Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008964.1 Hibiscus syriacus cultivar Beakdansim tig00112305_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: 2156694
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 9 of 11
Found at i:1543457 original size:160 final size:161
Alignment explanation
Indices: 1543111--1543521 Score: 524
Period size: 160 Copynumber: 2.6 Consensus size: 161
1543101 ATAATTCCTT
* * * * * * * *
1543111 TATTCTTTTACCCAAAGGTATTTAGCTTTTAATCTAACTTGCATATTTTACACTTTTATGTCAAA
1 TATTCTTTTACTCAAAGGTATTTAACTATTCATCTAACTGGCATAATTGACACTTTTATGCCAAA
* * *
1543176 TGCACAACTAGTCTATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTG
66 TGCACAACTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTAATCTAACTGGCATAATTG
* *
1543241 ATACCTTTTTGCCAAATGCACAGTTAGGCCA
131 ATACCTTTCTGCCAAATGCACAATTAGGCCA
* * * * * *
1543272 TTTATCTTTTACT--ACGGTCTTTAACTGTTCATCTAACTGGCATAATTGACACATTTCTGCCAA
1 TAT-TCTTTTACTCAAAGGTATTTAACTATTCATCTAACTGGCATAATTGACACTTTTATGCCAA
* *
1543335 ATTCACAACTAGGCCATTGTTCTTTTACTCAACGGTATTT-ACCGTTAATCTAACTGGCATAATT
65 ATGCACAACTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTAATCTAACTGGCATAATT
1543399 GACT-CCTTTCTGCCAAATGCACAATTAGGCCA
130 GA-TACCTTTCTGCCAAATGCACAATTAGGCCA
* * * *
1543431 TATTCTTTTACTCAATGGTATTTAACTATTCATATAACTGGCATAATTGACATTTTTTTGCCAAA
1 TATTCTTTTACTCAAAGGTATTTAACTATTCATCTAACTGGCATAATTGACACTTTTATGCCAAA
** *
1543496 TGCACAGTTAGGCCATTAATCTTTTA
66 TGCACAACTAGGCCATTATTCTTTTA
1543522 TTTTTTTTAA
Statistics
Matches: 213, Mismatches: 33, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
158 9 0.04
159 53 0.25
160 141 0.66
161 2 0.01
162 8 0.04
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (161 bp):
TATTCTTTTACTCAAAGGTATTTAACTATTCATCTAACTGGCATAATTGACACTTTTATGCCAAA
TGCACAACTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTAATCTAACTGGCATAATTG
ATACCTTTCTGCCAAATGCACAATTAGGCCA
Found at i:1543744 original size:55 final size:55
Alignment explanation
Indices: 1543685--1543800 Score: 155
Period size: 55 Copynumber: 2.1 Consensus size: 55
1543675 TATACGATAG
* ***
1543685 TTCATCAACTCATGATGAATTCTGTC-GATTTG-AACACATAGTGCCCGTACGGTTA
1 TTCATCAACTCATGATGAATTCCG-CAGATTTGCAA-ACATAGTGCAAATACGGTTA
*
1543740 TTCATCAACTCATGATGAATTCCGCAGATTTGCAAACTTAGTGCAAATACGGTTA
1 TTCATCAACTCATGATGAATTCCGCAGATTTGCAAACATAGTGCAAATACGGTTA
1543795 TTCATC
1 TTCATC
1543801 CATGTAGGAT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
54 1 0.02
55 51 0.94
56 2 0.04
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (55 bp):
TTCATCAACTCATGATGAATTCCGCAGATTTGCAAACATAGTGCAAATACGGTTA
Found at i:1545200 original size:54 final size:54
Alignment explanation
Indices: 1545106--1545562 Score: 571
Period size: 54 Copynumber: 8.5 Consensus size: 54
1545096 TAAATAAATT
** ** * * * * *
1545106 ATGAATTCCGTGGGTTGCA-AACTAGTGCCAAAACGATTGTTCATCAATAAATT
1 ATGAATTCCGTGAATTGCACATTTAGTGCCGAAACGGTTGTTCATCAACATATG
* * *
1545159 ATG-AGTCCTGTGAATTGCACACTTAGTGCCGAAACGGTTGTTCATCAATATATG
1 ATGAATTCC-GTGAATTGCACATTTAGTGCCGAAACGGTTGTTCATCAACATATG
* *
1545213 ATGAATTCCGTGAATTGCATATTCAGTGCC-AGAACGGTTGTTCATCAACATATG
1 ATGAATTCCGTGAATTGCACATTTAGTGCCGA-AACGGTTGTTCATCAACATATG
* * *
1545267 ATGAATTCCATGAAATGCACATTTAGTGCCGAAACGGTTATTCATCAACATATG
1 ATGAATTCCGTGAATTGCACATTTAGTGCCGAAACGGTTGTTCATCAACATATG
* * *
1545321 TTGAATTTCGTGAATTGCACATTTAGTGCCGAAACGGTTGTTCATCAACATACG
1 ATGAATTCCGTGAATTGCACATTTAGTGCCGAAACGGTTGTTCATCAACATATG
* ** *
1545375 ATGAATTCCGTTAATTGCACACATAGTGCCGAAACGGCTGTTCATCAACATATG
1 ATGAATTCCGTGAATTGCACATTTAGTGCCGAAACGGTTGTTCATCAACATATG
* * *
1545429 ATGAATTCTGTGAATTTCATATTTAGTGCCGAAACGGTTGTTCATCAACATATG
1 ATGAATTCCGTGAATTGCACATTTAGTGCCGAAACGGTTGTTCATCAACATATG
** **
1545483 ATGAATTCCGTGAATTATACATTTAGTGCCGAAA-TATTGTTCATCAACATATG
1 ATGAATTCCGTGAATTGCACATTTAGTGCCGAAACGGTTGTTCATCAACATATG
* *
1545536 ATGAATTCTGTGAATTGCATATTTAGT
1 ATGAATTCCGTGAATTGCACATTTAGT
1545563 ACCCATTTGG
Statistics
Matches: 350, Mismatches: 49, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
52 4 0.01
53 52 0.15
54 289 0.83
55 5 0.01
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (54 bp):
ATGAATTCCGTGAATTGCACATTTAGTGCCGAAACGGTTGTTCATCAACATATG
Found at i:1552153 original size:54 final size:54
Alignment explanation
Indices: 1552088--1552554 Score: 481
Period size: 54 Copynumber: 8.8 Consensus size: 54
1552078 TATATGATCA
* * * ** *
1552088 TTCATAAACATATTATGAATTCCATGGGTTGCACACCTAGT-CTCGAAATGGTTG
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGC-CGAAATGGTTG
* * * *
1552142 TTCATCAACATATGATGAATTCTGTTAATTACACACTTAGTGCCGAAACGGTTG
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAATGGTTG
* *
1552196 TTCATCAACATATGATGAATTCCGTGAATTGTACA-TTCAGTGCCGAAATAGTTG
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTT-AGTGCCGAAATGGTTG
* * * * *
1552250 TTCATCAACATATGATGAATTTCGTGAACTGCACATTTAGTGCCAAAACGGTTG
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAATGGTTG
* * * * * *
1552304 TTCATTAATATATGATGAATTCCATGAATTGCACATTTAGTGCCGAAATAGTTA
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAATGGTTG
* * * * * *
1552358 TTCATCAACATATGATAAATTCAGTGAATTGCACACTTATTGTCGAAACGATTG
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAATGGTTG
* * *
1552412 TTCATCAACATATGATGAATTCCGTGAATTGCACATTTAGTGCTGAAACT-GTGG
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAA-TGGTTG
* * *
1552466 TTCTTCAAC--AT-ATG-A-----TGAATTGCACATTTAGTGCTGAAATGGTTG
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAATGGTTG
* * *
1552511 CTCATCATCATATGATGAATTCCGTGAATTGCACATTTAGTGCC
1 TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCC
1552555 CATTTGGTAA
Statistics
Matches: 341, Mismatches: 58, Indels: 28
0.80 0.14 0.07
Matches are distributed among these distances:
44 1 0.00
45 33 0.10
47 2 0.01
48 3 0.01
49 1 0.00
50 1 0.00
51 3 0.01
52 2 0.01
53 2 0.01
54 290 0.85
55 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (54 bp):
TTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCCGAAATGGTTG
Found at i:1552260 original size:108 final size:107
Alignment explanation
Indices: 1552088--1552554 Score: 531
Period size: 108 Copynumber: 4.4 Consensus size: 107
1552078 TATATGATCA
* * * ** ** *
1552088 TTCATAAACATATTATGAATTCCATGGGTTGCACACCTAGT-CTCGAAATGGTTGTTCATCAACA
1 TTCATCAACATATGATGAATTCCGTGAATTGCACATTTAGTGC-CGAAATAGTTGTTCATCAACA
* *
1552152 TATGATGAATTCTGTTAATTACACACTTAGTGCCGAAACGGTTG
65 TATGATGAATT-TGTGAATTGCACACTTAGTGCCGAAACGGTTG
* *
1552196 TTCATCAACATATGATGAATTCCGTGAATTGTACATTCAGTGCCGAAATAGTTGTTCATCAACAT
1 TTCATCAACATATGATGAATTCCGTGAATTGCACATTTAGTGCCGAAATAGTTGTTCATCAACAT
* * *
1552261 ATGATGAATTTCGTGAACTGCACATTTAGTGCCAAAACGGTTG
66 ATGATGAATTT-GTGAATTGCACACTTAGTGCCGAAACGGTTG
* * * *
1552304 TTCATTAATATATGATGAATTCCATGAATTGCACATTTAGTGCCGAAATAGTTATTCATCAACAT
1 TTCATCAACATATGATGAATTCCGTGAATTGCACATTTAGTGCCGAAATAGTTGTTCATCAACAT
* * * * *
1552369 ATGATAAATTCAGTGAATTGCACACTTATTGTCGAAACGATTG
66 ATGATGAATT-TGTGAATTGCACACTTAGTGCCGAAACGGTTG
* * *
1552412 TTCATCAACATATGATGAATTCCGTGAATTGCACATTTAGTGCTGAAACT-GTGGTTCTTCAAC-
1 TTCATCAACATATGATGAATTCCGTGAATTGCACATTTAGTGCCGAAA-TAGTTGTTCATCAACA
* * *
1552475 -AT-ATG-A----TGAATTGCACATTTAGTGCTGAAATGGTTG
65 TATGATGAATTTGTGAATTGCACACTTAGTGCCGAAACGGTTG
* *
1552511 CTCATCATCATATGATGAATTCCGTGAATTGCACATTTAGTGCC
1 TTCATCAACATATGATGAATTCCGTGAATTGCACATTTAGTGCC
1552555 CATTTGGTAA
Statistics
Matches: 309, Mismatches: 46, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
99 65 0.21
104 1 0.00
105 2 0.01
106 2 0.01
107 1 0.00
108 236 0.76
109 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (107 bp):
TTCATCAACATATGATGAATTCCGTGAATTGCACATTTAGTGCCGAAATAGTTGTTCATCAACAT
ATGATGAATTTGTGAATTGCACACTTAGTGCCGAAACGGTTG
Found at i:1552500 original size:45 final size:45
Alignment explanation
Indices: 1552436--1552531 Score: 140
Period size: 45 Copynumber: 2.1 Consensus size: 45
1552426 ATGAATTCCG
* *
1552436 TGAATTGCACATTTAGTGCTGAAACT-GTGGTTCTTCAACATATGA
1 TGAATTGCACATTTAGTGCTGAAA-TGGTGGCTCATCAACATATGA
* *
1552481 TGAATTGCACATTTAGTGCTGAAATGGTTGCTCATCATCATATGA
1 TGAATTGCACATTTAGTGCTGAAATGGTGGCTCATCAACATATGA
1552526 TGAATT
1 TGAATT
1552532 CCGTGAATTG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 1 0.02
45 45 0.98
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (45 bp):
TGAATTGCACATTTAGTGCTGAAATGGTGGCTCATCAACATATGA
Found at i:1552932 original size:19 final size:19
Alignment explanation
Indices: 1552905--1552945 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1552895 GTATCGATAC
*
1552905 TACTATATTATGGTACCGA
1 TACTATATTACGGTACCGA
* *
1552924 TACTCTATTACGGTATCGA
1 TACTATATTACGGTACCGA
1552943 TAC
1 TAC
1552946 CATTTTTGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (19 bp):
TACTATATTACGGTACCGA
Found at i:1562784 original size:46 final size:46
Alignment explanation
Indices: 1562726--1562817 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
1562716 TTTTAAACAT
1562726 GATTACGAAACACAATAGTCTGAAATGTACATATGTCAAACATTAG
1 GATTACGAAACACAATAGTCTGAAATGTACATATGTCAAACATTAG
1562772 GATTACGAAACACAATAGTCTGAAATGTACATATGTCAAACATTAG
1 GATTACGAAACACAATAGTCTGAAATGTACATATGTCAAACATTAG
1562818 TGTCAAAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (46 bp):
GATTACGAAACACAATAGTCTGAAATGTACATATGTCAAACATTAG
Found at i:1562934 original size:19 final size:19
Alignment explanation
Indices: 1562911--1562974 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
1562901 TCCAATATAT
1562911 AATCTGGATTGCAACATAA
1 AATCTGGATTGCAACATAA
* * * *
1562930 TATCTGGTTTCCAACTTAA
1 AATCTGGATTGCAACATAA
* *
1562949 AATTCTGGGTTGCAACCTAA
1 AA-TCTGGATTGCAACATAA
1562969 AATCTG
1 AATCTG
1562975 ATTTCCAATA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (19 bp):
AATCTGGATTGCAACATAA
Found at i:1562964 original size:20 final size:20
Alignment explanation
Indices: 1562913--1562971 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
1562903 CAATATATAA
*
1562913 TCTGGATTGCAACATAATA-
1 TCTGGATTGCAACATAAAAT
* * *
1562932 TCTGGTTTCCAACTTAAAAT
1 TCTGGATTGCAACATAAAAT
* *
1562952 TCTGGGTTGCAACCTAAAAT
1 TCTGGATTGCAACATAAAAT
1562972 CTGATTTCCA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (20 bp):
TCTGGATTGCAACATAAAAT
Found at i:1563577 original size:17 final size:17
Alignment explanation
Indices: 1563555--1563588 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1563545 TTTCTTGAAA
1563555 ATTTTAAATTTTCTTAT
1 ATTTTAAATTTTCTTAT
* *
1563572 ATTTTAGATTTTTTTAT
1 ATTTTAAATTTTCTTAT
1563589 TGATAATTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTAAATTTTCTTAT
Found at i:1564686 original size:16 final size:17
Alignment explanation
Indices: 1564654--1564686 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1564644 TGCAAATAAA
*
1564654 TTTTTAAATAATATATT
1 TTTTTAAAAAATATATT
1564671 TTTTTAAAAAAT-TATT
1 TTTTTAAAAAATATATT
1564687 ACTATAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTTAAAAAATATATT
Found at i:1567513 original size:37 final size:38
Alignment explanation
Indices: 1567472--1567546 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 38
1567462 ACTAAGTGTA
* *
1567472 TATGGTGAGCACGACCTTATGTAT-AGCACTTCGATGC
1 TATGGTGAGCAAGACCTTATGTATAAGCACTACGATGC
* * *
1567509 TATGGTGGGCAAGATCTTATGTGTAAGCACTACGATGC
1 TATGGTGAGCAAGACCTTATGTATAAGCACTACGATGC
1567547 AAATATTACT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
37 20 0.62
38 12 0.38
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (38 bp):
TATGGTGAGCAAGACCTTATGTATAAGCACTACGATGC
Found at i:1569299 original size:20 final size:19
Alignment explanation
Indices: 1569274--1569328 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
1569264 TGATTCAATC
*
1569274 AGTATCGATACCAATGAGG
1 AGTATCGATACCAATAAGG
1569293 TAGTATCGATACCATGATAAGG
1 -AGTATCGATACCA--ATAAGG
*
1569315 GGTATCGATACCAA
1 AGTATCGATACCAA
1569329 GAAACATCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.03
20 13 0.42
21 12 0.39
22 5 0.16
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (19 bp):
AGTATCGATACCAATAAGG
Found at i:1569829 original size:59 final size:59
Alignment explanation
Indices: 1569749--1569970 Score: 297
Period size: 59 Copynumber: 3.8 Consensus size: 59
1569739 ATGGCACTAA
**
1569749 GTGTGC-AAAATGTTAAGGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTT
1 GTGTGCTAAAATGAGAA-GGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTT
* * *
1569808 GTGTGCTAATATGAGAAGGAATTCATACTAAGTATATGAATTTCCATGTAGGGCACTTT
1 GTGTGCTAAAATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTT
* * * *
1569867 GTGTGCTAACATGGGAAGGAATTCATACTAAGTGTATGAATTTCCAGAT-GGGCACCTT
1 GTGTGCTAAAATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTT
* * * *
1569925 GTGTGCTAAAATGATAAGAAATT-TTCCTAAGTGTATGAATTTCCAT
1 GTGTGCTAAAATGAGAAGGAATTCATACTAAGTGTATGAATTTCCAT
1569971 GTGGGAAATA
Statistics
Matches: 144, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
57 20 0.14
58 27 0.19
59 90 0.62
60 7 0.05
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (59 bp):
GTGTGCTAAAATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTT
Found at i:1570269 original size:68 final size:67
Alignment explanation
Indices: 1570153--1570411 Score: 365
Period size: 68 Copynumber: 3.8 Consensus size: 67
1570143 AAATAAAAGA
* * * * * *
1570153 TTTGAGGCCTAAATGTGCATTTGATAGAAATGTGCCAATTATGTCAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
1570218 GTC
66 G-C
*
1570221 TTTGTGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
1570286 GCC
66 G-C
* * *
1570289 TTTGAGGCCTAACTGTGCATATGAAAAAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
1570354 GC
66 GC
* * * *
1570356 ATTTGAGGCCTAACTGTGTATTTGACAGAAAGATGTCAATTATGCTAGTTAGATGA
1 -TTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGA
1570412 GCGGTTGAGT
Statistics
Matches: 171, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
67 1 0.01
68 170 0.99
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.31
Consensus pattern (67 bp):
TTTGAGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
GC
Found at i:1570397 original size:136 final size:136
Alignment explanation
Indices: 1570153--1570411 Score: 403
Period size: 136 Copynumber: 1.9 Consensus size: 136
1570143 AAATAAAAGA
* * * *
1570153 TTTGAGGCCTAAATGTGCATTTGATAGAAATGTGCCAATTATGTCAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAAATGTGCATATGAAAAAAATGTGCCAATTATGCCAGTTAGATGAAAGGCTAAGT
* *
1570218 GTCTTTGTGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTA
66 GTCTTTGAGGCCTAACTGTGCATATGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGCTA
1570283 AGTGCC
131 AGTGCC
* *
1570289 TTTGAGGCCTAACTGTGCATATGAAAAAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAAATGTGCATATGAAAAAAATGTGCCAATTATGCCAGTTAGATGAAAGGCTAAGT
* * *
1570354 G-CATTTGAGGCCTAACTGTGTATTTGACAGAAAGATGTCAATTATGCTAGTTAGATGA
66 GTC-TTTGAGGCCTAACTGTGCATATGACAGAAAGATGTCAATTATGCCAGTTAGATGA
1570412 GCGGTTGAGT
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
135 1 0.01
136 110 0.99
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.31
Consensus pattern (136 bp):
TTTGAGGCCTAAATGTGCATATGAAAAAAATGTGCCAATTATGCCAGTTAGATGAAAGGCTAAGT
GTCTTTGAGGCCTAACTGTGCATATGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGCTA
AGTGCC
Found at i:1570561 original size:79 final size:79
Alignment explanation
Indices: 1570430--1570792 Score: 543
Period size: 79 Copynumber: 4.6 Consensus size: 79
1570420 GTATCGTTGA
* *
1570430 ATAAAAGAATAATGCATATGGGTACACTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
*
1570495 GGTACATTGTCAGT
66 GGTACATTGTCAGC
*
1570509 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCATAGCTGAAATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
* * *
1570574 GTTACATTGTTAAC
66 GGTACATTGTCAGC
* * * *
1570588 ATAAAATAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCTAAAATGTATGTG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
* *
1570653 GGTAAACTGTCAGC
66 GGTACATTGTCAGC
* *
1570667 AT--AA-AATAATACATATGGATGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
1570729 GGTACATTGTCAGC
66 GGTACATTGTCAGC
* * *
1570743 ATAATAGAATAATGCATATGGGTGCATTATTGGCATGAAAAGATACCATA
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATA
1570793 AATGAAAATG
Statistics
Matches: 252, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
76 67 0.27
77 2 0.01
78 1 0.00
79 182 0.72
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
GGTACATTGTCAGC
Found at i:1570735 original size:155 final size:157
Alignment explanation
Indices: 1570430--1570782 Score: 539
Period size: 155 Copynumber: 2.3 Consensus size: 157
1570420 GTATCGTTGA
* * * *
1570430 ATAAAAGAATAATGCATATGGGTACACTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCTAAAATGTATATG
* * * * * *
1570495 GGTACATTGTCAGTATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCATAG
66 GGTAAACTGTCAGCAT-AAAGAATAATACATATGGATGCATTATTGGCATGAAAGGATGCCATAG
* *
1570560 CTGAAATGTATATGGTTACATTGTTAAC
130 CTGAAATGTATATGGGTACATTGTCAAC
* *
1570588 ATAAAATAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCTAAAATGTATGTG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCTAAAATGTATATG
1570653 GGTAAACTGTCAGCAT-AA-AATAATACATATGGATGCATTATTGGCATGAAAGGATGCCATAGC
66 GGTAAACTGTCAGCATAAAGAATAATACATATGGATGCATTATTGGCATGAAAGGATGCCATAGC
*
1570716 TGAAATGTATATGGGTACATTGTCAGC
131 TGAAATGTATATGGGTACATTGTCAAC
*
1570743 ATAATAGAATAATGCATATGGGTGCATTATTGGCATGAAA
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAA
1570783 AGATACCATA
Statistics
Matches: 178, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
155 104 0.58
156 2 0.01
158 72 0.40
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (157 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCTAAAATGTATATG
GGTAAACTGTCAGCATAAAGAATAATACATATGGATGCATTATTGGCATGAAAGGATGCCATAGC
TGAAATGTATATGGGTACATTGTCAAC
Found at i:1579482 original size:83 final size:81
Alignment explanation
Indices: 1579335--1579487 Score: 177
Period size: 80 Copynumber: 1.9 Consensus size: 81
1579325 ATTAATAAGT
* * *
1579335 AAAATATTTTTAATTAATTCAACTTAAATATACATTAAAGATTTATAATCAGAATTAGAATC-TT
1 AAAATATTTTTAATTAATTCAAATTAAATATACATTAAAGAGTTATAATCAGAATTACAATCTTT
1579399 TAATGTTTAATTATAA
66 TAATGTTTAATTATAA
* * * *
1579415 AAAAT-TTATTTAATTATTTCAAATTATATATATCAATTAAAAGAGTTGTAATCTA-AATTACAT
1 AAAATATT-TTTAATTAATTCAAATTAAATATA-C-ATT-AAAGAGTTATAATC-AGAATTACAA
1579478 TCTTTTAATG
61 TCTTTTAATG
1579488 CTTACTTAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
79 2 0.03
80 26 0.43
81 1 0.02
82 3 0.05
83 20 0.33
84 8 0.13
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (81 bp):
AAAATATTTTTAATTAATTCAAATTAAATATACATTAAAGAGTTATAATCAGAATTACAATCTTT
TAATGTTTAATTATAA
Found at i:1584039 original size:31 final size:31
Alignment explanation
Indices: 1584004--1584064 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1583994 TTGACTTATT
1584004 GAAGATGATAAGGTTGAGGTGTATTGGTTTG
1 GAAGATGATAAGGTTGAGGTGTATTGGTTTG
* *
1584035 GAAGATGATAAGGTTTAGGTGTCTTGGTTT
1 GAAGATGATAAGGTTGAGGTGTATTGGTTT
1584065 AATGGTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.02, G:0.36, T:0.38
Consensus pattern (31 bp):
GAAGATGATAAGGTTGAGGTGTATTGGTTTG
Found at i:1585708 original size:26 final size:26
Alignment explanation
Indices: 1585672--1585750 Score: 142
Period size: 26 Copynumber: 3.1 Consensus size: 26
1585662 AGGATACTAA
1585672 GTGTA-TATGGTGGGCACGACCTTAT
1 GTGTATTATGGTGGGCACGACCTTAT
1585697 GTGTATTATGGTGGGCACGACCTTAT
1 GTGTATTATGGTGGGCACGACCTTAT
*
1585723 ATGTATTATGGTGGGCACGACCTTAT
1 GTGTATTATGGTGGGCACGACCTTAT
1585749 GT
1 GT
1585751 ATAGCACTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
25 5 0.10
26 46 0.90
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.34
Consensus pattern (26 bp):
GTGTATTATGGTGGGCACGACCTTAT
Found at i:1589052 original size:15 final size:15
Alignment explanation
Indices: 1589032--1589070 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1589022 GGAATAAATT
*
1589032 AAAGAAAGGAAAACA
1 AAAGAAAGCAAAACA
*
1589047 AAAGAAAACAAAACA
1 AAAGAAAGCAAAACA
1589062 AAAGGAAAG
1 AAA-GAAAG
1589071 AGAATTAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.74, C:0.08, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAGAAAGCAAAACA
Found at i:1593878 original size:37 final size:37
Alignment explanation
Indices: 1593780--1593878 Score: 153
Period size: 37 Copynumber: 2.7 Consensus size: 37
1593770 GAGTTGAGGG
*
1593780 TTACCTATGTTCTTCGGGACATATCGACAATTACAAA
1 TTACCTATGTTCTTCGGGACATATGGACAATTACAAA
* * * *
1593817 TTACCTATGTTCTTCGGGATATATGGACAGTTATAGA
1 TTACCTATGTTCTTCGGGACATATGGACAATTACAAA
1593854 TTACCTATGTTCTTCGGGACATATG
1 TTACCTATGTTCTTCGGGACATATG
1593879 AATTGATTAC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (37 bp):
TTACCTATGTTCTTCGGGACATATGGACAATTACAAA
Found at i:1594750 original size:21 final size:22
Alignment explanation
Indices: 1594685--1594750 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 22
1594675 ATTCGATTAT
*
1594685 GTTCACGGT-CTGTTCATTACT
1 GTTCACGGTACTGTTCATTACC
* * *
1594706 GTTCACAGTATTGTTTATTACC
1 GTTCACGGTACTGTTCATTACC
1594728 GTTCACGGTACTGTTCA-TACC
1 GTTCACGGTACTGTTCATTACC
1594749 GT
1 GT
1594751 ATAGTACTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
21 14 0.38
22 23 0.62
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (22 bp):
GTTCACGGTACTGTTCATTACC
Found at i:1598646 original size:37 final size:37
Alignment explanation
Indices: 1598585--1598686 Score: 159
Period size: 37 Copynumber: 2.8 Consensus size: 37
1598575 GAGTCGAGGG
*
1598585 TTACATATGTTCTTCGGGACATATGGACAATTACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAATTACAGA
* * * *
1598622 TTACCTATGTTCTTCAGGATATATGGACAGTTATAGA
1 TTACCTATGTTCTTCGGGACATATGGACAATTACAGA
1598659 TTACCTATGTTCTTCGGGACATATGGAC
1 TTACCTATGTTCTTCGGGACATATGGAC
1598687 TGATTACCTA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (37 bp):
TTACCTATGTTCTTCGGGACATATGGACAATTACAGA
Found at i:1598719 original size:31 final size:31
Alignment explanation
Indices: 1598657--1598719 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
1598647 GACAGTTATA
*
1598657 GATTACCTATGTTCTTCGGGACATATGGACT
1 GATTACCTATGTTCTTCGGGACATATAGACT
1598688 GATTACCTA-GATTCTTCGGGATC-TATAGACT
1 GATTACCTATG-TTCTTCGGGA-CATATAGACT
1598719 G
1 G
1598720 GTCATTCGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 1 0.03
31 27 0.93
32 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (31 bp):
GATTACCTATGTTCTTCGGGACATATAGACT
Found at i:1599406 original size:21 final size:22
Alignment explanation
Indices: 1599381--1599422 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1599371 TATTGTAGCA
*
1599381 AGGGTATCGGTACAC-TGTAGT
1 AGGGTATCGATACACTTGTAGT
*
1599402 AGGGTATTGATACACTTGTAG
1 AGGGTATCGATACACTTGTAG
1599423 CATTCTGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.26, C:0.12, G:0.31, T:0.31
Consensus pattern (22 bp):
AGGGTATCGATACACTTGTAGT
Found at i:1599517 original size:19 final size:22
Alignment explanation
Indices: 1599464--1599519 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
1599454 TCATGGTACT
* *
1599464 GTTCACAGTACTGTTTATTACC
1 GTTCATAGTACTATTTATTACC
*
1599486 GTTCATGGTACTATTTA-TACC
1 GTTCATAGTACTATTTATTACC
1599507 G-T-ATAGTACTATT
1 GTTCATAGTACTATT
1599520 CATAAAAAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 10 0.33
20 1 0.03
21 5 0.17
22 14 0.47
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (22 bp):
GTTCATAGTACTATTTATTACC
Found at i:1601676 original size:4 final size:4
Alignment explanation
Indices: 1601660--1601692 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
1601650 AACCGAACAA
*
1601660 AAAT AAA- AAAT AAAT AAAT ATAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1601693 GAAAATGGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1602229 original size:17 final size:20
Alignment explanation
Indices: 1602188--1602236 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 20
1602178 ATTATATATG
1602188 TTATTATATATATAATAATA
1 TTATTATATATATAATAATA
*
1602208 ATATTATA-ATAT-A-AATA
1 TTATTATATATATAATAATA
*
1602225 TTATTATTTATA
1 TTATTATATATA
1602237 AAGCCCGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 10 0.40
18 4 0.16
19 4 0.16
20 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATTATATATATAATAATA
Found at i:1607123 original size:198 final size:201
Alignment explanation
Indices: 1606783--1607185 Score: 785
Period size: 198 Copynumber: 2.0 Consensus size: 201
1606773 TGACTCATGG
1606783 AATTATAGAAGTGGATGCCAACAGTCAATCTATTTTGATTAAACATTTGGAAGTCAACAACATGA
1 AATTATAGAAGTGGATGCCAACAGTCAATCTATTTTGATTAAACATTTGGAAGTCAACAACATGA
1606848 ATGAAGTTGATAGTGTCAAACCAAATGGAGGACAAGGCCAAGCCAAGAAAGATGAAGTATGTATG
66 ATGAAGTTGATAGTGTCAAACCAAATGGAGGACAAGGCCAAGCCAAGAAAGATGAAGTATGTATG
1606913 ACAGATTTAATTCTCAATACTTCTCTCAAGCTGAAAGAATATGC-AAAATGAGCAAAGCAAAAGG
131 ACAGATTTAATTCTCAATACTTCTCTCAAGCTGAAAGAATATGCAAAAATGAGCAAAGCAAAAGG
1606977 AAAGGT
196 AAAGGT
1606983 AATTATAGAAGTGGATGCCAACAGTC-ATCTA-TTTGATTAAACATTTGGAAGTCAACAACATGA
1 AATTATAGAAGTGGATGCCAACAGTCAATCTATTTTGATTAAACATTTGGAAGTCAACAACATGA
1607046 ATGAAGTTGATAGTGTCAAACCAAATGGAGGACAAGGCCAAGCCAAGAAAGATGAAGTATGTATG
66 ATGAAGTTGATAGTGTCAAACCAAATGGAGGACAAGGCCAAGCCAAGAAAGATGAAGTATGTATG
1607111 ACAGATTTAATTCTCAATACTTCTCTCAAGCTGAAAGAATATGCAAAAATGAGCAAAGCAAAAGG
131 ACAGATTTAATTCTCAATACTTCTCTCAAGCTGAAAGAATATGCAAAAATGAGCAAAGCAAAAGG
1607176 AAAGGT
196 AAAGGT
1607182 AATT
1 AATT
1607186 CGAGACTGGC
Statistics
Matches: 202, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
198 141 0.70
199 35 0.17
200 26 0.13
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (201 bp):
AATTATAGAAGTGGATGCCAACAGTCAATCTATTTTGATTAAACATTTGGAAGTCAACAACATGA
ATGAAGTTGATAGTGTCAAACCAAATGGAGGACAAGGCCAAGCCAAGAAAGATGAAGTATGTATG
ACAGATTTAATTCTCAATACTTCTCTCAAGCTGAAAGAATATGCAAAAATGAGCAAAGCAAAAGG
AAAGGT
Found at i:1609262 original size:42 final size:42
Alignment explanation
Indices: 1609181--1609262 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
1609171 CTTGGAGTGT
* *
1609181 TGGGGCATGCTGAAGGCCTATTTCAGTCAGAAATAATCCATG
1 TGGGGCATGCTGAAGGCCTATTTCAGACAAAAATAATCCATG
* * *
1609223 TGGGGTATGCTGAAGGCCTATTTTAGACAAAAATGATCCA
1 TGGGGCATGCTGAAGGCCTATTTCAGACAAAAATAATCCA
1609263 AGTAGGATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (42 bp):
TGGGGCATGCTGAAGGCCTATTTCAGACAAAAATAATCCATG
Found at i:1610114 original size:22 final size:22
Alignment explanation
Indices: 1610088--1610130 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1610078 TTCTGCAAGG
1610088 ATGATAGATTCTCTTTTCAAAT
1 ATGATAGATTCTCTTTTCAAAT
1610110 ATGATAGATTCTCTTTTCAAA
1 ATGATAGATTCTCTTTTCAAA
1610131 GACCAAAGTT
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:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (22 bp):
ATGATAGATTCTCTTTTCAAAT
Found at i:1610898 original size:45 final size:45
Alignment explanation
Indices: 1610764--1610908 Score: 122
Period size: 45 Copynumber: 3.2 Consensus size: 45
1610754 AATTTTCACG
* *
1610764 AAAGAGTAGTGGAATGAATTTTTCAGCAAAGTATCAAACTCCAGGGA
1 AAAGAGTAGAGGAATGAATTTTTCAGCAAAGTATCAAACTCCA--CA
* * * *
1610811 AGAGAGTA-ATGGAA-GCAA--ATTCAATCATAA--ATCTGAACTCCACA
1 AAAGAGTAGA-GGAATG-AATTTTTC-AGCA-AAGTATC-AAACTCCACA
1610855 AAAGAGTAGAGGAATGAATTTTTCAGCAAAGTATCAAACTCCACA
1 AAAGAGTAGAGGAATGAATTTTTCAGCAAAGTATCAAACTCCACA
*
1610900 GAAGAGTAG
1 AAAGAGTAG
1610909 TGAAAGCAGA
Statistics
Matches: 76, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
44 16 0.21
45 28 0.37
46 17 0.22
47 15 0.20
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (45 bp):
AAAGAGTAGAGGAATGAATTTTTCAGCAAAGTATCAAACTCCACA
Found at i:1617939 original size:42 final size:41
Alignment explanation
Indices: 1617892--1617980 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 41
1617882 AATTAGTAAG
*
1617892 TCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGTCATCAGTAAGTCTTTCGAGCAAGATGA-TAAA
* * *
1617934 TCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAG
1 TCCTTCGGGTCATCAGTAAGTCTTTCGAGCAAGATGATAAA
1617975 TCCTTC
1 TCCTTC
1617981 AGGCCATCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 9 0.21
42 34 0.79
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.34
Consensus pattern (41 bp):
TCCTTCGGGTCATCAGTAAGTCTTTCGAGCAAGATGATAAA
Found at i:1618159 original size:197 final size:196
Alignment explanation
Indices: 1617846--1618252 Score: 661
Period size: 197 Copynumber: 2.1 Consensus size: 196
1617836 GTAAAAATAT
* * * *
1617846 GATTTCCAAAGTGTCTTACCCAGTAAACTATTTCAGAATTAGTAAGTCCTTCGGGTCATCAGTAA
1 GATTTCCAAAGTTTATTACCCAGTAAACTATTTCAAAATTAGTAAGTCCTTCGGGCCATCAGTAA
* * * * *
1617911 GTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGT
66 ATCTTTCAAGCATAATGATTAAATCCTTCGGGTCATATGTCAGCCTTTCGAGCAAGATGATAAGT
* * *
1617976 CCTTCAGGCCATCTATAAGACCTTTGGGCATGATGTTTTCATATGATTTTTGAAAAATGAGAAAG
131 CCTTCAGGCCATCTATAAGACCTTCGGGCATGATGTTTTCACAAGATTTTTGAAAAATGAGAAAG
1618041 C
196 C
1618042 GATTTCCAAAGTTTATTACCCAGTAAACTATTTCAAAAATTAGTAAGTCCTTCGGGCCATCAGTA
1 GATTTCCAAAGTTTATTACCCAGTAAACTATTTC-AAAATTAGTAAGTCCTTCGGGCCATCAGTA
* *
1618107 AATCTTTCAAGCATAATGATTAAATCCTTTGGTTCATATGTCAGCCTTTCGAGCAAGATGATAAG
65 AATCTTTCAAGCATAATGATTAAATCCTTCGGGTCATATGTCAGCCTTTCGAGCAAGATGATAAG
* *
1618172 TCTTTCAGGCCATCTATAAGACCTTCGGGTATGATGTTTTCACAAGATTTTTGAAAAATGAGAAA
130 TCCTTCAGGCCATCTATAAGACCTTCGGGCATGATGTTTTCACAAGATTTTTGAAAAATGAGAAA
1618237 GC
195 GC
1618239 GATTTCCAAAGTTT
1 GATTTCCAAAGTTT
1618253 CTCATTTAAA
Statistics
Matches: 194, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
196 32 0.16
197 162 0.84
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (196 bp):
GATTTCCAAAGTTTATTACCCAGTAAACTATTTCAAAATTAGTAAGTCCTTCGGGCCATCAGTAA
ATCTTTCAAGCATAATGATTAAATCCTTCGGGTCATATGTCAGCCTTTCGAGCAAGATGATAAGT
CCTTCAGGCCATCTATAAGACCTTCGGGCATGATGTTTTCACAAGATTTTTGAAAAATGAGAAAG
C
Found at i:1618927 original size:42 final size:41
Alignment explanation
Indices: 1618863--1618966 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 41
1618853 AATTGGGTAG
* * **
1618863 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGTCATCTATAAGTCTTTCGAGCAACATGA-TAAA
* * *
1618905 TCCTTCGGGTCATCTGTCAGTCTTTCGAGCAACATGATAAG
1 TCCTTCGGGTCATCTATAAGTCTTTCGAGCAACATGATAAA
*
1618946 TCCTTTGGGGTCATCTATAAG
1 TCC-TTCGGGTCATCTATAAG
1618967 ACCTTTGGAC
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 6 0.12
42 45 0.88
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (41 bp):
TCCTTCGGGTCATCTATAAGTCTTTCGAGCAACATGATAAA
Found at i:1619103 original size:260 final size:259
Alignment explanation
Indices: 1618021--1619869 Score: 2344
Period size: 260 Copynumber: 7.2 Consensus size: 259
1618011 TTTTCATATG
* * * * *
1618021 ATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTATTACCCAGTAAACTATTTCAAAAATTAGT
1 ATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGT
* * * * * *
1618086 AAGTCCTTCGGGCCATCAGTAAATCTTTCAAGCATAATGATTAAATCCTTTGGTTCATATGTCAG
66 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAG
* * * * * *
1618151 CCTTTCGAGCAAGATGATAAGTCTTTCAGGCCATCTATAAGACCTTCGGGTATGATGTTTTCACA
131 TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAGGATGTTTTCACA
* *
1618216 AGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTTAG-AAATGAA
196 TGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCAGAAAATGAA
* * * *
1618279 ATTTTTTG-AAAGTAAGAAAGGGATTTCCAAATTTTCTTACCCAGTAAACTATTTTCAAAATTAG
1 A-TTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGG
*
1618343 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTACGGGTCATCTGTCA
65 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCA
** * * * * *
1618408 GTAATT-GAGCAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTCGGACATGATGTTTCCAC
130 GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAGGATGTTTTCAC
* * *
1618472 ATGATTTTCGAAAAATAAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTTTCAGAAAATGAA
195 ATGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCAGAAAATGAA
* *
1618537 ATTTTTGAAAAGTAAGAAAGTGGTTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGT
1 ATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGT
* * * * *
1618602 AAGTCCTTCGAGCCATCATTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTGGCAA
66 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAG
* * *
1618667 TCTTTCGAGCAAAATGATAAGTCCTTCGGGCCATCTATAAGA-CATTCGGCAGGATGTTTTCACA
131 TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAGGATGTTTTCACA
* * * * *
1618731 TGACTTTTGAAAAATGAGAAAGTGATTTCCAAAGTTTCTCGTTTAAATATTTTCAAAAAATGAA
196 TGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCAGAAAATGAA
* * *
1618795 ATTTTTGAAAAGTAAGAAAGCTATTTCCAAAGTTTCTTACCAAGTAAACTACTTCCAAAATTGGG
1 ATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATT-GG
*
1618860 T-AGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCA
65 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCA
* * * * *
1618924 GTCTTTCGAGCAACATGATAAGTCCTTTGGGGTCATCTATAAGACCTTTGGACAGGATGTTTCCA
130 GTCTTTCGAGCAAGATGATAAGTCC-TTCGGGCCATCTATAAGACCTTTGGGCAGGATGTTTTCA
* * *
1618989 CATGATTTTTGAAAAACGAGAAAACGATTTCCAAAGTTTTTCATTTAAATCTTTTCAGAAAATGA
194 CATGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCAGAAAATGA
1619054 A
259 A
* * * *
1619055 ATTTTGGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAAACTATATCCAAAATTAGT
1 ATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGT
* * *
1619120 AAGTCTTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTCATCTATCAG
66 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAG
* * ** * * *
1619185 ----TCGGGCCATCT-ATAAGACC-T-------TC-----G-----T--GCAGGATGATTCCACA
131 TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAGGATGTTTTCACA
* * * * * *
1619225 TGATTTTCGAAAAATAAGAAAACGGTTTCCAAAGTTTCTCATTTAAATCTTTTCAAAAAATAAA
196 TGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCAGAAAATGAA
* *
1619289 ATTTTTGAAAAGTAATAAAGCAATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGT
1 ATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGT
*
1619354 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTGTCAG
66 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAG
* ** *
1619419 TCTTTTGAGTGAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAGGATCTTTTCACA
131 TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAGGATGTTTTCACA
** * * * *
1619484 TGATTTTCAAAAAAAATAAGAAAGCGATTTTCAAAGTTTCTCATTTAGTAT-TTTT-AAAAAATG
196 TGATTTT--TGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTA-AATCTTTTCAGAAAATG
1619547 AA
258 AA
** * *
1619549 AACTTTGAAGAA-TAAGAAAGCGATTTCCAAAGTTTTTTACCTAGTAAACTATTTCCAAAATTGG
1 ATTTTTGAA-AAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGG
* * * * * *
1619613 GAAGTCATTCGGTCTATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTCATCTATCA
65 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCA
* * * *
1619678 TTCTTTCGAGCAAGATGATAAGTCCTTCGCGTCATCTATAAGACCTTTGGGCATGATGTTTTCAC
130 GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAGGATGTTTTCAC
** * *
1619743 ATGATTTTCAAAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTT-AATGTTTTCAGAAAATG
195 ATGATTTT--TGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCAGAAAATG
1619807 AA
258 AA
* * *
1619809 AGTTTTGAAAAGTAAGAAAGCGATTTCCAAATTTTCTTACCTAGTAAACTATTTCCAAAAT
1 ATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAAT
1619870 CGGACCATCA
Statistics
Matches: 1392, Mismatches: 159, Indels: 78
0.85 0.10 0.05
Matches are distributed among these distances:
234 191 0.14
236 1 0.00
238 5 0.00
239 7 0.01
240 1 0.00
241 1 0.00
246 2 0.00
247 2 0.00
252 1 0.00
253 1 0.00
255 7 0.01
256 7 0.01
257 112 0.08
258 448 0.32
259 87 0.06
260 478 0.34
261 39 0.03
262 2 0.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (259 bp):
ATTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGT
AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAG
TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTGGGCAGGATGTTTTCACA
TGATTTTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCAGAAAATGAA
Found at i:1619404 original size:42 final size:41
Alignment explanation
Indices: 1619357--1619453 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 41
1619347 AATTGGTAAG
1619357 TCCTTCGGGCCATCAGTAAGTCTTTCGAG-CATGATGATTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGTCA-GATGA-TAAA
* * * * * * *
1619399 TCCTTCGAGTCATCTGTCAGTCTTTTGAGTGAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGTCAGATGATAAA
1619440 TCCTTCGGGCCATC
1 TCCTTCGGGCCATC
1619454 TATAAGACCT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 15 0.33
42 29 0.64
43 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.33
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCGAGTCAGATGATAAA
Found at i:1619642 original size:494 final size:493
Alignment explanation
Indices: 1618692--1619677 Score: 1455
Period size: 494 Copynumber: 2.0 Consensus size: 493
1618682 GATAAGTCCT
* * * **
1618692 TCGGGCCATCTATAAGACATTCGGCAGGATGTTTTCACATGACTTTTGAAAAATGAGAAAGTGAT
1 TCGGGCCATCTATAAGACATTCGGCAGGATGATTCCACATGACTTTTGAAAAATAAGAAAACGAT
* * *
1618757 TTCCAAAGTTTCTCGTTTAAATATTTTCAAAAAATGAAATTTTTGAAAAGTAAGAAAGCTATTTC
66 TTCCAAAGTTTCTCATTTAAATATTTTCAAAAAATAAAATTTTTGAAAAGTAAGAAAGCAATTTC
1618822 CAAAGTTTCTTACCAAGTAAACTACTTCCAAAATTGGGTAGTCCTTCGGGCCATCAATAAGTCTT
131 CAAAGTTTCTTACCAAGTAAACTACTTCCAAAATTGGGTAGTCCTTCGGGCCATCAATAAGTCTT
*
1618887 TCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAACATGATAAGTCCTTT
196 TCGAGCATGATGATTAAATCCTTCGAGTCATCTGTCAGTCTTTCGAGCAACATGATAAGTCCTTT
* * * ** *
1618952 GGGGTCATCTATAAGACCTTTGGACAGGATGTTTCCACATGATTTTTGAAAAACGAGAAAACGAT
261 CGGGCCATCTATAAGACCTTTGGACAGGATCTTTCCACATGATTTTAAAAAAACAAGAAAACGAT
* * * *
1619017 TTCCAAAGTTTTTCATTTAAATCTTTTCAGAAAATGAAATTTTGGAAAAGTAAGAAAGTGATTTC
326 TTCCAAAGTTTCTCATTTAAATCTTTTCAAAAAATGAAACTTTGGAAAAGTAAGAAAGCGATTTC
* *
1619082 CAAAGTTTCTTACCCAGTAAACTATATCCAAAATTAGTAAGTCTTTCGGGCCATCAGTAAGTCTT
391 CAAAGTTTCTTACCCAGTAAACTATATCCAAAATTAGGAAGTCATTCGGGCCATCAGTAAGTCTT
1619147 TTGAGCATGATGATTAAATCCTTCGGGTCATCTATCAG
456 TTGAGCATGATGATTAAATCCTTCGGGTCATCTATCAG
*
1619185 TCGGGCCATCTATAAGACCTTCGTGCAGGATGATTCCACATGA-TTTTCGAAAAATAAGAAAACG
1 TCGGGCCATCTATAAGACATTCG-GCAGGATGATTCCACATGACTTTT-GAAAAATAAGAAAACG
* * *
1619249 GTTTCCAAAGTTTCTCATTTAAATCTTTTCAAAAAATAAAATTTTTGAAAAGTAATAAAGCAATT
64 ATTTCCAAAGTTTCTCATTTAAATATTTTCAAAAAATAAAATTTTTGAAAAGTAAGAAAGCAATT
* * *
1619314 TCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATT-GGTAAGTCCTTCGGGCCATCAGTAAGT
129 TCCAAAGTTTCTTACCAAGTAAACTACTTCCAAAATTGGGT-AGTCCTTCGGGCCATCAATAAGT
* ** *
1619378 CTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTGTCAGTCTTTTGAGTGAGATGATAAGTCC
193 CTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTGTCAGTCTTTCGAGCAACATGATAAGTCC
* * *
1619443 -TTCGGGCCATCTATAAGACCTTTGGGCAGGATCTTTTCACATGATTTTCAAAAAAAATAAGAAA
258 TTTCGGGCCATCTATAAGACCTTTGGACAGGATCTTTCCACATGATTTT--AAAAAAACAAGAAA
* * *
1619507 GCGATTTTCAAAGTTTCTCATTTAGTAT-TTTT-AAAAAATGAAAACTTT-GAAGAA-TAAGAAA
321 ACGATTTCCAAAGTTTCTCATTTA-AATCTTTTCAAAAAATG-AAACTTTGGAA-AAGTAAGAAA
* * * * * *
1619568 GCGATTTCCAAAGTTTTTTACCTAGTAAACTATTTCCAAAATTGGGAAGTCATTCGGTCTATCAG
383 GCGATTTCCAAAGTTTCTTACCCAGTAAACTATATCCAAAATTAGGAAGTCATTCGGGCCATCAG
1619633 TAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTCATCTATCA
448 TAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTCATCTATCA
1619678 TTCTTTCGAG
Statistics
Matches: 441, Mismatches: 44, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
493 72 0.16
494 324 0.73
495 43 0.10
496 2 0.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (493 bp):
TCGGGCCATCTATAAGACATTCGGCAGGATGATTCCACATGACTTTTGAAAAATAAGAAAACGAT
TTCCAAAGTTTCTCATTTAAATATTTTCAAAAAATAAAATTTTTGAAAAGTAAGAAAGCAATTTC
CAAAGTTTCTTACCAAGTAAACTACTTCCAAAATTGGGTAGTCCTTCGGGCCATCAATAAGTCTT
TCGAGCATGATGATTAAATCCTTCGAGTCATCTGTCAGTCTTTCGAGCAACATGATAAGTCCTTT
CGGGCCATCTATAAGACCTTTGGACAGGATCTTTCCACATGATTTTAAAAAAACAAGAAAACGAT
TTCCAAAGTTTCTCATTTAAATCTTTTCAAAAAATGAAACTTTGGAAAAGTAAGAAAGCGATTTC
CAAAGTTTCTTACCCAGTAAACTATATCCAAAATTAGGAAGTCATTCGGGCCATCAGTAAGTCTT
TTGAGCATGATGATTAAATCCTTCGGGTCATCTATCAG
Found at i:1619716 original size:41 final size:42
Alignment explanation
Indices: 1619637--1619716 Score: 117
Period size: 41 Copynumber: 1.9 Consensus size: 42
1619627 TATCAGTAAG
* * *
1619637 TCTTTTGAGCATGATGATTAAATCCTTCGGGTCATCTATCAT
1 TCTTTCGAGCAAGATGATTAAATCCTTCGCGTCATCTATCAT
*
1619679 TCTTTCGAGCAAGATGA-TAAGTCCTTCGCGTCATCTAT
1 TCTTTCGAGCAAGATGATTAAATCCTTCGCGTCATCTAT
1619717 AAGACCTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
41 19 0.56
42 15 0.44
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (42 bp):
TCTTTCGAGCAAGATGATTAAATCCTTCGCGTCATCTATCAT
Found at i:1620128 original size:44 final size:44
Alignment explanation
Indices: 1620031--1620425 Score: 388
Period size: 44 Copynumber: 9.0 Consensus size: 44
1620021 AATAGATTGA
* * * *
1620031 AAGATGAGTCAA-CTTTAGTGTTGTCATTCTTGACTTTTTTCGTG
1 AAGAGGAGTCAATCTTTAGTGTTATTATTCTTGAC-TTTCTCGTG
* * *
1620075 AAGATGAGTCAATCTTTAATGTTATTATTCTTGACTTTCTCGAG
1 AAGAGGAGTCAATCTTTAGTGTTATTATTCTTGACTTTCTCGTG
* * * *
1620119 AAGGGGAGTCAATCTTTAGTGTTTTTATTCTTGACTTTTTCTTG
1 AAGAGGAGTCAATCTTTAGTGTTATTATTCTTGACTTTCTCGTG
* * * *
1620163 AAGATGAGTCCATCTTTAATGTTATTATTCTTGACTTTCTCATG
1 AAGAGGAGTCAATCTTTAGTGTTATTATTCTTGACTTTCTCGTG
* * * *
1620207 AAGAGGGGTCAATATATAGTGTTTTTATTCTTGACTTTCTCGTG
1 AAGAGGAGTCAATCTTTAGTGTTATTATTCTTGACTTTCTCGTG
* * * *
1620251 AAGAGGAGTCAACCTTTAGTGGTGTTGTTCTTGACTTTCTCGTG
1 AAGAGGAGTCAATCTTTAGTGTTATTATTCTTGACTTTCTCGTG
* * * * * *
1620295 GAGAGAAGTCAACCTTTTAGTGATGTCATTCTTGACTTTCTCGTG
1 AAGAGGAGTCAATC-TTTAGTGTTATTATTCTTGACTTTCTCGTG
* * * *
1620340 AAGA-GACTCAATCTTTCAATG----TATTCTTGACTTTTTCGTA
1 AAGAGGAGTCAATCTTT-AGTGTTATTATTCTTGACTTTCTCGTG
* * *
1620380 AAGAGGAGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCGTG
1 AAGAGGAGTCAATCTTT-AGTGTTATTATTCTTGACTTTCTCGTG
1620425 A
1 A
1620426 TGAGAAATTG
Statistics
Matches: 290, Mismatches: 53, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
40 20 0.07
41 14 0.05
43 3 0.01
44 187 0.64
45 66 0.23
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (44 bp):
AAGAGGAGTCAATCTTTAGTGTTATTATTCTTGACTTTCTCGTG
Found at i:1620185 original size:88 final size:88
Alignment explanation
Indices: 1620031--1620425 Score: 437
Period size: 88 Copynumber: 4.5 Consensus size: 88
1620021 AATAGATTGA
* *
1620031 AAGATGAGTCAA-CTTTAGTGTTGTCATTCTTGACTTTTTTCGTGAAGATGAGTCAATCTTTAAT
1 AAGAGGAGTCAATCTTTAGTGTTGTCATTCTTGAC-TTTCTCGTGAAGATGAGTCAATCTTTAAT
1620095 GTTATTATTCTTGACTTTCTCGAG
65 GTTATTATTCTTGACTTTCTCGAG
* * * * * *
1620119 AAGGGGAGTCAATCTTTAGTGTTTTTATTCTTGACTTTTTCTTGAAGATGAGTCCATCTTTAATG
1 AAGAGGAGTCAATCTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGATGAGTCAATCTTTAATG
1620184 TTATTATTCTTGACTTTCTC-ATG
66 TTATTATTCTTGACTTTCTCGA-G
* * * * * * * *
1620207 AAGAGGGGTCAATATATAGTGTTTTTATTCTTGACTTTCTCGTGAAGAGGAGTCAACCTTTAGTG
1 AAGAGGAGTCAATCTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGATGAGTCAATCTTTAATG
* * * *
1620272 GTGTTGTTCTTGACTTTCTCGTG
66 TTATTATTCTTGACTTTCTCGAG
* * * * *
1620295 GAGAGAAGTCAACCTTTTAGTGATGTCATTCTTGACTTTCTCGTGAAGA-GACTCAATCTTTCAA
1 AAGAGGAGTCAATC-TTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGATGAGTCAATCTTT-AA
*
1620359 TG----TATTCTTGACTTTTTCGTA-
64 TGTTATTATTCTTGACTTTCTCG-AG
*
1620380 AAGAGGAGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCGTGA
1 AAGAGGAGTCAATCTTT-AGTGTTGTCATTCTTGACTTTCTCGTGA
1620426 TGAGAAATTG
Statistics
Matches: 260, Mismatches: 40, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
84 3 0.01
85 52 0.20
87 1 0.00
88 151 0.58
89 53 0.20
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (88 bp):
AAGAGGAGTCAATCTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGATGAGTCAATCTTTAATG
TTATTATTCTTGACTTTCTCGAG
Found at i:1620473 original size:130 final size:129
Alignment explanation
Indices: 1620232--1620473 Score: 288
Period size: 130 Copynumber: 1.9 Consensus size: 129
1620222 ATAGTGTTTT
* * **
1620232 TATTCTTGACTTTCTCGTGAAGAGGAGTCAACCTTTAGTGGTGTTGTTCTTGACTTTCTCGTGGA
1 TATTCTTGACTTTCTCGTAAAGAGGAGTCAACCTTTAGTAGTGTCATTCTTGACTTTCTCGTGGA
* * ***
1620297 GAGAAGTCAACCTTTTAGTGATGTCATTCTTGACTTTCTCGTGAAGAGACTCAATCTTTCAATG
66 GAGAAATCAACCTTTTAGTGATGTCATTCTTAACTTTCTAACGAAGAGACTCAATCTTTCAATG
* * *
1620361 TATTCTTGACTTTTTCGTAAAGAGGAGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCGT-G
1 TATTCTTGACTTTCTCGTAAAGAGGAGTCAACCTTT-AGTAGTGTCATTCTTGACTTTCTCGTGG
** * * * * *
1620425 ATGAGAAATTGATCTTTTGGTGTTGTCCTTTTTAACTTTCTAACGAAGA
65 A-GAGAAATCAACCTTTTAGTGATGTCATTCTTAACTTTCTAACGAAGA
1620474 ATAGTCAACC
Statistics
Matches: 92, Mismatches: 19, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
129 35 0.38
130 57 0.62
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (129 bp):
TATTCTTGACTTTCTCGTAAAGAGGAGTCAACCTTTAGTAGTGTCATTCTTGACTTTCTCGTGGA
GAGAAATCAACCTTTTAGTGATGTCATTCTTAACTTTCTAACGAAGAGACTCAATCTTTCAATG
Found at i:1621291 original size:134 final size:134
Alignment explanation
Indices: 1621111--1621643 Score: 678
Period size: 134 Copynumber: 4.0 Consensus size: 134
1621101 TGAAGAGCAT
* * * * *
1621111 TGAAGTAGATCAAAAATTTCTCGATTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTC
1 TGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCCTAAAAAGTAGTGGAGCAGATGCTTCTTC
* *
1621176 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGTAAATCGATTATGATTCAATCTTCTCTGAAGA
66 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTATGATTCAATCTTCCCTGAAGA
*
1621241 GTAG
131 ATAG
* *
1621245 TGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCTCTAAAAAGTAGTGGAGC-GTATG-TTTTA
1 TGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCCTAAAAAGTAGTGGAGCAG-ATGCTTCT-
* * * * * * *
1621308 TCTTTCAGATTTGGTCTTCTTGAAGAGCAATGAATCAAATTGATTCTAACTCAATCTTCCCTGAA
64 TCTTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTATGATTCAATCTTCCCTGAA
*
1621373 TAATAG
129 GAATAG
* ** * *
1621379 TGAAGTGGATCAAAGTTTTCTCGAGTCTGATCTCCCCTAAAGAA-TAGTATAGCATATGCCTCTT
1 TGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCCTAAA-AAGTAGTGGAGCAGATGCTTCTT
* * * * *
1621443 CTTTCAGATCTAGTCTTCCTAAAGAGGAGTGAAGCAAATCAATTATGATTCAATCTTCCCTGAA-
65 CTTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTATGATTCAATCTTCCCTGAAG
1621507 ATATAG
130 A-ATAG
* * * *
1621513 TGAAGTGGATCAAAGTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCATACGCTTCTTC
1 TGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCCTAAAAAGTAGTGGAGCAGATGCTTCTTC
* ** *
1621578 TTTCAGATTTGGTCTTCCTAAAGAGCAGTGAAGCAAATCGATTCCGATTCAATCTTCCCTAAAGA
66 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTATGATTCAATCTTCCCTGAAGA
1621643 A
131 A
1621644 CGATGGAATG
Statistics
Matches: 342, Mismatches: 49, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
133 6 0.02
134 331 0.97
135 5 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (134 bp):
TGAAGTGGATCAAAATTTTCTCGAGTCTGATCTCCCCTAAAAAGTAGTGGAGCAGATGCTTCTTC
TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTATGATTCAATCTTCCCTGAAGA
ATAG
Found at i:1621760 original size:3 final size:3
Alignment explanation
Indices: 1621747--1621787 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
1621737 AGACATGTTT
*
1621747 TTA TT- TTA TTA TTA TTA TCA TTA TTA TTTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TT
1621788 TTGTTTGCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1624247 original size:11 final size:12
Alignment explanation
Indices: 1624233--1624261 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1624223 ATTTTTTTTA
1624233 TATTTTAAAA-T
1 TATTTTAAAATT
1624244 TATTTTAAAATT
1 TATTTTAAAATT
1624256 TATTTT
1 TATTTT
1624262 TAGGCATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTTTAAAATT
Found at i:1628890 original size:95 final size:95
Alignment explanation
Indices: 1628713--1628919 Score: 222
Period size: 95 Copynumber: 2.2 Consensus size: 95
1628703 TACCTAATGA
* * ** *
1628713 AGTGGTATTGATACCATGGTGAGGGTATTGATACCGGGTAACATCGAACCTAATTTTGGTATCGA
1 AGTGGTATTGATACCATGGTAAAGGTATCAATACCGGGCAACATCGAACCTAATTTTGGTATCGA
*
1628778 TACCATATAGGGGTATCAGTACCATAGTAT
66 TACCATATAGGGGTATCAATACCATAGTAT
* * * * *
1628808 AGTGGTATTGATACCTATGGTAAAGGTATCAATACGGGGCCACATTGAATCTAATTTTTGGTATT
1 AGTGGTATTGATACC-ATGGTAAAGGTATCAATACCGGGCAACATCGAACCTAA-TTTTGGTATC
* *
1628873 GATA-C-TGGTA-GGGTATCAATACCATAGTAG
64 GATACCAT-ATAGGGGTATCAATACCATAGTAT
** *
1628903 AGAAGTATCGATACCAT
1 AGTGGTATTGATACCAT
1628920 AGTAGGGGTA
Statistics
Matches: 93, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
94 2 0.02
95 46 0.49
96 32 0.34
97 13 0.14
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (95 bp):
AGTGGTATTGATACCATGGTAAAGGTATCAATACCGGGCAACATCGAACCTAATTTTGGTATCGA
TACCATATAGGGGTATCAATACCATAGTAT
Found at i:1628932 original size:20 final size:21
Alignment explanation
Indices: 1628882--1628936 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
1628872 TGATACTGGT
*
1628882 AGGGTATCAATACCATAGTAG
1 AGGGTATCGATACCATAGTAG
*
1628903 AGAAGTATCGATACCATAGTAG
1 AG-GGTATCGATACCATAGTAG
1628925 -GGGTATCGATAC
1 AGGGTATCGATAC
1628937 TGAAGGGCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.33
21 3 0.10
22 17 0.57
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (21 bp):
AGGGTATCGATACCATAGTAG
Found at i:1629491 original size:45 final size:45
Alignment explanation
Indices: 1629427--1629776 Score: 371
Period size: 45 Copynumber: 7.8 Consensus size: 45
1629417 ATAAAAGAAT
*** * *
1629427 AATGCATATGGGTGCATTATTGGCATG-AAAGGATGCCAGAGTTGA
1 AATGCATATGGGTGCATTATCAACA-GAAAAGTATGCAAGAGTTGA
* *
1629472 AATGCATATGGGTGCATTATCAACAGAAAAGTATAG-GATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTAT-GCAAGAGTTGA
* * * * *
1629517 AATGTATATAGGTACATTATCAACATAAAAGTATGCAATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCAAGAGTTGA
* *
1629562 AATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCAAGAGTTGA
* * * * * * *
1629607 AATGTATATGGGTACATTATCAACTGAAAATTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCAAGAGTTGA
* ** * * * *
1629652 AATGTATATGGGTATATTATCAATAGAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCAAGAGTTGA
* * * *
1629697 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAATTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCAAGAGTTGA
*
1629742 AATGCATATGGGTGCATTATCAACAGAAAAATATG
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATG
1629777 TTATAGTTTA
Statistics
Matches: 266, Mismatches: 36, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
44 2 0.01
45 263 0.99
46 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATGCAAGAGTTGA
Found at i:1629502 original size:79 final size:79
Alignment explanation
Indices: 1629335--1629502 Score: 255
Period size: 79 Copynumber: 2.1 Consensus size: 79
1629325 CTCTAAAATG
* * *
1629335 AACATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGTAT
1 AACATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGAGCTGAAATGCAT
* *
1629400 GTGGGTACATTGTC
66 ATGGGTACATTATC
* *
1629414 AGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGAGTTGAAATGCAT
1 AACATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGAGCTGAAATGCAT
*
1629479 ATGGGTGCATTATC
66 ATGGGTACATTATC
*
1629493 AACAGAAAAG
1 AACATAAAAG
1629503 TATAGGATAG
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.26
Consensus pattern (79 bp):
AACATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGAGCTGAAATGCAT
ATGGGTACATTATC
Found at i:1629594 original size:90 final size:90
Alignment explanation
Indices: 1629466--1629784 Score: 437
Period size: 90 Copynumber: 3.5 Consensus size: 90
1629456 AGGATGCCAG
* *
1629466 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATAGGATAGTTGAAATGTATATAGGTA
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATAGTATAGTTGAAATGTATATGGGTA
* *
1629531 CATTATCAACATAAAAGTATGCAAT
66 CATTATCAACATAAAAGTATACTAT
* *
1629556 AGTTGAAATGCATATGGGTGCATTGTCAACAGAAAAGTAT-GCTAGAGTTGAAATGTATATGGGT
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATAG-TATAGTTGAAATGTATATGGGT
*
1629620 ACATTATCAAC-TGAAAATTATACTAT
65 ACATTATCAACAT-AAAAGTATACTAT
* ** * * * *
1629646 AGTTGAAATGTATATGGGTATATTATCAATAGAAAAGTATACTATAGTTGAAATGCATATGGGTG
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATAGTATAGTTGAAATGTATATGGGTA
*
1629711 CATTATCAACAGAAAAGTATACTAT
66 CATTATCAACATAAAAGTATACTAT
* *
1629736 AATTGAAATGCATATGGGTGCATTATCAACAGAAAAATAT-GTTATAGTT
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATAG-TATAGTT
1629785 TAAAGTACAT
Statistics
Matches: 199, Mismatches: 25, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
89 2 0.01
90 197 0.99
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (90 bp):
AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATAGTATAGTTGAAATGTATATGGGTA
CATTATCAACATAAAAGTATACTAT
Found at i:1629671 original size:135 final size:135
Alignment explanation
Indices: 1629427--1629771 Score: 485
Period size: 135 Copynumber: 2.6 Consensus size: 135
1629417 ATAAAAGAAT
*** * *
1629427 AATGCATATGGGTGCATTATTGGCATG-AAAGGATGCCAGAGTTGAAATGCATATGGGTGCATTA
1 AATGCATATGGGTGCATTATCAACA-GAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTA
* * *
1629491 TCAACAGAAAAGTATAGGATAGTTGAAATGTATATAGGTACATTATCAACATAAAAGTATGCAAT
65 TCAACAGAAAAGTATACGATAGTTGAAATGTATATAGGTACATTATCAACAGAAAAGTATACAAT
1629556 AGTTGA
130 AGTTGA
* * *
1629562 AATGCATATGGGTGCATTGTCAACAGAAAAGTATGCTAGAGTTGAAATGTATATGGGTACATTAT
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTAT
* * * * * * *
1629627 CAACTGAAAATTATACTATAGTTGAAATGTATATGGGTATATTATCAATAGAAAAGTATACTATA
66 CAACAGAAAAGTATACGATAGTTGAAATGTATATAGGTACATTATCAACAGAAAAGTATACAATA
1629692 GTTGA
131 GTTGA
* * *
1629697 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTATAATTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTAT
1629762 CAACAGAAAA
66 CAACAGAAAA
1629772 ATATGTTATA
Statistics
Matches: 184, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
134 1 0.01
135 183 0.99
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.30
Consensus pattern (135 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTAT
CAACAGAAAAGTATACGATAGTTGAAATGTATATAGGTACATTATCAACAGAAAAGTATACAATA
GTTGA
Found at i:1630312 original size:13 final size:13
Alignment explanation
Indices: 1630294--1630339 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1630284 GTCATAAATC
*
1630294 TATGACGCGTATT
1 TATGACGCGCATT
* *
1630307 TATGACACACATT
1 TATGACGCGCATT
*
1630320 TATGATGCGCATT
1 TATGACGCGCATT
1630333 TATGACG
1 TATGACG
1630340 TTCATTGAGC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:1630431 original size:85 final size:85
Alignment explanation
Indices: 1630317--1630482 Score: 194
Period size: 85 Copynumber: 2.0 Consensus size: 85
1630307 TATGACACAC
** * * * *
1630317 ATTTATGATGCGCATTTATGACGTTCATTG-AGCGTCATTGAAGCCCCCATCA-TAAATTAAGAT
1 ATTTATGACACGCATGTATGACGTTCATTGCA-CGTCATTGAAGCACACATCACTAAA-AAAGAT
*
1630380 GACACACATTTGTGTGTCATAA
64 GACACACATTCGTGTGTCATAA
* * *
1630402 ATTTATGACACGCATGTATGAC-TTACATTGCATGTCATTGAAGCACACGTCACTAAAAAATATG
1 ATTTATGACACGCATGTATGACGTT-CATTGCACGTCATTGAAGCACACATCACTAAAAAAGATG
1630466 ACACACATTCGTGTGTC
65 ACACACATTCGTGTGTC
1630483 GTAATTGTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
84 2 0.03
85 61 0.90
86 5 0.07
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACGTTCATTGCACGTCATTGAAGCACACATCACTAAAAAAGATGA
CACACATTCGTGTGTCATAA
Found at i:1637696 original size:17 final size:16
Alignment explanation
Indices: 1637670--1637701 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1637660 TTATTTTTCT
1637670 TAGTGTGTTTAAATTA
1 TAGTGTGTTTAAATTA
1637686 TAGTGGTGTTTAAATT
1 TAGT-GTGTTTAAATT
1637702 TTTTTGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (16 bp):
TAGTGTGTTTAAATTA
Found at i:1638289 original size:17 final size:18
Alignment explanation
Indices: 1638250--1638297 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
1638240 TGTTTCTGAG
1638250 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
1638268 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
1638285 GGAATTGGAATCT
1 GGAATTGGAATCT
1638298 AATTCCATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.29
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:1639107 original size:267 final size:244
Alignment explanation
Indices: 1638660--1639266 Score: 812
Period size: 267 Copynumber: 2.4 Consensus size: 244
1638650 CTCCATCCAA
1638660 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCCGAA
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCCGAA
* *
1638725 ATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAATATATATATATAGAG
66 ATAATAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAATAAATATATATAGA-
*
1638790 GGAGGGGTATTATTGTAATTATTTCTAAATATATAAGGTAAAATTATATATTTTTTGGTTCGGGT
130 GGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA---------T----T
*
1638855 CGGGTCGGGTATTGTTCACCCTAAACCCG-T-ACCTGACCCGAATATCACACTTAAAAAGAACC
182 CGGGTCGGGTATTGTTCACCCTAAACCCGATCACCCGACCCGAATATCACACTTAAAAAG-ACC
*
1638917 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAATCCGAC
1 GACCCGACCCGACCAAAATAAAGTTT----C-ACCCGACCCGAATATATGAATTAGAAACCCGA-
1638982 CCAACCTGAAATAATAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAA-AAAT
60 -C--CC-GAAATAATAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAATAAAT
*
1639046 -TATATATA-GAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATATT
121 ATATATAGAGGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGT-AAA--AT-TATATATT
*
1639109 CGGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAGAC
182 CGGGTCGGGTATTGTTCACCCTAAACCCG-A-TC-ACCCGACCCGAATATCACACTTAAAAAGAC
1639174 C
244 C
*
1639175 TACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCCGAA
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCCGAA
1639240 ATAAT-AAAAAAATATTTTTATTCAATA
66 ATAATAAAAAAAATATTTTTATTCAATA
1639267 TATGAATAAG
Statistics
Matches: 322, Mismatches: 9, Indels: 48
0.85 0.02 0.13
Matches are distributed among these distances:
247 22 0.07
248 8 0.02
249 2 0.01
251 1 0.00
253 31 0.10
254 30 0.09
257 27 0.08
258 29 0.09
259 27 0.08
261 1 0.00
262 31 0.10
263 37 0.11
264 4 0.01
265 7 0.02
266 7 0.02
267 58 0.18
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.27
Consensus pattern (244 bp):
GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCCGAA
ATAATAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAATAAATATATATAGAG
GAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTCGGGTCGGGTATTG
TTCACCCTAAACCCGATCACCCGACCCGAATATCACACTTAAAAAGACC
Found at i:1642652 original size:12 final size:12
Alignment explanation
Indices: 1642635--1642665 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1642625 TTAAATATAT
1642635 ATACCCGGCCCG
1 ATACCCGGCCCG
*
1642647 ATACCCTGCCCG
1 ATACCCGGCCCG
1642659 ATACCCG
1 ATACCCG
1642666 TTTAAATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.13
Consensus pattern (12 bp):
ATACCCGGCCCG
Found at i:1644810 original size:32 final size:33
Alignment explanation
Indices: 1644705--1644814 Score: 195
Period size: 33 Copynumber: 3.4 Consensus size: 33
1644695 TACTTAAATA
*
1644705 CAAGTTTGATAAATTCAAATACTTAAAAACTTT
1 CAAGTTCGATAAATTCAAATACTTAAAAACTTT
*
1644738 CAAGTTTGATAAATTCAAATACTTAAAAACTTT
1 CAAGTTCGATAAATTCAAATACTTAAAAACTTT
1644771 CAAGTTCGATAAATTCAAATACTTAAAAAC-TT
1 CAAGTTCGATAAATTCAAATACTTAAAAACTTT
1644803 CAAGTTCGATAA
1 CAAGTTCGATAA
1644815 TTGAAACAAA
Statistics
Matches: 76, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 14 0.18
33 62 0.82
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (33 bp):
CAAGTTCGATAAATTCAAATACTTAAAAACTTT
Found at i:1644833 original size:21 final size:21
Alignment explanation
Indices: 1644809--1644850 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1644799 ACTTCAAGTT
*
1644809 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAATTTA
*
1644830 CGATAATTGAAATAAAATTTA
1 CGATAATTGAAACAAAATTTA
1644851 AAAATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAATTTA
Found at i:1647461 original size:23 final size:23
Alignment explanation
Indices: 1647435--1647498 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
1647425 CACGAATATG
* *
1647435 TTTGCGAACAATAAATAAACACA
1 TTTGTGAATAATAAATAAACACA
* * * *
1647458 TTTGTGAATATTAAACAAATATA
1 TTTGTGAATAATAAATAAACACA
1647481 TTTGTGAATAATAAATAA
1 TTTGTGAATAATAAATAA
1647499 GCAAACACGA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (23 bp):
TTTGTGAATAATAAATAAACACA
Found at i:1652102 original size:18 final size:19
Alignment explanation
Indices: 1652067--1652105 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1652057 ATATATTTGA
1652067 TCTGATTATCCAAAAAAAT
1 TCTGATTATCCAAAAAAAT
*
1652086 TCTGA-TATCCGATAAAAAT
1 TCTGATTATCC-AAAAAAAT
1652105 T
1 T
1652106 ATTCAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (19 bp):
TCTGATTATCCAAAAAAAT
Found at i:1654015 original size:13 final size:13
Alignment explanation
Indices: 1653997--1654021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1653987 ATTTTGATAA
1653997 ATTTTTAAAAAAT
1 ATTTTTAAAAAAT
1654010 ATTTTTAAAAAA
1 ATTTTTAAAAAA
1654022 ACTTAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTTTAAAAAAT
Found at i:1654731 original size:20 final size:19
Alignment explanation
Indices: 1654706--1654748 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1654696 TTTTTTAATA
*
1654706 TATTATTAAATTATTATTAT
1 TATTATTAAAGTATTATT-T
*
1654726 TATTATTTAAGTATTATTT
1 TATTATTAAAGTATTATTT
1654745 TATT
1 TATT
1654749 TTCTTGCAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTATTAAAGTATTATTT
Found at i:1656150 original size:29 final size:29
Alignment explanation
Indices: 1656125--1656234 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 29
1656115 TATGTTTTTT
1656125 TTTATTTTAATTCAGCTATGTAGTTTTCA
1 TTTATTTTAATTCAGCTATGTAGTTTTCA
* * **
1656154 TTTATTTTAATTTAGCCCCATGTTCTCGAATATGTTTTTT
1 TTTATTTTAA-TT-----CA-GCTAT-G--TA-GTTTTCA
1656194 TTTATTTTAATTCAGCTATGTAGTTTTCA
1 TTTATTTTAATTCAGCTATGTAGTTTTCA
1656223 TTTATTTTAATT
1 TTTATTTTAATT
1656235 TAGCCCCATG
Statistics
Matches: 62, Mismatches: 8, Indels: 22
0.67 0.09 0.24
Matches are distributed among these distances:
29 27 0.44
30 4 0.06
32 1 0.02
33 3 0.05
34 2 0.03
35 2 0.03
36 3 0.05
37 1 0.02
39 4 0.06
40 15 0.24
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (29 bp):
TTTATTTTAATTCAGCTATGTAGTTTTCA
Found at i:1656187 original size:69 final size:69
Alignment explanation
Indices: 1656109--1656246 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
1656099 GCATTTCAAA
1656109 CTCGAATATGTTTTTTTTTATTTTAATTCAGCTATGTAGTTTTCATTTATTTTAATTTAGCCCCA
1 CTCGAATATGTTTTTTTTTATTTTAATTCAGCTATGTAGTTTTCATTTATTTTAATTTAGCCCCA
1656174 TGTT
66 TGTT
1656178 CTCGAATATGTTTTTTTTTATTTTAATTCAGCTATGTAGTTTTCATTTATTTTAATTTAGCCCCA
1 CTCGAATATGTTTTTTTTTATTTTAATTCAGCTATGTAGTTTTCATTTATTTTAATTTAGCCCCA
1656243 TGTT
66 TGTT
1656247 TTATTTATTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.22, C:0.13, G:0.10, T:0.55
Consensus pattern (69 bp):
CTCGAATATGTTTTTTTTTATTTTAATTCAGCTATGTAGTTTTCATTTATTTTAATTTAGCCCCA
TGTT
Found at i:1659366 original size:113 final size:113
Alignment explanation
Indices: 1659159--1659377 Score: 330
Period size: 113 Copynumber: 1.9 Consensus size: 113
1659149 TCCAGTTTCA
**
1659159 CAACACAGTTTTCAAATTCGCAACGTGATTATCCAAAATCGCAACGCGAATTTCATTTTCGCAAC
1 CAACACAGTTTTCAAATTCGCAACACGATTATCCAAAATCGCAACGCGAATTTCATTTTCGCAAC
*
1659224 TCAAATTTCGCAACGCTAATTACCTATATAGGTAAACACAACTATTTG
66 TCAAATTTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTTG
* * * * * *
1659272 CAACTCAGTTTTCAAATTTGTAACACGATTCTTCAAATTCGCAACGCGAATTTCATTTTCGCAAC
1 CAACACAGTTTTCAAATTCGCAACACGATTATCCAAAATCGCAACGCGAATTTCATTTTCGCAAC
* * *
1659337 TCGAATTTCTCAACGCTAATTACCGATATATGTAAACACAA
66 TCAAATTTCGCAACGCTAATTACCGATATAGGTAAACACAA
1659378 TTCAGTTTTT
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
113 94 1.00
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.31
Consensus pattern (113 bp):
CAACACAGTTTTCAAATTCGCAACACGATTATCCAAAATCGCAACGCGAATTTCATTTTCGCAAC
TCAAATTTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTTG
Found at i:1659523 original size:20 final size:20
Alignment explanation
Indices: 1659479--1659516 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1659469 ATTCGAGTTG
*
1659479 TGAAATTCACGTTGTGAAAA
1 TGAAATTCACGTTGCGAAAA
*
1659499 TGAAATTCGCGTTGCGAA
1 TGAAATTCACGTTGCGAA
1659517 TTTGAAAACT
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:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (20 bp):
TGAAATTCACGTTGCGAAAA
Found at i:1659632 original size:41 final size:42
Alignment explanation
Indices: 1659587--1659709 Score: 119
Period size: 41 Copynumber: 3.0 Consensus size: 42
1659577 CGAAATTTGC
1659587 GTTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAACTG-A
1 GTTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAACTGCA
* * *** *
1659628 GTTGCG-TGTATCGGTA-ATTATTGTTGCGAATTTGAAAACCGCA
1 GTTGCGAT-T-TTGG-AGAATCGCGTTGCGAATTTGAAAACTGCA
* *
1659671 -TTGCGATTTTGCAGAATCGGGTTGCGAATTTGAAAACTG
1 GTTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAACTG
1659710 GTGTTCGCCT
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
40 2 0.03
41 29 0.46
42 29 0.46
43 3 0.05
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (42 bp):
GTTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAACTGCA
Found at i:1659676 original size:20 final size:20
Alignment explanation
Indices: 1659651--1659707 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
1659641 GTAATTATTG
1659651 TTGCGAATTTGAAAACCGCA
1 TTGCGAATTTGAAAACCGCA
* * * **
1659671 TTGCGATTTTGCAGAATCGGG
1 TTGCGAATTTG-AAAACCGCA
1659692 TTGCGAATTTGAAAAC
1 TTGCGAATTTGAAAAC
1659708 TGGTGTTCGC
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (20 bp):
TTGCGAATTTGAAAACCGCA
Found at i:1660355 original size:82 final size:82
Alignment explanation
Indices: 1660259--1660420 Score: 324
Period size: 82 Copynumber: 2.0 Consensus size: 82
1660249 ATTTTAAGAT
1660259 TTTACAAAAGATTTTCTAAGTATATTCGATGTAATTATTCGAATATCAAAATATTACTCCAAGTA
1 TTTACAAAAGATTTTCTAAGTATATTCGATGTAATTATTCGAATATCAAAATATTACTCCAAGTA
1660324 TTTCAAAGTTCATTTAA
66 TTTCAAAGTTCATTTAA
1660341 TTTACAAAAGATTTTCTAAGTATATTCGATGTAATTATTCGAATATCAAAATATTACTCCAAGTA
1 TTTACAAAAGATTTTCTAAGTATATTCGATGTAATTATTCGAATATCAAAATATTACTCCAAGTA
1660406 TTTCAAAGTTCATTT
66 TTTCAAAGTTCATTT
1660421 TAATCCTTAC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (82 bp):
TTTACAAAAGATTTTCTAAGTATATTCGATGTAATTATTCGAATATCAAAATATTACTCCAAGTA
TTTCAAAGTTCATTTAA
Found at i:1660581 original size:22 final size:21
Alignment explanation
Indices: 1660552--1660659 Score: 130
Period size: 22 Copynumber: 5.0 Consensus size: 21
1660542 ATCAGATTGT
1660552 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
1660573 CACAGGGGGTACAGATTCCCCCC
1 C-CAGGGGGTACAGATT-CCCCC
*
1660596 CCAGGGGGGTACCGATTCCCCC
1 CCA-GGGGGTACAGATTCCCCC
*
1660618 CCAAGGGGGAACAGATT-CCCC
1 CC-AGGGGGTACAGATTCCCCC
* *
1660639 TCA-GGGGTACCGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
1660659 C
1 C
1660660 TGTCTAACGG
Statistics
Matches: 75, Mismatches: 7, Indels: 11
0.81 0.08 0.12
Matches are distributed among these distances:
19 10 0.13
20 5 0.07
21 6 0.08
22 35 0.47
23 19 0.25
ACGTcount: A:0.19, C:0.39, G:0.28, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:1660615 original size:45 final size:42
Alignment explanation
Indices: 1660552--1660659 Score: 139
Period size: 45 Copynumber: 2.5 Consensus size: 42
1660542 ATCAGATTGT
* *
1660552 CCAGGGGGTACAGATT-CCCCCCACAGGGGGTACAGATTCCCCCC
1 CCAGGGGGTACCGATTCCCCCCCA-AGGGGGAACAGATT--CCCC
1660596 CCAGGGGGGTACCGATTCCCCCCCAAGGGGGAACAGATTCCCC
1 CCA-GGGGGTACCGATTCCCCCCCAAGGGGGAACAGATTCCCC
*
1660639 TCA-GGGGTACCGATTCCCCCC
1 CCAGGGGGTACCGATTCCCCCC
1660660 TGTCTAACGG
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
41 18 0.31
43 6 0.10
44 3 0.05
45 25 0.42
46 7 0.12
ACGTcount: A:0.19, C:0.39, G:0.28, T:0.14
Consensus pattern (42 bp):
CCAGGGGGTACCGATTCCCCCCCAAGGGGGAACAGATTCCCC
Found at i:1664084 original size:21 final size:21
Alignment explanation
Indices: 1664045--1664108 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1664035 ATCAGATTGT
*
1664045 CCAGGGGGTACAG-TCTCCCCC
1 CCAGGGGGAACAGAT-TCCCCC
* **
1664066 CCAGGGGGTACCTATTCCCCC
1 CCAGGGGGAACAGATTCCCCC
*
1664087 TCAGGGGGAACAGATTCCCCC
1 CCAGGGGGAACAGATTCCCCC
1664108 C
1 C
1664109 TGTCTAACGA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 34 0.97
22 1 0.03
ACGTcount: A:0.17, C:0.41, G:0.27, T:0.16
Consensus pattern (21 bp):
CCAGGGGGAACAGATTCCCCC
Found at i:1667650 original size:2 final size:2
Alignment explanation
Indices: 1667643--1667670 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1667633 ACATATGTTC
1667643 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
1667671 CACATAACAC
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:1670003 original size:21 final size:21
Alignment explanation
Indices: 1669977--1670016 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1669967 AAGACTTTAT
*
1669977 TTTCAAAATTAAAAAATGATA
1 TTTCAAAATGAAAAAATGATA
*
1669998 TTTCAAAATGAAAATATGA
1 TTTCAAAATGAAAAAATGA
1670017 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
TTTCAAAATGAAAAAATGATA
Found at i:1673829 original size:22 final size:22
Alignment explanation
Indices: 1673801--1673905 Score: 106
Period size: 22 Copynumber: 4.8 Consensus size: 22
1673791 TTTGGTGCAG
*
1673801 GAGGAATCGATACCCCCTTAAA
1 GAGGAATCGATTCCCCCTTAAA
1673823 GAGGAATCGATTCCCCCTTAAA
1 GAGGAATCGATTCCCCCTTAAA
* * *
1673845 AAGGAATCGATTCCCCATTTGAA
1 GAGGAATCGATTCCCC-CTTAAA
* * *
1673868 GGGGAACCGATTCACCCC-TAGA
1 GAGGAATCGATTC-CCCCTTAAA
*
1673890 G-GGAATCGATACCCCC
1 GAGGAATCGATTCCCCC
1673906 CACGGGGTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.06
21 9 0.13
22 39 0.57
23 14 0.20
24 3 0.04
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (22 bp):
GAGGAATCGATTCCCCCTTAAA
Found at i:1679505 original size:22 final size:20
Alignment explanation
Indices: 1679474--1679535 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
1679464 AATCAGATTG
1679474 CCCA-GGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
1679493 CCTTCAGGGGGTACAGATTACC
1 CC--CAGGGGGTACAGATTCCC
* *
1679515 CCCAGGGGGAAAAGATTCCC
1 CCCAGGGGGTACAGATTCCC
1679535 C
1 C
1679536 TTGTCTAACG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.06
20 16 0.44
21 2 0.06
22 16 0.44
ACGTcount: A:0.24, C:0.32, G:0.27, T:0.16
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:1680835 original size:19 final size:20
Alignment explanation
Indices: 1680811--1680858 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1680801 AATGACTTTC
*
1680811 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1680830 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1680850 TTTTGAAAA
1 TTTTGAAAA
1680859 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1682351 original size:19 final size:20
Alignment explanation
Indices: 1682303--1682361 Score: 75
Period size: 22 Copynumber: 2.9 Consensus size: 20
1682293 AATCAGATTG
1682303 CCCAGGGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
1682323 CCTTCAGGGGGTATAGATT-CC
1 CC--CAGGGGGTACAGATTCCC
*
1682344 CCCAGGGGGTACCGATTC
1 CCCAGGGGGTACAGATTC
1682362 GCCCTGTCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 13 0.39
20 2 0.06
21 4 0.12
22 14 0.42
ACGTcount: A:0.19, C:0.31, G:0.31, T:0.20
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:1683354 original size:17 final size:16
Alignment explanation
Indices: 1683323--1683356 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1683313 AAAAGAAGAC
*
1683323 ATAAAAAATAGAAAAG
1 ATAAAAAATAAAAAAG
1683339 ATAAAAAGATAAAAAAG
1 ATAAAAA-ATAAAAAAG
1683356 A
1 A
1683357 AAGAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
ATAAAAAATAAAAAAG
Found at i:1683372 original size:36 final size:37
Alignment explanation
Indices: 1683289--1683373 Score: 86
Period size: 36 Copynumber: 2.3 Consensus size: 37
1683279 CGACACAGAG
** * *
1683289 AGAAAGAAGAAAAGATATAGCAGAAAAAGAAGACATAA
1 AGAAAG-AGAAAAGATATAAAAGAAAAAGAAGAAAGAA
*
1683327 A-AAATAGAAAAGATA-AAAAGATAAAA-AAGAAAGAA
1 AGAAAGAGAAAAGATATAAAAGA-AAAAGAAGAAAGAA
1683362 AGAAAGAGAAAA
1 AGAAAGAGAAAA
1683374 TAGAAGAACG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
35 12 0.31
36 23 0.59
37 3 0.08
38 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.07
Consensus pattern (37 bp):
AGAAAGAGAAAAGATATAAAAGAAAAAGAAGAAAGAA
Found at i:1683378 original size:21 final size:21
Alignment explanation
Indices: 1683327--1683378 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
1683317 GAAGACATAA
*
1683327 AAAATAGAAAAGATAAAAAGAT
1 AAAATAG-AAAGATAAAAAGAG
*
1683349 AAAAAAGAAAGA-AAGAAAGAG
1 AAAATAGAAAGATAA-AAAGAG
1683370 AAAATAGAA
1 AAAATAGAA
1683379 GAACGAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 2 0.08
21 18 0.69
22 6 0.23
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (21 bp):
AAAATAGAAAGATAAAAAGAG
Found at i:1684123 original size:28 final size:28
Alignment explanation
Indices: 1684047--1684115 Score: 138
Period size: 28 Copynumber: 2.5 Consensus size: 28
1684037 GAAGCCAACC
1684047 TGAAACACATTACTTCCCCAAATTAACT
1 TGAAACACATTACTTCCCCAAATTAACT
1684075 TGAAACACATTACTTCCCCAAATTAACT
1 TGAAACACATTACTTCCCCAAATTAACT
1684103 TGAAACACATTAC
1 TGAAACACATTAC
1684116 CTTACCAAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.41, C:0.28, G:0.04, T:0.28
Consensus pattern (28 bp):
TGAAACACATTACTTCCCCAAATTAACT
Found at i:1685425 original size:54 final size:54
Alignment explanation
Indices: 1685359--1685819 Score: 371
Period size: 54 Copynumber: 8.7 Consensus size: 54
1685349 TGAAGTGGGG
* * *
1685359 CAAAGAAACTAAGTCTGATTTTCAAAAGTTTCTTGACGATTTTTAAATGAGTTT
1 CAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAATTT
* * * *
1685413 TAAAGAAACTAAGTCTAATTTTCAGAAGTTTCTTGATTATTTTT-AATGAGCTTT
1 CAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGA-ATTT
* * *
1685467 CAATGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG-GTTGTAAATGAACTTT
1 CAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAA-TTT
* * * ** *
1685521 CAAAGAAATTAAGCCTAATTTTCAGGGGTTTCTTGATG-TTTTCAAATGAATTT
1 CAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAATTT
* * * **
1685574 GAAAGAAATTAAGCCTGATTTTCAGGGGTTTCTTGAT-ATTTTTAAATGAATTT
1 CAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAATTT
* * * * *
1685627 GAAAGAAACTAAGTCCGATTTT-TGAAAGTTTCTTGAT--TATTT-AA-G-CTTT
1 CAAAGAAACTAAGTCTGATTTTCAG-AAGTTTCTTGATGATTTTTAAATGAATTT
* * *
1685676 CAAAGAAAATAAG-CTGATTTTCA-AGGGTTTCTTGATG-TTTTCAAATGAATTT
1 CAAAGAAACTAAGTCTGATTTTCAGA-AGTTTCTTGATGATTTTTAAATGAATTT
** * ** * * *
1685728 CAAAGAAGTTAAGCCAAAATTTT-AG-GGATTTCTTGATG-TTTTCAAATGAGTTT
1 CAAAGAAACTAAGTC-TGATTTTCAGAAG-TTTCTTGATGATTTTTAAATGAATTT
** * **
1685781 -TTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAT
1 CAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGAT
1685820 GATTTTCAAT
Statistics
Matches: 337, Mismatches: 52, Indels: 37
0.79 0.12 0.09
Matches are distributed among these distances:
47 1 0.00
48 17 0.05
49 17 0.05
50 3 0.01
51 8 0.02
52 43 0.13
53 118 0.35
54 130 0.39
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (54 bp):
CAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAATTT
Found at i:1685487 original size:108 final size:107
Alignment explanation
Indices: 1685359--1685860 Score: 433
Period size: 108 Copynumber: 4.7 Consensus size: 107
1685349 TGAAGTGGGG
* *** * * *
1685359 CAAAGAAACTAAGTCTGATTTTCAAAAGTTTCTTGACGATTTTTAAATGAGTTTTAAAGAAACTA
1 CAAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTTTTAAATGAATTTCAAAGAAACTA
* **
1685424 AGTCTAATTTTCAGAAGTTTCTTGAT-TATTTTTAATGAGCTTT
66 AGCCTAATTTT-AGAAGTTTCTTGATGT-TTTCAAATGAGCTTT
* * ** * * *
1685467 CAATGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG-GTTGTAAATGAACTTTCAAAGAAATT
1 CAAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTTTTAAATGAA-TTTCAAAGAAACT
** *
1685531 AAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGA-ATTT
65 AAGCCTAATTTT-AGAAGTTTCTTGATGTTTTCAAATGAGCTTT
* * *
1685574 GAAAGAAATTAAGCCTGATTTTCAGGGGTTTCTTGAT-ATTTTTAAATGAATTTGAAAGAAACTA
1 CAAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTTTTAAATGAATTTCAAAGAAACTA
* *
1685638 AGTCC-GATTTTTGAAAGTTTCTTGAT-TATTT---A--AGCTTT
66 AG-CCTAATTTTAG-AAGTTTCTTGATGT-TTTCAAATGAGCTTT
* * * **
1685676 CAAAGAAAATAAG-CTGATTTTCAAGGGTTTCTTGATG-TTTTCAAATGAATTTCAAAGAAGTTA
1 CAAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTTTTAAATGAATTTCAAAGAAACTA
* *
1685739 AGCCAAAATTTTAG-GGATTTCTTGATGTTTTCAAATGAG-TTT
66 AGCC-TAATTTTAGAAG-TTTCTTGATGTTTTCAAATGAGCTTT
** * * *
1685781 -TTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATGATTTTCAATGAGTTTTTAAAAGGA
1 CAAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAT--TTTTAAATGA--ATTTCAAA-GA
1685845 AACTAAGCCTAATTTT
61 AACTAAGCCTAATTTT
1685861 TAGGGGTTCC
Statistics
Matches: 320, Mismatches: 50, Indels: 46
0.77 0.12 0.11
Matches are distributed among these distances:
100 3 0.01
101 59 0.18
102 21 0.07
103 1 0.00
104 10 0.03
105 28 0.09
106 35 0.11
107 55 0.17
108 86 0.27
109 1 0.00
110 12 0.04
111 9 0.03
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (107 bp):
CAAAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTTTTAAATGAATTTCAAAGAAACTA
AGCCTAATTTTAGAAGTTTCTTGATGTTTTCAAATGAGCTTT
Found at i:1685724 original size:154 final size:159
Alignment explanation
Indices: 1685359--1685819 Score: 476
Period size: 154 Copynumber: 2.9 Consensus size: 159
1685349 TGAAGTGGGG
* * ** * * * * *
1685359 CAAAGAAACTAAGTCTGATTTTCAAAAGTTTCTTGACGATTTTTAAATGAGTTTTAAAGAAACTA
1 CAAAGAAAATAAGCCTGATTTTCAAGGGTTTCTTGATG-TTTTCAAATGAATTTCAAAGAAATTA
* ** * * *
1685424 AGTCTAATTTTCAGAAGTTTCTTGATTATTTTT-AATGAGCTTTCAATGAAACTAAGTCTGA-TT
65 AGCCTAATTTTCAGGGGTTTCTTGA-TATTTTTAAATGA-ATTT-AAAGAAACTAAGTCCGATTT
*
1685487 TTCAGAAGTTTCTTGATGGTTGTAAATGAACTTT
127 TTCAGAAGTTTCTTGATGATTGTAAATG-ACTTT
* * * *
1685521 CAAAGAAATTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAATTAA
1 CAAAGAAAATAAGCCTGATTTTCAAGGGTTTCTTGATGTTTTCAAATGAATTTCAAAGAAATTAA
* *
1685586 GCCTGATTTTCAGGGGTTTCTTGATATTTTTAAATGAATTTGAAAGAAACTAAGTCCGATTTTTG
66 GCCTAATTTTCAGGGGTTTCTTGATATTTTTAAATGAATTT-AAAGAAACTAAGTCCGATTTTTC
*
1685651 A-AAGTTTCTTGATTATT-T-AA-G-CTTT
130 AGAAGTTTCTTGATGATTGTAAATGACTTT
*
1685676 CAAAGAAAATAAG-CTGATTTTCAAGGGTTTCTTGATGTTTTCAAATGAATTTCAAAGAAGTTAA
1 CAAAGAAAATAAGCCTGATTTTCAAGGGTTTCTTGATGTTTTCAAATGAATTTCAAAGAAATTAA
* * * * * **
1685740 GCCAAAATTTT-AGGGATTTCTTGATGTTTTCAAATGAGTTTTTAGAAACTAAG-CCTGA-TTTT
66 GCC-TAATTTTCAGGGGTTTCTTGATATTTTTAAATGAATTTAAAGAAACTAAGTCC-GATTTTT
**
1685802 CAGGGGTTTCTTGATGAT
129 CAGAAGTTTCTTGATGAT
1685820 GATTTTCAAT
Statistics
Matches: 255, Mismatches: 39, Indels: 19
0.81 0.12 0.06
Matches are distributed among these distances:
152 7 0.03
153 24 0.09
154 76 0.30
155 21 0.08
157 1 0.00
158 2 0.01
159 1 0.00
160 39 0.15
161 53 0.21
162 31 0.12
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (159 bp):
CAAAGAAAATAAGCCTGATTTTCAAGGGTTTCTTGATGTTTTCAAATGAATTTCAAAGAAATTAA
GCCTAATTTTCAGGGGTTTCTTGATATTTTTAAATGAATTTAAAGAAACTAAGTCCGATTTTTCA
GAAGTTTCTTGATGATTGTAAATGACTTT
Found at i:1685975 original size:42 final size:41
Alignment explanation
Indices: 1685912--1686018 Score: 133
Period size: 42 Copynumber: 2.6 Consensus size: 41
1685902 AGGGTTTCTT
* * **
1685912 GATGAGTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCGT
1 GATGA-TAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAA
* *
1685954 GATGCTTAAATCCTTCGGGCCATCTGTAAGTCTTTCGAGCAA
1 GATG-ATAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAA
*
1685996 GATGATAAGTCCTTCGGGCCATC
1 GATGATAAATCCTTCGGGCCATC
1686019 CATAAGACCT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 17 0.30
42 39 0.70
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.29
Consensus pattern (41 bp):
GATGATAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAA
Found at i:1686277 original size:144 final size:144
Alignment explanation
Indices: 1686001--1686513 Score: 710
Period size: 144 Copynumber: 3.6 Consensus size: 144
1685991 AGCAAGATGA
* * *
1686001 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTTAATATTTCCTTTGCTTGATT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCGATT
* * * *
1686066 CACAACACTTCGAATCAGCAACGCCCACCAGAGGGGTTAACATTTCCTATTGCTCGATTCACAAC
66 CACAACACTTCAAATCAACAACCCCCACCAGAAGGGTTAACATTTCCTATTGCTCGATTCACAAC
*
1686131 ACTTCGAATTAGCT
131 ACTTCGAATCAGCT
* *
1686145 TAAGTCCTTTGGGTCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCGATT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCGATT
1686210 CACAACACTTCAAATCAACAACACCCCACCAGAAGGGTTAACATTTCCTATTGCTCGATTCAC-A
66 CACAACACTTCAAATCAACAAC-CCCCACCAGAAGGGTTAACATTTCCTATTGCTCGATTCACAA
*
1686274 CACTTTGAATCAGCT
130 CACTTCGAATCAGCT
* * * * *
1686289 TAAGTCTTTTGGGTCATCCATAAGACCTCCGGGCAGGTTGTTTTCAACATTTCCTTTGCTCGATT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCGATT
* * * * *
1686354 CACAACACTTCGAATCAGA-AACGCCCCACCATAAGGGTT-ACACTTCATAATGCTCGATTCACA
66 CACAACACTTCAAATCA-ACAAC-CCCCACCAGAAGGGTTAACATTTCCTATTGCTCGATTCACA
1686417 ACACTTCGAATCAGCT
129 ACACTTCGAATCAGCT
** * * *
1686433 TAAGTTATTCGGGCCATCCATAAGACCTTCGGGCATGAT-ATTTCAACATTTCCTTTGCTTGATT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCGATT
** *
1686497 CACGGCATTTCAAATCA
66 CACAACACTTCAAATCA
1686514 GCGACACCTC
Statistics
Matches: 332, Mismatches: 34, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
143 56 0.17
144 237 0.71
145 39 0.12
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (144 bp):
TAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCGATT
CACAACACTTCAAATCAACAACCCCCACCAGAAGGGTTAACATTTCCTATTGCTCGATTCACAAC
ACTTCGAATCAGCT
Found at i:1686663 original size:73 final size:72
Alignment explanation
Indices: 1686540--1686794 Score: 314
Period size: 73 Copynumber: 3.5 Consensus size: 72
1686530 GGGATCTTTG
* * *
1686540 TCTCGCTTGAGATAGTTTTACTCGAAACAAAATTTTATCTCACTCGAGATTTTTTTCTTTAAAAC
1 TCTCGCTTGAGACAGTTTCACTCGAAACAAAAATTTATCTCACTCGAGATTTTTTTC-TTAAAAC
*
1686605 AAACTTCG
65 AAACTTCA
* *
1686613 TCTCGCTTGAGACAGTTTCACTCGAAACAAAACTTTATCTCACTCAAGATTGTTTTTCTTAAAAC
1 TCTCGCTTGAGACAGTTTCACTCGAAACAAAAATTTATCTCACTCGAGATT-TTTTTCTTAAAAC
1686678 AAACTTCA
65 AAACTTCA
* * * * * *
1686686 TCTCGCTTGAG-CGGATTTTACTCAAAACAAGAAATTTATCTCACTCGAGATTGTTTTCTTCAAC
1 TCTCGCTTGAGACAG-TTTCACTCGAAACAA-AAATTTATCTCACTCGAGATTTTTTTCTTAAAA
*
1686750 CAAATTTCA
64 CAAACTTCA
* * * *
1686759 TCTCGCTTGAGAAAGTTTCCCTTGAAAAAAAAATTT
1 TCTCGCTTGAGACAGTTTCACTCGAAACAAAAATTT
1686795 GAAATTGTTT
Statistics
Matches: 157, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
72 8 0.05
73 123 0.78
74 26 0.17
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (72 bp):
TCTCGCTTGAGACAGTTTCACTCGAAACAAAAATTTATCTCACTCGAGATTTTTTTCTTAAAACA
AACTTCA
Found at i:1686689 original size:36 final size:36
Alignment explanation
Indices: 1686576--1686762 Score: 110
Period size: 36 Copynumber: 5.1 Consensus size: 36
1686566 ACAAAATTTT
1686576 ATCTCACTCGAGATT-TTTTTCTTTAAAACAAACTTC
1 ATCTCACTCGAGATTGTTTTTC-TTAAAACAAACTTC
* * * ** ** ** *
1686612 GTCTCGCTTGAGACAGTTTCACTCGAAACAAAACTTT
1 ATCTCACTCGAGATTGTTTTTCTTAAAAC-AAACTTC
*
1686649 ATCTCACTCAAGATTGTTTTTCTTAAAACAAACTTC
1 ATCTCACTCGAGATTGTTTTTCTTAAAACAAACTTC
* * ** * * * *
1686685 ATCTCGCTTGAG-CGGATTTTACTCAAAACAAGAAATTT
1 ATCTCACTCGAGATTG-TTTTTCTTAAAAC-A-AACTTC
* * *
1686723 ATCTCACTCGAGATTG-TTTTCTTCAACCAAATTTC
1 ATCTCACTCGAGATTGTTTTTCTTAAAACAAACTTC
1686758 ATCTC
1 ATCTC
1686763 GCTTGAGAAA
Statistics
Matches: 105, Mismatches: 40, Indels: 13
0.66 0.25 0.08
Matches are distributed among these distances:
35 10 0.10
36 42 0.40
37 38 0.36
38 14 0.13
39 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.36
Consensus pattern (36 bp):
ATCTCACTCGAGATTGTTTTTCTTAAAACAAACTTC
Found at i:1687458 original size:139 final size:139
Alignment explanation
Indices: 1687208--1687871 Score: 641
Period size: 139 Copynumber: 4.8 Consensus size: 139
1687198 GGATAAACCA
* *
1687208 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGA-TGAGGGAGAA-AATTTTC
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAA-GTTC
* *
1687271 ATAATGAGAAGAACTTGTTCAACCTTAGC-CTGATTCATGACATATGGAGTTGAATCAACAATAC
65 ATAATGAGAAGAACTTGTTCAACCTTAGCTC-GATTCATCACATATGGAGTTGAATCAAC-ACAC
1687335 CTCACTCGAGGG
128 CTCACTCGAGGG
* * *
1687347 ATCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGA-AGAGGGAGATGAAGTTCA
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCA
*
1687411 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCCACACCT
66 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCA-ACACACCT
1687476 CACTCGAGGG
130 CACTCGAGGG
** * * * *
1687486 ATCAACATTTCCGGTGGAGAGTTCATAATGAGAATAACTCATCTGACAAAGGGAAAAGAAGTTCA
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCA
* * * * * * *
1687551 TAATAAGAAGAGCTTGTAT-AACCTATCGCTTGATTCA-CGACAT-T----TCGAATCAGCGACG
66 TAATGAGAAGAACTTGT-TCAACCT-TAGCTCGATTCATC-ACATATGGAGTTGAATCAAC-ACA
* *
1687609 CCTCGCTTGAGGG
127 CCTCACTCGAGGG
* * * * *
1687622 ATTAACACTTCAAATGGAGAGTTCATAATGACAA-AACTCATCCGATA-AGGGAGAAGAAGTTCA
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCA
* * * * * * *
1687685 TAATGAGAAGATCTTGTTCGACCTATCA-CTCAATTCA-CGACAT-TCGAATT-AGT---GACAC
66 TAATGAGAAGAACTTGTTCAACCT-T-AGCTCGATTCATC-ACATATGGAGTTGAATCAACACAC
* *
1687743 CTCGCTTGAGGG
128 CTCACTCGAGGG
** * * *
1687755 ATTGACATTT-CACATGGAGAGTTCATAATGAGAAGAAGTCATCCAACAGAGGGAGAAGAAGTTT
1 ATCAACATTTCCA-ATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTC
* * * * *
1687819 ATAATGAGAAGATCTTGTTCGACCTTAGCTTGTTTCCATCACATAAGGAGTTG
65 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATT-CATCACATATGGAGTTG
1687872 GAGCAGCACT
Statistics
Matches: 446, Mismatches: 57, Indels: 46
0.81 0.10 0.08
Matches are distributed among these distances:
132 1 0.00
133 45 0.10
134 65 0.15
135 57 0.13
136 53 0.12
137 2 0.00
138 1 0.00
139 166 0.37
140 41 0.09
141 15 0.03
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (139 bp):
ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAACACACCTC
ACTCGAGGG
Found at i:1687910 original size:41 final size:42
Alignment explanation
Indices: 1687853--1687956 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
1687843 TTAGCTTGTT
* *
1687853 TCCATCACATAAGGAGTTGGAGCAGCA-C-TGACTTTTGCTCA-
1 TCCATCACATAAGGAGTTGGAGCAGCATCATCA-TTTCGCT-AG
*
1687894 TCCATCACATAAGGAGTTGGATCAGCATCATCATTTCGCTAG
1 TCCATCACATAAGGAGTTGGAGCAGCATCATCATTTCGCTAG
1687936 TCCATCACATAAGGAGTTGGA
1 TCCATCACATAAGGAGTTGGA
1687957 TTAGTATCAC
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
41 27 0.47
42 28 0.49
43 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (42 bp):
TCCATCACATAAGGAGTTGGAGCAGCATCATCATTTCGCTAG
Found at i:1687953 original size:42 final size:41
Alignment explanation
Indices: 1687853--1687957 Score: 142
Period size: 41 Copynumber: 2.5 Consensus size: 41
1687843 TTAGCTTGTT
* * *
1687853 TCCATCACATAAGGAGTTGGAGCAGCACTGACTTTTGCTCA
1 TCCATCACATAAGGAGTTGGATCAGCACTCACTTTCGCTCA
1687894 TCCATCACATAAGGAGTTGGATCAGCA-TCATCATTTCGCT-A
1 TCCATCACATAAGGAGTTGGATCAGCACTCA-C-TTTCGCTCA
1687935 GTCCATCACATAAGGAGTTGGAT
1 -TCCATCACATAAGGAGTTGGAT
1687958 TAGTATCACC
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
40 2 0.03
41 28 0.48
42 28 0.48
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (41 bp):
TCCATCACATAAGGAGTTGGATCAGCACTCACTTTCGCTCA
Found at i:1688247 original size:25 final size:25
Alignment explanation
Indices: 1688218--1688280 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
1688208 GCTTTACAAC
* *
1688218 TCCAGGCCCAACTGACCTAGTTACA
1 TCCAGGCCCAACTGACCCAATTACA
* *
1688243 TCCAGACCCAACTGACCCAATTATA
1 TCCAGGCCCAACTGACCCAATTACA
1688268 TCCAGAGCCCAAC
1 TCCAG-GCCCAAC
1688281 AGCAACACCA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 26 0.81
26 6 0.19
ACGTcount: A:0.32, C:0.38, G:0.13, T:0.17
Consensus pattern (25 bp):
TCCAGGCCCAACTGACCCAATTACA
Found at i:1688523 original size:77 final size:77
Alignment explanation
Indices: 1688396--1688546 Score: 205
Period size: 77 Copynumber: 2.0 Consensus size: 77
1688386 CCGGTTCAAT
* * * ** * *
1688396 TCATCACCATGCTCTGCCATCTCTAGTACCCCATGTGAAACACCACCAACTGAGCATACCCATGT
1 TCATCACCATGCCCTGACATCTCCAGTACCCCACCTGAAACACCACCAACTGAGCAGACCCATGC
*
1688461 CCTCCTCCATAA
66 CCTACTCCATAA
*
1688473 TCATCACCATGCCCTGACATCTCCAGTACCCCACCTGAAGTC-CCACCAACTGAGCAGACCCATG
1 TCATCACCATGCCCTGACATCTCCAGTACCCCACCTGAA-ACACCACCAACTGAGCAGACCCATG
1688537 CCCTACTCCA
65 CCCTACTCCA
1688547 CAGTACACAT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
77 63 0.98
78 1 0.02
ACGTcount: A:0.26, C:0.42, G:0.11, T:0.21
Consensus pattern (77 bp):
TCATCACCATGCCCTGACATCTCCAGTACCCCACCTGAAACACCACCAACTGAGCAGACCCATGC
CCTACTCCATAA
Found at i:1694199 original size:2 final size:2
Alignment explanation
Indices: 1694192--1694230 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1694182 TGTTTACAAA
1694192 AT AT 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 AT AT A
1694231 ATCCTTTGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1694404 original size:14 final size:15
Alignment explanation
Indices: 1694377--1694405 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1694367 AATTATTTAA
1694377 TAAATATATATATTT
1 TAAATATATATATTT
1694392 TAAATAT-TATATTT
1 TAAATATATATATTT
1694406 ATATTGTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAATATATATATTT
Found at i:1694706 original size:38 final size:38
Alignment explanation
Indices: 1694664--1694786 Score: 104
Period size: 38 Copynumber: 3.0 Consensus size: 38
1694654 TAAAAATATT
1694664 ATAAAATATTTTCAATTACGTTTTAAAATTATTATAAA
1 ATAAAATATTTTCAATTACGTTTTAAAATTATTATAAA
* *
1694702 ATAAAATATTTTAAATTCAACCGACTCAACTTAAAA-TATTATAAA
1 ATAAAATATTTTCAATT--A-CG--T---TTTAAAATTATTATAAA
**
1694747 ATTTTATTATATTTTCAATTACGTTTTAAAATTATTATAA
1 A---TAAAATATTTTCAATTACGTTTTAAAATTATTATAA
1694787 TTTATTTTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 21
0.71 0.06 0.22
Matches are distributed among these distances:
38 16 0.24
40 7 0.10
41 10 0.15
43 2 0.03
45 12 0.18
46 7 0.10
48 13 0.19
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (38 bp):
ATAAAATATTTTCAATTACGTTTTAAAATTATTATAAA
Found at i:1696061 original size:6 final size:6
Alignment explanation
Indices: 1696045--1696083 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
1696035 GTCCGTCTCG
1696045 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1696084 ATACGTGTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.00, C:0.18, G:0.51, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:1696210 original size:42 final size:41
Alignment explanation
Indices: 1696164--1696248 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 41
1696154 TCAACGAATT
*
1696164 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAA
1 TGGAAAATCACAACG-CAACTGTCA-ACTATCGCAACGCGAAA
* * *
1696206 TGGAAAATCACAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCACAACGCAACTGTCAACTATCGCAACGCGAAA
1696247 TG
1 TG
1696249 CAACGCGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 23 0.61
42 15 0.39
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.18
Consensus pattern (41 bp):
TGGAAAATCACAACGCAACTGTCAACTATCGCAACGCGAAA
Found at i:1696252 original size:21 final size:21
Alignment explanation
Indices: 1696189--1696252 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
1696179 ACAACTGTAG
*
1696189 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
1696210 A-AATCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
1696230 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
1696251 AC
1 AC
1696253 GCGAATTTGC
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:1696304 original size:20 final size:20
Alignment explanation
Indices: 1696281--1696345 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
1696271 AGATCGCGTT
*
1696281 GCGATTTCAACTATCGCAAC
1 GCGATTCCAACTATCGCAAC
* ** *
1696301 GCGAAATGGAA-AATCGCAAC
1 GCG-ATTCCAACTATCGCAAC
1696321 GCGATCTCCAACTATCGCAAC
1 GCGAT-TCCAACTATCGCAAC
1696342 GCGA
1 GCGA
1696346 AATGGAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
19 1 0.03
20 17 0.50
21 16 0.47
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.17
Consensus pattern (20 bp):
GCGATTCCAACTATCGCAAC
Found at i:1696338 original size:41 final size:41
Alignment explanation
Indices: 1696288--1696390 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
1696278 GTTGCGATTT
*
1696288 CAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
* * *
1696329 CAACTATCGCAACGCGAAATGGAAAAACGTAACGCGATTTT
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
*
1696370 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
1696391 CAACGTGAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.17
Consensus pattern (41 bp):
CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
Found at i:1696394 original size:21 final size:21
Alignment explanation
Indices: 1696288--1696394 Score: 83
Period size: 21 Copynumber: 5.2 Consensus size: 21
1696278 GTTGCGATTT
1696288 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
1696309 GAA-AATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATG
1696329 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * * ** *
1696350 GAA-AAACGTAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
1696370 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
1696391 CAAC
1 CAAC
1696395 GTGAATTTGC
Statistics
Matches: 59, Mismatches: 25, Indels: 4
0.67 0.28 0.05
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:1698828 original size:2 final size:2
Alignment explanation
Indices: 1698821--1698847 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1698811 TGTTTACAAA
1698821 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
1698848 ATCCTTTGGT
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:1699315 original size:38 final size:38
Alignment explanation
Indices: 1699273--1699395 Score: 104
Period size: 38 Copynumber: 3.0 Consensus size: 38
1699263 TAAAAATATT
1699273 ATAAAATATTTTCAATTACGTTTTAAAATTATTATAAA
1 ATAAAATATTTTCAATTACGTTTTAAAATTATTATAAA
* *
1699311 ATAAAATATTTTAAATTCAACCGACTCAACTTAAAA-TATTATAAA
1 ATAAAATATTTTCAATT--A-CG--T---TTTAAAATTATTATAAA
**
1699356 ATTTTATTATATTTTCAATTACGTTTTAAAATTATTATAA
1 A---TAAAATATTTTCAATTACGTTTTAAAATTATTATAA
1699396 TTTATTTTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 21
0.71 0.06 0.22
Matches are distributed among these distances:
38 16 0.24
40 7 0.10
41 10 0.15
43 2 0.03
45 12 0.18
46 7 0.10
48 13 0.19
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (38 bp):
ATAAAATATTTTCAATTACGTTTTAAAATTATTATAAA
Found at i:1700164 original size:6 final size:6
Alignment explanation
Indices: 1700153--1700191 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
1700143 TGAAAATCGC
1700153 ACCACG ACCACG ACCACACG ACCACG ACCACG ACC-CG AC
1 ACCACG ACCACG A-C-CACG ACCACG ACCACG ACCACG AC
1700192 TCGACGGACG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 4 0.13
6 20 0.65
7 2 0.06
8 5 0.16
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1700174 original size:14 final size:14
Alignment explanation
Indices: 1700155--1700183 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1700145 AAAATCGCAC
1700155 CACGACCACGACCA
1 CACGACCACGACCA
1700169 CACGACCACGACCA
1 CACGACCACGACCA
1700183 C
1 C
1700184 GACCCGACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.52, G:0.14, T:0.00
Consensus pattern (14 bp):
CACGACCACGACCA
Found at i:1700694 original size:6 final size:6
Alignment explanation
Indices: 1700678--1700716 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
1700668 GTCCGTCTCG
1700678 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1700717 ATACGTGTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.00, C:0.18, G:0.51, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:1700846 original size:42 final size:41
Alignment explanation
Indices: 1700800--1700881 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
1700790 TCAACGAATT
*
1700800 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAA
1 TGGAAAATCACAACG-CAACTGTCA-ACTATCGCAACGCGAAA
* * *
1700842 TGGAAAATCACAACGCGATTTTCAACTATCGCAACGCGAA
1 TGGAAAATCACAACGCAACTGTCAACTATCGCAACGCGAA
1700882 TTTGCGATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 20 0.57
42 15 0.43
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (41 bp):
TGGAAAATCACAACGCAACTGTCAACTATCGCAACGCGAAA
Found at i:1700870 original size:41 final size:41
Alignment explanation
Indices: 1700825--1700969 Score: 148
Period size: 41 Copynumber: 3.4 Consensus size: 41
1700815 ACAACTGTAG
*
1700825 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* ***
1700866 ACTATCGCAACGCGAATTTGCGATGATTGAGATCGCGTTGCGA-TTTCA
1 ACTATCGCAACGCGAA-ATG-GA--A---A-ATCGCAACGCGATTTTCA
* *
1700914 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1700955 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
1700970 TTTTCAACTA
Statistics
Matches: 84, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
40 9 0.11
41 35 0.42
42 2 0.02
43 2 0.02
44 1 0.01
45 1 0.01
46 2 0.02
47 2 0.02
48 22 0.26
49 8 0.10
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.21
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:1700998 original size:21 final size:21
Alignment explanation
Indices: 1700912--1700998 Score: 86
Period size: 21 Copynumber: 4.2 Consensus size: 21
1700902 GTTGCGATTT
1700912 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
1700933 GAA-AATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATG
** *
1700953 CAACTATCGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
1700974 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
1700995 CAAC
1 CAAC
1700999 GTGAATTTGC
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 15 0.29
21 37 0.71
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.18
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:1704079 original size:60 final size:59
Alignment explanation
Indices: 1703993--1704118 Score: 173
Period size: 59 Copynumber: 2.1 Consensus size: 59
1703983 TTTTGGTCTG
** *
1703993 TTTTAGTACCTAAACTTTCATTTTTTTCAAAATCATACCTAA-AGTTTAGTTTTTATTTCA
1 TTTTAGTACCTAAACTTTCAAATTTTT-AAAACCATACCTAACA-TTTAGTTTTTATTTCA
* * *
1704053 TTTTAGTATCTAAACTTTCAAATTTTTAAAACCATAGCTAACATTTAGTTTTTGTTTCA
1 TTTTAGTACCTAAACTTTCAAATTTTTAAAACCATACCTAACATTTAGTTTTTATTTCA
1704112 TTTTAGT
1 TTTTAGT
1704119 TCTCCCATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
59 34 0.58
60 25 0.42
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.50
Consensus pattern (59 bp):
TTTTAGTACCTAAACTTTCAAATTTTTAAAACCATACCTAACATTTAGTTTTTATTTCA
Found at i:1707174 original size:20 final size:20
Alignment explanation
Indices: 1707149--1707306 Score: 154
Period size: 20 Copynumber: 7.8 Consensus size: 20
1707139 ATTCACGTTG
*
1707149 CATTTCACGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
1707169 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* * * *
1707189 CAGTTCGCGTTGTGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* ** *
1707210 AAAATGGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
*
1707230 CATTTCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTTTC
* *
1707250 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* ** *
1707271 AAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTTTC
1707291 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1707307 AGTCTACAAA
Statistics
Matches: 109, Mismatches: 27, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
20 81 0.74
21 28 0.26
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:1707228 original size:61 final size:61
Alignment explanation
Indices: 1707156--1707306 Score: 257
Period size: 61 Copynumber: 2.5 Consensus size: 61
1707146 TTGCATTTCA
* *
1707156 CGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGTGATAGTTGAAAATGG
1 CGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCG
* *
1707217 CGTTGCGATTTTCCATTTCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGTTGAAAATCG
1 CGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCG
*
1707278 CGTTGCGATTTTTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCCATTTCGCGTTGCGAT
1707307 AGTCTACAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 85 1.00
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.41
Consensus pattern (61 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCG
Found at i:1707924 original size:21 final size:21
Alignment explanation
Indices: 1707859--1707974 Score: 139
Period size: 21 Copynumber: 5.7 Consensus size: 21
1707849 AAATAACCAA
*
1707859 CAAATTCGCAATGCGA-TCT-
1 CAAATTCGCAACGCGATTCTC
* *
1707878 CAAATTCGCAACGCAATT-TT
1 CAAATTCGCAACGCGATTCTC
1707898 CAAATTCGCAACGCGATTCTC
1 CAAATTCGCAACGCGATTCTC
1707919 CAAATTCGCAACGCGATTCTC
1 CAAATTCGCAACGCGATTCTC
* * * *
1707940 CAAAATCACAATGCAATTCTC
1 CAAATTCGCAACGCGATTCTC
*
1707961 CAAAATCGCAACGC
1 CAAATTCGCAACGC
1707975 TAATTACCGA
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
19 15 0.18
20 18 0.21
21 51 0.61
ACGTcount: A:0.34, C:0.30, G:0.12, T:0.23
Consensus pattern (21 bp):
CAAATTCGCAACGCGATTCTC
Found at i:1708170 original size:112 final size:112
Alignment explanation
Indices: 1707966--1708469 Score: 376
Period size: 113 Copynumber: 4.6 Consensus size: 112
1707956 TTCTCCAAAA
1707966 TCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCACACTCAGTTTTCAAATTCGCAACG
1 TCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCACACTCAGTTTTCAAATTCGCAACG
1708031 CGATTCTCCTAAATCGCAACGCGAATTTCGTTTTCGCAACTTGAATT
66 CGATTCTCCTAAATCGCAACGCGAATTTCGTTTTCGCAACTTGAATT
* * *
1708078 TCGCAACGCTGATTACCGATATAGGTAAACACAACTATTCGCAACTCAGTTTTCAAATTCGTAAC
1 TCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCAC-ACTCAGTTTTCAAATTCGCAAC
* * * **** *
1708143 GCGATT-T-TTAAATTCGCACCGCTAATTTC-ACAACGCTAATTACTG-ATAT
65 GCGATTCTCCTAAA-TCGCAACGCGAATTTCGTTTTCGC-AACT--TGAAT-T
** * * * * *** *
1708192 AGGTAAACAC-AACTATTCGCA-ACTTA-GT--TTTCAA--ATTCGCAACTCAGTTTTCAAATTC
1 TCG-CAACGCTAATTA-CCG-ATA--TAGGTAAACACAACTATTCAC-ACTCAGTTTTCAAATTC
* * *
1708250 GCAACGCGATTCTCCAAAATCGAAACACGAA------TTT-G----TT---TT
60 GCAACGCGATTCTCCTAAATCGCAACGCGAATTTCGTTTTCGCAACTTGAATT
* ** * * *
1708289 -CGCAACGCTAATTACTGATATAAATAAACAAAACTCTTCGCAACTCAGTTTTCAAATTCGCAAC
1 TCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCAC-ACTCAGTTTTCAAATTCGCAAC
* *
1708353 GCGATTCTCCAAAATCGCAACGCGAATTTCGTTTTCGCAACTCGAATT
65 GCGATTCTCCTAAATCGCAACGCGAATTTCGTTTTCGCAACTTGAATT
* * * *
1708401 TTGCAACGCTAATTACCGATATAGGTAAACACAACAATTCGCAACTCAGTTTTTAAATTCGCAAC
1 TCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCAC-ACTCAGTTTTCAAATTCGCAAC
1708466 GCGA
65 GCGA
1708470 ATTTCGTTTT
Statistics
Matches: 303, Mismatches: 54, Indels: 69
0.71 0.13 0.16
Matches are distributed among these distances:
93 2 0.01
94 2 0.01
95 6 0.02
96 7 0.02
97 1 0.00
98 53 0.17
100 1 0.00
102 1 0.00
104 3 0.01
105 1 0.00
107 1 0.00
109 1 0.00
111 7 0.02
112 94 0.31
113 98 0.32
114 13 0.04
115 7 0.02
116 3 0.01
117 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.29
Consensus pattern (112 bp):
TCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCACACTCAGTTTTCAAATTCGCAACG
CGATTCTCCTAAATCGCAACGCGAATTTCGTTTTCGCAACTTGAATT
Done.