Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009643.1 Hibiscus syriacus cultivar Beakdansim tig00117056_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: 8859806
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 41
Found at i:1275403 original size:23 final size:23
Alignment explanation
Indices: 1275377--1275421 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1275367 CACCACAGCT
*
1275377 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
1275400 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1275422 ATATAATGAT
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:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1277250 original size:64 final size:63
Alignment explanation
Indices: 1277152--1277312 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
1277142 TAATGAAGGT
* *
1277152 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
1277215 GG
62 GC
*
1277217 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
1277281 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
1277313 CTGCATGTGC
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.67
65 24 0.28
66 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:1277306 original size:19 final size:19
Alignment explanation
Indices: 1277282--1277332 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
1277272 TTTAAATTCA
1277282 TGCATCGATGCACTGCATG
1 TGCATCGATGCACTGCATG
1277301 TGCATCGATGCACTGCATG
1 TGCATCGATGCACTGCATG
1277320 TGCATCGATGCAC
1 TGCATCGATGCAC
1277333 CTTAAACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.25
Consensus pattern (19 bp):
TGCATCGATGCACTGCATG
Found at i:1280199 original size:27 final size:27
Alignment explanation
Indices: 1280158--1280218 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
1280148 TTTATTTATA
*
1280158 AAATCATATCTCTATAGGAATAGTAAC
1 AAATCATATCACTATAGGAATAGTAAC
1280185 AAATCATATCACTATAGGAATAGTAAC
1 AAATCATATCACTATAGGAATAGTAAC
1280212 AAATCAT
1 AAATCAT
1280219 CTCTATAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.28
Consensus pattern (27 bp):
AAATCATATCACTATAGGAATAGTAAC
Found at i:1289670 original size:58 final size:58
Alignment explanation
Indices: 1289580--1289692 Score: 226
Period size: 58 Copynumber: 1.9 Consensus size: 58
1289570 TTCTCTCGTA
1289580 CCATTAAACTAACCGTATCTTTGTTTCCCTTTTTCACTTCGACAATAACACTTCCGTT
1 CCATTAAACTAACCGTATCTTTGTTTCCCTTTTTCACTTCGACAATAACACTTCCGTT
1289638 CCATTAAACTAACCGTATCTTTGTTTCCCTTTTTCACTTCGACAATAACACTTCC
1 CCATTAAACTAACCGTATCTTTGTTTCCCTTTTTCACTTCGACAATAACACTTCC
1289693 ATCGACAATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.25, C:0.30, G:0.06, T:0.39
Consensus pattern (58 bp):
CCATTAAACTAACCGTATCTTTGTTTCCCTTTTTCACTTCGACAATAACACTTCCGTT
Found at i:1296145 original size:25 final size:24
Alignment explanation
Indices: 1296110--1296156 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
1296100 AACTGGTTTT
1296110 AAATATAATT-AAATAGTTTTATAA
1 AAATATAATTAAAATA-TTTTATAA
1296134 AAATATTAATTAAAATATTTTAT
1 AAATA-TAATTAAAATATTTTAT
1296157 TATAACATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.24
25 11 0.52
26 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
AAATATAATTAAAATATTTTATAA
Found at i:1301571 original size:56 final size:56
Alignment explanation
Indices: 1301487--1301597 Score: 186
Period size: 56 Copynumber: 2.0 Consensus size: 56
1301477 GTTCCACAAA
* * *
1301487 AGAAAAATAATTTATTTAGAACATCTTTCCATAGATATTACATGCTTGCTCAAAAT
1 AGAAAAATAATTTACTTAGAACACCTTTCCATAAATATTACATGCTTGCTCAAAAT
*
1301543 AGAAAAATATTTTACTTAGAACACCTTTCCATAAATATTACATGCTTGCTCAAAA
1 AGAAAAATAATTTACTTAGAACACCTTTCCATAAATATTACATGCTTGCTCAAAA
1301598 ATATAGAGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.34
Consensus pattern (56 bp):
AGAAAAATAATTTACTTAGAACACCTTTCCATAAATATTACATGCTTGCTCAAAAT
Found at i:1304012 original size:3 final size:3
Alignment explanation
Indices: 1304004--1304056 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
1303994 TTTTTATCCA
*
1304004 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1304052 TAT TA
1 TAT TA
1304057 AATATATATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1304068 original size:11 final size:11
Alignment explanation
Indices: 1304052--1304076 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1304042 TTATTATTAT
1304052 TATTAAATATA
1 TATTAAATATA
1304063 TATTAAATATA
1 TATTAAATATA
1304074 TAT
1 TAT
1304077 ATAATTAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TATTAAATATA
Found at i:1306231 original size:18 final size:17
Alignment explanation
Indices: 1306208--1306258 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
1306198 TTCTTTTCAA
1306208 ATTTTTTATTTATTTAT
1 ATTTTTTATTTATTTAT
*
1306225 -TATTTTTATAATATTTAT
1 AT-TTTTTAT-TTATTTAT
*
1306243 ATGTTTTATTTTATTT
1 ATTTTTTA-TTTATTT
1306259 GCAAGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
16 1 0.04
17 7 0.26
18 17 0.63
19 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
ATTTTTTATTTATTTAT
Found at i:1313366 original size:17 final size:19
Alignment explanation
Indices: 1313339--1313374 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1313329 AGACGGCAAT
1313339 CATTCTTTACATTT-TTTA
1 CATTCTTTACATTTATTTA
1313357 CATT-TTTACATTTATTTA
1 CATTCTTTACATTTATTTA
1313375 TTTCATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.25, C:0.14, G:0.00, T:0.61
Consensus pattern (19 bp):
CATTCTTTACATTTATTTA
Found at i:1316078 original size:22 final size:22
Alignment explanation
Indices: 1316052--1316096 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1316042 GAAGATCAGC
1316052 TATTAGGTTTAG-TTTAATATAT
1 TATTAGGTTTAGTTTTAA-ATAT
1316074 TATTAGGTTTAGTTTTAAATAT
1 TATTAGGTTTAGTTTTAAATAT
1316096 T
1 T
1316097 GGTAATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (22 bp):
TATTAGGTTTAGTTTTAAATAT
Found at i:1325106 original size:42 final size:41
Alignment explanation
Indices: 1325059--1325155 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 41
1325049 ATAATTTAAG
* * *
1325059 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGAT-AAA
* * *
1325101 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
*
1325142 TCATTCGGGCCATC
1 TCCTTCGGGCCATC
1325156 CATAAAGCCT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 14 0.30
42 33 0.70
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.29
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
Found at i:1325164 original size:42 final size:41
Alignment explanation
Indices: 1325055--1325166 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 41
1325045 GTAAATAATT
* * *
1325055 TAAGTCCTTCGGGCCAT-CAGTAAGTCTTTCGAGCATGATGA
1 TAAGTCCTTCGGGCCATCCA-TAAGCCTTTAGAGCAAGATGA
* * **
1325096 TGAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGA
1 T-AAGTCCTTCGGGCCATCCATAAGCCTTTAGAGCAAGATGA
*
1325138 TAAGTCATTCGGGCCATCCATAAAGCCTT
1 TAAGTCCTTCGGGCCATCCAT-AAGCCTT
1325167 CGGGTAGGAT
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
41 16 0.29
42 40 0.71
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (41 bp):
TAAGTCCTTCGGGCCATCCATAAGCCTTTAGAGCAAGATGA
Found at i:1325448 original size:80 final size:79
Alignment explanation
Indices: 1325284--1325484 Score: 312
Period size: 80 Copynumber: 2.5 Consensus size: 79
1325274 GTCCTTCGGG
* * * **
1325284 CCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTAATTTTAAGCCTTCACCGAAGA
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGCAATGGTAAGCCTTCACCGAAGA
1325349 GTAGTGAAGCAAAC
66 GTAGTGAAGCAAAC
*
1325363 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGCAACTGGTAAGCCTTCACGGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGCAA-TGGTAAGCCTTCACCGAAG
*
1325428 AGTAGTGAAGCAAAT
65 AGTAGTGAAGCAAAC
* *
1325443 TCATCAGTAAGTCTTTCGAGAATGATGATTAAATCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
1325485 TCATCCATAA
Statistics
Matches: 112, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 42 0.38
80 70 0.62
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (79 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGCAATGGTAAGCCTTCACCGAAGA
GTAGTGAAGCAAAC
Found at i:1325986 original size:53 final size:53
Alignment explanation
Indices: 1325923--1326113 Score: 303
Period size: 53 Copynumber: 3.6 Consensus size: 53
1325913 AGAATCACAC
1325923 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
*
1325976 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * **
1326029 CAGAAGACTGTTCGAGTTCTACTCTCTGAAGCAAGAGGGAGCGAACCCGCCGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1326082 TC-GAAGATTGTTCGAGTTCTATACTCCCTGAA
1 -CAGAAGATTGTTCGAGTTC--TACTCCCTGAA
1326114 CGAATAGGGA
Statistics
Matches: 127, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
53 116 0.91
54 1 0.01
55 10 0.08
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.21
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:1326143 original size:55 final size:55
Alignment explanation
Indices: 1326084--1326235 Score: 174
Period size: 55 Copynumber: 2.8 Consensus size: 55
1326074 CCCGCCGGTC
* *
1326084 GAAGATTGTTCGAGT-TCTATACTCCCTGAACGAATAGGGAGCAGACTCGTTT-TAT
1 GAAGATTATTCGAGTCT-TATACTCCCTGAACGAATAGGGAGCAGACACGTTTGT-T
* *
1326139 GAAGATTATTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTT
1 GAAGATTATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTT
* *
1326194 GAAG---A-TCAAGTCTTATACTCTCTGAA-GAAATAGGGAGCAGAC
1 GAAGATTATTCGAGTCTTATACTCCCTGAACG-AATAGGGAGCAGAC
1326236 TTATCATTTG
Statistics
Matches: 89, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
50 1 0.01
51 34 0.38
52 1 0.01
55 51 0.57
56 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (55 bp):
GAAGATTATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTT
Found at i:1327368 original size:22 final size:22
Alignment explanation
Indices: 1327342--1327386 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1327332 GAAGATCAGC
1327342 TATTAGGTTTAG-TTTAATATAT
1 TATTAGGTTTAGTTTTAA-ATAT
1327364 TATTAGGTTTAGTTTTAAATAT
1 TATTAGGTTTAGTTTTAAATAT
1327386 T
1 T
1327387 GGTAATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (22 bp):
TATTAGGTTTAGTTTTAAATAT
Found at i:1330654 original size:12 final size:12
Alignment explanation
Indices: 1330637--1330674 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1330627 ATGCTTGAAG
1330637 AAAAAAAAAG--
1 AAAAAAAAAGAA
1330647 AAAAAAAAAGAA
1 AAAAAAAAAGAA
*
1330659 AAAAAAAGAGAA
1 AAAAAAAAAGAA
1330671 AAAA
1 AAAA
1330675 GAGGGGTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.40
12 15 0.60
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:1330677 original size:9 final size:10
Alignment explanation
Indices: 1330634--1330674 Score: 73
Period size: 10 Copynumber: 4.0 Consensus size: 10
1330624 ATTATGCTTG
1330634 AAGAAAAAAA
1 AAGAAAAAAA
1330644 AAGAAAAAAA
1 AAGAAAAAAA
1330654 AAGAAAAAAA
1 AAGAAAAAAA
1330664 AAGAGAAAAAA
1 AAGA-AAAAAA
1330675 GAGGGGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 24 0.80
11 6 0.20
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:1332011 original size:82 final size:82
Alignment explanation
Indices: 1331800--1332437 Score: 1107
Period size: 82 Copynumber: 7.7 Consensus size: 82
1331790 AAACATTAAA
*
1331800 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGAC
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
*
1331865 AGAATCAAGCATTGAGTT
66 AGAA-CAATCATTGAGTT
1331883 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
*
1331948 AGAACAATCATTGAATT
66 AGAACAATCATTGAGTT
* * **
1331965 TGGAAGATGAATGTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1332030 AGAACAATCATTGAGTT
66 AGAACAATCATTGAGTT
1332047 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1332112 AGAACAATCATTGAGTT
66 AGAACAATCATTGAGTT
*
1332129 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGAC
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
*
1332194 AGAATCAAGCATTGAGTT
66 AGAA-CAATCATTGAGTT
1332212 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1332277 AGAACAATCATTGAGTT
66 AGAACAATCATTGAGTT
1332294 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGA
*
1332358 CAGAACCAATCATTGAATT
65 CAGAA-CAATCATTGAGTT
* * **
1332377 TGGAAGATGAATGTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1332438 TGGTAAGAAC
Statistics
Matches: 531, Mismatches: 21, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
82 312 0.59
83 219 0.41
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (82 bp):
TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
AGAACAATCATTGAGTT
Found at i:1332289 original size:165 final size:165
Alignment explanation
Indices: 1331800--1332437 Score: 1118
Period size: 165 Copynumber: 3.9 Consensus size: 165
1331790 AAACATTAAA
1331800 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGAC
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGAC
1331865 AGAATCAAGCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
66 AGAATCAAGCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
*
1331930 TATCTGATCTGGTTGGACAGAACAATCATTGAATT
131 TATCTGATCTGGTTGGACAGAACAATCATTGAGTT
* * ** *
1331965 TGGAAGATGAATGTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGAC
*
1332030 AGAA-CAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
66 AGAATCAAGCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1332094 TATCTGATCTGGTTGGACAGAACAATCATTGAGTT
131 TATCTGATCTGGTTGGACAGAACAATCATTGAGTT
1332129 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGAC
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGAC
1332194 AGAATCAAGCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
66 AGAATCAAGCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
1332259 TATCTGATCTGGTTGGACAGAACAATCATTGAGTT
131 TATCTGATCTGGTTGGACAGAACAATCATTGAGTT
*
1332294 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-
1 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GATTGGA
* * * * * **
1332358 CAGAACCAATCATTGAATTTGGAAGATGAATGTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAG
65 CAGAATCAAGCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
1332423 TTATCTGATCTGGTT
130 TTATCTGATCTGGTT
1332438 TGGTAAGAAC
Statistics
Matches: 450, Mismatches: 21, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
164 157 0.35
165 288 0.64
166 5 0.01
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (165 bp):
TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGAC
AGAATCAAGCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
TATCTGATCTGGTTGGACAGAACAATCATTGAGTT
Found at i:1333529 original size:230 final size:230
Alignment explanation
Indices: 1333113--1333949 Score: 1237
Period size: 230 Copynumber: 3.6 Consensus size: 230
1333103 ATAGATTAGC
*
1333113 TTTTCCAGA-AAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAA
1 TTTTCCAGAGAAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
*
1333177 GAAGAATTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-GAAGAG
65 GAAGAACTTGTTCAACCTTTT-GTTTGAATTCATCATTTGATGGATCAACATTGCCAGAGAAGAG
1333241 TTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
129 TTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1333306 CAACCTTTTATCTGAATTCATCACTGGATGGATTATT
194 CAACCTTTTATCTGAATTCATCACTGGATGGATTATT
* *
1333343 TTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAG
1 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1333408 AAGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-GAAGAGT
66 AAGAACTTGTTCAACCTTTT-GTTTGAATTCATCATTTGATGGATCAACATTGCCAGAGAAGAGT
1333472 TCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
130 TCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1333537 AACCTTTTATCTGAATTCATCACTGGATGGATTATT
195 AACCTTTTATCTGAATTCATCACTGGATGGATTATT
*
1333573 TTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * * * * *
1333638 AAGAATTTGTTCAACCTTTT-TTCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAG-G
66 AAGAACTTGTTCAACCTTTTGTT-TGAATTCATC-ATTTGATGGATCAACATTGCCAGAGAAGAG
*
1333701 TTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
129 TTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * * * * **
1333763 CAATCTTTT-GCTTGAATTCATCATTTGATGGATCAAC
194 CAACCTTTTATC-TGAATTCATCACTGGATGGATTATT
* * *
1333800 ATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAA
1 TTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAA
* * * **
1333864 TGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGATGGATCATCATCCCCAGCA-AA
62 TGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-AGAA
* *
1333928 AAGTTCATAATAAGAAGAACTC
126 GAGTTCATAATGAGAAGAACTC
1333950 ATCTGGAGAG
Statistics
Matches: 558, Mismatches: 35, Indels: 26
0.90 0.06 0.04
Matches are distributed among these distances:
226 2 0.00
227 96 0.17
228 3 0.01
229 31 0.06
230 417 0.75
231 8 0.01
232 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (230 bp):
TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGAGAAGAGTT
CATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
ACCTTTTATCTGAATTCATCACTGGATGGATTATT
Found at i:1333816 original size:343 final size:342
Alignment explanation
Indices: 1333126--1333968 Score: 1291
Period size: 343 Copynumber: 2.4 Consensus size: 342
1333116 TCCAGAAAAG
*
1333126 GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGT
1 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* * *
1333188 TCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAG
66 TCAACCTTTT--TCTGAATTCATCATTTGATGGATCATCATTCCCAGAGAAG-GTTCATAATGAG
1333252 AAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAT
128 AAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAT
* * *
1333317 CTGAATTCATCACTGGATGGATTATTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
190 CTGAATTCATCAATGGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
1333382 AGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTG
255 AGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGGCTTGAATTCATCATTTG
1333447 ATGGATCAACATTGCCAGGAAGA
320 ATGGATCAACATTGCCAGGAAGA
1333470 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* * * ** *
1333535 TCAACCTTTTATCTGAATTCATCACTGGATGGATTATTTTTTCCAGAGAAGGTTCATAATGAGAA
66 TCAACCTTTT-TCTGAATTCATCATTTGATGGATCATCATTCCCAGAGAAGGTTCATAATGAGAA
*
1333600 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAA
130 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAA
* *
1333665 TTCATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAA
195 TTCATC-AATGGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
* *
1333730 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTT-GCTTGAATTCATCATTTGATGG
259 AGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGGCTTGAATTCATCATTTGATGG
*
1333794 ATCAACATTGCCAGGTAGA
324 ATCAACATTGCCAGGAAGA
*
1333813 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* * * * * *
1333878 TCAATCTTTTGCTTGAATTCATCATTTGATGGATCATCATCCCCAGCAAAAAGTTCATAATAAGA
66 TCAACCTTTTTC-TGAATTCATCATTTGATGGATCATCATTCCCAG-AGAAGGTTCATAATGAGA
*
1333943 AGAACTCATCTGGAGAGAGAGAAGAA
129 AGAACTCATCTGAAGA-AG-GAAGAA
1333969 TTTATTCAAT
Statistics
Matches: 456, Mismatches: 34, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
342 1 0.00
343 204 0.45
344 141 0.31
345 2 0.00
346 51 0.11
347 57 0.12
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (342 bp):
GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
TCAACCTTTTTCTGAATTCATCATTTGATGGATCATCATTCCCAGAGAAGGTTCATAATGAGAAG
AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAAT
TCATCAATGGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG
AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGGCTTGAATTCATCATTTGATGGAT
CAACATTGCCAGGAAGA
Found at i:1334113 original size:3 final size:3
Alignment explanation
Indices: 1334105--1334181 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
1334095 TTTTTATCCA
1334105 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1334153 TAT TAT CAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1334182 AATATATATT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1334193 original size:11 final size:11
Alignment explanation
Indices: 1334177--1334208 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
1334167 TTATTATTAT
1334177 TATTAAATATA
1 TATTAAATATA
1334188 TATTAAATATA
1 TATTAAATATA
1334199 TATATAAATA
1 TAT-TAAATA
1334209 ATTAATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATATA
Found at i:1338540 original size:21 final size:21
Alignment explanation
Indices: 1338515--1338580 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
1338505 CGGACTCATA
1338515 CCCATGTCGTTCATCCCCATT
1 CCCATGTCGTTCATCCCCATT
* * *
1338536 CCCATG-C-TTGGA--CTCATA
1 CCCATGTCGTT-CATCCCCATT
*
1338554 CCCATGTTGTTCATCCCCATT
1 CCCATGTCGTTCATCCCCATT
1338575 CCCATG
1 CCCATG
1338581 CTTGGACTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
18 10 0.30
19 3 0.09
20 4 0.12
21 16 0.48
ACGTcount: A:0.17, C:0.39, G:0.12, T:0.32
Consensus pattern (21 bp):
CCCATGTCGTTCATCCCCATT
Found at i:1338623 original size:45 final size:39
Alignment explanation
Indices: 1338492--1338618 Score: 218
Period size: 39 Copynumber: 3.3 Consensus size: 39
1338482 GCTCCCTGTA
* *
1338492 CCATTCCCATGCTCGGACTCATACCCATGTCGTTCATCC
1 CCATTCCCATGCTTGGACTCATACCCATGTTGTTCATCC
1338531 CCATTCCCATGCTTGGACTCATACCCATGTTGTTCATCC
1 CCATTCCCATGCTTGGACTCATACCCATGTTGTTCATCC
*
1338570 CCATTCCCATGCTTGGACTTATACCCATGTTGTTCATCC
1 CCATTCCCATGCTTGGACTCATACCCATGTTGTTCATCC
*
1338609 CCATCCCCAT
1 CCATTCCCAT
1338619 TCCCATGCCC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 84 1.00
ACGTcount: A:0.18, C:0.39, G:0.12, T:0.31
Consensus pattern (39 bp):
CCATTCCCATGCTTGGACTCATACCCATGTTGTTCATCC
Found at i:1339570 original size:33 final size:33
Alignment explanation
Indices: 1339519--1339631 Score: 129
Period size: 33 Copynumber: 3.4 Consensus size: 33
1339509 TTGGCAATGC
* *
1339519 GGATTAGCATTTGGCTGTGCTAGTTGACCATTT
1 GGATTAGCATTTGGCTGTGCAAGTTGGCCATTT
* * * * *
1339552 GGGTTAGTATTTGACTGTGCAAGTTGGGCATAT
1 GGATTAGCATTTGGCTGTGCAAGTTGGCCATTT
**
1339585 GGATTAGCATTTGGCTGTGCGGGTTGGCCATTT
1 GGATTAGCATTTGGCTGTGCAAGTTGGCCATTT
1339618 GGATTCA-CATTTGG
1 GGATT-AGCATTTGG
1339632 GTAAATATTT
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
33 64 0.98
34 1 0.02
ACGTcount: A:0.18, C:0.13, G:0.32, T:0.37
Consensus pattern (33 bp):
GGATTAGCATTTGGCTGTGCAAGTTGGCCATTT
Found at i:1339662 original size:33 final size:33
Alignment explanation
Indices: 1339638--1340371 Score: 492
Period size: 33 Copynumber: 22.2 Consensus size: 33
1339628 TTGGGTAAAT
* * * *
1339638 ATTTGGCTTTGCAGGTTGGCCATTTGGGTAAAT
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
* * *
1339671 ATTTGGATGTGCAGGTTGGCCATATGGATTAGC
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
* * *
1339704 ATTTGGCTGTGCAGGTTGGGCATATGGATTAGC
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
** * *
1339737 ATTTGGCTGAACGGGTTGGCCATTTGGATTCAC
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
* * * * * * *
1339770 ATTTGCCAGTGCAGGTAGTCCATTCGG-GTAAGT
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAA-C
* ** * *
1339803 ATTTGGCAGTGCAGGTTGATCATATGGATTAGC
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
* *
1339836 ATTTGGCTGTGTAGGTTGGCCATTTGGATTCAC
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
* * * ** *
1339869 ATTTGGCTGAGCGGGTTCGCCATGAGGATTCAC
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
* * * *
1339902 ATTTGGCTGAGCCGGTTGGCCATTTGG-GTAAGT
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAA-C
* * * * **
1339935 ATTTGGTTGTGCATGTTGACCATATGGATTAGT
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
* *
1339968 ATTTGGCTGTGCAGGTTGGTCATTTGGATTCAC
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
* * *
1340001 ATTTAGCT-TAGCAGGTTGGCCATTTGAATTCAC
1 ATTTGGCTGT-GCAGGTTGGCCATTTGGATTAAC
* * * * *
1340034 ATTT-GCTTGTGCAAGTAGGCTATTTGG-GTAAGT
1 ATTTGGC-TGTGCAGGTTGGCCATTTGGATTAA-C
* * * *
1340067 ATTTGGCTGAGCGGGTTGTCCATTTGGATTCAC
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
* * * *
1340100 ATTTGGCTGTGCAGGTAGGCTATTTGG-GTAAGT
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAA-C
* * *
1340133 ATTTGGCTGTGCAGGTTGGACATATGGATTAGC
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
* * ** *
1340166 ATTTGACTGTGCAGGTTGGACATAGGGATTAGC
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
* * * * * *
1340199 ATTTGACAGAGCAGGTTGCCCATATGGATTAGC
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
* * * * *
1340232 ATTTTGCTGAGCGGGTTGGACATTTGGATTAGC
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
* ** *
1340265 ATTTGGTTGTGCAGGTTGGCCATAGGGATTAGC
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
* * *** *
1340298 ATTTTGCTGAGTCA-GTTGGCCAAAGGGATTAGC
1 ATTTGGCTGTG-CAGGTTGGCCATTTGGATTAAC
* * * * *
1340331 ATCTGGCTGTGCGGGTTGGCCATTAGGATCATC
1 ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
1340364 ATTTGGCT
1 ATTTGGCT
1340372 TCGGTGGTTC
Statistics
Matches: 546, Mismatches: 141, Indels: 28
0.76 0.20 0.04
Matches are distributed among these distances:
32 12 0.02
33 521 0.95
34 13 0.02
ACGTcount: A:0.20, C:0.14, G:0.31, T:0.34
Consensus pattern (33 bp):
ATTTGGCTGTGCAGGTTGGCCATTTGGATTAAC
Found at i:1339719 original size:66 final size:66
Alignment explanation
Indices: 1339638--1340513 Score: 567
Period size: 66 Copynumber: 13.3 Consensus size: 66
1339628 TTGGGTAAAT
* ** *
1339638 ATTTGGCTTTGCAGGTTGGCCATTTGGGTAAATATTTGGATGTGCAGGTTGGCCATATGGATTAG
1 ATTTGGCTGTGCAGGTTGGCCATTTGGGTAAGCATTTGGCTGTGCAGGTTGGCCATATGGATTAG
1339703 C
66 C
* * * * ** * *
1339704 ATTTGGCTGTGCAGGTTGGGCATATGGATTAGCATTTGGCTGAACGGGTTGGCCATTTGGATTCA
1 ATTTGGCTGTGCAGGTTGGCCATTTGGGTAAGCATTTGGCTGTGCAGGTTGGCCATATGGATT-A
1339769 -C
65 GC
* * * * * * * **
1339770 ATTTGCCAGTGCAGGTAGTCCATTCGGGTAAGTATTTGGCAGTGCAGGTTGATCATATGGATTAG
1 ATTTGGCTGTGCAGGTTGGCCATTTGGGTAAGCATTTGGCTGTGCAGGTTGGCCATATGGATTAG
1339835 C
66 C
* * * * * *
1339836 ATTTGGCTGTGTAGGTTGGCCATTTGGATTCA-CATTTGGCTGAGCGGGTTCGCCATGA-GGATT
1 ATTTGGCTGTGCAGGTTGGCCATTTGG-GTAAGCATTTGGCTGTGCAGGTTGGCCAT-ATGGATT
1339899 CA-C
64 -AGC
* * * * * *
1339902 ATTTGGCTGAGCCGGTTGGCCATTTGGGTAAGTATTTGGTTGTGCATGTTGACCATATGGATTAG
1 ATTTGGCTGTGCAGGTTGGCCATTTGGGTAAGCATTTGGCTGTGCAGGTTGGCCATATGGATTAG
*
1339967 T
66 C
* * * * * *
1339968 ATTTGGCTGTGCAGGTTGGTCATTTGGATTCA-CATTTAGCT-TAGCAGGTTGGCCATTTGAATT
1 ATTTGGCTGTGCAGGTTGGCCATTTGG-GTAAGCATTTGGCTGT-GCAGGTTGGCCATATGGATT
1340031 CA-C
64 -AGC
* * * * * * * *
1340034 ATTT-GCTTGTGCAAGTAGGCTATTTGGGTAAGTATTTGGCTGAGCGGGTTGTCCATTTGGATTC
1 ATTTGGC-TGTGCAGGTTGGCCATTTGGGTAAGCATTTGGCTGTGCAGGTTGGCCATATGGATT-
1340098 A-C
64 AGC
* * * *
1340100 ATTTGGCTGTGCAGGTAGGCTATTTGGGTAAGTATTTGGCTGTGCAGGTTGGACATATGGATTAG
1 ATTTGGCTGTGCAGGTTGGCCATTTGGGTAAGCATTTGGCTGTGCAGGTTGGCCATATGGATTAG
1340165 C
66 C
* * * * * * * *
1340166 ATTTGACTGTGCAGGTTGGACA-TAGGGATTAGCATTTGACAGAGCAGGTTGCCCATATGGATTA
1 ATTTGGCTGTGCAGGTTGGCCATTTGGG-TAAGCATTTGGCTGTGCAGGTTGGCCATATGGATTA
1340230 GC
65 GC
* * * * * * * *
1340232 ATTTTGCTGAGCGGGTTGGACATTTGGATTAGCATTTGGTTGTGCAGGTTGGCCATAGGGATTAG
1 ATTTGGCTGTGCAGGTTGGCCATTTGGGTAAGCATTTGGCTGTGCAGGTTGGCCATATGGATTAG
1340297 C
66 C
* * ** * * *
1340298 ATTTTGCTGAGTCA-GTTGGCCA-AAGGGATTAGCATCTGGCTGTGCGGGTTGGCCAT-TAGGAT
1 ATTTGGCTGTG-CAGGTTGGCCATTTGGG-TAAGCATTTGGCTGTGCAGGTTGGCCATAT-GGAT
* *
1340360 CATC
63 TAGC
** ** ** ** * * * ** *
1340364 ATTTGGCT-TCGGTGGTTCTCCATAAGAATCATCATTTGGCTTTGGTGGTTGGCCATAAGGATTA
1 ATTTGGCTGT-GCAGGTTGGCCATTTGGGTAAGCATTTGGCTGTGCAGGTTGGCCATATGGATTA
*
1340428 AC
65 GC
* * * * * * * * * **
1340430 ACTTGACAGTGCAGATTGGACATGTGGAG-AAGCACTTGGCTGCGCAGGTTGGTCATACAGATTA
1 ATTTGGCTGTGCAGGTTGGCCATTTGG-GTAAGCATTTGGCTGTGCAGGTTGGCCATATGGATTA
1340494 GC
65 GC
* *
1340496 ACTTGGCTGTGTAGGTTG
1 ATTTGGCTGTGCAGGTTG
1340514 ACTGTACATA
Statistics
Matches: 615, Mismatches: 168, Indels: 54
0.73 0.20 0.06
Matches are distributed among these distances:
65 17 0.03
66 580 0.94
67 18 0.03
ACGTcount: A:0.20, C:0.15, G:0.31, T:0.34
Consensus pattern (66 bp):
ATTTGGCTGTGCAGGTTGGCCATTTGGGTAAGCATTTGGCTGTGCAGGTTGGCCATATGGATTAG
C
Found at i:1339721 original size:111 final size:111
Alignment explanation
Indices: 1339527--1339742 Score: 303
Period size: 111 Copynumber: 1.9 Consensus size: 111
1339517 GCGGATTAGC
* * *
1339527 ATTTGGCTGTGCTAGTTGACCATTTGGGTTAGTATTTGACTGTGCAAGTTGGGCATATGGATTAG
1 ATTTGGCTGTGCTAGTTGACCATTTGGGTAAATATTTGACTGTGCAAGTTGGCCATATGGATTAG
* *
1339592 CATTTGGCTGTGCGGGTTGGCCATTTGGATTCA-CATTTGGGTAAAT
66 CATTTGGCTGTGCAGGTTGGCCATATGGATT-AGCATTTGGGTAAAT
* * *
1339638 ATTTGGCTTTGC-AGGTTGGCCATTTGGGTAAATATTTGGA-TGTGCAGGTTGGCCATATGGATT
1 ATTTGGCTGTGCTA-GTTGACCATTTGGGTAAATATTT-GACTGTGCAAGTTGGCCATATGGATT
*
1339701 AGCATTTGGCTGTGCAGGTTGGGCATATGGATTAGCATTTGG
64 AGCATTTGGCTGTGCAGGTTGGCCATATGGATTAGCATTTGG
1339743 CTGAACGGGT
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
110 2 0.02
111 89 0.96
112 2 0.02
ACGTcount: A:0.19, C:0.12, G:0.32, T:0.37
Consensus pattern (111 bp):
ATTTGGCTGTGCTAGTTGACCATTTGGGTAAATATTTGACTGTGCAAGTTGGCCATATGGATTAG
CATTTGGCTGTGCAGGTTGGCCATATGGATTAGCATTTGGGTAAAT
Found at i:1339864 original size:132 final size:132
Alignment explanation
Indices: 1339638--1340287 Score: 664
Period size: 132 Copynumber: 4.9 Consensus size: 132
1339628 TTGGGTAAAT
* * * *
1339638 ATTTGGCTTTGCAGGTTGGCCATTTGGGTAAATATTTGG-ATGTGCAGGTTGGCCATATGGATTA
1 ATTTGCCTGTGCAGGTTGGCCATTTGGGTAAGTATTTGGCA-GTGCAGGTTGACCATATGGATTA
* * * *
1339702 GCATTTGGCTGTGCAGGTTGGGCATATGGATTAGCATTTGGCTGAACGGGTTGGCCATTTGGATT
65 GCATTTGGCTGTGCAGGTTGGCCATTTGGATTAGCATTTGGCTGAGCAGGTTGGCCATTTGGATT
1339767 CAC
130 CAC
* * * * *
1339770 ATTTGCCAGTGCAGGTAGTCCATTCGGGTAAGTATTTGGCAGTGCAGGTTGATCATATGGATTAG
1 ATTTGCCTGTGCAGGTTGGCCATTTGGGTAAGTATTTGGCAGTGCAGGTTGACCATATGGATTAG
* * * **
1339835 CATTTGGCTGTGTAGGTTGGCCATTTGGATTCA-CATTTGGCTGAGCGGGTTCGCCATGAGGATT
66 CATTTGGCTGTGCAGGTTGGCCATTTGGATT-AGCATTTGGCTGAGCAGGTTGGCCATTTGGATT
1339899 CAC
130 CAC
* * * ** *
1339902 ATTTGGCTGAGCCGGTTGGCCATTTGGGTAAGTATTTGGTTGTGCATGTTGACCATATGGATTAG
1 ATTTGCCTGTGCAGGTTGGCCATTTGGGTAAGTATTTGGCAGTGCAGGTTGACCATATGGATTAG
* * * * *
1339967 TATTTGGCTGTGCAGGTTGGTCATTTGGATTCA-CATTTAGCTTAGCAGGTTGGCCATTTGAATT
66 CATTTGGCTGTGCAGGTTGGCCATTTGGATT-AGCATTTGGCTGAGCAGGTTGGCCATTTGGATT
1340031 CAC
130 CAC
* * * * * * * * *
1340034 ATTTGCTTGTGCAAGTAGGCTATTTGGGTAAGTATTTGGCTGAGCGGGTTGTCCATTTGGATTCA
1 ATTTGCCTGTGCAGGTTGGCCATTTGGGTAAGTATTTGGCAGTGCAGGTTGACCATATGGATT-A
* * * * * * * *
1340099 -CATTTGGCTGTGCAGGTAGGCTATTTGGGTAAGTATTTGGCTGTGCAGGTTGGACATATGGATT
65 GCATTTGGCTGTGCAGGTTGGCCATTTGGATTAGCATTTGGCTGAGCAGGTTGGCCATTTGGATT
1340163 -AGC
130 CA-C
* * * * * * * *
1340166 ATTTGACTGTGCAGGTTGGACA-TAGGGATTAGCATTTGACAGAGCAGGTTGCCCATATGGATTA
1 ATTTGCCTGTGCAGGTTGGCCATTTGGG-TAAGTATTTGGCAGTGCAGGTTGACCATATGGATTA
* * * * * *
1340230 GCATTTTGCTGAGCGGGTTGGACATTTGGATTAGCATTTGGTTGTGCAGGTTGGCCAT
65 GCATTTGGCTGTGCAGGTTGGCCATTTGGATTAGCATTTGGCTGAGCAGGTTGGCCAT
1340288 AGGGATTAGC
Statistics
Matches: 423, Mismatches: 88, Indels: 14
0.81 0.17 0.03
Matches are distributed among these distances:
131 7 0.02
132 413 0.98
133 3 0.01
ACGTcount: A:0.20, C:0.14, G:0.31, T:0.35
Consensus pattern (132 bp):
ATTTGCCTGTGCAGGTTGGCCATTTGGGTAAGTATTTGGCAGTGCAGGTTGACCATATGGATTAG
CATTTGGCTGTGCAGGTTGGCCATTTGGATTAGCATTTGGCTGAGCAGGTTGGCCATTTGGATTC
AC
Found at i:1340395 original size:33 final size:33
Alignment explanation
Indices: 1340344--1340422 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
1340334 TGGCTGTGCG
* * *
1340344 GGTTGGCCATTAGGATCATCATTTGGCTTCGGT
1 GGTTCGCCATAAGAATCATCATTTGGCTTCGGT
* *
1340377 GGTTCTCCATAAGAATCATCATTTGGCTTTGGT
1 GGTTCGCCATAAGAATCATCATTTGGCTTCGGT
*
1340410 GGTTGGCCATAAG
1 GGTTCGCCATAAG
1340423 GATTAACACT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.35
Consensus pattern (33 bp):
GGTTCGCCATAAGAATCATCATTTGGCTTCGGT
Found at i:1341862 original size:17 final size:17
Alignment explanation
Indices: 1341840--1341889 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
1341830 GATTGCTTGA
1341840 ATGGTATCTATACCCCC
1 ATGGTATCTATACCCCC
*
1341857 ATGGTATCGATACCCCC
1 ATGGTATCTATACCCCC
*
1341874 AGGGTATCTATACCCC
1 ATGGTATCTATACCCC
1341890 TGGCTACAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (17 bp):
ATGGTATCTATACCCCC
Found at i:1341948 original size:21 final size:21
Alignment explanation
Indices: 1341922--1341961 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1341912 TTGGATTTTG
1341922 TGAAGGAGTACCGATACCCTA
1 TGAAGGAGTACCGATACCCTA
*
1341943 TGAAGGGGTACCGATACCC
1 TGAAGGAGTACCGATACCC
1341962 CTATCGTGGG
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:0.30, C:0.25, G:0.28, T:0.17
Consensus pattern (21 bp):
TGAAGGAGTACCGATACCCTA
Found at i:1342027 original size:20 final size:22
Alignment explanation
Indices: 1341989--1342028 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1341979 TTTGAGTAGA
1341989 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1342011 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1342029 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1345062 original size:21 final size:21
Alignment explanation
Indices: 1345036--1345075 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1345026 CAACAATTGG
1345036 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
1345057 TAACAATTGATATCTTTTT
1 TAACAATTGATATCATTTT
1345076 CATTAAACAT
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:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:1345529 original size:21 final size:21
Alignment explanation
Indices: 1345513--1345559 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
1345503 ATCATCTCCA
1345513 AACGGCTTC-AAAACATCCCC
1 AACGGCTTCTAAAACATCCCC
*
1345533 AACGTC-TCTAAAACATCCCC
1 AACGGCTTCTAAAACATCCCC
1345553 AACGGCT
1 AACGGCT
1345560 ATATATGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.34, C:0.38, G:0.11, T:0.17
Consensus pattern (21 bp):
AACGGCTTCTAAAACATCCCC
Found at i:1355512 original size:2 final size:2
Alignment explanation
Indices: 1355505--1355546 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1355495 TCATAAATTC
1355505 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
1355547 TTCCATAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1355796 original size:27 final size:27
Alignment explanation
Indices: 1355754--1355805 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1355744 ATCTATAATA
* *
1355754 AAATTTAAATTTAATATATTTATTTTT
1 AAATTTAAATTTAATAAATGTATTTTT
1355781 AAATTT-AATTTAAATAAATGTATTT
1 AAATTTAAATTT-AATAAATGTATTT
1355806 AATTTGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
AAATTTAAATTTAATAAATGTATTTTT
Found at i:1355954 original size:31 final size:31
Alignment explanation
Indices: 1355918--1355992 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
1355908 ATAAAAAGTA
* * *
1355918 TAATATTTGATCATTTTTATTTTTATTTCAT
1 TAATATGTGATCATATTCATTTTTATTTCAT
* *
1355949 TAATATGTGGTCATATTCATTTTTATTTAAT
1 TAATATGTGATCATATTCATTTTTATTTCAT
* *
1355980 TGAGATGTGATCA
1 TAATATGTGATCA
1355993 CTTACTTTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.28, C:0.07, G:0.11, T:0.55
Consensus pattern (31 bp):
TAATATGTGATCATATTCATTTTTATTTCAT
Found at i:1367633 original size:145 final size:145
Alignment explanation
Indices: 1367366--1367651 Score: 464
Period size: 145 Copynumber: 2.0 Consensus size: 145
1367356 CTGTAAGATG
1367366 TTAGAAAATTGACTTCTGAGCATTCTTTATAAAATCATCCTAGATCTTCAATTTCTTTATCCTTG
1 TTAGAAAATTGACTTCTGAGCATTCTTTATAAAATCATCCTAGATCTTCAATTTCTTTATCCTTG
*
1367431 AAATATGTAAACAAACATCCATAGGTATTTGATTTCATTAAGATGATACACCACTTAGAATTTGA
66 AAATATGTAAACAAACATCCATAGGTATTTGATTTCATTAAGATGACACACCACTTAGAATTTGA
1367496 TGTACAAGTTGCCAC
131 TGTACAAGTTGCCAC
* *
1367511 TTAGAAAATTGACTTCTGAGCATTCTTTATAAAATCATTCTAGATCTTCAGTTTCTTTATCCTTG
1 TTAGAAAATTGACTTCTGAGCATTCTTTATAAAATCATCCTAGATCTTCAATTTCTTTATCCTTG
* * * ** * * *
1367576 AAATATGTAAGCAAATATTCATAGGTATTTGATTTCATTAAGATGACATGCCCCTTAGACTTTGG
66 AAATATGTAAACAAACATCCATAGGTATTTGATTTCATTAAGATGACACACCACTTAGAATTTGA
*
1367641 TGTATAAGTTG
131 TGTACAAGTTG
1367652 TCAAAGCTTT
Statistics
Matches: 129, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
145 129 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (145 bp):
TTAGAAAATTGACTTCTGAGCATTCTTTATAAAATCATCCTAGATCTTCAATTTCTTTATCCTTG
AAATATGTAAACAAACATCCATAGGTATTTGATTTCATTAAGATGACACACCACTTAGAATTTGA
TGTACAAGTTGCCAC
Found at i:1370157 original size:2 final size:2
Alignment explanation
Indices: 1370150--1370183 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1370140 CAGTATCTTA
1370150 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
1370184 TATCATCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1382178 original size:21 final size:21
Alignment explanation
Indices: 1382152--1382205 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
1382142 GTTTCCAGAT
*
1382152 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
1382173 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
1382194 TCGCAATGCGAA
1 TCGCAATGCGAA
1382206 TATGTAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:1382809 original size:21 final size:21
Alignment explanation
Indices: 1382783--1382832 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
1382773 TACATATTCA
1382783 CATTGCGATAGTCGAAGTTCG
1 CATTGCGATAGTCGAAGTTCG
1382804 CATTGCGATAGTCGAAGTTCG
1 CATTGCGATAGTCGAAGTTCG
*
1382825 CGTTGCGA
1 CATTGCGA
1382833 ATCTGAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (21 bp):
CATTGCGATAGTCGAAGTTCG
Found at i:1385652 original size:19 final size:19
Alignment explanation
Indices: 1385628--1385669 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1385618 GACGATGTAA
*
1385628 AAATATGATAAA-TATAAAT
1 AAATAT-ATAAAGTAAAAAT
1385647 AAATATATAAAGTAAAAAT
1 AAATATATAAAGTAAAAAT
1385666 AAAT
1 AAAT
1385670 TAATTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
AAATATATAAAGTAAAAAT
Found at i:1385686 original size:24 final size:23
Alignment explanation
Indices: 1385635--1385700 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
1385625 TAAAAATATG
*
1385635 ATAAATATAAATAAATATATAAA
1 ATAAAAATAAATAAATATATAAA
* * *
1385658 GTAAAAATAAATTAATTTAATAAA
1 ATAAAAATAAATAAATAT-ATAAA
*
1385682 ATAAAAATTATATAAATAT
1 ATAAAAA-TAAATAAATAT
1385701 TTTTATAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
23 14 0.42
24 11 0.33
25 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
ATAAAAATAAATAAATATATAAA
Found at i:1389384 original size:19 final size:20
Alignment explanation
Indices: 1389360--1389406 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
1389350 ATAACAAACA
1389360 AATTCGCAACGCG-ATTTCG
1 AATTCGCAACGCGAATTTCG
* *
1389379 AATTCGCGACGCGAATTTCT
1 AATTCGCAACGCGAATTTCG
1389399 AATTCGCA
1 AATTCGCA
1389407 CAACACGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (20 bp):
AATTCGCAACGCGAATTTCG
Found at i:1389943 original size:20 final size:20
Alignment explanation
Indices: 1389920--1389965 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1389910 ATTCGCGGTT
1389920 CGAATTAGGAATTAACGTCG
1 CGAATTAGGAATTAACGTCG
*
1389940 CGAATTAGGAATTAGCGTCG
1 CGAATTAGGAATTAACGTCG
1389960 CGAATT
1 CGAATT
1389966 CGAAATCGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (20 bp):
CGAATTAGGAATTAACGTCG
Found at i:1391532 original size:29 final size:29
Alignment explanation
Indices: 1391447--1391532 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 29
1391437 ATGTTCTTGG
** * * *
1391447 GGTAGGTCGCCATGCAGTCCCGGATGCCCT
1 GGTAGGTCGCCATGCACACCC-GACGACAT
* * ** *
1391477 GGTAGGTCGCTATGCACGCTGGGCGACAT
1 GGTAGGTCGCCATGCACACCCGACGACAT
1391506 GGTAGGTCGCCATGCACACCCGACGAC
1 GGTAGGTCGCCATGCACACCCGACGAC
1391533 CAAGCTTTAA
Statistics
Matches: 42, Mismatches: 14, Indels: 1
0.74 0.25 0.02
Matches are distributed among these distances:
29 26 0.62
30 16 0.38
ACGTcount: A:0.17, C:0.31, G:0.34, T:0.17
Consensus pattern (29 bp):
GGTAGGTCGCCATGCACACCCGACGACAT
Found at i:1391984 original size:21 final size:21
Alignment explanation
Indices: 1391955--1391998 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1391945 AATTTAGTTA
*
1391955 ATTATTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1391976 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1391997 AT
1 AT
1391999 ATATTATATT
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:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1394386 original size:49 final size:49
Alignment explanation
Indices: 1394269--1394537 Score: 374
Period size: 49 Copynumber: 5.6 Consensus size: 49
1394259 TTTGATTTAG
* * * *
1394269 TAATGATTTGATAATCATGATT--TAATAATGAATTTA-TATTTAAAATT
1 TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTA-TTAATATT
* *
1394316 ATAATAATTAT-TTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1 -TAATGATT-TGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1394366 TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1394415 TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
*
1394464 TAATGATTTG---GTAATGATTAGTAATAATTAAATTATTATTAATATT
1 TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
*
1394510 TGATGATTTGATAGTAAT-ATTTAGTAAT
1 TAATGATTTGATAGTAATGA-TTAGTAAT
1394538 TGTTAGTAAT
Statistics
Matches: 202, Mismatches: 10, Indels: 17
0.88 0.04 0.07
Matches are distributed among these distances:
46 44 0.22
48 18 0.09
49 118 0.58
50 20 0.10
51 2 0.01
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.46
Consensus pattern (49 bp):
TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
Found at i:1394517 original size:95 final size:96
Alignment explanation
Indices: 1394328--1394537 Score: 361
Period size: 95 Copynumber: 2.2 Consensus size: 96
1394318 AATAATTATT
1394328 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTG--AGTAATGATTAGTAA
1394393 TAATGAAATTATTATTAATATTTAATGATTTGA
64 TAATGAAATTATTATTAATATTTAATGATTTGA
1394426 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTG-GTAATGATTAGTAATA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGAGTAATGATTAGTAATA
* *
1394490 ATTAAATTATTATTAATATTTGATGATTTGA
66 ATGAAATTATTATTAATATTTAATGATTTGA
1394521 TAGTAAT-ATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
1394538 TGTTAGTAAT
Statistics
Matches: 109, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
94 1 0.01
95 60 0.55
98 48 0.44
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (96 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGAGTAATGATTAGTAATA
ATGAAATTATTATTAATATTTAATGATTTGA
Found at i:1394766 original size:12 final size:11
Alignment explanation
Indices: 1394744--1394965 Score: 93
Period size: 12 Copynumber: 19.1 Consensus size: 11
1394734 TAACCGTAAA
1394744 AATGATTTAAT
1 AATGATTTAAT
1394755 AATGATTT--T
1 AATGATTTAAT
1394764 AAT-A-TT--T
1 AATGATTTAAT
*
1394771 AATGATTTGAT
1 AATGATTTAAT
*
1394782 -A--ATTTAGT
1 AATGATTTAAT
1394790 AATGATTTGATAAT
1 AATGA-TT--TAAT
*
1394804 AATCATTATAAT
1 AATGATT-TAAT
1394816 AATGATTTAGTAAT
1 AATGA-TT--TAAT
*
1394830 AATCATTATAAT
1 AATGATT-TAAT
*
1394842 AGTGATTTAAT
1 AATGATTTAAT
* *
1394853 AATAATGATAAT
1 AATGAT-TTAAT
1394865 AATGATTTAATAAT
1 AATGA-TT--TAAT
*
1394879 AATCATTATAAT
1 AATGATT-TAAT
1394891 AATGATTTAATAAT
1 AATGA-TT--TAAT
*
1394905 AATCATTATAAT
1 AATGATT-TAAT
1394917 AATGATTTAATAAT
1 AATGA-TT--TAAT
*
1394931 AATGATTTAGT
1 AATGATTTAAT
*
1394942 AATGATTTGAT
1 AATGATTTAAT
1394953 AATGATTTTAAT
1 AATGA-TTTAAT
1394965 A
1 A
1394966 TTTAATGATT
Statistics
Matches: 167, Mismatches: 23, Indels: 41
0.72 0.10 0.18
Matches are distributed among these distances:
7 6 0.04
8 7 0.04
9 7 0.04
10 1 0.01
11 35 0.21
12 52 0.31
13 17 0.10
14 42 0.25
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (11 bp):
AATGATTTAAT
Found at i:1394786 original size:16 final size:17
Alignment explanation
Indices: 1394753--1394803 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
1394743 AAATGATTTA
1394753 ATAATGATTT--TAATAT
1 ATAATGATTTGATAAT-T
*
1394769 TTAATGATTTGATAATTT
1 ATAATGATTTGATAA-TT
1394787 AGTAATGATTTGATAAT
1 A-TAATGATTTGATAAT
1394804 AATCATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 9 0.31
18 5 0.17
19 15 0.52
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (17 bp):
ATAATGATTTGATAATT
Found at i:1394818 original size:26 final size:26
Alignment explanation
Indices: 1394789--1394955 Score: 243
Period size: 26 Copynumber: 6.6 Consensus size: 26
1394779 GATAATTTAG
*
1394789 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
*
1394815 TAATGATTTAGTAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
* *
1394841 TAGTGATTTAATAAT-A--ATGATAA
1 TAATGATTTAATAATAATCATTATAA
1394864 TAATGATTTAATAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
1394890 TAATGATTTAATAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAA
* *
1394916 TAATGATTTAATAATAATGATT-TAG
1 TAATGATTTAATAATAATCATTATAA
*
1394941 TAATGATTTGATAAT
1 TAATGATTTAATAAT
1394956 GATTTTAATA
Statistics
Matches: 128, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
23 20 0.16
24 1 0.01
25 17 0.13
26 90 0.70
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (26 bp):
TAATGATTTAATAATAATCATTATAA
Found at i:1394857 original size:3 final size:3
Alignment explanation
Indices: 1394849--1394933 Score: 50
Period size: 3 Copynumber: 29.3 Consensus size: 3
1394839 AATAGTGATT
* * * * * *
1394849 TAA TAA TAA TGA TAA TAA TGA T-T TAA TAA TAA TCA TTA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
1394896 T-T TAA TAA TAA TCA TTA TAA TAA TGA T-T TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1394934 GATTTAGTAA
Statistics
Matches: 62, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
2 3 0.05
3 59 0.95
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:1394868 original size:75 final size:76
Alignment explanation
Indices: 1394789--1394955 Score: 282
Period size: 75 Copynumber: 2.2 Consensus size: 76
1394779 GATAATTTAG
* *
1394789 TAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAGTGATTTAATA
1 TAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATCATTATAATAATGATTTAATA
1394854 ATAATGA-TAA
66 ATAATGATTAA
*
1394864 TAATGATTTAATAATAATCATTATAATAATGATTTAATAATAATCATTATAATAATGATTTAATA
1 TAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATCATTATAATAATGATTTAATA
*
1394929 ATAATGATTTAG
66 ATAATGA-TTAA
1394941 TAATGATTTGATAAT
1 TAATGATTTGATAAT
1394956 GATTTTAATA
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
75 69 0.81
77 16 0.19
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (76 bp):
TAATGATTTGATAATAATCATTATAATAATGATTTAATAATAATCATTATAATAATGATTTAATA
ATAATGATTAA
Found at i:1394976 original size:52 final size:52
Alignment explanation
Indices: 1394789--1394955 Score: 243
Period size: 49 Copynumber: 3.3 Consensus size: 52
1394779 GATAATTTAG
* *
1394789 TAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAATAATGATTTAATAATAATCATTATAA
* *
1394841 TAGTGATTTAATAAT-A--ATGATAATAATGATTTAATAATAATCATTATAA
1 TAATGATTTAATAATAATCATTATAATAATGATTTAATAATAATCATTATAA
* *
1394890 TAATGATTTAATAATAATCATTATAATAATGATTTAATAATAATGATT-TAG
1 TAATGATTTAATAATAATCATTATAATAATGATTTAATAATAATCATTATAA
*
1394941 TAATGATTTGATAAT
1 TAATGATTTAATAAT
1394956 GATTTTAATA
Statistics
Matches: 103, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
49 45 0.44
50 1 0.01
51 17 0.17
52 40 0.39
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (52 bp):
TAATGATTTAATAATAATCATTATAATAATGATTTAATAATAATCATTATAA
Found at i:1394994 original size:11 final size:10
Alignment explanation
Indices: 1394930--1394996 Score: 65
Period size: 11 Copynumber: 7.0 Consensus size: 10
1394920 GATTTAATAA
1394930 TAATGATTTAG
1 TAATGATTT-G
1394941 TAATGATTTG
1 TAATGATTTG
1394951 ATAATGATTT-
1 -TAATGATTTG
1394961 TAAT-A-TT-
1 TAATGATTTG
1394968 TAATGATTTG
1 TAATGATTTG
1394978 --ATGATTTAG
1 TAATGATTT-G
1394987 TAATGATTTG
1 TAATGATTTG
1394997 ATACCATGTC
Statistics
Matches: 49, Mismatches: 0, Indels: 15
0.77 0.00 0.23
Matches are distributed among these distances:
7 6 0.12
8 9 0.18
9 7 0.14
10 2 0.04
11 25 0.51
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.49
Consensus pattern (10 bp):
TAATGATTTG
Found at i:1395047 original size:29 final size:29
Alignment explanation
Indices: 1394998--1395057 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
1394988 AATGATTTGA
*
1394998 TACCATGTCGCCTAGCATGCATGGCGACC
1 TACCATGTCGCCCAGCATGCATGGCGACC
*
1395027 TACCATGTCGCCCAGCGTGCATGGCGACC
1 TACCATGTCGCCCAGCATGCATGGCGACC
1395056 TA
1 TA
1395058 GCCTTTCTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (29 bp):
TACCATGTCGCCCAGCATGCATGGCGACC
Found at i:1395131 original size:23 final size:23
Alignment explanation
Indices: 1395067--1395131 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
1395057 AGCCTTTCTC
*
1395067 GCTCGCTCGGATGCCCTCACATA
1 GCTCGCTCGGATGCCCTCGCATA
* *
1395090 GCTCGCTCAGATGCCCTCGTATA
1 GCTCGCTCGGATGCCCTCGCATA
* *
1395113 GCTCGCTTGGATGGCCTCG
1 GCTCGCTCGGATGCCCTCG
1395132 GATGCCCAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.14, C:0.35, G:0.26, T:0.25
Consensus pattern (23 bp):
GCTCGCTCGGATGCCCTCGCATA
Found at i:1395594 original size:30 final size:30
Alignment explanation
Indices: 1395558--1395623 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
1395548 TGTTGCTCCA
* *
1395558 GAGGTCGTCGTGTGCTCTTGGAGACCTATG
1 GAGGTCGCCATGTGCTCTTGGAGACCTATG
1395588 GAGGTCGCCATGTGCTCTTGGAGACCTATG
1 GAGGTCGCCATGTGCTCTTGGAGACCTATG
*
1395618 GTGGTC
1 GAGGTC
1395624 ATTGTAACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.14, C:0.21, G:0.36, T:0.29
Consensus pattern (30 bp):
GAGGTCGCCATGTGCTCTTGGAGACCTATG
Found at i:1402257 original size:3 final size:3
Alignment explanation
Indices: 1402246--1402318 Score: 137
Period size: 3 Copynumber: 24.0 Consensus size: 3
1402236 CAGATTGTTG
1402246 TTA TGTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1402292 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1402319 GTGATTTATA
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 66 0.96
4 3 0.04
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1402657 original size:16 final size:16
Alignment explanation
Indices: 1402638--1402668 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1402628 AAGACATTTG
*
1402638 TTGCAAAATGTGTTTC
1 TTGCAAAACGTGTTTC
1402654 TTGCAAAACGTGTTT
1 TTGCAAAACGTGTTT
1402669 TTATAAAACG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (16 bp):
TTGCAAAACGTGTTTC
Found at i:1409305 original size:24 final size:24
Alignment explanation
Indices: 1409267--1409331 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
1409257 ACGAGTTTGT
*
1409267 GTCCGAATTTTGCGATGCTAATTC
1 GTCCGAATTTCGCGATGCTAATTC
* **
1409291 GTTCGAATTTCGCGATATTAATTC
1 GTCCGAATTTCGCGATGCTAATTC
1409315 GTCCGAATTTCGCGATG
1 GTCCGAATTTCGCGATG
1409332 TTTCATAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (24 bp):
GTCCGAATTTCGCGATGCTAATTC
Found at i:1418755 original size:60 final size:60
Alignment explanation
Indices: 1418625--1418748 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
1418615 AAATTATTAT
* * * * *
1418625 TTTGCAACTTTTAATAGTTGACTGACTCAACAAAACAACTCCTTATAGTCGATTGATCAA
1 TTTGTAACTTTTAATAGTTAACGGACTCAACAAAACAACTCCTTATAGTCGATGGAACAA
* * * *
1418685 TTTGTAACTTTTAATAGTTAAGGGACTCAATAAAACAA-TATCTTATAGTC-ATGGAACCA
1 TTTGTAACTTTTAATAGTTAACGGACTCAACAAAACAACT-CCTTATAGTCGATGGAACAA
1418744 TTTGT
1 TTTGT
1418749 GTACTTTACC
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
59 12 0.22
60 42 0.78
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (60 bp):
TTTGTAACTTTTAATAGTTAACGGACTCAACAAAACAACTCCTTATAGTCGATGGAACAA
Found at i:1424648 original size:2 final size:2
Alignment explanation
Indices: 1424641--1424666 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1424631 CTTTCACAAC
1424641 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
1424667 GGAACCCTCA
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):
TA
Found at i:1426353 original size:2 final size:2
Alignment explanation
Indices: 1426346--1426388 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1426336 CCTAAGGGGA
1426346 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
1426388 A
1 A
1426389 ATTTGATTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1427451 original size:23 final size:23
Alignment explanation
Indices: 1427404--1427455 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1427394 TCAATTTTAT
* * *
1427404 TATAATATTCTCTCTTGATTTTC
1 TATAATATTCTCTCTTAAATGTC
1427427 TATAATATTCTCTCTTAAATGTC
1 TATAATATTCTCTCTTAAATGTC
1427450 TATAAT
1 TATAAT
1427456 TAAATTATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.04, T:0.52
Consensus pattern (23 bp):
TATAATATTCTCTCTTAAATGTC
Found at i:1427949 original size:60 final size:59
Alignment explanation
Indices: 1427873--1427991 Score: 145
Period size: 60 Copynumber: 2.0 Consensus size: 59
1427863 CACAAATGGT
* *
1427873 CCCTGATTATAAGACATTGTCTTAT-T-GAGTCC-CATGATTATTAAAAGTTATAAAATGATC
1 CCCTAATTATAAGACATTG-CTT-TGTGGAGTCCTCA--ACTATTAAAAGTTATAAAATGATC
*
1427933 CCCTAATTATAGGACATTGCTTTGTGGAGTCCTTCAACTATTAAAAGTTATAAAATGAT
1 CCCTAATTATAAGACATTGCTTTGTGGAGTCC-TCAACTATTAAAAGTTATAAAATGAT
1427992 TACTCGACTA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
58 1 0.02
59 4 0.08
60 45 0.87
62 2 0.04
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (59 bp):
CCCTAATTATAAGACATTGCTTTGTGGAGTCCTCAACTATTAAAAGTTATAAAATGATC
Found at i:1430841 original size:2 final size:2
Alignment explanation
Indices: 1430836--1430864 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1430826 GTGTGAATGA
1430836 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 A
1430865 AAATTTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1433393 original size:21 final size:22
Alignment explanation
Indices: 1433352--1433401 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
1433342 TCATTTGGAT
1433352 AAAAT-ATTTTAAGTGTGTTTA
1 AAAATAATTTTAAGTGTGTTTA
1433373 AAAATAATTTTAAAGT-T-TTTA
1 AAAATAATTTT-AAGTGTGTTTA
1433394 AAATATAA
1 AAA-ATAA
1433402 AAGTATTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 12 0.46
22 10 0.38
23 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (22 bp):
AAAATAATTTTAAGTGTGTTTA
Found at i:1436852 original size:23 final size:23
Alignment explanation
Indices: 1436818--1436990 Score: 213
Period size: 23 Copynumber: 7.5 Consensus size: 23
1436808 TATACGAATT
* *
1436818 GAAGAAGGAGAAATGGGTTTATG
1 GAAGAAGAAGAAATGTGTTTATG
*
1436841 GAAGAAAAAGAAATGTGTTTATG
1 GAAGAAGAAGAAATGTGTTTATG
*
1436864 GAAGAAAAAAGAAATGTGTTTATG
1 GAAG-AAGAAGAAATGTGTTTATG
* *
1436888 GAAGAAGAAGAAACGAGTTTATG
1 GAAGAAGAAGAAATGTGTTTATG
* * *
1436911 AAAGAAGAAGCAATGGGTTTATG
1 GAAGAAGAAGAAATGTGTTTATG
* *
1436934 GAATAAGAAGAAA-ATGTTTATG
1 GAAGAAGAAGAAATGTGTTTATG
**
1436956 GAAGAAGAAGAAACATGTTTATG
1 GAAGAAGAAGAAATGTGTTTATG
1436979 GAAGAAGAAGAA
1 GAAGAAGAAGAA
1436991 TGGTTCATAA
Statistics
Matches: 132, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
22 19 0.14
23 90 0.68
24 23 0.17
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (23 bp):
GAAGAAGAAGAAATGTGTTTATG
Found at i:1436977 original size:68 final size:69
Alignment explanation
Indices: 1436818--1436993 Score: 223
Period size: 70 Copynumber: 2.6 Consensus size: 69
1436808 TATACGAATT
* * * * * *
1436818 GAAGAAGGAGAAATGGGTTTATGGAAGAAAAAGAAATGTGTTTATGGAAGAAAAAAGAAATGTGT
1 GAAGAAGAAGAAACGAGTTTATGGAAGAAGAAG-AATGGGTTTATGGAAGAAAAAAGAAATATGT
1436883 TTATG
65 TTATG
* * *
1436888 GAAGAAGAAGAAACGAGTTTATGAAAGAAGAAGCAATGGGTTTATGGAA-TAAGAAGAAA-ATGT
1 GAAGAAGAAGAAACGAGTTTATGGAAGAAGAAG-AATGGGTTTATGGAAGAAAAAAGAAATATGT
1436951 TTATG
65 TTATG
1436956 GAAGAAGAAGAAAC-ATGTTTATGGAAGAAGAAGAATGG
1 GAAGAAGAAGAAACGA-GTTTATGGAAGAAGAAGAATGG
1436994 TTCATAATGG
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
67 6 0.06
68 38 0.40
69 8 0.09
70 42 0.45
ACGTcount: A:0.47, C:0.02, G:0.30, T:0.22
Consensus pattern (69 bp):
GAAGAAGAAGAAACGAGTTTATGGAAGAAGAAGAATGGGTTTATGGAAGAAAAAAGAAATATGTT
TATG
Found at i:1439270 original size:22 final size:24
Alignment explanation
Indices: 1439240--1439288 Score: 75
Period size: 22 Copynumber: 2.1 Consensus size: 24
1439230 ATGCGTATAT
1439240 AAATATTAAAATT-TT-TTATTTA
1 AAATATTAAAATTATTATTATTTA
*
1439262 AAATTTTAAAATTATTATTATTTA
1 AAATATTAAAATTATTATTATTTA
1439286 AAA
1 AAA
1439289 AACATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 12 0.50
23 2 0.08
24 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATATTAAAATTATTATTATTTA
Found at i:1439279 original size:21 final size:22
Alignment explanation
Indices: 1439240--1439288 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
1439230 ATGCGTATAT
*
1439240 AAATATTAAAATTTTTTATTTA
1 AAATATTAAAATTTATTATTTA
*
1439262 AAATTTTAAAATTATTATTATTTA
1 AAATATTAAAA-T-TTATTATTTA
1439286 AAA
1 AAA
1439289 AACATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 1 0.04
24 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATATTAAAATTTATTATTTA
Found at i:1441195 original size:24 final size:25
Alignment explanation
Indices: 1441167--1441215 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1441157 AAATTGAAAA
*
1441167 AAATAATCTTGTAA-TATTTATTTT
1 AAATAAACTTGTAATTATTTATTTT
* *
1441191 AAATAAACTTTTAATTTTTTATTTT
1 AAATAAACTTGTAATTATTTATTTT
1441216 TGATTATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (25 bp):
AAATAAACTTGTAATTATTTATTTT
Found at i:1443442 original size:60 final size:60
Alignment explanation
Indices: 1443301--1443458 Score: 172
Period size: 60 Copynumber: 2.6 Consensus size: 60
1443291 TATGTCTTTG
* * * * *
1443301 AACTATGATCCTCATTTTAAATTAGTTCTTAGACTTTTAAATATTTTAATTTCATCCCCA
1 AACTATGACCCTCATTTTAAATTAGTCCTTAAACTTTTAAATATTCTAATTTAATCCCCA
** * ** * *
1443361 AACTATGACTTTTATTTTAAATTAGTCCTTAAACTTTTTCATATTCTAGTTTAATCCTCA
1 AACTATGACCCTCATTTTAAATTAGTCCTTAAACTTTTAAATATTCTAATTTAATCCCCA
* * * *
1443421 AACTATGGCCCTCATTCTAAATTGGTCCCTAAACTTTT
1 AACTATGACCCTCATTTTAAATTAGTCCTTAAACTTTT
1443459 GATTCTTTCA
Statistics
Matches: 79, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 79 1.00
ACGTcount: A:0.30, C:0.20, G:0.06, T:0.44
Consensus pattern (60 bp):
AACTATGACCCTCATTTTAAATTAGTCCTTAAACTTTTAAATATTCTAATTTAATCCCCA
Found at i:1443725 original size:60 final size:60
Alignment explanation
Indices: 1443613--1443772 Score: 164
Period size: 60 Copynumber: 2.6 Consensus size: 60
1443603 ACATGGTTTA
* * * * * ** *
1443613 GATGAAATTGAAATGTTCAAAAAATTTGGGGACCAATTTAGAATGAAGGTCATAGTTTAAT
1 GATGAAATTAAAATGTTC-TAAAGTTTGAGGACTAATTTAGAATGAAGGTCATAACTTAAG
* *
1443674 GATGAAAATAAAATGTTCTAAAGTTTGAGGACTAATTTAGAATGATA-GTCATAACTTAGG
1 GATGAAATTAAAATGTTCTAAAGTTTGAGGACTAATTTAGAATGA-AGGTCATAACTTAAG
*
1443734 GATGAAGTTAAAATGTT-TAAAAGTTT-AGAGACTAATTTA
1 GATGAAATTAAAATGTTCT-AAAGTTTGAG-GACTAATTTA
1443773 ATGACATATG
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
59 3 0.04
60 64 0.76
61 17 0.20
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.33
Consensus pattern (60 bp):
GATGAAATTAAAATGTTCTAAAGTTTGAGGACTAATTTAGAATGAAGGTCATAACTTAAG
Found at i:1446616 original size:28 final size:29
Alignment explanation
Indices: 1446581--1446648 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 29
1446571 TTATTCTATA
* * *
1446581 TAGGGTTTTAAAGTTTAAGATT-TAAATT
1 TAGGGTTTTAAAGCTTAAGATTGAAAACT
*
1446609 TAGGG-TTTAAAGCTTATGATTGAAAACT
1 TAGGGTTTTAAAGCTTAAGATTGAAAACT
*
1446637 TAAGGTTTTAAA
1 TAGGGTTTTAAA
1446649 CACAACAACA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 14 0.42
28 13 0.39
29 6 0.18
ACGTcount: A:0.37, C:0.03, G:0.19, T:0.41
Consensus pattern (29 bp):
TAGGGTTTTAAAGCTTAAGATTGAAAACT
Found at i:1446848 original size:43 final size:43
Alignment explanation
Indices: 1446800--1447008 Score: 316
Period size: 43 Copynumber: 4.9 Consensus size: 43
1446790 TGATAACAAA
* * *
1446800 AAACGCCGCAAAAGGTCGAGATATATAGCGACATTTTTGAAAC
1 AAACGCCGCAAAAGGTCGAGATATATAGCGGCGTTTTTGGAAC
* *
1446843 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATC
1 AAACGCCGCAAAAGGTCGAGATATATAGCGGCGTTTTTGGAAC
*
1446886 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCG-TTTTGGAAC
1 AAACGCCGCAAAAGGTCGAGATATATAGCGGCGTTTTTGGAAC
*
1446928 AAACGCCGCTAAAA-GTCGAGATTTATAGCGGCGTTTTTGGAAC
1 AAACGCCGC-AAAAGGTCGAGATATATAGCGGCGTTTTTGGAAC
1446971 AAACGCCGCAAAAGGTCGAGA-ATTATAGCGGCGTTTTT
1 AAACGCCGCAAAAGGTCGAGATA-TATAGCGGCGTTTTT
1447009 TATACAAACG
Statistics
Matches: 154, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
42 39 0.25
43 115 0.75
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGAGATATATAGCGGCGTTTTTGGAAC
Found at i:1446959 original size:85 final size:84
Alignment explanation
Indices: 1446800--1447007 Score: 319
Period size: 85 Copynumber: 2.4 Consensus size: 84
1446790 TGATAACAAA
* *
1446800 AAACGCCGCAAAAGGTCGAGATATATAGCGACATTTTTGAAACAAACGCCGCAAAAGGTCGAGAT
1 AAACGCCGCAAAAGGTCGAGAT-TATAGCGGC-GTTTTGAAACAAACGCCGCAAAAGGTCGAGAT
*
1446865 CTATAGCGGCGTTTTTGGATC
64 CTATAGCGGCGTTTTTGGAAC
*
1446886 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTGGAACAAACGCCGCTAAAA-GTCGAGAT
1 AAACGCCGCAAAAGGTCGAGAT-TATAGCGGCGTTTTGAAACAAACGCCGC-AAAAGGTCGAGAT
*
1446950 TTATAGCGGCGTTTTTGGAAC
64 CTATAGCGGCGTTTTTGGAAC
1446971 AAACGCCGCAAAAGGTCGAGAATTATAGCGGCGTTTT
1 AAACGCCGCAAAAGGTCGAG-ATTATAGCGGCGTTTT
1447008 TTATACAAAC
Statistics
Matches: 114, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
85 78 0.68
86 36 0.32
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (84 bp):
AAACGCCGCAAAAGGTCGAGATTATAGCGGCGTTTTGAAACAAACGCCGCAAAAGGTCGAGATCT
ATAGCGGCGTTTTTGGAAC
Found at i:1447166 original size:21 final size:21
Alignment explanation
Indices: 1447142--1447202 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
1447132 TAATTAAGAC
1447142 ACAAACTTGAAATCCATAACA
1 ACAAACTTGAAATCCATAACA
1447163 ACAAACTTGAAATCCATAACA
1 ACAAACTTGAAATCCATAACA
*
1447184 AGAAACTTGAAATCCATAA
1 ACAAACTTGAAATCCATAA
1447203 TAATAAATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.20
Consensus pattern (21 bp):
ACAAACTTGAAATCCATAACA
Found at i:1451159 original size:42 final size:43
Alignment explanation
Indices: 1451053--1451167 Score: 139
Period size: 42 Copynumber: 2.7 Consensus size: 43
1451043 AATGGTTAAA
* * **
1451053 CGCCAATAAAGTACTAGGTTTTAGCGGCG--TTTGTCTAAAAT
1 CGCCACTAAAGTATTAGGTTTTAGCGGCGTTTTTGAATAAAAT
* *
1451094 CGTCACTAAAGTATGA-GTATTTAGCGGCGTTTTTGAATAAAAT
1 CGCCACTAAAGTATTAGGT-TTTAGCGGCGTTTTTGAATAAAAT
1451137 -GCCACTAAAGTATTAGGTTTTAGCGGCGTTT
1 CGCCACTAAAGTATTAGGTTTTAGCGGCGTTT
1451168 ATTTAAAAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
40 2 0.03
41 22 0.35
42 26 0.42
43 12 0.19
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34
Consensus pattern (43 bp):
CGCCACTAAAGTATTAGGTTTTAGCGGCGTTTTTGAATAAAAT
Found at i:1451327 original size:41 final size:41
Alignment explanation
Indices: 1451050--1451385 Score: 179
Period size: 41 Copynumber: 8.2 Consensus size: 41
1451040 GTTAATGGTT
* * *
1451050 AAACGCCAATAAAGTACTAGGT-TTTAGCGGCGTTTGTCTAA
1 AAACGCCACTAAAGTATTA-GTCTTTAGCGGCGTTTGTTTAA
* * * * *
1451091 AATCGTCACTAAAGTATGAGTATTTAGCGGCGTTT-TTGAATA
1 AAACGCCACTAAAGTATTAGTCTTTAGCGGCGTTTGTT-TA-A
* *
1451133 AAATGCCACTAAAGTATTAGGT-TTTAGCGGCGTTTATTTAA
1 AAACGCCACTAAAGTATTA-GTCTTTAGCGGCGTTTGTTTAA
* * * * ** *
1451174 AAACACAACGATA-TATATACCCTATTA-CGGAGTTTGTTTAA
1 AAACGCCACTAAAGTAT-TAGTCT-TTAGCGGCGTTTGTTTAA
* ** * * * * *
1451215 AAACGCCACTAAAGAACGATTCTATGGCGGCGTTTATCTAA
1 AAACGCCACTAAAGTATTAGTCTTTAGCGGCGTTTGTTTAA
* **
1451256 AAATGCCAC-AATA-TATGTACCCTATT-GCGGCGTTTGTTTAA
1 AAACGCCACTAA-AGTAT-TAGTCT-TTAGCGGCGTTTGTTTAA
* **
1451297 AAACGCCACTAAAGTACTTA-TCTTTAGCGGCGCTTGTCGAA
1 AAACGCCACTAAAGTA-TTAGTCTTTAGCGGCGTTTGTTTAA
* ** * *
1451338 TAAATGCCACTAAAGTACGAGT-TTAAGCGGCGTTTGTTGAA
1 -AAACGCCACTAAAGTATTAGTCTTTAGCGGCGTTTGTTTAA
1451379 AAACGCC
1 AAACGCC
1451386 GTTAATGTTA
Statistics
Matches: 220, Mismatches: 56, Indels: 39
0.70 0.18 0.12
Matches are distributed among these distances:
40 18 0.08
41 140 0.64
42 57 0.26
43 5 0.02
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (41 bp):
AAACGCCACTAAAGTATTAGTCTTTAGCGGCGTTTGTTTAA
Found at i:1451327 original size:82 final size:83
Alignment explanation
Indices: 1451132--1451347 Score: 233
Period size: 82 Copynumber: 2.6 Consensus size: 83
1451122 GTTTTTGAAT
* * ** * *
1451132 AAAATGCCACTAAAGTA-TTAGGT-TTTAGCGGCGTTTATTTAAAAACACAACGATATATATACC
1 AAAACGCCACTAAAGTACTTA-GTCTTTAGCGGCGTTTATCTAAAAATGCCACAATATATATACC
1451195 CTATTACGGAGTTTGTTTA
65 CTATTACGGAGTTTGTTTA
* * * * * *
1451214 AAAACGCCACTAAAGAAC-GATTCTATGGCGGCGTTTATCTAAAAATGCCACAATATATGTACCC
1 AAAACGCCACTAAAGTACTTAGTCTTTAGCGGCGTTTATCTAAAAATGCCACAATATATATACCC
* *
1451278 TATTGCGGCGTTTGTTTA
66 TATTACGGAGTTTGTTTA
* * *
1451296 AAAACGCCACTAAAGTACTTA-TCTTTAGCGGCGCTTGTCGAATAAATGCCAC
1 AAAACGCCACTAAAGTACTTAGTCTTTAGCGGCGTTTATCTAA-AAATGCCAC
1451348 TAAAGTACGA
Statistics
Matches: 109, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
81 1 0.01
82 98 0.90
83 10 0.09
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (83 bp):
AAAACGCCACTAAAGTACTTAGTCTTTAGCGGCGTTTATCTAAAAATGCCACAATATATATACCC
TATTACGGAGTTTGTTTA
Found at i:1451732 original size:21 final size:20
Alignment explanation
Indices: 1451646--1451803 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1451636 AAATGACCAA
**
1451646 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1451665 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1451685 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1451705 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1451726 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1451747 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1451767 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1451788 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1451804 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1451819 original size:40 final size:40
Alignment explanation
Indices: 1451770--1451924 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
1451760 CGATTTTCCA
* ** *
1451770 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
1451810 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
1451850 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
1451890 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1451925 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:1451832 original size:20 final size:20
Alignment explanation
Indices: 1451770--1451923 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
1451760 CGATTTTCCA
* ** *
1451770 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1451790 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1451810 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1451830 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1451850 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1451870 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1451890 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1451911 AAATCGCAACGCG
1 AAATCGCAACGCG
1451924 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1452345 original size:33 final size:33
Alignment explanation
Indices: 1452306--1452376 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1452296 TTCACTTAGA
*
1452306 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1452339 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1452372 TTTCA
1 TTTCA
1452377 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1452500 original size:20 final size:20
Alignment explanation
Indices: 1452456--1452565 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
1452446 TGCAGAAGAG
*
1452456 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
1452477 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
1452497 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
1452518 TCGCAACGAGAG-AT-----
1 TCGCAACGAGAGAATGAAAA
*
1452532 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
1452551 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
1452566 CGCAACGCGA
Statistics
Matches: 72, Mismatches: 9, Indels: 17
0.73 0.09 0.17
Matches are distributed among these distances:
14 12 0.17
19 12 0.17
20 20 0.28
21 28 0.39
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:1452513 original size:41 final size:40
Alignment explanation
Indices: 1452455--1452565 Score: 146
Period size: 41 Copynumber: 2.9 Consensus size: 40
1452445 TTGCAGAAGA
*
1452455 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGA-T
1452496 GTCGCAACGAGAGAAATGAAAATCGCAAC--GAG-A-GAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGAT
*
1452532 -TCGCAAC--GCGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1452566 CGCAACGCGA
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
33 18 0.28
35 10 0.16
36 2 0.03
37 2 0.03
38 1 0.02
39 3 0.05
41 28 0.44
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (40 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGAT
Found at i:1452548 original size:33 final size:33
Alignment explanation
Indices: 1452508--1452588 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
1452498 CGCAACGAGA
*
1452508 GAAATGAAAATCGCAACGAGAGATTCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1452541 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1452574 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1452589 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1452568 original size:14 final size:14
Alignment explanation
Indices: 1452516--1452572 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1452506 GAGAAATGAA
1452516 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
1452530 ATTCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1452549 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1452563 AATCGCAACG
1 AATCGCAACG
1452573 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1452606 original size:19 final size:19
Alignment explanation
Indices: 1452584--1452648 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
1452574 GAAACCAAAA
*
1452584 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1452603 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1452617 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1452636 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1452649 CTCTCGTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 22 0.58
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1452625 original size:14 final size:14
Alignment explanation
Indices: 1452606--1452662 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1452596 TTTCATTTCG
1452606 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1452620 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1452639 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1452653 CGTTGCGATT
1 CGTTGCGATT
1452663 TTCATTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1452631 original size:33 final size:33
Alignment explanation
Indices: 1452589--1452670 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
1452579 CAAAATCGCA
1452589 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1452622 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1452655 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1452671 AACCAAAAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1454526 original size:93 final size:93
Alignment explanation
Indices: 1454367--1454649 Score: 541
Period size: 93 Copynumber: 3.1 Consensus size: 93
1454357 TAGATTGCTT
*
1454367 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1454432 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1454460 AGTAAATTTGTTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1454525 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1454553 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1454618 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1454645 AGTAA
1 AGTAA
1454650 TGCAATCCAT
Statistics
Matches: 187, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
92 6 0.03
93 181 0.97
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1454737 original size:19 final size:19
Alignment explanation
Indices: 1454697--1454773 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
1454687 TAGTTTACTT
* *
1454697 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1454717 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1454736 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1454750 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1454769 TCGCA
1 TCGCA
1454774 TTGCGATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
14 10 0.21
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 19 0.40
20 13 0.27
ACGTcount: A:0.45, C:0.30, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1454791 original size:19 final size:19
Alignment explanation
Indices: 1454769--1454889 Score: 135
Period size: 19 Copynumber: 6.6 Consensus size: 19
1454759 GAAACCAAAA
*
1454769 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1454788 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1454807 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1454823 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1454840 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1454859 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1454879 TCGTGTTGCGA
1 TCGCGTTGCGA
1454890 AAGTAAACTA
Statistics
Matches: 86, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
14 7 0.08
16 5 0.06
17 5 0.06
19 57 0.66
20 12 0.14
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1456835 original size:14 final size:14
Alignment explanation
Indices: 1456816--1456851 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1456806 ATTGTTTAAT
1456816 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1456830 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1456844 TGATTTGT
1 TGATTTGT
1456852 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1456982 original size:19 final size:19
Alignment explanation
Indices: 1456958--1457055 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1456948 AAAATTGACT
1456958 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1456977 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1456996 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1457010 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1457029 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1457049 ATCGCAA
1 ATCGCAA
1457056 CGGGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1457087 original size:53 final size:53
Alignment explanation
Indices: 1456958--1457074 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
1456948 AAAATTGACT
1456958 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
1457010 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1457063 ATCGCAATGCGA
1 ATCGCAATGCGA
1457075 TTTTAATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:1457092 original size:19 final size:19
Alignment explanation
Indices: 1457064--1457233 Score: 181
Period size: 19 Copynumber: 9.7 Consensus size: 19
1457054 AACGGGAGAA
* *
1457064 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
1457083 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1457099 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1457116 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1457132 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1457149 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1457168 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1457187 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1457205 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1457221 TCGCATTGCGATT
1 TCGCATTGCGATT
1457234 CTCTCGTTGC
Statistics
Matches: 127, Mismatches: 8, Indels: 32
0.76 0.05 0.19
Matches are distributed among these distances:
14 23 0.18
16 16 0.13
17 14 0.11
18 1 0.01
19 57 0.45
20 16 0.13
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1457107 original size:14 final size:14
Alignment explanation
Indices: 1457088--1457142 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1457078 TAATTTCGCA
1457088 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1457102 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1457119 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1457135 TTGCGATT
1 TTGCGATT
1457143 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1457107 original size:33 final size:33
Alignment explanation
Indices: 1457070--1457247 Score: 250
Period size: 33 Copynumber: 5.2 Consensus size: 33
1457060 AGAATCGCAA
*
1457070 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1457103 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
1457136 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
*
1457174 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
1457208 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1457241 TGCGATT
1 TGCGATT
1457248 GTAATTTTCG
Statistics
Matches: 130, Mismatches: 7, Indels: 16
0.85 0.05 0.10
Matches are distributed among these distances:
32 1 0.01
33 78 0.60
34 14 0.11
35 3 0.02
36 6 0.05
37 3 0.02
38 15 0.12
39 10 0.08
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1457215 original size:72 final size:68
Alignment explanation
Indices: 1457070--1457247 Score: 240
Period size: 72 Copynumber: 2.6 Consensus size: 68
1457060 AGAATCGCAA
*
1457070 TGCGATTTTAATTTCGCATTGCGA--TTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 TGCGATTTTCATTTCGCATTGCGATTTTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1457133 CGT
66 CGT
*
1457136 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTC-TCTCG--TTGCGATTTTCATTT-CGCATTGCGATT
*
1457201 TTCAT-GT
62 CTC-TCGT
*
1457208 TGGGATTTTCATTTCGCATTGCGA--TTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCTCTCGTTGCGATT
1457248 GTAATTTTCG
Statistics
Matches: 100, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
66 23 0.23
67 8 0.08
68 3 0.03
69 8 0.08
70 3 0.03
71 15 0.15
72 39 0.39
73 1 0.01
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (68 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCT
CGT
Found at i:1459496 original size:12 final size:12
Alignment explanation
Indices: 1459479--1459503 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1459469 TCTTCGGGGA
1459479 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1459491 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1459503 C
1 C
1459504 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1459712 original size:24 final size:24
Alignment explanation
Indices: 1459678--1459724 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1459668 CTGAAACATC
1459678 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1459702 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1459725 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1460433 original size:20 final size:20
Alignment explanation
Indices: 1460405--1460634 Score: 246
Period size: 20 Copynumber: 11.5 Consensus size: 20
1460395 AAATTTCAGT
* * *
1460405 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1460425 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1460445 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1460465 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1460485 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1460505 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1460525 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
1460545 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1460565 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1460585 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1460605 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1460625 GTTGCGATTT
1 GTTGCGATTT
1460635 TTGAAAATCG
Statistics
Matches: 184, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 183 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1460645 original size:21 final size:20
Alignment explanation
Indices: 1460601--1460699 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
1460591 ATTTATGTGT
* * *
1460601 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTGAAAA
1460621 TCGCGTTGCGATTTTTGAAAA
1 TCGCGTTGCGA-TTTTGAAAA
** * **
1460642 TCGCAATGCGAATTTGTACTA
1 TCGCGTTGCGATTTTG-AAAA
* *
1460663 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTGAA-AA
1460684 TCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTG
1460700 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTGAAAA
Found at i:1460694 original size:42 final size:43
Alignment explanation
Indices: 1460601--1460699 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1460591 ATTTATGTGT
* *
1460601 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTTCAAAA
**
1460642 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGA-TTTTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTTCAA-AA
*
1460684 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1460700 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 14 0.30
42 30 0.64
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTTCAAAA
Found at i:1462477 original size:3 final size:3
Alignment explanation
Indices: 1462469--1462560 Score: 175
Period size: 3 Copynumber: 30.7 Consensus size: 3
1462459 TTTTTATCCA
1462469 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1462517 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1462561 AATATATTAA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1463132 original size:16 final size:15
Alignment explanation
Indices: 1463102--1463137 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1463092 AATCAGTAGC
*
1463102 AAAGAAACAGAAGAG
1 AAAGAAAAAGAAGAG
1463117 AAAGAAAAAGGAAGAG
1 AAAGAAAAA-GAAGAG
1463133 AAAGA
1 AAAGA
1463138 CTTACCGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.69, C:0.03, G:0.28, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGAAGAG
Found at i:1476761 original size:83 final size:83
Alignment explanation
Indices: 1476534--1477007 Score: 650
Period size: 83 Copynumber: 5.7 Consensus size: 83
1476524 GAACAAATGT
*
1476534 AATGTGCTCATAGCATCTTCTGGAAGTTTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
*
1476599 CATTGAATTTAGAGGATG
66 CATTGAATTTAGAAGATG
* * * * *
1476617 AAGGAGACTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCA
1 AATGTG-C-TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCA
*
1476682 ATCATTGAATTTTGAAGATG
64 ATCATTGAATTTAGAAGATG
* *
1476702 AATGTGCTCATAGCATCCTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
*
1476767 CATTGAATTTGGAAGATG
66 CATTGAATTTAGAAGATG
* * *
1476785 AATTTGC-CAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAA
1 AATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAA
1476849 TCATTGAATTT-GAAAGATG
65 TCATTGAATTTAG-AAGATG
* *
1476868 AATTTGC-CAATAGCATCTTCTGGAGGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCA
1 AATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCA
*
1476931 ATCATTGAATTTAGAGGATG
64 ATCATTGAATTTAGAAGATG
* * * * *
1476951 AAGGAGACTTAATAGTATCTTCTGTAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 AATGTG-C-TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1477008 TAAGAACTAC
Statistics
Matches: 351, Mismatches: 30, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
82 6 0.02
83 225 0.64
84 4 0.01
85 112 0.32
86 4 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (83 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
CATTGAATTTAGAAGATG
Found at i:1476883 original size:166 final size:167
Alignment explanation
Indices: 1476534--1477007 Score: 722
Period size: 166 Copynumber: 2.8 Consensus size: 167
1476524 GAACAAATGT
*
1476534 AATGTGCTCATAGCATCTTCTGGAAGTTTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGGCAGAACCAAT
1476599 CATTGAATTTAGAGGATGAAGGAGACTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
65 CATTGAATTTAGAGGATGAAGGAGACTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
* *
1476664 TCTGGTTAGACAGAACCAATCATTGAATTTTGAAGATG
130 TCTGGTTTGGCAGAACCAATCATTGAATTTTGAAGATG
*
1476702 AATGTGCTCATAGCATCCTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG-TTTGGCAGAACCAAT
* * *** * *
1476767 CATTGAATTTGGAAGATGAATTTG-C-CAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
65 CATTGAATTTAGAGGATGAAGGAGACTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA
*
1476830 TCTGATTTGGCAGAACCAATCATTGAA-TTTGAAAGATG
130 TCTGGTTTGGCAGAACCAATCATTGAATTTTG-AAGATG
* * *
1476868 AATTTGC-CAATAGCATCTTCTGGAGGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
1 AATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGG-CAGAACCAA
* *
1476932 TCATTGAATTTAGAGGATGAAGGAGACTTAATAGTATCTTCTGTAAGTGTTCTTTGAGTTATCTG
64 TCATTGAATTTAGAGGATGAAGGAGACTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1476997 ATCTGGTTTGG
129 ATCTGGTTTGG
1477008 TAAGAACTAC
Statistics
Matches: 274, Mismatches: 26, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
165 9 0.03
166 139 0.51
167 3 0.01
168 123 0.45
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (167 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGGCAGAACCAATC
ATTGAATTTAGAGGATGAAGGAGACTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
CTGGTTTGGCAGAACCAATCATTGAATTTTGAAGATG
Found at i:1477853 original size:113 final size:114
Alignment explanation
Indices: 1477661--1478197 Score: 868
Period size: 113 Copynumber: 4.7 Consensus size: 114
1477651 AATTTATCAT
* *
1477661 TTGATGGATT-GACATTTCAAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATTAG-CTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* *
1477725 AAATTCATAATGAGAAGAATTTGTTCAACCTTCTGCCT-AATTCTATC-AC
65 AAGTTCATAATGAGAAGAATTTGTTCAACCTTCTGCCTGAATTC-ATCAAA
*
1477774 TTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
1477839 AATTCATAATGAGAAGCATTTGTTCAACCTTCTGCCT-AATTCTATC-AC
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTCTGCCTGAATTC-ATCAAA
1477887 TTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* **
1477952 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCAAA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTCTGCCTGAATTCATCAAA
*
1478001 TTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* **
1478066 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCAAA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTCTGCCTGAATTCATCAAA
*
1478115 TTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1478180 AGTTCATAATGAGAAGAA
66 AGTTCATAATGAGAAGAA
1478198 CTCATCTGAA
Statistics
Matches: 409, Mismatches: 12, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
113 206 0.50
114 203 0.50
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (114 bp):
TTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAATTTGTTCAACCTTCTGCCTGAATTCATCAAA
Found at i:1478187 original size:154 final size:153
Alignment explanation
Indices: 1478022--1478350 Score: 561
Period size: 153 Copynumber: 2.1 Consensus size: 153
1478012 TCTTTTCCAG
*
1478022 AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
1 AGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTT
* * * * *
1478087 GTTCAACCTTTT-TTCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATG
65 GTTCAACCTTTTACT-TGAATCCATC-AATTGATGGATCATCATTTCCAGAGAAAGTTCATAATG
1478151 AGAAGAACTCATCTGAAGAAGGAAGA
128 AGAAGAACTCATCTGAAGAAGGAAGA
1478177 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTG
1 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTG
*
1478242 TTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGA
66 TTCAACCTTTTACTTGAATCCATCAATTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGA
1478307 AGAACTCATCTGAAGAAGGAAGA
131 AGAACTCATCTGAAGAAGGAAGA
1478330 AGAAGTTCATAATGAGAAGAA
1 AGAAGTTCATAATGAGAAGAA
1478351 TTTGTTCAAC
Statistics
Matches: 166, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
153 81 0.49
154 80 0.48
155 5 0.03
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (153 bp):
AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTG
TTCAACCTTTTACTTGAATCCATCAATTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGA
AGAACTCATCTGAAGAAGGAAGA
Done.