Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008091.1 Hibiscus syriacus cultivar Beakdansim tig00110602_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2471235
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1940369 original size:17 final size:17
Alignment explanation
Indices: 1940273--1940369 Score: 54
Period size: 17 Copynumber: 5.6 Consensus size: 17
1940263 AAATCTTAAG
*
1940273 TGAGATAAAATTCATTT
1 TGAGAAAAAATTCATTT
**
1940290 TGAGAAAAACAATCTC-TAG
1 TGAG-AAAA-AAT-TCATTT
** **
1940309 TGAGACGAAATTTGTTT
1 TGAGAAAAAATTCATTT
* *
1940326 TAAGAAAAAATCTCA-TG
1 TGAGAAAAAAT-TCATTT
*
1940343 TGAGATAAAATTCATTT
1 TGAGAAAAAATTCATTT
1940360 TGAGAAAAAA
1 TGAGAAAAAA
1940370 ATCACTAGTG
Statistics
Matches: 56, Mismatches: 18, Indels: 12
0.65 0.21 0.14
Matches are distributed among these distances:
16 4 0.07
17 36 0.64
18 6 0.11
19 8 0.14
20 2 0.04
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.31
Consensus pattern (17 bp):
TGAGAAAAAATTCATTT
Found at i:1940502 original size:71 final size:70
Alignment explanation
Indices: 1940173--1940530 Score: 336
Period size: 71 Copynumber: 5.1 Consensus size: 70
1940163 ATGGAAGATG
* *
1940173 AAATTTATTTTAAGAAAAACAATCTTAAGTAAGATAAAAATT-TGTTTTGAGAAAAAAATCTCTA
1 AAATTTGTTTTAAGAAAAACAATCTTAAGTGAGAT--AAATTCT-TTTTGAGAAAAAAATCTCTA
1940237 GTGAGACA
63 GTGAGACA
* *
1940245 AAATTTGTTTTAAGTAAAA-AATCTTAAGTGAGATAAAATTCATTTTGAGAAAAACAATCTCTAG
1 AAATTTGTTTTAAGAAAAACAATCTTAAGTGAGAT-AAATTCTTTTTGAGAAAAA-AATCTCTAG
*
1940309 TGAGACG
64 TGAGACA
* * * *
1940316 AAATTTGTTTTAAG-AAAA-AATCTCATGTGAGATAAAATTCATTTTGAGAAAAAAATCACTAGT
1 AAATTTGTTTTAAGAAAAACAATCTTAAGTGAGAT-AAATTCTTTTTGAGAAAAAAATCTCTAGT
1940379 GAGAC-
65 GAGACA
* * * * * * * * *
1940384 -GATTTTTTTTAAGAAAAACAATATCAAGTAAGATAAAATTTGTTTTTAAGAAAAATACTCTGTA
1 AAATTTGTTTTAAGAAAAACAATCTTAAGTGAGAT-AAA-TTCTTTTTGAGAAAAA-AATCTCTA
1940448 GTGAGACA
63 GTGAGACA
* * * *
1940456 AAATTTTGTTTTAAGAAAAAACAATCTTAAATGAGAT-AATT-TTTTTAATAAAAACAATCTCAA
1 AAA-TTTGTTTTAAG-AAAAACAATCTTAAGTGAGATAAATTCTTTTTGAGAAAAA-AATCTCTA
* *
1940519 TTGAGATA
63 GTGAGACA
1940527 AAAT
1 AAAT
1940531 CTTGAGTGAA
Statistics
Matches: 244, Mismatches: 32, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
67 11 0.05
68 4 0.02
69 30 0.12
70 69 0.28
71 81 0.33
72 19 0.08
73 3 0.01
74 10 0.04
75 17 0.07
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (70 bp):
AAATTTGTTTTAAGAAAAACAATCTTAAGTGAGATAAATTCTTTTTGAGAAAAAAATCTCTAGTG
AGACA
Found at i:1943076 original size:28 final size:26
Alignment explanation
Indices: 1943035--1943089 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 26
1943025 AGAAACACAT
*
1943035 AAAAAAGAAGAGAAAAAGGAAGAGAAAA
1 AAAAAAGAAAAGAAAAAGG--GAGAAAA
1943063 AAAAAAGAAAAGAAAAAGGGAGAAAA
1 AAAAAAGAAAAGAAAAAGGGAGAAAA
1943089 A
1 A
1943090 GGGGAAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 8 0.31
28 18 0.69
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (26 bp):
AAAAAAGAAAAGAAAAAGGGAGAAAA
Found at i:1943079 original size:12 final size:12
Alignment explanation
Indices: 1943035--1943073 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1943025 AGAAACACAT
1943035 AAAAAAGAAGAG
1 AAAAAAGAAGAG
*
1943047 AAAAAGGAAGAG
1 AAAAAAGAAGAG
*
1943059 AAAAAA-AAAAG
1 AAAAAAGAAGAG
1943070 AAAA
1 AAAA
1943074 GAAAAAGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAGAG
Found at i:1945408 original size:22 final size:22
Alignment explanation
Indices: 1945375--1945430 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
1945365 TATCACACAC
1945375 GAGGAAAGGGAAAATATAGAAGA
1 GAGG-AAGGGAAAATATAGAAGA
*
1945398 GATGAAGGGAAAATATAGAAGA
1 GAGGAAGGGAAAATATAGAAGA
1945420 GAGGAAGGGAA
1 GAGGAAGGGAA
1945431 GCGGGGATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.38, T:0.09
Consensus pattern (22 bp):
GAGGAAGGGAAAATATAGAAGA
Found at i:1951667 original size:23 final size:22
Alignment explanation
Indices: 1951637--1951715 Score: 81
Period size: 21 Copynumber: 3.5 Consensus size: 22
1951627 TGGCCATGTA
1951637 CATCGATGCACATTCAAAGCGTG
1 CATCGATGCACATTCAAAG-GTG
* *
1951660 CATCGATGCATC-TTC-ATGATG
1 CATCGATGCA-CATTCAAAGGTG
*
1951681 TATCGATGCACATTCAAAGGGATG
1 CATCGATGCACATTCAAA-GG-TG
1951705 CATCGATGCAC
1 CATCGATGCAC
1951716 TGTTAAGTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 1 0.02
21 14 0.31
22 3 0.07
23 14 0.31
24 13 0.29
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (22 bp):
CATCGATGCACATTCAAAGGTG
Found at i:1951727 original size:44 final size:44
Alignment explanation
Indices: 1951638--1951734 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
1951628 GGCCATGTAC
*
1951638 ATCGATGCACATTCAAAGCGTGCATCGATGCATCTTCATGATGT
1 ATCGATGCACATTCAAAGCGTGCATCGATGCATCTTCAAGATGT
* *
1951682 ATCGATGCACATTCAAAGGGATGCATCGATGCA-CTGTTAAG-TGT
1 ATCGATGCACATTCAAAGCG-TGCATCGATGCATCT-TCAAGATGT
1951726 ATCGATGCA
1 ATCGATGCA
1951735 TTAAACACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
44 33 0.69
45 15 0.31
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (44 bp):
ATCGATGCACATTCAAAGCGTGCATCGATGCATCTTCAAGATGT
Found at i:1951943 original size:3 final size:3
Alignment explanation
Indices: 1951935--1951960 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1951925 GCAATCAAAA
1951935 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1951961 AAGCATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1958363 original size:49 final size:48
Alignment explanation
Indices: 1958309--1958419 Score: 134
Period size: 49 Copynumber: 2.2 Consensus size: 48
1958299 TTAGTAGAAA
* * *
1958309 AGCGCCCCCCTGCACCACGCTATATGC-TGATTTGGCGCCACATGGGTAT
1 AGCGCCCCCCTGC-CC-CGCGATATACATGATCTGGCGCCACATGGGTAT
**
1958358 AGCGCCCCCCTGCCCCGCGATATACAGTGATCTGGCGCCATGTGGGTAT
1 AGCGCCCCCCTGCCCCGCGATATACA-TGATCTGGCGCCACATGGGTAT
1958407 AGCGCGCCCCCTG
1 AGCGC-CCCCCTG
1958420 ATCTGCGCTA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
47 8 0.15
48 2 0.04
49 37 0.69
50 7 0.13
ACGTcount: A:0.16, C:0.37, G:0.27, T:0.20
Consensus pattern (48 bp):
AGCGCCCCCCTGCCCCGCGATATACATGATCTGGCGCCACATGGGTAT
Found at i:1958436 original size:39 final size:39
Alignment explanation
Indices: 1958393--1958492 Score: 155
Period size: 39 Copynumber: 2.5 Consensus size: 39
1958383 AGTGATCTGG
* *
1958393 CGCCATGTGGGTATAGCGCGCCCCCTGATCTGCGCTATA
1 CGCCACGTGGGTATAGCGCGCCCCCTGATCCGCGCTATA
1958432 CGCCACGTGGGTATAGCGCGCCCCCTGATCCGCGCTATA
1 CGCCACGTGGGTATAGCGCGCCCCCTGATCCGCGCTATA
*
1958471 TGCCACGTAGGGGTATAGCGCG
1 CGCCACGT--GGGTATAGCGCG
1958493 GATCAGGGGT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 44 0.79
41 12 0.21
ACGTcount: A:0.16, C:0.33, G:0.31, T:0.20
Consensus pattern (39 bp):
CGCCACGTGGGTATAGCGCGCCCCCTGATCCGCGCTATA
Found at i:1961961 original size:35 final size:36
Alignment explanation
Indices: 1961917--1962003 Score: 103
Period size: 35 Copynumber: 2.5 Consensus size: 36
1961907 ATTTGATATT
1961917 TAAATACAA-CAAACTTACAATAA-GA-ATTAAATGG
1 TAAATACAACCAAA-TTACAATAACGATATTAAATGG
1961951 TAAATGACAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACCAAATTACAATAAC-GATATTAAATGG
*
1961989 T-AATA-AACAAAATTA
1 TAAATACAACCAAATTA
1962004 ACTAAAATAT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
34 5 0.11
35 22 0.47
36 5 0.11
37 5 0.11
38 10 0.21
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.25
Consensus pattern (36 bp):
TAAATACAACCAAATTACAATAACGATATTAAATGG
Found at i:1962242 original size:21 final size:21
Alignment explanation
Indices: 1962216--1962266 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1962206 ACTCCTCGCT
*
1962216 GTCATCGTCGTCGTCACCATC
1 GTCATCGTCGTCATCACCATC
*
1962237 GTCATCGTCGTCATCATCATC
1 GTCATCGTCGTCATCACCATC
*
1962258 GTCGTCGTC
1 GTCATCGTC
1962267 CTGAGCAGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.14, C:0.35, G:0.20, T:0.31
Consensus pattern (21 bp):
GTCATCGTCGTCATCACCATC
Found at i:1962246 original size:18 final size:18
Alignment explanation
Indices: 1962217--1962266 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
1962207 CTCCTCGCTG
*
1962217 TCATCGTCGTCGTCACCA
1 TCATCATCGTCGTCACCA
* *
1962235 TCGTCATCGTCGTCATCA
1 TCATCATCGTCGTCACCA
*
1962253 TCATCGTCGTCGTC
1 TCATCATCGTCGTC
1962267 CTGAGCAGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.14, C:0.36, G:0.18, T:0.32
Consensus pattern (18 bp):
TCATCATCGTCGTCACCA
Found at i:1962251 original size:15 final size:15
Alignment explanation
Indices: 1962216--1962263 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1962206 ACTCCTCGCT
*
1962216 GTCATCGTCGTCGTC
1 GTCATCGTCATCGTC
**
1962231 ACCATCGTCATCGTC
1 GTCATCGTCATCGTC
*
1962246 GTCATCATCATCGTC
1 GTCATCGTCATCGTC
1962261 GTC
1 GTC
1962264 GTCCTGAGCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.15, C:0.35, G:0.19, T:0.31
Consensus pattern (15 bp):
GTCATCGTCATCGTC
Found at i:1962381 original size:9 final size:9
Alignment explanation
Indices: 1962367--1962391 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1962357 ACCGGCATGC
1962367 GAAAACTGG
1 GAAAACTGG
1962376 GAAAACTGG
1 GAAAACTGG
1962385 GAAAACT
1 GAAAACT
1962392 CATACATCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.28, T:0.12
Consensus pattern (9 bp):
GAAAACTGG
Found at i:1964348 original size:111 final size:111
Alignment explanation
Indices: 1964154--1964367 Score: 367
Period size: 111 Copynumber: 1.9 Consensus size: 111
1964144 ATTACAAAAA
* * *
1964154 TTAATTTTTAATCTAATAACCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAACCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
1964219 AATTAAAACGTTAAAATGTTATCGTATCA-TCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGT-AAAGTGTCGAGATAT
*
1964265 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAACCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1964330 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGT
66 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGT
1964368 AGATATATAT
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
111 96 0.99
112 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAACCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTCGAGATAT
Found at i:1964768 original size:49 final size:49
Alignment explanation
Indices: 1964661--1964768 Score: 119
Period size: 49 Copynumber: 2.2 Consensus size: 49
1964651 GATATCCAGG
* * * * *
1964661 TATAGCGCGGATCAGGGGGCGCGCTATATCCCGTGGCGCCAGATCACCG
1 TATAGCGCGGAGCAGGGGGCGCGCTATATCACGTGACGCCAAATCACCA
* * * *
1964710 TATATCGCGG-GCAGGGGGCGTGTTATACTCACGTGACGCCAAATCAGCA
1 TATAGCGCGGAGCAGGGGGCGCGCTATA-TCACGTGACGCCAAATCACCA
1964759 TATAGCGCGG
1 TATAGCGCGG
1964769 TGCATGGGCG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
48 14 0.29
49 34 0.71
ACGTcount: A:0.21, C:0.27, G:0.33, T:0.19
Consensus pattern (49 bp):
TATAGCGCGGAGCAGGGGGCGCGCTATATCACGTGACGCCAAATCACCA
Found at i:1967069 original size:33 final size:31
Alignment explanation
Indices: 1967019--1967101 Score: 80
Period size: 33 Copynumber: 2.6 Consensus size: 31
1967009 TAATATATTT
* **
1967019 ATAAT-TA-TTTATTATATTTAAACTTTTTAA
1 ATAATATATTTTATAATATTTAAA-TAATTAA
*
1967049 ATTAATATATTTTATAATATTTTTAATAATTAA
1 A-TAATATATTTTATAATA-TTTAAATAATTAA
1967082 ATAATATATTTTAATAATAT
1 ATAATATATTTT-ATAATAT
1967102 AAAATAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
30 1 0.02
31 4 0.09
32 14 0.32
33 20 0.45
34 5 0.11
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (31 bp):
ATAATATATTTTATAATATTTAAATAATTAA
Found at i:1967074 original size:21 final size:21
Alignment explanation
Indices: 1967062--1967104 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
1967052 AATATATTTT
1967062 ATAATAT-TTTTAATAATTAA
1 ATAATATATTTTAATAATTAA
1967082 ATAATATATTTTAATAATATAA
1 ATAATATATTTTAATAAT-TAA
1967104 A
1 A
1967105 ATAAAAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
21 10 0.48
22 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAATATATTTTAATAATTAA
Found at i:1967082 original size:42 final size:42
Alignment explanation
Indices: 1967001--1967082 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
1966991 AAATAATATA
*
1967001 TTTTAGAATAATATATTTATAATTATTTATTATATTTAAACT
1 TTTTAGAATAATATATTTATAATTATTTATTATAATTAAACT
1967043 TTTTA-AATTAATATATTTTATAA-TATTT-TTAATAATTAAA
1 TTTTAGAA-TAATATA-TTTATAATTATTTATT-ATAATTAAA
1967083 TAATATATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
41 4 0.11
42 25 0.69
43 7 0.19
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (42 bp):
TTTTAGAATAATATATTTATAATTATTTATTATAATTAAACT
Found at i:1967096 original size:42 final size:45
Alignment explanation
Indices: 1966983--1967102 Score: 106
Period size: 42 Copynumber: 2.6 Consensus size: 45
1966973 ATATTTTAAA
1966983 AATAATTAAAATAATATATTTTAGAATAATATATTTATAATTATTTATT
1 AATAATT-AAATAATATATTTT--AAT-ATATATTTATAATTATTTATT
* * * **
1967032 -ATATTTAAACT-TTTTAAATTAATATAT-TTTATAA-TATTT-TT
1 AATAATTAAA-TAATATATTTTAATATATATTTATAATTATTTATT
1967073 AATAATTAAATAATATATTTTAATAATATA
1 AATAATTAAATAATATATTTTAAT-ATATA
1967103 AAATAAAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
41 3 0.05
42 21 0.38
43 11 0.20
44 4 0.07
45 3 0.05
47 8 0.14
48 6 0.11
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (45 bp):
AATAATTAAATAATATATTTTAATATATATTTATAATTATTTATT
Found at i:1967338 original size:18 final size:18
Alignment explanation
Indices: 1967315--1967352 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1967305 TAATTATATT
1967315 TAAGGTAAAGTACACAAC
1 TAAGGTAAAGTACACAAC
1967333 TAAGGTAAAGTACACAAC
1 TAAGGTAAAGTACACAAC
1967351 TA
1 TA
1967353 GTCCCCCGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (18 bp):
TAAGGTAAAGTACACAAC
Found at i:1969159 original size:14 final size:14
Alignment explanation
Indices: 1969140--1969167 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1969130 GAATTCTCCA
1969140 CGCCTTATATGACT
1 CGCCTTATATGACT
1969154 CGCCTTATATGACT
1 CGCCTTATATGACT
1969168 ACCCCCCTCC
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:0.21, C:0.29, G:0.14, T:0.36
Consensus pattern (14 bp):
CGCCTTATATGACT
Found at i:1973711 original size:8 final size:8
Alignment explanation
Indices: 1973698--1973792 Score: 58
Period size: 8 Copynumber: 12.2 Consensus size: 8
1973688 GTTTCTATAA
1973698 TTTATTAT
1 TTTATTAT
1973706 TTTATTCA-
1 TTTATT-AT
*
1973714 -TTATTTT
1 TTTATTAT
1973721 TTTATTAT
1 TTTATTAT
* * *
1973729 TTAAGTAA
1 TTTATTAT
*
1973737 TTAATTAT
1 TTTATTAT
1973745 TTTATTA-
1 TTTATTAT
1973752 -TTATTAT
1 TTTATTAT
1973759 TTTATT-T
1 TTTATTAT
*
1973766 TAGTATATAT
1 T-TTAT-TAT
*
1973776 TTTTTTAT
1 TTTATTAT
1973784 TTT-TTAT
1 TTTATTAT
1973791 TT
1 TT
1973793 GACTATTTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
6 6 0.09
7 13 0.19
8 43 0.63
9 4 0.06
10 2 0.03
ACGTcount: A:0.26, C:0.01, G:0.02, T:0.71
Consensus pattern (8 bp):
TTTATTAT
Found at i:1973781 original size:20 final size:19
Alignment explanation
Indices: 1973741--1973786 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
1973731 AAGTAATTAA
*
1973741 TTATTTTATTATTATTATT
1 TTATTTTAGTATTATTATT
*
1973760 TTATTTTAGTATATATTTTT
1 TTATTTTAGTAT-TATTATT
1973780 TTATTTT
1 TTATTTT
1973787 TTATTTGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (19 bp):
TTATTTTAGTATTATTATT
Found at i:1976073 original size:24 final size:20
Alignment explanation
Indices: 1976020--1976077 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1976010 TTCCCCTTGG
*
1976020 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
1976040 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
1976063 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1976078 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1976188 original size:64 final size:63
Alignment explanation
Indices: 1976065--1976201 Score: 161
Period size: 64 Copynumber: 2.2 Consensus size: 63
1976055 TCTTTAACAT
* * *
1976065 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACATTCGATGTTTTCATTTTAA-AGA
* * * * *
1976129 GTGCATCGATGCACT-CCTTATGCATCGATGCACTAATTACATTCGATG-TTTCTTCTTTAAAGA
1 GTGCATCGATGCACTACC-CATGCATCGATACACCAATCACATTCGATGTTTTCAT-TTTAAAGA
1976192 GTGCATCGAT
1 GTGCATCGAT
1976202 ACACATTGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
63 18 0.29
64 45 0.71
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACCAATCACATTCGATGTTTTCATTTTAAAGA
Found at i:1977391 original size:14 final size:14
Alignment explanation
Indices: 1977372--1977410 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1977362 TAGATGTATG
1977372 TTTTTTAATTTTAT
1 TTTTTTAATTTTAT
*
1977386 TTTTTTAATTGTAT
1 TTTTTTAATTTTAT
*
1977400 TTATTTAATTT
1 TTTTTTAATTT
1977411 GAATCTCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTTTAATTTTAT
Found at i:1978477 original size:36 final size:36
Alignment explanation
Indices: 1978401--1978484 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 36
1978391 TAAGAGGGAT
* * *
1978401 GATGGCGATGAGGAGGATGAGAATAAAGATGAAGAA
1 GATGACGAGGAGGAGGATGAGAATAAAGACGAAGAA
* * * ** *
1978437 GATGATGAGGAGGATGATGAGAATGAAGACGGTGAG
1 GATGACGAGGAGGAGGATGAGAATAAAGACGAAGAA
1978473 GATGACGAGGAG
1 GATGACGAGGAG
1978485 CAACATATAA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.39, C:0.04, G:0.43, T:0.14
Consensus pattern (36 bp):
GATGACGAGGAGGAGGATGAGAATAAAGACGAAGAA
Found at i:1980407 original size:83 final size:82
Alignment explanation
Indices: 1980302--1981023 Score: 490
Period size: 83 Copynumber: 8.8 Consensus size: 82
1980292 ATGTCATAGT
* * ** *
1980302 ATTTTCCATTATTATTCAGAGAATCTCTATCAAG-CTGTAGTGTTTTA-TCCTATCCGAAATGAA
1 ATTTTCCATTATTATTCAGAGAATCTCTACCAAGTC-ATAGTGTTCCATTCC-ATCCAAAATGAA
*
1980365 AGGCGCGTTCCAGGGGAAAC
64 AGGCACGTTCCA-GGGAAAC
* * * *
1980385 GTTTGT-CATTATTATTCTGAGAATCTCTGCCATGTCATAGTGTTCCATTCCATCCAAAATGAAA
1 ATTT-TCCATTATTATTCAGAGAATCTCTACCAAGTCATAGTGTTCCATTCCATCCAAAATGAAA
1980449 GGCACGTTCCAGGGAAAC
65 GGCACGTTCCAGGGAAAC
* * * ** * *
1980467 ATTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAGTGTTCCATCCCTTCTGAAATAAAAA
1 ATTTTCCATTATTATTCAGAGAATCTCTACCAAGTCATAGTGTTCCATTCCATCCAAAATGAAAG
* * *
1980532 GCGCGTTCCTGGGAAATT
66 GCACGTTCCAGGGAAA-C
* ** * * * * **
1980550 ATTTTCCATTATTATTCACAGAAT-T-TGTCATA-TCTTAGTGCTCCATCCCATCCGAAACAAAA
1 ATTTTCCATTATTATTCAGAGAATCTCTACCA-AGTCATAGTGTTCCATTCCATCCAAAATGAAA
* * * * * *
1980612 GACGCATTCCATGAAAAGT
65 GGCACGTTCCAGGGAAA-C
* *
1980631 ATTTTCCATTATTATTCAAAGAATCTCT-----GTC--A-TGTTCCATCCCATCCAAAATGAAAG
1 ATTTTCCATTATTATTCAGAGAATCTCTACCAAGTCATAGTGTTCCATTCCATCCAAAATGAAAG
** *
1980688 GTGCGTTCCAGGGTAAGC
66 GCACGTTCCAGGG-AAAC
* * * * *
1980706 ATATTCCATTATTATTCAGAGAATCTCTGA-CATGTCATAGTGTTCAATAT-CATCCGAATTGAA
1 ATTTTCCATTATTATTCAGAGAATCTCT-ACCAAGTCATAGTGTTCCAT-TCCATCCAAAATGAA
* ** *
1980769 AGGCGCGTTTTAGGGGAATC
64 AGGCACGTTCCA-GGGAAAC
* * * * * ** * ** *
1980789 GTTTTCCATTATTATTCAGAGAATATCTGCCATGTTATAGTGTTATATCCCATCTGAAATGAAAT
1 ATTTTCCATTATTATTCAGAGAATCTCTACCAAGTCATAGTGTTCCATTCCATCCAAAATGAAAG
* * ** * *
1980854 GAATGTTCTTGTAGAAGC
66 GCACGTTCCAG-GGAAAC
* * * * *
1980872 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
1 ATTTTCCATTATTATTCAGAGAATCTCTACCAAGTCATAGTGTTCCATTCCATCCAAAATGAAAG
**
1980937 ATACGTTCCAGGGGAAAC
66 GCACGTTCCA-GGGAAAC
* * * *
1980955 ATTTTCCATTATTATTCAGAGAATCTTTGCTATA-TCATAGTGTTCCA-TCTCATCCGAAATGAA
1 ATTTTCCATTATTATTCAGAGAATCTCTACCA-AGTCATAGTGTTCCATTC-CATCCAAAATGAA
1981018 AGGCAC
64 AGGCAC
1981024 ATGTTTCATT
Statistics
Matches: 515, Mismatches: 98, Indels: 52
0.77 0.15 0.08
Matches are distributed among these distances:
75 55 0.11
76 3 0.01
78 2 0.00
80 3 0.01
81 64 0.12
82 80 0.16
83 299 0.58
84 9 0.02
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (82 bp):
ATTTTCCATTATTATTCAGAGAATCTCTACCAAGTCATAGTGTTCCATTCCATCCAAAATGAAAG
GCACGTTCCAGGGAAAC
Found at i:1980972 original size:249 final size:245
Alignment explanation
Indices: 1980391--1981021 Score: 723
Period size: 239 Copynumber: 2.6 Consensus size: 245
1980381 AAACGTTTGT
* * *
1980391 CATTATTATTCTGAGAATCTCTGCCATGTCATAGTGTTCCATTCCATCCAAAATGAAAGGCACGT
1 CATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCAAAATGAAAGGTACGT
* *
1980456 TCCA-GGGAAACATTTTCCATTATTATTCAGAGAATCTCT-ACCATGTCATAGTGTTCCATCCCT
66 TCCAGGGGAAACATTTTCCATTATTATTCAGAGAATCTCTGA-CATGTCATAGTGTTCCATCTCA
* * * * *
1980519 TCTGAAATAAAAAGCGCGTTCCTGGGAAATTATTTTCCATTATTATTCACAGAATTTGTCATATC
130 TCCGAAATGAAAGGCGCGTTCCTGGGAAATCATTTTCCATTATTATTCACAGAATTTGCCATATC
* *
1980584 TTAGTGCTCCATCCCATCCGAAACAAAAGACGCATTCCATGAAAAGTATTTTC
195 TTAGTGCTACATCCCATCCGAAACAAAAGA--CATTCCATGAAAAGCATTTTC
* *
1980637 CATTATTATTCAAAGAA--TCT--C-TGTC--A-TGTTCCATCCCATCCAAAATGAAAGGTGCGT
1 CATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCAAAATGAAAGGTACGT
* * * * *
1980694 TCCAGGGTAAGCATATTCCATTATTATTCAGAGAATCTCTGACATGTCATAGTGTTCAATATCAT
66 TCCAGGGGAAACATTTTCCATTATTATTCAGAGAATCTCTGACATGTCATAGTGTTCCATCTCAT
* * * * * *
1980759 CCGAATTGAAAGGCGCGTT-TTAGGGGAATCGTTTTCCATTATTATTCAGAGAATATCTGCCATG
131 CCGAAATGAAAGGCGCGTTCCT-GGGAAATCATTTTCCATTATTATTCACAGAAT-T-TGCCATA
* * * * * * * * *
1980823 T-TATAGTGTTATATCCCATCTGAAATGAAATGA-ATGTTCTTGTAGAAGCGTTTTC
193 TCT-TAGTGCTACATCCCATCCGAAA-CAAAAGACAT-TCCATG-AAAAGCATTTTC
* *
1980878 CATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAGATACGT
1 CATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCAAAATGAAAGGTACGT
* *
1980943 TCCAGGGGAAACATTTTCCATTATTATTCAGAGAATCTTTG-CTATATCATAGTGTTCCATCTCA
66 TCCAGGGGAAACATTTTCCATTATTATTCAGAGAATCTCTGAC-ATGTCATAGTGTTCCATCTCA
1981007 TCCGAAATGAAAGGC
130 TCCGAAATGAAAGGC
1981022 ACATGTTTCA
Statistics
Matches: 321, Mismatches: 46, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
238 33 0.10
239 97 0.30
240 7 0.02
241 53 0.17
242 6 0.02
243 3 0.01
244 3 0.01
245 1 0.00
246 19 0.06
248 2 0.01
249 97 0.30
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (245 bp):
CATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCAAAATGAAAGGTACGT
TCCAGGGGAAACATTTTCCATTATTATTCAGAGAATCTCTGACATGTCATAGTGTTCCATCTCAT
CCGAAATGAAAGGCGCGTTCCTGGGAAATCATTTTCCATTATTATTCACAGAATTTGCCATATCT
TAGTGCTACATCCCATCCGAAACAAAAGACATTCCATGAAAAGCATTTTC
Found at i:1980997 original size:166 final size:165
Alignment explanation
Indices: 1980302--1981018 Score: 661
Period size: 166 Copynumber: 4.4 Consensus size: 165
1980292 ATGTCATAGT
** * * ** *
1980302 ATTTTCCATTATTATTCAGAGAATCTCTATCAAG-CTGTAGTGTTTTATCCTATCCGAAATGAAA
1 ATTTTCCATTATTATTCAGAGAATCTCTGCCATGTC-ATAGTGTTCCATCCCATCCGAAATGAAA
* * * * *
1980366 GGCGCGTTCCAGGGGAAA-CGTTTGT-CATTATTATTCTGAGAATCTCTGCCATGTCATAGTGTT
65 AGAGCGTTCC-TGGGAAAGCATTT-TCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTT
* * *
1980429 CCATTCCATCCAAAATGAAAGGCACGTTCCAGGGAAAC
128 CCATCCCATCCGAAATGAAAGACACGTTCCAGGGAAAC
* * * *
1980467 ATTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAGTGTTCCATCCCTTCTGAAATAAAAA
1 ATTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAA
* ** * * * * *
1980532 GCGCGTTCCTGGGAAATTATTTTCCATTATTATTCACAGAAT-T-TGTCATATCTTAGTGCTCCA
66 GAGCGTTCCTGGGAAAGCATTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCA
** * * * * *
1980595 TCCCATCCGAAACAAAAGACGCATTCCATGAAAAGT
131 TCCCATCCGAAATGAAAGACACGTTCCAGGGAAA-C
* * *
1980631 ATTTTCCATTATTATTCAAAGAA--TCT--C-TGTC--A-TGTTCCATCCCATCCAAAATGAAAG
1 ATTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAA
* * * * * *
1980688 GTGCGTTCCAGGGTAAGCATATTCCATTATTATTCAGAGAATCTCTGACATGTCATAGTGTTCAA
66 GAGCGTTCCTGGGAAAGCATTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCA
** * * * ** *
1980753 TATCATCCGAATTGAAAGGCGCGTTTTAGGGGAATC
131 TCCCATCCGAAATGAAAGACACGTTCCA-GGGAAAC
* * * ** * *
1980789 GTTTTCCATTATTATTCAGAGAATATCTGCCATGTTATAGTGTTATATCCCATCTGAAATGAAAT
1 ATTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAA
** * * *
1980854 GAATGTT-CTTGTAGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCC
66 GAGCGTTCCTGGGA-AAGCATTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCC
*
1980918 ATCCCATCCGAAATGAAAGATACGTTCCAGGGGAAAC
130 ATCCCATCCGAAATGAAAGACACGTTCCA-GGGAAAC
* * * *
1980955 ATTTTCCATTATTATTCAGAGAATCTTTGCTATATCATAGTGTTCCATCTCATCCGAAATGAAA
1 ATTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAA
1981019 GGCACATGTT
Statistics
Matches: 438, Mismatches: 98, Indels: 31
0.77 0.17 0.05
Matches are distributed among these distances:
156 55 0.13
157 2 0.00
158 55 0.13
159 7 0.02
160 4 0.01
162 4 0.01
163 44 0.10
164 30 0.07
165 84 0.19
166 153 0.35
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (165 bp):
ATTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAA
GAGCGTTCCTGGGAAAGCATTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCA
TCCCATCCGAAATGAAAGACACGTTCCAGGGAAAC
Found at i:1987041 original size:32 final size:32
Alignment explanation
Indices: 1986986--1987050 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
1986976 ATCCATTTGT
1986986 TTTTATTTATATTTTTAACATTATTATAAATA
1 TTTTATTTATATTTTTAACATTATTATAAATA
** *
1987018 TTTTATTT-TATTTATTATTATTATTATTAATA
1 TTTTATTTATATTT-TTAACATTATTATAAATA
1987050 T
1 T
1987051 AATAAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 5 0.17
32 24 0.83
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (32 bp):
TTTTATTTATATTTTTAACATTATTATAAATA
Found at i:1992615 original size:15 final size:15
Alignment explanation
Indices: 1992595--1992626 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1992585 GATCAATACC
1992595 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1992610 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1992625 TT
1 TT
1992627 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1999922 original size:20 final size:21
Alignment explanation
Indices: 1999899--1999951 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
1999889 ATTATGCTTG
*
1999899 AAGAAGAAAAAAT-TATGAAA
1 AAGAAGAAAAAATAAATGAAA
1999919 AAG-A-AAAAAATGAAATGAAA
1 AAGAAGAAAAAAT-AAATGAAA
*
1999939 AAAAAGAAAAAAT
1 AAGAAGAAAAAAT
1999952 GATAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 7 0.26
19 1 0.04
20 11 0.41
21 1 0.04
22 7 0.26
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.11
Consensus pattern (21 bp):
AAGAAGAAAAAATAAATGAAA
Found at i:2001706 original size:113 final size:113
Alignment explanation
Indices: 2001503--2001952 Score: 733
Period size: 113 Copynumber: 4.0 Consensus size: 113
2001493 GCAAAGATTC
*
2001503 GAATCCATCATTCGATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATTCATCATTCGATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAG
*
2001568 AAGGAAAAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTT
66 AAGGAAAAAGAAGTTCATAATAAGAAGAACTTGTTTAACCTTTTGCTT
* * *
2001616 GAATTCATCATTCAATAGATCAACTGTTCCATAAGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATTCATCATTCGATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * *
2001681 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTTCTT
66 AAGGAAAAAGAAGTTCATAATAAGAAGAACTTGTTTAACCTTTTGCTT
2001729 GAATTCATCATTCGATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATTCATCATTCGATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAG
2001794 AAGGAAAAAGAAGTTCATAATAAGAAGAACTTGTTTAACCTTTTGCTT
66 AAGGAAAAAGAAGTTCATAATAAGAAGAACTTGTTTAACCTTTTGCTT
* *
2001842 GAATTCATCATTCGATGGATCAACTGTTCCTG-AGAGAGTTCATAATGAGAAGAAATCATCTGAA
1 GAATTCATCATTCGATGGATCAACTGTTCCAGAAGA-AGTTCATAATGAGAAGAACTCATCTGAA
* * * * *
2001906 -AAAGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACTTTTTGCT
65 GAAGGAAAAAGAAGTTCATAATAAGAAGAACTTGTTTAACCTTTTGCT
2001953 AGATTATATC
Statistics
Matches: 315, Mismatches: 21, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
112 45 0.14
113 270 0.86
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
GAATTCATCATTCGATGGATCAACTGTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAAAAGAAGTTCATAATAAGAAGAACTTGTTTAACCTTTTGCTT
Found at i:2002241 original size:4 final size:4
Alignment explanation
Indices: 2002227--2002261 Score: 61
Period size: 4 Copynumber: 8.5 Consensus size: 4
2002217 TATAAATATT
2002227 TTTA TTTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
2002262 ATTATTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2004738 original size:23 final size:23
Alignment explanation
Indices: 2004694--2004738 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2004684 ACTTAATTAC
*
2004694 TCAACAATACAAAACATTTCATA
1 TCAACAATACAAAACATATCATA
*
2004717 TCAACAATACAAAACGTATCAT
1 TCAACAATACAAAACATATCAT
2004739 GTCATATCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.22, G:0.02, T:0.24
Consensus pattern (23 bp):
TCAACAATACAAAACATATCATA
Found at i:2005039 original size:23 final size:24
Alignment explanation
Indices: 2005013--2005073 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
2005003 AGCTCGTATA
*
2005013 AAATACACCGAAGTGA-CACGTAG
1 AAATGCACCGAAGTGACCACGTAG
* *
2005036 AAATGCATCGAAGT-ACCGCGTAG
1 AAATGCACCGAAGTGACCACGTAG
2005059 AAATGCACCGAAGTG
1 AAATGCACCGAAGTG
2005074 TCATATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.15
Consensus pattern (24 bp):
AAATGCACCGAAGTGACCACGTAG
Found at i:2013521 original size:4 final size:4
Alignment explanation
Indices: 2013512--2013554 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
2013502 TAATGCATGT
2013512 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
2013555 CATAGTTGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:2015957 original size:31 final size:30
Alignment explanation
Indices: 2015900--2015957 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
2015890 ATTAATACAT
* *
2015900 TGAAATAATATAAAATAATGATTAAATTGA
1 TGAAATAATATAAAATAAGGACTAAATTGA
2015930 TGAAAT-ATATAAATAATAAGGACTAAAT
1 TGAAATAATAT-AA-AATAAGGACTAAAT
2015958 ATATAATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.17
30 8 0.33
31 12 0.50
ACGTcount: A:0.57, C:0.02, G:0.10, T:0.31
Consensus pattern (30 bp):
TGAAATAATATAAAATAAGGACTAAATTGA
Found at i:2016507 original size:3 final size:3
Alignment explanation
Indices: 2016499--2016603 Score: 203
Period size: 3 Copynumber: 35.3 Consensus size: 3
2016489 CATTAATCAA
2016499 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2016547 AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2016594 AAT AAT AAT A
1 AAT AAT AAT A
2016604 TAGTCTAGTG
Statistics
Matches: 101, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 99 0.98
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2020097 original size:21 final size:21
Alignment explanation
Indices: 2020073--2020141 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
2020063 ATTTTCTAAA
*
2020073 ATAATTAAAATAATATATTTT
1 ATAATTAAATTAATATATTTT
* *
2020094 ATAA-TATATTTATTATATTTT
1 ATAATTA-AATTAATATATTTT
*
2020115 AATGATTAAATTAATATATTTT
1 -ATAATTAAATTAATATATTTT
2020137 ATAAT
1 ATAAT
2020142 AATTTTTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
20 2 0.05
21 19 0.50
22 15 0.39
23 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (21 bp):
ATAATTAAATTAATATATTTT
Found at i:2020130 original size:43 final size:41
Alignment explanation
Indices: 2020076--2020158 Score: 139
Period size: 43 Copynumber: 2.0 Consensus size: 41
2020066 TTCTAAAATA
2020076 ATTAAAATAATATATTTTATAATATATTTATTATATTTTAATG
1 ATTAAAATAATATATTTTATAATA-ATTT-TTATATTTTAATG
*
2020119 ATTAAATTAATATATTTTATAATAATTTTTATATTTTAAT
1 ATTAAAATAATATATTTTATAATAATTTTTATATTTTAAT
2020159 AAAATAAAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 12 0.31
42 4 0.10
43 23 0.59
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (41 bp):
ATTAAAATAATATATTTTATAATAATTTTTATATTTTAATG
Found at i:2021208 original size:40 final size:40
Alignment explanation
Indices: 2021149--2021239 Score: 157
Period size: 40 Copynumber: 2.3 Consensus size: 40
2021139 TTTCTCTTAC
2021149 CACT-TAAAATATTAGCGAACTCGTCTAATTATCTCATAT
1 CACTCTAAAATATTAGCGAACTCGTCTAATTATCTCATAT
*
2021188 CACTCTAAAATATTAGCGAACTCGTCTCATTATCTCATAT
1 CACTCTAAAATATTAGCGAACTCGTCTAATTATCTCATAT
2021228 CACTCTATAAAT
1 CACTCTA-AAAT
2021240 TTATATTTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
39 4 0.08
40 41 0.84
41 4 0.08
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (40 bp):
CACTCTAAAATATTAGCGAACTCGTCTAATTATCTCATAT
Found at i:2026823 original size:149 final size:149
Alignment explanation
Indices: 2026553--2026856 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
2026543 CGAAGTGCCC
2026553 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
2026618 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
2026683 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
*
2026702 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
2026767 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
2026832 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
2026851 CGTAGA
1 CGTAGA
2026857 CCCTCTACCC
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
CATATGTCCTAAAGAACCG
Found at i:2026987 original size:30 final size:28
Alignment explanation
Indices: 2026942--2026998 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
2026932 ATCGCGTAGT
* *
2026942 CATATTATTTCCATACCTTTATCACATAGG
1 CATATCATTTACATACC-TT-TCACATAGG
2026972 CATATCATTTACATACCTTTCACATAG
1 CATATCATTTACATACCTTTCACATAG
2026999 CTCATATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.32
29 2 0.08
30 15 0.60
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.39
Consensus pattern (28 bp):
CATATCATTTACATACCTTTCACATAGG
Found at i:2027083 original size:29 final size:28
Alignment explanation
Indices: 2027020--2027090 Score: 106
Period size: 29 Copynumber: 2.5 Consensus size: 28
2027010 TTTTCTGCAT
* *
2027020 ATTCATGTCATGCAATACATAAATATGA
1 ATTCATGTCATGTAATACATAAATATAA
*
2027048 ATTCATGTCATGTAATACATTTAATATAA
1 ATTCATGTCATGTAATACA-TAAATATAA
2027077 ATTCATGTCATGTA
1 ATTCATGTCATGTA
2027091 TCATAATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 18 0.46
29 21 0.54
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (28 bp):
ATTCATGTCATGTAATACATAAATATAA
Found at i:2027529 original size:66 final size:66
Alignment explanation
Indices: 2027388--2027535 Score: 219
Period size: 65 Copynumber: 2.2 Consensus size: 66
2027378 TTTTTCTCAT
* *
2027388 GGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATTTCATATACGAT
1 GGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATATACGAT
2027453 GA
65 GA
* * *
2027455 -GGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTTG
1 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATATACGATG
2027518 A
66 A
2027519 GGGGGTATCGGTTCCCC
1 -GGGGTATCGGTTCCCC
2027536 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
64 6 0.08
65 43 0.58
66 25 0.34
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (66 bp):
GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATATACGATG
A
Found at i:2030209 original size:54 final size:54
Alignment explanation
Indices: 2030147--2030464 Score: 451
Period size: 54 Copynumber: 6.1 Consensus size: 54
2030137 TTACCAAATA
* *
2030147 GGCACTAAGTGTTCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
2030201 GGCACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
2030255 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTTGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
2030309 GGCACTAAGTGTGCATTTCACGGAATTCATCTTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
2030363 GACACTAAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAA-C---T-
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
2030412 ---A--AA-TGTTCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
2030460 GGCAC
1 GGCAC
2030465 CGAGTGTGTA
Statistics
Matches: 239, Mismatches: 16, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
43 36 0.15
44 3 0.01
46 1 0.00
47 1 0.00
50 1 0.00
51 1 0.00
53 1 0.00
54 195 0.82
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:2030427 original size:43 final size:43
Alignment explanation
Indices: 2030366--2030453 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
2030356 CCGTTTCGAC
* *
2030366 ACTAAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATA
1 ACTAAATGTGCATTTCACGGAATTCATCCTATGTGGATGAATA
*
2030409 ACTAAATGTTCATTTCACGGAATTCATCCTATGTGGATGAATA
1 ACTAAATGTGCATTTCACGGAATTCATCCTATGTGGATGAATA
2030452 AC
1 AC
2030454 CATTTTGGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (43 bp):
ACTAAATGTGCATTTCACGGAATTCATCCTATGTGGATGAATA
Found at i:2030487 original size:97 final size:97
Alignment explanation
Indices: 2030312--2030489 Score: 232
Period size: 97 Copynumber: 1.8 Consensus size: 97
2030302 TCGTTTCGGC
* * * *
2030312 ACTAAGTGTGCATTTCACGGAATTCATCTTATGTGGATGAATAACCGTTTCGACACTAAGTGTGC
1 ACTAAATGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGACACCAAGTGTGC
***
2030377 ATTTCACGGAATTCATTCTATGTGGATGAATA
66 AAAACACGGAATTCATTCTATGTGGATGAATA
* * * * *
2030409 ACTAAATGTTCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTTGGCACCGAGTGTGT
1 ACTAAATGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGACACCAAGTGTGC
2030474 AAAACA-GGTAATTCAT
66 AAAACACGG-AATTCAT
2030490 AATATGTTTA
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
96 2 0.03
97 66 0.97
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (97 bp):
ACTAAATGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCGACACCAAGTGTGC
AAAACACGGAATTCATTCTATGTGGATGAATA
Found at i:2031210 original size:21 final size:21
Alignment explanation
Indices: 2031184--2031234 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
2031174 AACTTTCTGG
2031184 GAGTTTCGAAACTATAACTTA
1 GAGTTTCGAAACTATAACTTA
2031205 GAGTTTCGAAACTATAACTTA
1 GAGTTTCGAAACTATAACTTA
2031226 GAGTTTCGA
1 GAGTTTCGA
2031235 TACTCTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (21 bp):
GAGTTTCGAAACTATAACTTA
Found at i:2033471 original size:9 final size:9
Alignment explanation
Indices: 2033457--2033483 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2033447 AATCTAAACA
2033457 CAGATGCCT
1 CAGATGCCT
2033466 CAGATGCCT
1 CAGATGCCT
2033475 CAGATGCCT
1 CAGATGCCT
2033484 GATCTCATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (9 bp):
CAGATGCCT
Found at i:2034728 original size:21 final size:21
Alignment explanation
Indices: 2034698--2034988 Score: 201
Period size: 21 Copynumber: 14.0 Consensus size: 21
2034688 GATTTACATA
* *
2034698 TTCGCATTGCGATAGTCTAAG
1 TTCGCGTTGCGATAGTCCAAG
*
2034719 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
2034740 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
2034761 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
2034780 TTTGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
2034803 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
2034822 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
* *
2034845 TT--CATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
2034864 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
**
2034887 TT--CGTTGCGATAGTTGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
2034906 TTCGCTTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
2034929 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
2034948 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
2034971 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
2034989 AATCGCAACG
Statistics
Matches: 210, Mismatches: 40, Indels: 42
0.72 0.14 0.14
Matches are distributed among these distances:
19 55 0.26
21 114 0.54
23 41 0.20
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:2034750 original size:42 final size:41
Alignment explanation
Indices: 2034723--2034985 Score: 420
Period size: 42 Copynumber: 6.3 Consensus size: 41
2034713 TCTAAGTTCG
2034723 CGTTGCGATAGTCGAAGTTCGCGTTGCGATT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAATT
*
2034763 CGTTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
* *
2034805 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
*
2034847 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
* *
2034889 CGTTGCGATAGTTGAAGTTCGCTTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
2034931 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
2034973 CGTTGCGATAGTC
1 CGTTGCGATAGTC
2034986 CAAAATCGCA
Statistics
Matches: 209, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 28 0.13
41 2 0.01
42 179 0.86
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAATT
Found at i:2035718 original size:21 final size:21
Alignment explanation
Indices: 2035692--2035925 Score: 104
Period size: 21 Copynumber: 11.4 Consensus size: 21
2035682 ATTTTGGACT
*
2035692 ATCGCAATGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
2035713 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
2035734 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
2035755 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
2035776 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAATTTGGAATAA
* * *
2035795 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
2035816 ATCGCAATGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * * *
2035837 ATCACAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
2035858 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAATTTGGAATAA
* * *
2035877 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
2035898 ATCGCAACGAATTT-GAA-AA
1 ATCGCAACGAATTTGGAATAA
2035917 ATCGCAACG
1 ATCGCAACG
2035926 CGAACTTCGA
Statistics
Matches: 155, Mismatches: 34, Indels: 50
0.65 0.14 0.21
Matches are distributed among these distances:
18 2 0.01
19 60 0.39
21 68 0.44
23 25 0.16
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:2035808 original size:40 final size:42
Alignment explanation
Indices: 2035688--2035946 Score: 449
Period size: 40 Copynumber: 6.3 Consensus size: 42
2035678 TGCGATTTTG
*
2035688 GACTATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
2035730 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
2035772 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
2035812 GACTATCGCAATGAATTTGGAATAAATCACAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
2035854 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
2035894 GACTATCGCAACGAATTT-GAA-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
2035934 GACTATCGCAACG
1 GACTATCGCAACG
2035947 CGAACTTGGA
Statistics
Matches: 209, Mismatches: 5, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
39 1 0.00
40 107 0.51
41 3 0.01
42 98 0.47
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:2035971 original size:82 final size:82
Alignment explanation
Indices: 2035688--2035946 Score: 459
Period size: 82 Copynumber: 3.2 Consensus size: 82
2035678 TGCGATTTTG
*
2035688 GACTATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAT
1 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAT
2035753 AAATCGCAACGCGAACTTC
64 AAATCGCAACGCGAACTTC
*
2035772 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAATGAATTTGGAATAA
1 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
*
2035837 ATCACAACGCGAACTTC
66 ATCGCAACGCGAACTTC
2035854 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTT-GAA-AA
1 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
2035917 ATCGCAACGCGAACTTC
66 ATCGCAACGCGAACTTC
2035934 GACTATCGCAACG
1 GACTATCGCAACG
2035947 CGAACTTGGA
Statistics
Matches: 170, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
80 31 0.18
81 3 0.02
82 116 0.68
83 1 0.01
84 19 0.11
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (82 bp):
GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
ATCGCAACGCGAACTTC
Found at i:2036005 original size:21 final size:21
Alignment explanation
Indices: 2035980--2036032 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2035970 AATATGTAAA
2035980 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
2036001 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
2036022 TCGCGTTGCGA
1 TCGCATTGCGA
2036033 ATCTGTAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:2036771 original size:13 final size:13
Alignment explanation
Indices: 2036753--2036806 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 13
2036743 GTTCCGACCC
*
2036753 GACCCGACCCTTT
1 GACCCGACCCGTT
2036766 GACCCGACCC---
1 GACCCGACCCGTT
**
2036776 GACCTAACCCGTT
1 GACCCGACCCGTT
2036789 GACCCGACCCGTT
1 GACCCGACCCGTT
2036802 GACCC
1 GACCC
2036807 TTGACCGACG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 8 0.24
13 26 0.76
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2036772 original size:23 final size:23
Alignment explanation
Indices: 2036746--2036799 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
2036736 TTGACCGGTT
* *
2036746 CCGACCCGACCCGACCCTTTGAC
1 CCGACCCGACCCAACCCGTTGAC
*
2036769 CCGACCCGACCTAACCCGTTGAC
1 CCGACCCGACCCAACCCGTTGAC
2036792 CCGACCCG
1 CCGACCCG
2036800 TTGACCCTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.19, C:0.52, G:0.19, T:0.11
Consensus pattern (23 bp):
CCGACCCGACCCAACCCGTTGAC
Found at i:2039235 original size:24 final size:24
Alignment explanation
Indices: 2039201--2039272 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
2039191 AATACATTAC
* *
2039201 CTGAATGCTGTTCTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
* *
2039225 CTGGATTCTGTTATGATATCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
* *
2039249 CTGAATTCTGTTTTGATTTATGAT
1 CTGAATTCTGTTATGATTTCTGAT
2039273 ATCTTCATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.49
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:2043801 original size:12 final size:12
Alignment explanation
Indices: 2043781--2043840 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
2043771 GATACATTAC
2043781 CTGAATTCTGTT
1 CTGAATTCTGTT
*
2043793 CTGATTTCTGTT
1 CTGAATTCTGTT
*
2043805 CTGGATTCTGTT
1 CTGAATTCTGTT
* *
2043817 ATG-ATATCTGAT
1 CTGAAT-TCTGTT
2043829 CTGAATTCTGTT
1 CTGAATTCTGTT
2043841 TTTATTTATG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 2 0.05
12 35 0.90
13 2 0.05
ACGTcount: A:0.17, C:0.15, G:0.18, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:2043852 original size:24 final size:24
Alignment explanation
Indices: 2043781--2043840 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
2043771 GATACATTAC
* *
2043781 CTGAATTCTGTTCTGATTTCTGTT
1 CTGAATTCTGTTATGATTTCTGAT
* *
2043805 CTGGATTCTGTTATGATATCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
2043829 CTGAATTCTGTT
1 CTGAATTCTGTT
2043841 TTTATTTATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.17, C:0.15, G:0.18, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:2053466 original size:106 final size:106
Alignment explanation
Indices: 2053324--2053536 Score: 408
Period size: 106 Copynumber: 2.0 Consensus size: 106
2053314 CATTTATCAT
2053324 GCTTTATAACATCAAAAATAGTATTCTACCATGAATACACTTACATGCTTAAAGAACTCATACAA
1 GCTTTATAACATCAAAAATAGTATTCTACCATGAATACACTTACATGCTTAAAGAACTCATACAA
2053389 ACTAACCAACAAATATAATAACTTACAAGTGGTATAGATGA
66 ACTAACCAACAAATATAATAACTTACAAGTGGTATAGATGA
*
2053430 GCTTTATAACATCAAAAGTAGTATTCTACCATGAATACACTTACATGCTTAAAGAACTCATACAA
1 GCTTTATAACATCAAAAATAGTATTCTACCATGAATACACTTACATGCTTAAAGAACTCATACAA
*
2053495 GCTAACCAACAAATATAATAACTTACAAGTGGTATAGATGA
66 ACTAACCAACAAATATAATAACTTACAAGTGGTATAGATGA
2053536 G
1 G
2053537 TTAGAAATAT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 105 1.00
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (106 bp):
GCTTTATAACATCAAAAATAGTATTCTACCATGAATACACTTACATGCTTAAAGAACTCATACAA
ACTAACCAACAAATATAATAACTTACAAGTGGTATAGATGA
Found at i:2053938 original size:14 final size:14
Alignment explanation
Indices: 2053919--2053959 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
2053909 CTTGGGAAGG
2053919 AAGAGGGAAAAGAT
1 AAGAGGGAAAAGAT
2053933 AAGAGGGAAAAGAT
1 AAGAGGGAAAAGAT
2053947 AAGAGGGAAAAGA
1 AAGAGGGAAAAGA
2053960 AGACAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.37, T:0.05
Consensus pattern (14 bp):
AAGAGGGAAAAGAT
Found at i:2055183 original size:12 final size:12
Alignment explanation
Indices: 2055166--2055195 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2055156 CTCACATATC
2055166 TTATATTCATAA
1 TTATATTCATAA
2055178 TTATATTCATAA
1 TTATATTCATAA
*
2055190 CTATAT
1 TTATAT
2055196 ATCGTAGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (12 bp):
TTATATTCATAA
Found at i:2055662 original size:18 final size:18
Alignment explanation
Indices: 2055639--2055739 Score: 132
Period size: 18 Copynumber: 5.4 Consensus size: 18
2055629 AACTTGCCAA
2055639 ATTCATAATTTATTTTAG
1 ATTCATAATTTATTTTAG
2055657 ATTCATAATTTATTTTAG
1 ATTCATAATTTATTTTAG
2055675 ATTCATAATTTATTTTAG
1 ATTCATAATTTATTTTAG
*
2055693 ATTCATAGCTTTACTTTCT-G
1 ATTCATA-ATTTA-TTT-TAG
*
2055713 ATTCATAACTTTTCTTTTAG
1 ATTCATAA--TTTATTTTAG
2055733 ATTCATA
1 ATTCATA
2055740 GCCAAATGTA
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
18 43 0.58
19 5 0.07
20 22 0.30
21 4 0.05
ACGTcount: A:0.30, C:0.11, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTCATAATTTATTTTAG
Found at i:2057147 original size:10 final size:10
Alignment explanation
Indices: 2057132--2057156 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2057122 GTCATATCAT
2057132 TTTAGTTGCA
1 TTTAGTTGCA
2057142 TTTAGTTGCA
1 TTTAGTTGCA
2057152 TTTAG
1 TTTAG
2057157 GTCATTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (10 bp):
TTTAGTTGCA
Found at i:2057457 original size:26 final size:26
Alignment explanation
Indices: 2057428--2057481 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
2057418 CTGATTCCAG
* *
2057428 TAGTTGGTTTGACCAACTGATTTGAT
1 TAGTTGATTTGACAAACTGATTTGAT
*
2057454 TAGTTGATTTGAGAAACTGATTTGAT
1 TAGTTGATTTGACAAACTGATTTGAT
2057480 TA
1 TA
2057482 ACTGTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (26 bp):
TAGTTGATTTGACAAACTGATTTGAT
Found at i:2057484 original size:13 final size:13
Alignment explanation
Indices: 2057442--2057485 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
2057432 TGGTTTGACC
2057442 AACTGATTTGATT
1 AACTGATTTGATT
** **
2057455 AGTTGATTTGAGA
1 AACTGATTTGATT
2057468 AACTGATTTGATT
1 AACTGATTTGATT
2057481 AACTG
1 AACTG
2057486 TTTATATAGA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (13 bp):
AACTGATTTGATT
Found at i:2066492 original size:2 final size:2
Alignment explanation
Indices: 2066485--2067606 Score: 737
Period size: 2 Copynumber: 563.5 Consensus size: 2
2066475 CAAAATCCCA
* *
2066485 AC AC AC AC AC AC AC A- AC AC AC AC AC GC AC AC AC AC GC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * * *
2066526 AC AC GC AC AT AT AT AC AT AC AC AC AC GC AC AC AC AC AC AC GC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * *
2066568 AC AC AC AT GC AT AC AC AC GC AC AC AC AC GC AC AC AC A- AGC GC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A-C AC
* * * * * * * * *
2066610 GC GC GC GC AC AC AC AC AC AC AC AT AC AT AT AT AC AT AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * * * *
2066652 AC GC AC AT GC AC AC AC AC AC GC GC GC GC AC AC AC AC AC GC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * *
2066694 AC GC AC AC AC AC GC AC AC AC AC GC AC AC AC GC AC AC TC AC GC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * *
2066736 AC AC AC AC GC AC AC AC AC GC AC AC AC AC GC GC AC AC AT AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
** * * *
2066778 AC AC AC AC GT AC AC AC AC AC AC GC AC AC AC AC AC AC AC GC GC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * *
2066820 AC AC AC AC AC GC AC AC GC AC AC AC AC GC AC AC AC GC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * *
2066862 AC GC AC AC AC AC GC AC AC AC AC -C AC AC AC GC AC AC AC AC GC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
** * * * *
2066903 GT AC AC AC AC AC AT AT AT AC AT AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * *
2066945 GC AC AC AT GC AT AC AC AC -C AC AC AC AC GC AC AC AC A- AGC GC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A-C AC
* * * * * * * * *
2066986 GC GC GC AC -C AC AC AC AC AT AC AT AT AT AC AT AC AC AC AC GC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * ** *
2067027 AC AC GC AC AC AC AC AC GC GC GC AC AC AC AC AC AT GT AC AC GC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * *
2067069 AC AC AC AC GC AC AC AC AC AC AC GC AC AC AC AC GC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
** * * * * * * * *
2067111 GT GC AC AT AT AC AC AC AC AC GC AC AC GC AC AC AC AC GC GC GC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * *
2067153 AC AC AC AC AC AC GC GC AC AC AC AC GC GC GC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * *
2067195 GC AC AC GC GC AC AC AC AC AC AC AC AC AC AC AC AC AT AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * *
2067237 AT GC AC AC AC AC GC AC GC AC AC AC AC GC AC AC GC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * *
2067279 AC AC AC AC AC AC AC AC AC GC AC AC AC AC GC AC AC AC AC GC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * *
2067321 AC AC AC AC GC AC AC GC AC AC GC AC AC AC AC AC AC AC AC GC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * *
2067363 AC AC AC AC AC AC GC AC AC AC AC AC GC -C AC AC AC GC AT AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * *
2067404 AC GC AC AC AC AC AC AC GC GC GC AC AC AC AC AC AC AC AC GC TC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * * *
2067446 GC AC AC AC GC AC AC AC AC GC AC AC GC AC GC AC AC GC AC GC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * * * *
2067488 GC AC GC AC GC AC AC CC AC GC AC AC AC AC GC GC GC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * * * * *
2067530 GC AC AC GC AC GC AC AC GC AC GC AC GC AC GC AC GC AC GC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * *
2067572 CC AC GC AC AC AC AC GC GC GC GC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2067607 TACATACATA
Statistics
Matches: 872, Mismatches: 239, Indels: 18
0.77 0.21 0.02
Matches are distributed among these distances:
1 7 0.01
2 865 0.99
ACGTcount: A:0.39, C:0.47, G:0.11, T:0.03
Consensus pattern (2 bp):
AC
Found at i:2067598 original size:18 final size:18
Alignment explanation
Indices: 2066485--2067606 Score: 811
Period size: 18 Copynumber: 61.4 Consensus size: 18
2066475 CAAAATCCCA
*
2066485 ACACACACACACACA-AC
1 ACACACACGCACACACAC
2066502 ACACACACGCACACACACGC
1 ACACACACGCACACACA--C
* * *
2066522 ACACACACGCACATATAT
1 ACACACACGCACACACAC
* * *
2066540 ACATACACACACGCACAC
1 ACACACACGCACACACAC
2066558 ACACACACGCACACACATGC
1 ACACACACGCACACACA--C
*
2066578 ATACACACGCACACACAC
1 ACACACACGCACACACAC
* * *
2066596 GCACACA--CA-AGCGCGC
1 ACACACACGCACA-CACAC
* * *
2066612 GCGCGCA--CACACACAC
1 ACACACACGCACACACAC
* ** * * *
2066628 ACACATACATATATACAT
1 ACACACACGCACACACAC
**
2066646 ACACACACGCACATGCAC
1 ACACACACGCACACACAC
* * *
2066664 ACACACACGCGCGCGCAC
1 ACACACACGCACACACAC
*
2066682 ACACACACG--CACACGC
1 ACACACACGCACACACAC
2066698 ACACACACGCACACACAC
1 ACACACACGCACACACAC
* *
2066716 GCACACACGCACACTCACGC
1 ACACACACGCACA--CACAC
2066736 ACACACACGCACACACACGC
1 ACACACACGCACACACA--C
* *
2066756 ACACACACGCGCACACAT
1 ACACACACGCACACACAC
* **
2066774 ACACACACACACGTACAC
1 ACACACACGCACACACAC
2066792 ACACACACGCACACACAC
1 ACACACACGCACACACAC
*
2066810 ACACACGCGCACACACAC
1 ACACACACGCACACACAC
*
2066828 ACGCACACGCACACACAC
1 ACACACACGCACACACAC
*
2066846 GCACACACGCACACACACGC
1 ACACACACGCACACACA--C
2066866 ACACACACGCACACACAC
1 ACACACACGCACACACAC
2066884 -CACACACGCACACACACGC
1 ACACACACGCACACACA--C
* * *
2066903 GTACACACACACATATATACATAC
1 --ACACACACGC----ACACACAC
*
2066927 ACACACACACACACACAC
1 ACACACACGCACACACAC
* * *
2066945 GCACACATGCATACACACC
1 ACACACACGCACACACA-C
2066964 ACACACACGCACACACA-
1 ACACACACGCACACACAC
* * *
2066981 AGCGCGCGCGCAC-CACAC
1 A-CACACACGCACACACAC
* ** * * *
2066999 ACACATACATATATACAT
1 ACACACACGCACACACAC
*
2067017 ACACACACGCACACGCAC
1 ACACACACGCACACACAC
* *
2067035 ACACACACGCGCGCACAC
1 ACACACACGCACACACAC
* * *
2067053 ACACACATG--TACACGC
1 ACACACACGCACACACAC
2067069 ACACACACGCACACACAC
1 ACACACACGCACACACAC
* * *
2067087 ACACGCACACACACGCAC
1 ACACACACGCACACACAC
** * *
2067105 ACACACGTGCACATATAC
1 ACACACACGCACACACAC
*
2067123 ACACACACGCACACGCAC
1 ACACACACGCACACACAC
* *
2067141 ACACACGCGCGCACACAC
1 ACACACACGCACACACAC
*
2067159 ACACACGCGCACACACAC
1 ACACACACGCACACACAC
* * * *
2067177 GCGCGCACACACACACAC
1 ACACACACGCACACACAC
* *
2067195 GCACACGCGCACACACAC
1 ACACACACGCACACACAC
* *
2067213 ACACACACACACACACAT
1 ACACACACGCACACACAC
*
2067231 ACACACATGCACACACACGC
1 ACACACACGCACACACA--C
* * *
2067251 ACGCACACACACGCACACGC
1 A--CACACACGCACACACAC
*
2067271 ACACACACACACACACAC
1 ACACACACGCACACACAC
2067289 ACACACACGCACACACACGC
1 ACACACACGCACACACA--C
2067309 ACACACACGCACACACAC
1 ACACACACGCACACACAC
* *
2067327 ACGCACACGCACACGCAC
1 ACACACACGCACACACAC
*
2067345 ACACACA--CACACACGC
1 ACACACACGCACACACAC
* *
2067361 ACACACACACACACGCAC
1 ACACACACGCACACACAC
*
2067379 ACACACACGCCACACACGC
1 ACACACACG-CACACACAC
*
2067398 ATACACACGCACACACAC
1 ACACACACGCACACACAC
* *
2067416 ACACGCGCGCACACACAC
1 ACACACACGCACACACAC
*
2067434 ACACACACGCTCGCACACACGC
1 ACACACA----CGCACACACAC
*
2067456 ACACACACGCACACGCACGC
1 ACACACACGCACA--CACAC
* * *
2067476 ACACGCACGCACGCACGC
1 ACACACACGCACACACAC
* *
2067494 ACGCACAC-C-CACGCAC
1 ACACACACGCACACACAC
* *
2067510 ACACACGCGCGCACACAC
1 ACACACACGCACACACAC
* *
2067528 ACGCACACGCACGCACAC
1 ACACACACGCACACACAC
* * * *
2067546 GCACGCACGCACGCACGC
1 ACACACACGCACACACAC
* * *
2067564 ACGCACACCCACGCACAC
1 ACACACACGCACACACAC
* * *
2067582 ACACGCGCGCGCACACAC
1 ACACACACGCACACACAC
2067600 ACACACA
1 ACACACA
2067607 TACATACATA
Statistics
Matches: 861, Mismatches: 195, Indels: 97
0.75 0.17 0.08
Matches are distributed among these distances:
15 1 0.00
16 67 0.08
17 42 0.05
18 547 0.64
19 31 0.04
20 120 0.14
22 47 0.05
24 1 0.00
26 5 0.01
ACGTcount: A:0.39, C:0.47, G:0.11, T:0.03
Consensus pattern (18 bp):
ACACACACGCACACACAC
Found at i:2071495 original size:13 final size:13
Alignment explanation
Indices: 2071477--2071517 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
2071467 TTAACAGAAA
2071477 AAAGTCAATGGTC
1 AAAGTCAATGGTC
* *
2071490 AAAGTCAACGATC
1 AAAGTCAATGGTC
2071503 AAAGTCAATGGTC
1 AAAGTCAATGGTC
2071516 AA
1 AA
2071518 CAGTTAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.20
Consensus pattern (13 bp):
AAAGTCAATGGTC
Found at i:2071513 original size:26 final size:27
Alignment explanation
Indices: 2071477--2071531 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
2071467 TTAACAGAAA
*
2071477 AAAGTCAATGGTCAA-AGTCAACGATC
1 AAAGTCAATGGTCAACAGTCAAAGATC
*
2071503 AAAGTCAATGGTCAACAGTTAAAGATC
1 AAAGTCAATGGTCAACAGTCAAAGATC
2071530 AA
1 AA
2071532 TGGTCAACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.20
Consensus pattern (27 bp):
AAAGTCAATGGTCAACAGTCAAAGATC
Found at i:2071516 original size:20 final size:21
Alignment explanation
Indices: 2071493--2071559 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
2071483 AATGGTCAAA
2071493 GTCAAC-GATCAAAG-TCAATG
1 GTCAACAG-TCAAAGATCAATG
*
2071513 GTCAACAGTTAAAGATCAATG
1 GTCAACAGTCAAAGATCAATG
* *
2071534 GTCAACAGTTAACGATCAATG
1 GTCAACAGTCAAAGATCAATG
2071555 GTCAA
1 GTCAA
2071560 ACAATATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 11 0.26
21 32 0.74
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.22
Consensus pattern (21 bp):
GTCAACAGTCAAAGATCAATG
Found at i:2071533 original size:21 final size:21
Alignment explanation
Indices: 2071503--2071559 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
2071493 GTCAACGATC
2071503 AAAG-TCAATGGTCAACAGTT
1 AAAGATCAATGGTCAACAGTT
2071523 AAAGATCAATGGTCAACAGTT
1 AAAGATCAATGGTCAACAGTT
*
2071544 AACGATCAATGGTCAA
1 AAAGATCAATGGTCAA
2071560 ACAATATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 4 0.11
21 31 0.89
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (21 bp):
AAAGATCAATGGTCAACAGTT
Found at i:2074544 original size:3 final size:3
Alignment explanation
Indices: 2074536--2074597 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
2074526 AAGGGAAGGA
2074536 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2074584 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
2074598 CATGCAAGGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2076433 original size:31 final size:28
Alignment explanation
Indices: 2076386--2076480 Score: 93
Period size: 31 Copynumber: 3.2 Consensus size: 28
2076376 TAAGTACTTG
*
2076386 AAGTATTTTTTAGTCAAAATAAGTACCAA
1 AAGTATTTTTT-GTCAAAATAGGTACCAA
* **
2076415 AAGTTATTTTTTTGGTCAAGATAGGTATTAA
1 AAG-TA-TTTTTT-GTCAAAATAGGTACCAA
*
2076446 AAGTATTTTATGTCAAAATAGGTACCTAA
1 AAGTATTTTTTGTCAAAATAGGTACC-AA
2076475 AA-TATT
1 AAGTATT
2076481 CAATATTTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
28 16 0.30
29 12 0.22
30 4 0.07
31 22 0.41
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (28 bp):
AAGTATTTTTTGTCAAAATAGGTACCAA
Found at i:2076621 original size:31 final size:31
Alignment explanation
Indices: 2076562--2076621 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
2076552 ATGAAAATTG
* * *
2076562 AATACTTTAGGTATCTATTTTGATAAAAAAA
1 AATACTTTAAGTACCTATTTTGACAAAAAAA
*
2076593 AATACTTTAAGTACCTA-TTTGACCAAAAA
1 AATACTTTAAGTACCTATTTTGACAAAAAA
2076622 GAGAACTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (31 bp):
AATACTTTAAGTACCTATTTTGACAAAAAAA
Found at i:2094972 original size:18 final size:19
Alignment explanation
Indices: 2094949--2094985 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2094939 TAGCCCGCCT
2094949 AATTTA-ATTATTTTTTAC
1 AATTTATATTATTTTTTAC
*
2094967 AATTTATTTTATTTTTTAC
1 AATTTATATTATTTTTTAC
2094986 GGAAGACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
AATTTATATTATTTTTTAC
Found at i:2100897 original size:469 final size:467
Alignment explanation
Indices: 2100015--2100953 Score: 1716
Period size: 469 Copynumber: 2.0 Consensus size: 467
2100005 GTCATCCACA
*
2100015 TATAGATAAGAAAACAAATTTTAATCTCATTGACCTTCTGGTATATACATTGATCCAAGATTTTC
1 TATAGATAAGAAAACAAATTTTAATCTCATTGACCTTCTAGTATATACATTGATCCAAGATTTTC
2100080 TAAACAAAACCAAATGAAGAGATAACTTCATAGAATTTTAAATACCACTGTCTGGAGGCTTGTTT
66 TAAACAAAACCAAATGAAGAGATAACTTCATAGAATTTTAAATACCACTGTCTGGAGGCTTGTTT
*
2100145 CAATCCATATATTAACTTTTTCAACTTAAATACCAAGTGTTCACAATCACTAGAGAATAATCCTT
131 CAATCCATATATTAACTTTTTCAACTTAAATACCAAGTGTTCACAATCACTAGAGAAGAATCCTT
*
2100210 TAGGTTGTTTCATGTATACCTCTTCCTCAAGGTCACCATTGAGAAAAGTAGTTTTCACATACATT
196 TAGGTTGTTTCATGTATACCTCTTCCTCAAGGTCACCATTGAGAAAAGTAGCTTTCACATACATT
* * * *
2100275 TGTTTTAACATAAGGTCAAAATGAGCTACTAATGCTAACACGATGTATAAAGAATCTTTCTTAGA
261 TGTTTTAACACAAGGTCAAAATGAGATACTAATGCTAACACGATGCATAAAGAATCTATCTTAGA
* *
2100340 TACTGGACTAAAAGTTTCAGTGTAATCGATTTCTTCACGCTGAGTGAAACCTTTTGCAACGAGTC
326 TACTGGACTAAAAGTCTCAGTGTAATCGATTTCTTCACGCTGAGTGAAACCTTTTACAACGAGTC
*
2100405 TTTCTTTATATCTTTCAATGTTGCCCATTGAGTCTCTTTTTGTTTTAAAAACCTATTTACATCCA
391 TTGCTTTATATCTTTCAATGTTGCCCATTGAGTCTCTTTTTGTTTTAAAAACCTATTTACATCCA
2100470 TTGATTTTTACAC
456 TTGATTTTT-CAC
2100483 TATAGGATAAGAAAACAAATTTTAATCTCATTGACCTTCTAGTATATACATTGATCCAAGATTTT
1 TATA-GATAAGAAAACAAATTTTAATCTCATTGACCTTCTAGTATATACATTGATCCAAGATTTT
*
2100548 CTAAACAAAACCAAATGAAGAGATAACTTCATTGAATTTTAAATACCACTGTCTGGAGGCTTGTT
65 CTAAACAAAACCAAATGAAGAGATAACTTCATAGAATTTTAAATACCACTGTCTGGAGGCTTGTT
*
2100613 TCAATCCATATATTAACTTTTTCAACTTAAATACCAAGTGTTCACCATCACTAGAGAAGAATCCT
130 TCAATCCATATATTAACTTTTTCAACTTAAATACCAAGTGTTCACAATCACTAGAGAAGAATCCT
*
2100678 TTAGGTTGTTTCATGTATACCTCTTCCTCAAGGTCACCATTGAGAAAAGTAGCTTTCATATACAT
195 TTAGGTTGTTTCATGTATACCTCTTCCTCAAGGTCACCATTGAGAAAAGTAGCTTTCACATACAT
2100743 TTGTTTTAACACAAGGTCAAAATGAGATACTAATGCTAACACGATGCATAAAGAATCTATCTTAG
260 TTGTTTTAACACAAGGTCAAAATGAGATACTAATGCTAACACGATGCATAAAGAATCTATCTTAG
* *
2100808 ATATTGGACTAAAAGTCTCAGTGTAATTGATTTCTTCACGCTGAGTGAAACCTTTTACAACGAGT
325 ATACTGGACTAAAAGTCTCAGTGTAATCGATTTCTTCACGCTGAGTGAAACCTTTTACAACGAGT
*
2100873 CTTGCTTTATATCTTTCAATGTTGCCCATTGAGTCTCTTTTTGTTTTAAAGACCTATTTACATCC
390 CTTGCTTTATATCTTTCAATGTTGCCCATTGAGTCTCTTTTTGTTTTAAAAACCTATTTACATCC
2100938 ATTGATTTTTCAC
455 ATTGATTTTTCAC
2100951 TAT
1 TAT
2100954 CAAGCAACGA
Statistics
Matches: 454, Mismatches: 16, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
468 10 0.02
469 444 0.98
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (467 bp):
TATAGATAAGAAAACAAATTTTAATCTCATTGACCTTCTAGTATATACATTGATCCAAGATTTTC
TAAACAAAACCAAATGAAGAGATAACTTCATAGAATTTTAAATACCACTGTCTGGAGGCTTGTTT
CAATCCATATATTAACTTTTTCAACTTAAATACCAAGTGTTCACAATCACTAGAGAAGAATCCTT
TAGGTTGTTTCATGTATACCTCTTCCTCAAGGTCACCATTGAGAAAAGTAGCTTTCACATACATT
TGTTTTAACACAAGGTCAAAATGAGATACTAATGCTAACACGATGCATAAAGAATCTATCTTAGA
TACTGGACTAAAAGTCTCAGTGTAATCGATTTCTTCACGCTGAGTGAAACCTTTTACAACGAGTC
TTGCTTTATATCTTTCAATGTTGCCCATTGAGTCTCTTTTTGTTTTAAAAACCTATTTACATCCA
TTGATTTTTCAC
Found at i:2108664 original size:16 final size:16
Alignment explanation
Indices: 2108643--2108675 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2108633 ATGACTTAAC
2108643 GGATGACATTATATAT
1 GGATGACATTATATAT
2108659 GGATGACATTATATAT
1 GGATGACATTATATAT
2108675 G
1 G
2108676 AGCTAAACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (16 bp):
GGATGACATTATATAT
Found at i:2118187 original size:874 final size:875
Alignment explanation
Indices: 2116496--2118203 Score: 2324
Period size: 874 Copynumber: 2.0 Consensus size: 875
2116486 GCACTAATTT
* * **
2116496 GGATCATTATATTGCTAAAGTAACTCAGGTGTCCTCACCGTTTCCTATGTGACAACAAAGGTGTA
1 GGATCATTATACTGCTAAAGTAACTCAGGTGTCCTCACCGTTTCCTATGTGACAAAAAAGGCATA
* * * * *
2116561 AGTCTTATGGAATCTTACCTCATAAGGCTCTTATGGTTATCACACAATTAATGTTATTATCTCAT
66 AGTCTTATGGAATCTTACCTCATAAGGCTCTTATGGTTATCAAAAAATTAATGTCACTATCTAAT
* *
2116626 TATTATAATAAGTCTTTACTCTAGAGCGAACATCTTAATCCATGTTAACTGATACCACACTAAGG
131 TATTATAATAAATCTTTACTCTAGAGAGAACATCTTAA-CCATGTTAACTGATACCACACTAAGG
* ** * * * *
2116691 CGACCGAAGTAGCTTGGCTACTCAATACAAAACTTATTGAAGTCAGGTGAGGTCATTTCCCCTTC
195 CAACAAAAGTAGCTCGACTACTCAATACAAAACTTATTGAAGCCAGGTGAGATCATTTCCCCTTC
* * ** *
2116756 ACTCGAACTATCCCGCTCGTCCTCTTTCCTAGGACGTAAAGAAAAGGTTTATTAGAACTTAAAGG
260 ACCCGAACTATCCCGCTCATCCTCTCGCCTAGGACGTAAAGAAAAGGTTTACTAGAACTTAAAGG
* * * * * ** *
2116821 GTATTTTAGTCATCTCTGTCTCTGAAGAGATCTCTAAGTGTTTTATGATTTCCTGACGATTATGG
325 GTATTTTAGTCATCGCTATCTCTGAAGAGATCTATAAGTATTTCACAATTCCCTGACGATTATGG
* *
2116886 TGTTTGTTATTCACAGACTGAATCACTAGTTAGCCCAATACCTGACTTGGGTTCATTACTGGGTA
390 TGTTTGTTATTCACAGACTAAATCACTAGTTAGCCCAATACCTGACTCGGGTTCATTACTGGGTA
* * * * *
2116951 ACAACACTCCTAACACTTTTAGTGTACTTCTCCCAAAACCCCCTTGAAGTAGTGGGACGACTTAT
455 ACAACACTCCTAACACTCTTAGTGTACTTCTCCCAAAACCACATTGAAGTAGTAGGACGAATTAT
* ** *
2117016 ACATTCTCGATTCACTGACATTCTCGAAGTACCATGTTCTTCTTCAATAATAAATATGTCATATT
520 ACATTCTCGATTCACTGACATTCTCGAAGCACCACATTCTTCGTCAATAATAAATATGTCATATT
* **
2117081 CTTTGTACGATATATCATATATCTCTTGTAACGATCCTCGATCCCAACTATTTGTATATGTCCTC
585 CTTTGTACGATATATCAGATATCTCTTGTAACGATCCTCGATCCCAACTATTTGTATACATCCTC
* * * *
2117146 GATTGAAGATAATTTGGTGTATTACACTTAATATGTTTACACCTGATGTAACCTACTCCTATGAG
650 GATTGAAGATAATTTGGCGTATTACACTTAATATGGTTACACCCGATGTAACCTACTCCTACGAG
* * *
2117211 TTTTTTAGATACGTTTGGTCATTCATGTCCTTTACAGACTAAGTCTTACTATTAAGGGTCGTCCT
715 TGTTTTAGATACGTTTGGTCATTCATGTCCTTCACAAACTAAGTCTTACTATTAAGGGTCGTCCT
* ***
2117276 TAGTCCTTATCGACCTTAATCAGGTCAAATCTGACCATTTTAAGTGAGTAGTATAAATACCCTAG
780 TAGTCCTTATCGACCTTAATCAGGTCAAATATGACCATCCCAAGTGAGTAGTATAAATACCCTAG
2117341 GGTCAAGTATCGATACCCAAATAAGTATCAA
845 GGTCAAGTATCGATACCCAAATAAGTATCAA
* * *
2117372 GGATCATTATACTGCTAAAGTAACTTAGGTGTCCTCATCGTTTCTTGA-GTGACAAAAAAGGCAT
1 GGATCATTATACTGCTAAAGTAACTCAGGTGTCCTCACCGTTTCCT-ATGTGACAAAAAAGGCAT
2117436 AAGTCTTATGGAATCTTACCTCATAAGGCTCTTATGGTTATCAAAAAATTAATGTCACTATCTAA
65 AAGTCTTATGGAATCTTACCTCATAAGGCTCTTATGGTTATCAAAAAATTAATGTCACTATCTAA
* *
2117501 TTATTATAATAAATCTTTGCTCTAGAGAGAACGTCTTAA-CATACGTTAACTGATACCACACTAA
130 TTATTATAATAAATCTTTACTCTAGAGAGAACATCTTAACCAT--GTTAACTGATACCACACTAA
* * ** ** * * * *
2117565 GTCAACAAAATTAGCTCGACTACTTTATACCGAACTTATTGAAGCCATGTGAGAT-TTTTTCTCT
193 GGCAACAAAAGTAGCTCGACTACTCAATACAAAACTTATTGAAGCCAGGTGAGATCATTTCCCCT
* *
2117629 TCACCCGAACTATCCCGCTCATCCTCTCGCGTAGGACGTAAAGAAAAGGTTTACTAGCACTTAAA
258 TCACCCGAACTATCCCGCTCATCCTCTCGCCTAGGACGTAAAGAAAAGGTTTACTAGAACTTAAA
*
2117694 GGGTATTTTAGTCATCGCTATCTCTGGAGAGATCTATAAGTATTTCACAATTCCCTGAC-ATTAT
323 GGGTATTTTAGTCATCGCTATCTCTGAAGAGATCTATAAGTATTTCACAATTCCCTGACGATTAT
* * * *
2117758 GGTGTTTGTTGTTCACTGACTAAATCACTAGTTATCCCAATACTTGACTCGGGTTCATTACTGGG
388 GGTGTTTGTTATTCACAGACTAAATCACTAGTTAGCCCAATACCTGACTCGGGTTCATTACTGGG
* * * *
2117823 TAACAACACTTCTAACTCTCTTA-TCGTACTTGTCCCAAAACCATATTGAAGTAGTAGGAC-ATA
453 TAACAACACTCCTAACACTCTTAGT-GTACTTCTCCCAAAACCACATTGAAGTAGTAGGACGA-A
* * * * * * *
2117886 TTATCCATTCTTGGTTCACTGACGTTCTCGAAGCACCACATTCTTCGTCAATACTGAATCTGTCA
516 TTATACATTCTCGATTCACTGACATTCTCGAAGCACCACATTCTTCGTCAATAATAAATATGTCA
* * *
2117951 TATTCTTCATG-CCG-TATATCGGATATCT-TCTGTAATGATCCTCGATCCCAACTATTTGTATA
581 TATTCTT--TGTACGATATATCAGATATCTCT-TGTAACGATCCTCGATCCCAACTATTTGTATA
* * ** *
2118013 CATCCTTGATTGAAGATACTTTGGCGTATTATGCTTAATATGGTTACACCCGATGTAACTTACTC
643 CATCCTCGATTGAAGATAATTTGGCGTATTACACTTAATATGGTTACACCCGATGTAACCTACTC
*
2118078 CTACGAGTGTTTTAGATACGTTTGGTCATTCATGTCCTTCACAAACTAAGTCTTACTATTATGGG
708 CTACGAGTGTTTTAGATACGTTTGGTCATTCATGTCCTTCACAAACTAAGTCTTACTATTAAGGG
* *
2118143 TCGT-CTGTAGTCCTTA-CTGGCCTTAA-CCGTGTCAAATATGACCATCCCAAGTGAGTAGTAT
773 TCGTCCT-TAGTCCTTATC-GACCTTAATCAG-GTCAAATATGACCATCCCAAGTGAGTAGTAT
2118204 TGATACTTTA
Statistics
Matches: 721, Mismatches: 100, Indels: 24
0.85 0.12 0.03
Matches are distributed among these distances:
873 8 0.01
874 383 0.53
875 116 0.16
876 213 0.30
877 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (875 bp):
GGATCATTATACTGCTAAAGTAACTCAGGTGTCCTCACCGTTTCCTATGTGACAAAAAAGGCATA
AGTCTTATGGAATCTTACCTCATAAGGCTCTTATGGTTATCAAAAAATTAATGTCACTATCTAAT
TATTATAATAAATCTTTACTCTAGAGAGAACATCTTAACCATGTTAACTGATACCACACTAAGGC
AACAAAAGTAGCTCGACTACTCAATACAAAACTTATTGAAGCCAGGTGAGATCATTTCCCCTTCA
CCCGAACTATCCCGCTCATCCTCTCGCCTAGGACGTAAAGAAAAGGTTTACTAGAACTTAAAGGG
TATTTTAGTCATCGCTATCTCTGAAGAGATCTATAAGTATTTCACAATTCCCTGACGATTATGGT
GTTTGTTATTCACAGACTAAATCACTAGTTAGCCCAATACCTGACTCGGGTTCATTACTGGGTAA
CAACACTCCTAACACTCTTAGTGTACTTCTCCCAAAACCACATTGAAGTAGTAGGACGAATTATA
CATTCTCGATTCACTGACATTCTCGAAGCACCACATTCTTCGTCAATAATAAATATGTCATATTC
TTTGTACGATATATCAGATATCTCTTGTAACGATCCTCGATCCCAACTATTTGTATACATCCTCG
ATTGAAGATAATTTGGCGTATTACACTTAATATGGTTACACCCGATGTAACCTACTCCTACGAGT
GTTTTAGATACGTTTGGTCATTCATGTCCTTCACAAACTAAGTCTTACTATTAAGGGTCGTCCTT
AGTCCTTATCGACCTTAATCAGGTCAAATATGACCATCCCAAGTGAGTAGTATAAATACCCTAGG
GTCAAGTATCGATACCCAAATAAGTATCAA
Found at i:2118820 original size:21 final size:22
Alignment explanation
Indices: 2118796--2118837 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2118786 AACAAATAAC
*
2118796 CCATG-GCTTGAATGGTTAAAT
1 CCATGCGCTTGAAGGGTTAAAT
2118817 CCATGCTGCTTGAAGGGTTAA
1 CCATGC-GCTTGAAGGGTTAA
2118838 GAATGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
23 13 0.72
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (22 bp):
CCATGCGCTTGAAGGGTTAAAT
Found at i:2120675 original size:4 final size:4
Alignment explanation
Indices: 2120666--2120691 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2120656 TTTAGAATAG
2120666 TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TA
2120692 TCACGTGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:2124705 original size:22 final size:22
Alignment explanation
Indices: 2124677--2124727 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
2124667 TCCTCTGCAT
2124677 TAACAACTACATTGAAGTCCCC
1 TAACAACTACATTGAAGTCCCC
2124699 TAACAACTACATTGAAGTCCCC
1 TAACAACTACATTGAAGTCCCC
*
2124721 TATCAAC
1 TAACAAC
2124728 AAATGATAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.31, G:0.08, T:0.24
Consensus pattern (22 bp):
TAACAACTACATTGAAGTCCCC
Found at i:2127444 original size:26 final size:26
Alignment explanation
Indices: 2127415--2127472 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 26
2127405 TAAAAGAGCT
2127415 AATAAATCTCTTATAATAAAAGAAGA
1 AATAAATCTCTTATAATAAAAGAAGA
* *
2127441 AAT-AATCTCTTTTAATAAAAGAGGA
1 AATAAATCTCTTATAATAAAAGAAGA
*
2127466 ATTAAAT
1 AATAAAT
2127473 TATCTTTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 22 0.79
26 6 0.21
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (26 bp):
AATAAATCTCTTATAATAAAAGAAGA
Found at i:2129020 original size:18 final size:18
Alignment explanation
Indices: 2128957--2129023 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 18
2128947 AGTTTCTCAA
*
2128957 TATCGATACTGAGCCTGCCAG
1 TATCGATACTG-GCCT--TAG
*
2128978 TATCGATATTGGCCTTAGGG
1 TATCGATACTGGCCTTA--G
2128998 TATCGATACTGGCCTTAG
1 TATCGATACTGGCCTTAG
2129016 TATCGATA
1 TATCGATA
2129024 TCATTTTTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 10 0.24
20 21 0.51
21 10 0.24
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (18 bp):
TATCGATACTGGCCTTAG
Found at i:2132950 original size:24 final size:23
Alignment explanation
Indices: 2132923--2132977 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
2132913 ACTTAAACAT
2132923 TATTTTTTCTACCTAAAATGTTAA
1 TATTTTTTCTACCTAAAATGTT-A
***
2132947 TATTTGGAGCTACCTAAAATGTTA
1 TATTT-TTTCTACCTAAAATGTTA
2132971 T-TTTTTT
1 TATTTTTT
2132978 ACCGATTTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
23 3 0.12
24 7 0.29
25 14 0.58
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (23 bp):
TATTTTTTCTACCTAAAATGTTA
Found at i:2137972 original size:2 final size:2
Alignment explanation
Indices: 2137967--2137993 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2137957 ATATATTTGA
2137967 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2137994 AATTTTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2145437 original size:5 final size:5
Alignment explanation
Indices: 2145427--2145471 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
2145417 ATTCAACATT
2145427 ATAAA ATAAA AT-AA A-AAA ATAATA A-AGAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAA-A ATA-AA ATAAA ATAAA ATAAA A
2145472 GTATAATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
4 6 0.17
5 25 0.71
6 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (5 bp):
ATAAA
Found at i:2146272 original size:21 final size:21
Alignment explanation
Indices: 2146246--2146286 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2146236 CGGTGAACAG
*
2146246 TGCTACAGTGTATCGATGCAC
1 TGCTACAGTGTACCGATGCAC
2146267 TGCTACAGTGTACCGATGCA
1 TGCTACAGTGTACCGATGCA
2146287 TAAAAACATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (21 bp):
TGCTACAGTGTACCGATGCAC
Found at i:2146333 original size:21 final size:21
Alignment explanation
Indices: 2146308--2146368 Score: 106
Period size: 21 Copynumber: 2.9 Consensus size: 21
2146298 AATATAAATT
2146308 GTGTATCGATGCACTGCTAGA
1 GTGTATCGATGCACTGCTAGA
2146329 GTGTATCGATGCACTGCTAGA
1 GTGTATCGATGCACTGCTAGA
2146350 GTGTA-CTGATGCACTGCTA
1 GTGTATC-GATGCACTGCTA
2146369 CAGTAACTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 1 0.03
21 38 0.97
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (21 bp):
GTGTATCGATGCACTGCTAGA
Found at i:2146885 original size:22 final size:22
Alignment explanation
Indices: 2146857--2146917 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
2146847 GGCATGTGAA
*
2146857 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCCGAAAGACCTATGT
* * *
2146879 ATTTGTCTCGAAGGACCTCTGT
1 ATTTGTCCCGAAAGACCTATGT
2146901 ATTTGTCCCGAAAGACC
1 ATTTGTCCCGAAAGACC
2146918 ACGTAGAACC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (22 bp):
ATTTGTCCCGAAAGACCTATGT
Found at i:2148209 original size:46 final size:45
Alignment explanation
Indices: 2148111--2148216 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 45
2148101 GTGCACTAAG
* * *
2148111 AGTGCATTGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
* *
2148156 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTC
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAC
*
2148202 AGTGCATCAATGCAT
1 AGTGCATCGATGCAT
2148217 GGTATGTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
45 28 0.53
46 22 0.42
47 3 0.06
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (45 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
Found at i:2148534 original size:20 final size:20
Alignment explanation
Indices: 2148509--2148552 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
2148499 AAATTCATTT
2148509 AAACTTAATTTGTTATATTG
1 AAACTTAATTTGTTATATTG
2148529 AAACTTAATTTGTTATATTG
1 AAACTTAATTTGTTATATTG
2148549 AAAC
1 AAAC
2148553 ATAAAAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (20 bp):
AAACTTAATTTGTTATATTG
Found at i:2152162 original size:36 final size:36
Alignment explanation
Indices: 2152121--2152196 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2152111 ATTTTCGGGA
*
2152121 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
2152157 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
2152193 TTTT
1 TTTT
2152197 TTTAGCTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:2153416 original size:21 final size:21
Alignment explanation
Indices: 2153391--2153438 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2153381 CCTAATATTG
2153391 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
2153412 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
2153433 TAATGT
1 CAATGT
2153439 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:2158077 original size:21 final size:21
Alignment explanation
Indices: 2158052--2158099 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2158042 CCTAATATTG
2158052 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
2158073 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
2158094 TAATGT
1 CAATGT
2158100 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:2163227 original size:3 final size:3
Alignment explanation
Indices: 2163219--2163277 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
2163209 AATCATTCTG
*
2163219 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2163267 ATT ATT -TT ATT
1 ATT ATT ATT ATT
2163278 TTTTTTGCTG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2171984 original size:2 final size:2
Alignment explanation
Indices: 2171977--2172004 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2171967 TGCGAAACCA
2171977 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2172005 ATGTATGTGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2173052 original size:2 final size:2
Alignment explanation
Indices: 2173045--2173108 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
2173035 TGTGTTTTTA
2173045 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2173087 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
2173109 TTTAAAATTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2179883 original size:39 final size:40
Alignment explanation
Indices: 2179768--2179884 Score: 120
Period size: 39 Copynumber: 3.0 Consensus size: 40
2179758 TATTAAATGT
*
2179768 ATTTATAATTT-TCAAATTATTTCAC-TATAACATTCT-AA
1 ATTTATAATTTCTTAAATTATTTCACAT-TAACATTCTAAA
* * *
2179806 ATTTCTAATTTCTTAAATT-TTGCTACCA-TAATATTCTAAA
1 ATTTATAATTTCTTAAATTATTTC-A-CATTAACATTCTAAA
*
2179846 ATTT-TAATTTCTTAAATTATTTCACATTAACAATCTAAA
1 ATTTATAATTTCTTAAATTATTTCACATTAACATTCTAAA
2179885 TTATTTTTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
38 15 0.23
39 40 0.62
40 10 0.15
ACGTcount: A:0.38, C:0.14, G:0.01, T:0.47
Consensus pattern (40 bp):
ATTTATAATTTCTTAAATTATTTCACATTAACATTCTAAA
Found at i:2180049 original size:2 final size:2
Alignment explanation
Indices: 2180042--2180090 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2180032 ATTTTAGAAT
2180042 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2180084 TA TA TA T
1 TA TA TA T
2180091 TTTAAAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2181533 original size:13 final size:14
Alignment explanation
Indices: 2181515--2181548 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2181505 ATAACCTTAC
*
2181515 CCCTAACTTA-AAA
1 CCCTAAATTATAAA
2181528 CCCTAAATTATAAA
1 CCCTAAATTATAAA
2181542 CCCTAAA
1 CCCTAAA
2181549 CCCTATTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAAATTATAAA
Found at i:2182868 original size:20 final size:20
Alignment explanation
Indices: 2182841--2183088 Score: 154
Period size: 20 Copynumber: 12.3 Consensus size: 20
2182831 AATTTGTAAA
2182841 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
2182861 TCGTAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
2182881 TCGCAACGC-GATAATCAAAT
1 TCGCAACACAGA-AGTCAAAT
* *
2182901 TCGTAATAC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* **
2182921 TCACAACATTGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
2182941 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
**
2182961 TCGCAAC-GTGAA-TCTGTAAA-
1 TCGCAACACAGAAGTC---AAAT
* **
2182981 TCACAAC-GTGAATTTGT-AAA-
1 TCGCAACACAGAA---GTCAAAT
*
2183001 TCGTAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
2183021 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
2183041 TCGCAACGC-GATAGTTAAAT
1 TCGCAACACAGA-AGTCAAAT
* * *
2183061 TCGCAACACTGAATTTCAAAC
1 TCGCAACACAGAA-GTCAAAT
2183082 TCGCAAC
1 TCGCAAC
2183089 TGAATTTCAA
Statistics
Matches: 180, Mismatches: 33, Indels: 29
0.74 0.14 0.12
Matches are distributed among these distances:
18 4 0.02
19 8 0.04
20 146 0.81
21 21 0.12
24 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:2182988 original size:100 final size:100
Alignment explanation
Indices: 2182884--2183067 Score: 221
Period size: 100 Copynumber: 1.8 Consensus size: 100
2182874 GTCAAATTCG
* **
2182884 CAACGCG-ATAAT-CAAATTCGTAATAC-GATAGTCAAATTCACAACATTGAAGTCAAATTCGCA
1 CAACGCGAAT-ATGCAAA-TCGTAACACAGA-AGTCAAATTCACAACACAGAAGTCAAATTCGCA
2182946 ACACAAAAGTCAAATTCGCAACGTGAATCTGTAAATCA
63 ACACAAAAGTCAAATTCGCAACGTGAATCTGTAAATCA
* * * * *
2182984 CAACGTGAATTTGTAAATCGTAACACAGAAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACG
1 CAACGCGAATATGCAAATCGTAACACAGAAGTCAAATTCACAACACAGAAGTCAAATTCGCAACA
* * *
2183049 CGATAGTTAAATTCGCAAC
66 CAAAAGTCAAATTCGCAAC
2183068 ACTGAATTTC
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
100 63 0.90
101 7 0.10
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (100 bp):
CAACGCGAATATGCAAATCGTAACACAGAAGTCAAATTCACAACACAGAAGTCAAATTCGCAACA
CAAAAGTCAAATTCGCAACGTGAATCTGTAAATCA
Found at i:2183015 original size:80 final size:81
Alignment explanation
Indices: 2182811--2183076 Score: 278
Period size: 80 Copynumber: 3.3 Consensus size: 81
2182801 TCCCAATGCC
* *
2182811 AATCTGTAAATCGCAACACAAATTTGTAAATCGCAACACAGAAGTCAAATTCGTAACACAAAAGT
1 AATCTGTAAATCGCAACACGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGT
2182876 CAAATTCGCAACGCGA
66 CAAATTCGCAACGCGA
* * * * **
2182892 TAATC---AAATTCGTAATACG-A-TAGTCAAATTCACAACATTGAAGTCAAATTCGCAACACAA
1 -AATCTGTAAA-TCGCAACACGAATTTGT-AAA-TCGCAACACAGAAGTCAAATTCGCAACACAA
*
2182952 AAGTCAAATTCGCAACGTG-
62 AAGTCAAATTCGCAACGCGA
* ** * *
2182971 AATCTGTAAATCACAACGTGAATTTGTAAATCGTAACACAGAAGTCAAATTCGCAACACAGAAGT
1 AATCTGTAAATCGCAACACGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGT
2183036 CAAATTCGCAACGCGA
66 CAAATTCGCAACGCGA
* *
2183052 TA-GT-TAAATTCGCAACACTGAATTT
1 AATCTGTAAA-TCGCAACAC-GAATTT
2183077 CAAACTCGCA
Statistics
Matches: 147, Mismatches: 26, Indels: 23
0.75 0.13 0.12
Matches are distributed among these distances:
78 7 0.05
79 11 0.07
80 108 0.73
81 14 0.10
82 7 0.05
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (81 bp):
AATCTGTAAATCGCAACACGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAAAAGT
CAAATTCGCAACGCGA
Found at i:2183099 original size:80 final size:78
Alignment explanation
Indices: 2182817--2183107 Score: 236
Period size: 80 Copynumber: 3.6 Consensus size: 78
2182807 TGCCAATCTG
* * * *
2182817 TAAA-TCGCAACAC-AAATTTGTAAATCGCAACACAGAAGTCAAATTCGTAACACAAAAGTCAAA
1 TAAATTCGCAACACTGAATTT-CAAATCGC-A-ACTGAAGTCAAATTCGCAACACAAAAGTCAAA
2182880 TTCGCAACGCGATAAT
63 TTCGCAACGCGATAAT
* * * * *
2182896 CAAATTCGTAATAC-G-ATAGTCAAATTCACAACATTGAAGTCAAATTCGCAACACAAAAGTCAA
1 TAAATTCGCAACACTGAAT-TTCAAA-TCGCAAC--TGAAGTCAAATTCGCAACACAAAAGTCAA
* *
2182959 ATTCGCAACGTGA-ATCT
62 ATTCGCAACGCGATA-AT
* * * * * *
2182976 GTAAA-TCACAAC-GTGAATTTGTAAATCGTAACACAGAAGTCAAATTCGCAACACAGAAGTCAA
1 -TAAATTCGCAACACTGAATTT-CAAATCG-CA-ACTGAAGTCAAATTCGCAACACAAAAGTCAA
*
2183039 ATTCGCAACGCGATAGT
62 ATTCGCAACGCGATAAT
*
2183056 TAAATTCGCAACACTGAATTTCAAACTCGCAACTGAATTTCAAATTCGCAAC
1 TAAATTCGCAACACTGAATTTCAAA-TCGCAACTGAA-GTCAAATTCGCAAC
2183108 TCGATTTTCG
Statistics
Matches: 165, Mismatches: 30, Indels: 33
0.72 0.13 0.14
Matches are distributed among these distances:
78 2 0.01
79 19 0.12
80 122 0.74
81 20 0.12
82 2 0.01
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.23
Consensus pattern (78 bp):
TAAATTCGCAACACTGAATTTCAAATCGCAACTGAAGTCAAATTCGCAACACAAAAGTCAAATTC
GCAACGCGATAAT
Found at i:2183101 original size:40 final size:39
Alignment explanation
Indices: 2182915--2183147 Score: 141
Period size: 40 Copynumber: 5.8 Consensus size: 39
2182905 AATACGATAG
* * * * **
2182915 TCAAATTCACAACATTGAAGTCAAATTCGCAACACAAAAG
1 TCAAATTCGCAACA-TGAATTTAAATTCGCAACACGAATT
* * **
2182955 TCAAATTCGCAACGTGAATCTGTAAA-TCACAACGTGAATT
1 TCAAATTCGCAACATGAAT-T-TAAATTCGCAACACGAATT
* * * * * *
2182995 TGTAAA-TCGTAACACAGAAGTCAAATTCGCAACACAGAA-G
1 T-CAAATTCGCAACA-TGAATTTAAATTCGCAACAC-GAATT
** *
2183035 TCAAATTCGCAACGCGATAGTTAAATTCGCAACACTGAATT
1 TCAAATTCGCAACATGA-ATTTAAATTCGCAACAC-GAATT
* * *
2183076 TCAAACTCGCAAC-TGAATTTCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACATGAATTT-AAATTCGCAACACGAATT
* *
2183115 TCGAATTCGCAACATGAATTTAATTTCGCAACA
1 TCAAATTCGCAACATGAATTTAAATTCGCAACA
2183148 GGTTTTAGTT
Statistics
Matches: 146, Mismatches: 36, Indels: 23
0.71 0.18 0.11
Matches are distributed among these distances:
39 40 0.27
40 82 0.56
41 24 0.16
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.25
Consensus pattern (39 bp):
TCAAATTCGCAACATGAATTTAAATTCGCAACACGAATT
Found at i:2183147 original size:19 final size:20
Alignment explanation
Indices: 2182915--2183147 Score: 117
Period size: 20 Copynumber: 11.7 Consensus size: 20
2182905 AATACGATAG
* *
2182915 TCAAATTCACAACATTGAA-G
1 TCAAATTCGCAACA-TGAATT
** **
2182935 TCAAATTCGCAACACAAAAG
1 TCAAATTCGCAACATGAATT
*
2182955 TCAAATTCGCAACGTGAATCT
1 TCAAATTCGCAACATGAAT-T
* *
2182976 GT-AAA-TCACAACGTGAATT
1 -TCAAATTCGCAACATGAATT
* * * *
2182995 TGTAAA-TCGTAACACAGAA-G
1 T-CAAATTCGCAACA-TGAATT
* *
2183015 TCAAATTCGCAACACAGAA-G
1 TCAAATTCGCAACA-TGAATT
** *
2183035 TCAAATTCGCAACGCGATAGT
1 TCAAATTCGCAACATGA-ATT
2183056 T-AAATTCGCAACACTGAATT
1 TCAAATTCGCAACA-TGAATT
*
2183076 TCAAACTCGCAAC-TGAATT
1 TCAAATTCGCAACATGAATT
*
2183095 TCAAATTCGCAAC-TCGATTT
1 TCAAATTCGCAACAT-GAATT
*
2183115 TCGAATTCGCAACATGAATT
1 TCAAATTCGCAACATGAATT
*
2183135 T-AATTTCGCAACA
1 TCAAATTCGCAACA
2183148 GGTTTTAGTT
Statistics
Matches: 171, Mismatches: 29, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
18 1 0.01
19 37 0.22
20 112 0.65
21 20 0.12
22 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.25
Consensus pattern (20 bp):
TCAAATTCGCAACATGAATT
Found at i:2183323 original size:15 final size:16
Alignment explanation
Indices: 2183303--2183340 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2183293 TCTCCATCTC
*
2183303 TAATTTTCTTT-TACA
1 TAATTTTATTTCTACA
*
2183318 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
2183334 TAATTTT
1 TAATTTT
2183341 TCAATGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:2186859 original size:28 final size:28
Alignment explanation
Indices: 2186827--2186880 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
2186817 ATAATTCTTA
*
2186827 TTTACACATCAAATTAAACAAATCAACT
1 TTTACAAATCAAATTAAACAAATCAACT
* **
2186855 TTTACAAATCAACTTTTACAAATCAA
1 TTTACAAATCAAATTAAACAAATCAA
2186881 TTAAACAAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (28 bp):
TTTACAAATCAAATTAAACAAATCAACT
Found at i:2186861 original size:14 final size:14
Alignment explanation
Indices: 2186844--2186880 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2186834 ATCAAATTAA
2186844 ACAAATCAACTTTT
1 ACAAATCAACTTTT
2186858 ACAAATCAACTTTT
1 ACAAATCAACTTTT
2186872 ACAAATCAA
1 ACAAATCAA
2186881 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2186916 original size:79 final size:78
Alignment explanation
Indices: 2186779--2186934 Score: 276
Period size: 79 Copynumber: 2.0 Consensus size: 78
2186769 ATTTAAAACA
2186779 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATC-AATTAA
*
2186844 ACAAATCAACTTTT
65 ACAAATAAACTTTT
* *
2186858 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTAAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTAAA
2186923 CAAATAAACTTT
66 CAAATAAACTTT
2186935 CAATGTAAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 18 0.24
79 56 0.76
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.31
Consensus pattern (78 bp):
ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTAAA
CAAATAAACTTTT
Found at i:2188257 original size:17 final size:17
Alignment explanation
Indices: 2188235--2188268 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2188225 ACGCATCCAT
*
2188235 CATATTGGGCACGGGAG
1 CATATTAGGCACGGGAG
2188252 CATATTAGGCACGGGAG
1 CATATTAGGCACGGGAG
2188269 GGGGTTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.18, G:0.38, T:0.18
Consensus pattern (17 bp):
CATATTAGGCACGGGAG
Found at i:2188360 original size:21 final size:21
Alignment explanation
Indices: 2188336--2188455 Score: 116
Period size: 21 Copynumber: 5.7 Consensus size: 21
2188326 GAGAGACCCA
2188336 TTGAACGATGACAGGGGCCTC
1 TTGAACGATGACAGGGGCCTC
*
2188357 TTGAACGATGACAGTGGCCTC
1 TTGAACGATGACAGGGGCCTC
* **
2188378 TTGAACGGTGGGAGGGGCCTC
1 TTGAACGATGACAGGGGCCTC
* * **
2188399 TTGAATGATGAGAGAAGCCTC
1 TTGAACGATGACAGGGGCCTC
* * * *
2188420 TTGAATGAT-AGGAGGCGTCTC
1 TTGAACGATGA-CAGGGGCCTC
2188441 TTGAACGATGACAGG
1 TTGAACGATGACAGG
2188456 TGAATCGGGC
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
20 1 0.01
21 80 0.98
22 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (21 bp):
TTGAACGATGACAGGGGCCTC
Found at i:2188382 original size:42 final size:42
Alignment explanation
Indices: 2188336--2188454 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
2188326 GAGAGACCCA
* **
2188336 TTGAACGATGACAGGGGCCTCTTGAACGATGACAGTGGCCTC
1 TTGAACGATGAGAGGGGCCTCTTGAACGATGACAGAAGCCTC
* * * *
2188378 TTGAACGGTGGGAGGGGCCTCTTGAATGATGAGAGAAGCCTC
1 TTGAACGATGAGAGGGGCCTCTTGAACGATGACAGAAGCCTC
* * *
2188420 TTGAATGAT-AGGAGGCGTCTCTTGAACGATGACAG
1 TTGAACGATGA-GAGGGGCCTCTTGAACGATGACAG
2188455 GTGAATCGGG
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (42 bp):
TTGAACGATGAGAGGGGCCTCTTGAACGATGACAGAAGCCTC
Done.