Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold162
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: 1959167
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.30
Warning! 205334 characters in sequence are not A, C, G, or T
File 8 of 12
Found at i:1175811 original size:23 final size:24
Alignment explanation
Indices: 1175766--1175812 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1175756 CAAAGAATTG
*
1175766 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
1175790 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
1175813 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:1178414 original size:34 final size:35
Alignment explanation
Indices: 1178376--1178442 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1178366 CCTTACAACA
1178376 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1178410 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1178443 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1178939 original size:13 final size:13
Alignment explanation
Indices: 1178921--1178946 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1178911 CTATTTATGA
1178921 TGTATCGATACAC
1 TGTATCGATACAC
1178934 TGTATCGATACAC
1 TGTATCGATACAC
1178947 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1179069 original size:21 final size:21
Alignment explanation
Indices: 1179043--1179084 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1179033 CCTATGAAAC
*
1179043 AGTGATTTATCGATACATGAA
1 AGTGATGTATCGATACATGAA
1179064 AGTGATGTATCGATACATGAA
1 AGTGATGTATCGATACATGAA
1179085 CAGTTATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (21 bp):
AGTGATGTATCGATACATGAA
Found at i:1179198 original size:53 final size:53
Alignment explanation
Indices: 1179134--1179270 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
1179124 CTACTTTCAA
1179134 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
1179187 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1179240 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
1179271 TATGCAATCT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:1179303 original size:20 final size:20
Alignment explanation
Indices: 1179240--1179310 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1179230 GCCAATGTCC
**
1179240 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
1179260 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
1179280 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
1179300 TGTATCGATAC
1 TGTATCGATAC
1179311 TTTTCAAGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:1179374 original size:21 final size:21
Alignment explanation
Indices: 1179350--1179390 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1179340 GTCAACCTTG
1179350 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
1179371 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
1179391 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:1186165 original size:25 final size:25
Alignment explanation
Indices: 1186120--1186168 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1186110 CGTTAGCTAT
*
1186120 GTTTGACTTGACATTGGGTTCAATG
1 GTTTGACTTGACATTGAGTTCAATG
*
1186145 GTTTCGACTTGATATT-AGTTCAAT
1 GTTT-GACTTGACATTGAGTTCAAT
1186169 ACGATCCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.43
Consensus pattern (25 bp):
GTTTGACTTGACATTGAGTTCAATG
Found at i:1188252 original size:14 final size:14
Alignment explanation
Indices: 1188233--1188269 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1188223 AAGATCATTT
1188233 GAATAAAAAAAGAA
1 GAATAAAAAAAGAA
*
1188247 GAATAAAAAAATAA
1 GAATAAAAAAAGAA
*
1188261 TAATAAAAA
1 GAATAAAAA
1188270 TAATCATGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (14 bp):
GAATAAAAAAAGAA
Found at i:1188546 original size:14 final size:13
Alignment explanation
Indices: 1188524--1188565 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1188514 TTCTTCTCTC
1188524 TTTTCTTTCTCTTT
1 TTTTCTTTCT-TTT
*
1188538 TTTT-TTT-TCTT
1 TTTTCTTTCTTTT
1188549 TTTTCTTTCTTTT
1 TTTTCTTTCTTTT
1188562 TTTT
1 TTTT
1188566 GGTTGAACCT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 6 0.25
12 4 0.17
13 10 0.42
14 4 0.17
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTCTTTCTTTT
Found at i:1188549 original size:23 final size:23
Alignment explanation
Indices: 1188522--1188565 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1188512 ATTTCTTCTC
1188522 TCTTTTCTT-TCTCTTTTTTTTTT
1 TCTTTT-TTCTCTCTTTTTTTTTT
*
1188545 TCTTTTTTCTTTCTTTTTTTT
1 TCTTTTTTCTCTCTTTTTTTT
1188566 GGTTGAACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (23 bp):
TCTTTTTTCTCTCTTTTTTTTTT
Found at i:1188562 original size:11 final size:12
Alignment explanation
Indices: 1188513--1188563 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
1188503 TTTGTTTCTA
*
1188513 TTTCTTCTCTCT
1 TTTCTTCTCTTT
1188525 TTTCTTTCTCTTT
1 TTTC-TTCTCTTT
* *
1188538 TTTTTTTTCTTT
1 TTTCTTCTCTTT
1188550 TTTCTT-TCTTT
1 TTTCTTCTCTTT
1188561 TTT
1 TTT
1188564 TTGGTTGAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
11 8 0.24
12 16 0.47
13 10 0.29
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTCTTCTCTTT
Found at i:1188562 original size:12 final size:12
Alignment explanation
Indices: 1188507--1188564 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 12
1188497 TACCTCTTTG
*
1188507 TTTCTATTTCTTC
1 TTTCT-TTTTTTC
*
1188520 TCTCTTTTCTTTC
1 TTTCTTTT-TTTC
*
1188533 --TCTTTTTTTT
1 TTTCTTTTTTTC
1188543 TTTC-TTTTTTC
1 TTTCTTTTTTTC
1188554 TTTCTTTTTTT
1 TTTCTTTTTTT
1188565 TGGTTGAACC
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
10 3 0.08
11 16 0.43
12 11 0.30
13 7 0.19
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:1190025 original size:20 final size:20
Alignment explanation
Indices: 1189928--1190026 Score: 117
Period size: 20 Copynumber: 4.8 Consensus size: 20
1189918 TCCCGTATAA
*
1189928 ATGTATCGATACAATTTGGG
1 ATGTATCGATACATTTTGGG
**
1189948 ATGTATCGATACATGCATTTGAAA
1 ATGTATCGATACAT---TTTG-GG
* *
1189972 ATATATCGATACATTTTCGG
1 ATGTATCGATACATTTTGGG
1189992 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATTTTGGG
1190012 ATGTATCGATACATT
1 ATGTATCGATACATT
1190027 GTATCGATAC
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
20 46 0.70
21 3 0.05
23 4 0.06
24 13 0.20
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTTTGGG
Found at i:1190031 original size:13 final size:13
Alignment explanation
Indices: 1190013--1190038 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1190003 CATTTTGGGA
1190013 TGTATCGATACAT
1 TGTATCGATACAT
1190026 TGTATCGATACAT
1 TGTATCGATACAT
1190039 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1190035 original size:33 final size:32
Alignment explanation
Indices: 1189993--1190056 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1189983 CATTTTCGGA
*
1189993 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
1190026 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
1190057 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:1190145 original size:13 final size:13
Alignment explanation
Indices: 1190127--1190151 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1190117 ACATTTGGTC
1190127 ATGTATCGATACA
1 ATGTATCGATACA
1190140 ATGTATCGATAC
1 ATGTATCGATAC
1190152 TGTGCAATAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1195072 original size:52 final size:52
Alignment explanation
Indices: 1194924--1195052 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1194914 TGAAATATGA
1194924 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
1194976 AAATTTGCCTGTATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1195028 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1195053 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1195079 original size:13 final size:13
Alignment explanation
Indices: 1195061--1195085 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1195051 CAAAGATCAG
1195061 TGTATCGATACAA
1 TGTATCGATACAA
1195074 TGTATCGATACA
1 TGTATCGATACA
1195086 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1195165 original size:32 final size:32
Alignment explanation
Indices: 1195124--1195224 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
1195114 GGCAGTAGCT
* *
1195124 TACATTGTATCGATACAAAACTTATGTATAGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1195156 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
1195188 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
1195221 TACA
1 TACA
1195225 AATCATTGAA
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 51 0.77
33 15 0.23
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:1195170 original size:13 final size:13
Alignment explanation
Indices: 1195148--1195204 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
1195138 ACAAAACTTA
*
1195148 TGTATAGATACAT
1 TGTATCGATACAT
1195161 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1195179 ATGTATCGATACAT
1 -TGTATCGATACAT
1195193 TGTATCGATACA
1 TGTATCGATACA
1195205 ACACTTTATG
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 20 0.54
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1195185 original size:19 final size:19
Alignment explanation
Indices: 1195129--1195225 Score: 83
Period size: 19 Copynumber: 5.7 Consensus size: 19
1195119 TAGCTTACAT
*
1195129 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
*
1195148 TGTATAGAT---ACA--T-
1 TGTATCGATACAACACTTA
1195161 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1195180 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1195193 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
1195213 TGTATCGATACAA
1 TGTATCGATACAA
1195226 ATCATTGAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 25
0.69 0.03 0.28
Matches are distributed among these distances:
13 17 0.27
14 2 0.03
16 11 0.18
18 1 0.02
19 18 0.29
20 13 0.21
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1196068 original size:49 final size:49
Alignment explanation
Indices: 1195946--1196068 Score: 210
Period size: 49 Copynumber: 2.5 Consensus size: 49
1195936 ATATGCAGCT
* * *
1195946 AGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTTAAGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1195995 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
*
1196044 AGCGACATTGGACTTAAAGGTGAAG
1 AGCGACATTGGACTTAAAGATGAAG
1196069 ATGAGAAAAG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 70 1.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (49 bp):
AGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
Found at i:1196467 original size:101 final size:95
Alignment explanation
Indices: 1196137--1196571 Score: 547
Period size: 101 Copynumber: 4.5 Consensus size: 95
1196127 AAGCTGAGAA
* * * * * *
1196137 AAAAGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAAT
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-GAAAAGGCGCCAAT
* *
1196202 ATGCTGATTCAAGGCCATCTATATTGGACTT
65 ATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * **
1196233 -AAAGGTGCCAATGTGCTGATTTAAAGGCCAGCTACATTGGACTTAAAGA--AGAAGGTTCCAAT
1 AAAAGGTGCCAATGTGCTGA-TTCAAGGCCAGCGACATTGGACTTAAAGATGAAAAGGCGCCAAT
* * *
1196295 ATGCTAATTCAAGGCTAGCTATATTGGACTT
65 ATGCTGATTCAAGGCCAGCGATATTGGACTT
1196326 AAAA-GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAAT
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-AAAGGCGCCAAT
*
1196390 ATGCTGATTCAAGGCTAGCGATATTGGACTT
65 ATGCTGATTCAAGGCCAGCGATATTGGACTT
1196421 AAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCG
1 --A-A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-AAAGGCG
1196486 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
60 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1196522 AAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC-GACGACATTGGACTTA
1 --A-A--AAGGTGCCAATGTGCTGATTCAAGGCCAG-CGACATTGGACTTA
1196572 GAAGGGTTGC
Statistics
Matches: 309, Mismatches: 18, Indels: 19
0.89 0.05 0.05
Matches are distributed among these distances:
92 27 0.09
93 53 0.17
94 4 0.01
95 55 0.18
96 27 0.09
97 1 0.00
98 1 0.00
100 3 0.01
101 138 0.45
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (95 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAAAGGCGCCAATA
TGCTGATTCAAGGCCAGCGATATTGGACTT
Found at i:1196566 original size:49 final size:49
Alignment explanation
Indices: 1196146--1196571 Score: 455
Period size: 52 Copynumber: 8.7 Consensus size: 49
1196136 AAAAAGATGT
* * *
1196146 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-G--AAGGTGC
* * * *
1196198 CAATATGCTGATTCAAGGCCATCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * * *
1196241 CAATGTGCTGATTTAAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTTC
1 CAATGTGCTGA-TTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * * * *
1196291 CAATATGCTAATTCAAGGCTAGCTATATTGGACTT--A-A--AA-GTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
*
1196334 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG---AAGGTGC
* * *
1196386 CAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
*
1196435 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG---AAGGTGC
* *
1196487 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
1196536 CAATGTGCTGATTCAAGGCC-GACGACATTGGACTTA
1 CAATGTGCTGATTCAAGGCCAG-CGACATTGGACTTA
1196572 GAAGGGTTGC
Statistics
Matches: 319, Mismatches: 35, Indels: 43
0.80 0.09 0.11
Matches are distributed among these distances:
43 49 0.15
44 23 0.07
45 1 0.00
46 2 0.01
47 1 0.00
48 3 0.01
49 104 0.33
50 15 0.05
51 2 0.01
52 119 0.37
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
Found at i:1196613 original size:33 final size:33
Alignment explanation
Indices: 1196571--1197031 Score: 678
Period size: 33 Copynumber: 14.0 Consensus size: 33
1196561 CATTGGACTT
* *
1196571 AGAAGGGTTGCCACCAACTTGCGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
1196604 AGAATGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1196637 AG-AGGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
1196668 AAAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1196701 AAGAA-GGTTGCCACCGACTTGTGTGGGCTTTAG
1 -AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1196734 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* * * *
1196767 AAAAAGGTTACCACCGACTTGTATGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1196800 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* * * *
1196833 AAAAAGGTTACCACCGACTTGTGTGGGCTTTTG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
1196866 AAAAAGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* * * *
1196899 AAAAAGGTTACCACCGACTTGTGTGGGCTTTTG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1196932 AAGAA-GGTTGCCACCGACTTGTGTGGGCTTTAG
1 -AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* * *
1196965 AAAAAGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1196998 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1197031 A
1 A
1197032 AAAAGAGAAA
Statistics
Matches: 392, Mismatches: 30, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
31 2 0.01
32 61 0.16
33 323 0.82
34 6 0.02
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:1197076 original size:27 final size:27
Alignment explanation
Indices: 1197044--1197312 Score: 178
Period size: 27 Copynumber: 9.0 Consensus size: 27
1197034 AAGAGAAAGA
1197044 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * * *
1197071 TGCCACGAAATTATGGACTTAGAAGGAAAAAAAAG
1 TGCCACGGAGTTGTGGACTTAAAAGG--------G
1197106 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
1197133 TGCCACGGAGTTGTGGGCTTTAAAAAGAG
1 TGCCACGGAGTTGTGGAC-TT-AAAAGGG
*
1197162 TGCCACGGAGTTATGGACTTTGAAAAGAAAAAGG
1 TGCCACGGAGTTGTGGAC-TT-AAAAG-----GG
*
1197196 TGCCATGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
1197223 TGCCACGGAATTGTGGGCTTTTAAAGGGAAAAAGAG
1 TGCCACGGAGTTGTGGAC--TT-------AAAAGGG
*
1197259 TGCCACGGAGTTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
*
1197287 TGCCACGGAGTTGTGGACTTAGAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGG
1197313 AAAAAAAGTG
Statistics
Matches: 194, Mismatches: 24, Indels: 48
0.73 0.09 0.18
Matches are distributed among these distances:
27 64 0.33
28 25 0.13
29 32 0.16
32 5 0.03
33 2 0.01
34 17 0.09
35 26 0.13
36 23 0.12
ACGTcount: A:0.31, C:0.13, G:0.34, T:0.22
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:1197200 original size:34 final size:34
Alignment explanation
Indices: 1197126--1197537 Score: 250
Period size: 32 Copynumber: 13.0 Consensus size: 34
1197116 TTGTGGACTT
* *
1197126 AAAAGGGTGCCACGGAGTTGTGGGCTTT---AA-
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAG
* *
1197156 AAAGA-GTGCCACGGAGTTATGGACTTTGAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAG
*
1197189 AAAAAGGTGCCATGGAGTTGTGGAC-TT-AAAAG
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAG
* * * *
1197221 -----GGTGCCACGGAATTGTGGGCTTTTAAAGGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAA-AG
*
1197251 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
1 AAAAAG-GTGCCACGGAGTTGTGGACTTTGAAAAG
*
1197285 -----GGTGCCACGGAGTTGTGGACTTAGAAGGAA-
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAA--AAG
* *
1197315 AAAAA-GTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAG
* *
1197348 AAAAAGGTGGCACGGAGTTGTGGGCTTTG--AAG
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAG
* * *
1197380 AAAAA-ATGCCACTGAGTCGTGGACTTTG---AG
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAG
* *
1197410 ACAAAA--TGCCACTGAGTCGTGGACTTT--AAAG
1 A-AAAAGGTGCCACGGAGTTGTGGACTTTGAAAAG
* *
1197441 -AAAAGGATGCCACTGAGTCGTGGACTTTG--AAG
1 AAAAAGG-TGCCACGGAGTTGTGGACTTTGAAAAG
* * *
1197473 -AAAAGGATGCCACTGAGTCGTGGACTTTGAGAAG
1 AAAAAGG-TGCCACGGAGTTGTGGACTTTGAAAAG
* * *
1197507 --AAA-TTGCCACTGAGTTGTGGACTTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAG
1197538 GCATTTGAAG
Statistics
Matches: 320, Mismatches: 29, Indels: 65
0.77 0.07 0.16
Matches are distributed among these distances:
27 17 0.05
28 22 0.07
29 30 0.09
30 28 0.09
31 50 0.16
32 70 0.22
33 14 0.04
34 64 0.20
35 4 0.01
36 21 0.07
ACGTcount: A:0.32, C:0.13, G:0.32, T:0.23
Consensus pattern (34 bp):
AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAG
Found at i:1197262 original size:63 final size:63
Alignment explanation
Indices: 1197126--1197345 Score: 295
Period size: 62 Copynumber: 3.5 Consensus size: 63
1197116 TTGTGGACTT
* * * * *
1197126 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTATGGACTTTGAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGGGTGCCACGGAGTTGTGGACTTTTAAAGGA
* * * *
1197190 AAAAG-GTGCCATGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAATTGTGGGCTTTTAAAGGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTTTAAA-GGA
1197252 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGAC--TTAGAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTTTA-AAGGA
*
1197314 AAAAAAGTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
1197346 AGAAAAAGGT
Statistics
Matches: 139, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
61 27 0.19
62 46 0.33
63 36 0.26
64 30 0.22
ACGTcount: A:0.31, C:0.12, G:0.34, T:0.22
Consensus pattern (63 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTTTAAAGGA
Found at i:1197351 original size:35 final size:34
Alignment explanation
Indices: 1197286--1197406 Score: 124
Period size: 34 Copynumber: 3.6 Consensus size: 34
1197276 CTTTAAAAGG
* * *
1197286 GTGCCACGGAGTTGTGGAC-TTAGAAGGAAAAAAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAAG-AAAAAA
*
1197320 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG
1 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAA
* *
1197354 GTGGCACGGAGTTGTGGGCTTT--GAAGAAAAAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAA
* * *
1197386 -TGCCACTGAGTCGTGGACTTT
1 GTGCCACGGAGTTGTGGGCTTT
1197407 GAGACAAAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
31 17 0.23
32 8 0.11
34 44 0.59
35 6 0.08
ACGTcount: A:0.31, C:0.13, G:0.33, T:0.22
Consensus pattern (34 bp):
GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAA
Found at i:1197367 original size:68 final size:65
Alignment explanation
Indices: 1197280--1197537 Score: 203
Period size: 63 Copynumber: 4.0 Consensus size: 65
1197270 TGTGGGCTTT
* * *
1197280 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAAAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAAAGGTGCCACGGAGTTGTGGACTTAGAA-G-AAAAAA-TGCCACGGAGTCGTGGACTTTAAA
1197345 AAG
63 AAG
* * * * *
1197348 AAAAAGGTGGCACGGAGTTGTGGGCTTTGAAGAAAAAATGCCACTGAGTCGTGGACTTT---GAG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAGAAGAAAAAATGCCACGGAGTCGTGGACTTTAAAAAG
* * * * *
1197410 ACAAAA--TGCCACTGAGTCGTGGACTTTA-AAGAAAAGGATGCCACTGAGTCGTGGACTTT--G
1 A-AAAAGGTGCCACGGAGTTGTGGAC-TTAGAAGAAAA-AATGCCACGGAGTCGTGGACTTTAAA
1197470 AAG
63 AAG
* * * * * *
1197473 -AAAAGGATGCCACTGAGTCGTGGACTTTG-AGAAGAAATTGCCACTGAGTTGTGGACTTTAAAA
1 AAAAAGG-TGCCACGGAGTTGTGGACTTAGAAGAA-AAAATGCCACGGAGTCGTGGACTTTAAAA
1197536 AG
64 AG
1197538 GCATTTGAAG
Statistics
Matches: 159, Mismatches: 20, Indels: 25
0.78 0.10 0.12
Matches are distributed among these distances:
61 25 0.16
62 27 0.17
63 32 0.20
64 20 0.13
65 21 0.13
66 6 0.04
67 1 0.01
68 27 0.17
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.22
Consensus pattern (65 bp):
AAAAAGGTGCCACGGAGTTGTGGACTTAGAAGAAAAAATGCCACGGAGTCGTGGACTTTAAAAAG
Found at i:1198578 original size:20 final size:21
Alignment explanation
Indices: 1198543--1198585 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1198533 CTCACCGAGA
* *
1198543 TTTTCTGTTTTGTTTTTTTGT
1 TTTTCTCTTTTGTTTTTGTGT
1198564 TTTTCTCTTTT-TTTTTGTGT
1 TTTTCTCTTTTGTTTTTGTGT
1198584 TT
1 TT
1198586 GGAAAAGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.00, C:0.07, G:0.12, T:0.81
Consensus pattern (21 bp):
TTTTCTCTTTTGTTTTTGTGT
Found at i:1202424 original size:21 final size:21
Alignment explanation
Indices: 1202393--1202437 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
1202383 GCTATGAGTG
*
1202393 TGGGGGCTGCCCGGTTGCGACC
1 TGGGGGCTG-CCGGTCGCGACC
*
1202415 TGGGGG-TGCCGGTCGTGACC
1 TGGGGGCTGCCGGTCGCGACC
1202435 TGG
1 TGG
1202438 TGAGTGCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.04, C:0.27, G:0.49, T:0.20
Consensus pattern (21 bp):
TGGGGGCTGCCGGTCGCGACC
Found at i:1205263 original size:33 final size:33
Alignment explanation
Indices: 1205221--1205286 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1205211 AGATTGTCTT
1205221 TTCCATTATTTAAAACAAAACATTTGCATTCAA
1 TTCCATTATTTAAAACAAAACATTTGCATTCAA
1205254 TTCCATTATTTAAAACAAAACATTTGCATTCAA
1 TTCCATTATTTAAAACAAAACATTTGCATTCAA
1205287 ACGGATGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.36
Consensus pattern (33 bp):
TTCCATTATTTAAAACAAAACATTTGCATTCAA
Found at i:1207010 original size:15 final size:16
Alignment explanation
Indices: 1206987--1207024 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1206977 TTTGACAATC
*
1206987 TTATCTTCAAGA-TTT
1 TTATTTTCAAGAGTTT
*
1207002 TTATTTTCAATAGTTT
1 TTATTTTCAAGAGTTT
1207018 TTATTTT
1 TTATTTT
1207025 ATTTTCTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (16 bp):
TTATTTTCAAGAGTTT
Found at i:1209071 original size:13 final size:13
Alignment explanation
Indices: 1209053--1209078 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1209043 CATTTTGGGA
1209053 TGTATCGATACAT
1 TGTATCGATACAT
1209066 TGTATCGATACAT
1 TGTATCGATACAT
1209079 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1209075 original size:33 final size:32
Alignment explanation
Indices: 1209033--1209096 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1209023 TACAAGCCAA
*
1209033 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
1209066 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
1209097 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:1214865 original size:20 final size:20
Alignment explanation
Indices: 1214837--1214911 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1214827 TCATACCCTG
1214837 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1214857 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1214877 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1214897 ATGTATCGATACATT
1 ATGTATCGATACATT
1214912 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1214904 original size:40 final size:39
Alignment explanation
Indices: 1214837--1214914 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1214827 TCATACCCTG
* *
1214837 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1214877 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1214915 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1215856 original size:24 final size:22
Alignment explanation
Indices: 1215824--1215877 Score: 76
Period size: 20 Copynumber: 2.5 Consensus size: 22
1215814 AGCCTTTGAC
1215824 CATGCATTTTTTTTGATTATGTTT
1 CATGCATTTTTTTT-ATTATG-TT
1215848 CATGCA--TTTTTTATTATGTT
1 CATGCATTTTTTTTATTATGTT
1215868 CATGCATTTT
1 CATGCATTTT
1215878 AACATGTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 8 0.29
21 6 0.21
22 8 0.29
24 6 0.21
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.59
Consensus pattern (22 bp):
CATGCATTTTTTTTATTATGTT
Found at i:1215869 original size:20 final size:22
Alignment explanation
Indices: 1215832--1215877 Score: 78
Period size: 20 Copynumber: 2.2 Consensus size: 22
1215822 ACCATGCATT
1215832 TTTTTTGATTATGTTTCATGCA
1 TTTTTTGATTATGTTTCATGCA
1215854 TTTTTT-ATTATG-TTCATGCA
1 TTTTTTGATTATGTTTCATGCA
1215874 TTTT
1 TTTT
1215878 AACATGTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.50
21 6 0.25
22 6 0.25
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.63
Consensus pattern (22 bp):
TTTTTTGATTATGTTTCATGCA
Found at i:1222011 original size:15 final size:17
Alignment explanation
Indices: 1221975--1222017 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
1221965 AAAGTCAAAA
*
1221975 GCAAAAGCACAAAAGAT
1 GCAAAAGCAAAAAAGAT
1221992 G-AAAAG-AAAAAAG-T
1 GCAAAAGCAAAAAAGAT
1222006 GCAAAAGCAAAA
1 GCAAAAGCAAAA
1222018 TAAAAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 9 0.39
17 1 0.04
ACGTcount: A:0.65, C:0.12, G:0.19, T:0.05
Consensus pattern (17 bp):
GCAAAAGCAAAAAAGAT
Found at i:1222024 original size:23 final size:23
Alignment explanation
Indices: 1221998--1222049 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1221988 AGATGAAAAG
1221998 AAAAAAGTGCAA-AAGC-AAAATAA
1 AAAAAAG-GCAACAA-CAAAAATAA
*
1222021 AAAAAAGGGAACAACAAAAATAA
1 AAAAAAGGCAACAACAAAAATAA
1222044 AAAAAA
1 AAAAAA
1222050 CGAGGACACG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.75, C:0.08, G:0.12, T:0.06
Consensus pattern (23 bp):
AAAAAAGGCAACAACAAAAATAA
Found at i:1223420 original size:55 final size:54
Alignment explanation
Indices: 1223334--1224807 Score: 861
Period size: 57 Copynumber: 26.0 Consensus size: 54
1223324 ACTGTGACCT
* * *
1223334 CTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAATTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAAGTCAGTGGCA-CC
* *
1223389 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAATTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAAGTCAGTGGCACC
* *
1223443 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAAGTCAGTGGCACC
* * *
1223498 CTTTTAAGTCCACAACTCTGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAAGTCAGTGGCACC
* *
1223553 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAAGTCAGTGGCACC
* **
1223608 CTTTTAAAGTCCACAACTCCGTGGCATCCCTTTCAAAGAACACAAGTCAGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCA-CCCTTT-TAAGTCCACAAGTCAGTGGCACC
* * * * ** *
1223665 CTTTCAAAG-CCTACAAGTCAGTGGCACCCTTTCAAAACCCACAAGTCAGTGGCACT
1 CTTT-TAAGTCC-ACAACTCCGTGGCACCCTTT-TAAGTCCACAAGTCAGTGGCACC
* * * * *
1223721 CTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTTT--AAGTCCACAACTCCGTGGCACCCTTTT--AAGTCCACAAGTCAGTGGCAC-C
* * * * * * * *
1223780 CTTTCAAAGCCCACAAATCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACT
1 CTTT-TAAGTCCACAACTCCGTGGCAC-CCTTT-TAAGTCCACAAGTCAGTGGCACC
* * * * *
1223837 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTT--AAGTCCACAACTCCGTGGCACCCTTT-TAAGTCCACAAGTCAGTGGCACC
* * * ** * * * *
1223894 CTTTCAAAGCCCACAAGTTAGTGGTACTCCTTTCAAAGCCCACAAGTCAGTGGCACTT
1 CTTT-TAAGTCCACAACTCCGTGGCAC-CCTTT-TAAGTCCACAAGTCAGTGGCAC-C
* * * * * * *
1223952 CTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTT-TAAGTCCACAACTCCGTGGCACCCTTTT--AAGTCCACAAGTCAGTGGCACC
* * * * * * *
1224009 CTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTT-TAAGTCCACAACTCCGTGGCAC-CCTTT-TAAGTCCACAAGTCAGTGGCACC
* * * * * *
1224066 TTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTT--AAGTCCACAACTCCGTGGCACCCTTTT--AAGTCCACAAGTCAGTGGCACC
* * ** * *
1224124 CTTTCAAAG-CGCACAAGTTAGTGGCACCCTTTCAGAGCCCACAAGTCAGTGGCA-C
1 CTTT-TAAGTC-CACAACTCCGTGGCACCCTTTTA-AGTCCACAAGTCAGTGGCACC
* * * * ** * * *
1224179 CTTTTCGAAGCCCACAAGTCAGTGGCACCATTGCGAAGCCCACAATTCAGTGGCACT
1 CTTTT--AAGTCCACAACTCCGTGGCACCCTT-TTAAGTCCACAAGTCAGTGGCACC
* * * * *
1224236 CTTTCAAAGGCCACAAGTCAGTGGCACCCTTTTAAAGCCCACACAAGTCAGTGGCACTC
1 CTTT-TAAGTCCACAACTCCGTGGCACCCTTTT-AAG-TC-CACAAGTCAGTGGCAC-C
* * * * * * *
1224295 CTTTTAAAGCTCACGCAAGTCAGTGGTA-CCTTTTCAAAGCCCACGAGTCAGTGGCACT
1 CTTTT-AAG-TC-CACAACTCCGTGGCACCCTTTT--AAGTCCACAAGTCAGTGGCACC
* * * ** * *
1224353 CTTTCAAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTT-TAAGTCCACAACTCCGTGGCAC-CCTTT-TAAGTCCACAAGTCAGTGGCAC-C
* * * * * *
1224411 CTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA-C
1 CTTT-TAAGTCCACAACTCCGTGGCACCCTTTT--AAGTCCACAAGTCAGTGGCACC
* * * * * * *
1224467 CTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACCAGTCAGTGGCACTC
1 CTTT-TAAGTCCACAACTCCGTGGCACCCTTT-TAAGTCCACAAGTCAGTGGCAC-C
* * * ** * * * * *
1224524 CTTTCAAAGCCCACAAGTCAATGGCACTCTTTTCAAAGCCCAGAAATCAGTGGCACT
1 CTTT-TAAGTCCACAACTCCGTGGCACCCTTTT--AAGTCCACAAGTCAGTGGCACC
* * ** * *
1224581 CTTTTAAAGGCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTT-TAAGTCCACAAGTCAGTGGCAC-C
* * * * ** ** * *
1224638 CTTTCAAAGCCCACAAGTCAGTGGCACTTTTTTCAAAACCCACAAATCAGTGGCACT
1 CTTT-TAAGTCCACAACTCCGTGGCACCCTTTT--AAGTCCACAAGTCAGTGGCACC
* * * * * *
1224695 CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTTT--AAGTCCACAACTCCGTGGCACCCTTT-TAAGTCCACAAGTCAGTGGCACC
* * * * *
1224752 CTTTTAGAGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAAGTCAGTGGCACC
1 CTTTTA-AGTCCACAACTCCGTGGCACCCTTT-TAAGTCCACAAGTCAGTGGCACC
1224808 ATTGCGAAGC
Statistics
Matches: 1223, Mismatches: 130, Indels: 131
0.82 0.09 0.09
Matches are distributed among these distances:
54 27 0.02
55 218 0.18
56 272 0.22
57 342 0.28
58 308 0.25
59 30 0.02
60 9 0.01
61 17 0.01
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (54 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAAGTCAGTGGCACC
Found at i:1223795 original size:143 final size:140
Alignment explanation
Indices: 1223330--1225253 Score: 1859
Period size: 143 Copynumber: 13.2 Consensus size: 140
1223320 TAGTACTGTG
* * * * * * *
1223330 ACCTCTTT-AAAGTCCACAACTCCGTGGCACCCTTT-TAAGTCCACAATTCCGTGGCATCCCTTT
1 ACCT-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTT
* * * * * * * * *
1223393 -TAAGTCCACAACTCCGTGGCACCCTTT-TAAGTCCACAATTCCGTGGCACCCTTTT--AAGTCC
64 CAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCC
* *
1223454 ACAACTCCGTGGC
128 ACAAGTCAGTGGC
* * * * * * *
1223467 ATCCCTTTT--AAGTCCACAACTCCGTGGCACCCTTT-TAAGTCCACAACTCTGTGGCATCCCTT
1 A--CCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCCTT
* * * * * * * * *
1223529 T-TAAGTCCACAACTCCGTGGCACCCTTT-TAAGTCCACAACTCCGTGGCATCCCTTTT--AAGT
63 TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA--CCTTTTCAAAGC
* *
1223590 CCACAACTCCGTGGC
126 CCACAAGTCAGTGGC
* * * **
1223605 ACCCTTTT-AAAGTCCACAACTCCGTGGCATCCCTTTCAAAGAACACAAGTCAGTGGCACCCTTT
1 A-CCTTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTT
* *
1223669 CAAAGCCTACAAGTCAGTGGCACCCTTTCAAAACCCACAAGTCAGTGGCACTCTTTTCAAAGCCC
64 CAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCC
*
1223734 ACAAATCAGTGGC
128 ACAAGTCAGTGGC
*
1223747 ACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCCTT
1 AC-CTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTT
* * *
1223812 TCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
63 TCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
1223877 CACAAGTCAGTGGC
127 CACAAGTCAGTGGC
* * * *
1223891 ACCCTTTCAAAGCCCACAAGTTAGTGGTACTCCTTTCAAAGCCCACAAGTCAGTGGCACTTCTTT
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTT
* * * *
1223956 CAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCC
64 CAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCC
1224021 ACAAGTCAGTGGC
128 ACAAGTCAGTGGC
* ** * *
1224034 ACTCCTTTCAAAGCCCACAAGTCAGTGGCACTTTTTTCAAAGCCCACAAATCAGTGGCACTCTTT
1 AC-CTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTT
* * * *
1224099 TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCGCACAAGTTAGTGGCACCCTTTCAGAGCCC
63 TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCC
1224164 ACAAGTCAGTGGC
128 ACAAGTCAGTGGC
* * * * * *
1224177 ACCTTTTCGAAGCCCACAAGTCAGTGGCACCATTGCGAAGCCCACAATTCAGTGGCACTCTTTCA
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
* *
1224242 AAGGCCACAAGTCAGTGGCACCCTTTTAAAGCCCACACAAGTCAGTGGCACTCCTTTT-AAAGCT
66 AAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGCA--CCTTTTCAAAGC-
* *
1224306 CACGCAAGTCAGTGGT
126 C-CACAAGTCAGTGGC
* * *
1224322 ACCTTTTCAAAGCCCACGAGTCAGTGGCACTCTTTCAAAGCCCACAAGTTAGTGGCACTCCTTTC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTC
*
1224387 AAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCC
65 AAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCC
1224452 ACAAGTCAGTGGC
128 ACAAGTCAGTGGC
*
1224465 ACC-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACCAGTCAGTGGCACTCCTTTC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTC
* * * * *
1224529 AAAGCCCACAAGTCAATGGCACTCTTTTCAAAGCCCAGAAATCAGTGGCACTCTTTT-AAAGGCC
65 AAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCC
*
1224593 ACAAGTTAGTGGC
128 ACAAGTCAGTGGC
* **
1224606 ACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTTTTTT
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTT
* * * *
1224671 CAAAACCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCC
64 CAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCC
*
1224736 ACAAGTTAGTGGC
128 ACAAGTCAGTGGC
* * * *
1224749 ACCCTTTT-AGAGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAAGTCAGTGGCACCATTGC
1 A-CCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
* * * * *
1224813 GAAGCCCACAATTCAGTGGCACTCTTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGC
65 AAAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGC-A-CCTTTTCAAAG-
*
1224878 CCACACAAGTCGGTGGC
125 CC-CACAAGTCAGTGGC
* *
1224895 AACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCA
1 -A-CCTTTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAG-CC-CACAAGTCAGTGGC-
* **
1224960 ACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTTGGTGGCAA
57 ACCC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAG-CC-CACAAGTCAGTGGC-A
*
1225025 CCATTTTCAAAGCCCACACATGTCGGTGGC
114 CC-TTTTCAAAGCCCACA-A-GTCAGTGGC
* * *
1225055 AACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCATTCCAAAGCCCACACAAGTCGGTGGCA
1 -A-CCTTTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAG-CC-CACAAGTCAGTGGC-
* *
1225120 ACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACATAAGTCGGTGGCAA
57 ACCC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTCAAAGCCCAC--AAGTCAGTGGC-A
* *
1225185 CCCATTTCAAAGCCCACACAAGTCGGTGGC
114 -CCTTTTCAAAG-CC-CACAAGTCAGTGGC
* * *
1225215 AATTCTTTTCAAGGCCCACATAAGTTAGTGGCACCCTTT
1 -A-CCTTTTCAAAGCCCAC--AAGTCAGTGGCACCCTTT
1225254 TTTTTTAAAA
Statistics
Matches: 1589, Mismatches: 137, Indels: 101
0.87 0.07 0.06
Matches are distributed among these distances:
137 107 0.07
138 50 0.03
139 16 0.01
140 85 0.05
141 86 0.05
142 244 0.15
143 373 0.23
144 157 0.10
145 109 0.07
146 40 0.03
147 17 0.01
148 3 0.00
149 2 0.00
150 13 0.01
151 4 0.00
152 7 0.00
153 2 0.00
154 13 0.01
155 3 0.00
156 6 0.00
157 2 0.00
158 24 0.02
159 16 0.01
160 201 0.13
161 5 0.00
162 4 0.00
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (140 bp):
ACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
AAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACA
AGTCAGTGGC
Found at i:1224815 original size:28 final size:29
Alignment explanation
Indices: 1223334--1225253 Score: 1828
Period size: 28 Copynumber: 66.1 Consensus size: 29
1223324 ACTGTGACCT
* * *
1223334 CTTT-AAAGTCCACAACTCCGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* * * *
1223361 CTTT-TAAGTCCACAATTCCGTGGCA-TCC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT-C
* * * *
1223389 CTTT-TAAGTCCACAACTCCGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* * * *
1223416 CTTT-TAAGTCCACAATTCCGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* * * *
1223443 CTTT-TAAGTCCACAACTCCGTGGCA-TCC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT-C
* * * *
1223471 CTTT-TAAGTCCACAACTCCGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* * * *
1223498 CTTT-TAAGTCCACAACTCTGTGGCA-TCC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT-C
* * * *
1223526 CTTT-TAAGTCCACAACTCCGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* * * *
1223553 CTTT-TAAGTCCACAACTCCGTGGCA-TCC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT-C
* * * *
1223581 CTTT-TAAGTCCACAACTCCGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* * * *
1223608 CTTTTAAAGTCCACAACTCCGTGGCA-TCC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT-C
**
1223637 CTTTCAAAGAACACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1223665 CTTTCAAAGCCTACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1223693 CTTTCAAAACCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1223722 TTTTCAAAGCCCACAAATCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1223751 TTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1223780 CTTTCAAAGCCCACAAATCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1223809 CTTTCAAAGCCCACAAATCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1223838 TTTTCAAAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1223866 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1223894 CTTTCAAAGCCCACAAGTTAGTGGTACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1223923 CTTTCAAAGCCCACAAGTCAGTGGCACTT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1223952 CTTTCAAAGCCCACAAATCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1223981 TTTTCAAAGCCCACAAGTTAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1224009 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1224038 CTTTCAAAGCCCACAAGTCAGTGGCACTT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1224067 TTTTCAAAGCCCACAAATCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1224096 TTTTCAAAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1224124 CTTTCAAAGCGCACAAGTTAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1224152 CTTTCAGAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1224180 TTTTCGAAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* * * *
1224208 ATTGCGAAGCCCACAATTCAGTGGCACT-
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1224236 CTTTCAAAGGCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1224264 CTTTTAAAGCCCACACAAGTCAGTGGCACTC
1 CTTTCAAAG-CC-CACAAGTCAGTGGCACTC
* * *
1224295 CTTTTAAAGCTCACGCAAGTCAGTGGTAC-C
1 CTTTCAAAGC-C-CACAAGTCAGTGGCACTC
* *
1224325 TTTTCAAAGCCCACGAGTCAGTGGCACT-
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1224353 CTTTCAAAGCCCACAAGTTAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1224382 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1224411 CTTTCAAAGCCCACAAATCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1224440 TTTTCAAAGCCCACAAGTCAGTGGCA--C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1224467 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1224495 CTTTCAAAGCCCACCAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1224524 CTTTCAAAGCCCACAAGTCAATGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* * *
1224553 TTTTCAAAGCCCAGAAATCAGTGGCACT-
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* * *
1224581 CTTTTAAAGGCCACAAGTTAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1224609 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1224638 CTTTCAAAGCCCACAAGTCAGTGGCACTT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* * *
1224667 TTTTCAAAACCCACAAATCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1224696 TTTTCAAAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1224724 CTTTCAAAGCCCACAAGTTAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* *
1224752 CTTTTAGAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1224780 CTTTCGAAGCCCACAAGTCAGTGGCAC-C
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
* * * *
1224808 ATTGCGAAGCCCACAATTCAGTGGCACT-
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC
*
1224836 CTTTCAAAGCCCACACAAGTCGGTGGCAAC-C
1 CTTTCAAAG-CC-CACAAGTCAGTGGC-ACTC
*
1224867 CATTTCAAAGCCCACACAAGTCGGTGGCAAC-C
1 C-TTTCAAAG-CC-CACAAGTCAGTGGC-ACTC
*
1224899 CTTTTCAAAGCCCACACAAGTCGGTGGCAAC-C
1 C-TTTCAAAG-CC-CACAAGTCAGTGGC-ACTC
*
1224931 CATTTCAAAGCCCACACAAGTCGGTGGCAAC-C
1 C-TTTCAAAG-CC-CACAAGTCAGTGGC-ACTC
*
1224963 CATTTCAAAGCCCACACAAGTCGGTGGCAAC-C
1 C-TTTCAAAG-CC-CACAAGTCAGTGGC-ACTC
**
1224995 CATTTCAAAGCCCACACAAGTTGGTGGCAAC-C
1 C-TTTCAAAG-CC-CACAAGTCAGTGGC-ACTC
* *
1225027 ATTTTCAAAGCCCACACATGTCGGTGGCAAC-C
1 -CTTTCAAAGCCCACA-A-GTCAGTGGC-ACTC
*
1225059 CTTTTCAAAGCCCACACAAGTCGGTGGCAAC-C
1 C-TTTCAAAG-CC-CACAAGTCAGTGGC-ACTC
* *
1225091 CATTCCAAAGCCCACACAAGTCGGTGGCAAC-C
1 C-TTTCAAAG-CC-CACAAGTCAGTGGC-ACTC
*
1225123 CATTTCAAAGCCCACACAAGTCGGTGGCAAC-C
1 C-TTTCAAAG-CC-CACAAGTCAGTGGC-ACTC
*
1225155 CTTTTCAAAGCCCACATAAGTCGGTGGCAAC-C
1 C-TTTCAAAGCCCAC--AAGTCAGTGGC-ACTC
* *
1225187 CATTTCAAAGCCCACACAAGTCGGTGGCAATTC
1 C-TTTCAAAG-CC-CACAAGTCAGTGGC-ACTC
* * *
1225220 TTTTCAAGGCCCACATAAGTTAGTGGCAC-C
1 CTTTCAAAGCCCAC--AAGTCAGTGGCACTC
1225250 CTTT
1 CTTT
1225254 TTTTTTAAAA
Statistics
Matches: 1708, Mismatches: 135, Indels: 97
0.88 0.07 0.05
Matches are distributed among these distances:
27 156 0.09
28 599 0.35
29 532 0.31
30 52 0.03
31 37 0.02
32 319 0.19
33 6 0.00
34 7 0.00
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (29 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACTC
Found at i:1225843 original size:20 final size:20
Alignment explanation
Indices: 1225815--1225889 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1225805 TCATACCCTG
1225815 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1225835 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
1225855 ATGTATCGATATC-TTCTACA
1 ATGTATCGATA-CATTTTTCA
1225875 ATGTATCGATACATT
1 ATGTATCGATACATT
1225890 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1225882 original size:40 final size:39
Alignment explanation
Indices: 1225815--1225892 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
1225805 TCATACCCTG
* *
1225815 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
*
1225855 ATGTATCGATATC-TTCTACAATGTATCGATACATTATG
1 ATGTATCGATA-CATTCTACAATATATCGATACATTATG
1225893 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 4 0.12
40 29 0.85
41 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1226836 original size:25 final size:25
Alignment explanation
Indices: 1226802--1226859 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 25
1226792 AGCCTTTGAC
1226802 CATGCATTTTTTTTTTATTATGTTT
1 CATGCATTTTTTTTTTATTATGTTT
1226827 CATGCA---TTTTTTTATTATGTTT
1 CATGCATTTTTTTTTTATTATGTTT
1226849 CATGCATTTTT
1 CATGCATTTTT
1226860 AACATGTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 22 0.73
25 8 0.27
ACGTcount: A:0.17, C:0.10, G:0.09, T:0.64
Consensus pattern (25 bp):
CATGCATTTTTTTTTTATTATGTTT
Found at i:1226839 original size:22 final size:22
Alignment explanation
Indices: 1226811--1226859 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1226801 CCATGCATTT
1226811 TTTTTTTATTATGTTTCATGCA
1 TTTTTTTATTATGTTTCATGCA
1226833 TTTTTTTATTATGTTTCATGCA
1 TTTTTTTATTATGTTTCATGCA
1226855 TTTTT
1 TTTTT
1226860 AACATGTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.67
Consensus pattern (22 bp):
TTTTTTTATTATGTTTCATGCA
Found at i:1226866 original size:20 final size:21
Alignment explanation
Indices: 1226812--1226866 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
1226802 CATGCATTTT
**
1226812 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
1226833 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
1226855 -TTTTTAACATGT
1 TTTTTTAACATGT
1226867 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:1232395 original size:11 final size:11
Alignment explanation
Indices: 1232371--1232419 Score: 80
Period size: 11 Copynumber: 4.4 Consensus size: 11
1232361 CTTCATATAA
1232371 AATTAATTAAAT
1 AATT-ATTAAAT
*
1232383 AATTATCAAAT
1 AATTATTAAAT
1232394 AATTATTAAAT
1 AATTATTAAAT
1232405 AATTATTAAAT
1 AATTATTAAAT
1232416 AATT
1 AATT
1232420 GCCTTAGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
11 31 0.89
12 4 0.11
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
AATTATTAAAT
Found at i:1234939 original size:21 final size:20
Alignment explanation
Indices: 1234898--1234941 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1234888 CTCTCCTTTA
1234898 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCG-TTATTAATAAT
1234919 TCTCCCCC-TTATTCAAGTAAT
1 TCTCCCCCGTTATT-AA-TAAT
1234940 TC
1 TC
1234942 ATATCAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.24
20 2 0.10
21 14 0.67
ACGTcount: A:0.23, C:0.32, G:0.05, T:0.41
Consensus pattern (20 bp):
TCTCCCCCGTTATTAATAAT
Found at i:1236767 original size:13 final size:13
Alignment explanation
Indices: 1236749--1236785 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1236739 AATCACCCTG
1236749 TATCGATACAATA
1 TATCGATACAATA
*
1236762 TATCGATACAATG
1 TATCGATACAATA
1236775 TATCGATACAA
1 TATCGATACAA
1236786 AGCAAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:1238884 original size:15 final size:15
Alignment explanation
Indices: 1238864--1238894 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1238854 ATTTCGTTTG
*
1238864 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1238879 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1238894 G
1 G
1238895 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1240726 original size:21 final size:21
Alignment explanation
Indices: 1240697--1240741 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1240687 AAGTTTTCAT
*
1240697 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1240717 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1240739 TTT
1 TTT
1240742 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1242985 original size:13 final size:13
Alignment explanation
Indices: 1242967--1242992 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1242957 CAATTTTTTG
1242967 TGTATCGATACAT
1 TGTATCGATACAT
1242980 TGTATCGATACAT
1 TGTATCGATACAT
1242993 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1250067 original size:642 final size:642
Alignment explanation
Indices: 1248844--1250130 Score: 2547
Period size: 642 Copynumber: 2.0 Consensus size: 642
1248834 AAAGTTTTAA
1248844 TCTCATATACAACCCAAAGAGATGGGGAACATAGAGATATAAAATGACCTCCAGATTTTATTTTG
1 TCTCATATACAACCCAAAGAGATGGGGAACATAGAGATATAAAATGACCTCCAGATTTTATTTTG
* *
1248909 AAAACTAAATATTCTTATCAGGCACTAGAAAGATACCGACATGAAACATTGTCTTTGCGATTTTT
66 AAAACTAAATATTCTTATCAGGCACTAGAAAGATACCGACATGAAACATTGCCTTTGCAATTTTT
1248974 AAAACAAATTTTTGGAAAACATGAATGCACATAATCATCATAAGGAAAATATGTTAGTATGACAA
131 AAAACAAATTTTTGGAAAACATGAATGCACATAATCATCATAAGGAAAATATGTTAGTATGACAA
1249039 TAAGTGCAATAAAGTTGCATAAATTAATCCACACAAAATAACAATAAAGAAAATGAGAGGCGGTC
196 TAAGTGCAATAAAGTTGCATAAATTAATCCACACAAAATAACAATAAAGAAAATGAGAGGCGGTC
1249104 GGAATGTATCTCACAATTATCCTCGATTATTCAAAAAAATAACCAAATTGACAATAATGGAGACG
261 GGAATGTATCTCACAATTATCCTCGATTATTCAAAAAAATAACCAAATTGACAATAATGGAGACG
1249169 TGTCTGAAGTCATTGATTAATTGAAGTCAAAAACGGACATGACTCAAAATTTGAGAGAGAGAAAA
326 TGTCTGAAGTCATTGATTAATTGAAGTCAAAAACGGACATGACTCAAAATTTGAGAGAGAGAAAA
1249234 TGATTTAATTTTTGATTGAAAAACGAGGTAGGAGTATCCCTTCGGAGGAATGGGGTTAGAGTGTC
391 TGATTTAATTTTTGATTGAAAAACGAGGTAGGAGTATCCCTTCGGAGGAATGGGGTTAGAGTGTC
1249299 CCCAGTGATGACAATTTAAGCAAAAATAAGATTTAAATTTTGATGAGTTTAAAAGCGGAGTTGGA
456 CCCAGTGATGACAATTTAAGCAAAAATAAGATTTAAATTTTGATGAGTTTAAAAGCGGAGTTGGA
1249364 GTATCCCCTCGGAAGAATAGGGTTGGAGTATCCCCGATAAATAAAATTTTAATATTTTTTATACT
521 GTATCCCCTCGGAAGAATAGGGTTGGAGTATCCCCGATAAATAAAATTTTAATATTTTTTATACT
1249429 GAAAATTGATGTAAATGAGGATGGTAAAGATGTAAAAGCATTTGTGCCTTGACATGG
586 GAAAATTGATGTAAATGAGGATGGTAAAGATGTAAAAGCATTTGTGCCTTGACATGG
*
1249486 TCTCATATACAACCCAGAGAGATGGGGAACATAGAGATATAAAATGACCTCCAGATTTTATTTTG
1 TCTCATATACAACCCAAAGAGATGGGGAACATAGAGATATAAAATGACCTCCAGATTTTATTTTG
1249551 AAAACTAAATATTCTTATCAGGCACTAGAAAGATACCGACATGAAACATTGCCTTTGCAATTTTT
66 AAAACTAAATATTCTTATCAGGCACTAGAAAGATACCGACATGAAACATTGCCTTTGCAATTTTT
1249616 AAAACAAATTTTTGGAAAACATGAATGCACATAATCATCATAAGGAAAATATGTTAGTATGACAA
131 AAAACAAATTTTTGGAAAACATGAATGCACATAATCATCATAAGGAAAATATGTTAGTATGACAA
1249681 TAAGTGCAATAAAGTTGCATAAATTAATCCACACAAAATAACAATAAAGAAAATGAGAGGCGGTC
196 TAAGTGCAATAAAGTTGCATAAATTAATCCACACAAAATAACAATAAAGAAAATGAGAGGCGGTC
1249746 GGAATGTATCTCACAATTATCCTCGATTATTCAAAAAAATAACCAAATTGACAATAATGGAGACG
261 GGAATGTATCTCACAATTATCCTCGATTATTCAAAAAAATAACCAAATTGACAATAATGGAGACG
1249811 TGTCTGAAGTCATTGATTAATTGAAGTCAAAAACGGACATGACTCAAAATTTGAGAGAGAGAAAA
326 TGTCTGAAGTCATTGATTAATTGAAGTCAAAAACGGACATGACTCAAAATTTGAGAGAGAGAAAA
1249876 TGATTTAATTTTTGATTGAAAAACGAGGTAGGAGTATCCCTTCGGAGGAATGGGGTTAGAGTGTC
391 TGATTTAATTTTTGATTGAAAAACGAGGTAGGAGTATCCCTTCGGAGGAATGGGGTTAGAGTGTC
1249941 CCCAGTGATGACAATTTAAGCAAAAATAAGATTTAAATTTTGATGAGTTTAAAAGCGGAGTTGGA
456 CCCAGTGATGACAATTTAAGCAAAAATAAGATTTAAATTTTGATGAGTTTAAAAGCGGAGTTGGA
1250006 GTATCCCCTCGGAAGAATAGGGTTGGAGTATCCCCGATAAATAAAATTTTAATATTTTTTATACT
521 GTATCCCCTCGGAAGAATAGGGTTGGAGTATCCCCGATAAATAAAATTTTAATATTTTTTATACT
1250071 GAAAATTGATGTAAATGAGGATGGTAAAGATGTAAAAGCATTTGTGCCTTGACATGG
586 GAAAATTGATGTAAATGAGGATGGTAAAGATGTAAAAGCATTTGTGCCTTGACATGG
1250128 TCT
1 TCT
1250131 GAGAGAGGTC
Statistics
Matches: 642, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
642 642 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (642 bp):
TCTCATATACAACCCAAAGAGATGGGGAACATAGAGATATAAAATGACCTCCAGATTTTATTTTG
AAAACTAAATATTCTTATCAGGCACTAGAAAGATACCGACATGAAACATTGCCTTTGCAATTTTT
AAAACAAATTTTTGGAAAACATGAATGCACATAATCATCATAAGGAAAATATGTTAGTATGACAA
TAAGTGCAATAAAGTTGCATAAATTAATCCACACAAAATAACAATAAAGAAAATGAGAGGCGGTC
GGAATGTATCTCACAATTATCCTCGATTATTCAAAAAAATAACCAAATTGACAATAATGGAGACG
TGTCTGAAGTCATTGATTAATTGAAGTCAAAAACGGACATGACTCAAAATTTGAGAGAGAGAAAA
TGATTTAATTTTTGATTGAAAAACGAGGTAGGAGTATCCCTTCGGAGGAATGGGGTTAGAGTGTC
CCCAGTGATGACAATTTAAGCAAAAATAAGATTTAAATTTTGATGAGTTTAAAAGCGGAGTTGGA
GTATCCCCTCGGAAGAATAGGGTTGGAGTATCCCCGATAAATAAAATTTTAATATTTTTTATACT
GAAAATTGATGTAAATGAGGATGGTAAAGATGTAAAAGCATTTGTGCCTTGACATGG
Found at i:1253887 original size:20 final size:20
Alignment explanation
Indices: 1253864--1253901 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1253854 TACAAGTAGG
1253864 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
1253884 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
1253902 ATCTTTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:1256990 original size:20 final size:20
Alignment explanation
Indices: 1256967--1257039 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1256957 ACAATTCAAA
1256967 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1256987 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1257008 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1257028 GTATCGATACAT
1 GTATCGATACAT
1257040 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1257011 original size:21 final size:21
Alignment explanation
Indices: 1256985--1257060 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1256975 ACATGTTGCA
1256985 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1257006 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1257026 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
1257047 ATGTATCGATACAT
1 ATGTATCGATACAT
1257061 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1257018 original size:41 final size:41
Alignment explanation
Indices: 1256967--1257060 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1256957 ACAATTCAAA
*
1256967 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1257008 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1257049 GTATCGATACAT
1 GTATCGATACAT
1257061 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1257117 original size:13 final size:13
Alignment explanation
Indices: 1257099--1257124 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1257089 TACAACAAGT
1257099 ATGTATCGATACA
1 ATGTATCGATACA
1257112 ATGTATCGATACA
1 ATGTATCGATACA
1257125 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1261207 original size:15 final size:15
Alignment explanation
Indices: 1261187--1261217 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1261177 TAAAAATGTC
*
1261187 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1261202 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1261217 C
1 C
1261218 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1263315 original size:13 final size:13
Alignment explanation
Indices: 1263297--1263334 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1263287 CATTTTTATT
1263297 TGTATCGATACAA
1 TGTATCGATACAA
*
1263310 TGTATCGATACAC
1 TGTATCGATACAA
1263323 TGTATCGATACA
1 TGTATCGATACA
1263335 GGGTGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1265811 original size:20 final size:20
Alignment explanation
Indices: 1265788--1265860 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1265778 ACAATTCAAA
1265788 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1265808 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1265829 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1265849 GTATCGATACAT
1 GTATCGATACAT
1265861 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1265832 original size:21 final size:21
Alignment explanation
Indices: 1265806--1265881 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1265796 ACATGTTGCA
1265806 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1265827 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1265847 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
1265868 ATGTATCGATACAT
1 ATGTATCGATACAT
1265882 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1265839 original size:41 final size:41
Alignment explanation
Indices: 1265788--1265881 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1265778 ACAATTCAAA
*
1265788 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1265829 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1265870 GTATCGATACAT
1 GTATCGATACAT
1265882 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1265938 original size:13 final size:13
Alignment explanation
Indices: 1265920--1265945 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1265910 TACAGCAAGT
1265920 ATGTATCGATACA
1 ATGTATCGATACA
1265933 ATGTATCGATACA
1 ATGTATCGATACA
1265946 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1270802 original size:21 final size:21
Alignment explanation
Indices: 1270769--1270809 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1270759 CTAAGTAAAA
1270769 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
1270790 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
1270810 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:1270874 original size:20 final size:19
Alignment explanation
Indices: 1270849--1270919 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
1270839 ACCCTGAAAA
1270849 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
1270869 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
1270888 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
1270909 GTATCGATACA
1 GTATCGATACA
1270920 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:1270972 original size:53 final size:53
Alignment explanation
Indices: 1270889--1271025 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
1270879 AGATTGCATA
1270889 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
1270943 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
1270996 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
1271026 TTGGAAGTAG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
53 67 0.83
54 14 0.17
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:1271101 original size:21 final size:22
Alignment explanation
Indices: 1271067--1271122 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
1271057 CATCACTATT
1271067 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
1271089 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
1271110 CATCACTGTTCAT
1 CATCACTGTTCAT
1271123 ACTGTTCACG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:1271202 original size:13 final size:13
Alignment explanation
Indices: 1271184--1271209 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1271174 ATAGATTTGT
1271184 GTGTATCGATACA
1 GTGTATCGATACA
1271197 GTGTATCGATACA
1 GTGTATCGATACA
1271210 TCATAAATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:1279684 original size:10 final size:10
Alignment explanation
Indices: 1279662--1279725 Score: 64
Period size: 9 Copynumber: 6.7 Consensus size: 10
1279652 CTTTATACTC
*
1279662 AAAAAAA-AG
1 AAAAAAACAA
*
1279671 AAAAATAC-A
1 AAAAAAACAA
*
1279680 AAAAATAC-A
1 AAAAAAACAA
1279689 A-AAAAACAA
1 AAAAAAACAA
1279698 AAAAAAACAA
1 AAAAAAACAA
1279708 AAAAAAACAA
1 AAAAAAACAA
1279718 GAAAAAAA
1 -AAAAAAA
1279726 TAGCAAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
8 5 0.10
9 18 0.38
10 18 0.38
11 7 0.15
ACGTcount: A:0.86, C:0.08, G:0.03, T:0.03
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:1279712 original size:9 final size:9
Alignment explanation
Indices: 1279661--1279724 Score: 60
Period size: 10 Copynumber: 7.0 Consensus size: 9
1279651 CCTTTATACT
1279661 CAAAAAAAA
1 CAAAAAAAA
* *
1279670 -GAAAAATA
1 CAAAAAAAA
*
1279678 CAAAAAATA
1 CAAAAAAAA
1279687 C-AAAAAAA
1 CAAAAAAAA
1279695 CAAAAAAAAA
1 C-AAAAAAAA
1279705 CAAAAAAAAA
1 C-AAAAAAAA
1279715 CAAGAAAAAA
1 CAA-AAAAAA
1279725 ATAGCAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
8 13 0.28
9 10 0.21
10 24 0.51
ACGTcount: A:0.84, C:0.09, G:0.03, T:0.03
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:1279740 original size:12 final size:10
Alignment explanation
Indices: 1279688--1279725 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
1279678 CAAAAAATAC
1279688 AAAAAAACAA
1 AAAAAAACAA
1279698 AAAAAAACAA
1 AAAAAAACAA
1279708 AAAAAAACAA
1 AAAAAAACAA
1279718 GAAAAAAA
1 -AAAAAAA
1279726 TAGCAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 20 0.74
11 7 0.26
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:1279744 original size:10 final size:10
Alignment explanation
Indices: 1279679--1279744 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
1279669 AGAAAAATAC
*
1279679 AAAAAATACA
1 AAAAAATAGA
* *
1279689 AAAAAACAAA
1 AAAAAATAGA
* *
1279699 AAAAAACAAA
1 AAAAAATAGA
*
1279709 AAAAAACAAGA
1 AAAAAA-TAGA
1279720 AAAAAATAGCAA
1 AAAAAATAG--A
1279732 AAAAAATAGA
1 AAAAAATAGA
1279742 AAA
1 AAA
1279745 GGGGTCCAGA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
10 30 0.62
11 8 0.17
12 10 0.21
ACGTcount: A:0.83, C:0.08, G:0.05, T:0.05
Consensus pattern (10 bp):
AAAAAATAGA
Found at i:1280990 original size:28 final size:28
Alignment explanation
Indices: 1280953--1282203 Score: 1433
Period size: 28 Copynumber: 43.6 Consensus size: 28
1280943 GAATGTTCAT
* * *
1280953 CTTTTCAAAGCCCACAATTTAGTGGCAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
1280981 CTTTTCAAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
1281009 CCTTTCAAAGCCCACAAGTTAGGGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
1281038 CTTTT-AAAGCCCACAAGTCAGTGGCAAC
1 CTTTTCAAAGCCCACAAGTCAGTGGC-AC
* **
1281066 C-TTTCAAAGCTCACAAGTCAGTGATAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
1281093 CCTTTCAAAGCCTACAAGTCAGTGGTAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
1281121 TCTTTTCAAAGCCCACGAGTCAGTGGCACC
1 -CTTTTCAAAGCCCACAAGTCAGTGGCA-C
*
1281151 CTTTTCAAAACCCACAAGTCAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
1281180 CTTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
1281209 C-TTTCAAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
1281236 CCTTTCAAAGCCCACGCAAGTCAGTGGCAC
1 CTTTTCAAAGCCCA--CAAGTCAGTGGCAC
* *
1281266 CCTTTCAAAGCCCACGAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
1281294 TCTTTTCAAAGTCCACAAGTCAGTGGCAC
1 -CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
1281323 CCTTTCAAAGCCCACAAGTCAGTAGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
1281352 CTTTTCAAAGCCCACAAGGT-AGTGGCATC
1 CTTTTCAAAGCCCACAA-GTCAGTGGCA-C
* *
1281381 C-ATTCAAAGCCCACAAGTCAGTGACAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
1281408 CTTTTCAAAGCCTACAAGTCAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* * *
1281437 CTTTTCAAAGCCCAAAACTTAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
1281466 C-TTTCAAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
1281493 CCTTTCAAAGCCCACAAGTCAGTCGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
1281521 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
1281549 CCTTTCGAAGCCCACGCAAGTTAGTGGCGC
1 CTTTTCAAAGCCCA--CAAGTCAGTGGCAC
* *
1281579 CCTTTCAAAGCCCACAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
1281607 TCTTTTCAAAGCCCACAAGTCAGTGCCAC
1 -CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
1281636 C-CTTCAAAGCCCACAAGTTAGTAGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
1281663 TATTTTTAAAGCCCACAAGTTAGTGGCAC
1 -CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
1281692 CCTTTCAAAGCTCACAAGTTAATGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
1281720 CGTTTCAAAGCCCACAAGTTAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
*
1281749 C-TTTCAAAGCCCATAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
1281776 CTTTTCAAAGCCCACAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
1281804 TCTTTTCAAAGCCCACAAGTCAATGGCAC
1 -CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
1281833 CTTTTCAAAGCCCATAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
1281861 CCTTACAAAGCCAACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
1281889 TCTTTTCAAAGCCCACAAGTCAGTGGCATC
1 -CTTTTCAAAGCCCACAAGTCAGTGGCA-C
*
1281919 C-TTTCAAAGCCCATAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
1281946 CCTTTCAAAGCCCATAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
1281974 CCTTTCAAAGCCCACAAG-CTAGTGGTAAC
1 CTTTTCAAAGCCCACAAGTC-AGTGG-CAC
*
1282003 TCTTTTCAAAGCCCACACGAGTCGGTGGCAAC
1 -CTTTTCAAAGCCCACA--AGTCAGTGGC-AC
* *
1282035 TCTTTTCAAAGCCCACATGTCAGTGGTAC
1 -CTTTTCAAAGCCCACAAGTCAGTGGCAC
*
1282064 TCTTTTCAAAGCCCACACGAGTCGGTGGCAAC
1 -CTTTTCAAAGCCCACA--AGTCAGTGGC-AC
*
1282096 TCTTTTCAAAGCCCACAAGTTAGTGGCAC
1 -CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
1282125 TCTTTTCAAAGCCCACAAGCCAGTGGTAAC
1 -CTTTTCAAAGCCCACAAGTCAGTGG-CAC
* *
1282155 TCTTTACAAAGCCCACACAAGTCGGTGGCAAC
1 -CTTTTCAAAG-CC-CACAAGTCAGTGGC-AC
1282187 TCTTTTCAAAGCCCACA
1 -CTTTTCAAAGCCCACA
1282204 CAAGTTAATA
Statistics
Matches: 1071, Mismatches: 111, Indels: 80
0.85 0.09 0.06
Matches are distributed among these distances:
27 41 0.04
28 540 0.50
29 308 0.29
30 103 0.10
31 11 0.01
32 67 0.06
33 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:1281396 original size:85 final size:84
Alignment explanation
Indices: 1280950--1282203 Score: 1445
Period size: 85 Copynumber: 14.6 Consensus size: 84
1280940 CTAGAATGTT
* * * * *
1280950 CATCTTTTCAAAGCCCACAATTTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
1 CATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
* *
1281015 AAAGCCCACAAGTTAGGGG
66 AAAGCCCACAAGTCAGTGG
* * * * **
1281034 CACCCTTTTAAAGCCCACAAGTCAGTGGCAACCTTTCAAAGCTCACAAGTCAGTGATACCCTTTC
1 CATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
*
1281099 AAAGCCTACAAGTCAGTGG
66 AAAGCCCACAAGTCAGTGG
* * * *
1281118 TACTCTTTTCAAAGCCCACGAGTCAGTGGCACCCTTTTCAAAACCCACAAGTCAGTGGCACCCTT
1 CA-TCCTTTCAAAGCCCACAAGTCAGTGGCACCC-TTTCAAAGCCCACAAGTCAGTGGCACCC-T
1281183 TTCAAAGCCCACAAGTCAGTGG
63 TTCAAAGCCCACAAGTCAGTGG
1281205 CATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACGCAAGTCAGTGGCACCCTT
1 CATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTT
*
1281270 TCAAAGCCCACGAGTCAGTGG
64 TCAAAGCCCACAAGTCAGTGG
* * *
1281291 CACTCTTTTCAAAGTCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTAGCACCCTTT
1 CA-TCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC-TT
1281356 TCAAAGCCCACAAGGT-AGTGG
64 TCAAAGCCCACAA-GTCAGTGG
* * * *
1281377 CATCCATTCAAAGCCCACAAGTCAGTGACACCTTTTCAAAGCCTACAAGTCAGTGGCACCCTTTT
1 CATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC-TTT
* * *
1281442 CAAAGCCCAAAACTTAGTGG
65 CAAAGCCCACAAGTCAGTGG
*
1281462 CATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTCGCACCCTTTC
1 CATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
1281527 AAAGCCCACAAGTCAGTGG
66 AAAGCCCACAAGTCAGTGG
* * * * * *
1281546 CACCCTTTCGAAGCCCACGCAAGTTAGTGGCGCCCTTTCAAAGCCCACAAGTTAGTGGCACTCTT
1 CATCCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
*
1281611 TTCAAAGCCCACAAGTCAGTGC
63 TTCAAAGCCCACAAGTCAGTGG
* * * ** * *
1281633 CA-CCCTTCAAAGCCCACAAGTTAGTAGCACTATTTTTAAAGCCCACAAGTTAGTGGCACCCTTT
1 CATCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTT
* * *
1281697 CAAAGCTCACAAGTTAATGG
65 CAAAGCCCACAAGTCAGTGG
* * * *
1281717 CA-CCGTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGGCACCTTTT
1 CATCC-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTT
*
1281781 CAAAGCCCACAAGTTAGTGG
65 CAAAGCCCACAAGTCAGTGG
* * * * * *
1281801 CACTCTTTTCAAAGCCCACAAGTCAATGGCACCTTTTCAAAGCCCATAAGTTAGTGGCACCCTTA
1 CA-TCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTT
*
1281866 CAAAGCCAACAAGTCAGTGG
65 CAAAGCCCACAAGTCAGTGG
* * *
1281886 CACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGGCACCCTTT
1 CA-TCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTT
*
1281951 CAAAGCCCATAAGTCAGTGG
65 CAAAGCCCACAAGTCAGTGG
* * * *
1281971 CACCCTTTCAAAGCCCACAAG-CTAGTGGTAACTCTTTTCAAAGCCCACACGAGTCGGTGGCAAC
1 CATCCTTTCAAAGCCCACAAGTC-AGTGG-CAC-CCTTTCAAAGCCCACA--AGTCAGTGGC-AC
* *
1282035 TCTTTTCAAAGCCCACATGTCAGTGG
60 -CCTTTCAAAGCCCACAAGTCAGTGG
* * * * *
1282061 TACTCTTTTCAAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGCACT
1 CA-TCCTTTCAAAGCCCACA--AGTCAGTGGC-AC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-
* *
1282126 CTTTTCAAAGCCCACAAGCCAGTGG
60 CCTTTCAAAGCCCACAAGTCAGTGG
* * * *
1282151 TAACTCTTTACAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCACA
1 CATC-CTTT-CAAAG-CC-CACAAGTCAGTGGC-AC-CCTTTCAAAGCCCACA
1282204 CAAGTTAATA
Statistics
Matches: 1019, Mismatches: 119, Indels: 57
0.85 0.10 0.05
Matches are distributed among these distances:
83 1 0.00
84 213 0.21
85 379 0.37
86 163 0.16
87 107 0.11
88 9 0.01
89 3 0.00
90 54 0.05
91 58 0.06
92 2 0.00
93 29 0.03
94 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (84 bp):
CATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
AAAGCCCACAAGTCAGTGG
Found at i:1282631 original size:21 final size:21
Alignment explanation
Indices: 1282598--1282638 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1282588 CTAAGTAAAA
1282598 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
1282619 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
1282639 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:1282706 original size:20 final size:19
Alignment explanation
Indices: 1282678--1282748 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
1282668 ACCCTGAAAA
*
1282678 GTATTGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
1282698 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
1282717 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
1282738 GTATCGATACA
1 GTATCGATACA
1282749 GGACATTGGC
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 4 0.10
20 34 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:1282796 original size:53 final size:53
Alignment explanation
Indices: 1282718--1282854 Score: 213
Period size: 53 Copynumber: 2.6 Consensus size: 53
1282708 AGATTGCATA
*
1282718 GTATCGATACACACAAATATGTATCGATACAGGACATTGGC-GATAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACACTGGCAG-TAGCCAAATTT
* *
1282772 GTATTGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
*
1282825 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
1282855 TTGGAAGTAG
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
53 63 0.82
54 14 0.18
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
Found at i:1282897 original size:10 final size:10
Alignment explanation
Indices: 1282878--1282908 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1282868 AATCTCATTT
1282878 TCACTGTTCA
1 TCACTGTTCA
*
1282888 TCACTATTCA
1 TCACTGTTCA
1282898 TCACTGTTCA
1 TCACTGTTCA
1282908 T
1 T
1282909 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:1282983 original size:48 final size:47
Alignment explanation
Indices: 1282919--1283016 Score: 160
Period size: 48 Copynumber: 2.1 Consensus size: 47
1282909 GTATCGATAC
*
1282919 ATCACTTTCATGTATCGTTAAAAATCACTATTCATCACTGTTCACGT
1 ATCACTTTCATGTATCGTTAAAAATCACTATTCATCACTCTTCACGT
* *
1282966 ATCACTATTCATGTATCGTTAAAAATCACTGTTCATCACTCTTCATGT
1 ATCACT-TTCATGTATCGTTAAAAATCACTATTCATCACTCTTCACGT
1283014 ATC
1 ATC
1283017 GATACATCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 6 0.13
48 41 0.87
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (47 bp):
ATCACTTTCATGTATCGTTAAAAATCACTATTCATCACTCTTCACGT
Found at i:1282993 original size:24 final size:24
Alignment explanation
Indices: 1282897--1283001 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
1282887 ATCACTATTC
* * *
1282897 ATCACTGTTCATGTATCG--ATAC
1 ATCACTATTCATGTATCGTTAAAA
1282919 ATCACT-TTCATGTATCGTTAAAA
1 ATCACTATTCATGTATCGTTAAAA
* ***
1282942 ATCACTATTCAT-CA-CTGTTCACGT
1 ATCACTATTCATGTATC-GTT-AAAA
1282966 ATCACTATTCATGTATCGTTAAAA
1 ATCACTATTCATGTATCGTTAAAA
*
1282990 ATCACTGTTCAT
1 ATCACTATTCAT
1283002 CACTCTTCAT
Statistics
Matches: 65, Mismatches: 11, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
21 11 0.17
22 7 0.11
23 12 0.18
24 30 0.46
25 4 0.06
26 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (24 bp):
ATCACTATTCATGTATCGTTAAAA
Found at i:1286486 original size:13 final size:13
Alignment explanation
Indices: 1286468--1286492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1286458 TTTTCCAGAT
1286468 TGTATCGATACAA
1 TGTATCGATACAA
1286481 TGTATCGATACA
1 TGTATCGATACA
1286493 TTACTTCAGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1287724 original size:243 final size:242
Alignment explanation
Indices: 1287296--1287782 Score: 947
Period size: 243 Copynumber: 2.0 Consensus size: 242
1287286 TGACAATGTA
1287296 TTAAGGGGGAGAGTTGGTAAACATTTGTATTAAGGGGGAGAGTTTGCATAAACTTTTGGTATTAG
1 TTAAGGGGGAGAGTTGGTAAACATTTGTATTAAGGGGGAGAGTTTGCATAAACTTTTGGTATTAG
1287361 TTGCATGAATAACAAAAAGGGAGAGAATAGATTTGGCCTAATAAAAAAGGGGAGAAAAGAGATGT
66 TTGCATGAATAACAAAAAGGGAGAGAATAGATTTGGCCTAATAAAAAAGGGGAGAAAAGAGATGT
1287426 TTCACAAAGAGGGAGAATTATAGAGAAATAGAATTGATTATTTGTTATAAAGGAAGAAACTGAAA
131 TTCACAAAGAGGGAGAATTATAGAGAAATAGAATTGATTATTTGTTATAAAGGAAGAAACTGAAA
1287491 ATATTGAAGAATATTGGTATAAAATTTCTTTATAACAAAATGAGAGAT
196 ATATTGAAGAATATTGGTAT-AAATTTCTTTATAACAAAATGAGAGAT
1287539 TTAAGGGGGAGAGTTGGTAAACATTTGTATTAAGGGGGAGAGTTTGCATAAACTTTTGGTATTAG
1 TTAAGGGGGAGAGTTGGTAAACATTTGTATTAAGGGGGAGAGTTTGCATAAACTTTTGGTATTAG
*
1287604 TTGCATGAATAACAAAAAGGGAGAGAATAGATTTGGCCTAATAAAAAGGGGGAGAAAAGAGATGT
66 TTGCATGAATAACAAAAAGGGAGAGAATAGATTTGGCCTAATAAAAAAGGGGAGAAAAGAGATGT
*
1287669 TTCACAAAGGGGGAGAATTATAGAGAAATAGAATTGATTATTTGTTATAAAGGAAGAAACTGAAA
131 TTCACAAAGAGGGAGAATTATAGAGAAATAGAATTGATTATTTGTTATAAAGGAAGAAACTGAAA
1287734 ATATTGAAGAATATTGGTATAAATTTCTTTATAACAAAATGAGAGAT
196 ATATTGAAGAATATTGGTATAAATTTCTTTATAACAAAATGAGAGAT
1287781 TT
1 TT
1287783 TTGCATAAAA
Statistics
Matches: 242, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
242 29 0.12
243 213 0.88
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (242 bp):
TTAAGGGGGAGAGTTGGTAAACATTTGTATTAAGGGGGAGAGTTTGCATAAACTTTTGGTATTAG
TTGCATGAATAACAAAAAGGGAGAGAATAGATTTGGCCTAATAAAAAAGGGGAGAAAAGAGATGT
TTCACAAAGAGGGAGAATTATAGAGAAATAGAATTGATTATTTGTTATAAAGGAAGAAACTGAAA
ATATTGAAGAATATTGGTATAAATTTCTTTATAACAAAATGAGAGAT
Found at i:1288361 original size:21 final size:21
Alignment explanation
Indices: 1288328--1288368 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1288318 CTAAGTAAAA
1288328 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
1288349 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
1288369 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:1288433 original size:20 final size:19
Alignment explanation
Indices: 1288408--1288478 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
1288398 ACCCTGAAAA
1288408 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
1288428 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
1288447 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
1288468 GTATCGATACA
1 GTATCGATACA
1288479 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:1288531 original size:53 final size:53
Alignment explanation
Indices: 1288448--1288584 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
1288438 AGATTGCATA
*
1288448 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
*
1288502 GTATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
*
1288555 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
1288585 TTGGTAGTAG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 66 0.82
54 14 0.17
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
Found at i:1288624 original size:10 final size:10
Alignment explanation
Indices: 1288609--1288639 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1288599 ATCTCATTTT
1288609 TCACTATTCA
1 TCACTATTCA
1288619 TCACTATTCA
1 TCACTATTCA
*
1288629 TCACTGTTCA
1 TCACTATTCA
1288639 T
1 T
1288640 TTTTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.03, T:0.42
Consensus pattern (10 bp):
TCACTATTCA
Found at i:1289064 original size:20 final size:20
Alignment explanation
Indices: 1289039--1289110 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
1289029 TACCCAGACA
1289039 TATCGATACATTTTTCAATG
1 TATCGATACATTTTTCAATG
* * *
1289059 TATCGATACATGTATGAATG
1 TATCGATACATTTTTCAATG
* *
1289079 TATCAATACATTCTTCAATG
1 TATCGATACATTTTTCAATG
1289099 TATCGATACATT
1 TATCGATACATT
1289111 CTGTCTTTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.40
Consensus pattern (20 bp):
TATCGATACATTTTTCAATG
Found at i:1294495 original size:12 final size:12
Alignment explanation
Indices: 1294478--1294521 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
1294468 AAAAAATCAC
1294478 TATAATAATAAT
1 TATAATAATAAT
*
1294490 TATAATAATATT
1 TATAATAATAAT
* * *
1294502 TTTTATATTAAT
1 TATAATAATAAT
1294514 TATAATAA
1 TATAATAA
1294522 ATATAACACT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATAATAATAAT
Found at i:1298030 original size:2 final size:2
Alignment explanation
Indices: 1298023--1298054 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1298013 TTCAAAGGGT
1298023 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1298055 GAGAGAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1298059 original size:2 final size:2
Alignment explanation
Indices: 1298054--1298087 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1298044 ATATATATAT
1298054 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1298088 GGGAAAGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1298656 original size:21 final size:21
Alignment explanation
Indices: 1298606--1298645 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1298596 ATTTTATTAA
*
1298606 AAAGAAAAAGAAAAATTGACC
1 AAAGAAAAAGAAAAATAGACC
*
1298627 AAAAAAAAAGAAAAATAGA
1 AAAGAAAAAGAAAAATAGA
1298646 TAAAGACAAA
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:0.75, C:0.05, G:0.12, T:0.07
Consensus pattern (21 bp):
AAAGAAAAAGAAAAATAGACC
Found at i:1299113 original size:23 final size:22
Alignment explanation
Indices: 1299070--1299113 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1299060 TTGAATATTT
*
1299070 AATTATATTTATATATTAAAAG
1 AATTATATTTATATATAAAAAG
*
1299092 AATTATATTTTTAATATAAAAA
1 AATTATATTTAT-ATATAAAAA
1299114 TTCAATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
AATTATATTTATATATAAAAAG
Found at i:1300122 original size:20 final size:21
Alignment explanation
Indices: 1300076--1300123 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
1300066 ACTATAAACT
*
1300076 ATAAATATTGTTAATTTAGTA
1 ATAAATTTTGTTAATTTAGTA
* **
1300097 ACAAATTTTG-TAATTTTTTA
1 ATAAATTTTGTTAATTTAGTA
1300117 ATAAATT
1 ATAAATT
1300124 GAGAAGAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (21 bp):
ATAAATTTTGTTAATTTAGTA
Found at i:1300213 original size:3 final size:3
Alignment explanation
Indices: 1300205--1300239 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1300195 ATAGTTATAG
1300205 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1300240 ATGATTTGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1300460 original size:10 final size:10
Alignment explanation
Indices: 1300427--1300469 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
1300417 ACTATATGTA
*
1300427 ATTTATCTAT
1 ATTTATATAT
1300437 AATTTATAATAT
1 -ATTTAT-ATAT
1300449 ATTTATATAT
1 ATTTATATAT
*
1300459 ATATATATAT
1 ATTTATATAT
1300469 A
1 A
1300470 AAAGCATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 14 0.48
11 12 0.41
12 3 0.10
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTTATATAT
Found at i:1301314 original size:21 final size:21
Alignment explanation
Indices: 1301273--1301314 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1301263 TTCATTAATT
* *
1301273 TTAATTATTTATAAAATATAA
1 TTAAATATTTATAAAAAATAA
1301294 TTAAATATTTA-AAATAAATAA
1 TTAAATATTTATAAA-AAATAA
1301315 AGTTACAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAATATTTATAAAAAATAA
Found at i:1302218 original size:2 final size:2
Alignment explanation
Indices: 1302211--1302239 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1302201 ATCTATTAAT
1302211 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1302240 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1302244 original size:2 final size:2
Alignment explanation
Indices: 1302239--1302267 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1302229 TCTCTCTCTC
1302239 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1302268 GCATGGCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1303128 original size:18 final size:18
Alignment explanation
Indices: 1303105--1303156 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
1303095 TTTTTTAAAA
1303105 TTATTATTATAAATATTT
1 TTATTATTATAAATATTT
1303123 TTATTATTA-ATAATATTT
1 TTATTATTATA-AATATTT
* *
1303141 ATATAATTAATAAATA
1 TTATTATT-ATAAATA
1303157 AGAAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 1 0.03
18 22 0.76
19 5 0.17
20 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATTATTATAAATATTT
Found at i:1304213 original size:15 final size:15
Alignment explanation
Indices: 1304172--1304216 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1304162 AACGAGTCAA
*
1304172 AATTTATATAACTTTT
1 AATTT-TATAAGTTTT
*
1304188 TATTTTCATAAGTTTT
1 AATTTT-ATAAGTTTT
1304204 AATTTTATAAGTT
1 AATTTTATAAGTT
1304217 AAAAAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (15 bp):
AATTTTATAAGTTTT
Found at i:1308549 original size:14 final size:16
Alignment explanation
Indices: 1308524--1308563 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1308514 TAATTATATT
1308524 TTTTTAATATATAAGA
1 TTTTTAATATATAAGA
1308540 TTTTTAATATATAAGA
1 TTTTTAATATATAAGA
1308556 TTTTTAAT
1 TTTTTAAT
1308564 TCTATACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (16 bp):
TTTTTAATATATAAGA
Found at i:1308876 original size:25 final size:24
Alignment explanation
Indices: 1308835--1308881 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1308825 GGGTGAATAA
1308835 ATATTTTTTAAAAAAGTTATTATAT
1 ATATTTTTTAAAAAAG-TATTATAT
**
1308860 ATATTTTTTAAGTAAGTATTAT
1 ATATTTTTTAAAAAAGTATTAT
1308882 TTTTAGTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (24 bp):
ATATTTTTTAAAAAAGTATTATAT
Found at i:1308893 original size:16 final size:18
Alignment explanation
Indices: 1308864--1308905 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1308854 TTATATATAT
1308864 TTTTTAAGTAAGT-ATTA
1 TTTTTAAGTAAGTAATTA
*
1308881 TTTTT-AGTGAGTAATTA
1 TTTTTAAGTAAGTAATTA
1308898 TTTATTAA
1 TTT-TTAA
1308906 AAATTAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.29
17 12 0.57
18 2 0.10
19 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (18 bp):
TTTTTAAGTAAGTAATTA
Found at i:1313340 original size:23 final size:23
Alignment explanation
Indices: 1313313--1313360 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1313303 AGTAAAAAGT
* *
1313313 AATAATTATTTTTAAAATATAAA
1 AATAATTATTTATAAAATAGAAA
1313336 AATAATTATTTATAAAATAGAAA
1 AATAATTATTTATAAAATAGAAA
1313359 AA
1 AA
1313361 GCTTGCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
AATAATTATTTATAAAATAGAAA
Found at i:1315509 original size:28 final size:29
Alignment explanation
Indices: 1315457--1315514 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
1315447 TTAAACCTTT
** * *
1315457 TAAAATAATTTTAATTTATTTATTTTAAA
1 TAAAATAATTTTAATAAATTCATTTCAAA
1315486 TAAAATAA-TTTAATAAATTCATTTCAAA
1 TAAAATAATTTTAATAAATTCATTTCAAA
1315514 T
1 T
1315515 TTAATATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (29 bp):
TAAAATAATTTTAATAAATTCATTTCAAA
Found at i:1315593 original size:2 final size:2
Alignment explanation
Indices: 1315586--1315618 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1315576 TGATTAAAAC
1315586 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 A
1315619 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1315623 original size:2 final size:2
Alignment explanation
Indices: 1315618--1315678 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1315608 ATATATATAT
1315618 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1315660 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
1315679 AGAAAATATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1316034 original size:57 final size:57
Alignment explanation
Indices: 1315941--1316048 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 57
1315931 AATAAGAAAC
* * * *
1315941 ATAACACATTCATCTCAAAGTTAATATATTTGATTAAAGATAAGTTTAAAATATGTT
1 ATAACACAATCATATCAAAATTAATATATTTAATTAAAGATAAGTTTAAAATATGTT
* *
1315998 ATAATACAATCATATCAAAATTAATATTTTTAATTAAAGATAAGTTTAAAA
1 ATAACACAATCATATCAAAATTAATATATTTAATTAAAGATAAGTTTAAAA
1316049 CATTTAGCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.38
Consensus pattern (57 bp):
ATAACACAATCATATCAAAATTAATATATTTAATTAAAGATAAGTTTAAAATATGTT
Found at i:1317657 original size:82 final size:82
Alignment explanation
Indices: 1317478--1317650 Score: 319
Period size: 82 Copynumber: 2.1 Consensus size: 82
1317468 TCCAGTCTGG
*
1317478 ATTTATCATGTAACTTTATACCTTGTTATATTATATTTATATATGATTTACTTAGTAAATAAAAA
1 ATTTATCATGCAACTTTATACCTTGTTATATTATATTTATATATGATTTACTTAGTAAATAAAAA
1317543 CCTTAGGGGATTAATAT
66 CCTTAGGGGATTAATAT
1317560 ATTTATCATGCAACTTTATACCTTGTTATATTATATTTATATATGATTTACTTAGTAAATAAAAA
1 ATTTATCATGCAACTTTATACCTTGTTATATTATATTTATATATGATTTACTTAGTAAATAAAAA
1317625 CCTTAGGGGATTAATAT
66 CCTTAGGGGATTAATAT
* *
1317642 GTTTTTCAT
1 ATTTATCAT
1317651 CAAACTTGGA
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 88 1.00
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.46
Consensus pattern (82 bp):
ATTTATCATGCAACTTTATACCTTGTTATATTATATTTATATATGATTTACTTAGTAAATAAAAA
CCTTAGGGGATTAATAT
Found at i:1317675 original size:82 final size:82
Alignment explanation
Indices: 1317478--1317676 Score: 285
Period size: 82 Copynumber: 2.4 Consensus size: 82
1317468 TCCAGTCTGG
* * *
1317478 ATTTATCATGTAACTTTATACCTTGTTATATTATATTTATATATGATTTACTTAGTAAATAAAAA
1 ATTTATCATGCAACTTGATACCTTGTTAAATTATATTTATATATGATTTACTTAGTAAATAAAAA
1317543 CCTTAGGGGATTAATAT
66 CCTTAGGGGATTAATAT
* *
1317560 ATTTATCATGCAACTTTATACCTTGTTATATTATATTTATATATGATTTACTTAGTAAATAAAAA
1 ATTTATCATGCAACTTGATACCTTGTTAAATTATATTTATATATGATTTACTTAGTAAATAAAAA
1317625 CCTTAGGGGATTAATAT
66 CCTTAGGGGATTAATAT
* * * *
1317642 GTTTTTCAT-CAAACTTGGATA-TTTTTTAAATTATA
1 ATTTATCATGC-AACTT-GATACCTTGTTAAATTATA
1317677 AAAATAAATG
Statistics
Matches: 108, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
81 1 0.01
82 104 0.96
83 3 0.03
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.46
Consensus pattern (82 bp):
ATTTATCATGCAACTTGATACCTTGTTAAATTATATTTATATATGATTTACTTAGTAAATAAAAA
CCTTAGGGGATTAATAT
Found at i:1318032 original size:7 final size:7
Alignment explanation
Indices: 1318020--1318044 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1318010 ATAAACAAAG
1318020 TAAATAT
1 TAAATAT
1318027 TAAATAT
1 TAAATAT
1318034 TAAATAT
1 TAAATAT
1318041 TAAA
1 TAAA
1318045 AAATTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAATAT
Found at i:1319405 original size:32 final size:28
Alignment explanation
Indices: 1319336--1319407 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
1319326 TTAAATATTT
1319336 AATTTAAAATTAATTAAAAATAAATAAA
1 AATTTAAAATTAATTAAAAATAAATAAA
* *
1319364 AAATT-AAATTATATTAAATATGATAATATAA
1 AATTTAAAATTA-ATTAAAAAT-A-AATA-AA
*
1319395 ATTTTAAAATTAA
1 AATTTAAAATTAA
1319408 GCATATATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
27 6 0.17
28 12 0.34
29 1 0.03
30 4 0.11
31 6 0.17
32 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (28 bp):
AATTTAAAATTAATTAAAAATAAATAAA
Found at i:1320617 original size:17 final size:17
Alignment explanation
Indices: 1320576--1320634 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
1320566 AATTAATTTG
* *
1320576 ATAATAAAAAATTATTAAA
1 ATAATATAAAA-TA-TAAT
1320595 ATAATATAAAATATAAT
1 ATAATATAAAATATAAT
1320612 ATAATATAAAA-ATAATT
1 ATAATATAAAATATAA-T
1320629 ATAATA
1 ATAATA
1320635 AGATGTGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.11
17 21 0.57
18 2 0.05
19 10 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATATAAAATATAAT
Found at i:1325321 original size:8 final size:8
Alignment explanation
Indices: 1325310--1325398 Score: 50
Period size: 9 Copynumber: 11.5 Consensus size: 8
1325300 ACATATATTT
1325310 ATATTAAA
1 ATATTAAA
1325318 ATA-T-AA
1 ATATTAAA
1325324 AT-TTAAA
1 ATATTAAA
1325331 A-ATTATAA
1 ATATTA-AA
*
1325339 ATATT-TA
1 ATATTAAA
1325346 ATATTTAAA
1 ATA-TTAAA
*
1325355 ACTTTTAAA
1 A-TATTAAA
1325364 A-ATT-AA
1 ATATTAAA
*
1325370 ATA-AATAA
1 ATATTA-AA
1325378 ATATTAAA
1 ATATTAAA
1325386 ATATTTAAA
1 ATA-TTAAA
1325395 ATAT
1 ATAT
1325399 ATAGTAACTA
Statistics
Matches: 62, Mismatches: 6, Indels: 26
0.66 0.06 0.28
Matches are distributed among these distances:
6 8 0.13
7 14 0.23
8 19 0.31
9 20 0.32
10 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATTAAA
Done.