Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008228.1 Hibiscus syriacus cultivar Beakdansim tig00110864_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: 3739947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 20
Found at i:2068040 original size:55 final size:55
Alignment explanation
Indices: 2067955--2068061 Score: 151
Period size: 55 Copynumber: 1.9 Consensus size: 55
2067945 AAGAGAAATC
* * *
2067955 AATCTTTGTTATTATTGACTTCCTCGTGAAGAGAAGTCAATCCTTATTATTAGTG
1 AATCTTTCTTATTATTGAATTCCTCATGAAGAGAAGTCAATCCTTATTATTAGTG
* * * *
2068010 AATCTTTCTTATTCTTGAATTCTTCATGAAGAGAAGTCAATCTTTGTTATTA
1 AATCTTTCTTATTATTGAATTCCTCATGAAGAGAAGTCAATCCTTATTATTA
2068062 TTGACTTCCT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (55 bp):
AATCTTTCTTATTATTGAATTCCTCATGAAGAGAAGTCAATCCTTATTATTAGTG
Found at i:2068076 original size:93 final size:93
Alignment explanation
Indices: 2067917--2068098 Score: 301
Period size: 93 Copynumber: 2.0 Consensus size: 93
2067907 AAGAGAAGTC
* * *
2067917 AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAATCAATCTTTGTTATTATTGACTTCCTCGT
1 AATCTTTCTTATTCTTGAATTCCTCATGAAGAGAAATCAATCTTTGTTATTATTGACTTCCTCGT
2067982 GAAGAGAAGTCAATCCTTATTATTAGTG
66 GAAGAGAAGTCAATCCTTATTATTAGTG
* *
2068010 AATCTTTCTTATTCTTGAATTCTTCATGAAGAGAAGTCAATCTTTGTTATTATTGACTTCCTCGT
1 AATCTTTCTTATTCTTGAATTCCTCATGAAGAGAAATCAATCTTTGTTATTATTGACTTCCTCGT
* *
2068075 GAAGAGAAGTCAATCTTTGTTATT
66 GAAGAGAAGTCAATCCTTATTATT
2068099 CTTGACTTCC
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 82 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (93 bp):
AATCTTTCTTATTCTTGAATTCCTCATGAAGAGAAATCAATCTTTGTTATTATTGACTTCCTCGT
GAAGAGAAGTCAATCCTTATTATTAGTG
Found at i:2068116 original size:131 final size:131
Alignment explanation
Indices: 2067879--2068136 Score: 426
Period size: 131 Copynumber: 2.0 Consensus size: 131
2067869 AAGAGAAGTC
* * * *
2067879 AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCGT
1 AATCTTTCTTATTCTTGAATTCCTCATGAAGAGAAGTCAATCTTTGTTATTATTGACTTCCTCGT
2067944 GAAGAGAAATCAATCTTTGTTATTATTGACTTCCTCGTGAAGAGAAGTCAATCCTTATTATTAGT
66 GAAGAGAAATCAATCTTTGTTATTATTGACTTCCTCGTGAAGAGAAGTCAATCCTTATTATTAGT
2068009 G
131 G
*
2068010 AATCTTTCTTATTCTTGAATTCTTCATGAAGAGAAGTCAATCTTTGTTATTATTGACTTCCTCGT
1 AATCTTTCTTATTCTTGAATTCCTCATGAAGAGAAGTCAATCTTTGTTATTATTGACTTCCTCGT
* * * * *
2068075 GAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCTTGAAGAGAAGTCAATCTTTGTTATT
66 GAAGAGAAATCAATCTTTGTTATTATTGACTTCCTCGTGAAGAGAAGTCAATCCTTATTATT
2068137 CTTGACTTCC
Statistics
Matches: 117, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
131 117 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (131 bp):
AATCTTTCTTATTCTTGAATTCCTCATGAAGAGAAGTCAATCTTTGTTATTATTGACTTCCTCGT
GAAGAGAAATCAATCTTTGTTATTATTGACTTCCTCGTGAAGAGAAGTCAATCCTTATTATTAGT
G
Found at i:2068131 original size:169 final size:169
Alignment explanation
Indices: 2067852--2068165 Score: 547
Period size: 169 Copynumber: 1.9 Consensus size: 169
2067842 CTTTTTTTAT
* * *
2067852 TTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTC
1 TTCTTGAATTCCTCATGAAGAGAAGTCAATCTTTGTTATTATTGACTTCCTCGTGAAGAGAAGTC
*
2067917 AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAATCAATCTTTGTTATTATTGACTTCCTCGT
66 AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAATCAATCTTTGTTATTATTGACTTCCTCAT
*
2067982 GAAGAGAAGTCAATCCTTATTATTAGTGAATCTTTCTTA
131 AAAGAGAAGTCAATCCTTATTATTAGTGAATCTTTCTTA
*
2068021 TTCTTGAATTCTTCATGAAGAGAAGTCAATCTTTGTTATTATTGACTTCCTCGTGAAGAGAAGTC
1 TTCTTGAATTCCTCATGAAGAGAAGTCAATCTTTGTTATTATTGACTTCCTCGTGAAGAGAAGTC
* * *
2068086 AATCTTTGTTATTCTTGACTTCCTCTTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCAT
66 AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAATCAATCTTTGTTATTATTGACTTCCTCAT
2068151 AAAGAGAAGTCAATC
131 AAAGAGAAGTCAATC
2068166 TCTCGGTATT
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
169 136 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (169 bp):
TTCTTGAATTCCTCATGAAGAGAAGTCAATCTTTGTTATTATTGACTTCCTCGTGAAGAGAAGTC
AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAATCAATCTTTGTTATTATTGACTTCCTCAT
AAAGAGAAGTCAATCCTTATTATTAGTGAATCTTTCTTA
Found at i:2068207 original size:45 final size:44
Alignment explanation
Indices: 2068129--2068306 Score: 167
Period size: 45 Copynumber: 4.0 Consensus size: 44
2068119 AAGTCAATCT
* * * * * *
2068129 TTGTTATTCTTGACTTCCTCATAAAGAGAAGTCAATCTCTCGGTA
1 TTGTT-TTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTA
* * * * *
2068174 TTGTTATTCTCGACTTTATCGTGCAGAGGAGTCAATATTTCAGTG
1 TTGTT-TTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTA
* * *
2068219 TTGTCTTCCTTGACTTTCTCGTGAAGATGAGTCAATCTTTTAGTA
1 TTGT-TTTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTA
* * *
2068264 TTGTCCTTCTTGAATTTCTCGTGAAGAGGAGTCAATATTTCAG
1 TTGT-TTTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAG
2068307 ATTTGGTCTG
Statistics
Matches: 107, Mismatches: 25, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
45 106 0.99
46 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (44 bp):
TTGTTTTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTA
Found at i:2068730 original size:15 final size:16
Alignment explanation
Indices: 2068712--2068745 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2068702 TAGAGTTTCC
2068712 TTTTGTTTAG-TTTAT
1 TTTTGTTTAGTTTTAT
*
2068727 TTTTGTTTTGTTTTAT
1 TTTTGTTTAGTTTTAT
2068743 TTT
1 TTT
2068746 GATTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.09, C:0.00, G:0.12, T:0.79
Consensus pattern (16 bp):
TTTTGTTTAGTTTTAT
Found at i:2068793 original size:26 final size:25
Alignment explanation
Indices: 2068749--2068813 Score: 112
Period size: 26 Copynumber: 2.6 Consensus size: 25
2068739 TTATTTTGAT
2068749 TATATATATATAATTTTGAAATATA
1 TATATATATATAATTTTGAAATATA
*
2068774 TATATATAGTATAGTTTTGAAATATA
1 TATATATA-TATAATTTTGAAATATA
2068800 TATATATATATAAT
1 TATATATATATAAT
2068814 ATAGTTTTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 13 0.35
26 24 0.65
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (25 bp):
TATATATATATAATTTTGAAATATA
Found at i:2068832 original size:26 final size:26
Alignment explanation
Indices: 2068749--2068833 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 26
2068739 TTATTTTGAT
* *
2068749 TATATAT-ATATAATTTTGAAATATA
1 TATATATAATATAGTTTTGAAATAAA
*
2068774 TATATATAGTATAGTTTTGAAATATATATA
1 TATATATAATATAGTTTTG-AA-ATA-A-A
2068804 TATATATAATATAGTTTTAGAAA-AAA
1 TATATATAATATAGTTTT-GAAATAAA
2068830 TATA
1 TATA
2068834 GTTTGAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
25 7 0.14
26 14 0.28
27 3 0.06
28 4 0.08
29 1 0.02
30 20 0.40
31 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (26 bp):
TATATATAATATAGTTTTGAAATAAA
Found at i:2068833 original size:30 final size:30
Alignment explanation
Indices: 2068767--2068833 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
2068757 TATAATTTTG
*
2068767 AAATATATATATATAGTATAGTTTTGAAAT
1 AAATATATATATATAATATAGTTTTGAAAT
*
2068797 ATATATATATATATAATATAGTTTTAGAAA-
1 AAATATATATATATAATATAGTTTT-GAAAT
2068827 AAATATA
1 AAATATA
2068834 GTTTGAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 29 0.88
31 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (30 bp):
AAATATATATATATAATATAGTTTTGAAAT
Found at i:2068853 original size:19 final size:18
Alignment explanation
Indices: 2068811--2068864 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 18
2068801 ATATATATAT
* *
2068811 AATATAGTTTTAGAA-AA
1 AATATAGTTTAAAAATAA
*
2068828 AATATAGTTTGAAAATAA
1 AATATAGTTTAAAAATAA
2068846 ATATATAGTATTAAAAATA
1 A-ATATAGT-TTAAAAATA
2068865 TATAGATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 13 0.42
18 3 0.10
19 7 0.23
20 8 0.26
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (18 bp):
AATATAGTTTAAAAATAA
Found at i:2068965 original size:3 final size:3
Alignment explanation
Indices: 2068950--2068986 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2068940 ATATGCTTGC
*
2068950 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2068987 ATTCCAAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2074060 original size:63 final size:64
Alignment explanation
Indices: 2073946--2074073 Score: 172
Period size: 63 Copynumber: 2.0 Consensus size: 64
2073936 CATAAATGAA
* *
2073946 ATATCTAACAGTATAATCAGTTGTTTAGTTGAGAAATATTACATAAATG-AAACAAACCTCAAT
1 ATATCTAACAATATAATCAGTTGTTTAGCTGAGAAATATTACATAAATGAAAACAAACCTCAAT
* * *
2074009 ATATCTAACAATATAATCAGTTGTTTTA-CTGAGAAGT-TCTACGTAAGTGAAAACAAACCTCAA
1 ATATCTAACAATATAATCAGTTG-TTTAGCTGAGAAATAT-TACATAAATGAAAACAAACCTCAA
2074072 T
64 T
2074073 A
1 A
2074074 CCTCTATTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
62 1 0.02
63 37 0.65
64 19 0.33
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (64 bp):
ATATCTAACAATATAATCAGTTGTTTAGCTGAGAAATATTACATAAATGAAAACAAACCTCAAT
Found at i:2077269 original size:2 final size:2
Alignment explanation
Indices: 2077232--2077260 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2077222 CAAGAAAAGC
2077232 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2077261 ACCTATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2079813 original size:20 final size:20
Alignment explanation
Indices: 2079788--2079855 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
2079778 AATTTTTTTA
*
2079788 TGGTTTTGAAACCTCTTGAT
1 TGGTTTCGAAACCTCTTGAT
* *
2079808 TGGTTTCGAAACATCTTGAC
1 TGGTTTCGAAACCTCTTGAT
* *
2079828 TGGTTTCGAAACCCACATGAT
1 TGGTTTCGAAA-CCTCTTGAT
2079849 TGGTTTC
1 TGGTTTC
2079856 TAACCCCTGT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 28 0.70
21 12 0.30
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TGGTTTCGAAACCTCTTGAT
Found at i:2080658 original size:31 final size:31
Alignment explanation
Indices: 2080623--2080690 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
2080613 TTTTATTATT
2080623 TCGGGTCGGGTTTCTAATTCATATATTCGGG
1 TCGGGTCGGGTTTCTAATTCATATATTCGGG
*
2080654 TCGGGTCGTGTTTCTAATTCATATATTCGGG
1 TCGGGTCGGGTTTCTAATTCATATATTCGGG
2080685 TCGGGT
1 TCGGGT
2080691 GAAACTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.15, C:0.16, G:0.29, T:0.40
Consensus pattern (31 bp):
TCGGGTCGGGTTTCTAATTCATATATTCGGG
Found at i:2081049 original size:28 final size:28
Alignment explanation
Indices: 2081005--2081068 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
2080995 GGGTCGAGTC
*
2081005 GGTCGGG-CTTTTTAAGTGTGATATTCG
1 GGTCGGGTCTTTTTAAGTATGATATTCG
*
2081032 GGTCGGGTTTTTTTAAGTATGATATTCG
1 GGTCGGGTCTTTTTAAGTATGATATTCG
2081060 GGTCGGGTC
1 GGTCGGGTC
2081069 AGGTTCGTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 7 0.21
28 26 0.79
ACGTcount: A:0.14, C:0.11, G:0.34, T:0.41
Consensus pattern (28 bp):
GGTCGGGTCTTTTTAAGTATGATATTCG
Found at i:2082673 original size:17 final size:17
Alignment explanation
Indices: 2082651--2082705 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 17
2082641 AACGATCAAC
2082651 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2082668 GGTCAACGGTCGAGTCGGTTCG
1 GGTCAACGGTC--G--GG-TCG
2082690 GGTCAACGGTCGGGTC
1 GGTCAACGGTCGGGTC
2082706 AGACCGGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 13 0.39
18 2 0.06
19 1 0.03
20 1 0.03
21 2 0.06
22 14 0.42
ACGTcount: A:0.13, C:0.24, G:0.44, T:0.20
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:2082678 original size:7 final size:7
Alignment explanation
Indices: 2082624--2082661 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
2082614 GTCAAAGAAA
2082624 GTCAACG
1 GTCAACG
2082631 GTCAACG
1 GTCAACG
*
2082638 ATCAACG
1 GTCAACG
*
2082645 ATCAACG
1 GTCAACG
2082652 GTCAACG
1 GTCAACG
2082659 GTC
1 GTC
2082662 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:2082690 original size:22 final size:22
Alignment explanation
Indices: 2082659--2082701 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2082649 ACGGTCAACG
2082659 GTCGGGTCGGGTCAACGGTCGA
1 GTCGGGTCGGGTCAACGGTCGA
*
2082681 GTCGGTTCGGGTCAACGGTCG
1 GTCGGGTCGGGTCAACGGTCG
2082702 GGTCAGACCG
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:0.12, C:0.23, G:0.44, T:0.21
Consensus pattern (22 bp):
GTCGGGTCGGGTCAACGGTCGA
Found at i:2082728 original size:19 final size:19
Alignment explanation
Indices: 2082704--2082743 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2082694 AACGGTCGGG
2082704 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
2082723 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
2082742 TC
1 TC
2082744 GAACCAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:2082732 original size:10 final size:9
Alignment explanation
Indices: 2082702--2082791 Score: 54
Period size: 9 Copynumber: 9.3 Consensus size: 9
2082692 TCAACGGTCG
*
2082702 GGTCAGACC
1 GGTCAAACC
2082711 GGTCAAACC
1 GGTCAAACC
*
2082720 GGTTCAGACC
1 GG-TCAAACC
2082730 GGTCAAACC
1 GGTCAAACC
*
2082739 GGTTCGAACC
1 GG-TCAAACC
** *
2082749 AATTGAAACC
1 -GGTCAAACC
2082759 GGTCAGAACC
1 GGTCA-AACC
*
2082769 GGTTAAAAACC
1 GG-T-CAAACC
*
2082780 GGTTAAACC
1 GGTCAAACC
2082789 GGT
1 GGT
2082792 TTCCAACAGC
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
9 28 0.45
10 26 0.42
11 7 0.11
12 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.26, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2082788 original size:30 final size:29
Alignment explanation
Indices: 2082708--2082792 Score: 50
Period size: 29 Copynumber: 2.9 Consensus size: 29
2082698 GTCGGGTCAG
* *
2082708 ACCGGTCAAACCGGTTCAGACCGG-TCAA
1 ACCGGTCAAACCGGTTAAAACCGGTTCAA
* ** *
2082736 ACCGGTTCGAACCAATTGAAACCGG-TCAGA
1 ACCGG-TCAAACCGGTTAAAACCGGTTCA-A
*
2082766 ACCGGTTAAAAACCGGTT-AAACCGGTT
1 ACCGG-T-CAAACCGGTTAAAACCGGTT
2082793 TCCAACAGCC
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
28 5 0.11
29 17 0.39
30 15 0.34
31 7 0.16
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.18
Consensus pattern (29 bp):
ACCGGTCAAACCGGTTAAAACCGGTTCAA
Found at i:2082790 original size:20 final size:21
Alignment explanation
Indices: 2082754--2082792 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2082744 GAACCAATTG
2082754 AAACCGGTCAGAACCGGTTAA
1 AAACCGGTCAGAACCGGTTAA
*
2082775 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
2082793 TCCAACAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTAA
Found at i:2090006 original size:22 final size:22
Alignment explanation
Indices: 2089981--2090030 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
2089971 CAACGGTCAA
2089981 CGGGTCGGGTCAACGGTCGGGT
1 CGGGTCGGGTCAACGGTCGGGT
2090003 CGGGTCGGGTCAACGGTCGGGT
1 CGGGTCGGGTCAACGGTCGGGT
2090025 CGGGTC
1 CGGGTC
2090031 AGAACGGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.08, C:0.24, G:0.50, T:0.18
Consensus pattern (22 bp):
CGGGTCGGGTCAACGGTCGGGT
Found at i:2090068 original size:10 final size:10
Alignment explanation
Indices: 2090038--2090127 Score: 71
Period size: 9 Copynumber: 9.1 Consensus size: 10
2090028 GTCAGAACGG
*
2090038 TCAAACCGAT
1 TCAAACCGGT
*
2090048 TCAGACC-GT
1 TCAAACCGGT
2090057 TCAAACCGGT
1 TCAAACCGGT
*
2090067 TCGAACCGGTT
1 TCAAACCGG-T
*
2090078 TTAAACCGG-
1 TCAAACCGGT
*
2090087 TCGAACCGG-
1 TCAAACCGGT
2090096 TCAGAACCGGT
1 TCA-AACCGGT
*
2090107 TGAAAACCGGT
1 T-CAAACCGGT
2090118 T-AAACCGGT
1 TCAAACCGGT
2090127 T
1 T
2090128 TCCAGCAGCC
Statistics
Matches: 65, Mismatches: 10, Indels: 11
0.76 0.12 0.13
Matches are distributed among these distances:
9 25 0.38
10 22 0.34
11 17 0.26
12 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:2090074 original size:19 final size:19
Alignment explanation
Indices: 2090038--2090107 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
2090028 GTCAGAACGG
*
2090038 TCAAACCGATTC-AGACCGT
1 TCAAACCGGTTCGA-ACCGT
2090057 TCAAACCGGTTCGAACCGGTT
1 TCAAACCGGTTCGAACC-G-T
* *
2090078 TTAAACCGG-TCGAACCGG
1 TCAAACCGGTTCGAACCGT
2090096 TCAGAACCGGTT
1 TCA-AACCGGTT
2090108 GAAAACCGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
18 2 0.05
19 21 0.50
20 10 0.24
21 9 0.21
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (19 bp):
TCAAACCGGTTCGAACCGT
Found at i:2090094 original size:30 final size:31
Alignment explanation
Indices: 2090052--2090127 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
2090042 ACCGATTCAG
* **
2090052 ACCGTTCAAACCGGTTC-GAACCGGTTTTAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
2090082 ACCGGTCGAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
2090112 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
2090128 TCCAGCAGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 2 0.05
30 35 0.92
31 1 0.03
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:2096641 original size:72 final size:72
Alignment explanation
Indices: 2096515--2096648 Score: 223
Period size: 72 Copynumber: 1.9 Consensus size: 72
2096505 GGTGATAGTG
** * *
2096515 TTTGGTAAGACTGAAGATTTAACCAGTTGCTTTGTGTAATTGTTACTATTGTAATTTATGCCCAA
1 TTTGGTAAGACTGAAGATTTAACCAACTGCTTTGTGTAATTGTTACTATAGTAATGTATGCCCAA
2096580 AAATATC
66 AAATATC
*
2096587 TTTGGTAAGACTGAAGATTTAACCAACTGCTTTGTGTAATTGTTTCTATAGTAATGTATGCC
1 TTTGGTAAGACTGAAGATTTAACCAACTGCTTTGTGTAATTGTTACTATAGTAATGTATGCC
2096649 TTTTTAATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (72 bp):
TTTGGTAAGACTGAAGATTTAACCAACTGCTTTGTGTAATTGTTACTATAGTAATGTATGCCCAA
AAATATC
Found at i:2099884 original size:90 final size:90
Alignment explanation
Indices: 2099651--2099876 Score: 416
Period size: 90 Copynumber: 2.5 Consensus size: 90
2099641 ATGCTAAAAT
* * *
2099651 TTGATTTGGCTTTTTTATACAAAAAGTAATGGAAATTGAGTTTCCAGCATTTTAATACTGATCTA
1 TTGATTTGGCTTTTCTGTACAAAAAGTAATGGAAATTGAGTTTCCAGCATTTTAATACTGATATA
2099716 CTCGTTTCCAACTATGAGTGGGAAA
66 CTCGTTTCCAACTATGAGTGGGAAA
*
2099741 TTGATTTGGCTTTGCTGTACAAAAAGTAATGGAAATTGAGTTTCCAGCATTTTAATACTGATATA
1 TTGATTTGGCTTTTCTGTACAAAAAGTAATGGAAATTGAGTTTCCAGCATTTTAATACTGATATA
2099806 CTCGTTTCCAACTATGAGTGGGAAA
66 CTCGTTTCCAACTATGAGTGGGAAA
2099831 TTGATTTGGCTTTTCTGTACAAAAAGTAATGGAAATTGAGTTTCCA
1 TTGATTTGGCTTTTCTGTACAAAAAGTAATGGAAATTGAGTTTCCA
2099877 TTGTTTTACT
Statistics
Matches: 131, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 131 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (90 bp):
TTGATTTGGCTTTTCTGTACAAAAAGTAATGGAAATTGAGTTTCCAGCATTTTAATACTGATATA
CTCGTTTCCAACTATGAGTGGGAAA
Found at i:2116009 original size:95 final size:95
Alignment explanation
Indices: 2115846--2116037 Score: 357
Period size: 95 Copynumber: 2.0 Consensus size: 95
2115836 CATCACAGCT
* *
2115846 TTAGGGTTATTTGAAATTTGAAAGTCCTTTATTTGTGAAGGTATTTTAATTGATTATTTAATTGT
1 TTAGGGTTATTTGAAATTTGAAAGTCCTTTATTTATGAAGGTATTTTAATTGATCATTTAATTGT
2115911 GCACATTTTCGAAACTTAGGCAGATGATTA
66 GCACATTTTCGAAACTTAGGCAGATGATTA
*
2115941 TTAGGGTTATTTGAAATTTGAAAGTCCTTTCTTTATGAAGGTATTTTAATTGATCATTTAATTGT
1 TTAGGGTTATTTGAAATTTGAAAGTCCTTTATTTATGAAGGTATTTTAATTGATCATTTAATTGT
2116006 GCACATTTTCGAAACTTAGGCAGATGATTA
66 GCACATTTTCGAAACTTAGGCAGATGATTA
2116036 TT
1 TT
2116038 TAATTATGCA
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.44
Consensus pattern (95 bp):
TTAGGGTTATTTGAAATTTGAAAGTCCTTTATTTATGAAGGTATTTTAATTGATCATTTAATTGT
GCACATTTTCGAAACTTAGGCAGATGATTA
Found at i:2116050 original size:39 final size:39
Alignment explanation
Indices: 2115991--2116067 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
2115981 GTATTTTAAT
* **
2115991 TGATCATTTAATTGTGCACATTTTCGAAACTTAGGCAGA
1 TGATCATTTAATTATGCACATTTTAAAAACTTAGGCAGA
* *
2116030 TGATTATTTAATTATGCACATTTTAAAAACTTATGCAG
1 TGATCATTTAATTATGCACATTTTAAAAACTTAGGCAG
2116068 GTGGCTGAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (39 bp):
TGATCATTTAATTATGCACATTTTAAAAACTTAGGCAGA
Found at i:2117039 original size:212 final size:212
Alignment explanation
Indices: 2116672--2117096 Score: 832
Period size: 212 Copynumber: 2.0 Consensus size: 212
2116662 TGTCTGATGT
*
2116672 ATGCTTTAGACCCAAGTTTAAGGGTAATGCTCCTCACTTTGAGCTTGAATTGTGTTTCGGTTGTT
1 ATGCTTTAGACCCAAGTTTAAGGGTAATGCTCCTCACTTTGAGCTTGAATTGTGCTTCGGTTGTT
2116737 TGCTGCCGAGTCTCCCCTTTACAGAAAGCACAGGTAGGTTCTTGTTGGCAGCTGTATTGAAACTT
66 TGCTGCCGAGTCTCCCCTTTACAGAAAGCACAGGTAGGTTCTTGTTGGCAGCTGTATTGAAACTT
2116802 ATTAATTTTGCTTTCAGTACAGTGTGTGAATAAAAGGTTTGTACAAAAAAAAAGGACATGCTGTA
131 ATTAATTTTGCTTTCAGTACAGTGTGTGAATAAAAGGTTTGTACAAAAAAAAAGGACATGCTGTA
2116867 CATAAATGATAATTTAA
196 CATAAATGATAATTTAA
2116884 ATGCTTTAGACCCAAGTTTAAGGGTAATGCTCCTCACTTTGAGCTTGAATTGTGCTTCGGTTGTT
1 ATGCTTTAGACCCAAGTTTAAGGGTAATGCTCCTCACTTTGAGCTTGAATTGTGCTTCGGTTGTT
2116949 TGCTGCCGAGTCTCCCCTTTACAGAAAGCACAGGTAGGTTCTTGTTGGCAGCTGTATTGAAACTT
66 TGCTGCCGAGTCTCCCCTTTACAGAAAGCACAGGTAGGTTCTTGTTGGCAGCTGTATTGAAACTT
*
2117014 ATTAGTTTTGCTTTCAGTACAGTGTGTGAATAAAAGGTTTGTACAAAAAAAAAGGACATGCTGTA
131 ATTAATTTTGCTTTCAGTACAGTGTGTGAATAAAAGGTTTGTACAAAAAAAAAGGACATGCTGTA
2117079 CATAAATGATAATTTAA
196 CATAAATGATAATTTAA
2117096 A
1 A
2117097 AGACTAGGAA
Statistics
Matches: 211, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
212 211 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (212 bp):
ATGCTTTAGACCCAAGTTTAAGGGTAATGCTCCTCACTTTGAGCTTGAATTGTGCTTCGGTTGTT
TGCTGCCGAGTCTCCCCTTTACAGAAAGCACAGGTAGGTTCTTGTTGGCAGCTGTATTGAAACTT
ATTAATTTTGCTTTCAGTACAGTGTGTGAATAAAAGGTTTGTACAAAAAAAAAGGACATGCTGTA
CATAAATGATAATTTAA
Found at i:2130066 original size:37 final size:37
Alignment explanation
Indices: 2130016--2130098 Score: 166
Period size: 37 Copynumber: 2.2 Consensus size: 37
2130006 AAATATAAAC
2130016 ACAAAAATATTTAAAAGCAAATAAGGACTAAATTACA
1 ACAAAAATATTTAAAAGCAAATAAGGACTAAATTACA
2130053 ACAAAAATATTTAAAAGCAAATAAGGACTAAATTACA
1 ACAAAAATATTTAAAAGCAAATAAGGACTAAATTACA
2130090 ACAAAAATA
1 ACAAAAATA
2130099 AAATAAGAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.61, C:0.11, G:0.07, T:0.20
Consensus pattern (37 bp):
ACAAAAATATTTAAAAGCAAATAAGGACTAAATTACA
Found at i:2134396 original size:2 final size:2
Alignment explanation
Indices: 2134389--2134419 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2134379 AAATGGTGAA
2134389 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2134420 ATAATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2134491 original size:24 final size:22
Alignment explanation
Indices: 2134464--2134514 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
2134454 GTTAAAAGCA
2134464 AAAAAGAAAAGAGAGAAAAAATAT
1 AAAAAGAAAAGA-AG-AAAAATAT
* *
2134488 AAAAATAAAATAAGAAAAATAT
1 AAAAAGAAAAGAAGAAAAATAT
*
2134510 TAAAA
1 AAAAA
2134515 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 12 0.50
23 2 0.08
24 10 0.42
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (22 bp):
AAAAAGAAAAGAAGAAAAATAT
Found at i:2134583 original size:20 final size:19
Alignment explanation
Indices: 2134560--2134606 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2134550 TGAAAGAATA
*
2134560 AAGAAAATGGGAAAAATGTT
1 AAGAAAA-GGAAAAAATGTT
2134580 AAGAGAAAGGAAAAAATGTT
1 AAGA-AAAGGAAAAAATGTT
*
2134600 AATAAAA
1 AAGAAAA
2134607 ATACAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 18 0.75
21 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (19 bp):
AAGAAAAGGAAAAAATGTT
Found at i:2135891 original size:35 final size:36
Alignment explanation
Indices: 2135852--2135946 Score: 138
Period size: 37 Copynumber: 2.6 Consensus size: 36
2135842 AATGAAAATG
*
2135852 AAAATTACATATTATATATATTT-AAAAATGTTTTC
1 AAAATTATATATTATATATATTTCAAAAATGTTTTC
* *
2135887 AAAATCATATATTATATATATTTTCGAAAATGTTTTC
1 AAAATTATATATTATATATA-TTTCAAAAATGTTTTC
*
2135924 TAAATTATATATTATATATATTT
1 AAAATTATATATTATATATATTT
2135947 TTCAGAACTT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
35 18 0.34
36 6 0.11
37 29 0.55
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (36 bp):
AAAATTATATATTATATATATTTCAAAAATGTTTTC
Found at i:2135960 original size:37 final size:37
Alignment explanation
Indices: 2135852--2135965 Score: 137
Period size: 37 Copynumber: 3.1 Consensus size: 37
2135842 AATGAAAATG
* *
2135852 AAAATTACATATTATATATA-TTT-AAAAATGTTTTC
1 AAAATTATATATTATATATATTTTCAGAAATGTTTTC
*
2135887 AAAATCATATATTATATATATTTTC-GAAAATGTTTTC
1 AAAATTATATATTATATATATTTTCAG-AAATGTTTTC
* *
2135924 TAAATTATATATTATATATATTTTTCAGAACT-TTTTC
1 AAAATTATATATTATATATA-TTTTCAGAAATGTTTTC
2135961 AAAAT
1 AAAAT
2135966 GTTTTCAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
35 18 0.27
36 3 0.04
37 37 0.55
38 8 0.12
39 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (37 bp):
AAAATTATATATTATATATATTTTCAGAAATGTTTTC
Found at i:2135970 original size:12 final size:12
Alignment explanation
Indices: 2135955--2135988 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
2135945 TTTTCAGAAC
2135955 TTTTTCAAAATG
1 TTTTTCAAAATG
2135967 -TTTTCAAAAATG
1 TTTTTC-AAAATG
2135979 TTTTTCAAAA
1 TTTTTCAAAA
2135989 CTATATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.25
12 10 0.50
13 5 0.25
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (12 bp):
TTTTTCAAAATG
Found at i:2135985 original size:13 final size:13
Alignment explanation
Indices: 2135955--2135988 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2135945 TTTTCAGAAC
2135955 TTTTTC-AAAATG
1 TTTTTCAAAAATG
2135967 -TTTTCAAAAATG
1 TTTTTCAAAAATG
2135979 TTTTTCAAAA
1 TTTTTCAAAA
2135989 CTATATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.25
12 6 0.30
13 9 0.45
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (13 bp):
TTTTTCAAAAATG
Found at i:2136008 original size:38 final size:37
Alignment explanation
Indices: 2135967--2136177 Score: 157
Period size: 39 Copynumber: 5.9 Consensus size: 37
2135957 TTTCAAAATG
2135967 TTTTCAAAAA-TGTTTTTCAAAACTATATATTATATAT
1 TTTTCAAAAATTG-TTTTCAAAACTATATATTATATAT
*
2136004 GTTTTCAAAAATTTGTTTTCAAAACTATATAATATATAT
1 -TTTTCAAAAA-TTGTTTTCAAAACTATATATTATATAT
* * *
2136043 ATATTC-AAAA-------CTATA-TA-ATA-TATATA-
1 -TTTTCAAAAATTGTTTTCAAAACTATATATTATATAT
*
2136069 TTTTCAAAAATTATTTTCAAAACTATATAATTTATATAT
1 TTTTCAAAAATTGTTTTCAAAACTATAT-A-TTATATAT
*
2136108 ATATTCAAAAATTGTTTTCAAAACTATATA-TAT-T-T
1 -TTTTCAAAAATTGTTTTCAAAACTATATATTATATAT
** *
2136143 TTTTCAAAAATTGTTTTTTTAAAGTATATATTATA
1 TTTTCAAAAATTG-TTTTCAAAACTATATATTATA
2136178 AAAAATCATT
Statistics
Matches: 139, Mismatches: 14, Indels: 41
0.72 0.07 0.21
Matches are distributed among these distances:
25 4 0.03
26 4 0.03
27 6 0.04
28 3 0.02
29 2 0.01
30 3 0.02
33 3 0.02
34 14 0.10
35 16 0.12
36 5 0.04
37 3 0.02
38 20 0.14
39 28 0.20
40 28 0.20
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (37 bp):
TTTTCAAAAATTGTTTTCAAAACTATATATTATATAT
Found at i:2136059 original size:64 final size:64
Alignment explanation
Indices: 2135982--2136117 Score: 220
Period size: 64 Copynumber: 2.1 Consensus size: 64
2135972 AAAAATGTTT
* * *
2135982 TTCAAAACTATATATTATATATGTTTTCAAAAATTTGTTTTCAAAACTATATAA-TATATATATA
1 TTCAAAACTATATAATATATATATTTTCAAAAA-TTATTTTCAAAACTATATAATTATATATATA
2136046 TTCAAAACTATATAATATATATATTTTCAAAAATTATTTTCAAAACTATATAATTTATATATATA
1 TTCAAAACTATATAATATATATATTTTCAAAAATTATTTTCAAAACTATATAA-TTATATATATA
2136111 TTCAAAA
1 TTCAAAA
2136118 ATTGTTTTCA
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
63 19 0.28
64 31 0.46
65 17 0.25
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.44
Consensus pattern (64 bp):
TTCAAAACTATATAATATATATATTTTCAAAAATTATTTTCAAAACTATATAATTATATATATA
Found at i:2136063 original size:23 final size:25
Alignment explanation
Indices: 2136021--2136077 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
2136011 AAAATTTGTT
2136021 TTCAAAACTATATAATATATATATA
1 TTCAAAACTATATAATATATATATA
*
2136046 TTCAAAACTATATAATATATATATT
1 TTCAAAACTATATAATATATATATA
2136071 TTCAAAA
1 TTCAAAA
2136078 ATTATTTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (25 bp):
TTCAAAACTATATAATATATATATA
Found at i:2136116 original size:40 final size:40
Alignment explanation
Indices: 2136046--2136142 Score: 153
Period size: 40 Copynumber: 2.5 Consensus size: 40
2136036 TATATATATA
*
2136046 TTCAAAACTATATAA--TATATATATTTTCAAAAATTATT
1 TTCAAAACTATATAATTTATATATATATTCAAAAATTATT
*
2136084 TTCAAAACTATATAATTTATATATATATTCAAAAATTGTT
1 TTCAAAACTATATAATTTATATATATATTCAAAAATTATT
2136124 TTCAAAACTATATATATTT
1 TTCAAAACTATATA-ATTT
2136143 TTTTCAAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
38 15 0.28
40 35 0.65
41 4 0.07
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.45
Consensus pattern (40 bp):
TTCAAAACTATATAATTTATATATATATTCAAAAATTATT
Found at i:2136137 original size:142 final size:144
Alignment explanation
Indices: 2135969--2136257 Score: 344
Period size: 144 Copynumber: 2.0 Consensus size: 144
2135959 TCAAAATGTT
2135969 TTCAAAAATGTTTTTCAAAACTATATATTATATATGTTTTCAAAAATT-TGTTTTCAAA-ACTAT
1 TTCAAAAATGTTTTTCAAAACTATATA-TAT-T-T-TTTTCAAAAATTGTGTTTTCAAAGA-TAT
* *
2136032 ATAAT-ATATAT-ATATTC-AAAACTATATAATATATATATTTTCAAAAATTATTTTC-AAAACT
61 ATAATAAAAAATCATATTCAAAAACTATATAATATATATATTTTCAAAAA-TATTTTCAAAAACT
*
2136093 ATA-TA-ATTTATATATATA
125 ATACTATATTAATATATATA
* * *
2136111 TTCAAAAAT-TGTTTTCAAAACTATATATATTTTTTTCAAAAATTGTTTTTTTAAAGTATATATT
1 TTCAAAAATGT-TTTTCAAAACTATATATATTTTTTTCAAAAATTGTGTTTTCAAAG-ATATATA
* * * *
2136175 ATAAAAAATCATTTTCTAAAAACTATATATTATATTTTTTTTCAAAAATATTTTCAAAAACTATA
64 ATAAAAAATCATATTC-AAAAACTATATAATATATATATTTTCAAAAATATTTTCAAAAACTATA
2136240 CTATATTAATATATATA
128 CTATATTAATATATATA
2136257 T
1 T
2136258 ATATACTAAA
Statistics
Matches: 126, Mismatches: 10, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
138 12 0.10
139 9 0.07
140 8 0.06
141 9 0.07
142 30 0.24
143 7 0.06
144 36 0.29
145 2 0.02
146 13 0.10
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (144 bp):
TTCAAAAATGTTTTTCAAAACTATATATATTTTTTTCAAAAATTGTGTTTTCAAAGATATATAAT
AAAAAATCATATTCAAAAACTATATAATATATATATTTTCAAAAATATTTTCAAAAACTATACTA
TATTAATATATATA
Found at i:2136182 original size:104 final size:99
Alignment explanation
Indices: 2135864--2136253 Score: 286
Period size: 104 Copynumber: 3.9 Consensus size: 99
2135854 AATTACATAT
* *
2135864 TATATATATT-T-AAAAA-TGTTTTCAAAA-TCATATATTATATATATTTTCGAAAA-TGTTTTC
1 TATATATATTATAAAAAATTATTTTCAAAACT-ATATATTATATATATTTTCAAAAATTGTTTTC
* * * * * *
2135924 TAAATTATATATTATATATATTTTTCAGAACTTTTTCAA
65 AAAACTATATA-TAT-TATA-TATTCAAAACTATAT-AA
* * *
2135963 -A-ATGT-TT-TCAAAAATGT-TTTTCAAAACTATATATTATATATGTTTTCAAAAATTTGTTTT
1 TATATATATTATAAAAAAT-TATTTTCAAAACTATATATTATATATATTTTCAAAAA-TTGTTTT
2136023 CAAAACTATATAATATATATATATTCAAAACTATATAA
64 CAAAACTATAT-ATAT-TATATATTCAAAACTATATAA
* * *
2136061 TATATATATTTTCAAAAATTATTTTCAAAACTATATAATTTATATATATATTCAAAAATTGTTTT
1 TATATATATTATAAAAAATTATTTTCAAAACTATAT-A-TTATATATATTTTCAAAAATTGTTTT
* * * *
2136126 CAAAACTATATATATT-T-TTTTCAAAAATTGTTTTTTTAA
64 CAAAACTATATATATTATATATTC-AAAA----CTATATAA
* * * *
2136165 -AGTATATATTATAAAAAATCATTTTCTAAAAACTATATATTATATTTTTTTTCAAAAA-TATTT
1 TA-TATATATTATAAAAAATTATTTTC--AAAACTATATATTATATATATTTTCAAAAATTGTTT
2136228 TCAAAAACTATACTATATTAATATAT
63 TC-AAAACTATA-TATATT-ATATAT
2136254 ATATATATAC
Statistics
Matches: 240, Mismatches: 24, Indels: 45
0.78 0.08 0.15
Matches are distributed among these distances:
96 3 0.01
97 8 0.03
98 34 0.14
99 18 0.08
100 31 0.13
101 5 0.02
102 27 0.11
103 26 0.11
104 68 0.28
105 7 0.03
106 10 0.04
107 1 0.00
108 2 0.01
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (99 bp):
TATATATATTATAAAAAATTATTTTCAAAACTATATATTATATATATTTTCAAAAATTGTTTTCA
AAACTATATATATTATATATTCAAAACTATATAA
Found at i:2136209 original size:38 final size:37
Alignment explanation
Indices: 2136167--2136239 Score: 85
Period size: 38 Copynumber: 1.9 Consensus size: 37
2136157 TTTTTTAAAG
2136167 TATA-TATTATAAAAAATCATTTTCTAAAAACTATATAT
1 TATATTATTATAAAAAAT-ATTTTC-AAAAACTATATAT
* * *
2136205 TATATTTTTTTTCAAAAATATTTTCAAAAACTATA
1 TATA-TTATTATAAAAAATATTTTCAAAAACTATA
2136240 CTATATTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
38 14 0.47
39 6 0.20
40 10 0.33
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (37 bp):
TATATTATTATAAAAAATATTTTCAAAAACTATATAT
Found at i:2136374 original size:22 final size:20
Alignment explanation
Indices: 2136345--2136396 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
2136335 ACTATTGAAC
2136345 TATATATAAACTACATAGTT
1 TATATATAAACTACATAGTT
* *
2136365 TATTAATATAAATTATATAGTT
1 TA-T-ATATAAACTACATAGTT
2136387 TATATATAAA
1 TATATATAAA
2136397 TTATATATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 9 0.32
21 2 0.07
22 17 0.61
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (20 bp):
TATATATAAACTACATAGTT
Found at i:2136394 original size:11 final size:11
Alignment explanation
Indices: 2136366--2136423 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
2136356 TACATAGTTT
2136366 ATTA-ATATAA
1 ATTATATATAA
2136376 ATTATATAGT--
1 ATTATATA-TAA
2136386 -TTATATATAA
1 ATTATATATAA
*
2136396 ATTATATATGA
1 ATTATATATAA
*
2136407 ATTACATATAA
1 ATTATATATAA
*
2136418 ACTATA
1 ATTATA
2136424 CAATTTATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
8 1 0.03
9 7 0.18
10 4 0.11
11 25 0.66
12 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (11 bp):
ATTATATATAA
Found at i:2136395 original size:42 final size:40
Alignment explanation
Indices: 2136345--2136517 Score: 138
Period size: 42 Copynumber: 4.2 Consensus size: 40
2136335 ACTATTGAAC
* * *
2136345 TATATATAAACTACATAGTTTATTAATATAAATTATATAGTT
1 TATATATAAA-TATATA-TGTATTAATATAAACTATATAGTT
* * *
2136387 TATATATAAATTATATATGAATTACATATAAACTATACAATT
1 TATATATAAA-TATATATGTATTA-ATATAAACTATATAGTT
* * * *
2136429 TATATTTATATA-ATATGTA-TAATTATAAATTATATA-TAC
1 TATATATAAATATATATGTATTAA-TATAAACTATATAGT-T
*
2136468 TATGCATA-AAATATATAGTTTATTAATATAAACTATATAGTT
1 TAT--ATATAAATATATA-TGTATTAATATAAACTATATAGTT
2136510 TATATATA
1 TATATATA
2136518 TACATATAGT
Statistics
Matches: 103, Mismatches: 18, Indels: 21
0.73 0.13 0.15
Matches are distributed among these distances:
38 2 0.02
39 16 0.16
40 13 0.13
41 13 0.13
42 55 0.53
43 4 0.04
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (40 bp):
TATATATAAATATATATGTATTAATATAAACTATATAGTT
Found at i:2136403 original size:22 final size:21
Alignment explanation
Indices: 2136345--2136533 Score: 73
Period size: 20 Copynumber: 9.2 Consensus size: 21
2136335 ACTATTGAAC
* *
2136345 TATATATAAA-CTACATAGTT
1 TATATATAAATATATATAGTT
2136365 TATTAATATAAAT-TATATAGTT
1 TA-T-ATATAAATATATATAGTT
*
2136387 TATATATAAAT-TATATATGAAT
1 TATATATAAATATATATA-G-TT
* *
2136409 TACATATAAACTATACA-A-TT
1 TATATATAAA-TATATATAGTT
* * *
2136429 TATATTTATATA-ATAT-GTA
1 TATATATAAATATATATAGTT
*
2136448 TA-ATTATAAAT-TATATA-TAC
1 TATA-TATAAATATATATAGT-T
**
2136468 TATGCATAAA-ATATATAGTT
1 TATATATAAATATATATAGTT
*
2136488 TATTAATATAAA-CTATATAGTT
1 TA-T-ATATAAATATATATAGTT
* *
2136510 TATATAT--ATACATATAGTA
1 TATATATAAATATATATAGTT
2136529 TATAT
1 TATAT
2136534 GGTTAAGGTT
Statistics
Matches: 128, Mismatches: 22, Indels: 39
0.68 0.12 0.21
Matches are distributed among these distances:
18 4 0.03
19 27 0.21
20 43 0.34
21 6 0.05
22 43 0.34
23 2 0.02
24 3 0.02
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (21 bp):
TATATATAAATATATATAGTT
Found at i:2136689 original size:42 final size:42
Alignment explanation
Indices: 2136634--2136767 Score: 232
Period size: 42 Copynumber: 3.2 Consensus size: 42
2136624 TAACTTATAC
* * * *
2136634 TATATGTAAACTATATATACTATATAGTTTACATATAAACTA
1 TATATATAAACTATGTAAACTATATAGTTTACATATGAACTA
2136676 TATATATAAACTATGTAAACTATATAGTTTACATATGAACTA
1 TATATATAAACTATGTAAACTATATAGTTTACATATGAACTA
2136718 TATATATAAACTATGTAAACTATATAGTTTACATATGAACTA
1 TATATATAAACTATGTAAACTATATAGTTTACATATGAACTA
2136760 TATATATA
1 TATATATA
2136768 GTTTATTAGT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (42 bp):
TATATATAAACTATGTAAACTATATAGTTTACATATGAACTA
Found at i:2136799 original size:13 final size:13
Alignment explanation
Indices: 2136781--2136837 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
2136771 TATTAGTGAA
2136781 TTATATAA-ACTAT
1 TTATATAATA-TAT
2136794 TTATATAATATA-
1 TTATATAATATAT
2136806 TTATAT-ATATAT
1 TTATATAATATAT
*
2136818 ATATA-AACTATAGT
1 TTATATAA-TATA-T
2136832 TTATAT
1 TTATAT
2136838 TTATATACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
11 5 0.14
12 11 0.31
13 14 0.39
14 6 0.17
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (13 bp):
TTATATAATATAT
Found at i:2136800 original size:2 final size:2
Alignment explanation
Indices: 2136795--2136901 Score: 60
Period size: 2 Copynumber: 51.5 Consensus size: 2
2136785 ATAAACTATT
* *
2136795 TA TA TA -A TA TA T- TA TA TA TA TA TA TA TA AA CTA TA GTT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA
* * *
2136837 TT TA TA TA CTA CA TA CTA TA GT- TGA TA TT TA TA TA CTA TA TA T-
1 TA TA TA TA -TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA TA TA
*
2136880 TA TA TA TA TA AA CTA TA TA TA T
1 TA TA TA TA TA TA -TA TA TA TA T
2136902 TGTATAGTAT
Statistics
Matches: 81, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
1 4 0.05
2 66 0.81
3 11 0.14
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2136811 original size:7 final size:7
Alignment explanation
Indices: 2136791--2136899 Score: 54
Period size: 7 Copynumber: 16.4 Consensus size: 7
2136781 TTATATAAAC
2136791 TATT-TA
1 TATTATA
*
2136797 TATAATA
1 TATTATA
2136804 TATTATA
1 TATTATA
2136811 TA-TATA
1 TATTATA
2136817 TA-TATA
1 TATTATA
* *
2136823 AACTATA
1 TATTATA
2136830 GT-TTATA
1 -TATTATA
2136837 T-TTATA
1 TATTATA
* *
2136843 TACTACA
1 TATTATA
*
2136850 TACTATA
1 TATTATA
*
2136857 GT-TGATA
1 -TATTATA
2136864 T-TTATA
1 TATTATA
*
2136870 TACTATA
1 TATTATA
2136877 TATTATA
1 TATTATA
2136884 TA-TATA
1 TATTATA
* *
2136890 AACTATA
1 TATTATA
2136897 TAT
1 TAT
2136900 ATTGTATAGT
Statistics
Matches: 80, Mismatches: 16, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
6 32 0.40
7 47 0.59
8 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (7 bp):
TATTATA
Found at i:2136864 original size:27 final size:27
Alignment explanation
Indices: 2136824--2136883 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
2136814 ATATATATAA
*
2136824 ACTATAGTTTATATTTATATACTACAT
1 ACTATAGTTGATATTTATATACTACAT
*
2136851 ACTATAGTTGATATTTATATACTATAT
1 ACTATAGTTGATATTTATATACTACAT
*
2136878 ATTATA
1 ACTATA
2136884 TATATAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.48
Consensus pattern (27 bp):
ACTATAGTTGATATTTATATACTACAT
Found at i:2136897 original size:20 final size:20
Alignment explanation
Indices: 2136645--2137279 Score: 136
Period size: 20 Copynumber: 30.8 Consensus size: 20
2136635 ATATGTAAAC
*
2136645 TATATATACTATATAGTT-TA
1 TATATAAACTATATA-TTATA
* *
2136665 CATATAAACTATATATATAAA
1 TATATAAACTATATAT-TATA
*
2136686 CTATGTAAACTATATAGTT-TA
1 -TATATAAACTATATA-TTATA
* * *
2136707 CATATGAACTATATATATAAA
1 TATATAAACTATATAT-TATA
*
2136728 CTATGTAAACTATATAGTT-TA
1 -TATATAAACTATATA-TTATA
* * *
2136749 CATATGAACTATATATATAGTT
1 TATATAAACTATATAT-TA-TA
* * * *
2136771 TATTAGTGAATTATATAAACTATT
1 TA-TA-TAAACTATAT--ATTATA
2136795 TATATAATA-TATTATATATATA
1 TATATAA-ACTA-TATAT-TATA
2136817 TATATAAACTATAGT-TTATA
1 TATATAAACTATA-TATTATA
*
2136837 TTTATATACTACATACTATAGTTGATA
1 --TATATA-AAC-TA-TATA-TT-ATA
* *
2136864 TTTATATACTATATATTATA
1 TATATAAACTATATATTATA
2136884 TATATAAACTATATA-TAT-
1 TATATAAACTATATATTATA
* *
2136902 TGTAT--AGTATA-ATT-TA
1 TATATAAACTATATATTATA
* * * * *
2136918 CATATGAACTAAATATAAAAA
1 TATATAAACTATATAT-TATA
*
2136939 CTATATAAACTATA-GTT-TA
1 -TATATAAACTATATATTATA
*
2136958 TATATAAACTATATACTATA
1 TATATAAACTATATATTATA
* ** * *
2136978 GTTTAT-ATTTATATATAATC
1 -TATATAAACTATATATTATA
2136998 TATATAAACTATATAGTT-TA
1 TATATAAACTATATA-TTATA
*
2137018 TATATGAACTATA-ATT-TA
1 TATATAAACTATATATTATA
* * *
2137036 CATATGAACTATATA-TAAA
1 TATATAAACTATATATTATA
*
2137055 CTAGAGTTAAACTATATAGTT-TA
1 -TATA--TAAACTATATA-TTATA
*
2137078 TATATGAA-T-TATAGTT-TA
1 TATATAAACTATATA-TTATA
* *
2137096 CATATAAACTATAGTTGATATTTA
1 TATATAAACTATA--T-AT-TATA
* * *
2137120 CATATGAACTATA-GTT-TA
1 TATATAAACTATATATTATA
* * * *
2137138 CATATGAACTATACATATAGTT
1 TATATAAACTATATAT-TA-TA
* *
2137160 TATTAGTGAACTATATA-AACTA
1 TA-TA-TAAACTATATATTA-TA
* * * * *
2137182 TTTATATAGTATATACTGTA
1 TATATAAACTATATATTATA
2137202 TATATAAACTATAGT-TTATA
1 TATATAAACTATA-TATTATA
* *
2137222 TTTATATACTATATTATATATA
1 TATATAAACTATA-TAT-TATA
*
2137244 TATATATA-TATATATATATA
1 TATATAAACTATATAT-TATA
*
2137264 CTATATATACTATATA
1 -TATATAAACTATATA
2137280 GTATTATTTA
Statistics
Matches: 458, Mismatches: 90, Indels: 132
0.67 0.13 0.19
Matches are distributed among these distances:
15 2 0.00
16 9 0.02
18 68 0.15
19 21 0.05
20 143 0.31
21 34 0.07
22 103 0.22
23 19 0.04
24 44 0.10
25 9 0.02
26 3 0.01
27 3 0.01
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (20 bp):
TATATAAACTATATATTATA
Found at i:2136961 original size:18 final size:18
Alignment explanation
Indices: 2136940--2137116 Score: 63
Period size: 18 Copynumber: 9.2 Consensus size: 18
2136930 ATATAAAAAC
2136940 TATATAAACTATAGTTTA
1 TATATAAACTATAGTTTA
*
2136958 TATATAAACTATA-TACTA
1 TATATAAACTATAGT-TTA
* ** *
2136976 TAGTTTATATTTATA-TATAATC
1 TA-TATA-AACTATAGT-T--TA
2136998 TATATAAACTATATAGTTTA
1 TATATAAAC--TATAGTTTA
* *
2137018 TATATGAACTATAATTTA
1 TATATAAACTATAGTTTA
* * *
2137036 CATATGAACTATA-TATAAA
1 TATATAAACTATAGT-T-TA
*
2137055 CTAGAGTTAAACTATATAGTTTA
1 -TATA--TAAAC--TATAGTTTA
* *
2137078 TATATGAATTATAGTTTA
1 TATATAAACTATAGTTTA
* *
2137096 CATATAAACTATAGTTGA
1 TATATAAACTATAGTTTA
2137114 TAT
1 TAT
2137117 TTACATATGA
Statistics
Matches: 117, Mismatches: 26, Indels: 32
0.67 0.15 0.18
Matches are distributed among these distances:
17 2 0.02
18 63 0.54
19 4 0.03
20 22 0.19
21 3 0.03
22 15 0.13
23 2 0.02
24 5 0.04
25 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.43
Consensus pattern (18 bp):
TATATAAACTATAGTTTA
Found at i:2137028 original size:60 final size:58
Alignment explanation
Indices: 2136909--2137108 Score: 190
Period size: 60 Copynumber: 3.4 Consensus size: 58
2136899 TATTGTATAG
* * *
2136909 TATAATTTACATATGAACTAAATATAAAAACTATATAAAC--TATAGTTTATATATAAAC
1 TATAATATACATATGAACT--ATATATAAACTATATAAACTATATAGTTTATATATGAAC
** ** *
2136967 TATATACTATAGTTTAT-ATTTATATATAATCTATATAAACTATATAGTTTATATATGAAC
1 TATA-A-TATA-CATATGAACTATATATAAACTATATAAACTATATAGTTTATATATGAAC
* * *
2137027 TATAATTTACATATGAACTATATATAAACTAGAGTTAAACTATATAGTTTATATATGAAT
1 TATAATATACATATGAACTATATATAAACTATA--TAAACTATATAGTTTATATATGAAC
* * *
2137087 TATAGTTTACATATAAACTATA
1 TATAATATACATATGAACTATA
2137109 GTTGATATTT
Statistics
Matches: 116, Mismatches: 18, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
57 3 0.03
58 38 0.33
59 2 0.02
60 70 0.60
61 3 0.03
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (58 bp):
TATAATATACATATGAACTATATATAAACTATATAAACTATATAGTTTATATATGAAC
Found at i:2137139 original size:18 final size:18
Alignment explanation
Indices: 2137009--2137150 Score: 88
Period size: 18 Copynumber: 7.2 Consensus size: 18
2136999 ATATAAACTA
*
2137009 TATAGTTTATATATGAAC
1 TATAGTTTACATATGAAC
*
2137027 TATAATTTACATATGAAC
1 TATAGTTTACATATGAAC
* * *
2137045 TATA-TATAAACTAGAGTTAAAC
1 TATAGT-T-TAC-ATA--TGAAC
* *
2137067 TATATAGTTTATATATGAAT
1 --TATAGTTTACATATGAAC
*
2137087 TATAGTTTACATATAAAC
1 TATAGTTTACATATGAAC
2137105 TATAGTTGATATTTACATATGAAC
1 TATA---G---TTTACATATGAAC
2137129 TATAGTTTACATATGAAC
1 TATAGTTTACATATGAAC
2137147 TATA
1 TATA
2137151 CATATAGTTT
Statistics
Matches: 96, Mismatches: 14, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
17 1 0.01
18 57 0.59
19 2 0.02
20 5 0.05
21 2 0.02
22 6 0.06
23 1 0.01
24 21 0.22
25 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (18 bp):
TATAGTTTACATATGAAC
Found at i:2137156 original size:24 final size:24
Alignment explanation
Indices: 2137129--2137174 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2137119 ACATATGAAC
2137129 TATAGTTTACATA-TGAACTATACA
1 TATAGTTTA-ATAGTGAACTATACA
*
2137153 TATAGTTTATTAGTGAACTATA
1 TATAGTTTAATAGTGAACTATA
2137175 TAAACTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (24 bp):
TATAGTTTAATAGTGAACTATACA
Found at i:2137170 original size:42 final size:41
Alignment explanation
Indices: 2137068--2137174 Score: 126
Period size: 42 Copynumber: 2.5 Consensus size: 41
2137058 GAGTTAAACT
* *
2137068 ATATAGTTTATATATGAATTATAGTTTACATATAAACTATAG
1 ATATAGTTTAT-TATGAACTATAGTTTACATATAAACTATAC
* * *
2137110 TTGATA-TTTACATATGAACTATAGTTTACATATGAACTATAC
1 AT-ATAGTTTA-TTATGAACTATAGTTTACATATAAACTATAC
2137152 ATATAGTTTATTAGTGAACTATA
1 ATATAGTTTATTA-TGAACTATA
2137175 TAAACTATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
41 5 0.09
42 46 0.85
43 3 0.06
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (41 bp):
ATATAGTTTATTATGAACTATAGTTTACATATAAACTATAC
Found at i:2137189 original size:2 final size:2
Alignment explanation
Indices: 2137184--2137279 Score: 86
Period size: 2 Copynumber: 45.0 Consensus size: 2
2137174 ATAAACTATT
* * * *
2137184 TA TA TA GTA TA TA CTG TA TA TA TA AA CTA TA GTT TA TA TT TA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA
2137228 TA CTA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
2137271 TA CTA TA TA
1 TA -TA TA TA
2137280 GTATTATTTA
Statistics
Matches: 78, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
1 1 0.01
2 66 0.85
3 11 0.14
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2137205 original size:18 final size:17
Alignment explanation
Indices: 2137171--2137279 Score: 107
Period size: 18 Copynumber: 6.4 Consensus size: 17
2137161 ATTAGTGAAC
* *
2137171 TATATAAACTATTTATA
1 TATATATACTATATATA
*
2137188 TAGTATATACTGTATATA
1 TA-TATATACTATATATA
* *
2137206 TAAACTATAGT-T-TATA
1 TATA-TATACTATATATA
*
2137222 TTTATATACTATATTATA
1 TATATATACTATA-TATA
2137240 TATATATA-TATATATA
1 TATATATACTATATATA
2137256 TATATATACTATATATA
1 TATATATACTATATATA
2137273 CTATATA
1 -TATATA
2137280 GTATTATTTA
Statistics
Matches: 76, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
15 5 0.07
16 19 0.25
17 16 0.21
18 36 0.47
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (17 bp):
TATATATACTATATATA
Found at i:2137227 original size:6 final size:6
Alignment explanation
Indices: 2137184--2137279 Score: 86
Period size: 7 Copynumber: 15.0 Consensus size: 6
2137174 ATAAACTATT
* * * *
2137184 TATATA GTATATA CTGTATA TATAAA CTATAGTT TATATT TATATA CTATAT-
1 TATATA -TATATA -TATATA TATATA -TATA-TA TATATA TATATA -TATATA
2137236 TATATA TATATA TATATA TATATA TATACTA TATATA CTATATA
1 TATATA TATATA TATATA TATATA TATA-TA TATATA -TATATA
2137280 GTATTATTTA
Statistics
Matches: 76, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
5 5 0.07
6 35 0.46
7 36 0.47
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (6 bp):
TATATA
Found at i:2137548 original size:13 final size:13
Alignment explanation
Indices: 2137529--2137566 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
2137519 TAATTTAATG
2137529 ATTATAAATAA-A
1 ATTATAAATAAGA
2137541 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
2137556 ATTATAAATAA
1 ATTATAAATAA
2137567 TATAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:2137576 original size:19 final size:19
Alignment explanation
Indices: 2137545--2137591 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2137535 AATAAAATTT
*
2137545 ATAATAT-AAGAATTATAA
1 ATAATATAAAGAATTAGAA
*
2137563 ATAATATAAAGAATTGGAA
1 ATAATATAAAGAATTAGAA
*
2137582 TTAATATAAA
1 ATAATATAAA
2137592 ACCAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.32
Consensus pattern (19 bp):
ATAATATAAAGAATTAGAA
Found at i:2140847 original size:31 final size:31
Alignment explanation
Indices: 2140806--2140871 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
2140796 TCATTCCAAT
* * *
2140806 TAACAGAAATAACAATAAAATACTTATTTTA
1 TAACAAAAATAAAAATAAAACACTTATTTTA
**
2140837 TAACAAAAATAAAAATTGAACACTTATTTTA
1 TAACAAAAATAAAAATAAAACACTTATTTTA
2140868 TAAC
1 TAAC
2140872 TTTTAATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (31 bp):
TAACAAAAATAAAAATAAAACACTTATTTTA
Found at i:2143399 original size:2 final size:2
Alignment explanation
Indices: 2143394--2143419 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2143384 ACACACACAC
2143394 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
2143420 GTTGGGGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2147984 original size:19 final size:19
Alignment explanation
Indices: 2147960--2148005 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
2147950 AAATTTGGTT
*
2147960 TTTATATTAATTCCAATTC
1 TTTATATTAATTACAATTC
* *
2147979 TTTATATTATTTATAATTC
1 TTTATATTAATTACAATTC
2147998 -TTATATTA
1 TTTATATTA
2148006 TAAATTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATATTAATTACAATTC
Found at i:2148019 original size:13 final size:14
Alignment explanation
Indices: 2147985--2148021 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
2147975 ATTCTTTATA
2147985 TTATTTAT-AATTC
1 TTATTTATAAATTC
2147998 TTATATTATAAATT-
1 TTAT-TTATAAATTC
2148012 TTATTTATAA
1 TTATTTATAA
2148022 TCATTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATAAATTC
Found at i:2148292 original size:7 final size:6
Alignment explanation
Indices: 2148279--2148358 Score: 63
Period size: 7 Copynumber: 12.5 Consensus size: 6
2148269 ATACTATACA
* *
2148279 ATATAT ATAGTAT ATATAT ATATAT ATA-AT ATAGTAT ATAAAT ATAAACT
1 ATATAT ATA-TAT ATATAT ATATAT ATATAT ATA-TAT ATATAT ATATA-T
* *
2148329 ATAGTTT ATATAT ACAGTAT ATACTAT ATA
1 ATA-TAT ATATAT ATA-TAT ATA-TAT ATA
2148359 AATAGTTTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
5 5 0.08
6 26 0.43
7 30 0.49
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (6 bp):
ATATAT
Found at i:2148297 original size:13 final size:13
Alignment explanation
Indices: 2148279--2148324 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
2148269 ATACTATACA
2148279 ATATATATAGTAT
1 ATATATATAGTAT
2148292 ATATATATA-TAT
1 ATATATATAGTAT
2148304 ATA-ATATAGTAT
1 ATATATATAGTAT
*
2148316 ATAAATATA
1 ATATATATA
2148325 AACTATAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 5 0.16
12 12 0.39
13 14 0.45
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (13 bp):
ATATATATAGTAT
Found at i:2148300 original size:24 final size:24
Alignment explanation
Indices: 2148268--2148331 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
2148258 CTATATAAAT
2148268 TATACTATACAATAT-ATATAGTATA
1 TATA-TATA-AATATAATATAGTATA
*
2148293 TATATATATATATAATATAGTATA
1 TATATATAAATATAATATAGTATA
*
2148317 TAAATATAAACTATA
1 TATATATAAA-TATA
2148332 GTTTATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.12
24 22 0.65
25 8 0.24
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (24 bp):
TATATATAAATATAATATAGTATA
Found at i:2148304 original size:28 final size:30
Alignment explanation
Indices: 2148259--2148324 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 30
2148249 ACTTGAATAC
*
2148259 TATATAAATTATACTATACAATATA-TATA
1 TATATATATTATACTATACAATATAGTATA
*
2148288 GTATATATA-TATA-TATATAATATAGTATA
1 -TATATATATTATACTATACAATATAGTATA
*
2148317 TAAATATA
1 TATATATA
2148325 AACTATAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 17 0.53
29 8 0.25
30 7 0.22
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (30 bp):
TATATATATTATACTATACAATATAGTATA
Found at i:2148358 original size:20 final size:19
Alignment explanation
Indices: 2148279--2148371 Score: 77
Period size: 20 Copynumber: 4.9 Consensus size: 19
2148269 ATACTATACA
2148279 ATATATATAGTATATATAT
1 ATATATATAGTATATATAT
*
2148298 ATATATATAATATAGTATAT
1 ATATATATAGTATA-TATAT
* * *
2148318 AAATATAAACTATAGT-T-T
1 ATATATATAGTATA-TATAT
*
2148336 ATATATACAGTATATACTAT
1 ATATATATAGTATATA-TAT
*
2148356 ATA-A-ATAGTTTATATA
1 ATATATATAGTATATATA
2148372 GTTCACTAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
17 3 0.05
18 20 0.33
19 16 0.26
20 22 0.36
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (19 bp):
ATATATATAGTATATATAT
Found at i:2148371 original size:2 final size:2
Alignment explanation
Indices: 2148279--2148358 Score: 63
Period size: 2 Copynumber: 37.5 Consensus size: 2
2148269 ATACTATACA
*
2148279 AT AT AT AT AGT AT AT AT AT AT AT AT AT A- AT AT AGT AT AT AA AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * *
2148322 AT AA ACT AT AGT TT AT AT AT AC AGT AT AT ACT AT AT A
1 AT AT A-T AT A-T AT AT AT AT AT A-T AT AT A-T AT AT A
2148359 AATAGTTTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
1 1 0.02
2 53 0.84
3 9 0.14
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (2 bp):
AT
Found at i:2148395 original size:24 final size:24
Alignment explanation
Indices: 2148368--2148413 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2148358 AAATAGTTTA
2148368 TATAGTTCACTA-ATAAACTATATG
1 TATAGTTCA-TATATAAACTATATG
*
2148392 TATAGTTCATATGTAAACTATA
1 TATAGTTCATATATAAACTATA
2148414 GTTCATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (24 bp):
TATAGTTCATATATAAACTATATG
Found at i:2148397 original size:33 final size:31
Alignment explanation
Indices: 2148315--2148413 Score: 83
Period size: 31 Copynumber: 3.1 Consensus size: 31
2148305 TAATATAGTA
* *
2148315 TATAAA-TATAAACTATAGTTTATATATACAG
1 TATAAACTATATA-TATAGTTTATATATACAC
* * *
2148346 TATATACTATATAAATAGTTTATATAGTTCAC
1 TATAAACTATATATATAGTTTATATA-TACAC
* * * *
2148378 TAATAAACTATATGTATAGTTCATATGTAAAC
1 T-ATAAACTATATATATAGTTTATATATACAC
2148410 TATA
1 TATA
2148414 GTTCATATGT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
31 20 0.38
32 13 0.25
33 20 0.38
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.40
Consensus pattern (31 bp):
TATAAACTATATATATAGTTTATATATACAC
Found at i:2148415 original size:18 final size:18
Alignment explanation
Indices: 2148392--2148533 Score: 88
Period size: 18 Copynumber: 7.2 Consensus size: 18
2148382 AAACTATATG
2148392 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
2148410 TATAGTTCATATGTAAATATCAAC
1 TATAGTTCATATG----TA--AAC
*
2148434 TATAGTTTATATGTAAAC
1 TATAGTTCATATGTAAAC
* *
2148452 TATAATTCATATATAAAC
1 TATAGTTCATATGTAAAC
* * *
2148470 TATATAGTTTAACTCTAGTTTATA-
1 --TATAG-TT--C-ATA-TGTAAAC
*
2148494 TATAGTTCATATGTAAAT
1 TATAGTTCATATGTAAAC
*
2148512 TATAGTTCATATATAAAC
1 TATAGTTCATATGTAAAC
2148530 TATA
1 TATA
2148534 TAGTTTATAT
Statistics
Matches: 97, Mismatches: 13, Indels: 28
0.70 0.09 0.20
Matches are distributed among these distances:
17 4 0.04
18 53 0.55
19 1 0.01
20 6 0.06
21 4 0.04
22 7 0.07
23 1 0.01
24 17 0.18
25 4 0.04
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:2148415 original size:42 final size:42
Alignment explanation
Indices: 2148368--2148474 Score: 137
Period size: 42 Copynumber: 2.5 Consensus size: 42
2148358 AAATAGTTTA
*
2148368 TATAGTTCACTA-ATAAACTATATGTATAGTTCATATGTAAAC
1 TATAGTTCA-TATATAAACTATATCTATAGTTCATATGTAAAC
* * *
2148410 TATAGTTCATATGTAAA-TATCAACTATAGTTTATATGTAAAC
1 TATAGTTCATATATAAACTAT-ATCTATAGTTCATATGTAAAC
*
2148452 TATAATTCATATATAAACTATAT
1 TATAGTTCATATATAAACTATAT
2148475 AGTTTAACTC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
41 5 0.09
42 47 0.85
43 3 0.05
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.40
Consensus pattern (42 bp):
TATAGTTCATATATAAACTATATCTATAGTTCATATGTAAAC
Found at i:2148534 original size:40 final size:39
Alignment explanation
Indices: 2148490--2148633 Score: 102
Period size: 40 Copynumber: 3.7 Consensus size: 39
2148480 AACTCTAGTT
*
2148490 TATATATAGTTCATATGTAAATTATAGTTCATATATAAAC
1 TATATATAGTTCATATATAAATTATAGTT-ATATATAAAC
* *
2148530 --TATATAGTT--TATATAGATTATA-TATAAATATAAAC
1 TATATATAGTTCATATATAAATTATAGT-TATATATAAAC
* * ***
2148565 TATAGTATATAGTTTATATATAAACTATAGTT-TATATAGTTTT
1 --TA-TATATAGTTCATATATAAATTATAGTTATATATA--AAC
*
2148608 TATATATAGTTCATATGTAAATTATA
1 TATATATAGTTCATATATAAATTATA
2148634 CTATACAATA
Statistics
Matches: 81, Mismatches: 12, Indels: 22
0.70 0.10 0.19
Matches are distributed among these distances:
35 10 0.12
36 12 0.15
38 9 0.11
40 30 0.37
41 7 0.09
42 12 0.15
43 1 0.01
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (39 bp):
TATATATAGTTCATATATAAATTATAGTTATATATAAAC
Found at i:2148554 original size:60 final size:60
Alignment explanation
Indices: 2148434--2148671 Score: 209
Period size: 60 Copynumber: 4.1 Consensus size: 60
2148424 AAATATCAAC
* * * *
2148434 TATAGTTTATATGTAAACTATAATTCATATATAAACTATATAGTTTAACTCTAG-TT-TATA
1 TATAGTTCATATGTAAATTATAGTTCATATATAAACTATATAGTTT-A-TATAGATTATATA
2148494 TATAGTTCATATGTAAATTATAGTTCATATATAAACTATATAGTTTATATAGATTATATA
1 TATAGTTCATATGTAAATTATAGTTCATATATAAACTATATAGTTTATATAGATTATATA
** * * *
2148554 TAAATA-TAAACTATAGT--A-TATAGTTTATATATAAAC--TATAGTTTATATAGTTTTTATA
1 T--ATAGTTCA-TAT-GTAAATTATAGTTCATATATAAACTATATAGTTTATATAGATTATATA
* *
2148612 TATAGTTCATATGTAAATTATA---C-TATACAATA-TATATAGTTTATATATA-TATA-A
1 TATAGTTCATATGTAAATTATAGTTCATATATAA-ACTATATAGTTTATATAGATTATATA
2148666 TATAGT
1 TATAGT
2148672 ATATAAATAT
Statistics
Matches: 149, Mismatches: 16, Indels: 32
0.76 0.08 0.16
Matches are distributed among these distances:
54 13 0.09
55 6 0.04
56 19 0.13
57 3 0.02
58 29 0.19
59 3 0.02
60 65 0.44
61 3 0.02
62 6 0.04
63 2 0.01
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (60 bp):
TATAGTTCATATGTAAATTATAGTTCATATATAAACTATATAGTTTATATAGATTATATA
Found at i:2148586 original size:18 final size:18
Alignment explanation
Indices: 2148426--2148602 Score: 63
Period size: 18 Copynumber: 9.2 Consensus size: 18
2148416 TCATATGTAA
*
2148426 ATATCAACTATAGTTTAT
1 ATATAAACTATAGTTTAT
* * *
2148444 ATGTAAACTATAATTCAT
1 ATATAAACTATAGTTTAT
2148462 ATATAAACTATATAGTTTAACTCT
1 ATATAAAC--TATAGTTT-A---T
* * *
2148486 AGTTTATA-TATAGTTCAT
1 A-TATAAACTATAGTTTAT
* * *
2148504 ATGTAAATTATAGTTCAT
1 ATATAAACTATAGTTTAT
2148522 ATATAAACTATATAGTTTAT
1 ATATAAAC--TATAGTTTAT
* * * *
2148542 ATAGATTATA-TATAAATATAA
1 AT--A-TAAACTAT-AGTTTAT
*
2148563 ACTATAGTA-TATAGTTTAT
1 A-TATA-AACTATAGTTTAT
2148582 ATATAAACTATAGTTTAT
1 ATATAAACTATAGTTTAT
2148600 ATA
1 ATA
2148603 GTTTTTATAT
Statistics
Matches: 119, Mismatches: 23, Indels: 34
0.68 0.13 0.19
Matches are distributed among these distances:
17 5 0.04
18 56 0.47
19 7 0.06
20 26 0.22
21 7 0.06
22 9 0.08
23 3 0.03
24 2 0.02
25 4 0.03
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.44
Consensus pattern (18 bp):
ATATAAACTATAGTTTAT
Found at i:2148601 original size:27 final size:25
Alignment explanation
Indices: 2148557--2148752 Score: 103
Period size: 27 Copynumber: 8.0 Consensus size: 25
2148547 TTATATATAA
2148557 ATATAAACTATAGTATATAGTTTAT
1 ATATAAACTATAGTATATAGTTTAT
*
2148582 ATATAAACTATAGTTTATATAGTTTTT
1 ATATAAACTATAG--TATATAGTTTAT
* * * **
2148609 ATATATAGT-TCA-TATGTAAATTAT
1 ATATAAACTAT-AGTATATAGTTTAT
*
2148633 ACTAT--ACAATA-TATATAGTTTAT
1 A-TATAAACTATAGTATATAGTTTAT
*
2148656 ATAT--A-TATA--ATATAGTATATAA
1 ATATAAACTATAGTATATAGT-T-TAT
* * *
2148678 ATATCAACTATAGTATGTAGTATATAA
1 ATATAAACTATAGTATATAGT-T-TAT
* *
2148705 ATATAAACTATAGTTTATA-TATAT
1 ATATAAACTATAGTATATAGTTTAT
*
2148729 ATAT-AA-TATATTATATAGTTTAT
1 ATATAAACTATAGTATATAGTTTAT
2148752 A
1 A
2148753 ATTCACTAAT
Statistics
Matches: 135, Mismatches: 23, Indels: 28
0.73 0.12 0.15
Matches are distributed among these distances:
20 7 0.05
21 4 0.03
22 19 0.14
23 19 0.14
24 17 0.13
25 20 0.15
26 2 0.01
27 47 0.35
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (25 bp):
ATATAAACTATAGTATATAGTTTAT
Found at i:2148648 original size:2 final size:2
Alignment explanation
Indices: 2148641--2148745 Score: 56
Period size: 2 Copynumber: 50.5 Consensus size: 2
2148631 ATACTATACA
* *
2148641 AT AT AT AT AGT TT AT AT AT AT AT A- AT AT AGT AT AT AA AT AT CA-
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT -AT
* * * *
2148684 ACT AT AGT AT GT AGT AT AT AA AT AT AA ACT AT AGT TT AT AT AT AT
1 A-T AT A-T AT AT A-T AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT
2148729 AT AT A- AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT A
2148746 GTTTATAATT
Statistics
Matches: 79, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
1 4 0.05
2 64 0.81
3 11 0.14
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2148742 original size:20 final size:20
Alignment explanation
Indices: 2148641--2148745 Score: 63
Period size: 20 Copynumber: 4.8 Consensus size: 20
2148631 ATACTATACA
2148641 ATAT-ATATAGTT-TATATAT
1 ATATAATATA-TTATATATAT
* *
2148660 ATATAATATAGTATATAAAT
1 ATATAATATATTATATATAT
*
2148680 ATCA-ACTATAGTATGTAGTATATAA
1 AT-ATA--ATA-TAT-TA-TATATAT
2148705 ATATAAACTATAGTTTATATATAT
1 ATAT-AA-TATA--TTATATATAT
2148729 ATATAATATATTATATA
1 ATATAATATATTATATA
2148746 GTTTATAATT
Statistics
Matches: 67, Mismatches: 6, Indels: 25
0.68 0.06 0.26
Matches are distributed among these distances:
19 5 0.07
20 21 0.31
21 1 0.01
22 7 0.10
23 4 0.06
24 16 0.24
25 11 0.16
26 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.44
Consensus pattern (20 bp):
ATATAATATATTATATATAT
Found at i:2148781 original size:24 final size:24
Alignment explanation
Indices: 2148749--2148796 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2148739 TTATATAGTT
2148749 TATAATTCACTA-ATAAACTATATA
1 TATAATTCA-TATATAAACTATATA
* *
2148773 TATAGTTCATATGTAAACTATATA
1 TATAATTCATATATAAACTATATA
2148797 GTTTACATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (24 bp):
TATAATTCATATATAAACTATATA
Found at i:2148794 original size:22 final size:22
Alignment explanation
Indices: 2148769--2148838 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
2148759 TAATAAACTA
2148769 TATATATAGTTCATATGTAAAC
1 TATATATAGTTCATATGTAAAC
**
2148791 --TATATAGTTTACATA-GTTTA-
1 TATATATAG-TT-CATATGTAAAC
2148811 TATATATAGTTCATATGTAAAC
1 TATATATAGTTCATATGTAAAC
2148833 TATATA
1 TATATA
2148839 GTATATATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
20 11 0.29
21 10 0.26
22 17 0.45
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (22 bp):
TATATATAGTTCATATGTAAAC
Found at i:2148818 original size:42 final size:42
Alignment explanation
Indices: 2148767--2148858 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
2148757 ACTAATAAAC
*
2148767 TATATATATAGTTCATATGTAAACTATATAGTTTACATAGTT
1 TATATATATAGTTCATATGTAAACTATATAGTATACATAGTT
*
2148809 TATATATATAGTTCATATGTAAACTATATAGTATATATAGTT
1 TATATATATAGTTCATATGTAAACTATATAGTATACATAGTT
*
2148851 TACATATA
1 TATATATA
2148859 GTATAAGTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.45
Consensus pattern (42 bp):
TATATATATAGTTCATATGTAAACTATATAGTATACATAGTT
Found at i:2148846 original size:20 final size:20
Alignment explanation
Indices: 2148771--2148840 Score: 88
Period size: 20 Copynumber: 3.4 Consensus size: 20
2148761 ATAAACTATA
2148771 TATATAGTTCATATGTAAAC
1 TATATAGTTCATATGTAAAC
* *
2148791 TATATAGTTTACATAGTTTATA-
1 TATATAG-TT-CATA-TGTAAAC
2148813 TATATAGTTCATATGTAAAC
1 TATATAGTTCATATGTAAAC
2148833 TATATAGT
1 TATATAGT
2148841 ATATATAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 4 0.10
20 19 0.45
21 4 0.10
22 11 0.26
23 4 0.10
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (20 bp):
TATATAGTTCATATGTAAAC
Found at i:2149010 original size:22 final size:22
Alignment explanation
Indices: 2148962--2149024 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
2148952 ACCTTAAACC
* *
2148962 ATATATACTATAT-GTATATAT
1 ATATAAACTATATAGTTTATAT
2148983 ATATAAACTATATAGTTTATAT
1 ATATAAACTATATAGTTTATAT
*
2149005 -TAATAAACTATATATTTTAT
1 AT-ATAAACTATATAGTTTAT
2149025 GCATAGTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.35
22 24 0.65
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (22 bp):
ATATAAACTATATAGTTTATAT
Found at i:2149397 original size:40 final size:38
Alignment explanation
Indices: 2149321--2149487 Score: 213
Period size: 38 Copynumber: 4.4 Consensus size: 38
2149311 TACTTTAAAA
2149321 AAAACAATTTTTGAAAA-A-AT--A-TATATAGTTTTG
1 AAAACAATTTTTGAAAATATATAAATTATATAGTTTTG
2149354 AAAACAATTTTTGAATATATATATAAATTATATAGTTTTG
1 AAAACAATTTTTGAA-A-ATATATAAATTATATAGTTTTG
* *
2149394 AAAATAATTTTTGAAAATATATATATTATATAGTTTTG
1 AAAACAATTTTTGAAAATATATAAATTATATAGTTTTG
*
2149432 AAAACAAATTTTTGAAAACATATATAA-TATATAGTTTTG
1 AAAAC-AATTTTTGAAAATATATA-AATTATATAGTTTTG
2149471 AAAA-ACATTTTTGAAAA
1 AAAACA-ATTTTTGAAAA
2149488 CATTTTGAAA
Statistics
Matches: 119, Mismatches: 5, Indels: 15
0.86 0.04 0.11
Matches are distributed among these distances:
33 15 0.13
34 1 0.01
35 1 0.01
36 1 0.01
37 3 0.03
38 36 0.30
39 35 0.29
40 27 0.23
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (38 bp):
AAAACAATTTTTGAAAATATATAAATTATATAGTTTTG
Found at i:2149490 original size:38 final size:39
Alignment explanation
Indices: 2149341--2149490 Score: 207
Period size: 39 Copynumber: 3.9 Consensus size: 39
2149331 TTGAAAAAAT
* *
2149341 ATATATAGTTTTGAAAACA-ATTTTTGAATATATATATAA
1 ATATATAGTTTTGAAAACACATTTTTGAAAACATATAT-A
* *
2149380 ATTATATAGTTTTGAAAATA-ATTTTTGAAAATATATATA
1 A-TATATAGTTTTGAAAACACATTTTTGAAAACATATATA
* *
2149419 TTATATAGTTTTGAAAACAAATTTTTGAAAACATATATA
1 ATATATAGTTTTGAAAACACATTTTTGAAAACATATATA
2149458 ATATATAGTTTTGAAAA-ACATTTTTGAAAACAT
1 ATATATAGTTTTGAAAACACATTTTTGAAAACAT
2149491 TTTGAAAAAG
Statistics
Matches: 102, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
38 32 0.31
39 36 0.35
40 34 0.33
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (39 bp):
ATATATAGTTTTGAAAACACATTTTTGAAAACATATATA
Found at i:2149495 original size:11 final size:12
Alignment explanation
Indices: 2149466--2149498 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2149456 TAATATATAG
2149466 TTTTGAAAAACAT
1 TTTTG-AAAACAT
2149479 TTTTGAAAACA-
1 TTTTGAAAACAT
2149490 TTTTGAAAA
1 TTTTGAAAA
2149499 AGTTCTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 6 0.30
13 5 0.25
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:2149499 original size:12 final size:13
Alignment explanation
Indices: 2149466--2149499 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
2149456 TAATATATAG
2149466 TTTTGAAAAACAT
1 TTTTGAAAAACAT
2149479 TTTTG-AAAACA-
1 TTTTGAAAAACAT
2149490 TTTTGAAAAA
1 TTTTGAAAAA
2149500 GTTCTGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.25
12 10 0.50
13 5 0.25
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (13 bp):
TTTTGAAAAACAT
Found at i:2149548 original size:37 final size:35
Alignment explanation
Indices: 2149507--2149602 Score: 120
Period size: 37 Copynumber: 2.7 Consensus size: 35
2149497 AAAGTTCTGA
2149507 AAAATATATAAAATATATAATTTAGAAAACATTTT
1 AAAATATATAAAATATATAATTTAGAAAACATTTT
* * *
2149542 CGAAAATATATATAATATATGATTTTGAAAACATTTT
1 --AAAATATATAAAATATATAATTTAGAAAACATTTT
* *
2149579 TAAATATATATAAATATGTAATTT
1 AAAATATATA-AAATATATAATTT
2149603 TCATTTTCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
35 9 0.18
36 10 0.20
37 32 0.63
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (35 bp):
AAAATATATAAAATATATAATTTAGAAAACATTTT
Found at i:2149640 original size:11 final size:11
Alignment explanation
Indices: 2149600--2149645 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
2149590 AAATATGTAA
*
2149600 TTTTCATTTTCA
1 TTTTCA-TTTCT
2149612 TTTTCATTT-T
1 TTTTCATTTCT
*
2149622 ATTT-ATTTCT
1 TTTTCATTTCT
2149632 TTTTCATTTCT
1 TTTTCATTTCT
2149643 TTT
1 TTT
2149646 GCTATTTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
9 4 0.14
10 7 0.24
11 12 0.41
12 6 0.21
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTCATTTCT
Found at i:2150171 original size:32 final size:29
Alignment explanation
Indices: 2150135--2150193 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 29
2150125 AGAAACCGAG
2150135 CCAAAGCAAAAGCGAAAATAAAGAAAAACAGT
1 CCAAAGCAAAAGC-AAAA-AAA-AAAAACAGT
* *
2150167 CCAAATCAAGAGCAAAAAAAAAAAACA
1 CCAAAGCAAAAGCAAAAAAAAAAAACA
2150194 AAGCTCGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 3 0.12
31 4 0.16
32 11 0.44
ACGTcount: A:0.66, C:0.17, G:0.12, T:0.05
Consensus pattern (29 bp):
CCAAAGCAAAAGCAAAAAAAAAAAACAGT
Found at i:2150373 original size:15 final size:15
Alignment explanation
Indices: 2150353--2150382 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2150343 TTGGCCAATC
2150353 GGGTTTCAGATTGGT
1 GGGTTTCAGATTGGT
2150368 GGGTTTCAGATTGGT
1 GGGTTTCAGATTGGT
2150383 ATTGAGGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.40, T:0.40
Consensus pattern (15 bp):
GGGTTTCAGATTGGT
Found at i:2150966 original size:17 final size:17
Alignment explanation
Indices: 2150946--2150979 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2150936 TTCCTCTTTC
2150946 ATTTTT-TTAATTTTAAT
1 ATTTTTCTT-ATTTTAAT
2150963 ATTTTTCTTATTTTAAT
1 ATTTTTCTTATTTTAAT
2150980 TTTATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTCTTATTTTAAT
Found at i:2156967 original size:201 final size:202
Alignment explanation
Indices: 2156689--2157067 Score: 519
Period size: 201 Copynumber: 1.9 Consensus size: 202
2156679 GAAGGCCTGG
* * ** * * **
2156689 GTTGGTTGTGATTTAGCAACAATGAACTATATCCCAGTCAAATTTACAGTATAGCTCAAGGCGAG
1 GTTGGTTGCGATTTAGCAACAATGAACTATATCACAACCAAATTCACAGCATAGCTCAACACGAG
* *
2156754 AAGGGCTATCTGTCAACAAAAACCTTCGAGTTCAATTCCATTCAACTCGAGGGCACATCAACCTC
66 AAGGGCTATCTGTCAACAAAAACCTTCGAGTCCAATTCCATTCAACTCGAGGGCACATCAACCAC
*
2156819 ATGGTAGCAACGAGGAACTACTTTCCAGTCGAATTTT-AAACCAAGGTATTTTAGCCTAGAAGAA
131 ATGGTAGCAACAAGGAACTACTTTCCAGTCGAATTTTCAAACCAAGGTATTTTAGCCTAGAAGAA
2156883 GACCTAT
196 GACCTAT
* * *
2156890 GTTGGTTGCGATTTAGCAACAA-GAGACTATTTCATAACCTAATTCACAGCATAGCTCAACACGA
1 GTTGGTTGCGATTTAGCAACAATGA-ACTATATCACAACCAAATTCACAGCATAGCTCAACACGA
* * * * * *
2156954 GAATGGTTATCTGTCAACAAAAACCTTTGAGTCCGATTCCATTCAGCTCGAGGGCATATCAACCA
65 GAAGGGCTATCTGTCAACAAAAACCTTCGAGTCCAATTCCATTCAACTCGAGGGCACATCAACCA
** * *
2157019 CATGGTAGCCTCAAGGAACTACTTTCCGGTTGAATTTTCAAACCAAGGT
130 CATGGTAGCAACAAGGAACTACTTTCCAGTCGAATTTTCAAACCAAGGT
2157068 CTTTAAACCG
Statistics
Matches: 152, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
200 2 0.01
201 140 0.92
202 10 0.07
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (202 bp):
GTTGGTTGCGATTTAGCAACAATGAACTATATCACAACCAAATTCACAGCATAGCTCAACACGAG
AAGGGCTATCTGTCAACAAAAACCTTCGAGTCCAATTCCATTCAACTCGAGGGCACATCAACCAC
ATGGTAGCAACAAGGAACTACTTTCCAGTCGAATTTTCAAACCAAGGTATTTTAGCCTAGAAGAA
GACCTAT
Found at i:2157627 original size:39 final size:38
Alignment explanation
Indices: 2157518--2157628 Score: 169
Period size: 38 Copynumber: 3.0 Consensus size: 38
2157508 TTTAAAAAAC
2157518 ACAATTTTTG-AAA-A-A-ATA-TATATAGTTTTGAAA
1 ACAATTTTTGAAAATATATATATTATATAGTTTTGAAA
2157551 ACAATTTTTGAAAATATATATATTATATAGTTTTGAAA
1 ACAATTTTTGAAAATATATATATTATATAGTTTTGAAA
*
2157589 ACAATTTTTGAATATATATATATTTATATAGTTTTGAAA
1 ACAATTTTTGAAAATATATATA-TTATATAGTTTTGAAA
2157628 A
1 A
2157629 TATATATGTT
Statistics
Matches: 71, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
33 10 0.14
34 3 0.04
35 1 0.01
36 1 0.01
37 3 0.04
38 36 0.51
39 17 0.24
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (38 bp):
ACAATTTTTGAAAATATATATATTATATAGTTTTGAAA
Found at i:2157646 original size:25 final size:26
Alignment explanation
Indices: 2157594--2157652 Score: 95
Period size: 25 Copynumber: 2.3 Consensus size: 26
2157584 TGAAAACAAT
2157594 TTTTGAATATATATATATTTATATAG
1 TTTTGAATATATATATATTTATATAG
2157620 TTTTGAA-A-ATATATATGTTATATAG
1 TTTTGAATATATATATAT-TTATATAG
2157645 TTTTGAAT
1 TTTTGAAT
2157653 TTTTTTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
24 8 0.26
25 16 0.52
26 7 0.23
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (26 bp):
TTTTGAATATATATATATTTATATAG
Found at i:2157707 original size:39 final size:38
Alignment explanation
Indices: 2157620--2157740 Score: 130
Period size: 39 Copynumber: 3.3 Consensus size: 38
2157610 ATTTATATAG
* * **
2157620 TTTTGAAAATATATATGTTATATAGTTTTG--AATTTT
1 TTTTGAAAACATATATATTATATAGTTTTGAAAACATT
2157656 TTTTG--AA-A-ATATATTATATAGTTTTGAAAACAATT
1 TTTTGAAAACATATATATTATATAGTTTTGAAAAC-ATT
*
2157691 TTTTGAAAACATATATAATATATAGTTTTGAAAAGCA-T
1 TTTTGAAAACATATATATTATATAGTTTTGAAAA-CATT
2157729 TTTTGAAAACAT
1 TTTTGAAAACAT
2157741 TTTGAAAACG
Statistics
Matches: 73, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
32 17 0.23
33 1 0.01
34 4 0.05
35 7 0.10
36 5 0.07
37 2 0.03
38 14 0.19
39 22 0.30
40 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.46
Consensus pattern (38 bp):
TTTTGAAAACATATATATTATATAGTTTTGAAAACATT
Found at i:2157745 original size:11 final size:11
Alignment explanation
Indices: 2157716--2157759 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
2157706 TAATATATAG
2157716 TTTTGAAAAGCA
1 TTTTGAAAA-CA
2157728 TTTTTGAAAACA
1 -TTTTGAAAACA
*
2157740 TTTTGAAAACG
1 TTTTGAAAACA
2157751 TTTTGAAAA
1 TTTTGAAAA
2157760 ATATAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 19 0.63
12 2 0.07
13 9 0.30
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.39
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:2157761 original size:96 final size:95
Alignment explanation
Indices: 2157568--2157834 Score: 265
Period size: 96 Copynumber: 2.8 Consensus size: 95
2157558 TTGAAAATAT
* * * *
2157568 ATATATTATATAGTTTTGAAAACAATTTTTGAATATATATATATTTATATAGTTTTGAAAATATA
1 ATATATTATATAGTTTTGAAAACAATTTTTGAAAATATATATA-ATATATAGTTTTGAAAACATT
* * * * ****
2157633 TATGTTATATAGTTTTGAATTTTTTTTGAAA
65 TTTGTAAAACAGTTTTGAAAACGTTTTGAAA
*
2157664 ATATATTATATAGTTTTGAAAACAATTTTTTGAAAACATATATAATATATAGTTTTGAAAAGCAT
1 ATATATTATATAGTTTTGAAAACAA-TTTTTGAAAATATATATAATATATAGTTTTGAAAA-CAT
2157729 TTTTG-AAAACA-TTTTGAAAACGTTTTGAAAA
64 TTTTGTAAAACAGTTTTGAAAACGTTTTG-AAA
* *
2157760 ATATAAATAATATATAATTTAT-AAAAC-ATTTTCGAAAATATATATAATATAT-GATTTTGAAA
1 ATAT--AT--TATATAGTTT-TGAAAACAATTTTTGAAAATATATATAATATATAG-TTTTGAAA
*
2157822 ACATTTTTTTAAA
60 ACATTTTTGTAAA
2157835 TATATATAAT
Statistics
Matches: 144, Mismatches: 17, Indels: 18
0.80 0.09 0.10
Matches are distributed among these distances:
95 12 0.08
96 51 0.35
97 29 0.20
98 36 0.25
99 1 0.01
100 14 0.10
101 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (95 bp):
ATATATTATATAGTTTTGAAAACAATTTTTGAAAATATATATAATATATAGTTTTGAAAACATTT
TTGTAAAACAGTTTTGAAAACGTTTTGAAA
Found at i:2157798 original size:37 final size:37
Alignment explanation
Indices: 2157739--2157854 Score: 137
Period size: 37 Copynumber: 3.1 Consensus size: 37
2157729 TTTTGAAAAC
* *
2157739 ATTTTGAAAACGTTTT-GAAAAATATAAATAATATATA
1 ATTTTGAAAACATTTTCG-AAAATATATATAATATATA
*
2157776 ATTTAT-AAAACATTTTCGAAAATATATATAATATATG
1 ATTT-TGAAAACATTTTCGAAAATATATATAATATATA
*** *
2157813 ATTTTGAAAACATTTTTTTAAATATATATAATATGTA
1 ATTTTGAAAACATTTTCGAAAATATATATAATATATA
2157850 ATTTT
1 ATTTT
2157855 AATTTACATT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
36 1 0.01
37 65 0.96
38 2 0.03
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (37 bp):
ATTTTGAAAACATTTTCGAAAATATATATAATATATA
Found at i:2163086 original size:105 final size:109
Alignment explanation
Indices: 2162965--2163219 Score: 322
Period size: 112 Copynumber: 2.3 Consensus size: 109
2162955 TGTATCAAGC
*
2162965 AATTTATAGAGAGACATGAAAAAATTAAAATAAAAATATAAAATTT-G-AGAAGAAG-AAA-AAT
1 AATTTATAGAGAGACATGAAAAAATTAAAATAAAAATATAAAATTTAGAAGAAGAAGAAAAGAAG
* * *
2163026 AAGAAAGCCAAATATGCAAACTTATCAATCTGACGTAGTAAACG
66 AAGAAAGACAAATATGCAAACTTACCAATCCGACGTAGTAAACG
* *
2163070 AATTTATAGAGAGACATGAAAAAATAAAAATAAAAAATATAGAATTTGAGAAGAAGAAGAAAAAG
1 AATTTATAGAGAGACATGAAAAAATTAAAAT-AAAAATATAAAATTT-AGAAGAAGAAG-AAAAG
* *
2163135 AAGAAGAAAGACAAATATGCAGACTTACCAATCCGATGTAGTAAACG
63 AAGAAGAAAGACAAATATGCAAACTTACCAATCCGACGTAGTAAACG
* ***
2163182 AATTGA-AGAGAGGGTTGAAAATAATTAAAATAATAAAT
1 AATTTATAGAGAGACATGAAAA-AATTAAAATAA-AAAT
2163220 GAAAAAAATA
Statistics
Matches: 128, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
105 30 0.23
106 14 0.11
108 1 0.01
109 8 0.06
111 17 0.13
112 58 0.45
ACGTcount: A:0.56, C:0.07, G:0.16, T:0.21
Consensus pattern (109 bp):
AATTTATAGAGAGACATGAAAAAATTAAAATAAAAATATAAAATTTAGAAGAAGAAGAAAAGAAG
AAGAAAGACAAATATGCAAACTTACCAATCCGACGTAGTAAACG
Found at i:2164880 original size:24 final size:24
Alignment explanation
Indices: 2164853--2164909 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
2164843 GCTTCTTTTA
2164853 CAGCTTCAGCCACTTCCATGTATT
1 CAGCTTCAGCCACTTCCATGTATT
2164877 CAGCTTCAGCCACTTCCATGTATT
1 CAGCTTCAGCCACTTCCATGTATT
2164901 CAGCTTCAG
1 CAGCTTCAG
2164910 TTGTAGATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.32
Consensus pattern (24 bp):
CAGCTTCAGCCACTTCCATGTATT
Found at i:2169612 original size:20 final size:20
Alignment explanation
Indices: 2169579--2169616 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2169569 TGTTTTAATG
*
2169579 AGCTCATTGTACATGTGTGCA
1 AGCTCATTGAACAT-TGTGCA
2169600 AGCT-ATTGAACATTGTG
1 AGCTCATTGAACATTGTG
2169617 ACTTCCTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 8 0.50
21 4 0.25
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (20 bp):
AGCTCATTGAACATTGTGCA
Found at i:2170862 original size:12 final size:12
Alignment explanation
Indices: 2170845--2170878 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
2170835 AGAGTGTTTG
2170845 GAATTTAAAGTA
1 GAATTTAAAGTA
*
2170857 GAATTTAGAGTA
1 GAATTTAAAGTA
2170869 GAATTTAAAG
1 GAATTTAAAG
2170879 GTTAGGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (12 bp):
GAATTTAAAGTA
Found at i:2175907 original size:20 final size:21
Alignment explanation
Indices: 2175882--2175922 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2175872 ATACATCAAG
*
2175882 ATCTTT-ATGGAGGCCATGAA
1 ATCTTTCATCGAGGCCATGAA
*
2175902 ATCTTTCGTCGAGGCCATGAA
1 ATCTTTCATCGAGGCCATGAA
2175923 TTCCTGCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (21 bp):
ATCTTTCATCGAGGCCATGAA
Found at i:2184274 original size:14 final size:13
Alignment explanation
Indices: 2184250--2184280 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
2184240 TTTTTGTTTA
2184250 TTTTAATTTTAAT
1 TTTTAATTTTAAT
2184263 TTTTATATTTTAAT
1 TTTTA-ATTTTAAT
2184277 TTTT
1 TTTT
2184281 CATCAAGACG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTAATTTTAAT
Found at i:2190020 original size:21 final size:21
Alignment explanation
Indices: 2189925--2190021 Score: 52
Period size: 21 Copynumber: 4.6 Consensus size: 21
2189915 TCGAGGGTTC
* * * *
2189925 TATGTGGTCCTTCGGGATATA
1 TATGTGATCCTTTGGAACATA
*
2189946 TATGTAATCCTTTTGGAACATA
1 TATGTGATCC-TTTGGAACATA
* * * * *
2189968 TATG-CAGTTCTTAGGGACACA
1 TATGTGA-TCCTTTGGAACATA
* * *
2189989 TATTTGGTCCTTTGGAATATA
1 TATGTGATCCTTTGGAACATA
2190010 TATGTGATCCTT
1 TATGTGATCCTT
2190022 AAGGAGTGGT
Statistics
Matches: 53, Mismatches: 20, Indels: 6
0.67 0.25 0.08
Matches are distributed among these distances:
21 39 0.74
22 14 0.26
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (21 bp):
TATGTGATCCTTTGGAACATA
Found at i:2190054 original size:21 final size:21
Alignment explanation
Indices: 2190027--2190106 Score: 126
Period size: 21 Copynumber: 3.8 Consensus size: 21
2190017 TCCTTAAGGA
*
2190027 GTGGTCCTTCGGAACAT-CTAT
1 GTGGTCCTTCGGGACATAC-AT
*
2190048 ATGGTCCTTCGGGACATACAT
1 GTGGTCCTTCGGGACATACAT
2190069 GTGGTCCTTCGGGACATACAT
1 GTGGTCCTTCGGGACATACAT
2190090 GTGGTCCTTCGGGACAT
1 GTGGTCCTTCGGGACAT
2190107 TTCTAAATAG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
21 54 0.98
22 1 0.02
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.30
Consensus pattern (21 bp):
GTGGTCCTTCGGGACATACAT
Found at i:2191928 original size:18 final size:18
Alignment explanation
Indices: 2191905--2191940 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2191895 CATTGAAAAA
*
2191905 CATAAAATATGTCTTTTT
1 CATAAAATATGACTTTTT
*
2191923 CATAAAATTTGACTTTTT
1 CATAAAATATGACTTTTT
2191941 GGGTCCAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (18 bp):
CATAAAATATGACTTTTT
Found at i:2192695 original size:21 final size:20
Alignment explanation
Indices: 2192671--2192736 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 20
2192661 TCTGCCACTA
2192671 CATTATTATATT-TATAGTGCC
1 CATTATT-TATTCT-TAGTGCC
2192692 CATTATTTCATTCTTAGTGCC
1 CATTATTT-ATTCTTAGTGCC
*
2192713 CATGATTTTATTCTTAGTGCC
1 CATTA-TTTATTCTTAGTGCC
2192734 CAT
1 CAT
2192737 AAGATATATT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
20 1 0.02
21 36 0.88
22 4 0.10
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.47
Consensus pattern (20 bp):
CATTATTTATTCTTAGTGCC
Found at i:2192749 original size:25 final size:21
Alignment explanation
Indices: 2192685--2192736 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
2192675 ATTATATTTA
* *
2192685 TAGTGCCCATTATTTCATTCT
1 TAGTGCCCATGATTTTATTCT
2192706 TAGTGCCCATGATTTTATTCT
1 TAGTGCCCATGATTTTATTCT
2192727 TAGTGCCCAT
1 TAGTGCCCAT
2192737 AAGATATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.44
Consensus pattern (21 bp):
TAGTGCCCATGATTTTATTCT
Found at i:2195266 original size:31 final size:31
Alignment explanation
Indices: 2195192--2195266 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 31
2195182 GGGGCCTACG
** *
2195192 AGCCTACCCAAGGCAATTCTTAGGGCCACTA
1 AGCCTACCCAAGAAAATTCTCAGGGCCACTA
* *
2195223 AGGCTTACCCAAGAAAATTCTCAGGGCCGC-A
1 A-GCCTACCCAAGAAAATTCTCAGGGCCACTA
2195254 TAGCCTACCCAAG
1 -AGCCTACCCAAG
2195267 GCTCGACTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
31 12 0.33
32 24 0.67
ACGTcount: A:0.31, C:0.32, G:0.20, T:0.17
Consensus pattern (31 bp):
AGCCTACCCAAGAAAATTCTCAGGGCCACTA
Done.