Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 54
Found at i:1257151 original size:43 final size:40
Alignment explanation
Indices: 1257052--1257156 Score: 111
Period size: 40 Copynumber: 2.5 Consensus size: 40
1257042 AAGATGTCAT
* * * *
1257052 GTCATCCTCATCATGTAGGAACCGTGTCATCCACTGACCA
1 GTCATCCTCATCACGTAGGAACCGTGTCACCCAATAACCA
* * * *
1257092 GACCTCCTCATAACGTAGGAGCCGTGTCACCCTTAGATAACCA
1 GTCATCCTCATCACGTAGGAACCGTGTCACCC--A-ATAACCA
1257135 GTCATCCTCATCACGTAGGAAC
1 GTCATCCTCATCACGTAGGAAC
1257157 TATGTTATCA
Statistics
Matches: 50, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
40 26 0.52
42 1 0.02
43 23 0.46
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (40 bp):
GTCATCCTCATCACGTAGGAACCGTGTCACCCAATAACCA
Found at i:1257190 original size:48 final size:48
Alignment explanation
Indices: 1257135--1257251 Score: 189
Period size: 48 Copynumber: 2.4 Consensus size: 48
1257125 TAGATAACCA
* *
1257135 GTCATCCTCATCACGTAGGAACTATGTTATCATCCCTAAAGATGGTAT
1 GTCATCCTCATCACGTAGGAACTATGATATCATCCCTAAAGATGATAT
* *
1257183 GTCATCCTCATCATGTAGGAACTGTGATATCATCCCTAAAGATGATAT
1 GTCATCCTCATCACGTAGGAACTATGATATCATCCCTAAAGATGATAT
*
1257231 GCCATCCTCATCACGTAGGAA
1 GTCATCCTCATCACGTAGGAA
1257252 TCATGTCATC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 63 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (48 bp):
GTCATCCTCATCACGTAGGAACTATGATATCATCCCTAAAGATGATAT
Found at i:1272572 original size:2 final size:2
Alignment explanation
Indices: 1272565--1272594 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1272555 TCTAAAGCTT
1272565 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1272595 GTTAACTGGA
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):
TA
Found at i:1274854 original size:13 final size:13
Alignment explanation
Indices: 1274836--1274861 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1274826 TTTCACATTC
1274836 TTCCTTCTATCAA
1 TTCCTTCTATCAA
1274849 TTCCTTCTATCAA
1 TTCCTTCTATCAA
1274862 GCTACGTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (13 bp):
TTCCTTCTATCAA
Found at i:1276029 original size:21 final size:21
Alignment explanation
Indices: 1276003--1276044 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1275993 TATCGACATC
1276003 ACAGAGGAACCCTCAACTCCA
1 ACAGAGGAACCCTCAACTCCA
*
1276024 ACAGAGGAACCCTCATCTCCA
1 ACAGAGGAACCCTCAACTCCA
1276045 GCAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.38, G:0.14, T:0.12
Consensus pattern (21 bp):
ACAGAGGAACCCTCAACTCCA
Found at i:1276661 original size:21 final size:21
Alignment explanation
Indices: 1276603--1276650 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1276593 AAACCCTGTG
*
1276603 GTGGTGGCAT-ATAAAATGATT
1 GTGGTGGCATCA-GAAATGATT
*
1276624 GTGGTGGCATCAGAAATGGTT
1 GTGGTGGCATCAGAAATGATT
1276645 GTGGTG
1 GTGGTG
1276651 TCATTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.25, C:0.06, G:0.38, T:0.31
Consensus pattern (21 bp):
GTGGTGGCATCAGAAATGATT
Found at i:1277191 original size:64 final size:65
Alignment explanation
Indices: 1277118--1277305 Score: 230
Period size: 65 Copynumber: 2.9 Consensus size: 65
1277108 TTTCAAAGTG
**
1277118 ATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATTGCATGCATCGATGCACATAC
1 ATGCATCGATGCACTCATGGAATATTTTGAAACATCGAATGCATTGCATGCATCGATGCACA-AC
1277181 T
65 T
*
1277182 ATGCATCGATGCACTCA--GAGT-TTTATGAAAACATCGAATGCATTTG-ATGCATCGATGCACC
1 ATGCATCGATGCACTCATGGAATATTT-TG-AAACATCGAATGCA-TTGCATGCATCGATGCA-C
1277243 AACT
62 AACT
* *
1277247 ATGCATCGATGCACTC-TGG-CTATTTTGAAACATCGAATGCATTTCATGCATCGATGCAC
1 ATGCATCGATGCACTCATGGAATATTTTGAAACATCGAATGCATTGCATGCATCGATGCAC
1277306 TCTCAGTGCA
Statistics
Matches: 109, Mismatches: 5, Indels: 21
0.81 0.04 0.16
Matches are distributed among these distances:
62 1 0.01
63 8 0.07
64 41 0.38
65 50 0.46
66 9 0.08
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (65 bp):
ATGCATCGATGCACTCATGGAATATTTTGAAACATCGAATGCATTGCATGCATCGATGCACAACT
Found at i:1283156 original size:23 final size:23
Alignment explanation
Indices: 1283103--1283167 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
1283093 ATGAATCCCT
1283103 TTGAATGTGCATCGAT--ACACC
1 TTGAATGTGCATCGATGCACACC
* * * *
1283124 ATGAAGGTGCACCGATGCACGCC
1 TTGAATGTGCATCGATGCACACC
1283147 TTGAATGTGCATCGATGCACA
1 TTGAATGTGCATCGATGCACA
1283168 AGGCCATGCA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 13 0.38
23 21 0.62
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (23 bp):
TTGAATGTGCATCGATGCACACC
Found at i:1283602 original size:13 final size:13
Alignment explanation
Indices: 1283586--1283610 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1283576 AAATCGAAAA
1283586 TCTAAATTTGATT
1 TCTAAATTTGATT
1283599 TCTAAATTTGAT
1 TCTAAATTTGAT
1283611 GTTTTTGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
TCTAAATTTGATT
Found at i:1285206 original size:2 final size:2
Alignment explanation
Indices: 1285199--1285250 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1285189 CAACTTAAGC
1285199 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1285240 TA TA TA TA TA T
1 TA TA TA TA TA T
1285251 CAATTGACTA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1285906 original size:64 final size:64
Alignment explanation
Indices: 1285705--1285912 Score: 237
Period size: 65 Copynumber: 3.2 Consensus size: 64
1285695 TTTCAAAGTG
* * **
1285705 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGAAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCACCAA-CCATGCATCGATGCACTC-T-AGATATTTTGAAACATCGAATGCATT
1285768 TC
63 TC
* *
1285770 ATGCATCAATGCA-CATACTATGCATCGATGCACTC-AGAGT-TTTATGAAAACATCGAATGCAT
1 ATGCATCGATGCACCA-ACCATGCATCGATGCACTCTAGA-TATTT-TG-AAACATCGAATGCAT
*
1285832 TTG
62 TTC
* *
1285835 ATGCATCGATGCACCAACCATGTATCGATGCACTCTAGCTATTTTGAAACATCGAATGCATTTC
1 ATGCATCGATGCACCAACCATGCATCGATGCACTCTAGATATTTTGAAACATCGAATGCATTTC
1285899 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1285913 TCTTAGTGCA
Statistics
Matches: 122, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 48 0.39
65 61 0.50
66 7 0.06
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (64 bp):
ATGCATCGATGCACCAACCATGCATCGATGCACTCTAGATATTTTGAAACATCGAATGCATTTC
Found at i:1287020 original size:2 final size:2
Alignment explanation
Indices: 1287013--1287084 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
1287003 AAACTAAAAC
1287013 AT 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 AT
1287055 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
1287085 TCTTATCAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1290353 original size:73 final size:73
Alignment explanation
Indices: 1290234--1290381 Score: 278
Period size: 73 Copynumber: 2.0 Consensus size: 73
1290224 AACGTATAGC
*
1290234 TTAGACATCTAAATGATAACATTGATAACCTTAGGATAAAAGGAATTAAGTACTTAAATGTATTT
1 TTAGACATCTAAATGATAACATTGATAACCTTAAGATAAAAGGAATTAAGTACTTAAATGTATTT
1290299 TAGATATT
66 TAGATATT
*
1290307 TTAGACATCTAAATGATAACATTGATAACCTTAAGATAAAAGGAATTAAGTATTTAAATGTATTT
1 TTAGACATCTAAATGATAACATTGATAACCTTAAGATAAAAGGAATTAAGTACTTAAATGTATTT
1290372 TAGATATT
66 TAGATATT
1290380 TT
1 TT
1290382 TTTATTAAGT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (73 bp):
TTAGACATCTAAATGATAACATTGATAACCTTAAGATAAAAGGAATTAAGTACTTAAATGTATTT
TAGATATT
Found at i:1292938 original size:11 final size:11
Alignment explanation
Indices: 1292922--1292946 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1292912 TAATTTATGG
1292922 TAAAAATATAT
1 TAAAAATATAT
1292933 TAAAAATATAT
1 TAAAAATATAT
1292944 TAA
1 TAA
1292947 TGTTTACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAAAATATAT
Found at i:1296074 original size:19 final size:20
Alignment explanation
Indices: 1296040--1296079 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
1296030 AAGGGAAAAA
1296040 AGAATATTTTCTAAGA-AAG
1 AGAATATTTTCTAAGAGAAG
1296059 AGAATATTTT-TCAAGAGAAG
1 AGAATATTTTCT-AAGAGAAG
1296079 A
1 A
1296080 AAACTTCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.05
19 14 0.74
20 4 0.21
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.30
Consensus pattern (20 bp):
AGAATATTTTCTAAGAGAAG
Found at i:1296251 original size:83 final size:83
Alignment explanation
Indices: 1296146--1296390 Score: 361
Period size: 83 Copynumber: 3.0 Consensus size: 83
1296136 GGAATTTTGA
* *
1296146 GAGAGTTTTACTCAAACTAAAACTCTTTTAATATCTAAATTTAAACAGAAAATAATATATTTTAA
1 GAGAGTTTTAATCAAACCAAAACTCTTTTAATATCTAAATTTAAACAGAAAATAATATATTTTAA
1296211 ATTTAAAATATTAAACCT
66 ATTTAAAATATTAAACCT
* * *
1296229 GAGAGTTTTAAT-ATAATCAAAACTCTTTTAATATCTAAATTTAAACA-AATAATATTATCTTTT
1 GAGAGTTTTAATCA-AACCAAAACTCTTTTAATATCTAAATTTAAACAGAA-AATAATATATTTT
1296292 AAATTTAAAATATTAAACCT
64 AAATTTAAAATATTAAACCT
* * * *
1296312 GAGAGTTTTACTCAAACCAAAACTCTTTTAATATCTAAATTTAAATAGATAATAATATTTTTTAA
1 GAGAGTTTTAATCAAACCAAAACTCTTTTAATATCTAAATTTAAACAGAAAATAATATATTTTAA
*
1296377 ATTT-ATATATTAAA
66 ATTTAAAATATTAAA
1296391 TATATATTTT
Statistics
Matches: 146, Mismatches: 12, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
82 12 0.08
83 132 0.90
84 2 0.01
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (83 bp):
GAGAGTTTTAATCAAACCAAAACTCTTTTAATATCTAAATTTAAACAGAAAATAATATATTTTAA
ATTTAAAATATTAAACCT
Found at i:1301900 original size:41 final size:41
Alignment explanation
Indices: 1301855--1301937 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
1301845 CATTTTTAGA
* * *
1301855 TATGGCATACTTTCATTCTTTAAAGTAT-ATTTTCATGCATT
1 TATGGCATACTTTCATGCCTTAAAGCATCA-TTTCATGCATT
* *
1301896 TATGGCATTCTTTCATGCCTTAATGCATCATTTCATGCATT
1 TATGGCATACTTTCATGCCTTAAAGCATCATTTCATGCATT
1301937 T
1 T
1301938 TTAGTTATGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
41 35 0.97
42 1 0.03
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (41 bp):
TATGGCATACTTTCATGCCTTAAAGCATCATTTCATGCATT
Found at i:1301956 original size:47 final size:47
Alignment explanation
Indices: 1301805--1301980 Score: 170
Period size: 47 Copynumber: 3.9 Consensus size: 47
1301795 ATTTAATTTC
* **
1301805 AGTTATGGCCT-CTTTTCATGCCTTAATGCATCCGTTCATGCATTTTT
1 AGTTATGGCATAC-TTTCATGCCTTAATGCATCATTTCATGCATTTTT
* * * * *
1301852 AGATATGGCATACTTTCATTCTTTAAAGTAT-ATTTTCATGCA----T
1 AGTTATGGCATACTTTCATGCCTTAATGCATCA-TTTCATGCATTTTT
*
1301895 --TTATGGCATTCTTTCATGCCTTAATGCATCATTTCATGCATTTTT
1 AGTTATGGCATACTTTCATGCCTTAATGCATCATTTCATGCATTTTT
* * *
1301940 AGTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 AGTTATGGCATACTTTCATGCCTTAATGCATCATTTCATGC
1301981 CTTAATGCAT
Statistics
Matches: 103, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
41 32 0.31
42 1 0.01
43 1 0.01
45 1 0.01
47 67 0.65
48 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.44
Consensus pattern (47 bp):
AGTTATGGCATACTTTCATGCCTTAATGCATCATTTCATGCATTTTT
Found at i:1301977 original size:88 final size:88
Alignment explanation
Indices: 1301818--1301980 Score: 227
Period size: 88 Copynumber: 1.9 Consensus size: 88
1301808 TATGGCCTCT
* * * * *
1301818 TTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGATATGGCATACTTTCATTCTTTAAAGTAT
1 TTTCATGCCTTAATGCATCAGTTCATGCATTTTTAGATATGGAATACTTTCATGCCTTAAAGCAT
*
1301883 ATTTTCATGCATTTATGGCATTC
66 ACTTTCATGCATTTATGGCATTC
* * * *
1301906 TTTCATGCCTTAATGCATCATTTCATGCATTTTTAGTTATGGAATCCTTTCATGCCTTAATGCAT
1 TTTCATGCCTTAATGCATCAGTTCATGCATTTTTAGATATGGAATACTTTCATGCCTTAAAGCAT
*
1301971 CCTTTCATGC
66 ACTTTCATGC
1301981 CTTAATGCAT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
88 64 1.00
ACGTcount: A:0.23, C:0.20, G:0.12, T:0.45
Consensus pattern (88 bp):
TTTCATGCCTTAATGCATCAGTTCATGCATTTTTAGATATGGAATACTTTCATGCCTTAAAGCAT
ACTTTCATGCATTTATGGCATTC
Found at i:1301994 original size:67 final size:67
Alignment explanation
Indices: 1301885--1302047 Score: 263
Period size: 67 Copynumber: 2.4 Consensus size: 67
1301875 TAAAGTATAT
* * *
1301885 TTTCATGCATTTATGGCATTCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAGTTATGGAA
1 TTTCATGCCTTAAT-GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAGTTATGGAA
1301950 TCC
65 TCC
**
1301953 TTTCATGCCTTAATGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAGTTATGTCAT
1 TTTCATGCCTTAATGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAGTTATGGAAT
1302018 CC
66 CC
*
1302020 TTTCATGCCTTAATGCATCCGTTCATGC
1 TTTCATGCCTTAATGCATCCTTTCATGC
1302048 ATTTTTATTT
Statistics
Matches: 89, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
67 77 0.87
68 12 0.13
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (67 bp):
TTTCATGCCTTAATGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAGTTATGGAAT
CC
Found at i:1302019 original size:47 final size:47
Alignment explanation
Indices: 1301968--1302195 Score: 330
Period size: 47 Copynumber: 4.9 Consensus size: 47
1301958 TGCCTTAATG
** *
1301968 CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTTAGTTATGT
1 CATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGA
* *
1302015 CATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTATTTATGG
1 CATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGA
** * * * *
1302062 CATTATTTCATGCCGTAATGCATCCGTTCAAGTAGTTTTAGTTATGA
1 CATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGA
*
1302109 CATCCTTTCATTCCTTAATGCATCCGTTCATGCATTTTTAGTTATGA
1 CATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGA
* *
1302156 CATCCTTTCATACCTTAATGCATCCATTCATGCATTTTTA
1 CATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTA
1302196 TTTAGGAATT
Statistics
Matches: 160, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 160 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (47 bp):
CATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGA
Found at i:1302044 original size:20 final size:20
Alignment explanation
Indices: 1301885--1302047 Score: 110
Period size: 20 Copynumber: 7.4 Consensus size: 20
1301875 TAAAGTATAT
* * *
1301885 TTTCATGCATTTATGGCATTC
1 TTTCATGCCTTAAT-GCATCC
*
1301906 TTTCATGCCTTAATGCATCA
1 TTTCATGCCTTAATGCATCC
* *
1301926 TTTCATGCATTTTTAGTTATGGAATCC
1 TTTCATGC---CTTA---AT-GCATCC
1301953 TTTCATGCCTTAATGCATCC
1 TTTCATGCCTTAATGCATCC
*
1301973 TTTCATGCCTTAATGCATCA
1 TTTCATGCCTTAATGCATCC
*
1301993 TTTCATGCATTTTTAGTTATGTCATCC
1 TTTCATGC---CTTA---ATG-CATCC
1302020 TTTCATGCCTTAATGCATCC
1 TTTCATGCCTTAATGCATCC
*
1302040 GTTCATGC
1 TTTCATGC
1302048 ATTTTTATTT
Statistics
Matches: 114, Mismatches: 14, Indels: 29
0.73 0.09 0.18
Matches are distributed among these distances:
20 56 0.49
21 17 0.15
23 6 0.05
24 6 0.05
26 5 0.04
27 24 0.21
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (20 bp):
TTTCATGCCTTAATGCATCC
Found at i:1302657 original size:41 final size:41
Alignment explanation
Indices: 1302610--1302755 Score: 112
Period size: 41 Copynumber: 3.2 Consensus size: 41
1302600 TACTACCCTG
1302610 GTATCGATACTTCTATACTATGGTACCGATACCCCCTTTCA
1 GTATCGATACTTCTATACTATGGTACCGATACCCCCTTTCA
* * * *
1302651 ATATCGATACCATTTCTATATTCTATGTTGCATGGTATCGATACCCTTCTCTCA
1 GTATCGATA-C--TTCTATA--C-----T--ATGGTACCGATACCC-CCTTTCA
* *
1302705 GTATCGATACTTCTATATTATGGTACCGATACTCCCTTTCA
1 GTATCGATACTTCTATACTATGGTACCGATACCCCCTTTCA
*
1302746 GTATTGATAC
1 GTATCGATAC
1302756 CATTTTGACA
Statistics
Matches: 81, Mismatches: 11, Indels: 26
0.69 0.09 0.22
Matches are distributed among these distances:
41 22 0.27
42 14 0.17
44 8 0.10
46 1 0.01
51 8 0.10
53 15 0.19
54 13 0.16
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (41 bp):
GTATCGATACTTCTATACTATGGTACCGATACCCCCTTTCA
Found at i:1307082 original size:21 final size:21
Alignment explanation
Indices: 1307056--1307102 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1307046 AAACAAGCTT
1307056 CACTGAGAAGTCTGCATGCTC
1 CACTGAGAAGTCTGCATGCTC
1307077 CACTGAGAAGTCTGCATGCTC
1 CACTGAGAAGTCTGCATGCTC
1307098 CACTG
1 CACTG
1307103 TGCAATTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.23
Consensus pattern (21 bp):
CACTGAGAAGTCTGCATGCTC
Found at i:1311155 original size:20 final size:20
Alignment explanation
Indices: 1311132--1311169 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1311122 GTCTACGCTG
1311132 TCCTTC-GAGACATATATGTA
1 TCCTTCGGA-ACATATATGTA
*
1311152 TCCTTTGGAACATATATG
1 TCCTTCGGAACATATATG
1311170 AGGTCTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (20 bp):
TCCTTCGGAACATATATGTA
Found at i:1317452 original size:20 final size:20
Alignment explanation
Indices: 1317429--1317501 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 20
1317419 TTGCATCCTA
1317429 TCATGCCTTAATGCATCATT
1 TCATGCCTTAATGCATCATT
* *
1317449 TCATGCATTTTTAGTTATGACATCCTT
1 TCATGC---CTTA---ATG-CATCATT
*
1317476 TCATGTCTTAATGCATCATT
1 TCATGCCTTAATGCATCATT
1317496 TCATGC
1 TCATGC
1317502 ATTTTTAGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
20 17 0.43
21 3 0.08
23 3 0.08
24 3 0.08
26 3 0.08
27 11 0.28
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (20 bp):
TCATGCCTTAATGCATCATT
Found at i:1317480 original size:27 final size:26
Alignment explanation
Indices: 1317439--1317528 Score: 84
Period size: 27 Copynumber: 3.6 Consensus size: 26
1317429 TCATGCCTTA
1317439 ATGCATCATTTCATGCATTTTTAGTT
1 ATGCATCATTTCATGCATTTTTAGTT
* *
1317465 ATGACATCCTTTCATG---TCTTA---
1 ATG-CATCATTTCATGCATTTTTAGTT
1317486 ATGCATCATTTCATGCATTTTTAGTT
1 ATGCATCATTTCATGCATTTTTAGTT
* *
1317512 ATGGCATCCTTTTATGC
1 AT-GCATCATTTCATGC
1317529 CTTAATGTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
20 11 0.22
21 3 0.06
23 4 0.08
24 4 0.08
26 5 0.10
27 23 0.46
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (26 bp):
ATGCATCATTTCATGCATTTTTAGTT
Found at i:1317480 original size:47 final size:47
Alignment explanation
Indices: 1317407--1317689 Score: 397
Period size: 47 Copynumber: 6.0 Consensus size: 47
1317397 GGGGGTGTTA
* * *
1317407 CATTTTTAGTTATTGCATCCTATCATGCCTTAATGCATCATTTCATG
1 CATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCAGTTCATG
* * *
1317454 CATTTTTAGTTATGACATCCTTTCATGTCTTAATGCATCATTTCATG
1 CATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCAGTTCATG
* * *
1317501 CATTTTTAGTTATGGCATCCTTTTATGCCTTAATGTATCCGTTCATG
1 CATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCAGTTCATG
* ** * * *
1317548 CATTTTTATTTATGTTATCATTTTATGCCTTAATGCATCTGTTCATG
1 CATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCAGTTCATG
*
1317595 CATTTTTAGTTATGGCATCCTTCCATGCCTTAATGCAT-ACGTTCATG
1 CATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCA-GTTCATG
*
1317642 CATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATG
1 CATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCAGTTCATG
1317689 C
1 C
1317690 CTTAATGCAT
Statistics
Matches: 209, Mismatches: 25, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
47 209 1.00
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (47 bp):
CATTTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCAGTTCATG
Found at i:1317546 original size:67 final size:67
Alignment explanation
Indices: 1317469--1317756 Score: 261
Period size: 67 Copynumber: 4.2 Consensus size: 67
1317459 TTAGTTATGA
* * * *
1317469 CATCCTTTCATGTCTTAATGCATCATTTCATGCATTTTTAGTTATGGCATCCTTTTATGCCTTAA
1 CATCCGTTCATGCCTTAATGCATCAGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAA
1317534 TG
66 TG
* * ** *
1317536 TATCCGTTCATGCATT--TTTATTTATGTT-AT-CA-TTTTATGCCTTAAT-GCAT-CTGTTCAT
1 CATCCGTTCATGCCTTAATGCA-TCA-GTTCATGCATTTTTA-G--TT-ATGGCATCCT-TTCAT
*
1317594 GCATTTTTAGTTATGG
59 GC---CTTA---AT-G
1317610 CATCC-TTCCATGCCTTAATGCAT-ACGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTT
1 CATCCGTT-CATGCCTTAATGCATCA-GTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTT
1317673 AATG
64 AATG
* *
1317677 CATCCGTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCATTTCATGCCTTAA
1 CATCCGTTCATGCCTTAATGCATCAGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAA
1317742 TG
66 TG
1317744 CATCCGTTCATGC
1 CATCCGTTCATGC
1317757 ATTTTTATTT
Statistics
Matches: 179, Mismatches: 18, Indels: 48
0.73 0.07 0.20
Matches are distributed among these distances:
64 5 0.03
65 5 0.03
66 6 0.03
67 101 0.56
68 6 0.03
70 3 0.02
71 3 0.02
73 6 0.03
74 29 0.16
75 5 0.03
76 5 0.03
77 5 0.03
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (67 bp):
CATCCGTTCATGCCTTAATGCATCAGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAA
TG
Found at i:1317621 original size:27 final size:26
Alignment explanation
Indices: 1317589--1317669 Score: 68
Period size: 27 Copynumber: 3.3 Consensus size: 26
1317579 AATGCATCTG
1317589 TTCATGCATTTTTAGTTATGGCATCC
1 TTCATGCATTTTTAGTTATGGCATCC
* *
1317615 TTCCATGC---CTTA---AT-GCATACG
1 TT-CATGCATTTTTAGTTATGGCAT-CC
1317636 TTCATGCATTTTTAGTTATGGCATCC
1 TTCATGCATTTTTAGTTATGGCATCC
1317662 TTTCATGC
1 -TTCATGC
1317670 CTTAATGCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 19
0.64 0.06 0.30
Matches are distributed among these distances:
20 9 0.22
21 5 0.12
23 3 0.07
24 3 0.07
26 5 0.12
27 16 0.39
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (26 bp):
TTCATGCATTTTTAGTTATGGCATCC
Found at i:1317681 original size:20 final size:20
Alignment explanation
Indices: 1317656--1317756 Score: 103
Period size: 20 Copynumber: 4.7 Consensus size: 20
1317646 TTTAGTTATG
*
1317656 GCATCCTTTCATGCCTTAAT
1 GCATCCGTTCATGCCTTAAT
1317676 GCATCCGTTCATGCCTTAAT
1 GCATCCGTTCATGCCTTAAT
*
1317696 GCATCCGTTCATGCATTTTTAGTTAT
1 GCATCCGTTCATGC---CTTA---AT
**
1317722 GGCATCATTTCATGCCTTAAT
1 -GCATCCGTTCATGCCTTAAT
1317743 GCATCCGTTCATGC
1 GCATCCGTTCATGC
1317757 ATTTTTATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
20 45 0.67
21 2 0.03
23 3 0.04
24 3 0.04
26 2 0.03
27 12 0.18
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.39
Consensus pattern (20 bp):
GCATCCGTTCATGCCTTAAT
Found at i:1332010 original size:64 final size:63
Alignment explanation
Indices: 1331936--1332096 Score: 216
Period size: 64 Copynumber: 2.5 Consensus size: 63
1331926 TTGTTTAAGG
*
1331936 TGCATCGATGCATATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATATGCAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAGGATTTA
* * * *
1332000 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATATGCAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAGGATTTA
* *
1332064 TGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCAT-ATGCAGTGCATCGATGCAT
1332097 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 62 0.72
65 23 0.27
66 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATATGCAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATAGGATTTA
Found at i:1333665 original size:149 final size:149
Alignment explanation
Indices: 1333491--1333797 Score: 605
Period size: 149 Copynumber: 2.1 Consensus size: 149
1333481 GAGTCGAGGG
1333491 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1333556 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
1333621 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
1333640 TCTACGCGGTCCTTTGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1333705 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
1333770 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1333789 TCTACGCGG
1 TCTACGCGG
1333798 CACTTCAGTG
Statistics
Matches: 157, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 157 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:1333808 original size:23 final size:23
Alignment explanation
Indices: 1333773--1333817 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1333763 ATTATTATAT
* *
1333773 GGCACTACGGTGCAATTCTACGC
1 GGCACTACAGTGCAATTATACGC
*
1333796 GGCACTTCAGTGCAATTATACG
1 GGCACTACAGTGCAATTATACG
1333818 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (23 bp):
GGCACTACAGTGCAATTATACGC
Found at i:1339050 original size:3 final size:3
Alignment explanation
Indices: 1339037--1339094 Score: 55
Period size: 3 Copynumber: 18.0 Consensus size: 3
1339027 AATGTAACAT
*
1339037 TAA TAA T-A TAA TAA TTA TAAA TAA TAA TAA TAA TAAA TATA TATA TAAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA T-AA TA-A TA-A T-AA
1339086 TAA TAA TAA
1 TAA TAA TAA
1339095 AAAAGACCCG
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 2 0.04
3 32 0.67
4 13 0.27
5 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1339072 original size:22 final size:22
Alignment explanation
Indices: 1339037--1339095 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
1339027 AATGTAACAT
*
1339037 TAATAAT-ATAATAATTATAAA
1 TAATAATAATAATAAATATAAA
*
1339058 TAATAATAATAATAAATATATA
1 TAATAATAATAATAAATATAAA
1339080 T-ATAAATAATAATAAA
1 TAAT-AATAATAATAAA
1339096 AAAGACCCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 9 0.26
22 25 0.74
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TAATAATAATAATAAATATAAA
Found at i:1339084 original size:12 final size:10
Alignment explanation
Indices: 1339037--1339095 Score: 61
Period size: 10 Copynumber: 6.0 Consensus size: 10
1339027 AATGTAACAT
1339037 TAATAATATAA
1 TAATAATA-AA
*
1339048 TAATTATAAA
1 TAATAATAAA
1339058 TAATAAT-AA
1 TAATAATAAA
*
1339067 TAATAA-ATA
1 TAATAATAAA
1339076 T-ATATATAAA
1 TAATA-ATAAA
1339086 TAATAATAAA
1 TAATAATAAA
1339096 AAAGACCCGG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
8 3 0.08
9 11 0.28
10 16 0.40
11 10 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TAATAATAAA
Found at i:1346663 original size:19 final size:20
Alignment explanation
Indices: 1346634--1346671 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1346624 CATGTTCACA
1346634 CCAAGGGAAGATGAATTCAG
1 CCAAGGGAAGATGAATTCAG
*
1346654 CCAA-GGAAGATTAATTCA
1 CCAAGGGAAGATGAATTCA
1346672 TTAATTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (20 bp):
CCAAGGGAAGATGAATTCAG
Found at i:1349649 original size:2 final size:2
Alignment explanation
Indices: 1349644--1349670 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1349634 ATTTTTTGTG
1349644 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 T
1349671 GTAGGAACTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1354638 original size:18 final size:17
Alignment explanation
Indices: 1354612--1354645 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1354602 CGACTACTCT
1354612 TAAAATCTAAATGAATTA
1 TAAAATCTAAAT-AATTA
*
1354630 TAAACTCTAAATAATT
1 TAAAATCTAAATAATT
1354646 GAAAAGGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (17 bp):
TAAAATCTAAATAATTA
Found at i:1358365 original size:19 final size:19
Alignment explanation
Indices: 1358320--1358356 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1358310 TACAATCTCA
*
1358320 AAGGTTATGATTGATTAAC
1 AAGGTTATGATCGATTAAC
1358339 AAGGTTATGATCGATTAA
1 AAGGTTATGATCGATTAA
1358357 TAGGGTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (19 bp):
AAGGTTATGATCGATTAAC
Found at i:1358958 original size:17 final size:17
Alignment explanation
Indices: 1358932--1358965 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1358922 TTGAAAACAT
1358932 AAAATATGACTTTTTGG
1 AAAATATGACTTTTTGG
*
1358949 AAAATTTGACTTTTTGG
1 AAAATATGACTTTTTGG
1358966 TCAAAGTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (17 bp):
AAAATATGACTTTTTGG
Found at i:1363336 original size:22 final size:22
Alignment explanation
Indices: 1363308--1363364 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
1363298 TTTGACATTT
1363308 TGGTCAAAGTCAAAGTCAACAC
1 TGGTCAAAGTCAAAGTCAACAC
*
1363330 TGGTCAAAGTCAAAGTCAACTC
1 TGGTCAAAGTCAAAGTCAACAC
* *
1363352 TAGTTAAAGTCAA
1 TGGTCAAAGTCAA
1363365 CGTCTAGGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (22 bp):
TGGTCAAAGTCAAAGTCAACAC
Found at i:1375754 original size:19 final size:21
Alignment explanation
Indices: 1375719--1375762 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
1375709 AGGCGTCATG
1375719 TTCACACCAAGGGAAGATGAA
1 TTCACACCAAGGGAAGATGAA
*
1375740 TTCA-ACCAA-GGAAGATTAA
1 TTCACACCAAGGGAAGATGAA
1375759 TTCA
1 TTCA
1375763 TTAATTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.59
20 5 0.23
21 4 0.18
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (21 bp):
TTCACACCAAGGGAAGATGAA
Found at i:1377145 original size:13 final size:13
Alignment explanation
Indices: 1377107--1377137 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1377097 ATCATAAATC
*
1377107 TATGACGCGCATT
1 TATGACACGCATT
1377120 TATGACACGCATT
1 TATGACACGCATT
1377133 TATGA
1 TATGA
1377138 TTCGCATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (13 bp):
TATGACACGCATT
Found at i:1377264 original size:85 final size:85
Alignment explanation
Indices: 1377117--1377274 Score: 223
Period size: 85 Copynumber: 1.9 Consensus size: 85
1377107 TATGACGCGC
* * **
1377117 ATTTATGACACGCATTTATGATTCGCATTGAGCGTCATTGAAGCCCCCATCATAGATTAAGATGA
1 ATTTATGACACGCATGTATGATTCACATTGAGCGTCATTGAAGCCCCCATCATAGAAAAAGATGA
1377182 CACACATTTGTGTGTCATAA
66 CACACATTTGTGTGTCATAA
*
1377202 ATTTATGACACGCATGTATGACTT-ACATTGAGCGTCATTGAAG-CTCCAGTCATTA-AAAAAGA
1 ATTTATGACACGCATGTATGA-TTCACATTGAGCGTCATTGAAGCCCCCA-TCA-TAGAAAAAGA
1377264 TGACACACATT
63 TGACACACATT
1377275 CAGGGGTCGT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
84 4 0.06
85 57 0.88
86 4 0.06
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGATTCACATTGAGCGTCATTGAAGCCCCCATCATAGAAAAAGATGA
CACACATTTGTGTGTCATAA
Found at i:1378909 original size:17 final size:17
Alignment explanation
Indices: 1378889--1378924 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1378879 ATGCCTGCTA
1378889 AAGAATAAAACTATATG
1 AAGAATAAAACTATATG
*
1378906 AAGAATAAGACTATATG
1 AAGAATAAAACTATATG
1378923 AA
1 AA
1378925 CAAAGCTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (17 bp):
AAGAATAAAACTATATG
Found at i:1385613 original size:45 final size:45
Alignment explanation
Indices: 1385465--1385752 Score: 363
Period size: 45 Copynumber: 6.4 Consensus size: 45
1385455 TAAATCTATG
* *
1385465 ATCGTCATAAAA-GTACCATAAATGAAAATGCATAACGG-GCATT
1 ATCGACATAAAAGGTGCCATAAATGAAAATGCATAACGGTGCATT
1385508 ATC-AGCATAAAAGGTGCCATAAATGAAAATGCATAACGGTTGCATT
1 ATCGA-CATAAAAGGTGCCATAAATGAAAATGCATAACGG-TGCATT
* * *
1385554 ATCGGCATAAAAGGTGCCATAAATGAAAATGCATAATGGCGCATT
1 ATCGACATAAAAGGTGCCATAAATGAAAATGCATAACGGTGCATT
* * *
1385599 ATCGACATAAAAGGTGCCATAAATAAAAATGCATAACTGTGCATA
1 ATCGACATAAAAGGTGCCATAAATGAAAATGCATAACGGTGCATT
* *
1385644 ATC-AGCATAAAAAGTG-CATAAATGAAAATGTATAACGGTGCATT
1 ATCGA-CATAAAAGGTGCCATAAATGAAAATGCATAACGGTGCATT
* * *
1385688 ATCGGCATAAAAGGTACCACT-AATGAAAATACATAACGGTGCATT
1 ATCGACATAAAAGGTGCCA-TAAATGAAAATGCATAACGGTGCATT
* *
1385733 ATTGGCATAAAAGGTGCCAT
1 ATCGACATAAAAGGTGCCAT
1385753 TCATGGTATT
Statistics
Matches: 213, Mismatches: 23, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
43 10 0.05
44 63 0.30
45 98 0.46
46 42 0.20
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (45 bp):
ATCGACATAAAAGGTGCCATAAATGAAAATGCATAACGGTGCATT
Found at i:1385717 original size:89 final size:88
Alignment explanation
Indices: 1385481--1385749 Score: 378
Period size: 89 Copynumber: 3.0 Consensus size: 88
1385471 ATAAAAGTAC
*
1385481 CATAAATGAAAATGCATAACGGGCATTATCAGCATAAAAGGTGCCATAAATGAAAATGCATAACG
1 CATAAATGAAAATGCATAACGGGCATTATCGGCATAAAAGGTGCCATAAATGAAAATGCATAACG
1385546 GTTGCATTATCGGCATAAAAGGTG
66 G-TGCATTATCGGCATAAAAGGTG
* * *
1385570 CCATAAATGAAAATGCATAATGGCGCATTATCGACATAAAAGGTGCCATAAATAAAAATGCATAA
1 -CATAAATGAAAATGCATAACGG-GCATTATCGGCATAAAAGGTGCCATAAATGAAAATGCATAA
* * * *
1385635 CTGTGCATAATCAGCATAAAAAGTG
64 CGGTGCATTATCGGCATAAAAGGTG
* * *
1385660 CATAAATGAAAATGTATAACGGTGCATTATCGGCATAAAAGGTACCACT-AATGAAAATACATAA
1 CATAAATGAAAATGCATAACGG-GCATTATCGGCATAAAAGGTGCCA-TAAATGAAAATGCATAA
*
1385724 CGGTGCATTATTGGCATAAAAGGTG
64 CGGTGCATTATCGGCATAAAAGGTG
1385749 C
1 C
1385750 CATTCATGGT
Statistics
Matches: 157, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
89 76 0.48
90 41 0.26
91 40 0.25
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (88 bp):
CATAAATGAAAATGCATAACGGGCATTATCGGCATAAAAGGTGCCATAAATGAAAATGCATAACG
GTGCATTATCGGCATAAAAGGTG
Found at i:1385723 original size:134 final size:135
Alignment explanation
Indices: 1385465--1385752 Score: 413
Period size: 134 Copynumber: 2.1 Consensus size: 135
1385455 TAAATCTATG
* * * * *
1385465 ATCGTCATAAAA-GTACCATAAATGAAAATGCATAACGGGCATTATCAGCATAAAAGGTGCCATA
1 ATCGACATAAAAGGTGCCATAAATAAAAATGCATAACGGGCATAATCAGCATAAAAAGTGCCATA
* * *
1385529 AATGAAAATGCATAACGGTTGCATTATCGGCATAAAAGGTGCCATAAATGAAAATGCATAATGGC
66 AATGAAAATGCATAACGGTTGCATTATCGGCATAAAAGGTACCATAAATGAAAATACATAACGGC
1385594 GCATT
131 GCATT
*
1385599 ATCGACATAAAAGGTGCCATAAATAAAAATGCATAACTGTGCATAATCAGCATAAAAAGTG-CAT
1 ATCGACATAAAAGGTGCCATAAATAAAAATGCATAAC-GGGCATAATCAGCATAAAAAGTGCCAT
*
1385663 AAATGAAAATGTATAACGG-TGCATTATCGGCATAAAAGGTACCACT-AATGAAAATACATAACG
65 AAATGAAAATGCATAACGGTTGCATTATCGGCATAAAAGGTACCA-TAAATGAAAATACATAACG
*
1385726 GTGCATT
129 GCGCATT
* *
1385733 ATTGGCATAAAAGGTGCCAT
1 ATCGACATAAAAGGTGCCAT
1385753 TCATGGTATT
Statistics
Matches: 138, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
134 74 0.54
135 44 0.32
136 20 0.14
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (135 bp):
ATCGACATAAAAGGTGCCATAAATAAAAATGCATAACGGGCATAATCAGCATAAAAAGTGCCATA
AATGAAAATGCATAACGGTTGCATTATCGGCATAAAAGGTACCATAAATGAAAATACATAACGGC
GCATT
Found at i:1386580 original size:3 final size:3
Alignment explanation
Indices: 1386567--1386623 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
1386557 CGGGTCTTTT
** **
1386567 TTA TATA TTA TTA TTA TCG TTA TT- TTAA TTA TTA TTA TTA GCA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
1386613 TTA TTA TTA TT
1 TTA TTA TTA TT
1386624 TATTTACATA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 2 0.05
3 36 0.84
4 5 0.12
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1387121 original size:20 final size:18
Alignment explanation
Indices: 1387070--1387104 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1387060 AGGGGAGAAC
1387070 AAAAAAAACAGAGAATAA
1 AAAAAAAACAGAGAATAA
1387088 AAAAAAAACAGAGAATA
1 AAAAAAAACAGAGAATA
1387105 GAGGAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.77, C:0.06, G:0.11, T:0.06
Consensus pattern (18 bp):
AAAAAAAACAGAGAATAA
Found at i:1391445 original size:85 final size:83
Alignment explanation
Indices: 1391336--1391500 Score: 235
Period size: 85 Copynumber: 2.0 Consensus size: 83
1391326 AAAGGCACCA
* * *
1391336 TAAATGAAAATTATAACGTGCATTATCGGCATAAAATGTGCCA-TAATGAAAATGCATAACAGTG
1 TAAATGAAAATCATAACGTACATTATCGGCATAAAAGGTGCCACTAATGAAAATGC-TAACAGTG
1391400 CATATAT-CATAAAGGGCCG
65 CAT-TATGCATAAAGGGCCG
*
1391419 TAAATGAAAATGCATAACGATACATTATCGGCATAAAAGGTGCCACTAATGAAAATGCTAACGGT
1 TAAATGAAAAT-CATAACG-TACATTATCGGCATAAAAGGTGCCACTAATGAAAATGCTAACAGT
1391484 GCATTATGGCATAAAGG
64 GCATTAT-GCATAAAGG
1391501 TGCCACTATG
Statistics
Matches: 73, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
83 11 0.15
84 9 0.12
85 33 0.45
86 20 0.27
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (83 bp):
TAAATGAAAATCATAACGTACATTATCGGCATAAAAGGTGCCACTAATGAAAATGCTAACAGTGC
ATTATGCATAAAGGGCCG
Found at i:1391506 original size:42 final size:45
Alignment explanation
Indices: 1391317--1391508 Score: 194
Period size: 43 Copynumber: 4.5 Consensus size: 45
1391307 AAATCTATGA
** *
1391317 ATCGGCATAAAAGGCACCA-TAAATGAAAAT-TATAAC-GTGCATT
1 ATCGGCATAAAAGGTGCCACT-AATGAAAATGCATAACGGTGCATT
* *
1391360 ATCGGCATAAAATGTGCCA-TAATGAAAATGCATAACAGTGCATAT
1 ATCGGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCAT-T
* * *
1391405 AT---CAT-AAAGG-GCC-GTAAATGAAAATGCATAACGATACATT
1 ATCGGCATAAAAGGTGCCACT-AATGAAAATGCATAACGGTGCATT
1391445 ATCGGCATAAAAGGTGCCACTAATGAAAATGC-TAACGGTGCATT
1 ATCGGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATT
1391489 AT-GGCAT-AAAGGTGCCACTA
1 ATCGGCATAAAAGGTGCCACTA
1391509 TGGTATTCAT
Statistics
Matches: 127, Mismatches: 11, Indels: 23
0.79 0.07 0.14
Matches are distributed among these distances:
40 7 0.06
41 24 0.19
42 25 0.20
43 30 0.24
44 23 0.18
45 17 0.13
46 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (45 bp):
ATCGGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATT
Found at i:1394135 original size:16 final size:16
Alignment explanation
Indices: 1394116--1394146 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1394106 ATTTAACTTT
1394116 TTGGTCAAAGTCAACG
1 TTGGTCAAAGTCAACG
1394132 TTGGTCAAAGTCAAC
1 TTGGTCAAAGTCAAC
1394147 AGTTAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (16 bp):
TTGGTCAAAGTCAACG
Found at i:1394159 original size:17 final size:18
Alignment explanation
Indices: 1394137--1394171 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1394127 CAACGTTGGT
1394137 CAAAGTCAAC-AGTTAAA
1 CAAAGTCAACAAGTTAAA
1394154 CAAAGTCAACAAGTTAAA
1 CAAAGTCAACAAGTTAAA
1394172 TATATTCGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.54, C:0.17, G:0.11, T:0.17
Consensus pattern (18 bp):
CAAAGTCAACAAGTTAAA
Found at i:1408268 original size:47 final size:45
Alignment explanation
Indices: 1408174--1408299 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
1408164 ATAACCATGC
* * *
1408174 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * * *
1408218 AAATAAGCTTACAAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
1408265 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
1408300 AGATTTTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 21 0.30
45 11 0.16
46 1 0.01
47 37 0.53
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:1409899 original size:6 final size:6
Alignment explanation
Indices: 1409883--1409918 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
1409873 AACGGAAGAC
1409883 TCATAGG TCATGG TCATGG TCATGG TCATGG TCATG
1 TCAT-GG TCATGG TCATGG TCATGG TCATGG TCATG
1409919 ATACAAGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (6 bp):
TCATGG
Found at i:1411029 original size:12 final size:12
Alignment explanation
Indices: 1411013--1411061 Score: 64
Period size: 13 Copynumber: 3.9 Consensus size: 12
1411003 TATAAGAAGA
1411013 AGAAAAAACAAA-
1 AGAAAAAA-AAAC
1411025 AGAAAAAAAAAC
1 AGAAAAAAAAAC
1411037 AGAAGAAAAAAAC
1 AGAA-AAAAAAAC
1411050 AGAAAAAGAAAA
1 AGAAAAA-AAAA
1411062 TGAAAACGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.09
12 15 0.44
13 16 0.47
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAC
Found at i:1411031 original size:6 final size:6
Alignment explanation
Indices: 1411006--1411113 Score: 62
Period size: 6 Copynumber: 17.3 Consensus size: 6
1410996 TATATATTAT
*
1411006 AAGAAG AAGAAA AA-ACAA AAGAAA AA-AAA ACAGAAGA AA-AAA ACAGAAA
1 AAGAAA AAGAAA AAGA-AA AAGAAA AAGAAA A-AGAA-A AAGAAA A-AGAAA
* * * * *
1411055 AAGAAA ATGAAA ACGAAGA AGAAAAA AATGAAA ACGAGA AAG-AA AAGAAA
1 AAGAAA AAGAAA AAGAA-A A-AGAAA AA-GAAA AAGAAA AAGAAA AAGAAA
1411105 AAGAGAA AA
1 AAGA-AA AA
1411114 AATGAGAGAT
Statistics
Matches: 80, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
5 11 0.14
6 45 0.56
7 20 0.25
8 4 0.05
ACGTcount: A:0.76, C:0.05, G:0.18, T:0.02
Consensus pattern (6 bp):
AAGAAA
Found at i:1411033 original size:15 final size:15
Alignment explanation
Indices: 1411009--1411082 Score: 69
Period size: 15 Copynumber: 4.7 Consensus size: 15
1410999 ATATTATAAG
*
1411009 AAGAAGAAAAAACAA
1 AAGAAAAAAAAACAA
*
1411024 AAGAAAAAAAAACAG
1 AAGAAAAAAAAACAA
1411039 AAGAAAAAAACAGA-AA
1 AAGAAAAAAA-A-ACAA
*
1411055 AAGAAAATGAAAACGAA
1 AAGAAAA-AAAAAC-AA
1411072 GAAGAAAAAAA
1 -AAGAAAAAAA
1411083 TGAAAACGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
15 24 0.50
16 10 0.21
17 7 0.15
18 7 0.15
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.01
Consensus pattern (15 bp):
AAGAAAAAAAAACAA
Found at i:1411082 original size:27 final size:26
Alignment explanation
Indices: 1411017--1411106 Score: 69
Period size: 27 Copynumber: 3.4 Consensus size: 26
1411007 AGAAGAAGAA
* *
1411017 AAAACAAAAGAAAAAAAAAC-AG-AAG
1 AAAAGAAAA-AAAAGAAAACGAGAAAG
* *
1411042 AAAAAAACAGAAAAAGAAAATGA-AAACG
1 AAAAGAA-A-AAAAAGAAAACGAGAAA-G
*
1411070 AAGAAGAAAAAAATGAAAACGAGAAAG
1 AA-AAGAAAAAAAAGAAAACGAGAAAG
1411097 AAAAGAAAAA
1 AAAAGAAAAA
1411107 GAGAAAAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
25 6 0.12
26 17 0.33
27 18 0.35
28 7 0.13
29 4 0.08
ACGTcount: A:0.77, C:0.06, G:0.16, T:0.02
Consensus pattern (26 bp):
AAAAGAAAAAAAAGAAAACGAGAAAG
Found at i:1411090 original size:21 final size:20
Alignment explanation
Indices: 1411045--1411100 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
1411035 ACAGAAGAAA
1411045 AAAAC-AGAA-AAAGAAAATG
1 AAAACGAGAAGAAA-AAAATG
1411064 AAAACGAAGAAGAAAAAAATG
1 AAAACG-AGAAGAAAAAAATG
1411085 AAAACGAGAAAGAAAA
1 AAAACGAG-AAGAAAA
1411101 GAAAAAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.15
20 2 0.06
21 23 0.70
22 3 0.09
ACGTcount: A:0.73, C:0.05, G:0.18, T:0.04
Consensus pattern (20 bp):
AAAACGAGAAGAAAAAAATG
Found at i:1415204 original size:47 final size:45
Alignment explanation
Indices: 1415110--1415235 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
1415100 GTAACCATGC
* * *
1415110 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * * *
1415154 AAATAAGCTTACAAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
1415201 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
1415236 AGATTTTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 21 0.30
45 11 0.16
46 1 0.01
47 37 0.53
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:1417616 original size:22 final size:22
Alignment explanation
Indices: 1417591--1417633 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1417581 GGTAAATGTC
1417591 AAAGTCAACAT-TGGTCAAAGTT
1 AAAGTCAAC-TCTGGTCAAAGTT
1417613 AAAGTCAACTCTGGTCAAAGT
1 AAAGTCAACTCTGGTCAAAGT
1417634 CAACGGTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (22 bp):
AAAGTCAACTCTGGTCAAAGTT
Found at i:1426584 original size:54 final size:54
Alignment explanation
Indices: 1426462--1426987 Score: 788
Period size: 54 Copynumber: 9.8 Consensus size: 54
1426452 ATTAAACGGT
* * * * * *
1426462 TTGCAAACCTAGTGCCAATATGAAAATTCATAAACTTTATTATGAATTCCTTAAG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAAC-TCATTATGAATTTCTTAAG
* * * *
1426517 TTGCACACATAGTGCCAATAAGGAAATTCATAAACTCATTATGCATTTTTTAGG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
* * * *
1426571 TTGTACACATAGTGCCGATATGGAAATTCATAAACTCATTGTGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
* * *
1426625 TTGCACACATAGTGTCAATACGAAAATTCATAAACTCGTTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
*
1426679 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCCTTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
*
1426733 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCCTTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
*
1426787 TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
* *
1426841 TTGCACACATAGTGCCAATATGGAAATTCATAAACTCGTTATGAATTTCTTAAG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
* * *
1426895 TTGCACACATAGTGCCAAAACGGAAATTCAT--ACTCATTATGAATTTATTTAG
1 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
1426947 TTGCACACATAGTGCCAATAC-GATAATTCATAAACTCATTA
1 TTGCACACATAGTGCCAATACGGA-AATTCATAAACTCATTA
1426988 AGCAACATGC
Statistics
Matches: 431, Mismatches: 37, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
51 2 0.00
52 45 0.10
54 353 0.82
55 31 0.07
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (54 bp):
TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
Found at i:1432102 original size:19 final size:21
Alignment explanation
Indices: 1432051--1432103 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 21
1432041 ACTTTTCTCC
*
1432051 TAGTATCGATACTTCTATACTA
1 TAGTATCGATACTTCCATA-TA
* *
1432073 TGGTATTGATAC-TCCAT-TA
1 TAGTATCGATACTTCCATATA
1432092 TAGTATCGATAC
1 TAGTATCGATAC
1432104 CATTTCTACA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 12 0.46
21 4 0.15
22 10 0.38
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (21 bp):
TAGTATCGATACTTCCATATA
Found at i:1432156 original size:20 final size:20
Alignment explanation
Indices: 1432128--1432178 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1432118 GGAAACAATG
*
1432128 GTATCGATACCTTCCTCATA
1 GTATAGATACCTTCCTCATA
* *
1432148 GTATTGATACATTCCTCATA
1 GTATAGATACCTTCCTCATA
1432168 GTATAGATACC
1 GTATAGATACC
1432179 CACATCAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (20 bp):
GTATAGATACCTTCCTCATA
Found at i:1437972 original size:19 final size:21
Alignment explanation
Indices: 1437950--1437988 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1437940 AATTTCAAAA
1437950 TTTTTG-GAAAATTA-TTGTG
1 TTTTTGAGAAAATTAGTTGTG
*
1437969 TTTTTGATAAAATTAGTTGT
1 TTTTTGAGAAAATTAGTTGT
1437989 AATATCTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (21 bp):
TTTTTGAGAAAATTAGTTGTG
Found at i:1438352 original size:20 final size:20
Alignment explanation
Indices: 1438323--1438360 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1438313 AGAACCCCAG
*
1438323 GGGGGTATCGATTCCCCTAA
1 GGGGGAATCGATTCCCCTAA
1438343 GGGGGAATCGATTCCCCT
1 GGGGGAATCGATTCCCCT
1438361 TCAATAGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTAA
Found at i:1438374 original size:23 final size:20
Alignment explanation
Indices: 1438324--1438381 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1438314 GAACCCCAGG
* *
1438324 GGGGTATCGATTCCCCTAAG
1 GGGGAATCGATTCCCCTAAA
1438344 GGGGAATCGATTCCCCTTCAATA
1 GGGGAATCGATTCCCC-T-AA-A
*
1438367 GGGGAATCGGTTCCC
1 GGGGAATCGATTCCC
1438382 TCATGAGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.47
21 1 0.03
22 2 0.06
23 14 0.44
ACGTcount: A:0.21, C:0.26, G:0.29, T:0.24
Consensus pattern (20 bp):
GGGGAATCGATTCCCCTAAA
Found at i:1440634 original size:30 final size:31
Alignment explanation
Indices: 1440582--1440641 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
1440572 CTTAGCTTTA
**
1440582 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
1440612 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
1440642 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:1441546 original size:19 final size:20
Alignment explanation
Indices: 1441522--1441571 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1441512 CGTCCAAGAG
* *
1441522 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
1441541 CATGTATTTTCATAAAAAAT
1 CATGTATTTTCATAAAAAAT
1441561 -ATGTATTTTCA
1 CATGTATTTTCA
1441572 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 23 0.82
20 5 0.18
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:1442300 original size:24 final size:24
Alignment explanation
Indices: 1442273--1442318 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1442263 GCAAAAAGAA
1442273 AGAAAAGATA-AAAAGAAAAAAACC
1 AGAAAAGA-AGAAAAGAAAAAAACC
*
1442297 AGAATAGAAGAAAAGAAAAAAA
1 AGAAAAGAAGAAAAGAAAAAAA
1442319 AGAAGAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.76, C:0.04, G:0.15, T:0.04
Consensus pattern (24 bp):
AGAAAAGAAGAAAAGAAAAAAACC
Found at i:1451109 original size:72 final size:72
Alignment explanation
Indices: 1451026--1451170 Score: 281
Period size: 72 Copynumber: 2.0 Consensus size: 72
1451016 ATTCATATAT
1451026 TACAAATAAATCATACAAGTTTCAGAATGAGATATAGAAATAGAATACAACCTATAATCACATGC
1 TACAAATAAATCATACAAGTTTCAGAATGAGATATAGAAATAGAATACAACCTATAATCACATGC
1451091 ACCGTAC
66 ACCGTAC
1451098 TACAAATAAATCATACAAGTTTCAGAATGAGATATAGAAATAGAATACAACCTATAATCACATGC
1 TACAAATAAATCATACAAGTTTCAGAATGAGATATAGAAATAGAATACAACCTATAATCACATGC
*
1451163 ATCGTAC
66 ACCGTAC
1451170 T
1 T
1451171 CCGTAAGCAA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.25
Consensus pattern (72 bp):
TACAAATAAATCATACAAGTTTCAGAATGAGATATAGAAATAGAATACAACCTATAATCACATGC
ACCGTAC
Found at i:1468588 original size:31 final size:31
Alignment explanation
Indices: 1468553--1468664 Score: 86
Period size: 31 Copynumber: 3.6 Consensus size: 31
1468543 TTATTAAAAA
*
1468553 TAGGTGATTAATGTTTTATTTGTTGCATTTT
1 TAGGTGATTAATGTTTTATATGTTGCATTTT
* * *
1468584 TAGGTGCA-CAATCTTTTATCTGTTGCACTTTT
1 TAGGTG-ATTAATGTTTTATATGTTGCA-TTTT
* ** * *
1468616 T-GGTGCTTGTTGTTTT-TCATGTTCCACTTT
1 TAGGTGATTAATGTTTTAT-ATGTTGCATTTT
*
1468646 TAGGTGTTTAATGTTTTAT
1 TAGGTGATTAATGTTTTAT
1468665 CCCTTACACT
Statistics
Matches: 61, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
30 5 0.08
31 49 0.80
32 7 0.11
ACGTcount: A:0.16, C:0.11, G:0.19, T:0.54
Consensus pattern (31 bp):
TAGGTGATTAATGTTTTATATGTTGCATTTT
Found at i:1470193 original size:17 final size:17
Alignment explanation
Indices: 1470160--1470209 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
1470150 ACTTTTTTTT
*
1470160 GTCAA-AGTCAACGGTTG
1 GTCAACAGTCAA-TGTTG
1470177 GTCAACAGTCAATGTTG
1 GTCAACAGTCAATGTTG
1470194 GTCAAC-GATCAATGTT
1 GTCAACAG-TCAATGTT
1470210 AGTTCGAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 1 0.03
17 23 0.77
18 6 0.20
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (17 bp):
GTCAACAGTCAATGTTG
Found at i:1476796 original size:19 final size:19
Alignment explanation
Indices: 1476772--1476809 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1476762 ACTTATTAGT
1476772 ATTATTCATTTTTT-TAAAA
1 ATTATT-ATTTTTTCTAAAA
*
1476791 ATTATTTTTTTTTCTAAAA
1 ATTATTATTTTTTCTAAAA
1476810 TTACAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTATTATTTTTTCTAAAA
Found at i:1477422 original size:30 final size:30
Alignment explanation
Indices: 1477386--1477442 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1477376 CATTACTCCG
*
1477386 TAGACACCTAAAAATGTAATGAGAAAATGT
1 TAGACACCTAAAAATGTAATGAAAAAATGT
*
1477416 TAGACACCTAAAATTGTAATGAAAAAA
1 TAGACACCTAAAAATGTAATGAAAAAA
1477443 AATTAGGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.53, C:0.11, G:0.14, T:0.23
Consensus pattern (30 bp):
TAGACACCTAAAAATGTAATGAAAAAATGT
Found at i:1478213 original size:21 final size:20
Alignment explanation
Indices: 1478191--1478230 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1478181 AAGTTATGGA
1478191 AAACATCATAAAAGGTTTTG
1 AAACATCATAAAAGGTTTTG
* **
1478211 AAATATCATTCAAGGTTTTG
1 AAACATCATAAAAGGTTTTG
1478231 GAGTAATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (20 bp):
AAACATCATAAAAGGTTTTG
Found at i:1479140 original size:13 final size:14
Alignment explanation
Indices: 1479104--1479147 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
1479094 GCCTCAGACA
1479104 ACCCGTTGACTTTG
1 ACCCGTTGACTTTG
1479118 ACCCGTTGACTTTG
1 ACCCGTTGACTTTG
**
1479132 A-GTGTTGACTTTG
1 ACCCGTTGACTTTG
1479145 ACC
1 ACC
1479148 GAAAAGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (14 bp):
ACCCGTTGACTTTG
Found at i:1500245 original size:7 final size:7
Alignment explanation
Indices: 1500233--1500262 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1500223 ATTATCCAGA
1500233 AAAAAAT
1 AAAAAAT
1500240 AAAAAAT
1 AAAAAAT
1500247 AAAAAAT
1 AAAAAAT
1500254 -AAAAAT
1 AAAAAAT
1500260 AAA
1 AAA
1500263 GATGATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:1500252 original size:14 final size:13
Alignment explanation
Indices: 1500233--1500262 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
1500223 ATTATCCAGA
1500233 AAAAAATAAAAAAT
1 AAAAAAT-AAAAAT
1500247 AAAAAATAAAAAT
1 AAAAAATAAAAAT
1500260 AAA
1 AAA
1500263 GATGATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:1508819 original size:2 final size:2
Alignment explanation
Indices: 1508812--1508846 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1508802 CAAAACAAAC
1508812 AT AT AT AT 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 AT AT AT AT A
1508847 CATACATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1517338 original size:21 final size:21
Alignment explanation
Indices: 1517312--1517352 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1517302 GAAGAGTGAA
*
1517312 AATCAAGAAGAAAGGAACAAG
1 AATCAAGAACAAAGGAACAAG
*
1517333 AATCAATAACAAAGGAACAA
1 AATCAAGAACAAAGGAACAA
1517353 AAAGAATGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.12, G:0.17, T:0.07
Consensus pattern (21 bp):
AATCAAGAACAAAGGAACAAG
Found at i:1524248 original size:23 final size:23
Alignment explanation
Indices: 1524222--1524270 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1524212 ACTCGATCCA
1524222 ACCCGACCCGAACTGTTAACCAG
1 ACCCGACCCGAACTGTTAACCAG
* *
1524245 ACCCGAGCCGAACTGTTAACCCG
1 ACCCGACCCGAACTGTTAACCAG
1524268 ACC
1 ACC
1524271 AAACCCGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.41, G:0.18, T:0.12
Consensus pattern (23 bp):
ACCCGACCCGAACTGTTAACCAG
Found at i:1524317 original size:16 final size:16
Alignment explanation
Indices: 1524296--1524339 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1524286 TCCTGACCCT
* *
1524296 TTGACTATGACCATAG
1 TTGACTTTGACCAGAG
*
1524312 TTGACTTTGATCAGAG
1 TTGACTTTGACCAGAG
1524328 TTGACTTTGACC
1 TTGACTTTGACC
1524340 CGAAAAGACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (16 bp):
TTGACTTTGACCAGAG
Found at i:1528081 original size:23 final size:23
Alignment explanation
Indices: 1528032--1528081 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
1528022 ACCAGCCCAT
* *
1528032 CCCGACCAGAACCATTGACCTGG
1 CCCGACCAGAACCATTAACCTGA
* * *
1528055 CCCGACCCGAACTATTAACTTGA
1 CCCGACCAGAACCATTAACCTGA
1528078 CCCG
1 CCCG
1528082 TTGAGTTTGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.40, G:0.18, T:0.16
Consensus pattern (23 bp):
CCCGACCAGAACCATTAACCTGA
Found at i:1532080 original size:131 final size:132
Alignment explanation
Indices: 1531770--1532120 Score: 553
Period size: 131 Copynumber: 2.7 Consensus size: 132
1531760 ATAATATATT
* * *
1531770 TTCATTTCGGTTTGATTAATAAATGATTGCTTTAAGGCATGAGAGGT-ATTTTATTCTCGATTTG
1 TTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCA-TTTATTCTCGATTTG
* * * * * *
1531834 AAATAATTAAATATTATCATTTTCTCTCGAATCAATATTTATTTTTTAAGACGAAATAGTGATAT
65 AAATAATTAGATATTATCGTTTTCACTCGAATCAATATTGATATTTTAAGACAAAATAGTGATAT
1531899 CTC
130 CTC
* *
1531902 TTCATTACGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGA
1 TTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTTGA
*
1531967 AATCATTAGATATTATCGTTTTCACTCGAATCAATATTGA-ATTTTAAGACAAAATAGTGATATC
66 AATAATTAGATATTATCGTTTTCACTCGAATCAATATTGATATTTTAAGACAAAATAGTGATATC
1532031 TC
131 TC
*
1532033 TTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTTGA
1 TTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTTGA
*
1532098 AATAATTAGATTTTATCGTTTTC
66 AATAATTAGATATTATCGTTTTC
1532121 TCTCTTAAAA
Statistics
Matches: 201, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
131 107 0.53
132 93 0.46
133 1 0.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (132 bp):
TTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTTGA
AATAATTAGATATTATCGTTTTCACTCGAATCAATATTGATATTTTAAGACAAAATAGTGATATC
TC
Found at i:1533092 original size:28 final size:28
Alignment explanation
Indices: 1533049--1533111 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
1533039 TCGTGATGGT
*
1533049 TTTCACCTCCTTATGGATATAAGAAGGTG
1 TTTC-CCTCCGTATGGATATAAGAAGGTG
*
1533078 TTTCCCTCCGTATGGATATAAGGAGGTG
1 TTTCCCTCCGTATGGATATAAGAAGGTG
1533106 TTTCCC
1 TTTCCC
1533112 CTCGAATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 28 0.88
29 4 0.12
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (28 bp):
TTTCCCTCCGTATGGATATAAGAAGGTG
Found at i:1537026 original size:46 final size:45
Alignment explanation
Indices: 1536974--1537100 Score: 168
Period size: 46 Copynumber: 2.8 Consensus size: 45
1536964 ATAAACTGGC
* *
1536974 AAATAAGCTTACGAGTTTATGAGATTAAATGGTTAGTATATTGGTA
1 AAATAAGCTTACAAGTTTATG-GATTAAATGGTAAGTATATTGGTA
*
1537020 AAATAAGCTTA-AAATCTTATGGTATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACAAGT-TTATGG-ATTAAATGGTAAGTATATTGGTA
*
1537066 AAATAAGCTTACAAGCTTATGGGA-TAAATGGTAAG
1 AAATAAGCTTACAAGTTTAT-GGATTAAATGGTAAG
1537101 AGATTTTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
45 14 0.19
46 54 0.75
47 4 0.06
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (45 bp):
AAATAAGCTTACAAGTTTATGGATTAAATGGTAAGTATATTGGTA
Found at i:1537571 original size:23 final size:23
Alignment explanation
Indices: 1537545--1537590 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1537535 TTTTCCATAA
1537545 TGCTACAGGGGTACCGATTCCCC
1 TGCTACAGGGGTACCGATTCCCC
1537568 TGCTACAGGGGTACCGATTCCCC
1 TGCTACAGGGGTACCGATTCCCC
1537591 CACTGTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.35, G:0.26, T:0.22
Consensus pattern (23 bp):
TGCTACAGGGGTACCGATTCCCC
Found at i:1549208 original size:29 final size:29
Alignment explanation
Indices: 1549166--1549223 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1549156 TCACTAGCAT
1549166 CCAAGTATGAAATACCGAAATCGAGAGGA
1 CCAAGTATGAAATACCGAAATCGAGAGGA
1549195 CCAAGTATGAAATACCGAAATCGAGAGGA
1 CCAAGTATGAAATACCGAAATCGAGAGGA
1549224 AGAGATGCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (29 bp):
CCAAGTATGAAATACCGAAATCGAGAGGA
Found at i:1549603 original size:90 final size:89
Alignment explanation
Indices: 1549446--1549613 Score: 300
Period size: 90 Copynumber: 1.9 Consensus size: 89
1549436 TACCTAACAC
*
1549446 ATCCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTA
1 ATCCTCTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTA
1549511 TATTTAATTAATTGGAATTTAATA
66 TATTTAATTAATTGGAATTTAATA
* *
1549535 ATCCTCTTATATCCAAGTTACCCTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATCT
1 ATCCTCTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCT
1549600 ATATTTAATTAATT
65 ATATTTAATTAATT
1549614 AATTGAAATT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 34 0.45
90 41 0.55
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.45
Consensus pattern (89 bp):
ATCCTCTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTA
TATTTAATTAATTGGAATTTAATA
Found at i:1564991 original size:134 final size:131
Alignment explanation
Indices: 1564810--1565216 Score: 393
Period size: 131 Copynumber: 3.1 Consensus size: 131
1564800 ATCTAACTTT
* * * *
1564810 CCTGAAGAAATAGTG-GAATATATCCCCTCTATTT-TCAGATTTGATCTTCCTTGAGTAGCAGTG
1 CCTGAAGAAATAATGCAAATA-ATCCCCTCTCTTTCT-AGATTT-ATCTTCCATGAGTAGCAGTG
* * *
1564873 GAACAAGTCTGCCTTGATTCAATCTTCCCTAAATAACAATGGAATAAATCACATCTCCAAATCTG
63 GAACAAGTCTTCCTTGATTCAATCTTCCCTAAA-AACAGTGGAATGAATCA-ATCTCCAAATCTG
1564938 ATTTTC
126 ATTTTC
* *
1564944 CCTGAA-AAA-AATAGCATAATAGATCCCCTCTCTTTCTAGATTTATCTTCCATGA--A-TAGTA
1 CCTGAAGAAATAAT-GCA-AATA-ATCCCCTCTCTTTCTAGATTTATCTTCCATGAGTAGCAGTG
* * * *
1565004 GAACAAGTCTTCCTCGATTCAATCTTCCCTGAAAAACGGTGGAATGAATCAATGTCTATATATCT
63 GAACAAGTCTTCCTTGATTCAATCTTCCCT-AAAAACAGTGGAATGAATCAATCTCCA-A-ATCT
1565069 GATTTT-
125 GATTTTC
* * * * * *
1565075 CTTGAAGAAATAATGGAACAT-ATCCCCTCTCTTTCCAGACTTGATCTTCCCTGAGTAGCTGTGG
1 CCTGAAGAAATAATGCAA-ATAATCCCCTCTCTTTCTAGA-TTTATCTTCCATGAGTAGCAGTGG
* * * *
1565139 AACAAGTCTTCCTTGATTAAATCTT-CCTAAGAACAGTGGAATGAATCAATGTTTCCATATCTGA
64 AACAAGTCTTCCTTGATTCAATCTTCCCTAAAAACAGTGGAATGAATCAA--TCTCCAAATCTGA
*
1565203 CTTTC
127 TTTTC
1565208 CCTGAAGAA
1 CCTGAAGAA
1565217 GCAGCGGAAC
Statistics
Matches: 225, Mismatches: 31, Indels: 35
0.77 0.11 0.12
Matches are distributed among these distances:
130 22 0.10
131 64 0.28
132 51 0.23
133 19 0.08
134 46 0.20
135 22 0.10
136 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (131 bp):
CCTGAAGAAATAATGCAAATAATCCCCTCTCTTTCTAGATTTATCTTCCATGAGTAGCAGTGGAA
CAAGTCTTCCTTGATTCAATCTTCCCTAAAAACAGTGGAATGAATCAATCTCCAAATCTGATTTT
C
Found at i:1567795 original size:135 final size:130
Alignment explanation
Indices: 1567430--1567797 Score: 434
Period size: 130 Copynumber: 2.8 Consensus size: 130
1567420 ATCAATATTG
* ** * * * * * * *
1567430 AAAATAGTAATATCTTTTCATTTTGGTTGGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCA
1 AAAATAGTGATATCACTTCATTTCGATTGAAGTAATAAATAACTACTTTAAGGCATGAGAGGTCA
* * * *
1567495 TTTATTCTCGATTGGAAATAATTAGATATTACCGTTTTCTCTTGAATCAATTGATTTTTTAAGAC
66 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTTGAATAAATTGATATTTTAAGAC
** * *
1567560 GGAATAGTGATATCACTTCATTTCGATTGAAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
1 AAAATAGTGATATCACTTCATTTCGATTGAAGTAATAAATAACTACTTTAAGGCATGAGAGGTCA
* *
1567625 TTTCTTCTCGATTGGAAATTATTAGATATTATCGTTTTCACTCT-AATAAATATTGA-ATTTTAA
66 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACT-TGAAT-AA-ATTGATATTTTAA
1567688 GAC
128 GAC
* * * *
1567691 AAAATAGTGATATCTCTTCATTTCTATTGGATTAATAAATAACTACTTTAAGGAAGCCATGAGAG
1 AAAATAGTGATATCACTTCATTTCGATTGAAGTAATAAATAACTACTTTAA-G--G-CATGAGAG
*
1567756 GTCATTTATTCTTGATTGGAAATAATTAGATATTATCGTTTT
62 GTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTT
1567798 ATCTCTTAAC
Statistics
Matches: 204, Mismatches: 27, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
130 96 0.47
131 54 0.26
132 6 0.03
134 1 0.00
135 47 0.23
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (130 bp):
AAAATAGTGATATCACTTCATTTCGATTGAAGTAATAAATAACTACTTTAAGGCATGAGAGGTCA
TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTTGAATAAATTGATATTTTAAGAC
Found at i:1571358 original size:19 final size:19
Alignment explanation
Indices: 1571334--1571372 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1571324 TAATGTACAC
1571334 CTGGCTAACTTACTTCTCG
1 CTGGCTAACTTACTTCTCG
1571353 CTGGCTAACTTACTTCTCG
1 CTGGCTAACTTACTTCTCG
1571372 C
1 C
1571373 AAGTACTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.33, G:0.15, T:0.36
Consensus pattern (19 bp):
CTGGCTAACTTACTTCTCG
Found at i:1584985 original size:23 final size:23
Alignment explanation
Indices: 1584940--1584985 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1584930 ACCCATAATA
* *
1584940 CACATATAGTGCCATATAGAATG
1 CACATATAGTGCCACATAAAATG
* *
1584963 CACATGTAGTGCCACGTAAAATG
1 CACATATAGTGCCACATAAAATG
1584986 TACAAATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (23 bp):
CACATATAGTGCCACATAAAATG
Found at i:1585756 original size:31 final size:31
Alignment explanation
Indices: 1585719--1585797 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
1585709 TTGAAACTCC
1585719 TGTGCATTATCTGAATGCAAACCTGACATAA
1 TGTGCATTATCTGAATGCAAACCTGACATAA
* *
1585750 TGTGCATTATCTAAATGCAAACCTGACATAT
1 TGTGCATTATCTGAATGCAAACCTGACATAA
* *
1585781 TCTGCATCATCTGAATG
1 TGTGCATTATCTGAATG
1585798 AGAATTTTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (31 bp):
TGTGCATTATCTGAATGCAAACCTGACATAA
Found at i:1587919 original size:21 final size:21
Alignment explanation
Indices: 1587895--1587934 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1587885 ATCGATATTG
1587895 TAGCGTTAAGAATCGACACTA
1 TAGCGTTAAGAATCGACACTA
*
1587916 TAGCGTTAAGTATCGACAC
1 TAGCGTTAAGAATCGACAC
1587935 GCCTATGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (21 bp):
TAGCGTTAAGAATCGACACTA
Found at i:1593217 original size:29 final size:29
Alignment explanation
Indices: 1593175--1593242 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
1593165 CCTTATCCGC
1593175 CCAAACCTAAAACTACTAGCCAAAGTAAA
1 CCAAACCTAAAACTACTAGCCAAAGTAAA
1593204 CCAAACCTAAAACTACTAGCCAAAGTAAA
1 CCAAACCTAAAACTACTAGCCAAAGTAAA
* *
1593233 TCTAACCTAA
1 CCAAACCTAA
1593243 TTGAATATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.50, C:0.28, G:0.06, T:0.16
Consensus pattern (29 bp):
CCAAACCTAAAACTACTAGCCAAAGTAAA
Found at i:1619973 original size:12 final size:12
Alignment explanation
Indices: 1619956--1619980 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1619946 TCACATTCTA
1619956 CACTTCTTTTTT
1 CACTTCTTTTTT
1619968 CACTTCTTTTTT
1 CACTTCTTTTTT
1619980 C
1 C
1619981 TTCTATTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (12 bp):
CACTTCTTTTTT
Found at i:1624779 original size:20 final size:19
Alignment explanation
Indices: 1624745--1624785 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
1624735 CTTAACCTAC
*
1624745 CCGTTAACTTTGACTTTGA
1 CCGTTAACGTTGACTTTGA
1624764 CCGTTAACCGTTGACTTTGA
1 CCGTTAA-CGTTGACTTTGA
1624784 CC
1 CC
1624786 AAAAAGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.37
Consensus pattern (19 bp):
CCGTTAACGTTGACTTTGA
Found at i:1627633 original size:24 final size:24
Alignment explanation
Indices: 1627606--1627652 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1627596 GTCAACCGAC
*
1627606 ACATCTCTTAGATCTTCAAGTGAA
1 ACATCTCTTAGAACTTCAAGTGAA
* *
1627630 ACATCTTTTGGAACTTCAAGTGA
1 ACATCTCTTAGAACTTCAAGTGA
1627653 CATGTCTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (24 bp):
ACATCTCTTAGAACTTCAAGTGAA
Found at i:1627660 original size:24 final size:24
Alignment explanation
Indices: 1627619--1627672 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1627609 TCTCTTAGAT
*
1627619 CTTCAAGTGAAACATCTTTTGGAA
1 CTTCAAGTGAAACATCTTGTGGAA
* **
1627643 CTTCAAGTGACATGTCTTGTGGAA
1 CTTCAAGTGAAACATCTTGTGGAA
1627667 CTTCAA
1 CTTCAA
1627673 AAGTCATGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (24 bp):
CTTCAAGTGAAACATCTTGTGGAA
Found at i:1627680 original size:24 final size:24
Alignment explanation
Indices: 1627633--1627681 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1627623 AAGTGAAACA
* **
1627633 TCTTTTGGAACTTCAAGTGACATG
1 TCTTGTGGAACTTCAAAAGACATG
*
1627657 TCTTGTGGAACTTCAAAAGTCATG
1 TCTTGTGGAACTTCAAAAGACATG
1627681 T
1 T
1627682 TCATTGGTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (24 bp):
TCTTGTGGAACTTCAAAAGACATG
Found at i:1635767 original size:2 final size:2
Alignment explanation
Indices: 1635760--1635807 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1635750 TTTAAGGTTA
1635760 AT 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 AT
1635802 AT AT AT
1 AT AT AT
1635808 TTAGGTCTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1636758 original size:20 final size:18
Alignment explanation
Indices: 1636722--1636770 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
1636712 CGAAAATAAA
*
1636722 ATAAAATATAAAACAAAG
1 ATAAAAAATAAAACAAAG
* *
1636740 CTAAAAAATAAATATCAAAT
1 ATAAAAAATAAA-A-CAAAG
1636760 ATAAAAAATAA
1 ATAAAAAATAA
1636771 CCTTTGCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 10 0.40
19 1 0.04
20 14 0.56
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.20
Consensus pattern (18 bp):
ATAAAAAATAAAACAAAG
Found at i:1637448 original size:113 final size:113
Alignment explanation
Indices: 1637284--1637547 Score: 284
Period size: 113 Copynumber: 2.3 Consensus size: 113
1637274 CGAACTACGG
* ** *
1637284 TTGAACAAGTTCTTCTCATTATGAACTATTCTTCTTCAGACGAGTTATTCTTATTATG-A-TTCT
1 TTGAACAAGTTATTAACATTATGAAC--TTCTTCTTCAGACGAGATATTCTTATTATGAACTTC-
* * **
1637347 TTCTGGAATTGTTGATGTGCTCCATCTCCTTATGCGATAGAGTTGAGC-AAA-A
63 TTCTGGAATTGAT-A-CT-CTCCATCTCCTTATGCGATAGAGTCAAGCGAAAGA
* * * * *
1637399 TTGAATAAGTTCTTAAGATTATGAACTTCTTCTTCAGATGAGATCTTCTTATTATGAACTTCTTC
1 TTGAACAAGTTATTAACATTATGAACTTCTTCTTCAGACGAGATATTCTTATTATGAACTTCTTC
* * *
1637464 TGGAATTGATACTCTCTATCTCCTTATGTGATAGAGTCAAGCGAAAGG
66 TGGAATTGATACTCTCCATCTCCTTATGCGATAGAGTCAAGCGAAAGA
**
1637512 TTGAACAAGTTATTCTCATTATGAACTTCTTCTTCA
1 TTGAACAAGTTATTAACATTATGAACTTCTTCTTCA
1637548 ACTTCAGATG
Statistics
Matches: 126, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
111 25 0.20
112 4 0.03
113 59 0.47
114 13 0.10
115 25 0.20
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.41
Consensus pattern (113 bp):
TTGAACAAGTTATTAACATTATGAACTTCTTCTTCAGACGAGATATTCTTATTATGAACTTCTTC
TGGAATTGATACTCTCCATCTCCTTATGCGATAGAGTCAAGCGAAAGA
Found at i:1637767 original size:71 final size:72
Alignment explanation
Indices: 1637589--1637938 Score: 518
Period size: 71 Copynumber: 5.0 Consensus size: 72
1637579 TCTCTGGAAA
* *
1637589 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGATATTTCGAGTGAAACTTTATCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCAAGCGAG
1637654 AAAAAGTT
66 AAAAAG-T
* *
1637662 TGTTTTAAGAAAAACAAACTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTC-AGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCAAGCGAG
1637726 AAAAAGT
66 AAAAAGT
* *
1637733 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCGAGTGAAACTTTCTCAAGCGCG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCAAGCGAG
* *
1637798 AAACACT
66 AAAAAGT
* * *
1637805 TTTTTTAAG-AAAACAACCTCAAGT--GATAAATTGCTATTTCAAGTG-AACTTT-TC-AGCGA-
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCAAGCGAG
1637863 AAAAAGT
66 AAAAAGT
* *
1637870 TCTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCTATTTCGAGTGAAACTTTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCAAGCGAG
1637935 AAAA
66 AAAA
1637939 GGTTCTGTTG
Statistics
Matches: 248, Mismatches: 21, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
65 13 0.05
66 18 0.07
67 2 0.01
68 25 0.10
69 25 0.10
70 2 0.01
71 75 0.30
72 34 0.14
73 54 0.22
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (72 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAGTGAAACTTTCTCAAGCGAG
AAAAAGT
Found at i:1637791 original size:37 final size:37
Alignment explanation
Indices: 1637606--1637935 Score: 149
Period size: 37 Copynumber: 9.3 Consensus size: 37
1637596 AGAAAAACAA
* *
1637606 TCTCAAGTGAGATAAATTGATATTTCGAGTGAAACTT
1 TCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTT
* * * * * * ** **
1637643 TATCAAGCGAGAAAAAGT-TTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTT
* *
1637679 ACTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTT
1 TCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTT
* * ** **
1637716 TCTC-AGCGAGAAAAAGTTG-T-TTT-AAGAAAAACAA
1 TCTCAAGTGAGATAAA-TTGTTATTTCAAGTGAAACTT
*
1637750 TCTCAAGTGAGATAAATTGTTATTTCGAGTGAAACTT
1 TCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTT
* * * **
1637787 TCTCAAGCGCGA-AACACTT-TT-TTT-AAG-AAAACAA
1 TCTCAAGTGAGATAA-A-TTGTTATTTCAAGTGAAACTT
* *
1637821 CCTCAAGT--GATAAATTGCTATTTCAAGTG-AACTT
1 TCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTT
* * * * ** **
1637855 T-TC-AGCGA-A-AAA-AGTTCTTTTAAGAAAAACAA
1 TCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTT
*
1637887 TCTCAAGTGAGATAAATT-TCTATTTCGAGTGAAACTT
1 TCTCAAGTGAGATAAATTGT-TATTTCAAGTGAAACTT
*
1637924 TCTCAAGCGAGA
1 TCTCAAGTGAGA
1637936 AAAGGTTCTG
Statistics
Matches: 201, Mismatches: 70, Indels: 44
0.64 0.22 0.14
Matches are distributed among these distances:
31 10 0.05
32 13 0.06
33 10 0.05
34 34 0.17
35 16 0.08
36 45 0.22
37 71 0.35
38 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (37 bp):
TCTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTT
Found at i:1637912 original size:137 final size:142
Alignment explanation
Indices: 1637591--1637938 Score: 555
Period size: 137 Copynumber: 2.5 Consensus size: 142
1637581 TCTGGAAATG
* *
1637591 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTGATATTTCGAGTGAAACTTTATCAAGCGAGAA
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATT-TTATTTCGAGTGAAACTTTCTCAAGCGAGAA
*
1637656 AAAGTTTGTTTTAAGAAAAACAAACTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCA
65 AAACTTTGTTTTAAGAAAAACAAACTCAAGT-AGATAAATTGCTATTTCAAGTGAAACTTTCTCA
*
1637721 GCGAGAAAAAGTTG
129 GCGAGAAAAAGTTC
*
1637735 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCGAGTGAAACTTTCTCAAGCGCGAA
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATT-TTATTTCGAGTGAAACTTTCTCAAGCGAGAA
* *
1637800 ACACTTT-TTTTAAG-AAAACAACCTCAAGT-GATAAATTGCTATTTCAAGTG-AACTTT-TCAG
65 AAACTTTGTTTTAAGAAAAACAAACTCAAGTAGATAAATTGCTATTTCAAGTGAAACTTTCTCAG
1637860 CGA-AAAAAGTTC
130 CGAGAAAAAGTTC
1637872 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCTATTTCGAGTGAAACTTTCTCAAGCGAGAA
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTT-TATTTCGAGTGAAACTTTCTCAAGCGAGAA
1637937 AA
65 AA
1637939 GGTTCTGTTG
Statistics
Matches: 194, Mismatches: 9, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
136 1 0.01
137 71 0.37
138 7 0.04
139 6 0.03
140 21 0.11
142 14 0.07
143 7 0.04
144 67 0.35
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (142 bp):
TTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTATTTCGAGTGAAACTTTCTCAAGCGAGAAA
AACTTTGTTTTAAGAAAAACAAACTCAAGTAGATAAATTGCTATTTCAAGTGAAACTTTCTCAGC
GAGAAAAAGTTC
Found at i:1638268 original size:17 final size:17
Alignment explanation
Indices: 1638246--1638323 Score: 120
Period size: 17 Copynumber: 4.5 Consensus size: 17
1638236 TGAACATCGA
1638246 ATGCATTCCATGCACCG
1 ATGCATTCCATGCACCG
1638263 ATGCATTCCATGCACCG
1 ATGCATTCCATGCACCG
*
1638280 ATGCATTCCATGCACCA
1 ATGCATTCCATGCACCG
*
1638297 ATGCACTCTCCATGCATCG
1 ATGCA-T-TCCATGCACCG
1638316 ATGCATTC
1 ATGCATTC
1638324 TGAATATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
17 40 0.71
18 2 0.04
19 14 0.25
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (17 bp):
ATGCATTCCATGCACCG
Found at i:1638358 original size:65 final size:63
Alignment explanation
Indices: 1638306--1638431 Score: 189
Period size: 63 Copynumber: 2.0 Consensus size: 63
1638296 AATGCACTCT
* * *
1638306 CCATGCATCGATGCATTCTGAATATTTTCAAAACATCGAATGCATTTGATGCATCGATGCACAAG
1 CCATGCATCGATGCA-CCAGAATATTTTC-AAACATCGAATGCATTTAATGCATCGATGCACAAG
**
1638371 CCATGCATCGATGCACCAGGCTATTTTCAAACATCGAATGCATTTAATGCATCGATGCACA
1 CCATGCATCGATGCACCAGAATATTTTCAAACATCGAATGCATTTAATGCATCGATGCACA
1638432 CTTGGTGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
63 32 0.57
64 9 0.16
65 15 0.27
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (63 bp):
CCATGCATCGATGCACCAGAATATTTTCAAACATCGAATGCATTTAATGCATCGATGCACAAG
Found at i:1644204 original size:42 final size:41
Alignment explanation
Indices: 1644130--1644208 Score: 113
Period size: 42 Copynumber: 1.9 Consensus size: 41
1644120 TTTGTGCTTC
* *
1644130 ATGCACCGATGCATTAACAATGCATCGATGCATCCTTGAAT
1 ATGCACCGATGCATAAACAATGCACCGATGCATCCTTGAAT
* *
1644171 ATGCATCGATGCATAAGACCATGCACCGATGCATCCTT
1 ATGCACCGATGCATAA-ACAATGCACCGATGCATCCTT
1644209 CGGGTTTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 14 0.42
42 19 0.58
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (41 bp):
ATGCACCGATGCATAAACAATGCACCGATGCATCCTTGAAT
Found at i:1646788 original size:65 final size:63
Alignment explanation
Indices: 1646655--1646861 Score: 204
Period size: 64 Copynumber: 3.2 Consensus size: 63
1646645 ATTCAAATGC
* *
1646655 ATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAATA-ATT-GAACATCGAATGCATT
1 ATGCACCGATGCACTC--TCCATGCATCGATGCATC--TGAATATTTTCAAACATCGAATGCATT
**
1646717 CC
62 TA
*
1646719 ATGCACCGATGCACTCTCCATGCATCGATGCATTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCACCGATGCACTCTCCATGCATCGATGCA-TCTGAATATTTTC-AAACATCGAATGCATTTA
* *** * * **
1646784 ATGCATCGATGCACAAGCCATGCATCGATGCACCAGGCTATTTTTCAAACATCGAATGCATTTA
1 ATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATA-TTTTCAAACATCGAATGCATTTA
*
1646848 ATGCATCGATGCAC
1 ATGCACCGATGCAC
1646862 ACTTGGTGCA
Statistics
Matches: 124, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
62 6 0.05
63 18 0.15
64 50 0.40
65 50 0.40
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (63 bp):
ATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATATTTTCAAACATCGAATGCATTTA
Found at i:1647838 original size:143 final size:142
Alignment explanation
Indices: 1647574--1647899 Score: 442
Period size: 143 Copynumber: 2.3 Consensus size: 142
1647564 CGATTAACTC
* * * *
1647574 AACAGGTTCGTTTTAAGAAAAACAATATCAAGT-GAT-AATGCTATTTCAAGTGAAACTTTTTCC
1 AACA-GTTTGTTTTAAG-AAAACAATCTCAAGTAGATAAATGCTATTTCAAGTGAAACTTTCTCA
* * *
1647637 AGCGAGAAAAAGTTGTTTTAAGAAAAACAATTTCAAGTGAGATAAATTGTTATTTCAAGTGAAAC
64 AGCGAGAAAAAGTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAAA
*
1647702 CTTCTCTAGCGACA
129 CTTCTCCAGCGACA
1647716 AA-AGTTTGTTTTAAGAAAACAATCTCAAGTGAGATAAATGCTATTTCAAGTGAAACTTTCTCAA
1 AACAGTTTGTTTTAAGAAAACAATCTCAAGT-AGATAAATGCTATTTCAAGTGAAACTTTCTCAA
** *
1647780 GCGAGAAACTGTTTGTTTTAAGAACAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAAA
65 GCGAGAAAAAG-TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAAA
* *
1647845 TTTCTCCAGCGAGA
129 CTTCTCCAGCGACA
* *
1647859 AACAGTTTGTTTTAAAAAAAACAATCTCAATTAAGATAAAT
1 AACAGTTTGTTTT-AAGAAAACAATCTCAAGT-AGATAAAT
1647900 CTTTGTTTTG
Statistics
Matches: 162, Mismatches: 16, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
139 14 0.09
140 11 0.07
141 4 0.02
142 37 0.23
143 62 0.38
144 10 0.06
145 24 0.15
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (142 bp):
AACAGTTTGTTTTAAGAAAACAATCTCAAGTAGATAAATGCTATTTCAAGTGAAACTTTCTCAAG
CGAGAAAAAGTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAAACT
TCTCCAGCGACA
Found at i:1647849 original size:73 final size:73
Alignment explanation
Indices: 1647574--1647899 Score: 443
Period size: 73 Copynumber: 4.6 Consensus size: 73
1647564 CGATTAACTC
* * *
1647574 AACAGGTTCGTTTTAAGAAAAACAATATCAAGT--GAT-AA-TGCTATTTCAAGTGAAACTTTTT
1 AACA-GTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCT
1647635 CCAGCGAGA
65 CCAGCGAGA
* * * *
1647644 AAAAG-TTGTTTTAAGAAAAACAATTTCAAGTGAGATAAATTGTTATTTCAAGTGAAACCTTCTC
1 AACAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTC
* *
1647708 TAGCGACA
66 CAGCGAGA
1647716 AA-AGTTTGTTTTAAG-AAAACAATCTCAAGTGAGATAAA-TGCTATTTCAAGTGAAACTTTCTC
1 AACAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTC
*
1647778 AAGCGAGA
66 CAGCGAGA
* * *
1647786 AACTGTTTGTTTTAAGAACAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAAATTTCTC
1 AACAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTC
1647851 CAGCGAGA
66 CAGCGAGA
* * *
1647859 AACAGTTTGTTTTAAAAAAAACAATCTCAATTAAGATAAAT
1 AACAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAT
1647900 CTTTGTTTTG
Statistics
Matches: 226, Mismatches: 22, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
68 24 0.11
69 1 0.00
70 36 0.16
71 38 0.17
72 61 0.27
73 66 0.29
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (73 bp):
AACAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTC
CAGCGAGA
Found at i:1649759 original size:15 final size:14
Alignment explanation
Indices: 1649741--1649790 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 14
1649731 TTATAGCCTC
1649741 TCTTTTTTTTCTTT
1 TCTTTTTTTTCTTT
1649755 CTCTTTTTTTTTCTTT
1 -TC-TTTTTTTTCTTT
1649771 T-TTTTATTTT-TTT
1 TCTTTT-TTTTCTTT
1649784 TCTTTTT
1 TCTTTTT
1649791 ACTATTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 9 0.28
14 8 0.25
15 3 0.09
16 12 0.38
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (14 bp):
TCTTTTTTTTCTTT
Found at i:1649766 original size:18 final size:16
Alignment explanation
Indices: 1649743--1649790 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
1649733 ATAGCCTCTC
1649743 TTTTTTTTCTTTCTCTT-
1 TTTTTTTTCTTT-T-TTA
*
1649760 TTTTTTTCTTTTTTTTA
1 TTTTTTT-TCTTTTTTA
1649777 TTTTTTTTCTTTTT
1 TTTTTTTTCTTTTT
1649791 ACTATTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.30
17 15 0.56
18 4 0.15
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTTTCTTTTTTA
Done.