Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008887.1 Hibiscus syriacus cultivar Beakdansim tig00112152_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: 452931
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
File 2 of 2
Found at i:368866 original size:20 final size:20
Alignment explanation
Indices: 368822--368866 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
368812 AGATCCTTGA
368822 GAAAGTGCTCAACCCAAGCC
1 GAAAGTGCTCAACCCAAGCC
* * *
368842 AAAAGTGGTCAACCCAAGCT
1 GAAAGTGCTCAACCCAAGCC
368862 GAAAG
1 GAAAG
368867 GGGTGGTCAC
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:0.40, C:0.27, G:0.22, T:0.11
Consensus pattern (20 bp):
GAAAGTGCTCAACCCAAGCC
Found at i:370904 original size:15 final size:15
Alignment explanation
Indices: 370881--370916 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
370871 GATATGTAAC
*
370881 ACCCATCTCCCGTAT
1 ACCCTTCTCCCGTAT
370896 ACCCTTCTCCCGTAT
1 ACCCTTCTCCCGTAT
370911 ACCCTT
1 ACCCTT
370917 TGTACATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.17, C:0.47, G:0.06, T:0.31
Consensus pattern (15 bp):
ACCCTTCTCCCGTAT
Found at i:371306 original size:2 final size:2
Alignment explanation
Indices: 371299--371332 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
371289 ATTGAAATCA
371299 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
371333 CATTATTCTT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:371491 original size:54 final size:54
Alignment explanation
Indices: 371448--372065 Score: 423
Period size: 54 Copynumber: 11.3 Consensus size: 54
371438 TTTCGTGTTT
*
371448 TCCATACCTAGTGCCGAAATGGTTATTCATCCACTTAGGATGAATTCCGTGAAA
1 TCCACACCTAGTGCCGAAATGGTTATTCATCCACTTAGGATGAATTCCGTGAAA
* * * * * * *
371502 TGCACACTTAGTGCTGAAATGGTTATTCATCCACATAGAATAAATTCCTTGAAA
1 TCCACACCTAGTGCCGAAATGGTTATTCATCCACTTAGGATGAATTCCGTGAAA
* * * * * * * *
371556 TGCACACTTAGTGTCAAAACGGTTATTCATCCCCATAGGATGAATTCCATGAAA
1 TCCACACCTAGTGCCGAAATGGTTATTCATCCACTTAGGATGAATTCCGTGAAA
* * * * * * *
371610 TGCACACTTTA-TGCCAAAACGATTATTCATCCACATAGGATGAATTCCATGAAA
1 TCCACAC-CTAGTGCCGAAATGGTTATTCATCCACTTAGGATGAATTCCGTGAAA
* * * * **
371664 TACACACTTAGTGTCGAAACGGTTATTCATCCAAATAGGATGAATTCCGTGAAA
1 TCCACACCTAGTGCCGAAATGGTTATTCATCCACTTAGGATGAATTCCGTGAAA
* * * * * * * *
371718 TGCACACAC-AGTGCCAAAATAGTTATTCATCCCCATAGGATGAATTTCGCGACA
1 TCCACAC-CTAGTGCCGAAATGGTTATTCATCCACTTAGGATGAATTCCGTGAAA
* * * * * *
371772 TGCACACTTTGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCTGTGAAA
1 TCCACACCTAGTGCCGAAATGGTTATTCATCCACTTAGGATGAATTCCGTGAAA
* * * * * *
371826 TGCACACTTAGTGTCGAAACGATTATTCATCCACATAAGATACATAGGATGAATTGCGTGAAA
1 TCCACACCTAGTGCCGAAATGGTTATTCATCCAC------T---TAGGATGAATTCCGTGAAA
* * * * ** * * *
371889 TGCACTCTTAGTGCCAAAACAGTTATTCATCCACATAGGATGAATTCCATGAAT
1 TCCACACCTAGTGCCGAAATGGTTATTCATCCACTTAGGATGAATTCCGTGAAA
* * * * * * *
371943 TGCACACTTAGTGACGAAATGGTTATTCATCCCCATATGATGAATTCCGTTAAA
1 TCCACACCTAGTGCCGAAATGGTTATTCATCCACTTAGGATGAATTCCGTGAAA
* * ** ** * * *
371997 TGCACACTTTTTTTCGAAACGATTATTCATCCA-TATAGGATGAATTCTGTGAAA
1 TCCACACCTAGTGCCGAAATGGTTATTCATCCACT-TAGGATGAATTCCGTGAAA
* *
372051 TGCACACTTAGTGCC
1 TCCACACCTAGTGCC
372066 TATTTGGTAA
Statistics
Matches: 464, Mismatches: 86, Indels: 28
0.80 0.15 0.05
Matches are distributed among these distances:
53 3 0.01
54 412 0.89
55 3 0.01
63 46 0.10
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (54 bp):
TCCACACCTAGTGCCGAAATGGTTATTCATCCACTTAGGATGAATTCCGTGAAA
Found at i:371598 original size:108 final size:108
Alignment explanation
Indices: 371456--372065 Score: 684
Period size: 108 Copynumber: 5.6 Consensus size: 108
371446 TTTCCATACC
* * * *
371456 TAGTGCCGAAATGGTTATTCATCCACTTAGGATGAATTCCGTGAAATGCACACTTAGTGCTGAAA
1 TAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAA
* *
371521 TGGTTATTCATCCACATAGAATAAATTCCTTGAAATGCACACT
66 TGGTTATTCATCCACATAGAATGAATTCCGTGAAATGCACACT
* * * *
371564 TAGTGTCAAAACGGTTATTCATCCCCATAGGATGAATTCCATGAAATGCACACTTTA-TGCCAAA
1 TAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACAC-TTAGTGCCGAA
* * * * *
371628 ACGATTATTCATCCACATAGGATGAATTCCATGAAATACACACT
65 ATGGTTATTCATCCACATAGAATGAATTCCGTGAAATGCACACT
* ** *
371672 TAGTGTCGAAACGGTTATTCATCCAAATAGGATGAATTCCGTGAAATGCACACACAGTGCCAAAA
1 TAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAA
* * * * * *
371737 TAGTTATTCATCCCCATAGGATGAATTTCGCGACATGCACACT
66 TGGTTATTCATCCACATAGAATGAATTCCGTGAAATGCACACT
* * * *
371780 TTGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCTGTGAAATGCACACTTAGTGTCGAAA
1 TAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAA
* * * *
371845 CGATTATTCATCCACATAAGATACATAGGATGAATTGCGTGAAATGCACTCT
66 TGGTTATTCATCCACAT-AG------A--ATGAATTCCGTGAAATGCACACT
* * * * * *
371897 TAGTGCCAAAACAGTTATTCATCCACATAGGATGAATTCCATGAATTGCACACTTAGTGACGAAA
1 TAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAA
* *
371962 TGGTTATTCATCCCCATATG-ATGAATTCCGTTAAATGCACACT
66 TGGTTATTCATCCACATA-GAATGAATTCCGTGAAATGCACACT
** * * * *
372005 TTTTTTCGAAACGATTATTCATCCATATAGGATGAATTCTGTGAAATGCACACTTAGTGCC
1 TAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCC
372066 TATTTGGTAA
Statistics
Matches: 419, Mismatches: 71, Indels: 24
0.82 0.14 0.05
Matches are distributed among these distances:
107 1 0.00
108 320 0.76
109 5 0.01
116 1 0.00
117 92 0.22
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29
Consensus pattern (108 bp):
TAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAA
TGGTTATTCATCCACATAGAATGAATTCCGTGAAATGCACACT
Found at i:371672 original size:162 final size:162
Alignment explanation
Indices: 371459--372065 Score: 741
Period size: 162 Copynumber: 3.7 Consensus size: 162
371449 CCATACCTAG
* * *
371459 TGCCGAAATGGTTATTCATCCACTTAGGATGAATTCCGTGAAATGCACACTTAGTG-CTGAAATG
1 TGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTC-GAAACG
* * * *
371523 GTTATTCATCCACATAGAATAAATTCCTTGAAATGCACACTTAGTGTCAAAACGGTTATTCATCC
65 ATTATTCATCCACATAGAATAAATTCCGTGAAATGCACACTTAGTGCCAAAACAGTTATTCATCC
371588 CCATAGGATGAATTCCATGAAATGCACACTTTA
130 CCATAGGATGAATTCCATGAAATGCACACTTTA
* * * * *
371621 TGCCAAAACGATTATTCATCCACATAGGATGAATTCCATGAAATACACACTTAGTGTCGAAACGG
1 TGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAAACGA
* * * ** *
371686 TTATTCATCCAAATAGGATGAATTCCGTGAAATGCACACACAGTGCCAAAATAGTTATTCATCCC
66 TTATTCATCCACATAGAATAAATTCCGTGAAATGCACACTTAGTGCCAAAACAGTTATTCATCCC
* ** * *
371751 CATAGGATGAATTTCGCGACATGCACACTTTG
131 CATAGGATGAATTCCATGAAATGCACACTTTA
*
371783 TGCCGAAACGGTTATTCATCCACATAGGATGAATTCTGTGAAATGCACACTTAGTGTCGAAACGA
1 TGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAAACGA
* *
371848 TTATTCATCCACATAAGATACATAGGATGAATTGCGTGAAATGCACTCTTAGTGCCAAAACAGTT
66 TTATTCATCCACAT-AG--A-AT---A--AATTCCGTGAAATGCACACTTAGTGCCAAAACAGTT
* *
371913 ATTCATCCACATAGGATGAATTCCATGAATTGCACAC-TTA
122 ATTCATCCCCATAGGATGAATTCCATGAAATGCACACTTTA
* * * * * ** *
371953 GTGACGAAATGGTTATTCATCCCCATATGATGAATTCCGTTAAATGCACACTTTTTTTCGAAACG
1 -TGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAAACG
* * * *
372018 ATTATTCATCCATATAGGATGAATTCTGTGAAATGCACACTTAGTGCC
65 ATTATTCATCCACATAGAATAAATTCCGTGAAATGCACACTTAGTGCC
372066 TATTTGGTAA
Statistics
Matches: 377, Mismatches: 57, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
162 235 0.62
163 3 0.01
166 2 0.01
167 2 0.01
170 4 0.01
171 131 0.35
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (162 bp):
TGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAAACGA
TTATTCATCCACATAGAATAAATTCCGTGAAATGCACACTTAGTGCCAAAACAGTTATTCATCCC
CATAGGATGAATTCCATGAAATGCACACTTTA
Found at i:371915 original size:63 final size:63
Alignment explanation
Indices: 371804--371925 Score: 185
Period size: 63 Copynumber: 1.9 Consensus size: 63
371794 TTATTCATCC
* *
371804 ACATAGGATGAATTCTGTGAAATGCACACTTAGTGTCGAAACGATTATTCATCCACATAAGAT
1 ACATAGGATGAATTCTGTGAAATGCACACTTAGTGCCAAAACGATTATTCATCCACATAAGAT
*
371867 ACATAGGATGAATTGC-GTGAAATGCACTCTTAGTGCCAAAAC-AGTTATTCATCCACATA
1 ACATAGGATGAATT-CTGTGAAATGCACACTTAGTGCCAAAACGA-TTATTCATCCACATA
371926 GGATGAATTC
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
62 1 0.02
63 52 0.96
64 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (63 bp):
ACATAGGATGAATTCTGTGAAATGCACACTTAGTGCCAAAACGATTATTCATCCACATAAGAT
Found at i:371941 original size:63 final size:64
Alignment explanation
Indices: 371811--371945 Score: 161
Period size: 63 Copynumber: 2.1 Consensus size: 64
371801 TCCACATAGG
* * **
371811 ATGAATT-CTGTGAAATGCACACTTAGTGTCGAAACGATTATTCATCCACATAAGATACATAGG
1 ATGAATTGCTGTGAAATGCACACTTAGTGCCAAAACGATTATTCATCCACATAAGATACATACC
* * *
371874 ATGAATTGC-GTGAAATGCACTCTTAGTGCCAAAAC-AGTTATTCATCCACATAGGATGA-ATTC
1 ATGAATTGCTGTGAAATGCACACTTAGTGCCAAAACGA-TTATTCATCCACATAAGAT-ACATAC
371936 C
64 C
371937 ATGAATTGC
1 ATGAATTGC
371946 ACACTTAGTG
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
62 1 0.02
63 59 0.95
64 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (64 bp):
ATGAATTGCTGTGAAATGCACACTTAGTGCCAAAACGATTATTCATCCACATAAGATACATACC
Found at i:371961 original size:117 final size:117
Alignment explanation
Indices: 371751--371979 Score: 332
Period size: 117 Copynumber: 2.0 Consensus size: 117
371741 TATTCATCCC
* * * * *
371751 CATAGGATGAATTTCGCGACATGCACACTTTGTGCCGAAACGGTTATTCATCCACATAGGATGAA
1 CATAGGATGAATTGCGCGAAATGCACACTTAGTGCCAAAACAGTTATTCATCCACATAGGATGAA
** *
371816 TTCTGTGAAATGCACACTTAGTGTCGAAACGATTATTCATCCACATAAGATA
66 TTCCATGAAATGCACACTTAGTGACGAAACGATTATTCATCCACATAAGATA
* *
371868 CATAGGATGAATTGCGTGAAATGCACTCTTAGTGCCAAAACAGTTATTCATCCACATAGGATGAA
1 CATAGGATGAATTGCGCGAAATGCACACTTAGTGCCAAAACAGTTATTCATCCACATAGGATGAA
* * * *
371933 TTCCATGAATTGCACACTTAGTGACGAAATGGTTATTCATCCCCATA
66 TTCCATGAAATGCACACTTAGTGACGAAACGATTATTCATCCACATA
371980 TGATGAATTC
Statistics
Matches: 98, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
117 98 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (117 bp):
CATAGGATGAATTGCGCGAAATGCACACTTAGTGCCAAAACAGTTATTCATCCACATAGGATGAA
TTCCATGAAATGCACACTTAGTGACGAAACGATTATTCATCCACATAAGATA
Found at i:372413 original size:20 final size:21
Alignment explanation
Indices: 372385--372443 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
372375 ATTTTTGGCT
*
372385 CCATAGTATCGATACCCT-TA
1 CCATGGTATCGATACCCTATA
*
372405 CCATGGTATCGATACTACTATA
1 CCATGGTATCGATAC-CCTATA
* *
372427 CTATGGTACCGATACCC
1 CCATGGTATCGATACCC
372444 CCTTCCAGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 14 0.44
21 3 0.09
22 15 0.47
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (21 bp):
CCATGGTATCGATACCCTATA
Found at i:378597 original size:54 final size:54
Alignment explanation
Indices: 378515--378931 Score: 443
Period size: 54 Copynumber: 7.8 Consensus size: 54
378505 CGTACTTAGT
* * *
378515 GTTATTCATCCCCATATGATGAATTCCGTGAAATGTACACTTTATGCCGAAACG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTTATGCCGAAACG
* *
378569 GTTATTCATCCACATAGGATGAATTCCGTGAAATG--CA--TTAGTGTCGAAATG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTTA-TGCCGAAACG
* * **
378620 GTTATTCATCCACATAGGATAAATTCCATGAAATGCACACTTGGTGCCGAAACG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTTATGCCGAAACG
* * * * * *
378674 ATTATTCATCCTCATAGGATGAATTCTGTGAAATGCACAATTTATACCGAAATG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTTATGCCGAAACG
* * * * *
378728 GTTATTCATCCACTTAAGATGAATTCCGTGAAACGTACAC-TTAGTACCGAAACG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTTA-TGCCGAAACG
* * * *
378782 GTT-TTCCATCCACATAGGATGAATTCTGTGAAATACACAC-TTAGTACCAAAACG
1 GTTATT-CATCCACATAGGATGAATTCCGTGAAATGCACACTTTA-TGCCGAAACG
* * * ** * *
378836 TTTATTCATCCCCATAGGATAAATTATGTGAAATACACACTTTGTGCCGAAACG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTTATGCCGAAACG
* * *
378890 GTTATTCATCCACATACGATGAATTCCGAGAAATGAACACTT
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTT
378932 AGTGACTGTT
Statistics
Matches: 302, Mismatches: 52, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
50 3 0.01
51 41 0.14
52 2 0.01
53 7 0.02
54 244 0.81
55 5 0.02
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (54 bp):
GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTTATGCCGAAACG
Found at i:378868 original size:162 final size:161
Alignment explanation
Indices: 378516--378934 Score: 538
Period size: 162 Copynumber: 2.6 Consensus size: 161
378506 GTACTTAGTG
* * *
378516 TTATTCATCCCCATATGATGAATTCCGTGAAATGTACACTTTATGCCGAAACGGTTATTCATCCA
1 TTATTCATCCCCATAGGATGAATTCTGTGAAATGCACACTTTATGCCGAAACGGTTATTCATCCA
* * ** *
378581 CATAGGATGAATTCCGTGAAA-TGCA-TTAGTGTCGAAATGGTTATTCATCCACATAGGATAAAT
66 CATAAGATGAATTCCGTGAAAGTACACTTAGTACCGAAACGGTTATTCATCCACATAGGATAAAT
* * * *
378644 TCCATGAAATGCACACTTGGTGCCGAAACGA
131 TCCATGAAATACACACTTAGTACCAAAACGA
* * * *
378675 TTATTCATCCTCATAGGATGAATTCTGTGAAATGCACAATTTATACCGAAATGGTTATTCATCCA
1 TTATTCATCCCCATAGGATGAATTCTGTGAAATGCACACTTTATGCCGAAACGGTTATTCATCCA
* *
378740 CTTAAGATGAATTCCGTGAAACGTACACTTAGTACCGAAACGGTT-TTCCATCCACATAGGATGA
66 CATAAGATGAATTCCGTGAAA-GTACACTTAGTACCGAAACGGTTATT-CATCCACATAGGATAA
** *
378804 ATTCTGTGAAATACACACTTAGTACCAAAACGT
129 ATTCCATGAAATACACACTTAGTACCAAAACGA
* * * *
378837 TTATTCATCCCCATAGGATAAATTATGTGAAATACACACTTTGTGCCGAAACGGTTATTCATCCA
1 TTATTCATCCCCATAGGATGAATTCTGTGAAATGCACACTTTATGCCGAAACGGTTATTCATCCA
* * *
378902 CATACGATGAATTCCGAGAAATGAACACTTAGT
66 CATAAGATGAATTCCGTGAAA-GTACACTTAGT
378935 GACTGTTTGG
Statistics
Matches: 222, Mismatches: 34, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
159 77 0.35
161 5 0.02
162 140 0.63
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (161 bp):
TTATTCATCCCCATAGGATGAATTCTGTGAAATGCACACTTTATGCCGAAACGGTTATTCATCCA
CATAAGATGAATTCCGTGAAAGTACACTTAGTACCGAAACGGTTATTCATCCACATAGGATAAAT
TCCATGAAATACACACTTAGTACCAAAACGA
Found at i:379401 original size:22 final size:21
Alignment explanation
Indices: 379356--379426 Score: 85
Period size: 19 Copynumber: 3.5 Consensus size: 21
379346 ATATTACCTA
*
379356 GTATCGATAC-CCTTACCATG
1 GTATCGATACTCCTTACTATG
*
379376 GTATCGATACTACCATACTATG
1 GTATCGATACT-CCTTACTATG
*
379398 GTATCGAT--TCCTTCCTATG
1 GTATCGATACTCCTTACTATG
379417 GTATCGATAC
1 GTATCGATAC
379427 CATTTTTGCT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 16 0.37
20 11 0.26
22 16 0.37
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (21 bp):
GTATCGATACTCCTTACTATG
Found at i:383765 original size:22 final size:22
Alignment explanation
Indices: 383737--383787 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
383727 TCGAGGTAGT
383737 GGCAAGCTAGACCTCCTATAGG
1 GGCAAGCTAGACCTCCTATAGG
*
383759 GGCAAGCTATACCTCCTATAGG
1 GGCAAGCTAGACCTCCTATAGG
*
383781 AGCAAGC
1 GGCAAGC
383788 ATGCTAAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.18
Consensus pattern (22 bp):
GGCAAGCTAGACCTCCTATAGG
Found at i:393951 original size:20 final size:21
Alignment explanation
Indices: 393912--393969 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
393902 TTTTGGTGCA
* * *
393912 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCACCTTT
393932 GAGGGAACCGATTCCACCTTT
1 GAGGGAACCGATTCCACCTTT
393953 GAAGGGGAACCGATTCC
1 G-A-GGGAACCGATTCC
393970 CCCCACAGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.31
21 8 0.25
22 1 0.03
23 13 0.41
ACGTcount: A:0.24, C:0.29, G:0.28, T:0.19
Consensus pattern (21 bp):
GAGGGAACCGATTCCACCTTT
Found at i:393999 original size:20 final size:21
Alignment explanation
Indices: 393955--393994 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
393945 CCACCTTTGA
*
393955 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
393976 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
393995 TAGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:396873 original size:109 final size:107
Alignment explanation
Indices: 396684--396899 Score: 414
Period size: 109 Copynumber: 2.0 Consensus size: 107
396674 AAACGGCTAT
396684 ATGATCTTCACTAATCATTCCCACGTTAGAAGTAATTCAAGGTGTATTTAAGCAAGCTTAGAAGT
1 ATGATCTTCACTAATCATTCCCACGTTAGAAGTAATTCAAGGTGTATTTAAGCAAGCTTAGAAGT
396749 CATTGATCAACAACAAGAAACATCAAGCAATTAGAATCAAGA
66 CATTGATCAACAACAAGAAACATCAAGCAATTAGAATCAAGA
396791 ATGATCTTCACTAATCATTCCCAACGTTTAGAAGTAATTCAAGGTGTATTTAAGCAAGCTTAGAA
1 ATGATCTTCACTAATCATTCCC-ACG-TTAGAAGTAATTCAAGGTGTATTTAAGCAAGCTTAGAA
396856 GTCATTGATCAACAACAAGAAACATCAAGCAATTAGAATCAAGA
64 GTCATTGATCAACAACAAGAAACATCAAGCAATTAGAATCAAGA
396900 GAGAATCAAA
Statistics
Matches: 107, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
107 22 0.21
108 3 0.03
109 82 0.77
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (107 bp):
ATGATCTTCACTAATCATTCCCACGTTAGAAGTAATTCAAGGTGTATTTAAGCAAGCTTAGAAGT
CATTGATCAACAACAAGAAACATCAAGCAATTAGAATCAAGA
Found at i:397557 original size:25 final size:25
Alignment explanation
Indices: 397484--397544 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
397474 GAGGGTATTT
* ** *
397484 GGTACCGATACCAATATCAAAAAAG
1 GGTACCTATACCAATGCCAGAAAAG
397509 GGTACCTATACCAATGCCAGAAAAG
1 GGTACCTATACCAATGCCAGAAAAG
397534 GGTACCTATAC
1 GGTACCTATAC
397545 TAGTGCTGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (25 bp):
GGTACCTATACCAATGCCAGAAAAG
Found at i:398361 original size:68 final size:68
Alignment explanation
Indices: 398248--398666 Score: 538
Period size: 68 Copynumber: 6.2 Consensus size: 68
398238 ACTAAAAAGC
* * *
398248 CAGTTAGATGAAATGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACATAAATATGTCAATTA
1 CAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAAGATGTCAATTA
*
398313 TGC
66 TGA
**
398316 CAAATAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAA-AGTGTCAATT
1 CAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAAGA-TGTCAATT
*
398380 ATGT
65 ATGA
* * * * *
398384 TAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCATAAGTGTGTATTTGACAGAAAGGTGTCAATTA
1 CAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAAGATGTCAATTA
398449 TGA
66 TGA
* * * *
398452 CTGTTAGATGAAAGGCTAAATGCCTTTGAGGCCTAACTGTGCATTTGATAGAAAGATGCCAATTA
1 CAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAAGATGTCAATTA
*
398517 TGC
66 TGA
* * ** *
398520 CAGTTAGATGAAAGGCTAAGTGTCTTTGAGGCCTAACTGTACATTTGGTAGAAAGGTGTCAATTA
1 CAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAAGATGTCAATTA
398585 T-A
66 TGA
* * * * * *
398587 CTAGTCAGATGAAAGGCTAAATACCTTTGAGGCCTAA-TGTGTATTTGGCATAAAGATGTCAATT
1 C-AGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAAGATGTCAATT
*
398651 ATGT
65 ATGA
398655 CAGTTAGATGAA
1 CAGTTAGATGAA
398667 CAATTAAAGA
Statistics
Matches: 305, Mismatches: 42, Indels: 9
0.86 0.12 0.03
Matches are distributed among these distances:
67 36 0.12
68 269 0.88
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (68 bp):
CAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAAGATGTCAATTA
TGA
Found at i:398600 original size:204 final size:203
Alignment explanation
Indices: 398248--398666 Score: 613
Period size: 204 Copynumber: 2.1 Consensus size: 203
398238 ACTAAAAAGC
* * * * *
398248 CAGTTAGATGAAATGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACATAAATATGTCAATTA
1 CAGTTAGATGAAAGGCTAAATGCCTTTGAGGCCTAACTGTGCATTTGACAGAAAGATGCCAATTA
*
398313 TGCCAAATAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAAAGTGTCAA
66 TGCCAAATAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTACATTTGACAGAAAAGTGTCAA
** * * * *
398378 TTATGTTAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCATAAGTGTGTATTTGACAGAAAGGTGT
131 TTATACTAGTCAGATGAAAGGCTAAATACCTTTGAGGCATAA-TGTGTATTTGACAGAAAGATGT
398443 CAATTATGA
195 CAATTATGA
* *
398452 CTGTTAGATGAAAGGCTAAATGCCTTTGAGGCCTAACTGTGCATTTGATAGAAAGATGCCAATTA
1 CAGTTAGATGAAAGGCTAAATGCCTTTGAGGCCTAACTGTGCATTTGACAGAAAGATGCCAATTA
** * ** *
398517 TGCCAGTTAGATGAAAGGCTAAGTGTCTTTGAGGCCTAACTGTACATTTGGTAGAAAGGTGTCAA
66 TGCCAAATAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTACATTTGACAGAAAAGTGTCAA
* * *
398582 TTATACTAGTCAGATGAAAGGCTAAATACCTTTGAGGCCTAATGTGTATTTGGCATAAAGATGTC
131 TTATACTAGTCAGATGAAAGGCTAAATACCTTTGAGGCATAATGTGTATTTGACAGAAAGATGTC
*
398647 AATTATGT
196 AATTATGA
398655 CAGTTAGATGAA
1 CAGTTAGATGAA
398667 CAATTAAAGA
Statistics
Matches: 190, Mismatches: 25, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
203 38 0.20
204 152 0.80
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (203 bp):
CAGTTAGATGAAAGGCTAAATGCCTTTGAGGCCTAACTGTGCATTTGACAGAAAGATGCCAATTA
TGCCAAATAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTACATTTGACAGAAAAGTGTCAA
TTATACTAGTCAGATGAAAGGCTAAATACCTTTGAGGCATAATGTGTATTTGACAGAAAGATGTC
AATTATGA
Found at i:398758 original size:81 final size:81
Alignment explanation
Indices: 398624--398960 Score: 424
Period size: 81 Copynumber: 4.2 Consensus size: 81
398614 TGAGGCCTAA
* * * * *
398624 TGTGTATTTGGCATAAAGATGTCAATTATGTCAGTTAGATGAACAATTAAAGACCATTGAGTAAA
1 TGTGCATTTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAA
* *
398689 AGATAAATGACCTAGA
66 AGATAAATGGCCTAGC
* *
398705 TGTGCATTTGGCATAAAGATGTCAATTATGCCAGTTAGATGAACGATTAAAGACTGTTGAGTAAA
1 TGTGCATTTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAA
*
398770 AGATAAATTGCCTAGC
66 AGATAAATGGCCTAGC
* * * * * * *
398786 CGTGCATTTGGTAGAAA-AGTGTCAATTATGCCAGTTAGAAGAACGGTTAAATATCGTTGAATAA
1 TGTGCATTTGGCAGAAAGA-TGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAA
398850 AAGATAAATGGCCTAGC
65 AAGATAAATGGCCTAGC
* ** * * * **
398867 TTTGCATTTTTCAGAAAGGTGTCAATTATGCTAGTTAGATGAACGGTTAAAGATTGTTGAGTAAA
1 TGTGCATTTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAA
*
398932 AGATAAATGGTCTAGC
66 AGATAAATGGCCTAGC
398948 TGTGCATTTGGCA
1 TGTGCATTTGGCA
398961 ATCAAGTGTC
Statistics
Matches: 221, Mismatches: 33, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
80 1 0.00
81 220 1.00
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.31
Consensus pattern (81 bp):
TGTGCATTTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAA
AGATAAATGGCCTAGC
Found at i:398970 original size:81 final size:81
Alignment explanation
Indices: 398624--399019 Score: 415
Period size: 81 Copynumber: 4.9 Consensus size: 81
398614 TGAGGCCTAA
* * ** *
398624 TGTGTATTTGGC-ATAAAGATGTCAATTATGTCAGTTAGATGAACAATTAAAGACCATTGAGTAA
1 TGTGCATTTGGCAATAAAG-TGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAA
* *
398688 AAGATAAATGACCTAGA
65 AAGATAAATGGCCTAGC
* *
398705 TGTGCATTTGGC-ATAAAGATGTCAATTATGCCAGTTAGATGAACGATTAAAGACTGTTGAGTAA
1 TGTGCATTTGGCAATAAAG-TGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAA
*
398769 AAGATAAATTGCCTAGC
65 AAGATAAATGGCCTAGC
* * * * * *
398786 CGTGCATTTGGTAGA-AAAGTGTCAATTATGCCAGTTAGAAGAACGGTTAAATATCGTTGAATAA
1 TGTGCATTTGGCA-ATAAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAA
398850 AAGATAAATGGCCTAGC
65 AAGATAAATGGCCTAGC
* ** * * **
398867 TTTGCATTTTTCAGA-AAGGTGTCAATTATGCTAGTTAGATGAACGGTTAAAGATTGTTGAGTAA
1 TGTGCATTTGGCA-ATAAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAA
*
398931 AAGATAAATGGTCTAGC
65 AAGATAAATGGCCTAGC
* * * * * * * * *
398948 TGTGCATTTGGCAATCAAGTGTCAGTCATACAAGTTAGATGAAAGGTTAATG-CCTTTGGGTAAA
1 TGTGCATTTGGCAATAAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAA
399012 AGACTAAA
66 AGA-TAAA
399020 GGAATTATAA
Statistics
Matches: 267, Mismatches: 44, Indels: 8
0.84 0.14 0.03
Matches are distributed among these distances:
80 12 0.04
81 250 0.94
82 4 0.01
83 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.30
Consensus pattern (81 bp):
TGTGCATTTGGCAATAAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAA
AGATAAATGGCCTAGC
Found at i:400222 original size:34 final size:34
Alignment explanation
Indices: 400177--400244 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 34
400167 ATATATATAT
400177 ATATATATATATAATTAATAAATTTAATTTAAATTA
1 ATATATATATAT-ATT-ATAAATTTAATTTAAATTA
*
400213 ATATATATATATATTATATATTTAATTTAAAT
1 ATATATATATATATTATAAATTTAATTTAAAT
400245 ATATACCCGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 16 0.52
35 3 0.10
36 12 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
ATATATATATATATTATAAATTTAATTTAAATTA
Found at i:400249 original size:2 final size:2
Alignment explanation
Indices: 400154--400233 Score: 61
Period size: 2 Copynumber: 44.5 Consensus size: 2
400144 ATAATTATTT
400154 TA TA TA TA -A T- TA TA TA TA TA TA TA TA TA TA TA TA TA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
400192 TA -A TA AA TT TA -A TT TA AA T- TA -A TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
400229 TA TA T
1 TA TA T
400234 TTAATTTAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
1 9 0.15
2 52 0.85
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:403364 original size:19 final size:19
Alignment explanation
Indices: 403336--403385 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
403326 ATCGACACCA
* *
403336 TATCGGTACCGTAATAGAG
1 TATCGATACCATAATAGAG
* *
403355 TATCGATACCATAGTATAG
1 TATCGATACCATAATAGAG
403374 TATCGATACCAT
1 TATCGATACCAT
403386 GATGGGGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
TATCGATACCATAATAGAG
Found at i:403784 original size:55 final size:54
Alignment explanation
Indices: 403686--403886 Score: 214
Period size: 55 Copynumber: 3.8 Consensus size: 54
403676 AAGCGCGCAA
* * * *
403686 AAACTTAAG-AATCCATACCAAGTGTATGAATTTTGGTATGGGCACTTTGTGTAC
1 AAAC-TAAGAAATCCATACTAAGTGTATGAATTTTCGTATGGGCACTATGTGTGC
* * * *
403740 AAATCTAAGAAATTCATACTAAGTGTATAAATTTCCGTACGGGCACTATGTGTGC
1 AAA-CTAAGAAATCCATACTAAGTGTATGAATTTTCGTATGGGCACTATGTGTGC
* * * *
403795 AAAACTAAGAAATTCATACAAATTGTATGAA--TT--TATGAGCACTATGTGTGC
1 -AAACTAAGAAATCCATACTAAGTGTATGAATTTTCGTATGGGCACTATGTGTGC
* *
403846 AAACTAAGAAATCCATACTAAGAGTATTAATTTTCGTATGG
1 AAACTAAGAAATCCATACTAAGTGTATGAATTTTCGTATGG
403887 AAATATATGT
Statistics
Matches: 120, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
50 25 0.21
51 16 0.13
52 2 0.02
53 1 0.01
54 11 0.09
55 62 0.52
56 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (54 bp):
AAACTAAGAAATCCATACTAAGTGTATGAATTTTCGTATGGGCACTATGTGTGC
Found at i:404368 original size:204 final size:204
Alignment explanation
Indices: 404018--404402 Score: 583
Period size: 204 Copynumber: 1.9 Consensus size: 204
404008 TATATGGTTA
* * * *
404018 ACTGTGCATTTGACAGAAAGGTGTCAATTATACCAGTTAGATGAAAGGCCAAGTTCATTTGAGGC
1 ACTGTGCATTTAAAAGAAAGGTGCCAATTATACCAGTTAGATGAAAGGCCAAGTGCATTTGAGGC
* * *
404083 CTAATTGTGCATTTGACAGAAAGGTATCAATTATGCCAGTTAGATGAAAGGCTAAGCGCCTTTGA
66 CTAACTGTACATTTGACAGAAAGGTATCAATTATGCCAGTTAGATGAAAGGCTAAGCGCCTTTCA
* *
404148 GGCCTAAATGTGCATTTGATAGAAATGTGTCAATTATGCCAGTTAAATGAAAGGCTAAGTGCCTT
131 GGCCTAAATATGCATTTGATAGAAATGTGTCAATTATGCCAATTAAATGAAAGGCTAAGTGCCTT
404213 TGAGGCCTG
196 TGAGGCCTG
* * * *
404222 ACTGTGCATTTAAAAGAAATGTGCCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGC
1 ACTGTGCATTTAAAAGAAAGGTGCCAATTATACCAGTTAGATGAAAGGCCAAGTGCATTTGAGGC
* * *
404287 CTAACTGTACATTTGACA-AGAAGGTGTCAATTATGCCAGTTAGATGAAAGTCTAAGTGCCTTTC
66 CTAACTGTACATTTGACAGA-AAGGTATCAATTATGCCAGTTAGATGAAAGGCTAAGCGCCTTTC
* * *
404351 AGGCCTAACTATGCATTTGGTAGAAATGTGTCAATTATGTCAATTAAATGAA
130 AGGCCTAAATATGCATTTGATAGAAATGTGTCAATTATGCCAATTAAATGAA
404403 TAGTTAAAGA
Statistics
Matches: 161, Mismatches: 19, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
203 1 0.01
204 160 0.99
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (204 bp):
ACTGTGCATTTAAAAGAAAGGTGCCAATTATACCAGTTAGATGAAAGGCCAAGTGCATTTGAGGC
CTAACTGTACATTTGACAGAAAGGTATCAATTATGCCAGTTAGATGAAAGGCTAAGCGCCTTTCA
GGCCTAAATATGCATTTGATAGAAATGTGTCAATTATGCCAATTAAATGAAAGGCTAAGTGCCTT
TGAGGCCTG
Found at i:404402 original size:68 final size:68
Alignment explanation
Indices: 404016--404389 Score: 525
Period size: 68 Copynumber: 5.5 Consensus size: 68
404006 ATTATATGGT
* * * *
404016 TAACTGTGCATTTGACAGAAAGGTGTCAATTATACCAGTTAGATGAAAGGCCAAGTTCATTTGAG
1 TAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
404081 GCC
66 GCC
* * *
404084 TAATTGTGCATTTGACAGAAAGGTATCAATTATGCCAGTTAGATGAAAGGCTAAGCGCCTTTGAG
1 TAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
404149 GCC
66 GCC
* * * *
404152 TAAATGTGCATTTGATAGAAATGTGTCAATTATGCCAGTTAAATGAAAGGCTAAGTGCCTTTGAG
1 TAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
404217 GCC
66 GCC
* * * * *
404220 TGACTGTGCATTTAAAAGAAATGTGCCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
1 TAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
404285 GCC
66 GCC
* * *
404288 TAACTGTACATTTGACA-AGAAGGTGTCAATTATGCCAGTTAGATGAAAGTCTAAGTGCCTTTCA
1 TAACTGTGCATTTGACAGA-AAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
404352 GGCC
65 GGCC
* ** *
404356 TAACTATGCATTTGGTAGAAATGTGTCAATTATG
1 TAACTGTGCATTTGACAGAAAGGTGTCAATTATG
404390 TCAATTAAAT
Statistics
Matches: 272, Mismatches: 32, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
67 1 0.00
68 270 0.99
69 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.30
Consensus pattern (68 bp):
TAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
GCC
Found at i:404527 original size:80 final size:80
Alignment explanation
Indices: 404362--404673 Score: 355
Period size: 80 Copynumber: 3.9 Consensus size: 80
404352 GGCCTAACTA
* * * ** *
404362 TGCATTTGGTAGAAATGTGTCAATTATGTCAATTAAATGAATAGTTAAAGATCGTTGAGTAAAAG
1 TGCATTTGGTAGAAA-GTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAG
404427 ATAAATGGCCTAGCTT-
65 ATAAATGGCCTAG-TTG
404443 TGCATTTGGCT-GAAAGATGTCAATTATGCCAGTTAGATGAACGGTT-AAGACCGTTGAGTAAAA
1 TGCATTTGG-TAGAAAG-TGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAA
*
404506 TATAAATGGCCTAGTTG
64 GATAAATGGCCTAGTTG
* * *
404523 TGCATTTGGTAGAAAGGTGTCAATTATCCCGGTTAGATGAACGGTTAAAGGCCGTTGAGTAAAAG
1 TGCATTTGGTAGAAA-GTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAG
*
404588 AT-AATGGCCTAGCTG
65 ATAAATGGCCTAGTTG
* * * * * * *
404603 TGGATTTGGCAGACAAGTGTCAATCATGCAAGTTAGATGAAAGGTTAAATG-CCTTTGGGTAAAA
1 TGCATTTGGTAGA-AAGTGTCAATTATGCCAGTTAGATGAACGGTTAAA-GACCGTTGAGTAAAA
404667 GACTAAA
64 GA-TAAA
404674 GCAATTATAA
Statistics
Matches: 200, Mismatches: 21, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
79 3 0.01
80 134 0.67
81 60 0.30
82 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (80 bp):
TGCATTTGGTAGAAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGA
TAAATGGCCTAGTTG
Found at i:404690 original size:161 final size:160
Alignment explanation
Indices: 404361--404650 Score: 377
Period size: 161 Copynumber: 1.8 Consensus size: 160
404351 AGGCCTAACT
* ** * *
404361 ATGCATTTGGTAGAAATGTGTCAATTATGTCAATTAAATGAATAGTTAAAGATCGTTGAGTAAAA
1 ATGCATTTGGTAGAAAGGTGTCAATTATCCCAATTAAATGAACAGTTAAAGACCGTTGAGTAAAA
* * * * *
404426 GATAAATGGCCTAGCTTTGCATTTGGCTGAAAGATGTCAATTATGCCAGTTAGATGAACGGTTAA
66 GATAAATGGCCTAGCTGTGCATTTGGCAGAAAGATGTCAATCATGCAAGTTAGATGAAAGGTTAA
* *
404491 GACCGTTGAGTAAAATATAAATGGCCTAGTT
131 GACCGTTGAGTAAAAGATAAA-GGCCTAGTA
* ** * * *
404522 GTGCATTTGGTAGAAAGGTGTCAATTATCCCGGTTAGATGAACGGTTAAAGGCCGTTGAGTAAAA
1 ATGCATTTGGTAGAAAGGTGTCAATTATCCCAATTAAATGAACAGTTAAAGACCGTTGAGTAAAA
*
404587 GAT-AATGGCCTAGCTGTGGATTTGGCAGACAAG-TGTCAATCATGCAAGTTAGATGAAAGGTTA
66 GATAAATGGCCTAGCTGTGCATTTGGCAGA-AAGATGTCAATCATGCAAGTTAGATGAAAGGTTA
404650 A
130 A
404651 ATGCCTTTGG
Statistics
Matches: 111, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
160 51 0.46
161 60 0.54
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (160 bp):
ATGCATTTGGTAGAAAGGTGTCAATTATCCCAATTAAATGAACAGTTAAAGACCGTTGAGTAAAA
GATAAATGGCCTAGCTGTGCATTTGGCAGAAAGATGTCAATCATGCAAGTTAGATGAAAGGTTAA
GACCGTTGAGTAAAAGATAAAGGCCTAGTA
Found at i:419231 original size:43 final size:43
Alignment explanation
Indices: 419139--419231 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
419129 GTAGATATGA
* *
419139 AAAATG-AATGTGAAAGTTTTGAAAAGTATCTGAAAGGAAATG
1 AAAATGAAATGTGAAAGTTCTGAAAAGTATCTGAAAAGAAATG
* *
419181 AAAATGAAATGTGAAAGTTCTG-AATGTGTCTGAATAAGAAA-G
1 AAAATGAAATGTGAAAGTTCTGAAAAGTATCTGAA-AAGAAATG
419223 AAACATGAA
1 AAA-ATGAA
419232 TTGATTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
42 20 0.45
43 24 0.55
ACGTcount: A:0.48, C:0.04, G:0.23, T:0.25
Consensus pattern (43 bp):
AAAATGAAATGTGAAAGTTCTGAAAAGTATCTGAAAAGAAATG
Found at i:423557 original size:30 final size:31
Alignment explanation
Indices: 423516--423574 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
423506 TAAAATTTAA
*
423516 GGACCATTTTGTAATTTTT-GAAAAGTTAGG
1 GGACCAATTTGTAATTTTTGGAAAAGTTAGG
423546 GGACCAATTTGTAATTTTTGGAAAAGTTA
1 GGACCAATTTGTAATTTTTGGAAAAGTTA
423575 TAAATAGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.39
Consensus pattern (31 bp):
GGACCAATTTGTAATTTTTGGAAAAGTTAGG
Found at i:424719 original size:28 final size:28
Alignment explanation
Indices: 424677--424730 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
424667 GTTTACACAT
* * *
424677 ACATGTGGTATGTGACAGAAGAGAAGGA
1 ACATGTGATACGTGACAGAAAAGAAGGA
424705 ACATGTGATACGTGACAGAAAAGAAG
1 ACATGTGATACGTGACAGAAAAGAAG
424731 AGATATATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.31, T:0.17
Consensus pattern (28 bp):
ACATGTGATACGTGACAGAAAAGAAGGA
Found at i:424892 original size:22 final size:22
Alignment explanation
Indices: 424864--424911 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
424854 GGCTCTACGC
* *
424864 GGTCCTTCGGGACATATACAGA
1 GGTCCTTCAGGACAAATACAGA
* *
424886 GGTCCTTTAGGACAAATACATA
1 GGTCCTTCAGGACAAATACAGA
424908 GGTC
1 GGTC
424912 ATTGGGGTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (22 bp):
GGTCCTTCAGGACAAATACAGA
Found at i:425221 original size:18 final size:17
Alignment explanation
Indices: 425185--425223 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
425175 TAAAAGGTAT
* *
425185 TAATGATAATAATAGGA
1 TAATGATAAAAATAAGA
425202 TAATGATAAGAAATAAGA
1 TAATGATAA-AAATAAGA
425220 TAAT
1 TAAT
425224 CATATATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.28
Consensus pattern (17 bp):
TAATGATAAAAATAAGA
Found at i:436169 original size:21 final size:23
Alignment explanation
Indices: 436143--436184 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
436133 TTATAGTGCT
436143 AATTTG-GGATG-TTTTTATTCG
1 AATTTGTGGATGATTTTTATTCG
*
436164 AATTTGTGTATGATTTTTATT
1 AATTTGTGGATGATTTTTATT
436185 TTTAGGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 4 0.22
23 8 0.44
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.57
Consensus pattern (23 bp):
AATTTGTGGATGATTTTTATTCG
Found at i:448191 original size:29 final size:29
Alignment explanation
Indices: 448148--448230 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
448138 CTCACCTAAC
448148 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
448178 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
448207 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
448231 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Done.