Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008001.1 Hibiscus syriacus cultivar Beakdansim tig00110458_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: 3902382
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 18
Found at i:1140257 original size:22 final size:22
Alignment explanation
Indices: 1140232--1140282 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
1140222 ATTTAAACTT
*
1140232 TTACCCTCTAAATTTTAATAAG
1 TTACCCTCTAAATTTAAATAAG
* * *
1140254 TTACCATTTTAAATTTAAATAAT
1 TTACC-CTCTAAATTTAAATAAG
1140277 TTACCC
1 TTACCC
1140283 CCTTCTAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.43
Consensus pattern (22 bp):
TTACCCTCTAAATTTAAATAAG
Found at i:1141610 original size:17 final size:17
Alignment explanation
Indices: 1141585--1141619 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1141575 ATTCTAACAC
*
1141585 AACATAACATAAATTCT
1 AACACAACATAAATTCT
1141602 AACACAACATAAATTCT
1 AACACAACATAAATTCT
1141619 A
1 A
1141620 GAAGCTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.26
Consensus pattern (17 bp):
AACACAACATAAATTCT
Found at i:1156235 original size:38 final size:38
Alignment explanation
Indices: 1156163--1156236 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 38
1156153 TCGGGTCGGG
*
1156163 TTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCGGAC
1 TTTTTTAAGTGTGATATTCGGGTCGAGTCAGGTCGGAC
*
1156201 TTTTTTAAGTGTGATATTCGGTTC-AGGTCAGGTCGG
1 TTTTTTAAGTGTGATATTCGGGTCGA-GTCAGGTCGG
1156237 GTTCGGGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.16, C:0.12, G:0.32, T:0.39
Consensus pattern (38 bp):
TTTTTTAAGTGTGATATTCGGGTCGAGTCAGGTCGGAC
Found at i:1156843 original size:18 final size:18
Alignment explanation
Indices: 1156820--1156855 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1156810 TATAGAATTG
*
1156820 GATTCCAATTCCTTCATA
1 GATTCCAATTCCCTCATA
1156838 GATTCCAATTCCCTCATA
1 GATTCCAATTCCCTCATA
1156856 AATATTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.31, G:0.06, T:0.36
Consensus pattern (18 bp):
GATTCCAATTCCCTCATA
Found at i:1165455 original size:26 final size:26
Alignment explanation
Indices: 1165419--1165485 Score: 134
Period size: 26 Copynumber: 2.6 Consensus size: 26
1165409 GTCTCGTACG
1165419 CCAAAACGGCGTCGTCCCGTTTAGTT
1 CCAAAACGGCGTCGTCCCGTTTAGTT
1165445 CCAAAACGGCGTCGTCCCGTTTAGTT
1 CCAAAACGGCGTCGTCCCGTTTAGTT
1165471 CCAAAACGGCGTCGT
1 CCAAAACGGCGTCGT
1165486 ATTGACCTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.24
Consensus pattern (26 bp):
CCAAAACGGCGTCGTCCCGTTTAGTT
Found at i:1165979 original size:3 final size:3
Alignment explanation
Indices: 1165971--1166002 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1165961 TATGTGTGGT
1165971 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1166003 TTTTTTTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1174183 original size:8 final size:8
Alignment explanation
Indices: 1174170--1174197 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1174160 AGATTCTCCC
1174170 ATATGTAT
1 ATATGTAT
1174178 ATATGTAT
1 ATATGTAT
1174186 ATATGTAT
1 ATATGTAT
1174194 ATAT
1 ATAT
1174198 CTTCTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:1177694 original size:8 final size:8
Alignment explanation
Indices: 1177681--1177734 Score: 64
Period size: 8 Copynumber: 7.4 Consensus size: 8
1177671 AAAATGAGTG
1177681 AAAATGAA
1 AAAATGAA
1177689 AAAATGAA
1 AAAATGAA
*
1177697 AAAATAAA
1 AAAATGAA
1177705 AAAAT-AA
1 AAAATGAA
1177712 AAAATG--
1 AAAATGAA
1177718 --AATGAA
1 AAAATGAA
1177724 AAAATGAA
1 AAAATGAA
1177732 AAA
1 AAA
1177735 TGAGGGTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
4 4 0.10
7 7 0.17
8 29 0.73
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.13
Consensus pattern (8 bp):
AAAATGAA
Found at i:1178820 original size:55 final size:55
Alignment explanation
Indices: 1178736--1179324 Score: 857
Period size: 55 Copynumber: 10.7 Consensus size: 55
1178726 CCAACGATAA
* *
1178736 TTGAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
1178791 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* *
1178846 TTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
1178901 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
*
1178956 TTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* *
1179011 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAGATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
*
1179066 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAG-AAATAGGGAGCAGACACGATTG
* * * *
1179122 TTGAAGATTGTTCGAGTCTCATTCTCTCTGAAGAAAATAGGGAGCAGGCACGATTA
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAG-AAATAGGGAGCAGACACGATTG
* * * *
1179178 TTG-AGAATTGTTCGAGTCTCATACTCTCTGAAAAAATAGGGAGCAGACATGATTA
1 TTGAAG-ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* * * * * *
1179233 TCG-AGAATCGTTTGAGTCTTGTACTCTCTGGA-AAATGGGGAGCAGACACGATTG
1 TTGAAG-ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
** * * *
1179287 ACGAAGATT-TTCGAGT-TT-TACTCCCTGGAGCAATAGGG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG
1179325 GATAAAACCA
Statistics
Matches: 497, Mismatches: 33, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
51 10 0.02
52 8 0.02
53 6 0.01
54 23 0.05
55 348 0.70
56 102 0.21
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (55 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
Found at i:1181012 original size:26 final size:26
Alignment explanation
Indices: 1180976--1181042 Score: 134
Period size: 26 Copynumber: 2.6 Consensus size: 26
1180966 GTCTCGTACG
1180976 CCAAAACGGCGTCGTCCCGTTTAGTT
1 CCAAAACGGCGTCGTCCCGTTTAGTT
1181002 CCAAAACGGCGTCGTCCCGTTTAGTT
1 CCAAAACGGCGTCGTCCCGTTTAGTT
1181028 CCAAAACGGCGTCGT
1 CCAAAACGGCGTCGT
1181043 ATTGACCTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.24
Consensus pattern (26 bp):
CCAAAACGGCGTCGTCCCGTTTAGTT
Found at i:1181536 original size:3 final size:3
Alignment explanation
Indices: 1181528--1181556 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1181518 TATGTGTGGT
1181528 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1181557 TTTTTTTTGA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1183846 original size:22 final size:21
Alignment explanation
Indices: 1183814--1183888 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
1183804 TAATAATGGA
1183814 ATCGAT-CTTTTAAGGGAAGGG
1 ATCGATCCTTTT-AGGGAAGGG
* **
1183835 ATCGAACCTTTTCATCG-AGGG
1 ATCGATCCTTTT-AGGGAAGGG
1183856 ATCGATCCTTTT-GGTGAAGGG
1 ATCGATCCTTTTAGG-GAAGGG
1183877 ATCGATCCTTTT
1 ATCGATCCTTTT
1183889 GGTGAAATGA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
20 1 0.02
21 36 0.82
22 7 0.16
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (21 bp):
ATCGATCCTTTTAGGGAAGGG
Found at i:1183876 original size:21 final size:21
Alignment explanation
Indices: 1183829--1183904 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
1183819 TCTTTTAAGG
* **
1183829 GAAGGGATCGAACCTTTTCAT
1 GAAGGGATCGATCCTTTTGGT
1183850 CG-AGGGATCGATCCTTTTGGT
1 -GAAGGGATCGATCCTTTTGGT
1183871 GAAGGGATCGATCCTTTTGGT
1 GAAGGGATCGATCCTTTTGGT
**
1183892 GAAATGATCGATC
1 GAAGGGATCGATC
1183905 TCAAACTCAC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
20 1 0.02
21 46 0.96
22 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (21 bp):
GAAGGGATCGATCCTTTTGGT
Found at i:1187884 original size:6 final size:6
Alignment explanation
Indices: 1187875--1187901 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1187865 TTAAAACTCA
1187875 AACTTG AACTTG AACTTG AACTTG AAC
1 AACTTG AACTTG AACTTG AACTTG AAC
1187902 CTTAAGTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (6 bp):
AACTTG
Found at i:1187982 original size:15 final size:15
Alignment explanation
Indices: 1187971--1188000 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1187961 TTATTAATAA
1187971 TTTAAAATTTAAAAT
1 TTTAAAATTTAAAAT
1187986 TTTAAAATTTTAAAA
1 TTTAAAA-TTTAAAA
1188001 ATTAATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAAAATTTAAAAT
Found at i:1188003 original size:9 final size:8
Alignment explanation
Indices: 1187971--1188000 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1187961 TTATTAATAA
1187971 TTTAAAA-
1 TTTAAAAT
1187978 TTTAAAAT
1 TTTAAAAT
1187986 TTTAAAAT
1 TTTAAAAT
1187994 TTTAAAA
1 TTTAAAA
1188001 ATTAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TTTAAAAT
Found at i:1188012 original size:8 final size:8
Alignment explanation
Indices: 1187950--1188012 Score: 51
Period size: 8 Copynumber: 8.0 Consensus size: 8
1187940 AATAACATAT
1187950 AAATATTA
1 AAATATTA
*
1187958 ATATTATTA
1 A-AATATTA
1187967 ATAAT-TTA
1 A-AATATTA
1187975 AAAT-TTA
1 AAATATTA
*
1187982 AAATTTTA
1 AAATATTA
*
1187990 AAATTTTA
1 AAATATTA
1187998 AAA-ATTA
1 AAATATTA
*
1188005 ATATATTA
1 AAATATTA
1188013 TTTTTAGTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
7 15 0.31
8 23 0.48
9 10 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAATATTA
Found at i:1194239 original size:18 final size:18
Alignment explanation
Indices: 1194216--1194265 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
1194206 AAGCTTTTCC
*
1194216 TGCGGTTGGGGTTGCAGT
1 TGCGGTTGCGGTTGCAGT
* *
1194234 TGCGGTTGCGGCTGGAGT
1 TGCGGTTGCGGTTGCAGT
*
1194252 TGCAGTTGCGGTTG
1 TGCGGTTGCGGTTG
1194266 TAGGTGCTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.06, C:0.14, G:0.48, T:0.32
Consensus pattern (18 bp):
TGCGGTTGCGGTTGCAGT
Found at i:1194253 original size:24 final size:24
Alignment explanation
Indices: 1194216--1194265 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
1194206 AAGCTTTTCC
* *
1194216 TGCGGTTGGGGTTGCAGTTGCGGT
1 TGCGGCTGGAGTTGCAGTTGCGGT
1194240 TGCGGCTGGAGTTGCAGTTGCGGT
1 TGCGGCTGGAGTTGCAGTTGCGGT
1194264 TG
1 TG
1194266 TAGGTGCTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.06, C:0.14, G:0.48, T:0.32
Consensus pattern (24 bp):
TGCGGCTGGAGTTGCAGTTGCGGT
Found at i:1194765 original size:30 final size:30
Alignment explanation
Indices: 1194724--1194807 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
1194714 CTGTCGCTTG
*
1194724 ACTGTTGTGCCTGTCGTCGGTGTATCCAGA
1 ACTGCTGTGCCTGTCGTCGGTGTATCCAGA
* *
1194754 ACTGCTGTGCCTATCGTCGGTGTATCCGGA
1 ACTGCTGTGCCTGTCGTCGGTGTATCCAGA
* *
1194784 ACTGCTGTGCCTGTTGCCGGTGTA
1 ACTGCTGTGCCTGTCGTCGGTGTA
1194808 GTTGAAGTCT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.12, C:0.25, G:0.31, T:0.32
Consensus pattern (30 bp):
ACTGCTGTGCCTGTCGTCGGTGTATCCAGA
Found at i:1197611 original size:23 final size:22
Alignment explanation
Indices: 1197553--1197642 Score: 67
Period size: 22 Copynumber: 3.9 Consensus size: 22
1197543 ATTTGAAAAT
1197553 AATAATATATATTTTAATTTTTG
1 AATAAT-TATATTTTAATTTTTG
*
1197576 AATAATT-TAATTTTTATTTTTGG
1 AATAATTAT-ATTTTAATTTTT-G
* *
1197599 TATTATTATA-TTTAAGTTTTTG
1 AATAATTATATTTTAA-TTTTTG
*
1197621 AATATTTTTATATTTTGAATTT
1 AATA--ATTATATTTT-AATTT
1197643 AAAATATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
21 1 0.02
22 19 0.37
23 18 0.35
24 6 0.12
25 6 0.12
26 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
AATAATTATATTTTAATTTTTG
Found at i:1197669 original size:23 final size:24
Alignment explanation
Indices: 1197621--1197670 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
1197611 TAAGTTTTTG
**
1197621 AATATTTTTATATTTTGAATTTAA
1 AATATTTTTATATTTTGAATAAAA
*
1197645 AATATTTTT-TATTTTTAATAAAA
1 AATATTTTTATATTTTGAATAAAA
1197668 AAT
1 AAT
1197671 TAAATAATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
AATATTTTTATATTTTGAATAAAA
Found at i:1199805 original size:15 final size:15
Alignment explanation
Indices: 1199785--1199887 Score: 91
Period size: 15 Copynumber: 6.5 Consensus size: 15
1199775 TAATAAGGTT
1199785 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1199800 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
1199815 ATTTACTTTAAAATA
1 ATTTATTTTAAAATA
* *
1199830 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
*
1199849 TTGATTTATTTTTAAATA
1 ---ATTTATTTTAAAATA
1199867 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
1199881 ATTTATT
1 ATTTATT
1199888 AGTATGGATT
Statistics
Matches: 72, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
14 12 0.17
15 41 0.57
16 4 0.06
17 2 0.03
18 1 0.01
19 1 0.01
20 2 0.03
21 3 0.04
22 6 0.08
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1199825 original size:30 final size:30
Alignment explanation
Indices: 1199785--1199844 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1199775 TAATAAGGTT
* *
1199785 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTACTTTAAAATAAATTATTATAAAATA
1199815 ATTTACTTTAAAATAAATTATTATAAAATA
1 ATTTACTTTAAAATAAATTATTATAAAATA
1199845 TGGATTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (30 bp):
ATTTACTTTAAAATAAATTATTATAAAATA
Found at i:1199865 original size:22 final size:22
Alignment explanation
Indices: 1199840--1199934 Score: 77
Period size: 22 Copynumber: 4.2 Consensus size: 22
1199830 AATTATTATA
1199840 AAATATGGATTGATTTATTTTT
1 AAATATGGATTGATTTATTTTT
** * * *
1199862 AAATAATTTATTTTAAATAATTTATT
1 AAAT-ATGGA--TTGATTTATTT-TT
* *
1199888 -AGTATGGATTGATTTATTTTA
1 AAATATGGATTGATTTATTTTT
1199909 AAATATGGATTGATTTA-TTTT
1 AAATATGGATTGATTTATTTTT
1199930 AAATA
1 AAATA
1199935 ATTTATTAGT
Statistics
Matches: 54, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
21 9 0.17
22 27 0.50
23 3 0.06
24 3 0.06
25 10 0.19
26 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.52
Consensus pattern (22 bp):
AAATATGGATTGATTTATTTTT
Found at i:1199877 original size:14 final size:14
Alignment explanation
Indices: 1199852--1199887 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
1199842 ATATGGATTG
1199852 ATTTATTTTTAAATA
1 ATTTA-TTTTAAATA
1199867 ATTTATTTTAAATA
1 ATTTATTTTAAATA
1199881 ATTTATT
1 ATTTATT
1199888 AGTATGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:1199905 original size:32 final size:32
Alignment explanation
Indices: 1199867--1199964 Score: 117
Period size: 32 Copynumber: 3.4 Consensus size: 32
1199857 TTTTTAAATA
1199867 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1199899 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
1199921 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1199953 ATTTATTTTAAA
1 ATTTATTTTAAA
1199965 ATATGGATTA
Statistics
Matches: 55, Mismatches: 1, Indels: 20
0.72 0.01 0.26
Matches are distributed among these distances:
22 14 0.25
23 4 0.07
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.07
32 25 0.45
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:1199932 original size:54 final size:54
Alignment explanation
Indices: 1199867--1200274 Score: 271
Period size: 54 Copynumber: 7.4 Consensus size: 54
1199857 TTTTTAAATA
1199867 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
1199921 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * * *
1199975 ATTTATTATT--GTAGTTGTA-T-GAATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATT-TTAAATAATT-TATTAGTATGGATTGA-TTT--AT--TTTA-AAATATGGATTG
** ** * ** * * *
1200033 ATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTG
* *
1200087 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * ** * * * * ***
1200137 ATTTGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
*
1200199 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1200253 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
1200275 TTATAGTTGT
Statistics
Matches: 274, Mismatches: 52, Indels: 56
0.72 0.14 0.15
Matches are distributed among these distances:
50 16 0.06
52 10 0.04
53 11 0.04
54 141 0.51
55 17 0.06
56 8 0.03
57 8 0.03
58 36 0.13
59 9 0.03
60 2 0.01
62 16 0.06
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:1200011 original size:80 final size:82
Alignment explanation
Indices: 1199912--1200130 Score: 320
Period size: 80 Copynumber: 2.6 Consensus size: 82
1199902 TATTTTAAAA
1199912 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTAAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAAATATGGATTAAT
1199977 TTA-TT-AT-TGTAGTT-G
65 TTATTTAATATGTA-TTAG
* *
1199992 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAAATATGGATTAAT
*
1200057 TTATTTTAAATAATTTATTAG
65 TTA-TTT-AAT-ATGTATTAG
1200078 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTTTAAA
1200131 TAATTTATTT
Statistics
Matches: 126, Mismatches: 5, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
80 65 0.52
82 2 0.02
84 2 0.02
85 3 0.02
86 54 0.43
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (82 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAAATATGGATTAATT
TATTTAATATGTATTAG
Found at i:1200033 original size:32 final size:32
Alignment explanation
Indices: 1199991--1200162 Score: 247
Period size: 32 Copynumber: 5.7 Consensus size: 32
1199981 TATTGTAGTT
*
1199991 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1200023 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1200046 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1200077 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
1200109 GTATGAATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1200141 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
1200163 ATATGAATTG
Statistics
Matches: 126, Mismatches: 4, Indels: 20
0.84 0.03 0.13
Matches are distributed among these distances:
22 14 0.11
23 4 0.03
25 1 0.01
26 3 0.02
28 3 0.02
29 1 0.01
31 4 0.03
32 96 0.76
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:1200049 original size:22 final size:22
Alignment explanation
Indices: 1200024--1200066 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1200014 AATTTATTAG
1200024 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1200046 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1200067 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1200074 original size:14 final size:14
Alignment explanation
Indices: 1200055--1200140 Score: 55
Period size: 14 Copynumber: 5.6 Consensus size: 14
1200045 ATATGGATTG
1200055 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* * *
1200069 ATTTATTAGTATGGATTG
1 ATTTATT--T-T-AAATA
1200087 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
1200101 ATTTATTAGTATGAATTG
1 ATTTATT--T-T-AAATA
1200119 ATTTATTTTAAATA
1 ATTTATTTTAAATA
1200133 ATTTATTT
1 ATTTATTT
1200141 GTATGGATTG
Statistics
Matches: 54, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
14 27 0.50
15 2 0.04
16 4 0.07
17 2 0.04
18 19 0.35
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:1200145 original size:118 final size:112
Alignment explanation
Indices: 1199991--1200242 Score: 391
Period size: 118 Copynumber: 2.2 Consensus size: 112
1199981 TATTGTAGTT
*
1199991 GTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1 GTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGA
*
1200056 TTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAATAATTTATTA
66 TTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTA
*
1200109 GTATGAATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGAATTGA
1 GTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGA
1200174 TTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTA
66 TTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTA
1200221 GTAT-AGATTGATTTATTTTAAA
1 GTATGA-ATTGATTTATTTTAAA
1200243 ATATGGATTG
Statistics
Matches: 129, Mismatches: 3, Indels: 10
0.91 0.02 0.07
Matches are distributed among these distances:
111 1 0.01
112 55 0.43
113 2 0.02
114 2 0.02
116 2 0.02
118 67 0.52
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.53
Consensus pattern (112 bp):
GTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGA
TTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:1200164 original size:198 final size:188
Alignment explanation
Indices: 1199867--1200274 Score: 672
Period size: 198 Copynumber: 2.1 Consensus size: 188
1199857 TTTTTAAATA
1199867 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
*
1199932 ATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAGTTGTATGA
66 ATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTAATTTATTATTGTAGTTGTATGA
*
1199997 ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
131 ATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1200055 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-T-G---G-ATTGA
* * *
1200120 TTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTGT
56 TTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTAATTTATTATTGT
*
1200185 AGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGA
121 AGTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGA
1200250 TTG
186 TTG
1200253 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
1200275 TTATAGTTGT
Statistics
Matches: 204, Mismatches: 6, Indels: 10
0.93 0.03 0.05
Matches are distributed among these distances:
188 41 0.20
189 2 0.01
190 2 0.01
192 2 0.01
193 1 0.00
194 1 0.00
197 1 0.00
198 154 0.75
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (188 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
ATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTAATTTATTATTGTAGTTGTATGA
ATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
Found at i:1200230 original size:80 final size:80
Alignment explanation
Indices: 1200109--1200259 Score: 266
Period size: 80 Copynumber: 1.9 Consensus size: 80
1200099 TAATTTATTA
* *
1200109 GTATGAATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGAATTGA
1 GTATGAATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTGA
1200174 TTTATTATTGTAGTT
66 TTTATTATTGTAGTT
* *
1200189 GTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGA
1 GTATGAATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTGA
1200254 TTTATT
66 TTTATT
1200260 TTAAATAATT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (80 bp):
GTATGAATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTGA
TTTATTATTGTAGTT
Found at i:1200324 original size:31 final size:31
Alignment explanation
Indices: 1200289--1200347 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1200279 AGTTGTATGG
* *
1200289 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATATCAGTATTGCAAAACTAAA
1200320 ATTATTTAAATATCAGTATTGCAAAACT
1 ATTATTTAAATATCAGTATTGCAAAACT
1200348 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATATCAGTATTGCAAAACTAAA
Found at i:1201244 original size:17 final size:17
Alignment explanation
Indices: 1201222--1201260 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1201212 TGAATCAAAT
1201222 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1201239 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1201256 -AATTA
1 TAATTA
1201261 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:1203208 original size:29 final size:30
Alignment explanation
Indices: 1203152--1203211 Score: 113
Period size: 29 Copynumber: 2.0 Consensus size: 30
1203142 ATTTTCACCT
1203152 AACTAAATTGATGTTAAGCAATGACATCAA
1 AACTAAATTGATGTTAAGCAATGACATCAA
1203182 AACTAAATTGATG-TAAGCAATGACATCAA
1 AACTAAATTGATGTTAAGCAATGACATCAA
1203211 A
1 A
1203212 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.25
Consensus pattern (30 bp):
AACTAAATTGATGTTAAGCAATGACATCAA
Found at i:1208634 original size:29 final size:29
Alignment explanation
Indices: 1208592--1208650 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1208582 ATTTTTACCT
*
1208592 AACTAAATTGATGTAAACAATGGCATCAA
1 AACTAAATTGATGTAAACAATGACATCAA
*
1208621 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAACAATGACATCAA
1208650 A
1 A
1208651 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAACAATGACATCAA
Found at i:1219877 original size:34 final size:35
Alignment explanation
Indices: 1219824--1219904 Score: 137
Period size: 34 Copynumber: 2.3 Consensus size: 35
1219814 GTCCAGGGGT
1219824 ACAGATTCCCCCCAGGGGGTATCGATTCCCCAGGA
1 ACAGATTCCCCCCAGGGGGTATCGATTCCCCAGGA
* *
1219859 ACAGATTCCCCCCA-GGGGTATCGATTCCCCGGGT
1 ACAGATTCCCCCCAGGGGGTATCGATTCCCCAGGA
1219893 ACAGATTCCCCC
1 ACAGATTCCCCC
1219905 TGCATGGTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 30 0.68
35 14 0.32
ACGTcount: A:0.21, C:0.37, G:0.23, T:0.19
Consensus pattern (35 bp):
ACAGATTCCCCCCAGGGGGTATCGATTCCCCAGGA
Found at i:1220055 original size:21 final size:21
Alignment explanation
Indices: 1220017--1220058 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1220007 ATTTGAATAT
* **
1220017 TATGAAGGGGTATTGATTCCC
1 TATGAAGGGATACCGATTCCC
1220038 TATGAAGGGATACCGATTCCC
1 TATGAAGGGATACCGATTCCC
1220059 CCCATTCTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (21 bp):
TATGAAGGGATACCGATTCCC
Found at i:1220381 original size:34 final size:32
Alignment explanation
Indices: 1220342--1220411 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
1220332 TTTTGTAAAG
*
1220342 GGGAAAGGTTCTAGCTAATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAATCCCG-G-AAAAACTA
* * *
1220376 GGGAAATGTTCTAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
1220408 GGGA
1 GGGA
1220412 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
Found at i:1222091 original size:24 final size:24
Alignment explanation
Indices: 1222057--1222125 Score: 129
Period size: 24 Copynumber: 2.9 Consensus size: 24
1222047 GAGTAGAGGG
*
1222057 TCTACGCGGTCCTTCGGGACAAAT
1 TCTACGTGGTCCTTCGGGACAAAT
1222081 TCTACGTGGTCCTTCGGGACAAAT
1 TCTACGTGGTCCTTCGGGACAAAT
1222105 TCTACGTGGTCCTTCGGGACA
1 TCTACGTGGTCCTTCGGGACA
1222126 TATATGTATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.28
Consensus pattern (24 bp):
TCTACGTGGTCCTTCGGGACAAAT
Found at i:1222815 original size:18 final size:18
Alignment explanation
Indices: 1222794--1222832 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1222784 TTTTGTATAA
1222794 TAATGAAAGGCTAAATTT
1 TAATGAAAGGCTAAATTT
1222812 TAATGAAAGGCTAAATTT
1 TAATGAAAGGCTAAATTT
1222830 TAA
1 TAA
1222833 GAGTGTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.33
Consensus pattern (18 bp):
TAATGAAAGGCTAAATTT
Found at i:1224805 original size:45 final size:45
Alignment explanation
Indices: 1224754--1224855 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
1224744 AAGACTTTTA
1224754 ATTATTGGGTTGCCAAAAGTAAAATCAAAGGATTAAT-TCTT-TCCG
1 ATTATTGGGTTGCCAAAAGTAAAATCAAAGGATTAATATCTTGT--G
* * * * * *
1224799 ATTATTGGATTACGAAAATTAAAATCAAATGATTAGTATCTTGTG
1 ATTATTGGGTTGCCAAAAGTAAAATCAAAGGATTAATATCTTGTG
1224844 ATTATTGGGTTG
1 ATTATTGGGTTG
1224856 GTAAAATTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
45 42 0.89
46 4 0.09
47 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (45 bp):
ATTATTGGGTTGCCAAAAGTAAAATCAAAGGATTAATATCTTGTG
Found at i:1225114 original size:58 final size:58
Alignment explanation
Indices: 1225032--1225192 Score: 187
Period size: 58 Copynumber: 2.8 Consensus size: 58
1225022 TCTAGCTTCG
* * * *
1225032 TAAGGAAACTAAATAGTTAGATTTATTTCCTTGAGAATCCTGAATGATTATAACTTTC
1 TAAGAAAAATAAATAGTTAAATTTATTTCCTTGAGAATCTTGAATGATTATAACTTTC
* * * * * * * *
1225090 TAATAAAATTATATTGTTAAATTTATTTCTTTGATAATCTTGAATGATTCTAACTTTG
1 TAAGAAAAATAAATAGTTAAATTTATTTCCTTGAGAATCTTGAATGATTATAACTTTC
* * *
1225148 TAAGAAAAATAAATAGTTGAATTTATTTTCTTGAGGATCTTGAAT
1 TAAGAAAAATAAATAGTTAAATTTATTTCCTTGAGAATCTTGAAT
1225193 AATTTTATTT
Statistics
Matches: 83, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 83 1.00
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (58 bp):
TAAGAAAAATAAATAGTTAAATTTATTTCCTTGAGAATCTTGAATGATTATAACTTTC
Found at i:1225936 original size:18 final size:19
Alignment explanation
Indices: 1225909--1225950 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1225899 AACTAGCCGT
1225909 TACT-TGATCA-GTATCGA
1 TACTATGATCAGGTATCGA
1225926 TACTATGATCATGGTATCGA
1 TACTATGATCA-GGTATCGA
1225946 TACTA
1 TACTA
1225951 CTGTGTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.18
18 6 0.27
20 12 0.55
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (19 bp):
TACTATGATCAGGTATCGA
Found at i:1227466 original size:20 final size:19
Alignment explanation
Indices: 1227429--1227476 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1227419 TCTAAATCAT
*
1227429 TTTTCAAAATTTCATTTTG
1 TTTTCAAAATCTCATTTTG
1227448 ATTTTCAAAATCT-ATTTTTG
1 -TTTTCAAAATCTCA-TTTTG
*
1227468 CTTTCAAAA
1 TTTTCAAAA
1227477 GAAAATCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.52
Consensus pattern (19 bp):
TTTTCAAAATCTCATTTTG
Found at i:1228581 original size:20 final size:20
Alignment explanation
Indices: 1228540--1228654 Score: 81
Period size: 20 Copynumber: 5.8 Consensus size: 20
1228530 AAATAACCAA
* *
1228540 CAAATTCGCAACGCGAA-CTC
1 CAAATTCGCAACAC-AATTTC
* *
1228560 CAATTTCGCAACACAGTTTC
1 CAAATTCGCAACACAATTTC
* ** *
1228580 CAAATTCACAATGCGATTTTC
1 CAAATTCGCAACAC-AATTTC
* *
1228601 CAATTTTGCAACACAATTTC
1 CAAATTCGCAACACAATTTC
* * *
1228621 CAAATTCGCAACTCGATCT-
1 CAAATTCGCAACACAATTTC
1228640 CAAATTCGCAACACA
1 CAAATTCGCAACACA
1228655 TAATTAAAAT
Statistics
Matches: 71, Mismatches: 22, Indels: 5
0.72 0.22 0.05
Matches are distributed among these distances:
19 14 0.20
20 43 0.61
21 14 0.20
ACGTcount: A:0.35, C:0.30, G:0.10, T:0.26
Consensus pattern (20 bp):
CAAATTCGCAACACAATTTC
Found at i:1228732 original size:40 final size:40
Alignment explanation
Indices: 1228645--1228732 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 40
1228635 GATCTCAAAT
* * * *
1228645 TCGCAACACATAATTAAAATTCGCATTGCGAATTTCAATT
1 TCGCAACACAGAATTAAAATTCGCATTACAAATTTCAATA
** * * *
1228685 TAACAACACAGAATTGAAATTCGCGTTACAAATTTCACTA
1 TCGCAACACAGAATTAAAATTCGCATTACAAATTTCAATA
1228725 TCGCAACA
1 TCGCAACA
1228733 ACACACCTTT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (40 bp):
TCGCAACACAGAATTAAAATTCGCATTACAAATTTCAATA
Found at i:1228983 original size:39 final size:40
Alignment explanation
Indices: 1228920--1229047 Score: 159
Period size: 40 Copynumber: 3.2 Consensus size: 40
1228910 GTTGCGATAG
* * *
1228920 TGAAATCCGTAACGCGAATTTCAATTTTGTGTTGCTAAAT
1 TGAAATTCGCAACGCGAATTTCAATTATGTGTTGCTAAAT
* *
1228960 TGAAATTCGCAA-GCGAATTTCAATTCTGTGTTGTTAAAT
1 TGAAATTCGCAACGCGAATTTCAATTATGTGTTGCTAAAT
* * * *
1228999 TGAAATTCGCAACGCGAATTTTAATTATGTATTGCGAATT
1 TGAAATTCGCAACGCGAATTTCAATTATGTGTTGCTAAAT
*
1229039 TTAAATTCG
1 TGAAATTCG
1229048 AGTTGTGAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
39 37 0.49
40 39 0.51
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.38
Consensus pattern (40 bp):
TGAAATTCGCAACGCGAATTTCAATTATGTGTTGCTAAAT
Found at i:1229065 original size:21 final size:20
Alignment explanation
Indices: 1229041--1229084 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1229031 TGCGAATTTT
* *
1229041 AAATTCGAGTTGTGAATTTGG
1 AAATT-GAGTTGCGAAATTGG
*
1229062 AAATTGTGTTGCGAAATTGG
1 AAATTGAGTTGCGAAATTGG
1229082 AAA
1 AAA
1229085 ACCGCATTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (20 bp):
AAATTGAGTTGCGAAATTGG
Found at i:1229141 original size:21 final size:20
Alignment explanation
Indices: 1229049--1229144 Score: 75
Period size: 21 Copynumber: 4.7 Consensus size: 20
1229039 TTAAATTCGA
* * *
1229049 GTTGTGAATTTGGAAATTGT
1 GTTGCGAATTTGGAAACTGC
* *
1229069 GTTGCGAAATTGGAAAACCGC
1 GTTGCGAATTTGG-AAACTGC
* * * *
1229090 ATTACGAATTTGAAAAATCGC
1 GTTGCGAATTTGGAAACT-GC
*
1229111 GTTGCGAATTTGGAAACTGT
1 GTTGCGAATTTGGAAACTGC
*
1229131 GTTGCGAAATTGGA
1 GTTGCGAATTTGGA
1229145 GTTCGCGTTG
Statistics
Matches: 57, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 28 0.49
21 29 0.51
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.31
Consensus pattern (20 bp):
GTTGCGAATTTGGAAACTGC
Found at i:1230918 original size:3 final size:3
Alignment explanation
Indices: 1230902--1230941 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
1230892 TTATTATTAT
*
1230902 TAA TAG TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1230942 TCAAATGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1234925 original size:49 final size:48
Alignment explanation
Indices: 1234816--1234964 Score: 210
Period size: 49 Copynumber: 3.0 Consensus size: 48
1234806 GTATATGCTG
* * *
1234816 ATGTGGCATTCAACTTGTAGATCCCTGAAAGTT-GAGTTTAACACTGAA
1 ATGTGACATTCAACTTGTAGATTCTTGAAAGTTAGAGTTTAACA-TGAA
1234864 ATGTGACATTCAACTTGTAGATTCTTGAAAGTTAGAGTTTAACATAGAA
1 ATGTGACATTCAACTTGTAGATTCTTGAAAGTTAGAGTTTAACAT-GAA
*
1234913 ATGTGACCTTCAACTTGTAGATTCTTGAAAGTTAGAGAGTTTAACATTGAA
1 ATGTGACATTCAACTTGTAGATTCTTGAAAGTT--AGAGTTTAACA-TGAA
1234964 A
1 A
1234965 AACAATCCAG
Statistics
Matches: 92, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
48 31 0.34
49 45 0.49
51 15 0.16
52 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (48 bp):
ATGTGACATTCAACTTGTAGATTCTTGAAAGTTAGAGTTTAACATGAA
Found at i:1238568 original size:2 final size:2
Alignment explanation
Indices: 1238561--1238609 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1238551 ATTATCAATA
1238561 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
1238603 AT AT AT A
1 AT AT AT A
1238610 AACAAAGAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1239452 original size:56 final size:56
Alignment explanation
Indices: 1239376--1239488 Score: 208
Period size: 56 Copynumber: 2.0 Consensus size: 56
1239366 TATTTTAGTC
*
1239376 ATTAAAAGGTTGAATGTACGTAAACACGTATCTCTATTTTAATTCATTATGAGTTT
1 ATTAAAAGGTTGAATATACGTAAACACGTATCTCTATTTTAATTCATTATGAGTTT
*
1239432 ATTACAAGGTTGAATATACGTAAACACGTATCTCTATTTTAATTCATTATGAGTTT
1 ATTAAAAGGTTGAATATACGTAAACACGTATCTCTATTTTAATTCATTATGAGTTT
1239488 A
1 A
1239489 ATATTATGGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (56 bp):
ATTAAAAGGTTGAATATACGTAAACACGTATCTCTATTTTAATTCATTATGAGTTT
Found at i:1240716 original size:20 final size:20
Alignment explanation
Indices: 1240691--1240783 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
1240681 TTTTCCCAAT
1240691 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1240711 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
1240731 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
1240752 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1240773 TCGCAATGCGA
1 TCGCAATGCGA
1240784 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1240733 original size:41 final size:41
Alignment explanation
Indices: 1240688--1240783 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
1240678 CGATTTTCCC
1240688 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1240729 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
1240770 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1240784 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:1240737 original size:21 final size:20
Alignment explanation
Indices: 1240691--1240783 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1240681 TTTTCCCAAT
*
1240691 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
1240711 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
1240731 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
1240752 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
1240773 TCGCAATGCGA
1 TCGCAATGCGA
1240784 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:1240796 original size:41 final size:41
Alignment explanation
Indices: 1240710--1240844 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
1240700 GAATAAGTAA
* * *
1240710 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
1240751 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * *
1240792 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTGACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
1240833 TTCGCAACGCGA
1 ATCGCAACGCGA
1240845 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:1240797 original size:20 final size:20
Alignment explanation
Indices: 1240772--1240865 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1240762 AATTGGGAAA
*
1240772 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1240792 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
*
1240813 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1240833 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1240853 TTCGTAACGCGAT
1 ATCGCAACGCGAT
1240866 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1241432 original size:19 final size:19
Alignment explanation
Indices: 1241410--1241453 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1241400 GGAAATGACT
*
1241410 ATCGCAACGAGAAATAAAA
1 ATCGCAACGAGAAACAAAA
* *
1241429 ATCGCAACGCGAAACCAAA
1 ATCGCAACGAGAAACAAAA
1241448 ATCGCA
1 ATCGCA
1241454 TTGTGATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (19 bp):
ATCGCAACGAGAAACAAAA
Found at i:1241471 original size:19 final size:19
Alignment explanation
Indices: 1241458--1241652 Score: 203
Period size: 19 Copynumber: 10.6 Consensus size: 19
1241448 ATCGCATTGT
1241458 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
1241477 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
1241496 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
*
1241515 GATTTTAATTTCGCGGTTGC
1 GATTTTCATTTCGC-GTTGC
1241535 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
* *
1241554 GATTGTC---T-G-GTCGC
1 GATTTTCATTTCGCGTTGC
**
1241568 GATAGTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
*
1241587 GA--TTC---TCTCGTTGC
1 GATTTTCATTTCGCGTTGC
**
1241601 GATAGTCATTTCCGCGTTGC
1 GATTTTCATTT-CGCGTTGC
* *
1241621 GATTCTCATTATCTCGTTGC
1 GATTTTCATT-TCGCGTTGC
1241641 GATTTTCATTTC
1 GATTTTCATTTC
1241653 AACCAAAAGA
Statistics
Matches: 149, Mismatches: 14, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
14 20 0.13
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 71 0.48
20 49 0.33
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
GATTTTCATTTCGCGTTGC
Found at i:1241568 original size:39 final size:38
Alignment explanation
Indices: 1241458--1241652 Score: 171
Period size: 33 Copynumber: 5.3 Consensus size: 38
1241448 ATCGCATTGT
1241458 GATTTTCATTTCGCGTTGCGATTTTCATTTCGC-GTTGC
1 GATTTTCATTTCGCGTTGCGATTTTC-TTTCGCGGTTGC
*
1241496 GATTTTCATTTCGCGTTGCGATTTTAATTTCGCGGTTGC
1 GATTTTCATTTCGCGTTGCGATTTT-CTTTCGCGGTTGC
* *
1241535 GATTTTCATTTCGCGTTGCGATTGTC--T---GGTCGC
1 GATTTTCATTTCGCGTTGCGATTTTCTTTCGCGGTTGC
** *
1241568 GATAGTCATTTCGCGTTGCGA--TTC--TCTC-GTTGC
1 GATTTTCATTTCGCGTTGCGATTTTCTTTCGCGGTTGC
** * *
1241601 GATAGTCATTTCCGCGTTGCGATTCTCATTATCTC-GTTGC
1 GATTTTCATTT-CGCGTTGCGATTTTC-TT-TCGCGGTTGC
1241641 GATTTTCATTTC
1 GATTTTCATTTC
1241653 AACCAAAAGA
Statistics
Matches: 134, Mismatches: 11, Indels: 23
0.80 0.07 0.14
Matches are distributed among these distances:
31 3 0.02
33 39 0.29
34 10 0.07
36 3 0.02
38 31 0.23
39 30 0.22
40 18 0.13
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
GATTTTCATTTCGCGTTGCGATTTTCTTTCGCGGTTGC
Found at i:1241568 original size:58 final size:57
Alignment explanation
Indices: 1241449--1241652 Score: 176
Period size: 58 Copynumber: 3.7 Consensus size: 57
1241439 GAAACCAAAA
* * * * *
1241449 TCGCATTGTGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTGTCATG
1241506 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATTTCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATTTCGCGTTGCGATTGTCATG
* ** * * * *
1241561 T-G-GTCGCGATAGTCATTTCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTGTCATG
* * *
1241611 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATTTC
1 T-CGCGTTGCGATTTTAATT-TCGCGTTGCGATTTTCATTTC
1241653 AACCAAAAGA
Statistics
Matches: 120, Mismatches: 14, Indels: 24
0.76 0.09 0.15
Matches are distributed among these distances:
47 14 0.12
50 4 0.03
52 8 0.07
53 27 0.22
54 11 0.09
55 1 0.01
56 3 0.03
57 20 0.17
58 30 0.25
59 2 0.02
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (57 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTGTCATG
Found at i:1241629 original size:20 final size:20
Alignment explanation
Indices: 1241595--1241652 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1241585 GCGATTCTCT
**
1241595 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
1241615 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1241635 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1241653 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1243711 original size:42 final size:42
Alignment explanation
Indices: 1243651--1243773 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
1243641 GCCTGACTCG
* * *
1243651 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1243693 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
1243735 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1243774 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1243731 original size:21 final size:21
Alignment explanation
Indices: 1243707--1243773 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1243697 TCATTCCTCG
1243707 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1243728 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1243749 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1243770 AGAG
1 AGAG
1243774 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1245148 original size:14 final size:14
Alignment explanation
Indices: 1245129--1245164 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1245119 ATTGTTTAAT
1245129 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1245143 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1245157 TGATTTGT
1 TGATTTGT
1245165 TTAATTGATG
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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1245344 original size:19 final size:19
Alignment explanation
Indices: 1245322--1245419 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
1245312 CGAAATTAAA
*
1245322 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1245341 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
1245357 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1245374 TTCGCATTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
*
1245389 -TCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1245407 TTCGCATTGCGAT
1 TTCGCATTGCGAT
1245420 AGTAATTTCC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 16 0.26
16 9 0.15
17 9 0.15
19 28 0.45
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1245368 original size:33 final size:33
Alignment explanation
Indices: 1245326--1245419 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
1245316 ATTAAATTCG
1245326 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
1245359 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
1245392 CATTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1245420 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:1246438 original size:20 final size:20
Alignment explanation
Indices: 1246413--1246463 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1246403 ATTCATTTGA
1246413 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGTGAAAATGG
1246433 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGTGAAAATGG
* *
1246453 TTATCACAACG
1 CTATCGCAACG
1246464 AGAATATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (20 bp):
CTATCGCAACGTGAAAATGG
Found at i:1246513 original size:14 final size:15
Alignment explanation
Indices: 1246493--1246565 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
1246483 TGATAATCGC
1246493 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
1246508 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
1246525 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
1246543 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
1246559 -TTGCGAT
1 ATTGCGAT
1246566 AGCCATTTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:1246530 original size:19 final size:19
Alignment explanation
Indices: 1246489--1246555 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
1246479 GAAATGATAA
1246489 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1246505 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1246522 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
1246540 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1246556 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1246691 original size:14 final size:14
Alignment explanation
Indices: 1246672--1246708 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1246662 CATCAATTAA
1246672 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1246686 ACAAATCATCTTTT
1 ACAAATCAACATTT
1246700 ACAAATCAA
1 ACAAATCAA
1246709 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1248609 original size:20 final size:19
Alignment explanation
Indices: 1248574--1248640 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1248564 GAAACTTAAA
1248574 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1248593 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* * **
1248613 ATCGCAATGAGAAATGAAA
1 ATCGCAACGCGAAATGACT
1248632 ATCGCAACG
1 ATCGCAACG
1248641 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 24 0.60
20 16 0.40
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1248648 original size:14 final size:14
Alignment explanation
Indices: 1248629--1248686 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1248619 ATGAGAAATG
1248629 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1248643 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1248659 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1248675 AAAATCGCAACG
1 AAAATCGCAACG
1248687 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1248671 original size:32 final size:33
Alignment explanation
Indices: 1248613--1248691 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1248603 GGAAATGGCT
* *
1248613 ATCGCAATGAGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1248646 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1248678 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1248692 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 30 0.68
33 14 0.32
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1248720 original size:19 final size:17
Alignment explanation
Indices: 1248698--1248793 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
1248688 GAAACACAAA
1248698 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
1248717 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
1248733 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
1248749 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
1248765 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
1248782 TCGCATTGCGAT
1 TCGC-TTGCGAT
1248794 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:1248739 original size:14 final size:14
Alignment explanation
Indices: 1248720--1248777 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1248710 TTTCATTTCG
1248720 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1248734 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1248750 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1248766 CGTTGCGATTTT
1 CGTTGCGATTTT
1248778 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1248784 original size:33 final size:33
Alignment explanation
Indices: 1248703--1248793 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1248693 ACAAATCGCA
1248703 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1248736 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
1248768 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
1248794 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:1248812 original size:20 final size:19
Alignment explanation
Indices: 1248778--1248832 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1248768 TTGCGATTTT
*
1248778 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1248797 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1248817 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1248833 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1249327 original size:18 final size:18
Alignment explanation
Indices: 1249301--1249345 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1249291 GTCGATCAGA
*
1249301 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
1249319 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
1249337 TGATGGCTC
1 TGATGGCTC
1249346 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:1250686 original size:20 final size:20
Alignment explanation
Indices: 1250661--1250698 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1250651 AATATTTTCT
1250661 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1250681 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1250699 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1251217 original size:20 final size:20
Alignment explanation
Indices: 1251192--1251244 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1251182 GATTATGTAT
*
1251192 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
1251212 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
1251232 TATCTCGTTGCGA
1 TATCGCGTTGCGA
1251245 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:1251257 original size:41 final size:41
Alignment explanation
Indices: 1251212--1251289 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1251202 CGAAAGTCAG
* * *
1251212 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCACATTGCGATTTTTTAT
* *
1251253 TATCGCATTGCGATAGTCAGTATCACATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCACATTGCGATTTT
1251290 CTCAATTTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCACATTGCGATTTTTTAT
Found at i:1251305 original size:41 final size:41
Alignment explanation
Indices: 1251212--1251307 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
1251202 CGAAAGTCAG
* * * *
1251212 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCACATTGCGATTTTTAAT
* *
1251253 TATCGCATTGCGATAGTCAGTATCACATTGCGATTTTCTCAAT
1 TATCGCGTTGCGATAGTAAGTATCACATTGCGATTTT-T-AAT
1251296 T-T-GCGTTGCGAT
1 TATCGCGTTGCGAT
1251308 TTACTTATTC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 41 0.89
42 2 0.04
43 3 0.07
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCACATTGCGATTTTTAAT
Found at i:1251306 original size:21 final size:21
Alignment explanation
Indices: 1251280--1251367 Score: 81
Period size: 20 Copynumber: 4.3 Consensus size: 21
1251270 CAGTATCACA
*
1251280 TTGCGATTTTCTCAATTTGCG
1 TTGCGATTTTCTCAATTCGCG
* * *
1251301 TTGCGATTTACT-TATTCGCA
1 TTGCGATTTTCTCAATTCGCG
* *
1251321 TTGCGAATTTCCCAATTCGCG
1 TTGCGATTTTCTCAATTCGCG
* * *
1251342 TTGCGATTTACT-TATTCGCA
1 TTGCGATTTTCTCAATTCGCG
1251362 TTGCGA
1 TTGCGA
1251368 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 14, Indels: 3
0.75 0.20 0.04
Matches are distributed among these distances:
20 26 0.50
21 26 0.50
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (21 bp):
TTGCGATTTTCTCAATTCGCG
Found at i:1251323 original size:41 final size:41
Alignment explanation
Indices: 1251278--1251370 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
1251268 GTCAGTATCA
* * *
1251278 CATTGCGATTTTCTCAATTTGCGTTGCGATTTACTTATTCG
1 CATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCG
1251319 CATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 CATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCG
1251360 CATTGCGAATT
1 CATTGCGAATT
1251371 GGGAAAATCG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (41 bp):
CATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTATTCG
Found at i:1251326 original size:20 final size:20
Alignment explanation
Indices: 1251278--1251367 Score: 90
Period size: 21 Copynumber: 4.4 Consensus size: 20
1251268 GTCAGTATCA
* *
1251278 CATTGCGATTTTCTCAATTTG
1 CATTGCGATTTACT-AATTCG
* *
1251299 CGTTGCGATTTACTTATTCG
1 CATTGCGATTTACTAATTCG
* *
1251319 CATTGCGAATTTCCCAATTCG
1 CATTGCG-ATTTACTAATTCG
* *
1251340 CGTTGCGATTTACTTATTCG
1 CATTGCGATTTACTAATTCG
1251360 CATTGCGA
1 CATTGCGA
1251368 ATTGGGAAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 3
0.77 0.18 0.04
Matches are distributed among these distances:
20 27 0.49
21 28 0.51
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (20 bp):
CATTGCGATTTACTAATTCG
Found at i:1252428 original size:20 final size:20
Alignment explanation
Indices: 1252405--1252471 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
1252395 GTTTCCAAAT
1252405 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
1252425 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
** *
1252445 TCGCAATACGAATTTGTAAT
1 TCGCAACGCGAATTTGTAAA
1252465 TCGCAAC
1 TCGCAAC
1252472 ACAGAAGTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:1252429 original size:40 final size:39
Alignment explanation
Indices: 1252385--1252475 Score: 101
Period size: 40 Copynumber: 2.3 Consensus size: 39
1252375 AACTCCAACT
*
1252385 TCGCAACACAGTTTCCAAATTCGCAACGCGAATTTGTAAA
1 TCGCAACACAGTTTCCAAA-TCGCAACACGAATTTGTAAA
* * ** * *
1252425 TCGCAACGCGAATTTGTAAATCGCAATACGAATTTGTAAT
1 TCGCAACAC-AGTTTCCAAATCGCAACACGAATTTGTAAA
1252465 TCGCAACACAG
1 TCGCAACACAG
1252476 AAGTCAAATT
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
39 1 0.02
40 33 0.80
41 7 0.17
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (39 bp):
TCGCAACACAGTTTCCAAATCGCAACACGAATTTGTAAA
Found at i:1252489 original size:40 final size:40
Alignment explanation
Indices: 1252400--1252593 Score: 96
Period size: 40 Copynumber: 4.8 Consensus size: 40
1252390 ACACAGTTTC
* *
1252400 CAAATTCGCAACGCGAATTTGTAAATCGCAACGCGAATTTGT
1 CAAATTCGCAACACGAATTTGTAAATCGCAACACGAA--TGT
* *
1252442 -AAA-TCGCAATACGAATTTGTAATTCGCAACACAGAA-GT
1 CAAATTCGCAACACGAATTTGTAAATCGCAACAC-GAATGT
* * ** * * *
1252480 CAAATTCGCAGCGCG-ATTTCCAAATTCGTAATACTGAATTT
1 CAAATTCGCAACACGAATTTGTAAA-TCGCAACAC-GAATGT
* * * * *
1252521 CAAATTCGCAACTA-G-ATTTCTGAATTCGCAACTCGATTTT
1 CAAATTCGCAAC-ACGAATTTGT-AAATCGCAACACGAATGT
* * *
1252561 CGAATTCGTAACACGAATTT-TAATTTCGCAACA
1 CAAATTCGCAACACGAATTTGTAA-ATCGCAACA
1252594 GGTTTTATTT
Statistics
Matches: 117, Mismatches: 25, Indels: 22
0.71 0.15 0.13
Matches are distributed among these distances:
38 2 0.02
39 12 0.10
40 67 0.57
41 34 0.29
42 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (40 bp):
CAAATTCGCAACACGAATTTGTAAATCGCAACACGAATGT
Found at i:1252531 original size:61 final size:61
Alignment explanation
Indices: 1252360--1252593 Score: 165
Period size: 60 Copynumber: 3.9 Consensus size: 61
1252350 AAATGACCAA
** * * * * * * *
1252360 TAAATTCGCAACGCGAACTCCAACTTCGCAACAC-AGTTTCCAAATTCGCAACGC-GAATTTG
1 TAAATTCGCAACGCGATTTCCAAATTCGTAATACGAATTT-CAAATTCGCAACACAGAA-GTC
** * **
1252421 TAAA-TCGCAACGCGAATTTGTAAA-TCGCAATACGAATTTGTAATTCGCAACACAGAAGTC
1 TAAATTCGCAACGCG-ATTTCCAAATTCGTAATACGAATTTCAAATTCGCAACACAGAAGTC
* * **
1252481 -AAATTCGCAGCGCGATTTCCAAATTCGTAATACTGAATTTCAAATTCGCAAC-TAGATTTC
1 TAAATTCGCAACGCGATTTCCAAATTCGTAATAC-GAATTTCAAATTCGCAACACAGAAGTC
* * * * * * *
1252541 TGAATTCGCAACTCGATTTTCGAATTCGTAACACGAATTTTAATTTCGCAACA
1 TAAATTCGCAACGCGATTTCCAAATTCGTAATACGAATTTCAAATTCGCAACA
1252594 GGTTTTATTT
Statistics
Matches: 136, Mismatches: 29, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
59 10 0.07
60 68 0.50
61 58 0.43
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (61 bp):
TAAATTCGCAACGCGATTTCCAAATTCGTAATACGAATTTCAAATTCGCAACACAGAAGTC
Found at i:1252548 original size:20 final size:20
Alignment explanation
Indices: 1252518--1252568 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1252508 TAATACTGAA
*
1252518 TTTCAAATTCGCAACTAGA-
1 TTTCGAATTCGCAACTAGAT
*
1252537 TTTCTGAATTCGCAACTCGAT
1 TTTC-GAATTCGCAACTAGAT
1252558 TTTCGAATTCG
1 TTTCGAATTCG
1252569 TAACACGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 20 0.71
21 4 0.14
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (20 bp):
TTTCGAATTCGCAACTAGAT
Found at i:1252593 original size:20 final size:19
Alignment explanation
Indices: 1252545--1252612 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
1252535 GATTTCTGAA
*
1252545 TTCGCAACTCGATTTTCGAA-
1 TTCGCAACACGATTTT--AAT
*
1252565 TTCGTAACACGAATTTTAAT
1 TTCGCAACACG-ATTTTAAT
* *
1252585 TTCGCAACA-GGTTTTATT
1 TTCGCAACACGATTTTAAT
1252603 TTCGCAACAC
1 TTCGCAACAC
1252613 AAATGTTTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
18 15 0.38
19 3 0.08
20 17 0.43
21 5 0.12
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (19 bp):
TTCGCAACACGATTTTAAT
Found at i:1253402 original size:12 final size:12
Alignment explanation
Indices: 1253381--1253414 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1253371 ACCACATTTC
*
1253381 CAATACCAAACA
1 CAATATCAAACA
1253393 CAATATCAAACA
1 CAATATCAAACA
*
1253405 CAATCTCAAA
1 CAATATCAAA
1253415 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1253572 original size:24 final size:24
Alignment explanation
Indices: 1253540--1253593 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1253530 GTATTCGAAA
1253540 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1253564 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1253588 TTTGAT
1 TTTGAT
1253594 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1255862 original size:12 final size:12
Alignment explanation
Indices: 1255845--1255891 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
1255835 AACAAAAGGA
1255845 AATCAAAATC-G
1 AATCAAAATCAG
1255856 CAATCAAAATCAG
1 -AATCAAAATCAG
1255869 AATCAAAATCAG
1 AATCAAAATCAG
*
1255881 AATCACAATCA
1 AATCAAAATCA
1255892 CAAACGGCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
12 32 0.97
13 1 0.03
ACGTcount: A:0.55, C:0.21, G:0.06, T:0.17
Consensus pattern (12 bp):
AATCAAAATCAG
Found at i:1255878 original size:18 final size:18
Alignment explanation
Indices: 1255844--1255894 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1255834 AAACAAAAGG
*
1255844 AAATCAAAATCGCAATCA
1 AAATCAAAATCACAATCA
* *
1255862 AAATCAGAATCAAAATCA
1 AAATCAAAATCACAATCA
* *
1255880 GAATCACAATCACAA
1 AAATCAAAATCACAA
1255895 ACGGCTTCAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.57, C:0.22, G:0.06, T:0.16
Consensus pattern (18 bp):
AAATCAAAATCACAATCA
Found at i:1255894 original size:6 final size:6
Alignment explanation
Indices: 1255844--1255891 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
1255834 AAACAAAAGG
* * * * *
1255844 AAATCA AAATCG CAATCA AAATCA GAATCA AAATCA GAATCA CAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
1255892 CAAACGGCTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.56, C:0.21, G:0.06, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:1256173 original size:20 final size:20
Alignment explanation
Indices: 1256144--1256198 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
1256134 ACGATTGTTG
*
1256144 CGAAAGTCAAATTCGCAACA
1 CGAAAATCAAATTCGCAACA
1256164 CGAAAATCAAATTCGCAACA
1 CGAAAATCAAATTCGCAACA
1256184 CGAAAATCAAATTCG
1 CGAAAATCAAATTCG
1256199 TAACGTGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.47, C:0.24, G:0.13, T:0.16
Consensus pattern (20 bp):
CGAAAATCAAATTCGCAACA
Found at i:1256272 original size:20 final size:20
Alignment explanation
Indices: 1256247--1256285 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1256237 AATCGCACGT
*
1256247 GAATTTGACTTTCGCGTTGC
1 GAATTTGACTTTCACGTTGC
*
1256267 GAATTTGATTTTCACGTTG
1 GAATTTGACTTTCACGTTG
1256286 AAAAAGTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.44
Consensus pattern (20 bp):
GAATTTGACTTTCACGTTGC
Found at i:1257656 original size:40 final size:39
Alignment explanation
Indices: 1257605--1257689 Score: 136
Period size: 40 Copynumber: 2.2 Consensus size: 39
1257595 TCGGGCCGGG
1257605 TATATA-TATTTAAATTAAATATATAAATATTATATATA
1 TATATATTATTTAAATTAAATATATAAATATTATATATA
* *
1257643 TATATATTAATTTAAATTAAATTTATTAATATTATATATA
1 TATATATT-ATTTAAATTAAATATATAAATATTATATATA
1257683 TATATAT
1 TATATAT
1257690 AATAATTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
38 6 0.14
39 1 0.02
40 36 0.84
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (39 bp):
TATATATTATTTAAATTAAATATATAAATATTATATATA
Found at i:1257801 original size:35 final size:35
Alignment explanation
Indices: 1257752--1257830 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
1257742 GATTACCAAA
1257752 CCCGTCCCCATCCCCGTTTAACATAAATAG-TTTTC
1 CCCGTCCCCATCCCCGTTTAACATAAA-AGATTTTC
* * * *
1257787 CCCGTCCTCGTCCCCGTTTAGCATAAACGATTTTC
1 CCCGTCCCCATCCCCGTTTAACATAAAAGATTTTC
1257822 CCCGTCCCC
1 CCCGTCCCC
1257831 GTTTAATTCG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
34 1 0.03
35 37 0.97
ACGTcount: A:0.18, C:0.42, G:0.11, T:0.29
Consensus pattern (35 bp):
CCCGTCCCCATCCCCGTTTAACATAAAAGATTTTC
Found at i:1258275 original size:21 final size:21
Alignment explanation
Indices: 1258251--1258309 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1258241 GGGAGAGACA
*
1258251 TCTTGAATGATGACATGGGCC
1 TCTTGAATGATGACAGGGGCC
* **
1258272 TCTTGAATGGTGGGAGGGGCC
1 TCTTGAATGATGACAGGGGCC
*
1258293 TCTTGAACGATGACAGG
1 TCTTGAATGATGACAGG
1258310 TGAATCGGGC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.25
Consensus pattern (21 bp):
TCTTGAATGATGACAGGGGCC
Found at i:1258673 original size:21 final size:21
Alignment explanation
Indices: 1258653--1258692 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1258643 TCATCGCGTA
1258653 AAACATC-TACCTCACCACGT
1 AAACATCGTACCTCACCACGT
* *
1258673 AAAGATCGTACCTCATCACG
1 AAACATCGTACCTCACCACG
1258693 CCATGCACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.35, C:0.35, G:0.10, T:0.20
Consensus pattern (21 bp):
AAACATCGTACCTCACCACGT
Found at i:1258738 original size:21 final size:21
Alignment explanation
Indices: 1258709--1258758 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1258699 ACCATTGTCG
* *
1258709 TCACATAAAGTACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
* *
1258730 TCACGTAAAGCACTGATCTCA
1 TCACGTAAAGCACCGACCTCA
1258751 TCACGTAA
1 TCACGTAA
1258759 CTCCCCTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:1260337 original size:20 final size:20
Alignment explanation
Indices: 1260277--1260330 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1260267 AAACTAAAAC
1260277 CGCGTTGCGAATTTCATTTT
1 CGCGTTGCGAATTTCATTTT
*
1260297 TGCGTTGCGAATTTCATTTT
1 CGCGTTGCGAATTTCATTTT
*
1260317 CGTGTTGCGAATTT
1 CGCGTTGCGAATTT
1260331 AAGTTTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (20 bp):
CGCGTTGCGAATTTCATTTT
Found at i:1260679 original size:20 final size:21
Alignment explanation
Indices: 1260656--1260698 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1260646 TCTGAGAGAT
1260656 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
*
1260676 GGAGATGGGGACGGATTTCGCC
1 GGAGAT-GAGACGGATTTCGCC
1260698 G
1 G
1260699 TAGAGAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.21, C:0.19, G:0.42, T:0.19
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:1260889 original size:20 final size:20
Alignment explanation
Indices: 1260866--1260935 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1260856 GACTTCTGTA
*
1260866 TTGCAAATTACAAATTCGCG
1 TTGCGAATTACAAATTCGCG
* *
1260886 TTGCGATTTACATATTCGCG
1 TTGCGAATTACAAATTCGCG
*
1260906 TTGCGAATTTAGAAAATT-GCG
1 TTGCGAA-TTA-CAAATTCGCG
1260927 TTGCGAATT
1 TTGCGAATT
1260936 TGGAAACTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
20 25 0.60
21 13 0.31
22 4 0.10
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (20 bp):
TTGCGAATTACAAATTCGCG
Found at i:1260951 original size:20 final size:21
Alignment explanation
Indices: 1260903--1260977 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 21
1260893 TTACATATTC
*
1260903 GCGTTGCGAATTTAGAAAATT
1 GCGTTGCGAATTTAGAAAACT
*
1260924 GCGTTGCGAATTT-GGAAACT
1 GCGTTGCGAATTTAGAAAACT
* * * * *
1260944 GTGTTGCGAAATTCGAGATC-
1 GCGTTGCGAATTTAGAAAACT
1260964 GCGTTGCGAATTTA
1 GCGTTGCGAATTTA
1260978 TTGGTCATTT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.32
Consensus pattern (21 bp):
GCGTTGCGAATTTAGAAAACT
Found at i:1262495 original size:38 final size:38
Alignment explanation
Indices: 1262447--1262541 Score: 172
Period size: 38 Copynumber: 2.5 Consensus size: 38
1262437 CTGGCTCTTA
*
1262447 TTTGGAATTTATTCATGCAATTCATGGAAATCTTATGC
1 TTTGTAATTTATTCATGCAATTCATGGAAATCTTATGC
*
1262485 TTTGTAATTTATTCCTGCAATTCATGGAAATCTTATGC
1 TTTGTAATTTATTCATGCAATTCATGGAAATCTTATGC
1262523 TTTGTAATTTATTCATGCA
1 TTTGTAATTTATTCATGCA
1262542 TTGCAGAGTC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (38 bp):
TTTGTAATTTATTCATGCAATTCATGGAAATCTTATGC
Found at i:1264252 original size:21 final size:20
Alignment explanation
Indices: 1264226--1264338 Score: 77
Period size: 21 Copynumber: 5.5 Consensus size: 20
1264216 CAGTTCCCAT
1264226 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
1264246 GAATCGCAATGCGA-TA-GCACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
1264267 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
*
1264289 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
* *
1264309 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
*
1264329 TATCGCAACG
1 AATCGCAACG
1264339 AGTATCCGTA
Statistics
Matches: 71, Mismatches: 15, Indels: 13
0.72 0.15 0.13
Matches are distributed among these distances:
19 1 0.01
20 32 0.45
21 34 0.48
22 3 0.04
23 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:1264314 original size:20 final size:20
Alignment explanation
Indices: 1264289--1264544 Score: 221
Period size: 20 Copynumber: 12.7 Consensus size: 20
1264279 GATTTTCCAG
** *
1264289 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
* *
1264309 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * *
1264328 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCCGT-A
* *
1264350 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
1264370 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
*
1264391 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* * *
1264411 AATCGCAATGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
1264431 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
* *
1264451 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
1264471 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
1264491 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
* *
1264512 AATTGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
1264532 AATCGCAACGCGA
1 AATCGCAACGCGA
1264545 TTTTTAAAGC
Statistics
Matches: 187, Mismatches: 40, Indels: 18
0.76 0.16 0.07
Matches are distributed among these distances:
19 1 0.01
20 136 0.73
21 49 0.26
22 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:1264445 original size:40 final size:41
Alignment explanation
Indices: 1264289--1264541 Score: 336
Period size: 41 Copynumber: 6.2 Consensus size: 41
1264279 GATTTTCCAG
* * *
1264289 AATCGCAACGCGAATATG-AAAATCGCAACGCG-ATTC-TGA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT-A
* * * *
1264328 CTATCGCAACGAGTATCCGTAAAATCGTAACGCGTATCCGTA
1 -AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
*
1264370 AATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
* *
1264411 AATCGCAATGAGAATACGT-AAATCGCAACGCGTATCTGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
*
1264451 AATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
* *
1264491 AATCGCAACGACAATACGTAAAATTGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
1264532 AATCGCAACG
1 AATCGCAACG
1264542 CGATTTTTAA
Statistics
Matches: 188, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
40 88 0.47
41 95 0.51
42 4 0.02
43 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (41 bp):
AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
Found at i:1264731 original size:24 final size:23
Alignment explanation
Indices: 1264704--1264754 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
1264694 AATCTCTCAC
*
1264704 TCTCTACGACGAAATCCGTCCCCA
1 TCTCT-CGAAGAAATCCGTCCCCA
**
1264728 TCTC-CGAAGATTTCCGTCCCCA
1 TCTCTCGAAGAAATCCGTCCCCA
1264750 TCTCT
1 TCTCT
1264755 GGCGAAATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 19 0.83
24 4 0.17
ACGTcount: A:0.20, C:0.41, G:0.12, T:0.27
Consensus pattern (23 bp):
TCTCTCGAAGAAATCCGTCCCCA
Found at i:1265162 original size:21 final size:21
Alignment explanation
Indices: 1265101--1265179 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
1265091 TTCTAAACTT
1265101 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
1265121 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
1265141 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
1265162 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
1265180 TCGCAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:1267069 original size:94 final size:94
Alignment explanation
Indices: 1266908--1267287 Score: 656
Period size: 94 Copynumber: 4.1 Consensus size: 94
1266898 TAGATTGCTT
* *
1266908 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1266973 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
1267002 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1267067 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
1267096 AGTAAATTTGTTCGGTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1267161 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
1267190 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTAAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1267255 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1267283 AGTAA
1 AGTAA
1267288 TGCAATCCAT
Statistics
Matches: 275, Mismatches: 10, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
93 26 0.09
94 249 0.91
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Done.