Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_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: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 35 of 43
Found at i:7053506 original size:120 final size:120
Alignment explanation
Indices: 7053293--7053526 Score: 360
Period size: 120 Copynumber: 1.9 Consensus size: 120
7053283 CCTGAAGATG
* *
7053293 ATTGTTGCTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACTGTGGATGACCCCTAAGTCGT
1 ATTGTTGCTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATAAGTCGT
*
7053358 GAAGTTAAGCCTTGACTTGAATATCCTTCATCGTGAAGCTAAAATCCAAGCTTAT
66 GAAGTTAAGCCTTGAATTGAATATCCTTCATCGTGAAGCTAAAATCCAAGCTTAT
* ** *
7053413 ATTGTTGCTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGT
1 ATTGTTGCTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATAAGTCGT
* * * * *
7053478 GAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
66 GAAGTTAAGCCTTGAATTGAATATCCTTCATCGTGAAGCTAAAATCCAA
7053527 TGTAAGTTAC
Statistics
Matches: 102, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
120 102 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (120 bp):
ATTGTTGCTGGTGAGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGACCCATAAGTCGT
GAAGTTAAGCCTTGAATTGAATATCCTTCATCGTGAAGCTAAAATCCAAGCTTAT
Found at i:7054118 original size:106 final size:106
Alignment explanation
Indices: 7053798--7054280 Score: 511
Period size: 106 Copynumber: 4.5 Consensus size: 106
7053788 GTATTTCTCC
* * * *
7053798 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCT-AGAATTGGAAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-AACTGGGAAATTATTTGTTGACA
* * *
7053862 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTC
65 GTCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
** * * * *
7053904 GAGTTTAAAATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAGAAGTTATTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC----TGAAACTG-GGAAATTATTTGTT
* * *
7053969 GACATTTATCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
61 GACAGTCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
*
7054015 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTTGTTGACAG
* * * * *
7054080 CCAACTGCCCATTCGTTGTGAAGTTGATCTTGTGTTGTCTT
66 TCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
* * * * *
7054121 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACT-GAAAAGTTGTTTATT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC----TGAAACTGGGAAA-TTATTTGTT
* * * * * * *
7054185 AACAATCAATCACCCTTTCGTTGTGAAGTTGAGCTTGTGTTTTCTT
61 GACAGTCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
* * * *
7054231 GAGTCCAATATCCTTTGCTGTAAAGTTGAACTTGGCTCTGAAATTGGGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAA
7054281 TCCCCTTCGT
Statistics
Matches: 313, Mismatches: 52, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
106 123 0.39
107 11 0.04
109 4 0.01
110 89 0.28
111 86 0.27
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTTGTTGACAG
TCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
Found at i:7058313 original size:14 final size:13
Alignment explanation
Indices: 7058286--7058343 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
7058276 GAGAAAAGAA
*
7058286 TAATAAAAAATAT
1 TAATAAATAATAT
7058299 TAATATAATAATAT
1 TAATA-AATAATAT
7058313 TAATAAATAA-AT
1 TAATAAATAATAT
*
7058325 AAATAAAT-ATAT
1 TAATAAATAATAT
7058337 ATAATAA
1 -TAATAA
7058344 TGTAAAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
11 1 0.03
12 11 0.28
13 15 0.38
14 12 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TAATAAATAATAT
Found at i:7058813 original size:33 final size:33
Alignment explanation
Indices: 7058715--7058814 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
7058705 AAAATGCTTC
*
7058715 GGTTTTAGTGTTTTAATAAGACTCAAATACGTG
1 GGTTTTAGTGTTTTAATAAGACTCAAATACGTT
* *
7058748 GGTTTTAGTGTTTTAATAGGACTTAAATACGTT
1 GGTTTTAGTGTTTTAATAAGACTCAAATACGTT
*
7058781 GGTTTTAGTGTTTCAATAAGACTCAAATACGTT
1 GGTTTTAGTGTTTTAATAAGACTCAAATACGTT
7058814 G
1 G
7058815 ATTTATTTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (33 bp):
GGTTTTAGTGTTTTAATAAGACTCAAATACGTT
Found at i:7058879 original size:8 final size:8
Alignment explanation
Indices: 7058866--7058933 Score: 54
Period size: 8 Copynumber: 8.8 Consensus size: 8
7058856 GGGGCCTACA
7058866 AAAATAAT
1 AAAATAAT
*
7058874 AAAATAAA
1 AAAATAAT
*
7058882 AAAATATT
1 AAAATAAT
7058890 AATAATAAT
1 AA-AATAAT
*
7058899 AATA-AAT
1 AAAATAAT
7058906 -AAATAA-
1 AAAATAAT
7058912 ATAAAT-AT
1 A-AAATAAT
*
7058920 AATATAAT
1 AAAATAAT
7058928 AAAATA
1 AAAATA
7058934 TTTTTATAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
6 2 0.04
7 9 0.20
8 28 0.61
9 7 0.15
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
AAAATAAT
Found at i:7058932 original size:27 final size:28
Alignment explanation
Indices: 7058868--7058933 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
7058858 GGCCTACAAA
*
7058868 AATAATAAAATAAAAAAATATTAATAAT
1 AATAATAAAATAAAAAAATAATAATAAT
*
7058896 AATAAT-AAATAAATAAATAA-ATATAAT
1 AATAATAAAATAAAAAAATAATA-ATAAT
7058923 -ATAATAAAATA
1 AATAATAAAATA
7058934 TTTTTATAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 6 0.18
27 22 0.65
28 6 0.18
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (28 bp):
AATAATAAAATAAAAAAATAATAATAAT
Found at i:7060616 original size:12 final size:12
Alignment explanation
Indices: 7060599--7060624 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
7060589 GTGAATTCGG
7060599 CCGAAACCATGA
1 CCGAAACCATGA
7060611 CCGAAACCATGA
1 CCGAAACCATGA
7060623 CC
1 CC
7060625 CAGATTTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.38, G:0.15, T:0.08
Consensus pattern (12 bp):
CCGAAACCATGA
Found at i:7061819 original size:13 final size:13
Alignment explanation
Indices: 7061801--7061828 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
7061791 GTGCCTACCT
7061801 GGATGTTTGGATA
1 GGATGTTTGGATA
7061814 GGATGTTTGGATA
1 GGATGTTTGGATA
7061827 GG
1 GG
7061829 TCAAATGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.43, T:0.36
Consensus pattern (13 bp):
GGATGTTTGGATA
Found at i:7073170 original size:21 final size:20
Alignment explanation
Indices: 7073148--7073187 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
7073138 CTAGCATTGA
*
7073148 AAAAAAAATTAGAAACTTTG
1 AAAAAAAATCAGAAACTTTG
* *
7073168 AAACAAGATCAGAAACTTTG
1 AAAAAAAATCAGAAACTTTG
7073188 TCTTTTTGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (20 bp):
AAAAAAAATCAGAAACTTTG
Found at i:7073256 original size:51 final size:52
Alignment explanation
Indices: 7073168--7073265 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 52
7073158 AGAAACTTTG
* *
7073168 AAACAAGATCAGAAACTTTGTCTTTTTGTAGCACAAAATTTAGATGACATTA
1 AAACAAGATCAGAAACTTTGTCCTTTTCTAGCACAAAATTTAGATGACATTA
*
7073220 AAACAAGATCAGAAAGTTTG-CCTTTTCTAGCACAAAATTTAGATGA
1 AAACAAGATCAGAAACTTTGTCCTTTTCTAGCACAAAATTTAGATGA
7073266 ACCTATTACT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
51 24 0.56
52 19 0.44
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (52 bp):
AAACAAGATCAGAAACTTTGTCCTTTTCTAGCACAAAATTTAGATGACATTA
Found at i:7073933 original size:43 final size:42
Alignment explanation
Indices: 7073823--7073933 Score: 102
Period size: 42 Copynumber: 2.6 Consensus size: 42
7073813 AAAATATCGT
* * * *
7073823 TAAATGACCAACCTATTGCGGCGTTTATGCCTAAAATGCCGC
1 TAAATGACCAACCTATTGTGGTGTTTATGACTAAAAAGCCGC
* * *
7073865 TAAAT-ATCAA-ATA-TGTTGCGATGTTTATGACTAAAACAGCTGC
1 TAAATGACCAACCTATTG-TG-G-TGTTTATGACTAAAA-AGCCGC
7073908 TAAATGACCAACCTATTGTGGTGTTT
1 TAAATGACCAACCTATTGTGGTGTTT
7073934 GTGCCCAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
39 2 0.04
40 3 0.06
41 5 0.09
42 18 0.34
43 14 0.26
44 5 0.09
45 4 0.08
46 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (42 bp):
TAAATGACCAACCTATTGTGGTGTTTATGACTAAAAAGCCGC
Found at i:7075649 original size:22 final size:22
Alignment explanation
Indices: 7075624--7075668 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
7075614 AATTCGGTGC
7075624 CCCCATGCGCCTCCATTCTTGA
1 CCCCATGCGCCTCCATTCTTGA
* * *
7075646 CCCCATGTGCTTCCATTTTTGA
1 CCCCATGCGCCTCCATTCTTGA
7075668 C
1 C
7075669 TTTACAATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.13, C:0.40, G:0.13, T:0.33
Consensus pattern (22 bp):
CCCCATGCGCCTCCATTCTTGA
Found at i:7077198 original size:23 final size:23
Alignment explanation
Indices: 7077154--7077202 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
7077144 ATAAAGAACC
*
7077154 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
7077177 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
7077200 AAA
1 AAA
7077203 CCAACACCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:7087489 original size:21 final size:21
Alignment explanation
Indices: 7087465--7087507 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
7087455 AATTCGGTGC
7087465 CCCATGCGCCTCCATTCTTGA
1 CCCATGCGCCTCCATTCTTGA
* * *
7087486 CCCATGTGCTTCCATTTTTGA
1 CCCATGCGCCTCCATTCTTGA
7087507 C
1 C
7087508 TTTACACTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.37, G:0.14, T:0.35
Consensus pattern (21 bp):
CCCATGCGCCTCCATTCTTGA
Found at i:7092950 original size:2 final size:2
Alignment explanation
Indices: 7092933--7092973 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
7092923 ATTACATAGC
7092933 AT AT A- AT AT A- 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 AT AT AT
7092973 A
1 A
7092974 CACATTACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:7094147 original size:36 final size:34
Alignment explanation
Indices: 7094106--7094185 Score: 99
Period size: 36 Copynumber: 2.3 Consensus size: 34
7094096 ATTTAATTAT
*
7094106 TTTTTATTATTATTTTATTTT-TTTCTTCTTAAATTG
1 TTTTAATT-TTATTTTATTTTCTTT-TT-TTAAATTG
7094142 CTTTTAATTTTATTTTATTTTCTTTTTTTAAATTG
1 -TTTTAATTTTATTTTATTTTCTTTTTTTAAATTG
*
7094177 TTTTGATTT
1 TTTTAATTT
7094186 AGTTCTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
34 8 0.20
35 8 0.20
36 14 0.35
37 10 0.25
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.72
Consensus pattern (34 bp):
TTTTAATTTTATTTTATTTTCTTTTTTTAAATTG
Found at i:7094303 original size:20 final size:20
Alignment explanation
Indices: 7094278--7094352 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
7094268 TTCTTCTCCT
7094278 TTTAATTGTTTTTAATTTAA
1 TTTAATTGTTTTTAATTTAA
* * **
7094298 TTTAATTATTTATTTATTTCT
1 TTTAATTGTTT-TTAATTTAA
7094319 TTTAATTGATTTTT-ATTTAA
1 TTTAATTG-TTTTTAATTTAA
*
7094339 TTTAATTTTTTTTA
1 TTTAATTGTTTTTA
7094353 TTTCTTTTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 5 0.11
20 21 0.48
21 15 0.34
22 3 0.07
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTAATTGTTTTTAATTTAA
Found at i:7094322 original size:41 final size:39
Alignment explanation
Indices: 7094276--7094360 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 39
7094266 CTTTCTTCTC
7094276 CTTTTAATTG-TTTTTAATTTAATTTAATTATTTATTTATTT
1 CTTTTAATTGATTTTT-ATTTAATTTAATT-TTT-TTTATTT
7094317 CTTTTAATTGATTTTTATTTAATTTAATTTTTTTTATTT
1 CTTTTAATTGATTTTTATTTAATTTAATTTTTTTTATTT
7094356 CTTTT
1 CTTTT
7094361 TCTTCTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
39 12 0.28
40 3 0.07
41 23 0.53
42 5 0.12
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (39 bp):
CTTTTAATTGATTTTTATTTAATTTAATTTTTTTTATTT
Found at i:7094546 original size:10 final size:10
Alignment explanation
Indices: 7094531--7094565 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
7094521 ATTTCTGTTA
7094531 TTTTTTATTT
1 TTTTTTATTT
7094541 TTTTTTATTT
1 TTTTTTATTT
7094551 TTTTTTATTT
1 TTTTTTATTT
7094561 TTTTT
1 TTTTT
7094566 GTTTGATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:7094579 original size:20 final size:19
Alignment explanation
Indices: 7094513--7094580 Score: 61
Period size: 18 Copynumber: 3.7 Consensus size: 19
7094503 ATATGTTTGT
* *
7094513 TTTA-TTATATTTCTGTTA
1 TTTATTTATATTTTTTTTA
7094531 TTT-TTTAT-TTTTTTTTA
1 TTTATTTATATTTTTTTTA
* * *
7094548 TTTTTTTTTATTTTTTTTG
1 TTTATTTATATTTTTTTTA
7094567 TTTGATTTATATTT
1 TTT-ATTTATATTT
7094581 AATTTCACGA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
17 10 0.25
18 11 0.28
19 11 0.28
20 8 0.20
ACGTcount: A:0.15, C:0.01, G:0.04, T:0.79
Consensus pattern (19 bp):
TTTATTTATATTTTTTTTA
Found at i:7103228 original size:32 final size:32
Alignment explanation
Indices: 7103191--7103251 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
7103181 TTTTAAGAAC
*
7103191 AAACTTTAATATGATTCAAGCACCATAATAAG
1 AAACTTCAATATGATTCAAGCACCATAATAAG
7103223 AAACTTCAATATGATTCAAGCACCATAAT
1 AAACTTCAATATGATTCAAGCACCATAAT
7103252 TGATAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (32 bp):
AAACTTCAATATGATTCAAGCACCATAATAAG
Found at i:7112103 original size:20 final size:19
Alignment explanation
Indices: 7112078--7112143 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 19
7112068 AAAAACAGAA
*
7112078 CCCTAGGGGGGTATCGATTC
1 CCCTA-GGGGGAATCGATTC
*
7112098 CCCTAGGGGGAATCGGTTC
1 CCCTAGGGGGAATCGATTC
*
7112117 CCCTTCAAAGGGGGAATCGGTTC
1 CCC-T---AGGGGGAATCGATTC
7112140 CCCT
1 CCCT
7112144 TCAAGGGGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 15 0.38
20 6 0.15
22 1 0.03
23 18 0.45
ACGTcount: A:0.17, C:0.29, G:0.32, T:0.23
Consensus pattern (19 bp):
CCCTAGGGGGAATCGATTC
Found at i:7112149 original size:22 final size:23
Alignment explanation
Indices: 7112102--7112151 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
7112092 CGATTCCCCT
7112102 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
7112125 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
7112147 AGGGG
1 AGGGG
7112152 TATCGATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.20, C:0.24, G:0.36, T:0.20
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:7126146 original size:18 final size:18
Alignment explanation
Indices: 7126123--7126158 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
7126113 ATTTATCACC
7126123 ATCAAATCTGATCCCGGT
1 ATCAAATCTGATCCCGGT
7126141 ATCAAATCTGATCCCGGT
1 ATCAAATCTGATCCCGGT
7126159 CAAACATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (18 bp):
ATCAAATCTGATCCCGGT
Found at i:7131531 original size:25 final size:24
Alignment explanation
Indices: 7131497--7131554 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
7131487 GCATTTGTAA
*
7131497 ATTTGATATATAAA-TAATTATATTT
1 ATTTAATATA-AAATTAA-TATATTT
*
7131522 ATTTAATATAAAATTAATATCTTT
1 ATTTAATATAAAATTAATATATTT
*
7131546 CTTTAATAT
1 ATTTAATAT
7131555 TTGGAATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTTAATATAAAATTAATATATTT
Found at i:7133259 original size:24 final size:25
Alignment explanation
Indices: 7133230--7133276 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
7133220 TTTATCCCTA
7133230 CTATTATTATA-TATTATATTTTCC
1 CTATTATTATATTATTATATTTTCC
*
7133254 CTATTATTATATTTTTATATTTT
1 CTATTATTATATTATTATATTTT
7133277 ATTCCCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.64
Consensus pattern (25 bp):
CTATTATTATATTATTATATTTTCC
Found at i:7133261 original size:27 final size:25
Alignment explanation
Indices: 7133224--7133276 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
7133214 TCTAATTTTA
7133224 TCCCTACTATTATTATATATTATATTT
1 TCCCTACTATTA-TAT-TATTATATTT
* *
7133251 TCCCTATTATTATATTTTTATATTT
1 TCCCTACTATTATATTATTATATTT
7133276 T
1 T
7133277 ATTCCCTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 11 0.46
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.60
Consensus pattern (25 bp):
TCCCTACTATTATATTATTATATTT
Found at i:7133335 original size:2 final size:2
Alignment explanation
Indices: 7133328--7133352 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7133318 GATTTTATTT
7133328 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 T
7133353 TTGTAGCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7133552 original size:19 final size:19
Alignment explanation
Indices: 7133528--7133575 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
7133518 ATTTAATACA
7133528 TGTTTTATTTTTATTTCTT
1 TGTTTTATTTTTATTTCTT
* * *
7133547 TGTTTTTATGTTTGTTTTTT
1 TG-TTTTATTTTTATTTCTT
*
7133567 TCTTTTATT
1 TGTTTTATT
7133576 ACTATTCACG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.08, C:0.04, G:0.08, T:0.79
Consensus pattern (19 bp):
TGTTTTATTTTTATTTCTT
Found at i:7133656 original size:15 final size:14
Alignment explanation
Indices: 7133630--7133663 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
7133620 TATGCTTTTT
*
7133630 TTTATTT-TTTCCC
1 TTTATTTCTTTTCC
7133643 TTTATTTCTTTTCC
1 TTTATTTCTTTTCC
7133657 TTTATTT
1 TTTATTT
7133664 ATACTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTCTTTTCC
Found at i:7133803 original size:20 final size:21
Alignment explanation
Indices: 7133778--7133824 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
7133768 CCAAAAACAA
*
7133778 TCGCAACTC-AGTTTCCAAAT
1 TCGCAACGCGAGTTTCCAAAT
*
7133798 TCGCAACGCGATTTTCCAAAT
1 TCGCAACGCGAGTTTCCAAAT
7133819 TCGCAA
1 TCGCAA
7133825 TGCTAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.28
Consensus pattern (21 bp):
TCGCAACGCGAGTTTCCAAAT
Found at i:7133881 original size:20 final size:20
Alignment explanation
Indices: 7133856--7133925 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
7133846 AACAGTACTA
7133856 TCGCAACGCGATTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
**
7133876 TCGCAATACGATTTTCCAAAT
1 TCGCAACGCGATTTT-CAAAT
*
7133897 TCGCAACGTGATTTTCAAA-
1 TCGCAACGCGATTTTCAAAT
7133916 TCTGCAACGC
1 TC-GCAACGC
7133926 TAATTACTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.05
20 23 0.55
21 17 0.40
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (20 bp):
TCGCAACGCGATTTTCAAAT
Found at i:7133897 original size:21 final size:20
Alignment explanation
Indices: 7133864--7133916 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
7133854 TATCGCAACG
7133864 CGATTTTCAAATTCGCAATA
1 CGATTTTCAAATTCGCAATA
**
7133884 CGATTTTCCAAATTCGCAACG
1 CGATTTT-CAAATTCGCAATA
*
7133905 TGATTTTCAAAT
1 CGATTTTCAAAT
7133917 CTGCAACGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (20 bp):
CGATTTTCAAATTCGCAATA
Found at i:7133966 original size:56 final size:57
Alignment explanation
Indices: 7133897--7134025 Score: 163
Period size: 56 Copynumber: 2.3 Consensus size: 57
7133887 TTTTCCAAAT
* * * * *
7133897 TCGCAACGTGATTTTCAAATCT-GCAACGCTAATTACTGATATAGGT-AACACTATTA
1 TCGCAACGCGATTTTCAAAT-TAGCAACGCTAATTACCGACATAGGTAAACACAACTA
*
7133953 TCGCAACGCGATTTTCAAATTAGCAACGCTAATTACCGACATTGGTAAACACAACTA
1 TCGCAACGCGATTTTCAAATTAGCAACGCTAATTACCGACATAGGTAAACACAACTA
* *
7134010 TCGCAACACGAATTTC
1 TCGCAACGCGATTTTC
7134026 GTTTTCGCAA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
55 1 0.02
56 40 0.63
57 22 0.35
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (57 bp):
TCGCAACGCGATTTTCAAATTAGCAACGCTAATTACCGACATAGGTAAACACAACTA
Found at i:7134507 original size:57 final size:57
Alignment explanation
Indices: 7134414--7134554 Score: 219
Period size: 57 Copynumber: 2.5 Consensus size: 57
7134404 GAAAATAACG
* * * * *
7134414 TTGCGAATTTGAAAATCGTGTTGTGATATTAGTGTTTACCTATGTCGGTAATTAGCA
1 TTGCGAATTTGAAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGCA
*
7134471 TTGCGAATTTGAAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGCG
1 TTGCGAATTTGAAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGCA
7134528 TTGCGAATTTGGAAAATCGCGTTGCGA
1 TTGCGAATTT-GAAAATCGCGTTGCGA
7134555 AAAAGAAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
57 61 0.79
58 16 0.21
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.36
Consensus pattern (57 bp):
TTGCGAATTTGAAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGCA
Found at i:7141990 original size:18 final size:16
Alignment explanation
Indices: 7141965--7142004 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
7141955 GCCCTAAATT
7141965 GAAAAAAATAGAAAAAA
1 GAAAAAAATA-AAAAAA
*
7141982 GAGAAAAAATAACAAAA
1 GA-AAAAAATAAAAAAA
7141999 GAAAAA
1 GAAAAA
7142005 GAGAAGAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.19
17 9 0.43
18 8 0.38
ACGTcount: A:0.80, C:0.03, G:0.12, T:0.05
Consensus pattern (16 bp):
GAAAAAAATAAAAAAA
Found at i:7143005 original size:111 final size:110
Alignment explanation
Indices: 7142768--7143255 Score: 637
Period size: 110 Copynumber: 4.5 Consensus size: 110
7142758 GGTTTTAGCT
* * ** * * *
7142768 AGAGTAAATTTCAACTTCACAGCGAATAATATTGGACTCAAGACAACACAAGCACAACTTCACAA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAG
* *
7142833 CGAAAGGGCGACTAACTGTCAACAAACAACTTTTCAGTTTCATTC
66 CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
* * *
7142878 AGAGTCAATTTCAACTTAACAGCGAAGGATATT-GAACTCAAGATAACACAAGCTCAACTTCACA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTAG-ACTCAAGACAACACAAGCTCAACTTCACA
*
7142942 GCGAAGGGGGCGACTGACTGTCAACAAACAGCTTTTCAGTTTCATTC
65 GCGAA-GGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
* * *
7142989 AGAGTCAATTTTAACTTCACAACGAATGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAG
*
7143054 AGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
66 CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
* * *
7143099 AGAGTCAATTTCAACATCACAACGAAGGATATTAGACTCGAGACAACACAAGATCAACTTCACAG
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAG
* * *
7143164 CGAAGGGGCGGCTGGCTGTCAACAAACAA-TTTCCCAG-TT--TT-
66 CGAAGGGGCGACTGACTGTCAACAAACAACTTT-TCAGTTTCATTC
* ** * * * *
7143205 AGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTCAAAACAATACAA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAA
7143256 CTTACTTGGA
Statistics
Matches: 339, Mismatches: 35, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
106 42 0.12
107 2 0.01
109 6 0.02
110 190 0.56
111 98 0.29
112 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (110 bp):
AGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAG
CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
Found at i:7143163 original size:221 final size:220
Alignment explanation
Indices: 7142768--7143191 Score: 654
Period size: 221 Copynumber: 1.9 Consensus size: 220
7142758 GGTTTTAGCT
* *
7142768 AGAGTAAATTTCAACTTCACAGCGAATAATATTGGACTCAAGACAACACAAGCACAACTTCACAA
1 AGAGTAAATTTCAACTTCACAACGAATAATATTAGACTCAAGACAACACAAGCACAACTTCACAA
*
7142833 CGAAAGGGCGACTAACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTAAC
66 CGAAAGGGCGACTAACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACATAAC
* * *
7142898 AGCGAAGGATATTGAACTCAAGATAACACAAGCTCAACTTCACAGCGAAGGGGGCGACTGACTGT
131 AACGAAGGATATTGAACTCAAGACAACACAAGATCAACTTCACAGCGAA-GGGGCGACTGACTGT
7142963 CAACAAACAGCTTTTCAGTTTCATTC
195 CAACAAACAGCTTTTCAGTTTCATTC
* * * * *
7142989 AGAGTCAATTTTAACTTCACAACGAATGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
1 AGAGTAAATTTCAACTTCACAACGAATAATATTAGACTCAAGACAACACAAGCACAACTTCACA-
* * *
7143054 A-GAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACATCA
65 ACGAAAGGGCGACTAACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACATAA
* * *
7143118 CAACGAAGGATATT-AGACTCGAGACAACACAAGATCAACTTCACAGCGAAGGGGCGGCTGGCTG
130 CAACGAAGGATATTGA-ACTCAAGACAACACAAGATCAACTTCACAGCGAAGGGGCGACTGACTG
7143182 TCAACAAACA
194 TCAACAAACA
7143192 ATTTCCCAGT
Statistics
Matches: 184, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
220 23 0.12
221 160 0.87
222 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (220 bp):
AGAGTAAATTTCAACTTCACAACGAATAATATTAGACTCAAGACAACACAAGCACAACTTCACAA
CGAAAGGGCGACTAACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACATAAC
AACGAAGGATATTGAACTCAAGACAACACAAGATCAACTTCACAGCGAAGGGGCGACTGACTGTC
AACAAACAGCTTTTCAGTTTCATTC
Found at i:7143697 original size:18 final size:18
Alignment explanation
Indices: 7143674--7143724 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
7143664 AAAACCGAAG
7143674 TCTTCAGGACAAGTTTCA
1 TCTTCAGGACAAGTTTCA
*
7143692 TCTTCACGACAAGTTTCA
1 TCTTCAGGACAAGTTTCA
7143710 TCTTCAGGACGAAGT
1 TCTTCAGGAC-AAGT
7143725 ATCTTGAGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (18 bp):
TCTTCAGGACAAGTTTCA
Found at i:7145118 original size:24 final size:24
Alignment explanation
Indices: 7145073--7145117 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
7145063 TTAATCCCTA
7145073 CTATTATTATATATTATATTTTCC
1 CTATTATTATATATTATATTTTCC
*
7145097 CTATTATTATAT-TTTTATTTT
1 CTATTATTATATATTATATTTT
7145118 TTATTCCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (24 bp):
CTATTATTATATATTATATTTTCC
Found at i:7156404 original size:7 final size:7
Alignment explanation
Indices: 7156392--7156424 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
7156382 CTATTATCAT
7156392 TTTTTTA
1 TTTTTTA
7156399 TTTTTTA
1 TTTTTTA
7156406 TTTTTTA
1 TTTTTTA
7156413 TTTTTTA
1 TTTTTTA
7156420 TTTTT
1 TTTTT
7156425 GTCGCTGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:7158253 original size:2 final size:2
Alignment explanation
Indices: 7158246--7158281 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
7158236 GACTCTTCAA
7158246 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
7158282 CAAAGTGGTG
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:7160674 original size:2 final size:2
Alignment explanation
Indices: 7160667--7160696 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7160657 TACATAACAA
7160667 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
7160697 GCATGTCTGT
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:7167217 original size:16 final size:15
Alignment explanation
Indices: 7167195--7167238 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
7167185 TTTTAAATTA
**
7167195 TAAATATAAAACTAT
1 TAAATATAAAAAAAT
7167210 TCAAATATTAAAAAAAT
1 T-AAATA-TAAAAAAAT
7167227 TAAATATAAAAA
1 TAAATATAAAAA
7167239 TACTAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 7 0.28
16 10 0.40
17 8 0.32
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAATATAAAAAAAT
Found at i:7167230 original size:39 final size:40
Alignment explanation
Indices: 7167187--7167316 Score: 103
Period size: 40 Copynumber: 3.3 Consensus size: 40
7167177 AAAATTTATT
7167187 TTAAAT-TATAAATA-TAAAACTATTCAAA-TATTAAAAAAA
1 TTAAATATATAAATACTAAAA-TATT-AAACTATTAAAAAAA
* *
7167226 TTAAATATAAAAATACTAAAA-ACTTAAATTATTAAAAAAA
1 TTAAATATATAAATACTAAAATA-TTAAACTATTAAAAAAA
* * *
7167266 -T-GA-ATATACATATTACAAATATTAAAACTATTATAAAAAA
1 TTAAATATATAAATACTA-AAATATT-AAACTATTA-AAAAAA
*
7167306 TTATATATATA
1 TTAAATATATA
7167317 TATATATATA
Statistics
Matches: 73, Mismatches: 7, Indels: 18
0.74 0.07 0.18
Matches are distributed among these distances:
37 9 0.12
38 6 0.08
39 20 0.27
40 26 0.36
41 6 0.08
42 1 0.01
43 5 0.07
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (40 bp):
TTAAATATATAAATACTAAAATATTAAACTATTAAAAAAA
Found at i:7167312 original size:2 final size:2
Alignment explanation
Indices: 7167307--7167445 Score: 73
Period size: 2 Copynumber: 74.0 Consensus size: 2
7167297 TATAAAAAAT
* *
7167307 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA -A TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
7167347 TA AA CTA -A T- TA TT TA TA AA T- TG T- TA -A 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
* * * * * * *
7167385 TA TA TG TA TG TA TA TG TA TA T- TA AA AA AA TA T- TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
7167425 -A CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
7167446 CTTGTAAAAT
Statistics
Matches: 107, Mismatches: 19, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
1 10 0.09
2 96 0.90
3 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:7168265 original size:20 final size:20
Alignment explanation
Indices: 7168227--7168264 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
7168217 ATATTTTAAT
*
7168227 TTTTAGTAATTTAATTTTTG
1 TTTTAGTAAGTTAATTTTTG
7168247 TTTTAGT-AGTTAATTTTT
1 TTTTAGTAAGTTAATTTTT
7168265 TAAATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.66
Consensus pattern (20 bp):
TTTTAGTAAGTTAATTTTTG
Found at i:7168296 original size:24 final size:25
Alignment explanation
Indices: 7168268--7168318 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
7168258 AATTTTTTAA
*
7168268 ATATTT-AAATATTCAAATAA-TTTT
1 ATATTTAAAAT-TTAAAATAACTTTT
7168292 ATATTTAAAATTTAAAATAACTTTT
1 ATATTTAAAATTTAAAATAACTTTT
7168317 AT
1 AT
7168319 TTCAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (25 bp):
ATATTTAAAATTTAAAATAACTTTT
Found at i:7168451 original size:21 final size:21
Alignment explanation
Indices: 7168427--7168466 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
7168417 GTCACATTGG
7168427 ACTGTCACGTCAGCATCGTGA
1 ACTGTCACGTCAGCATCGTGA
7168448 ACTGTCACGTCAGCATCGT
1 ACTGTCACGTCAGCATCGT
7168467 AACAATCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (21 bp):
ACTGTCACGTCAGCATCGTGA
Found at i:7170194 original size:37 final size:36
Alignment explanation
Indices: 7170118--7170194 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
7170108 TTTTTATATT
*
7170118 TTTAATTTTGTAAAAAAATTTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAA-TTATATAAATATTATCAA
* *
7170155 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
7170192 TTT
1 TTT
7170195 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 18 0.51
38 4 0.11
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:7170734 original size:26 final size:26
Alignment explanation
Indices: 7170703--7170791 Score: 169
Period size: 26 Copynumber: 3.4 Consensus size: 26
7170693 ATGTATATAG
7170703 ACACCCCCCATATAACCATAAATATT
1 ACACCCCCCATATAACCATAAATATT
7170729 ACACCCCCCATATAACCATAAATATT
1 ACACCCCCCATATAACCATAAATATT
7170755 ACACCCCCCATATAACCATAAATATT
1 ACACCCCCCATATAACCATAAATATT
*
7170781 ACACCCACCAT
1 ACACCCCCCAT
7170792 GAACCCTAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 62 1.00
ACGTcount: A:0.42, C:0.37, G:0.00, T:0.21
Consensus pattern (26 bp):
ACACCCCCCATATAACCATAAATATT
Found at i:7172398 original size:153 final size:152
Alignment explanation
Indices: 7172111--7172575 Score: 648
Period size: 153 Copynumber: 3.0 Consensus size: 152
7172101 CATATCTTTT
* * *
7172111 TAAAACATATTTAAAAAACATA-ATAATCCCTCCAACCG-ACAAGTCCAAATGTGTAAGTTCCCC
1 TAAAACA-ATTTAAAAACCATAGA-AATCCCTCCAACCGAACACGTCCAAATGTGTAGGTTCCCC
* * *
7172174 AGAACCATACATCCACCGTCAAGTCCAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTTCATGTA
64 AGAACCATACACCCACCGTCAAGTCCAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCAAGTA
* *
7172239 TGCTTCCTCCAACAATGCCCCCAAA
129 TACTTCCTCCAATAAT-CCCCCAAA
* * *
7172264 TAAAATAATTTAAAAACCATAGAAATTTCC-CCAACCGAACACGTCCAAATCTGTAGGTTCCCCA
1 TAAAACAATTTAAAAACCATAGAAA-TCCCTCCAACCGAACACGTCCAAATGTGTAGGTTCCCCA
* * ** *
7172328 GAACCATACACCCACCGTCACGTCCAGCAAGGCCCTGAGCTGAAAGCCGAGAAGCCTGCAAGTAT
65 GAACCATACACCCACCGTCAAGTCCAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCAAGTAT
*
7172393 ACTTCCTCCAATAATACCCTCAAA
130 ACTTCCTCCAATAAT-CCCCCAAA
* * *
7172417 TAAAACATTTTAAAAACCATAGAAATCCCTCCAACCAAACACGTCCAAATGTGTAGGTTCCCCAA
1 TAAAACAATTTAAAAACCATAGAAATCCCTCCAACCGAACACGTCCAAATGTGTAGGTTCCCCAG
* *
7172482 AACCATACACCCACCGTCAAGTCCAGTAAGGCCCTAAGCACAAAGCCGAGGAGCCTGTAAGTATA
66 AACCATACACCCACCGTCAAGTCCAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCAAGTATA
* *
7172547 CTTCCTCTAATAATACCCCAAA
131 CTTCCTCCAATAATCCCCCAAA
7172569 TAAAACA
1 TAAAACA
7172576 TTTTCCGTCA
Statistics
Matches: 274, Mismatches: 34, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
152 38 0.14
153 236 0.86
ACGTcount: A:0.37, C:0.31, G:0.13, T:0.19
Consensus pattern (152 bp):
TAAAACAATTTAAAAACCATAGAAATCCCTCCAACCGAACACGTCCAAATGTGTAGGTTCCCCAG
AACCATACACCCACCGTCAAGTCCAGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCAAGTATA
CTTCCTCCAATAATCCCCCAAA
Found at i:7176331 original size:47 final size:47
Alignment explanation
Indices: 7176226--7176473 Score: 376
Period size: 47 Copynumber: 5.3 Consensus size: 47
7176216 AGTTTCTTAT
* * *
7176226 CAATATAATTTCCATTT-ATCCCATAAGCTCGTAAGCTTA-TTTTAC
1 CAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTTAC
* * * * *
7176271 CAATGTACTTACCATTTAATTCAATAAGCTTGTAAGCATATTTTTAC
1 CAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTTAC
7176318 CAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTTAC
1 CAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTTAC
*
7176365 CAATATACTTACCATTTAATACCATAAGTTCGTAAGCTTATTTTTAC
1 CAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTTAC
7176412 CAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTA-TTTTAC
1 CAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTTAC
* *
7176458 CAATACACTTGCCATT
1 CAATATACTTACCATT
7176474 ATTCCATAAC
Statistics
Matches: 185, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
45 14 0.08
46 38 0.21
47 133 0.72
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (47 bp):
CAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTTAC
Found at i:7176435 original size:22 final size:22
Alignment explanation
Indices: 7176315--7176388 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 22
7176305 AGCATATTTT
7176315 TACCAATATACTTACCATTTAA
1 TACCAATATACTTACCATTTAA
* *
7176337 TACC-ATA-AGCTCGTAAGCTTATTT-T
1 TACCAATATA-CT--T-A-C-CATTTAA
7176362 TACCAATATACTTACCATTTAA
1 TACCAATATACTTACCATTTAA
7176384 TACCA
1 TACCA
7176389 TAAGTTCGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 18
0.64 0.07 0.30
Matches are distributed among these distances:
20 1 0.03
21 9 0.23
22 10 0.26
23 2 0.05
24 2 0.05
25 5 0.13
26 9 0.23
27 1 0.03
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.36
Consensus pattern (22 bp):
TACCAATATACTTACCATTTAA
Found at i:7176654 original size:59 final size:59
Alignment explanation
Indices: 7176562--7176689 Score: 157
Period size: 59 Copynumber: 2.2 Consensus size: 59
7176552 CGTAATGCAA
* * * * **
7176562 TCCCGAGTATGACACATAAGGTCGTGTCCACCATTTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
* * ** *
7176621 TCCCGAATATGACACATAAGGTTATGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
7176680 TCCCGAATAT
1 TCCCGAATAT
7176690 ACAACCTGTT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:7180421 original size:30 final size:30
Alignment explanation
Indices: 7180348--7180422 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
7180338 TTGAATTTTT
* ***
7180348 GGTCAAAGTCAACAATCAATGGGTTAACTC
1 GGTCAAAGTCAACGATCAACAAGTTAACTC
*
7180378 GGTCAAAGTCAACGATCAACAAGTTGACTC
1 GGTCAAAGTCAACGATCAACAAGTTAACTC
7180408 GGTCAAAGTCAACGA
1 GGTCAAAGTCAACGA
7180423 GTTGACCTAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.20
Consensus pattern (30 bp):
GGTCAAAGTCAACGATCAACAAGTTAACTC
Found at i:7180474 original size:15 final size:14
Alignment explanation
Indices: 7180420--7180477 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
7180410 TCAAAGTCAA
7180420 CGAGTTGAC-CTAGT
1 CGAGTTGACTC-AGT
7180434 -GAGTTGACTCAGT
1 CGAGTTGACTCAGT
*
7180447 CGAGTTAACTCAGT
1 CGAGTTGACTCAGT
7180461 GCG-GATTGACTCAGT
1 -CGAG-TTGACTCAGT
7180476 CG
1 CG
7180478 GGTTAAGCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 11 0.29
14 16 0.42
15 11 0.29
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (14 bp):
CGAGTTGACTCAGT
Found at i:7183494 original size:14 final size:14
Alignment explanation
Indices: 7183477--7183515 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
7183467 TACGATTTGT
7183477 GACGAACGATGAGC
1 GACGAACGATGAGC
*
7183491 GACGACCGATGAGC
1 GACGAACGATGAGC
7183505 GACG-ACGATGA
1 GACGAACGATGA
7183516 TCTGATGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.33, C:0.23, G:0.36, T:0.08
Consensus pattern (14 bp):
GACGAACGATGAGC
Found at i:7185054 original size:14 final size:15
Alignment explanation
Indices: 7185035--7185064 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7185025 AAACCCTAAA
7185035 AAACTG-CCCCCAAC
1 AAACTGCCCCCCAAC
7185049 AAACTGCCCCCCAAC
1 AAACTGCCCCCCAAC
7185064 A
1 A
7185065 TGTTGTCCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.50, G:0.07, T:0.07
Consensus pattern (15 bp):
AAACTGCCCCCCAAC
Found at i:7186006 original size:4 final size:4
Alignment explanation
Indices: 7185997--7186043 Score: 87
Period size: 4 Copynumber: 12.0 Consensus size: 4
7185987 ACGTTTGGCT
7185997 CATA CATA CATA CATA CATA CATA CATA CAT- CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
7186044 TTGTAATGGC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.07
4 39 0.93
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:7186606 original size:2 final size:2
Alignment explanation
Indices: 7186599--7186657 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
7186589 TGGATGGTTG
7186599 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
7186641 GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA G
7186658 CTTCAAAGTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:7188408 original size:43 final size:43
Alignment explanation
Indices: 7188354--7188443 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
7188344 CACAAGAGAA
7188354 ACACTACATCCAGCAATACAAACCCCAAACCACAACAAAACAC
1 ACACTACATCCAGCAATACAAACCCCAAACCACAACAAAACAC
* ** *
7188397 ACACTACATCCAGCAATGCATTCCCCAAACTACAACAAAACAC
1 ACACTACATCCAGCAATACAAACCCCAAACCACAACAAAACAC
7188440 ACAC
1 ACAC
7188444 AACACCCATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.48, C:0.39, G:0.03, T:0.10
Consensus pattern (43 bp):
ACACTACATCCAGCAATACAAACCCCAAACCACAACAAAACAC
Found at i:7191607 original size:117 final size:117
Alignment explanation
Indices: 7191468--7191706 Score: 338
Period size: 116 Copynumber: 2.0 Consensus size: 117
7191458 TTGAAAAAGA
*
7191468 AAAAAACATGATTAAATTTAATTCAAAATTGAATGAATAAATAAGAGAAACGAAAAAAGAGGGTC
1 AAAAAACATGATTAAATTTAATTCAAAATTGAATGAATAAATAAGAGAAACG-AAAAAGAAGGTC
* *
7191533 AAAAACTAAACATTTTATTAACTTATAAAAATTAG-GGCCCTAATTATAAATAG
65 AAAAACTAAA-ATTTTATGAACTTATAAAAATTAGAAGCCCTAATTATAAATAG
* * * * *
7191586 AAAAAA-ATGGTTAAATTTAATTCAAATTTGGATGAATTAATAAGAGAAATGAAAAAGAAGGTCA
1 AAAAAACATGATTAAATTTAATTCAAAATTGAATGAATAAATAAGAGAAACGAAAAAGAAGGTCA
* * * *
7191650 AAAATTTAAATTTTATGAAGTTATAAAAATTAGAAGCCCTAATTATAAATAT
66 AAAACTAAAATTTTATGAACTTATAAAAATTAGAAGCCCTAATTATAAATAG
7191702 AAAAA
1 AAAAA
7191707 GTTAGAGACT
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
115 22 0.20
116 40 0.37
117 40 0.37
118 6 0.06
ACGTcount: A:0.54, C:0.06, G:0.12, T:0.28
Consensus pattern (117 bp):
AAAAAACATGATTAAATTTAATTCAAAATTGAATGAATAAATAAGAGAAACGAAAAAGAAGGTCA
AAAACTAAAATTTTATGAACTTATAAAAATTAGAAGCCCTAATTATAAATAG
Found at i:7191712 original size:29 final size:28
Alignment explanation
Indices: 7191671--7191735 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
7191661 TTTATGAAGT
7191671 TATAAAAATTAGA-AGCCCTAATTATAAA
1 TATAAAAATTAGAGA-CCCTAATTATAAA
*
7191699 TATAAAAAGTTAGAGACTCTAATTATAAA
1 TATAAAAA-TTAGAGACCCTAATTATAAA
*
7191728 TAAAAAAA
1 TATAAAAA
7191736 AATTAGATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 8 0.24
29 24 0.73
30 1 0.03
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.28
Consensus pattern (28 bp):
TATAAAAATTAGAGACCCTAATTATAAA
Found at i:7193261 original size:22 final size:22
Alignment explanation
Indices: 7193233--7193279 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
7193223 ATATGCAGTG
7193233 ATGGATATTTTCATGAATACAT
1 ATGGATATTTTCATGAATACAT
7193255 ATGGATATTTTCATGAATACAT
1 ATGGATATTTTCATGAATACAT
7193277 ATG
1 ATG
7193280 CATGGTGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (22 bp):
ATGGATATTTTCATGAATACAT
Found at i:7193356 original size:37 final size:37
Alignment explanation
Indices: 7193305--7193410 Score: 149
Period size: 38 Copynumber: 2.8 Consensus size: 37
7193295 CCTTTTCGTC
*
7193305 CTACTAGGATTCAAACTTCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
7193342 TTACTAGGATTCAAACTCCTAAAAATAGGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATA-GGATAGAATT
* * *
7193380 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
7193411 CCACAAGCAC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
37 29 0.48
38 32 0.52
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:7194403 original size:20 final size:20
Alignment explanation
Indices: 7194359--7194447 Score: 83
Period size: 21 Copynumber: 4.3 Consensus size: 20
7194349 GATTCTGACT
* *
7194359 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATACGT-AA
*
7194380 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATACGTAA
* *
7194400 ATCGCAATGAC-AATACGCTAA
1 ATCGCAACG-CGTATACG-TAA
7194421 ATCGCAACGCG-ATTACGTAA
1 ATCGCAACGCGTA-TACGTAA
7194441 ATCGCAA
1 ATCGCAA
7194448 TGAGATTCTG
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
20 26 0.44
21 33 0.56
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATACGTAA
Found at i:7194454 original size:20 final size:20
Alignment explanation
Indices: 7194395--7194454 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
7194385 AACGCGTATC
* *
7194395 CGTAAATCGCAATGACAATA
1 CGTAAATCGCAATGAGATTA
* *
7194415 CGCTAAATCGCAACGCGATTA
1 CG-TAAATCGCAATGAGATTA
7194436 CGTAAATCGCAATGAGATT
1 CGTAAATCGCAATGAGATT
7194455 CTGACTATCG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
CGTAAATCGCAATGAGATTA
Found at i:7197942 original size:19 final size:18
Alignment explanation
Indices: 7197895--7198017 Score: 73
Period size: 19 Copynumber: 6.9 Consensus size: 18
7197885 AATCACAACG
*
7197895 TGAAAATTGCAACGCGGAAA
1 TGAAAATCGCAA-GC-GAAA
**
7197915 TGACTATCGCAATGCGAAA
1 TGAAAATCGCAA-GCGAAA
7197934 TGAAAATCGCAA-CG--A
1 TGAAAATCGCAAGCGAAA
* *
7197949 -GAGAATCGCAATACGAAA
1 TGAAAATCGCAA-GCGAAA
7197967 TGAAAATCGCAA-CG--A
1 TGAAAATCGCAAGCGAAA
**
7197982 -GGGAATCGCAAAGCGAAA
1 TGAAAATCGC-AAGCGAAA
7198000 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAA-GCGAA
7198018 TTTAGTTTCG
Statistics
Matches: 80, Mismatches: 12, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
14 17 0.21
15 4 0.05
16 4 0.05
17 4 0.05
18 4 0.05
19 36 0.45
20 11 0.14
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.13
Consensus pattern (18 bp):
TGAAAATCGCAAGCGAAA
Found at i:7197966 original size:33 final size:33
Alignment explanation
Indices: 7197920--7198013 Score: 154
Period size: 33 Copynumber: 2.8 Consensus size: 33
7197910 GGAAATGACT
*
7197920 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
*
7197953 ATCGCAATACGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
7197986 ATCGCAA-AGCGAAATGAAAATCGCAACG
1 ATCGCAATA-CGAAATGAAAATCGCAACG
7198014 CGAATTTAGT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 1 0.02
33 57 0.98
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAATACGAAATGAAAATCGCAACGAGAGA
Found at i:7198040 original size:19 final size:19
Alignment explanation
Indices: 7198018--7198058 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
7198008 GCAACGCGAA
7198018 TTTAGTTTCGCGTTGAGAT
1 TTTAGTTTCGCGTTGAGAT
*
7198037 TTTAGTTTCGCGTTGCGAT
1 TTTAGTTTCGCGTTGAGAT
7198056 TTT
1 TTT
7198059 CATTTCGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.12, C:0.12, G:0.24, T:0.51
Consensus pattern (19 bp):
TTTAGTTTCGCGTTGAGAT
Found at i:7198064 original size:19 final size:19
Alignment explanation
Indices: 7198023--7198107 Score: 65
Period size: 19 Copynumber: 4.7 Consensus size: 19
7198013 GCGAATTTAG
*
7198023 TTTCGCGTTGAGATTTT-A
1 TTTCGCGTTGCGATTTTCA
7198041 GTTTCGCGTTGCGATTTTCA
1 -TTTCGCGTTGCGATTTTCA
**
7198061 TTTCGTATTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
**
7198077 --TCTAGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
7198094 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
7198108 AGTCATTTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
14 8 0.16
16 3 0.06
17 3 0.06
19 36 0.71
20 1 0.02
ACGTcount: A:0.14, C:0.18, G:0.21, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:7199649 original size:21 final size:21
Alignment explanation
Indices: 7199583--7199649 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
7199573 GTGAATCGGG
*
7199583 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
7199603 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
7199625 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
7199646 CTCT
1 CTCT
7199650 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:7199668 original size:42 final size:41
Alignment explanation
Indices: 7199583--7199705 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
7199573 GTGAATCGGG
* * * *
7199583 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
7199625 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
7199667 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
7199706 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:7201677 original size:19 final size:19
Alignment explanation
Indices: 7201653--7201739 Score: 94
Period size: 19 Copynumber: 4.8 Consensus size: 19
7201643 TCTTTTGGTT
7201653 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
7201672 GAAATGAAAATCGCAA--T
1 GAAATGAAAATCGCAACGC
* *
7201689 G--A-GAGAATCGCAACAC
1 GAAATGAAAATCGCAACGC
*
7201705 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
7201724 GAAATGAAATTCGCAA
1 GAAATGAAAATCGCAA
7201740 TGCAATTTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 41 0.75
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:7202407 original size:20 final size:20
Alignment explanation
Indices: 7202382--7202595 Score: 177
Period size: 20 Copynumber: 10.6 Consensus size: 20
7202372 CTTTAAAAAT
7202382 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
7202402 CGCGTTACGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
7202422 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
7202443 CGCATTACGATTTACGTAT-
1 CGCGTTGCGATTTACGGATA
* *
7202462 TGTCGTTGCGATTTACAGATA
1 CG-CGTTGCGATTTACGGATA
* * *
7202483 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
7202503 CGCATTGCGATTTAC--ATAA
1 CGCGTTGCGATTTACGGAT-A
* *
7202522 TCGTGTTGCGATTTTACGTAT-
1 -CGCGTTGCGA-TTTACGGATA
*
7202543 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
7202564 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
7202585 CTCGTTGCGAT
1 CGCGTTGCGAT
7202596 AGTCAGAATC
Statistics
Matches: 154, Mismatches: 27, Indels: 26
0.74 0.13 0.13
Matches are distributed among these distances:
18 2 0.01
19 1 0.01
20 100 0.65
21 49 0.32
23 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:7202468 original size:40 final size:41
Alignment explanation
Indices: 7202384--7202676 Score: 275
Period size: 40 Copynumber: 7.2 Consensus size: 41
7202374 TTAAAAATCG
*
7202384 CGTTGCGATTTACGGATACGCGTTACGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
* *
7202425 CGTTGCGATTTACGGATACGCATTACGA-TTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
* *
7202465 CGTTGCGATTTACAGATACGCATTGCGA-TTTACGTATTCG-
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATT-GT
* *
7202505 CATTGCGATTTAC--ATAATCGTGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGAT-A-CGCGTTGCGATTTTACGTATTGT
* **
7202546 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
* * * *
7202587 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGT-TCG-
1 CGTTGCGAT-TTACGGATA-CGCGTTGCGATTT-TACGTATTGT
* ** * *
7202627 CGTTGCGATTTTCATATTCGCGTTGCGATTTT-CATATTCG-
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATT-GT
7202667 CGTTGCGATT
1 CGTTGCGATT
7202677 ATGGAAAATC
Statistics
Matches: 215, Mismatches: 23, Indels: 29
0.81 0.09 0.11
Matches are distributed among these distances:
38 3 0.01
39 4 0.02
40 106 0.49
41 95 0.44
42 5 0.02
43 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
Found at i:7202627 original size:20 final size:20
Alignment explanation
Indices: 7202604--7202676 Score: 121
Period size: 20 Copynumber: 3.6 Consensus size: 20
7202594 ATAGTCAGAA
*
7202604 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
7202624 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
7202644 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
7202664 TCGCGTTGCGATT
1 TCGCGTTGCGATT
7202677 ATGGAAAATC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 1 0.02
20 50 0.98
ACGTcount: A:0.14, C:0.19, G:0.23, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:7202655 original size:162 final size:162
Alignment explanation
Indices: 7202384--7202676 Score: 376
Period size: 162 Copynumber: 1.8 Consensus size: 162
7202374 TTAAAAATCG
* ** * *
7202384 CGTTGCGATTTACGGATACGCGTTACGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
1 CGTTGCGATTTACGGATACGCGTTACGATTTTACGGATACTCGTTGCGATTCACGAATACGCATT
* *
7202449 ACGATTTACGTATTGTCGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCGCATTGCGAT
66 ACGATTTACATATTGTCGTTGCGATTTACAGATACGCATTGCGATTTACATATTCGCATTGCGAT
7202514 TTACATAATCGTGTTGCGATTTTACGTATTGT
131 TTACATAATCGTGTTGCGATTTTACGTATTGT
* *
7202546 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGTCA-GAAT-CGCG
1 CGTTGCGATTTACGGATACGCGTTACGATTTTACGGATACTCGTTGCGAT--TCACGAATACGCA
* * * * * * * * *
7202609 TTGCGATTTATATGTTCG-CGTTGCGATTTTCATATTCGCGTTGCGATTTTCATATTCGCGTTGC
64 TTACGATTTACATATT-GTCGTTGCGATTTACAGATACGCATTGCGATTTACATATTCGCATTGC
7202673 GATT
128 GATT
7202677 ATGGAAAATC
Statistics
Matches: 110, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
162 104 0.95
163 4 0.04
164 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.39
Consensus pattern (162 bp):
CGTTGCGATTTACGGATACGCGTTACGATTTTACGGATACTCGTTGCGATTCACGAATACGCATT
ACGATTTACATATTGTCGTTGCGATTTACAGATACGCATTGCGATTTACATATTCGCATTGCGAT
TTACATAATCGTGTTGCGATTTTACGTATTGT
Found at i:7202687 original size:81 final size:82
Alignment explanation
Indices: 7202380--7202687 Score: 258
Period size: 81 Copynumber: 3.8 Consensus size: 82
7202370 CACTTTAAAA
* * * **
7202380 ATCG-CGTTGCGATTTACGGATACGCGTTACGATTTTACGTATT-GTCGTTGCGATT-TAC-GGA
1 ATCGTCGTTGCGATTTACAGATACGCGTTGCGATTTT-CGTATTCG-CGTTGCGATTATGCAAAA
* *
7202441 TACGCATTACGA-TTTACGT
64 T-CGCGTTGCGATTTTACGT
* * * * * *
7202460 ATTGTCGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCGCATTGCGATT-TACATAATC
1 ATCGTCGTTGCGATTTACAGATACGCGTTGCGATTTTCGTATTCGCGTTGCGATTATGCAAAATC
*
7202524 GTGTTGCGATTTTACGT
66 GCGTTGCGATTTTACGT
* * * * * *
7202541 ATTGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGA-TA-GTCAGAA
1 ATCGTCGTTGCGATTTACAGATACGCGTTGCGATTTT-CGTATTCGCGTTGCGATTATG-CAAAA
*
7202604 TCGCGTTGCGATTTATATGT
64 TCGCGTTGCGATTT-TACGT
* * * * *
7202624 -TCG-CGTTGCGATTTTCATATTCGCGTTGCGATTTTCATATTCGCGTTGCGATTATGGAAAATC
1 ATCGTCGTTGCGATTTACAGATACGCGTTGCGATTTTCGTATTCGCGTTGCGATTATGCAAAATC
7202687 G
66 G
7202688 TAATGCGAAT
Statistics
Matches: 185, Mismatches: 33, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
80 40 0.22
81 109 0.59
82 32 0.17
83 4 0.02
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (82 bp):
ATCGTCGTTGCGATTTACAGATACGCGTTGCGATTTTCGTATTCGCGTTGCGATTATGCAAAATC
GCGTTGCGATTTTACGT
Found at i:7202737 original size:42 final size:39
Alignment explanation
Indices: 7202465--7202739 Score: 146
Period size: 41 Copynumber: 6.8 Consensus size: 39
7202455 TACGTATTGT
* * *
7202465 CGTTGCGATTTAC-AGATACGCATTGCGA-TTTACGTATTCG
1 CGTTGCGATTTTCAAAAT-CGCGTTGCGATTTTAC-TA-TCG
* * * * *
7202505 CATTGCGATTTACATAATCGTGTTGCGATTTTACGTATTG
1 CGTTGCGATTTTCAAAATCGCGTTGCGATTTTAC-TATCG
* ** * *
7202545 TCGTTGCGATTTAC-GGATACGCGTTGCGATTTTACGGATACT
1 -CGTTGCGATTTTCAAAAT-CGCGTTGCGATTTTAC-TAT-CG
** * *
7202587 CGTTGCGATAGTCAGAATCGCGTTGCGATTTATA-TGTTCG
1 CGTTGCGATTTTCAAAATCGCGTTGCGATTT-TACT-ATCG
* *
7202627 CGTTGCGATTTTCATATTCGCGTTGCGATTTT-CATATTCG
1 CGTTGCGATTTTCAAAATCGCGTTGCGATTTTAC-TA-TCG
** ***
7202667 CGTTGCGATTATGGAAAATCGTAATGCGAATTTGTACTATCG
1 CGTTGCGATT-TTCAAAATCGCGTTGCG-ATTT-TACTATCG
*
7202709 CATTGCGATTCTTCAAAATCGCGTTGCGATT
1 CGTTGCGATT-TTCAAAATCGCGTTGCGATT
7202740 CTGGGAACTG
Statistics
Matches: 181, Mismatches: 39, Indels: 29
0.73 0.16 0.12
Matches are distributed among these distances:
39 1 0.01
40 66 0.36
41 77 0.43
42 33 0.18
43 3 0.02
44 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (39 bp):
CGTTGCGATTTTCAAAATCGCGTTGCGATTTTACTATCG
Found at i:7202932 original size:7 final size:8
Alignment explanation
Indices: 7202902--7202930 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
7202892 TTATACATAC
7202902 ATTTTTAT
1 ATTTTTAT
7202910 ATTTTTAT
1 ATTTTTAT
7202918 ATTTTTAT
1 ATTTTTAT
7202926 ATTTT
1 ATTTT
7202931 ATTTATACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
ATTTTTAT
Found at i:7202950 original size:22 final size:22
Alignment explanation
Indices: 7202883--7202952 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 22
7202873 TTATTTTTTC
**
7202883 TTTATTTTA-TTATAC-ATACA
1 TTTATTTTATTTATACTATTTA
* *
7202903 TTT-TTATATTTTTA-TATTT-
1 TTTATTTTATTTATACTATTTA
7202922 TTATATTTTATTTATACTATTTA
1 TT-TATTTTATTTATACTATTTA
7202945 TTTATTTT
1 TTTATTTT
7202953 CATTATGTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
19 6 0.16
20 10 0.26
21 9 0.24
22 11 0.29
23 2 0.05
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTATTTTATTTATACTATTTA
Found at i:7203066 original size:18 final size:20
Alignment explanation
Indices: 7203043--7203081 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
7203033 TATATATATA
*
7203043 TATTTTCTTC-ATTT-ATTT
1 TATTTTATTCAATTTCATTT
7203061 TATTTTATTCAATTTCATTT
1 TATTTTATTCAATTTCATTT
7203081 T
1 T
7203082 TTTAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 4 0.22
20 5 0.28
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTTTATTCAATTTCATTT
Found at i:7204259 original size:19 final size:19
Alignment explanation
Indices: 7204235--7204271 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
7204225 ACCTTACTAA
7204235 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
7204254 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
7204272 ATCATGCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:7205623 original size:15 final size:15
Alignment explanation
Indices: 7205599--7205648 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
7205589 AAAAAGGGCA
7205599 AAAACAAAAAAGAA-
1 AAAACAAAAAAGAAC
*
7205613 AAGAAGCAAAAAAGAAG
1 AA-AA-CAAAAAAGAAC
7205630 AAAACAAAAAAGAAC
1 AAAACAAAAAAGAAC
7205645 AAAA
1 AAAA
7205649 ATCAAAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
14 2 0.06
15 16 0.50
16 12 0.38
17 2 0.06
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAACAAAAAAGAAC
Found at i:7205648 original size:8 final size:7
Alignment explanation
Indices: 7205598--7205662 Score: 51
Period size: 7 Copynumber: 8.6 Consensus size: 7
7205588 AAAAAAGGGC
*
7205598 AAAAACA
1 AAAAAGA
7205605 AAAAAGA
1 AAAAAGA
7205612 AAAGAAGCA
1 AAA-AAG-A
7205621 AAAAAGA
1 AAAAAGA
*
7205628 AGAAAACA
1 A-AAAAGA
7205636 AAAAAGA
1 AAAAAGA
7205643 ACAAAA-A
1 A-AAAAGA
7205650 TCAAAAAGA
1 --AAAAAGA
7205659 AAAA
1 AAAA
7205663 GGGACAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
7 22 0.46
8 20 0.42
9 6 0.12
ACGTcount: A:0.80, C:0.08, G:0.11, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:7205649 original size:16 final size:15
Alignment explanation
Indices: 7205598--7205662 Score: 78
Period size: 16 Copynumber: 4.2 Consensus size: 15
7205588 AAAAAAGGGC
7205598 AAAAACAAAAAAGAA
1 AAAAACAAAAAAGAA
*
7205613 AAGAAGCAAAAAAGAA
1 AA-AAACAAAAAAGAA
*
7205629 GAAAACAAAAAAGAA
1 AAAAACAAAAAAGAA
7205644 CAAAAATC-AAAAAGAA
1 -AAAAA-CAAAAAAGAA
7205660 AAA
1 AAA
7205663 GGGACAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
15 17 0.40
16 25 0.58
17 1 0.02
ACGTcount: A:0.80, C:0.08, G:0.11, T:0.02
Consensus pattern (15 bp):
AAAAACAAAAAAGAA
Found at i:7206293 original size:22 final size:22
Alignment explanation
Indices: 7206265--7206319 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
7206255 GCTACCCCAT
7206265 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
7206287 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
7206309 CAAACCTTTGA
1 CAAACCTTTGA
7206320 CCAAACAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:7208556 original size:106 final size:106
Alignment explanation
Indices: 7207293--7208555 Score: 1914
Period size: 106 Copynumber: 11.9 Consensus size: 106
7207283 CGAGAAAACA
* * * *
7207293 CAAGTTCAACTTCACAACGAAGGGACTGCTAGTTGTCAACAAACAACTTCCCAATTTCATAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
7207358 ATTTCAGCTTCACAACGAAGGATATTGGACTCTAGACAACT
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* **
7207399 TAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTTAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
7207464 ATTTCAACTTCACGACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
7207505 CAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
7207570 ATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * * *
7207611 CAATTTCAACTTCATGACGAAGGGACCGTTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCGA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
7207676 ATTTTAACTTCACAGCGAAGGATATTGGACTCCAAACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
7207717 CAAGTTCAACTTCACGATGAAGGGACCGTTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
**
7207782 ATTTCAACTTCACAATAAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
7207823 CAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAACAAATAACTTCCCAATTTCAAAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
7207888 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
7207929 CAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
7207994 ATTTCAACTTCACGACGAAAGATATTGGACTCCAAACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * *
7208035 CAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * *
7208100 ATTTTAACTTCACAGCAAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
7208141 CAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
7208206 ATTTCAACTTCACAACGAAGGATGTTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
7208247 CAAGTTTAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTTCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
7208312 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
7208353 CAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * *
7208418 ATTTCAACTTCACAACAAAGGATATTGGACTCGAGCCAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * * *
7208459 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGATTCCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * *
7208524 ATTTTAACTTCACGATGGAGGATATTGGACTC
66 ATTTCAACTTCACAACGAAGGATATTGGACTC
7208556 GGAACAATGC
Statistics
Matches: 1054, Mismatches: 103, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 1054 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
Found at i:7209344 original size:37 final size:37
Alignment explanation
Indices: 7209291--7209395 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
7209281 CCTTTTCGTC
7209291 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
7209328 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
7209365 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
7209396 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:7210155 original size:22 final size:22
Alignment explanation
Indices: 7210055--7210158 Score: 67
Period size: 22 Copynumber: 4.6 Consensus size: 22
7210045 TTTATTTTTC
7210055 ATTTATTTATTATTATTGT-TACT
1 ATTTATTTATT-TTATT-TATACT
7210078 ATTTAGTATTTTATTTTA-TTATACAT
1 A-TT--TA-TTTATTTTATTTATAC-T
* *
7210104 ACATT-TTTATATT-TTTATA-T
1 A-TTTATTTATTTTATTTATACT
7210124 ATTT-TATTATTTTATTTATACT
1 ATTTAT-TTATTTTATTTATACT
7210146 ATTTATTTATTTT
1 ATTTATTTATTTT
7210159 CATTATGTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 23
0.70 0.05 0.25
Matches are distributed among these distances:
19 3 0.05
20 8 0.12
21 6 0.09
22 24 0.37
23 2 0.03
24 4 0.06
25 4 0.06
26 8 0.12
27 6 0.09
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTTATTTATTTTATTTATACT
Found at i:7210164 original size:22 final size:21
Alignment explanation
Indices: 7210117--7210158 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
7210107 TTTTTATATT
7210117 TTTATATATTTTATTATTTTA
1 TTTATATATTTTATTATTTTA
7210138 TTTATACTA-TTTATTTATTTT
1 TTTATA-TATTTTA-TTATTTT
7210159 CATTATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTATATATTTTATTATTTTA
Found at i:7210263 original size:18 final size:19
Alignment explanation
Indices: 7210240--7210286 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
7210230 CTTTTTTATA
*
7210240 TATTTTTTTTTCTTC-ATT
1 TATTTTTTTTTATTCAATT
*
7210258 TATTTTATTTTATTCAATT
1 TATTTTTTTTTATTCAATT
7210277 TCATTTTTTT
1 T-ATTTTTTT
7210287 AAATATTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 13 0.54
19 4 0.17
20 7 0.29
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTTTTTTATTCAATT
Found at i:7211015 original size:31 final size:31
Alignment explanation
Indices: 7210980--7211051 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
7210970 AGAGTATATT
*
7210980 ATATGGTCACTTTCGTTTTTATTTAATTAAG
1 ATATGGTCACTTTCGTATTTATTTAATTAAG
* * *
7211011 ATAT-GACTACTTTCGTATTTGTTTAGTTAAG
1 ATATGGTC-ACTTTCGTATTTATTTAATTAAG
*
7211042 ATGTGGTCAC
1 ATATGGTCAC
7211052 CACGGGTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
30 2 0.06
31 29 0.88
32 2 0.06
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.47
Consensus pattern (31 bp):
ATATGGTCACTTTCGTATTTATTTAATTAAG
Found at i:7213956 original size:20 final size:20
Alignment explanation
Indices: 7213931--7213977 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
7213921 TCCATTTTTC
7213931 AAAAATAAATAAAATAAAAT
1 AAAAATAAATAAAATAAAAT
* **
7213951 AAAAATGAATAAAATTCAAT
1 AAAAATAAATAAAATAAAAT
7213971 AAAAATA
1 AAAAATA
7213978 GAATGTAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (20 bp):
AAAAATAAATAAAATAAAAT
Found at i:7215212 original size:2 final size:2
Alignment explanation
Indices: 7215157--7215192 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
7215147 GAAATTCACC
7215157 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
7215193 GCTATTAAAT
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:7216469 original size:36 final size:38
Alignment explanation
Indices: 7216428--7216508 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
7216418 TTTGTTCAGG
7216428 GTCGGGT-AGG-TTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCGA
* *
7216464 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGG
1 GTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCGA
7216502 GTCGGGT
1 GTCGGGT
7216509 TCGGGTTTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 7 0.17
37 2 0.05
38 32 0.78
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (38 bp):
GTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:7216487 original size:38 final size:39
Alignment explanation
Indices: 7216438--7216516 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 39
7216428 GTCGGGTAGG
7216438 TTTTTTAAGTGTGATATTCGGGTCGAGTCGGG-TCGGGT
1 TTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTTCGGGT
*
7216476 TTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGT
1 TTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTTCGGGT
7216515 TT
1 TT
7216517 AGGGTGAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 31 0.79
39 8 0.21
ACGTcount: A:0.11, C:0.10, G:0.37, T:0.42
Consensus pattern (39 bp):
TTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTTCGGGT
Found at i:7216960 original size:20 final size:20
Alignment explanation
Indices: 7216935--7217021 Score: 63
Period size: 20 Copynumber: 4.3 Consensus size: 20
7216925 GACCAACAAA
*
7216935 ATCGCAATGCGATCTCCAAT
1 ATCGCAACGCGATCTCCAAT
** *
7216955 ATCGCAAATC-AGTTTCCAGAT
1 ATCGCAACGCGA-TCTCCA-AT
* *
7216976 -TCGCAACGCGAT-TCTGACT
1 ATCGCAACGCGATCTC-CAAT
*
7216995 ATCGCAACGCGATCTCCAGT
1 ATCGCAACGCGATCTCCAAT
7217015 ATCGCAA
1 ATCGCAA
7217022 ATCAGTTTCT
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
19 4 0.08
20 43 0.83
21 5 0.10
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATCTCCAAT
Found at i:7217028 original size:60 final size:60
Alignment explanation
Indices: 7216935--7217066 Score: 210
Period size: 60 Copynumber: 2.2 Consensus size: 60
7216925 GACCAACAAA
7216935 ATCGCAATGCGATCTCCAATATCGCAAATCAGTTTCCAGATTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATCTCCAATATCGCAAATCAGTTTCCAGATTCGCAACGCGATTCTGACT
* * * * *
7216995 ATCGCAACGCGATCTCCAGTATCGCAAATCAGTTTCTAGATTCGTAACGCGATTTTGACT
1 ATCGCAATGCGATCTCCAATATCGCAAATCAGTTTCCAGATTCGCAACGCGATTCTGACT
*
7217055 AGCGCAATGCGA
1 ATCGCAATGCGA
7217067 ATATGTAAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (60 bp):
ATCGCAATGCGATCTCCAATATCGCAAATCAGTTTCCAGATTCGCAACGCGATTCTGACT
Found at i:7217102 original size:20 final size:20
Alignment explanation
Indices: 7216976--7217148 Score: 102
Period size: 20 Copynumber: 8.6 Consensus size: 20
7216966 GTTTCCAGAT
7216976 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* *
7216996 TCGCAACGCGA-TCTCCAGTA
1 TCGCAACGCGATTCT-GACTA
** *
7217016 TCGCAAATCAGTTTCTAGA-T-
1 TCGCAACGC-GATTCT-GACTA
* *
7217036 TCGTAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
* * * * *
7217056 GCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
*
7217076 TCACAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* ** * *
7217096 TTGCAACGCGATAATACACAA
1 TCGCAACGCGATTCT-GACTA
7217117 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
7217137 TCGCAATGCGAT
1 TCGCAACGCGAT
7217149 AATACAAAAC
Statistics
Matches: 109, Mismatches: 36, Indels: 16
0.68 0.22 0.10
Matches are distributed among these distances:
18 2 0.02
19 9 0.08
20 76 0.70
21 18 0.17
22 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:7217124 original size:21 final size:21
Alignment explanation
Indices: 7217098--7217169 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
7217088 TCTGACTATT
7217098 GCAACGCGATAATACACAATC
1 GCAACGCGATAATACACAATC
** * *
7217119 GCAACGCGATTCT-GACTATC
1 GCAACGCGATAATACACAATC
* * *
7217139 GCAATGCGATAATACAAAACC
1 GCAACGCGATAATACACAATC
*
7217160 GCAATGCGAT
1 GCAACGCGAT
7217170 TTCTTAAGAA
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 15 0.38
21 24 0.62
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (21 bp):
GCAACGCGATAATACACAATC
Found at i:7217128 original size:41 final size:41
Alignment explanation
Indices: 7217073--7217170 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
7217063 GCGAATATGT
* *
7217073 AAATCACAACGCGATTCTGACTATTGCAACGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
* *
7217114 CAATCGCAACGCGATTCTGACTATCGCAATGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
* *
7217155 AAACCGCAATGCGATT
1 AAATCGCAACGCGATT
7217171 TCTTAAGAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (41 bp):
AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
Found at i:7217572 original size:19 final size:20
Alignment explanation
Indices: 7217547--7217637 Score: 96
Period size: 19 Copynumber: 4.4 Consensus size: 20
7217537 CTTATTTTGG
7217547 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
*
7217567 -TTTTTCAATATCGCAACAAC
1 ATTTTTCACTATCGCAAC-AC
*
7217587 ATGTTTTTCAAACTCTCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
*
7217611 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
7217630 ATTTTTCA
1 ATTTTTCA
7217638 AAATAGCGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
19 29 0.50
20 7 0.12
21 4 0.07
23 6 0.10
24 3 0.05
25 9 0.16
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.36
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:7217609 original size:44 final size:41
Alignment explanation
Indices: 7217558--7217639 Score: 112
Period size: 44 Copynumber: 1.9 Consensus size: 41
7217548 TTTTTCACTA
*
7217558 TCGCAACACTTTTTCAA-TATCGCAACAACATGTTTTTCAAACTC
1 TCGCAACACATTTT-AACTATCGCAAC-ACA--TTTTTCAAACTC
7217602 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
1 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
7217640 ATAGCGTTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
41 9 0.25
43 5 0.14
44 22 0.61
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (41 bp):
TCGCAACACATTTTAACTATCGCAACACATTTTTCAAACTC
Found at i:7220969 original size:3 final size:3
Alignment explanation
Indices: 7220961--7221140 Score: 306
Period size: 3 Copynumber: 60.0 Consensus size: 3
7220951 CTCAACTTTC
*
7220961 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
7221009 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TGA TGA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
7221057 TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
7221105 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
7221141 CAACGATTAC
Statistics
Matches: 167, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 167 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:7222495 original size:2 final size:2
Alignment explanation
Indices: 7222488--7222517 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
7222478 TATTGTTATG
*
7222488 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7222518 AAAATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7226850 original size:17 final size:18
Alignment explanation
Indices: 7226828--7226861 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
7226818 CACAGGACGA
7226828 GTAAGAATT-AAATATTG
1 GTAAGAATTGAAATATTG
7226845 GTAAGAATTGAAATATT
1 GTAAGAATTGAAATATT
7226862 AGATTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (18 bp):
GTAAGAATTGAAATATTG
Found at i:7235046 original size:218 final size:219
Alignment explanation
Indices: 7234666--7235104 Score: 772
Period size: 218 Copynumber: 2.0 Consensus size: 219
7234656 GGACAAGGTT
7234666 TATTATCGTCATTCTAGTCATTTAAGTACTCTAGACTCTCTAGAGGCATATACATATACAAACAC
1 TATTATCGTCATTCTAGTCATTTAAGTACTCTAGACTCTCTAGAGGCATATA-ATATACAAACAC
*
7234731 TGACTGAATCTAACTCGCGGGTCCTAGAAATGACTAAACTTGGATGTTCTGATACCACTAAATAT
65 TGACTGAATCTAACTCGCGAGTCCTAGAAATGACTAAACTTGGATGTTCTGATACCACTAAATAT
*
7234796 AACACCCTAATCTAGATAGACCTGAAGATCCATGGATTACAATGTTACACGGGACTAACAAAATA
130 AACACCCTAATCTAGATAGACCCGAAGATCCATGGATTACAATGTTACACGGGACTAACAAAATA
7234861 GTGACCCAAAATTTTCTTTTAAAAC
195 GTGACCCAAAATTTTCTTTTAAAAC
* * *
7234886 TATTATCGTCATTCTAGTCATTTAAGTACTCTAGACTCTTTAGAGGCATAT-ATATATAGACACT
1 TATTATCGTCATTCTAGTCATTTAAGTACTCTAGACTCTCTAGAGGCATATAATATACAAACACT
* * *
7234950 GATTGAATCTAACTCGCGATTCCTATAAATGACTAAACTTGGATGTTCTGATACCACTAAATATA
66 GACTGAATCTAACTCGCGAGTCCTAGAAATGACTAAACTTGGATGTTCTGATACCACTAAATATA
* *
7235015 ACACCCTAATCTATATATACCCGAAGATCCATGGATTACAATGTTACACGGGACTAACAAAATAG
131 ACACCCTAATCTAGATAGACCCGAAGATCCATGGATTACAATGTTACACGGGACTAACAAAATAG
7235080 TGACCCAAAATTTTCTTTTAAAAC
196 TGACCCAAAATTTTCTTTTAAAAC
7235104 T
1 T
7235105 GCTTGTAAAT
Statistics
Matches: 209, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
218 159 0.76
220 50 0.24
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (219 bp):
TATTATCGTCATTCTAGTCATTTAAGTACTCTAGACTCTCTAGAGGCATATAATATACAAACACT
GACTGAATCTAACTCGCGAGTCCTAGAAATGACTAAACTTGGATGTTCTGATACCACTAAATATA
ACACCCTAATCTAGATAGACCCGAAGATCCATGGATTACAATGTTACACGGGACTAACAAAATAG
TGACCCAAAATTTTCTTTTAAAAC
Found at i:7238641 original size:153 final size:154
Alignment explanation
Indices: 7238363--7238673 Score: 615
Period size: 153 Copynumber: 2.0 Consensus size: 154
7238353 TAAATAAAAT
7238363 ATCACATATAGATATAAGGTATCATAATAAATCCAAGTACGAAAAATATCATATAAAAATATATG
1 ATCACATATAGATATAAGGTATCATAATAAATCCAAGTACGAAAAATATCATATAAAAATATATG
7238428 AACGTATAAAACTAATTTTTCAAAGTCATTTCTTTTATCATATAACATGTAACAATGGTTCAAGT
66 AACGTATAAAACTAATTTTTCAAAGTCATTTCTTTTATCATATAACATGTAACAATGGTTCAAGT
7238493 ATAAAACAA-TTATGCCAAATCAA
131 ATAAAACAATTTATGCCAAATCAA
7238516 ATCACATATAGATATAAGGTATCATAATAAATCCAAGTACGAAAAATATCATATAAAAATATATG
1 ATCACATATAGATATAAGGTATCATAATAAATCCAAGTACGAAAAATATCATATAAAAATATATG
7238581 AACGTATAAAACTAATTTTTCAAAGTCATTTCTTTTATCATATAACATGTAACAATGGTTCAAGT
66 AACGTATAAAACTAATTTTTCAAAGTCATTTCTTTTATCATATAACATGTAACAATGGTTCAAGT
7238646 ATAAAACAATTTATGCCAAATCAA
131 ATAAAACAATTTATGCCAAATCAA
7238670 ATCA
1 ATCA
7238674 AAGTATTCTA
Statistics
Matches: 157, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
153 139 0.89
154 18 0.11
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (154 bp):
ATCACATATAGATATAAGGTATCATAATAAATCCAAGTACGAAAAATATCATATAAAAATATATG
AACGTATAAAACTAATTTTTCAAAGTCATTTCTTTTATCATATAACATGTAACAATGGTTCAAGT
ATAAAACAATTTATGCCAAATCAA
Found at i:7241843 original size:23 final size:23
Alignment explanation
Indices: 7241813--7241872 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
7241803 CATTTTATAT
7241813 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
7241836 GGCACTTCGGTGCAATTCTATGG
1 GGCACTTCGGTGCAATTCTACGC
*
7241859 GGTACTTCGGTGCA
1 GGCACTTCGGTGCA
7241873 TTTATACGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:7243989 original size:29 final size:29
Alignment explanation
Indices: 7243922--7243998 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
7243912 TGTCAAAATA
7243922 CATAAATTTTCAAAA-TTATACTTTCGTC
1 CATAAATTTTCAAAATTTATACTTTCGTC
* *
7243950 TATGAACTTTTCCAAAATTTATACTTT-G-C
1 CAT-AAATTTT-CAAAATTTATACTTTCGTC
7243979 CACTAAATTTTCAAAATTTA
1 CA-TAAATTTTCAAAATTTA
7243999 CATTTTGGTC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 11 0.27
29 14 0.34
30 7 0.17
31 9 0.22
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.43
Consensus pattern (29 bp):
CATAAATTTTCAAAATTTATACTTTCGTC
Found at i:7244011 original size:29 final size:27
Alignment explanation
Indices: 7243924--7244012 Score: 65
Period size: 29 Copynumber: 3.1 Consensus size: 27
7243914 TCAAAATACA
7243924 TAAATTTTCAAAATTATAC-TTTCGTCTA-
1 TAAATTTTCAAAATT-TACATTT-GTC-AC
* * *
7243952 TGAACTTTTCCAAAATTTATACTTTGCCAC
1 T-AAATTTT-CAAAATTTACA-TTTGTCAC
7243982 TAAATTTTCAAAATTTACATTTTGGTCAC
1 TAAATTTTCAAAATTTACA-TTT-GTCAC
7244011 TA
1 TA
7244013 GCCAAAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
28 14 0.29
29 21 0.44
30 10 0.21
31 3 0.06
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.44
Consensus pattern (27 bp):
TAAATTTTCAAAATTTACATTTGTCAC
Found at i:7248579 original size:17 final size:17
Alignment explanation
Indices: 7248559--7248597 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
7248549 CAAAGGAGAT
*
7248559 CAAAGATTAATGTACAA
1 CAAAAATTAATGTACAA
7248576 CAAAAATTAATGTACAA
1 CAAAAATTAATGTACAA
7248593 CAAAA
1 CAAAA
7248598 TCAGCCTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.13, G:0.08, T:0.21
Consensus pattern (17 bp):
CAAAAATTAATGTACAA
Found at i:7255101 original size:21 final size:20
Alignment explanation
Indices: 7255077--7255123 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
7255067 ATTTAACAAG
*
7255077 TAAAACTTTAATATTAAA-TTA
1 TAAAA-TTTAA-ATGAAATTTA
7255098 TAAATATTTAAATGAAATTTA
1 TAAA-ATTTAAATGAAATTTA
7255119 TAAAA
1 TAAAA
7255124 AAATATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 6 0.26
21 16 0.70
22 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
TAAAATTTAAATGAAATTTA
Found at i:7255499 original size:3 final size:3
Alignment explanation
Indices: 7255491--7255516 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7255481 TAAACTCGTA
7255491 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
7255517 AATTTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:7261126 original size:22 final size:22
Alignment explanation
Indices: 7261086--7261127 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
7261076 CGCCATGAAA
*
7261086 TTATAAAATAATTATTAAATTG
1 TTATAAAATAATTACTAAATTG
**
7261108 TTATAAAATGTTTACTAAAT
1 TTATAAAATAATTACTAAAT
7261128 GTAATGGTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
TTATAAAATAATTACTAAATTG
Found at i:7262336 original size:30 final size:31
Alignment explanation
Indices: 7262295--7262372 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
7262285 GTCCCTGAAT
7262295 TTTAGA-AAAATATCAATATA-ACCTTAAAC
1 TTTAGATAAAATATCAATATATACCTTAAAC
* * **
7262324 TTTAGATAAAATATTAATTTATTTCTTAAAC
1 TTTAGATAAAATATCAATATATACCTTAAAC
7262355 TTTAGATAAAATATCAAT
1 TTTAGATAAAATATCAAT
7262373 TGATCATTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 6 0.14
30 12 0.29
31 24 0.57
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (31 bp):
TTTAGATAAAATATCAATATATACCTTAAAC
Found at i:7270206 original size:2 final size:2
Alignment explanation
Indices: 7270199--7270257 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
7270189 ATCATAACCC
7270199 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7270241 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
7270258 GATCAACTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.