Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 35
Found at i:1084340 original size:22 final size:22
Alignment explanation
Indices: 1084287--1084343 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
1084277 TACATCTACA
1084287 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* * *
1084309 TCTCCGAAGATGATATATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
1084331 TTTTCAAAGATGA
1 TCTTCAAAGATGA
1084344 AAGCTTTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:1084927 original size:113 final size:113
Alignment explanation
Indices: 1084701--1085269 Score: 556
Period size: 113 Copynumber: 5.0 Consensus size: 113
1084691 TTAGCAAATA
* * * * * ** * * *
1084701 TTTGAATCCATTACTCAATGGATCAACA-TGCCAGGTAGAGTTCATAATGAGAATAGCTCATTTG
1 TTTGAATTCATCACTCGATGGATCAGCATTACCAGAAAGAGTTCATAATGAGAAGAACTCATCTG
* * * *
1084765 AATAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACTTTTTG
66 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTG
* * * * * *
1084813 TTTTAATTCATCACCCGATGGATTAGCATTGCCAGAAAAAGTTCATAATGAGAAGAACTTATCTG
1 TTTGAATTCATCACTCGATGGATCAGCATTACCAGAAAGAGTTCATAATGAGAAGAACTCATCTG
*
1084878 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
66 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTG
* * * **
1084926 TTTGAATTCATCATTTGATGTATCAGCATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTG
1 TTTGAATTCATCACTCGATGGATCAGCATTACCAGAAAGAGTTCATAATGAGAAGAACTCATCTG
* * * **
1084991 AAGATGGAAGAAGAAATTCATAATAAGAAGAATTTGTTCAAATTTTTG
66 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTG
* * * * *
1085039 TTTGAATTCATCACTCGATTGATCAACTTTTCCAGAGAAGAGTTCATAATGAGAAGAACTTATCT
1 TTTGAATTCATCACTCGATGGATCAGCATTACCAGA-AAGAGTTCATAATGAGAAGAACTCATCT
*
1085104 GAAG-AGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACC-TTTG
65 GAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTG
* * ** * * *
1085151 TTTG-ACTCTATCACGGAAGGAGATAGATCAACATCAACATTTCCAG-AAGTGTTCATAATGAGA
1 TTTGAATTC-ATCAC---------TCGAT--GGATCAGCATTACCAGAAAGAGTTCATAATGAGA
* * *
1085214 AGAACTCATCTGAAGAAGG-AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTT
54 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTT
1085270 GCCTTAATTT
Statistics
Matches: 384, Mismatches: 57, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
111 3 0.01
112 34 0.09
113 233 0.61
114 30 0.08
121 67 0.17
122 4 0.01
123 13 0.03
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (113 bp):
TTTGAATTCATCACTCGATGGATCAGCATTACCAGAAAGAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTG
Found at i:1085125 original size:226 final size:230
Alignment explanation
Indices: 1084722--1085265 Score: 676
Period size: 226 Copynumber: 2.4 Consensus size: 230
1084712 TACTCAATGG
* * * * * *
1084722 ATCAACA-TGCCAGGTAGAGTTCATAATGAGAATAGCTCATTTGAATAAGGAAGAAGAAGTTCAT
1 ATCAACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
* * * * * *
1084786 AATGAGAAGAACTTGTTCGACTTTTTGTTTTAATTCATCACCCGATGGATTAGCATTGCCAGAAA
66 AATGAGAAGAATTTGTTCAAATTTTTGTTTGAATTCATCACCCGATGGATCAACATTGCCAGAAA
*
1084851 AAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
131 AAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
* ***
1084916 CAACCTTTTGTTTGAAT-TCAT-C-ATTTGAT-G-T-
196 CAACC-TTTGTTTGACTCT-ATACGAGGAGATAGATA
* *
1084947 ATCAGCATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGATGGAAGAAGAAATTCAT
1 ATCAACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
* * * * *
1085012 AATAAGAAGAATTTGTTCAAATTTTTGTTTGAATTCATCACTCGATTGATCAACTTTTCCAGAGA
66 AATGAGAAGAATTTGTTCAAATTTTTGTTTGAATTCATCACCCGATGGATCAACATTGCCAGA-A
* *
1085077 AGAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATAAGAAGAATTTGT
130 AAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGT
1085141 TCAACCTTTGTTTGACTCTATCACGGAAGGAGATAGATCAA
195 TCAACCTTTGTTTGACTCTAT-AC-G-AGGAGATAGAT--A
* * *
1085182 CATCAACATTTCCA-GAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAATTCA
1 -ATCAACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCA
1085245 TAATGAGAAGAATTTGTTCAA
65 TAATGAGAAGAATTTGTTCAA
1085266 CCTTGCCTTA
Statistics
Matches: 273, Mismatches: 32, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
225 18 0.07
226 140 0.51
227 32 0.12
230 4 0.01
231 1 0.00
232 1 0.00
234 32 0.12
235 34 0.12
236 11 0.04
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (230 bp):
ATCAACATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
AATGAGAAGAATTTGTTCAAATTTTTGTTTGAATTCATCACCCGATGGATCAACATTGCCAGAAA
AAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
CAACCTTTGTTTGACTCTATACGAGGAGATAGATA
Found at i:1087124 original size:3 final size:3
Alignment explanation
Indices: 1087116--1087157 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1087106 ATATATTTAT
*
1087116 TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1087158 CAAATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1087519 original size:21 final size:19
Alignment explanation
Indices: 1087471--1087512 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1087461 ATTTATAAGT
*
1087471 AAATAAATATATTATATAA
1 AAATTAATATATTATATAA
* *
1087490 AAATTAATATATTTTATTA
1 AAATTAATATATTATATAA
1087509 AAAT
1 AAAT
1087513 CATAATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATTAATATATTATATAA
Found at i:1088231 original size:23 final size:22
Alignment explanation
Indices: 1088204--1088253 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1088194 TAATGAAATT
*
1088204 TTCAATTAATGATAATATAAAAA
1 TTCAATT-ATGATAAAATAAAAA
*
1088227 TTCAA-TATTATAAAATAAAAA
1 TTCAATTATGATAAAATAAAAA
1088248 TT-AATT
1 TTCAATT
1088254 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.08
21 16 0.67
22 1 0.04
23 5 0.21
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
TTCAATTATGATAAAATAAAAA
Found at i:1088265 original size:20 final size:21
Alignment explanation
Indices: 1088215--1088260 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1088205 TCAATTAATG
*
1088215 ATAATATAAAAATTCAATATT
1 ATAAAATAAAAATTCAATATT
1088236 ATAAAATAAAAATT-AAT-TT
1 ATAAAATAAAAATTCAATATT
1088255 -TAAAAT
1 ATAAAAT
1088261 TTAAAATGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 2 0.08
20 3 0.12
21 13 0.54
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAAAATAAAAATTCAATATT
Found at i:1094930 original size:10 final size:10
Alignment explanation
Indices: 1094917--1094941 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1094907 ATTAAAAAAG
1094917 AAAAAAATAA
1 AAAAAAATAA
1094927 AAAAAAATAA
1 AAAAAAATAA
1094937 AAAAA
1 AAAAA
1094942 TAAAGGACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:1094933 original size:18 final size:18
Alignment explanation
Indices: 1094910--1094945 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1094900 ATTTAAAATT
1094910 AAAAAAGAAAAAAATAAA
1 AAAAAAGAAAAAAATAAA
*
1094928 AAAAAATAAAAAAATAAA
1 AAAAAAGAAAAAAATAAA
1094946 GGACAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.03, T:0.08
Consensus pattern (18 bp):
AAAAAAGAAAAAAATAAA
Found at i:1097399 original size:33 final size:32
Alignment explanation
Indices: 1097362--1097423 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
1097352 AAAAAGCCAC
* *
1097362 TTAAGGAAATGTGAAGATCTTCAACGAAAAGAA
1 TTAAGGAAATGTAAAGAGCTTCAAC-AAAAGAA
1097395 TTAAGGAAATGTAAAGAGCTTCAACAAAA
1 TTAAGGAAATGTAAAGAGCTTCAACAAAA
1097424 TAATAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.50, C:0.10, G:0.19, T:0.21
Consensus pattern (32 bp):
TTAAGGAAATGTAAAGAGCTTCAACAAAAGAA
Found at i:1104615 original size:29 final size:29
Alignment explanation
Indices: 1104573--1104650 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
1104563 CGTTGATCGG
* *
1104573 TGCTATTCTGGTAAATAATTCGGTTTTGA
1 TGCTATTATGGTAAATAATTCGGTTATGA
* *
1104602 TGCTATTTTGGTAAATAATTCGGTTATGG
1 TGCTATTATGGTAAATAATTCGGTTATGA
*
1104631 TGCTATTATGGTAATTAATT
1 TGCTATTATGGTAAATAATT
1104651 TGAAATGGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (29 bp):
TGCTATTATGGTAAATAATTCGGTTATGA
Found at i:1104696 original size:29 final size:29
Alignment explanation
Indices: 1104629--1104696 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
1104619 ATTCGGTTAT
* * *
1104629 GGTGCTATTATGGTAATTAATTTGAAATG
1 GGTGCTATTTTGGTAATTAATTTAAAAAG
*
1104658 GGTGCTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGTAATTAATTTAAAAAG
1104687 GGTGCTATTT
1 GGTGCTATTT
1104697 GTGTAAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.28, C:0.04, G:0.24, T:0.44
Consensus pattern (29 bp):
GGTGCTATTTTGGTAATTAATTTAAAAAG
Found at i:1112009 original size:18 final size:18
Alignment explanation
Indices: 1111986--1112038 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
1111976 TGACCGGTCA
1111986 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
1112004 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
1112022 CGACCCGA-TCGTTGACC
1 CGACCCGACCCGTTGACC
1112039 GTTGACCGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 8 0.24
18 26 0.76
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:1112088 original size:29 final size:29
Alignment explanation
Indices: 1112046--1112125 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
1112036 ACCGTTGACC
1112046 GGTGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
1112075 GGTGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
1112104 GGTGCTATTCTGGTAATTAATT
1 GGTGCTATTCTGGTAAATAATT
1112126 TGAAATGGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.45
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:1112136 original size:29 final size:29
Alignment explanation
Indices: 1112046--1112148 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 29
1112036 ACCGTTGACC
***
1112046 GGTGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGAAATT
***
1112075 GGTGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGAAATT
* * *
1112104 GGTGCTATTCTGGTAATTAATTTGAAATG
1 GGTGCTATTCTGGTAAATAATTCGAAATT
*
1112133 GGTGCTATTTTGGTAA
1 GGTGCTATTCTGGTAA
1112149 TTATTTTAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.22, C:0.09, G:0.25, T:0.44
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGAAATT
Found at i:1112165 original size:28 final size:29
Alignment explanation
Indices: 1112104--1112170 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
1112094 ATTCGGTTTT
* **
1112104 GGTGCTATTCTGGTAATTAATTTGAAATG
1 GGTGCTATTTTGGTAATTAATTTGAAAAA
*
1112133 GGTGCTATTTTGGTAATT-ATTTTAAAAA
1 GGTGCTATTTTGGTAATTAATTTGAAAAA
1112161 GGTGCTATTT
1 GGTGCTATTT
1112171 GTGTAAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 17 0.50
29 17 0.50
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.45
Consensus pattern (29 bp):
GGTGCTATTTTGGTAATTAATTTGAAAAA
Found at i:1114781 original size:20 final size:21
Alignment explanation
Indices: 1114756--1114804 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1114746 TGCATTTCGG
1114756 GTTGCGATA-ATGAAAACCGC
1 GTTGCGATAGATGAAAACCGC
* *
1114776 GTTGCGATAGTTGAAAATCGC
1 GTTGCGATAGATGAAAACCGC
1114797 GTTGCGAT
1 GTTGCGAT
1114805 TTTCCATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (21 bp):
GTTGCGATAGATGAAAACCGC
Found at i:1114818 original size:20 final size:20
Alignment explanation
Indices: 1114793--1115154 Score: 152
Period size: 20 Copynumber: 18.4 Consensus size: 20
1114783 TAGTTGAAAA
*
1114793 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAAT
* **
1114813 TCGCGTTGTGATTTTCCGTT
1 TCGCGTTGCGATTTTCCAAT
*
1114833 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAAT
* * ** *
1114853 TCACGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAAT
* * *
1114874 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAAT
1114896 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCC-AAT
* * *
1114917 T--CGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAAT
1114937 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AAT
*
1114958 T--CGTTGCGA------AAA
1 TCGCGTTGCGATTTTCCAAT
*
1114970 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAAT
* ** *
1114990 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAAT
*** *
1115011 TCGCAACGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAAT
*
1115031 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAAT
* * *
1115051 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAAT
1115073 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AAT
*
1115094 T--CGTTGCGA------AAA
1 TCGCGTTGCGATTTTCCAAT
* *
1115106 TCGCGTTGCAATTTTCCATT
1 TCGCGTTGCGATTTTCCAAT
* *
1115126 TCGCGTTGCGATTTTTCAGT
1 TCGCGTTGCGATTTTCCAAT
1115146 TCGCGTTGC
1 TCGCGTTGC
1115155 AATAGTCTAC
Statistics
Matches: 253, Mismatches: 60, Indels: 58
0.68 0.16 0.16
Matches are distributed among these distances:
12 6 0.02
14 15 0.06
19 25 0.10
20 130 0.51
21 39 0.15
22 38 0.15
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAAT
Found at i:1114835 original size:81 final size:82
Alignment explanation
Indices: 1114750--1114912 Score: 193
Period size: 81 Copynumber: 2.0 Consensus size: 82
1114740 TCGCGTTGCA
* * * * * *
1114750 TTTCGGGTTGCGATAATGAAAACCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCATTT
1 TTTCGCGTTGCGATAATCAAAACCACGTTGCGATAGTTGAAAATCGCGTTGCGATATCTACAGTT
*
1114814 CGCGTTGTGATTTTCCG
66 CGCGTTGCGATTTTCCG
** * ***
1114831 TTTCGCGTTGCGATTTTCCAGTTCACGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGT
1 TTTCGCGTTGCGATAATCAAAACCACGTTGCGATAGTTGAAAATCGCGTTGCGATA-TCTACAGT
1114896 TCGCGTTGCGATTTTCC
65 TCGCGTTGCGATTTTCC
1114913 AAATTCGTTG
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
81 46 0.69
83 21 0.31
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.36
Consensus pattern (82 bp):
TTTCGCGTTGCGATAATCAAAACCACGTTGCGATAGTTGAAAATCGCGTTGCGATATCTACAGTT
CGCGTTGCGATTTTCCG
Found at i:1114902 original size:22 final size:22
Alignment explanation
Indices: 1114832--1114948 Score: 79
Period size: 22 Copynumber: 5.6 Consensus size: 22
1114822 GATTTTCCGT
* *
1114832 TTCGCGTTGCGAT--TTTCCAG
1 TTCGCGTTGCGATAGTCTACAG
* *
1114852 TTCACGTTGCGATAGT-TGA-AA
1 TTCGCGTTGCGATAGTCT-ACAG
*
1114873 ATCGCGTTGCGATAGTCTACAG
1 TTCGCGTTGCGATAGTCTACAG
** * *
1114895 TTCGCGTTGCGATTTTCCA-AA
1 TTCGCGTTGCGATAGTCTACAG
1114916 TT--CGTTGCGATAGTCTACAG
1 TTCGCGTTGCGATAGTCTACAG
1114936 TT-GTCGTTGCGAT
1 TTCG-CGTTGCGAT
1114949 TTTCCAAATT
Statistics
Matches: 74, Mismatches: 15, Indels: 14
0.72 0.15 0.14
Matches are distributed among these distances:
19 12 0.16
20 15 0.20
21 20 0.27
22 27 0.36
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.36
Consensus pattern (22 bp):
TTCGCGTTGCGATAGTCTACAG
Found at i:1114922 original size:41 final size:41
Alignment explanation
Indices: 1114877--1114966 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
1114867 TTGAAAATCG
1114877 CGTTGCGATAGTCTACAGTTCG-CGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTT-GTCGTTGCGATTTTCCAAATT
1114918 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1114959 CGTTGCGA
1 CGTTGCGA
1114967 AAATCGCGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 1 0.02
41 47 0.98
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:1114923 original size:19 final size:19
Alignment explanation
Indices: 1114899--1114966 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 19
1114889 CTACAGTTCG
1114899 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
* * **
1114918 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGAT--TTTCCAAAT-T
1114940 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
1114959 CGTTGCGA
1 CGTTGCGA
1114967 AAATCGCGTT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 18 0.47
20 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:1115098 original size:136 final size:136
Alignment explanation
Indices: 1114833--1115197 Score: 486
Period size: 136 Copynumber: 2.7 Consensus size: 136
1114823 ATTTTCCGTT
* * ***
1114833 TCGCGTTGCGATTTTCCAGTTCACGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTTC
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATA-TCTACAGTTC
1114898 GCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTT
65 GCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTT
1114963 GCGAAAA
130 GCGAAAA
* * *
1114970 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGAT-TTTCCATTTCG
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATATCTACAGTTCG
*
1115034 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGT
66 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGT
1115098 TGCGAAAA
129 TGCGAAAA
* * ** ** *** *
1115106 TCGCGTTGCAATTTTCCATTTCGCGTTGCGAT-TTTTCAGTTCGCGTTGCAATAGTCTACAGTT-
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATA-TCTACAGTTC
1115169 GTCGTTGCGATTTTCCAAATTCGTTGCGA
65 G-CGTTGCGATTTTCCAAATTCGTTGCGA
1115198 AAATTCGTTG
Statistics
Matches: 199, Mismatches: 23, Indels: 13
0.85 0.10 0.06
Matches are distributed among these distances:
134 3 0.02
135 33 0.17
136 92 0.46
137 68 0.34
138 3 0.02
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (136 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATATCTACAGTTCG
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTG
CGAAAA
Found at i:1115108 original size:95 final size:95
Alignment explanation
Indices: 1115006--1115201 Score: 329
Period size: 95 Copynumber: 2.1 Consensus size: 95
1114996 TGCGATAGTT
* * *
1115006 GAAAATCGCAACGCGATTTTCCATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
1 GAAAATCGCAACGCAATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCAATAGTCTACA
1115071 GTTGTCGTTGCGATTTTCCAAATTCGTTGC
66 GTTGTCGTTGCGATTTTCCAAATTCGTTGC
*** *
1115101 GAAAATCGCGTTGCAATTTTCCATTTCGCGTTGCGATTTTTCAGTTCGCGTTGCAATAGTCTACA
1 GAAAATCGCAACGCAATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCAATAGTCTACA
1115166 GTTGTCGTTGCGATTTTCCAAATTCGTTGC
66 GTTGTCGTTGCGATTTTCCAAATTCGTTGC
1115196 GAAAAT
1 GAAAAT
1115202 TCGTTGTGAT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (95 bp):
GAAAATCGCAACGCAATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCAATAGTCTACA
GTTGTCGTTGCGATTTTCCAAATTCGTTGC
Found at i:1115835 original size:6 final size:6
Alignment explanation
Indices: 1115809--1115851 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
1115799 TCTCGTCTCA
1115809 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1115852 ATACGTGTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.41
6 22 0.59
ACGTcount: A:0.00, C:0.19, G:0.53, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:1115979 original size:22 final size:22
Alignment explanation
Indices: 1115950--1116042 Score: 95
Period size: 22 Copynumber: 4.4 Consensus size: 22
1115940 AATTTGAAAA
1115950 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
1115972 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
1115994 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
1116013 ATCGCAACGAC-ATTGTAGACT
1 ATCGCAACGACAACTGTAGACT
1116034 ATCGCAACG
1 ATCGCAACG
1116043 CGAAATGGAA
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
19 13 0.23
20 3 0.05
21 13 0.23
22 27 0.48
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:1116059 original size:20 final size:20
Alignment explanation
Indices: 1116034--1116188 Score: 103
Period size: 20 Copynumber: 7.6 Consensus size: 20
1116024 ATTGTAGACT
1116034 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
1116054 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
1116075 ATCGCAGCGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
1116095 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
1116116 ATCGCAGCGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
1116136 ATCGTAACGCGATTTTCAATT
1 ATCGCAACGCGAAATGGAA-A
*
1116157 ATCGCAACGCAAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
1116177 ATCGCAATGCGA
1 ATCGCAACGCGA
1116189 TTTTCAACTA
Statistics
Matches: 93, Mismatches: 39, Indels: 6
0.67 0.28 0.04
Matches are distributed among these distances:
20 52 0.56
21 41 0.44
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1116080 original size:21 final size:20
Alignment explanation
Indices: 1116054--1116209 Score: 96
Period size: 21 Copynumber: 7.6 Consensus size: 20
1116044 GAAATGGAAA
1116054 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAA-T
* ** ** *
1116075 ATCGCAGCGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAAT
1116095 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAA-T
* ** ** *
1116116 ATCGCAGCGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAAT
*
1116136 ATCGTAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAA-T
* ** ** *
1116157 ATCGCAACGCAAAATGGAAA
1 ATCGCAACGCGATTTTCAAT
*
1116177 ATCGCAATGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAA-T
1116198 ATCGCAACGCGA
1 ATCGCAACGCGA
1116210 ATTTGCGATA
Statistics
Matches: 92, Mismatches: 40, Indels: 6
0.67 0.29 0.04
Matches are distributed among these distances:
20 40 0.43
21 52 0.57
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTTTCAAT
Found at i:1116103 original size:41 final size:41
Alignment explanation
Indices: 1115991--1116210 Score: 313
Period size: 41 Copynumber: 5.4 Consensus size: 41
1115981 ACAACTGTAG
* *
1115991 ACTATCGCAA--CGAATTTGGAAAATCGCAACGAC-ATTGT-A
1 ACTATCGCAACGCGAA-ATGGAAAATCGCAACG-CGATTTTCA
1116030 GACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
1116072 ACTATCGCAGCGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* *
1116113 ACTATCGCAGCGCGAAATGGAAAATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* * *
1116154 ATTATCGCAACGCAAAATGGAAAATCGCAATGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1116195 ACTATCGCAACGCGAA
1 ACTATCGCAACGCGAA
1116211 TTTGCGATAG
Statistics
Matches: 165, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
40 11 0.07
41 149 0.90
42 5 0.03
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:1116403 original size:32 final size:32
Alignment explanation
Indices: 1116344--1116405 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
1116334 TATTTTCTCA
*
1116344 TTAAAAAAATCTTATTTTTTATATTTTTAAAT
1 TTAAAAAAATCTTAATTTTTATATTTTTAAAT
*
1116376 TTAAAAAATTTCTTAATTTTTAT-TTTTTAA
1 TTAAAAAA-ATCTTAATTTTTATATTTTTAA
1116406 TTAAACAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (32 bp):
TTAAAAAAATCTTAATTTTTATATTTTTAAAT
Found at i:1116706 original size:22 final size:23
Alignment explanation
Indices: 1116676--1116719 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1116666 TCAAGTACCA
1116676 TAAAGTCA-TGATTTTCTATCTCT
1 TAAAGTCATTGATTTT-TATCTCT
*
1116699 TAAA-TCATTGGTTTTTATCTC
1 TAAAGTCATTGATTTTTATCTC
1116720 CAAAATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.50
Consensus pattern (23 bp):
TAAAGTCATTGATTTTTATCTCT
Found at i:1119592 original size:51 final size:51
Alignment explanation
Indices: 1119509--1119611 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 51
1119499 GATATATGCG
*
1119509 TTGTTTAGTGTTTGTCTGAACAGATACTGATTTCTTCATTCACCATGACTC
1 TTGTTTAGTGTTTGTCTGAACAGATACTGATTTCTTCATTCACCATAACTC
* *
1119560 TTGTTTAGTGTTTGTCTGAATAGGTA-TCGATTTCTTCATTCACCATAACTC
1 TTGTTTAGTGTTTGTCTGAACAGATACT-GATTTCTTCATTCACCATAACTC
1119611 T
1 T
1119612 ATTACGCGGG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
50 1 0.02
51 47 0.98
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (51 bp):
TTGTTTAGTGTTTGTCTGAACAGATACTGATTTCTTCATTCACCATAACTC
Found at i:1120883 original size:28 final size:28
Alignment explanation
Indices: 1120843--1120901 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
1120833 TGTATCTTTC
1120843 CTTGCTAATATATCTGTTTTATT-ATTTA
1 CTTGCTAATATATCTGTTTTATTGA-TTA
* *
1120871 CTTGCTATTATATTTGTTTTATTGATTA
1 CTTGCTAATATATCTGTTTTATTGATTA
1120899 CTT
1 CTT
1120902 TTAAATATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.22, C:0.10, G:0.08, T:0.59
Consensus pattern (28 bp):
CTTGCTAATATATCTGTTTTATTGATTA
Found at i:1125384 original size:2 final size:2
Alignment explanation
Indices: 1125377--1125406 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1125367 GAACATGTGA
1125377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1125407 GTTTAAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1126077 original size:13 final size:13
Alignment explanation
Indices: 1126059--1126121 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
1126049 TTATATGGCA
1126059 CTACGGTGCAATT
1 CTACGGTGCAATT
1126072 CTACGG-GC-A--
1 CTACGGTGCAATT
*
1126081 CTTCGGTGCAATT
1 CTACGGTGCAATT
1126094 CTACGG-GC-A--
1 CTACGGTGCAATT
*
1126103 CTTCGGTGCAATT
1 CTACGGTGCAATT
1126116 CTACGG
1 CTACGG
1126122 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:1126087 original size:22 final size:22
Alignment explanation
Indices: 1126055--1126135 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
1126045 ATCATTATAT
*
1126055 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
1126077 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
1126099 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
1126122 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1126136 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:1129204 original size:21 final size:21
Alignment explanation
Indices: 1129178--1129222 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1129168 GATTTCTGGG
* *
1129178 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1129199 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1129220 CAA
1 CAA
1129223 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1130246 original size:2 final size:2
Alignment explanation
Indices: 1130239--1130278 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1130229 GAACATGTGA
1130239 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1130279 GTTTAAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1130951 original size:13 final size:13
Alignment explanation
Indices: 1130933--1130995 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
1130923 TTATATGGCA
1130933 CTACGGTGCAATT
1 CTACGGTGCAATT
1130946 CTACGG-GC-A--
1 CTACGGTGCAATT
*
1130955 CTTCGGTGCAATT
1 CTACGGTGCAATT
1130968 CTACGG-GC-A--
1 CTACGGTGCAATT
*
1130977 CTTCGGTGCAATT
1 CTACGGTGCAATT
1130990 CTACGG
1 CTACGG
1130996 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:1130961 original size:22 final size:22
Alignment explanation
Indices: 1130929--1131009 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
1130919 ATCATTATAT
*
1130929 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
1130951 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
1130973 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
1130996 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1131010 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:1134084 original size:21 final size:21
Alignment explanation
Indices: 1134058--1134102 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1134048 GATTTCTGGG
* *
1134058 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1134079 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1134100 CAA
1 CAA
1134103 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1135132 original size:2 final size:2
Alignment explanation
Indices: 1135125--1135150 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1135115 GAACATGTGA
1135125 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1135151 GTTTAAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1135823 original size:13 final size:13
Alignment explanation
Indices: 1135805--1135867 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
1135795 TTATATGGCA
1135805 CTACGGTGCAATT
1 CTACGGTGCAATT
1135818 CTACGG-GC-A--
1 CTACGGTGCAATT
*
1135827 CTTCGGTGCAATT
1 CTACGGTGCAATT
1135840 CTACGG-GC-A--
1 CTACGGTGCAATT
*
1135849 CTTCGGTGCAATT
1 CTACGGTGCAATT
1135862 CTACGG
1 CTACGG
1135868 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:1135833 original size:22 final size:22
Alignment explanation
Indices: 1135801--1135881 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
1135791 ATCATTATAT
*
1135801 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
1135823 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
1135845 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
1135868 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1135882 TTTATATGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:1138089 original size:2 final size:2
Alignment explanation
Indices: 1138084--1138108 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1138074 ATATATACAT
1138084 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1138109 TTGCCAGTAT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1140853 original size:144 final size:144
Alignment explanation
Indices: 1140692--1141146 Score: 680
Period size: 144 Copynumber: 3.2 Consensus size: 144
1140682 CTCTGACAAA
*
1140692 TTATTAGAGATCCAATCATGAGACTGTTGTCATCTAGAGAATACGAGATTTTGGATAAATAGTAA
1 TTATTAGAGATCCAATCATGAGACTGTTGTCATCTAGAGAATACAAGATTTTGGATAAATAGTAA
* * * *
1140757 GTGAGGGTGCAATTTTTGAAGGGTATCTTCAAAAAATAGTTTCAAGGGTATAATAATTATTACTT
66 GTGAGGGTGCAATTTTCGAAGGGTATCTTCAAAAAATATTTTCAAAGGTATAATAATTATCACTT
1140822 AGATATATGTGGAT
131 AGATATATGTGGAT
* * * *
1140836 TTATTATAGATCCAATCATGAGACTGTCGTCGTCTAGAGAATACAATATTTTGGATAAATAGTAA
1 TTATTAGAGATCCAATCATGAGACTGTTGTCATCTAGAGAATACAAGATTTTGGATAAATAGTAA
* * *
1140901 GTGA-GGTGCAATTTTCGAAGGGTATCTTTAAAAAAATATTTTTAAAGATATAATAATTATCACT
66 GTGAGGGTGCAATTTTCGAAGGGTATC-TTCAAAAAATATTTTCAAAGGTATAATAATTATCACT
**
1140965 CGGATATATGTGGAT
130 TAGATATATGTGGAT
* * *
1140980 TTATTAGAGATCCAATCATGAGACTATTGGCATTTAGAGAATACAAGATTTTGGATAAATAGTAA
1 TTATTAGAGATCCAATCATGAGACTGTTGTCATCTAGAGAATACAAGATTTTGGATAAATAGTAA
* *
1141045 ATGAGGGTGCAATTTTCGAAGGGTATATTCAAAAAATATTTTCAAAGGTATAATAATTATCAC-T
66 GTGAGGGTGCAATTTTCGAAGGGTATCTTCAAAAAATATTTTCAAAGGTATAATAATTATCACTT
*
1141109 CGAATATATGTGGAT
131 AG-ATATATGTGGAT
* *
1141124 TTATTAGAAATTCAATCATGAGA
1 TTATTAGAGATCCAATCATGAGA
1141147 TTGTCGTGGA
Statistics
Matches: 278, Mismatches: 30, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
143 22 0.08
144 235 0.85
145 21 0.08
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (144 bp):
TTATTAGAGATCCAATCATGAGACTGTTGTCATCTAGAGAATACAAGATTTTGGATAAATAGTAA
GTGAGGGTGCAATTTTCGAAGGGTATCTTCAAAAAATATTTTCAAAGGTATAATAATTATCACTT
AGATATATGTGGAT
Found at i:1142438 original size:79 final size:78
Alignment explanation
Indices: 1142341--1142490 Score: 203
Period size: 78 Copynumber: 1.9 Consensus size: 78
1142331 TTATTATTTT
* * *
1142341 TTTAACATTTCCCGTAAAGTACTATCTAAAACATTATTTTTTATACCGGAAATGTTAATATTGGG
1 TTTAACATTTCCCGTAAAGCACTACCT-AAACATTATTTTTTATACCAGAAATGTTAATATTGGG
1142406 TGCTACCTAAAATA
65 TGCTACCTAAAATA
* * * *
1142420 TTTAACACTTT-CTGTAAAGCGCTACCTAAACATTATTTTTTCTACCATAAATGTTAATATTGGG
1 TTTAACA-TTTCCCGTAAAGCACTACCTAAACATTATTTTTTATACCAGAAATGTTAATATTGGG
*
1142484 TTCTACC
65 TGCTACC
1142491 GGAAATTAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
78 40 0.65
79 19 0.31
80 3 0.05
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (78 bp):
TTTAACATTTCCCGTAAAGCACTACCTAAACATTATTTTTTATACCAGAAATGTTAATATTGGGT
GCTACCTAAAATA
Found at i:1142895 original size:2 final size:2
Alignment explanation
Indices: 1142888--1142917 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1142878 AATAATACCC
1142888 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1142918 TTCAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1142964 original size:19 final size:19
Alignment explanation
Indices: 1142940--1142977 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1142930 CTTATTTTTA
1142940 TTTAATAAAAATAATATTT
1 TTTAATAAAAATAATATTT
* *
1142959 TTTAATAAATATATTATTT
1 TTTAATAAAAATAATATTT
1142978 CGGATCGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAATAAAAATAATATTT
Found at i:1143472 original size:21 final size:23
Alignment explanation
Indices: 1143446--1143495 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
1143436 TAATTATTAG
1143446 AATATTTAGAAT-ATATT-TATT
1 AATATTTAGAATAATATTATATT
**
1143467 AATATTTCTAATAATATTATATT
1 AATATTTAGAATAATATTATATT
1143490 -ATATTT
1 AATATTT
1143496 TTAATATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.40
22 11 0.44
23 4 0.16
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
AATATTTAGAATAATATTATATT
Found at i:1143493 original size:22 final size:22
Alignment explanation
Indices: 1143458--1143501 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1143448 TATTTAGAAT
1143458 ATATTTATTAATATTTCTAATA
1 ATATTTATTAATATTTCTAATA
*
1143480 ATATTATATT-ATATTTTTAATA
1 ATATT-TATTAATATTTCTAATA
1143502 TTATAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTTATTAATATTTCTAATA
Found at i:1143523 original size:32 final size:32
Alignment explanation
Indices: 1143457--1143525 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
1143447 ATATTTAGAA
* * *
1143457 TATATTTATTAATATTTCTAATAATATTATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
1143489 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
1143521 TATAT
1 TATAT
1143526 AATAATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 12 0.38
31 6 0.19
32 14 0.44
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:1143715 original size:23 final size:22
Alignment explanation
Indices: 1143689--1143732 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1143679 AATAATATTT
1143689 TAATAAAGATATTTAAAATATAC
1 TAATAAAGA-ATTTAAAATATAC
* * *
1143712 TAATTAATAATTTTAAATATA
1 TAATAAAGAATTTAAAATATA
1143733 ATATAACACT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
TAATAAAGAATTTAAAATATAC
Found at i:1144071 original size:14 final size:14
Alignment explanation
Indices: 1144038--1144071 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1144028 AATATTATTC
* *
1144038 ATTTTACGGAAAAC
1 ATTTTCCGGAAAAA
1144052 ATTTTCCGGAAAAA
1 ATTTTCCGGAAAAA
1144066 ATTTTC
1 ATTTTC
1144072 AGTGAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (14 bp):
ATTTTCCGGAAAAA
Found at i:1144226 original size:3 final size:3
Alignment explanation
Indices: 1144218--1144264 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1144208 CTGAGTTGAT
1144218 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1144265 GACCACGGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1146121 original size:16 final size:16
Alignment explanation
Indices: 1146102--1146135 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1146092 CAATATACGA
1146102 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
1146118 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
1146134 AT
1 AT
1146136 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:1146207 original size:16 final size:18
Alignment explanation
Indices: 1146175--1146208 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1146165 TATTAATGTA
1146175 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
1146193 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
1146209 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:1146880 original size:130 final size:130
Alignment explanation
Indices: 1146676--1146923 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
1146666 AATTTTCTTC
* * *
1146676 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATATCAGAT
**
1146741 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
1146806 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATATCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATATCAGAT
1146871 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
1146924 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATATCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:1147381 original size:35 final size:35
Alignment explanation
Indices: 1147320--1147395 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
1147310 AATTAAATTT
* *
1147320 AATTGAATTATTTTAGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTAGAAATTAGGGTTTAGAATGA
* *
1147355 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTAGAAATTAGGGTTTAGAATGA
1147390 AATTGA
1 AATTGA
1147396 TGATTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTAGAAATTAGGGTTTAGAATGA
Found at i:1149040 original size:20 final size:20
Alignment explanation
Indices: 1149015--1149146 Score: 192
Period size: 20 Copynumber: 6.6 Consensus size: 20
1149005 GCGATTTTCC
* *
1149015 GACTATCGCAATGCGATTAT
1 GACTATCGCAACGCGATTCT
1149035 GACTATCGCAACGCGATTCT
1 GACTATCGCAACGCGATTCT
*
1149055 GACTATCGCAACGAGATTCT
1 GACTATCGCAACGCGATTCT
* *
1149075 GACTATCGCAACGTGGTTCT
1 GACTATCGCAACGCGATTCT
*
1149095 GACTATCGCAACGCGATGCT
1 GACTATCGCAACGCGATTCT
*
1149115 GACTATCGCAATGCGATTCT
1 GACTATCGCAACGCGATTCT
*
1149135 GACTGTCGCAAC
1 GACTATCGCAAC
1149147 ACTGAATTTC
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 100 1.00
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (20 bp):
GACTATCGCAACGCGATTCT
Found at i:1152596 original size:140 final size:140
Alignment explanation
Indices: 1152344--1152613 Score: 495
Period size: 140 Copynumber: 1.9 Consensus size: 140
1152334 AAACGTTGTA
*
1152344 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTG
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* * *
1152409 TGATTTGTTCAGTTGTTATCACTTATTACATATTCATTTGAATATCGCAACGTGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
1152474 TATGTGTATT
131 TATGTGTATT
*
1152484 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGTTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1152549 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
1152614 CGCAACGCGA
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 125 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:1152609 original size:20 final size:20
Alignment explanation
Indices: 1152584--1152848 Score: 250
Period size: 20 Copynumber: 13.8 Consensus size: 20
1152574 TTACACATTC
*
1152584 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1152604 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1152624 ATTTGATTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1152644 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
1152664 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
*
1152683 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1152698 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
1152718 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
* * *
1152738 ATTTTACTATAGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
1152758 A----A--ATTGCAACGCAA
1 ATTTGACTATCGCAACGCGA
* *
1152772 ATTTTATTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1152792 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
1152812 ATTTGATTATCGTAAC-AGA
1 ATTTGACTATCGCAACGCGA
*
1152831 TATTTGGCTATCGCAACG
1 -ATTTGACTATCGCAACG
1152849 AGAAAATCGC
Statistics
Matches: 200, Mismatches: 31, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
14 20 0.10
15 3 0.01
16 1 0.00
18 1 0.00
19 4 0.02
20 171 0.86
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1152709 original size:74 final size:73
Alignment explanation
Indices: 1152612--1152823 Score: 282
Period size: 74 Copynumber: 2.9 Consensus size: 73
1152602 GAATTTGACT
* *
1152612 ATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGC
1 ATCGCAACGCGAATTTG-TTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
1152677 AACGCA-AAA
65 AACG-AGAAA
* * * * *
1152686 ATCGCAACGCGAATTTGTCTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTTACTATAGC
1 ATCGCAACGCGAATTTGT-TATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
1152751 AACGAGAAA
65 AACGAGAAA
* * * *
1152760 ATTGCAACGCAAATTTTATTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCG
1 ATCGCAACGCGAA-TTTGTTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCG
1152824 TAACAGATAT
Statistics
Matches: 119, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
73 2 0.02
74 113 0.95
75 4 0.03
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (73 bp):
ATCGCAACGCGAATTTGTTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCA
ACGAGAAA
Found at i:1152753 original size:94 final size:90
Alignment explanation
Indices: 1152590--1152888 Score: 318
Period size: 94 Copynumber: 3.2 Consensus size: 90
1152580 ATTCATTTGA
*
1152590 ATATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATC
1 ATATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATA
1152655 GCAAC-ACGAATATGACTATCGCAACGCAAA-
66 GCAACGA-GAA-A--A-T-T-GCAACGCAAAT
* * * *
1152685 A-ATCGCAACGCGAATTTGTCTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTTACTATA
1 ATATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATA
1152749 GCAACGAGAAAATTGCAACGCAAATTTT
66 GCAACGAGAAAATTGCAACGCAAA---T
* * *
1152777 ATTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGTAAC-AGATATTTGGCTA
1 A-TATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCGA-ATTTGACTA
* * * *
1152841 TCGCAACGAGAAAATCGCAAAGCATATTAG
64 TAGCAACGAGAAAATTGCAACGCA-A--AT
1152871 ACTATCGCAACGCGAATT
1 A-TATCGCAACGCGAATT
1152889 GTCTTTCGCG
Statistics
Matches: 177, Mismatches: 16, Indels: 23
0.82 0.07 0.11
Matches are distributed among these distances:
88 10 0.06
89 1 0.01
90 1 0.01
91 1 0.01
92 1 0.01
93 2 0.01
94 157 0.89
95 3 0.02
97 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (90 bp):
ATATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCGAATTTGACTATA
GCAACGAGAAAATTGCAACGCAAAT
Found at i:1153083 original size:14 final size:14
Alignment explanation
Indices: 1153023--1153084 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
1153013 CACAAATAAG
*
1153023 AATTATTTACACATC
1 AATT-TTTACAAATC
**
1153038 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
1153053 AACTTTTACAAATC
1 AATTTTTACAAATC
*
1153067 AATTTTTATAAATC
1 AATTTTTACAAATC
1153081 AATT
1 AATT
1153085 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:1154588 original size:42 final size:42
Alignment explanation
Indices: 1154481--1154592 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 42
1154471 TCTAGAATGT
* * * * *
1154481 TGGGAGAGACCTCTTCAACGATTACAGTGGCCTCTTGAACGG
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** *
1154523 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
1154565 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
1154593 TGAGTCGGGC
Statistics
Matches: 54, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
42 51 0.94
43 3 0.06
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:1155108 original size:18 final size:18
Alignment explanation
Indices: 1155078--1155144 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 18
1155068 GAAACTTAAA
*
1155078 ATCGCAACACGAATGACT
1 ATCGCAACGCGAATGACT
*
1155096 ATTGCAACGCGAAAATGACT
1 ATCGCAACGCG--AATGACT
*
1155116 ATCGTAACGCGAATTTGACT
1 ATCGCAACGCGAA--TGACT
1155136 ATCGCAACG
1 ATCGCAACG
1155145 AGAGAATCGC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 11 0.28
20 29 0.73
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (18 bp):
ATCGCAACGCGAATGACT
Found at i:1155114 original size:20 final size:20
Alignment explanation
Indices: 1155089--1155144 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1155079 TCGCAACACG
*
1155089 AATGACTATTGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
1155109 AATGACTATCGTAACGCGAA
1 AATGACTATCGCAACGCGAA
**
1155129 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
1155145 AGAGAATCGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:1155214 original size:20 final size:20
Alignment explanation
Indices: 1155189--1155231 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1155179 GATTCTTTCA
1155189 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCG
1155209 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCG
1155229 TTG
1 TTG
1155232 GGAAAGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:1155540 original size:20 final size:20
Alignment explanation
Indices: 1155515--1155562 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1155505 GCGATTCTTT
1155515 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
1155535 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
1155555 CGTTGCGA
1 CGTTGCGA
1155563 AAGTAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1155774 original size:20 final size:20
Alignment explanation
Indices: 1155749--1155816 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
1155739 TAGTTTACTT
**
1155749 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAATTTGACTA
1155769 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAATTTGACTA
1155789 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAATTTGACTA
1155809 TCGCAACG
1 TCGCAACG
1155817 AGAGAATCGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATTTGACTA
Found at i:1155851 original size:344 final size:348
Alignment explanation
Indices: 1155425--1156057 Score: 1139
Period size: 344 Copynumber: 1.8 Consensus size: 348
1155415 TAGTTTACTT
*
1155425 TCGCAACGCGAAAATGACTATCACAATGCGAATTTGACTATCGCAACGAGAGAATCGCAATGCGA
1 TCGCAACGCGAAAATGACTATCACAACGCGAATTTGACTATCGCAACGAGAGAATCGCAATGCGA
1155490 TTTTCATTTCACATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCG
66 TTTTCATTTCACATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCG
*
1155555 CGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTAAATGGATTGCATTACTTCAACC
131 CGTTGCGAAAGTAAACTATTCTTCTACTGCAAATTGAAACTTAAATGGATTGCATTACTTCAACC
*
1155620 AAAAGACAACCAAAAAC-AA-A-T-ACTTCACAAGGTTAAAGAATAAACATTTTAGCAGTATTGG
196 AAAAGACAACCAAAAACAAATACTAACTTCACAAGGTTAAAGAATAAACAGTTTAGCAGTATTGG
*
1155681 CTGCAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAGTTTA
261 CAGCAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAGTTTA
1155746 CTTTCGCAACGCGAAAATGACTA
326 CTTTCGCAACGCGAAAATGACTA
** *
1155769 TCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGAGAATCGCAATGCGA
1 TCGCAACGCGAAAATGACTATCACAACGCGAATTTGACTATCGCAACGAGAGAATCGCAATGCGA
* *
1155834 TTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAGTTCGCGTTGCGATAGTCATTTTCG
66 TTTTCATTTCACATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCG
*
1155899 CGTTGCGAAAGTAAACTATTCTTCTACTGCAAATTGAAACTTGAATGGATTGCATTACTTCAACC
131 CGTTGCGAAAGTAAACTATTCTTCTACTGCAAATTGAAACTTAAATGGATTGCATTACTTCAACC
*
1155964 AAAAGACAACCAAAAACAAATACTAACTTCACAGGGTTAAAGAATAAACAGTTTAGCAGTATTGG
196 AAAAGACAACCAAAAACAAATACTAACTTCACAAGGTTAAAGAATAAACAGTTTAGCAGTATTGG
1156029 CAGCAACCGAATGAATTTACTAAGCAATC
261 CAGCAACCGAATGAATTTACTAAGCAATC
1156058 TAAGTGAAAT
Statistics
Matches: 274, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
344 204 0.74
345 2 0.01
346 1 0.00
347 1 0.00
348 66 0.24
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (348 bp):
TCGCAACGCGAAAATGACTATCACAACGCGAATTTGACTATCGCAACGAGAGAATCGCAATGCGA
TTTTCATTTCACATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCG
CGTTGCGAAAGTAAACTATTCTTCTACTGCAAATTGAAACTTAAATGGATTGCATTACTTCAACC
AAAAGACAACCAAAAACAAATACTAACTTCACAAGGTTAAAGAATAAACAGTTTAGCAGTATTGG
CAGCAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAGTTTA
CTTTCGCAACGCGAAAATGACTA
Found at i:1155865 original size:324 final size:327
Alignment explanation
Indices: 1155099--1156057 Score: 1271
Period size: 328 Copynumber: 2.9 Consensus size: 327
1155089 AATGACTATT
** *
1155099 GCAACGCGAAAATGACTATCGTAACGCGAATTTGACTATCGCAACGAGAGAATCGCAATGCAATT
1 GCAACGCGAAAATGACTATCACAACGCGAATTTGACTATCGCAACGAGAGAATCGCAA-GCGA-T
** * * * * *
1155164 TTCATTTCGCATTGCGATTCTTTCATTGCGA-TA-GTCATTTTCG-CGTTGCGATAGTCATTTTC
64 GACATATCACAATGCGATTCTTTCGTTGCGATTATG-CA-TATCGCCGTTGCGATAGTCATTTTC
*
1155226 GCGTTGGGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAATGGATTGCATTACTTCAAC
127 GCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAATGGATTGCATTACTTCAAC
*
1155291 CAAAAGATAACCAAAAACAAATACTAACTTCAC-AGGATTAAAGAATAAACAGTTTAGCAGTATT
192 CAAAAGACAACCAAAAACAAATACTAACTTCACAAGG-TTAAAGAATAAACAGTTTAGCAGTATT
1155355 GGCAGCAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAGTT
256 GGCAGCAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAGTT
1155420 TACTTTC
321 TACTTTC
*
1155427 GCAACGCGAAAATGACTATCACAATGCGAATTTGACTATCGCAACGAGAGAATCGCAATGCGATT
1 GCAACGCGAAAATGACTATCACAACGCGAATTTGACTATCGCAACGAGAGAATCGCAA-GCGA-T
** * * *
1155492 TTCATTTCACATTGCGATTCTTTCGTTGCGA-TA-GTCAAATTCG-CGTTGCGATAGTCATTTTC
64 GACATATCACAATGCGATTCTTTCGTTGCGATTATG-CATA-TCGCCGTTGCGATAGTCATTTTC
*
1155554 GCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTAAATGGATTGCATTACTTCAAC
127 GCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAATGGATTGCATTACTTCAAC
*
1155619 CAAAAGACAACCAAAAAC-AA-A-T-ACTTCACAAGGTTAAAGAATAAACATTTTAGCAGTATTG
192 CAAAAGACAACCAAAAACAAATACTAACTTCACAAGGTTAAAGAATAAACAGTTTAGCAGTATTG
*
1155680 GCTGCAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAGTTT
257 GCAGCAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAGTTT
1155745 ACTTTC
322 ACTTTC
* *
1155751 GCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAA-
1 GCAACGCGAAAATGACTATCACAACGCGAATTTGACTATCGCAACGAG-A---GA--ATCGCAAG
* * *
1155815 CGA-GAGA-ATCGCAATGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAGTTC
60 CGATGACATATCACAATGCGA--TTC-TTTCG--TTGCGA----TT--ATGC-ATA-TC--G--C
*
1155878 GCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTACTGCAAATTGAAACTTGA
108 -CGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGA
*
1155943 ATGGATTGCATTACTTCAACCAAAAGACAACCAAAAACAAATACTAACTTCACAGGGTTAAAGAA
172 ATGGATTGCATTACTTCAACCAAAAGACAACCAAAAACAAATACTAACTTCACAAGGTTAAAGAA
1156008 TAAACAGTTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAAGCAATC
237 TAAACAGTTTAGCAGTATTGGCAGCAACCGAATGAATTTACTAAGCAATC
1156058 TAAGTGAAAT
Statistics
Matches: 569, Mismatches: 30, Indels: 44
0.88 0.05 0.07
Matches are distributed among these distances:
324 149 0.26
325 14 0.02
326 2 0.00
327 5 0.01
328 208 0.37
330 13 0.02
335 1 0.00
337 1 0.00
338 5 0.01
340 1 0.00
344 100 0.18
345 2 0.00
346 1 0.00
347 1 0.00
348 66 0.12
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (327 bp):
GCAACGCGAAAATGACTATCACAACGCGAATTTGACTATCGCAACGAGAGAATCGCAAGCGATGA
CATATCACAATGCGATTCTTTCGTTGCGATTATGCATATCGCCGTTGCGATAGTCATTTTCGCGT
TGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAATGGATTGCATTACTTCAACCAAA
AGACAACCAAAAACAAATACTAACTTCACAAGGTTAAAGAATAAACAGTTTAGCAGTATTGGCAG
CAACCGAATGAATTTACTAAGCAATCCATTCAAGTTTCAATTTGCAGAAGAAGAATAGTTTACTT
TC
Found at i:1155884 original size:20 final size:20
Alignment explanation
Indices: 1155859--1155906 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1155849 GCGATTCTTT
1155859 CGTTGCGATAGTCAAGTTCG
1 CGTTGCGATAGTCAAGTTCG
**
1155879 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAGTTCG
1155899 CGTTGCGA
1 CGTTGCGA
1155907 AAGTAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAGTTCG
Found at i:1157834 original size:20 final size:20
Alignment explanation
Indices: 1157811--1157877 Score: 102
Period size: 19 Copynumber: 3.5 Consensus size: 20
1157801 TCTGAAACTT
*
1157811 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
1157831 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
*
1157850 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
1157869 AAAATCGCA
1 AAAATCGCA
1157878 TTGCGATTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
19 28 0.64
20 16 0.36
ACGTcount: A:0.51, C:0.22, G:0.16, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:1158506 original size:20 final size:20
Alignment explanation
Indices: 1158481--1158573 Score: 150
Period size: 20 Copynumber: 4.7 Consensus size: 20
1158471 CGCTTTGAAA
1158481 ATCGCATTGCGATAGTCAGC
1 ATCGCATTGCGATAGTCAGC
1158501 ATCGCATTGCGATAGTCAGC
1 ATCGCATTGCGATAGTCAGC
*
1158521 ATCGCGTTGCGATAGTCAGC
1 ATCGCATTGCGATAGTCAGC
* *
1158541 ATCGCGTTGCGATAGTCAGA
1 ATCGCATTGCGATAGTCAGC
*
1158561 ATCGCATTTCGAT
1 ATCGCATTGCGAT
1158574 TTATATATTC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.27
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGC
Found at i:1159847 original size:23 final size:25
Alignment explanation
Indices: 1159813--1159866 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
1159803 TACACTTTTC
1159813 ATAATTTTATAAT-TTTT-AAAAATT
1 ATAA-TTTATAATATTTTGAAAAATT
*
1159837 ATAATTTATAATATTTTGGAAAATT
1 ATAATTTATAATATTTTGAAAAATT
1159862 A-AATT
1 ATAATT
1159867 GTTTATTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 8 0.30
24 12 0.44
25 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
ATAATTTATAATATTTTGAAAAATT
Found at i:1161979 original size:16 final size:16
Alignment explanation
Indices: 1161954--1161988 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1161944 ATTCATACAG
1161954 AGCATCTGAATCATTC
1 AGCATCTGAATCATTC
*
1161970 AGCATTTGAATCATTC
1 AGCATCTGAATCATTC
1161986 AGC
1 AGC
1161989 GCTTAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (16 bp):
AGCATCTGAATCATTC
Found at i:1172931 original size:74 final size:74
Alignment explanation
Indices: 1172847--1172999 Score: 236
Period size: 74 Copynumber: 2.1 Consensus size: 74
1172837 GCAATCATAT
1172847 ATTGAGTTTTTTAACTATTTAAATATAATATTTTAAATCTATTTAAGAAAATAT-AGTATTTTAA
1 ATTGAGTTTTTTAACTATTTAAATATAATATTTTAAATCTATTTAAGAAAATATAAG-ATTTTAA
1172911 ATAAATACTC
65 ATAAATACTC
** * * *
1172921 ATTGAGTTTTTTAGTTGTTTAAATATAATATTTTAAATTTATTTAAGAAGATATAAGATTTTAAA
1 ATTGAGTTTTTTAACTATTTAAATATAATATTTTAAATCTATTTAAGAAAATATAAGATTTTAAA
*
1172986 TAAATATTC
66 TAAATACTC
1172995 ATTGA
1 ATTGA
1173000 ATGATTGAAT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
74 70 0.97
75 2 0.03
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (74 bp):
ATTGAGTTTTTTAACTATTTAAATATAATATTTTAAATCTATTTAAGAAAATATAAGATTTTAAA
TAAATACTC
Found at i:1175584 original size:13 final size:15
Alignment explanation
Indices: 1175566--1175600 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1175556 AAATCATTTT
1175566 TTATTTTT-T-AAAA
1 TTATTTTTCTCAAAA
1175579 TTATTTTTCTCAAAA
1 TTATTTTTCTCAAAA
1175594 TTATTTT
1 TTATTTT
1175601 AAAAGGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.40
14 1 0.05
15 11 0.55
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTTTTCTCAAAA
Found at i:1185227 original size:26 final size:26
Alignment explanation
Indices: 1185198--1185290 Score: 70
Period size: 26 Copynumber: 3.6 Consensus size: 26
1185188 TAGTTGAGGA
1185198 TATTTTATATTTTATAATTTAAATTT
1 TATTTTATATTTTATAATTTAAATTT
* * *
1185224 TATTTGATATTTTTTTA-TTAAA-TT
1 TATTTTATATTTTATAATTTAAATTT
* *
1185248 GAGTTTATA-TTTA-AATTT-AATTGT
1 TATTTTATATTTTATAATTTAAATT-T
1185272 TAATATTTATAATTTTATA
1 T-AT-TTTAT-ATTTTATA
1185291 GTATTATTTG
Statistics
Matches: 49, Mismatches: 10, Indels: 13
0.68 0.14 0.18
Matches are distributed among these distances:
22 3 0.06
23 6 0.12
24 9 0.18
25 6 0.12
26 19 0.39
27 1 0.02
28 4 0.08
29 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.61
Consensus pattern (26 bp):
TATTTTATATTTTATAATTTAAATTT
Found at i:1185477 original size:18 final size:18
Alignment explanation
Indices: 1185456--1185492 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1185446 AATCATTTAA
* *
1185456 AATTTTAATTTATAATTT
1 AATTCTAATTTAAAATTT
1185474 AATTCTAATTTAAAATTT
1 AATTCTAATTTAAAATTT
1185492 A
1 A
1185493 TTGAGTCGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTCTAATTTAAAATTT
Found at i:1189033 original size:25 final size:26
Alignment explanation
Indices: 1188996--1189045 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1188986 TTAATAATAT
* *
1188996 ATTTTTATCCTC-TAAAATTTTATGA
1 ATTTATATCCTCTTAAAATTATATGA
*
1189021 ATTTATATTCTCTTAAAATTATATG
1 ATTTATATCCTCTTAAAATTATATG
1189046 GATTAACCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.34, C:0.10, G:0.04, T:0.52
Consensus pattern (26 bp):
ATTTATATCCTCTTAAAATTATATGA
Found at i:1195979 original size:15 final size:15
Alignment explanation
Indices: 1195940--1195979 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
1195930 CAACCATGTT
1195940 AGGGACTTAAACAAA
1 AGGGACTTAAACAAA
*
1195955 AGAGACTTAAACAAA
1 AGGGACTTAAACAAA
*
1195970 AGGGAGTTAA
1 AGGGACTTAA
1195980 CGGAAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.53, C:0.10, G:0.23, T:0.15
Consensus pattern (15 bp):
AGGGACTTAAACAAA
Found at i:1196634 original size:21 final size:21
Alignment explanation
Indices: 1196605--1196657 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1196595 ATTCTGACTA
1196605 TCGCATTGCGATTTTACAAAT
1 TCGCATTGCGATTTTACAAAT
* * *
1196626 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTACAAAT
*
1196647 TCGCAATGCGA
1 TCGCATTGCGA
1196658 ATATGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1196672 original size:20 final size:20
Alignment explanation
Indices: 1196647--1196717 Score: 133
Period size: 20 Copynumber: 3.5 Consensus size: 20
1196637 TTTTCCGAAT
*
1196647 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATATAAA
1196667 TCGCAATGCGAATATATAAA
1 TCGCAATGCGAATATATAAA
1196687 TCGCAATGCGAATATATAAA
1 TCGCAATGCGAATATATAAA
1196707 TCGCAATGCGA
1 TCGCAATGCGA
1196718 TTATGACTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATATATAAA
Found at i:1196729 original size:20 final size:20
Alignment explanation
Indices: 1196647--1196819 Score: 122
Period size: 20 Copynumber: 8.7 Consensus size: 20
1196637 TTTTCCGAAT
* *
1196647 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTATG-ACTA
*
1196667 TCGCAATGCGAATATAT-A-AA
1 TCGCAATGCG-AT-TATGACTA
*
1196687 TCGCAATGCGAATATAT-A-AA
1 TCGCAATGCG-AT-TATGACTA
1196707 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTATGACTA
* *
1196727 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTATGACTA
* * *
1196747 TCGCAACGAGATTCTGACTA
1 TCGCAATGCGATTATGACTA
* * *
1196767 TCGCAACGTGATTCTGACTA
1 TCGCAATGCGATTATGACTA
* **
1196787 TCGCAACGCGATGCTGACTA
1 TCGCAATGCGATTATGACTA
*
1196807 TCGTAATGCGATT
1 TCGCAATGCGATT
1196820 TTCAAAGCGC
Statistics
Matches: 138, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
18 3 0.02
19 3 0.02
20 128 0.93
21 1 0.01
22 3 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (20 bp):
TCGCAATGCGATTATGACTA
Found at i:1196730 original size:40 final size:40
Alignment explanation
Indices: 1196585--1196737 Score: 123
Period size: 40 Copynumber: 3.8 Consensus size: 40
1196575 GTTTCCAGAT
* * * * * *
1196585 TCGCAACGCGATTCTGACTATCGCATTGCGATTTTACAAA
1 TCGCAATGCGATTATGACTATCGCAATGCGAATATATAAA
** * * *
1196625 TTCGCGTTGCGATTTTCCGAAT-TCGCAATGCGAATATGTAAA
1 -TCGCAATGCGATTAT--GACTATCGCAATGCGAATATATAAA
*
1196667 TCGCAATGCGAATATAT-A-AATCGCAATGCGAATATATAAA
1 TCGCAATGCG-AT-TATGACTATCGCAATGCGAATATATAAA
*
1196707 TCGCAATGCGATTATGACTATCGCAACGCGA
1 TCGCAATGCGATTATGACTATCGCAATGCGA
1196738 TTCTGACTAT
Statistics
Matches: 88, Mismatches: 17, Indels: 15
0.73 0.14 0.12
Matches are distributed among these distances:
38 3 0.03
39 3 0.03
40 41 0.47
41 19 0.22
42 17 0.19
43 5 0.06
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (40 bp):
TCGCAATGCGATTATGACTATCGCAATGCGAATATATAAA
Found at i:1196750 original size:40 final size:40
Alignment explanation
Indices: 1196706--1196819 Score: 165
Period size: 40 Copynumber: 2.9 Consensus size: 40
1196696 GAATATATAA
* *
1196706 ATCGCAATGCGATTATGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATTCTGACT
* *
1196746 ATCGCAACGAGATTCTGACTATCGCAACGTGATTCTGACT
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATTCTGACT
* * *
1196786 ATCGCAACGCGATGCTGACTATCGTAATGCGATT
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATT
1196820 TTCAAAGCGC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (40 bp):
ATCGCAACGCGATTCTGACTATCGCAACGCGATTCTGACT
Found at i:1196750 original size:60 final size:62
Alignment explanation
Indices: 1196686--1196817 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 62
1196676 GAATATATAA
* *
1196686 ATCGCAATGCGA-ATATAT-A-AATCGCAATGCGATTATGACTATCGCAACGCGATTCTGACT
1 ATCGCAATGCGAGAT-TATGACAATCGCAACGCGATTATGACTATCGCAACGCGATGCTGACT
* * * *
1196746 ATCGCAA--CGAGATTCTGACTATCGCAACGTGATTCTGACTATCGCAACGCGATGCTGACT
1 ATCGCAATGCGAGATTATGACAATCGCAACGCGATTATGACTATCGCAACGCGATGCTGACT
*
1196806 ATCGTAATGCGA
1 ATCGCAATGCGA
1196818 TTTTCAAAGC
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
58 5 0.08
59 3 0.05
60 49 0.82
62 3 0.05
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (62 bp):
ATCGCAATGCGAGATTATGACAATCGCAACGCGATTATGACTATCGCAACGCGATGCTGACT
Found at i:1197002 original size:22 final size:22
Alignment explanation
Indices: 1196977--1197031 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
1196967 GGCGACATCC
1196977 GTCCCTATCTCCAACGAAATCA
1 GTCCCTATCTCCAACGAAATCA
* * *
1196999 GTCCCCATCTCCGACGAAATCC
1 GTCCCTATCTCCAACGAAATCA
1197021 GT--CTATCTCCA
1 GTCCCTATCTCCA
1197032 TCTCTTAGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 7 0.25
22 21 0.75
ACGTcount: A:0.25, C:0.40, G:0.11, T:0.24
Consensus pattern (22 bp):
GTCCCTATCTCCAACGAAATCA
Found at i:1197442 original size:20 final size:20
Alignment explanation
Indices: 1197417--1197469 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1197407 CTATTTTAGT
1197417 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
**
1197437 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
1197457 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
1197470 TTTAAGTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:1199228 original size:18 final size:18
Alignment explanation
Indices: 1199205--1199254 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
1199195 TTTACTCGTA
1199205 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
*
1199223 ATTTCACTTAGATTAACT
1 ATTTCACTTAGATTAACC
1199241 ATTTCACTTAGATT
1 ATTTCACTTAGATT
1199255 GCTTAGTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:1199427 original size:20 final size:20
Alignment explanation
Indices: 1199402--1199469 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
1199392 TAGTTTACTT
1199402 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
1199422 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* **
1199442 TCACAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
1199462 TCGCAACG
1 TCGCAACG
1199470 AAAGAATCAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:1199555 original size:18 final size:19
Alignment explanation
Indices: 1199512--1199558 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1199502 GCGATTCTCT
1199512 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-AATTCG
*
1199532 CATTGCGATAGTC-ATTCG
1 CGTTGCGATAGTCAATTCG
*
1199550 TGTTGCGAT
1 CGTTGCGAT
1199559 TTTAAGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 12 0.50
20 12 0.50
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (19 bp):
CGTTGCGATAGTCAATTCG
Found at i:1200082 original size:18 final size:19
Alignment explanation
Indices: 1200043--1200084 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1200033 CTCACCTGTC
1200043 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
1200064 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
1200082 ATC
1 ATC
1200085 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:1201562 original size:14 final size:14
Alignment explanation
Indices: 1201543--1201604 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
1201533 TGTCTTGTTT
1201543 AATTGATTTGTAAA
1 AATTGATTTGTAAA
1201557 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
1201571 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1201586 TATTGATGTGTAAA
1 AATTGATTTGTAAA
1201600 TAATT
1 -AATT
1201605 CTTATTTGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 13 0.33
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1201576 original size:28 final size:29
Alignment explanation
Indices: 1201545--1201599 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1201535 TCTTGTTTAA
*
1201545 TTGATTTG-TAAAAATTGATTTGTAAAAG
1 TTGATTTGTTAAAAATTGATGTGTAAAAG
* *
1201573 TTGATTTGTTTAATATTGATGTGTAAA
1 TTGATTTGTTAAAAATTGATGTGTAAA
1201600 TAATTCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (29 bp):
TTGATTTGTTAAAAATTGATGTGTAAAAG
Found at i:1201728 original size:20 final size:20
Alignment explanation
Indices: 1201703--1201756 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1201693 AGGTACACTT
*
1201703 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
*
1201723 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
1201743 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
1201757 TCAATTCGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.28, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:1201825 original size:20 final size:20
Alignment explanation
Indices: 1201800--1201907 Score: 144
Period size: 20 Copynumber: 5.4 Consensus size: 20
1201790 CGATTTTCTG
* * *
1201800 GTTGCGATAGTCGAATACCC
1 GTTGCGATAGTCAAATTCGC
* *
1201820 GTTGCGATAATCAAATTCAC
1 GTTGCGATAGTCAAATTCGC
**
1201840 GTTGCGATAGTCAAATTCTT
1 GTTGCGATAGTCAAATTCGC
*
1201860 GTTGCGATAGTTAAATTCGC
1 GTTGCGATAGTCAAATTCGC
1201880 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
1201900 GTTGCGAT
1 GTTGCGAT
1201908 TTTTTCGTTA
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:1201894 original size:60 final size:54
Alignment explanation
Indices: 1201759--1201941 Score: 179
Period size: 54 Copynumber: 3.3 Consensus size: 54
1201749 CGCGAAAGTC
* * * * * * **
1201759 AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTGGTTGCGATAGTCG
1 AATTCGCGTTGCGATAATCAAATTCACGTTGCGATTTTCTTGTTGCGATAGTTA
* *
1201813 AATACCCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCTTGTTGCGATAGTTA
1 AATTCGCGTTGCGATAATCAAATTCACGTTGCGAT--T----TTCTTGTTGCGATAGTTA
* * *
1201873 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TTCGTTACGATAGTTA
1 AATTCGCGTTGCGATAATCAAATTCACGTTGCGATTTTCTT-GTTGCGATAGTTA
1201927 AATTCGCGTTGCGAT
1 AATTCGCGTTGCGAT
1201942 TTTTGAGTTA
Statistics
Matches: 107, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
53 2 0.02
54 57 0.53
56 1 0.01
58 1 0.01
60 46 0.43
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.36
Consensus pattern (54 bp):
AATTCGCGTTGCGATAATCAAATTCACGTTGCGATTTTCTTGTTGCGATAGTTA
Found at i:1201930 original size:34 final size:34
Alignment explanation
Indices: 1201878--1201975 Score: 160
Period size: 34 Copynumber: 2.9 Consensus size: 34
1201868 AGTTAAATTC
*
1201878 GCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
1 GCGTTACGATAGTCAAATTCGCGTTGCGATTTTT
* *
1201912 TCGTTACGATAGTTAAATTCGCGTTGCGATTTTT
1 GCGTTACGATAGTCAAATTCGCGTTGCGATTTTT
*
1201946 GAGTTACGATAGTCAAATTCGCGTTGCGAT
1 GCGTTACGATAGTCAAATTCGCGTTGCGAT
1201976 ATTCAAATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.38
Consensus pattern (34 bp):
GCGTTACGATAGTCAAATTCGCGTTGCGATTTTT
Found at i:1201981 original size:20 final size:20
Alignment explanation
Indices: 1201800--1201983 Score: 117
Period size: 20 Copynumber: 9.8 Consensus size: 20
1201790 CGATTTTCTG
* * * *
1201800 GTTGCGATAGTCGAATACCC
1 GTTGCGATATTCAAATTCGC
* *
1201820 GTTGCGATAATCAAATTCAC
1 GTTGCGATATTCAAATTCGC
* **
1201840 GTTGCGATAGTCAAATTCTT
1 GTTGCGATATTCAAATTCGC
1201860 GTTGCGATAGTT-AAATTCGC
1 GTTGCGATA-TTCAAATTCGC
*
1201880 GTTGCGATAGTCAAATTCGC
1 GTTGCGATATTCAAATTCGC
*
1201900 GTTGCGAT-TT----TT-TC
1 GTTGCGATATTCAAATTCGC
*
1201914 GTTACGATAGTT-AAATTCGC
1 GTTGCGATA-TTCAAATTCGC
*
1201934 GTTGCGAT-TT----TT-GA
1 GTTGCGATATTCAAATTCGC
* *
1201948 GTTACGATAGTCAAATTCGC
1 GTTGCGATATTCAAATTCGC
1201968 GTTGCGATATTCAAAT
1 GTTGCGATATTCAAAT
1201984 GAATGTGTAA
Statistics
Matches: 128, Mismatches: 22, Indels: 28
0.72 0.12 0.16
Matches are distributed among these distances:
14 16 0.12
15 5 0.04
16 2 0.02
18 2 0.02
19 6 0.05
20 96 0.75
21 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.36
Consensus pattern (20 bp):
GTTGCGATATTCAAATTCGC
Found at i:1204468 original size:24 final size:24
Alignment explanation
Indices: 1204434--1204487 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1204424 CTGAAACATC
1204434 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1204458 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1204482 ATCAAA
1 ATCAAA
1204488 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1204501 original size:24 final size:24
Alignment explanation
Indices: 1204434--1204501 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1204424 CTGAAACATC
* * *
1204434 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1204458 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1204482 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1204502 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1205333 original size:20 final size:20
Alignment explanation
Indices: 1205308--1205395 Score: 140
Period size: 20 Copynumber: 4.4 Consensus size: 20
1205298 GAAATTCAGT
*
1205308 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1205328 GTTGCGATAGTCAGAATCTC
1 GTTGCGATAGTCAGAATCGC
*
1205348 GTTGCGATAATCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
1205368 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1205388 ATTGCGAT
1 GTTGCGAT
1205396 TTACATATTC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:1205413 original size:40 final size:40
Alignment explanation
Indices: 1205322--1205476 Score: 118
Period size: 40 Copynumber: 3.8 Consensus size: 40
1205312 CGACAGTCAG
* * * * *
1205322 AATCGCGTTGCGATAGTCAGAATCTCGTTGCGA-TAATCAG
1 AATCGCATTGCGATAGTCAGAATCGCATTGCGATTTA-CAA
* *
1205362 AATCGCGTTGCGATAGTCAGAATCGCATTGCGATTTACAT
1 AATCGCATTGCGATAGTCAGAATCGCATTGCGATTTACAA
* * * * *
1205402 ATTCGCATTGCGAT-TTCGAAAAATCGCAATGCAAATTTGA-AA
1 AATCGCATTGCGATAGTC--AGAATCGCATTGC-GATTT-ACAA
* *
1205444 AATCGCAATGCGATAGTCAGAATCGCGTTGCGA
1 AATCGCATTGCGATAGTCAGAATCGCATTGCGA
1205477 ATCTGGAAAC
Statistics
Matches: 91, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
39 2 0.02
40 46 0.51
41 23 0.25
42 17 0.19
43 3 0.03
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (40 bp):
AATCGCATTGCGATAGTCAGAATCGCATTGCGATTTACAA
Found at i:1205443 original size:21 final size:22
Alignment explanation
Indices: 1205414--1205454 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
1205404 TCGCATTGCG
1205414 ATTTCGAAAAATCGCAATGCAA
1 ATTTCGAAAAATCGCAATGCAA
1205436 ATTT-GAAAAATCGCAATGC
1 ATTTCGAAAAATCGCAATGC
1205455 GATAGTCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (22 bp):
ATTTCGAAAAATCGCAATGCAA
Found at i:1205536 original size:19 final size:19
Alignment explanation
Indices: 1205512--1205554 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1205502 AAGATTGCGC
1205512 TGCGAATTATCGATCGCAT
1 TGCGAATTATCGATCGCAT
1205531 TGCGAATTATCGATCGCAT
1 TGCGAATTATCGATCGCAT
1205550 TGCGA
1 TGCGA
1205555 TTTAGTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (19 bp):
TGCGAATTATCGATCGCAT
Found at i:1206775 original size:30 final size:30
Alignment explanation
Indices: 1206718--1206775 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
1206708 TCCACACTCT
* * *
1206718 TTCTTGATTTTTCTCTTCTCTCGGTGCTGG
1 TTCTTGATTTTTCTCTACGCTCAGTGCTGG
* *
1206748 TTCTTGCTTTTTCTCTACGGTCAGTGCT
1 TTCTTGATTTTTCTCTACGCTCAGTGCT
1206776 TAACTTTGGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.05, C:0.24, G:0.19, T:0.52
Consensus pattern (30 bp):
TTCTTGATTTTTCTCTACGCTCAGTGCTGG
Found at i:1210735 original size:22 final size:22
Alignment explanation
Indices: 1210707--1210754 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
1210697 AATAATATTT
1210707 TATTTTTAAAAAATAAAAAATA
1 TATTTTTAAAAAATAAAAAATA
1210729 TATTTTTAAAAAATAAAAAATA
1 TATTTTTAAAAAATAAAAAATA
1210751 TATT
1 TATT
1210755 AGTAAAGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TATTTTTAAAAAATAAAAAATA
Found at i:1210760 original size:22 final size:22
Alignment explanation
Indices: 1210713--1210760 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1210703 ATTTTATTTT
**
1210713 TAAAAAATAAAAAATATATTTT
1 TAAAAAATAAAAAATATATTAG
1210735 TAAAAAATAAAAAATATATTAG
1 TAAAAAATAAAAAATATATTAG
1210757 TAAA
1 TAAA
1210761 GGTTATTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAAAATAAAAAATATATTAG
Found at i:1210829 original size:23 final size:23
Alignment explanation
Indices: 1210802--1210849 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1210792 GAATTTTAGC
1210802 ATCATACACTTAAGTAATAAAAG
1 ATCATACACTTAAGTAATAAAAG
1210825 ATCATACACTTAAGTAATAAAAG
1 ATCATACACTTAAGTAATAAAAG
1210848 AT
1 AT
1210850 AAATTTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.27
Consensus pattern (23 bp):
ATCATACACTTAAGTAATAAAAG
Found at i:1211766 original size:23 final size:23
Alignment explanation
Indices: 1211735--1211872 Score: 168
Period size: 23 Copynumber: 6.0 Consensus size: 23
1211725 CACCACAGCT
* *
1211735 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
*
1211758 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
* *
1211781 CGTAGAAATGCACCAAAGCGCCG
1 CGTAGAAATGCACCAAAGTGCCA
* * *
1211804 CATAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
* *
1211827 CGTAGAAATGCACCAAAGCGCCG
1 CGTAGAAATGCACCAAAGTGCCA
* *
1211850 CATAGAATTGCACCAAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
1211873 TATAAAATGT
Statistics
Matches: 97, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 97 1.00
ACGTcount: A:0.36, C:0.28, G:0.23, T:0.14
Consensus pattern (23 bp):
CGTAGAAATGCACCAAAGTGCCA
Found at i:1211793 original size:46 final size:46
Alignment explanation
Indices: 1211735--1211872 Score: 213
Period size: 46 Copynumber: 3.0 Consensus size: 46
1211725 CACCACAGCT
* * * * * *
1211735 CGTATAAATGCACCGAAGTGCCACGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCAAAGCGCCGCATAGAATTGCACCGAAGTGCCA
1211781 CGTAGAAATGCACCAAAGCGCCGCATAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGCACCAAAGCGCCGCATAGAATTGCACCGAAGTGCCA
*
1211827 CGTAGAAATGCACCAAAGCGCCGCATAGAATTGCACCAAAGTGCCA
1 CGTAGAAATGCACCAAAGCGCCGCATAGAATTGCACCGAAGTGCCA
1211873 TATAAAATGT
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.36, C:0.28, G:0.23, T:0.14
Consensus pattern (46 bp):
CGTAGAAATGCACCAAAGCGCCGCATAGAATTGCACCGAAGTGCCA
Found at i:1214258 original size:65 final size:64
Alignment explanation
Indices: 1214060--1214269 Score: 232
Period size: 65 Copynumber: 3.2 Consensus size: 64
1214050 TGCACTAAGA
* * ** *
1214060 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTTG
* *
1214124 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGTTGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGT
1214187 AT-
63 -TG
* *
1214189 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGG-TT
1214253 G
64 G
*
1214254 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
1214270 CTTTGATAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 51 0.41
65 63 0.51
66 1 0.01
67 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTTG
Found at i:1215283 original size:21 final size:21
Alignment explanation
Indices: 1215259--1215302 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1215249 CCGAAGGAAG
*
1215259 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
* *
1215280 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
1215301 AG
1 AG
1215303 CTCCCGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.41, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAGCT
Found at i:1215757 original size:15 final size:15
Alignment explanation
Indices: 1215734--1215763 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1215724 ATTTTCATTC
*
1215734 TCATTATATAACCCA
1 TCATCATATAACCCA
1215749 TCATCATATAACCCA
1 TCATCATATAACCCA
1215764 AAAAGGAAAG
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:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (15 bp):
TCATCATATAACCCA
Found at i:1216882 original size:23 final size:23
Alignment explanation
Indices: 1216854--1216932 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 23
1216844 CATGGCCTTG
*
1216854 TGCATCGATGCACATTCAAGGTG
1 TGCATCGATGCACATTCAAGGTA
* * *
1216877 TGCATCGGTGCACCTTCATGGTA
1 TGCATCGATGCACATTCAAGGTA
* *
1216900 T--ATCAATGCACATTCAAAG-A
1 TGCATCGATGCACATTCAAGGTA
1216920 TGCATCGATGCAC
1 TGCATCGATGCAC
1216933 TGTTAGGTGT
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.05
21 13 0.30
22 9 0.20
23 20 0.45
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.27
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGTA
Found at i:1222825 original size:65 final size:65
Alignment explanation
Indices: 1222721--1222862 Score: 182
Period size: 65 Copynumber: 2.2 Consensus size: 65
1222711 CCACCCTTAG
*
1222721 TGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCAATGCATGGCT-GGTGCATCGATGCATCAA
1 TGCATTCGATGTTTTCAAAATAGCCACAGTGCATCAATGCATGG-TAGGTGCATCGATGCATCAA
1222784 A
65 A
* * * * *
1222785 TGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGGTATGTGCATCGATGCATGAA
1 TGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCAATGCATGGTAGGTGCATCGATGCATCAA
1222849 A
65 A
*
1222850 TGCATTTGATGTT
1 TGCATTCGATGTT
1222863 CAATTTAATT
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 12 0.18
65 53 0.78
66 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (65 bp):
TGCATTCGATGTTTTCAAAATAGCCACAGTGCATCAATGCATGGTAGGTGCATCGATGCATCAAA
Done.