Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008010.1 Hibiscus syriacus cultivar Beakdansim tig00110472_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: 3152856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 14
Found at i:2428172 original size:60 final size:60
Alignment explanation
Indices: 2428098--2428257 Score: 155
Period size: 60 Copynumber: 2.7 Consensus size: 60
2428088 TTTGGATGAC
* ** *
2428098 TTTGGGAATGAAATT-GAAAGATTCAAAAGCTTGGGGACCAATTTAGAATGAGAGTCATAG
1 TTTGGGGATGAAATTGGAAAG-TTCAAAAGCTTAAGGACCAATTTAGAATGAAAGTCATAG
* * * ** *
2428158 TTTGGGGATGAAATTGGAATGTTCAAAGGTTTAAGGATTAATTTAGAATGAAAGTCATGG
1 TTTGGGGATGAAATTGGAAAGTTCAAAAGCTTAAGGACCAATTTAGAATGAAAGTCATAG
** * *
2428218 TTTAAGGATGAAA-TGGAATA-CTCAAAAGTTTAAGGACCAA
1 TTTGGGGATGAAATTGGAA-AGTTCAAAAGCTTAAGGACCAA
2428258 ATTAAAGTAA
Statistics
Matches: 81, Mismatches: 17, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
59 21 0.26
60 56 0.69
61 4 0.05
ACGTcount: A:0.39, C:0.07, G:0.26, T:0.29
Consensus pattern (60 bp):
TTTGGGGATGAAATTGGAAAGTTCAAAAGCTTAAGGACCAATTTAGAATGAAAGTCATAG
Found at i:2440721 original size:2 final size:2
Alignment explanation
Indices: 2440709--2440765 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
2440699 GTTGTAATCC
*
2440709 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2440751 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
2440766 TGATTAAACT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2441981 original size:16 final size:17
Alignment explanation
Indices: 2441947--2441989 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2441937 TGATATTAAG
2441947 AAAA-AAAATAATAGAA
1 AAAATAAAATAATAGAA
*
2441963 AAAATAAAATAA-AGTA
1 AAAATAAAATAATAGAA
*
2441979 AAAATAGAATA
1 AAAATAAAATA
2441990 TTAAGTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (17 bp):
AAAATAAAATAATAGAA
Found at i:2442018 original size:37 final size:39
Alignment explanation
Indices: 2441975--2442055 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 39
2441965 AATAAAATAA
* *
2441975 AGTAAAAATAGAATATTAAG-TAATATATATATAAACAT
1 AGTAAAAATAGAATATTAAGAAAAAATATATATAAACAT
* *
2442013 A-T-AAAATATAATATTAAGAAAAAATATATATATACAT
1 AGTAAAAATAGAATATTAAGAAAAAATATATATAAACAT
2442050 AGTAAA
1 AGTAAA
2442056 TGGAGAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
36 15 0.42
37 17 0.47
38 2 0.06
39 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.31
Consensus pattern (39 bp):
AGTAAAAATAGAATATTAAGAAAAAATATATATAAACAT
Found at i:2442096 original size:8 final size:8
Alignment explanation
Indices: 2442085--2442115 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
2442075 TATAATATCT
2442085 ATATATAC
1 ATATATAC
2442093 ATATATAC
1 ATATATAC
*
2442101 ATATACAC
1 ATATATAC
2442109 ATATATA
1 ATATATA
2442116 TATAATGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (8 bp):
ATATATAC
Found at i:2442126 original size:14 final size:13
Alignment explanation
Indices: 2442068--2442148 Score: 69
Period size: 14 Copynumber: 6.2 Consensus size: 13
2442058 GAGAAAATTA
*
2442068 ATATATCTATAAT
1 ATATATATATAAT
*
2442081 ATCTATATATACAT
1 ATATATATATA-AT
* *
2442095 ATATACATATACAC
1 ATATATATATA-AT
2442109 ATATATATATAAT
1 ATATATATATAAT
2442122 GATATATA-ATAAT
1 -ATATATATATAAT
*
2442135 A-A-AAATATAAT
1 ATATATATATAAT
2442146 ATA
1 ATA
2442149 AATAAAAAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
10 2 0.04
11 7 0.12
12 2 0.04
13 15 0.27
14 30 0.54
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.38
Consensus pattern (13 bp):
ATATATATATAAT
Found at i:2442149 original size:19 final size:19
Alignment explanation
Indices: 2442125--2442184 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 19
2442115 ATATAATGAT
2442125 ATATAATAATAAAAATATA
1 ATATAATAATAAAAATATA
*
2442144 ATATAAATAAAAAAGGAATATA
1 ATAT-AATAATAAA--AATATA
*
2442166 GTA-AATAAATAAAAATATA
1 ATATAAT-AATAAAAATATA
2442185 TAATTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
19 10 0.29
20 11 0.32
21 5 0.15
22 8 0.24
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
ATATAATAATAAAAATATA
Found at i:2443798 original size:106 final size:106
Alignment explanation
Indices: 2443537--2444018 Score: 575
Period size: 106 Copynumber: 4.6 Consensus size: 106
2443527 AATTGGCTCT
* * * *
2443537 GGAAATTGTTTGTTGACAGTCAACCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTC
1 GGAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* * * *
2443602 TAATATCATTCGTTGTGAAGTTGAAATTGACTCTG-AA-T-
66 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
* * ** *
2443640 -GAAA-T-TTTATTGACAATCAGCCTCCCCTTCG-TCACGAAGTTGAGCTTGTGTTGTCTTGGGT
1 GGAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCT-GTGAAGTTGAGCTTGTGTTGTCTTGAGT
*
2443701 CCAATATCCTTCGCT-TGGAAGTTGAAATTGGCCCTGAAATTG
65 CCAATATCCTTCGCTGT-GAAGTTGAAATTGGCTCTGAAATTG
* * *
2443743 GGAAGTTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTATGTTGTCTTGAGTC
1 GGAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
2443808 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
66 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
* * * ** * ** * *
2443849 GGAAGTTGTTTGTTGACAACCAGTCGTTCCTTCGTTGTGAAGTTGAATTTGTGTTGTCTCGAATC
1 GGAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
* *
2443914 CAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAACTG
66 CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
* * * * * *
2443955 GGAAATTGTTTGTTGACAACCAGTCGTCACTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
1 GGAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGT
2444019 GGCACGATAT
Statistics
Matches: 327, Mismatches: 42, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
99 2 0.01
100 74 0.23
101 3 0.01
102 5 0.02
104 3 0.01
105 1 0.00
106 237 0.72
107 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (106 bp):
GGAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTC
CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
Found at i:2444860 original size:65 final size:67
Alignment explanation
Indices: 2444665--2444863 Score: 244
Period size: 67 Copynumber: 3.0 Consensus size: 67
2444655 AATTCATTTC
* * * * *
2444665 AAGGGAAAT-GATCTCAAAGATATCTGTTGTTTCATGA-AAACGGTCTCAAGGGAAACAAAATTT
1 AAGGGAAATAAAT-TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
2444728 TTTTT
63 GTTTT
**
2444733 AAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTT
1 AAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTT
2444798 TT
66 TT
* * *
2444800 AGGGGAAATAAATTCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
1 AAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTT
2444863 T
66 T
2444864 CAAGAGAGAC
Statistics
Matches: 116, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
65 39 0.34
66 12 0.10
67 48 0.41
68 15 0.13
69 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.32
Consensus pattern (67 bp):
AAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTT
TT
Found at i:2444986 original size:123 final size:123
Alignment explanation
Indices: 2444767--2444990 Score: 331
Period size: 123 Copynumber: 1.8 Consensus size: 123
2444757 GTGTTTCAAG
* ** * * *
2444767 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
2444832 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAGACAAAACTTAGTTCCAAA
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAGACAAAACTTAGTTCCAAA
* * * * *
2444890 AGAAACTGTCTTAAGGGAGACGAAATTTGTTTCAAATAAAACATATTCAAATAATTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
* *
2444955 GGAAATTGTCTTAAGAGAGACAAAATTTGTTTCAAG
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG
2444991 GGAAACTGTC
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
123 88 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (123 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAGACAAAACTTAGTTCCAAA
Found at i:2444989 original size:36 final size:36
Alignment explanation
Indices: 2444942--2445220 Score: 205
Period size: 36 Copynumber: 8.1 Consensus size: 36
2444932 ATATTCAAAT
* *
2444942 AATTTGTTTCAAGGGAAATTGTCTTAAGAGAGACAA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
**
2444978 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGATGA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* * *
2445014 AATTTATTTCAAGGGAAA-TGTTTTC-A-A-TG----
1 AATTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAA
* *
2445043 -TTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
1 AATT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
2445079 AATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
1 AA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* * * **
2445116 AATTCGTTTCAAGGGAAA-TGTTTTCAA-TG-TTC--
1 AATTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAA
* *
2445148 -A--TGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* * * *
2445181 TATTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAA
1 -AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
2445218 AAT
1 AAT
2445221 CTTCTTTTTA
Statistics
Matches: 188, Mismatches: 33, Indels: 44
0.71 0.12 0.17
Matches are distributed among these distances:
28 2 0.01
29 32 0.17
30 6 0.03
31 3 0.02
32 1 0.01
33 1 0.01
34 2 0.01
35 5 0.03
36 74 0.39
37 60 0.32
38 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (36 bp):
AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
Found at i:2445016 original size:101 final size:101
Alignment explanation
Indices: 2444863--2445220 Score: 396
Period size: 102 Copynumber: 3.5 Consensus size: 101
2444853 AAAATTTGTT
* * ** * * * * ***
2444863 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTTAAGGGAGACGAAATTTGTTTCAAATA
1 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGG
** * * *
2444928 AAACATATTCAAATAATT-TGTTTCAAGGGAAATTGTC
66 AAATGTTTTC-AAT-ATTATGTTTCAAGAGAAACTGTC
* * ** *
2444965 TTAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATGAAATTTATTTCAAGGG
1 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGG
*
2445029 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTC
66 AAATGTTTTCAAT-ATTATGTTTCAAGAGAAACTGTC
* *
2445066 TCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGG
1 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGG
*
2445131 AAATGTTTTCAATGTTCATGTTTCAAGAGAAACTGTC
66 AAATGTTTTCAATATT-ATGTTTCAAGAGAAACTGTC
* * * * *
2445168 TCAAGGGAGACAATATTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
2445221 CTTCTTTTTA
Statistics
Matches: 223, Mismatches: 30, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
100 5 0.02
101 78 0.35
102 140 0.63
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (101 bp):
TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGG
AAATGTTTTCAATATTATGTTTCAAGAGAAACTGTC
Found at i:2445098 original size:37 final size:37
Alignment explanation
Indices: 2445047--2445220 Score: 152
Period size: 37 Copynumber: 4.9 Consensus size: 37
2445037 TCAATGTTTA
*
2445047 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
2445084 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * * **
2445120 CGTTTCAAGGGAAA-TGTTTTCAA-TG-TTC---A---
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * *
2445149 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAATATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
2445186 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
2445221 CTTCTTTTTA
Statistics
Matches: 108, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
29 17 0.16
30 3 0.03
31 2 0.02
34 2 0.02
35 2 0.02
36 20 0.19
37 62 0.57
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:2445126 original size:102 final size:102
Alignment explanation
Indices: 2444946--2445220 Score: 435
Period size: 102 Copynumber: 2.7 Consensus size: 102
2444936 TCAAATAATT
* * * *
2444946 TGTTTCAAGGGAAATTGTCTTAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* * *
2445010 ATGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
66 ATAAAATTCATTTCAAGGGAAATGTTTTCAATGTTCA
2445047 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
2445112 ACAAAATTCGTTTCAAGGGAAATGTTTTCAATGTTCA
66 ATAAAATTCATTTCAAGGGAAATGTTTTCAATGTTCA
* * *
2445149 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAATATTTTGTTTCAAGGGAAACTATCTCAAGCGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
2445214 ATAAAAT
66 ATAAAAT
2445221 CTTCTTTTTA
Statistics
Matches: 160, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
101 31 0.19
102 129 0.81
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ATAAAATTCATTTCAAGGGAAATGTTTTCAATGTTCA
Found at i:2446796 original size:69 final size:69
Alignment explanation
Indices: 2446681--2446818 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
2446671 TGTCTCTCTC
* *
2446681 TTGATGCTCTATGGTCTTCGAGTGGAGTGATTCAGTGATTCAGAAATGATTGTGCTCGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTCGATCAATC
2446746 TCAT
66 TCAT
* * *
2446750 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCGGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTCGATCAATC
2446815 TCAT
66 TCAT
2446819 AGTTTGAATC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTCGATCAATC
TCAT
Found at i:2446906 original size:12 final size:13
Alignment explanation
Indices: 2446891--2446951 Score: 65
Period size: 12 Copynumber: 4.8 Consensus size: 13
2446881 TTTTCTTCAA
2446891 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
2446903 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
2446915 ATTTTCTCTTTGCTT
1 -TTTTCTCTTTG-TT
* *
2446930 TTTTCTCTCT-CT
1 TTTTCTCTTTGTT
2446942 TTTTCTCTTT
1 TTTTCTCTTT
2446952 TGTTCTGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 17 0.40
13 14 0.33
14 9 0.21
15 2 0.05
ACGTcount: A:0.02, C:0.21, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:2446932 original size:26 final size:27
Alignment explanation
Indices: 2446890--2446951 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
2446880 TTTTTCTTCA
* *
2446890 ATTTTC-CTTTG-TTTTTTCTCTTTTT
1 ATTTTCTCTTTGCTTTTTTCTCTCTCT
2446915 ATTTTCTCTTTGCTTTTTTCTCTCTCT
1 ATTTTCTCTTTGCTTTTTTCTCTCTCT
2446942 -TTTTCTCTTT
1 ATTTTCTCTTT
2446952 TGTTCTGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 6 0.18
26 15 0.45
27 12 0.36
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.73
Consensus pattern (27 bp):
ATTTTCTCTTTGCTTTTTTCTCTCTCT
Found at i:2448561 original size:15 final size:16
Alignment explanation
Indices: 2448543--2448607 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 16
2448533 AAATAAAAAT
2448543 AAAA-ATAATATTAAG
1 AAAATATAATATTAAG
*
2448558 AAAATATATATATATAATAT
1 AAAATATA-ATAT-T-A-AG
2448578 AAAATATAATATTAAG
1 AAAATATAATATTAAG
2448594 AAATATATATATAT
1 AAA-ATATA-ATAT
2448608 GGTAAATGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
15 4 0.10
16 7 0.17
17 10 0.24
18 6 0.15
19 5 0.12
20 9 0.22
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
AAAATATAATATTAAG
Found at i:2448565 original size:39 final size:38
Alignment explanation
Indices: 2448520--2448606 Score: 117
Period size: 36 Copynumber: 2.3 Consensus size: 38
2448510 TAAAATATAT
2448520 ATATATATATAATAAATAAAAATAAAA-ATAATATTAAGAA
1 ATATATATATAAT--AT-AAAATAAAATATAATATTAAGAA
*
2448560 A-ATATATAT-ATATAATATAAAATATAATATTAAGAA
1 ATATATATATAATATAAAATAAAATATAATATTAAGAA
2448596 ATATATATATA
1 ATATATATATA
2448607 TGGTAAATGG
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
35 8 0.19
36 16 0.37
37 8 0.19
38 2 0.05
39 8 0.19
40 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (38 bp):
ATATATATATAATATAAAATAAAATATAATATTAAGAA
Found at i:2448580 original size:35 final size:35
Alignment explanation
Indices: 2448541--2448607 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
2448531 ATAAATAAAA
2448541 ATAAAA-ATAATATTAAGAAAATATATATATATAAT
1 ATAAAATATAATATTAAG-AAATATATATATATAAT
2448576 ATAAAATATAATATTAAGAAATATATATATAT
1 ATAAAATATAATATTAAGAAATATATATATAT
2448608 GGTAAATGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (35 bp):
ATAAAATATAATATTAAGAAATATATATATATAAT
Found at i:2448648 original size:2 final size:2
Alignment explanation
Indices: 2448631--2448709 Score: 115
Period size: 2 Copynumber: 40.0 Consensus size: 2
2448621 AAATTACATC
* * *
2448631 TA TA CA TA TC TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2448673 TA TA TA TA TA TA TA TA TA TA TA TA TA -A GA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2448710 ATAAAAATAA
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2448722 original size:14 final size:14
Alignment explanation
Indices: 2448705--2448733 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2448695 TATAAGATAT
2448705 ATATAATAAAAATA
1 ATATAATAAAAATA
2448719 ATATAATAAAAATA
1 ATATAATAAAAATA
2448733 A
1 A
2448734 AAAAGGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATATAATAAAAATA
Found at i:2448743 original size:22 final size:20
Alignment explanation
Indices: 2448709--2448777 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 20
2448699 AGATATATAT
*
2448709 AATAAAAATAATATAATAAA
1 AATAAAAAAAATATAATAAA
*
2448729 AATAAAAAAGGAATATAGTAAATA
1 AATAAAAAA--AATATAAT-AA-A
*
2448753 AATAAAAAATATATAATTAAA
1 AATAAAAAAAATATAA-TAAA
2448774 AATA
1 AATA
2448778 TATATATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
20 8 0.20
21 5 0.12
22 14 0.35
23 3 0.08
24 10 0.25
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (20 bp):
AATAAAAAAAATATAATAAA
Found at i:2449244 original size:23 final size:23
Alignment explanation
Indices: 2449218--2449270 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
2449208 CCTTGCTCGA
*
2449218 TTGTTGCACGTTTGTTGGTGTGG
1 TTGTTGCACGTTTGTTGGTATGG
2449241 TTGTTGCACGTTTGTTGGTATGG
1 TTGTTGCACGTTTGTTGGTATGG
2449264 TTGTTGC
1 TTGTTGC
2449271 TTTAAAAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.06, C:0.09, G:0.36, T:0.49
Consensus pattern (23 bp):
TTGTTGCACGTTTGTTGGTATGG
Found at i:2452949 original size:3 final size:3
Alignment explanation
Indices: 2452941--2452970 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2452931 TATGTTATCT
2452941 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2452971 ATGGTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2454425 original size:6 final size:6
Alignment explanation
Indices: 2454414--2454474 Score: 122
Period size: 6 Copynumber: 10.2 Consensus size: 6
2454404 TCCAAAGCTT
2454414 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
2454462 TATGTA TATGTA T
1 TATGTA TATGTA T
2454475 GGACTGTGTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
TATGTA
Found at i:2460845 original size:20 final size:20
Alignment explanation
Indices: 2460778--2460850 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
2460768 AATATTTTTA
* *
2460778 TGAATAGTAT-TATACTGTA
1 TGAATAGTATCGATACTGTG
* *
2460797 TGAATAGTATCAATACTATG
1 TGAATAGTATCGATACTGTG
*
2460817 TAAATAGTATCGATACTGTG
1 TGAATAGTATCGATACTGTG
* *
2460837 TGAACAGTACCGAT
1 TGAATAGTATCGAT
2460851 GCACAAAACA
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 10 0.23
20 34 0.77
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
TGAATAGTATCGATACTGTG
Found at i:2465408 original size:2 final size:2
Alignment explanation
Indices: 2465401--2465426 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2465391 ACAGTTGATA
2465401 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
2465427 GTTTATTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2477232 original size:26 final size:26
Alignment explanation
Indices: 2477189--2477239 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2477179 GTATTGGGAG
*
2477189 AAAGCTAGAATGATTTAGGATGATTTT
1 AAAGCTAGAATGAGTTAGGAT-ATTTT
*
2477216 AAAGCTA-AATGGGTTAGGATATTT
1 AAAGCTAGAATGAGTTAGGATATTT
2477240 ATAGTTGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 11 0.50
27 7 0.32
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (26 bp):
AAAGCTAGAATGAGTTAGGATATTTT
Found at i:2479664 original size:26 final size:26
Alignment explanation
Indices: 2479635--2479691 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
2479625 CTAAAAGATA
*
2479635 AAAATATAAAATAATTATATTTTAAT
1 AAAATATAAAATAACTATATTTTAAT
* ** *
2479661 AAAAAATAATTTAACTATATTTTATT
1 AAAATATAAAATAACTATATTTTAAT
2479687 AAAAT
1 AAAAT
2479692 TAATCTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (26 bp):
AAAATATAAAATAACTATATTTTAAT
Found at i:2489835 original size:7 final size:7
Alignment explanation
Indices: 2489823--2489875 Score: 79
Period size: 7 Copynumber: 7.6 Consensus size: 7
2489813 CTTCATAACC
2489823 TTTCCAT
1 TTTCCAT
2489830 TTTCCAT
1 TTTCCAT
2489837 TTTCCAT
1 TTTCCAT
2489844 TTTCCAT
1 TTTCCAT
*
2489851 TTTCAAT
1 TTTCCAT
*
2489858 TTTCAAT
1 TTTCCAT
*
2489865 TTTCAAT
1 TTTCCAT
2489872 TTTC
1 TTTC
2489876 AATTATACTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTCCAT
Found at i:2489849 original size:21 final size:21
Alignment explanation
Indices: 2489823--2489879 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
2489813 CTTCATAACC
* *
2489823 TTTCCATTTTCCATTTTCCAT
1 TTTCCATTTTCAATTTTCAAT
2489844 TTTCCATTTTCAATTTTCAAT
1 TTTCCATTTTCAATTTTCAAT
*
2489865 TTTCAATTTTCAATT
1 TTTCCATTTTCAATT
2489880 ATACTATGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTCCATTTTCAATTTTCAAT
Found at i:2496191 original size:20 final size:20
Alignment explanation
Indices: 2496166--2496213 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2496156 TTTTCCTGAT
*
2496166 TCGCAACGCGAATAC-GTAAA
1 TCGCAACGCGAAT-CTATAAA
*
2496186 TCGCAATGCGAATCTATAAA
1 TCGCAACGCGAATCTATAAA
2496206 TCGCAACG
1 TCGCAACG
2496214 AGATTCTGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATCTATAAA
Found at i:2497100 original size:24 final size:24
Alignment explanation
Indices: 2497073--2497126 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2497063 GTATTCGAAA
2497073 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2497097 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2497121 TTTGAT
1 TTTGAT
2497127 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2499586 original size:20 final size:20
Alignment explanation
Indices: 2499561--2499646 Score: 120
Period size: 20 Copynumber: 4.3 Consensus size: 20
2499551 CAACGTGGAA
*
2499561 ATCGCAACGC-GAATATGACT
1 ATCGCAACACGGAA-ATGACT
2499581 ATCGCAACACGGAAATGACT
1 ATCGCAACACGGAAATGACT
** *
2499601 ATCGCAATGCGGAATTGACT
1 ATCGCAACACGGAAATGACT
2499621 ATCGCAACACGGAAATGACT
1 ATCGCAACACGGAAATGACT
2499641 ATCGCA
1 ATCGCA
2499647 GTGAGAGAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 55 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACACGGAAATGACT
Found at i:2499595 original size:34 final size:34
Alignment explanation
Indices: 2499541--2499636 Score: 86
Period size: 40 Copynumber: 2.6 Consensus size: 34
2499531 AGACATTCAT
* **
2499541 TTGACTATAGCAACGTGGAAATCGCAACGC-GAA
1 TTGACTATCGCAACACGGAAATCGCAACGCGGAA
*
2499574 TATGACTATCGCAACACGGAAATGACTATCGCAATGCGGAA
1 T-TGACTATCGCAACACGG--A--A--ATCGCAACGCGGAA
2499615 TTGACTATCGCAACACGGAAAT
1 TTGACTATCGCAACACGGAAAT
2499637 GACTATCGCA
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
33 1 0.02
34 16 0.31
36 2 0.04
38 2 0.04
40 26 0.51
41 4 0.08
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (34 bp):
TTGACTATCGCAACACGGAAATCGCAACGCGGAA
Found at i:2499620 original size:40 final size:40
Alignment explanation
Indices: 2499561--2499646 Score: 147
Period size: 40 Copynumber: 2.1 Consensus size: 40
2499551 CAACGTGGAA
2499561 ATCGCAACGCGAATATGACTATCGCAACACGGAAATGACT
1 ATCGCAACGCGAATATGACTATCGCAACACGGAAATGACT
*
2499601 ATCGCAATGCGGAAT-TGACTATCGCAACACGGAAATGACT
1 ATCGCAACGC-GAATATGACTATCGCAACACGGAAATGACT
2499641 ATCGCA
1 ATCGCA
2499647 GTGAGAGAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 40 0.91
41 4 0.09
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (40 bp):
ATCGCAACGCGAATATGACTATCGCAACACGGAAATGACT
Found at i:2499709 original size:34 final size:33
Alignment explanation
Indices: 2499653--2499716 Score: 119
Period size: 34 Copynumber: 1.9 Consensus size: 33
2499643 CGCAGTGAGA
2499653 GAATCGCAATGCGAAATGAAAATCGCAACGAGT
1 GAATCGCAATGCGAAATGAAAATCGCAACGAGT
2499686 GAATCGCAATGCGAAAATGAAAATCGCAACG
1 GAATCGCAATGCG-AAATGAAAATCGCAACG
2499717 TGAAATTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 13 0.43
34 17 0.57
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (33 bp):
GAATCGCAATGCGAAATGAAAATCGCAACGAGT
Found at i:2499774 original size:34 final size:34
Alignment explanation
Indices: 2499731--2499826 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
2499721 ATTAGTTTCG
2499731 CGTTGCAATTTTCATTTTCGCATTGCGATTC-ACT
1 CGTTGCAATTTTCATTTTCGCATTGCGATTCTA-T
2499765 CGTTGCAATTTTCA-TTTCGCATTGCGATTCTAT
1 CGTTGCAATTTTCATTTTCGCATTGCGATTCTAT
* ** * *
2499798 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCAATTTTCATTTTCGCATTGCGAT
2499827 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.42
Consensus pattern (34 bp):
CGTTGCAATTTTCATTTTCGCATTGCGATTCTAT
Found at i:2499947 original size:14 final size:14
Alignment explanation
Indices: 2499928--2499964 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2499918 CATCAATTAA
2499928 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2499942 ACAAATCATCTTTT
1 ACAAATCAACATTT
2499956 ACAAATCAA
1 ACAAATCAA
2499965 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2500951 original size:42 final size:42
Alignment explanation
Indices: 2500794--2501127 Score: 368
Period size: 42 Copynumber: 8.0 Consensus size: 42
2500784 CAAAATACTA
* *
2500794 TACTTTAGTGGCGTTTGTATA-AAAACGCCGCTAAAGA-ATCG
1 TACTTTAGTGGCGTTT-TATACCAAACGCCGCTATAGACATCG
* * * *
2500835 TAATGTAGTGGCGTTTTTATA-CAAACGCCGCTATAAAC-TAG
1 TACTTTAGTGGCG-TTTTATACCAAACGCCGCTATAGACATCG
*
2500876 TATTTTAGTGGCGTTTT-TACACAAACGCCGCTATAGACAT-G
1 TACTTTAGTGGCGTTTTATAC-CAAACGCCGCTATAGACATCG
*
2500917 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGAC-TCG
1 TACTTTAGTGGCGTTTT-ATACCAAACGCCGCTATAGACATCG
* * *
2500959 TACTTTAGTGACATTTT-TACACAAACGCCGCTATAAACA-CG
1 TACTTTAGTGGCGTTTTATAC-CAAACGCCGCTATAGACATCG
* *
2501000 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGA-TTCG
1 TACTTTAGTGGCGTTTT-ATACCAAACGCCGCTATAGACATCG
*
2501042 TACTTTAGTGGCGTTTTTTACACAAACGCCGCTATAGACA-CG
1 TACTTTAGTGGCGTTTTATAC-CAAACGCCGCTATAGACATCG
* *
2501084 TACTTTTGTGGCGTTTTAATACCAAACGTCGCTATAGAC-TCG
1 TACTTTAGTGGCGTTTT-ATACCAAACGCCGCTATAGACATCG
2501126 TA
1 TA
2501128 ATTTGATTGT
Statistics
Matches: 250, Mismatches: 26, Indels: 33
0.81 0.08 0.11
Matches are distributed among these distances:
39 2 0.01
40 7 0.03
41 109 0.44
42 123 0.49
43 9 0.04
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (42 bp):
TACTTTAGTGGCGTTTTATACCAAACGCCGCTATAGACATCG
Found at i:2500976 original size:83 final size:83
Alignment explanation
Indices: 2500794--2501127 Score: 465
Period size: 83 Copynumber: 4.0 Consensus size: 83
2500784 CAAAATACTA
* * * * * * * * *
2500794 TACTTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGA-ATCGTAATGTAGTGGCGTTTTTATA-C
1 TACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACA-CGTACTTTTGTGGCGTTTTAATACC
* *
2500857 AAACGCCGCTATAAACTAG
65 AAACGCCGCTATAGACTCG
* * *
2500876 TATTTTAGTGGCGTTTTTACACAAACGCCGCTATAGACATGTACTTTTGTGGCGTTTTAATACCA
1 TACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCA
2500941 AACGCCGCTATAGACTCG
66 AACGCCGCTATAGACTCG
* *
2500959 TACTTTAGTGACATTTTTACACAAACGCCGCTATAAACACGTACTTTTGTGGCGTTTTAATACCA
1 TACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCA
*
2501024 AACGCCGCTATAGATTCG
66 AACGCCGCTATAGACTCG
*
2501042 TACTTTAGTGGCGTTTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
1 TACTTTAGTGGC-ATTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
*
2501107 AAACGTCGCTATAGACTCG
65 AAACGCCGCTATAGACTCG
2501126 TA
1 TA
2501128 ATTTGATTGT
Statistics
Matches: 226, Mismatches: 23, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
82 50 0.22
83 107 0.47
84 69 0.31
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (83 bp):
TACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCA
AACGCCGCTATAGACTCG
Found at i:2503065 original size:22 final size:22
Alignment explanation
Indices: 2503040--2503086 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
2503030 TTTGTAAAGC
2503040 CTTCTTGATCCTTGAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
*
2503062 CTTCTTGATCCTTTAATGTTTA
1 CTTCTTGATCCTTGAATGTTTA
2503084 CTT
1 CTT
2503087 TTTGTAAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.19, G:0.11, T:0.53
Consensus pattern (22 bp):
CTTCTTGATCCTTGAATGTTTA
Found at i:2504904 original size:43 final size:42
Alignment explanation
Indices: 2504857--2505110 Score: 190
Period size: 43 Copynumber: 6.0 Consensus size: 42
2504847 TGTTTTCGAT
* * * *
2504857 AAAAACGCCGCTAAATC-TCAACGCTTATTGCGGCGCTTGTTT-G
1 AAAAACGCCGCTAAA-CAACAACACCTATTGCGGC-ATT-TTTGG
*
2504900 AAAAACACCGCTAAACAACAACACCTATTGCGGCATTTTTGGG
1 AAAAACGCCGCTAAACAACAACACCTATTGCGGCATTTTT-GG
* * * * **
2504943 AAAAACGCCGCTAAACAACGATACCTACTGCGGCGTTTGGGG
1 AAAAACGCCGCTAAACAACAACACCTATTGCGGCATTTTTGG
* * * *
2504985 GAAAACGCCGCTAAACGACAACACCTATTGCGGCGTTTTTAAG
1 AAAAACGCCGCTAAACAACAACACCTATTGCGGCATTTTT-GG
* * * **
2505028 ACAAAA-GCCGCTAAATAGCAACACCTATTGCGGCGTTTTTTC
1 A-AAAACGCCGCTAAACAACAACACCTATTGCGGCATTTTTGG
* * * ** *
2505070 AACAAACGCCGCTATATATCGTCACCTATTGCGGCGTTTTT
1 AA-AAACGCCGCTAAACAACAACACCTATTGCGGCATTTTT
2505111 CGTTAACAAA
Statistics
Matches: 174, Mismatches: 30, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
41 4 0.02
42 42 0.24
43 124 0.71
44 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAACAACAACACCTATTGCGGCATTTTTGG
Found at i:2505014 original size:85 final size:85
Alignment explanation
Indices: 2504901--2505065 Score: 224
Period size: 85 Copynumber: 1.9 Consensus size: 85
2504891 GCTTGTTTGA
** * *
2504901 AAAACACCGCTAAACAACAACACCTATTGCGGCATTTTTGGGA-AAAACGCCGCTAAACAACGAT
1 AAAACACCGCTAAACAACAACACCTATTGCGGCATTTTTAAGACAAAA-GCCGCTAAACAACAAC
2504965 ACCTACTGCGGCGTTTGGGGG
65 ACCTACTGCGGCGTTTGGGGG
* * * * *
2504986 AAAACGCCGCTAAACGACAACACCTATTGCGGCGTTTTTAAGACAAAAGCCGCTAAATAGCAACA
1 AAAACACCGCTAAACAACAACACCTATTGCGGCATTTTTAAGACAAAAGCCGCTAAACAACAACA
*
2505051 CCTATTGCGGCGTTT
66 CCTACTGCGGCGTTT
2505066 TTTCAACAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
85 65 0.94
86 4 0.06
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (85 bp):
AAAACACCGCTAAACAACAACACCTATTGCGGCATTTTTAAGACAAAAGCCGCTAAACAACAACA
CCTACTGCGGCGTTTGGGGG
Found at i:2506483 original size:20 final size:20
Alignment explanation
Indices: 2506460--2506613 Score: 111
Period size: 20 Copynumber: 8.3 Consensus size: 20
2506450 GAAACTTAAA
*
2506460 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
2506480 ATCGCAATGCGAAAATAACT
1 ATCGCAATGCGAAAATGACT
**
2506500 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
*
2506520 ATCGCAA--CG-AGA-GA--
1 ATCGCAATGCGAAAATGACT
**
2506534 ATCGCAATGCG-AAATGAAA
1 ATCGCAATGCGAAAATGACT
2506553 ATCGCAA--C-AACAA--A--
1 ATCGCAATGCGAA-AATGACT
*
2506567 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
2506587 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
2506607 ATCGCAA
1 ATCGCAA
2506614 CGAGAGAATC
Statistics
Matches: 109, Mismatches: 11, Indels: 28
0.74 0.07 0.19
Matches are distributed among these distances:
14 14 0.13
16 10 0.09
17 7 0.06
18 5 0.05
19 7 0.06
20 66 0.61
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:2506543 original size:34 final size:33
Alignment explanation
Indices: 2506457--2506593 Score: 112
Period size: 34 Copynumber: 3.9 Consensus size: 33
2506447 TCTGAAACTT
* *
2506457 AAAATCGCAACGCGAAAATGACTATCGCAATGCGAAA
1 AAAATCGCAATGCG-AAATGACTATCGCAA--C-AAC
* * *
2506494 ATAACTATCGCAATGCGAATTTGACTATCGCAACGAG
1 A-AA--ATCGCAATGCGAA-ATGACTATCGCAACAAC
* **
2506531 AGAATCGCAATGCGAAATGAAAATCGCAACAAC
1 AAAATCGCAATGCGAAATGACTATCGCAACAAC
*
2506564 AAAATCGCAACGCGAAAATGACTATCGCAA
1 AAAATCGCAATGCG-AAATGACTATCGCAA
2506594 TGCGAATTTG
Statistics
Matches: 81, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
33 24 0.30
34 26 0.32
36 1 0.01
37 3 0.04
38 3 0.04
39 2 0.02
40 22 0.27
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (33 bp):
AAAATCGCAATGCGAAATGACTATCGCAACAAC
Found at i:2506570 original size:33 final size:33
Alignment explanation
Indices: 2506500--2506580 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
2506490 GAAAATAACT
* ** * * *
2506500 ATCGCAATGCGAATTTGACTATCGCAACGAGAGA
1 ATCGCAATGCGAA-ATGAAAATCGCAACAACAAA
2506534 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
*
2506567 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
2506581 ATGACTATCG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 27 0.68
34 13 0.32
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACAACAAA
Found at i:2506688 original size:20 final size:20
Alignment explanation
Indices: 2506660--2506783 Score: 98
Period size: 20 Copynumber: 6.5 Consensus size: 20
2506650 GATTCTCTCG
* **
2506660 TTGCGATAGTCAAATTCGCA
1 TTGCAATAGTCATTTTCGCA
* *
2506680 TTGCAATAGTCATTTTTGTA
1 TTGCAATAGTCATTTTCGCA
2506700 TTGCAATAGTCATTTTCGCA
1 TTGCAATAGTCATTTTCGCA
* *
2506720 TTGCGAT--TC--TCTCG--
1 TTGCAATAGTCATTTTCGCA
* *
2506734 TTGCGATAGTCATTTTCGCG
1 TTGCAATAGTCATTTTCGCA
* *
2506754 TTGCGATAGTCATTTTCGCG
1 TTGCAATAGTCATTTTCGCA
*
2506774 TTGCGATAGT
1 TTGCAATAGT
2506784 AAACTATTCT
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
14 7 0.08
16 6 0.07
18 6 0.07
20 69 0.78
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCAATAGTCATTTTCGCA
Found at i:2506748 original size:34 final size:34
Alignment explanation
Indices: 2506639--2506760 Score: 118
Period size: 34 Copynumber: 3.4 Consensus size: 34
2506629 GCGATTTTCA
* *
2506639 TTTCGCATTGTGATTCTCTCGTTGCGATAGTCAA
1 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
* * * * *
2506673 ATTCGCATTGCAATAGTCATTTTTGTATTGCAATAGTCAT
1 TTTCGCATTGCGAT--TC--TCTCG--TTGCGATAGTCAT
2506713 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
1 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
*
2506747 TTTCGCGTTGCGAT
1 TTTCGCATTGCGAT
2506761 AGTCATTTTC
Statistics
Matches: 69, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
34 36 0.52
36 5 0.07
38 5 0.07
40 23 0.33
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.42
Consensus pattern (34 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
Found at i:2506783 original size:74 final size:74
Alignment explanation
Indices: 2506639--2506783 Score: 209
Period size: 74 Copynumber: 2.0 Consensus size: 74
2506629 GCGATTTTCA
* * *
2506639 TTTCGCATTGTGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCAATAGTCATTTTTGTATTGC
1 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCAATAGTCATTTTCGCATTGC
2506704 AATAGTCAT
66 AATAGTCAT
** * * *
2506713 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCGTTGC
1 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCAATAGTCATTTTCGCATTGC
*
2506778 GATAGT
66 AATAGT
2506784 AAACTATTCT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 62 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (74 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCAATAGTCATTTTCGCATTGC
AATAGTCAT
Found at i:2508722 original size:20 final size:20
Alignment explanation
Indices: 2508664--2508733 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
2508654 GAAACTTTAA
* **
2508664 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
2508684 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
2508704 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
2508724 ATCGCAACGC
1 ATCGCAACGC
2508734 AAGAATCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2508800 original size:20 final size:20
Alignment explanation
Indices: 2508775--2508823 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
2508765 GCGATTCTCT
2508775 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
2508795 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
2508815 CGTTGCGAT
1 CGTTGCGAT
2508824 TCACTCGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2509434 original size:20 final size:20
Alignment explanation
Indices: 2509411--2509484 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
2509401 GCGATAGTCA
*
2509411 TATTCGTATTGCGATTTACG
1 TATTCGCATTGCGATTTACG
*
2509431 TATTCGGATTGCGATTTACG
1 TATTCGCATTGCGATTTACG
* *
2509451 TAATCGCGTTGCGATTTACG
1 TATTCGCATTGCGATTTACG
2509471 TATTCGCATTGCGA
1 TATTCGCATTGCGA
2509485 ATCAGGAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (20 bp):
TATTCGCATTGCGATTTACG
Found at i:2510833 original size:23 final size:22
Alignment explanation
Indices: 2510807--2510849 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
2510797 TATAAAAAAT
2510807 TATTTTTTATTAAATATTTTTGG
1 TATTTTTTATTAAAT-TTTTTGG
*
2510830 TATTTTTTATTTAATTTTTT
1 TATTTTTTATTAAATTTTTT
2510850 AAATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (22 bp):
TATTTTTTATTAAATTTTTTGG
Found at i:2515995 original size:87 final size:87
Alignment explanation
Indices: 2515849--2516011 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
2515839 TATGTTATAT
* *
2515849 TATTTAACCGGAAATATTATTAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
*
2515914 AGCGCTTATATAATAAAATAGG
66 AACGCTTATATAATAAAATAGG
* *
2515936 TATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
2516001 AACGCTTATAT
66 AACGCTTATAT
2516012 TGACCTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (87 bp):
TATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AACGCTTATATAATAAAATAGG
Found at i:2516671 original size:363 final size:364
Alignment explanation
Indices: 2516147--2516806 Score: 1189
Period size: 363 Copynumber: 1.8 Consensus size: 364
2516137 TGCGTTCACC
* *
2516147 TTTTGTCATTTATAGACCGGTTTTATCATATTTTTACATATTATATTATTATGGATCGATACATT
1 TTTTGTCATTTAGAGACCGGTTTTATCATATTATTACATATTATATTATTATGGATCGATACATT
*
2516212 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTATTAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGTGTCGA
*
2516277 TACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTCG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCG
2516342 AGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATC
196 AGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATC
* *
2516407 GACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAA
261 GACACTTTATTGACGATATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAA
2516472 TTATCGACACTTTCAACATAACCAGTAGCGCTTTACCTG
326 TTATCGACACTTTCAACATAACCAGTAGCGCTTTACCTG
* * * *
2516511 TTTTGTCATTTCGAGACCGGTTTTGTCATATTATTACCTGTTATATTATTATGGATCGATACA-T
1 TTTTGTCATTTAGAGACCGGTTTTATCATATTATTACATATTATATTATTATGGATCGATACATT
*
2516575 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTTCAAAAGTGTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATT-AATTCCAAAAGTGTCG
2516639 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTC
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTC
2516704 GAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTAT
195 GAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTAT
*
2516769 CGACACTTTATTGATGATATAACTTATTCTCTTTTAAA
260 CGACACTTTATTGACGATATAACTTATTCTCTTTTAAA
2516807 AAAGATAAAA
Statistics
Matches: 283, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
362 2 0.01
363 224 0.79
364 57 0.20
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (364 bp):
TTTTGTCATTTAGAGACCGGTTTTATCATATTATTACATATTATATTATTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGTGTCGA
TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCG
AGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATC
GACACTTTATTGACGATATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAAA
TTATCGACACTTTCAACATAACCAGTAGCGCTTTACCTG
Found at i:2516673 original size:181 final size:182
Alignment explanation
Indices: 2516147--2516806 Score: 1144
Period size: 182 Copynumber: 3.6 Consensus size: 182
2516137 TGCGTTCACC
** * *
2516147 TTTTGTCATTTATAGACCGGTTTTATCATATTTTTACATATTATATTATTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATT
* *
2516212 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTATT-AATTCCAAAAGTGTCG
66 TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
*
2516276 ATACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
2516329 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATT
2516394 TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
2516459 TACTTATAATAAATTATCGACACTTTCAACATAACCAGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
2516511 TTTTGTCATTTCGAGACCGGTTTTGTCATATTATTACCTGTTATATTATTATGGATCGATACA-T
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATT
* *
2516575 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
2516640 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
2516692 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATT
* * *
2516757 TTTATAAAGTATCGACACTTTATTGATGATATAACTTATTCTCTTTTAAA
66 TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAA
2516807 AAAGATAAAA
Statistics
Matches: 454, Mismatches: 22, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
181 177 0.39
182 277 0.61
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
Found at i:2519448 original size:17 final size:18
Alignment explanation
Indices: 2519426--2519468 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
2519416 ATATATCCGG
2519426 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
2519443 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
2519463 TATCAT
1 TATCAT
2519469 ATTTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:2519862 original size:182 final size:180
Alignment explanation
Indices: 2519398--2519870 Score: 671
Period size: 181 Copynumber: 2.6 Consensus size: 180
2519388 CGTACTTACG
* * *
2519398 AAAGTATCGACACTTTTAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCATTTTACCGGTTTTATCATTTTGATACTGGTTT
*
2519463 TATCATATTTTTACATGTTATATCTTTGTTTGATCGATACATTTTTTAAAATATCGACACTTTAT
66 TATCATATTTTTACATGTTATATCGTTG-TTGATCGATACATTTTTTAAAATATCGACACTTTAT
* *
2519528 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCGTTATAT
130 AGGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATAT
* * * * *
2519579 AAAGTTTCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTCATCATTTTGATATCAT--T
1 AAAGTATCGACACTTTAAATATATCCGGTACCATTTTACCGGTTTTATCATTTTGATA-C-TGGT
* *
2519642 TTTATCATATTTTTACATGTTATATCGTTGTTGATCGATATATTTTTTGAAAGTATCGACACTTT
64 TTTATCATATTTTTACATGTTATATCGTTGTTGATCGATACATTTTTT-AAAATATCGACACTTT
*
2519707 ATAGGCGCTAAAACTGCTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATATT
128 ATAGGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATA-T
* * * * **
2519761 AAAGTACCGACACTTTAAATATATTCAGTACCACTTTACCGGTTTTATCATTTCAATACTGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCATTTTACCGGTTTTATCATTTTGATACTGGTTT
* * * *
2519826 TGTCATAGTTTTATATGTTATATCGTTGTGGATCGATACATTTTT
66 TATCATATTTTTACATGTTATATCGTTGTTGATCGATACATTTTT
2519871 AATTTGGATC
Statistics
Matches: 258, Mismatches: 28, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
180 18 0.07
181 148 0.57
182 92 0.36
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (180 bp):
AAAGTATCGACACTTTAAATATATCCGGTACCATTTTACCGGTTTTATCATTTTGATACTGGTTT
TATCATATTTTTACATGTTATATCGTTGTTGATCGATACATTTTTTAAAATATCGACACTTTATA
GGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATAT
Found at i:2522847 original size:16 final size:17
Alignment explanation
Indices: 2522813--2522849 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
2522803 TAATTTTAAA
2522813 AAATATATTTATATATT
1 AAATATATTTATATATT
2522830 AAATAATATTT-T-TATT
1 AAAT-ATATTTATATATT
2522846 AAAT
1 AAAT
2522850 TATGAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 5 0.26
18 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATATATTTATATATT
Found at i:2522918 original size:2 final size:2
Alignment explanation
Indices: 2522911--2522950 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2522901 CATTTTATTT
2522911 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2522951 CATTACAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2523056 original size:39 final size:39
Alignment explanation
Indices: 2522972--2523305 Score: 277
Period size: 39 Copynumber: 8.5 Consensus size: 39
2522962 GCAAATGGTG
* * * *
2522972 TTTGAAAATACATATATAATATATAGTCTTTAAAAAAAACATT
1 TTTG-AAA-ACATATATATTATATAGT-TTTGAAAATAA-TTT
* * *
2523015 TTTGAAAACATATACATTATATAGTTTTTAAAACAATTTT
1 TTTGAAAACATATATATTATATAGTTTTGAAAATAA-TTT
* *
2523055 TTTG-AAATATATATATTATATAGTTTTGAAAATTAGTTT
1 TTTGAAAACATATATATTATATAGTTTTGAAAA-TAATTT
* * * *
2523094 TTT-TAAATATATATATTATATAGTTTTGAAAATTA-GT
1 TTTGAAAACATATATATTATATAGTTTTGAAAATAATTT
* * * *
2523131 TTTAAAAAAATATATATTATATAGTTTTGAAAATTAGTT
1 TTTGAAAACATATATATTATATAGTTTTGAAAATAATTT
* *
2523170 TTT-AAAA-ATTATATATTATATAATTTTGAAAATTATTTT
1 TTTGAAAACA-TATATATTATATAGTTTTGAAAA-TAATTT
* * * * *
2523209 TTTCAAAAC-TATATATTATGTGGTTTTGAAAGTTATTT
1 TTTGAAAACATATATATTATATAGTTTTGAAAATAATTT
* * *
2523247 TTTTAAAA-ATATATATTATATGGTTTTGAAAATTATTTT
1 TTTGAAAACATATATATTATATAGTTTTGAAAA-TAATTT
*
2523286 CTTTAAAAACATATATATTA
1 -TTTGAAAACATATATATTA
2523306 CAACAACAAC
Statistics
Matches: 246, Mismatches: 33, Indels: 26
0.81 0.11 0.09
Matches are distributed among these distances:
37 5 0.02
38 89 0.36
39 92 0.37
40 27 0.11
41 26 0.11
42 3 0.01
43 4 0.02
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (39 bp):
TTTGAAAACATATATATTATATAGTTTTGAAAATAATTT
Found at i:2523153 original size:38 final size:38
Alignment explanation
Indices: 2523013--2523305 Score: 316
Period size: 38 Copynumber: 7.5 Consensus size: 38
2523003 AAAAAAAACA
* * * ** *
2523013 TTTTTGAAAACATATACATTATATAGTTTTTAAAACAATT
1 TTTTT-AAAAAATATATATTATATAGTTTTGAAAATTA-G
* *
2523053 TTTTTGAAATATATATATTATATAGTTTTGAAAATTAG
1 TTTTTAAAAAATATATATTATATAGTTTTGAAAATTAG
* *
2523091 TTTTTTTAAATATATATATTATATAGTTTTGAAAATTAG
1 -TTTTTAAAAAATATATATTATATAGTTTTGAAAATTAG
*
2523130 TTTTAAAAAAATATATATTATATAGTTTTGAAAATTAG
1 TTTTTAAAAAATATATATTATATAGTTTTGAAAATTAG
* * *
2523168 TTTTTAAAAATTATATATTATATAATTTTGAAAATTATT
1 TTTTTAAAAAATATATATTATATAGTTTTGAAAATTA-G
* * * * * *
2523207 TTTTTCAAAACTATATATTATGTGGTTTTGAAAGTTAT
1 TTTTTAAAAAATATATATTATATAGTTTTGAAAATTAG
* * *
2523245 TTTTTTAAAAATATATATTATATGGTTTTGAAAATTATT
1 TTTTTAAAAAATATATATTATATAGTTTTGAAAATTA-G
2523284 TTCTTTAAAAACATATATATTA
1 TT-TTTAAAAA-ATATATATTA
2523306 CAACAACAAC
Statistics
Matches: 222, Mismatches: 26, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
38 103 0.46
39 97 0.44
40 12 0.05
41 10 0.05
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (38 bp):
TTTTTAAAAAATATATATTATATAGTTTTGAAAATTAG
Found at i:2523162 original size:77 final size:78
Alignment explanation
Indices: 2523024--2523305 Score: 345
Period size: 77 Copynumber: 3.6 Consensus size: 78
2523014 TTTTGAAAAC
* * ** ** *
2523024 ATATACATTATATAGTTTTTAAAACAATTTTTTTGAAATATATATATTATATAGTTTTGAAAATT
1 ATATATATTATATAGTTTTGAAAATTATTTTTTAAAAAAATATATATTATATAGTTTTGAAAATT
2523089 AGTTTTTTTAAAT
66 AGTTTTTTTAAAT
*
2523102 ATATATATTATATAGTTTTGAAAATTA-GTTTTAAAAAAATATATATTATATAGTTTTGAAAATT
1 ATATATATTATATAGTTTTGAAAATTATTTTTTAAAAAAATATATATTATATAGTTTTGAAAATT
**
2523166 AGTTTTTAAAAAT
66 AGTTTTTTTAAAT
* ** * * * *
2523179 -TATATATTATATAATTTTGAAAATTATTTTTTTCAAAACTATATATTATGTGGTTTTGAAAGTT
1 ATATATATTATATAGTTTTGAAAATTATTTTTTAAAAAAATATATATTATATAGTTTTGAAAATT
*
2523243 A-TTTTTTTAAAA
66 AGTTTTTTTAAAT
* *
2523255 ATATATATTATATGGTTTTGAAAATTATTTTCTTTAAAAACATATATATTA
1 ATATATATTATATAGTTTTGAAAATTA-TTT-TTTAAAAAAATATATATTA
2523306 CAACAACAAC
Statistics
Matches: 173, Mismatches: 27, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
76 33 0.19
77 99 0.57
78 26 0.15
79 15 0.09
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (78 bp):
ATATATATTATATAGTTTTGAAAATTATTTTTTAAAAAAATATATATTATATAGTTTTGAAAATT
AGTTTTTTTAAAT
Found at i:2523434 original size:14 final size:14
Alignment explanation
Indices: 2523415--2523460 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
2523405 TTTTTCTTTA
2523415 TTTCTTTATTTATT
1 TTTCTTTATTTATT
2523429 TTTCTTTATTTCATT
1 TTTCTTTATTT-ATT
*
2523444 TATTATTTA-TTATT
1 T-TTCTTTATTTATT
2523458 TTT
1 TTT
2523461 TATTTCTCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 2 0.07
14 15 0.52
15 6 0.21
16 6 0.21
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCTTTATTTATT
Found at i:2523454 original size:26 final size:22
Alignment explanation
Indices: 2523403--2523451 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
2523393 TTTAAAAAAA
2523403 TATTTTTCTTTATTTCTTTATT
1 TATTTTTCTTTATTTCTTTATT
2523425 TATTTTTCTTTATTTCATTTA-T
1 TATTTTTCTTTATTTC-TTTATT
2523447 TATTT
1 TATTT
2523452 ATTATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (22 bp):
TATTTTTCTTTATTTCTTTATT
Found at i:2523463 original size:14 final size:15
Alignment explanation
Indices: 2523412--2523465 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 15
2523402 ATATTTTTCT
2523412 TTATTTCTTTATTTA
1 TTATTTCTTTATTTA
2523427 TT-TTTCTTTA-TT-
1 TTATTTCTTTATTTA
* *
2523439 TCATTT-ATTATTTA
1 TTATTTCTTTATTTA
2523453 TTATTT-TTTATTT
1 TTATTTCTTTATTT
2523466 CTCGTTTCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
12 4 0.12
13 7 0.22
14 19 0.59
15 2 0.06
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTTCTTTATTTA
Found at i:2537423 original size:14 final size:16
Alignment explanation
Indices: 2537404--2537436 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2537394 AAATATTGTC
2537404 CATGGT-AAAA-AAAA
1 CATGGTGAAAATAAAA
2537418 CATGGTGAAAATAAAA
1 CATGGTGAAAATAAAA
2537434 CAT
1 CAT
2537437 AACTACTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 4 0.24
16 7 0.41
ACGTcount: A:0.58, C:0.09, G:0.15, T:0.18
Consensus pattern (16 bp):
CATGGTGAAAATAAAA
Found at i:2539532 original size:25 final size:25
Alignment explanation
Indices: 2539503--2539553 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
2539493 TAAATAATAC
2539503 ATAGAATACGTTTAAGATAAAATGT
1 ATAGAATACGTTTAAGATAAAATGT
*
2539528 ATAGAATACGTTTAAGTTAAAATGT
1 ATAGAATACGTTTAAGATAAAATGT
2539553 A
1 A
2539554 CTTTAAGTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (25 bp):
ATAGAATACGTTTAAGATAAAATGT
Found at i:2549298 original size:21 final size:20
Alignment explanation
Indices: 2549274--2549317 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2549264 TTAAATATTT
*
2549274 TTAATTCAAAAAAGTGTATAA
1 TTAATTCAAAAAA-TATATAA
* *
2549295 TTAATTTAAATAATATATAA
1 TTAATTCAAAAAATATATAA
2549315 TTA
1 TTA
2549318 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (20 bp):
TTAATTCAAAAAATATATAA
Found at i:2549605 original size:185 final size:182
Alignment explanation
Indices: 2549254--2549640 Score: 598
Period size: 185 Copynumber: 2.1 Consensus size: 182
2549244 TTTTCTAATT
* * * *
2549254 TATATAA-AAATTAAATATTTTTAATTCAAAAAAGTGTATAATTAATTTAAATAATATATAATTA
1 TATATAATATATTTAATATTTTTAATTAAAAAAAGTGTACAATTAATTTAAATAATATATAATTA
2549318 TAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGG
66 TAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGG
* *
2549383 ATCTTAAATTATTAATTGAGTTTTAAATTGTTTGGGCTTAGCCCAAATGTTA
131 ATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTA
*
2549435 TATATAATATATTTAATATGTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATAT-TTTTAATT-AAAAAA-AGTGTACAATTAATTTAAATAATATATAA
* * *
2549500 TTATAAAATAAAAAATTT-ATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
63 TTATAAAAT-AAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTA
* * *
2549564 TTGGATCTTAAATTATTAATTGTGTTTTAAATGGTTTGGGCTGAGTCCATATGTTA
127 TTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTA
*
2549620 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
2549641 AAAATTTAAT
Statistics
Matches: 187, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
181 7 0.04
182 9 0.05
183 8 0.04
184 7 0.04
185 148 0.79
186 8 0.04
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (182 bp):
TATATAATATATTTAATATTTTTAATTAAAAAAAGTGTACAATTAATTTAAATAATATATAATTA
TAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGG
ATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATGTTA
Found at i:2557786 original size:15 final size:16
Alignment explanation
Indices: 2557740--2557787 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 16
2557730 TCCCATATGT
2557740 ATATAATTAGATATTG
1 ATATAATTAGATATTG
2557756 TATATATAATTTAGATATTG
1 ---ATATAA-TTAGATATTG
2557776 -TATAATTAGATA
1 ATATAATTAGATA
2557788 ATTTAGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 7 0.25
16 5 0.18
19 6 0.21
20 10 0.36
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (16 bp):
ATATAATTAGATATTG
Found at i:2557793 original size:24 final size:22
Alignment explanation
Indices: 2557741--2557806 Score: 84
Period size: 24 Copynumber: 3.0 Consensus size: 22
2557731 CCCATATGTA
2557741 TATAA-TTAGATATTGTAT-A-
1 TATAATTTAGATATTGTATAAT
2557760 TATAATTTAGATATTGTATAAT
1 TATAATTTAGATATTGTATAAT
*
2557782 TAGATAATTTAGATATTTTATAAT
1 T--ATAATTTAGATATTGTATAAT
2557806 T
1 T
2557807 TGTTATTCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 5 0.12
20 13 0.32
21 1 0.02
22 1 0.02
24 21 0.51
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (22 bp):
TATAATTTAGATATTGTATAAT
Found at i:2557905 original size:22 final size:22
Alignment explanation
Indices: 2557879--2557921 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2557869 ATAAAAATAA
*
2557879 TAAATGTTATTTCCAAATAGTG
1 TAAATGTTATTCCCAAATAGTG
2557901 TAAATGTTATTCCCAAATAGT
1 TAAATGTTATTCCCAAATAGT
2557922 AAGAAATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (22 bp):
TAAATGTTATTCCCAAATAGTG
Found at i:2570009 original size:17 final size:16
Alignment explanation
Indices: 2569983--2570016 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2569973 TTTCACTAGT
*
2569983 AGAGGAAATATTACAA
1 AGAGGAAATAGTACAA
2569999 AGAGAGAAATAGTACAA
1 AGAG-GAAATAGTACAA
2570016 A
1 A
2570017 TAGCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.06, G:0.21, T:0.15
Consensus pattern (16 bp):
AGAGGAAATAGTACAA
Found at i:2571495 original size:18 final size:18
Alignment explanation
Indices: 2571472--2571518 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
2571462 TGAACTAGTT
2571472 CCAAATCCAACTGTGCTA
1 CCAAATCCAACTGTGCTA
2571490 CCAAATCCAACTGTGCTA
1 CCAAATCCAACTGTGCTA
*
2571508 CCAAAGCCAAC
1 CCAAATCCAAC
2571519 AAAATTCTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.36, C:0.36, G:0.11, T:0.17
Consensus pattern (18 bp):
CCAAATCCAACTGTGCTA
Found at i:2578195 original size:21 final size:21
Alignment explanation
Indices: 2578166--2578218 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2578156 ATTTTTACTA
2578166 TCGCATTGCGATTCTCCAAAT
1 TCGCATTGCGATTCTCCAAAT
* * *
2578187 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTCTCCAAAT
*
2578208 TCGCAATGCGA
1 TCGCATTGCGA
2578219 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTCTCCAAAT
Found at i:2578233 original size:20 final size:20
Alignment explanation
Indices: 2578208--2578354 Score: 206
Period size: 20 Copynumber: 7.3 Consensus size: 20
2578198 TTTTCCTAAT
2578208 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
2578228 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
2578249 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2578269 TCGCAATGCGAATACTTAAA
1 TCGCAATGCGAATACGTAAA
*
2578289 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
2578309 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
2578329 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
2578349 TCGCAA
1 TCGCAA
2578355 CGAGATTCTG
Statistics
Matches: 111, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
19 1 0.01
20 95 0.86
21 15 0.14
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2578372 original size:60 final size:60
Alignment explanation
Indices: 2578208--2578375 Score: 211
Period size: 60 Copynumber: 2.8 Consensus size: 60
2578198 TTTTCCTAAT
*
2578208 TCGCAATGCGAATAC-GTAAATCGCAACGCGAATT-TGGAAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACTGTAAATCGCAACGCG-ATTCT-G-AAATCGCAATGCGAATACGTAAA
*
2578269 TCGCAATGCGAATACT-TAAATCGCAATGCGATTAC-GTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACTGTAAATCGCAACGCGATT-CTG-AAATCGCAATGCGAATACGTAAA
* *
2578329 TCGCAATGCGAAT-CTGTAAATCGCAACGAGATTCTGACTATCGCAAT
1 TCGCAATGCGAATACTGTAAATCGCAACGCGATTCTGA-AATCGCAAT
2578376 ACTGAATTTC
Statistics
Matches: 95, Mismatches: 6, Indels: 13
0.83 0.05 0.11
Matches are distributed among these distances:
59 4 0.04
60 63 0.66
61 28 0.29
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (60 bp):
TCGCAATGCGAATACTGTAAATCGCAACGCGATTCTGAAATCGCAATGCGAATACGTAAA
Found at i:2579243 original size:24 final size:24
Alignment explanation
Indices: 2579216--2579269 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2579206 GTATTCGAAA
2579216 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2579240 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2579264 TTTGAT
1 TTTGAT
2579270 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2581726 original size:20 final size:20
Alignment explanation
Indices: 2581701--2581789 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
2581691 CAACACGGAA
2581701 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
2581721 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
2581741 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
2581761 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
2581781 ATCGCAACG
1 ATCGCAACG
2581790 AGAGAATCGC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 59 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:2581818 original size:19 final size:19
Alignment explanation
Indices: 2581794--2581881 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
2581784 GCAACGAGAG
2581794 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2581813 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2581832 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
2581846 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
2581866 AATCGCAAAGCGAAAT
1 AATCGCAATGCGAAAT
2581882 TAGTTTCGCG
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
14 8 0.13
16 5 0.08
17 2 0.03
18 3 0.05
19 31 0.52
20 11 0.18
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2581867 original size:53 final size:52
Alignment explanation
Indices: 2581741--2581881 Score: 183
Period size: 53 Copynumber: 2.7 Consensus size: 52
2581731 GGAAATGACT
* ** * **
2581741 ATCGCAATGCGGAATTGACTATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAAAGC-GAAATGAAAATCGCAACGAGAGA
* *
2581795 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAAAGCGAAATGAAAATCGCAACGAGAGA
2581847 ATCGCAATGCGAAAATGAAAATCGCAAAGCGAAAT
1 ATCGCAATGCG-AAATGAAAATCGCAAAGCGAAAT
2581882 TAGTTTCGCG
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
52 31 0.40
53 37 0.47
54 10 0.13
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAAAGCGAAATGAAAATCGCAACGAGAGA
Found at i:2581933 original size:34 final size:34
Alignment explanation
Indices: 2581890--2581985 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
2581880 ATTAGTTTCG
2581890 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
2581924 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** * *
2581957 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
2581986 AGTCTGTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:2582106 original size:14 final size:14
Alignment explanation
Indices: 2582087--2582123 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2582077 CATCAATTAA
2582087 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2582101 ACAAATCATCTTTT
1 ACAAATCAACATTT
2582115 ACAAATCAA
1 ACAAATCAA
2582124 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2583426 original size:20 final size:20
Alignment explanation
Indices: 2583403--2583451 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2583393 GAAACTTAAA
2583403 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
2583423 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
2583443 ATCGCAACG
1 ATCGCAACG
2583452 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2583515 original size:20 final size:20
Alignment explanation
Indices: 2583490--2583538 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2583480 CAACAACAAA
2583490 ATCGCAACGCGAAA-ATGACT
1 ATCGCAACGC-AAATATGACT
* *
2583510 ATCGCAATGCAAATTTGACT
1 ATCGCAACGCAAATATGACT
*
2583530 AGCGCAACG
1 ATCGCAACG
2583539 AGAGAATCGC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCAAATATGACT
Found at i:2583608 original size:20 final size:20
Alignment explanation
Indices: 2583583--2583722 Score: 193
Period size: 20 Copynumber: 7.3 Consensus size: 20
2583573 GATTCTTTCG
**
2583583 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
2583603 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2583623 TTGCGATAGCCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
2583643 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2583663 TTGCGAT--T-ATCTT-G--
1 TTGCGATAGTCATTTTCGCA
*
2583677 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
2583697 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
2583717 TTGCGA
1 TTGCGA
2583723 CAGTAAACTA
Statistics
Matches: 107, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
14 7 0.07
16 2 0.02
17 8 0.07
18 2 0.02
20 88 0.82
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:2583631 original size:40 final size:40
Alignment explanation
Indices: 2583545--2583722 Score: 193
Period size: 40 Copynumber: 4.8 Consensus size: 40
2583535 AACGAGAGAA
* **
2583545 TCGCAATGCGATTTTCA-TTTCGCATTGCGAT--TC--TT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
**
2583580 TCG--TTGCGATAGTCAAATTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
2583618 TCGCATTGCGATAGCCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
2583658 TCGCATTGCGAT--T-ATCTT-G--TTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
2583692 TCGCGTTGCGATAGTCATTTTCGCATTGCGA
1 TCGCATTGCGATAGTCATTTTCGCATTGCGA
2583723 CAGTAAACTA
Statistics
Matches: 119, Mismatches: 11, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
33 9 0.08
34 39 0.33
35 3 0.03
36 4 0.03
37 8 0.07
38 6 0.05
40 50 0.42
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
Found at i:2585615 original size:20 final size:20
Alignment explanation
Indices: 2585592--2585641 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
2585582 CTGAAACTTT
2585592 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
2585612 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
**
2585632 CTATCGCAAC
1 AAATCGCAAC
2585642 GCAAGAATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.24, G:0.14, T:0.12
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:2585712 original size:20 final size:20
Alignment explanation
Indices: 2585687--2585733 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2585677 GATTCTCTCG
2585687 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
2585707 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
2585727 TTGCGAT
1 TTGCGAT
2585734 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:2586346 original size:21 final size:21
Alignment explanation
Indices: 2586322--2586362 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2586312 TATTCGCATT
2586322 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
2586343 GCGAATTTGGGAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
2586363 TGTGATAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:2588227 original size:21 final size:21
Alignment explanation
Indices: 2588202--2588241 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2588192 TCTCAATTCT
*
2588202 GAAAGTTCCAATCTTTCATAC
1 GAAAGTCCCAATCTTTCATAC
*
2588223 GAAAGTCCCAGTCTTTCAT
1 GAAAGTCCCAATCTTTCAT
2588242 CAATGGCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (21 bp):
GAAAGTCCCAATCTTTCATAC
Found at i:2593687 original size:24 final size:26
Alignment explanation
Indices: 2593651--2593700 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
2593641 CGTTGACGTC
*
2593651 TAATAGAACAATC-AA-TAAAATGAT
1 TAATAAAACAATCTAATTAAAATGAT
*
2593675 TAATAAAAGAATCTAATTAAAATGAT
1 TAATAAAACAATCTAATTAAAATGAT
2593701 AATTAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
25 2 0.09
26 9 0.41
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (26 bp):
TAATAAAACAATCTAATTAAAATGAT
Found at i:2601126 original size:23 final size:23
Alignment explanation
Indices: 2601096--2601139 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2601086 GATTTTGCCA
*
2601096 TGTCACTTTTCAACCATTATTAG
1 TGTCACTTATCAACCATTATTAG
*
2601119 TGTCACTTATGAACCATTATT
1 TGTCACTTATCAACCATTATT
2601140 GTTGCCAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.43
Consensus pattern (23 bp):
TGTCACTTATCAACCATTATTAG
Found at i:2601194 original size:21 final size:20
Alignment explanation
Indices: 2601154--2601195 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2601144 CCAACTTACA
*
2601154 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
2601174 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
2601195 A
1 A
2601196 GTTGCATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:2604338 original size:42 final size:42
Alignment explanation
Indices: 2604277--2604393 Score: 225
Period size: 42 Copynumber: 2.8 Consensus size: 42
2604267 CCCCGAAATT
*
2604277 CCGTGTTTGTTTCATGTAATTCGTTTTCCGGAAAATGTTTTC
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTC
2604319 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTC
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTC
2604361 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
2604394 CGTAATTCAT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.16, C:0.19, G:0.20, T:0.45
Consensus pattern (42 bp):
CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTC
Found at i:2604609 original size:23 final size:23
Alignment explanation
Indices: 2604565--2604625 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
2604555 TATTTTCATC
*
2604565 AAAATATTAATTATTAAAATATTT
1 AAAATA-TAATTATTAAAATATAT
* *
2604589 AAAATATATTTATTAATATATAT
1 AAAATATAATTATTAAAATATAT
*
2604612 ATAATATAATTATT
1 AAAATATAATTATT
2604626 TTTTAGTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 26 0.81
24 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATATAATTATTAAAATATAT
Found at i:2604625 original size:27 final size:26
Alignment explanation
Indices: 2604590--2604736 Score: 81
Period size: 28 Copynumber: 5.4 Consensus size: 26
2604580 AAAATATTTA
2604590 AAATATATTTATTAATATATATATAAT
1 AAAT-TATTTATTAATATATATATAAT
* * *
2604617 ATAATTATTTTTTAGTTTAATAATATAAT
1 A-AATTATTTATTAATAT-AT-ATATAAT
* *
2604646 AAATTATATTA-TAATAATATAAGATATT
1 AAATTAT-TTATTAAT-ATAT-ATATAAT
* *
2604674 ATATTTTTTATTTTAATA-ATATATAAT
1 AAATTATTTA--TTAATATATATATAAT
2604701 AAATT-TTT-TT-ATATA-ATAATGAAT
1 AAATTATTTATTAATATATAT-AT-AAT
2604725 AATATTATTTAT
1 AA-ATTATTTAT
2604737 ATATTTAAAT
Statistics
Matches: 93, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
22 5 0.05
23 5 0.05
24 5 0.05
25 3 0.03
26 6 0.06
27 24 0.26
28 29 0.31
29 12 0.13
30 4 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
AAATTATTTATTAATATATATATAAT
Found at i:2604664 original size:23 final size:23
Alignment explanation
Indices: 2604634--2604678 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2604624 TTTTTTAGTT
*
2604634 TAATAATATAATAAATTATATTA
1 TAATAATATAAGAAATTATATTA
*
2604657 TAATAATATAAGATATTATATT
1 TAATAATATAAGAAATTATATT
2604679 TTTTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TAATAATATAAGAAATTATATTA
Found at i:2604725 original size:24 final size:26
Alignment explanation
Indices: 2604582--2604740 Score: 77
Period size: 25 Copynumber: 6.0 Consensus size: 26
2604572 TAATTATTAA
*
2604582 AATATTTAA-AATA-TATTTATTA-AT
1 AATATATAATAATATTATTT-TTATAT
*
2604606 ATATATATAAT-ATAATTATTTTTTAGTTT
1 A-ATATATAATAAT-ATTA-TTTTTA-TAT
*
2604635 AATAATATAATAA-ATTA-TATTATAAT
1 AAT-ATATAATAATATTATTTTTAT-AT
* *
2604661 AATATA-AGATATTATATTTTTTATTTTAAT
1 AATATATA-ATA--ATATTATTT-TTAT-AT
2604691 AATATATAATAA-ATT-TTTTTATAT
1 AATATATAATAATATTATTTTTATAT
*
2604715 AATA-ATGAATAATATTATTTATATAT
1 AATATAT-AATAATATTATTTTTATAT
2604741 TTAAATAATA
Statistics
Matches: 106, Mismatches: 9, Indels: 38
0.69 0.06 0.25
Matches are distributed among these distances:
23 2 0.02
24 13 0.12
25 22 0.21
26 20 0.19
27 9 0.08
28 13 0.12
29 10 0.09
30 16 0.15
31 1 0.01
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
AATATATAATAATATTATTTTTATAT
Found at i:2604922 original size:20 final size:20
Alignment explanation
Indices: 2604893--2604932 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2604883 TAATAAAATT
2604893 ATAAAAAAA-TATATTTAATA
1 ATAAAAAAATTAT-TTTAATA
*
2604913 ATAAATAAATTATTTTAATA
1 ATAAAAAAATTATTTTAATA
2604933 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAAAAATTATTTTAATA
Found at i:2605103 original size:14 final size:14
Alignment explanation
Indices: 2605084--2605128 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
2605074 CCAGAAATGT
2605084 AATTCATTTTCCAG
1 AATTCATTTTCCAG
** *
2605098 AATTCAAATTCTAG
1 AATTCATTTTCCAG
2605112 TAATTCATTTTCCAG
1 -AATTCATTTTCCAG
2605127 AA
1 AA
2605129 AACCAATTAC
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.40
Consensus pattern (14 bp):
AATTCATTTTCCAG
Found at i:2605107 original size:20 final size:20
Alignment explanation
Indices: 2605070--2605108 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2605060 TCATAAAACG
**
2605070 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
2605090 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
2605109 TAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:2616508 original size:20 final size:20
Alignment explanation
Indices: 2616483--2616523 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2616473 TCTTGAATAT
* *
2616483 TTTTTTTATGTTTTTTAATC
1 TTTTTTTATATTTTATAATC
*
2616503 TTTTTTTGTATTTTATAATC
1 TTTTTTTATATTTTATAATC
2616523 T
1 T
2616524 AAATGAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (20 bp):
TTTTTTTATATTTTATAATC
Found at i:2619348 original size:24 final size:23
Alignment explanation
Indices: 2619295--2619348 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
2619285 ATAGTTTTAG
2619295 TATTTTTTTTTAATTTACATATT
1 TATTTTTTTTTAATTTACATATT
* * *
2619318 CAATTTTTTTAGTAATTTA-ATTTT
1 -TATTTTTTT-TTAATTTACATATT
2619342 TATTTTT
1 TATTTTT
2619349 AATATTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 6 0.24
24 12 0.48
25 7 0.28
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.69
Consensus pattern (23 bp):
TATTTTTTTTTAATTTACATATT
Found at i:2619370 original size:14 final size:14
Alignment explanation
Indices: 2619322--2619401 Score: 63
Period size: 14 Copynumber: 5.3 Consensus size: 14
2619312 CATATTCAAT
2619322 TTTTTTAGTAATTTAA
1 TTTTTTA-T-ATTTAA
*
2619338 -TTTTTATTTTTAA
1 TTTTTTATATTTAA
*
2619351 TATTTTATATTTAA
1 TTTTTTATATTTAA
*
2619365 TTTTTTGAATATCTAAA
1 TTTTTT--ATAT-TTAA
2619382 TATTTTTATATTTAAA
1 T-TTTTTATATTT-AA
2619398 TTTT
1 TTTT
2619402 AAATAATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
13 5 0.10
14 17 0.33
15 10 0.19
16 11 0.21
17 4 0.08
18 5 0.10
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (14 bp):
TTTTTTATATTTAA
Found at i:2625374 original size:20 final size:20
Alignment explanation
Indices: 2625327--2625397 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
2625317 GCGATTTTCC
2625327 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGAATAT
*
2625347 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGAATAT
* * *
2625367 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGAATAT
*
2625387 GACTGTCGCAA
1 GACTATCGCAA
2625398 CACTGAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (20 bp):
GACTATCGCAATGCGAATAT
Found at i:2626253 original size:24 final size:24
Alignment explanation
Indices: 2626219--2626272 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2626209 GTATTCGAAA
2626219 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* * *
2626243 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
2626267 TTTGAT
1 TTTGAT
2626273 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:2626488 original size:14 final size:14
Alignment explanation
Indices: 2626469--2626498 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2626459 GAAGAAAAAG
2626469 AAATCCCCGAAGAA
1 AAATCCCCGAAGAA
2626483 AAATCCCCGAAGAA
1 AAATCCCCGAAGAA
2626497 AA
1 AA
2626499 TGCCACGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.27, G:0.13, T:0.07
Consensus pattern (14 bp):
AAATCCCCGAAGAA
Found at i:2628567 original size:18 final size:18
Alignment explanation
Indices: 2628535--2628569 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2628525 AGAAAGAGGC
**
2628535 AATCAAAATTGCAATCAA
1 AATCAAAATCCCAATCAA
2628553 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
2628570 CAACCGGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:2628881 original size:140 final size:140
Alignment explanation
Indices: 2628629--2628898 Score: 495
Period size: 140 Copynumber: 1.9 Consensus size: 140
2628619 AAACGTTGTA
2628629 TTATGTGTAAACTTTTAAAATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAAAATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
2628694 TGATCTGTTCAGTTGTTATCACTTATTACACATTTATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
2628759 TATGTGTATT
131 TATGTGTATT
* * *
2628769 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGATTTTGAACATTGTTA
1 TTATGTGTAAACTTTTAAAATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
2628834 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
2628899 CGCAACGCGA
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 125 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAAAATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:2628894 original size:20 final size:20
Alignment explanation
Indices: 2628869--2629147 Score: 256
Period size: 20 Copynumber: 14.8 Consensus size: 20
2628859 TTACACATTC
*
2628869 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
2628889 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
2628909 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
2628928 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2628943 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* *
2628963 ATATGACTATCACAACGC-A
1 ATTTGACTATCGCAACGCGA
*
2628982 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2628997 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2629017 ATTTGACTATCGCAACG-GCT
1 ATTTGACTATCGCAACGCG-A
*
2629037 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
*
2629057 A----A--ATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
2629071 ATTTGACTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2629091 ATTTGAGTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2629111 ATTTGATTATCGCAACG-GA
1 ATTTGACTATCGCAACGCGA
*
2629130 TATTTAACTATCGCAACG
1 -ATTTGACTATCGCAACG
2629148 AGAAAATCAC
Statistics
Matches: 212, Mismatches: 26, Indels: 42
0.76 0.09 0.15
Matches are distributed among these distances:
14 29 0.14
15 6 0.03
16 1 0.00
18 1 0.00
19 8 0.04
20 166 0.78
21 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:2628964 original size:54 final size:54
Alignment explanation
Indices: 2628877--2629196 Score: 271
Period size: 54 Copynumber: 5.8 Consensus size: 54
2628867 TCATTTGAAT
* *
2628877 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAA
* * *
2628931 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCACAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAA
* **
2628985 ATCGCAACGCGAATTTGTCTATCGCAACGCGAATTTGACTATCGCAACGGCTATTTGACT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAAC-GC-A----AAA
* * * *
2629045 ATCGCAACGAGAA----A--ATCGCAACACGAATTTGACTATCACAACGCGAATTTGAGT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGC-AA----A-A
* *
2629099 ATCGCAACGCGAATTTGATTATCGCAACG-GATATTTAACTATCGCAACG-AGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGA-ATTTGACTATCGCAACGCA-AAA
* * * * * *
2629153 ATCACAAAGTGTATTAGACTATCGCAACGCGAA-TTGACTTTCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
2629197 GTTGCGATTT
Statistics
Matches: 216, Mismatches: 30, Indels: 41
0.75 0.10 0.14
Matches are distributed among these distances:
49 1 0.00
53 12 0.06
54 156 0.72
55 5 0.02
56 1 0.00
58 2 0.01
59 3 0.01
60 36 0.17
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAA
Found at i:2629009 original size:74 final size:73
Alignment explanation
Indices: 2628931--2629127 Score: 270
Period size: 74 Copynumber: 2.7 Consensus size: 73
2628921 CAACTCAAAA
* * *
2628931 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCACAACGCA-AAAATCGCAACGC
1 ATCGCAACGCGAATTTGACTATCGCAAC-CGAATTTGACTATCGCAACG-AGAAAATCGCAACAC
*
2628995 GAATTTGTCT
64 GAATTTGACT
* *
2629005 ATCGCAACGCGAATTTGACTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATCGCAACACG
1 ATCGCAACGCGAATTTGACTATCGCAACCG-AATTTGACTATCGCAACGAGAAAATCGCAACACG
2629070 AATTTGACT
65 AATTTGACT
* * *
2629079 ATCACAACGCGAATTTGAGTATCGCAACGCGAATTTGATTATCGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAAC-CGAATTTGACTATCGCAACG
2629128 GATATTTAAC
Statistics
Matches: 109, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
73 2 0.02
74 106 0.97
75 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (73 bp):
ATCGCAACGCGAATTTGACTATCGCAACCGAATTTGACTATCGCAACGAGAAAATCGCAACACGA
ATTTGACT
Found at i:2629087 original size:94 final size:94
Alignment explanation
Indices: 2628989--2629196 Score: 294
Period size: 94 Copynumber: 2.2 Consensus size: 94
2628979 GCAAAAATCG
* * *
2628989 CAACGCGAATTTGTCTATCGCAACGCGAATTTGACTATCGCAACGGCTATTTGACTATCGCAACG
1 CAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGGATATTTAACTATCGCAACG
* *
2629054 AGAAAATCGCAACA-CGAATTTGACTATCA
66 AGAAAATCACAA-AGCGAATTAGACTATCA
* *
2629083 CAACGCGAATTTGAGTATCGCAACGCGAATTTGATTATCGCAACGGATATTTAACTATCGCAACG
1 CAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGGATATTTAACTATCGCAACG
* * *
2629148 AGAAAATCACAAAGTGTATTAGACTATCG
66 AGAAAATCACAAAGCGAATTAGACTATCA
*
2629177 CAACGCGAA-TTGACTTTCGC
1 CAACGCGAATTTGACTATCGC
2629197 GTTGCGATTT
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
93 10 0.10
94 91 0.90
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (94 bp):
CAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGGATATTTAACTATCGCAACG
AGAAAATCACAAAGCGAATTAGACTATCA
Found at i:2629215 original size:20 final size:20
Alignment explanation
Indices: 2629186--2629243 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
2629176 GCAACGCGAA
2629186 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
2629206 TTGTCTTTCGCATTGCGATT
1 TTGACTTTCGCGTTGCGATT
* *
2629226 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCGTTGCGA
2629244 AAGTGTACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.12, C:0.17, G:0.26, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGATT
Found at i:2630856 original size:21 final size:22
Alignment explanation
Indices: 2630832--2630908 Score: 56
Period size: 21 Copynumber: 3.7 Consensus size: 22
2630822 TAACAGTGGC
*
2630832 CTCTTGAACGG-TGGGAGGGGA
1 CTCTTGAACGGATGAGAGGGGA
* * *
2630853 CTCTT-AAGGGATGATAGGGGC
1 CTCTTGAACGGATGAGAGGGGA
* *
2630874 CTCTTGAAC-GAT-AGGGGAGGC
1 CTCTTGAACGGATGAGAGG-GGA
2630895 CTCTTGAAC-GATGA
1 CTCTTGAACGGATGA
2630909 CAGATGAGTC
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 7 0.16
21 35 0.78
22 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (22 bp):
CTCTTGAACGGATGAGAGGGGA
Found at i:2630908 original size:42 final size:41
Alignment explanation
Indices: 2630801--2630911 Score: 100
Period size: 42 Copynumber: 2.6 Consensus size: 41
2630791 TCTAGAATGC
* * *
2630801 TGGGAG-GGACCTCTTCAACGATAACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTT-AACGATGACAGGGGCCTCTTGAACGA
* * * *
2630843 TGGGAGGGGACTCTTAAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTAA-CGATGACAGGGGCCTCTTGAACGA
2630885 TAGGG-GAGGCCTCTTGAACGATGACAG
1 T-GGGAGAGGCCTCTT-AACGATGACAG
2630912 ATGAGTCAGG
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
41 2 0.04
42 46 0.84
43 7 0.13
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (41 bp):
TGGGAGAGGCCTCTTAACGATGACAGGGGCCTCTTGAACGA
Done.