCACCGATGCACT
1 AACATCGAATGCACTTGATGCATCGATGAAC-CAGACATGCACCGATGCACT
214354 CTTAGTGCAC
Statistics
Matches: 95, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
64 42 0.44
65 49 0.52
66 4 0.04
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCACTTGATGCATCGATGAACCAGACATGCACCGATGCACTGAGGATTTTATGAA
Found at i:214369 original size:19 final size:19
Alignment explanation
Indices: 214321--214372 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
214311 ATGCACTTGA
* *
214321 TGCATCGATGAACTCTTAC
1 TGCACCGATGCACTCTTAC
*
214340 TGCACCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAC
214359 TGCACCGATGCACT
1 TGCACCGATGCACT
214373 AAGGGTCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (19 bp):
TGCACCGATGCACTCTTAC
Found at i:221514 original size:54 final size:54
Alignment explanation
Indices: 221498--221660 Score: 310
Period size: 54 Copynumber: 3.0 Consensus size: 54
221488 ACACTTAGTA
221498 CCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
1 CCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
*
221552 CCAGTACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
1 CCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
221606 CCAATACGGAAATTCATAAACTTATTATGAATTTC-TAAGTTGCACACACAGTG
1 CCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
221659 CC
1 CC
221661 CATGTGGTAA
Statistics
Matches: 107, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
53 20 0.19
54 87 0.81
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (54 bp):
CCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
Found at i:231279 original size:40 final size:40
Alignment explanation
Indices: 231235--231361 Score: 102
Period size: 40 Copynumber: 3.2 Consensus size: 40
231225 GTTCATTAAG
231235 AAATAGGTTGTGATATGTAATTTTAATATTTTTATTAATA
1 AAATAGGTTGTGATATGTAATTTTAATATTTTTATTAATA
* * * * * * *
231275 AAATAGGTTGCG-TCCAAG-AA-TGTCATA-ATTTACTAA-G
1 AAATAGGTTGTGAT--ATGTAATTTTAATATTTTTATTAATA
* * *
231312 AAATAGGTTGTGATCTGTAATGTTAATATTTTTATTAGTA
1 AAATAGGTTGTGATATGTAATTTTAATATTTTTATTAATA
*
231352 AAATAAGTTG
1 AAATAGGTTG
231362 CACCAAATAA
Statistics
Matches: 62, Mismatches: 18, Indels: 14
0.66 0.19 0.15
Matches are distributed among these distances:
36 1 0.02
37 13 0.21
38 12 0.19
39 12 0.19
40 22 0.35
41 2 0.03
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.42
Consensus pattern (40 bp):
AAATAGGTTGTGATATGTAATTTTAATATTTTTATTAATA
Found at i:231293 original size:77 final size:76
Alignment explanation
Indices: 231212--231390 Score: 241
Period size: 77 Copynumber: 2.3 Consensus size: 76
231202 TGATTGTGTT
* * *
231212 CAAGAATATCATGGTTCATTAAGAAATAGGTTGTGATATGTAATTTTAATATTTTTATTAATAAA
1 CAAGAATGTCATGGTTCACTAAGAAATAGGTTGTGATATGTAATGTTAATATTTTTATTAATAAA
* *
231277 ATAGGTTGCGTC
66 ATAAGTTGC-AC
** * * *
231289 CAAGAATGTCATAATTTACTAAGAAATAGGTTGTGATCTGTAATGTTAATATTTTTATTAGTAAA
1 CAAGAATGTCATGGTTCACTAAGAAATAGGTTGTGATATGTAATGTTAATATTTTTATTAATAAA
231354 ATAAGTTGCAC
66 ATAAGTTGCAC
*
231365 CAAATAATGTCATGGTTCACTAAGAA
1 C-AAGAATGTCATGGTTCACTAAGAA
231391 TATTAATATT
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
76 2 0.02
77 85 0.98
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.37
Consensus pattern (76 bp):
CAAGAATGTCATGGTTCACTAAGAAATAGGTTGTGATATGTAATGTTAATATTTTTATTAATAAA
ATAAGTTGCAC
Found at i:232180 original size:29 final size:29
Alignment explanation
Indices: 232144--232337 Score: 110
Period size: 29 Copynumber: 6.7 Consensus size: 29
232134 ATAAATTACT
*
232144 TTTTTATAAATTACATTTAA-GGACAAAGA
1 TTTTTATAAATTACA-ATAATGGACAAAGA
* * **
232173 TTTTTATAAACTATAATAATGGACAAATC
1 TTTTTATAAATTACAATAATGGACAAAGA
* * * **
232202 TTTTTATAAATTATAATAGA-AGATAAATC
1 TTTTTATAAATTACAATA-ATGGACAAAGA
* * **
232231 TTCTTATAAATTACAATAAAGGACAAATC
1 TTTTTATAAATTACAATAATGGACAAAGA
* * * * *
232260 TTTTTATAATTTAAAATAGA-GAAAAAAATA
1 TTTTTATAAATTACAATA-ATG-GACAAAGA
* *
232290 TTTTTATAAATTACAATAAT-GACATATA
1 TTTTTATAAATTACAATAATGGACAAAGA
232318 TTTTT-TGCAAATTACAATAA
1 TTTTTAT--AAATTACAATAA
232338 CAACTCATAA
Statistics
Matches: 134, Mismatches: 23, Indels: 16
0.77 0.13 0.09
Matches are distributed among these distances:
27 1 0.01
28 14 0.10
29 96 0.72
30 23 0.17
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (29 bp):
TTTTTATAAATTACAATAATGGACAAAGA
Found at i:232206 original size:58 final size:58
Alignment explanation
Indices: 232144--232308 Score: 152
Period size: 58 Copynumber: 2.8 Consensus size: 58
232134 ATAAATTACT
* * * * *
232144 TTTTTATAAATTACATTTA-AGGACAAAGATTTTTATAAACTATAATAATGGACAAATC
1 TTTTTATAAATTACA-ATAGAAGACAAAGATTCTTATAAACTACAATAAAGGACAAATC
* * ** *
232202 TTTTTATAAATTATAATAGAAGATAAATCTTCTTATAAATTACAATAAAGGACAAATC
1 TTTTTATAAATTACAATAGAAGACAAAGATTCTTATAAACTACAATAAAGGACAAATC
* * * * * * *
232260 TTTTTATAATTTAAAATAGAGAAAAAAATATTTTTATAAATTACAATAA
1 TTTTTATAAATTACAATAGA-AGACAAAGATTCTTATAAACTACAATAA
232309 TGACATATAT
Statistics
Matches: 89, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
57 2 0.02
58 63 0.71
59 24 0.27
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (58 bp):
TTTTTATAAATTACAATAGAAGACAAAGATTCTTATAAACTACAATAAAGGACAAATC
Found at i:232322 original size:58 final size:57
Alignment explanation
Indices: 232172--232322 Score: 176
Period size: 58 Copynumber: 2.6 Consensus size: 57
232162 AAGGACAAAG
* * * * *
232172 ATTTTTATAAACTATAATAATGGACAAATCTTTTTATAAATTATAATAGAAGATAAAT
1 ATTTTTATAAATTACAATAAT-GACAAATCTTTTTATAAATTAAAATAGAAAAAAAAT
* * * *
232230 CTTCTTATAAATTACAATAAAGGACAAATCTTTTTATAATTTAAAATAGAGAAAAAAAT
1 ATTTTTATAAATTACAAT-AATGACAAATCTTTTTATAAATTAAAATAGA-AAAAAAAT
* *
232289 ATTTTTATAAATTACAATAATGACATATATTTTT
1 ATTTTTATAAATTACAATAATGACAAATCTTTTT
232323 TGCAAATTAC
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
58 53 0.69
59 24 0.31
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.40
Consensus pattern (57 bp):
ATTTTTATAAATTACAATAATGACAAATCTTTTTATAAATTAAAATAGAAAAAAAAT
Found at i:232379 original size:28 final size:28
Alignment explanation
Indices: 232287--232379 Score: 98
Period size: 28 Copynumber: 3.3 Consensus size: 28
232277 AGAGAAAAAA
* ** *
232287 ATATTTTTATAAATTACAATAATGACAT
1 ATATTTTTACAAATTACAATAACAACCT
*
232315 ATATTTTTTGCAAATTACAATAACAA-CT
1 ATA-TTTTTACAAATTACAATAACAACCT
* *
232343 CATAATTTTACATATTACAATAACAACCT
1 -ATATTTTTACAAATTACAATAACAACCT
232372 ATATTTTT
1 ATATTTTT
232380 GCAATCACTA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
28 30 0.57
29 23 0.43
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.42
Consensus pattern (28 bp):
ATATTTTTACAAATTACAATAACAACCT
Found at i:235344 original size:5 final size:5
Alignment explanation
Indices: 235334--235387 Score: 72
Period size: 5 Copynumber: 10.4 Consensus size: 5
235324 AAGAGAAAAC
* *
235334 AAGAA AAGAAA GAAGAA AAGAA AAGAA AAGAG AAGAG AAGAA AAGAA AAGAA
1 AAGAA AAG-AA -AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
235386 AA
1 AA
235388 ATTAATTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 38 0.84
6 4 0.09
7 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:235352 original size:20 final size:18
Alignment explanation
Indices: 235324--235388 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
235314 GAAAGATCAT
235324 AAGAGAAAACAAGAAAAGA
1 AAGAGAAAA-AAGAAAAGA
*
235343 AAGA-AGAAAAGAAAAGAA
1 AAGAGAAAAAAGAAAAG-A
*
235361 AAGAGAAGAGAAGAAAAGA
1 AAGAGAA-AAAAGAAAAGA
235380 AA-AGAAAAA
1 AAGAGAAAAA
235389 TTAATTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 10 0.26
18 12 0.31
19 8 0.21
20 9 0.23
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (18 bp):
AAGAGAAAAAAGAAAAGA
Found at i:235372 original size:25 final size:24
Alignment explanation
Indices: 235340--235387 Score: 87
Period size: 25 Copynumber: 2.0 Consensus size: 24
235330 AAACAAGAAA
235340 AGAAAGAAGAAAAGAAAAGAAAAG
1 AGAAAGAAGAAAAGAAAAGAAAAG
235364 AGAAGAGAAGAAAAGAAAAGAAAA
1 AGAA-AGAAGAAAAGAAAAGAAAA
235388 ATTAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (24 bp):
AGAAAGAAGAAAAGAAAAGAAAAG
Found at i:243125 original size:46 final size:47
Alignment explanation
Indices: 243072--243184 Score: 131
Period size: 46 Copynumber: 2.4 Consensus size: 47
243062 GTAACCATGC
243072 AAATAAGCTTATGAGCTTACGGAA-T-AATGGCAAGTATATTGAAAAA
1 AAATAAGCTTATGAGCTTACGGAATTAAATGGCAAGTATATTG-AAAA
** * * * **
243118 AAATAAGCTTACAAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTACGGAA-TTAAATGGCAAGTATATTGAAAA
243166 AAATAAGCTTATGAGCTTA
1 AAATAAGCTTATGAGCTTA
243185 TGGGATAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
46 21 0.38
48 20 0.36
49 14 0.25
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (47 bp):
AAATAAGCTTATGAGCTTACGGAATTAAATGGCAAGTATATTGAAAA
Found at i:243183 original size:48 final size:46
Alignment explanation
Indices: 243072--243192 Score: 136
Period size: 48 Copynumber: 2.6 Consensus size: 46
243062 GTAACCATGC
*
243072 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAAA
** * * **
243118 AAATAAGCTTACAAGCTTATGGAATTTAAATGGTAAGTATTTTG-GTAA
1 AAATAAGCTTATGAGCTTATGGAA--T-AATGGCAAGTATATTGAAAAA
*
243166 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
243193 AAGGTAAGAA
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
45 2 0.03
46 22 0.35
48 24 0.39
49 14 0.23
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (46 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAAA
Found at i:252295 original size:18 final size:16
Alignment explanation
Indices: 252252--252282 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
252242 ATCATCCATG
252252 CACACTTTCACTTATT
1 CACACTTTCACTTATT
252268 CACACTTTCACTTAT
1 CACACTTTCACTTAT
252283 ATATACACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (16 bp):
CACACTTTCACTTATT
Found at i:253931 original size:13 final size:14
Alignment explanation
Indices: 253913--253947 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
253903 TAAGATTTTC
253913 TTTGAAAATC-ATT
1 TTTGAAAATCAATT
253926 TTTG-AAATCAATT
1 TTTGAAAATCAATT
253939 TTTGAAAAT
1 TTTGAAAAT
253948 TACTCTCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 11 0.55
14 4 0.20
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (14 bp):
TTTGAAAATCAATT
Found at i:263187 original size:22 final size:21
Alignment explanation
Indices: 263157--263198 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
263147 ATAAACATTT
*
263157 TTTATTATTATAAAAAATCATA
1 TTTAATATTAT-AAAAATCATA
*
263179 TTTAATATTCTAAAAATCAT
1 TTTAATATTATAAAAATCAT
263199 TTAAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTAATATTATAAAAATCATA
Found at i:267540 original size:75 final size:75
Alignment explanation
Indices: 267399--267540 Score: 160
Period size: 75 Copynumber: 1.9 Consensus size: 75
267389 ATTGACAAAA
* * * ** * ** *
267399 TTGAAAGATTGGTGGCAAAAGTATAAGGACTAAATAATTAGATTGTCATTGATATAATTTACTCT
1 TTGAAAGATTGATGGCAAAAGTAAAAGGACTAAATAATTAAATAATCATTGATAAAATCCAATCT
267464 TTTTTTAGTG
66 TTTTTTAGTG
* * *
267474 TTGAAAGATTGATGGCAAAAGTAAAATGACTAAATAGTTTAAATAATTATTGA-AAAATCCAATC
1 TTGAAAGATTGATGGCAAAAGTAAAAGGACTAAATA-ATTAAATAATCATTGATAAAATCCAATC
267538 TTT
65 TTT
267541 CCAATCAGGG
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
75 43 0.80
76 11 0.20
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (75 bp):
TTGAAAGATTGATGGCAAAAGTAAAAGGACTAAATAATTAAATAATCATTGATAAAATCCAATCT
TTTTTTAGTG
Found at i:269704 original size:19 final size:20
Alignment explanation
Indices: 269661--269706 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
269651 TACTATATTG
* * *
269661 GAAATTAATTTTAGAGTGTT
1 GAAATTGATGTTAGAATGTT
269681 GAAATTGATGTTAGAATG-T
1 GAAATTGATGTTAGAATGTT
269700 GAAATTG
1 GAAATTG
269707 GGTCATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:271125 original size:34 final size:34
Alignment explanation
Indices: 271087--271169 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 34
271077 CATAATTGGT
271087 AGCACTAGAGTGTATAGAAAAGACACATAGTAC-A
1 AGCACTAGAGTGTATA-AAAAGACACATAGTACAA
* * *
271121 AGCACTATAGTGTAT-AAGAGACACATAGTGCAA
1 AGCACTAGAGTGTATAAAAAGACACATAGTACAA
*
271154 AACACTAGAGTGTATA
1 AGCACTAGAGTGTATA
271170 CCCATGACAG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 14 0.33
33 14 0.33
34 14 0.33
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.20
Consensus pattern (34 bp):
AGCACTAGAGTGTATAAAAAGACACATAGTACAA
Found at i:271881 original size:18 final size:18
Alignment explanation
Indices: 271855--271907 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
271845 ATTTTATACT
*
271855 ACATCTTAACTTAAATTC
1 ACATCTTAACTTAAATTA
* * *
271873 ACATATTAAATTAAACTA
1 ACATCTTAACTTAAATTA
271891 ACATCTTAACATTAAAT
1 ACATCTTAAC-TTAAAT
271908 ATATATATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (18 bp):
ACATCTTAACTTAAATTA
Found at i:271913 original size:2 final size:2
Alignment explanation
Indices: 271906--271935 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
271896 TTAACATTAA
271906 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
271936 TAGTTTAACT
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:272013 original size:26 final size:28
Alignment explanation
Indices: 271984--272041 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
271974 AATTTTAATT
271984 TAACTTAAA-A-ATATAATATATTCTTA
1 TAACTTAAATATATATAATATATTCTTA
* * *
272010 TAACTTAAATATTTATATTTTATTCTTA
1 TAACTTAAATATATATAATATATTCTTA
272038 TAAC
1 TAAC
272042 ATTTTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
27 1 0.04
28 17 0.63
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (28 bp):
TAACTTAAATATATATAATATATTCTTA
Found at i:272094 original size:31 final size:31
Alignment explanation
Indices: 272042--272101 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
272032 TTCTTATAAC
* * *
272042 ATTTTTAAATTAAGATAATAATAAAATATGT
1 ATTTCTAAACTAAAATAATAATAAAATATGT
272073 ATTTCTAAACTAAAATAATAATAAAATAT
1 ATTTCTAAACTAAAATAATAATAAAATAT
272102 AAATTTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (31 bp):
ATTTCTAAACTAAAATAATAATAAAATATGT
Found at i:272111 original size:18 final size:18
Alignment explanation
Indices: 272090--272152 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
272080 AACTAAAATA
*
272090 ATAATAAAATATAAATTT
1 ATAATAAAATATATATTT
272108 ATAAATAAAA-ATATATATT
1 AT-AATAAAATATATAT-TT
272127 A-AATTAAAATATATATTT
1 ATAA-TAAAATATATATTT
*
272145 ATATTAAA
1 ATAATAAA
272153 GTAAGAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 2 0.05
18 19 0.50
19 17 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATAAAATATATATTT
Found at i:272116 original size:19 final size:19
Alignment explanation
Indices: 272092--272147 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
272082 CTAAAATAAT
*
272092 AATAAAATATAAATTTATA
1 AATAAAATATATATTTATA
272111 AATAAAA-ATATATATTA-A
1 AATAAAATATATAT-TTATA
*
272129 ATTAAAATATATATTTATA
1 AATAAAATATATATTTATA
272148 TTAAAGTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAAAATATATATTTATA
Found at i:272120 original size:31 final size:30
Alignment explanation
Indices: 272036--272117 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 30
272026 ATTTTATTCT
* *
272036 TATAACATTTTTAAATTAAGATAATAATAAAA
1 TATAA-ATTTATAAA-TAAAATAATAATAAAA
** *
272068 TATGTATTTCTAAACTAAAATAATAATAAAA
1 TATAAATTTATAAA-TAAAATAATAATAAAA
272099 TATAAATTTATAAATAAAA
1 TATAAATTTATAAATAAAA
272118 ATATATATTA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 5 0.12
31 34 0.81
32 3 0.07
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (30 bp):
TATAAATTTATAAATAAAATAATAATAAAA
Found at i:272135 original size:17 final size:17
Alignment explanation
Indices: 272109--272143 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
272099 TATAAATTTA
272109 TAAATAAAAATATATAT
1 TAAATAAAAATATATAT
*
272126 TAAATTAAAATATATAT
1 TAAATAAAAATATATAT
272143 T
1 T
272144 TATATTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATAAAAATATATAT
Found at i:272169 original size:21 final size:20
Alignment explanation
Indices: 272116--272170 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 20
272106 TTATAAATAA
*
272116 AAATATATATTAAATTAAAAT
1 AAAT-TATATTAAAGTAAAAT
272137 ATATATTTATATTAAAGTAAGAAT
1 A-A-A-TTATATTAAAGTAA-AAT
272161 AAATTATATT
1 AAATTATATT
272171 TTTCTAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
21 8 0.28
22 2 0.07
23 14 0.48
24 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (20 bp):
AAATTATATTAAAGTAAAAT
Found at i:273570 original size:3 final size:3
Alignment explanation
Indices: 273562--273596 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
273552 AATAGAAAGT
273562 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
273597 GTTAAAGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:277849 original size:12 final size:12
Alignment explanation
Indices: 277832--277856 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
277822 AAACAGTATC
277832 AATACCCAATGA
1 AATACCCAATGA
277844 AATACCCAATGA
1 AATACCCAATGA
277856 A
1 A
277857 CTAGTATCAA
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:0.52, C:0.24, G:0.08, T:0.16
Consensus pattern (12 bp):
AATACCCAATGA
Found at i:277945 original size:20 final size:20
Alignment explanation
Indices: 277916--277962 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
277906 AGAACAATAT
* *
277916 CGATAGTGTTCATCTAGTAC
1 CGATACTGTTAATCTAGTAC
*
277936 CGATACTGTTAATTTAGTAC
1 CGATACTGTTAATCTAGTAC
*
277956 CTATACT
1 CGATACT
277963 CAAGCCCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (20 bp):
CGATACTGTTAATCTAGTAC
Found at i:285483 original size:21 final size:21
Alignment explanation
Indices: 285457--285511 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
285447 GGGCTCGTGC
*
285457 TGGTGTTGGTTGTTCTTCGGT
1 TGGTGTTGGTTGTTCTTCCGT
285478 TGGTGTTGGTTGTTCTTCCGT
1 TGGTGTTGGTTGTTCTTCCGT
* *
285499 TGGAGTGGGTTGT
1 TGGTGTTGGTTGT
285512 ACAGGAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.02, C:0.09, G:0.40, T:0.49
Consensus pattern (21 bp):
TGGTGTTGGTTGTTCTTCCGT
Found at i:289833 original size:2 final size:2
Alignment explanation
Indices: 289828--289883 Score: 103
Period size: 2 Copynumber: 27.5 Consensus size: 2
289818 CGTGTGTGTG
289828 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
289870 TA TA TA TA TGA TA T
1 TA TA TA TA T-A TA T
289884 GCTTGTTTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 51 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:303534 original size:20 final size:20
Alignment explanation
Indices: 303511--303548 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
303501 GGTTATAAAT
303511 ATTATAATATAATTATTACG
1 ATTATAATATAATTATTACG
* *
303531 ATTATATTATTATTATTA
1 ATTATAATATAATTATTA
303549 TAACAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
ATTATAATATAATTATTACG
Found at i:303541 original size:3 final size:3
Alignment explanation
Indices: 303531--303594 Score: 51
Period size: 3 Copynumber: 22.0 Consensus size: 3
303521 AATTATTACG
* ** * * *
303531 ATT A-T ATT ATT ATT ATT ATA ACA ATT A-T ATT ATA ATA ATT ATT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
303577 ATT ATT ATT AGT ATT ATT
1 ATT ATT ATT ATT ATT ATT
303595 TATGTTTTCT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 4 0.08
3 45 0.92
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (3 bp):
ATT
Found at i:303557 original size:23 final size:23
Alignment explanation
Indices: 303509--303572 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
303499 CCGGTTATAA
* *
303509 ATATTATAATATAATTATTACGATT
1 ATATTAT-A-ATAATTATAACAATT
* *
303534 ATATTATTATTATTATAACAATT
1 ATATTATAATAATTATAACAATT
303557 ATATTATAATAATTAT
1 ATATTATAATAATTAT
303573 TAGTATTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 26 0.79
25 7 0.21
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (23 bp):
ATATTATAATAATTATAACAATT
Found at i:303580 original size:23 final size:22
Alignment explanation
Indices: 303509--303586 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 22
303499 CCGGTTATAA
303509 ATATTATAATATAATTATTACGATT
1 ATATTAT-A-ATAATTATTA-GATT
* * * *
303534 ATATTATTATTATTATAACAATT
1 ATATTATAATAATTATTA-GATT
303557 ATATTATAATAATTATTAGTATT
1 ATATTATAATAATTATTAG-ATT
303580 ATTATTA
1 A-TATTA
303587 GTATTATTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
23 31 0.72
24 5 0.12
25 7 0.16
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (22 bp):
ATATTATAATAATTATTAGATT
Found at i:303583 original size:12 final size:12
Alignment explanation
Indices: 303522--303594 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
303512 TTATAATATA
303522 ATTATTACG-ATT
1 ATTATTA-GTATT
*
303534 A-TATTATTATT
1 ATTATTAGTATT
* **
303545 ATTATAACAATT
1 ATTATTAGTATT
*
303557 A-TATTA-TAATA
1 ATTATTAGT-ATT
303568 ATTATTAGTATT
1 ATTATTAGTATT
303580 ATTATTAGTATT
1 ATTATTAGTATT
303592 ATT
1 ATT
303595 TATGTTTTCT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
11 16 0.33
12 31 0.65
13 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (12 bp):
ATTATTAGTATT
Found at i:303929 original size:12 final size:12
Alignment explanation
Indices: 303912--303936 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
303902 AAATATGGAC
303912 CTACTGCCCATG
1 CTACTGCCCATG
303924 CTACTGCCCATG
1 CTACTGCCCATG
303936 C
1 C
303937 CTTACTCTAC
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:0.16, C:0.44, G:0.16, T:0.24
Consensus pattern (12 bp):
CTACTGCCCATG
Found at i:311878 original size:23 final size:22
Alignment explanation
Indices: 311827--311941 Score: 86
Period size: 22 Copynumber: 5.4 Consensus size: 22
311817 TTTCTTGAAG
311827 AAGAAAAGAGAAAAAATGGAAA
1 AAGAAAAGAGAAAAAATGGAAA
*
311849 AAAAAAAGTAGAAAAAAT-GAAA
1 AAGAAAAG-AGAAAAAATGGAAA
* *
311871 AAGGAAAAAAG-GAAAA-GGAAAA
1 AA-GAAAAGAGAAAAAATGG-AAA
*
311893 AATGAAAA-AGGAAAAA-GGAAA
1 AA-GAAAAGAGAAAAAATGGAAA
311914 AAGGAAAA-AGAAAAAA---AAA
1 AA-GAAAAGAGAAAAAATGGAAA
311933 AAGAAAAGA
1 AAGAAAAGA
311942 AAATAAAAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
18 5 0.06
19 6 0.08
21 24 0.30
22 31 0.39
23 13 0.16
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (22 bp):
AAGAAAAGAGAAAAAATGGAAA
Found at i:311879 original size:29 final size:28
Alignment explanation
Indices: 311838--311944 Score: 118
Period size: 29 Copynumber: 3.9 Consensus size: 28
311828 AGAAAAGAGA
311838 AAAAATGGAAAAAA-AAAAGTAGAAAAAATG
1 AAAAA-GGAAAAAAGAAAAG--GAAAAAATG
311868 AAAAAGGAAAAAAGGAAAAGGAAAAAATG
1 AAAAAGGAAAAAA-GAAAAGGAAAAAATG
*
311897 AAAAAGGAAAAAGGAAAAAGG-AAAAA-G
1 AAAAAGGAAAAAAG-AAAAGGAAAAAATG
311924 AAAAA--AAAAAAGAAAA-GAAAA
1 AAAAAGGAAAAAAGAAAAGGAAAA
311945 TAAAAAAGAA
Statistics
Matches: 71, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
23 1 0.01
24 7 0.10
25 6 0.08
27 6 0.08
28 6 0.08
29 35 0.49
30 5 0.07
31 5 0.07
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.04
Consensus pattern (28 bp):
AAAAAGGAAAAAAGAAAAGGAAAAAATG
Found at i:311929 original size:7 final size:7
Alignment explanation
Indices: 311827--311956 Score: 86
Period size: 7 Copynumber: 18.0 Consensus size: 7
311817 TTTCTTGAAG
311827 AAGAAAA
1 AAGAAAA
*
311834 GAGAAAA
1 AAGAAAA
311841 AATGGAAAA
1 AA--GAAAA
311850 AA-AAAA
1 AAGAAAA
*
311856 GTAGAAAA
1 -AAGAAAA
311864 AATGAAAA
1 AA-GAAAA
*
311872 AGGAAAA
1 AAGAAAA
*
311879 AAGGAAA
1 AAGAAAA
*
311886 AGGAAAA
1 AAGAAAA
311893 AATG-AAA
1 AA-GAAAA
*
311900 AAGGAAA
1 AAGAAAA
*
311907 AAGGAAA
1 AAGAAAA
*
311914 AAGGAAA
1 AAGAAAA
311921 AAGAAAA
1 AAGAAAA
311928 AA-AAAA
1 AAGAAAA
*
311934 AGAAAAGAA
1 A-AGAA-AA
*
311943 AATAAAA
1 AAGAAAA
311950 AAGAAAA
1 AAGAAAA
311957 CAAAAATCAA
Statistics
Matches: 100, Mismatches: 13, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
6 10 0.10
7 64 0.64
8 16 0.16
9 10 0.10
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (7 bp):
AAGAAAA
Found at i:311929 original size:14 final size:13
Alignment explanation
Indices: 311845--311956 Score: 97
Period size: 14 Copynumber: 8.4 Consensus size: 13
311835 AGAAAAAATG
311845 GAAAAAA-AAAAGTA
1 GAAAAAAGAAAA--A
311859 GAAAAAATGAAAAA
1 GAAAAAA-GAAAAA
*
311873 GGAAAAAAGGAAAAG
1 -GAAAAAA-GAAAAA
311888 GAAAAAATGAAAAA
1 GAAAAAA-GAAAAA
*
311902 GGAAAAAGGAAAAA
1 -GAAAAAAGAAAAA
*
311916 GGAAAAAGAAAAA
1 GAAAAAAGAAAAA
311929 -AAAAAAG-AAAA
1 GAAAAAAGAAAAA
*
311940 GAAAATA-AAAAA
1 GAAAAAAGAAAAA
311952 GAAAA
1 GAAAA
311957 CAAAAATCAA
Statistics
Matches: 83, Mismatches: 9, Indels: 14
0.78 0.08 0.13
Matches are distributed among these distances:
11 4 0.05
12 20 0.24
13 11 0.13
14 26 0.31
15 18 0.22
16 4 0.05
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (13 bp):
GAAAAAAGAAAAA
Found at i:311939 original size:17 final size:17
Alignment explanation
Indices: 311919--311962 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
311909 GGAAAAAGGA
311919 AAAAGAAAAAAAAAAAG
1 AAAAGAAAAAAAAAAAG
*
311936 AAAAGAAAATAAAAAAG
1 AAAAGAAAAAAAAAAAG
*
311953 AAAACAAAAA
1 AAAAGAAAAA
311963 TCAAGTCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.86, C:0.02, G:0.09, T:0.02
Consensus pattern (17 bp):
AAAAGAAAAAAAAAAAG
Found at i:313265 original size:37 final size:37
Alignment explanation
Indices: 313222--313338 Score: 180
Period size: 37 Copynumber: 3.2 Consensus size: 37
313212 TGAAGAAGTG
*
313222 AATCCATCTTAAGCCTTCACTGAAGAGTAGTGAAGCA
1 AATCCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCA
* * *
313259 AATCCATCATAAGCCTTCACCGAAGAGTAGTGAAGTA
1 AATCCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCA
* *
313296 AATCCATCTTAAGCATTTACAGAAGAGTAGTGAAGCA
1 AATCCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCA
313333 AATCCA
1 AATCCA
313339 CCAGTAAGTC
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (37 bp):
AATCCATCTTAAGCCTTCACAGAAGAGTAGTGAAGCA
Found at i:313385 original size:41 final size:41
Alignment explanation
Indices: 313340--313418 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
313330 GCAAATCCAC
*
313340 CAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTTGGGCCA
1 CAGTAAGTCTTTCGAGCATGATGATGAAATCCTTTGGGCCA
*
313381 CAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGG
1 CAGTAAGTCTTTCGAGCATGATGATGAAATCCTTTGGG
313419 TAATTTGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (41 bp):
CAGTAAGTCTTTCGAGCATGATGATGAAATCCTTTGGGCCA
Found at i:313524 original size:42 final size:42
Alignment explanation
Indices: 313340--313570 Score: 155
Period size: 42 Copynumber: 5.3 Consensus size: 42
313330 GCAAATCCAC
* * *
313340 CAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTTGGGCCA-
1 CAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCAT
* * *
313381 CAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTAAT
1 CAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCAT
** * * * * *
313423 TTGTAAGCCTTCACGGAAG-A-GTAGTGAAGCAAATCCATCAGTAAGTGCAAT
1 CAGTAAGTCTT-TC-G-AGCATG-A-TGATG-AAATCCTTC-G--GGT-C-AT
* *
313474 CACTAAGTCTTTCGAGTATGATGATGAAATCCTTCGGGTCAT
1 CAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCAT
* * * *
313516 CAGTAAGTCTTTCAAGCATGATGATTAAATTCTTCGGGTAATT
1 CAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCA-T
313559 CA-TAAGTCTTTC
1 CAGTAAGTCTTTC
313571 TCAATCAAAG
Statistics
Matches: 147, Mismatches: 28, Indels: 29
0.72 0.14 0.14
Matches are distributed among these distances:
41 37 0.25
42 55 0.37
43 6 0.04
44 5 0.03
45 5 0.03
46 8 0.05
47 9 0.06
48 6 0.04
49 5 0.03
50 2 0.01
51 9 0.06
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (42 bp):
CAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCAT
Found at i:317770 original size:156 final size:154
Alignment explanation
Indices: 317487--317809 Score: 603
Period size: 156 Copynumber: 2.1 Consensus size: 154
317477 AAAGGTCGAC
*
317487 TTAAGTGAAGTGTATAACCTACTTACCCATTAAACAACAAGTTATATACTATTAACTAAAAGTCT
1 TTAAG-GAAGTATATAACCTACTTACCCATTAAACAACAAGTTATATACTATTAACTAAAAGTCT
317552 AATAAAAGTCAGATTGAAGATCTTAGTGGAAAGTTGGGTTTGATCAATATATGCACACCAGATTT
65 AATAAAAGTCAGATTGAAGATCTTAGTGGAAAGTTGGGTTTGATCAATATATGCACACCAGATTT
317617 AGGGGGAGTGTTAGAATTCTGAGAA
130 AGGGGGAGTGTTAGAATTCTGAGAA
317642 TTAAGGAAGTATATAACCTACTTACCCATTAAACAACAAGTTATATACTTATTAACTAAAAGTCT
1 TTAAGGAAGTATATAACCTACTTACCCATTAAACAACAAGTTATATAC-TATTAACTAAAAGTCT
317707 AAATAAAAGTCAGATTGAAGATCTTAGTGGAAAGTTGGGTTTGATCAATATATGCACACCAGATT
65 -AATAAAAGTCAGATTGAAGATCTTAGTGGAAAGTTGGGTTTGATCAATATATGCACACCAGATT
317772 TAGGGGGAGTGTTAGAATTCTGAGAA
129 TAGGGGGAGTGTTAGAATTCTGAGAA
317798 TTAAGGAA-TATA
1 TTAAGGAAGTATA
317810 ATTATTCCTT
Statistics
Matches: 165, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
154 42 0.25
155 25 0.15
156 98 0.59
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (154 bp):
TTAAGGAAGTATATAACCTACTTACCCATTAAACAACAAGTTATATACTATTAACTAAAAGTCTA
ATAAAAGTCAGATTGAAGATCTTAGTGGAAAGTTGGGTTTGATCAATATATGCACACCAGATTTA
GGGGGAGTGTTAGAATTCTGAGAA
Found at i:319770 original size:18 final size:18
Alignment explanation
Indices: 319743--319792 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
319733 ATACTCTACA
319743 CTTG-GTATCGATACACC
1 CTTGAGTATCGATACACC
319760 CTTGAGTATCGATACACC
1 CTTGAGTATCGATACACC
319778 CTTGAGTATCGATAC
1 CTTGAGTATCGATAC
319793 CACAAATGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 4 0.12
18 28 0.88
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (18 bp):
CTTGAGTATCGATACACC
Found at i:320698 original size:39 final size:39
Alignment explanation
Indices: 320644--320722 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
320634 ATTTTGTGCT
320644 ATAGTTGTTCTCATAATTTTTTACAAGAGTTATAGGGAG
1 ATAGTTGTTCTCATAATTTTTTACAAGAGTTATAGGGAG
320683 ATAGTTGTTCTCATAATTTTTTACAAGAGTTATAGGGAG
1 ATAGTTGTTCTCATAATTTTTTACAAGAGTTATAGGGAG
320722 A
1 A
320723 GAAAGAACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.41
Consensus pattern (39 bp):
ATAGTTGTTCTCATAATTTTTTACAAGAGTTATAGGGAG
Found at i:322716 original size:12 final size:12
Alignment explanation
Indices: 322699--322738 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
322689 CTATTCAGGA
322699 TGATGTGCATGG
1 TGATGTGCATGG
* *
322711 TGATGTTCAAGG
1 TGATGTGCATGG
*
322723 TCATGTGCATGG
1 TGATGTGCATGG
322735 TGAT
1 TGAT
322739 CTTCATGATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.20, C:0.10, G:0.35, T:0.35
Consensus pattern (12 bp):
TGATGTGCATGG
Found at i:335785 original size:24 final size:23
Alignment explanation
Indices: 335758--335809 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
335748 CTAGATCCTA
335758 TTCAGGATGATGTGCATGATGATG
1 TTCAGG-TGATGTGCATGATGATG
* *
335782 TTCAAGGTGATGTGCATGGTGATT
1 TTC-AGGTGATGTGCATGATGATG
335806 TTCA
1 TTCA
335810 TGTTAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.04
24 21 0.84
25 3 0.12
ACGTcount: A:0.23, C:0.10, G:0.31, T:0.37
Consensus pattern (23 bp):
TTCAGGTGATGTGCATGATGATG
Found at i:341632 original size:55 final size:55
Alignment explanation
Indices: 341485--341650 Score: 199
Period size: 55 Copynumber: 3.0 Consensus size: 55
341475 CTCCAAAAGA
* * * * * *
341485 GCTCTGAAATCGAATATATCTATCTGTTGTTGCCATTAATAAGCATAAAAATAAG
1 GCTCCGAAATCGAGTATATCAATCAGTTGTTGCCATTAAAAAGCATAAAAATAGG
** * * *
341540 AATCCCGAAATCGAGTATATCAATAAGTTGTT-TCATTAAAAAACATAAAAATAGG
1 GCT-CCGAAATCGAGTATATCAATCAGTTGTTGCCATTAAAAAGCATAAAAATAGG
* *
341595 GCTCCGAAATCGAGTATATCAATCAGTTGTTGCCATTAAGAAGTATAAAAATAGG
1 GCTCCGAAATCGAGTATATCAATCAGTTGTTGCCATTAAAAAGCATAAAAATAGG
341650 G
1 G
341651 GCCCAAAATC
Statistics
Matches: 91, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
54 27 0.30
55 41 0.45
56 23 0.25
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (55 bp):
GCTCCGAAATCGAGTATATCAATCAGTTGTTGCCATTAAAAAGCATAAAAATAGG
Found at i:341660 original size:55 final size:55
Alignment explanation
Indices: 341490--341669 Score: 193
Period size: 55 Copynumber: 3.3 Consensus size: 55
341480 AAAGAGCTCT
* * * ***
341490 GAAATCGAATATATCTATCTGTTGTTGCCATTAATAAGCATAAAAATAAGAATCCC
1 GAAATCGAATATATCAATCAGTTGTTGCCATTAAAAAGCATAAAAAT-AGGGGCCC
* * * *
341546 GAAATCGAGTATATCAATAAGTTGTT-TCATTAAAAAACATAAAAATA-GGGCTCC
1 GAAATCGAATATATCAATCAGTTGTTGCCATTAAAAAGCATAAAAATAGGGGC-CC
* * *
341600 GAAATCGAGTATATCAATCAGTTGTTGCCATTAAGAAGTATAAAAATAGGGGCCC
1 GAAATCGAATATATCAATCAGTTGTTGCCATTAAAAAGCATAAAAATAGGGGCCC
* *
341655 AAAATCTAATATATC
1 GAAATCGAATATATC
341670 TATAAAATAG
Statistics
Matches: 103, Mismatches: 18, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
53 1 0.01
54 28 0.27
55 48 0.47
56 26 0.25
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.28
Consensus pattern (55 bp):
GAAATCGAATATATCAATCAGTTGTTGCCATTAAAAAGCATAAAAATAGGGGCCC
Found at i:350035 original size:15 final size:15
Alignment explanation
Indices: 350015--350044 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
350005 TATTAGACTA
350015 TTTGTATTCTAGTAT
1 TTTGTATTCTAGTAT
*
350030 TTTGTATTCTGGTAT
1 TTTGTATTCTAGTAT
350045 CCTATTCAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.17, T:0.60
Consensus pattern (15 bp):
TTTGTATTCTAGTAT
Found at i:358942 original size:13 final size:13
Alignment explanation
Indices: 358920--358951 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
358910 TTAATCAATG
*
358920 AATGGCAGTGGAA
1 AATGGTAGTGGAA
358933 AATGGTAGTGGAA
1 AATGGTAGTGGAA
358946 AATGGT
1 AATGGT
358952 CATTCTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.38, T:0.22
Consensus pattern (13 bp):
AATGGTAGTGGAA
Found at i:365110 original size:30 final size:30
Alignment explanation
Indices: 365074--365200 Score: 245
Period size: 30 Copynumber: 4.2 Consensus size: 30
365064 GCACACCTTG
365074 ATATATTAACTAATTAAATATCATTTATAC
1 ATATATTAACTAATTAAATATCATTTATAC
365104 ATATATTAACTAATTAAATATCATTTATAC
1 ATATATTAACTAATTAAATATCATTTATAC
365134 ATATATTAACTAATTAAATATCATTTATAC
1 ATATATTAACTAATTAAATATCATTTATAC
*
365164 ATATATTATCTAATTAAATATCATTTATAC
1 ATATATTAACTAATTAAATATCATTTATAC
365194 ATATATT
1 ATATATT
365201 TTTAATCAAT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 96 1.00
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45
Consensus pattern (30 bp):
ATATATTAACTAATTAAATATCATTTATAC
Found at i:365111 original size:22 final size:21
Alignment explanation
Indices: 365086--365171 Score: 58
Period size: 22 Copynumber: 4.2 Consensus size: 21
365076 ATATTAACTA
365086 ATTAAATATCATTTATACATAT
1 ATTAAATAT-ATTTATACATAT
* * *
365108 ATTAACTA-ATTAAATATCATTT
1 ATTAAATATATT-TATA-CATAT
*
365130 A-TACATATA-TTA-AC-TA-
1 ATTAAATATATTTATACATAT
365146 ATTAAATATCATTTATACATAT
1 ATTAAATAT-ATTTATACATAT
365168 ATTA
1 ATTA
365172 TCTAATTAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 18
0.64 0.11 0.25
Matches are distributed among these distances:
16 1 0.02
17 7 0.15
18 2 0.04
19 4 0.09
20 6 0.13
21 10 0.21
22 17 0.36
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTAAATATATTTATACATAT
Found at i:366764 original size:68 final size:71
Alignment explanation
Indices: 366644--366781 Score: 167
Period size: 68 Copynumber: 2.0 Consensus size: 71
366634 TAATTTGTTA
* * ** *
366644 TAATTTAAATTTTATATATTTATTACTTTTAAGTTATTTAATATTAATCATTTTATGTGAT-TTT
1 TAATTAAAAGTTTATATATTTATTAC-TTTAAGTTATTTAATACGAACCATTTTATGTGATGTTT
366708 AGATAATT
65 -GATAATT
* *
366716 TAATTAAAAGTTTAT-TATTT-TTA-TTTAATTTATTTAATACGAACCATTTTGTGTGATGTTTG
1 TAATTAAAAGTTTATATATTTATTACTTTAAGTTATTTAATACGAACCATTTTATGTGATGTTTG
366778 ATAA
66 ATAA
366782 ATATTAGTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
68 34 0.59
69 3 0.05
70 3 0.05
71 5 0.09
72 13 0.22
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.54
Consensus pattern (71 bp):
TAATTAAAAGTTTATATATTTATTACTTTAAGTTATTTAATACGAACCATTTTATGTGATGTTTG
ATAATT
Found at i:369134 original size:82 final size:83
Alignment explanation
Indices: 368987--369150 Score: 242
Period size: 82 Copynumber: 2.0 Consensus size: 83
368977 GAATATTTTT
*
368987 TCATTTTCTACCGTTAATCTCAACCTTTAATTTCTCTAATCCAATGGTCTTAAAAAGGTGCAAAA
1 TCATTTTCTACCGTTAATCTCAAACTTTAATTTCTCTAATCCAATGGTCTTAAAAAGGTGCAAAA
369052 CTAAAAG-AGTTTTACACC
66 CTAAAAGCA-TTTTACACC
* * * * * *
369070 TCATTTTCTACTGTTAATCTCAAAC-TTAATTTCTTTCATCTAATGGTCTTAAAAATGTGTAAAA
1 TCATTTTCTACCGTTAATCTCAAACTTTAATTTCTCTAATCCAATGGTCTTAAAAAGGTGCAAAA
369134 CTAAAAGCATTTTACAC
66 CTAAAAGCATTTTACAC
369151 AATGTAATTG
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
82 49 0.67
83 24 0.33
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.38
Consensus pattern (83 bp):
TCATTTTCTACCGTTAATCTCAAACTTTAATTTCTCTAATCCAATGGTCTTAAAAAGGTGCAAAA
CTAAAAGCATTTTACACC
Found at i:369461 original size:6 final size:6
Alignment explanation
Indices: 369452--369477 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
369442 CATATATATA
369452 TATAAT TATAAT TATAAT TATAAT TA
1 TATAAT TATAAT TATAAT TATAAT TA
369478 AAAAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATAAT
Found at i:372604 original size:2 final size:2
Alignment explanation
Indices: 372597--372626 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
372587 ATGCATGTAT
*
372597 AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
372627 CAAATAGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Done.