Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 49 of 91
Found at i:10411978 original size:18 final size:18
Alignment explanation
Indices: 10411955--10412007 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 18
10411945 TCATGTTTGT
10411955 TTTAATTAATTTTTTTAA
1 TTTAATTAATTTTTTTAA
10411973 TTTAATTATTATATTTTTTAA
1 TTTAATTA--AT-TTTTTTAA
10411994 TCTTAATTTAATTT
1 T-TTAA-TTAATTT
10412008 AGTTGGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 8 0.27
20 4 0.13
21 11 0.37
22 4 0.13
23 3 0.10
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTAATTAATTTTTTTAA
Found at i:10414903 original size:19 final size:19
Alignment explanation
Indices: 10414845--10414903 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
10414835 ACACCCTGCA
10414845 TTTGCATATGCATTTTTATTT
1 TTTGCA-ATGCA-TTTTATTT
*
10414866 TTTTCAATGCATTTATATTT
1 TTTGCAATGCATTT-TATTT
* *
10414886 TTTGCATTGTATTTTATT
1 TTTGCAATGCATTTTATT
10414904 CATTCATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 7 0.21
20 21 0.64
21 5 0.15
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.63
Consensus pattern (19 bp):
TTTGCAATGCATTTTATTT
Found at i:10420756 original size:37 final size:37
Alignment explanation
Indices: 10420698--10420782 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
10420688 GCCTTCGAAT
* * *
10420698 AAAATCAATCTTAATCATTCACAGAAGAA-TAGTGAAG
1 AAAATTAATCTTAAACATTCACA-AAAAAGTAGTGAAG
* *
10420735 CAAATTAATCTTAAACCTTCACAAAAAAGTAGTGAAG
1 AAAATTAATCTTAAACATTCACAAAAAAGTAGTGAAG
10420772 AAAATTAATCT
1 AAAATTAATCT
10420783 AGAGTCTCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 4 0.10
37 37 0.90
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (37 bp):
AAAATTAATCTTAAACATTCACAAAAAAGTAGTGAAG
Found at i:10427287 original size:11 final size:10
Alignment explanation
Indices: 10427254--10427286 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
10427244 TTTTTTGAAA
10427254 TTTTGGC-TT
1 TTTTGGCTTT
10427263 TTTTGGCTTT
1 TTTTGGCTTT
*
10427273 TTTTGTCTTT
1 TTTTGGCTTT
10427283 TTTT
1 TTTT
10427287 TTGTTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.00, C:0.09, G:0.15, T:0.76
Consensus pattern (10 bp):
TTTTGGCTTT
Found at i:10428695 original size:55 final size:53
Alignment explanation
Indices: 10428636--10429818 Score: 852
Period size: 55 Copynumber: 21.6 Consensus size: 53
10428626 CCTCTTTGAT
* * * *
10428636 GAAGATTGTTTGAGTCCTATACTCCCTGAAAGAAGAGGTAGCGTACACGTCTACC
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGG-AGCG-ACACATTTTCC
* * * * **
10428691 GAAGATTGTTCAAGTCTTATACTCCTTGGAAA-AAGGGGGAGCGGA-ACCATTTTTT
1 GAAGATTGTTCGAGTCCTATACTCCCT-GAAAGAA-GAGGAGC-GACA-CATTTTCC
* * * *
10428746 GAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAAGGAGCATACCCATTTTCT
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAG-AGGAGC-GACACATTTTCC
* * *** * * *
10428801 GAAGATCGTTCAAGTCCTATACTATATGAAAGAAAAAGGAGCGGACCCATTTCCC
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAG-AAGAGGAGC-GACACATTTTCC
* * * *
10428856 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGAAGACACATTTGCT
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGA-GGAG-CGACACATTTTCC
* ** * * * * **
10428911 GAAGATTGTTCAAGTCCTATACTCTTTGAAAAAAGAAGTG-GACCCATTTTTT
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGAGCGACACATTTTCC
* * * * * *
10428963 GAAGTTTTTTCAAGTCTTATACTCCCTGAAAGAAGAGGGAGCGGAC-CTGTTTTCT
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGA-GGAGC-GACAC-ATTTTCC
* * ** * * * *
10429018 GAAGTTTGTTTGAGTCCTATACTTTCTAAAAGAAGATGGAGCAGACCCGTTTTCT
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGA-GGAGC-GACACATTTTCC
* * * **
10429073 GAAGATTTTTCGAGTCCTGTACTCCTTGAAAGAAGAGGGAGCAGACATGTTTTCC
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGA-GGAGC-GACACATTTTCC
* * * * * * **
10429128 AAAGATTGTCCAACTCCTATAATCCCTGAAAGAAGAGAGAGCGGGCTTATTTTCC
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAG-GAGC-GACACATTTTCC
** *
10429183 GAAGATTGTTTAAGTCCTATACTCCCTGAAAGAAGAGGGAGTCGACCCATTTTCC
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGA-GGAG-CGACACATTTTCC
* * * * * * * *
10429238 GAAGATCGTTCAAGTCCTATACTCCTTGAAAAAAGAAGGAACAAACCCATTTTTC
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAG-AGGAGC-GACACATTTTCC
* * * *
10429293 AAAGATTGATT-GAGTCTTATACTCCCTGAAAGAAGAGGGAGCGGACACATCTGCC
1 GAAGATTG-TTCGAGTCCTATACTCCCTGAAAGAAGA-GGAGC-GACACATTTTCC
* * * * * *
10429348 GAA-ATTTGTTTGAGTCCTATACTCCTTGGAAGAAGAAGGAGTGAACCCATTTTCT
1 GAAGA-TTGTTCGAGTCCTATACTCCCTGAAAGAAG-AGGAGCG-ACACATTTTCC
* * * *
10429403 GAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGATAGAGCG-GACATGTTTGTC
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGA-GGAGCGACACAT-TTT-CC
* * * *
10429458 GAAGATTGTTCGAGTCCTATACTCCTTGAAAAAAGAAGGAGCCGACTCATTTTTC
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAG-AGGAG-CGACACATTTTCC
* * * * *
10429513 GAAAATTATTCGAGTTCTATACTCCCTGAAAGAACAGAGAGCAGACACATTTACC
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAG-GAGC-GACACATTTTCC
* * * * *
10429568 GAAGATTGTTCGGGTCCTATAATCCTTGAAAGAAGAAGGAGCGGACCCATTTTTC
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAG-AGGAGC-GACACATTTTCC
* *
10429623 GAAGATTGTTCGAGTCTTATACTCCCTGAAAGAAGAGGGAGCGA-ACATGTCATCC
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGA-GGAGCGACACAT-T-TTCC
* * * *
10429678 AAAGATTGTTCGAGTCCTATACTCCTTGGAAGAAGAAGGAGCTGACTCATTTTCC
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAG-AGGAGC-GACACATTTTCC
* * * * *
10429733 AAAAATTGTTCGAGTTCTATACTCCCTGAAAGAACATGGAGCAGACACATTTACC
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGA-GGAGC-GACACATTTTCC
* * *
10429788 GAAGATTGTTCGGGTCCTATAATCCTTGAAA
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAA
10429819 TTAGAGTGGA
Statistics
Matches: 896, Mismatches: 189, Indels: 86
0.77 0.16 0.07
Matches are distributed among these distances:
52 39 0.04
53 8 0.01
54 31 0.03
55 782 0.87
56 30 0.03
57 6 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (53 bp):
GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGAGCGACACATTTTCC
Found at i:10428805 original size:110 final size:110
Alignment explanation
Indices: 10428636--10429815 Score: 1002
Period size: 110 Copynumber: 10.8 Consensus size: 110
10428626 CCTCTTTGAT
* * * * *
10428636 GAAGATTGTTTGAGTCCTATACTCCCTGAAAGAAGAGGTAGC-GTACACGTCTACCGAAGATTGT
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCAG-ACACATTTTCCGAAGATTGT
* ** **
10428700 TCAAGTCTTATACTCCTTGGAAAAAGGGGGAGCGGAACCATTTTTT
65 TCAAGTCCTATACTCCTTGGAAAAAGAAGGAGCGGAACCATTTTCC
* * * * * *
10428746 GAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGAAGGAGCATACCCATTTTCTGAAGATCGTT
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACATTTTCCGAAGATTGTT
* * * *
10428811 CAAGTCCTATACT-ATAT-GAAAGAAAAAGGAGCGGACCCATTTCCC
66 CAAGTCCTATACTCCT-TGGAAA-AAGAAGGAGCGGAACCATTTTCC
* * * *
10428856 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGAAGACACATTTGCTGAAGATTGTT
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACATTTTCCGAAGATTGTT
* * * * **
10428921 CAAGTCCTATACT-CTTTG-AAAA-AAGAAGTGGACCCATTTTTT
66 CAAGTCCTATACTCCTTGGAAAAAGAAGGAGCGGAACCATTTTCC
* * * * * * * *
10428963 GAAGTTTTTTCAAGTCTTATACTCCCTGAAAGAAGAGGGAGCGGAC-CTGTTTTCTGAAGTTTGT
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACAC-ATTTTCCGAAGATTGT
** ** * * * * *
10429027 TTGAGTCCTATACT--TTCTAAAAGAAGATGGAGCAGACCCGTTTTCT
65 TCAAGTCCTATACTCCTT-GGAAA-AAGAAGGAGCGGAACCATTTTCC
* * * ** * *
10429073 GAAGATTTTTCGAGTCCTGTACTCCTTGAAAGAAGAGGGAGCAGACATGTTTTCCAAAGATTGTC
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACATTTTCCGAAGATTGTT
* * * * *
10429138 CAACTCCTATAATCCCT-GAAAGAAG-AGAGAGCGG-GCTTATTTTCC
66 CAAGTCCTATACTCCTTGGAAA-AAGAAG-GAGCGGAAC-CATTTTCC
** * *
10429183 GAAGATTGTTTAAGTCCTATACTCCCTGAAAGAAGAGGGAGTC-GACCCATTTTCCGAAGATCGT
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAG-CAGACACATTTTCCGAAGATTGT
* * * *
10429247 TCAAGTCCTATACTCCTTGAAAAAAGAAGGAAC-AAACCCATTTTTC
65 TCAAGTCCTATACTCCTTGGAAAAAGAAGGAGCGGAA-CCATTTTCC
* * * * *
10429293 AAAGATTGATT-GAGTCTTATACTCCCTGAAAGAAGAGGGAGCGGACACATCTGCCGAA-ATTTG
1 GAAGATTG-TTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACATTTTCCGAAGA-TTG
** * * *
10429356 TTTGAGTCCTATACTCCTTGGAAGAAGAAGGAG-TGAACCCATTTTCT
64 TTCAAGTCCTATACTCCTTGGAAAAAGAAGGAGCGGAA-CCATTTTCC
* ** * **
10429403 GAAGATTGTTCAAGTCCTATACTCCCTGAAAGAAGATAGAGCGGACATGTTTGT-CGAAGATTGT
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACATTT-TCCGAAGATTGT
* * * *
10429467 TCGAGTCCTATACTCCTTGAAAAAAGAAGGAGCCG-ACTCATTTTTC
65 TCAAGTCCTATACTCCTTGGAAAAAGAAGGAGCGGAAC-CATTTTCC
* * * * * *
10429513 GAAAATTATTCGAGTTCTATACTCCCTGAAAGAACAGAGAGCAGACACATTTACCGAAGATTGTT
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACATTTTCCGAAGATTGTT
** * * *
10429578 CGGGTCCTATAATCCTT-GAAAGAAGAAGGAGCGGACCCATTTTTC
66 CAAGTCCTATACTCCTTGGAAA-AAGAAGGAGCGGAACCATTTTCC
* * *
10429623 GAAGATTGTTCGAGTCTTATACTCCCTGAAAGAAGAGGGAGC-GA-ACATGTCATCCAAAGATTG
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACAT-T-TTCCGAAGATTG
* * *
10429686 TTCGAGTCCTATACTCCTTGGAAGAAGAAGGAGCTG-ACTCATTTTCC
64 TTCAAGTCCTATACTCCTTGGAAAAAGAAGGAGCGGAAC-CATTTTCC
* * * * * *
10429733 AAAAATTGTTCGAGTTCTATACTCCCTGAAAGAACATGGAGCAGACACATTTACCGAAGATTGTT
1 GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACATTTTCCGAAGATTGTT
** *
10429798 CGGGTCCTATAATCCTTG
66 CAAGTCCTATACTCCTTG
10429816 AAATTAGAGT
Statistics
Matches: 866, Mismatches: 167, Indels: 74
0.78 0.15 0.07
Matches are distributed among these distances:
106 3 0.00
107 80 0.09
108 8 0.01
109 24 0.03
110 728 0.84
111 18 0.02
112 5 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (110 bp):
GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACACATTTTCCGAAGATTGTT
CAAGTCCTATACTCCTTGGAAAAAGAAGGAGCGGAACCATTTTCC
Found at i:10428879 original size:165 final size:165
Alignment explanation
Indices: 10428635--10429818 Score: 947
Period size: 165 Copynumber: 7.2 Consensus size: 165
10428625 ACCTCTTTGA
* * * * * *
10428635 TGAAGATTGTTTGAGTCCTATACTCCCTGAAAG-AAGAGGTAGCGTACACGTCTACCGAAGATTG
1 TGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAAAAGG-AGCGGACACATTTTCCGAAGATTG
* * * * *
10428699 TTCAAGTCTTATACTCCTTGGAAA-AAGGGGGAGCGGAACCATTTTTTGAAGATTGTTCAAGTCC
65 TTCGAGTCCTATACTCCTT-GAAAGAAGAGGGAGCAGAACCATTTTCTGAAGATTGTTCAAGTCC
* *
10428763 TATACTCCCTGAAAGAAGAAGGAGCATACCCATTTTC
129 TATACTCCTTGAAAGAAGAAGGAGCAGACCCATTTTC
* * *** * *
10428800 TGAAGATCGTTCAAGTCCTATACTATATGAAAGAAAAAGGAGCGGACCCATTTCCCGAAGATTGT
1 TGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAAAAGGAGCGGACACATTTTCCGAAGATTGT
* * * *
10428865 TCGAGTCCTATACTCCCTGAAAGAATAGGGAGAAG-ACACATTTGCTGAAGATTGTTCAAGTCCT
66 TCGAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGAAC-CATTTTCTGAAGATTGTTCAAGTCCT
* * * *
10428929 ATACTCTTTGAAAAAAGAA-GTG--GACCCATTTTT
130 ATACTCCTTGAAAGAAGAAGGAGCAGACCCATTTTC
* * * * * * * * *
10428962 TGAAGTTTTTTCAAGTCTTATACTCCCTGAAAGAAGAGGGAGCGGAC-CTGTTTTCTGAAGTTTG
1 TGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAAAAGGAGCGGACAC-ATTTTCCGAAGATTG
* * * * * * * *
10429026 TTTGAGTCCTATACT-TTCTAAAAGAAGATGGAGCAGACCCGTTTTCTGAAGATTTTTCGAGTCC
65 TTCGAGTCCTATACTCCT-TGAAAGAAGAGGGAGCAGAACCATTTTCTGAAGATTGTTCAAGTCC
* * ***
10429090 TGTACTCCTTGAAAGAAGAGGGAGCAGACATGTTTTC
129 TATACTCCTTGAAAGAAGAAGGAGCAGACCCATTTTC
** * * * * * * **
10429127 CAAAGATTGTCCAACTCCTATAATCCCTGAAAG-AAGAGAGAGCGGGCTTATTTTCCGAAGATTG
1 TGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAAAAG-GAGCGGACACATTTTCCGAAGATTG
** * * * *
10429191 TTTAAGTCCTATACTCCCTGAAAGAAGAGGGAGTC-GACCCATTTTCCGAAGATCGTTCAAGTCC
65 TTCGAGTCCTATACTCCTTGAAAGAAGAGGGAG-CAGAACCATTTTCTGAAGATTGTTCAAGTCC
* * *
10429255 TATACTCCTTGAAAAAAGAAGGAACAAACCCATTTT-
129 TATACTCCTTGAAAGAAGAAGGAGCAGACCCATTTTC
* * * * * *
10429291 TCAAAGATTGATT-GAGTCTTATACTCCCTGAAAGAAGAGGGAGCGGACACATCTGCCGAA-ATT
1 T-GAAGATTG-TTCGAGTCCTATACTCCCTGAAAGAAAAAGGAGCGGACACATTTTCCGAAGA-T
* * * *
10429354 TGTTTGAGTCCTATACTCCTTGGAAGAAGAAGGAG-TGAACCCATTTTCTGAAGATTGTTCAAGT
63 TGTTCGAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGAA-CCATTTTCTGAAGATTGTTCAAGT
* * *
10429418 CCTATACTCCCTGAAAGAAGATA-GAGCGGA--CATGTTTG
127 CCTATACTCCTTGAAAGAAGA-AGGAGCAGACCCAT-TTTC
* * * * *
10429456 TCGAAGATTGTTCGAGTCCTATACTCCTTGAAA-AAAGAAGGAGCCGACTCATTTTTCGAAAATT
1 T-GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAA-AAGGAGCGGACACATTTTCCGAAGATT
* * * * * * * **
10429520 ATTCGAGTTCTATACTCCCTGAAAGAACAGAGAGCAG-ACACATTTACCGAAGATTGTTCGGGTC
64 GTTCGAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGAAC-CATTTTCTGAAGATTGTTCAAGTC
* *
10429584 CTATAATCCTTGAAAGAAGAAGGAGCGGACCCATTTT-
128 CTATACTCCTTGAAAGAAGAAGGAGCAGACCCATTTTC
* * * * *
10429621 TCGAAGATTGTTCGAGTCTTATACTCCCTGAAAGAAGAGGGAGC-GA-ACATGTCATCCAAAGAT
1 T-GAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAAAAGGAGCGGACACAT-T-TTCCGAAGAT
* * * ** * *
10429684 TGTTCGAGTCCTATACTCCTTGGAAGAAGAAGGAGCTG-ACTCATTTTCCAAAAATTGTTCGAGT
63 TGTTCGAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGAAC-CATTTTCTGAAGATTGTTCAAGT
* * * * * *
10429748 TCTATACTCCCTGAAAGAACATGGAGCAGACACATTTAC
127 CCTATACTCCTTGAAAGAAGAAGGAGCAGACCCATTTTC
* * * *
10429787 CGAAGATTGTTCGGGTCCTATAATCCTTGAAA
1 TGAAGATTGTTCGAGTCCTATACTCCCTGAAA
10429819 TTAGAGTGGA
Statistics
Matches: 804, Mismatches: 181, Indels: 68
0.76 0.17 0.06
Matches are distributed among these distances:
161 1 0.00
162 123 0.15
163 9 0.01
164 25 0.03
165 626 0.78
166 17 0.02
167 3 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (165 bp):
TGAAGATTGTTCGAGTCCTATACTCCCTGAAAGAAAAAGGAGCGGACACATTTTCCGAAGATTGT
TCGAGTCCTATACTCCTTGAAAGAAGAGGGAGCAGAACCATTTTCTGAAGATTGTTCAAGTCCTA
TACTCCTTGAAAGAAGAAGGAGCAGACCCATTTTC
Found at i:10434625 original size:39 final size:38
Alignment explanation
Indices: 10434501--10434622 Score: 183
Period size: 38 Copynumber: 3.2 Consensus size: 38
10434491 CTTTGATATT
10434501 CGGTGCAAATGGTGGGCACGACCTTATGTGTAGCACTTA
1 CGGTGCAAATGGTGGGCACGACCTTATGTGTAGCAC-TA
* * *
10434540 -GGTGCAAATGGTGCGCACGACCTTATATGTAGCACTT
1 CGGTGCAAATGGTGGGCACGACCTTATGTGTAGCACTA
*
10434577 CGGTGCATATGGTGGGCACGACCTTATGTGTAAGCACTA
1 CGGTGCAAATGGTGGGCACGACCTTATGTGT-AGCACTA
10434616 CGGTGCA
1 CGGTGCA
10434623 TATATTTGAC
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.01
38 60 0.81
39 13 0.18
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.25
Consensus pattern (38 bp):
CGGTGCAAATGGTGGGCACGACCTTATGTGTAGCACTA
Found at i:10436137 original size:20 final size:21
Alignment explanation
Indices: 10436114--10436159 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
10436104 TTAACCTTAT
*
10436114 TAAAATAATATT-TAATATTC
1 TAAAATAATATTAAAATATTC
* *
10436134 TAAAATTATATTAAAATATTT
1 TAAAATAATATTAAAATATTC
10436155 TAAAA
1 TAAAA
10436160 ATATTTTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAAATAATATTAAAATATTC
Found at i:10437504 original size:3 final size:3
Alignment explanation
Indices: 10437498--10437561 Score: 101
Period size: 3 Copynumber: 21.0 Consensus size: 3
10437488 GCTTGTTTCT
10437498 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
10437544 TTA TGA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA
10437562 CTACTACATA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:10438515 original size:18 final size:21
Alignment explanation
Indices: 10438475--10438516 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 21
10438465 TGGTTGGCTG
*
10438475 AAAGAATAATGTATAAAGTAA
1 AAAGAATAATGTATAAAGAAA
10438496 AAAGAA-AAT-TA-AAAGAAA
1 AAAGAATAATGTATAAAGAAA
10438514 AAA
1 AAA
10438517 TTATCGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 3 0.15
21 6 0.30
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (21 bp):
AAAGAATAATGTATAAAGAAA
Found at i:10438675 original size:16 final size:16
Alignment explanation
Indices: 10438654--10438688 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
10438644 TTGAAACAAG
10438654 AACAAAA-AATAAGAAT
1 AACAAAATAA-AAGAAT
10438670 AACAAAATAAAAGAAT
1 AACAAAATAAAAGAAT
10438686 AAC
1 AAC
10438689 CTTTTAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.74, C:0.09, G:0.06, T:0.11
Consensus pattern (16 bp):
AACAAAATAAAAGAAT
Found at i:10441043 original size:112 final size:111
Alignment explanation
Indices: 10440878--10441104 Score: 319
Period size: 112 Copynumber: 2.0 Consensus size: 111
10440868 TTATAGGTGC
* * * * **
10440878 TTTCCACATACTTTGTGTATGATAGTATCAATCGATTTTGTTTAATGCATAACGGTGCATTTTTT
1 TTTCAACATACTTCGTGTATGAAAGTATCAATCGATTTTGCTTAATGCATAACGGTGCATTTTCG
* * *
10440943 ACATAAAATGTGCCACCCATGGTATTCATAATGAGGTGAATTACCA
66 ACATAAAAGGTGCCACCCATGGTATTCATAATAAGGTGAATTACAA
* *
10440989 TTTCAACATACTTCGTTTATGAAAGTTATCGATCGATTTTGCTTAATGCATAACGGTGCATTTTC
1 TTTCAACATACTTCGTGTATGAAAG-TATCAATCGATTTTGCTTAATGCATAACGGTGCATTTTC
* * *
10441054 GGCATAAAAGGTGCCGCTCATGGTATTCATAATAAGGTGAATTACAA
65 GACATAAAAGGTGCCACCCATGGTATTCATAATAAGGTGAATTACAA
10441101 TTTC
1 TTTC
10441105 GGCACTTCGG
Statistics
Matches: 101, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
111 21 0.21
112 80 0.79
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (111 bp):
TTTCAACATACTTCGTGTATGAAAGTATCAATCGATTTTGCTTAATGCATAACGGTGCATTTTCG
ACATAAAAGGTGCCACCCATGGTATTCATAATAAGGTGAATTACAA
Found at i:10455555 original size:28 final size:26
Alignment explanation
Indices: 10455496--10455570 Score: 61
Period size: 28 Copynumber: 2.9 Consensus size: 26
10455486 GTATATTATA
10455496 CATATAATATTTAACTAAAATAAATT
1 CATATAATATTTAACTAAAATAAATT
*
10455522 -ATTATAATTATTGTAATTATAAAT-AATT
1 CA-TATAA-TATT-TAACTA-AAATAAATT
10455550 CATAT-AT-TTTAAC-AATAATAA
1 CATATAATATTTAACTAA-AATAA
10455571 TTATTTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
22 1 0.03
23 4 0.10
24 4 0.10
25 3 0.08
26 6 0.15
27 5 0.12
28 12 0.30
29 5 0.12
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (26 bp):
CATATAATATTTAACTAAAATAAATT
Found at i:10455602 original size:104 final size:107
Alignment explanation
Indices: 10455457--10455683 Score: 297
Period size: 106 Copynumber: 2.1 Consensus size: 107
10455447 AGTTGCGCAC
* * * *
10455457 AAATAAGATATTTAGTTAAAA-TATTATATGTATATTATACATATAATA-TTTAACTAAAATAA-
1 AAAT-AGATAATTATTTAAAATTAATAAATGTATATTATACATATAATATTTTAACTAAAATAAC
* *
10455519 ATTATTATAATTATTGTAATT-ATAAATAATTCATA-TATTTTAA
65 ATTATTATAATTATTATAATTGA-AAATAATT-ATATTATTTAAA
*
10455562 CAATA-ATAATTATTTAAAATTAATAAATGTAT-TTGATACATATAATATTTTAACTAAAATAAC
1 AAATAGATAATTATTTAAAATTAATAAATGTATATT-ATACATATAATATTTTAACTAAAATAAC
10455625 ATTATTATAATTATTATAATTGAAAATAATTATATTTATTTAAA
65 ATTATTATAATTATTATAATTGAAAATAATTATA-TTATTTAAA
10455669 AAATAGATAATTATT
1 AAATAGATAATTATT
10455684 AGGAAAAATA
Statistics
Matches: 106, Mismatches: 8, Indels: 13
0.83 0.06 0.10
Matches are distributed among these distances:
103 14 0.13
104 23 0.22
105 20 0.19
106 28 0.26
107 12 0.11
108 9 0.08
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (107 bp):
AAATAGATAATTATTTAAAATTAATAAATGTATATTATACATATAATATTTTAACTAAAATAACA
TTATTATAATTATTATAATTGAAAATAATTATATTATTTAAA
Found at i:10456047 original size:15 final size:15
Alignment explanation
Indices: 10455997--10456056 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
10455987 AATAATTTAT
*
10455997 TTAAATATAAAATTAA
1 TTAAATATAAAAAT-A
* *
10456013 TAAAATATTCAAAA-A
1 TTAAATA-TAAAAATA
*
10456028 CTAAATATAAAAATA
1 TTAAATATAAAAATA
*
10456043 TTAAAAATAAAAAT
1 TTAAATATAAAAAT
10456057 TAAATTATTA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
14 5 0.15
15 19 0.56
16 6 0.18
17 4 0.12
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TTAAATATAAAAATA
Found at i:10456065 original size:21 final size:22
Alignment explanation
Indices: 10456013--10456068 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
10456003 ATAAAATTAA
*
10456013 TAAAATATTCAAAAACTAAATAT
1 TAAAATATT-AAAAACTAAAAAT
*
10456036 AAAAATATTAAAAA-TAAAAAT
1 TAAAATATTAAAAACTAAAAAT
*
10456057 TAAATTATTAAA
1 TAAAATATTAAA
10456069 TAAATTGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 16 0.55
22 5 0.17
23 8 0.28
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAATATTAAAAACTAAAAAT
Found at i:10456620 original size:16 final size:16
Alignment explanation
Indices: 10456593--10456639 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
10456583 TTATTATTAG
10456593 TATTTTAATATTTAAT
1 TATTTTAATATTTAAT
*
10456609 T-TTTTAAATATTTTAT
1 TATTTT-AATATTTAAT
10456625 TATTTTAATATTTAA
1 TATTTTAATATTTAA
10456640 AATTTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 4 0.15
16 19 0.70
17 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTTAATATTTAAT
Found at i:10456636 original size:8 final size:8
Alignment explanation
Indices: 10456593--10456637 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
10456583 TTATTATTAG
10456593 TATTTTAA
1 TATTTTAA
10456601 TA-TTTAA
1 TATTTTAA
*
10456608 TTTTTTAAA
1 TATTTT-AA
*
10456617 TATTTTAT
1 TATTTTAA
10456625 TATTTTAA
1 TATTTTAA
10456633 TATTT
1 TATTT
10456638 AAAATTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
7 6 0.19
8 18 0.58
9 7 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TATTTTAA
Found at i:10456707 original size:28 final size:28
Alignment explanation
Indices: 10456658--10456713 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
10456648 ATGATTTTTT
* *
10456658 TTTTAAAAAATTAAATAAGCCCTTGAAC
1 TTTTAAAAAATCAAATAAGCCCTCGAAC
**
10456686 TTTTAAAAAATCAAATTGGCCCTCGAAC
1 TTTTAAAAAATCAAATAAGCCCTCGAAC
10456714 AAAACAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (28 bp):
TTTTAAAAAATCAAATAAGCCCTCGAAC
Found at i:10456921 original size:28 final size:31
Alignment explanation
Indices: 10456858--10456914 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
10456848 AGGTTGGTCA
* *
10456858 AAGGGTCACATTGGGTTTGTTTTATGAGTTG
1 AAGGGTCACATTGGATTTGTTTTATAAGTTG
10456889 AAGGGTCACATT-GATTT-TTTTA-AAGT
1 AAGGGTCACATTGGATTTGTTTTATAAGT
10456915 ATAAGGGCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 5 0.21
30 4 0.17
31 12 0.50
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.42
Consensus pattern (31 bp):
AAGGGTCACATTGGATTTGTTTTATAAGTTG
Found at i:10459435 original size:21 final size:21
Alignment explanation
Indices: 10459411--10459454 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
10459401 GTGCCGGAGG
* *
10459411 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAACT
* *
10459432 AGGAGCAGCTCGTGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
10459453 AG
1 AG
10459455 CTCCCGGACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:10460562 original size:8 final size:8
Alignment explanation
Indices: 10460551--10460578 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
10460541 TTTTTTTATT
10460551 TTCAAAAA
1 TTCAAAAA
10460559 TTCAAAAA
1 TTCAAAAA
10460567 TTCAAAAA
1 TTCAAAAA
10460575 TTCA
1 TTCA
10460579 TTGAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (8 bp):
TTCAAAAA
Found at i:10466504 original size:19 final size:19
Alignment explanation
Indices: 10466480--10466531 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
10466470 AATAGCCAGA
*
10466480 GTGCATTGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
10466499 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
10466518 GTGCATCGATGCAT
1 GTGCATCGATGCAT
10466532 CAAATGCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTG
Found at i:10466610 original size:83 final size:83
Alignment explanation
Indices: 10466436--10466611 Score: 189
Period size: 84 Copynumber: 2.1 Consensus size: 83
10466426 GCACTAAGAG
* *
10466436 TGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATTGATGCATGGCTGGT
1 TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGGT
***
10466501 GCATCGATGCATGGCTGG
66 GCATCGATGCATGGCAAA
* ** **
10466519 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTTAGTGTGTCGATGCATGG-TA
1 TGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAGAGTGCATCGATGCATGGCT-
*
10466582 TGTGCATCGATGCAT-G-AAA
63 GGTGCATCGATGCATGGCAAA
10466601 TGCATTCGATG
1 TGCA-TCGATG
10466612 TTCAATTTAT
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
82 4 0.05
83 35 0.45
84 36 0.46
85 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (83 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGGT
GCATCGATGCATGGCAAA
Found at i:10466652 original size:65 final size:64
Alignment explanation
Indices: 10466497--10466663 Score: 176
Period size: 65 Copynumber: 2.6 Consensus size: 64
10466487 GATGCATGGC
* *
10466497 TGGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCT
1 TGGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCA
* ** * ** *
10466562 TAGTGTGTCGATGCATGGTAT-GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCC
1 TGGTGCATCGATGCATGGT-TGGTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCC
10466625 A
64 A
* * *
10466626 TGGTGCATCAATACATGGATTGGTGCATCGGTGCATCA
1 TGGTGCATCGATGCATGG-TTGGTGCATCGATGCATCA
10466664 CTTTGAAAAA
Statistics
Matches: 82, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
63 3 0.04
64 20 0.24
65 58 0.71
66 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (64 bp):
TGGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCA
Found at i:10477786 original size:20 final size:20
Alignment explanation
Indices: 10477757--10477799 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
10477747 GGATTGGTAA
10477757 AAACTATGAATCTATCATGG
1 AAACTATGAATCTATCATGG
*
10477777 AAACTGTGAATCTATCATGG
1 AAACTATGAATCTATCATGG
10477797 AAA
1 AAA
10477800 GGGATACAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (20 bp):
AAACTATGAATCTATCATGG
Found at i:10479402 original size:43 final size:43
Alignment explanation
Indices: 10479341--10479425 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
10479331 AGAAATGCAT
10479341 TTTTTATGTCTAGTTGGTGAGGTATCCAATCCTTGTTCACTGG
1 TTTTTATGTCTAGTTGGTGAGGTATCCAATCCTTGTTCACTGG
10479384 TTTTTATGTCTAGTTGGTGAGGTATCCAATCCTTGTTCACTG
1 TTTTTATGTCTAGTTGGTGAGGTATCCAATCCTTGTTCACTG
10479426 CCACGGATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.45
Consensus pattern (43 bp):
TTTTTATGTCTAGTTGGTGAGGTATCCAATCCTTGTTCACTGG
Found at i:10483058 original size:23 final size:23
Alignment explanation
Indices: 10483024--10483097 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
10483014 TACCACGTAG
10483024 AAACAACA-TTTTTCGGCTCTAGT
1 AAACAA-AGTTTTTCGGCTCTAGT
* * * *
10483047 AAACAAAGTTTTCCGACCCTTGT
1 AAACAAAGTTTTTCGGCTCTAGT
* * * *
10483070 AAACAGAGTTTTTTGGTTCTGGT
1 AAACAAAGTTTTTCGGCTCTAGT
10483093 AAACA
1 AAACA
10483098 GGGTTTTTTT
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
22 1 0.03
23 38 0.97
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (23 bp):
AAACAAAGTTTTTCGGCTCTAGT
Found at i:10483112 original size:23 final size:23
Alignment explanation
Indices: 10483068--10483113 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
10483058 TCCGACCCTT
*
10483068 GTAAACAGAGTTTTTTGGTTCTG
1 GTAAACAGAGTTTTTTGATTCTG
* *
10483091 GTAAACAGGGTTTTTTTATTCTG
1 GTAAACAGAGTTTTTTGATTCTG
10483114 AAATTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.46
Consensus pattern (23 bp):
GTAAACAGAGTTTTTTGATTCTG
Found at i:10499256 original size:22 final size:23
Alignment explanation
Indices: 10499229--10499281 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
10499219 AAAATTAGCA
10499229 AAGAAA-TCGAAGCACTC-AAAAG
1 AAGAAATTC-AAGCACTCAAAAAG
10499251 AAGAAAAATTCAAGCACTCAAAAAG
1 AAG--AAATTCAAGCACTCAAAAAG
10499276 AAGAAA
1 AAGAAA
10499282 AAAAAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
22 3 0.11
23 3 0.11
24 11 0.41
25 10 0.37
ACGTcount: A:0.60, C:0.15, G:0.15, T:0.09
Consensus pattern (23 bp):
AAGAAATTCAAGCACTCAAAAAG
Found at i:10507831 original size:88 final size:85
Alignment explanation
Indices: 10507684--10507849 Score: 235
Period size: 88 Copynumber: 1.9 Consensus size: 85
10507674 TATCAATAGC
* * **
10507684 AATAAGATATCTGATGTCACCTAGCATCCAGTAATAAATTCCTATGAGTTATCTGGTATCACCTA
1 AATAAGATATCTGATGTCACCTAGCATCAAGTAATAAATTCCTATGAGTTACCAAGTATCACCTA
10507749 GAAATCAAGTAATAAGTAGA
66 GAAATCAAGTAATAAGTAGA
*
10507769 AATAAGATATCTTATGTGACGACCTAGCATCAAGTAATAAATAT-CTATGAGTTACCAAGTATCA
1 AATAAGATATCTGATGT--C-ACCTAGCATCAAGTAATAAAT-TCCTATGAGTTACCAAGTATCA
*
10507833 CTTAGAAATCAAGTAAT
62 CCTAGAAATCAAGTAAT
10507850 TAAAAACAAC
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
85 16 0.23
87 1 0.01
88 53 0.75
89 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (85 bp):
AATAAGATATCTGATGTCACCTAGCATCAAGTAATAAATTCCTATGAGTTACCAAGTATCACCTA
GAAATCAAGTAATAAGTAGA
Found at i:10511035 original size:16 final size:17
Alignment explanation
Indices: 10511011--10511043 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
10511001 TACGGGTCAT
10511011 ATCTGGGTC-GGATCAG
1 ATCTGGGTCTGGATCAG
*
10511027 ATCTTGGTCTGGATCAG
1 ATCTGGGTCTGGATCAG
10511044 CTGTTGGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.30
Consensus pattern (17 bp):
ATCTGGGTCTGGATCAG
Found at i:10511171 original size:3 final size:3
Alignment explanation
Indices: 10511163--10511200 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
10511153 ATAATTTTCT
10511163 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
10511201 TTTTTTAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:10520905 original size:7 final size:7
Alignment explanation
Indices: 10520902--10521010 Score: 107
Period size: 7 Copynumber: 15.4 Consensus size: 7
10520892 AGAAAAAGGA
*
10520902 AAAAATA
1 AAAAATG
10520909 AAAAGATG
1 AAAA-ATG
10520917 ATAAAA-G
1 A-AAAATG
10520924 AAAAATG
1 AAAAATG
10520931 AAAAATG
1 AAAAATG
10520938 AAAAATG
1 AAAAATG
*
10520945 AAAAATA
1 AAAAATG
*
10520952 AAAAATA
1 AAAAATG
*
10520959 AAAAATA
1 AAAAATG
10520966 AAAAAT-
1 AAAAATG
10520972 AAAAGATG
1 AAAA-ATG
10520980 AAAAAT-
1 AAAAATG
10520986 AAAAGATG
1 AAAA-ATG
*
10520994 AAAAAAG
1 AAAAATG
*
10521001 AAAAAAG
1 AAAAATG
10521008 AAA
1 AAA
10521011 GAAAATATGA
Statistics
Matches: 92, Mismatches: 3, Indels: 14
0.84 0.03 0.13
Matches are distributed among these distances:
6 12 0.13
7 65 0.71
8 12 0.13
9 3 0.03
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:10522047 original size:105 final size:105
Alignment explanation
Indices: 10521906--10522630 Score: 1004
Period size: 105 Copynumber: 6.9 Consensus size: 105
10521896 TGGTCCATCG
* * *
10521906 CAGAAGGAGGTGAACCAACATTTCTA-ATAGAGTTCATAACGAGAAGAACTCATCCTAAAGGAGA
1 CAGAAGGAGGTGAACCAACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCCCAAAGGAGA
10521970 AAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCACCA
65 AAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCACCA
* * * * *
10522011 CAAAAGGAGGTAAACAAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCCAAAGAAGAA
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCCAAAGGAGAA
*
10522076 AGTTCATAATGAGAAGAACTTGTTCCTTTAAAATTCACCA
66 AGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCACCA
* * ** *
10522116 CAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGATAAGAACTCATCTTAGAGGAGAA
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCCAAAGGAGAA
***
10522181 AGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCATTG
66 AGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCACCA
* * *
10522221 CAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGCGAAGAACTCGTCCCAAAGGAGAA
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCCAAAGGAGAA
10522286 AGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCACCA
66 AGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCACCA
* * * * * *
10522326 CAGAAAGAGGTGAACCAAAATTTCCATAAAAGTTCATAATGAGAAGAACTCGTCCCAAAGAAGAA
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCCAAAGGAGAA
* *
10522391 AGTTCATAATGAGAATAACTTGTTCCTTTCAAAATTCACTA
66 AGTTCATAATGAGAAGAACTTGTTCCTTTC-AAATTCACCA
* ** **
10522432 TAGAAGGAGGTGAACCAACATTTCTTGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAA
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCCAAAGGAGAA
* * *
10522497 ATTTCATAATGAGAAGAACGTGTTCCTTTCAAATTCACCG
66 AGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCACCA
* * * *
10522537 CAGAAGGAGGTGAACCAACACTTCCAGGACAATTCATAATGAGAAGAACTCAT-CCAATGAGGGA
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCCAA--A-GGA
*
10522601 TGAGAAGTTTATAATGAGAAGAACTTGTTC
63 -GA-AAGTTCATAATGAGAAGAACTTGTTC
10522631 AACCTTGCAT
Statistics
Matches: 545, Mismatches: 68, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
104 2 0.00
105 423 0.78
106 92 0.17
107 3 0.01
108 2 0.00
109 23 0.04
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (105 bp):
CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCCAAAGGAGAA
AGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCACCA
Found at i:10522489 original size:19 final size:18
Alignment explanation
Indices: 10522465--10522515 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
10522455 CTTGAAGAGT
10522465 TCATAATGAGAAGAACTCA
1 TCATAATGAGAAGAACT-A
* * *
10522484 TCATAA--AGGAGAAATT
1 TCATAATGAGAAGAACTA
10522500 TCATAATGAGAAGAAC
1 TCATAATGAGAAGAAC
10522516 GTGTTCCTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
16 6 0.24
17 7 0.28
18 6 0.24
19 6 0.24
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.22
Consensus pattern (18 bp):
TCATAATGAGAAGAACTA
Found at i:10522819 original size:38 final size:38
Alignment explanation
Indices: 10522757--10522860 Score: 118
Period size: 38 Copynumber: 2.7 Consensus size: 38
10522747 CAACATTTTC
**
10522757 AGTGGAGAGTTCCTAATGAGAAGAACTCATCCAATGAG
1 AGTGGAGAGTTAATAATGAGAAGAACTCATCCAATGAG
* *
10522795 AGTGGAGAGTTAATAGTGATAAGAACTCATCCAATGAG
1 AGTGGAGAGTTAATAATGAGAAGAACTCATCCAATGAG
* * * * *
10522833 GGAGGATAAGTTCATAATGAGATGAACT
1 AGTGGA-GAGTTAATAATGAGAAGAACT
10522861 TATTCAACCT
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
38 38 0.70
39 16 0.30
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (38 bp):
AGTGGAGAGTTAATAATGAGAAGAACTCATCCAATGAG
Found at i:10522873 original size:155 final size:155
Alignment explanation
Indices: 10522650--10522945 Score: 425
Period size: 155 Copynumber: 1.9 Consensus size: 155
10522640 TTAGCATTTG
* * *
10522650 TAATAGAGAGAAGAACTCATCCAATAAGGAAGAAGAATTTCATAATGAGAATAACTTGTTCAATC
1 TAATAGAGAGAAGAACTCATCCAATAAGGAAGAAGAAGTTCATAATGAGAATAACTTATTCAACC
* * * *
10522715 TTGGTTTAATTCCATCACAAAAGT-AGGTGGATCAACATTTTCAGTGGAGAGTTCCTAATGAGAA
66 TTGGTTCAATTCCATCACAAAA-TAAGGTGGATCAACATTTCCAGCGGAGAGTTCATAATGAGAA
10522779 GAACTCATCCAATGAGAGTGGAGAGT
130 GAACTCATCCAATGAGAGTGGAGAGT
* * * * * *
10522805 TAATAGTGATAAGAACTCATCCAATGAGGGAGGATAAGTTCATAATGAG-ATGAACTTATTCAAC
1 TAATAGAGAGAAGAACTCATCCAATAAGGAAGAAGAAGTTCATAATGAGAAT-AACTTATTCAAC
* *
10522869 CTTGGTTCGATTCCATCACAGAATAAGGTGGATCAACATTTCCAGCGGAGAGTTCATAATGAGAA
65 CTTGGTTCAATTCCATCACAAAATAAGGTGGATCAACATTTCCAGCGGAGAGTTCATAATGAGAA
10522934 GAACTCATCCAA
130 GAACTCATCCAA
10522946 CAAGGAAGAA
Statistics
Matches: 124, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
154 3 0.02
155 121 0.98
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (155 bp):
TAATAGAGAGAAGAACTCATCCAATAAGGAAGAAGAAGTTCATAATGAGAATAACTTATTCAACC
TTGGTTCAATTCCATCACAAAATAAGGTGGATCAACATTTCCAGCGGAGAGTTCATAATGAGAAG
AACTCATCCAATGAGAGTGGAGAGT
Found at i:10523062 original size:91 final size:91
Alignment explanation
Indices: 10522907--10523075 Score: 295
Period size: 91 Copynumber: 1.9 Consensus size: 91
10522897 TGGATCAACA
*
10522907 TTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCGTAATGAGA
1 TTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATGAGA
10522972 AGAACTTGTTCAACCTTGCATCAGTG
66 AGAACTTGTTCAACCTTGCATCAGTG
* *
10522998 TTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACAA-GAGAGAAGAAGTTTATAATGAG
1 TTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGA-AGAAGAAGTTCATAATGAG
10523062 AAGAACTTGTTCAA
65 AAGAACTTGTTCAA
10523076 TCCAACAATG
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
90 2 0.03
91 72 0.97
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.24
Consensus pattern (91 bp):
TTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTGCATCAGTG
Found at i:10535758 original size:33 final size:32
Alignment explanation
Indices: 10535696--10535758 Score: 74
Period size: 33 Copynumber: 1.9 Consensus size: 32
10535686 TCATAAAAGC
**
10535696 TTTATTGTTATTTAATTTATTATGTAAATCGG
1 TTTATTGTTATTTAATTTATTATCAAAATCGG
*
10535728 TTTATTTGTTATTT-ATTATATTTTCAAAATC
1 TTTA-TTGTTATTTAATT-TATTATCAAAATC
10535759 TTATGTATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
32 7 0.27
33 19 0.73
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.59
Consensus pattern (32 bp):
TTTATTGTTATTTAATTTATTATCAAAATCGG
Found at i:10539821 original size:20 final size:20
Alignment explanation
Indices: 10539788--10539835 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
10539778 AATGATTATC
*
10539788 TTTTG-AAAGCAAAATTG-GA
1 TTTTGAAAAGCAAAA-TGAAA
*
10539807 TTTTGAAAAGTAAAATGAAA
1 TTTTGAAAAGCAAAATGAAA
10539827 TTTTGAAAA
1 TTTTGAAAA
10539836 ATGATTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.48, C:0.02, G:0.17, T:0.33
Consensus pattern (20 bp):
TTTTGAAAAGCAAAATGAAA
Found at i:10546290 original size:45 final size:45
Alignment explanation
Indices: 10546231--10546363 Score: 196
Period size: 45 Copynumber: 3.0 Consensus size: 45
10546221 TGTAATTTCA
* * *
10546231 ATGAAAGGGCTTAACCTT-TTGATTAAAAGACTTAACCTTTAATTT
1 ATGAAAGGGTTTAACCTTATTCATAAAAAGACTTAA-CTTTAATTT
* *
10546276 ATGAAAGGGTTTAACCTTACTCATAAAAAGACTTGACTTTAATTT
1 ATGAAAGGGTTTAACCTTATTCATAAAAAGACTTAACTTTAATTT
*
10546321 ATGAAAGGGTTTAACCTTATTCATAAAAAGACTCAACTTTAAT
1 ATGAAAGGGTTTAACCTTATTCATAAAAAGACTTAACTTTAAT
10546364 AGTCAAACTA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 66 0.84
46 13 0.16
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (45 bp):
ATGAAAGGGTTTAACCTTATTCATAAAAAGACTTAACTTTAATTT
Found at i:10546291 original size:24 final size:24
Alignment explanation
Indices: 10546262--10546338 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 24
10546252 ATTAAAAGAC
10546262 TTAACCTTTAATTTATGAAAGGGT
1 TTAACCTTTAATTTATGAAAGGGT
* * * * **
10546286 TTAACC-TT-ACTCATAAAAAGAC
1 TTAACCTTTAATTTATGAAAGGGT
*
10546308 TTGA-CTTTAATTTATGAAAGGGT
1 TTAACCTTTAATTTATGAAAGGGT
10546331 TTAACCTT
1 TTAACCTT
10546339 ATTCATAAAA
Statistics
Matches: 36, Mismatches: 14, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
21 1 0.03
22 13 0.36
23 13 0.36
24 9 0.25
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (24 bp):
TTAACCTTTAATTTATGAAAGGGT
Found at i:10547800 original size:289 final size:290
Alignment explanation
Indices: 10547261--10547839 Score: 1052
Period size: 289 Copynumber: 2.0 Consensus size: 290
10547251 AAGTGGTCAC
* *
10547261 ATATCCCATTCAGAGGTATTTTTTTTAAACAACTTATAATACATTAGATATAATACAAAACAAAA
1 ATATCCCATTAAGAGGTATCTTTTTTAAACAACTTATAATACATTAGATATAATACAAAACAAAA
10547326 TATTAATAATACAAATATATCCAAAACGATAGCAAATACATGTCACCAGAAACAACAGAAAGCAT
66 TATTAATAATACAAATATATCCAAAACGATAGCAAATACATGTCACCAGAAACAACAGAAAGCAT
*
10547391 GTAAAGATATATGTTCGTACAAAATAAGTAGTTGATCTCCCCTGATGCCAAATCTGCTAGCTTAC
131 GTAAAGATATATGTTCGTACAAAATAAGTAGTTGATCTCCCCTGATGCCAAATCTACTAGCTTAC
* *
10547456 GGTCTGCTGTTATCTGAAAAGGGGTAAAAACTATAGAATGAGCTAAAAAGCCCAGTGTGCTTCAA
196 GGTCTGCTATTATCTGAAAAAGGGTAAAAACTATAGAATGAGCTAAAAAGCCCAGTGTGCTTCAA
10547521 ACAGCGTATAAAAACATTTTAATAAAATAT
261 ACAGCGTATAAAAACATTTTAATAAAATAT
*
10547551 ATATCCCATTAAGAGGTA-CTTTTTTAAACAACTTATAATACATTAGATATATTACAAAACAAAA
1 ATATCCCATTAAGAGGTATCTTTTTTAAACAACTTATAATACATTAGATATAATACAAAACAAAA
* * *
10547615 TATTAATAATACAAATATGTCCAAAACGATAGCAAATACATGTCACCAGATACAACGGAAAGCAT
66 TATTAATAATACAAATATATCCAAAACGATAGCAAATACATGTCACCAGAAACAACAGAAAGCAT
10547680 GTAAAGATATATGTTCGTACAAAATAAGTAGTTGATCTCCCCTGATGCCAAATCTACTAGCTTAC
131 GTAAAGATATATGTTCGTACAAAATAAGTAGTTGATCTCCCCTGATGCCAAATCTACTAGCTTAC
10547745 GGTCTGCTATTATCTGAAAAAGGGTAAAAACTATAGAATGAGCTAAAAAGCCCAGTGTGCTTCAA
196 GGTCTGCTATTATCTGAAAAAGGGTAAAAACTATAGAATGAGCTAAAAAGCCCAGTGTGCTTCAA
* *
10547810 ACAGTGTATAGAAACATTTTAATAAAATAT
261 ACAGCGTATAAAAACATTTTAATAAAATAT
10547840 TGCAGTAAAA
Statistics
Matches: 278, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
289 261 0.94
290 17 0.06
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (290 bp):
ATATCCCATTAAGAGGTATCTTTTTTAAACAACTTATAATACATTAGATATAATACAAAACAAAA
TATTAATAATACAAATATATCCAAAACGATAGCAAATACATGTCACCAGAAACAACAGAAAGCAT
GTAAAGATATATGTTCGTACAAAATAAGTAGTTGATCTCCCCTGATGCCAAATCTACTAGCTTAC
GGTCTGCTATTATCTGAAAAAGGGTAAAAACTATAGAATGAGCTAAAAAGCCCAGTGTGCTTCAA
ACAGCGTATAAAAACATTTTAATAAAATAT
Found at i:10548968 original size:30 final size:30
Alignment explanation
Indices: 10548916--10549066 Score: 195
Period size: 29 Copynumber: 5.2 Consensus size: 30
10548906 AATAATTATT
10548916 AAAATAGCACCTTTTT-GAATTAAATTCCC
1 AAAATAGCACCTTTTTCGAATTAAATTCCC
10548945 AAAATAGCACCTTTTTCGAATTAAATTCCC
1 AAAATAGCACCTTTTTCGAATTAAATTCCC
* *
10548975 AATATAGCACC-TTTTCAAATTAAATTCCC
1 AAAATAGCACCTTTTTCGAATTAAATTCCC
*
10549004 AAAATAGCACCCATTTT-GAATT-AATTCCC
1 AAAATAGCA-CCTTTTTCGAATTAAATTCCC
* ** *
10549033 AAAATAACACCCATTTCAAATT-AATTCCC
1 AAAATAGCACCTTTTTCGAATTAAATTCCC
10549062 AAAAT
1 AAAAT
10549067 GTCACACGAT
Statistics
Matches: 110, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
28 5 0.05
29 72 0.65
30 29 0.26
31 4 0.04
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.32
Consensus pattern (30 bp):
AAAATAGCACCTTTTTCGAATTAAATTCCC
Found at i:10548984 original size:59 final size:58
Alignment explanation
Indices: 10548916--10549066 Score: 207
Period size: 59 Copynumber: 2.6 Consensus size: 58
10548906 AATAATTATT
** *
10548916 AAAATAGCACCTTTTTGAATTAAATTCCCAAAATAGCA-CCTTTTTCGAATTAAATTCCC
1 AAAATAGCACCTTTTCAAATTAAATTCCCAAAATAGCACCCATTTT-GAATT-AATTCCC
*
10548975 AATATAGCACCTTTTCAAATTAAATTCCCAAAATAGCACCCATTTTGAATTAATTCCC
1 AAAATAGCACCTTTTCAAATTAAATTCCCAAAATAGCACCCATTTTGAATTAATTCCC
* *
10549033 AAAATAACACCCATTTCAAATT-AATTCCCAAAAT
1 AAAATAGCA-CCTTTTCAAATTAAATTCCCAAAAT
10549067 GTCACACGAT
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
58 26 0.31
59 51 0.61
60 6 0.07
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.32
Consensus pattern (58 bp):
AAAATAGCACCTTTTCAAATTAAATTCCCAAAATAGCACCCATTTTGAATTAATTCCC
Found at i:10552324 original size:12 final size:12
Alignment explanation
Indices: 10552307--10552338 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
10552297 GGTTAAAGTC
10552307 GGTCAAAGTTCT
1 GGTCAAAGTTCT
*
10552319 GGTCAATGTTCT
1 GGTCAAAGTTCT
10552331 GGTCAAAG
1 GGTCAAAG
10552339 GAGGTCAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (12 bp):
GGTCAAAGTTCT
Found at i:10552496 original size:18 final size:18
Alignment explanation
Indices: 10552473--10552526 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
10552463 AATGTCACTC
10552473 GGTCAACGGGTCAGGTCG
1 GGTCAACGGGTCAGGTCG
10552491 GGTCAACGGGTCAGGTC-
1 GGTCAACGGGTCAGGTCG
* *
10552508 GGTCAACAGGTCGGGTCG
1 GGTCAACGGGTCAGGTCG
10552526 G
1 G
10552527 AACCAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
17 15 0.45
18 18 0.55
ACGTcount: A:0.17, C:0.22, G:0.44, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCAGGTCG
Found at i:10552513 original size:17 final size:17
Alignment explanation
Indices: 10552471--10552526 Score: 85
Period size: 17 Copynumber: 3.2 Consensus size: 17
10552461 AAAATGTCAC
10552471 TCGGTCAACGGGTCAGG
1 TCGGTCAACGGGTCAGG
10552488 TCGGGTCAACGGGTCAGG
1 TC-GGTCAACGGGTCAGG
* *
10552506 TCGGTCAACAGGTCGGG
1 TCGGTCAACGGGTCAGG
10552523 TCGG
1 TCGG
10552527 AACCAATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 19 0.53
18 17 0.47
ACGTcount: A:0.16, C:0.23, G:0.43, T:0.18
Consensus pattern (17 bp):
TCGGTCAACGGGTCAGG
Found at i:10552560 original size:20 final size:20
Alignment explanation
Indices: 10552535--10552573 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10552525 GGAACCAATT
10552535 AAACCGGTCAAACCAGTTAA
1 AAACCGGTCAAACCAGTTAA
* *
10552555 AAACCGGTTAAACCGGTTA
1 AAACCGGTCAAACCAGTTA
10552574 TTTCAACCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (20 bp):
AAACCGGTCAAACCAGTTAA
Found at i:10559575 original size:29 final size:29
Alignment explanation
Indices: 10559550--10559670 Score: 140
Period size: 29 Copynumber: 4.2 Consensus size: 29
10559540 AATAATTACT
*
10559550 AAAATAGTACCTTTCCGAATTAAATTCCC
1 AAAATAGCACCTTTCCGAATTAAATTCCC
**
10559579 AAAATAGCACCTTTTTGAATTAAATTCCC
1 AAAATAGCACCTTTCCGAATTAAATTCCC
** *
10559608 AAAATAGCACCCATCTTGAATT-AATTCCC
1 AAAATAGCACCTTTC-CGAATTAAATTCCC
10559637 AAAATAGCACCCATTT-CGAATT-AATTCCC
1 AAAATAGCA-CC-TTTCCGAATTAAATTCCC
10559666 AAAAT
1 AAAAT
10559671 GTCACCCGAT
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
29 71 0.89
30 8 0.10
31 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.30
Consensus pattern (29 bp):
AAAATAGCACCTTTCCGAATTAAATTCCC
Found at i:10559677 original size:29 final size:30
Alignment explanation
Indices: 10559565--10559670 Score: 157
Period size: 29 Copynumber: 3.6 Consensus size: 30
10559555 AGTACCTTTC
*
10559565 CGAATTAAATTCCCAAAATAGCA-CCTTTT
1 CGAATTAAATTCCCAAAATAGCACCCATTT
*
10559594 TGAATTAAATTCCCAAAATAGCACCCATCTT
1 CGAATTAAATTCCCAAAATAGCACCCAT-TT
10559625 -GAATT-AATTCCCAAAATAGCACCCATTT
1 CGAATTAAATTCCCAAAATAGCACCCATTT
10559653 CGAATT-AATTCCCAAAAT
1 CGAATTAAATTCCCAAAAT
10559671 GTCACCCGAT
Statistics
Matches: 72, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
28 2 0.03
29 60 0.83
30 8 0.11
31 2 0.03
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.29
Consensus pattern (30 bp):
CGAATTAAATTCCCAAAATAGCACCCATTT
Found at i:10559708 original size:18 final size:17
Alignment explanation
Indices: 10559684--10559735 Score: 68
Period size: 18 Copynumber: 3.0 Consensus size: 17
10559674 ACCCGATCAA
10559684 CGGTCAACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
* *
10559701 CGGGTCAACGAGTAGGGT
1 C-GGTCAACGGGTCGGGT
*
10559719 CGGTCAATGGGTCGGGT
1 CGGTCAACGGGTCGGGT
10559736 TAAACCGGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.15, C:0.19, G:0.46, T:0.19
Consensus pattern (17 bp):
CGGTCAACGGGTCGGGT
Found at i:10563007 original size:29 final size:29
Alignment explanation
Indices: 10562970--10563069 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
10562960 TTTTTTAAAT
* *
10562970 AATTACTAAAATAGCATATTTTCGAATTA
1 AATTCCTAAAATAGCACATTTTCGAATTA
* * *
10562999 AATTCCTAATATAACACCTTTTCGAATTA
1 AATTCCTAAAATAGCACATTTTCGAATTA
*
10563028 AATTTCC-AAAATAGCACCCA-TTTCG-ATTT
1 AA-TTCCTAAAATAGCA--CATTTTCGAATTA
*
10563057 AATTCCCAAAATA
1 AATTCCTAAAATA
10563070 TCACCCAGTC
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
28 4 0.07
29 44 0.76
30 9 0.16
31 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (29 bp):
AATTCCTAAAATAGCACATTTTCGAATTA
Found at i:10563074 original size:29 final size:30
Alignment explanation
Indices: 10562989--10563076 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 30
10562979 AATAGCATAT
* * * *
10562989 TTTCGAATTAAATTCCTAATATAACA-CCT
1 TTTCGAATTAAATTCCCAAAATAGCACCCA
*
10563018 TTTCGAATTAAATTTCCAAAATAGCACCCA
1 TTTCGAATTAAATTCCCAAAATAGCACCCA
* *
10563048 TTTCG-ATTTAATTCCCAAAATATCACCCA
1 TTTCGAATTAAATTCCCAAAATAGCACCCA
10563077 GTCAATGGTA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
29 43 0.86
30 7 0.14
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.34
Consensus pattern (30 bp):
TTTCGAATTAAATTCCCAAAATAGCACCCA
Found at i:10572061 original size:18 final size:19
Alignment explanation
Indices: 10572038--10572074 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
10572028 TCAATCTCAT
*
10572038 ATCAAA-TTCAATTTAAAC
1 ATCAAATTTCAATATAAAC
10572056 ATCAAATTTCAATATAAAC
1 ATCAAATTTCAATATAAAC
10572075 CCTAGGTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.32
Consensus pattern (19 bp):
ATCAAATTTCAATATAAAC
Found at i:10572889 original size:29 final size:28
Alignment explanation
Indices: 10572868--10572965 Score: 151
Period size: 29 Copynumber: 3.4 Consensus size: 28
10572858 ATTGTTAAAC
*
10572868 AAGTGATATTTTGATAATTATTTCAAAAA
1 AAGTGATATTTTGGTAATTATTTC-AAAA
*
10572897 AAGTGATATTTTGGTAATTATTTCGAAA
1 AAGTGATATTTTGGTAATTATTTCAAAA
10572925 AAGTGATATTTTGGTAATTATTTCGAAAA
1 AAGTGATATTTTGGTAATTATTTC-AAAA
*
10572954 AGGTGATATTTT
1 AAGTGATATTTT
10572966 CGTATTTAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
28 27 0.42
29 37 0.58
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (28 bp):
AAGTGATATTTTGGTAATTATTTCAAAA
Found at i:10572934 original size:28 final size:28
Alignment explanation
Indices: 10572868--10572965 Score: 160
Period size: 28 Copynumber: 3.4 Consensus size: 28
10572858 ATTGTTAAAC
* *
10572868 AAGTGATATTTTGATAATTATTTCAAAAA
1 AAGTGATATTTTGGTAATTATTTC-GAAA
10572897 AAGTGATATTTTGGTAATTATTTCGAAA
1 AAGTGATATTTTGGTAATTATTTCGAAA
10572925 AAGTGATATTTTGGTAATTATTTCGAAA
1 AAGTGATATTTTGGTAATTATTTCGAAA
10572953 AAGGTGATATTTT
1 AA-GTGATATTTT
10572966 CGTATTTAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
28 33 0.50
29 33 0.50
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (28 bp):
AAGTGATATTTTGGTAATTATTTCGAAA
Found at i:10577138 original size:29 final size:29
Alignment explanation
Indices: 10577096--10577152 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
10577086 AATTTCGGTT
* *
10577096 ATGGTGGTATTTTCATAAATATTGTTAAG
1 ATGGTGGTAGTTTCATAAATATTATTAAG
* *
10577125 ATGGTGTTAGTTTCGTAAATATTATTAA
1 ATGGTGGTAGTTTCATAAATATTATTAA
10577153 ACAAGTGATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.46
Consensus pattern (29 bp):
ATGGTGGTAGTTTCATAAATATTATTAAG
Found at i:10577286 original size:28 final size:28
Alignment explanation
Indices: 10577155--10577278 Score: 196
Period size: 28 Copynumber: 4.4 Consensus size: 28
10577145 ATTATTAAAC
10577155 AAGTGATATTTTGGTAATTATTT-AAAA
1 AAGTGATATTTTGGTAATTATTTCAAAA
10577182 AAGTGATATTTTGGTAATTATTTCAAAAA
1 AAGTGATATTTTGGTAATTATTTC-AAAA
* *
10577211 AAGTGAAATTTTGGTAATTATTTCCAAA
1 AAGTGATATTTTGGTAATTATTTCAAAA
* *
10577239 ATGTGATATTTTGGTAATTATTTCGAAA
1 AAGTGATATTTTGGTAATTATTTCAAAA
10577267 AAGTGATATTTT
1 AAGTGATATTTT
10577279 CATAATTAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
27 23 0.26
28 39 0.44
29 27 0.30
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (28 bp):
AAGTGATATTTTGGTAATTATTTCAAAA
Found at i:10581411 original size:29 final size:29
Alignment explanation
Indices: 10581368--10581425 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
10581358 TAATTTCGGT
*
10581368 TATGGTGGTATTTTCGTAAATATTGTTAA
1 TATGGTGGTAGTTTCGTAAATATTGTTAA
*
10581397 TATGGTGTTAGTTTCGTAAATATTGTTAA
1 TATGGTGGTAGTTTCGTAAATATTGTTAA
10581426 ACAAGTGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.48
Consensus pattern (29 bp):
TATGGTGGTAGTTTCGTAAATATTGTTAA
Found at i:10581444 original size:29 final size:28
Alignment explanation
Indices: 10581376--10581501 Score: 103
Period size: 29 Copynumber: 4.4 Consensus size: 28
10581366 GTTATGGTGG
** *
10581376 TATTTTCGTAAATATTGTTAATATGGTGT
1 TATTTTCGTAAATATTGTTAA-AAAGTGA
*
10581405 TAGTTTCGTAAATATTGTTAAACAAGTGA
1 TATTTTCGTAAATATTGTTAAA-AAGTGA
* *
10581434 TATTTTGGTAATTATT-TTGAAAAAGTGA
1 TATTTTCGTAAATATTGTT-AAAAAGTGA
* * * *
10581462 TATTTTGGTAATTATT-TCGAAAAAGGTAA
1 TATTTTCGTAAATATTGT-TAAAAA-GTGA
10581491 TATTTTCGTAA
1 TATTTTCGTAA
10581502 TTAAAAAAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
28 31 0.37
29 52 0.63
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (28 bp):
TATTTTCGTAAATATTGTTAAAAAGTGA
Found at i:10581463 original size:28 final size:28
Alignment explanation
Indices: 10581428--10581504 Score: 118
Period size: 28 Copynumber: 2.7 Consensus size: 28
10581418 ATTGTTAAAC
*
10581428 AAGTGATATTTTGGTAATTATTTTGAAA
1 AAGTGATATTTTGGTAATTATTTCGAAA
10581456 AAGTGATATTTTGGTAATTATTTCGAAA
1 AAGTGATATTTTGGTAATTATTTCGAAA
* *
10581484 AAGGTAATATTTTCGTAATTA
1 AA-GTGATATTTTGGTAATTA
10581505 AAAAAATGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 29 0.64
29 16 0.36
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (28 bp):
AAGTGATATTTTGGTAATTATTTCGAAA
Found at i:10590469 original size:29 final size:29
Alignment explanation
Indices: 10590427--10590483 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
10590417 AATTTCGGAT
* *
10590427 ATGGTGGTATTTTCGTAAATATTGTTAAG
1 ATGGTGGTAGTTTCGTAAATATTATTAAG
*
10590456 ATGGTGTTAGTTTCGTAAATATTATTAA
1 ATGGTGGTAGTTTCGTAAATATTATTAA
10590484 ACAAGTGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.46
Consensus pattern (29 bp):
ATGGTGGTAGTTTCGTAAATATTATTAAG
Found at i:10590502 original size:29 final size:28
Alignment explanation
Indices: 10590486--10590618 Score: 171
Period size: 29 Copynumber: 4.7 Consensus size: 28
10590476 ATTATTAAAC
10590486 AAGTGATATTTTGGTAATTATTTAAAAAA
1 AAGTGATATTTTGGTAATTATTT-AAAAA
*
10590515 AAGTGATATTTTGGTAATTATTTCAAAA
1 AAGTGATATTTTGGTAATTATTTAAAAA
*
10590543 AAGTGATA-TTTGGTAATTA-TTAGGAAA
1 AAGTGATATTTTGGTAATTATTTA-AAAA
* *
10590570 AGGTGATATTTTGGTAATTATTTCAGAAA
1 AAGTGATATTTTGGTAATTATTT-AAAAA
* *
10590599 AGGTGATATTTTCGTAATTA
1 AAGTGATATTTTGGTAATTA
10590619 AAAAAATGTT
Statistics
Matches: 95, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
26 2 0.02
27 21 0.22
28 23 0.24
29 48 0.51
30 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.41
Consensus pattern (28 bp):
AAGTGATATTTTGGTAATTATTTAAAAA
Found at i:10590578 original size:55 final size:58
Alignment explanation
Indices: 10590486--10590618 Score: 200
Period size: 55 Copynumber: 2.3 Consensus size: 58
10590476 ATTATTAAAC
10590486 AAGTGATATTTTGGTAATTATTTAAAAAAAAGTGATATTTTGGTAATTATTTCA-AAA
1 AAGTGATATTTTGGTAATTATTTAAAAAAAAGTGATATTTTGGTAATTATTTCAGAAA
** *
10590543 AAGTGATA-TTTGGTAATTA-TTAGGAAAAGGTGATATTTTGGTAATTATTTCAGAAA
1 AAGTGATATTTTGGTAATTATTTAAAAAAAAGTGATATTTTGGTAATTATTTCAGAAA
* *
10590599 AGGTGATATTTTCGTAATTA
1 AAGTGATATTTTGGTAATTA
10590619 AAAAAATGTT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
55 30 0.43
56 21 0.30
57 18 0.26
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.41
Consensus pattern (58 bp):
AAGTGATATTTTGGTAATTATTTAAAAAAAAGTGATATTTTGGTAATTATTTCAGAAA
Found at i:10600554 original size:19 final size:20
Alignment explanation
Indices: 10600530--10600568 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
10600520 AAGCTAAAAA
10600530 TGGTATC-ATTACTC-AGGGT
1 TGGTATCGA-TACTCAAGGGT
10600549 TGGTATCGATACTCAAGGGT
1 TGGTATCGATACTCAAGGGT
10600569 CATTACGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (20 bp):
TGGTATCGATACTCAAGGGT
Found at i:10603473 original size:30 final size:30
Alignment explanation
Indices: 10603417--10603474 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
10603407 ATGCCATTGG
* *
10603417 AAGAGAATGCAAGTGTGCAAACTGAAGTGA
1 AAGAGAATGCAAGTATACAAACTGAAGTGA
*
10603447 AAGAGAATG-AATGTATACAAAGTGAAGT
1 AAGAGAATGCAA-GTATACAAACTGAAGT
10603475 CAATGCCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.47, C:0.07, G:0.28, T:0.19
Consensus pattern (30 bp):
AAGAGAATGCAAGTATACAAACTGAAGTGA
Found at i:10607384 original size:58 final size:58
Alignment explanation
Indices: 10607320--10607461 Score: 160
Period size: 58 Copynumber: 2.4 Consensus size: 58
10607310 CACAAATCAT
* * *
10607320 AAACCCAACATAAACCCTAACAGAAAGCCCAATA-TTTAAGAAAACAAATCATTTCTAG
1 AAACCCAACATAAACCCTAACA-AAAACACAACATTTTAAGAAAACAAATCATTTCTAG
* * **** **
10607378 AAACCCAACTTAAACCCTAACAAAAACACAACATTTTAAGCAAATTTTTTTTTTCTAG
1 AAACCCAACATAAACCCTAACAAAAACACAACATTTTAAGAAAACAAATCATTTCTAG
*
10607436 AAACCCAACATAAGCCCTAACAAAAA
1 AAACCCAACATAAACCCTAACAAAAA
10607462 ACTCAAACAA
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
57 8 0.11
58 62 0.89
ACGTcount: A:0.49, C:0.25, G:0.05, T:0.22
Consensus pattern (58 bp):
AAACCCAACATAAACCCTAACAAAAACACAACATTTTAAGAAAACAAATCATTTCTAG
Found at i:10607847 original size:27 final size:27
Alignment explanation
Indices: 10607817--10607875 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
10607807 GAGAAGGTTG
10607817 GGGAAAATCAAGTTTATTATTAGAAAA
1 GGGAAAATCAAGTTTATTATTAGAAAA
*
10607844 GGGAAAATCAAGTTTATTATTATAAAA
1 GGGAAAATCAAGTTTATTATTAGAAAA
*
10607871 AGGAA
1 GGGAA
10607876 TAACATCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.49, C:0.03, G:0.19, T:0.29
Consensus pattern (27 bp):
GGGAAAATCAAGTTTATTATTAGAAAA
Found at i:10626169 original size:29 final size:29
Alignment explanation
Indices: 10626127--10626185 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 29
10626117 ATTTTCACCT
10626127 AACTAAATTGATGTAAGCAAT-GACATCAA
1 AACTAAATTGATGTAAGCAATGGA-ATCAA
10626156 AACTAAATTGATGTAAGCAATGGAATCAA
1 AACTAAATTGATGTAAGCAATGGAATCAA
10626185 A
1 A
10626186 TTAGTTTAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 27 0.93
30 2 0.07
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGGAATCAA
Found at i:10646110 original size:24 final size:24
Alignment explanation
Indices: 10646083--10646151 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
10646073 AAACGGAGAT
*
10646083 ATCAGAAATCAAAACAAAATTCAG
1 ATCAGAAATCAGAACAAAATTCAG
*
10646107 ATCA-AATATCAGAACAAAATCCAG
1 ATCAGAA-ATCAGAACAAAATTCAG
*
10646131 ATCAGAAATCAGAACAGAATT
1 ATCAGAAATCAGAACAAAATT
10646152 AAGGTAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.05
24 35 0.90
25 2 0.05
ACGTcount: A:0.55, C:0.17, G:0.10, T:0.17
Consensus pattern (24 bp):
ATCAGAAATCAGAACAAAATTCAG
Found at i:10646149 original size:12 final size:11
Alignment explanation
Indices: 10646088--10646146 Score: 55
Period size: 12 Copynumber: 5.0 Consensus size: 11
10646078 GAGATATCAG
*
10646088 AAATCAAAACA
1 AAATCAGAACA
*
10646099 AAATTCAGATCA
1 AAA-TCAGAACA
10646111 AATATCAGAACA
1 AA-ATCAGAACA
*
10646123 AAATCCAGATCA
1 AAAT-CAGAACA
10646135 GAAATCAGAACA
1 -AAATCAGAACA
10646147 GAATTAAGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 5 0.13
12 29 0.74
13 5 0.13
ACGTcount: A:0.58, C:0.19, G:0.08, T:0.15
Consensus pattern (11 bp):
AAATCAGAACA
Found at i:10646191 original size:24 final size:25
Alignment explanation
Indices: 10646083--10646189 Score: 82
Period size: 24 Copynumber: 4.4 Consensus size: 25
10646073 AAACGGAGAT
* *
10646083 ATCAGAAATCAAAACAAAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* *
10646107 ATCA-AATATCAGAACA-AAATCCAG
1 ATCAGAA-ATCAGAACAGAATTCAAG
10646131 ATCAGAAATCAGAACAGAATT-AAG
1 ATCAGAAATCAGAACAGAATTCAAG
* * * *
10646155 GTAATG-TATCATAACAGAATTCAAG
1 ATCA-GAAATCAGAACAGAATTCAAG
10646180 -TCAGAAATCA
1 ATCAGAAATCA
10646190 TATAAAATAT
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
23 7 0.11
24 50 0.76
25 9 0.14
ACGTcount: A:0.52, C:0.16, G:0.12, T:0.20
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:10648742 original size:55 final size:55
Alignment explanation
Indices: 10648682--10649005 Score: 447
Period size: 55 Copynumber: 5.9 Consensus size: 55
10648672 ACGTAGTGCT
* *
10648682 GATACGGTCGTTCATAAACATATTATGAATTTTGTGGTTTTGCACACTTAATGTC
1 GATACGGTCGTTCATAAACATATTATGAATTTCGTGGTTTTGCACACTTAGTGTC
* *
10648737 AATACGGTCTTTCATAAACATATTATGAATTAT-GTGGTTTTGCACACTTAGTGTC
1 GATACGGTCGTTCATAAACATATTATGAATT-TCGTGGTTTTGCACACTTAGTGTC
** * * *
10648792 GATACATTCGTTCATAAACATACTATGAATTTCGTGGTTTTGCACACCTAGT-AC
1 GATACGGTCGTTCATAAACATATTATGAATTTCGTGGTTTTGCACACTTAGTGTC
* * * *
10648846 TGATACGGTCGTTCATAAACATATTATGAA-TTCCTAGGTTTTGCACAGTTAGTTTT
1 -GATACGGTCGTTCATAAACATATTATGAATTTCGT-GGTTTTGCACACTTAGTGTC
*
10648902 GATACGGTCGTTCATAAACATATTATGAATTTCGTGGTTTTACACACTTAGTGTC
1 GATACGGTCGTTCATAAACATATTATGAATTTCGTGGTTTTGCACACTTAGTGTC
** *
10648957 GATACAATCGTTCATAAACATATTATAAATTTCGTGGTTTTGCACACTT
1 GATACGGTCGTTCATAAACATATTATGAATTTCGTGGTTTTGCACACTT
10649006 TCTTTTCTCT
Statistics
Matches: 236, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
54 6 0.03
55 225 0.95
56 5 0.02
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (55 bp):
GATACGGTCGTTCATAAACATATTATGAATTTCGTGGTTTTGCACACTTAGTGTC
Found at i:10648952 original size:165 final size:165
Alignment explanation
Indices: 10648670--10649003 Score: 510
Period size: 165 Copynumber: 2.0 Consensus size: 165
10648660 TTTAAAGTGT
* * * *
10648670 ACACGTAGTGCTGATACGGTCGTTCATAAACATATTATGAATTTTGTGGTTTTGCACACTTAATG
1 ACACCTAGTACTGATACGGTCGTTCATAAACATATTATGAATTCTGAGGTTTTGCACACTTAATG
* * *
10648735 TCAATACGGTCTTTCATAAACATATTATGAATTATGTGGTTTTGCACACTTAGTGTCGATACATT
66 TCAATACGGTCGTTCATAAACATATTATGAATTATGTGGTTTTACACACTTAGTGTCGATACAAT
*
10648800 CGTTCATAAACATACTATGAATTTCGTGGTTTTGC
131 CGTTCATAAACATACTATAAATTTCGTGGTTTTGC
* *
10648835 ACACCTAGTACTGATACGGTCGTTCATAAACATATTATGAATTCCT-AGGTTTTGCACAGTTAGT
1 ACACCTAGTACTGATACGGTCGTTCATAAACATATTATGAATT-CTGAGGTTTTGCACACTTAAT
* **
10648899 TTTGATACGGTCGTTCATAAACATATTATGAATT-TCGTGGTTTTACACACTTAGTGTCGATACA
65 GTCAATACGGTCGTTCATAAACATATTATGAATTAT-GTGGTTTTACACACTTAGTGTCGATACA
*
10648963 ATCGTTCATAAACATATTATAAATTTCGTGGTTTTGC
129 ATCGTTCATAAACATACTATAAATTTCGTGGTTTTGC
10649000 ACAC
1 ACAC
10649004 TTTCTTTTCT
Statistics
Matches: 153, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
164 1 0.01
165 151 0.99
166 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (165 bp):
ACACCTAGTACTGATACGGTCGTTCATAAACATATTATGAATTCTGAGGTTTTGCACACTTAATG
TCAATACGGTCGTTCATAAACATATTATGAATTATGTGGTTTTACACACTTAGTGTCGATACAAT
CGTTCATAAACATACTATAAATTTCGTGGTTTTGC
Found at i:10649108 original size:21 final size:21
Alignment explanation
Indices: 10649084--10649123 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
10649074 TTCATTTTCA
10649084 CTCTCAAT-TCTCTTTTCAATG
1 CTCTCAATGTCT-TTTTCAATG
10649105 CTCTCAATGTCTTTTTCAA
1 CTCTCAATGTCTTTTTCAA
10649124 CTCTTGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.20, C:0.28, G:0.05, T:0.47
Consensus pattern (21 bp):
CTCTCAATGTCTTTTTCAATG
Found at i:10657508 original size:23 final size:23
Alignment explanation
Indices: 10657482--10657526 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
10657472 TAGCTATAGA
*
10657482 TATAATAT-ATATATGATAATAAT
1 TATAATATAACATATGA-AATAAT
*
10657505 TATATTATAACATATGAAATAA
1 TATAATATAACATATGAAATAA
10657527 GCATATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
TATAATATAACATATGAAATAAT
Found at i:10662338 original size:7 final size:7
Alignment explanation
Indices: 10662326--10662368 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
10662316 TAGGAGTATT
10662326 TTTTTTC
1 TTTTTTC
10662333 TTTTTTC
1 TTTTTTC
10662340 -TTTTTC
1 TTTTTTC
*
10662346 TTCTTTC
1 TTTTTTC
10662353 -TTTTTC
1 TTTTTTC
10662359 TTTTTT-
1 TTTTTTC
10662365 TTTT
1 TTTT
10662369 GTTGCAGCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 15 0.47
7 17 0.53
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:10662343 original size:6 final size:6
Alignment explanation
Indices: 10662327--10662368 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
10662317 AGGAGTATTT
10662327 TTTTTC TTTTTTC TTTTTC TTCTTTC TTTTTC TTTTT- TTTTT
1 TTTTTC -TTTTTC TTTTTC TT-TTTC TTTTTC TTTTTC TTTTT
10662369 GTTGCAGCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.15
6 17 0.50
7 12 0.35
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:10662345 original size:13 final size:13
Alignment explanation
Indices: 10662327--10662368 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
10662317 AGGAGTATTT
10662327 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
*
10662340 TTTTTCTTCTTTC
1 TTTTTCTTTTTTC
10662353 TTTTTCTTTTTT-
1 TTTTTCTTTTTTC
10662365 TTTT
1 TTTT
10662369 GTTGCAGCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 4 0.15
13 23 0.85
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:10662584 original size:15 final size:15
Alignment explanation
Indices: 10662564--10662599 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
10662554 AATATGGAAG
10662564 AAGAAAGGAAATGAT
1 AAGAAAGGAAATGAT
*
10662579 AAGAAAGGAAATGGT
1 AAGAAAGGAAATGAT
10662594 AAGAAA
1 AAGAAA
10662600 TTATATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.28, T:0.11
Consensus pattern (15 bp):
AAGAAAGGAAATGAT
Found at i:10665958 original size:15 final size:15
Alignment explanation
Indices: 10665935--10665973 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
10665925 AGTAAATGAG
10665935 AAAAGATGAAATAAA-
1 AAAA-ATGAAATAAAT
10665950 AATAAATGAAATAAAT
1 AA-AAATGAAATAAAT
10665966 AAAAATGA
1 AAAAATGA
10665974 GGATAACTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (15 bp):
AAAAATGAAATAAAT
Found at i:10666194 original size:13 final size:12
Alignment explanation
Indices: 10666170--10666205 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
10666160 TGTAGGAGTC
10666170 TTTTTCTTTTTG
1 TTTTTCTTTTTG
10666182 TTTTTCTTCTTTG
1 TTTTTCTT-TTTG
*
10666195 TTTTGCTTTTT
1 TTTTTCTTTTT
10666206 TTTGTTGCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTTTG
Found at i:10666627 original size:14 final size:14
Alignment explanation
Indices: 10666608--10666635 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10666598 TGTTGTGAAG
10666608 GATGGTGATGGAAA
1 GATGGTGATGGAAA
10666622 GATGGTGATGGAAA
1 GATGGTGATGGAAA
10666636 TAGTATCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (14 bp):
GATGGTGATGGAAA
Found at i:10668614 original size:59 final size:59
Alignment explanation
Indices: 10668522--10668650 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
10668512 CGTAATGCAA
* * **
10668522 TCCCGAGTATGACACATAAGGTCATGTCCACCATATGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
* * ** *
10668581 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
10668640 TCCCGAATATG
1 TCCCGAATATG
10668651 CAGCCTACTG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:10672718 original size:7 final size:6
Alignment explanation
Indices: 10672689--10672731 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
10672679 GTTGTAGGAA
*
10672689 TCTTTT TC-TTT TCTTTT TCTTTT TCTTTTT TCTTTT GCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TC-TTTT TCTTTT TCTTTT T
10672732 TTGTTGCAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (6 bp):
TCTTTT
Found at i:10672720 original size:13 final size:13
Alignment explanation
Indices: 10672691--10672732 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
10672681 TGTAGGAATC
10672691 TTTTTC-TTTTC-
1 TTTTTCTTTTTCT
10672702 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
*
10672715 TTTTTCTTTTGCT
1 TTTTTCTTTTTCT
10672728 TTTTT
1 TTTTT
10672733 TGTTGCAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 6 0.21
12 5 0.18
13 17 0.61
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.83
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:10674381 original size:10 final size:10
Alignment explanation
Indices: 10674368--10674433 Score: 60
Period size: 10 Copynumber: 6.4 Consensus size: 10
10674358 TCTTTTTGAC
10674368 TTTTTTTTCT
1 TTTTTTTTCT
*
10674378 TTTTCTTTCT
1 TTTTTTTTCT
*
10674388 TTTTTTTTGAAT
1 TTTTTTTT--CT
*
10674400 TTTTTCTTCT
1 TTTTTTTTCT
* *
10674410 TCTTTTTGCT
1 TTTTTTTTCT
*
10674420 TTTCTTTTCT
1 TTTTTTTTCT
10674430 TTTT
1 TTTT
10674434 GTACTCTAAT
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
10 34 0.81
12 8 0.19
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:10674403 original size:31 final size:32
Alignment explanation
Indices: 10674352--10674427 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
10674342 TTTTCTTGGC
* *
10674352 TTGCTTTCTTTTTGACTTTTTT-TTCTT-TTT
1 TTGCTTTTTTTTTGAATTTTTTCTTCTTCTTT
*
10674382 CTTTCTTTTTTTTTGAATTTTTTCTTCTTCTTT
1 -TTGCTTTTTTTTTGAATTTTTTCTTCTTCTTT
*
10674415 TTGCTTTTCTTTT
1 TTGCTTTTTTTTT
10674428 CTTTTTGTAC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
31 19 0.50
32 16 0.42
33 3 0.08
ACGTcount: A:0.04, C:0.14, G:0.05, T:0.76
Consensus pattern (32 bp):
TTGCTTTTTTTTTGAATTTTTTCTTCTTCTTT
Found at i:10674758 original size:22 final size:21
Alignment explanation
Indices: 10674732--10674772 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
10674722 GGCTGCGAAA
10674732 TTGATGGTCTTGATGGATGATG
1 TTGATGGTCTTGAT-GATGATG
*
10674754 TTGATGGTGTTGATGATGA
1 TTGATGGTCTTGATGATGA
10674773 AATGGAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.20, C:0.02, G:0.37, T:0.41
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGATG
Found at i:10679828 original size:15 final size:15
Alignment explanation
Indices: 10679804--10679839 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
10679794 TTTGATAACT
*
10679804 ATTCTATCCATTTCA
1 ATTCTTTCCATTTCA
10679819 ATTCTTTCCATTTCA
1 ATTCTTTCCATTTCA
10679834 ATTCTT
1 ATTCTT
10679840 AATTATTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.22, C:0.25, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTCTTTCCATTTCA
Found at i:10683997 original size:30 final size:30
Alignment explanation
Indices: 10683961--10684027 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
10683951 ATTCTTTGTG
*
10683961 AGCTGTTTATGTC-TCCCAAATGCTCCACTA
1 AGCTGTTTATGTCTTCCC-AATGCTCCACCA
*
10683991 AGCTGTTTATGTCTTCTCAATGCTCCACCA
1 AGCTGTTTATGTCTTCCCAATGCTCCACCA
10684021 AGCTGTT
1 AGCTGTT
10684028 CCAACGTGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 31 0.91
31 3 0.09
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (30 bp):
AGCTGTTTATGTCTTCCCAATGCTCCACCA
Found at i:10685875 original size:30 final size:29
Alignment explanation
Indices: 10685840--10685933 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 29
10685830 CACACGTTGG
*
10685840 AACAGCTTGGTAGAGCATTTGGAAGATATA
1 AACAGCTTGGT-GAGCATTTGGAAGACATA
* *
10685870 TACAGCTTGGTGGAGCATTTAGAAGACATA
1 AACAGCTTGGT-GAGCATTTGGAAGACATA
* * *
10685900 AACAACTTAGTGAAGCATTTGGGAGACATA
1 AACAGCTTGGTG-AGCATTTGGAAGACATA
10685930 AACA
1 AACA
10685934 ACTCAAAAAG
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 1 0.02
30 53 0.98
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.24
Consensus pattern (29 bp):
AACAGCTTGGTGAGCATTTGGAAGACATA
Found at i:10694116 original size:5 final size:5
Alignment explanation
Indices: 10694103--10694167 Score: 69
Period size: 5 Copynumber: 13.0 Consensus size: 5
10694093 TTGGAGTTTA
* * * *
10694103 AAAAG AAAAT AAAAG AAAAA AAGAAG AAAAA AAAAG AAAAA AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAAAG
*
10694154 AAAA- AGAAG AAAAG
1 AAAAG AAAAG AAAAG
10694168 TCAAAAAGGA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
4 3 0.06
5 41 0.85
6 4 0.08
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:10694118 original size:10 final size:10
Alignment explanation
Indices: 10694102--10694166 Score: 94
Period size: 10 Copynumber: 6.2 Consensus size: 10
10694092 ATTGGAGTTT
10694102 AAAAAGAAAA
1 AAAAAGAAAA
*
10694112 TAAAAGAAAA
1 AAAAAGAAAA
10694122 AAAGAAGAAAA
1 AAA-AAGAAAA
10694133 AAAAAGAAAA
1 AAAAAGAAAA
10694143 AAAAAGAAAA
1 AAAAAGAAAA
10694153 GAAAAAGAAGAA
1 -AAAAAGAA-AA
10694165 AA
1 AA
10694167 GTCAAAAAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
10 28 0.56
11 20 0.40
12 2 0.04
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:10694131 original size:21 final size:21
Alignment explanation
Indices: 10694105--10694167 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
10694095 GGAGTTTAAA
*
10694105 AAGAAAATAAAAGAAAAAAAG
1 AAGAAAAAAAAAGAAAAAAAG
10694126 AAGAAAAAAAAAGAAAAAAA-
1 AAGAAAAAAAAAGAAAAAAAG
*
10694146 AAGAAAAGAAAAAGAAGAAAAG
1 AAGAAAA-AAAAAGAAAAAAAG
10694168 TCAAAAAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 7 0.18
21 31 0.82
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.02
Consensus pattern (21 bp):
AAGAAAAAAAAAGAAAAAAAG
Found at i:10694140 original size:31 final size:31
Alignment explanation
Indices: 10694102--10694166 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
10694092 ATTGGAGTTT
*
10694102 AAAAAGAAAATAAAAGAAAA-AAAGAAGAAAA
1 AAAAAGAAAAAAAAAGAAAAGAAA-AAGAAAA
*
10694133 AAAAAGAAAAAAAAAGAAAAGAAAAAGAAGA
1 AAAAAGAAAAAAAAAGAAAAGAAAAAGAAAA
10694164 AAA
1 AAA
10694167 GTCAAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.02
Consensus pattern (31 bp):
AAAAAGAAAAAAAAAGAAAAGAAAAAGAAAA
Found at i:10694754 original size:14 final size:14
Alignment explanation
Indices: 10694725--10694764 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
10694715 TTGGTGTGAA
*
10694725 GGTGATGG-ACTAT
1 GGTGATGGAAATAT
10694738 GGTGATGGAAATAT
1 GGTGATGGAAATAT
*
10694752 GGTGATGAAAATA
1 GGTGATGGAAATA
10694765 GTGTCATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.35, C:0.03, G:0.35, T:0.28
Consensus pattern (14 bp):
GGTGATGGAAATAT
Found at i:10695134 original size:19 final size:20
Alignment explanation
Indices: 10695096--10695138 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
10695086 GAAACCCCTT
*
10695096 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
10695116 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
10695135 TGAA
1 TGAA
10695139 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:10701103 original size:23 final size:24
Alignment explanation
Indices: 10701065--10701117 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
10701055 AACTTTTCTT
10701065 TTTCTTCTTTTTGAGTGCTTTCAA
1 TTTCTTCTTTTTGAGTGCTTTCAA
* *
10701089 TTTCTTC-TTTTGAGTGCTTTTAT
1 TTTCTTCTTTTTGAGTGCTTTCAA
10701112 TTTCTT
1 TTTCTT
10701118 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.09, C:0.15, G:0.11, T:0.64
Consensus pattern (24 bp):
TTTCTTCTTTTTGAGTGCTTTCAA
Found at i:10705407 original size:18 final size:16
Alignment explanation
Indices: 10705380--10705434 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
10705370 ATGATAAAGT
10705380 AATG-AAAATAAGAAA
1 AATGAAAAATAAGAAA
*
10705395 AGATGAAAGAATAAG-GA
1 A-ATGAAA-AATAAGAAA
10705412 AATGAAAAAGTAAGAAA
1 AATGAAAAA-TAAGAAA
10705429 AATGAA
1 AATGAA
10705435 GATAACTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 3 0.09
16 13 0.39
17 11 0.33
18 6 0.18
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (16 bp):
AATGAAAAATAAGAAA
Found at i:10705413 original size:27 final size:26
Alignment explanation
Indices: 10705362--10705413 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
10705352 AAAAAAAGGT
* *
10705362 TAAGAAAAATGATAAAGTAATGAAAA
1 TAAGAAAAATGATAAAATAAGGAAAA
10705388 TAAGAAAAGATGA-AAGAATAAGGAAA
1 TAAGAAAA-ATGATAA-AATAAGGAAA
10705414 TGAAAAAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.15
Consensus pattern (26 bp):
TAAGAAAAATGATAAAATAAGGAAAA
Found at i:10706474 original size:20 final size:20
Alignment explanation
Indices: 10706449--10706486 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10706439 TGAAACCCCT
*
10706449 TTGAAAACACATGATTTTTA
1 TTGAAAACACATAATTTTTA
*
10706469 TTGAAAATACATAATTTT
1 TTGAAAACACATAATTTT
10706487 AATGAAGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (20 bp):
TTGAAAACACATAATTTTTA
Found at i:10706492 original size:19 final size:20
Alignment explanation
Indices: 10706450--10706492 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
10706440 GAAACCCCTT
* *
10706450 TGAAAACACATGATTTTTAT
1 TGAAAACACATGAATTTTAA
*
10706470 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
10706489 TGAA
1 TGAA
10706493 GATAAATGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:10707667 original size:17 final size:18
Alignment explanation
Indices: 10707647--10707682 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
10707637 CACCTCATAT
10707647 TTTCTTCTA-CCTTTCTA
1 TTTCTTCTATCCTTTCTA
10707664 TTTCTTCTATTCCTTTCTA
1 TTTCTTCTA-TCCTTTCTA
10707683 CCCTAACGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.11, C:0.28, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTCTTCTATCCTTTCTA
Found at i:10710500 original size:23 final size:25
Alignment explanation
Indices: 10710472--10710526 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
10710462 AAATCCAGCA
10710472 AAGAAAATCAAAGCACTC-AAAA-G
1 AAGAAAATCAAAGCACTCAAAAAGG
* *
10710495 AAGAAATTGAAAGCACTCAAAAAGG
1 AAGAAAATCAAAGCACTCAAAAAGG
10710520 AAGAAAA
1 AAGAAAA
10710527 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 16 0.59
24 4 0.15
25 7 0.26
ACGTcount: A:0.62, C:0.13, G:0.16, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAAAGG
Found at i:10714901 original size:22 final size:22
Alignment explanation
Indices: 10714876--10714929 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
10714866 CTAGAAATGC
* *
10714876 ATGCATGGACGTAGGTTACAAT
1 ATGCATGGACGAAGATTACAAT
* *
10714898 ATGCATGGCCGAATATTACAAT
1 ATGCATGGACGAAGATTACAAT
*
10714920 TTGCATGGAC
1 ATGCATGGAC
10714930 TCATGGTGCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (22 bp):
ATGCATGGACGAAGATTACAAT
Found at i:10722953 original size:36 final size:36
Alignment explanation
Indices: 10722906--10722987 Score: 137
Period size: 36 Copynumber: 2.3 Consensus size: 36
10722896 TGCATGGGAT
*
10722906 GCTGGCCATATGGCACACACATGGATGTTCTAGGGG
1 GCTGGTCATATGGCACACACATGGATGTTCTAGGGG
* *
10722942 GCTGGTCATATGGCACGCACATGGGTGTTCTAGGGG
1 GCTGGTCATATGGCACACACATGGATGTTCTAGGGG
10722978 GCTGGTCATA
1 GCTGGTCATA
10722988 CGTACATGGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.20, C:0.21, G:0.35, T:0.24
Consensus pattern (36 bp):
GCTGGTCATATGGCACACACATGGATGTTCTAGGGG
Found at i:10722998 original size:31 final size:31
Alignment explanation
Indices: 10722923--10723017 Score: 111
Period size: 36 Copynumber: 2.9 Consensus size: 31
10722913 ATATGGCACA
*
10722923 CACATGGATGTTCTAGGGGGCTGGTCATATGGCACG
1 CACATGGGTGTTCTAGGGGGCTGGTC--AT---ACG
10722959 CACATGGGTGTTCTAGGGGGCTGGTCATACG
1 CACATGGGTGTTCTAGGGGGCTGGTCATACG
* *
10722990 TACATGGGTGTTCTA-AGGGCTGGTCATA
1 CACATGGGTGTTCTAGGGGGCTGGTCATA
10723018 TGTTCTCCAT
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
30 12 0.21
31 17 0.30
34 2 0.04
36 25 0.45
ACGTcount: A:0.19, C:0.18, G:0.36, T:0.27
Consensus pattern (31 bp):
CACATGGGTGTTCTAGGGGGCTGGTCATACG
Found at i:10726701 original size:35 final size:37
Alignment explanation
Indices: 10726606--10726711 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
10726596 GATACAATCT
*
10726606 GTCCATCACCATTATCACGACTATATCATCACCATAA
1 GTCCATCACCATTATCACGCCTATATCATCACCATAA
10726643 GTCCATCACCATTATCACGCCTATATCATCACCAT-A
1 GTCCATCACCATTATCACGCCTATATCATCACCATAA
* * *
10726679 TTCTATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
10726712 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
35 21 0.32
36 10 0.15
37 34 0.52
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (37 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATAA
Found at i:10732348 original size:37 final size:36
Alignment explanation
Indices: 10732298--10732402 Score: 149
Period size: 37 Copynumber: 2.9 Consensus size: 36
10732288 ATACAATCTA
**
10732298 TCCATCACCATTATCACAACTATATCATCACCATAAG
1 TCCATCACCATTATCACGCCTATATCATCACCAT-AG
* *
10732335 TCCATCACCATTATCACGCCTATATCACCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
10732371 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
10732403 ACTTATAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
35 20 0.32
36 11 0.18
37 31 0.50
ACGTcount: A:0.33, C:0.36, G:0.03, T:0.28
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:10736398 original size:13 final size:13
Alignment explanation
Indices: 10736380--10736437 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
10736370 ACTACCTAAA
10736380 CATCACCATATTC
1 CATCACCATATTC
*
10736393 CATCACCAT-TTT
1 CATCACCATATTC
**
10736405 CA-CACC-TATAA
1 CATCACCATATTC
*
10736416 CATCACCATCTTC
1 CATCACCATATTC
*
10736429 CATTACCAT
1 CATCACCAT
10736438 TGCACGCCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 1 0.03
11 7 0.20
12 8 0.23
13 19 0.54
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (13 bp):
CATCACCATATTC
Found at i:10736485 original size:35 final size:35
Alignment explanation
Indices: 10736380--10736485 Score: 140
Period size: 35 Copynumber: 3.0 Consensus size: 35
10736370 ACTACCTAAA
* * *
10736380 CATCACCATATTCCATCACCATTTTCACACCTATAA
1 CATCACCATCTTCCATCACCA-TTTCACGCCTATAT
* *
10736416 CATCACCATCTTCCATTACCATTGCACGCCTATAT
1 CATCACCATCTTCCATCACCATTTCACGCCTATAT
* *
10736451 CATTACCATCTTCTATCACCATTTCACGCCTATAT
1 CATCACCATCTTCCATCACCATTTCACGCCTATAT
10736486 AACCATAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 42 0.69
36 19 0.31
ACGTcount: A:0.28, C:0.36, G:0.03, T:0.33
Consensus pattern (35 bp):
CATCACCATCTTCCATCACCATTTCACGCCTATAT
Found at i:10737133 original size:16 final size:16
Alignment explanation
Indices: 10737107--10737165 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
10737097 GAGTTGTAAG
10737107 TTATCTTCATTTTCTCT
1 TTAT-TTCATTTTCTCT
* *
10737124 TTATTTCATTTCCTTT
1 TTATTTCATTTTCTCT
*
10737140 TTCTTTCATCTTT-TC-
1 TTATTTCAT-TTTCTCT
10737155 TTATTTCATTT
1 TTATTTCATTT
10737166 CCTTATTCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 2 0.06
15 8 0.23
16 19 0.54
17 6 0.17
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTCATTTTCTCT
Found at i:10742041 original size:13 final size:13
Alignment explanation
Indices: 10742023--10742048 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10742013 ACTACCTAAA
10742023 CATCACCATTTTC
1 CATCACCATTTTC
10742036 CATCACCATTTTC
1 CATCACCATTTTC
10742049 ACGCCTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (13 bp):
CATCACCATTTTC
Found at i:10742073 original size:36 final size:35
Alignment explanation
Indices: 10742017--10742126 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 35
10742007 TAAGATACTA
*
10742017 CCTA-AACATCACCATTTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* * * *
10742052 CCTATAACATCATCATCTTCCATTACCATTGCATG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * *
10742087 CCTATATCATTACCATCTTCTA-CACCATTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
10742121 CCTATA
1 CCTATA
10742127 TAACCACCAA
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
34 15 0.24
35 27 0.44
36 20 0.32
ACGTcount: A:0.28, C:0.35, G:0.04, T:0.34
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:10743633 original size:15 final size:15
Alignment explanation
Indices: 10743614--10743648 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
10743604 TGGCTGCGGA
10743614 ATTGATGGTCTTGAT
1 ATTGATGGTCTTGAT
* *
10743629 GTTGATGGTGTTGAT
1 ATTGATGGTCTTGAT
10743644 ATTGA
1 ATTGA
10743649 AATGGAGATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.20, C:0.03, G:0.31, T:0.46
Consensus pattern (15 bp):
ATTGATGGTCTTGAT
Found at i:10749474 original size:15 final size:15
Alignment explanation
Indices: 10749454--10749482 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10749444 ATAACATTTC
10749454 TTTCCATTTCAATTA
1 TTTCCATTTCAATTA
10749469 TTTCCATTTCAATT
1 TTTCCATTTCAATT
10749483 TCCTTTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTCCATTTCAATTA
Done.