Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008543.1 Hibiscus syriacus cultivar Beakdansim tig00111432_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: 282078
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 2 of 3
Found at i:80630 original size:20 final size:20
Alignment explanation
Indices: 80605--80648 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
80595 TTTTTTACTA
*
80605 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
80625 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
80645 TTCT
1 TTCT
80649 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:80658 original size:20 final size:20
Alignment explanation
Indices: 80635--80907 Score: 105
Period size: 20 Copynumber: 13.6 Consensus size: 20
80625 TTCTTTTTAA
80635 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
80655 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * *
80675 CATTGCGA--TTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
80693 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
80716 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
80736 CATTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
80756 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
80776 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** * *
80799 CGTTGCGAACTTGGAAGCTTG
1 CGTTGCGATTTTCTAA-ATCG
* *
80820 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
* *
80838 ACCGTTGCGATTTCTTTTAA---
1 --CGTTGCGATTT-TCTAAATCG
80858 CGTTGCGA-TTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
80877 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
80896 CGTTGCGATTTT
1 CGTTGCGATTTT
80908 ATTGGTCATT
Statistics
Matches: 198, Mismatches: 37, Indels: 37
0.73 0.14 0.14
Matches are distributed among these distances:
16 4 0.02
17 2 0.01
18 28 0.14
19 25 0.13
20 94 0.47
21 15 0.08
22 2 0.01
23 28 0.14
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:80722 original size:61 final size:63
Alignment explanation
Indices: 80645--80765 Score: 201
Period size: 61 Copynumber: 2.0 Consensus size: 63
80635 CGTTGCGATT
* * *
80645 TTCTAAATCGCGTTGCGATTCTCTCAGTCGCATTGCGA-T-TCTCAGTCGCATTGCGATTTTC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGACTCTCTCAATCGCATTGCGATTTTC
80706 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGACTCTCTCAATCGCATTGCGATT
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGACTCTCTCAATCGCATTGCGATT
80766 CAATCAATCG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 36 0.65
62 1 0.02
63 18 0.33
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (63 bp):
TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGACTCTCTCAATCGCATTGCGATTTTC
Found at i:80742 original size:81 final size:82
Alignment explanation
Indices: 80635--80806 Score: 265
Period size: 81 Copynumber: 2.1 Consensus size: 82
80625 TTCTTTTTAA
* * * * * *
80635 CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAGTCGCATTGCGATTC-TCAGTCGCATTGC
1 CGTTGCGACTCTCTAAATCGCATTGCGACTCTCTCAATCGCATTGCGATTCATCAATCGCATTGC
80699 GATTTTCTTCTAAATCG
66 GATTTTCTTCTAAATCG
*
80716 CGTTGCGACTCTCTCAATCGCATTGCGACTCTCTCAATCGCATTGCGATTCAATCAATCGCATTG
1 CGTTGCGACTCTCTAAATCGCATTGCGACTCTCTCAATCGCATTGCGATTC-ATCAATCGCATTG
80781 CGATTTTCTTCTAAATCG
65 CGATTTTCTTCTAAATCG
80799 CGTTGCGA
1 CGTTGCGA
80807 ACTTGGAAGC
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
81 45 0.55
83 37 0.45
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (82 bp):
CGTTGCGACTCTCTAAATCGCATTGCGACTCTCTCAATCGCATTGCGATTCATCAATCGCATTGC
GATTTTCTTCTAAATCG
Found at i:80863 original size:18 final size:19
Alignment explanation
Indices: 80820--80870 Score: 77
Period size: 18 Copynumber: 2.7 Consensus size: 19
80810 TGGAAGCTTG
*
80820 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGA-TTTCTTTTGAA
80840 CGTTGCGATTTCTTTT-AA
1 CGTTGCGATTTCTTTTGAA
80858 CGTTGCGATTTCT
1 CGTTGCGATTTCT
80871 AAATCGCGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 14 0.47
19 8 0.27
20 8 0.27
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.49
Consensus pattern (19 bp):
CGTTGCGATTTCTTTTGAA
Found at i:80882 original size:19 final size:19
Alignment explanation
Indices: 80858--80907 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
80848 TTTCTTTTAA
80858 CGTTGCGATTTCT-AAATCG
1 CGTTGCGATTT-TGAAATCG
*
80877 CGTTGCGATTTTGATATCG
1 CGTTGCGATTTTGAAATCG
80896 CGTTGCGATTTT
1 CGTTGCGATTTT
80908 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 1 0.03
19 28 0.97
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTGAAATCG
Found at i:87267 original size:23 final size:23
Alignment explanation
Indices: 87220--87269 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
87210 AATAACATAT
**
87220 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
87243 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
87266 TAGG
1 TAGG
87270 CATTTAACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:87806 original size:201 final size:196
Alignment explanation
Indices: 87363--88073 Score: 656
Period size: 201 Copynumber: 3.5 Consensus size: 196
87353 TTTTCGAAGT
* * *
87363 AAACCGGTATATTTATACCGGTAACATTGAAAATTTACTTATTACATTATTATTATCGGTTTCGA
1 AAACCGGTATATTTATACTGGTTACATTGAAAATTTACCTATTACATTA-TATTATCGGTTTCGA
* ** * * * **
87428 TATTTTTTAGATCTATACAATTTT-TAAATGTATCGACACTTTATGTTTGCACCTCGTTGGTCAT
65 TGTTTTTGGGATCGATAC-TTTTTATAAATGTATCGACACTTTATGGTTGCACC-C-TT--TTTT
* * *
87492 T-CATATTTCATTCTGGAAAAAAATATCGACACAAACTAACAAAGTGTCGATACATGT-T-TTAG
125 TGC--A-TTCATTCTGGAAAAAAGTATCGACACAAATTAAC-AAGTGTCGATAC-TTTATGTTA-
*
87554 ACCAATTCTCTCATA
184 ACCTATT-T-TCATA
87569 AAACCGGTATATTTATACTGGTTACATTGAAAATTTACCTATTACATTATACTTAT-GAGTTTCG
1 AAACCGGTATATTTATACTGGTTACATTGAAAATTTACCTATTACATTATA-TTATCG-GTTTCG
* *
87633 ATGTTTTCGGGATCGATACTTTTTATAAATATATCGACACTTTATGGTTGCACCCTTTTTTTGCA
64 ATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTTTGCA
* *
87698 TTCATTCTGGACCAAAAGTAACGACACAAATTTAACAAGTGTCGATACTTTATGTTAACCTATTT
129 TTCATTCTGGA-AAAAAGTATCGACACAAA-TTAACAAGTGTCGATACTTTATGTTAACCTATTT
87763 TAGCATA
192 T--CATA
* * * *
87770 AAACCGGTATATTTATA-TCAGTTACATTGTAAATTTATCTAATACATTATATATATCGGTTTCG
1 AAACCGGTATATTTATACT-GGTTACATTGAAAATTTACCTATTACATTATAT-TATCGGTTTCG
* * **
87834 ATGTTTTTGGGATCGATA-TCTTTAATAAATGTATCGACACTTTAT-GTGTGCA-CCTCGTTTGG
64 ATGTTTTTGGGATCGATACT-TTTTATAAATGTATCGACACTTTATGGT-TGCACCCT-TTTTTT
* * * * * * *
87896 GCATTCATCCT-GAATAATAAGTATCGACACAAATTACACAACTATTGATACATTATGTTGACAT
126 GCATTCATTCTGGAA-AA-AAGTATCGACACAAATTA-ACAAGTGTCGATACTTTATGTTAACCT
*
87960 GTTTTC-TA
188 ATTTTCATA
* ** * *
87968 ATTAACTGGTATATTTATACTGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTT
1 A--AACCGGTATATTTATACTGGTTACATTGAAAATTTACCTATTACATTAT-ATTATCGGTTTC
* *
88033 GATGTTTTTTGGG-TCGATAC-TTGTAGAAAATGTATCGACAC
63 GATG-TTTTTGGGATCGATACTTTTTA-TAAATGTATCGACAC
88074 ATATTTAGGT
Statistics
Matches: 430, Mismatches: 49, Indels: 58
0.80 0.09 0.11
Matches are distributed among these distances:
198 3 0.01
199 5 0.01
200 103 0.24
201 200 0.47
202 11 0.03
203 1 0.00
204 2 0.00
205 8 0.02
206 97 0.23
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (196 bp):
AAACCGGTATATTTATACTGGTTACATTGAAAATTTACCTATTACATTATATTATCGGTTTCGAT
GTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTTTGCATT
CATTCTGGAAAAAAGTATCGACACAAATTAACAAGTGTCGATACTTTATGTTAACCTATTTTCAT
A
Found at i:90567 original size:182 final size:180
Alignment explanation
Indices: 90079--90553 Score: 666
Period size: 182 Copynumber: 2.6 Consensus size: 180
90069 CGTACTTACG
* * *
90079 AAAGTATCGACACTTTCAATATATCCGGTAACGCTTTACCAGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCGGTTTTATC-TTTTGATACCGGTTT
* *
90144 TATCATATTTTTACATGTTATGTCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGTTATATCG-TGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
*
90209 AGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
129 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
* * * * * *
90261 AAAGTATCAACACTTTAAATATATCTGGTAGCGCTTTACCGGTTTTACCATTTGGATATCAGTTT
1 AAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCGGTTTTATC-TTTTGATACCGGTTT
*
90326 TGTCATATTTTTACCTGTTATATCGTCGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGTTATATCGT-GTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
*
90391 AGGC-CTTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
129 AGGCGC-TAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
* * * *
90443 AAAGTATCGACACGTTCAATATATCTGGTAGGGCTTTACCGGTATTGTCTTTTCG-TGACCGGTT
1 AAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCGGTTTTATCTTTT-GAT-ACCGGTT
* * * *
90507 TTAACATATTTTTACCTGTTATATTGATATGTATCGATACATTTTTA
64 TTATCATATTTTTACCTGTTATATCG-TGTGGATCGATACATTTTTA
90554 ATTTGGATCG
Statistics
Matches: 259, Mismatches: 29, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
181 6 0.02
182 252 0.97
183 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41
Consensus pattern (180 bp):
AAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCGGTTTTATCTTTTGATACCGGTTTT
ATCATATTTTTACCTGTTATATCGTGTGGATCGATACATTTTTATAAAGTATCGACACTTTATAG
GCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
Found at i:96888 original size:47 final size:47
Alignment explanation
Indices: 96837--96928 Score: 139
Period size: 47 Copynumber: 2.0 Consensus size: 47
96827 GATGTAAACA
* *
96837 AACATAAACGAACACAATAGACAAACGTAAACGAATACAAATGAACG
1 AACATAAACGAACACAATAAACAAACGTAAACGAAAACAAATGAACG
** *
96884 AACATAAACGAACACAATAAATGAACGTAAACGAAAATAAATGAA
1 AACATAAACGAACACAATAAACAAACGTAAACGAAAACAAATGAA
96929 AAAATATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.60, C:0.16, G:0.12, T:0.12
Consensus pattern (47 bp):
AACATAAACGAACACAATAAACAAACGTAAACGAAAACAAATGAACG
Found at i:96900 original size:24 final size:24
Alignment explanation
Indices: 96792--96928 Score: 100
Period size: 24 Copynumber: 5.8 Consensus size: 24
96782 CATTTAAATG
* *
96792 ATAAACGAACATAAATGAACGAAA
1 ATAAACGAACACAAATGAACGAAC
** ** * *
96816 ATAAACGAACGGATGTAAACAAAC
1 ATAAACGAACACAAATGAACGAAC
*
96840 ATAAACGAACAC-AAT-AGACAAAC
1 ATAAACGAACACAAATGA-ACGAAC
* *
96863 GTAAACGAATACAAATGAACGAAC
1 ATAAACGAACACAAATGAACGAAC
* *
96887 ATAAACGAACAC-AATAAATGAAC
1 ATAAACGAACACAAATGAACGAAC
* * *
96910 GTAAACGAAAATAAATGAA
1 ATAAACGAACACAAATGAA
96929 AAAATATATT
Statistics
Matches: 87, Mismatches: 22, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
22 1 0.01
23 35 0.40
24 50 0.57
25 1 0.01
ACGTcount: A:0.59, C:0.15, G:0.13, T:0.12
Consensus pattern (24 bp):
ATAAACGAACACAAATGAACGAAC
Found at i:96914 original size:23 final size:23
Alignment explanation
Indices: 96831--96918 Score: 95
Period size: 23 Copynumber: 3.8 Consensus size: 23
96821 CGAACGGATG
* *
96831 TAAACAAACATAAACGAACACAA
1 TAAACGAACGTAAACGAACACAA
* * *
96854 TAGACAAACGTAAACGAATACAAA
1 TAAACGAACGTAAACGAACAC-AA
* *
96878 TGAACGAACATAAACGAACACAA
1 TAAACGAACGTAAACGAACACAA
*
96901 TAAATGAACGTAAACGAA
1 TAAACGAACGTAAACGAA
96919 AATAAATGAA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
23 35 0.66
24 18 0.34
ACGTcount: A:0.59, C:0.18, G:0.11, T:0.11
Consensus pattern (23 bp):
TAAACGAACGTAAACGAACACAA
Found at i:97135 original size:23 final size:24
Alignment explanation
Indices: 97094--97143 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
97084 GATTATGCTA
* *
97094 AACATAAATGAACGTACATAAACG
1 AACATAAACGAACGAACATAAACG
*
97118 AACAT-AACGAACGAACATAAATG
1 AACATAAACGAACGAACATAAACG
97141 AAC
1 AAC
97144 GAACATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.56, C:0.18, G:0.12, T:0.14
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAACG
Found at i:97145 original size:14 final size:14
Alignment explanation
Indices: 97094--97150 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
97084 GATTATGCTA
97094 AACATAAATGAACG
1 AACATAAATGAACG
*
97108 TACAT--A--AACG
1 AACATAAATGAACG
*
97118 AACAT-AACGAACG
1 AACATAAATGAACG
97131 AACATAAATGAACG
1 AACATAAATGAACG
97145 AACATA
1 AACATA
97151 TTACCTAACG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 8 0.22
11 1 0.03
12 1 0.03
13 9 0.25
14 17 0.47
ACGTcount: A:0.56, C:0.18, G:0.12, T:0.14
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:100944 original size:10 final size:10
Alignment explanation
Indices: 100931--101002 Score: 54
Period size: 10 Copynumber: 6.4 Consensus size: 10
100921 GTTCGTGAAC
*
100931 GTTCTTTTAT
1 GTTCGTTTAT
100941 GTTCGTTTAT
1 GTTCGTTTAT
100951 GTTCGTTCGGTTAT
1 GTTCG-T---TTAT
100965 GTTCGTTTATGTTT
1 GTTCGTTTA----T
*
100979 GTTCGGTTAT
1 GTTCGTTTAT
100989 GTTCGTTTAT
1 GTTCGTTTAT
100999 GTTC
1 GTTC
101003 ATTCATTTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
10 31 0.61
11 1 0.02
13 1 0.02
14 18 0.35
ACGTcount: A:0.08, C:0.11, G:0.22, T:0.58
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:100958 original size:14 final size:14
Alignment explanation
Indices: 100941--100995 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
100931 GTTCTTTTAT
*
100941 GTTCGTTTATGTTC
1 GTTCGGTTATGTTC
100955 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
*
100969 G-T---TTATGTTT
1 GTTCGGTTATGTTC
100979 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
100993 GTT
1 GTT
100996 TATGTTCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
13 1 0.03
14 24 0.71
ACGTcount: A:0.07, C:0.11, G:0.25, T:0.56
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:101015 original size:24 final size:24
Alignment explanation
Indices: 100937--101002 Score: 123
Period size: 24 Copynumber: 2.8 Consensus size: 24
100927 GAACGTTCTT
100937 TTATGTTCGTTTATGTTCGTTCGG
1 TTATGTTCGTTTATGTTCGTTCGG
*
100961 TTATGTTCGTTTATGTTTGTTCGG
1 TTATGTTCGTTTATGTTCGTTCGG
100985 TTATGTTCGTTTATGTTC
1 TTATGTTCGTTTATGTTC
101003 ATTCATTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.09, C:0.11, G:0.23, T:0.58
Consensus pattern (24 bp):
TTATGTTCGTTTATGTTCGTTCGG
Found at i:102105 original size:10 final size:10
Alignment explanation
Indices: 102090--102131 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
102080 GGTCTCCAAA
102090 GTTTATGTTC
1 GTTTATGTTC
102100 GTTTATGTTC
1 GTTTATGTTC
102110 G----TGTTC
1 GTTTATGTTC
102116 GTTTATGTTC
1 GTTTATGTTC
102126 GTTTAT
1 GTTTAT
102132 TTATTAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 6 0.21
10 22 0.79
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.60
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:102116 original size:16 final size:16
Alignment explanation
Indices: 102095--102127 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
102085 CCAAAGTTTA
102095 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
102111 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
102127 T
1 T
102128 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:104474 original size:8 final size:8
Alignment explanation
Indices: 104457--104490 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
104447 CATGAGCTAG
*
104457 ACAACGAC
1 ACAACAAC
104465 ACAACAAC
1 ACAACAAC
104473 ACAACAAC
1 ACAACAAC
104481 ACAACAAC
1 ACAACAAC
104489 AC
1 AC
104491 GTATATGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.59, C:0.38, G:0.03, T:0.00
Consensus pattern (8 bp):
ACAACAAC
Found at i:104547 original size:37 final size:37
Alignment explanation
Indices: 104506--104577 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
104496 TGTATGAAGT
104506 TTATCTTTAATAACTCAATAAGTGTATGTTTAAAAAC
1 TTATCTTTAATAACTCAATAAGTGTATGTTTAAAAAC
* * *
104543 TTATCTTTAATAATTTAATGAGTGTATGTTTAAAA
1 TTATCTTTAATAACTCAATAAGTGTATGTTTAAAA
104578 TATTATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (37 bp):
TTATCTTTAATAACTCAATAAGTGTATGTTTAAAAAC
Found at i:110477 original size:24 final size:24
Alignment explanation
Indices: 110445--110492 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
110435 AGAAACTCTC
*
110445 GCTCATACTCTATCACTGAGCGAT
1 GCTCATACTCCATCACTGAGCGAT
110469 GCTCATACTCCATCACTGAGCGAT
1 GCTCATACTCCATCACTGAGCGAT
110493 CTCTCTGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (24 bp):
GCTCATACTCCATCACTGAGCGAT
Found at i:114859 original size:168 final size:168
Alignment explanation
Indices: 114581--114895 Score: 612
Period size: 168 Copynumber: 1.9 Consensus size: 168
114571 ATCACTTAAT
*
114581 AATTTTTTAACTCATCAATAGAACCTGTAGATGCCTAGGTTATTGAGAAAATTTTATGATTTCCC
1 AATTTTTCAACTCATCAATAGAACCTGTAGATGCCTAGGTTATTGAGAAAATTTTATGATTTCCC
114646 ATATATCTACTTGACCTTTAGCAACATTTAGTAATTTTATATTATTGAGCTTTCCTAAAGCTCAT
66 ATATATCTACTTGACCTTTAGCAACATTTAGTAATTTTATATTATTGAGCTTTCCTAAAGCTCAT
114711 TTTATTATTTATTATTTATTATTTCAGATTAAAAAGGA
131 TTTATTATTTATTATTTATTATTTCAGATTAAAAAGGA
114749 AATTTTTCAACTCATCAATAGAACCTGTAGATGCCTAGGTTATTGAGAAAATTTTATGATTTCCC
1 AATTTTTCAACTCATCAATAGAACCTGTAGATGCCTAGGTTATTGAGAAAATTTTATGATTTCCC
*
114814 ATATATCTACTTGACCTTTAGCAGCATTTAGTAATTTTATATTATTGAGCTTTCCTAAAGCTCAT
66 ATATATCTACTTGACCTTTAGCAACATTTAGTAATTTTATATTATTGAGCTTTCCTAAAGCTCAT
114879 TTTATTATTTATTATTT
131 TTTATTATTTATTATTT
114896 CAGATTAAAA
Statistics
Matches: 145, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 145 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (168 bp):
AATTTTTCAACTCATCAATAGAACCTGTAGATGCCTAGGTTATTGAGAAAATTTTATGATTTCCC
ATATATCTACTTGACCTTTAGCAACATTTAGTAATTTTATATTATTGAGCTTTCCTAAAGCTCAT
TTTATTATTTATTATTTATTATTTCAGATTAAAAAGGA
Found at i:115893 original size:2 final size:2
Alignment explanation
Indices: 115888--115915 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
115878 TTTTAAAAAT
115888 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
115916 ATTATTTAAA
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):
TA
Found at i:116285 original size:2 final size:2
Alignment explanation
Indices: 116278--116364 Score: 55
Period size: 2 Copynumber: 47.5 Consensus size: 2
116268 TAAAAATAAT
* * *
116278 TA TA TA TA TA TA TA -A TA T- TA -A TA AA T- TA -A TT TA AA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
116314 TA TA TA TA TA TA TA -A TA TT TA TA TA TT TA -A TT TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
116354 TA TA TA TA TA T
1 TA TA TA TA TA T
116365 CGGTCCGATA
Statistics
Matches: 63, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
1 8 0.13
2 55 0.87
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:116315 original size:36 final size:37
Alignment explanation
Indices: 116275--116364 Score: 146
Period size: 36 Copynumber: 2.4 Consensus size: 37
116265 TATTAAAAAT
116275 AATTATATATATATATAATATTAATA-AATTAATTTA
1 AATTATATATATATATAATATTAATATAATTAATTTA
* *
116311 AATTATATATATATATAATATTTATATATTTAATTTA
1 AATTATATATATATATAATATTAATATAATTAATTTA
116348 AATATATATATATATAT
1 AAT-TATATATATATAT
116365 CGGTCCGATA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
36 25 0.50
37 12 0.24
38 13 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (37 bp):
AATTATATATATATATAATATTAATATAATTAATTTA
Found at i:118396 original size:32 final size:32
Alignment explanation
Indices: 118360--118426 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
118350 GGATTGATTG
* *
118360 TTTTTGGATTGGGTCAATATCGAATTAGTCGA
1 TTTTTGCATTGGGTCAATATCAAATTAGTCGA
* *
118392 TTTTTTCATTGGGTTAATATCAAATTAGTCGA
1 TTTTTGCATTGGGTCAATATCAAATTAGTCGA
118424 TTT
1 TTT
118427 CTAGATCGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.09, G:0.19, T:0.46
Consensus pattern (32 bp):
TTTTTGCATTGGGTCAATATCAAATTAGTCGA
Found at i:118441 original size:32 final size:32
Alignment explanation
Indices: 118375--118445 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
118365 GGATTGGGTC
* * * * *
118375 AATATCGAATTAGTCGATTTTTTCATTGGGTT
1 AATATCAAATTAGTCGATTTCTACATCGGATT
*
118407 AATATCAAATTAGTCGATTTCTAGATCGGATT
1 AATATCAAATTAGTCGATTTCTACATCGGATT
118439 AATATCA
1 AATATCA
118446 TATTGGTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.41
Consensus pattern (32 bp):
AATATCAAATTAGTCGATTTCTACATCGGATT
Found at i:121777 original size:18 final size:19
Alignment explanation
Indices: 121754--121793 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
121744 CAGCAGCTCA
*
121754 TAACTGCTC-TTAACAAGC
1 TAACTGCTCTTTAACAAAC
*
121772 TAACTGGTCTTTAACAAAC
1 TAACTGCTCTTTAACAAAC
121791 TAA
1 TAA
121794 TAGTTCCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.30
Consensus pattern (19 bp):
TAACTGCTCTTTAACAAAC
Found at i:123788 original size:63 final size:63
Alignment explanation
Indices: 123689--123810 Score: 172
Period size: 63 Copynumber: 1.9 Consensus size: 63
123679 AACCATCTCG
* * ***
123689 ACTTCATTATGGATTTCTGCATTACCAACTTCTTCATGCACGGTGGTGGTATTTGGTAACTCT
1 ACTTCATTATAGATTTCTGCATCACCAACTTCTTCATGCACGACAGTGGTATTTGGTAACTCT
* * *
123752 ACTTCATTATATATTTCTGCATCACCATCTTCTTCATGTACGACAGTGGTATTTGGTAA
1 ACTTCATTATAGATTTCTGCATCACCAACTTCTTCATGCACGACAGTGGTATTTGGTAA
123811 GTGACTTGGT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.40
Consensus pattern (63 bp):
ACTTCATTATAGATTTCTGCATCACCAACTTCTTCATGCACGACAGTGGTATTTGGTAACTCT
Found at i:130466 original size:21 final size:21
Alignment explanation
Indices: 130415--130473 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
130405 TTTGGTGCAG
* *
130415 AGGGAATCGA-TACCCCCATA
1 AGGGAATCGATTCCCCCCACA
* *
130435 AGGCAACCGATTCCCCCCACA
1 AGGGAATCGATTCCCCCCACA
* *
130456 GGGGAATCGATACCCCCC
1 AGGGAATCGATTCCCCCC
130474 TGGGGTACTG
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
20 8 0.27
21 22 0.73
ACGTcount: A:0.29, C:0.39, G:0.20, T:0.12
Consensus pattern (21 bp):
AGGGAATCGATTCCCCCCACA
Found at i:131198 original size:15 final size:15
Alignment explanation
Indices: 131178--131217 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
131168 CAAATCCTCC
*
131178 TCCTATTCTTGAAAT
1 TCCTATTCCTGAAAT
131193 TCCTATTCCTGAAAT
1 TCCTATTCCTGAAAT
*
131208 TCCAATTCCT
1 TCCTATTCCT
131218 AATCCTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.25, C:0.28, G:0.05, T:0.42
Consensus pattern (15 bp):
TCCTATTCCTGAAAT
Found at i:132782 original size:23 final size:23
Alignment explanation
Indices: 132749--132794 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
132739 TTAAGTGTTT
*
132749 TAAATGGGAGAAGTATTAAAGTA
1 TAAATGAGAGAAGTATTAAAGTA
*
132772 TAAATGAGAGAAGTGTTAAAGTA
1 TAAATGAGAGAAGTATTAAAGTA
132795 AGGGGGAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (23 bp):
TAAATGAGAGAAGTATTAAAGTA
Found at i:132829 original size:26 final size:26
Alignment explanation
Indices: 132793--132845 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
132783 AGTGTTAAAG
132793 TAAGGGGGAGTAATTTCAAAACTTGA
1 TAAGGGGGAGTAATTTCAAAACTTGA
132819 TAAGGGGGAGTAATTTCAAAACTTGA
1 TAAGGGGGAGTAATTTCAAAACTTGA
132845 T
1 T
132846 TTCAAAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (26 bp):
TAAGGGGGAGTAATTTCAAAACTTGA
Found at i:135438 original size:18 final size:19
Alignment explanation
Indices: 135415--135455 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
135405 CAGCAGCTCA
*
135415 TAACTGCTC-TTAACAAGC
1 TAACTGCTCTTTAACAAAC
*
135433 TAACTGGTCTTTAACAAAC
1 TAACTGCTCTTTAACAAAC
135452 TAAC
1 TAAC
135456 AGTTCCTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (19 bp):
TAACTGCTCTTTAACAAAC
Found at i:135465 original size:19 final size:19
Alignment explanation
Indices: 135423--135466 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
135413 CATAACTGCT
* *
135423 CTTAACAAGCTAACTGGTC
1 CTTAACAAACTAACAGGTC
* *
135442 TTTAACAAACTAACAGTTC
1 CTTAACAAACTAACAGGTC
135461 CTTAAC
1 CTTAAC
135467 TACCATTTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (19 bp):
CTTAACAAACTAACAGGTC
Found at i:135820 original size:29 final size:30
Alignment explanation
Indices: 135763--135820 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
135753 AAAGTGACCA
* *
135763 AAATAAGAAGAATTTGAAAGTTCAATGAGC
1 AAATAAGAAGAATTTAAAAGTACAATGAGC
* *
135793 AAATTAGAA-AATTTAAAAGTACAGTGAG
1 AAATAAGAAGAATTTAAAAGTACAATGAG
135821 TAAAATAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.52, C:0.05, G:0.19, T:0.24
Consensus pattern (30 bp):
AAATAAGAAGAATTTAAAAGTACAATGAGC
Found at i:136862 original size:112 final size:112
Alignment explanation
Indices: 136648--136863 Score: 378
Period size: 112 Copynumber: 1.9 Consensus size: 112
136638 TAAAAATAAA
* *
136648 TCATTTATTCACTTTTACTCATTTGTCGGGTTAAAAATTAGGTCAAGGTTCGATTTGAATCAAAT
1 TCATTCATTCACTTTTACTCATTTGTCGAGTTAAAAATTAGGTCAAGGTTCGATTTGAATCAAAT
* * * *
136713 TTAAGTAAATTAAATCCGATTTATTTTTGGTTTGGGTTGCTTTCGAT
66 TTAAGTAAATTAAATCCGAATTAGTTTTAGTTCGGGTTGCTTTCGAT
136760 TCATTCATTCACTTTTACTCATTTGTCGAGTTAAAAATTAGGTCAAGGTTCGATTTGAATCAAAT
1 TCATTCATTCACTTTTACTCATTTGTCGAGTTAAAAATTAGGTCAAGGTTCGATTTGAATCAAAT
136825 TTAAGTAAATTAAATCCGAATTAGTTTTAGTTCGGGTTG
66 TTAAGTAAATTAAATCCGAATTAGTTTTAGTTCGGGTTG
136864 TTTTTCGTTC
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 98 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.43
Consensus pattern (112 bp):
TCATTCATTCACTTTTACTCATTTGTCGAGTTAAAAATTAGGTCAAGGTTCGATTTGAATCAAAT
TTAAGTAAATTAAATCCGAATTAGTTTTAGTTCGGGTTGCTTTCGAT
Found at i:136873 original size:16 final size:16
Alignment explanation
Indices: 136849--136883 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
136839 TCCGAATTAG
*
136849 TTTTAGTTCGGGTTGT
1 TTTTAGTTCGGGTTAT
*
136865 TTTTCGTTCGGGTTAT
1 TTTTAGTTCGGGTTAT
136881 TTT
1 TTT
136884 CGATTCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.09, G:0.26, T:0.60
Consensus pattern (16 bp):
TTTTAGTTCGGGTTAT
Found at i:136917 original size:32 final size:32
Alignment explanation
Indices: 136861--136938 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
136851 TTAGTTCGGG
* * *
136861 TTGTTTTTCGTTCGGGTTATTTTCGATTCAAA
1 TTGTTTTTCGTTTGAGTTAATTTCGATTCAAA
* *
136893 TTGTTTTTGGTTTGAGTTAATTTCGATTCTAA
1 TTGTTTTTCGTTTGAGTTAATTTCGATTCAAA
* *
136925 TTATTTTTTGTTTG
1 TTGTTTTTCGTTTG
136939 GGTCAAACTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.15, C:0.08, G:0.18, T:0.59
Consensus pattern (32 bp):
TTGTTTTTCGTTTGAGTTAATTTCGATTCAAA
Found at i:138936 original size:24 final size:24
Alignment explanation
Indices: 138890--138936 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
138880 TAAAACGAAG
* **
138890 ATAAAGAATAAAAATAAGTAATAA
1 ATAAAAAATAAAAATAAACAATAA
138914 ATAAAAAATAAAAATAAACAATA
1 ATAAAAAATAAAAATAAACAATA
138937 TTAACATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.19
Consensus pattern (24 bp):
ATAAAAAATAAAAATAAACAATAA
Found at i:139099 original size:2 final size:2
Alignment explanation
Indices: 139087--139160 Score: 141
Period size: 2 Copynumber: 37.5 Consensus size: 2
139077 TCAAAAACTC
139087 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
139128 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 T
139161 GTTTTCAAAA
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 70 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:139202 original size:39 final size:39
Alignment explanation
Indices: 139144--139320 Score: 235
Period size: 39 Copynumber: 4.7 Consensus size: 39
139134 TATATATATA
139144 TATATATATATATATATGTTTTCAAAATGTTTTCAAAAAC
1 TATATAT-TATATATATGTTTTCAAAATGTTTTCAAAAAC
*
139184 TATATATTATATACATGTTTTCAAAAATGTTTT--AAAAC
1 TATATATTATATATATGTTTTC-AAAATGTTTTCAAAAAC
*
139222 --TAT-GTAT-TATATGTTTTCAAAATGTTTTCAAAAAC
1 TATATATTATATATATGTTTTCAAAATGTTTTCAAAAAC
*
139257 TATATATTATATATATTTTTTCAAAATGTTTTCAAAAAC
1 TATATATTATATATATGTTTTCAAAATGTTTTCAAAAAC
*
139296 TATATTATT-TATAT-TTTTTTCAAAA
1 TATA-TATTATATATATGTTTTCAAAA
139321 ATCGATTTAA
Statistics
Matches: 124, Mismatches: 5, Indels: 18
0.84 0.03 0.12
Matches are distributed among these distances:
33 10 0.08
34 10 0.08
35 8 0.06
36 3 0.02
37 3 0.02
38 19 0.15
39 50 0.40
40 21 0.17
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (39 bp):
TATATATTATATATATGTTTTCAAAATGTTTTCAAAAAC
Found at i:139233 original size:73 final size:73
Alignment explanation
Indices: 139156--139298 Score: 243
Period size: 73 Copynumber: 1.9 Consensus size: 73
139146 TATATATATA
139156 TATATGTTTTCAAAATGTTTTCAAAAACTATATATTATATACATGTTTTCAAAAATGTTTT-AAA
1 TATATGTTTTCAAAATGTTTTCAAAAACTATATATTATATACATGTTTTC-AAAATGTTTTAAAA
139220 ACTATGTAT
65 ACTATGTAT
* *
139229 TATATGTTTTCAAAATGTTTTCAAAAACTATATATTATATATATTTTTTCAAAATGTTTTCAAAA
1 TATATGTTTTCAAAATGTTTTCAAAAACTATATATTATATACATGTTTTCAAAATGTTTT-AAAA
139294 ACTAT
65 ACTAT
139299 ATTATTTATA
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
72 10 0.15
73 48 0.73
74 8 0.12
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (73 bp):
TATATGTTTTCAAAATGTTTTCAAAAACTATATATTATATACATGTTTTCAAAATGTTTTAAAAA
CTATGTAT
Found at i:140681 original size:36 final size:36
Alignment explanation
Indices: 140623--140705 Score: 143
Period size: 36 Copynumber: 2.4 Consensus size: 36
140613 ATTATTGTGA
140623 ATATTTT-ATTT-ATTTAATTTTTTAGTATTAGTTT
1 ATATTTTAATTTGATTTAATTTTTTAGTATTAGTTT
*
140657 ATATTTTAATTTGATTTATTTTTTTAGTATTAGTTT
1 ATATTTTAATTTGATTTAATTTTTTAGTATTAGTTT
140693 ATATTTTAATTTG
1 ATATTTTAATTTG
140706 TATACTATTT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
34 7 0.15
35 4 0.09
36 35 0.76
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (36 bp):
ATATTTTAATTTGATTTAATTTTTTAGTATTAGTTT
Found at i:140725 original size:36 final size:35
Alignment explanation
Indices: 140623--140725 Score: 106
Period size: 36 Copynumber: 2.9 Consensus size: 35
140613 ATTATTGTGA
*
140623 ATATTTT-ATTT-ATTTAATTT-TTTAGTATTAGTTT
1 ATATTTTAATTTGATCT-ATTTATTTAG-ATTAGTTT
* *
140657 ATATTTTAATTTGATTTATTTTTTTAGTATTAGTTT
1 ATATTTTAATTTGATCTATTTATTTAG-ATTAGTTT
140693 ATATTTTAATTTGTATACTATTTATTTA-ATTAG
1 ATATTTTAATTTG-AT-CTATTTATTTAGATTAG
140726 GGGAATGACC
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
34 7 0.11
35 8 0.13
36 36 0.58
37 2 0.03
38 9 0.15
ACGTcount: A:0.28, C:0.01, G:0.07, T:0.64
Consensus pattern (35 bp):
ATATTTTAATTTGATCTATTTATTTAGATTAGTTT
Found at i:155198 original size:42 final size:42
Alignment explanation
Indices: 155041--155445 Score: 513
Period size: 42 Copynumber: 9.8 Consensus size: 42
155031 CAAAATACTA
* * *
155041 TACTTTAGTGGCGTTTTTATA-AAAACGCCGCTAAAGA-ATCG
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACA-CG
* * * *
155082 TAATGTAGTGGCGTTTTTATA-CAAACGCCGCTATAAACTA-G
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGAC-ACG
* * *
155123 TATTTTAGTGGCGTTTTTATA-CAAACGCTGCTATAGACACG
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACACG
* * * *
155164 TACTTTTGTGGCGTTTTAATACCAAACGACGCTATAGACTCA
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACACG
*
155206 TACTTTAGTGGCATTTT--TACACAAACGCCGCTATAGACACG
1 TACTTTAGTGGCGTTTTAATAC-CAAACGCCGCTATAGACACG
*
155247 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACG
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACACG
* **
155289 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGATTCG
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACACG
155331 TACTTTAGTGGCGTTTT--TACACAAACGCCGCTATAGACACG
1 TACTTTAGTGGCGTTTTAATAC-CAAACGCCGCTATAGACACG
* * *
155372 TACTTTTGTGGCGTTTTAATAACAAACGCCGCTATAGACTCG
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACACG
155414 TACTTTAGTGGCGTTTTAATACCAAACGCCGC
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGC
155446 AATTATCATA
Statistics
Matches: 321, Mismatches: 33, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
40 7 0.02
41 152 0.47
42 156 0.49
43 6 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (42 bp):
TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACACG
Found at i:155230 original size:83 final size:83
Alignment explanation
Indices: 155040--155445 Score: 495
Period size: 83 Copynumber: 4.9 Consensus size: 83
155030 GCAAAATACT
* * * * * *
155040 ATACTTTAGTGGCGTTTTTATAAAAACGCCGCTAAAGA-ATCGTAATGTAGTGGCGTTTTTATA-
1 ATACTTTAGTGGCGTTTTTACACAAACGCCGCTATAGACA-CGTACTTTAGTGGCGTTTTAATAC
155103 CAAACGCCGCTATA-A-AC
65 CAAACGCCGCTATAGACAC
* * * *
155120 TAGTATTTTAGTGGCGTTTTTATACAAACGCTGCTATAGACACGTACTTTTGTGGCGTTTTAATA
1 -A-TACTTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATA
* *
155185 CCAAACGACGCTATAGACTC
64 CCAAACGCCGCTATAGACAC
* *
155205 ATACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
1 ATACTTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATACC
155270 AAACGCCGCTATAGACAC
66 AAACGCCGCTATAGACAC
* * **
155288 GTACTTTTGTGGCGTTTTAATAC-CAAACGCCGCTATAGATTCGTACTTTAGTGGCGTTTT--TA
1 ATACTTTAGTGGCGTTTT--TACACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATA
155350 CACAAACGCCGCTATAGACAC
64 C-CAAACGCCGCTATAGACAC
* * *
155371 GTACTTTTGTGGCGTTTTAATA-ACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTAATA
1 ATACTTTAGTGGCGTTTT--TACACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATA
155435 CCAAACGCCGC
64 CCAAACGCCGC
155446 AATTATCATA
Statistics
Matches: 291, Mismatches: 23, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
81 1 0.00
82 55 0.19
83 182 0.63
84 46 0.16
85 7 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (83 bp):
ATACTTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATACC
AAACGCCGCTATAGACAC
Found at i:155315 original size:125 final size:124
Alignment explanation
Indices: 155041--155445 Score: 600
Period size: 125 Copynumber: 3.3 Consensus size: 124
155031 CAAAATACTA
* * * * * *
155041 TACTTTAGTGGCGTTTTTATA-AAAACGCCGCTAAAGAATCGTAATGTAGTGGCGTTTTTATACA
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTACACA
* * *
155105 AACGCCGCTATAAACTA-GTA-TTTTAGTGGCGTTTTTATACAAACGCTGCTATAGACACG
66 AACGCCGCTATAGAC-ACGTACTTTT-GTGGCGTTTTAATACAAACGCCGCTATAGACACG
* * * * *
155164 TACTTTTGTGGCGTTTTAATACCAAACGACGCTATAGACTCATACTTTAGTGGCATTTTTACACA
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTACACA
155229 AACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACG
66 AACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATA-CAAACGCCGCTATAGACACG
* *
155289 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGATTCGTACTTTAGTGGCGTTTTTACACA
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTACACA
*
155354 AACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATAACAAACGCCGCTATAGACTCG
66 AACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAAT-ACAAACGCCGCTATAGACACG
155414 TACTTTAGTGGCGTTTTAATACCAAACGCCGC
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGC
155446 AATTATCATA
Statistics
Matches: 257, Mismatches: 20, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
123 20 0.08
124 64 0.25
125 172 0.67
126 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (124 bp):
TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTACACA
AACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACAAACGCCGCTATAGACACG
Found at i:160235 original size:21 final size:21
Alignment explanation
Indices: 160193--160251 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
160183 TGATTTATTA
**
160193 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
160214 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
* *
160235 TTATCGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
160252 ATTGGAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:160451 original size:43 final size:43
Alignment explanation
Indices: 160404--160628 Score: 274
Period size: 43 Copynumber: 5.3 Consensus size: 43
160394 ACCAGATCTT
* * *
160404 TTGCGGTGTTTGTGGGAAAAACGCCACTAAATATCAAGACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
*
160447 TTGCGGCATTTGT-GGACAAAACGCCGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTGGGA-AAAACGCCGCTAAATATCAACACCTA
* * *
160490 TTGCGGCGTTTGTGGAAAAAACGCCGCTAAATCTCAACACATA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
* * *
160533 TTGCGGCGTTTGTTGGAAAAA-GCCACCAAATATCAACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
* * * ***
160575 TTGCGGCGTTTGTTGGACAAACGCCGCTATATATCGTTACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
*
160618 TTGCGGTGTTT
1 TTGCGGCGTTT
160629 TTTGTTACCA
Statistics
Matches: 157, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
42 40 0.25
43 115 0.73
44 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (43 bp):
TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
Found at i:160620 original size:85 final size:86
Alignment explanation
Indices: 160404--160628 Score: 276
Period size: 85 Copynumber: 2.6 Consensus size: 86
160394 ACCAGATCTT
* * * * *
160404 TTGCGGTGTTTGTGGGAAAAACGCCACTAAATATCAAGACCTATTGCGGCATTTGTGGACAAAAC
1 TTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTGGACAAAAC
* *
160469 GCCGCTAAATATCAACACCTA
66 GCCACCAAATATCAACACCTA
* *
160490 TTGCGGCGTTTG-TGGAAAAAACGCCGCTAAATCTCAACACATATTGCGGCGTTTGTTGGA-AAA
1 TTGCGGCGTTTGTTGG-AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTG-TGGACAAA
160553 A-GCCACCAAATATCAACACCTA
64 ACGCCACCAAATATCAACACCTA
* * *** *
160575 TTGCGGCGTTTGTTGGACAAACGCCGCTATATATCGTTACCTATTGCGGTGTTT
1 TTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
160629 TTTGTTACCA
Statistics
Matches: 119, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
85 63 0.53
86 52 0.44
87 4 0.03
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (86 bp):
TTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTGGACAAAAC
GCCACCAAATATCAACACCTA
Found at i:161592 original size:35 final size:35
Alignment explanation
Indices: 161545--161614 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
161535 ATGAAGGGGG
*
161545 GGGGGGGGAATTGTTGAGTTATTCTCTCTTTGGAA
1 GGGGGGGAAATTGTTGAGTTATTCTCTCTTTGGAA
161580 GGGGGGGAAATTGTTGAGTTATTCTCTCTTTGGAA
1 GGGGGGGAAATTGTTGAGTTATTCTCTCTTTGGAA
161615 TACAAATTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.19, C:0.09, G:0.36, T:0.37
Consensus pattern (35 bp):
GGGGGGGAAATTGTTGAGTTATTCTCTCTTTGGAA
Found at i:166325 original size:16 final size:17
Alignment explanation
Indices: 166298--166336 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
166288 CAAATTCTCT
166298 CTCAAACACTCTCAAAG
1 CTCAAACACTCTCAAAG
* *
166315 C-CAAACCCTCTTAAAG
1 CTCAAACACTCTCAAAG
166331 CTCAAA
1 CTCAAA
166337 TCTTGTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.41, C:0.36, G:0.05, T:0.18
Consensus pattern (17 bp):
CTCAAACACTCTCAAAG
Found at i:168666 original size:17 final size:16
Alignment explanation
Indices: 168644--168691 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
168634 ATTATTTACC
168644 TTTTATTACTTAATTT
1 TTTTATTACTTAATTT
** **
168660 ATTTTATTTTTTAAAAT
1 -TTTTATTACTTAATTT
168677 TTTTATTACTTAATT
1 TTTTATTACTTAATT
168692 GTTCAAATAT
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTATTACTTAATTT
Found at i:172047 original size:47 final size:47
Alignment explanation
Indices: 171987--172194 Score: 307
Period size: 47 Copynumber: 4.5 Consensus size: 47
171977 CTTACCATTA
*
171987 TCCATAAAGCTCGTAAGCTTATTTTACCAAAATATTTACCATTTAAAT
1 TCCAT-AAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAAT
172035 TCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAAT
1 TCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAAT
* * * *
172082 TCCATAAGCTTGCAAGCTTATTTTATCAATATACTTACCATTTAAAT
1 TCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAAT
* * *
172129 TCCATAAGCTCGTAAGCTTATTTTATCAATATACTTGCCA-TT--AT
1 TCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAAT
172173 T-CATAAGCTCGTAAGCTTATTT
1 TCCATAAGCTCGTAAGCTTATTT
172195 GCATACTTAC
Statistics
Matches: 152, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
43 21 0.14
44 3 0.02
46 2 0.01
47 121 0.80
48 5 0.03
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.39
Consensus pattern (47 bp):
TCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAAT
Found at i:174017 original size:30 final size:30
Alignment explanation
Indices: 173983--174040 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
173973 TTGGTCCATG
*
173983 AACTTTTCAAAATTTAT-ACTTTGGTCACCA
1 AACTTTACAAAATTTATAAC-TTGGTCACCA
*
174013 AACTTTACCAAATTTATAACTTGGTCAC
1 AACTTTACAAAATTTATAACTTGGTCAC
174041 TAAATACATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTACAAAATTTATAACTTGGTCACCA
Found at i:174290 original size:21 final size:18
Alignment explanation
Indices: 174265--174303 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 18
174255 TTTTGTCCAA
174265 ATAATCATATATAAAATAAAT
1 ATAAT-ATAT-TAAAA-AAAT
174286 ATAATATATTAAAAAAAT
1 ATAATATATTAAAAAAAT
174304 TTACCTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 4 0.22
21 5 0.28
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAATATATTAAAAAAAT
Found at i:184226 original size:32 final size:32
Alignment explanation
Indices: 184185--184246 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
184175 AGGGTCAAGG
* *
184185 GTTACCTATGTCTTTCGAGACATATGGACAGT
1 GTTACCTATGTCCTTCGAGACACATGGACAGT
*
184217 GTTACCTATGTCCTTCGGGACACATGGACA
1 GTTACCTATGTCCTTCGAGACACATGGACA
184247 ATTACCAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (32 bp):
GTTACCTATGTCCTTCGAGACACATGGACAGT
Found at i:188717 original size:32 final size:32
Alignment explanation
Indices: 188681--188783 Score: 97
Period size: 32 Copynumber: 3.2 Consensus size: 32
188671 AGAGTCGAGG
*
188681 GTTACCTATATCTTTCAAGACATATGGACAGT
1 GTTACCTATGTCTTTCAAGACATATGGACAGT
* ** *
188713 GTTACCTATGTCCTTCGGGACATATAGACAG-
1 GTTACCTATGTCTTTCAAGACATATGGACAGT
*
188744 GATTACCTATGT-TCT-AAGGAACATATGGACAGT
1 G-TTACCTATGTCTTTCAA-G-ACATATGGACAGT
188777 -TTACCTA
1 GTTACCTA
188784 GGTTCTTTGG
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
31 10 0.18
32 47 0.82
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (32 bp):
GTTACCTATGTCTTTCAAGACATATGGACAGT
Found at i:188789 original size:31 final size:31
Alignment explanation
Indices: 188699--188808 Score: 121
Period size: 32 Copynumber: 3.5 Consensus size: 31
188689 TATCTTTCAA
* *
188699 GACATATGGACAGTGTTACCTATGTCCTTCGG
1 GACATATGGACAGT-TTACCTATGTTCTTAGG
* * *
188731 GACATATAGACAGGATTACCTATGTTCTAAGG
1 GACATATGGACA-GTTTACCTATGTTCTTAGG
* * *
188763 AACATATGGACAGTTTACCTAGGTTCTTTGG
1 GACATATGGACAGTTTACCTATGTTCTTAGG
*
188794 GACCTATGGACAGTT
1 GACATATGGACAGTT
188809 GCCGAGGTTC
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
31 28 0.44
32 35 0.55
33 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (31 bp):
GACATATGGACAGTTTACCTATGTTCTTAGG
Found at i:193473 original size:14 final size:14
Alignment explanation
Indices: 193454--193483 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
193444 GTAATTGGTT
*
193454 TTCTGGAAATTGAA
1 TTCTGGAAAATGAA
193468 TTCTGGAAAATGAA
1 TTCTGGAAAATGAA
193482 TT
1 TT
193484 ACATTTCTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (14 bp):
TTCTGGAAAATGAA
Found at i:193812 original size:23 final size:23
Alignment explanation
Indices: 193763--193813 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
193753 GTGTTATATT
**
193763 ATATTTTAAAAATATTAATTATT
1 ATATTTTAAAAATATTAATTAAA
* * *
193786 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
193809 ATATT
1 ATATT
193814 ATTACATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:193867 original size:27 final size:26
Alignment explanation
Indices: 193832--193920 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 26
193822 ATTATATTAA
193832 TATTAAATATATAAATAATATT-ATTC
1 TATT-AATATATAAATAATATTAATTC
*
193858 ATTATTAATA-ATTTAATAATATTAATTC
1 --TATTAATATA-TAAATAATATTAATTC
* * * *
193886 TATGAAATTTATAAATAATATAAATTT
1 TAT-TAATATATAAATAATATTAATTC
193913 TATTAATA
1 TATTAATA
193921 ATTTATTATA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
26 7 0.14
27 33 0.67
28 9 0.18
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (26 bp):
TATTAATATATAAATAATATTAATTC
Found at i:193869 original size:19 final size:19
Alignment explanation
Indices: 193801--193869 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
193791 TTAAATATCT
193801 TTATTAA-AATATTATTACA
1 TTATTAATAATATTATT-CA
*
193820 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTCA
*
193839 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTCA
193859 TTATTAATAAT
1 TTATTAATAAT
193870 TTAATAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
18 8 0.20
19 18 0.45
20 7 0.17
22 7 0.17
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTCA
Found at i:193875 original size:8 final size:9
Alignment explanation
Indices: 193802--193883 Score: 53
Period size: 9 Copynumber: 8.8 Consensus size: 9
193792 TAAATATCTT
193802 TATTAA-AA
1 TATTAATAA
*
193810 TATTATTACA
1 TATTAATA-A
193820 TTATTATATTAA
1 -TATTA-A-TAA
193832 TATTAA-ATA
1 TATTAATA-A
*
193841 TATAAATAA
1 TATTAATAA
* *
193850 TATTATTCAT
1 TATTAAT-AA
193860 TATTAATAA
1 TATTAATAA
193869 T-TTAATAA
1 TATTAATAA
193877 TATTAAT
1 TATTAAT
193884 TCTATGAAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 17
0.70 0.10 0.21
Matches are distributed among these distances:
8 14 0.25
9 20 0.35
10 10 0.18
11 10 0.18
12 1 0.02
13 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (9 bp):
TATTAATAA
Found at i:193933 original size:27 final size:27
Alignment explanation
Indices: 193859--193933 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 27
193849 ATATTATTCA
* *
193859 TTATTAATAATTTAATA-ATATTAATT
1 TTATTAATAATTTATTATATATAAATT
* * *
193885 CTA-TGA-AATTTATAAATAATATAAATT
1 TTATTAATAATTTAT-TAT-ATATAAATT
193912 TTATTAATAATTTATTATATAT
1 TTATTAATAATTTATTATATAT
193934 TATTAAAATA
Statistics
Matches: 36, Mismatches: 8, Indels: 9
0.68 0.15 0.17
Matches are distributed among these distances:
24 6 0.17
25 3 0.08
26 2 0.06
27 14 0.39
28 4 0.11
29 7 0.19
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
TTATTAATAATTTATTATATATAAATT
Found at i:193993 original size:20 final size:19
Alignment explanation
Indices: 193946--194009 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
193936 TTAAAATAAA
* *
193946 ATATAATAACTTATTATTATA
1 ATATATTAA-TTATT-TTATT
*
193967 ATATATTGATTATTTTATT
1 ATATATTAATTATTTTATT
* *
193986 ATAGTATTAAGTATATTATT
1 ATA-TATTAATTATTTTATT
194006 ATAT
1 ATAT
194010 TAAATATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 8 0.22
20 21 0.58
21 7 0.19
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (19 bp):
ATATATTAATTATTTTATT
Found at i:194855 original size:15 final size:15
Alignment explanation
Indices: 194835--194866 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
194825 AATTTTGATA
*
194835 ATATTATATTAATAT
1 ATATTATAATAATAT
194850 ATATTATAATAATAT
1 ATATTATAATAATAT
194865 AT
1 AT
194867 GATATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTATAATAATAT
Found at i:194875 original size:23 final size:23
Alignment explanation
Indices: 194832--194877 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
194822 TATAATTTTG
* *
194832 ATAATATTATATTAATATATATT
1 ATAATAATATATGAATATATATT
194855 ATAATAATATATG-ATATTATATT
1 ATAATAATATATGAATA-TATATT
194878 TTTAAATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATAATAATATATGAATATATATT
Found at i:196932 original size:18 final size:18
Alignment explanation
Indices: 196909--196943 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
196899 GTTTGATAGT
*
196909 TGTAATTGATTTTCCTAA
1 TGTAATTCATTTTCCTAA
196927 TGTAATTCATTTTCCTA
1 TGTAATTCATTTTCCTA
196944 GTTCCTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (18 bp):
TGTAATTCATTTTCCTAA
Found at i:199112 original size:42 final size:42
Alignment explanation
Indices: 199046--199154 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 42
199036 TTCTAAGGGT
* * * ** *
199046 GTGTTTGATAGCTGGAAAAT-GTTTTTCGGAAAATGTTTTCCG
1 GTGTTTGATAGCT-GTAATTGGTTTTACGGAAAACATTTTCCA
* **
199088 GTGTTTGATAGCTGTAATTGGTTTTACGTAAAACATTTTTTA
1 GTGTTTGATAGCTGTAATTGGTTTTACGGAAAACATTTTCCA
* *
199130 GTGTTTGATAGTTGTAATTGATTTT
1 GTGTTTGATAGCTGTAATTGGTTTT
199155 CCTAATGTAA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 4 0.07
42 51 0.93
ACGTcount: A:0.24, C:0.06, G:0.23, T:0.47
Consensus pattern (42 bp):
GTGTTTGATAGCTGTAATTGGTTTTACGGAAAACATTTTCCA
Found at i:199165 original size:18 final size:18
Alignment explanation
Indices: 199142--199176 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
199132 GTTTGATAGT
*
199142 TGTAATTGATTTTCCTAA
1 TGTAATTCATTTTCCTAA
199160 TGTAATTCATTTTCCTA
1 TGTAATTCATTTTCCTA
199177 GTTCCTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (18 bp):
TGTAATTCATTTTCCTAA
Found at i:199341 original size:13 final size:13
Alignment explanation
Indices: 199296--199348 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
199286 ATATTACATT
199296 AATATTTTAATAAA
1 AATA-TTTAATAAA
*
199310 AATATTAATTATGAAA
1 AATATT--TAAT-AAA
199326 AATATTTAATAAA
1 AATATTTAATAAA
*
199339 AATATATAAT
1 AATATTTAAT
199349 TTTAATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 14 0.42
14 7 0.21
15 3 0.09
16 9 0.27
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
AATATTTAATAAA
Found at i:199358 original size:29 final size:29
Alignment explanation
Indices: 199295--199360 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
199285 AATATTACAT
199295 TAATATTTTAATAAAAATATTAATTATGAA
1 TAATA-TTTAATAAAAATATTAATTATGAA
* *
199325 AAATATTTAATAAAAATATATAATT-TTAA
1 TAATATTTAATAAAAATAT-TAATTATGAA
199354 TAATATT
1 TAATATT
199361 ATATTAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (29 bp):
TAATATTTAATAAAAATATTAATTATGAA
Found at i:199538 original size:19 final size:19
Alignment explanation
Indices: 199516--199554 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
199506 TAATTTATAT
199516 ATTTAATATTA-GTATAATA
1 ATTTAATATTATGT-TAATA
*
199535 ATTTAGTATTATGTTAATA
1 ATTTAATATTATGTTAATA
199554 A
1 A
199555 AATACTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (19 bp):
ATTTAATATTATGTTAATA
Found at i:201423 original size:42 final size:41
Alignment explanation
Indices: 201350--201458 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 41
201340 TTCTAAAGGT
* * **
201350 GTGTTTGATAGCTGGAAAAT-ATTTTTAGGAAAATGTTTTCTA
1 GTGTTTGATAGCT-GTAATTGA-TTTTAGGAAAACATTTTCTA
* *
201392 GTGTTTGATAGCTGTAATTGGTTTTACGGAAAACATTTTTTA
1 GTGTTTGATAGCTGTAATTGATTTTA-GGAAAACATTTTCTA
*
201434 GTGTTTGATAGTTGTAATTGATTTT
1 GTGTTTGATAGCTGTAATTGATTTT
201459 CCTAATGTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
41 9 0.16
42 48 0.84
ACGTcount: A:0.27, C:0.05, G:0.22, T:0.47
Consensus pattern (41 bp):
GTGTTTGATAGCTGTAATTGATTTTAGGAAAACATTTTCTA
Found at i:201469 original size:18 final size:18
Alignment explanation
Indices: 201446--201480 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
201436 GTTTGATAGT
*
201446 TGTAATTGATTTTCCTAA
1 TGTAATTCATTTTCCTAA
201464 TGTAATTCATTTTCCTA
1 TGTAATTCATTTTCCTA
201481 GTTCCTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (18 bp):
TGTAATTCATTTTCCTAA
Found at i:201663 original size:29 final size:29
Alignment explanation
Indices: 201600--201665 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
201590 AATATTACAT
201600 TAATATTTTAATAAAAATATTAATTATGAA
1 TAATA-TTTAATAAAAATATTAATTATGAA
* * *
201630 AAATATTTAATAAACATATATAATT-TTAA
1 TAATATTTAATAAAAATAT-TAATTATGAA
201659 TAATATT
1 TAATATT
201666 ATATTAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 22 0.71
30 9 0.29
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
TAATATTTAATAAAAATATTAATTATGAA
Found at i:201696 original size:18 final size:18
Alignment explanation
Indices: 201645--201714 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
201635 TTTAATAAAC
*
201645 ATATATAATTTTAATAATA
1 ATATATAATATT-ATAATA
* *
201664 TTATATTAATA-TATACTCA
1 ATATA-TAATATTATAAT-A
201683 A-ATATAATATTATAATA
1 ATATATAATATTATAATA
*
201700 ATATATGATATTATA
1 ATATATAATATTATA
201715 TTTTTAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
17 7 0.17
18 24 0.59
19 6 0.15
20 4 0.10
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (18 bp):
ATATATAATATTATAATA
Found at i:201851 original size:19 final size:19
Alignment explanation
Indices: 201816--201861 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
201806 AGTAATATAA
201816 TTAATATATTTAATATTA-G
1 TTAATA-ATTTAATATTATG
*
201835 TATAATAATTTAGTATTATG
1 T-TAATAATTTAATATTATG
201855 TTAATAA
1 TTAATAA
201862 AATACTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (19 bp):
TTAATAATTTAATATTATG
Found at i:204540 original size:20 final size:20
Alignment explanation
Indices: 204507--204552 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
204497 TCATGGGTAC
**
204507 CGATACTAGCCCTTCAGTAT
1 CGATACTAAACCTTCAGTAT
**
204527 CGATACTAAACCTTTGGTAT
1 CGATACTAAACCTTCAGTAT
204547 CGATAC
1 CGATAC
204553 CCACCTGCTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (20 bp):
CGATACTAAACCTTCAGTAT
Found at i:214346 original size:23 final size:23
Alignment explanation
Indices: 214272--214394 Score: 111
Period size: 24 Copynumber: 5.2 Consensus size: 23
214262 ATTTAAATGG
* *
214272 TAAACAAACACAAATGAACGAACA
1 TAAACGAACAC-AATAAACGAACA
*** * *
214296 TAAACGAATGGATGTAAACGATCA
1 TAAACGAACACA-ATAAACGAACA
*
214320 TAAACGAACACAATAAACGAACG
1 TAAACGAACACAATAAACGAACA
* *
214343 TAAACGAATACAAATGAACGAACA
1 TAAACGAACAC-AATAAACGAACA
* *
214367 TAAACAAACACAATAAATGAACA
1 TAAACGAACACAATAAACGAACA
214390 TAAAC
1 TAAAC
214395 AAATATAAAT
Statistics
Matches: 77, Mismatches: 20, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
23 34 0.44
24 43 0.56
ACGTcount: A:0.58, C:0.18, G:0.11, T:0.13
Consensus pattern (23 bp):
TAAACGAACACAATAAACGAACA
Found at i:214347 original size:47 final size:47
Alignment explanation
Indices: 214272--214404 Score: 149
Period size: 47 Copynumber: 2.8 Consensus size: 47
214262 ATTTAAATGG
* ** ** *
214272 TAAACAAACACAAATGAACGAACATAAACGAATGGATGTAAACGATCA
1 TAAACAAACAC-AATAAACGAACATAAACGAATACAAATAAACGAACA
* * *
214320 TAAACGAACACAATAAACGAACGTAAACGAATACAAATGAACGAACA
1 TAAACAAACACAATAAACGAACATAAACGAATACAAATAAACGAACA
* * *
214367 TAAACAAACACAATAAATGAACATAAACAAATATAAAT
1 TAAACAAACACAATAAACGAACATAAACGAATACAAAT
214405 GAAAATAGAT
Statistics
Matches: 71, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
47 61 0.86
48 10 0.14
ACGTcount: A:0.59, C:0.17, G:0.11, T:0.14
Consensus pattern (47 bp):
TAAACAAACACAATAAACGAACATAAACGAATACAAATAAACGAACA
Found at i:218835 original size:108 final size:107
Alignment explanation
Indices: 218647--218863 Score: 398
Period size: 108 Copynumber: 2.0 Consensus size: 107
218637 ACACGTTATG
* *
218647 AATCTTATTCATCTCCAAAGGAATGCTAACTGATAAGCTATTGAACAAACTCTTTTTGTAATCTC
1 AATCTTATCCATCTCCAAAGGAATGCCAACTGATAAGCTATTGAACAAACTCTTTTTGTAATCTC
218712 GTATGGGTCAATGAATCTCGAACTCAACTTTCCTTTGCGCTC
66 GTATGGGTCAATGAATCTCGAACTCAACTTTCCTTTGCGCTC
218754 AATCTTATCCATCTCCAAAGGTAATGCCAACTGATAAGCTATTGAACAAACTCTTTTTGTAATCT
1 AATCTTATCCATCTCCAAAGG-AATGCCAACTGATAAGCTATTGAACAAACTCTTTTTGTAATCT
*
218819 CGTATGGGTTAATGAATCTCGAACTCAACTTTCCTTTGCGCTC
65 CGTATGGGTCAATGAATCTCGAACTCAACTTTCCTTTGCGCTC
218862 AA
1 AA
218864 ATATCAGAAC
Statistics
Matches: 106, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
107 20 0.19
108 86 0.81
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (107 bp):
AATCTTATCCATCTCCAAAGGAATGCCAACTGATAAGCTATTGAACAAACTCTTTTTGTAATCTC
GTATGGGTCAATGAATCTCGAACTCAACTTTCCTTTGCGCTC
Found at i:229591 original size:13 final size:14
Alignment explanation
Indices: 229573--229614 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 14
229563 TGATTTATCA
229573 AAAT-AAATTAAAG
1 AAATAAAATTAAAG
*
229586 AAATAAAACT-AA-
1 AAATAAAATTAAAG
229598 AAATAAAATTAAAG
1 AAATAAAATTAAAG
229612 AAA
1 AAA
229615 ATCAATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 9 0.38
13 8 0.33
14 7 0.29
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (14 bp):
AAATAAAATTAAAG
Found at i:230545 original size:156 final size:158
Alignment explanation
Indices: 230385--230744 Score: 510
Period size: 156 Copynumber: 2.3 Consensus size: 158
230375 AGTTACATAG
* * * * *
230385 GTATTCTATTGTGGTATATGAGCATGTGGTTCTAATTTGTTAAAAAAAAGACTTAAAATAAATCA
1 GTATTCTACTATGGTATAGGAGCATGTGGTTCAAATTTGATAAAAAAAAGACTTAAAATAAATCA
* *
230450 TAAATTGAAGGAATAAGGAGATTATGAAA-AATTGAAGGACTAAATTGAAAAATAAAAAAAAT-T
66 T-AATTGAAGAAATAAGAAGATTATGAAACAATTGAAGGACTAAATTGAAAAATAAAAAAAATGT
230513 -ATAAAAAAGAGGAATTGAAAGTACACAT
130 AATAAAAAAGAGGAATTGAAAGTACACAT
* * ** * * *
230541 GTATTCGACTATGGTATAGGAGCACGTGGCACAAATTTGGTAAAAAACAGACTTAAAATAAATGA
1 GTATTCTACTATGGTATAGGAGCATGTGGTTCAAATTTGATAAAAAAAAGACTTAAAATAAATCA
* *
230606 TGATTGAAGAAATAAGAAGATTATGAAACAATTGAAGGACTAAATTGAAAAATAAAAAAATTGTA
66 TAATTGAAGAAATAAGAAGATTATGAAACAATTGAAGGACTAAATTGAAAAATAAAAAAAATGTA
* *
230671 ATCAAAAAGAGGATTTGAAAGTACACAT
131 ATAAAAAAGAGGAATTGAAAGTACACAT
* *
230699 GTATTATACTATGGTTTAGGAGCATGTGGTTCAAATTTGATAAAAA
1 GTATTCTACTATGGTATAGGAGCATGTGGTTCAAATTTGATAAAAA
230745 TGGACTTAAA
Statistics
Matches: 177, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
155 24 0.14
156 87 0.49
157 1 0.01
158 65 0.37
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.28
Consensus pattern (158 bp):
GTATTCTACTATGGTATAGGAGCATGTGGTTCAAATTTGATAAAAAAAAGACTTAAAATAAATCA
TAATTGAAGAAATAAGAAGATTATGAAACAATTGAAGGACTAAATTGAAAAATAAAAAAAATGTA
ATAAAAAAGAGGAATTGAAAGTACACAT
Found at i:231437 original size:17 final size:17
Alignment explanation
Indices: 231415--231449 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
231405 TAAATCAAAT
* *
231415 AAGGAAAGTTAAAATAA
1 AAGGAAAATCAAAATAA
231432 AAGGAAAATCAAAATAA
1 AAGGAAAATCAAAATAA
231449 A
1 A
231450 TAAAGTCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.14, T:0.14
Consensus pattern (17 bp):
AAGGAAAATCAAAATAA
Found at i:232426 original size:46 final size:46
Alignment explanation
Indices: 232359--232451 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
232349 TATTCTCACA
*
232359 TCTCATTCAAGCGCTAAATAATTTGGAGAATCAACATTTGATTACT
1 TCTCATTCAAGCACTAAATAATTTGGAGAATCAACATTTGATTACT
232405 TCTCATTCAAGCACTAAATAATTTGGAGAATCAACATTTGATTACT
1 TCTCATTCAAGCACTAAATAATTTGGAGAATCAACATTTGATTACT
232451 T
1 T
232452 TTGTAAACAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (46 bp):
TCTCATTCAAGCACTAAATAATTTGGAGAATCAACATTTGATTACT
Found at i:244279 original size:32 final size:32
Alignment explanation
Indices: 244238--244301 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
244228 CTGATATTGA
244238 CCCTTGGGTAGGCTCTT-AGGCCCCAAGACACT
1 CCCTTGGGTAGGCT-TTAAGGCCCCAAGACACT
*
244270 CCCTTGGGTAGGCTTTAAGGCCCCAAGGCACT
1 CCCTTGGGTAGGCTTTAAGGCCCCAAGACACT
244302 TTATTAGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 2 0.07
32 28 0.93
ACGTcount: A:0.19, C:0.33, G:0.27, T:0.22
Consensus pattern (32 bp):
CCCTTGGGTAGGCTTTAAGGCCCCAAGACACT
Found at i:244640 original size:32 final size:31
Alignment explanation
Indices: 244602--244682 Score: 90
Period size: 32 Copynumber: 2.6 Consensus size: 31
244592 CGAAATATTC
* *
244602 CCTTGGGTAGGTTCTCAGGCCCCAAGATACT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGATACT
* * * * *
244633 CCATTGGGCAAGCTCTAAGGCCTCAAGGTATT
1 CC-TTGGGTAGGCTCTAAGGCCCCAAGATACT
244665 CCTTGGGTAGGCTCTAAG
1 CCTTGGGTAGGCTCTAAG
244683 ACCCAAGGTA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
31 16 0.40
32 24 0.60
ACGTcount: A:0.21, C:0.26, G:0.27, T:0.26
Consensus pattern (31 bp):
CCTTGGGTAGGCTCTAAGGCCCCAAGATACT
Found at i:244692 original size:30 final size:30
Alignment explanation
Indices: 244597--244696 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 30
244587 AGCCCCGAAA
* * * *
244597 TATTCCCTTGGGTAGGTTCTCAGGCCCCAAGA
1 TATT-CCTTGGGTAGGCTCT-AAGACCCAAGG
* * * *
244629 TACTCCATTGGGCAAGCTCTAAGGCCTCAAGG
1 TATTCC-TTGGGTAGGCTCTAAGACC-CAAGG
244661 TATTCCTTGGGTAGGCTCTAAGACCCAAGG
1 TATTCCTTGGGTAGGCTCTAAGACCCAAGG
244691 TATTCC
1 TATTCC
244697 CTTAGGTTGG
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
30 11 0.20
31 22 0.40
32 22 0.40
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (30 bp):
TATTCCTTGGGTAGGCTCTAAGACCCAAGG
Found at i:244709 original size:31 final size:31
Alignment explanation
Indices: 244644--244709 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
244634 CATTGGGCAA
* *
244644 GCTCTAAGGCCTCAAGGTATTCCTTGGGTAG
1 GCTCTAAGACCTCAAGGTATTCCTTAGGTAG
*
244675 GCTCTAAGACC-CAAGGTATTCCCTTAGGTTG
1 GCTCTAAGACCTCAAGGTATT-CCTTAGGTAG
244706 GCTC
1 GCTC
244710 CTATGCCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.29
Consensus pattern (31 bp):
GCTCTAAGACCTCAAGGTATTCCTTAGGTAG
Found at i:246659 original size:93 final size:95
Alignment explanation
Indices: 246488--246683 Score: 333
Period size: 93 Copynumber: 2.1 Consensus size: 95
246478 ATTGAATTCT
* * *
246488 ATTTTAATATATTAATGATTTTCTAAAATTATGTTTTTATTTATAAATTGTTTTGCGATTTGAAA
1 ATTTTGATATATGAATGATTTTCTAAAATTATGTTTTTATTTATAAATTGTTTTACGATTTGAAA
*
246553 TGGTTTAACAAAAATTTTAATATTTCTTGG
66 TGGTTTAACAAAAATTTTAATATTTATTGG
*
246583 ATTTTGATATATGAATGATTTTCTAAAATTATG-TTTT-TTTATAAATTGTTTTACGGTTTGAAA
1 ATTTTGATATATGAATGATTTTCTAAAATTATGTTTTTATTTATAAATTGTTTTACGATTTGAAA
246646 TGGTTTAACAAAAATTTTAATATTTATTGG
66 TGGTTTAACAAAAATTTTAATATTTATTGG
246676 ATTTTGAT
1 ATTTTGAT
246684 TGTGGGTCGC
Statistics
Matches: 96, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
93 61 0.64
94 4 0.04
95 31 0.32
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.52
Consensus pattern (95 bp):
ATTTTGATATATGAATGATTTTCTAAAATTATGTTTTTATTTATAAATTGTTTTACGATTTGAAA
TGGTTTAACAAAAATTTTAATATTTATTGG
Found at i:247167 original size:20 final size:20
Alignment explanation
Indices: 247144--247202 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 20
247134 AAGCTCCTCC
247144 TTTATATGTAAAGATTTTAT
1 TTTATATGTAAAGATTTTAT
247164 TTTATA--T-AA-ATTTTA-
1 TTTATATGTAAAGATTTTAT
247179 ---ATATGTAAAGATTTTAT
1 TTTATATGTAAAGATTTTAT
247196 TTTATAT
1 TTTATAT
247203 AAATTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 16
0.66 0.00 0.34
Matches are distributed among these distances:
12 3 0.10
14 1 0.03
15 2 0.06
16 12 0.39
17 2 0.06
18 1 0.03
20 10 0.32
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
TTTATATGTAAAGATTTTAT
Found at i:247178 original size:16 final size:16
Alignment explanation
Indices: 247157--247210 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
247147 ATATGTAAAG
247157 ATTTTATTTTATATAA
1 ATTTTATTTTATATAA
* * *
247173 ATTTTAATATGTA-AA
1 ATTTTATTTTATATAA
247188 GATTTTATTTTATATAA
1 -ATTTTATTTTATATAA
247205 ATTTTA
1 ATTTTA
247211 AAATTTTCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 2 0.07
16 26 0.87
17 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (16 bp):
ATTTTATTTTATATAA
Found at i:247183 original size:32 final size:32
Alignment explanation
Indices: 247147--247211 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
247137 CTCCTCCTTT
247147 ATATGTAAAGATTTTATTTTATATAAATTTTA
1 ATATGTAAAGATTTTATTTTATATAAATTTTA
247179 ATATGTAAAGATTTTATTTTATATAAATTTTA
1 ATATGTAAAGATTTTATTTTATATAAATTTTA
247211 A
1 A
247212 AATTTTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (32 bp):
ATATGTAAAGATTTTATTTTATATAAATTTTA
Found at i:252196 original size:20 final size:21
Alignment explanation
Indices: 252158--252196 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
252148 TCGGATCGGG
* *
252158 TTTCAGATAGAGATTAGATAT
1 TTTCAGATACAGATAAGATAT
252179 TTTCAGAT-CAGATAAGAT
1 TTTCAGATACAGATAAGAT
252197 TACCCAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (21 bp):
TTTCAGATACAGATAAGATAT
Found at i:252562 original size:20 final size:20
Alignment explanation
Indices: 252539--252679 Score: 149
Period size: 20 Copynumber: 7.0 Consensus size: 20
252529 GTTTCCAGAT
252539 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
** *
252559 TCGCATTGCGATTTTCCGACTA
1 TCGCAACGCGA--TTCTGACTA
* * * *
252581 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
* *
252601 TCGCAATGCGATTATGACTA
1 TCGCAACGCGATTCTGACTA
252621 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
252641 TCGCAACGAGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
252661 TCGCAACGCGATTTTGACT
1 TCGCAACGCGATTCTGACT
252680 GTCGTAACAC
Statistics
Matches: 102, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.01
20 82 0.80
21 1 0.01
22 18 0.18
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:253535 original size:24 final size:24
Alignment explanation
Indices: 253508--253561 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
253498 GTATTCGAAA
253508 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
253532 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
253556 TTTGAT
1 TTTGAT
253562 GATGTTTCAG
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:255843 original size:18 final size:18
Alignment explanation
Indices: 255820--255854 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
255810 AGAAAAAGGC
*
255820 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
255838 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
255855 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:256044 original size:20 final size:20
Alignment explanation
Indices: 256021--256311 Score: 179
Period size: 20 Copynumber: 15.4 Consensus size: 20
256011 TTCATTTAAA
*
256021 TATCGCAATGCAAATTTGAC
1 TATCGCAACGCAAATTTGAC
* * *
256041 TATCGTAACGCGAATTTGAT
1 TATCGCAACGCAAATTTGAC
*
256061 TATCGCAACTCAAA----A-
1 TATCGCAACGCAAATTTGAC
* *
256076 -ATTGCAACGCGAATTTGAC
1 TATCGCAACGCAAATTTGAC
* * *
256095 TATCGCAACACGAATATGAC
1 TATCGCAACGCAAATTTGAC
*
256115 TATGGCAACGCAAA----A-
1 TATCGCAACGCAAATTTGAC
* * *
256130 -ATCACAACGCGAATTTGTC
1 TATCGCAACGCAAATTTGAC
*
256149 TATCGCAACGCGAATTTGAC
1 TATCGCAACGCAAATTTGAC
*
256169 TATCGCAACGCAAATTTGAT
1 TATCGCAACGCAAATTTGAC
***
256189 TATCGCAACGGGTATTTGAC
1 TATCGCAACGCAAATTTGAC
*
256209 TATTGCAACG-AGAA----A-
1 TATCGCAACGCA-AATTTGAC
*
256224 -ATCGCAACACAAATTTGAC
1 TATCGCAACGCAAATTTGAC
**
256243 TATCGCAACGTGAATTTGAC
1 TATCGCAACGCAAATTTGAC
* *
256263 TATCGCAACGCGAATTTGAT
1 TATCGCAACGCAAATTTGAC
* ***
256283 TATCGCAATGGGTATTTGAC
1 TATCGCAACGCAAATTTGAC
256303 TATCGCAAC
1 TATCGCAAC
256312 TAGAAAATCG
Statistics
Matches: 208, Mismatches: 43, Indels: 40
0.71 0.15 0.14
Matches are distributed among these distances:
14 29 0.14
15 1 0.00
16 3 0.01
18 2 0.01
20 173 0.83
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (20 bp):
TATCGCAACGCAAATTTGAC
Found at i:256109 original size:54 final size:54
Alignment explanation
Indices: 256033--256182 Score: 219
Period size: 54 Copynumber: 2.8 Consensus size: 54
256023 TCGCAATGCA
* * * **
256033 AATTTGACTATCGTAACGCGAATTTGATTATCGCAACTCAAAAATTGCAACGCG
1 AATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCACAACGCG
* * *
256087 AATTTGACTATCGCAACACGAATATGACTATGGCAACGCAAAAATCACAACGCG
1 AATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCACAACGCG
*
256141 AATTTGTCTATCGCAACGCGAATTTGACTATCGCAACGCAAA
1 AATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAA
256183 TTTGATTATC
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 84 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.24
Consensus pattern (54 bp):
AATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCACAACGCG
Found at i:256195 original size:94 final size:94
Alignment explanation
Indices: 256079--256356 Score: 301
Period size: 94 Copynumber: 3.0 Consensus size: 94
256069 CTCAAAAATT
* * *
256079 GCAACGCGAATTTGACTATCGCAACACGAATATGACTATGGCAACGCA-AAAATCACAACGCGAA
1 GCAACGCGAATTTGATTATCGCAACACGAATATGACTATGGCAACG-AGAAAATCACAACACAAA
*
256143 TTTGTCTATCGCAACGCGAATTTGACTATC
65 TTTGACTATCGCAACGCGAATTTGACTATC
* ** * * * *
256173 GCAACGCAAATTTGATTATCGCAACGGGTATTTGACTATTGCAACGAGAAAATCGCAACACAAAT
1 GCAACGCGAATTTGATTATCGCAACACGAATATGACTATGGCAACGAGAAAATCACAACACAAAT
*
256238 TTGACTATCGCAACGTGAATTTGACTATC
66 TTGACTATCGCAACGCGAATTTGACTATC
*** * * * * * ***
256267 GCAACGCGAATTTGATTATCGCAATGGGTATTTGACTATCGCAACTAGAAAATCGCAA-AGTGTA
1 GCAACGCGAATTTGATTATCGCAACACGAATATGACTATGGCAACGAGAAAATCACAACA-CAAA
*
256331 TTAGACTATCGCAACGCGAA-TTGACT
65 TTTGACTATCGCAACGCGAATTTGACT
256357 TTCGTGTTGC
Statistics
Matches: 161, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
93 8 0.05
94 153 0.95
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (94 bp):
GCAACGCGAATTTGATTATCGCAACACGAATATGACTATGGCAACGAGAAAATCACAACACAAAT
TTGACTATCGCAACGCGAATTTGACTATC
Found at i:256228 original size:74 final size:74
Alignment explanation
Indices: 256021--256290 Score: 229
Period size: 74 Copynumber: 3.6 Consensus size: 74
256011 TTCATTTAAA
* * * * * *
256021 TATCGCAATGCAAATTTGACTATCGTAACGCGAATTTGATTATCGCAACTCA-AAAATTGCAACG
1 TATCGCAACGCAAATTTGACTATCGCAACGCGAATTTGACTATCGCAAC-GAGAAAATCGCAACA
*
256085 CGAATTTGAC
65 CAAATTTGAC
* * * * * ** * * *** *** *
256095 TATCGCAACACGAATATGACTATGGCAACGCAAAAATCAC-AACGCGAATTTGTCTATCGCAACG
1 TATCGCAACGCAAATTTGACTATCGCAACGCGAATTTGACTATCGC-AACGAGAAAATCGCAACA
*
256159 CGAATTTGAC
65 CAAATTTGAC
* * * *
256169 TATCGCAACGCAAATTTGATTATCGCAACGGGTATTTGACTATTGCAACGAGAAAATCGCAACAC
1 TATCGCAACGCAAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGAAAATCGCAACAC
256234 AAATTTGAC
66 AAATTTGAC
** *
256243 TATCGCAACGTGAATTTGACTATCGCAACGCGAATTTGATTATCGCAA
1 TATCGCAACGCAAATTTGACTATCGCAACGCGAATTTGACTATCGCAA
256291 TGGGTATTTG
Statistics
Matches: 146, Mismatches: 47, Indels: 6
0.73 0.24 0.03
Matches are distributed among these distances:
73 4 0.03
74 139 0.95
75 3 0.02
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (74 bp):
TATCGCAACGCAAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGAAAATCGCAACAC
AAATTTGAC
Found at i:256229 original size:54 final size:54
Alignment explanation
Indices: 256170--256272 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 54
256160 GAATTTGACT
* * * *
256170 ATCGCAACGCAAATTTGATTATCGCAACGGGTATTTGACTATTGCAACGAGAAA
1 ATCGCAACACAAATTTGACTATCGCAACGGGAATTTGACTATCGCAACGAGAAA
*
256224 ATCGCAACACAAATTTGACTATCGCAACGTGAATTTGACTATCGCAACG
1 ATCGCAACACAAATTTGACTATCGCAACGGGAATTTGACTATCGCAACG
256273 CGAATTTGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.25
Consensus pattern (54 bp):
ATCGCAACACAAATTTGACTATCGCAACGGGAATTTGACTATCGCAACGAGAAA
Found at i:256406 original size:20 final size:20
Alignment explanation
Indices: 256351--256408 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
256341 GCAACGCGAA
* *
256351 TTGACTTTCGTGTTGCGATT
1 TTGACTTTAGCGTTGCGATT
* * *
256371 TTGTCTTTCGCATTGCGATT
1 TTGACTTTAGCGTTGCGATT
*
256391 TTGAGTTTAGCGTTGCGA
1 TTGACTTTAGCGTTGCGA
256409 AAGTGTACCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.47
Consensus pattern (20 bp):
TTGACTTTAGCGTTGCGATT
Found at i:256567 original size:14 final size:14
Alignment explanation
Indices: 256507--256568 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
256497 AACAAATAAA
*
256507 AATTATTTACACATC
1 AATT-TTTACAAATC
**
256522 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
256537 AACTTTTACAAATC
1 AATTTTTACAAATC
*
256551 AATTTTTATAAATC
1 AATTTTTACAAATC
256565 AATT
1 AATT
256569 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:258033 original size:21 final size:18
Alignment explanation
Indices: 258009--258053 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
257999 GAACGGTGGG
258009 AGGGGACTCTTGAGGGATGAT
1 AGGGGACTCTTGA---ATGAT
*
258030 AGGGGCCTCTTGAATGAT
1 AGGGGACTCTTGAATGAT
258048 AGGGGA
1 AGGGGA
258054 GGCCTCTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 10 0.45
21 12 0.55
ACGTcount: A:0.24, C:0.11, G:0.42, T:0.22
Consensus pattern (18 bp):
AGGGGACTCTTGAATGAT
Found at i:258600 original size:20 final size:20
Alignment explanation
Indices: 258575--258629 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
258565 AACACGAATT
*
258575 ACTATCGCAATGTGAAAATG
1 ACTATCGCAATGCGAAAATG
* * **
258595 ACTATCGTAAAGCGAATTTG
1 ACTATCGCAATGCGAAAATG
258615 ACTATCGCAATGCGA
1 ACTATCGCAATGCGA
258630 TTTTCATTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:258699 original size:18 final size:20
Alignment explanation
Indices: 258655--258701 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
258645 GCGATTCTTT
*
258655 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
258675 CGTTGCGATAGT-AATTT-G
1 CGTTGCGATAGTCAATTTCG
*
258693 TGTTGCGAT
1 CGTTGCGAT
258702 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.36
19 4 0.16
20 12 0.48
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:258853 original size:20 final size:20
Alignment explanation
Indices: 258797--258854 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
258787 TTGCAACACA
*
258797 AAAATGACTATCGCAACGCG
1 AAAATGACTATCGCAATGCG
258817 AAAATGACTATCGCAATGCG
1 AAAATGACTATCGCAATGCG
**
258837 AATTTGACTATCGCAATG
1 AAAATGACTATCGCAATG
258855 AAATAATCGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
AAAATGACTATCGCAATGCG
Found at i:258921 original size:20 final size:20
Alignment explanation
Indices: 258895--258942 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
258885 GTGATTCTTT
258895 CGTTGCGATAGTCAATTTCG
1 CGTTGCGATAGTCAATTTCG
* *
258915 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
258935 CGTTGCGA
1 CGTTGCGA
258943 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:259158 original size:20 final size:20
Alignment explanation
Indices: 259133--259180 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
259123 TAGTTTACTT
259133 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* **
259153 TCGCAACGTGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
259173 TCGCAACG
1 TCGCAACG
259181 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:259276 original size:20 final size:20
Alignment explanation
Indices: 259222--259280 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
259212 GCGATTCTCT
**
259222 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
259242 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
259262 CGTTGCGATAGTCATTTTC
1 CGTTGCGATAGTCATTTTC
259281 ACAATGCGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:259288 original size:20 final size:20
Alignment explanation
Indices: 259245--259289 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
259235 AAATTCGCGT
* **
259245 TGCGATAGTCATTTTCGCGT
1 TGCGATAGTCATTTTCACAA
259265 TGCGATAGTCATTTTCACAA
1 TGCGATAGTCATTTTCACAA
259285 TGCGA
1 TGCGA
259290 AAGTAAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (20 bp):
TGCGATAGTCATTTTCACAA
Found at i:259460 original size:18 final size:18
Alignment explanation
Indices: 259437--259486 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
259427 TTTACTAAGC
259437 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
259455 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
259473 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
259487 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:261247 original size:20 final size:20
Alignment explanation
Indices: 261208--261295 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 20
261198 TCTGAAACTT
*
261208 AAAATTGCAACACGGAAAATG
1 AAAATCGCAACAC-GAAAATG
261229 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
261249 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
261269 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
261288 -AAATCGCA
1 AAAATCGCA
261296 TTGCGATTCT
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
18 6 0.11
19 3 0.05
20 36 0.63
21 12 0.21
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:261701 original size:22 final size:22
Alignment explanation
Indices: 261670--261711 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
261660 GAGATAGATG
*
261670 GATTTTGTCGGAGATGGGGATT
1 GATTTCGTCGGAGATGGGGATT
261692 GATTTCGTCGGAGATGGGGA
1 GATTTCGTCGGAGATGGGGA
261712 CGGATGTCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.07, G:0.43, T:0.31
Consensus pattern (22 bp):
GATTTCGTCGGAGATGGGGATT
Found at i:261922 original size:20 final size:20
Alignment explanation
Indices: 261894--262000 Score: 151
Period size: 20 Copynumber: 5.3 Consensus size: 20
261884 GAAAATCGCA
*
261894 TTGCGATAGTCAGCATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
261914 TTGCTATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCTCG
261934 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
*
261954 TTGCGATAGTCAGAATCACG
1 TTGCGATAGTCAGAATCTCG
* * *
261974 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCTCG
261994 TTGCGAT
1 TTGCGAT
262001 TTACATATTC
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 78 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Done.