Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 35
Found at i:1222901 original size:65 final size:63
Alignment explanation
Indices: 1222721--1222904 Score: 180
Period size: 65 Copynumber: 2.8 Consensus size: 63
1222711 CCACCCTTAG
* * *
1222721 TGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCAATGCATGGCTGGTGCATCGATGCATCAA
1 TGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAA
1222784 A
63 A
*
1222785 TGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTAT-GTGCATCGATGCATGAA
1 TGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-TGGTGCATCGATGCATCAA
1222849 A
63 A
* **
1222850 TGCATTTGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGATTGGTGCATCG
1 TGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-TTGGTGCATCG
1222905 GTGCCTCACT
Statistics
Matches: 103, Mismatches: 7, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 33 0.32
65 58 0.56
66 5 0.05
67 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (63 bp):
TGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAA
Found at i:1223165 original size:2 final size:2
Alignment explanation
Indices: 1223158--1223213 Score: 82
Period size: 2 Copynumber: 29.0 Consensus size: 2
1223148 TGTTTTCAAC
1223158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GA- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1223200 A- AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT
1223214 GTTTATGTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.06
2 46 0.92
3 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1223507 original size:18 final size:18
Alignment explanation
Indices: 1223466--1223507 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1223456 CGGTCCTTCA
*
1223466 GGACACAGTGGTCATTCG
1 GGACATAGTGGTCATTCG
1223484 GGACATAGTGGTCATTCG
1 GGACATAGTGGTCATTCG
1223502 GGACAT
1 GGACAT
1223508 TTCATAGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (18 bp):
GGACATAGTGGTCATTCG
Found at i:1227848 original size:18 final size:18
Alignment explanation
Indices: 1227825--1227947 Score: 149
Period size: 18 Copynumber: 6.8 Consensus size: 18
1227815 GGGTCTACGC
1227825 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
* * *
1227843 GGTCCTTCGTGACACATT
1 GGTCCTTCGGGACATAGT
* *
1227861 GGTCCTTCGTGACACAGT
1 GGTCCTTCGGGACATAGT
1227879 GGTCCTTCGGGACACT-GT
1 GGTCCTTCGGGACA-TAGT
*
1227897 GGTCCTTCGGGACACAGT
1 GGTCCTTCGGGACATAGT
* *
1227915 GGTCTTTCGGAACATAGT
1 GGTCCTTCGGGACATAGT
*
1227933 GGTCCTTTGGGACAT
1 GGTCCTTCGGGACAT
1227948 TTCATAGTGG
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
18 90 1.00
ACGTcount: A:0.16, C:0.24, G:0.30, T:0.29
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:1227911 original size:54 final size:54
Alignment explanation
Indices: 1227825--1227947 Score: 169
Period size: 54 Copynumber: 2.3 Consensus size: 54
1227815 GGGTCTACGC
* *
1227825 GGTCCTTCGGGACATAGTGGTCCTTCGTGACACATTGGTCCTTCGTG-ACACAGT
1 GGTCCTTCGGGACATAGTGGTCCTTCGGGACACAGTGGTCCTTCG-GAACACAGT
* *
1227879 GGTCCTTCGGGACACT-GTGGTCCTTCGGGACACAGTGGTCTTTCGGAACATAGT
1 GGTCCTTCGGGACA-TAGTGGTCCTTCGGGACACAGTGGTCCTTCGGAACACAGT
*
1227933 GGTCCTTTGGGACAT
1 GGTCCTTCGGGACAT
1227948 TTCATAGTGG
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
53 2 0.03
54 59 0.95
55 1 0.02
ACGTcount: A:0.16, C:0.24, G:0.30, T:0.29
Consensus pattern (54 bp):
GGTCCTTCGGGACATAGTGGTCCTTCGGGACACAGTGGTCCTTCGGAACACAGT
Found at i:1227957 original size:23 final size:24
Alignment explanation
Indices: 1227927--1227979 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
1227917 TCTTTCGGAA
* *
1227927 CATAGTGGTCCTTTGGGAC-ATTT
1 CATAGTGGTCATTCGGGACAATTT
1227950 CATAGTGGTCATTCGGGACAAATTT
1 CATAGTGGTCATTCGGGAC-AATTT
1227975 CATAG
1 CATAG
1227980 CCCCTAGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 17 0.65
25 9 0.35
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (24 bp):
CATAGTGGTCATTCGGGACAATTT
Found at i:1228273 original size:18 final size:18
Alignment explanation
Indices: 1228250--1228307 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
1228240 ATATTGATAG
*
1228250 TAAATGAGTCATGTTGAT
1 TAAATGAGTCATGTTGGT
1228268 TAAATGAGTCATGTTGGT
1 TAAATGAGTCATGTTGGT
1228286 TAAATGAGTCATGTTGGT
1 TAAATGAGTCATGTTGGT
1228304 TAAA
1 TAAA
1228308 ATAATTATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (18 bp):
TAAATGAGTCATGTTGGT
Found at i:1228388 original size:2 final size:2
Alignment explanation
Indices: 1228376--1228408 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1228366 ACACATTTTC
1228376 AT AT A- 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
1228409 GTTTTACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1229184 original size:24 final size:24
Alignment explanation
Indices: 1229152--1229208 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
1229142 TACACCGTGT
1229152 ATCGATGCATCCCTTGACGGGTGC
1 ATCGATGCATCCCTTGACGGGTGC
*
1229176 ATCGATGCATCCCTTGATGGGTGC
1 ATCGATGCATCCCTTGACGGGTGC
1229200 ATCGATGCA
1 ATCGATGCA
1229209 CTATATATGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.26
Consensus pattern (24 bp):
ATCGATGCATCCCTTGACGGGTGC
Found at i:1232952 original size:23 final size:23
Alignment explanation
Indices: 1232934--1232994 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1232924 CTCGTATAAA
*
1232934 TGCACCGAAGTGCCACGTAGAAT
1 TGCACAGAAGTGCCACGTAGAAT
*
1232957 TGCACAGAAGTGCCGCGTAGAAT
1 TGCACAGAAGTGCCACGTAGAAT
*
1232980 TGCACTGAAGTGCCA
1 TGCACAGAAGTGCCA
1232995 TATAAAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.25, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACAGAAGTGCCACGTAGAAT
Found at i:1233266 original size:24 final size:24
Alignment explanation
Indices: 1233238--1233290 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1233228 CATAGTTCTT
*
1233238 TCACATAGCTCAT-TGACATATAAA
1 TCACATAGCACATAT-ACATATAAA
*
1233262 TCACATATCACATATACATATAAA
1 TCACATAGCACATATACATATAAA
1233286 -CACAT
1 TCACAT
1233291 TGTTCACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 5 0.19
24 20 0.77
25 1 0.04
ACGTcount: A:0.45, C:0.23, G:0.04, T:0.28
Consensus pattern (24 bp):
TCACATAGCACATATACATATAAA
Found at i:1234143 original size:22 final size:23
Alignment explanation
Indices: 1234109--1234169 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
1234099 ATCTCAGGTT
* *
1234109 CATATAACTCATATAA-CATTTTC
1 CATATAACACATATAATCA-TTGC
*
1234132 C-TATAATACATA-AATCATTGC
1 CATATAACACATATAATCATTGC
1234153 CATATAACACATATAAT
1 CATATAACACATATAAT
1234170 ATAAATTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
21 6 0.19
22 21 0.68
23 4 0.13
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (23 bp):
CATATAACACATATAATCATTGC
Found at i:1238354 original size:23 final size:23
Alignment explanation
Indices: 1238321--1238381 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
1238311 CTCATATAAA
*
1238321 TGCACCGAAGTGCCACGTAGAAT
1 TGCACTGAAGTGCCACGTAGAAT
*
1238344 TGCACAT-AAGTGCCGCGTAGAAT
1 TGCAC-TGAAGTGCCACGTAGAAT
1238367 TGCACTGAAGTGCCA
1 TGCACTGAAGTGCCA
1238382 TATAAAATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.03
23 32 0.97
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACTGAAGTGCCACGTAGAAT
Found at i:1239172 original size:2 final size:2
Alignment explanation
Indices: 1239165--1239191 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1239155 CATTTTCATA
1239165 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1239192 ACTCCATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1239612 original size:24 final size:26
Alignment explanation
Indices: 1239583--1239630 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
1239573 TACCACATAA
*
1239583 CATGTAATAT-GAAC-TAAGCATATT
1 CATGTAATATCAAACATAAGCATATT
1239607 CATGTAATATCAAACATAAGCATA
1 CATGTAATATCAAACATAAGCATA
1239631 CTTCTAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 3 0.14
26 8 0.38
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (26 bp):
CATGTAATATCAAACATAAGCATATT
Found at i:1245242 original size:19 final size:21
Alignment explanation
Indices: 1245220--1245276 Score: 73
Period size: 19 Copynumber: 2.8 Consensus size: 21
1245210 AGAACCCCAG
1245220 GGGGGTATCGATTCCCC-T-A
1 GGGGGTATCGATTCCCCTTAA
* *
1245239 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGTATCGATTCCCCTT-AA
1245261 GGGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
1245277 TCTGCCCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 15 0.48
20 1 0.03
22 15 0.48
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCTTAA
Found at i:1248900 original size:22 final size:23
Alignment explanation
Indices: 1248875--1248918 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1248865 AATTAAGTTT
1248875 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
1248897 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
1248919 CCATTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:1254629 original size:20 final size:21
Alignment explanation
Indices: 1254606--1254685 Score: 83
Period size: 20 Copynumber: 3.8 Consensus size: 21
1254596 TTGGTGCAGA
1254606 GGGAATCGATACCCCCATGA-
1 GGGAATCGATACCCCCATGAG
* *
1254626 GGGAATCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC-ATG-AG
* *
1254649 GGGAACCGATTACCCCCA-CAG
1 GGGAATCGA-TACCCCCATGAG
1254670 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
1254686 CTGGGGTTCT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 22 0.45
21 12 0.24
22 1 0.02
23 8 0.16
24 6 0.12
ACGTcount: A:0.26, C:0.33, G:0.25, T:0.16
Consensus pattern (21 bp):
GGGAATCGATACCCCCATGAG
Found at i:1254686 original size:21 final size:21
Alignment explanation
Indices: 1254647--1254685 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1254637 CCCCCTTTGA
1254647 AGGGGAACCGATTACCCCCAC
1 AGGGGAACCGATTACCCCCAC
*
1254668 AGGGGAATCGA-TACCCCC
1 AGGGGAACCGATTACCCCC
1254686 CTGGGGTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.36, G:0.26, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATTACCCCCAC
Found at i:1262309 original size:16 final size:14
Alignment explanation
Indices: 1262273--1262301 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1262263 TTATCAATAT
1262273 TCTTATAATTTATA
1 TCTTATAATTTATA
1262287 TCTTATAA-TTATA
1 TCTTATAATTTATA
1262300 TC
1 TC
1262302 CTCTTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (14 bp):
TCTTATAATTTATA
Found at i:1262654 original size:23 final size:23
Alignment explanation
Indices: 1262628--1262672 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1262618 CACCACAGCT
* *
1262628 CGTATAAATGAACTGAAGTGCCA
1 CGTAGAAATGAACCGAAGTGCCA
* *
1262651 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGAACCGAAGTGCC
1262673 GTGTAGAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGAACCGAAGTGCCA
Found at i:1262678 original size:23 final size:23
Alignment explanation
Indices: 1262642--1262694 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1262632 TAAATGAACT
1262642 GAAGTGCCACGTAGAATTGCACC
1 GAAGTGCCACGTAGAATTGCACC
** *
1262665 GAAGTGCCGTGTAGAATTGCATC
1 GAAGTGCCACGTAGAATTGCACC
1262688 GAAGTGC
1 GAAGTGC
1262695 TATATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (23 bp):
GAAGTGCCACGTAGAATTGCACC
Found at i:1266797 original size:36 final size:36
Alignment explanation
Indices: 1266756--1266865 Score: 132
Period size: 36 Copynumber: 3.1 Consensus size: 36
1266746 AAGATGAACA
* *
1266756 CTTGAATCGAAAGTGTTGATGCTTTCTTTCGTTCTT
1 CTTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTT
* * * * * *
1266792 CTTGAATCAAAAGTGCCAATGATTCCTTCCGTTC-A
1 CTTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTT
*
1266827 CTTGAATCGAAAGTGTCGATGCTTCCTTTTGTTCTT
1 CTTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTT
1266863 CTT
1 CTT
1266866 ATTCACCTTC
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
35 28 0.48
36 30 0.52
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (36 bp):
CTTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTT
Found at i:1268118 original size:3 final size:3
Alignment explanation
Indices: 1268082--1268110 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1268072 ATTCCCTCTA
1268082 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1268111 GTTCTTCTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:1271001 original size:39 final size:39
Alignment explanation
Indices: 1270942--1271025 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
1270932 TTCACCCTAA
* *
1270942 ACCCAACCCCGACCCGAATATCACACTTAAAAAAACCCG
1 ACCCGACCCCGACCCGAATATCAAACTTAAAAAAACCCG
*
1270981 ACCCGACCCCGACCCGAATATCAAACTTACAAAAACCCG
1 ACCCGACCCCGACCCGAATATCAAACTTAAAAAAACCCG
1271020 ACCCGA
1 ACCCGA
1271026 ACTCGAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.39, C:0.42, G:0.10, T:0.10
Consensus pattern (39 bp):
ACCCGACCCCGACCCGAATATCAAACTTAAAAAAACCCG
Found at i:1280541 original size:20 final size:20
Alignment explanation
Indices: 1280512--1280549 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1280502 TTCCTTCAAA
*
1280512 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
1280532 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
1280550 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:1284961 original size:19 final size:19
Alignment explanation
Indices: 1284937--1284976 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1284927 GGAGTGACCC
1284937 AATTAGCTCTTCAAGAGTT
1 AATTAGCTCTTCAAGAGTT
1284956 AATTAGCTCTTCAAGAGTT
1 AATTAGCTCTTCAAGAGTT
1284975 AA
1 AA
1284977 GGACGTTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (19 bp):
AATTAGCTCTTCAAGAGTT
Found at i:1297253 original size:20 final size:20
Alignment explanation
Indices: 1297211--1297344 Score: 155
Period size: 20 Copynumber: 6.7 Consensus size: 20
1297201 GTGAATATGA
* *
1297211 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1297231 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
1297251 AAACCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1297271 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1297291 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
1297311 AAATCGCAACGAC-AATACGT
1 AAATCGCAACG-CGTATCCGT
1297331 AAAATCGCAACGCG
1 -AAATCGCAACGCG
1297345 ATTTTTAAAG
Statistics
Matches: 98, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
20 84 0.86
21 14 0.14
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1297763 original size:33 final size:33
Alignment explanation
Indices: 1297724--1297794 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1297714 TTCACTTAGA
1297724 TTTCATTTCGCGTTACGATTCTCTCGTTACGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTACGAT
* * *
1297757 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTACGAT
1297790 TTTCA
1 TTTCA
1297795 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:0.13, C:0.24, G:0.15, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTACGAT
Found at i:1297898 original size:21 final size:21
Alignment explanation
Indices: 1297874--1297950 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
1297864 TGCAAAAGAG
1297874 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
1297895 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
*
1297915 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
1297937 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1297951 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.19
21 29 0.62
22 9 0.19
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:1297954 original size:14 final size:14
Alignment explanation
Indices: 1297935--1297991 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1297925 GAAAAATGAA
1297935 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1297949 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1297968 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1297982 AATCGCAACG
1 AATCGCAACG
1297992 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1297966 original size:33 final size:33
Alignment explanation
Indices: 1297928--1298005 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
1297918 GCAACGAGAA
1297928 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1297961 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
1297994 AAACCAAAATCG
1 AAATGAAAATCG
1298006 TATTGCGATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:1298054 original size:33 final size:33
Alignment explanation
Indices: 1298008--1298089 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
1297998 CAAAATCGTA
1298008 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1298041 TTGTGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1298074 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1298090 TCTCATTGCG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.10, C:0.22, G:0.20, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1298077 original size:14 final size:14
Alignment explanation
Indices: 1298025--1298081 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1298015 TTTCATTTCG
1298025 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
1298039 CGTTGTGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1298058 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1298072 CGTTGCGATT
1 CGTTGCGATT
1298082 TTCATTTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1298092 original size:21 final size:21
Alignment explanation
Indices: 1298066--1298130 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
1298056 CGCGTTGCGA
1298066 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
* ***
1298087 TTCTCTCATTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1298107 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1298128 TTC
1 TTC
1298131 AACCAAAAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.12, C:0.26, G:0.14, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1298127 original size:20 final size:20
Alignment explanation
Indices: 1298065--1298128 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
1298055 TCGCGTTGCG
1298065 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* ***
1298085 ATTTCTCTCATTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
1298106 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
1298126 ATT
1 ATT
1298129 TCAACCAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.14, C:0.25, G:0.14, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1299973 original size:93 final size:93
Alignment explanation
Indices: 1299814--1300036 Score: 419
Period size: 93 Copynumber: 2.4 Consensus size: 93
1299804 TAGATTGCTT
* *
1299814 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAAAAGTA
1299879 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1299907 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAAAAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAAAAGTA
1299972 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1300000 AGTAAATTTGTTCGGTTGCTGCCAATTTTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1300037 AATACCCTGA
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 127 1.00
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAAAAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1300214 original size:52 final size:53
Alignment explanation
Indices: 1300134--1300243 Score: 150
Period size: 52 Copynumber: 2.1 Consensus size: 53
1300124 TAGTTTACTT
* * * **
1300134 TCGCAACACGAAACTTAAAATCGCAACGAGAGAATCACAACGCGAAATGAAAA
1 TCGCAACACGAAACTCAAAATCGCAACGACAAAATCACAACGCGAAACCAAAA
* *
1300187 TCGCAACGCGAAAC-CAAAATCGCAACGACAAAATCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACTCAAAATCGCAACGACAAAATCACAACGCGAAACCAAAA
1300239 TCGCA
1 TCGCA
1300244 TTGCGATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 37 0.74
53 13 0.26
ACGTcount: A:0.47, C:0.27, G:0.16, T:0.09
Consensus pattern (53 bp):
TCGCAACACGAAACTCAAAATCGCAACGACAAAATCACAACGCGAAACCAAAA
Found at i:1300218 original size:14 final size:14
Alignment explanation
Indices: 1300201--1300227 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1300191 AACGCGAAAC
1300201 CAAAATCGCAACGA
1 CAAAATCGCAACGA
1300215 CAAAATCGCAACG
1 CAAAATCGCAACG
1300228 CGAAACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:1300249 original size:19 final size:19
Alignment explanation
Indices: 1300166--1300243 Score: 94
Period size: 19 Copynumber: 4.4 Consensus size: 19
1300156 GCAACGAGAG
* **
1300166 AATCACAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
1300185 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
1300204 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
1300218 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
1300237 AATCGCA
1 AATCGCA
1300244 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
14 11 0.22
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 34 0.67
ACGTcount: A:0.49, C:0.28, G:0.15, T:0.08
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:1300261 original size:19 final size:19
Alignment explanation
Indices: 1300239--1300392 Score: 130
Period size: 19 Copynumber: 8.6 Consensus size: 19
1300229 GAAACCAAAA
*
1300239 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1300258 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1300272 TCTCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1300291 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1300307 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1300324 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
1300343 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
1300362 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1300382 TCGTGTTGCGA
1 TCGCGTTGCGA
1300393 AAGTAAACTA
Statistics
Matches: 107, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
14 16 0.15
16 8 0.07
17 8 0.07
19 63 0.59
20 12 0.11
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1300284 original size:33 final size:33
Alignment explanation
Indices: 1300242--1300374 Score: 167
Period size: 33 Copynumber: 3.9 Consensus size: 33
1300232 ACCAAAATCG
1300242 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
1300275 CATTGCGATTTTCATTTCGCATTGCGATTCTGT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
1300308 CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCT
1 CATTGCGATTTTCATTTCGCGTTGCGA---T--TCTCT
* *
1300346 CGTTGCGATTCTCATTTCGCGTTGCGATT
1 CATTGCGATTTTCATTTCGCGTTGCGATT
1300375 TTAAGTTTCG
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
33 57 0.65
35 1 0.01
36 1 0.01
38 29 0.33
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.46
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:1302338 original size:14 final size:14
Alignment explanation
Indices: 1302319--1302354 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1302309 ATTGTTTAAT
1302319 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1302333 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1302347 TGATTTGT
1 TGATTTGT
1302355 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:1302477 original size:19 final size:19
Alignment explanation
Indices: 1302461--1302558 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1302451 AAAAATGACT
1302461 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1302480 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1302499 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1302513 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1302532 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1302552 ATCGCAA
1 ATCGCAA
1302559 CGAGAGAATC
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:1302590 original size:53 final size:53
Alignment explanation
Indices: 1302461--1302577 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
1302451 AAAAATGACT
1302461 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1302513 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1302566 ATCGCAATGCGA
1 ATCGCAATGCGA
1302578 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:1302612 original size:20 final size:19
Alignment explanation
Indices: 1302567--1302738 Score: 176
Period size: 19 Copynumber: 9.7 Consensus size: 19
1302557 AACGAGAGAA
*
1302567 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1302586 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1302605 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
1302622 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1302639 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1302658 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
1302675 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1302692 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1302710 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1302726 TCGCATTGCGATT
1 TCGCATTGCGATT
1302739 CTCTCGTTGC
Statistics
Matches: 128, Mismatches: 7, Indels: 36
0.75 0.04 0.21
Matches are distributed among these distances:
14 23 0.18
16 12 0.09
17 11 0.09
18 9 0.07
19 41 0.32
20 32 0.25
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1302636 original size:53 final size:53
Alignment explanation
Indices: 1302573--1302710 Score: 267
Period size: 53 Copynumber: 2.6 Consensus size: 53
1302563 AGAATCGCAA
1302573 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1302626 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1302679 TGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 TGCGATTTTCATTT-CGCATTGCGATTTTCAT
1302711 GTTGGGATTT
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
53 67 0.80
54 17 0.20
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:1302687 original size:34 final size:34
Alignment explanation
Indices: 1302644--1302771 Score: 188
Period size: 34 Copynumber: 3.8 Consensus size: 34
1302634 TCATTTCGCA
1302644 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
*
1302678 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTTCCGCATTGCGATTCTC-TCG
*
1302712 TTGGGATTTTCATTT-CGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
* * *
1302745 TTGCGATTGTAATTTCCGTATTGCGAT
1 TTGCGATTTTCATTTCCGCATTGCGAT
1302772 AGTCAAATGC
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
32 1 0.01
33 27 0.32
34 55 0.65
35 1 0.01
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (34 bp):
TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
Found at i:1302769 original size:87 final size:85
Alignment explanation
Indices: 1302573--1302771 Score: 226
Period size: 87 Copynumber: 2.3 Consensus size: 85
1302563 AGAATCGCAA
* *
1302573 TGCGATTTTCATTT-CGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCA
1 TGCGATTGTAATTTCCG-ATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCA
*
1302637 TTTCGCATTGCGATTTTCATT
65 TTTCGCATTGCGATTTTCAGT
* ** * *
1302658 TCCGCATTGCGATTCTCTCG-TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTT
1 TGCG-ATTGTAATT-TC-CGATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGATTT
1302721 TCATTTCGCATTGCGATTCTCTC-GT
62 TCATTTCGCATTGCGATT-T-TCAGT
1302746 TGCGATTGTAATTTCCGTATTGCGAT
1 TGCGATTGTAATTTCCG-ATTGCGAT
1302772 AGTCAAATGC
Statistics
Matches: 95, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
85 5 0.05
86 8 0.08
87 72 0.76
88 6 0.06
89 4 0.04
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (85 bp):
TGCGATTGTAATTTCCGATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCAGT
Found at i:1305040 original size:20 final size:20
Alignment explanation
Indices: 1305012--1305103 Score: 130
Period size: 20 Copynumber: 4.6 Consensus size: 20
1305002 AAATTTCAGT
* * *
1305012 GTTGTGATTTAAAGATTCTC
1 GTTGCGATTTACAGATTATC
*
1305032 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTATC
*
1305052 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTATC
*
1305072 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTATC
1305092 GTTGCGATTTAC
1 GTTGCGATTTAC
1305104 GGATACGCGT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (20 bp):
GTTGCGATTTACAGATTATC
Found at i:1305072 original size:40 final size:40
Alignment explanation
Indices: 1305012--1305240 Score: 214
Period size: 40 Copynumber: 5.7 Consensus size: 40
1305002 AAATTTCAGT
* * * *
1305012 GTTGTGATTTAAAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTAGC
* *
1305052 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTAGC
* * *
1305092 GTTGCGATTTACGGATACGCGTTGCGATATACGGA-TACGC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTA-GC
* * * * *
1305132 ATTGCGGTTTACGGATAT-GCGTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACAGAT-TCGCGTTGCGATTTACG-GATTAGC
* * * *
1305172 GTTGCGATTTTCATATTCGCGTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACG-GATTAGC
* *
1305212 GTTGCGATTTTCATATTCGCGTTGCGATT
1 GTTGCGATTTACAGATTCGCGTTGCGATT
1305241 CTGGAAAATC
Statistics
Matches: 166, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.02
40 161 0.97
41 2 0.01
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.40
Consensus pattern (40 bp):
GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTAGC
Found at i:1305104 original size:20 final size:20
Alignment explanation
Indices: 1305025--1305162 Score: 158
Period size: 20 Copynumber: 6.9 Consensus size: 20
1305015 GTGATTTAAA
*
1305025 GATTCTCGTTGCGATTTACG
1 GATTATCGTTGCGATTTACG
*
1305045 GATTATCGTTGCGATTTACA
1 GATTATCGTTGCGATTTACG
*
1305065 GATTCTCGTTGCGATTTACG
1 GATTATCGTTGCGATTTACG
1305085 GATTATCGTTGCGATTTACG
1 GATTATCGTTGCGATTTACG
* *
1305105 GA-TACGCGTTGCGATATACG
1 GATTA-TCGTTGCGATTTACG
*
1305125 GA-TA-CGCATTGCGGTTTACG
1 GATTATCG--TTGCGATTTACG
1305145 GA-TATGCGTTGCGATTTA
1 GATTAT-CGTTGCGATTTA
1305163 TGTGTTCGCG
Statistics
Matches: 103, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.02
19 2 0.02
20 97 0.94
22 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.36
Consensus pattern (20 bp):
GATTATCGTTGCGATTTACG
Found at i:1305115 original size:60 final size:60
Alignment explanation
Indices: 1305025--1305202 Score: 200
Period size: 60 Copynumber: 3.0 Consensus size: 60
1305015 GTGATTTAAA
* * *
1305025 GATTCTCGTTGCGATTTACGGATTA-TCGTTGCGATTTACAGATTCTCGTTGCGATTTACG
1 GATTATCGTTGCGATTTACGGA-TACGCGTTGCGATTTACAGATTCGCGTTGCGATTTACG
* * * * *
1305085 GATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGCATTGCGGTTTACG
1 GATTATCGTTGCGATTTACGGATACGCGTTGCGATTTACAGATTCGCGTTGCGATTTACG
* * * *
1305145 GA-TATGCGTTGCGATTTATGTG-TTCGCGTTGCGATTTTCATATTCGCGTTGCGATTTA
1 GATTAT-CGTTGCGATTTACG-GATACGCGTTGCGATTTACAGATTCGCGTTGCGATTTA
1305203 TGTGTTCGCG
Statistics
Matches: 98, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
59 5 0.05
60 92 0.94
61 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (60 bp):
GATTATCGTTGCGATTTACGGATACGCGTTGCGATTTACAGATTCGCGTTGCGATTTACG
Found at i:1305173 original size:20 final size:20
Alignment explanation
Indices: 1305167--1305240 Score: 114
Period size: 20 Copynumber: 3.7 Consensus size: 20
1305157 GATTTATGTG
1305167 TTCGCGTTGCGATTTTCATA
1 TTCGCGTTGCGATTTTCATA
* *
1305187 TTCGCGTTGCGATTTAT-GTG
1 TTCGCGTTGCGATTT-TCATA
1305207 TTCGCGTTGCGATTTTCATA
1 TTCGCGTTGCGATTTTCATA
1305227 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
1305241 CTGGAAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.45
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATA
Found at i:1305622 original size:16 final size:16
Alignment explanation
Indices: 1305603--1305670 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
1305593 AATTAACCCG
1305603 AACCGAAATCGAAA-TA
1 AACCG-AATCGAAAGTA
* *
1305619 AACCAGAATCAAAAGCA
1 AACC-GAATCGAAAGTA
* *
1305636 AACTGAATCGAAATTA
1 AACCGAATCGAAAGTA
*
1305652 ACCCGAATCGAAAG-A
1 AACCGAATCGAAAGTA
1305667 AACC
1 AACC
1305671 AACACCAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
15 4 0.10
16 31 0.77
17 5 0.12
ACGTcount: A:0.53, C:0.22, G:0.13, T:0.12
Consensus pattern (16 bp):
AACCGAATCGAAAGTA
Found at i:1305660 original size:32 final size:31
Alignment explanation
Indices: 1305609--1305669 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
1305599 CCCGAACCGA
1305609 AATCGAAATAAACCAGAATCAAAAGCAAACTG
1 AATCGAAATAAACCAGAATCAAAAG-AAACTG
* * *
1305641 AATCGAAATTAACCCGAATCGAAAGAAAC
1 AATCGAAATAAACCAGAATCAAAAGAAAC
1305670 CAACACCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 4 0.15
32 22 0.85
ACGTcount: A:0.54, C:0.20, G:0.13, T:0.13
Consensus pattern (31 bp):
AATCGAAATAAACCAGAATCAAAAGAAACTG
Found at i:1305770 original size:17 final size:17
Alignment explanation
Indices: 1305748--1305781 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1305738 GACATATTGA
1305748 AATTGATAAAAGTTATT
1 AATTGATAAAAGTTATT
1305765 AATTGATAAAAGTTATT
1 AATTGATAAAAGTTATT
1305782 TTCAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (17 bp):
AATTGATAAAAGTTATT
Found at i:1305816 original size:18 final size:17
Alignment explanation
Indices: 1305795--1305850 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
1305785 AATAATAAAT
1305795 TAATTTAAATAAAATTAA
1 TAATTTAAATAAAA-TAA
* *
1305813 TAATTT-ATTAAAAATAT
1 TAATTTAAAT-AAAATAA
1305830 TATATTTATAATAAAATAA
1 TA-ATTTA-AATAAAATAA
1305849 TA
1 TA
1305851 GAAAATTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 6 0.20
18 14 0.47
19 8 0.27
20 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATTTAAATAAAATAA
Found at i:1305965 original size:24 final size:24
Alignment explanation
Indices: 1305938--1306026 Score: 63
Period size: 24 Copynumber: 3.5 Consensus size: 24
1305928 TTGTTATAGA
1305938 AATATTAAATTTATAATAAAAAGT
1 AATATTAAATTTATAATAAAAAGT
* * * *
1305962 AATA-GAAAATAACTAAAACAAAAGAAAT
1 AATATTAAATTTA-TAATA-AAAAG---T
* *
1305990 AATATTATATTTATAATAAAAAAT
1 AATATTAAATTTATAATAAAAAGT
*
1306014 AATATAAAATTTA
1 AATATTAAATTTA
1306027 CTTATGTTAC
Statistics
Matches: 47, Mismatches: 12, Indels: 12
0.66 0.17 0.17
Matches are distributed among these distances:
23 5 0.11
24 20 0.43
25 5 0.11
27 4 0.09
28 9 0.19
29 4 0.09
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.31
Consensus pattern (24 bp):
AATATTAAATTTATAATAAAAAGT
Found at i:1306747 original size:16 final size:16
Alignment explanation
Indices: 1306726--1306756 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1306716 AAATTATCTG
1306726 ACTCAAACCCGATCCA
1 ACTCAAACCCGATCCA
1306742 ACTCAAACCCGATCC
1 ACTCAAACCCGATCC
1306757 GAATAACTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.45, G:0.06, T:0.13
Consensus pattern (16 bp):
ACTCAAACCCGATCCA
Found at i:1311567 original size:15 final size:15
Alignment explanation
Indices: 1311547--1311592 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1311537 ATTCAAATTG
1311547 ACTCGAATTGAGTCA
1 ACTCGAATTGAGTCA
*
1311562 ACTCG-ATCGAGTCA
1 ACTCGAATTGAGTCA
* *
1311576 ATTCAAATTGAGTCA
1 ACTCGAATTGAGTCA
1311591 AC
1 AC
1311593 CCGTTGACTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (15 bp):
ACTCGAATTGAGTCA
Found at i:1321403 original size:2 final size:2
Alignment explanation
Indices: 1321396--1321430 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1321386 TATTAAACCA
1321396 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1321431 GAGTTATGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1330359 original size:19 final size:18
Alignment explanation
Indices: 1330331--1330370 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
1330321 TGAATAATAA
1330331 TGGGTAGTTTTATTTTAG
1 TGGGTAGTTTTATTTTAG
*
1330349 TGGGATAGTTTTGTTTTAG
1 TGGG-TAGTTTTATTTTAG
1330368 TGG
1 TGG
1330371 TAAAAGTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.53
Consensus pattern (18 bp):
TGGGTAGTTTTATTTTAG
Found at i:1337843 original size:25 final size:24
Alignment explanation
Indices: 1337797--1337844 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1337787 ATTAATAATC
1337797 TAATTTCATATCCTAAAATTTTTA
1 TAATTTCATATCCTAAAATTTTTA
*
1337821 TAATTTTATATCTCT-AAATTTTTA
1 TAATTTCATATC-CTAAAATTTTTA
1337845 ATATAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.54
Consensus pattern (24 bp):
TAATTTCATATCCTAAAATTTTTA
Found at i:1344849 original size:2 final size:2
Alignment explanation
Indices: 1344842--1344889 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
1344832 TATTTTATTA
*
1344842 AT AT AT AT AA AT AT -T AT AT -T AT -T A- 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
1344880 AT AT AT AT AT
1 AT AT AT AT AT
1344890 TCATTTTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 4 0.10
2 36 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1347442 original size:2 final size:2
Alignment explanation
Indices: 1347437--1347464 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1347427 TATTTAATCC
1347437 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
1347465 TGTATTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1351299 original size:8 final size:8
Alignment explanation
Indices: 1351286--1351326 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1351276 CTCATTTTCA
1351286 GAGAATTT
1 GAGAATTT
1351294 GAGAATTT
1 GAGAATTT
*
1351302 -AGAGTTT
1 GAGAATTT
*
1351309 GGGAATTT
1 GAGAATTT
1351317 GAGAATTT
1 GAGAATTT
1351325 GA
1 GA
1351327 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1351637 original size:128 final size:128
Alignment explanation
Indices: 1351406--1351880 Score: 833
Period size: 128 Copynumber: 3.7 Consensus size: 128
1351396 ACTATTCACA
* *
1351406 TGAAGGCGCGTTCCCGGGGTCGCGCCTTCCATTATTTTTTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
1351471 TTATATCACTCATGTCCCTCGGGGACACTATTCATATCAGTTCCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
1351534 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
1351599 TTATGTCACTCATGTCCCTCAGGGACACTATTCCTATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* * *
1351662 TGAAGGCGTGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGACTATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
1351727 TTATGTCACTCATGTCCCTCGGGGATACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* * *
1351790 TGAAGGCGCGTTCCCGGGGGCGCGCCTTACATTATTTTGTCAGAAAATATGTTATCATTGCACTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1351855 TTATGTCACTCATGTCCCTCGGGGAC
66 TTATGTCACTCATGTCCCTCGGGGAC
1351881 TGTAACATCC
Statistics
Matches: 328, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 328 1.00
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:1352724 original size:63 final size:63
Alignment explanation
Indices: 1352650--1352809 Score: 180
Period size: 63 Copynumber: 2.5 Consensus size: 63
1352640 TTGTTTAAGG
*
1352650 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCACATGCAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * * * * *
1352714 TGCATC-ATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCACATGCAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
** *
1352777 TGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCA-CATGCAGTGCATCGATGCAT
1352810 ACCTTCATTA
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
63 47 0.58
64 17 0.21
65 17 0.21
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCACATGCAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:1353534 original size:31 final size:30
Alignment explanation
Indices: 1353496--1353591 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
1353486 GTCAAAGAAC
1353496 TACCTATG-TCTTTCGAGACATATGGACAGT
1 TACCTATGTTCTTT-GAGACATATGGACAGT
** *
1353526 ATACCTATGTTCTAAG-GAACATATGGATAGTT
1 -TACCTATGTTCTTTGAG-ACATATGGACAG-T
* * *
1353558 TACCTAGGTTCTTTGGGACCTATGGACAGT
1 TACCTATGTTCTTTGAGACATATGGACAGT
1353588 TACC
1 TACC
1353592 GAGGATCTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
30 6 0.11
31 42 0.79
32 5 0.09
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (30 bp):
TACCTATGTTCTTTGAGACATATGGACAGT
Found at i:1353601 original size:30 final size:30
Alignment explanation
Indices: 1353547--1353646 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 30
1353537 CTAAGGAACA
* * *
1353547 TATGGATAGTTTACCTAGGTTCTTTGGGACC
1 TATGGATAG-TTACCGAGGATCTTTAGGACC
* **
1353578 TATGGACAGTTACCGAGGATCTTTATTACC
1 TATGGATAGTTACCGAGGATCTTTAGGACC
* *
1353608 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTAGGACC
*
1353638 TCTGGATAG
1 TATGGATAG
1353647 GTCATGCGGG
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
30 52 0.87
31 8 0.13
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (30 bp):
TATGGATAGTTACCGAGGATCTTTAGGACC
Found at i:1356036 original size:2 final size:2
Alignment explanation
Indices: 1356029--1356097 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1356019 CATTATATGA
1356029 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
1356071 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1356098 AAGGAAAAAG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1357116 original size:64 final size:63
Alignment explanation
Indices: 1357031--1357191 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
1357021 TTGTTTAAGG
* * * *
1357031 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * *
1357095 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
* *
1357159 TGCATCAATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
1357192 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:1357916 original size:31 final size:30
Alignment explanation
Indices: 1357878--1357973 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
1357868 GTCAAAGAAC
1357878 TACCTATG-TCTTTCGAGACATATGGACAGT
1 TACCTATGTTCTTT-GAGACATATGGACAGT
** *
1357908 ATACCTATGTTCTAAG-GAACATATGGATAGTT
1 -TACCTATGTTCTTTGAG-ACATATGGACAG-T
* * *
1357940 TACCTAGGTTCTTTGGGACCTATGGACAGT
1 TACCTATGTTCTTTGAGACATATGGACAGT
1357970 TACC
1 TACC
1357974 GAGGATCTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
30 6 0.11
31 42 0.79
32 5 0.09
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (30 bp):
TACCTATGTTCTTTGAGACATATGGACAGT
Found at i:1359027 original size:128 final size:128
Alignment explanation
Indices: 1358780--1359303 Score: 897
Period size: 128 Copynumber: 4.1 Consensus size: 128
1358770 GGGTGTTACA
* * *
1358780 GGGACACTATTCATATCAGTACCTATTATTTCTCAAGGGACTTGAAGGTGCATTCCCGGGGGGGG
1 GGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCC---GGGGG
* * * *
1358845 GGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTTATATCCCTC
63 CGAGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTC
1358910 G
128 G
*
1358911 GGGACACTATTCATATCAGTACATATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGA
1 GGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGA
*
1358976 TCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCG
66 GCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCG
* * *
1359039 GGGACACTATTCATATCAGTACCTATTATTTCTCAGGTGACTTAAAGGCGCGTTCCCGGGGGCGC
1 GGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGA
1359104 GCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCG
66 GCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCG
1359167 GGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGC-A
1 GGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGA
1359231 CGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCG
66 -GCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCG
1359295 GGGACACTA
1 GGGACACTA
1359304 GATGGATTGT
Statistics
Matches: 375, Mismatches: 17, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
128 322 0.86
131 53 0.14
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (128 bp):
GGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGA
GCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCG
Found at i:1359768 original size:34 final size:34
Alignment explanation
Indices: 1359699--1359804 Score: 124
Period size: 34 Copynumber: 3.1 Consensus size: 34
1359689 TAAGTTGAAA
* * * * *
1359699 TTTAATGTTAAGTTTCAAATACTATAA-TTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTGTAT
* *
1359732 TTTAATTTTAAATTTCGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTGTAT
* *
1359766 TTTTATTTTAAATTTTGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTGTAT
1359800 TTTAA
1 TTTAA
1359805 AAACATTTAT
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
33 22 0.36
34 39 0.64
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.56
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTGTAT
Found at i:1360359 original size:21 final size:20
Alignment explanation
Indices: 1360335--1360417 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 20
1360325 AACCCTACGA
*
1360335 GCTAGGCATGTAACCTGGCGG
1 GCTAGGAATGTAACCT-GCGG
1360356 GCTAGGAATGTAACCCTGCGG
1 GCTAGGAATGTAA-CCTGCGG
* **
1360377 GCTCGGAATGTAACCCTGTAG
1 GCTAGGAATGTAA-CCTGCGG
*
1360398 GCTCGGAATGTAACCCTGCG
1 GCTAGGAATGTAA-CCTGCG
1360418 AAGATGGCAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
21 52 0.95
22 3 0.05
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.20
Consensus pattern (20 bp):
GCTAGGAATGTAACCTGCGG
Found at i:1362241 original size:31 final size:33
Alignment explanation
Indices: 1362176--1362255 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
1362166 TTAATAATTC
* *
1362176 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
1362210 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
1362241 TATAAAATATAATAA
1 TA-AAAAAATAATAA
1362256 CTATTTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.15
32 10 0.25
33 2 0.05
34 22 0.55
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:1363695 original size:22 final size:23
Alignment explanation
Indices: 1363661--1363703 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1363651 ATATAATAAA
*
1363661 TAATATTATTTATTATAAAAACT
1 TAATATTAGTTATTATAAAAACT
*
1363684 TAATATT-GTTATTTTAAAAA
1 TAATATTAGTTATTATAAAAA
1363704 TATTAGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TAATATTAGTTATTATAAAAACT
Found at i:1369147 original size:18 final size:19
Alignment explanation
Indices: 1369108--1369149 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1369098 ATTAAAATAT
1369108 TATTAGACTACTATATTAA
1 TATTAGACTACTATATTAA
1369127 TATTAGA-TAC-ATATGTAA
1 TATTAGACTACTATAT-TAA
1369145 TATTA
1 TATTA
1369150 TTCACTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.18
18 11 0.50
19 7 0.32
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (19 bp):
TATTAGACTACTATATTAA
Found at i:1371436 original size:16 final size:16
Alignment explanation
Indices: 1371417--1371459 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
1371407 ATATATAAAA
1371417 AATATTTGT-GAGGAAC
1 AATATTT-TCGAGGAAC
1371433 AATATTTTCGGAGGAAC
1 AATATTTTC-GAGGAAC
1371450 AATATTTTCG
1 AATATTTTCG
1371460 GGAGAGACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.04
16 8 0.32
17 16 0.64
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (16 bp):
AATATTTTCGAGGAAC
Found at i:1371448 original size:17 final size:17
Alignment explanation
Indices: 1371426--1371460 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1371416 AAATATTTGT
1371426 GAGGAACAATATTTTCG
1 GAGGAACAATATTTTCG
1371443 GAGGAACAATATTTTCG
1 GAGGAACAATATTTTCG
1371460 G
1 G
1371461 GAGAGACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (17 bp):
GAGGAACAATATTTTCG
Found at i:1371835 original size:20 final size:20
Alignment explanation
Indices: 1371810--1371865 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
1371800 AATTCGACTA
1371810 TCGCATTGCGATTTACATA-T
1 TCGCATTGCGATTTACA-AGT
* *
1371830 TCGCATTGCGATGGTCCAAGT
1 TCGCATTGCGAT-TTACAAGT
1371851 TCGCATTGCGATTTA
1 TCGCATTGCGATTTA
1371866 TTCCAAATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAGT
Found at i:1371897 original size:42 final size:40
Alignment explanation
Indices: 1371809--1371897 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 40
1371799 AAATTCGACT
* * *
1371809 ATCGCATTGCGATTTACATATTCGCATTGCGATGGTCCAAG
1 ATCGCATTGCGATTTACAAATTCG-ATTGCGATAGTCCAAA
*
1371850 TTCGCATTGCGATTTATTCCAAATTCG-TTGCGATAGTCCAAA
1 ATCGCATTGCGATTTA---CAAATTCGATTGCGATAGTCCAAA
1371892 ATCGCA
1 ATCGCA
1371898 ACGACTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
41 15 0.38
42 18 0.45
44 7 0.17
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (40 bp):
ATCGCATTGCGATTTACAAATTCGATTGCGATAGTCCAAA
Found at i:1372486 original size:6 final size:6
Alignment explanation
Indices: 1372475--1372529 Score: 101
Period size: 6 Copynumber: 9.2 Consensus size: 6
1372465 CCGTCTCGTC
*
1372475 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TTGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1372523 TCGTGG T
1 TCGTGG T
1372530 AATACGTGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.00, C:0.15, G:0.49, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:1372680 original size:42 final size:42
Alignment explanation
Indices: 1372618--1372794 Score: 227
Period size: 42 Copynumber: 4.3 Consensus size: 42
1372608 TGCGATTTTG
* *
1372618 GACTATCGCAACGAATTTGGAATAAATAGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * * *
1372660 GACTATCACAACGAACTTGGACT--ATCGCAA--CGAATTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
1372698 GAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1372742 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1372784 GACTATCGCAA
1 GACTATCGCAA
1372795 TGCGAATAGT
Statistics
Matches: 114, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
38 9 0.08
40 22 0.19
42 74 0.65
44 9 0.08
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:1372800 original size:21 final size:19
Alignment explanation
Indices: 1372615--1372794 Score: 135
Period size: 21 Copynumber: 8.7 Consensus size: 19
1372605 CGTTGCGATT
*
1372615 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
* *
1372634 TTGGAATAAATAGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
* *
1372657 TTCGACTATCACAACGAAC
1 TTGGACTATCGCAACGAAC
*
1372676 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
* *
1372695 TTGGAATAAATCGCAACGAAT
1 TTGGACT--ATCGCAACGAAC
*
1372716 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
1372739 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
1372758 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
1372781 TTGGACTATCGCAA
1 TTGGACTATCGCAA
1372795 TGCGAATAGT
Statistics
Matches: 132, Mismatches: 17, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
19 43 0.33
21 60 0.45
23 29 0.22
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:1378702 original size:18 final size:17
Alignment explanation
Indices: 1378679--1378754 Score: 50
Period size: 18 Copynumber: 4.4 Consensus size: 17
1378669 TTAAAAAGAT
1378679 TATGATATGTGAATGATA
1 TATGATAT-TGAATGATA
1378697 TATGATACTTGAATG-TA
1 TATGATA-TTGAATGATA
* *
1378714 -ATGATGTTTGAAAAGAT-
1 TATGAT-ATTG-AATGATA
* *
1378731 TCTGATAAATGAATGATA
1 TATGAT-ATTGAATGATA
1378749 TATGAT
1 TATGAT
1378755 TTAAAGAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
16 8 0.18
17 10 0.23
18 25 0.57
19 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.38
Consensus pattern (17 bp):
TATGATATTGAATGATA
Found at i:1379823 original size:24 final size:24
Alignment explanation
Indices: 1379779--1379826 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1379769 CCACATAGTT
*
1379779 TTTGTCCCGAAGAACCGTATAGAA
1 TTTGTCCCGAAGAACCATATAGAA
1379803 TTTGTCCCGAATG-ACCATATAGAA
1 TTTGTCCCGAA-GAACCATATAGAA
1379827 ATGTCCTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (24 bp):
TTTGTCCCGAAGAACCATATAGAA
Found at i:1380040 original size:28 final size:28
Alignment explanation
Indices: 1380008--1380061 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
1379998 GGTATCTTCG
**
1380008 CGTAGAACTTTTTCACTTAGCACATTCA
1 CGTAGAACCATTTCACTTAGCACATTCA
1380036 CGTAGAACCATTTCACTTAGCACATT
1 CGTAGAACCATTTCACTTAGCACATT
1380062 ATCATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (28 bp):
CGTAGAACCATTTCACTTAGCACATTCA
Found at i:1382833 original size:18 final size:17
Alignment explanation
Indices: 1382779--1382827 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1382769 TTGGACCCTT
* *
1382779 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1382797 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1382815 AGTGCATTCGATG
1 AGTGCA-TCGATG
1382828 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1382860 original size:45 final size:46
Alignment explanation
Indices: 1382796--1382903 Score: 157
Period size: 45 Copynumber: 2.4 Consensus size: 46
1382786 CGGTGCACTA
*
1382796 AGAGTGCATCGATGCATCAAGTGCATTCGATG-TTTCA-AAATAGCC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGATTTCATAAA-AGCC
*
1382841 AGAGTGCATCGATGCATCAAATGCATTCGATGATTTCATAAAATCC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGATTTCATAAAAGCC
**
1382887 TCAGTGCATCGATGCAT
1 AGAGTGCATCGATGCAT
1382904 GGTATGTGCA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
45 31 0.54
46 23 0.40
47 3 0.05
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (46 bp):
AGAGTGCATCGATGCATCAAATGCATTCGATGATTTCATAAAAGCC
Found at i:1384196 original size:29 final size:28
Alignment explanation
Indices: 1384154--1384312 Score: 201
Period size: 29 Copynumber: 5.5 Consensus size: 28
1384144 ACCGACCCGA
*
1384154 TGATATTTTAGTAATTATTTTGAAACCGG
1 TGATATTTTAGTAATTATTTTGAAA-AGG
*
1384183 TGATATTTTAGTAATTATTTTGAAACCGG
1 TGATATTTTAGTAATTATTTTGAAA-AGG
* *
1384212 TGATATTTTGGTAATTATTTTGAAAAAG
1 TGATATTTTAGTAATTATTTTGAAAAGG
* *
1384240 TGATATTTTGGTAATTATTTTTGAAAAAG
1 TGATATTTTAGTAATTA-TTTTGAAAAGG
*
1384269 TGATATTTTAGTAATTATTTTTAAAAAGG
1 TGATATTTTAGTAATTA-TTTTGAAAAGG
* *
1384298 TGCTATTTTCGTAAT
1 TGATATTTTAGTAAT
1384313 AGTTGACTGT
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
28 18 0.15
29 103 0.85
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (28 bp):
TGATATTTTAGTAATTATTTTGAAAAGG
Found at i:1384305 original size:86 final size:86
Alignment explanation
Indices: 1384154--1384312 Score: 230
Period size: 86 Copynumber: 1.8 Consensus size: 86
1384144 ACCGACCCGA
** **
1384154 TGATATTTTAGTAATTATTTTGAAACCGGTGATATTTTAGTAATTATTTTGAAACCGGTGATATT
1 TGATATTTTAGTAATTATTTTGAAACAAGTGATATTTTAGTAATTATTTTGAAAAAGGTGATATT
*
1384219 TTGGTAATTATTTTGAAAAAG
66 TTCGTAATTATTTTGAAAAAG
* * *
1384240 TGATATTTTGGTAATTATTTTTGAAA-AAGTGATATTTTAGTAATTATTTTTAAAAAGGTGCTAT
1 TGATATTTTAGTAATTA-TTTTGAAACAAGTGATATTTTAGTAATTATTTTGAAAAAGGTGATAT
1384304 TTTCGTAAT
65 TTTCGTAAT
1384313 AGTTGACTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
86 56 0.88
87 8 0.12
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (86 bp):
TGATATTTTAGTAATTATTTTGAAACAAGTGATATTTTAGTAATTATTTTGAAAAAGGTGATATT
TTCGTAATTATTTTGAAAAAG
Found at i:1391544 original size:17 final size:18
Alignment explanation
Indices: 1391516--1391551 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1391506 TCCGAACCGG
1391516 GTTGACCCGACCCGACCC
1 GTTGACCCGACCCGACCC
*
1391534 GTTGA-CCGACCTGACCC
1 GTTGACCCGACCCGACCC
1391551 G
1 G
1391552 GTGATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.17, C:0.44, G:0.25, T:0.14
Consensus pattern (18 bp):
GTTGACCCGACCCGACCC
Found at i:1391598 original size:29 final size:29
Alignment explanation
Indices: 1391550--1391606 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1391540 CGACCTGACC
*
1391550 CGGTGATATTTTAGTGATTATTTTGAAAT
1 CGGTGATATTTTAGTAATTATTTTGAAAT
*
1391579 CGGTGATATTTTGGTAATTATTTTGAAA
1 CGGTGATATTTTAGTAATTATTTTGAAA
1391607 AAAACTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (29 bp):
CGGTGATATTTTAGTAATTATTTTGAAAT
Found at i:1393609 original size:14 final size:15
Alignment explanation
Indices: 1393590--1393618 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1393580 TCAAGCATTT
1393590 AACAATCCA-AAATA
1 AACAATCCAGAAATA
1393604 AACAATCCAGAAATA
1 AACAATCCAGAAATA
1393619 TCAAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.21, G:0.03, T:0.14
Consensus pattern (15 bp):
AACAATCCAGAAATA
Found at i:1396547 original size:3 final size:3
Alignment explanation
Indices: 1396535--1396570 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1396525 ATATTTTTCA
1396535 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1396571 GGTTTTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:1398875 original size:23 final size:23
Alignment explanation
Indices: 1398844--1398957 Score: 165
Period size: 23 Copynumber: 5.0 Consensus size: 23
1398834 CACCACAGCT
* * *
1398844 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCG
* *
1398867 TGTAGAATTACACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCG
*
1398890 CGTAGAATTACACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCG
1398913 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCG
*
1398936 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGGAGTGCC
1398958 ATATAATAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 83 1.00
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCG
Found at i:1399099 original size:103 final size:103
Alignment explanation
Indices: 1398974--1399186 Score: 399
Period size: 103 Copynumber: 2.1 Consensus size: 103
1398964 TAATGTCCAT
* *
1398974 AAGGACCACATATCATTCCTTAAGAATCATATATATATACTAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1399039 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1399077 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1399142 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1399180 AAGGACC
1 AAGGACC
1399187 GCGTAGACCC
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1400583 original size:22 final size:21
Alignment explanation
Indices: 1400558--1400617 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
1400548 TTCGCTTGAG
1400558 GGGTATCGATTCCCCATTGAAT
1 GGGTATCGATTCCCC-TTGAAT
*
1400580 GGGTACCGATT-CCCTTGAAT
1 GGGTATCGATTCCCCTTGAAT
1400600 GGGTATCGATTCCCCTTG
1 GGGTATCGATTCCCCTTG
1400618 CCCAGAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 16 0.46
21 9 0.26
22 10 0.29
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (21 bp):
GGGTATCGATTCCCCTTGAAT
Found at i:1402819 original size:16 final size:16
Alignment explanation
Indices: 1402798--1402831 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1402788 GCATGTCCCT
1402798 TCTGAACTTGAGATAG
1 TCTGAACTTGAGATAG
1402814 TCTGAACTTGAGATAG
1 TCTGAACTTGAGATAG
1402830 TC
1 TC
1402832 AAGGCAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (16 bp):
TCTGAACTTGAGATAG
Found at i:1411337 original size:14 final size:14
Alignment explanation
Indices: 1411318--1411344 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1411308 GATCGAAACT
1411318 TCAAGATTCCAGAG
1 TCAAGATTCCAGAG
1411332 TCAAGATTCCAGA
1 TCAAGATTCCAGA
1411345 AAGATTTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAG
Found at i:1411993 original size:106 final size:106
Alignment explanation
Indices: 1411656--1412194 Score: 781
Period size: 106 Copynumber: 5.0 Consensus size: 106
1411646 ATATCACGTC
* * * * * *
1411656 ACTCGAGACAACACAAGTTCAACTTCAGAACGAAGGGACGATTGGTTGTCAATAAACGATTACTC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
*
1411721 AGTTTTATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 A---AT-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
1411766 ACTCAAGACAACACAAGTTCAACTTCGCAATGAAGGGATGACTGGTTGTCAATAAAACAACTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAA-CAAACAATTTCC
* *
1411831 CAATTTTAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1411873 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
*
1411938 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1411979 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
*
1412044 AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1412085 ACTCGAGACAACATAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAAAAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
* * * *
1412150 AGTTCCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
1412191 ACTC
1 ACTC
1412195 AAAACAGTAC
Statistics
Matches: 395, Mismatches: 33, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
106 255 0.65
107 84 0.21
108 1 0.00
110 46 0.12
111 9 0.02
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1413649 original size:2 final size:2
Alignment explanation
Indices: 1413644--1413669 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1413634 ACGTTTACTA
1413644 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
1413670 TATTTTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1414802 original size:23 final size:22
Alignment explanation
Indices: 1414766--1414864 Score: 94
Period size: 23 Copynumber: 4.5 Consensus size: 22
1414756 CATGGCCTTG
* *
1414766 TGCATCAATACACATTCAAGGCA
1 TGCATCGATGCACATTCAAGG-A
1414789 TGCATCGATGCACATTCAAGTCG-
1 TGCATCGATGCACATTCAAG--GA
* * *
1414812 TGCATCGGTGCACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
* *
1414833 TGTATCGATGCACATTCACGGA
1 TGCATCGATGCACATTCAAGGA
1414855 TGCATCGATG
1 TGCATCGATG
1414865 TACTATTAGG
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
21 18 0.29
22 9 0.14
23 35 0.56
25 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:1414844 original size:21 final size:21
Alignment explanation
Indices: 1414765--1414886 Score: 86
Period size: 23 Copynumber: 5.6 Consensus size: 21
1414755 GCATGGCCTT
* * *
1414765 GTGCATCAATACACATTCAAG
1 GTGCATCGATGCACATTCATG
*
1414786 GCATGCATCGATGCACATTCAAGTC
1 G--TGCATCGATGCACATTC-A-TG
* *
1414811 GTGCATCGGTGCACCTTCATG
1 GTGCATCGATGCACATTCATG
* *
1414832 GTGTATCGATGCACATTCACG
1 GTGCATCGATGCACATTCATG
*
1414853 GATGCATCGATGTACTATT-A-G
1 G-TGCATCGATGCAC-ATTCATG
*
1414874 GTGTATCGATGCA
1 GTGCATCGATGCA
1414887 TTAAGCACAA
Statistics
Matches: 80, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
20 10 0.12
21 22 0.28
22 13 0.16
23 33 0.41
24 1 0.01
25 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (21 bp):
GTGCATCGATGCACATTCATG
Found at i:1414883 original size:20 final size:21
Alignment explanation
Indices: 1414792--1414886 Score: 77
Period size: 21 Copynumber: 4.4 Consensus size: 21
1414782 CAAGGCATGC
* *
1414792 ATCGATGCACATTCAAGTCGTGC
1 ATCGATGCACATTCACG--GTGT
* * *
1414815 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCACGGTGT
*
1414836 ATCGATGCACATTCACGGATGC
1 ATCGATGCACATTCACGG-TGT
*
1414858 ATCGATGTACTATT-A-GGTGT
1 ATCGATGCAC-ATTCACGGTGT
1414878 ATCGATGCA
1 ATCGATGCA
1414887 TTAAGCACAA
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
20 10 0.17
21 20 0.34
22 12 0.20
23 17 0.29
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (21 bp):
ATCGATGCACATTCACGGTGT
Found at i:1420778 original size:35 final size:35
Alignment explanation
Indices: 1420749--1420815 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1420739 TAATTAAAGT
*
1420749 ATTTTGGAATTTGAGGG-TTAAAATATAATTGAAAC
1 ATTTTAGAATTT-AGGGTTTAAAATATAATTGAAAC
*
1420784 ATTTTAGAATTTAGGGTTTAAAATGTAATTGA
1 ATTTTAGAATTTAGGGTTTAAAATATAATTGA
1420816 TGATTGTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 4 0.14
35 25 0.86
ACGTcount: A:0.39, C:0.01, G:0.19, T:0.40
Consensus pattern (35 bp):
ATTTTAGAATTTAGGGTTTAAAATATAATTGAAAC
Found at i:1427055 original size:16 final size:15
Alignment explanation
Indices: 1427027--1427065 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1427017 TATTTTGGTA
*
1427027 TTTTT-AAATAATAAT
1 TTTTTAAAAAAAT-AT
1427042 TTTTTAAAAAAATAT
1 TTTTTAAAAAAATAT
1427057 TTTTTAAAA
1 TTTTTAAAA
1427066 TATATGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTTTAAAAAAATAT
Found at i:1427065 original size:14 final size:14
Alignment explanation
Indices: 1427027--1427070 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
1427017 TATTTTGGTA
*
1427027 TTTTTAAATAATAAT
1 TTTTTAAAAAAT-AT
1427042 TTTTTAAAAAAATAT
1 TTTTT-AAAAAATAT
*
1427057 TTTTTAAAATATAT
1 TTTTTAAAAAATAT
1427071 GATAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 8 0.31
15 12 0.46
16 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTTTAAAAAATAT
Found at i:1427110 original size:18 final size:18
Alignment explanation
Indices: 1427074--1427123 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1427064 AATATATGAT
* *
1427074 AATTATAATCTATTCTTAA
1 AATTATAA-ATATTTTTAA
*
1427093 AGTTATAAATATTTTTAA
1 AATTATAAATATTTTTAA
1427111 AATTATAAA-ATTT
1 AATTATAAATATTT
1427124 AATTTTTTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 4 0.15
18 16 0.59
19 7 0.26
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (18 bp):
AATTATAAATATTTTTAA
Found at i:1435565 original size:42 final size:42
Alignment explanation
Indices: 1435517--1435606 Score: 171
Period size: 42 Copynumber: 2.1 Consensus size: 42
1435507 ACATATCTTT
1435517 TGATTTTTTAATGATGAATAACCAAAATGAAATACTAAAATA
1 TGATTTTTTAATGATGAATAACCAAAATGAAATACTAAAATA
*
1435559 TGATTTTTTAATGATGAATAATCAAAATGAAATACTAAAATA
1 TGATTTTTTAATGATGAATAACCAAAATGAAATACTAAAATA
1435601 TGATTT
1 TGATTT
1435607 AAAAAAAAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.37
Consensus pattern (42 bp):
TGATTTTTTAATGATGAATAACCAAAATGAAATACTAAAATA
Found at i:1445946 original size:15 final size:16
Alignment explanation
Indices: 1445921--1445958 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
1445911 ATAAGTAAAA
1445921 TTATATTAAATTATTT
1 TTATATTAAATTATTT
1445937 TTAT-TTAAATTATTT
1 TTATATTAAATTATTT
1445952 TTCATAT
1 TT-ATAT
1445959 ATTATGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 13 0.65
16 6 0.30
17 1 0.05
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATATTAAATTATTT
Found at i:1447428 original size:17 final size:18
Alignment explanation
Indices: 1447406--1447444 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1447396 TTGGAAGGAA
1447406 TTTTTT-CAAGTCTTTCT
1 TTTTTTCCAAGTCTTTCT
1447423 TTTTTTCCAAGTCTTTCT
1 TTTTTTCCAAGTCTTTCT
1447441 TTTT
1 TTTT
1447445 CTAACTTGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.10, C:0.18, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTTTCCAAGTCTTTCT
Found at i:1450282 original size:12 final size:12
Alignment explanation
Indices: 1450265--1450293 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1450255 ATAACAAATA
1450265 TTTGAGGTCAGG
1 TTTGAGGTCAGG
1450277 TTTGAGGTCAGG
1 TTTGAGGTCAGG
1450289 TTTGA
1 TTTGA
1450294 TTTGTTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.07, G:0.38, T:0.38
Consensus pattern (12 bp):
TTTGAGGTCAGG
Found at i:1454537 original size:17 final size:18
Alignment explanation
Indices: 1454517--1454562 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
1454507 ATTTGTGTGC
1454517 TTATTTTATTTTACTT-T
1 TTATTTTATTTTACTTGT
*
1454534 TTATTTTA-TTTATTTGT
1 TTATTTTATTTTACTTGT
1454551 TTATTTTATTTT
1 TTATTTTATTTT
1454563 CACATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.23
17 17 0.65
18 3 0.12
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (18 bp):
TTATTTTATTTTACTTGT
Found at i:1456656 original size:40 final size:40
Alignment explanation
Indices: 1456601--1456691 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
1456591 GTAAAACTTT
* * * *
1456601 AATTTTGATGCAGCTTTAAAAACTTTGATTGA-TCGCTATA
1 AATTTTGGTGTAGCTTTAAAAACTTTGA-TAATTCGCTAGA
*
1456641 AATTTTGGTGTAGCTTTAACAACTTTGATAATTCGCTAGA
1 AATTTTGGTGTAGCTTTAAAAACTTTGATAATTCGCTAGA
1456681 AATTTTGGTGT
1 AATTTTGGTGT
1456692 TTTTTTTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
39 2 0.04
40 43 0.96
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.42
Consensus pattern (40 bp):
AATTTTGGTGTAGCTTTAAAAACTTTGATAATTCGCTAGA
Found at i:1458651 original size:30 final size:30
Alignment explanation
Indices: 1458612--1458670 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
1458602 TAGAAATGAT
*
1458612 TTGGGGACC-ATTTGATAATTTTTGAAAAG
1 TTGGGGACCAATTCGATAATTTTTGAAAAG
*
1458641 TTGGGAGACCAATTCGGTAATTTTTGAAAA
1 TTGGG-GACCAATTCGATAATTTTTGAAAA
1458671 ATAGTGGGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 5 0.19
30 4 0.15
31 17 0.65
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (30 bp):
TTGGGGACCAATTCGATAATTTTTGAAAAG
Found at i:1461524 original size:18 final size:18
Alignment explanation
Indices: 1461498--1461555 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1461488 AATATATTAC
1461498 AAATAAACATATAAAATT
1 AAATAAACATATAAAATT
*
1461516 AAATCAACA-ACTAAAA-T
1 AAATAAACATA-TAAAATT
*
1461533 AAATGAA-AT-TAAAATT
1 AAATAAACATATAAAATT
*
1461549 ATATAAA
1 AAATAAA
1461556 AATGATTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 5 0.15
16 7 0.21
17 8 0.24
18 13 0.39
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATAAACATATAAAATT
Done.