Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008092.1 Hibiscus syriacus cultivar Beakdansim tig00110607_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: 2324158
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2179832 original size:21 final size:21
Alignment explanation
Indices: 2179806--2179888 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 21
2179796 TATTAAAATA
2179806 TTATAA-AAATCATAATAAAAG
1 TTATAATAAAT-ATAATAAAAG
* *
2179827 TTATAATGAATATAATAAAAAAA
1 TTATAATAAATATAAT--AAAAG
*
2179850 TT-TAA-AAACTATATTAAAAG
1 TTATAATAAA-TATAATAAAAG
*
2179870 TTATAATGAATATAA-AAAA
1 TTATAATAAATATAATAAAA
2179889 TAAATTTTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
20 10 0.20
21 20 0.41
22 13 0.27
23 6 0.12
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.31
Consensus pattern (21 bp):
TTATAATAAATATAATAAAAG
Found at i:2179856 original size:43 final size:42
Alignment explanation
Indices: 2179800--2179905 Score: 133
Period size: 43 Copynumber: 2.4 Consensus size: 42
2179790 TAAAAATATT
*
2179800 AAAATATTATAAAAATCATAATAAAAGTTATAATGAATATAATA
1 AAAAAATT-TAAAAATCATAATAAAAGTTATAATGAATATAA-A
*
2179844 AAAAAATTTAAAAA-CTATATTAAAAGTTATAATGAATATAAA
1 AAAAAATTTAAAAATC-ATAATAAAAGTTATAATGAATATAAA
*
2179886 AAATAAATTTTATAAATCAT
1 AAA-AAA-TTTAAAAATCAT
2179906 TAAAAAATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
42 5 0.09
43 33 0.60
44 16 0.29
45 1 0.02
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (42 bp):
AAAAAATTTAAAAATCATAATAAAAGTTATAATGAATATAAA
Found at i:2180092 original size:20 final size:20
Alignment explanation
Indices: 2180067--2180125 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
2180057 TTTTATGATT
2180067 ATTTTAATATATTTTTAAAA
1 ATTTTAATATATTTTTAAAA
*
2180087 ATTTTAA-A-ATTTTAATAAA
1 ATTTTAATATATTTTTA-AAA
*
2180106 ATTTTAATTTATTATTTAAA
1 ATTTTAATATATT-TTTAAA
2180126 GAATAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
20 7 0.22
21 5 0.16
22 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTTAATATATTTTTAAAA
Found at i:2181634 original size:20 final size:20
Alignment explanation
Indices: 2181609--2181655 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2181599 AAATTCAGTA
*
2181609 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
2181629 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
2181649 TTGCGAT
1 TTGCGAT
2181656 TTACATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:2181665 original size:20 final size:20
Alignment explanation
Indices: 2181642--2181775 Score: 169
Period size: 20 Copynumber: 6.7 Consensus size: 20
2181632 CGATAGTCAG
* *
2181642 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
2181662 ATTCGCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
*
2181682 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
2181702 ATTCACATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
* **
2181722 ATTCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
2181743 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2181763 ATTCGCATTGCGA
1 ATTCGCATTGCGA
2181776 ATTAGGAAAA
Statistics
Matches: 97, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 81 0.84
21 16 0.16
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2181796 original size:21 final size:21
Alignment explanation
Indices: 2181772--2181859 Score: 149
Period size: 21 Copynumber: 4.2 Consensus size: 21
2181762 TATTCGCATT
* *
2181772 GCGAATTAGGAAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
2181793 GCGAATTTGGGAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
2181814 GCGAATTTGGGAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
*
2181835 GCGAATTTGGGAAATCGCAAT
1 GCGAATTTGGGAAATCGCAAC
2181856 GCGA
1 GCGA
2181860 TAGTCAAAAT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.18
Consensus pattern (21 bp):
GCGAATTTGGGAAATCGCAAC
Found at i:2185877 original size:32 final size:34
Alignment explanation
Indices: 2185826--2185888 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 34
2185816 ATAAATAAAT
2185826 AAATAAATAAATATTGATAAAATAT-TTATTTAA
1 AAATAAATAAATATTGATAAAATATATTATTTAA
*
2185859 AAAT-AATAAA-ATTAGATAATATATATTATT
1 AAATAAATAAATATT-GATAAAATATATTATT
2185889 GATAAAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 3 0.11
32 15 0.56
33 9 0.33
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (34 bp):
AAATAAATAAATATTGATAAAATATATTATTTAA
Found at i:2186197 original size:15 final size:15
Alignment explanation
Indices: 2186177--2186206 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2186167 ATAATTATTA
2186177 ATCAATGATTAAAAT
1 ATCAATGATTAAAAT
*
2186192 ATCAATTATTAAAAT
1 ATCAATGATTAAAAT
2186207 TAAGAAATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (15 bp):
ATCAATGATTAAAAT
Found at i:2187444 original size:17 final size:20
Alignment explanation
Indices: 2187388--2187465 Score: 69
Period size: 19 Copynumber: 4.0 Consensus size: 20
2187378 GCTTCTGATG
*
2187388 TAATTTGTAATATAT-AT-A
1 TAATTTATAATATATAATAA
2187406 TATATATT-TAATA-ATAAT-A
1 TA-AT-TTATAATATATAATAA
*
2187425 TAATATTATTATAT-TAATAA
1 TAAT-TTATAATATATAATAA
2187445 TAATTTATAATATATAATAA
1 TAATTTATAATATATAATAA
2187465 T
1 T
2187466 TTTAATAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
18 9 0.18
19 28 0.55
20 14 0.27
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (20 bp):
TAATTTATAATATATAATAA
Found at i:2187475 original size:32 final size:36
Alignment explanation
Indices: 2187411--2187479 Score: 94
Period size: 34 Copynumber: 2.0 Consensus size: 36
2187401 ATATATATAT
2187411 ATTTAATAATAATATAATATTATTATATTAATAATA
1 ATTTAATAATAATATAATATTATTATATTAATAATA
2187447 ATTT-ATAAT-ATATAATAATT-TTA-A-TAATAATA
1 ATTTAATAATAATATAAT-ATTATTATATTAATAATA
2187479 A
1 A
2187480 CGAAAAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
32 9 0.28
33 1 0.03
34 10 0.31
35 8 0.25
36 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (36 bp):
ATTTAATAATAATATAATATTATTATATTAATAATA
Found at i:2187747 original size:76 final size:76
Alignment explanation
Indices: 2187621--2188330 Score: 1275
Period size: 76 Copynumber: 9.4 Consensus size: 76
2187611 GAGGTCTTAA
* *
2187621 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2187686 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2187697 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2187762 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2187773 AAACATCATGCACTGTAGGACTTACAGAT-ACCCTAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2187836 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2187847 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2187912 AGGCTTTTTGG
66 AGGCTTTTTGG
**
2187923 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2187988 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2187999 AAACATCATGCACTGCAGGACTTACAGATGACCTTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2188064 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2188075 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGCTCCTGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
2188139 AGGCTTTTTGA
66 AGGCTTTTTGG
*
2188150 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTTAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2188215 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2188226 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2188291 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2188302 AAACATCAT-CACTGCAGGACTCACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
2188331 TGGAAATAGT
Statistics
Matches: 611, Mismatches: 20, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
74 51 0.08
75 135 0.22
76 425 0.70
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:2188228 original size:151 final size:152
Alignment explanation
Indices: 2187621--2188330 Score: 1275
Period size: 151 Copynumber: 4.7 Consensus size: 152
2187611 GAGGTCTTAA
* *
2187621 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
2187686 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
*
2187751 AAAGCTCCCAAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
*
2187773 AAACATCATGCACTGTAGGACTTACAGAT-ACCCTAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
2187836 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
2187901 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
**
2187923 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
2187988 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCTTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
2188053 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
*
2188075 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGCTCCTGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* *
2188139 AGGCTTTTTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTTAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
2188204 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
*
2188226 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
2188291 AGGCTTTTTGGAAACATCAT-CACTGCAGGACTCACAGATG
66 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
2188331 TGGAAATAGT
Statistics
Matches: 538, Mismatches: 17, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
150 125 0.23
151 210 0.39
152 203 0.38
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (152 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGG
Found at i:2188604 original size:166 final size:166
Alignment explanation
Indices: 2188331--2188658 Score: 493
Period size: 166 Copynumber: 2.0 Consensus size: 166
2188321 CTCACAGATG
* *
2188331 TGGAAATAGTTTATTAAGTAAAAACTAAGGAAATCGTTTTTCTTACTTTTCAACAATTTCATTTT
1 TGGAAATAGTTTACTAAGTAAAAACTAAGAAAATCGTTTTTCTTACTTTTCAACAATTTCATTTT
** *
2188396 TAGAAAAGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTA-TTTTTCAAAATAACATGTTG
66 TAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTTCAAAATAACATGTTG
*
2188460 ATTGGGTAACATG-CCCTAATTTCAAGATAAGGCTGT
131 ATTGGGTAACATGACCC-AATCTCAAGATAAGGCTGT
2188496 TGGAAATAGTTTACTAAGTAAAAAAAACTAAGAAAATCG-TTTTCTTACTTTTCAACAATTTCA-
1 TGGAAATAGTTTACTAAGT---AAAAACTAAGAAAATCGTTTTTCTTACTTTTCAACAATTTCAT
**
2188559 TTTTAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATGTTTTTTTGAAATAACA
63 TTTTAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTA--TTTTTTCAAAATAACA
*
2188624 TGTTGATTGGGTAACATGACCCAATCTGAAGATAA
126 TGTTGATTGGGTAACATGACCCAATCTCAAGATAA
2188659 TGCTCATTTT
Statistics
Matches: 147, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
165 18 0.12
166 44 0.30
167 24 0.16
168 16 0.11
169 42 0.29
170 3 0.02
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (166 bp):
TGGAAATAGTTTACTAAGTAAAAACTAAGAAAATCGTTTTTCTTACTTTTCAACAATTTCATTTT
TAGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTTCAAAATAACATGTTG
ATTGGGTAACATGACCCAATCTCAAGATAAGGCTGT
Found at i:2189216 original size:187 final size:187
Alignment explanation
Indices: 2188901--2189274 Score: 748
Period size: 187 Copynumber: 2.0 Consensus size: 187
2188891 TTGACTTCAA
2188901 AGTGGTGAACTTGGTCTTCCTTCACTTCATCATTTATTGCCATGGTTACCTCTGGATATCAGTAT
1 AGTGGTGAACTTGGTCTTCCTTCACTTCATCATTTATTGCCATGGTTACCTCTGGATATCAGTAT
2188966 AGAAACTTATGCTGTCAAGCTTGCATTTCTACAGAATCATCTGATCAATTTGTATCTTTGCATTT
66 AGAAACTTATGCTGTCAAGCTTGCATTTCTACAGAATCATCTGATCAATTTGTATCTTTGCATTT
2189031 TCTTTGATTCATTTAAGTCTCAGAAGAAATGTTTCACTTGTGGAACTCTTGTCGTAG
131 TCTTTGATTCATTTAAGTCTCAGAAGAAATGTTTCACTTGTGGAACTCTTGTCGTAG
2189088 AGTGGTGAACTTGGTCTTCCTTCACTTCATCATTTATTGCCATGGTTACCTCTGGATATCAGTAT
1 AGTGGTGAACTTGGTCTTCCTTCACTTCATCATTTATTGCCATGGTTACCTCTGGATATCAGTAT
2189153 AGAAACTTATGCTGTCAAGCTTGCATTTCTACAGAATCATCTGATCAATTTGTATCTTTGCATTT
66 AGAAACTTATGCTGTCAAGCTTGCATTTCTACAGAATCATCTGATCAATTTGTATCTTTGCATTT
2189218 TCTTTGATTCATTTAAGTCTCAGAAGAAATGTTTCACTTGTGGAACTCTTGTCGTAG
131 TCTTTGATTCATTTAAGTCTCAGAAGAAATGTTTCACTTGTGGAACTCTTGTCGTAG
2189275 TCAAAATTAT
Statistics
Matches: 187, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
187 187 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (187 bp):
AGTGGTGAACTTGGTCTTCCTTCACTTCATCATTTATTGCCATGGTTACCTCTGGATATCAGTAT
AGAAACTTATGCTGTCAAGCTTGCATTTCTACAGAATCATCTGATCAATTTGTATCTTTGCATTT
TCTTTGATTCATTTAAGTCTCAGAAGAAATGTTTCACTTGTGGAACTCTTGTCGTAG
Found at i:2191726 original size:31 final size:31
Alignment explanation
Indices: 2191691--2191753 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
2191681 AGAGATGTGG
2191691 TCTGAATTCATCAATTACAGAGTTGACAGAT
1 TCTGAATTCATCAATTACAGAGTTGACAGAT
*
2191722 TCTGAATTCATCAATTGCAGAGTTGACAGAT
1 TCTGAATTCATCAATTACAGAGTTGACAGAT
2191753 T
1 T
2191754 TTATATGTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (31 bp):
TCTGAATTCATCAATTACAGAGTTGACAGAT
Found at i:2199392 original size:15 final size:15
Alignment explanation
Indices: 2199372--2199401 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2199362 ATAATTATTA
2199372 ATCAATGATTAAAAT
1 ATCAATGATTAAAAT
*
2199387 ATCAATTATTAAAAT
1 ATCAATGATTAAAAT
2199402 TAAGAAATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (15 bp):
ATCAATGATTAAAAT
Found at i:2200616 original size:3 final size:3
Alignment explanation
Indices: 2200608--2200679 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
2200598 TATATATATT
* * * * *
2200608 TAA TAA TAAA TAA TAA TAA TAT TTA TAT TAA TAA TAA TAT TTA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2200654 TAA TAA TAA TAA T-T TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
2200680 ACGAAAAATT
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
2 1 0.02
3 51 0.93
4 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:2200641 original size:18 final size:17
Alignment explanation
Indices: 2200617--2200679 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 17
2200607 TTAATAATAA
2200617 ATAATAATAATATTTAT
1 ATAATAATAATATTTAT
2200634 ATTAATAATAATATTTAT
1 A-TAATAATAATATTTAT
2200652 AATAATAATAATAATTTA-
1 -ATAATAATAAT-ATTTAT
2200670 ATAATAATAA
1 ATAATAATAA
2200680 ACGAAAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.26
18 26 0.60
19 6 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATAATAATATTTAT
Found at i:2214200 original size:6 final size:6
Alignment explanation
Indices: 2214189--2214360 Score: 63
Period size: 6 Copynumber: 28.5 Consensus size: 6
2214179 AAGAGAAAAT
** *
2214189 AAATAA AAAT-A AAATAA ATAATTAAA AAAGTCAA AAGGAA AAA-AA GAATAA
1 AAATAA AAATAA AAATAA A-AA-T-AA AAA-T-AA AAATAA AAATAA AAATAA
* * *
2214240 AAATAA AGAA-AA AAAGAA AAGTCAA AAGA-AA ATAAAAA AAATAA AAA-AA
1 AAATAA A-AATAA AAATAA AAAT-AA AA-ATAA A-AATAA AAATAA AAATAA
* * * * * * *
2214289 ATATCA TAATAA TAAT-A AAATAA AAATAG AGATAA AAA-AA TAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
* * *
2214335 CAATAA TAATAA TAAT-A AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
2214361 AGGTTAAATA
Statistics
Matches: 126, Mismatches: 25, Indels: 30
0.70 0.14 0.17
Matches are distributed among these distances:
5 27 0.21
6 76 0.60
7 12 0.10
8 8 0.06
9 3 0.02
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:2214255 original size:8 final size:9
Alignment explanation
Indices: 2214239--2214291 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
2214229 AAAAAGAATA
2214239 AAAATAAAG
1 AAAATAAAG
2214248 AAAA-AAAG
1 AAAATAAAG
2214256 AAAAGTCAAAAG
1 AAAA-T--AAAG
*
2214268 AAAATAAAA
1 AAAATAAAG
*
2214277 AAAATAAAA
1 AAAATAAAG
2214286 AAAATA
1 AAAATA
2214292 TCATAATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
8 8 0.21
9 22 0.56
11 1 0.03
12 8 0.21
ACGTcount: A:0.81, C:0.02, G:0.08, T:0.09
Consensus pattern (9 bp):
AAAATAAAG
Found at i:2214279 original size:20 final size:20
Alignment explanation
Indices: 2214182--2214291 Score: 70
Period size: 20 Copynumber: 5.4 Consensus size: 20
2214172 GGACAAAAAG
*
2214182 AGAAAATAAATAAAAATAAA
1 AGAAAATAAAGAAAAATAAA
*
2214202 A-TAAATAATTA-AAAAAGTCAAA
1 AGAAAATAA--AGAAAAA-T-AAA
*
2214224 AGGAAAA-AAAGAATAAAAATAA
1 A-GAAAATAAAGAA-AAATA-AA
*
2214246 AGAAAA-AAAGAAAAGTCAAA
1 AGAAAATAAAGAAAAAT-AAA
2214266 AGAAAATAAA-AAAAATAAA
1 AGAAAATAAAGAAAAATAAA
2214285 A-AAAATA
1 AGAAAATA
2214292 TCATAATAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 24
0.71 0.06 0.23
Matches are distributed among these distances:
18 6 0.08
19 10 0.14
20 21 0.29
21 19 0.26
22 9 0.12
23 5 0.07
24 3 0.04
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.13
Consensus pattern (20 bp):
AGAAAATAAAGAAAAATAAA
Found at i:2214289 original size:35 final size:35
Alignment explanation
Indices: 2214193--2214289 Score: 90
Period size: 35 Copynumber: 2.7 Consensus size: 35
2214183 GAAAATAAAT
* *
2214193 AAAAATAAAATAAATAATTAAAAAAGTCAAAAGGAAAA
1 AAAAATAAAAAAAATAA--AAAAAAG-CAAAAGCAAAA
*
2214231 AAAGAATAAAAATAAA-GAAAAAAAG-AAAAGTCAAAA
1 AAA-AATAAAAA-AAATAAAAAAAAGCAAAAG-CAAAA
*
2214267 GAAAATAAAAAAAATAAAAAAAA
1 AAAAATAAAAAAAATAAAAAAAA
2214290 TATCATAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
34 3 0.06
35 20 0.40
36 6 0.12
37 7 0.14
38 3 0.06
39 8 0.16
40 3 0.06
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.11
Consensus pattern (35 bp):
AAAAATAAAAAAAATAAAAAAAAGCAAAAGCAAAA
Found at i:2214300 original size:3 final size:3
Alignment explanation
Indices: 2214294--2214357 Score: 55
Period size: 3 Copynumber: 22.3 Consensus size: 3
2214284 AAAAAATATC
* * * *
2214294 ATA ATA ATA ATA A-A ATA AAA ATA GA-G ATA A-A AAA ATA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
2214337 ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
2214358 AAAAGGTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
2 7 0.14
3 41 0.84
4 1 0.02
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (3 bp):
ATA
Found at i:2214387 original size:17 final size:17
Alignment explanation
Indices: 2214365--2214398 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2214355 TAAAAAAGGT
2214365 TAAATAAA-AAATTAAAA
1 TAAATAAATAAA-TAAAA
2214382 TAAATAAATAAATAAAA
1 TAAATAAATAAATAAAA
2214399 AGGGACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAATAAATAAATAAAA
Found at i:2215426 original size:14 final size:14
Alignment explanation
Indices: 2215409--2215443 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2215399 AATAAAACCG
2215409 TATAATAATAATAA
1 TATAATAATAATAA
*
2215423 TATACTAATAATAA
1 TATAATAATAATAA
2215437 TATAATA
1 TATAATA
2215444 TAAACTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (14 bp):
TATAATAATAATAA
Found at i:2215601 original size:39 final size:39
Alignment explanation
Indices: 2215504--2215638 Score: 131
Period size: 39 Copynumber: 3.6 Consensus size: 39
2215494 TATTTTTTTT
* * * *
2215504 AAAAAA-GTTTTCAAAACTATATATCATATAGT-TTT--
1 AAAAAATGTTTTTAAAATTATATATTATATAATCTTTCA
* * *
2215539 AAAAAATG-ATTTAAAA-AAAATATTATATAA-CTTTCA
1 AAAAAATGTTTTTAAAATTATATATTATATAATCTTTCA
*
2215575 AAAAAATGTTTTTTAAAATTATATATTATATAATTTTTCA
1 AAAAAATG-TTTTTAAAATTATATATTATATAATCTTTCA
*
2215615 AAAAAATGTTTTTAGAATTATATA
1 AAAAAATGTTTTTAAAATTATATA
2215639 AGTTTTTCAA
Statistics
Matches: 81, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
34 13 0.16
35 12 0.15
36 9 0.11
38 7 0.09
39 27 0.33
40 13 0.16
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (39 bp):
AAAAAATGTTTTTAAAATTATATATTATATAATCTTTCA
Found at i:2215724 original size:36 final size:34
Alignment explanation
Indices: 2215642--2215786 Score: 159
Period size: 34 Copynumber: 4.0 Consensus size: 34
2215632 TTATATAAGT
2215642 TTTTCAAAATGTTTTTTTAAAAACTATATATTATATA
1 TTTTCAAAATG---TTTTAAAAACTATATATTATATA
* *
2215679 TATTT-AAAATGATTTCAAAACTATATATTATATA
1 T-TTTCAAAATGTTTTAAAAACTATATATTATATA
2215713 GGTTTTCAAAATGTTTTAAAAACCT-TATATTATATA
1 --TTTTCAAAATGTTTTAAAAA-CTATATATTATATA
*
2215749 TTTTCAAAATGTTTTTTTTAAAACTATATATTATATA
1 TTTTCAAAATG---TTTTAAAAACTATATATTATATA
2215786 T
1 T
2215787 ATATATATAT
Statistics
Matches: 94, Mismatches: 5, Indels: 18
0.80 0.04 0.15
Matches are distributed among these distances:
34 32 0.34
35 3 0.03
36 27 0.29
37 29 0.31
38 3 0.03
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (34 bp):
TTTTCAAAATGTTTTAAAAACTATATATTATATA
Found at i:2216344 original size:12 final size:12
Alignment explanation
Indices: 2216327--2216355 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2216317 CGAGGGCTGT
2216327 TAGGCACTTATC
1 TAGGCACTTATC
2216339 TAGGCACTTATC
1 TAGGCACTTATC
2216351 T-GGCA
1 TAGGCA
2216356 GTGGTTGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (12 bp):
TAGGCACTTATC
Found at i:2216522 original size:35 final size:35
Alignment explanation
Indices: 2216480--2216547 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
2216470 AATAGAAGAA
*
2216480 TTGGATTAGGACTCAAATACTAGTCTAAAATAGAG
1 TTGGATTAAGACTCAAATACTAGTCTAAAATAGAG
2216515 TTGGATTAAGACTCAAATACTAGTCTAAAATAG
1 TTGGATTAAGACTCAAATACTAGTCTAAAATAG
2216548 GGTTTTTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (35 bp):
TTGGATTAAGACTCAAATACTAGTCTAAAATAGAG
Found at i:2216947 original size:17 final size:18
Alignment explanation
Indices: 2216925--2216960 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2216915 ATATGGATAT
*
2216925 TTATTCAT-TTATTTTTA
1 TTATTCATGTTATTATTA
2216942 TTATTCATGTTATTATTA
1 TTATTCATGTTATTATTA
2216960 T
1 T
2216961 ACGTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.67
Consensus pattern (18 bp):
TTATTCATGTTATTATTA
Found at i:2217030 original size:2 final size:2
Alignment explanation
Indices: 2217023--2217047 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2217013 TTTATTTTAT
2217023 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 T
2217048 CTTTAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2217229 original size:2 final size:2
Alignment explanation
Indices: 2217224--2217248 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2217214 CTTATAACTT
2217224 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 T
2217249 TATTTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2217505 original size:38 final size:40
Alignment explanation
Indices: 2217454--2217533 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
2217444 AGTGAAAGGG
*
2217454 TAGCTTTTCTATTTT-TAAATA-TTTGTTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
2217492 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
2217532 TA
1 TA
2217534 TATATTTTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.56
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:2217638 original size:15 final size:14
Alignment explanation
Indices: 2217596--2217628 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2217586 TTTCCTTATC
*
2217596 TTATTTATTT-ATT
1 TTATTTATTTCCTT
2217609 TTATTTATTTCCTT
1 TTATTTATTTCCTT
2217623 TTATTT
1 TTATTT
2217629 TATTCTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTTATTTCCTT
Found at i:2226163 original size:106 final size:106
Alignment explanation
Indices: 2225902--2226775 Score: 1071
Period size: 106 Copynumber: 8.3 Consensus size: 106
2225892 GCCATCAGCG
* * *
2225902 ATTTCAACTTCAC-GACGGAGGATATCGCGCCACTCGAGATAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATATTG-G--ACTCGAGACAACACAAGTTCAACTTCACAACGA
* * * *
2225966 AGGGACGGCTGGTTGTCAACAAACCACTTT-TCAGTTTCATTCAGAGCCA
62 AGGGACGACTGGTTGTCAACAAA-CAATTTCCCA--AT--TTCAGAGCCA
*
2226015 ATTTCAACTTCACAGCGAAGGATATTGGAC-CTGGGACAACACAAGTTCAACTTCACAACGAAGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTC-GAGACAACACAAGTTCAACTTCACAACGAAGG
* *
2226079 GATGACTGGTTATCAACAAACAATTTCCCAATTTCAGAGCCA
65 GACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
2226121 ATTTCAACTTCACATCGAAGGATGTTGGACTCGGGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
2226186 ACGACTGGTTGTCAACAAACAATTTCCCAATTTCATAGTCA
66 ACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
**
2226227 ATTTCAACTTCACAGCGAAGGATATTGGACTTAAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
*
2226292 ACGACTGGTTGTCAACAAACAATCTCCCAATTTCAGAG-C-
66 ACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
2226331 ----CAA--T---AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAATGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * *
2226387 ATGACTGGTTGTCAATAAACAATTTCCCAATTTCAGGGTCA
66 ACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
** *
2226428 ATTTCAACTTCACATTGAAGGATATTGGACTCCAGAC--CACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
2226491 ACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
66 ACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
2226532 ATTTCAACTTCACAGCGAAAGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * *
2226597 ACGGCTGGTTGTCAATAAACAATTTCCCAATTTCAGGGTCA
66 ACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * * * * *
2226638 ATTTCAACTTCACATCGAAGGATATTAGACGCAAGACAACACAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* ** * * * *
2226703 GCGGTTGGCTGTCAACAAACAATTTTCCAGTTCCA-ATGCCA
66 ACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGA-GCCA
* * *
2226744 ATTTCAACTTCACGGCGGAGGATATTTGACTC
1 ATTTCAACTTCACAGCGAAGGATATTGGACTC
2226776 AGAACAATAC
Statistics
Matches: 672, Mismatches: 71, Indels: 43
0.85 0.09 0.05
Matches are distributed among these distances:
95 82 0.12
96 1 0.00
98 1 0.00
100 3 0.00
101 3 0.00
103 1 0.00
104 93 0.14
105 1 0.00
106 403 0.60
107 1 0.00
108 1 0.00
109 6 0.01
110 51 0.08
112 1 0.00
113 23 0.03
114 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (106 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
Found at i:2226518 original size:411 final size:414
Alignment explanation
Indices: 2225933--2226725 Score: 1164
Period size: 411 Copynumber: 1.9 Consensus size: 414
2225923 ATATCGCGCC
* * * *
2225933 ACTCGAGATAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCACTTTTC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACCAATTTCC
* **
2225998 AGTTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCTGGGACAACACAAGTTC
66 AG-AT-ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCTCAGAC-ACACAAGTTC
*
2226063 AACTTCACAACGAAGGGATGACTGGTTATCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAA
128 AACTTCACAACGAAGGGACGACTGGTTATCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAA
* * * *
2226128 CTTCACATCGAAGGATGTTGGACTCGGGACAACACAAGTTCAACTTCACAACGAAGGGACGACTG
193 CTTCACAGCGAAAGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTG
* * *
2226193 GTTGTCAACAAACAATTTCCCAATTTCATAGTCAATTTCAACTTCACAGCGAAGGATATTGGACT
258 GTTGTCAACAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACG
* * *
2226258 TAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATCTCCCAAT
323 CAAGACAACACAAGCTCAACTTCACAACGAAGGGACGACTGGCTGTCAACAAACAATCTCCCAAT
2226323 TTCAGAGCCAATAGCGAAGGATATTGG
388 TTCAGAGCCAATAGCGAAGGATATTGG
* * * *
2226350 ACTCGAGACGACACAAGTTCAACTTCACAACGAATGGATGACTGGTTGTCAATAAA-CAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACCAATTT-C
* * **
2226414 CA-AT-TTCAGGGTCAATTTCAACTTCACATTGAAGGATATTGGA-CTCCAGAC-CACAAGTTCA
65 CAGATATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCT-CAGACACACAAGTTCA
* * *
2226475 ACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCAATTTCAAC
129 ACTTCACAACGAAGGGACGACTGGTTATCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAAC
* *
2226540 TTCACAGCGAAAGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGG
194 TTCACAGCGAAAGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGG
* * *
2226605 TTGTCAATAAACAATTTCCCAATTTCAGGGTCAATTTCAACTTCACATCGAAGGATATTAGACGC
259 TTGTCAACAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACGC
* * **
2226670 AAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGTTGGCTGTCAACAAACAAT
324 AAGACAACACAAGCTCAACTTCACAACGAAGGGACGACTGGCTGTCAACAAACAAT
2226726 TTTCCAGTTC
Statistics
Matches: 336, Mismatches: 38, Indels: 10
0.88 0.10 0.03
Matches are distributed among these distances:
411 238 0.71
412 2 0.01
413 38 0.11
415 1 0.00
416 5 0.01
417 52 0.15
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (414 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACCAATTTCC
AGATATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCTCAGACACACAAGTTCAAC
TTCACAACGAAGGGACGACTGGTTATCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTT
CACAGCGAAAGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTT
GTCAACAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACGCAA
GACAACACAAGCTCAACTTCACAACGAAGGGACGACTGGCTGTCAACAAACAATCTCCCAATTTC
AGAGCCAATAGCGAAGGATATTGG
Found at i:2226583 original size:305 final size:306
Alignment explanation
Indices: 2226028--2226632 Score: 980
Period size: 305 Copynumber: 2.0 Consensus size: 306
2226018 TCAACTTCAC
*
2226028 AGCGAAGGATATTGGACCTGGGACAACACAAGTTCAACTTCACAACGAAGGGATGACTGGTTATC
1 AGCGAAGGATATTGGACCTGAGACAACACAAGTTCAACTTCACAACGAAGGGATGACTGGTTATC
* **
2226093 AACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATGTTGGACTCGGGAC
66 AACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCCAGAC
*
2226158 AACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCATA
131 -ACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGA
* * *
2226223 GTCAATTTCAACTTCACAGCGAAGGATATTGGACTTAAGACAACACAAGTTCAACTTCACAACGA
195 GCCAATTTCAACTTCACAGCGAAAGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGA
2226288 AGGGACGACTGGTTGTCAACAAACAATCTCCCAATTTCAGAGCCAAT
260 AGGGACGACTGGTTGTCAACAAACAATCTCCCAATTTCAGAGCCAAT
* * *
2226335 AGCGAAGGATATTGGA-CTCGAGACGACACAAGTTCAACTTCACAACGAATGGATGACTGGTTGT
1 AGCGAAGGATATTGGACCT-GAGACAACACAAGTTCAACTTCACAACGAAGGGATGACTGGTTAT
* * * *
2226399 CAATAAACAATTTCCCAATTTCAGGGTCAATTTCAACTTCACATTGAAGGATATTGGACTCCAGA
65 CAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCCAGA
* *
2226464 C-CACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGA
130 CACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGA
* *
2226528 GCCAATTTCAACTTCACAGCGAAAGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGA
195 GCCAATTTCAACTTCACAGCGAAAGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGA
* * *
2226593 AGGGACGGCTGGTTGTCAATAAACAATTTCCCAATTTCAG
260 AGGGACGACTGGTTGTCAACAAACAATCTCCCAATTTCAG
2226633 GGTCAATTTC
Statistics
Matches: 275, Mismatches: 22, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
305 157 0.57
306 2 0.01
307 116 0.42
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (306 bp):
AGCGAAGGATATTGGACCTGAGACAACACAAGTTCAACTTCACAACGAAGGGATGACTGGTTATC
AACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCCAGAC
ACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAG
CCAATTTCAACTTCACAGCGAAAGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAA
GGGACGACTGGTTGTCAACAAACAATCTCCCAATTTCAGAGCCAAT
Found at i:2227352 original size:35 final size:35
Alignment explanation
Indices: 2227260--2227331 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
2227250 CCAAAAAAGA
2227260 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
2227295 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
2227330 AG
1 AG
2227332 GGTTTTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:2227759 original size:2 final size:2
Alignment explanation
Indices: 2227752--2227778 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2227742 TTATACATAC
2227752 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2227779 GTTTAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2227823 original size:2 final size:2
Alignment explanation
Indices: 2227818--2227842 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2227808 TATATTTTAT
2227818 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 T
2227843 CTTTAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2228307 original size:38 final size:40
Alignment explanation
Indices: 2228256--2228335 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
2228246 AGTGAGAGGG
*
2228256 TAACTTTTCTATTTT-TAAATA-TTTGTTGTATATATATA
1 TAACTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
2228294 TAACTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAACTT-TTCTATTTTATAAATACTTTGATGTATATATATA
2228334 TA
1 TA
2228336 TATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (40 bp):
TAACTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:2231863 original size:19 final size:18
Alignment explanation
Indices: 2231838--2231888 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
2231828 TACAAAAATA
*
2231838 TTTTATTATATTATTATT
1 TTTTATTATATTAATATT
2231856 TATTTATTATTATTAATATT
1 T-TTTATTA-TATTAATATT
2231876 TTTTATTTATATT
1 TTTTA-TTATATT
2231889 TTTTTGTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 15 0.52
20 13 0.45
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATTATATTAATATT
Found at i:2231865 original size:14 final size:15
Alignment explanation
Indices: 2231839--2231869 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2231829 ACAAAAATAT
2231839 TTTATTATATTATTA
1 TTTATTATATTATTA
2231854 TTTATT-TATTATTA
1 TTTATTATATTATTA
2231868 TT
1 TT
2231870 AATATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTATATTATTA
Found at i:2231880 original size:23 final size:22
Alignment explanation
Indices: 2231840--2231885 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
2231830 CAAAAATATT
*
2231840 TTATTATATTATTATTTATTTA
1 TTATTATAATATTATTTATTTA
*
2231862 TTATTATTAATATTTTTTATTTA
1 TTATTA-TAATATTATTTATTTA
2231885 T
1 T
2231886 ATTTTTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATTATAATATTATTTATTTA
Found at i:2237662 original size:64 final size:64
Alignment explanation
Indices: 2237561--2237870 Score: 467
Period size: 64 Copynumber: 4.8 Consensus size: 64
2237551 TGCAGCTTTT
* * *
2237561 AGAGTCAATTTCAACTTCACAAAGAAGGATATTGGACTCAACAAACAACTTTCCAATTTTATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * * *
2237625 AGAGTCAATTTTAACTTCACAGCGAAAGATATTGGACTCAACAAACAACTTTTCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* *
2237689 AGAGTCAATTTCAACTTCACAACGAATGATATTGGACTCAACAAACAACTTTCCAGTTTCATTT
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * *
2237753 AGAGTAAATTTCAACTTCACAACGAAGGATATTGAACTCAACAAACAACTTTTCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* *
2237817 AGAGTTAATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACAATACAACTT
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTC--AACAA-ACAACTT
2237871 ACACCCTTGG
Statistics
Matches: 223, Mismatches: 20, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
64 211 0.95
66 5 0.02
67 7 0.03
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (64 bp):
AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
Found at i:2238165 original size:121 final size:121
Alignment explanation
Indices: 2237873--2238466 Score: 812
Period size: 121 Copynumber: 4.9 Consensus size: 121
2237863 TACAACTTAC
* * * * *
2237873 ACCCTTGGATTTTAACTTCACGACGAAGGATATCCAATTCAAAGATCAACTTCACAACGAATGAG
1 ACCCTTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGGG
* * * * * *
2237938 CCAACCATGATTTCAACTTCAAGACGAAGGATATCGTGCCCACCAGTAAC-ATCCA
66 CCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAATGCA
* ** * * *
2237993 TCTTTATATTGGATTTCAACTTCATGATGAAGGATATCCAATTCAAGGCTCAACTTCATAACGAA
1 AC----CCTTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAA
* *
2238058 GGGGCCATCCACGATTTCAACTTCACGAAGAAGGATATCGTGCCCACAAGCAGCAATGCA
62 GGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAATGCA
* * *
2238118 ACCCTTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCATAACGAATGAG
1 ACCCTTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGGG
*
2238183 CCATCCACGATTTCAACTTCACGACGAAGGATATCGTACCCACAAGCAACAATGCA
66 CCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAATGCA
* *
2238239 ACCCTTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGG
1 ACCCTTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGGG
* * * * * *
2238304 TCATCCACGATTTCAACTTCATGACGAATGATATCGTGCCCACAAGCAGCAGTACA
66 CCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAATGCA
** * * *
2238360 ACCCTTATATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACAAAGTGG
1 ACCCTTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGGG
*
2238425 CCATCCACGATTTCAACTTCACGACGAAGGATATCGTTCCCA
66 CCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCA
2238467 ACGGACCGAC
Statistics
Matches: 419, Mismatches: 50, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
120 1 0.00
121 317 0.76
124 96 0.23
125 5 0.01
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (121 bp):
ACCCTTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGGG
CCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAATGCA
Found at i:2238674 original size:85 final size:85
Alignment explanation
Indices: 2238524--2238816 Score: 370
Period size: 86 Copynumber: 3.4 Consensus size: 85
2238514 TCCGGTGCAG
* * *
2238524 CATAACTCAAGGTGAGAAGGGTTATCTGTCATCAAAAGACCTTCGAGTTTGATTACACTCAGCTC
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
2238589 AAAGGCACATCCAATTTACAA
65 AAAGGCACATCAAATTTATAA
*
2238610 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCA
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
*
2238675 AAGGCACATCAAATTTATAG
66 AAGGCACATCAAATTTATAA
* * * * * * * * *
2238695 CATAGCTCAAGACGAGAAGGGCTATCTGTCAATAAAATACATTCGAATTCTATTACATTCAGCTC
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTCGATTACACTCAGCTC
* * *
2238760 AGATGCATATCAAATTTATAA
65 AAAGGCACATCAAATTTATAA
* * *
2238781 CATAGCTCAAGGCGAGAAGGGATATTTGTCAACAAA
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAA
2238817 AATTGACGAG
Statistics
Matches: 181, Mismatches: 25, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
85 79 0.44
86 102 0.56
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (85 bp):
CATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
AAGGCACATCAAATTTATAA
Found at i:2238829 original size:171 final size:171
Alignment explanation
Indices: 2238522--2238844 Score: 393
Period size: 171 Copynumber: 1.9 Consensus size: 171
2238512 AGTCCGGTGC
** * * *
2238522 AGCATAACTCAAGGTGAGAAGGGTTATCTGTCATCAAAAGACCTTCGAGTTTGATTACACTCAGC
1 AGCATAACTCAAGACGAGAAGGGCTATCTGTCATCAAAAGACATTCGAATTTGATTACACTCAGC
* * **
2238587 TCAAAGGCACATCCAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTT
66 TCAAAGGCACATCAAATTTACAACATAACTCAAGGCGAGAAGGGATATCTGTCAACCAAGAAATT
*
2238652 CGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTAT
131 CGAGTTCAATTACACTCAGCTCAAAGGCACATCAAATTTAT
* * *
2238693 AGCATAGCTCAAGACGAGAAGGGCTATCTGTCAAT-AAAATACATTCGAATTCT-ATTACATTCA
1 AGCATAACTCAAGACGAGAAGGGCTATCTGTC-ATCAAAAGACATTCGAATT-TGATTACACTCA
* * * * * *
2238756 GCTCAGATGCATATCAAATTTATAACATAGCTCAAGGCGAGAAGGGATATTTGTCAA-CAA-AAA
64 GCTCAAAGGCACATCAAATTTACAACATAACTCAAGGCGAGAAGGGATATCTGTCAACCAAGAAA
* *
2238819 TTGACGAGTTCAATTTCATTCAGCTC
129 TT--CGAGTTCAATTACACTCAGCTC
2238845 GATGACAACG
Statistics
Matches: 127, Mismatches: 21, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
169 3 0.02
170 3 0.02
171 118 0.93
172 3 0.02
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (171 bp):
AGCATAACTCAAGACGAGAAGGGCTATCTGTCATCAAAAGACATTCGAATTTGATTACACTCAGC
TCAAAGGCACATCAAATTTACAACATAACTCAAGGCGAGAAGGGATATCTGTCAACCAAGAAATT
CGAGTTCAATTACACTCAGCTCAAAGGCACATCAAATTTAT
Found at i:2245908 original size:51 final size:51
Alignment explanation
Indices: 2245832--2245933 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
2245822 TGATCTTCCT
*
2245832 TGTAGAGTTAAGATTCTATCATCGATATGTATATGCTACTTAACTATGCAC
1 TGTAGAGTTAAGATTCTATCATCGATATGTATATGCTACATAACTATGCAC
2245883 TGTAGAGTTAAGATTCTATCATCGATATGTATATGCTACATAACTATGCAC
1 TGTAGAGTTAAGATTCTATCATCGATATGTATATGCTACATAACTATGCAC
2245934 ATAAAAAGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (51 bp):
TGTAGAGTTAAGATTCTATCATCGATATGTATATGCTACATAACTATGCAC
Found at i:2248880 original size:26 final size:26
Alignment explanation
Indices: 2248840--2248900 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
2248830 CCTAGTATTG
*
2248840 GTTTTGGTGCTTGGTGCTCTGTCCCTT
1 GTTTT-GTGCTTGGTGCTATGTCCCTT
*
2248867 GTTTTGTTCTTGGTGCTATGTCCCTT
1 GTTTTGTGCTTGGTGCTATGTCCCTT
2248893 GTTTTGTG
1 GTTTTGTG
2248901 TGTCTGCAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 26 0.84
27 5 0.16
ACGTcount: A:0.02, C:0.18, G:0.28, T:0.52
Consensus pattern (26 bp):
GTTTTGTGCTTGGTGCTATGTCCCTT
Found at i:2256560 original size:37 final size:36
Alignment explanation
Indices: 2256519--2256605 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 36
2256509 TGCACATACC
*
2256519 ATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGA
1 ATGCATCGATGCACTCAGGATATTT-TG-AAACATCGA
* *
2256556 ATGCATCGATGCACTCTGGCTATTTTGAAACATCGA
1 ATGCATCGATGCACTCAGGATATTTTGAAACATCGA
*
2256592 ATGCACTTGATGCA
1 ATGCA-TCGATGCA
2256606 TCGATGCACT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
36 14 0.32
37 27 0.61
38 3 0.07
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (36 bp):
ATGCATCGATGCACTCAGGATATTTTGAAACATCGA
Found at i:2256614 original size:17 final size:19
Alignment explanation
Indices: 2256586--2256634 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2256576 TATTTTGAAA
2256586 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
2256604 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
2256623 CACCGATGCACT
1 CATCGATGCACT
2256635 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:2262128 original size:21 final size:21
Alignment explanation
Indices: 2262082--2262157 Score: 55
Period size: 23 Copynumber: 3.5 Consensus size: 21
2262072 ACACCTAACA
* *
2262082 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATACA-CCTTGAAG
2262104 GTGCATCGATACA-CTATGAAG
1 GTGCATCGATACACCT-TGAAG
* * *
2262125 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGAT--ACACCTTGAAG
*
2262148 ATGCATCGAT
1 GTGCATCGAT
2262158 GCACAAGGCC
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
20 2 0.05
21 13 0.30
22 12 0.28
23 14 0.33
24 2 0.05
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (21 bp):
GTGCATCGATACACCTTGAAG
Found at i:2262178 original size:43 final size:42
Alignment explanation
Indices: 2262081--2262180 Score: 103
Period size: 43 Copynumber: 2.3 Consensus size: 42
2262071 TACACCTAAC
* * * *
2262081 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACTATGA
1 AGTGCATCGATGCAGCCTTGAATATGCATCGATACACAAGGA
* * *
2262123 AGGTGCACCGATGCACGCCTTGAATATGCATCGATGCACAAGGCC
1 A-GTGCATCGATGCA-GCCTTGAATATGCATCGATACACAAGG-A
2262168 A-TGCATCGATGCA
1 AGTGCATCGATGCA
2262181 TCTGTCGGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
42 1 0.02
43 23 0.49
44 22 0.47
45 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (42 bp):
AGTGCATCGATGCAGCCTTGAATATGCATCGATACACAAGGA
Found at i:2263737 original size:21 final size:21
Alignment explanation
Indices: 2263695--2263738 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2263685 ACCCCGAGAG
* *
2263695 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
2263716 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
2263737 CT
1 CT
2263739 CCTCTGGTAC
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:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:2264833 original size:65 final size:63
Alignment explanation
Indices: 2264716--2264923 Score: 226
Period size: 65 Copynumber: 3.2 Consensus size: 63
2264706 TATCAAAGTG
* *
2264716 ATGCATCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGTAT
1 ATGCATCGATGCA-CAA-CCATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATGCAT
2264778 TTC
61 TTC
*
2264781 ATGCATCGATGCACATACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTT
1 ATGCATCGATGCACA-ACCATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCATTT
*
2264845 T
63 C
* * * * *
2264846 ATGCATCGATGCATCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTC
2264910 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2264924 TCTTAGTGCA
Statistics
Matches: 125, Mismatches: 10, Indels: 18
0.82 0.07 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 47 0.38
65 69 0.55
66 5 0.04
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTC
Found at i:2264923 original size:17 final size:19
Alignment explanation
Indices: 2264895--2264943 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2264885 TATTTTGAAA
2264895 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
2264913 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
2264932 CACCGATGCACT
1 CATCGATGCACT
2264944 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:2267726 original size:2 final size:2
Alignment explanation
Indices: 2267721--2267757 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2267711 TATACTTTTG
2267721 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2267758 CTTACACATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2271699 original size:19 final size:19
Alignment explanation
Indices: 2271675--2271723 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
2271665 TGCAATAAGC
*
2271675 AGCAGCGGCAACAAGAAAG
1 AGCAGCAGCAACAAGAAAG
2271694 AGCAGCAGCAACAAGAAAG
1 AGCAGCAGCAACAAGAAAG
*
2271713 AGCATCAGCAA
1 AGCAGCAGCAA
2271724 GCGTATAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.49, C:0.22, G:0.27, T:0.02
Consensus pattern (19 bp):
AGCAGCAGCAACAAGAAAG
Found at i:2272600 original size:28 final size:28
Alignment explanation
Indices: 2272563--2272617 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
2272553 TATGATACAA
*
2272563 ATATGAGTTTCGTAGAATATTGGAATAC
1 ATATGAGTTTCGGAGAATATTGGAATAC
*
2272591 ATATGTGTTTCGGAGAATATTGGAATA
1 ATATGAGTTTCGGAGAATATTGGAATA
2272618 ATGCATTGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (28 bp):
ATATGAGTTTCGGAGAATATTGGAATAC
Found at i:2273583 original size:19 final size:19
Alignment explanation
Indices: 2273561--2273604 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
2273551 GACAATGGAA
*
2273561 TGGATCTAAGGGGATGGTT
1 TGGATCTAAGGGGATAGTT
2273580 TGGATCTAAGGGGATAGTT
1 TGGATCTAAGGGGATAGTT
2273599 TGGATC
1 TGGATC
2273605 GCGGTTCGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.23, C:0.07, G:0.39, T:0.32
Consensus pattern (19 bp):
TGGATCTAAGGGGATAGTT
Found at i:2275053 original size:18 final size:18
Alignment explanation
Indices: 2275030--2275071 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2275020 GCCACTTGCC
2275030 AACTTGAATCAAATTGTA
1 AACTTGAATCAAATTGTA
* *
2275048 AACTTGAATCAACTTGTC
1 AACTTGAATCAAATTGTA
2275066 AACTTG
1 AACTTG
2275072 TGTAGCCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (18 bp):
AACTTGAATCAAATTGTA
Found at i:2286096 original size:15 final size:16
Alignment explanation
Indices: 2286068--2286099 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2286058 AAAATCTTTC
2286068 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
2286084 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
2286099 T
1 T
2286100 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:2286873 original size:16 final size:16
Alignment explanation
Indices: 2286849--2286882 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2286839 TATCGCCGAC
*
2286849 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
2286865 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
2286881 CG
1 CG
2286883 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:2290118 original size:106 final size:106
Alignment explanation
Indices: 2289992--2290203 Score: 361
Period size: 106 Copynumber: 2.0 Consensus size: 106
2289982 ATATTTAACT
* * *
2289992 AGTCACATATTTTGTTAAAAAAATCCAAACATGTATAACACATTGCAAAAATAAATGGATGTTGT
1 AGTCACATATTTCGATAAAAAAATCCAAACATGTATAACAAATTGCAAAAATAAATGGATGTTGT
2290057 TTATAGGTAGTAAAGTATATATATTAAAATGGTATGAGGTA
66 TTATAGGTAGTAAAGTATATATATTAAAATGGTATGAGGTA
* *
2290098 AGTCACATATTTCGATAAAAAAATCCAAACATGTATAACAAATTTCAAATATAAATGGATGTTGT
1 AGTCACATATTTCGATAAAAAAATCCAAACATGTATAACAAATTGCAAAAATAAATGGATGTTGT
* *
2290163 TTATAGGTCGTAAAGTATATATATTAAAATGGTTTGAGGTA
66 TTATAGGTAGTAAAGTATATATATTAAAATGGTATGAGGTA
2290204 GCGAGGTGGT
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 99 1.00
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (106 bp):
AGTCACATATTTCGATAAAAAAATCCAAACATGTATAACAAATTGCAAAAATAAATGGATGTTGT
TTATAGGTAGTAAAGTATATATATTAAAATGGTATGAGGTA
Found at i:2291866 original size:34 final size:33
Alignment explanation
Indices: 2291813--2291876 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
2291803 TGTGTGCTTG
2291813 GTTCGTTTAGTTCACGAACAA-CTCATTTATGA
1 GTTCGTTTAGTTCACGAACAAGCTCATTTATGA
* *
2291845 GTTCGTTATATGTTCATGAACAAGCTCGTTTA
1 GTTCGTT-TA-GTTCACGAACAAGCTCATTTA
2291877 ATTTTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 7 0.26
33 2 0.07
34 11 0.41
35 7 0.26
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (33 bp):
GTTCGTTTAGTTCACGAACAAGCTCATTTATGA
Found at i:2292141 original size:194 final size:191
Alignment explanation
Indices: 2291758--2292143 Score: 727
Period size: 191 Copynumber: 2.0 Consensus size: 191
2291748 ACGAGTATAA
2291758 ACAAAAATTTTATGTTCGTTTAATAAACGAATGAATACAAACATATGTGTGCTTGGTTCGTTTAG
1 ACAAAAATTTTATGTTCGTTTAATAAACGAATGAATACAAACATATGTGTGCTTGGTTCGTTTAG
2291823 TTCACGAACAACTCATTTATGAGTTCGTTATATGTTCATGAACAAGCTCGTTTAATTTTTTTATA
66 TTCACGAACAACTCATTTATGAGTTCGTTATATGTTCATGAACAAGCTCGTTTAATTTTTTTATA
2291888 TTTTAAATATCAGTGAAGGTACATATTAAATTAAATACACGGTAAAACATGGAGTTTAAAT
131 TTTTAAATATCAGTGAAGGTACATATTAAATTAAATACACGGTAAAACATGGAGTTTAAAT
*
2291949 ACAAACATTTTATGTTCGTTTAATAAACGAATGAATACAAACATATGTGTGCTTGGTTCGTTTAG
1 ACAAAAATTTTATGTTCGTTTAATAAACGAATGAATACAAACATATGTGTGCTTGGTTCGTTTAG
*
2292014 TTCACGAACAAACTCATTTATGAGTTCGTTTATATGTTCATGAACAAGTTCGTTTAATTTTTTTT
66 TTCACGAAC-AACTCATTTATGAGTTCG-TTATATGTTCATGAACAAGCTCGTTTAA-TTTTTTT
2292079 ATATTTTAAATATCAGTGAAGGTACATATTAAATTAAATACACGGTAAAACATGGAGTTTAAAT
128 ATATTTTAAATATCAGTGAAGGTACATATTAAATTAAATACACGGTAAAACATGGAGTTTAAAT
2292143 A
1 A
2292144 ATAAATACTA
Statistics
Matches: 190, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
191 73 0.38
192 18 0.09
193 27 0.14
194 72 0.38
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (191 bp):
ACAAAAATTTTATGTTCGTTTAATAAACGAATGAATACAAACATATGTGTGCTTGGTTCGTTTAG
TTCACGAACAACTCATTTATGAGTTCGTTATATGTTCATGAACAAGCTCGTTTAATTTTTTTATA
TTTTAAATATCAGTGAAGGTACATATTAAATTAAATACACGGTAAAACATGGAGTTTAAAT
Found at i:2293250 original size:19 final size:19
Alignment explanation
Indices: 2293226--2293268 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2293216 TGTACCCAAT
*
2293226 AATCTAG-TTTCTAACCTAA
1 AATCTAGATTTC-AAACTAA
2293245 AATCTAGATTTCAAACTAA
1 AATCTAGATTTCAAACTAA
2293264 AATCT
1 AATCT
2293269 GAATTCCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.35
Consensus pattern (19 bp):
AATCTAGATTTCAAACTAA
Found at i:2293282 original size:19 final size:19
Alignment explanation
Indices: 2293238--2293386 Score: 136
Period size: 19 Copynumber: 7.5 Consensus size: 19
2293228 TCTAGTTTCT
* *
2293238 AACCTAAAATCTAGATTTC
1 AACCTAAAATCTGGATTCC
* *
2293257 AAACTAAAATCTGAATTCC
1 AACCTAAAATCTGGATTCC
*
2293276 AACCTAACTTAAAATTTGGATTCC
1 AA-C---C-TAAAATCTGGATTCC
* * *
2293300 AACTTAAAATCTAGTTTCC
1 AACCTAAAATCTGGATTCC
*
2293319 AACCTAAAATTTGGATTCC
1 AACCTAAAATCTGGATTCC
*
2293338 AACCCAAAATCTGGATTCCC
1 AACCTAAAATCTGGATT-CC
* *
2293358 AACCTAAAATTTGGATTTC
1 AACCTAAAATCTGGATTCC
2293377 AACCTAAAAT
1 AACCTAAAAT
2293387 ATTAGGTTCT
Statistics
Matches: 104, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
19 70 0.67
20 17 0.16
23 2 0.02
24 15 0.14
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.30
Consensus pattern (19 bp):
AACCTAAAATCTGGATTCC
Found at i:2293308 original size:43 final size:42
Alignment explanation
Indices: 2293236--2293386 Score: 122
Period size: 43 Copynumber: 3.7 Consensus size: 42
2293226 AATCTAGTTT
* * * *
2293236 CTAACCTAAAATCTAGATTTCAAACTAAAATCTGAATTCCAAC
1 CTAA-CTAAAATTTGGATTCCAACCTAAAATCTGAATTCCAAC
* *
2293279 CTAACTTAAAATTTGGATTCCAACTTAAAATCT-AGTTTCCAA-
1 CTAAC-TAAAATTTGGATTCCAACCTAAAATCTGA-ATTCCAAC
* *
2293321 C---CTAAAATTTGGATTCCAACCCAAAATCTGGATT-C--C
1 CTAACTAAAATTTGGATTCCAACCTAAAATCTGAATTCCAAC
*
2293357 C-AACCTAAAATTTGGATTTCAACCTAAAAT
1 CTAA-CTAAAATTTGGATTCCAACCTAAAAT
2293387 ATTAGGTTCT
Statistics
Matches: 89, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 27 0.30
39 25 0.28
42 3 0.03
43 32 0.36
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (42 bp):
CTAACTAAAATTTGGATTCCAACCTAAAATCTGAATTCCAAC
Found at i:2293371 original size:39 final size:38
Alignment explanation
Indices: 2293226--2293386 Score: 151
Period size: 39 Copynumber: 4.1 Consensus size: 38
2293216 TGTACCCAAT
* * * * * *
2293226 AATCTAGTTTCTAACCTAAAATCTAGATTTCAAACTAA
1 AATCTAGTTCCCAACCTAAAATTTGGATTCCAACCTAA
* * *
2293264 AATCTGAATTCCAACCTAACTTAAAATTTGGATTCCAACTTAA
1 AATCT-AGTT-C--CC-AACCTAAAATTTGGATTCCAACCTAA
* *
2293307 AATCTAGTTTCCAACCTAAAATTTGGATTCCAACCCAA
1 AATCTAGTTCCCAACCTAAAATTTGGATTCCAACCTAA
* *
2293345 AATCTGGATTCCCAACCTAAAATTTGGATTTCAACCTAA
1 AATCTAG-TTCCCAACCTAAAATTTGGATTCCAACCTAA
2293384 AAT
1 AAT
2293387 ATTAGGTTCT
Statistics
Matches: 99, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
38 34 0.34
39 36 0.36
42 4 0.04
43 25 0.25
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (38 bp):
AATCTAGTTCCCAACCTAAAATTTGGATTCCAACCTAA
Found at i:2293494 original size:113 final size:113
Alignment explanation
Indices: 2293357--2293581 Score: 432
Period size: 113 Copynumber: 2.0 Consensus size: 113
2293347 TCTGGATTCC
2293357 CAACCTAAAATTTGGATTTCAACCTAAAATATTAGGTTCTGAATATCTAGTTTTATTTCATTATT
1 CAACCTAAAATTTGGATTTCAACCTAAAATATTAGGTTCTGAATATCTAGTTTTATTTCATTATT
*
2293422 TATTAATTTTCATTATGATATTTAATTTAATGTGTTTTTTCTTTTATG
66 TATTAATTTTCATTATGATATTTAATTTAACGTGTTTTTTCTTTTATG
2293470 CAACCTAAAATTTGGATTTCAACCTAAAATATTAGGTTCTGAATATCTAGTTTTATTTCATTATT
1 CAACCTAAAATTTGGATTTCAACCTAAAATATTAGGTTCTGAATATCTAGTTTTATTTCATTATT
*
2293535 TATTAATTTTTATTATGATATTTAATTTAACGTGTTTTTTCTTTTAT
66 TATTAATTTTCATTATGATATTTAATTTAACGTGTTTTTTCTTTTAT
2293582 AAAGTTTAGG
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 110 1.00
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (113 bp):
CAACCTAAAATTTGGATTTCAACCTAAAATATTAGGTTCTGAATATCTAGTTTTATTTCATTATT
TATTAATTTTCATTATGATATTTAATTTAACGTGTTTTTTCTTTTATG
Found at i:2299404 original size:27 final size:29
Alignment explanation
Indices: 2299374--2299435 Score: 74
Period size: 33 Copynumber: 2.1 Consensus size: 29
2299364 GTTAATTATT
2299374 GTCCTA-T-TAAAATTACTTGTCTTGGTA
1 GTCCTACTATAAAATTACTTGTCTTGGTA
2299401 GTCCTATCTAAGGTAAAATTACTTGTCTTGGTA
1 GTCCTA-CT-A--TAAAATTACTTGTCTTGGTA
2299434 GT
1 GT
2299436 TCTGTCTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
27 6 0.21
29 1 0.03
33 22 0.76
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.42
Consensus pattern (29 bp):
GTCCTACTATAAAATTACTTGTCTTGGTA
Found at i:2299423 original size:33 final size:33
Alignment explanation
Indices: 2299381--2299446 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
2299371 ATTGTCCTAT
2299381 TAAAATTACTTGTCTTGGTAGTCCTATCTAAGG
1 TAAAATTACTTGTCTTGGTAGTCCTATCTAAGG
* *
2299414 TAAAATTACTTGTCTTGGTAGTTCTGTCTAAGG
1 TAAAATTACTTGTCTTGGTAGTCCTATCTAAGG
2299447 AGAGTTAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.41
Consensus pattern (33 bp):
TAAAATTACTTGTCTTGGTAGTCCTATCTAAGG
Found at i:2305303 original size:23 final size:23
Alignment explanation
Indices: 2305277--2305351 Score: 141
Period size: 23 Copynumber: 3.3 Consensus size: 23
2305267 TAACATGCTT
*
2305277 ACGAACATGTTCATAAACGCTAA
1 ACGAACATGTTCATAAACGTTAA
2305300 ACGAACATGTTCATAAACGTTAA
1 ACGAACATGTTCATAAACGTTAA
2305323 ACGAACATGTTCATAAACGTTAA
1 ACGAACATGTTCATAAACGTTAA
2305346 ACGAAC
1 ACGAAC
2305352 GCTAAACGAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (23 bp):
ACGAACATGTTCATAAACGTTAA
Found at i:2305359 original size:34 final size:34
Alignment explanation
Indices: 2305315--2305395 Score: 117
Period size: 34 Copynumber: 2.4 Consensus size: 34
2305305 CATGTTCATA
* *
2305315 AACGTTAAACGAACATGTTCATAAACGTTAAACG
1 AACGCTAAACGAACATGTTCACAAACGTTAAACG
* * *
2305349 AACGCTAAACGAACATGTTTACAAATGTTAAATG
1 AACGCTAAACGAACATGTTCACAAACGTTAAACG
2305383 AACGCTAAACGAA
1 AACGCTAAACGAA
2305396 TGTTAAATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.22
Consensus pattern (34 bp):
AACGCTAAACGAACATGTTCACAAACGTTAAACG
Found at i:2305412 original size:22 final size:22
Alignment explanation
Indices: 2305372--2305418 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2305362 CATGTTTACA
*
2305372 AATGTTAAATGAACGCTAAACG
1 AATGTTAAATGAACACTAAACG
* *
2305394 AATGTTAAATGAGCACTAAATG
1 AATGTTAAATGAACACTAAACG
2305416 AAT
1 AAT
2305419 ACATTCACGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.26
Consensus pattern (22 bp):
AATGTTAAATGAACACTAAACG
Found at i:2307225 original size:31 final size:32
Alignment explanation
Indices: 2307154--2307244 Score: 107
Period size: 31 Copynumber: 2.9 Consensus size: 32
2307144 GAATGACCTA
* *
2307154 TCCATATGTTCC-GAAGAACATATGTAACACTG
1 TCCATATG-TCCTGAAGGACATAGGTAACACTG
2307186 TCCATATGTCCTGAAGGACATAGGTAA-ACTG
1 TCCATATGTCCTGAAGGACATAGGTAACACTG
* *
2307217 TCCGTATGT-CTCGAAAGACATAGGTAAC
1 TCCATATGTCCT-GAAGGACATAGGTAAC
2307245 CCTCGACTCT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
30 2 0.04
31 29 0.56
32 21 0.40
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (32 bp):
TCCATATGTCCTGAAGGACATAGGTAACACTG
Found at i:2314818 original size:35 final size:36
Alignment explanation
Indices: 2314772--2314842 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
2314762 AATCAGAGGA
2314772 AAAACTTAGGTTTTTTATGTTTG-TTTTTTTTCCTT
1 AAAACTTAGGTTTTTTATGTTTGTTTTTTTTTCCTT
2314807 AAAACTTAGGTTTTTTATGTTTGTTTTTTTTTCCTT
1 AAAACTTAGGTTTTTTATGTTTGTTTTTTTTTCCTT
2314843 CTGAATTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.17, C:0.08, G:0.11, T:0.63
Consensus pattern (36 bp):
AAAACTTAGGTTTTTTATGTTTGTTTTTTTTTCCTT
Done.