Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 29
Found at i:1933599 original size:12 final size:12
Alignment explanation
Indices: 1933582--1933607 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1933572 TTACGTACTG
1933582 AAAATACTCAAT
1 AAAATACTCAAT
1933594 AAAATACTCAAT
1 AAAATACTCAAT
1933606 AA
1 AA
1933608 GGATCCTACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATACTCAAT
Found at i:1934474 original size:131 final size:131
Alignment explanation
Indices: 1934240--1934504 Score: 530
Period size: 131 Copynumber: 2.0 Consensus size: 131
1934230 GGAGACGGTG
1934240 GTGACCTCGGGGTCTTTCCGAGATTAAGAACTATGGATTCCAATAATTGTTTCCCAATTGTTGCT
1 GTGACCTCGGGGTCTTTCCGAGATTAAGAACTATGGATTCCAATAATTGTTTCCCAATTGTTGCT
1934305 TGATGTCTCGATGGTGCTGGCTTTGGAGACGGCGGTGATTTTGGGGTCTTTCCGAAATTGAAAAC
66 TGATGTCTCGATGGTGCTGGCTTTGGAGACGGCGGTGATTTTGGGGTCTTTCCGAAATTGAAAAC
1934370 C
131 C
1934371 GTGACCTCGGGGTCTTTCCGAGATTAAGAACTATGGATTCCAATAATTGTTTCCCAATTGTTGCT
1 GTGACCTCGGGGTCTTTCCGAGATTAAGAACTATGGATTCCAATAATTGTTTCCCAATTGTTGCT
1934436 TGATGTCTCGATGGTGCTGGCTTTGGAGACGGCGGTGATTTTGGGGTCTTTCCGAAATTGAAAAC
66 TGATGTCTCGATGGTGCTGGCTTTGGAGACGGCGGTGATTTTGGGGTCTTTCCGAAATTGAAAAC
1934501 C
131 C
1934502 GTG
1 GTG
1934505 GAACCCCATG
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
131 134 1.00
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (131 bp):
GTGACCTCGGGGTCTTTCCGAGATTAAGAACTATGGATTCCAATAATTGTTTCCCAATTGTTGCT
TGATGTCTCGATGGTGCTGGCTTTGGAGACGGCGGTGATTTTGGGGTCTTTCCGAAATTGAAAAC
C
Found at i:1938943 original size:15 final size:15
Alignment explanation
Indices: 1938925--1938956 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1938915 CTACTAATAG
*
1938925 TGACAAAATTAATTT
1 TGACAAAATTAAATT
1938940 TGACAAAATTAAATT
1 TGACAAAATTAAATT
1938955 TG
1 TG
1938957 TCACAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (15 bp):
TGACAAAATTAAATT
Found at i:1945439 original size:18 final size:17
Alignment explanation
Indices: 1945413--1945463 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
1945403 TAATAAAAAA
1945413 TAAACAAATTAAATTAAT
1 TAAA-AAATTAAATTAAT
* *
1945431 TAATAAAATGAAAATAAT
1 TAA-AAAATTAAATTAAT
1945449 TAAAAAATTACAATT
1 TAAAAAATTA-AATT
1945464 GTTAGCAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 6 0.22
18 20 0.74
19 1 0.04
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (17 bp):
TAAAAAATTAAATTAAT
Found at i:1945498 original size:16 final size:15
Alignment explanation
Indices: 1945474--1945503 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1945464 GTTAGCAAAT
1945474 AAAAAAATTAAATAC
1 AAAAAAATTAAATAC
1945489 AAAAATAATTAAATA
1 AAAAA-AATTAAATA
1945504 TATGAATCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAAAATTAAATAC
Found at i:1947559 original size:18 final size:18
Alignment explanation
Indices: 1947500--1947560 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
1947490 ATATTATAGA
*
1947500 AATTAAAATATAAACTAAT
1 AATTAAAATATTAAC-AAT
* * *
1947519 -ACTAAAAAATTTA-AAT
1 AATTAAAATATTAACAAT
*
1947535 AAATAAAATATTAACAAT
1 AATTAAAATATTAACAAT
1947553 AATTAAAA
1 AATTAAAA
1947561 GTAAAATATA
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
16 3 0.09
17 10 0.31
18 19 0.59
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (18 bp):
AATTAAAATATTAACAAT
Found at i:1948053 original size:16 final size:16
Alignment explanation
Indices: 1948034--1948066 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1948024 TAATTTATCA
1948034 TTTGTTT-TTATTATTT
1 TTTGTTTATT-TTATTT
1948050 TTTGTTTATTTTATTT
1 TTTGTTTATTTTATTT
1948066 T
1 T
1948067 AGAACAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTGTTTATTTTATTT
Found at i:1949603 original size:13 final size:14
Alignment explanation
Indices: 1949585--1949613 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1949575 TGATACGTTA
1949585 ATAATA-TAAAATT
1 ATAATATTAAAATT
1949598 ATAATATTAAAATT
1 ATAATATTAAAATT
1949612 AT
1 AT
1949614 TGTTAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATATTAAAATT
Found at i:1951462 original size:18 final size:18
Alignment explanation
Indices: 1951439--1951494 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
1951429 AGGCATTTTA
1951439 TCCTCTGGCTGTGCTTGT
1 TCCTCTGGCTGTGCTTGT
*
1951457 TCCTCT-GCTTATGCTTGT
1 TCCTCTGGC-TGTGCTTGT
*
1951475 TCCTC-GTGCTGTTCTTGT
1 TCCTCTG-GCTGTGCTTGT
1951493 TC
1 TC
1951495 ATCGTCGGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 2 0.06
18 28 0.88
19 2 0.06
ACGTcount: A:0.02, C:0.29, G:0.21, T:0.48
Consensus pattern (18 bp):
TCCTCTGGCTGTGCTTGT
Found at i:1953116 original size:22 final size:22
Alignment explanation
Indices: 1953060--1953119 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 22
1953050 GGGGTATTGA
*
1953060 TTCCCCTAC-AGGGGGAATCGG
1 TTCCCCTTCAAGGGGGAATCGG
1953081 TTCCCCTTCAAAGGGGGAATCGG
1 TTCCCCTTC-AAGGGGGAATCGG
1953104 TTCCCCTTCAAGGGGG
1 TTCCCCTTCAAGGGGG
1953120 GTATCGATTC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
21 8 0.22
22 7 0.19
23 21 0.58
ACGTcount: A:0.18, C:0.28, G:0.32, T:0.22
Consensus pattern (22 bp):
TTCCCCTTCAAGGGGGAATCGG
Found at i:1953132 original size:22 final size:23
Alignment explanation
Indices: 1953069--1953131 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1953059 ATTCCCCTAC
1953069 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
1953092 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
* * *
1953115 GGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
1953132 TCTGCACTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.22
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:1956928 original size:22 final size:21
Alignment explanation
Indices: 1956886--1956925 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1956876 GAGTTTGTTT
*
1956886 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1956907 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1956926 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1960951 original size:12 final size:12
Alignment explanation
Indices: 1960934--1960963 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1960924 ATATACTTAG
1960934 AAAATCTTTTGT
1 AAAATCTTTTGT
1960946 AAAATCTTTTGT
1 AAAATCTTTTGT
1960958 AAAATC
1 AAAATC
1960964 ATAAAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (12 bp):
AAAATCTTTTGT
Found at i:1966354 original size:18 final size:18
Alignment explanation
Indices: 1966328--1966362 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1966318 AGTTCTTGAA
*
1966328 AAATCGATATCAATTATT
1 AAATAGATATCAATTATT
1966346 AAATAGATATCAATTAT
1 AAATAGATATCAATTAT
1966363 ATTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (18 bp):
AAATAGATATCAATTATT
Found at i:1968456 original size:64 final size:65
Alignment explanation
Indices: 1968386--1968510 Score: 182
Period size: 64 Copynumber: 1.9 Consensus size: 65
1968376 TGCACTAAGA
* *
1968386 GTGCATCGATACATCAAGTGCATTCGATG-TTTCA-AAATAGCCAGAGTGCATCGATGCATGGCA
1 GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAA-AGCCACAGTGCATCGATGCATGGCA
1968449 G
65 G
* * *
1968450 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATG
1 GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATG
1968511 AAATGCATTC
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
64 27 0.50
65 24 0.44
66 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (65 bp):
GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGCAG
Found at i:1968523 original size:64 final size:64
Alignment explanation
Indices: 1968387--1968524 Score: 165
Period size: 64 Copynumber: 2.2 Consensus size: 64
1968377 GCACTAAGAG
* * * **
1968387 TGCATCGATACATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCAGG
1 TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCAAA
* *
1968451 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCAT-G-AA
1 TGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGGCAA
1968513 A
64 A
1968514 TGCATTCGATG
1 TGCA-TCGATG
1968525 TTCAATTTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
63 5 0.08
64 33 0.52
65 23 0.36
66 3 0.05
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (64 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCAAA
Found at i:1969291 original size:18 final size:18
Alignment explanation
Indices: 1969270--1969314 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1969260 TATTTATTTA
*
1969270 TTTATTTTATCCTTATCT
1 TTTATTTTATCCATATCT
*
1969288 TTTATTTTATGCATATCT
1 TTTATTTTATCCATATCT
1969306 TTTATTTTA
1 TTTATTTTA
1969315 AAACAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.20, C:0.11, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTTTATCCATATCT
Found at i:1969857 original size:12 final size:12
Alignment explanation
Indices: 1969840--1969865 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1969830 TTACATACTG
1969840 AAAATACTCAAT
1 AAAATACTCAAT
1969852 AAAATACTCAAT
1 AAAATACTCAAT
1969864 AA
1 AA
1969866 GGATCCTACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATACTCAAT
Found at i:1971398 original size:18 final size:18
Alignment explanation
Indices: 1971357--1971407 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
1971347 TATTATCTAC
* * *
1971357 AATTATTTATTTAAATGT
1 AATTATATATATAAATGA
*
1971375 ATTTATATATATAAATGA
1 AATTATATATATAAATGA
1971393 AATTATA-A-ATAAATG
1 AATTATATATATAAATG
1971408 GCTATTTGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 7 0.25
17 1 0.04
18 20 0.71
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (18 bp):
AATTATATATATAAATGA
Found at i:1980909 original size:5 final size:5
Alignment explanation
Indices: 1980896--1980949 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
1980886 GTCCGTCCGT
* * * *
1980896 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
1980946 CTCG
1 CTCG
1980950 TGGTCGTGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.06, C:0.41, G:0.37, T:0.17
Consensus pattern (5 bp):
CTCGG
Found at i:1981274 original size:6 final size:6
Alignment explanation
Indices: 1980951--1981273 Score: 484
Period size: 6 Copynumber: 53.8 Consensus size: 6
1980941 CTCGGCTCGT
* * * *
1980951 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGA GGTCGA GGTCGA GGTCGA
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
* * * * * *
1980999 GGTCGA GGTCGT GGGCGT GGTCGT GGTCGT GGTCGA GGTCGA GGTCGT
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
1981047 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
* * *
1981095 GGTCGA GGTCGT GGTCGA GGTCGA GGTCGA GGTCGT GGTCGT GGTCGA
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
*
1981143 GGTCGA GGTCGT GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
1981191 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
* * * *
1981239 GGTCGA GGTCGT GGTCGT GGTCGT GGTCGT GGTCG
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCG
1981274 TACGTGTCTT
Statistics
Matches: 303, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 303 1.00
ACGTcount: A:0.11, C:0.17, G:0.50, T:0.22
Consensus pattern (6 bp):
GGTCGA
Found at i:1981453 original size:22 final size:22
Alignment explanation
Indices: 1981428--1981482 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1981418 TCAGGAGTTA
* *
1981428 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1981450 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1981472 CGGGAGTTATA
1 CAGGAGTTATA
1981483 ACAGCGGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1987024 original size:5 final size:5
Alignment explanation
Indices: 1987010--1987063 Score: 54
Period size: 5 Copynumber: 10.8 Consensus size: 5
1987000 GTCCGTCCGT
* * * * * *
1987010 CTCGT CTCGG CTCGG CACGG CACGG CACGG CACGG CTTGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
1987060 CTCG
1 CTCG
1987064 TGGTCGTGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.07, C:0.39, G:0.37, T:0.17
Consensus pattern (5 bp):
CTCGG
Found at i:1987055 original size:15 final size:15
Alignment explanation
Indices: 1987015--1987063 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
1987005 TCCGTCTCGT
1987015 CTCGGCTCGGCACGG
1 CTCGGCTCGGCACGG
* *
1987030 CACGGCACGGCACGG
1 CTCGGCTCGGCACGG
* *
1987045 CTTGGCTCGGCTCGG
1 CTCGGCTCGGCACGG
1987060 CTCG
1 CTCG
1987064 TGGTCGTGGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.08, C:0.39, G:0.39, T:0.14
Consensus pattern (15 bp):
CTCGGCTCGGCACGG
Found at i:1987072 original size:6 final size:6
Alignment explanation
Indices: 1987061--1987127 Score: 107
Period size: 6 Copynumber: 11.2 Consensus size: 6
1987051 TCGGCTCGGC
* * *
1987061 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1987109 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
1987128 AATACGTGTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.04, C:0.16, G:0.49, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:1987426 original size:22 final size:22
Alignment explanation
Indices: 1987401--1987455 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1987391 TCAGGAGTTA
* *
1987401 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1987423 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1987445 CGGGAGTTATA
1 CAGGAGTTATA
1987456 ATAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1993005 original size:5 final size:5
Alignment explanation
Indices: 1992995--1993048 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
1992985 CTCGTCTTGT
* * * *
1992995 CTCGG CACGG CACGG CACGG CACGG CTCGG CTCGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
1993045 CTCG
1 CTCG
1993049 TGGTCGTGGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.07, C:0.41, G:0.39, T:0.13
Consensus pattern (5 bp):
CTCGG
Found at i:1993057 original size:6 final size:6
Alignment explanation
Indices: 1993046--1993100 Score: 83
Period size: 6 Copynumber: 9.2 Consensus size: 6
1993036 TCGGCTCGGC
* * *
1993046 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1993094 TCGTGG T
1 TCGTGG T
1993101 AATACGTGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.05, C:0.16, G:0.49, T:0.29
Consensus pattern (6 bp):
TCGTGG
Found at i:1993399 original size:22 final size:22
Alignment explanation
Indices: 1993374--1993428 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1993364 TCAGGAGTTA
* *
1993374 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1993396 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1993418 CGGGAGTTATA
1 CAGGAGTTATA
1993429 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1998975 original size:5 final size:5
Alignment explanation
Indices: 1998956--1999004 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
1998946 GTCCGTCCGT
* * *
1998956 CTCGT CTCGT CTCGG CTCGG CACGG CTCGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
1999005 TGGTCGTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.02, C:0.41, G:0.35, T:0.22
Consensus pattern (5 bp):
CTCGG
Found at i:1999013 original size:6 final size:6
Alignment explanation
Indices: 1999002--1999062 Score: 86
Period size: 6 Copynumber: 10.2 Consensus size: 6
1998992 TCGGCTCGGC
* * * *
1999002 TCGTGG TCGTGG TCGTGG TTGAGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1999050 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
1999063 AATACGTGTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.05, C:0.15, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:1999361 original size:22 final size:22
Alignment explanation
Indices: 1999336--1999390 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1999326 TCAGGAGTTA
* *
1999336 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1999358 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1999380 CGGGAGTTATA
1 CAGGAGTTATA
1999391 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:2010207 original size:27 final size:27
Alignment explanation
Indices: 2010136--2010208 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
2010126 TGTTGACGCT
*
2010136 ATATTTTAATGAATGTGATTAATATCA
1 ATATTTGAATGAATGTGATTAATATCA
* * *
2010163 GT-TGTTG-ACGTAACGTGATTAATATCA
1 ATAT-TTGAATG-AATGTGATTAATATCA
2010190 ATATTTGAATGAATGTGAT
1 ATATTTGAATGAATGTGAT
2010209 GGATATTAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
26 3 0.09
27 29 0.83
28 3 0.09
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (27 bp):
ATATTTGAATGAATGTGATTAATATCA
Found at i:2012591 original size:12 final size:12
Alignment explanation
Indices: 2012567--2012603 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
2012557 ATTAGTTTAT
2012567 AATAAAT-ACAA
1 AATAAATAACAA
2012578 AATAAATAACAA
1 AATAAATAACAA
*
2012590 AAT-AATAAAAA
1 AATAAATAACAA
2012601 AAT
1 AAT
2012604 TTACAAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 17 0.71
12 7 0.29
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (12 bp):
AATAAATAACAA
Found at i:2029014 original size:24 final size:24
Alignment explanation
Indices: 2028982--2029030 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2028972 ACAAGTGGTT
2028982 ATGGAGATACGCAAAAGAATCTGA
1 ATGGAGATACGCAAAAGAATCTGA
2029006 ATGGAGATACGCAAAAGAATCTGA
1 ATGGAGATACGCAAAAGAATCTGA
2029030 A
1 A
2029031 AGTCTGTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.16
Consensus pattern (24 bp):
ATGGAGATACGCAAAAGAATCTGA
Found at i:2031129 original size:35 final size:35
Alignment explanation
Indices: 2031082--2031182 Score: 130
Period size: 35 Copynumber: 2.9 Consensus size: 35
2031072 AAAATAGTCC
* * *
2031082 TCAATTTCATTCTAAACCCTAAATTCCAAAGTAAT
1 TCAATTTTATTCTAAACCCAAAATTCCAAAATAAT
*
2031117 TCAATTTTATTCTAAACCCCAAATTCCAAAATAAT
1 TCAATTTTATTCTAAACCCAAAATTCCAAAATAAT
* * * *
2031152 ACAATTTTATTTTAAATCCAAAATTCTAAAA
1 TCAATTTTATTCTAAACCCAAAATTCCAAAA
2031183 CAATCCAAGC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.44, C:0.20, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTTATTCTAAACCCAAAATTCCAAAATAAT
Found at i:2038497 original size:35 final size:35
Alignment explanation
Indices: 2038447--2038521 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
2038437 TTCATTTTCA
* *
2038447 AAATTCCAAAGTAATTCAATT-TCATTCTAAACCCT
1 AAATTCCAAAATAATTAAATTAT-ATTCTAAACCCT
* *
2038482 AAATTCCAAAATAATTAAATTATATTTTAAACCTT
1 AAATTCCAAAATAATTAAATTATATTCTAAACCCT
2038517 AAATT
1 AAATT
2038522 GAAGTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 34 0.97
36 1 0.03
ACGTcount: A:0.45, C:0.16, G:0.01, T:0.37
Consensus pattern (35 bp):
AAATTCCAAAATAATTAAATTATATTCTAAACCCT
Found at i:2038592 original size:35 final size:35
Alignment explanation
Indices: 2038517--2038626 Score: 96
Period size: 35 Copynumber: 3.1 Consensus size: 35
2038507 TTTAAACCTT
* *
2038517 AAATTGAAGTATTTTAGAATTTGAGGTTTAAAATT
1 AAATTGAAGTATTTTAGAATTTAAGGTTTAAAATA
* * * **
2038552 TAATTGAATTGTTTTAGAATTTAAGGTTTGGAATA
1 AAATTGAAGTATTTTAGAATTTAAGGTTTAAAATA
* * * * *
2038587 AAATTGAACTACTTT-GAAATTTAGGGTTTAGAATG
1 AAATTGAAGTATTTTAG-AATTTAAGGTTTAAAATA
2038622 AAATT
1 AAATT
2038627 AAAGACTGTT
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
34 1 0.02
35 59 0.98
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.42
Consensus pattern (35 bp):
AAATTGAAGTATTTTAGAATTTAAGGTTTAAAATA
Found at i:2041142 original size:24 final size:24
Alignment explanation
Indices: 2041076--2041145 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
2041066 ATAAGAATTG
*
2041076 TGCCACAAGAGTAAAGAAAATATTA
1 TGCCACAAGAGTAAAGAAAA-AGTA
** *
2041101 TGCCACAAGAACATAGAAAAAGTA
1 TGCCACAAGAGTAAAGAAAAAGTA
* *
2041125 TGCTACAAGAGTAGAGAAAAA
1 TGCCACAAGAGTAAAGAAAAA
2041146 CGTGTCAAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
24 20 0.54
25 17 0.46
ACGTcount: A:0.53, C:0.13, G:0.19, T:0.16
Consensus pattern (24 bp):
TGCCACAAGAGTAAAGAAAAAGTA
Found at i:2041592 original size:21 final size:21
Alignment explanation
Indices: 2041566--2041627 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 21
2041556 TAATATTACA
2041566 TATTTTATTATTTATTATATG
1 TATTTTATTATTTATTATATG
* * *
2041587 -CTTTT-TTA-TTAATATGATA
1 TATTTTATTATTTATTAT-ATG
*
2041606 TATTTTGTTATTTATTATATG
1 TATTTTATTATTTATTATATG
2041627 T
1 T
2041628 GGTTATCACA
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
18 6 0.19
19 5 0.16
20 8 0.26
21 6 0.19
22 6 0.19
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (21 bp):
TATTTTATTATTTATTATATG
Found at i:2041597 original size:40 final size:40
Alignment explanation
Indices: 2041548--2041626 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
2041538 ATATGTCATG
*
2041548 TTTTTTATTAATATTACATATTTTATTATTTATTATATGC
1 TTTTTTATTAATATGACATATTTTATTATTTATTATATGC
* *
2041588 TTTTTTATTAATATGATATATTTTGTTATTTATTATATG
1 TTTTTTATTAATATGACATATTTTATTATTTATTATATG
2041627 TGGTTATCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (40 bp):
TTTTTTATTAATATGACATATTTTATTATTTATTATATGC
Found at i:2041625 original size:19 final size:18
Alignment explanation
Indices: 2041548--2041625 Score: 66
Period size: 19 Copynumber: 3.9 Consensus size: 18
2041538 ATATGTCATG
*
2041548 TTTTTTATTAATATTACATA
1 TTTTTTATT--TATTATATA
*
2041568 TTTTATTATTTATTATATGC
1 TTTT-TTATTTATTATAT-A
*
2041588 TTTTTTATTAATATGATATA
1 TTTTTTATT--TATTATATA
2041608 TTTTGTTATTTATTATAT
1 TTTT-TTATTTATTATAT
2041626 GTGGTTATCA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
19 19 0.40
20 12 0.25
21 17 0.35
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (18 bp):
TTTTTTATTTATTATATA
Found at i:2045067 original size:14 final size:14
Alignment explanation
Indices: 2045029--2045095 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 14
2045019 CAATGAATCC
*
2045029 TAAACCCTAAACCA
1 TAAACCTTAAACCA
* * *
2045043 TATATCATAAAACC-
1 TA-AACCTTAAACCA
*
2045057 TAAACCTTAAACCT
1 TAAACCTTAAACCA
*
2045071 TAAACATTAAACCA
1 TAAACCTTAAACCA
2045085 TAAACCCTTAA
1 TAAA-CCTTAA
2045096 TTCGATTATG
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
13 8 0.20
14 20 0.50
15 12 0.30
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:2045067 original size:28 final size:27
Alignment explanation
Indices: 2045027--2045095 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
2045017 TGCAATGAAT
* *
2045027 CCTAAACCCTAAACCATATATCATAAAA
1 CCTAAACCTTAAACCATA-AACATAAAA
* *
2045055 CCTAAACCTTAAACCTTAAACATTAAA
1 CCTAAACCTTAAACCATAAACATAAAA
2045082 CCATAAACCCTTAA
1 CC-TAAA-CCTTAA
2045096 TTCGATTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.26
28 20 0.57
29 6 0.17
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (27 bp):
CCTAAACCTTAAACCATAAACATAAAA
Found at i:2046461 original size:40 final size:40
Alignment explanation
Indices: 2046402--2046496 Score: 111
Period size: 40 Copynumber: 2.3 Consensus size: 40
2046392 ATAAATTGGA
* * * *
2046402 TTTAAAAAATAAATAAATAAATAAATATATATATATATATA-
1 TTTAAATAAT-AAT-AATAAATAAATATATAAACATATAGAG
*
2046443 TTTATAATAATAATAATAATTAAATATATAAACATATAGAG
1 TTTA-AATAATAATAATAAATAAATATATAAACATATAGAG
2046484 TTTAAATAATAAT
1 TTTAAATAATAAT
2046497 TAAATTTAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
40 31 0.66
41 11 0.23
42 5 0.11
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (40 bp):
TTTAAATAATAATAATAAATAAATATATAAACATATAGAG
Found at i:2047021 original size:10 final size:10
Alignment explanation
Indices: 2046999--2047031 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2046989 AATTTTCATT
2046999 TCTC-TTCTC
1 TCTCATTCTC
*
2047008 TCTCATTTTC
1 TCTCATTCTC
2047018 TCTCATTCTC
1 TCTCATTCTC
2047028 TCTC
1 TCTC
2047032 TAAAATGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (10 bp):
TCTCATTCTC
Found at i:2047782 original size:3 final size:3
Alignment explanation
Indices: 2047769--2047837 Score: 68
Period size: 3 Copynumber: 22.7 Consensus size: 3
2047759 ATATATTATT
* * * *
2047769 TAA TAA CAA TAA T-A TAA TAA TATA TAA TAT TAA TTA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
*
2047814 TAA TATT TAA TAA TAA TAA TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TA
2047838 TACAGTGAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
2 2 0.04
3 46 0.87
4 5 0.09
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2047809 original size:19 final size:19
Alignment explanation
Indices: 2047782--2047838 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
2047772 TAACAATAAT
2047782 ATAATAATATATAATATTA
1 ATAATAATATATAATATTA
*
2047801 ATTATAATAATGATAATATTTA
1 ATAATAAT-AT-ATAATA-TTA
2047823 ATAATAATA-ATAATAT
1 ATAATAATATATAATAT
2047839 ACAGTGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 1 0.03
19 13 0.39
20 2 0.06
21 7 0.21
22 10 0.30
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATAATAATATATAATATTA
Found at i:2047809 original size:22 final size:23
Alignment explanation
Indices: 2047781--2047839 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
2047771 ATAACAATAA
2047781 TATAATAATATATAATA-TTAAT
1 TATAATAATATATAATATTTAAT
*
2047803 TATAATAAT-GATAATATTTAAT
1 TATAATAATATATAATATTTAAT
*
2047825 AATAATAATAATATA
1 TATAATAAT-ATATA
2047840 CAGTGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 6 0.19
22 22 0.71
24 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TATAATAATATATAATATTTAAT
Found at i:2047817 original size:31 final size:31
Alignment explanation
Indices: 2047757--2047818 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
2047747 CTGTATATAT
*
2047757 ATATATATTATTTAATAACAATAATATAATA
1 ATATATAATATTTAATAACAATAATATAATA
* *
2047788 ATATATAATA-TTAATTATAATAATGATAATA
1 ATATATAATATTTAATAACAATAAT-ATAATA
2047819 TTTAATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (31 bp):
ATATATAATATTTAATAACAATAATATAATA
Found at i:2047825 original size:28 final size:28
Alignment explanation
Indices: 2047769--2047837 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
2047759 ATATATTATT
*
2047769 TAATAACAATAAT-ATAATAATATATAA
1 TAATAATAATAATAATAATAATATATAA
* * * *
2047796 TATTAATTATAATAATGATAATATTTAA
1 TAATAATAATAATAATAATAATATATAA
2047824 TAATAATAATAATA
1 TAATAATAATAATA
2047838 TACAGTGAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 10 0.29
28 24 0.71
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (28 bp):
TAATAATAATAATAATAATAATATATAA
Found at i:2048365 original size:114 final size:113
Alignment explanation
Indices: 2048178--2048853 Score: 966
Period size: 113 Copynumber: 6.0 Consensus size: 113
2048168 AGAGTCATGC
* * * * *
2048178 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTTAGATAAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
2048242 ATGAACTT-TCTCTGGAAAAGTTGATGCATCGAGTGATGAATTCGAGCA
66 ATGAACTTCT-TCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCA
* * * * *
2048290 AAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTT-CTTCTTTAGATGAGTTCTTTTCA
1 AAAGG-TTAAACAAGTTCTTCTCATTATGAACTTCTT-TTTCCTTCTTCAGATGAGTTCTTCTCA
* *
2048354 TTATGAACTT-TCTCTGGAAAAGTTGATCAATCGAGTGATGAATTCGAGCA
64 TTATGAACTTCT-TCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCA
* * * *
2048404 AAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTTTTCCTTCATCAGATGAGTTCTTCTCAT
1 AAAGG-TTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
2048469 TATGATCTTCTTCTGGAATAGTTGATCCATCAAATGATGAATTCAAGCA
65 TATGAACTTCTTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCA
* * * *
2048518 AAAGGTTAAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGATTTATTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
2048583 ATGAACTTCTTCTGGAACAGTTGATCCATCGAATGATGAATTCAAGCA
66 ATGAACTTCTTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCA
*
2048631 AAAGGTTAAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATT
*
2048696 ATGAACTTCTTCTGGAATAGTTGATCCATCGTA-TGATGAATTCAAGCA
66 ATGAACTTCTTCTGGAAAAGTTGATCCATCG-AGTGATGAATTCAAGCA
*
2048744 AAAGGTTAAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
2048809 ATGAACTTCTTCTGGAACAGTTGATCCATCAAGTGATGAATTCAA
66 ATGAACTTCTTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
2048854 ATTTTTGCTA
Statistics
Matches: 523, Mismatches: 34, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
112 6 0.01
113 342 0.65
114 174 0.33
115 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (113 bp):
AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTCTTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCA
Found at i:2050420 original size:13 final size:13
Alignment explanation
Indices: 2050402--2050426 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2050392 CTTTTTATCA
2050402 TTTTTTCTTCTTT
1 TTTTTTCTTCTTT
2050415 TTTTTTCTTCTT
1 TTTTTTCTTCTT
2050427 CAAGCATAAT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTCTTCTTT
Found at i:2057748 original size:15 final size:15
Alignment explanation
Indices: 2057728--2057759 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2057718 TGCAATGAAT
2057728 AATGAATATATGCAA
1 AATGAATATATGCAA
*
2057743 AATGAATGTATGCAA
1 AATGAATATATGCAA
2057758 AA
1 AA
2057760 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (15 bp):
AATGAATATATGCAA
Found at i:2061864 original size:2 final size:2
Alignment explanation
Indices: 2061857--2061887 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2061847 ATTGGATTTA
*
2061857 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2061888 ACAATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 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):
AT
Found at i:2063181 original size:2 final size:2
Alignment explanation
Indices: 2063174--2063222 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2063164 AATGGGCCTG
2063174 TA TA TA TA TA 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 TA TA TA TA TA
2063216 TA TA TA T
1 TA TA TA T
2063223 TTAATAATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2063232 original size:3 final size:3
Alignment explanation
Indices: 2063224--2063286 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
2063214 TATATATATT
* ** *
2063224 TAA TAA TAA TAA -ATA TAA TAT TAA TAA TAA TTT TAA TAA TGA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2063269 TATT TAA TAA TAA TAA TA
1 TA-A TAA TAA TAA TAA TA
2063287 TACAGTGAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
2 1 0.02
3 43 0.91
4 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:2063247 original size:21 final size:23
Alignment explanation
Indices: 2063187--2063288 Score: 84
Period size: 23 Copynumber: 4.2 Consensus size: 23
2063177 ATATATATAT
* *
2063187 ATATATATATATATATATATATATAT
1 ATATATATATTTA-ATA-ATA-ATAA
2063213 ATATATATATTTAATAATAATAA
1 ATATATATATTTAATAATAATAA
*
2063236 ATATA-ATA-TTAATAATAATTTTA
1 ATATATATATTTAATAATAA--TAA
2063259 ATAATGATAATATTTAATAATAAT-A
1 AT-AT-AT-ATATTTAATAATAATAA
2063284 ATATA
1 ATATA
2063289 CAGTGAAAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 17
0.77 0.03 0.20
Matches are distributed among these distances:
21 10 0.15
22 3 0.05
23 13 0.20
24 7 0.11
25 7 0.11
26 13 0.20
27 3 0.05
28 10 0.15
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (23 bp):
ATATATATATTTAATAATAATAA
Found at i:2072995 original size:22 final size:22
Alignment explanation
Indices: 2072970--2073035 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
2072960 GGCAACATCT
2072970 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
2072992 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* **
2073014 GTCTCCATCTCCGGTGAAATCA
1 GTCCCCATCTCCGACGAAATCA
2073036 TTCACGGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:2073424 original size:20 final size:20
Alignment explanation
Indices: 2073402--2073537 Score: 115
Period size: 20 Copynumber: 7.2 Consensus size: 20
2073392 AATTCTTGCA
* *
2073402 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAATTTCGCG
* * *
2073422 TTGCGATAGTCATTTTTGTG
1 TTGCGATAGTCAATTTCGCG
**
2073442 TTGCGATTTTC-ATTTCGCG
1 TTGCGATAGTCAATTTCGCG
2073461 TTGCGAT--TC---TT-GCG
1 TTGCGATAGTCAATTTCGCG
*
2073475 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAATTTCGCG
* *
2073495 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCAATTTCGCG
* *
2073515 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCAATTTCGCG
2073535 TTG
1 TTG
2073538 TGATTTTCAT
Statistics
Matches: 97, Mismatches: 13, Indels: 12
0.80 0.11 0.10
Matches are distributed among these distances:
14 10 0.10
15 2 0.02
16 2 0.02
17 2 0.02
19 14 0.14
20 67 0.69
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCAATTTCGCG
Found at i:2073456 original size:73 final size:73
Alignment explanation
Indices: 2073368--2073521 Score: 263
Period size: 73 Copynumber: 2.1 Consensus size: 73
2073358 CGATTCTGTC
*
2073368 GTTGTGATTTTCATTTCGCGTTGCAATTCTTGCATTGCGATAGTCAAATTCGCATTGCGATAGTC
1 GTTGCGATTTTCATTTCGCGTTGCAATTCTTGCATTGCGATAGTCAAATTCGCATTGCGATAGTC
*
2073433 ATTTTTGT
66 ATTTTCGT
* * *
2073441 GTTGCGATTTTCATTTCGCGTTGCGATTCTTGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTC
1 GTTGCGATTTTCATTTCGCGTTGCAATTCTTGCATTGCGATAGTCAAATTCGCATTGCGATAGTC
2073506 ATTTTCGT
66 ATTTTCGT
2073514 GTTGCGAT
1 GTTGCGAT
2073522 AGTCATTTTC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.42
Consensus pattern (73 bp):
GTTGCGATTTTCATTTCGCGTTGCAATTCTTGCATTGCGATAGTCAAATTCGCATTGCGATAGTC
ATTTTCGT
Found at i:2073499 original size:34 final size:34
Alignment explanation
Indices: 2073382--2073501 Score: 116
Period size: 34 Copynumber: 3.4 Consensus size: 34
2073372 TGATTTTCAT
* *
2073382 TTCGCGTTGCAATTCTTGCATTGCGATAGTCAAA
1 TTCGCGTTGCGATTCTTGCGTTGCGATAGTCAAA
* * ** *
2073416 TTCGCATTGCGATAGTCATTTTTGTGTTGCGATTTTC-AT
1 TTCGCGTTGCGAT--TC----TTGCGTTGCGATAGTCAAA
2073455 TTCGCGTTGCGATTCTTGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATTCTTGCGTTGCGATAGTCAAA
2073489 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
2073502 AGTCATTTTC
Statistics
Matches: 67, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
33 13 0.19
34 25 0.37
36 2 0.03
37 2 0.03
39 13 0.19
40 12 0.18
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.40
Consensus pattern (34 bp):
TTCGCGTTGCGATTCTTGCGTTGCGATAGTCAAA
Found at i:2073547 original size:20 final size:20
Alignment explanation
Indices: 2073431--2073564 Score: 93
Period size: 20 Copynumber: 7.0 Consensus size: 20
2073421 ATTGCGATAG
*
2073431 TCATTTTTGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
*
2073451 TCA-TTTCGCGTTGCGA--T
1 TCATTTTCGTGTTGCGATTT
* **
2073468 TC---TT-GCGTTGCGATAG
1 TCATTTTCGTGTTGCGATTT
** * **
2073484 TCAAATTCGCGTTGCGATAG
1 TCATTTTCGTGTTGCGATTT
**
2073504 TCATTTTCGTGTTGCGATAG
1 TCATTTTCGTGTTGCGATTT
*
2073524 TCATTTTCGTGTTGTGATTT
1 TCATTTTCGTGTTGCGATTT
*
2073544 TCATTTTCATGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
2073564 T
1 T
2073565 AAGTTTCAGA
Statistics
Matches: 97, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
14 9 0.09
15 2 0.02
16 2 0.02
17 3 0.03
19 13 0.13
20 68 0.70
ACGTcount: A:0.14, C:0.16, G:0.22, T:0.48
Consensus pattern (20 bp):
TCATTTTCGTGTTGCGATTT
Found at i:2073548 original size:40 final size:40
Alignment explanation
Indices: 2073402--2073561 Score: 145
Period size: 40 Copynumber: 4.2 Consensus size: 40
2073392 AATTCTTGCA
* **
2073402 TTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTTGTG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCATG
** * *
2073442 TTGCGATTTTC-ATTTCGCGTTGCGAT--TC--TTGC--G
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCATG
*
2073475 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCATG
** * * **
2073515 TTGCGATAGTCATTTTCGTGTTGTGATTTTCATTTTCATG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCATG
2073555 TTGCGAT
1 TTGCGAT
2073562 TTTAAGTTTC
Statistics
Matches: 96, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
33 10 0.10
34 14 0.15
35 2 0.02
36 2 0.02
37 2 0.02
38 3 0.03
39 13 0.14
40 50 0.52
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.44
Consensus pattern (40 bp):
TTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCATG
Found at i:2073571 original size:20 final size:20
Alignment explanation
Indices: 2073528--2073572 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2073518 CGATAGTCAT
* * * *
2073528 TTTCGTGTTGTGATTTTCAT
1 TTTCATGTTGCGATTTTAAG
2073548 TTTCATGTTGCGATTTTAAG
1 TTTCATGTTGCGATTTTAAG
2073568 TTTCA
1 TTTCA
2073573 GAAACTATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.56
Consensus pattern (20 bp):
TTTCATGTTGCGATTTTAAG
Found at i:2075977 original size:14 final size:14
Alignment explanation
Indices: 2075958--2075993 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2075948 ATTGTTTAAT
2075958 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2075972 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2075986 TGATTTGT
1 TGATTTGT
2075994 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2076156 original size:33 final size:34
Alignment explanation
Indices: 2076099--2076193 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 34
2076089 AAAACAGACT
** **
2076099 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATACGAAAATGAAAATCGCAACGAGAGA
**
2076133 ATCGCAATGTG-AAATGAAAATCGCAACGAGAGA
1 ATCGCAATACGAAAATGAAAATCGCAACGAGAGA
*
2076166 ATCGTAATACGAAAATGAAAATCGCAAC
1 ATCGCAATACGAAAATGAAAATCGCAAC
2076194 ACGAAACTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
33 28 0.53
34 25 0.47
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (34 bp):
ATCGCAATACGAAAATGAAAATCGCAACGAGAGA
Found at i:2076273 original size:20 final size:20
Alignment explanation
Indices: 2076244--2076316 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
2076234 CGATTCTCTC
2076244 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
* *
2076264 GTTGCAATAGTCATTTCCGT
1 GTTGCGATAGTCATTTTCGT
* *
2076284 GTTGCGATAGTCATATTCGC
1 GTTGCGATAGTCATTTTCGT
2076304 GTTGCGATAGTCA
1 GTTGCGATAGTCA
2076317 AATGAATGTC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:2078797 original size:24 final size:24
Alignment explanation
Indices: 2078737--2078789 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
2078727 ATCATTAAAA
2078737 TTCGAGTATTGACCAAGATCAAAG
1 TTCGAGTATTGACCAAGATCAAAG
* * *
2078761 TCCGGGTATTGACCAAGATCAAAT
1 TTCGAGTATTGACCAAGATCAAAG
2078785 TTCGA
1 TTCGA
2078790 ATACTGACTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (24 bp):
TTCGAGTATTGACCAAGATCAAAG
Found at i:2079650 original size:20 final size:20
Alignment explanation
Indices: 2079625--2079711 Score: 147
Period size: 20 Copynumber: 4.3 Consensus size: 20
2079615 AAATTCAGTA
2079625 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
*
2079645 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
2079665 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
2079685 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
2079705 TTGCGAT
1 TTGCGAT
2079712 TTACATATTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:2079721 original size:20 final size:20
Alignment explanation
Indices: 2079698--2079824 Score: 159
Period size: 20 Copynumber: 6.3 Consensus size: 20
2079688 CGATAGTCAG
* *
2079698 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
2079718 ATTCGCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
*
2079738 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
2079758 ATTCGCATTGCGATAGT-CAG-
1 ATTCGCATTGCGAT-TTAC-GT
2079778 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
2079798 ATTCTCATTGGGATTTACGT
1 ATTCGCATTGCGATTTACGT
2079818 ATTCGCA
1 ATTCGCA
2079825 ACGCGAATTT
Statistics
Matches: 92, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.02
20 88 0.96
21 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2079729 original size:40 final size:40
Alignment explanation
Indices: 2079685--2079807 Score: 160
Period size: 40 Copynumber: 3.1 Consensus size: 40
2079675 CAGAATCTCG
*
2079685 TTGCGATAGTCAGATTCGCGTTGCGATTTACATATTCGCA
1 TTGCGATAGTCAGATTCGCATTGCGATTTACATATTCGCA
* * *
2079725 TTGCGAT--TTATGTATTCACATTGCGATTTACGTATTCGCA
1 TTGCGATAGTCA-G-ATTCGCATTGCGATTTACATATTCGCA
* *
2079765 TTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCTCA
1 TTGCGATAGTCAGATTCGCATTGCGATTTACATATTCGCA
2079805 TTG
1 TTG
2079808 GGATTTACGT
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
38 2 0.03
39 1 0.01
40 66 0.92
41 1 0.01
42 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (40 bp):
TTGCGATAGTCAGATTCGCATTGCGATTTACATATTCGCA
Found at i:2080256 original size:19 final size:20
Alignment explanation
Indices: 2080230--2080282 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
2080220 TTTTATTAAC
*
2080230 ATAAAATTGTTTACAAAATA
1 ATAAAATTATTTACAAAATA
*
2080250 A-AAAATTATTTACAATATA
1 ATAAAATTATTTACAAAATA
2080269 ATAAAATTTATTTA
1 ATAAAA-TTATTTA
2080283 TATTTCCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 17 0.59
20 5 0.17
21 7 0.24
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (20 bp):
ATAAAATTATTTACAAAATA
Found at i:2082895 original size:17 final size:18
Alignment explanation
Indices: 2082862--2082895 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2082852 ATTTGATCTT
*
2082862 TTCACATAATTTGTTTTC
1 TTCACATAATTTCTTTTC
2082880 TTCACAT-ATTTCTTTT
1 TTCACATAATTTCTTTT
2082896 ATTTTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.21, C:0.18, G:0.03, T:0.59
Consensus pattern (18 bp):
TTCACATAATTTCTTTTC
Found at i:2099339 original size:26 final size:26
Alignment explanation
Indices: 2099262--2099340 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 26
2099252 ACATAACAGA
* *
2099262 TATAGTAACAAATAAGATGCAATGGT
1 TATAGCAACAAATAAGATGCAATAGT
*
2099288 TATAGC-ACAAA-AACA---AATAGT
1 TATAGCAACAAATAAGATGCAATAGT
*
2099309 TATAGCAATAAATAAGATGCAATAGT
1 TATAGCAACAAATAAGATGCAATAGT
2099335 TATAGC
1 TATAGC
2099341 CCAAAAATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
21 11 0.26
22 4 0.09
23 3 0.07
24 3 0.07
25 5 0.12
26 17 0.40
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.25
Consensus pattern (26 bp):
TATAGCAACAAATAAGATGCAATAGT
Found at i:2102616 original size:32 final size:31
Alignment explanation
Indices: 2102578--2102654 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
2102568 CGGGGTCATG
*
2102578 GAGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GAGCCTACCTAAGAA-ACATCTCAGGGCCGCA
* ** ** *
2102610 GGGCCTACCCGAGAATGATCTCAGGGCTGCA
1 GAGCCTACCTAAGAAACATCTCAGGGCCGCA
2102641 GAGCCTACCTAAGA
1 GAGCCTACCTAAGA
2102655 GTCACATTAG
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.16
Consensus pattern (31 bp):
GAGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:2122117 original size:59 final size:60
Alignment explanation
Indices: 2122045--2122161 Score: 155
Period size: 59 Copynumber: 1.9 Consensus size: 60
2122035 TGCACTAAGC
* * * *
2122045 TTACGCTCTAGTGCTGATTCAGATATGACA-TACGGTTGTGCACACCTCCTACACTAGGT
1 TTACACTCTAGTGCTCATTCAGATATGACACTAAGGTTGTGCACACCACCTACACTAGGT
* * *
2122104 TTACACTCTAGTGCTCATTCGGATATGACACGTAAGGTTGTGCCCACCACCTGCACTA
1 TTACACTCTAGTGCTCATTCAGATATGACAC-TAAGGTTGTGCACACCACCTACACTA
2122162 AGTGTCCTCG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
59 27 0.55
61 22 0.45
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (60 bp):
TTACACTCTAGTGCTCATTCAGATATGACACTAAGGTTGTGCACACCACCTACACTAGGT
Found at i:2132875 original size:30 final size:30
Alignment explanation
Indices: 2132841--2132923 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
2132831 CCAGGCCAGG
* **
2132841 GTGAGGATGATTGTTCTGATTTTCAGGTAA
1 GTGAGGATGATTGTTTTGATTTTCAGAAAA
*
2132871 GTGAGGATAATTGTTTTGATTTTCAGAAAA
1 GTGAGGATGATTGTTTTGATTTTCAGAAAA
*
2132901 GTGAGGATGATTATTTTGATTTT
1 GTGAGGATGATTGTTTTGATTTT
2132924 TGGGATAGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.27, C:0.04, G:0.27, T:0.43
Consensus pattern (30 bp):
GTGAGGATGATTGTTTTGATTTTCAGAAAA
Found at i:2138230 original size:44 final size:44
Alignment explanation
Indices: 2138167--2138255 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
2138157 CATCTTCCGG
2138167 GAGCACTGTAGATTCCTCCCTACTTAAGAAAATAAAATATCAAT
1 GAGCACTGTAGATTCCTCCCTACTTAAGAAAATAAAATATCAAT
2138211 GAGCACTGTAGATTCCTCCCTACTTAAGAAAATAAAATATCAAT
1 GAGCACTGTAGATTCCTCCCTACTTAAGAAAATAAAATATCAAT
2138255 G
1 G
2138256 GCAACACACT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.27
Consensus pattern (44 bp):
GAGCACTGTAGATTCCTCCCTACTTAAGAAAATAAAATATCAAT
Found at i:2141492 original size:2 final size:2
Alignment explanation
Indices: 2141487--2141519 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2141477 TCTCTCTCTC
2141487 TA TA 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 TA TA T
2141520 TTAAAAATGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2141756 original size:3 final size:3
Alignment explanation
Indices: 2141748--2141807 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
2141738 TTACCTACAA
*
2141748 AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAAT AAT AAT GAT AAT AA-
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT AAT AAT
* *
2141794 AAA AAT AAA AAT AA
1 AAT AAT AAT AAT AA
2141808 AAATGGGTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
2 2 0.04
3 41 0.84
4 6 0.12
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:2141783 original size:26 final size:24
Alignment explanation
Indices: 2141746--2141807 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 24
2141736 TTTTACCTAC
2141746 AAAAT-AATAATAATAATAATAAA
1 AAAATAAATAATAATAATAATAAA
*
2141769 TAATAATAAATAATAATGATAATAAA
1 -AA-AATAAATAATAATAATAATAAA
2141795 AAAATAAA-AATAA
1 AAAATAAATAATAA
2141808 AAATGGGTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
23 5 0.14
24 8 0.23
25 5 0.14
26 17 0.49
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAATAATAATAATAATAAA
Found at i:2141812 original size:26 final size:28
Alignment explanation
Indices: 2141746--2141812 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 28
2141736 TTTTACCTAC
*
2141746 AAAATAATAATAATAATAATAAATAATA
1 AAAATAATAATGATAATAATAAATAATA
2141774 ATAAATAATAATGATAATAA-AAA-AATA
1 A-AAATAATAATGATAATAATAAATAATA
*
2141801 AAAATAAAAATG
1 AAAATAATAATG
2141813 GGTCTCTAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
26 10 0.28
27 5 0.14
28 4 0.11
29 17 0.47
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (28 bp):
AAAATAATAATGATAATAATAAATAATA
Found at i:2145759 original size:3 final size:3
Alignment explanation
Indices: 2145746--2145835 Score: 54
Period size: 3 Copynumber: 29.7 Consensus size: 3
2145736 TCCGTCCCAT
* * * * * * * *
2145746 TTA TGA TTA TTA TTA TTA TTA TTA CTA TTA CTA CTA CTA CTA CTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
2145794 CTA CTA TTA TTG TTG TTA TTA TAAA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TT
2145836 TAAGGCTTTA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
3 74 0.97
4 2 0.03
ACGTcount: A:0.32, C:0.10, G:0.03, T:0.54
Consensus pattern (3 bp):
TTA
Found at i:2148192 original size:131 final size:131
Alignment explanation
Indices: 2147828--2148192 Score: 459
Period size: 131 Copynumber: 2.8 Consensus size: 131
2147818 TCGGTATTGA
* *
2147828 GAATAGTAATATCTTTTCATTTC-AGTTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTTA
1 GAATAGTAATATCTCTTCATTTCGA-TTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCA
* * * *
2147892 TTTATTCTCGATTGGAAATAATTCA-ATATTACCGCTTTCTCTCGAATCACTATTGATTTTTAAG
65 TTTATTCTCGATTGGAAATAATT-AGATATTATCGTTTTCACTCGAATCACTATTGAATTTTAAG
2147956 ACG
129 ACG
* * * * *
2147959 AAATGGTGATATCTCTTCATTTCGATTGGAG-AAGTAAATGACTGCTTTAAGGTATGAGAGGTCA
1 GAATAGTAATATCTCTTCATTTCGATTGGAGTAA-TAAATGAATGCTTTAAGGCATGAGAGGTCA
* *
2148023 TTTATTCTCGATTGGAAATCATTAGATATTATTGTTTTCACTCGAATCGA-TATTGAATTTTAAG
65 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAATC-ACTATTGAATTTTAAG
*
2148087 ATG
129 ACG
* * * * * *
2148090 GAATAATAATATCTCTTCATTTCGATTGGAGTAATAAATGATTGTTTTAAGGCAGGAAATGTCAT
1 GAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
* * *
2148155 TTATTATCGGTTGGAAATAATTAGATATTATCATTTTC
66 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTC
2148193 TCTATTAAAA
Statistics
Matches: 200, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
130 3 0.01
131 193 0.96
132 4 0.02
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (131 bp):
GAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTCGAATCACTATTGAATTTTAAGAC
G
Found at i:2156593 original size:134 final size:133
Alignment explanation
Indices: 2156450--2156946 Score: 556
Period size: 134 Copynumber: 3.7 Consensus size: 133
2156440 AACAAGTCTA
* * *
2156450 TCTCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAATAATTCTATCTCGATTCAATCTTCCC
1 TCTCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCC
* * * *
2156515 TGAAGAACAGTGGAATGAATCAACG-TCCTCATATAC-GATTTTCCTTTAAGAAGAAGTATAAAA
66 TGAAGAACAGTGGAATGAATCAACGTTTC-CAGAT-CTAATTTTCC-ATAAGAAGAAGTATAAAA
2156578 TATCCC
128 TATCCC
* * *
2156584 TCTCTTTCAAGATTTGATCTTTCCTGACTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCT
1 TCTCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCC
* * * * *
2156649 TGAATAATAGTGGAATGAATCAATGTTTCCAGATCTAATTTTACCACAAGAAGAAGCGA-AATAA
66 TGAAGAACAGTGGAATGAATCAACGTTTCCAGATCTAATTTT-CCATAAGAAGAAG-TATAA-AA
**
2156713 -ATCAT
128 TATCCC
* * * * *
2156718 TCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAATAAATCTACCTCAATTCAATCTTCAC
1 TCTCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCC
* * ** * *
2156783 TGAAGAACAATTGAATGAATCAATATTTCCAGATCTAATTTTCCCTCAG--GAAGTAATGAAACA
66 TGAAGAACAGTGGAATGAATCAACGTTTCCAGATCTAATTTTCCATAAGAAGAAGT-AT-AAA-A
*
2156846 TATTCC
128 TATCCC
* ** * *
2156852 TCTCTTTCAAAGACTTGATCTAACCTGAGTAACAGTGGAACAAGTCTTCCTTGATTCAATCTTCC
1 TCTCTTTC-AAGATTTGATCTTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCC
2156917 CTGAAGAACAGTGGAATGAATCAACGTTTC
65 CTGAAGAACAGTGGAATGAATCAACGTTTC
2156947 TCGATCTGAT
Statistics
Matches: 301, Mismatches: 51, Indels: 21
0.81 0.14 0.06
Matches are distributed among these distances:
131 5 0.02
132 1 0.00
133 8 0.03
134 208 0.69
135 79 0.26
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (133 bp):
TCTCTTTCAAGATTTGATCTTCCCTGAGTAACAGTGGAACAAGTCTACCTCGATTCAATCTTCCC
TGAAGAACAGTGGAATGAATCAACGTTTCCAGATCTAATTTTCCATAAGAAGAAGTATAAAATAT
CCC
Found at i:2157117 original size:3 final size:3
Alignment explanation
Indices: 2157109--2157153 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
2157099 TTTTTGTCCC
2157109 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2157154 TTCAAGCTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2159348 original size:131 final size:130
Alignment explanation
Indices: 2159141--2159500 Score: 431
Period size: 131 Copynumber: 2.7 Consensus size: 130
2159131 TGACATTTAG
* * *
2159141 AATAGTAATATTTTTTCATTTCAG-TTGGAGTAATAAATGATTG-CTCTAAGGCATGAGAGGTCA
1 AATAGTAATATCTCTTCATTT-AGATTGGAGTAATAAATGATTGCCT-TAAGGTATGAGAGGTCA
* * *
2159204 TTTATTCAT-AATTGGAAATAATTCAATATTATCATTTTCTCTCAAATCAATATTGATTTTTAAG
64 TTTATTC-TCAATTGGAAATAATT-AATATTATCATTTTCACTCAAATCAATATTAAATTTTAAG
2159268 ACAA
127 ACAA
* * * *
2159272 AATGGTGATATCTCTTCATTTAGATTAGAGCAATAAATGATTGCCTTAAGGTATGAGAGGTCATT
1 AATAGTAATATCTCTTCATTTAGATTGGAGTAATAAATGATTGCCTTAAGGTATGAGAGGTCATT
* * *
2159337 TATTCTCAATTGGAAATCATTAGATATTATCATTTTCACTCGAATCGATATTAAATTTTAAGACA
66 TATTCTCAATTGGAAATAATTA-ATATTATCATTTTCACTCAAATCAATATTAAATTTTAAGACA
2159402 A
130 A
* * * * * * *
2159403 AATAGTAATATCTTTTCATTTCGATTGGAGTGAGAACTGATTTCTTTAAGGTATGAGAGGTCGA-
1 AATAGTAATATCTCTTCATTTAGATTGGAGTAATAAATGATTGCCTTAAGGTATGAGAGGTC-AT
* *
2159467 TTATTCTCGATAGGAAATAATTAAATATTATCAT
65 TTATTCTCAATTGGAAATAATT-AATATTATCAT
2159501 ACTTTGTCCT
Statistics
Matches: 196, Mismatches: 27, Indels: 12
0.83 0.11 0.05
Matches are distributed among these distances:
130 4 0.02
131 188 0.96
132 4 0.02
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (130 bp):
AATAGTAATATCTCTTCATTTAGATTGGAGTAATAAATGATTGCCTTAAGGTATGAGAGGTCATT
TATTCTCAATTGGAAATAATTAATATTATCATTTTCACTCAAATCAATATTAAATTTTAAGACAA
Found at i:2162705 original size:20 final size:20
Alignment explanation
Indices: 2162676--2162714 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2162666 AGAGCTCATA
*
2162676 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
2162696 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
2162715 ATGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:2171853 original size:3 final size:3
Alignment explanation
Indices: 2171845--2171876 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2171835 AACAGTTAGA
2171845 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2171877 AACAATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2178566 original size:2 final size:2
Alignment explanation
Indices: 2178559--2178595 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2178549 TATTCTTCAA
2178559 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2178596 AAATACGTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2181276 original size:29 final size:29
Alignment explanation
Indices: 2181195--2181280 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 29
2181185 GTCAAAATGT
* *
2181195 AACTTTTTAAAATTATCATTTTGGTCCCTA
1 AACTTTTTAAAATT-TTATTTTGGTCACTA
* *
2181225 AACTTTTTAAAGTTTATACTTTGGTCACTA
1 AACTTTTTAAAATTT-TATTTTGGTCACTA
* *
2181255 ATCTTTTAAAAATTTTATTTTGGTCA
1 AACTTTTTAAAATTTTATTTTGGTCA
2181281 TTAACCAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 11 0.23
30 36 0.77
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (29 bp):
AACTTTTTAAAATTTTATTTTGGTCACTA
Found at i:2182116 original size:39 final size:39
Alignment explanation
Indices: 2182061--2182207 Score: 138
Period size: 39 Copynumber: 3.8 Consensus size: 39
2182051 ACCCAGTAAG
* *
2182061 GACTTACTCTGTGCACAAAGCAGAGGAGCCTGCAATAAA
1 GACTTACCCTGAGCACAAAGCAGAGGAGCCTGCAATAAA
* * * *
2182100 GACTTACCCTGAGCACAAAGCCGTGGAGCTTGC-ATTAA
1 GACTTACCCTGAGCACAAAGCAGAGGAGCCTGCAATAAA
* * * * * * *
2182138 G-GTTACCTTGAACACAAAGCCGAGGAGTCTTCAGTAAA
1 GACTTACCCTGAGCACAAAGCAGAGGAGCCTGCAATAAA
*
2182176 GACTTACCCTGAGCACAAAACCA-AGGAGCCTG
1 GACTTACCCTGAGCAC-AAAGCAGAGGAGCCTG
2182208 TGGAAAGCAG
Statistics
Matches: 83, Mismatches: 22, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
37 24 0.29
38 9 0.11
39 46 0.55
40 4 0.05
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.18
Consensus pattern (39 bp):
GACTTACCCTGAGCACAAAGCAGAGGAGCCTGCAATAAA
Found at i:2182279 original size:44 final size:44
Alignment explanation
Indices: 2182217--2182302 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
2182207 GTGGAAAGCA
* *
2182217 GTAAGGTCTCACCGTTGCACATAGCAGATGAGCCTTCAGAAATG
1 GTAAGGTCTCACCCTTGCACATAACAGATGAGCCTTCAGAAATG
* * *
2182261 GTAAGGTCTTACCCTTGCACATAACATATGAGCCTTTAGAAA
1 GTAAGGTCTCACCCTTGCACATAACAGATGAGCCTTCAGAAA
2182303 CTTCCTCTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (44 bp):
GTAAGGTCTCACCCTTGCACATAACAGATGAGCCTTCAGAAATG
Found at i:2188772 original size:38 final size:38
Alignment explanation
Indices: 2188702--2188774 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 38
2188692 ATACAAATGT
* * * *
2188702 CAGAAAACTGTATAAAACATATGCATATCAAAATACCA
1 CAGAAAACCGTATAAAACATATACAGAACAAAATACCA
* *
2188740 CAGAAAACCGTATAAAACATTTACGGAACAAAATA
1 CAGAAAACCGTATAAAACATATACAGAACAAAATA
2188775 TCGGTAATAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 29 1.00
ACGTcount: A:0.53, C:0.18, G:0.10, T:0.19
Consensus pattern (38 bp):
CAGAAAACCGTATAAAACATATACAGAACAAAATACCA
Found at i:2189170 original size:39 final size:39
Alignment explanation
Indices: 2189106--2189222 Score: 137
Period size: 39 Copynumber: 3.0 Consensus size: 39
2189096 CCTGTACACC
* * * *
2189106 CAGTAAGGACTTACCTTGTGCACAAAGTAGAGGAGCCTG
1 CAGTAAGAACTTACCCTGAGCACAAAGTCGAGGAGCCTG
* * * *
2189145 CAGTAA-AGATTTACCCTGAGTACAAAGCCGAGGAGCCTA
1 CAGTAAGA-ACTTACCCTGAGCACAAAGTCGAGGAGCCTG
*
2189184 CAGTAAGAACTTACTCTGAGCACAAAGTCGAGGAGCCTG
1 CAGTAAGAACTTACCCTGAGCACAAAGTCGAGGAGCCTG
2189223 TGGAAAGAGG
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
39 62 0.98
40 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (39 bp):
CAGTAAGAACTTACCCTGAGCACAAAGTCGAGGAGCCTG
Found at i:2189337 original size:44 final size:44
Alignment explanation
Indices: 2189231--2189361 Score: 192
Period size: 44 Copynumber: 3.0 Consensus size: 44
2189221 TGTGGAAAGA
* * * * * *
2189231 GGTAAGGCCTCACCCTTGCACATAGGAGATGAGACTTCAG-AAT
1 GGTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAAC
2189274 GGTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAAC
1 GGTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAAC
*
2189318 GGTAAGGTCTTACCCTTGCACATAGCATAGGAGCCTTCAGAAAC
1 GGTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAAC
2189362 TTCCTTCAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
43 35 0.44
44 45 0.56
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.21
Consensus pattern (44 bp):
GGTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAAC
Found at i:2202426 original size:19 final size:19
Alignment explanation
Indices: 2202385--2202461 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 19
2202375 CAATTATTAT
2202385 TATTATTTATTTTTA--ATA
1 TATT-TTTATTTTTATGATA
2202403 -A-TTTTATTTTTATGATA
1 TATTTTTATTTTTATGATA
*
2202420 TA---TT-TTTTTATGACA
1 TATTTTTATTTTTATGATA
*
2202435 CATTTTTTATTTTT-TGATA
1 TA-TTTTTATTTTTATGATA
2202454 TATTTTTA
1 TATTTTTA
2202462 AGATTGAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
15 21 0.45
16 3 0.06
17 4 0.09
18 7 0.15
19 7 0.15
20 5 0.11
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (19 bp):
TATTTTTATTTTTATGATA
Found at i:2210035 original size:17 final size:17
Alignment explanation
Indices: 2210013--2210051 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2210003 CTCTTCGGAT
*
2210013 GGTGCGATAGGCATAAG
1 GGTGCGACAGGCATAAG
*
2210030 GGTGCGACAGGCGTAAG
1 GGTGCGACAGGCATAAG
*
2210047 AGTGC
1 GGTGC
2210052 ATAATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.44, T:0.15
Consensus pattern (17 bp):
GGTGCGACAGGCATAAG
Found at i:2211689 original size:12 final size:12
Alignment explanation
Indices: 2211672--2211706 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
2211662 ATTATGTAAT
2211672 ATGATGATATCC
1 ATGATGATATCC
2211684 ATGATGATATCC
1 ATGATGATATCC
2211696 ATGATGATATC
1 ATGATGATATC
2211707 ACCCTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (12 bp):
ATGATGATATCC
Found at i:2215119 original size:20 final size:20
Alignment explanation
Indices: 2215094--2215143 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
2215084 ACTGCTGTGA
2215094 GTATCGATACTAAGAGAAAG
1 GTATCGATACTAAGAGAAAG
*
2215114 GTATCGTTACTAAGAGAAAG
1 GTATCGATACTAAGAGAAAG
2215134 GTATCGATAC
1 GTATCGATAC
2215144 CATGGATTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (20 bp):
GTATCGATACTAAGAGAAAG
Found at i:2215171 original size:34 final size:34
Alignment explanation
Indices: 2215128--2215211 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
2215118 CGTTACTAAG
2215128 AGAAA-GGTATCGATACCATGGATTCCAGAATGC
1 AGAAATGGTATCGATACCATGGATTCCAGAATGC
2215161 AGAAATGGTATCGATACCATGGATTCCAGAATGC
1 AGAAATGGTATCGATACCATGGATTCCAGAATGC
2215195 AGAAATGGTATCGATAC
1 AGAAATGGTATCGATAC
2215212 TAAAAGGGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 5 0.10
34 45 0.90
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.23
Consensus pattern (34 bp):
AGAAATGGTATCGATACCATGGATTCCAGAATGC
Found at i:2215810 original size:49 final size:49
Alignment explanation
Indices: 2215699--2215812 Score: 183
Period size: 49 Copynumber: 2.3 Consensus size: 49
2215689 GTTCAATCGA
* *
2215699 CATAAAAGACGCCACTAATGAAAGTTAAATGCATAACGGTGTATTTCGG
1 CATAAAAGATGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGG
*
2215748 CATAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGG
1 CATAAAAGATGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGG
* *
2215797 TATAAAAGTTGCCACT
1 CATAAAAGATGCCACT
2215813 CATAGTATTC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 60 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (49 bp):
CATAAAAGATGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGG
Found at i:2220703 original size:9 final size:9
Alignment explanation
Indices: 2220689--2220715 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2220679 CCATAGTGTT
2220689 TTATACACC
1 TTATACACC
2220698 TTATACACC
1 TTATACACC
2220707 TTATACACC
1 TTATACACC
2220716 GTAGTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (9 bp):
TTATACACC
Found at i:2224671 original size:44 final size:45
Alignment explanation
Indices: 2224615--2224717 Score: 145
Period size: 44 Copynumber: 2.3 Consensus size: 45
2224605 ATGGTTTATG
* **
2224615 GTATATTGGTAAAATAAGCTTATGAGCTT-TGGGATAAATGGTAA
1 GTATATTGGTAAAATAAACTTACAAGCTTATGGGATAAATGGTAA
**
2224659 GTATATTGGTAAAATAAACTTACAAGCTTATGGGATAAATTTTAA
1 GTATATTGGTAAAATAAACTTACAAGCTTATGGGATAAATGGTAA
*
2224704 GTATATTGATAAAA
1 GTATATTGGTAAAA
2224718 ATTTTATATT
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 26 0.50
45 26 0.50
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (45 bp):
GTATATTGGTAAAATAAACTTACAAGCTTATGGGATAAATGGTAA
Found at i:2230667 original size:13 final size:13
Alignment explanation
Indices: 2230651--2230680 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2230641 CTTAATTGCG
2230651 AAAATTAAAATTT
1 AAAATTAAAATTT
*
2230664 AAAATTTAAATTT
1 AAAATTAAAATTT
2230677 AAAA
1 AAAA
2230681 GCATTCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:2232925 original size:36 final size:36
Alignment explanation
Indices: 2232873--2232945 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
2232863 GGTTGACATA
*
2232873 TAGCTCTTCTCGACTTAAGCTATACTGCAAATGATG
1 TAGCCCTTCTCGACTTAAGCTATACTGCAAATGATG
*
2232909 TAGCCCTTCTTGACTTAAGCTATACTGCAAATGATG
1 TAGCCCTTCTCGACTTAAGCTATACTGCAAATGATG
2232945 T
1 T
2232946 GCCTTTGAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.34
Consensus pattern (36 bp):
TAGCCCTTCTCGACTTAAGCTATACTGCAAATGATG
Found at i:2233017 original size:120 final size:121
Alignment explanation
Indices: 2232787--2233034 Score: 281
Period size: 120 Copynumber: 2.1 Consensus size: 121
2232777 TATTGACAGA
* * * * *
2232787 TAGCCCTTCTTGCCTTGAGCTATGCTGTAAATCTGATTCGCCTCTGAGCTGAGTGTAATCGAACT
1 TAGCCCTTCTTGACTTAAGCTATACTGCAAA-CTGATTCGCCTCTGAGCTGAGCGTAATCGAACT
* * * * *
2232852 CGAAGGTTTTTGGTTGACATATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATG
65 CGAAGGTTTTTAGTTGACATATAACCCTTATAGACTTAAGCTATACTGCAAATGATG
* *
2232909 TAGCCCTTCTTGACTTAAGCTATACTGCAAA-TGATGT-GCCTTTGAGCTGAGCGTAGTCGAACT
1 TAGCCCTTCTTGACTTAAGCTATACTGCAAACTGAT-TCGCCTCTGAGCTGAGCGTAATCGAACT
* * * *
2232972 CGAAGGTTTTTTAG-TGAC-TGATAACCCTTATAGCCTTGAGTTATACTGTAAATGATG
65 CGAAGG-TTTTTAGTTGACAT-ATAACCCTTATAGACTTAAGCTATACTGCAAATGATG
2233029 T-GCCCT
1 TAGCCCT
2233035 CGAAGCTGAA
Statistics
Matches: 107, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
119 6 0.06
120 67 0.63
121 7 0.07
122 27 0.25
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (121 bp):
TAGCCCTTCTTGACTTAAGCTATACTGCAAACTGATTCGCCTCTGAGCTGAGCGTAATCGAACTC
GAAGGTTTTTAGTTGACATATAACCCTTATAGACTTAAGCTATACTGCAAATGATG
Found at i:2233029 original size:84 final size:80
Alignment explanation
Indices: 2232912--2233596 Score: 584
Period size: 84 Copynumber: 8.3 Consensus size: 80
2232902 AATGATGTAG
* * *
2232912 CCCTTCTTGACTTAAGCTATACTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* *
2232977 GTTTTTTAGTGACTGATAA
66 G-TCTTT-G-G-CAGATAA
* * * * * * ** * ** * *
2232996 CCCTTATAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAATGTAATTAAACTTGAG
1 CCCTTCTAGACTTAAGTTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA
2233061 GGTCTTTGGCAGATAA
65 GGTCTTTGGCAGATAA
* * * * * * *
2233077 CCCTTCTAGCCTTGAGCTATACTGCAAATGATATGCCGTT-GAGCTGAGTGTAATCGAACTCAAA
1 CCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAA
*
2233141 GGTCTTTGGCAGATAG
65 GGTCTTTGGCAGATAA
* ** * * *
2233157 CCCTTCTCGACTTAAGTTATACTATAAATGTTGTGACTTGGAGCTGAGCGTAGTCAAACTCGAAG
1 CCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
2233222 GTCTTTTGGTTACAGATAA
66 GTC-TTTGG---CAGATAA
* * * * * * * * * *
2233241 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGATGAGTGTAATCGAACTCGAG
1 CCCTTCTAGACTTAAGTTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA
*
2233306 GGTCTTTGGCAGATAG
65 GGTCTTTGGCAGATAA
* ** * * * *
2233322 CCTTTCCCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAG
1 CCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
2233387 GTCTTTGGTTGGAAGATAA
66 GTC--T--TTGGCAGATAA
*
2233406 CCCTTC-ACGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
1 CCCTTCTA-GACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
*
2233470 GGTCTTTGGATGGCAGGTAA
65 GGTC-TT---TGGCAGATAA
* * * **
2233490 CCTTTCTTGATTTAAACTATACTGCAAAT-ATTGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
1 CCCTTCTAGACTTAAGTTATACTGCAAATGA-TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
2233554 GGTCTTTAGTTGGCAGATAA
65 GGTC--T--TTGGCAGATAA
* *
2233574 CCCTTCTAGCCTTGAGTTATACT
1 CCCTTCTAGACTTAAGTTATACT
2233597 AAAATGTTAT
Statistics
Matches: 482, Mismatches: 98, Indels: 42
0.77 0.16 0.07
Matches are distributed among these distances:
79 2 0.00
80 112 0.23
81 77 0.16
82 2 0.00
83 4 0.01
84 236 0.49
85 48 0.10
87 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (80 bp):
CCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
GTCTTTGGCAGATAA
Found at i:2233349 original size:245 final size:247
Alignment explanation
Indices: 2232909--2233476 Score: 782
Period size: 245 Copynumber: 2.3 Consensus size: 247
2232899 GCAAATGATG
* * *
2232909 TAGCCCTTCTTGACTTAAGCTATACTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCG
1 TAGCCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCG
* *
2232974 AAGGTTTTTTAGTGACTGATAACCCTTATAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAA
66 AAGGTCTTTTAGTGACAGATAACCCTTATAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAA
* * * * * *
2233039 GCTGAATGTAATTAAACTTGAGGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGCTATACTGCAA
131 GATGAATGTAATCAAACTCGAGGGTCTTTGGCAGATAACCCTTCCAGACTTAAGCTATACTGCAA
* * *
2233104 ATGATATGCCGTT-GAGCTGAGTGTAATCGAACTCAAAGGTC-T-TTGGCAGA
196 ATGATATGCC-TTGGAGCTGAGCGTAATCAAACTCAAAGGTCTTGTTGGAAGA
** * * *
2233154 TAGCCCTTCTCGACTTAAGTTATACTATAAATGTTGTGACTTGGAGCTGAGCGTAGTCAAACTCG
1 TAGCCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCG
* * * *
2233219 AAGGTCTTTTGGTTACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAA
66 AAGGTCTTTTAGTGACAGATAACCCTTATAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAA
* * * * * *
2233284 GATGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCTTTCCCGACTTAAGCTATGCTGCAA
131 GATGAATGTAATCAAACTCGAGGGTCTTTGGCAGATAACCCTTCCAGACTTAAGCTATACTGCAA
* *
2233349 ATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGAAGA
196 ATGATATGCCTTGGAGCTGAGCGTAATCAAACTCAAAGGTC-TT-GTTGGAAGA
* * *
2233403 TAACCCTTCACGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCG
1 TAGCCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCG
2233468 AAGGTCTTT
66 AAGGTCTTT
2233477 GGATGGCAGG
Statistics
Matches: 279, Mismatches: 39, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
244 2 0.01
245 203 0.73
247 1 0.00
249 73 0.26
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (247 bp):
TAGCCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCG
AAGGTCTTTTAGTGACAGATAACCCTTATAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAA
GATGAATGTAATCAAACTCGAGGGTCTTTGGCAGATAACCCTTCCAGACTTAAGCTATACTGCAA
ATGATATGCCTTGGAGCTGAGCGTAATCAAACTCAAAGGTCTTGTTGGAAGA
Found at i:2233364 original size:165 final size:164
Alignment explanation
Indices: 2232933--2233593 Score: 665
Period size: 165 Copynumber: 4.0 Consensus size: 164
2232923 TTAAGCTATA
* * * * * *
2232933 CTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTAGTGACTGATAACC
1 CTGCAAATGATGTGCCCTTGAGCTGAGTGTAATCGAACTCGAAGG-TCTTT-G-G-CAGATAGCC
* * * * * * * * * ** * * * *
2232998 CTTATAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAATGTAATTAAACTTGAGGG
62 TTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCAAACTCGAAGG
* *
2233063 TCTTT-G--G-CAGATAACCCTTCTAGCCTTGAGCTATA
126 TCTTTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * *
2233098 CTGCAAATGATATGCCGTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGCAGATAGCCCTTC
1 CTGCAAATGATGTGCCCTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCTTTC
* ** * *
2233163 TCGACTTAAGTTATACTATAAATGTTGTGACTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTT
66 TCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC-TT
2233228 TGGTT-ACAGATAACCCTTCTAGCCTTGAGTTATG
130 TGGTTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * *
2233262 CTGTAAATGATGTGCCCTCGAAGATGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCTTT
1 CTGCAAATGATGTGCCCTTG-AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCTTT
* * *
2233327 CCCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTT
65 CTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTT
* *
2233392 TGGTTGGA-AGATAACCCTTC-ACGACTTAAGTTATG
130 TGGTT-GACAGATAACCCTTCTA-GCCTTGAGTTATG
* * * *
2233427 CTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGATGGCAGGTAAC
1 CTGCAAATGATGTGCCCTT-GAGCTGAGTGTAATCGAACTCGAAGGTC-TT---TGGCAGATAGC
* * * *
2233491 CTTTCTTGATTTAAACTATACTGCAAAT-ATTGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
61 CTTTCTCGACTTAAGCTATACTGCAAATGA-TGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAG
* *
2233555 GTCTTTAGTTGGCAGATAACCCTTCTAGCCTTGAGTTAT
125 GTCTTTGGTTGACAGATAACCCTTCTAGCCTTGAGTTAT
2233594 ACTAAAATGT
Statistics
Matches: 417, Mismatches: 62, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
160 24 0.06
161 37 0.09
162 2 0.00
163 1 0.00
164 80 0.19
165 174 0.42
166 1 0.00
167 2 0.00
168 95 0.23
169 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (164 bp):
CTGCAAATGATGTGCCCTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCTTTC
TCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTT
GGTTGACAGATAACCCTTCTAGCCTTGAGTTATG
Found at i:2234949 original size:95 final size:94
Alignment explanation
Indices: 2234782--2234979 Score: 274
Period size: 95 Copynumber: 2.1 Consensus size: 94
2234772 GGACAACTTA
** * * * *
2234782 ATATATAAACACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAATTG
1 ATATATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCATTTAACCAATTG
*
2234847 CCTTAGAGGGACAACTCAAGCTTTATTGT
66 CCTTAGAGGGACAACTCAAGCTTTATTAT
* *
2234876 ATAGTATAATTACCTTTATTAGGCTAGTTGAATATTATCCATAAAGCC-GAGGCATTTAACCAAT
1 ATA-TATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAG-GGCATTTAACCAAT
2234940 TG-CTCTAGAGGGACAACTCAAGCTTTATTAT
64 TGCCT-TAGAGGGACAACTCAAGCTTTATTAT
2234971 ATATATAAT
1 ATATATAAT
2234980 ATTATAATCT
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
94 12 0.13
95 80 0.87
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (94 bp):
ATATATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGGGCATTTAACCAATTG
CCTTAGAGGGACAACTCAAGCTTTATTAT
Found at i:2238702 original size:23 final size:23
Alignment explanation
Indices: 2238678--2238720 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2238668 TAATTTTTTA
2238678 AAAAATA-ATAATA-AAATAAAGT
1 AAAAATAGATAA-ACAAATAAAGT
2238700 AAAAATAGATAAACAAATAAA
1 AAAAATAGATAAACAAATAAA
2238721 ACAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (23 bp):
AAAAATAGATAAACAAATAAAGT
Found at i:2240435 original size:24 final size:24
Alignment explanation
Indices: 2240408--2240456 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
2240398 TGCATGACAT
*
2240408 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATATTTTATACATCA
*
2240432 TGTATATAGATATTTTATACATCA
1 TGTACATAGATATTTTATACATCA
2240456 T
1 T
2240457 CGGGAAGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (24 bp):
TGTACATAGATATTTTATACATCA
Found at i:2241042 original size:45 final size:45
Alignment explanation
Indices: 2240985--2241087 Score: 154
Period size: 45 Copynumber: 2.3 Consensus size: 45
2240975 ATGGTTTATG
2240985 GTATATTGGTAAAATAAGA-TTACAAGCTTATAAGATAAATGGTAA
1 GTATATTGGTAAAATAA-ACTTACAAGCTTATAAGATAAATGGTAA
** *
2241030 GTATATTGGTAAAATAAACTTACAAGCTTATGGGATATATGGTAA
1 GTATATTGGTAAAATAAACTTACAAGCTTATAAGATAAATGGTAA
*
2241075 GTATATTGATAAA
1 GTATATTGGTAAA
2241088 GAATTTATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 1 0.02
45 52 0.98
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (45 bp):
GTATATTGGTAAAATAAACTTACAAGCTTATAAGATAAATGGTAA
Found at i:2243732 original size:14 final size:14
Alignment explanation
Indices: 2243713--2243753 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
2243703 GGCATAAGAG
2243713 AAAAAGAAAAAAAA
1 AAAAAGAAAAAAAA
2243727 AAAAAG-AAAAAAA
1 AAAAAGAAAAAAAA
*
2243740 AAAGAGAAAAAAAA
1 AAAAAGAAAAAAAA
2243754 TGAGAGATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAA
Found at i:2243758 original size:12 final size:12
Alignment explanation
Indices: 2243708--2243758 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
2243698 AAGAAGGCAT
*
2243708 AAGAGAAAAAGA
1 AAGAGAAAAAAA
2243720 AA-A-AAAAAAA
1 AAGAGAAAAAAA
2243730 AAGA-AAAAAAA
1 AAGAGAAAAAAA
2243741 AAGAGAAAAAAA
1 AAGAGAAAAAAA
*
2243753 ATGAGA
1 AAGAGA
2243759 GATGCTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 8 0.23
11 13 0.37
12 14 0.40
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (12 bp):
AAGAGAAAAAAA
Found at i:2243760 original size:14 final size:13
Alignment explanation
Indices: 2243713--2243753 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
2243703 GGCATAAGAG
2243713 AAAAAGA-AAAAA
1 AAAAAGAGAAAAA
*
2243725 AAAAAAAGAAAAA
1 AAAAAGAGAAAAA
2243738 AAAAAGAGAAAAA
1 AAAAAGAGAAAAA
2243751 AAA
1 AAA
2243754 TGAGAGATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 6 0.23
13 20 0.77
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAGAGAAAAA
Found at i:2247759 original size:45 final size:45
Alignment explanation
Indices: 2247702--2247805 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
2247692 TGGTTTATGG
*
2247702 TATATTGGTAAAATAAGCTTACGAGCTTATAGGATAACTGGTAAA
1 TATATTGGTAAAATAAGCTTACGAGCTTATAGGATAAATGGTAAA
* * *
2247747 TATATTGGTAAAATAAGCTTATGAGCTTATGGGATAAATGGTAAG
1 TATATTGGTAAAATAAGCTTACGAGCTTATAGGATAAATGGTAAA
*
2247792 TATATTGATAAAAT
1 TATATTGGTAAAAT
2247806 TTTATATTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (45 bp):
TATATTGGTAAAATAAGCTTACGAGCTTATAGGATAAATGGTAAA
Found at i:2251471 original size:19 final size:19
Alignment explanation
Indices: 2251447--2251487 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2251437 GCACACCATA
2251447 AAAACAGATTAATTTTAAT
1 AAAACAGATTAATTTTAAT
** *
2251466 AAAACATTTTAATTTTATT
1 AAAACAGATTAATTTTAAT
2251485 AAA
1 AAA
2251488 GTACCAAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (19 bp):
AAAACAGATTAATTTTAAT
Done.