Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008162.1 Hibiscus syriacus cultivar Beakdansim tig00110733_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: 3688897
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 16
Found at i:1758846 original size:21 final size:21
Alignment explanation
Indices: 1758796--1758851 Score: 89
Period size: 21 Copynumber: 2.7 Consensus size: 21
1758786 AATTATGTGA
1758796 TAGAGTTTAGAGTTTAGGATT
1 TAGAGTTTAGAGTTTAGGATT
1758817 TAG-GATTTAGAGTTTAGGATT
1 TAGAG-TTTAGAGTTTAGGATT
1758838 TAGAGTTTAG-GTTT
1 TAGAGTTTAGAGTTT
1758852 TTAGGGATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.15
21 27 0.82
22 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.45
Consensus pattern (21 bp):
TAGAGTTTAGAGTTTAGGATT
Found at i:1758869 original size:7 final size:6
Alignment explanation
Indices: 1758800--1758851 Score: 50
Period size: 7 Copynumber: 7.7 Consensus size: 6
1758790 ATGTGATAGA
1758800 GTTTAG AGTTTAG GATTTAG GATTTAG AGTTTAG GATTTAG AGTTTAG
1 GTTTAG -GTTTAG G-TTTAG G-TTTAG -GTTTAG G-TTTAG -GTTTAG
1758848 GTTT
1 GTTT
1758852 TTAGGGATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.15
7 33 0.80
8 2 0.05
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (6 bp):
GTTTAG
Found at i:1759209 original size:16 final size:17
Alignment explanation
Indices: 1759177--1759210 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1759167 ATATATAAAG
1759177 ACCTAATTATAAACTAA
1 ACCTAATTATAAACTAA
*
1759194 ACCTAA-TATGAACTAA
1 ACCTAATTATAAACTAA
1759210 A
1 A
1759211 ACTATCCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (17 bp):
ACCTAATTATAAACTAA
Found at i:1759212 original size:17 final size:18
Alignment explanation
Indices: 1759172--1759212 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
1759162 ATTTAATATA
1759172 TAAAGACCTAATTATAAAC
1 TAAA-ACCTAATTATAAAC
*
1759191 T-AAACCTAA-TATGAAC
1 TAAAACCTAATTATAAAC
1759207 TAAAAC
1 TAAAAC
1759213 TATCCTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 7 0.35
17 10 0.50
18 2 0.10
19 1 0.05
ACGTcount: A:0.54, C:0.17, G:0.05, T:0.24
Consensus pattern (18 bp):
TAAAACCTAATTATAAAC
Found at i:1761863 original size:30 final size:30
Alignment explanation
Indices: 1761807--1761863 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1761797 GTTCGAGCCT
*
1761807 TTTCGAGTTCGAGTCGAGTTTAATAATATA
1 TTTCGAGTTCGAGTCGAGCTTAATAATATA
* * *
1761837 TTTCGAGTTGGAGTTGAGCTTCATAAT
1 TTTCGAGTTCGAGTCGAGCTTAATAAT
1761864 TTTTAGTTCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (30 bp):
TTTCGAGTTCGAGTCGAGCTTAATAATATA
Found at i:1765493 original size:66 final size:64
Alignment explanation
Indices: 1765389--1765511 Score: 167
Period size: 66 Copynumber: 1.9 Consensus size: 64
1765379 TTTGATTTGA
* * *
1765389 AAAAAATAATTTTCTTGATTCGATTCGATTTACGGTTCGTAATTTTATAAATTTGATATAATTTT
1 AAAAAATAATTTTCTTGATTCAATTCAATTTAC-GTTCGTAATTTTATAAACTTGATATAATTTT
*
1765454 AAAAAATAAATTTTCTTGATTTAATTCAAATTGTA-GTTCGTAATTTTATAAACTTGAT
1 AAAAAAT-AATTTTCTTGATTCAATTC-AATT-TACGTTCGTAATTTTATAAACTTGAT
1765512 TTGAGTTGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
65 7 0.14
66 39 0.76
67 3 0.06
68 2 0.04
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (64 bp):
AAAAAATAATTTTCTTGATTCAATTCAATTTACGTTCGTAATTTTATAAACTTGATATAATTTT
Found at i:1765812 original size:19 final size:19
Alignment explanation
Indices: 1765769--1765827 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
1765759 CTATTACTAT
*
1765769 AATATAAA-AATATATTATCA
1 AATATAAATAAAATATT-T-A
1765789 AATATAAATAAAATATTTA
1 AATATAAATAAAATATTTA
*
1765808 AATATATATAAAA-ATTTA
1 AATATAAATAAAATATTTA
1765826 AA
1 AA
1765828 AACTTCAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.19
19 13 0.36
20 9 0.25
21 7 0.19
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
AATATAAATAAAATATTTA
Found at i:1768119 original size:84 final size:85
Alignment explanation
Indices: 1768015--1768198 Score: 201
Period size: 84 Copynumber: 2.1 Consensus size: 85
1768005 CAGAACAATA
* ** * * *
1768015 AAAAATTTAAAGGACCAAAATATGATTAACATAAACTT-GAGGACCAAAATAGAAAAAATAGAAA
1 AAAAATTTAAAGGAACAAAATA-GAAAAACAAAAACTTAAAGGACCAAAATAGAAAAAATAAAAA
1768079 CTCAAAGGACTAAAATAGAAT
65 CTCAAAGGACTAAAATAGAAT
* * * *
1768100 AAAAA-TTAAAGGAATAAAATAGAAAAACAAAAATTTAAAGGACTAAAATAGCAAAAATAAAAAC
1 AAAAATTTAAAGGAACAAAATAGAAAAACAAAAACTTAAAGGACCAAAATAGAAAAAATAAAAAC
* *
1768164 TTAAAGGACTACAATAGCAAAAAT
66 TCAAAGGACTAAAATAG----AAT
1768188 AAAAATTTAAA
1 AAAAATTTAAA
1768199 TGTCTAAACC
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
83 11 0.14
84 52 0.64
85 5 0.06
88 8 0.10
89 5 0.06
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (85 bp):
AAAAATTTAAAGGAACAAAATAGAAAAACAAAAACTTAAAGGACCAAAATAGAAAAAATAAAAAC
TCAAAGGACTAAAATAGAAT
Found at i:1768141 original size:29 final size:30
Alignment explanation
Indices: 1768054--1768198 Score: 167
Period size: 30 Copynumber: 5.0 Consensus size: 30
1768044 CATAAACTTG
* * * * *
1768054 AGGACCAAAATAGAAAAAATAGAAACTCAA
1 AGGACTAAAATAGCAAAAATAAAAATTTAA
1768084 AGGACTAAAATAG----AATAAAAA-TTAA
1 AGGACTAAAATAGCAAAAATAAAAATTTAA
* *
1768109 AGGAATAAAATAG-AAAAACAAAAATTTAA
1 AGGACTAAAATAGCAAAAATAAAAATTTAA
*
1768138 AGGACTAAAATAGCAAAAATAAAAACTTAA
1 AGGACTAAAATAGCAAAAATAAAAATTTAA
*
1768168 AGGACTACAATAGCAAAAATAAAAATTTAA
1 AGGACTAAAATAGCAAAAATAAAAATTTAA
1768198 A
1 A
1768199 TGTCTAAACC
Statistics
Matches: 100, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.15
26 7 0.07
28 7 0.07
29 16 0.16
30 55 0.55
ACGTcount: A:0.64, C:0.08, G:0.11, T:0.17
Consensus pattern (30 bp):
AGGACTAAAATAGCAAAAATAAAAATTTAA
Found at i:1768143 original size:54 final size:55
Alignment explanation
Indices: 1768000--1768198 Score: 161
Period size: 59 Copynumber: 3.4 Consensus size: 55
1767990 CATAAGGGAT
* * * * * *
1768000 TAAAACAGAACAATAAAAAATTTAAAGGACCAAAATATGATTAACATAAACTT-GAGGAC
1 TAAAATAGAA-AA-AAAAAATTTAAAGGACTAAAATA-GA--AATAAAAACTTAAAGGAA
* * *
1768059 CAAAATAGAAAAAATAGAAACTCAAAGGACTAAAATAG-AATAAAAA-TTAAAGGAA
1 TAAAATAGAAAAAA-A-AAATTTAAAGGACTAAAATAGAAATAAAAACTTAAAGGAA
*
1768114 TAAAATAGAAAAACAAAAATTTAAAGGACTAAAATAGCAAAAATAAAAACTTAAAGGAC
1 TAAAATAGAAAAA-AAAAATTTAAAGGACTAAAATAG---AAATAAAAACTTAAAGGAA
*
1768173 TACAATAGCAAAAATAAAAATTTAAA
1 TAAAATAG-AAAAA-AAAAATTTAAA
1768199 TGTCTAAACC
Statistics
Matches: 115, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
54 21 0.18
55 23 0.20
56 1 0.01
57 2 0.02
58 12 0.10
59 40 0.35
60 16 0.14
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (55 bp):
TAAAATAGAAAAAAAAAATTTAAAGGACTAAAATAGAAATAAAAACTTAAAGGAA
Found at i:1768192 original size:30 final size:29
Alignment explanation
Indices: 1768000--1768198 Score: 165
Period size: 30 Copynumber: 6.9 Consensus size: 29
1767990 CATAAGGGAT
* * *
1768000 TAAAACAGAACAATAAAAAATTTAAAGGAC
1 TAAAATAGAAAAAT-AAAAACTTAAAGGAC
* ** * * *
1768030 CAAAATATGATTAACATAAACTT-GAGGAC
1 TAAAATA-GAAAAATAAAAACTTAAAGGAC
* * *
1768059 CAAAATAGAAAAAATAGAAACTCAAAGGAC
1 TAAAATAG-AAAAATAAAAACTTAAAGGAC
*
1768089 TAAAATAG---AATAAAAA-TTAAAGGAA
1 TAAAATAGAAAAATAAAAACTTAAAGGAC
* *
1768114 TAAAATAGAAAAACAAAAATTTAAAGGAC
1 TAAAATAGAAAAATAAAAACTTAAAGGAC
1768143 TAAAATAGCAAAAATAAAAACTTAAAGGAC
1 TAAAATAG-AAAAATAAAAACTTAAAGGAC
* *
1768173 TACAATAGCAAAAATAAAAATTTAAA
1 TAAAATAG-AAAAATAAAAACTTAAA
1768199 TGTCTAAACC
Statistics
Matches: 137, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
25 15 0.11
26 7 0.05
28 8 0.06
29 37 0.27
30 66 0.48
31 4 0.03
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (29 bp):
TAAAATAGAAAAATAAAAACTTAAAGGAC
Found at i:1769640 original size:3 final size:3
Alignment explanation
Indices: 1769632--1769683 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
1769622 GTAATAAATG
*
1769632 TAA TAA TAA TAA TAA TAA TAA TAA TAA -ACA TAA TAA TAA TAA -AT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
1769676 TAA TAA TA
1 TAA TAA TA
1769684 TTTTTGTAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 41 0.93
4 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1769932 original size:39 final size:41
Alignment explanation
Indices: 1769835--1769946 Score: 129
Period size: 39 Copynumber: 2.7 Consensus size: 41
1769825 GTTGGGGGAC
* * *
1769835 GACACTGCTCATACGTGATGAAGAGTTCAGGTCGTCTAAGGGT
1 GACACAGCTCATACGTGATGAAGAGTTCTGGTCG-CT-AGGAT
* * * *
1769878 GACACAACTCCTACGTGATGATGAGATCTGGTCG-T-GGAT
1 GACACAGCTCATACGTGATGAAGAGTTCTGGTCGCTAGGAT
1769917 GACACAGCTCATACGTGATGAAGAGTTCTG
1 GACACAGCTCATACGTGATGAAGAGTTCTG
1769947 ACCATCTTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
39 29 0.50
41 1 0.02
43 28 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.25
Consensus pattern (41 bp):
GACACAGCTCATACGTGATGAAGAGTTCTGGTCGCTAGGAT
Found at i:1770042 original size:43 final size:43
Alignment explanation
Indices: 1769995--1770172 Score: 105
Period size: 43 Copynumber: 4.1 Consensus size: 43
1769985 ATGAAGACAA
1769995 CTGGTTATCTAAGGGTGACACGACTCCTACGTGATGAGGAGGT
1 CTGGTTATCTAAGGGTGACACGACTCCTACGTGATGAGGAGGT
* ** ** * *
1770038 CTGG---TC-GAGAATGACACGGTTCCTACGTGATGAGGATGA
1 CTGGTTATCTAAGGGTGACACGACTCCTACGTGATGAGGAGGT
** * * * * * *
1770077 CAT-GCCATCTTTAGGGATGATAACACAATTCCTATGTGATGAGGACGC
1 C-TGGTTATC-TAAGGG-TG---ACACGACTCCTACGTGATGAGGAGGT
* * *
1770125 CTGGTTATCTAGGGGTGACACGGCTCCTATGTGATGAGGAGGT
1 CTGGTTATCTAAGGGTGACACGACTCCTACGTGATGAGGAGGT
1770168 CTGGT
1 CTGGT
1770173 CGGGGATGAC
Statistics
Matches: 100, Mismatches: 24, Indels: 22
0.68 0.16 0.15
Matches are distributed among these distances:
39 28 0.28
40 3 0.03
42 2 0.02
43 30 0.30
44 2 0.02
45 2 0.02
46 2 0.02
47 5 0.05
48 26 0.26
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (43 bp):
CTGGTTATCTAAGGGTGACACGACTCCTACGTGATGAGGAGGT
Found at i:1770089 original size:133 final size:129
Alignment explanation
Indices: 1769869--1770223 Score: 415
Period size: 130 Copynumber: 2.7 Consensus size: 129
1769859 GTTCAGGTCG
* * * * * * *
1769869 TCTAAGGGTGACACAACTCCTACGTGATGATGAGATCTGGTCGTGGATGACACAGCTCATACGTG
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGAGGATGACACGGTTCCTACGTG
* * **
1769934 ATGAAGAGTTC-TGACCATCTTTAGGAAAGGTGATAACACGGTTCCCACGCGATGAAGACAACTG
66 ATGAGGAG-TCATG-CCATCTTTAGG---GATGATAACACAATTCCCACGCGATGAAGACAACTG
1769998 GTTA
126 GTTA
*
1770002 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGAGAATGACACGGTTCCTACGTG
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGAGGATGACACGGTTCCTACGTG
* * * * * **
1770067 ATGAGGATGACATGCCATCTTTAGGGATGATAACACAATTCCTATGTGATGAGGACGCCTGGTTA
66 ATGAGGA-GTCATGCCATCTTTAGGGATGATAACACAATTCCCACGCGATGAAGACAACTGGTTA
* * * * * *
1770132 TCTAGGGGTGACACGGCTCCTATGTGATGAGGAGGTCTGGTCGGGGATGACACGGTTCCTATGTA
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGAGGATGACACGGTTCCTACGTG
1770197 ATGAGGACGTCATGCCATCTTTAGGGA
66 ATGAGGA-GTCATGCCATCTTTAGGGA
1770224 GACTATCTCA
Statistics
Matches: 192, Mismatches: 28, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
130 114 0.59
133 75 0.39
134 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (129 bp):
TCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGAGGATGACACGGTTCCTACGTG
ATGAGGAGTCATGCCATCTTTAGGGATGATAACACAATTCCCACGCGATGAAGACAACTGGTTA
Found at i:1770194 original size:39 final size:40
Alignment explanation
Indices: 1770010--1770203 Score: 115
Period size: 39 Copynumber: 4.6 Consensus size: 40
1770000 TATCTAAGGG
** * * *
1770010 TGACACGACTCCTACGTGATGAGGAGGTCTGGTC-GAGAA
1 TGACACGGTTCCTATGTGATGAGGAGGTCTGGTCTGGGGA
* * * *
1770049 TGACACGGTTCCTACGTGATGAGGATGACATGCCATCTTTAGGGATGA
1 TGACACGGTTCCTATGTGATGAGGAGGTC-TG--GTC--T-GGG--GA
* ** * *
1770097 TAACACAATTCCTATGTGATGAGGACGCCTGGTTATCTAGGGG-
1 TGACACGGTTCCTATGTGATGAGGAGGTCTGG---TCT-GGGGA
*
1770140 TGACACGGCTCCTATGTGATGAGGAGGTCTGGTC-GGGGA
1 TGACACGGTTCCTATGTGATGAGGAGGTCTGGTCTGGGGA
*
1770179 TGACACGGTTCCTATGTAATGAGGA
1 TGACACGGTTCCTATGTGATGAGGA
1770204 CGTCATGCCA
Statistics
Matches: 120, Mismatches: 22, Indels: 26
0.71 0.13 0.15
Matches are distributed among these distances:
38 4 0.03
39 48 0.40
40 4 0.03
42 2 0.02
43 26 0.22
44 1 0.01
46 7 0.06
47 2 0.02
48 26 0.22
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (40 bp):
TGACACGGTTCCTATGTGATGAGGAGGTCTGGTCTGGGGA
Found at i:1770366 original size:29 final size:27
Alignment explanation
Indices: 1770316--1770375 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
1770306 GACAAAATTC
* *
1770316 GTTTCAAGGGAAACGATCTCAAAGATCTT
1 GTTTCAAGAGAAACAATCTCAAAG-T-TT
* *
1770345 GTTTCAAGAGAAATAATTTCAAAGTTT
1 GTTTCAAGAGAAACAATCTCAAAGTTT
1770372 GTTT
1 GTTT
1770376 TAAGGAATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 6 0.22
28 1 0.04
29 20 0.74
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (27 bp):
GTTTCAAGAGAAACAATCTCAAAGTTT
Found at i:1770537 original size:36 final size:37
Alignment explanation
Indices: 1770490--1770642 Score: 161
Period size: 36 Copynumber: 4.2 Consensus size: 37
1770480 AGGAAAAAAA
* *
1770490 TGTCTCAAGCGAGACGAAATTTG-TTTTAAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGCTTTTAAGAGAAAC
* *
1770526 TGTCTCAAGCGAGACAAAATTTG-TTTTTAGGGAAAGC
1 TGTCTCAAGCGAGACAAAATTTGCTTTTAAGAGAAA-C
*
1770563 TGTCTCAAGTGAGACAAAATTTGCTTTT-AGA-AAAC
1 TGTCTCAAGCGAGACAAAATTTGCTTTTAAGAGAAAC
** * * * * *
1770598 CATCTCAAACGAGACAAAATTTGTTTTTAAAATAAAT
1 TGTCTCAAGCGAGACAAAATTTGCTTTTAAGAGAAAC
1770635 TGTCTCAA
1 TGTCTCAA
1770643 AGGCAACAAC
Statistics
Matches: 98, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
35 24 0.24
36 37 0.38
37 33 0.34
38 4 0.04
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (37 bp):
TGTCTCAAGCGAGACAAAATTTGCTTTTAAGAGAAAC
Found at i:1770567 original size:37 final size:35
Alignment explanation
Indices: 1770490--1770626 Score: 166
Period size: 36 Copynumber: 3.8 Consensus size: 35
1770480 AGGAAAAAAA
* * *
1770490 TGTCTCAAGCGAGACGAAATTTGTTTTAAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAG-GAAAC
1770526 TGTCTCAAGCGAGACAAAATTTGTTTTTAGGGAAAGC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTA-GGAAA-C
* * *
1770563 TGTCTCAAGTGAGACAAAATTTGCTTTTAGAAAAC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGGAAAC
** *
1770598 CATCTCAAACGAGACAAAATTTGTTTTTA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTA
1770627 AAATAAATTG
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
35 25 0.28
36 35 0.40
37 28 0.32
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGGAAAC
Found at i:1770612 original size:35 final size:35
Alignment explanation
Indices: 1770485--1770626 Score: 167
Period size: 35 Copynumber: 4.0 Consensus size: 35
1770475 CTCAAAGGAA
* * *
1770485 AAAAATGTCTCAAGCGAGACGAAATTTGTTTTAAG
1 AAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAG
*
1770520 AGAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAGGG
1 A-AAACTGTCTCAAGCGAGACAAAATTTGTTTTTA--G
* * *
1770558 AAAGCTGTCTCAAGTGAGACAAAATTTGCTTTTAG
1 AAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAG
** *
1770593 AAAACCATCTCAAACGAGACAAAATTTGTTTTTA
1 AAAACTGTCTCAAGCGAGACAAAATTTGTTTTTA
1770627 AAATAAATTG
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
35 30 0.33
36 30 0.33
37 29 0.32
38 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (35 bp):
AAAACTGTCTCAAGCGAGACAAAATTTGTTTTTAG
Found at i:1770639 original size:72 final size:71
Alignment explanation
Indices: 1770483--1770642 Score: 180
Period size: 72 Copynumber: 2.2 Consensus size: 71
1770473 TTCTCAAAGG
* *** *
1770483 AAAAAAATGTCTCAAGCGAGACGAAATTTGTTTTAAGAGAAATTGTCTCAAGCGAGACAAAATTT
1 AAAAAAATGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAACCATCTCAAACGAGACAAAATTT
1770548 GTTTTT
66 GTTTTT
* ** *
1770554 AGGGAAAGCTGTCTCAAGTGAGACAAAATTTGCTTTT-AGA-AAACCATCTCAAACGAGACAAAA
1 A--AAAAAATGTCTCAAGCGAGACAAAATTTG-TTTTAAGAGAAACCATCTCAAACGAGACAAAA
1770617 TTTGTTTTT
63 TTTGTTTTT
1770626 AAAATAAATTGTCTCAA
1 AAAA-AAA-TGTCTCAA
1770643 AGGCAACAAC
Statistics
Matches: 72, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
70 2 0.03
71 2 0.03
72 37 0.51
73 27 0.38
74 4 0.06
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (71 bp):
AAAAAAATGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAACCATCTCAAACGAGACAAAATTT
GTTTTT
Found at i:1771829 original size:20 final size:21
Alignment explanation
Indices: 1771804--1771843 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1771794 TTTGCATATG
1771804 TTTCTTATCTT-TTTTTTTCC
1 TTTCTTATCTTCTTTTTTTCC
* *
1771824 TTTCTTTTGTTCTTTTTTTC
1 TTTCTTATCTTCTTTTTTTC
1771844 TTTGATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTCTTATCTTCTTTTTTTCC
Found at i:1773089 original size:13 final size:13
Alignment explanation
Indices: 1773071--1773114 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
1773061 GCTTAAAAAT
1773071 AAAATGCAGATGC
1 AAAATGCAGATGC
*
1773084 AAAATGCAAAGATAC
1 AAAATGC--AGATGC
1773099 -AAATGCAGATGC
1 AAAATGCAGATGC
1773111 AAAA
1 AAAA
1773115 ATGTTGAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 5 0.19
13 10 0.38
14 6 0.23
15 5 0.19
ACGTcount: A:0.55, C:0.14, G:0.18, T:0.14
Consensus pattern (13 bp):
AAAATGCAGATGC
Found at i:1774538 original size:59 final size:60
Alignment explanation
Indices: 1774463--1774675 Score: 189
Period size: 59 Copynumber: 3.6 Consensus size: 60
1774453 ATAAGGGATT
* * * * ** **
1774463 AAAATAG-AACAATAAAAAATTAAAGGACCAAAATATGATTAACAGAAAAT-TGAGGACC
1 AAAATAGCAAAAATAAAAACTTAAAGGACTAAAATAGGAAAAACAGAAAATCAAAGGACC
* * * *
1774521 AAAATAGCAAAAATAAAAACTTAAAGGATTAAAATAGGAAAAATAGAAACTCAAAGGACT
1 AAAATAGCAAAAATAAAAACTTAAAGGACTAAAATAGGAAAAACAGAAAATCAAAGGACC
* * * * * * *
1774581 AAAATAGCACAAACAAAAACTTAAAGGACTAAAATA-GAAAAATAGAAATTTAAATGACT
1 AAAATAGCAAAAATAAAAACTTAAAGGACTAAAATAGGAAAAACAGAAAATCAAAGGACC
* * * * *
1774640 GAAATAGAAAAAACATAAACTTAAATGACTAAAATA
1 AAAATAGCAAAAATAAAAACTTAAAGGACTAAAATA
1774676 ACAAAAATAG
Statistics
Matches: 130, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
58 7 0.05
59 85 0.65
60 38 0.29
ACGTcount: A:0.61, C:0.09, G:0.12, T:0.18
Consensus pattern (60 bp):
AAAATAGCAAAAATAAAAACTTAAAGGACTAAAATAGGAAAAACAGAAAATCAAAGGACC
Found at i:1774555 original size:30 final size:30
Alignment explanation
Indices: 1774515--1774694 Score: 200
Period size: 30 Copynumber: 6.0 Consensus size: 30
1774505 CAGAAAATTG
* *
1774515 AGGACCAAAATAGCAAAAATAAAAACTTAA
1 AGGACTAAAATAGCAAAAATAGAAACTTAA
* * *
1774545 AGGATTAAAATAGGAAAAATAGAAACTCAA
1 AGGACTAAAATAGCAAAAATAGAAACTTAA
* * *
1774575 AGGACTAAAATAGCACAAACAAAAACTTAA
1 AGGACTAAAATAGCAAAAATAGAAACTTAA
*
1774605 AGGACTAAAATAG-AAAAATAGAAATTTAA
1 AGGACTAAAATAGCAAAAATAGAAACTTAA
* * * * *
1774634 ATGACTGAAATAGAAAAAACATAAACTTAA
1 AGGACTAAAATAGCAAAAATAGAAACTTAA
* * *
1774664 ATGACTAAAATAACAAAAATAGAAATTTAA
1 AGGACTAAAATAGCAAAAATAGAAACTTAA
1774694 A
1 A
1774695 CGATTGAACC
Statistics
Matches: 123, Mismatches: 26, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
29 23 0.19
30 100 0.81
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (30 bp):
AGGACTAAAATAGCAAAAATAGAAACTTAA
Found at i:1774599 original size:60 final size:59
Alignment explanation
Indices: 1774515--1774688 Score: 222
Period size: 59 Copynumber: 2.9 Consensus size: 59
1774505 CAGAAAATTG
* * *
1774515 AGGACCAAAATAGCAAAAATAAAAACTTAAAGGATTAAAATAGGAAAAATAGAAACTCAA
1 AGGACTAAAATAGCAAAAACAAAAACTTAAAGGACTAAAATA-GAAAAATAGAAACTCAA
* * *
1774575 AGGACTAAAATAGCACAAACAAAAACTTAAAGGACTAAAATAGAAAAATAGAAATTTAA
1 AGGACTAAAATAGCAAAAACAAAAACTTAAAGGACTAAAATAGAAAAATAGAAACTCAA
* * * * * *
1774634 ATGACTGAAATAGAAAAAACATAAACTTAAATGACTAAAATAACAAAAATAGAAA
1 AGGACTAAAATAGCAAAAACAAAAACTTAAAGGACTAAAAT-AGAAAAATAGAAA
1774689 TTTAAACGAT
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
59 50 0.50
60 50 0.50
ACGTcount: A:0.62, C:0.10, G:0.11, T:0.17
Consensus pattern (59 bp):
AGGACTAAAATAGCAAAAACAAAAACTTAAAGGACTAAAATAGAAAAATAGAAACTCAA
Found at i:1780415 original size:6 final size:6
Alignment explanation
Indices: 1780404--1780430 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1780394 CGACTACACC
1780404 GGATAG GGATAG GGATAG GGATAG GGA
1 GGATAG GGATAG GGATAG GGATAG GGA
1780431 AATGGGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.52, T:0.15
Consensus pattern (6 bp):
GGATAG
Found at i:1781711 original size:24 final size:23
Alignment explanation
Indices: 1781683--1781760 Score: 102
Period size: 24 Copynumber: 3.3 Consensus size: 23
1781673 ATTCAACTCA
* *
1781683 AGTATCAGAGCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCATGTC
1781706 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCATGTC
* *
1781730 AATATCATATCAGAATCCATGTC
1 AGTATCAGATCAGAATCCATGTC
1781753 AGGTATCA
1 A-GTATCA
1781761 TAACAAAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
23 22 0.46
24 26 0.54
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCATGTC
Found at i:1783130 original size:33 final size:35
Alignment explanation
Indices: 1783086--1783157 Score: 112
Period size: 34 Copynumber: 2.1 Consensus size: 35
1783076 CGTCACGAAT
*
1783086 AGTAAGGCCCTGAGCACAAAGC-GAGGAGCCTGCA
1 AGTAAGGCCCTGAGCACAAAGCTGAGGAGCCTCCA
*
1783120 AGTAA-GCCCTGAGCACAAAGCTGATGAGCCTCCA
1 AGTAAGGCCCTGAGCACAAAGCTGAGGAGCCTCCA
1783154 AGTA
1 AGTA
1783158 TTCTTCCTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 16 0.46
34 19 0.54
ACGTcount: A:0.33, C:0.26, G:0.28, T:0.12
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACAAAGCTGAGGAGCCTCCA
Found at i:1783263 original size:24 final size:24
Alignment explanation
Indices: 1783236--1783317 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
1783226 CATAATTCAA
1783236 GTCAAGTATCAGATCAGAATCCTG
1 GTCAAGTATCAGATCAGAATCCTG
* *
1783260 GTCATGTATTAGATCAGAATCCAT-
1 GTCAAGTATCAGATCAGAATCC-TG
* * *
1783284 GTCAA-TATCATATCTGAATCCAG
1 GTCAAGTATCAGATCAGAATCCTG
*
1783307 GTCAGGTATCA
1 GTCAAGTATCA
1783318 TAACAAAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
23 17 0.36
24 29 0.62
25 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCTG
Found at i:1785772 original size:17 final size:17
Alignment explanation
Indices: 1785750--1785790 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1785740 GGTCAACAGT
**
1785750 GGTCAACGCCTGTCAAC
1 GGTCAACGCAAGTCAAC
*
1785767 GGTCAACGCAAGTCAAT
1 GGTCAACGCAAGTCAAC
1785784 GGTCAAC
1 GGTCAAC
1785791 AATCGACCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (17 bp):
GGTCAACGCAAGTCAAC
Found at i:1787857 original size:24 final size:24
Alignment explanation
Indices: 1787830--1787911 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 24
1787820 CATAATTCAA
1787830 GTCAAGTATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
1787854 GTCATGTATCAGATCATAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
* *
1787878 GTCAA-TATCATATCTGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
*
1787901 GTCAGGTATCA
1 GTCAAGTATCA
1787912 TAACAAAATT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
23 18 0.38
24 30 0.62
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:1787898 original size:47 final size:48
Alignment explanation
Indices: 1787820--1787911 Score: 132
Period size: 47 Copynumber: 1.9 Consensus size: 48
1787810 AATATTAAAA
* *
1787820 CATAATTCAAGTCAAGTATCAGATCAGAATCCAGGTCATGTATCAGAT
1 CATAATCCAAGTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAT
* * *
1787868 CATAATCCATGTCAA-TATCATATCTGAATCCAGGTCAGGTATCA
1 CATAATCCAAGTCAAGTATCAGATCAGAATCCAGGTCAGGTATCA
1787912 TAACAAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 26 0.67
48 13 0.33
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (48 bp):
CATAATCCAAGTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAT
Found at i:1792604 original size:24 final size:24
Alignment explanation
Indices: 1792577--1792624 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1792567 GATTTTGAAA
* *
1792577 CTCTTCAAGAATTATATTTCAAAG
1 CTCTTCAAGAATTACAATTCAAAG
* *
1792601 CTCTTCGAGAGTTACAATTCAAAG
1 CTCTTCAAGAATTACAATTCAAAG
1792625 TTTACAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (24 bp):
CTCTTCAAGAATTACAATTCAAAG
Found at i:1793384 original size:176 final size:176
Alignment explanation
Indices: 1793090--1793442 Score: 688
Period size: 176 Copynumber: 2.0 Consensus size: 176
1793080 AAATTTCAGC
1793090 TCAAGATCCTCATTTTAATTCTTTACTTCTATAGAAATATTGTTTGTAAAATCATTGTTGATAAC
1 TCAAGATCCTCATTTTAATTCTTTACTTCTATAGAAATATTGTTTGTAAAATCATTGTTGATAAC
* *
1793155 TTTTCTATTTTGGTTCCATTATTTTCTCGTAATGACATAACTTATCGAGCTCTCTTCATTATTTT
66 TTTTCTATTTTGGTTCCATTATTTTATAGTAATGACATAACTTATCGAGCTCTCTTCATTATTTT
1793220 CATTTTCATTTTTCAGGTACATGAAACTCTTCTAGATTTGTATTAT
131 CATTTTCATTTTTCAGGTACATGAAACTCTTCTAGATTTGTATTAT
1793266 TCAAGATCCTCATTTTAATTCTTTACTTCTATAGAAATATTGTTTGTAAAATCATTGTTGATAAC
1 TCAAGATCCTCATTTTAATTCTTTACTTCTATAGAAATATTGTTTGTAAAATCATTGTTGATAAC
1793331 TTTTCTATTTTGGTTCCATTATTTTATAGTAATGACATAACTTATCGAGCTCTCTTCATTATTTT
66 TTTTCTATTTTGGTTCCATTATTTTATAGTAATGACATAACTTATCGAGCTCTCTTCATTATTTT
1793396 CATTTTCATTTTTCAGGTACATGAAACTCTTCTAGATTTGTATTAT
131 CATTTTCATTTTTCAGGTACATGAAACTCTTCTAGATTTGTATTAT
1793442 T
1 T
1793443 AGTTATGCCT
Statistics
Matches: 175, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 175 1.00
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (176 bp):
TCAAGATCCTCATTTTAATTCTTTACTTCTATAGAAATATTGTTTGTAAAATCATTGTTGATAAC
TTTTCTATTTTGGTTCCATTATTTTATAGTAATGACATAACTTATCGAGCTCTCTTCATTATTTT
CATTTTCATTTTTCAGGTACATGAAACTCTTCTAGATTTGTATTAT
Found at i:1805505 original size:2 final size:2
Alignment explanation
Indices: 1805498--1805534 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1805488 AATTTTAGTG
1805498 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1805535 GTATTTGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1810171 original size:29 final size:28
Alignment explanation
Indices: 1810129--1810202 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
1810119 GTCAAACACT
*
1810129 TTACACAAATAGCACCCTTTTTAAAATAA
1 TTAC-CAAATAGCACCCTTTTCAAAATAA
* * *
1810158 TTACCAATATAGCACACTTTTCGAATTAA
1 TTACCAA-ATAGCACCCTTTTCAAAATAA
*
1810187 TTCCCAAAATAGCACC
1 TTACC-AAATAGCACC
1810203 AAAACCAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
28 3 0.08
29 32 0.86
30 2 0.05
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (28 bp):
TTACCAAATAGCACCCTTTTCAAAATAA
Found at i:1810283 original size:18 final size:18
Alignment explanation
Indices: 1810255--1810295 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1810245 GGTCACGGTC
1810255 GGGTC-GGTCAACGGGTA
1 GGGTCGGGTCAACGGGTA
*
1810272 GGGTCGGGTCAACGGGTC
1 GGGTCGGGTCAACGGGTA
1810290 GGGTCG
1 GGGTCG
1810296 TGACCGGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.12, C:0.20, G:0.51, T:0.17
Consensus pattern (18 bp):
GGGTCGGGTCAACGGGTA
Found at i:1810311 original size:10 final size:10
Alignment explanation
Indices: 1810298--1810343 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
1810288 TCGGGTCGTG
1810298 ACCGGTCAAA
1 ACCGGTCAAA
1810308 ACCGGTTCAAA
1 ACCGG-TCAAA
1810319 ACC-GT-ATAA
1 ACCGGTCA-AA
1810328 ACCGGTCAAA
1 ACCGGTCAAA
1810338 ACCGGT
1 ACCGGT
1810344 TTCCAGCGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 1 0.03
9 6 0.19
10 16 0.50
11 9 0.28
ACGTcount: A:0.37, C:0.28, G:0.20, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:1817345 original size:29 final size:28
Alignment explanation
Indices: 1817303--1817376 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
1817293 GTCAAACATT
*
1817303 TTACACAAATAGCACCCTTTTTAAAATAA
1 TTAC-CAAATAGCACCCTTTTCAAAATAA
* *
1817332 TTACCAATATAGCACCCTTTTCGAATTAA
1 TTACCAA-ATAGCACCCTTTTCAAAATAA
*
1817361 TTCCCAAAATAGCACC
1 TTACC-AAATAGCACC
1817377 AAAACCAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 3 0.08
29 34 0.87
30 2 0.05
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.30
Consensus pattern (28 bp):
TTACCAAATAGCACCCTTTTCAAAATAA
Found at i:1817440 original size:18 final size:18
Alignment explanation
Indices: 1817407--1817458 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
1817397 AATAGCACCA
1817407 GTCAAC-GGTCGGGTCGG
1 GTCAACGGGTCGGGTCGG
*
1817424 GTCAACGGGTAGGGTCGG
1 GTCAACGGGTCGGGTCGG
1817442 GTCAACGGGTCGGGTCG
1 GTCAACGGGTCGGGTCG
1817459 TGACCGGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 6 0.19
18 26 0.81
ACGTcount: A:0.13, C:0.21, G:0.48, T:0.17
Consensus pattern (18 bp):
GTCAACGGGTCGGGTCGG
Found at i:1817475 original size:9 final size:9
Alignment explanation
Indices: 1817461--1817494 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1817451 TCGGGTCGTG
1817461 ACCGGTTAA
1 ACCGGTTAA
*
1817470 ACCGGTCAAA
1 ACCGGT-TAA
1817480 ACCGGTTAA
1 ACCGGTTAA
1817489 ACCGGT
1 ACCGGT
1817495 CAAAACCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:1817483 original size:10 final size:10
Alignment explanation
Indices: 1817468--1817501 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1817458 GTGACCGGTT
1817468 AAACCGGTCA
1 AAACCGGTCA
*
1817478 AAACCGGT-T
1 AAACCGGTCA
1817487 AAACCGGTCA
1 AAACCGGTCA
1817497 AAACC
1 AAACC
1817502 AGTTTCCAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.41, C:0.29, G:0.18, T:0.12
Consensus pattern (10 bp):
AAACCGGTCA
Found at i:1817483 original size:19 final size:19
Alignment explanation
Indices: 1817461--1817501 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1817451 TCGGGTCGTG
1817461 ACCGGTTAAACCGGTCAAA
1 ACCGGTTAAACCGGTCAAA
1817480 ACCGGTTAAACCGGTCAAA
1 ACCGGTTAAACCGGTCAAA
1817499 ACC
1 ACC
1817502 AGTTTCCAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.29, G:0.20, T:0.15
Consensus pattern (19 bp):
ACCGGTTAAACCGGTCAAA
Found at i:1818833 original size:24 final size:23
Alignment explanation
Indices: 1818800--1818859 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
1818790 AATTTAATTG
* *
1818800 AATTTAAAATTCA-ATTAATGAGA
1 AATTGAAAATTAACATTAATGA-A
1818823 AATTGCAAAATCTAACATTAATGAA
1 AATTG-AAAAT-TAACATTAATGAA
*
1818848 TATTGAAAATTA
1 AATTGAAAATTA
1818860 TCAAATGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.19
24 10 0.32
25 7 0.23
26 8 0.26
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (23 bp):
AATTGAAAATTAACATTAATGAA
Found at i:1830707 original size:3 final size:3
Alignment explanation
Indices: 1830685--1830739 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
1830675 CCCGAATCTT
* * *
1830685 TTA TTA TTG TTG TTA TTTA TTA TTA TTA TTA TTA TTA TT- TTT TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1830730 TTA TT- TTA TT
1 TTA TTA TTA TT
1830740 TATAGGCCCT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:1831191 original size:15 final size:15
Alignment explanation
Indices: 1831173--1831202 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1831163 AAAGGAATTT
1831173 TAAAAGAAAGAAAAA
1 TAAAAGAAAGAAAAA
*
1831188 TAAAAGAGAGAAAAA
1 TAAAAGAAAGAAAAA
1831203 AATTAAAGCT
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:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (15 bp):
TAAAAGAAAGAAAAA
Found at i:1831463 original size:13 final size:13
Alignment explanation
Indices: 1831445--1831478 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
1831435 GGGTTTTTGC
1831445 AAGAAAAATAAAA
1 AAGAAAAATAAAA
1831458 AAGAAAAATAAAA
1 AAGAAAAATAAAA
1831471 AAGAAAAA
1 AAGAAAAA
1831479 AGAGAGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (13 bp):
AAGAAAAATAAAA
Found at i:1843810 original size:63 final size:63
Alignment explanation
Indices: 1843711--1843830 Score: 222
Period size: 63 Copynumber: 1.9 Consensus size: 63
1843701 GAATTATACC
1843711 ATTGAGAATTTCAAAAACTGAAAAGTTCTTAATTGTAGGTAATCTCACGTTGTCCTCACTCTT
1 ATTGAGAATTTCAAAAACTGAAAAGTTCTTAATTGTAGGTAATCTCACGTTGTCCTCACTCTT
* *
1843774 ATTGAGAATTTCAAAAGCTGAAGAGTTCTTAATTGTAGGTAATCTCACGTTGTCCTC
1 ATTGAGAATTTCAAAAACTGAAAAGTTCTTAATTGTAGGTAATCTCACGTTGTCCTC
1843831 TCCATCTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (63 bp):
ATTGAGAATTTCAAAAACTGAAAAGTTCTTAATTGTAGGTAATCTCACGTTGTCCTCACTCTT
Found at i:1847946 original size:70 final size:71
Alignment explanation
Indices: 1847588--1848149 Score: 557
Period size: 71 Copynumber: 7.9 Consensus size: 71
1847578 GGAAATAAAT
* * * * *
1847588 TTTTCAAGAGACAATATCTCAAGTGAGATAAAATTTTGGTTTCGACG-GAAATTGTCTCGAGTGA
1 TTTTCAAGGGA-AATATCTCAAGGGAGATGAAATTTTTGTTTCGA-GAGAAACTGTCTCGAGTGA
*
1847652 GGCGAAACA
64 GACGAAA-A
* * *
1847661 TTTTCAAGGGAAAACATCTCAAGGGAGATGGAATTTTTGTTTCGAGAGAAACTATCTCGAGTGAG
1 TTTTCAAGGG-AAATATCTCAAGGGAGATGAAATTTTTGTTTCGAGAGAAACTGTCTCGAGTGAG
1847726 --GAAAAA
65 ACG-AAAA
* * * * *
1847732 TTTCCAAGAGAAAATATCTCAAGGGAGATGTAATTTTAT-TTT-TAGAGAAACTGTCTCGATTGA
1 TTTTCAAG-GGAAATATCTCAAGGGAGATGAAATTTT-TGTTTCGAGAGAAACTGTCTCGAGTGA
* *
1847795 AACAAAAAA
64 GAC-GAAAA
* * **
1847804 TTTTCAAGGGAAAATATCTTAAGAGAGATGTCA-TTTTGTTTCGAGAGAAACTGTCTCGAGTGAG
1 TTTTCAAGGG-AAATATCTCAAGGGAGATGAAATTTTTGTTTCGAGAGAAACTGTCTCGAGTGAG
1847868 ACGAAAA
65 ACGAAAA
* * * *
1847875 ATTTAAAGGGAAATATCTCAAGGGAGATGAAATTTTTGTTTCGATATAAACTGTCTCGAGTGAGA
1 TTTTCAAGGGAAATATCTCAAGGGAGATGAAATTTTTGTTTCGAGAGAAACTGTCTCGAGTGAGA
*
1847940 TGAAAA
66 CGAAAA
* * * *
1847946 TTTTCAAGGGAAAATATCTCAAGTGAGATGCAA-TTTTGTTTCGAGTGAAACTTTCTCGAGTGAG
1 TTTTCAAGGG-AAATATCTCAAGGGAGATGAAATTTTTGTTTCGAGAGAAACTGTCTCGAGTGAG
*
1848010 ACAAAAA
65 ACGAAAA
* * * ** * *
1848017 TTTTCAAGGGAAATATCTGAAGCGAGAT-AAAATTTTGTTTAAAGAGAAATTGTCCCGAGTGAGA
1 TTTTCAAGGGAAATATCTCAAGGGAGATGAAATTTTTGTTTCGAGAGAAACTGTCTCGAGTGAGA
*
1848081 TGAAAA
66 CGAAAA
* * * * * * *
1848087 TTTTCAAGGAGAAATATCTCAAGAGAGATGTATTTTTTGTTGCAAG-GAAATTGTCTCAAGTGA
1 TTTTCAAGG-GAAATATCTCAAGGGAGATGAAATTTTTGTTTCGAGAGAAACTGTCTCGAGTGA
1848150 AATGAAATTT
Statistics
Matches: 408, Mismatches: 65, Indels: 34
0.80 0.13 0.07
Matches are distributed among these distances:
69 2 0.00
70 92 0.23
71 172 0.42
72 88 0.22
73 53 0.13
74 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (71 bp):
TTTTCAAGGGAAATATCTCAAGGGAGATGAAATTTTTGTTTCGAGAGAAACTGTCTCGAGTGAGA
CGAAAA
Found at i:1853689 original size:26 final size:27
Alignment explanation
Indices: 1853645--1853695 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
1853635 TTAATAATTT
1853645 TCAAATAAATTTCGATTCGATTAATGG
1 TCAAATAAATTTCGATTCGATTAATGG
*
1853672 TCAAAT-AATTTCGGTTCGATTAAT
1 TCAAATAAATTTCGATTCGATTAAT
1853696 ATCAAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (27 bp):
TCAAATAAATTTCGATTCGATTAATGG
Found at i:1853781 original size:26 final size:27
Alignment explanation
Indices: 1853741--1853792 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
1853731 AATAATTTTT
1853741 AAATAAATTTCGGTTCGATTAATGGTC
1 AAATAAATTTCGGTTCGATTAATGGTC
1853768 AAAT-AATTTCGGTTCGATTAATGGT
1 AAATAAATTTCGGTTCGATTAATGGT
1853793 TAAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (27 bp):
AAATAAATTTCGGTTCGATTAATGGTC
Found at i:1853802 original size:94 final size:94
Alignment explanation
Indices: 1853631--1853814 Score: 314
Period size: 94 Copynumber: 1.9 Consensus size: 94
1853621 TAACCTTTAA
1853631 TCGGTTAATAATTTTCAAATAAATTTCGATTCGATTAATGGTCAAATAATTTCGGTTCGATTAAT
1 TCGGTTAATAATTTTCAAATAAATTTCGATTCGATTAATGGTCAAATAATTTCGGTTCGATTAAT
*
1853696 ATCAAAGAAAAAAATTCGGTTAATATGGT
66 ATCAAAGAAAAAAATTCGATTAATATGGT
* *
1853725 TCGGTTAATAATTTTTAAATAAATTTCGGTTCGATTAATGGTCAAATAATTTCGGTTCGATTAAT
1 TCGGTTAATAATTTTCAAATAAATTTCGATTCGATTAATGGTCAAATAATTTCGGTTCGATTAAT
* *
1853790 GGTTAAAGAAAAAAATTCGATTAAT
66 -ATCAAAGAAAAAAATTCGATTAAT
1853815 TCGATTTTTT
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
94 63 0.75
95 21 0.25
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (94 bp):
TCGGTTAATAATTTTCAAATAAATTTCGATTCGATTAATGGTCAAATAATTTCGGTTCGATTAAT
ATCAAAGAAAAAAATTCGATTAATATGGT
Found at i:1853975 original size:93 final size:94
Alignment explanation
Indices: 1853875--1854101 Score: 366
Period size: 93 Copynumber: 2.4 Consensus size: 94
1853865 ATTTATTTTA
* * *
1853875 TTCGGTTAATAATTTTAAAATAAATTTTGATTCGATTAACAGCCAAATAATTTCAGTTCGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACAGCCAAATAATTTCAGTTCGATTAA
1853940 TGTTAAAGAAAAAAA-TCGGTTAATTTGG
66 TGTTAAAGAAAAAAATTCGGTTAATTTGG
* * **
1853968 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCAATTAACAGTCAAATAATTTTGGTTCGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACAGCCAAATAATTTCAGTTCGATTAA
*
1854033 TGTTAACGAAAAAAATTCGGTTAATTTGG
66 TGTTAAAGAAAAAAATTCGGTTAATTTGG
*
1854062 TTTGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAAC
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAAC
1854102 GGTTAAAAAA
Statistics
Matches: 123, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
93 72 0.59
94 51 0.41
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (94 bp):
TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACAGCCAAATAATTTCAGTTCGATTAA
TGTTAAAGAAAAAAATTCGGTTAATTTGG
Found at i:1855594 original size:21 final size:21
Alignment explanation
Indices: 1855570--1855641 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
1855560 AAATTTTATT
1855570 TAATTACTCACATCAAACATA
1 TAATTACTCACATCAAACATA
* **
1855591 TAATTAGT-A-ATCTAGGATAGGTTA
1 TAATTACTCACATC-A--A-ACAT-A
1855615 TAATTACTCACATCAAACATA
1 TAATTACTCACATCAAACATA
1855636 TAATTA
1 TAATTA
1855642 GTAATATAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
19 3 0.08
20 2 0.05
21 14 0.37
22 3 0.08
23 3 0.08
24 8 0.21
25 2 0.05
26 3 0.08
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (21 bp):
TAATTACTCACATCAAACATA
Found at i:1861230 original size:182 final size:182
Alignment explanation
Indices: 1860922--1861335 Score: 618
Period size: 182 Copynumber: 2.3 Consensus size: 182
1860912 TCGATCAAAT
* * *
1860922 TAAAAATGTATCGATCCATAT-TATTATAATAGGTAAAAATATGATAAAACCAGTCACTAAAAGA
1 TAAAAATGTATCGATCCACATCTA-TATAACAGGTAAAAATATGATAAAACCAGTCACGAAAAGA
* * *
1860986 CAATACCGGTAAAGCCCTACCGGATATATTGAACGTGTCGATACTTTAATATAAGGATCGACACT
65 CAAAACCAGTAAAGCCCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACT
1861051 TTGAGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
130 TTGAGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
* * *
1861104 TAAAAATGTATCGATCCACATCGATATAACAGGTAAAAATATGACAAAACC-GAT-ATCGAAATG
1 TAAAAATGTATCGATCCACATCTATATAACAGGTAAAAATATGATAAAACCAG-TCA-CGAAAAG
* ** * * *
1861167 ATAAAACCAGTAAAGTGCTACCGGATATATTTAAAGTGTCGGTACTTTAATATAAGTATCGACAC
64 ACAAAACCAGTAAAGCCCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACAC
* *
1861232 TTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTA
129 TTTGAGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
*
1861286 TAAAAATGTATCGATCCACAACTATATAACAGGTAAAAATATGATAAAAC
1 TAAAAATGTATCGATCCACATCTATATAACAGGTAAAAATATGATAAAAC
1861336 TGGTAAAGCG
Statistics
Matches: 209, Mismatches: 20, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
181 2 0.01
182 206 0.99
183 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (182 bp):
TAAAAATGTATCGATCCACATCTATATAACAGGTAAAAATATGATAAAACCAGTCACGAAAAGAC
AAAACCAGTAAAGCCCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTT
TGAGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
Found at i:1863183 original size:22 final size:24
Alignment explanation
Indices: 1863138--1863188 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1863128 TTTTGTGTTT
*
1863138 TTATATAAAATGATAGTATATTTA
1 TTATATAAAATGATAGAATATTTA
*
1863162 TTATATAAAATTATA-AAT-TTTA
1 TTATATAAAATGATAGAATATTTA
1863184 TTATA
1 TTATA
1863189 AATGCAGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.36
23 2 0.08
24 14 0.56
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
TTATATAAAATGATAGAATATTTA
Found at i:1863487 original size:15 final size:15
Alignment explanation
Indices: 1863467--1863496 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1863457 TGGTTGTATT
1863467 GGGGGATGACGGTGA
1 GGGGGATGACGGTGA
1863482 GGGGGATGACGGTGA
1 GGGGGATGACGGTGA
1863497 ATGAAAACAG
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:0.20, C:0.07, G:0.60, T:0.13
Consensus pattern (15 bp):
GGGGGATGACGGTGA
Found at i:1863605 original size:21 final size:21
Alignment explanation
Indices: 1863581--1863645 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
1863571 AAGATAATCA
1863581 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1863602 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
** * *
1863623 AGAGTTAAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1863644 AG
1 AG
1863646 GAATAAGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.43, C:0.09, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1863716 original size:33 final size:33
Alignment explanation
Indices: 1863679--1863742 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
1863669 AAATAGATGG
*
1863679 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTAA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTAA
*
1863712 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGT
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGT
1863743 GATCTTAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.45, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTAA
Found at i:1863955 original size:21 final size:21
Alignment explanation
Indices: 1863929--1863969 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1863919 GAAAAAATAT
1863929 GAAGAAGAAAAGAGGGAAGAG
1 GAAGAAGAAAAGAGGGAAGAG
*
1863950 GAAGAAGAAAAGATGGAAGA
1 GAAGAAGAAAAGAGGGAAGA
1863970 AATGAGGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.39, T:0.02
Consensus pattern (21 bp):
GAAGAAGAAAAGAGGGAAGAG
Found at i:1865556 original size:19 final size:19
Alignment explanation
Indices: 1865529--1865577 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1865519 AATGTAGGGT
*
1865529 TAATGTTGTATA-AGATTTA
1 TAATTTTGTATACA-ATTTA
1865548 TAATTTTGTATACAATTTA
1 TAATTTTGTATACAATTTA
1865567 TAATTTTGTAT
1 TAATTTTGTAT
1865578 GTGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 27 0.96
20 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.53
Consensus pattern (19 bp):
TAATTTTGTATACAATTTA
Found at i:1866371 original size:199 final size:200
Alignment explanation
Indices: 1865820--1866973 Score: 1868
Period size: 200 Copynumber: 5.8 Consensus size: 200
1865810 AAGCATATGC
* * *
1865820 GTCGATCCATATATAAAAAGTATCGATCCCAGAAACATCAAAACTCATAAGTATAATGTAATAGG
1 GTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATAGG
* * * * * *
1865885 TAATTTTTCAATGTAACCGGTATAAATTTGCCGGTTTTACGAGACAATATGTCTACAATATGTAT
66 TAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGTAT
*
1865950 CGACACTTTTTTATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCAT
131 CGACACTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCAT
1866015 AAAGT
196 AAAGT
*
1866020 GTCGATCCATTTATAAAAAGTATTGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATAGG
1 GTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATAGG
1866085 TAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGTAT
66 TAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGTAT
*
1866150 CGGCACTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCAT
131 CGACACTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCAT
1866215 AAAGT
196 AAAGT
* * * * *
1866220 GTCGATCCATTTATAAAATGTATCGATCTCAGAAACTTCGAAA-CCATAAGTATAATATAATATG
1 GTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATAGG
* * *
1866284 TAATTTTTCAATGTAACCGGTATAAATATACCAGTTTTACGAGAGAATAGATCTACAACATGTAT
66 TAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGTAT
* *
1866349 CGACATTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTACAACCAT
131 CGACACTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCAT
1866414 AAAGT
196 AAAGT
* * *
1866419 ATCGATCCATTTATAAAAAATATCGATCCCAGAAACATCGAAACACATAAGTATAATGTAATAGG
1 GTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATAGG
* *
1866484 TAAATTTTCAATGTAACCGGTATAAATATACC-GTTTTATGAGAGAATAGGTTTACAACATGTAT
66 TAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGTAT
*
1866548 CGA-ACCTTTTTAATTTTGTGTCGATACTTTTAGTCCAGAATGAATGCCAAAAAGGGTGCAACCA
131 CGACA-CTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCA
1866612 TAAAGT
195 TAAAGT
** *
1866618 GTCGATATATTTATAAAAAGTATCGATCCTAGAAACATCGAAACCCATAAGTATAATGTAATAGG
1 GTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATAGG
* * *
1866683 TAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTACGAGAAAATAGGTCTACAACATGTAT
66 TAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGTAT
* *
1866748 CGACACTTTTTAATTTTGTGTCGATACTTTTGGTCCATAATGAATCCCAAAAAGGGTGCAACCAT
131 CGACACTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCAT
1866813 AAAGT
196 AAAGT
* * *
1866818 GTCGTTTCATTTATAAAAAGTATTGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATAGG
1 GTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATAGG
* * *
1866883 TAAATTATCAATGTAACCGGTATAAATAT--CGGTTTTATGAGAGAATATGTCTACAACATGTAT
66 TAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGTAT
* *
1866946 CAACACTTTTTAATTTTATGTCGATACT
131 CGACACTTTTTAATTTTGTGTCGATACT
1866974 ATTTTAAATA
Statistics
Matches: 884, Mismatches: 66, Indels: 10
0.92 0.07 0.01
Matches are distributed among these distances:
198 58 0.07
199 369 0.42
200 456 0.52
201 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (200 bp):
GTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATAGG
TAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGTAT
CGACACTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCAT
AAAGT
Found at i:1866501 original size:399 final size:396
Alignment explanation
Indices: 1865820--1866973 Score: 1884
Period size: 399 Copynumber: 2.9 Consensus size: 396
1865810 AAGCATATGC
* *
1865820 GTCGATCCATATATAAAAAGTATCGATCCCAGAAACATCAAAACTCATAAGTATAATGTAATAGG
1 GTCGATCCATTTATAAAAAGTATCGAT-CCAGAAACATCGAAAC-CATAAGTATAATGTAATAGG
* * *
1865885 TAATTTTTCAATGTAACCGGTATAAATTTGCCGGTTTTACGAGACAATATGTCTACAATATGTAT
64 TAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTACGAGAAAATA-GTCTACAACATGTAT
1865950 CGACACTTTTTT-ATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCA
128 CGACA-TTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCA
1866014 TAAAGTGTCGATCCATTTATAAAAAGTATTGATCCCAGAAACATCGAAACCCATAAGTATAATGT
192 TAAAGTGTCGATCCATTTATAAAAAGTATTGATCCCAGAAACATCGAAACCCATAAGTATAATGT
*
1866079 AATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAAC
257 AATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAAC
*
1866144 ATGTATCGGCACTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGC
322 ATGTATC-GCACTTTTTAATTTTGTGTCGATACTTTTAGTCCAGAATGAATGCCAAAAAGGGTGC
1866209 AACCATAAAGT
386 AACCATAAAGT
* * * *
1866220 GTCGATCCATTTATAAAATGTATCGATCTCAGAAACTTCGAAACCATAAGTATAATATAATATGT
1 GTCGATCCATTTATAAAAAGTATCGATC-CAGAAACATCGAAACCATAAGTATAATGTAATAGGT
* * *
1866285 AATTTTTCAATGTAACCGGTATAAATATACCAGTTTTACGAGAGAATAGATCTACAACATGTATC
65 AATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTACGAGAAAATAG-TCTACAACATGTATC
*
1866350 GACATTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTACAACCATA
129 GACATTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATA
* * * *
1866415 AAGTATCGATCCATTTATAAAAAATATCGATCCCAGAAACATCGAAACACATAAGTATAATGTAA
194 AAGTGTCGATCCATTTATAAAAAGTATTGATCCCAGAAACATCGAAACCCATAAGTATAATGTAA
*
1866480 TAGGTAAATTTTCAATGTAACCGGTATAAATATACC-GTTTTATGAGAGAATAGGTTTACAACAT
259 TAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACAT
*
1866544 GTATCGAACCTTTTTAATTTTGTGTCGATACTTTTAGTCCAGAATGAATGCCAAAAAGGGTGCAA
324 GTATCGCA-CTTTTTAATTTTGTGTCGATACTTTTAGTCCAGAATGAATGCCAAAAAGGGTGCAA
1866609 CCATAAAGT
388 CCATAAAGT
**
1866618 GTCGATATATTTATAAAAAGTATCGATCCTAGAAACATCGAAACCCATAAGTATAATGTAATAGG
1 GTCGATCCATTTATAAAAAGTATCGATCC-AGAAACATCGAAA-CCATAAGTATAATGTAATAGG
1866683 TAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTACGAGAAAATAGGTCTACAACATGTAT
64 TAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTACGAGAAAATA-GTCTACAACATGTAT
* * *
1866748 CGACACTTTTTAATTTTGTGTCGATACTTTTGGTCCATAATGAATCCCAAAAAGGGTGCAACCAT
128 CGACATTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCAT
* *
1866813 AAAGTGTCGTTTCATTTATAAAAAGTATTGATCCCAGAAACATCGAAACCCATAAGTATAATGTA
193 AAAGTGTCGATCCATTTATAAAAAGTATTGATCCCAGAAACATCGAAACCCATAAGTATAATGTA
* *
1866878 ATAGGTAAATTATCAATGTAACCGGTATAAATAT--CGGTTTTATGAGAGAATATGTCTACAACA
258 ATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACA
* *
1866941 TGTATCAACACTTTTTAATTTTATGTCGATACT
323 TGTATC-GCACTTTTTAATTTTGTGTCGATACT
1866974 ATTTTAAATA
Statistics
Matches: 700, Mismatches: 45, Indels: 20
0.92 0.06 0.03
Matches are distributed among these distances:
397 4 0.01
398 192 0.27
399 465 0.66
400 39 0.06
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (396 bp):
GTCGATCCATTTATAAAAAGTATCGATCCAGAAACATCGAAACCATAAGTATAATGTAATAGGTA
ATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTACGAGAAAATAGTCTACAACATGTATCGA
CATTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACCATAAA
GTGTCGATCCATTTATAAAAAGTATTGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
GGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
ATCGCACTTTTTAATTTTGTGTCGATACTTTTAGTCCAGAATGAATGCCAAAAAGGGTGCAACCA
TAAAGT
Found at i:1868484 original size:18 final size:18
Alignment explanation
Indices: 1868457--1868502 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1868447 CAAGCGGTCA
1868457 ATGAAGATGAAGATGACG
1 ATGAAGATGAAGATGACG
* * *
1868475 ATGAATATGACGATGATG
1 ATGAAGATGAAGATGACG
*
1868493 ATGATGATGA
1 ATGAAGATGA
1868503 TGATCCAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.04, G:0.30, T:0.24
Consensus pattern (18 bp):
ATGAAGATGAAGATGACG
Found at i:1868503 original size:12 final size:12
Alignment explanation
Indices: 1868457--1868506 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
1868447 CAAGCGGTCA
* *
1868457 ATGAAGATGAAG
1 ATGACGATGATG
1868469 ATGACGATGAAT-
1 ATGACGATG-ATG
1868481 ATGACGATGATG
1 ATGACGATGATG
*
1868493 ATGATGATGATG
1 ATGACGATGATG
1868505 AT
1 AT
1868507 CCAAACAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 2 0.06
12 30 0.91
13 1 0.03
ACGTcount: A:0.40, C:0.04, G:0.30, T:0.26
Consensus pattern (12 bp):
ATGACGATGATG
Found at i:1870009 original size:50 final size:53
Alignment explanation
Indices: 1869955--1870063 Score: 138
Period size: 51 Copynumber: 2.1 Consensus size: 53
1869945 AGAATGGATG
1869955 CCAAAAAGGG-TGAACGCAT-AAGTGTCGATACATTT-TCAAAGAGTGTCGAT-
1 CCAAAAAGGGTTGAACGCATAAAGTGTCGATACATTTATCAAA-AGTGTCGATC
* * * *
1870005 CC-AAAAGGGTTGCACGCATAAAGTTTCGATACATTTATTAAAAGTGTTGATC
1 CCAAAAAGGGTTGAACGCATAAAGTGTCGATACATTTATCAAAAGTGTCGATC
1870057 CCAAAAA
1 CCAAAAA
1870064 CATCGAAACC
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
49 7 0.14
50 10 0.20
51 23 0.46
52 6 0.12
53 4 0.08
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (53 bp):
CCAAAAAGGGTTGAACGCATAAAGTGTCGATACATTTATCAAAAGTGTCGATC
Found at i:1870329 original size:177 final size:177
Alignment explanation
Indices: 1870128--1870475 Score: 556
Period size: 177 Copynumber: 2.0 Consensus size: 177
1870118 ACATATACCG
* * * *
1870128 GTTTTATGAGAGAATAGATCTATAACATGTATCGACACT-TCTTAATATTGTGTCGATAATTTTT
1 GTTTTATGAGAGAATAGATCTATAACATGTATCAACACTATATAAAT-TTGTGTCGATAAGTTTT
* * *
1870192 GTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTTGATACATTTTCAAA-AAGCGTCGA
65 GTCCAGAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATTTTCAAAGAA-CGTCGA
*
1870256 TCCCGAAAACATCGAAACCCATAATTATAATGTAATAGGTAATATAAAT
129 TCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATATAAAT
* *
1870305 GTTTTATGAGAGAATAGGTCTATAACATGTATCAACACTATATAAATTTGTGTCGATACGTTTTG
1 GTTTTATGAGAGAATAGATCTATAACATGTATCAACACTATATAAATTTGTGTCGATAAGTTTTG
* *
1870370 TCCAGAATGGATGCCAAAAAGGATGAACGTACAAAGTGTCGATACATTTTCAAAGAATGTCGATC
66 TCCAGAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATTTTCAAAGAACGTCGATC
1870435 CCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAT
131 CCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAT
1870476 TTTGTAATAT
Statistics
Matches: 157, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
177 150 0.96
178 7 0.04
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (177 bp):
GTTTTATGAGAGAATAGATCTATAACATGTATCAACACTATATAAATTTGTGTCGATAAGTTTTG
TCCAGAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCGATACATTTTCAAAGAACGTCGATC
CCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATATAAAT
Found at i:1870648 original size:200 final size:199
Alignment explanation
Indices: 1870305--1870746 Score: 667
Period size: 200 Copynumber: 2.2 Consensus size: 199
1870295 TAATATAAAT
* * * * *
1870305 GTTTTATGAGAGAATAGGTCTATAACATGTATCAACACTATATAAATTTGTGTCGATACGTTTTG
1 GTTTTATAAGAGAATAGGTCTACAACATGTATCGACACTTTTTAAATTTGTGTCGATACGTTTTG
* *
1870370 TCCAGAATGGATGCCAAAAAGGATGAACGTACAAAGTGTCGATACATTTTCAAAGAATGTCGATC
66 TCCAGAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCAATACATTTTCAAAGAATGTCGATC
*
1870435 CCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACC-AGTATAAAT
131 CCAAAAACATCGAAACCCATAATTATAATATAATAGGTAATTTTGTAATATAACCGA-TATAAAT
1870499 ATACC
195 ATACC
* *
1870504 AGTTTTATAAGAGGATAGGTCTACAAGATGTATCGACACTTTTT-AATATTGTGTCGATAC-TTT
1 -GTTTTATAAGAGAATAGGTCTACAACATGTATCGACACTTTTTAAAT-TTGTGTCGATACGTTT
* *
1870567 ATGTCCAGAATGGATGTCAAAAAGGGTGAACGCACAAAGTGTCAATACATTTTCAAA-AAGTGTC
64 -TGTCCAGAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCAATACATTTTCAAAGAA-TGTC
*
1870631 GATCCCAAAAACATCGAAACCCATAATTATAATATAATAGGTAATTTTTTAATATAACCGATATA
127 GATCCCAAAAACATCGAAACCCATAATTATAATATAATAGGTAATTTTGTAATATAACCGATATA
*
1870696 AATATATC
192 AATATACC
* *
1870704 GTTTTATAAGAGAATATGTCTACAACATGTAGCGACACTTTTT
1 GTTTTATAAGAGAATAGGTCTACAACATGTATCGACACTTTTT
1870747 TTATTTTGAT
Statistics
Matches: 220, Mismatches: 18, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
199 47 0.21
200 172 0.78
201 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (199 bp):
GTTTTATAAGAGAATAGGTCTACAACATGTATCGACACTTTTTAAATTTGTGTCGATACGTTTTG
TCCAGAATGGATGCCAAAAAGGATGAACGCACAAAGTGTCAATACATTTTCAAAGAATGTCGATC
CCAAAAACATCGAAACCCATAATTATAATATAATAGGTAATTTTGTAATATAACCGATATAAATA
TACC
Found at i:1872673 original size:200 final size:196
Alignment explanation
Indices: 1872245--1872950 Score: 748
Period size: 200 Copynumber: 3.5 Consensus size: 196
1872235 ACCTAAATAT
* * *
1872245 GTGTCGATACATTT-TATACAAGTATCGA-CCCAAAAAACATCAAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTATA-AAAAGTATCGATCCC-AAAAACATCGAAACCGATAATTATAATGTAA
* * * **
1872308 TATGTAAATTAACAATGTAACCGGTATAAATATACCGGTTAAATAGAAAACATGTCAACATAATG
64 TAGGTAAATTTATAATGTAACCGGTATAAATATACCGGTTTTAT-GAAAA-ATGTCAACATAATG
* * *
1872373 TATCGACACTTGTGAATTTGTTTCGATACTTATT-GTCCAATATGAATG-CACAAACGAGGTGC-
127 TATCGACACTTGTAAATTTGTGTCGATACTT-TTGGTCCAATATGAATGCCA-AAAAG-GGTGCA
1872435 ACGCATAAA
189 AC-CATAAA
* * *
1872444 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATTGAAACCGATAATTATAATGTATTA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * **
1872509 GGTAAATTTATAATATAACCGATATAAATATACCGGTTTTATGATAAAATGGGTCAACATAAAAT
66 GGTAAATTTATAATGTAACCGGTATAAATATACCGGTTTTATGA-AAAAT--GTCAACATAATGT
1872574 ATCGACACTTGCTAAATTTGTGTCGATACTTTTGGTCCAGA-ATGAATGCCAAAAAGGGTGCAAC
128 ATCGACACTTG-TAAATTTGTGTCGATACTTTTGGTCCA-ATATGAATGCCAAAAAGGGTGCAAC
1872638 CATAAA
191 CATAAA
* ** * *
1872644 GTGTCGATACATTTATAAAAAGCATCGATCCCGGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * *
1872709 GGTAAATTT-TCAATGTAACTGGTATAAATATACTGGTTTTATGAGAGAATAAGTCTAA-ATAAT
66 GGTAAATTTAT-AATGTAACCGGTATAAATATACCGGTTTTATGA-A-AA-ATGTC-AACATAAT
* * * * ** **
1872772 GTATCGACACTTTGTTAGTTTGTGTCGATATTTTTTTAGAATGAAATATGAATGCTCAACCA-GG
126 GTATCGACAC-TTGTAAATTTGTGTCGATA--CTTTT-G-GTCCAATATGAATGC-CAAAAAGGG
*
1872836 TGCAAGCATAAA
185 TGCAACCATAAA
** ** *
1872848 GTGTCGATACATTTA-AAATTGTATCGATCTAAAAAACATCGAAACCGATAATAATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* *
1872912 GGTAAATTTGTAATGTTACCGGTATAAATATACCGGTTT
66 GGTAAATTTATAATGTAACCGGTATAAATATACCGGTTT
1872951 ACTTCGAAAA
Statistics
Matches: 429, Mismatches: 56, Indels: 40
0.82 0.11 0.08
Matches are distributed among these distances:
198 4 0.01
199 92 0.21
200 165 0.38
201 42 0.10
202 8 0.02
203 75 0.17
204 39 0.09
205 4 0.01
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (196 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTATAATGTAACCGGTATAAATATACCGGTTTTATGAAAAATGTCAACATAATGTATC
GACACTTGTAAATTTGTGTCGATACTTTTGGTCCAATATGAATGCCAAAAAGGGTGCAACCATAA
A
Found at i:1873061 original size:64 final size:64
Alignment explanation
Indices: 1872988--1873107 Score: 213
Period size: 64 Copynumber: 1.9 Consensus size: 64
1872978 TACCTATTAC
*
1872988 ATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGTCTAATTT
1 ATTATATAAGAGCTACCTAATATATTATTGTACTTGATAATATTTCCGGTTAAATGTCTAATTT
* *
1873052 ATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTTCTGGTTAAATG
1 ATTATATAAGAGCTACCTAATATATTATTGTACTTGATAATATTTCCGGTTAAATG
1873108 ATATAACATT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.43
Consensus pattern (64 bp):
ATTATATAAGAGCTACCTAATATATTATTGTACTTGATAATATTTCCGGTTAAATGTCTAATTT
Found at i:1893195 original size:20 final size:21
Alignment explanation
Indices: 1893170--1893214 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
1893160 TATTATGAGA
*
1893170 AAAATATATAGAATTATAA-T
1 AAAATATATAGAATCATAATT
*
1893190 AAAATATTTAGAATCATAATT
1 AAAATATATAGAATCATAATT
1893211 AAAA
1 AAAA
1893215 ATTAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
AAAATATATAGAATCATAATT
Found at i:1895132 original size:23 final size:23
Alignment explanation
Indices: 1895080--1895124 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1895070 ATTATTTTTG
*
1895080 AAAAATAACTTTTAAAAGTGTGGT
1 AAAAA-AACTTTTAAAAGTGTCGT
1895104 AAAAAAACTTTTAAAAGTGTC
1 AAAAAAACTTTTAAAAGTGTC
1895125 TTTCAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.31
Consensus pattern (23 bp):
AAAAAAACTTTTAAAAGTGTCGT
Found at i:1909846 original size:15 final size:16
Alignment explanation
Indices: 1909826--1909859 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1909816 ACTTGATTAT
1909826 ATTGCAA-ACATTTCC
1 ATTGCAAGACATTTCC
1909841 ATTGCAATGACATTTCC
1 ATTGCAA-GACATTTCC
1909858 AT
1 AT
1909860 CCATTTTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (16 bp):
ATTGCAAGACATTTCC
Found at i:1913762 original size:20 final size:19
Alignment explanation
Indices: 1913739--1913782 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1913729 TTGTTCATGG
**
1913739 GTATCAATATTAACCCTTAA
1 GTATCAATACCAACCC-TAA
*
1913759 GTATCGATACCAACCCTAA
1 GTATCAATACCAACCCTAA
1913778 GTATC
1 GTATC
1913783 GATAGCAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (19 bp):
GTATCAATACCAACCCTAA
Found at i:1914651 original size:42 final size:42
Alignment explanation
Indices: 1914592--1914680 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
1914582 TGGCCAAAAC
* *
1914592 TTGATCTTGGGGTCTCAAATGGAATCTCTAGAGGTGTTAAGA
1 TTGATCTTGGGGTCTCAAATGGAAGCTCTAAAGGTGTTAAGA
*
1914634 TTGATCTTGGGGTCTCAAATGGAAGCTCTAAAGGTGTTAAGT
1 TTGATCTTGGGGTCTCAAATGGAAGCTCTAAAGGTGTTAAGA
1914676 TTGAT
1 TTGAT
1914681 TTTTATCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.35
Consensus pattern (42 bp):
TTGATCTTGGGGTCTCAAATGGAAGCTCTAAAGGTGTTAAGA
Found at i:1919166 original size:30 final size:30
Alignment explanation
Indices: 1919108--1919166 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1919098 GCATAACCAA
* *
1919108 AGGCCTCCTCAACAACAACCATATCAACCG
1 AGGCCACCTCAACAACAACCATACCAACCG
1919138 AGGCCACCTCAACAACAA-CAGTACCAACC
1 AGGCCACCTCAACAACAACCA-TACCAACC
1919167 ATCAAAACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.39, C:0.41, G:0.10, T:0.10
Consensus pattern (30 bp):
AGGCCACCTCAACAACAACCATACCAACCG
Found at i:1920807 original size:13 final size:14
Alignment explanation
Indices: 1920770--1920824 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
1920760 CATTTTTTAC
1920770 TATTTACTTTATTTT
1 TATTTA-TTTATTTT
1920785 TATTTATTTATTTT
1 TATTTATTTATTTT
*
1920799 TA-TTGTTTATTTT
1 TATTTATTTATTTT
* *
1920812 TCTTTATATATTT
1 TATTTATTTATTT
1920825 ATGTACCTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.31
14 18 0.51
15 6 0.17
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (14 bp):
TATTTATTTATTTT
Found at i:1922827 original size:2 final size:2
Alignment explanation
Indices: 1922820--1922849 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1922810 AGTAGCATTG
1922820 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
1922850 GATAATAAAA
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:1923489 original size:21 final size:21
Alignment explanation
Indices: 1923463--1923505 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1923453 TCGAGGGTTC
*
1923463 TATGTGGTCCTTCGGGAAAAA
1 TATGTGGTCCTTCAGGAAAAA
*
1923484 TATGTGGTCCTTCAGGAGAAA
1 TATGTGGTCCTTCAGGAAAAA
1923505 T
1 T
1923506 CCTATGTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (21 bp):
TATGTGGTCCTTCAGGAAAAA
Found at i:1924164 original size:17 final size:18
Alignment explanation
Indices: 1924114--1924153 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1924104 ATTTAAAATT
1924114 TAACCAATTTGTAAAGGA
1 TAACCAATTTGTAAAGGA
1924132 TAACCAATTTGTAAAGGA
1 TAACCAATTTGTAAAGGA
1924150 TAAC
1 TAAC
1924154 ACTTTGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (18 bp):
TAACCAATTTGTAAAGGA
Found at i:1926781 original size:20 final size:20
Alignment explanation
Indices: 1926756--1926807 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1926746 GGTTGAAGGG
1926756 GTATTGATACCAAGTATCTA
1 GTATTGATACCAAGTATCTA
1926776 GTATTGATACCAAGTATCTA
1 GTATTGATACCAAGTATCTA
*
1926796 GTATCGATACCA
1 GTATTGATACCA
1926808 TTATCAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
GTATTGATACCAAGTATCTA
Found at i:1930590 original size:2 final size:2
Alignment explanation
Indices: 1930583--1930610 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1930573 GAATGGTCAG
1930583 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
1930611 TTTAAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1931475 original size:2 final size:2
Alignment explanation
Indices: 1931468--1931500 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1931458 TCAATCTACA
1931468 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1931501 ATAATTTACG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1931684 original size:13 final size:13
Alignment explanation
Indices: 1931660--1931701 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1931650 AATGACGCGC
*
1931660 AATGAGCATCATA
1 AATGCGCATCATA
*
1931673 AATGCGCGTCATA
1 AATGCGCATCATA
*
1931686 AATGTGCATCATA
1 AATGCGCATCATA
1931699 AAT
1 AAT
1931702 TTATGACGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (13 bp):
AATGCGCATCATA
Found at i:1932861 original size:20 final size:20
Alignment explanation
Indices: 1932832--1932882 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1932822 CGTTAAGGGA
*
1932832 TGTACTGATACACTATAGAG
1 TGTACCGATACACTATAGAG
1932852 TGTACCGATACACTATAGAG
1 TGTACCGATACACTATAGAG
1932872 TGTACCGATAC
1 TGTACCGATAC
1932883 CTACCTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (20 bp):
TGTACCGATACACTATAGAG
Found at i:1934846 original size:23 final size:23
Alignment explanation
Indices: 1934816--1934861 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1934806 CGGGTTGGGG
1934816 GTGTTACAGTATATCTATTCCTT
1 GTGTTACAGTATATCTATTCCTT
1934839 GTGTTACAGTATATCTATTCCTT
1 GTGTTACAGTATATCTATTCCTT
1934862 CTCCTATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.48
Consensus pattern (23 bp):
GTGTTACAGTATATCTATTCCTT
Found at i:1935605 original size:21 final size:21
Alignment explanation
Indices: 1935581--1935624 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1935571 CGAACAGGAA
1935581 AAAAACAAAAAAAAAGCAAGG
1 AAAAACAAAAAAAAAGCAAGG
* * *
1935602 AAAAATAAAAAAAATGGAAGG
1 AAAAACAAAAAAAAAGCAAGG
1935623 AA
1 AA
1935625 GAAGAAAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.75, C:0.05, G:0.16, T:0.05
Consensus pattern (21 bp):
AAAAACAAAAAAAAAGCAAGG
Found at i:1936931 original size:22 final size:22
Alignment explanation
Indices: 1936899--1936995 Score: 99
Period size: 22 Copynumber: 4.4 Consensus size: 22
1936889 CCATTAAATA
*
1936899 ACAAAAATGCCTCAGCACTGAT
1 ACAAAAGTGCCTCAGCACTGAT
1936921 ACAAAAGTGCCTCAGCACTGAT
1 ACAAAAGTGCCTCAGCACTGAT
**
1936943 ACAAAAGTGTATTC-GCACTGAGT
1 ACAAAAGTG-CCTCAGCACTGA-T
* * **
1936966 -CAAAAGGGCATTTGCACTGAT
1 ACAAAAGTGCCTCAGCACTGAT
1936987 ACAAAAGTG
1 ACAAAAGTG
1936996 TCATAGCACT
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.03
22 58 0.92
23 3 0.05
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (22 bp):
ACAAAAGTGCCTCAGCACTGAT
Found at i:1936962 original size:44 final size:44
Alignment explanation
Indices: 1936913--1936996 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
1936903 AAATGCCTCA
* *
1936913 GCACTGA-TACAAAAGTGCCTCAGCACTGATACAAAAGTGTATTC
1 GCACTGAGT-CAAAAGGGCATCAGCACTGATACAAAAGTGTATTC
**
1936957 GCACTGAGTCAAAAGGGCATTTGCACTGATACAAAAGTGT
1 GCACTGAGTCAAAAGGGCATCAGCACTGATACAAAAGTGT
1936997 CATAGCACTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
44 34 0.97
45 1 0.03
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (44 bp):
GCACTGAGTCAAAAGGGCATCAGCACTGATACAAAAGTGTATTC
Found at i:1937004 original size:22 final size:23
Alignment explanation
Indices: 1936912--1937007 Score: 103
Period size: 22 Copynumber: 4.3 Consensus size: 23
1936902 AAAATGCCTC
* *
1936912 AGCACTGATACAAAAGTG-CCTC
1 AGCACTGATACAAAAGTGTCATT
1936934 AGCACTGATACAAAAGTGT-ATT
1 AGCACTGATACAAAAGTGTCATT
* *
1936956 CGCACTGAGT-CAAAAG-GGCATT
1 AGCACTGA-TACAAAAGTGTCATT
*
1936978 TGCACTGATACAAAAGTGTCA-T
1 AGCACTGATACAAAAGTGTCATT
1937000 AGCACTGA
1 AGCACTGA
1937008 GAAGAGAATC
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
21 2 0.03
22 56 0.90
23 4 0.06
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (23 bp):
AGCACTGATACAAAAGTGTCATT
Found at i:1938042 original size:14 final size:14
Alignment explanation
Indices: 1938023--1938055 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1938013 AGACACTCTC
1938023 AAGCCCTCAAACTA
1 AAGCCCTCAAACTA
1938037 AAGCCCTCAAACTA
1 AAGCCCTCAAACTA
1938051 AAGCC
1 AAGCC
1938056 TCTCTATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.36, G:0.09, T:0.12
Consensus pattern (14 bp):
AAGCCCTCAAACTA
Found at i:1941546 original size:87 final size:87
Alignment explanation
Indices: 1941400--1941649 Score: 473
Period size: 87 Copynumber: 2.9 Consensus size: 87
1941390 TATGTTATAT
*
1941400 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1941465 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
*
1941487 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATGTAATAGAT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1941552 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
*
1941574 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGGT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1941639 AGCGCTTATAT
66 AGCGCTTATAT
1941650 TGACCTATTT
Statistics
Matches: 159, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 159 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (87 bp):
TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:1942118 original size:260 final size:246
Alignment explanation
Indices: 1941762--1942279 Score: 759
Period size: 260 Copynumber: 2.0 Consensus size: 246
1941752 CTTTTTATAA
*
1941762 AAGTATCGACACTTTATGCTTGCACCTCGTTGGGCATTAATATTTCATTCTGGATAAAAATATCG
1 AAGTATCGACACTTTATGCTTGCACCTCGTTGGGCATTAATATTTCATTCTGGACAAAAATATCG
* * *
1941827 ACACAAACTAAAAAAGTGTTGATATATGATTTAGACATATTCTCTCATAAAACTGGTATAATTAT
66 ACACAAACTAAAAAAGTGTCGATACATGATTTAGACATATTCTCTCATAAAACCGGTATAATTAT
* *
1941892 ACCGGTTTCATTGACCATTTACCTATTACATTATACTTATGGGTTTCGATGTTTTAGGGATCGAT
131 ACAGGTTTCATTG-----------A--ACATTATACTTATGGGTTTCGATATTTTAGGGATCGAT
*
1941957 ATTTTTTTAATAAATGTATCGACACTTTTTAAGGGTACACCTTTTTTGGCATTCATTCTAGACCG
183 ACTTTTTTAATAAATGTATCGACAC--TTTAAGGGTACACCTTTTTTGGCATTCATTCTAGACCG
1942022 T
246 T
* * * **
1942023 AAGTATCAACACTTTATGTTTGCACCTTGTT-GGTTTTAATATTTCATTCTGGACAAAAATATCG
1 AAGTATCGACACTTTATGCTTGCACCTCGTTGGGCATTAATATTTCATTCTGGACAAAAATATCG
*
1942087 ACACAAACTAAAAAAGTGTCGATACATGATTTAGACCTATTCTCTCATAAAACCGGTATAATTAT
66 ACACAAACTAAAAAAGTGTCGATACATGATTTAGACATATTCTCTCATAAAACCGGTATAATTAT
* *
1942152 ACATGTTTCATTGAACATTATACTTATGGGTTTTGATATTTTAGGGATCGATACTTTTTTAATAA
131 ACAGGTTTCATTGAACATTATACTTATGGGTTTCGATATTTTAGGGATCGATACTTTTTTAATAA
1942217 ATGTATCGACACTTTAAGGGTACACCTTTTTTGGCATTCATTCTAGACCGT
196 ATGTATCGACACTTTAAGGGTACACCTTTTTTGGCATTCATTCTAGACCGT
1942268 AAGTATCGACAC
1 AAGTATCGACAC
1942280 AACTTTAACA
Statistics
Matches: 241, Mismatches: 16, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
245 50 0.21
247 60 0.25
249 1 0.00
260 102 0.42
261 28 0.12
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (246 bp):
AAGTATCGACACTTTATGCTTGCACCTCGTTGGGCATTAATATTTCATTCTGGACAAAAATATCG
ACACAAACTAAAAAAGTGTCGATACATGATTTAGACATATTCTCTCATAAAACCGGTATAATTAT
ACAGGTTTCATTGAACATTATACTTATGGGTTTCGATATTTTAGGGATCGATACTTTTTTAATAA
ATGTATCGACACTTTAAGGGTACACCTTTTTTGGCATTCATTCTAGACCGT
Found at i:1945305 original size:183 final size:183
Alignment explanation
Indices: 1944997--1945567 Score: 993
Period size: 183 Copynumber: 3.1 Consensus size: 183
1944987 TTAAAATTAG
*
1944997 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
1945062 ATACCGATTATATTACAAAATTATATATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
* *
1945127 CACTTTTTGACAAGGTATCGACATATTTTTCTTCCATTCTCGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
*
1945180 CGACACAATATTAAAAAGTGTTGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
1945245 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
1945310 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
*
1945363 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAATCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* * * *
1945428 ATATCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTTTTTTCAA--T
66 ATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATG---TGTAAATGT
*
1945491 CGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
128 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
1945547 CGACACAATATTAAAAAGTGT
1 CGACACAATATTAAAAAGTGT
1945568 GAAAACTTTG
Statistics
Matches: 371, Mismatches: 14, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
183 290 0.78
184 77 0.21
186 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTAC
Found at i:1946785 original size:3 final size:3
Alignment explanation
Indices: 1946777--1946842 Score: 78
Period size: 3 Copynumber: 22.0 Consensus size: 3
1946767 ACTTGTTTGG
* * *
1946777 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC GTC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
1946825 TTC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC
1946843 GTCAGCTTCA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:1946843 original size:12 final size:12
Alignment explanation
Indices: 1946778--1946859 Score: 83
Period size: 12 Copynumber: 6.8 Consensus size: 12
1946768 CTTGTTTGGA
*
1946778 TCATCATCATCA
1 TCATCATCATCT
*
1946790 TCATCATCATCA
1 TCATCATCATCT
*
1946802 TCATCATCATCG
1 TCATCATCATCT
* *
1946814 TCGTCGTCATCT
1 TCATCATCATCT
*
1946826 TCATCGTCATCT
1 TCATCATCATCT
* *
1946838 TCATCGTCAGCT
1 TCATCATCATCT
*
1946850 TCATCTTCAT
1 TCATCATCAT
1946860 TGACCGCTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 62 1.00
ACGTcount: A:0.22, C:0.33, G:0.07, T:0.38
Consensus pattern (12 bp):
TCATCATCATCT
Found at i:1949082 original size:14 final size:13
Alignment explanation
Indices: 1949049--1949074 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1949039 TCGATATTGA
1949049 AAAATAATTTATT
1 AAAATAATTTATT
1949062 AAAATAATTTATT
1 AAAATAATTTATT
1949075 TGAAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAATAATTTATT
Found at i:1950438 original size:3 final size:3
Alignment explanation
Indices: 1950430--1950486 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
1950420 TTAATATATT
* * *
1950430 TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1950478 TAA TAA TAA
1 TAA TAA TAA
1950487 ATAAATCAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1950903 original size:113 final size:113
Alignment explanation
Indices: 1950718--1951616 Score: 1229
Period size: 113 Copynumber: 8.0 Consensus size: 113
1950708 GTGACAGAGT
* ** * *
1950718 CAAAAGGTTGAATAAGCTCTTCTTATTATGAACTTC--C-T-CTTCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*** * *
1950779 TTATGAACTTTCTCTGGAAATTTTAATCCATCAAGTGATAGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
* *
1950827 CGAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
1950892 TTATGAACTTTCTCTGGAAAAGCGGATCCATCAAGTGATGGATTTGAA
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
1950940 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
* * ** * * * * ** *
1951005 TCATTGTGAACTCTAC-CTGGCTATGTTGATCCATCAAATGATGAATTCAAA
63 TCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
* *
1951056 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT-AGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
1951120 TTATGAACTTTCTCTGGAAAAGCGGATCCATCAAGTGATGGATTTGGG
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
* * * * *
1951168 CAAACGGTTAAATAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCG
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
1951233 TTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTAAG
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
*
1951281 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
1951346 TTATGAACTTTCTCTGGAAAAGCGGATCCATCAAGTGATGGATTTG-G
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
* *
1951393 ACAAAAGGTTAAATAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 -CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
1951458 GTTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTAAG
65 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
*
1951507 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*** * *
1951572 TTATGAACTTGAACTGGAAAAGTTGATCCATTGAA-TGATGGATTT
66 TTATGAACTTTCTCTGGAAAAGCTGATCCA-TCAAGTGATGGATTT
1951617 AAATCTTTGC
Statistics
Matches: 695, Mismatches: 82, Indels: 22
0.87 0.10 0.03
Matches are distributed among these distances:
109 31 0.04
111 3 0.00
112 88 0.13
113 471 0.68
114 4 0.01
115 4 0.01
116 92 0.13
117 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
Found at i:1952475 original size:83 final size:83
Alignment explanation
Indices: 1952335--1953128 Score: 1254
Period size: 83 Copynumber: 9.6 Consensus size: 83
1952325 TCTATAGTTC
* * *
1952335 CTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTC
1 CTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTT
*
1952400 CAAATTTAATAACTGGTT
66 CAAATTTAATGACTGGTT
* *
1952418 TTACCAAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTT
1 CTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTT
*
1952483 CAAATTCAATGACTGGTT
66 CAAATTTAATGACTGGTT
*
1952501 TTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTT
1 CTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTT
*
1952566 CAAATTCAATGACTGGTT
66 CAAATTTAATGACTGGTT
* *
1952584 TTACCAAACCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCTATGAGCACATTCATCTTT
1 CTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTT
* *
1952649 CAAATTCAATGACTAGTT
66 CAAATTTAATGACTGGTT
* *
1952667 TTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTT
1 CTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTT
* * *
1952732 C-GATTTCAATGATTAGTT
66 CAAATTT-AATGACTGGTT
*
1952750 CTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTT
1 CTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTT
*
1952815 C-AATTTCAATGATTGGTT
66 CAAATTT-AATGACTGGTT
* *
1952833 CTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTT
1 CTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTT
*
1952898 C-AATTTCAATGATTGGTT
66 CAAATTT-AATGACTGGTT
*
1952916 CTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTT
1 CTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTT
*
1952981 C-AATTTCAATGATTGGTT
66 CAAATTT-AATGACTGGTT
*
1952999 CTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTT
1 CTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTT
* * *
1953064 TAAATTCAATGGCTGGTT
66 CAAATTTAATGACTGGTT
*
1953082 CTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 CTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1953129 TTTCCATTGA
Statistics
Matches: 683, Mismatches: 26, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
82 3 0.00
83 676 0.99
84 4 0.01
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (83 bp):
CTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTT
CAAATTTAATGACTGGTT
Found at i:1954114 original size:10 final size:10
Alignment explanation
Indices: 1954101--1954148 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
1954091 TTGACCCCCC
1954101 TTTTCCTTTT
1 TTTTCCTTTT
*
1954111 TTTTCTTTTT
1 TTTTCCTTTT
*
1954121 TCTTTCTTTTT
1 T-TTTCCTTTT
1954132 TTTTCTTCTTTT
1 TTTTC--CTTTT
1954144 TTTTC
1 TTTTC
1954149 TTCAAGCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 14 0.42
11 10 0.30
12 9 0.27
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTCCTTTT
Found at i:1954126 original size:21 final size:22
Alignment explanation
Indices: 1954102--1954148 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
1954092 TGACCCCCCT
1954102 TTTCCTTTTTTTTCTT-TTTTC
1 TTTCCTTTTTTTTCTTCTTTTC
* *
1954123 TTTCTTTTTTTTTCTTCTTTTT
1 TTTCCTTTTTTTTCTTCTTTTC
1954145 TTTC
1 TTTC
1954149 TTCAAGCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTCCTTTTTTTTCTTCTTTTC
Found at i:1954130 original size:17 final size:16
Alignment explanation
Indices: 1954101--1954150 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
1954091 TTGACCCCCC
*
1954101 TTTTCCTTTTTTTTCT
1 TTTTTCTTTTTTTTCT
1954117 TTTTTCTTTCTTTTT-T
1 TTTTTCTTT-TTTTTCT
1954133 TTTCTTCTTTTTTTTCT
1 TTT-TTCTTTTTTTTCT
1954150 T
1 T
1954151 CAAGCATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTCTTTTTTTTCT
Found at i:1954134 original size:13 final size:13
Alignment explanation
Indices: 1954116--1954150 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
1954106 CTTTTTTTTC
1954116 TTTTTTCTTTCTT
1 TTTTTTCTTTCTT
1954129 TTTTTT-TCTTCTT
1 TTTTTTCT-TTCTT
1954142 TTTTTTCTT
1 TTTTTTCTT
1954151 CAAGCATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.05
13 18 0.90
14 1 0.05
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTCTTTCTT
Found at i:1954147 original size:12 final size:12
Alignment explanation
Indices: 1954106--1954151 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
1954096 CCCCCTTTTC
1954106 CTTTTTTTTCTT
1 CTTTTTTTTCTT
*
1954118 -TTTTCTTTC-T
1 CTTTTTTTTCTT
1954128 -TTTTTTTTCTT
1 CTTTTTTTTCTT
1954139 CTTTTTTTTCTT
1 CTTTTTTTTCTT
1954151 C
1 C
1954152 AAGCATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 9 0.30
11 9 0.30
12 12 0.40
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
CTTTTTTTTCTT
Found at i:1964808 original size:19 final size:18
Alignment explanation
Indices: 1964758--1964808 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
1964748 CTCTGACAGA
1964758 AAAATAAATAATAAAAT-
1 AAAATAAATAATAAAATG
**
1964775 AAAATACTTGCAATAAAATG
1 AAAATAAAT--AATAAAATG
1964795 AAATATAAATAATA
1 AAA-ATAAATAATA
1964809 TATAAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
17 7 0.27
19 12 0.46
20 3 0.12
21 4 0.15
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (18 bp):
AAAATAAATAATAAAATG
Found at i:1964811 original size:11 final size:11
Alignment explanation
Indices: 1964797--1964835 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1964787 ATAAAATGAA
1964797 ATATAAATAAT
1 ATATAAATAAT
*
1964808 ATATAAAAAAT
1 ATATAAATAAT
*
1964819 ATATATAT-AT
1 ATATAAATAAT
1964829 ATATAAA
1 ATATAAA
1964836 AAAAATTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATATAAATAAT
Found at i:1964832 original size:21 final size:20
Alignment explanation
Indices: 1964795--1964838 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
1964785 CAATAAAATG
1964795 AAATATAAATAATATATAAA
1 AAATATAAATAATATATAAA
*
1964815 AAATATATATATATATATAAA
1 AAATATAAATA-ATATATAAA
1964836 AAA
1 AAA
1964839 AATTATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATATAAATAATATATAAA
Found at i:1965526 original size:14 final size:13
Alignment explanation
Indices: 1965492--1965517 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1965482 TCGATATTGA
1965492 AAAATAATTTATT
1 AAAATAATTTATT
1965505 AAAATAATTTATT
1 AAAATAATTTATT
1965518 TGAAATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAATAATTTATT
Found at i:1965532 original size:16 final size:16
Alignment explanation
Indices: 1965498--1965548 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1965488 TTGAAAAATA
1965498 ATTTA-TTAAA-ATA-
1 ATTTATTTAAATATAT
1965511 ATTTATTTGAAATA-AT
1 ATTTATTT-AAATATAT
*
1965527 ATTTATTTATATATAT
1 ATTTATTTAAATATAT
1965543 ATTTAT
1 ATTTAT
1965549 GACTACATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
13 5 0.16
14 2 0.06
15 8 0.25
16 17 0.53
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTATTTAAATATAT
Found at i:1966878 original size:12 final size:12
Alignment explanation
Indices: 1966863--1966939 Score: 66
Period size: 12 Copynumber: 6.4 Consensus size: 12
1966853 TATATATATT
*
1966863 TAATATTTTTAA
1 TAATATTTATAA
* *
1966875 TAATAATAATAA
1 TAATATTTATAA
1966887 TAATATTTATAA
1 TAATATTTATAA
* *
1966899 TAATAATAATAA
1 TAATATTTATAA
* *
1966911 TAATAATAATAA
1 TAATATTTATAA
*
1966923 -ATATAATTATAA
1 TA-ATATTTATAA
1966935 TAATA
1 TAATA
1966940 ATAAATAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
11 1 0.02
12 53 0.96
13 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATTTATAA
Found at i:1966880 original size:3 final size:3
Alignment explanation
Indices: 1966872--1966943 Score: 101
Period size: 3 Copynumber: 24.0 Consensus size: 3
1966862 TTAATATTTT
* *
1966872 TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1966920 TAA -ATA TAA TTA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA
1966944 ATAAATCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
2 1 0.02
3 59 0.97
4 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1966894 original size:24 final size:24
Alignment explanation
Indices: 1966863--1966939 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
1966853 TATATATATT
*
1966863 TAATATTTTTAATAATAATAATAA
1 TAATATTTATAATAATAATAATAA
1966887 TAATATTTATAATAATAATAATAA
1 TAATATTTATAATAATAATAATAA
* * *
1966911 TAATAATAATAA-ATATAATTATAA
1 TAATATTTATAATA-ATAATAATAA
1966935 TAATA
1 TAATA
1966940 ATAAATAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 1 0.02
24 47 0.98
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAATATTTATAATAATAATAATAA
Found at i:1967459 original size:200 final size:199
Alignment explanation
Indices: 1966978--1967552 Score: 1028
Period size: 200 Copynumber: 2.9 Consensus size: 199
1966968 AGTATCTTCA
* *
1966978 GACACAAACTACAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTG
1 GACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTG
*
1967043 TACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATAGGTTTCGATGTTTATGGGATCGA
66 TACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGA
1967108 CAC-TTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAA
131 CACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAA
1967172 TATC
196 TATC
*
1967176 GACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTATCATAAAACCGGTATACTTG
1 GACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTG
*
1967241 TACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGA
66 TACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGA
1967306 CACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAA
131 CACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACC-AAA
1967371 ATATC
195 ATATC
1967376 GACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTG
1 GACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTG
* *
1967441 TACCGATTAGATTGAAAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGA
66 TACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGA
* * *
1967506 TACTTTTTATATATGGATCGACACTTTA-TGATTGCATCCTATTTGCC
131 CACTTTTTATATATGGATCGACACTTTATTG-TTGCACCCTGTTTGCC
1967553 GTATTGTAAA
Statistics
Matches: 362, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
198 128 0.35
199 59 0.16
200 175 0.48
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (199 bp):
GACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTG
TACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGA
CACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAA
TATC
Found at i:1967810 original size:19 final size:19
Alignment explanation
Indices: 1967786--1967834 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1967776 AATTATTCAC
1967786 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
1967805 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1967824 ATACAAAATTA
1 ATACAAAATTA
1967835 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1969660 original size:33 final size:33
Alignment explanation
Indices: 1969623--1969688 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1969613 CATCTTAATA
*
1969623 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
***
1969656 TCACCCCTCAACACCTTTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1969689 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1969747 original size:21 final size:21
Alignment explanation
Indices: 1969722--1969782 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
1969712 CCCCTTATGC
* *
1969722 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1969743 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
**
1969764 CAATCAAGTTTCTCTTCGA
1 CTCTCAAGTTTCTCTTCGA
1969783 ATCTTGATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.20, C:0.30, G:0.11, T:0.39
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1971989 original size:172 final size:174
Alignment explanation
Indices: 1971701--1972151 Score: 615
Period size: 172 Copynumber: 2.6 Consensus size: 174
1971691 CGTACTTACG
* *
1971701 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACGTTTTT
1 AAAGTATCGACACTTTC-A-ATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACGTTTTA
*
1971766 TCATATTTTTACCTGTTATATCGTTGTGGATCGATATTTTTTAAAGTATCGACAC-TTATAGGCG
64 TCATATTTTTACCTGTTATATCGTT-TGGATCGATATTTTTTAAAGTATCGACACTTTATAGGAG
1971830 CTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGAT-CTTATA-T
128 CTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
1971875 AAAGTATCGACACTTTCAATATCCGGTAACGTTTTA-CGGTTTTATCATTTTGATACGATTTTAT
1 AAAGTATCGACACTTTCAATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACG-TTTTAT
* *
1971939 CATATTTTTACCTGGTATATCGTTTGG-TCGATATTTTTTTAAAAGTATCGACACTTTATAGGAT
65 CATATTTTTACCTGTTATATCGTTTGGATCGATA-TTTTTT-AAAGTATCGACACTTTATAGGAG
* *
1972003 TTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
128 CTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * **
1972050 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAA--TATCCGGTAACGTTTTACCGGTTTTATCATTTTGATA-C-G-TT
* * *
1972115 TTGTCATAGTTTTACCTGTTACATCGTTTTGGATCGA
61 TTATCATATTTTTACCTGTTATATCG-TTTGGATCGA
1972152 CACATTTTTA
Statistics
Matches: 246, Mismatches: 18, Indels: 18
0.87 0.06 0.06
Matches are distributed among these distances:
170 6 0.02
171 30 0.12
172 58 0.24
173 44 0.18
174 23 0.09
175 18 0.07
177 15 0.06
178 17 0.07
179 1 0.00
180 25 0.10
181 5 0.02
182 4 0.02
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (174 bp):
AAAGTATCGACACTTTCAATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACGTTTTATC
ATATTTTTACCTGTTATATCGTTTGGATCGATATTTTTTAAAGTATCGACACTTTATAGGAGCTA
AAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:1973565 original size:17 final size:17
Alignment explanation
Indices: 1973536--1973585 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
1973526 TATTTTTTAG
1973536 TAATTTATTTAATTATTT
1 TAATTTATTTAA-TATTT
1973554 TAATTT-TTTAATATTT
1 TAATTTATTTAATATTT
*
1973570 T-ATTTAATTAAT-TTT
1 TAATTTATTTAATATTT
1973585 T
1 T
1973586 TTTGCAGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 8 0.27
16 11 0.37
17 5 0.17
18 6 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TAATTTATTTAATATTT
Done.