Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009614.1 Hibiscus syriacus cultivar Beakdansim tig00117000_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: 2129691
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 10
Found at i:855253 original size:5 final size:5
Alignment explanation
Indices: 855231--855265 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
855221 CGTATTACCA
855231 CGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
855266 GACGGACGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.26, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:855761 original size:6 final size:6
Alignment explanation
Indices: 855750--855785 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
855740 TCTCGTCTCG
*
855750 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT CGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
855786 CGTCCGCGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.19, G:0.47, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:855773 original size:18 final size:18
Alignment explanation
Indices: 855742--855785 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
855732 CGCCGTCGTC
855742 TCGTC-TCG-GGTCGTGG
1 TCGTCGTCGTGGTCGTGG
*
855758 TCGTGGTCGTGGTCGTGG
1 TCGTCGTCGTGGTCGTGG
855776 TCGTCGTCGT
1 TCGTCGTCGT
855786 CGTCCGCGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 3 0.12
18 17 0.71
ACGTcount: A:0.00, C:0.23, G:0.43, T:0.34
Consensus pattern (18 bp):
TCGTCGTCGTGGTCGTGG
Found at i:857209 original size:20 final size:20
Alignment explanation
Indices: 857184--857223 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
857174 ATGATTTCAG
857184 TATTAGAATAGACTCTAATA
1 TATTAGAATAGACTCTAATA
*
857204 TATTAGAATATACTCTAATA
1 TATTAGAATAGACTCTAATA
857224 GCCAGGTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (20 bp):
TATTAGAATAGACTCTAATA
Found at i:859178 original size:122 final size:119
Alignment explanation
Indices: 858965--859185 Score: 334
Period size: 122 Copynumber: 1.8 Consensus size: 119
858955 TAAGTATAAA
* *
858965 ATAAATGTTTAAATTAAATATTTTTTTATGATTAAGTTTTTAAATTATTTTTTGAATAATTTTAA
1 ATAAATATTTAAATTAAATATTTTTTTATGATTAAGTGTTTAAATTATTTTTTGAATAATTTTAA
*
859030 TGTCTAACATGATAAATGTTATCACTTAAGGTTTTTAGATTATCATCGGCATTT
66 TGTCTAACACGATAAATGTTATCACTTAAGGTTTTTAGATTATCATCGGCATTT
* * * *
859084 ATAAATATTTAAATTAAATTGTTTTTTTATGATTAGGTGTTTAAATTGTTTTTTTTTAATAATTT
1 ATAAATATTTAAATTAAA-TATTTTTTTATGATTAAGTGTTTAAA-T-TATTTTTTGAATAATTT
* *
859149 TGATGTCTAACACGATAAATGTTATCACTTAGGGTTT
63 TAATGTCTAACACGATAAATGTTATCACTTAAGGTTT
859186 GTTTGTTTGT
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
119 17 0.19
120 23 0.26
121 1 0.01
122 49 0.54
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.50
Consensus pattern (119 bp):
ATAAATATTTAAATTAAATATTTTTTTATGATTAAGTGTTTAAATTATTTTTTGAATAATTTTAA
TGTCTAACACGATAAATGTTATCACTTAAGGTTTTTAGATTATCATCGGCATTT
Found at i:859287 original size:42 final size:42
Alignment explanation
Indices: 859231--859325 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
859221 TTCCCCGAAA
* * *
859231 TCCCGTGTTTGTTTCACATAATTCATTTTTCGGAAAATGTTT
1 TCCCATGTTTGTTTCACATAATTCATTTTCCGAAAAATGTTT
* *
859273 TCCCATGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTT
1 TCCCATGTTTGTTTCACATAATTCATTTTCCGAAAAATGTTT
859315 T-CCAGTGTTTG
1 TCCCA-TGTTTG
859326 GTTCGAGGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 3 0.06
42 44 0.94
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.46
Consensus pattern (42 bp):
TCCCATGTTTGTTTCACATAATTCATTTTCCGAAAAATGTTT
Found at i:859572 original size:21 final size:21
Alignment explanation
Indices: 859524--859601 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 21
859514 TTTTAATCAA
*
859524 AATAT-TAATTATTAAAATATTT
1 AATATATAA-TATTAATAT-TTT
* *
859546 AAAATATATTTATTAATATTTCT
1 AATATATA-ATATTAATATTT-T
859569 AATAATATAATATT-ATATTTT
1 AAT-ATATAATATTAATATTTT
859590 AATATTATAATA
1 AATA-TATAATA
859602 AAATTAATCA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
20 1 0.02
21 11 0.24
22 12 0.26
23 17 0.37
24 5 0.11
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATATAATATTAATATTTT
Found at i:860708 original size:15 final size:16
Alignment explanation
Indices: 860677--860715 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
860667 TCATATATCC
860677 AACAA-CCAAAGTAAA
1 AACAATCCAAAGTAAA
860692 AACAATCCAAAGT-AA
1 AACAATCCAAAGTAAA
860707 AACAATCCA
1 AACAATCCA
860716 TGAACATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.62, C:0.23, G:0.05, T:0.10
Consensus pattern (16 bp):
AACAATCCAAAGTAAA
Found at i:862271 original size:23 final size:23
Alignment explanation
Indices: 862235--862311 Score: 111
Period size: 23 Copynumber: 3.3 Consensus size: 23
862225 TCGATTCCCT
862235 AAAGGAGGGAATCGGTTCCCATTC
1 AAAGG-GGGAATCGGTTCCCATTC
*
862259 AAAGGGGGAATCGGTTCCTATTC
1 AAAGGGGGAATCGGTTCCCATTC
* *
862282 AAAGGGGGAATCGATTCCCCTTC
1 AAAGGGGGAATCGGTTCCCATTC
862305 -AAGGGGG
1 AAAGGGGG
862312 TATCAATTCC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 7 0.14
23 37 0.76
24 5 0.10
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.21
Consensus pattern (23 bp):
AAAGGGGGAATCGGTTCCCATTC
Found at i:862308 original size:22 final size:23
Alignment explanation
Indices: 862218--862322 Score: 110
Period size: 23 Copynumber: 4.7 Consensus size: 23
862208 CAGAATTCGT
*
862218 GGGGGTATCGATTCCC--T-AAA
1 GGGGGAATCGATTCCCATTCAAA
*
862238 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGATTCCCATTCAAA
* *
862262 GGGGGAATCGGTTCCTATTCAAA
1 GGGGGAATCGATTCCCATTCAAA
*
862285 GGGGGAATCGATTCCCCTTC-AA
1 GGGGGAATCGATTCCCATTCAAA
* *
862307 GGGGGTATCAATTCCC
1 GGGGGAATCGATTCCC
862323 TCTGCACTAA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
20 2 0.03
21 12 0.16
22 16 0.22
23 38 0.52
24 5 0.07
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.24
Consensus pattern (23 bp):
GGGGGAATCGATTCCCATTCAAA
Found at i:866404 original size:117 final size:117
Alignment explanation
Indices: 866184--866405 Score: 279
Period size: 117 Copynumber: 1.9 Consensus size: 117
866174 CTTTCAAATC
* *
866184 GAAATTTTCATTTTCAATACTTTTAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTT
1 GAAAATTTCATTTTCAATACTTTTAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* *
866249 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTATTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTATTTAATTT
* * * * *
866301 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAACAT
1 GAAAATTTCATTTTCAATACTTTT-AAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAACAT
* * **
866364 TTCATTTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
64 TTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
866406 ATCATTTTTA
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
116 6 0.07
117 79 0.89
118 4 0.04
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (117 bp):
GAAAATTTCATTTTCAATACTTTTAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTATTTAATTT
Found at i:867654 original size:24 final size:24
Alignment explanation
Indices: 867610--867659 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
867600 ATAAAGAACC
*
867610 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
867634 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
867658 AA
1 AA
867660 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:877812 original size:24 final size:24
Alignment explanation
Indices: 877768--877817 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
877758 ATAAAGAACC
*
877768 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
877792 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
877816 AA
1 AA
877818 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:882151 original size:24 final size:24
Alignment explanation
Indices: 882107--882156 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
882097 ATAAAGAACC
*
882107 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
882131 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
882155 AA
1 AA
882157 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:883907 original size:17 final size:18
Alignment explanation
Indices: 883880--883916 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
883870 ATTTATTAAT
883880 TTCATAGAAATAATATTA
1 TTCATAGAAATAATATTA
883898 TTCA-AGAAATAATATTA
1 TTCATAGAAATAATATTA
883915 TT
1 TT
883917 AAATTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (18 bp):
TTCATAGAAATAATATTA
Found at i:883943 original size:19 final size:19
Alignment explanation
Indices: 883907--883987 Score: 62
Period size: 19 Copynumber: 4.3 Consensus size: 19
883897 ATTCAAGAAA
*
883907 TAAT-ATTATTAA-ATTAT
1 TAATAATTAATAATATTAT
*
883924 TAATAATGAATAATATTATT
1 TAATAATTAATAATATTA-T
* * *
883944 TATATATTTAATACTAATA-
1 TA-ATAATTAATAATATTAT
883963 TAATAATCTAATAATATT-T
1 TAATAAT-TAATAATATTAT
883982 TAATAA
1 TAATAA
883988 AGATATTTGA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
17 4 0.08
18 10 0.20
19 20 0.41
20 3 0.06
21 12 0.24
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (19 bp):
TAATAATTAATAATATTAT
Found at i:884008 original size:23 final size:23
Alignment explanation
Indices: 883982--884026 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
883972 AATAATATTT
*
883982 TAATAAAGATATTTGAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
884005 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
884027 ATATAACATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:884186 original size:22 final size:22
Alignment explanation
Indices: 884160--884201 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
884150 TATTTTAATA
884160 TTTTAAAA-ATAATAATATTAAG
1 TTTTAAAATA-AATAATATTAAG
*
884182 TTTTATAATAAATAATATTA
1 TTTTAAAATAAATAATATTA
884202 TTTATTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TTTTAAAATAAATAATATTAAG
Found at i:884392 original size:14 final size:14
Alignment explanation
Indices: 884373--884431 Score: 73
Period size: 14 Copynumber: 4.1 Consensus size: 14
884363 TCAGAAATGT
*
884373 AATTCATTTTCCAG
1 AATTCAATTTCCAG
*
884387 AATTCAAATTCCAG
1 AATTCAATTTCCAG
* *
884401 TAATTTATTTTCCAG
1 -AATTCAATTTCCAG
884416 AATTCAATTTCCAG
1 AATTCAATTTCCAG
884430 AA
1 AA
884432 AACCAATTAC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
14 26 0.70
15 11 0.30
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.39
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:884404 original size:29 final size:29
Alignment explanation
Indices: 884371--884429 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
884361 TTTCAGAAAT
884371 GTAATTCATTTTCCAGAATTCAAATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
* *
884400 GTAATTTATTTTCCAGAATTCAATTTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
884429 G
1 G
884430 AAAACCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTCCA
Found at i:885631 original size:18 final size:18
Alignment explanation
Indices: 885608--885643 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
885598 ATTTATGTGT
*
885608 TTTTAAATATAATTTTAA
1 TTTTAAATAAAATTTTAA
885626 TTTTAAATAAAATTTTAA
1 TTTTAAATAAAATTTTAA
885644 AATTATCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTAAATAAAATTTTAA
Found at i:887627 original size:37 final size:37
Alignment explanation
Indices: 887572--887651 Score: 133
Period size: 37 Copynumber: 2.2 Consensus size: 37
887562 CAATGGGATT
*
887572 TTATTAATCAAAGAATGATAAGGACATACATAAAATG
1 TTATTAATCAAAGAATGATAAGGACATACATAAAATA
* *
887609 TTATTAATCAATGTATGATAAGGACATACATAAAATA
1 TTATTAATCAAAGAATGATAAGGACATACATAAAATA
887646 TTATTA
1 TTATTA
887652 GCAATTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (37 bp):
TTATTAATCAAAGAATGATAAGGACATACATAAAATA
Found at i:887767 original size:26 final size:25
Alignment explanation
Indices: 887737--887787 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
887727 TAATGCACCG
*
887737 AAAGTGTATTAGTTGGCATCAATGAT
1 AAAGTGCATTAGTTGGCAT-AATGAT
887763 AAAGTGCATTAGTTGGCATAATGAT
1 AAAGTGCATTAGTTGGCATAATGAT
887788 TCATCAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (25 bp):
AAAGTGCATTAGTTGGCATAATGAT
Found at i:904479 original size:28 final size:28
Alignment explanation
Indices: 904447--904504 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
904437 TCAATCGGTC
904447 GAATTAATTCGATCGGTCGGAAGAACCG
1 GAATTAATTCGATCGGTCGGAAGAACCG
904475 GAATTAATTCGATCGGTCGGAAGAACCG
1 GAATTAATTCGATCGGTCGGAAGAACCG
904503 GA
1 GA
904505 CGACATCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (28 bp):
GAATTAATTCGATCGGTCGGAAGAACCG
Found at i:909949 original size:19 final size:20
Alignment explanation
Indices: 909912--909949 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
909902 CACTCACTAT
*
909912 TGTATTACTTGCATCGATTG
1 TGTATTACTTGCATAGATTG
*
909932 TGTA-TACTTGTATAGATT
1 TGTATTACTTGCATAGATT
909950 TACGTACCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (20 bp):
TGTATTACTTGCATAGATTG
Found at i:911799 original size:23 final size:23
Alignment explanation
Indices: 911763--911835 Score: 96
Period size: 23 Copynumber: 3.3 Consensus size: 23
911753 CACCACAGCT
*
911763 CATATA-AA-TGCACCGAAGTGC
1 CATATAGAATTGCACCGTAGTGC
911784 CATATAGAATTGCACCGTAGTGC
1 CATATAGAATTGCACCGTAGTGC
***
911807 CGCGTAGAATTGCACCGTAGTGC
1 CATATAGAATTGCACCGTAGTGC
911830 CATATA
1 CATATA
911836 ATAATGTCCA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.14
22 2 0.05
23 35 0.81
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (23 bp):
CATATAGAATTGCACCGTAGTGC
Found at i:911965 original size:18 final size:18
Alignment explanation
Indices: 911942--911995 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
911932 GAATACATAT
911942 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
911960 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
*
911978 ATGTCCCAAAGGACCACA
1 ATGTCCCGAAGGACCACA
911996 TATCATTCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.35, C:0.33, G:0.20, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:912093 original size:139 final size:139
Alignment explanation
Indices: 911838--912098 Score: 461
Period size: 139 Copynumber: 1.9 Consensus size: 139
911828 GCCATATAAT
* *
911838 AATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
1 AATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
*
911903 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATGTCCCG
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCAAAGGACCACAATGTCCCG
911968 AAGGACCAC
131 AAGGACCAC
*
911977 AATGTCCCA-AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATG
1 AATGT-CCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATG
*
912041 TGTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCTCAAAGGACCACA
65 TGTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCAAAGGACCACA
912099 TATCATTCCT
Statistics
Matches: 116, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
139 113 0.97
140 3 0.03
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (139 bp):
AATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCAAAGGACCACAATGTCCCG
AAGGACCAC
Found at i:912157 original size:103 final size:103
Alignment explanation
Indices: 911978--912203 Score: 416
Period size: 103 Copynumber: 2.2 Consensus size: 103
911968 AAGGACCACA
*
911978 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
1 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTG
*
912043 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACTTCACACATATTCCAAAGAATACATAT
*
912081 ATGTCTCAAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTG
1 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTG
912146 TCTCACCAGACTTCACACATATTCCAAAGAATACATAT
66 TCTCACCAGACTTCACACATATTCCAAAGAATACATAT
*
912184 ATGTCCCGAAGGACCACATA
1 ATGTCCCAAAGGACCACATA
912204 GACCCTCGAC
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 118 1.00
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (103 bp):
ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTG
TCTCACCAGACTTCACACATATTCCAAAGAATACATAT
Found at i:913411 original size:21 final size:21
Alignment explanation
Indices: 913381--913425 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
913371 TTTTGCTCGT
* *
913381 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
913402 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
913423 TTG
1 TTG
913426 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:917386 original size:23 final size:23
Alignment explanation
Indices: 917360--917420 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
917350 CTCATATAAA
917360 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* *
917383 TGCACC-ATAGTGCCGCGTAGAAT
1 TGCACCGA-AGTGCCACATAGAAT
*
917406 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
917421 TATAATAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:917554 original size:18 final size:18
Alignment explanation
Indices: 917531--917566 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
917521 GAATACATAT
917531 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
917549 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
917567 TATCATTCCT
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:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:917641 original size:121 final size:121
Alignment explanation
Indices: 917427--917790 Score: 665
Period size: 121 Copynumber: 3.0 Consensus size: 121
917417 GCCATATAAT
** * * *
917427 AATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
*
917492 GTCTTACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
917548 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
917613 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
*
917669 AATATCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
917734 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
917790 A
1 A
917791 TAGACCCTCG
Statistics
Matches: 236, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 236 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (121 bp):
AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
Found at i:917673 original size:20 final size:18
Alignment explanation
Indices: 917655--917691 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
917645 TACATATATG
917655 TCCCGAAGGACCACAATA
1 TCCCGAAGGACCACAATA
917673 TCCCGAAGGACCAC-ATA
1 TCCCGAAGGACCACAATA
917690 TC
1 TC
917692 ATTCCTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.35, C:0.35, G:0.16, T:0.14
Consensus pattern (18 bp):
TCCCGAAGGACCACAATA
Found at i:918994 original size:21 final size:21
Alignment explanation
Indices: 918970--919014 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
918960 TTTTGTTCGT
* *
918970 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
918991 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
919012 TTG
1 TTG
919015 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:920838 original size:26 final size:26
Alignment explanation
Indices: 920809--920862 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
920799 GCTAAACAAT
* **
920809 TAATCAAATTAGTTTTTCAAACCAGC
1 TAATCAAATCAGTTGGTCAAACCAGC
920835 TAATCAAATCAGTTGGTCAAACCAGC
1 TAATCAAATCAGTTGGTCAAACCAGC
920861 TA
1 TA
920863 TTGGAATCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (26 bp):
TAATCAAATCAGTTGGTCAAACCAGC
Found at i:925767 original size:25 final size:26
Alignment explanation
Indices: 925738--925792 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
925728 TATTTTATTA
925738 TATTTTTAATATTTT-GTAATTAATT
1 TATTTTTAATATTTTAGTAATTAATT
*
925763 TA--TTTAATATTTTACTTAATTAATT
1 TATTTTTAATATTTTA-GTAATTAATT
925788 T-TTTT
1 TATTTT
925793 GCAGAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
23 11 0.44
25 12 0.48
26 2 0.08
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
TATTTTTAATATTTTAGTAATTAATT
Found at i:925781 original size:21 final size:20
Alignment explanation
Indices: 925727--925788 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
925717 TGTCTAAGGT
925727 ATATTTTATT-ATATT-TTTA
1 ATATTTTATTAAT-TTATTTA
925746 ATATTTTGTAATTAATTTATTTA
1 ATA-TTT-T-ATTAATTTATTTA
*
925769 ATATTTTACTTAATTAATTT
1 ATATTTTA-TTAATTTATTT
925789 TTTTGCAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
19 3 0.08
20 4 0.11
21 12 0.33
22 8 0.22
23 9 0.25
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
ATATTTTATTAATTTATTTA
Found at i:929606 original size:14 final size:14
Alignment explanation
Indices: 929587--929617 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
929577 TCAAATTATT
929587 TAAATAAATTCAAA
1 TAAATAAATTCAAA
*
929601 TAAATAAATTCTAA
1 TAAATAAATTCAAA
929615 TAA
1 TAA
929618 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATAAATTCAAA
Found at i:929634 original size:19 final size:19
Alignment explanation
Indices: 929612--929661 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
929602 AAATAAATTC
929612 TAATAATTTAAATAATATA
1 TAATAATTTAAATAATATA
* *
929631 TAATTAATTT-CATAATATT
1 TAA-TAATTTAAATAATATA
929650 TACA-AATTTAAA
1 TA-ATAATTTAAA
929662 ACTAATGTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
18 5 0.20
19 13 0.52
20 7 0.28
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAATTTAAATAATATA
Found at i:929852 original size:21 final size:21
Alignment explanation
Indices: 929791--929840 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
929781 GTTTATAATT
*
929791 AAATAATCAAATA--AAAATA
1 AAATAATTAAATACTAAAATA
929810 AAATAATTAAATACTAAAATA
1 AAATAATTAAATACTAAAATA
929831 AAATAATTAA
1 AAATAATTAA
929841 TTATTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 12 0.43
21 16 0.57
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATAATTAAATACTAAAATA
Found at i:929862 original size:16 final size:16
Alignment explanation
Indices: 929845--929875 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
929835 AATTAATTAT
929845 TTTAAT-AATAAAAAA
1 TTTAATGAATAAAAAA
929860 TTTAATGAATAAAAAA
1 TTTAATGAATAAAAAA
929876 ATAAATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
TTTAATGAATAAAAAA
Found at i:929865 original size:15 final size:15
Alignment explanation
Indices: 929845--929889 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
929835 AATTAATTAT
929845 TTTAATAATAAAAAA
1 TTTAATAATAAAAAA
929860 TTTAATGAATAAAAAA
1 TTTAAT-AATAAAAAA
* * *
929876 ATAAATTATAAAAA
1 TTTAATAATAAAAA
929890 CAATTGTACC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (15 bp):
TTTAATAATAAAAAA
Found at i:930199 original size:29 final size:30
Alignment explanation
Indices: 930166--930251 Score: 122
Period size: 29 Copynumber: 2.9 Consensus size: 30
930156 GTCCCAACAC
* *
930166 ATAGGTCGTCATGCCCTCCGGGTGACCTT-
1 ATAGGTCGCCATGCACTCCGGGTGACCTTG
* *
930195 ATAGGTCGCCATGCTCTCCGGGCGACCTTG
1 ATAGGTCGCCATGCACTCCGGGTGACCTTG
930225 A-AGGTCGCCATGCACTCCGGGTGACCT
1 ATAGGTCGCCATGCACTCCGGGTGACCT
930252 ACCCTTGCTC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
29 50 0.98
30 1 0.02
ACGTcount: A:0.15, C:0.33, G:0.29, T:0.23
Consensus pattern (30 bp):
ATAGGTCGCCATGCACTCCGGGTGACCTTG
Found at i:935769 original size:18 final size:19
Alignment explanation
Indices: 935748--935800 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 19
935738 TGAAACATAG
935748 AAATTAA-ATGAATA-TAAT
1 AAATTAATAT-AATATTAAT
*
935766 AAATGAATATAATATTAAT
1 AAATTAATATAATATTAAT
935785 -AATT-A-ATAATATTAAT
1 AAATTAATATAATATTAAT
935801 TATTAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 11 0.35
17 1 0.03
18 13 0.42
19 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
AAATTAATATAATATTAAT
Found at i:935770 original size:13 final size:13
Alignment explanation
Indices: 935752--935779 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
935742 ACATAGAAAT
935752 TAAATGAATATAA
1 TAAATGAATATAA
935765 TAAATGAATATAA
1 TAAATGAATATAA
935778 TA
1 TA
935780 TTAATAATTA
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:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (13 bp):
TAAATGAATATAA
Found at i:935822 original size:17 final size:17
Alignment explanation
Indices: 935758--935835 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 17
935748 AAATTAAATG
935758 AATATAATAAATGAA-TAT
1 AATAT-ATAAAT-AATTAT
935776 AATAT-T-AATAATTAAT
1 AATATATAAATAATT-AT
*
935792 AATAT-T-AATTATTA-
1 AATATATAAATAATTAT
935806 AATATACTAAATAATTAT
1 AATATA-TAAATAATTAT
*
935824 GATATATAAATA
1 AATATATAAATA
935836 TAGAAATATA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
14 7 0.14
15 5 0.10
16 16 0.31
17 13 0.25
18 10 0.20
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (17 bp):
AATATATAAATAATTAT
Found at i:937143 original size:15 final size:15
Alignment explanation
Indices: 937113--937145 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
937103 ATTTGACTGC
937113 TTATGGTAAATTAAT
1 TTATGGTAAATTAAT
*
937128 TTAT-GTAAATTAAA
1 TTATGGTAAATTAAT
937142 TTAT
1 TTAT
937146 TGAGTTAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (15 bp):
TTATGGTAAATTAAT
Found at i:940122 original size:7 final size:7
Alignment explanation
Indices: 940110--940282 Score: 73
Period size: 7 Copynumber: 24.6 Consensus size: 7
940100 GTGCATAACT
940110 TAAACCC
1 TAAACCC
940117 TAAACCC
1 TAAACCC
**
940124 TAACACAT
1 TAA-ACCC
*
940132 TAAACAC
1 TAAACCC
*
940139 AAAACCC
1 TAAACCC
**
940146 TAAACTT
1 TAAACCC
*
940153 TAAACCT
1 TAAACCC
* *
940160 TAAATCA
1 TAAACCC
*
940167 TAACACAC
1 TAA-ACCC
940175 -AAACCC
1 TAAACCC
940181 TAAACCC
1 TAAACCC
*
940188 TAAACCT
1 TAAACCC
940195 TAAA-CC
1 TAAACCC
*
940201 TCAAACCT
1 T-AAACCC
**
940209 TAAACTT
1 TAAACCC
*
940216 TAAACCT
1 TAAACCC
*
940223 TAAATCC
1 TAAACCC
* *
940230 T-ATCACA
1 TAAAC-CC
**
940237 TAAACTA
1 TAAACCC
*
940244 TAAACAC
1 TAAACCC
*
940251 TAAACCT
1 TAAACCC
*
940258 TAAACTC
1 TAAACCC
*
940265 TAAATCC
1 TAAACCC
940272 TAAACCC
1 TAAACCC
940279 TAAA
1 TAAA
940283 TCTTATCAAA
Statistics
Matches: 123, Mismatches: 36, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
6 6 0.05
7 107 0.87
8 10 0.08
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:940192 original size:35 final size:35
Alignment explanation
Indices: 940110--940199 Score: 112
Period size: 35 Copynumber: 2.5 Consensus size: 35
940100 GTGCATAACT
*
940110 TAAACCCTAAACCCTAACACATTAAACACAAAACCC
1 TAAACCCTAAACCTTAA-ACATTAAACACAAAACCC
**
940146 TAAACTTTAAACCTTAAATCA-T-AACACACAAACCC
1 TAAACCCTAAACCTTAAA-CATTAAACACA-AAACCC
940181 TAAACCCTAAACCTTAAAC
1 TAAACCCTAAACCTTAAAC
940200 CTCAAACCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
34 7 0.15
35 24 0.51
36 16 0.34
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.19
Consensus pattern (35 bp):
TAAACCCTAAACCTTAAACATTAAACACAAAACCC
Found at i:940199 original size:21 final size:21
Alignment explanation
Indices: 940108--940282 Score: 106
Period size: 21 Copynumber: 8.3 Consensus size: 21
940098 ATGTGCATAA
940108 CTTAAACCCTAAACCCTAACAC
1 CTTAAACCCTAAACCCTAA-AC
* * *
940130 ATTAAACACAAAACCCTAAAC
1 CTTAAACCCTAAACCCTAAAC
* * * *
940151 TTTAAACCTTAAATCATAACAC
1 CTTAAACCCTAAACCCTAA-AC
940173 AC--AAACCCTAAACCCTAAAC
1 -CTTAAACCCTAAACCCTAAAC
*
940193 CTTAAA-CCTCAAACCTTAAAC
1 CTTAAACCCT-AAACCCTAAAC
* * * *
940214 TTTAAACCTTAAATCCT-ATC
1 CTTAAACCCTAAACCCTAAAC
* ** *
940234 ACATAAACTATAAACACTAAAC
1 -CTTAAACCCTAAACCCTAAAC
* *
940256 CTTAAACTCTAAATCCTAAAC
1 CTTAAACCCTAAACCCTAAAC
*
940277 CCTAAA
1 CTTAAA
940283 TCTTATCAAA
Statistics
Matches: 114, Mismatches: 31, Indels: 17
0.70 0.19 0.10
Matches are distributed among these distances:
19 1 0.01
20 7 0.06
21 84 0.74
22 22 0.19
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (21 bp):
CTTAAACCCTAAACCCTAAAC
Found at i:940218 original size:63 final size:63
Alignment explanation
Indices: 940111--940276 Score: 199
Period size: 63 Copynumber: 2.6 Consensus size: 63
940101 TGCATAACTT
*
940111 AAACCCTAAACCCTAACACATTAAACACAAAACCCTAAACTTTAAACCTTAAATCATAACACAC
1 AAACCCTAAACCCTAA-ACCTTAAACACAAAACCCTAAACTTTAAACCTTAAATCATAACACAC
* * * * *
940175 AAACCCTAAACCCTAAACCTTAAAC-CTCAAACCTTAAACTTTAAACCTTAAATCCTATCACAT
1 AAACCCTAAACCCTAAACCTTAAACAC-AAAACCCTAAACTTTAAACCTTAAATCATAACACAC
** * * * *
940238 AAACTATAAACACTAAACCTTAAACTCTAAATCCTAAAC
1 AAACCCTAAACCCTAAACCTTAAACACAAAACCCTAAAC
940277 CCTAAATCTT
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
62 1 0.01
63 70 0.80
64 17 0.19
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (63 bp):
AAACCCTAAACCCTAAACCTTAAACACAAAACCCTAAACTTTAAACCTTAAATCATAACACAC
Found at i:940427 original size:15 final size:14
Alignment explanation
Indices: 940402--940439 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
940392 CAATTTAAAA
940402 AAATA-ATTATTAC
1 AAATATATTATTAC
*
940415 AAATATTATTATTAG
1 AAATA-TATTATTAC
940430 AAATATATTA
1 AAATATATTA
940440 AATATTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 5 0.23
15 12 0.55
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (14 bp):
AAATATATTATTAC
Found at i:940564 original size:14 final size:14
Alignment explanation
Indices: 940547--940587 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
940537 TTTATTTATC
940547 AATAATGTATTTTT
1 AATAATGTATTTTT
940561 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
940572 AATAATGTAATTTT
1 AATAATGTATTTTT
940586 AA
1 AA
940588 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:945098 original size:12 final size:13
Alignment explanation
Indices: 945076--945104 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
945066 ACTCGTTTAC
945076 TGAATAGTGAAAG
1 TGAATAGTGAAAG
945089 TGAA-AGTGAAAG
1 TGAATAGTGAAAG
945101 TGAA
1 TGAA
945105 GGGGAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (13 bp):
TGAATAGTGAAAG
Found at i:945860 original size:2 final size:2
Alignment explanation
Indices: 945853--945893 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
945843 TTGCACTCTG
945853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
945894 GACTCAATGG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:947597 original size:7 final size:8
Alignment explanation
Indices: 947573--947599 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
947563 AAACCTTAAC
947573 AAAGGAAA
1 AAAGGAAA
947581 AAAGGAAA
1 AAAGGAAA
947589 AAAGGAAA
1 AAAGGAAA
947597 AAA
1 AAA
947600 CAATCAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (8 bp):
AAAGGAAA
Found at i:949152 original size:162 final size:162
Alignment explanation
Indices: 948885--949209 Score: 650
Period size: 162 Copynumber: 2.0 Consensus size: 162
948875 GTGGTACTTA
948885 ATATCTGATTGAATAAAGAGAATAACCTTTCCCTCCAGAGGCGCCGATAGCAATACGCTCACCAG
1 ATATCTGATTGAATAAAGAGAATAACCTTTCCCTCCAGAGGCGCCGATAGCAATACGCTCACCAG
948950 GCTTGAACAGTTTGTTCTCTAAAATAACCTGGTGAATCTCCTCCTCGAACACCGCGTAAAAACAC
66 GCTTGAACAGTTTGTTCTCTAAAATAACCTGGTGAATCTCCTCCTCGAACACCGCGTAAAAACAC
949015 TCTCTGCATATCTTTAACCATGGCACAATTTT
131 TCTCTGCATATCTTTAACCATGGCACAATTTT
949047 ATATCTGATTGAATAAAGAGAATAACCTTTCCCTCCAGAGGCGCCGATAGCAATACGCTCACCAG
1 ATATCTGATTGAATAAAGAGAATAACCTTTCCCTCCAGAGGCGCCGATAGCAATACGCTCACCAG
949112 GCTTGAACAGTTTGTTCTCTAAAATAACCTGGTGAATCTCCTCCTCGAACACCGCGTAAAAACAC
66 GCTTGAACAGTTTGTTCTCTAAAATAACCTGGTGAATCTCCTCCTCGAACACCGCGTAAAAACAC
949177 TCTCTGCATATCTTTAACCATGGCACAATTTT
131 TCTCTGCATATCTTTAACCATGGCACAATTTT
949209 A
1 A
949210 GAATCCATGA
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
162 163 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.27
Consensus pattern (162 bp):
ATATCTGATTGAATAAAGAGAATAACCTTTCCCTCCAGAGGCGCCGATAGCAATACGCTCACCAG
GCTTGAACAGTTTGTTCTCTAAAATAACCTGGTGAATCTCCTCCTCGAACACCGCGTAAAAACAC
TCTCTGCATATCTTTAACCATGGCACAATTTT
Found at i:953068 original size:2 final size:2
Alignment explanation
Indices: 953061--953096 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
953051 AAACTCTCCC
953061 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
953097 TTTTGTTAAC
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:957686 original size:13 final size:13
Alignment explanation
Indices: 957670--957761 Score: 66
Period size: 13 Copynumber: 7.2 Consensus size: 13
957660 TAAAAAAGGT
*
957670 AAATCAAATAAAA
1 AAATAAAATAAAA
957683 AAATAAAATAAAA
1 AAATAAAATAAAA
957696 AAA-AAAA-AAAA
1 AAATAAAATAAAA
* * *
957707 CAACAAAA-AATA
1 AAATAAAATAAAA
* *
957719 ACA-AAAGTAAAA
1 AAATAAAATAAAA
*
957731 AAATACAAAGAAAA
1 AAATA-AAATAAAA
*
957745 TAATAAAATAGAAA
1 AAATAAAATA-AAA
957759 AAA
1 AAA
957762 AGGAAAAAAT
Statistics
Matches: 61, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
11 9 0.15
12 17 0.28
13 20 0.33
14 15 0.25
ACGTcount: A:0.80, C:0.05, G:0.03, T:0.11
Consensus pattern (13 bp):
AAATAAAATAAAA
Found at i:957688 original size:8 final size:8
Alignment explanation
Indices: 957675--957776 Score: 68
Period size: 8 Copynumber: 12.1 Consensus size: 8
957665 AAGGTAAATC
957675 AAATAAAA
1 AAATAAAA
957683 AAATAAAA
1 AAATAAAA
957691 TAAA-AAAA
1 -AAATAAAA
957699 AAA-AAAA
1 AAATAAAA
*
957706 ACAA-CAAA
1 A-AATAAAA
957714 AAATAACAA
1 AAATAA-AA
*
957723 AAGTAAAA
1 AAATAAAA
957731 AAATACAAAGA
1 AAAT--AAA-A
*
957742 AAATAATA
1 AAATAAAA
957750 AAATAGAAA
1 AAATA-AAA
957759 AAA-AGGAAA
1 AAATA--AAA
957768 AAATAAAA
1 AAATAAAA
957776 A
1 A
957777 TCATTAAAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
7 10 0.13
8 35 0.45
9 24 0.31
10 4 0.05
11 5 0.06
ACGTcount: A:0.81, C:0.04, G:0.05, T:0.10
Consensus pattern (8 bp):
AAATAAAA
Found at i:957691 original size:18 final size:17
Alignment explanation
Indices: 957657--957775 Score: 61
Period size: 18 Copynumber: 6.9 Consensus size: 17
957647 AAAAAGTTAG
*
957657 AAATAAAAAAGGT-AAAT
1 AAATAAAAAA-ATAAAAT
957674 CAAATAAAAAAATAAAAT
1 -AAATAAAAAAATAAAAT
957692 AAA-AAAAAAA-AAAA-
1 AAATAAAAAAATAAAAT
*
957706 ACAA-CAAAAAATAACAA-
1 A-AATAAAAAAATAA-AAT
* *
957723 AAGTAAAAAAATACAAAGA
1 AAATAAAAAAATA-AAA-T
* *
957742 AAATAATAAAATAGAAAA
1 AAATAAAAAAATA-AAAT
**
957760 AAAGGAAAAAATAAAA
1 AAATAAAAAAATAAAA
957776 ATCATTAAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 17
0.75 0.09 0.15
Matches are distributed among these distances:
14 1 0.01
15 12 0.14
16 10 0.12
17 20 0.24
18 26 0.31
19 14 0.17
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.11
Consensus pattern (17 bp):
AAATAAAAAAATAAAAT
Found at i:957730 original size:29 final size:26
Alignment explanation
Indices: 957682--957776 Score: 86
Period size: 26 Copynumber: 3.5 Consensus size: 26
957672 ATCAAATAAA
957682 AAAATAAAATAAAAAA-AAAAAAAAAC
1 AAAA-AAAATAAAAAATAAAAAAAAAC
*
957708 AACAAAAAATAACAAAAGTAAAAAAATAC
1 AA-AAAAAATAA-AAAA-TAAAAAAAAAC
* *
957737 AAAGAAAATAATAAAATAGAAAAAAA-
1 AAAAAAAATAA-AAAATAAAAAAAAAC
**
957763 GGAAAAAATAAAAA
1 AAAAAAAATAAAAA
957777 TCATTAAAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
25 3 0.05
26 17 0.30
27 14 0.25
28 12 0.21
29 11 0.19
ACGTcount: A:0.81, C:0.04, G:0.05, T:0.09
Consensus pattern (26 bp):
AAAAAAAATAAAAAATAAAAAAAAAC
Found at i:957878 original size:13 final size:13
Alignment explanation
Indices: 957852--957894 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
957842 GATATGAAAG
*
957852 AATAAAAAAGAATA
1 AATAAAATA-AATA
957866 AATAAAATAAATA
1 AATAAAATAAATA
*
957879 AATAAATTAAAATA
1 AATAAAAT-AAATA
957893 AA
1 AA
957895 ACTTAGAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (13 bp):
AATAAAATAAATA
Found at i:959006 original size:4 final size:4
Alignment explanation
Indices: 958997--959023 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
958987 AAAATAACTA
958997 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
959024 ATATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:959037 original size:13 final size:13
Alignment explanation
Indices: 959021--959046 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
959011 ATAAATAAAT
959021 AAAATATTTTTTA
1 AAAATATTTTTTA
959034 AAAATATTTTTTA
1 AAAATATTTTTTA
959047 TATATGATTT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAATATTTTTTA
Found at i:959156 original size:37 final size:36
Alignment explanation
Indices: 959114--959411 Score: 187
Period size: 36 Copynumber: 8.2 Consensus size: 36
959104 ATTTTAAAAC
*
959114 TATATATATTTTCAAACATGTTTTTAAAAAACTGTATAA
1 TATATATATTTTCAAA-ATGTTTTT-AAAAACTATAT-A
*
959153 TATATAATTATTTTCAAAAT-ATTTTAAAAACTATATA
1 TATAT-A-TATTTTCAAAATGTTTTTAAAAACTATATA
* *
959190 T-TATATAAGTTTTCAAAATGTTTTAAAAAATTATATA
1 TATATAT-A-TTTTCAAAATGTTTTTAAAAACTATATA
*
959227 TTATATATATTTTCAAAATGATTTTTAATAAC--TATA
1 -TATATATATTTTCAAAATG-TTTTTAAAAACTATATA
* *
959263 TA-ATATA---T--AAATG-TTTTCAAAACTGTATA
1 TATATATATTTTCAAAATGTTTTTAAAAACTATATA
*** * **
959292 TTATATAT-TTCAAAAATGT-TTTCAAA-AACTATATA
1 -TATATATATTTTCAAA-ATGTTTTTAAAAACTATATA
*
959327 TTATATTTATTTTCAAAATG-TTTTAAAAACTATATAA
1 -TATATATATTTTCAAAATGTTTTTAAAAACTATAT-A
* *
959364 TATATAAATGTTTTCAAACATG-TTTTCAAAACTATATTA
1 TATAT--ATATTTTCAAA-ATGTTTTTAAAAACTATA-TA
959403 TATATATAT
1 TATATATAT
959412 ATATATATAT
Statistics
Matches: 205, Mismatches: 27, Indels: 56
0.71 0.09 0.19
Matches are distributed among these distances:
27 8 0.04
29 9 0.04
30 2 0.01
31 5 0.02
34 6 0.03
35 26 0.13
36 39 0.19
37 31 0.15
38 29 0.14
39 36 0.18
40 4 0.02
41 10 0.05
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (36 bp):
TATATATATTTTCAAAATGTTTTTAAAAACTATATA
Found at i:959195 original size:38 final size:39
Alignment explanation
Indices: 959114--959284 Score: 192
Period size: 38 Copynumber: 4.5 Consensus size: 39
959104 ATTTTAAAAC
* *
959114 TATAT-ATATTTTCAAACATGTTTTTAAAAAACTGTATAA
1 TATATAATATTTTCAAA-ATGATTTTAAAAAACTATATAA
*
959153 TATATAATTATTTTCAAAAT-ATTTT-AAAAACTATATAT
1 TATATAA-TATTTTCAAAATGATTTTAAAAAACTATATAA
* * *
959191 TATATAA-GTTTTCAAAATG-TTTTAAAAAATTATATAT
1 TATATAATATTTTCAAAATGATTTTAAAAAACTATATAA
* *
959228 TATAT-ATATTTTCAAAATGATTTTTAATAACTATATAA
1 TATATAATATTTTCAAAATGATTTTAAAAAACTATATAA
*
959266 TATATAAATGTTTTCAAAA
1 TATAT-AATATTTTCAAAA
959285 CTGTATATTA
Statistics
Matches: 113, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
36 15 0.13
37 28 0.25
38 37 0.33
39 9 0.08
40 14 0.12
41 10 0.09
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (39 bp):
TATATAATATTTTCAAAATGATTTTAAAAAACTATATAA
Found at i:959218 original size:75 final size:76
Alignment explanation
Indices: 959114--959284 Score: 215
Period size: 75 Copynumber: 2.2 Consensus size: 76
959104 ATTTTAAAAC
*
959114 TATATATA-TTTTCAAACATGTTTTTAAAAAACTGTATAATATATAATTATTTTCAAAAT-A-TT
1 TATATA-AGTTTTCAAA-ATGTTTTTAAAAAACTATATAATATAT-A-TATTTTCAAAATGATTT
*
959176 TTAAAAACTATATAT
62 TTAAAAACTATATAA
* *
959191 TATATAAGTTTTCAAAATG-TTTTAAAAAATTATATATTATATATATTTTCAAAATGATTTTTAA
1 TATATAAGTTTTCAAAATGTTTTTAAAAAACTATATAATATATATATTTTCAAAATGATTTTTAA
*
959255 TAACTATATAA
66 AAACTATATAA
959266 TATATAAATGTTTTCAAAA
1 TATAT-AA-GTTTTCAAAA
959285 CTGTATATTA
Statistics
Matches: 84, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
73 12 0.14
74 2 0.02
75 40 0.48
76 6 0.07
77 24 0.29
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (76 bp):
TATATAAGTTTTCAAAATGTTTTTAAAAAACTATATAATATATATATTTTCAAAATGATTTTTAA
AAACTATATAA
Found at i:959274 original size:29 final size:27
Alignment explanation
Indices: 959242--959298 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
959232 TATATTTTCA
*
959242 AAATGATTTTTAATAACTATATAATATAT
1 AAATG-TTTTCAA-AACTATATAATATAT
* *
959271 AAATGTTTTCAAAACTGTATATTATAT
1 AAATGTTTTCAAAACTATATAATATAT
959298 A
1 A
959299 TTTCAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 14 0.56
28 6 0.24
29 5 0.20
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (27 bp):
AAATGTTTTCAAAACTATATAATATAT
Found at i:959297 original size:34 final size:35
Alignment explanation
Indices: 959168--959369 Score: 133
Period size: 37 Copynumber: 5.9 Consensus size: 35
959158 AATTATTTTC
* *
959168 AAAATATTTT-AAAAACTATATATTATATAAGTTTTC-
1 AAAATGTTTTCAAAAACTATATATTATAT-A--TATCA
* *
959204 AAAATGTTTTAAAAAATTATATATTATATATATTTTC-
1 AAAATGTTTTCAAAAACTATATATTATATATA---TCA
* *
959241 AAAATGATTTTTAATAAC--TATA-TA-ATATAT--
1 AAAATG-TTTTCAAAAACTATATATTATATATATCA
* *
959271 -AAATGTTTTC-AAAACTGTATATTATATATTTCA
1 AAAATGTTTTCAAAAACTATATATTATATATATCA
*
959304 AAAATGTTTTCAAAAACTATATATTATATTTATTTTC-
1 AAAATGTTTTCAAAAACTATATATTATA--TA-TATCA
*
959341 AAAATGTTTT-AAAAACTATATAATATATA
1 AAAATGTTTTCAAAAACTATATATTATATA
959370 AATGTTTTCA
Statistics
Matches: 139, Mismatches: 11, Indels: 34
0.76 0.06 0.18
Matches are distributed among these distances:
27 4 0.03
28 4 0.03
29 9 0.06
30 2 0.01
31 6 0.04
34 18 0.13
35 17 0.12
36 30 0.22
37 37 0.27
38 12 0.09
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.45
Consensus pattern (35 bp):
AAAATGTTTTCAAAAACTATATATTATATATATCA
Found at i:959327 original size:100 final size:99
Alignment explanation
Indices: 959169--959381 Score: 313
Period size: 100 Copynumber: 2.1 Consensus size: 99
959159 ATTATTTTCA
* * *
959169 AAATATTTTAAAAACTATATATTATATAAGTTTTCAAAATGTTTTAAAAAATTATATATTATATA
1 AAATGTTTTCAAAACTATATATTATATAAG-TTTCAAAATGTTTTAAAAAACTATATATTATATA
*
959234 TATTTTCAAAATGATTTTTAATAACTATATAATATAT
65 TATTTTCAAAATG--TTTTAAAAACTATATAATATAT
* * *
959271 AAATGTTTTCAAAACTGTATATTATAT-A-TTTCAAAAATGTTTTCAAAAACTATATATTATATT
1 AAATGTTTTCAAAACTATATATTATATAAGTTTC-AAAATGTTTTAAAAAACTATATATTATATA
959334 TATTTTCAAAATGTTTTAAAAACTATATAATATAT
65 TATTTTCAAAATGTTTTAAAAACTATATAATATAT
959369 AAATGTTTTCAAA
1 AAATGTTTTCAAA
959382 CATGTTTTCA
Statistics
Matches: 103, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
98 34 0.33
99 4 0.04
100 40 0.39
101 1 0.01
102 24 0.23
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (99 bp):
AAATGTTTTCAAAACTATATATTATATAAGTTTCAAAATGTTTTAAAAAACTATATATTATATAT
ATTTTCAAAATGTTTTAAAAACTATATAATATAT
Found at i:959347 original size:137 final size:140
Alignment explanation
Indices: 959141--959408 Score: 356
Period size: 137 Copynumber: 1.9 Consensus size: 140
959131 ATGTTTTTAA
959141 AAAACTGTATAATATATAATTATTTTCAAAATATTTTAAAAACTATATATTATATAAGTTTTCAA
1 AAAACTGTATAATATATAATTATTTTCAAAATATTTTAAAAACTATATATTATATAAGTTTTCAA
* * *
959206 AATGTTTTAAAAAAT-TAT-ATATTATATATATTTTCAAA-ATGATTTTTAATAACTATATAATA
66 AATGTTTTAAAAACTATATAATA-TATAAATATTTTCAAACATG-TTTTCAA-AACTATATAATA
959268 TATAAATGTTTTC
128 TATAAATGTTTTC
* *
959281 AAAACTGTAT-AT-TAT-A-TA-TTTCAAAAATGTTTTCAAAAACTATATATTATATTTA-TTTT
1 AAAACTGTATAATATATAATTATTTTC-AAAATATTTT-AAAAACTATATATTATA-TAAGTTTT
* *
959340 CAAAATGTTTTAAAAACTATATAATATATAAATGTTTTCAAACATGTTTTCAAAACTATATTATA
63 CAAAATGTTTTAAAAACTATATAATATATAAATATTTTCAAACATGTTTTCAAAACTATATAATA
959405 TATA
128 TATA
959409 TATATATATA
Statistics
Matches: 115, Mismatches: 7, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
135 4 0.03
136 11 0.10
137 54 0.47
138 28 0.24
139 8 0.07
140 10 0.09
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (140 bp):
AAAACTGTATAATATATAATTATTTTCAAAATATTTTAAAAACTATATATTATATAAGTTTTCAA
AATGTTTTAAAAACTATATAATATATAAATATTTTCAAACATGTTTTCAAAACTATATAATATAT
AAATGTTTTC
Found at i:959395 original size:39 final size:37
Alignment explanation
Indices: 959271--959413 Score: 152
Period size: 39 Copynumber: 3.9 Consensus size: 37
959261 TATAATATAT
*
959271 AAATGTTTTCAAAACTGTATAT-TAT--ATA-TTTCAA
1 AAATGTTTTCAAAACTATATATATATAAATATTTTC-A
**
959305 AAATGTTTTCAAAAACTATATAT-TATATTTATTTTCA
1 AAATGTTTTC-AAAACTATATATATATAAATATTTTCA
* *
959342 AAATGTTTTAAAAACTATATAATATATAAATGTTTTCA
1 AAATGTTTTCAAAACTATAT-ATATATAAATATTTTCA
*
959380 AACATGTTTTCAAAACTATATTATATATATATAT
1 AA-ATGTTTTCAAAACTATA-TATATATAAATAT
959414 ATATATATAT
Statistics
Matches: 92, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
34 10 0.11
35 14 0.15
36 10 0.11
37 14 0.15
38 17 0.18
39 26 0.28
40 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (37 bp):
AAATGTTTTCAAAACTATATATATATAAATATTTTCA
Found at i:959408 original size:2 final size:2
Alignment explanation
Indices: 959396--959425 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
959386 TTTTCAAAAC
959396 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
959426 TCAAAAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:961466 original size:13 final size:13
Alignment explanation
Indices: 961440--961478 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
961430 TATATGAAAG
961440 AAAA-AATATAAA
1 AAAATAATATAAA
*
961452 AAAATAAT-TTAA
1 AAAATAATATAAA
961464 AAAATAATATAAA
1 AAAATAATATAAA
961477 AA
1 AA
961479 TATTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 15 0.65
13 8 0.35
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAATAATATAAA
Found at i:963753 original size:57 final size:57
Alignment explanation
Indices: 963687--963798 Score: 224
Period size: 57 Copynumber: 2.0 Consensus size: 57
963677 GTTTTGGCTC
963687 CCCGAGTCAAATCCGTTGTCATTTTCCCCAAAAATTACTTCGATGATCACAAATCCT
1 CCCGAGTCAAATCCGTTGTCATTTTCCCCAAAAATTACTTCGATGATCACAAATCCT
963744 CCCGAGTCAAATCCGTTGTCATTTTCCCCAAAAATTACTTCGATGATCACAAATC
1 CCCGAGTCAAATCCGTTGTCATTTTCCCCAAAAATTACTTCGATGATCACAAATC
963799 TACAAAAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.30, C:0.29, G:0.11, T:0.29
Consensus pattern (57 bp):
CCCGAGTCAAATCCGTTGTCATTTTCCCCAAAAATTACTTCGATGATCACAAATCCT
Found at i:966319 original size:7 final size:7
Alignment explanation
Indices: 966307--966331 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
966297 GTCTAGCGGG
966307 TTTTATA
1 TTTTATA
966314 TTTTATA
1 TTTTATA
966321 TTTTATA
1 TTTTATA
966328 TTTT
1 TTTT
966332 CAACTGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTATA
Found at i:969443 original size:140 final size:143
Alignment explanation
Indices: 969290--969657 Score: 417
Period size: 140 Copynumber: 2.6 Consensus size: 143
969280 TATGTATAAA
* * *
969290 ATATTTATTTATTT-AGAAATATCAGAAAAGGGCTTTTAGGTGCTTTAAGACAGCTCTTTTCTTG
1 ATATTTATTTATTTAAG-AATATCAGAAAAGGACTTATAGGTGTTTTAAGACAGCTCTTTTCTTG
* *
969354 ATATTAATAAATAAATAA-CTAAAAAAACATTTTTTTTAAAAAAATAATT-AATATA-TAAT-T-
65 ATATTAATAAATAAATAAGCTAAAAAAACA-TTTATCT--AAAAATAATTAAATATATTAATATA
969414 T-ATAAAAAAAAACAGG
127 TGATAAAAAAAAACAGG
* * * * *
969430 ATATTTATTTATTTAAGAATATCAGAAAAGAACTTCTAGTTGTTTTAAGACAGCTCCTTTCTTAA
1 ATATTTATTTATTTAAGAATATCAGAAAAGGACTTATAGGTGTTTTAAGACAGCTCTTTTCTTGA
* *
969495 TATTAATAAATAAATAAATGTTAATAAAACATTTATCTAAAAATAATTAAAATATATTAATATAT
66 TATTAATAAATAAAT-AA-GCTAAAAAAACATTTATCTAAAAATAATT-AAATATATTAATATAT
** * *
969560 GATTTATAAAAATAGG
128 GATAAAAAAAAACAGG
* * * * *
969576 ACATTTATTTATTTAATATTATCAGAAAAGGACTTAGAGGTATTTTAAGACAGCTCTTTTCTTAG
1 ATATTTATTTATTTAAGAATATCAGAAAAGGACTTATAGGTGTTTTAAGACAGCTCTTTTCTT-G
*
969641 ATATTAAAAAATAAATA
65 ATATTAATAAATAAATA
969658 CATATCAAAA
Statistics
Matches: 191, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
140 80 0.42
141 4 0.02
142 11 0.06
143 13 0.07
144 1 0.01
145 1 0.01
146 66 0.35
147 15 0.08
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.38
Consensus pattern (143 bp):
ATATTTATTTATTTAAGAATATCAGAAAAGGACTTATAGGTGTTTTAAGACAGCTCTTTTCTTGA
TATTAATAAATAAATAAGCTAAAAAAACATTTATCTAAAAATAATTAAATATATTAATATATGAT
AAAAAAAAACAGG
Found at i:971189 original size:3 final size:3
Alignment explanation
Indices: 971170--971233 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
971160 TTTGTCATAT
*
971170 TAA TAAA TAA TATA TAA TAA TAA T-A TAA TAA TAA TAC TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
971216 TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
971234 ATTTAAATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 44 0.85
4 6 0.12
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:971195 original size:11 final size:11
Alignment explanation
Indices: 971170--971217 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
971160 TTTGTCATAT
971170 TAATA-AATAA
1 TAATATAATAA
971180 T-ATATAATAA
1 TAATATAATAA
971190 TAATATAATAA
1 TAATATAATAA
971201 TAATACTAATAA
1 TAATA-TAATAA
971213 TAATA
1 TAATA
971218 ATTTTAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
9 3 0.09
10 7 0.20
11 14 0.40
12 11 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATATAATAA
Found at i:971865 original size:74 final size:76
Alignment explanation
Indices: 971403--972217 Score: 1433
Period size: 76 Copynumber: 10.9 Consensus size: 76
971393 CCGAAGGTTT
971403 TTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCA-TGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
*
971466 GACCCGAAGG-
66 GACCCTAAGGC
*
971476 TTTGAAAACGTCAAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
1 TTTGAAAACATC-AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
971541 TGACCCTAAGGC
65 TGACCCTAAGGC
*
971553 TTTGAAAACATCAAAAATCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
971618 GACCCTAAGGC
66 GACCCTAAGGC
*
971629 TTTGAAAACATCAAAAAGCTCCCGAACGCTTTTTGGAAACA-CATGCACTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
971693 GACCCTAAGGC
66 GACCCTAAGGC
971704 TTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
1 TTTG-AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
971769 TGACCCTAAGGC
65 TGACCCTAAGGC
*
971781 TTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCA-GCACTGTAGGACTTACAAAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
971844 GACCCTAAGGC
66 GACCCTAAGGC
971855 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGG-CTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
971919 GA-CCTAAGGC
66 GACCCTAAGGC
*
971929 -TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGTCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
971993 GACCCTAAGGC
66 GACCCTAAGGC
972004 TTTGAAAACATCAAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGTAGGACTTACAGA
1 TTTGAAAACATC-AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
972068 TGA-CCTAAGG-
65 TGACCCTAAGGC
*
972078 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAAAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
972143 GA-CCTAAGGC
66 GACCCTAAGGC
*
972153 TTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCACGCACTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
972217 G
66 G
972218 TGAGAAATAG
Statistics
Matches: 715, Mismatches: 13, Indels: 27
0.95 0.02 0.04
Matches are distributed among these distances:
73 82 0.11
74 184 0.26
75 138 0.19
76 245 0.34
77 66 0.09
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
GACCCTAAGGC
Found at i:972668 original size:22 final size:22
Alignment explanation
Indices: 972634--972685 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
972624 CATAAAGCTT
* *
972634 TCATTTTTGAAAAGAGAATATA
1 TCATCTTTAAAAAGAGAATATA
*
972656 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATATA
972678 TCATCTTT
1 TCATCTTT
972686 GAAGAGTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATATA
Found at i:975440 original size:115 final size:114
Alignment explanation
Indices: 975231--975566 Score: 495
Period size: 115 Copynumber: 3.0 Consensus size: 114
975221 GATCATGCAG
* * * * *
975231 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACC-AATCAGATCAGATAACTCAAAGA
*
975296 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAAA
65 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAAA
*
975346 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACC-AATCAGATCAGATAACTCAAAGA
* *
975411 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGC-AAA
65 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAAA
* *
975460 TTCATCTTTAAAATCCAATGATTGGTTTTTGGGGTTCATA-C---CAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATT-GATTTTGGGGTTCATACCAATCAGATCAGATAACTCAAAGA
*
975521 A-ACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
65 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
975567 CATGGCACTT
Statistics
Matches: 203, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
109 41 0.20
110 21 0.10
114 26 0.13
115 115 0.57
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAATCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAAA
Found at i:976441 original size:43 final size:43
Alignment explanation
Indices: 976392--976477 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
976382 CTATATAAAA
976392 GGCCTATAAGGGTAGATTCTGTTCCAATGTCTTATTCTGTGCC
1 GGCCTATAAGGGTAGATTCTGTTCCAATGTCTTATTCTGTGCC
976435 GGCCTATAAGGGTAGATTCTGTTCCAATGTCTTATTCTGTGCC
1 GGCCTATAAGGGTAGATTCTGTTCCAATGTCTTATTCTGTGCC
976478 ATAAGTCCTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (43 bp):
GGCCTATAAGGGTAGATTCTGTTCCAATGTCTTATTCTGTGCC
Found at i:977613 original size:15 final size:16
Alignment explanation
Indices: 977595--977624 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
977585 TCGATTTTCC
977595 TTTTCTTC-TTCTTTT
1 TTTTCTTCTTTCTTTT
977610 TTTTCTTCTTTCTTT
1 TTTTCTTCTTTCTTT
977625 GTTGGATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTCTTCTTTCTTTT
Found at i:978371 original size:19 final size:19
Alignment explanation
Indices: 978347--978390 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
978337 AAAGAACATT
978347 TAATCTACTTGATACTCAA
1 TAATCTACTTGATACTCAA
978366 TAATCTACTTGATACTCAA
1 TAATCTACTTGATACTCAA
978385 TAATCT
1 TAATCT
978391 CAAGATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (19 bp):
TAATCTACTTGATACTCAA
Found at i:982115 original size:15 final size:15
Alignment explanation
Indices: 982083--982149 Score: 57
Period size: 15 Copynumber: 4.3 Consensus size: 15
982073 TGAATATAAT
* *
982083 AAATAAATAAAATAAA
1 AAAT-AATAATATTAA
982099 AAATAATAATATTAA
1 AAATAATAATATTAA
*
982114 AAATAATAAGTAATGAA
1 AAATAATAA-T-ATTAA
982131 AAATTAA-AA-ATTAA
1 AAA-TAATAATATTAA
982145 AAATA
1 AAATA
982150 TGAATTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
13 2 0.05
14 7 0.16
15 18 0.41
16 5 0.11
17 9 0.20
18 3 0.07
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (15 bp):
AAATAATAATATTAA
Found at i:982118 original size:31 final size:32
Alignment explanation
Indices: 982075--982149 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 32
982065 TTAATTCTTG
982075 AATA-TAATAAATAAATAA-AAT-AAAAAATAA
1 AATATTAA-AAATAAATAAGAATGAAAAAATAA
*
982105 TAATATTAAAAAT-AATAAGTAATGAAAAATTAA
1 -AATATTAAAAATAAATAAG-AATGAAAAAATAA
982138 AA-ATTAAAAATA
1 AATATTAAAAATA
982150 TGAATTTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
30 5 0.13
31 17 0.45
32 8 0.21
33 8 0.21
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.27
Consensus pattern (32 bp):
AATATTAAAAATAAATAAGAATGAAAAAATAA
Found at i:982133 original size:18 final size:15
Alignment explanation
Indices: 982075--982122 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
982065 TTAATTCTTG
*
982075 AATATAATAAATAAAT
1 AATATAAAAAAT-AAT
*
982091 AAAATAAAAAATAAT
1 AATATAAAAAATAAT
*
982106 AATATTAAAAATAAT
1 AATATAAAAAATAAT
982121 AA
1 AA
982123 GTAATGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 18 0.64
16 10 0.36
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATATAAAAAATAAT
Found at i:984476 original size:3 final size:3
Alignment explanation
Indices: 984457--984525 Score: 84
Period size: 3 Copynumber: 22.3 Consensus size: 3
984447 TTGTAATATT
* *
984457 TAA TAAA TAA TATA TAA TAA TAA TTA TAA TAA TAA TAC TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
984504 TAA TTT TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
984526 TTTAAATGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 50 0.89
4 6 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:985084 original size:157 final size:157
Alignment explanation
Indices: 984798--985112 Score: 630
Period size: 157 Copynumber: 2.0 Consensus size: 157
984788 TTATGCACTG
984798 AAAGGTATAAGCATTACACAAATCCTTTACAAAAAAATGTATTAGGAAAAGGAACATTTTTTTTA
1 AAAGGTATAAGCATTACACAAATCCTTTACAAAAAAATGTATTAGGAAAAGGAACATTTTTTTTA
984863 AGTTTGATCTAGTAAAGTTTTATAACTAGCACTATGAACCAACATCTTTAACCGCATCGATAGTG
66 AGTTTGATCTAGTAAAGTTTTATAACTAGCACTATGAACCAACATCTTTAACCGCATCGATAGTG
984928 AATTGTAGTATTTAATAAAATGAAATC
131 AATTGTAGTATTTAATAAAATGAAATC
984955 AAAGGTATAAGCATTACACAAATCCTTTACAAAAAAATGTATTAGGAAAAGGAACATTTTTTTTA
1 AAAGGTATAAGCATTACACAAATCCTTTACAAAAAAATGTATTAGGAAAAGGAACATTTTTTTTA
985020 AGTTTGATCTAGTAAAGTTTTATAACTAGCACTATGAACCAACATCTTTAACCGCATCGATAGTG
66 AGTTTGATCTAGTAAAGTTTTATAACTAGCACTATGAACCAACATCTTTAACCGCATCGATAGTG
985085 AATTGTAGTATTTAATAAAATGAAATC
131 AATTGTAGTATTTAATAAAATGAAATC
985112 A
1 A
985113 TTGGCTTATG
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 158 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (157 bp):
AAAGGTATAAGCATTACACAAATCCTTTACAAAAAAATGTATTAGGAAAAGGAACATTTTTTTTA
AGTTTGATCTAGTAAAGTTTTATAACTAGCACTATGAACCAACATCTTTAACCGCATCGATAGTG
AATTGTAGTATTTAATAAAATGAAATC
Found at i:987248 original size:17 final size:17
Alignment explanation
Indices: 987223--987279 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
987213 GTATGGTGTT
*
987223 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
987240 CATTTAAGCATGCATTG
1 CATTTAAGCATGCATTG
* * *
987257 CATTTAAACATGTATTT
1 CATTTAAGCATGCATTG
987274 CATTTA
1 CATTTA
987280 GGGAAGTAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:987306 original size:17 final size:17
Alignment explanation
Indices: 987286--987344 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
987276 TTTAGGGAAG
987286 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
987303 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
987319 TAATTCATTCATGCATT
1 TAGTTCATTTATGCATC
987336 TAGTTCATT
1 TAGTTCATT
987345 GAATAATGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:992501 original size:22 final size:23
Alignment explanation
Indices: 992455--992497 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
992445 TTTTCCCACT
*
992455 TTTTCTATTTATTTATTTATTTA
1 TTTTCTATTTATTTATATATTTA
992478 TTTTC-ATTTATTT-TATATTT
1 TTTTCTATTTATTTATATATTT
992498 TATTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTCTATTTATTTATATATTTA
Found at i:992508 original size:17 final size:17
Alignment explanation
Indices: 992462--992546 Score: 50
Period size: 17 Copynumber: 4.8 Consensus size: 17
992452 ACTTTTTCTA
992462 TTTATTTATTTATTTAT-T
1 TTTA-TTATTT-TTTATAT
* *
992480 TTCATT-TATTTTATAT
1 TTTATTATTTTTTATAT
*
992496 TTTATTATTTTTT-TGT
1 TTTATTATTTTTTATAT
*
992512 TAGTATTATTATTTCTATTAT
1 T-TTATTATT-TTT-TA-TAT
992533 TTTATTATTATTTT
1 TTTATTATT-TTTT
992547 CTCTCAAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
15 5 0.10
16 11 0.21
17 14 0.27
18 6 0.12
19 2 0.04
20 11 0.21
21 3 0.06
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTATTATTTTTTATAT
Found at i:992532 original size:9 final size:8
Alignment explanation
Indices: 992470--992541 Score: 55
Period size: 8 Copynumber: 9.1 Consensus size: 8
992460 TATTTATTTA
992470 TTTATTTAT
1 TTTA-TTAT
992479 TTTCATTTAT
1 TTT-A-TTAT
992489 TTTA-TAT
1 TTTATTAT
992496 TTTATTAT
1 TTTATTAT
992504 TTT-TT-T
1 TTTATTAT
* *
992510 GTTAGTA-
1 TTTATTAT
992517 -TTATTAT
1 TTTATTAT
992524 TTCTATTAT
1 TT-TATTAT
992533 TTTATTAT
1 TTTATTAT
992541 T
1 T
992542 ATTTTCTCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
6 8 0.15
7 10 0.19
8 14 0.26
9 12 0.23
10 9 0.17
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (8 bp):
TTTATTAT
Found at i:996130 original size:21 final size:21
Alignment explanation
Indices: 996104--996148 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
996094 GATTTCTGGG
*
996104 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
996125 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
996146 CAA
1 CAA
996149 ACGAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:996612 original size:20 final size:22
Alignment explanation
Indices: 996572--996628 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
996562 TGAATGTGTG
*
996572 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
996594 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
996614 ATATGAATATG-TGAT
1 ATATG-ATATGATGAT
996629 TATGAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:997194 original size:31 final size:31
Alignment explanation
Indices: 997156--997342 Score: 340
Period size: 31 Copynumber: 6.0 Consensus size: 31
997146 AGGGTCGAGG
997156 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
997187 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
997218 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
997249 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
997280 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
997311 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
997342 G
1 G
997343 GTCCTTCGGG
Statistics
Matches: 153, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
31 152 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1000385 original size:21 final size:21
Alignment explanation
Indices: 1000359--1000403 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1000349 GATTTCTGGG
* *
1000359 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1000380 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1000401 CAA
1 CAA
1000404 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1000871 original size:20 final size:22
Alignment explanation
Indices: 1000831--1000887 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
1000821 TGAATGTGTG
*
1000831 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
1000853 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
1000873 ATATGAATATG-TGAT
1 ATATG-ATATGATGAT
1000888 TATGAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:1001455 original size:31 final size:31
Alignment explanation
Indices: 1001417--1001572 Score: 278
Period size: 31 Copynumber: 5.0 Consensus size: 31
1001407 AGGGTCGAGG
1001417 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1001448 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1001479 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1001510 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1001541 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1001572 G
1 G
1001573 GTCCTTCGGG
Statistics
Matches: 122, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 121 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1003655 original size:165 final size:164
Alignment explanation
Indices: 1003243--1004646 Score: 1225
Period size: 165 Copynumber: 8.5 Consensus size: 164
1003233 TTTTAAAGAA
* * * *
1003243 ATCATTTGCAGCATAACTCAATGATAGAAGGGCTATCTGCCACCAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
* * * *
1003308 ACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTCAAGACTAG-AGGGTTATCTGCCACCAA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCT---ACC-A
* * * * *
1003372 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAT
127 AAGACCCTCGAGTTCGACTACACTCAGTTCGAAGGCAC
* * ** * * *
1003410 ATCATTTGCAGTATAACTTAACTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTTGAGTTCGAC
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAAGACCTTCGAGTTCGAC
* *
1003474 TACGCTCAGTTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAG
65 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTACCAAAG
* * * * *
1003539 ACCCTCGAGTTTGATTATACTCAGTTTCGAGGGAAC
130 ACCCTCGAGTTCGACTACACTCAG-TTCGAAGGCAC
* * * * *
1003575 ATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTATCACCAAAAGACTTTCGAGTTCGATT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
* * * *
1003640 ACGCTCAGCTCCAAGGCACATAATTTGCAACATAACTTAAGTTGAGAAGGGTTATCTGCCAACCA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCT----ACCA
* * * * *
1003705 AAGACCTTTGAGTTTGACTACGCTCAGTTCCAAGGCAC
127 AAGACCCTCGAGTTCGACTACACTCAGTTCGAAGGCAC
* * * * * * * * *
1003743 ATCATTTGCAGCATAGCTTAAGTCGAGAAAGGCTATC--T-ATC-AAAGACCCTCGAGTTCGATT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
** * * * * * * *
1003804 ATACTCAGTTTCAAGGGCACATCATTTACAGTATAAG-TCAAGGCTAGAAGGGTTATCTGTCACC
66 ACGCTCAGCTCCAA-GGCACATCATTTGCAGCAT-AGCTTAAGTCGAGAAGGGTTATC--T-ACC
* * * *
1003868 GAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCAC
126 -AAAGACCCTCGAGTTCGACTACACTCAGTTCGAAGGCAC
* * * * * * *
1003908 ATAATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAA-ACCTTTGAGTTCGAC
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAAGACCTTCGAGTTCGAC
* * *
1003972 TACGCTCAGCTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
65 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTACCAAAG
* * * *
1004037 ACCCTGGATTTCGATTACACTCAGCTTCGAGGGCAC
130 ACCCTCGAGTTCGACTACACTCAG-TTCGAAGGCAC
** * * *
1004073 ATCATTTATAGTATAACTCAAGGCTAGAATGGTTATCTGTCACCAAAAGACCTTCGTGTTCGACT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
* * * * *
1004138 ACGCTCAGCTCGAAGGTACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATTTACCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTACCAAAGA
* *
1004203 CCCTCGAGTTCGATTACACTCAGTTTCGAGGGCAC
131 CCCTCGAGTTCGACTACACTCAG-TTCGAAGGCAC
* * *
1004238 ATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAACACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
* *
1004303 ACGCTCAACTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCT----ACCA
* * * * * *
1004368 AAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGACAC
127 AAGACCCTCGAGTTCGACTACACTCAGTTCGAAGGCAC
* ** * * * * * * **
1004406 ATCATTTGTAGCATTGCTTAAGTCGAGAAGGGATATCTG---CC-AAATACCCTCGAGTTCGTTT
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
* * * * * * * * *
1004467 ACACTAAGCTTCGAGGGCACATCATTTACACCATAACTTAAGGCTAGAAGGGTTATCTGTCACCA
66 ACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATC--T-ACC-
* * * *
1004532 AAATACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCAC
126 AAAGACCCTCGAGTTCGACTACACTCAGTTCGAAGGCAC
* * * * * * * * *
1004571 GTCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTAT-TTTCCAACC-GAAGACCTTCGAGTTCGA
1 ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGT-C-ACCAAAAGACCTTCGAGTTCGA
* *
1004634 TTACACTCAGCTC
64 CTACGCTCAGCTC
1004647 ATAGACAATC
Statistics
Matches: 1014, Mismatches: 189, Indels: 67
0.80 0.15 0.05
Matches are distributed among these distances:
164 113 0.11
165 573 0.57
166 3 0.00
167 98 0.10
168 120 0.12
169 104 0.10
170 3 0.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (164 bp):
ATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTACCAAAGA
CCCTCGAGTTCGACTACACTCAGTTCGAAGGCAC
Found at i:1003689 original size:249 final size:249
Alignment explanation
Indices: 1003243--1004448 Score: 1462
Period size: 249 Copynumber: 4.8 Consensus size: 249
1003233 TTTTAAAGAA
* * *
1003243 ATCATTTGCAGCATAACTCAA-T-GATAGAAGGGCTATCTGCCACCAAAAGACCTTCGAGTTCGA
1 ATCATTTGCAGCATAGCTTAAGTCG--AGAAGGGCTATCT---ACC-AAAGACCCTCGAGTTCGA
* * * * * * * * * *
1003306 CTACGCTCAG-CTCCAAGGCATATCATTTGCAGCATAGCTCAAGACTAG-AGGGTTATCTGCCAC
60 TTACACTCAGTTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAC
* * *
1003369 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTAACTC
125 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
1003434 GAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGTTCCAAGGCAC
190 GAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGTTCCAAGGCAC
* *
1003494 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCCTCGAGTTTGATTATAC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCCTCGAGTTCGATTACAC
* * *
1003559 TCAGTTTCGAGGGAACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTATCACCAAAAG
66 TCAGTTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAG
* * * * *
1003624 ACTTTCGAGTTCGATTACGCTCAGCTCCAAGGCACATAATTTGCAACATAACTTAAGTTGAGAAG
131 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAG
*
1003689 GGTTATCTGCCAACCAAAGACCTTTGAGTTTGACTACGCTCAGTTCCAAGGCAC
196 GGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGTTCCAAGGCAC
* * *
1003743 ATCATTTGCAGCATAGCTTAAGTCGAGAAAGGCTATCTATCAAAGACCCTCGAGTTCGATTATAC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCCTCGAGTTCGATTACAC
* * * *
1003808 TCAGTTTCAAGGGCACATCATTTACAGTATAAGTCAAGGCTAGAAGGGTTATCTGTCACCGAAAG
66 TCAGTTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAG
* * *
1003873 ACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATAATTTGCAACATAACTTAAGTCGAGAAG
131 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAG
* *
1003938 GGTTATCTGCCAACCAAAAACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
196 GGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGTTCCAAGGCAC
* * * *
1003992 ATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTGGATTTCGATTACAC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCCTCGAGTTCGATTACAC
* * * *
1004057 TCAGCTTCGAGGGCACATCATTTATAGTATAACTCAAGGCTAGAATGGTTATCTGTCACCAAAAG
66 TCAGTTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAG
* * * * *
1004122 ACCTTCGTGTTCGACTACGCTCAGCTCGAAGGTACATCATTTACAGCATAGCTTAAGTCGAGAAG
131 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAG
* * * * * * * *
1004187 GGCTAT-T---TACCAAAGACCCTCGAGTTCGATTACACTCAGTTTCGAGGGCAC
196 GGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAG-TTCCAAGGCAC
* * * * * * * *
1004238 ATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAA-ACACCTTCGAGTTCGAC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--T-ACCAAAGAC-CC-TCGAGTTCGAT
* ** * * * * * * *
1004302 TACGCTCA-ACTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC
61 TACACTCAGTTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-AC
* * * **
1004366 C-AAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGACACATCATTTGTAGCATTGCTTAAGTC
125 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
*
1004430 GAGAAGGGATATCTGCCAA
190 GAGAAGGGTTATCTGCCAA
1004449 ATACCCTCGA
Statistics
Matches: 831, Mismatches: 109, Indels: 28
0.86 0.11 0.03
Matches are distributed among these distances:
245 26 0.03
246 37 0.04
247 23 0.03
248 36 0.04
249 655 0.79
250 19 0.02
251 32 0.04
252 1 0.00
253 2 0.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (249 bp):
ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCCTCGAGTTCGATTACAC
TCAGTTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAG
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAG
GGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGTTCCAAGGCAC
Found at i:1004074 original size:414 final size:413
Alignment explanation
Indices: 1003243--1004643 Score: 1695
Period size: 414 Copynumber: 3.4 Consensus size: 413
1003233 TTTTAAAGAA
* * * *
1003243 ATCATTTGCAGCATAACTCAATGATAGAAGGGCTATCTGCCACCAAAAGACCTTCGAGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACT
* * * * *
1003308 ACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTCAAGACTAG-AGGGTTATCTGCCACCAA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT---ACC-A
* * * * * * * * ** *
1003372 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCATATCATTTGCAGTATAACTTAACTCGA
127 AAGACCCTCGAGTTCGATTACACTCAGTTTCAAGGGCACATCATTTACAGTATAACTCAAGGCTA
* * *
1003436 GAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGTTCCAAGGCACATCATTT
192 GAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * * * * **
1003501 GCAGCATAGCTTAAGTCGAGAAGGGCTATCT----ACCAAAGACCCTCGAGTTTGATTATACTCA
256 GCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * * * ** * * * * * * * *
1003562 GTTTCGAGGGAACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTATCACCAAAAGACT
321 G-CTCCAAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGATATC--T-GCC-AAAGACC
* * * *
1003627 TTCGAGTTCGATTACGCTCAGC-TCCAAGGCAC
381 CTCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * * * * *
1003659 ATAATTTGCAACATAACTTAA-GTTGAGAAGGGTTATCTGCCAACC-AAAGACCTTTGAGTTTGA
1 ATCATTTACAGCATAACTCAAGGCT-AGAAGGGTTATCTGCC-ACCAAAAGACCTTCGAGTTCGA
* * *
1003722 CTACGCTCAGTTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAAGGCTATCTATCAAA
64 CTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAA
* *
1003787 GACCCTCGAGTTCGATTATACTCAGTTTCAAGGGCACATCATTTACAGTATAAGTCAAGGCTAGA
129 GACCCTCGAGTTCGATTACACTCAGTTTCAAGGGCACATCATTTACAGTATAACTCAAGGCTAGA
* *
1003852 AGGGTTATCTGTCACCGAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATAATTTGC
194 AGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGC
* * *
1003917 AACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAAACCTTTGAGTTCGACTACGCTCAGC
258 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
* * *
1003982 TCCAAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTGGATT
323 TCCAAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGATATCTGCCAAAGACCCTCGAGT
1004047 TCGATTACACTCAGCTTCGAGGGCAC
388 TCGATTACACTCAGCTTCGAGGGCAC
* * * * *
1004073 ATCATTTATAGTATAACTCAAGGCTAGAATGGTTATCTGTCACCAAAAGACCTTCGTGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACT
* * * *
1004138 ACGCTCAGCTCGAAGGTACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATTTACCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGA
* **
1004203 CCCTCGAGTTCGATTACACTCAGTTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAG
131 CCCTCGAGTTCGATTACACTCAGTTTCAAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAG
* *
1004268 GGTTATCTGTCACCAAAACACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAG
196 GGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAG
*
1004333 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCAACTACGCTCAGCTC
260 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * *
1004398 CAAGACACATCATTTGTAGCATTGCTTAAGTCGAGAAGGGATATCTGCCAAATACCCTCGAGTTC
325 CAAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGATATCTGCCAAAGACCCTCGAGTTC
* *
1004463 GTTTACACTAAGCTTCGAGGGCAC
390 GATTACACTCAGCTTCGAGGGCAC
* * * *
1004487 ATCATTTACACCATAACTTAAGGCTAGAAGGGTTATCTGTCACCAAAATACCTTCGAGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACT
* * * * *
1004552 ACGCTCAGCTCGAAGGCACGTCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATTTTCCAACCG
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA---T-CTACCA
*
1004617 AAGACCTTCGAGTTCGATTACACTCAG
127 AAGACCCTCGAGTTCGATTACACTCAG
1004644 CTCATAGACA
Statistics
Matches: 850, Mismatches: 119, Indels: 30
0.85 0.12 0.03
Matches are distributed among these distances:
413 58 0.07
414 594 0.70
415 5 0.01
416 92 0.11
417 48 0.06
418 53 0.06
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (413 bp):
ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGA
CCCTCGAGTTCGATTACACTCAGTTTCAAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAG
GGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
ATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
AAGGCACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGATATCTGCCAAAGACCCTCGAGTTCG
ATTACACTCAGCTTCGAGGGCAC
Found at i:1004512 original size:249 final size:247
Alignment explanation
Indices: 1003243--1004646 Score: 1412
Period size: 249 Copynumber: 5.6 Consensus size: 247
1003233 TTTTAAAGAA
* * ** * *
1003243 ATCATTTGCAGCATAACTCAATGATAGAAGGGCTATCTGCCACCAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGGCGAGAAGGGCTATCTGTCACC-AAA-ACCCTCGAGTTCGACT
* * * * *
1003308 ACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTCAAGACTAG-AGGGTTATCTGCCACCAA
64 ACACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAA
* * *
1003372 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTAACTCGAG
129 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
1003437 AAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGTTCCAAGGCAC
194 AAGGGTTATCTG---ACCAAAGACCTTTGAGTTCGACTACGCTCAGTTCCAAGGCAC
* * * *
1003494 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--T-ACCAAAGACCCTCGAGTTTGATTA
1 ATCATTTGCAGCATAACTTAAGGCGAGAAGGGCTATCTGTCACCAAA-ACCCTCGAGTTCGACTA
* * * * * * **
1003556 TACTCAGTTTCGAGGGAACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTATCACCAA
65 CACTCAG-CTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAA
* * * * *
1003621 AAGACTTTCGAGTTCGATTACGCTCAGCTCCAAGGCACATAATTTGCAACATAACTTAAGTTGAG
129 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
*
1003686 AAGGGTTATCTGCCAACCAAAGACCTTTGAGTTTGACTACGCTCAGTTCCAAGGCAC
194 AAGGGTTATCTG---ACCAAAGACCTTTGAGTTCGACTACGCTCAGTTCCAAGGCAC
* * * * * * *
1003743 ATCATTTGCAGCATAGCTTAAGTCGAGAAAGGCTATCTATCA--AAGACCCTCGAGTTCGATTAT
1 ATCATTTGCAGCATAACTTAAGGCGAGAAGGGCTATCTGTCACCAAAACCCTCGAGTTCGACTAC
* * * * * *
1003806 ACTCAGTTTCAAGGGCACATCATTTACAGTATAAGTCAAGGCTAGAAGGGTTATCTGTCACCGAA
66 ACTCAGCTCCAA-GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAA
* * *
1003871 AGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATAATTTGCAACATAACTTAAGTCGAGA
130 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGA
* *
1003936 AGGGTTATCTGCCAACCAAAAACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
195 AGGGTTATCTG---ACCAAAGACCTTTGAGTTCGACTACGCTCAGTTCCAAGGCAC
* * * * * *
1003992 ATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCTGGATTTCGATTA
1 ATCATTTGCAGCATAACTTAAGGCGAGAAGGGCTATCTGTCACCAAA-ACCCTCGAGTTCGACTA
* * * * * *
1004054 CACTCAGCTTCGAGGGCACATCATTTATAGTATAACTCAAGGCTAGAATGGTTATCTGTCACCAA
65 CACTCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAA
* * * * *
1004119 AAGACCTTCGTGTTCGACTACGCTCAGCTCGAAGGTACATCATTTACAGCATAGCTTAAGTCGAG
129 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
* * * * * * * *
1004184 AAGGGCTAT-TTACCAAAGACCCTCGAGTTCGATTACACTCAGTTTCGAGGGCAC
194 AAGGGTTATCTGACCAAAGACCTTTGAGTTCGACTACGCTCAG-TTCCAAGGCAC
* * * * *
1004238 ATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAACACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGGCGAGAAGGGCTATCTGTCACCAAAAC-CC-TCGAGTTCGACT
* * * * * *
1004303 ACGCTCAACTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-
64 ACACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCC-ACCA
* * * **
1004367 AAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGACACATCATTTGTAGCATTGCTTAAGTCGA
128 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
* * * * ** * * * *
1004432 GAAGGGATATCTG-CCAAATACCCTCGAGTTCGTTTACACTAAGCTTCGAGGGCAC
193 GAAGGGTTATCTGACCAAAGACCTTTGAGTTCGACTACGCTCAG-TTCCAAGGCAC
* * * * *
1004487 ATCATTTACACCATAACTTAAGGCTAGAAGGGTTATCTGTCACCAAAATACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGGCGAGAAGGGCTATCTGTCACC-AAA-ACCCTCGAGTTCGACT
* * * * * * * * * * * *
1004552 ACGCTCAGCTCGAAGGCACGTCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATTTTCCAACC-
64 ACACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCC-ACCA
* * *
1004616 GAAGACCTTCGAGTTCGATTACACTCAGCTC
128 AAAGACCTTCGAGTTCGACTACGCTCAGCTC
1004647 ATAGACAATC
Statistics
Matches: 998, Mismatches: 135, Indels: 42
0.85 0.11 0.04
Matches are distributed among these distances:
245 26 0.03
246 39 0.04
247 23 0.02
248 40 0.04
249 807 0.81
250 28 0.03
251 34 0.03
252 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (247 bp):
ATCATTTGCAGCATAACTTAAGGCGAGAAGGGCTATCTGTCACCAAAACCCTCGAGTTCGACTAC
ACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAA
GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAA
GGGTTATCTGACCAAAGACCTTTGAGTTCGACTACGCTCAGTTCCAAGGCAC
Found at i:1006142 original size:27 final size:26
Alignment explanation
Indices: 1006112--1006193 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 26
1006102 ATTTTCCTAC
1006112 TTTTTCTATTTATTTATTTATTTTAT
1 TTTTTCTATTTATTTATTTATTTTAT
*
1006138 ATTTTAT-TATTT-TTT-TGTTAGTATTAT
1 -TTTT-TCTATTTATTTAT-TTA-TTTTAT
*
1006165 TATTTCTA-TTATTTTATTTTATTTTAT
1 TTTTTCTATTTA-TTTA-TTTATTTTAT
1006192 TT
1 TT
1006194 CTCTCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 16
0.68 0.06 0.25
Matches are distributed among these distances:
25 4 0.09
26 11 0.26
27 23 0.53
28 4 0.09
29 1 0.02
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (26 bp):
TTTTTCTATTTATTTATTTATTTTAT
Found at i:1013797 original size:41 final size:41
Alignment explanation
Indices: 1013726--1013804 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
1013716 TAATTCAAAG
* *
1013726 TTAAGAAATGATAGAGAATAAATGTGATTAAAAATATTTTA
1 TTAAAAAATGATAGAGAATAAATGTAATTAAAAATATTTTA
*
1013767 TTAAAAAATGATAGAGAATATATGTAATTAAAAATATT
1 TTAAAAAATGATAGAGAATAAATGTAATTAAAAATATT
1013805 ATAAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (41 bp):
TTAAAAAATGATAGAGAATAAATGTAATTAAAAATATTTTA
Found at i:1018624 original size:48 final size:48
Alignment explanation
Indices: 1018568--1018678 Score: 138
Period size: 48 Copynumber: 2.3 Consensus size: 48
1018558 TAAATATTTA
*
1018568 TCTGATTTCTGACT-TGAATTCTGTTCTGATA-CATTA-CTTGAATTCTGT
1 TCTGATTTCTGA-TATGAATTCTGTTCTGATATC-TGATC-TGAATTCTGT
*
1018616 TCTGATTTCTGATATGGATTCTGTTCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGTTCTGATATCTGATCTGAATTCTGT
* *
1018664 TTTGATTTCTAATAT
1 TCTGATTTCTGATAT
1018679 CTCCGTTTAC
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
47 1 0.02
48 53 0.95
49 2 0.04
ACGTcount: A:0.21, C:0.14, G:0.15, T:0.50
Consensus pattern (48 bp):
TCTGATTTCTGATATGAATTCTGTTCTGATATCTGATCTGAATTCTGT
Found at i:1018636 original size:24 final size:24
Alignment explanation
Indices: 1018568--1018678 Score: 111
Period size: 24 Copynumber: 4.6 Consensus size: 24
1018558 TAAATATTTA
1018568 TCTGATTTCTGACT-TGAATTCTGT
1 TCTGATTTCTGA-TATGAATTCTGT
* *
1018592 TCTGA-TACATTACT-TGAATTCTGT
1 TCTGATTTC-TGA-TATGAATTCTGT
*
1018616 TCTGATTTCTGATATGGATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* *
1018640 TCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* *
1018664 TTTGATTTCTAATAT
1 TCTGATTTCTGATAT
1018679 CTCCGTTTAC
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
23 3 0.04
24 67 0.93
25 2 0.03
ACGTcount: A:0.21, C:0.14, G:0.15, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTCTGT
Found at i:1018673 original size:12 final size:12
Alignment explanation
Indices: 1018610--1018673 Score: 58
Period size: 12 Copynumber: 5.3 Consensus size: 12
1018600 ATTACTTGAA
1018610 TTCTGTTCTGAT
1 TTCTGTTCTGAT
* *
1018622 TTCTGATATGGA-
1 TTCTGTTCT-GAT
1018634 TTCTGTTCTGAT
1 TTCTGTTCTGAT
* * *
1018646 ATCTGATCTGAA
1 TTCTGTTCTGAT
*
1018658 TTCTGTTTTGAT
1 TTCTGTTCTGAT
1018670 TTCT
1 TTCT
1018674 AATATCTCCG
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 35 0.90
13 2 0.05
ACGTcount: A:0.16, C:0.14, G:0.17, T:0.53
Consensus pattern (12 bp):
TTCTGTTCTGAT
Found at i:1022413 original size:24 final size:23
Alignment explanation
Indices: 1022375--1022452 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 23
1022365 ATATGTAAAA
*
1022375 ATTA-TTATTTAATTTTTAAATCAT
1 ATTATTTATTT-A-TTTTAAATAAT
* * *
1022399 GTTATTTATTTATTTGAAATGAT
1 ATTATTTATTTATTTTAAATAAT
*
1022422 ATTAAATTATTTATTTTAAATAAT
1 ATT-ATTTATTTATTTTAAATAAT
1022446 ATTATTT
1 ATTATTT
1022453 TTAGATTATA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
23 14 0.32
24 24 0.55
25 6 0.14
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (23 bp):
ATTATTTATTTATTTTAAATAAT
Found at i:1022451 original size:19 final size:19
Alignment explanation
Indices: 1022427--1022485 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
1022417 ATGATATTAA
1022427 ATTATTTATTTTAAATAAT
1 ATTATTTATTTTAAATAAT
* *
1022446 ATTA--T-TTTTAGATTAT
1 ATTATTTATTTTAAATAAT
*
1022462 A-TATTTAAATTTAAATAAT
1 ATTATTT-ATTTTAAATAAT
1022481 ATTAT
1 ATTAT
1022486 ACAGAACCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 9
0.68 0.11 0.20
Matches are distributed among these distances:
15 2 0.07
16 10 0.33
17 2 0.07
19 13 0.43
20 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTATTTATTTTAAATAAT
Found at i:1022654 original size:23 final size:25
Alignment explanation
Indices: 1022611--1022659 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
1022601 ATTTTAAAAC
1022611 TTAAATAAATATTTTTATAAT-ATT
1 TTAAATAAATATTTTTATAATGATT
*
1022635 TTAAATATATATTTTT-TAATGATT
1 TTAAATAAATATTTTTATAATGATT
1022659 T
1 T
1022660 CATATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAAATAAATATTTTTATAATGATT
Found at i:1029935 original size:36 final size:36
Alignment explanation
Indices: 1029853--1030062 Score: 245
Period size: 35 Copynumber: 5.8 Consensus size: 36
1029843 CTCCACACCC
*
1029853 AAAA-TATATAATATATAGTTTTGAAATCA-TTTTT-
1 AAAACTATATAATATATAGTTTT-AAAACATTTTTTG
1029887 AAAACATTTATATAATATATAGTTTTAAAACATTTTTTG
1 AAAAC---TATATAATATATAGTTTTAAAACATTTTTTG
*
1029926 AAAACTATATAATATATAAGTTTAAAAAAACATTTTTTG
1 AAAACTATATAATATAT-AGTTT--TAAAACATTTTTTG
*
1029965 AAAAC-ATATAATATATAGTTTTATAACA-TTTTTG
1 AAAACTATATAATATATAGTTTTAAAACATTTTTTG
*
1029999 AAAACTATATAATATATAATTTTAAAAACATTTTTT-
1 AAAACTATATAATATATAGTTTT-AAAACATTTTTTG
1030035 AAAA-TATATAATATATAGTATTTTAAAA
1 AAAACTATATAATATATAG--TTTTAAAA
1030063 GATATATTAT
Statistics
Matches: 155, Mismatches: 7, Indels: 26
0.82 0.04 0.14
Matches are distributed among these distances:
34 15 0.10
35 34 0.22
36 25 0.16
37 24 0.15
38 34 0.22
39 23 0.15
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (36 bp):
AAAACTATATAATATATAGTTTTAAAACATTTTTTG
Found at i:1030057 original size:26 final size:26
Alignment explanation
Indices: 1030028--1030092 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 26
1030018 TTTTAAAAAC
*
1030028 ATTTTTTAAAATATATAATATATAGT
1 ATTTTTTAAAATATATAATATATAAT
* *
1030054 A--TTTTAAAAGATATATTATATAAT
1 ATTTTTTAAAATATATAATATATAAT
*
1030078 TTTTTTTGAAAATAT
1 ATTTTTT-AAAATAT
1030093 TTGTGTATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 20 0.65
26 5 0.16
27 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.51
Consensus pattern (26 bp):
ATTTTTTAAAATATATAATATATAAT
Found at i:1030082 original size:24 final size:24
Alignment explanation
Indices: 1030028--1030082 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
1030018 TTTTAAAAAC
*
1030028 ATTTTTTAAAATATATAATATATA
1 ATTTTTTAAAAGATATAATATATA
* * *
1030052 GTATTTTAAAAGATATATTATATA
1 ATTTTTTAAAAGATATAATATATA
1030076 ATTTTTT
1 ATTTTTT
1030083 TTGAAAATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
ATTTTTTAAAAGATATAATATATA
Found at i:1030118 original size:4 final size:4
Alignment explanation
Indices: 1030109--1030148 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
1030099 ATATAATATA
1030109 TTAT TTAT TTAT TTAT TTAT TTA- TTAT TT-T TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1030149 CCTTTTTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 6 0.18
4 28 0.82
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTAT
Found at i:1031329 original size:24 final size:24
Alignment explanation
Indices: 1031302--1031355 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
1031292 TACTCTTAAA
*
1031302 ATTTAACACTTTTTTCTTTAG-TTT
1 ATTTAACACTTTTTTATTT-GTTTT
*
1031326 ATTTAACATTTTTTTATTTGTTTT
1 ATTTAACACTTTTTTATTTGTTTT
1031350 ATTTAA
1 ATTTAA
1031356 TTTGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (24 bp):
ATTTAACACTTTTTTATTTGTTTT
Done.