Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009461.1 Hibiscus syriacus cultivar Beakdansim tig00113724_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: 2346588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2100232 original size:20 final size:19
Alignment explanation
Indices: 2100204--2100246 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2100194 AATAAAGTAC
* *
2100204 TATTAAATTTTAAGATTTTA
1 TATTAAA-TTTAAAATTATA
*
2100224 TATTCAATTTAAAATTATA
1 TATTAAATTTAAAATTATA
2100243 TATT
1 TATT
2100247 TCATTAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
TATTAAATTTAAAATTATA
Found at i:2100511 original size:63 final size:63
Alignment explanation
Indices: 2100433--2100560 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 63
2100423 CTTGGATGTA
2100433 TCGATACACCCCCAACTTCGAATGGAATAAGGGTATCGATACACAGCTAAAGTATCGATACAC
1 TCGATACACCCCCAACTTCGAATGGAATAAGGGTATCGATACACAGCTAAAGTATCGATACAC
* *
2100496 TCGATACACCCCCAACTTCGAATGGAATAAGGGTATCGATACACAGCTGAAGTATCGATGCAC
1 TCGATACACCCCCAACTTCGAATGGAATAAGGGTATCGATACACAGCTAAAGTATCGATACAC
2100559 TC
1 TC
2100561 CTGGCTCCGA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (63 bp):
TCGATACACCCCCAACTTCGAATGGAATAAGGGTATCGATACACAGCTAAAGTATCGATACAC
Found at i:2103435 original size:17 final size:16
Alignment explanation
Indices: 2103415--2103462 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
2103405 ATATACTCAT
*
2103415 AATATATATATTTATA
1 AATAAATATATTTATA
*
2103431 GAATAAAATAAATTTATA
1 -AAT-AAATATATTTATA
2103449 AATAAATAATATTT
1 AATAAAT-ATATTT
2103463 TTACAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 4 0.15
17 11 0.42
18 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
AATAAATATATTTATA
Found at i:2106077 original size:27 final size:21
Alignment explanation
Indices: 2106022--2106064 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2106012 TCCTAATTCT
2106022 TAAATAAATAAAATAAATAAA
1 TAAATAAATAAAATAAATAAA
2106043 TAAATAAATATTAAATAAATAA
1 TAAATAAATA--AAATAAATAA
2106065 TAGTAATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.50
23 10 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAATAAATAAAATAAATAAA
Found at i:2106083 original size:4 final size:4
Alignment explanation
Indices: 2106022--2106064 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
2106012 TCCTAATTCT
*
2106022 TAAA TAAA TAAAA TAAA TAAA TAAA TAAA T-AT TAAA TAAA TAA
1 TAAA TAAA T-AAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
2106065 TAGTAATGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 2 0.06
4 29 0.83
5 4 0.11
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:2106703 original size:13 final size:13
Alignment explanation
Indices: 2106687--2106717 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2106677 GTGAAAATAC
2106687 AATAATAAAAGAA
1 AATAATAAAAGAA
*
2106700 AATAATGAAAGAA
1 AATAATAAAAGAA
2106713 AATAA
1 AATAA
2106718 AGAATAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (13 bp):
AATAATAAAAGAA
Found at i:2111780 original size:13 final size:13
Alignment explanation
Indices: 2111762--2111786 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2111752 TTGTGAAAAG
2111762 AAAATAAAGAAAT
1 AAAATAAAGAAAT
2111775 AAAATAAAGAAA
1 AAAATAAAGAAA
2111787 GATGAAGATG
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:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AAAATAAAGAAAT
Found at i:2115527 original size:20 final size:20
Alignment explanation
Indices: 2115489--2115527 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2115479 TGTTGAAGTG
*
2115489 GTATCGATACTCGGGGCCTA
1 GTATCGATACTCGAGGCCTA
*
2115509 GTATCGATACTCGATGCCT
1 GTATCGATACTCGAGGCCT
2115528 TGATCAAAAA
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:0.21, C:0.26, G:0.26, T:0.28
Consensus pattern (20 bp):
GTATCGATACTCGAGGCCTA
Found at i:2119531 original size:2 final size:2
Alignment explanation
Indices: 2119524--2119565 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2119514 AGTTGGAGAT
2119524 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
2119565 T
1 T
2119566 GCAAGTAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2129757 original size:22 final size:21
Alignment explanation
Indices: 2129718--2129760 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
2129708 AATTTATCCT
2129718 ACTAAGTATTAAAGCTAAGAA
1 ACTAAGTATTAAAGCTAAGAA
2129739 ACTAA-TATTAAGGAGCTAAGAA
1 ACTAAGTATTAA--AGCTAAGAA
2129761 TAATGATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.23
Consensus pattern (21 bp):
ACTAAGTATTAAAGCTAAGAA
Found at i:2148256 original size:57 final size:58
Alignment explanation
Indices: 2148130--2148245 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 58
2148120 ATATCTAGAT
* *
2148130 TCTCCAATAATCACTAGCTGCTCTCCACATGCCCTAAAGGCCATGCCTCAGCCATTCA
1 TCTCCAATAATCACTAGCTGCTCTCCACATGCCCTAAAGGACATGCCTCAGCCATGCA
*
2148188 TCTCCAATAATCACTAGCTGCTGTCCACATG-CCTAAAGGACATGCCTCAGCCATGCA
1 TCTCCAATAATCACTAGCTGCTCTCCACATGCCCTAAAGGACATGCCTCAGCCATGCA
2148245 T
1 T
2148246 TGAGTCTAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
57 25 0.45
58 30 0.55
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.24
Consensus pattern (58 bp):
TCTCCAATAATCACTAGCTGCTCTCCACATGCCCTAAAGGACATGCCTCAGCCATGCA
Found at i:2149162 original size:20 final size:20
Alignment explanation
Indices: 2149111--2149201 Score: 93
Period size: 20 Copynumber: 4.8 Consensus size: 20
2149101 AGGTTGTCAA
* *
2149111 AGTGTATCCATACACCCTGT
1 AGTGTATCCATGCACCCTGC
* *
2149131 AGTGCATCCATGCACTCTGC
1 AGTGTATCCATGCACCCTGC
2149151 AGTGTATCCATGCA-----C
1 AGTGTATCCATGCACCCTGC
*
2149166 AGTGTATCGATGCACCCTGC
1 AGTGTATCCATGCACCCTGC
*
2149186 AGTGCATCCATGCACC
1 AGTGTATCCATGCACC
2149202 TATGACTGCT
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
15 14 0.24
20 44 0.76
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (20 bp):
AGTGTATCCATGCACCCTGC
Found at i:2149168 original size:15 final size:15
Alignment explanation
Indices: 2149150--2149180 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2149140 ATGCACTCTG
2149150 CAGTGTATCCATGCA
1 CAGTGTATCCATGCA
*
2149165 CAGTGTATCGATGCA
1 CAGTGTATCCATGCA
2149180 C
1 C
2149181 CCTGCAGTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (15 bp):
CAGTGTATCCATGCA
Found at i:2149186 original size:35 final size:35
Alignment explanation
Indices: 2149131--2149200 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
2149121 TACACCCTGT
* *
2149131 AGTGCATCCATGCACTCTGCAGTGTATCCATGCAC
1 AGTGCATCCATGCACCCTGCAGTGCATCCATGCAC
* *
2149166 AGTGTATCGATGCACCCTGCAGTGCATCCATGCAC
1 AGTGCATCCATGCACCCTGCAGTGCATCCATGCAC
2149201 CTATGACTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.24
Consensus pattern (35 bp):
AGTGCATCCATGCACCCTGCAGTGCATCCATGCAC
Found at i:2149409 original size:21 final size:21
Alignment explanation
Indices: 2149380--2149419 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2149370 TTATTGCAGA
2149380 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCC-AACGGCTCC
*
2149402 AAAA-CATCCTCAACGGCT
1 AAAATCATCCCCAACGGCT
2149420 ATATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:2151694 original size:11 final size:12
Alignment explanation
Indices: 2151674--2151698 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2151664 CCAATGTTTG
2151674 TTTTATTTTTTT
1 TTTTATTTTTTT
2151686 TTTTATTTTTTT
1 TTTTATTTTTTT
2151698 T
1 T
2151699 AAATAACCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTATTTTTTT
Found at i:2162844 original size:2 final size:2
Alignment explanation
Indices: 2162839--2162865 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2162829 TGTGTGTGTG
2162839 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 T
2162866 GCGCGCGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2164860 original size:2 final size:2
Alignment explanation
Indices: 2164853--2164882 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2164843 TGAGACTTTA
2164853 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
2164883 CCTATTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2168187 original size:42 final size:42
Alignment explanation
Indices: 2168140--2168224 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
2168130 AATATAAGAA
* *
2168140 ATGAGAATTACAATGCATCCAAATATATAAAGAAAATTAGAG
1 ATGAGAATTACAATGCAACCAAATATAGAAAGAAAATTAGAG
2168182 ATGAGAATTACAATGCAACCAAATATAGAAAGAAAATTAGAG
1 ATGAGAATTACAATGCAACCAAATATAGAAAGAAAATTAGAG
2168224 A
1 A
2168225 CAATGGTCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.54, C:0.09, G:0.15, T:0.21
Consensus pattern (42 bp):
ATGAGAATTACAATGCAACCAAATATAGAAAGAAAATTAGAG
Found at i:2181726 original size:24 final size:28
Alignment explanation
Indices: 2181693--2181745 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
2181683 CGGCCTCGCG
2181693 ATATGGTACAA-GG-TTATTT-TTATAA
1 ATATGGTACAAGGGTTTATTTATTATAA
2181718 ATAT-GTACAAGGGTTTATTTATTATAA
1 ATATGGTACAAGGGTTTATTTATTATAA
2181745 A
1 A
2181746 AGGAGATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 6 0.24
25 6 0.24
26 6 0.24
27 7 0.28
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.43
Consensus pattern (28 bp):
ATATGGTACAAGGGTTTATTTATTATAA
Found at i:2185475 original size:24 final size:24
Alignment explanation
Indices: 2185443--2185503 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
2185433 GGCATTATCT
*
2185443 ACAACTGAAGCTGAATACATGGCA
1 ACAAATGAAGCTGAATACATGGCA
2185467 ACAAATGAAGCTGAATACATGGCA
1 ACAAATGAAGCTGAATACATGGCA
*
2185491 GCAAATGAAGCTG
1 ACAAATGAAGCTG
2185504 CAAAAGAAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (24 bp):
ACAAATGAAGCTGAATACATGGCA
Found at i:2186777 original size:16 final size:16
Alignment explanation
Indices: 2186756--2186789 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2186746 AATTAATCCG
2186756 AATTTATAGTATTGAA
1 AATTTATAGTATTGAA
* *
2186772 AATTTATGGTTTTGAA
1 AATTTATAGTATTGAA
2186788 AA
1 AA
2186790 ATCTTACCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (16 bp):
AATTTATAGTATTGAA
Found at i:2187061 original size:21 final size:21
Alignment explanation
Indices: 2187037--2187076 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2187027 ATCATTCGCA
*
2187037 AAAAGGAATTGATCCTTTTGG
1 AAAAGGAATCGATCCTTTTGG
2187058 AAAAGGAATCGATCCTTTT
1 AAAAGGAATCGATCCTTTT
2187077 ACAAAGGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (21 bp):
AAAAGGAATCGATCCTTTTGG
Found at i:2187096 original size:20 final size:20
Alignment explanation
Indices: 2187038--2187095 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
2187028 TCATTCGCAA
*
2187038 AAAGGAATTGATCCTTTTGGA-
1 AAAGGAATCGATCCTTTT--AC
2187059 AAAGGAATCGATCCTTTTAC
1 AAAGGAATCGATCCTTTTAC
*
2187079 AAAGGGATCGAT-CTTTT
1 AAAGGAATCGATCCTTTT
2187096 TTCTGGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.18
20 11 0.32
21 17 0.50
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (20 bp):
AAAGGAATCGATCCTTTTAC
Found at i:2187147 original size:50 final size:49
Alignment explanation
Indices: 2187060--2187156 Score: 142
Period size: 50 Copynumber: 2.0 Consensus size: 49
2187050 CCTTTTGGAA
* *
2187060 AAGGAATCGATCCTTTTACAAAGGGATCGATCTTTTTTCTGGAAAATGC
1 AAGGAATCGATCCTTTTACAAAGGGATCAATCATTTTTCTGGAAAATGC
*
2187109 AAGGGATCGATCCTTTT-CTAAAAGGGATCAATCATTTTTCTGGAAAAT
1 AAGGAATCGATCCTTTTAC--AAAGGGATCAATCATTTTTCTGGAAAAT
2187157 TGCATTTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
48 1 0.02
49 16 0.37
50 26 0.60
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (49 bp):
AAGGAATCGATCCTTTTACAAAGGGATCAATCATTTTTCTGGAAAATGC
Found at i:2187642 original size:16 final size:17
Alignment explanation
Indices: 2187621--2187653 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2187611 CTCAATCATA
2187621 CATATAAA-TATAAAAT
1 CATATAAAGTATAAAAT
2187637 CATATAAAGTATAAAAT
1 CATATAAAGTATAAAAT
2187654 TTCAGACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (17 bp):
CATATAAAGTATAAAAT
Found at i:2191850 original size:21 final size:21
Alignment explanation
Indices: 2191826--2191867 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2191816 AGTTTATTTT
2191826 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
2191847 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
2191868 AACTTGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:2191909 original size:33 final size:33
Alignment explanation
Indices: 2191856--2191932 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
2191846 GTAAACTTTG
*
2191856 TTTCAA-TTATCGAACTTGGAAGTTTTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTATTTAAGTA
* *
2191888 TTTGAATTTATTGAACTTGGAAGTATTTAAGTA
1 TTTCAATTTATCGAACTTGGAAGTATTTAAGTA
2191921 TTTCAA-TTATCG
1 TTTCAATTTATCG
2191933 TAAACTTTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 10 0.26
33 29 0.74
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (33 bp):
TTTCAATTTATCGAACTTGGAAGTATTTAAGTA
Found at i:2205049 original size:43 final size:45
Alignment explanation
Indices: 2205001--2205122 Score: 160
Period size: 43 Copynumber: 2.8 Consensus size: 45
2204991 GTCACTCAGT
*
2205001 TGTTTAGAAGTTTGGAGAGCATAGGGAATGTTGATCCT-TAA-AC
1 TGTTTAGAAGTTTGGAGAGCATAGGGAATGTTGATCCTCAAATAC
* *
2205044 TGTTTAAAAGGTTGGAGAGCATAGGG-ATGTTGATCCTCAAATTAC
1 TGTTTAGAAGTTTGGAGAGCATAGGGAATGTTGATCCTCAAA-TAC
* * *
2205089 TATTTAGAAGTTTGGAAAGCATTGGGAATGTTGA
1 TGTTTAGAAGTTTGGAGAGCATAGGGAATGTTGA
2205123 GACTTTATGG
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
42 11 0.16
43 26 0.39
45 23 0.34
46 7 0.10
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.33
Consensus pattern (45 bp):
TGTTTAGAAGTTTGGAGAGCATAGGGAATGTTGATCCTCAAATAC
Found at i:2206951 original size:2 final size:2
Alignment explanation
Indices: 2206944--2206975 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2206934 TATAGAATCC
2206944 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
2206976 TGACCTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2208107 original size:30 final size:30
Alignment explanation
Indices: 2208071--2208174 Score: 99
Period size: 30 Copynumber: 3.5 Consensus size: 30
2208061 TATTTTTGTG
2208071 TTCGTTTATTTATTTTTG-AAGATGTTTATA
1 TTCGTTTATTTATTTTTGAAAG-TGTTTATA
** *
2208101 TTCGTTTA---AAATTTGAATATTGTGTTCATA
1 TTCGTTTATTTATTTTTGAA-A--GTGTTTATA
* *
2208131 TTCGTTTATTTATTTTTGAAAGTGTTCATG
1 TTCGTTTATTTATTTTTGAAAGTGTTTATA
2208161 TTCGTTTATTTATT
1 TTCGTTTATTTATT
2208175 GTTCACGAAC
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
27 5 0.08
28 1 0.02
29 1 0.02
30 45 0.74
31 1 0.02
32 1 0.02
33 7 0.11
ACGTcount: A:0.23, C:0.06, G:0.13, T:0.58
Consensus pattern (30 bp):
TTCGTTTATTTATTTTTGAAAGTGTTTATA
Found at i:2208200 original size:23 final size:22
Alignment explanation
Indices: 2208168--2208230 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
2208158 ATGTTCGTTT
*
2208168 ATTTATTGTTCACGAACATGTTC
1 ATTTAATGTTCACGAACATG-TC
* * *
2208191 ATTTAATGTTCGCAAACTTGTC
1 ATTTAATGTTCACGAACATGTC
*
2208213 ATTTATATGCTCACGAAC
1 ATTTA-ATGTTCACGAAC
2208231 GTCTTCATGA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
22 7 0.22
23 25 0.78
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (22 bp):
ATTTAATGTTCACGAACATGTC
Found at i:2208365 original size:21 final size:22
Alignment explanation
Indices: 2208302--2208365 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
2208292 TTCACGAATA
* *
2208302 TGTTCGTTTAGTGTTCATTTAG
1 TGTTTGTTTAGCGTTCATTTAG
*
2208324 TGTTTGTTTAGCATT-ATTTTAG
1 TGTTTGTTTAGCGTTCA-TTTAG
*
2208346 TG-TTGTTTATCGTTCATTTA
1 TGTTTGTTTAGCGTTCATTTA
2208366 CATATTTGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 15 0.43
22 20 0.57
ACGTcount: A:0.16, C:0.08, G:0.19, T:0.58
Consensus pattern (22 bp):
TGTTTGTTTAGCGTTCATTTAG
Found at i:2212211 original size:17 final size:18
Alignment explanation
Indices: 2212181--2212215 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2212171 GTAGAAGATA
*
2212181 TATTTTATTAATTTTAAT
1 TATTTAATTAATTTTAAT
2212199 TATTTAATT-ATTTTAAT
1 TATTTAATTAATTTTAAT
2212216 ATATAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTAATTAATTTTAAT
Found at i:2212547 original size:160 final size:161
Alignment explanation
Indices: 2212361--2212684 Score: 560
Period size: 160 Copynumber: 2.0 Consensus size: 161
2212351 GAAAAGTAAC
* *
2212361 AATTGAAGGGGATTGAACTCGATCTTTTGTGTTGTTGAGGCACGTTCATATCGCTAGACCAACAC
1 AATTGAAGGGGATTGAACTCGATCTTTTGTGTTGTTGAGGCACGCTCATATCACTAGACCAACAC
* *
2212426 TCAATTTGAGATCTTATTTTACAACATATTATATTTAGCATGTATTATAACAAAAACAATAAAAT
66 TCAATTTGAGATCTTAGTTTAAAACATATTATATTTAGCATGTATTATAACAAAAACAATAAAAT
2212491 GAATAAAACTTTGA-TTTTTTAGAGAATATT
131 GAATAAAACTTTGATTTTTTTAGAGAATATT
* * *
2212521 AATTGCAGGGGATTGAACTCGATCTTTTGTGTTGTTGAGGCATGCTGATATCACTAGACCAACAC
1 AATTGAAGGGGATTGAACTCGATCTTTTGTGTTGTTGAGGCACGCTCATATCACTAGACCAACAC
*
2212586 TCAATTTGAGATCTTAGTTTAAAACATATTATATTTAGCATGTATTATAACGAAAACAATAAAAT
66 TCAATTTGAGATCTTAGTTTAAAACATATTATATTTAGCATGTATTATAACAAAAACAATAAAAT
2212651 GAATAAAACTTTGATTTTTTTTAGAGAATATT
131 GAATAAAACTTTGA-TTTTTTTAGAGAATATT
2212683 AA
1 AA
2212685 ATATATAAGC
Statistics
Matches: 154, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
160 136 0.88
162 18 0.12
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (161 bp):
AATTGAAGGGGATTGAACTCGATCTTTTGTGTTGTTGAGGCACGCTCATATCACTAGACCAACAC
TCAATTTGAGATCTTAGTTTAAAACATATTATATTTAGCATGTATTATAACAAAAACAATAAAAT
GAATAAAACTTTGATTTTTTTAGAGAATATT
Found at i:2214285 original size:27 final size:27
Alignment explanation
Indices: 2214242--2214294 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2214232 GACTGAATTT
2214242 ATTAAAATGACAAAAATACCCATGAGC
1 ATTAAAATGACAAAAATACCCATGAGC
** *
2214269 ATTAAAATGACCGAAATACCCTTGAG
1 ATTAAAATGACAAAAATACCCATGAG
2214295 TTCTAGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (27 bp):
ATTAAAATGACAAAAATACCCATGAGC
Found at i:2215297 original size:39 final size:39
Alignment explanation
Indices: 2215249--2215383 Score: 146
Period size: 39 Copynumber: 3.5 Consensus size: 39
2215239 CTGCTTCGTT
* * *
2215249 CACATGGTAAGTCCTTACCGCAAGCTCCTTTATTTTATG
1 CACAGGGTAAGTCCTTACCGTAAGCTCCTTTATTTTGTG
* * *
2215288 CACAGGGTAAGCCCTTACCGTAGGCTCATTTATTTTGTG
1 CACAGGGTAAGTCCTTACCGTAAGCTCCTTTATTTTGTG
* * * *
2215327 CACAGGGTAA-ACTCTTACCATAAGCTCCTCTACTTTGTG
1 CACAGGGTAAGTC-CTTACCGTAAGCTCCTTTATTTTGTG
* *
2215366 CACAAGATAAGTCCTTAC
1 CACAGGGTAAGTCCTTAC
2215384 TGTAGACCCT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
38 1 0.01
39 77 0.97
40 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (39 bp):
CACAGGGTAAGTCCTTACCGTAAGCTCCTTTATTTTGTG
Found at i:2218387 original size:32 final size:32
Alignment explanation
Indices: 2218346--2218412 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
2218336 GGCCAATCTG
2218346 ACCCCCTATCCCATATCCGACCTGATCACCTA
1 ACCCCCTATCCCATATCCGACCTGATCACCTA
2218378 ACCCCCTATCCCATATCCGACCTGATCACCTA
1 ACCCCCTATCCCATATCCGACCTGATCACCTA
2218410 ACC
1 ACC
2218413 TAACCCACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.25, C:0.48, G:0.06, T:0.21
Consensus pattern (32 bp):
ACCCCCTATCCCATATCCGACCTGATCACCTA
Found at i:2221365 original size:23 final size:23
Alignment explanation
Indices: 2221332--2221389 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
2221322 AGGGTGTTAC
2221332 ATAATTTAATAT-ATATTTTAAAA
1 ATAA-TTAATATGATATTTTAAAA
2221355 TATAATTAATATGATATTTTAAAA
1 -ATAATTAATATGATATTTTAAAA
*
2221379 AAAATTAATAT
1 ATAATTAATAT
2221390 TTTAAATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 17 0.53
24 15 0.47
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAATTAATATGATATTTTAAAA
Found at i:2221413 original size:24 final size:22
Alignment explanation
Indices: 2221332--2221415 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 22
2221322 AGGGTGTTAC
*
2221332 ATAATTTAATAT-ATATTTTAAA
1 ATAAATTAATATAATATTTT-AA
*
2221354 ATATAATTAATATGATATTTTAA
1 ATA-AATTAATATAATATTTTAA
2221377 A-AAA--AAT-TAATATTTTAA
1 ATAAATTAATATAATATTTTAA
2221395 ATTTAAATTTAATATATATAT
1 A--TAAA-TTAATATA-ATAT
2221416 ATATAAAATA
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
18 11 0.22
19 3 0.06
21 5 0.10
22 4 0.08
23 11 0.22
24 10 0.20
25 2 0.04
26 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (22 bp):
ATAAATTAATATAATATTTTAA
Found at i:2230908 original size:11 final size:11
Alignment explanation
Indices: 2230892--2230924 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
2230882 CATTGCATGG
2230892 TATTTAGTTTA
1 TATTTAGTTTA
2230903 TATTTAGTTTA
1 TATTTAGTTTA
2230914 TATTTAGTTTA
1 TATTTAGTTTA
2230925 GTTGTCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (11 bp):
TATTTAGTTTA
Found at i:2244238 original size:13 final size:13
Alignment explanation
Indices: 2244220--2244245 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2244210 TGTCGACATA
2244220 TGCCAAATTTCTC
1 TGCCAAATTTCTC
2244233 TGCCAAATTTCTC
1 TGCCAAATTTCTC
2244246 AAGGAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (13 bp):
TGCCAAATTTCTC
Found at i:2248246 original size:13 final size:13
Alignment explanation
Indices: 2248228--2248258 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2248218 GTCTTATCTT
2248228 CTTTTCACTTTTA
1 CTTTTCACTTTTA
2248241 CTTTTCACTTTTA
1 CTTTTCACTTTTA
2248254 CTTTT
1 CTTTT
2248259 TTTCATCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.65
Consensus pattern (13 bp):
CTTTTCACTTTTA
Found at i:2256356 original size:19 final size:19
Alignment explanation
Indices: 2256332--2256372 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2256322 ACTGCCAATG
2256332 TGGCACATCCAACGTGGCA
1 TGGCACATCCAACGTGGCA
2256351 TGGCACATCCAACGTGGCA
1 TGGCACATCCAACGTGGCA
2256370 TGG
1 TGG
2256373 TATGCAGGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.17
Consensus pattern (19 bp):
TGGCACATCCAACGTGGCA
Found at i:2258102 original size:62 final size:62
Alignment explanation
Indices: 2257944--2258104 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 62
2257934 CATCTCAATT
* *
2257944 ATATTCTAACCACTTTCCTTACAAAATGAAAACCACACTTAAACAAATTATCGTCTCTCTTTAA
1 ATATTCTAACCACTTTCCTTACAAAA-GAAAATCACACTTAAACAAATAATC-TCTCTCTTTAA
* * * *
2258008 ATATTCTAACCACTTTCCTTACAAAAGAAAAATCGCACTTAAACAAACTAAT-T-TGTTTTTAG
1 ATATTCTAACCACTTTCCTTACAAAAG-AAAATCACACTTAAACAAA-TAATCTCTCTCTTTAA
* *
2258070 ATGTTCTAACCACTTTCCTTACGAAACGAAAATCA
1 ATATTCTAACCACTTTCCTTAC-AAAAGAAAATCA
2258105 TCCCAAAAGC
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
62 33 0.39
63 6 0.07
64 43 0.51
65 3 0.04
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.32
Consensus pattern (62 bp):
ATATTCTAACCACTTTCCTTACAAAAGAAAATCACACTTAAACAAATAATCTCTCTCTTTAA
Found at i:2259852 original size:30 final size:30
Alignment explanation
Indices: 2259813--2259876 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 30
2259803 TATATATGAT
*
2259813 ATGATCTATGTGATCC-TATGAGAATGTGAC
1 ATGAACTATGTGA-CCATATGAGAATGTGAC
2259843 ATGAACTATGTGACCATATGAGAATGTGAC
1 ATGAACTATGTGACCATATGAGAATGTGAC
2259873 ATGA
1 ATGA
2259877 GATTATATGC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.06
30 30 0.94
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (30 bp):
ATGAACTATGTGACCATATGAGAATGTGAC
Found at i:2260446 original size:9 final size:9
Alignment explanation
Indices: 2260400--2260447 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
2260390 ACTAAGAGAT
2260400 ATAATTGATA
1 ATAA-TGATA
*
2260410 ATAATGCTA
1 ATAATGATA
2260419 ATAATGATA
1 ATAATGATA
* *
2260428 AGAATAATA
1 ATAATGATA
*
2260437 ATAAGGATA
1 ATAATGATA
2260446 AT
1 AT
2260448 GAAATGATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
9 27 0.87
10 4 0.13
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.31
Consensus pattern (9 bp):
ATAATGATA
Found at i:2263900 original size:44 final size:44
Alignment explanation
Indices: 2263807--2263902 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 44
2263797 GAAATACAAG
**
2263807 CTATGTGAATAAATGATCACAAGATATAAGTCATGTGACAGGAT
1 CTATGTGAATAAATGAGAACAAGATATAAGTCATGTGACAGGAT
* * * * * *
2263851 ATATGTGAATATATGAGAACATGATATCAG-CTATGTGATATGAT
1 CTATGTGAATAAATGAGAACAAGATATAAGTC-ATGTGACAGGAT
2263895 CTATGTGA
1 CTATGTGA
2263903 TCCTATGAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (44 bp):
CTATGTGAATAAATGAGAACAAGATATAAGTCATGTGACAGGAT
Found at i:2264232 original size:24 final size:24
Alignment explanation
Indices: 2264198--2264248 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
2264188 TGTGTTATAT
2264198 GTGGTCATTCGGGACAAATTCTAC
1 GTGGTCATTCGGGACAAATTCTAC
*
2264222 GTGGTCCTTCGGGACAAATTCTAC
1 GTGGTCATTCGGGACAAATTCTAC
2264246 GTG
1 GTG
2264249 CCCTTAGTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (24 bp):
GTGGTCATTCGGGACAAATTCTAC
Found at i:2264525 original size:9 final size:9
Alignment explanation
Indices: 2264484--2264526 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
2264474 GAGATATGAT
2264484 TGATAATAA
1 TGATAATAA
*
2264493 TGCTAATAA
1 TGATAATAA
*
2264502 TGATAAGAA
1 TGATAATAA
*
2264511 TAATAATAA
1 TGATAATAA
*
2264520 GGATAAT
1 TGATAAT
2264527 GAAATGATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.14, T:0.30
Consensus pattern (9 bp):
TGATAATAA
Found at i:2280262 original size:16 final size:16
Alignment explanation
Indices: 2280241--2280272 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2280231 ATTGGTTATT
2280241 TTTTTTAATCATTTAA
1 TTTTTTAATCATTTAA
*
2280257 TTTTTTAATTATTTAA
1 TTTTTTAATCATTTAA
2280273 ATCGAGTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTTAATCATTTAA
Found at i:2282436 original size:194 final size:194
Alignment explanation
Indices: 2282107--2282495 Score: 778
Period size: 194 Copynumber: 2.0 Consensus size: 194
2282097 AGCTGGTTAT
2282107 AACTTGGTCAGTTACACAACTTTCACATCTATTCTTTCAGTTTTACCCGGTTTGATTTAAATGGA
1 AACTTGGTCAGTTACACAACTTTCACATCTATTCTTTCAGTTTTACCCGGTTTGATTTAAATGGA
2282172 AAAAGAACTACATTCCTGTTAGTCGACTGTTAGCTCTGTGTACCAGTTTCATGAAAGCAAATTGC
66 AAAAGAACTACATTCCTGTTAGTCGACTGTTAGCTCTGTGTACCAGTTTCATGAAAGCAAATTGC
2282237 TTCCCACTAGGAAGCCAGTGAATGACTATTAATTTCTGGTTTTATATTCAATTTGATTAATTGA
131 TTCCCACTAGGAAGCCAGTGAATGACTATTAATTTCTGGTTTTATATTCAATTTGATTAATTGA
2282301 AACTTGGTCAGTTACACAACTTTCACATCTATTCTTTCAGTTTTACCCGGTTTGATTTAAATGGA
1 AACTTGGTCAGTTACACAACTTTCACATCTATTCTTTCAGTTTTACCCGGTTTGATTTAAATGGA
2282366 AAAAGAACTACATTCCTGTTAGTCGACTGTTAGCTCTGTGTACCAGTTTCATGAAAGCAAATTGC
66 AAAAGAACTACATTCCTGTTAGTCGACTGTTAGCTCTGTGTACCAGTTTCATGAAAGCAAATTGC
2282431 TTCCCACTAGGAAGCCAGTGAATGACTATTAATTTCTGGTTTTATATTCAATTTGATTAATTGA
131 TTCCCACTAGGAAGCCAGTGAATGACTATTAATTTCTGGTTTTATATTCAATTTGATTAATTGA
2282495 A
1 A
2282496 TACCCTTGGC
Statistics
Matches: 195, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
194 195 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (194 bp):
AACTTGGTCAGTTACACAACTTTCACATCTATTCTTTCAGTTTTACCCGGTTTGATTTAAATGGA
AAAAGAACTACATTCCTGTTAGTCGACTGTTAGCTCTGTGTACCAGTTTCATGAAAGCAAATTGC
TTCCCACTAGGAAGCCAGTGAATGACTATTAATTTCTGGTTTTATATTCAATTTGATTAATTGA
Found at i:2285300 original size:153 final size:154
Alignment explanation
Indices: 2285068--2285460 Score: 474
Period size: 153 Copynumber: 2.6 Consensus size: 154
2285058 ATTTAGTCCC
* * * * * *
2285068 TAATTTCATTATTTTTTCAATTCCTCCTTCATTTTAAGTCCATTTTTATC--ATTTGAATCACAT
1 TAATATCATTATTTCTTCAATTCGTCATTTATTTTAAGT-CATTTTTATCAAATTTGAACCACAT
* * * *
2285131 GCACTTAAACCATAGTAGAATACATGTGTACTTTCAATTCCACTTTTTGAT-A-ATTTTTTTATT
65 GCTCATAAACCATAGTAGAATACATGTCTACTTTCAATTCCACTTTTTGATAACAATTTTTT-TT
2285194 TTTAAATTTAGTCCTTCAATTTTTCA
129 TTTAAATTTAGTCCTTCAATTTTTCA
* *
2285220 TAATATCATTATTTCTCCAATTCGTCATTTATTTTAAGTCATTTTTATCAAATTTGAGCCACATG
1 TAATATCATTATTTCTTCAATTCGTCATTTATTTTAAGTCATTTTTATCAAATTTGAACCACATG
* * *
2285285 CTCCTAAACCATAGTAGAATACATGTCTACTTTCAATTCCTCTTTTTTATAACAATTTTTTTTTT
66 CTCATAAACCATAGTAGAATACATGTCTACTTTCAATTCCACTTTTTGATAACAATTTTTTTTTT
*
2285350 TCAATTTAGTCCTTCAATTTTTCA
131 TAAATTTAGTCCTTCAATTTTTCA
** * * * * *
2285374 T-ACCTCCTTATTCCTTCAATTTGTAATTTA-TTTAAGTCAATTTTTTACCAAATTTGAACCACA
1 TAATATCATTATTTCTTCAATTCGTCATTTATTTTAAGTC-A-TTTTTATCAAATTTGAACCACA
* * *
2285437 TGCTCATATACCACAATAGAATAC
64 TGCTCATAAACCATAGTAGAATAC
2285461 CTATATAACT
Statistics
Matches: 207, Mismatches: 28, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
151 10 0.05
152 41 0.20
153 80 0.39
154 69 0.33
155 7 0.03
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (154 bp):
TAATATCATTATTTCTTCAATTCGTCATTTATTTTAAGTCATTTTTATCAAATTTGAACCACATG
CTCATAAACCATAGTAGAATACATGTCTACTTTCAATTCCACTTTTTGATAACAATTTTTTTTTT
TAAATTTAGTCCTTCAATTTTTCA
Found at i:2285485 original size:154 final size:154
Alignment explanation
Indices: 2285098--2285490 Score: 397
Period size: 154 Copynumber: 2.6 Consensus size: 154
2285088 TTCCTCCTTC
* * * * * * * *
2285098 ATTTTAAGTCCATTTTTATC--ATTTGAATCACATGCACTTAAACCATAGTAGAATACATGTGTA
1 ATTTTAAGT-CATTTTTACCAAATTTGAACCACATGCTCATAAACCACAATAGAATACATATATA
* * * *
2285161 CTTTCAATTCC-ACTTTTTGATA-ATTTTTTTATTTTTAAATTTAGTCCTTCAATTTTTCATAAT
65 CTTTCAATTCCTATTTTTTTA-ACAATTTTTTATTTTTAAATTTAGTCCTTCAATTTTTCATAAC
* *
2285224 ATCATTATTTCTCCAATTCGTCATTT
129 ATCATTATTCCTCCAATTCGTAATTT
* * * * * * *
2285250 ATTTTAAGTCATTTTTATCAAATTTGAGCCACATGCTCCTAAACCATAGTAGAATACATGTCTAC
1 ATTTTAAGTCATTTTTACCAAATTTGAACCACATGCTCATAAACCACAATAGAATACATATATAC
* * *
2285315 TTTCAATTCCTCTTTTTTATAACAATTTTTT-TTTTTCAATTTAGTCCTTCAATTTTTCAT-ACC
66 TTTCAATTCCTATTTTTT-TAACAATTTTTTATTTTTAAATTTAGTCCTTCAATTTTTCATAACA
* * *
2285378 TCCTTATTCCTTCAATTTGTAATTT
130 TCATTATTCCTCCAATTCGTAATTT
* *
2285403 A-TTTAAGTCAATTTTTTACCAAATTTGAACCACATGCTCATATACCACAATAGAATACCTATAT
1 ATTTTAAGTC-A-TTTTTACCAAATTTGAACCACATGCTCATAAACCACAATAGAATACATATAT
**
2285467 AACTTT-AATTGTTATTTTTTTAAC
64 -ACTTTCAATTCCTATTTTTTTAAC
2285491 TAAGATATAC
Statistics
Matches: 204, Mismatches: 29, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
151 10 0.05
152 17 0.08
153 76 0.37
154 88 0.43
155 13 0.06
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.46
Consensus pattern (154 bp):
ATTTTAAGTCATTTTTACCAAATTTGAACCACATGCTCATAAACCACAATAGAATACATATATAC
TTTCAATTCCTATTTTTTTAACAATTTTTTATTTTTAAATTTAGTCCTTCAATTTTTCATAACAT
CATTATTCCTCCAATTCGTAATTT
Found at i:2285723 original size:2 final size:2
Alignment explanation
Indices: 2285716--2285751 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2285706 ATATGAAAGA
2285716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2285752 TATGGTTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2293362 original size:31 final size:31
Alignment explanation
Indices: 2293289--2293355 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
2293279 CAGTTACATC
*
2293289 AGGGACCATATTGCAAACGGACTAAATGTTG
1 AGGGACCATATTGCAAACAGACTAAATGTTG
2293320 AGGGACCATATTGCAAACAGACTAAATGTTG
1 AGGGACCATATTGCAAACAGACTAAATGTTG
*
2293351 GGGGA
1 AGGGA
2293356 TTATATTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (31 bp):
AGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:2294440 original size:31 final size:31
Alignment explanation
Indices: 2294405--2294475 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
2294395 CTTTTAAAAC
**
2294405 TTGCAATA-CATTCCCCCAACATTTAGTCTGT
1 TTGCAATATCA-TCCCCCAACATTTAGTCCAT
* *
2294436 TTGCAATATGATCCCTCAACATTTAGTCCAT
1 TTGCAATATCATCCCCCAACATTTAGTCCAT
2294467 TTGCAATAT
1 TTGCAATAT
2294476 GGTCCCCGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.37
Consensus pattern (31 bp):
TTGCAATATCATCCCCCAACATTTAGTCCAT
Found at i:2294476 original size:31 final size:31
Alignment explanation
Indices: 2294416--2294482 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
2294406 TGCAATACAT
**
2294416 TCCCCCAACATTTAGTCTGTTTGCAATATGA
1 TCCCCCAACATTTAGTCCATTTGCAATATGA
* *
2294447 TCCCTCAACATTTAGTCCATTTGCAATATGG
1 TCCCCCAACATTTAGTCCATTTGCAATATGA
2294478 TCCCC
1 TCCCC
2294483 GACGTAACTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.24, C:0.30, G:0.12, T:0.34
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCATTTGCAATATGA
Found at i:2295270 original size:2 final size:2
Alignment explanation
Indices: 2295263--2295330 Score: 76
Period size: 2 Copynumber: 37.0 Consensus size: 2
2295253 CCGCCCCGAT
2295263 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2295303 TT TA TA TA T- TT TA TA T- TA -A T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2295331 AAATATTTTC
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
1 6 0.10
2 52 0.90
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2295893 original size:24 final size:24
Alignment explanation
Indices: 2295866--2295917 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
2295856 AAGGACAGTC
*
2295866 TACGCATATGGGTTACGTTAGATG
1 TACGCATACGGGTTACGTTAGATG
2295890 TACGCATACGGGTTACGTTAGATG
1 TACGCATACGGGTTACGTTAGATG
2295914 TACG
1 TACG
2295918 AAAACCACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (24 bp):
TACGCATACGGGTTACGTTAGATG
Found at i:2307131 original size:17 final size:17
Alignment explanation
Indices: 2307109--2307143 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2307099 ATTCTTGATC
2307109 TTGATCAGTGTTTAGAA
1 TTGATCAGTGTTTAGAA
2307126 TTGATCAGTGTTTAGAA
1 TTGATCAGTGTTTAGAA
2307143 T
1 T
2307144 CTGGTTGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.43
Consensus pattern (17 bp):
TTGATCAGTGTTTAGAA
Found at i:2315512 original size:228 final size:227
Alignment explanation
Indices: 2315111--2315619 Score: 848
Period size: 228 Copynumber: 2.3 Consensus size: 227
2315101 TTATTAGTTC
*
2315111 AAAGAAAAAAAGGCAAAAAGAGGTTGAGAACAAGATCATTGTAGATTGGAAAAGAATATTGAATA
1 AAAGAAAAAAAGGCAAAAAGAGGTTGAGAACAAGATCATTGTAGATTGGAAAAGAATACTGAATA
*
2315176 AAGAACAATAAAATGACAAGCAATAAATTCAAGAAACTCTAAATAATTTGACAATGAATGTTCAA
66 AAGAACAATAAAATGACAAGCAATAAATTCAAGAAACTCTAAATAATTTGACAATAAATGTTCAA
* * **
2315241 ACACTCATACAGACGTCATGCTCAAACTTGAGACCTTTAAAGATAACAAACATCACTTAACCATT
131 ACAATCATACAAACGTCATGCTCAAACCCGAGACCTTTAAAGATAACAAACATCACTTAACCATT
*
2315306 TATTAGTTTTAAGCCTTAAATAATGAATTCGT
196 TATTAGTTGTAAGCCTTAAATAATGAATTCGT
2315338 AAAGAAAAAAAAGGCAAAAAGAGGTTGAGAACAAGATCATTGTAGATTGGAAAAGAATACTGAAT
1 AAAG-AAAAAAAGGCAAAAAGAGGTTGAGAACAAGATCATTGTAGATTGGAAAAGAATACTGAAT
* * *
2315403 AAAGAACAATCAAATGACAAGCAATAAATTCGAGAAACTCTCAATAATTTGACAATAAATGTTCA
65 AAAGAACAATAAAATGACAAGCAATAAATTCAAGAAACTCTAAATAATTTGACAATAAATGTTCA
* * *
2315468 AACAATCCTTCAAACGTCATGCTCAAACCCGAGACCTTTAAAGATAACAAATATCACTTAACCAT
130 AACAATCATACAAACGTCATGCTCAAACCCGAGACCTTTAAAGATAACAAACATCACTTAACCAT
2315533 TTATTAGTTGTAAGCCTTAAATAATGAATTCGT
195 TTATTAGTTGTAAGCCTTAAATAATGAATTCGT
*
2315566 -AAG-GAAAAA---AAAAAGAGGTTGAGAACAAGATCATTGTAGATTGGAAAAGAATAC
1 AAAGAAAAAAAGGCAAAAAGAGGTTGAGAACAAGATCATTGTAGATTGGAAAAGAATAC
2315620 CATATAACTG
Statistics
Matches: 267, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
222 45 0.17
225 5 0.02
227 7 0.03
228 210 0.79
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.24
Consensus pattern (227 bp):
AAAGAAAAAAAGGCAAAAAGAGGTTGAGAACAAGATCATTGTAGATTGGAAAAGAATACTGAATA
AAGAACAATAAAATGACAAGCAATAAATTCAAGAAACTCTAAATAATTTGACAATAAATGTTCAA
ACAATCATACAAACGTCATGCTCAAACCCGAGACCTTTAAAGATAACAAACATCACTTAACCATT
TATTAGTTGTAAGCCTTAAATAATGAATTCGT
Found at i:2317248 original size:27 final size:27
Alignment explanation
Indices: 2317218--2317269 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
2317208 CTTCATGTCA
*
2317218 AGTGGTGAGCATATAATTCTCGAATCC
1 AGTGGAGAGCATATAATTCTCGAATCC
* * *
2317245 AGTGGAGTGTATATGATTCTCGAAT
1 AGTGGAGAGCATATAATTCTCGAAT
2317270 TAGGCCGTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (27 bp):
AGTGGAGAGCATATAATTCTCGAATCC
Found at i:2319163 original size:111 final size:111
Alignment explanation
Indices: 2318963--2319330 Score: 540
Period size: 111 Copynumber: 3.3 Consensus size: 111
2318953 TTCAAAAAAT
** * * * *
2318963 TATCGATCATTTTTATAAAAAATATCTATACTTTCAACATATTAGGTAAATGTTACTGGTTTTGT
1 TATCGATCATTTTTAT-AAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACTGTTTTTGT
*
2319028 CATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTATAAAG
65 CATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAG
*
2319075 TATCTATCATTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACTGTTTTTGTC
1 TATCGATCATTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACTGTTTTTGTC
*
2319140 ATAATGAAACTGGTTTTGTCATATTTTTACTTGTTATATTGTAAAG
66 ATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAG
* * * * * *
2319186 TATCTATCCTTTTTATAAAAGGATCAATACTTTCAATATATCAGGTAAATTTTACCGTTTTTGTT
1 TATCGATCATTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACTGTTTTTGTC
* *
2319251 ATAATGAAACTAGTTTTGTCATATTTTTACCTGTTATATTGTAAAAA
66 ATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT-AAAG
*
2319298 TATCGATACATTTTTAT-AAAGTATCGATACTTT
1 TATCGAT-CATTTTTATAAAAGGATCGATACTTT
2319331 ATAGGCACTA
Statistics
Matches: 233, Mismatches: 21, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
111 187 0.80
112 38 0.16
113 8 0.03
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (111 bp):
TATCGATCATTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACTGTTTTTGTC
ATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAG
Found at i:2319930 original size:111 final size:111
Alignment explanation
Indices: 2319799--2320212 Score: 670
Period size: 111 Copynumber: 3.7 Consensus size: 111
2319789 ATATATATAT
* *
2319799 TTTCAACATATCAGGTAAATTTTACCGATTTTGTCATAATCAAACTGGTTTTGTCATATTTTTAC
1 TTTCAACATATCAAGTAAATTTTACCGATTTTGTCATAATGAAACTGGTTTTGTCATATTTTTAC
2319864 CTGTTATATTGTAAAATATCTATTCTTTTTATAAAAAGATCGATAC
66 CTGTTATATTGTAAAATATCTATTCTTTTTATAAAAAGATCGATAC
* *
2319910 TTTCAACATATCAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTAC
1 TTTCAACATATCAAGTAAATTTTACCGATTTTGTCATAATGAAACTGGTTTTGTCATATTTTTAC
* *
2319975 CTGTTATATTGTAAAGTATCTA-TCATTTTTATAAAAGGATCGATAC
66 CTGTTATATTGTAAAATATCTATTC-TTTTTATAAAAAGATCGATAC
* *
2320021 TTTCAATATATCAAGTAAATTTTACCGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTAC
1 TTTCAACATATCAAGTAAATTTTACCGATTTTGTCATAATGAAACTGGTTTTGTCATATTTTTAC
* * *
2320086 CTGTTATATTGTAAAGTATCTATCCTTTTTATAAAATGATCGATAC
66 CTGTTATATTGTAAAATATCTATTCTTTTTATAAAAAGATCGATAC
* * *
2320132 TTTCAACATATCAAGTAAATTTTACCGATTTTATCATAATAAAATTGGTGTTT-TCATATTTTTA
1 TTTCAACATATCAAGTAAATTTTACCGATTTTGTCATAATGAAACTGGT-TTTGTCATATTTTTA
2320196 CCTGTTATATTGTAAAA
65 CCTGTTATATTGTAAAA
2320213 CATCGATATA
Statistics
Matches: 286, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
110 2 0.01
111 280 0.98
112 4 0.01
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (111 bp):
TTTCAACATATCAAGTAAATTTTACCGATTTTGTCATAATGAAACTGGTTTTGTCATATTTTTAC
CTGTTATATTGTAAAATATCTATTCTTTTTATAAAAAGATCGATAC
Found at i:2320939 original size:111 final size:111
Alignment explanation
Indices: 2320688--2321154 Score: 654
Period size: 111 Copynumber: 4.2 Consensus size: 111
2320678 GTATCGATAA
* * * * *
2320688 TTTTTATAAAAGTATCTATACTTTCAACATATTAGGTAAATGTTA-TCGGTTTTGTCATAATGAA
1 TTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACT-GTTTTTGTCATAATGAA
2320752 ACTGGTTTTGTCATA-TTTTACCTGTTATATTGTAAAGTATCTATCT
65 ACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCT
* *
2320798 TTTTTATAAAAGGATCGATACTCTCTACATATCAGGTAAATTTTACTGTTTTTGTCATAATGAAA
1 TTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACTGTTTTTGTCATAATGAAA
* * *
2320863 CTGTTTTTGTCATATTTTTACCTTTTATATTATAAAGTATCTATCT
66 CTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCT
* *
2320909 TTTTTATAAAATGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTTTGTCATAATGAAA
1 TTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACTGTTTTTGTCATAATGAAA
* * *
2320974 CTGGTTTTGTCATATTTTTACCTGTTACATTGTAAAGTATTTATCC
66 CTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCT
* *
2321020 TTTTTATAAAAGGATCGATACTTTCAACATATCAAGTAAATTTTACCGGTTTTT-TCATAATGAA
1 TTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTA-CTGTTTTTGTCATAATGAA
* * * * * **
2321084 ATTGTTTTTATCATATTTTTACCTGTTATATTGTAAAATATCGATAGA
65 ACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTAT-CT
*
2321132 TTTTTAT-AAAGTATCGATACTTT
1 TTTTTATAAAAGGATCGATACTTT
2321155 ATAGGCGCTA
Statistics
Matches: 320, Mismatches: 33, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
110 69 0.22
111 237 0.74
112 14 0.04
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (111 bp):
TTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACTGTTTTTGTCATAATGAAA
CTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCT
Found at i:2321010 original size:909 final size:913
Alignment explanation
Indices: 2318958--2321260 Score: 3719
Period size: 909 Copynumber: 2.5 Consensus size: 913
2318948 TAACTTTCAA
* * * * * * *
2318958 AAAATTATCGATCATTTTTATAAAAAATATCTATACTTTCAACATATTAGGTAAATGTTACTGGT
1 AAAA-TATCTATCTTTTTTAT-AAAAAGATCGATACTTTCAACATATCAGGTAAATTTTACTGTT
2319023 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTATAAAGTATCTATCATTTT
64 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTATAAAGTATCTATCATTTT
*
2319088 TATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACTGTTTTTGTCATAATGAAACTGG
129 TATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGG
* *
2319153 TTTTGTCATATTTTTACTTGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGGATCAATACTT
194 TTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGGATCGATACTT
* * * * * * *
2319218 TCAATATATCAGGTAAATTTTACCGTTTTTGTTATAATGAAACTAGTTTTGTCATATTTTTACCT
259 TCAACATATCAAGTAAATTTTACCGATTTTATCATAATGAAA-TTGTTTTATCATATTTTTACCT
*
2319283 GTTATATTGTAAAAATATCGATACATTTTTATAAAGTATCGATACTTTATAGGCACTATTACT-T
323 GTTATATTGT-AAAATATCGATACATTTTTATAAAGTATCGATACTTTATAGGCGCTATTACTGT
* *
2319347 CTTTTCTTTTAAATTCCAAAAGTTGCAATACTTATTTAAATGGAATCGATACTTTCAACATATTC
387 -TTTTCTTTTAAATTCCAAAAGTTTCGATACTTATTTAAATGGAATCGATACTTTCAACATATTC
* *
2319412 GGTAGGTAGTTTAATGTAATAGGTAGGTATTTGACTGTAAAAAATATTAATTTAAGATTATCTTT
451 GGTAGGTAGTTTAATGTAATAGGTAGGTATTTCACTGTAAAAAACATTAATTTAAGATTATCTTT
* ** *
2319477 TGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGCGTCTAGTGATTTATTTTTTATGTTACG
516 TGAGTGAGATTTAAGATATTAATTTAGTAATTATACACGTCTAATGATTTA-TTTTTATGTTACG
*
2319542 GTATATATTATTATTAAATTAAAAACAATAAACATAGATATTACATATTTATTATTATCATTGGT
580 ATATATATTATTATTAAATTAAAAACAATAAACATAGATATTACATATTTATTATTATCATTGGT
2319607 TAAAATTATTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAATGTT
645 TAAAATTATTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAATGTT
* * * *
2319672 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAATACTATTAAAAACTTTT
710 TATGTAAATGAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATTAAAAAATTTT
* ** *
2319737 GAAACATAAATTATATAACTTTCAAAAAAGTATAAATCCTTTTTATAAAAATATATATATATTTT
775 GAAACATAAATTACATAACTTTCAAAAAAGTATAAATAATTTTTATAAAAATATATATATACTTT
*
2319802 CAACATATCAGGTAAATTTTACCGATTTTGTCATAATCAAACTGGTTTTGTCATATTTTTACCTG
840 CAACATATCAGGTAAATGTTACCGATTTTGTCATAATCAAACTGGTTTTGTCATATTTTTACCTG
2319867 TTATATTGT
905 TTATATTGT
*
2319876 AAAATATCTAT-TCTTTTTATAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTT
1 AAAATATCTATCT-TTTTTATAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTACTGTTT
*
2319940 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCATTTTT
65 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTATAAAGTATCTATCATTTTT
* *
2320005 ATAAAAGGATCGATACTTTCAATATATCAAGTAAATTTTACCGTTTTTGTCATAATGAAACTGGT
130 ATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGT
*
2320070 TTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCCTTTTTATAAAATGATCGATACTTT
195 TTTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGGATCGATACTTT
*
2320135 CAACATATCAAGTAAATTTTACCGATTTTATCATAATAAAATTGGTGTTT-TCATATTTTTACCT
260 CAACATATCAAGTAAATTTTACCGATTTTATCATAATGAAATT-GT-TTTATCATATTTTTACCT
* * *
2320199 GTTATATTGTAAAACATCGATATAGTTTTATAAAGTATCGATACTTTATAGGCGCTATTACTGTT
323 GTTATATTGTAAAATATCGATACATTTTTATAAAGTATCGATACTTTATAGGCGCTATTACTGTT
2320264 TTTCTTTTAAATTCCAAAAGTTTCGATACTTATTTAAATGGAATCGATACTTTCAACATATTCGG
388 TTTCTTTTAAATTCCAAAAGTTTCGATACTTATTTAAATGGAATCGATACTTTCAACATATTCGG
* * *
2320329 TAGGTAGTTTAATGTAATAAGTAGGTA-TTCACTGTGAAAAACATTAATTTAAGGTTATCTTTTG
453 TAGGTAGTTTAATGTAATAGGTAGGTATTTCACTGTAAAAAACATTAATTTAAGATTATCTTTTG
2320393 AGTGAGATTTAAGATATTAATTTAGTAATTATACACGTCTAATGATTTA-TTTTATGTTACGATA
518 AGTGAGATTTAAGATATTAATTTAGTAATTATACACGTCTAATGATTTATTTTTATGTTACGATA
* *
2320457 TATATTATTATTAAATTAAAAATAATAAACATAGATATTACATATTTATTATTATCTTTGGTTAA
583 TATATTATTATTAAATTAAAAACAATAAACATAGATATTACATATTTATTATTATCATTGGTTAA
* * *
2320522 AATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTAT
648 AATTATTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAATGTTTAT
2320587 GTAAATGAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATTAAAAAATTTTGAA
713 GTAAATGAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATTAAAAAATTTTGAA
** * *
2320652 ACATAAATTACATAACTTTCAAAAAAGTATCGATAATTTTTAT-AAAA-GTATCTATACTTTCAA
778 ACATAAATTACATAACTTTCAAAAAAGTATAAATAATTTTTATAAAAATATATATATACTTTCAA
* * * *
2320715 CATATTAGGTAAATGTTATCGGTTTTGTCATAATGAAACTGGTTTTGTCATA-TTTTACCTGTTA
843 CATATCAGGTAAATGTTACCGATTTTGTCATAATCAAACTGGTTTTGTCATATTTTTACCTGTTA
2320779 TATTGT
908 TATTGT
* * * *
2320785 AAAGTATCTATCTTTTTTATAAAAGGATCGATACTCTCTACATATCAGGTAAATTTTACTGTTTT
1 AAAATATCTATCTTTTTTATAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTACTGTTTT
* * *
2320850 TGTCATAATGAAACTGTTTTTGTCATATTTTTACCTTTTATATTATAAAGTATCTATCTTTTTTA
66 TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTATAAAGTATCTATCATTTTTA
*
2320915 TAAAATGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGTT
131 TAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGTT
* *
2320980 TTGTCATATTTTTACCTGTTACATTGTAAAGTATTTATCCTTTTTATAAAAGGATCGATACTTTC
196 TTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGGATCGATACTTTC
* *
2321045 AACATATCAAGTAAATTTTACCGGTTTTTTCATAATGAAATTGTTTTTATCATATTTTTACCTGT
261 AACATATCAAGTAAATTTTACCGATTTTATCATAATGAAATTG-TTTTATCATATTTTTACCTGT
* *
2321110 TATATTGTAAAATATCGATAGATTTTTATAAAGTATCGATACTTTATAGGCGCTATTACTG-CTT
325 TATATTGTAAAATATCGATACATTTTTATAAAGTATCGATACTTTATAGGCGCTATTACTGTTTT
* *
2321174 TCTTTTAAATTCCAAAAGTGTCGATACTTATTTAAATGAAATCGATACTTTCAACATACCTT--G
390 TCTTTTAAATTCCAAAAGTTTCGATACTTATTTAAATGGAATCGATACTTTCAACATA--TTCGG
*
2321237 TAGGTAGTTTAATATAATAGGTAG
453 TAGGTAGTTTAATGTAATAGGTAG
2321261 CACCTATTTT
Statistics
Matches: 1290, Mismatches: 86, Indels: 28
0.92 0.06 0.02
Matches are distributed among these distances:
908 85 0.07
909 375 0.29
910 63 0.05
911 4 0.00
912 238 0.18
914 78 0.06
915 139 0.11
916 288 0.22
917 16 0.01
918 4 0.00
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (913 bp):
AAAATATCTATCTTTTTTATAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTACTGTTTT
TGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTATAAAGTATCTATCATTTTTA
TAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGTTTTTGTCATAATGAAACTGGTT
TTGTCATATTTTTACCTGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGGATCGATACTTTC
AACATATCAAGTAAATTTTACCGATTTTATCATAATGAAATTGTTTTATCATATTTTTACCTGTT
ATATTGTAAAATATCGATACATTTTTATAAAGTATCGATACTTTATAGGCGCTATTACTGTTTTT
CTTTTAAATTCCAAAAGTTTCGATACTTATTTAAATGGAATCGATACTTTCAACATATTCGGTAG
GTAGTTTAATGTAATAGGTAGGTATTTCACTGTAAAAAACATTAATTTAAGATTATCTTTTGAGT
GAGATTTAAGATATTAATTTAGTAATTATACACGTCTAATGATTTATTTTTATGTTACGATATAT
ATTATTATTAAATTAAAAACAATAAACATAGATATTACATATTTATTATTATCATTGGTTAAAAT
TATTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAATGTTTATGTA
AATGAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATTAAAAAATTTTGAAACA
TAAATTACATAACTTTCAAAAAAGTATAAATAATTTTTATAAAAATATATATATACTTTCAACAT
ATCAGGTAAATGTTACCGATTTTGTCATAATCAAACTGGTTTTGTCATATTTTTACCTGTTATAT
TGT
Found at i:2321658 original size:23 final size:23
Alignment explanation
Indices: 2321632--2321760 Score: 85
Period size: 23 Copynumber: 5.8 Consensus size: 23
2321622 AACATATTTT
2321632 ATTATATAAGCGTTACCTATTAC
1 ATTATATAAGCGTTACCTATTAC
* *
2321655 ATTATATAAGCGCTACCTATTAT
1 ATTATATAAGCGTTACCTATTAC
* *
2321678 ATTAT-TATGC-TTGA--TAATA-
1 ATTATATAAGCGTT-ACCTATTAC
* * * **
2321697 TTTCTAGTAA---TTAATCTATTTT
1 ATTATA-TAAGCGTT-ACCTATTAC
2321719 ATTATATAAGCGTTACCTATTAC
1 ATTATATAAGCGTTACCTATTAC
*
2321742 ATTATATAAGCGGTACCTA
1 ATTATATAAGCGTTACCTA
2321761 ATATGTTATT
Statistics
Matches: 80, Mismatches: 17, Indels: 18
0.70 0.15 0.16
Matches are distributed among these distances:
19 6 0.08
20 4 0.05
21 9 0.11
22 9 0.11
23 50 0.62
24 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (23 bp):
ATTATATAAGCGTTACCTATTAC
Found at i:2321683 original size:87 final size:86
Alignment explanation
Indices: 2321528--2321786 Score: 374
Period size: 87 Copynumber: 3.0 Consensus size: 86
2321518 TAACAAATTA
* * * * *
2321528 AGTAATTAACCTATTTTAATATATAAACGCTACCTATTACGTTTTATAAGCGCTACCTAATATGT
1 AGTAATTAA-CTATTTTATTATATAAGCGTTACCTATTACATTATATAAGCGCTACCTAATATGT
*
2321593 TATTGTGCTTGATAATGTTTCC
65 TATTGTGCTTGATAATATTTCC
* *
2321615 AGTAATTAACATATTTTATTATATAAGCGTTACCTATTACATTATATAAGCGCTACCTATTATAT
1 AGTAATTAAC-TATTTTATTATATAAGCGTTACCTATTACATTATATAAGCGCTACCTAATATGT
* *
2321680 TATTATGCTTGATAATATTTCT
65 TATTGTGCTTGATAATATTTCC
*
2321702 AGTAATTAATCTATTTTATTATATAAGCGTTACCTATTACATTATATAAGCGGTACCTAATATGT
1 AGTAATTAA-CTATTTTATTATATAAGCGTTACCTATTACATTATATAAGCGCTACCTAATATGT
**
2321767 TATTGTATTTGATAATATTT
65 TATTGTGCTTGATAATATTT
2321787 TCGATTAAAT
Statistics
Matches: 154, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
86 1 0.01
87 152 0.99
88 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (86 bp):
AGTAATTAACTATTTTATTATATAAGCGTTACCTATTACATTATATAAGCGCTACCTAATATGTT
ATTGTGCTTGATAATATTTCC
Found at i:2321854 original size:17 final size:16
Alignment explanation
Indices: 2321820--2321855 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2321810 TGGTCTAAAT
*
2321820 TTTAACCGATCACTTA
1 TTTAACCGATCACCTA
2321836 TTTAACCGATCACACTA
1 TTTAACCGATCAC-CTA
2321853 TTT
1 TTT
2321856 TTTAACCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.39
Consensus pattern (16 bp):
TTTAACCGATCACCTA
Found at i:2322626 original size:25 final size:25
Alignment explanation
Indices: 2322598--2322672 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 25
2322588 TATTTAATAT
2322598 TATATATTTATTAATATAATATGAA
1 TATATATTTATTAATATAATATGAA
*
2322623 TATATA---A-T-ATAAAATATGATA
1 TATATATTTATTAATATAATATGA-A
2322644 TTCATATATTTATTAATATAATATGAA
1 -T-ATATATTTATTAATATAATATGAA
2322671 TA
1 TA
2322673 GTAAATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
20 10 0.25
21 2 0.05
22 2 0.05
23 5 0.12
25 7 0.17
26 2 0.05
27 2 0.05
28 10 0.25
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (25 bp):
TATATATTTATTAATATAATATGAA
Found at i:2322661 original size:23 final size:22
Alignment explanation
Indices: 2322592--2322667 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 22
2322582 TGTTAATATT
2322592 TAATATTATATATTTATTAATA
1 TAATATTATATATTTATTAATA
* * *
2322614 TAATATGAATATATAATATAAAATA
1 TAATAT-TATATAT-TTAT-TAATA
*
2322639 TGATATTCATATATTTATTAATA
1 TAATATT-ATATATTTATTAATA
2322662 TAATAT
1 TAATAT
2322668 GAATAGTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
22 6 0.14
23 15 0.36
24 6 0.14
25 15 0.36
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (22 bp):
TAATATTATATATTTATTAATA
Found at i:2326110 original size:19 final size:19
Alignment explanation
Indices: 2326080--2326128 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
2326070 GGATATATGT
2326080 ACAAGT-ATACACAATCGA
1 ACAAGTAATACACAATCGA
2326098 ACAAGTAATACACAATCGA
1 ACAAGTAATACACAATCGA
2326117 ACAAGTAATACA
1 ACAAGTAATACA
2326129 GTTATAAGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 6 0.20
19 24 0.80
ACGTcount: A:0.53, C:0.20, G:0.10, T:0.16
Consensus pattern (19 bp):
ACAAGTAATACACAATCGA
Found at i:2326496 original size:159 final size:159
Alignment explanation
Indices: 2326207--2326529 Score: 628
Period size: 159 Copynumber: 2.0 Consensus size: 159
2326197 TGTCACCTAA
2326207 GTAAAGTTAGTGATGGTATGTACAAATGAGAATGTTGTGGCAAACTGAGATGGGTGTTGTGGAAA
1 GTAAAGTTAGTGATGGTATGTACAAATGAGAATGTTGTGGCAAACTGAGATGGGTGTTGTGGAAA
2326272 TGGAATGACGGTAGTATGGTAGCAAATGGATATGTCGTGGCAAATTGAATTGTGTTGAGTGCAAA
66 TGGAATGACGGTAGTATGGTAGCAAATGGATATGTCGTGGCAAATTGAATTGTGTTGAGTGCAAA
*
2326337 CAAATGGAAATGTCAAGGCAAAATGAAAT
131 CAAATAGAAATGTCAAGGCAAAATGAAAT
2326366 GTAAAGTTAGTGATGGTATGTACAAATGAGAATGTTGTGGCAAACTGAGATGGGTGTTGTGGAAA
1 GTAAAGTTAGTGATGGTATGTACAAATGAGAATGTTGTGGCAAACTGAGATGGGTGTTGTGGAAA
*
2326431 TGTAATGACGGTAGTATGGTAGCAAATGGATATGTCGTGGCAAATTGAATTGTGTTGAGTGCAAA
66 TGGAATGACGGTAGTATGGTAGCAAATGGATATGTCGTGGCAAATTGAATTGTGTTGAGTGCAAA
2326496 CAAATAGAAATGTCAAGGCAAAATGAAAT
131 CAAATAGAAATGTCAAGGCAAAATGAAAT
2326525 GTAAA
1 GTAAA
2326530 TATACAATTT
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
159 162 1.00
ACGTcount: A:0.36, C:0.07, G:0.30, T:0.27
Consensus pattern (159 bp):
GTAAAGTTAGTGATGGTATGTACAAATGAGAATGTTGTGGCAAACTGAGATGGGTGTTGTGGAAA
TGGAATGACGGTAGTATGGTAGCAAATGGATATGTCGTGGCAAATTGAATTGTGTTGAGTGCAAA
CAAATAGAAATGTCAAGGCAAAATGAAAT
Found at i:2328967 original size:20 final size:20
Alignment explanation
Indices: 2328950--2328987 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2328940 GTGGTGCAGC
2328950 AGTCGCACGACGGGTGCACT
1 AGTCGCACGACGGGTGCACT
2328970 AGTCGCACGACGGGTGCA
1 AGTCGCACGACGGGTGCA
2328988 TTTTCTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.37, T:0.13
Consensus pattern (20 bp):
AGTCGCACGACGGGTGCACT
Done.