Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 94 of 126
Found at i:28599107 original size:23 final size:23
Alignment explanation
Indices: 28599063--28599108 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28599053 TTTGTTTCTT
* *
28599063 GTTTAGTTTTATTTCTATTTGTA
1 GTTTAGGTTTATTTCTAGTTGTA
* *
28599086 GTTTAGGTTTCTTTTTAGTTGTA
1 GTTTAGGTTTATTTCTAGTTGTA
28599109 ATCGTAGTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.15, C:0.04, G:0.17, T:0.63
Consensus pattern (23 bp):
GTTTAGGTTTATTTCTAGTTGTA
Found at i:28609681 original size:33 final size:33
Alignment explanation
Indices: 28609644--28609713 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
28609634 CTGACCTCTC
* *
28609644 TTCACTAATAATGAATTATCTCGTTGTACAGAA
1 TTCACTAAAAATGAATTATCTCGTTGTACAAAA
*
28609677 TTCACTAAAAATGAATTATCTTGTTGTACAAAA
1 TTCACTAAAAATGAATTATCTCGTTGTACAAAA
28609710 TTCA
1 TTCA
28609714 GATGATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (33 bp):
TTCACTAAAAATGAATTATCTCGTTGTACAAAA
Found at i:28610325 original size:51 final size:50
Alignment explanation
Indices: 28610254--28610456 Score: 198
Period size: 51 Copynumber: 4.0 Consensus size: 50
28610244 TAATTAATGA
* * * *
28610254 TATCGGTTCACATAGTAGCCTGCACATAGTACTAGACATGTGACCATCAC
1 TATCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCAC
* * * *
28610304 TATCAGATACACGTAGTAGCCTGCACATAGTACTACGCACGTTATCGA--AGC
1 TATC-GGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-C
* * * * * *
28610355 TATTCGGCACGCATAGTAGGCTGCACATAGTACTACACATGCGACCTATCA-
1 TA-TCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC-ATCAC
28610406 T-TCTGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCAC
1 TATC-GGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCAC
28610456 T
1 T
28610457 TTCACTTTCA
Statistics
Matches: 120, Mismatches: 24, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
49 6 0.05
50 42 0.35
51 67 0.56
52 4 0.03
53 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (50 bp):
TATCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCAC
Found at i:28610430 original size:101 final size:102
Alignment explanation
Indices: 28610264--28610446 Score: 289
Period size: 101 Copynumber: 1.8 Consensus size: 102
28610254 TATCGGTTCA
* *
28610264 CATAGTAGCCTGCACATAGTACTAGACATGTGACCATCACTATCAGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCAGATACACGTAGTAGCCTGCA
*
28610329 CATAGTACTACGCACGTTATCGAAGCTATTCGGCACG
66 CATAGTACTACACACGTTATCGAAGCTATTCGGCACG
* * *
28610366 CATAGTAGGCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCAGATACACGTAGTAGCCTGC
28610429 ACATAGTACTACACACGT
65 ACATAGTACTACACACGT
28610447 GACCATCACT
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 37 0.50
102 33 0.45
103 4 0.05
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCAGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTTATCGAAGCTATTCGGCACG
Found at i:28611904 original size:122 final size:122
Alignment explanation
Indices: 28611704--28611925 Score: 331
Period size: 122 Copynumber: 1.8 Consensus size: 122
28611694 ACTCTAATGG
* * * *
28611704 TTTCATTTGGTATTGGTAGAACCCATCAAAATATCGATAGAAATGTAGGGGAGGCTAAACTTTGA
1 TTTCAATTGGTATTGGTAGAACCCAACAAAACATCGATAGAAATGCAGGGGAGGCTAAACTTTGA
* *
28611769 CTACTAATTTGACTTGTTTCAGTAAAATTCCTCAATGTAGCGGTAGAACTCCGGTGC
66 CTACTAATTTGACTTGTTTCACTAAAAGTCCTCAATGTAGCGGTAGAACTCCGGTGC
28611826 TTTCAATTGGTATTGGTAGAACCCAACAAAACATCGATAGAAATGCAGGAGG-GGCTGAAA-TTT
1 TTTCAATTGGTATTGGTAGAACCCAACAAAACATCGATAGAAATGCAGG-GGAGGCT-AAACTTT
* * *
28611889 GGCTACTATTTTGACTTGTTTCACTAGAAGTCCTCAA
64 GACTACTAATTTGACTTGTTTCACTAAAAGTCCTCAA
28611926 GGTATCAATA
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
122 84 0.94
123 5 0.06
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (122 bp):
TTTCAATTGGTATTGGTAGAACCCAACAAAACATCGATAGAAATGCAGGGGAGGCTAAACTTTGA
CTACTAATTTGACTTGTTTCACTAAAAGTCCTCAATGTAGCGGTAGAACTCCGGTGC
Found at i:28613242 original size:52 final size:51
Alignment explanation
Indices: 28613177--28613305 Score: 163
Period size: 52 Copynumber: 2.5 Consensus size: 51
28613167 AATAGTGACT
* *
28613177 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGTTTTGG-TCA
1 CAAGTGGGGTACTATGTGAAGGCCACTTTGTGAAG-AAGATAGCTTTGGCT-A
* *
28613229 CAAGTGGGGTACTATGTGAAGGCCAGTTTGTGAAGAAGGTAGCTTTGGCTA
1 CAAGTGGGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGCTA
* *
28613280 CAAG-GGTGGTATTATGTGCAGGCCAC
1 CAAGTGG-GGTACTATGTGAAGGCCAC
28613306 CGGGTATCCG
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
50 2 0.03
51 32 0.47
52 34 0.50
ACGTcount: A:0.26, C:0.13, G:0.33, T:0.28
Consensus pattern (51 bp):
CAAGTGGGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGCTA
Found at i:28613297 original size:51 final size:52
Alignment explanation
Indices: 28613177--28613305 Score: 165
Period size: 51 Copynumber: 2.5 Consensus size: 52
28613167 AATAGTGACT
* *
28613177 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGTTTTGGTCA
1 CAAGGGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
* *
28613229 CAAGTGG-GGTACTATGTGAAGGCCAGTTTGTGAAG-AAGGTAGCTTTGG-CTA
1 CAAG-GGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTC-A
* *
28613280 CAAGGGTGGTATTATGTGCAGGCCAC
1 CAAGGGTGGTACTATGTGAAGGCCAC
28613306 CGGGTATCCG
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
50 3 0.04
51 32 0.48
52 31 0.46
53 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.33, T:0.28
Consensus pattern (52 bp):
CAAGGGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
Found at i:28615254 original size:22 final size:22
Alignment explanation
Indices: 28615219--28615274 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
28615209 TGATATAATC
*
28615219 CAACCAAAAAGTATATAAAAAG
1 CAACCAAGAAGTATATAAAAAG
*
28615241 CAATCAAGAAGTATATAAAAAG
1 CAACCAAGAAGTATATAAAAAG
28615263 CAACCAAGAAGT
1 CAACCAAGAAGT
28615275 GAGGTCATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.59, C:0.14, G:0.12, T:0.14
Consensus pattern (22 bp):
CAACCAAGAAGTATATAAAAAG
Found at i:28629759 original size:41 final size:41
Alignment explanation
Indices: 28629692--28629773 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
28629682 TCGGTCCAAC
* *
28629692 CTCTTTATAACCTCCCACAGACAAGTACCACAAGGCAAATG
1 CTCTTTATAACCTCCCACAAACAAGTACCACAAAGCAAATG
* * *
28629733 CTCTTTATAATCTCCCTCAAATAAGTACCACAAAGCAAATG
1 CTCTTTATAACCTCCCACAAACAAGTACCACAAAGCAAATG
28629774 GTCGAGAGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.23
Consensus pattern (41 bp):
CTCTTTATAACCTCCCACAAACAAGTACCACAAAGCAAATG
Found at i:28638151 original size:19 final size:19
Alignment explanation
Indices: 28638104--28638153 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
28638094 TAAACTATTT
* *
28638104 CAACCCAAATGAGCTAAAT
1 CAACCCAAATGAACTAAAA
*
28638123 GAAGCCCAAATGAACTAAAA
1 CAA-CCCAAATGAACTAAAA
28638143 CAACCCAAATG
1 CAACCCAAATG
28638154 GCCATATTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.50, C:0.26, G:0.12, T:0.12
Consensus pattern (19 bp):
CAACCCAAATGAACTAAAA
Found at i:28641122 original size:12 final size:12
Alignment explanation
Indices: 28641105--28641129 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28641095 GTTCAAAGTG
28641105 AAAATTAAATTA
1 AAAATTAAATTA
28641117 AAAATTAAATTA
1 AAAATTAAATTA
28641129 A
1 A
28641130 TTGGTTATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTAAATTA
Found at i:28646942 original size:21 final size:21
Alignment explanation
Indices: 28646903--28646942 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28646893 TTATTAGTTT
*
28646903 TTTTAAAAATATATTTTTATA
1 TTTTAAAAATATATATTTATA
28646924 TTTT-AAAATAATATATTTA
1 TTTTAAAAAT-ATATATTTA
28646943 ATAGATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTAAAAATATATATTTATA
Found at i:28647017 original size:16 final size:16
Alignment explanation
Indices: 28646998--28647031 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28646988 GCTTTTCTAT
*
28646998 TTTTCTATTTTTACAA
1 TTTTCTATTTTTAAAA
*
28647014 TTTTTTATTTTTAAAA
1 TTTTCTATTTTTAAAA
28647030 TT
1 TT
28647032 ATTTGATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTCTATTTTTAAAA
Found at i:28659147 original size:11 final size:11
Alignment explanation
Indices: 28659131--28659169 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
28659121 TTTATAAATA
28659131 TATAAATTAAT
1 TATAAATTAAT
*
28659142 TATAAAGTATAT
1 TATAAATTA-AT
28659154 TATTAAATTAAT
1 TA-TAAATTAAT
28659166 TATA
1 TATA
28659170 TTATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:28659167 original size:28 final size:28
Alignment explanation
Indices: 28659135--28659188 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
28659125 TAAATATATA
28659135 AATTA-ATTATAAAGTA-TATTATTAAATT
1 AATTATATTATAAA-TATTA-TATTAAATT
28659163 AATTATATTATAAATATTATATTAAA
1 AATTATATTATAAATATTATATTAAA
28659189 AAATAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
AATTATATTATAAATATTATATTAAATT
Found at i:28659181 original size:14 final size:17
Alignment explanation
Indices: 28659149--28659186 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
28659139 AATTATAAAG
28659149 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
28659166 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
28659180 TATATTA
1 TATATTA
28659187 AAAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:28659412 original size:19 final size:20
Alignment explanation
Indices: 28659385--28659432 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
28659375 GCTGGTAAAT
*
28659385 ACATGTGTA-ATAATAATAA
1 ACATATGTATATAATAATAA
*
28659404 ACATATGTATTTAATAATAA
1 ACATATGTATATAATAATAA
28659424 A-ATATGTAT
1 ACATATGTAT
28659433 TGCTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (20 bp):
ACATATGTATATAATAATAA
Found at i:28659433 original size:19 final size:20
Alignment explanation
Indices: 28659395--28659433 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
28659385 ACATGTGTAA
28659395 TAATAATAAACATATGTATT
1 TAATAATAAACATATGTATT
28659415 TAATAATAAA-ATATGTATT
1 TAATAATAAACATATGTATT
28659434 GCTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TAATAATAAACATATGTATT
Found at i:28659959 original size:17 final size:18
Alignment explanation
Indices: 28659937--28659970 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28659927 TAAATGAGTT
28659937 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
28659954 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
28659971 AATAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:28660291 original size:18 final size:18
Alignment explanation
Indices: 28660268--28660305 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
28660258 GTATATTGAT
28660268 TTGAAT-GTGAAATTGAAA
1 TTGAATAGTGAAATT-AAA
*
28660286 TTGAATAGTGATATTAAA
1 TTGAATAGTGAAATTAAA
28660304 TT
1 TT
28660306 TGGTATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (18 bp):
TTGAATAGTGAAATTAAA
Found at i:28660412 original size:23 final size:23
Alignment explanation
Indices: 28660382--28660444 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
28660372 TTTTTCGATT
28660382 AGGCACTTTATGTGTCGTATTTC
1 AGGCACTTTATGTGTCGTATTTC
**
28660405 AGGCACTTCGTGTGTC--ATTTC
1 AGGCACTTTATGTGTCGTATTTC
*
28660426 AGGCAC-TTATGTGTGGTAT
1 AGGCACTTTATGTGTCGTAT
28660445 ACTGATCAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
20 6 0.18
21 11 0.33
22 2 0.06
23 14 0.42
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.40
Consensus pattern (23 bp):
AGGCACTTTATGTGTCGTATTTC
Found at i:28665227 original size:15 final size:15
Alignment explanation
Indices: 28665187--28665227 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
28665177 TTAATTTCAC
28665187 ATTTTACTA-TTATGT
1 ATTTTA-TATTTATGT
28665202 ATTTTATATTTATGT
1 ATTTTATATTTATGT
*
28665217 CTTTTATATTT
1 ATTTTATATTT
28665228 TGCATGCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 22 0.92
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (15 bp):
ATTTTATATTTATGT
Found at i:28668048 original size:29 final size:29
Alignment explanation
Indices: 28668016--28668086 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
28668006 AATCTCGAGA
*
28668016 TATTTTTTCAGGA-TCCATCTAATCAAAAT
1 TATTTTTTCAGAACT-CATCTAATCAAAAT
* *
28668045 TATTTTTTTAGAACTCATCTCATCAAAAT
1 TATTTTTTCAGAACTCATCTAATCAAAAT
*
28668074 TATTTTTTTAGAA
1 TATTTTTTCAGAA
28668087 TCCCTAAACC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 37 0.97
30 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (29 bp):
TATTTTTTCAGAACTCATCTAATCAAAAT
Found at i:28668134 original size:14 final size:14
Alignment explanation
Indices: 28668117--28668144 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28668107 ATTTATGAAT
28668117 AATAAAACCCTAAA
1 AATAAAACCCTAAA
28668131 AATAAAACCCTAAA
1 AATAAAACCCTAAA
28668145 CCCTAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.14
Consensus pattern (14 bp):
AATAAAACCCTAAA
Found at i:28668313 original size:21 final size:22
Alignment explanation
Indices: 28668250--28668311 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
28668240 AACTTAAATA
*
28668250 AAACACAAAACCCTAATTTAAT
1 AAACACCAAACCCTAATTTAAT
* *
28668272 TAACACCAAAACCTAATTTAAT
1 AAACACCAAACCCTAATTTAAT
28668294 AAAC-CCTAAACCCTAATT
1 AAACACC-AAACCCTAATT
28668312 AAACAATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 2 0.06
22 32 0.94
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (22 bp):
AAACACCAAACCCTAATTTAAT
Found at i:28674565 original size:3 final size:3
Alignment explanation
Indices: 28674559--28674604 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
28674549 ATAAATTACG
* * * *
28674559 TTA TTA TTA TTA GTA TTA TTA TTA ATA TTA TTG TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28674605 ATTTTCATTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:28674794 original size:28 final size:28
Alignment explanation
Indices: 28674763--28674824 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
28674753 ATATACTTAT
*
28674763 ATATTTTTATAT-TTTATAACTTATATAC
1 ATATTTTTATATCTATATAAC-TATATAC
* * *
28674791 ATATCTATATATCTATATATCTATATAC
1 ATATTTTTATATCTATATAACTATATAC
28674819 AT-TTTT
1 ATATTTT
28674825 AAATTTTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
27 2 0.07
28 19 0.70
29 6 0.22
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (28 bp):
ATATTTTTATATCTATATAACTATATAC
Found at i:28674804 original size:8 final size:8
Alignment explanation
Indices: 28674791--28674817 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
28674781 ACTTATATAC
28674791 ATATCTAT
1 ATATCTAT
28674799 ATATCTAT
1 ATATCTAT
28674807 ATATCTAT
1 ATATCTAT
28674815 ATA
1 ATA
28674818 CATTTTTAAA
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:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (8 bp):
ATATCTAT
Found at i:28674841 original size:52 final size:51
Alignment explanation
Indices: 28674682--28674841 Score: 129
Period size: 50 Copynumber: 3.2 Consensus size: 51
28674672 AATTTTGTTA
* * * * *
28674682 TATGTATATACATAC-ATACATTTATATATATATGTACATATTTT-AATTTT
1 TATGAATATACATACTATATATCTATATATCTATATACAT-TTTTAAATTTT
* * * *
28674732 TATAAATATACATA-TGTATA-C-ATATA-CT-TATATATTTTTATATTTT
1 TATGAATATACATACTATATATCTATATATCTATATACATTTTTAAATTTT
*
28674778 ATAACT-TATATACATATCTATATATCTATATATCTATATACATTTTTAAATTTT
1 -T-A-TGAATATACATA-CTATATATCTATATATCTATATACATTTTTAAATTTT
28674832 TATGAATATA
1 TATGAATATA
28674842 TAAATACATG
Statistics
Matches: 84, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
45 4 0.05
46 10 0.12
47 2 0.02
48 15 0.18
49 1 0.01
50 20 0.24
51 2 0.02
52 11 0.13
53 3 0.04
54 16 0.19
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (51 bp):
TATGAATATACATACTATATATCTATATATCTATATACATTTTTAAATTTT
Found at i:28674842 original size:54 final size:52
Alignment explanation
Indices: 28674686--28674848 Score: 146
Period size: 54 Copynumber: 3.2 Consensus size: 52
28674676 TTGTTATATG
* * * *
28674686 TATATACATAC-ATACATTTATATATATATGTACATATTTT-AATTTTTATAA
1 TATATACATACTATATATCTATATATCTATATACAT-TTTTAAATTTTTATAA
* * *
28674737 -ATATACATA-TGTATA-C-ATATA-CT-TATATATTTTTATA-TTTTATAA
1 TATATACATACTATATATCTATATATCTATATACATTTTTAAATTTTTATAA
28674782 CTTATATACATATCTATATATCTATATATCTATATACATTTTTAAATTTTTATGAA
1 --TATATACATA-CTATATATCTATATATCTATATACATTTTTAAATTTTTAT-AA
*
28674838 TATATAAATAC
1 TATATACATAC
28674849 ATGCTTATAT
Statistics
Matches: 88, Mismatches: 11, Indels: 24
0.72 0.09 0.20
Matches are distributed among these distances:
45 12 0.14
46 6 0.07
47 1 0.01
48 14 0.16
50 17 0.19
51 1 0.01
52 5 0.06
53 3 0.03
54 21 0.24
55 6 0.07
56 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (52 bp):
TATATACATACTATATATCTATATATCTATATACATTTTTAAATTTTTATAA
Found at i:28678233 original size:60 final size:60
Alignment explanation
Indices: 28678076--28678243 Score: 176
Period size: 60 Copynumber: 2.8 Consensus size: 60
28678066 TATATTTTTT
* *
28678076 ATTTTTAGAGTTAGGACTAAATTGATAGATTTTTGTAAATATTGAAGGCTAAATTTATTGA
1 ATTTTTAGAATTAGGACTAAATTGATAGA-ATTTGTAAATATTGAAGGCTAAATTTATTGA
* * ** * * * *
28678137 ATTTTTAGAATTAGAACCAAAACGACA-AATTTTGTAAACATTGAAGGTTAAATTTGTTGA
1 ATTTTTAGAATTAGGACTAAATTGATAGAA-TTTGTAAATATTGAAGGCTAAATTTATTGA
* * * * *
28678197 ATTTTTATATTTAGGATTAAATTGATAGAATGTGTAAATATTAAAGG
1 ATTTTTAGAATTAGGACTAAATTGATAGAATTTGTAAATATTGAAGG
28678244 GATAATTTTA
Statistics
Matches: 84, Mismatches: 21, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
60 61 0.73
61 23 0.27
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.40
Consensus pattern (60 bp):
ATTTTTAGAATTAGGACTAAATTGATAGAATTTGTAAATATTGAAGGCTAAATTTATTGA
Found at i:28679172 original size:125 final size:123
Alignment explanation
Indices: 28678942--28679365 Score: 573
Period size: 125 Copynumber: 3.4 Consensus size: 123
28678932 ACGTGGACGC
* * * * *
28678942 GAAGAATTTGTGAAATCGCGCCCTCCTAGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
1 GAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCT-GAAAAAATAA
* *
28679007 TTTCGAATTAACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACTAGGATGCTTTATGA
65 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAC-AGGATGCTTTATGA
* * * *
28679067 GAAGAATTTGTTAAATCGTGCCCACGTGGACGCGCTTTTCCTACAGTAGGTCCTGAAAAAATTAT
1 GAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAAT
*
28679132 TTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTT-TAAGCAGGATGCTATT-TGA
66 TTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAATCGCTTCT-A-CAGGATGCT-TTATGA
* * * * * *
28679192 GAAGAATTTCTGAAATCGTGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCTTGAAAGAACTAA
1 GAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAA-AAATAA
28679257 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGA
65 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTA-CAGGATGCTTTATGA
* * *
28679317 GAAGAATTTGTGAAATCGCGCTCACATGGACACGCTTTTGCTACAGTAG
1 GAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
28679366 CATGTTTGGG
Statistics
Matches: 263, Mismatches: 29, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
124 40 0.15
125 184 0.70
126 39 0.15
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (123 bp):
GAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAAT
TTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACAGGATGCTTTATGA
Found at i:28680435 original size:9 final size:9
Alignment explanation
Indices: 28680417--28680448 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
28680407 ATTCTCAAAT
28680417 AATA-TCAA
1 AATATTCAA
28680425 AATATTCAA
1 AATATTCAA
28680434 AATATTCAA
1 AATATTCAA
28680443 AATATT
1 AATATT
28680449 TGTACAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (9 bp):
AATATTCAA
Found at i:28680553 original size:70 final size:69
Alignment explanation
Indices: 28680472--28680601 Score: 224
Period size: 70 Copynumber: 1.9 Consensus size: 69
28680462 TAAGCTCATG
* *
28680472 TTATTACATCAAATAATATCAAAATAAATCAAAAAAAATTCTATTTTATTACATCAAATAAACTT
1 TTATTACATCAAATAATATCAAAATAAATC-AAAAAAATTCTATTTAATTACATAAAATAAACTT
28680537 CTATT
65 CTATT
*
28680542 TTATTACATCAAATAATATCAAAATAACTCAAAAAAATTCTATTTAATTACATAAAATAA
1 TTATTACATCAAATAATATCAAAATAAATCAAAAAAATTCTATTTAATTACATAAAATAA
28680602 TATCAAAATA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
69 28 0.49
70 29 0.51
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (69 bp):
TTATTACATCAAATAATATCAAAATAAATCAAAAAAATTCTATTTAATTACATAAAATAAACTTC
TATT
Found at i:28680555 original size:25 final size:25
Alignment explanation
Indices: 28680499--28680557 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
28680489 ATCAAAATAA
*
28680499 ATCAAAAAAAATTCTATTTTATTAC
1 ATCAAATAAAATTCTATTTTATTAC
*
28680524 ATCAAATAAACTTCTATTTTATTAC
1 ATCAAATAAAATTCTATTTTATTAC
28680549 ATCAAATAA
1 ATCAAATAA
28680558 TATCAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (25 bp):
ATCAAATAAAATTCTATTTTATTAC
Found at i:28680592 original size:44 final size:45
Alignment explanation
Indices: 28680525--28680611 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 45
28680515 TTTTATTACA
* * *
28680525 TCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAATAAAATTCTATTTAATTACATAAAATAATATCAAAATAAC
28680570 TCAAA-AAAATTCTATTTAATTACATAAAATAATATCAAAATA
1 TCAAATAAAATTCTATTTAATTACATAAAATAATATCAAAATA
28680612 TTCAAAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 34 0.87
45 5 0.13
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (45 bp):
TCAAATAAAATTCTATTTAATTACATAAAATAATATCAAAATAAC
Found at i:28682368 original size:11 final size:12
Alignment explanation
Indices: 28682354--28682396 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
28682344 TTAAATATGG
28682354 ATTTGAGA-GAA
1 ATTTGAGAGGAA
28682365 ATTTTGA-AGGAA
1 A-TTTGAGAGGAA
28682377 A-TTGAGAGGAA
1 ATTTGAGAGGAA
28682388 ATTTGAGAG
1 ATTTGAGAG
28682397 AGGATTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.14
11 8 0.29
12 16 0.57
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.28
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:28684610 original size:55 final size:55
Alignment explanation
Indices: 28684541--28684789 Score: 426
Period size: 55 Copynumber: 4.5 Consensus size: 55
28684531 AAAAATAGAG
* * * *
28684541 TGTTTATATGTTTAAATCAATTGTTATGTTGGAATATTGATTCTTTTGAATCGAT
1 TGTTTATACGTTTAAATCGATTATTATGTTGGAATATTGCTTCTTTTGAATCGAT
*
28684596 TCTTTATACGTTTAAATCGATTATTATGTTGGAATATTGCTTCTTTTGAATCGAT
1 TGTTTATACGTTTAAATCGATTATTATGTTGGAATATTGCTTCTTTTGAATCGAT
28684651 TGTTTATACGTTTAAATCGATTATTATGTTGGAATATTGCTTCTTTTGAATCGAT
1 TGTTTATACGTTTAAATCGATTATTATGTTGGAATATTGCTTCTTTTGAATCGAT
* *
28684706 TGTTTATATGTTTAAATCGATTATTATGTTGGAATATTGCTTCTTTTGAATCAAT
1 TGTTTATACGTTTAAATCGATTATTATGTTGGAATATTGCTTCTTTTGAATCGAT
*
28684761 TGTTTATACGTTTAAATCGATTGTTATGT
1 TGTTTATACGTTTAAATCGATTATTATGT
28684790 AGCACATATA
Statistics
Matches: 184, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 184 1.00
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (55 bp):
TGTTTATACGTTTAAATCGATTATTATGTTGGAATATTGCTTCTTTTGAATCGAT
Found at i:28684913 original size:13 final size:13
Alignment explanation
Indices: 28684891--28684923 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
28684881 AGATATAACT
*
28684891 ATAAATCTCGAAA
1 ATAAACCTCGAAA
28684904 ATAAACCTCGAAA
1 ATAAACCTCGAAA
28684917 ATAAACC
1 ATAAACC
28684924 GTAAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.55, C:0.21, G:0.06, T:0.18
Consensus pattern (13 bp):
ATAAACCTCGAAA
Found at i:28684940 original size:8 final size:8
Alignment explanation
Indices: 28684927--28684954 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
28684917 ATAAACCGTA
28684927 AAAAATAT
1 AAAAATAT
28684935 AAAAATAT
1 AAAAATAT
28684943 AAAAATAT
1 AAAAATAT
28684951 AAAA
1 AAAA
28684955 GAAAACATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATAT
Found at i:28685667 original size:8 final size:9
Alignment explanation
Indices: 28685579--28685707 Score: 73
Period size: 10 Copynumber: 13.4 Consensus size: 9
28685569 ACATGTGACA
28685579 AAAAATTAT
1 AAAAATTAT
28685588 AAAAA--AT
1 AAAAATTAT
*
28685595 AAAAATCAAT
1 AAAAAT-TAT
*
28685605 AAAAGTTAT
1 AAAAATTAT
28685614 AAAAATTATT
1 AAAAATTA-T
**
28685624 AAATTTTAAT
1 AAAAATT-AT
28685634 AAAAATATAATT
1 AAAAAT-T-A-T
* * *
28685646 TAAAATGAA
1 AAAAATTAT
28685655 AAAAATTAT
1 AAAAATTAT
28685664 AAAAATTAT
1 AAAAATTAT
*
28685673 AAAAAATTGT
1 -AAAAATTAT
*
28685683 AAAATTTTAT
1 AAAA-ATTAT
28685693 AAAAAATTTAT
1 -AAAAA-TTAT
28685704 AAAA
1 AAAA
28685708 TGCATCAAAA
Statistics
Matches: 92, Mismatches: 17, Indels: 21
0.71 0.13 0.16
Matches are distributed among these distances:
7 7 0.08
9 33 0.36
10 34 0.37
11 12 0.13
12 6 0.07
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:28685678 original size:19 final size:19
Alignment explanation
Indices: 28685578--28685707 Score: 81
Period size: 19 Copynumber: 6.7 Consensus size: 19
28685568 AACATGTGAC
28685578 AAAAAATTATAAAAA--AT
1 AAAAAATTATAAAAATTAT
* *
28685595 -AAAAATCAATAAAAGTTAT
1 AAAAAAT-TATAAAAATTAT
**
28685614 -AAAAATTATTAAATTTTAAT
1 AAAAAATTA-TAAAAATT-AT
* * *
28685634 AAAAATATAATTTAAAATGA-
1 AAAAA-ATTA-TAAAAATTAT
28685654 AAAAAATTATAAAAATTAT
1 AAAAAATTATAAAAATTAT
* *
28685673 AAAAAATTGTAAAATTTTAT
1 AAAAAATTATAAAA-ATTAT
28685693 AAAAAATTTATAAAA
1 AAAAAA-TTATAAAA
28685708 TGCATCAAAA
Statistics
Matches: 87, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
16 6 0.07
17 6 0.07
18 8 0.09
19 30 0.34
20 17 0.20
21 12 0.14
22 8 0.09
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAAAATTATAAAAATTAT
Found at i:28685996 original size:9 final size:9
Alignment explanation
Indices: 28685982--28686047 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
28685972 TTCTACATTT
*
28685982 TTTTTATGA
1 TTTTTATAA
28685991 TTTTTATAAAA
1 TTTTTAT--AA
* **
28686002 TTTTAATTT
1 TTTTTATAA
28686011 TTTTTATAA
1 TTTTTATAA
**
28686020 TTTCTTACGA
1 TTT-TTATAA
28686030 TTTTTATAA
1 TTTTTATAA
28686039 TTTTTATAA
1 TTTTTATAA
28686048 CTTTAATTTA
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
9 29 0.67
10 7 0.16
11 7 0.16
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:28687826 original size:198 final size:199
Alignment explanation
Indices: 28687396--28687809 Score: 661
Period size: 202 Copynumber: 2.1 Consensus size: 199
28687386 TAAAAAAAAT
* * * *
28687396 TTAAAAGAATATCCATTGATTCAAGATTTAAGAAATCGCGGCCCAATACGTTAGGGCACAATTTC
1 TTAAGAGAATA-CCATTAATTCAAGATTTAAGAAATCGCAGCCCAATACGTTAGGGCACAATTCC
28687461 TTTAAAATCCCAAACTCGGAATATTTCCTTTATTATTTTTTTTAGAAAAAAATCTTCATTTCGAG
65 TTTAAAATCCCAAACTCGGAATATTTCCTTTATTA--TTTTTTAGAAAAAAATCTTCATTTCGAG
* *
28687526 AAATCAATATGTCACATCCAATACGTTAGGACACAACGTGTTGAATTCCCAACAATGAACTCTTA
128 AAATCAATACGTCACATCCAATACGTTAGGACACAACGTGTTAAATTCCCAACAATGAACTCTTA
28687591 TTTTTGA
193 TTTTTGA
*
28687598 TTAAGAGAATATCCATTTATTCAAGATTTAAGAAATCGCAGCCCAATACGTTAGGGCACAATTCC
1 TTAAGAGAATA-CCATTAATTCAAGATTTAAGAAATCGCAGCCCAATACGTTAGGGCACAATTCC
* *
28687663 TTTAAAATCCCAAACTTGGAATATTTCCTTTATTA-TTTTTAG-GAAAAATCTTCATTTCGAGAA
65 TTTAAAATCCCAAACTCGGAATATTTCCTTTATTATTTTTTAGAAAAAAATCTTCATTTCGAGAA
* *
28687726 ATCAATGCGTCACATCCAATACGTTAGGACACAACGTGTTAAATTCCCAATAATGAACTCTTATT
130 ATCAATACGTCACATCCAATACGTTAGGACACAACGTGTTAAATTCCCAACAATGAACTCTTATT
28687791 TTTGA
195 TTTGA
28687796 TTAAAGAAGAATAC
1 TT-AAG-AGAATAC
28687810 TTGAATGTCA
Statistics
Matches: 200, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
198 88 0.44
199 11 0.05
200 6 0.03
202 95 0.47
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (199 bp):
TTAAGAGAATACCATTAATTCAAGATTTAAGAAATCGCAGCCCAATACGTTAGGGCACAATTCCT
TTAAAATCCCAAACTCGGAATATTTCCTTTATTATTTTTTAGAAAAAAATCTTCATTTCGAGAAA
TCAATACGTCACATCCAATACGTTAGGACACAACGTGTTAAATTCCCAACAATGAACTCTTATTT
TTGA
Found at i:28690007 original size:2 final size:2
Alignment explanation
Indices: 28690000--28690027 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28689990 GATAGAGACG
28690000 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
28690028 CTGTTGTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28691913 original size:28 final size:26
Alignment explanation
Indices: 28691868--28691922 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
28691858 ACCTTTCACT
* *
28691868 TACATATATATCTGCATGTCTACATTCA
1 TACATATATATATACATG-C-ACATTCA
28691896 TACATATATATATACATGCACATTCA
1 TACATATATATATACATGCACATTCA
28691922 T
1 T
28691923 GAACGCATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.32
27 1 0.04
28 16 0.64
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.38
Consensus pattern (26 bp):
TACATATATATATACATGCACATTCA
Found at i:28696807 original size:56 final size:55
Alignment explanation
Indices: 28696720--28696827 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 55
28696710 TTATAGATTG
*
28696720 CAAATTAATTATTCATGAGCACTATTCAAATTAAAAGTCATGATTTATCATCTTA
1 CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTCATGATTTATCATCTTA
* *
28696775 CAAATTTAATTATTCATAAGCACTATTTAAATTAAAAGTGATGATTTATCATC
1 CAAA-TTAATTATTCATAAGCACTATTCAAATTAAAAGTCATGATTTATCATC
28696828 CAATGGATAC
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
55 4 0.08
56 45 0.92
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (55 bp):
CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTCATGATTTATCATCTTA
Found at i:28699438 original size:24 final size:24
Alignment explanation
Indices: 28699385--28699439 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
28699375 GACATGAGTA
*
28699385 TGTGAGACAATTGATTAAGGACGG
1 TGTGATACAATTGATTAAGGACGG
28699409 TGTGATACAATTGATTAAGGACGG
1 TGTGATACAATTGATTAAGGACGG
28699433 TGTGATA
1 TGTGATA
28699440 ACTGTTACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.33, C:0.07, G:0.31, T:0.29
Consensus pattern (24 bp):
TGTGATACAATTGATTAAGGACGG
Found at i:28700497 original size:56 final size:56
Alignment explanation
Indices: 28700411--28701247 Score: 1649
Period size: 56 Copynumber: 15.0 Consensus size: 56
28700401 TGTATCCATT
28700411 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
1 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
28700467 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
1 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
28700523 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
1 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
28700579 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
1 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
28700635 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
1 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
28700691 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
1 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
28700747 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
1 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
28700803 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
1 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
28700859 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
1 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
28700915 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
1 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
28700971 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
1 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
28701027 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
1 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
28701083 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
1 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
28701139 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
1 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
* *
28701195 AGATGATAAATCATCACTTTTAATTTGAATAATGCTCATGAATAATT-AATTTG
1 AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTG
28701248 CAATCTATAA
Statistics
Matches: 779, Mismatches: 2, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
55 6 0.01
56 773 0.99
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (56 bp):
AGATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTA
Found at i:28703254 original size:126 final size:125
Alignment explanation
Indices: 28703019--28703580 Score: 650
Period size: 126 Copynumber: 4.5 Consensus size: 125
28703009 AAATCAAAGG
* * * * * * * *
28703019 AGGATGATTTATCAGAA-AGATTTTTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTAAAGTAGG
1 AGGATGCTTTATGAGAAGA-ATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGG
*
28703083 TCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTCAAGC
65 TCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGC
* * *
28703144 AGGATGTTTTGTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTACTACAGTTGGT
1 AGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGGT
* * * *
28703209 CCTGGAAGAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGTTTAAAAAGCGCTTCAAGC
66 CCTGGAA-AAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGC
* * * *
28703270 AGGGTGCTTTATAAGAAGAATTTGTGAAGTCGCG-CCTATGTGGACGCGCTTTTGCTACA-TTAG
1 AGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCT-CGTGGACGCGCTTTTGCTACAGTT-G
* ** * * * * *
28703333 GTCCT-AAAAAAGTAATTTTAAGTTTACGTTTCTGAGTAAATAGTATAAAATAACACTGCAAGC
64 GTCCTGGAAAAA-TAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAA-AACGCTTCAAGC
** *
28703396 AACATGCTATT-TGATAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGG
1 AGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGG
* * * * **
28703460 TCTTGGAAAAATAATTTTGACTTGACGTTTCTGAACAAATAGTAT-AAAATCGCTTTTAGC
65 TCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGC
* * * *
28703520 AGGATACTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTAGACGCGTTTTTGCTACAGT
1 AGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
28703581 AACATGTTTG
Statistics
Matches: 370, Mismatches: 56, Indels: 23
0.82 0.12 0.05
Matches are distributed among these distances:
123 2 0.01
124 61 0.16
125 102 0.28
126 193 0.52
127 12 0.03
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (125 bp):
AGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGGT
CCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGC
Found at i:28703487 original size:251 final size:250
Alignment explanation
Indices: 28703038--28703581 Score: 716
Period size: 251 Copynumber: 2.2 Consensus size: 250
28703028 TATCAGAAAG
* * * * *
28703038 ATTTTTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTAAAGTAGGTCCTGGAAAAATAATTTCGA
1 ATTTGTGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCAA
* * * ** *
28703103 CTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTCAAGCAGGATGTTTTGTGAGAAGAATTTG
66 CTTGACGTTTCTGAGCAAATAGTATAAAAAACACTGCAAGCAACATGTATTGTGAGAAGAATTTG
*
28703168 TGAAATCGCGCCCTCGTGGACGCGCTTTTACTACAGTTGGTCCTGGAAGAAATAATTTCGAGTTG
131 TGAAATCGCGCCCTCGTGGACGCGCTTTTACTACAGTTGGTCCTGGAAGAAATAATTTCGACTTG
* * * * *
28703233 ACGTTTTTGAGCAAATAGTTTAAAAAGCGCTTCAAGCAGGGTGCTTTATAAGAAGA
196 ACGTTTCTGAACAAATAGTAT-AAAAGCGCTTCAAGCAGGATACTTTATAAGAAGA
* * * *
28703289 ATTTGTGAAGTCGCGCCTATGTGGACGCGCTTTTGCTACATTAGGTCCT-AAAAAAGTAATTTTA
1 ATTTGTGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAA-TAATTTCA
* * * *
28703353 AGTTTACGTTTCTGAGTAAATAGTATAAAATAACACTGCAAGCAACATGCTATT-TGATAAGAAT
65 ACTTGACGTTTCTGAGCAAATAGTATAAAA-AACACTGCAAGCAACATG-TATTGTGAGAAGAAT
* * *
28703417 TTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCTTGGAA-AAATAATTTTGAC
128 TTGTGAAATCGCGCCCTCGTGGACGCGCTTTTACTACAGTTGGTCCTGGAAGAAATAATTTCGAC
* ** *
28703481 TTGACGTTTCTGAACAAATAGTATAAAATCGCTTTTAGCAGGATACTTTATGAGAAGA
193 TTGACGTTTCTGAACAAATAGTATAAAAGCGCTTCAAGCAGGATACTTTATAAGAAGA
* * *
28703539 ATTTGTGAAATCGCGCCCACGTAGACGCGTTTTTGCTACAGTA
1 ATTTGTGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAGTA
28703582 ACATGTTTGG
Statistics
Matches: 252, Mismatches: 38, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
250 70 0.28
251 107 0.42
252 72 0.29
253 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (250 bp):
ATTTGTGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCAA
CTTGACGTTTCTGAGCAAATAGTATAAAAAACACTGCAAGCAACATGTATTGTGAGAAGAATTTG
TGAAATCGCGCCCTCGTGGACGCGCTTTTACTACAGTTGGTCCTGGAAGAAATAATTTCGACTTG
ACGTTTCTGAACAAATAGTATAAAAGCGCTTCAAGCAGGATACTTTATAAGAAGA
Found at i:28706797 original size:22 final size:22
Alignment explanation
Indices: 28706756--28707633 Score: 769
Period size: 21 Copynumber: 40.0 Consensus size: 22
28706746 TCAAATTATA
28706756 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
28706777 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
28706799 TTAAAGTTAAGAGTATAGGGTTT
1 TTTAAGTTAAGGGTTTAGGG-TT
* *
28706822 TAAAGTTAATGGTTTAGGGTTTAGGGGT
1 T----TTAA--GTTAAGGGTTTAGGGTT
* *
28706850 TTTAATTTAAGAG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
28706871 TTTAAGTTAACGATTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
28706893 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
28706915 TTAAAGTT-ATGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
28706936 TTTAGGTTAAGGG-TTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
28706957 TTTAGGTTAAGGGTTTAGAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
28706979 TTTAATTTAATGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
28707000 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
28707022 TTTAAGTTAAAGGTCTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
28707044 CTAAAATTAA-GGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
28707065 TTCAGGTTAAGGG-TTAGGGTG
1 TTTAAGTTAAGGGTTTAGGGTT
* * **
28707086 TTTAGGTTAAGTGTTTAAAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
28707108 TTTAATTTAA-GGATTGGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
28707129 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
28707151 TTTAAGTTAAGGGTCTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
28707173 TTAAAGTTAA-GGTTTTGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
28707194 TTTAGGTTAAGGG-TTAGGATT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
28707215 TTTAGGTTAAGAGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
28707237 TTT-ACTTTAGGG-CTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
28707257 TTTAAGTTAAGGGTTCAAGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
28707278 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
28707300 TTAAAGTTAA-GGTTTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
* *
28707320 TTTAGGTTAAGTG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
28707341 TTTAGGTTAAGGGTTAAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
28707363 TTTAATTTAAGGG-CTAGAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
28707384 TTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
28707406 TTTAGGTTAAGGGTCTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
28707427 TTTAACGTTAA-GGTTTAGGGTT
1 TTTAA-GTTAAGGGTTTAGGGTT
* *
28707449 TTCAGGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
28707470 TTAAAGTTAATGG-TTAGGGTTTT
1 TTTAAGTTAAGGGTTTAGGG--TT
*
28707493 TCGGTTAAGAATTTAGGG-TTAGGGTT
1 T---TTAAG--TTAAGGGTTTAGGGTT
* *
28707519 TTTAGGTTAAGGGTTTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* **
28707541 TTAAAGTTAAGGG-TTAATGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
28707562 TTTAGGTTAAGGGGTTAAGGG-T
1 TTTAAGTTAA-GGGTTTAGGGTT
28707584 TTTAAGTTAAGGGTGAGGATTAGGGTT
1 TTTAAGTTAAGGGT-----TTAGGGTT
* *
28707611 TTTAGGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
28707633 T
1 T
28707634 GTGAATTAAA
Statistics
Matches: 690, Mismatches: 124, Indels: 85
0.77 0.14 0.09
Matches are distributed among these distances:
20 25 0.04
21 306 0.44
22 288 0.42
23 13 0.02
24 4 0.01
26 12 0.02
27 17 0.02
28 13 0.02
29 12 0.02
ACGTcount: A:0.24, C:0.01, G:0.31, T:0.44
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTTAGGGTT
Found at i:28706823 original size:43 final size:42
Alignment explanation
Indices: 28706756--28707597 Score: 741
Period size: 43 Copynumber: 19.3 Consensus size: 42
28706746 TCAAATTATA
28706756 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
* * *
28706799 TTAAAGTTAAGAGTATAGGGTTTTAAAGTTAATGGTTTAGGGTTTAGGGGT
1 TTTAAGTTAAGGGT-TAGGGTTTT-AAGTT-A------AGGGTTTAGGGTT
* * * *
28706850 TTTAATTTAAGAGTTAGGGTTTTTAAGTTAACGATTTAGGGTT
1 TTTAAGTTAAGGGTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
*
28706893 TTTAAGTTAAGGGTTTAGGGTTTTAAAGTT-ATGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTT-AAGTTAAGGGTTTAGGGTT
* * * *
28706936 TTTAGGTTAAGGGTTAGTGTTTTTAGGTTAAGGGTTTAGAGTT
1 TTTAAGTTAAGGGTTAG-GGTTTTAAGTTAAGGGTTTAGGGTT
* *
28706979 TTTAATTTAATGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
* * *
28707022 TTTAAGTTAAAGGTCTAGGGTTCTAAAATTAA-GGTTTAGGGTT
1 TTTAAGTTAAGGGT-TAGGGTT-TTAAGTTAAGGGTTTAGGGTT
* * * * **
28707065 TTCAGGTTAAGGGTTAGGGTGTTTAGGTTAAGTGTTTAAAGTT
1 TTTAAGTTAAGGGTTAGGGT-TTTAAGTTAAGGGTTTAGGGTT
* * *
28707108 TTTAATTTAAGGATTGGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
* *
28707151 TTTAAGTTAAGGGTCTAAGGTTTTAAAGTTAA-GGTTTTGGGTT
1 TTTAAGTTAAGGGT-TAGGGTTTT-AAGTTAAGGGTTTAGGGTT
* * * *
28707194 TTTAGGTTAAGGGTTAGGATTTTTAGGTTAAGAGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGG-GTTTTAAGTTAAGGGTTTAGGGTT
* * * * *
28707237 TTT-ACTTTAGGGCTAGGGTTTTTAAGTTAAGGGTTCAAGG-T
1 TTTAAGTTAAGGGTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
28707278 TTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAA-GGTTTAGGG-T
1 TTTAAGTTAAGGG-TTAGGGTTTT-AAGTTAAGGGTTTAGGGTT
* * * *
28707320 TTTAGGTTAAGTGTTAGGGTTTTTAGGTTAAGGGTTAAGGGTT
1 TTTAAGTTAAGGGTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
* * * *
28707363 TTTAATTTAAGGGCTAGAGTTTTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTAG-GGTTTTAAGTTAAGGGTTTAGGGTT
*
28707406 TTTAGGTTAAGGGTCTAGGGTTTTAACGTTAA-GGTTTAGGGTT
1 TTTAAGTTAAGGGT-TAGGGTTTTAA-GTTAAGGGTTTAGGGTT
* * *
28707449 TTCAGGTTAAGGGTTAGGGTTTTAAAGTTAATGG-TTAGGGTTTT
1 TTTAAGTTAAGGGTTAGGGTTTT-AAGTTAAGGGTTTAGGG--TT
* * *
28707493 TCGGTTAAGAATTTAGGGTTAGGGTTTTTAGGTTAAGGGTTTAGTGTT
1 T---TTAAG--TTAAGGGTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
* * * * *
28707541 TTAAAGTTAAGGGTTAATGTTTTTAGGTTAAGGGGTTAAGGG-T
1 TTTAAGTTAAGGGTT-AGGGTTTTAAGTTAA-GGGTTTAGGGTT
28707584 TTTAAGTTAAGGGT
1 TTTAAGTTAAGGGT
28707598 GAGGATTAGG
Statistics
Matches: 651, Mismatches: 101, Indels: 94
0.77 0.12 0.11
Matches are distributed among these distances:
41 16 0.02
42 119 0.18
43 371 0.57
44 66 0.10
45 5 0.01
47 3 0.00
48 3 0.00
49 21 0.03
50 19 0.03
51 28 0.04
ACGTcount: A:0.24, C:0.02, G:0.30, T:0.44
Consensus pattern (42 bp):
TTTAAGTTAAGGGTTAGGGTTTTAAGTTAAGGGTTTAGGGTT
Found at i:28706859 original size:29 final size:29
Alignment explanation
Indices: 28706816--28706871 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 29
28706806 TAAGAGTATA
28706816 GGGTTTTAAAGTTAATG-GTTTAGGGTTTAG
1 GGGTTTTAAAGTTAA-GAG-TTAGGGTTTAG
*
28706846 GGGTTTT-AATTTAAGAGTTAGGGTTT
1 GGGTTTTAAAGTTAAGAGTTAGGGTTT
28706872 TTAAGTTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 10 0.42
29 7 0.29
30 7 0.29
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (29 bp):
GGGTTTTAAAGTTAAGAGTTAGGGTTTAG
Found at i:28706880 original size:72 final size:73
Alignment explanation
Indices: 28706765--28706915 Score: 209
Period size: 72 Copynumber: 2.1 Consensus size: 73
28706755 ATTTAAGTTA
* *
28706765 AGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAA-GAGTATAGGGTTTTAAAGT
1 AGGGTTTAGGGGTTTTAAGTTAAGAGTTTAGGGTTTTAAAGTTAACGA-TATAGGGTTTTAAAGT
*
28706828 TAATGGTTT
65 TAAGGGTTT
* * * *
28706837 AGGGTTTAGGGGTTTTAATTTAAGAG-TTAGGGTTTTTAAGTTAACGATTTAGGGTTTTTAAGTT
1 AGGGTTTAGGGGTTTTAAGTTAAGAGTTTAGGGTTTTAAAGTTAACGATATAGGGTTTTAAAGTT
28706901 AAGGGTTT
66 AAGGGTTT
28706909 AGGGTTT
1 AGGGTTT
28706916 TAAAGTTATG
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
72 50 0.71
73 20 0.29
ACGTcount: A:0.26, C:0.01, G:0.30, T:0.43
Consensus pattern (73 bp):
AGGGTTTAGGGGTTTTAAGTTAAGAGTTTAGGGTTTTAAAGTTAACGATATAGGGTTTTAAAGTT
AAGGGTTT
Found at i:28707563 original size:71 final size:70
Alignment explanation
Indices: 28707441--28707572 Score: 201
Period size: 71 Copynumber: 1.9 Consensus size: 70
28707431 ACGTTAAGGT
* * *
28707441 TTAGGGTTTTCAGGTTAAGGGTTAGGGTTTTAAAGTTAATGGTTAGGGTTTTTCGGTTAAGAATT
1 TTAGGGTTTTCAGGTTAAGGGTTAGGGTTTTAAAGTTAAGGGTTAAGGTTTTTAGGTTAAGAATT
28707506 TAGGG
66 TAGGG
* * *
28707511 TTAGGGTTTTTAGGTTAAGGGTTTAGTGTTTTAAAGTTAAGGGTTAATGTTTTTAGGTTAAG
1 TTAGGGTTTTCAGGTTAAGGG-TTAGGGTTTTAAAGTTAAGGGTTAAGGTTTTTAGGTTAAG
28707573 GGGTTAAGGG
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
70 20 0.36
71 35 0.64
ACGTcount: A:0.23, C:0.02, G:0.31, T:0.44
Consensus pattern (70 bp):
TTAGGGTTTTCAGGTTAAGGGTTAGGGTTTTAAAGTTAAGGGTTAAGGTTTTTAGGTTAAGAATT
TAGGG
Found at i:28708839 original size:7 final size:7
Alignment explanation
Indices: 28708829--28708889 Score: 122
Period size: 7 Copynumber: 8.7 Consensus size: 7
28708819 TTATATACAT
28708829 AATACTA
1 AATACTA
28708836 AATACTA
1 AATACTA
28708843 AATACTA
1 AATACTA
28708850 AATACTA
1 AATACTA
28708857 AATACTA
1 AATACTA
28708864 AATACTA
1 AATACTA
28708871 AATACTA
1 AATACTA
28708878 AATACTA
1 AATACTA
28708885 AATAC
1 AATAC
28708890 CAATCGACTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 54 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:28709095 original size:20 final size:20
Alignment explanation
Indices: 28709058--28709095 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28709048 TTTATTTTTA
*
28709058 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
28709078 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
28709096 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:28710107 original size:11 final size:11
Alignment explanation
Indices: 28710107--28710168 Score: 90
Period size: 11 Copynumber: 5.6 Consensus size: 11
28710097 GAGAGAAATT
28710107 TTGA-AGGAAA
1 TTGAGAGGAAA
28710117 TTGAGAGGAAA
1 TTGAGAGGAAA
28710128 TTGAGAGGAAA
1 TTGAGAGGAAA
* *
28710139 TTCAGAAGAAA
1 TTGAGAGGAAA
28710150 TTGAGAGGAAA
1 TTGAGAGGAAA
28710161 TTTGAGAG
1 -TTGAGAG
28710169 AGTATTAGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
10 4 0.09
11 35 0.76
12 7 0.15
ACGTcount: A:0.45, C:0.02, G:0.32, T:0.21
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:28710115 original size:51 final size:51
Alignment explanation
Indices: 28710034--28710131 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
28710024 AATTATTTAA
* *
28710034 AAATAGGGATTTAAGAGAAATTTAAGAGGAACTTTAGAGCAAATTGAAAAT
1 AAATAGGGATTTAAGAGAAATTTAAGAGGAAATTGAGAGCAAATTGAAAAT
* * * *
28710085 AAATATGGATTTGAGAGAAATTT-TGAAGGAAATTGAGAGGAAATTGA
1 AAATAGGGATTTAAGAGAAATTTAAG-AGGAAATTGAGAGCAAATTGA
28710132 GAGGAAATTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
50 1 0.03
51 39 0.98
ACGTcount: A:0.47, C:0.02, G:0.24, T:0.27
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAAGAGGAAATTGAGAGCAAATTGAAAAT
Found at i:28710120 original size:22 final size:21
Alignment explanation
Indices: 28710095--28710169 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 21
28710085 AAATATGGAT
28710095 TTGAGAGAAATTTTGA-AGGAAA
1 TTGAGAGAAA--TTGAGAGGAAA
28710117 TTGAGAGGAAATTGAGAGGAAA
1 TTGAGA-GAAATTGAGAGGAAA
*
28710139 TTCAGAAGAAATTGAGAGGAAA
1 TTGAG-AGAAATTGAGAGGAAA
28710161 TTTGAGAGA
1 -TTGAGAGA
28710170 GTATTAGTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.09
22 34 0.72
23 9 0.19
ACGTcount: A:0.45, C:0.01, G:0.31, T:0.23
Consensus pattern (21 bp):
TTGAGAGAAATTGAGAGGAAA
Found at i:28710132 original size:33 final size:33
Alignment explanation
Indices: 28710093--28710169 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 33
28710083 ATAAATATGG
**
28710093 ATTTGAGAGAAATTTTGAAGGAAATTGAGAGGAA
1 ATTTGAGAGAAATTCAGAA-GAAATTGAGAGGAA
28710127 A-TTGAGAGGAAATTCAGAAGAAATTGAGAGGAA
1 ATTTGAGA-GAAATTCAGAAGAAATTGAGAGGAA
28710160 ATTTGAGAGA
1 ATTTGAGAGA
28710170 GTATTAGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
33 23 0.59
34 16 0.41
ACGTcount: A:0.45, C:0.01, G:0.30, T:0.23
Consensus pattern (33 bp):
ATTTGAGAGAAATTCAGAAGAAATTGAGAGGAA
Found at i:28712550 original size:93 final size:93
Alignment explanation
Indices: 28712383--28712619 Score: 298
Period size: 93 Copynumber: 2.5 Consensus size: 93
28712373 TTACTCTAAA
* * * * *
28712383 TACAAGTTGTTCTAAACAATGATTGTTCTAAACATAACTATTCCCGGAACACTATTGTTCTAAAA
1 TACAAATTGTTCTAAACAATGATTGTTCTAAATATAACTATTCTCGAAACACTATTATTCTAAAA
28712448 AAGAGTTGTTTCAAACTTTAATTGTTAT
66 AAGAGTTGTTTCAAACTTTAATTGTTAT
*
28712476 TACAAATTGTTCTAAACAATGATTGTTCTAAATATAACTATTCTCGAAACACTATTATTCTAAAT
1 TACAAATTGTTCTAAACAATGATTGTTCTAAATATAACTATTCTCGAAACACTATTATTCTAAAA
* ** *
28712541 AAGATTTGTTTTGAACTTTAGTTGTTAT
66 AAGAGTTGTTTCAAACTTTAATTGTTAT
* * *
28712569 AACTAAAGTCCTGTTCTAAAC-AT-ATCTATTCTAGATATAACTATTCTCGAA
1 TAC-AAA-T--TGTTCTAAACAATGAT-TGTTCTAAATATAACTATTCTCGAA
28712620 CAACAATTGT
Statistics
Matches: 126, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
93 85 0.67
94 3 0.02
95 3 0.02
96 25 0.20
97 10 0.08
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (93 bp):
TACAAATTGTTCTAAACAATGATTGTTCTAAATATAACTATTCTCGAAACACTATTATTCTAAAA
AAGAGTTGTTTCAAACTTTAATTGTTAT
Found at i:28714407 original size:93 final size:93
Alignment explanation
Indices: 28714296--28714956 Score: 1124
Period size: 93 Copynumber: 7.1 Consensus size: 93
28714286 CTAACTATAC
28714296 TACATATTACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTTGA
1 TACATA-TACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTTGA
28714361 CAGCATTGATTCACCAAAATTGGGCAGCA
65 CAGCATTGATTCACCAAAATTGGGCAGCA
*
28714390 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATGTACAAAATTTGAC
1 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTTGAC
*
28714455 AGCATTGCTTCACCAAAATTGGGCAGCA
66 AGCATTGATTCACCAAAATTGGGCAGCA
* * *
28714483 TACATACACAAATTTGGACAGCACTTATACACAAAATTTAACAGCATGTATATACAAAATTGGAC
1 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTTGAC
28714548 AGCATTGATTCACCAAAATTGGGCAGCA
66 AGCATTGATTCACCAAAATTGGGCAGCA
* * *
28714576 TACATATACAAATTTGGACGGCACTTATACACAATATATAACAGCATGTATATACAAAATTGGAC
1 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTTGAC
28714641 AGCATTGATTCACCAAAATTGGGCAGCA
66 AGCATTGATTCACCAAAATTGGGCAGCA
* * *
28714669 TACATATACAAATTTGGACGGCACTTATACACAATATATAACAGCATGTATATACAAAATTGGAC
1 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTTGAC
28714734 AGCATTGATTCACCAAAATTGGGCAGCA
66 AGCATTGATTCACCAAAATTGGGCAGCA
*
28714762 TACATATACAAAATTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTTGAC
1 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTTGAC
* *
28714827 AGCATTTATTCACCCAAAATTAGGCAGCA
66 AGCATTGATTCA-CCAAAATTGGGCAGCA
* * *
28714856 TACATAAACAAATTTGGACAGCATTTATACACAAAATTTAACAGCATGTATATACAAAATTTGAC
1 TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTTGAC
* *
28714921 AGCATTGATTTATCAAAATTGGGCAGCA
66 AGCATTGATTCACCAAAATTGGGCAGCA
*
28714949 TACCTATA
1 TACATATA
28714957 ACAATTGGGC
Statistics
Matches: 539, Mismatches: 27, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
93 447 0.83
94 92 0.17
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (93 bp):
TACATATACAAATTTGGACAGCACTTATACACAAAATATAACAGCATGTATATACAAAATTTGAC
AGCATTGATTCACCAAAATTGGGCAGCA
Found at i:28714925 original size:23 final size:22
Alignment explanation
Indices: 28714306--28714949 Score: 329
Period size: 23 Copynumber: 27.6 Consensus size: 22
28714296 TACATATTAC
*
28714306 AAATTTGGACAGCACTTATACACA
1 AAATTT-GACAGCA-TTATATACA
* *
28714330 AAATATAACAGCATGTATATACA
1 AAATTTGACAGCAT-TATATACA
28714353 AAATTTGACAGCATTGAT-TCACCA
1 AAATTTGACAGCATT-ATAT-A-CA
* * *
28714377 AAATTGGGCAGCATACATATAC-
1 AAATTTGACAGCAT-TATATACA
*
28714399 AAATTTGGACAGCACTTATACACA
1 AAATTT-GACAGCA-TTATATACA
* * *
28714423 AAATATAACAGCATGTATGTACA
1 AAATTTGACAGCAT-TATATACA
*
28714446 AAATTTGACAGCATTGCT-TCACCA
1 AAATTTGACAGCATT-ATAT-A-CA
* * *
28714470 AAATTGGGCAGCA-TACATACA
1 AAATTTGACAGCATTATATACA
*
28714491 CAAATTTGGACAGCACTTATACACA
1 -AAATTT-GACAGCA-TTATATACA
*
28714516 AAATTTAACAGCATGTATATACA
1 AAATTTGACAGCAT-TATATACA
*
28714539 AAATTGGACAGCATTGAT-TCACCA
1 AAATTTGACAGCATT-ATAT-A-CA
* * *
28714563 AAATTGGGCAGCATACATATAC-
1 AAATTTGACAGCAT-TATATACA
* *
28714585 AAATTTGGACGGCACTTATACACA
1 AAATTT-GACAGCA-TTATATACA
* * *
28714609 ATATATAACAGCATGTATATACA
1 AAATTTGACAGCAT-TATATACA
*
28714632 AAATTGGACAGCATTGAT-TCACCA
1 AAATTTGACAGCATT-ATAT-A-CA
* * *
28714656 AAATTGGGCAGCATACATATAC-
1 AAATTTGACAGCAT-TATATACA
* *
28714678 AAATTTGGACGGCACTTATACACA
1 AAATTT-GACAGCA-TTATATACA
* * *
28714702 ATATATAACAGCATGTATATACA
1 AAATTTGACAGCAT-TATATACA
*
28714725 AAATTGGACAGCATTGAT-TCACCA
1 AAATTTGACAGCATT-ATAT-A-CA
* * *
28714749 AAATTGGGCAGCATACATATACA
1 AAATTTGACAGCAT-TATATACA
* *
28714772 AAATTGGACAGCACTTATACACA
1 AAATTTGACAGCA-TTATATACA
* *
28714795 AAATATAACAGCATGTATATACA
1 AAATTTGACAGCAT-TATATACA
28714818 AAATTTGACAGCATT-TATTCACCCA
1 AAATTTGACAGCATTATA-T-A--CA
* * * *
28714843 AAATTAGGCAGCA-TACATAAA
1 AAATTTGACAGCATTATATACA
*
28714864 CAAATTTGGACAGCATTTATACACA
1 -AAATTT-GACAGCA-TTATATACA
*
28714889 AAATTTAACAGCATGTATATACA
1 AAATTTGACAGCAT-TATATACA
*
28714912 AAATTTGACAGCATTGATTTATCA
1 AAATTTGACAGCATT-ATATA-CA
* *
28714936 AAATTGGGCAGCAT
1 AAATTTGACAGCAT
28714950 ACCTATAACA
Statistics
Matches: 475, Mismatches: 89, Indels: 112
0.70 0.13 0.17
Matches are distributed among these distances:
21 5 0.01
22 46 0.10
23 261 0.55
24 134 0.28
25 29 0.06
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (22 bp):
AAATTTGACAGCATTATATACA
Found at i:28715729 original size:28 final size:28
Alignment explanation
Indices: 28715697--28715851 Score: 193
Period size: 28 Copynumber: 5.5 Consensus size: 28
28715687 ATTTAATAAG
* * *
28715697 CTCGCACACTTAGTGCTCAATAATCAAA
1 CTCGCACACTTAGTGCTCTACAATTAAA
* *
28715725 CTCGCACACTTAGTGCTTTACCATTAAA
1 CTCGCACACTTAGTGCTCTACAATTAAA
* *
28715753 CTCGCACACTTAGTGCTTTACCATTAAA
1 CTCGCACACTTAGTGCTCTACAATTAAA
28715781 CTCGCACACTTAGTGCTCTACAATTAAA
1 CTCGCACACTTAGTGCTCTACAATTAAA
* * * *
28715809 CTCACGCACTTAGTGCTTTATAATTAAA
1 CTCGCACACTTAGTGCTCTACAATTAAA
* *
28715837 TTCACACACTTAGTG
1 CTCGCACACTTAGTG
28715852 TCAAAAATCA
Statistics
Matches: 114, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 114 1.00
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (28 bp):
CTCGCACACTTAGTGCTCTACAATTAAA
Found at i:28715845 original size:84 final size:84
Alignment explanation
Indices: 28715697--28715851 Score: 229
Period size: 84 Copynumber: 1.8 Consensus size: 84
28715687 ATTTAATAAG
* * * *
28715697 CTCGCACACTTAGTGCTCAATAATCAAACTCGCACACTTAGTGCTTTACCATTAAACTCGCACAC
1 CTCGCACACTTAGTGCTCAACAATCAAACTCACACACTTAGTGCTTTACAATTAAACTCACACAC
28715762 TTAGTGCTTTACCATTAAA
66 TTAGTGCTTTACCATTAAA
* * * * *
28715781 CTCGCACACTTAGTGCTCTACAATTAAACTCACGCACTTAGTGCTTTATAATTAAATTCACACAC
1 CTCGCACACTTAGTGCTCAACAATCAAACTCACACACTTAGTGCTTTACAATTAAACTCACACAC
28715846 TTAGTG
66 TTAGTG
28715852 TCAAAAATCA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 62 1.00
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (84 bp):
CTCGCACACTTAGTGCTCAACAATCAAACTCACACACTTAGTGCTTTACAATTAAACTCACACAC
TTAGTGCTTTACCATTAAA
Found at i:28725704 original size:28 final size:28
Alignment explanation
Indices: 28725664--28725720 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
28725654 ATTTAACCGA
28725664 TAATTTATTTTGGTAAGCTAAAGATCGC
1 TAATTTATTTTGGTAAGCTAAAGATCGC
28725692 TAATTTATTTTGGTAAGCTAAAGATCGC
1 TAATTTATTTTGGTAAGCTAAAGATCGC
28725720 T
1 T
28725721 CACCGCCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.40
Consensus pattern (28 bp):
TAATTTATTTTGGTAAGCTAAAGATCGC
Found at i:28728259 original size:41 final size:40
Alignment explanation
Indices: 28728188--28728488 Score: 207
Period size: 41 Copynumber: 7.4 Consensus size: 40
28728178 ATTTTTAAAC
* * *
28728188 CTTTAGCGGCGTTTTTATTTTAGTGCCACTAATTCTCCGAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCACTAATTCT-CGAT
* * * * *
28728229 CTTTAGCGGTGTTTTTATCTGAGCGTCACTAATGT-TCTAGC
1 CTTTAGCGGCGTTTTTATCTAAGCGCCACTAAT-TCTCGA-T
* * *
28728270 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGTAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCACTAATTCTCG-AT
* * * * * *
28728311 CATTAGTGGCGTTATTGTCTGAGCGCCACTAATTCTCTGTT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCACTAATTCTC-GAT
* *
28728352 CTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGTTCGT-G-T
1 CTTTAGCGGCGTTTTTATCTAAGCGCCACT-AA-TTC-TCGAT
* ** * * **
28728393 TTTTAATGGCGTTTTTATCTGAGCGCCACTAATACTCTGGC
1 CTTTAGCGGCGTTTTTATCTAAGCGCCACTAATTCTC-GAT
* * * *
28728434 CTTTAGCGGCGTTTTATATGTAAGCGCCGCTAATGCT--AC
1 CTTTAGCGGCGTTTT-TATCTAAGCGCCACTAATTCTCGAT
28728473 CTTTAGCGGCGTTTTT
1 CTTTAGCGGCGTTTTT
28728489 CCGAAGCGCC
Statistics
Matches: 204, Mismatches: 44, Indels: 27
0.74 0.16 0.10
Matches are distributed among these distances:
38 2 0.01
39 18 0.09
40 5 0.02
41 152 0.75
42 23 0.11
43 3 0.01
44 1 0.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.40
Consensus pattern (40 bp):
CTTTAGCGGCGTTTTTATCTAAGCGCCACTAATTCTCGAT
Found at i:28728335 original size:82 final size:80
Alignment explanation
Indices: 28728187--28728470 Score: 300
Period size: 82 Copynumber: 3.5 Consensus size: 80
28728177 GATTTTTAAA
* * * * * * *
28728187 CCTTTAGCGGCGTTTTTATTTTAGTGCCACTAATTCTCCG-ATCTTTAGCGGTGTTTTTATCTGA
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCT-CGTATCTTTAGTGGCGTTTTTATCTGA
*
28728251 GCGTCACTAATGTTCTAG
65 GCGCCACTAAT-TTCT-G
* * * *
28728269 CCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGTATCATTAGTGGCGTTATTGTCTGAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
28728334 CGCCACTAATTCTCTG
66 CGCCACTAATT-TCTG
* * * * * * *
28728350 TTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGTTCGTGTTTTTAATGGCGTTTTTATCTGA
1 -CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGA
*
28728415 GCGCCACTAATACTCTGG
65 GCGCCACTAAT-TTCT-G
*
28728433 CCTTTAGCGGCGTTTTATATGTAAGCGCCGCTAATGCT
1 CCTTTAGCGGCGTTTT-TATCTAAGCGCCGCTAATGCT
28728471 ACCTTTAGCG
Statistics
Matches: 168, Mismatches: 28, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
81 4 0.02
82 146 0.87
83 18 0.11
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (80 bp):
CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
CGCCACTAATTTCTG
Found at i:28728445 original size:123 final size:123
Alignment explanation
Indices: 28728186--28728488 Score: 267
Period size: 123 Copynumber: 2.5 Consensus size: 123
28728176 CGATTTTTAA
* * * * * *
28728186 ACCTTTAGCGGCGTTTTTATTTTAGTGCCACTAATTCTCCGATCTTTAGCGGTGTTTTTATCTGA
1 ACCTTTAGCGGCGTTATTATCTGAGCGCCACTAATTCTCCGATCTTTAGCGGCGTTTTTATCTAA
* * * * * *
28728251 GCGTCACTAATGTTCTAGCCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGT
66 GCGCCACTAAAGTTCTAGCCTTTAACGGCGTTTTTATCTAAGCGCCACTAATACTCGT
* * * * * * *
28728309 ATCATTAGTGGCGTTATTGTCTGAGCGCCACTAATTCTCTGTTCTTTAGCGGCGTTTTTTTCTAA
1 ACCTTTAGCGGCGTTATTATCTGAGCGCCACTAATTCTCCGATCTTTAGCGGCGTTTTTATCTAA
* ** * *
28728374 GCGCCGCTAAAGTTCGT-GTTTTTAATGGCGTTTTTATCTGAGCGCCACTAATACTC-T
66 GCGCCACTAAAGTTC-TAGCCTTTAACGGCGTTTTTATCTAAGCGCCACTAATACTCGT
* * * * *
28728431 GGCCTTTAGCGGCGTT-TTATATGTAAGCGCCGCTAATGCT---ACCTTTAGCGGCGTTTTT
1 -ACCTTTAGCGGCGTTATTATCTG--AGCGCCACTAATTCTCCGATCTTTAGCGGCGTTTTT
28728489 CCGAAGCGCC
Statistics
Matches: 142, Mismatches: 34, Indels: 10
0.76 0.18 0.05
Matches are distributed among these distances:
121 16 0.11
122 6 0.04
123 106 0.75
124 14 0.10
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (123 bp):
ACCTTTAGCGGCGTTATTATCTGAGCGCCACTAATTCTCCGATCTTTAGCGGCGTTTTTATCTAA
GCGCCACTAAAGTTCTAGCCTTTAACGGCGTTTTTATCTAAGCGCCACTAATACTCGT
Found at i:28730769 original size:8 final size:10
Alignment explanation
Indices: 28730746--28730783 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
28730736 ATATTTTTAC
28730746 ATATATATGG
1 ATATATATGG
*
28730756 ATATATATGA
1 ATATATATGG
28730766 ATATATATGG
1 ATATATATGG
28730776 ATATATAT
1 ATATATAT
28730784 ATAGTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (10 bp):
ATATATATGG
Found at i:28730769 original size:20 final size:20
Alignment explanation
Indices: 28730746--28730783 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
28730736 ATATTTTTAC
28730746 ATATATATGGATATATATGA
1 ATATATATGGATATATATGA
28730766 ATATATATGGATATATAT
1 ATATATATGGATATATAT
28730784 ATAGTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (20 bp):
ATATATATGGATATATATGA
Found at i:28730892 original size:27 final size:27
Alignment explanation
Indices: 28730851--28730902 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
28730841 AATAAACAAA
* *
28730851 TAAATAAGTTAGTAATTATTTATTTGT
1 TAAATAAATTAGTAATTAATTATTTGT
*
28730878 TAAATAAATTGGTAATTAATTATTT
1 TAAATAAATTAGTAATTAATTATTT
28730903 AAAAGTCGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (27 bp):
TAAATAAATTAGTAATTAATTATTTGT
Found at i:28741218 original size:72 final size:71
Alignment explanation
Indices: 28741101--28741458 Score: 405
Period size: 71 Copynumber: 5.0 Consensus size: 71
28741091 TCATGGAATA
* * * * *
28741101 TCAGCTGAGAGCGTATGCTTGCGCTAACTATTTTTGGAAGTTACGGTATTAAACCTATGAGCCTT
1 TCAGCTGAGAGCGTAGGCTCGCGCTAACTA-TTTTGGAGGCTACGGTATTGAACCTATGAGCCTT
28741166 AAGATAT
65 AAGATAT
* * * * *
28741173 TCAGCTGAGAGCGTAGGCTCGCGCTAATTTTTTTTGGAGGCTACGGTATTAAACTTGTGAGCCTT
1 TCAGCTGAGAGCGTAGGCTCGCGCTAA-CTATTTTGGAGGCTACGGTATTGAACCTATGAGCCTT
*
28741238 AAAATAT
65 AAGATAT
* * * * ** * *
28741245 TCAGCTGAGAGAGTCGGCTCGCGCTAACTATTTTGGAGGTTGCGGGGTTGAGCTCT-TAAGCCTT
1 TCAGCTGAGAGCGTAGGCTCGCGCTAACTATTTTGGAGGCTACGGTATTGAAC-CTATGAGCCTT
28741309 AAGATAT
65 AAGATAT
* * * *
28741316 TTAGAT-AGAAGCGTAGGCTCGCGCTAACTATTTTGGAGGCTACGGTATTGAATCTACGAGCCTT
1 TCAGCTGAG-AGCGTAGGCTCGCGCTAACTATTTTGGAGGCTACGGTATTGAACCTATGAGCCTT
28741380 AAGATAT
65 AAGATAT
*** * * *
28741387 TTTTCTGAGAGCGTAGGCTCGCGCTAACTATTTTGGAGGCTGCAGTATTGAACCTACGAGCCTTA
1 TCAGCTGAGAGCGTAGGCTCGCGCTAACTATTTTGGAGGCTACGGTATTGAACCTATGAGCCTTA
28741452 AGATAT
66 AGATAT
28741458 T
1 T
28741459 TCCAAGTACA
Statistics
Matches: 241, Mismatches: 40, Indels: 11
0.83 0.14 0.04
Matches are distributed among these distances:
70 4 0.02
71 147 0.61
72 89 0.37
73 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (71 bp):
TCAGCTGAGAGCGTAGGCTCGCGCTAACTATTTTGGAGGCTACGGTATTGAACCTATGAGCCTTA
AGATAT
Found at i:28743475 original size:16 final size:16
Alignment explanation
Indices: 28743454--28743489 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
28743444 TTTGCTTCGC
28743454 TGTATTAGATTAGAGG
1 TGTATTAGATTAGAGG
*
28743470 TGTATTGGATTAGAGG
1 TGTATTAGATTAGAGG
28743486 TGTA
1 TGTA
28743490 AAGGAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.39
Consensus pattern (16 bp):
TGTATTAGATTAGAGG
Found at i:28743499 original size:16 final size:16
Alignment explanation
Indices: 28743464--28743506 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
28743454 TGTATTAGAT
** *
28743464 TAGAGGTGTATTGGAT
1 TAGAGGTGTAAAGGAA
28743480 TAGAGGTGTAAAGGAA
1 TAGAGGTGTAAAGGAA
28743496 TAGAGGTGTAA
1 TAGAGGTGTAA
28743507 TAGCAAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (16 bp):
TAGAGGTGTAAAGGAA
Found at i:28743758 original size:16 final size:16
Alignment explanation
Indices: 28743721--28743762 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28743711 TTAATCATAT
*
28743721 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28743737 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28743752 TTAAAATATAT
1 TTAAAATATAT
28743763 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28743769 original size:14 final size:15
Alignment explanation
Indices: 28743730--28743771 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28743720 TTTAAACATA
*
28743730 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28743745 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28743759 A-TATAATTTAATA
1 ATTATAATTAAATA
28743772 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28743880 original size:16 final size:16
Alignment explanation
Indices: 28743859--28743900 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
28743849 AATTAATATT
28743859 AAATATAT-TTTAATTA
1 AAATATATATTTAA-TA
28743875 AAATATATGATTTAATA
1 AAATATAT-ATTTAATA
*
28743892 AAATTTATA
1 AAATATATA
28743901 ATAATTATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 9 0.39
18 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
AAATATATATTTAATA
Found at i:28743953 original size:101 final size:95
Alignment explanation
Indices: 28743835--28744155 Score: 428
Period size: 91 Copynumber: 3.4 Consensus size: 95
28743825 ATACTATAAA
* *
28743835 ATATAATTTGAAATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTT-A
1 ATATAATTTAAAATAATTAATATTAAATATAATTTAATT--AATA-ATGA--TAAT-AAATTTCA
* ***
28743899 TAATAATTATACCTAATAAATTTTCTTATATGAATTT
60 TAA-AATTCTTGATAATAAATTTTCTTATATGAATTT
* *
28743936 GTATAATTTAAAATAATTATTATTAAATATAATTTAA-TAATAAT-AT-AT-AATTTCATAAAAT
1 ATATAATTTAAAATAATTAATATTAAATATAATTTAATTAATAATGATAATAAATTTCATAAAAT
28743997 TCTTGATAATAAATTTTCTTATATGAATTT
66 TCTTGATAATAAATTTTCTTATATGAATTT
28744027 ATATAATTTAAAATAATTAATATTAAATATAA--T--TTAATAATGA-AATATAATTTCATAAAA
1 ATATAATTTAAAATAATTAATATTAAATATAATTTAATTAATAATGATAATA-AATTTCATAAAA
28744087 TTCTTGATAATAAATTTTCTTATATGAATTT
65 TTCTTGATAATAAATTTTCTTATATGAATTT
28744118 ATATAATTTAAAATAATTAATATTAAATATAATTTAAT
1 ATATAATTTAAAATAATTAATATTAAATATAATTTAAT
28744156 AATGATATAT
Statistics
Matches: 200, Mismatches: 10, Indels: 26
0.85 0.04 0.11
Matches are distributed among these distances:
88 7 0.04
89 4 0.02
91 139 0.69
92 4 0.02
93 3 0.01
94 1 0.00
95 1 0.00
96 1 0.00
97 2 0.01
98 4 0.02
100 1 0.00
101 33 0.17
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (95 bp):
ATATAATTTAAAATAATTAATATTAAATATAATTTAATTAATAATGATAATAAATTTCATAAAAT
TCTTGATAATAAATTTTCTTATATGAATTT
Found at i:28744008 original size:91 final size:91
Alignment explanation
Indices: 28743912--28744170 Score: 475
Period size: 91 Copynumber: 2.8 Consensus size: 91
28743902 TAATTATACC
* *
28743912 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
28743977 AATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTGA
28744003 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
28744068 GAA-ATATAATTTCATAAAATTCTTGA
66 -AATATATAATTTCATAAAATTCTTGA
28744094 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
28744159 GATATATAATTT
66 AATATATAATTT
28744171 ATACATTTAA
Statistics
Matches: 163, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
90 1 0.01
91 160 0.98
92 2 0.01
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTGA
Found at i:28744074 original size:18 final size:18
Alignment explanation
Indices: 28744017--28744084 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
28744007 AAATTTTCTT
28744017 ATATGAATTTATATAATTTAA
1 ATAT-AATTTA-ATAA-TTAA
28744038 A-ATAA-TTAAT-ATTAA
1 ATATAATTTAATAATTAA
*
28744053 ATATAATTTAATAATGAA
1 ATATAATTTAATAATTAA
*
28744071 ATATAATTTCATAA
1 ATATAATTTAATAA
28744085 AATTCTTGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 5 0.12
16 5 0.12
17 7 0.17
18 20 0.48
19 2 0.05
20 2 0.05
21 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (18 bp):
ATATAATTTAATAATTAA
Found at i:28745189 original size:17 final size:17
Alignment explanation
Indices: 28745167--28745202 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
28745157 GCACCTAATA
28745167 TAACTCATATTTCAAAT
1 TAACTCATATTTCAAAT
28745184 TAACTCATATTTCAAAT
1 TAACTCATATTTCAAAT
28745201 TA
1 TA
28745203 CAGCAAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (17 bp):
TAACTCATATTTCAAAT
Found at i:28752465 original size:18 final size:19
Alignment explanation
Indices: 28752431--28752471 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
28752421 ATCATTTTAG
28752431 ATTTTAAATTAATTTTCAA
1 ATTTTAAATTAATTTTCAA
28752450 ATTTT-AATATAA-TTTCAA
1 ATTTTAAAT-TAATTTTCAA
28752468 ATTT
1 ATTT
28752472 CAGAATCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTAAATTAATTTTCAA
Found at i:28753976 original size:16 final size:16
Alignment explanation
Indices: 28753940--28753971 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
28753930 AATATTTTTG
28753940 ATAAATGTTATATATT
1 ATAAATGTTATATATT
28753956 ATAAAT-TT-TATATT
1 ATAAATGTTATATATT
28753970 AT
1 AT
28753972 TTAAACAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
ATAAATGTTATATATT
Found at i:28753980 original size:79 final size:79
Alignment explanation
Indices: 28753883--28754056 Score: 348
Period size: 79 Copynumber: 2.2 Consensus size: 79
28753873 ATGACAAAAA
28753883 TTTATATTATTTAAACAGTGTAGTGAAAGTTATTGGACACTTTACAAAATATTTTTGATAAATGT
1 TTTATATTATTTAAACAGTGTAGTGAAAGTTATTGGACACTTTACAAAATATTTTTGATAAATGT
28753948 TATATATTATAAAT
66 TATATATTATAAAT
28753962 TTTATATTATTTAAACAGTGTAGTGAAAGTTATTGGACACTTTACAAAATATTTTTGATAAATGT
1 TTTATATTATTTAAACAGTGTAGTGAAAGTTATTGGACACTTTACAAAATATTTTTGATAAATGT
28754027 TATATATTATAAAT
66 TATATATTATAAAT
28754041 TTTATATTATTTAAAC
1 TTTATATTATTTAAAC
28754057 CAAATTTACA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 95 1.00
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.45
Consensus pattern (79 bp):
TTTATATTATTTAAACAGTGTAGTGAAAGTTATTGGACACTTTACAAAATATTTTTGATAAATGT
TATATATTATAAAT
Found at i:28754055 original size:16 final size:16
Alignment explanation
Indices: 28754019--28754050 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
28754009 AATATTTTTG
28754019 ATAAATGTTATATATT
1 ATAAATGTTATATATT
28754035 ATAAAT-TT-TATATT
1 ATAAATGTTATATATT
28754049 AT
1 AT
28754051 TTAAACCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
ATAAATGTTATATATT
Found at i:28760839 original size:20 final size:21
Alignment explanation
Indices: 28760790--28760853 Score: 69
Period size: 22 Copynumber: 3.1 Consensus size: 21
28760780 GGATATTTGT
* *
28760790 TTAGCACTTTTATGCTCTCTAA
1 TTAGCACTTTTGTGCTCTCT-G
*
28760812 TTAACACTTTTGTGCTCTCTG
1 TTAGCACTTTTGTGCTCTCTG
*
28760833 TT-GCACTTTGGTGC-CTCTG
1 TTAGCACTTTTGTGCTCTCTG
28760852 TT
1 TT
28760854 CAGCTATACG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.19
20 10 0.27
21 2 0.05
22 18 0.49
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.47
Consensus pattern (21 bp):
TTAGCACTTTTGTGCTCTCTG
Found at i:28760850 original size:19 final size:20
Alignment explanation
Indices: 28760816--28760853 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28760806 CTCTAATTAA
*
28760816 CACTTTTGTGCTCTCTGTTG
1 CACTTTGGTGCTCTCTGTTG
28760836 CACTTTGGTGC-CTCTGTT
1 CACTTTGGTGCTCTCTGTT
28760854 CAGCTATACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.05, C:0.26, G:0.21, T:0.47
Consensus pattern (20 bp):
CACTTTGGTGCTCTCTGTTG
Found at i:28766171 original size:21 final size:21
Alignment explanation
Indices: 28766147--28766200 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
28766137 AAATTAGATT
*
28766147 TCTGTTTGCACTTTTGTGCTC
1 TCTGTTAGCACTTTTGTGCTC
*
28766168 TCTGTTAGCATTTTTGTGC-C
1 TCTGTTAGCACTTTTGTGCTC
*
28766188 TTTGTTCAGCACT
1 TCTGTT-AGCACT
28766201 GCGATGCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.09, C:0.22, G:0.19, T:0.50
Consensus pattern (21 bp):
TCTGTTAGCACTTTTGTGCTC
Found at i:28767427 original size:22 final size:22
Alignment explanation
Indices: 28767397--28767445 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
28767387 AAAAAAACAG
*
28767397 AAAAA-AAGCAAAAAGCGCAAA
1 AAAAAGAAGCAAAAAGCACAAA
28767418 AAAAAGAAGCAAAAAGCACAAA
1 AAAAAGAAGCAAAAAGCACAAA
28767440 AAAAAG
1 AAAAAG
28767446 TTGCCTACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.73, C:0.12, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAAGAAGCAAAAAGCACAAA
Found at i:28776058 original size:11 final size:11
Alignment explanation
Indices: 28776042--28776072 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
28776032 ATACCCATAC
28776042 CCCATACCTTG
1 CCCATACCTTG
*
28776053 CCCATACCTTT
1 CCCATACCTTG
28776064 CCCATACCT
1 CCCATACCT
28776073 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:28776646 original size:18 final size:18
Alignment explanation
Indices: 28776619--28776711 Score: 168
Period size: 18 Copynumber: 5.2 Consensus size: 18
28776609 TACGACCGTT
28776619 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
28776637 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
28776655 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
28776673 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
28776691 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
28776709 TAC
1 TAC
28776712 AGTAGTTGGG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 72 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:28780781 original size:11 final size:11
Alignment explanation
Indices: 28780765--28780795 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
28780755 ATACCCATAC
28780765 CCCATACCTTG
1 CCCATACCTTG
*
28780776 CCCATACCTTT
1 CCCATACCTTG
28780787 CCCATACCT
1 CCCATACCT
28780796 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:28788756 original size:16 final size:17
Alignment explanation
Indices: 28788728--28788759 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28788718 GAAGATAAGT
28788728 ATTAAATTATATTAAAC
1 ATTAAATTATATTAAAC
28788745 ATTAAA-TATATTAAA
1 ATTAAATTATATTAAA
28788760 ATAATATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAAATTATATTAAAC
Found at i:28815380 original size:19 final size:19
Alignment explanation
Indices: 28815356--28815392 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28815346 GCATACTGGC
*
28815356 GCATGAAGCTCATCCTAGT
1 GCATGAAGCACATCCTAGT
28815375 GCATGAAGCACATCCTAG
1 GCATGAAGCACATCCTAG
28815393 CACACGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (19 bp):
GCATGAAGCACATCCTAGT
Found at i:28816196 original size:15 final size:15
Alignment explanation
Indices: 28816147--28816200 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
28816137 CCTAAAAGTG
28816147 TTAATTAAGCTTAAT
1 TTAATTAAGCTTAAT
*
28816162 ATTAATTAAGCATAGA-
1 -TTAATTAAGCTTA-AT
28816178 TTAATTAAG-TTAAT
1 TTAATTAAGCTTAAT
28816192 CTTAATTAA
1 -TTAATTAA
28816201 TAACTAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 1 0.03
14 2 0.06
15 17 0.52
16 12 0.36
17 1 0.03
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (15 bp):
TTAATTAAGCTTAAT
Found at i:28821382 original size:25 final size:25
Alignment explanation
Indices: 28821354--28821517 Score: 82
Period size: 25 Copynumber: 6.6 Consensus size: 25
28821344 GAATTCTCTA
28821354 GAAAGTCTTTT-TGGCATATCATTGG
1 GAAAG-CTTTTGTGGCATATCATTGG
* *
28821379 GAAAGCTTTTGTGGTATATCATTTG
1 GAAAGCTTTTGTGGCATATCATTGG
* * * * **
28821404 GAAAGCCTTTGTAGTAAATTTTCTGG
1 GAAAGCTTTTGTGGCATATCAT-TGG
* * * *
28821430 G-AAGCCTTTATGGCGTATCATTTG
1 GAAAGCTTTTGTGGCATATCATTGG
* * * *
28821454 GAAAGCCTTTGTGGTGATTTCACT-G
1 GAAAGCTTTTGTGG-CATATCATTGG
* * * **
28821479 GAAAGCCTCTGTGGCGTATCATTTA
1 GAAAGCTTTTGTGGCATATCATTGG
*
28821504 GAAAGCCTTTGTGG
1 GAAAGCTTTTGTGG
28821518 TGAACTCTCT
Statistics
Matches: 106, Mismatches: 28, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
24 13 0.12
25 85 0.80
26 8 0.08
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (25 bp):
GAAAGCTTTTGTGGCATATCATTGG
Found at i:28821449 original size:50 final size:50
Alignment explanation
Indices: 28821378--28821773 Score: 400
Period size: 50 Copynumber: 7.9 Consensus size: 50
28821368 CATATCATTG
* ** * *
28821378 GGAAAGCTTTTGTGGTATATCATTTGGAAAGCCTTTGTAGTAAATT-TTCT
1 GGAAAGCCTTTGTGGCGTATCATTTGGAAAGCCTTTGTGGTGAATTATT-T
* * * *
28821428 GGGAAGCCTTTATGGCGTATCATTTGGAAAGCCTTTGTGGTGATTTCA-CT
1 GGAAAGCCTTTGTGGCGTATCATTTGGAAAGCCTTTGTGGTGAATT-ATTT
* * * * *
28821478 GGAAAGCCTCTGTGGCGTATCATTTAGAAAGCCTTTGTGGTGAACTCTCT
1 GGAAAGCCTTTGTGGCGTATCATTTGGAAAGCCTTTGTGGTGAATTATTT
* ** * * ** *
28821528 AGAAAGATTTTTTGACGTATCATTTGGAAAGCCTTTGTGGCAAATTCTTT
1 GGAAAGCCTTTGTGGCGTATCATTTGGAAAGCCTTTGTGGTGAATTATTT
* ** * * * * *
28821578 GGAAAGCCTTTATGAAGAATTATCTGGAAAGCCTTTATGGCGAATTATTT
1 GGAAAGCCTTTGTGGCGTATCATTTGGAAAGCCTTTGTGGTGAATTATTT
* * *
28821628 GAAAAACCCTTGTGGCGTATCATTTGGAAAGCCTTTGTGGTGAATTATTT
1 GGAAAGCCTTTGTGGCGTATCATTTGGAAAGCCTTTGTGGTGAATTATTT
* * *
28821678 GGAGAGCCCTTGTGGCGTATCATTTGGAAAGCCTTTATGGTGAATTATTT
1 GGAAAGCCTTTGTGGCGTATCATTTGGAAAGCCTTTGTGGTGAATTATTT
* * * *
28821728 GGAAAGCCCTTGTGGTGTATCATTTAGAAAGCCTTTATGGTGAATT
1 GGAAAGCCTTTGTGGCGTATCATTTGGAAAGCCTTTGTGGTGAATT
28821774 CTCTAGAAAT
Statistics
Matches: 287, Mismatches: 56, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
50 287 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.36
Consensus pattern (50 bp):
GGAAAGCCTTTGTGGCGTATCATTTGGAAAGCCTTTGTGGTGAATTATTT
Found at i:28821578 original size:25 final size:25
Alignment explanation
Indices: 28821400--28821775 Score: 208
Period size: 25 Copynumber: 15.0 Consensus size: 25
28821390 TGGTATATCA
* **
28821400 TTTGGAAAGCCTTTGTAGTAAATT-
1 TTTGGAAAGCCTTTGTGGCGAATTC
* * *
28821424 TTCTGGGAAGCCTTTATGGCGTA-TC
1 TT-TGGAAAGCCTTTGTGGCGAATTC
* *
28821449 ATTTGGAAAGCCTTTGTGGTGATTTC
1 -TTTGGAAAGCCTTTGTGGCGAATTC
** * *
28821475 ACTGGAAAGCCTCTGTGGCGTA-TC
1 TTTGGAAAGCCTTTGTGGCGAATTC
* * *
28821499 ATTTAGAAAGCCTTTGTGGTGAACTC
1 -TTTGGAAAGCCTTTGTGGCGAATTC
* * ** * * *
28821525 TCTAGAAAGATTTTTTGACGTA-TC
1 TTTGGAAAGCCTTTGTGGCGAATTC
*
28821549 ATTTGGAAAGCCTTTGTGGCAAATTC
1 -TTTGGAAAGCCTTTGTGGCGAATTC
* ** *
28821575 TTTGGAAAGCCTTTATGAAGAATTA
1 TTTGGAAAGCCTTTGTGGCGAATTC
* * *
28821600 TCTGGAAAGCCTTTATGGCGAATTA
1 TTTGGAAAGCCTTTGTGGCGAATTC
* * * *
28821625 TTTGAAAAACCCTTGTGGCGTA-TC
1 TTTGGAAAGCCTTTGTGGCGAATTC
* *
28821649 ATTTGGAAAGCCTTTGTGGTGAATTA
1 -TTTGGAAAGCCTTTGTGGCGAATTC
* * *
28821675 TTTGGAGAGCCCTTGTGGCGTA-TC
1 TTTGGAAAGCCTTTGTGGCGAATTC
* * *
28821699 ATTTGGAAAGCCTTTATGGTGAATTA
1 -TTTGGAAAGCCTTTGTGGCGAATTC
* * *
28821725 TTTGGAAAGCCCTTGTGGTGTA-TC
1 TTTGGAAAGCCTTTGTGGCGAATTC
* * *
28821749 ATTTAGAAAGCCTTTATGGTGAATTC
1 -TTTGGAAAGCCTTTGTGGCGAATTC
28821775 T
1 T
28821776 CTAGAAATTT
Statistics
Matches: 260, Mismatches: 78, Indels: 27
0.71 0.21 0.07
Matches are distributed among these distances:
24 10 0.04
25 238 0.92
26 12 0.05
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.36
Consensus pattern (25 bp):
TTTGGAAAGCCTTTGTGGCGAATTC
Found at i:28828612 original size:45 final size:45
Alignment explanation
Indices: 28828549--28828638 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
28828539 GGTCGGTCCA
28828549 ACTACTAATTGGACCGCCAATCCAGTTTTACATACTATGCCTGAT
1 ACTACTAATTGGACCGCCAATCCAGTTTTACATACTATGCCTGAT
28828594 ACTACTAATTGGACCGCCAATCCAGTTTTACATACTATGCCTGAT
1 ACTACTAATTGGACCGCCAATCCAGTTTTACATACTATGCCTGAT
28828639 TTGACCAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (45 bp):
ACTACTAATTGGACCGCCAATCCAGTTTTACATACTATGCCTGAT
Found at i:28830154 original size:27 final size:27
Alignment explanation
Indices: 28830124--28830429 Score: 225
Period size: 27 Copynumber: 11.4 Consensus size: 27
28830114 CGGCCTAGAT
28830124 GTCATTTTACCCTTTAGGGGTATTTCG
1 GTCATTTTACCCTTTAGGGGTATTTCG
* *
28830151 GTCATTTTACCCTTT-GAGGATATTTCA
1 GTCATTTTACCCTTTAG-GGGTATTTCG
* * *
28830178 GTCATTTCA-CCTTTCAGAGGTATTTCA
1 GTCATTTTACCCTTT-AGGGGTATTTCG
* *
28830205 ATCATTTTACCCTTT-GAGGGTATTTTG
1 GTCATTTTACCCTTTAG-GGGTATTTCG
*
28830232 GTCA-TTTACCC-TTCGGGGTATTTCG
1 GTCATTTTACCCTTTAGGGGTATTTCG
* * **
28830257 GTCATTTTATCCTTCAAAGGTATTTCG
1 GTCATTTTACCCTTTAGGGGTATTTCG
** * *
28830284 GTCATTTTACCAATCAAGGGTATTTCG
1 GTCATTTTACCCTTTAGGGGTATTTCG
* * *
28830311 GTTATTTTACCCATT-GAAGGTATTTCG
1 GTCATTTTACCCTTTAG-GGGTATTTCG
* * * *
28830338 GCCATTTCACCCATT-GAGGGTATTTTG
1 GTCATTTTACCCTTTAG-GGGTATTTCG
* * *
28830365 ATCATTTTACCC-ATCGAGGGTATTTCG
1 GTCATTTTACCCTTTAG-GGGTATTTCG
* * *
28830392 GTCATTTTACCCATCAAGGGTATTTCG
1 GTCATTTTACCCTTTAGGGGTATTTCG
*
28830419 GTTA-TTTACCC
1 GTCATTTTACCC
28830430 ACGAATCGCA
Statistics
Matches: 226, Mismatches: 42, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
25 15 0.07
26 29 0.13
27 176 0.78
28 6 0.03
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTTTAGGGGTATTTCG
Found at i:28830210 original size:54 final size:53
Alignment explanation
Indices: 28830124--28830429 Score: 248
Period size: 54 Copynumber: 5.7 Consensus size: 53
28830114 CGGCCTAGAT
* * * * *
28830124 GTCATTTTACCCTTTAGGGGTATTTCGGTCATTTTACCCTTTGAGGATATTTCA
1 GTCATTTCACCATTCAGAGGTATTTCGGTCATTTTACCCTTTGAGG-TATTTCG
* ** *
28830178 GTCATTTCACCTTTCAGAGGTATTTCAATCATTTTACCCTTTGAGGGTATTTTG
1 GTCATTTCACCATTCAGAGGTATTTCGGTCATTTTACCCTTTGA-GGTATTTCG
* * * **
28830232 GTCATTT-ACCCTTC-GGGGTATTTCGGTCATTTTATCCTTCAAAGGTATTTCG
1 GTCATTTCACCATTCAGAGGTATTTCGGTCATTTTACCCTT-TGAGGTATTTCG
* * * *
28830284 GTCATTTTACCAATCA-AGGGTATTTCGGTTATTTTACCCATTGAAGGTATTTCG
1 GTCATTTCACCATTCAGA-GGTATTTCGGTCATTTTACCCTTTG-AGGTATTTCG
* * * * * *
28830338 GCCATTTCACCCATTGAG-GGTATTTTGATCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTCA-CCATTCAGAGGTATTTCGGTCATTTTACCCTTTGA-GGTATTTCG
* *
28830392 GTCATTTTACCCA-TCA-AGGGTATTTCGGTTA-TTTACCC
1 GTCATTTCA-CCATTCAGA-GGTATTTCGGTCATTTTACCC
28830430 ACGAATCGCA
Statistics
Matches: 203, Mismatches: 38, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
52 36 0.18
53 22 0.11
54 138 0.68
55 7 0.03
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (53 bp):
GTCATTTCACCATTCAGAGGTATTTCGGTCATTTTACCCTTTGAGGTATTTCG
Found at i:28830361 original size:81 final size:78
Alignment explanation
Indices: 28830141--28830425 Score: 286
Period size: 81 Copynumber: 3.6 Consensus size: 78
28830131 TACCCTTTAG
* * * *
28830141 GGGTATTTCGGTCATTTTACCCTTTGAGGATATTTCAGTCATTTCACCTTTCAGAGGTATTTCAA
1 GGGTATTTCGGTCATTTTACCCATTGAGG-TATTTCGGTCATTTCACC-TTAAG-GGTATTTCGA
* *
28830206 TCATTTTACCCTTTGA
63 TCATTTTACCCATCGA
* * * * *
28830222 GGGTATTTTGGTCA-TTTACCC-TTCGGGGTATTTCGGTCATTTTATCCTTCAAAGGTATTTCGG
1 GGGTATTTCGGTCATTTTACCCATT-GAGGTATTTCGGTCATTTCA-CCTT-AAGGGTATTTCGA
* *
28830285 TCATTTTACCAATCAA
63 TCATTTTACCCATCGA
* * * *
28830301 GGGTATTTCGGTTATTTTACCCATTGAAGGTATTTCGGCCATTTCACCCATTGAGGGTATTTTGA
1 GGGTATTTCGGTCATTTTACCCATTG-AGGTATTTCGGTCATTTCA-CC-TTAAGGGTATTTCGA
28830366 TCATTTTACCCATCGA
63 TCATTTTACCCATCGA
** *
28830382 GGGTATTTCGGTCATTTTACCCATCAAGGGTATTTCGGTTATTT
1 GGGTATTTCGGTCATTTTACCCATTGA-GGTATTTCGGTCATTT
28830426 ACCCACGAAT
Statistics
Matches: 167, Mismatches: 29, Indels: 16
0.79 0.14 0.08
Matches are distributed among these distances:
79 50 0.30
80 22 0.13
81 93 0.56
82 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (78 bp):
GGGTATTTCGGTCATTTTACCCATTGAGGTATTTCGGTCATTTCACCTTAAGGGTATTTCGATCA
TTTTACCCATCGA
Found at i:28839003 original size:51 final size:51
Alignment explanation
Indices: 28838948--28839397 Score: 396
Period size: 51 Copynumber: 8.9 Consensus size: 51
28838938 GTGAAAGTGT
*
28838948 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
* * * * * * * * * *
28838999 TGGTCACATGTTTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAA-ATAA
28839050 TGGTCACGTGTGTAGTAC-AGTGTGAAGGCTACTACGTGAATCGATAAATAA
1 TGGTCACGTGTGTAGTACTA-TGTGAAGGCTACTACGTGAATCGATAAATAA
* * * * ** * * * * *
28839101 TGATCACATGTGTAGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAA-ATAA
* * *
28839152 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
* * * * * * *
28839203 TGGTCACATGAGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAA--TAA
* * * *
28839254 TAGTCACATATGTAGTACTATGTGAAGGCTACTACGTGAATCG-TAAA-ACT
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-A
* * * *
28839304 TGATCACGTGTATAGTACTATGTGAAGGCTATTACGTGAACCG-TAAA-AA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
* *
28839353 TTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 -TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
28839398 ATGATAAAAG
Statistics
Matches: 313, Mismatches: 73, Indels: 26
0.76 0.18 0.06
Matches are distributed among these distances:
50 87 0.28
51 222 0.71
52 4 0.01
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (51 bp):
TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAA
Found at i:28839123 original size:102 final size:102
Alignment explanation
Indices: 28838947--28839397 Score: 590
Period size: 102 Copynumber: 4.4 Consensus size: 102
28838937 AGTGAAAGTG
* * *
28838947 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTTT
1 TTGGTCACGTGTGTAGTACAGTGTGAAGGCTACTACGTGAATCGATAAATAATGATCACATGTGT
28839012 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
28839049 TTGGTCACGTGTGTAGTACAGTGTGAAGGCTACTACGTGAATCGATAAATAATGATCACATGTGT
1 TTGGTCACGTGTGTAGTACAGTGTGAAGGCTACTACGTGAATCGATAAATAATGATCACATGTGT
*
28839114 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
* * * * *
28839151 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACATGAGT
1 TTGGTCACGTGTGTAGTACAGTGTGAAGGCTACTACGTGAATCGATAAATAATGATCACATGTGT
* *
28839216 AGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCT
66 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
* * * * *
28839253 TTAGTCACATATGTAGTACTA-TGTGAAGGCTACTACGTGAATCG-TAAA-ACTTGATCACGTGT
1 TTGGTCACGTGTGTAGTAC-AGTGTGAAGGCTACTACGTGAATCGATAAATA-ATGATCACATGT
* * ** * * **
28839315 ATAGTACTATGTGAAGGCTATTACGTGAACCGTA-AA-AA
64 GTAGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCT
* *
28839353 TTGATCACGTGTGTAGTACTA-TGTGAAGGCTACTACGTGTATCGA
1 TTGGTCACGTGTGTAGTAC-AGTGTGAAGGCTACTACGTGAATCGA
28839398 ATGATAAAAG
Statistics
Matches: 311, Mismatches: 34, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
100 39 0.13
101 41 0.13
102 231 0.74
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (102 bp):
TTGGTCACGTGTGTAGTACAGTGTGAAGGCTACTACGTGAATCGATAAATAATGATCACATGTGT
AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT
Found at i:28845147 original size:51 final size:46
Alignment explanation
Indices: 28845082--28845186 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 46
28845072 ATAAATAATA
*
28845082 TAAACAAATATTTATATTTATGTAAAAACACCAGATCTAAAGAAAACATAT
1 TAAATAAATATTTATATTTAT-TAAAAACACCAGATCT---GAAAACA-AT
* *
28845133 TAAATAAATATTTATATTTATTTAAAACATCAGATCTGAAAACAAT
1 TAAATAAATATTTATATTTATTAAAAACACCAGATCTGAAAACAAT
28845179 TAAATAAA
1 TAAATAAA
28845187 CAAGATCTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
46 10 0.20
47 7 0.14
50 14 0.27
51 20 0.39
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (46 bp):
TAAATAAATATTTATATTTATTAAAAACACCAGATCTGAAAACAAT
Found at i:28847387 original size:25 final size:23
Alignment explanation
Indices: 28847351--28847415 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 23
28847341 ACATGTTTGA
* *
28847351 GAACATATTCATTTAATATTCGT
1 GAACATGTTCATTTAATATTCAT
* *
28847374 GACCATATGTTCATTTAATGTTCAT
1 GA--ACATGTTCATTTAATATTCAT
28847399 GAACATGTTCATTTAAT
1 GAACATGTTCATTTAAT
28847416 GTTTCCTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 16 0.46
25 19 0.54
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (23 bp):
GAACATGTTCATTTAATATTCAT
Found at i:28847396 original size:11 final size:11
Alignment explanation
Indices: 28847380--28847418 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
28847370 TCGTGACCAT
28847380 ATGTTCATTTA
1 ATGTTCATTTA
**
28847391 ATGTTCATGAA
1 ATGTTCATTTA
28847402 CATGTTCATTTA
1 -ATGTTCATTTA
28847414 ATGTT
1 ATGTT
28847419 TCCTATAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (11 bp):
ATGTTCATTTA
Found at i:28847410 original size:23 final size:23
Alignment explanation
Indices: 28847351--28847418 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
28847341 ACATGTTTGA
* * *
28847351 GAACATATTCATTTAATATTCGT
1 GAACATGTTCATTTAATGTTCAT
*
28847374 GACCATATGTTCATTTAATGTTCAT
1 GA--ACATGTTCATTTAATGTTCAT
28847399 GAACATGTTCATTTAATGTT
1 GAACATGTTCATTTAATGTT
28847419 TCCTATAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
23 19 0.50
25 19 0.50
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (23 bp):
GAACATGTTCATTTAATGTTCAT
Found at i:28852103 original size:43 final size:43
Alignment explanation
Indices: 28852056--28852168 Score: 156
Period size: 43 Copynumber: 2.6 Consensus size: 43
28852046 CACATATTGC
* * * * *
28852056 TGCCACTGCCCCAGACATGGTCTTATACGAAATCA-TATAACGA
1 TGCCAATGTCCCAGACATGGTCTTACACGAAATCACAAT-ACAA
*
28852099 TGCCAATGTCCCAGACATGGTCTTACACGTAATCACAATACAA
1 TGCCAATGTCCCAGACATGGTCTTACACGAAATCACAATACAA
28852142 TGCCAATGTCCCAGACATGGTCTTACA
1 TGCCAATGTCCCAGACATGGTCTTACA
28852169 TGTTATCACC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
43 61 0.97
44 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (43 bp):
TGCCAATGTCCCAGACATGGTCTTACACGAAATCACAATACAA
Found at i:28852177 original size:43 final size:42
Alignment explanation
Indices: 28852024--28852177 Score: 150
Period size: 43 Copynumber: 3.6 Consensus size: 42
28852014 TGTCATATCT
* * * * * *
28852024 CAGATATGGTCTTACATGTTATCACATATTGC-TGCCACTGCCC
1 CAGACATGGTCTTACACGTAATCACA-A-TACATGCCAATGTCC
* * *
28852067 CAGACATGGTCTTATACGAAATCA-TATAACGATGCCAATGTCC
1 CAGACATGGTCTTACACGTAATCACAAT-AC-ATGCCAATGTCC
28852110 CAGACATGGTCTTACACGTAATCACAATACAATGCCAATGTCC
1 CAGACATGGTCTTACACGTAATCACAATAC-ATGCCAATGTCC
* *
28852153 CAGACATGGTCTTACATGTTATCAC
1 CAGACATGGTCTTACACGTAATCAC
28852178 CACTTAGTAA
Statistics
Matches: 92, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
43 87 0.95
44 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (42 bp):
CAGACATGGTCTTACACGTAATCACAATACATGCCAATGTCC
Found at i:28856718 original size:28 final size:28
Alignment explanation
Indices: 28856687--28856742 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
28856677 ACAAAGTGAA
* *
28856687 AATAATGATAAGCACCGAACTGCAAATT
1 AATAACGATAAGCACCAAACTGCAAATT
*
28856715 AATAACGATAAGCACCAAAGTGCAAATT
1 AATAACGATAAGCACCAAACTGCAAATT
28856743 TTTACAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (28 bp):
AATAACGATAAGCACCAAACTGCAAATT
Found at i:28871815 original size:3 final size:3
Alignment explanation
Indices: 28871807--28871835 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28871797 CTTTAGCACT
28871807 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
28871836 TGCTGCTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:28875853 original size:25 final size:25
Alignment explanation
Indices: 28875819--28875870 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
28875809 AACACAAGTC
* *
28875819 ACTTCAAAGCATTTGAACTTAACCA
1 ACTTCAAAGCATTTGAACATAAACA
28875844 ACTTCAAAGCATTTGAACATAAACA
1 ACTTCAAAGCATTTGAACATAAACA
28875869 AC
1 AC
28875871 AAATGGCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (25 bp):
ACTTCAAAGCATTTGAACATAAACA
Found at i:28882647 original size:280 final size:279
Alignment explanation
Indices: 28882299--28882860 Score: 1004
Period size: 280 Copynumber: 2.0 Consensus size: 279
28882289 TTCGTTGAAT
*
28882299 CTTCATATTGTGAGAGTTAGGCTGACTTAAGCGTTTTTTTTAACTTTTTTTATTTATCCATTTAA
1 CTTCATATTGTGAGAGTTAGGCTGACTTAAGCGTTTTTTTTAACCTTTTTTATTTATCCATTTAA
* *
28882364 TTGTTTAATTATTAATTATTCTTATACTTTTATTCGTTTATTTATCCATCAACTTTCTTATTTAC
66 TTGTTTAATCATTAATTATTCTTATACTTTTATTCATTTATTTATCCATCAACTTTCTTATTTAC
28882429 ATATTGTTCATTCATTTAACCATTCTTATCATTCTTTTATTTTCTTCCATTAATTATATACTTTA
131 ATATTGTTCATTCATTTAACCATTCTTATCATTCTTTTATTTTCTTCCATTAATTATATACTTTA
*
28882494 TTTGTTTTTAATATTATGTCACACATGTTGTTTATTTTTTAAAAACTCGTGTTATAAATCAT-TC
196 TTTGTTTTTAATATTATGTCACACA---TGTTTATTTTTTAAAAACTCGTGTTATAAATAATCT-
28882558 ATTTTAAATTGTTTGATTATTTG
257 ATTTTAAATTGTTTGATTATTTG
28882581 CTTCA-ATTGTGAGAGTTAGGCTGACTTAAGCG-TTTTTTTAACCTTTTTTATTTATCCATTTAA
1 CTTCATATTGTGAGAGTTAGGCTGACTTAAGCGTTTTTTTTAACCTTTTTTATTTATCCATTTAA
28882644 TTGTTTAATCATTAATTATTCTTATACTTTTATTCATTTATTTATCCATCAACTTTCTTATTTAC
66 TTGTTTAATCATTAATTATTCTTATACTTTTATTCATTTATTTATCCATCAACTTTCTTATTTAC
* *
28882709 ATATTGTTTATTCATTTAATCATTCTTATCATTCTTTTATTTTCTTCCATTAATTATATACTTTA
131 ATATTGTTCATTCATTTAACCATTCTTATCATTCTTTTATTTTCTTCCATTAATTATATACTTTA
28882774 TTTGTTTTTAATATTATGTCACACATGTTTATTTTTTAAAAACTCGTGTTATAAATAATCTATTT
196 TTTGTTTTTAATATTATGTCACACATGTTTATTTTTTAAAAACTCGTGTTATAAATAATCTATTT
*
28882839 TAAATTTTTTGATTATTTG
261 TAAATTGTTTGATTATTTG
28882858 CTT
1 CTT
28882861 TTTATGTCAC
Statistics
Matches: 272, Mismatches: 7, Indels: 7
0.95 0.02 0.02
Matches are distributed among these distances:
277 58 0.21
278 1 0.00
280 181 0.67
281 27 0.10
282 5 0.02
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.55
Consensus pattern (279 bp):
CTTCATATTGTGAGAGTTAGGCTGACTTAAGCGTTTTTTTTAACCTTTTTTATTTATCCATTTAA
TTGTTTAATCATTAATTATTCTTATACTTTTATTCATTTATTTATCCATCAACTTTCTTATTTAC
ATATTGTTCATTCATTTAACCATTCTTATCATTCTTTTATTTTCTTCCATTAATTATATACTTTA
TTTGTTTTTAATATTATGTCACACATGTTTATTTTTTAAAAACTCGTGTTATAAATAATCTATTT
TAAATTGTTTGATTATTTG
Found at i:28882917 original size:78 final size:75
Alignment explanation
Indices: 28882787--28882938 Score: 243
Period size: 78 Copynumber: 2.0 Consensus size: 75
28882777 GTTTTTAATA
*
28882787 TTATGTCACACATGTTTATTTTTTAAAAACTCGTGTTATAAATAATCTATTTTAAATTTTTTGAT
1 TTATGTCACACATGTTTATTTTTTAAAAACTCGTGTTATAAATAATCTATTTTAAATTGTTTGAT
28882852 TATTTGCTTT
66 TATTTGCTTT
*
28882862 TTATGTCACACATGTTGTTTATTTTTTAAAAACTCGTGTTATAAATCAT-TCATTTTAAATTGTT
1 TTATGTCACACA---TGTTTATTTTTTAAAAACTCGTGTTATAAATAATCT-ATTTTAAATTGTT
28882926 TGATTATTTGCTT
62 TGATTATTTGCTT
28882939 CAAATTTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
75 12 0.17
77 1 0.01
78 58 0.82
ACGTcount: A:0.28, C:0.10, G:0.09, T:0.53
Consensus pattern (75 bp):
TTATGTCACACATGTTTATTTTTTAAAAACTCGTGTTATAAATAATCTATTTTAAATTGTTTGAT
TATTTGCTTT
Found at i:28888937 original size:24 final size:24
Alignment explanation
Indices: 28888910--28888958 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28888900 AACCTGAAAC
28888910 AAGACTATTGTTTAGAACGCACTA
1 AAGACTATTGTTTAGAACGCACTA
28888934 AAGACTATTGTTTAGAACGCACTA
1 AAGACTATTGTTTAGAACGCACTA
28888958 A
1 A
28888959 GTATAAAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (24 bp):
AAGACTATTGTTTAGAACGCACTA
Found at i:28889779 original size:45 final size:45
Alignment explanation
Indices: 28889659--28889902 Score: 160
Period size: 45 Copynumber: 5.5 Consensus size: 45
28889649 AAGTTATAAG
* * * ** *
28889659 TCTTATCTCCCTAAAGTTGTAGTGCAGCAGACTGAAGAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAA
* *
28889704 TCTTAT-TCCCTTGAAGCTGTAGTGTG-GCAGACTGAAGATGGCAAA
1 TCTTATCTCCC-TGAAGTTGCAGTG-GAGCAGACTGAAGATGGCAAA
* * * *
28889749 TCTTATCTCCCTGAATTTGCAATGGAGCAGA-TTAA-A-GCCAATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGC-A-AA
* * * * * ** *
28889793 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAG-TTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAA
* * ** *
28889837 TCTTATCTCCCTGAAGTTACAGTGAAGCAGACTGAAGAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAA
*
28889882 TTTTATC-CCCATGAAGTTGCA
1 TCTTATCTCCC-TGAAGTTGCA
28889903 ACGGGGCACT
Statistics
Matches: 157, Mismatches: 31, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
42 2 0.01
43 2 0.01
44 72 0.46
45 76 0.48
46 5 0.03
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAA
Done.